CAMSAP CH domain; This domain is the N-terminal CH domain from the CAMSAP proteins.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568953494   108 RAIARRAPCFPNVTTL-QDLASGAALAATIHCYCPQLLRLEEVCLKDPMSVADSLYNLQLVQDFCASHLP-RGCPLSLED 185
Cdd:pfam11971    1 PLSQRSLPLSPPVEDLlRDLSDGCALAALIHFYCPQLIDLEDICLKESMSLADSLYNIQLLQEFCQRHLGnRCCHLTLED 80

                   ....*
gi 568953494   186 LLYVP 190
Cdd:pfam11971   81 LLYAR 85

DNA double-strand break repair Rad50 ATPase;

                          10        20        30        40        50        60        70        80
                  ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568953494  789 EDEMAQKRASLlERQQRRVEEARRRKQWQEAEKEQKREEAARLAQEAPGLAFT--------TPVVASAAPVATLAPTTRA 860
Cdd:PRK02224  522 EELIAERRETI-EEKRERAEELRERAAELEAEAEEKREAAAEAEEEAEEAREEvaelnsklAELKERIESLERIRTLLAA 600

                          90       100       110
                  ....*....|....*....|....*....|
gi 568953494  861 MAPAEEEVG---PRRGDFTRLEYERRAQLK 887
Cdd:PRK02224  601 IADAEDEIErlrEKREALAELNDERRERLA 630

Microtubule-binding calmodulin-regulated spectrin-associated; This is the C-terminal domain of a family of eumetazoan proteins collectively defined as calmodulin-regulated spectrin-associated, or CAMSAP, proteins. CAMSAP proteins carry an N-terminal region that includes the CH domain, a central region including a predicted coiled-coil and this C-terminal, or CKK, domain - defined as being present in CAMSAP, KIAA1078 and KIAA1543, The C-terminal domain is the part of the CAMSAP proteins that binds to microtubules. The domain appears to act by producing inhibition of neurite extension, probably by blocking microtubule function. CKK represents a domain that has evolved with the metazoa. The structure of a murine hypothetical protein from RIKEN cDNA has shown the domain to adopt a mainly beta barrel structure with an associated alpha-helical hairpin.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568953494  1008 PRLYKEPSAKSNKFIIHNALSHCCLAGKVNEPQKNRILEEIEKSKANHFLILFRDSSCQFRALYTLSGETEELSRLAGYG 1087
Cdd:pfam08683    1 PKLFKKPSAKSNKKIIHNALSHCCLAGKVNEDQKNKILEELEKSESKHFLILFRDSGCQFRALYSYNPETEELVKLHGIG 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 568953494  1088 PRTVTPAMVEGIYKYNSDRKRFTQIPAKTMSMSVDAFTI 1126
Cdd:pfam08683   81 PRVVTPKMIEKFYKYNSGRKQFTEIPTKTLSVSIDAFTI 119

Spectrin-binding region of Ca2+-Calmodulin; CAMSAP_CC1 is the conserved region on calmodulin-regulated spectrin-associated proteins in eukaryotes that binds spectrin. CAMSAPs are vertebrate microtubule-binding proteins, representatives of a family of cytoskeletal proteins that arose in animals. This conserved CC1 region binds to both spectrin and Ca2+/calmodulin in vitro, although the binding of Ca2+/calmodulin inhibited the binding of spectrin. CC1 appears to be a functional region of CAMSAP1 that links spectrin-binding to neurite outgrowth.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 568953494   482 PTSTPVAPEALSSEMSELGARLEEKRRAIEAQKRRIEAIFAKHRQRLGKSAFLQVQPR 539
Cdd:pfam17095    2 GDDSPSASPELASELSQLRLKLEEKRRAIEQQKKRMEAAFARQRQKLGKAAFLQVVKK 59

FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like subfamily of structure-specific, 5' nucleases (FEN-like family). Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 568953494  795 KRASLLERQQRRvEEARrrKQWQEAEKEQKREEAARLAQ 833
Cdd:cd09867    85 KSGELEKRRERR-EEAE--EKLEEALEEGDLEEARKYAK 120

Domain of unknown function (DUF4670); This family of proteins is found in eukaryotes. Proteins in this family are typically between 373 and 763 amino acids in length.

                           10        20        30        40        50        60        70
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|.
gi 568953494   766 EEASSEGEPRSGLGFFYKDEDKPEDEMAQKrasllER--QQRRVEEARRRKQWQEAEKEQKREEAARLAQE 834
Cdd:pfam15709  445 ERAEAEKQRQKELEMQLAEEQKRLMEMAEE-----ERleYQRQKQEAEEKARLEAEERRQKEEEAARLALE 510

Microtubule-binding calmodulin-regulated spectrin-associated; This is the C-terminal domain of a family of eumetazoan proteins collectively defined as calmodulin-regulated spectrin-associated, or CAMSAP, proteins. CAMSAP proteins carry an N-terminal region that includes the CH domain, a central region including a predicted coiled-coil and this C-terminal, or CKK, domain - defined as being present in CAMSAP, KIAA1078 and KIAA1543, The C-terminal domain is the part of the CAMSAP proteins that binds to microtubules. The domain appears to act by producing inhibition of neurite extension, probably by blocking microtubule function. CKK represents a domain that has evolved with the metazoa. The structure of a murine hypothetical protein from RIKEN cDNA has shown the domain to adopt a mainly beta barrel structure with an associated alpha-helical hairpin.

