RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11858
(267 letters)
>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 = 36.9 bits (86), Expect = 5e-04
Identities = 13/52 (25%), Positives = 20/52 (38%), Gaps = 4/52 (7%)
Query: 28 ESFLTCGTCLCMYDGGEHTPKLLPCSHTVCLHCLSRIAASQTRETGTLRCPI 79
S C + E+ P +LPC H L ++A + G +CP
Sbjct: 8 HSIFVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLA----KNGGKFKCPY 55
>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 = 36.7 bits (85), Expect = 6e-04
Identities = 16/53 (30%), Positives = 22/53 (41%), Gaps = 8/53 (15%)
Query: 32 TCGTCLCMYDGGEHTPKLLPCSHTVCLHCLSRIAASQTRETGTLRCPICREQI 84
C CL + LLPC H C C+ + ++G CP+CR I
Sbjct: 1 ECPICLEEFR---EPVVLLPCGHVFCRSCIDKW-----LKSGKNTCPLCRTPI 45
>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 = 34.0 bits (78), Expect = 0.004
Identities = 18/48 (37%), Positives = 22/48 (45%), Gaps = 8/48 (16%)
Query: 33 CGTCLCMYDGGEHTPKLLPCSHTVCLHCLSRIAASQTRETGTLRCPIC 80
C CL Y P +LPC HT C C+ + E+G CPIC
Sbjct: 1 CPICLEEY---LKDPVILPCGHTFCRSCIRKW-----LESGNNTCPIC 40
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 33.5 bits (77), Expect = 0.007
Identities = 12/47 (25%), Positives = 18/47 (38%), Gaps = 7/47 (14%)
Query: 36 CLCMYD-GGEHTPKLLPCSHTVCLHCLSRIAASQTRETGTLRCPICR 81
+C+ + +LPC H CL + S CP+CR
Sbjct: 4 PICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSS------NTCPLCR 44
>gnl|CDD|197662 smart00336, BBOX, B-Box-type zinc finger.
Length = 42
Score = 32.3 bits (74), Expect = 0.017
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 116 PKCSTHNSQEL-LFCETCDTVFCLQCT 141
PKC +H + FCE C + C C
Sbjct: 4 PKCDSHGDEPAEFFCEECGALLCRTCD 30
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 31.6 bits (72), Expect = 0.041
Identities = 13/38 (34%), Positives = 18/38 (47%), Gaps = 8/38 (21%)
Query: 49 LLPCSHTV-CLHCLSRIAASQTRETGTLRCPICREQIT 85
LPC H C C R+ + + +CPICR+ I
Sbjct: 17 FLPCGHLCLCEECAKRLRSKK-------KCPICRQPIE 47
>gnl|CDD|237988 cd00021, BBOX, B-Box-type zinc finger; zinc binding domain
(CHC3H2); often present in combination with other
motifs, like RING zinc finger, NHL motif, coiled-coil or
RFP domain in functionally unrelated proteins, most
likely mediating protein-protein interaction.
Length = 39
Score = 30.7 bits (70), Expect = 0.052
Identities = 10/27 (37%), Positives = 13/27 (48%), Gaps = 1/27 (3%)
Query: 116 PKCSTHNSQEL-LFCETCDTVFCLQCT 141
C H + L LFCET + C+ C
Sbjct: 1 RLCDEHGEEPLSLFCETDRALLCVDCD 27
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 33.8 bits (77), Expect = 0.091
Identities = 19/41 (46%), Positives = 22/41 (53%), Gaps = 8/41 (19%)
Query: 42 GGEHTPKLLPCSHTVCLHCLSR-IAASQTRETGTLRCPICR 81
G + TPK LPC H + LHCL + QT CPICR
Sbjct: 308 GLDMTPKRLPCGHILHLHCLKNWLERQQT-------CPICR 341
>gnl|CDD|216039 pfam00643, zf-B_box, B-box zinc finger.
