RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy3513
(140 letters)
>gnl|CDD|233902 TIGR02506, NrdE_NrdA, ribonucleoside-diphosphate reductase, alpha
subunit. This model represents the alpha (large) chain
of the class I ribonucleotide reductase (RNR). RNR's are
responsible for the conversion of the ribose sugar of
RNA into the deoxyribose sugar of DNA. This is the
rate-limiting step of DNA biosynthesis. Class I RNR's
generate the required radical (on tyrosine) via a
"non-heme" iron cofactor which resides in the beta
(small) subunit. The alpha subunit contains the
catalytic and allosteric regulatory sites. The mechanism
of this enzyme requires molecular oxygen. E. Coli
contains two versions of this enzyme which are regulated
independently (NrdAB and NrdEF, where NrdA and NrdE are
the large chains ). Most organisms contain only one, but
the application of the gene symbols NrdA and NrdE are
somewhat arbitrary. This model identifies RNR's in
diverse clades of bacteria, eukaryotes as well as
numerous DNA viruses and phage [Purines, pyrimidines,
nucleosides, and nucleotides, 2'-Deoxyribonucleotide
metabolism].
Length = 617
Score = 31.2 bits (71), Expect = 0.15
Identities = 9/34 (26%), Positives = 14/34 (41%)
Query: 104 YTFKECFKSIFRVHTETGNIWTHLLDILNKPLQN 137
+ ++ K I R ETG + D +NK
Sbjct: 249 VSARDLMKDILRTRVETGRPYILFKDAVNKHNPF 282
>gnl|CDD|217315 pfam03006, HlyIII, Haemolysin-III related. Members of this family
are integral membrane proteins. This family includes a
protein with hemolytic activity from Bacillus cereus. It
has been proposed that YOL002c encodes a Saccharomyces
cerevisiae protein that plays a key role in metabolic
pathways that regulate lipid and phosphate metabolism.
In eukaryotes, members are seven-transmembrane pass
molecules found to encode functional receptors with a
broad range of apparent ligand specificities, including
progestin and adipoQ receptors, and hence have been
named PAQR proteins. The mammalian members include
progesterone binding proteins. Unlike the case with GPCR
receptor proteins, the evolutionary ancestry of the
members of this family can be traced back to the
Archaea.
Length = 207
Score = 30.7 bits (70), Expect = 0.16
Identities = 10/15 (66%), Positives = 12/15 (80%)
Query: 114 FRVHTETGNIWTHLL 128
F +H ET NIWTHL+
Sbjct: 1 FSLHNETANIWTHLI 15
>gnl|CDD|224191 COG1272, COG1272, Predicted membrane protein, hemolysin III homolog
[General function prediction only].
Length = 226
Score = 30.3 bits (69), Expect = 0.28
Identities = 11/39 (28%), Positives = 18/39 (46%), Gaps = 10/39 (25%)
Query: 90 QDNDFLHTGHRPPLYTFKECFKSIFRVHTETGNIWTHLL 128
+DN+++ G R Y++ E E N THL+
Sbjct: 2 RDNNYIAEGKRSKSYSWHE----------EIANAITHLI 30
>gnl|CDD|147874 pfam05957, DUF883, Bacterial protein of unknown function
(DUF883). This family consists of several hypothetical
bacterial proteins of unknown function.
Length = 94
Score = 27.1 bits (61), Expect = 1.6
Identities = 11/30 (36%), Positives = 16/30 (53%), Gaps = 1/30 (3%)
Query: 47 VEDGLDAMNHMAHDAVEHAEEFVR-KVWQA 75
+ D DA A DA + A+++V WQA
Sbjct: 47 LGDAADAAAERARDAADAADDYVHENPWQA 76
>gnl|CDD|182670 PRK10715, flk, flagella biosynthesis regulator; Provisional.
