RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14236
(290 letters)
>gnl|CDD|153423 cd07977, TFIIE_beta_winged_helix, TFIIE_beta_winged_helix domain,
located at the central core region of TFIIE beta, with
double-stranded DNA binding activity. Transcription
Factor IIE (TFIIE) beta winged-helix (or forkhead)
domain is located at the central core region of TFIIE
beta. The winged-helix is a form of helix-turn-helix
(HTH) domain which typically binds DNA with the 3rd
helix. The winged-helix domain is distinguished by the
presence of a C-terminal beta-strand hairpin unit (the
wing) that packs against the cleft of the tri-helical
core. Although most winged-helix domains are
multi-member families, TFIIE beta winged-helix domain is
typically found as a single orthologous group. TFIIE is
one of the six eukaryotic general transcription factors
(TFIIA, TFIIB, TFIID, TFIIE, TFIIF and TFIIH) that are
required for transcription initiation of protein-coding
genes. TFIIE is a heterotetramer consisting of two
copies each of alpha and beta subunits. TFIIE beta
contains several functional domains, an N-terminal
serine-rich region, a central core domain exhibiting a
winged-helix structure capable of binding
double-stranded DNA, a leucine repeat, a sigma3 region,
and a C-terminal domain containing two basic regions.
The assembly of transcription preinitiation complex
(PIC) includes the general transcription factors and RNA
polymerase II (pol II) initiated by the binding of the
TBP subunit of TFIID to the TATA box, followed by either
the sequential assembly of other general transcription
factors and pol II or a preassembled pol II holoenzyme
pathway. TFIIE interacts directly with TFIIF, TFIIB, pol
II, and promoter DNA. TFIIE recruits TFIIH and regulates
its activities. TFIIE and TFIIH are also important for
the transition from initiation to elongation.
Length = 75
Score = 95.4 bits (238), Expect = 3e-25
Identities = 42/80 (52%), Positives = 56/80 (70%), Gaps = 5/80 (6%)
Query: 66 SGSSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNN 125
+GS + F LAKIV +MK+RHQ HPLT+DEILD + LD+G K+K WL +EAL NN
Sbjct: 1 TGSGTHVFTQLAKIVDYMKKRHQ----HPLTLDEILDYLSLLDIGPKLKEWLKSEALVNN 56
Query: 126 PKIEVIEGNKYIFKPVFKIK 145
PKI+ +G + FKP + I+
Sbjct: 57 PKIDPKDG-TFSFKPKYNIR 75
>gnl|CDD|216922 pfam02186, TFIIE_beta, TFIIE beta subunit core domain. General
transcription factor TFIIE consists of two subunits,
TFIIE alpha pfam02002 and TFIIE beta. TFIIE beta has
been found to bind to the region where the promoter
starts to open to be single-stranded upon transcription
initiation by RNA polymerase II. The structure of the
DNA binding core region has been solved and has a winged
helix fold.
Length = 65
Score = 73.1 bits (180), Expect = 6e-17
Identities = 34/76 (44%), Positives = 48/76 (63%), Gaps = 12/76 (15%)
Query: 70 QYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIE 129
+ F VLAK V++MK+R DHPLT++EILD + LD+G V W L+NNPKI+
Sbjct: 1 SHLFTVLAKAVEYMKER-----DHPLTVEEILDYLS-LDIGPTVLPW-----LKNNPKIK 49
Query: 130 VI-EGNKYIFKPVFKI 144
+G + FKP++ I
Sbjct: 50 FDPKGGTFAFKPLYNI 65
>gnl|CDD|227501 COG5174, TFA2, Transcription initiation factor IIE, beta subunit
[Transcription].
