GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Escherichia coli BW25113

Align Ornithine carbamoyltransferase subunit F; OTCase-2; EC 2.1.3.3 (characterized)
to candidate 14411 b0273 CP4-6 prophage; ornithine carbamoyltransferase 2, chain F (NCBI)

Query= SwissProt::P06960
         (334 letters)



>FitnessBrowser__Keio:14411
          Length = 334

 Score =  670 bits (1728), Expect = 0.0
 Identities = 334/334 (100%), Positives = 334/334 (100%)

Query: 1   MSDLYKKHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTR 60
           MSDLYKKHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTR
Sbjct: 1   MSDLYKKHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTR 60

Query: 61  CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQY 120
           CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQY
Sbjct: 61  CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQY 120

Query: 121 AGVPVWNGLTNEFHPTQLLADLMTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALT 180
           AGVPVWNGLTNEFHPTQLLADLMTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALT
Sbjct: 121 AGVPVWNGLTNEFHPTQLLADLMTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALT 180

Query: 181 GLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEA 240
           GLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEA
Sbjct: 181 GLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEA 240

Query: 241 KEKWAERIALLRGYQVNAQMMALTDNPNVKFLHCLPAFHDDQTTLGKQMAKEFDLHGGME 300
           KEKWAERIALLRGYQVNAQMMALTDNPNVKFLHCLPAFHDDQTTLGKQMAKEFDLHGGME
Sbjct: 241 KEKWAERIALLRGYQVNAQMMALTDNPNVKFLHCLPAFHDDQTTLGKQMAKEFDLHGGME 300

Query: 301 VTDEVFESAASIVFDQAENRMHTIKAVMMATLGE 334
           VTDEVFESAASIVFDQAENRMHTIKAVMMATLGE
Sbjct: 301 VTDEVFESAASIVFDQAENRMHTIKAVMMATLGE 334


Lambda     K      H
   0.318    0.132    0.385 

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: 554
Number of extensions: 15
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: 334
Length of database: 334
Length adjustment: 28
Effective length of query: 306
Effective length of database: 306
Effective search space:    93636
Effective search space used:    93636
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: 49 (23.5 bits)

Align candidate 14411 b0273 (CP4-6 prophage; ornithine carbamoyltransferase 2, chain F (NCBI))
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.15044.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.15044.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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