GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcC in Pseudomonas stutzeri RCH2

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate GFF269 Psest_0270 carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__psRCH2:GFF269
          Length = 307

 Score =  482 bits (1241), Expect = e-141
 Identities = 237/307 (77%), Positives = 273/307 (88%), Gaps = 1/307 (0%)

Query: 1   MRIVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQ 60
           MRIV+ALGGNALLRRGEP++ADNQRENVR A  QIA++A GNELV+AHGNGPQVGLLALQ
Sbjct: 1   MRIVIALGGNALLRRGEPLSADNQRENVRTACMQIARIAAGNELVVAHGNGPQVGLLALQ 60

Query: 61  GAAYDKVSPYPLDVLGAETEGMIGYMIEQEMGNLLPFEVPFATILTQVEVDGKDPAFQNP 120
           GAAY  V  YPLDVLGAETEGMIGY+IEQE+GNLLPFEVP AT+LTQVEVD +DPAF+ P
Sbjct: 61  GAAYKDVPVYPLDVLGAETEGMIGYIIEQELGNLLPFEVPMATLLTQVEVDPEDPAFKQP 120

Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180
           +KPIGPVYSREEAERLA EKGW+IA DGD+FRRVVPSPRPKRIFEIRP+ WLL+KG++VI
Sbjct: 121 SKPIGPVYSREEAERLAEEKGWAIAADGDRFRRVVPSPRPKRIFEIRPIGWLLDKGSVVI 180

Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240
           CAGGGGIPT+YD++G +L GVEAVIDKDLCS+LLA++L AD+L+IATDVD AY+DWG P 
Sbjct: 181 CAGGGGIPTVYDQSG-RLQGVEAVIDKDLCSALLAEQLKADLLVIATDVDGAYLDWGTPQ 239

Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGTRV 300
           Q+ I++AHPD+L+  GFAAGSMGPKVQAA EFAR TG  AVIGSL  I AI +G+AGTRV
Sbjct: 240 QRRISEAHPDQLQSRGFAAGSMGPKVQAACEFARNTGNVAVIGSLEQIEAIIKGQAGTRV 299

Query: 301 STRKAGI 307
           S   AG+
Sbjct: 300 SLEAAGL 306


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: 384
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: 310
Length of database: 307
Length adjustment: 27
Effective length of query: 283
Effective length of database: 280
Effective search space:    79240
Effective search space used:    79240
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 GFF269 Psest_0270 (carbamate kinase)
to HMM TIGR00746 (arcC: carbamate kinase (EC 2.7.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.3295.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.3295.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.