RPS-BLAST 2.2.22 [Sep-27-2009] Database: CddB 21,608 sequences; 5,994,473 total letters Searching..................................................done Query= gi|254780688|ref|YP_003065101.1| putative flagellar motor switch protein [Candidatus Liberibacter asiaticus str. psy62] (147 letters) >gnl|CDD|131533 TIGR02480, fliN, flagellar motor switch protein FliN. Proteins that consist largely of the domain described by this model can be designated flagellar motor switch protein FliN. Longer proteins in which this region is a C-terminal domain typically are designated FliY. More distantly related sequences, outside the scope of this family, are associated with type III secretion and include the surface presentation of antigens protein SpaO required or invasion of host cells by Salmonella enterica. Length = 77 Score = 74.9 bits (185), Expect = 8e-15 Identities = 32/80 (40%), Positives = 55/80 (68%), Gaps = 3/80 (3%) Query: 68 NFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEIT 127 N DLI++IPV++ + LG + + +L+ L +G VI LDK GE +DI +N + IA+GE+ Sbjct: 1 NIDLILDIPVELTVELGRTRITLGDLLKLGEGSVIELDKLAGEPLDILVNGRLIARGEVV 60 Query: 128 IMEEDDTHFGVRVIEILNAQ 147 ++E+ FG+R+ EI+++ Sbjct: 61 VVEDK---FGIRITEIVDSS 77 >gnl|CDD|181236 PRK08119, PRK08119, flagellar motor switch protein; Validated. Length = 382 Score = 71.4 bits (176), Expect = 8e-14 Identities = 31/78 (39%), Positives = 53/78 (67%), Gaps = 3/78 (3%) Query: 68 NFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEIT 127 N DLI+++P+++ + LG I +++ L G +I LDK GE VDI +N + IAKGE+ Sbjct: 299 NLDLILDVPLQVTVELGRTKKSIKDILELGTGSIIELDKLAGEPVDILVNGKLIAKGEVV 358 Query: 128 IMEEDDTHFGVRVIEILN 145 +++E+ FGVR+ +I++ Sbjct: 359 VIDEN---FGVRITDIVS 373 >gnl|CDD|181582 PRK08916, PRK08916, flagellar motor switch protein; Reviewed. Length = 116 Score = 65.5 bits (160), Expect = 5e-12 Identities = 36/119 (30%), Positives = 63/119 (52%), Gaps = 10/119 (8%) Query: 28 DTNVSSPTNNSEMLIQKNDVDNISEPISSDSNNILEKSTDNFDLIMNIPVKMQIILGSCC 87 D V P N ++DV E + + LE + ++PV++ +LG Sbjct: 5 DLQVPLPDLNGADAPPEDDVGYNEEEQADRTAADLEA-------VFDVPVQVSAVLGRSK 57 Query: 88 MQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNA 146 M + L+ L G V+ LD++VGE++DI +NN+ +A+GE+ ++E+ GV + EI+ A Sbjct: 58 MDVGQLLKLGPGSVLELDRKVGEAIDIYVNNRLVARGEVVLVED---RLGVTMTEIIKA 113 >gnl|CDD|181183 PRK07963, fliN, flagellar motor switch protein FliN; Validated. Length = 137 Score = 64.8 bits (158), Expect = 7e-12 Identities = 32/75 (42%), Positives = 49/75 (65%), Gaps = 3/75 (4%) Query: 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIM 129 DLIM+IPVK+ + LG M I L+ L++G V+ LD GE +DI IN IA+GE+ ++ Sbjct: 55 DLIMDIPVKLTVELGRTRMTIKELLRLTQGSVVALDGLAGEPLDILINGYLIAQGEVVVV 114 Query: 130 EEDDTHFGVRVIEIL 144 + +GVR+ +I+ Sbjct: 115 ADK---YGVRITDII 126 >gnl|CDD|168189 PRK05698, fliN, flagellar motor switch protein; Validated. Length = 155 Score = 57.5 bits (139), Expect = 1e-09 Identities = 29/77 (37%), Positives = 51/77 (66%), Gaps = 3/77 (3%) Query: 68 NFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEIT 127 N D+I++IPV + + +GS + I NL+ L++G VI LD+ GE +D+ +N IA GE+ Sbjct: 72 NLDVILDIPVSISMEVGSTDINIRNLLQLNQGSVIELDRLAGEPLDVLVNGTLIAHGEVV 131 Query: 128 IMEEDDTHFGVRVIEIL 144 ++ E FG+R+ +++ Sbjct: 132 VVNEK---FGIRLTDVI 145 >gnl|CDD|162918 TIGR02551, SpaO_YscQ, type III secretion system apparatus protein YscQ/HrcQ. Genes in this family are