RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy1283
(123 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 = 79.0 bits (195), Expect = 1e-18
Identities = 26/39 (66%), Positives = 35/39 (89%)
Query: 11 KLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKL 49
K+Y++VI DVIN+V+E F++EGVDEQVLQ+LK +WE KL
Sbjct: 1 KVYESVIEDVINDVREDFEDEGVDEQVLQDLKKLWEKKL 39
>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 = 74.1 bits (183), Expect = 1e-18
Identities = 27/41 (65%), Positives = 34/41 (82%)
Query: 9 TMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKL 49
K+Y++VI DVINNV+E F++EGVDE VLQELK +WE KL
Sbjct: 1 VSKVYESVIEDVINNVREDFEDEGVDESVLQELKQLWEEKL 41
>gnl|CDD|227478 COG5149, TOA1, Transcription initiation factor IIA, large chain
[Transcription].
Length = 293
Score = 57.4 bits (138), Expect = 7e-11
Identities = 26/93 (27%), Positives = 43/93 (46%), Gaps = 6/93 (6%)
Query: 7 SLTMKLYQAVIADVINNVKEAFQEEGVDEQVLQELKHIWEAKLFGIGVGKLSKRKEWMSK 66
S+ ++Y VI DVI N + F+E GVD+ L+EL+++W++KL V W ++
Sbjct: 4 SIVGEVYHHVILDVIANSRSDFEENGVDDATLRELQNLWQSKLVATDVATFP----W-AQ 58
Query: 67 CYRSSNISG-RPSLSGNLKARLVYQPCLTQPVE 98
+ + G R + P L Q
Sbjct: 59 AFPIGQLFGLRTDSLDVTAPAVANSPILNQSAT 91
>gnl|CDD|145649 pfam02610, Arabinose_Isome, L-arabinose isomerase. This is a
family of L-arabinose isomerases, AraA, EC:5.3.1.4.
These enzymes catalyze the reaction: L-arabinose <=>
L-ribulose. This reaction is the first step in the
pathway of L-arabinose utilisation as a carbon source
after entering the cell L-arabinose is converted into
L-ribulose by the L-arabinose isomerases enzyme.
Length = 359
Score = 27.6 bits (62), Expect = 1.5
Identities = 14/60 (23%), Positives = 26/60 (43%), Gaps = 23/60 (38%)
Query: 80 SGNLKARLVYQPCLTQPVELLSIC-AADHE----------------------LQAIRKPL 116
SG L ++V +P +T P E+ ++C A+++ L ++KPL
Sbjct: 41 SGKLPVKIVLKPVVTTPDEITALCREANYDENCAGVITWMHTFSPAKMWIRGLSELQKPL 100
>gnl|CDD|179503 PRK02929, PRK02929, L-arabinose isomerase; Provisional.
Length = 499
Score = 27.5 bits (62), Expect = 1.7
Identities = 16/60 (26%), Positives = 27/60 (45%), Gaps = 23/60 (38%)
Query: 80 SGNLKARLVYQPCLTQPVELLSIC-AADHE----------------------LQAIRKPL 116
SG L ++V +P LT P E+ ++C A+++ L A++KPL
Sbjct: 41 SGKLPVKIVLKPVLTTPDEITAVCREANYDDNCAGVITWMHTFSPAKMWIRGLSALQKPL 100
>gnl|CDD|224165 COG1244, COG1244, Predicted Fe-S oxidoreductase [General function
prediction only].
Length = 358
Score = 27.7 bits (62), Expect = 1.7
Identities = 13/38 (34%), Positives = 21/38 (55%), Gaps = 3/38 (7%)
Query: 21 INNVKEAFQE---EGVDEQVLQELKHIWEAKLFGIGVG 55
+NVKE E E + E+ L+E+ I E K+ + +G
Sbjct: 133 NDNVKEVVVESRPEFIREERLEEITEILEGKIVEVAIG 170
>gnl|CDD|223394 COG0317, SpoT, Guanosine polyphosphate
pyrophosphohydrolases/synthetases [Signal transduction
mechanisms / Transcription].
