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Conserved domains on  [gi|513183311|ref|XP_004941236|]
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protein RUFY3 isoform X12 [Gallus gallus]

Protein Classification

Graphical summary

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List of domain hits

 Name Accession Description Interval E-value
RUN_RUFY3 cd17696
RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; ...
 68-223 7.45e-101

RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. This model represents the RUN domain of RUFY3.


:

Pssm-ID: 439058  Cd Length: 156  Bit Score: 298.45  E-value: 7.45e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17696    1 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 223
Cdd:cd17696   81 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 156
SMC_prok_B super family cl37069
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 243-463 1.50e-10

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


The actual alignment was detected with superfamily member TIGR02168:

Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 63.54  E-value: 1.50e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   243 KDGNSTKGSegDGQITAILDQKNYVEELNRH---LSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE 319
Cdd:TIGR02168  657 PGGVITGGS--AKTNSSILERRREIEELEEKieeLEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   320 SSYILESNRKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDD 399
Cdd:TIGR02168  735 LARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTL 814

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 513183311   400 LRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 463
Cdd:TIGR02168  815 LNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEAL 878
 
Name Accession Description Interval E-value
RUN_RUFY3 cd17696
RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; ...
 68-223 7.45e-101

RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. This model represents the RUN domain of RUFY3.


Pssm-ID: 439058  Cd Length: 156  Bit Score: 298.45  E-value: 7.45e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17696    1 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 223
Cdd:cd17696   81 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 156
RUN pfam02759
RUN domain; This domain is present in several proteins that are linked to the functions of ...
 103-226 1.25e-45

RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.


Pssm-ID: 460679  Cd Length: 134  Bit Score: 155.13  E-value: 1.25e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  103 QFFVVMEHCLKHGLKA------KKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKT---PVGRGRAWLRLALMQ 173
Cdd:pfam02759   1 QLCAALEALLSHGLKRssllilRAAGLLPERSFWALLERVGKLVPPAEELLSSVQELEQIHTpysPDGRGRAWIRLALNE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 513183311  174 KKLSEYMKALINRKDLLSEFYEPNALMMEEEGA-IIAGLLVGLNVIDANFCMKG 226
Cdd:pfam02759  81 KLLDQWLKLLLSNKELLSEYYEPWALLADPEFGeILLGLLVGLSALDFNLCLKL 134
RUN smart00593
domain involved in Ras-like GTPase signaling;
163-225 1.04e-17

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 76.88  E-value: 1.04e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 513183311   163 GRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGLNVIDANFCMK 225
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLRdPEEGEQLLGLLVGLSALDFNLPVD 64
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 243-463 1.50e-10

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 63.54  E-value: 1.50e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   243 KDGNSTKGSegDGQITAILDQKNYVEELNRH---LSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE 319
Cdd:TIGR02168  657 PGGVITGGS--AKTNSSILERRREIEELEEKieeLEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   320 SSYILESNRKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDD 399
Cdd:TIGR02168  735 LARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTL 814

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 513183311   400 LRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 463
Cdd:TIGR02168  815 LNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEAL 878
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 255-463 1.20e-07

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 53.61  E-value: 1.20e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 255 GQITAILDQKNYVEELNRHLSAtvnnLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDR 334
Cdd:COG4942   17 AQADAAAEAEAELEQLQQEIAE----LEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 335 TADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQE----MELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFK 410
Cdd:COG4942   93 AELRAELEAQKEELAELLRALYRLGRQPPLALLLSPEdfldAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAE 172

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 513183311 411 LQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 463
Cdd:COG4942  173 RAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEEL 225
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 312-449 4.12e-06

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 49.35  E-value: 4.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  312 EMERVKEES---SYILESNRKVTKDRTADGQAL-TEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQ 387
Cdd:pfam17380 447 EMERVRLEEqerQQQVERLRQQEEERKRKKLELeKEKRDRKRAEEQRRKILEKELEERKQAMIEEERKRKLLEKEMEERQ 526

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311  388 DALV--ALRQQLDDLRALKHELSFKLQSSDMgVKQKSELNSRLE--EKTNQMAATIKQLEQSEKDL 449
Cdd:pfam17380 527 KAIYeeERRREAEEERRKQQEMEERRRIQEQ-MRKATEERSRLEamEREREMMRQIVESEKARAEY 591
PRK11281 PRK11281
mechanosensitive channel MscK;
272-466 2.29e-04

mechanosensitive channel MscK;


Pssm-ID: 236892 [Multi-domain]  Cd Length: 1113  Bit Score: 43.75  E-value: 2.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  272 RHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE----SSYILESNRKVTKDRTADGQALTEARKQ 347
Cdd:PRK11281  117 TLSTLSLRQLESRLAQTLDQLQNAQNDLAEYNSQLVSLQTQPERAQAAlyanSQRLQQIRNLLKGGKVGGKALRPSQRVL 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  348 LKEETQLrldvekeLEAQIGMRQEmELAMKMLEKDVCEKQDALVALRQQLddlraLKHELSFklqssdmgvkqkselnsr 427
Cdd:PRK11281  197 LQAEQAL-------LNAQNDLQRK-SLEGNTQLQDLLQKQRDYLTARIQR-----LEHQLQL------------------ 245

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 513183311  428 LEEKTNQmaatiKQLEQSEKDlVKQAKTLNSAA----NKLIQK 466
Cdd:PRK11281  246 LQEAINS-----KRLTLSEKT-VQEAQSQDEAAriqaNPLVAQ 282
 
Name Accession Description Interval E-value
RUN_RUFY3 cd17696
RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; ...
 68-223 7.45e-101

RUN domain found in RUN and FYVE domain-containing protein 3 (RUFY3) and similar proteins; RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. This model represents the RUN domain of RUFY3.


Pssm-ID: 439058  Cd Length: 156  Bit Score: 298.45  E-value: 7.45e-101
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17696    1 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 223
Cdd:cd17696   81 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 156
RUN_RUFY2 cd17695
RUN domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins; ...
 68-223 3.61e-99

RUN domain found in RUN and FYVE domain-containing protein 2 (RUFY2) and similar proteins; RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between. It is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. This model represents the RUN domain of RUFY2.


Pssm-ID: 439057  Cd Length: 156  Bit Score: 294.19  E-value: 3.61e-99
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17695    1 ERANLLNMAKLSIKGLIESALSFGRTLDSDYPPLQQFFVVMEHCLKHGLKVRKSFLSYNKTIWGPLELVEKLCPEAEEIA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 223
Cdd:cd17695   81 ASVRDLPGLKTPLGRARAWLRLALMQKKLADYLRCLIIRRDLLSEFYEYHALMMEEEGAVIVGLLVGLNVIDANLC 156
RUN_RUFY1_like cd17681
RUN domain found in RUN and FYVE domain-containing proteins, RUFY1, RUFY2, RUFY3 and similar ...
 68-222 6.59e-96

RUN domain found in RUN and FYVE domain-containing proteins, RUFY1, RUFY2, RUFY3 and similar proteins; This family includes RUN and FYVE domain-containing protein RUFY1, RUFY2, and RUFY3. RUFY1, also called FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homolog of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY2, also called Rab4-interacting protein related, is a novel embryonic factor that is present in the nucleus at early stages of embryonic development. It may have both endosomal functions in the cytoplasm and nuclear functions. RUFY3, also called Rap2-interacting protein x (RIPx or RPIPx), or single axon-regulated protein (singar), is an N-terminal RUN domain and a C-terminal FYVE domain containing protein predominantly expressed in the brain. It suppresses formation of surplus axons for neuronal polarity. Unlike other RUFY proteins, RUFY3 can associate with the GTP-bound active form of Rab5. RUFY1, RUFY2, and RUFY3 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.


