RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780804|ref|YP_003065217.1| DNA polymerase III subunit
delta [Candidatus Liberibacter asiaticus str. psy62]
         (352 letters)



>1jr3_D DNA polymerase III, delta subunit; processivity, processivity
           clamp, clamp loader, AAA+ ATPase, transferase; HET: DNA;
           2.70A {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB:
           1jqj_C* 1xxh_A* 1xxi_A* 3glf_A* 3glg_A* 3glh_A* 3gli_A*
          Length = 343

 Score = 77.6 bits (190), Expect = 4e-15
 Identities = 41/316 (12%), Positives = 110/316 (34%), Gaps = 14/316 (4%)

Query: 1   MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNA 60
           M  +   +   +  + L      ++  G+D  L+ E  +  ++  +      F      +
Sbjct: 1   MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAA---AQGFEEHHTFS 54

Query: 61  LEIQKNISTFWNEINSTSLFSKKKIILIENLSTEK--KVLDCLEEIIIKNICNHIIIIKS 118
           ++   + +  ++   + SLF+ ++              + + L  +      + ++I++ 
Sbjct: 55  IDPNTDWNAIFSLCQAMSLFASRQTXXXXXPENGPNAAINEQLLTLTGLLHDDLLLIVRG 114

Query: 119 NEIKKNNTLRKIAEKFTSV-LAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANL 177
           N++ K            +  + ++C    +  L   +          +   A Q+L    
Sbjct: 115 NKLSKAQENAAWFTALANRSVQVTCQTPEQAQLPRWVAARAKQLNLELDDAANQVLCYCY 174

Query: 178 GGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLA 237
            G+ +A    L++LS     D  +T   V+  + D         ++A + GK   A+ + 
Sbjct: 175 EGNLLALAQALERLSLLW-PDGKLTLPRVEQAVNDAAHFTPFHWVDALLMGKSKRALHIL 233

Query: 238 DFFLASKMPSHALLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQES 297
                       LL    ++  LL  +       +     +  K    +   +R ++ E+
Sbjct: 234 QQLRLEGSEPVILLRTLQRELLLLVNLKRQSA--HTPLRALFDKH--RVWQNRRGMMGEA 289

Query: 298 LRIWNKNLVRETLHKI 313
           L   ++  +R+ +  +
Sbjct: 290 LNRLSQTQLRQAVQLL 305


>1jql_B DNA polymerase III, delta subunit; processivity clamp, clamp
           loader, DNA replication, AAA+ ATPase, transferase; HET:
           DNA; 2.50A {Escherichia coli} SCOP: c.37.1.20
          Length = 140

 Score = 36.1 bits (83), Expect = 0.011
 Identities = 15/145 (10%), Positives = 52/145 (35%), Gaps = 9/145 (6%)

Query: 1   MATIESHKFIQKSTKNLFLSHFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNA 60
           M  +   +   +  + L      ++  G+D  L+ E  +  ++  +      F      +
Sbjct: 1   MIRLYPEQLRAQLNEGL---RAAYLLLGNDPLLLQESQDAVRQVAA---AQGFEEHHTFS 54

Query: 61  LEIQKNISTFWNEINSTSLFSKKKIILIENLSTEK--KVLDCLEEIIIKNICNHIIIIKS 118
           ++   + +  ++   + SLF+ ++              + + L  +      + ++I++ 
Sbjct: 55  IDPNTDWNAIFSLCQAMSLFASRQTXXXXXPENGPNAAINEQLLTLTGLLHDDLLLIVRG 114

Query: 119 NEIKKNNTLRKIAEKFTSV-LAISC 142
           N++ K            +  + ++C
Sbjct: 115 NKLSKAQENAAWFTALANRSVQVTC 139


>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 = 33.4 bits (76), Expect = 0.089
 Identities = 23/157 (14%), Positives = 50/157 (31%), Gaps = 43/157 (27%)

Query: 112 HIIIIKSNEIKKNNTLRKIAEKFTSVL-------AISCYPDNKIHL----MDLIEESLLI 160
           H++++ +      + L+   E+F  +L       A    P     L    +  +   +  
Sbjct: 18  HVLLVPTASFFIASQLQ---EQFNKILPEPTEGFAADDEPTTPAELVGKFLGYVSSLVEP 74

Query: 161 GQKSISKEAKQILL-----ANLGGDRIASRNELQKLSSYCLEDILITEQHVKDIICDTHV 215
            +     +   + L       L G      N++  L++  L++   T    K++I +   
Sbjct: 75  SKVGQFDQVLNLCLTEFENCYLEG------NDIHALAAKLLQENDTTLVKTKELIKN--- 125

