RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy7662
(220 letters)
>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 = 127 bits (321), Expect = 4e-38
Identities = 52/92 (56%), Positives = 77/92 (83%), Gaps = 2/92 (2%)
Query: 123 KRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMG--RTGRVQVEDI 180
KR+F+KE+R MMYGFGD +NP E+VD+LED V+++++++ KA E+ R G+V+VED+
Sbjct: 1 KRLFTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGKVKVEDL 60
Query: 181 VFLVRKDNRKYARVKDLLTMNEELKKARKAFD 212
+FL+RKD +K AR+++LL+M +ELKKARKAFD
Sbjct: 61 IFLLRKDPKKLARLRELLSMKDELKKARKAFD 92
Score = 72.2 bits (178), Expect = 8e-17
Identities = 25/57 (43%), Positives = 42/57 (73%)
Query: 35 KRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGRTGPTFLSL 91
KR+F+KE+R MMYGFGD +NP E+VD+LED V+++++++ KA E+ + + +
Sbjct: 1 KRLFTKEIRQMMYGFGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQRRRGKVKV 57
>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 = 120 bits (302), Expect = 2e-35
Identities = 48/93 (51%), Positives = 67/93 (72%), Gaps = 3/93 (3%)
Query: 124 RMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGRTG---RVQVEDI 180
+F KEL+ MMYGFGD ++P E+V +LED V L+++ Q+AM+ + ++ +EDI
Sbjct: 1 HLFRKELQSMMYGFGDVQDPLQETVQLLEDLVRGQLIELLQQAMKTAQLRGSRKITLEDI 60
Query: 181 VFLVRKDNRKYARVKDLLTMNEELKKARKAFDE 213
FL+RKD +K R+KDLL+MNE LKKARK FDE
Sbjct: 61 KFLIRKDPKKLNRLKDLLSMNELLKKARKQFDE 93
Score = 68.6 bits (168), Expect = 2e-15
Identities = 22/48 (45%), Positives = 34/48 (70%)
Query: 36 RMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEMGR 83
+F KEL+ MMYGFGD ++P E+V +LED V L+++ Q+AM+ +
Sbjct: 1 HLFRKELQSMMYGFGDVQDPLQETVQLLEDLVRGQLIELLQQAMKTAQ 48
>gnl|CDD|227573 COG5248, TAF19, Transcription initiation factor TFIID, subunit
TAF13 [Transcription].
Length = 126
Score = 79.2 bits (195), Expect = 4e-19
Identities = 31/97 (31%), Positives = 56/97 (57%), Gaps = 1/97 (1%)
Query: 119 PSGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEM-GRTGRVQV 177
+ R +F K+++ +MY +GD P ++ + L + V+D++ + A M + +
Sbjct: 4 EARRVNLFMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNMAQVRNKTKT 63
Query: 178 EDIVFLVRKDNRKYARVKDLLTMNEELKKARKAFDEV 214
ED F +R+D +K RV++LL NEE+K A+KAF+
Sbjct: 64 EDFKFALRRDPKKLGRVEELLITNEEIKLAKKAFEPK 100
Score = 45.3 bits (107), Expect = 2e-06
Identities = 13/51 (25%), Positives = 28/51 (54%)
Query: 31 PSGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDAVIDFLVDMTQKAMEM 81
+ R +F K+++ +MY +GD P ++ + L + V+D++ + A M
Sbjct: 4 EARRVNLFMKDIKSLMYAYGDVVAPRYDTAEALHEYVLDYMSILCTNAHNM 54
>gnl|CDD|224036 COG1111, MPH1, ERCC4-like helicases [DNA replication,
recombination, and repair].
Length = 542
Score = 30.4 bits (69), Expect = 0.70
Identities = 12/48 (25%), Positives = 18/48 (37%), Gaps = 4/48 (8%)
Query: 169 MGRTGRVQVEDIVFLVRKDNRKYAR----VKDLLTMNEELKKARKAFD 212
GRTGR + +V LV + R A + M E ++
Sbjct: 463 KGRTGRKRKGRVVVLVTEGTRDEAYYYSSRRKEQKMIESIRGLSLELK 510
>gnl|CDD|182725 PRK10781, rcsF, outer membrane lipoprotein; Reviewed.
Length = 133
Score = 29.3 bits (66), Expect = 0.90
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 24 QDTPVNLPSGRKRMFSK 40
QD+P ++P+ RKRM
Sbjct: 79 QDSPPSIPTARKRMQIN 95
Score = 29.3 bits (66), Expect = 0.90
Identities = 8/17 (47%), Positives = 12/17 (70%)
Query: 112 QDTPVNLPSGRKRMFSK 128
QD+P ++P+ RKRM
Sbjct: 79 QDSPPSIPTARKRMQIN 95
>gnl|CDD|217388 pfam03144, GTP_EFTU_D2, Elongation factor Tu domain 2. Elongation
factor Tu consists of three structural domains, this is
the second domain. This domain adopts a beta barrel
structure. This the second domain is involved in binding
to charged tRNA. This domain is also found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This domain is structurally
related to pfam03143, and in fact has weak sequence
matches to this domain.
