RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14441
(365 letters)
>gnl|CDD|173964 cd07981, TAF12, TATA Binding Protein (TBP) Associated Factor 12
(TAF12) 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 12 (TAF12) is one of several TAFs that bind TBP
and are involved in forming the TFIID complex. TFIID is
one of the seven General Transcription Factors (GTFs)
(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 are named after their
electrophoretic mobility in polyacrylamide gels in
different species. A new, unified nomenclature has been
suggested for the pol II TAFs to show the relationship
between TAF orthologs and paralogs. Several hypotheses
are proposed for TAFs function such as serving as
activator-binding sites, core-promoter recognition or a
role in essential catalytic activity. These TAFs, with
the help of specific activators, are required only for
expression of a subset of genes and are 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; the 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. TAF12 domain interacts with
TAF4 and makes a novel histone-like heterodimer that
binds DNA and has a core promoter function of a subset
of genes.
Length = 72
Score = 107 bits (270), Expect = 2e-29
Identities = 38/72 (52%), Positives = 53/72 (73%)
Query: 260 ILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDL 319
IL K KL EL++++D Q+D +V + EIA+DFVD++V AC+LAKHR S TL+ KD+
Sbjct: 1 ILTKRKLQELLKEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDV 60
Query: 320 QFVLAKDWNISI 331
Q L ++WNISI
Sbjct: 61 QLHLERNWNISI 72
>gnl|CDD|112650 pfam03847, TFIID_20kDa, Transcription initiation factor TFIID
subunit A.
Length = 67
Score = 89.7 bits (223), Expect = 9e-23
Identities = 31/67 (46%), Positives = 48/67 (71%)
Query: 262 GKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQF 321
K KL +L++Q+DS ++DE+V D EIA+DFV+++ AC+LAKHR S L+ +D+Q
Sbjct: 1 SKRKLQDLVQQIDSNTKLDEDVEDLLLEIADDFVESVTTFACKLAKHRKSDKLEVRDIQL 60
Query: 322 VLAKDWN 328
L ++WN
Sbjct: 61 HLERNWN 67
>gnl|CDD|227911 COG5624, TAF61, Transcription initiation factor TFIID, subunit
TAF12 (also component of histone acetyltransferase SAGA)
[Transcription].
Length = 505
Score = 69.3 bits (169), Expect = 6e-13
Identities = 35/102 (34%), Positives = 56/102 (54%), Gaps = 2/102 (1%)
Query: 259 QILGKDKLDELMRQ-VDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPK 317
++ K KL+EL VD +I+ EV + A+ FV+ + +C+LAKHR S TL+ +
Sbjct: 382 RLDSKRKLEELQHGGVDEEEKIENEVEELLLSRADGFVEPVTEFSCRLAKHRKSDTLEVR 441
Query: 318 DLQFVLAKDWNISIPGYGTDEL-KPYKRPMATEAHKQRLALI 358
D Q L ++WNI PG+ D + Y++ T + Q+ I
Sbjct: 442 DGQLHLERNWNIRCPGFVDDIIHMSYRKQKPTVEYCQKKLAI 483
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 36.9 bits (86), Expect = 0.002
Identities = 13/69 (18%), Positives = 31/69 (44%), Gaps = 1/69 (1%)
Query: 256 PNDQILGKDKLDELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLD 315
D +L K + ++R+ ++ + E ++++ I A +LA+H T+
Sbjct: 15 STDLLLPKAPVRRILRKA-GAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVK 73
Query: 316 PKDLQFVLA 324
+D++ L
Sbjct: 74 AEDIKLALK 82
>gnl|CDD|201453 pfam00808, CBFD_NFYB_HMF, Histone-like transcription factor
(CBF/NF-Y) and archaeal histone. This family includes
archaebacterial histones and histone like transcription
factors from eukaryotes.