Pssm-ID: 439043  Cd Length: 155  Bit Score: 285.62  E-value: 6.59e-96
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17681    1 ERRNLLNLAKLSIKELIESALSFGRTLDSDHVPLQQFFVILEHVLRHGLKVKKSFLGPNKSFWPVLEHVEKLVPEANEIT 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 513183311 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANF 222
Cdd:cd17681   81 ASVRDLPGIKTPLGRARAWLRLALMQKKLADYFRALIENKDLLSEFYEPGALMMSEEAVVIAGLLVGLNVIDCNL 155
RUN_RUFY1 cd17694
RUN domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins; ...
 68-223 3.44e-93

RUN domain found in RUN and FYVE domain-containing protein 1 (RUFY1) and similar proteins; RUFY1, also called FYVE-finger protein EIP1, or La-binding protein 1, or Rab4-interacting protein (Rabip4), or Zinc finger FYVE domain-containing protein 12 (ZFY12), a human homolog of mouse Rabip4, an effector of Rab4 GTPase that regulates recycling of endocytosed cargo. RUFY1 is an endosomal protein that functions as a dual effector of Rab4 and Rab14 and is involved in efficient recycling of transferrin (Tfn). It is a downstream effector of Etk, a downstream tyrosine kinase of PI3-kinase that is involved in regulation of vesicle trafficking. RUFY1 contains an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.


Pssm-ID: 439056  Cd Length: 156  Bit Score: 279.10  E-value: 3.44e-93
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17694    1 ERANLMNMMKLSIKVLIQSALSLGRTLDSDYPPLQQFFVVLEHCLKHGLKVKKSFIGQNKSFFGPLELVEKLCPEASDIA 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 223
Cdd:cd17694   81 TSARNLPELKTAVGRGRAWLHLALMQKKLADYLKVLIDRKDLLSEFYEPGALMMEEEGAVIVGLLVGLNVIDANLC 156
RUN pfam02759
RUN domain; This domain is present in several proteins that are linked to the functions of ...
 103-226 1.25e-45

RUN domain; This domain is present in several proteins that are linked to the functions of GTPases in the Rap and Rab families. They could hence play important roles in multiple Ras-like GTPase signalling pathways. The domain is comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases.


Pssm-ID: 460679  Cd Length: 134  Bit Score: 155.13  E-value: 1.25e-45
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  103 QFFVVMEHCLKHGLKA------KKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKT---PVGRGRAWLRLALMQ 173
Cdd:pfam02759   1 QLCAALEALLSHGLKRssllilRAAGLLPERSFWALLERVGKLVPPAEELLSSVQELEQIHTpysPDGRGRAWIRLALNE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 513183311  174 KKLSEYMKALINRKDLLSEFYEPNALMMEEEGA-IIAGLLVGLNVIDANFCMKG 226
Cdd:pfam02759  81 KLLDQWLKLLLSNKELLSEYYEPWALLADPEFGeILLGLLVGLSALDFNLCLKL 134
RUN_RUNDC3 cd17684
RUN domain found in RUN domain-containing protein 3 (RUNDC3) and similar proteins; RUNDC3 ...
 71-222 4.84e-36

RUN domain found in RUN domain-containing protein 3 (RUNDC3) and similar proteins; RUNDC3 contains two isoforms, RUNDC3A and RUNDC3B. RUNDC3A, also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. RUNDC3B, also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. Both RUNDC3A and RUNDC3B contain a RUN domain.


Pssm-ID: 439046  Cd Length: 150  Bit Score: 130.21  E-value: 4.84e-36
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  71 NLMNMAKLSIKGLIESALNlgRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLG--QNKSFWGPLELVEKLVPEAAeiTA 148
Cdd:cd17684    1 NLVTVCRLSVKSLIDKACL--ETIDDSSEELINFAAILEQILSHRLKPVKPWYGseEPRTFWDYIRVACKKVPQNC--IA 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 513183311 149 SVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANF 222
Cdd:cd17684   77 SIEQMENIKSPKAKGRAWIRVALMEKRLSEYLSTALKQTRLTRNFYQDGAIMLSEDATVLCGMLIGLNAIDFSF 150
RUN cd17671
RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new ...
 79-222 8.89e-33

RUN domain; RUN domain, named after RPIP8 (Rap2 interacting protein 8), UNC-14 and NESCA (new molecule containing SH3 at the carboxyl-terminus), is a less conserved protein motif that comprises six conserved regions, which in some proteins have considerable insertions between them. The domain core is thought to take up a predominantly alpha fold, with basic amino acids in regions A and D possibly playing a functional role in interactions with Ras GTPases. RUN domains are often found in proteins linked particularly to the functions of GTPases in the Rap and Rab families, suggesting the RUN domain may be involved in Rab-mediated membrane trafficking, possibly as a Rab-binding site. RUN domain-containing proteins could hence play important roles in multiple Ras-like GTPase signalling pathways.


Pssm-ID: 439038  Cd Length: 154  Bit Score: 121.76  E-value: 8.89e-33
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  79 SIKGLIESALNLGR-------TLDSDYAPLQQFFVVMEHCLKHGLKAKKtFLGQNKSFWGPLELVEKLVPEAAEITA--S 149
Cdd:cd17671    2 AVKELLESFADNGEaddsaalTLTDDDPVVGRLCAALEAILSHGLKPKR-FGGGKVSFWDFLEALEKLLPAPSLKQAirD 80

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 513183311 150 VKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGLNVIDANF 222
Cdd:cd17671   81 INSLSNVKTDDGRGRAWIRLALNEKSLESYLAALLSDQSLLRKYYEPWALLRdPEEAELFLSLLVGLSSLDFNL 154
RUN_RUNDC3B cd17700
RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins; RUN ...
 71-223 1.84e-26

RUN domain found in RUN domain-containing protein 3B (RUNDC3B) and similar proteins; RUN domain-containing protein 3B (RUNDC3B), also called Rap2-binding protein 9, or Rap2-interacting protein 9 (RPIP-9), contains a RUN domain in its N-terminal region that mediates interaction with Rap2, an important component of the Mitogen-Activated Protein Kinase (MAPK) cascade, which regulates cellular proliferation and differentiation. It also contains characteristic binding sites for MAPK intermediates. RUNDC3B contains a RUN domain.


Pssm-ID: 439062  Cd Length: 151  Bit Score: 104.28  E-value: 1.84e-26
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  71 NLMNMAKLSIKGLIESALNlgRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQN--KSFWGPLELVEKLVPEAAeiTA 148
Cdd:cd17700    1 NLITVCRFSVKTLIDRSCF--ETIDDSSPEFVNFAAILEQILSHRLKGQVTWFGYEspRSFWDYIRVACSKVPHNC--IC 76

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 513183311 149 SVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 223
Cdd:cd17700   77 SIENMENVSSSRAKGRAWIRVALMEKRLSEYISTALRDFKTTRRFYEDGAIVLGEEANMLAGMLLGLNAIDFSFC 151
RUN_RUNDC3A cd17699
RUN domain found in RUN domain-containing protein 3A (RUNDC3A) and similar proteins; RUN ...
 71-223 8.83e-24

RUN domain found in RUN domain-containing protein 3A (RUNDC3A) and similar proteins; RUN domain-containing protein 3A (RUNDC3A), also called Rap2-interacting protein 8 (RPIP8), may act as an effector of Rap2A GTPase in neuronal cells. It contains a RUN domain.


