RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy18180
(143 letters)
>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 = 43.6 bits (103), Expect = 4e-07
Identities = 13/44 (29%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 37 CLVCQGILIKPIKL-PCNHHVCLECLQRICDNSNLSCPMCRKRL 79
C +C +P+ L PC H C C+ + + +CP+CR +
Sbjct: 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 45
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 39.8 bits (93), Expect = 1e-05
Identities = 16/46 (34%), Positives = 24/46 (52%), Gaps = 2/46 (4%)
Query: 33 DSVLCLVCQGILIKPIKL-PCNHHVCLECLQRICDNSNLSCPMCRK 77
+ + C +C +L P+ L PC H C EC+ R + CP+CR
Sbjct: 1 EELECPICLDLLRDPVVLTPCGHVFCRECILRYLKKKS-KCPICRT 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 = 39.4 bits (92), Expect = 2e-05
Identities = 14/40 (35%), Positives = 24/40 (60%), Gaps = 1/40 (2%)
Query: 37 CLVCQGILIK-PIKLPCNHHVCLECLQRICDNSNLSCPMC 75
C +C +K P+ LPC H C C+++ ++ N +CP+C
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 40
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 42.4 bits (99), Expect = 2e-05
Identities = 16/46 (34%), Positives = 25/46 (54%), Gaps = 1/46 (2%)
Query: 34 SVLCLVCQGILIKPIKLP-CNHHVCLECLQRICDNSNLSCPMCRKR 78
S+ C +C +L P+K P C H C EC+ +S+ CP C ++
Sbjct: 274 SLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRK 319
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 38.9 bits (91), Expect = 3e-05
Identities = 15/45 (33%), Positives = 22/45 (48%), Gaps = 4/45 (8%)
Query: 37 CLVCQGILI---KPIKLPCNHHVCLECLQRICDNSNLSCPMCRKR 78
C +C + + LPC H ECL + +SN +CP+CR
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVFHKECLDKWLRSSN-TCPLCRAP 46
>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 = 37.3 bits (86), Expect = 0.001
Identities = 14/43 (32%), Positives = 24/43 (55%), Gaps = 1/43 (2%)
Query: 34 SVLCLVCQGILIKPIKLPCNHHVCLECLQRICDNSNLSCPMCR 76
S+ C +C+ P+ C+H C C++R C ++ CP+CR
Sbjct: 26 SLRCHICKDFFDVPVLTSCSHTFCSLCIRR-CLSNQPKCPLCR 67
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 33.5 bits (77), Expect = 0.003
Identities = 15/46 (32%), Positives = 23/46 (50%), Gaps = 3/46 (6%)
Query: 33 DSVLCLVCQGILIKPIKLPCNHHV-CLECLQRICDNSNLSCPMCRK 77
+ LC++C + LPC H C EC +R+ CP+CR+
Sbjct: 1 EDDLCVICLERPRNVVFLPCGHLCLCEECAKRLRSKKK--CPICRQ 44
>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 = 33.2 bits (76), Expect = 0.004
Identities = 13/40 (32%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 37 CLVCQGILIKPIK-LPCNHHVCLECLQRICDNSNLSCPMC 75
C +C P+ LPC H C +C+ ++ N++CP+C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>gnl|CDD|227568 COG5243, HRD1, HRD ubiquitin ligase complex, ER membrane component
[Posttranslational modification, protein turnover,
chaperones].
