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Conserved domains on  [gi|68341991|ref|NP_001020298|]
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protein RUFY3 isoform 4 [Rattus norvegicus]

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 1.74e-99

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: 294.98  E-value: 1.74e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17696   1 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 68341991 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEEGAIIAGLLVGLNVIDANFC 223
Cdd:cd17696  81 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINRKDLLSEFYEPNALMMEEEGAIIAGLLVGLNVIDANFC 156
SMC_prok_B super family cl37069
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 243-464 1.86e-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]


The actual alignment was detected with superfamily member TIGR02168:

Pssm-ID: 274008 [Multi-domain]  Cd Length: 1179  Bit Score: 53.91  E-value: 1.86e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    243 KDGNSSKGSegDGQITAILDQKNYVEELNRHLN---ATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE 319
Cdd:TIGR02168  657 PGGVITGGS--AKTNSSILERRREIEELEEKIEeleEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    320 SSYLLESNRKGpKQDRTAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLD 399
Cdd:TIGR02168  735 LARLEAEVEQL-EERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELT 813

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68341991    400 DLRALKHELAFKLQSSDLGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:TIGR02168  814 LLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEAL 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 1.74e-99

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: 294.98  E-value: 1.74e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17696   1 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 68341991 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEEGAIIAGLLVGLNVIDANFC 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 1.14e-43

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: 150.12  E-value: 1.14e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   103 QFFVVMEHCLKHGLKA------KKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKT---PVGRGRAWLRLALMQ 173
Cdd:pfam02759   1 QLCAALEALLSHGLKRssllilRAAGLLPERSFWALLERVGKLVPPAEELLSSVQELEQIHTpysPDGRGRAWIRLALNE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 68341991   174 KKLSEYMKALINKKELLSEFYEANALMMEEEGA-IIAGLLVGLNVIDANFCMKG 226
Cdd:pfam02759  81 KLLDQWLKLLLSNKELLSEYYEPWALLADPEFGeILLGLLVGLSALDFNLCLKL 134
RUN smart00593
domain involved in Ras-like GTPase signaling;
163-225 6.15e-17

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 74.96  E-value: 6.15e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 68341991    163 GRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMM-EEEGAIIAGLLVGLNVIDANFCMK 225
Cdd:smart00593   1 FRAWIRLALNEKLLSSWLNLLLSDEELLSKYYEPWAFLRdPEEGEQLLGLLVGLSALDFNLPVD 64
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 243-464 1.86e-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: 53.91  E-value: 1.86e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    243 KDGNSSKGSegDGQITAILDQKNYVEELNRHLN---ATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE 319
Cdd:TIGR02168  657 PGGVITGGS--AKTNSSILERRREIEELEEKIEeleEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    320 SSYLLESNRKGpKQDRTAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLD 399
Cdd:TIGR02168  735 LARLEAEVEQL-EERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELT 813

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68341991    400 DLRALKHELAFKLQSSDLGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:TIGR02168  814 LLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEAL 878
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 255-464 4.63e-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: 51.69  E-value: 4.63e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 255 GQITAILDQKNYVEELNRHLNAtvnnLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSyLLESNRKGPKQD 334
Cdd:COG4942  17 AQADAAAEAEAELEQLQQEIAE----LEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELA-ALEAELAELEKE 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 335 RTAEGQALSEARKHLKEE--TQLRLDVEKELELQISMR--QEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAF 410
Cdd:COG4942  92 IAELRAELEAQKEELAELlrALYRLGRQPPLALLLSPEdfLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEA 171

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 68341991 411 KLQSSDLGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:COG4942 172 ERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEEL 225
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 312-450 7.57e-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: 48.58  E-value: 7.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   312 EMERVKEES---SYLLESNRKGPKQDRTAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQ 388
Cdd:pfam17380 447 EMERVRLEEqerQQQVERLRQQEEERKRKKLELEKEKRDRKRAEEQRRKILEKELEERKQAMIEEERKRKLLEKEMEERQ 526

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 68341991   389 DALV--SLRQQLDDLRALKHELAFKLQSSDlGVKQKSELNSRLE--EKTNQMAATIKQLEQSEKDL 450
Cdd:pfam17380 527 KAIYeeERRREAEEERRKQQEMEERRRIQE-QMRKATEERSRLEamEREREMMRQIVESEKARAEY 591
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
277-464 2.81e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 43.51  E-value: 2.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  277 TVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYLLESNRKGPKQDRTAEgqalSEARKHLKEETQLR 356
Cdd:PRK03918 385 TPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGKCPVCGRELT----EEHRKELLEEYTAE 460

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  357 L-DVEKELELQISMRQEMELAMKMLEKdVCEKQDALVSLRQQLDDLRALKHELAfKLQSSDLgvKQKSELNSRLEEKTNQ 435
Cdd:PRK03918 461 LkRIEKELKEIEEKERKLRKELRELEK-VLKKESELIKLKELAEQLKELEEKLK-KYNLEEL--EKKAEEYEKLKEKLIK 536

                        170       180       190
                 ....*....|....*....|....*....|..
gi 68341991  436 MAATIKQLE---QSEKDLVKQAKTLNSAANKL 464
Cdd:PRK03918 537 LKGEIKSLKkelEKLEELKKKLAELEKKLDEL 568
 
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 1.74e-99

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: 294.98  E-value: 1.74e-99
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17696   1 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 68341991 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEEGAIIAGLLVGLNVIDANFC 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 6.75e-97

