GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Sinorhizobium meliloti 1021

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate SM_b21184 SM_b21184 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>FitnessBrowser__Smeli:SM_b21184
          Length = 392

 Score =  257 bits (656), Expect = 5e-73
 Identities = 161/402 (40%), Positives = 235/402 (58%), Gaps = 22/402 (5%)

Query: 3   VLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGS-RLVHRVGDEKHVIEREL----- 56
           +LVIN+GSSS+K+Q+  +    +  +  A+  GI    RL     D   +I R L     
Sbjct: 4   LLVINAGSSSLKFQIFGIATAGLERQVRAKLDGIATQPRLKATAADGTELINRRLDATAV 63

Query: 57  PDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVS 116
           PD  EAL     ++  + L  ++   ++ A+GHRVVHGG  +   VL++  VL  +    
Sbjct: 64  PDLPEAL-----SVARDWLATLRGF-DLRAIGHRVVHGGPDYVRPVLIETTVLDRLASYQ 117

Query: 117 PLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRY 176
            LAPLH P NL  I+ AM + P VP VA FDTAFH+   +    YA+P  +YE+  +RRY
Sbjct: 118 DLAPLHQPNNLAPIRLAMDIKPDVPQVACFDTAFHRGRTEHTDCYALPRTFYEQ-GVRRY 176

Query: 177 GFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLV 236
           GFHG S+ Y++ R  E+   ++   ++I  H+G+GAS+ A+K G+ V+T+MGFT L+GL 
Sbjct: 177 GFHGISYEYIAGRLREV-APEVARGRVIVAHLGSGASMCALKDGRSVETTMGFTALDGLP 235

Query: 237 MGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDE 296
           MGTR G LDP +   ++  +G+S Q + D+L  +SG+ GLS G S+DMR++  +    D 
Sbjct: 236 MGTRPGQLDPGVVLHLLTDQGMSAQAVSDLLYHRSGLKGLS-GISNDMRELLGS---DDP 291

Query: 297 WCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDK 356
                ++ + +R A   G  AAA+ G+DA VFTAG+GENS   R  V   L +LG +LD 
Sbjct: 292 RASFAIDHFVHRCALDAGMLAAALGGLDAFVFTAGIGENSAPIRARVSEGLAWLGAELDP 351

Query: 357 QKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398
             N+        +IS   SRV + V+PT+EELMIAR T  I+
Sbjct: 352 AAND----AGASVISKAGSRVALHVMPTDEELMIARHTLAII 389


Lambda     K      H
   0.318    0.138    0.391 

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: 360
Number of extensions: 17
Number of successful extensions: 6
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: 403
Length of database: 392
Length adjustment: 31
Effective length of query: 372
Effective length of database: 361
Effective search space:   134292
Effective search space used:   134292
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: 50 (23.9 bits)

Align candidate SM_b21184 SM_b21184 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.18698.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18698.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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