RPS-BLAST 2.2.22 [Sep-27-2009]

Database: mmdb70 
           33,805 sequences; 4,956,049 total letters

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

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



>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription,
           initiation, class I, activator, RNA polymerase,
           holoenzyme, sigma70, open complex, CAP, CRP,
           CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli
           k-12} (A:49-180)
          Length = 132

 Score =  156 bits (397), Expect = 3e-39
 Identities = 60/132 (45%), Positives = 87/132 (65%), Gaps = 4/132 (3%)

Query: 53  SSLRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           SS+ G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G
Sbjct: 1   SSMPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIG 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPI 168
            VTA DI    D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PI
Sbjct: 61  PVTAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPI 120

Query: 169 GLITIDALYSPI 180
           G + +DA YSP+
Sbjct: 121 GRLLVDACYSPV 132


>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase
           holoenzyme, streptolydigin, antibiotic, transcription
           regulation; HET: STD; 2.40A {Thermus thermophilus}
           (A:48-172)
          Length = 125

 Score =  149 bits (378), Expect = 5e-37
 Identities = 52/126 (41%), Positives = 77/126 (61%), Gaps = 3/126 (2%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTI--FKRGPG 112
           + G A+T+V I+ VLHE S+I GV ED+ +IILN+K + ++    S + VT+     GP 
Sbjct: 1   IPGTAVTSVYIEDVLHEFSTIPGVKEDVVEIILNLKELVVRFLNPSLQTVTLLLKAEGPK 60

Query: 113 VVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPAKHHRTENDPIGLIT 172
            V A D   V D+E++NPD  I  L+    + ME+ V +G GYVPA+ H  + D I  I 
Sbjct: 61  EVKARDFLPVADVEIMNPDLHIATLEEGGRLNMEVRVDRGVGYVPAEKHGIK-DRINAIP 119

Query: 173 IDALYS 178
           +DA++S
Sbjct: 120 VDAVFS 125


>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase,
           assemble; 2.50A {Escherichia coli} (A:51-178)
          Length = 128

 Score =  148 bits (376), Expect = 7e-37
 Identities = 57/128 (44%), Positives = 83/128 (64%), Gaps = 4/128 (3%)

Query: 55  LRGAAITAVQIDGVLHEISSIKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           + G A+T V+IDGVLHE S+ +GV ED+ +I+LN+KG+ +++ G     +T+ K G G V
Sbjct: 1   MPGCAVTEVEIDGVLHEYSTKEGVQEDILEILLNLKGLAVRVQGKDEVILTLNKSGIGPV 60

Query: 115 TAGDIQTVNDIEVLNPDHVICNL-DVDAVVRMELTVSKGHGYVPA---KHHRTENDPIGL 170
           TA DI    D+E++ P HVIC+L D +A + M + V +G GYVPA    H   +  PIG 
Sbjct: 61  TAADITHDGDVEIVKPQHVICHLTDENASISMRIKVQRGRGYVPASTRIHSEEDERPIGR 120

Query: 171 ITIDALYS 178
           + +DA YS
Sbjct: 121 LLVDACYS 128


>2a6h_A DNA-directed RNA polymerase alpha chain; RNA polymerase
           holoenzyme, streptolydigin, antibiotic, transcription
           regulation; HET: STD; 2.40A {Thermus thermophilus}
           (A:1-47,A:173-315)
          Length = 190

 Score =  140 bits (353), Expect = 3e-34
 Identities = 47/144 (32%), Positives = 70/144 (48%), Gaps = 2/144 (1%)

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFE 235
           L SP+++V++ VE  R GQ  D DKL++ I TDGS+T  +++  A  IL++ L  F N +
Sbjct: 45  LSSPVRRVAFQVEDTRLGQRTDLDKLTLRIWTDGSVTPLEALNQAVEILREHLTYFSNPQ 104