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: 288.42  E-value: 6.75e-97
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17695   1 ERANLLNMAKLSIKGLIESALSFGRTLDSDYPPLQQFFVVMEHCLKHGLKVRKSFLSYNKTIWGPLELVEKLCPEAEEIA 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 68341991 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEEGAIIAGLLVGLNVIDANFC 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 1.09e-92

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: 277.53  E-value: 1.09e-92
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17681   1 ERRNLLNLAKLSIKELIESALSFGRTLDSDHVPLQQFFVILEHVLRHGLKVKKSFLGPNKSFWPVLEHVEKLVPEANEIT 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68341991 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEEGAIIAGLLVGLNVIDANF 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 1.17e-89

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: 269.85  E-value: 1.17e-89
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  68 ERMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEIT 147
Cdd:cd17694   1 ERANLMNMMKLSIKVLIQSALSLGRTLDSDYPPLQQFFVVLEHCLKHGLKVKKSFIGQNKSFFGPLELVEKLCPEASDIA 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 68341991 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEEGAIIAGLLVGLNVIDANFC 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 1.14e-43

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: 150.12  E-value: 1.14e-43
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   103 QFFVVMEHCLKHGLKA------KKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKT---PVGRGRAWLRLALMQ 173
Cdd:pfam02759   1 QLCAALEALLSHGLKRssllilRAAGLLPERSFWALLERVGKLVPPAEELLSSVQELEQIHTpysPDGRGRAWIRLALNE 80

                          90       100       110       120       130
                  ....*....|....*....|....*....|....*....|....*....|....
gi 68341991   174 KKLSEYMKALINKKELLSEFYEANALMMEEEGA-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 2.97e-35

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: 128.28  E-value: 2.97e-35
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  71 NLMNMAKLSIKGLIESALNlgRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLG--QNKSFWGPLELVEKLVPEAAeiTA 148
Cdd:cd17684   1 NLVTVCRLSVKSLIDKACL--ETIDDSSEELINFAAILEQILSHRLKPVKPWYGseEPRTFWDYIRVACKKVPQNC--IA 76

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 68341991 149 SVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEEGAIIAGLLVGLNVIDANF 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 6.22e-31

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: 116.76  E-value: 6.22e-31
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  79 SIKGLIESALNLGR-------TLDSDYAPLQQFFVVMEHCLKHGLKAKKtFLGQNKSFWGPLELVEKLVPEAAEITA--S 149
Cdd:cd17671   2 AVKELLESFADNGEaddsaalTLTDDDPVVGRLCAALEAILSHGLKPKR-FGGGKVSFWDFLEALEKLLPAPSLKQAirD 80

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....
gi 68341991 150 VKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMM-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 8.47e-27

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: 105.44  E-value: 8.47e-27
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  71 NLMNMAKLSIKGLIESALNlgRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFLGQN--KSFWGPLELVEKLVPEAAeiTA 148
Cdd:cd17700   1 NLITVCRFSVKTLIDRSCF--ETIDDSSPEFVNFAAILEQILSHRLKGQVTWFGYEspRSFWDYIRVACSKVPHNC--IC 76

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68341991 149 SVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEEGAIIAGLLVGLNVIDANFC 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 3.19e-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: 98.17  E-value: 3.19e-24
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  71 NLMNMAKLSIKGLIESALnlGRTLDSDYAPLQQFFVVMEHCLKHGLKAKKTFL---GQnKSFWGPLELVEKLVPEaaEIT 147
Cdd:cd17699   1 NLITVCRFSVKTLLEKYT--AEPIDDSSEEFVNFAAILEQILSHRFKGPVSWFssdGQ-RGFWDYIRLACSKVPN--NCI 75

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 68341991 148 ASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEEGAIIAGLLVGLNVIDANFC 223
Cdd:cd17699  76 SSIENMENISTSRAKGRAWIRVALMEKRLSEYIATALRDTRTTRRFYDDGAIMLREESTVLTGMLIGLSAIDFSFC 151
RUN smart00593
domain involved in Ras-like GTPase signaling;
163-225 6.15e-17

domain involved in Ras-like GTPase signaling;


Pssm-ID: 214736 [Multi-domain]  Cd Length: 64  Bit Score: 74.96  E-value: 6.15e-17
                           10        20        30        40        50        60
                   ....*....|....*....|....*....|....*....|....*....|....*....|....
gi 68341991    163 GRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMM-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 1.90e-15

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: 73.41  E-value: 1.90e-15
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  80 IKGLIESALNLGRTLDSDYAP-LQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLE-LVEKLVPEA---AEITASVKDLP 154
Cdd:cd17682   2 LKGCVLDLKSEFGEITDPDNPyLRPFCETLEKILRKGLKEKVSLGGRRKDYWDWLEeLLKKLNKIPkslSDAVKFVKSCK 81

                        90       100       110       120       130       140
                ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 68341991 155 GLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMMEEE-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 2.24e-12

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: 65.30  E-value: 2.24e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  69 RMNLMNMAKLSIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAK-----KTFLGQN------KSFWGPLELV- 136
Cdd:cd17679   1 KKSLTKELSSSVKELQLEYVSSDEVVTSSDDGANTLCCVLEAIFLHGLKDKfiskvSSVFSGDvdklpePNFWPLLLKFs 80

