RPS-BLAST 2.2.22 [Sep-27-2009]

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

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

Query= gi|254780868|ref|YP_003065281.1| birA bifunctional protein
[Candidatus Liberibacter asiaticus str. psy62]
         (252 letters)



>3bfm_A Biotin protein ligase-like protein of unknown function;
           YP_612389.1, structural genomics, joint center for
           structural genomics, JCSG; HET: 2PE; 1.70A {Silicibacter
           SP}
          Length = 235

 Score =  121 bits (305), Expect = 1e-28
 Identities = 35/225 (15%), Positives = 68/225 (30%), Gaps = 10/225 (4%)

Query: 32  RALSGDLGNLWIVASCQTAGRGRRDNKWISDKGNLYASLLLIDSISKDSLTLLSFAIAVA 91
            A         +       G       +      L A+L+L   +       +     V 
Sbjct: 15  EAAGPGQDPFDLACQKAELGVDAGLVVYELGTDVLRAALVLAPEVPLAKAMAMLPVCGVG 74

Query: 92  MRSVIASTLPVGTDVKIKWPNDILVFQRKIAGILIETLNLKNGLQA--VVVGIGLNVKHC 149
            ++ + +  P    V + W   + +   +   + I         Q   +VVG+ L +   
Sbjct: 75  FQNALGALAPPEVAVHLDWNGALRINGARCGRLRIAASTDDPDTQPDWLVVGLDLPLWPE 134

Query: 150 PVDTP-YPVTSLQRE-GGCIDLKDIFSLLFQDVARVLDLWKKDTGREEIMNLWRCFACGI 207
                    T+L  E    +    +     +     ++    +   E I   WR  A G+
Sbjct: 135 GDGGETPDETALYAEGCADVAAPRLLESWARHCLHWIN-RWDEGELETIHGEWRGLAHGM 193

Query: 208 GDLITIKLSYGSILGRFVGVDDFGYLLLEEKKGCVRQIFTGDIFT 252
           G+  T         G F+GVD+   +LL ++      I    +  
Sbjct: 194 GEARTEA----GRSGTFLGVDEDFGMLLRDETT-THLIPLTTVLV 233


>2ej9_A Putative biotin ligase; biotin biosynthesis, monomer, X-RAY
           diffraction, structural genomics, NPPSFA; HET: BTN;
           2.00A {Methanocaldococcus jannaschii}
          Length = 237

 Score =  110 bits (276), Expect = 3e-25
 Identities = 61/240 (25%), Positives = 104/240 (43%), Gaps = 16/240 (6%)

Query: 18  FFDTISSTNDECMKRALSGDLGNLWIVASCQTAGRGRRDNKWISDKGNLYASLLLIDSIS 77
               I STND   + A  G      ++A  Q  G+GR    W SD+G LY S++L   + 
Sbjct: 5   HLSEIDSTNDYAKELAKEGKRN-FIVLADKQNNGKGRWGRVWYSDEGGLYFSMVLDSKLY 63

Query: 78  KDSLTLLSFAIAVAMRSVIASTLPVGTDVKIKWPNDILV----FQRKIAGILIETLNLKN 133
              +  L   I +           V  ++ +K+PNDI+V      +K+ GIL E   L +
Sbjct: 64  NPKVINLLVPICIIE----VLKNYVDKELGLKFPNDIMVKVNDNYKKLGGILTE---LTD 116

Query: 134 GLQAVVVGIGLNVKHCPVDTPYPVTSLQREGGCIDLKDIFSLLFQDVARVLDLWK-KDTG 192
               + +GI +N +         ++  +  G  +D  +I S   +     L+  K K+  
Sbjct: 117 DYMIIGIGINVNNQIRNEIREIAISLKEITGKELDKVEILSNFLKTFESYLEKLKNKEID 176

Query: 193 REEIMNLWRCFACGIGDLITIKLSYGSIL-GRFVGVDDFGYLLLEEKKGCVRQIFTGDIF 251
             EI+  ++ ++  IG  + I LS   I+ G+   +D  G +L  EK   + +I +G   
Sbjct: 177 DYEILKKYKKYSITIGKQVKILLSNNEIITGKVYDIDFDGIVLGTEKG--IERIPSGICI 234


>1bia_A BIRA bifunctional protein; transcription regulation; 2.30A
           {Escherichia coli} SCOP: a.4.5.1 b.34.1.1 d.104.1.2 PDB:
           1bib_A* 1hxd_A* 2ewn_A*
          Length = 321

 Score =  109 bits (272), Expect = 7e-25
 Identities = 61/247 (24%), Positives = 104/247 (42%), Gaps = 9/247 (3%)

