GapMind for catabolism of small carbon sources

 

Alignments for a candidate for ackA in Dechlorosoma suillum PS

Align acetate kinase (EC 2.7.2.1) (characterized)
to candidate Dsui_3033 Dsui_3033 acetate kinase

Query= BRENDA::G4T0C7
         (401 letters)



>FitnessBrowser__PS:Dsui_3033
          Length = 397

 Score =  279 bits (713), Expect = 1e-79
 Identities = 167/405 (41%), Positives = 249/405 (61%), Gaps = 28/405 (6%)

Query: 8   ILVINSGSSSIKYRLIALPQ------EQVLADGLLERIGEQESRIIHRADDSGR-LNEIK 60
           +L +N+GSSSIK+ L  L        E VL+ G ++ IG +    I   DD G+ L+++ 
Sbjct: 5   VLTLNAGSSSIKFSLYELENGGGIAAEPVLS-GQIDGIGVKAH--IKAKDDKGKKLDDVD 61

Query: 61  ---QSVIAADHHQAFKAVFEILGEN---CSVDAIGHRVVHGGDRFSGPALVDDDTIASMR 114
              Q    + HH+A + +   L ++     + A+GHRVVHGG+R+S P  +DD+ I  + 
Sbjct: 62  IPLQGDAESQHHEALEFLISWLHDHEKGWKIVAVGHRVVHGGERYSRPMKLDDNIIEHLT 121

Query: 115 ALCRIAPLHNPVNLLGIESCLAHFPGVPQVAVFDTAFHQTMPPHAYRYAIPETWYSDYGI 174
            L  +APLH P NL G+++     P VPQVA FDTAFH+T  P A  +A+P  W +  G+
Sbjct: 122 RLIPLAPLHQPHNLDGVDALRTMMPEVPQVACFDTAFHRTQAPVAQAFALPR-WITGEGV 180

Query: 175 RRFGFHGTSHHYVARRAAEFIGKPFDRSHLITLHLGNGASATAIANGRSVDTSMGFTPLE 234
           +R+GFHG S+ Y+AR   ++   P     ++  HLGNGAS   + + +S  ++MGFT +E
Sbjct: 181 KRYGFHGLSYEYIARVLPDY--SPRANGRVVVAHLGNGASMCGMVDRKSQVSTMGFTAVE 238

Query: 235 GLVMGTRSGDLDPAIPLFVEQTENTDTDAIDRALNRESGLKGLCGTN-DLRTVLEQTNAG 293
           GL+MGTR+G LDP + L++ + +  D  A+ + L +ESGL G+ G + D+RT+L    A 
Sbjct: 239 GLMMGTRTGALDPGVMLYLMENKGMDVKALTKLLYKESGLLGVSGISPDMRTLL----AS 294

Query: 294 DE-RARLALDLYCYRIKKYIGAYYAVLGEVDALVFTGGVGENAAEVRRLACEGLSRLGIA 352
           D+  A+ A+DL+CYR+ + +G+  A +G +DALVFTGG+GE+AAEVRR  C   S LGI+
Sbjct: 295 DKPEAKEAVDLFCYRVVRELGSLAAAIGGIDALVFTGGIGEHAAEVRRRVCLQASWLGIS 354

Query: 353 IDEAANSDVTGAIAEIGLAESRTRILVIKTDEELQIAREAMAVLD 397
           IDE+AN+     I+E     S   +LVI T+EE  IAR    +L+
Sbjct: 355 IDESANALHANRISE---PRSTVDVLVIPTNEEWMIARHTATLLN 396


Lambda     K      H
   0.320    0.137    0.400 

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: 441
Number of extensions: 22
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: 397
Length adjustment: 31
Effective length of query: 370
Effective length of database: 366
Effective search space:   135420
Effective search space used:   135420
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 Dsui_3033 Dsui_3033 (acetate kinase)
to HMM TIGR00016 (ackA: acetate kinase (EC 2.7.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.17764.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17764.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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