Length = 491
Score = 35.7 bits (82), Expect = 0.005
Identities = 17/63 (26%), Positives = 29/63 (46%), Gaps = 14/63 (22%)
Query: 30 LTPDSVLCLVC-------------QGILIKPIKLPCNHHVCLECLQRICDNSNLSCPMCR 76
LT C +C +G+ + P +LPC H + L CL+ + +CP+CR
Sbjct: 283 LTNSDRTCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLERQQ-TCPICR 341
Query: 77 KRL 79
+ +
Sbjct: 342 RPV 344
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 33.1 bits (75), Expect = 0.040
Identities = 22/83 (26%), Positives = 34/83 (40%), Gaps = 17/83 (20%)
Query: 3 DKKVFR------DVSL--LLVNSKMDNEDCNSNNTLTPDSVLCLVCQGILIKPIKLPCNH 54
D+K FR ++S L S D+ D +++ C +C G + PC H
Sbjct: 30 DRKNFRRKQKKNNLSAEPNLTTSSADDTD--------EENMNCQICAGSTTYSARYPCGH 81
Query: 55 HVCLECLQRICDNSNLS-CPMCR 76
+C C R+ CP+CR
Sbjct: 82 QICHACAVRLRALYMQKGCPLCR 104
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 32.8 bits (74), Expect = 0.049
Identities = 12/43 (27%), Positives = 19/43 (44%), Gaps = 1/43 (2%)
Query: 34 SVLCLVCQGILIKPIKLPCNHHVCLECLQRICDNSNLSCPMCR 76
+ C +C + P + C H C C++R CP+CR
Sbjct: 25 MLRCRICDCRISIPCETTCGHTFCSLCIRRHLGTQPF-CPVCR 66
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 32.3 bits (73), Expect = 0.071
Identities = 14/45 (31%), Positives = 22/45 (48%), Gaps = 3/45 (6%)
Query: 35 VLCLVCQGILIKPIK---LPCNHHVCLECLQRICDNSNLSCPMCR 76
V C +C IK + LPC+H + C+ + + CP+CR
Sbjct: 324 VECAICMSNFIKNDRLRVLPCDHRFHVGCVDKWLLGYSNKCPVCR 368
>gnl|CDD|219128 pfam06666, DUF1173, Protein of unknown function (DUF1173). This
family contains a group of hypothetical bacterial
proteins that contain three conserved cysteine residues
towards the N-terminal. The function of these proteins
is unknown.
Length = 385
Score = 31.5 bits (72), Expect = 0.11
Identities = 13/40 (32%), Positives = 24/40 (60%), Gaps = 2/40 (5%)
Query: 81 IWLRRNKDFSLLIDENLWNQIQKYYKKEVDQKLFDQDDGV 120
I +R D L++DE+LW ++ K + E++ L+ +GV
Sbjct: 233 IVIRHLPDAPLMLDEDLWRRLLKRFAAELE--LWRAGEGV 270
>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 = 29.2 bits (66), Expect = 0.12
Identities = 12/45 (26%), Positives = 16/45 (35%), Gaps = 5/45 (11%)
Query: 37 CLVCQGILIKPIKLPCNHHVCLECLQRICDNSNLS-CPMCRKRLS 80
CL C + K + LPC H + D + CP C
Sbjct: 10 CLFCGTVGTKGVLLPCGHLIPDGTF----DGERYNGCPFCGTPFE 50
>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 = 28.8 bits (65), Expect = 0.22
Identities = 10/49 (20%), Positives = 20/49 (40%), Gaps = 5/49 (10%)
Query: 31 TPDSVLCLVCQGILI----KPIKLPCNHHVCLECLQRICDNSN-LSCPM 74
+C + + ++ P+ LPC H + L+++ N CP
Sbjct: 7 FHSIFVCPISKEVMTDEENPPVMLPCGHVYSRKALEKLAKNGGKFKCPY 55
>gnl|CDD|227502 COG5175, MOT2, Transcriptional repressor [Transcription].
Length = 480
Score = 30.8 bits (69), Expect = 0.23
Identities = 11/28 (39%), Positives = 15/28 (53%)
Query: 51 PCNHHVCLECLQRICDNSNLSCPMCRKR 78
PC + +C C I N N CP CR++
Sbjct: 35 PCGYQICQFCYNNIRQNLNGRCPACRRK 62
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 30.2 bits (68), Expect = 0.26
Identities = 14/41 (34%), Positives = 16/41 (39%), Gaps = 1/41 (2%)
Query: 37 CLVCQGILIKPIKLPCNHHVCLECL-QRICDNSNLSCPMCR 76
C +C P PC H CL CL CP+CR
Sbjct: 218 CFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLCR 258
>gnl|CDD|218995 pfam06337, DUSP, DUSP domain. The DUSP (domain present in
ubiquitin-specific protease) domain is found at the
N-terminus of Ubiquitin-specific proteases. The
structure of this domain has been solved. Its
tripod-like structure consists of a 3-fold alpha-helical
bundle supporting a triple-stranded anti-parallel
beta-sheet.
