GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Desulfovibrio vulgaris Miyazaki F

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 8501129 DvMF_1865 acetate kinase (RefSeq)

Query= BRENDA::Q9WYB1
         (403 letters)



>FitnessBrowser__Miya:8501129
          Length = 404

 Score =  422 bits (1085), Expect = e-123
 Identities = 216/403 (53%), Positives = 283/403 (70%), Gaps = 8/403 (1%)

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

Query: 56  LPDHEEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEV 115
             +H E +K +++ + D   GVI D  EI AVGHRV+ GGE  K+SV +DE     I + 
Sbjct: 61  FANHVEGMKKVVDLITDADKGVIADKGEIYAVGHRVLLGGEEIKQSVKIDEWAKGIIRDY 120

Query: 116 SPLAPLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRR 175
            PL PLHNPANL GI+ A +L P  P+V VFDT FHQT+P+KAYLY +PY+ Y+  +IRR
Sbjct: 121 IPLGPLHNPANLAGIEVAEELFPHAPSVGVFDTEFHQTMPKKAYLYPLPYDLYKTLRIRR 180

Query: 176 YGFHGTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGL 235
           YGFHGTSHRY++K+ AE LGK L+EL IITCH+GNG S+AAVK G+CVDT+MG TPLEGL
Sbjct: 181 YGFHGTSHRYITKKTAEFLGKPLDELNIITCHLGNGCSMAAVKNGRCVDTTMGITPLEGL 240

Query: 236 VMGTRSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGD 295
           +MGTR GD+DPA+  F+MEK+G S  E+  ++NK+SG+ G+     +DMRDI  A  KGD
Sbjct: 241 MMGTRCGDIDPALVPFLMEKKGWSGAEIDTVMNKQSGLKGICG--MNDMRDIHAAREKGD 298

Query: 296 EWCKLVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLD 355
           E  +L  +++ YRI KYIG++A  +  +DAIVFTAG+GEN  + R  VC  ++ LG+ +D
Sbjct: 299 EMAELAFQMFVYRIRKYIGSFAVVVGKLDAIVFTAGIGENDDLVRAAVCKDMDILGIDID 358

Query: 356 KQKNEETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIV 398
           +  N +   G+   I  P  RV VLVVPTNEEL IA+ T  ++
Sbjct: 359 EAVNAKR-SGQARHIGKPGQRVPVLVVPTNEELEIAQTTVAVL 400


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: 498
Number of extensions: 16
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: 404
Length adjustment: 31
Effective length of query: 372
Effective length of database: 373
Effective search space:   138756
Effective search space used:   138756
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 8501129 DvMF_1865 (acetate kinase (RefSeq))
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.2381.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2381.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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