GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Phaeobacter inhibens BS107

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate GFF653 PGA1_c06670 carbamoyl-phosphate synthase small chain

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__Phaeo:GFF653
          Length = 387

 Score =  343 bits (880), Expect = 5e-99
 Identities = 177/378 (46%), Positives = 241/378 (63%), Gaps = 7/378 (1%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A L L DG+I+    FGA G  +AEL FNT++TGYQEI+TDPSYAGQ V  T P IGNTG
Sbjct: 11  ACLALADGTIFYGNGFGAYGETVAELCFNTAMTGYQEIMTDPSYAGQIVTFTFPHIGNTG 70

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
           V P+D+E+      G+V++      SNWR T+ L D+LT  + + +  +DTR +TR +R+
Sbjct: 71  VTPEDDETADPVAAGMVVKWDPTLASNWRATEELKDWLTRTNRIAIGGIDTRRLTRAIRQ 130

Query: 178 DGSLIGVLSTEQSKTDD--ELLQMSRSWD-IVGIDLISDVSCKSPYEWVDKTNAEWDFNT 234
            G+    L+ +     D   L+  +R W  + G+DL  DV+C   Y W D+    W    
Sbjct: 131 LGAPHVALAHDPDGNFDIEALVAKAREWSGLEGLDLAKDVTCSQSYRW-DEMRWAWPEGY 189

Query: 235 NSRDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGPGD 294
             ++   +KV+A D+G K+NILR L+S GC +TV+P++  A E L  +PDG+  SNGPGD
Sbjct: 190 TRQEAPKHKVVAIDYGAKRNILRCLASAGCDVTVLPASATAEEVLAHSPDGVFLSNGPGD 249

Query: 295 PSAV-PYAVETVKELLGK--VPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNRT 351
           P+A   YAV  ++++L    +P++GIC+GHQ+L  ALGGKT KM  GHHG NHPV+ N T
Sbjct: 250 PAATGEYAVPMIQQILDTTDLPMFGICLGHQMLALALGGKTVKMNHGHHGANHPVKENAT 309

Query: 352 GQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPHD 411
           G+VEI++ NH +AVD  SLP GVE THV+L DGS  G+   +  V S+Q+HPEASPGP D
Sbjct: 310 GKVEITSMNHGFAVDGQSLPDGVEETHVSLFDGSNCGIRISDRPVYSVQHHPEASPGPQD 369

Query: 412 SDNAFREFIELMKRSKQS 429
           S   F  F E M   K +
Sbjct: 370 SFYLFERFAEAMAARKSA 387


Lambda     K      H
   0.316    0.134    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: 532
Number of extensions: 23
Number of successful extensions: 4
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: 430
Length of database: 387
Length adjustment: 31
Effective length of query: 399
Effective length of database: 356
Effective search space:   142044
Effective search space used:   142044
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 GFF653 PGA1_c06670 (carbamoyl-phosphate synthase small chain)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.18684.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18684.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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