RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3674
(306 letters)
>gnl|CDD|128983 smart00744, RINGv, The RING-variant domain is a C4HC3 zinc-finger
like motif found in a number of cellular and viral
proteins. Some of these proteins have been shown both
in vivo and in vitro to have ubiquitin E3 ligase
activity. The RING-variant domain is reminiscent of both
the RING and the PHD domains and may represent an
evolutionary intermediate. To describe this domain the
term PHD/LAP domain has been used in the past. Extended
description: The RING-variant (RINGv) domain contains a
C4HC3 zinc-finger-like motif similar to the PHD domain,
while some of the spacing between the Cys/His residues
follow a pattern somewhat closer to that found in the
RING domain. The RINGv domain, similar to the RING, PHD
and LIM domains, is thought to bind two zinc ions
co-ordinated by the highly conserved Cys and His
residues. RING variant domain: C-x (2) -C-x(10-45)-C-x
(1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a
PHD: C-x(1-2) -C-x
(7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C
Classical RING domain: C-x (2) -C-x
(9-39)-C-x(1-3)-H-x(2-3)-C-x(2)-C-x(4-48) -C-x(2)-C.
Length = 49
Score = 62.7 bits (153), Expect = 3e-13
Identities = 22/49 (44%), Positives = 31/49 (63%), Gaps = 3/49 (6%)
Query: 90 VCRICHG---SHENLKALCECRGTMGLVHAECLTQWLSESGRSCCEICN 135
+CRICH + L + C C+G++ VH ECL +W++ESG CEIC
Sbjct: 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49
>gnl|CDD|221845 pfam12906, RINGv, RING-variant domain.
Length = 47
Score = 61.6 bits (150), Expect = 8e-13
Identities = 22/47 (46%), Positives = 26/47 (55%), Gaps = 3/47 (6%)
Query: 91 CRICH---GSHENLKALCECRGTMGLVHAECLTQWLSESGRSCCEIC 134
CRIC E L C CRG++ VH CL +WL SG + CEIC
Sbjct: 1 CRICLEGEEEDEPLIRPCRCRGSLKYVHQSCLERWLKTSGNTTCEIC 47
>gnl|CDD|227510 COG5183, SSM4, Protein involved in mRNA turnover and stability [RNA
processing and modification].
Length = 1175
Score = 63.1 bits (153), Expect = 5e-11
Identities = 24/71 (33%), Positives = 39/71 (54%), Gaps = 3/71 (4%)
Query: 85 DENAPVCRICHGSHENLKAL---CECRGTMGLVHAECLTQWLSESGRSCCEICNFKYKFK 141
+E+ CRIC L C+C G++ +H ECL +W+ SG C+IC+++YKFK
Sbjct: 9 NEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDICHYEYKFK 68
Query: 142 RTLKRPLWETM 152
K + + +
Sbjct: 69 DIYKEDMPQII 79
>gnl|CDD|177491 PHA02825, PHA02825, LAP/PHD finger-like protein; Provisional.
Length = 162
Score = 52.5 bits (126), Expect = 2e-08
Identities = 19/62 (30%), Positives = 30/62 (48%)
Query: 85 DENAPVCRICHGSHENLKALCECRGTMGLVHAECLTQWLSESGRSCCEICNFKYKFKRTL 144
C IC ++ + C C+ +VH ECL +W++ S C+ICN Y K+
Sbjct: 5 SLMDKCCWICKDEYDVVTNYCNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKKNY 64
Query: 145 KR 146
K+
Sbjct: 65 KK 66
>gnl|CDD|165197 PHA02862, PHA02862, 5L protein; Provisional.
Length = 156
Score = 39.9 bits (93), Expect = 3e-04
Identities = 20/99 (20%), Positives = 43/99 (43%), Gaps = 5/99 (5%)
Query: 90 VCRICHGSHENLKALCECRGTMGLVHAECLTQWLSESGRSCCEICNFKYKFKRTLKRPLW 149
+C IC+ + C C +VH +C+ W++ S + C +C KY K+T +
Sbjct: 4 ICWICNDVCDERNNFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKKT-----Y 58
Query: 150 ETMAGWLYKVVENSQVFIILSWLMAITPIVLLAAALTNN 188
+ W + + + +++ + L +L+N+
Sbjct: 59 VSFKKWNWCFNDKKTTLSKIFFILFALVFIFLTISLSND 97
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 35.0 bits (80), Expect = 0.060
Identities = 24/81 (29%), Positives = 33/81 (40%), Gaps = 7/81 (8%)
Query: 63 NSICNDILQLLEGEIDEIGSEHDENAPVCRICHG---SHENLKALCECRGTMGLVHAECL 119
N D+L L + IDE S H+E C IC+ + C H CL
Sbjct: 1448 NGSFMDLLGLWKKNIDEKFSGHEE----CAICYSVLDMVDRSLPSKRCATCKNKFHTRCL 1503
Query: 120 TQWLSESGRSCCEICNFKYKF 140
+W + S RS C +C + F
Sbjct: 1504 YKWFASSARSNCPLCRSEITF 1524
>gnl|CDD|236712 PRK10547, PRK10547, chemotaxis protein CheA; Provisional.
