RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy5990
(119 letters)
>gnl|CDD|227446 COG5116, RPN2, 26S proteasome regulatory complex component
[Posttranslational modification, protein turnover,
chaperones].
Length = 926
Score = 93.5 bits (232), Expect = 2e-23
Identities = 38/102 (37%), Positives = 61/102 (59%)
Query: 1 MNTVAGVISLLDDPMIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAA 60
M T + +LL + + +L +N VD WPE+S+ ++ IE L++D F ++AA
Sbjct: 3 MTTARILPALLAELRDGRESEALDVINAHVDQLWPEISDDLRYIEALYDDDSFDPREMAA 62
Query: 61 LVASKVYFHLGSFSDSLQYALGAGDLFDVRNDTVYVKTIICK 102
L SKVY+ LG + +++YAL AGD F V + + Y +TI+ K
Sbjct: 63 LCLSKVYYVLGEYQQAIEYALRAGDRFLVDDGSFYYETIVYK 104
>gnl|CDD|178128 PLN02512, PLN02512, acetylglutamate kinase.
Length = 309
Score = 29.7 bits (67), Expect = 0.34
Identities = 11/32 (34%), Positives = 18/32 (56%)
Query: 1 MNTVAGVISLLDDPMIELKEFSLKKLNDIVDD 32
+ VAGV+ DDP +KE +K + ++ D
Sbjct: 226 LTDVAGVLEDKDDPGSLVKELDIKGVRKLIAD 257
>gnl|CDD|215419 PLN02784, PLN02784, alpha-amylase.
Length = 894
Score = 28.1 bits (62), Expect = 1.3
Identities = 11/23 (47%), Positives = 14/23 (60%)
Query: 63 ASKVYFHLGSFSDSLQYALGAGD 85
AS+ YF +G + DSL Y G D
Sbjct: 689 ASEPYFAVGEYWDSLSYTYGEMD 711
>gnl|CDD|129694 TIGR00606, rad50, rad50. All proteins in this family for which
functions are known are involvedin recombination,
recombinational repair, and/or non-homologous end
joining.They are components of an exonuclease complex
with MRE11 homologs. This family is distantly related to
the SbcC family of bacterial proteins.This family is
based on the phylogenomic analysis of JA Eisen (1999,
Ph.D. Thesis, Stanford University).
Length = 1311
Score = 26.9 bits (59), Expect = 3.0
Identities = 10/38 (26%), Positives = 20/38 (52%), Gaps = 2/38 (5%)
Query: 11 LDDPMIELKEFSLKKLNDIVDDFWPEV--SEAIQKIEI 46
LD +++ ++++N I+ D W + I+ IEI
Sbjct: 1127 LDQAIMKFHSMKMEEINKIIRDLWRSTYRGQDIEYIEI 1164
>gnl|CDD|169401 PRK08359, PRK08359, transcription factor; Validated.
Length = 176
Score = 26.4 bits (58), Expect = 4.1
Identities = 10/16 (62%), Positives = 12/16 (75%)
Query: 28 DIVDDFWPEVSEAIQK 43
DIV+D+ V EAIQK
Sbjct: 81 DIVEDYAERVYEAIQK 96
>gnl|CDD|236452 PRK09285, PRK09285, adenylosuccinate lyase; Provisional.
Length = 456
Score = 26.3 bits (59), Expect = 4.2
Identities = 15/42 (35%), Positives = 22/42 (52%), Gaps = 4/42 (9%)
Query: 8 ISLLDDPMI-ELKEFS---LKKLNDIVDDFWPEVSEAIQKIE 45
I+L P I E+ FS L IV++F E + I++IE
Sbjct: 45 IALAAHPGIPEVPPFSAEANAFLRAIVENFSEEDAARIKEIE 86
>gnl|CDD|233701 TIGR02055, APS_reductase, thioredoxin-dependent adenylylsulfate APS
reductase. This model describes recently identified
adenosine 5'-phosphosulfate (APS) reductase activity
found in sulfate-assimilatory prokaryotes, thus
separating it from the traditionally described
phosphoadenosine 5'-phosphosulfate (PAPS) reductases
found in bacteria and fungi. Homologous to PAPS
reductase in enterobacteria, cyanobacteria, and yeast,
APS reductase here clusters with, and demonstrates
greater homology to plant APS reductase. Additionally,
the presence of two conserved C-terminal motifs
(CCXXRKXXPL & SXGCXXCT) distinguishes APS substrate
specificity and serves as a FeS cluster [Central
intermediary metabolism, Sulfur metabolism].