Query: 236 EPKKEVKEDINVKS--LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADML 293
                  E+             L   +EEL LS R  + L+ E I  +  L+     D+ 
Sbjct: 105 AAAVAAPEEAKEPEAPPEQEEELDLPLEELGLSTRVLHSLKEEGIESVRALLALNLKDLK 164

Query: 294 RMANFGRKSLVEIKGVLGTMGLFL 317
            +   G +SL EIK  L   G  L
Sbjct: 165 NIPGIGERSLEEIKEALEKKGFTL 188



 Score = 50.7 bits (121), Expect = 3e-07
 Identities = 17/48 (35%), Positives = 22/48 (45%), Gaps = 3/48 (6%)

Query: 7  QELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSS 54
             +K           +       + EPL RGF  TLGN LRR+L+SS
Sbjct: 3  DSKLKAPVFTVR---TQGREYGEFVLEPLERGFGVTLGNPLRRILLSS 47


>1coo_A RNA polymerase alpha subunit; transcription regulation,
           nucleotidyl transferase; NMR {Escherichia coli K12} (A:)
          Length = 98

 Score =  107 bits (269), Expect = 2e-24
 Identities = 46/100 (46%), Positives = 69/100 (69%), Gaps = 3/100 (3%)

Query: 232 INFEEPKKEVKEDINVKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEAD 291
           ++  + ++   ++   +   F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE +
Sbjct: 1   MDLRDVREPEVKE---EKPEFDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVE 57

Query: 292 MLRMANFGRKSLVEIKGVLGTMGLFLGMNLPDWPPESIEE 331
           +L+  N G+KSL EIK VL + GL LGM L +WPP SI +
Sbjct: 58  LLKTPNLGKKSLTEIKDVLASRGLSLGMRLENWPPASIAD 97


>1lb2_B DNA-directed RNA polymerase alpha chain; protein-DNA
           complex, gene-regulatory, gene regulation/DNA complex;
           HET: CMP; 3.10A {Escherichia coli} (B:)
          Length = 84

 Score =  105 bits (264), Expect = 7e-24
 Identities = 46/80 (57%), Positives = 61/80 (76%)

Query: 252 FNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGVLG 311
           F+P LL+ V++LEL+VRS NCL+ E I Y+GDL+QRTE ++L+  N G+KSL EIK VL 
Sbjct: 4   FDPILLRPVDDLELTVRSANCLKAEAIHYIGDLVQRTEVELLKTPNLGKKSLTEIKDVLA 63

Query: 312 TMGLFLGMNLPDWPPESIEE 331
           + GL LGM L +WPP SI +
Sbjct: 64  SRGLSLGMRLENWPPASIAD 83


>3gfk_B DNA-directed RNA polymerase subunit alpha; protein-protein
           complex, cytoplasm, redox-active center, stress
           response, transcription; 2.30A {Bacillus subtilis} (B:)
          Length = 79

 Score = 87.8 bits (218), Expect = 2e-18
 Identities = 30/74 (40%), Positives = 43/74 (58%)

Query: 247 VKSLPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEI 306
            +       L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+
Sbjct: 5   KEEDQKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEV 64

Query: 307 KGVLGTMGLFLGMN 320
           K  L  +GL L  +
Sbjct: 65  KAKLEELGLGLRKD 78


>1z3e_B DNA-directed RNA polymerase alpha chain; bacterial
           transcription regulation, disulfide stress; 1.50A
           {Bacillus subtilis} (B:)
          Length = 73

 Score = 86.6 bits (215), Expect = 5e-18
 Identities = 30/71 (42%), Positives = 43/71 (60%)

Query: 250 LPFNPALLKKVEELELSVRSTNCLRGENIVYMGDLIQRTEADMLRMANFGRKSLVEIKGV 309
           +     L   +EEL+LSVRS NCL+   I  + +L  +TE DM+++ N GRKSL E+K  
Sbjct: 1   MEKEKVLEMTIEELDLSVRSYNCLKRAGINTVQELANKTEEDMMKVRNLGRKSLEEVKAK 60

