RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10659
(140 letters)
>gnl|CDD|233043 TIGR00599, rad18, DNA repair protein rad18. All proteins in this
family for which functions are known are involved in
nucleotide excision repair.This family is based on the
phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis,
Stanford University) [DNA metabolism, DNA replication,
recombination, and repair].
Length = 397
Score = 55.0 bits (132), Expect = 8e-10
Identities = 32/83 (38%), Positives = 42/83 (50%), Gaps = 7/83 (8%)
Query: 4 TSTPSRSLKRQHSPPDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSA 63
+TP SL P D L C IC + +T C HTFC CI +C+ Q KCP C A
Sbjct: 13 LTTPIPSLY----PLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRA 68
Query: 64 SLPDMNSVF-PNFLLNELVQKHK 85
D S N+L++E+V+ K
Sbjct: 69 --EDQESKLRSNWLVSEIVESFK 89
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 49.4 bits (118), Expect = 3e-09
Identities = 19/43 (44%), Positives = 28/43 (65%), Gaps = 1/43 (2%)
Query: 20 NDLLCPICFELIREAHI-TRCGHTFCFSCISKCVELQIKCPKC 61
+L CPIC +L+R+ + T CGH FC CI + ++ + KCP C
Sbjct: 1 EELECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPIC 43
>gnl|CDD|238093 cd00162, RING, RING-finger (Really Interesting New Gene) domain,
a specialized type of Zn-finger of 40 to 60 residues
that binds two atoms of zinc; defined by the
'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)-
H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved
in mediating protein-protein interactions; identified
in a proteins with a wide range of functions such as
viral replication, signal transduction, and
development; has two variants, the C3HC4-type and a
C3H2C3-type (RING-H2 finger), which have different
cysteine/histidine pattern; a subset of RINGs are
associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H).
Length = 45
Score = 45.5 bits (108), Expect = 9e-08
Identities = 19/44 (43%), Positives = 24/44 (54%), Gaps = 2/44 (4%)
Query: 24 CPICFELIRE-AHITRCGHTFCFSCISKCVEL-QIKCPKCSASL 65
CPIC E RE + CGH FC SCI K ++ + CP C +
Sbjct: 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|214546 smart00184, RING, Ring finger. E3 ubiquitin-protein ligase
activity is intrinsic to the RING domain of c-Cbl and
is likely to be a general function of this domain;
Various RING fingers exhibit binding activity towards
E2 ubiquitin-conjugating enzymes (Ubc' s).
Length = 40
Score = 45.2 bits (107), Expect = 9e-08
Identities = 20/40 (50%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 24 CPICFE-LIREAHITRCGHTFCFSCISKCVELQ-IKCPKC 61
CPIC E +++ I CGHTFC SCI K +E CP C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 48.9 bits (116), Expect = 1e-07
Identities = 23/79 (29%), Positives = 29/79 (36%), Gaps = 3/79 (3%)
Query: 19 DNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFP-NFLL 77
D+ L C IC I T CGHTFC CI + + Q CP C S +
Sbjct: 23 DSMLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCRE--DPCESRLRGSSGS 80
Query: 78 NELVQKHKIKSAQDSDGLR 96
E+ + H L
Sbjct: 81 REINESHARNRDLLRKVLE 99
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 44.3 bits (105), Expect = 3e-07
Identities = 15/44 (34%), Positives = 19/44 (43%), Gaps = 3/44 (6%)
Query: 24 CPICFELI---REAHITRCGHTFCFSCISKCVELQIKCPKCSAS 64
CPIC + E + CGH F C+ K + CP C A
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSNTCPLCRAP 46
>gnl|CDD|215715 pfam00097, zf-C3HC4, Zinc finger, C3HC4 type (RING finger). The
C3HC4 type zinc-finger (RING finger) is a cysteine-rich
domain of 40 to 60 residues that coordinates two zinc
ions, and has the consensus sequence:
C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C
where X is any amino acid. Many proteins containing a
RING finger play a key role in the ubiquitination
pathway.
