RPS-BLAST 2.2.22 [Sep-27-2009]
Database: CddB
21,608 sequences; 5,994,473 total letters
Searching..................................................done
Query= gi|254780547|ref|YP_003064960.1| OmpA/MotB [Candidatus
Liberibacter asiaticus str. psy62]
(160 letters)
>gnl|CDD|131849 TIGR02802, Pal_lipo, peptidoglycan-associated lipoprotein. Members
of this protein are Pal (also called OprL), the
Peptidoglycan-Associated Lipoprotein of the Tol-Pal
system. The system appears to be involved both in the
maintenance of outer membrane integrity and in the
import of certain organic molecules as nutrients.
Members of this family contain a hydrodrophobic
lipoprotein signal sequence, a conserved N-terminal
cleavage and modification site, a poorly conserved
low-complexity region, together comprising about 65
amino acids, and a well-conserved C-terminal domain. The
seed alignment for this model includes only the
conserved C-terminal domain.
Length = 104
Score = 127 bits (321), Expect = 2e-30
Identities = 45/102 (44%), Positives = 67/102 (65%), Gaps = 1/102 (0%)
Query: 51 SVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYAV 109
V+FD S ++ +L ++L+K+ IEGH DE G+R ++ALG RRA AV
Sbjct: 1 RVYFDFDSSDLKSEAQAILDAHAAYLKKNPSVRVTIEGHTDERGTREYNLALGERRANAV 60
Query: 110 FNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIV 151
+Y A+G+SAS+++ SYG+E P+ GHDE A+AKNRRA++
Sbjct: 61 KDYLQAKGVSASQIETVSYGEEKPACLGHDEAAWAKNRRAVL 102
>gnl|CDD|182744 PRK10802, PRK10802, peptidoglycan-associated outer membrane
lipoprotein; Provisional.
Length = 173
Score = 95.7 bits (238), Expect = 4e-21
Identities = 48/101 (47%), Positives = 64/101 (63%), Gaps = 1/101 (0%)
Query: 52 VFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYAVF 110
V+FD Y IR Q+L ++L + +EGHADE G+ +IALG RRA AV
Sbjct: 71 VYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNIALGERRANAVK 130
Query: 111 NYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIV 151
Y +G+SA ++ + SYGKE P+V GHDE AYAKNRRA++
Sbjct: 131 MYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYAKNRRAVL 171
>gnl|CDD|182507 PRK10510, PRK10510, putative outer membrane lipoprotein;
Provisional.
Length = 219
Score = 50.6 bits (121), Expect = 2e-07
Identities = 28/105 (26%), Positives = 56/105 (53%), Gaps = 1/105 (0%)
Query: 50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFL-IEGHADELGSRNSSIALGLRRAYA 108
++V FD+SS +++PA L+ + L+++ + + G+ D GS + ++ L +RA +
Sbjct: 112 NNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVVGYTDSTGSHDLNMRLSQQRADS 171
Query: 109 VFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153
V + + +G+ ASR++ G P + A+NRR + L
Sbjct: 172 VASALITQGVDASRIRTQGMGPANPIASNSTAEGKAQNRRVEITL 216
>gnl|CDD|181435 PRK08457, motB, flagellar motor protein MotB; Reviewed.
Length = 257
Score = 49.7 bits (119), Expect = 4e-07
Identities = 27/123 (21%), Positives = 47/123 (38%), Gaps = 9/123 (7%)
Query: 40 LQEQFSSSVGDSVFFDTSSYSIRPAD----IQVLSNLGSWLEKHDCDFLIEGHADELGSR 95
+ + + + F+ S I AD ++ ++ + + L K + G+ D
Sbjct: 112 IDNGIALKLPSKLLFENGSAEIINADMMDYLKRIAKIITKLPK-QVKINVRGYTDNSPLN 170
Query: 96 NSSIA----LGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIV 151
S L RAY V + GI+ +R+ +SYG P + KN R +
Sbjct: 171 KSRYKDHYELAAARAYNVMKVLIQYGINPNRLSFSSYGSNNPIAPNDSLENRLKNNRVEI 230
Query: 152 FLK 154
F K
Sbjct: 231 FFK 233
>gnl|CDD|182748 PRK10808, PRK10808, outer membrane protein A; Reviewed.
