RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1168
(229 letters)
>gnl|CDD|227640 COG5333, CCL1, Cdk activating kinase (CAK)/RNA polymerase II
transcription initiation/nucleotide excision repair
factor TFIIH/TFIIK, cyclin H subunit [Cell division and
chromosome partitioning / Transcription / DNA
replication, recombination, and repair].
Length = 297
Score = 120 bits (302), Expect = 6e-33
Identities = 67/173 (38%), Positives = 101/173 (58%), Gaps = 13/173 (7%)
Query: 35 ILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTC 94
L+ E+ + I++ I L +L L Q V+ATA ++F RFY +NS++ I + TC
Sbjct: 35 ELTLEKELNLVIYYLKLIMDLCTRLNLPQTVLATAILFFSRFYLKNSVEEISLYSVVTTC 94
Query: 95 VFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRT-NHILECEFYLLENLDCC 153
V+LA KVE+ + R +S ++ E P + ILE EF LLE LD
Sbjct: 95 VYLACKVED-----TPRDISIESFEARDL-----WSEEPKSSRERILEYEFELLEALDFD 144
Query: 154 LIVYQPYRPLLQLVQDIGHED--QLLALAWRVINDSLRTDVCLLYPPYQIAIG 204
L V+ PY+ L ++D+ +D +LL +AW++IND+LRTD+CLLYPP+ IA+
Sbjct: 145 LHVHHPYKYLEGFLKDLQEKDKYKLLQIAWKIINDALRTDLCLLYPPHIIALA 197
>gnl|CDD|129660 TIGR00569, ccl1, cyclin ccl1. All proteins in this family for
which functions are known are cyclins that are
components of TFIIH, a complex that is involved in
nucleotide excision repair and transcription initiation.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, StanfordUniversity) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 305
Score = 89.9 bits (223), Expect = 2e-21
Identities = 57/178 (32%), Positives = 82/178 (46%), Gaps = 22/178 (12%)
Query: 36 LSDEEYQKIFIFFANFIQILGEQLK--LRQQVIATATVYFKRFYARNSLKCIDPLLLAPT 93
L+ EE + ++ + K + V+ TA +YFKRFY NS+ P ++ T
Sbjct: 47 LTPEEELDLVKYYEKRLLDFCSAFKPTMPTSVVGTAIMYFKRFYLNNSVMEYHPKIIMLT 106
Query: 94 CVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCC 153
CVFLA KVEEF V + + L +LE E L++ L+
Sbjct: 107 CVFLACKVEEFNVSID----QFVGNLKETPLK---------ALEQVLEYELLLIQQLNFH 153
Query: 154 LIVYQPYRPLLQLVQDI-------GHEDQLLALAWRVINDSLRTDVCLLYPPYQIAIG 204
LIV+ PYRPL + DI + + L A + +N +L TD LLY P QIA+
Sbjct: 154 LIVHNPYRPLEGFLIDIKTRLPGLENPEYLRKHADKFLNRTLLTDAYLLYTPSQIALA 211
>gnl|CDD|238003 cd00043, CYCLIN, Cyclin box fold. Protein binding domain
functioning in cell-cycle and transcription control.
Present in cyclins, TFIIB and Retinoblastoma (RB).The
cyclins consist of 8 classes of cell cycle regulators
that regulate cyclin dependent kinases (CDKs). TFIIB is
a transcription factor that binds the TATA box. Cyclins,
TFIIB and RB contain 2 copies of the domain.
Length = 88
Score = 56.9 bits (138), Expect = 5e-11
Identities = 23/98 (23%), Positives = 35/98 (35%), Gaps = 16/98 (16%)
Query: 50 NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISS 109
+F++ + + L L + + A RF S+ P L+A ++LA+KVEE
Sbjct: 7 DFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAAAALYLAAKVEEI----- 61
Query: 110 SRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLL 147
L V IL E LL
Sbjct: 62 PPWLKDLVHVTGY-----------ATEEEILRMEKLLL 88
Score = 26.4 bits (59), Expect = 5.3
Identities = 10/48 (20%), Positives = 19/48 (39%)
Query: 156 VYQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAI 203
P L ++ + +G + L LA +++ L L P +A
Sbjct: 2 RPTPLDFLRRVAKALGLSPETLTLAVNLLDRFLLDYSVLGRSPSLVAA 49
>gnl|CDD|215740 pfam00134, Cyclin_N, Cyclin, N-terminal domain. Cyclins regulate
cyclin dependent kinases (CDKs). Human cyclin-O is a
Uracil-DNA glycosylase that is related to other cyclins.
