GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcB in Marinobacter adhaerens HP15

Align Ornithine carbamoyltransferase, catabolic; OTCase; EC 2.1.3.3 (characterized)
to candidate GFF4047 HP15_3987 ornithine carbamoyltransferase

Query= SwissProt::P08308
         (336 letters)



>FitnessBrowser__Marino:GFF4047
          Length = 333

 Score =  449 bits (1155), Expect = e-131
 Identities = 219/333 (65%), Positives = 268/333 (80%), Gaps = 2/333 (0%)

Query: 1   MAFNMHNRNLLSLMHHSTRELRYLLDLSRDLKRAKYTGTEQQHLKRKNIALIFEKTSTRT 60
           MAFN+ NR+ L+L   S RE+ +LL LS DLK AKY GTE   L+ K+IALIFEK STRT
Sbjct: 1   MAFNLKNRHFLTLRDFSPREIAFLLKLSADLKTAKYAGTEVPKLEGKDIALIFEKNSTRT 60

Query: 61  RCAFEVAAYDQGANVTYIDPNSSQIGHKESMKDTARVLGRMYDAIEYRGFKQEIVEELAK 120
           R  FEVAA+DQGA VTY+ P  + IGHKES+KDTARVLGR+YDAIEYRGF Q +V+ELA+
Sbjct: 61  RVGFEVAAFDQGARVTYLGPTGTHIGHKESVKDTARVLGRVYDAIEYRGFGQSVVDELAQ 120

Query: 121 FAGVPVFNGLTDEYHPTQMLADVLTMREHSDKPLHDISYAYLGDARNNMGNSLLLIGAKL 180
           +AGVPV+NGLT+E+HPTQ+LAD LTM+EH +KPL D++Y ++GDA NNMG+SLL+ GAK+
Sbjct: 121 YAGVPVYNGLTNEFHPTQILADFLTMQEHVEKPLRDVAYVFIGDAANNMGDSLLIGGAKM 180

Query: 181 GMDVRIAAPKALWPHDEFVAQCKKFAEESGAKLTLTEDPKEAVKGVDFVHTDVWVSMGEP 240
           GMDVR+ APKA WP      + +  A E+GA++T+TED   AV GVDFV+TDVWVSMGEP
Sbjct: 181 GMDVRLCAPKACWPGQAVQEEAQALAAETGARITITEDVDAAVAGVDFVYTDVWVSMGEP 240

Query: 241 VEAWGERIKELLPYQVNMEIMKATGNPRAKFMHCLPAFHNSETKVGKQIAEQYPNLANGI 300
            E W ERIK L+PYQVN  +M  TGNPRA+FMHCLPAFHN+ET VGK+I E Y    + +
Sbjct: 241 KEKWAERIKLLMPYQVNAALMAKTGNPRARFMHCLPAFHNTETVVGKEIQETYG--IDAM 298

Query: 301 EVTEDVFESPYNIAFEQAENRMHTIKAILVSTL 333
           EVTE+VFESP +I F+QAENRMHTIKA+LV+TL
Sbjct: 299 EVTEEVFESPASIVFDQAENRMHTIKAVLVATL 331


Lambda     K      H
   0.318    0.133    0.387 

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: 386
Number of extensions: 6
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: 336
Length of database: 333
Length adjustment: 28
Effective length of query: 308
Effective length of database: 305
Effective search space:    93940
Effective search space used:    93940
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 GFF4047 HP15_3987 (ornithine carbamoyltransferase)
to HMM TIGR00658 (argF: ornithine carbamoyltransferase (EC 2.1.3.3))

Software error:

../bin/blast/fastacmd -i /tmp/list.27670.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.27670.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

For help, please send mail to the webmaster (help@microbesonline.org), giving this error message and the time and date of the error.