                           10        20        30        40        50        60        70        80
                   ....*....|....*....|....*....|....*....|....*....|....*....|....*....|....*....|
gi 568953494  1008 PRLYKEPSAKSNKFIIHNALSHCCLAGKVNEPQKNRILEEIEKSKANHFLILFRDSSCQFRALYTLSGETEELSRLAGYG 1087
Cdd:pfam08683    1 PKLFKKPSAKSNKKIIHNALSHCCLAGKVNEDQKNKILEELEKSESKHFLILFRDSGCQFRALYSYNPETEELVKLHGIG 80

                           90       100       110
                   ....*....|....*....|....*....|....*....
gi 568953494  1088 PRTVTPAMVEGIYKYNSDRKRFTQIPAKTMSMSVDAFTI 1126
Cdd:pfam08683   81 PRVVTPKMIEKFYKYNSGRKQFTEIPTKTLSVSIDAFTI 119

Spectrin-binding region of Ca2+-Calmodulin; CAMSAP_CC1 is the conserved region on calmodulin-regulated spectrin-associated proteins in eukaryotes that binds spectrin. CAMSAPs are vertebrate microtubule-binding proteins, representatives of a family of cytoskeletal proteins that arose in animals. This conserved CC1 region binds to both spectrin and Ca2+/calmodulin in vitro, although the binding of Ca2+/calmodulin inhibited the binding of spectrin. CC1 appears to be a functional region of CAMSAP1 that links spectrin-binding to neurite outgrowth.

                           10        20        30        40        50
                   ....*....|....*....|....*....|....*....|....*....|....*...
gi 568953494   482 PTSTPVAPEALSSEMSELGARLEEKRRAIEAQKRRIEAIFAKHRQRLGKSAFLQVQPR 539
Cdd:pfam17095    2 GDDSPSASPELASELSQLRLKLEEKRRAIEQQKKRMEAAFARQRQKLGKAAFLQVVKK 59

FEN-like PIN domains of Flap endonuclease-1, a structure-specific, divalent-metal-ion dependent, 5' nuclease and homologs; Flap endonuclease-1 (FEN1) is involved in multiple DNA metabolic pathways, including DNA replication processes (5' flap DNA endonuclease activity and double stranded DNA 5'-exonuclease activity) and DNA repair processes (long-patch base excision repair) in eukaryotes and archaea. Interaction between FEN1 and PCNA (Proliferating cell nuclear antigen) is an essential prerequisite to FEN1's DNA replication functionality and stimulates FEN1 nuclease activity by 10-50 fold. FEN1 belongs to the FEN1-EXO1-like subfamily of structure-specific, 5' nucleases (FEN-like family). Canonical members of the FEN-like family possess a PIN domain with a two-helical structure insert (also known as the helical arch, helical clamp or I domain) of variable length (approximately 16 to 800 residues), and at the C-terminus of the PIN domain a H3TH (helix-3-turn-helix) domain, an atypical helix-hairpin-helix-2-like region. Both the H3TH domain (not included in this model) and the helical arch/clamp region are involved in DNA binding. The PIN domain belongs to a large nuclease superfamily. The structural properties of the PIN domain indicate its putative active center, consisting of invariant acidic amino acid residues (putative metal-binding residues), is geometrically similar in the active center of structure-specific 5' nucleases, PIN-domain ribonucleases of eukaryotic rRNA editing proteins, and bacterial toxins of toxin-antitoxin (TA) operons. FEN1 has a C-terminal extension containing residues forming the consensus PIP-box - Qxx(M/L/I)xxF(Y/F) which serves to anchor FEN1 to PCNA.

                          10        20        30
                  ....*....|....*....|....*....|....*....
gi 568953494  795 KRASLLERQQRRvEEARrrKQWQEAEKEQKREEAARLAQ 833
Cdd:cd09867    85 KSGELEKRRERR-EEAE--EKLEEALEEGDLEEARKYAK 120

Membrane protein TolA involved in colicin uptake [Cell wall/membrane/envelope biogenesis];

                          10        20        30        40        50
                  ....*....|....*....|....*....|....*....|....*....|...
gi 568953494  783 KDEDKPEDEMAQKRASLLERQQRRVEEARRRKQWQEAEKEQKREEAARLAQEA 835
Cdd:COG3064     4 ALEEKAAEAAAQERLEQAEAEKRAAAEAEQKAKEEAEEERLAELEAKRQAEEE 56

Trichohyalin-plectin-homology domain; This family is a mixtrue of two different families of eukaryotic proteins. Trichoplein or mitostatin, was first defined as a meiosis-specific nuclear structural protein. It has since been linked with mitochondrial movement. It is associated with the mitochondrial outer membrane, and over-expression leads to reduction in mitochondrial motility whereas lack of it enhances mitochondrial movement. The activity appears to be mediated through binding the mitochondria to the actin intermediate filaments (IFs). The family is in the trichohyalin-plectin-homology domain.

                           10        20        30        40
                   ....*....|....*....|....*....|....*....|....*..
gi 568953494   789 EDEMAQKRASLLERQQRRVEEARRRKQWQEAEKEQKREEAARLAQEA 835
Cdd:pfam13868  197 QDEKAERDELRAKLYQEEQERKERQKEREEAEKKARQRQELQQAREE 243