GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Shewanella oneidensis MR-1

Align succinyl-diaminopimelate desuccinylase (EC 3.5.1.18) (characterized)
to candidate 201612 SO2471 succinyl-diaminopimelate desuccinylase (NCBI ptt file)

Query= BRENDA::Q9KQ52
         (377 letters)



>FitnessBrowser__MR1:201612
          Length = 384

 Score =  521 bits (1341), Expect = e-152
 Identities = 253/372 (68%), Positives = 293/372 (78%)

Query: 5   PVLALAKELISRQSVTPADAGCQDLMIERLKALGFEIESMVFEDTTNFWARRGTQSPLFV 64
           PV  L K LI+R SVTP D GCQ LM ERL A+GF IE+MVFEDTTN WARRG   P+F 
Sbjct: 12  PVTELTKALIARPSVTPLDEGCQTLMAERLAAIGFNIEAMVFEDTTNMWARRGNTGPVFC 71

Query: 65  FAGHTDVVPAGPLSQWHTPPFEPTVIDGFLHGRGAADMKGSLACMIVAVERFIAEHPDHQ 124
           FAGHTDVVP G LS+WHTPPFEPT+IDG+L+GRGAADMKGSLA M+VA ERF+A+HP+H 
Sbjct: 72  FAGHTDVVPTGDLSRWHTPPFEPTIIDGYLYGRGAADMKGSLAAMVVATERFVAKHPNHP 131

Query: 125 GSIGFLITSDEEGPFINGTVRVVETLMARNELIDMCIVGEPSSTLAVGDVVKNGRRGSIT 184
           GSI FLITSDEEGPFINGT RV++TL ARNE I   +VGEPSSTL +GDVVKNGRRGS+T
Sbjct: 132 GSIAFLITSDEEGPFINGTTRVIDTLEARNEKITWALVGEPSSTLKLGDVVKNGRRGSLT 191

Query: 185 GDLKVKGTQGHVAYPHLANNPVHKALPALAELAATQWDEGNAYFPPTSFQIPNLQAGTGA 244
            +L VKG QGHVAYPHLA+NP+HKA P LAEL+ T WD GNA+FPPTS QI N+  GTGA
Sbjct: 192 ANLTVKGVQGHVAYPHLADNPIHKAAPFLAELSQTHWDNGNAFFPPTSMQIANINGGTGA 251

Query: 245 SNVIPGEFDVQFNFRFSTELTDEEIKRRVHSVLDAHGLDYDVKWTLSGQPFLTDTGELLA 304
           SNVIPG  +V FNFR+STE+T E +  RV ++L AH LDYD++WT +G PFLT  G LL 
Sbjct: 252 SNVIPGALEVMFNFRYSTEVTAEILIERVETLLTAHELDYDIRWTFNGLPFLTGEGPLLD 311

Query: 305 AVVAAVEEVNHQAPALLTTGGTSDGRFIAQMGAQVVELGPVNATIHKVNECVRIADLEKL 364
           A   A+ +V        TTGGTSDGRFIA  GA+V+ELGPVNATIHKVNECV++ DLE+L
Sbjct: 312 ATRHAIRQVTGYDTDPQTTGGTSDGRFIAPTGAKVLELGPVNATIHKVNECVKVDDLEQL 371

Query: 365 TDMYQKTLNHLL 376
              Y+  L  LL
Sbjct: 372 ALCYEVILEQLL 383


Lambda     K      H
   0.318    0.135    0.403 

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: 533
Number of extensions: 16
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: 377
Length of database: 384
Length adjustment: 30
Effective length of query: 347
Effective length of database: 354
Effective search space:   122838
Effective search space used:   122838
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 (21.7 bits)
S2: 50 (23.9 bits)

Align candidate 201612 SO2471 (succinyl-diaminopimelate desuccinylase (NCBI ptt file))
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.21860.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21860.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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