RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10641
(97 letters)
>gnl|CDD|236973 PRK11767, PRK11767, SpoVR family protein; Provisional.
Length = 498
Score = 30.2 bits (69), Expect = 0.14
Identities = 14/28 (50%), Positives = 18/28 (64%), Gaps = 1/28 (3%)
Query: 58 PRRIASLTEDVNRQKEREAVLQERFGAL 85
P++I SL E+ RQKERE LQ + L
Sbjct: 182 PQKI-SLQEEKARQKEREEYLQSQVNDL 208
>gnl|CDD|184281 PRK13729, PRK13729, conjugal transfer pilus assembly protein TraB;
Provisional.
Length = 475
Score = 27.5 bits (61), Expect = 1.1
Identities = 12/59 (20%), Positives = 25/59 (42%), Gaps = 12/59 (20%)
Query: 19 QARAQELLKQYKVLESQIDQCYVDLSTFSFLKTQEEASIPRRIASLTEDVNR-QKEREA 76
Q A ++ KQY+ + ++D + ++ RRI L +D ++ +A
Sbjct: 75 QVTAAQMQKQYEEIRRELD-----------VLNKQRGDDQRRIEKLGQDNAALAEQVKA 122
>gnl|CDD|220716 pfam10359, Fmp27_WPPW, RNA pol II promoter Fmp27 protein domain.
Fmp27_WPPW is a conserved domain of a family of proteins
involved in RNA polymerase II transcription initiation.
It contains characteristic HQR and WPPW sequence motifs.
and is towards the C-terminal in members which contain
Fmp27_SW pfam10305.
Length = 470
Score = 27.3 bits (61), Expect = 1.2
Identities = 18/83 (21%), Positives = 37/83 (44%), Gaps = 14/83 (16%)
Query: 9 VQMKILLGGYQARAQELLKQYKVLESQIDQCYVDLSTFSFLKTQEEASIPRRIASLTEDV 68
VQ ++L + R ++L +Q K LE ++D L+ + + + L E++
Sbjct: 161 VQRELL----EERLKQLEEQIKKLEEKLD----------DLELNDTEELQSDLEELEEEL 206
Query: 69 NRQKEREAVLQERFGALDAQLKQ 91
+ KER L++ L+ +
Sbjct: 207 SVLKERLEFLEKLLEDLERSEES 229
>gnl|CDD|233758 TIGR02169, SMC_prok_A, chromosome segregation protein SMC,
primarily archaeal type. SMC (structural maintenance of
chromosomes) proteins bind DNA and act in organizing and
segregating chromosomes for partition. SMC proteins are
found in bacteria, archaea, and eukaryotes. It is found
in a single copy and is homodimeric in prokaryotes, but
six paralogs (excluded from this family) are found in
eukarotes, where SMC proteins are heterodimeric. This
family represents the SMC protein of archaea and a few
bacteria (Aquifex, Synechocystis, etc); the SMC of other
bacteria is described by TIGR02168. The N- and
C-terminal domains of this protein are well conserved,
but the central hinge region is skewed in composition
and highly divergent [Cellular processes, Cell division,
DNA metabolism, Chromosome-associated proteins].
