RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781063|ref|YP_003065476.1| hypothetical protein
CLIBASIA_04825 [Candidatus Liberibacter asiaticus str. psy62]
(129 letters)
>gnl|CDD|131990 TIGR02945, SUF_assoc, FeS assembly SUF system protein. Members of
this family belong to the broader Pfam family pfam01883,
or Domain of Unknown Function DUF59. Many members of
DUF59 are candidate ring hydroxylating complex subunits.
However, members of the narrower family defined here all
are found in genomes that carry the FeS assembly SUF
system. For 70 % of these species, the member of this
protein family is found as part of the SUF locus,
usually immediately downstream of the sufS gene.
Length = 99
Score = 152 bits (386), Expect = 3e-38
Identities = 60/99 (60%), Positives = 75/99 (75%)
Query: 31 RISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWI 90
R+ + +I ALKTVYDPEIP +I+ELGLIY IDV++D V I MTLTAP CPVAG MP +
Sbjct: 1 RLKDAVIEALKTVYDPEIPVNIYELGLIYDIDVDDDGHVDIQMTLTAPNCPVAGSMPGEV 60
Query: 91 ENAVGAVEGISGVEVSITFDPPWTPDLMSEEAQIATGYY 129
ENAV AV G+ V V + +DPPWTP+ MSEEA++ G +
Sbjct: 61 ENAVRAVPGVGSVTVELVWDPPWTPERMSEEARLELGMF 99
>gnl|CDD|132447 TIGR03406, FeS_long_SufT, probable FeS assembly SUF system protein
SufT. The function is unknown for this protein family,
but members are found almost always in operons for the
the SUF system of iron-sulfur cluster biosynthesis. The
SUF system is present elsewhere on the chromosome for
those few species where SUF genes are not adjacent. This
family shares this property of association with the SUF
system with a related family, TIGR02945. TIGR02945
consists largely of a DUF59 domain (see Pfam family
pfam01883), while this protein is about double the
length, with a unique N-terminal domain and DUF59
C-terminal domain. A location immediately downstream of
the cysteine desulfurase gene sufS in many contexts
suggests the gene symbol sufT. Note that some other
homologs of this family and of TIGR02945, but no actual
members of this family, are found in operons associated
with phenylacetic acid (or other ring-hydroxylating)
degradation pathways.
Length = 174
Score = 103 bits (260), Expect = 9e-24
Identities = 51/126 (40%), Positives = 69/126 (54%), Gaps = 15/126 (11%)
Query: 13 ADKIALSP--ESTIPPEDLERISNDII-AALKTVYDPEIPCDIFELGLIYKIDVE----N 65
AD + P +P + D + L+TVYDPEIP +I +LGL+Y VE
Sbjct: 52 ADALGKEPPPPLDLPENADGEDNEDQVWEQLRTVYDPEIPVNIVDLGLVYGCRVEKLGEG 111
Query: 66 DYMVKILMTLTAPGC---PV-AGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLMSEE 121
+ V I MTLTAPGC PV D +E+ V AV + VEV + FDPPW+ ++MSE
Sbjct: 112 QFRVDIEMTLTAPGCGMGPVLVED----VEDKVLAVPNVDEVEVELVFDPPWSREMMSEA 167
Query: 122 AQIATG 127
A++ G
Sbjct: 168 AKLELG 173
>gnl|CDD|131214 TIGR02159, PA_CoA_Oxy4, phenylacetate-CoA oxygenase, PaaJ subunit.
Phenylacetate-CoA oxygenase is comprised of a five gene
complex responsible for the hydroxylation of
phenylacetate-CoA (PA-CoA) as the second catabolic step
in phenylacetic acid (PA) degradation. Although the
exact function of this enzyme has not been determined,
it has been shown to be required for phenylacetic acid
degradation and has been proposed to function in a
multicomponent oxygenase acting on phenylacetate-CoA.
