GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapC in Pseudomonas fluorescens GW456-L13

Align succinyldiaminopimelate transaminase (EC 2.6.1.17) (characterized)
to candidate PfGW456L13_4713 N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17)

Query= BRENDA::Q9ZEX3
         (397 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_4713
          Length = 399

 Score =  413 bits (1062), Expect = e-120
 Identities = 217/395 (54%), Positives = 264/395 (66%), Gaps = 4/395 (1%)

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

Query: 61  VYPSTKGEPALRQAISQWLSRRYSIPAP--DPESEVLPVLGSREALFAFAQTVIDPSAGA 118
           VYP+T G P LR+AI+ W  RR+ +P    DP   VLPV G+REALFAF QTV++    A
Sbjct: 60  VYPTTLGIPELREAIAAWCERRFDVPKGWIDPARNVLPVNGTREALFAFTQTVVNRGDDA 119

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

Query: 179 AGNVMSLEEWRTLFELSDRHGFVIAAYECYSEIYLDEDTPPLGSLQAARRLGRDRYTNLV 238
            G ++ +E  + L  L+D + FVIAA ECYSE+Y DE TPP G L A   LGR  +   V
Sbjct: 180 TGALIPVETLKKLIALADEYDFVIAADECYSELYFDEQTPPPGLLSACAELGRKDFKRCV 239

Query: 239 AFSSLSKRSNVPGMRSGFVAGDAALLARFLLYRTYHGSAMSPVVSAASIAAWSMRRMCR- 297
            F SLSKRSN+PG+RSGFVAGDA +L  FLLYRTYHG AM      AS+AAW+     R 
Sbjct: 240 VFHSLSKRSNLPGLRSGFVAGDADVLKGFLLYRTYHGCAMPVQTQLASVAAWNDEVHVRA 299

Query: 298 KTAQYRAKFEAVLPILQNVLDVRAPQASFYLWAGTPGSDTAFARELYGRTGVTVLPGSLL 357
             A YR KF+AVL IL  VLDV+ P  SFYLW    G D AF R+L+ +  VTV+PGS L
Sbjct: 300 NRALYREKFDAVLEILSPVLDVQRPDGSFYLWPNVAGDDAAFCRDLFEQEHVTVVPGSYL 359

Query: 358 AREAHNANPGQGRIRIALVAPLDQCVQAAERIAHF 392
           +R+    NPG GR+R+ALVAPL +CV+AAERI  F
Sbjct: 360 SRDVDGVNPGAGRVRMALVAPLAECVEAAERIRDF 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: 512
Number of extensions: 27
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 PfGW456L13_4713 (N-succinyl-L,L-diaminopimelate aminotransferase alternative (EC 2.6.1.17))
to HMM TIGR03538 (dapC: succinyldiaminopimelate transaminase (EC 2.6.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.1125.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.1125.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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