RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy843
(109 letters)
>gnl|CDD|220631 pfam10210, MRP-S32, Mitochondrial 28S ribosomal protein S32.
This entry is of a family of short, approximately 100
amino acid residues, proteins which are mitochondrial
28S ribosomal proteins named as MRP-S32. Their exact
function could not be confirmed.
Length = 96
Score = 85.6 bits (212), Expect = 3e-23
Identities = 34/85 (40%), Positives = 52/85 (61%)
Query: 13 IAITADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFVR 72
+A+T+DG T+VCWHP PYEH+ PLP + +N+ Q ++ FK K E +R
Sbjct: 6 VALTSDGRTIVCWHPSVDVPYEHTKPLPRPDPLHSNAETHEQVLKTALEKFKHKHPEPMR 65
Query: 73 QDLMNITFTNKHRWFPVRKMRQKKR 97
++L + FT KHRW+P + R+ K+
Sbjct: 66 EELSKVFFTTKHRWYPRGRDRRAKK 90
>gnl|CDD|234031 TIGR02840, spore_YtaF, putative sporulation protein YtaF. This
protein family was identified, at the time of the
publication of the Carboxydothermus hydrogenoformans
genome, as having a phylogenetic profile that exactly
matches the subset of the Firmicutes capable of forming
endospores. The species include Bacillus anthracis,
Clostridium tetani, Thermoanaerobacter tengcongensis,
Geobacillus kaustophilus, etc. This protein, previously
named YtaF, is therefore a putative sporulation protein
[Cellular processes, Sporulation and germination].
Length = 206
Score = 27.2 bits (61), Expect = 1.3
Identities = 22/70 (31%), Positives = 29/70 (41%), Gaps = 7/70 (10%)
Query: 37 LPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFVRQDLMNITFTNKHRWFPVRKMRQKK 96
LP VTE IL + IYN F+PKKE R + T K F ++ +R
Sbjct: 58 LPPKVTEILGA-FILIAIGIWIIYNAFRPKKEVKDRSSEPDSTKELKSFGFVIQILR--- 113
Query: 97 RYFKPLIPDR 106
P + D
Sbjct: 114 ---NPEVADL 120
>gnl|CDD|236552 PRK09534, btuF, corrinoid ABC transporter substrate-binding
protein; Reviewed.
Length = 359
Score = 26.8 bits (59), Expect = 2.8
Identities = 15/65 (23%), Positives = 26/65 (40%)
Query: 1 MRTKRLVPLTHKIAITADGTTVVCWHPEQPFPYEHSLPLPVTEQQSTNSILKVQNVQEIY 60
MR + LV + + +TA G + Q + + PVTE +T + + + E
Sbjct: 4 MRFRSLVIVALAVTMTAAGGALAPAPAAQHADADRACSFPVTETDATGTEITLDERPERV 63
Query: 61 NVFKP 65
P
Sbjct: 64 VTLNP 68
>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 = 25.9 bits (57), Expect = 4.6
Identities = 15/76 (19%), Positives = 28/76 (36%), Gaps = 9/76 (11%)
Query: 33 YEHSLPLPVTEQQSTNSILKVQNVQEIYNVFKPKKEEFVRQDLMNITFTNKHRW--FPVR 90
Y+ PLP + + V N++E Y+ P+ EF+R + RW
Sbjct: 163 YDVPAPLPTGNEPKGTADEAVNNIREXYSRLSPEYAEFLRYAF-------EERWIDAVAN 215
Query: 91 KMRQKKRYFKPLIPDR 106
K ++ + +
Sbjct: 216 KGKRPGAFCTYIYDYA 231
>gnl|CDD|129670 TIGR00581, moaC, molybdenum cofactor biosynthesis protein MoaC.
MoaC catalyzes an early step in molybdenum cofactor
biosynthesis in E. coli. The Arabidopsis homolog Cnx3
complements MoaC deficiency in E. coli (MUID:95197640).
Eukarotic members of this family branch within the
bacterial branch, with the archaeal members as an
apparent outgroup. This protein is absent in a number
of the pathogens with smaller genomes, including
Mycoplasmas, Chlamydias, and spirochetes, but is found
in most other complete genomes to date. The homolog
form Synechocystis sp. is fused to a MobA-homologous
region and is an outlier to all other bacterial forms
by both neighbor-joining and UPGMA analyses. Members of
this family are well-conserved. The seed for this model
excludes both archaeal sequences and the most divergent
bacterial sequences, but still finds all candidate MoaC
sequences easily between trusted and noise cutoffs. We
suggest that sequences branching outside the set that
contains all seed members be regarded only as putative
functional equivalents of MoaC unless and until a
member of the archaeal outgroup is shown to have
equivalent function [Biosynthesis of cofactors,
prosthetic groups, and carriers, Molybdopterin].
Length = 147
Score = 25.5 bits (56), Expect = 4.8
Identities = 6/16 (37%), Positives = 10/16 (62%)
Query: 2 RTKRLVPLTHKIAITA 17
RT L+PL H + ++
Sbjct: 65 RTGDLIPLCHPLPLSK 80
>gnl|CDD|215391 PLN02735, PLN02735, carbamoyl-phosphate synthase.
Length = 1102
Score = 25.5 bits (56), Expect = 8.0
Identities = 9/44 (20%), Positives = 23/44 (52%), Gaps = 3/44 (6%)
Query: 51 LKVQNVQEIYNVFKPKKEEFVRQDLMNITFTNKHRWFPVRKMRQ 94
L+V N I+ ++ K+ ++ +TF + WF + ++++
Sbjct: 444 LRVPNPDRIHAIYAAMKKGMTVDEIHELTFIDP--WF-LTQLKE 484
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
0.322 0.136 0.424
Gapped
Lambda K H
0.267 0.0649 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 5,548,908
Number of extensions: 446513
Number of successful extensions: 456
Number of sequences better than 10.0: 1
Number of HSP's gapped: 456
Number of HSP's successfully gapped: 17
Length of query: 109
Length of database: 10,937,602
Length adjustment: 74
Effective length of query: 35
Effective length of database: 7,655,406
Effective search space: 267939210
Effective search space used: 267939210
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 (24.4 bits)