RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7895
(108 letters)
>gnl|CDD|227452 COG5123, TOA2, Transcription initiation factor IIA, gamma subunit
[Transcription].
Length = 113
Score = 99.3 bits (247), Expect = 2e-28
Identities = 51/109 (46%), Positives = 66/109 (60%), Gaps = 8/109 (7%)
Query: 3 YQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALPSKVKSRLTFKSGK 62
Y+LYR + +G L+++LDELI G I+P LAM VL FDKS+ L V S LTFK GK
Sbjct: 5 YELYRRSMIGKVLEDALDELISAGVISPNLAMHVLETFDKSVPEVLNKSVTSSLTFK-GK 63
Query: 63 LNTYRFCDNVWTFVLT------DVEFREVAEIA-RVNKLKIVACDGKSS 104
L+TY FCD VWTF+ + E+ E+ K +IVAC G+ S
Sbjct: 64 LDTYNFCDGVWTFITKNFVMSLNNEYFNAGEVNIVACKARIVACAGRRS 112
>gnl|CDD|145428 pfam02268, TFIIA_gamma_N, Transcription initiation factor IIA,
gamma subunit, helical domain. Accurate transcription
in vivo requires at least six general transcription
initiation factors, in addition to RNA polymerase II.
Transcription initiation factor IIA (TFIIA) is a
multimeric protein which facilitates the binding of
TFIID to the TATA box. The N-terminal domain of the
gamma subunit is a 4 helix bundle.
Length = 49
Score = 86.9 bits (216), Expect = 2e-24
Identities = 34/49 (69%), Positives = 38/49 (77%)
Query: 1 MSYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALP 49
M Y+LYR +TLG L ++LDELI G ITP LAMKVLLQFDKSIN AL
Sbjct: 1 MYYELYRRSTLGMALTDALDELISDGRITPQLAMKVLLQFDKSINEALA 49
>gnl|CDD|199901 cd10145, TFIIA_gamma_N, Gamma subunit of transcription initiation
factor IIA, N-terminal helical domain. Transcription
factor II A (TFIIA) is one of the general transcription
factors for RNA polymerase II. TFIIA increases the
affinity of the 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 TFIIA_alpha_beta gene
and 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. The TFIIA gamma subunit is highly
conserved between humans, Drosophila and yeast and it
is required for TFIIA function. The N-terminal domain
of the gamma subunit forms a 4-helix bundle together
with the alpha subunit.
Length = 49
Score = 85.7 bits (213), Expect = 6e-24
Identities = 37/48 (77%), Positives = 40/48 (83%)
Query: 2 SYQLYRNTTLGNTLQESLDELIQYGTITPTLAMKVLLQFDKSINGALP 49
Y+LYRNTTLG LQ++LDELIQ G ITP LAMKVLLQFDKSIN AL
Sbjct: 1 YYELYRNTTLGIALQDALDELIQDGQITPQLAMKVLLQFDKSINEALA 48
>gnl|CDD|190407 pfam02751, TFIIA_gamma_C, Transcription initiation factor IIA,
gamma subunit. Accurate transcription in vivo requires
at least six general transcription initiation factors,
in addition to RNA polymerase II. Transcription
initiation factor IIA (TFIIA) is a multimeric protein
which facilitates the binding of TFIID to the TATA box.
The C-terminal domain of the gamma subunit is a 12
stranded beta-barrel.
Length = 51
Score = 82.3 bits (204), Expect = 1e-22
Identities = 31/52 (59%), Positives = 40/52 (76%), Gaps = 2/52 (3%)
Query: 51 KVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEFRE-VAEIARVNKLKIVACDG 101
KVKS+LTFK G L+TYRFCDNVWTF++ + +F+ E V+K+KIVACD
Sbjct: 1 KVKSKLTFK-GHLDTYRFCDNVWTFIVKNAQFKLDDQETVTVDKVKIVACDS 51
>gnl|CDD|199900 cd10014, TFIIA_gamma_C, Gamma subunit of transcription initiation
factor IIA, C-terminal domain. Transcription factor II
A (TFIIA) is one of the general transcription factors
for RNA polymerase II. TFIIA increases the affinity of
the 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 TFIIA_alpha_beta gene and 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. The TFIIA
gamma subunit is highly conserved between humans,
Drosophila and yeast and it is required for TFIIA
function. The C-terminal domain of the gamma
(TFIIA_gamma_C) subunit forms a beta-barrel structure
together with TFIIA beta.