found in type III secretion operons. The gene (YscQ) in Yersinia is essential for YOPs secretion, while SpaO in Shigella is involved in the Surface Presentation of Antigens apparatus found on the virulence plasmid, and HrcQ is involved in the Harpin secretory system in organisms like Pseudomonas syringae. Length = 298 Score = 55.5 bits (134), Expect = 5e-09 Identities = 24/108 (22%), Positives = 49/108 (45%), Gaps = 10/108 (9%) Query: 40 MLIQKNDVDN--ISEPISSDSNNILEKSTDNFDLI-MN-IPVKMQIILGSCCMQISNLVN 95 LI DN +S+ ++S + + ++ +PV ++ LG + ++ L Sbjct: 197 ELIDGITADNLDLSDLTDTESPDE---PAAPTPEVDLDQLPVTLEFELGRLTLTLAELAA 253 Query: 96 LSKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEI 143 L G V+ L+ V V + N + + +GE+ + GVR++E+ Sbjct: 254 LQPGSVLELNVPVDGPVRLRANGRLLGRGELVDVGG---RLGVRILEL 298 >gnl|CDD|181603 PRK08983, fliN, flagellar motor switch protein; Validated. Length = 127 Score = 52.1 bits (125), Expect = 5e-08 Identities = 29/93 (31%), Positives = 54/93 (58%), Gaps = 3/93 (3%) Query: 52 EPISSDSNNILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGES 111 + + DS I E D I++IPV + + +G + I NL+ L++G V+ LD+ GE Sbjct: 28 DELVDDSAPITEDEARKLDTILDIPVTISMEVGRSFISIRNLLQLNQGSVVELDRVAGEP 87 Query: 112 VDITINNQKIAKGEITIMEEDDTHFGVRVIEIL 144 +D+ +N IA GE+ ++ + FG+R+ +++ Sbjct: 88 LDVMVNGTLIAHGEVVVVNDK---FGIRLTDVI 117 >gnl|CDD|181423 PRK08433, PRK08433, flagellar motor switch protein; Validated. Length = 111 Score = 51.3 bits (123), Expect = 1e-07 Identities = 27/91 (29%), Positives = 53/91 (58%), Gaps = 3/91 (3%) Query: 56 SDSNNILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDIT 115 + + LE+ +++ +++I V LG+ + + ++ KG VI L+K GESV++ Sbjct: 13 LELSTYLEELICDYENLLDIEVDFSAELGTTQISLLEILKFEKGSVIDLEKPAGESVELY 72 Query: 116 INNQKIAKGEITIMEEDDTHFGVRVIEILNA 146 IN + I KGE+ + E++ +R+ EIL++ Sbjct: 73 INGRIIGKGEVMVYEKN---LAIRINEILDS 100 >gnl|CDD|180692 PRK06782, PRK06782, flagellar motor switch protein; Reviewed. Length = 528 Score = 50.6 bits (121), Expect = 2e-07 Identities = 23/95 (24%), Positives = 52/95 (54%), Gaps = 3/95 (3%) Query: 50 ISEPISSDSNNILEKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVG 109 + +PI +E + ++ ++P+ ++++ GS I ++++L + +V+ LD+ + Sbjct: 437 VVQPIEFKEVKQMEPVYMDTSILQDVPMNVKVVFGSTKKTIQDILSLQENEVVVLDEDID 496 Query: 110 ESVDITINNQKIAKGEITIMEEDDTHFGVRVIEIL 144 E + I +N +A GE+ + D FGV+V + L Sbjct: 497 EPIRIYVNGVLVAYGELVNV---DGFFGVKVTKSL 528 >gnl|CDD|180693 PRK06788, PRK06788, flagellar motor switch protein; Validated. Length = 119 Score = 46.4 bits (110), Expect = 2e-06 Identities = 24/81 (29%), Positives = 47/81 (58%), Gaps = 3/81 (3%) Query: 63 EKSTDNFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIA 122 E S + D + +I +++ + LG + + ++ L GDV+ ++K +G VD+ ++N K+ Sbjct: 22 EASKAHIDTVSDISIELGVKLGKASITLGDVKQLKVGDVLEVEKNLGHKVDVYLSNMKVG 81 Query: 123 KGEITIMEEDDTHFGVRVIEI 143 GE +M+E FG+ + EI Sbjct: 82 IGEAIVMDEK---FGIIISEI 99 >gnl|CDD|180359 PRK06033, PRK06033, hypothetical protein; Validated. Length = 83 Score = 43.2 bits (102), Expect = 3e-05 Identities = 19/58 (32%), Positives = 31/58 (53%) Query: 74 NIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEITIMEE 131 + V++ ++LG M I ++ + +G VI LD + V I NN IA+GE+ I Sbjct: 6 AVSVELMVVLGRSSMPIHQVLRMGRGAVIPLDATEADEVWILANNHPIARGEVLIDRN 63 >gnl|CDD|181422 PRK08432, PRK08432, flagellar motor switch protein FliY; Validated. Length = 283 Score = 40.8 bits (96), Expect = 1e-04 Identities = 19/76 (25%), Positives = 51/76 (67%), Gaps = 3/76 (3%) Query: 68 NFDLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEIT 127 N ++I+++ + +++ +G M + +++++ G V+ L++ + ++I ++++ IAKGE+ Sbjct: 199 NINMILDVKLPVRVRIGQKKMLLKDVLSMDIGSVVELNQLANDPLEILVDDKVIAKGEVV 258 Query: 128 IMEEDDTHFGVRVIEI 143 I+ D +FG+++ EI Sbjct: 259 IV---DGNFGIQITEI 271 >gnl|CDD|180651 PRK06666, fliM, flagellar motor switch protein FliM; Validated. Length = 337 Score = 38.7 bits (91), Expect = 6e-04 Identities = 12/57 (21%), Positives = 27/57 (47%) Query: 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEI 126 + V++ LG + +S ++NL GDVI L+K + + + ++ + + Sbjct: 253 QQVQQAEVELVAELGEIKLTLSEILNLKVGDVIPLEKPADDPLIVYVDGKPKFLCQY 309 >gnl|CDD|130464 TIGR01397, fliM_switch, flagellar motor switch protein FliM. Members of this family are the flagellar motor switch protein FliM. The family excludes FliM homologs that lack an N-terminal region critical to interaction with phosphorylated CheY. One set lacking this N-terminal region is found in Rhizobium meliloti, in which the direction of flagellar rotation is not reversible (i.e. the FliM homolog does not act to reverse the motor direction), and in related species. Another is found in Buchnera, an obligate intracellular endosymbiont with genes for many of the components of the flagellar apparatus, but not, apparently, for flagellin iself. Length = 320 Score = 35.4 bits (82), Expect = 0.006 Identities = 15/52 (28%), Positives = 27/52 (51%) Query: 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKI 121 + +PV M+ +LG + + L+NL GDVI L+ + E V + + + Sbjct: 248 RELSTVPVDMRAVLGEVEVSLRQLLNLQVGDVIPLNTDMPEEVSLRVGGRPK 299 >gnl|CDD|180694 PRK06789, PRK06789, flagellar motor switch protein; Validated. Length = 74 Score = 32.1 bits (73), Expect = 0.056 Identities = 13/53 (24%), Positives = 32/53 (60%) Query: 74 NIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEI 126 +IP+ + +G+ +I +L++++KG + L+ +V + + N++I G+I Sbjct: 6 DIPLTIYFEIGNTKKKIEDLLHITKGTLYRLENSTKNTVRLMLENEEIGTGKI 58 >gnl|CDD|181204 PRK08035, PRK08035, type III secretion system protein SsaQ; Validated. Length = 323 Score = 30.2 bits (68), Expect = 0.20 Identities = 29/117 (24%), Positives = 44/117 (37%), Gaps = 23/117 (19%) Query: 10 YIKDNLEGRSMHIDNPLQDTNVSSPTNNSEMLIQKNDVDNISEPISSDSNNILEKSTDNF 69 YI EG +M ID QD + L+ + S SS L + Sbjct: 209 YILLT-EGNTMTIDELNQD---------IDTLLASGSPMSKSPGTSSVELEQLPQQ---- 254 Query: 70 DLIMNIPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINNQKIAKGEI 126 ++M I G + I L L+ GDV+ + V I +N + I +GE+ Sbjct: 255 -VVMEI--------GRLSLPIGQLRQLAVGDVLPVGGCFYPEVTIRLNGRIIGQGEL 302 >gnl|CDD|180315 PRK05933, PRK05933, type III secretion system protein; Validated. Length = 372 Score = 29.8 bits (67), Expect = 0.26 Identities = 15/57 (26%), Positives = 28/57 (49%), Gaps = 4/57 (7%) Query: 88 MQISNLVNLSKGDVITLDK-RVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEI 143 + + + L G ++ D VDI +N K+ +GEI + + G+RV+E+ Sbjct: 319 LSVGEFLKLGPGSILQFDGVHPTLGVDIILNGAKVGRGEIIALGD---VLGIRVLEV 372 >gnl|CDD|181259 PRK08158, PRK08158, type III secretion system protein SpaO; Validated. Length = 303 Score = 29.1 bits (65), Expect = 0.44 Identities = 21/86 (24%), Positives = 41/86 (47%), Gaps = 7/86 (8%) Query: 63 EKSTDNFDLIMN----IPVKMQIILGSCCMQISNLVNLSKGDVITLDKRVGESVDITINN 118 E +T + +PVK++ +L + ++ L L + +++L +V+I N Sbjct: 214 ENNTTETAETLPGLNQLPVKLEFVLYRKNVTLAELEELCQQQLLSLPTNAELNVEIRANG 273 Query: 119 QKIAKGEITIMEEDDTHFGVRVIEIL 144 + GE +++ DDT GV + E L Sbjct: 274 ALLGNGE--LVQMDDT-LGVEIHEWL 296 >gnl|CDD|177583 PHA03323, PHA03323, nuclear egress membrane protein UL34; Provisional. Length = 272 Score = 26.6 bits (59), Expect = 2.7 Identities = 6/15 (40%), Positives = 12/15 (80%) Query: 53 PISSDSNNILEKSTD 67 I+++ NN++ KST+ Sbjct: 105 AITAEQNNVILKSTE 119 >gnl|CDD|130587 TIGR01524, ATPase-IIIB_Mg, magnesium-translocating P-type ATPase. The magnesium ATPases have been classified as type IIIB by a phylogenetic analysis. Length = 867 Score = 26.4 bits (58), Expect = 3.2 Identities = 14/34 (41%), Positives = 20/34 (58%), Gaps = 1/34 (2%) Query: 92 NLVNLSKGDVITLDKRVGESVDITINNQKIAKGE 125 +L+ L+ GD+I D RV + D+ I NQ GE Sbjct: 153 DLIELAAGDIIPADARVISARDLFI-NQSALTGE 185 >gnl|CDD|147848 pfam05919, Mitovir_RNA_pol, Mitovirus RNA-dependent RNA polymerase. This family consists of several Mitovirus RNA-dependent RNA polymerase proteins. The family also contains fragment matches in the mitochondria of Arabidopsis thaliana. Length = 495 Score = 25.8 bits (57), Expect = 4.5 Identities = 9/19 (47%), Positives = 12/19 (63%) Query: 113 DITINNQKIAKGEITIMEE 131 DI I N K+AK + IM + Sbjct: 246 DIVIANDKVAKKYLEIMTD 264 >gnl|CDD|178766 PLN03227, PLN03227, serine palmitoyltransferase-like protein; Provisional. Length = 392 Score = 25.6 bits (56), Expect = 4.7 Identities = 11/51 (21%), Positives = 26/51 (50%), Gaps = 3/51 (5%) Query: 97 SKGDVITLDKRVGESVDITINNQKIAKGEITIMEEDDTHFGVRVIEILNAQ 147 +GD++ +D+ V E++ + +++ + +D RV+E + AQ Sbjct: 80 KRGDLLVVDRGVNEAL---LVGVSLSRANVRWFRHNDMKDLRRVLEQVRAQ 127 >gnl|CDD|183286 PRK11713, PRK11713, 16S ribosomal RNA methyltransferase RsmE; Provisional. Length = 234 Score = 25.6 bits (57), Expect = 5.6 Identities = 11/67 (16%), Positives = 25/67 (37%), Gaps = 14/67 (20%) Query: 93 LVNLSKGDVITLDK------------RVGESVDITINNQKIAKGEITIMEEDDTHFGVRV 140 V L+ G+ + LD + G+ + + + EIT + + + + Sbjct: 5 FVLLAAGETLILDGEEAHHLVRVLRLKEGDELRLFDGDGGEYLAEITEIGKK--EVELEI 62 Query: 141 IEILNAQ 147 +E L + Sbjct: 63 LEKLELE 69 >gnl|CDD|180440 PRK06172, PRK06172, short chain dehydrogenase; Provisional. Length = 253 Score = 25.1 bits (55), Expect = 6.8 Identities = 8/18 (44%), Positives = 10/18 (55%) Query: 61 ILEKSTDNFDLIMNIPVK 78 + E S FD IM + VK Sbjct: 101 LAEGSEAEFDAIMGVNVK 118 >gnl|CDD|185135 PRK15213, PRK15213, fimbrial outer membrane usher protein PefC; Provisional. Length = 797 Score = 24.7 bits (54), Expect = 10.0 Identities = 7/22 (31%), Positives = 13/22 (59%) Query: 111 SVDITINNQKIAKGEITIMEED 132 VD+ N +KI K ++I ++ Sbjct: 60 LVDVIFNGKKIGKAILSITPQE 81 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 0.313 0.131 0.351 Gapped Lambda K H 0.267 0.0762 0.140 Matrix: BLOSUM62 Gap Penalties: Existence: 11, Extension: 1 Number of Sequences: 21608 Number of Hits to DB: 2,161,976 Number of extensions: 121572 Number of successful extensions: 213 Number of sequences better than 10.0: 1 Number of HSP's gapped: 210 Number of HSP's successfully gapped: 43 Length of query: 147 Length of database: 5,994,473 Length adjustment: 85 Effective length of query: 62 Effective length of database: 4,157,793 Effective search space: 257783166 Effective search space used: 257783166 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: 52 (23.7 bits)