RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7782
(225 letters)
>gnl|CDD|185575 PTZ00361, PTZ00361, 26 proteosome regulatory subunit 4-like
protein; Provisional.
Length = 438
Score = 261 bits (668), Expect = 4e-86
Identities = 114/165 (69%), Positives = 139/165 (84%)
Query: 61 GAGSNSDKKDDKDKKKKYEPPIPTRVGKKKRKAKGPDAAIKLPQVTPHTKCRLKLLKLER 120
G G+N K+ K +KKK E P P K+K+K KGPDAA KLP+VTP+TKCRL+LLKLER
Sbjct: 6 GQGNNQKDKNKKKEKKKKESPPPPHEIKRKKKRKGPDAASKLPKVTPNTKCRLRLLKLER 65
Query: 121 IKDYLLMEEEFIRNQERLKPQEEKNEEERSRVDDLRGTPMSVGTLEEIIDDNHAIVSTSV 180
IKDYLL+EEEFI NQE KP +EKNE E +VDDLRG+P+SVGTLEEIID+NHAIVS+SV
Sbjct: 66 IKDYLLLEEEFITNQEAQKPAQEKNEAELKKVDDLRGSPLSVGTLEEIIDENHAIVSSSV 125
Query: 181 GSEHYVSILSFVDKDQLEPGCSVLLNHKVHAVVGVLSDDTDPMVT 225
G E+YV+ILSFVDK+QLEPGCSVLL++K H+VVG+L D+ DP+V+
Sbjct: 126 GPEYYVNILSFVDKEQLEPGCSVLLHNKTHSVVGILLDEVDPLVS 170
Score = 97.1 bits (242), Expect = 1e-23
Identities = 38/45 (84%), Positives = 43/45 (95%)
Query: 3 LDVQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
L+ QIQEIKE+VELPLTHPE Y+++GIKPPKGVILYGPPGTGKTL
Sbjct: 188 LEQQIQEIKEAVELPLTHPELYDDIGIKPPKGVILYGPPGTGKTL 232
>gnl|CDD|224143 COG1222, RPT1, ATP-dependent 26S proteasome regulatory subunit
[Posttranslational modification, protein turnover,
chaperones].
Length = 406
Score = 120 bits (303), Expect = 3e-32
Identities = 51/140 (36%), Positives = 75/140 (53%), Gaps = 4/140 (2%)
Query: 87 GKKKRKAKGPDAAIKLPQVTPHTKCRLKLLKLERIKDYLLMEEEFIR-NQERLKPQEEKN 145
D PQ + KL LE+ K LL+EE+ + RLK + ++
Sbjct: 2 ELDALDEILGDLESYEPQEYLNKLEDTKLKLLEKEKRLLLLEEQRLEAEGLRLKREVDRL 61
Query: 146 EEERSRVDDLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSFVDKDQLEPGCSVLL 205
EE ++ L+ P+ VGT+ E++DD AIV +S G + V+ILSFVD+D LEPG V L
Sbjct: 62 REE---IERLKEPPLIVGTVLEVLDDGRAIVKSSTGPKFVVNILSFVDRDLLEPGMRVAL 118
Query: 206 NHKVHAVVGVLSDDTDPMVT 225
N +++V VL + DP V+
Sbjct: 119 NRDSYSIVRVLPPEVDPRVS 138
Score = 99.6 bits (249), Expect = 2e-24
Identities = 35/45 (77%), Positives = 40/45 (88%)
Query: 3 LDVQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
LD QIQEI+E VELPL +PE +EE+GI PPKGV+LYGPPGTGKTL
Sbjct: 156 LDEQIQEIREVVELPLKNPELFEELGIDPPKGVLLYGPPGTGKTL 200
>gnl|CDD|179699 PRK03992, PRK03992, proteasome-activating nucleotidase;
Provisional.
Length = 389
Score = 94.5 bits (236), Expect = 8e-23
Identities = 32/45 (71%), Positives = 41/45 (91%)
Query: 3 LDVQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
L+ QI+E++E+VELPL PE +EE+GI+PPKGV+LYGPPGTGKTL
Sbjct: 136 LEEQIREVREAVELPLKKPELFEEVGIEPPKGVLLYGPPGTGKTL 180
Score = 71.8 bits (177), Expect = 1e-14
Identities = 39/116 (33%), Positives = 66/116 (56%), Gaps = 8/116 (6%)
Query: 117 KLERIKDYLLMEEEFIRNQER----LKPQEEKNEEE----RSRVDDLRGTPMSVGTLEEI 168
+LE +++ EE IR E L+ + EK E E +S ++ L+ P+ V T+ E+
Sbjct: 2 RLEALEERNSELEEQIRQLELKLRDLEAENEKLERELERLKSELEKLKSPPLIVATVLEV 61
Query: 169 IDDNHAIVSTSVGSEHYVSILSFVDKDQLEPGCSVLLNHKVHAVVGVLSDDTDPMV 224
+DD +V +S G + V++ F+D+++L+PG V LN + A+V VL + DP V
Sbjct: 62 LDDGRVVVKSSGGPQFLVNVSPFIDREKLKPGARVALNQQSLAIVEVLPSEKDPRV 117
>gnl|CDD|240423 PTZ00454, PTZ00454, 26S protease regulatory subunit 6B-like
protein; Provisional.
Length = 398
Score = 85.2 bits (211), Expect = 2e-19
Identities = 33/45 (73%), Positives = 41/45 (91%)
Query: 3 LDVQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
LD+Q QEI+E+VELPLT PE YE++GI PP+GV+LYGPPGTGKT+
Sbjct: 150 LDIQKQEIREAVELPLTCPELYEQIGIDPPRGVLLYGPPGTGKTM 194
Score = 83.7 bits (207), Expect = 8e-19
Identities = 47/128 (36%), Positives = 78/128 (60%), Gaps = 6/128 (4%)
Query: 97 DAAIKLPQVTPHTKCRL--KLLKLERIKDYLLMEEEFIRN-QERLKPQEEKNEEERSRVD 153
AA + T HT+ L KL +LE+ ++L ++EE+I+ Q+ LK + + +EE R+
Sbjct: 4 TAAAAVASSTTHTERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRI- 62
Query: 154 DLRGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSFVDKDQLEPGCSVLLNHKVHAVV 213
+ P+ +G E+ID N+ IVS++ GS +YV ILS ++++ L+P SV L+ HAVV
Sbjct: 63 --QSVPLVIGQFLEMIDSNYGIVSSTSGSNYYVRILSTLNRELLKPNASVALHRHSHAVV 120
Query: 214 GVLSDDTD 221
+L + D
Sbjct: 121 DILPPEAD 128
>gnl|CDD|130309 TIGR01242, 26Sp45, 26S proteasome subunit P45 family. Many
proteins may score above the trusted cutoff because an
internal.
