GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Herbaspirillum seropedicae SmR1

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate HSERO_RS06920 HSERO_RS06920 carbamoyl phosphate synthase small subunit

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__HerbieS:HSERO_RS06920
          Length = 387

 Score =  331 bits (849), Expect = 2e-95
 Identities = 171/379 (45%), Positives = 241/379 (63%), Gaps = 10/379 (2%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A L L DGS++   S GA G    E+VFNT++TGYQEILTDPSY+ Q V +T P IGNTG
Sbjct: 12  AVLALADGSVFQGFSIGAAGNTTGEVVFNTAMTGYQEILTDPSYSRQIVTLTYPHIGNTG 71

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLRE 177
           VN +D E+ Q    GL+I++L    SN+R  ++L+DYL E +I+ +  +DTR +TR LRE
Sbjct: 72  VNREDVEASQIHAAGLIIKDLPRLLSNFRSQQSLSDYLKEGNIVSIAGIDTRKLTRILRE 131

Query: 178 DGSLIGVL---STEQSKTDDELLQMSRSWD-IVGIDLISDVSCKSPYEWVDKTNAEWDFN 233
            G+  G +     + +    + L+++R++  + G+DL   VS +  Y W   T  EW   
Sbjct: 132 KGAQNGAIVAGEADIAAATAKALELARAFPGLAGMDLAKVVSTQKAYNW---TETEWRLG 188

Query: 234 TN--SRDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNG 291
                +    + V+A+D+G+K NILR L+  GC++TV+P+   AAEAL +NPDGI  SNG
Sbjct: 189 RGYGQQITPKFHVVAFDYGVKYNILRMLAERGCKVTVLPAQATAAEALALNPDGIFLSNG 248

Query: 292 PGDPSAVPYAVETVKELLGK-VPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNR 350
           PGDP    YA+   KEL+ + +P +GIC+GHQ++  A G KT KMKFGHHG NHPV++  
Sbjct: 249 PGDPEPCDYAIAASKELIERGIPTFGICLGHQIMALASGAKTLKMKFGHHGANHPVQDLD 308

Query: 351 TGQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPH 410
           + QV I++QNH +AVD A+LP    VTHV+L DGS  G    +      Q HPEASPGPH
Sbjct: 309 SKQVMITSQNHGFAVDQATLPANCRVTHVSLFDGSLQGFERTDKPAFCFQGHPEASPGPH 368

Query: 411 DSDNAFREFIELMKRSKQS 429
           D    F +F+ +M++ + +
Sbjct: 369 DIAPLFDKFVAMMEKKQNA 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: 431
Number of extensions: 14
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 HSERO_RS06920 HSERO_RS06920 (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.6912.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6912.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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