RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|255764488|ref|YP_003065099.2| flagellar motor protein MotA
[Candidatus Liberibacter asiaticus str. psy62]
         (290 letters)



>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 = 38.0 bits (88), Expect = 0.002
 Identities = 52/274 (18%), Positives = 97/274 (35%), Gaps = 100/274 (36%)

Query: 51  LKVIKDSGVSLLEIFGYKALGQ---DTYCDVLKLLYILMYNLKKGSRNETENHIDDPYNS 107
            + + +    L+ IFG    GQ   D Y + L+ LY   Y             + D    
Sbjct: 146 FRAVGEGNAQLVAIFG----GQGNTDDYFEELRDLY-QTY----------HVLVGD---- 186

Query: 108 TIFTSIPTVLENNELTTFICDYMRMIIVGNARSYEIENLMDEEIDIILYEKLK-----P- 161
            +       L  +EL                 + + E +  + ++I+ +  L+     P 
Sbjct: 187 -LIKFSAETL--SELI--------------RTTLDAEKVFTQGLNILEW--LENPSNTPD 227

Query: 162 --YHA---ISHMGESLPAIGIVG----AILGIIKAMGNLSQSPKILGTAI-GVSLTGTLL 211
             Y     IS      P IG++      +    K +G    +P  L + + G   TG   
Sbjct: 228 KDYLLSIPIS-----CPLIGVIQLAHYVV--TAKLLG---FTPGELRSYLKGA--TGHSQ 275

Query: 212 GIILSYSLCNPLTSQIKSTRLKQHRLYIIVKKAL-----I------AYMNGAIP----QV 256
           G++ + ++     ++  S        ++ V+KA+     I      AY N ++P    + 
Sbjct: 276 GLVTAVAI-----AETDSWE----SFFVSVRKAITVLFFIGVRCYEAYPNTSLPPSILED 326

Query: 257 AIEYGRKVLP---LSER-PSIEIVAQEVL-QYNH 285
           ++E    V P   LS    + E V Q+ + + N 
Sbjct: 327 SLENNEGV-PSPMLSISNLTQEQV-QDYVNKTNS 358



 Score = 32.6 bits (74), Expect = 0.10
 Identities = 38/265 (14%), Positives = 77/265 (29%), Gaps = 120/265 (45%)

Query: 50  PLKVIKDSGVSLLEIFGYKALGQDTYCDVLKLLYILMYNLKKGSRNETENHIDD-----P 104
           P  +++DS +   E       G  +           M ++   ++ + +++++      P
Sbjct: 320 PPSILEDS-LENNE-------GVPSP----------MLSISNLTQEQVQDYVNKTNSHLP 361

Query: 105 YNSTIFTSIPTVLENNELTTFICDYMRMIIV-GNARS-YEIENLMDE-----EIDI--IL 155
               +  S    L N           + ++V G  +S Y +   + +      +D   I 
Sbjct: 362 AGKQVEIS----LVNGA---------KNLVVSGPPQSLYGLNLTLRKAKAPSGLDQSRIP 408

Query: 156 YEKLK------------PYH------AISHMGESLPAIGIV--GAILGI----------I 185
           + + K            P+H      A   + + L    +      + I          +
Sbjct: 409 FSERKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGSDL 468

Query: 186 KAM-GNLSQS------------PKIL---GTAI------GVSLTGTLLGIILSYSLCNPL 223
           + + G++S+                     T I      G S  G  LG          L
Sbjct: 469 RVLSGSISERIVDCIIRLPVKWETTTQFKATHILDFGPGGAS--G--LG---------VL 515

Query: 224 TSQIKS---TRLKQHRLYIIVKKAL 245
           T + K     R       +IV   L
Sbjct: 516 THRNKDGTGVR-------VIVAGTL 533



 Score = 32.2 bits (73), Expect = 0.14
 Identities = 52/312 (16%), Positives = 84/312 (26%), Gaps = 143/312 (45%)

Query: 4   IIGLF------ITILCIIGGFYAMGGNPYILIQPFEIVIVAGAGLG---GFVMANPLKVI 54
           +IG+       +T    +     +G  P  L          GA  G   G V A     I
Sbjct: 240 LIGVIQLAHYVVT--AKL-----LGFTPGELRSYL-----KGAT-GHSQGLVTA---VAI 283

