RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14787
(81 letters)
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 50.0 bits (119), Expect = 9e-09
Identities = 21/62 (33%), Positives = 32/62 (51%), Gaps = 4/62 (6%)
Query: 9 VDQWLSSNKRCPICRVDI----ETHLNKDLLQPTWRLPCMHLFHVECVDQWLSSNKRCPI 64
+Q +S++ C IC ++ L + L RLPC H+ H+ C+ WL + CPI
Sbjct: 280 EEQLTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQTCPI 339
Query: 65 CR 66
CR
Sbjct: 340 CR 341
Score = 35.7 bits (82), Expect = 0.001
Identities = 10/22 (45%), Positives = 14/22 (63%)
Query: 2 HLFHVECVDQWLSSNKRCPICR 23
H+ H+ C+ WL + CPICR
Sbjct: 320 HILHLHCLKNWLERQQTCPICR 341
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 44.3 bits (105), Expect = 5e-08
Identities = 21/48 (43%), Positives = 28/48 (58%), Gaps = 6/48 (12%)
Query: 19 CPICRVDIETHLNKDLLQPTWRLPCMHLFHVECVDQWLSSNKRCPICR 66
CPIC + E + LPC H+FH EC+D+WL S+ CP+CR
Sbjct: 3 CPICLDEFEPG------EEVVVLPCGHVFHKECLDKWLRSSNTCPLCR 44
Score = 34.7 bits (80), Expect = 2e-04
Identities = 13/22 (59%), Positives = 18/22 (81%)
Query: 2 HLFHVECVDQWLSSNKRCPICR 23
H+FH EC+D+WL S+ CP+CR
Sbjct: 23 HVFHKECLDKWLRSSNTCPLCR 44
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 44.3 bits (104), Expect = 9e-07
Identities = 19/64 (29%), Positives = 32/64 (50%), Gaps = 6/64 (9%)
Query: 9 VDQWLSSNKRCPICRVDIETHLNKDLLQPTWRLP-CMHLFHVECVDQWL--SSNKRCPIC 65
+D+ S ++ C IC ++ D P+ R C + FH C+ +W S+ CP+C
Sbjct: 1462 IDEKFSGHEECAICYSVLDMV---DRSLPSKRCATCKNKFHTRCLYKWFASSARSNCPLC 1518
Query: 66 RVDI 69
R +I
Sbjct: 1519 RSEI 1522
Score = 32.7 bits (74), Expect = 0.009
Identities = 10/27 (37%), Positives = 16/27 (59%), Gaps = 2/27 (7%)
Query: 2 HLFHVECVDQWL--SSNKRCPICRVDI 26
+ FH C+ +W S+ CP+CR +I
Sbjct: 1496 NKFHTRCLYKWFASSARSNCPLCRSEI 1522
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 42.7 bits (100), Expect = 3e-06
Identities = 17/30 (56%), Positives = 20/30 (66%), Gaps = 1/30 (3%)
Query: 41 LPCMHLFHVECVDQWLSSNK-RCPICRVDI 69
LPC H FHV CVD+WL +CP+CR I
Sbjct: 342 LPCDHRFHVGCVDKWLLGYSNKCPVCRTAI 371
Score = 35.4 bits (81), Expect = 0.001
Identities = 14/26 (53%), Positives = 17/26 (65%), Gaps = 1/26 (3%)
Query: 2 HLFHVECVDQWLSSNK-RCPICRVDI 26
H FHV CVD+WL +CP+CR I
Sbjct: 346 HRFHVGCVDKWLLGYSNKCPVCRTAI 371
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 38.2 bits (89), Expect = 1e-05
Identities = 18/52 (34%), Positives = 23/52 (44%), Gaps = 8/52 (15%)
Query: 15 SNKRCPICRVDIETHLNKDLLQPTWRLPCMHLFHVECVDQWLSSNKRCPICR 66
CPIC L P PC H+F EC+ ++L +CPICR
Sbjct: 1 EELECPIC--------LDLLRDPVVLTPCGHVFCRECILRYLKKKSKCPICR 44
Score = 30.2 bits (68), Expect = 0.015