Length = 146
Score = 57.1 bits (138), Expect = 1e-09
Identities = 33/82 (40%), Positives = 51/82 (62%), Gaps = 3/82 (3%)
Query: 43 VYDPEIPC-DIFELGLIYKIDVENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGIS 101
V DPEIP + +LG++ ++DV+ V + T T GCP + + I +AV A+ G+
Sbjct: 1 VPDPEIPVVSVTDLGMVREVDVDGG-GVVVKFTPTYSGCPALEVIRQDIRDAVRAL-GVE 58
Query: 102 GVEVSITFDPPWTPDLMSEEAQ 123
VEVS + DPPWT D ++E+A+
Sbjct: 59 VVEVSTSLDPPWTTDWITEDAR 80
>gnl|CDD|183761 PRK12806, PRK12806, flagellin; Provisional.
Length = 475
Score = 30.0 bits (67), Expect = 0.18
Identities = 24/125 (19%), Positives = 44/125 (35%), Gaps = 5/125 (4%)
Query: 7 DTENNIADKIALSPESTIPPEDLERISNDIIAALKTVYDPEIPCDIFELGL----IYKID 62
++ NN +D+ ++ E + +LERI+ + + + D F++G
Sbjct: 101 NSTNNSSDRASIQSEISQLKSELERIAQNTEFNGQRILDGSFSGASFQVGANSNQTINFS 160
Query: 63 VENDYMVKILMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLMSEEA 122
+ + I TA G VAG I A+G + + S F +
Sbjct: 161 IGSIKASSIGGIATATGTEVAGAAATDITIAIGGGA-ATSINSSANFTGALNGQDATSAY 219
Query: 123 QIATG 127
A
Sbjct: 220 AKAAA 224
>gnl|CDD|179579 PRK03437, PRK03437, 3-isopropylmalate dehydrogenase; Provisional.
Length = 344
Score = 27.2 bits (61), Expect = 1.2
Identities = 20/65 (30%), Positives = 32/65 (49%), Gaps = 4/65 (6%)
Query: 23 TIPPEDLERI-SNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPG-- 79
T+P L + +D I L + DP +P + E GL+ K+ D+ V + + PG
Sbjct: 55 TLPDSVLAELRQHDAIL-LGAIGDPSVPSGVLERGLLLKLRFALDHYVNLRPSKLYPGVT 113
Query: 80 CPVAG 84
P+AG
Sbjct: 114 SPLAG 118
>gnl|CDD|118064 pfam09528, Ehrlichia_rpt, Ehrlichia tandem repeat (Ehrlichia_rpt).
This entry represents 77 residues of an 80 amino acid
(240 nucleotide) tandem repeat, found in a variable
number of copies in an immunodominant outer membrane
protein of Ehrlichia chaffeensis, a tick-borne obligate
intracellular pathogen.
Length = 707
Score = 26.5 bits (57), Expect = 2.0
Identities = 10/43 (23%), Positives = 23/43 (53%)
Query: 83 AGDMPKWIENAVGAVEGISGVEVSITFDPPWTPDLMSEEAQIA 125
A D+P +++++ G +V F + P++++E+ Q A
Sbjct: 521 AEDLPPAVDDSLEHSIPEVGEKVDEMFAEEFNPEVIAEDLQPA 563
>gnl|CDD|184487 PRK14071, PRK14071, 6-phosphofructokinase; Provisional.
Length = 360
Score = 26.2 bits (58), Expect = 2.5
Identities = 26/79 (32%), Positives = 32/79 (40%), Gaps = 20/79 (25%)
Query: 33 SNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDYMVKILMTLTAPG-CPVAGDMPKWIE 91
S +II LGL I + D + IL L G + G +PK I+
Sbjct: 96 SQEIIDGYH------------SLGLDALIGIGGDGSLAILRRLAQQGGINLVG-IPKTID 142
Query: 92 NAVGAVEGISGVEVSITFD 110
N VGA EVSI FD
Sbjct: 143 NDVGA------TEVSIGFD 155
>gnl|CDD|131709 TIGR02661, MauD, methylamine dehydrogenase accessory protein MauD.