Query: 310 LGTMGLFLGMN 320
           L  +GL L  +
Sbjct: 61  LEELGLGLRKD 71


>3iyd_A DNA-directed RNA polymerase subunit alpha; transcription,
           initiation, class I, activator, RNA polymerase,
           holoenzyme, sigma70, open complex, CAP, CRP,
           CAMP-dependent; HET: DNA CMP; 19.80A {Escherichia coli
           k-12} (A:1-48,A:181-246)
          Length = 114

 Score = 84.4 bits (209), Expect = 2e-17
 Identities = 20/65 (30%), Positives = 43/65 (66%)

Query: 180 IKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKK 239
           +++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++  + ++
Sbjct: 48  LERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDLRDVRQ 107

Query: 240 EVKED 244
              ++
Sbjct: 108 PEVKE 112



 Score = 64.7 bits (158), Expect = 2e-11
 Identities = 21/51 (41%), Positives = 29/51 (56%), Gaps = 3/51 (5%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLM 52
          +Q +  E +KP  ++     Q       +  EPL RGF HTLGNALRR+L+
Sbjct: 1  MQGSVTEFLKPRLVDIE---QVSSTHAKVTLEPLERGFGHTLGNALRRILL 48


>1bdf_A RNA polymerase alpha subunit; nucleotidyltransferase,
           assemble; 2.50A {Escherichia coli} (A:1-50,A:179-235)
          Length = 107

 Score = 82.8 bits (205), Expect = 6e-17
 Identities = 23/59 (38%), Positives = 41/59 (69%)

Query: 176 LYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINF 234
           L SP+++++Y VE+AR  Q  D DKL + ++T+G+I  E+++  A+ IL +QL  F++ 
Sbjct: 48  LSSPVERIAYNVEAARVEQRTDLDKLVIEMETNGTIDPEEAIRRAATILAEQLEAFVDL 106



 Score = 61.3 bits (149), Expect = 2e-10
 Identities = 22/53 (41%), Positives = 31/53 (58%), Gaps = 3/53 (5%)

Query: 2  IQKNWQELIKPNNIEYIVLGQEEENRTLMIAEPLPRGFAHTLGNALRRVLMSS 54
          +Q +  E +KP  ++   + Q       +  EPL RGF HTLGNALR +L+SS
Sbjct: 1  MQGSVTEFLKPRLVD---IEQVSSTHAKVTLEPLERGFGHTLGNALRAILLSS 50


>3fho_A ATP-dependent RNA helicase DBP5; mRNA export, ATPase,
           translation termination, ATP-binding, cytoplasm,
           hydrolase, membrane; 2.80A {Schizosaccharomyces pombe}
           (A:1-326)
          Length = 326

 Score = 27.8 bits (61), Expect = 1.9
 Identities = 13/69 (18%), Positives = 25/69 (36%), Gaps = 19/69 (27%)

Query: 283 DLIQRTEADMLRMANFGRKSLVEIKGVLGTMGL-----FLGMNLPD----------WPPE 327
           DL++R +   L   +     L E   +L   GL      +   LP           +   
Sbjct: 248 DLMKRRQ---LDARDIKVFVLDEADNMLDQQGLGDQSMRIKHLLPRNTQIVLFSATFSER 304

Query: 328 SIEELAKKY 336
            +E+ A+++
Sbjct: 305 -VEKYAERF 312


>2j9l_A Chloride channel protein 5; domain, membrane, transport, CBS
           domain, CLC, disease mutation, ION channel, ION
           transport, transmembrane; HET: ATP; 2.30A {Homo sapiens}
           (A:1-114)
          Length = 114

 Score = 27.9 bits (62), Expect = 2.0
 Identities = 8/129 (6%), Positives = 22/129 (17%), Gaps = 21/129 (16%)

Query: 99  DSHKRVTIFKRGPGVVTAGDIQTVNDIEVLNPDHVICNLDVDAVVRMELTVSKGHGYVPA 158
           ++ +          V+            +      +     D    +       +   P 
Sbjct: 2   EAKEEFAHKTLAMDVMKPRRNDP-LLTVLTQDSMTV----EDVETIIS---ETTYSGFPV 53

