RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddA
21,609 sequences; 6,263,737 total letters
Searching..................................................done
Query= gi|254780170|ref|YP_003064583.1| cationic amino acid ABC
transporter, periplasmic binding protein [Candidatus Liberibacter
asiaticus str. psy62]
(342 letters)
>gnl|CDD|29040 cd00134, PBPb, Bacterial periplasmic transport systems use
membrane-bound complexes and substrate-bound,
membrane-associated, periplasmic binding proteins (PBPs)
to transport a wide variety of substrates, such as,
amino acids, peptides, sugars, vitamins and inorganic
ions. PBPs have two cell-membrane translocation
functions: bind substrate, and interact with the
membrane bound complex. A diverse group of periplasmic
transport receptors for lysine/arginine/ornithine (LAO),
glutamine, histidine, sulfate, phosphate, molybdate, and
methanol are included in the PBPb CD..
Length = 218
Score = 112 bits (280), Expect = 2e-25
Identities = 59/229 (25%), Positives = 96/229 (41%), Gaps = 14/229 (6%)
Query: 36 LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95
L G F+ ANG+ GFDVD +A++ + K++++ ++ AL+S
Sbjct: 1 LTVGTAGTYPPFSFRDANGELTGFDVDLAKAIAKEL---GVKVKFVEVDWDGLITALKSG 57
Query: 96 QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKKKGISSVSQLSGASICVQAGTT 155
++D+++ T R + F Y GQ ++ K I SV L G + VQ G+T
Sbjct: 58 KVDLIAAGMTITPERAKQV--DFSDPYYKSGQVILVKKGSPIKSVKDLKGKKVAVQKGST 115
Query: 156 TELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHV 215
E Y K + + ++ E AA R DA D AL AL + P E
Sbjct: 116 AE----KYLKKALPEAKVVSYDDNAEALAALENGRADAVIVDEIALAALLKKH--PPELK 169
Query: 216 ILPDIISKSPLAPAII--QGDTEWYNIVSWTHYAMVTAEEL-GITQKNI 261
I+ I PL + + + E + V+ + EL I++K
Sbjct: 170 IVGPSIDLEPLGFGVAVGKDNKELLDAVNKALKELRADGELKKISKKWF 218
>gnl|CDD|31176 COG0834, HisJ, ABC-type amino acid transport/signal transduction
systems, periplasmic component/domain [Amino acid
transport and metabolism / Signal transduction
mechanisms].
Length = 275
Score = 103 bits (258), Expect = 6e-23
Identities = 66/260 (25%), Positives = 106/260 (40%), Gaps = 11/260 (4%)
Query: 7 VSILCLIILFFTSFSTNASILGDIKKRGFLKCGIN-TGLVGFAEVKA-NGDWKGFDVDFC 64
+++ L+ + A +L IK RG L+ G T F + A G GFDVD
Sbjct: 7 LALAALLAALLLAACAAADLLDKIKARGKLRVGTEATYAPPFEFLDAKGGKLVGFDVDLA 66
Query: 65 RALSSAIFDDPSKIQYLPLNAKERFLALQSKQIDILSRNTDWTLLREISLGLAFRPITYF 124
+A++ + D K++++P+ AL++ ++DI+ T R+ + F Y+
Sbjct: 67 KAIAKRLGGDK-KVEFVPVAWDGLIPALKAGKVDIIIAGMTITPERKKKV--DFSDPYYY 123
Query: 125 DGQGFIMHKKK--GISSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEI 182
GQ ++ K GI S+ L G + VQ GTT E N K + ++ E
Sbjct: 124 SGQVLLVKKDSDIGIKSLEDLKGKKVGVQLGTTDEAEEKAKKPGPNAK--IVAYDSNAEA 181
Query: 183 DAAYRAHRCDAYTGDISALYALKLTNDRPSEHVILPDIISK-SPLAPAIIQG-DTEWYNI 240
A + R DA D + L LKL P +V+L L A+ +G D E
Sbjct: 182 LLALKNGRADAVVSDSAVLAGLKLLKKNPGLYVLLVFPGLSVEYLGIALRKGDDPELLEA 241
Query: 241 VSWTHYAMVTAEELGITQKN 260
V+ + L
Sbjct: 242 VNKALKELKADGTLQKISDK 261
>gnl|CDD|144186 pfam00497, SBP_bac_3, Bacterial extracellular solute-binding
proteins, family 3.
