RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy8740
(252 letters)
>gnl|CDD|219849 pfam08454, RIH_assoc, RyR and IP3R Homology associated. This
eukaryotic domain is found in ryanodine receptors (RyR)
and inositol 1,4,5-trisphosphate receptors (IP3R) which
together form a superfamily of homotetrameric
ligand-gated intracellular Ca2+ channels. There seems to
be no known function for this domain. Also see the
IP3-binding domain pfam01365 and pfam02815.
Length = 109
Score = 63.7 bits (156), Expect = 3e-13
Identities = 23/81 (28%), Positives = 33/81 (40%), Gaps = 10/81 (12%)
Query: 9 TEPNISTTVN--ESIMDFYWHYSSKELIDPAGKANFFKAIGVASQVFNTLSEVIQGPCTQ 66
+ N + N +D L+ GK K + Q +TL+E+IQGPC +
Sbjct: 35 QQTNSKNSYNIINETVDL--------LLTLLGKNINKKNYELIVQCLDTLTELIQGPCHE 86
Query: 67 NQQALAHSRLWDAVGGFLFLF 87
NQ AL S+ D L
Sbjct: 87 NQIALCESKFLDIATDLLQKK 107
>gnl|CDD|222407 pfam13833, EF_hand_6, EF-hand domain pair.
Length = 53
Score = 29.4 bits (67), Expect = 0.21
Identities = 9/44 (20%), Positives = 20/44 (45%), Gaps = 1/44 (2%)
Query: 181 PKDFKEKM-EQQKSYTPEDIEFMLACCETNHDGKIDYVGFTDRF 223
++ K + S + E+++ + +T+ DGKI + F
Sbjct: 7 REELKRALALLGISLSEEEVDILFREFDTDGDGKISFEEFCVLL 50
>gnl|CDD|206240 pfam14070, YjfB_motility, Putative motility protein. This family
of proteins is regulated in B. subtilis by SigD, and is
likely to be involved in motility or flagellin
production, Proteins in this family are approximately 60
amino acids in length, and contain two highly conserved
asparagine residues.
Length = 57
Score = 28.3 bits (64), Expect = 0.59
Identities = 8/41 (19%), Positives = 17/41 (41%), Gaps = 1/41 (2%)
Query: 100 QVDLLKILLNLQKDMITMMLSMLEGNVVNGTIGKQMVDTLV 140
+ +LK ++ Q+ +L M+ V +G +D
Sbjct: 18 SIAVLKKAMDTQEQSAAQLLQMMPQASVPPNLG-GNIDVKA 57
>gnl|CDD|238008 cd00051, EFh, EF-hand, calcium binding motif; A diverse superfamily
of calcium sensors and calcium signal modulators; most
examples in this alignment model have 2 active canonical
EF hands. Ca2+ binding induces a conformational change
in the EF-hand motif, leading to the activation or
inactivation of target proteins. EF-hands tend to occur
in pairs or higher copy numbers.
Length = 63
Score = 28.3 bits (64), Expect = 0.80
Identities = 12/50 (24%), Positives = 24/50 (48%), Gaps = 1/50 (2%)
Query: 168 FMEIDINNEGWVYPKDFKEKMEQQKSYTP-EDIEFMLACCETNHDGKIDY 216
F D + +G + + K ++ E+I+ M+ + + DGKID+
Sbjct: 6 FRLFDKDGDGTISADELKAALKSLGEGLSEEEIDEMIREVDKDGDGKIDF 55
>gnl|CDD|232843 TIGR00133, gatB, aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase,
B subunit. The heterotrimer GatABC is responsible for
transferring the NH2 group that converts Glu to Gln, or
Asp to Asn after the Glu or Asp has been ligated to the
tRNA for Gln or Asn, respectively. In Lactobacillus,
GatABC is responsible only for tRNA(Gln). In the
Archaea, GatABC is responsible only for tRNA(Asn), while
GatDE is responsible for tRNA(Gln). In lineages that
include Thermus, Chlamydia, or Acidithiobacillus, the
GatABC complex catalyzes both [Protein synthesis, tRNA
aminoacylation].
