GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Paraburkholderia bryophila 376MFSha3.1

Align Probable propionate kinase; EC 2.7.2.15 (characterized)
to candidate H281DRAFT_02796 H281DRAFT_02796 acetate kinase

Query= SwissProt::P74879
         (404 letters)



>FitnessBrowser__Burk376:H281DRAFT_02796
          Length = 385

 Score =  242 bits (618), Expect = 1e-68
 Identities = 157/389 (40%), Positives = 207/389 (53%), Gaps = 28/389 (7%)

Query: 3   YKIMAINAGSSSLKFQLLEMPQGD--MLCQGLIERIGMADAQVTIKTHSQKW--QETVPV 58
           + I+ +N+GSSSLKF L E    D  +L +G  + IG  D ++ I     +   QE   +
Sbjct: 10  HTILVLNSGSSSLKFGLFEHSGDDESLLLEGSAQGIGRRDGRLRIAAPDGRVLVQEEHVL 69

Query: 59  ADHRDAVTLLLEKLLGYQIINSLRDIDGVGHRVAHGGEFFKDSTLVTDETLAQIERLAEL 118
               DA    L+KL              VGHRV HGG   +    +T E   +++     
Sbjct: 70  ESQTDA----LQKLSTVLAQQHHEQPTAVGHRVVHGGPHLRSHQRLTPEVRRRLQDAVHF 125

Query: 119 APLHNPVNALGIHVFRQLLPDAPSVAVFDTAFHQTLDEPAYIYPLPWHYYAELGIRRYGF 178
           APLH P     I   +++   A   A FDTAFH TL   A    LP   Y+E G+ RYGF
Sbjct: 126 APLHIPPALDLIDEAQKIFGGAQHFACFDTAFHATLPPRAAQLALP-RRYSEAGVIRYGF 184

Query: 179 HGTSHKYVSGVLAEKLGVPLSALRVICCHLGNGSSICAIKNGRSVNTSMGFTPQSGVMMG 238
           HG S++     L  +LG  L A RV+C HLGNGSS+CA+++GRSV+TSMG TP  GV MG
Sbjct: 185 HGLSYES----LVAQLGATLPA-RVVCAHLGNGSSVCALRDGRSVDTSMGMTPTGGVPMG 239

Query: 239 TRSGDIDPSILPWIAQRESKTPQQLNQLLNNESGLLGVSGVSSDYRDVEQAANTGNRQAK 298
           TR GD+DP +L ++ + E      L  LLN  SGL G +   SD + +EQ A  G+  A 
Sbjct: 240 TRCGDLDPGVLLYLMRVEKLDANGLETLLNRHSGLAGYADGESDMQALEQRAAAGDPHAS 299

Query: 299 LALTLFAERIRATIGSYIMQMGGLDALVFTGGIGENSARARSAVCHNLQFLGLAVDEEKN 358
           LAL  FA  +R TIG Y   +GG+D LVFTGGIGE+S + R  +C  L FLGL       
Sbjct: 300 LALDAFATAVRKTIGGYAALLGGIDLLVFTGGIGEHSVQMRKRICEGLSFLGL------- 352

Query: 359 QRNATFIQTENALVKVAVINTNEELMIAQ 387
                     +A  KV V++T EE  IA+
Sbjct: 353 -------HEGDASGKVRVLHTEEEKQIAR 374


Lambda     K      H
   0.319    0.135    0.392 

Gapped
Lambda     K      H
   0.267   0.0410    0.140 


Matrix: BLOSUM62
Gap Penalties: Existence: 11, Extension: 1
Number of Sequences: 1
Number of Hits to DB: 363
Number of extensions: 15
Number of successful extensions: 4
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 1
Number of HSP's successfully gapped: 1
Length of query: 404
Length of database: 385
Length adjustment: 31
Effective length of query: 373
Effective length of database: 354
Effective search space:   132042
Effective search space used:   132042
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate H281DRAFT_02796 H281DRAFT_02796 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.2205.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2205.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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