GapMind for catabolism of small carbon sources

 

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

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (characterized)
to candidate 5207682 Shew_0204 ornithine carbamoyltransferase (RefSeq)

Query= SwissProt::Q9K4Y9
         (301 letters)



>FitnessBrowser__PV4:5207682
          Length = 301

 Score =  389 bits (1000), Expect = e-113
 Identities = 180/300 (60%), Positives = 242/300 (80%)

Query: 1   MENLLSVKDLSKQQILDLLALAKAVKANPAEYSQALAGKSIVTIYEKPSLRTRVTFDIGI 60
           M +LLS+K+L++QQ++DLLALAK +KANP +Y +AL GKS+V ++EKPSLRTRV+FDIGI
Sbjct: 1   MNHLLSIKELTQQQLIDLLALAKTIKANPEDYRKALDGKSVVMLFEKPSLRTRVSFDIGI 60

Query: 61  HKLGGHAVYLDAQNGAIGERETVKDFAANISRWADAIVARVVSHKTLEGLVEHGSVPVVN 120
           +KLGGH +YLD QNGA+G+RE V DFAANIS WADAIVAR  +H T+E L EHG+VPV+N
Sbjct: 61  NKLGGHCLYLDQQNGALGKREPVSDFAANISCWADAIVARTFAHSTIEQLAEHGTVPVIN 120

Query: 121 SLCDLYHPCQALADFLTISEHYEDVSKVKLAYVGEGNNVTHSLMLTGAILGAEVTAVCPR 180
           +L D+YHPCQ LADFLT++E ++DVSKVKLAYVG+GNNVTHSLM   A+LGA++T +CP+
Sbjct: 121 ALSDMYHPCQGLADFLTLAEQFDDVSKVKLAYVGDGNNVTHSLMYGAALLGAKMTVICPQ 180

Query: 181 GSSPDAQIVKQAMALAEISGGKINVTDNLDDIVDYDVIYGDTWVSMGDDTPLAQVKEKYM 240
           G  PD ++V +A A+AE  GG++ ++ +++ I  +D IY DTW+SMGD   L ++K K+ 
Sbjct: 181 GHFPDGKVVLEAQAIAEAHGGELVLSSDVEAIAGHDAIYTDTWISMGDKASLDEIKAKFA 240

Query: 241 PYQINKALLMRTGIKHVLHCQPAHRELEITSEVMDGEHSLIFDQAENRMHAQNAVLLTLL 300
           PY ++  ++ + G K  +HC PA+R +E+ +EV+DG  SLI  QAENRMHAQNAVL+TLL
Sbjct: 241 PYHVDTDMMNKAGAKFFMHCLPAYRGVEVAAEVVDGAGSLILQQAENRMHAQNAVLVTLL 300


Lambda     K      H
   0.317    0.133    0.379 

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: 261
Number of extensions: 6
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: 301
Length of database: 301
Length adjustment: 27
Effective length of query: 274
Effective length of database: 274
Effective search space:    75076
Effective search space used:    75076
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: 48 (23.1 bits)

Align candidate 5207682 Shew_0204 (ornithine carbamoyltransferase (RefSeq))
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.22296.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22296.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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