Pssm-ID: 439061  Cd Length: 151  Bit Score: 97.02  E-value: 8.83e-24
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  71 NLMNMAKLSIKGLIESALnlGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFL---GQnKSFWGPLELVEKLVPEaaEIT 147
Cdd:cd17699    1 NLITVCRFSVKTLLEKYT--AEPIDDSSEEFVNFAAILEQILSHRFKGPVSWFssdGQ-RGFWDYIRLACSKVPN--NCI 75

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 223
Cdd:cd17699   76 SSIENMENISTSRAKGRAWIRVALMEKRLSEYIATALRDTRTTRRFYDDGAIMLREESTVLTGMLIGLSAIDFSFC 151
RUN smart00593
domain involved in Ras-like GTPase signaling;
163-225 1.04e-17

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 76.88  E-value: 1.04e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 513183311   163 GRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGLNVIDANFCMK 225
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLRdPEEGEQLLGLLVGLSALDFNLPVD 64
RUN_RUFY4_like cd17682
RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4), FYVE and coiled-coil ...
 80-219 3.94e-17

RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4), FYVE and coiled-coil domain-containing protein 1 (FYCO1), and similar proteins; The family includes RUFY4 and FYCO1. RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. FYCO1, also called zinc finger FYVE domain-containing protein 7 (ZFYVE7), is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport. Both RUFY4 and FYCO1 contain an N-terminal RUN domain and a C-terminal FYVE domain with two coiled-coil domains in-between; this model represents the RUN domain.


Pssm-ID: 439044  Cd Length: 150  Bit Score: 78.04  E-value: 3.94e-17
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  80 IKGLIESALNLGRTLDSDYAP-LQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLE-LVEKLVPEA---AEITASVKDLP 154
Cdd:cd17682    2 LKGCVLDLKSEFGEITDPDNPyLRPFCETLEKILRKGLKEKVSLGGRRKDYWDWLEeLLKKLNKIPkslSDAVKFVKSCK 81

                         90       100       110       120       130       140
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311 155 GLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEE-GAIIAGLLVGLNVID 219
Cdd:cd17682   82 KVKTNQGRGRLFIRYALNKKCLHDPVQQLVKNPKLLSDYYSPDSILGNEIlSEILLSLLYQLNEIN 147
RUN_PLEKHM1 cd17679
RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and ...
 69-215 1.12e-13

RUN domain found in pleckstrin homology domain-containing family M member 1 (PLEKHM1) and similar proteins; PLEKHM1, also called PH domain-containing family M member 1, or 162 kDa adapter protein (AP162), may act as a multivalent adapter protein that regulates Rab7-dependent and HOPS complex-dependent fusion events in the endolysosomal system and couples autophagic and the endocytic trafficking pathways. This model represents the RUN domain of PLEKHM1.


Pssm-ID: 439041 [Multi-domain]  Cd Length: 171  Bit Score: 68.77  E-value: 1.12e-13
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  69 RMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAK-----KTFLGQN------KSFWGPLELV- 136
Cdd:cd17679    1 KKSLTKELSSSVKELQLEYVSSDEVVTSSDDGANTLCCVLEAIFLHGLKDKfiskvSSVFSGDvdklpePNFWPLLLKFs 80

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 137 EKlvpeaaEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGL 215
Cdd:cd17679   81 HR------DVIDQIEHLSQITTDVGRCRAWIRLALNDGLLESYLEAILKDKSALKSYYNPSAFLRdPEQLDILKSLLQGL 154
RUN_SNX29 cd17689
RUN domain found in sorting nexin-29 (SNX29) and similar proteins; SNX29, also called RUN ...
 153-218 1.92e-12

RUN domain found in sorting nexin-29 (SNX29) and similar proteins; SNX29, also called RUN domain-containing protein 2A (RUNDC2A), belongs to the sorting nexin family. Sorting nexins are a large group of proteins that are localized in the cytoplasm and have the potential for membrane association either through their lipid-binding PX domain, a phospholipid-binding motif, or through protein-protein interactions with membrane-associated protein complexes. Some sorting nexin family members have been shown to facilitate protein sorting. This model contains the RUN domain of SNX29.


Pssm-ID: 439051  Cd Length: 166  Bit Score: 65.33  E-value: 1.92e-12
                         10        20        30        40        50        60
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 513183311 153 LPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMM-EEEGAIIAGLLVGLNVI 218
Cdd:cd17689   93 LKNIWTDIGRGRAWLRSALNEHSLERYLHILLSNENLLRQYYEDWAFLRdEERSSMLPNMAAGLGSI 159
RUN_RUFY4 cd17697
RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; ...
 108-218 2.66e-11

RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; RUFY4 acts as a positive regulator that enhances autophagy and lysosome tethering in response to Interleukin-4. It is expressed in a cell-specific manner or under specific immunological conditions associated with IL4 expression such as allergic asthma. RUFY4 belongs to the FUFY protein family which is characterized by the presence of an N-terminal RUN domain and a C-terminal FYVE domain; this model represents the RUN domain of RUFY4.


Pssm-ID: 439059  Cd Length: 150  Bit Score: 61.35  E-value: 2.66e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 108 MEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRK 187
Cdd:cd17697   35 LEYLLQFDQKEKKSFFGSRKDYWDFLCLCLNRHRGGTEGIHFVNSTDKLKTPLGKGRAFIRYCLVQQQLAESLQLCLLNP 114

                         90       100       110
                 ....*....|....*....|....*....|..
gi 513183311 188 DLLSEFYEPNA-LMMEEEGAIIAGLLVGLNVI 218
Cdd:cd17697  115 ELTGEWYYARSpFLSPELRSDILDSLYELNGV 146
RUN_SGSM1_like cd17687
RUN domain found in small G protein signaling modulators, SGSM1, SGSM2, and similar proteins; ...
 109-219 6.80e-11

RUN domain found in small G protein signaling modulators, SGSM1, SGSM2, and similar proteins; SGSM1, also called RUN and TBC1 domain-containing protein 2 (RUTBC2), interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. It is a Rab9A effector and GTPase-activating protein for Rab36, and links Rab9A function to Rab36 function in the endosomal system. SGSM2, also called RUN and TBC1 domain-containing protein 1 (RUTBC1), is a GTPase-activating protein for Rab32/38, and regulates melanogenic enzyme trafficking in melanocytes. It also acts as a Rab9A effector that activates GTP hydrolysis by Rab32 and Rab33B proteins. This model contains the RUN domain of SGSM1 and SGSM2.


Pssm-ID: 439049  Cd Length: 161  Bit Score: 60.76  E-value: 6.80e-11
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 109 EHCLKHGLKAKK-TFLGQNKSFwGPLELVEKLVPEAAEITASVKDL------PGLKTPVGRGRA-------------WLR 168
Cdd:cd17687   31 DACLLHGLRKRAlGLFRSSSTF-SLLQKVAKSCPPAADILRKVQEIenlsenKRSSSSSGSNSSnshgnsssnrkilWIR 109

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|..
gi 513183311 169 LALMQKKLSEYMKALINRKdllSEFYEPNALMME-EEGAIIAGLLVGLNVID 219
Cdd:cd17687  110 IALFEKVLDKIVDYLVENA---SKYYEKEALMADpVDGPLLASLLVGPCALD 158
RUN_PLEKHM2 cd17680
RUN domain found in pleckstrin homology domain-containing family M member 2 (PLEKHM2) and ...
 79-200 1.40e-10

RUN domain found in pleckstrin homology domain-containing family M member 2 (PLEKHM2) and similar proteins; PLEKHM2, also called PH domain-containing family M member 2, or Salmonella-induced filaments A (SifA) and Kinesin-Interacting Protein (SKIP), is the lysosome, melanosome and lytic granule cargo adaptor that controls lysosome positioning using a composite kinesin-1 heavy and light chain-binding domain. In addition to kinesin-1, it also interacts with several Rabs to affect endosomal trafficking. This model represents the RUN domain of PLEKHM2.


