RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy12404
(123 letters)
>gnl|CDD|218703 pfam05700, BCAS2, Breast carcinoma amplified sequence 2 (BCAS2).
This family consists of several eukaryotic sequences of
unknown function. The mammalian members of this family
are annotated as breast carcinoma amplified sequence 2
(BCAS2) proteins. BCAS2 is a putative spliceosome
associated protein.
Length = 221
Score = 131 bits (331), Expect = 1e-39
Identities = 59/126 (46%), Positives = 85/126 (67%), Gaps = 3/126 (2%)
Query: 1 MVEEETRRYRPTKNYLEHIPPL---DINKFETEIMRKDFERIQQRLPMEPLSMIRYKLPQ 57
+VEEE +RYRPTKNYLEH+P L D + FET ++R +FER+Q PM+ L M RY+LP+
Sbjct: 31 LVEEEMKRYRPTKNYLEHLPSLQGPDYSLFETPLLRNEFERVQAGQPMKGLDMSRYELPE 90
Query: 58 PPTGKMSDIAAWTECVENSMSQLEHQSTRIVNLQLMLEYGPETWKEYLQTLVNCVSQAQS 117
PP GK +D AW + N+ +QLEHQ RI+NL+L+ +YG W Y + L + + +
Sbjct: 91 PPAGKANDDKAWKAALNNARAQLEHQLIRIINLELLSKYGKNAWLVYNEQLEALLKRLEK 150
Query: 118 KLIQLR 123
+L +L+
Sbjct: 151 ELAELK 156
>gnl|CDD|153088 cd01679, RNR_I, Class I ribonucleotide reductase. Ribonucleotide
reductase (RNR) catalyzes the reductive synthesis of
deoxyribonucleotides from their corresponding
ribonucleotides. It provides the precursors necessary
for DNA synthesis. RNRs are separated into three classes
based on their metallocofactor usage. Class I RNRs,
found in eukaryotes, bacteria, and many viruses, use a
diiron-tyrosyl radical. Class II RNRs, found in
bacteria, bacteriophage, algae and archaea, use coenzyme
B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found
in anaerobic bacteria, bacteriophages, and archaea, use
an FeS cluster and S-adenosylmethionine to generate a
glycyl radical. Many organisms have more than one class
of RNR present in their genomes. All three RNRs have a
ten-stranded alpha-beta barrel domain that is
structurally similar to the domain of PFL (pyruvate
formate lyase). Class I RNR is oxygen-dependent and can
be subdivided into classes Ia (eukaryotes, prokaryotes,
viruses and phages) and Ib (which is found in
prokaryotes only). It is a tetrameric enzyme of two
alpha and two beta subunits; this model covers the major
part of the alpha or large subunit, called R1 in class
Ia and R1E in class Ib.
Length = 460
Score = 27.9 bits (63), Expect = 1.6
Identities = 17/68 (25%), Positives = 27/68 (39%), Gaps = 10/68 (14%)
Query: 59 PTGKMSDIAAWTECVENSMSQLEHQS-----TRIVN---LQLMLEYGPE-TWKEYLQ-TL 108
PT +S I T +E S + + +VN + + EYG T E Q L
Sbjct: 351 PTASISQILGATPSIEPITSNIYVRRVLSGEFPVVNPHLEKDLWEYGLYKTAYEIDQRWL 410
Query: 109 VNCVSQAQ 116
++ + Q
Sbjct: 411 IDLAADRQ 418
>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 = 27.7 bits (62), Expect = 2.0
Identities = 8/31 (25%), Positives = 15/31 (48%)
Query: 13 KNYLEHIPPLDINKFETEIMRKDFERIQQRL 43
+ ++ P ++ KF +I D +RI L
Sbjct: 29 QRFIRSFPIENVQKFMEKIDEWDIQRILPGL 59
>gnl|CDD|220450 pfam09869, DUF2096, Uncharacterized protein conserved in archaea
(DUF2096). This domain, found in various hypothetical
prokaryotic proteins, has no known function.
Length = 169
Score = 26.2 bits (58), Expect = 3.9
Identities = 11/38 (28%), Positives = 16/38 (42%), Gaps = 1/38 (2%)
Query: 10 RPTKNYLEHIPPLDINKFETEI-MRKDFERIQQRLPME 46
+ + PL +KF E+ K FE I+ LP
Sbjct: 85 KALRGEEVFEFPLKKSKFNVEVKRPKGFETIRVNLPEP 122
>gnl|CDD|235612 PRK05800, cobU, adenosylcobinamide
kinase/adenosylcobinamide-phosphate guanylyltransferase;
Validated.
Length = 170
Score = 25.9 bits (58), Expect = 4.6
Identities = 8/29 (27%), Positives = 14/29 (48%)
Query: 92 LMLEYGPETWKEYLQTLVNCVSQAQSKLI 120
L+ E G E + L+ + Q +K+I
Sbjct: 92 LLFEEGEEAIAAEIDALLAALQQLPAKII 120
>gnl|CDD|236448 PRK09281, PRK09281, F0F1 ATP synthase subunit alpha; Validated.
Length = 502
Score = 26.2 bits (59), Expect = 5.0
Identities = 7/20 (35%), Positives = 12/20 (60%)
Query: 12 TKNYLEHIPPLDINKFETEI 31
T YL+ +P + +FE E+
Sbjct: 441 TNGYLDDVPVEKVRRFEAEL 460
>gnl|CDD|225309 COG2511, GatE, Archaeal Glu-tRNAGln amidotransferase subunit E
(contains GAD domain) [Translation, ribosomal structure
and biogenesis].