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 137 EKlvpeaaEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMM-EEEGAIIAGLLVGL 215
Cdd:cd17679  81 HR------DVIDQIEHLSQITTDVGRCRAWIRLALNDGLLESYLEAILKDKSALKSYYNPSAFLRdPEQLDILKSLLQGL 154
RUN_RUFY4 cd17697
RUN domain found in RUN and FYVE domain-containing protein 4 (RUFY4) and similar proteins; ...
 108-218 9.51e-12

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: 62.89  E-value: 9.51e-12
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 108 MEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKK 187
Cdd:cd17697  35 LEYLLQFDQKEKKSFFGSRKDYWDFLCLCLNRHRGGTEGIHFVNSTDKLKTPLGKGRAFIRYCLVQQQLAESLQLCLLNP 114

                        90       100       110
                ....*....|....*....|....*....|..
gi 68341991 188 ELLSEFYEANA-LMMEEEGAIIAGLLVGLNVI 218
Cdd:cd17697 115 ELTGEWYYARSpFLSPELRSDILDSLYELNGV 146
RUN_SNX29 cd17689
RUN domain found in sorting nexin-29 (SNX29) and similar proteins; SNX29, also called RUN ...
 153-218 2.43e-11

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: 61.86  E-value: 2.43e-11
                        10        20        30        40        50        60
                ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 68341991 153 LPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALMM-EEEGAIIAGLLVGLNVI 218
Cdd:cd17689  93 LKNIWTDIGRGRAWLRSALNEHSLERYLHILLSNENLLRQYYEDWAFLRdEERSSMLPNMAAGLGSI 159
RUN_FYCO1 cd17698
RUN domain found in FYVE and coiled-coil domain-containing protein 1 (FYCO1) and similar ...
 74-222 1.25e-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: 57.01  E-value: 1.25e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  74 NMAKLSIKGLIESALNLGRTLDSDYAP-------LQQFFVVMEHCLKHGLKAKKTFLGQNKSFWGPLELVEKLVPEAAEI 146
Cdd:cd17698   2 SQLQKIIRDLQDCVTELKKEFEETGEPitddsttLHKFCAKLEYLLQFDQKEKTTLLGGRKDYWDYFCECLAKVKGLNDG 81

                        90       100       110       120       130       140       150
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 68341991 147 TASVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSE-FYEANALMMEEEGAIIAGLLVGLNviDANF 222
Cdd:cd17698  82 IRFVKSLKEVRTSLGKGRAFIRYSLVHQRLADTLQQCVMNGKVTSDwYYPRSVFLNHKYSSDIINSLYDLN--EVQF 156
RUN_SGSM1_like cd17687
RUN domain found in small G protein signaling modulators, SGSM1, SGSM2, and similar proteins; ...
 109-219 2.82e-09

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: 55.76  E-value: 2.82e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 109 EHCLKHGLKAKK-TFLGQNKSFwGPLELVEKLVPEAAEITASVKDL------PGLKTPVGRGRA-------------WLR 168
Cdd:cd17687  31 DACLLHGLRKRAlGLFRSSSTF-SLLQKVAKSCPPAADILRKVQEIenlsenKRSSSSSGSNSSnshgnsssnrkilWIR 109

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 68341991 169 LALMQKKLSEYMKALINKKellSEFYEANALMME-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 2.96e-09

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: 55.33  E-value: 2.96e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  79 SIKGLIESALNLGRTLDSDYAPLQQFFVVMEHCLKHGLKAKktflgqNKSFWGpleLVEKLVPEAAEItaSVKDLPGLKT 158
Cdd:cd17680  12 SLQSYSSSQEEEDVLITNENRELQRLCEALDHALLHGLRRG------NRGYWP---FVKEFTHKETIK--QIENLPNVTT 80

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 68341991 159 PVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANALM 200
Cdd:cd17680  81 DLGRGRAWLYLALNEGSLESYLRSFLENRKLVKKFYHKHALL 122
RUN_RUBCN cd17686
RUN domain found in Run domain Beclin-1-interacting and cysteine-rich domain-containing ...
 101-221 6.81e-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: 54.58  E-value: 6.81e-09
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 101 LQQFFVVMEHCLKHGLKAKKTFLGQNkSFWGPLELVEKLVPEAAEITASVKDLPGLKTPVG-RGRAWLRLALMQKKLSEY 179
Cdd:cd17686  21 LQRLCRAVENILQHGLKEFQGLNKEI-DDWEFVQGLRWLQPTLAPSIEQQSRSSPSESEVSdKGRLWLRQSLQQHCLSSQ 99

                        90       100       110       120
                ....*....|....*....|....*....|....*....|..
gi 68341991 180 MKALINKKELLSEFYEANALMMEEEGAiiAGLLVGLNVIDAN 221
Cdd:cd17686 100 LQWLVSDKELLRKYYEDEAFLRQEGYA--TALLICLTAVELN 139
RUN1_DENND5 cd17677
RUN1 domain found in DENN domain-containing protein 5 (DENND5) and similar proteins; DENND5 ...
 114-223 3.56e-08

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: 53.17  E-value: 3.56e-08
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 114 HGLKAKktflgQNKS-FWGPL----ELVEKLVPEAAEITA---SVKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALIN 185
Cdd:cd17677  65 HGLQTK-----QGKSaLWSHLlayqENEERLKPLPESLLFdmkNVQNMKEIKTDVGYARAWIRLALEKKLLSKHLKTLLS 139

