RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy14772
(191 letters)
>gnl|CDD|227533 COG5208, HAP5, CCAAT-binding factor, subunit C [Transcription].
Length = 286
Score = 134 bits (339), Expect = 3e-39
Identities = 59/98 (60%), Positives = 77/98 (78%)
Query: 6 KEHVNRVIQVTELDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIR 65
++ + + ++ LK LPLARIKK+MK D+ VKMISAEAP+LF+K E+FI ELT+R
Sbjct: 91 QQTIKAAEEERQILLKDHNLPLARIKKVMKTDEDVKMISAEAPVLFAKITEIFIEELTMR 150
Query: 66 AWIHTEDNKRRTLQRNDIAMAITKYDMFDFLIDIVPRE 103
AWI+ E+NKRRTLQ++DIA A+ K +MFDFLIDIVPR
Sbjct: 151 AWINAEENKRRTLQKSDIAAAVKKSEMFDFLIDIVPRN 188
>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 = 79.6 bits (197), Expect = 3e-20
Identities = 22/63 (34%), Positives = 34/63 (53%)
Query: 25 LPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIA 84
LP+AR+K+IMK D IS +A L ++ E FI + A + KR+T+ I
Sbjct: 3 LPIARVKRIMKSDPDAGRISQDAKELIAECVEEFIEFIASEAAEICKKEKRKTINAEHIK 62
Query: 85 MAI 87
+A+
Sbjct: 63 LAV 65
>gnl|CDD|201020 pfam00125, Histone, Core histone H2A/H2B/H3/H4.
Length = 75
Score = 52.9 bits (128), Expect = 6e-10
Identities = 19/70 (27%), Positives = 34/70 (48%), Gaps = 1/70 (1%)
Query: 19 DLKTQALPLARIKKIMKLDDGV-KMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRT 77
L LP +R+ + +K IS++AP+ +A E + E+ A + KR+T
Sbjct: 3 RLLILKLPFSRVVRELKEGFYAELRISSKAPVALQEALEDLLEEILEDAGLLARHAKRKT 62
Query: 78 LQRNDIAMAI 87
+ DI +A+
Sbjct: 63 ITPRDIQLAV 72
>gnl|CDD|227572 COG5247, BUR6, Class 2 transcription repressor NC2, alpha subunit
(DRAP1 homolog) [Transcription].
Length = 113
Score = 46.5 bits (110), Expect = 4e-07
Identities = 22/82 (26%), Positives = 42/82 (51%)
Query: 26 PLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAM 85
P+AR+KKIM+LD+ + + P++ SKA E+F+ E+ + + + +
Sbjct: 25 PIARLKKIMQLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKR 84
Query: 86 AITKYDMFDFLIDIVPREEVKT 107
A + FDFL ++ + +T
Sbjct: 85 ATESDEKFDFLKNMEQFKNRET 106
>gnl|CDD|224947 COG2036, HHT1, Histones H3 and H4 [Chromatin structure and
dynamics].
Length = 91
Score = 41.5 bits (98), Expect = 1e-05
Identities = 18/72 (25%), Positives = 36/72 (50%), Gaps = 1/72 (1%)
Query: 22 TQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRN 81
LP A +++I++ G + +S+ A +A E ++ E+ A E KR+T++
Sbjct: 17 DLLLPKAPVRRILR-KAGAERVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAE 75
Query: 82 DIAMAITKYDMF 93
DI +A+ +
Sbjct: 76 DIKLALKRLGRR 87
>gnl|CDD|227587 COG5262, HTA1, Histone H2A [Chromatin structure and dynamics].
Length = 132
Score = 40.2 bits (94), Expect = 9e-05
Identities = 22/94 (23%), Positives = 39/94 (41%), Gaps = 1/94 (1%)
Query: 4 GEKEHVNRVIQVTELDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELT 63
G K RV Q P+ R+K+++K + I A AP+ + E E+
Sbjct: 7 GGKAADARVSQSRSAKAGLI-FPVGRVKRLLKKGNYRMRIGAGAPVYLAAVLEYLAAEIL 65
Query: 64 IRAWIHTEDNKRRTLQRNDIAMAITKYDMFDFLI 97
A DNK++ + + +AI + + L+
Sbjct: 66 ELAGNAARDNKKKRIIPRHLQLAIRNDEELNKLL 99
>gnl|CDD|185139 PRK15217, PRK15217, fimbrial outer membrane usher protein;
Provisional.
