GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Shewanella amazonensis SB2B

Align 3-deoxy-7-phosphoheptulonate synthase, Trp-sensitive (EC 2.5.1.54) (characterized)
to candidate 6937933 Sama_2074 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

Query= ecocyc::AROH-MONOMER
         (348 letters)



>FitnessBrowser__SB2B:6937933
          Length = 353

 Score =  451 bits (1159), Expect = e-131
 Identities = 219/345 (63%), Positives = 267/345 (77%)

Query: 3   RTDELRTARIESLVTPAELALRYPVTPGVATHVTDSRRRIEKILNGEDKRLLVIIGPCSI 62
           +TDELRT+ +  +++P++LA  YP+T   A ++   RR +E IL G+DKRLLVIIGPCSI
Sbjct: 4   KTDELRTSLLCKVISPSQLAAEYPLTQEAADYLVAQRREVEAILTGQDKRLLVIIGPCSI 63

Query: 63  HDLTAAMEYATRLQSLRNQYQSRLEIVMRTYFEKPRTVVGWKGLISDPDLNGSYRVNHGL 122
           HD  AA+EYA RL  L ++ +  L I+MR YFEKPRT+VGWKGLISDPDL+GS+  N GL
Sbjct: 64  HDTEAALEYAGRLAKLHHELKDDLCILMRVYFEKPRTIVGWKGLISDPDLDGSFSANKGL 123

Query: 123 ELARKLLLQVNELGVPTATEFLDMVTGQFIADLISWGAIGARTTESQIHREMASALSCPV 182
            LAR LL Q+ EL +P ATEFLDMV GQ+IADLI+WGAIGARTTESQIHREMASALSCPV
Sbjct: 124 RLARHLLQQITELKLPIATEFLDMVNGQYIADLITWGAIGARTTESQIHREMASALSCPV 183

Query: 183 GFKNGTDGNTRIAVDAIRAARASHMFLSPDKNGQMTIYQTSGNPYGHIIMRGGKKPNYHA 242
           GFKNGTDGN  IAVDA+RAA+  H+F SPDK+G M++Y+T GNPYGHII+RGGK PNY  
Sbjct: 184 GFKNGTDGNINIAVDAVRAAKVPHIFYSPDKDGHMSVYRTHGNPYGHIILRGGKNPNYAQ 243

Query: 243 DDIAAACDTLHEFDLPEHLVVDFSHGNCQKQHRRQLEVCEDICQQIRNGSTAIAGIMAES 302
           + +  A + L    +   +V+DFSHGN QKQH++QLEV E++  QIR GSTAIAGIMAES
Sbjct: 244 EHVQKAHEQLKATGIDTGMVIDFSHGNSQKQHKKQLEVAENVMAQIRAGSTAIAGIMAES 303

Query: 303 FLREGTQKIVGSQPLTYGQSITDPCLGWEDTERLVEKLASAVDTR 347
           F+ EG Q +V  QPL YG+SITD CL W DTE L+  LA+A   R
Sbjct: 304 FIEEGNQAVVEGQPLCYGKSITDACLSWGDTEPLLRNLAAAARVR 348


Lambda     K      H
   0.320    0.135    0.399 

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: 408
Number of extensions: 8
Number of successful extensions: 1
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: 348
Length of database: 353
Length adjustment: 29
Effective length of query: 319
Effective length of database: 324
Effective search space:   103356
Effective search space used:   103356
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 49 (23.5 bits)

Align candidate 6937933 Sama_2074 (phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq))
to HMM TIGR00034 (3-deoxy-7-phosphoheptulonate synthase (EC 2.5.1.54))

Software error:

../bin/blast/fastacmd -i /tmp/list.16241.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.16241.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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