GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Shewanella amazonensis SB2B

Align Ornithine carbamoyltransferase; OTCase; EC 2.1.3.3 (characterized)
to candidate 6936061 Sama_0258 ornithine carbamoyltransferase (RefSeq)

Query= SwissProt::Q9K4Y9
         (301 letters)



>FitnessBrowser__SB2B:6936061
          Length = 301

 Score =  400 bits (1029), Expect = e-116
 Identities = 186/300 (62%), Positives = 249/300 (83%)

Query: 1   MENLLSVKDLSKQQILDLLALAKAVKANPAEYSQALAGKSIVTIYEKPSLRTRVTFDIGI 60
           M++L+S+K+L+++Q+LDLL LAK +KA+PA+YS+ALAGKS+V ++EKPSLRTRV+FDIGI
Sbjct: 1   MKHLISIKELTQKQMLDLLTLAKEIKADPAKYSRALAGKSVVMLFEKPSLRTRVSFDIGI 60

Query: 61  HKLGGHAVYLDAQNGAIGERETVKDFAANISRWADAIVARVVSHKTLEGLVEHGSVPVVN 120
           +KLGGH +YLD QNGA+G+RE+VKDFA+N+S WADAIVAR  +H+T+EGL ++G VPV+N
Sbjct: 61  NKLGGHCLYLDQQNGALGKRESVKDFASNLSCWADAIVARTFAHETVEGLAKYGRVPVIN 120

Query: 121 SLCDLYHPCQALADFLTISEHYEDVSKVKLAYVGEGNNVTHSLMLTGAILGAEVTAVCPR 180
           +L DLYHPCQ LADFL+++E ++D+SKV+LAYVG+GNNV+HSLM   A+LGA +T +CP 
Sbjct: 121 ALSDLYHPCQGLADFLSLAEKFDDLSKVRLAYVGDGNNVSHSLMYGAALLGATMTVICPP 180

Query: 181 GSSPDAQIVKQAMALAEISGGKINVTDNLDDIVDYDVIYGDTWVSMGDDTPLAQVKEKYM 240
           G  PD   V+QA  +A   GGK+ +T +++ I  +D +Y DTW+SMGD+T L  +K K+ 
Sbjct: 181 GHFPDGFEVQQAQQIAAAHGGKLVLTSDINAIEGHDAVYTDTWISMGDNTALTDIKAKFA 240

Query: 241 PYQINKALLMRTGIKHVLHCQPAHRELEITSEVMDGEHSLIFDQAENRMHAQNAVLLTLL 300
           PYQ+NKAL+ + G  + +HC PAHR LE+T EVMDGE SLI DQAENRMHAQNAVL+TLL
Sbjct: 241 PYQVNKALMNKAGASYFMHCLPAHRGLEVTDEVMDGEGSLILDQAENRMHAQNAVLVTLL 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: 272
Number of extensions: 2
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 6936061 Sama_0258 (ornithine carbamoyltransferase (RefSeq))
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.2662.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2662.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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