GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Klebsiella michiganensis M5al

Align Ornithine carbamoyltransferase subunit F; OTCase-2; EC 2.1.3.3 (characterized)
to candidate BWI76_RS03010 BWI76_RS03010 ornithine carbamoyltransferase

Query= SwissProt::P06960
         (334 letters)



>FitnessBrowser__Koxy:BWI76_RS03010
          Length = 334

 Score =  608 bits (1569), Expect = e-179
 Identities = 299/334 (89%), Positives = 317/334 (94%)

Query: 1   MSDLYKKHFLKLLDFTPAQFTSLLTLAAQLKADKKNGKEVQKLTGKNIALIFEKDSTRTR 60
           MS  Y+KHFLKLLDFTPA+ T+LL LAA+LKADKKN  E+Q LTGKNIALIFEKDSTRTR
Sbjct: 1   MSAFYQKHFLKLLDFTPAEITALLELAARLKADKKNNIEIQHLTGKNIALIFEKDSTRTR 60

Query: 61  CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAQY 120
           CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLA+Y
Sbjct: 61  CSFEVAAFDQGARVTYLGPSGSQIGHKESIKDTARVLGRMYDGIQYRGHGQEVVETLAEY 120

Query: 121 AGVPVWNGLTNEFHPTQLLADLMTMQEHLPGKAFNEMTLVYAGDARNNMGNSMLEAAALT 180
           AGVPVWNGLTNEFHPTQLLADL+TMQEHLPGKAFN+MTLVYAGDARNNMGNSMLEAAALT
Sbjct: 121 AGVPVWNGLTNEFHPTQLLADLLTMQEHLPGKAFNQMTLVYAGDARNNMGNSMLEAAALT 180

Query: 181 GLDLRLLAPKACWPEESLVAECSALAEKHGGKITLTEDVAAGVKGADFIYTDVWVSMGEA 240
           GLDLRL+AP ACWPEE LV +C ALA+K+GG ITLTED+AAGVKGADFIYTDVWVSMGEA
Sbjct: 181 GLDLRLVAPTACWPEEKLVEQCRALAQKNGGNITLTEDIAAGVKGADFIYTDVWVSMGEA 240

Query: 241 KEKWAERIALLRGYQVNAQMMALTDNPNVKFLHCLPAFHDDQTTLGKQMAKEFDLHGGME 300
           KEKWAERIALLR YQVN++MMALT NP VKFLHCLPAFHDDQTTLGKQMA E+ LHGGME
Sbjct: 241 KEKWAERIALLRAYQVNSEMMALTGNPQVKFLHCLPAFHDDQTTLGKQMAAEYGLHGGME 300

Query: 301 VTDEVFESAASIVFDQAENRMHTIKAVMMATLGE 334
           VTDEVFESAASIVFDQAENRMHTIKAVM+ATLG+
Sbjct: 301 VTDEVFESAASIVFDQAENRMHTIKAVMVATLGK 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: 486
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: 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 BWI76_RS03010 BWI76_RS03010 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.6623.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6623.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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