                        90       100       110
                ....*....|....*....|....*....|....*....
gi 68341991 186 KKELLSEFYEANA-LMMEEEGAIIAGLLVGLNVIDAnFC 223
Cdd:cd17677 140 NQDLLRSLYKRYAfLRCEDEREQFLYHLLSLNAVDY-FC 177
RUN1_DENND5B cd17691
RUN1 domain found in DENN domain-containing protein 5B (DENND5B) and similar proteins; DENND5B, ...
 150-223 5.95e-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: 5.95e-08
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68341991 150 VKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANA-LMMEEEGAIIAGLLVGLNVIDAnFC 223
Cdd:cd17691 127 IQNMSEIKTDVGRARAWIRLSLEKKLLSQHLKQLLSNQALTKKLYKRYAfLRCEEEKEQFLYHLLSLNAVDY-FC 200
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 243-464 1.86e-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: 53.91  E-value: 1.86e-07
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    243 KDGNSSKGSegDGQITAILDQKNYVEELNRHLN---ATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE 319
Cdd:TIGR02168  657 PGGVITGGS--AKTNSSILERRREIEELEEKIEeleEKIAELEKALAELRKELEELEEELEQLRKELEELSRQISALRKD 734

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    320 SSYLLESNRKGpKQDRTAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLD 399
Cdd:TIGR02168  735 LARLEAEVEQL-EERIAQLSKELTELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELT 813

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68341991    400 DLRALKHELAFKLQSSDLGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:TIGR02168  814 LLNEEAANLRERLESLERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEAL 878
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 255-464 4.63e-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: 51.69  E-value: 4.63e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 255 GQITAILDQKNYVEELNRHLNAtvnnLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSyLLESNRKGPKQD 334
Cdd:COG4942  17 AQADAAAEAEAELEQLQQEIAE----LEKELAALKKEEKALLKQLAALERRIAALARRIRALEQELA-ALEAELAELEKE 91

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 335 RTAEGQALSEARKHLKEE--TQLRLDVEKELELQISMR--QEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAF 410
Cdd:COG4942  92 IAELRAELEAQKEELAELlrALYRLGRQPPLALLLSPEdfLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEA 171

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|....
gi 68341991 411 KLQSSDLGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:COG4942 172 ERAELEALLAELEEERAALEALKAERQKLLARLEKELAELAAELAELQQEAEEL 225
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 272-465 8.28e-07

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 51.48  E-value: 8.28e-07
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 272 RHLNATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESS------YLLESNRKGPKQDRTAEGQALSEA 345
Cdd:COG1196 235 RELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEeaqaeeYELLAELARLEQDIARLEERRREL 314

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 346 RKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHElafKLQSSDLGVKQKSEL 425
Cdd:COG1196 315 EERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAE---AEEELEELAEELLEA 391

                       170       180       190       200
                ....*....|....*....|....*....|....*....|
gi 68341991 426 NSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKLI 465
Cdd:COG1196 392 LRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALA 431
EnvC COG4942
Septal ring factor EnvC, activator of murein hydrolases AmiA and AmiB [Cell cycle control, ...
 256-463 1.22e-06

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: 50.53  E-value: 1.22e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 256 QITAILDQKNYVEELNRHLNATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYLLESNRKGPKQDR 335
Cdd:COG4942  42 ELAALKKEEKALLKQLAALERRIAALARRIRALEQELAALEAELAELEKEIAELRAELEAQKEELAELLRALYRLGRQPP 121

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 336 TA---EGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKL 412
Cdd:COG4942 122 LAlllSPEDFLDAVRRLQYLKYLAPARREQAEELRADLAELAALRAELEAERAELEALLAELEEERAALEALKAERQKLL 201

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|.
gi 68341991 413 QSSDLGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANK 463
Cdd:COG4942 202 ARLEKELAELAAELAELQQEAEELEALIARLEAEAAAAAERTPAAGFAALK 252
RUN_SGSM1 cd17703
RUN domain found in small G protein signaling modulator 1 (SGSM1) and similar proteins; SGSM1, ...
 80-214 1.39e-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: 1.39e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  80 IKGLIESALNLgRTLDSDYAPLQQFFVVMEHCLKHGLKAKKT-FLGQNK----------SFWGPLELVEKL--------- 139
Cdd:cd17703   3 VKQIMEEAVTR-KFVHEDSSHIISFCAAVEACVLHGLKRRAAgFLRSNKiaalfmkvgkSFPPAEELCRKVqeleqllen 81

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 140 ----VPEAAEITASVKDLPGLkTPVGRGRAWLRLALMQKKLSEYMKALInkkELLSEFYEANALMMEE-EGAIIAGLLVG 214
Cdd:cd17703  82 krnqMQGLQENVRKMPKLPNL-SPQAIKHLWIRTALFEKVLDKIVHYLV---ENSSKYYEKEALLMDPvDGPILASLLVG 157
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 264-464 1.94e-06

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: 50.44  E-value: 1.94e-06
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    264 KNYVEELNRhLNATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYLLESNRKGpKQDRTAEGQALS 343
Cdd:TIGR02168  263 QELEEKLEE-LRLEVSELEEEIEELQKELYALANEISRLEQQKQILRERLANLERQLEELEAQLEEL-ESKLDELAEELA 340

