GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Magnetospirillum magneticum AMB-1

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate WP_011384935.1 AMB_RS12860 acetate/propionate family kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>NCBI__GCF_000009985.1:WP_011384935.1
          Length = 397

 Score =  290 bits (741), Expect = 7e-83
 Identities = 161/409 (39%), Positives = 265/409 (64%), Gaps = 28/409 (6%)

Query: 3   VLVINSGSSSIKYQLIEMEGEK---VLCKGIAERIGIEGSRLVHRVGDEKH---VIEREL 56
           +LVIN+GSSSIK+ L    G++   + CKG  E I +      H +    H   + E+  
Sbjct: 5   ILVINAGSSSIKFSLYISNGDEKPLLSCKGQVEGINVAP----HFIAKSPHGGVLNEQRW 60

Query: 57  PDH----EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAI 112
           PD      EAL   +   ++ +LG      E+ A GHRVVHGG ++ + +LV++E+++ +
Sbjct: 61  PDQPNMSHEALFKYMIEWIEAQLGDA----ELKAAGHRVVHGGSQYSQPLLVNDELMEEL 116

Query: 113 EEVSPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYK 172
           E++ PLAPLH P NL  I+A  K+ PG+  VA FDTAFH++ P  A  +A+P +   +  
Sbjct: 117 EKLIPLAPLHQPHNLAPIRALTKVHPGLTQVACFDTAFHRSNPWTAQSFALPRKITGE-G 175

Query: 173 IRRYGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPL 232
           ++RYGFHG S+ +++++  + L       K++ CH+G+GAS+ A+  GK V ++MGFT +
Sbjct: 176 VKRYGFHGLSYEFIARQMRQ-LSPAAARGKVVVCHLGSGASMCAIDGGKSVASTMGFTAV 234

Query: 233 EGLVMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAAL 292
           +GL MGTR+G +D  +  ++++++G++P+E+ D+L K+SG+ G+S G S+DMR + E++ 
Sbjct: 235 DGLPMGTRTGTMDAGVILYLLQQKGMTPKEIEDLLYKQSGLLGVS-GVSNDMRILLESS- 292

Query: 293 KGDEWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGV 352
             +      +E++ YRI++ +G+ AAAM G+DA+VFTAG+GE SP  RE VC++ E+LGV
Sbjct: 293 --EPHAAEAVELFVYRISRELGSLAAAMGGLDALVFTAGIGERSPQIRERVCAHAEWLGV 350

Query: 353 KLDKQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEKI 401
           ++D++ N+        +IS  DS V V V+PT+EE+MIA+ T+E++  +
Sbjct: 351 EMDQEANQR----DSLLISAADSPVSVWVIPTDEEMMIAKHTRELLRSL 395


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: 423
Number of extensions: 27
Number of successful extensions: 5
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: 397
Length adjustment: 31
Effective length of query: 372
Effective length of database: 366
Effective search space:   136152
Effective search space used:   136152
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 WP_011384935.1 AMB_RS12860 (acetate/propionate family kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.4357.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.4357.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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