Length = 40
Score = 43.2 bits (102), Expect = 5e-07
Identities = 17/40 (42%), Positives = 20/40 (50%), Gaps = 2/40 (5%)
Query: 24 CPICFELIREAH-ITRCGHTFCFSCISKCVELQI-KCPKC 61
CPIC E ++ I CGH FC CI +E CP C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 42.4 bits (99), Expect = 2e-05
Identities = 30/98 (30%), Positives = 43/98 (43%), Gaps = 2/98 (2%)
Query: 17 PPDNDLLCPICFELIREAHITR-CGHTFCFSCI-SKCVELQIKCPKCSASLPDMNSVFPN 74
PP+ L CP+C L+R T CGHTFC CI + ++ KCP CS ++ + P+
Sbjct: 270 PPNISLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLTPD 329
Query: 75 FLLNELVQKHKIKSAQDSDGLRDFVASESQNLSLPDVN 112
V+K K + D S+ D N
Sbjct: 330 IDKKLEVEKALKKQRKKVGTSDDNNTPMSEKRKREDPN 367
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 37.0 bits (86), Expect = 2e-04
Identities = 16/43 (37%), Positives = 18/43 (41%), Gaps = 2/43 (4%)
Query: 20 NDLLCPICFELIREAHITRCGHT-FCFSCISKCVELQIKCPKC 61
D LC IC E R CGH C C + + KCP C
Sbjct: 1 EDDLCVICLERPRNVVFLPCGHLCLCEECAKRLRSKK-KCPIC 42
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 39.1 bits (91), Expect = 2e-04
Identities = 18/48 (37%), Positives = 21/48 (43%), Gaps = 2/48 (4%)
Query: 18 PDNDLLCPICFELIREAHITRCGHTFCFSCI--SKCVELQIKCPKCSA 63
P D C +C E T CGH FC SC+ S + CP C A
Sbjct: 212 PLADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCRA 259
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 39.3 bits (91), Expect = 2e-04
Identities = 16/68 (23%), Positives = 27/68 (39%), Gaps = 2/68 (2%)
Query: 18 PDNDLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLL 77
LC IC + +T CGH+FC C + + +C C + V +
Sbjct: 193 EKIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGDECGVCGKATYGRFWVVSDL-- 250
Query: 78 NELVQKHK 85
+++ K K
Sbjct: 251 QKMLNKRK 258
>gnl|CDD|222135 pfam13445, zf-RING_LisH, RING-type zinc-finger, LisH dimerisation
motif. This zinc-finger is the dimerisation motif for
LisH proteins, and is also a typical RING-type of plant
ubiquitin ligases.
Length = 55
Score = 36.5 bits (85), Expect = 3e-04
Identities = 11/44 (25%), Positives = 20/44 (45%), Gaps = 6/44 (13%)
Query: 22 LLCPICFELIREAH----ITRCGHTFCFSCISKCVE--LQIKCP 59
+CPI E++ + + CGH + + K + + KCP
Sbjct: 11 FVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCP 54
>gnl|CDD|128780 smart00504, Ubox, Modified RING finger domain. Modified RING
finger domain, without the full complement of
Zn2+-binding ligands. Probable involvement in
E2-dependent ubiquitination.
Length = 63
Score = 36.4 bits (85), Expect = 3e-04
Identities = 17/63 (26%), Positives = 27/63 (42%), Gaps = 1/63 (1%)
Query: 21 DLLCPICFELIREAHITRCGHTFCFSCISKCVELQIKCPKCSASLPDMNSVFPNFLLNEL 80
+ LCPI E++++ I G T+ S I K + P L + PN L
Sbjct: 1 EFLCPISLEVMKDPVILPSGQTYERSAIEKWLLSHGTDPVTGQPLTH-EDLIPNLALKSA 59
Query: 81 VQK 83
+Q+
Sbjct: 60 IQE 62
>gnl|CDD|178747 PLN03208, PLN03208, E3 ubiquitin-protein ligase RMA2;
Provisional.
Length = 193
Score = 37.4 bits (86), Expect = 8e-04
Identities = 14/30 (46%), Positives = 19/30 (63%)
Query: 21 DLLCPICFELIREAHITRCGHTFCFSCISK 50
D C IC + +R+ +T CGH FC+ CI K
Sbjct: 18 DFDCNICLDQVRDPVVTLCGHLFCWPCIHK 47
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 30.9 bits (70), Expect = 0.16
Identities = 14/46 (30%), Positives = 19/46 (41%), Gaps = 8/46 (17%)
Query: 24 CPICFELIREAHI--------TRCGHTFCFSCISKCVELQIKCPKC 61
C IC E + + I + C H FC CI + + CP C
Sbjct: 177 CAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKEKNTCPVC 222
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 29.9 bits (67), Expect = 0.45
Identities = 9/27 (33%), Positives = 12/27 (44%)
Query: 39 CGHTFCFSCISKCVELQIKCPKCSASL 65
CGH C+ +E Q CP C +
Sbjct: 318 CGHILHLHCLKNWLERQQTCPICRRPV 344
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 29.3 bits (65), Expect = 0.68
Identities = 22/87 (25%), Positives = 36/87 (41%), Gaps = 9/87 (10%)
Query: 15 HSPPDNDLLCPICFELI----REAHITRCGHTFCFSCISKCVE-LQIKCPKCSASLPDMN 69
H+ D + CP+C E + + CG+ C C + + L +CP C D N
Sbjct: 8 HNSEDEEDYCPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLNGRCPACRRKYDDEN 67
Query: 70 ----SVFPNFLLNELVQKHKIKSAQDS 92
++ P L EL +K + K +
Sbjct: 68 VRYVTLSPEELKMELARKEERKMREKE 94
>gnl|CDD|221705 pfam12678, zf-rbx1, RING-H2 zinc finger. There are 8 cysteine/
histidine residues which are proposed to be the
conserved residues involved in zinc binding. The
protein, of which this domain is the conserved region,
participates in diverse functions relevant to
chromosome metabolism and cell cycle control.
