RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780980|ref|YP_003065393.1| hypothetical protein
CLIBASIA_04405 [Candidatus Liberibacter asiaticus str. psy62]
(121 letters)
>gnl|CDD|130083 TIGR01010, BexC_CtrB_KpsE, polysaccharide export inner-membrane
protein, BexC/CtrB/KpsE family. This family contains
gamma proteobacterial proteins involved in capsule
polysaccharide export.
Length = 362
Score = 33.9 bits (78), Expect = 0.010
Identities = 17/60 (28%), Positives = 32/60 (53%), Gaps = 2/60 (3%)
Query: 36 QKNSTQMIKEANFKISE-THRLAQERVEAAEKRVKEVEERATASR-KLSVDELANAFWDL 93
QK + +++KE I+ R ++ + AE VKE E+R A++ +L ++ N +D
Sbjct: 146 QKINQRLLKEGERLINRLNERARKDTIAFAENEVKEAEQRLNATKAELLKYQIKNKVFDP 205
>gnl|CDD|182956 PRK11091, PRK11091, aerobic respiration control sensor protein
ArcB; Provisional.
Length = 779
Score = 30.3 bits (69), Expect = 0.12
Identities = 19/57 (33%), Positives = 30/57 (52%), Gaps = 6/57 (10%)
Query: 27 RTEDL-LN-KLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKL 81
R DL LN +L+ N I + N +I+E + + R EA E+ E++ER +L
Sbjct: 98 RERDLELNVQLKDN----IAQLNQEIAEREKAEEARQEAFEQLKNEIKEREETQIEL 150
>gnl|CDD|178527 PLN02939, PLN02939, transferase, transferring glycosyl groups.
Length = 977
Score = 29.9 bits (67), Expect = 0.19
Identities = 16/56 (28%), Positives = 32/56 (57%), Gaps = 6/56 (10%)
Query: 23 IVIGRTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATAS 78
+V+ + +DL +K+ K EA+ K + + + +VE ++++K +EER AS
Sbjct: 321 LVLDQNQDLRDKVDK------LEASLKEANVSKFSSYKVELLQQKLKLLEERLQAS 370
>gnl|CDD|182386 PRK10334, PRK10334, mechanosensitive channel MscS; Provisional.
Length = 286
Score = 28.0 bits (62), Expect = 0.67
Identities = 24/120 (20%), Positives = 46/120 (38%), Gaps = 20/120 (16%)
Query: 5 ILMTSAFSTTLLTIGGCDIVIGRTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAA 64
+L FSTT+ T G IVI + + + S + ++ F I + ++V+
Sbjct: 145 VLSVQIFSTTMRTADGKIIVIPNGKIIAGNIINFSREPVRRNEFIIGVAYDSDIDQVKQI 204
Query: 65 EKRVKEVEERATASRKLSV--------------------DELANAFWDLSDEDKNAFTGN 104
+ + E+R R+++V +L N +WD+ + K F
Sbjct: 205 LTNIIQSEDRILKDREMTVRLNELGASSINFVVRVWSNSGDLQNVYWDVLERIKREFDAA 264
>gnl|CDD|161812 TIGR00308, TRM1, tRNA(guanine-26,N2-N2) methyltransferase. This
enzyme is responsible for two methylations of a
characteristic guanine of most tRNA molecules. The
activity has been demonstrated for eukaryotic and
archaeal proteins, which are active when expressed in E.
coli, a species that lacks this enzyme. At least one
Eubacterium, Aquifex aeolicus, has an ortholog, as do
all completed archaeal genomes.
Length = 374
Score = 27.5 bits (61), Expect = 0.83
Identities = 12/58 (20%), Positives = 28/58 (48%), Gaps = 4/58 (6%)
Query: 62 EAAEKRVKEVEERATASRKLSVDELANAFWDLSDEDKNAFTGNVKQEVCKVKKITVPP 119
E E+ ++ EE+ +RK V ++ + + + ++ + + V K++VPP
Sbjct: 277 EFIEEVLRIAEEKEYGTRK-RVLKMLSLIKNELSDPPGYYSPH---HIASVLKLSVPP 330
>gnl|CDD|180652 PRK06667, motB, flagellar motor protein MotB; Validated.