Length = 224
Score = 96.2 bits (240), Expect = 1e-20
Identities = 52/211 (24%), Positives = 91/211 (43%), Gaps = 15/211 (7%)
Query: 36 LKCGINTGLVGFAEVKANGDWKGFDVDFCRALSSAIFDDPSKIQYLPLNAKERFLALQSK 95
L+ G + F+ + +G GFDVD +A++ + K++++P++ ALQS
Sbjct: 1 LRVGTDADYPPFSYLDEDGKLVGFDVDLAKAIAKRLGV---KVEFVPVSWDGLIPALQSG 57
Query: 96 QIDILSRNTDWTLLREISLGLAFRPITYFDGQGFIMHKK-----KGISSVSQLSGASICV 150
+ID++ T R+ + F Y+ GQ ++ K K I ++ L G + V
Sbjct: 58 KIDVIIAGMTITPERKKK--VDFSDPYYYSGQVLVVRKDSPPKIKSIKDLADLKGKKVGV 115
Query: 151 QAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDR 210
Q GTT E L + ++++ E A A R DA D L
Sbjct: 116 QKGTTQEDLLKELAP---KGAEIVLYDDQAEALQALAAGRVDAVVADSPVAAY--LIKKN 170
Query: 211 PSEHVILPDIISKSPLAPAIIQGDTEWYNIV 241
P ++++ + +S P A+ +GD E V
Sbjct: 171 PGLNLVVGEPLSGEPYGIAVRKGDPELLAAV 201
>gnl|CDD|35943 KOG0724, KOG0724, KOG0724, Zuotin and related molecular chaperones
(DnaJ superfamily), contains DNA-binding domains
[Posttranslational modification, protein turnover,
chaperones].
Length = 335
Score = 29.5 bits (65), Expect = 1.2
Identities = 16/133 (12%), Positives = 27/133 (20%), Gaps = 13/133 (9%)
Query: 159 TLADYFKAHNMKYHPIVFERVEEIDAAYRAHRCDAYTGDISALYALKLTNDRPSEHVILP 218
L D E + Y G + + N R S P
Sbjct: 48 ILDDDEPRRTPDSWDKFAEALPLEKRLEDKIE--EYIGLVFDV------NIRESGQKPFP 99
Query: 219 DIISKSPLAPAIIQGDTEWYNIVSWTHYAMVTAEELG-----ITQKNINQVSKDTTNPDV 273
+ + W SW Y + + + +N +
Sbjct: 100 KYGKSDTSLAEVEEFYNFWPKFKSWRQYPQKDEPDEEDSENRSQSRYSGGTQRGKSNAEE 159
Query: 274 QRFLGIDKSSNIG 286
R G +
Sbjct: 160 LRRKGTPVTERER 172
>gnl|CDD|36214 KOG0996, KOG0996, KOG0996, Structural maintenance of chromosome
protein 4 (chromosome condensation complex Condensin,
subunit C) [Chromatin structure and dynamics, Cell cycle
control, cell division, chromosome partitioning].
Length = 1293
Score = 28.8 bits (64), Expect = 2.0
Identities = 19/56 (33%), Positives = 25/56 (44%), Gaps = 9/56 (16%)
Query: 130 IMHKKKGISSVSQLSGASICVQAGTTTELTLADYFKAHNMKYHPIVFERVEEIDAA 185
+ KK ++S LSG G T +LA F H Y P ++EIDAA
Sbjct: 1183 VRPPKKSWKNISNLSG-------GEKTLSSLALVFALH--HYKPTPLYVMDEIDAA 1229
>gnl|CDD|146223 pfam03468, XS, XS domain. The XS (rice gene X and SGS3) domain
is found in a family of plant proteins including gene X
and SGS3. SGS3 is thought to be involved in
post-transcriptional gene silencing (PTGS). This domain
contains a conserved aspartate residue that may be
functionally important. The XS domain has recently been
predicted to possess an RRM-like RNA-binding domain by
fold recognition.
Length = 118
Score = 28.1 bits (63), Expect = 3.3
Identities = 14/44 (31%), Positives = 17/44 (38%), Gaps = 9/44 (20%)
Query: 23 NASILGDIKKRGFLKCGI-------NTGLVGFAEVKANGDWKGF 59
A + + K GF + G GFA VK DW GF
Sbjct: 31 GAKLDDKLSKLGF--NPLKVKPLWNREGHTGFAIVKFAKDWSGF 72
>gnl|CDD|173948 cd08189, Fe-ADH5, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenase-like. Alcohol
dehydrogenase catalyzes the reduction of acetaldehyde to
alcohol with NADP as cofactor. Its activity requires
iron ions. The protein structure represents a
dehydroquinate synthase-like fold and belongs to the
alcohol dehydrogenase-like superfamily. They are
distinct from other alcohol dehydrogenases which
contains different protein domain. Proteins of this
family have not been characterized. Their specific
function is unknown.
Length = 374
Score = 27.9 bits (63), Expect = 3.6
Identities = 11/44 (25%), Positives = 18/44 (40%), Gaps = 11/44 (25%)
Query: 159 TLADYFKAHNMKYHPIVF---------ERVEEIDAAYRAHRCDA 193
+ + + ++Y V+ E VE A YR + CDA
Sbjct: 45 KVLEALEGAGIEY--AVYDGVPPDPTIENVEAGLALYRENGCDA 86
>gnl|CDD|173942 cd08183, Fe-ADH2, Iron-containing alcohol dehydrogenases-like.