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 2 HLFHVECVDQWLSSNKRCPICR 23
H+F EC+ ++L +CPICR
Sbjct: 23 HVFCRECILRYLKKKSKCPICR 44
>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 = 38.2 bits (89), Expect = 1e-05
Identities = 20/52 (38%), Positives = 27/52 (51%), Gaps = 9/52 (17%)
Query: 19 CPICRVDIETHLNKDLLQPTWRLPCMHLFHVECVDQWL-SSNKRCPICRVDI 69
CPIC ++ +P LPC H+F C+D+WL S CP+CR I
Sbjct: 2 CPIC--------LEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
Score = 31.3 bits (71), Expect = 0.005
Identities = 12/26 (46%), Positives = 16/26 (61%), Gaps = 1/26 (3%)
Query: 2 HLFHVECVDQWL-SSNKRCPICRVDI 26
H+F C+D+WL S CP+CR I
Sbjct: 20 HVFCRSCIDKWLKSGKNTCPLCRTPI 45
>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 = 38.2 bits (89), Expect = 2e-05
Identities = 17/59 (28%), Positives = 25/59 (42%), Gaps = 4/59 (6%)
Query: 12 WLSSNKRCPICRVDIETHLNKDLLQ----PTWRLPCMHLFHVECVDQWLSSNKRCPICR 66
W + C ICR + + P C H FH+ C+ +WL + CP+CR
Sbjct: 15 WDIEDDVCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRNTCPLCR 73
Score = 32.4 bits (74), Expect = 0.003
Identities = 10/22 (45%), Positives = 15/22 (68%)
Query: 2 HLFHVECVDQWLSSNKRCPICR 23
H FH+ C+ +WL + CP+CR
Sbjct: 52 HAFHLHCISRWLKTRNTCPLCR 73
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 37.5 bits (87), Expect = 2e-04
Identities = 11/25 (44%), Positives = 15/25 (60%)
Query: 43 CMHLFHVECVDQWLSSNKRCPICRV 67
C H+F +EC+D W CP+CR
Sbjct: 200 CNHVFCIECIDIWKKEKNTCPVCRT 224
Score = 34.8 bits (80), Expect = 0.001
Identities = 10/23 (43%), Positives = 14/23 (60%)
Query: 2 HLFHVECVDQWLSSNKRCPICRV 24
H+F +EC+D W CP+CR
Sbjct: 202 HVFCIECIDIWKKEKNTCPVCRT 224
>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 = 31.3 bits (71), Expect = 0.005
Identities = 19/48 (39%), Positives = 24/48 (50%), Gaps = 9/48 (18%)
Query: 19 CPICRVDIETHLNKDLLQPTWRLPCMHLFHVECVDQWL-SSNKRCPIC 65
CPIC ++ L+ LPC H F C+ +WL S N CPIC
Sbjct: 1 CPIC--------LEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
Score = 25.5 bits (56), Expect = 0.85
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 1/23 (4%)
Query: 1 MHLFHVECVDQWL-SSNKRCPIC 22
H F C+ +WL S N CPIC
Sbjct: 18 GHTFCRSCIRKWLESGNNTCPIC 40
>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 = 29.7 bits (67), Expect = 0.019
Identities = 18/48 (37%), Positives = 23/48 (47%), Gaps = 9/48 (18%)
Query: 19 CPICRVDIETHLNKDLLQPTWRLPCMHLFHVECVDQWLSSNKR-CPIC 65
CPIC + + P LPC HLF +C+ WL S CP+C
Sbjct: 1 CPICLEEPK--------DPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>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 = 31.0 bits (70), Expect = 0.020
