GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Magnetospirillum magneticum AMB-1

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate WP_011386228.1 AMB_RS19600 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>NCBI__GCF_000009985.1:WP_011386228.1
          Length = 379

 Score =  298 bits (764), Expect = 1e-85
 Identities = 170/381 (44%), Positives = 232/381 (60%), Gaps = 8/381 (2%)

Query: 1   MTETQSLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFG----DTKNIWLRR 56
           M+    + LA+ LI  PSVTP+D     +LA  L ++GFA   +       + +N++ R 
Sbjct: 1   MSFRDPVPLAQALIRCPSVTPEDAGALDVLAGALEELGFACHHIRSATGGPEIRNLYARL 60

Query: 57  GTKAPVVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERF 116
           GT+AP +CFAGHTDVVP G  + W   PF      GRL+GRG+ADMK +IACFV A  R 
Sbjct: 61  GTEAPNLCFAGHTDVVPPG--KGWTVEPFAAGIDQGRLFGRGSADMKGAIACFVAAVARL 118

Query: 117 VAKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIK 176
           + +    +GS++LLIT DEEG A+DGT KV+D L AR E ID CIVGEPT   KLGDM+K
Sbjct: 119 L-EDGAPKGSLSLLITGDEEGPAVDGTVKVLDWLAARGERIDCCIVGEPTNPRKLGDMMK 177

Query: 177 NGRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQIS 236
            GRRGSL+  LTV G QGH AYPHLA NP+      L  LT+   DEG  +F  ++  ++
Sbjct: 178 IGRRGSLNCRLTVFGTQGHSAYPHLADNPIPRLLDILRRLTEAPLDEGTPHFQASTLALT 237

Query: 237 NINGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFL 296
            ++ G  ATNVIP E    FN RF+   + A L++ +   + + G + +++   SG+ FL
Sbjct: 238 TVDVGNPATNVIPAEARAGFNIRFNDLHSGASLERWIRDTVAQAGGEVEIKVEVSGESFL 297

Query: 297 TQAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENV 356
           T  G L+D    A  E  G+  ELST+GGTSD RFIK     ++E G    T+H+ +E+V
Sbjct: 298 TPPGALSDALAEAAFEVTGLRPELSTSGGTSDARFIKNHC-PVVEFGLVGQTMHKSDEHV 356

Query: 357 RLNDIPKLSAVYEGILARLLA 377
            + D+  L+ +Y  +L RL A
Sbjct: 357 SVADMEALTEIYRRVLVRLAA 377


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: 426
Number of extensions: 25
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: 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 WP_011386228.1 AMB_RS19600 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.30003.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30003.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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