RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18179
(108 letters)
>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 = 39.7 bits (93), Expect = 6e-06
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 19 CLVCQGILIKPIKL-PCNHHVCLECLQRICDNSNLSCPMCRKRL 61
C +C +P+ L PC H C C+ + + +CP+CR +
Sbjct: 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 41.7 bits (97), Expect = 2e-05
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 16 SVLCLVCQGILIKPIKLP-CNHHVCLECLQRICDNSNLSCPMCRKR 60
S+ C +C +L P+K P C H C EC+ +S+ CP C ++
Sbjct: 274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK 319
>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 = 35.6 bits (82), Expect = 2e-04
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 19 CLVCQGILIK-PIKLPCNHHVCLECLQRICDNSNLSCPMC 57
C +C +K P+ LPC H C C+++ ++ N +CP+C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 35.2 bits (81), Expect = 4e-04
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 15 DSVLCLVCQGILIKPIKL-PCNHHVCLECLQRICDNSNLSCPMCRK 59
+ + C +C +L P+ L PC H C EC+ R + CP+CR
Sbjct: 1 EELECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKS-KCPICRT 45
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 35.1 bits (81), Expect = 5e-04
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 19 CLVCQGILI---KPIKLPCNHHVCLECLQRICDNSNLSCPMCRKR 60
C +C + + LPC H ECL + +SN +CP+CR
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSN-TCPLCRAP 46
>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 = 36.5 bits (84), Expect = 0.001
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 16 SVLCLVCQGILIKPIKLPCNHHVCLECLQRICDNSNLSCPMCR 58
S+ C +C+ P+ C+H C C++R C ++ CP+CR
Sbjct: 26 SLRCHICKDFFDVPVLTSCSHTFCSLCIRR-CLSNQPKCPLCR 67
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 36.5 bits (84), Expect = 0.001
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 14/63 (22%)
Query: 12 LTPDSVLCLVC-------------QGILIKPIKLPCNHHVCLECLQRICDNSNLSCPMCR 58
LT C +C +G+ + P +LPC H + L CL+ + +CP+CR
Sbjct: 283 LTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ-TCPICR 341
Query: 59 KRL 61
+ +
Sbjct: 342 RPV 344
>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 = 30.1 bits (68), Expect = 0.033
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 19 CLVCQGILIKPIK-LPCNHHVCLECLQRICDNSNLSCPMC 57
C +C P+ LPC H C +C+ ++ N++CP+C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>gnl|CDD|219128 pfam06666, DUF1173, Protein of unknown function (DUF1173). This
family contains a group of hypothetical bacterial
proteins that contain three conserved cysteine residues
towards the N-terminal. The function of these proteins
is unknown.
Length = 385
Score = 31.9 bits (73), Expect = 0.039
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 63 IWLRRNKDFSLLIDENLWNQIQKYYKKEVDQKLFDQDDGV 102
I +R D L++DE+LW ++ K + E++ L+ +GV
Sbjct: 233 IVIRHLPDAPLMLDEDLWRRLLKRFAAELE--LWRAGEGV 270
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 31.9 bits (72), Expect = 0.040
Identities = 13/45 (28%), Positives = 21/45 (46%), Gaps = 1/45 (2%)
Query: 15 DSVLCLVCQGILIKPIKLPCNHHVCLECLQRICDNSNLS-CPMCR 58
+++ C +C G + PC H +C C R+ CP+CR
Sbjct: 60 ENMNCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLCR 104
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 32.0 bits (72), Expect = 0.042
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 16 SVLCLVCQGILIKPIKLPCNHHVCLECLQRICDNSNLSCPMCR 58
+ C +C + P + C H C C++R CP+CR
Sbjct: 25 MLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPF-CPVCR 66
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 31.9 bits (72), Expect = 0.045
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 17 VLCLVCQGILIKPIK---LPCNHHVCLECLQRICDNSNLSCPMCR 58
V C +C IK + LPC+H + C+ + + CP+CR
Sbjct: 324 VECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCR 368
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 29.7 bits (67), Expect = 0.047
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 15 DSVLCLVCQGILIKPIKLPCNHHV-CLECLQRICDNSNLSCPMCRK 59
+ LC++C + LPC H C EC +R+ CP+CR+
Sbjct: 1 EDDLCVICLERPRNVVFLPCGHLCLCEECAKRLRSKKK--CPICRQ 44
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 30.4 bits (68), Expect = 0.13
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 33 PCNHHVCLECLQRICDNSNLSCPMCRKR 60
PC + +C C I N N CP CR++
Sbjct: 35 PCGYQICQFCYNNIRQNLNGRCPACRRK 62
>gnl|CDD|218995 pfam06337, DUSP, DUSP domain. The DUSP (domain present in
ubiquitin-specific protease) domain is found at the
N-terminus of Ubiquitin-specific proteases. The
structure of this domain has been solved. Its
tripod-like structure consists of a 3-fold
alpha-helical bundle supporting a triple-stranded
anti-parallel beta-sheet.