Pssm-ID: 439042  Cd Length: 145  Bit Score: 59.18  E-value: 1.40e-10
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  79 SIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKktflgqNKSFWGpleLVEKLVPEAAEItaSVKDLPGLKT 158
Cdd:cd17680   12 SLQSYSSSQEEEDVLITNENRELQRLCEALDHALLHGLRRG------NRGYWP---FVKEFTHKETIK--QIENLPNVTT 80

                         90       100       110       120
                 ....*....|....*....|....*....|....*....|..
gi 513183311 159 PVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALM 200
Cdd:cd17680   81 DLGRGRAWLYLALNEGSLESYLRSFLENRKLVKKFYHKHALL 122
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 243-463 1.50e-10

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 63.54  E-value: 1.50e-10
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   243 KDGNSTKGSegDGQITAILDQKNYVEELNRH---LSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE 319
Cdd:TIGR02168  657 PGGVITGGS--AKTNSSILERRREIEELEEKieeLEEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   320 SSYILESNRKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDD 399
Cdd:TIGR02168  735 LARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTL 814

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 513183311   400 LRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 463
Cdd:TIGR02168  815 LNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEAL 878
RUN_FYCO1 cd17698
RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar ...
 74-222 1.56e-09

RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar proteins; FYCO1, also called zinc finger FYVE domain-containing protein 7 (ZFYVE7), is a multidomain autophagy adaptor protein that interacts with kinesin motor proteins and with the autophagosomal membrane components microtubule-associated protein 1 light chain 3 (LC3), Rab7, and Phosphatidylinositol 3-phosphate (PI3P), to mediate microtubule plus-end-directed autophagosome transport. This model represents the RUN domain of FYCO1.


Pssm-ID: 439060  Cd Length: 158  Bit Score: 56.63  E-value: 1.56e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  74 NMAKLSIKGLIESALNLGRTLDSDYAP-------LQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEI 146
Cdd:cd17698    2 SQLQKIIRDLQDCVTELKKEFEETGEPitddsttLHKFCAKLEYLLQFDQKEKTTLLGGRKDYWDYFCECLAKVKGLNDG 81

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 513183311 147 TASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEP-NALMMEEEGAIIAGLLVGLNviDANF 222
Cdd:cd17698   82 IRFVKSLKEVRTSLGKGRAFIRYSLVHQRLADTLQQCVMNGKVTSDWYYPrSVFLNHKYSSDIINSLYDLN--EVQF 156
RUN1_DENND5 cd17677
RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins; DENND5 ...
 114-223 2.74e-09

RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins; DENND5 has been characterized as Rab6-interacting protein which is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. It functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. DENND5 has two isoforms, DENND5A and DENND5B. This model represents the first RUN domain of DENND5.


Pssm-ID: 439039  Cd Length: 183  Bit Score: 56.64  E-value: 2.74e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 114 HGLKAKktflgQNKS-FWGPL----ELVEKLVPEAAEITA---SVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALIN 185
Cdd:cd17677   65 HGLQTK-----QGKSaLWSHLlayqENEERLKPLPESLLFdmkNVQNMKEIKTDVGYARAWIRLALEKKLLSKHLKTLLS 139

                         90       100       110
                 ....*....|....*....|....*....|....*....
gi 513183311 186 RKDLLSEFYEPNA-LMMEEEGAIIAGLLVGLNVIDAnFC 223
Cdd:cd17677  140 NQDLLRSLYKRYAfLRCEDEREQFLYHLLSLNAVDY-FC 177
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 264-465 3.18e-09

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 59.30  E-value: 3.18e-09
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   264 KNYVEELNRHLSAtVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTE 343
Cdd:TIGR02168  263 QELEEKLEELRLE-VSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEELESKLDELAEELAE 341

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   344 ARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDMGVKQKSE 423
Cdd:TIGR02168  342 LEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQQ 421

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....
gi 513183311   424 LNSRLEEK--TNQMAATIKQLEQSEKDLVKQAKTLNSAANKLIQ 465
Cdd:TIGR02168  422 EIEELLKKleEAELKELQAELEELEEELEELQEELERLEEALEE 465
RUN_RUBCN cd17686
RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing ...
 88-221 5.50e-09

RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing protein (RUBCN) and similar proteins; RUBCN, also called rubicon, or beclin-1 associated RUN domain containing protein (Baron), is part of a Beclin-1-Vps34-containing autophagy complex. It negatively regulates endosome maturation and degradative endocytic trafficking and impairs autophagosome maturation process. It is also an important negative regulator of the innate immune response, enhances viral replication and may play a role in viral immune evasion. This model contains the RUN domain of RUBCN.


Pssm-ID: 439048  Cd Length: 151  Bit Score: 54.97  E-value: 5.50e-09
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  88 LNLGRTLD--SDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNkSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVG-RGR 164
Cdd:cd17686    6 LLLSRSSNvwSTYGGLQRLCRAVENILQHGLKEFQGLNKEI-DDWEFVQGLRWLQPTLAPSIEQQSRSSPSESEVSdKGR 84

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|....*..
gi 513183311 165 AWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAiiAGLLVGLNVIDAN 221
Cdd:cd17686   85 LWLRQSLQQHCLSSQLQWLVSDKELLRKYYEDEAFLRQEGYA--TALLICLTAVELN 139
RUN1_DENND5B cd17691
RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins; DENND5B, ...
 150-223 5.20e-08

RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins; DENND5B, also called Rab6-interacting protein 1 (Rab6IP1)-like protein, functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the first RUN domain of DENND5B.


Pssm-ID: 439053 [Multi-domain]  Cd Length: 206  Bit Score: 53.14  E-value: 5.20e-08
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 513183311 150 VKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNA-LMMEEEGAIIAGLLVGLNVIDAnFC 223
Cdd:cd17691  127 IQNMSEIKTDVGRARAWIRLSLEKKLLSQHLKQLLSNQALTKKLYKRYAfLRCEEEKEQFLYHLLSLNAVDY-FC 200
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 255-463 1.20e-07

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 53.61  E-value: 1.20e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 255 GQITAILDQKNYVEELNRHLSAtvnnLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDR 334
Cdd:COG4942   17 AQADAAAEAEAELEQLQQEIAE----LEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEI 92

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 335 TADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQE----MELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFK 410
Cdd:COG4942   93 AELRAELEAQKEELAELLRALYRLGRQPPLALLLSPEdfldAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAE 172

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|...
gi 513183311 411 LQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 463
Cdd:COG4942  173 RAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEEL 225
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 256-463 1.30e-07

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 54.17  E-value: 1.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 256 QITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRT 335
Cdd:COG1196  296 ELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELA 375

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 336 ADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSfklqssd 415
Cdd:COG1196  376 EAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAA------- 448

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|....*...
gi 513183311 416 mgvKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 463
Cdd:COG1196  449 ---EEEAELEEEEEALLELLAELLEEAALLEAALAELLEELAEAAARL 493
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 256-467 1.30e-07

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 54.17  E-value: 1.30e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 256 QITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRT 335
Cdd:COG1196  233 KLRELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELARLEQDIARLEERRR 312

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 336 ADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSD 415
Cdd:COG1196  313 ELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEAL 392

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|..
gi 513183311 416 mgvKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKLIQKH 467
Cdd:COG1196  393 ---RAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEE 441
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 247-461 2.34e-07

chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. This family represents the SMC protein of most bacteria. The smc gene is often associated with scpB (TIGR00281) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 53.52  E-value: 2.34e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   247 STKGSEGDGQITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE---SSYI 323
Cdd:TIGR02168  725 SRQISALRKDLARLEAEVEQLEERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEElkaLREA 804

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   324 LESNRKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQE----MELAMKMLEKDVCEKQDALVALRQQLDD 399
Cdd:TIGR02168  805 LDELRAELTLLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEdiesLAAEIEELEELIEELESELEALLNERAS 884

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311   400 LRALKHELSFKLQSSDMGV----KQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAAN 461
Cdd:TIGR02168  885 LEEALALLRSELEELSEELreleSKRSELRRELEELREKLAQLELRLEGLEVRIDNLQERLSEEYS 950
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 248-437 4.50e-07

Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function unknown];


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 51.75  E-value: 4.50e-07
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 248 TKGSEGDGQITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE------SS 321
Cdd:COG3883   16 PQIQAKQKELSELQAELEAAQAELDALQAELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAEIEERREElgerarAL 95

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 322 Y-----------ILESN---------RKVTKDRTADGQALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEK 381
Cdd:COG3883   96 YrsggsvsyldvLLGSEsfsdfldrlSALSKIADADADLLEELKADKAELEAKKAELEAKLAELEALKAELEAAKAELEA 175

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311 382 DVCEKQDALVALRQQLDDLRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAA 437
Cdd:COG3883  176 QQAEQEALLAQLSAEEAAAEAQLAELEAELAAAEAAAAAAAAAAAAAAAAAAAAAA 231
RUN_SGSM1 cd17703
RUN domain found in small G protein signaling modulator 1 (SGSM1) and similar proteins; SGSM1, ...
 80-214 1.51e-06

RUN domain found in small G protein signaling modulator 1 (SGSM1) and similar proteins; SGSM1, also called RUN and TBC1 domain-containing protein 2 (RUTBC2), interacts with numerous Rab family members, functioning as Rab effector for some, and as GTPase activator for others. It is a Rab9A effector and GTPase-activating protein for Rab36, and links Rab9A function to Rab36 function in the endosomal system. This model contains the RUN domain of SGSM1.


