RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780472|ref|YP_003064885.1| cytochrome o ubiquinol oxidase
subunit III [Candidatus Liberibacter asiaticus str. psy62]
         (210 letters)



>1fft_C Ubiquinol oxidase; electron transport, cytochrome oxidase, membrane
           protein, oxidoreductase; HET: HEM HEO; 3.50A
           {Escherichia coli} SCOP: f.25.1.1
          Length = 204

 Score =  125 bits (315), Expect = 7e-30
 Identities = 96/184 (52%), Positives = 125/184 (67%), Gaps = 1/184 (0%)

Query: 27  HDGTYLGFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSL 86
                 GFWIYLMSDC++F++ F TYAVL    A GP   D+F++  + V T +LL SS+
Sbjct: 22  GGTKIFGFWIYLMSDCILFSILFATYAVLVNGTAGGPTGKDIFELPFVLVETFLLLFSSI 81

Query: 87  SCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFF 146
           +   A +A        + +SWL +T  FG  FI MEIYEF HLI     P RS FLS+FF
Sbjct: 82  TYGMAAIAMYKNN-KSQVISWLALTWLFGAGFIGMEIYEFHHLIVNGMGPDRSGFLSAFF 140

Query: 147 ALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFSFVYL 206
           ALVG HGLHV  GLIW+ VL++QI ++GL S N+ R++CLS+FWHFLD++WICVF+ VYL
Sbjct: 141 ALVGTHGLHVTSGLIWMAVLMVQIARRGLTSTNRTRIMCLSLFWHFLDVVWICVFTVVYL 200

Query: 207 MGVV 210
           MG +
Sbjct: 201 MGAM 204


>1qle_C Cytochrome C oxidase polypeptide III; oxidoreductase/immune system,
           complex (oxidoreductase/antibody), electron transport;
           HET: HEA PC1; 3.0A {Paracoccus denitrificans} SCOP:
           f.25.1.1
          Length = 273

 Score = 97.4 bits (242), Expect = 2e-21
 Identities = 47/188 (25%), Positives = 90/188 (47%), Gaps = 14/188 (7%)

Query: 32  LGFWIYLMSDCLMFAVFFVTYAVLGKNYAAG----------PAPIDVFDISGI-FVSTIV 80
            GF +++MS+ + F  +F  +                    P  I  FD   +  ++T++
Sbjct: 88  YGFILFIMSEVMFFVAWFWAFIKNALYPMGPDSPIKDGVWPPEGIVTFDPWHLPLINTLI 147

Query: 81  LLLSSLSCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSA 140
           LLLS ++ ++A  A   +     T++ L+V    G+ F  ++ YE++H          + 
Sbjct: 148 LLLSGVAVTWAHHAFVLEGDRKTTINGLIVAVILGVCFTGLQAYEYSHAAFG---LADTV 204

Query: 141 FLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICV 200
           +  +F+   G HG HV  G I+LFV +I++LK  +           + +WHF+D++W+ +
Sbjct: 205 YAGAFYMATGFHGAHVIIGTIFLFVCLIRLLKGQMTQKQHVGFEAAAWYWHFVDVVWLFL 264

Query: 201 FSFVYLMG 208
           F  +Y+ G
Sbjct: 265 FVVIYIWG 272


>1m56_C Cytochrome C oxidase; membrane protein, oxidoreductase; HET: HEA
           PEH; 2.30A {Rhodobacter sphaeroides} SCOP: f.25.1.1 PDB:
           1m57_C*
          Length = 266

 Score = 95.1 bits (236), Expect = 9e-21
 Identities = 43/191 (22%), Positives = 86/191 (45%), Gaps = 14/191 (7%)

Query: 29  GTYLGFWIYLMSDCLMFAVFFVTYAVLGKNYAAGPAP----------IDVFDISGI-FVS 77
           G   GF +++MS+ + F+ +F ++           +P          I  FD   +  ++
Sbjct: 78  GLRWGFILFIMSEVMFFSAWFWSFFKHALYPMGPESPIIDGIFPPEGIITFDPWHLPLIN 137

Query: 78  TIVLLLSSLSCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQ 137
           T++LL S  + ++A  A   +         L +    G +F + + YE++H         
Sbjct: 138 TLILLCSGCAATWAHHALVHENNRRDVAWGLALAIALGALFTVFQAYEYSH---AAFGFA 194

Query: 138 RSAFLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIW 197
            + + ++FF   G HG HV  G I+L V +I++ +                +WHF+D++W
Sbjct: 195 GNIYGANFFMATGFHGFHVIVGTIFLLVCLIRVQRGHFTPEKHVGFEAAIWYWHFVDVVW 254