Length = 701
Score = 26.8 bits (60), Expect = 3.6
Identities = 8/33 (24%), Positives = 18/33 (54%)
Query: 13 YQAVIADVINNVKEAFQEEGVDEQVLQELKHIW 45
+ I +V++ ++E + G+ +V KHI+
Sbjct: 214 REQYIENVVSELREELKAAGIKAEVSGRPKHIY 246
>gnl|CDD|216215 pfam00961, LAGLIDADG_1, LAGLIDADG endonuclease.
Length = 99
Score = 25.3 bits (56), Expect = 5.5
Identities = 13/42 (30%), Positives = 23/42 (54%), Gaps = 7/42 (16%)
Query: 34 DEQVLQELKHIWEAKLFGIGVGKLSKRKEWMSKCYRSSNISG 75
DE++L ++K+ +G+G + KRK+ + YR SN
Sbjct: 38 DEKLLYKIKNY-------LGIGSIKKRKKDNTVRYRVSNKKL 72
>gnl|CDD|239619 cd03557, L-arabinose_isomerase, L-Arabinose isomerase (AI)
catalyzes the isomerization of L-arabinose to
L-ribulose, the first reaction in its conversion into
D-xylulose-5-phosphate, an intermediate in the pentose
phosphate pathway, which allows L-arabinose to be used
as a carbon source. AI can also convert D-galactose to
D-tagatose at elevated temperatures in the presence of
divalent metal ions. D-tagatose, rarely found in nature,
is of commercial interest as a low-calorie sugar
substitute.
Length = 484
Score = 26.1 bits (58), Expect = 6.1
Identities = 13/36 (36%), Positives = 21/36 (58%)
Query: 70 SSNISGRPSLSGNLKARLVYQPCLTQPVELLSICAA 105
S I + SG L ++V++P LT P E+L++C
Sbjct: 25 SREIVDGLNASGKLPVKIVFKPVLTTPDEILAVCRE 60
>gnl|CDD|235437 PRK05380, pyrG, CTP synthetase; Validated.
Length = 533
Score = 25.8 bits (58), Expect = 8.0
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 4/33 (12%)
Query: 14 QAVI----ADVINNVKEAFQEEGVDEQVLQELK 42
+AVI D I V E+G+D+ VL+ L
Sbjct: 232 EAVISAPDVDSIYEVPLLLHEQGLDDIVLERLG 264
>gnl|CDD|100084 cd06163, S2P-M50_PDZ_RseP-like, RseP-like Site-2 proteases (S2P),
zinc metalloproteases (MEROPS family M50A), cleave
transmembrane domains of substrate proteins, regulating
intramembrane proteolysis (RIP) of diverse signal
transduction mechanisms. In Escherichia coli, the S2P
homolog RseP is involved in the sigmaE pathway of
extracytoplasmic stress responses. Also included in
this group are such homologs as Bacillus subtilis YluC,
Mycobacterium tuberculosis Rv2869c S2P, and Bordetella
bronchiseptica HurP. Rv2869c S2P appears to have a
role in the regulation of prokaryotic lipid
biosynthesis and membrane composition and YluC of
Bacillus has a role in transducing membrane stress.
This group includes bacterial and eukaryotic S2P/M50s
homologs with either one or two PDZ domains present.
PDZ domains are believed to have a regulatory role. The
RseP PDZ domain is required for the inhibitory reaction
that prevents cleavage of its substrate, RseA.
Length = 182
Score = 25.1 bits (56), Expect = 9.5
Identities = 10/22 (45%), Positives = 13/22 (59%)
Query: 37 VLQELKHIWEAKLFGIGVGKLS 58
+ EL H AKLFG+ V + S
Sbjct: 13 FVHELGHFLVAKLFGVKVEEFS 34
>gnl|CDD|236872 PRK11183, PRK11183, D-lactate dehydrogenase; Provisional.
Length = 564
Score = 25.6 bits (57), Expect = 9.8
Identities = 10/18 (55%), Positives = 11/18 (61%)
Query: 50 FGIGVGKLSKRKEWMSKC 67
F G+GK SKRK W C
Sbjct: 547 FNPGIGKTSKRKNWQECC 564
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 0.132 0.383
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,122,407
Number of extensions: 516601
Number of successful extensions: 475
Number of sequences better than 10.0: 1
Number of HSP's gapped: 475
Number of HSP's successfully gapped: 21
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 bits)
S2: 53 (24.1 bits)