This protein, MauD, appears critical to proper formation
of the small subunit of methylamine dehydrogenase, which
has both an unusual tryptophan tryptophylquinone
cofactor and multiple disulfide bonds. MauD shares
sequence similarity, including a CPxC motif, with a
number of thiol:disulfide interchange proteins. In MauD
mutants, the small subunit apparently does not form
properly and is rapidly degraded.
Length = 189
Score = 26.0 bits (57), Expect = 2.7
Identities = 11/35 (31%), Positives = 17/35 (48%), Gaps = 1/35 (2%)
Query: 72 LMTLTAPGCPVAGDMPKWIENAVGAVEGISGVEVS 106
L+ TAP CPV + I+ ++ E V +S
Sbjct: 78 LLMFTAPSCPVCDKLFPIIK-SIARAEETDVVMIS 111
>gnl|CDD|132287 TIGR03243, arg_catab_AOST, arginine and ornithine
succinyltransferase subunits. In many bacteria, the
sole member of this protein family is arginine
N-succinyltransferase (EC 2.3.1.109), the AstA protein
of the arginine succinyltransferase (ast) pathway.
However, in Pseudomonas aeruginosa and several other
species, a tandem gene pair encodes alpha and beta
subunits of a heterodimer that is designated arginine
and ornithine succinyltransferase (AOST).
Length = 335
Score = 26.1 bits (58), Expect = 3.1
Identities = 7/19 (36%), Positives = 12/19 (63%)
Query: 95 GAVEGISGVEVSITFDPPW 113
G V G+S +E ++ D P+
Sbjct: 66 GTVAGVSAIEAAVGLDEPF 84
>gnl|CDD|179052 PRK00513, minC, septum formation inhibitor; Reviewed.
Length = 214
Score = 25.6 bits (57), Expect = 3.9
Identities = 11/28 (39%), Positives = 13/28 (46%), Gaps = 2/28 (7%)
Query: 12 IADKIALSPESTIPPEDLE--RISNDII 37
IAD IA +PE P E I + I
Sbjct: 174 IADVIARAPEDKEKPNYPEVAYIKDGGI 201
>gnl|CDD|173066 PRK14602, ruvA, Holliday junction DNA helicase RuvA; Provisional.
Length = 203
Score = 25.4 bits (56), Expect = 4.5
Identities = 24/74 (32%), Positives = 33/74 (44%), Gaps = 4/74 (5%)
Query: 15 KIALSPESTIPPEDLERI-SNDIIAALKTV--YDPEIPCDIFELGLIYKIDVENDYMVKI 71
K AL+ S P+DL R+ + + +AAL V + IF L L YK+ VE +
Sbjct: 85 KTALAILSQFRPDDLRRLVAEEDVAALTRVSGIGKKTAQHIF-LELKYKLKVEGLPAAAV 143
Query: 72 LMTLTAPGCPVAGD 85
L A V D
Sbjct: 144 LAGTGAVPGSVFRD 157
>gnl|CDD|179038 PRK00464, nrdR, transcriptional regulator NrdR; Validated.
Length = 154
Score = 25.1 bits (56), Expect = 4.8
Identities = 6/26 (23%), Positives = 12/26 (46%)
Query: 24 IPPEDLERISNDIIAALKTVYDPEIP 49
+ E +E + I L+ + E+P
Sbjct: 79 VSSEQIEAAVSRIERQLRASGEREVP 104
>gnl|CDD|148093 pfam06278, DUF1032, Protein of unknown function (DUF1032). This
family consists of several conserved eukaryotic proteins
of unknown function.
Length = 565
Score = 25.3 bits (55), Expect = 5.2
Identities = 13/39 (33%), Positives = 20/39 (51%), Gaps = 10/39 (25%)
Query: 6 PDTENNIADK----------IALSPESTIPPEDLERISN 34
D+E N+ K I L P + +PPE++E+ SN
Sbjct: 74 EDSEANVDLKDDQITSPVLIIPLLPMALVPPEEVEKNSN 112
>gnl|CDD|165553 PHA03296, PHA03296, envelope glycoprotein H; Provisional.
