GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Paraburkholderia bryophila 376MFSha3.1

Align acetate kinase monomer (EC 2.7.2.15) (characterized)
to candidate H281DRAFT_01409 H281DRAFT_01409 acetate kinase

Query= metacyc::ACKCLOS-MONOMER
         (401 letters)



>FitnessBrowser__Burk376:H281DRAFT_01409
          Length = 393

 Score =  253 bits (645), Expect = 9e-72
 Identities = 151/401 (37%), Positives = 224/401 (55%), Gaps = 20/401 (4%)

Query: 4   LVINCGSSSIKYQFIDMKDETV--LAKGLVERIGIKGSVITHKVNGEKYVTETPME---- 57
           LV+N GSSSIK+   D +   +  + +G ++ +            G +       +    
Sbjct: 6   LVLNAGSSSIKFSAFDAQTAELACVLRGQIDGLFSSPHFAAFDAAGAQAGAHAWGDGASL 65

Query: 58  DHKKAIKLVLDALLNDEYGVIKNIDEISAVGHRIVHGGEKYANSVLIDEDVMKSIEDCVS 117
           DH +AI  + D L     G       ++AVGHR+VHGG ++   VL+D  V+  +     
Sbjct: 66  DHAEAIAHIADFLRGHREG-----HRLTAVGHRVVHGGARFVAPVLVDASVLAELHTLTP 120

Query: 118 LAPLHNPPHIIGINACKELMPNVPMVAVFDTAFHQTIPDYAYMYAIPYEYYDKYKIRKYG 177
           LAPLH P ++  I    E    +P +A FDTAFH T P+ A  +A+P    ++  +R+YG
Sbjct: 121 LAPLHQPHNLKPIAIIAERNSAMPQIACFDTAFHATQPEQAKAFALPAAVTER-GVRRYG 179

Query: 178 FHGTSHKYVSRTAAEFIGKKVEDLKMVVCHMGNGASITAVENGKSVDTSMGFTPLGGLAM 237
           FHG S++Y++    E         + VV H+GNGAS+ A+   +SV T+MGFT L GL M
Sbjct: 180 FHGLSYEYIASRLPEMSPAAAAG-RTVVAHLGNGASLCALSACRSVATTMGFTALDGLMM 238

Query: 238 GTRSGDMDPAVVTFLMDKLNINASEVNNLLNKKSGIEGLSGISSDMRDIKKGNYVDKDPK 297
           GTRSG +DP V+ +L+++LN+   EV NLL  +SG+ G+SGIS DMR +        DP+
Sbjct: 239 GTRSGSLDPGVILYLLNELNMTTREVENLLYSQSGLLGVSGISGDMRVL----LASDDPR 294

Query: 298 AMLAYSVFNYKIKQFIGSYTAVMNGLDCLVFTGGIGENSFENRREICKNMDYLGIKIDDK 357
           A  A  ++ Y+I + +GS  A + G+D LVFT GIGE++ + R+ I +   + GI ID  
Sbjct: 295 ARFAVELYVYRICRELGSLIAALKGIDALVFTAGIGEHATQVRQRIGEYAQWCGIDIDSD 354

Query: 358 KNDETMGIPMDISAEGSKVRVLVIPTNEELMIARDTKDIVG 398
            N         IS   S+V V ++PTNEELMIAR T+ ++G
Sbjct: 355 ANQANDSC---ISTPTSRVGVWIVPTNEELMIARHTRALIG 392


Lambda     K      H
   0.317    0.136    0.390 

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: 352
Number of extensions: 24
Number of successful extensions: 6
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: 393
Length adjustment: 31
Effective length of query: 370
Effective length of database: 362
Effective search space:   133940
Effective search space used:   133940
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate H281DRAFT_01409 H281DRAFT_01409 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.25026.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.25026.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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