RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy2696
(180 letters)
>gnl|CDD|227481 COG5152, COG5152, Uncharacterized conserved protein, contains RING
and CCCH-type Zn-fingers [General function prediction
only].
Length = 259
Score = 47.4 bits (112), Expect = 8e-07
Identities = 24/61 (39%), Positives = 31/61 (50%), Gaps = 1/61 (1%)
Query: 22 EGEEAPTPTSCGPKNPLLCHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPICGQH 81
E EEAP + G K P LC +C Y P + C HSFC+ C + G C +CG+
Sbjct: 181 EYEEAPVISGPGEKIPFLCGICKKDYESPVVTECGHSFCSLCAIRKYQKGD-ECGVCGKA 239
Query: 82 T 82
T
Sbjct: 240 T 240
>gnl|CDD|227719 COG5432, RAD18, RING-finger-containing E3 ubiquitin ligase
[Signal transduction mechanisms].
Length = 391
Score = 47.4 bits (112), Expect = 9e-07
Identities = 20/61 (32%), Positives = 33/61 (54%), Gaps = 1/61 (1%)
Query: 18 TGPPEGEEAPTPTSCGPKNPLLCHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPI 77
T P + + P+ G + L C +CD + PC +C H+FC+ C+R R + + CP+
Sbjct: 6 TDPSDWNQTKIPSLKGLDSMLRCRICDCRISIPCETTCGHTFCSLCIR-RHLGTQPFCPV 64
Query: 78 C 78
C
Sbjct: 65 C 65
>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 = 46.1 bits (109), Expect = 3e-06
Identities = 20/52 (38%), Positives = 30/52 (57%), Gaps = 1/52 (1%)
Query: 27 PTPTSCGPKNPLLCHVCDDYYTEPCLLSCYHSFCARCLRGRTVDGKLSCPIC 78
P P+ L CH+C D++ P L SC H+FC+ C+R R + + CP+C
Sbjct: 16 PIPSLYPLDTSLRCHICKDFFDVPVLTSCSHTFCSLCIR-RCLSNQPKCPLC 66
>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 = 40.1 bits (94), Expect = 2e-05
Identities = 16/44 (36%), Positives = 22/44 (50%), Gaps = 1/44 (2%)
Query: 40 CHVCDDYYTEPC-LLSCYHSFCARCLRGRTVDGKLSCPICGQHT 82
C +C + + EP LL C H FC C+ GK +CP+C
Sbjct: 2 CPICLEEFREPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRTPI 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 = 37.1 bits (86), Expect = 2e-04
Identities = 16/40 (40%), Positives = 23/40 (57%), Gaps = 1/40 (2%)
Query: 40 CHVCDDYY-TEPCLLSCYHSFCARCLRGRTVDGKLSCPIC 78
C +C + Y +P +L C H+FC C+R G +CPIC
Sbjct: 1 CPICLEEYLKDPVILPCGHTFCRSCIRKWLESGNNTCPIC 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 = 34.0 bits (78), Expect = 0.003
Identities = 12/40 (30%), Positives = 22/40 (55%), Gaps = 1/40 (2%)
Query: 40 CHVCDDYYTEPCLLS-CYHSFCARCLRGRTVDGKLSCPIC 78
C +C + +P + C H FC++C+ G ++CP+C
Sbjct: 1 CPICLEEPKDPVTILPCGHLFCSKCILSWLESGNVTCPLC 40
>gnl|CDD|227547 COG5222, COG5222, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 427
Score = 35.5 bits (81), Expect = 0.010
Identities = 22/72 (30%), Positives = 30/72 (41%), Gaps = 4/72 (5%)
Query: 34 PKNPLLCHVCDDYYTEPC-LLSCYHSFCARCLRGRTVDGKLSCPICGQHTLLKEGSTLPP 92
P L C +C P C H+FC C+ +D CP C + +L +G T
Sbjct: 271 PNISLKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLDSDFKCPNCSRKDVLLDGLT--- 327
Query: 93 PDNVLKQLIEVA 104
PD K +E A
Sbjct: 328 PDIDKKLEVEKA 339
>gnl|CDD|222279 pfam13639, zf-RING_2, Ring finger domain.