Query: 198 ICVFSFVYLMG 208
           + +F+ +Y+ G
Sbjct: 255 LFLFASIYIWG 265


>1v54_C Cytochrome C oxidase polypeptide III; oxidoreductase; HET: FME TPO
           HEA TGL PGV CHD CDL PEK PSC DMU; 1.80A {Bos taurus}
           SCOP: f.25.1.1 PDB: 1v55_C* 2dyr_C* 2eij_C* 2eik_C*
           2eil_C* 2eim_C* 2ein_C* 2zxw_C* 2occ_C* 1oco_C* 1occ_C*
           1ocz_C* 1ocr_C* 2dys_C*
          Length = 261

 Score = 84.3 bits (208), Expect = 2e-17
 Identities = 40/186 (21%), Positives = 72/186 (38%), Gaps = 9/186 (4%)

Query: 29  GTYLGFWIYLMSDCLMFAVFF------VTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLL 82
           G   G  ++++S+ L F  FF                   P  I   +   + +    +L
Sbjct: 78  GLRYGMILFIISEVLFFTGFFWAFYHSSLAPTPELGGCWPPTGIHPLNPLEVPLLNTSVL 137

Query: 83  LSSLSCSFAMLASATKRLIHKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFL 142
           L+S         S  +      +  L +T   G+ F +++  E+              + 
Sbjct: 138 LASGVSITWAHHSLMEGDRKHMLQALFITITLGVYFTLLQASEYYE---APFTISDGVYG 194

Query: 143 SSFFALVGLHGLHVFFGLIWLFVLVIQILKKGLISGNQRRLICLSMFWHFLDLIWICVFS 202
           S+FF   G HGLHV  G  +L V   + LK    S +       + +WHF+D++W+ ++ 
Sbjct: 195 STFFVATGFHGLHVIIGSTFLIVCFFRQLKFHFTSNHHFGFEAAAWYWHFVDVVWLFLYV 254

Query: 203 FVYLMG 208
            +Y  G
Sbjct: 255 SIYWWG 260


>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 = 29.5 bits (66), Expect = 0.55
 Identities = 20/136 (14%), Positives = 42/136 (30%), Gaps = 51/136 (37%)

Query: 4   QKIGKSP-NFSLFYVK--------DKKESCVDHDGTYLGFWIYLMS---DC-----LMFA 46
            ++ ++  +    + +        +   +  D D        YL+S    C     +  A
Sbjct: 196 SELIRTTLDAEKVFTQGLNILEWLENPSNTPDKD--------YLLSIPISCPLIGVIQLA 247

Query: 47  VFFVTYAVLGKNYAAGPAPIDVFD-IS-------GIFVSTIVLLLSSLSCSFAMLASATK 98
            + VT  +LG        P ++   +        G+  +  +    S   SF +      
Sbjct: 248 HYVVTAKLLGFT------PGELRSYLKGATGHSQGLVTAVAIAETDSWE-SFFVSV---- 296

Query: 99  RLIHKTVSWLLVTAFF 114
               K ++ L    FF
Sbjct: 297 ---RKAITVL----FF 305



 Score = 29.1 bits (65), Expect = 0.80
 Identities = 31/209 (14%), Positives = 55/209 (26%), Gaps = 96/209 (45%)

Query: 1   MSRQKIGKSPNFSLF-YVKDKKESCVDHDGTYLGFWIYLMSDCLMFAVF----------- 48
           M+++   K  N +LF  V +                        + A+F           
Sbjct: 132 MAKRPFDKKSNSALFRAVGEGNAQ--------------------LVAIFGGQGNTDDYFE 171

Query: 49  -----FVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSFAMLASATKRLIHK 103
                + TY VL            V D     +      LS L           +++  +
Sbjct: 172 ELRDLYQTYHVL------------VGD----LIKFSAETLSELI----RTTLDAEKVFTQ 211

Query: 104 ---TVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSF---FALVGLHGL-HV 156
               + WL                   +       P +  +L S      L+G+  L H 
Sbjct: 212 GLNILEWL------------------ENP---SNTPDK-DYLLSIPISCPLIGVIQLAH- 248

Query: 157 FFGLIWLFVLVIQILKKGLISGNQRRLIC 185
                  +V+  ++L  G   G  R  + 
Sbjct: 249 -------YVVTAKLL--GFTPGELRSYLK 268



 Score = 25.7 bits (56), Expect = 8.0
 Identities = 8/33 (24%), Positives = 12/33 (36%), Gaps = 11/33 (33%)

Query: 94  ASATKRLI----HKTVSWLLVTAF-------FG 115
            S ++R++       V W   T F       FG
Sbjct: 473 GSISERIVDCIIRLPVKWETTTQFKATHILDFG 505