Length = 252
Score = 27.5 bits (61), Expect = 0.90
Identities = 17/91 (18%), Positives = 40/91 (43%), Gaps = 13/91 (14%)
Query: 6 LMTSAFSTTLLTIGGCDIVIGRTEDLLNKLQKNSTQMIKEANFKISETHRLAQ----ERV 61
+++++F+ T GG + G+ +L N + + E ++S+ + A +
Sbjct: 49 IISASFTGTGFFKGGQTLSKGKLSELGNSIMSLPST---EKGKQLSQAKKNASSLFKPEI 105
Query: 62 EAAEKRVKEVEERATASRKLSVDELANAFWD 92
++ + V E E R L + ++AF+
Sbjct: 106 QSNKVAVTEDE------RGLVISLASDAFFY 130
>gnl|CDD|163537 TIGR03825, FliH_bacil, flagellar assembly protein FliH. This
bacillus clade of FliH proteins is not found by the Pfam
FliH model pfam02108, but is closely related to the
sequences identified by that model. Sequences identified
by this model are observed in flagellar operons in an
analogous position relative to other flagellar operon
genes.
Length = 255
Score = 25.9 bits (57), Expect = 2.4
Identities = 24/83 (28%), Positives = 37/83 (44%), Gaps = 17/83 (20%)
Query: 43 IKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELANAFWDLS-DEDKNAF 101
I EAN + E +E++E+A+ + E+ LA +S EDKNAF
Sbjct: 113 IDEANAIVEEAKDDYEEKIESAQPLIIEL-----------ACALAEKVIGVSLAEDKNAF 161
Query: 102 TGNVKQEVCKVK-----KITVPP 119
V+Q + +V+ I V P
Sbjct: 162 QALVRQVLSEVREFDEVSIYVHP 184
>gnl|CDD|161889 TIGR00462, genX, lysyl-tRNA synthetase-like protein GenX. Many
Gram-negative bacteria have a protein closely homologous
to the C-terminal region of lysyl-tRNA synthetase
(LysS). Multiple sequence alignment of these proteins
with the homologous regions of collected LysS proteins
shows that these proteins form a distinct set rather
than just similar truncations of LysS. The protein is
termed GenX after its designation in E. coli.
Interestingly, genX often is located near a homolog of
lysine-2,3-aminomutase. Its function is unknown.
Length = 304
Score = 25.6 bits (57), Expect = 3.2
Identities = 7/11 (63%), Positives = 9/11 (81%)
Query: 85 ELANAFWDLSD 95
ELAN F +L+D
Sbjct: 228 ELANGFHELTD 238
>gnl|CDD|179675 PRK03918, PRK03918, chromosome segregation protein; Provisional.
Length = 880
Score = 25.8 bits (57), Expect = 3.2
Identities = 16/47 (34%), Positives = 28/47 (59%), Gaps = 1/47 (2%)
Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERA 75
E+L+ + +K ++++E N +IS +E +E EK VKE+EE
Sbjct: 192 EELIKEKEKELEEVLREIN-EISSELPELREELEKLEKEVKELEELK 237
>gnl|CDD|184422 PRK13962, PRK13962, bifunctional phosphoglycerate
kinase/triosephosphate isomerase; Provisional.
Length = 645
Score = 25.5 bits (56), Expect = 3.7
Identities = 24/83 (28%), Positives = 38/83 (45%), Gaps = 18/83 (21%)
Query: 37 KNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEER--------ATASRKLSVDELA- 87
KN + I N+K+++T A+E V +K VK+ + A S K +VD
Sbjct: 394 KNPRKPIIAGNWKMNKTPAEAKEFVNELKKYVKDAQAEVVVCPPFTALPSVKEAVDGSNI 453
Query: 88 -----NAFWDLSDEDKNAFTGNV 105
N F+ E+K A+TG +
Sbjct: 454 KLGAQNVFY----EEKGAYTGEI 472
>gnl|CDD|149170 pfam07946, DUF1682, Protein of unknown function (DUF1682). The
members of this family are all hypothetical eukaryotic
proteins of unknown function. One member is described as
being an adipocyte-specific protein, but no evidence of
this was found.