Pssm-ID: 439065  Cd Length: 177  Bit Score: 48.47  E-value: 1.51e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  80 IKGLIESALNLgRTLDSDYAPLQQFFVVMEHCLKHGLKAKKT-FLGQNK----------SFWGPLELVEKL--------- 139
Cdd:cd17703    3 VKQIMEEAVTR-KFVHEDSSHIISFCAAVEACVLHGLKRRAAgFLRSNKiaalfmkvgkSFPPAEELCRKVqeleqllen 81

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 140 ----VPEAAEITASVKDLPGLkTPVGRGRAWLRLALMQKKLSEYMKALINRKdllSEFYEPNALMMEE-EGAIIAGLLVG 214
Cdd:cd17703   82 krnqMQGLQENVRKMPKLPNL-SPQAIKHLWIRTALFEKVLDKIVHYLVENS---SKYYEKEALLMDPvDGPILASLLVG 157
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 281-466 3.09e-06

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 49.94  E-value: 3.09e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 281 LQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESsyilesnRKVTKDRTADGQALTEARKQLKEETQLRLDVEK 360
Cdd:COG1196  307 LEERRRELEERLEELEEELAELEEELEELEEELEELEEEL-------EEAEEELEEAEAELAEAEEALLEAEAELAEAEE 379

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 361 ELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIK 440
Cdd:COG1196  380 ELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAELEEEEE 459

                        170       180
                 ....*....|....*....|....*.
gi 513183311 441 QLEQSEKDLVKQAKTLNSAANKLIQK 466
Cdd:COG1196  460 ALLELLAELLEEAALLEAALAELLEE 485
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 268-466 3.70e-06

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 49.55  E-value: 3.70e-06
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 268 EELNRhLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTEARKQ 347
Cdd:COG1196  281 LELEE-AQAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAE 359

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 348 LKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSfklqssdmgvKQKSELNSR 427
Cdd:COG1196  360 LAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLE----------EELEELEEA 429

                        170       180       190
                 ....*....|....*....|....*....|....*....
gi 513183311 428 LEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKLIQK 466
Cdd:COG1196  430 LAELEEEEEEEEEALEEAAEEEAELEEEEEALLELLAEL 468
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 312-449 4.12e-06

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 49.35  E-value: 4.12e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  312 EMERVKEES---SYILESNRKVTKDRTADGQAL-TEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQ 387
Cdd:pfam17380 447 EMERVRLEEqerQQQVERLRQQEEERKRKKLELeKEKRDRKRAEEQRRKILEKELEERKQAMIEEERKRKLLEKEMEERQ 526

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 513183311  388 DALV--ALRQQLDDLRALKHELSFKLQSSDMgVKQKSELNSRLE--EKTNQMAATIKQLEQSEKDL 449
Cdd:pfam17380 527 KAIYeeERRREAEEERRKQQEMEERRRIQEQ-MRKATEERSRLEamEREREMMRQIVESEKARAEY 591
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 256-462 1.05e-05

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 47.45  E-value: 1.05e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 256 QITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE------SSYILESNRK 329
Cdd:COG4942   42 ELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRAELEAQKEElaellrALYRLGRQPP 121

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 330 VTKDRTADGQALTEARKQ-LKEETQLRLDVEKELEAQigmRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELS 408
Cdd:COG4942  122 LALLLSPEDFLDAVRRLQyLKYLAPARREQAEELRAD---LAELAALRAELEAERAELEALLAELEEERAALEALKAERQ 198

                        170       180       190       200       210
                 ....*....|....*....|....*....|....*....|....*....|....
gi 513183311 409 FKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANK 462
Cdd:COG4942  199 KLLARLEKELAELAAELAELQQEAEELEALIARLEAEAAAAAERTPAAGFAALK 252
Golgin_A5 pfam09787
Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining ...
 277-463 1.77e-05

Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining Golgi structure. They stimulate the formation of Golgi stacks and ribbons, and are involved in intra-Golgi retrograde transport. Two main interactions have been characterized: one with RAB1A that has been activated by GTP-binding and another with isoform CASP of CUTL1.


Pssm-ID: 462900 [Multi-domain]  Cd Length: 305  Bit Score: 46.67  E-value: 1.77e-05
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  277 TVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRkvtkdrtadgQALTEARKQLKEETQLRL 356
Cdd:pfam09787  41 SSTALTLELEELRQERDLLREEIQKLRGQIQQLRTELQELEAQQQEEAESSR----------EQLQELEEQLATERSARR 110

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  357 DVEKELEAQigmRQEMElamKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSdmgvKQKSELNSRLEEKTNQMA 436
Cdd:pfam09787 111 EAEAELERL---QEELR---YLEEELRRSKATLQSRIKDREAEIEKLRNQLTSKSQSS----SSQSELENRLHQLTETLI 180

                         170       180       190
                  ....*....|....*....|....*....|
gi 513183311  437 ATIKQLE--QSEKD-LVKQAKTLNSAANKL 463
Cdd:pfam09787 181 QKQTMLEalSTEKNsLVLQLERMEQQIKEL 210
RUN1_DENND5A cd17690
RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins; DENND5A, ...
 150-223 7.22e-05

RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins; DENND5A, also called Rab6-interacting protein 1 (Rab6IP1), is present predominantly in developing neuronal tissue, and functions in membrane trafficking at a crossroads between the Golgi and the endosomal system. It is composed of an N-terminal DENN (Differentially Expressed in Normal and Neoplastic cells) domain followed by two RUN (RPIP8 [RaP2-interacting protein 8], UNC-14, and NESCA [new molecule containing SH3 at the carboxyl terminus]) domains flanking a PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain. This model represents the first RUN domain of DENND5A.


Pssm-ID: 439052 [Multi-domain]  Cd Length: 209  Bit Score: 43.84  E-value: 7.22e-05
                         10        20        30        40        50        60        70
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 513183311 150 VKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNA-LMMEEEGAIIAGLLVGLNVIDAnFC 223
Cdd:cd17690  130 IQNIGEIKTDVGKARAWVRLSMEKKLLSRHLKQLLSDHELTKKLYKRYAfLRCDDEKEQFLYHLLSFNAVDY-FC 203
GumC COG3206
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];
279-466 7.26e-05

Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];


Pssm-ID: 442439 [Multi-domain]  Cd Length: 687  Bit Score: 45.39  E-value: 7.26e-05
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 279 NNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYI-LESNRKVTKDRTAD-GQALTEARKQLkEETQLRL 356
Cdd:COG3206  164 QNLELRREEARKALEFLEEQLPELRKELEEAEAALEEFRQKNGLVdLSEEAKLLLQQLSElESQLAEARAEL-AEAEARL 242

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 357 DvekELEAQIGMRQEmELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDmgvKQKSELNSRLEEKTNQMA 436
Cdd:COG3206  243 A---ALRAQLGSGPD-ALPELLQSPVIQQLRAQLAELEAELAELSARYTPNHPDVIALR---AQIAALRAQLQQEAQRIL 315

                        170       180       190
                 ....*....|....*....|....*....|....
gi 513183311 437 ATIK----QLEQSEKDLVKQAKTLNSAANKLIQK 466
Cdd:COG3206  316 ASLEaeleALQAREASLQAQLAQLEARLAELPEL 349
CagA_N pfam18971
CagA protein; The Helicobacter pylori type IV secretion effector CagA is a major bacterial ...
 279-463 1.10e-04

CagA protein; The Helicobacter pylori type IV secretion effector CagA is a major bacterial virulence determinant and critical for gastric carcinogenesis. X-ray crystallographic analysis of the N-terminal CagA fragment (residues 1-876) revealed that the region has a structure comprised of three discrete domains. Domain I constitutes a mobile CagA N terminus, while Domain II tethers CagA to the plasma membrane by interacting with membrane phosphatidylserine. Domain III interacts intramolecularly with the intrinsically disordered C-terminal region, and this interaction potentiates the pathogenic scaffold/hub function of CagA.


