RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy13513
(71 letters)
>gnl|CDD|173967 cd08048, TAF11, TATA Binding Protein (TBP) Associated Factor 11
(TAF11) is one of several TAFs that bind TBP and is
involved in forming Transcription Factor IID (TFIID)
complex. The TATA Binding Protein (TBP) Associated
Factor 11 (TAF11) is one of several TAFs that bind TBP
and are involved in forming the Transcription Factor
IID (TFIID) complex. TFIID is one of seven General
Transcription Factors (GTF) (TFIIA, TFIIB, TFIID,
TFIIE, TFIIF, and TFIID) that are involved in accurate
initiation of transcription by RNA polymerase II in
eukaryotes. TFIID plays an important role in the
recognition of promoter DNA and assembly of the
pre-initiation complex. TFIID complex is composed of
the TBP and at least 13 TAFs. TAFs from various species
were originally named by their predicted molecular
weight or their electrophoretic mobility in
polyacrylamide gels. A new, unified nomenclature for
the pol II TAFs has been suggested to show the
relationship between TAF orthologs and paralogs.
Several hypotheses are proposed for TAFs functions such
as serving as activator-binding sites, core-promoter
recognition or a role in essential catalytic activity.
TAF11 interacts with the ligand binding domains of the
nuclear receptors for vitamin D3 and thyroid hormone.
TAF11 also directly interacts with TFIIA, acting as a
bridging factor that stabilizes the TFIIA-TBP-DNA
complex. Each TAF, with the help of a specific
activator, is required only for the expression of
subset of genes and is not universally involved for
transcription as are GTFs. In yeast and human cells,
TAFs have been found as components of other complexes
besides TFIID. Several TAFs interact via histone-fold
(HFD) motifs; HFD is the interaction motif involved in
heterodimerization of the core histones and their
assembly into nucleosome octamers. The minimal HFD
contains three alpha-helices linked by two loops and is
found in core histones, TAFS and many other
transcription factors. TFIID has a histone octamer-like
substructure. The TAF11 domain is structurally
analogous to histone H3 and interacts with TAF13,
making a novel histone-like heterodimer. The dimer may
be structurally and functionally similar to the spt3
protein within the SAGA histone acetyltransferase
complex.
Length = 85
Score = 99 bits (250), Expect = 8e-30
Identities = 42/55 (76%), Positives = 54/55 (98%)
Query: 16 FTEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70
F+E+Q++RYEM+RR++FPKAAIKRLIQ+++G SVSQNVVIA++GIAKVFVGEIVE
Sbjct: 1 FSEEQMNRYEMFRRSSFPKAAIKRLIQSVTGQSVSQNVVIAVAGIAKVFVGEIVE 55
>gnl|CDD|218227 pfam04719, TAFII28, hTAFII28-like protein conserved region. The
general transcription factor, TFIID, consists of the
TATA-binding protein (TBP) associated with a series of
TBP-associated factors (TAFs) that together participate
in the assembly of the transcription preinitiation
complex. The conserved region is found at the
C-terminal of most member proteins. The crystal
structure of hTAFII28 with hTAFII18 shows that this
region is involved in the binding of these two
subunits. The conserved region contains four alpha
helices and three loops arranged as in histone H3.
Length = 89
Score = 97.4 bits (243), Expect = 9e-29
Identities = 44/62 (70%), Positives = 56/62 (90%)
Query: 9 MQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEI 68
MQVLVSNFTE+QL+RYE++RR++ KA +K+LI ++G SVS+NVVIA+SGIAKVFVGEI
Sbjct: 1 MQVLVSNFTEEQLNRYEVFRRSSLKKAQVKKLISQVTGQSVSENVVIAISGIAKVFVGEI 60
Query: 69 VE 70
VE
Sbjct: 61 VE 62
>gnl|CDD|227576 COG5251, TAF40, Transcription initiation factor TFIID, subunit
TAF11 [Transcription].
Length = 199
Score = 80.1 bits (197), Expect = 1e-20
Identities = 29/69 (42%), Positives = 48/69 (69%)
Query: 2 EEEEREKMQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIA 61
E + E+ ++LV+N E+Q +RYE++RR + K +K+L T++ +VS N+ I + G+
Sbjct: 86 ELAQDERFKLLVTNLDEEQTNRYEVFRRTSLNKTQVKKLASTVANQTVSPNIRIFLQGVG 145
Query: 62 KVFVGEIVE 70
KVFVGEI+E
Sbjct: 146 KVFVGEIIE 154
>gnl|CDD|131525 TIGR02472, sucr_P_syn_N, sucrose-phosphate synthase, putative,
glycosyltransferase domain. This family consists of the
N-terminal regions, or in some cases the entirety, of
bacterial proteins closely related to plant
sucrose-phosphate synthases (SPS). The C-terminal domain
(TIGR02471), found with most members of this family,
resembles both bona fide plant sucrose-phosphate
phosphatases (SPP) and the SPP-like domain of plant SPS.
