RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy338
(72 letters)
>gnl|CDD|107299 cd06304, PBP1_BmpA_like, Periplasmic binding component of a
family of basic membrane lipoproteins from Borrelia and
various putative lipoproteins from other bacteria.
Periplasmic binding component of a family of basic
membrane lipoproteins from Borrelia and various
putative lipoproteins from other bacteria. These outer
membrane proteins include Med, a cell-surface localized
protein regulating the competence transcription factor
gene comK in Bacillus subtilis, and PnrA, a periplasmic
purine nucleoside binding protein of an ATP-binding
cassette (ABC) transport system in Treponema pallidum.
All contain the type I periplasmic sugar-binding
protein-like fold.
Length = 260
Score = 28.6 bits (65), Expect = 0.19
Identities = 10/37 (27%), Positives = 20/37 (54%)
Query: 15 HQAALLKLEEKCKIEMDQHKSLLDKEYETLLQQFSRE 51
L K E++ +E+ +S+ D +YE L+Q + +
Sbjct: 19 AYEGLEKAEKELGVEVKYVESVEDADYEPNLRQLAAQ 55
>gnl|CDD|221737 pfam12726, SEN1_N, SEN1 N terminal. This domain is found at the N
terminal of the helicase SEN1. SEN1 is a Pol II
termination factor for noncoding RNA genes. The N
terminal of SEN1, unlike the C terminal, is not required
for growth.
Length = 724
Score = 28.4 bits (64), Expect = 0.24
Identities = 15/47 (31%), Positives = 23/47 (48%)
Query: 19 LLKLEEKCKIEMDQHKSLLDKEYETLLQQFSRELEKLTLKHTSELEK 65
L K K K E+ K+ +K + L + S+ LE+L+ SEL
Sbjct: 469 LEKFPPKGKDELTAEKTQFNKIVQQLTELISQILERLSDFDPSELSS 515
>gnl|CDD|216179 pfam00898, Orbi_VP2, Orbivirus outer capsid protein VP2. VP2 acts
as an anchor for VP1 and VP3. VP2 contains a
non-specific DNA and RNA binding domain in the
N-terminus.
Length = 946
Score = 26.9 bits (60), Expect = 0.89
Identities = 12/52 (23%), Positives = 23/52 (44%), Gaps = 6/52 (11%)
Query: 21 KLEEKCKIEMDQHKSLLDKEYETLLQQFSRELEKLTLKHTSELEKKAKLNTS 72
K E CKI + +LD E E ++ L+++ +L++K +
Sbjct: 260 KALELCKILSAIGRKMLDTEEE------PKDEMDLSVRFQFKLDEKFRRTDQ 305
>gnl|CDD|215168 PLN02299, PLN02299, 1-aminocyclopropane-1-carboxylate oxidase.
Length = 321
Score = 25.9 bits (57), Expect = 2.1
Identities = 10/19 (52%), Positives = 14/19 (73%)
Query: 37 LDKEYETLLQQFSRELEKL 55
LD EY +++ F+ ELEKL
Sbjct: 109 LDDEYRKVMKDFALELEKL 127
>gnl|CDD|233051 TIGR00611, recf, recF protein. All proteins in this family for
which functions are known are DNA binding proteins that
assist the filamentation of RecA onto DNA for the
initiation of recombination or recombinational repair.
This family is based on the phylogenomic analysis of JA
Eisen (1999, Ph.D. Thesis, Stanford University) [DNA
metabolism, DNA replication, recombination, and repair].
Length = 365
Score = 24.6 bits (54), Expect = 4.8
Identities = 11/31 (35%), Positives = 15/31 (48%)
Query: 37 LDKEYETLLQQFSRELEKLTLKHTSELEKKA 67
L+ E + Q ELE L+L + EL K
Sbjct: 204 LEPEAQKAHQLLLPELESLSLFYRGELWDKE 234
>gnl|CDD|237026 PRK11930, PRK11930, putative bifunctional
UDP-N-acetylmuramoyl-tripeptide:D-alanyl-D-alanine
ligase/alanine racemase; Provisional.