Length = 478
Score = 28.1 bits (63), Expect = 4.3
Identities = 7/42 (16%), Positives = 23/42 (54%), Gaps = 2/42 (4%)
Query: 100 QVDLLKILLNLQKDMITMMLSMLEGNVVNGTIGKQMVDTLVE 141
Q+ L + L+ + ++ +++ ++G KQ+++ ++E
Sbjct: 361 QISLAE--CGLKPSDLAELIKLIKEGKISGKSAKQLIEEMLE 400
>gnl|CDD|239133 cd02668, Peptidase_C19L, A subfamily of Peptidase C19. Peptidase
C19 contains ubiquitinyl hydrolases. They are
intracellular peptidases that remove ubiquitin molecules
from polyubiquinated peptides by cleavage of isopeptide
bonds. They hydrolyze bonds involving the carboxyl group
of the C-terminal Gly residue of ubiquitin. The purpose
of the de-ubiquitination is thought to be editing of the
ubiquitin conjugates, which could rescue them from
degradation, as well as recycling of the ubiquitin. The
ubiquitin/proteasome system is responsible for most
protein turnover in the mammalian cell, and with over 50
members, family C19 is one of the largest families of
peptidases in the human genome.
Length = 324
Score = 28.2 bits (63), Expect = 4.7
Identities = 20/81 (24%), Positives = 32/81 (39%), Gaps = 27/81 (33%)
Query: 27 HYSSKELIDPAGKANFFKAIGVASQVFNTLSEVIQGPCTQNQQALAHSRLWDAVGGFLFL 86
+ ++ ++DP+G F KA+G+ T QQ DA
Sbjct: 65 QFGNRSVVDPSG---FVKALGL---------------DTGQQQ--------DAQEFSKLF 98
Query: 87 FSHMQDKLSKHSSQVDLLKIL 107
S ++ KLSK + DL I+
Sbjct: 99 LSLLEAKLSKSKNP-DLKNIV 118
>gnl|CDD|130652 TIGR01591, Fdh-alpha, formate dehydrogenase, alpha subunit,
archaeal-type. This model describes a subset of formate
dehydrogenase alpha chains found mainly archaea but also
in alpha and gamma proteobacteria and a small number of
gram positive bacteria. The alpha chain contains domains
for molybdopterin dinucleotide binding and molybdopterin
oxidoreductase (pfam01568 and pfam00384, respectively).
The holo-enzyme also contains beta and gamma subunits.
The enzyme catalyzes the oxidation of formate (produced
from pyruvate during anaerobic growth) to carbon dioxide
with the concomitant release of two electrons and two
protons. The enzyme's purpose is to allow growth on
formate in some circumstances and, in the case of FdhH
in gamma proteobacteria, to pass electrons to
hydrogenase (by which process acid is neutralized). This
model is well-defined, with only a single fragmentary
sequence falling between trusted and noise. The alpha
subunit of a version of nitrate reductase is closely
related.
Length = 671
Score = 28.2 bits (63), Expect = 5.4
Identities = 20/63 (31%), Positives = 26/63 (41%), Gaps = 13/63 (20%)
Query: 149 ILKYFDMFLKLK---DLTSSASFMEIDINNEGWVYPKDFKEK--------MEQQKSYTPE 197
K D+ + LK D+ + + I EG Y K F EK E K YTPE
Sbjct: 197 TAKIADLHIPLKPGTDIALLNAMANVIIE-EGL-YDKAFIEKRTEGFEEFREIVKGYTPE 254
Query: 198 DIE 200
+E
Sbjct: 255 YVE 257
>gnl|CDD|235389 PRK05287, PRK05287, hypothetical protein; Provisional.
Length = 250
Score = 27.5 bits (62), Expect = 6.4
Identities = 9/12 (75%), Positives = 9/12 (75%)
Query: 195 TPEDIEFMLACC 206
EDIEF LACC
Sbjct: 238 VDEDIEFELACC 249
>gnl|CDD|213580 TIGR01060, eno, phosphopyruvate hydratase. Alternate name: enolase
[Energy metabolism, Glycolysis/gluconeogenesis].