Length = 70
Score = 28.0 bits (63), Expect = 0.91
Identities = 9/38 (23%), Positives = 17/38 (44%)
Query: 172 TGRVQVEDIVFLVRKDNRKYARVKDLLTMNEELKKARK 209
+G ++ D V + K RV L + +L++A
Sbjct: 10 SGTLKKGDKVVIGPNGTGKKGRVTSLEMFHGDLREAVA 47
>gnl|CDD|234018 TIGR02799, thio_ybgC, tol-pal system-associated acyl-CoA
thioesterase. The tol-pal system consists of five
critical genes. Inner membrane proteins TolQ and TolR
convert protomotive force to energy that is transduced
through TolA to an outer membrane complex of TolB and
Pal. The system is known to be required to maintain
outer membrane integrity. In a system with several
homologous parts, ExbB and ExbD transduces energy
through TonB to a variety of outer membrane proteins,
many of which are siderophore receptors. The tol-pal
system therefore may also be involved in transport. This
family consists of a protein nearly always found in
operons with the genes of the tol-pal system. The
significance of this thioesterase to the tol-pal system
is unclear, but either of two observations may be
relevant. First, Pal, or peptidoglycan-associated
lipoprotein, has a conserved N-terminal cleavage and
acylation that makes it a lipoprotein. Second, the
tol-pal system is implicated not only in the import of
certain organics but also in the maintenance of outer
membrane integrity (by an unknown mechanism).
Length = 126
Score = 28.7 bits (65), Expect = 1.0
Identities = 13/36 (36%), Positives = 20/36 (55%), Gaps = 3/36 (8%)
Query: 178 EDIVFLVRK---DNRKYARVKDLLTMNEELKKARKA 210
+VF+VR D K AR+ DLLT+ + + + A
Sbjct: 49 TGLVFVVRSMELDYLKPARLDDLLTVTTRVVELKGA 84
>gnl|CDD|202823 pfam03947, Ribosomal_L2_C, Ribosomal Proteins L2, C-terminal
domain.
Length = 130
Score = 28.3 bits (64), Expect = 1.7
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 28 VNLPSGRKRMFSKELRC 44
+ LPSG R+ S R
Sbjct: 51 LKLPSGEVRLVSSNCRA 67
Score = 28.3 bits (64), Expect = 1.7
Identities = 7/17 (41%), Positives = 9/17 (52%)
Query: 116 VNLPSGRKRMFSKELRC 132
+ LPSG R+ S R
Sbjct: 51 LKLPSGEVRLVSSNCRA 67
>gnl|CDD|184277 PRK13725, PRK13725, plasmid maintenance protein; Provisional.
Length = 132
Score = 28.1 bits (62), Expect = 1.9
Identities = 15/46 (32%), Positives = 26/46 (56%)
Query: 91 LLKFKSNKNVCVFSFQFEEEEQDTPVNLPSGRKRMFSKELRCMMYG 136
+LKF + N+C+F+ + + E NL +GR + S L ++YG
Sbjct: 1 MLKFMLDTNICIFTIKNKPEHVRERFNLNTGRMCISSVTLMELIYG 46
>gnl|CDD|99972 cd03799, GT1_amsK_like, This is a family of GT1
glycosyltransferases found specifically in certain
bacteria. amsK in Erwinia amylovora, has been reported
to be involved in the biosynthesis of amylovoran, a
exopolysaccharide acting as a virulence factor.
Length = 355
Score = 28.7 bits (65), Expect = 2.8
Identities = 12/33 (36%), Positives = 16/33 (48%), Gaps = 1/33 (3%)
Query: 146 ESVDILEDAVIDFLVDMTQKAMEMGRTGRVQVE 178
+ L DA+ L D + EMG GR +VE
Sbjct: 312 GDPEALADAIERLL-DDPELRREMGEAGRARVE 343
>gnl|CDD|238652 cd01342, Translation_Factor_II_like, Translation_Factor_II_like:
Elongation factor Tu (EF-Tu) domain II-like proteins.
Elongation factor Tu consists of three structural
domains, this family represents the second domain.
Domain II adopts a beta barrel structure and is involved
in binding to charged tRNA. Domain II is found in other
proteins such as elongation factor G and translation
initiation factor IF-2. This group also includes the C2
subdomain of domain IV of IF-2 that has the same fold as
domain II of (EF-Tu). Like IF-2 from certain prokaryotes
such as Thermus thermophilus, mitochondrial IF-2 lacks
domain II, which is thought to be involved in binding
of E.coli IF-2 to 30S subunits.