Query: 216 LYIEEIINATIQGKIYNAIMLADFFLASKMPSHALLH 252
            Y               A ++A      K  + AL  
Sbjct: 126 -Y-------------ITARIMAKRPF-DKKSNSALFR 147


>1jr3_A DNA polymerase III subunit gamma; processivity, processivity clamp,
           clamp loader, AAA+ ATPase, transferase; HET: DNA; 2.70A
           {Escherichia coli} SCOP: a.80.1.1 c.37.1.20 PDB: 1xxh_B*
           3glh_B* 3glf_B* 3gli_B* 3glg_B* 1xxi_B*
          Length = 373

 Score = 33.2 bits (75), Expect = 0.10
 Identities = 24/215 (11%), Positives = 68/215 (31%), Gaps = 10/215 (4%)

Query: 72  NEINSTSLFSKKKIILIENL-STEKKVLDCLEEIIIKNICNHIIIIKSNEIKK-NNTLRK 129
           + +       + K+ LI+ +    +   + L + + +   +   ++ + + +K   T+  
Sbjct: 109 DNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILS 168

Query: 130 IAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQ 189
              +F           +   +   +E  L     +    A Q+L     G    + +   
Sbjct: 169 RCLQFH------LKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTD 222

Query: 190 KLSSYCLEDILITEQHVKDIICDTHVLYIEEIINATIQGKIYNAIMLADFFLASKMPSHA 249
           +  +    D  ++ Q V  ++          ++ A ++      + L +   A  +   A
Sbjct: 223 QAIASG--DGQVSTQAVSAMLGTLDDDQALSLVEAMVEANGERVMALINEAAARGIEWEA 280

Query: 250 LLHGFLQKFQLLEKIHIIKECSNISFEKIIQKTEK 284
           LL   L     +  + +           I  +  +
Sbjct: 281 LLVEMLGLLHRIAMVQLSPAALGNDMAAIELRMRE 315


>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 = 32.7 bits (73), Expect = 0.13
 Identities = 9/33 (27%), Positives = 18/33 (54%), Gaps = 9/33 (27%)

Query: 283 EKNIIPMKRNILQESLRIWNKN----L-VRETL 310
           EK    +K+  LQ SL+++  +    L ++ T+
Sbjct: 18  EKQ--ALKK--LQASLKLYADDSAPALAIKATM 46


>1njg_A DNA polymerase III subunit gamma; rossman-like fold, AAA+ ATPase
           domains, sensor 1, sensor 2, transferase; HET: DNA;
           2.20A {Escherichia coli} SCOP: c.37.1.20 PDB: 1njf_A*
          Length = 250

 Score = 30.8 bits (69), Expect = 0.43
 Identities = 16/141 (11%), Positives = 48/141 (34%), Gaps = 10/141 (7%)

Query: 72  NEINSTSLFSKKKIILIENL-STEKKVLDCLEEIIIKNICNHIIIIKSNEIKK-NNTLRK 129
           + +       + K+ LI+ +    +   + L + + +   +   ++ + + +K   T+  
Sbjct: 116 DNVQYAPARGRFKVYLIDEVHMLSRHSFNALLKTLEEPPEHVKFLLATTDPQKLPVTILS 175

Query: 130 IAEKFTSVLAISCYPDNKIHLMDLIEESLLIGQKSISKEAKQILLANLGGDRIASRNELQ 189
              +F           +   +   +E  L     +    A Q+L     G    + +   
Sbjct: 176 RCLQFH------LKALDVEQIRHQLEHILNEEHIAHEPRALQLLARAAEGSLRDALSLTD 229

Query: 190 KLSSYCLEDILITEQHVKDII 210
           +  +    D  ++ Q V  ++
Sbjct: 230 QAIASG--DGQVSTQAVSAML 248


>3ikm_A DNA polymerase subunit gamma-1; human mitochondrial DNA polymerase,
           disease mutation, DNA replication, DNA-binding,
           DNA-directed DNA polymerase; HET: DNA; 3.24A {Homo
           sapiens}
          Length = 1172

 Score = 30.3 bits (68), Expect = 0.76
 Identities = 12/45 (26%), Positives = 20/45 (44%), Gaps = 3/45 (6%)

Query: 158 LLIGQKSISKEAKQILLANLGGDRIASRNELQKLSSYCLEDILIT 202
           L +G   + KE +++ +    G     R   Q L  YC +D+  T
Sbjct: 295 LYVGGPPLEKEPRELFVK---GTMKDIRENFQDLMQYCAQDVWAT 336