Length = 814
Score = 25.0 bits (54), Expect = 6.0
Identities = 19/65 (29%), Positives = 29/65 (44%), Gaps = 2/65 (3%)
Query: 15 KIALSPESTIPPEDLERISNDIIAALKTVYDPEIPCDIF--ELGLIYKIDVENDYMVKIL 72
KI LS E + L S IAA + + P+ D F EL + D+E+ + I
Sbjct: 571 KIFLSGEGELETAALLDDSARAIAAAQALGGPKALADAFFPELAKCFDWDLEHHIVFFIA 630
Query: 73 MTLTA 77
++ A
Sbjct: 631 ISAHA 635
>gnl|CDD|181078 PRK07678, PRK07678, aminotransferase; Validated.
Length = 451
Score = 25.0 bits (55), Expect = 6.4
Identities = 14/43 (32%), Positives = 21/43 (48%), Gaps = 6/43 (13%)
Query: 4 KNPDT---ENNIADKIALSPESTIPPEDLERISNDIIAALKTV 43
KN DT NN+ + LSP I E++ I + AL+ +
Sbjct: 411 KNGDTVAGYNNV---LTLSPPLVISSEEIAFIVGTLKTALERI 450
>gnl|CDD|147801 pfam05843, Suf, Suppressor of forked protein (Suf). This family
consists of several eukaryotic suppressor of forked
(Suf) like proteins. The Drosophila melanogaster
Suppressor of forked [Su(f)] protein shares homology
with the yeast RNA14 protein and the 77-kDa subunit of
human cleavage stimulation factor, which are proteins
involved in mRNA 3' end formation. This suggests a role
for Su(f) in mRNA 3' end formation in Drosophila. The
su(f) gene produces three transcripts; two of them are
polyadenylated at the end of the transcription unit,
and one is a truncated transcript, polyadenylated in
intron 4. It is thought that su(f) plays a role in the
regulation of poly(A) site utilisation and an important
role of the GU-rich sequence for this regulation to
occur.
Length = 275
Score = 25.0 bits (55), Expect = 6.6
Identities = 8/13 (61%), Positives = 9/13 (69%)
Query: 45 DPEIPCDIFELGL 57
DP+ IFELGL
Sbjct: 51 DPKTAFKIFELGL 63
>gnl|CDD|183738 PRK12775, PRK12775, putative trifunctional 2-polyprenylphenol
hydroxylase/glutamate synthase subunit beta/ferritin
domain-containing protein; Provisional.
Length = 1006
Score = 24.9 bits (54), Expect = 6.9
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 5/27 (18%)
Query: 79 GCPVAGDMPKWIENAV-----GAVEGI 100
GCPV D+P +I + V GA+E I
Sbjct: 344 GCPVQIDIPVFIRHVVVRDFDGALEVI 370
>gnl|CDD|132288 TIGR03244, arg_catab_AstA, arginine N-succinyltransferase. In many
bacteria, the arginine succinyltransferase (ast) pathway
operon consists of five genes, including this protein,
arginine N-succinyltransferase (EC 2.3.1.109). In a few
species, such as Pseudomonas aeruginosa, the member of
this family is encoded adjacent to a paralog, and the
two polypeptides form a heterodimeric enzyme, active on
both arginine and ornithine. In such species, this
polypeptide may be treated as the beta subunit of an
enzyme that may be named either arginine
N-succinyltransferase (AST) or arginine and orthithine
N-succinyltransferase (AOST).
Length = 336
Score = 24.6 bits (54), Expect = 7.9
Identities = 6/19 (31%), Positives = 12/19 (63%)
Query: 95 GAVEGISGVEVSITFDPPW 113
G V G+S +E ++ + P+
Sbjct: 66 GTVAGVSAIEAAVGLEEPF 84
>gnl|CDD|149445 pfam08385, DHC_N1, Dynein heavy chain, N-terminal region 1. Dynein
heavy chains interact with other heavy chains to form
dimers, and with intermediate chain-light chain
complexes to form a basal cargo binding unit. The region
featured in this family includes the sequences
implicated in mediating these interactions. It is
thought to be flexible and not to adopt a rigid
conformation.
