GapMind for catabolism of small carbon sources

 

Alignments for a candidate for sdaB in Escherichia coli BW25113

Align L-serine ammonia-lyase (EC 4.3.1.17) (characterized)
to candidate 15932 b1814 L-serine deaminase I (NCBI)

Query= BRENDA::P16095
         (454 letters)



>FitnessBrowser__Keio:15932
          Length = 454

 Score =  910 bits (2351), Expect = 0.0
 Identities = 454/454 (100%), Positives = 454/454 (100%)

Query: 1   MISLFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLDSVTRVAVDVYGSLSLTGKGH 60
           MISLFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLDSVTRVAVDVYGSLSLTGKGH
Sbjct: 1   MISLFDMFKVGIGPSSSHTVGPMKAGKQFVDDLVEKGLLDSVTRVAVDVYGSLSLTGKGH 60

Query: 61  HTDIAIIMGLAGNEPATVDIDSIPGFIRDVEERERLLLAQGRHEVDFPRDNGMRFHNGNL 120
           HTDIAIIMGLAGNEPATVDIDSIPGFIRDVEERERLLLAQGRHEVDFPRDNGMRFHNGNL
Sbjct: 61  HTDIAIIMGLAGNEPATVDIDSIPGFIRDVEERERLLLAQGRHEVDFPRDNGMRFHNGNL 120

Query: 121 PLHENGMQIHAYNGDEVVYSKTYYSIGGGFIVDEEHFGQDAANEVSVPYPFKSATELLAY 180
           PLHENGMQIHAYNGDEVVYSKTYYSIGGGFIVDEEHFGQDAANEVSVPYPFKSATELLAY
Sbjct: 121 PLHENGMQIHAYNGDEVVYSKTYYSIGGGFIVDEEHFGQDAANEVSVPYPFKSATELLAY 180

Query: 181 CNETGYSLSGLAMQNELALHSKKEIDEYFAHVWQTMQACIDRGMNTEGVLPGPLRVPRRA 240
           CNETGYSLSGLAMQNELALHSKKEIDEYFAHVWQTMQACIDRGMNTEGVLPGPLRVPRRA
Sbjct: 181 CNETGYSLSGLAMQNELALHSKKEIDEYFAHVWQTMQACIDRGMNTEGVLPGPLRVPRRA 240

Query: 241 SALRRMLVSSDKLSNDPMNVIDWVNMFALAVNEENAAGGRVVTAPTNGACGIVPAVLAYY 300
           SALRRMLVSSDKLSNDPMNVIDWVNMFALAVNEENAAGGRVVTAPTNGACGIVPAVLAYY
Sbjct: 241 SALRRMLVSSDKLSNDPMNVIDWVNMFALAVNEENAAGGRVVTAPTNGACGIVPAVLAYY 300

Query: 301 DHFIESVSPDIYTRYFMAAGAIGALYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGG 360
           DHFIESVSPDIYTRYFMAAGAIGALYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGG
Sbjct: 301 DHFIESVSPDIYTRYFMAAGAIGALYKMNASISGAEVGCQGEVGVACSMAAAGLAELLGG 360

Query: 361 SPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINAARMALRRTSAPRVS 420
           SPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINAARMALRRTSAPRVS
Sbjct: 361 SPEQVCVAAEIGMEHNLGLTCDPVAGQVQVPCIERNAIASVKAINAARMALRRTSAPRVS 420

Query: 421 LDKVIETMYETGKDMNAKYRETSRGGLAIKVQCD 454
           LDKVIETMYETGKDMNAKYRETSRGGLAIKVQCD
Sbjct: 421 LDKVIETMYETGKDMNAKYRETSRGGLAIKVQCD 454


Lambda     K      H
   0.318    0.135    0.396 

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: 841
Number of extensions: 22
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: 454
Length of database: 454
Length adjustment: 33
Effective length of query: 421
Effective length of database: 421
Effective search space:   177241
Effective search space used:   177241
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 (21.7 bits)
S2: 51 (24.3 bits)

Align candidate 15932 b1814 (L-serine deaminase I (NCBI))
to HMM TIGR00720 (L-serine ammonia-lyase (EC 4.3.1.17))

Software error:

../bin/blast/fastacmd -i /tmp/list.22837.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22837.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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