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 43 CMHLFHVECVDQWLSSNKRCPICR 66
C H FH C+ +WL + CP+ R
Sbjct: 54 CNHAFHDHCIYRWLDTKGVCPLDR 77
Score = 28.6 bits (64), Expect = 0.15
Identities = 9/22 (40%), Positives = 13/22 (59%)
Query: 2 HLFHVECVDQWLSSNKRCPICR 23
H FH C+ +WL + CP+ R
Sbjct: 56 HAFHDHCIYRWLDTKGVCPLDR 77
>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 = 31.1 bits (70), Expect = 0.039
Identities = 21/67 (31%), Positives = 30/67 (44%), Gaps = 10/67 (14%)
Query: 13 LSSNKRCPICRVDIETHLNKDLLQPTWRLPCMHLFHVECVDQWLSSNKRCPICRV-DIET 71
L ++ RC IC KD C H F C+ + LS+ +CP+CR D E+
Sbjct: 23 LDTSLRCHIC---------KDFFDVPVLTSCSHTFCSLCIRRCLSNQPKCPLCRAEDQES 73
Query: 72 HLNKDLL 78
L + L
Sbjct: 74 KLRSNWL 80
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 28.7 bits (64), Expect = 0.21
Identities = 15/65 (23%), Positives = 27/65 (41%), Gaps = 13/65 (20%)
Query: 16 NKRCPICRVDIETHLNKDLLQPTWRLPCMHLFHVECVDQWLSSNK--RCPICRVDIETHL 73
+ +C +C + E PC HLF + C+ + K CP+CR + +
Sbjct: 215 DYKCFLCLEEPEVPS---------CTPCGHLFCLSCLLISWTKKKYEFCPLCRA--KVYP 263
Query: 74 NKDLL 78
K ++
Sbjct: 264 KKVII 268
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 28.9 bits (64), Expect = 0.22
Identities = 16/56 (28%), Positives = 21/56 (37%), Gaps = 9/56 (16%)
Query: 13 LSSNKRCPICRVDIETHLNKDLLQPTWRLPCMHLFHVECVDQWLSSNKRCPICRVD 68
L S RC IC + C H F C+ + L + CP+CR D
Sbjct: 22 LDSMLRCRIC---------DCRISIPCETTCGHTFCSLCIRRHLGTQPFCPVCRED 68
>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 = 28.4 bits (63), Expect = 0.33
Identities = 18/52 (34%), Positives = 26/52 (50%), Gaps = 10/52 (19%)
Query: 16 NKRCPICRVDIETHLNKD---LLQPTWRLPCMHLFHVECVDQWLSSNK-RCP 63
++RCP+C+ D +LN D L+ P C H CVD+ S +CP
Sbjct: 10 DRRCPVCKSDR--YLNPDIKILINP----ECYHRMCESCVDRIFSRGPAQCP 55
>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 = 27.4 bits (61), Expect = 0.35
Identities = 12/27 (44%), Positives = 17/27 (62%), Gaps = 3/27 (11%)
Query: 43 CMHLFHVECVDQWL---SSNKRCPICR 66
C H FH+ C+ +WL +S CP+CR
Sbjct: 52 CKHNFHMHCILKWLATETSKGLCPMCR 78
Score = 25.1 bits (55), Expect = 2.8
Identities = 11/25 (44%), Positives = 16/25 (64%), Gaps = 3/25 (12%)
Query: 2 HLFHVECVDQWL---SSNKRCPICR 23
H FH+ C+ +WL +S CP+CR
Sbjct: 54 HNFHMHCILKWLATETSKGLCPMCR 78
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 27.0 bits (60), Expect = 0.36
Identities = 16/32 (50%), Positives = 19/32 (59%), Gaps = 2/32 (6%)
Query: 41 LPCMHL-FHVECVDQWLSSNKRCPICRVDIET 71
LPC HL EC + S K+CPICR IE+
Sbjct: 18 LPCGHLCLCEECAKRLRS-KKKCPICRQPIES 48
>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional.