Length = 351
Score = 48.1 bits (115), Expect = 9e-07
Identities = 32/116 (27%), Positives = 53/116 (45%), Gaps = 12/116 (10%)
Query: 52 VFFDTSSYSIRPADIQVLSNLGSWLEK---HDCDFLIEGHADELGSRNSSIALGLRRAYA 108
V F+ + +++P Q L L S L D ++ G+ D +GS + L +RA +
Sbjct: 226 VLFNFNKATLKPEGQQALDQLYSQLSNLDPKDGSVVVLGYTDRIGSDAYNQGLSEKRAQS 285
Query: 109 VFNYFVARGISASRMKVTSYGKEMP-------SVYGHDE--DAYAKNRRAIVFLKG 155
V +Y V++GI A ++ GK P +V D A +RR + +KG
Sbjct: 286 VVDYLVSKGIPADKISARGMGKSNPVTGNTCDNVKPRAALIDCLAPDRRVEIEVKG 341
>gnl|CDD|181619 PRK09039, PRK09039, hypothetical protein; Validated.
Length = 343
Score = 46.5 bits (111), Expect = 3e-06
Identities = 30/120 (25%), Positives = 52/120 (43%), Gaps = 19/120 (15%)
Query: 48 VGD------SVFFDTSSYSIRPADIQVLSNLGSWLEK------HDCDFLI--EGHADEL- 92
VGD V F T S + P ++ L + L + + ++++ +GH D +
Sbjct: 216 VGDRFVFQSEVLFPTGSAELNPEGQAEIAKLAAALIELAKEIPPEINWVLRVDGHTDNVP 275
Query: 93 ----GSRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148
G + L RA +V + +A G+ A R+ +G+ P G +A A+NRR
Sbjct: 276 LSGTGRFRDNWELSSARAISVVKFLIALGVPADRLAAAGFGEFQPLDPGDTPEARARNRR 335
>gnl|CDD|102525 PRK06742, PRK06742, flagellar motor protein MotS; Reviewed.
Length = 225
Score = 45.4 bits (107), Expect = 6e-06
Identities = 25/110 (22%), Positives = 49/110 (44%), Gaps = 5/110 (4%)
Query: 50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRN----SSIALGLRR 105
D++ FDT +++P +++S L + + ++EGH D N S+ L R
Sbjct: 115 DNLIFDTGDANVKPEAKEIISQLVGFFQSVPNPIVVEGHTDSRPIHNDKFPSNWELSSAR 174
Query: 106 AYAVFNYFV-ARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK 154
A + ++ + + R+ Y P V + KNRR ++++K
Sbjct: 175 AANMIHHLIEVYNVDDKRLAAVGYADTKPVVPNDSPQNWEKNRRVVIYIK 224
>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 = 43.6 bits (103), Expect = 2e-05
Identities = 25/99 (25%), Positives = 45/99 (45%), Gaps = 5/99 (5%)
Query: 41 QEQFSSS--VGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIE--GHADELGSRN 96
Q+Q +G +V F T S I P L + + L K + ++ G+AD G
Sbjct: 124 QQQLLEELALGMNVQFRTGSSDIEPHFQPQLDEVAT-LMKQSPELKLDLSGYADRRGDSQ 182
Query: 97 SSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSV 135
+ AL +R V +Y + +G+ +R+ ++G+ P
Sbjct: 183 YNQALSEQRVLEVRSYLIKQGVDEARLTTQAFGESAPLK 221
>gnl|CDD|182172 PRK09967, PRK09967, putative outer membrane lipoprotein;
Provisional.
Length = 160
Score = 42.7 bits (100), Expect = 5e-05
Identities = 29/116 (25%), Positives = 50/116 (43%), Gaps = 10/116 (8%)
Query: 44 FSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLE----KHDCDFLIEGHADELGSRNSSI 99
+S + D++ F + Y + P Q + + + L H ++GH D G + +
Sbjct: 46 WSLGLSDAILFAKNDYKLLPESQQQIQTMAAKLASTGLTHA---RMDGHTDNYGEDSYNE 102
Query: 100 ALGLRRAYAVFNYFVARGISASRMKVTS--YGKEMPSVYGHDEDAYAKNRRAIVFL 153
L L+RA V + + A G R +T+ GK+ P A+NRR V +
Sbjct: 103 GLSLKRANVVADAW-AMGGQIPRSNLTTQGLGKKYPIASNKTAQGRAENRRVAVVI 157
>gnl|CDD|181620 PRK09040, PRK09040, hypothetical protein; Provisional.
