RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254781214|ref|YP_003065627.1| hypothetical protein
CLIBASIA_05605 [Candidatus Liberibacter asiaticus str. psy62]
(110 letters)
>gnl|CDD|163501 TIGR03789, pdsO, proteobacterial sortase system OmpA family
protein. A newly defined histidine kinase (TIGR03785)
and response regulator (TIGR03787) gene pair occurs
exclusively in Proteobacteria, mostly of marine origin,
nearly all of which contain a subfamily 6 sortase
(TIGR03784) and its single dedicated target protein
(TIGR03788) adjacent to to the sortase. This protein
family shows up in only in those species with the
histidine kinase/response regulator gene pair, and
often adjacent to that pair. It belongs to the OmpA
protein family (pfam00691). Its function is unknown. We
assign the gene symbol pdsO, for Proteobacterial
Dedicated Sortase system OmpA family protein.
Length = 239
Score = 31.3 bits (71), Expect = 0.052
Identities = 15/28 (53%), Positives = 19/28 (67%), Gaps = 1/28 (3%)
Query: 14 LSSGFKLGSIF-GPVGGVIGGLMGGAAG 40
L SG LG++ GPVG +IGG+ GG G
Sbjct: 47 LGSGALLGALVGGPVGAIIGGITGGLIG 74
Score = 25.1 bits (55), Expect = 4.3
Identities = 10/26 (38%), Positives = 15/26 (57%), Gaps = 1/26 (3%)
Query: 17 GFKLGSIFGP-VGGVIGGLMGGAAGL 41
G G++ G VGG +G ++GG G
Sbjct: 46 GLGSGALLGALVGGPVGAIIGGITGG 71
>gnl|CDD|173412 PTZ00121, PTZ00121, MAEBL; Provisional.
Length = 2084
Score = 29.0 bits (64), Expect = 0.26
Identities = 14/45 (31%), Positives = 19/45 (42%), Gaps = 1/45 (2%)
Query: 54 SSQKEGKKEEEGVRPLEGDELAE-VRRQESLRAYEMNRIPIPARR 97
+E KK+ E R E AE R+ E R E + AR+
Sbjct: 1115 RKAEEAKKKAEDARKAEEARKAEDARKAEEARKAEDAKRVEIARK 1159
Score = 27.0 bits (59), Expect = 1.2
Identities = 13/42 (30%), Positives = 20/42 (47%)
Query: 57 KEGKKEEEGVRPLEGDELAEVRRQESLRAYEMNRIPIPARRF 98
+E +K E+ + + EVR+ E LR E R AR+
Sbjct: 1167 EEARKAEDAKKAEAARKAEEVRKAEELRKAEDARKAEAARKA 1208
Score = 26.3 bits (57), Expect = 2.0
Identities = 11/42 (26%), Positives = 19/42 (45%)
Query: 57 KEGKKEEEGVRPLEGDELAEVRRQESLRAYEMNRIPIPARRF 98
+ +K EE + E + + R+ E+ R E R AR+
Sbjct: 1179 EAARKAEEVRKAEELRKAEDARKAEAARKAEEERKAEEARKA 1220
Score = 25.1 bits (54), Expect = 4.0
Identities = 14/41 (34%), Positives = 20/41 (48%), Gaps = 5/41 (12%)
Query: 57 KEGKKEEEGVRPLEGDELAEVRRQESLRAYEMNRIPIPARR 97
+E KK+ E + E E R E +R +E R+ ARR
Sbjct: 1233 EEAKKDAEEAKKAE-----EERNNEEIRKFEEARMAHFARR 1268
>gnl|CDD|162098 TIGR00900, 2A0121, H+ Antiporter protein.
Length = 365
Score = 27.3 bits (61), Expect = 0.86
Identities = 21/89 (23%), Positives = 29/89 (32%), Gaps = 20/89 (22%)
Query: 12 SSLSSGFKLGSIFGPVGGVIGGLMGGAAGLYSE-WDTIGGFFGSS--------QKEGKKE 62
S + L I GP IGGLM G+ W GF S+ + E
Sbjct: 131 SLSQAVRSLFYIVGPG---IGGLMYATLGIKWAIWVDAVGFAISALLIVSVRIPELAASE 187
Query: 63 EEGVRP------LEGDELAEVRRQESLRA 85
+ + EG + V + LR
Sbjct: 188 IQALSNAVLRDTREG--IKFVLKNPLLRT 214
>gnl|CDD|150018 pfam09187, DUF1950, Domain of unknown function(DUF1950). Members
of this family pertain to a set of functionally
uncharacterized hypothetical eukaryotic proteins.