Pssm-ID: 408741 [Multi-domain]  Cd Length: 876  Bit Score: 44.76  E-value: 1.10e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  279 NNLQAKVDALEKSNtKLTEELAVANnriitlqeemervKEESSYILESNRKVTKDRTADG-----QALTEARKQLKEETQ 353
Cdd:pfam18971 563 NKLTAKGLSLQEAN-KLIKDFLSSN-------------KELAGKALNFNKAVAEAKSTGNydevkKAQKDLEKSLRKREH 628

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  354 LRLDVEKELEAQIGMRQEMEL-AMKMLEKDVC-------EKQDALVALRQQldDLRALKHELSFKLQ--SSDMGVKQKS- 422
Cdd:pfam18971 629 LEKEVEKKLESKSGNKNKMEAkAQANSQKDEIfalinkeANRDARAIAYTQ--NLKGIKRELSDKLEkiSKDLKDFSKSf 706

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|....*...
gi 513183311  423 -ELNSRLEEKTNQMAATIKQLEQSEKDL------VKQAKTLNSAANKL 463
Cdd:pfam18971 707 dEFKNGKNKDFSKAEETLKALKGSVKDLginpewISKVENLNAALNEF 754
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 299-467 1.30e-04

Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 443969 [Multi-domain]  Cd Length: 377  Bit Score: 43.98  E-value: 1.30e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 299 LAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTEARKQLKEETQLRldveKELEAQIgmrQEMELAMKM 378
Cdd:COG4942   15 AAAQADAAAEAEAELEQLQQEIAELEKELAALKKEEKALLKQLAALERRIAALARRI----RALEQEL---AALEAELAE 87

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 379 LEKDVCEKQDALVALRQQLDD-LRAL-----KHELSFKLQSSDMGVKQKS-----ELNSRLEEKTNQMAATIKQLEQSEK 447
Cdd:COG4942   88 LEKEIAELRAELEAQKEELAElLRALyrlgrQPPLALLLSPEDFLDAVRRlqylkYLAPARREQAEELRADLAELAALRA 167

                        170       180
                 ....*....|....*....|
gi 513183311 448 DLVKQAKTLNSAANKLIQKH 467
Cdd:COG4942  168 ELEAERAELEALLAELEEER 187
PRK11281 PRK11281
mechanosensitive channel MscK;
272-466 2.29e-04

mechanosensitive channel MscK;


Pssm-ID: 236892 [Multi-domain]  Cd Length: 1113  Bit Score: 43.75  E-value: 2.29e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  272 RHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE----SSYILESNRKVTKDRTADGQALTEARKQ 347
Cdd:PRK11281  117 TLSTLSLRQLESRLAQTLDQLQNAQNDLAEYNSQLVSLQTQPERAQAAlyanSQRLQQIRNLLKGGKVGGKALRPSQRVL 196

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  348 LKEETQLrldvekeLEAQIGMRQEmELAMKMLEKDVCEKQDALVALRQQLddlraLKHELSFklqssdmgvkqkselnsr 427
Cdd:PRK11281  197 LQAEQAL-------LNAQNDLQRK-SLEGNTQLQDLLQKQRDYLTARIQR-----LEHQLQL------------------ 245

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|...
gi 513183311  428 LEEKTNQmaatiKQLEQSEKDlVKQAKTLNSAA----NKLIQK 466
Cdd:PRK11281  246 LQEAINS-----KRLTLSEKT-VQEAQSQDEAAriqaNPLVAQ 282
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
256-444 2.38e-04

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 43.75  E-value: 2.38e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  256 QITAILDQKNYVEELNRHLSATVNnlQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEEssyILESNRKVtkdRT 335
Cdd:COG4913   263 RYAAARERLAELEYLRAALRLWFA--QRRLELLEAELEELRAELARLEAELERLEARLDALREE---LDELEAQI---RG 334

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  336 ADGQALTEARKQLKeetqlrlDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSS- 414
Cdd:COG4913   335 NGGDRLEQLEREIE-------RLERELEERERRRARLEALLAALGLPLPASAEEFAALRAEAAALLEALEEELEALEEAl 407

                         170       180       190
                  ....*....|....*....|....*....|
gi 513183311  415 DMGVKQKSELNSRLEEKTNQmaatIKQLEQ 444
Cdd:COG4913   408 AEAEAALRDLRRELRELEAE----IASLER 433
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
282-467 2.44e-04

Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 43.75  E-value: 2.44e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  282 QAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEessyILESNRKVTKDRTA--DGQALTEARKQLKEE-TQLRLDV 358
Cdd:COG4913   609 RAKLAALEAELAELEEELAEAEERLEALEAELDALQE----RREALQRLAEYSWDeiDVASAEREIAELEAElERLDASS 684

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  359 E--KELEAQIgmrQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQssDMGVKQKSELNSRLEEK----- 431
Cdd:COG4913   685 DdlAALEEQL---EELEAELEELEEELDELKGEIGRLEKELEQAEEELDELQDRLE--AAEDLARLELRALLEERfaaal 759

                         170       180       190
                  ....*....|....*....|....*....|....*..
gi 513183311  432 -TNQMAATIKQLEQSEKDLVKQAKTLNSAANKLIQKH 467
Cdd:COG4913   760 gDAVERELRENLEERIDALRARLNRAEEELERAMRAF 796
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 260-458 2.89e-04

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 43.52  E-value: 2.89e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   260 ILDQK--NYVEELnRHLSATVNNLQAKVDALEKSNTKLTEELAvaNNRIITLQEEMERVKEESSyileSNRKVTKDRTAD 337
Cdd:TIGR02169  748 SLEQEieNVKSEL-KELEARIEELEEDLHKLEEALNDLEARLS--HSRIPEIQAELSKLEEEVS----RIEARLREIEQK 820

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   338 GQALTEARKQLKEETQLRLDVEKELEAQIGM-RQEMELAMKMLEK---DVCEKQDALVALRQQLDDLRALKHELSFKLqs 413
Cdd:TIGR02169  821 LNRLTLEKEYLEKEIQELQEQRIDLKEQIKSiEKEIENLNGKKEEleeELEELEAALRDLESRLGDLKKERDELEAQL-- 898

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*
gi 513183311   414 sdmgvkqkselnSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNS 458
Cdd:TIGR02169  899 ------------RELERKIEELEAQIEKKRKRLSELKAKLEALEE 931
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
277-463 6.04e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 42.36  E-value: 6.04e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 277 TVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEEssyiLESNRKVTKDRTADGQALTEA-RKQLKEETQLR 355
Cdd:PRK03918 385 TPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKA----IEELKKAKGKCPVCGRELTEEhRKELLEEYTAE 460