Cyclins contain two domains of similar all-alpha fold,
of which this family corresponds with the N-terminal
domain.
Length = 127
Score = 56.8 bits (138), Expect = 1e-10
Identities = 23/105 (21%), Positives = 43/105 (40%), Gaps = 14/105 (13%)
Query: 50 NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISS 109
+++ + E+ KL + + A Y RF ++ + L+ TC+ +A+K EE
Sbjct: 36 DWLVEVHEEFKLLPETLYLAVNYLDRFLSKQPVPRTKLQLVGVTCLLIAAKYEEI----- 90
Query: 110 SRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLENLDCCL 154
+V ++ Y + Y IL E +L L+ L
Sbjct: 91 -----YPPSV----EDFVYITDNAYTKEEILRMELLILSTLNWDL 126
>gnl|CDD|214641 smart00385, CYCLIN, domain present in cyclins, TFIIB and
Retinoblastoma. A helical domain present in cyclins and
TFIIB (twice) and Retinoblastoma (once). A protein
recognition domain functioning in cell-cycle and
transcription control.
Length = 83
Score = 52.2 bits (126), Expect = 3e-09
Identities = 24/99 (24%), Positives = 35/99 (35%), Gaps = 16/99 (16%)
Query: 50 NFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISS 109
+F++ + + L L + + A RF + P L+A ++LASK EE
Sbjct: 1 DFLRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAAAALYLASKTEETP---- 56
Query: 110 SRLLSTCQTVVKNKLNYAYAQEFPYRTNHILECEFYLLE 148
K Y F IL E LLE
Sbjct: 57 ----------PWTKELVHYTGYFTE--EEILRMERLLLE 83
Score = 27.6 bits (62), Expect = 1.5
Identities = 10/41 (24%), Positives = 19/41 (46%)
Query: 163 LLQLVQDIGHEDQLLALAWRVINDSLRTDVCLLYPPYQIAI 203
L ++ + + + + L LA +++ L L Y P IA
Sbjct: 3 LRRVCKALNLDPETLNLAVNLLDRFLSDYKFLKYSPSLIAA 43
>gnl|CDD|224323 COG1405, SUA7, Transcription initiation factor TFIIIB, Brf1
subunit/Transcription initiation factor TFIIB
[Transcription].
Length = 285
Score = 29.6 bits (67), Expect = 1.1
Identities = 15/85 (17%), Positives = 34/85 (40%)
Query: 19 VLDRQDLIRERKHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYA 78
D+ + R RK + I ++ I ++ + L L + V TA +++
Sbjct: 71 WGDKDKMYRLRKWQIRIRVSSAKERNLITALEELERIASALGLPESVRETAARIYRKAVD 130
Query: 79 RNSLKCIDPLLLAPTCVFLASKVEE 103
+ L+ +A C++ A ++
Sbjct: 131 KGLLRGRSIESVAAACIYAACRING 155
>gnl|CDD|227357 COG5024, COG5024, Cyclin [Cell division and chromosome
partitioning].
Length = 440
Score = 29.7 bits (67), Expect = 1.3
Identities = 19/77 (24%), Positives = 33/77 (42%), Gaps = 14/77 (18%)
Query: 75 RFYARNSLKCIDPLLLAPTCVFLASKVEEFGVISSSRLLSTCQTVVKNKLNYAYAQEFPY 134
RF + + L+ + +F+ASK EE C ++ + YA + +
Sbjct: 243 RFLSSRVVSLEKYQLVGISALFIASKYEEV----------NCPSIK----DLVYATDGAF 288
Query: 135 RTNHILECEFYLLENLD 151
+ I+ E Y+LE LD
Sbjct: 289 TRDDIIRAERYMLEVLD 305
>gnl|CDD|181738 PRK09265, PRK09265, aminotransferase AlaT; Validated.