Length = 119
Score = 26.8 bits (59), Expect = 1.4
Identities = 11/21 (52%), Positives = 15/21 (71%), Gaps = 1/21 (4%)
Query: 77 VRRQESLRAYEMNRIPIPARR 97
+RR E + Y M +IPIPA+R
Sbjct: 2 LRRAEMYQEY-MKQIPIPAKR 21
>gnl|CDD|129972 TIGR00894, 2A0114euk, Na(+)-dependent inorganic phosphate
cotransporter.
Length = 465
Score = 26.6 bits (59), Expect = 1.5
Identities = 15/46 (32%), Positives = 21/46 (45%), Gaps = 8/46 (17%)
Query: 9 KFGSSLSSGFKLGS-IFGPVGGVIGGLMGGAAGLYSEWDTIGGFFG 53
+ +SGF+LG+ IF P+ G + GG W I FG
Sbjct: 167 RLLGMSTSGFQLGTFIFLPISGWLCESWGG-------WPMIFYVFG 205
>gnl|CDD|177560 PHA03231, PHA03231, glycoprotein BALF4; Provisional.
Length = 829
Score = 26.4 bits (59), Expect = 1.5
Identities = 9/35 (25%), Positives = 13/35 (37%), Gaps = 5/35 (14%)
Query: 20 LGSIF---GPVGGVIGGLMGGAAGLYSEWDTIGGF 51
L G VG +G ++ G AG + G
Sbjct: 664 LAEFMQGLGAVGKAVGNVVSGVAGAVG--SIVSGV 696
>gnl|CDD|132173 TIGR03129, one_C_dehyd_B, formylmethanofuran dehydrogenase subunit
B. Members of this largely archaeal protein family are
subunit B of the formylmethanofuran dehydrogenase.
Nomenclature in some bacteria may reflect inclusion of
the formyltransferase described by TIGR03119 as part of
the complex, and therefore call this protein
formyltransferase/hydrolase complex Fhc subunit C. Note
that this model does not distinguish tungsten (FwdB)
from molybdenum-containing (FmdB) forms of this enzyme.
Length = 421
Score = 26.1 bits (58), Expect = 2.0
Identities = 8/25 (32%), Positives = 12/25 (48%)
Query: 85 AYEMNRIPIPARRFTSSSLLSGVHV 109
AY M+ +PI R+ S S +
Sbjct: 389 AYRMDNVPIRLRKVIESPEPSDEEI 413
>gnl|CDD|179189 PRK00968, PRK00968, tetrahydromethanopterin S-methyltransferase
subunit D; Provisional.
Length = 240
Score = 26.1 bits (58), Expect = 2.2
Identities = 9/14 (64%), Positives = 10/14 (71%)
Query: 27 VGGVIGGLMGGAAG 40
V GVIGG +GG G
Sbjct: 143 VSGVIGGALGGIGG 156
>gnl|CDD|102546 PRK06772, PRK06772, salicylate synthase Irp9; Reviewed.
Length = 434
Score = 25.9 bits (56), Expect = 2.3
Identities = 12/33 (36%), Positives = 20/33 (60%)
Query: 74 LAEVRRQESLRAYEMNRIPIPARRFTSSSLLSG 106
+AE+RR E ++ IP+P+R ++LL G
Sbjct: 183 VAEIRRGEYVKVIVSRAIPLPSRIDMPATLLYG 215
>gnl|CDD|151016 pfam10439, Bacteriocin_IIc, Bacteriocin class II with
double-glycine leader peptide. This is a family of
bacteriocidal bacteriocins secreted by Streptococcal
species in order to kill off closely-related competitor
Gram-positives. The sequence includes the peptide
precursor, this being cleaved off proteolytically at
the double-glycine. The family does not carry the
YGNGVXC motif characteristic of pediocin-like
Bacteriocins, Bacteriocin_II pfam01721. The producer
bacteria are protected from the effects of their own
bacteriocins by production of a specific immunity
protein which is co-transcribed with the genes encoding
the bacteriocins, eg family EntA_Immun pfam08951. The
bacteriocins are structurally more specific than their
immunity-protein counterparts. Typically, production of
the bacteriocin gene is from within an operon carrying
up to 6 genes including a typical two-component
regulatory system (R and H), a small peptide pheromone
(C), and a dedicated ABC transporter (A and -B) as well
as an immunity protein. The ABC transporter is thought
to recognize the N termini of both the pheromone and
the bacteriocins and to transport these peptides across
the cytoplasmic membrane, concurrent with cleavage at
the conserved double-glycine motif. Cleaved
extracellular C can then bind to the sensor kinase, H,
resulting in activation of R and up-regulation of the
entire gene cluster via binding to consensus sequences
within each promoter. It seems likely that this whole
regulon is carried on a transmissible plasmid which is
passed between closely related Firmicute species since
many clinical isolates from different Firmicutes can
produce at least two bacteriocins. and the same
bacteriocins can be produced by different species.