Length = 73
Score = 27.8 bits (62), Expect = 0.73
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 38 RCGHTFCFSCISKCVELQIKCPKC 61
CGH F CIS+ ++ + CP C
Sbjct: 49 ECGHAFHLHCISRWLKTRNTCPLC 72
>gnl|CDD|239127 cd02662, Peptidase_C19F, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 240
Score = 28.5 bits (64), Expect = 1.0
Identities = 10/49 (20%), Positives = 17/49 (34%), Gaps = 1/49 (2%)
Query: 55 QIKCPKCSASLPDMNSVFPNFLLNELVQKHKIKSAQDSDGLRDFVASES 103
+I C +C S F L + + L DF+++E
Sbjct: 63 RIVCLQCGESSKVRYESFTMLSLP-VPNQSSGSGTTLEHCLDDFLSTEI 110
>gnl|CDD|177987 PLN02354, PLN02354, copper ion binding / oxidoreductase.
Length = 552
Score = 28.2 bits (63), Expect = 1.7
Identities = 9/19 (47%), Positives = 15/19 (78%)
Query: 6 TPSRSLKRQHSPPDNDLLC 24
+P RSL+ +++ P+N LLC
Sbjct: 520 SPERSLRDEYNMPENALLC 538
>gnl|CDD|150760 pfam10122, Mu-like_Com, Mu-like prophage protein Com. Members of
this family of proteins comprise the translational
regulator of mom.
Length = 51
Score = 25.6 bits (56), Expect = 2.4
Identities = 13/27 (48%), Positives = 17/27 (62%), Gaps = 5/27 (18%)
Query: 38 RCGHTFCFSCISKC---VELQIKCPKC 61
RCGH C +++ ELQIKCP+C
Sbjct: 6 RCGH--CNKLLARAGAFSELQIKCPRC 30
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 27.3 bits (60), Expect = 3.1
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 2/45 (4%)
Query: 19 DNDLLCPICFELIREAHITRCGHTFCFSCISKCVEL--QIKCPKC 61
+ ++ C IC + CGH C +C + L Q CP C
Sbjct: 59 EENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLC 103
>gnl|CDD|172952 PRK14477, PRK14477, bifunctional nitrogenase molybdenum-cofactor
biosynthesis protein NifE/NifN; Provisional.
Length = 917
Score = 27.4 bits (61), Expect = 3.1
Identities = 10/43 (23%), Positives = 25/43 (58%)
Query: 97 DFVASESQNLSLPDVNLMLEVLNQRKHLLEAESSVAQYKLLYE 139
+ +A+ +QN +L D M ++++ H++E S+ +++ E
Sbjct: 345 EVLAAGTQNSTLEDFARMKALMHKDAHIIEDTSTAGLLRVMRE 387
>gnl|CDD|222981 PHA03096, PHA03096, p28-like protein; Provisional.
Length = 284
Score = 27.1 bits (60), Expect = 3.5
Identities = 14/77 (18%), Positives = 25/77 (32%), Gaps = 16/77 (20%)
Query: 24 CPICFELIREAHI--------TRCGHTFCFSCI------SKCVELQIKCPKCSASLPDMN 69
C IC E I+ +I + H F CI S E + + + + + +
Sbjct: 181 CGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESLYKETEPENRRLNTVIVFIE 240
Query: 70 SVFPNFLLNELVQKHKI 86
+ N L +
Sbjct: 241 KI--NEDLKNNIPSRYW 255
>gnl|CDD|176479 cd08642, DNA_pol_A_pol_I_A, Polymerase I functions primarily to
fill DNA gaps that arise during DNA repair,
recombination and replication. Family A polymerase
(polymerase I) functions primarily to fill DNA gaps that
arise during DNA repair, recombination and replication.