Query: 159 KHHRTENDPIGLITIDALYSPIKKVSYTVESAREGQVLDYDKLSMTIDTDGSITGEDSVA 218
              R     +G +    L                 +  D     +   +    T      
Sbjct: 54  VVSRESQRLVGFVLRRDLII---------SIENARKKQDG----VVSTSIIYFTEHSPPL 100

Query: 219 LASRILQDQ 227
                   +
Sbjct: 101 PPYTPPTLK 109


>1zau_A DNA ligase; AMP; HET: DNA AMP; 3.15A {Mycobacterium
          tuberculosis} (A:126-246)
          Length = 121

 Score = 27.9 bits (62), Expect = 2.1
 Identities = 11/47 (23%), Positives = 20/47 (42%), Gaps = 6/47 (12%)

Query: 57 GAAITAVQIDGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGD 99
          G A++ V  +G L   S+      G  ED+T     I  +  +++  
Sbjct: 1  GVALSLVYREGRLTRASTRGDGRTG--EDVTLNARTIADVPERLTPG 45


>2owo_A DNA ligase; protein/DNA complex, ligase/DNA complex; HET:
           DNA OMC AMP; 2.30A {Escherichia coli K12}
           (A:1-60,A:117-236)
          Length = 180

 Score = 27.5 bits (61), Expect = 2.7
 Identities = 17/70 (24%), Positives = 32/70 (45%), Gaps = 3/70 (4%)

Query: 57  GAAITAVQIDGVLHE-ISSIKGVH-EDLTDIILNIKGINLKMSGDSHKRVTIFKRGPGVV 114
           G A++ +  +GVL    +   G   ED+T  +  I+ I LK+ G++        RG   +
Sbjct: 62  GLAVSILYENGVLVSAATRGDGTTGEDITSNVRTIRAIPLKLHGENIPARLEV-RGEVFL 120

Query: 115 TAGDIQTVND 124
                + +N+
Sbjct: 121 PQAGFEKINE 130


>3jsl_A DNA ligase; NAD+-dependent, DNA damage, DNA repair, DNA
           replication, magnesium, manganese, metal-binding, NAD,
           zinc; HET: DNA; 1.80A {Staphylococcus aureus} PDB:
           3jsn_A* (A:115-227)
          Length = 113

 Score = 27.1 bits (60), Expect = 3.5
 Identities = 13/48 (27%), Positives = 23/48 (47%), Gaps = 4/48 (8%)

Query: 57  GAAITAVQIDGVLHEISSIKG---VHEDLTDIILNIKGINLKMSGDSH 101
           G A++   +DG   +  + +G     ED+T+ +  I  I LKM    +
Sbjct: 1   GLAVSLKYVDGYFVQGLT-RGDGTTGEDITENLKTIHAIPLKMKEPLN 47


>3h0g_C DNA-directed RNA polymerase II subunit RPB3; transcription,
           multi-protein complex, DNA- binding, magnesium; 3.65A
           {Schizosaccharomyces pombe} (C:1-38,C:171-297)
          Length = 165

 Score = 26.7 bits (59), Expect = 4.1
 Identities = 11/55 (20%), Positives = 26/55 (47%), Gaps = 2/55 (3%)

Query: 197 DYDKLSMTIDTDGSITGEDSVALASRILQDQLGMFINFEEPKKEVKEDINVKSLP 251
           +  +  M +++ GSI   + +    RILQ++L + +   +  +E    ++   L 
Sbjct: 93  EPRRFYMDVESVGSIPPNEIMVQGLRILQEKLAVLV--RDLDEEQPTQLSANELN 145


>3bac_A DNA ligase; adenylation domain, DNA damage, DNA repair, DNA
           replication, NAD; HET: DNA 3B9; 3.00A {Haemophilus
           influenzae} (A:56-173)
          Length = 118

