RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy16471
(153 letters)
>gnl|CDD|227521 COG5194, APC11, Component of SCF ubiquitin ligase and
anaphase-promoting complex [Posttranslational
modification, protein turnover, chaperones / Cell
division and chromosome partitioning].
Length = 88
Score = 119 bits (299), Expect = 6e-36
Identities = 52/129 (40%), Positives = 60/129 (46%), Gaps = 42/129 (32%)
Query: 25 KRFDVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASTTSEECTVAWGVCNHAF 84
+ +KKW+AVALW+WDI +D CAICRNHIM C ECQ
Sbjct: 1 MKVKIKKWHAVALWSWDIPIDVCAICRNHIMGTCPECQFG-------------------- 40
Query: 85 HFHCISRNHIMDLCIECQANQASTTSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDNR 144
T +EC V WGVCNHAFH HCI RWL T+ VCPLD +
Sbjct: 41 ----------------------MTPGDECPVVWGVCNHAFHDHCIYRWLDTKGVCPLDRQ 78
Query: 145 EWEFQKYGH 153
W G
Sbjct: 79 TWVLADGGA 87
>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 = 102 bits (255), Expect = 2e-29
Identities = 46/118 (38%), Positives = 52/118 (44%), Gaps = 45/118 (38%)
Query: 26 RFDVKKWNAVALWAWDIVVDNCAICRNHIMDLCIECQANQASTTSEECTVAWGVCNHAFH 85
R ++KKWNAVALW+WDI D CAICRNH C EC
Sbjct: 1 RVEIKKWNAVALWSWDIEDDVCAICRNHFDGTCPEC------------------------ 36
Query: 86 FHCISRNHIMDLCIECQANQASTTSEECTVAWGVCNHAFHFHCISRWLKTRQVCPLDN 143
+ ++C V WG C HAFH HCISRWLKTR CPL
Sbjct: 37 ---------------------KSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73
>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 = 48.6 bits (116), Expect = 2e-08
Identities = 26/64 (40%), Positives = 34/64 (53%), Gaps = 6/64 (9%)
Query: 29 VKKWNAVALWAWDIVVD-NCAICRNHIMDLCIECQANQASTTSEECTVAWGVCNHAFHFH 87
+K+WNAVA W WD D C ICR C +C+ ++C + WG C H FH H
Sbjct: 5 IKEWNAVATWTWDTPSDDVCGICRVSFDGTCPQCK-----FPGDDCPLVWGKCKHNFHMH 59
Query: 88 CISR 91
CI +
Sbjct: 60 CILK 63
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 38.0 bits (88), Expect = 0.001
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 120 CNHAFHFHCISRWLKTRQVCPL 141
C H H HC+ WL+ +Q CP+
Sbjct: 318 CGHILHLHCLKNWLERQQTCPI 339
Score = 28.4 bits (63), Expect = 1.7
Identities = 10/43 (23%), Positives = 14/43 (32%), Gaps = 5/43 (11%)
Query: 47 CAICRNHIMDLCIECQANQASTTSEECTVAWGVCNHAFHFHCI 89
C IC + + E T + C H H HC+
Sbjct: 290 CTICMDEMFHPDHEPLPRGLDMTPKRLP-----CGHILHLHCL 327
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 34.3 bits (79), Expect = 0.002
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 120 CNHAFHFHCISRWLKTRQVCPL 141
C H FH C+ +WL++ CPL
Sbjct: 21 CGHVFHKECLDKWLRSSNTCPL 42
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 33.2 bits (76), Expect = 0.032
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 120 CNHAFHFHCISRWLKTRQVCPL 141
CNH F CI W K + CP+
Sbjct: 200 CNHVFCIECIDIWKKEKNTCPV 221
>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 = 29.7 bits (67), Expect = 0.077
Identities = 12/31 (38%), Positives = 15/31 (48%), Gaps = 1/31 (3%)
Query: 112 ECTVAWGVCNHAFHFHCISRWLKTRQV-CPL 141
V C H F CI +WLK+ + CPL
Sbjct: 10 REPVVLLPCGHVFCRSCIDKWLKSGKNTCPL 40
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 32.3 bits (73), Expect = 0.087
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 2/33 (6%)
Query: 118 GVCNHAFHFHCISRWLKT--RQVCPLDNREWEF 148
C + FH C+ +W + R CPL E F
Sbjct: 1492 ATCKNKFHTRCLYKWFASSARSNCPLCRSEITF 1524
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 31.1 bits (70), Expect = 0.22
