GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Paraburkholderia bryophila 376MFSha3.1

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate H281DRAFT_00597 H281DRAFT_00597 succinyldiaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__Burk376:H281DRAFT_00597
          Length = 379

 Score =  474 bits (1221), Expect = e-138
 Identities = 232/376 (61%), Positives = 282/376 (75%), Gaps = 4/376 (1%)

Query: 6   SLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGDTKNIWLRR----GTKAP 61
           +L L ++LI+R SVTPDD+ CQ+LL ERL  +GF  E +      N+W  +    G    
Sbjct: 4   TLALTEQLIARASVTPDDQHCQRLLIERLSALGFEHETIESNGVTNLWAVKRGVDGRAGK 63

Query: 62  VVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFVAKHP 121
           ++ FAGHTDVVPTGP+E+W S PFEP  RDG+LYGRGAADMKTSIA FV A E FVA HP
Sbjct: 64  LLAFAGHTDVVPTGPLEQWQSAPFEPTHRDGKLYGRGAADMKTSIAGFVVASEEFVAAHP 123

Query: 122 NHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKNGRRG 181
            H+GSIA LITSDEEG A DGT KVV+ L+AR E +DYCIVGEPT+  + GD +KNGRRG
Sbjct: 124 RHRGSIAFLITSDEEGPATDGTVKVVEALQARGERMDYCIVGEPTSSTQFGDTVKNGRRG 183

Query: 182 SLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISNINGG 241
           S+SG L VKG QGHIAYPHLA NPVH  APAL EL  E WD+GNEYFPPT++Q+SNI+ G
Sbjct: 184 SMSGKLVVKGVQGHIAYPHLARNPVHLLAPALAELVAERWDDGNEYFPPTTWQVSNIHSG 243

Query: 242 TGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLTQAGK 301
           TGATNVIPG  +V FNFRFST ST  GL+QRVHAILD+HG++YDLQW+ SG PFLT  G 
Sbjct: 244 TGATNVIPGHADVMFNFRFSTASTVEGLQQRVHAILDRHGLEYDLQWTVSGLPFLTPHGD 303

Query: 302 LTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVRLNDI 361
           L++    AI +  G+  ELSTTGGTSDGRFI  I Q+++E GP NA+IH+I+E++ +  I
Sbjct: 304 LSNALAKAIKDETGVSTELSTTGGTSDGRFIARICQQVVEFGPLNASIHKIDEHIDVAHI 363

Query: 362 PKLSAVYEGILARLLA 377
             L  VY  +L +L+A
Sbjct: 364 EPLKNVYRRVLEQLIA 379


Lambda     K      H
   0.317    0.135    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: 506
Number of extensions: 18
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: 381
Length of database: 379
Length adjustment: 30
Effective length of query: 351
Effective length of database: 349
Effective search space:   122499
Effective search space used:   122499
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: 50 (23.9 bits)

Align candidate H281DRAFT_00597 H281DRAFT_00597 (succinyldiaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.6680.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6680.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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