GapMind for Amino acid biosynthesis

 

Alignments for a candidate for hisF in Marinobacter adhaerens HP15

Align Imidazole glycerol phosphate synthase subunit HisF; IGP synthase cyclase subunit; IGP synthase subunit HisF; ImGP synthase subunit HisF; IGPS subunit HisF; EC 4.3.2.10 (characterized)
to candidate GFF3065 HP15_3009 protein containing histidine biosynthesis, HisF domain

Query= SwissProt::Q7SIB9
         (252 letters)



>FitnessBrowser__Marino:GFF3065
          Length = 257

 Score =  306 bits (784), Expect = 3e-88
 Identities = 157/256 (61%), Positives = 198/256 (77%), Gaps = 6/256 (2%)

Query: 1   MSLAKRIVPCLDVHAGRVVKGVNFVNLRDAGDPVEAARAYDEAGADELVFLDISATHEER 60
           M+LAKRI+PCLDV  GRVVKGVNFV++RDAGDPVE AR Y+E GADE+ FLDI+A+HE R
Sbjct: 1   MALAKRIIPCLDVDKGRVVKGVNFVDIRDAGDPVEVARRYNEQGADEITFLDITASHESR 60

Query: 61  AILLDVVARVAERVFIPLTVGGGVRSLEDARKLLLSGADKVSVNSAAVRRPELIRELADH 120
               + V R+A  VFIPLTVGGGVR+++D RKLL +GADKVS+N+AAV  PE +RE AD 
Sbjct: 61  DTTYETVERMAAEVFIPLTVGGGVRTVDDIRKLLNAGADKVSINTAAVFNPEFVREAADR 120

Query: 121 FGAQAVVLAIDAR---WRGDFP--EVHVAGGRVPTGLHAVEWAVKGVELGAGEILLTSMD 175
           FG+Q +V+AIDA+     G+ P  E+   GGR PTGL AVEWA K VE+GAGE+LLTSMD
Sbjct: 121 FGSQCIVVAIDAKRVSEEGEEPRWEIFTHGGRKPTGLDAVEWARKMVEMGAGELLLTSMD 180

Query: 176 RDGTKEGYDLRLTRMVAEAVGVPVIASGGAGRMEHFLEAF-QAGAEAALAASVFHFGEIP 234
           RDGTK G+DL LT+ +++AV VPVIASGG G ++H  +   Q GA+A LAAS+FHFG+  
Sbjct: 181 RDGTKIGFDLGLTKAISDAVIVPVIASGGVGELQHLADGVTQGGADAVLAASIFHFGQHT 240

Query: 235 IPKLKRYLAEKGVHVR 250
           IP+ K ++  +G+ VR
Sbjct: 241 IPEAKAFMKAQGIEVR 256


Lambda     K      H
   0.321    0.138    0.398 

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: 246
Number of extensions: 10
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: 252
Length of database: 257
Length adjustment: 24
Effective length of query: 228
Effective length of database: 233
Effective search space:    53124
Effective search space used:    53124
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: 47 (22.7 bits)

Align candidate GFF3065 HP15_3009 (protein containing histidine biosynthesis, HisF domain)
to HMM TIGR00735 (hisF: imidazoleglycerol phosphate synthase, cyclase subunit)

Software error:

../bin/blast/fastacmd -i /tmp/list.3078.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3078.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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