Length = 214
Score = 42.3 bits (100), Expect = 6e-05
Identities = 30/108 (27%), Positives = 49/108 (45%), Gaps = 10/108 (9%)
Query: 51 SVFFDTSSYSIRPADIQVLSNL----GSWLEKHDCDFLIEGHADELGSR--NSSIA---- 100
SV F +S ++P ++L +L ++L D ++ G D+ R N A
Sbjct: 89 SVLFALNSDQLQPEGRELLKSLAGPLAAYLRARDEILMVSGFTDDQPVRAGNRRFADNWE 148
Query: 101 LGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148
L +RA V + G+ AS + ++G E P D++ AKNRR
Sbjct: 149 LSAQRALTVTRALIDAGVPASSVFAAAFGSEQPVASNADDEGRAKNRR 196
>gnl|CDD|180754 PRK06925, PRK06925, flagellar motor protein MotS; Reviewed.
Length = 230
Score = 40.1 bits (94), Expect = 3e-04
Identities = 33/123 (26%), Positives = 46/123 (37%), Gaps = 19/123 (15%)
Query: 40 LQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRN--- 96
LQE V F+T I L +G L D +EGH D SR
Sbjct: 116 LQEA--------VLFETGEADILKQAEPFLHKIGVLLSTIPNDIKVEGHTD---SRPIST 164
Query: 97 ----SSIALGLRRAYAVFNYFVAR-GISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIV 151
S+ L RA +V YF ++ + +SR Y P V E+ +NRR +
Sbjct: 165 YRYPSNWELSAARASSVIRYFTSKEKLDSSRFIAVGYADTKPVVPNTTEENMQENRRVEI 224
Query: 152 FLK 154
+
Sbjct: 225 VIS 227
>gnl|CDD|181618 PRK09038, PRK09038, flagellar motor protein MotD; Reviewed.
Length = 281
Score = 39.6 bits (93), Expect = 3e-04
Identities = 21/103 (20%), Positives = 37/103 (35%), Gaps = 4/103 (3%)
Query: 50 DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIA----LGLRR 105
S+ F + + +L + L+ +EG D + + L R
Sbjct: 133 SSLLFGSGDAMLSDQAFAILEKVAEVLKPAPNPIHVEGFTDNVPIATAQFPSNWELSAAR 192
Query: 106 AYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148
A +V G++ SR+ YG+ P + A+NRR
Sbjct: 193 AASVVRLLADDGVAPSRLAAVGYGEFQPVADNDTAEGRARNRR 235
>gnl|CDD|132393 TIGR03350, type_VI_ompA, type VI secretion system OmpA/MotB family
protein. The flagellar motor protein MotB and the
Gram-negative bacterial outer membrane protein OmpA
share a region of sequence homology. This model
describes a domain found fused to type VI secretion
system homologs of the type IV system protein DotU (see
model TIGR03349), with OmpA/MotB homology.
Length = 137
Score = 36.9 bits (86), Expect = 0.002
Identities = 24/104 (23%), Positives = 37/104 (35%), Gaps = 4/104 (3%)
Query: 54 FDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIA----LGLRRAYAV 109
F + S +R +L + L + GH D + R S L RA AV
Sbjct: 34 FASGSAEVRADFEPLLDRIAKALAAVPGRITVVGHTDNVPIRTSRFPSNWHLSEARAKAV 93
Query: 110 FNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153
+ G+ A R++ G P A+NRR + +
Sbjct: 94 ADVLAQGGVPAGRVRAEGRGDSEPIASNATAAGRAQNRRVEIDV 137
>gnl|CDD|181590 PRK08944, motB, flagellar motor protein MotB; Reviewed.