DNA-dependent DNA polymerases can be classified in six
main groups based upon phylogenetic relationships with
E. coli polymerase I (classA), E. coli polymerase II
(class B), E.coli polymerase III (class C),
euryarchaaeota polymerase II (class D), human polymerase
beta (class x), E. coli UmuC/DinB and eukaryotic RAP
30/Xeroderma pigmentosum variant (class Y). Family A
polymerase are found primarily in organisms related to
prokaryotes and include prokaryotic DNA polymerase I
,mitochondrial polymerase delta, and several
bacteriphage polymerases including those from
odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is
have two functional domains located on the same
polypeptide; a 5'-3' polymerase and 5'-3' exonuclease.
Pol I uses its 5' nuclease activity to remove the
ribonucleotide portion of newly synthesized Okazaki
fragments and DNA polymerase activity to fill in the
resulting gap. A combination of phylogenomic and
signature sequence-based (or phonetic) approaches is
used to understand the evolutionary relationships among
bacteria. DNA polymerase I is one of the conserved
proteins that is used to search for protein signatures.
The structure of these polymerases resembles in overall
morphology a cupped human right hand, with fingers
(which bind an incoming nucleotide and interact with the
single-stranded template), palm (which harbors the
catalytic amino acid residues and also binds an incoming
dNTP) and thumb (which binds double-stranded DNA)
subdomains.
Length = 378
Score = 26.8 bits (60), Expect = 4.0
Identities = 11/23 (47%), Positives = 12/23 (52%), Gaps = 3/23 (13%)
Query: 29 ELIREAHITRCGHTFC---FSCI 48
+LIR A I GH F FS I
Sbjct: 158 QLIRTAFIPSEGHRFIVSDFSAI 180
>gnl|CDD|233856 TIGR02411, leuko_A4_hydro, leukotriene A-4
hydrolase/aminopeptidase. Members of this family
represent a distinctive subset within the zinc
metallopeptidase family M1 (pfam01433). The majority of
the members of pfam01433 are aminopeptidases, but the
sequences in this family for which the function is known
are leukotriene A-4 hydrolase. A dual epoxide hydrolase
and aminopeptidase activity at the same active site is
indicated. The physiological substrate for
aminopeptidase activity is not known.
Length = 602
Score = 26.7 bits (59), Expect = 4.6
Identities = 20/64 (31%), Positives = 30/64 (46%), Gaps = 8/64 (12%)
Query: 66 PDMNSVFPNF---LLNE---LVQKHKIKSAQDSDGLRDFVASESQNLSLPDVNLMLEVLN 119
P M V PNF L +E L + + +A+ D L F A + ++ S + L LE L
Sbjct: 443 PGMPPVKPNFDTTLADECYALADRW-VDAAKADD-LSSFNAKDIKDFSSHQLVLFLETLT 500
Query: 120 QRKH 123
+R
Sbjct: 501 ERGG 504
>gnl|CDD|116857 pfam08273, Prim_Zn_Ribbon, Zinc-binding domain of
primase-helicase.
Length = 39
Score = 24.3 bits (53), Expect = 5.7
Identities = 12/39 (30%), Positives = 15/39 (38%), Gaps = 13/39 (33%)
Query: 14 QHSPPDNDLLCPIC-----FELIREAHITRCGHTFCFSC 47
+H P CP C F + + G FCFSC
Sbjct: 2 RHGP------CPNCGGSDRFRIFDDKDGR--GTWFCFSC 32
>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional.
Length = 242
Score = 26.2 bits (57), Expect = 7.0
Identities = 10/35 (28%), Positives = 16/35 (45%), Gaps = 9/35 (25%)
Query: 24 CPICFELIREAHITR---------CGHTFCFSCIS 49
C IC+E++ + C H FC +CI+
Sbjct: 173 CGICYEVVYSKRLENDRYFGLLDSCNHIFCITCIN 207
>gnl|CDD|234932 PRK01269, PRK01269, tRNA s(4)U8 sulfurtransferase; Provisional.
Length = 482
Score = 25.9 bits (58), Expect = 8.2
Identities = 11/35 (31%), Positives = 18/35 (51%)
Query: 93 DGLRDFVASESQNLSLPDVNLMLEVLNQRKHLLEA 127
GL + S +L PDV + LE+ + R +L+
Sbjct: 130 GGLNQHIESAGVDLKNPDVTVHLEIRDDRLYLVTE 164
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
0.321 0.133 0.397
Gapped
Lambda K H
0.267 0.0775 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,416,506
Number of extensions: 516262
Number of successful extensions: 531
Number of sequences better than 10.0: 1
Number of HSP's gapped: 524
Number of HSP's successfully gapped: 54
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 54 (24.5 bits)