Alignments for a candidate for carA in Pseudomonas stutzeri RCH2

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate GFF938 Psest_0967 carbamoyl-phosphate synthase, small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__psRCH2:GFF938
          Length = 382

 Score =  533 bits (1372), Expect = e-156
 Identities = 261/374 (69%), Positives = 299/374 (79%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           A+L L DG+ F G +IGA G  +GEVVFNT+MTGYQEILTDPSY++QIVTLTYPH+GN G
Sbjct: 9   AILALADGSIFRGESIGADGQTIGEVVFNTAMTGYQEILTDPSYAKQIVTLTYPHVGNTG 68

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
           T   D ES +V A GLVIRDLPLI+SN+R+ + L  YLK +  VAIA IDTR+LTR+LRE
Sbjct: 69  TTPEDAESWKVWAAGLVIRDLPLISSNWRDKQPLPDYLKANGTVAIAGIDTRRLTRILRE 128

Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184
           KGAQNGCI+AG +     ALE AR+FPGL GMDLAKEV+  E Y W    W L       
Sbjct: 129 KGAQNGCILAGSDATEEKALELARSFPGLKGMDLAKEVSVKERYEWRSSVWCLKDDGHAE 188

Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244
               ELP+HVVA+D+G K NILRMLV RGCR+T++PAQT A + L +NPDGIFL+NGPGD
Sbjct: 189 IPASELPYHVVAFDYGVKYNILRMLVARGCRVTVLPAQTPASEALALNPDGIFLANGPGD 248

Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304
           P PCDYAI AIQ+ LETDIPVFGICLGHQLLALASGAKTVKM  GHHG NHPV+D++  V
Sbjct: 249 PEPCDYAIKAIQEVLETDIPVFGICLGHQLLALASGAKTVKMPNGHHGANHPVQDLKTGV 308

Query: 305 VMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHDAA 364
           VMIT+QNHGFAVDEA+LPAN+R THKSLFDGTLQGI RTDK AFSFQGHPEASPGPHD A
Sbjct: 309 VMITSQNHGFAVDEASLPANVRATHKSLFDGTLQGIERTDKAAFSFQGHPEASPGPHDVA 368

Query: 365 PLFDHFIELIEQYR 378
           PLFD FIE + + R
Sbjct: 369 PLFDRFIETMAKRR 382


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: 527
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: 382
Length of database: 382
Length adjustment: 30
Effective length of query: 352
Effective length of database: 352
Effective search space:   123904
Effective search space used:   123904
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 GFF938 Psest_0967 (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.26338.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.26338.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.