Length = 404
Score = 29.8 bits (68), Expect = 1.3
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 29 RKHDLSILSDEEYQKI 44
R+H+L I +DE Y KI
Sbjct: 198 RQHNLIIFADEIYDKI 213
>gnl|CDD|109440 pfam00382, TFIIB, Transcription factor TFIIB repeat.
Length = 71
Score = 27.2 bits (61), Expect = 2.0
Identities = 15/54 (27%), Positives = 26/54 (48%)
Query: 52 IQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLLLAPTCVFLASKVEEFG 105
I+ + L+L ++V A K N LK P +A C+++A ++EE
Sbjct: 1 IKRFADALELPKKVADAANELAKLALDDNLLKGRSPESIAAACLYIACRLEEVK 54
>gnl|CDD|235596 PRK05764, PRK05764, aspartate aminotransferase; Provisional.
Length = 393
Score = 28.9 bits (66), Expect = 2.1
Identities = 11/30 (36%), Positives = 19/30 (63%), Gaps = 4/30 (13%)
Query: 19 VLDRQDL--IRE--RKHDLSILSDEEYQKI 44
V ++L I + +HD+ +LSDE Y+K+
Sbjct: 180 VYSPEELEAIADVAVEHDIWVLSDEIYEKL 209
>gnl|CDD|180404 PRK06108, PRK06108, aspartate aminotransferase; Provisional.
Length = 382
Score = 29.1 bits (66), Expect = 2.1
Identities = 11/28 (39%), Positives = 14/28 (50%), Gaps = 4/28 (14%)
Query: 18 WVLDRQD----LIRERKHDLSILSDEEY 41
W R D L R+H L I++DE Y
Sbjct: 173 WTASRDDLRAILAHCRRHGLWIVADEVY 200
>gnl|CDD|237361 PRK13355, PRK13355, bifunctional HTH-domain containing
protein/aminotransferase; Provisional.
Length = 517
Score = 28.9 bits (65), Expect = 2.7
Identities = 17/38 (44%), Positives = 21/38 (55%), Gaps = 7/38 (18%)
Query: 8 GRFYP-EWIQQWVLDRQDLIRERKHDLSILSDEEYQKI 44
G YP E +QQ V D+ RE H L I SDE Y ++
Sbjct: 295 GALYPREVLQQIV----DIARE--HQLIIFSDEIYDRL 326
>gnl|CDD|240391 PTZ00377, PTZ00377, alanine aminotransferase; Provisional.
Length = 481
Score = 28.4 bits (64), Expect = 3.8
Identities = 8/29 (27%), Positives = 14/29 (48%), Gaps = 6/29 (20%)
Query: 19 VLDRQDLIRE-----RKHDLSILSDEEYQ 42
VL R + E + + +++DE YQ
Sbjct: 234 VLTRDV-MEEIIKFCYEKGIVLMADEVYQ 261
>gnl|CDD|181036 PRK07568, PRK07568, aspartate aminotransferase; Provisional.
Length = 397
Score = 28.3 bits (64), Expect = 3.9
Identities = 17/54 (31%), Positives = 31/54 (57%), Gaps = 10/54 (18%)
Query: 29 RKHDLSILSDEEYQKIFIF----FANFIQILGEQLKLRQQVIATATVYFKRFYA 78
+KHDL ++SDE Y++ F++ + + + + G L +VI +V KR+ A
Sbjct: 192 KKHDLFLISDEVYRE-FVYDGLKYTSALSLEG----LEDRVIIIDSVS-KRYSA 239
>gnl|CDD|111360 pfam02454, Sigma_1s, Sigma 1s protein. The reoviral gene S1
encodes for haemagglutinin (sigma 1 protein), an outer
capsid protein and a major factor in determining
virus-host cell interactions. Sigma 1s is one of two
translation products of the S1 gene.
Length = 116
Score = 27.2 bits (60), Expect = 4.0
Identities = 7/17 (41%), Positives = 11/17 (64%)
Query: 9 RFYPEWIQQWVLDRQDL 25
R YP W+ + +L Q+L
Sbjct: 77 RVYPSWVTESMLLNQEL 93
>gnl|CDD|176487 cd08666, APC10-HECTD3, APC10-like DOC1 domain of HECTD3, a HECT E3
ubiquitin ligase protein that mediates substrate
ubiquitination. This model represents the APC10/DOC1
domain present in HECTD3, a HECT (Homologous to the
E6-AP Carboxyl Terminus) E3 ubiquitin ligase protein.
