GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Shewanella sp. ANA-3

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 7024360 Shewana3_1552 acetate kinase (RefSeq)

Query= BRENDA::E3W769
         (401 letters)



>FitnessBrowser__ANA3:7024360
          Length = 399

 Score =  683 bits (1762), Expect = 0.0
 Identities = 336/399 (84%), Positives = 371/399 (92%), Gaps = 1/399 (0%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           MS+KLVLVLNCGSSSLKFA+IDAQ+GDD+ISGLAECFGLEDSRIKWK NG K+E+ LGAF
Sbjct: 1   MSNKLVLVLNCGSSSLKFAVIDAQTGDDQISGLAECFGLEDSRIKWKINGEKHESSLGAF 60

Query: 61  TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120
           TAHREAVEF IVN ILA  PELAAQI+A+GHRIVHGGEKFTRSVII   VI+GIE+C+SL
Sbjct: 61  TAHREAVEF-IVNKILAGQPELAAQIQAVGHRIVHGGEKFTRSVIIDEHVIKGIEECSSL 119

Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180
           APLHNPAHLIGIRAAIASFP+LPQV VFDTAFHQ+MPE+AYIYALPYKLYREH IRRYGM
Sbjct: 120 APLHNPAHLIGIRAAIASFPKLPQVAVFDTAFHQSMPERAYIYALPYKLYREHGIRRYGM 179

Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240
           HGTSH +V REAAKVL K +++ NVICAHLGNGASV A+KGGKSVDTSMGLTPLEGLVMG
Sbjct: 180 HGTSHLFVSREAAKVLNKPLEETNVICAHLGNGASVTAVKGGKSVDTSMGLTPLEGLVMG 239

Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300
           TRCGDLDPSII+HLV QLGYTL+EVNNL+NKQSGLLGISELTNDCRGIEEGY DGHKGAT
Sbjct: 240 TRCGDLDPSIIYHLVHQLGYTLEEVNNLMNKQSGLLGISELTNDCRGIEEGYADGHKGAT 299

Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360
           LAL+IFCYRLAKYIASYTVPLGRLDA++FTGGIGENS++IREKVLN+L+IFNF VD   N
Sbjct: 300 LALEIFCYRLAKYIASYTVPLGRLDAVVFTGGIGENSDIIREKVLNMLQIFNFHVDSERN 359

Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLIT 399
           KAARFG++G+IT   + +AMVIPTNEEWVIAED+IKLIT
Sbjct: 360 KAARFGKKGIITTDNSTVAMVIPTNEEWVIAEDSIKLIT 398


Lambda     K      H
   0.321    0.139    0.409 

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: 630
Number of extensions: 17
Number of successful extensions: 2
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: 401
Length of database: 399
Length adjustment: 31
Effective length of query: 370
Effective length of database: 368
Effective search space:   136160
Effective search space used:   136160
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 50 (23.9 bits)

Align candidate 7024360 Shewana3_1552 (acetate kinase (RefSeq))
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.13247.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13247.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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