Length = 1164
Score = 27.3 bits (61), Expect = 1.4
Identities = 14/76 (18%), Positives = 35/76 (46%), Gaps = 11/76 (14%)
Query: 18 YQARAQELLKQYKVLESQIDQCYVDLSTFSFLKTQEEASIPRRIASLTEDVNRQKEREAV 77
+A ++L + L+ + D+ L + R+I L + ++++R +
Sbjct: 873 LEAALRDLESRLGDLKKERDELEAQLR-----------ELERKIEELEAQIEKKRKRLSE 921
Query: 78 LQERFGALDAQLKQLE 93
L+ + AL+ +L ++E
Sbjct: 922 LKAKLEALEEELSEIE 937
>gnl|CDD|217372 pfam03105, SPX, SPX domain. We have named this region the SPX
domain after (SYG1, Pho81 and XPR1). This 180 residue
length domain is found at the amino terminus of a
variety of proteins. In the yeast protein SYG1, the
N-terminus directly binds to the G- protein beta subunit
and inhibits transduction of the mating pheromone
signal. This finding suggests that all the members of
this family are involved in G-protein associated signal
transduction. The N-termini of several proteins involved
in the regulation of phosphate transport, including the
putative phosphate level sensors PHO81 from
Saccharomyces cerevisiae and NUC-2 from Neurospora
crassa, are also members of this family. The SPX domain
of S. cerevisiae low-affinity phosphate transporters
Pho87 and Pho90 auto-regulates uptake and prevents
efflux. This SPX dependent inhibition is mediated by the
physical interaction with Spl2 NUC-2 contains several
ankyrin repeats pfam00023. Several members of this
family are annotated as XPR1 proteins: the xenotropic
and polytropic retrovirus receptor confers
susceptibility to infection with murine leukaemia
viruses (MLV). The similarity between SYG1, phosphate
regulators and XPR1 sequences has been previously noted,
as has the additional similarity to several predicted
proteins, of unknown function, from Drosophila
melanogaster, Arabidopsis thaliana, Caenorhabditis
elegans, Schizosaccharomyces pombe, and Saccharomyces
cerevisiae. In addition, given the similarities between
XPR1 and SYG1 and phosphate regulatory proteins, it has
been proposed that XPR1 might be involved in G-protein
associated signal transduction and may itself function
as a phosphate sensor.
Length = 176
Score = 26.2 bits (58), Expect = 2.7
Identities = 16/91 (17%), Positives = 34/91 (37%), Gaps = 13/91 (14%)
Query: 3 FVACLCVQMKILLGGYQARAQELLKQYKVLESQIDQCYVDLSTFSFLKTQEEASIPRRIA 62
F L +++ + Y+ + ELL++ + LE Q++ EE A
Sbjct: 65 FFEALDKELEKVNSFYKEKEAELLERLEELEKQLE-------------ELEERRDETSSA 111
Query: 63 SLTEDVNRQKEREAVLQERFGALDAQLKQLE 93
+ + L++ L +L+ L+
Sbjct: 112 KSSPSDKNLLKAFEELKKALLELYRELQLLK 142
>gnl|CDD|234799 PRK00578, prfB, peptide chain release factor 2; Validated.
Length = 367
Score = 26.0 bits (58), Expect = 3.6
Identities = 20/77 (25%), Positives = 36/77 (46%), Gaps = 12/77 (15%)
Query: 19 QARAQELLKQYKVLESQIDQCYVDLSTFSFLKTQ-EEASIPRRIASLTEDVNRQKEREAV 77
Q RAQ++ K+ L++++D T L+ + ++ +A +D E EA
Sbjct: 48 QERAQKVTKELSSLKAKLD-------TLEELRQRLDDLEELLELAEEEDDEETLAEAEAE 100
Query: 78 LQERFGALDAQLKQLEL 94
L+ L+ +L LEL
Sbjct: 101 LKA----LEKKLAALEL 113
>gnl|CDD|237329 PRK13278, purP,
5-formaminoimidazole-4-carboxamide-1-(beta)-D-
ribofuranosyl 5'-monophosphate synthetase; Provisional.
Length = 358
Score = 25.2 bits (56), Expect = 6.0
Identities = 10/23 (43%), Positives = 15/23 (65%)
Query: 40 YVDLSTFSFLKTQEEASIPRRIA 62
Y++ S +S+L E S+ RRIA
Sbjct: 319 YMNGSPYSYLYWDEPMSMGRRIA 341
>gnl|CDD|223496 COG0419, SbcC, ATPase involved in DNA repair [DNA replication,
recombination, and repair].