HECT E3 ubiquitin ligases mediate substrate
ubiquitination (or ubiquitylation), and are a component
of the ubiquitin-26S proteasome pathway for selective
proteolytic degradation. They also regulate the
trafficking of many receptors, channels, transporters
and viral proteins. HECTD3 (HECT domain-containing
protein3) contains a C-terminal HECT domain with the
active site for ubiquitin transfer onto substrates, and
an N-terminal APC10/DOC1 domain, which is responsible
for substrate recognition and binding. HECTD3
specifically recognizes the Trio-binding protein, Tara
(Trio-associated repeat on actin), implicated in
regulating actin cytoskeletal, cell motility and cell
growth. Tara also binds to TRF1 and may participate in
telomere maintenance and/or mitotic regulation through
interacting with TRF1. HECTD3 interacts with and
promotes the ubiquitination of Syntaxin 8, an endosomal
syntaxin proposed to mediate distinct steps of endosomal
protein trafficking. HECTD3-mediated Syntaxin 8
degradation has been suggested to contribute to the
pathophysiology of neurodegenerative diseases.
Length = 134
Score = 26.6 bits (59), Expect = 6.8
Identities = 18/56 (32%), Positives = 24/56 (42%), Gaps = 10/56 (17%)
Query: 157 YQPYRPLLQLVQDIGHEDQLLALAWRVINDSLRTDVCLL------YPPYQIAIGEC 206
Y P R + G D L L I+++L DVC+L P +I I EC
Sbjct: 68 YMPKR----VAVYGGEGDNLKKLNDVSIDETLIGDVCILEDMTTHLPVIEIRIKEC 119
>gnl|CDD|219442 pfam07514, TraI_2, Putative helicase. Some members of this
family have been annotated as helicases.
Length = 326
Score = 27.3 bits (61), Expect = 8.2
Identities = 12/54 (22%), Positives = 21/54 (38%), Gaps = 7/54 (12%)
Query: 8 GRFYPEWIQQW--VLDRQDLIRERKHDLSILSDEE----YQKIFIFFANFIQIL 55
G P + RQ+L+ +L + S E+ Y +A +Q+L
Sbjct: 1 GYPAPLSAEDLLATERRQELLERIWQNLGL-SREDFERLYLPPIRRYAELVQLL 53
>gnl|CDD|180537 PRK06348, PRK06348, aspartate aminotransferase; Provisional.
Length = 384
Score = 27.0 bits (60), Expect = 8.9
Identities = 27/139 (19%), Positives = 56/139 (40%), Gaps = 24/139 (17%)
Query: 30 KHDLSILSDEEYQKIFIFFANFIQILGEQLKLRQQVIATATVYFKRFYARNSLKCIDPLL 89
++DL I+SDE Y F F+ +F+ + + ++ I + F + +A + +
Sbjct: 193 EYDLFIISDEVYDG-FSFYEDFVPMATLA-GMPERTITFGS--FSKDFAMTGWRI--GYV 246
Query: 90 LAPTCV------------FLASKVEEFGVISSSRLLSTCQTVV----KNKLNYAYAQ--E 131
+AP + F A + + I + + T ++ + +L YAY +
Sbjct: 247 IAPDYIIETAKIINEGICFSAPTISQRAAIYALKHRDTIVPLIKEEFQKRLEYAYKRIES 306
Query: 132 FPYRTNHILECEFYLLENL 150
P + H + Y N+
Sbjct: 307 IPNLSLHPPKGSIYAFINI 325
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
0.327 0.142 0.437
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,801,760
Number of extensions: 1112225
Number of successful extensions: 1127
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1121
Number of HSP's successfully gapped: 27
Length of query: 229
Length of database: 10,937,602
Length adjustment: 94
Effective length of query: 135
Effective length of database: 6,768,326
Effective search space: 913724010
Effective search space used: 913724010
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 (21.7 bits)
S2: 57 (25.6 bits)