GapMind for Amino acid biosynthesis

 

Alignments for a candidate for dapF in Pseudomonas putida KT2440

Align Diaminopimelate epimerase; DAP epimerase; EC 5.1.1.7; PLP-independent amino acid racemase (uncharacterized)
to candidate PP_3790 PP_3790 diaminopimelate epimerase

Query= curated2:Q8R9S4
         (274 letters)



>FitnessBrowser__Putida:PP_3790
          Length = 268

 Score =  168 bits (426), Expect = 1e-46
 Identities = 92/265 (34%), Positives = 150/265 (56%), Gaps = 15/265 (5%)

Query: 1   MRFTKMHGLGNDFIVIEAVEGVDYSELAV-KLCDRHFGIGADGLLVVEPSHIADIKMRIF 59
           M+F K H  GND++V       D S+  + ++CDRH G+G+DG+LV        + +RI+
Sbjct: 1   MQFYKYHAAGNDYLVYRDCVPFDCSKPMISRICDRHRGLGSDGILVPVIKEGERLSVRIY 60

Query: 60  NADGSEAEMCGNGSRCFAKYVYEKGIVSKQKMTVETLAGVIMPELFVENGKIKSVKVYMG 119
           N DGS+AE  GNG R   +Y++++ IV+     + T  G++  ++ ++NG+   + + MG
Sbjct: 61  NTDGSQAEKSGNGLRILCRYLWDQNIVAGSPFEISTKGGIVTCQV-LDNGQ--RISIAMG 117

Query: 120 SPIFESSKIPVKSEKQKFIDEPVKIDGKTYRLSSVRVGVPHTILFVSSFEESFMKELGPK 179
              F ++               V +DG   +L  V +G PH ++FV    E+  ++LGP 
Sbjct: 118 QAAFANTAAFT-----------VDVDGTPLQLHPVSMGNPHCVVFVDQPTETLARQLGPL 166

Query: 180 IEKSSLFPEGTNVDFVKVEDEENISVRTWERGVGLTLACGSGASASAVVSSLLGRTRRSV 239
           IE+ S+FP+ TNV FV+V D + + V+ WERGVG TL+ G+ + A+A VS  LG     V
Sbjct: 167 IERLSIFPDRTNVQFVRVIDRQTLEVQIWERGVGYTLSSGTSSCAAAAVSRRLGLVGPRV 226

Query: 240 NVHFKAGVLLVEWKEDNSIYLSGEV 264
            V+   GV+++E  +D  + + G V
Sbjct: 227 AVNMAGGVIMIELDDDYHVLMQGPV 251


Lambda     K      H
   0.318    0.136    0.386 

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: 183
Number of extensions: 9
Number of successful extensions: 3
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: 274
Length of database: 268
Length adjustment: 25
Effective length of query: 249
Effective length of database: 243
Effective search space:    60507
Effective search space used:    60507
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 (21.7 bits)
S2: 47 (22.7 bits)

Align candidate PP_3790 PP_3790 (diaminopimelate epimerase)
to HMM TIGR00652 (dapF: diaminopimelate epimerase (EC 5.1.1.7))

Software error:

../bin/blast/fastacmd -i /tmp/list.32122.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.32122.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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