Length = 42
Score = 30.1 bits (68), Expect = 0.12
Identities = 14/45 (31%), Positives = 20/45 (44%), Gaps = 8/45 (17%)
Query: 116 PKCSTHNSQEL-LFCETCDTVFCLQCTGGSNHSSTSGDSEHTIIP 159
C H + L L+CE C + C +C SG HT++P
Sbjct: 4 RLCPEHEEKPLELYCEDCQQLLCEECA-------LSGHKGHTVVP 41
>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 = 30.5 bits (69), Expect = 0.22
Identities = 17/63 (26%), Positives = 28/63 (44%), Gaps = 12/63 (19%)
Query: 33 CGTCLCMYDG--------GEHTPKLL-PCSHTVCLHCLSRIAASQTRETGTLRCPICREQ 83
CG C +DG G+ P + C H +HC+ + A++T + CP+CR+
Sbjct: 24 CGICRVSFDGTCPQCKFPGDDCPLVWGKCKHNFHMHCILKWLATETSKG---LCPMCRQT 80
Query: 84 ITI 86
Sbjct: 81 FVF 83
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 29.0 bits (65), Expect = 0.25
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 6/34 (17%)
Query: 49 LLPCSHTVCLHCLSRIAASQTRETGTLRCPICRE 82
L PC H C C+ R ++ +CPICR
Sbjct: 18 LTPCGHVFCRECILRYLKKKS------KCPICRT 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 = 29.7 bits (67), Expect = 0.25
Identities = 15/59 (25%), Positives = 20/59 (33%), Gaps = 15/59 (25%)
Query: 32 TCGTCL---------CMYDGGEHTPKLLPCSHTVCLHCLSRIAASQTRETGTLRCPICR 81
C C C G + C H LHC+SR ++ CP+CR
Sbjct: 21 VCAICRNHFDGTCPECKSPGDDCPVVWGECGHAFHLHCISRWLKTRN------TCPLCR 73
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 31.4 bits (71), Expect = 0.37
Identities = 12/37 (32%), Positives = 17/37 (45%), Gaps = 4/37 (10%)
Query: 45 HTPKLLPCSHTVCLHCLSRIAASQTRETGTLRCPICR 81
P PC H CL CL + + ++ CP+CR
Sbjct: 226 EVPSCTPCGHLFCLSCL--LISWTKKKYE--FCPLCR 258
>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 = 31.5 bits (71), Expect = 0.40
Identities = 18/54 (33%), Positives = 26/54 (48%), Gaps = 10/54 (18%)
Query: 28 ESFLTCGTCLCMYDGGEHTPKLLPCSHTVCLHCLSRIAASQTRETGTLRCPICR 81
++ L C C +D P L CSHT C C+ R ++Q +CP+CR
Sbjct: 24 DTSLRCHICKDFFD----VPVLTSCSHTFCSLCIRRCLSNQP------KCPLCR 67
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase [Signal
transduction mechanisms].