Length = 364
Score = 83.7 bits (207), Expect = 6e-19
Identities = 34/45 (75%), Positives = 42/45 (93%)
Query: 3 LDVQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
L+ QI+EI+E+VELPL HPE +EE+GI+PPKGV+LYGPPGTGKTL
Sbjct: 127 LEEQIREIREAVELPLKHPELFEEVGIEPPKGVLLYGPPGTGKTL 171
Score = 71.8 bits (176), Expect = 1e-14
Identities = 39/118 (33%), Positives = 65/118 (55%), Gaps = 9/118 (7%)
Query: 108 HTKCRLKLLKLERIKDYLLMEEEFIRNQERLKPQEEKNEEERSRVDDLRGTPMSVGTLEE 167
++ +++ KLE + +E+E IR E + E RS ++ LR P+ VGT+ E
Sbjct: 1 ISELDVRIRKLE--DEKRSLEKEKIR-------LERELERLRSEIERLRSPPLIVGTVLE 51
Query: 168 IIDDNHAIVSTSVGSEHYVSILSFVDKDQLEPGCSVLLNHKVHAVVGVLSDDTDPMVT 225
++DDN +V +S G V++ +F+D+ L+PG V LN + +V VL DP+V
Sbjct: 52 VLDDNRVVVKSSTGPNFVVNVSAFIDRKSLKPGARVALNQQTLTIVDVLPTSKDPLVK 109
>gnl|CDD|200312 TIGR03689, pup_AAA, proteasome ATPase. In the Actinobacteria, as
shown for Mycobacterium tuberculosis, some proteins are
modified by ligation between an epsilon-amino group of a
lysine side chain and the C-terminal carboxylate of the
ubiquitin-like protein Pup. This modification leads to
protein degradation by the archaeal-like proteasome
found in the Actinobacteria. Members of this protein
family belong to the AAA family of ATPases and tend to
be clustered with the genes for Pup, the Pup ligase
PafA, and structural components of the proteasome. This
protein forms hexameric rings with ATPase activity
[Protein fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 512
Score = 78.6 bits (194), Expect = 5e-17
Identities = 30/45 (66%), Positives = 37/45 (82%)
Query: 3 LDVQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
L QI++I+++VELP HPE Y E G+KPPKGV+LYGPPG GKTL
Sbjct: 187 LGSQIEQIRDAVELPFLHPELYREYGLKPPKGVLLYGPPGCGKTL 231
Score = 38.5 bits (90), Expect = 0.002
Identities = 29/91 (31%), Positives = 43/91 (47%), Gaps = 2/91 (2%)
Query: 136 ERLKPQEEKNEEERSRVDDLRGTPMSVGT-LEEIIDDNHAIVSTSVGSEHYVSILSFVDK 194
E LK ++ E + ++D L P + GT L+ DD A V T+ G V + VD
Sbjct: 22 EALKAARDELAELKEQLDALAQPPSTYGTLLQVATDDRTAEVFTA-GRRMRVGVSPNVDA 80
Query: 195 DQLEPGCSVLLNHKVHAVVGVLSDDTDPMVT 225
+L PG +V LN + V + T +VT
Sbjct: 81 AELVPGQTVRLNEALQVVEACDFERTGEIVT 111
Score = 30.4 bits (69), Expect = 0.70
Identities = 14/46 (30%), Positives = 27/46 (58%)
Query: 164 TLEEIIDDNHAIVSTSVGSEHYVSILSFVDKDQLEPGCSVLLNHKV 209
TL+E++DD A+V+ G E V + + + L PG ++L++ +
Sbjct: 111 TLKEVLDDGRALVTDRSGEERVVKLAGALADEGLRPGDTLLVDPRA 156
>gnl|CDD|233328 TIGR01243, CDC48, AAA family ATPase, CDC48 subfamily. This
subfamily of the AAA family ATPases includes two members
each from three archaeal species. It also includes yeast
CDC48 (cell division control protein 48) and the human
ortholog, transitional endoplasmic reticulum ATPase
(valosin-containing protein). These proteins in
eukaryotes are involved in the budding and transfer of
membrane from the transitional endoplasmic reticulum to
the Golgi apparatus.
Length = 733
Score = 71.1 bits (174), Expect = 2e-14
Identities = 29/45 (64%), Positives = 37/45 (82%)
Query: 3 LDVQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
L ++I+E VELP+ HPE +E +GI+PPKGV+LYGPPGTGKTL
Sbjct: 183 LKEAKEKIREMVELPMKHPELFEHLGIEPPKGVLLYGPPGTGKTL 227
Score = 69.2 bits (169), Expect = 1e-13
Identities = 29/40 (72%), Positives = 37/40 (92%)
Query: 8 QEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
QE++E+VE PL HPE +E+MGI+PPKGV+L+GPPGTGKTL
Sbjct: 463 QELREAVEWPLKHPEIFEKMGIRPPKGVLLFGPPGTGKTL 502
>gnl|CDD|223540 COG0464, SpoVK, ATPases of the AAA+ class [Posttranslational
modification, protein turnover, chaperones].
Length = 494
Score = 68.7 bits (168), Expect = 1e-13
Identities = 26/46 (56%), Positives = 37/46 (80%)
Query: 2 SLDVQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
L+ +E+KE++E PL PE + ++G++PPKGV+LYGPPGTGKTL
Sbjct: 246 GLEEAKEELKEAIETPLKRPELFRKLGLRPPKGVLLYGPPGTGKTL 291
Score = 42.1 bits (99), Expect = 1e-04
Identities = 23/33 (69%), Positives = 30/33 (90%)
Query: 15 ELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
ELPL PE ++++GI+PPKGV+L+GPPGTGKTL
Sbjct: 1 ELPLKEPELFKKLGIEPPKGVLLHGPPGTGKTL 33
>gnl|CDD|233327 TIGR01241, FtsH_fam, ATP-dependent metalloprotease FtsH.
HflB(FtsH) is a pleiotropic protein required for correct
cell division in bacteria. It has ATP-dependent zinc
metalloprotease activity. It was formerly designated
cell division protein FtsH [Cellular processes, Cell
division, Protein fate, Degradation of proteins,
peptides, and glycopeptides].
Length = 495
Score = 61.9 bits (151), Expect = 3e-11
Identities = 21/40 (52%), Positives = 29/40 (72%), Gaps = 1/40 (2%)
Query: 8 QEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
+E+ E V+ L +P + ++G K PKGV+L GPPGTGKTL
Sbjct: 65 EELMEIVDF-LKNPSKFTKLGAKIPKGVLLVGPPGTGKTL 103
>gnl|CDD|223541 COG0465, HflB, ATP-dependent Zn proteases [Posttranslational
modification, protein turnover, chaperones].
Length = 596
Score = 56.2 bits (136), Expect = 2e-09
Identities = 23/44 (52%), Positives = 31/44 (70%), Gaps = 1/44 (2%)
Query: 4 DVQIQEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
D +E+ E V+ L +P+ Y+ +G K PKGV+L GPPGTGKTL
Sbjct: 156 DEAKEELSELVD-FLKNPKKYQALGAKIPKGVLLVGPPGTGKTL 198
>gnl|CDD|214386 CHL00176, ftsH, cell division protein; Validated.
Length = 638
Score = 52.4 bits (126), Expect = 5e-08
Identities = 22/40 (55%), Positives = 27/40 (67%), Gaps = 1/40 (2%)
Query: 8 QEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
+E +E V L PE + +G K PKGV+L GPPGTGKTL
Sbjct: 193 EEFEEVVSF-LKKPERFTAVGAKIPKGVLLVGPPGTGKTL 231
>gnl|CDD|182683 PRK10733, hflB, ATP-dependent metalloprotease; Reviewed.
Length = 644
Score = 43.9 bits (103), Expect = 3e-05
Identities = 21/40 (52%), Positives = 29/40 (72%), Gaps = 1/40 (2%)
Query: 8 QEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
+E+ E VE L P ++++G K PKGV++ GPPGTGKTL
Sbjct: 162 EEVAELVEY-LREPSRFQKLGGKIPKGVLMVGPPGTGKTL 200
>gnl|CDD|99707 cd00009, AAA, The AAA+ (ATPases Associated with a wide variety of
cellular Activities) superfamily represents an ancient
group of ATPases belonging to the ASCE (for additional
strand, catalytic E) division of the P-loop NTPase
fold. The ASCE division also includes ABC, RecA-like,
VirD4-like, PilT-like, and SF1/2 helicases. Members of
the AAA+ ATPases function as molecular chaperons,
ATPase subunits of proteases, helicases, or
nucleic-acid stimulated ATPases. The AAA+ proteins
contain several distinct features in addition to the
conserved alpha-beta-alpha core domain structure and
the Walker A and B motifs of the P-loop NTPases.