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    344 EARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKLQSSDLGVKQKS 423
Cdd:TIGR02168  341 ELEEKLEELKEELESLEAELEELEAELEELESRLEELEEQLETLRSKVAQLELQIASLNNEIERLEARLERLEDRRERLQ 420

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|...
gi 68341991    424 ELNSRLEEK--TNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:TIGR02168  421 QEIEELLKKleEAELKELQAELEELEEELEELQEELERLEEAL 463
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 256-461 3.41e-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: 3.41e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 256 QITAILDQKNYVEELNRHLNATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSyLLESNRKGPKQDR 335
Cdd:COG1196 296 ELARLEQDIARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELA-EAEEALLEAEAEL 374

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 336 TAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKLQSS 415
Cdd:COG1196 375 AEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEEEEEEALEEAAEEEAEL 454

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....*.
gi 68341991 416 DLGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAA 461
Cdd:COG1196 455 EEEEEALLELLAELLEEAALLEAALAELLEELAEAAARLLLLLEAE 500
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 256-465 5.58e-06

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 49.16  E-value: 5.58e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 256 QITAILDQKNYVEELNRHLNATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSyLLESNRKGPKQDR 335
Cdd:COG1196 233 KLRELEAELEELEAELEELEAELEELEAELAELEAELEELRLELEELELELEEAQAEEYELLAELA-RLEQDIARLEERR 311

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 336 TAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKLQSS 415
Cdd:COG1196 312 RELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEA 391

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 68341991 416 DlgvKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKLI 465
Cdd:COG1196 392 L---RAAAELAAQLEELEEAEEALLERLERLEEELEELEEALAELEEEEE 438
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 312-450 7.57e-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: 48.58  E-value: 7.57e-06
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   312 EMERVKEES---SYLLESNRKGPKQDRTAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQ 388
Cdd:pfam17380 447 EMERVRLEEqerQQQVERLRQQEEERKRKKLELEKEKRDRKRAEEQRRKILEKELEERKQAMIEEERKRKLLEKEMEERQ 526

                          90       100       110       120       130       140
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*.
gi 68341991   389 DALV--SLRQQLDDLRALKHELAFKLQSSDlGVKQKSELNSRLE--EKTNQMAATIKQLEQSEKDL 450
Cdd:pfam17380 527 KAIYeeERRREAEEERRKQQEMEERRRIQE-QMRKATEERSRLEamEREREMMRQIVESEKARAEY 591
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 283-464 8.43e-06

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 48.39  E-value: 8.43e-06
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 283 AKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEEssylLESNRkgpkQDRTAEGQALSEARKHLKEETQLRLDVEKE 362
Cdd:COG1196 232 LKLRELEAELEELEAELEELEAELEELEAELAELEAE----LEELR----LELEELELELEEAQAEEYELLAELARLEQD 303

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 363 LELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKLQSSDlgvKQKSELNSRLEEKTNQMAATIKQ 442
Cdd:COG1196 304 IARLEERRRELEERLEELEEELAELEEELEELEEELEELEEELEEAEEELEEAE---AELAEAEEALLEAEAELAEAEEE 380

                       170       180
                ....*....|....*....|..
gi 68341991 443 LEQSEKDLVKQAKTLNSAANKL 464
Cdd:COG1196 381 LEELAEELLEALRAAAELAAQL 402
CwlO1 COG3883
Uncharacterized N-terminal coiled-coil domain of peptidoglycan hydrolase CwlO [Function ...
 262-438 1.43e-05

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


Pssm-ID: 443091 [Multi-domain]  Cd Length: 379  Bit Score: 47.13  E-value: 1.43e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 262 DQKNYVEELNRhLNATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEE------SSY-----------LL 324
Cdd:COG3883  31 ELEAAQAELDA-LQAELEELNEEYNELQAELEALQAEIDKLQAEIAEAEAEIEERREElgerarALYrsggsvsyldvLL 109

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 325 ESnrKGPKQ--DR--------TAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSL 394
Cdd:COG3883 110 GS--ESFSDflDRlsalskiaDADADLLEELKADKAELEAKKAELEAKLAELEALKAELEAAKAELEAQQAEQEALLAQL 187

                       170       180       190       200
                ....*....|....*....|....*....|....*....|....
gi 68341991 395 RQQLDDLRALKHELAFKLQSSDLGVKQKSELNSRLEEKTNQMAA 438
Cdd:COG3883 188 SAEEAAAEAQLAELEAELAAAEAAAAAAAAAAAAAAAAAAAAAA 231
Smc COG1196
Chromosome segregation ATPase Smc [Cell cycle control, cell division, chromosome partitioning]; ...
 258-464 4.16e-05

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


Pssm-ID: 440809 [Multi-domain]  Cd Length: 983  Bit Score: 46.08  E-value: 4.16e-05
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 258 TAILDQKNYVEELNRHLN---ATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSyLLESNRKGPKQD 334
Cdd:COG1196 267 AELEELRLELEELELELEeaqAEEYELLAELARLEQDIARLEERRRELEERLEELEEELAELEEELE-ELEEELEELEEE 345

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 335 RTAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKLQS 414
Cdd:COG1196 346 LEEAEEELEEAEAELAEAEEALLEAEAELAEAEEELEELAEELLEALRAAAELAAQLEELEEAEEALLERLERLEEELEE 425

