Alignments for a candidate for carA in Methylococcus capsulatus Bath

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_010961105.1 MCA_RS09105 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_000008325.1:WP_010961105.1
          Length = 378

 Score =  507 bits (1306), Expect = e-148
 Identities = 245/367 (66%), Positives = 292/367 (79%), Gaps = 3/367 (0%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           ALL L+DGT F G AIGA G++VGEVVFNTS+TGYQEILTDPSY+RQIV LTYPHIGN G
Sbjct: 5   ALLALDDGTVFRGYAIGAEGASVGEVVFNTSITGYQEILTDPSYARQIVALTYPHIGNTG 64

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
            N+ D ES+ + A GLVIRDLPL ASN+R    L  YL++  +V IA +DTR+LTR+LR+
Sbjct: 65  INEEDTESTGIFASGLVIRDLPLRASNWRCERRLDEYLRQRGVVGIAGLDTRRLTRILRD 124

Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184
           KGAQ GCI AG+  DA  A+  AR FPGL GMDLA+ VTT + Y WT+GSW       E 
Sbjct: 125 KGAQRGCIAAGNGLDADAAVAMARGFPGLQGMDLAQVVTTPQRYEWTEGSWRFGA---EP 181

Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244
            +  +  FHVVAYDFG KRNILR+L DRGCR+T+VPA+T A + L + PDG+FLSNGPGD
Sbjct: 182 VQSGQGGFHVVAYDFGVKRNILRLLADRGCRVTVVPARTPAAEALALKPDGLFLSNGPGD 241

Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304
           P PCDYA+ AI++FL+T IPVFGICLGHQLLALA+GA+T KMKFGHHG NHPV+D+    
Sbjct: 242 PEPCDYAVAAIREFLDTGIPVFGICLGHQLLALAAGARTSKMKFGHHGANHPVQDLSTGR 301

Query: 305 VMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAA 364
           V+IT+QNHGFAV+EA+LPAN+R TH+SLFDG+LQGI  TD+ AFSFQGHPEASPGPHD  
Sbjct: 302 VVITSQNHGFAVEEASLPANVRPTHRSLFDGSLQGIEFTDRSAFSFQGHPEASPGPHDLC 361

Query: 365 PLFDHFI 371
            LFD F+
Sbjct: 362 DLFDRFV 368


Lambda     K      H
   0.318    0.135    0.400 

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: 515
Number of extensions: 16
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: 382
Length of database: 378
Length adjustment: 30
Effective length of query: 352
Effective length of database: 348
Effective search space:   122496
Effective search space used:   122496
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: 50 (23.9 bits)

Align candidate WP_010961105.1 MCA_RS09105 (glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.11419.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.11419.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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