GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Shewanella amazonensis SB2B

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate 6937325 Sama_1495 acetate kinase (RefSeq)

Query= BRENDA::E3W769
         (401 letters)



>FitnessBrowser__SB2B:6937325
          Length = 399

 Score =  672 bits (1733), Expect = 0.0
 Identities = 332/398 (83%), Positives = 362/398 (90%), Gaps = 1/398 (0%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           MS+ LVLVLNCGSSSLKFAI+DA +GD+KISGLAECFGLE++RIKWK  G K+EA LGAF
Sbjct: 1   MSNTLVLVLNCGSSSLKFAILDATNGDEKISGLAECFGLENARIKWKLRGEKHEASLGAF 60

Query: 61  TAHREAVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASL 120
           +AHREAVE+ IVN IL   PEL  Q+ AIGHRIVHGGEKFT SVII   V++GIEDCASL
Sbjct: 61  SAHREAVEY-IVNKILVNEPELKGQLIAIGHRIVHGGEKFTHSVIIDDAVLKGIEDCASL 119

Query: 121 APLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGM 180
           APLHNPAHLIGIRAA ASFP LPQV VFDTAFHQ+MP++AYIYALPYKLYREH IRRYGM
Sbjct: 120 APLHNPAHLIGIRAAQASFPSLPQVAVFDTAFHQSMPDRAYIYALPYKLYREHGIRRYGM 179

Query: 181 HGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMG 240
           HGTSH +V REAAK LGKDV D NVICAHLGNGASV A+KGGKSVDTSMGLTPLEGLVMG
Sbjct: 180 HGTSHLFVSREAAKALGKDVNDTNVICAHLGNGASVTAVKGGKSVDTSMGLTPLEGLVMG 239

Query: 241 TRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGAT 300
           TRCGDLDPSII+HLV QLGYTLDEVNNL+NKQSGLLGISELTNDCRGIEEGY +GHKGAT
Sbjct: 240 TRCGDLDPSIIYHLVHQLGYTLDEVNNLMNKQSGLLGISELTNDCRGIEEGYAEGHKGAT 299

Query: 301 LALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN 360
           LAL+IFCYRLAKYIASYTVPLGRLDAI+FTGGIGENS+LIREKVLNLLEIF F+VD   N
Sbjct: 300 LALEIFCYRLAKYIASYTVPLGRLDAIVFTGGIGENSDLIREKVLNLLEIFKFEVDSERN 359

Query: 361 KAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLI 398
           KAARFG QGVIT+ G+PIAMVIPTNEEWVIAED+++L+
Sbjct: 360 KAARFGNQGVITKEGSPIAMVIPTNEEWVIAEDSLRLV 397


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: 610
Number of extensions: 24
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 6937325 Sama_1495 (acetate kinase (RefSeq))
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.12005.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.12005.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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