GapMind for catabolism of small carbon sources

 

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

Align N-acetylgalactosamine-6-phosphate deacetylase; GalNAc-6-P deacetylase; N-acetylglucosamine-6-phosphate deacetylase; GlcNAc-6-P deacetylase; EC 3.5.1.-; EC 3.5.1.25 (characterized)
to candidate 7025546 Shewana3_2697 N-acetylglucosamine 6-phosphate deacetylase (RefSeq)

Query= SwissProt::A0KYQ5
         (394 letters)



>FitnessBrowser__ANA3:7025546
          Length = 394

 Score =  788 bits (2034), Expect = 0.0
 Identities = 394/394 (100%), Positives = 394/394 (100%)

Query: 1   MKPNTDFMLIADGAKVLTQGNLTEHCAIEVSDGIICGLKSTISAEWTADKPHYRLTSGTL 60
           MKPNTDFMLIADGAKVLTQGNLTEHCAIEVSDGIICGLKSTISAEWTADKPHYRLTSGTL
Sbjct: 1   MKPNTDFMLIADGAKVLTQGNLTEHCAIEVSDGIICGLKSTISAEWTADKPHYRLTSGTL 60

Query: 61  VAGFIDTQVNGGGGLMFNHVPTLETLRLMMQAHRQFGTTAMLPTVITDDIEVMQAAADAV 120
           VAGFIDTQVNGGGGLMFNHVPTLETLRLMMQAHRQFGTTAMLPTVITDDIEVMQAAADAV
Sbjct: 61  VAGFIDTQVNGGGGLMFNHVPTLETLRLMMQAHRQFGTTAMLPTVITDDIEVMQAAADAV 120

Query: 121 AEAIDCQVPGIIGIHFEGPHLSVAKRGCHPPAHLRGITEREWLLYLRQDLGVRLITLAPE 180
           AEAIDCQVPGIIGIHFEGPHLSVAKRGCHPPAHLRGITEREWLLYLRQDLGVRLITLAPE
Sbjct: 121 AEAIDCQVPGIIGIHFEGPHLSVAKRGCHPPAHLRGITEREWLLYLRQDLGVRLITLAPE 180

Query: 181 SVTPEQIKRLVASGAIISLGHSNADGETVLKAIEAGASGFTHLYNGMSALTSREPGMVGA 240
           SVTPEQIKRLVASGAIISLGHSNADGETVLKAIEAGASGFTHLYNGMSALTSREPGMVGA
Sbjct: 181 SVTPEQIKRLVASGAIISLGHSNADGETVLKAIEAGASGFTHLYNGMSALTSREPGMVGA 240

Query: 241 AFASENTYCGIILDGQHVHPISALAAWRAKGTEHLMLVTDAMSPLGSDQTEFQFFDGKVV 300
           AFASENTYCGIILDGQHVHPISALAAWRAKGTEHLMLVTDAMSPLGSDQTEFQFFDGKVV
Sbjct: 241 AFASENTYCGIILDGQHVHPISALAAWRAKGTEHLMLVTDAMSPLGSDQTEFQFFDGKVV 300

Query: 301 REGMTLRDQHGSLAGSVLDMASAVRYAATELNLGLSNAVQMATRTPAEFIQRPQLGDIAE 360
           REGMTLRDQHGSLAGSVLDMASAVRYAATELNLGLSNAVQMATRTPAEFIQRPQLGDIAE
Sbjct: 301 REGMTLRDQHGSLAGSVLDMASAVRYAATELNLGLSNAVQMATRTPAEFIQRPQLGDIAE 360

Query: 361 GKQADWVWLDDDQRVLAVWIAGELLYQAEQARFA 394
           GKQADWVWLDDDQRVLAVWIAGELLYQAEQARFA
Sbjct: 361 GKQADWVWLDDDQRVLAVWIAGELLYQAEQARFA 394


Lambda     K      H
   0.320    0.134    0.400 

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: 712
Number of extensions: 9
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: 394
Length of database: 394
Length adjustment: 31
Effective length of query: 363
Effective length of database: 363
Effective search space:   131769
Effective search space used:   131769
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: 50 (23.9 bits)

Align candidate 7025546 Shewana3_2697 (N-acetylglucosamine 6-phosphate deacetylase (RefSeq))
to HMM TIGR00221 (nagA: N-acetylglucosamine-6-phosphate deacetylase (EC 3.5.1.25))

Software error:

../bin/blast/fastacmd -i /tmp/list.14674.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14674.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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