                       170       180       190       200       210
                ....*....|....*....|....*....|....*....|....*....|
gi 68341991 415 SDLGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:COG1196 426 LEEALAELEEEEEEEEEALEEAAEEEAELEEEEEALLELLAELLEEAALL 475
RUN1_DENND5A cd17690
RUN1 domain found in DENN domain-containing protein 5A (DENND5A) and similar proteins; DENND5A, ...
 150-223 6.02e-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: 44.23  E-value: 6.02e-05
                        10        20        30        40        50        60        70
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*
gi 68341991 150 VKDLPGLKTPVGRGRAWLRLALMQKKLSEYMKALINKKELLSEFYEANA-LMMEEEGAIIAGLLVGLNVIDAnFC 223
Cdd:cd17690 130 IQNIGEIKTDVGKARAWVRLSMEKKLLSRHLKQLLSDHELTKKLYKRYAfLRCDDEKEQFLYHLLSFNAVDY-FC 203
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 247-457 6.62e-05

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: 45.44  E-value: 6.62e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    247 SSKGSEGDGQITAILDQKNYVEELNRHLNATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYLLES 326
Cdd:TIGR02169  708 SQELSDASRKIGEIEKEIEQLEQEEEKLKERLEELEEDLSSLEQEIENVKSELKELEARIEELEEDLHKLEEALNDLEAR 787

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    327 NRKGPKQDRTAEGQALSEARKHLKEETQlrlDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRAlkh 406
Cdd:TIGR02169  788 LSHSRIPEIQAELSKLEEEVSRIEARLR---EIEQKLNRLTLEKEYLEKEIQELQEQRIDLKEQIKSIEKEIENLNG--- 861

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|.
gi 68341991    407 elafklqssdlgvkQKSELNSRLEEKTNQmaatIKQLEQSEKDLVKQAKTL 457
Cdd:TIGR02169  862 --------------KKEELEEELEELEAA----LRDLESRLGDLKKERDEL 894
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 251-462 6.69e-05

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: 45.43  E-value: 6.69e-05
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    251 SEGDGQITAILDQKNYVEELNRHLNATVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEEssyllesnRKG 330
Cdd:TIGR02168  757 TELEAEIEELEERLEEAEEELAEAEAEIEELEAQIEQLKEELKALREALDELRAELTLLNEEAANLRER--------LES 828

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    331 PKQDRTAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAf 410
Cdd:TIGR02168  829 LERRIAATERRLEDLEEQIEELSEDIESLAAEIEELEELIEELESELEALLNERASLEEALALLRSELEELSEELRELE- 907

                          170       180       190       200       210
                   ....*....|....*....|....*....|....*....|....*....|..
gi 68341991    411 klqssdlgvKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAAN 462
Cdd:TIGR02168  908 ---------SKRSELRRELEELREKLAQLELRLEGLEVRIDNLQERLSEEYS 950
Golgin_A5 pfam09787
Golgin subfamily A member 5; Members of this family of proteins are involved in maintaining ...
 277-464 1.45e-04

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: 43.59  E-value: 1.45e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   277 TVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYLLESNRkgpkqdrtaegQALSEARKHLKEETQLR 356
Cdd:pfam09787  41 SSTALTLELEELRQERDLLREEIQKLRGQIQQLRTELQELEAQQQEEAESSR-----------EQLQELEEQLATERSAR 109

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   357 LDVEKELElqiSMRQEMElamKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFKLQSSdlgvKQKSELNSRLEEKTNQM 436
Cdd:pfam09787 110 REAEAELE---RLQEELR---YLEEELRRSKATLQSRIKDREAEIEKLRNQLTSKSQSS----SSQSELENRLHQLTETL 179

                         170       180       190
                  ....*....|....*....|....*....|.
gi 68341991   437 AATIKQLE--QSEKD-LVKQAKTLNSAANKL 464
Cdd:pfam09787 180 IQKQTMLEalSTEKNsLVLQLERMEQQIKEL 210
PRK03918 PRK03918
DNA double-strand break repair ATPase Rad50;
277-464 2.81e-04

DNA double-strand break repair ATPase Rad50;


Pssm-ID: 235175 [Multi-domain]  Cd Length: 880  Bit Score: 43.51  E-value: 2.81e-04
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  277 TVNNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYLLESNRKGPKQDRTAEgqalSEARKHLKEETQLR 356
Cdd:PRK03918 385 TPEKLEKELEELEKAKEEIEEEISKITARIGELKKEIKELKKAIEELKKAKGKCPVCGRELT----EEHRKELLEEYTAE 460

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  357 L-DVEKELELQISMRQEMELAMKMLEKdVCEKQDALVSLRQQLDDLRALKHELAfKLQSSDLgvKQKSELNSRLEEKTNQ 435
Cdd:PRK03918 461 LkRIEKELKEIEEKERKLRKELRELEK-VLKKESELIKLKELAEQLKELEEKLK-KYNLEEL--EKKAEEYEKLKEKLIK 536

                        170       180       190
                 ....*....|....*....|....*....|..
gi 68341991  436 MAATIKQLE---QSEKDLVKQAKTLNSAANKL 464
Cdd:PRK03918 537 LKGEIKSLKkelEKLEELKKKLAELEKKLDEL 568
SMC_prok_B TIGR02168
chromosome segregation protein SMC, common bacterial type; SMC (structural maintenance of ...
 256-408 3.48e-04