Query: 8   CQNPYSFRYEFFDTISSTNDECMKRALSGDLGNLWIVASCQTAGRGRRDNKWISDKG-NL 66
                         I STN   + R      G+   +A  Q AGRGRR  KW S  G NL
Sbjct: 73  LGQLDGGSVAVLPVIDSTNQYLLDRIGELKSGD-ACIAEYQQAGRGRRGRKWFSPFGANL 131

Query: 67  YASLLLIDSISKDSLTLLSFAIAVAMRSVIASTLPVGTDVKIKWPNDILVFQRKIAGILI 126
           Y S+         +      ++ + +             V++KWPND+ +  RK+AGIL+
Sbjct: 132 YLSMFWRLEQGPAAAI--GLSLVIGIVMAEVLRKLGADKVRVKWPNDLYLQDRKLAGILV 189

Query: 127 ETLNLKNGLQAVVVGIGLNVKHCPVDTP---YPVTSLQREGGCIDLKDIFSLLFQDVARV 183
           E          +V+G G+N+    V+         +LQ  G  +D   + ++L +++   
Sbjct: 190 ELTGKTGDAAQIVIGAGINMAMRRVEESVVNQGWITLQEAGINLDRNTLAAMLIRELRAA 249

Query: 184 LDLWKKDTGREEIMNLWRCFACGIGDLITIKLSYGSILGRFVGVDDFGYLLLEEKKGCVR 243
           L+L++++ G    ++ W      I   + + +    I G   G+D  G LLLE+    ++
Sbjct: 250 LELFEQE-GLAPYLSRWEKLDNFINRPVKLIIGDKEIFGISRGIDKQGALLLEQDGI-IK 307

Query: 244 QIFTGDI 250
               G+I
Sbjct: 308 PWMGGEI 314


>2cgh_A Biotin ligase; 1.8A {Mycobacterium tuberculosis}
          Length = 268

 Score =  104 bits (260), Expect = 2e-23
 Identities = 64/243 (26%), Positives = 106/243 (43%), Gaps = 14/243 (5%)

Query: 14  FRYEFFDTISSTNDECMKRALSGDLGN-LWIVASCQTAGRGRRDNKWISDKG-NLYASLL 71
            + +      STN + + RA SG   + + ++A  QTAGRGR    W +     +  S+ 
Sbjct: 30  RQLDVVAQTGSTNADLLARAASGADIDGVVLIAEHQTAGRGRHGRGWAATARAQIILSVG 89

Query: 72  L-IDSISKDSLTLLSFAIAVAMRSVIASTLPVGTD-VKIKWPNDILVFQRKIAGILIETL 129
           + +  +   +   LS A  +A+   +A  + V      +KWPND+L    K+AGIL E  
Sbjct: 90  VRVVDVPVQAWGWLSLAAGLAVLDSVAPLIAVPPAETGLKWPNDVLARGGKLAGILAEVA 149

Query: 130 NLKNGLQAVVVGIGLNVKHCP-VDTPYPVTSLQREGGCIDLKDIFSLLFQDVARVLDLWK 188
                   VV+G+GLNV   P    P   + L       D   I S L +++   +  W 
Sbjct: 150 Q-----PFVVLGVGLNVTQAPEEVDPDATSLLDLGVAAPDRNRIASRLLRELEARIIQW- 203

Query: 189 KDTGREEIMNLWRCFACGIGDLITIKLSYG-SILGRFVGVDDFGYLLLEEKKGCVRQIFT 247
                 ++   +R  +  IG  + ++L  G  ++G    +DD G L L +  G    +  
Sbjct: 204 -RNANPQLAADYRARSLTIGSRVRVELPGGQDVVGIARDIDDQGRLCL-DVGGRTVVVSA 261

Query: 248 GDI 250
           GD+
Sbjct: 262 GDV 264


>2eay_A Biotin [acetyl-COA-carboxylase] ligase; biotin biosynthesis, dimer,
           X-RAY diffraction, structural genomics, NPPSFA; 1.95A
           {Aquifex aeolicus} PDB: 3efs_A* 3fjp_A 3efr_A*
          Length = 233

 Score =  101 bits (251), Expect = 2e-22
 Identities = 54/233 (23%), Positives = 97/233 (41%), Gaps = 11/233 (4%)

Query: 18  FFDTISSTNDECMKRALSGDLGNLWIVASCQTAGRGRRDNKWISDKGNLYASLLLIDSIS 77
           +   + ST +   +  +S       +VA  QT GRGR   KW+S +G LY S LL     
Sbjct: 7   WLKEVDSTQERLKEWNVSY---GTALVADRQTKGRGRLGRKWLSQEGGLYFSFLLNPKEF 63

