GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Cupriavidus basilensis 4G11

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate RR42_RS17175 RR42_RS17175 ornithine carbamoyltransferase

Query= reanno::HerbieS:HSERO_RS07185
         (304 letters)



>FitnessBrowser__Cup4G11:RR42_RS17175
          Length = 307

 Score =  457 bits (1177), Expect = e-133
 Identities = 222/303 (73%), Positives = 253/303 (83%), Gaps = 1/303 (0%)

Query: 2   AIKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFE 61
           +IKHYLQFSD T DEYEY+++R+R++K KFKNYE  H L DRTL M+FEKNSTRTRLSFE
Sbjct: 5   SIKHYLQFSDLTPDEYEYLLDRARILKTKFKNYETWHPLHDRTLSMIFEKNSTRTRLSFE 64

Query: 62  AGMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVP 121
           AG+HQ+GG A++LNTRDSQLGRGEP+EDAAQV+SRM D+IMIRT+GQEIIERFA HSRVP
Sbjct: 65  AGIHQLGGHAVFLNTRDSQLGRGEPIEDAAQVISRMVDIIMIRTFGQEIIERFAAHSRVP 124

Query: 122 VINGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVS 181
           VINGLTNE HPCQVLADVFTYIE  GSI+GK VAW+GDANNM Y+W+QAAE  GF  + S
Sbjct: 125 VINGLTNEYHPCQVLADVFTYIEQRGSIRGKTVAWIGDANNMAYTWIQAAERLGFTFHFS 184

Query: 182 TPKGYDIDPAQVSPGNKNYT-FFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGW 240
            P GY +DPA V     +    F DP  ACQ ADLVTTDVWTSMG+EAEN+AR +AF  W
Sbjct: 185 APPGYQLDPAMVPATAAHLVKVFDDPLTACQGADLVTTDVWTSMGYEAENDARKRAFQNW 244

Query: 241 IVDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVH 300
           +V  A M RA  DALFMHCLPAHRGEEV A VIDGP+SVVWEEAENRLHVQKAL+EYL+ 
Sbjct: 245 MVTTAMMDRAGDDALFMHCLPAHRGEEVEAAVIDGPKSVVWEEAENRLHVQKALMEYLLC 304

Query: 301 GRF 303
           GR+
Sbjct: 305 GRY 307


Lambda     K      H
   0.321    0.135    0.409 

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: 383
Number of extensions: 10
Number of successful extensions: 2
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: 304
Length of database: 307
Length adjustment: 27
Effective length of query: 277
Effective length of database: 280
Effective search space:    77560
Effective search space used:    77560
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

Align candidate RR42_RS17175 RR42_RS17175 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.20430.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.20430.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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