Length = 83
Score = 26.9 bits (60), Expect = 2.9
Identities = 11/45 (24%), Positives = 17/45 (37%), Gaps = 1/45 (2%)
Query: 173 GRVQVEDIVFLVRKDNRKYARVKDLLTMNEELKKARKAFDEVKFV 217
G ++ D V + +VK L E+ +A D V V
Sbjct: 25 GTLKKGDKVRVGPGGGGVKGKVKSLKRFKGEVDEAVAG-DIVGIV 68
>gnl|CDD|130337 TIGR01270, Trp_5_monoox, tryptophan 5-monooxygenase, tetrameric.
This model describes tryptophan 5-monooxygenase, a
member of the family of tetrameric, biopterin-dependent
aromatic amino acid hydroxylases found in metazoans. It
is closely related to tetrameric
phenylalanine-4-hydroxylase and tyrosine
3-monooxygenase, and more distantly related to the
monomeric phenylalanine-4-hydroxylase found in some
Gram-negative bacteria [Energy metabolism, Amino acids
and amines].
Length = 464
Score = 28.7 bits (64), Expect = 3.0
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 12/57 (21%)
Query: 10 KNVCVFSFQFEEEEQDTPVNLPSGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDA 66
+N ++ FEE ++ + R F+ + FG NPYTESV++L+++
Sbjct: 395 QNAYFYTRSFEEAKE---------KMREFTNT---IKRPFGVRYNPYTESVEVLKNS 439
Score = 28.7 bits (64), Expect = 3.0
Identities = 16/57 (28%), Positives = 29/57 (50%), Gaps = 12/57 (21%)
Query: 98 KNVCVFSFQFEEEEQDTPVNLPSGRKRMFSKELRCMMYGFGDDRNPYTESVDILEDA 154
+N ++ FEE ++ + R F+ + FG NPYTESV++L+++
Sbjct: 395 QNAYFYTRSFEEAKE---------KMREFTNT---IKRPFGVRYNPYTESVEVLKNS 439
>gnl|CDD|235009 PRK02141, PRK02141, Maf-like protein; Reviewed.
Length = 207
Score = 27.8 bits (62), Expect = 4.2
Identities = 9/16 (56%), Positives = 10/16 (62%)
Query: 170 GRTGRVQVEDIVFLVR 185
RTG Q ED+V VR
Sbjct: 121 SRTGETQSEDVVTRVR 136
>gnl|CDD|223168 COG0090, RplB, Ribosomal protein L2 [Translation, ribosomal
structure and biogenesis].
Length = 275
Score = 27.6 bits (62), Expect = 5.6
Identities = 9/23 (39%), Positives = 9/23 (39%)
Query: 22 EEQDTPVNLPSGRKRMFSKELRC 44
E V LPSG R E R
Sbjct: 168 EGNYVIVRLPSGEMRKVLSECRA 190
Score = 27.6 bits (62), Expect = 5.6
Identities = 9/23 (39%), Positives = 9/23 (39%)
Query: 110 EEQDTPVNLPSGRKRMFSKELRC 132
E V LPSG R E R
Sbjct: 168 EGNYVIVRLPSGEMRKVLSECRA 190
>gnl|CDD|177773 PLN00178, PLN00178, sulfite reductase.
Length = 623
Score = 27.8 bits (62), Expect = 6.1
Identities = 17/55 (30%), Positives = 24/55 (43%), Gaps = 25/55 (45%)
Query: 169 MGRT--------------GRVQVEDIVFLV-----------RKDNRKYARVKDLL 198
MGRT G V EDI++ V R+D+RK +R+K L+
Sbjct: 307 MGRTHRNETTFPRLADPLGYVPKEDILYAVKAIVATQRDYGRRDDRKQSRMKYLV 361
>gnl|CDD|221281 pfam11871, DUF3391, Domain of unknown function (DUF3391). This
domain is functionally uncharacterized. This domain is
found in bacteria. This presumed domain is typically
between 122 to 139 amino acids in length. This domain is
found associated with pfam01966.
Length = 127
Score = 26.5 bits (59), Expect = 6.9
Identities = 10/27 (37%), Positives = 15/27 (55%)
Query: 189 RKYARVKDLLTMNEELKKARKAFDEVK 215
A VK ++ EL++A+K F E K
Sbjct: 78 EPPAPVKKKVSFERELRRAKKLFQEAK 104
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
0.321 0.136 0.388
Gapped
Lambda K H
0.267 0.0736 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 11,447,443
Number of extensions: 1095349
Number of successful extensions: 1148
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1145
Number of HSP's successfully gapped: 41
Length of query: 220
Length of database: 10,937,602
Length adjustment: 93
Effective length of query: 127
Effective length of database: 6,812,680
Effective search space: 865210360
Effective search space used: 865210360
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: 57 (25.7 bits)