Length = 908
Score = 25.5 bits (56), Expect = 6.3
Identities = 15/74 (20%), Positives = 34/74 (45%)
Query: 20 ARAQELLKQYKVLESQIDQCYVDLSTFSFLKTQEEASIPRRIASLTEDVNRQKEREAVLQ 79
+E L+ + L ++++ L + + E + + + L E + E +L+
Sbjct: 301 EELEEELEGLRALLEELEELLEKLKSLEERLEKLEEKLEKLESELEELAEEKNELAKLLE 360
Query: 80 ERFGALDAQLKQLE 93
ER L+ +L++LE
Sbjct: 361 ERLKELEERLEELE 374
>gnl|CDD|232965 TIGR00414, serS, seryl-tRNA synthetase. This model represents the
seryl-tRNA synthetase found in most organisms. This
protein is a class II tRNA synthetase, and is recognized
by the pfam model tRNA-synt_2b. The seryl-tRNA
synthetases of two archaeal species, Methanococcus
jannaschii and Methanobacterium thermoautotrophicum,
differ considerably and are included in a different
model [Protein synthesis, tRNA aminoacylation].
Length = 418
Score = 25.0 bits (55), Expect = 6.9
Identities = 15/74 (20%), Positives = 31/74 (41%)
Query: 21 RAQELLKQYKVLESQIDQCYVDLSTFSFLKTQEEASIPRRIASLTEDVNRQKEREAVLQE 80
+ L + K L S+I++ + S + + +I + +++ KE L
Sbjct: 31 KLIALDDERKKLLSEIEELQAKRNELSKQIGKAKGQKKDKIEEIKKELKELKEELTELSA 90
Query: 81 RFGALDAQLKQLEL 94
AL+A+L+ L
Sbjct: 91 ALKALEAELQDKLL 104
>gnl|CDD|221991 pfam13226, DUF4034, Domain of unknown function (DUF4034). This
presumed domain is functionally uncharacterized. This
domain family is found in bacteria, and is
approximately 280 amino acids in length. There is a
conserved PRW sequence motif.
Length = 277
Score = 24.7 bits (54), Expect = 8.3
Identities = 8/20 (40%), Positives = 11/20 (55%)
Query: 74 REAVLQERFGALDAQLKQLE 93
RE + + RF LD L+Q
Sbjct: 8 RELLRENRFDELDHFLEQAL 27
>gnl|CDD|181432 PRK08453, fliD, flagellar capping protein; Validated.
Length = 673
Score = 24.8 bits (54), Expect = 9.1
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 54 EASIPRRIASLTED----VNRQKEREAVLQERFGALDAQLKQ 91
E S+ R SLT+D K R ++ ERF A D+Q+ +
Sbjct: 623 EDSLTRDAKSLTKDKENAQELLKTRYDIMAERFAAYDSQISK 664
>gnl|CDD|227393 COG5061, ERO1, Oxidoreductin, endoplasmic reticulum
membrane-associated protein involved in disulfide bond
formation [Posttranslational modification, protein
turnover, chaperones / Intracellular trafficking and
secretion].
Length = 425
Score = 24.8 bits (54), Expect = 9.4
Identities = 11/37 (29%), Positives = 20/37 (54%)
Query: 15 LGGYQARAQELLKQYKVLESQIDQCYVDLSTFSFLKT 51
+G + R + Y ++ S + + VDLS+F+F T
Sbjct: 221 VGNFPDRIENFYFNYALVRSALGKIDVDLSSFTFCPT 257
>gnl|CDD|180820 PRK07064, PRK07064, hypothetical protein; Provisional.
Length = 544
Score = 24.6 bits (54), Expect = 9.7
Identities = 13/45 (28%), Positives = 19/45 (42%), Gaps = 8/45 (17%)
Query: 37 DQCYVDLSTFSFLKTQEEASIP-RRIASLTEDVNRQKEREAVLQE 80
+ YV+L T F +P R+ S + EAVL+E
Sbjct: 476 RRYYVELHTPDFALLAASLGLPHWRVTSA-------DDFEAVLRE 513
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 0.135 0.366
Gapped
Lambda K H
0.267 0.0856 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,757,762
Number of extensions: 383727
Number of successful extensions: 689
Number of sequences better than 10.0: 1
Number of HSP's gapped: 676
Number of HSP's successfully gapped: 99
Length of query: 97
Length of database: 10,937,602
Length adjustment: 64
Effective length of query: 33
Effective length of database: 8,098,946
Effective search space: 267265218
Effective search space used: 267265218
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: 53 (24.0 bits)