Length = 191
Score = 25.9 bits (57), Expect = 5.2
Identities = 17/46 (36%), Positives = 25/46 (54%), Gaps = 6/46 (13%)
Query: 14 PMIELKE-FSLKKLNDIVDDFWPEVSEAIQKIEI----LHEDKGFP 54
P +E+ E F L K+N + D +V E I E+ LH D+G+P
Sbjct: 113 PFLEIDEAFGLVKINPLADWTSEDVWEYIADNELPYNPLH-DRGYP 157
>gnl|CDD|233709 TIGR02073, PBP_1c, penicillin-binding protein 1C. This subfamily
of the penicillin binding proteins includes the member
from E. coli designated penicillin-binding protein 1C.
Members have both transglycosylase and transpeptidase
domains and are involved in forming cross-links in the
late stages of peptidoglycan biosynthesis. All members
of this subfamily are presumed to have the same basic
function [Cell envelope, Biosynthesis and degradation
of murein sacculus and peptidoglycan].
Length = 727
Score = 26.2 bits (58), Expect = 5.7
Identities = 9/36 (25%), Positives = 15/36 (41%), Gaps = 13/36 (36%)
Query: 36 EVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLG 71
++S + +L+EDK F Y+H G
Sbjct: 40 DISPKFLQALLLYEDKRF-------------YWHPG 62
>gnl|CDD|183464 PRK12352, PRK12352, putative carbamate kinase; Reviewed.
Length = 316
Score = 25.5 bits (56), Expect = 7.0
Identities = 12/29 (41%), Positives = 17/29 (58%)
Query: 35 PEVSEAIQKIEILHEDKGFPQYKLAALVA 63
P+V +++ EI HE +G P LA VA
Sbjct: 55 PQVGLDLRRAEIAHEREGLPLTPLANCVA 83
>gnl|CDD|216950 pfam02259, FAT, FAT domain. The FAT domain is named after FRAP,
ATM and TRRAP.
Length = 350
Score = 25.8 bits (57), Expect = 7.4
Identities = 18/75 (24%), Positives = 31/75 (41%), Gaps = 3/75 (4%)
Query: 15 MIELKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFS 74
+ +L+EF L+ V SE + + +Y A L+A + + LG +
Sbjct: 205 IQKLREFVSCYLSKPVGSS--SDSELLLGLTYEVISSTNLEYFEAKLLA-RCFLKLGEWL 261
Query: 75 DSLQYALGAGDLFDV 89
D LQ G G ++
Sbjct: 262 DKLQMNWGQGKKDEI 276
>gnl|CDD|223293 COG0215, CysS, Cysteinyl-tRNA synthetase [Translation, ribosomal
structure and biogenesis].
Length = 464
Score = 25.7 bits (57), Expect = 7.5
Identities = 19/59 (32%), Positives = 26/59 (44%), Gaps = 13/59 (22%)
Query: 23 LKKLNDIVDDFWPEVSEAIQK----IEILHEDKGFPQYKLAALVASK--VYFHLGSFSD 75
+ LN + D P +E I + IE L +KG+ A VA VYF + F D
Sbjct: 100 MDALNVLPPDIEPRATEHIDEIIEFIEKL-IEKGY------AYVADDGDVYFDVSKFKD 151
>gnl|CDD|176470 cd01598, PurB, PurB_like adenylosuccinases (adenylsuccinate
lyase, ASL). This subgroup contains EcASL, the product
of the purB gene in Escherichia coli, and related
proteins. It is a member of the Lyase class I family of
the Lyase_I superfamily. Members of the Lyase class I
family function as homotetramers to catalyze similar
beta-elimination reactions in which a Calpha-N or
Calpha-O bond is cleaved with the subsequent release of
fumarate as one of the products. The four active sites
of the homotetrameric enzyme are each formed by
residues from three different subunits. ASL catalyzes
two non-sequential steps in the de novo purine
biosynthesis pathway: the conversion of
5-aminoimidazole-(N-succinylocarboxamide) ribotide
(SAICAR) into 5-aminoimidazole-4-carboxamide ribotide
(AICAR) and; the conversion of adenylsuccinate (SAMP)
into adenosine monophosphate (AMP).
Length = 425
Score = 25.7 bits (57), Expect = 7.5
Identities = 13/43 (30%), Positives = 24/43 (55%), Gaps = 4/43 (9%)
Query: 7 VISLLDDPMI-ELKEFS---LKKLNDIVDDFWPEVSEAIQKIE 45
+I+L + I E+ + LK L I+++F E + I++IE
Sbjct: 22 LIALSNLEEIPEVPPLTKEELKFLRAIIENFSEEDALRIKEIE 64
>gnl|CDD|227327 COG4994, COG4994, Uncharacterized protein conserved in bacteria
[Function unknown].
