RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy11212
(448 letters)
>gnl|CDD|173968 cd08050, TAF6, TATA Binding Protein (TBP) Associated Factor 6
(TAF6) 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 6 (TAF6) is one of several TAFs that bind TBP and
are involved in forming Transcription Factor IID (TFIID)
complex. TFIID is one of 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
functions 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. TAF6 is a shared subunit of histone
acetyltransferase complex SAGA and TFIID complexes. TAF6
domain interacts with TAF9 and makes a novel
histone-like heterodimer that is structurally related to
histones H4 and H3. TAF6 may also interact with the
downstream core promoter element (DPE).
Length = 343
Score = 390 bits (1005), Expect = e-135
Identities = 164/311 (52%), Positives = 218/311 (70%), Gaps = 18/311 (5%)
Query: 130 KCMSHSKRVKLLPVDIDDALNMKNIEPIYGLTVSQFLPFKHASGGGRELHFTDEKEVDFE 189
K M HSKR KL D++ AL ++N+EP+YG + S+ LPF+ ++GGG+EL++ ++KE+D +
Sbjct: 42 KFMRHSKRRKLTTSDVNHALRLRNVEPLYGFSSSEPLPFRVSTGGGQELYYVEDKEIDLK 101
Query: 190 DLLTNLNPKSALETHLRTHWLAIEGVQPTVPENPPPVDKSAQKLESIDPISKLGKKDKDT 249
DL+ PK L+ ++ HWLAIEGVQP +PENPPP QK ES
Sbjct: 102 DLINTPLPKVPLDVSVKAHWLAIEGVQPLIPENPPPSAIEVQKKES-------------- 147
Query: 250 SGKPTSAKLEKLRNVETVHVKQLATHELSVEQQLYYKEITEACVGSDEGRRFEALQSLAT 309
+A +++L+ E V +K L H LS E QLY++EITEA VGS+E +R EALQSL T
Sbjct: 148 ---LANAAVKRLKKDEQVLLKPLVRHVLSKELQLYFEEITEALVGSNEEKRREALQSLRT 204
Query: 310 DPGLHEMLPRMCTFIAEGVKVNVVQNNLALLIYLMRMVKALLDNQSLYLEKYLHELLPSI 369
DPGL ++LP FIAEGV VN+ QN LALLIYLMRMV+ALLDN +L+LE YLH+L+PS+
Sbjct: 205 DPGLQQLLPYFVRFIAEGVTVNLDQN-LALLIYLMRMVRALLDNPNLHLEPYLHQLIPSV 263
Query: 370 LSCIVSKQLCGRPEADNHWALRDFASRLLTQVSKNFNTSTNNIQTRVTRLLSNAINDPKI 429
L+C+V+KQLC RP DNHWALRD+A+RLL Q+ + F+TS N +Q R+TR L A+ DPK
Sbjct: 264 LTCLVAKQLCSRPPDDNHWALRDYAARLLAQICRKFSTSYNTLQPRITRTLLKALLDPKK 323
Query: 430 NFPSLYGAIAG 440
+ YGAI G
Sbjct: 324 PLTTHYGAIVG 334
Score = 122 bits (309), Expect = 2e-31
Identities = 57/145 (39%), Positives = 86/145 (59%), Gaps = 29/145 (20%)
Query: 11 ESMKVIAESIGIPNLPDDAAKELSDNITYCCKVIIQ------------------------ 46
ES+K+IAES+GI +L D+ A+ L++++ Y + IIQ
Sbjct: 3 ESIKLIAESLGIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALR 62
Query: 47 -----PIYGLTVSQFLPFKHASGGGRELHFTDEKEVDFEDLLTNLNPKSALETHLRTHWL 101
P+YG + S+ LPF+ ++GGG+EL++ ++KE+D +DL+ PK L+ ++ HWL
Sbjct: 63 LRNVEPLYGFSSSEPLPFRVSTGGGQELYYVEDKEIDLKDLINTPLPKVPLDVSVKAHWL 122
Query: 102 AIEGVQPTVPENPPPVDKSAQKLES 126
AIEGVQP +PENPPP QK ES
Sbjct: 123 AIEGVQPLIPENPPPSAIEVQKKES 147
>gnl|CDD|227426 COG5095, TAF6, Transcription initiation factor TFIID, subunit TAF6
(also component of histone acetyltransferase SAGA)
[Transcription].