At least two members of this family lack the SPP-like
domain, which may have binding or regulatory rather than
enzymatic activity by analogy to plant SPS. This enzyme
produces sucrose 6-phosphate and UDP from UDP-glucose
and D-fructose 6-phosphate, and may be encoded near the
gene for fructokinase.
Length = 439
Score = 28.9 bits (65), Expect = 0.17
Identities = 12/35 (34%), Positives = 22/35 (62%), Gaps = 5/35 (14%)
Query: 1 MEEEEREKMQVLVSNFTEDQLDRYEMYRRAAFPKA 35
ME ++RE +Q ++ +DRY++Y + A+PK
Sbjct: 295 MESQQREVLQKVL-----LLIDRYDLYGKVAYPKH 324
>gnl|CDD|227572 COG5247, BUR6, Class 2 transcription repressor NC2, alpha subunit
(DRAP1 homolog) [Transcription].
Length = 113
Score = 26.8 bits (59), Expect = 0.70
Identities = 13/48 (27%), Positives = 25/48 (52%), Gaps = 1/48 (2%)
Query: 25 EMYRRAAFPKAAIKRLIQTISG-GSVSQNVVIAMSGIAKVFVGEIVEQ 71
+ ++ FP A +K+++Q G V Q+ + S ++F+ EIV
Sbjct: 17 QKKKKTRFPIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGL 64
>gnl|CDD|177867 PLN02221, PLN02221, asparaginyl-tRNA synthetase.
Length = 572
Score = 26.5 bits (58), Expect = 1.00
Identities = 13/53 (24%), Positives = 23/53 (43%), Gaps = 4/53 (7%)
Query: 6 REKMQVLVSNFTEDQLDRYEMYRRAAFPK----AAIKRLIQTISGGSVSQNVV 54
+ M+++ NF +DR M F + AI+ L + ++ G N V
Sbjct: 385 FDDMELMAKNFDSGCIDRLRMVASTPFGRITYTEAIELLEEAVAKGKEFDNNV 437
>gnl|CDD|213984 cd12109, Hr_FBXL5, Hemerythrin-like domain of FBXL5-like proteins.
Human FBXL5 (F-box and leucine-rich repeat protein 5)
protein plays a role in cellular iron homeostasis. It is
part of an E3 ubiquitin ligase complex that targets the
iron regulatory protein IRP2 for proteasomal
degradation. The FBXL5's stability is regulated by iron
concentration, with its iron- and oxygen-binding
hemerythrin domain acting as a ligand-dependent
regulatory switch.
Length = 158
Score = 26.1 bits (58), Expect = 1.2
Identities = 7/21 (33%), Positives = 12/21 (57%)
Query: 1 MEEEEREKMQVLVSNFTEDQL 21
M EEE +L F++++L
Sbjct: 125 MHEEETVFQPLLWEYFSDEEL 145
>gnl|CDD|226092 COG3562, KpsS, Capsule polysaccharide export protein [Cell
envelope biogenesis, outer membrane].
Length = 403
Score = 26.0 bits (57), Expect = 1.5
Identities = 5/23 (21%), Positives = 11/23 (47%)
Query: 19 DQLDRYEMYRRAAFPKAAIKRLI 41
D LD + + R + +I ++
Sbjct: 64 DNLDDFPTFLRKFIAQHSIDAIV 86
>gnl|CDD|233608 TIGR01869, casC_Cse4, CRISPR-associated protein Cas7/Cse4/CasC,
subtype I-E/ECOLI. CRISPR is a term for Clustered,
Regularly Interspaced Short Palidromic Repeats. A number
of protein families appear only in association with
these repeats and are designated Cas (CRISPR-Associated)
proteins. This family is represented by CT1975 of
Chlorobium tepidum and is part of the Ecoli subtype of
CRISPR/Cas locis. It is designated Cse4, for CRISPR/Cas
Subtype Ecoli protein 4 [Mobile and extrachromosomal
element functions, Other].
