RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13810
(386 letters)
>gnl|CDD|233058 TIGR00625, tfb2, Transcription factor tfb2. All proteins in this
family are part of the TFIIH complex which is involved
in the initiation of transcription and 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 = 448
Score = 415 bits (1068), Expect = e-144
Identities = 197/415 (47%), Positives = 266/415 (64%), Gaps = 40/415 (9%)
Query: 1 ELSEIAKHYVIRLLFVEQPVPQAVIASWLSKTHAKEHKEATDTLTEL------------- 47
EL +AK++V+R+LF EQPVP A + W+ K K +E+T L+ L
Sbjct: 30 ELPSLAKNWVMRMLFNEQPVPLADVDLWVKKEFKKAQEESTGLLSGLHIWHTQLLPGLQG 89
Query: 48 -------RRNAKVALLGGGKPWSM-SAKLEVDSKARDLDFLNQYALERWECILRFMVGSQ 99
R+N ++AL GGGK S ++L D A D+D L++YA ERWE IL FMVG+
Sbjct: 90 IILNPIFRQNLRIALTGGGKANSFGVSQLGPDKHAVDVDSLDKYAEERWETILHFMVGTP 149
Query: 100 QTEGISADAVRTLFNEGA--------ENPVITKDGFQFLLLETPAQVWYFILKYLETVES 151
+ + ++ V L + E P IT GFQFLL + AQ+W +L+YL+T ES
Sbjct: 150 SAK-VPSEDVLQLLKQAGLMKSTEPGEPPCITSAGFQFLLQDINAQLWTLLLQYLKTAES 208
Query: 152 KGLDLVECLTFLFQLKFSTFGTDYSTEGMSDKLQVFLQHLREFGLVYQRKRKAGRFYPTK 211
+G+DLVE L FLF L F T G YS +G+SD + LQ LRE+GLV+QRKRK+ RFYPT+
Sbjct: 209 RGMDLVEVLHFLFMLGFLTLGKAYSVDGLSDTQLIMLQDLREYGLVFQRKRKSRRFYPTR 268
Query: 212 LALNMAT-----RGTLKQIREP-GFLIVETNFRVYAYTDSNLKVALIGLFCELMYRFPNL 265
LA+N+ + G + + GF+IVETN+R+YAYT+S L++ALI LF EL+ RFPN+
Sbjct: 269 LAINLTSDTKTVSGAGGTVDDDLGFIIVETNYRLYAYTESPLQIALIALFSELLARFPNM 328
Query: 266 TVGVLTRDSVRAALRSGITAAQIIGFLRLHALPSVSCP----LPPVVSDQIRLWEGERER 321
VG +TR+S+R AL +GITA QII +LR HA P + LPP + DQIRLWE ER+R
Sbjct: 329 VVGQITRESIRRALANGITAQQIIHYLRTHAHPQMRKEQTPVLPPTIVDQIRLWELERDR 388
Query: 322 LTTSEGVLYSQFVSQADFEKLRDYAQDLGVLTWQNEKKRTVVVTKQGHSDIKKFW 376
L +EGVLY+ F++Q DFE L YA++LGVL W+N KR +T GHSD+K+FW
Sbjct: 389 LRFTEGVLYNDFLTQVDFELLLAYARELGVLVWENSAKRLFFITPAGHSDVKRFW 443
>gnl|CDD|217760 pfam03849, Tfb2, Transcription factor Tfb2.
Length = 365
Score = 376 bits (968), Expect = e-129
Identities = 141/339 (41%), Positives = 194/339 (57%), Gaps = 41/339 (12%)
Query: 1 ELSEIAKHYVIRLLFVEQPVPQAVIASWLSKTHAKEHKEATDTLTEL------------- 47
L +AK +++R+LFV+QPVP A + W+ K+H+EA L L
Sbjct: 27 LLPPLAKQFIMRMLFVDQPVPAADLDKWVKPESKKQHEEAIKRLKSLHIITETPSGGKKQ 86
Query: 48 --------RRNAKVALLGGGKPWSM-SAKLEVDSKARDLDFLNQYALERWECILRFMVGS 98
++N + AL GGG S E D K D+ FL+ YA E+WE IL +MVGS
Sbjct: 87 SIRLNPTFKKNLRRALTGGGVNNSFGVPSDEPDKKLVDVAFLDSYAREKWETILHYMVGS 146
Query: 99 QQTEGISADAVRTLF------NEGAENPVITKDGFQFLLLETPAQVWYFILKYLETVESK 152
+ + + +V L IT +GFQFLL + AQ+W +L+YL+ E +
Sbjct: 147 SEAKTQPSKSVLNLLKHGGLMERSDGGLRITNEGFQFLLQDVNAQIWTLLLQYLKLAEER 206
Query: 153 GLDLVECLTFLFQLKFSTFGTDYSTEGMSDKLQVFLQHLREFGLVYQRKRKAGRFYPTKL 212
G+D V+ L+FLF L F G YST+G+S+ + LQ LR++GLVYQRKRK+ RFYPT+L
Sbjct: 207 GMDPVDVLSFLFMLGFLELGKAYSTDGLSETQRNMLQDLRDYGLVYQRKRKSRRFYPTRL 266
Query: 213 ALNMAT-------------RGTLKQIREPGFLIVETNFRVYAYTDSNLKVALIGLFCELM 259
A + + T + GF+IVETNFR+YAYT S L++A++ LF EL
Sbjct: 267 ATTLTSDSSALRTASSAMEAATSSEAASKGFIIVETNFRLYAYTSSPLQIAILALFVELK 326
Query: 260 YRFPNLTVGVLTRDSVRAALRSGITAAQIIGFLRLHALP 298
YRFPNL VG +TR+S+R AL +GITA QII +L HA P
Sbjct: 327 YRFPNLVVGQITRESIRNALENGITADQIISYLETHAHP 365
>gnl|CDD|227473 COG5144, TFB2, RNA polymerase II transcription
initiation/nucleotide excision repair factor TFIIH,
subunit TFB2 [Transcription / DNA replication,
recombination, and repair].