Length = 65
Score = 25.8 bits (57), Expect = 2.7
Identities = 13/31 (41%), Positives = 18/31 (58%), Gaps = 1/31 (3%)
Query: 11 GSSLSSGFKLGSIFG-PVGGVIGGLMGGAAG 40
G ++G G+ G PVGG+ G L+GG G
Sbjct: 30 GGGAAAGAVAGAAGGGPVGGLAGALVGGVVG 60
>gnl|CDD|185040 PRK15082, PRK15082, glutathione ABC transporter permease GsiD;
Provisional.
Length = 301
Score = 25.5 bits (56), Expect = 2.9
Identities = 13/33 (39%), Positives = 19/33 (57%), Gaps = 4/33 (12%)
Query: 13 SLSSGFKLGSIFGPVGGVIGGLMGGAAGLYSEW 45
SL++GF S+ +G IG ++G AG Y W
Sbjct: 102 SLAAGFF--SVA--IGAAIGTVLGLLAGYYEGW 130
>gnl|CDD|179524 PRK03001, PRK03001, M48 family peptidase; Provisional.
Length = 283
Score = 25.4 bits (56), Expect = 3.0
Identities = 9/31 (29%), Positives = 13/31 (41%), Gaps = 8/31 (25%)
Query: 23 IFGPVGGVIGG--------LMGGAAGLYSEW 45
+F +GG+IGG L +S W
Sbjct: 16 LFIVIGGMIGGSQGMLIALLFALGMNFFSYW 46
>gnl|CDD|177604 PHA03367, PHA03367, single-stranded DNA binding protein;
Provisional.
Length = 1115
Score = 25.3 bits (56), Expect = 3.1
Identities = 10/35 (28%), Positives = 18/35 (51%), Gaps = 2/35 (5%)
Query: 35 MGGAAGLYSEWDTIGGF--FGSSQKEGKKEEEGVR 67
+ G +G Y++ D +G F F + +G + EE
Sbjct: 487 VTGVSGFYNDLDILGNFGRFRDKEDDGNQREETPS 521
>gnl|CDD|185557 PTZ00327, PTZ00327, eukaryotic translation initiation factor 2
gamma subunit; Provisional.
Length = 460
Score = 25.3 bits (56), Expect = 3.7
Identities = 8/19 (42%), Positives = 10/19 (52%)
Query: 86 YEMNRIPIPARRFTSSSLL 104
Y +IPIP R TS +
Sbjct: 227 YICTQIPIPKRDLTSPPRM 245
>gnl|CDD|162896 TIGR02512, Fe_only_hydrog, hydrogenases, Fe-only. This model
describes iron-only hydrogenases of anaerobic and
microaerophilic bacteria and protozoa. This model is
narrower, and covers a longer stretch of sequence, than
Pfam model pfam02906. This family represents a division
among families that belong to pfam02906, which also
includes proteins such as nuclear prelamin A recognition
factor in animals. Note that this family shows some
heterogeneity in terms of periplasmic, cytosolic, or
hydrogenosome location, NAD or NADP dependence, and
overal protein protein length.
Length = 374
Score = 25.4 bits (56), Expect = 3.9
Identities = 17/57 (29%), Positives = 28/57 (49%), Gaps = 11/57 (19%)
Query: 21 GSIFGPVGGVIGGLMGGAAGLYSEWDTIGGFFGSSQKEGKKEEEGVRPLEGDELAEV 77
G+IFG GGV+ A L + ++ + G ++ E + VR L+G + A V
Sbjct: 276 GAIFGATGGVM------EAALRTAYEIVTG-----KELELIEFKAVRGLDGVKEATV 321
>gnl|CDD|183779 PRK12830, PRK12830, UDP-N-acetylglucosamine
1-carboxyvinyltransferase; Reviewed.
