GapMind for Amino acid biosynthesis

 

Alignments for a candidate for argH in Escherichia coli BW25113

Align argininosuccinate lyase (EC 4.3.2.1) (characterized)
to candidate 17999 b3960 argininosuccinate lyase (NCBI)

Query= ecocyc::ARGSUCCINLYA-MONOMER
         (457 letters)



>FitnessBrowser__Keio:17999
          Length = 457

 Score =  901 bits (2329), Expect = 0.0
 Identities = 457/457 (100%), Positives = 457/457 (100%)

Query: 1   MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60
           MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE
Sbjct: 1   MALWGGRFTQAADQRFKQFNDSLRFDYRLAEQDIVGSVAWSKALVTVGVLTAEEQAQLEE 60

Query: 61  ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120
           ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW
Sbjct: 61  ALNVLLEDVRARPQQILESDAEDIHSWVEGKLIDKVGQLGKKLHTGRSRNDQVATDLKLW 120

Query: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180
           CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE
Sbjct: 121 CKDTVSELLTANRQLQSALVETAQNNQDAVMPGYTHLQRAQPVTFAHWCLAYVEMLARDE 180

Query: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240
           SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS
Sbjct: 181 SRLQDALKRLDVSPLGCGALAGTAYEIDREQLAGWLGFASATRNSLDSVSDRDHVLELLS 240

Query: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300
           AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ
Sbjct: 241 AAAIGMVHLSRFAEDLIFFNTGEAGFVELSDRVTSGSSLMPQKKNPDALELIRGKCGRVQ 300

Query: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA 360
           GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA
Sbjct: 301 GALTGMMMTLKGLPLAYNKDMQEDKEGLFDALDTWLDCLHMAALVLDGIQVKRPRCQEAA 360

Query: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420
           QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED
Sbjct: 361 QQGYANATELADYLVAKGVPFREAHHIVGEAVVEAIRQGKPLEDLPLSELQKFSQVIDED 420

Query: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQARLG 457
           VYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQARLG
Sbjct: 421 VYPILSLQSCLDKRAAKGGVSPQQVAQAIAFAQARLG 457


Lambda     K      H
   0.318    0.133    0.386 

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: 794
Number of extensions: 21
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: 457
Length of database: 457
Length adjustment: 33
Effective length of query: 424
Effective length of database: 424
Effective search space:   179776
Effective search space used:   179776
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 17999 b3960 (argininosuccinate lyase (NCBI))
to HMM TIGR00838 (argH: argininosuccinate lyase (EC 4.3.2.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.13492.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.13492.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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