GapMind for Amino acid biosynthesis

 

Alignments for a candidate for cysK in Escherichia coli BW25113

Align cysteine synthase (EC 2.5.1.47) (characterized)
to candidate 16513 b2414 cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI)

Query= BRENDA::P0ABK5
         (323 letters)



>FitnessBrowser__Keio:16513
          Length = 323

 Score =  626 bits (1614), Expect = 0.0
 Identities = 323/323 (100%), Positives = 323/323 (100%)

Query: 1   MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK 60
           MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK
Sbjct: 1   MSKIFEDNSLTIGHTPLVRLNRIGNGRILAKVESRNPSFSVKCRIGANMIWDAEKRGVLK 60

Query: 61  PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM 120
           PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM
Sbjct: 61  PGVELVEPTSGNTGIALAYVAAARGYKLTLTMPETMSIERRKLLKALGANLVLTEGAKGM 120

Query: 121 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG 180
           KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG
Sbjct: 121 KGAIQKAEEIVASNPEKYLLLQQFSNPANPEIHEKTTGPEIWEDTDGQVDVFIAGVGTGG 180

Query: 181 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD 240
           TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD
Sbjct: 181 TLTGVSRYIKGTKGKTDLISVAVEPTDSPVIAQALAGEEIKPGPHKIQGIGAGFIPANLD 240

Query: 241 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP 300
           LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP
Sbjct: 241 LKLVDKVIGITNEEAISTARRLMEEEGILAGISSGAAVAAALKLQEDESFTNKNIVVILP 300

Query: 301 SSGERYLSTALFADLFTEKELQQ 323
           SSGERYLSTALFADLFTEKELQQ
Sbjct: 301 SSGERYLSTALFADLFTEKELQQ 323


Lambda     K      H
   0.313    0.133    0.368 

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: 507
Number of extensions: 12
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: 323
Length of database: 323
Length adjustment: 28
Effective length of query: 295
Effective length of database: 295
Effective search space:    87025
Effective search space used:    87025
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate 16513 b2414 (cysteine synthase A, O-acetylserine sulfhydrolase A subunit (NCBI))
to HMM TIGR01139 (cysK: cysteine synthase A (EC 2.5.1.47))

Software error:

../bin/blast/fastacmd -i /tmp/list.18763.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.18763.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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