Length = 325
Score = 25.5 bits (56), Expect = 2.5
Identities = 8/32 (25%), Positives = 12/32 (37%)
Query: 28 RRAAFPKAAIKRLIQTISGGSVSQNVVIAMSG 59
+ A KA K + + V IA+ G
Sbjct: 135 QDAVADKALKKNFKALLDAARLPGGVDIALFG 166
>gnl|CDD|179651 PRK03806, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 438
Score = 25.3 bits (56), Expect = 2.8
Identities = 10/22 (45%), Positives = 13/22 (59%), Gaps = 4/22 (18%)
Query: 13 VSNFTEDQLDRY----EMYRRA 30
+ N TED +DRY + YR A
Sbjct: 177 ILNVTEDHMDRYPFGLQQYRAA 198
>gnl|CDD|233840 TIGR02386, rpoC_TIGR, DNA-directed RNA polymerase, beta' subunit,
predominant form. Bacteria have a single DNA-directed
RNA polymerase, with required subunits that include
alpha, beta, and beta-prime. This model describes the
predominant architecture of the beta-prime subunit in
most bacteria. This model excludes from among the
bacterial mostly sequences from the cyanobacteria, where
RpoC is replaced by two tandem genes homologous to it
but also encoding an additional domain [Transcription,
DNA-dependent RNA polymerase].
Length = 1140
Score = 25.0 bits (55), Expect = 3.3
Identities = 13/42 (30%), Positives = 20/42 (47%)
Query: 3 EEEREKMQVLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQTI 44
+ + +K +VL + L RY RA AIK L++ I
Sbjct: 133 DTKLDKKEVLDETEYREVLKRYGDGFRAGMGAEAIKELLEKI 174
>gnl|CDD|225611 COG3069, DcuC, C4-dicarboxylate transporter [Energy production and
conversion].
Length = 451
Score = 24.7 bits (54), Expect = 4.3
Identities = 13/36 (36%), Positives = 23/36 (63%), Gaps = 6/36 (16%)
Query: 35 AAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70
+A+ R + +SG VV+A++G+AKV E+V+
Sbjct: 400 SALGRTLSPVSG------VVVAVAGMAKVSPFEVVK 429
>gnl|CDD|224249 COG1330, RecC, Exonuclease V gamma subunit [DNA replication,
recombination, and repair].
Length = 1078
Score = 24.7 bits (54), Expect = 4.4
Identities = 15/49 (30%), Positives = 24/49 (48%), Gaps = 6/49 (12%)
Query: 11 VLVSNFTEDQLDRYEMYRRAAFPKAAIKRLIQ-TISGGSVSQNVVIAMS 58
VLV + D Y Y A F +A I+R + ++S S+SQ + +
Sbjct: 377 VLVPDI-----DSYTPYIEAVFGQAPIERHLPYSLSDRSLSQTEPLLNA 420
>gnl|CDD|107260 cd01575, PBP1_GntR, Ligand-binding domain of DNA transcription
repressor GntR specific for gluconate, a member of the
LacI-GalR family of bacterial transcription regulators.
This group represents the ligand-binding domain of DNA
transcription repressor GntR specific for gluconate, a
member of the LacI-GalR family of bacterial
transcription regulators. The ligand-binding domain of
GntR is structurally homologous to the periplasmic
sugar-binding domain of ABC-type transporters and both
domains contain the type I periplasmic binding
protein-like fold. The LacI-GalR family repressors are
composed of two functional domains: an N-terminal HTH
(helix-turn-helix) domain, which is responsible for the
DNA-binding specificity, and a C-terminal ligand-binding
domain, which is homologous to the type I periplasmic
binding proteins. As also observed in the periplasmic
binding proteins, the C-terminal domain of the bacterial
transcription repressor undergoes a conformational
change upon ligand binding, which in turn changes the
DNA binding affinity of the repressor.
Length = 268
Score = 24.8 bits (55), Expect = 4.4
Identities = 9/33 (27%), Positives = 15/33 (45%), Gaps = 6/33 (18%)
Query: 22 DRYEMYRRAAFPKAAIKRLIQTISGGSVSQNVV 54
R E+ RRAA + L+ ++G +V
Sbjct: 231 PRREIGRRAA------ELLLARLAGEEPEPRIV 257
>gnl|CDD|215755 pfam00154, RecA, recA bacterial DNA recombination protein. RecA
is a DNA-dependent ATPase and functions in DNA repair
systems. RecA protein catalyzes an ATP-dependent DNA
strand-exchange reaction that is the central step in
the repair of dsDNA breaks by homologous recombination.