Length = 151
Score = 37.9 bits (88), Expect = 0.001
Identities = 13/18 (72%), Positives = 15/18 (83%)
Query: 30 KPPKGVILYGPPGTGKTL 47
PPK ++LYGPPGTGKT
Sbjct: 17 PPPKNLLLYGPPGTGKTT 34
>gnl|CDD|235250 PRK04195, PRK04195, replication factor C large subunit;
Provisional.
Length = 482
Score = 37.6 bits (88), Expect = 0.004
Identities = 12/17 (70%), Positives = 14/17 (82%)
Query: 30 KPPKGVILYGPPGTGKT 46
KP K ++LYGPPG GKT
Sbjct: 37 KPKKALLLYGPPGVGKT 53
>gnl|CDD|215649 pfam00004, AAA, ATPase family associated with various cellular
activities (AAA). AAA family proteins often perform
chaperone-like functions that assist in the assembly,
operation, or disassembly of protein complexes.
Length = 131
Score = 35.7 bits (83), Expect = 0.005
Identities = 10/13 (76%), Positives = 12/13 (92%)
Query: 35 VILYGPPGTGKTL 47
++LYGPPGTGKT
Sbjct: 1 LLLYGPPGTGKTT 13
>gnl|CDD|221912 pfam13086, AAA_11, AAA domain. This family of domains contain a
P-loop motif that is characteristic of the AAA
superfamily. Many of the proteins in this family are
conjugative transfer proteins.
Length = 220
Score = 35.8 bits (83), Expect = 0.010
Identities = 34/181 (18%), Positives = 68/181 (37%), Gaps = 30/181 (16%)
Query: 11 KESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTLPFSPALGY-HYYCRG------AG 63
+E+++ L+ + ++ GPPGTGKT + G A
Sbjct: 7 REAIKKALSSSDIT-----------LIQGPPGTGKTTTIVEIIKQLLSNAPGKKVLVCAP 55
Query: 64 SNS--DKKDDKDKKKKYEPPIPTRVGKKKRKAKGPDAAIKLPQVTPHTKCRLKLLKLERI 121
SNS D ++ ++K+ I R+G R V ++ L K E++
Sbjct: 56 SNSAVDNILERLLEQKFGLKI-VRIGSPAR--------EIHEDVLQYSLEYLLEAKFEQL 106
Query: 122 KDYLLMEEEFIRNQERLKPQEEKNEEERSRVDDLRGTPMSVGTLEEIIDDNHAIVSTSVG 181
+ + + + +LK + K E ++ + +EI+D+ + +T G
Sbjct: 107 LKRIRKLKSLLEEKSKLKRERRKLRSEIKKLKK-ELERLRKSIRKEILDEADVVCTTLSG 165
Query: 182 S 182
+
Sbjct: 166 A 166
>gnl|CDD|237355 PRK13342, PRK13342, recombination factor protein RarA; Reviewed.
Length = 413
Score = 35.4 bits (83), Expect = 0.016
Identities = 10/12 (83%), Positives = 12/12 (100%)
Query: 35 VILYGPPGTGKT 46
+IL+GPPGTGKT
Sbjct: 39 MILWGPPGTGKT 50
>gnl|CDD|224144 COG1223, COG1223, Predicted ATPase (AAA+ superfamily) [General
function prediction only].
Length = 368
Score = 34.4 bits (79), Expect = 0.036
Identities = 18/40 (45%), Positives = 23/40 (57%)
Query: 8 QEIKESVELPLTHPEYYEEMGIKPPKGVILYGPPGTGKTL 47
+E K L + + E E G PK V+ YGPPGTGKT+
Sbjct: 127 EEAKRKCRLIMEYLENPERFGDWAPKNVLFYGPPGTGKTM 166
>gnl|CDD|214640 smart00382, AAA, ATPases associated with a variety of cellular
activities. AAA - ATPases associated with a variety of
cellular activities. This profile/alignment only
detects a fraction of this vast family. The poorly
conserved N-terminal helix is missing from the
alignment.
Length = 148
Score = 32.7 bits (74), Expect = 0.061
Identities = 8/16 (50%), Positives = 13/16 (81%)
Query: 31 PPKGVILYGPPGTGKT 46
P + +++ GPPG+GKT
Sbjct: 1 PGEVILIVGPPGSGKT 16
>gnl|CDD|237354 PRK13341, PRK13341, recombination factor protein RarA/unknown
domain fusion protein; Reviewed.
Length = 725
Score = 33.5 bits (77), Expect = 0.085
Identities = 10/11 (90%), Positives = 10/11 (90%)
Query: 36 ILYGPPGTGKT 46
ILYGPPG GKT
Sbjct: 56 ILYGPPGVGKT 66
>gnl|CDD|201659 pfam01201, Ribosomal_S8e, Ribosomal protein S8e.
Length = 129
Score = 32.1 bits (74), Expect = 0.086
Identities = 12/30 (40%), Positives = 18/30 (60%), Gaps = 3/30 (10%)
Query: 68 KKDDKDKKKKYE---PPIPTRVGKKKRKAK 94
+ D KK+K+E PP PT++GK + K
Sbjct: 17 RLDHHRKKRKFELGRPPAPTKLGKNRVKQV 46
>gnl|CDD|225165 COG2256, MGS1, ATPase related to the helicase subunit of the
Holliday junction resolvase [DNA replication,
recombination, and repair].
Length = 436
Score = 33.4 bits (77), Expect = 0.090
Identities = 10/12 (83%), Positives = 12/12 (100%)
Query: 35 VILYGPPGTGKT 46
+IL+GPPGTGKT
Sbjct: 51 MILWGPPGTGKT 62
>gnl|CDD|131948 TIGR02902, spore_lonB, ATP-dependent protease LonB. Members of
this protein are LonB, a paralog of the ATP-dependent
protease La (LonA, TIGR00763). LonB proteins are found
strictly, and almost universally, in endospore-forming
bacteria. This protease was shown, in Bacillus subtilis,
to be expressed specifically in the forespore, during
sporulation, under control of sigma(F). The lonB gene,
despite location immediately upstream of lonA, was shown
to be monocistronic. LonB appears able to act on
sigma(H) for post-translation control, but lonB mutation
did not produce an obvious sporulation defect under the
conditions tested. Note that additional paralogs of LonA
and LonB occur in the Clostridium lineage and this model
selects only one per species as the protein that
corresponds to LonB in B. subtilis [Protein fate,
Degradation of proteins, peptides, and glycopeptides,
Cellular processes, Sporulation and germination].
Length = 531
Score = 32.4 bits (74), Expect = 0.17
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 32 PKGVILYGPPGTGKT 46
P+ VI+YGPPG GKT
Sbjct: 86 PQHVIIYGPPGVGKT 100
>gnl|CDD|188437 TIGR03922, T7SS_EccA, type VII secretion AAA-ATPase EccA. This
model represents the AAA family ATPase, EccA, of the
actinobacterial flavor of type VII secretion systems.
Species such as Mycobacterium tuberculosis have several
instances of this system per genome, designated EccA1,
EccA2, etc [Protein fate, Protein and peptide secretion
and trafficking].
Length = 557
Score = 32.1 bits (73), Expect = 0.19
Identities = 14/44 (31%), Positives = 20/44 (45%), Gaps = 7/44 (15%)
Query: 6 QIQEIKESVELPLTHPEYYEEMGIKPP---KGVILYGPPGTGKT 46
Q+ +K S + L E G+ ++ GPPGTGKT
Sbjct: 287 QVAALKSSTAMALAR----AERGLPVAQTSNHMLFAGPPGTGKT 326
>gnl|CDD|204405 pfam10146, zf-C4H2, Zinc finger-containing protein. This is a
family of proteins which appears to have a highly
conserved zinc finger domain at the C terminal end,
described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is
predicted to contain a coiled coil. Members are
annotated as being tumour-associated antigen HCA127 in
humans but this could not confirmed.
