GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcC in Pseudomonas fluorescens GW456-L13

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate PfGW456L13_1872 Carbamate kinase (EC 2.7.2.2)

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1872
          Length = 309

 Score =  511 bits (1317), Expect = e-150
 Identities = 253/310 (81%), Positives = 283/310 (91%), Gaps = 1/310 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60
           MRIVVALGGNALLRRGEPMTADNQR N+RIA EQIAK+ PGN+LVIAHGNGPQVGLL+LQ
Sbjct: 1   MRIVVALGGNALLRRGEPMTADNQRANIRIATEQIAKIHPGNQLVIAHGNGPQVGLLSLQ 60

Query: 61  GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120
            AAY  VSPYPLDVLGAETEGMIGY+IEQE+GNLL FEVPFAT+LTQVEVD  DPAF+NP
Sbjct: 61  AAAYTSVSPYPLDVLGAETEGMIGYIIEQELGNLLDFEVPFATLLTQVEVDANDPAFKNP 120

Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180
           TKPIGPVY++EEAE LAAEKGW+IAPDGDK+RRVV SP+PKRIFEIRP+KWLLEK +IVI
Sbjct: 121 TKPIGPVYTKEEAEALAAEKGWAIAPDGDKYRRVVASPKPKRIFEIRPIKWLLEKSSIVI 180

Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240
           CAGGGGIPTMY   G KL GVEAVIDKDLCS+LLA++L AD+L+IATDV+AA++D+GKPT
Sbjct: 181 CAGGGGIPTMYTSPG-KLEGVEAVIDKDLCSALLAEQLEADLLVIATDVNAAFIDFGKPT 239

Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300
           QKAIAQAHPDE+E+LGFAAGSMGPKVQAA EFAR TGK AVIGSL+DI AI +GKAGTR+
Sbjct: 240 QKAIAQAHPDEMEKLGFAAGSMGPKVQAACEFARHTGKVAVIGSLSDIEAIVQGKAGTRI 299

Query: 301 STRKAGIEYR 310
           ST   GI Y+
Sbjct: 300 STATPGISYQ 309


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: 399
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: 310
Length of database: 309
Length adjustment: 27
Effective length of query: 283
Effective length of database: 282
Effective search space:    79806
Effective search space used:    79806
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 PfGW456L13_1872 (Carbamate kinase (EC 2.7.2.2))
to HMM TIGR00746 (arcC: carbamate kinase (EC 2.7.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.3080.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3080.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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