Length = 47
Score = 78.8 bits (195), Expect = 3e-21
Identities = 34/48 (70%), Positives = 39/48 (81%), Gaps = 2/48 (4%)
Query: 56 LTFKSGKLNTYRFCDNVWTFVLTDVEFREV-AEIARVNKLKIVACDGK 102
LTFK G L TYRFCDNVWTF+L DVEF+E E+ V+K+KIVACDGK
Sbjct: 1 LTFK-GHLKTYRFCDNVWTFILNDVEFKESNTEVVTVDKVKIVACDGK 47
>gnl|CDD|130941 TIGR01886, dipeptidase, dipeptidase PepV. This model represents a
small clade of dipeptidase enzymes which are members of
the larger M25 subfamily of metalloproteases. Two
characterized enzymes are included in the seed. One,
from Lactococcus lactis has been shown to act on a wide
range of dipeptides, but not larger peptides. The enzyme
from Lactobacillus delbrueckii was originally
characterized as a Xaa-His dipeptidase, specifically a
carnosinase (beta-Ala-His) by complementation of an E.
coli mutant. Further study, including the
crystallization of the enzyme , has shown it to also be
a non-specific dipeptidase. This group also includes
enzymes from Streptococcus and Enterococcus [Protein
fate, Degradation of proteins, peptides, and
glycopeptides].
Length = 466
Score = 27.5 bits (61), Expect = 1.4
Identities = 12/41 (29%), Positives = 16/41 (39%)
Query: 42 KSINGALPSKVKSRLTFKSGKLNTYRFCDNVWTFVLTDVEF 82
K +GA P + TF + LN Y F F+ E
Sbjct: 264 KGAHGAAPQVGINSATFLALFLNQYAFAGGAKNFIHFLAEV 304
>gnl|CDD|200384 TIGR04133, rSAM_w_lipo, radical SAM enzyme, rSAM/lipoprotein
system. Members of this protein family are radical SAM
enzymes with an additional 4Fe4S cluster-binding
C-terminal domain (TIGR04085) shared with PqqE and many
other peptide and protein-modifying radical SAM enzymes.
All members occur in the context of a predicted
lipoprotein that usually is encoded by an adjacent gene.
Length = 350
Score = 27.4 bits (61), Expect = 1.7
Identities = 11/33 (33%), Positives = 15/33 (45%), Gaps = 5/33 (15%)
Query: 74 TFVLTDVEFREVAE-IARVNKLKIV----ACDG 101
LTD EFR+V + I K + C+G
Sbjct: 213 ELQLTDEEFRQVLDFIRDTRKEGRINLSYGCEG 245
>gnl|CDD|150923 pfam10327, 7TM_GPCR_Sri, Serpentine type 7TM GPCR chemoreceptor
Sri. Chemoreception is mediated in Caenorhabditis
elegans by members of the seven-transmembrane
G-protein-coupled receptor class (7TM GPCRs) of
proteins which are of the serpentine type. Sri is part
of the Str superfamily of chemoreceptors.
Chemoperception is one of the central senses of soil
nematodes like C. elegans which are otherwise 'blind'
and 'deaf'.
Length = 303
Score = 26.4 bits (59), Expect = 3.2
Identities = 6/14 (42%), Positives = 11/14 (78%)
Query: 56 LTFKSGKLNTYRFC 69
+ FKSGK++ +R+
Sbjct: 33 IIFKSGKIDNFRYY 46
>gnl|CDD|178283 PLN02679, PLN02679, hydrolase, alpha/beta fold family protein.