Length = 215
Score = 31.7 bits (72), Expect = 0.20
Identities = 19/63 (30%), Positives = 33/63 (52%), Gaps = 5/63 (7%)
Query: 112 RLKLLKLERIKDYLLMEEEFIRNQERLKPQ-----EEKNEEERSRVDDLRGTPMSVGTLE 166
R K +LE++KD + EEE + ++E+ + EE EE+ V++LR + +E
Sbjct: 7 RNKTDELEKLKDEIKAEEEALESEEKHLKEYDKEMEELLEEKMQHVEELRQIHADINDME 66
Query: 167 EII 169
I
Sbjct: 67 TEI 69
>gnl|CDD|222022 pfam13280, WYL, WYL domain. This presumed domain is around 170
amino acids in length. It is found to the C-terminus of
a DNA-binding helix-turn-helix domain. This domain may
be involved in binding to an as yet unknown ligand that
allows a transcriptional regulation response to that
molecule. There are a number of proteins that contain
two tandem copies of this domain. This suggests that
this domain may form a dimeric arrangement.
Length = 172
Score = 31.4 bits (72), Expect = 0.21
Identities = 21/98 (21%), Positives = 39/98 (39%), Gaps = 14/98 (14%)
Query: 108 HTKCRLKLLKLERIKDYLLMEEEFIRN-----QERLKPQEEKNEEER-------SRVDDL 155
H + L+ +L+RI+D +++E F +E LK E + L
Sbjct: 51 HDRNDLRTFRLDRIEDVEILDETFEPPEDFDLEEYLKKSFGVFEPIEVKLRFDPEAAEYL 110
Query: 156 RGTPMSVGTLEEIIDDNHAIVSTSVGSEHYVS--ILSF 191
+ P+ + E DD +++ V + +LSF
Sbjct: 111 KERPLHDQQIIEEDDDGSILLTFPVSDLEELLRWLLSF 148
>gnl|CDD|234063 TIGR02928, TIGR02928, orc1/cdc6 family replication initiation
protein. Members of this protein family are found
exclusively in the archaea. This set of DNA binding
proteins shows homology to the origin recognition
complex subunit 1/cell division control protein 6
family in eukaryotes. Several members may be found in
genome and interact with each other [DNA metabolism,
DNA replication, recombination, and repair].
Length = 365
Score = 31.8 bits (73), Expect = 0.21
Identities = 9/17 (52%), Positives = 10/17 (58%)
Query: 31 PPKGVILYGPPGTGKTL 47
P V +YG GTGKT
Sbjct: 39 RPSNVFIYGKTGTGKTA 55
>gnl|CDD|216186 pfam00910, RNA_helicase, RNA helicase. This family includes RNA
helicases thought to be involved in duplex unwinding
during viral RNA replication. Members of this family
are found in a variety of single stranded RNA viruses.
Length = 105
Score = 30.3 bits (69), Expect = 0.29
Identities = 13/42 (30%), Positives = 17/42 (40%), Gaps = 11/42 (26%)
Query: 35 VILYGPPGTGKTL---PFSPALGYHY--------YCRGAGSN 65
+ LYGPPG GK+ + AL H Y R +
Sbjct: 1 IWLYGPPGCGKSTLAKYLARALLKHLGLPKKDSVYSRNPDDD 42
>gnl|CDD|234619 PRK00080, ruvB, Holliday junction DNA helicase RuvB; Reviewed.
Length = 328
Score = 31.6 bits (73), Expect = 0.30
Identities = 10/12 (83%), Positives = 11/12 (91%)
Query: 35 VILYGPPGTGKT 46
V+LYGPPG GKT
Sbjct: 54 VLLYGPPGLGKT 65
>gnl|CDD|221970 pfam13191, AAA_16, AAA ATPase domain. This family of domains
contain a P-loop motif that is characteristic of the
AAA superfamily.
Length = 154
Score = 30.6 bits (69), Expect = 0.31
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 22 EYYEEMGIKPPKGVILYGPPGTGKT 46
+ P V+L GP GTGKT
Sbjct: 14 DALRRARSGGPPSVLLTGPSGTGKT 38
>gnl|CDD|219538 pfam07728, AAA_5, AAA domain (dynein-related subfamily). This
Pfam entry includes some of the AAA proteins not
detected by the pfam00004 model.
Length = 135
Score = 30.3 bits (69), Expect = 0.33
Identities = 10/14 (71%), Positives = 12/14 (85%)
Query: 34 GVILYGPPGTGKTL 47
GV+L GPPGTGK+
Sbjct: 1 GVLLVGPPGTGKSE 14
>gnl|CDD|187747 cd09289, Photosystem-II_D1, D1 subunit of photosystem II (PS
II). Photosystem II (PS II), D2 subunit. PS II is a
multi-subunit protein found in the photosynthetic
membranes of plants, algae, and cyanobacteria. It
utilizes light-induced electron transfer and
water-splitting reactions to produce protons,
electrons, and molecular oxygen. The protons generated
are instrumental in ATP formation. Molecular dioxygen
is released as a by-product. PS II can be described as
containing two parts: the photochemical part and the
catalytic part. The photochemical portion promotes the
fast, efficient light-induced charge separation and
stabilization that occur when light is absorbed by
chlorophyll. The catalytic portion, where water is
oxidized, involves a cluster of Mn ions close to a
redox-active tyrosine residue. The Mn cluster and its
ligands form a functional unit called the
oxygen-evolving complex (OEC) or the water-oxidizing
complex (WOC). The D1 and D2 subunits are a pair of
interwined polypeptides. They contain all the cofactors
involved directly in water oxidation and plastoquinone
reduction. The D1 subunit contains the Mn cluster that
constitutes the site of water oxidation. D1 and D2 are
highly homologous and are also similar to the L and M
proteins in bacterial photosynthetic reaction centers.
Length = 338
Score = 31.0 bits (70), Expect = 0.43
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 28 GIKPP-KGVILYGPP-GTGKTLPFSPALGYHYY 58
GI+ P G +LYG +G +P S A+G H+Y
Sbjct: 56 GIREPVSGSLLYGNNIISGAVVPTSNAIGLHFY 88
>gnl|CDD|234053 TIGR02903, spore_lon_C, ATP-dependent protease, Lon family.
Members of this protein family resemble the widely
distributed ATP-dependent protease La, also called Lon
and LonA. It resembles even more closely LonB, which is
a LonA paralog found in genomes if and only if the
species is capable of endospore formation (as in
Bacillus subtilis, Clostridium tetani, and select other
members of the Firmicutes) and expressed specifically in
the forespore compartment. Members of this family are
restricted to a subset of spore-forming species, and are
very likely to participate in the program of endospore
formation. We propose the designation LonC [Protein
fate, Degradation of proteins, peptides, and
glycopeptides, Cellular processes, Sporulation and
germination].
Length = 615
Score = 30.9 bits (70), Expect = 0.51
Identities = 11/15 (73%), Positives = 13/15 (86%)
Query: 32 PKGVILYGPPGTGKT 46
P+ +ILYGPPG GKT
Sbjct: 175 PQHIILYGPPGVGKT 189
>gnl|CDD|144608 pfam01078, Mg_chelatase, Magnesium chelatase, subunit ChlI.
Magnesium-chelatase is a three-component enzyme that
catalyzes the insertion of Mg2+ into protoporphyrin IX.
This is the first unique step in the synthesis of
(bacterio)chlorophyll. Due to this, it is thought that
Mg-chelatase has an important role in channelling
inter- mediates into the (bacterio)chlorophyll branch
in response to conditions suitable for photosynthetic
growth. ChlI and BchD have molecular weight between
38-42 kDa.