Length = 46
Score = 30.4 bits (69), Expect = 0.053
Identities = 13/42 (30%), Positives = 20/42 (47%), Gaps = 4/42 (9%)
Query: 40 CHVCDDYYT---EPCLLSCYHSFCARCLRGRTVDGKLSCPIC 78
C +C D + E +L C H F CL + + +CP+C
Sbjct: 3 CPICLDEFEPGEEVVVLPCGHVFHKECLD-KWLRSSNTCPLC 43
>gnl|CDD|227861 COG5574, PEX10, RING-finger-containing E3 ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 271
Score = 32.6 bits (74), Expect = 0.073
Identities = 16/68 (23%), Positives = 20/68 (29%), Gaps = 1/68 (1%)
Query: 20 PPEGEEAPTPTSCGPKNPLLCHVCDDYYTEPCLLSCYHSFCARCLRG-RTVDGKLSCPIC 78
E P C +C + P C H FC CL T CP+C
Sbjct: 198 TKENLSKKNGLPFIPLADYKCFLCLEEPEVPSCTPCGHLFCLSCLLISWTKKKYEFCPLC 257
Query: 79 GQHTLLKE 86
K+
Sbjct: 258 RAKVYPKK 265
>gnl|CDD|206094 pfam13923, zf-C3HC4_2, Zinc finger, C3HC4 type (RING finger).
Length = 45
Score = 29.8 bits (67), Expect = 0.11
Identities = 17/46 (36%), Positives = 21/46 (45%), Gaps = 2/46 (4%)
Query: 36 NPLLCHVCDDYYTEP-CLLSCYHSFCARCLRGRTVDGKLSCPICGQ 80
L C +C D +P L C H FC C+ R + K CPIC
Sbjct: 1 EELECPICLDLLRDPVVLTPCGHVFCRECIL-RYLKKKSKCPICRT 45
>gnl|CDD|225449 COG2896, MoaA, Molybdenum cofactor biosynthesis enzyme [Coenzyme
metabolism].
Length = 322
Score = 31.8 bits (73), Expect = 0.15
Identities = 19/57 (33%), Positives = 24/57 (42%), Gaps = 4/57 (7%)
Query: 57 HSFCARCLRGR-TVDGKLSCPICGQHTL--LKEGSTLPPPDNVLKQLIEVANAENPP 110
+ FCA C R R T DGKL P + L++ D L + I A PP
Sbjct: 248 NPFCATCNRLRLTADGKL-KPCLFREDGIDLRDLLRSGASDEELVEAIREALRRRPP 303
>gnl|CDD|227561 COG5236, COG5236, Uncharacterized conserved protein, contains RING
Zn-finger [General function prediction only].
Length = 493
Score = 31.9 bits (72), Expect = 0.15
Identities = 12/41 (29%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 39 LCHVCDDYYTEPCLLSCYHSFCARC-LRGRTVDGKLSCPIC 78
C +C T C H C C +R R + + CP+C
Sbjct: 63 NCQICAGSTTYSARYPCGHQICHACAVRLRALYMQKGCPLC 103
>gnl|CDD|234133 TIGR03168, 1-PFK, hexose kinase, 1-phosphofructokinase family.
This family consists largely of 1-phosphofructokinases,
but also includes tagatose-6-kinases and
6-phosphofructokinases.
Length = 303
Score = 29.5 bits (67), Expect = 0.78
Identities = 11/31 (35%), Positives = 13/31 (41%), Gaps = 4/31 (12%)
Query: 87 GSTLPP--PDNVLKQLIEVANAENPPCANCD 115
GS LPP P + QLI +A D
Sbjct: 135 GS-LPPGVPPDFYAQLIAIARKRGAKVI-LD 163
>gnl|CDD|202502 pfam02992, Transposase_21, Transposase family tnp2.
Length = 226
Score = 29.2 bits (66), Expect = 0.92
Identities = 11/19 (57%), Positives = 13/19 (68%)
Query: 64 LRGRTVDGKLSCPICGQHT 82
L G T GKL+CPIC + T
Sbjct: 149 LSGWTTKGKLACPICMEDT 167
>gnl|CDD|115392 pfam06730, FAM92, FAM92 protein. This family of proteins has a
role in embryogenesis. During embryogenesis it is
essential for ectoderm and axial mesoderm development.
It may regulate cell proliferation and apoptosis.