Length = 447
Score = 285 bits (731), Expect = 6e-93
Identities = 145/404 (35%), Positives = 201/404 (49%), Gaps = 32/404 (7%)
Query: 2 LSEIAKHYVIRLLFVEQPVPQAVIASWLSKTHAKEHKEATDTL----------------T 45
L E+A +V+ +LF V W+ +T +
Sbjct: 39 LPELATKFVMDMLFNSHSVSLLDEDEWIKETLKILLRIQVIGKKGNHIYLDEGLMIRLNP 98
Query: 46 ELRRNAKVALLGGGKPWSMSAKLEVDSKARDLDFLNQYALERWECILRFMVGSQQ----T 101
E + + AL GG S + + K +D L+ Y+ +WE IL FMVG+ +
Sbjct: 99 EFKISLMDALTGGTM--ENSFGVCIGEKLVSVDMLDSYSSRKWETILHFMVGTPEAKIPA 156
Query: 102 EGISADAVRTLFNEGAENPV-ITKDGFQFLLLETPAQVWYFILKYLETVESKGLDLVECL 160
EG+ N IT GFQFLL Q+W +L YL+ E +D V L
Sbjct: 157 EGVLELLKFGGLMGRDRNEFKITNRGFQFLLQTINEQLWTLLLLYLKYFEGSVMDEVAVL 216
Query: 161 TFLFQLKFSTFGTDYSTEGMSDKLQVFLQHLREFGLVYQRKRKAGRFYPTKLALNMATRG 220
FLF L GT Y + +SD Q+ L R +GLV Q FYPT LA+ +
Sbjct: 217 HFLFMLGALAVGTAYKIDALSDTQQIMLMDRRLYGLVEQLGILRKIFYPTGLAIGLTFDQ 276
Query: 221 TL---KQIRE---PGFLIVETNFRVYAYTDSNLKVALIGLFCELMYRFPNLTVGVLTRDS 274
+Q R GF+IVETN ++YAYT+S L++A+I LFC L RFPNL G++TR+S
Sbjct: 277 LFEASEQNRREDDKGFIIVETNNKIYAYTNSPLQIAVIHLFCNLTARFPNLVKGIITRES 336
Query: 275 VRAALRSGITAAQIIGFLRLHALP---SVSCPLPPVVSDQIRLWEGERERLTTSEGVLYS 331
+R AL +GITA QII +L HA P LPP + DQI LWE ER R+ G LYS
Sbjct: 337 IRRALDNGITAKQIIHYLETHAHPQMRKKLELLPPTIVDQIVLWELERNRIFMVPGYLYS 396
Query: 332 QFVSQADFEKLRDYAQDLGVLTWQNEKKRTVVVTKQGHSDIKKF 375
F++ +D++K+ +YA GVL W + KR + +GHS +K+F
Sbjct: 397 DFLTLSDYQKVLEYAIRGGVLVWSDVDKRMFFIKLEGHSLVKEF 440
>gnl|CDD|205803 pfam13625, Helicase_C_3, Helicase conserved C-terminal domain.
This domain family is found in a wide variety of
helicases and helicase-related proteins.
