GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Acidovorax sp. GW101-3H11

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate Ac3H11_435 Carbamoyl-phosphate synthase small chain (EC 6.3.5.5)

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__acidovorax_3H11:Ac3H11_435
          Length = 405

 Score =  330 bits (847), Expect = 4e-95
 Identities = 167/378 (44%), Positives = 240/378 (63%), Gaps = 13/378 (3%)

Query: 58  ARLVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTG 117
           A L L DG+++   S GA GT + E+VFNT++TGYQEILTDPSY  Q V +T P IGN G
Sbjct: 30  AILALADGTVFIGNSIGATGTTVGEVVFNTAITGYQEILTDPSYCQQIVTLTYPHIGNYG 89

Query: 118 VNPDDEESGQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRLR- 176
           VN +D E+ +    GL+I++L +  SN+R T+TL+ YL     + + ++DTR +TR LR 
Sbjct: 90  VNAEDIEADKVHAAGLIIKDLPLLASNFRSTETLSQYLVREKTVAIANIDTRKLTRLLRT 149

Query: 177 ---EDGSLIGVLSTE---QSKTDDELLQMSRSWDIVGIDLISDVSCKSPYEWVDKTNAEW 230
              ++G+++G+ + +   Q   D+ + +   + ++ G+DL   V+  S YEW   T  EW
Sbjct: 150 QGAQNGAIVGLAAGQVVTQGLIDEAIAKAKAAPNMAGLDLAKVVTTASRYEW---TQTEW 206

Query: 231 DFNT--NSRDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILF 288
              +         + V+AYDFG+K+NILR L+  GC++TVVP+  PAAE L MNPDG+  
Sbjct: 207 QLGSGYGVLAQPRFHVVAYDFGVKKNILRMLAERGCKVTVVPAQTPAAEVLAMNPDGVFL 266

Query: 289 SNGPGDPSAVPYAVETVKELL-GKVPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVR 347
           SNGPGDP+   YA+E  ++++   VP +GIC+GHQ++  A G  TFKM   HHG NHPV+
Sbjct: 267 SNGPGDPAPCDYAIEATRQIIDAGVPTFGICLGHQIMALASGATTFKMDNSHHGANHPVK 326

Query: 348 NNRTGQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASP 407
           +   G+V I++QNH +AVD ASLP  +  TH++L DG+  GL+  +      Q HPEASP
Sbjct: 327 DLDNGRVSITSQNHGFAVDMASLPATLRATHISLFDGTLQGLARTDKPAFCFQGHPEASP 386

Query: 408 GPHDSDNAFREFIELMKR 425
           GPHD    F  F  LM++
Sbjct: 387 GPHDIAYLFDRFTALMEK 404


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: 458
Number of extensions: 17
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: 405
Length adjustment: 32
Effective length of query: 398
Effective length of database: 373
Effective search space:   148454
Effective search space used:   148454
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 Ac3H11_435 (Carbamoyl-phosphate synthase small chain (EC 6.3.5.5))
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.8036.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.8036.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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