Length = 322
Score = 25.3 bits (56), Expect = 3.8
Identities = 14/59 (23%), Positives = 24/59 (40%), Gaps = 4/59 (6%)
Query: 28 TEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDEL 86
+ ++L K+ K + ++ QE +K K+ EER KLS +E
Sbjct: 254 SPEVLRKVDKTREEEEEKIL---KAAEEERQE-EAQEKKEEKKKEEREAKLAKLSPEEQ 308
>gnl|CDD|177394 PHA02562, 46, endonuclease subunit; Provisional.
Length = 562
Score = 25.4 bits (56), Expect = 4.1
Identities = 18/66 (27%), Positives = 31/66 (46%), Gaps = 2/66 (3%)
Query: 22 DIVIGRTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKL 81
D I E+++++ + S + + E KIS + V+ A K+VK E A
Sbjct: 319 DTAIDELEEIMDEFNEQSKK-LLELKNKISTNKQSLITLVDKA-KKVKAAIEELQAEFVD 376
Query: 82 SVDELA 87
+ +ELA
Sbjct: 377 NAEELA 382
>gnl|CDD|181030 PRK07561, PRK07561, DNA topoisomerase I subunit omega; Validated.
Length = 859
Score = 25.1 bits (56), Expect = 4.1
Identities = 12/41 (29%), Positives = 15/41 (36%), Gaps = 16/41 (39%)
Query: 57 AQERVEAAEKRVKEVEERAT----------------ASRKL 81
A +E A V VE++ T ASRKL
Sbjct: 244 AVAALEGARYSVASVEDKPTTRKPSAPFTTSTLQQEASRKL 284
>gnl|CDD|148033 pfam06188, HrpE, HrpE protein. This family consists of several
bacterial HrpE proteins. The exact function of this
family is unknown but it is thought that HrpE is
involved in the secretion of HrpZ (harpinPss).
Length = 191
Score = 25.1 bits (55), Expect = 4.5
Identities = 14/53 (26%), Positives = 26/53 (49%), Gaps = 5/53 (9%)
Query: 56 LAQERVEAAEKRVKEVEERATASRKLSVDELANAFWDLSDEDKNAFTGNVKQE 108
L R +A E+ + EE+A A ++ + ++ AFW + NA +Q+
Sbjct: 36 LEDARQQA-EQILDLAEEKAEALQQRAEEQAEAAFW----QQANALLQEWQQQ 83
>gnl|CDD|184480 PRK14056, PRK14056, phenylalanine 4-monooxygenase; Provisional.
Length = 578
Score = 25.0 bits (55), Expect = 4.7
Identities = 10/37 (27%), Positives = 15/37 (40%)
Query: 43 IKEANFKISETHRLAQERVEAAEKRVKEVEERATASR 79
+KE+ E A+ RV + V + E SR
Sbjct: 169 VKESPTSTPEEVAAAENRVIEKQNLVSGLSEAEQISR 205
>gnl|CDD|152881 pfam12447, DUF3683, Protein of unknown function (DUF3683). This
domain family is found in bacteria, and is approximately
120 amino acids in length. The family is found in
association with pfam02754, pfam01565, pfam02913.
Length = 117
Score = 25.2 bits (56), Expect = 4.9
Identities = 11/29 (37%), Positives = 16/29 (55%), Gaps = 2/29 (6%)
Query: 61 VEAAEKRVKEVEERATASRKLSVDELANA 89
EA R+ E+E+RA + + V EL A
Sbjct: 80 FEALRHRLDEIEKRANGNER--VLELVAA 106
>gnl|CDD|179009 PRK00409, PRK00409, recombination and DNA strand exchange inhibitor
protein; Reviewed.