Length = 822
Score = 24.5 bits (54), Expect = 5.2
Identities = 8/37 (21%), Positives = 16/37 (43%)
Query: 21 KLEEKCKIEMDQHKSLLDKEYETLLQQFSRELEKLTL 57
K+ EK K+ D + + + E + ++ L L
Sbjct: 205 KIMEKLKLFKDCDVIIYNGDNELISSCITKSNLTLKL 241
>gnl|CDD|241183 cd12739, RRM2_ESRP1, RNA recognition motif 2 in epithelial splicing
regulatory protein 1 (ESRP1) and similar proteins. This
subgroup corresponds to the RRM2 of ESRP1, also termed
RNA-binding motif protein 35A (RBM35A), which has been
identified as an epithelial cell type-specific regulator
of fibroblast growth factor receptor 2 (FGFR2) splicing.
It is required for expression of epithelial FGFR2-IIIb
and the regulation of CD44, CTNND1 (also termed
p120-Catenin) and ENAH (also termed hMena) splicing. It
enhances epithelial-specific exons of CD44 and ENAH,
silences mesenchymal exons of CTNND1, or both within
FGFR2. Additional research indicated that ESRP1
functions as a tumor suppressor in colon cancer cells.
It may be involved in posttranscriptional regulation of
various genes by exerting a differential effect on
protein translation via 5' untranslated regions (UTRs)
of mRNAs. ESRP1 contains three RNA recognition motifs
(RRMs), also termed RBDs (RNA binding domains) or RNPs
(ribonucleoprotein domains). .
Length = 109
Score = 24.2 bits (52), Expect = 5.6
Identities = 12/43 (27%), Positives = 24/43 (55%)
Query: 19 LLKLEEKCKIEMDQHKSLLDKEYETLLQQFSRELEKLTLKHTS 61
L EE + + +HK LL K Y L + + E++++ +++S
Sbjct: 67 LFACEEYAQNALKKHKDLLGKRYIELFRSTAAEVQQVLNRYSS 109
>gnl|CDD|236510 PRK09428, pssA, phosphatidylserine synthase; Provisional.
Length = 451
Score = 24.4 bits (54), Expect = 5.6
Identities = 12/37 (32%), Positives = 19/37 (51%), Gaps = 5/37 (13%)
Query: 36 LLDKEYETLLQQFSRELEKL-----TLKHTSELEKKA 67
L+ + L +Q +ELE + +KH S+LE A
Sbjct: 389 LIHDPKQELAEQREKELELIRTHTTRVKHYSQLESIA 425
>gnl|CDD|107271 cd06276, PBP1_FucR_like, Ligand-binding domain of a transcription
repressor, FucR, which functions as a molecular sensor
of L-fucose availability. Ligand-binding domain of a
transcription repressor, FucR, which functions as a
molecular sensor of L-fucose availability. FcuR acts as
an inducer of fucRRIAK and as a corepressor of another
locus that regulates production of fucosylated glycans.
FcuR and its close homologs in this group are a member
of the LacI-GalR family repressors that 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 sugar-binding domain
of ABC-type transport systems that contain the type I
periplasmic binding protein-like fold. 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 = 247
Score = 24.5 bits (54), Expect = 6.0
Identities = 15/54 (27%), Positives = 24/54 (44%)
Query: 16 QAALLKLEEKCKIEMDQHKSLLDKEYETLLQQFSRELEKLTLKHTSELEKKAKL 69
Q LLK K K+ + H EY ++ Q F + + + +L+K KL
Sbjct: 67 QYFLLKKIPKEKLLILDHSIPEGGEYSSVAQDFEKAIYNALQEGLEKLKKYKKL 120
>gnl|CDD|220565 pfam10095, DUF2333, Uncharacterized protein conserved in bacteria
(DUF2333). Members of this family of hypothetical
bacterial proteins have no known function.
Length = 337
Score = 24.2 bits (53), Expect = 6.4
Identities = 12/26 (46%), Positives = 13/26 (50%)
Query: 28 IEMDQHKSLLDKEYETLLQQFSRELE 53
IE+D L K LQQ RELE
Sbjct: 264 IEVDFADVLEKKNATVSLQQIIRELE 289
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
0.311 0.124 0.325
Gapped
Lambda K H
0.267 0.0783 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 3,440,053
Number of extensions: 263513
Number of successful extensions: 439
Number of sequences better than 10.0: 1
Number of HSP's gapped: 437
Number of HSP's successfully gapped: 68
Length of query: 72
Length of database: 10,937,602
Length adjustment: 42
Effective length of query: 30
Effective length of database: 9,074,734
Effective search space: 272242020
Effective search space used: 272242020
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)