RPS-BLAST 2.2.22 [Sep-27-2009]

Database: pdb70 
           24,244 sequences; 5,693,230 total letters

Searching..................................................done

Query= gi|254780547|ref|YP_003064960.1| OmpA/MotB [Candidatus
Liberibacter asiaticus str. psy62]
         (160 letters)



>2kgw_A Outer membrane protein A; OMPA- like, cell membrane, transmembrane;
           NMR {Mycobacterium tuberculosis}
          Length = 129

 Score =  105 bits (263), Expect = 5e-24
 Identities = 33/110 (30%), Positives = 50/110 (45%), Gaps = 1/110 (0%)

Query: 40  LQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSS 98
           LQ   ++  G  + F     S+ PAD ++L+ +   L+   D    I G+ D  GS   +
Sbjct: 14  LQSAINAVTGGPIAFGNDGASLIPADYEILNRVADKLKACPDARVTINGYTDNTGSEGIN 73

Query: 99  IALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148
           I L  +RA  V +Y VARG++   +     G   P       +  AKNRR
Sbjct: 74  IPLSAQRAKIVADYLVARGVAGDHIATVGLGSVNPIASNATPEGRAKNRR 123


>2zf8_A MOTY, component of sodium-driven polar flagellar motor; beta
           barrel, 2-layer sandwich, flagellum, structural protein;
           2.85A {Vibrio alginolyticus}
          Length = 278

 Score = 96.9 bits (241), Expect = 2e-21
 Identities = 26/116 (22%), Positives = 51/116 (43%), Gaps = 2/116 (1%)

Query: 40  LQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHD--CDFLIEGHADELGSRNS 97
           L+  F       + ++     +  A  + LS +  ++  +      L+  + D    +++
Sbjct: 152 LKYSFEDIAFTILHYERQGDQLTKASKKRLSQIADYIRHNQDIDLVLVATYTDSTDGKSA 211

Query: 98  SIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153
           S +L  RRA ++ +YF + G+   R++V  YGK  P           KNRR ++ L
Sbjct: 212 SQSLSERRAESLRDYFQSLGLPEDRIQVQGYGKRRPIADNGSPIGKDKNRRVVISL 267


>3ldt_A Outer membrane protein, OMPA family protein; OMPA-like domain,
           PSI-II, NYSGXRC, structural genomics, protein structure
           initiative; 2.30A {Legionella pneumophila}
          Length = 169

 Score = 95.4 bits (237), Expect = 5e-21
 Identities = 25/103 (24%), Positives = 41/103 (39%), Gaps = 1/103 (0%)

Query: 47  SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRR 105
            +    +F  SS  +       L+N+   L  +      + G  D +GSR+    L   +
Sbjct: 51  IIPTDKYFMFSSPRLNEICYPGLNNVIRLLNFYPQSTIYVAGFTDNVGSRSHKRKLSQAQ 110

Query: 106 AYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRR 148
           A  +  +  A GI+A R+K   YG +            A+NRR
Sbjct: 111 AETMMTFLWANGIAAKRLKAEGYGDKNAISDNAIIHGSAQNRR 153


>1r1m_A Outer membrane protein class 4; 1.90A {Neisseria meningitidis}
           SCOP: d.79.7.1
          Length = 164

 Score = 95.2 bits (236), Expect = 6e-21
 Identities = 31/113 (27%), Positives = 43/113 (38%), Gaps = 1/113 (0%)

Query: 47  SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRR 105
           S+     F     S+R      L  L   L +       +EGH D +GS   + AL  RR
Sbjct: 12  SLSAKTLFGFDKDSLRAEAQDNLKVLAQRLSRTNIQSVRVEGHTDFMGSDKYNQALSERR 71

Query: 106 AYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLKGCRA 158
           AY V N  V+ G+  SR+     G+    +    E   AK    +   K   A
Sbjct: 72  AYVVANNLVSNGVPVSRISAVGLGESQAQMTQVCEAEVAKLGAKVSKAKKREA 124


>3oon_A Outer membrane protein (TPN50); protein structure initiative,
           PSI-2, structural genomics, MI center for structural
           genomics, MCSG; 1.79A {Borrelia burgdorferi}
          Length = 123

 Score = 84.8 bits (210), Expect = 8e-18
 Identities = 26/104 (25%), Positives = 46/104 (44%), Gaps = 3/104 (2%)