Length = 219
Score = 28.8 bits (64), Expect = 1.3
Identities = 14/67 (20%), Positives = 23/67 (34%), Gaps = 4/67 (5%)
Query: 118 DRNAMYFCSTCASVRTGLMNCRSSLDEL----QLNCDTEKMTIQSFCQGMIDAITKTQNS 173
+++ C A+ R D L DTE ++ + D K Q+
Sbjct: 24 EKHFGELCQIFAAYVRKTARLRDKADLLVNEINSYADTETPNLKLGLKSFADEFAKLQDY 83
Query: 174 MIMEVQR 180
EV+R
Sbjct: 84 RQAEVER 90
>gnl|CDD|227827 COG5540, COG5540, RING-finger-containing ubiquitin ligase
[Posttranslational modification, protein turnover,
chaperones].
Length = 374
Score = 28.8 bits (64), Expect = 1.7
Identities = 11/41 (26%), Positives = 16/41 (39%), Gaps = 8/41 (19%)
Query: 53 LSCYHSFCARCLRGRTVDGKLSCPICGQHTLLKEGSTLPPP 93
L C H F C+ + CP+C + +PPP
Sbjct: 342 LPCDHRFHVGCVDKWLLGYSNKCPVC--------RTAIPPP 374
>gnl|CDD|178608 PLN03046, PLN03046, D-glycerate 3-kinase; Provisional.
Length = 460
Score = 28.7 bits (64), Expect = 1.7
Identities = 13/32 (40%), Positives = 18/32 (56%), Gaps = 2/32 (6%)
Query: 82 TLLKEGSTLPPPDNVLKQLIEVANAENPPCAN 113
TL EG + PD+VL +I++ NP AN
Sbjct: 431 TLYAEGPSGSDPDHVL--VIDIDEERNPILAN 460
>gnl|CDD|115139 pfam06463, Mob_synth_C, Molybdenum Cofactor Synthesis C. This
region contains two iron-sulphur (3Fe-4S) binding
sites. Mutations in this region of human MOCS1 cause
MOCOD (Molybdenum Co-Factor Deficiency) type A.
Length = 127
Score = 27.6 bits (62), Expect = 1.9
Identities = 11/18 (61%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 57 HSFCARCLRGR-TVDGKL 73
+ FCA C R R T DGKL
Sbjct: 69 NPFCASCNRLRLTADGKL 86
>gnl|CDD|185626 PTZ00447, PTZ00447, apical membrane antigen 1-like protein;
Provisional.
Length = 508
Score = 28.4 bits (63), Expect = 2.6
Identities = 11/29 (37%), Positives = 13/29 (44%), Gaps = 4/29 (13%)
Query: 86 EGSTLPPPDNVLK----QLIEVANAENPP 110
EG P+N L Q+ E ENPP
Sbjct: 469 EGKNDHIPNNTLPKGHIQMDEHGRGENPP 497
>gnl|CDD|182276 PRK10160, PRK10160, taurine transporter subunit; Provisional.
Length = 275
Score = 27.8 bits (62), Expect = 3.4
Identities = 8/18 (44%), Positives = 12/18 (66%)
Query: 90 LPPPDNVLKQLIEVANAE 107
LPPP VL +L+ +A +
Sbjct: 52 LPPPQQVLAKLLTIAGPQ 69
>gnl|CDD|215935 pfam00471, Ribosomal_L33, Ribosomal protein L33.
Length = 48
Score = 25.2 bits (56), Expect = 4.4
Identities = 8/12 (66%), Positives = 9/12 (75%)
Query: 75 CPICGQHTLLKE 86
CP C +HTL KE
Sbjct: 35 CPKCRKHTLHKE 46
>gnl|CDD|214584 smart00249, PHD, PHD zinc finger. The plant homeodomain (PHD)
finger is a C4HC3 zinc-finger-like motif found in
nuclear proteins thought to be involved in epigenetics
and chromatin-mediated transcriptional regulation. The
PHD finger binds two zinc ions using the so-called
'cross-brace' motif and is thus structurally related to
the RING finger and the FYVE finger. It is not yet
known if PHD fingers have a common molecular function.
Several reports suggest that it can function as a
protein-protein interacton domain and it was recently
demonstrated that the PHD finger of p300 can cooperate
with the adjacent BROMO domain in nucleosome binding in
vitro. Other reports suggesting that the PHD finger is
a ubiquitin ligase have been refuted as these domains
were RING fingers misidentified as PHD fingers.