Length = 302
Score = 35.4 bits (82), Expect = 0.007
Identities = 19/69 (27%), Positives = 29/69 (42%), Gaps = 5/69 (7%)
Query: 85 IEGHADELGSRN----SSIALGLRRAYAVFNYFVA-RGISASRMKVTSYGKEMPSVYGHD 139
+ GH D + + S+ L RA AV + + +G R+KV P V
Sbjct: 214 VSGHTDNVPISSELYRSNWDLSSARAVAVAHELLKVKGFDPQRLKVVGMADTQPLVPNDT 273
Query: 140 EDAYAKNRR 148
+ A+NRR
Sbjct: 274 AENRARNRR 282
>gnl|CDD|180652 PRK06667, motB, flagellar motor protein MotB; Validated.
Length = 252
Score = 34.0 bits (78), Expect = 0.018
Identities = 29/113 (25%), Positives = 45/113 (39%), Gaps = 11/113 (9%)
Query: 46 SSVGDSVFFDTSSYSIRPADIQ-VLSNLGSWLEKHDCD---FLIEGHADEL-----GSRN 96
S D+ FF S ++ + + L + S++ D F IEGH D + G
Sbjct: 122 SLASDA-FFYPGSAEVKLEENRETLQKIASFIGFLDLAGRNFRIEGHTDNVDVNPEGPWK 180
Query: 97 SSIALGLRRAYAVFNYFVARG-ISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148
S+ L RA + Y + G S S +V+ + P + A NRR
Sbjct: 181 SNWELSGARAVNMLEYILNYGDQSESWFQVSGFAGSRPLATEDTPEGRAYNRR 233
>gnl|CDD|181095 PRK07734, motB, flagellar motor protein MotB; Reviewed.
Length = 259
Score = 33.2 bits (76), Expect = 0.032
Identities = 30/147 (20%), Positives = 50/147 (34%), Gaps = 35/147 (23%)
Query: 32 DTVLNESSLQEQFSSS---------VGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDC- 81
D + E L + + D++ FD+ +R D+ + + + L +
Sbjct: 115 DQYIKEKQLSSSLQTKLTEEGLLITILDNILFDSGKADVRLEDLPLAKEISNLLVSNPPR 174
Query: 82 DFLIEGHADELGSRNSSIA----LGLRRAYAVFN-----------YFVARGISASRMKVT 126
+ I GH D + N+ A L + RA F A+G
Sbjct: 175 NITISGHTDNVPIANAQFASNWELSVMRAVNFMQVLLENKELDPEKFSAKG--------- 225
Query: 127 SYGKEMPSVYGHDEDAYAKNRRAIVFL 153
YG+ P + AKNRR V +
Sbjct: 226 -YGEYKPIASNDTAEGRAKNRRVEVLI 251
>gnl|CDD|180801 PRK07033, PRK07033, hypothetical protein; Provisional.
Length = 427
Score = 29.2 bits (66), Expect = 0.50
Identities = 28/104 (26%), Positives = 44/104 (42%), Gaps = 5/104 (4%)
Query: 49 GDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRN----SSIALGLR 104
GD +F ++S S+R VL+ + L + + L+ G++D + R S+ L
Sbjct: 314 GDGLF-ASASTSVRDRYQPVLARVADALNQVKGNVLVTGYSDNVPIRTARFPSNWELSQA 372
Query: 105 RAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148
RA AV AR R+ G P + A+NRR
Sbjct: 373 RAQAVRALLAARLGQPERVTAEGRGDSDPVAPNDSAENRARNRR 416
>gnl|CDD|151822 pfam11382, DUF3186, Protein of unknown function (DUF3186). This
bacterial family of proteins has no known function.
Length = 307
Score = 28.5 bits (64), Expect = 0.91
Identities = 12/33 (36%), Positives = 17/33 (51%), Gaps = 3/33 (9%)
Query: 18 ISGIDNLDTKISSPDTVLNESSLQEQFSSSVGD 50
+S +DN+DT TVL +L EQ + G
Sbjct: 265 VSTVDNVDTVPGQVTTVL---ALVEQLNGGAGH 294
>gnl|CDD|184472 PRK14040, PRK14040, oxaloacetate decarboxylase; Provisional.
Length = 593
Score = 27.6 bits (62), Expect = 1.5
Identities = 8/12 (66%), Positives = 10/12 (83%)
Query: 19 SGIDNLDTKISS 30
+GID +DT ISS
Sbjct: 222 AGIDGVDTAISS 233
>gnl|CDD|179846 PRK04423, PRK04423, organic solvent tolerance protein; Provisional.
