GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aroG in Shewanella sp. ANA-3

Align 3-deoxy-7-phosphoheptulonate synthase, Trp-sensitive (EC 2.5.1.54) (characterized)
to candidate 7024556 Shewana3_1734 phospho-2-dehydro-3-deoxyheptonate aldolase (RefSeq)

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



>FitnessBrowser__ANA3:7024556
          Length = 354

 Score =  450 bits (1157), Expect = e-131
 Identities = 217/341 (63%), Positives = 267/341 (78%)

Query: 3   RTDELRTARIESLVTPAELALRYPVTPGVATHVTDSRRRIEKILNGEDKRLLVIIGPCSI 62
           +TDELRT+ +  +++PA+LA  YP+T   A ++   RR +E I+ GED+RLLVIIGPCSI
Sbjct: 4   KTDELRTSLLAKVISPAQLASEYPLTQDAADYLVQQRREVEAIIMGEDQRLLVIIGPCSI 63

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

Query: 123 ELARKLLLQVNELGVPTATEFLDMVTGQFIADLISWGAIGARTTESQIHREMASALSCPV 182
            +AR+LL Q+ EL +P ATEFLDMV GQ+IADLI+WGAIGARTTESQ+HREMASALSCPV
Sbjct: 124 RIARELLQQITELKLPIATEFLDMVNGQYIADLITWGAIGARTTESQVHREMASALSCPV 183

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

Query: 243 DDIAAACDTLHEFDLPEHLVVDFSHGNCQKQHRRQLEVCEDICQQIRNGSTAIAGIMAES 302
            DI  A   L   D+   +VVDFSHGN +K H +QL V ++I  Q+R GSTAIAG+MAES
Sbjct: 244 QDIEEARLKLESVDVTPRMVVDFSHGNSEKNHLKQLVVADNIMAQMRAGSTAIAGVMAES 303

Query: 303 FLREGTQKIVGSQPLTYGQSITDPCLGWEDTERLVEKLASA 343
           FL+EG QK+V  QPL YGQSITD CL W+D+E+L+  LA A
Sbjct: 304 FLQEGNQKVVEGQPLCYGQSITDACLHWDDSEKLLRDLAKA 344


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: 400
Number of extensions: 7
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: 354
Length adjustment: 29
Effective length of query: 319
Effective length of database: 325
Effective search space:   103675
Effective search space used:   103675
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 7024556 Shewana3_1734 (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.29704.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.29704.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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