GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Paraburkholderia bryophila 376MFSha3.1

Align Ornithine carbamoyltransferase (EC 2.1.3.3) (characterized)
to candidate H281DRAFT_04119 H281DRAFT_04119 ornithine carbamoyltransferase

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



>FitnessBrowser__Burk376:H281DRAFT_04119
          Length = 309

 Score =  456 bits (1174), Expect = e-133
 Identities = 215/303 (70%), Positives = 260/303 (85%), Gaps = 1/303 (0%)

Query: 3   IKHYLQFSDFTLDEYEYVIERSRVIKRKFKNYEPHHTLADRTLVMVFEKNSTRTRLSFEA 62
           I+HYLQF DF+LD+YEYV+ER+R++KRKFKNYE +H L DRTL M+FEKNSTRTRLSFEA
Sbjct: 6   IRHYLQFKDFSLDDYEYVLERARILKRKFKNYETYHPLHDRTLAMIFEKNSTRTRLSFEA 65

Query: 63  GMHQMGGAAIYLNTRDSQLGRGEPVEDAAQVMSRMCDVIMIRTYGQEIIERFAKHSRVPV 122
           G+ Q+GG A++++TRD+QLGRGEP+EDAAQV+SRM D+IMIRT+GQ+II+RFA++SRVPV
Sbjct: 66  GIFQLGGHAVFMSTRDTQLGRGEPIEDAAQVISRMVDIIMIRTFGQDIIQRFAENSRVPV 125

Query: 123 INGLTNEQHPCQVLADVFTYIEHHGSIQGKIVAWVGDANNMLYSWLQAAEVFGFHVNVST 182
           INGLTNE HPCQVLAD+FTY EH G I+GK VAWVGDANNMLY+W++AA++ GF + +ST
Sbjct: 126 INGLTNEYHPCQVLADIFTYFEHRGPIRGKTVAWVGDANNMLYTWIEAAQILGFKLRLST 185

Query: 183 PKGYDIDPAQVSPGNKN-YTFFADPADACQDADLVTTDVWTSMGFEAENNARLKAFDGWI 241
           P GY +D A V+  +   +  F DP +AC  ADLVTTDVWTSMGFEAEN AR KAF  W 
Sbjct: 186 PPGYKLDRALVAAESAPFFQEFDDPNEACAGADLVTTDVWTSMGFEAENEARKKAFADWC 245

Query: 242 VDQAKMARAKKDALFMHCLPAHRGEEVAAEVIDGPQSVVWEEAENRLHVQKALLEYLVHG 301
           VD   M+RA  DALFMHCLPAHRGEEV+AEVIDGPQSVVW+EAENRLHVQKAL+EYL+ G
Sbjct: 246 VDAEMMSRANADALFMHCLPAHRGEEVSAEVIDGPQSVVWDEAENRLHVQKALMEYLLLG 305

Query: 302 RFD 304
           + +
Sbjct: 306 KLN 308


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: 377
Number of extensions: 14
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: 309
Length adjustment: 27
Effective length of query: 277
Effective length of database: 282
Effective search space:    78114
Effective search space used:    78114
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 H281DRAFT_04119 H281DRAFT_04119 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.2024.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2024.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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