Query: 55  KDSGVSLLEIFGYKALGQDTYCDVLKLL-YILMYNLKKGSRNETENHIDDPYNSTIFTSI 113
             +     E F             + +L +I       G R     +   P      TS+
Sbjct: 284 --AETDSWESFFVSVR------KAITVLFFI-------GVRC----YEAYPN-----TSL 319

Query: 114 -PTVL----ENNELT-TFICDYMRMIIVGNARSYEIENLMDEEIDIILYEKLKPYHAISH 167
            P++L    ENNE   +     M  I      +   E +  + ++               
Sbjct: 320 PPSILEDSLENNEGVPS----PMLSI-----SNLTQEQV-QDYVN--------------K 355

Query: 168 MGESLPA---IGIVGAILGIIKAMGNLSQSPK---ILGTAIGVSLTGTLLGIILSYSLCN 221
               LPA   + I         ++ N     K   + G     SL          Y L  
Sbjct: 356 TNSHLPAGKQVEI---------SLVN---GAKNLVVSGPPQ--SL----------YGLNL 391

Query: 222 PLTSQIKSTRLKQHRLYIIVKKALIAYMNGAIP--QVAIEYGRKV------LPLS---ER 270
            L      + L Q R                IP  +      RK+      LP++     
Sbjct: 392 TLRKAKAPSGLDQSR----------------IPFSE------RKLKFSNRFLPVASPFHS 429

Query: 271 PSIEIVAQEVLQ 282
             +   +  + +
Sbjct: 430 HLLVPASDLINK 441



 Score = 31.8 bits (72), Expect = 0.18
 Identities = 50/227 (22%), Positives = 77/227 (33%), Gaps = 62/227 (27%)

Query: 86   MYNLKKGSR---NETENHIDDPYNSTIFTSIPTVLENN-ELTTFICDYMRMIIVGNARSY 141
            +Y   K ++   N  +NH  D Y    F+ +  V+ N   LT         I  G  +  
Sbjct: 1635 LYKTSKAAQDVWNRADNHFKDTYG---FSILDIVINNPVNLT---------IHFGGEKGK 1682

Query: 142  EI-ENLMDEEIDIILYEKLKP--------YHAISHMGES----LPAIGIVGAILGIIK-- 186
             I EN      + I+  KLK          H+ S+   S    L A       L +++  
Sbjct: 1683 RIRENYSAMIFETIVDGKLKTEKIFKEINEHSTSYTFRSEKGLLSATQFTQPALTLMEKA 1742

Query: 187  AMGNLSQSPKILGTAIGVSLTGTLLGIILSYSLCNPLTSQIKSTRLKQHRLYIIVKKALI 246
            A  +L     I   A   +  G  LG    Y+    L   +    L +    ++  + + 
Sbjct: 1743 AFEDLKSKGLIPADA---TFAGHSLG---EYAALASLADVMSIESLVE----VVFYRGMT 1792

Query: 247  AYMNGAIPQ----------VAIEYGRKVLPLSERPSIEIVAQEVLQY 283
              M  A+P+          +AI  GR     S         QE LQY
Sbjct: 1793 --MQVAVPRDELGRSNYGMIAINPGRVAASFS---------QEALQY 1828


>3c96_A Flavin-containing monooxygenase; FAD, oxidoreductase, PF01266,
          NESG, PAR240, structural genomics, PSI-2; HET: FAD;
          1.90A {Pseudomonas aeruginosa PAO1} SCOP: c.3.1.2
          d.16.1.2 PDB: 2rgj_A*
          Length = 410

 Score = 33.2 bits (74), Expect = 0.067
 Identities = 14/34 (41%), Positives = 19/34 (55%), Gaps = 1/34 (2%)

Query: 30 QPFEIVIVAGAGLGGFVMANPLKVIKDSGVSLLE 63
          +P +I+I  GAG+GG   A  L       V+LLE
Sbjct: 3  EPIDILIA-GAGIGGLSCALALHQAGIGKVTLLE 35


>1td6_A F10_ORF294, hypothetical protein Mg237 homolog; alpha helical,
           structural genomics, PSI, protein structure initiative;
           2.50A {Mycoplasma pneumoniae} SCOP: a.234.1.1
          Length = 306

