RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10138
(183 letters)
>gnl|CDD|115928 pfam07303, Occludin_ELL, Occludin homology domain. This domain
represents a conserved region approximately 100 residues
long within eukaryotic occludin proteins and the RNA
polymerase II elongation factor ELL. Occludin is an
integral membrane protein that localises to tight
junctions, while ELL is an elongation factor that can
increase the catalytic rate of RNA polymerase II
transcription by suppressing transient pausing by
polymerase at multiple sites along the DNA. This shared
domain is thought to mediate protein interactions.
Length = 101
Score = 65.0 bits (159), Expect = 2e-14
Identities = 39/154 (25%), Positives = 58/154 (37%), Gaps = 54/154 (35%)
Query: 25 YTTIVDLEQRRRYKNDFSESYKEYQMLHAKIETVASRFASLQNQLRRETPGSFAHKAQGR 84
Y I EQR+RYK +F Y+EY+ L A+++ + R L +L GS +K
Sbjct: 1 YPPITSDEQRQRYKAEFDSDYQEYKELQAEVDAINKRLQQLDAELDSLPEGSQEYKTVAA 60
Query: 85 GSELFHAKMEPCCFRFRLSIAAAKIETVASRFASLQNQLRRETPGSFAHKQIQDTIVREY 144
+ + N+L++ +P Y
Sbjct: 61 QLDEY-------------------------------NRLKKRSPD--------------Y 75
Query: 145 HENKTDRKFEDCRRRFEYLHNKLSHIKKLVFIYD 178
E K R +YL NKLSHIK++V YD
Sbjct: 76 QEKK---------ERCKYLKNKLSHIKRMVSDYD 100
>gnl|CDD|115634 pfam06992, Phage_lambda_P, Replication protein P. This family
consists of several Bacteriophage lambda replication
protein P like proteins. The bacteriophage lambda P
protein promoters replication of the phage chromosome by
recruiting a key component of the cellular replication
machinery to the viral origin. Specifically, P protein
delivers one or more molecules of Escherichia coli DnaB
helicase to a nucleoprotein structure formed by the
lambda O initiator at the lambda replication origin.
Length = 233
Score = 31.7 bits (71), Expect = 0.15
Identities = 36/136 (26%), Positives = 56/136 (41%), Gaps = 10/136 (7%)
Query: 30 DLEQRRRYKNDFSESYKEYQMLHAKIETVASRFASLQNQLRRETPGSFAHKAQGRGSELF 89
D EQ RR N+ E Y E +++ VA + +QL P S A++ Q +E+
Sbjct: 12 DREQMRRIANNMPEQYDE----KPQVQQVAQIINGVFSQLLATFPASLANRDQNELNEI- 66
Query: 90 HAKMEPCCFRFRLSIAAAKIETVASRFASLQNQLRRETPGSFAHKQIQDTIVREYHENKT 149
+ FR I + + R A QN+ +PG F ++ V N +
Sbjct: 67 -RRQWVLAFR-ENGITSMEQVNAGMRVARRQNRPFLPSPGQFVAWCREEASVIAGLPNVS 124
Query: 150 ---DRKFEDCRRRFEY 162
D +E CR+R Y
Sbjct: 125 ELVDMVYEYCRKRGLY 140
>gnl|CDD|206357 pfam14189, DUF4312, Domain of unknown function (DUF4312). This
family of proteins is functionally uncharacterized. This
family of proteins is found in bacteria. Proteins in
this family are typically between 99 and 118 amino acids
in length.
Length = 85
Score = 28.0 bits (63), Expect = 0.95
Identities = 11/46 (23%), Positives = 18/46 (39%)
Query: 108 KIETVASRFASLQNQLRRETPGSFAHKQIQDTIVREYHENKTDRKF 153
K + A +S+Q + + T G + D V + E KF
Sbjct: 15 KEKAFAKALSSIQKTVLKNTNGVLLRIEPVDVYVLKAKEKVKTEKF 60
>gnl|CDD|238995 cd02038, FleN-like, FleN is a member of the Fer4_NifH superfamily.
It shares the common function as an ATPase, with the
ATP-binding domain at the N-terminus. In Pseudomonas
aeruginosa, FleN gene is involved in regulating the
number of flagella and chemotactic motility by
influencing FleQ activity.