Length = 450
Score = 220 bits (561), Expect = 7e-67
Identities = 115/313 (36%), Positives = 174/313 (55%), Gaps = 9/313 (2%)
Query: 130 KCMSHSKRVKLLPVDIDDALNMKNIEPIYGLTVSQFLPF-KHASGGGRELHFTDEKEVDF 188
K M HSKR L DI AL N+EP+YG S+ L F G G+ +++ D++EVDF
Sbjct: 48 KFMVHSKRTVLTIDDISYALRSLNVEPLYGYDPSRPLQFSLVFRGLGQSVYYLDDEEVDF 107
Query: 189 EDLLTNLNPKSALETHLRTHWLAIEGVQPTVPENPPPVDKSAQKLESIDPISKLGKKDKD 248
E+ + PK +++HWLAIEGVQP +P+NP +DK K S D + +
Sbjct: 108 EEYINRPLPKVPRRVSIQSHWLAIEGVQPAIPQNPILLDKPVAKWASKDTLGVMPGAST- 166
Query: 249 TSGKPTSAKLEKLRNVETVHVKQLATHELSVEQQLYYKEITEACVG-SDEGRRFEALQSL 307
+ ++E +K L H LS E Q+Y+ ++ A + SDE R AL+SL
Sbjct: 167 ----AAYQARNGVTSMENAELKPLVKHVLSKELQMYFDKVISALLDESDEQTRDAALESL 222
Query: 308 ATDPGLHEMLPRMCTFIAEGVKVNVVQNNLALLIYLMRMVKALLDNQSLYLEKYLHELLP 367
D GLH+++P F E + N+ NL L ++ M +LL N+ ++++ YLH+L+P
Sbjct: 223 RNDSGLHQLVPYFIHFFNEQITKNL--KNLEKLTTVVMMYSSLLKNKYIFVDPYLHQLMP 280
Query: 368 SILSCIVSKQLCGRPEADNHWALRDFASRLLTQVSKNFNTSTNNIQTRVTRLLSNAINDP 427
SIL+C+++K+L P+ H+ALRD A+ LL V NF++S ++ RVTR L A D
Sbjct: 281 SILTCLIAKKLGNVPDDHEHYALRDVAADLLKYVFSNFSSSYKTLKPRVTRTLLKAFLDR 340
Query: 428 KINFPSLYGAIAG 440
+ + YGA+ G
Sbjct: 341 EKTESTQYGALKG 353
Score = 92.0 bits (228), Expect = 5e-20
Identities = 50/151 (33%), Positives = 77/151 (50%), Gaps = 30/151 (19%)
Query: 6 TSFSIESMKVIAESIGIPNLPDDAAKELSDNITYCCKVIIQ------------------- 46
T +S E++K +AES+GI N+ DDA + L+ ++ Y K + Q
Sbjct: 4 TLWSKETLKDVAESLGISNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDI 63
Query: 47 ----------PIYGLTVSQFLPF-KHASGGGRELHFTDEKEVDFEDLLTNLNPKSALETH 95
P+YG S+ L F G G+ +++ D++EVDFE+ + PK
Sbjct: 64 SYALRSLNVEPLYGYDPSRPLQFSLVFRGLGQSVYYLDDEEVDFEEYINRPLPKVPRRVS 123
Query: 96 LRTHWLAIEGVQPTVPENPPPVDKSAQKLES 126
+++HWLAIEGVQP +P+NP +DK K S
Sbjct: 124 IQSHWLAIEGVQPAIPQNPILLDKPVAKWAS 154
>gnl|CDD|203686 pfam07571, DUF1546, Protein of unknown function (DUF1546).
Associated with pfam02969 in Transcription initiation
factor TFIID subunit 6 (TAF6).
Length = 92
Score = 101 bits (254), Expect = 3e-26
Identities = 34/72 (47%), Positives = 50/72 (69%)
Query: 369 ILSCIVSKQLCGRPEADNHWALRDFASRLLTQVSKNFNTSTNNIQTRVTRLLSNAINDPK 428
+L+C++ K+L G P DNHWALRDFA+ LL+ + + F+ S N+++ R+TR L A+ DPK
Sbjct: 1 VLTCLLGKKLGGSPPLDNHWALRDFAASLLSHICRKFSDSYNSLRPRLTRTLLKALLDPK 60
Query: 429 INFPSLYGAIAG 440
+ YGAI G
Sbjct: 61 KPLGTHYGAIRG 72
>gnl|CDD|145884 pfam02969, TAF, TATA box binding protein associated factor (TAF).
