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)