 Score = 31.1 bits (70), Expect = 0.29
 Identities = 24/86 (27%), Positives = 37/86 (43%), Gaps = 11/86 (12%)

Query: 77  DVLKLLYILMYNLKKGSRNETENHIDDPYNSTIFTSIPTVLENNELTTFICDYMRMIIVG 136
            ++  +  L    K+    E  N I D +  + F   P V    +L   I +Y+  I++ 
Sbjct: 221 QLITQIQQLFL--KEPVNAEFANEIIDAFLVSYFPLHPPV-PLAQLAAKIYEYVSQIVLN 277

Query: 137 NARSYEIENLMDEEIDII---LYEKL 159
                E  NL DE I +I   LYE+L
Sbjct: 278 -----EAVNLKDELIKLIVHTLYEQL 298


>1qzv_F Plant photosystem I: subunit PSAF; photosynthesis,plant
           photosynthetic reaction center, peripheral antenna; HET:
           CL1 PQN; 4.44A {Pisum sativum} SCOP: i.5.1.1
          Length = 154

 Score = 30.7 bits (68), Expect = 0.34
 Identities = 13/38 (34%), Positives = 16/38 (42%), Gaps = 15/38 (39%)

Query: 157 EK--LKPYHAIS---HMGESLPAIGIVGAILGIIKA-M 188
           EK  LK   A S   +  +S PA+         IKA M
Sbjct: 18  EKQALKKLQA-SLKLYADDSAPALA--------IKATM 46



 Score = 30.4 bits (67), Expect = 0.56
 Identities = 9/30 (30%), Positives = 15/30 (50%), Gaps = 8/30 (26%)

Query: 233 KQHRLYIIVKK---ALIAYMNGAIPQVAIE 259
           KQ      +KK   +L  Y + + P +AI+
Sbjct: 19  KQ-----ALKKLQASLKLYADDSAPALAIK 43


>1cf3_A Protein (glucose oxidase); oxidoreductase(flavoprotein); HET: NAG
          BMA MAN FAD; 1.90A {Aspergillus niger} SCOP: c.3.1.2
          d.16.1.1 PDB: 1gal_A*
          Length = 583

 Score = 30.8 bits (68), Expect = 0.35
 Identities = 9/34 (26%), Positives = 15/34 (44%), Gaps = 1/34 (2%)

Query: 30 QPFEIVIVAGAGLGGFVMANPLKVIKDSGVSLLE 63
          +  + +I  G GL G   A  L    +  V ++E
Sbjct: 18 RTVDYIIA-GGGLTGLTTAARLTENPNISVLVIE 50


>3fim_B ARYL-alcohol oxidase; AAO, lignin degradation, oxidoreductase,
          flavoprotein; HET: FAD; 2.55A {Pleurotus eryngii}
          Length = 566

 Score = 30.4 bits (67), Expect = 0.43
 Identities = 12/29 (41%), Positives = 15/29 (51%)

Query: 35 VIVAGAGLGGFVMANPLKVIKDSGVSLLE 63
           +V GAG  G V+A  L    D  V +LE
Sbjct: 5  YVVVGAGNAGNVVAARLTEDPDVSVLVLE 33


>2jbv_A Choline oxidase; alcohol oxidation, flavoenyzme oxidase,
          covalently linked FAD, C4A-adduct, flavoprotein,
          oxidoreductase; HET: FAO; 1.86A {Arthrobacter
          globiformis}
          Length = 546

 Score = 30.4 bits (67), Expect = 0.43
 Identities = 10/29 (34%), Positives = 13/29 (44%)

Query: 35 VIVAGAGLGGFVMANPLKVIKDSGVSLLE 63
           IV G G  G  +A  L       V+L+E
Sbjct: 16 YIVVGGGSAGAAVAARLSEDPAVSVALVE 44


>1n4w_A CHOD, cholesterol oxidase; flavoenzyme, steroid metabolism,
          oxidoreductase, atomic resolution; HET: FAD; 0.92A
          {Streptomyces SP} SCOP: c.3.1.2 d.16.1.1 PDB: 1b4v_A*
          1n1p_A* 1n4u_A* 1n4v_A* 1mxt_A* 2gew_A* 1b8s_A* 3gyi_A*
          1cc2_A* 3gyj_A* 1ijh_A* 1cbo_A* 3b3r_A* 3b6d_A* 3cnj_A*
          Length = 504