Length = 360
Score = 26.0 bits (57), Expect = 5.2
Identities = 13/46 (28%), Positives = 21/46 (45%), Gaps = 5/46 (10%)
Query: 32 LAMKVLLQFD-----KSINGALPSKVKSRLTFKSGKLNTYRFCDNV 72
L + +L D + I AL ++VK R K+ L+ Y + V
Sbjct: 206 LLLPLLWLIDFLLKQRGIASALFNRVKQRDNLKNILLSVYGNKEAV 251
>gnl|CDD|215341 PLN02635, PLN02635, disproportionating enzyme.
Length = 538
Score = 25.9 bits (57), Expect = 6.1
Identities = 18/58 (31%), Positives = 25/58 (43%), Gaps = 6/58 (10%)
Query: 12 GNTLQESLDELIQYGTIT------PTLAMKVLLQFDKSINGALPSKVKSRLTFKSGKL 63
GNTL SL+EL++ G + P KV + L +K RL G+L
Sbjct: 94 GNTLLISLEELVKDGLLEEDELPEPVPVGKVDFSAVAELKDPLIAKAAERLLLSDGEL 151
>gnl|CDD|216255 pfam01031, Dynamin_M, Dynamin central region. This region lies
between the GTPase domain, see pfam00350, and the
pleckstrin homology (PH) domain, see pfam00169.
Length = 296
Score = 25.6 bits (57), Expect = 6.8
Identities = 11/42 (26%), Positives = 16/42 (38%), Gaps = 7/42 (16%)
Query: 14 TLQESLDELIQYGTITPTLA---MKVLLQ----FDKSINGAL 48
LQE+ EL +YG P LL F++ +
Sbjct: 88 KLQETEKELERYGDDPPEDPAEKGAFLLDLITAFNQDFKNLI 129
>gnl|CDD|236095 PRK07777, PRK07777, aminotransferase; Validated.
Length = 387
Score = 25.4 bits (56), Expect = 7.4
Identities = 8/22 (36%), Positives = 13/22 (59%)
Query: 76 VLTDVEFREVAEIARVNKLKIV 97
VLT E +AE+A + L ++
Sbjct: 175 VLTAAELAAIAELAVEHDLLVI 196
>gnl|CDD|200328 TIGR03819, heli_sec_ATPase, helicase/secretion neighborhood ATPase.
Members of this protein family comprise a distinct
clade of putative ATPase associated with an integral
membrane complex likely to act in pilus formation,
secretion, or conjugal transfer. The association of most
members with a nearby gene for a DEAH-box helicase
suggests a role in conjugal transfer.
Length = 340
Score = 25.4 bits (56), Expect = 7.5
Identities = 9/16 (56%), Positives = 12/16 (75%)
Query: 18 SLDELIQYGTITPTLA 33
+LDEL+ GTI P +A
Sbjct: 153 TLDELVAAGTIPPGVA 168
>gnl|CDD|213656 TIGR01838, PHA_synth_I, poly(R)-hydroxyalkanoic acid synthase,
class I. This model represents the class I subfamily of
poly(R)-hydroxyalkanoate synthases, which polymerizes
hydroxyacyl-CoAs with three to five carbons in the
hydroxyacyl backbone into aliphatic esters termed
poly(R)-hydroxyalkanoic acids. These polymers accumulate
as carbon and energy storage inclusions in many species
and can amount to 90 percent of the dry weight of cell
[Fatty acid and phospholipid metabolism, Biosynthesis].
Length = 532
Score = 25.0 bits (55), Expect = 9.5
Identities = 17/47 (36%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 2 SYQLYRN--TTLGNTLQES-LDELIQYGTITPTLAMKVLLQFDKSIN 45
++++ RN TT G + E+ L +LIQY T T+ LL IN
Sbjct: 153 AFEVGRNLATTPGAVVFENELFQLIQYEPTTETVHKTPLLIVPPWIN 199
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
0.319 0.133 0.378
Gapped
Lambda K H
0.267 0.0564 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,218,490
Number of extensions: 420060
Number of successful extensions: 375
Number of sequences better than 10.0: 1
Number of HSP's gapped: 370
Number of HSP's successfully gapped: 19
Length of query: 108
Length of database: 10,937,602
Length adjustment: 73
Effective length of query: 35
Effective length of database: 7,699,760
Effective search space: 269491600
Effective search space used: 269491600
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: 53 (24.6 bits)