Length = 782
Score = 24.8 bits (55), Expect = 5.8
Identities = 13/55 (23%), Positives = 28/55 (50%), Gaps = 3/55 (5%)
Query: 27 RTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKL 81
E L +L++ ++ +E + + E + AQ+ ++ A+ KE +E R+L
Sbjct: 545 EAEKLKEELEEKKEKLQEEEDKLLEEAEKEAQQAIKEAK---KEADEIIKELRQL 596
>gnl|CDD|129130 TIGR00019, prfA, peptide chain release factor 1. This model
describes peptide chain release factor 1 (PrfA, RF-1),
and excludes the related peptide chain release factor 2
(PrfB, RF-2). RF-1 helps recognize and terminate
translation at UAA and UAG stop codons. The
mitochondrial release factors are prfA-like, although
not included above the trusted cutoff for this model.
RF-1 does not have a translational frameshift.
Length = 360
Score = 24.7 bits (54), Expect = 6.7
Identities = 10/39 (25%), Positives = 21/39 (53%), Gaps = 2/39 (5%)
Query: 36 QKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEER 74
+ I E + E +A+E +E E++++E+EE+
Sbjct: 61 DIKEAKEILEESDP--EMREMAKEELEELEEKIEELEEQ 97
>gnl|CDD|115824 pfam07195, FliD_C, Flagellar hook-associated protein 2 C-terminus.
The flagellar hook-associated protein 2 (HAP2 or FliD)
forms the distal end of the flagella, and plays a role
in mucin specific adhesion of the bacteria. This
alignment covers the C-terminal region of this family of
proteins.
Length = 230
Score = 24.6 bits (54), Expect = 6.9
Identities = 8/54 (14%), Positives = 24/54 (44%)
Query: 24 VIGRTEDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERATA 77
+ R +D L + ++ +++ + +++E ++R+ +E R A
Sbjct: 163 LAKRLDDSLKPYTGSGNGILASREDSLNKQIKRLNKQIEDLDRRLDTLEARLKA 216
>gnl|CDD|150781 pfam10147, CR6_interact, Growth arrest and DNA-damage-inducible
proteins-interacting protein 1. Members of this family
of proteins act as negative regulators of G1 to S cell
cycle phase progression by inhibiting cyclin-dependent
kinases. Inhibitory effects are additive with GADD45
proteins but occur also in the absence of GADD45
proteins. Furthermore, they act as a repressor of the
orphan nuclear receptor NR4A1 by inhibiting AB
domain-mediated transcriptional activity.
Length = 217
Score = 24.4 bits (53), Expect = 7.2
Identities = 11/46 (23%), Positives = 18/46 (39%)
Query: 29 EDLLNKLQKNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEER 74
E + K QMI + + + + A+ E E+ V E E
Sbjct: 123 EAEIAKNMAKMPQMIADWRAQKRKREQKARAAKERKERLVAEAREH 168
>gnl|CDD|179068 PRK00566, PRK00566, DNA-directed RNA polymerase subunit beta';
Provisional.
Length = 1156
Score = 24.3 bits (54), Expect = 8.1
Identities = 8/16 (50%), Positives = 12/16 (75%)
Query: 58 QERVEAAEKRVKEVEE 73
+E +E AEK V E+E+
Sbjct: 629 KEIIEEAEKEVAEIEK 644
>gnl|CDD|185576 PTZ00362, PTZ00362, hypothetical protein; Provisional.
Length = 479
Score = 24.3 bits (53), Expect = 8.2
Identities = 12/35 (34%), Positives = 19/35 (54%), Gaps = 2/35 (5%)
Query: 22 DIVIGRTEDLLNKL--QKNSTQMIKEANFKISETH 54
DI R + ++N L Q + +I N +ISET+
Sbjct: 408 DIRYKRLKKIMNHLENQDVHSSIIYIDNLQISETY 442
>gnl|CDD|130214 TIGR01144, ATP_synt_b, ATP synthase, F0 subunit b. This model
describes the F1/F0 ATP synthase b subunit in bacteria
only. Scoring just below the trusted cutoff are the
N-terminal domains of Mycobacterial b/delta fusion
proteins and a subunit from an archaeon, Methanosarcina
barkeri, in which the ATP synthase homolog differs in
architecture and is not experimentally confirmed. This
model helps resolve b from the related b' subunit.