Query: 78  KDSLTLLSFAIAVAMRSVIASTLPVGTDVKIKWPNDILVFQRKIAGILIETLNLKNGLQA 137
           ++    L   + + +    A          +KWPND+   ++K++G+L E          
Sbjct: 64  ENL---LQLPLVLGLSVSEALEEITEIPFSLKWPNDVYFQEKKVSGVLCEL---SKDKLI 117

Query: 138 VVVGIGLNVKHCPVDTPYPVTSLQREGGCIDLKDIFSLLFQDVARVLDLWKKDTGREEIM 197
           V +GI +N +  P +     T+L    G    +    L             K+   +E  
Sbjct: 118 VGIGINVNQREIPEEIKDRATTLYEITGKDWDRKEVLLKVLKRISENLKKFKEKSFKEFK 177

Query: 198 NLWRCFACGIGDLITIKLSYGSILGRFVGVDDFGYLLLEEKKGCVRQIFTGDI 250
                    +G+ + + L  G I G+ VG+ + G  L+  ++G +++I +G+ 
Sbjct: 178 GKIESKMLYLGEEVKL-LGEGKITGKLVGLSEKGGALILTEEG-IKEILSGEF 228


>2dxu_A Biotin--[acetyl-COA-carboxylase] ligase; biotin biosynthesis,
           dimer, X-RAY diffraction, structural genomics, NPPSFA;
           HET: BT5; 1.28A {Pyrococcus horikoshii} PDB: 2dzc_A
           2ejg_A* 2e3y_A* 2e41_A* 2e64_A 2ejf_A* 2zgw_A* 1wqw_A*
           1wpy_A* 1wq7_A 1wnl_A* 1x01_A* 2dkg_A* 2dth_A* 2dti_A*
           2dto_A* 2fyk_A* 2djz_A* 2hni_A 2e10_A ...
          Length = 235

 Score =  100 bits (250), Expect = 3e-22
 Identities = 64/236 (27%), Positives = 105/236 (44%), Gaps = 17/236 (7%)

Query: 15  RYEFFDTISSTNDECMKRALSGDLGNLWIVASCQTAGRGRRDNKWISDKGNLYASLLLID 74
           R  +F  I+STN+      L        IVA  QT G G  + KW S +G L+ S++L  
Sbjct: 12  RVIYFQEITSTNEFAKTSYLEE---GTVIVADKQTMGHGALNRKWESPEGGLWLSIVLSP 68

Query: 75  SISKDSLTLLSFAIAVAMRSVIASTLPVGTDVKIKWPNDILVFQRKIAGILIETLNLKNG 134
            + +  L      + +    V+ +      D +IKWPND+LV  +KIAG+L+E       
Sbjct: 69  KVPQKDLP---KIVFLGAVGVVETLKEFSIDGRIKWPNDVLVNYKKIAGVLVEGKG---- 121

Query: 135 LQAVVVGIGLNVKHCPVDTPYPVTSLQREGGCIDLKDIFSLLFQDVARVLDLWKKDTGRE 194
              +V+GIGLNV +   +    +         +    +F  L  ++ R+   + K+    
Sbjct: 122 -DKIVLGIGLNVNNKVPNGATSMKLELGSEVPLL--SVFRSLITNLDRLYLNFLKNPMD- 177

Query: 195 EIMNLWRCFACGIGDLITIKLSYGSILGRFVGVDDFGYLLLEEKKGCVRQIFTGDI 250
             +         +G  + I L  GS  G    +DDFG L++    G V+++  GD+
Sbjct: 178 --ILNLVRDNMILGVRVKI-LGDGSFEGIAEDIDDFGRLIIRLDSGEVKKVIYGDV 230


>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 = 31.1 bits (70), Expect = 0.23
 Identities = 27/208 (12%), Positives = 60/208 (28%), Gaps = 75/208 (36%)

Query: 73  IDSISKDSLTL----LSFAIAVA---------MRSVIASTLPVGTDVKIKWPNDI----- 114
           +D+ S   LTL    L   + V          ++      LP  T+      ++      
Sbjct: 1   MDAYSTRPLTLSHGSLEHVLLVPTASFFIASQLQEQFNKILPEPTEG-FAADDEPTTPAE 59

Query: 115 LV--FQRKIAGILIETLN------LKNGLQAVVVGI--GLNVKHC-----PVDTPYPVTS 159
           LV  F   ++ ++  +        L   L         G ++ H        +    +  
Sbjct: 60  LVGKFLGYVSSLVEPSKVGQFDQVLNLCLTEFENCYLEGNDI-HALAAKLLQENDTTLVK 118