Length = 207
Score = 30.2 bits (69), Expect = 0.63
Identities = 7/13 (53%), Positives = 12/13 (92%)
Query: 35 VILYGPPGTGKTL 47
+++ GPPG+GKT+
Sbjct: 25 LLMIGPPGSGKTM 37
>gnl|CDD|234751 PRK00411, cdc6, cell division control protein 6; Reviewed.
Length = 394
Score = 30.6 bits (70), Expect = 0.66
Identities = 10/12 (83%), Positives = 12/12 (100%)
Query: 35 VILYGPPGTGKT 46
V++YGPPGTGKT
Sbjct: 58 VLIYGPPGTGKT 69
>gnl|CDD|203260 pfam05496, RuvB_N, Holliday junction DNA helicase ruvB
N-terminus. The RuvB protein makes up part of the
RuvABC revolvasome which catalyzes the resolution of
Holliday junctions that arise during genetic
recombination and DNA repair. Branch migration is
catalyzed by the RuvB protein that is targeted to the
Holliday junction by the structure specific RuvA
protein. This family contains the N-terminal region of
the protein.
Length = 231
Score = 30.1 bits (69), Expect = 0.72
Identities = 10/12 (83%), Positives = 11/12 (91%)
Query: 35 VILYGPPGTGKT 46
V+LYGPPG GKT
Sbjct: 53 VLLYGPPGLGKT 64
>gnl|CDD|225164 COG2255, RuvB, Holliday junction resolvasome, helicase subunit
[DNA replication, recombination, and repair].
Length = 332
Score = 30.2 bits (69), Expect = 0.83
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 35 VILYGPPGTGKT 46
V+L+GPPG GKT
Sbjct: 55 VLLFGPPGLGKT 66
>gnl|CDD|224401 COG1484, DnaC, DNA replication protein [DNA replication,
recombination, and repair].
Length = 254
Score = 30.1 bits (68), Expect = 0.87
Identities = 8/15 (53%), Positives = 11/15 (73%)
Query: 32 PKGVILYGPPGTGKT 46
+ ++L GPPG GKT
Sbjct: 105 GENLVLLGPPGVGKT 119
>gnl|CDD|236482 PRK09361, radB, DNA repair and recombination protein RadB;
Provisional.
Length = 225
Score = 29.8 bits (68), Expect = 0.89
Identities = 10/16 (62%), Positives = 13/16 (81%), Gaps = 2/16 (12%)
Query: 33 KGVI--LYGPPGTGKT 46
+G I +YGPPG+GKT
Sbjct: 22 RGTITQIYGPPGSGKT 37
>gnl|CDD|222163 pfam13479, AAA_24, AAA domain. This AAA domain is found in a
wide variety of presumed phage proteins.
Length = 201
Score = 29.6 bits (67), Expect = 0.94
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 35 VILYGPPGTGKT 46
V++YGPPG GKT
Sbjct: 6 VLIYGPPGIGKT 17
>gnl|CDD|211394 cd11382, Ribosomal_S8e, Eukaryotic/archaeal ribosomal protein S8e
(RPS8). The eukaryotic/archaeal ribosomal protein S8
is a component of the small (40S in eukaryotes, 30S in
archaea) ribosomal subunits and interacts tightly with
18S rRNA (16S rRNA in archaea, presumably).
Length = 122
Score = 28.6 bits (65), Expect = 1.1
Identities = 10/22 (45%), Positives = 16/22 (72%), Gaps = 3/22 (13%)
Query: 74 KKKKYE---PPIPTRVGKKKRK 92
KK+KYE PP T++G+++ K
Sbjct: 19 KKRKYELGRPPANTKLGERRVK 40
>gnl|CDD|236153 PRK08116, PRK08116, hypothetical protein; Validated.
Length = 268
Score = 29.6 bits (67), Expect = 1.1
Identities = 12/23 (52%), Positives = 16/23 (69%), Gaps = 1/23 (4%)
Query: 24 YEEMGIKPPKGVILYGPPGTGKT 46
+EEM K G++L+G GTGKT
Sbjct: 107 FEEMK-KENVGLLLWGSVGTGKT 128
>gnl|CDD|179385 PRK02224, PRK02224, chromosome segregation protein; Provisional.
Length = 880
Score = 30.0 bits (68), Expect = 1.2
Identities = 16/55 (29%), Positives = 24/55 (43%), Gaps = 6/55 (10%)
Query: 118 LERIKDYLLMEEEFIRNQERLKPQEEKNEEERSRVDDLRGTPMSVGTLEEIIDDN 172
L I D E+E R +E+ + E N+E R R+ + R LE D+
Sbjct: 598 LAAIADA---EDEIERLREKREALAELNDERRERLAEKRE---RKRELEAEFDEA 646
>gnl|CDD|216619 pfam01637, Arch_ATPase, Archaeal ATPase. This family contain a
conserved P-loop motif that is involved in binding ATP.
This family is almost exclusively found in
archaebacteria and particularly in Methanococcus
jannaschii that encodes sixteen members of this family.
Length = 223
Score = 29.2 bits (66), Expect = 1.4
Identities = 22/85 (25%), Positives = 32/85 (37%), Gaps = 11/85 (12%)
Query: 26 EMGIKPPKGVILYGPPGTGKT------LPFSPALGYH--YYCRGAGSNSDKKDDKDKKKK 77
E G P +++YGP GKT L LGY YY +K D ++ K+
Sbjct: 16 ERGTYPI--IVVYGPRRCGKTALLREFLEELRELGYRVIYYDPLRREFEEKLDRFEEAKR 73
Query: 78 YEPPIPTRVGKKKRKAKGPDAAIKL 102
+ + K K A + L
Sbjct: 74 LAEALGDALPKIGIA-KSKLAFLSL 97
>gnl|CDD|218328 pfam04921, XAP5, XAP5, circadian clock regulator. This protein is
found in a wide range of eukaryotes. It is a nuclear
protein and is suggested to be DNA binding. In plants,
this family is essential for correct circadian clock
functioning by acting as a light-quality regulator
coordinating the activities of blue and red light
signalling pathways during plant growth - inhibiting
growth in red light but promoting growth in blue light.
Length = 233
Score = 28.9 bits (65), Expect = 1.8
Identities = 20/72 (27%), Positives = 29/72 (40%), Gaps = 10/72 (13%)
Query: 72 KDKKKKYEPPIPTRVGKKKRKAKGPDAAI-KLPQVTPHTKCRLKLLKLERIKDYLLMEEE 130
K K+ EP KK+ K P LP K R + R + + EE
Sbjct: 30 KVPKESSEPDEANVNPNKKKIGKNPSVDTSFLP-----DKAREEKEAELREE----LREE 80
Query: 131 FIRNQERLKPQE 142
F++ QE +K +E
Sbjct: 81 FLKKQEAVKEEE 92
>gnl|CDD|222104 pfam13401, AAA_22, AAA domain.
Length = 124
Score = 28.0 bits (63), Expect = 1.8
Identities = 6/13 (46%), Positives = 8/13 (61%)
Query: 35 VILYGPPGTGKTL 47
+L G G+GKT
Sbjct: 7 GVLTGESGSGKTT 19
>gnl|CDD|227346 COG5013, NarG, Nitrate reductase alpha subunit [Energy production and
conversion].
Length = 1227
Score = 29.3 bits (66), Expect = 2.0
Identities = 12/34 (35%), Positives = 17/34 (50%), Gaps = 1/34 (2%)
Query: 78 YEPPIPTR-VGKKKRKAKGPDAAIKLPQVTPHTK 110
Y PPI TR V + + + + L +TPH K
Sbjct: 1056 YRPPIDTRSVKEMREIKPNGNPELVLNYLTPHQK 1089
>gnl|CDD|110677 pfam01695, IstB_IS21, IstB-like ATP binding protein. This
protein contains an ATP/GTP binding P-loop motif. It is
found associated with IS21 family insertion sequences.