Length = 86
Score = 28.2 bits (63), Expect = 0.30
Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 48 DNSNLSCP--MCRKRLSIWLRRNKDFSLLIDENLWNQIQKYYKK 89
DNS+L K+L L+ D+ +L+ E +W + ++Y
Sbjct: 34 DNSSLLDDEENLLKQLKPNLQEGVDY-VLVPEEVWEFLVEWYGG 76
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 29.5 bits (66), Expect = 0.30
Identities = 14/41 (34%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 19 CLVCQGILIKPIKLPCNHHVCLECL-QRICDNSNLSCPMCR 58
C +C P PC H CL CL CP+CR
Sbjct: 218 CFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCR 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 = 27.7 bits (62), Expect = 0.36
Identities = 9/29 (31%), Positives = 14/29 (48%), Gaps = 1/29 (3%)
Query: 29 PIKLPCNHHVCLECLQRICDNSN-LSCPM 56
P+ LPC H + L+++ N CP
Sbjct: 27 PVMLPCGHVYSRKALEKLAKNGGKFKCPY 55
>gnl|CDD|206613 pfam14447, Prok-RING_4, Prokaryotic RING finger family 4. RING
finger family domain found sporadically in bacteria.
The finger is fused to an N-terminal alpha-helical
domain, ROT/Trove-like repeats and a C-terminal TerD
domain. The architecture suggests a possible role in an
RNA-processing complex.
Length = 55
Score = 27.3 bits (61), Expect = 0.43
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 5/45 (11%)
Query: 19 CLVCQGILIKPIKLPCNHHVCLECLQRICDNSNLS-CPMCRKRLS 62
CL C + K + LPC H + D + CP C
Sbjct: 10 CLFCGTVGTKGVLLPCGHLIPDGTF----DGERYNGCPFCGTPFE 50
>gnl|CDD|227085 COG4742, COG4742, Predicted transcriptional regulator
[Transcription].
Length = 260
Score = 27.2 bits (61), Expect = 1.4
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 65 LRRNKDFSLLIDENLWNQIQKYYKKEVDQKL 95
+ D SL++ E ++ +++ YK+E+ + L
Sbjct: 161 AEKGIDVSLILTEPVFERLKSDYKEELKEFL 191
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 27.1 bits (60), Expect = 1.7
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 34 CNHHVCLECLQRICDNSNLSCPMCRK 59
CNH C+EC+ N +CP+CR
Sbjct: 200 CNHVFCIECIDIWKKEKN-TCPVCRT 224
>gnl|CDD|112657 pfam03854, zf-P11, P-11 zinc finger.
Length = 50
Score = 25.2 bits (55), Expect = 2.5
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 35 NHHVCLECLQRICDNSNLSCPMCRKRLSIWLR 66
+H++CL CLQ + S CP+C+K L LR
Sbjct: 20 DHYLCLRCLQLLLSVSER-CPICKKPLPTKLR 50
>gnl|CDD|227545 COG5220, TFB3, Cdk activating kinase (CAK)/RNA polymerase II
transcription initiation/nucleotide excision repair
factor TFIIH, subunit TFB3 [Cell division and
chromosome partitioning / Transcription / DNA
replication, recombination, and repair].
Length = 314
Score = 26.5 bits (58), Expect = 2.8
Identities = 22/66 (33%), Positives = 26/66 (39%), Gaps = 16/66 (24%)
Query: 6 CNSNNTLTPDSVLCLVCQGILIKPIKLPCNHHVCLECLQRICDNSNLSCPM--CRKRLSI 63
C S+ L PD ILI P C H +C C+ RI CP C K
Sbjct: 16 CKSDRYLNPDIK-------ILINP---ECYHRMCESCVDRIFSRGPAQCPYKGCGK---- 61
Query: 64 WLRRNK 69
LR+ K
Sbjct: 62 ILRKIK 67
>gnl|CDD|236930 PRK11558, PRK11558, putative ssRNA endonuclease; Provisional.
