GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Pseudomonas stutzeri RCH2

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate GFF3154 Psest_3213 acetate kinase

Query= BRENDA::E3W769
         (401 letters)



>FitnessBrowser__psRCH2:GFF3154
          Length = 395

 Score =  384 bits (987), Expect = e-111
 Identities = 204/401 (50%), Positives = 269/401 (67%), Gaps = 7/401 (1%)

Query: 1   MSDKLVLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAF 60
           MS + +LV+NCGSSS+KFA+++       + GLAEC G  ++ I ++   GK   K+   
Sbjct: 1   MSARNILVINCGSSSIKFALVNEAQATFPLQGLAECIGSPEAVIHFESAAGKESVKVPN- 59

Query: 61  TAHREAVEFFIVNNILAEHPELAA-QIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCAS 119
             H+ A+       IL    E A   +  IGHR+VHGGEKF  S ++  E + GIE    
Sbjct: 60  ADHQAALA-----QILPRVEEAAGGHLDGIGHRVVHGGEKFFASSLLNDETLAGIEANIQ 114

Query: 120 LAPLHNPAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYG 179
           LAPLHNPA+L GI AAI  FP+LPQV VFDTAFHQTMPE AY YA+P  LY+EH +RRYG
Sbjct: 115 LAPLHNPANLSGIHAAINLFPELPQVGVFDTAFHQTMPEHAYRYAVPDVLYKEHGVRRYG 174

Query: 180 MHGTSHFYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVM 239
            HGTSH +V + AA++ G  V++ + + AHLGNG S  A+  G+S DTSMGLTPLEGLVM
Sbjct: 175 FHGTSHRFVSKRAAEMAGVPVENSSWLVAHLGNGCSTCAVVNGESRDTSMGLTPLEGLVM 234

Query: 240 GTRCGDLDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGA 299
           GTR GD+DPS+   L K LG+ L +++N+LNK+SGL G+S L+ND R + +  + GH GA
Sbjct: 235 GTRSGDVDPSLHNFLNKTLGWDLAKIDNMLNKESGLKGLSGLSNDMRTLADARNAGHPGA 294

Query: 300 TLALDIFCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDIL 359
            LA D+FCYRLAK +A+ +  L +LD ++FTGGIGENS+ +RE+ L  L++F FK+D   
Sbjct: 295 VLAFDVFCYRLAKSLAAMSCALPQLDGLVFTGGIGENSSAVRERTLEHLKLFGFKLDAEA 354

Query: 360 NKAARFGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKLITA 400
           N     G  G I  AG+P  MV+PTNEE  IA D + L+ A
Sbjct: 355 NARCTRGVAGEIQAAGSPRIMVVPTNEERQIALDTLALLDA 395


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: 487
Number of extensions: 19
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: 395
Length adjustment: 31
Effective length of query: 370
Effective length of database: 364
Effective search space:   134680
Effective search space used:   134680
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 GFF3154 Psest_3213 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.26263.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26263.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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