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: 43.12  E-value: 3.48e-04
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    256 QITAILDQKNYVEELNRHLNATVNNLQAKVDALEKSNT-------KLTEELAVANNRIITLQEEMERvkeessylLESNR 328
Cdd:TIGR02168  345 KLEELKEELESLEAELEELEAELEELESRLEELEEQLEtlrskvaQLELQIASLNNEIERLEARLER--------LEDRR 416

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    329 KGPKQDRTAEGQALSEARkhlKEETQLRLD-VEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHE 407
Cdd:TIGR02168  417 ERLQQEIEELLKKLEEAE---LKELQAELEeLEEELEELQEELERLEEALEELREELEEAEQALDAAERELAQLQARLDS 493


                   .
gi 68341991    408 L 408
Cdd:TIGR02168  494 L 494
DUF5401 pfam17380
Family of unknown function (DUF5401); This is a family of unknown function found in ...
 242-457 9.47e-04

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: 41.65  E-value: 9.47e-04
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   242 LKDGNSSKGSEGDGQITAILDQKNYVEELNRHLNATvnNLQAKVDALEKSNTkltEELAVANNRIITL-------QEEME 314
Cdd:pfam17380 318 LEEAEKARQAEMDRQAAIYAEQERMAMERERELERI--RQEERKRELERIRQ---EEIAMEISRMRELerlqmerQQKNE 392

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   315 RVKEE-----SSYLLESNRKGPKQDRTAEGQALSEARKHLKEETQLRLDVEKELELQISMRQEMElamkmlekdvceKQD 389
Cdd:pfam17380 393 RVRQEleaarKVKILEEERQRKIQQQKVEMEQIRAEQEEARQREVRRLEEERAREMERVRLEEQE------------RQQ 460

                         170       180       190       200       210       220
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....
gi 68341991   390 ALVSLRQQLDDLRALKHELAFKLQSSDLGVKQKSE-LNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTL 457
Cdd:pfam17380 461 QVERLRQQEEERKRKKLELEKEKRDRKRAEEQRRKiLEKELEERKQAMIEEERKRKLLEKEMEERQKAI 529
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 260-459 1.33e-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: 41.21  E-value: 1.33e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    260 ILDQK--NYVEELnRHLNATVNNLQAKVDALEKSNTKLTEELAvaNNRIITLQEEMERVKEESSYLLESNR--KGPKQDR 335
Cdd:TIGR02169  748 SLEQEieNVKSEL-KELEARIEELEEDLHKLEEALNDLEARLS--HSRIPEIQAELSKLEEEVSRIEARLReiEQKLNRL 824

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    336 TAEGQALSEARKHLKEETqlrldveKELELQISMRQ----EMELAMKMLEKDVCEKQDALVSLRQQLDDLRALKHELAFK 411
Cdd:TIGR02169  825 TLEKEYLEKEIQELQEQR-------IDLKEQIKSIEkeieNLNGKKEELEEELEELEAALRDLESRLGDLKKERDELEAQ 897

                          170       180       190       200
                   ....*....|....*....|....*....|....*....|....*...
gi 68341991    412 LqssdlgvkqkselnSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNS 459
Cdd:TIGR02169  898 L--------------RELERKIEELEAQIEKKRKRLSELKAKLEALEE 931
PRK11281 PRK11281
mechanosensitive channel MscK;
267-461 1.99e-03

mechanosensitive channel MscK;


Pssm-ID: 236892 [Multi-domain]  Cd Length: 1113  Bit Score: 40.67  E-value: 1.99e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   267 VEELNRHLNATVNNLQakvdaleksntKLTEELAVANNRIITLQEEMERVKEEssylLESNrkgpkQDRTAEGQAL---- 342
Cdd:PRK11281  123 LRQLESRLAQTLDQLQ-----------NAQNDLAEYNSQLVSLQTQPERAQAA----LYAN-----SQRLQQIRNLlkgg 182

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   343 SEARKHLKEETQLRLDVE-KELELQISMRQEmELAMKMLEKDVCEKQDALVSLRQQLddlraLKHELAFklqssdlgvkq 421
Cdd:PRK11281  183 KVGGKALRPSQRVLLQAEqALLNAQNDLQRK-SLEGNTQLQDLLQKQRDYLTARIQR-----LEHQLQL----------- 245

                         170       180       190       200
                  ....*....|....*....|....*....|....*....|
gi 68341991   422 kselnsrLEEKTNQmaatiKQLEQSEKDlVKQAKTLNSAA 461
Cdd:PRK11281  246 -------LQEAINS-----KRLTLSEKT-VQEAQSQDEAA 272
SMC_prok_A TIGR02169
chromosome segregation protein SMC, primarily archaeal type; SMC (structural maintenance of ...
 251-464 3.42e-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: 40.05  E-value: 3.42e-03
                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    251 SEGDGQITAILDQKNYVEELNRHLNATVNNLQAKVDALEKSNTKLTEElavannRIITLQEEMERVKEESSYLLESNRKG 330
Cdd:TIGR02169  240 EAIERQLASLEEELEKLTEEISELEKRLEEIEQLLEELNKKIKDLGEE------EQLRVKEKIGELEAEIASLERSIAEK 313

                           90       100       110       120       130       140       150       160
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991    331 PKQDRTAEGQA----------LSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLE---KDVCEKQDALVSLRQQ 397
Cdd:TIGR02169  314 ERELEDAEERLakleaeidklLAEIEELEREIEEERKRRDKLTEEYAELKEELEDLRAELEevdKEFAETRDELKDYREK 393

