RPS-BLAST 2.2.26 [Sep-21-2011]
Database: CDD.v3.10
44,354 sequences; 10,937,602 total letters
Searching..................................................done
Query= psy10256
(96 letters)
>gnl|CDD|214520 smart00112, CA, Cadherin repeats. Cadherins are glycoproteins
involved in Ca2+-mediated cell-cell adhesion. Cadherin
domains occur as repeats in the extracellular regions
which are thought to mediate cell-cell contact when
bound to calcium.
Length = 81
Score = 55.0 bits (133), Expect = 1e-11
Identities = 19/48 (39%), Positives = 27/48 (56%)
Query: 1 ELKTARGLDREKIARYTLNAHVQDRDQPAWECVSLITLTLTDINDNAP 48
E+ T + LDRE+ YTL D P + +T+T+ D+NDNAP
Sbjct: 34 EITTTKPLDREEQPEYTLTVEATDGGGPPLSSTATVTITVLDVNDNAP 81
>gnl|CDD|206637 cd11304, Cadherin_repeat, Cadherin tandem repeat domain.
Cadherins are glycoproteins involved in Ca2+-mediated
cell-cell adhesion. The cadherin repeat domains occur
as tandem repeats in the extracellular regions, which
are thought to mediate cell-cell contact when bound to
calcium. They play numerous roles in cell fate,
signalling, proliferation, differentiation, and
migration; members include E-, N-, P-, T-, VE-, CNR-,
proto-, and FAT-family cadherin, desmocollin, and
desmoglein, a large variety of domain architectures
with varying repeat copy numbers. Cadherin-repeat
containing proteins exist as monomers, homodimers, or
heterodimers.
Length = 98
Score = 50.8 bits (122), Expect = 7e-10
Identities = 18/46 (39%), Positives = 27/46 (58%)
Query: 1 ELKTARGLDREKIARYTLNAHVQDRDQPAWECVSLITLTLTDINDN 46
E+ TA+ LDRE+ + YTL D P + +T+T+ D+NDN
Sbjct: 53 EITTAKPLDREEQSSYTLTVTATDGGGPPLSSTATVTITVLDVNDN 98
>gnl|CDD|215665 pfam00028, Cadherin, Cadherin domain.
Length = 92
Score = 43.1 bits (102), Expect = 5e-07
Identities = 13/41 (31%), Positives = 19/41 (46%)
Query: 1 ELKTARGLDREKIARYTLNAHVQDRDQPAWECVSLITLTLT 41
+L T + LDRE I Y L D P + +T+T+
Sbjct: 52 DLSTTKPLDRESIGEYELTVLATDSGGPPLSSTTTVTITVL 92
>gnl|CDD|206635 cd00031, CA_like, Cadherin repeat-like domain. Cadherins are
glycoproteins involved in Ca2+-mediated cell-cell
adhesion. The cadherin repeat domains occur as tandem
repeats in the extracellular regions, which are thought
to mediate cell-cell contact when bound to calcium.
They play numerous roles in cell fate, signalling,
proliferation, differentiation, and migration; members
include E-, N-, P-, T-, VE-, CNR-, proto-, and
FAT-family cadherin, desmocollin, and desmoglein, a
large variety of domain architectures with varying
repeat copy numbers. Cadherin-repeat containing
proteins exist as monomers, homodimers, or
heterodimers. This family also includes the
cadherin-like repeats of extracellular
alpha-dystroglycan.
Length = 98
Score = 30.0 bits (67), Expect = 0.076
Identities = 10/45 (22%), Positives = 19/45 (42%)
Query: 2 LKTARGLDREKIARYTLNAHVQDRDQPAWECVSLITLTLTDINDN 46
L+ LDRE + ++ + S+ ++ + D NDN
Sbjct: 54 LEGLEKLDREDKGVHYISVSAASLGANVPQTSSVFSIEVYDENDN 98
>gnl|CDD|173170 PRK14707, PRK14707, hypothetical protein; Provisional.
Length = 2710
Score = 26.3 bits (57), Expect = 3.4
Identities = 22/67 (32%), Positives = 31/67 (46%), Gaps = 16/67 (23%)
Query: 3 KTARGLDREKIARYTLNAHVQDRDQPAWECVSLITLTLTDINDN------APEFASVINS 56
+ AR L RE AR TLNA + +SL + +DN AP FA+++ S
Sbjct: 145 RLARHLRREDKARQTLNA----------QNISLALNAFSKWSDNPDCQAVAPRFAALVAS 194
Query: 57 ASILENA 63
L +A
Sbjct: 195 DDRLRSA 201
>gnl|CDD|129992 TIGR00914, 2A0601, heavy metal efflux pump, CzcA family. This
model represents a family of H+/heavy metal cation
antiporters. This family is one of several subfamilies
within the scope of Pfam model pfam00873 [Cellular
processes, Detoxification, Transport and binding
proteins, Cations and iron carrying compounds].