TAF proteins adopt a histone-like fold.
Length = 66
Score = 51.6 bits (124), Expect = 8e-09
Identities = 23/42 (54%), Positives = 30/42 (71%)
Query: 5 GTSFSIESMKVIAESIGIPNLPDDAAKELSDNITYCCKVIIQ 46
T F ESMKVIAES+GI NL D+AA L++++ Y K I+Q
Sbjct: 1 TTIFPQESMKVIAESLGITNLSDEAAALLAEDVEYRLKEIVQ 42
Score = 32.4 bits (74), Expect = 0.047
Identities = 13/22 (59%), Positives = 14/22 (63%)
Query: 128 SFKCMSHSKRVKLLPVDIDDAL 149
+ K M HSKR KL DID AL
Sbjct: 44 AAKFMRHSKRQKLTVADIDSAL 65
>gnl|CDD|129039 smart00803, TAF, TATA box binding protein associated factor.
TAFs (TATA box binding protein associated factors) are
part of the transcription initiation factor TFIID
multimeric protein complex. TFIID is composed of the
TATA box binding protein (TBP) and a number of TAFs.
The TAFs provide binding sites for many different
transcriptional activators and co-activators that
modulate transcription initiation by Pol II. TAF
proteins adopt a histone-like fold.
Length = 65
Score = 48.4 bits (116), Expect = 9e-08
Identities = 18/39 (46%), Positives = 28/39 (71%)
Query: 8 FSIESMKVIAESIGIPNLPDDAAKELSDNITYCCKVIIQ 46
E++K +AES+GI NL D+AAK L++++ Y K I+Q
Sbjct: 3 LPKETIKDVAESLGIGNLSDEAAKLLAEDVEYRIKEIVQ 41
Score = 31.1 bits (71), Expect = 0.13
Identities = 12/20 (60%), Positives = 12/20 (60%)
Query: 130 KCMSHSKRVKLLPVDIDDAL 149
K M HSKR L DID AL
Sbjct: 45 KFMRHSKRTTLTTSDIDSAL 64
>gnl|CDD|187862 cd09731, Cse2_I-E, CRISPR/Cas system-associated protein Cse2.
CRISPR (Clustered Regularly Interspaced Short
Palindromic Repeats) and associated Cas proteins
comprise a system for heritable host defense by
prokaryotic cells against phage and other foreign DNA;
Small alpha-helical protein; also known as
Cse2/CasB/YgcK family; specific gene for I-E subtype;.
Length = 141
Score = 30.8 bits (70), Expect = 0.60
Identities = 19/77 (24%), Positives = 28/77 (36%), Gaps = 5/77 (6%)
Query: 267 VHVKQLATHELSVEQQLYYKEITEACVGSDEGRRFEALQSLATDPGLHEMLPRMCTFI-A 325
H K +S+ L S+ RRF L T L L R+ + +
Sbjct: 50 AHQKSDRKPGISLGAALARLREGSGSDVSE--RRFRQLLRADTPDELLRRLRRLVRLLKS 107
Query: 326 EGVKVNVVQNNLALLIY 342
+GV V+ Q LA +
Sbjct: 108 KGVPVDYGQ--LARDLL 122
>gnl|CDD|176893 cd08884, RHO_alpha_C_GbcA-like, C-terminal catalytic domain of GbcA
(glycine betaine catabolism A) from Pseudomonas
aeruginosa PAO1 and related aromatic ring hydroxylating
dioxygenases. C-terminal catalytic domain of GbcA
(glycine betaine catabolism A) from Pseudomonas
aeruginosa PAO1 and related Rieske-type non-heme iron
aromatic ring-hydroxylating oxygenases (RHOs, also known
as aromatic ring hydroxylating dioxygenases). RHOs
utilize non-heme Fe(II) to catalyze the addition of
hydroxyl groups to the aromatic ring, an initial step in
the oxidative degradation of aromatic compounds. RHOs
are composed of either two or three protein components,
and are comprised of an electron transport chain (ETC)
and an oxygenase. The ETC transfers reducing equivalents
from the electron donor to the oxygenase component,
which in turn transfers electrons to the oxygen
molecules. The oxygenase components are oligomers,
either (alpha)n or (alpha)n(beta)n. The alpha subunits
are the catalytic components and have an N-terminal
domain, which binds a Rieske-like 2Fe-2S cluster, and a
C-terminal domain which binds the non-heme Fe(II). The
Fe(II) is co-ordinated by conserved His and Asp
residues. GbcA is involved in glycine betaine (GB)
catabolism in Pseudomonas aeruginosa; it may remove a
methyl group from GB via a dioxygenase mechanism,
producing dimethylglycine and formaldehyde. This
subfamily belongs to the SRPBCC
(START/RHO_alpha_C/PITP/Bet_v1/CoxG/CalC) domain
superfamily of proteins that bind hydrophobic ligands.