The function of this protein is unknown, but it may
perform a transposase function.
Length = 178
Score = 28.4 bits (64), Expect = 2.0
Identities = 11/22 (50%), Positives = 15/22 (68%), Gaps = 1/22 (4%)
Query: 34 GVILYGPPGTGKTLPFSPALGY 55
++L GPPG GKT + ALG+
Sbjct: 49 NLLLLGPPGVGKTH-LACALGH 69
>gnl|CDD|220642 pfam10236, DAP3, Mitochondrial ribosomal death-associated protein
3. This is a family of conserved proteins which were
originally described as death-associated-protein-3
(DAP-3). The proteins carry a P-loop DNA-binding motif,
and induce apoptosis. DAP3 has been shown to be a
pro-apoptotic factor in the mitochondrial matrix and to
be crucial for mitochondrial biogenesis and so has also
been designated as MRP-S29 (mitochondrial ribosomal
protein subunit 29).
Length = 274
Score = 28.8 bits (65), Expect = 2.0
Identities = 6/18 (33%), Positives = 10/18 (55%)
Query: 30 KPPKGVILYGPPGTGKTL 47
K +L G G+GK++
Sbjct: 21 KKVVRFVLTGERGSGKSV 38
>gnl|CDD|235214 PRK04049, PRK04049, 30S ribosomal protein S8e; Validated.
Length = 127
Score = 27.9 bits (63), Expect = 2.1
Identities = 12/22 (54%), Positives = 14/22 (63%), Gaps = 3/22 (13%)
Query: 74 KKKKYE---PPIPTRVGKKKRK 92
KK+KYE P T VG+ KRK
Sbjct: 22 KKRKYELGREPTETTVGEDKRK 43
>gnl|CDD|222005 pfam13245, AAA_19, Part of AAA domain.
Length = 73
Score = 26.9 bits (60), Expect = 2.1
Identities = 7/12 (58%), Positives = 9/12 (75%)
Query: 35 VILYGPPGTGKT 46
++ G PGTGKT
Sbjct: 13 FVVDGGPGTGKT 24
>gnl|CDD|223542 COG0466, Lon, ATP-dependent Lon protease, bacterial type
[Posttranslational modification, protein turnover,
chaperones].
Length = 782
Score = 29.1 bits (66), Expect = 2.1
Identities = 11/16 (68%), Positives = 11/16 (68%), Gaps = 2/16 (12%)
Query: 33 KGVI--LYGPPGTGKT 46
KG I L GPPG GKT
Sbjct: 349 KGPILCLVGPPGVGKT 364
>gnl|CDD|224145 COG1224, TIP49, DNA helicase TIP49, TBP-interacting protein
[Transcription].
Length = 450
Score = 28.9 bits (65), Expect = 2.2
Identities = 9/14 (64%), Positives = 13/14 (92%)
Query: 33 KGVILYGPPGTGKT 46
+G+++ GPPGTGKT
Sbjct: 66 RGILIVGPPGTGKT 79
>gnl|CDD|238749 cd01472, vWA_collagen, von Willebrand factor (vWF) type A domain;
equivalent to the I-domain of integrins. This domain
has a variety of functions including: intermolecular
adhesion, cell migration, signalling, transcription, and
DNA repair. In integrins these domains form heterodimers
while in vWF it forms homodimers and multimers. There
are different interaction surfaces of this domain as
seen by its complexes with collagen with either integrin
or human vWFA. In integrins collagen binding occurs via
the metal ion-dependent adhesion site (MIDAS) and
involves three surface loops located on the upper
surface of the molecule. In human vWFA, collagen binding
is thought to occur on the bottom of the molecule and
does not involve the vestigial MIDAS motif.
Length = 164
Score = 28.3 bits (64), Expect = 2.2
Identities = 14/47 (29%), Positives = 23/47 (48%), Gaps = 11/47 (23%)
Query: 177 STSVGSEHYVSILSFVDK--DQLEPGCSVLLNHKVHAVVGVL--SDD 219
S S+G ++ + FV + ++L+ G V VGV+ SDD
Sbjct: 10 SESIGLSNFNLVKDFVKRVVERLDIG-----PDGVR--VGVVQYSDD 49
>gnl|CDD|223543 COG0467, RAD55, RecA-superfamily ATPases implicated in signal
transduction [Signal transduction mechanisms].
Length = 260
Score = 28.6 bits (64), Expect = 2.2
Identities = 13/35 (37%), Positives = 16/35 (45%), Gaps = 6/35 (17%)
Query: 31 PPKGVIL-YGPPGTGKTLPFSPALGYHYYCRGAGS 64
P V+L GPPGTGKT+ + GA
Sbjct: 21 PRGSVVLITGPPGTGKTI-----FALQFLYEGARE 50
>gnl|CDD|178596 PLN03025, PLN03025, replication factor C subunit; Provisional.
Length = 319
Score = 28.5 bits (64), Expect = 2.5
Identities = 10/12 (83%), Positives = 11/12 (91%)
Query: 35 VILYGPPGTGKT 46
+IL GPPGTGKT
Sbjct: 37 LILSGPPGTGKT 48
>gnl|CDD|224402 COG1485, COG1485, Predicted ATPase [General function prediction
only].
Length = 367
Score = 28.8 bits (65), Expect = 2.7
Identities = 8/16 (50%), Positives = 11/16 (68%)
Query: 31 PPKGVILYGPPGTGKT 46
P +G+ L+G G GKT
Sbjct: 64 PVRGLYLWGGVGRGKT 79
>gnl|CDD|224391 COG1474, CDC6, Cdc6-related protein, AAA superfamily ATPase [DNA
replication, recombination, and repair /
Posttranslational modification, protein turnover,
chaperones].
Length = 366
Score = 28.5 bits (64), Expect = 2.8
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 32 PKGVILYGPPGTGKTL 47
P +I+YGP GTGKT
Sbjct: 42 PSNIIIYGPTGTGKTA 57
>gnl|CDD|233793 TIGR02237, recomb_radB, DNA repair and recombination protein
RadB. This family consists exclusively of archaeal
RadB protein, a homolog of bacterial RecA (TIGR02012),
eukaryotic RAD51 (TIGR02239) and DMC1 (TIGR02238), and
archaeal RadA (TIGR02236).
Length = 209
Score = 28.1 bits (63), Expect = 3.4
Identities = 10/16 (62%), Positives = 13/16 (81%), Gaps = 2/16 (12%)
Query: 33 KGVI--LYGPPGTGKT 46
+G I +YGPPG+GKT
Sbjct: 11 RGTITQIYGPPGSGKT 26
>gnl|CDD|203138 pfam04977, DivIC, Septum formation initiator. DivIC from B.
subtilis is necessary for both vegetative and
sporulation septum formation. These proteins are mainly
composed of an amino terminal coiled-coil.
Length = 80
Score = 26.8 bits (60), Expect = 3.4
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 121 IKDYLLMEEEFIRNQERLKPQEEKNEEERSRVDDLRGTP 159
+ Y + +E Q L + +NEE + V DL+ P
Sbjct: 16 LSAYYQLNQEIAALQAELAKLKAENEELEAEVKDLKSDP 54
>gnl|CDD|238687 cd01393, recA_like, RecA is a bacterial enzyme which has roles
in homologous recombination, DNA repair, and the
induction of the SOS response. RecA couples ATP
hydrolysis to DNA strand exchange. While prokaryotes
have a single RecA protein, eukaryotes have multiple
RecA homologs such as Rad51, DMC1 and Rad55/57.
