RPS-BLAST 2.2.22 [Sep-27-2009]

Database: scop70_1_75 
           13,730 sequences; 2,407,596 total letters

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

Query= gi|254780237|ref|YP_003064650.1| DNA-directed RNA polymerase
subunit alpha [Candidatus Liberibacter asiaticus str. psy62]
         (340 letters)



>d1bdfa2 d.181.1.1 (A:53-178) RNA polymerase alpha subunit
           {Escherichia coli [TaxId: 562]}
          Length = 126

 Score =  132 bits (332), Expect = 6e-32
 Identities = 56/126 (44%), Positives = 81/126 (64%), Gaps = 4/126 (3%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTA 116
           G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G VTA
Sbjct: 1   GCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPVTA 60

Query: 117 GDIQTVNDIEVLNPDHVICNLDV-DAVVRMELTVSKGHGYVPA---KHHRTENDPIGLIT 172
            DI    D+E++ P HVIC+L   +A + M + V +G GYVPA    H   +  PIG + 
Sbjct: 61  ADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGRLL 120

Query: 173 IDALYS 178
           +DA YS
Sbjct: 121 VDACYS 126


>d1smya2 d.181.1.1 (A:50-172) RNA polymerase alpha subunit {Thermus
           thermophilus [TaxId: 274]}
          Length = 123

 Score =  130 bits (328), Expect = 2e-31
 Identities = 50/124 (40%), Positives = 75/124 (60%), Gaps = 3/124 (2%)

Query: 57  GAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHK--RVTIFKRGPGVV 114
           G A+T+V I+ VLHE S+I GV ED+ +IILN+K + ++    S +   + +   GP  V
Sbjct: 1   GTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPKEV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLITID 174
            A D   V D+E++NPD  I  L+    + ME+ V +G GYVPA+ H  + D I  I +D
Sbjct: 61  KARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIK-DRINAIPVD 119

Query: 175 ALYS 178
           A++S
Sbjct: 120 AVFS 123


>d1lb2b_ a.60.3.1 (B:) C-terminal domain of RNA polymerase alpha
           subunit {Escherichia coli [TaxId: 562]}
          Length = 72

 Score =  108 bits (272), Expect = 7e-25
 Identities = 41/72 (56%), Positives = 55/72 (76%)

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
           +P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL +
Sbjct: 1   DPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLAS 60

Query: 313 MGLFLGMNLPDW 324
            GL LGM L +W
Sbjct: 61  RGLSLGMRLENW 72


>d1bdfa1 d.74.3.1 (A:2-52,A:179-232) RNA polymerase alpha
           {Escherichia coli [TaxId: 562]}
          Length = 105

 Score = 90.7 bits (225), Expect = 2e-19
 Identities = 29/111 (26%), Positives = 54/111 (48%), Gaps = 9/111 (8%)

Query: 123 NDIEVLNPDHVICNLDVDAVVRMEL-TVSKGHGYVPAKHHRTENDPIGLITIDALYSPIK 181
           +  E L P  V          ++ L  + +G G+      R          + +   P++
Sbjct: 3   SVTEFLKPRLVDIEQVSSTHAKVTLEPLERGFGHTLGNALRA--------ILLSSMPPVE 54

Query: 182 KVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFI 232
           +++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F+
Sbjct: 55  RIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFV 105



 Score = 60.6 bits (147), Expect = 2e-10
 Identities = 26/88 (29%), Positives = 42/88 (47%), Gaps = 9/88 (10%)

Query: 3  QKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAITA 62
          Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALR +L+SS+      A
Sbjct: 1  QGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSSMPPVERIA 57

Query: 63 VQIDGVLHEISSIKGVHEDLTDIILNIK 90
            ++    E         DL  +++ ++
Sbjct: 58 YNVEAARVEQR------TDLDKLVIEME 79


>d1z3eb1 a.60.3.1 (B:245-311) C-terminal domain of RNA polymerase
           alpha subunit {Bacillus subtilis [TaxId: 1423]}
          Length = 67

 Score = 90.8 bits (226), Expect = 2e-19
 Identities = 30/65 (46%), Positives = 41/65 (63%)