SRPBCC domains have a deep hydrophobic ligand-binding
pocket.
Length = 205
Score = 29.2 bits (66), Expect = 3.5
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 4/23 (17%)
Query: 88 PKSALETHLRTHWL----AIEGV 106
P S ET +R WL A+EGV
Sbjct: 125 PLSPDETLVRCKWLVHPDAVEGV 147
Score = 29.2 bits (66), Expect = 3.5
Identities = 11/23 (47%), Positives = 13/23 (56%), Gaps = 4/23 (17%)
Query: 197 PKSALETHLRTHWL----AIEGV 215
P S ET +R WL A+EGV
Sbjct: 125 PLSPDETLVRCKWLVHPDAVEGV 147
>gnl|CDD|216913 pfam02169, LPP20, LPP20 lipoprotein. This family contains the
LPP20 lipoprotein, which is a non-essential class of
lipoprotein.
Length = 91
Score = 27.7 bits (62), Expect = 3.7
Identities = 10/42 (23%), Positives = 20/42 (47%), Gaps = 7/42 (16%)
Query: 389 ALRDFASRLLTQVSKNFNTSTNN-------IQTRVTRLLSNA 423
A R+ A ++ QV + +T+ +N ++T V + A
Sbjct: 30 AYRELAEQVYGQVISSQSTTVSNSVLTSDSVRTSVDSTIRGA 71
>gnl|CDD|112348 pfam03525, Meiotic_rec114, Meiotic recombination protein rec114.
Length = 328
Score = 29.2 bits (65), Expect = 4.6
Identities = 23/90 (25%), Positives = 32/90 (35%), Gaps = 10/90 (11%)
Query: 195 LNPKSALETHL-RTHWLAIEGVQPTVPENPPPVDKSAQKLESIDPISKLGKKDKDTSGKP 253
LN SA +T L R L ++ P V +S Q P ++ K
Sbjct: 221 LNTPSATQTVLARPEPLIVQ---------PLEVSQSLQNTTVCLPNTENQKYATLIPSDL 271
Query: 254 TSAKLEKLRNVETVHVKQLATHELSVEQQL 283
TS K+ L + V L E+QL
Sbjct: 272 TSRKIIALCKNGLLEVAHLPKERTEEEKQL 301
>gnl|CDD|224201 COG1282, PntB, NAD/NADP transhydrogenase beta subunit [Energy
production and conversion].
Length = 463
Score = 28.9 bits (65), Expect = 5.7
Identities = 12/30 (40%), Positives = 16/30 (53%), Gaps = 4/30 (13%)
Query: 26 PDDAAKELSDNITYCCKVIIQPIYGLTVSQ 55
+DAA+ L VII P YG+ V+Q
Sbjct: 298 AEDAAELL----KNASSVIIVPGYGMAVAQ 323
>gnl|CDD|220939 pfam11010, DUF2848, Protein of unknown function (DUF2848). This
bacterial family of proteins has no known function.
Length = 194
Score = 28.3 bits (64), Expect = 6.0
Identities = 12/27 (44%), Positives = 13/27 (48%)
Query: 371 SCIVSKQLCGRPEADNHWALRDFASRL 397
S VSKQ C +P A W L D A
Sbjct: 85 SVAVSKQACPKPVARRAWRLDDVADHW 111
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
0.316 0.133 0.386
Gapped
Lambda K H
0.267 0.0768 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 22,731,930
Number of extensions: 2199993
Number of successful extensions: 1824
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1817
Number of HSP's successfully gapped: 27
Length of query: 448
Length of database: 10,937,602
Length adjustment: 100
Effective length of query: 348
Effective length of database: 6,502,202
Effective search space: 2262766296
Effective search space used: 2262766296
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 (21.6 bits)
S2: 61 (27.2 bits)