Query: 47  SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRR 105
           ++   + F  +S+ I   + + +  +   LEK    + LIEGH ++ G       L  +R
Sbjct: 14  NLSFDIEFYPNSFQILQKEYKKIDLIAKLLEKFKKNNILIEGHTEQFGLEEEMHELSEKR 73

Query: 106 AYAVFNYFVARGISA-SRMKVTSYGKEMPSVYGHDEDAYAKNRR 148
           A A+ NY +   +    ++    +G + P  Y       AKNRR
Sbjct: 74  ARAIGNYLIKMKVKDKDQILFKGWGSQKP-KYPKSSPLKAKNRR 116


>3cyp_B Chemotaxis protein MOTB; bacterial flagellar motor, peptidoglycan
           binding, bacterial flagellum, flagellar rotation, inner
           membrane, membrane; 1.60A {Helicobacter pylori} PDB:
           3cyq_B*
          Length = 138

 Score = 82.6 bits (204), Expect = 4e-17
 Identities = 21/112 (18%), Positives = 41/112 (36%), Gaps = 7/112 (6%)

Query: 50  DSVFFDT-SSYSIRPADIQVLSNLGSWLEKH--DCDFLIEGHADELGSRNSSIA----LG 102
           D   F+  +S +I    +  +  +   ++K        + G  D+     +       L 
Sbjct: 3   DPFTFENATSDAINQDMMLYIERIAKIIQKLPKRVHINVRGFTDDTPLVKTRFKSHYELA 62

Query: 103 LRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK 154
             RAY V    +  G++ +++  +SYG   P       +   KN R  +F  
Sbjct: 63  ANRAYRVMKVLIQYGVNPNQLSFSSYGSTNPIAPNDSLENRMKNNRVEIFFS 114


>2zov_A Chemotaxis protein MOTB; 2-layer sandwich, bacterial flagellum,
           cell projection, flagellar rotation, inner membrane,
           membrane; 2.00A {Salmonella typhimurium}
          Length = 210

 Score = 75.1 bits (184), Expect = 7e-15
 Identities = 24/112 (21%), Positives = 36/112 (32%), Gaps = 9/112 (8%)

Query: 50  DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSS-----IALGLR 104
           +   F T S  + P    +L  +   L        + GH D+    N         L   
Sbjct: 71  NRPMFKTGSAEVEPYMRDILRAIAPVLNGIPNRISLAGHTDDFPYANGEKGYSNWELSAD 130

Query: 105 RAYAVFNYFVARGISASR-MKVTSYGKEMPSVYGHDEDAYAKNRRA-IVFLK 154
           RA A     VA G+   + ++V      M           A NRR  ++ L 
Sbjct: 131 RANASRRELVAGGLDNGKVLRVVGMAATMRLS--DRGPDDAINRRISLLVLN 180


>2k1s_A Inner membrane lipoprotein YIAD; abbababab, OMPA, alpha beta,
           palmitate, transmembrane, structural genomics, PSI-2;
           NMR {Escherichia coli K12}
          Length = 149

 Score = 67.9 bits (165), Expect = 9e-13
 Identities = 27/108 (25%), Positives = 56/108 (51%), Gaps = 1/108 (0%)

Query: 47  SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRR 105
           ++ ++V FD+SS +++PA    L+ +   L+++      + G+ D  G  + ++ L  +R
Sbjct: 31  NMPNNVTFDSSSATLKPAGANTLTGVAMVLKEYPKTAVNVIGYTDSTGGHDLNMRLSQQR 90

Query: 106 AYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153
           A +V +  + +G+ ASR++    G   P       +  A+NRR  + L
Sbjct: 91  ADSVASALITQGVDASRIRTQGLGPANPIASNSTAEGKAQNRRVEITL 138


>2hqs_H Peptidoglycan-associated lipoprotein; TOLB, PAL, TOL, transport
           protein/lipoprotein complex; 1.50A {Escherichia coli}
           SCOP: d.79.7.1 PDB: 2w8b_C 1oap_A
          Length = 118

 Score = 67.2 bits (163), Expect = 2e-12
 Identities = 48/107 (44%), Positives = 68/107 (63%), Gaps = 2/107 (1%)