Length = 826
Score = 31.3 bits (71), Expect = 0.30
Identities = 16/47 (34%), Positives = 20/47 (42%), Gaps = 2/47 (4%)
Query: 118 TKTALNPDQVQYYFQLAQQHQAALQQNNQGATTTSATPTLVVNGGNS 164
+ TA + DQ Y L+ Q Q + GA T P VNG S
Sbjct: 594 SGTAGSRDQFNYGVNLSHQRQG--NETTAGANLTWNAPVATVNGSYS 638
>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 = 28.7 bits (65), Expect = 0.40
Identities = 16/49 (32%), Positives = 24/49 (48%)
Query: 39 GVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAMAI 87
G+ +S EA L ++ E I E+ A +KR TL +DI A+
Sbjct: 16 GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSAL 64
>gnl|CDD|206093 pfam13922, PHD_3, PHD domain of transcriptional enhancer, Asx.
This is the DNA-binding domain on the additional sex
combs-like 1 proteins. The Asx protein acts as an
enhancer of trithorax and polycomb in displaying
bidirectional homoeotic phenotypes in Drosophila,
suggesting that it is required for maintenance of both
activation and silencing of Hox genes. Asx is required
for normal adult haematopoiesis and its function depends
on its cellular context.
Length = 64
Score = 27.8 bits (62), Expect = 0.72
Identities = 8/25 (32%), Positives = 9/25 (36%)
Query: 132 QLAQQHQAALQQNNQGATTTSATPT 156
+ Q QQN G T AT
Sbjct: 5 NGSGHSQHLPQQNFSGENTAEATAN 29
>gnl|CDD|133378 cd00592, HTH_MerR-like, Helix-Turn-Helix DNA binding domain of
MerR-like transcription regulators. Helix-turn-helix
(HTH) MerR-like transcription regulator, N-terminal
domain. The MerR family transcription regulators have
been shown to mediate responses to stress including
exposure to heavy metals, drugs, or oxygen radicals in
eubacterial and some archaeal species. They regulate
transcription of multidrug/metal ion transporter genes
and oxidative stress regulons by reconfiguring the
spacer between the -35 and -10 promoter elements. A
typical MerR regulator is comprised of two distinct
domains that harbor the regulatory (effector-binding)
site and the active (DNA-binding) site. Their
N-terminal domains are homologous and contain a
DNA-binding winged HTH motif, while the C-terminal
domains are often dissimilar and bind specific
coactivator molecules such as metal ions, drugs, and
organic substrates.
Length = 100
Score = 28.0 bits (63), Expect = 1.4
Identities = 13/51 (25%), Positives = 24/51 (47%), Gaps = 2/51 (3%)
Query: 7 EHVNRVIQVTELDLKTQALPLARIKKIMKLDDGVKMISAEAPMLFSKAAEL 57
E + R+ + L+ L L I++++ D ++A +L K AEL
Sbjct: 41 EDLERLRLI--RRLRELGLSLKEIRELLDARDEELSLAALLALLDEKLAEL 89
>gnl|CDD|185741 cd09000, GH43_XYL_1, Glycosyl hydrolase family 43,
beta-D-xylosidase. This glycosyl hydrolase family 43
(GH43) includes mostly enzymes that have been
characterized to have beta-1,4-xylosidase
(beta-D-xylosidase;xylan 1,4-beta-xylosidase; EC
3.2.1.37) activity. They are part of an array of
hemicellulases that are involved in the final breakdown
of plant cell-wall whereby they degrade xylan. They
hydrolyze beta-1,4 glycosidic bonds between two xylose
units in short xylooligosaccharides. These are inverting
enzymes (i.e. they invert the stereochemistry of the
anomeric carbon atom of the substrate) that have an
aspartate as the catalytic general base, a glutamate as
the catalytic general acid and another aspartate that is
responsible for pKa modulation and orienting the
catalytic acid. A common structural feature of GH43
enzymes is a 5-bladed beta-propeller domain that
contains the catalytic acid and catalytic base. A long
V-shaped groove, partially enclosed at one end, forms a
single extended substrate-binding surface across the
face of the propeller.
Length = 288
Score = 28.2 bits (64), Expect = 2.4
Identities = 11/50 (22%), Positives = 21/50 (42%), Gaps = 4/50 (8%)
Query: 2 DTGEKEHVNRVIQVTELDLKTQALPLARIKKIMKLDDGVKMISAEAPMLF 51
D + + I + E+DL+T L + + + +G E P L+
Sbjct: 138 DERRGYNGHGGIWLQEIDLETGKL----LGEPKVIWNGTGGRWPEGPHLY 183
>gnl|CDD|234964 PRK01611, argS, arginyl-tRNA synthetase; Reviewed.