Query: 160 LQREGGCIDLKDIF---------------SLLFQDVARVLDLWKKDTGREEIMNLW---- 200
            +     + +K+                 S LF+ V           G  +++ ++    
Sbjct: 119 TKE----L-IKNYITARIMAKRPFDKKSNSALFRAVG---------EGNAQLVAIFGGQG 164

Query: 201 ---RCFACGIGDLITIKLSYGSILGRFV 225
                F     +L  +  +Y  ++G  +
Sbjct: 165 NTDDYFE----ELRDLYQTYHVLVGDLI 188



 Score = 29.9 bits (67), Expect = 0.51
 Identities = 21/155 (13%), Positives = 41/155 (26%), Gaps = 72/155 (46%)

Query: 65  NLYASLL--LIDSISKDSLTLLSFAIAVAMRSVIASTLPVGTDVKIKW-------PN-DI 114
             Y  L+  LI   ++    L+   +              G ++ ++W       P+ D 
Sbjct: 178 QTYHVLVGDLIKFSAETLSELIRTTLDAE------KVFTQGLNI-LEWLENPSNTPDKDY 230

Query: 115 LV------------------------------FQRKIA-------GILI----------E 127
           L+                               +  +        G++           E
Sbjct: 231 LLSIPISCPLIGVIQLAHYVVTAKLLGFTPGELRSYLKGATGHSQGLVTAVAIAETDSWE 290

Query: 128 TLNLKNGLQAVVV--GIGLNVKHCPVDTPYPVTSL 160
           +    +  +A+ V   IG+          YP TSL
Sbjct: 291 SF-FVSVRKAITVLFFIGVRCYEA-----YPNTSL 319



 Score = 28.0 bits (62), Expect = 2.0
 Identities = 25/103 (24%), Positives = 45/103 (43%), Gaps = 18/103 (17%)

Query: 1    MFSNLSECQNPYSFRYEFFDTISSTND-----ECMKRALSGDLGNLWIVASCQT-AGRGR 54
            +F  ++E    Y+FR E    +S+T         M++A   DL +  ++ +  T AG   
Sbjct: 1706 IFKEINEHSTSYTFRSE-KGLLSATQFTQPALTLMEKAAFEDLKSKGLIPADATFAGHSL 1764

Query: 55   RDNKWISDKGNLYASLL-LIDSISKDSLTLLSFAIAVAMRSVI 96
             +          YA+L  L D +S +SL  + F   + M+  +
Sbjct: 1765 GE----------YAALASLADVMSIESLVEVVFYRGMTMQVAV 1797


>3sil_A Sialidase; glycosidase, hydrolase; HET: PO4 GOL; 1.05A {Salmonella
           typhimurium} SCOP: b.68.1.1 PDB: 1dim_A* 1dil_A* 2sil_A
           2sim_A*
          Length = 379

 Score = 26.8 bits (58), Expect = 5.0
 Identities = 11/75 (14%), Positives = 26/75 (34%), Gaps = 19/75 (25%)

Query: 18  FFDTISSTNDECMKRALSGDLGNLWIVASCQTAGRGRRDNKWISDKGNL--------YAS 69
              +  + N++  +  +S    NL+             + K I D            Y+ 
Sbjct: 293 AHSSAQNKNNDYTRSDISLYAHNLY-----------SGEVKLIDDFYPKVGNASGAGYSC 341

Query: 70  LLLIDSISKDSLTLL 84
           L    ++ K++L ++
Sbjct: 342 LSYRKNVDKETLYVV 356


>3m4i_A DNA gyrase subunit B; GYRB, toprim, type II topoisomerase,
           tuberculosi quinolone binding site, DNA binding site,
           ATP-binding; HET: DNA; 1.95A {Mycobacterium
           tuberculosis} PDB: 3ig0_A* 2zjt_A*
          Length = 242

 Score = 26.5 bits (58), Expect = 6.7
 Identities = 9/36 (25%), Positives = 13/36 (36%), Gaps = 1/36 (2%)

Query: 187 WKKDTGREEIMNLWRCFACGIGDLITI-KLSYGSIL 221
             +     E+  +      GI D   I KL Y  I+
Sbjct: 60  IDRVLKNTEVQAIITALGTGIHDEFDIGKLRYHKIV 95


  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
   0.324    0.141    0.433 

Gapped
Lambda     K      H
   0.267   0.0466    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 24244
Number of Hits to DB: 2,184,487
Number of extensions: 97535
Number of successful extensions: 222
Number of sequences better than 10.0: 1
Number of HSP's gapped: 209
Number of HSP's successfully gapped: 15
Length of query: 252
Length of database: 5,693,230
Length adjustment: 90
Effective length of query: 162
Effective length of database: 3,511,270
Effective search space: 568825740
Effective search space used: 568825740
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 55 (25.6 bits)