Query: 50  DSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELGSRNSSIALGLRRAYA 108
           + V+FD   Y IR    Q+L    ++L  +      +EGHADE G+   +I+LG RRA A
Sbjct: 6   NIVYFDLDKYDIRSDFAQMLDAHANFLRSNPSYKVTVEGHADERGTPEYNISLGERRANA 65

Query: 109 VFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRA-IVFLK 154
           V  Y   +G+SA ++ + SYGKE P+V GHDE AY+KNRRA +V+L+
Sbjct: 66  VKMYLQGKGVSADQISIVSYGKEKPAVLGHDEAAYSKNRRAVLVYLE 112


>2zvy_A Chemotaxis protein MOTB; 2-layer sandwich, bacterial flagellum,
           cell inner membrane, cell membrane, flagellar rotation,
           membrane; 1.75A {Salmonella typhimurium} PDB: 2zvz_A
          Length = 183

 Score = 64.0 bits (155), Expect = 2e-11
 Identities = 22/110 (20%), Positives = 33/110 (30%), Gaps = 8/110 (7%)

Query: 50  DSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSS-----IALGLR 104
           +   F T S  + P    +L  +   L        + GH D+    N         L   
Sbjct: 60  NRPMFKTGSAEVEPYMRDILRAIAPVLNGIPNRISLAGHTDDFPYANGEKGYSNWELSAD 119

Query: 105 RAYAVFNYFVA-RGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFL 153
           RA A     VA    +   ++V      M           A NRR  + +
Sbjct: 120 RANASRRELVAGGLDNGKVLRVVGMAATMRLS--DRGPDDAINRRISLLV 167


>2aiz_P Outer membrane protein P6; alpha-beta sandwich; HET: UDP AMU DGL
           6CL DAL; NMR {Haemophilus influenzae} SCOP: d.79.7.1
          Length = 134

 Score = 58.8 bits (141), Expect = 5e-10
 Identities = 44/120 (36%), Positives = 69/120 (57%), Gaps = 7/120 (5%)

Query: 35  LNESSLQEQFSSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH-DCDFLIEGHADELG 93
            + + LQ+++     ++V+F    Y I    +Q+L    ++L        L+EG+ DE G
Sbjct: 20  YSVADLQQRY-----NTVYFGFDKYDITGEYVQILDAHAAYLNATPAAKVLVEGNTDERG 74

Query: 94  SRNSSIALGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRA-IVF 152
           +   +IALG RRA AV  Y   +G+ A ++   SYG+E P+V GHDE AY+KNRRA + +
Sbjct: 75  TPEYNIALGQRRADAVKGYLAGKGVDAGKLGTVSYGEEKPAVLGHDEAAYSKNRRAVLAY 134


>3khn_A MOTB protein, putative; structural genomics, OMPA-like domain,
           PSI-2, protein structure initiative; 2.03A
           {Desulfovibrio vulgaris str}
          Length = 174

 Score = 56.0 bits (134), Expect = 4e-09
 Identities = 23/114 (20%), Positives = 40/114 (35%), Gaps = 6/114 (5%)

Query: 47  SVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKH------DCDFLIEGHADELGSRNSSIA 100
            V   V F   +  + P   +VL+ L     +          F  +           +  
Sbjct: 48  RVPSEVLFAPGAVELAPGADRVLATLKDLFIRRREQNINIKGFTDDVQPSANARFKDNWE 107

Query: 101 LGLRRAYAVFNYFVARGISASRMKVTSYGKEMPSVYGHDEDAYAKNRRAIVFLK 154
           +   R+  V  YF+  GI  +R+  T  G+  P      ++  A+NRR    L+
Sbjct: 108 VSALRSVNVLRYFLGAGIEPARLTATGLGELDPLFPNTSDENRARNRRVEFVLE 161


>2pff_B Fatty acid synthase subunit beta; fatty acid synthase,
           acyl-carrier-protein, beta-ketoacyl reductase,
           beta-ketoacyl synthase, dehydratase; 4.00A
           {Saccharomyces cerevisiae}
          Length = 2006

 Score = 36.1 bits (83), Expect = 0.004
 Identities = 30/192 (15%), Positives = 56/192 (29%), Gaps = 67/192 (34%)