 Score = 26.7 bits (59), Expect = 4.2
 Identities = 15/72 (20%), Positives = 32/72 (44%), Gaps = 7/72 (9%)

Query: 57  GAAITAVQIDGVLHEISS----IKGVHEDLTDIILNIKGINLKMSGDSHKRVTIFKRGPG 112
           G A++ + ++G L + ++      G  ED+T  I  I+ + L++  D+        RG  
Sbjct: 1   GLAVSILYVNGELTQAATRGDGTTG--EDITANIRTIRNVPLQLLTDNPPARLEV-RGEV 57

Query: 113 VVTAGDIQTVND 124
            +     + +N 
Sbjct: 58  FMPHAGFERLNK 69


>1ta8_A DNA ligase, NAD-dependent; nucleotidyl transferase fold;
          HET: DNA NMN; 1.80A {Enterococcus faecalis V583}
          (A:64-76,A:122-254)
          Length = 146

 Score = 25.6 bits (56), Expect = 8.8
 Identities = 9/43 (20%), Positives = 24/43 (55%), Gaps = 4/43 (9%)

Query: 57 GAAITAVQIDGVLHEISSIKG---VHEDLTDIILNIKGINLKM 96
          G AI+    +GV    ++ +G   V E++T+ +  ++ + +++
Sbjct: 15 GLAISLRYENGVFVRGAT-RGDGTVGENITENLRTVRSVPMRL 56


>1g8f_A Sulfate adenylyltransferase; alpha-beta protein,
           beta-barrel, rossmann-fold, kinase fold; 1.95A
           {Saccharomyces cerevisiae} (A:169-391)
          Length = 223

 Score = 25.7 bits (56), Expect = 8.9
 Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 2/27 (7%)

Query: 315 LFLGMNLPDW--PPESIEELAKKYEDK 339
           L +G  +P+W   PE ++ L +    +
Sbjct: 197 LRVGGEIPEWFSYPEVVKILRESNPPR 223


>1b04_A Protein (DNA ligase); DNA replication; 2.80A {Bacillus
          stearothermophilus} (A:117-248)
          Length = 132

 Score = 25.6 bits (56), Expect = 9.1
 Identities = 10/46 (21%), Positives = 23/46 (50%), Gaps = 4/46 (8%)

Query: 57 GAAITAVQIDGVLHEISSIKG---VHEDLTDIILNIKGINLKMSGD 99
          G A++    DG   + ++ +G     ED+T+ +  I+ + L++   
Sbjct: 1  GLAVSVRYEDGYFVQGAT-RGDGTTGEDITENLKTIRSLPLRLKEP 45


>1r6x_A ATP:sulfate adenylyltransferase; APS kinase-like domain;
           1.40A {Saccharomyces cerevisiae} (A:168-395)
          Length = 228

 Score = 25.8 bits (56), Expect = 9.3
 Identities = 7/27 (25%), Positives = 14/27 (51%), Gaps = 2/27 (7%)

Query: 315 LFLGMNLPDW--PPESIEELAKKYEDK 339
           L +G  +P+W   PE ++ L +    +
Sbjct: 197 LRVGGEIPEWFSYPEVVKILRESNPPR 223


  Database: mmdb70
    Posted date:  Jun 20, 2010  3:12 AM
  Number of letters in database: 4,956,049
  Number of sequences in database:  33,805
  
Lambda     K      H
   0.317    0.136    0.386 

Gapped
Lambda     K      H
   0.267   0.0623    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 33805
Number of Hits to DB: 2,535,118
Number of extensions: 114402
Number of successful extensions: 325
Number of sequences better than 10.0: 1
Number of HSP's gapped: 316
Number of HSP's successfully gapped: 37
Length of query: 340
Length of database: 4,956,049
Length adjustment: 89
Effective length of query: 251
Effective length of database: 1,947,404
Effective search space: 488798404
Effective search space used: 488798404
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 (25.2 bits)