RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11263
(80 letters)
>gnl|CDD|217392 pfam03153, TFIIA, Transcription factor IIA, alpha/beta subunit.
Transcription initiation factor IIA (TFIIA) is a
heterotrimer, the three subunits being known as alpha,
beta, and gamma, in order of molecular weight. The N and
C-terminal domains of the gamma subunit are represented
in pfam02268 and pfam02751, respectively. This family
represents the precursor that yields both the alpha and
beta subunits. The TFIIA heterotrimer is an essential
general transcription initiation factor for the
expression of genes transcribed by RNA polymerase II.
Together with TFIID, TFIIA binds to the promoter region;
this is the first step in the formation of a
pre-initiation complex (PIC). Binding of the rest of the
transcription machinery follows this step. After
initiation, the PIC does not completely dissociate from
the promoter. Some components, including TFIIA, remain
attached and re-initiate a subsequent round of
transcription.
Length = 332
Score = 132 bits (334), Expect = 1e-39
Identities = 43/68 (63%), Positives = 55/68 (80%), Gaps = 1/68 (1%)
Query: 14 IEDEPLNSSDDVSEED-PALFDTDNIVVCQYDKITRSRNKWKFYLKDGIMNLNGKDFVFL 72
IE + +S DDVS+ED LFDTDN+++CQYDK+ RS+NKWK LKDGIM +NGKD+VF
Sbjct: 265 IESDLDDSDDDVSDEDGEDLFDTDNVMLCQYDKVQRSKNKWKCTLKDGIMTINGKDYVFQ 324
Query: 73 KANGDADW 80
KA G+A+W
Sbjct: 325 KATGEAEW 332
>gnl|CDD|199899 cd07976, TFIIA_alpha_beta_like, Precursor of TFIIA alpha and beta
subunits and similar proteins. Transcription factor II
A (TFIIA) is one of the general transcription factors
for RNA polymerase II. TFIIA increases the affinity of
TATA-binding protein (TBP) for DNA in order to assemble
the initiation complex. TFIIA also functions as an
activator during development and differentiation, and is
involved in transcription from TATA-less promoters.
TFIIA is composed of more than one subunit in various
organisms. Mammalian TFIIA large subunits (TFIIA alpha
and beta) and the smaller subunit (TFIIA gamma) form a
heterotrimer. TFIIA alpha and beta are encoded by a
single gene (TFIIA_alpha_beta), its protein product is
post-translationally processed and cleaved. TOA1 and
TOA2 are the two subunits of Yeast TFIIA which
correspond to Mammalian TFIIA_alpha_beta and TFIIA
gamma, respectively. TOA1 and TOA2 form a heterodimeric
protein complex. TFIIA_alpha_beta alone is sufficient
for transcription in early embryogenesis, but the
cleaved forms, TFIIA alpha and TFIIA beta, represent the
vast majority of TFIIA in most differentiated cells. The
exact functional differences between cleaved and
uncleaved forms are not yet clear. This model also
contains paralogs of the canonical TFIIA_alpha_beta,
such as the human ALF, which may be involved in
gametogenesis and early embryogenesis (and is also
subject to proteolytic cleavage).
Length = 102
Score = 101 bits (255), Expect = 4e-30
Identities = 35/62 (56%), Positives = 44/62 (70%)
Query: 19 LNSSDDVSEEDPALFDTDNIVVCQYDKITRSRNKWKFYLKDGIMNLNGKDFVFLKANGDA 78
L+ S S +T+NIV+CQYDK+TR +NKWK LKDGIM LNGKD+VF KA G+
Sbjct: 41 LSQSGAASFPWDPKPETENIVLCQYDKVTRVKNKWKCTLKDGIMTLNGKDYVFQKATGEF 100
Query: 79 DW 80
+W
Sbjct: 101 EW 102
>gnl|CDD|227478 COG5149, TOA1, Transcription initiation factor IIA, large chain
[Transcription].