Iron-containing alcohol dehydrogenases (Fe-ADH). Alcohol
dehydrogenase catalyzes the reduction of acetaldehyde to
alcohol with NADP as cofactor. Its activity requires
iron ions. The protein structure represents a
dehydroquinate synthase-like fold and is a member of the
iron-activated alcohol dehydrogenase-like family. They
are distinct from other alcohol dehydrogenases which
contains different protein domain. Proteins of this
family have not been characterized. Their specific
function is unknown. They are mainly found in bacteria.
Length = 374
Score = 27.1 bits (61), Expect = 6.9
Identities = 11/40 (27%), Positives = 17/40 (42%), Gaps = 6/40 (15%)
Query: 160 LADYFKAHNMKYHPIVFER---VEEIDAA---YRAHRCDA 193
L + +A ++ +V VE +DAA R CD
Sbjct: 39 LIEALRAAGIEVTHVVVAGEPSVELVDAAVAEARNAGCDV 78
>gnl|CDD|173951 cd08192, Fe-ADH7, Iron-containing alcohol dehydrogenases-like,
involved in the linear alkylbenzenesulfonate (LAS)
degradation pathway. NAD-dependent iron-containing
alcohol dehydrogenase-like. Proteins in this family are
NAD-dependent alcohol dehydrogenases which are involved
in the linear alkylbenzenesulfonate (LAS) degradation
pathway. They catalyze the oxidation of beta-hydroxy CoA
ester to beta-oxo CoA ester, which then be subject to
CoA-dependent thiolysis to yield acetyl-CoA and
6-C8-SPC-CoA. The major laundry surfactant in worldwide
use is commercial linear alkylbenzenesulfonate (LAS)
which contains 20 congeners of linear alkanes (C10 to
C13). LAS is fully biodegradable in oxic environments.
Degradation involves microbial communities. Parvibaculum
lavamentivorans DS-1T is a representative member of many
heterotrophic, LAS-degrading communities, in which it
catalyzes the first steps of LAS degradation. Strain
DS-1T is a small heterotrophic bacterium able to
omega-oxygenate the commercial surfactant linear
alkylbenzenesulfonate (LAS) and shorten the side chain
by beta-oxidation to yield sulfophenylcarboxylates
(SPC). Parvibaculum lavamentivorans utilizes 3-C12-LAS
as the sole carbon and energy source, and excretes
largely 4-C6-SPC.
Length = 370
Score = 27.2 bits (61), Expect = 7.8
Identities = 11/35 (31%), Positives = 14/35 (40%), Gaps = 7/35 (20%)
Query: 184 AAYRAHRCDAYTG-------DISALYALKLTNDRP 211
AAYRA CD D++ AL + P
Sbjct: 75 AAYRAGGCDGVIAFGGGSALDLAKAVALMAGHPGP 109
>gnl|CDD|28977 cd00093, HTH_XRE, Helix-turn-helix XRE-family like proteins.
Prokaryotic DNA binding proteins belonging to the
xenobiotic response element family of transcriptional
regulators..
Length = 58
Score = 27.0 bits (60), Expect = 8.2
Identities = 11/45 (24%), Positives = 24/45 (53%), Gaps = 6/45 (13%)
Query: 251 AEELGITQKNINQVSKDTTNPDVQRFLGIDKSSNIGEALGLTKDW 295
AE+LG+++ I+++ NP ++ + +ALG++ D
Sbjct: 19 AEKLGVSRSTISRIENGKRNPSLETLE------KLAKALGVSLDE 57
>gnl|CDD|144194 pfam00508, PPV_E2_N, E2 (early) protein, N terminal.
Length = 201
Score = 26.7 bits (60), Expect = 9.8
Identities = 8/35 (22%), Positives = 16/35 (45%), Gaps = 8/35 (22%)
Query: 84 NAKERFLALQSKQIDILSRNTD--------WTLLR 110
ER ALQ + +++ +++ W L+R
Sbjct: 2 TLSERLDALQEQLLELYEKDSTDLEDQIEHWKLVR 36
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
0.322 0.138 0.418
Gapped
Lambda K H
0.267 0.0747 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21609
Number of Hits to DB: 4,243,682
Number of extensions: 220634
Number of successful extensions: 522
Number of sequences better than 10.0: 1
Number of HSP's gapped: 515
Number of HSP's successfully gapped: 16
Length of query: 342
Length of database: 6,263,737
Length adjustment: 95
Effective length of query: 247
Effective length of database: 4,210,882
Effective search space: 1040087854
Effective search space used: 1040087854
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: 58 (26.1 bits)