GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcC in Marinobacter adhaerens HP15

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate GFF4048 HP15_3988 bacterial carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__Marino:GFF4048
          Length = 302

 Score =  346 bits (888), Expect = e-100
 Identities = 183/304 (60%), Positives = 225/304 (74%), Gaps = 3/304 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVA-PGNELVIAHGNGPQVGLLAL 59
           M +V ALGGNALL+RGEP+TA+ QR NV+IAA  +A V   G+ LV+ HGNGPQVGLLAL
Sbjct: 1   MLVVAALGGNALLKRGEPLTAEVQRNNVQIAARSLAAVVRAGHNLVVTHGNGPQVGLLAL 60

Query: 60  QGAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQN 119
           QGA+Y     YPLDVLGAETEGMIGYMIEQE+ N L  + P AT+LTQV VD +DPAF+ 
Sbjct: 61  QGASYKPDEAYPLDVLGAETEGMIGYMIEQELENALGHDRPVATLLTQVVVDPRDPAFEK 120

Query: 120 PTKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIV 179
           PTK +GPVY REE ER AA  GWSIAPDGDK+RRVVPSP+P  I ++R +K LL++G +V
Sbjct: 121 PTKFVGPVYDREEGERRAAAAGWSIAPDGDKWRRVVPSPKPLEIPDMRVLKLLLDQGVVV 180

Query: 180 ICAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKP 239
           +CAGGGGIP +  + G  + G+EAVIDKD  S+LLA++L AD L++ TDV+A Y D+G  
Sbjct: 181 VCAGGGGIPVLRRDDG-SMVGIEAVIDKDAASALLARQLGADALLLLTDVEAVYRDFGTD 239

Query: 240 TQKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTR 299
              A+++    E   L   AGSMGPK+QAA +FA+A G    IG L D VAI EG AGTR
Sbjct: 240 RSTALSELTVSEARALEMPAGSMGPKLQAACDFAQAGGISG-IGRLQDAVAILEGSAGTR 298

Query: 300 VSTR 303
           VS +
Sbjct: 299 VSAK 302


Lambda     K      H
   0.317    0.136    0.393 

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: 324
Number of extensions: 17
Number of successful extensions: 4
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: 310
Length of database: 302
Length adjustment: 27
Effective length of query: 283
Effective length of database: 275
Effective search space:    77825
Effective search space used:    77825
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 (21.6 bits)
S2: 48 (23.1 bits)

Align candidate GFF4048 HP15_3988 (bacterial carbamate kinase)
to HMM TIGR00746 (arcC: carbamate kinase (EC 2.7.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.22131.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.22131.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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