Length = 577
Score = 24.5 bits (54), Expect = 7.9
Identities = 12/27 (44%), Positives = 16/27 (59%), Gaps = 3/27 (11%)
Query: 29 LERISNDIIAALKTVYDPEIPCDIFEL 55
LE+ISND+I LK+ P D+ L
Sbjct: 150 LEKISNDLIDQLKSYLSPS---DLMSL 173
>gnl|CDD|181589 PRK08943, PRK08943, lipid A biosynthesis (KDO)2-(lauroyl)-lipid IVA
acyltransferase; Validated.
Length = 314
Score = 24.4 bits (54), Expect = 8.1
Identities = 6/19 (31%), Positives = 9/19 (47%)
Query: 107 ITFDPPWTPDLMSEEAQIA 125
I PP L +++ IA
Sbjct: 260 IEIRPPMDDLLSADDETIA 278
>gnl|CDD|180329 PRK05964, PRK05964, adenosylmethionine--8-amino-7-oxononanoate
transaminase; Provisional.
Length = 423
Score = 24.4 bits (54), Expect = 8.2
Identities = 9/28 (32%), Positives = 15/28 (53%)
Query: 16 IALSPESTIPPEDLERISNDIIAALKTV 43
I L P I E+L+RI++ I+ +
Sbjct: 396 IYLMPPYIITAEELDRITDAIVEVADEL 423
>gnl|CDD|161821 TIGR00331, hrcA, heat shock gene repressor HrcA. In Bacillus
subtilis, hrcA is the first gene of the dnaK operon and
so is itself a heat shock gene.
Length = 337
Score = 24.2 bits (53), Expect = 9.3
Identities = 16/50 (32%), Positives = 22/50 (44%)
Query: 18 LSPESTIPPEDLERISNDIIAALKTVYDPEIPCDIFELGLIYKIDVENDY 67
+ + I EDLER N + L+ EI I EL KI++E
Sbjct: 161 IELPANISQEDLERAVNILNDRLRGRTLSEIREQIIELLSQLKIEIEEFE 210
>gnl|CDD|165212 PHA02884, PHA02884, ankyrin repeat protein; Provisional.
Length = 300
Score = 24.2 bits (52), Expect = 9.5
Identities = 21/48 (43%), Positives = 25/48 (52%), Gaps = 5/48 (10%)
Query: 35 DII-AALKTVYDPEIPCDIFELG----LIYKIDVENDYMVKILMTLTA 77
DII A LK DPE P + E LIY ID +ND K+L+ A
Sbjct: 47 DIIDAILKLGADPEAPFPLSENSKTNPLIYAIDCDNDDAAKLLIRYGA 94
>gnl|CDD|182474 PRK10456, PRK10456, arginine succinyltransferase; Provisional.
Length = 344
Score = 24.3 bits (53), Expect = 10.0
Identities = 8/19 (42%), Positives = 12/19 (63%)
Query: 95 GAVEGISGVEVSITFDPPW 113
G V GI +EV++ + PW
Sbjct: 68 GTVAGICAIEVAVGLNDPW 86
Database: CddB
Posted date: Feb 4, 2011 9:54 PM
Number of letters in database: 5,994,473
Number of sequences in database: 21,608
Lambda K H
0.314 0.136 0.404
Gapped
Lambda K H
0.267 0.0819 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 2,257,988
Number of extensions: 136224
Number of successful extensions: 251
Number of sequences better than 10.0: 1
Number of HSP's gapped: 249
Number of HSP's successfully gapped: 42
Length of query: 129
Length of database: 5,994,473
Length adjustment: 83
Effective length of query: 46
Effective length of database: 4,201,009
Effective search space: 193246414
Effective search space used: 193246414
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: 42 (21.9 bits)
S2: 51 (23.3 bits)