Length = 1051
Score = 25.9 bits (57), Expect = 3.8
Identities = 11/18 (61%), Positives = 12/18 (66%), Gaps = 1/18 (5%)
Query: 8 LDREKIARYTLN-AHVQD 24
+DREK ARY L VQD
Sbjct: 731 IDREKAARYGLTVGDVQD 748
>gnl|CDD|182036 PRK09700, PRK09700, D-allose transporter ATP-binding protein;
Provisional.
Length = 510
Score = 25.5 bits (56), Expect = 5.3
Identities = 12/27 (44%), Positives = 15/27 (55%), Gaps = 1/27 (3%)
Query: 52 SVINSASILENAEIGSLSTVNATIGVN 78
SVI+ ++LEN IG T GVN
Sbjct: 90 SVIDELTVLENLYIGRHLT-KKVCGVN 115
>gnl|CDD|223265 COG0187, GyrB, Type IIA topoisomerase (DNA gyrase/topo II,
topoisomerase IV), B subunit [DNA replication,
recombination, and repair].
Length = 635
Score = 25.2 bits (56), Expect = 6.0
Identities = 12/37 (32%), Positives = 18/37 (48%), Gaps = 9/37 (24%)
Query: 59 ILENAEIGSLSTVNATIGVNRCGH--TFRGKDLRCYN 93
IL+N EI ++ T +G G F + LR Y+
Sbjct: 462 ILKNEEIQTIIT---ALG---TGIGKDFDLEKLR-YH 491
>gnl|CDD|224129 COG1208, GCD1, Nucleoside-diphosphate-sugar pyrophosphorylase
involved in lipopolysaccharide biosynthesis/translation
initiation factor 2B, gamma/epsilon subunits
(eIF-2Bgamma/eIF-2Bepsilon) [Cell envelope biogenesis,
outer membrane / Translation, ribosomal structure and
biogenesis].
Length = 358
Score = 25.4 bits (56), Expect = 6.2
Identities = 11/44 (25%), Positives = 17/44 (38%), Gaps = 8/44 (18%)
Query: 41 TDINDNA-PEFASVINSASILENAEIGSLSTV-------NATIG 76
T I + I ++ I++N IG S + N IG
Sbjct: 280 TVIGEGVTIGNGVEIKNSIIMDNVVIGHGSYIGDSIIGENCKIG 323
>gnl|CDD|193581 cd09892, NGN_SP_RfaH, N-Utilization Substance G (NusG) N-terminal
domain in the NusG Specialized Paralog (SP), RfaH.
RfaH is an operon-specific virulence regulator, thought
to have arisen from an early duplication of
N-Utilization Substance G (NusG). Paralogs of
eubacterial NusG, NusG SP (Specialized Paralog of
NusG), are more diverse and often found as the first
ORF in operons encoding secreted proteins and LPS
biosynthesis genes. NusG SP family members are
operon-specific transcriptional antitermination
factors. NusG is essential in Escherichia coli and is
associated with RNA polymerase elongation and
Rho-termination in bacteria. In contrast, RfaH is a
non-essential protein that controls expression of
operons containing an ops (operon polarity suppressor)
element in their transcribed DNA. RfaH and NusG are
different in their response to Rho-dependent
terminators and regulatory targets. The NusG N-terminal
(NGN) domain is quite similar in all NusG orthologs,
but its C-terminal domains and the linker that separate
these two domains are different. The domain
organization of NusG and its homologs suggest that the
common properties of NusG and RfaH are due to their
similar NGN domains.
Length = 96
Score = 24.4 bits (54), Expect = 7.5
Identities = 5/18 (27%), Positives = 11/18 (61%)
Query: 62 NAEIGSLSTVNATIGVNR 79
+ E+ + + +T GV+R
Sbjct: 58 DPEVQNWRPIRSTRGVSR 75
>gnl|CDD|215637 PLN03223, PLN03223, Polycystin cation channel protein; Provisional.
Length = 1634
Score = 24.9 bits (54), Expect = 9.0
Identities = 10/41 (24%), Positives = 20/41 (48%)
Query: 33 VSLITLTLTDINDNAPEFASVINSASILENAEIGSLSTVNA 73
++ T D + N PE S ++S S + EI +++ +
Sbjct: 480 NNVRTDAKADADANFPEVKSWLSSESPVTFFEINTVAGTDP 520
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
0.318 0.133 0.390
Gapped
Lambda K H
0.267 0.0803 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 44354
Number of Hits to DB: 4,460,079
Number of extensions: 334351
Number of successful extensions: 254
Number of sequences better than 10.0: 1
Number of HSP's gapped: 253
Number of HSP's successfully gapped: 15
Length of query: 96
Length of database: 10,937,602
Length adjustment: 63
Effective length of query: 33
Effective length of database: 8,143,300
Effective search space: 268728900
Effective search space used: 268728900
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 (24.1 bits)