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 356 L-DVEKELEAQIGMRQEMELAMKMLEKdVCEKQDALVALRQQLDDLRALKHELS-FKLQSsdmgVKQKSELNSRLEEKTN 433
Cdd:PRK03918 461 LkRIEKELKEIEEKERKLRKELRELEK-VLKKESELIKLKELAEQLKELEEKLKkYNLEE----LEKKAEEYEKLKEKLI 535

                        170       180       190
                 ....*....|....*....|....*....|...
gi 513183311 434 QMAATIKQLE---QSEKDLVKQAKTLNSAANKL 463
Cdd:PRK03918 536 KLKGEIKSLKkelEKLEELKKKLAELEKKLDEL 568
HEC1 COG5185
Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell ...
 278-466 6.96e-04

Chromosome segregation protein NDC80, interacts with SMC proteins [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 444066 [Multi-domain]  Cd Length: 594  Bit Score: 42.25  E-value: 6.96e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 278 VNNLQAKVDALEKSNTKLTEELAVANNriiTLQEEMERVKEESSYILESNRKVTKDRTAD--GQALTEARKQLKEETQLR 355
Cdd:COG5185  324 EQELEESKRETETGIQNLTAEIEQGQE---SLTENLEAIKEEIENIVGEVELSKSSEELDsfKDTIESTKESLDEIPQNQ 400

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 356 LDVEKELEAQIgmrqemELAMKMLEKDVCEKQDALVALRQQLDD----LRALKHELSFKLQSSDMGVKQK-----SELNS 426
Cdd:COG5185  401 RGYAQEILATL------EDTLKAADRQIEELQRQIEQATSSNEEvsklLNELISELNKVMREADEESQSRleeayDEINR 474

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|
gi 513183311 427 RLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKLIQK 466
Cdd:COG5185  475 SVRSKKEDLNEELTQIESRVSTLKATLEKLRAKLERQLEG 514
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 339-463 1.87e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 39.91  E-value: 1.87e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 339 QALTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLD------DLRALKHELSFklQ 412
Cdd:COG1579   24 HRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEEVEARIKKYEEQLGnvrnnkEYEALQKEIES--L 101

                         90       100       110       120       130
                 ....*....|....*....|....*....|....*....|....*....|...
gi 513183311 413 SSDMGV--KQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 463
Cdd:COG1579  102 KRRISDleDEILELMERIEELEEELAELEAELAELEAELEEKKAELDEELAEL 154
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 281-456 1.92e-03

Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General function prediction only];


Pssm-ID: 441187 [Multi-domain]  Cd Length: 236  Bit Score: 39.91  E-value: 1.92e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 281 LQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTEARKQLKEETQLR--LDV 358
Cdd:COG1579   15 LDSELDRLEHRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEEVEARIKKYEEQLGNVRNNKeyEAL 94

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 359 EKELEAQigmrqemELAMKMLEKDVCEKQDALVALRQQLDDLRAlkhelsfklqssdmgvkQKSELNSRLEEKTNQMAAT 438
Cdd:COG1579   95 QKEIESL-------KRRISDLEDEILELMERIEELEEELAELEA-----------------ELAELEAELEEKKAELDEE 150

                        170
                 ....*....|....*...
gi 513183311 439 IKQLEQSEKDLVKQAKTL 456
Cdd:COG1579  151 LAELEAELEELEAEREEL 168
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 251-465 2.39e-03

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 40.44  E-value: 2.39e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   251 SEGDGQITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEElavannRIITLQEEMERVKEESSYiLESNRKV 330
Cdd:TIGR02169  240 EAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEE------EQLRVKEKIGELEAEIAS-LERSIAE 312

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   331 TKDRTADGQA-----LTEARKQLKEETQLRLDVE---KELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLR- 401
Cdd:TIGR02169  313 KERELEDAEErlaklEAEIDKLLAEIEELEREIEeerKRRDKLTEEYAELKEELEDLRAELEEVDKEFAETRDELKDYRe 392

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 513183311   402 ---ALKHELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKLIQ 465
Cdd:TIGR02169  393 kleKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKLEQ 459
PRK04778 PRK04778
septation ring formation regulator EzrA; Provisional
 267-466 2.68e-03

septation ring formation regulator EzrA; Provisional


Pssm-ID: 179877 [Multi-domain]  Cd Length: 569  Bit Score: 40.20  E-value: 2.68e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 267 VEELNRHLSATVNNL----QAKVDA---LEKSNTKLTEELAVANNRIITLQEEMERVKEesSYIL-----ESNRKVTKDR 334
Cdd:PRK04778 280 AEEKNEEIQERIDQLydilEREVKArkyVEKNSDTLPDFLEHAKEQNKELKEEIDRVKQ--SYTLneselESVRQLEKQL 357

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 335 TADGQALTEARKQLKEETQLRLDVEKELEaqigmrqEMELAMKMLEKDVCEKQDALVAL-------RQQLDDLRALKHEL 407
Cdd:PRK04778 358 ESLEKQYDEITERIAEQEIAYSELQEELE-------EILKQLEEIEKEQEKLSEMLQGLrkdeleaREKLERYRNKLHEI 430

                        170       180       190       200       210       220       230
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|..
gi 513183311 408 SFKLQSSDM-GVKQK------------SELNSRLEEKTNQMAATIKQLEQSEKDLvkqaKTLNSAANKLIQK 466
Cdd:PRK04778 431 KRYLEKSNLpGLPEDylemffevsdeiEALAEELEEKPINMEAVNRLLEEATEDV----ETLEEETEELVEN 498
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 242-456 2.75e-03

Family of unknown function (DUF5401); This is a family of unknown function found in Chromadorea.


Pssm-ID: 375164 [Multi-domain]  Cd Length: 722  Bit Score: 40.11  E-value: 2.75e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  242 LKDGNSTKGSEGDGQITAILDQKNYVEELNRHLSATvnNLQAKVDALEKSNTkltEELAVANNRIITL-------QEEME 314
Cdd:pfam17380 318 LEEAEKARQAEMDRQAAIYAEQERMAMERERELERI--RQEERKRELERIRQ---EEIAMEISRMRELerlqmerQQKNE 392

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  315 RVKEEssyiLESNRKVtkdRTADGQALTEARKQLKEETQLRLDVEKELEAQIG-MRQEMELAMKMLEKDVCEKQDALVAL 393
Cdd:pfam17380 393 RVRQE----LEAARKV---KILEEERQRKIQQQKVEMEQIRAEQEEARQREVRrLEEERAREMERVRLEEQERQQQVERL 465

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 513183311  394 RQQLDDLRALKHELSFKLQSSDMGVKQKSE-LNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTL 456
Cdd:pfam17380 466 RQQEEERKRKKLELEKEKRDRKRAEEQRRKiLEKELEERKQAMIEEERKRKLLEKEMEERQKAI 529
Mplasa_alph_rch TIGR04523
helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of ...
 254-465 3.16e-03

helix-rich Mycoplasma protein; Members of this family occur strictly within a subset of Mycoplasma species. Members average 750 amino acids in length, including signal peptide. Sequences are predicted (Jpred 3) to be almost entirely alpha-helical. These sequences show strong periodicity (consistent with long alpha helical structures) and low complexity rich in D,E,N,Q, and K. Genes encoding these proteins are often found in tandem. The function is unknown.