Within the family is an example from a
sodium-translocating rather than proton-translocating
ATP synthase.
Length = 147
Score = 24.3 bits (53), Expect = 8.5
Identities = 14/39 (35%), Positives = 19/39 (48%)
Query: 37 KNSTQMIKEANFKISETHRLAQERVEAAEKRVKEVEERA 75
K + K+A + E AQE +E A KR E+ E A
Sbjct: 43 KEAALAQKKAQVILKEAKDEAQEIIENANKRGSEILEEA 81
>gnl|CDD|148887 pfam07529, HSA, HSA. This domain is predicted to bind DNA and is
often found associated with helicases.
Length = 72
Score = 24.2 bits (53), Expect = 8.7
Identities = 10/52 (19%), Positives = 24/52 (46%), Gaps = 7/52 (13%)
Query: 30 DLLNKLQKNSTQMIKEANFKISETHRLAQ-------ERVEAAEKRVKEVEER 74
LL +++ S +E +KI++ +LA+ + ++R + +R
Sbjct: 15 HLLEEMKWMSKDFREERKWKIAKAKKLARAVAQYHKYIEKEEQRRKEREAQR 66
>gnl|CDD|162382 TIGR01479, GMP_PMI, mannose-1-phosphate
guanylyltransferase/mannose-6-phosphate isomerase. This
enzyme is known to be bifunctional, as both
mannose-6-phosphate isomerase (EC 5.3.1.8) (PMI) and
mannose-1-phosphate guanylyltransferase (EC 2.7.7.22) in
Pseudomonas aeruginosa, Xanthomonas campestris, and
Gluconacetobacter xylinus. The literature on the enzyme
from E. coli attributes mannose-6-phosphate isomerase
activity to an adjacent gene, but the present sequence
has not been shown to lack the activity. The PMI domain
is C-terminal.
Length = 468
Score = 24.2 bits (53), Expect = 8.9
Identities = 10/37 (27%), Positives = 20/37 (54%), Gaps = 2/37 (5%)
Query: 11 FSTTLL--TIGGCDIVIGRTEDLLNKLQKNSTQMIKE 45
+S + L +G D+V+ T+D + K+ Q +K+
Sbjct: 305 YSESRLVAVVGVEDLVVVETKDAVLVAHKDRVQDVKK 341
>gnl|CDD|180077 PRK05431, PRK05431, seryl-tRNA synthetase; Provisional.
Length = 425
Score = 24.3 bits (54), Expect = 9.0
Identities = 12/56 (21%), Positives = 23/56 (41%), Gaps = 7/56 (12%)
Query: 25 IGRTEDLLNKLQKNSTQMIK------EANFKISETHRLAQERVEAAEKRVKEVEER 74
E+L + S ++ + +A I+E L E ++A E + E+E
Sbjct: 41 QTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELK-EEIKALEAELDELEAE 95
>gnl|CDD|184697 PRK14475, PRK14475, F0F1 ATP synthase subunit B; Provisional.
Length = 167
Score = 24.1 bits (52), Expect = 9.5
Identities = 15/47 (31%), Positives = 25/47 (53%), Gaps = 3/47 (6%)
Query: 41 QMIKEANFKISETHRLAQERVEAAEKRVKEVEERATASRKLSVDELA 87
+M EA K+ E + R E AE+++ + E +A A K + +LA
Sbjct: 91 RMEAEAKEKLEEQ---IKRRAEMAERKIAQAEAQAAADVKAAAVDLA 134
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
0.312 0.126 0.337
Gapped
Lambda K H
0.267 0.0640 0.140
Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 21608
Number of Hits to DB: 1,799,740
Number of extensions: 100337
Number of successful extensions: 343
Number of sequences better than 10.0: 1
Number of HSP's gapped: 339
Number of HSP's successfully gapped: 76
Length of query: 121
Length of database: 5,994,473
Length adjustment: 81
Effective length of query: 40
Effective length of database: 4,244,225
Effective search space: 169769000
Effective search space used: 169769000
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: 51 (23.6 bits)