Alignments for a candidate for carA in Pedobacter sp. GW460-11-11-14-LB5

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate CA265_RS15240 CA265_RS15240 carbamoyl phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Pedo557:CA265_RS15240
          Length = 370

 Score =  310 bits (794), Expect = 4e-89
 Identities = 167/373 (44%), Positives = 229/373 (61%), Gaps = 18/373 (4%)

Query: 5   ALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNVG 64
           A+L+L DGT F+G+A G  G+  GE+ FNT MTGYQEI TDPSY  QI+  T  HIGN G
Sbjct: 9   AILLLADGTVFYGKAAGKIGTTTGEICFNTGMTGYQEIFTDPSYFGQIMVTTNAHIGNYG 68

Query: 65  TNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLLRE 124
            +  + ES  +   GLV ++  ++ S    TE +  Y +  N+VAI+DIDTR L R +R+
Sbjct: 69  IHKDEIESGSIKIAGLVCKNYNIVYSRKEATESIQDYFQNDNLVAISDIDTRALVRHIRD 128

Query: 125 KGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGGLPEA 184
           KGA N  II+ +  D     +K    P + G++L+ +V+T E Y +         G PEA
Sbjct: 129 KGAMNA-IISSEITDLEELKQKLAEVPSMEGLELSSKVSTTEPYFY---------GNPEA 178

Query: 185 KKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSNGPGD 244
             +      V A D G K+NILR   +R   + + PA+TS  ++ K +PDG F+SNGPGD
Sbjct: 179 SLK------VAALDLGIKKNILRNFENRDIYVQVFPAKTSFAEMEKFSPDGYFISNGPGD 232

Query: 245 PAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDVEKNV 304
           P+   YA+  I   L  D P+FGICLGHQLLA A+G  T+KM  GH G NHPVK++ KN 
Sbjct: 233 PSVMPYAVETITAILAVDKPLFGICLGHQLLAEANGIGTMKMFNGHRGLNHPVKNIIKNH 292

Query: 305 VMITAQNHGFAV--DEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGPHD 362
             +T+QNHGF V  DE      + +TH +L D +++GI    K AFS Q HPE+SPGPHD
Sbjct: 293 CEVTSQNHGFGVIPDEVRNSDKVEITHVNLNDKSIEGIRVKGKKAFSVQYHPESSPGPHD 352

Query: 363 AAPLFDHFIELIE 375
           +  LFD F+++++
Sbjct: 353 SRYLFDDFVDVMK 365


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: 386
Number of extensions: 16
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: 382
Length of database: 370
Length adjustment: 30
Effective length of query: 352
Effective length of database: 340
Effective search space:   119680
Effective search space used:   119680
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 CA265_RS15240 CA265_RS15240 (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.31063.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.31063.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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