GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Escherichia coli BW25113

Align Propionate kinase; EC 2.7.2.15 (characterized)
to candidate 17189 b3115 propionate kinase/acetate kinase C, anaerobic (RefSeq)

Query= SwissProt::P11868
         (402 letters)



>FitnessBrowser__Keio:17189
          Length = 402

 Score =  794 bits (2051), Expect = 0.0
 Identities = 402/402 (100%), Positives = 402/402 (100%)

Query: 1   MNEFPVVLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSY 60
           MNEFPVVLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSY
Sbjct: 1   MNEFPVVLVINCGSSSIKFSVLDASDCEVLMSGIADGINSENAFLSVNGGEPAPLAHHSY 60

Query: 61  EGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNY 120
           EGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNY
Sbjct: 61  EGALKAIAFELEKRNLNDSVALIGHRIAHGGSIFTESAIITDEVIDNIRRVSPLAPLHNY 120

Query: 121 ANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSHR 180
           ANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSHR
Sbjct: 121 ANLSGIESAQQLFPGVTQVAVFDTSFHQTMAPEAYLYGLPWKYYEELGVRRYGFHGTSHR 180

Query: 181 YVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV 240
           YVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV
Sbjct: 181 YVSQRAHSLLNLAEDDSGLVVAHLGNGASICAVRNGQSVDTSMGMTPLEGLMMGTRSGDV 240

Query: 241 DFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTF 300
           DFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTF
Sbjct: 241 DFGAMSWVASQTNQSLGDLERVVNKESGLLGISGLSSDLRVLEKAWHEGHERAQLAIKTF 300

Query: 301 VHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSC 360
           VHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSC
Sbjct: 301 VHRIARHIAGHAASLRRLDGIIFTGGIGENSSLIRRLVMEHLAVLGLEIDTEMNNRSNSC 360

Query: 361 GERIVSSENARVICAVIPTNEEKMIALDAIHLGKVNAPAEFA 402
           GERIVSSENARVICAVIPTNEEKMIALDAIHLGKVNAPAEFA
Sbjct: 361 GERIVSSENARVICAVIPTNEEKMIALDAIHLGKVNAPAEFA 402


Lambda     K      H
   0.318    0.134    0.386 

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: 680
Number of extensions: 16
Number of successful extensions: 1
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: 402
Length of database: 402
Length adjustment: 31
Effective length of query: 371
Effective length of database: 371
Effective search space:   137641
Effective search space used:   137641
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 17189 b3115 (propionate kinase/acetate kinase C, anaerobic (RefSeq))
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.989.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.989.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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