Length = 285
Score = 68.1 bits (166), Expect = 3e-13
Identities = 62/294 (21%), Positives = 114/294 (38%), Gaps = 42/294 (14%)
Query: 12 FKKKALSTPTVEKRKAETSKDEPWKAKKAKTSSSSSSSLSSSLGSSNNMAYKSM------ 65
FK K S P + + + ++ SS+ S S A
Sbjct: 11 FKSKVKSAPVIAPAQKKRMASPCHFEVGLNSNDGHSSTAWSKGSSPTKKARIPRMDRDRI 70
Query: 66 ----SGSSQYKFGVLAKIVKHMKQRHQDGDDHPLTIDEILDETNQLDVGNKVKIWLSTEA 121
G ++ L ++++KQ D PL+ +EI D +D+ N
Sbjct: 71 QSIDRGVQRHTNSYLHAAIEYLKQH-----DRPLSFEEIKDYL-SIDLHNNY-----VLL 119
Query: 122 LQNNPKIEVIEGNK-YIFKPVFKIKDRKGLLKLLKQHDLKGIGGILLDDVRESLPHCEKA 180
L+ +I + + ++FKP++ I+ + LLK+L+ G+ + + + P+
Sbjct: 120 LKKKRRIRIDATHSTFMFKPLYSIRSVEDLLKVLR--SQGTEEGLSMKKLMDGWPNVVPF 177
Query: 181 LKHLSLQNEIIYVTRPADKRKVMF-YNDKSAQLDLDEDFQKLWRSISVDGMDNDKIKEYL 239
++ L NEI+ + D V+ N ++ + +D +F+ LW + +I Y
Sbjct: 178 VEELEKSNEILILRTDKDGSPVVVWNNTQNLECPVDPEFKSLWNQV--------RIPTYH 229
Query: 240 EKQGIRPIQDHGFKK-PVLPGRKKNMNRKKQFKKPRD------NEHLADVLENY 286
+ IR + G K V P KK K + KK N H+ +L +Y
Sbjct: 230 DL--IRELNTAGLKPTSVDPNTKKRPTIKIKKKKRSRRKGKITNTHVKGILLDY 281
>gnl|CDD|233412 TIGR01438, TGR, thioredoxin and glutathione reductase
selenoprotein. This homodimeric, FAD-containing member
of the pyridine nucleotide disulfide oxidoreductase
family contains a C-terminal motif Cys-SeCys-Gly, where
SeCys is selenocysteine encoded by TGA (in some sequence
reports interpreted as a stop codon). In some members of
this subfamily, Cys-SeCys-Gly is replaced by
Cys-Cys-Gly. The reach of the selenium atom at the
C-term arm of the protein is proposed to allow broad
substrate specificity.
Length = 484
Score = 32.9 bits (75), Expect = 0.21
Identities = 15/58 (25%), Positives = 29/58 (50%), Gaps = 9/58 (15%)
Query: 214 LDEDFQKLWRSISVDGMDND---KIKEYLEKQGIRPIQDHGFKKPVLPGRKKNMNRKK 268
+ D + RSI + G D D K+ E++E+ G++ FK+ +P + + + K
Sbjct: 202 IGLDVTVMVRSILLRGFDQDCANKVGEHMEEHGVK------FKRQFVPIKVEQIEAKV 253
>gnl|CDD|219500 pfam07655, Secretin_N_2, Secretin N-terminal domain. This is a
short domain found in bacterial type II/III secretory
system proteins. The architecture of these proteins
suggest that this family may be functionally analogous
to pfam03958.
Length = 95
Score = 29.6 bits (67), Expect = 0.56
Identities = 13/28 (46%), Positives = 17/28 (60%)
Query: 42 TSSSSSSSLSSSLGSSNNMAYKSMSGSS 69
+SS S+SS SSS S+ + S SG S
Sbjct: 27 SSSGSNSSSSSSNSSNGGSSSSSSSGDS 54
>gnl|CDD|222332 pfam13708, Methyltransf_27, Methyltransferase domain. This family
contains methyltransferase domains.
Length = 194
Score = 30.7 bits (70), Expect = 0.68
Identities = 23/95 (24%), Positives = 38/95 (40%), Gaps = 19/95 (20%)
Query: 61 AYKSMSGSSQYKFGVLAK-IVKHMKQRHQDGDD--HPLTIDEI---------LDETNQLD 108
YK+ +S FG K I++++ + G + D++ LD D
Sbjct: 78 DYKT---NSPCGFGK--KIIIENLVPSDRWGYSLNYGWRRDKLDDLERILALLDGKPVPD 132
Query: 109 VGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPVFK 143
N + L E ++ NPK V EG + + FK
Sbjct: 133 HRNSASLRLH-EHIRANPKWIVFEGEYFRVR-YFK 165
>gnl|CDD|185416 PTZ00052, PTZ00052, thioredoxin reductase; Provisional.
