GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argC in Desulfovibrio vulgaris Miyazaki F

Align N-acetyl-gamma-glutamyl-phosphate reductase; AGPR; N-acetyl-glutamate semialdehyde dehydrogenase; NAGSA dehydrogenase; EC 1.2.1.38 (characterized)
to candidate 8500980 DvMF_1717 N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq)

Query= SwissProt::Q07906
         (345 letters)



>FitnessBrowser__Miya:8500980
          Length = 350

 Score =  295 bits (754), Expect = 2e-84
 Identities = 153/348 (43%), Positives = 219/348 (62%), Gaps = 3/348 (0%)

Query: 1   MMNVAIIGATGYSGAELFRLLYGHPHVSQCDVFSSSQDGIHLSESFPHVGAVDG--AVLH 58
           ++   ++G TGY+G EL RLL GHP++      S ++ G  LS+ +P +  + G  AV+ 
Sbjct: 3   IIRAGLVGVTGYTGMELTRLLAGHPNMRLVRATSRTEAGRPLSDIYPFLRGLPGGNAVMT 62

Query: 59  KLEIEALA-KYDAVFFATPPGVSGEWAPALVDRGVKVIDLSGDFRLKDGAVYAQWYGREA 117
             + + LA   D  F A P G + E    L  RG++V+DLS DFRL+D  VY  WY    
Sbjct: 63  APDPDDLADNCDVAFLAVPHGAAMEMGATLRQRGLRVVDLSADFRLRDPDVYEAWYKVPH 122

Query: 118 APSAYLERAVYGLTEWNREAVRGAVLLSNPGCYPTATLLGLAPLVKEGLIKEDSIIVDAK 177
              A L +AVYGL E   +AV+ A L++NPGCYPTAT+LGL   +K GL++ D I+VDAK
Sbjct: 123 TRRAELPQAVYGLPELYGDAVKKAGLVANPGCYPTATILGLYAALKHGLVETDGIVVDAK 182

Query: 178 SGVSGAGRKAGLGTHFSEVNENVKIYKVNAHQHIPEIEQALQTWNEAVAPITFSTHLIPM 237
           SG +GAGRKA +GT F EV++  + Y +  H+H PEIEQ L         ++F+ HL+P+
Sbjct: 183 SGATGAGRKAAVGTLFCEVSDTFRAYNIGKHRHTPEIEQELSAIAGTSMVVSFNPHLLPI 242

Query: 238 TRGIMATIYAKAKQSISPNDLVDLYKTSYEGSPFVRIRQLGQFPATKDVYGSNYCDIGLA 297
            RGI+ATIYAK  + +SP D+   ++ +++GS +VR+   GQ P T+ V G+ +CD+G+ 
Sbjct: 243 NRGILATIYAKLAKPVSPQDVQAAFEQTWQGSRWVRVLPAGQLPETRHVRGTMFCDVGVV 302

Query: 298 YDERTERVTVVSVIDNLMKGAAGQAVQNFNLMMGWDEAEGLRSLPIYP 345
            D+RT R+ ++S IDNL +GA+GQAV N NLM G     GL   P+ P
Sbjct: 303 TDQRTNRLVILSAIDNLCRGASGQAVANANLMFGLPVETGLMLAPLMP 350


Lambda     K      H
   0.318    0.135    0.404 

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: 334
Number of extensions: 14
Number of successful extensions: 2
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: 345
Length of database: 350
Length adjustment: 29
Effective length of query: 316
Effective length of database: 321
Effective search space:   101436
Effective search space used:   101436
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: 49 (23.5 bits)

Align candidate 8500980 DvMF_1717 (N-acetyl-gamma-glutamyl-phosphate reductase (RefSeq))
to HMM TIGR01850 (argC: N-acetyl-gamma-glutamyl-phosphate reductase (EC 1.2.1.38))

Software error:

../bin/blast/fastacmd -i /tmp/list.21151.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21151.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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