Length = 86
Score = 29.0 bits (65), Expect = 0.29
Identities = 12/44 (27%), Positives = 22/44 (50%), Gaps = 3/44 (6%)
Query: 66 DNSNLSCP--MCRKRLSIWLRRNKDFSLLIDENLWNQIQKYYKK 107
DNS+L K+L L+ D+ +L+ E +W + ++Y
Sbjct: 34 DNSSLLDDEENLLKQLKPNLQEGVDY-VLVPEEVWEFLVEWYGG 76
>gnl|CDD|112657 pfam03854, zf-P11, P-11 zinc finger.
Length = 50
Score = 27.5 bits (61), Expect = 0.58
Identities = 14/32 (43%), Positives = 20/32 (62%), Gaps = 1/32 (3%)
Query: 53 NHHVCLECLQRICDNSNLSCPMCRKRLSIWLR 84
+H++CL CLQ + S CP+C+K L LR
Sbjct: 20 DHYLCLRCLQLLLSVSER-CPICKKPLPTKLR 50
>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 = 28.1 bits (62), Expect = 1.8
Identities = 22/66 (33%), Positives = 26/66 (39%), Gaps = 16/66 (24%)
Query: 24 CNSNNTLTPDSVLCLVCQGILIKPIKLPCNHHVCLECLQRICDNSNLSCPM--CRKRLSI 81
C S+ L PD ILI P C H +C C+ RI CP C K
Sbjct: 16 CKSDRYLNPDIK-------ILINP---ECYHRMCESCVDRIFSRGPAQCPYKGCGK---- 61
Query: 82 WLRRNK 87
LR+ K
Sbjct: 62 ILRKIK 67
>gnl|CDD|222944 PHA02929, PHA02929, N1R/p28-like protein; Provisional.
Length = 238
Score = 27.8 bits (62), Expect = 1.8
Identities = 11/26 (42%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 52 CNHHVCLECLQRICDNSNLSCPMCRK 77
CNH C+EC+ N +CP+CR
Sbjct: 200 CNHVFCIECIDIWKKEKN-TCPVCRT 224
>gnl|CDD|153295 cd07611, BAR_Amphiphysin_I_II, The Bin/Amphiphysin/Rvs (BAR) domain
of Amphiphysin I and II. BAR domains are dimerization,
lipid binding and curvature sensing modules found in
many different proteins with diverse functions.
Amphiphysins function primarily in endocytosis and other
membrane remodeling events. They contain an N-terminal
BAR domain with an additional N-terminal amphipathic
helix (an N-BAR), a variable central domain, and a
C-terminal SH3 domain. Amphiphysin I proteins, enriched
in the brain and nervous system, contain domains that
bind clathrin, Adaptor Protein complex 2 (AP2), dynamin
and synaptojanin. They function in synaptic vesicle
endocytosis. Some amphiphysin II isoforms, also called
Bridging integrator 1 (Bin1), are localized in many
different tissues and may function in intracellular
vesicle trafficking. In skeletal muscle, Bin1 plays a
role in the organization and maintenance of the T-tubule
network. The N-BAR domain of amphiphysin forms a curved
dimer with a positively-charged concave face that can
drive membrane bending and curvature. Human
autoantibodies to amphiphysin-1 hinder GABAergic
signaling and contribute to the pathogenesis of
paraneoplastic stiff-person syndrome. Mutations in
amphiphysin-2 (BIN1) are associated with autosomal
recessive centronuclear myopathy.
Length = 211
Score = 27.2 bits (60), Expect = 3.2
Identities = 12/37 (32%), Positives = 23/37 (62%), Gaps = 1/37 (2%)
Query: 104 YYKKEVDQKLFDQDDGVWENYHQH-ISTYLLTAPTYL 139
+Y ++ + + ++ D +WE++HQ + LLT TYL
Sbjct: 64 WYGRDDVKTIGEKCDLLWEDFHQKLVDGALLTLDTYL 100
>gnl|CDD|227085 COG4742, COG4742, Predicted transcriptional regulator
[Transcription].