>1lox_A 15-lipoxygenase, 15LOX; oxidoreductase, 15LO_depot2; HET: RS7;
           2.40A {Oryctolagus cuniculus} SCOP: a.119.1.2 b.12.1.1
           PDB: 2p0m_A*
          Length = 662

 Score = 29.2 bits (65), Expect = 1.3
 Identities = 17/88 (19%), Positives = 35/88 (39%), Gaps = 7/88 (7%)

Query: 26  FYGSDKGLIFELINQF-KKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTSLFSKKK 84
           FY  D   ++E+I+++ +  + + Y       V + LE+Q    ++  EI    L   +K
Sbjct: 459 FYAQDALRLWEIISRYVQGIMGLYYKTD--EAVRDDLELQ----SWCREITEIGLQGAQK 512

Query: 85  IILIENLSTEKKVLDCLEEIIIKNICNH 112
                +L +  +    +   I      H
Sbjct: 513 QGFPTSLQSVAQACHFVTMCIFTCTGQH 540


>3ckj_A Putative uncharacterized protein; mycobacteria, unknown function;
           HET: CIT; 1.80A {Mycobacterium paratuberculosis} PDB:
           3ckn_A* 3cko_A* 3ckq_A* 3ckv_A* 3e26_A 3e25_A
          Length = 329

 Score = 29.1 bits (64), Expect = 1.4
 Identities = 13/103 (12%), Positives = 33/103 (32%)

Query: 56  VVLNALEIQKNISTFWNEINSTSLFSKKKIILIENLSTEKKVLDCLEEIIIKNICNHIII 115
           VVL AL+ +  I +  + I+        ++I++++ ST+   +  +            + 
Sbjct: 52  VVLPALDEEDTIGSVIDSISPLVDGLVDELIVLDSGSTDDTEIRAVAAGARVVSREQALP 111

Query: 116 IKSNEIKKNNTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESL 158
                  K   L +        + +    D        +   +
Sbjct: 112 EVPIRPGKGEALWRSLAASRGDIVVFVDSDLINPHPMFVPWLV 154


>3k7l_A Atragin; SVMP, metalloprotease, hydrolase; HET: NAG; 2.50A {Naja
          atra}
          Length = 422

 Score = 28.7 bits (63), Expect = 1.9
 Identities = 15/58 (25%), Positives = 26/58 (44%), Gaps = 4/58 (6%)

Query: 21 HFVFIFYGSDKGLIFELINQFKKNISITYHDPFSLVVLNALEIQKNISTFWNEINSTS 78
          + ++  Y  D+ +I   + +    +++ Y      + L  LEI  NI    NEIN  S
Sbjct: 24 NIMYRHYKRDQPVIKRKVYEMINTMNMIYRRLNFHIALIGLEIWSNI----NEINVQS 77


>3g5c_A ADAM 22; alpha/beta fold, cross-linked domain, alternative
          splicing, cell adhesion, cleavage on PAIR of basic
          residues, EGF-like domain; HET: NAG; 2.36A {Homo
          sapiens}
          Length = 510

 Score = 27.7 bits (60), Expect = 4.3
 Identities = 9/59 (15%), Positives = 16/59 (27%), Gaps = 5/59 (8%)

Query: 21 HFVFIFYGSDKGLIFELINQFKKNISITYHDPFSL-VVLNALEIQKNISTFWNEINSTS 78
          H +F  +                   + Y D     +VL A+E         N+   + 
Sbjct: 17 HLMFKKHRLSVVHTNTYAKSVVNMADLIYKDQLKTRIVLVAMETWATD----NKFAISE 71


>2pt0_A MYO-inositol hexaphosphate phosphohydrolase; PTP, protein tyrosine
           phosphatase, phytase, P-loop, cysteine-sulfonic acid,
           oxidized thiol.; 1.70A {Selenomonas ruminantium} SCOP:
           c.45.1.4 PDB: 2psz_A 3d1h_A 3d1o_A 3d1q_A 1u24_A 1u25_A*
           1u26_A* 2b4o_A 2b4p_A 2b4u_A
          Length = 340

 Score = 27.2 bits (60), Expect = 5.2
 Identities = 16/92 (17%), Positives = 31/92 (33%), Gaps = 6/92 (6%)

Query: 137 VLAISCYPDNKIHLMDLIEESLL-IGQKSISKEAKQILLANLGGDRIASRNELQKLSSYC 195
              +       I+ +DL +ES   +    +S   ++   ANLG     S++E      + 
Sbjct: 111 AAKLREKTAGPIYDVDLRQESHGYLDGIPVSWYGER-DWANLGK----SQHEALADERHR 165

