Alignments for a candidate for carA in Thiomicrospira cyclica ALM1

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate WP_013835598.1 THICY_RS05375 glutamine-hydrolyzing carbamoyl-phosphate synthase small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>NCBI__GCF_000214825.1:WP_013835598.1
          Length = 380

 Score =  554 bits (1427), Expect = e-162
 Identities = 273/381 (71%), Positives = 311/381 (81%), Gaps = 2/381 (0%)

Query: 1   MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60
           M  SALL L DGT F GRAIGA G  VGEVVFNTSMTGYQEILTDPSY +QIVTLTYPHI
Sbjct: 1   MEASALLALADGTLFWGRAIGAQGECVGEVVFNTSMTGYQEILTDPSYYKQIVTLTYPHI 60

Query: 61  GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120
           GNVG ND D ES  + AQGLV+RD P + SNFR T+ L  YLK  N+VAIADIDTRKLTR
Sbjct: 61  GNVGVNDDDRESPNIMAQGLVVRDCPRVMSNFRATQSLPDYLKAQNVVAIADIDTRKLTR 120

Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           LLREKGAQ+G I+AG   DAA A+ KA+AF GLNGMDLAKEVT ++AY+W +G+W L  G
Sbjct: 121 LLREKGAQSGVIVAGVQIDAAAAVAKAQAFAGLNGMDLAKEVTVSKAYTWHEGTWQLGEG 180

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
                +  +   HVVA+D+G KRNILRML DRGCRLT+VPAQTSA +VL MNPDG+FLSN
Sbjct: 181 --HVDRSAQATRHVVAFDYGIKRNILRMLADRGCRLTVVPAQTSAAEVLAMNPDGVFLSN 238

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDPAPCDYAI A+++ L   +PVFGICLGHQLLALA+GAKT+KMKFGHHGGNHPV+++
Sbjct: 239 GPGDPAPCDYAIEAVREILAAKVPVFGICLGHQLLALAAGAKTLKMKFGHHGGNHPVQEL 298

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
           E   VMIT+QNHGFAVD ATLPA+++VTH SLFDG+LQGI  TD+PAFSFQGHPEASPGP
Sbjct: 299 ETGRVMITSQNHGFAVDPATLPAHVKVTHNSLFDGSLQGITLTDRPAFSFQGHPEASPGP 358

Query: 361 HDAAPLFDHFIELIEQYRKTA 381
           HD APLFD FI  I QYR  +
Sbjct: 359 HDLAPLFDQFIVQINQYRSAS 379


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: 492
Number of extensions: 14
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: 380
Length adjustment: 30
Effective length of query: 352
Effective length of database: 350
Effective search space:   123200
Effective search space used:   123200
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_013835598.1 THICY_RS05375 (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.10393.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.10393.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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