Query: 10  LSAITMMSIS---GIDNLDTKISSPDTVL-NESSLQEQFSSS--------VGDSVFFDTS 57
           + A +   ++   G  +L+  +  P       S LQEQF+            D    + +
Sbjct: 1   MDAYSTRPLTLSHG--SLEHVLLVPTASFFIASQLQEQFNKILPEPTEGFAADD---EPT 55

Query: 58  S----------YSIRPAD-------IQVLSNLGSWLEKHDCDFL--IEGHADELGSRNSS 98
           +          Y     +        QVL+     L + +  +L   + HA         
Sbjct: 56  TPAELVGKFLGYVSSLVEPSKVGQFDQVLNLC---LTEFENCYLEGNDIHA-LAAKLLQE 111

Query: 99  IALGLRRAYAVF-NYFVARGISASRMKVTSYGKEMPSVYGH-------DEDA--YAKNRR 148
               L +   +  NY  AR ++          +               + +A   A    
Sbjct: 112 NDTTLVKTKELIKNYITARIMA---------KRPFDKKSNSALFRAVGEGNAQLVA---- 158

Query: 149 AIVFLKGCRANT 160
             +F  G + NT
Sbjct: 159 --IF--GGQGNT 166


>2wvx_A Mannosidase, putative alpha-1,2-mannosidase; glycoside hydrolase
           family 92, GH92, hydrolase, BT3990; HET: MSE; 1.90A
           {Bacteroides thetaiotaomicron} PDB: 2wvx_B*
          Length = 744

 Score = 27.7 bits (61), Expect = 1.4
 Identities = 24/113 (21%), Positives = 39/113 (34%), Gaps = 4/113 (3%)

Query: 1   MQYSTIFIILSAITMMSISGIDNLDTKISSPDTVLNESSLQEQFSSSVGDSVFFDTSSYS 60
           M  +    IL    M  +   D         + +++ +       SS G   +   +   
Sbjct: 375 MVGNNSASILVDAYMKGVKVDDIKTLY----EGLIHGTENVHPEVSSTGRLGYEYYNKLG 430

Query: 61  IRPADIQVLSNLGSWLEKHDCDFLIEGHADELGSRNSSIALGLRRAYAVFNYF 113
             P D+++  N    LE    D+ I   A EL      I+L  +RA    N F
Sbjct: 431 YVPYDVKINENAARTLEYAYDDWCIYRLAKELKRPKKEISLFAKRAMNYKNLF 483


>2fcl_A Hypothetical protein TM1012; structural genomics, PSI, protein
          structure initiative, joint center for structural
          genomics, JCSG; HET: MLY; 1.20A {Thermotoga maritima}
          SCOP: d.218.1.11 PDB: 2ewr_A
          Length = 169

 Score = 26.0 bits (57), Expect = 4.7
 Identities = 7/27 (25%), Positives = 14/27 (51%)

Query: 61 IRPADIQVLSNLGSWLEKHDCDFLIEG 87
          IRP  ++VL  +   L     ++++ G
Sbjct: 14 IRPEYLRVLRXIYDRLXNEXVNWVVTG 40


>1gxs_A HNL, hydroxynitrIle lyase; inhibitor complex, cyanogenesis
           mechanism; HET: NAG FUL FUC DKA; 2.3A {Sorghum bicolor}
           SCOP: c.69.1.5
          Length = 270

 Score = 25.4 bits (55), Expect = 6.9
 Identities = 7/40 (17%), Positives = 16/40 (40%)

Query: 45  SSSVGDSVFFDTSSYSIRPADIQVLSNLGSWLEKHDCDFL 84
            SS+G     +  ++ +      +L N  +W +  +  F 
Sbjct: 66  CSSIGLGAMQELGAFRVHTNGESLLLNEYAWNKAANILFA 105


  Database: pdb70
    Posted date:  Jan 26, 2011 11:21 AM
  Number of letters in database: 5,693,230
  Number of sequences in database:  24,244
  
Lambda     K      H
   0.318    0.132    0.372 

Gapped
Lambda     K      H
   0.267   0.0680    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,268,142
Number of extensions: 51598
Number of successful extensions: 118
Number of sequences better than 10.0: 1
Number of HSP's gapped: 106
Number of HSP's successfully gapped: 21
Length of query: 160
Length of database: 5,693,230
Length adjustment: 85
Effective length of query: 75
Effective length of database: 3,632,490
Effective search space: 272436750
Effective search space used: 272436750
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 (24.3 bits)