                          170       180       190       200       210       220
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*..
gi 68341991    398 LDDLralKHELAFKLQSSDLGVKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:TIGR02169  394 LEKL---KREINELKRELDRLQEELQRLSEELADLNAAIAGIEAKINELEEEKEDKALEIKKQEWKL 457
COG4913 COG4913
Uncharacterized conserved protein, contains a C-terminal ATPase domain [Function unknown];
282-469 3.60e-03

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


Pssm-ID: 443941 [Multi-domain]  Cd Length: 1089  Bit Score: 39.90  E-value: 3.60e-03
                         10        20        30        40        50        60        70        80
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  282 QAKVDALEKSNTKLTEELAVANNRIITLQEEMERVkeessyllesnrkgpkqdrtaegQALSEARKHLKEETQLRLDVEk 361
Cdd:COG4913  609 RAKLAALEAELAELEEELAEAEERLEALEAELDAL-----------------------QERREALQRLAEYSWDEIDVA- 664

                         90       100       110       120       130       140       150       160
                 ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991  362 ELELQISmrqemelamkmlekdvcEKQDALVSLRQQLDDLRALKHELAfKLQssdlgvKQKSELNSRLEEKTNQMAATIK 441
Cdd:COG4913  665 SAEREIA-----------------ELEAELERLDASSDDLAALEEQLE-ELE------AELEELEEELDELKGEIGRLEK 720

                        170       180
                 ....*....|....*....|....*...
gi 68341991  442 QLEQSEkDLVKQAKTLNSAANKLIPKHH 469
Cdd:COG4913  721 ELEQAE-EELDELQDRLEAAEDLARLEL 747
DR0291 COG1579
Predicted nucleic acid-binding protein DR0291, contains C4-type Zn-ribbon domain [General ...
 340-464 4.72e-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: 38.75  E-value: 4.72e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 340 QALSEARKHLKEETQLRLDVEKELELQISMRQEMELAMKMLEKDVCEKQDALVSLRQQLD------DLRALKHELAF-KL 412
Cdd:COG1579  24 HRLKELPAELAELEDELAALEARLEAAKTELEDLEKEIKRLELEIEEVEARIKKYEEQLGnvrnnkEYEALQKEIESlKR 103

                        90       100       110       120       130
                ....*....|....*....|....*....|....*....|....*....|..
gi 68341991 413 QSSDLGvKQKSELNSRLEEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:COG1579 104 RISDLE-DEILELMERIEELEEELAELEAELAELEAELEEKKAELDEELAEL 154
PRK10246 PRK10246
exonuclease subunit SbcC; Provisional
 274-447 9.22e-03

exonuclease subunit SbcC; Provisional


Pssm-ID: 182330 [Multi-domain]  Cd Length: 1047  Bit Score: 38.63  E-value: 9.22e-03
                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   274 LNATVNnlQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYLLESnrkgpKQDRTAEGQALSEA---RKHLK 350
Cdd:PRK10246  523 LEPGVN--QSRLDALEKEVKKLGEEGAALRGQLDALTKQLQRDESEAQSLRQE-----EQALTQQWQAVCASlniTLQPQ 595

                          90       100       110       120       130       140       150       160
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991   351 EETQLRLDVEKELELQ---ISMRQEMELAMKMLEKDVCEKQDALVSLRQQL-DDLRALKHE----------LAFKLQSSD 416
Cdd:PRK10246  596 DDIQPWLDAQEEHERQlrlLSQRHELQGQIAAHNQQIIQYQQQIEQRQQQLlTALAGYALTlpqedeeaswLATRQQEAQ 675

                         170       180       190
                  ....*....|....*....|....*....|.
gi 68341991   417 LGVKQKSELNsRLEEKTNQMAATIKQLEQSE 447
Cdd:PRK10246  676 SWQQRQNELT-ALQNRIQQLTPLLETLPQSD 705
GumC COG3206
Exopolysaccharide export protein/domain GumC/Wzc1 [Cell wall/membrane/envelope biogenesis];
279-464 9.73e-03

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


Pssm-ID: 442439 [Multi-domain]  Cd Length: 687  Bit Score: 38.46  E-value: 9.73e-03
                        10        20        30        40        50        60        70        80
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 279 NNLQAKVDALEKSNTKLTEELAVANNRIITLQEEMERVKEESSYLLESNRKGPKQDRTAE-GQALSEARKHLKEETQLRL 357
Cdd:COG3206 164 QNLELRREEARKALEFLEEQLPELRKELEEAEAALEEFRQKNGLVDLSEEAKLLLQQLSElESQLAEARAELAEAEARLA 243

                        90       100       110       120       130       140       150       160
                ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 68341991 358 DVEKELELQISMRQEMelamkmlekdvcEKQDALVSLRQQLDDLRALKHELAFKLQSSDLGVKQ--------KSELNSRL 429
Cdd:COG3206 244 ALRAQLGSGPDALPEL------------LQSPVIQQLRAQLAELEAELAELSARYTPNHPDVIAlraqiaalRAQLQQEA 311

                       170       180       190
                ....*....|....*....|....*....|....*
gi 68341991 430 EEKTNQMAATIKQLEQSEKDLVKQAKTLNSAANKL 464
Cdd:COG3206 312 QRILASLEAELEALQAREASLQAQLAQLEARLAEL 346
 
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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