Length = 631
Score = 26.2 bits (58), Expect = 5.1
Identities = 21/70 (30%), Positives = 27/70 (38%), Gaps = 9/70 (12%)
Query: 1 MVEEETRRYRP--TKNYLEHIPPLDINKFETEIMRKDFERIQQRLPMEPLSMIRYKLPQP 58
V EETR P T YL +P ET+I R+ E L I+ LP+
Sbjct: 403 GVPEETRGALPDGTTVYLRPLPGAARMYPETDIP-------PIRIDEELLEKIKENLPEL 455
Query: 59 PTGKMSDIAA 68
P K+
Sbjct: 456 PEEKVERYVK 465
>gnl|CDD|233211 TIGR00962, atpA, proton translocating ATP synthase, F1 alpha
subunit. The sequences of ATP synthase F1 alpha and
beta subunits are related and both contain a
nucleotide-binding site for ATP and ADP. They have a
common amino terminal domain but vary at the C-terminus.
The beta chain has catalytic activity, while the alpha
chain is a regulatory subunit. The alpha-subunit
contains a highly conserved adenine-specific
noncatalytic nucleotide-binding domain. The conserved
amino acid sequence is Gly-X-X-X-X-Gly-Lys. Proton
translocating ATP synthase F1, alpha subunit is
homologous to proton translocating ATP synthase
archaeal/vacuolar(V1), B subunit [Energy metabolism,
ATP-proton motive force interconversion].
Length = 501
Score = 26.2 bits (58), Expect = 5.3
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 9 YRPTKNYLEHIPPLDINKFETEIM 32
+ TK YL+ IP I KFE ++
Sbjct: 437 FAGTKGYLDDIPVDKIRKFEQALL 460
>gnl|CDD|131269 TIGR02214, spoVD_pbp, stage V sporulation protein D. This model
describes the spoVD subfamily of homologs of the cell
division protein FtsI, a penicillin binding protein.
This subfamily is restricted to Bacillus subtilis and
related Gram-positive species with known or suspected
endospore formation capability. In these species, the
functional equivalent of FtsI is desginated PBP-2B, a
paralog of spoVD [Cell envelope, Biosynthesis and
degradation of murein sacculus and peptidoglycan,
Cellular processes, Sporulation and germination].
Length = 636
Score = 26.3 bits (58), Expect = 5.4
Identities = 6/19 (31%), Positives = 12/19 (63%)
Query: 1 MVEEETRRYRPTKNYLEHI 19
V +++RY P ++L H+
Sbjct: 139 SVSPDSKRYYPNGDFLSHV 157
>gnl|CDD|188997 cd06459, M3B_PepF, Peptidase family M3B Oligopeptidase F (PepF).
Peptidase family M3B Oligopeptidase F (PepF;
Pz-peptidase B; EC 3.4.24.-) is mostly bacterial and
includes oligoendopeptidase F from Lactococcus lactis.
This enzyme hydrolyzes peptides containing between 7 and
17 amino acids with fairly broad specificity. The PepF
gene is duplicated in L. lactis on the plasmid that
bears it, while a shortened second copy is found in
Bacillus subtilis. Most bacterial PepFs are cytoplasmic
endopeptidases; however, the PepF Bacillus
amyloliquefaciens oligopeptidase is a secreted protein
and may facilitate the process of sporulation.
Specifically, the yjbG gene encoding the homolog of the
PepF1 and PepF2 oligoendopeptidases of Lactococcus
lactis has been identified in Bacillus subtilis as an
inhibitor of sporulation initiation when over expressed
from a multicopy plasmid.
Length = 450
Score = 25.5 bits (56), Expect = 8.8
Identities = 19/71 (26%), Positives = 23/71 (32%), Gaps = 15/71 (21%)
Query: 17 EHIPPLDINKFETEIMRKDFERIQQRLPMEPLSM--IRYKLPQPPTGKMSDIAAWTECVE 74
EH PL K ER Q+RL +E L + LP K + E V
Sbjct: 138 EHNVPL---------AAKFRERKQRRLGLEKLYFYDVPAPLPTGNEPKGT----ADEAVN 184
Query: 75 NSMSQLEHQST 85
N S
Sbjct: 185 NIREXYSRLSP 195
>gnl|CDD|205977 pfam13804, HERV-K_env_2, Retro-transcribing viruses envelope
glycoprotein. This family comes from human endogenous
retrovirus K envelope glycoproteins.
Length = 170
Score = 25.3 bits (55), Expect = 9.3
Identities = 16/60 (26%), Positives = 25/60 (41%), Gaps = 10/60 (16%)
Query: 58 PPTGKMSDIAAWTECVENSMSQLEHQSTRIVNLQLMLEYGPETWKEYLQTLVNCVSQAQS 117
P K +++ W ECV NS L++ + +++ P Q NC Q QS
Sbjct: 119 PKESKNTEVLVWEECVANSAVILQNNEFGTI-----IDWAPRG-----QFYHNCSGQTQS 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
0.317 0.132 0.387
Gapped
Lambda K H
0.267 0.0569 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,215,300
Number of extensions: 518310
Number of successful extensions: 503
Number of sequences better than 10.0: 1
Number of HSP's gapped: 502
Number of HSP's successfully gapped: 18
Length of query: 123
Length of database: 10,937,602
Length adjustment: 85
Effective length of query: 38
Effective length of database: 7,167,512
Effective search space: 272365456
Effective search space used: 272365456
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: 53 (24.6 bits)