RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3116
(177 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 = 60.0 bits (146), Expect = 5e-13
Identities = 25/49 (51%), Positives = 33/49 (67%), Gaps = 2/49 (4%)
Query: 40 ICRICYGADQ--QNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCK 86
ICRIC+ L+S C+CKGS+ YVH EC+ERW+ E G C++CK
Sbjct: 1 ICRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49
>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-12
Identities = 25/65 (38%), Positives = 40/65 (61%), Gaps = 2/65 (3%)
Query: 27 LDKPDSSDDEDMTICRICYGADQQN--LLSICQCKGSIAYVHIECIERWLQECGVDKCDL 84
++K ++ +ED CRIC D ++ L C+C GSI Y+H EC+ W++ G KCD+
Sbjct: 1 MEKENTPMNEDKRSCRICRTEDIRDDPLFHPCKCSGSIKYIHRECLMEWMECSGTKKCDI 60
Query: 85 CKYQF 89
C Y++
Sbjct: 61 CHYEY 65
>gnl|CDD|221845 pfam12906, RINGv, RING-variant domain.
Length = 47
Score = 56.6 bits (137), Expect = 1e-11
Identities = 20/47 (42%), Positives = 32/47 (68%), Gaps = 2/47 (4%)
Query: 41 CRICYGADQQN--LLSICQCKGSIAYVHIECIERWLQECGVDKCDLC 85
CRIC ++++ L+ C+C+GS+ YVH C+ERWL+ G C++C
Sbjct: 1 CRICLEGEEEDEPLIRPCRCRGSLKYVHQSCLERWLKTSGNTTCEIC 47
>gnl|CDD|165197 PHA02862, PHA02862, 5L protein; Provisional.
Length = 156
Score = 34.9 bits (80), Expect = 0.009
Identities = 17/55 (30%), Positives = 30/55 (54%), Gaps = 3/55 (5%)
Query: 40 ICRICYGA-DQQNLLSICQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTER 93
IC IC D++N + C C VHI+C++ W+ +C+LCK ++ ++
Sbjct: 4 ICWICNDVCDERN--NFCGCNEEYKVVHIKCMQLWINYSKKKECNLCKTKYNIKK 56
>gnl|CDD|177491 PHA02825, PHA02825, LAP/PHD finger-like protein; Provisional.
Length = 162
Score = 34.0 bits (78), Expect = 0.015
Identities = 13/52 (25%), Positives = 19/52 (36%), Gaps = 5/52 (9%)
Query: 56 CQCKGSIAYVHIECIERWLQECGVDKCDLCKYQFTTERLPTQTKLKSLLSWV 107
C CK VH EC+E W+ C +C + ++ K W
Sbjct: 25 CNCKNENKIVHKECLEEWINTSKNKSCKICNGPYNIKK-----NYKKCTKWR 71
>gnl|CDD|227470 COG5141, COG5141, PHD zinc finger-containing protein [General
function prediction only].
Length = 669
Score = 33.8 bits (77), Expect = 0.039
Identities = 19/70 (27%), Positives = 23/70 (32%), Gaps = 11/70 (15%)
Query: 29 KPDSSDDEDMTICRICYGADQQNLLSICQCKGSIAYVHIECI-------ERWLQECGVDK 81
+P DE IC C +N +I C G VH C WL K
Sbjct: 184 EPIEPSDEFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPEGFWL----CRK 239
Query: 82 CDLCKYQFTT 91
C +YQ
Sbjct: 240 CIYGEYQIRC 249
>gnl|CDD|193335 pfam12861, zf-Apc11, Anaphase-promoting complex subunit 11
RING-H2 finger. Apc11 is one of the subunits of the
anaphase-promoting complex or cyclosome. The APC
subunits are cullin family proteins with ubiquitin
ligase activity. Polyubiquitination marks proteins for
degradation by the 26S proteasome and is carried out by
a cascade of enzymes that includes ubiquitin-activating
enzymes (E1s), ubiquitin-conjugating enzymes (E2s), and
ubiquitin ligases (E3s). Apc11 acts as an E3 enzyme and
is responsible for recruiting E2s to the APC and for
mediating the subsequent transfer of ubiquitin to APC
substrates in vivo. In Saccharomyces cerevisiae this
RING-H2 finger protein defines the minimal ubiquitin
ligase activity of the APC, and the integrity of the
RING-H2 finger is essential for budding yeast cell
viability.
Length = 85
Score = 27.8 bits (62), Expect = 1.1
Identities = 17/71 (23%), Positives = 28/71 (39%), Gaps = 14/71 (19%)
Query: 31 DSSDDEDMTICRICYGA---------DQQNLLSICQCKGSIAYVHIECIERWLQECGVDK 81
D+ D+ ICR+ + D L+ +CK + H+ CI +WL
Sbjct: 17 DTPSDDVCGICRVSFDGTCPQCKFPGDDCPLV-WGKCKHNF---HMHCILKWLATETSKG 72
Query: 82 -CDLCKYQFTT 91
C +C+ F
Sbjct: 73 LCPMCRQTFVF 83
>gnl|CDD|165812 PLN02166, PLN02166, dTDP-glucose 4,6-dehydratase.