Pssm-ID: 275316 [Multi-domain]  Cd Length: 745  Bit Score: 40.00  E-value: 3.16e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  254 DGQITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYI---LESNRKV 330
Cdd:TIGR04523 411 DEQIKKLQQEKELLEKEIERLKETIIKNNSEIKDLTNQDSVKELIIKNLDNTRESLETQLKVLSRSINKIkqnLEQKQKE 490

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311  331 TKDRTADGQALTEARKQLKEETQ-------LRLDVEKELEAQIGMRQ-------------EMELAMKMLEKDVCEKQDAL 390
Cdd:TIGR04523 491 LKSKEKELKKLNEEKKELEEKVKdltkkisSLKEKIEKLESEKKEKEskisdledelnkdDFELKKENLEKEIDEKNKEI 570

                         170       180       190       200       210       220       230
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*...
gi 513183311  391 VALRQQLDDLRALKHELSFKLQSSDmgvKQKSELNSRLEEKTNQMAATIKQLEQSEK---DLVKQAKTLNSAANKLIQ 465
Cdd:TIGR04523 571 EELKQTQKSLKKKQEEKQELIDQKE---KEKKDLIKEIEEKEKKISSLEKELEKAKKeneKLSSIIKNIKSKKNKLKQ 645
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 268-444 4.93e-03

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 39.39  E-value: 4.93e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   268 EELNRHLSATVNNLQAKVDALEKsntKLTEELAvANNRI----ITLQEEMERVKEESSYILESNRKVTKDRTADGQALTE 343
Cdd:pfam01576   88 EERSQQLQNEKKKMQQHIQDLEE---QLDEEEA-ARQKLqlekVTTEAKIKKLEEDILLLEDQNSKLSKERKLLEERISE 163

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   344 ARKQLKEE-------TQLRL-------DVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRAL----KH 405
Cdd:pfam01576  164 FTSNLAEEeekakslSKLKNkheamisDLEERLKKEEKGRQELEKAKRKLEGESTDLQEQIAELQAQIAELRAQlakkEE 243

                          170       180       190
                   ....*....|....*....|....*....|....*....
gi 513183311   406 ELSFKLQSSDMGVKQKSELNSRLEEKTNQMAATIKQLEQ 444
Cdd:pfam01576  244 ELQAALARLEEETAQKNNALKKIRELEAQISELQEDLES 282
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 268-456 5.95e-03

chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of chromosomes) proteins bind DNA and act in organizing and segregating chromosomes for partition. SMC proteins are found in bacteria, archaea, and eukaryotes. It is found in a single copy and is homodimeric in prokaryotes, but six paralogs (excluded from this family) are found in eukarotes, where SMC proteins are heterodimeric. This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by TIGR02168. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent. [Cellular processes, Cell division, DNA metabolism, Chromosome-associated proteins]


Pssm-ID: 274009 [Multi-domain]  Cd Length: 1164  Bit Score: 39.28  E-value: 5.95e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   268 EELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTEARKQ 347
Cdd:TIGR02169  286 EEEQLRVKEKIGELEAEIASLERSIAEKERELEDAEERLAKLEAEIDKLLAEIEELEREIEEERKRRDKLTEEYAELKEE 365

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   348 LKEetqLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDMGVKQKSELNSR 427
Cdd:TIGR02169  366 LED---LRAELEEVDKEFAETRDELKDYREKLEKLKREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEE 442

                          170       180
                   ....*....|....*....|....*....
gi 513183311   428 LEEKTNQMAATIKQLEQSEKDLVKQAKTL 456
Cdd:TIGR02169  443 KEDKALEIKKQEWKLEQLAADLSKYEQEL 471
Myosin_tail_1 pfam01576
Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and ...
 264-458 6.66e-03

Myosin tail; The myosin molecule is a multi-subunit complex made up of two heavy chains and four light chains it is a fundamental contractile protein found in all eukaryote cell types. This family consists of the coiled-coil myosin heavy chain tail region. The coiled-coil is composed of the tail from two molecules of myosin. These can then assemble into the macromolecular thick filament. The coiled-coil region provides the structural backbone the thick filament.


Pssm-ID: 460256 [Multi-domain]  Cd Length: 1081  Bit Score: 39.00  E-value: 6.66e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   264 KNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAvannriiTLQEEMERVKEESSYILESNRKVTKDRTADGQALTE 343
Cdd:pfam01576  400 KQDSEHKRKKLEGQLQELQARLSESERQRAELAEKLS-------KLQSELESVSSLLNEAEGKNIKLSKDVSSLESQLQD 472

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311   344 ARKQLKEETQLRLDVEKELEAqigmrqemelamkmLEkdvcekqDALVALRQQLDDLRALKHELSFKLQSSDMgvkQKSE 423
Cdd:pfam01576  473 TQELLQEETRQKLNLSTRLRQ--------------LE-------DERNSLQEQLEEEEEAKRNVERQLSTLQA---QLSD 528

                          170       180       190
                   ....*....|....*....|....*....|....*
gi 513183311   424 LNSRLEEktnqMAATIKQLEQSEKDLVKQAKTLNS 458
Cdd:pfam01576  529 MKKKLEE----DAGTLEALEEGKKRLQRELEALTQ 559
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 298-466 8.44e-03

Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning];


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 38.76  E-value: 8.44e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 298 ELAVANNRIITLQEEMERVKEESSYILESNRKVTKDRTADGQALTEARKQLKEEtqlrldvEKELEAQIGMRQEMELAMK 377
Cdd:COG1196  226 EAELLLLKLRELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEEL-------ELELEEAQAEEYELLAELA 298

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 378 MLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQSSDmgvKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLN 457
Cdd:COG1196  299 RLEQDIARLEERRRELEERLEELEEELAELEEELEELE---EELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELA 375


                 ....*....
gi 513183311 458 SAANKLIQK 466
Cdd:COG1196  376 EAEEELEEL 384
YhaN COG4717
Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];
255-402 8.45e-03

Uncharacterized conserved protein YhaN, contains AAA domain [Function unknown];


Pssm-ID: 443752 [Multi-domain]  Cd Length: 641  Bit Score: 38.60  E-value: 8.45e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 255 GQITAILDQKNYVEELNRHLSATVNNLQAKVDALEK--SNTKLTEELAVANNRIITLQEEMERVKEEssyiLESNRKVTK 332
Cdd:COG4717   88 EEYAELQEELEELEEELEELEAELEELREELEKLEKllQLLPLYQELEALEAELAELPERLEELEER----LEELRELEE 163

                         90       100       110       120       130       140       150
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 513183311 333 DRTADGQALTEARKQLKEE-TQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRA 402
Cdd:COG4717  164 ELEELEAELAELQEELEELlEQLSLATEEELQDLAEELEELQQRLAELEEELEEAQEELEELEEELEQLEN 234
COG4372 COG4372
Uncharacterized protein, contains DUF3084 domain [Function unknown];
253-453 9.30e-03

Uncharacterized protein, contains DUF3084 domain [Function unknown];


Pssm-ID: 443500 [Multi-domain]  Cd Length: 370  Bit Score: 38.34  E-value: 9.30e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 253 GDGQITAILDQKNYVEELNRHLSATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEEssyilesnrkvtk 332
Cdd:COG4372    1 GDRLGEKVGKARLSLFGLRPKTGILIAALSEQLRKALFELDKLQEELEQLREELEQAREELEQLEEE------------- 67

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 513183311 333 drtadgqaLTEARKQLKEETQLRLDVEKELEAQIGMRQEMELAMKMLEKDVCEKQDALVALRQQLDDLRALKHELSFKLQ 412
Cdd:COG4372   68 --------LEQARSELEQLEEELEELNEQLQAAQAELAQAQEELESLQEEAEELQEELEELQKERQDLEQQRKQLEAQIA 139

                        170       180       190       200
                 ....*....|....*....|....*....|....*....|.
gi 513183311 413 SSDMGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQA 453
Cdd:COG4372  140 ELQSEIAEREEELKELEEQLESLQEELAALEQELQALSEAE 180
 
Blast search parameters
Data Source: Precalculated data, version = cdd.v.3.21
Preset Options:Database: CDSEARCH/cdd   Low complexity filter: no  Composition Based Adjustment: yes   E-value threshold: 0.01

References:

  • Wang J et al. (2023), "The conserved domain database in 2023", Nucleic Acids Res.51(D)384-8.
  • Lu S et al. (2020), "The conserved domain database in 2020", Nucleic Acids Res.48(D)265-8.
  • Marchler-Bauer A et al. (2017), "CDD/SPARCLE: functional classification of proteins via subfamily domain architectures.", Nucleic Acids Res.45(D)200-3.
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