GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Klebsiella michiganensis M5al

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; Aspartyl peptidase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate BWI76_RS20870 BWI76_RS20870 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q8ZN75
         (375 letters)



>FitnessBrowser__Koxy:BWI76_RS20870
          Length = 375

 Score =  711 bits (1835), Expect = 0.0
 Identities = 347/375 (92%), Positives = 362/375 (96%)

Query: 1   MSCPVIELTQQLIRRPSLSPDDAGCQALMIERLRKIGFTIEHMDFGDTQNFWAWRGRGET 60
           MSCPVIEL QQLIRRPSLSPDDAGCQALMIERLR IGFT+E MDFGDTQNFWAWRGRGET
Sbjct: 1   MSCPVIELAQQLIRRPSLSPDDAGCQALMIERLRAIGFTVEPMDFGDTQNFWAWRGRGET 60

Query: 61  LAFAGHTDVVPAGDVDRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQHPH 120
           LAFAGHTDVVP+GD DRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQ+P 
Sbjct: 61  LAFAGHTDVVPSGDADRWINPPFEPTIRDGMLFGRGAADMKGSLAAMVVAAERFVAQYPD 120

Query: 121 HRGRLAFLITSDEEASAKNGTVKVVEALMARNERLDYCLVGEPSSTEIVGDVVKNGRRGS 180
           H+GRLAFLITSDEEASAKNGTVKVVEALMARNERLDYCLVGEPSSTE+VGDVVKNGRRGS
Sbjct: 121 HKGRLAFLITSDEEASAKNGTVKVVEALMARNERLDYCLVGEPSSTEVVGDVVKNGRRGS 180

Query: 181 LTCNLTIHGVQGHVAYPHLADNPVHRAAPFLNELVAIEWDRGNDFFPATSMQVANIQAGT 240
           LTCNLTIHGVQGHVAYPHLADNPVHRAAP L ELV IEWD+GN+FFP TSMQ+AN+Q+GT
Sbjct: 181 LTCNLTIHGVQGHVAYPHLADNPVHRAAPMLAELVTIEWDKGNEFFPPTSMQIANVQSGT 240

Query: 241 GSNNVIPGELFVQFNFRFSTELTDEMIKERVHALLEKHQLRYTVDWWLSGQPFLTARGKL 300
           GSNNVIPG++FVQFNFRFSTELTDEMIK RV ALLEK+ LRY+VDWWLSGQPFLT+RGKL
Sbjct: 241 GSNNVIPGDMFVQFNFRFSTELTDEMIKARVVALLEKYALRYSVDWWLSGQPFLTSRGKL 300

Query: 301 VDAVVNAIEHYNEIKPQLLTTGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQ 360
           VDAVVNAIEHYNEIKPQLLT GGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQ
Sbjct: 301 VDAVVNAIEHYNEIKPQLLTNGGTSDGRFIARMGAQVVELGPVNATIHKINECVNAADLQ 360

Query: 361 LLARMYQRIMEQLVA 375
           LLARMYQRIMEQLVA
Sbjct: 361 LLARMYQRIMEQLVA 375


Lambda     K      H
   0.322    0.136    0.415 

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: 604
Number of extensions: 13
Number of successful extensions: 1
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: 375
Length of database: 375
Length adjustment: 30
Effective length of query: 345
Effective length of database: 345
Effective search space:   119025
Effective search space used:   119025
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 BWI76_RS20870 BWI76_RS20870 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.18277.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18277.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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