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  L  
Sbjct: 2   EKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAKLEE 61

Query: 313 MGLFL 317
           +GL L
Sbjct: 62  LGLGL 66


>d1doqa_ a.60.3.1 (A:) C-terminal domain of RNA polymerase alpha
           subunit {Thermus thermophilus [TaxId: 274]}
          Length = 69

 Score = 87.4 bits (217), Expect = 1e-18
 Identities = 21/65 (32%), Positives = 29/65 (44%)

Query: 253 NPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLGT 312
              L   +EEL LS R  + L+ E I  +  L+     D+  +   G +SL EIK  L  
Sbjct: 3   EEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLKNIPGIGERSLEEIKEALEK 62

Query: 313 MGLFL 317
            G  L
Sbjct: 63  KGFTL 67


>d1smya1 d.74.3.1 (A:1-49,A:173-229) RNA polymerase alpha {Thermus
           thermophilus [TaxId: 274]}
          Length = 106

 Score = 74.2 bits (182), Expect = 2e-14
 Identities = 30/106 (28%), Positives = 51/106 (48%), Gaps = 8/106 (7%)

Query: 137 LDVDAVVRMELTVSKGHGYVPAKHHR-------TENDPIGLITIDALYSPIKKVSYTVES 189
           LD      +    ++G  Y              T  +P+  I + +   P+++V++ VE 
Sbjct: 2   LDSKLKAPVFTVRTQGREYGEFVLEPLERGFGVTLGNPLRRI-LLSSIPPVRRVAFQVED 60

Query: 190 AREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
            R GQ  D DKL++ I TDGS+T  +++  A  IL++ L  F N +
Sbjct: 61  TRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQ 106



 Score = 55.7 bits (134), Expect = 5e-09
 Identities = 24/70 (34%), Positives = 33/70 (47%), Gaps = 8/70 (11%)

Query: 23 EEENRTLM--IAEPLPRGFAHTLGNALRRVLMSSLRGAAITAVQIDGVLHEISSIKGVHE 80
            + R     + EPL RGF  TLGN LRR+L+SS+      A Q++       +  G   
Sbjct: 14 RTQGREYGEFVLEPLERGFGVTLGNPLRRILLSSIPPVRRVAFQVE------DTRLGQRT 67

Query: 81 DLTDIILNIK 90
          DL  + L I 
Sbjct: 68 DLDKLTLRIW 77


>d1by5a_ f.4.3.3 (A:) Ferric hydroxamate uptake receptor FhuA
           {Escherichia coli [TaxId: 562]}
          Length = 697

 Score = 31.4 bits (69), Expect = 0.11
 Identities = 10/72 (13%), Positives = 27/72 (37%), Gaps = 2/72 (2%)

Query: 81  DLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVD 140
            + + +    G+++   G S+    +  RG           +N +++    +    +D  
Sbjct: 48  SVKEALSYTPGVSVGTRGASNTYDHLIIRGFAAEGQSQNNYLNGLKLQGNFYNDAVIDPY 107

Query: 141 AVVRMELTVSKG 152
            + R E  + +G
Sbjct: 108 MLERAE--IMRG 117


>d3bjha_ a.39.2.1 (A:) Pheromone-binding protein asp1 {Common
           honeybee (Apis mellifera) [TaxId: 7460]}
          Length = 117

 Score = 27.2 bits (60), Expect = 2.1
 Identities = 5/18 (27%), Positives = 10/18 (55%)

Query: 323 DWPPESIEELAKKYEDKC 340
           DW P  + +L  + + +C
Sbjct: 1   DWVPPEVFDLVAEDKARC 18


>d1twfc1 d.74.3.1 (C:3-41,C:173-268) RPB3 {Baker's yeast
           (Saccharomyces cerevisiae) [TaxId: 4932]}
          Length = 135

 Score = 27.1 bits (60), Expect = 2.4
 Identities = 14/59 (23%), Positives = 22/59 (37%), Gaps = 4/59 (6%)

