RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780688|ref|YP_003065101.1| putative flagellar motor
switch protein [Candidatus Liberibacter asiaticus str. psy62]
(147 letters)
>gnl|CDD|32070 COG1886, FliN, Flagellar motor switch/type III secretory pathway
protein [Cell motility and secretion / Intracellular
trafficking and secretion].
Length = 136
Score = 74.7 bits (183), Expect = 9e-15
Identities = 37/113 (32%), Positives = 64/113 (56%), Gaps = 3/113 (2%)
Query: 31 VSSPTNNSEMLIQKNDVDNISEPISSDSNNILEKSTDNFDLIMNIPVKMQIILGSCCMQI 90
V ++ L+ K+ + + + +LE ++ DL+++IPV++ + LG M +
Sbjct: 27 VPGSEATADSLLYKSVKEVAFAEVELTESTVLESLNESIDLLLDIPVRLSVELGRTKMPL 86
Query: 91 SNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEI 143
L+ L KG VI LDK GE VDI +N + I +GE+ ++++ FGVR+ EI
Sbjct: 87 GELLALGKGSVIELDKLAGEPVDILVNGRLIGRGEVVVVDDK---FGVRITEI 136
>gnl|CDD|144589 pfam01052, SpoA, Surface presentation of antigens (SPOA). This
family includes the C-terminal region of flagellar motor
switch proteins FliN and FliM. It is associated with
family FliM, pfam02154.
Length = 77
Score = 62.9 bits (154), Expect = 3e-11
Identities = 23/75 (30%), Positives = 45/75 (60%), Gaps = 3/75 (4%)
Query: 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIM 129
+ + ++PV+++ +LG + + L+NL GDVI LDK + V++ +N + I +GE+ ++
Sbjct: 3 EELSDVPVELEAVLGRTELTLGELLNLKVGDVIPLDKPAEDPVELYVNGRPIFRGELGVI 62
Query: 130 EEDDTHFGVRVIEIL 144
VR+ E+L
Sbjct: 63 GG---KLAVRITELL 74
>gnl|CDD|32053 COG1868, FliM, Flagellar motor switch protein [Cell motility and
secretion].
Length = 332
Score = 40.2 bits (94), Expect = 2e-04
Identities = 15/100 (15%), Positives = 44/100 (44%), Gaps = 4/100 (4%)
Query: 48 DNISEPISSDSNNILEKSTDNF-DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDK 106
+ +S + ++ + + + V+++ LG + + ++ L GDVI L+K
Sbjct: 225 EKLSSRMQENTREKDPEWRKELRQQVQRVEVELEARLGEISLTLREILRLEVGDVIPLEK 284
Query: 107 RVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNA 146
+ V +++ + + + V+++E++N+
Sbjct: 285 PADDRVTVSVGGKPKFLCQYGKSGG---QYAVKILELINS 321
>gnl|CDD|109627 pfam00577, Usher, Fimbrial Usher protein. This protein is involved
in biogenesis of gram negative bacterial pili.
Length = 784
Score = 28.4 bits (64), Expect = 0.81
Identities = 7/25 (28%), Positives = 12/25 (48%)
Query: 111 SVDITINNQKIAKGEITIMEEDDTH 135
VD+ +N +K +I DD+
Sbjct: 33 LVDVYLNGEKKGSQDINFTANDDSK 57
>gnl|CDD|173854 cd08489, PBP2_NikA, The substrate-binding component of an ABC-type
nickel import system contains the type 2 periplasmic
binding fold. This family represents the periplasmic
substrate-binding domain of nickel transport system,
which functions in the import of nickel and in the
control of chemotactic response away from nickel. The
ATP-binding cassette (ABC) type nickel transport system
is comprised of five subunits NikABCDE: the two
pore-forming integral inner membrane proteins NikB and
NikC; the two inner membrane-associated proteins with
ATPase activity NikD and NikE; and the periplasmic
nickel binding NikA, the initial nickel receptor. The
oligopeptide-binding protein OppA and the
dipeptide-binding protein DppA show significant sequence
similarity to NikA. The DppA binds dipeptides and some
tripeptides and is involved in chemotaxis toward
dipeptides, whereas the OppA binds peptides of a wide
range of lengths (2-35 amino acid residues) and plays a
role in recycling of cell wall peptides, which precludes
any involvement in chemotaxis. Most of other periplasmic
binding proteins are comprised of only two globular
subdomains corresponding to domains I and III of the
dipeptide/oligopeptide binding proteins. The structural
topology of these domains is most similar to that of the
type 2 periplasmic binding proteins (PBP2), which are
responsible for the uptake of a variety of substrates
such as phosphate, sulfate, polysaccharides,
lysine/arginine/ornithine, and histidine. The PBP2 bind
their ligand in the cleft between these domains in a
manner resembling a Venus flytrap. After binding their
specific ligand with high affinity, they can interact
with a cognate membrane transport complex comprised of
two integral membrane domains and two cytoplasmically
located ATPase domains. This interaction triggers the
ligand translocation across the cytoplasmic membrane
energized by ATP hydrolysis. Besides transport
proteins, the PBP2 superfamily includes the
ligand-binding domains from ionotropic glutamate
receptors, LysR-type transcriptional regulators, and
unorthodox sensor proteins involved in signal
transduction.