Length = 128
Score = 39.4 bits (93), Expect = 5e-04
Identities = 22/66 (33%), Positives = 30/66 (45%), Gaps = 4/66 (6%)
Query: 265 LTVGVLTRDSVRAALRSGITAAQIIGFLRLHALPSVSCPLPPVVSDQIRLWEGERERLTT 324
LT S+R AL +G+TA +II FL H+ P+P + IR RL
Sbjct: 36 AHTYRLTPLSLRRALDAGLTAEEIIEFLERHS----RTPVPQSLLYLIRDVARRHGRLRL 91
Query: 325 SEGVLY 330
+ LY
Sbjct: 92 GKAGLY 97
>gnl|CDD|177121 MTH00046, CYTB, cytochrome b; Validated.
Length = 355
Score = 33.4 bits (77), Expect = 0.19
Identities = 21/48 (43%), Positives = 26/48 (54%), Gaps = 9/48 (18%)
Query: 132 LETPAQV---WYFILKY--LETVESK--GLDLVECLTFLFQLKFSTFG 172
L TP + WYF+ Y L ++ SK GL LV L+FLF L TF
Sbjct: 254 LVTPVSIKPEWYFLAFYAMLRSINSKIGGLVLV--LSFLFFLWVPTFN 299
>gnl|CDD|225302 COG2469, COG2469, Uncharacterized conserved protein [Function
unknown].
Length = 284
Score = 30.9 bits (70), Expect = 1.1
Identities = 18/49 (36%), Positives = 26/49 (53%), Gaps = 1/49 (2%)
Query: 25 IASWLSKTHAKEHKEATDTLTELRRNAKVALLGGGKPWSMSAKLEVDSK 73
+ S+L KE KE +TL+E+ + VAL GG S+ L VD+
Sbjct: 196 LYSYLQNIKEKEIKEK-ETLSEIEKQILVALYSGGDSASLELFLGVDTD 243
>gnl|CDD|240010 cd04639, CBS_pair_26, The CBS domain, named after human CBS, is a
small domain originally identified in cystathionine
beta-synthase and is subsequently found in a wide range
of different proteins. CBS domains usually occur in
tandem repeats. They associate to form a so-called
Bateman domain or a CBS pair based on crystallographic
studies in bacteria. The CBS pair was used as a basis
for this cd hierarchy since the human CBS proteins can
adopt the typical core structure and form an
intramolecular CBS pair. The interface between the two
CBS domains forms a cleft that is a potential ligand
binding site. The CBS pair coexists with a variety of
other functional domains and this has been used to help
in its classification here. It has been proposed that
the CBS domain may play a regulatory role, although its
exact function is unknown. Mutations of conserved
residues within this domain are associated with a
variety of human hereditary diseases, including
congenital myotonia, idiopathic generalized epilepsy,
hypercalciuric nephrolithiasis, and classic Bartter
syndrome (CLC chloride channel family members),
Wolff-Parkinson-White syndrome (gamma 2 subunit of
AMP-activated protein kinase), retinitis pigmentosa (IMP
dehydrogenase-1), and homocystinuria (cystathionine
beta-synthase).
Length = 111
Score = 29.2 bits (66), Expect = 1.2
Identities = 19/63 (30%), Positives = 24/63 (38%), Gaps = 15/63 (23%)
Query: 267 VGVLTRDSVRAALRSGITAAQIIGFLR---------------LHALPSVSCPLPPVVSDQ 311
VG+LTRD + AL G A + G +R L + P PVV
Sbjct: 37 VGLLTRDDLIRALAEGGPDAPVRGVMRRDFPTVSPSATLDAVLRLMQQGGAPAVPVVDGS 96
Query: 312 IRL 314
RL
Sbjct: 97 GRL 99
>gnl|CDD|226766 COG4316, COG4316, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 138
Score = 28.0 bits (62), Expect = 4.1
Identities = 15/45 (33%), Positives = 23/45 (51%), Gaps = 4/45 (8%)
Query: 179 GMSDKLQVFLQHLREFGLVYQRKRKAGRFYPTKLALNMATRGTLK 223
G L+ F +H+ FG+V++ + G FY AL+M G L
Sbjct: 17 GTPKVLESFSKHIPRFGVVFEDDGETGYFY----ALDMRQDGILD 57
>gnl|CDD|233862 TIGR02424, TF_pcaQ, pca operon transcription factor PcaQ. Members
of this family are LysR-family transcription factors
associated with operons for catabolism of
protocatechuate. Members occur only in Proteobacteria
[Energy metabolism, Other, Regulatory functions, DNA
interactions].
