GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Burkholderia phytofirmans PsJN

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate BPHYT_RS14195 BPHYT_RS14195 carbamoyl phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__BFirm:BPHYT_RS14195
          Length = 384

 Score =  338 bits (867), Expect = 2e-97
 Identities = 174/376 (46%), Positives = 239/376 (63%), Gaps = 12/376 (3%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A L L DG+++   S GAPG  I E+VFNT++TGYQEILTDPSYA Q V +T P IGN G
Sbjct: 8   ALLALADGTVFRGYSIGAPGHTIGEVVFNTAITGYQEILTDPSYARQIVTLTYPHIGNVG 67

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
           VN +D E+ +    GL+IR+L +  SN+R  +TL  YL +  ++ +  LDTR +TR LR+
Sbjct: 68  VNAEDVEATKVHAAGLIIRDLPVLASNFRMERTLPQYLQDEGVVAIAGLDTRMLTRVLRD 127

Query: 178 DGSLIGVLSTEQSKTDDE--LLQMSRSW-DIVGIDLISDVSCKSPYEWVDKTNAEWDFNT 234
            G+  G +    + +DDE   ++++RS+  + G+DL   VS K  YEW   T  EW    
Sbjct: 128 KGAQNGAI---LAGSDDEAKAIELARSFPGLSGMDLAKVVSTKETYEW---TQTEWRLGE 181

Query: 235 --NSRDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGP 292
              ++    Y+V+A+D+G+K NILR L+  GC +TV+P+   AA+AL +NPDGI  SNGP
Sbjct: 182 GYGTQKAPKYRVVAFDYGVKYNILRMLAERGCHVTVLPAQASAADALALNPDGIFLSNGP 241

Query: 293 GDPSAVPYAVETVKELLGK-VPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNRT 351
           GDP    YA+   KEL+ + +P +GIC+GHQ++G A+G KT KMK GHHG NHPV++   
Sbjct: 242 GDPEPCDYAITATKELIERGIPTFGICLGHQIMGLAVGAKTMKMKTGHHGANHPVKDLDD 301

Query: 352 GQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPHD 411
           G+V I++QNH +AVD  +LP     THV+L DG+  G +  +      Q HPEASPGPHD
Sbjct: 302 GRVVITSQNHGFAVDADTLPANARATHVSLFDGTLQGFALTDKPAFCFQGHPEASPGPHD 361

Query: 412 SDNAFREFIELMKRSK 427
               F  F  LM   K
Sbjct: 362 IAYLFDRFTALMDTKK 377


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: 469
Number of extensions: 16
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: 384
Length adjustment: 31
Effective length of query: 399
Effective length of database: 353
Effective search space:   140847
Effective search space used:   140847
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 BPHYT_RS14195 BPHYT_RS14195 (carbamoyl phosphate synthase small subunit)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.23514.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.23514.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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