Length = 488
Score = 27.6 bits (62), Expect = 1.5
Identities = 19/94 (20%), Positives = 43/94 (45%), Gaps = 16/94 (17%)
Query: 34 PTNNSEML-IQKNDVDNI--SEPISSDSNNILEKSTDNFDLIMNIPVKMQIILGSCCMQI 90
P + +L +Q ++D I ++ IS+D+ L+K + ++ P + +
Sbjct: 195 PDAQTRLLALQSGEIDLIYGADGISADAFKQLKK-DKGYGTAVSEPTSTRFLA------- 246
Query: 91 SNLVNLSKGDVITLDKRVGESVDITINNQKIAKG 124
+N + D +V E+++ I+ + I+KG
Sbjct: 247 ---LNTASE--PLSDLKVREAINYAIDKEAISKG 275
>gnl|CDD|146878 pfam04452, Methyltrans_RNA, RNA methyltransferase. RNA
methyltransferases modify nucleotides during ribosomal
RNA maturation in a site-specific manner. The
Escherichia coli member is specific for U1498
methylation.
Length = 225
Score = 26.4 bits (59), Expect = 2.8
Identities = 7/41 (17%), Positives = 15/41 (36%), Gaps = 2/41 (4%)
Query: 107 RVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNAQ 147
+ G+ + + + EI E V+++E L
Sbjct: 18 KEGDEIKLFDGDGGEYLAEIE--EISKKSVLVKILEKLEVN 56
>gnl|CDD|144750 pfam01269, Fibrillarin, Fibrillarin.
Length = 229
Score = 26.0 bits (58), Expect = 3.6
Identities = 7/35 (20%), Positives = 17/35 (48%), Gaps = 4/35 (11%)
Query: 111 SVDITINNQKIAKGEITIMEEDDTHFGVRVIEILN 145
S+D+T +++ E+ ++E G + E +
Sbjct: 182 SIDVTKEPEEVFAREVEKLKE----EGFKPKEQVT 212
>gnl|CDD|32590 COG2520, COG2520, Predicted methyltransferase [General function
prediction only].
Length = 341
Score = 26.0 bits (57), Expect = 3.7
Identities = 10/39 (25%), Positives = 17/39 (43%)
Query: 42 IQKNDVDNISEPISSDSNNILEKSTDNFDLIMNIPVKMQ 80
I+ N V+ EPI D+ + + +IM +P
Sbjct: 231 IRLNKVEGRVEPILGDAREVAPELGVADRIIMGLPKSAH 269
>gnl|CDD|145730 pfam02731, SKIP_SNW, SKIP/SNW domain. This domain is found in
chromatin proteins.
Length = 158
Score = 25.7 bits (57), Expect = 5.0
Identities = 18/38 (47%), Positives = 20/38 (52%), Gaps = 6/38 (15%)
Query: 90 ISNLVNLSKGDVITLDKRV----GESVDITINNQKIAK 123
ISN N KG I LDKRV D+ IN+ K AK
Sbjct: 74 ISNWKN-PKGYTIPLDKRVAADGRGLQDVEIND-KFAK 109
>gnl|CDD|35153 COG5594, COG5594, Uncharacterized integral membrane protein
[Function unknown].
Length = 827
Score = 24.9 bits (54), Expect = 8.2
Identities = 10/34 (29%), Positives = 14/34 (41%)
Query: 3 KKVSKISYIKDNLEGRSMHIDNPLQDTNVSSPTN 36
KKV I Y L I+N + ++PT
Sbjct: 325 KKVDAIDYYSAKLTKLDAEIENARKSLYENTPTK 358
Database: CddA
Posted date: Feb 4, 2011 9:38 PM
Number of letters in database: 6,263,737
Number of sequences in database: 21,609
Lambda K H
0.313 0.131 0.351
Gapped
Lambda K H
0.267 0.0776 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 1,543,693
Number of extensions: 69524
Number of successful extensions: 122
Number of sequences better than 10.0: 1
Number of HSP's gapped: 122
Number of HSP's successfully gapped: 16
Length of query: 147
Length of database: 6,263,737
Length adjustment: 85
Effective length of query: 62
Effective length of database: 4,426,972
Effective search space: 274472264
Effective search space used: 274472264
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 53 (24.1 bits)