Length = 97
Score = 25.8 bits (57), Expect = 3.4
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 6/37 (16%)
Query: 55 PMCRKRLSIWLRRNK------DFSLLIDENLWNQIQK 85
P R RL++WL + D S I E +W Q+ +
Sbjct: 13 PRLRGRLAVWLLEVRAGVYVGDVSRRIREMIWQQVTQ 49
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 26.4 bits (59), Expect = 3.5
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 28 KPIKLPCNHHVCLECLQRICDNSNLSCP 55
KPI P + VC L R + C
Sbjct: 399 KPIPFPTHCPVCGSELVREEGEVVIRCT 426
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are
components of TFIIH, a complex that is involved in
nucleotide excision repair and transcription
initiation. Also known as MAT1 (menage a trois 1). 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 = 309
Score = 26.3 bits (58), Expect = 4.0
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 34 CNHHVCLECLQRICDNSNLSCPMCRKRLSIWLRRNKDFSLLIDENLWNQIQKYYKKEVD 92
C H +C C+ + + SCP C LR+N F + + E+ +KEVD
Sbjct: 26 CGHTLCESCVDLLFVRGSGSCPECDTP----LRKNN-FRVQLFEDP------TVEKEVD 73
>gnl|CDD|217015 pfam02395, Peptidase_S6, Immunoglobulin A1 protease. This family
consists of immunoglobulin A1 protease proteins. The
immunoglobulin A1 protease cleaves immunoglobulin IgA
and is found in pathogenic bacteria such as Neisseria
gonorrhoeae. Not all of the members of this family are
IgA proteases, espP from E. coli O157:H7 cleaves human
coagulation factor V and hbp is a hemoglobin protease
from E. coli EB1.
Length = 758
Score = 25.9 bits (57), Expect = 4.8
Identities = 8/21 (38%), Positives = 11/21 (52%)
Query: 77 ENLWNQIQKYYKKEVDQKLFD 97
N WN +K + +V QK D
Sbjct: 238 GNNWNVTKKDFLGQVLQKDTD 258
>gnl|CDD|221153 pfam11638, DnaA_N, DnaA N-terminal domain. This family of
proteins represents the N-terminal domain of DnaA, a
protein involved in the initiation of bacterial
chromosomal replication. The structure of this domain
is known. It is also found in three copies in some
proteins. The exact function of this domain is
uncertain but it has been suggested to play a role in
oligomerisation.
Length = 65
Score = 24.5 bits (54), Expect = 6.2
Identities = 5/21 (23%), Positives = 14/21 (66%)
Query: 77 ENLWNQIQKYYKKEVDQKLFD 97
+LW ++ + +KE+ ++ F+
Sbjct: 1 NSLWEKVLQRLRKELGEQTFN 21
>gnl|CDD|184418 PRK13958, PRK13958, N-(5'-phosphoribosyl)anthranilate isomerase;
Provisional.
Length = 207
Score = 25.1 bits (55), Expect = 7.9
Identities = 9/22 (40%), Positives = 11/22 (50%), Gaps = 1/22 (4%)
Query: 76 DENLWNQIQKYYKKEVDQKLFD 97
DEN+ I YK VD + D
Sbjct: 109 DENIIQNIN-KYKGFVDLFIID 129
>gnl|CDD|219663 pfam07957, DUF3294, Protein of unknown function (DUF3294). This
family was annotated as mitochondrial Ribosomal protein
MRP8, based on the presumed similarity of the
S.cerevisiae protein to an E.coli mitochondrial
ribosomal protein; however, this similarity is spurious,
and the function is not known [Wood, V].
Length = 217
Score = 25.1 bits (55), Expect = 8.1
Identities = 12/26 (46%), Positives = 19/26 (73%), Gaps = 1/26 (3%)
Query: 72 SLLIDENLWNQIQKYYKKEVDQKLFD 97
S DE++ +I+KY KKE+D+ +FD
Sbjct: 176 SEERDEDIEKEIKKYSKKELDE-IFD 200
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
0.324 0.140 0.476
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,221,461
Number of extensions: 412245
Number of successful extensions: 650
Number of sequences better than 10.0: 1
Number of HSP's gapped: 639
Number of HSP's successfully gapped: 60
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 53 (24.2 bits)