 Score = 30.3 bits (67), Expect = 0.53
 Identities = 11/31 (35%), Positives = 15/31 (48%), Gaps = 5/31 (16%)

Query: 35 VIVAGAGLGGFVMANPLKVIKDSGVS--LLE 63
           +V G G G  V A  L    ++GV   +LE
Sbjct: 8  AVVIGTGYGAAVSALRL---GEAGVQTLMLE 35


>1coy_A Cholesterol oxidase; oxidoreductase(oxygen receptor); HET: AND
          FAD; 1.80A {Brevibacterium sterolicum} SCOP: c.3.1.2
          d.16.1.1 PDB: 3cox_A*
          Length = 507

 Score = 29.8 bits (66), Expect = 0.69
 Identities = 10/31 (32%), Positives = 16/31 (51%), Gaps = 5/31 (16%)

Query: 35 VIVAGAGLGGFVMANPLKVIKDSGVS--LLE 63
           +V G+G GG V A  L     +G+   ++E
Sbjct: 14 ALVIGSGYGGAVAALRL---TQAGIPTQIVE 41


>1gpe_A Protein (glucose oxidase); oxidoreductase(flavoprotein); HET: NAG
          BMA MAN FAD; 1.80A {Penicillium amagasakiense} SCOP:
          c.3.1.2 d.16.1.1
          Length = 587

 Score = 29.5 bits (65), Expect = 1.00
 Identities = 10/29 (34%), Positives = 14/29 (48%)

Query: 35 VIVAGAGLGGFVMANPLKVIKDSGVSLLE 63
           I+AG GL G  +A  L       V ++E
Sbjct: 27 YIIAGGGLTGLTVAAKLTENPKIKVLVIE 55


>2f5v_A Pyranose 2-oxidase; flavoprotein, rossmann-fold, PHBH-fold, GMC
          oxidoreductase, glutathion-reductase related fold,
          tetramer; HET: KBG FAD PG4; 1.41A {Peniophora SP} SCOP:
          c.3.1.2 d.16.1.1 PDB: 1tzl_A* 1tt0_A* 2igk_A* 3bg6_A*
          2f6c_A* 3bg7_A* 2igm_A* 2ign_A* 2igo_A* 3bly_A* 3fdy_A*
          Length = 595

 Score = 29.3 bits (64), Expect = 1.1
 Identities = 7/31 (22%), Positives = 13/31 (41%), Gaps = 5/31 (16%)

Query: 35 VIVAGAGLGGFVMANPLKVIKDSGVS--LLE 63
          V++ G+G  G   A  L     +G    + +
Sbjct: 21 VVIVGSGPIGCTYAREL---VGAGYKVAMFD 48


>1kdg_A CDH, cellobiose dehydrogenase; GMC oxidoreductase, PHBH fold,
          alpha/beta structure, rossmann fold, 6-hydroxylated
          FAD; HET: NAG MAN 6FA EMT; 1.50A {Phanerochaete
          chrysosporium} SCOP: c.3.1.2 d.16.1.1 PDB: 1naa_A*
          Length = 546

 Score = 28.0 bits (61), Expect = 2.5
 Identities = 14/39 (35%), Positives = 20/39 (51%), Gaps = 12/39 (30%)

Query: 30 QPFEIVIVAGAGLGGFVMAN-----PLKVIKDSGVSLLE 63
           P++ +IV GAG GG + A+       KV+      LLE
Sbjct: 6  TPYDYIIV-GAGPGGIIAADRLSEAGKKVL------LLE 37


>1ju2_A HydroxynitrIle lyase; flavin, GMC oxidoreductase, almond,
          cyanogenesis; HET: NAG NDG FUC BMA MAN FAD; 1.47A
          {Prunus dulcis} SCOP: c.3.1.2 d.16.1.1 PDB: 3gdp_A*
          3gdn_A*
          Length = 536

 Score = 28.0 bits (61), Expect = 2.5
 Identities = 8/29 (27%), Positives = 13/29 (44%), Gaps = 2/29 (6%)

Query: 35 VIVAGAGLGGFVMANPLKVIKDSGVSLLE 63
           ++ G G  G  +A  L   +   V +LE
Sbjct: 29 YVIVGGGTSGCPLAATLS--EKYKVLVLE 55


