GapMind for Amino acid biosynthesis

 

Alignments for a candidate for proA in Caulobacter crescentus NA1000

Align Gamma-glutamyl phosphate reductase; GPR; Glutamate-5-semialdehyde dehydrogenase; Glutamyl-gamma-semialdehyde dehydrogenase; GSA dehydrogenase; EC 1.2.1.41 (characterized)
to candidate CCNA_03543 CCNA_03543 gamma-glutamyl phosphate reductase

Query= SwissProt::P07004
         (417 letters)



>FitnessBrowser__Caulo:CCNA_03543
          Length = 424

 Score =  323 bits (828), Expect = 6e-93
 Identities = 172/405 (42%), Positives = 256/405 (63%), Gaps = 5/405 (1%)

Query: 5   MGIAAKQASYKLAQLSSREKNRVLEKIADELEAQSEIILNANAQDVADARANGLSEAMLD 64
           MG  A++ +  L   +  ++   ++ +A  +   ++ IL ANA+D+A A ANG+S  MLD
Sbjct: 15  MGRTAREGARALRLATPEQRTAAIQAMAVAIREDADAILTANAKDLARAEANGVSGPMLD 74

Query: 65  RLALTPARLKGIADDVRQVCNLADPVGQVIDGGVLDSGLRLERRRVPLGVIGVIYEARPN 124
           RLAL  ARL+G+A  V  V  + DPVG         +GL + R R P+GVI +IYE+RPN
Sbjct: 75  RLALDAARLEGVAAGVEAVAAVPDPVGVATSRWTRPNGLDIARVRTPIGVIAMIYESRPN 134

Query: 125 VTVDVASLCLKTGNAVILRGGKETCRTNAATVAVIQDALKSCGLPAGAVQAIDNPDRALV 184
           VT D A+LC+++GNAVILRGG E   +N A  A I   L+  GLP  AVQA+  PDRA V
Sbjct: 135 VTADAAALCVRSGNAVILRGGSECIHSNLAIHAAIARGLQKAGLPTAAVQAVKTPDRAAV 194

Query: 185 SEMLR-MDKYIDMLIPRGGAGLHKLCREQSTIPVITGGIGVCHIYVDESVEIAEALKVIV 243
             +L  +D+ ID++IPRGG  L    + ++  PV+    G+ H++V  + ++ +A++V+V
Sbjct: 195 GMILAGLDRTIDLIIPRGGKSLVARVQAEARAPVLGHLEGLNHVFVHAAADLKKAVEVVV 254

Query: 244 NAKTQRPSTCNTVETLLVNKNIADSFLPALSKQMAESGVTLHADAAALAQLQAGPAKVVA 303
           NAK +R S C + ETLL+++  AD  LP ++  + ++G  L  DAAA    +A    +  
Sbjct: 255 NAKLRRVSVCGSAETLLIDQAAADKLLPPIADALIKAGCELRGDAAA----RAIEPTMKK 310

Query: 304 VKAEEYDDEFLSLDLNVKIVSDLDDAIAHIREHGTQHSDAILTRDMRNAQRFVNEVDSSA 363
              E++  E+L+  L+V +V  +  A  HI  +G+ H+DAI+T D   A+ F+ EVDS+ 
Sbjct: 311 ATVEDWTTEYLAPILSVAVVDGVAGAARHIASYGSGHTDAIITEDAAAAEAFIAEVDSAI 370

Query: 364 VYVNASTRFTDGGQFGLGAEVAVSTQKLHARGPMGLEALTTYKWI 408
           V VNAST+F DGG+FG GAE+ ++T KLHARGP+G E LTT+K++
Sbjct: 371 VLVNASTQFADGGEFGFGAEIGIATDKLHARGPVGAEQLTTFKYV 415


Lambda     K      H
   0.317    0.133    0.369 

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: 424
Number of extensions: 19
Number of successful extensions: 3
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: 417
Length of database: 424
Length adjustment: 32
Effective length of query: 385
Effective length of database: 392
Effective search space:   150920
Effective search space used:   150920
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: 50 (23.9 bits)

Align candidate CCNA_03543 CCNA_03543 (gamma-glutamyl phosphate reductase)
to HMM TIGR00407 (proA: glutamate-5-semialdehyde dehydrogenase (EC 1.2.1.41))

Software error:

../bin/blast/fastacmd -i /tmp/list.27035.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27035.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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