Length = 65
Score = 36.1 bits (84), Expect = 0.002
Identities = 8/55 (14%), Positives = 26/55 (47%)
Query: 269 LMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVL 323
+M+ +I ++ + +E +F++ I A ++ K T++ + ++ +
Sbjct: 11 IMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIKLAV 65
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 34.8 bits (81), Expect = 0.006
Identities = 16/59 (27%), Positives = 27/59 (45%)
Query: 268 ELMRQVDSTLQIDEEVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326
EL + L+I + E D ++ I+ A LA+H T+ P+D+Q + D
Sbjct: 17 ELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRKTITPRDIQLAVRLD 75
>gnl|CDD|190265 pfam02269, TFIID-18kDa, Transcription initiation factor IID, 18kD
subunit. This family includes the Spt3 yeast
transcription factors and the 18kD subunit from human
transcription initiation factor IID (TFIID-18).
Determination of the crystal structure reveals an
atypical histone fold.
Length = 93
Score = 31.6 bits (72), Expect = 0.13
Identities = 10/45 (22%), Positives = 24/45 (53%)
Query: 282 EVYDTFSEIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326
E ++ + ++ +A + A+ RGS + +D++F++ KD
Sbjct: 23 ETVQLLEDLVRGQLIELLQQAMKTAQLRGSRKITLEDIKFLIRKD 67
>gnl|CDD|236619 PRK09737, PRK09737, EcoKI restriction-modification system protein
HsdS; Provisional.
Length = 461
Score = 31.0 bits (70), Expect = 0.91
Identities = 30/123 (24%), Positives = 52/123 (42%), Gaps = 9/123 (7%)
Query: 155 KQNTKYNIQLLVGTVSLAATIGYLAVSDVFIWNFFPPTLPKNEVLSFPAKDLSMLNSVDS 214
+ +KY +Q +S A +IG+ ++ LP N V + A L +N
Sbjct: 67 EDVSKYQLQDRDIVISSAGSIGFSFLA--------QNPLPSNVVFASFAIRLKPVNYFSE 118
Query: 215 DH-SQVMNSFSNSMEVDQNSSQSSTQSPAAQVMQKTNMPSSTPNDQILGKDKLDELMRQV 273
+ S ++ S+ ++ Q+ AQ + P +Q + +KLD L+ QV
Sbjct: 119 YFLKHFLESSDYRNQLSLMSAGNAVQNINAQSLSTLTFPIPPIAEQKIIAEKLDTLLAQV 178
Query: 274 DST 276
DST
Sbjct: 179 DST 181
>gnl|CDD|149883 pfam08953, DUF1899, Domain of unknown function (DUF1899). This set
of domains is found in various eukaryotic proteins.
Function is unknown.
Length = 65
Score = 27.2 bits (61), Expect = 2.7
Identities = 9/43 (20%), Positives = 21/43 (48%), Gaps = 5/43 (11%)
Query: 123 QQVRRS---HAYSK--KPPVTIDDLPVPQGSWKAHYDKQNTKY 160
+ VR S H + + K +D+ + + +W +++ N K+
Sbjct: 1 RFVRSSKFRHVFGQPAKKEQCYEDIRISKNAWDSNFCAVNPKF 43
>gnl|CDD|221075 pfam11315, Med30, Mediator complex subunit 30. Med30 is a
metazoan-specific subunit of Mediator, having no
homologues in yeasts.
Length = 150
Score = 28.6 bits (64), Expect = 3.5
Identities = 9/26 (34%), Positives = 12/26 (46%)
Query: 41 RIQNITQHFNSHSFLFRKQRNVYLHC 66
+ I + + LFRK R VY C
Sbjct: 46 KCGKIQEQLRTLKLLFRKLRLVYEKC 71
>gnl|CDD|214579 smart00241, ZP, Zona pellucida (ZP) domain. ZP proteins are
responsible for sperm-adhesion fo the zona pellucida. ZP
domains are also present in multidomain transmembrane
proteins such as glycoprotein GP2, uromodulin and
TGF-beta receptor type III (betaglycan).