Length = 47
Score = 24.9 bits (54), Expect = 6.3
Identities = 16/46 (34%), Positives = 16/46 (34%), Gaps = 7/46 (15%)
Query: 40 CHVCDDYYTEPCLLSC------YHSFCARC-LRGRTVDGKLSCPIC 78
C VC LL C YH C L DGK CP C
Sbjct: 2 CSVCGKPDDGGELLQCDGCDRWYHQTCLGPPLLEEEPDGKWYCPKC 47
>gnl|CDD|234747 PRK00398, rpoP, DNA-directed RNA polymerase subunit P;
Provisional.
Length = 46
Score = 24.9 bits (55), Expect = 6.4
Identities = 14/32 (43%), Positives = 16/32 (50%), Gaps = 7/32 (21%)
Query: 60 CARCLRGRTVD-----GKLSCPICGQHTLLKE 86
CARC GR V+ + CP CG L KE
Sbjct: 6 CARC--GREVELDEYGTGVRCPYCGYRILFKE 35
>gnl|CDD|153282 cd07598, BAR_FAM92, The Bin/Amphiphysin/Rvs (BAR) domain of Family
with sequence similarity 92 (FAM92). BAR domains are
dimerization, lipid binding and curvature sensing
modules found in many different proteins with diverse
functions including organelle biogenesis, membrane
trafficking or remodeling, and cell division and
migration. This group is composed of proteins from the
family with sequence similarity 92 (FAM92), which were
originally identified by the presence of the unknown
domain DUF1208. This domain shows similarity to the BAR
domains of sorting nexins. Mammals contain at least two
member types, FAM92A and FAM92B, which may exist in many
variants. The Xenopus homolog of FAM92A1, xVAP019, is
essential for embryo survival and cell differentiation.
FAM92A1 may be involved in regulating cell proliferation
and apoptosis. BAR domains form dimers that bind to
membranes, induce membrane bending and curvature, and
may also be involved in protein-protein interactions.
Length = 211
Score = 26.5 bits (59), Expect = 6.8
Identities = 13/61 (21%), Positives = 22/61 (36%), Gaps = 4/61 (6%)
Query: 124 FCSTCASVRTGLMNCRSSLDEL----QLNCDTEKMTIQSFCQGMIDAITKTQNSMIMEVQ 179
C A+ R DEL DTE +++ + + + Q+ EV+
Sbjct: 23 LCQDFAAYTRKTARLRDKGDELAKSINAYADTENPSLKQGLKNFAECLAALQDYRQAEVE 82
Query: 180 R 180
R
Sbjct: 83 R 83
>gnl|CDD|222454 pfam13920, zf-C3HC4_3, Zinc finger, C3HC4 type (RING finger).
Length = 49
Score = 24.6 bits (54), Expect = 7.7
Identities = 14/47 (29%), Positives = 17/47 (36%), Gaps = 3/47 (6%)
Query: 36 NPLLCHVCDDYYTEPCLLSCYH-SFCARCLRGRTVDGKLSCPICGQH 81
LC +C + L C H C C + K CPIC Q
Sbjct: 1 EDDLCVICLERPRNVVFLPCGHLCLCEECAKRLRSKKK--CPICRQP 45
>gnl|CDD|213036 cd11728, ADDz_Dnmt3b, ADDz domain of DNA (cytosine-5)
methyltransferases (C5-MTases) 3 b (Dnmt3b).
ADDz_Dnmt3b is an active catalytic domain of Dnmt3b.
Dnmt3b is a member of the Dnmt3 family and is a de novo
DNA methyltransferases that has an N-terminal variable
region followed by a conserved PWWP region and the
cysteine-rich ADDz domain. DNA methylation is an
important epigenetic mechanism involved in diverse
biological processes such as embryonic development,
gene expression, and genomic imprinting. The
methyltransferase activity of Dnmt3a is not only
responsible for the establishment of DNA methylation
pattern, but is also essential for the inheritance of
these patterns during mitosis. Dnmt3b is ubiquitously
expressed in most adult tissues. The ADDz_Dnmt3 domain
is a PHD-like zinc finger motif that contains two
parts, a C2-C2 and a PHD-like zinc finger. PHD zinc
finger domains have been identified in more than 40
proteins that are mainly involved in chromatin mediated
transcriptional control; the classical PHD zinc finger
has a C4-H-C3 motif that spans about 50-80 amino acids.
