RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780801|ref|YP_003065214.1| hypothetical protein
CLIBASIA_03460 [Candidatus Liberibacter asiaticus str. psy62]
(222 letters)
>gnl|CDD|129155 TIGR00044, TIGR00044, pyridoxal phosphate enzyme, YggS family.
Members of this protein family include YggS from
Escherichia coli and YBL036C, an uncharacterized
pyridoxal protein of Saccharomyces cerevisiae.
Length = 229
Score = 134 bits (339), Expect = 1e-32
Identities = 78/223 (34%), Positives = 109/223 (48%), Gaps = 10/223 (4%)
Query: 6 KLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKW 65
L+ K KIE + R V L+AVSK + I++A GQ F EN +QE +K
Sbjct: 7 YLEDIKTKIEAANTHVNRNPSKVKLLAVSKTKPASAIQIAYDAGQRAFGENYVQELVEKI 66
Query: 66 IPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQ 125
L ++ FIG LQSNK +V FD + T+ K A L+ + K L V +Q
Sbjct: 67 KLLEDLGKLEWHFIGPLQSNKDRLVVENFDWVHTIDSLKIAKKLNEQREKLQPPLNVLLQ 126
Query: 126 VNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPH----------FY 175
+N E KSGI P + + I + L + GLM I + + F+
Sbjct: 127 INISDEESKSGIQPEELLELAIQIEELKHLKLRGLMTIGAPTDSHEDQEENFRFMKLLFW 186
Query: 176 LLSEIARECKLTKLSMGMTRDFELAIASGATSVRIGSGIFGER 218
+ + + + LSMGM+ DFE AIA+GAT VRIG+ IFG R
Sbjct: 187 QIKQDSPFGTIDTLSMGMSDDFEEAIAAGATMVRIGTAIFGAR 229
>gnl|CDD|178827 PRK00053, alr, alanine racemase; Reviewed.
Length = 363
Score = 35.9 bits (84), Expect = 0.008
Identities = 12/59 (20%), Positives = 30/59 (50%), Gaps = 5/59 (8%)
Query: 106 ASLLSLEMIKQSRF---LPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLM 161
SL LE ++++ L V+++++TG + + G+ P + + + + +EG+
Sbjct: 103 HSLEQLEALEKAELGKPLKVHLKIDTG--MHRLGVRPEEAEAALERLLACPNVRLEGIF 159
>gnl|CDD|129583 TIGR00492, alr, alanine racemase. This enzyme interconverts
L-alanine and D-alanine. Its primary function is to
generate D-alanine for cell wall formation. With
D-alanine-D-alanine ligase, it makes up the D-alanine
branch of the peptidoglycan biosynthetic route. It is a
monomer with one pyridoxal phosphate per subunit. In E.
coli, the ortholog is duplicated so that a second
isozyme, DadX, is present. DadX, a paralog of the
biosynthetic Alr, is induced by D- or L-alanine and is
involved in catabolism.
Length = 367
Score = 31.2 bits (71), Expect = 0.19
Identities = 19/74 (25%), Positives = 42/74 (56%), Gaps = 3/74 (4%)
Query: 89 EIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVIL 148
+I++ +D+ TV + L ++K+ + L V+++++TG + + G+ P++ FV
Sbjct: 89 KILAAWDLTTTVHSVEQLQALEEALLKEPKRLKVHLKIDTG--MNRLGVKPDEAALFVQK 146
Query: 149 CRQKYQ-LNVEGLM 161
RQ + L +EG+
Sbjct: 147 LRQLKKFLELEGIF 160
>gnl|CDD|181127 PRK07807, PRK07807, inosine 5-monophosphate dehydrogenase;
Validated.
Length = 479
Score = 30.6 bits (70), Expect = 0.29
Identities = 11/18 (61%), Positives = 15/18 (83%)
Query: 195 RDFELAIASGATSVRIGS 212
RD LA+A+GA++V IGS
Sbjct: 343 RDVALALAAGASNVMIGS 360
>gnl|CDD|184518 PRK14119, gpmA, phosphoglyceromutase; Provisional.