Length = 293
Score = 64.7 bits (157), Expect = 3e-14
Identities = 27/71 (38%), Positives = 40/71 (56%), Gaps = 6/71 (8%)
Query: 16 DEPLNS---SDDVSEEDPALFDTD---NIVVCQYDKITRSRNKWKFYLKDGIMNLNGKDF 69
DE + S DV D + T N ++C YDK+ S+ KWK KDG++++N D+
Sbjct: 222 DEGMFSDLDDSDVDSGDSEIEGTKGSTNCMLCLYDKVNMSKGKWKCTFKDGVVSINNIDY 281
Query: 70 VFLKANGDADW 80
VF KA G+ +W
Sbjct: 282 VFNKAQGELEW 292
>gnl|CDD|227346 COG5013, NarG, Nitrate reductase alpha subunit [Energy production
and conversion].
Length = 1227
Score = 28.9 bits (65), Expect = 0.19
Identities = 10/29 (34%), Positives = 17/29 (58%), Gaps = 8/29 (27%)
Query: 42 QYDKITRSRN--------KWKFYLKDGIM 62
Q+DK+ RS + WK Y+K+G++
Sbjct: 42 QHDKVVRSTHGVNCTGSCSWKIYVKNGLI 70
>gnl|CDD|162434 TIGR01580, narG, respiratory nitrate reductase, alpha subunit.
The Nitrate reductase enzyme complex allows bacteria to
use nitrate as an electron acceptor during anaerobic
growth. The enzyme complex consists of a tetramer that
has an alpha, beta and 2 gamma subunits. The alpha and
beta subunits have catalytic activity and the gamma
subunits attach the enzyme to the membrane and is a
b-type cytochrome that receives electrons from the
quinone pool and transfers them to the beta subunit.
This model is specific for the alpha subunit for
nitrate reductase I (narG) and nitrate reductase II
(narZ) for gram positive and gram negative bacteria.A
few thermophiles and archaea also match the model The
seed members used to make the model include Nitrate
reductases from Pseudomonas fluorescens (GP:11344601),
E.coli and B.subtilis. All seed members are
experimentally characterized. Some unpublished nitrate
reductases, that are shorter sequences, and probably
fragments fall in between the noise and trusted
cutoffs. Pfam models pfam00384 (Molybdopterin
oxidoreductase) and pfam01568(Molydopterin dinucleotide
binding domain) will also match the nitrate reductase,
alpha subunit [Energy metabolism, Anaerobic].
Length = 1235
Score = 28.0 bits (62), Expect = 0.41
Identities = 12/34 (35%), Positives = 18/34 (52%), Gaps = 8/34 (23%)
Query: 42 QYDKITRSRN--------KWKFYLKDGIMNLNGK 67
QYDKI RS + WK Y+K+G++ +
Sbjct: 40 QYDKIVRSTHGVNCTGSCSWKIYVKNGLVTWETQ 73
>gnl|CDD|145678 pfam02650, HTH_WhiA, Sporulation Regulator WhiA C terminal
domain. This domain is found at the C terminal of the
sporulation regulator WhiA. It is predicted to form a
DNA binding helix-turn-helix structure. WhiA is a
distant homologue of LAGLIDADG homing endonucleases.
Length = 191
Score = 27.2 bits (61), Expect = 0.77
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 45 KITRSRNKWKFYLKDG 60
KI RNK+ YLKD
Sbjct: 60 KIIERRNKYVVYLKDA 75
>gnl|CDD|222477 pfam13965, SID-1_RNA_chan, dsRNA-gated channel SID-1. This is a
family of proteins that are transmembrane dsRNA-gated
channels. They passively transport dsRNA into cells and
do not act as ATP-dependent pumps. They are required for
systemic RNA interference.
Length = 567
Score = 25.4 bits (56), Expect = 3.3
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 13 GIEDEPLNSSDDVSEEDPALFDTDNIVVCQYDKITRSR 50
E ++ D SEED + + D ++ Q + R +
Sbjct: 159 PSEQRAMDLQPDQSEEDSSERENDILMADQQIMVIREK 196
>gnl|CDD|224116 COG1195, RecF, Recombinational DNA repair ATPase (RecF pathway)
[DNA replication, recombination, and repair].
