GapMind for catabolism of small carbon sources

 

Alignments for a candidate for arcC in Klebsiella michiganensis M5al

Align Carbamate kinase; EC 2.7.2.2 (characterized, see rationale)
to candidate BWI76_RS07060 BWI76_RS07060 carbamate kinase

Query= uniprot:P13982
         (310 letters)



>FitnessBrowser__Koxy:BWI76_RS07060
          Length = 297

 Score =  270 bits (690), Expect = 3e-77
 Identities = 150/298 (50%), Positives = 191/298 (64%), Gaps = 10/298 (3%)

Query: 3   IVVALGGNALLRRGEPMTADNQRENVRIAAEQIAKVAPGNELVIAHGNGPQVGLLALQGA 62
           +VVALGGNALL+RGE +T +NQ  N+  A   +A++A    L I HGNGPQVGLL+LQ  
Sbjct: 4   LVVALGGNALLQRGEALTVENQYRNIDSAVPALARLAQKYRLAIVHGNGPQVGLLSLQNL 63

Query: 63  AYDKVSPYPLDVLGAETEGMIGYMIEQEMGN--LLPFEVPFATILTQVEVDGKDPAFQNP 120
           AY  V PYPLDVL AE++GMIGYM+ Q +    L+P   P +T++T++ V   DPAF  P
Sbjct: 64  AYGDVEPYPLDVLVAESQGMIGYMLAQRLAQEALMP---PVSTVMTRIAVASNDPAFSAP 120

Query: 121 TKPIGPVYSREEAERLAAEKGWSIAPDGDKFRRVVPSPRPKRIFEIRPVKWLLEKGTIVI 180
            K IGPVY  E   +L AE GW++  DG   RRVVPSP P RI E   ++ LL +G  VI
Sbjct: 121 EKFIGPVYEPELQAQLEAEYGWTMKRDGKYLRRVVPSPTPVRIEESESIERLLGEGHAVI 180

Query: 181 CAGGGGIPTMYDEAGKKLSGVEAVIDKDLCSSLLAQELVADILIIATDVDAAYVDWGKPT 240
           C GGGGIP +  E G+   G EAVIDKDL ++LLA+++ AD L+I TD DA Y  WG P 
Sbjct: 181 CCGGGGIPVL--ECGR---GAEAVIDKDLAAALLAEQINADGLVILTDADAVYEHWGTPM 235

Query: 241 QKAIAQAHPDELERLGFAAGSMGPKVQAAIEFARATGKDAVIGSLADIVAITEGKAGT 298
           Q+ I +A P+ L       G+MGPK+ A   + R  GK A IG+L+ I     G AGT
Sbjct: 236 QRPIREATPEALAPFARNDGAMGPKIAAVSGYVRRRGKRAWIGALSRIDDTLAGLAGT 293


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: 269
Number of extensions: 14
Number of successful extensions: 3
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: 297
Length adjustment: 27
Effective length of query: 283
Effective length of database: 270
Effective search space:    76410
Effective search space used:    76410
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 BWI76_RS07060 BWI76_RS07060 (carbamate kinase)
to HMM TIGR00746 (arcC: carbamate kinase (EC 2.7.2.2))

Software error:

../bin/blast/fastacmd -i /tmp/list.21694.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.21694.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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