GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Bacteroides thetaiotaomicron VPI-5482

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 353219 BT3693 acetate kinase (NCBI ptt file)

Query= BRENDA::Q9WYB1
         (403 letters)



>FitnessBrowser__Btheta:353219
          Length = 399

 Score =  466 bits (1199), Expect = e-136
 Identities = 235/401 (58%), Positives = 304/401 (75%), Gaps = 3/401 (0%)

Query: 1   MRVLVINSGSSSIKYQLIEMEGEKVLCKGIAERIGIEGSRLVHRVGD-EKHVIERELPDH 59
           M++LV+N GSSSIKY+L +M  ++V+ +G  E+IG++GS L   + + EK V+E+++P+H
Sbjct: 1   MKILVLNCGSSSIKYKLFDMTTKEVIAQGGIEKIGLKGSFLKLTLPNGEKKVLEKDIPEH 60

Query: 60  EEALKLILNTLVDEKLGVIKDLKEIDAVGHRVVHGGERFKESVLVDEEVLKAIEEVSPLA 119
              ++ ILNTL+  + G IK L EI+AVGHR+VHGGERF ESVL+++EVL+A    + LA
Sbjct: 61  TIGVEFILNTLISPEYGAIKSLDEINAVGHRMVHGGERFSESVLLNKEVLEAFAACNDLA 120

Query: 120 PLHNPANLMGIKAAMKLLPGVPNVAVFDTAFHQTIPQKAYLYAIPYEYYEKYKIRRYGFH 179
           PLHNPANL G+ A   +LP +P V VFDTAFHQT+P  AY+YAIPYE YEKY +RRYGFH
Sbjct: 121 PLHNPANLKGVNAVSAILPNIPQVGVFDTAFHQTMPDYAYMYAIPYEMYEKYGVRRYGFH 180

Query: 180 GTSHRYVSKRAAEILGKKLEELKIITCHIGNGASVAAVKYGKCVDTSMGFTPLEGLVMGT 239
           GTSHRYVSKR  E LG      KIITCHIGNG S+AA+K GKC+DT+MG TPLEGL+MGT
Sbjct: 181 GTSHRYVSKRVCEFLGVNPVGQKIITCHIGNGGSIAAIKDGKCIDTTMGLTPLEGLMMGT 240

Query: 240 RSGDLDPAIPFFIMEKEGISPQEMYDILNKKSGVYGLSKGFSSDMRDIEEAALKGDEWCK 299
           RSGD+D     FIMEKEG++   + ++LNKKSGV G+S G SSDMR++  A   G+E   
Sbjct: 241 RSGDIDAGAVTFIMEKEGLNTTGISNLLNKKSGVLGIS-GVSSDMRELLAACANGNERAI 299

Query: 300 LVLEIYDYRIAKYIGAYAAAMNGVDAIVFTAGVGENSPITREDVCSYLEFLGVKLDKQKN 359
           L  ++Y YRI KYIGAYAAA+ GVD I+FT GVGEN    RE VC  +EF+G+KLD   N
Sbjct: 300 LAEKMYYYRIKKYIGAYAAALGGVDIILFTGGVGENQFECRESVCKDMEFMGIKLDNNVN 359

Query: 360 EETIRGKEGIISTPDSRVKVLVVPTNEELMIARDTKEIVEK 400
            + +RG+E IIST DS+VKV+V+PT+EEL+IA DT +I++K
Sbjct: 360 AK-VRGEEAIISTADSKVKVVVIPTDEELLIASDTMDILKK 399


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: 536
Number of extensions: 18
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: 399
Length adjustment: 31
Effective length of query: 372
Effective length of database: 368
Effective search space:   136896
Effective search space used:   136896
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 353219 BT3693 (acetate kinase (NCBI ptt file))
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.9396.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9396.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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