Length = 335
Score = 27.3 bits (61), Expect = 3.2
Identities = 14/46 (30%), Positives = 18/46 (39%), Gaps = 11/46 (23%)
Query: 71 KVWQASWNVC-----------HFQHLPQWLQDNDFLHTGHRPPLYT 105
K+WQ+ + HF L QWLQ L H P L +
Sbjct: 187 KIWQSMLELSGVKSGELIPAKHFPLLSQWLQARQTLSQQHAPTLES 232
>gnl|CDD|233960 TIGR02642, phage_xxxx, uncharacterized phage protein. This
uncharacterized protein is found in prophage regions of
Shewanella oneidensis MR-1, Vibrio vulnificus YJ016,
Yersinia pseudotuberculosis IP 32953, and Aeromonas
hydrophila ATCC7966. It appears to have regions of
sequence similarity to phage lambda antitermination
protein Q [Mobile and extrachromosomal element
functions, Prophage functions].
Length = 186
Score = 26.8 bits (59), Expect = 3.5
Identities = 7/28 (25%), Positives = 12/28 (42%)
Query: 47 VEDGLDAMNHMAHDAVEHAEEFVRKVWQ 74
V +DA+ DA E +R ++
Sbjct: 159 VRAQVDALRRHESDAARVVERRIRLEFE 186
>gnl|CDD|225700 COG3158, Kup, K+ transporter [Inorganic ion transport and
metabolism].
Length = 627
Score = 27.2 bits (61), Expect = 3.7
Identities = 4/22 (18%), Positives = 7/22 (31%)
Query: 102 PLYTFKECFKSIFRVHTETGNI 123
PLY +E + +
Sbjct: 34 PLYALREALSGQGGLGVSRDEV 55
>gnl|CDD|237135 PRK12555, PRK12555, chemotaxis-specific methylesterase;
Provisional.
Length = 337
Score = 26.4 bits (59), Expect = 5.5
Identities = 14/51 (27%), Positives = 18/51 (35%), Gaps = 14/51 (27%)
Query: 41 VTQSL--NVEDGLDAMNHMAHDAV------------EHAEEFVRKVWQASW 77
VT N +AM A DAV E+A E + K+ Q
Sbjct: 79 VTSLTERNASRVFEAMGAGALDAVDTPTLGIGAGLEEYAAELLAKIDQIGR 129
>gnl|CDD|227886 COG5599, PTP2, Protein tyrosine phosphatase [Signal transduction
mechanisms].
Length = 302
Score = 26.0 bits (57), Expect = 9.1
Identities = 13/49 (26%), Positives = 19/49 (38%), Gaps = 8/49 (16%)
Query: 78 NVCHFQHLPQWLQDNDFLHTGHRPPLYTFKECFKSIFRVHTETGNIWTH 126
+ HFQ+ W+ DF P + + E S+ TG I H
Sbjct: 184 KIHHFQY-INWV---DFNV----PDIRSLTEVIHSLNDSPVRTGPIIVH 224
>gnl|CDD|221439 pfam12143, PPO1_KFDV, Protein of unknown function (DUF_B2219).
This domain family is found in eukaryotes, and is
typically between 138 and 152 amino acids in length. and
the family is found in association with pfam00264. Many
members are plant or plastid polyphenol oxidases, and
there is a highly conserved sequence motif: KFDV, from
which the name derives. This is the C-terminal domain of
these oxidases.
Length = 131
Score = 25.3 bits (56), Expect = 9.7
Identities = 12/20 (60%), Positives = 14/20 (70%)
Query: 4 LHLGIWELLEDELAEDDRDI 23
L LGI +LLED AEDD +
Sbjct: 90 LRLGITDLLEDLGAEDDDSV 109
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 0.137 0.451
Gapped
Lambda K H
0.267 0.0742 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 7,360,171
Number of extensions: 633056
Number of successful extensions: 565
Number of sequences better than 10.0: 1
Number of HSP's gapped: 564
Number of HSP's successfully gapped: 20
Length of query: 140
Length of database: 10,937,602
Length adjustment: 87
Effective length of query: 53
Effective length of database: 7,078,804
Effective search space: 375176612
Effective search space used: 375176612
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: 54 (24.6 bits)