Length = 322
Score = 24.5 bits (54), Expect = 4.7
Identities = 14/47 (29%), Positives = 24/47 (51%), Gaps = 10/47 (21%)
Query: 31 AFPKAAIKRL-------IQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70
F K +I RL ++ IS GS+ ++ + + G+ K G I+E
Sbjct: 13 QFGKGSIMRLGDKTVEDVEVISTGSLGLDIALGIGGLPK---GRIIE 56
>gnl|CDD|235160 PRK03803, murD, UDP-N-acetylmuramoyl-L-alanyl-D-glutamate
synthetase; Provisional.
Length = 448
Score = 24.5 bits (54), Expect = 4.9
Identities = 9/19 (47%), Positives = 12/19 (63%), Gaps = 3/19 (15%)
Query: 15 NFTEDQLDRY---EMYRRA 30
N +ED +DRY E Y +A
Sbjct: 182 NISEDHMDRYSDLEAYHQA 200
>gnl|CDD|116948 pfam08367, M16C_assoc, Peptidase M16C associated. This domain
appears in eukaryotes as well as bacteria and tends to
be found near the C-terminus of the metalloprotease
M16C (pfam05193).
Length = 248
Score = 24.5 bits (54), Expect = 5.4
Identities = 10/30 (33%), Positives = 18/30 (60%), Gaps = 2/30 (6%)
Query: 2 EEEEREKMQVLVSNFTEDQLDRYEMYRRAA 31
EEEREK++ S+ +E+ D+ ++ R
Sbjct: 12 NEEEREKLEKKKSSLSEE--DKEKIIERGL 39
>gnl|CDD|162659 TIGR02012, tigrfam_recA, protein RecA. This model describes
orthologs of the recA protein. RecA promotes
hybridization of homolgous regions of DNA. A segment of
ssDNA can be hybridized to another ssDNA region, or to
a dsDNA region. ATP is hydrolyzed in the process. Part
of the SOS respones, it is regulated by LexA via
autocatalytic cleavage [DNA metabolism, DNA
replication, recombination, and repair].
Length = 321
Score = 24.3 bits (53), Expect = 6.6
Identities = 15/47 (31%), Positives = 26/47 (55%), Gaps = 10/47 (21%)
Query: 31 AFPKAAIKRL-------IQTISGGSVSQNVVIAMSGIAKVFVGEIVE 70
F K +I RL ++TIS GS+S ++ + + G+ + G I+E
Sbjct: 16 QFGKGSIMRLGEKSVMDVETISTGSLSLDLALGVGGLPR---GRIIE 59
>gnl|CDD|215574 PLN03099, PIR, Protein PIR; Provisional.
Length = 1232
Score = 24.1 bits (52), Expect = 8.0
Identities = 12/40 (30%), Positives = 18/40 (45%), Gaps = 5/40 (12%)
Query: 17 TEDQLDRYEMYRRAAFPKAA----IKRLI-QTISGGSVSQ 51
D+ Y R P AA ++ LI + +SGGS +
Sbjct: 493 ENDESRPNFFYPRPVAPTAAQLHCLQFLIHELVSGGSPKK 532
>gnl|CDD|172486 PRK13984, PRK13984, putative oxidoreductase; Provisional.
Length = 604
Score = 24.0 bits (52), Expect = 8.0
Identities = 14/42 (33%), Positives = 24/42 (57%)
Query: 27 YRRAAFPKAAIKRLIQTISGGSVSQNVVIAMSGIAKVFVGEI 68
Y R PK I R + I GG+V+ ++ +M+ + K+ GE+
Sbjct: 407 YLRGEGPKPKIPRSLVVIGGGNVAMDIARSMARLQKMEYGEV 448
>gnl|CDD|225734 COG3193, GlcG, Uncharacterized protein, possibly involved in
utilization of glycolate and propanediol [General
function prediction only].
Length = 141
Score = 23.8 bits (52), Expect = 8.4
Identities = 9/20 (45%), Positives = 15/20 (75%)
Query: 44 ISGGSVSQNVVIAMSGIAKV 63
+SGG+ +Q+ IA +GIA +
Sbjct: 118 VSGGTGAQDEEIARAGIAAI 137
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
0.317 0.131 0.337
Gapped
Lambda K H
0.267 0.0778 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,658,121
Number of extensions: 284498
Number of successful extensions: 351
Number of sequences better than 10.0: 1
Number of HSP's gapped: 351
Number of HSP's successfully gapped: 27
Length of query: 71
Length of database: 10,937,602
Length adjustment: 41
Effective length of query: 30
Effective length of database: 9,119,088
Effective search space: 273572640
Effective search space used: 273572640
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)