GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Pedobacter sp. GW460-11-11-14-LB5

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate CA265_RS10080 CA265_RS10080 acetate kinase

Query= BRENDA::P38502
         (408 letters)



>FitnessBrowser__Pedo557:CA265_RS10080
          Length = 398

 Score =  383 bits (983), Expect = e-111
 Identities = 199/398 (50%), Positives = 271/398 (68%), Gaps = 7/398 (1%)

Query: 1   MKVLVINAGSSSLKYQLIDMTNESALAVGLCERIGIDNSIITQKKFDGKK---LEKLTDL 57
           M +LVIN+GSSSLKYQL +M  ++ L  GL ERIGI+ S I    +   +   +E+   +
Sbjct: 1   MNILVINSGSSSLKYQLFNMPEKAPLCSGLVERIGIEGSFIKHSVYRNNEKYNIEQSGFI 60

Query: 58  PTHKDALEEVVKALTDDEFGVIKDMGEINAVGHRVVHGGEKFTTSALYDEGVEKAIKDCF 117
             H + L++V+  LT+ E+ VI    +I AVGHRVVHGGE FT + L  + V+  IK  F
Sbjct: 61  ANHGEGLKQVLALLTEGEYAVIASPDDIAAVGHRVVHGGEHFTGATLITDEVKHQIKKLF 120

Query: 118 ELAPLHNPPNMMGISACAEIMPGTPMVIVFDTAFHQTMPPYAYMYALPYDLYEKHGVRKY 177
            LAPLHNP N   I    +       + VFDTAFHQT+P  AY YA+P   Y++HG+R Y
Sbjct: 121 SLAPLHNPVNYKCIEVAEQTFVNAKQIAVFDTAFHQTIPEQAYRYAIPEWYYKEHGIRVY 180

Query: 178 GFHGTSHKYVAERAALMLGKPAEETKIITCHLGNGSSITAVEGGKSVETSMGFTPLEGLA 237
           GFHGTSHKYV+E+A   L K   E+KII+ HLGNG SITA++ GKS++TSMGF PL GL 
Sbjct: 181 GFHGTSHKYVSEQAIKWLNK--AESKIISIHLGNGCSITAIKNGKSIDTSMGFGPLSGLM 238

Query: 238 MGTRCGSIDPAIVPFLMEKEGLTTREIDTLMNKKSGVLGVSGLSNDFRDLDEAASKGNRK 297
           MGTR G IDP+++  LME  G T  ++ TL+NK+SG+LGV G S+D RD+ +  S+GN  
Sbjct: 239 MGTRSGDIDPSVIFHLMEHSGYTLEQLSTLVNKQSGLLGVGG-SSDMRDIRKMVSEGNAA 297

Query: 298 AELALEIFAYKVKKFIGEYSAVLNGADAVVFTAGIGENSASIRKRILTGLDGIGIKIDDE 357
           A LAL+++AY++KKFIG Y+A+LNG DA+VFTAG+GEN +++R+ + + LD +GI++D  
Sbjct: 298 AILALKLYAYRIKKFIGAYAAILNGIDAIVFTAGVGENDSNMREAVCSALDYLGIELDPN 357

Query: 358 KN-KIRGQEIDISTPDAKVRVFVIPTNEELAIARETKE 394
           +N    G   +I+   AKV++ VIPTNEE  IA +  E
Sbjct: 358 QNAAYHGALKEINKTGAKVKILVIPTNEEYEIAHQCFE 395


Lambda     K      H
   0.316    0.135    0.380 

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: 442
Number of extensions: 14
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: 408
Length of database: 398
Length adjustment: 31
Effective length of query: 377
Effective length of database: 367
Effective search space:   138359
Effective search space used:   138359
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 CA265_RS10080 CA265_RS10080 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.13695.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13695.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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