>2wsc_3 LHCA3, type II chlorophyll A/B binding protein from photosystem I;
           photosynthesis, electron transfer, membrane proteins,
           large complexes; HET: CL1 PQN BCR LMU LMG SUC UNL; 3.30A
           {Glycine max} PDB: 2wse_3* 2wsf_3* 2o01_3*
          Length = 276

 Score = 28.2 bits (62), Expect = 2.6
 Identities = 6/16 (37%), Positives = 11/16 (68%)

Query: 99  NHIDDPYNSTIFTSIP 114
           +H+ DP ++ I TS+ 
Sbjct: 259 DHLTDPVHNNILTSLK 274


>2zkq_l 40S ribosomal protein S23E; protein-RNA complex, 40S ribosomal
           subunit, ribosomal protein/RNA complex; 8.70A {Canis
           familiaris} PDB: 1s1h_L
          Length = 143

 Score = 27.9 bits (62), Expect = 3.1
 Identities = 17/54 (31%), Positives = 25/54 (46%), Gaps = 4/54 (7%)

Query: 19  YAMGGNPYILIQPFEIVIVAGAG-LGGFVMANP---LKVIKDSGVSLLEIFGYK 68
           +         I+  + V+VAG G  G  V   P    KV+K + VSLL ++  K
Sbjct: 84  FVPNDGCLNFIEENDEVLVAGFGRKGHAVGDIPGVRFKVVKVANVSLLALYKGK 137


>1hyu_A AHPF, alkyl hydroperoxide reductase subunit F; thiol-thiolate
           hydrogen bond, nucleotide binding fold, thioredoxin
           reductase, thioredoxin; HET: FAD; 2.00A {Salmonella
           typhimurium} SCOP: c.3.1.5 c.3.1.5 c.47.1.2 c.47.1.2
           PDB: 1zyn_A 1zyp_A
          Length = 521

 Score = 26.6 bits (58), Expect = 6.8
 Identities = 14/134 (10%), Positives = 36/134 (26%), Gaps = 9/134 (6%)

Query: 31  PFEIVIVAGAGLGGFVMA--------NPLKVIKDSGVSLLEIFGYKALGQDTYCDVLKLL 82
            ++++IV G+G  G   A            + +  G  +L+    +        +  KL 
Sbjct: 212 AYDVLIV-GSGPAGAAAAVYSARKGIRTGLMGERFGGQVLDTVDIENYISVPKTEGQKLA 270

Query: 83  YILMYNLKKGSRNETENHIDDPYNSTIFTSIPTVLENNELTTFICDYMRMIIVGNARSYE 142
             L  ++     +  ++                 +E           + +      R+  
Sbjct: 271 GALKAHVSDYDVDVIDSQSASKLVPAATEGGLHQIETASGAVLKARSIIIATGAKWRNMN 330

Query: 143 IENLMDEEIDIILY 156
           +          + Y
Sbjct: 331 VPGEDQYRTKGVTY 344


>1ccw_B Protein (glutamate mutase); coenzyme B12, radical reaction, TIM-
           barrel, rossman-fold; HET: TAR CNC; 1.60A {Clostridium
           cochlearium} SCOP: c.1.19.2 PDB: 1cb7_B* 1i9c_B*
          Length = 483

 Score = 26.3 bits (58), Expect = 8.1
 Identities = 12/50 (24%), Positives = 20/50 (40%), Gaps = 7/50 (14%)

Query: 138 ARSYEIENLMDEEIDIILYEKLKPY-HAISHMGESLPAIGIVGAI-LGII 185
             S E+E  M       +  + K     +  +G+   AIG V A   G++
Sbjct: 360 PMSKELETEMAV-----IKAETKCILDKMFELGKGDLAIGTVKAFETGVM 404


  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
   0.322    0.141    0.402 

Gapped
Lambda     K      H
   0.267   0.0408    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,478,038
Number of extensions: 118913
Number of successful extensions: 458
Number of sequences better than 10.0: 1
Number of HSP's gapped: 457
Number of HSP's successfully gapped: 28
Length of query: 290
Length of database: 5,693,230
Length adjustment: 92
Effective length of query: 198
Effective length of database: 3,462,782
Effective search space: 685630836
Effective search space used: 685630836
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 56 (26.2 bits)