Length = 260
Score = 26.8 bits (60), Expect = 3.8
Identities = 8/31 (25%), Positives = 19/31 (61%)
Query: 83 LRRNKDFSLLIDENLWNQIQKYYKKEVDQKL 113
+ D SL++ E ++ +++ YK+E+ + L
Sbjct: 161 AEKGIDVSLILTEPVFERLKSDYKEELKEFL 191
>gnl|CDD|129661 TIGR00570, cdk7, CDK-activating kinase assembly factor MAT1. All
proteins in this family for which functions are known
are cyclin dependent protein kinases that are components
of TFIIH, a complex that is involved in nucleotide
excision repair and transcription initiation. Also known
as MAT1 (menage a trois 1). 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 = 309
Score = 26.7 bits (59), Expect = 4.2
Identities = 17/59 (28%), Positives = 26/59 (44%), Gaps = 11/59 (18%)
Query: 52 CNHHVCLECLQRICDNSNLSCPMCRKRLSIWLRRNKDFSLLIDENLWNQIQKYYKKEVD 110
C H +C C+ + + SCP C LR+N F + + E+ +KEVD
Sbjct: 26 CGHTLCESCVDLLFVRGSGSCPECDTP----LRKNN-FRVQLFEDP------TVEKEVD 73
>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 = 25.1 bits (55), Expect = 5.9
Identities = 9/30 (30%), Positives = 14/30 (46%), Gaps = 1/30 (3%)
Query: 47 PIKLPCNHHVCLECLQRICDNSNLSCPMCR 76
+ C H L C+ R + +CP+CR
Sbjct: 45 VVWGECGHAFHLHCISRWL-KTRNTCPLCR 73
>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 = 25.2 bits (55), Expect = 7.2
Identities = 9/26 (34%), Positives = 13/26 (50%), Gaps = 1/26 (3%)
Query: 52 CNHHVCLECLQRICDNSNLSCPMCRK 77
CNH C+ R D + CP+ R+
Sbjct: 54 CNHAFHDHCIYRWLDTKGV-CPLDRQ 78
>gnl|CDD|223350 COG0272, Lig, NAD-dependent DNA ligase (contains BRCT domain type
II) [DNA replication, recombination, and repair].
Length = 667
Score = 26.4 bits (59), Expect = 7.3
Identities = 9/28 (32%), Positives = 11/28 (39%)
Query: 46 KPIKLPCNHHVCLECLQRICDNSNLSCP 73
KPI P + VC L R + C
Sbjct: 399 KPIPFPTHCPVCGSELVREEGEVVIRCT 426
>gnl|CDD|221153 pfam11638, DnaA_N, DnaA N-terminal domain. This family of proteins
represents the N-terminal domain of DnaA, a protein
involved in the initiation of bacterial chromosomal
replication. The structure of this domain is known. It
is also found in three copies in some proteins. The
exact function of this domain is uncertain but it has
been suggested to play a role in oligomerisation.
Length = 65
Score = 24.5 bits (54), Expect = 8.4
Identities = 5/21 (23%), Positives = 14/21 (66%)
Query: 95 ENLWNQIQKYYKKEVDQKLFD 115
+LW ++ + +KE+ ++ F+
Sbjct: 1 NSLWEKVLQRLRKELGEQTFN 21
>gnl|CDD|181342 PRK08271, PRK08271, anaerobic ribonucleoside triphosphate
reductase; Provisional.
Length = 623
Score = 26.1 bits (58), Expect = 9.4
Identities = 15/56 (26%), Positives = 25/56 (44%), Gaps = 10/56 (17%)
Query: 86 NKDFSLLIDENL-WNQIQKYYKKEVDQKLFDQ---------DDGVWENYHQHISTY 131
KDF LI+ L WN+I++ + KE+ + Q D+ + Y + Y
Sbjct: 75 MKDFFKLINRYLVWNKIKELFGKELADEYLRQIENHEIYVHDETSLKPYCFSYTMY 130
>gnl|CDD|234628 PRK00093, PRK00093, GTP-binding protein Der; Reviewed.
Length = 435
Score = 25.8 bits (58), Expect = 9.8
Identities = 9/23 (39%), Positives = 14/23 (60%)
Query: 112 KLFDQDDGVWENYHQHISTYLLT 134
KL + D +EN ++ IST +L
Sbjct: 334 KLLEAIDEAYENANRRISTSVLN 356
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
0.324 0.138 0.448
Gapped
Lambda K H
0.267 0.0723 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,967,324
Number of extensions: 582528
Number of successful extensions: 811
Number of sequences better than 10.0: 1
Number of HSP's gapped: 800
Number of HSP's successfully gapped: 60
Length of query: 143
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 56
Effective length of database: 7,078,804
Effective search space: 396413024
Effective search space used: 396413024
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.6 bits)
S2: 54 (24.6 bits)