Length = 228
Score = 30.2 bits (68), Expect = 0.39
Identities = 14/30 (46%), Positives = 19/30 (63%), Gaps = 1/30 (3%)
Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQS-NK 86
L E+K++WIP+ K W + R G LQ NK
Sbjct: 69 LTESKQQWIPVYKSWRLNERHYGGLQGLNK 98
>gnl|CDD|152009 pfam11573, Med23, Mediator complex subunit 23. Med23 is one of the
subunits of the Tail portion of the Mediator complex
that regulates RNA polymerase II activity. Med23 is
required for heat-shock-specific gene expression, and
has been shown to mediate transcriptional activation of
E1A in mice.
Length = 1341
Score = 29.8 bits (67), Expect = 0.52
Identities = 28/145 (19%), Positives = 60/145 (41%), Gaps = 17/145 (11%)
Query: 1 MSLGNKLQVFKQKIENSAILAKRPKDSVSLVAVSKMVDSKKIRVALSCGQVIFAENKLQE 60
M K + ++ ++ +A++ + + + + V K I + C + + +E E
Sbjct: 57 MEQEEKESLVRELLKMVHHVAEKNRYERVVDVLLRYVHQKIIPATMLCEEGLISEKLFYE 116
Query: 61 AKKKWIPLRKEWDVQLRFIGSLQSNKVSEIV-----SLFDVIETVSREKTASLLSLEMI- 114
+ WI +++ + + IG + V EI+ +VS E LL++E +
Sbjct: 117 CSRFWI---EKFKLIRKVIGGVDYKGVREIMKYILEKALRFPYSVSPEIVPQLLAVEEVI 173
Query: 115 -----KQSRFLPVYIQVNTGYEIQK 134
+ + LP Y +N EI +
Sbjct: 174 LHIFDRNANLLPAYFTLN---EIMR 195
>gnl|CDD|130370 TIGR01303, IMP_DH_rel_1, IMP dehydrogenase family protein. This
model represents a family of proteins, often annotated
as a putative IMP dehydrogenase, related to IMP
dehydrogenase and GMP reductase and restricted to the
high GC Gram-positive bacteria. All species in which a
member is found so far (Corynebacterium glutamicum,
Mycobacterium tuberculosis, Streptomyces coelicolor,
etc.) also have IMP dehydrogenase as described by
TIGRFAMs entry TIGR01302.
Length = 475
Score = 29.9 bits (67), Expect = 0.52
Identities = 25/72 (34%), Positives = 34/72 (47%), Gaps = 13/72 (18%)
Query: 159 GLMCIPPAM-GNPKPHFYLLSEIARECKLTKLSMGM--------TRDFELAIASGATSVR 209
G MC M G +P F + E A E + KL + RD LA+A+GA++V
Sbjct: 298 GAMCTTRMMTGVGRPQFSAVLECAAEAR--KLGGHVWADGGVRHPRDVALALAAGASNVM 355
Query: 210 IGSGIFG--ERP 219
+GS G E P
Sbjct: 356 VGSWFAGTYESP 367
>gnl|CDD|184519 PRK14120, gpmA, phosphoglyceromutase; Provisional.
Length = 249
Score = 30.0 bits (68), Expect = 0.56
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83
L A + WIP+R+ W + R G+LQ
Sbjct: 72 LDAADRLWIPVRRSWRLNERHYGALQ 97
>gnl|CDD|130325 TIGR01258, pgm_1, phosphoglycerate mutase, BPG-dependent, family
1. Most members of this family are phosphoglycerate
mutase (EC 5.4.2.1). This enzyme interconverts
2-phosphoglycerate and 3-phosphoglycerate. The enzyme
is transiently phosphorylated on an active site
histidine by 2,3-diphosphoglyerate, which is both
substrate and product. Some members of this family have
are phosphoglycerate mutase as a minor activity and act
primarily as a bisphoglycerate mutase, interconverting
2,3-diphosphoglycerate and 1,3-diphosphoglycerate (EC
5.4.2.4). This model is designated as a subfamily for
this reason. The second and third paralogs in S.
cerevisiae are somewhat divergent and apparently
inactive (see PUBMED:9544241) but are also part of this
subfamily phylogenetically.