Length = 300
Score = 28.5 bits (64), Expect = 5.2
Identities = 20/63 (31%), Positives = 29/63 (46%), Gaps = 7/63 (11%)
Query: 277 AALRSGITAAQIIGF-----LRLHALPSVSCPL-PPVVSDQIRLWEGERERLTTSE-GVL 329
AALR G+ + +G +R+ ALP+V+ L P VV + R R+ T L
Sbjct: 75 AALRQGVASLSQLGEGEGPTVRIGALPTVAARLMPEVVKRFLARAPRLRVRIMTGPNAYL 134
Query: 330 YSQ 332
Q
Sbjct: 135 LDQ 137
>gnl|CDD|145736 pfam02741, FTR_C, FTR, proximal lobe. The FTR
(Formylmethanofuran--tetrahydromethanopterin
formyltransferase) enzyme EC:2.3.1.101 is involved in
archaebacteria in the formation of methane from carbon
dioxide. C-terminal proximal lobe of alpha+beta
ferredoxin-like fold. SCOP reports fold duplication with
N-terminal distal lobe.
Length = 150
Score = 27.9 bits (63), Expect = 5.5
Identities = 10/28 (35%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 270 LTRDSVRAALRSGITAA-QIIGFLRLHA 296
L+ ++V A+R+GI AA + G +++ A
Sbjct: 106 LSEEAVAEAMRAGIEAACAVPGVVKISA 133
>gnl|CDD|180404 PRK06108, PRK06108, aspartate aminotransferase; Provisional.
Length = 382
Score = 28.4 bits (64), Expect = 7.0
Identities = 20/84 (23%), Positives = 26/84 (30%), Gaps = 26/84 (30%)
Query: 272 RDSVRAALRSGITAAQIIGFLRLHALPSVSCPLPPVVSDQIRLWEGERERLTTSEGVLYS 331
R + RA SGI G R + LW GE + T
Sbjct: 2 RPAARALPESGIREVANAGRGR---------------EGVLPLWFGESDLPT-------P 39
Query: 332 QFVSQADFEKLRD----YAQDLGV 351
F+ A L D Y +LG+
Sbjct: 40 DFIRDAAAAALADGETFYTHNLGI 63
>gnl|CDD|235256 PRK04210, PRK04210, phosphoenolpyruvate carboxykinase; Provisional.
Length = 601
Score = 28.3 bits (64), Expect = 8.1
Identities = 9/27 (33%), Positives = 16/27 (59%)
Query: 335 SQADFEKLRDYAQDLGVLTWQNEKKRT 361
S+ ++++LRD A + G N +KR
Sbjct: 35 SEEEYDRLRDQAVEAGTEIKLNPEKRP 61
>gnl|CDD|233617 TIGR01884, cas_HTH, CRISPR locus-related DNA-binding protein. Most
but not all examples of this family are associated with
CRISPR loci, a combination of DNA repeats and
characteristic proteins encoded near the repeat cluster.
The C-terminal region of this protein is homologous to
DNA-binding helix-turn-helix domains with predicted
transcriptional regulatory activity [Regulatory
functions, DNA interactions, Mobile and extrachromosomal
element functions, Other].
Length = 203
Score = 27.7 bits (62), Expect = 8.3
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 191 LREFGLVYQRKRKAGRFYPTKLA 213
L + GLV Q+ RK R+ TKL
Sbjct: 181 LEKKGLVEQKGRKGKRYSLTKLG 203
>gnl|CDD|215486 PLN02898, PLN02898, HMP-P kinase/thiamin-monophosphate
pyrophosphorylase.
Length = 502
Score = 28.2 bits (63), Expect = 9.0
Identities = 17/53 (32%), Positives = 22/53 (41%), Gaps = 16/53 (30%)
Query: 236 NFRVYAYTDSNLKVALIGLFCELMYRFPNLTVGVLTRDSVRAALRSGITAAQI 288
N +YA TDS + N G T D+VRAA+ G T Q+
Sbjct: 290 NLFLYAVTDSGM----------------NKKWGRSTVDAVRAAIEGGATIVQL 326
>gnl|CDD|227586 COG5261, IQG1, Protein involved in regulation of cellular
morphogenesis/cytokinesis [Cell division and chromosome
partitioning / Signal transduction mechanisms].
Length = 1054
Score = 28.3 bits (63), Expect = 9.3
Identities = 12/58 (20%), Positives = 20/58 (34%), Gaps = 1/58 (1%)
Query: 197 VYQRKRKAGRFYPTKL-ALNMATRGTLKQIREPGFLIVETNFRVYAYTDSNLKVALIG 253
V + K K+ K A + RG L I P + F + + N + +
Sbjct: 943 VVRDKPKSISSGTFKYSAQQLYKRGVLVNITIPEPNVSNIYFTFSSDSTDNFVIEVYQ 1000
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 0.136 0.401
Gapped
Lambda K H
0.267 0.0777 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 19,577,004
Number of extensions: 1893516
Number of successful extensions: 1759
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1745
Number of HSP's successfully gapped: 27
Length of query: 386
Length of database: 10,937,602
Length adjustment: 99
Effective length of query: 287
Effective length of database: 6,546,556
Effective search space: 1878861572
Effective search space used: 1878861572
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: 60 (26.8 bits)