Length = 139
Score = 28.7 bits (65), Expect = 1.2
Identities = 13/46 (28%), Positives = 22/46 (47%), Gaps = 5/46 (10%)
Query: 25 YTTIVDLEQRRRYKNDF-----SESYKEYQMLHAKIETVASRFASL 65
Y I L ++ R N +ES KE + + ++ V++RF L
Sbjct: 85 YALIKKLAKQLRVLNFRVVVNRAESPKEGKKVFKRLSNVSNRFLGL 130
>gnl|CDD|219925 pfam08598, Sds3, Sds3-like. Repression of gene transcription is
mediated by histone deacetylases containing
repressor-co-repressor complexes, which are recruited
to promoters of target genes via interactions with
sequence-specific transcription factors. The
co-repressor complex contains a core of at least seven
proteins. This family represents the conserved region
found in Sds3, Dep1 and BRMS1-homologue p40 proteins.
Length = 184
Score = 28.8 bits (65), Expect = 1.3
Identities = 13/42 (30%), Positives = 22/42 (52%)
Query: 30 DLEQRRRYKNDFSESYKEYQMLHAKIETVASRFASLQNQLRR 71
DLE+RR + +E +EY++ + E A R A+ Q +
Sbjct: 50 DLEERRDDRLKVAELRREYKLECIEREYEAERQAAKQEFEKE 91
>gnl|CDD|220502 pfam09984, DUF2222, Uncharacterized signal transduction histidine
kinase domain (DUF2222). Members of this family of
domains are found in various BarA-like signal
transduction histidine kinases, which are involved in
the regulation of carbon metabolism via the csrA/csrB
regulatory system. The role of this domain has not, as
yet, been established.
Length = 146
Score = 27.6 bits (62), Expect = 2.7
Identities = 13/33 (39%), Positives = 19/33 (57%)
Query: 149 TDRKFEDCRRRFEYLHNKLSHIKKLVFIYDSNN 181
TD+ E RR Y H K S I + + ++D+NN
Sbjct: 31 TDKNRESVRRLISYTHRKHSPIVRSIAVFDANN 63
>gnl|CDD|235639 PRK05899, PRK05899, transketolase; Reviewed.
Length = 586
Score = 27.8 bits (63), Expect = 4.0
Identities = 8/19 (42%), Positives = 10/19 (52%), Gaps = 3/19 (15%)
Query: 164 HNKLSHIKKLVFIYDSNNL 182
H KL L+ IYD N +
Sbjct: 176 HLKLG---NLIVIYDDNRI 191
>gnl|CDD|219934 pfam08614, ATG16, Autophagy protein 16 (ATG16). Autophagy is a
ubiquitous intracellular degradation system for
eukaryotic cells. During autophagy, cytoplasmic
components are enclosed in autophagosomes and delivered
to lysosomes/vacuoles. ATG16 (also known as Apg16) has
been shown to be bind to Apg5 and is required for the
function of the Apg12p-Apg5p conjugate in the yeast
autophagy pathway.
Length = 194
Score = 27.1 bits (60), Expect = 4.6
Identities = 24/98 (24%), Positives = 44/98 (44%), Gaps = 3/98 (3%)
Query: 31 LEQRRRYKNDFSESYKEYQMLHAKIETVASRFASLQNQLRRET-PGSFAHKAQGRGSELF 89
L+ R R + FSE +++Y+ L + + +LQ + + S + A G GS+
Sbjct: 9 LKDRDRREKAFSELFEQYRQLADRTRLLKVENDALQAEKYEQQSSHSSSPSADGPGSDAA 68
Query: 90 HAKMEPCCFRFRLSIAAA--KIETVASRFASLQNQLRR 125
A+ME + R + K +A R L ++L +
Sbjct: 69 IAEMEQKLAKLREELTELHKKRGELAQRLLLLNDELEQ 106
>gnl|CDD|220019 pfam08795, DUF1796, Putative papain-like cysteine peptidase
(DUF1796).
