RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780374|ref|YP_003064787.1| flagellar basal body L-ring
protein [Candidatus Liberibacter asiaticus str. psy62]
         (238 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 = 42.2 bits (99), Expect = 1e-04
 Identities = 37/212 (17%), Positives = 66/212 (31%), Gaps = 84/212 (39%)

Query: 19  HSSISEI--------TGIPQMS-------------PMGSSLDENNRMPFLGIDFKNSDST 57
              IS +        +G P  S             P G  LD++ R+PF         S 
Sbjct: 365 QVEISLVNGAKNLVVSG-PPQSLYGLNLTLRKAKAPSG--LDQS-RIPF---------SE 411

Query: 58  KK---SYSLWRDS---HAALFKDSRALNVGDILTVDIRID-DQ---AVFDNQTGRSRNNS 107
           +K   S      +   H+ L   +  L   D++  ++  +       V+D   G      
Sbjct: 412 RKLKFSNRFLPVASPFHSHLLVPASDLINKDLVKNNVSFNAKDIQIPVYDTFDGS----D 467

Query: 108 LHRKLSGGF--SLFGQQT------PQMNGNLNYD-------GGGASSGKGSISRAEKLNL 152
           L R LSG     +                   +        G G +SG G +        
Sbjct: 468 L-RVLSGSISERIVDCIIRLPVKWETT---TQFKATHILDFGPGGASGLGVL-------- 515

Query: 153 LIAAIVTAILENGN---LIISGSQEVRVNDEI 181
                 T   ++G    +I++G+ ++  +D+ 
Sbjct: 516 ------THRNKDGTGVRVIVAGTLDINPDDDY 541



 Score = 30.3 bits (68), Expect = 0.43
 Identities = 21/120 (17%), Positives = 40/120 (33%), Gaps = 30/120 (25%)

Query: 145 SRAEKLNLLIAAIVTAILENGN--------LIISGSQEVRVNDEIRS----LNVTGIVRP 192
              + LNL +       LE  +        L  + +  V+  + I++      +      
Sbjct: 79  QFDQVLNLCLTEFENCYLEGNDIHALAAKLLQENDTTLVKTKELIKNYITARIMAKRPFD 138

Query: 193 QDVDAHNSVSYDKIAE--ARIS--YGGKGRT----TELLR------PPIGHQLIENLSPL 238
                 NS  +  + E  A++   +GG+G T     E LR        +   LI+  +  
Sbjct: 139 ---KKSNSALFRAVGEGNAQLVAIFGGQGNTDDYFEE-LRDLYQTYHVLVGDLIKFSAET 194


>2q28_A Oxalyl-COA decarboxylase; lyase, oxalate degradation, thiamine
           diphosphate; HET: TPP ADP MES; 1.74A {Escherichia coli}
           PDB: 2q27_A* 2q29_A*
          Length = 564

 Score = 32.4 bits (72), Expect = 0.084
 Identities = 15/72 (20%), Positives = 25/72 (34%), Gaps = 12/72 (16%)

Query: 154 IAAIVTAILENGNLIISGSQEVRVNDE----IRSLNVTGIVRPQDVDAHNSVSYDKIAEA 209
              I T    N  + I     V  N+        ++++G   P   D  +   YDK+ +A
Sbjct: 454 GMEIETICRYNLPVTI-----VIFNNGGIYRGDGVDLSGAGAPSPTDLLHHARYDKLMDA 508

Query: 210 RISYGGKGRTTE 221
              + G G    
Sbjct: 509 ---FRGVGYNVT 517


>3f8t_A Predicted ATPase involved in replication control, CDC46/MCM family;
           helicase, MCM homolog, DNA replication, ATP-binding,
           DNA-binding; 1.90A {Methanopyrus kandleri AV19}
          Length = 506

 Score = 29.2 bits (65), Expect = 0.74
 Identities = 14/82 (17%), Positives = 21/82 (25%), Gaps = 6/82 (7%)

Query: 158 VTAILENGNLIISGSQEVRVN--DEIRSLNVTGIVRPQDVDAHNSVSYDKIAEARISYGG 215
                    L+       R+     +    + GIVR   +DA      D I E       
Sbjct: 137 AIVDTG-SELVAVRLHGHRLGPGLRV---EILGIVRSATLDALEVHKKDPIPEVHPDPAE 192

Query: 216 KGRTTELLRPPIGHQLIENLSP 237
                EL            ++P
Sbjct: 193 LEEFRELADKDPLTTFARAIAP 214


>2h92_A Cytidylate kinase; rossmann fold, transferase; HET: C5P PG4; 2.30A
           {Staphylococcus aureus}
          Length = 219

 Score = 28.3 bits (62), Expect = 1.6
 Identities = 7/21 (33%), Positives = 16/21 (76%), Gaps = 2/21 (9%)

Query: 135 GGASSGKGSISR--AEKLNLL 153
           G A++GK +I++  A +L+++
Sbjct: 10  GPAAAGKSTIAKRVASELSMI 30


>1q3t_A Cytidylate kinase; nucleotide monophosphate kinase, CMP kinase,
           transferase; NMR {Streptococcus pneumoniae} SCOP:
           c.37.1.1
          Length = 236