Length = 425
Score = 27.7 bits (62), Expect = 6.7
Identities = 8/30 (26%), Positives = 20/30 (66%)
Query: 33 LIDPAGKANFFKAIGVASQVFNTLSEVIQG 62
+I P G +F +A+ + ++VF+ L ++++
Sbjct: 163 MIMPVGAPSFREALRMGAEVFHALKKLLKE 192
>gnl|CDD|153340 cd07656, F-BAR_srGAP, The F-BAR (FES-CIP4 Homology and
Bin/Amphiphysin/Rvs) domain of Slit-Robo GTPase
Activating Proteins. F-BAR domains are dimerization
modules that bind and bend membranes and are found in
proteins involved in membrane dynamics and actin
reorganization. Slit-Robo GTPase Activating Proteins
(srGAPs) are Rho GAPs that interact with Robo1, the
transmembrane receptor of Slit proteins. Slit proteins
are secreted proteins that control axon guidance and the
migration of neurons and leukocytes. Vertebrates contain
three isoforms of srGAPs, all of which are expressed
during embryonic and early development in the nervous
system but with different localization and timing.
srGAPs contain an N-terminal F-BAR domain, a Rho GAP
domain, and a C-terminal SH3 domain. F-BAR domains form
banana-shaped dimers with a positively-charged concave
surface that binds to negatively-charged lipid
membranes. They can induce membrane deformation in the
form of long tubules.
Length = 241
Score = 27.3 bits (61), Expect = 7.6
Identities = 16/59 (27%), Positives = 24/59 (40%), Gaps = 10/59 (16%)
Query: 68 QQALAHSRLWDAVGGFLFL-FSHMQD---KLSKHS------SQVDLLKILLNLQKDMIT 116
Q++ HS L D L M + ++SK +LL++L LQ M T
Sbjct: 81 QESRDHSTLSDIYSNNLVQRLGQMSEDLQRISKKCREIGSQLHDELLRVLNELQTAMKT 139
>gnl|CDD|197803 smart00609, VIT, Vault protein Inter-alpha-Trypsin domain.
Length = 130
Score = 26.6 bits (59), Expect = 7.7
Identities = 20/71 (28%), Positives = 28/71 (39%), Gaps = 8/71 (11%)
Query: 127 VNGTIGKQMVDTLVESAA---NVELILKYFDMFLKLKDLTSSASFMEIDINNEGWVYPKD 183
VN + + T+V S V FD+ L T+ S + I+ G Y +
Sbjct: 22 VNSKVTSRFAHTVVTSRVVNRAVPAQEVTFDVEL---PKTAFISNFAMTID--GKTYVGE 76
Query: 184 FKEKMEQQKSY 194
KEK QK Y
Sbjct: 77 IKEKEVAQKQY 87
>gnl|CDD|183940 PRK13276, PRK13276, cell wall biosynthesis protein ScdA;
Provisional.
Length = 224
Score = 26.7 bits (59), Expect = 9.6
Identities = 16/39 (41%), Positives = 21/39 (53%), Gaps = 3/39 (7%)
Query: 214 IDYVGFTDRFHEPAKEIGFNLAVLLTNLSE-HMPNEPRL 251
I Y+ +HEP +E NL +T LS+ H PN P L
Sbjct: 79 IQYI--QSAYHEPLREEFKNLTPYVTKLSKVHGPNHPYL 115
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
0.319 0.134 0.391
Gapped
Lambda K H
0.267 0.0833 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 12,508,440
Number of extensions: 1156132
Number of successful extensions: 1024
Number of sequences better than 10.0: 1
Number of HSP's gapped: 1024
Number of HSP's successfully gapped: 22
Length of query: 252
Length of database: 10,937,602
Length adjustment: 95
Effective length of query: 157
Effective length of database: 6,723,972
Effective search space: 1055663604
Effective search space used: 1055663604
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 (21.7 bits)
S2: 58 (25.9 bits)