Length = 162
Score = 26.5 bits (59), Expect = 6.3
Identities = 15/55 (27%), Positives = 23/55 (41%), Gaps = 5/55 (9%)
Query: 122 QLRRETPGSFAHKQIQDTIVREYHENKTDRKFEDCRRRFEYLHNKLSHIKKLVFI 176
L R+ G F+H D + EY+ R RRF ++ K ++FI
Sbjct: 70 ILFRKQYGLFSHHDFNDPVDSEYY-----RFKARYVRRFRRFLATINSSKPVLFI 119
>gnl|CDD|193205 pfam12729, 4HB_MCP_1, Four helix bundle sensory module for signal
transduction. This family is a four helix bundle that
operates as a ubiquitous sensory module in prokaryotic
signal-transduction. The 4HB_MCP is always found between
two predicted transmembrane helices indicating that it
detects only extracellular signals. In many cases the
domain is associated with a cytoplasmic HAMP domain
suggesting that most proteins carrying the bundle might
share the mechanism of transmembrane signalling which is
well-characterized in E coli chemoreceptors.
Length = 181
Score = 26.4 bits (59), Expect = 6.6
Identities = 14/44 (31%), Positives = 23/44 (52%), Gaps = 4/44 (9%)
Query: 12 NSTSTFLPKYEKDYTTIVDLEQRRRYKNDFSESYKEYQMLHAKI 55
L KYEK TI+ E+++ + N+F E K Y+ + K+
Sbjct: 89 AEIDKLLKKYEK---TILTEEEKKLF-NEFKEQLKAYRKVRNKV 128
>gnl|CDD|236848 PRK11107, PRK11107, hybrid sensory histidine kinase BarA;
Provisional.
Length = 919
Score = 27.1 bits (61), Expect = 6.7
Identities = 20/76 (26%), Positives = 32/76 (42%), Gaps = 18/76 (23%)
Query: 112 VASRFASLQNQLRRETPGSFAHKQIQDTIVR------EYHENKTDRKFEDCRRRFEYLHN 165
V +R+ LQ QL G+ +I+ EY T + E R+ LH
Sbjct: 30 VVNRYNELQRQL--IDAGA--------SIIEPLAIASEYG--MTLQNRESVRQLISVLHR 77
Query: 166 KLSHIKKLVFIYDSNN 181
+ S I + + ++D NN
Sbjct: 78 RHSDIVRSIAVFDENN 93
>gnl|CDD|203011 pfam04433, SWIRM, SWIRM domain. This SWIRM domain is a small
alpha-helical domain of about 85 amino acid residues
found in chromosomal proteins. It contains a helix-turn
helix motif and binds to DNA.
Length = 80
Score = 25.2 bits (56), Expect = 7.6
Identities = 9/39 (23%), Positives = 16/39 (41%), Gaps = 3/39 (7%)
Query: 123 LRRETPGSFAHKQIQDTIVREYHENKTDR-KFEDCRRRF 160
+TP + +I++ I+ E+ N D RR
Sbjct: 22 FFLKTPEVY--LKIRNFIINEWRLNPGKYLTKTDARRLL 58
>gnl|CDD|238970 cd02012, TPP_TK, Thiamine pyrophosphate (TPP) family, Transketolase
(TK) subfamily, TPP-binding module; TK catalyzes the
transfer of a two-carbon unit from ketose phosphates to
aldose phosphates. In heterotrophic organisms, TK
provides a link between glycolysis and the pentose
phosphate pathway and provides precursors for
nucleotide, aromatic amino acid and vitamin
biosynthesis. In addition, the enzyme plays a central
role in the Calvin cycle in plants. Typically, TKs are
homodimers. They require TPP and divalent cations, such
as magnesium ions, for activity.
Length = 255
Score = 26.3 bits (59), Expect = 8.4
Identities = 8/19 (42%), Positives = 10/19 (52%), Gaps = 3/19 (15%)
Query: 164 HNKLSHIKKLVFIYDSNNL 182
H KL L+ I DSN +
Sbjct: 153 HYKLD---NLIAIVDSNRI 168
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
0.320 0.131 0.373
Gapped
Lambda K H
0.267 0.0756 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 8,998,487
Number of extensions: 794142
Number of successful extensions: 882
Number of sequences better than 10.0: 1
Number of HSP's gapped: 880
Number of HSP's successfully gapped: 29
Length of query: 183
Length of database: 10,937,602
Length adjustment: 91
Effective length of query: 92
Effective length of database: 6,901,388
Effective search space: 634927696
Effective search space used: 634927696
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 (21.9 bits)
S2: 56 (25.3 bits)