Length = 245
Score = 29.7 bits (67), Expect = 0.64
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83
L E + WIP++K W + R G+LQ
Sbjct: 68 LDELDQLWIPVKKSWRLNERHYGALQ 93
>gnl|CDD|180614 PRK06546, PRK06546, pyruvate dehydrogenase; Provisional.
Length = 578
Score = 28.0 bits (63), Expect = 2.1
Identities = 12/19 (63%), Positives = 13/19 (68%)
Query: 199 LAIASGATSVRIGSGIFGE 217
LAIAS S +IGSG F E
Sbjct: 96 LAIASHIPSAQIGSGFFQE 114
>gnl|CDD|185556 PTZ00326, PTZ00326, phenylalanyl-tRNA synthetase alpha chain;
Provisional.
Length = 494
Score = 28.0 bits (63), Expect = 2.2
Identities = 15/73 (20%), Positives = 31/73 (42%), Gaps = 3/73 (4%)
Query: 62 KKKWIPLRKEWDVQLRFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLP 121
KKKWI L K D ++ L + V + L ++ S+ + L+ +K+ +
Sbjct: 112 KKKWIKLNKG-DKKVFLSRKLVDSVVDTVRLLLKIVAKGSQAEKIDSKELKELKKRKL-- 168
Query: 122 VYIQVNTGYEIQK 134
++ + + K
Sbjct: 169 ATLEKIKYFVVTK 181
>gnl|CDD|172606 PRK14116, gpmA, phosphoglyceromutase; Provisional.
Length = 228
Score = 28.0 bits (62), Expect = 2.2
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83
L+E+ + WIP K W + R G+LQ
Sbjct: 69 LEESDQLWIPETKTWRLNERHYGALQ 94
>gnl|CDD|148843 pfam07467, BLIP, Beta-lactamase inhibitor (BLIP). The structure of
BLIP reveals two structural domains, which form a polar,
concave surface that docks onto a predominantly polar,
convex protrusion on beta-lactamase. The ability of BLIP
to adapt to a variety of class A beta-lactamases is
thought to be due to flexibility between these two
domains.
Length = 183
Score = 27.6 bits (61), Expect = 2.5
Identities = 12/34 (35%), Positives = 16/34 (47%), Gaps = 1/34 (2%)
Query: 185 KLTKLSMGMTRDFELAIASGATSVRIGSGIFGER 218
K T++ GMTR IA + G G FG+
Sbjct: 35 KYTQIQFGMTRQQVWDIAGAEQNCETG-GSFGDS 67
>gnl|CDD|172608 PRK14118, gpmA, phosphoglyceromutase; Provisional.
Length = 227
Score = 27.6 bits (61), Expect = 2.6
Identities = 11/26 (42%), Positives = 16/26 (61%)
Query: 58 LQEAKKKWIPLRKEWDVQLRFIGSLQ 83
L+E+ + WIP K W + R G+LQ
Sbjct: 68 LEESNQLWIPQVKNWRLNERHYGALQ 93
>gnl|CDD|178757 PLN03218, PLN03218, maturation of RBCL 1; Provisional.