Length = 499
Score = 30.6 bits (69), Expect = 1.1
Identities = 15/48 (31%), Positives = 25/48 (52%), Gaps = 9/48 (18%)
Query: 223 RSISVDGMDN---DKIKEYLEKQGIRPIQDHGFKKPVLPGRKKNMNRK 267
RSI + G D +K+ EY+++QG F + V+P + M+ K
Sbjct: 213 RSIPLRGFDRQCSEKVVEYMKEQGTL------FLEGVVPINIEKMDDK 254
>gnl|CDD|235277 PRK04309, PRK04309, DNA-directed RNA polymerase subunit A'';
Validated.
Length = 383
Score = 29.0 bits (66), Expect = 3.0
Identities = 19/50 (38%), Positives = 25/50 (50%), Gaps = 6/50 (12%)
Query: 120 EALQNNPKIEV-IEGNKYIFKPVFKIKDRKGLLKL---LKQHDLKGIGGI 165
EA++ EV IEGN I P K + L KL ++ +KGI GI
Sbjct: 178 EAIEKKKGGEVEIEGNTLIISP--KEPSYRELRKLAEKIRNIKIKGIKGI 225
>gnl|CDD|221126 pfam11518, DUF3221, Protein of unknown function (DUF3221). This
family of proteins with unknown function appears to be
restricted to Bacillus. Some members in this family of
proteins are annotated as YobA however this cannot be
confirmed. YobA is a protein with unknown function.
Length = 99
Score = 27.0 bits (60), Expect = 4.6
Identities = 15/37 (40%), Positives = 22/37 (59%), Gaps = 7/37 (18%)
Query: 101 LDETNQLDVGNKVKIWLSTEALQNNP------KIEVI 131
LD +QL VG K+K+W ++ L++ P K EVI
Sbjct: 64 LDNYDQLKVGQKIKVW-YSQLLESYPAKMIVEKFEVI 99
>gnl|CDD|200387 TIGR04136, rSAM_FibroRumin, radical SAM peptide maturase,
FibroRumin system. Members of this protein family are
radical SAM enzymes proposed to act on small, Cys-rich
peptides encoded by tandem gene pairs. Members occur in
enzymes Fibrobacter succinogenes subsp. succinogenes S85
(genes for their target peptides missed) and in
Ruminococcus albus 8. This enzyme family is similar in
sequence to the SCIFF (Six Cysteines in Forty-Five)
system maturase (TIGR03974).
Length = 458
Score = 28.0 bits (62), Expect = 6.0
Identities = 25/100 (25%), Positives = 43/100 (43%), Gaps = 29/100 (29%)
Query: 144 IKDRKGLLKLLKQHDLKGIG-GILLDDVRESLPHCEKALKHLSLQNEIIYVTRPADKRKV 202
IKD++ ++ L+ ++ +KG+G I++ D R LP
Sbjct: 268 IKDQQDVIDLIDEYGIKGLGFNIMMGDDRFPLPAD------------------------- 302
Query: 203 MFYNDKSAQLDLDEDFQKLWRSISVDGMDNDKIKEYLEKQ 242
YNDK+AQ +DE + I D + K+K + + Q
Sbjct: 303 --YNDKAAQFIIDEFKELREIGIYEDRIMR-KLKAFAKAQ 339
>gnl|CDD|216824 pfam01978, TrmB, Sugar-specific transcriptional regulator TrmB.
One member of this family, TrmB, has been shown to be a
sugar-specific transcriptional regulator of the
trehalose/maltose ABC transporter in Thermococcus
litoralis.
Length = 68
Score = 25.6 bits (57), Expect = 9.2
Identities = 12/48 (25%), Positives = 22/48 (45%), Gaps = 4/48 (8%)
Query: 94 PLTIDEILDETNQLDVGNKVKIWLSTEALQNNPKIEVIEGNKYIFKPV 141
P T DEI +E V + K++ +L+ +E +G ++ V
Sbjct: 22 PATADEIAEE---SGVP-RSKVYEVLRSLEKKGLVEREKGRPKKYRAV 65
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
0.313 0.131 0.369
Gapped
Lambda K H
0.267 0.0588 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 14,594,305
Number of extensions: 1382443
Number of successful extensions: 1533
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1511
Number of HSP's successfully gapped: 40
Length of query: 290
Length of database: 10,937,602
Length adjustment: 96
Effective length of query: 194
Effective length of database: 6,679,618
Effective search space: 1295845892
Effective search space used: 1295845892
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 58 (26.4 bits)