GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argD'B in Marinobacter adhaerens HP15

Align Succinylornithine transaminase (EC 2.6.1.81) (characterized)
to candidate GFF3099 HP15_3042 bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein

Query= reanno::WCS417:GFF4238
         (406 letters)



>FitnessBrowser__Marino:GFF3099
          Length = 404

 Score =  537 bits (1383), Expect = e-157
 Identities = 262/403 (65%), Positives = 320/403 (79%), Gaps = 1/403 (0%)

Query: 3   VEQAPVQRADFDQVMVPNYAPAAFIPVRGEGSRVWDQAGRELIDFAGGIAVNVLGHAHPA 62
           + + PV R  FD+VMVPNYAP + IPVRGEGSR+WDQ GRE ID  GGIAV  LGH+HP 
Sbjct: 1   MNKEPVSRELFDEVMVPNYAPGSIIPVRGEGSRIWDQEGREFIDLQGGIAVTCLGHSHPG 60

Query: 63  LVGALTEQAHKLWHVSNVFTNEPALRLAHKLIDATFAERVFFCNSGAEANEAAFKLARRV 122
           LVGAL +QA K+WH+SNV TNEPALRLA  L D TFAERVFF NSGAEANEAAFKLARR 
Sbjct: 61  LVGALHDQAEKIWHLSNVMTNEPALRLAKTLCDLTFAERVFFANSGAEANEAAFKLARRY 120

Query: 123 AFDRFGSEKYEIIAALNSFHGRTLFTVNVGGQSKYSDGFGPKITGITHVPYNDLDALKAA 182
           A++  G EK EII+  NSFHGRTLFTV+VGGQ KY +GF P   GI H  +NDL+++K  
Sbjct: 121 AWEHHGKEKNEIISFKNSFHGRTLFTVSVGGQPKYLEGFEPAPGGIHHAEFNDLESVKKL 180

Query: 183 VS-DKTCAVVLEPIQGEGGVLPAELAYLQGARDLCDANNALLVFDEVQTGMGRSGHLFAY 241
           +S +KTCA+V+EPIQGEGGV+P + A+LQG RDLCD N+ALLVFDEVQ+G+GRSGH +AY
Sbjct: 181 ISKEKTCAIVVEPIQGEGGVMPGDQAFLQGLRDLCDENDALLVFDEVQSGVGRSGHFYAY 240

Query: 242 QHYGVTPDILTSAKSLGGGFPIAAMLTTEALAKHLVVGTHGTTYGGNPLACAVAEAVIDV 301
           Q YGV PDIL+SAK LGGGFP+AAMLTT  +A  L VGTHG+TYGGN LACAVA+ V+D 
Sbjct: 241 QMYGVVPDILSSAKGLGGGFPVAAMLTTAKVAASLGVGTHGSTYGGNALACAVAQRVVDT 300

Query: 302 INTPEVLAGVNAKHDLFKARLEQIGKQYGIFTEVRGMGLLLGCVLSDAFKGKAKDVFNAA 361
           ++ PE+L GV A+ D  +  +  IG++YG+FTEVRG GLLLGCVL++ ++GKAKD  NA 
Sbjct: 301 VSQPEILKGVKARSDKLRKGMMDIGERYGVFTEVRGAGLLLGCVLTEKWQGKAKDFLNAG 360

Query: 362 EKENLMILQAGPDVVRFAPSLVVEDADIKEGLDRFERAVKALT 404
            +E +M+L AG +V+R APSL++ + DI+  L+RFE AVK LT
Sbjct: 361 LEEGVMVLVAGANVIRLAPSLIIPEPDIELALERFEAAVKKLT 403


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: 522
Number of extensions: 13
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: 406
Length of database: 404
Length adjustment: 31
Effective length of query: 375
Effective length of database: 373
Effective search space:   139875
Effective search space used:   139875
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 GFF3099 HP15_3042 (bifunctional N-succinyldiaminopimelate-aminotransferase/acetylornithine transaminase protein)
to HMM TIGR03246 (astC: succinylornithine transaminase family (EC 2.6.1.81))

Software error:

../bin/blast/fastacmd -i /tmp/list.22934.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22934.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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