Length = 798
Score = 26.8 bits (59), Expect = 3.0
Identities = 12/51 (23%), Positives = 26/51 (50%), Gaps = 2/51 (3%)
Query: 35 LNESSLQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLI 85
L + +E+ S S G ++FD S +I ++ + +W+ D +++I
Sbjct: 579 LRQDDGKEKLSLSAGQILYFDDSLVTINNSEQTIEQGKSAWVA--DANYMI 627
>gnl|CDD|181240 PRK08126, PRK08126, hypothetical protein; Provisional.
Length = 432
Score = 26.6 bits (59), Expect = 3.2
Identities = 27/111 (24%), Positives = 48/111 (43%), Gaps = 8/111 (7%)
Query: 45 SSSV---GDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRN----S 97
SSV GD++F + ++ PA +++ + + + + GH D R+ S
Sbjct: 316 HSSVVFRGDAMFVPGQA-TVNPAMGPLIAKIAREIARVGGKVTVTGHTDNQPIRSAQFAS 374
Query: 98 SIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148
++ L +RA V + G+ ASR++ G P A+NRR
Sbjct: 375 NLVLSEKRAAQVAQMLQSAGVPASRLEAVGKGDAQPVADNRTPQGRAQNRR 425
>gnl|CDD|173127 PRK14664, PRK14664, tRNA-specific 2-thiouridylase MnmA;
Provisional.
Length = 362
Score = 26.5 bits (58), Expect = 3.4
Identities = 10/28 (35%), Positives = 13/28 (46%)
Query: 72 LGSWLEKHDCDFLIEGHADELGSRNSSI 99
L W +K C ++ GH L RN I
Sbjct: 100 LIEWADKLGCAWIATGHYSRLEERNGHI 127
>gnl|CDD|162335 TIGR01392, homoserO_Ac_trn, homoserine O-acetyltransferase. This
family describes homoserine-O-acetyltransferase, an
enzyme of methionine biosynthesis. This model has been
rebuilt to identify sequences more broadly, including a
number of sequences suggested to be homoserine
O-acetyltransferase based on proximity to other Met
biosynthesis genes.
Length = 351
Score = 25.0 bits (55), Expect = 8.5
Identities = 10/28 (35%), Positives = 17/28 (60%), Gaps = 2/28 (7%)
Query: 112 YFVARGISASRMKVTSYGKEMPSVYGHD 139
+A+ + A+ ++VT E+ S YGHD
Sbjct: 308 RELAKALPAAGLRVTYV--EIESPYGHD 333
>gnl|CDD|132642 TIGR03603, cyclo_dehy_ocin, bacteriocin biosynthesis
cyclodehydratase, SagC family. Members of this protein
family include enzymes related to SagC, a
cyclodehydratase involved in the biosynthesis of
streptolysin S in Streptococcus pyogenes from the
protoxin polypeptide (product of the sagA gene). This
protein family serves as a marker for widely distributed
prokaryotic systems for making a general class of
heterocycle-containing bacteriocins. Note that this
model does not find all possible examples of bacteriocin
biosynthesis cyclodehydratases, an in particular misses
the E. coli plasmid protein McbB of microcin B17
biosynthesis.
Length = 318
Score = 24.9 bits (54), Expect = 9.9
Identities = 7/32 (21%), Positives = 15/32 (46%)
Query: 3 YSTIFIILSAITMMSISGIDNLDTKISSPDTV 34
Y+ I I + + G++ L + P+T+
Sbjct: 152 YNYIIICTEHSNISLLRGLNKLSKETKKPNTI 183
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
0.318 0.132 0.372
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: 2,488,727
Number of extensions: 144404
Number of successful extensions: 293
Number of sequences better than 10.0: 1
Number of HSP's gapped: 285
Number of HSP's successfully gapped: 27
Length of query: 160
Length of database: 5,994,473
Length adjustment: 86
Effective length of query: 74
Effective length of database: 4,136,185
Effective search space: 306077690
Effective search space used: 306077690
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: 41 (21.8 bits)
S2: 53 (24.4 bits)