Archaea have the RecA-like homologs radA and radB.
Length = 226
Score = 27.9 bits (63), Expect = 3.5
Identities = 10/21 (47%), Positives = 13/21 (61%), Gaps = 4/21 (19%)
Query: 28 GIKPPKGVI--LYGPPGTGKT 46
GI P G I ++G G+GKT
Sbjct: 15 GI--PTGRITEIFGEFGSGKT 33
>gnl|CDD|180607 PRK06526, PRK06526, transposase; Provisional.
Length = 254
Score = 27.9 bits (62), Expect = 3.8
Identities = 9/12 (75%), Positives = 10/12 (83%)
Query: 35 VILYGPPGTGKT 46
V+ GPPGTGKT
Sbjct: 101 VVFLGPPGTGKT 112
>gnl|CDD|151829 pfam11389, Porin_OmpL1, Leptospira porin protein OmpL1. OmpL1 is a
member of the outer membrane (OM) proteins in the
mammalian pathogen Leptospira. Specifically, it is a
porin.
Length = 267
Score = 27.7 bits (61), Expect = 4.3
Identities = 18/67 (26%), Positives = 30/67 (44%), Gaps = 2/67 (2%)
Query: 159 PMSVGTLEEIIDDNHAIVSTSVGSEHYVSILSFVDKDQLEPGCSVLLNHKVHAVVGVLSD 218
P +VG + +D A V G ++ S + ++ G +L +V +LSD
Sbjct: 134 PATVGIKLNVTED--AAVYMGAGLNYFNGGWSLNGSNNIKGGHDILAAAGAGSVANLLSD 191
Query: 219 DTDPMVT 225
TDP+ T
Sbjct: 192 GTDPITT 198
>gnl|CDD|129721 TIGR00635, ruvB, Holliday junction DNA helicase, RuvB subunit.
All proteins in this family for which functions are
known are 5'-3' DNA helicases that, as part of a
complex with RuvA homologs serve as a 5'-3' Holliday
junction helicase. RuvA specifically binds Holliday
junctions as a sandwich of two tetramers and maintains
the configuration of the junction. It forms a complex
with two hexameric rings of RuvB, the subunit that
contains helicase activity. The complex drives
ATP-dependent branch migration of the Holliday junction
recombination intermediate. The endonuclease RuvC
resolves junctions [DNA metabolism, DNA replication,
recombination, and repair].
Length = 305
Score = 27.6 bits (62), Expect = 4.5
Identities = 9/12 (75%), Positives = 11/12 (91%)
Query: 35 VILYGPPGTGKT 46
++LYGPPG GKT
Sbjct: 33 LLLYGPPGLGKT 44
>gnl|CDD|225190 COG2308, COG2308, Uncharacterized conserved protein [Function
unknown].
Length = 488
Score = 28.1 bits (63), Expect = 4.5
Identities = 10/22 (45%), Positives = 14/22 (63%), Gaps = 1/22 (4%)
Query: 15 ELPLTHPEYYEEM-GIKPPKGV 35
EL ++P + EM GI+PP G
Sbjct: 122 ELVASNPGFLREMVGIRPPGGH 143
>gnl|CDD|221983 pfam13207, AAA_17, AAA domain.
Length = 114
Score = 26.9 bits (59), Expect = 4.5
Identities = 6/12 (50%), Positives = 11/12 (91%)
Query: 35 VILYGPPGTGKT 46
+++ GPPG+GK+
Sbjct: 2 ILITGPPGSGKS 13
>gnl|CDD|222194 pfam13521, AAA_28, AAA domain.
Length = 162
Score = 27.1 bits (61), Expect = 4.6
Identities = 6/12 (50%), Positives = 9/12 (75%)
Query: 35 VILYGPPGTGKT 46
+++ G P TGKT
Sbjct: 2 IVITGGPSTGKT 13
>gnl|CDD|238544 cd01124, KaiC, KaiC is a circadian clock protein primarily found
in cyanobacteria KaiC is a RecA-like ATPase, having
both Walker A and Walker B motifs. A related protein is
found in archaea.
Length = 187
Score = 27.7 bits (62), Expect = 4.6
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 35 VILYGPPGTGKTL 47
+L G PGTGKT
Sbjct: 2 TLLSGGPGTGKTT 14
>gnl|CDD|223679 COG0606, COG0606, Predicted ATPase with chaperone activity
[Posttranslational modification, protein turnover,
chaperones].
Length = 490
Score = 28.0 bits (63), Expect = 4.7
Identities = 11/22 (50%), Positives = 14/22 (63%)
Query: 33 KGVILYGPPGTGKTLPFSPALG 54
++L GPPGTGKT+ S G
Sbjct: 199 HNLLLVGPPGTGKTMLASRLPG 220
>gnl|CDD|147949 pfam06068, TIP49, TIP49 C-terminus. This family consists of the
C-terminal region of several eukaryotic and archaeal
RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin
or TIP49b) proteins. The N-terminal domain contains the
pfam00004 domain. In zebrafish, the liebeskummer (lik)
mutation, causes development of hyperplastic embryonic
hearts. lik encodes Reptin, a component of a
DNA-stimulated ATPase complex. Beta-catenin and Pontin,
a DNA-stimulated ATPase that is often part of complexes
with Reptin, are in the same genetic pathways. The
Reptin/Pontin ratio serves to regulate heart growth
during development, at least in part via the
beta-catenin pathway. TBP-interacting protein 49
(TIP49) was originally identified as a TBP-binding
protein, and two related proteins are encoded by
individual genes, tip49a and b. Although the function
of this gene family has not been elucidated, they are
supposed to play a critical role in nuclear events
because they interact with various kinds of nuclear
factors and have DNA helicase activities.TIP49a has
been suggested to act as an autoantigen in some
patients with autoimmune diseases.
Length = 395
Score = 28.0 bits (63), Expect = 4.8
Identities = 9/14 (64%), Positives = 12/14 (85%)
Query: 33 KGVILYGPPGTGKT 46
+ V++ GPPGTGKT
Sbjct: 51 RAVLIAGPPGTGKT 64
>gnl|CDD|235871 PRK06835, PRK06835, DNA replication protein DnaC; Validated.
Length = 329
Score = 27.9 bits (63), Expect = 4.8
Identities = 8/17 (47%), Positives = 11/17 (64%)
Query: 30 KPPKGVILYGPPGTGKT 46
K + ++ YG GTGKT
Sbjct: 181 KNNENLLFYGNTGTGKT 197
>gnl|CDD|238005 cd00046, DEXDc, DEAD-like helicases superfamily. A diverse family
of proteins involved in ATP-dependent RNA or DNA
unwinding. This domain contains the ATP-binding region.
Length = 144
Score = 27.3 bits (61), Expect = 4.9
Identities = 9/31 (29%), Positives = 13/31 (41%)
Query: 33 KGVILYGPPGTGKTLPFSPALGYHYYCRGAG 63
+ V+L P G+GKTL + G
Sbjct: 1 RDVLLAAPTGSGKTLAALLPILELLDSLKGG 31
>gnl|CDD|177094 CHL00195, ycf46, Ycf46; Provisional.
Length = 489
Score = 28.1 bits (63), Expect = 4.9
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 25 EEMGIKPPKGVILYGPPGTGKTL 47
G+ P+G++L G GTGK+L
Sbjct: 252 SNYGLPTPRGLLLVGIQGTGKSL 274
>gnl|CDD|222165 pfam13481, AAA_25, AAA domain. This AAA domain is found in a
wide variety of presumed DNA repair proteins.