Query: 179 PIKKVSYTVESAREGQVLDY----DKLSMTIDTDGSITGEDSVALASRILQDQLGMFIN 233
           P  K     +   EG   DY    D   M +++ GSI  +  V      LQ ++   + 
Sbjct: 69  PQSKNCEYEDPPNEGDPFDYKAQADTFYMNVESVGSIPVDQVVVRGIDTLQKKVASILL 127


>d1n8fa_ c.1.10.4 (A:) 3-deoxy-D-arabino-heptulosonate-7-phosphate
           synthase (DAHP synthase, AroG) {Escherichia coli,
           phenylalanine-regulated isozyme [TaxId: 562]}
          Length = 343

 Score = 26.7 bits (59), Expect = 2.5
 Identities = 12/71 (16%), Positives = 23/71 (32%), Gaps = 3/71 (4%)

Query: 271 NCLRGENIVYMGDLIQ--RTEADMLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPES 328
           N   G  I    D I         L +  +G  ++V   G      +  G   P++  + 
Sbjct: 180 NGTDG-TIKVAIDAINAAGAPHCFLSVTKWGHSAIVNTSGNGDCHIILRGGKEPNYSAKH 238

Query: 329 IEELAKKYEDK 339
           + E+ +     
Sbjct: 239 VAEVKEGLNKA 249


>d5ruba1 c.1.14.1 (A:138-457) Ribulose 1,5-bisphosphate
           carboxylase-oxygenase {Rhodospirillum rubrum [TaxId:
           1085]}
          Length = 320

 Score = 26.3 bits (58), Expect = 3.8
 Identities = 9/61 (14%), Positives = 24/61 (39%), Gaps = 1/61 (1%)

Query: 241 VKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGR 300
           +K D    + PF P L   +  +  ++R      GE  ++  ++      +++    +  
Sbjct: 53  IKNDEPQGNQPFAP-LRDTIALVADAMRRAQDETGEAKLFSANITADDPFEIIARGEYVL 111

Query: 301 K 301
           +
Sbjct: 112 E 112


>d1twfk_ d.74.3.2 (K:) RPB11 {Baker's yeast (Saccharomyces
          cerevisiae) [TaxId: 4932]}
          Length = 114

 Score = 26.3 bits (58), Expect = 4.0
 Identities = 13/50 (26%), Positives = 20/50 (40%), Gaps = 7/50 (14%)

Query: 11 KPNNIEYIVLGQEEENRTLMIAEPLPRGFA-------HTLGNALRRVLMS 53
           P+  E  +LG+ E    +      P           HTLGN +R  L++
Sbjct: 3  APDRFELFLLGEGESKLKIDPDTKAPNAVVITFEKEDHTLGNLIRAELLN 52


>d1g8pa_ c.37.1.20 (A:) ATPase subunit of magnesium chelatase,
          BchI {Rhodobacter capsulatus [TaxId: 1061]}
          Length = 333

 Score = 25.3 bits (54), Expect = 8.2
 Identities = 14/61 (22%), Positives = 26/61 (42%), Gaps = 11/61 (18%)

Query: 19 VLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSSLRGAAIT--AVQIDGVLHEISSIK 76
          ++GQE+    L++    P       G     VL+   RG   +     +  +L EI +++
Sbjct: 9  IVGQEDMKLALLLTAVDPGI-----GG----VLVFGDRGTGKSTAVRALAALLPEIEAVE 59

Query: 77 G 77
          G
Sbjct: 60 G 60


  Database: scop70_1_75
    Posted date:  Mar 27, 2010  6:21 PM
  Number of letters in database: 2,407,596
  Number of sequences in database:  13,730
  
Lambda     K      H
   0.317    0.136    0.386 

Gapped
Lambda     K      H
   0.267   0.0637    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 13730
Number of Hits to DB: 1,247,912
Number of extensions: 58395
Number of successful extensions: 189
Number of sequences better than 10.0: 1
Number of HSP's gapped: 183
Number of HSP's successfully gapped: 21
Length of query: 340
Length of database: 2,407,596
Length adjustment: 86
Effective length of query: 254
Effective length of database: 1,226,816
Effective search space: 311611264
Effective search space used: 311611264
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: 53 (24.4 bits)