GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas simiae WCS417

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate GFF1219 PS417_06195 succinyldiaminopimelate aminotransferase

Query= BRENDA::Q9ZEX3
         (397 letters)



>FitnessBrowser__WCS417:GFF1219
          Length = 399

 Score =  407 bits (1045), Expect = e-118
 Identities = 213/395 (53%), Positives = 262/395 (66%), Gaps = 4/395 (1%)

Query: 1   MNPRLDALHPYPFEKLRALLADAGKPTHDLPPINLSIGEPKHAAPACVGQAIAANLAGLS 60
           MN  L+ L PYPFEKLRALL     P  D  PI LSIGEPKH +P  V +A++ NL  ++
Sbjct: 1   MNNALNQLQPYPFEKLRALLGSV-TPNPDKRPIALSIGEPKHKSPTFVAEALSNNLDQMA 59

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAGA 118
           VYP+T G PALR+AI  W  RR+++P    DP   +LPV G+REALFAF QTV++    A
Sbjct: 60  VYPTTLGIPALREAIGAWCERRFNVPKGWLDPARNILPVNGTREALFAFTQTVVNRGDDA 119

Query: 119 LVVCPNPFYQIYEGAALLAGATPYYVNADPARDFGLRTGRVPDEVWRRTQLVFVCSPGNP 178
           LVV PNPFYQIYEGAA LAGA P+Y+    A  F      V  ++W+R Q++F+CSPGNP
Sbjct: 120 LVVSPNPFYQIYEGAAFLAGAKPHYLPCLDANGFNPDFEAVTPDIWKRCQILFLCSPGNP 179

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G ++ ++  + L  L+D + FVIAA ECYSE+Y DE +PP G L A   LGR  +   V
Sbjct: 180 TGALIPVDTLKKLIALADEYDFVIAADECYSELYFDEQSPPPGLLSACVELGRQDFKRCV 239

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAW-SMRRMCR 297
            F SLSKRSN+PG+RSGFVAGDA +L  FLLYRTYHG AM      ASIAAW     +  
Sbjct: 240 VFHSLSKRSNLPGLRSGFVAGDADILKAFLLYRTYHGCAMPVQTQLASIAAWQDEAHVLA 299

Query: 298 KTAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357
               YR KF+AVL IL+ VLDV +P   FYLW    G D  F R+L+    VTV+PGS L
Sbjct: 300 NRDLYREKFDAVLAILKPVLDVESPDGGFYLWPNVNGDDAGFCRDLFVEEHVTVVPGSYL 359

Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHF 392
           +RE    NPG GR+R+ALVAPL +CV+AAERI  F
Sbjct: 360 SREVDGFNPGAGRVRLALVAPLAECVEAAERIRDF 394


Lambda     K      H
   0.321    0.135    0.412 

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: 509
Number of extensions: 25
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: 397
Length of database: 399
Length adjustment: 31
Effective length of query: 366
Effective length of database: 368
Effective search space:   134688
Effective search space used:   134688
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: 50 (23.9 bits)

Align candidate GFF1219 PS417_06195 (succinyldiaminopimelate aminotransferase)
to HMM TIGR03538 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.17877.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.17877.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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