GapMind for Amino acid biosynthesis

 

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

Align 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19) (characterized)
to candidate 3607613 Dshi_1022 3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq)

Query= BRENDA::A6WUV8
         (450 letters)



>FitnessBrowser__Dino:3607613
          Length = 450

 Score =  461 bits (1186), Expect = e-134
 Identities = 248/446 (55%), Positives = 308/446 (69%), Gaps = 3/446 (0%)

Query: 1   MSHSAPPKPATARRSEALTGEIRIPGDKSISHRSFMFGGLASGETRITGLLEGEDVINTG 60
           MS    P P TA  S  L+G  ++PGDKSISHRS + G LA GET++TGLLEG+DV++T 
Sbjct: 1   MSAHGDPIPMTAHPSGPLSGTAQVPGDKSISHRSLILGALAVGETKVTGLLEGQDVLDTA 60

Query: 61  RAMQAMGAKIRKDGD-AWIINGVGNGCLLQPEAALDFGNAGTGARLTMGLVGTYDMRTSF 119
           RAMQA GA++ +    AW ++GVG G   +PE  +D GN+GTG RL MG + T  +  +F
Sbjct: 61  RAMQAFGAEVIQHAPGAWSVHGVGTGGFAEPEDVIDCGNSGTGVRLIMGAMATTPITATF 120

Query: 120 IGDASLSKRPMGRVLNPLREMGVQVEAAEGDRMPLTLIGPKTANPITYRVPMASAQVKSA 179
            GDASL  RPMGR+ +PL   G       G R+P+TL G     P+ Y VP+ SAQVKSA
Sbjct: 121 TGDASLRSRPMGRITDPLAGFGTTAVGRRGGRLPMTLTGAADPVPVRYTVPVPSAQVKSA 180

Query: 180 VLLAGLNTPGVTTVIEPVMTRDHTEKMLQGFGADLSVETDKDGVRHIRITGQGKLIGQTI 239
           VLLAGLN PG T VIE   TRDH+E+ML+GFGA++SVE+  +G   I +TGQ +L  QTI
Sbjct: 181 VLLAGLNAPGQTVVIEAEATRDHSERMLRGFGAEISVESAPEG-NVITLTGQPELRPQTI 239

Query: 240 DVPGDPSSTAFPLVAALLVEGSDVTIRNVLMNPTRTGLILTLQEMGADIEVLNARLAGGE 299
            VP DPSS AFP+   L+V GSDV +  + +NPTR GL  TLQEMGA++   N R  GGE
Sbjct: 240 VVPRDPSSAAFPVAVGLIVPGSDVLVPGIGLNPTRAGLYTTLQEMGAELSFENMREEGGE 299

Query: 300 DVADLRVKAS-KLKGVVVPPERAPSMIDEYPVLAIAAAFAEGETVMDGLDELRVKESDRL 358
            VADLR + S  ++G+ VPPERAPSMIDEYP+L++ AA+A G TVM G+ ELRVKESDR+
Sbjct: 300 PVADLRARFSDAMQGIEVPPERAPSMIDEYPILSVIAAYATGRTVMRGVKELRVKESDRI 359

Query: 359 AAVARGLEANGVDCTEGEMSLTVRGRPDGKGLGGGTVATHLDHRIAMSFLVMGLASEKPV 418
            A+ARGLEA GV   E E +L V G   G   GG T A+HLDHRIAMSFL  GLA++ PV
Sbjct: 360 DAMARGLEACGVRVEEDEDTLIVHGMGPGGVPGGATCASHLDHRIAMSFLCCGLAAQTPV 419

Query: 419 TVDDSTMIATSFPEFMDMMPGLGAKI 444
           +VDD   IATSFP F  +M  LGA +
Sbjct: 420 SVDDGGPIATSFPIFEPLMTALGATL 445


Lambda     K      H
   0.316    0.135    0.381 

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: 670
Number of extensions: 44
Number of successful extensions: 4
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: 450
Length of database: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
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: 51 (24.3 bits)

Align candidate 3607613 Dshi_1022 (3-phosphoshikimate 1-carboxyvinyltransferase (RefSeq))
to HMM TIGR01356 (aroA: 3-phosphoshikimate 1-carboxyvinyltransferase (EC 2.5.1.19))

Software error:

../bin/blast/fastacmd -i /tmp/list.24537.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.24537.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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