Length = 252
Score = 28.9 bits (65), Expect = 3.9
Identities = 11/54 (20%), Positives = 19/54 (35%), Gaps = 1/54 (1%)
Query: 29 PTIPQVEQNITYRI-QNITQHFNSHSFLFRKQRNVYLHCLLVMLNFMSFNLCQH 81
P ++ I Y F+ F F + VY HC + + + + C
Sbjct: 193 PVDGYLDSTIPYNSNPLHRARFSVKVFKFADRSLVYFHCQIRLCDKDDGSSCDG 246
>gnl|CDD|191179 pfam05053, Menin, Menin. MEN1, the gene responsible for multiple
endocrine neoplasia type 1, is a tumour suppressor gene
that encodes a protein called Menin which may be an
atypical GTPase stimulated by nm23.
Length = 618
Score = 28.8 bits (64), Expect = 5.1
Identities = 10/30 (33%), Positives = 16/30 (53%)
Query: 280 DEEVYDTFSEIANDFVDNIVHRACQLAKHR 309
DEE+Y F +IAND + ++ + R
Sbjct: 357 DEEIYKEFFDIANDVIPYLLKEEASGHEAR 386
>gnl|CDD|173962 cd07978, TAF13, The TATA Binding Protein (TBP) Associated Factor 13
(TAF13) 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 13 (TAF13) is one of several TAFs that bind TBP
and is 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 TAFs
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. Each TAF, with the help of a
specific activator, is required only for 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; the 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 are
found in core histones, TAFs and many other
transcription factors. TFIID has a histone octamer-like
substructure. TAF13 interacts with TAF11 and makes a
histone-like heterodimer similar to H3/H4-like proteins.
The dimer may be structurally and functionally similar
to the spt3 protein within the SAGA histone
acetyltransferase complex.
Length = 92
Score = 27.1 bits (61), Expect = 5.1
Identities = 11/38 (28%), Positives = 23/38 (60%), Gaps = 1/38 (2%)
Query: 289 EIANDFVDNIVHRACQLAKHRGSSTLDPKDLQFVLAKD 326
+I +++ + H+A ++A+ R + +DL F+L KD
Sbjct: 31 DIVVEYIIELCHKAAEVAQRRRGK-VKVEDLIFLLRKD 67
>gnl|CDD|223913 COG0843, CyoB, Heme/copper-type cytochrome/quinol oxidases, subunit
1 [Energy production and conversion].
Length = 566
Score = 28.0 bits (63), Expect = 8.8
Identities = 11/39 (28%), Positives = 18/39 (46%)
Query: 161 NIQLLVGTVSLAATIGYLAVSDVFIWNFFPPTLPKNEVL 199
I +L+ LAA + L + F +FF P + +L
Sbjct: 196 AILILLAFPVLAAALTMLLLDRNFGTSFFTPAGGGDPLL 234
>gnl|CDD|215326 PLN02606, PLN02606, palmitoyl-protein thioesterase.
Length = 306
Score = 27.6 bits (61), Expect = 9.9
Identities = 15/46 (32%), Positives = 20/46 (43%), Gaps = 2/46 (4%)
Query: 90 HASIHDMHMPVACHFVLSSLLKALLPVIGSQMVQQVRRSHAYSKKP 135
HA + + P C+ LLKA+ VI + Q Y KKP
Sbjct: 132 HAGVAAI--PKGCNSTFCELLKAVFAVIYTDFAQDHTAPSGYVKKP 175
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 0.131 0.386
Gapped
Lambda K H
0.267 0.0692 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 17,881,413
Number of extensions: 1655200
Number of successful extensions: 1635
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1635
Number of HSP's successfully gapped: 21
Length of query: 365
Length of database: 10,937,602
Length adjustment: 98
Effective length of query: 267
Effective length of database: 6,590,910
Effective search space: 1759772970
Effective search space used: 1759772970
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: 60 (27.0 bits)