>2pff_A Fatty acid synthase subunit alpha, 3-oxoacyl-[acyl-carrier-; fatty
            acid synthase, acyl-carrier-protein, beta-ketoacyl
            reductase, beta-ketoacyl synthase, dehydratase; 4.00A
            {Saccharomyces cerevisiae}
          Length = 1688

 Score = 27.5 bits (60), Expect = 2.4
 Identities = 8/19 (42%), Positives = 12/19 (63%)

Query: 162  WLFVLVIQILKKGLISGNQ 180
            W+    +QIL  G+I GN+
Sbjct: 1392 WMMNGALQILNSGIIPGNR 1410


>2r9r_B Paddle chimera voltage gated potassium channel KV1.2-KV2.1; voltage
           sensor, voltage dependent, ION channel, shaker, membrane
           protein; HET: NAP PGW; 2.40A {Rattus norvegicus} PDB:
           2a79_B*
          Length = 514

 Score = 27.1 bits (59), Expect = 3.0
 Identities = 19/143 (13%), Positives = 47/143 (32%), Gaps = 10/143 (6%)

Query: 66  IDVFDISGIFVSTIVLLLSSLSC-----SFAMLASATKRLIHKTVSWLLVTAFFGMIFII 120
           I +  +  I +S +   L +L               T     ++      +  F   F I
Sbjct: 184 IAIVSVMVILISIVSFCLETLPIFRDENEDMHGGGVTFHTYSQSTIGYQQSTSFTDPFFI 243

Query: 121 ME-----IYEFAHLISMEAVPQRSAFLSSFFALVGLHGLHVFFGLIWLFVLVIQILKKGL 175
           +E      + F  L+   A P ++ F ++   ++ +  +  ++  I+L      +L+   
Sbjct: 244 VETLCIIWFSFEFLVRFFACPSKAGFFTNIMNIIDIVAIIPYYVTIFLTESNKSVLQFQN 303

Query: 176 ISGNQRRLICLSMFWHFLDLIWI 198
           +    +    + +   F      
Sbjct: 304 VRRVVQIFRIMRILRIFKLSRHS 326


>1b22_A DNA repair protein RAD51; DNA binding, riken structural
          genomics/proteomics initiative, RSGI, structural
          genomics; HET: DNA; NMR {Homo sapiens} SCOP: a.60.4.1
          Length = 114

 Score = 26.4 bits (58), Expect = 5.4
 Identities = 10/38 (26%), Positives = 17/38 (44%)

Query: 62 GPAPIDVFDISGIFVSTIVLLLSSLSCSFAMLASATKR 99
          GP PI   +  GI  + +  L  +   +   +A A K+
Sbjct: 21 GPQPISRLEQCGINANDVKKLEEAGFHTVEAVAYAPKK 58


>1mhs_A Proton pump, plasma membrane ATPase; ION transport, membrane
           protein, P-type ATPase, active transport, cryo-electron
           microscopy; 8.00A {Neurospora crassa} SCOP: i.18.1.1
          Length = 920

 Score = 25.8 bits (56), Expect = 6.5
 Identities = 20/130 (15%), Positives = 40/130 (30%), Gaps = 25/130 (19%)

Query: 43  LMFAVFFVTYAVLGKNYAAGPAPIDVFDISGIFVSTIVLLLSSLSCSFAMLASATKR-LI 101
           ++    ++T   +   YA G     V +   +    ++ L  SL+ ++ +  +       
Sbjct: 765 VLAVGTWITVTTM---YAQGENGGIVQNFGNM--DEVLFLQISLTENWLIFITRANGPFW 819

Query: 102 HKTVSWLLVTAFFGMIFIIMEIYEFAHLISMEAVPQRSAFLSSFFALVGLHGLHVFFGLI 161
               SW L  A F +  +                     F  S  ++V           I
Sbjct: 820 SSIPSWQLSGAIFLVDILAT------------CFTIWGWFEHSDTSIVA-------VVRI 860

Query: 162 WLFVLVIQIL 171
           W+F   I  +
Sbjct: 861 WIFSFGIFCI 870


  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
   0.335    0.146    0.465 

Gapped
Lambda     K      H
   0.267   0.0455    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 1,792,869
Number of extensions: 74598
Number of successful extensions: 315
Number of sequences better than 10.0: 1
Number of HSP's gapped: 305
Number of HSP's successfully gapped: 42
Length of query: 210
Length of database: 5,693,230
Length adjustment: 88
Effective length of query: 122
Effective length of database: 3,559,758
Effective search space: 434290476
Effective search space used: 434290476
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 39 (21.6 bits)
S2: 54 (25.3 bits)