GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapE in Cupriavidus basilensis 4G11

Align Succinyl-diaminopimelate desuccinylase; SDAP desuccinylase; N-succinyl-LL-2,6-diaminoheptanedioate amidohydrolase; EC 3.5.1.18 (characterized)
to candidate RR42_RS11950 RR42_RS11950 succinyl-diaminopimelate desuccinylase

Query= SwissProt::Q9JYL2
         (381 letters)



>FitnessBrowser__Cup4G11:RR42_RS11950
          Length = 383

 Score =  469 bits (1206), Expect = e-137
 Identities = 235/380 (61%), Positives = 282/380 (74%), Gaps = 8/380 (2%)

Query: 6   SLELAKELISRPSVTPDDRDCQKLLAERLHKIGFAAEELHFGD----TKNIW-LRRGTKA 60
           +L L ++LI R SVTP D  CQ +L  RL  +GFA E +  G       N+W ++RGT+ 
Sbjct: 4   TLALTEDLIRRRSVTPADEGCQAVLETRLKALGFACEAIVSGPDDFRVTNLWAVKRGTRG 63

Query: 61  P---VVCFAGHTDVVPTGPVEKWDSPPFEPAERDGRLYGRGAADMKTSIACFVTACERFV 117
               ++ FAGHTDVVPTGP+E+W S PF P+ RDG+LYGRGAADMKTSIA FV A E FV
Sbjct: 64  QDGKLLAFAGHTDVVPTGPLEQWGSDPFLPSHRDGKLYGRGAADMKTSIAGFVVAVEEFV 123

Query: 118 AKHPNHQGSIALLITSDEEGDALDGTTKVVDVLKARDELIDYCIVGEPTAVDKLGDMIKN 177
             HP+H GSIA LITSDEEG A DGT KVV  LKAR E +DYC++GEPT+VD LGDM+KN
Sbjct: 124 QAHPDHAGSIAFLITSDEEGPAHDGTVKVVQALKARGERLDYCVIGEPTSVDTLGDMVKN 183

Query: 178 GRRGSLSGNLTVKGKQGHIAYPHLAINPVHTFAPALLELTQEVWDEGNEYFPPTSFQISN 237
           GRRGSLSG LTVKG QGHIAYPHLA NP+H  APAL +L  E WDEGNEYFP TS+Q+SN
Sbjct: 184 GRRGSLSGKLTVKGVQGHIAYPHLARNPIHLAAPALTDLVNERWDEGNEYFPATSWQMSN 243

Query: 238 INGGTGATNVIPGELNVKFNFRFSTESTEAGLKQRVHAILDKHGVQYDLQWSCSGQPFLT 297
           I+GGTGATNVIPG + V FNFRFST ST  GLK RVHAIL++H + YDL W+  G+PFLT
Sbjct: 244 IHGGTGATNVIPGHVTVDFNFRFSTASTPDGLKARVHAILERHQLDYDLDWTLGGEPFLT 303

Query: 298 QAGKLTDVARAAIAETCGIEAELSTTGGTSDGRFIKAIAQELIELGPSNATIHQINENVR 357
             G L++    AIA   G++ ELSTTGGTSDGRFI  I  ++IE GP NA+IH+I+E+V 
Sbjct: 304 ARGDLSEALAGAIAAETGVKTELSTTGGTSDGRFIAKICPQVIEFGPPNASIHKIDEHVE 363

Query: 358 LNDIPKLSAVYEGILARLLA 377
           +  I  L  +Y G+L RL+A
Sbjct: 364 VRFIEPLKNIYRGVLERLIA 383


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: 490
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: 383
Length adjustment: 30
Effective length of query: 351
Effective length of database: 353
Effective search space:   123903
Effective search space used:   123903
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 RR42_RS11950 RR42_RS11950 (succinyl-diaminopimelate desuccinylase)
to HMM TIGR01246 (dapE: succinyl-diaminopimelate desuccinylase (EC 3.5.1.18))

Software error:

../bin/blast/fastacmd -i /tmp/list.30611.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.30611.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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