Identities = 9/27 (33%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 120 CNHAFHFHCISRWLKT-RQVCPLDNRE 145
C+H FH C+ +WL CP+
Sbjct: 344 CDHRFHVGCVDKWLLGYSNKCPVCRTA 370
>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 = 27.9 bits (62), Expect = 0.35
Identities = 9/23 (39%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 120 CNHAFHFHCISRWLKTRQV-CPL 141
C H F CI +WL++ CP+
Sbjct: 17 CGHTFCRSCIRKWLESGNNTCPI 39
>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 = 27.1 bits (60), Expect = 0.74
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 120 CNHAFHFHCISRWLKTRQV-CPL 141
C H F CI WL++ V CPL
Sbjct: 17 CGHLFCSKCILSWLESGNVTCPL 39
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 27.1 bits (60), Expect = 0.83
Identities = 10/25 (40%), Positives = 13/25 (52%)
Query: 120 CNHAFHFHCISRWLKTRQVCPLDNR 144
C H F CI R+LK + CP+
Sbjct: 21 CGHVFCRECILRYLKKKSKCPICRT 45
>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 = 27.7 bits (61), Expect = 3.1
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 120 CNHAFHFHCISRWLKTRQVCPL 141
C+H F CI R L + CPL
Sbjct: 44 CSHTFCSLCIRRCLSNQPKCPL 65
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 27.4 bits (60), Expect = 4.0
Identities = 10/22 (45%), Positives = 12/22 (54%)
Query: 120 CNHAFHFHCISRWLKTRQVCPL 141
C H F CI R L T+ CP+
Sbjct: 43 CGHTFCSLCIRRHLGTQPFCPV 64
>gnl|CDD|233895 TIGR02494, PFLE_PFLC, glycyl-radical enzyme activating protein
family. This subset of the radical-SAM family
(pfam04055) includes a number of probable activating
proteins acting on different enzymes all requiring an
amino-acid-centered radical. The closest relatives to
this family are the pyruvate-formate lyase activating
enzyme (PflA, 1.97.1.4, TIGR02493) and the anaerobic
ribonucleotide reductase activating enzyme (TIGR02491).
Included within this subfamily are activators of
hydroxyphenyl acetate decarboxylase (HdpA, ),
benzylsuccinate synthase (BssD, ), gycerol dehydratase
(DhaB2,) as well as enzymes annotated in E. coli as
activators of different isozymes of pyruvate-formate
lyase (PFLC and PFLE) however, these appear to lack
characterization and may activate enzymes with
distinctive functions. Most of the sequence-level
variability between these forms is concentrated within
an N-terminal domain which follows a conserved group of
three cysteines and contains a variable pattern of 0 to
8 additional cysteines.
Length = 295
Score = 26.1 bits (58), Expect = 8.5
Identities = 9/59 (15%), Positives = 14/59 (23%), Gaps = 12/59 (20%)
Query: 56 DLCIECQANQASTTSEECTVAWGVCNHAFHFHCISRNHIMDL---CIECQANQASTTSE 111
+ C+ C +C RN I+ C C + S
Sbjct: 48 NRCLGC---------GKCVEVCPAGTARLSELADGRNRIIIRREKCTHCGKCTEACPSG 97
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 0.130 0.460
Gapped
Lambda K H
0.267 0.0598 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,965,603
Number of extensions: 525329
Number of successful extensions: 523
Number of sequences better than 10.0: 1
Number of HSP's gapped: 515
Number of HSP's successfully gapped: 38
Length of query: 153
Length of database: 10,937,602
Length adjustment: 89
Effective length of query: 64
Effective length of database: 6,990,096
Effective search space: 447366144
Effective search space used: 447366144
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: 40 (21.6 bits)
S2: 55 (25.3 bits)