GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Desulfovibrio vulgaris Hildenborough

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 208544 DVU3030 acetate kinase

Query= BRENDA::Q9WYB1
         (403 letters)



>MicrobesOnline__882:208544
          Length = 402

 Score =  433 bits (1114), Expect = e-126
 Identities = 222/404 (54%), Positives = 285/404 (70%), Gaps = 8/404 (1%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRV-----GDEKHVIERE 55
           M VLVINSGSSSIKYQLI+ME E  LC G+ ERIG    +L H++     G+EK   E+ 
Sbjct: 1   MNVLVINSGSSSIKYQLIDMEREVPLCSGLVERIGEPMGKLTHKIRPDAEGEEKLTFEQP 60

Query: 56  LPDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEV 115
             +H E +K ++  + D   GVIKD  EI A+GHRV+ GGE  K+SV +D+     I + 
Sbjct: 61  FTNHVEGMKRVVELITDADKGVIKDKSEIGAIGHRVLLGGEEIKQSVRIDDWAKGVIRDY 120

Query: 116 SPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRR 175
            PL PLHNPANL GI+ A +L PG+PNV VFDT FHQ++P KAYLY +P E YE+ KIRR
Sbjct: 121 IPLGPLHNPANLAGIEVAEELFPGLPNVGVFDTEFHQSMPAKAYLYPLPIELYEELKIRR 180

Query: 176 YGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGL 235
           YGFHGTSHRY++KR A+ LGK L+EL IITCH+GNG S+AAVK GKCVDT+MG TPLEGL
Sbjct: 181 YGFHGTSHRYITKRTAQYLGKPLDELNIITCHLGNGCSMAAVKNGKCVDTTMGITPLEGL 240

Query: 236 VMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295
           +MGTR GD+DPAI  F+MEK+ +SP E   ++NK+SG+ G+     +DMRD+  A   G+
Sbjct: 241 MMGTRCGDIDPAIVPFLMEKKNLSPAEADTLMNKQSGLKGMCG--MNDMRDLHAARENGN 298

Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355
           E  +L  E++ YRI KYIGAY A +  VDA+VFTAG+GEN    R +VC+ L+ LG+ +D
Sbjct: 299 ERAQLAFEMFTYRIKKYIGAYYAVLGRVDAVVFTAGIGENDDFVRAEVCAGLDSLGIAVD 358

Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVE 399
             +N     G+   IS   SRV VLVVPTNEEL IA+ T ++++
Sbjct: 359 PARN-AVRNGQPRHISPDGSRVAVLVVPTNEELEIAQATLDVLK 401


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: 484
Number of extensions: 23
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: 403
Length of database: 402
Length adjustment: 31
Effective length of query: 372
Effective length of database: 371
Effective search space:   138012
Effective search space used:   138012
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 208544 DVU3030 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.28983.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.28983.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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