Length = 1060
Score = 27.2 bits (60), Expect = 3.5
Identities = 46/200 (23%), Positives = 73/200 (36%), Gaps = 42/200 (21%)
Query: 31 VAVSKMVDSKKIRVALSCGQVIFAENKLQEAKKKWIPL--------------RKEWDVQL 76
V ++ S + VA G + A LQ+A+K+ I L K W L
Sbjct: 645 VKPDEVFFSALVDVAGHAGDLDKAFEILQDARKQGIKLGTVSYSSLMGACSNAKNWKKAL 704
Query: 77 RFIGSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIKQSRFLPVYIQVNTGYEIQKSG 136
++S K+ VS + + T E +LE++ E+++ G
Sbjct: 705 ELYEDIKSIKLRPTVSTMNALITALCEGNQLPKALEVLS---------------EMKRLG 749
Query: 137 IMPNQTKDFVIL--CRQKYQLNVEGLMCIPPAMGNP-KPHFYLLSEIARECKLTKLSMGM 193
+ PN ++L +K +V GL + A + KP+ + I C
Sbjct: 750 LCPNTITYSILLVASERKDDADV-GLDLLSQAKEDGIKPNLVMCRCITGLCL-------- 800
Query: 194 TRDFELAIASGATSVRIGSG 213
R FE A A G V SG
Sbjct: 801 -RRFEKACALGEPVVSFDSG 819
>gnl|CDD|132434 TIGR03393, indolpyr_decarb, indolepyruvate decarboxylase, Erwinia
family. A family of closely related, thiamine
pyrophosphate-dependent enzymes includes indolepyruvate
decarboxylase (EC 4.1.1.74), phenylpyruvate
decarboxylase (EC 4.1.1.43), pyruvate decarboxylase (EC
4.1.1.1), branched-chain alpha-ketoacid decarboxylase,
etc.. Members of this group of homologs may overlap in
specificity. Within the larger family, this model
represents a clade of bacterial indolepyruvate
decarboxylases, part of a pathway for biosynthesis of
the plant hormone indole-3-acetic acid. Typically, these
species interact with plants, as pathogens or as
beneficial, root-associated bacteria.
Length = 539
Score = 26.4 bits (58), Expect = 5.5
Identities = 11/36 (30%), Positives = 19/36 (52%)
Query: 80 GSLQSNKVSEIVSLFDVIETVSREKTASLLSLEMIK 115
+ +VSE L DV+E V+ + SL+ + + K
Sbjct: 493 PQSECWRVSEAEQLADVLEKVAAHERLSLIEVVLPK 528
>gnl|CDD|148471 pfam06872, EspG, EspG protein. This family consists of several
EspG like proteins from Citrobacter rodentium and
Escherichia coli. EspG is secreted by the type III
secretory system and is translocated into host
epithelial cells. EspG is homologous with Shigella
flexneri protein VirA and can rescue invasion in a
Shigella virA mutant, indicating that these proteins are
functionally equivalent in Shigella. EspG plays an
accessory but as yet undefined role in EPEC virulence
that may involve intestinal colonisation.
Length = 336
Score = 26.4 bits (58), Expect = 6.8
Identities = 16/67 (23%), Positives = 22/67 (32%), Gaps = 3/67 (4%)
Query: 114 IKQSRFLPVYIQVNTGYEIQKSGIMPNQTKDFVILCRQKYQLNVEGLMCIPPAMGNPKPH 173
I QS +Y+ +TG I PN R Y++ G C +
Sbjct: 269 ISQSSGGAIYVTSHTGVLIMAPEDRPNGVGMLTN--RTSYEVP-AGTKCEIEELVRAIKP 325
Query: 174 FYLLSEI 180
Y SE
Sbjct: 326 RYASSET 332
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
0.320 0.134 0.378
Gapped
Lambda K H
0.267 0.0725 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 3,354,946
Number of extensions: 197507
Number of successful extensions: 360
Number of sequences better than 10.0: 1
Number of HSP's gapped: 358
Number of HSP's successfully gapped: 26
Length of query: 222
Length of database: 5,994,473
Length adjustment: 90
Effective length of query: 132
Effective length of database: 4,049,753
Effective search space: 534567396
Effective search space used: 534567396
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 (21.8 bits)
S2: 55 (25.0 bits)