In ADDz, the conserved histidine residue of the PHD
finger is replaced by a cysteine, and an additional
zinc finger C2-C2 like motif is located about twenty
residues upstream of the C4-C-C3 motif. A knockout of
Dnmt3b has been shown to be lethal in the mouse model.
Length = 150
Score = 26.3 bits (58), Expect = 8.2
Identities = 16/51 (31%), Positives = 21/51 (41%), Gaps = 12/51 (23%)
Query: 31 SCGPKNPL---------LCHVCDDYYTEPCLL---SCYHSFCARCLRGRTV 69
SCG +NP LC C D + E + Y S+C C GR +
Sbjct: 22 SCGKRNPATFHPLFEGGLCQTCKDRFLELFYMYDDDGYQSYCTVCCEGREL 72
>gnl|CDD|234672 PRK00164, moaA, molybdenum cofactor biosynthesis protein A;
Reviewed.
Length = 331
Score = 26.6 bits (60), Expect = 8.4
Identities = 13/21 (61%), Positives = 13/21 (61%), Gaps = 2/21 (9%)
Query: 57 HSFCARCLRGR-TVDGKL-SC 75
H FCA C R R T DGKL C
Sbjct: 256 HDFCASCNRLRLTADGKLHLC 276
>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 = 26.3 bits (58), Expect = 8.8
Identities = 10/25 (40%), Positives = 12/25 (48%)
Query: 55 CYHSFCARCLRGRTVDGKLSCPICG 79
C H+ C C+ V G SCP C
Sbjct: 26 CGHTLCESCVDLLFVRGSGSCPECD 50
>gnl|CDD|219490 pfam07627, PSCyt3, Protein of unknown function (DUF1588). A region
of similarity shared by several Rhodopirellula baltica
cytochrome-like proteins that are predicted to be
secreted. These proteins also match pfam07626 and
pfam07624.
Length = 102
Score = 25.6 bits (57), Expect = 9.3
Identities = 14/39 (35%), Positives = 21/39 (53%), Gaps = 13/39 (33%)
Query: 91 PPPDNV------------LKQLIEVANAENPPCANCDKR 117
PPP NV L++ +E A+ ENP CA+C ++
Sbjct: 41 PPPPNVPALEPDDPGALTLRERLE-AHRENPACASCHRK 78
>gnl|CDD|176195 cd08233, butanediol_DH_like, (2R,3R)-2,3-butanediol dehydrogenase.
(2R,3R)-2,3-butanediol dehydrogenase, a zinc-dependent
medium chain alcohol dehydrogenase, catalyzes the
NAD(+)-dependent oxidation of (2R,3R)-2,3-butanediol and
meso-butanediol to acetoin. BDH functions as a
homodimer. NAD(P)(H)-dependent oxidoreductases are the
major enzymes in the interconversion of alcohols and
aldehydes, or ketones. The medium chain alcohol
dehydrogenase family (MDR) have a NAD(P)(H)-binding
domain in a Rossmann fold of a beta-alpha form. The
N-terminal region typically has an all-beta catalytic
domain. These proteins typically form dimers (typically
higher plants, mammals) or tetramers (yeast, bacteria),
and have 2 tightly bound zinc atoms per subunit.
Sorbitol and aldose reductase are NAD(+) binding
proteins of the polyol pathway, which interconverts
glucose and fructose. Sorbitol dehydrogenase is
tetrameric and has a single catalytic zinc per subunit.
Length = 351
Score = 26.3 bits (59), Expect = 9.4
Identities = 6/19 (31%), Positives = 8/19 (42%)
Query: 120 NAMYFCSTCASVRTGLMNC 138
C TC + + GL N
Sbjct: 95 EPTIKCGTCGACKRGLYNL 113
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
0.320 0.134 0.432
Gapped
Lambda K H
0.267 0.0718 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,372,836
Number of extensions: 686785
Number of successful extensions: 740
Number of sequences better than 10.0: 1
Number of HSP's gapped: 732
Number of HSP's successfully gapped: 45
Length of query: 180
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 89
Effective length of database: 6,901,388
Effective search space: 614223532
Effective search space used: 614223532
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 (21.8 bits)
S2: 56 (25.4 bits)