Length = 670
Score = 32.0 bits (73), Expect = 0.40
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 3/46 (6%)
Query: 48 LDAEEHSQQDDADFFNSICNDILQL-LE--GEIDEIGSEHDENAPV 90
LDA + SQ+ DA F IC + QL LE GE + A
Sbjct: 100 LDAYKTSQEPDAASFEYICQALRQLALEAKGETPSAVTRLSVVAIQ 145
>gnl|CDD|219160 pfam06749, DUF1218, Protein of unknown function (DUF1218). This
family contains hypothetical plant proteins of unknown
function. Family members contain a number of conserved
cysteine residues.
Length = 97
Score = 28.4 bits (64), Expect = 1.6
Identities = 12/43 (27%), Positives = 16/43 (37%), Gaps = 4/43 (9%)
Query: 165 VFIILSWLMAITPIV-LLAAALTNNFPFNHNDRKTHQQLQCGF 206
V +LSW+ + LLA A N H H + C
Sbjct: 39 VCFVLSWIAFVIAFALLLAGAARNA---YHTRYNVHFRPSCYT 78
>gnl|CDD|224048 COG1123, COG1123, ATPase components of various ABC-type transport
systems, contain duplicated ATPase [General function
prediction only].
Length = 539
Score = 28.7 bits (65), Expect = 4.2
Identities = 8/47 (17%), Positives = 14/47 (29%), Gaps = 6/47 (12%)
Query: 58 DADFFNSICNDILQLLEGEIDEIGSEHDENAPVCRICHGSHENLKAL 104
D I + + + +G I E G + H + L
Sbjct: 489 DLAVVRYIADRVAVMYDGRIVEEGPTEK------VFENPQHPYTRKL 529
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 28.8 bits (64), Expect = 4.5
Identities = 20/72 (27%), Positives = 25/72 (34%), Gaps = 15/72 (20%)
Query: 77 IDEIGSEHDENAPVCRICHGSH-ENLKALCECRGTMGLVHAECL-------TQWL----- 123
++ I DE +C C +H EN A+ C G VH C WL
Sbjct: 183 VEPIEPS-DEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWLCRKCI 241
Query: 124 -SESGRSCCEIC 134
E CC C
Sbjct: 242 YGEYQIRCCSFC 253
>gnl|CDD|214871 smart00868, zf-AD, Zinc-finger associated domain (zf-AD). The
zf-AD domain, also known as ZAD, forms an atypical
treble-cleft-like zinc co-ordinating fold. The zf-AD
domain is thought to be involved in mediating dimer
formation, but does not bind to DNA.
Length = 73
Score = 26.3 bits (58), Expect = 4.8
Identities = 12/47 (25%), Positives = 17/47 (36%), Gaps = 2/47 (4%)
Query: 90 VCRICHGSHENLKALCECRGTMGLVH--AECLTQWLSESGRSCCEIC 134
VCR+C ENL ++ + L EC + IC
Sbjct: 1 VCRLCLSESENLVSIFDESSEASLAEKIEECTGIEIEPDDGLPKVIC 47
>gnl|CDD|215516 PLN02957, PLN02957, copper, zinc superoxide dismutase.
Length = 238
Score = 27.8 bits (62), Expect = 5.9
Identities = 12/33 (36%), Positives = 12/33 (36%)
Query: 78 DEIGSEHDENAPVCRICHGSHENLKALCECRGT 110
S A V G EN K LC C GT
Sbjct: 191 TADKSGPGIAAAVIARSAGVGENYKKLCSCDGT 223
>gnl|CDD|236509 PRK09427, PRK09427, bifunctional indole-3-glycerol phosphate
synthase/phosphoribosylanthranilate isomerase;
Provisional.
Length = 454
Score = 27.5 bits (62), Expect = 9.7
Identities = 15/41 (36%), Positives = 21/41 (51%), Gaps = 10/41 (24%)
Query: 212 MIRKDSCPISITPIYEGYAMIRKDSCPISI-TPIYEGKYFK 251
+IR D P I +Y+ YA S IS+ T + KYF+
Sbjct: 65 LIRDDFDPAEIARVYKHYA-----SA-ISVLT---DEKYFQ 96
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
0.323 0.137 0.433
Gapped
Lambda K H
0.267 0.0633 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 15,473,910
Number of extensions: 1426052
Number of successful extensions: 1419
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1414
Number of HSP's successfully gapped: 25
Length of query: 306
Length of database: 10,937,602
Length adjustment: 97
Effective length of query: 209
Effective length of database: 6,635,264
Effective search space: 1386770176
Effective search space used: 1386770176
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 59 (26.7 bits)