Length = 417
Score = 25.2 bits (56), Expect = 4.4
Identities = 12/35 (34%), Positives = 20/35 (57%)
Query: 60 KKEEEGVRPLEGDELAEVRRQESLRAYEMNRIPIP 94
K EE GVR ++ V +Q +L+A ++ +P P
Sbjct: 265 KLEEMGVRVEVNEDSIFVEKQGNLKAVDIKTLPYP 299
>gnl|CDD|178676 PLN03130, PLN03130, ABC transporter C family member; Provisional.
Length = 1622
Score = 24.7 bits (54), Expect = 5.3
Identities = 18/61 (29%), Positives = 26/61 (42%), Gaps = 21/61 (34%)
Query: 66 VRPLEGDELAEVRRQESLRAYEM---NRIPI------------------PARRFTSSSLL 104
V+ + DEL+ R+ + L A+ N IP+ PAR FTS SL
Sbjct: 505 VQTVRDDELSWFRKAQLLSAFNSFILNSIPVLVTVVSFGVFTLLGGDLTPARAFTSLSLF 564
Query: 105 S 105
+
Sbjct: 565 A 565
>gnl|CDD|178177 PLN02563, PLN02563, aminoacyl-tRNA ligase.
Length = 963
Score = 24.4 bits (53), Expect = 6.0
Identities = 12/28 (42%), Positives = 17/28 (60%)
Query: 81 ESLRAYEMNRIPIPARRFTSSSLLSGVH 108
+SLR YEM P+ + S+S + GVH
Sbjct: 744 DSLRLYEMFMGPLRDSKTWSTSGVEGVH 771
>gnl|CDD|181907 PRK09494, glnP, glutamine ABC transporter permease protein;
Reviewed.
Length = 219
Score = 24.2 bits (53), Expect = 7.0
Identities = 10/24 (41%), Positives = 14/24 (58%)
Query: 22 SIFGPVGGVIGGLMGGAAGLYSEW 45
S+ G GG++ GL+ G A Y W
Sbjct: 26 SVLGLAGGLVIGLLAGFARAYGGW 49
>gnl|CDD|178198 PLN02587, PLN02587, L-galactose dehydrogenase.
Length = 314
Score = 24.4 bits (53), Expect = 7.4
Identities = 13/22 (59%), Positives = 15/22 (68%), Gaps = 5/22 (22%)
Query: 6 SSVKFGSSLSSGFKLGSIFGPV 27
SSV FG+S LGS+FGPV
Sbjct: 12 SSVGFGAS-----PLGSVFGPV 28
>gnl|CDD|178387 PLN02790, PLN02790, transketolase.
Length = 654
Score = 24.2 bits (53), Expect = 8.3
Identities = 15/44 (34%), Positives = 20/44 (45%), Gaps = 3/44 (6%)
Query: 27 VGGVIGGLMGGAAGLYSEWDT---IGGFFGSSQKEGKKEEEGVR 67
+ V+ GL+GG+A L S T G F E + GVR
Sbjct: 357 LAKVLPGLIGGSADLASSNMTLLKDFGDFQKDTPEERNVRFGVR 400
>gnl|CDD|172777 PRK14289, PRK14289, chaperone protein DnaJ; Provisional.
Length = 386
Score = 24.0 bits (52), Expect = 8.6
Identities = 14/51 (27%), Positives = 19/51 (37%), Gaps = 7/51 (13%)
Query: 17 GFKLGSIFGPVGGVIGGLMGGAAGLYSEWDTIGGFFGSSQKEGKKEEEGVR 67
G + IF G + GG GG G GGF G ++ +R
Sbjct: 88 GMSMEDIFSMFGDIFGGHGGGFGGF-------GGFGGGGSQQRVFRGSDLR 131
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
0.315 0.137 0.390
Gapped
Lambda K H
0.267 0.0643 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,839,532
Number of extensions: 109377
Number of successful extensions: 262
Number of sequences better than 10.0: 1
Number of HSP's gapped: 258
Number of HSP's successfully gapped: 55
Length of query: 110
Length of database: 5,994,473
Length adjustment: 76
Effective length of query: 34
Effective length of database: 4,352,265
Effective search space: 147977010
Effective search space used: 147977010
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 (22.0 bits)
S2: 50 (23.2 bits)