Length = 154
Score = 27.2 bits (61), Expect = 5.2
Identities = 10/20 (50%), Positives = 14/20 (70%), Gaps = 1/20 (5%)
Query: 28 GIKPPKGV-ILYGPPGTGKT 46
G+ P G+ +L G PGTGK+
Sbjct: 28 GLLPRGGLTLLAGAPGTGKS 47
>gnl|CDD|218528 pfam05272, VirE, Virulence-associated protein E. This family
contains several bacterial virulence-associated protein
E like proteins. These proteins contain a P-loop motif.
Length = 198
Score = 27.3 bits (61), Expect = 5.3
Identities = 14/43 (32%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 26 EMGIKPPKGVILYGPPGTGKTLPFSPALGYHYYCRGAGSNSDK 68
E G K +IL G G+GK+ F LG ++ S K
Sbjct: 46 EPGCKFDHVLILQGAQGSGKS-TFLKKLGGEWFTDSIRSFEGK 87
>gnl|CDD|214692 smart00487, DEXDc, DEAD-like helicases superfamily.
Length = 201
Score = 27.5 bits (61), Expect = 5.3
Identities = 10/32 (31%), Positives = 12/32 (37%)
Query: 33 KGVILYGPPGTGKTLPFSPALGYHYYCRGAGS 64
+ VIL P G+GKTL G
Sbjct: 25 RDVILAAPTGSGKTLAALLPALEALKRGKGGR 56
>gnl|CDD|129465 TIGR00368, TIGR00368, Mg chelatase-related protein. The N-terminal
end matches very strongly a pfam Mg_chelatase domain
[Unknown function, General].
Length = 499
Score = 27.9 bits (62), Expect = 5.7
Identities = 8/13 (61%), Positives = 13/13 (100%)
Query: 35 VILYGPPGTGKTL 47
++L+GPPG+GKT+
Sbjct: 214 LLLFGPPGSGKTM 226
>gnl|CDD|215599 PLN03140, PLN03140, ABC transporter G family member; Provisional.
Length = 1470
Score = 27.9 bits (62), Expect = 6.4
Identities = 10/18 (55%), Positives = 13/18 (72%)
Query: 29 IKPPKGVILYGPPGTGKT 46
IKP + +L GPP +GKT
Sbjct: 188 IKPSRMTLLLGPPSSGKT 205
>gnl|CDD|215832 pfam00270, DEAD, DEAD/DEAH box helicase. Members of this family
include the DEAD and DEAH box helicases. Helicases are
involved in unwinding nucleic acids. The DEAD box
helicases are involved in various aspects of RNA
metabolism, including nuclear transcription, pre mRNA
splicing, ribosome biogenesis, nucleocytoplasmic
transport, translation, RNA decay and organellar gene
expression.
Length = 169
Score = 26.8 bits (60), Expect = 7.1
Identities = 9/19 (47%), Positives = 12/19 (63%)
Query: 29 IKPPKGVILYGPPGTGKTL 47
I K V++ P G+GKTL
Sbjct: 11 ILSGKDVLVQAPTGSGKTL 29
>gnl|CDD|227570 COG5245, DYN1, Dynein, heavy chain [Cytoskeleton].
Length = 3164
Score = 27.6 bits (61), Expect = 7.3
Identities = 9/21 (42%), Positives = 13/21 (61%)
Query: 33 KGVILYGPPGTGKTLPFSPAL 53
+ I GPPG+GK + P+L
Sbjct: 1495 RSYIYCGPPGSGKEMLMCPSL 1515
>gnl|CDD|178279 PLN02674, PLN02674, adenylate kinase.
Length = 244
Score = 27.2 bits (60), Expect = 7.4
Identities = 11/16 (68%), Positives = 13/16 (81%)
Query: 30 KPPKGVILYGPPGTGK 45
KP K +IL GPPG+GK
Sbjct: 29 KPDKRLILIGPPGSGK 44
>gnl|CDD|192481 pfam10197, Cir_N, N-terminal domain of CBF1 interacting
co-repressor CIR. This is a 45 residue conserved region
at the N-terminal end of a family of proteins referred
to as CIRs (CBF1-interacting co-repressors). CBF1
(centromere-binding factor 1) acts as a transcription
factor that causes repression by binding specifically to
GTGGGAA motifs in responsive promoters, and it requires
CIR as a co-repressor. CIR binds to histone deacetylase
and to SAP30 and serves as a linker between CBF1 and the
histone deacetylase complex.
Length = 37
Score = 24.5 bits (54), Expect = 7.8
Identities = 9/24 (37%), Positives = 18/24 (75%)
Query: 133 RNQERLKPQEEKNEEERSRVDDLR 156
+NQE++ E+K EE+ ++++LR
Sbjct: 8 KNQEKVWEAEQKALEEQKKIEELR 31
>gnl|CDD|234763 PRK00440, rfc, replication factor C small subunit; Reviewed.
Length = 319
Score = 27.1 bits (61), Expect = 8.2
Identities = 8/9 (88%), Positives = 8/9 (88%)
Query: 38 YGPPGTGKT 46
GPPGTGKT
Sbjct: 44 AGPPGTGKT 52
>gnl|CDD|219158 pfam06745, KaiC, KaiC. This family represents a conserved region
within bacterial and archaeal proteins, most of which
are hypothetical. More than one copy is sometimes found
in each protein. This family includes KaiC, which is
one of the Kai proteins among which direct
protein-protein association may be a critical process
in the generation of circadian rhythms in
cyanobacteria.
Length = 231
Score = 26.8 bits (60), Expect = 8.8
Identities = 13/33 (39%), Positives = 18/33 (54%), Gaps = 7/33 (21%)
Query: 32 PKG--VILYGPPGTGKTLPFSPALGYHYYCRGA 62
P+G V++ G PGTGKT+ G + GA
Sbjct: 17 PRGRVVLITGGPGTGKTI-----FGLQFLYNGA 44
>gnl|CDD|202427 pfam02841, GBP_C, Guanylate-binding protein, C-terminal domain.
Transcription of the anti-viral guanylate-binding
protein (GBP) is induced by interferon-gamma during
macrophage induction. This family contains GBP1 and
GPB2, both GTPases capable of binding GTP, GDP and GMP.
Length = 297
Score = 26.9 bits (60), Expect = 9.2
Identities = 12/37 (32%), Positives = 21/37 (56%)
Query: 113 LKLLKLERIKDYLLMEEEFIRNQERLKPQEEKNEEER 149
+LL+ ++ ++ +ME + QE +K EK E ER
Sbjct: 220 QELLREKQKEEEQMMEAQERSYQEHVKQLIEKMEAER 256
>gnl|CDD|237090 PRK12402, PRK12402, replication factor C small subunit 2;
Reviewed.
Length = 337
Score = 26.9 bits (60), Expect = 9.5
Identities = 7/11 (63%), Positives = 10/11 (90%)
Query: 36 ILYGPPGTGKT 46
++ GPPG+GKT
Sbjct: 40 LVQGPPGSGKT 50
>gnl|CDD|238688 cd01394, radB, RadB. The archaeal protein radB shares similarity
radA, the archaeal functional homologue to the
bacterial RecA. The precise function of radB is
unclear.
Length = 218
Score = 26.7 bits (59), Expect = 9.7
Identities = 10/16 (62%), Positives = 13/16 (81%), Gaps = 2/16 (12%)
Query: 33 KGVI--LYGPPGTGKT 46
+G + +YGPPGTGKT
Sbjct: 18 RGTVTQVYGPPGTGKT 33
Database: CDD.v3.10
Posted date: Mar 20, 2013 7:55 AM
Number of letters in database: 10,937,602
Number of sequences in database: 44,354
Lambda K H
0.313 0.135 0.389
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,870,341
Number of extensions: 1144393
Number of successful extensions: 1390
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1375
Number of HSP's successfully gapped: 147
Length of query: 225
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 132
Effective length of database: 6,812,680
Effective search space: 899273760
Effective search space used: 899273760
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.8 bits)
S2: 57 (25.9 bits)