Length = 242
Score = 26.2 bits (57), Expect = 1.7
Identities = 10/30 (33%), Positives = 16/30 (53%), Gaps = 6/30 (20%)
Query: 43 CMHLFHVECVDQWLSSNKR------CPICR 66
C H+F + C++ W + + CPICR
Sbjct: 197 CNHIFCITCINIWHRTRRETGASDNCPICR 226
>gnl|CDD|221473 pfam12230, PRP21_like_P, Pre-mRNA splicing factor PRP21 like
protein. This domain family is found in eukaryotes, and
is typically between 212 and 238 amino acids in length.
The family is found in association with pfam01805. There
are two completely conserved residues (W and H) that may
be functionally important. PRP21 is required for
assembly of the prespliceosome and it interacts with U2
snRNP and/or pre-mRNA in the prespliceosome. This family
also contains proteins similar to PRP21, such as the
mammalian SF3a. SF3a also interacts with U2 snRNP from
the prespliceosome, converting it to its active form.
Length = 230
Score = 25.9 bits (57), Expect = 2.1
Identities = 7/28 (25%), Positives = 14/28 (50%), Gaps = 5/28 (17%)
Query: 18 RCPIC--RV---DIETHLNKDLLQPTWR 40
+CPI + + + H+ LL P ++
Sbjct: 171 KCPITGELIPEDEFDEHMRILLLDPRYK 198
>gnl|CDD|221845 pfam12906, RINGv, RING-variant domain.
Length = 47
Score = 24.3 bits (53), Expect = 3.5
Identities = 15/54 (27%), Positives = 19/54 (35%), Gaps = 14/54 (25%)
Query: 19 CPICRVDIETHLNKDLLQPTWRLPC-----MHLFHVECVDQWL--SSNKRCPIC 65
C IC E PC + H C+++WL S N C IC
Sbjct: 1 CRICLEGEEED-------EPLIRPCRCRGSLKYVHQSCLERWLKTSGNTTCEIC 47
>gnl|CDD|218794 pfam05883, Baculo_RING, Baculovirus U-box/Ring-like domain. This
family consists of several Baculovirus proteins of
around 130 residues in length. The function of this
family is unknown, but it appears to be related to the
U-box and ring finger domain by profile-profile
comparison.
Length = 135
Score = 25.3 bits (56), Expect = 3.7
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 2 HLFHVECVDQWLSSNKRCPICR 23
+FH EC +W KR P R
Sbjct: 55 KMFHAECDKRWKRERKRDPFNR 76
Score = 25.3 bits (56), Expect = 3.7
Identities = 9/22 (40%), Positives = 11/22 (50%)
Query: 45 HLFHVECVDQWLSSNKRCPICR 66
+FH EC +W KR P R
Sbjct: 55 KMFHAECDKRWKRERKRDPFNR 76
>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 = 23.8 bits (52), Expect = 4.7
Identities = 12/35 (34%), Positives = 18/35 (51%), Gaps = 7/35 (20%)
Query: 39 WRLPC-----MHLFHVECVDQWL--SSNKRCPICR 66
PC + H EC+++W+ S NK C IC+
Sbjct: 15 LVSPCRCKGSLKYVHQECLERWINESGNKTCEICK 49
Score = 23.4 bits (51), Expect = 6.0
Identities = 10/25 (40%), Positives = 16/25 (64%), Gaps = 2/25 (8%)
Query: 1 MHLFHVECVDQWL--SSNKRCPICR 23
+ H EC+++W+ S NK C IC+
Sbjct: 25 LKYVHQECLERWINESGNKTCEICK 49
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
0.328 0.140 0.504
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: 3,827,894
Number of extensions: 265268
Number of successful extensions: 354
Number of sequences better than 10.0: 1
Number of HSP's gapped: 341
Number of HSP's successfully gapped: 56
Length of query: 81
Length of database: 10,937,602
Length adjustment: 50
Effective length of query: 31
Effective length of database: 8,719,902
Effective search space: 270316962
Effective search space used: 270316962
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.8 bits)
S2: 53 (24.2 bits)