Length = 391
Score = 30.8 bits (69), Expect = 0.75
Identities = 23/84 (27%), Positives = 31/84 (36%), Gaps = 15/84 (17%)
Query: 28 ESFLTCGTCLCMYDGGEHTPKLLPCSHTVCLHCLSRIAASQTRETGTLRCPICREQITIP 87
+S L C C C P C HT C C+ R +Q CP+CRE
Sbjct: 23 DSMLRCRICDCRI----SIPCETTCGHTFCSLCIRRHLGTQP------FCPVCREDPCES 72
Query: 88 RGGVAALPPSFLVNQLLDLMSRQR 111
R L S ++ + +R R
Sbjct: 73 R-----LRGSSGSREINESHARNR 91
>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 = 28.1 bits (63), Expect = 0.81
Identities = 11/48 (22%), Positives = 13/48 (27%), Gaps = 14/48 (29%)
Query: 35 TCLCMYDGGEHTPKLLPCSHTVCLHC--LSRIAASQTRETGTLRCPIC 80
C G + LLPC H + R CP C
Sbjct: 10 CLFCGTVGTKGV--LLPCGHLIPDGTFDGERYNG----------CPFC 45
>gnl|CDD|227544 COG5219, COG5219, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 1525
Score = 30.8 bits (69), Expect = 1.0
Identities = 20/87 (22%), Positives = 31/87 (35%), Gaps = 13/87 (14%)
Query: 5 MSSTLSTNSTLVETVSINYEDFNESFLTCGTCLCMYDGGEHTPKLLP------CSHTVCL 58
M + L+ N ++ C C + D + + LP C +
Sbjct: 1444 MIKKNGSFMDLLGLWKKNIDEKFSGHEECAICYSVLDMVDRS---LPSKRCATCKNKFHT 1500
Query: 59 HCLSRIAASQTRETGTLRCPICREQIT 85
CL + AS R CP+CR +IT
Sbjct: 1501 RCLYKWFASSARS----NCPLCRSEIT 1523
>gnl|CDD|165237 PHA02926, PHA02926, zinc finger-like protein; Provisional.
Length = 242
Score = 29.6 bits (66), Expect = 1.3
Identities = 14/33 (42%), Positives = 20/33 (60%), Gaps = 2/33 (6%)
Query: 52 CSHTVCLHCLSRIAASQTRETG-TLRCPICREQ 83
C+H C+ C++ I RETG + CPICR +
Sbjct: 197 CNHIFCITCIN-IWHRTRRETGASDNCPICRTR 228
>gnl|CDD|192286 pfam09416, UPF1_Zn_bind, RNA helicase (UPF2 interacting domain).
UPF1 is an essential RNA helicase that detects mRNAs
containing premature stop codons and triggers their
degradation. This domain contains 3 zinc binding motifs
and forms interactions with another protein (UPF2) that
is also involved nonsense-mediated mRNA decay (NMD).
Length = 152
Score = 28.9 bits (65), Expect = 1.6
Identities = 10/33 (30%), Positives = 15/33 (45%), Gaps = 4/33 (12%)
Query: 118 CSTHNSQELLFCETCDTVFCLQCTGGSNHSSTS 150
C HN ++ C +C+ FC G +S S
Sbjct: 6 CGIHNPACVVKCNSCNKWFC----NGKGGTSGS 34
>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 = 26.3 bits (58), Expect = 2.5
Identities = 14/48 (29%), Positives = 19/48 (39%), Gaps = 8/48 (16%)
Query: 33 CGTCLCMYDGGEHTPKLLPCSHTVCLHCLSRIAASQTRETGTLRCPIC 80
C CL +LPC H C C+ E+G + CP+C
Sbjct: 1 CPICLEEPKD---PVTILPCGHLFCSKCILSW-----LESGNVTCPLC 40
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 27.3 bits (60), Expect = 9.9
Identities = 16/64 (25%), Positives = 26/64 (40%), Gaps = 8/64 (12%)
Query: 18 TVSINYEDFNESFLTCGTCLCMYDGGEHTPKLLPCSHTVCLHCLSRIAASQTRETGTLRC 77
+ + +D +E + C C G PC H +C C R+ A ++ C
Sbjct: 49 LTTSSADDTDEENMNCQICA----GSTTYSARYPCGHQICHACAVRLRALYMQKG----C 100
Query: 78 PICR 81
P+CR
Sbjct: 101 PLCR 104
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
0.321 0.132 0.407
Gapped
Lambda K H
0.267 0.0704 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,836,031
Number of extensions: 1140893
Number of successful extensions: 930
Number of sequences better than 10.0: 1
Number of HSP's gapped: 922
Number of HSP's successfully gapped: 37
Length of query: 267
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 172
Effective length of database: 6,723,972
Effective search space: 1156523184
Effective search space used: 1156523184
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: 58 (26.2 bits)