GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Marinobacter adhaerens HP15

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate GFF1535 HP15_1499 acetate/propionate kinase

Query= BRENDA::E3W769
         (401 letters)



>FitnessBrowser__Marino:GFF1535
          Length = 398

 Score =  349 bits (896), Expect = e-101
 Identities = 189/393 (48%), Positives = 255/393 (64%), Gaps = 7/393 (1%)

Query: 6   VLVLNCGSSSLKFAIIDAQSGDDKISGLAECFGLEDSRIKWKFNGGKNEAKLGAFTAHRE 65
           VLV+NCGSSSLK A+ + Q     +S LAE  G  D+      +G +    L A   H +
Sbjct: 5   VLVVNCGSSSLKLALFNNQHRK-LVSALAERLGQSDAFAH--IDGQEGTIPLDAGAGHDQ 61

Query: 66  AVEFFIVNNILAEHPELAAQIKAIGHRIVHGGEKFTRSVIITPEVIQGIEDCASLAPLHN 125
           A+E  +      +   +     AIGHR+VHGGE F  +V+I  +V++ IE CA LAPLHN
Sbjct: 62  ALETLVT--AFRDLGLMTTAPSAIGHRVVHGGETFHEAVLIDGDVLKAIESCAGLAPLHN 119

Query: 126 PAHLIGIRAAIASFPQLPQVTVFDTAFHQTMPEKAYIYALPYKLYREHSIRRYGMHGTSH 185
           P +L GIRA +A FP +PQ  VFDTAFHQT+P +A++YALP   YR+  IRRYG HGTSH
Sbjct: 120 PVNLSGIRATLAQFPDVPQTAVFDTAFHQTLPRRAFLYALPEAWYRDWGIRRYGFHGTSH 179

Query: 186 FYVCREAAKVLGKDVKDINVICAHLGNGASVAAIKGGKSVDTSMGLTPLEGLVMGTRCGD 245
            ++  EAA++LGK     +VI AHLGNG S+ AI+ G SVDTSMGLTPLEGLVMGTR GD
Sbjct: 180 AFMASEAARLLGKTPATTSVISAHLGNGCSITAIRDGISVDTSMGLTPLEGLVMGTRSGD 239

Query: 246 LDPSIIFHLVKQLGYTLDEVNNLLNKQSGLLGISELTNDCRGIEEGYHDGHKGATLALDI 305
           +DP  +F  ++  G   DEV+ +LN++SGLLG+S  TND R + E    GH+ +  A+D+
Sbjct: 240 VDPG-LFDFLRSKGIAADEVHRVLNQESGLLGLSGQTNDMRSLCELADHGHEPSQTAIDV 298

Query: 306 FCYRLAKYIASYTVPLGRLDAIIFTGGIGENSNLIREKVLNLLEIFNFKVDDILN-KAAR 364
           FC+RLA+Y+ +    L +LDA++FTGGIGENS  IRE+ +  L++  F++   LN    +
Sbjct: 299 FCFRLARYVGAMMASLSQLDALVFTGGIGENSPRIREETIRHLKLTGFELSQDLNIHHGQ 358

Query: 365 FGQQGVITQAGTPIAMVIPTNEEWVIAEDAIKL 397
           F    + +       +VIPTNEE VIA +A +L
Sbjct: 359 FSDGHIESPDSRFPVLVIPTNEELVIAREATRL 391


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: 425
Number of extensions: 20
Number of successful extensions: 4
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: 398
Length adjustment: 31
Effective length of query: 370
Effective length of database: 367
Effective search space:   135790
Effective search space used:   135790
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 GFF1535 HP15_1499 (acetate/propionate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.19543.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.19543.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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