 Score = 27.7 bits (61), Expect = 2.7
 Identities = 7/20 (35%), Positives = 12/20 (60%), Gaps = 2/20 (10%)

Query: 135 GGASSGKGSISR--AEKLNL 152
           G ASSGK ++++  A+    
Sbjct: 23  GPASSGKSTVAKIIAKDFGF 42


>1cke_A CK, MSSA, protein (cytidine monophosphate kinase); nucleotide
           monophosphate kinase,; 1.75A {Escherichia coli} SCOP:
           c.37.1.1 PDB: 1kdo_A* 1kdp_A* 1kdr_A* 1kdt_A* 2cmk_A*
           2fem_A 2feo_A*
          Length = 227

 Score = 27.0 bits (58), Expect = 4.0
 Identities = 7/20 (35%), Positives = 12/20 (60%), Gaps = 2/20 (10%)

Query: 135 GGASSGKGSISR--AEKLNL 152
           G + +GKG++ +  AE L  
Sbjct: 12  GPSGAGKGTLCKAMAEALQW 31


>2a6h_C DNA-directed RNA polymerase beta chain; RNA polymerase holoenzyme,
           streptolydigin, antibiotic, transcription regulation;
           HET: STD; 2.40A {Thermus thermophilus} SCOP: e.29.1.1
           PDB: 1smy_C* 1zyr_C* 1iw7_C* 2a69_C* 2a6e_C 2a68_C*
           2be5_C* 2cw0_C 2o5i_C 2o5j_C* 2ppb_C* 3dxj_C* 3eql_C*
           1ynj_C* 1ynn_C* 2gho_C 1hqm_C 1l9u_C 1l9z_C 1i6v_C*
          Length = 1119

 Score = 26.6 bits (58), Expect = 4.8
 Identities = 10/25 (40%), Positives = 15/25 (60%)

Query: 162 LENGNLIISGSQEVRVNDEIRSLNV 186
            E+G+ II+G+  V V+   RS  V
Sbjct: 122 TEDGSFIINGADRVIVSQIHRSPGV 146


>3iyd_C DNA-directed RNA polymerase subunit beta; transcription,
           initiation, class I, activator, RNA polymerase,
           holoenzyme, sigma70, open complex, CAP, CRP,
           CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli
           k-12}
          Length = 1342

 Score = 26.6 bits (58), Expect = 5.1
 Identities = 9/25 (36%), Positives = 15/25 (60%)

Query: 162 LENGNLIISGSQEVRVNDEIRSLNV 186
            +NG  +I+G++ V V+   RS  V
Sbjct: 131 TDNGTFVINGTERVIVSQLHRSPGV 155


>2it1_A 362AA long hypothetical maltose/maltodextrin transport ATP-binding
           protein; structural genomics, NPPSFA; 1.94A {Pyrococcus
           horikoshii}
          Length = 362

 Score = 26.4 bits (58), Expect = 5.3
 Identities = 5/34 (14%), Positives = 17/34 (50%)

Query: 70  ALFKDSRALNVGDILTVDIRIDDQAVFDNQTGRS 103
               +    + G+ +T+ ++ +   +FD +T ++
Sbjct: 323 VFAPEGEHFSFGEKVTIKVKEELLVLFDKKTEKA 356


>3elv_A PRE-mRNA leakage protein 1; intrinsically unstructured domain,
           forkhead-associated domain (FHA) domain, PRE-mRNA
           retention and splicing; 2.40A {Saccharomyces cerevisiae}
           PDB: 2jkd_A
          Length = 205

 Score = 26.1 bits (57), Expect = 7.1
 Identities = 10/60 (16%), Positives = 24/60 (40%), Gaps = 6/60 (10%)

Query: 36  SSLDENNRMPFLGIDFKNSDSTKKSYSLWRDSHAALFKDSRALNVGDILTVDIRIDDQAV 95
              ++ ++ P+   D       +  Y + R+   +L  D    +  +I+  DI I ++  
Sbjct: 84  YRKNDKDKGPWKRYDLNG----RSCYLVGRELGHSLDTDL--DDRTEIVVADIGIPEETS 137


>1g29_1 MALK, maltose transport protein MALK; ATPase, active transport,
           maltose uptake and regulation, sugar binding protein;
           1.90A {Thermococcus litoralis} SCOP: b.40.6.3 b.40.6.3
           c.37.1.12 PDB: 2d62_A
          Length = 372

 Score = 25.6 bits (56), Expect = 9.2
 Identities = 7/33 (21%), Positives = 13/33 (39%)

Query: 70  ALFKDSRALNVGDILTVDIRIDDQAVFDNQTGR 102
             F+    +  G  + V   +    +FD  TG+
Sbjct: 337 GSFRSESRVREGVEVDVVFDMKKIHIFDKTTGK 369


  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
   0.316    0.134    0.381 

Gapped
Lambda     K      H
   0.267   0.0522    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,967,788
Number of extensions: 86249
Number of successful extensions: 224
Number of sequences better than 10.0: 1
Number of HSP's gapped: 224
Number of HSP's successfully gapped: 15
Length of query: 238
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 148
Effective length of database: 3,511,270
Effective search space: 519667960
Effective search space used: 519667960
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 (21.6 bits)
S2: 55 (25.4 bits)