Length = 436
Score = 28.1 bits (62), Expect = 2.5
Identities = 12/32 (37%), Positives = 19/32 (59%)
Query: 92 ERLPTQTKLKSLLSWVKHVDNREDMEEMLTDF 123
+R P +K K LL+W + RE + M++DF
Sbjct: 392 KRKPDISKAKELLNWEPKISLREGLPLMVSDF 423
>gnl|CDD|177856 PLN02206, PLN02206, UDP-glucuronate decarboxylase.
Length = 442
Score = 28.0 bits (62), Expect = 2.6
Identities = 13/32 (40%), Positives = 17/32 (53%)
Query: 92 ERLPTQTKLKSLLSWVKHVDNREDMEEMLTDF 123
+R P TK K LL W V R+ + M+ DF
Sbjct: 391 KRKPDITKAKELLGWEPKVSLRQGLPLMVKDF 422
>gnl|CDD|176257 cd08297, CAD3, Cinnamyl alcohol dehydrogenases (CAD). These
alcohol dehydrogenases are related to the cinnamyl
alcohol dehydrogenases (CAD), members of the medium
chain dehydrogenase/reductase family.
NAD(P)(H)-dependent oxidoreductases are the major
enzymes in the interconversion of alcohols and
aldehydes, or ketones. Cinnamyl alcohol dehydrogenases
(CAD) reduce cinnamaldehydes to cinnamyl alcohols in the
last step of monolignal metabolism in plant cells walls.
CAD binds 2 zinc ions and is NADPH- dependent. CAD
family members are also found in non-plant species, e.g.
in yeast where they have an aldehyde reductase activity.
The medium chain dehydrogenases/reductase
(MDR)/zinc-dependent alcohol dehydrogenase-like family,
which contains the zinc-dependent alcohol dehydrogenase
(ADH-Zn) and related proteins, is a diverse group of
proteins related to the first identified member, class I
mammalian ADH. MDRs display a broad range of activities
and are distinguished from the smaller short chain
dehydrogenases (~ 250 amino acids vs. the ~ 350 amino
acids of the MDR). The MDR proteins have 2 domains: a
C-terminal NAD(P) binding-Rossmann fold domain of a
beta-alpha form and an N-terminal catalytic domain with
distant homology to GroES. The MDR group contains a
host of activities, including the founding alcohol
dehydrogenase (ADH), quinone reductase, sorbitol
dehydrogenase, formaldehyde dehydrogenase, butanediol
DH, ketose reductase, cinnamyl reductase, and numerous
others. The zinc-dependent alcohol dehydrogenases (ADHs)
catalyze the NAD(P)(H)-dependent interconversion of
alcohols to aldehydes or ketones. Active site zinc has
a catalytic role, while structural zinc aids in
stability. ADH-like proteins typically form dimers
(typically higher plants, mammals) or tetramers (yeast,
bacteria), and generally have 2 tightly bound zinc atoms
per subunit. The active site zinc is coordinated by a
histidine, two cysteines, and a water molecule. The
second zinc seems to play a structural role, affects
subunit interactions, and is typically coordinated by 4
cysteines.
Length = 341
Score = 27.5 bits (62), Expect = 3.9
Identities = 11/30 (36%), Positives = 17/30 (56%), Gaps = 1/30 (3%)
Query: 110 VDNREDMEEMLTDFAATFLFSPFIILLTLS 139
V R+D++E L +FAA P I ++ L
Sbjct: 291 VGTRQDLQEAL-EFAARGKVKPHIQVVPLE 319
>gnl|CDD|217143 pfam02614, UxaC, Glucuronate isomerase. This is a family of
Glucuronate isomerases also known as D-glucuronate
isomerase, uronic isomerase, uronate isomerase, or
uronic acid isomerase, EC:5.3.1.12. This enzyme
catalyzes the reactions: D-glucuronate <=>
D-fructuronate and D-galacturonate <=> D-tagaturonate.
It is not however clear where the experimental evidence
for this functional assignment came from and thus this
family has no literature reference.
Length = 469
Score = 27.6 bits (62), Expect = 4.5
Identities = 10/29 (34%), Positives = 15/29 (51%)
Query: 111 DNREDMEEMLTDFAATFLFSPFIILLTLS 139
D ++ ME + A L S F+ +LT S
Sbjct: 384 DTKDGMERQMNALANVGLLSNFVGMLTDS 412
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
0.322 0.136 0.412
Gapped
Lambda K H
0.267 0.0738 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,687,704
Number of extensions: 760995
Number of successful extensions: 750
Number of sequences better than 10.0: 1
Number of HSP's gapped: 747
Number of HSP's successfully gapped: 23
Length of query: 177
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 86
Effective length of database: 6,901,388
Effective search space: 593519368
Effective search space used: 593519368
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: 56 (25.3 bits)