Length = 507
Score = 28.2 bits (64), Expect = 3.1
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 12/46 (26%)
Query: 67 WIHTE---DNKRRTLQRN---------DIAMAITKYDMFDFLIDIV 100
W+ D+K R L ++ DIA + K++ FD +I +V
Sbjct: 234 WVRLTEFGDDKDRVLIKSDGTYTYFTRDIAYHLYKFERFDRVIYVV 279
>gnl|CDD|165721 PLN00153, PLN00153, histone H2A; Provisional.
Length = 129
Score = 27.0 bits (59), Expect = 4.3
Identities = 17/63 (26%), Positives = 27/63 (42%)
Query: 25 LPLARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIA 84
P+ RI + +K + I A AP+ + E E+ A DNK+ + I
Sbjct: 25 FPVGRIARYLKKGKYAERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQ 84
Query: 85 MAI 87
+AI
Sbjct: 85 LAI 87
>gnl|CDD|205352 pfam13171, DUF4004, Protein of unknown function (DUF4004). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are approximately 210 amino acids in length.
Length = 199
Score = 26.9 bits (60), Expect = 5.7
Identities = 21/115 (18%), Positives = 39/115 (33%), Gaps = 16/115 (13%)
Query: 27 LARIKKIMK------LDDGVKMISAEAPMLFSKAAELFIHELTIRAWIH---TEDNKRRT 77
L RI KI K LD+ KM S + EL + + K
Sbjct: 53 LKRINKIQKMKDDLSLDELAKMFSPNMEEVELTEEELLRKGIVSETALEVFEEIVGKAEV 112
Query: 78 LQRNDIAMAITKYDMFDFL-IDIVPREEVKTATGPHRRDDATKTALNPDQVQYYF 131
+ D+ ++ Y + + L I+ +E K +++ T+ ++
Sbjct: 113 FEFRDL---LSLYVLEELLQSGIISLDEAKELALVLKKNY---TSEEMKDMELII 161
>gnl|CDD|224565 COG1651, DsbG, Protein-disulfide isomerase [Posttranslational
modification, protein turnover, chaperones].
Length = 244
Score = 26.7 bits (59), Expect = 8.0
Identities = 26/139 (18%), Positives = 41/139 (29%), Gaps = 20/139 (14%)
Query: 27 LARIKKIMKLDDGVKMISAEAPMLFSKAAELFIHELTIRAWIHTEDNKRRTLQRNDIAMA 86
+KK D V+++ E P F A + A + R +D
Sbjct: 103 FPELKKKYIDDGKVRLVLREFP--FLDPACPYCRRAAQAARCAADQGIVRYWAFHDALFG 160
Query: 87 ITKYDMFDFLIDIVPREEVKTATGPHRRDDATKTALNPDQVQYYFQLAQQHQ-AALQQNN 145
+ A D K L +L Q+ A + +N
Sbjct: 161 ---------------SQAEAWAASILCAKDLAKADLAALDEGKKAKLNQKACDALIAKNY 205
Query: 146 QGATTT--SATPTLVVNGG 162
+ A + TPT +VNG
Sbjct: 206 KLAQQLGVNGTPTFIVNGK 224
>gnl|CDD|217451 pfam03249, TSA, Type specific antigen. There are several antigenic
variants in Rickettsia tsutsugamushi, and a
type-specific antigen (TSA) of 56-kilodaltons located on
the rickettsial surface is responsible for the
variation. TSA proteins are probably integral membrane
proteins.
Length = 502
Score = 26.8 bits (59), Expect = 8.6
Identities = 19/65 (29%), Positives = 24/65 (36%), Gaps = 8/65 (12%)
Query: 125 DQVQYYFQLAQ--QHQAALQQNNQGATTTSATPTLVVNGGNSGAQQIQTIPMLLPLRTTY 182
+Q+Q F + Q Q Q QQ AT A V N Q IQ +
Sbjct: 298 NQIQLNFVIPQQAQQQGQGQQQQAQATAQEAAAAAAVRLLNGNEQIIQL------YKDLV 351
Query: 183 KLTQH 187
KL +H
Sbjct: 352 KLQRH 356
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 0.130 0.365
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: 9,432,493
Number of extensions: 857092
Number of successful extensions: 786
Number of sequences better than 10.0: 1
Number of HSP's gapped: 786
Number of HSP's successfully gapped: 26
Length of query: 191
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 100
Effective length of database: 6,901,388
Effective search space: 690138800
Effective search space used: 690138800
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: 56 (25.3 bits)