GapMind for Amino acid biosynthesis

 

Alignments for a candidate for aceA in Shewanella loihica PV-4

Align Isocitrate lyase (EC 4.1.3.1) (characterized)
to candidate 5208774 Shew_1276 isocitrate lyase (RefSeq)

Query= reanno::PV4:5208774
         (450 letters)



>FitnessBrowser__PV4:5208774
          Length = 450

 Score =  907 bits (2344), Expect = 0.0
 Identities = 450/450 (100%), Positives = 450/450 (100%)

Query: 1   MLTPEMEKIMTKATTQISRQQQIDAIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENT 60
           MLTPEMEKIMTKATTQISRQQQIDAIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENT
Sbjct: 1   MLTPEMEKIMTKATTQISRQQQIDAIKQDWAENPRWAGVRRPYSAEDVVALRGSIVPENT 60

Query: 61  LATRGAEKLWQLVNGGAKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGT 120
           LATRGAEKLWQLVNGGAKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGT
Sbjct: 61  LATRGAEKLWQLVNGGAKKGYVNSLGALTGGQAVQQAKAGIEAIYLSGWQVAADANLAGT 120

Query: 121 MYPDQSLYPANSVPAVVQRINNSFRRADQIQWSNEIDPQDERYTDYFLPIVADAEAGFGG 180
           MYPDQSLYPANSVPAVVQRINNSFRRADQIQWSNEIDPQDERYTDYFLPIVADAEAGFGG
Sbjct: 121 MYPDQSLYPANSVPAVVQRINNSFRRADQIQWSNEIDPQDERYTDYFLPIVADAEAGFGG 180

Query: 181 VLNAYELMKNMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSG 240
           VLNAYELMKNMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSG
Sbjct: 181 VLNAYELMKNMIDAGAAGVHFEDQLASVKKCGHMGGKVLVPTQEAVQKLVSARLAADVSG 240

Query: 241 VPTLVIARTDANAADLLTSDCDPYDRDFITGERTSEGFYRVNAGIDQAISRGLAYAPYAD 300
           VPTLVIARTDANAADLLTSDCDPYDRDFITGERTSEGFYRVNAGIDQAISRGLAYAPYAD
Sbjct: 241 VPTLVIARTDANAADLLTSDCDPYDRDFITGERTSEGFYRVNAGIDQAISRGLAYAPYAD 300

Query: 301 LIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMG 360
           LIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMG
Sbjct: 301 LIWCETAKPDLEEARRFAEAIHAQYPDQLLAYNCSPSFNWKKNLDDATIARFQQELSDMG 360

Query: 361 YKYQFITLAGIHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVG 420
           YKYQFITLAGIHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVG
Sbjct: 361 YKYQFITLAGIHNMWYNMFDLAYDYARGEGMKHYVEKVQEVEFAAAKKGYTFVAHQQEVG 420

Query: 421 TGYFDKVTNVIQGGESSVTALTGSTEEEQF 450
           TGYFDKVTNVIQGGESSVTALTGSTEEEQF
Sbjct: 421 TGYFDKVTNVIQGGESSVTALTGSTEEEQF 450


Lambda     K      H
   0.316    0.132    0.389 

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: 900
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: 450
Length of database: 450
Length adjustment: 33
Effective length of query: 417
Effective length of database: 417
Effective search space:   173889
Effective search space used:   173889
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 (21.6 bits)
S2: 51 (24.3 bits)

Align candidate 5208774 Shew_1276 (isocitrate lyase (RefSeq))
to HMM TIGR01346 (aceA: isocitrate lyase (EC 4.1.3.1))

Software error:

../bin/blast/fastacmd -i /tmp/list.26689.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.26689.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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