GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Dinoroseobacter shibae DFL-12

Align Acetate kinase; EC 2.7.2.1; Acetokinase (uncharacterized)
to candidate 3607216 Dshi_0632 acetate kinase (RefSeq)

Query= curated2:B8EIS2
         (404 letters)



>FitnessBrowser__Dino:3607216
          Length = 382

 Score =  410 bits (1055), Expect = e-119
 Identities = 214/394 (54%), Positives = 277/394 (70%), Gaps = 17/394 (4%)

Query: 5   VITLNAGSSSIKFALFREGLTQEGSAKELTPMAIGLAEMVGEERRITVHDGAGAKIYEVK 64
           ++TLNAGSSS+KFA++        +A     +  G  + +G   R+ V+     K     
Sbjct: 4   LLTLNAGSSSVKFAVYE-------AANAPLLIVAGEVDGLGPAARLIVNTNPATK----- 51

Query: 65  RTEHVDAPFHAEALRRILAWRQSAFPDAEVVAAGHRVVHGGVHYSAPVIVTDEVLKYLHT 124
               +    HA AL  ILA  +      +VV  GHR+VHGG  ++APV +T +V++ L  
Sbjct: 52  --RDLGPTDHAAALHAILAALRPILSGRQVVGVGHRIVHGGGAFTAPVELTPDVIEALEA 109

Query: 125 LIPLAPLHEPYNIAGILGAREAWPHVEQVACFDTAFHRTHPFVNDVFALPRRFYDEGVRR 184
            +PLAPLH+P+N+A +  AR+A+P   Q+ CFDTAFH  HP+VND FALPRRFY+ GVRR
Sbjct: 110 FVPLAPLHQPHNLAMVAAARQAFPDAVQIGCFDTAFHAGHPWVNDTFALPRRFYEAGVRR 169

Query: 185 YGFHGLSYEYIVRRLREIAPLHAAGRVVVAHLGNGASMCAIRDGLSVASSMGFTALDGLP 244
           YGFHGLSY+YI  +LR   P  AAGRVV+AHLGNGASMCA+RDG SV S+MGF+ALDGLP
Sbjct: 170 YGFHGLSYDYITDKLRADCPELAAGRVVIAHLGNGASMCAVRDGRSVGSTMGFSALDGLP 229

Query: 245 MGTRCGQLDPGVVLYLMQEKKMSAAEITDLLYRESGLKGLSGLSHDMRELEAADTLEAQQ 304
           MGTRCGQLDPGV+LY+M E+ MS  EIT +LY ESGL+GLSG SHDMR L+A+D   A +
Sbjct: 230 MGTRCGQLDPGVLLYMM-EQGMSREEITSILYEESGLQGLSGFSHDMRTLQASDDPRAAE 288

Query: 305 AIEYFVFRIRRELGGLAAVLKGIDAIVFCGGIGENSRHVRERVLEGMEWIGVELDRSANS 364
           AI+Y+VFRIRRELG + AVL GIDA+VFCGGIGEN+  +R RV+EGM+++G+ LD  AN+
Sbjct: 289 AIDYYVFRIRRELGAMTAVLGGIDALVFCGGIGENAAVIRARVIEGMDYLGLSLDAEANA 348

Query: 365 ANAEVISSERSRTRVFVIPTDEEGMIARHTLALL 398
            NA  +++      + VIPT+EE +IAR   A L
Sbjct: 349 RNATRVAT--GPVPILVIPTNEELVIARAVSAAL 380


Lambda     K      H
   0.322    0.137    0.404 

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: 467
Number of extensions: 15
Number of successful extensions: 5
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: 404
Length of database: 382
Length adjustment: 31
Effective length of query: 373
Effective length of database: 351
Effective search space:   130923
Effective search space used:   130923
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 (21.9 bits)
S2: 50 (23.9 bits)

Align candidate 3607216 Dshi_0632 (acetate kinase (RefSeq))
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.9268.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.9268.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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