Length = 363
Score = 25.3 bits (56), Expect = 3.5
Identities = 6/24 (25%), Positives = 10/24 (41%), Gaps = 3/24 (12%)
Query: 42 QYDKITRSRNKWKFYLKDGIMNLN 65
Y+K+ + RN LK +
Sbjct: 153 NYEKLLKQRNA---LLKQLQGDYA 173
>gnl|CDD|225659 COG3117, COG3117, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 188
Score = 24.7 bits (54), Expect = 5.4
Identities = 11/47 (23%), Positives = 14/47 (29%), Gaps = 8/47 (17%)
Query: 21 SSDDVSEEDPALFDTDNIVVCQYDKITRSRNKWKFYLKDGIMNLNGK 67
+ D EDP V + + N LK NL K
Sbjct: 139 KTQDAQTEDP--------VTLYGGQFVSTANGMTGNLKTQQANLLSK 177
>gnl|CDD|217247 pfam02836, Glyco_hydro_2_C, Glycosyl hydrolases family 2, TIM
barrel domain. This family contains
beta-galactosidase, beta-mannosidase and
beta-glucuronidase activities.
Length = 297
Score = 24.7 bits (54), Expect = 5.4
Identities = 8/15 (53%), Positives = 10/15 (66%)
Query: 57 LKDGIMNLNGKDFVF 71
+KDG+ LNGK F
Sbjct: 3 VKDGLFLLNGKPLYF 17
>gnl|CDD|111058 pfam02121, IP_trans, Phosphatidylinositol transfer protein. Along
with the structurally unrelated Sec14p family (found in
pfam00650), this family can bind/exchange one molecule
of phosphatidylinositol (PI) or phosphatidylcholine (PC)
and thus aids their transfer between different membrane
compartments. There are three sub-families - all share
an N-terminal PITP-like domain, whose sequence is highly
conserved. It is described as consisting of three
regions. The N-terminal region is thought to bind the
lipid and contains two helices and an eight-stranded,
mostly antiparallel beta-sheet. An intervening loop
region, which is thought to play a role in
protein-protein interactions, separates this from the
C-terminal region, which exhibits the greatest sequence
variation and may be involved in membrane binding. PITP
alpha has a 16-fold greater affinity for PI than PC.
Together with PITP beta, it is expressed ubiquitously in
all tissues.
Length = 254
Score = 24.4 bits (53), Expect = 6.8
Identities = 9/27 (33%), Positives = 14/27 (51%)
Query: 10 VVCGIEDEPLNSSDDVSEEDPALFDTD 36
I + ++S D +EEDP LF +
Sbjct: 139 DYIDIVRDQVSSGDYKAEEDPKLFHSV 165
>gnl|CDD|131247 TIGR02192, HtrL_YibB, protein YibB. The protein from this rare,
uncharacterized protein family is designated HtrL or
YibB in E. coli, where its gene is found in a region of
LPS core biosynthesis genes. Homologs are found in
Shigella flexneri, Campylobacter jejuni, and
Caenorhabditis elegans only. The htrL gene may represent
an insertion to the LPS core biosynthesis region, rather
than an LPS biosynthetic protein [Hypothetical proteins,
Conserved].
Length = 270
Score = 24.5 bits (53), Expect = 7.8
Identities = 9/38 (23%), Positives = 18/38 (47%), Gaps = 5/38 (13%)
Query: 32 LFDTDNIV-----VCQYDKITRSRNKWKFYLKDGIMNL 64
LF++++ V + KW+F L +G ++L
Sbjct: 131 LFNSEHFVWLDFGYGHAENHFPYSYKWQFALPEGKISL 168
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
0.318 0.138 0.424
Gapped
Lambda K H
0.267 0.0690 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,140,970
Number of extensions: 326159
Number of successful extensions: 240
Number of sequences better than 10.0: 1
Number of HSP's gapped: 237
Number of HSP's successfully gapped: 14
Length of query: 80
Length of database: 10,937,602
Length adjustment: 49
Effective length of query: 31
Effective length of database: 8,764,256
Effective search space: 271691936
Effective search space used: 271691936
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 (21.7 bits)
S2: 53 (24.3 bits)