Length = 120
Score = 25.3 bits (55), Expect = 7.7
Identities = 19/73 (26%), Positives = 31/73 (42%), Gaps = 13/73 (17%)
Query: 5 AGVISLLDDPMIEL------KEFSLKKLND----IVDDFWPEVSEAIQKIEILHEDKGFP 54
+L+D E+ + + L L+ + D FW E+S+ +I+ L D
Sbjct: 25 EDFERMLEDDFWEVGASGYSRSYVLGVLDARHGHLGDAFW-EISDL--RIKALAPDNVLL 81
Query: 55 QYKLAALVASKVY 67
YKL LV + Y
Sbjct: 82 TYKLKTLVQNTRY 94
>gnl|CDD|234059 TIGR02917, PEP_TPR_lipo, putative PEP-CTERM system TPR-repeat
lipoprotein. This protein family occurs in strictly
within a subset of Gram-negative bacterial species with
the proposed PEP-CTERM/exosortase system, analogous to
the LPXTG/sortase system common in Gram-positive
bacteria. This protein occurs in a species if and only
if a transmembrane histidine kinase (TIGR02916) and a
DNA-binding response regulator (TIGR02915) also occur.
The present of tetratricopeptide repeats (TPR) suggests
protein-protein interaction, possibly for the regulation
of PEP-CTERM protein expression, since many PEP-CTERM
proteins in these genomes are preceded by a proposed DNA
binding site for the response regulator.
Length = 899
Score = 25.4 bits (56), Expect = 9.3
Identities = 9/26 (34%), Positives = 14/26 (53%)
Query: 54 PQYKLAALVASKVYFHLGSFSDSLQY 79
P+Y A L+A + LG+ + QY
Sbjct: 292 PEYLPALLLAGASEYQLGNLEQAYQY 317
>gnl|CDD|99863 cd06110, BSuCS-II_like, Bacillus subtilis (Bs) citrate synthase
(CS)-II_like. CS catalyzes the condensation of acetyl
coenzyme A (AcCoA) and oxalacetate (OAA) to form citrate
and coenzyme A (CoA), the first step in the citric acid
cycle (TCA or Krebs cycle). 2MCS catalyzes the
condensation of propionyl-coenzyme A (PrCoA) and OAA to
form 2-methylcitrate and CoA during propionate
metabolism. The overall CS reaction is thought to
proceed through three partial reactions: a) the
carbanion or equivalent is generated from AcCoA by base
abstraction of a proton, b) the nucleophilic attack of
this carbanion on OAA to generate citryl-CoA, and c) the
hydrolysis of citryl-CoA to produce citrate and CoA.
This group contains proteins similar to BsCS-II, the
major CS of the gram-positive bacterium Bacillus
subtilis. A mutation in the gene which encodes BsCS-II
(citZ gene) has been described which resulted in a
significant loss of CS activity, partial glutamate
auxotrophy, and a sporulation deficiency, all of which
are characteristic of strains defective in the Krebs
cycle. Streptococcus mutans CS, found in this group, may
participate in a pathway for the anaerobic biosynthesis
of glutamate. This group also contains functionally
uncharacterized CSs of various gram-negative bacteria.
Some of the gram-negative species represented in this
group have a second CS isozyme found in another group.
This group contains proteins which functions exclusively
as either a CS or a 2MCS, as well as those with relaxed
specificity which have dual functions as both a CS and a
2MCS.
Length = 356
Score = 25.3 bits (56), Expect = 10.0
Identities = 21/71 (29%), Positives = 29/71 (40%), Gaps = 16/71 (22%)
Query: 18 LKEFSLKKLNDIVDDFWPEVSEAIQKIEILHEDKGFPQYKLAALVASKVYFHLGSFSDSL 77
L+E S + + + W E+SEAI E + L V F +S S+
Sbjct: 267 LREMSRRLGKETGEPKWYEMSEAI-------EQAMRDEKGLNP----NVDF----YSASV 311
Query: 78 QYALG-AGDLF 87
Y LG DLF
Sbjct: 312 YYMLGIPVDLF 322
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
0.323 0.140 0.409
Gapped
Lambda K H
0.267 0.0722 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 6,057,972
Number of extensions: 534949
Number of successful extensions: 474
Number of sequences better than 10.0: 1
Number of HSP's gapped: 474
Number of HSP's successfully gapped: 26
Length of query: 119
Length of database: 10,937,602
Length adjustment: 82
Effective length of query: 37
Effective length of database: 7,300,574
Effective search space: 270121238
Effective search space used: 270121238
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 53 (24.2 bits)