Query: 196 LEDILITEQHVKDIICDTHVLYIEEIINATIQ 227
           L   L    ++  +         E      +Q
Sbjct: 166 LHAALHKTVYIAPLGKHKLPEGGEVRRVQKVQ 197


>1l5w_A Maltodextrin phosphorylase; enzymatic catalysis, substrate complex,
           transferase; HET: GLC PLP; 1.80A {Escherichia coli}
           SCOP: c.87.1.4 PDB: 1l5v_A* 1l6i_A* 2asv_A* 2av6_A*
           2aw3_A* 2azd_A* 1qm5_A* 1e4o_A* 2ecp_A* 1ahp_A*
          Length = 796

 Score = 26.9 bits (59), Expect = 6.9
 Identities = 23/136 (16%), Positives = 47/136 (34%), Gaps = 24/136 (17%)

Query: 213 THVLYIEEIINA-----TIQGKIYNAIMLADFFLASKMPSHALLHGFLQK---------- 257
           T VLY  +          +Q     A  +AD  L     +   LH               
Sbjct: 252 TKVLYPNDNAFEGKKLRLMQQYFQCACSVADI-LRRHHLAGRKLHELADYEVIQLNDTHP 310

Query: 258 -FQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVR-------ET 309
              + E + ++ +   +S++     T K        ++ E+L  W+  LV+       + 
Sbjct: 311 TIAIPELLRVLIDEHQMSWDDAWAITSKTFAYTNHTLMPEALERWDVKLVKGLLPRHMQI 370

Query: 310 LHKIDHRIHLARKKKY 325
           +++I+ R     +K +
Sbjct: 371 INEINTRFKTLVEKTW 386


>2gj4_A Glycogen phosphorylase, muscle form; transferase; HET: PLR 2TH;
           1.60A {Oryctolagus cuniculus} SCOP: c.87.1.4 PDB:
           2gm9_A* 1abb_A* 2pyi_A* 2pyd_A* 2qnb_A* 1c8l_A* 1axr_A*
           1gpy_A* 1e1y_A* 1lwo_A* 1pyg_A* 1uzu_A* 1lwn_A* 1xkx_A*
           1xl0_A* 1xl1_A* 1z62_A* 2amv_A* 2f3p_A* 2f3q_A* ...
          Length = 824

 Score = 26.5 bits (58), Expect = 8.1
 Identities = 11/62 (17%), Positives = 26/62 (41%)

Query: 258 FQLLEKIHIIKECSNISFEKIIQKTEKNIIPMKRNILQESLRIWNKNLVRETLHKIDHRI 317
             + E + ++ +   + ++K  + T K        +L E+L  W  +L+   L +    I
Sbjct: 333 LAIPELMRVLVDLERLDWDKAWEVTVKTCAYTNHTVLPEALERWPVHLLETLLPRHLQII 392

Query: 318 HL 319
           + 
Sbjct: 393 YE 394


>2wl2_A GYRA, DNA gyrase subunit A; isomerase, aminocoumarin antibiotic,
           drug target, protein-ligand complex; HET: DNA SM8; 2.62A
           {Escherichia coli} PDB: 1ab4_A 1x75_A*
          Length = 522

 Score = 26.4 bits (58), Expect = 9.8
 Identities = 19/124 (15%), Positives = 42/124 (33%), Gaps = 13/124 (10%)

Query: 101 LEEIIIKNICNHIIIIKSNEIKKN--NTLRKIAEKFTSVLAISCYPDNKIHLMDLIEESL 158
              + + NI   I +I+           L     +  +V A+     +     + +E   
Sbjct: 381 ALAVALANIDPIIELIRHAPTPAEAKTALVANPWQLGNVAAMLERAGDDAARPEWLEPEF 440

Query: 159 LIGQKSIS---KEAKQIL------LANLGGDRI-ASRNELQKLSSYCLEDILITEQHVKD 208
            +         ++A+ IL      L  L  +++     EL    +  L  IL +   + +
Sbjct: 441 GVRDGLYYLTEQQAQAILDLRLQKLTGLEHEKLLDEYKELLDQIAE-LLRILGSADRLME 499

Query: 209 IICD 212
           +I +
Sbjct: 500 VIRE 503


  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
   0.323    0.137    0.386 

Gapped
Lambda     K      H
   0.267   0.0686    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,972,961
Number of extensions: 141657
Number of successful extensions: 460
Number of sequences better than 10.0: 1
Number of HSP's gapped: 458
Number of HSP's successfully gapped: 42
Length of query: 352
Length of database: 5,693,230
Length adjustment: 93
Effective length of query: 259
Effective length of database: 3,438,538
Effective search space: 890581342
Effective search space used: 890581342
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 57 (25.8 bits)