Alignments for a candidate for carA in Shewanella loihica PV-4

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate 5210398 Shew_2839 carbamoyl phosphate synthase small subunit (RefSeq)

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__PV4:5210398
          Length = 390

 Score =  602 bits (1552), Expect = e-177
 Identities = 297/382 (77%), Positives = 323/382 (84%), Gaps = 1/382 (0%)

Query: 1   MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60
           + KSALLVLEDGT F G AIGA G AVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI
Sbjct: 10  LTKSALLVLEDGTVFSGTAIGADGLAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 69

Query: 61  GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120
           GN GTN  D ES  VHA GL+IRDLPL+ASNFRN + LS YLK +N+V IADIDTRKLTR
Sbjct: 70  GNTGTNSEDTESEAVHACGLIIRDLPLLASNFRNEQSLSDYLKSNNVVGIADIDTRKLTR 129

Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           +LREKGAQ G I+ GD  D A AL  A+AFPGL GMDLAKEVTT + Y W  GSW L GG
Sbjct: 130 ILREKGAQAGAILVGDM-DEAKALAAAKAFPGLKGMDLAKEVTTQKQYQWRSGSWRLVGG 188

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
           LP    E EL + VVAYD+G KRNILRMLVDRGC +T+VPAQT A +VL MNPDGIFLSN
Sbjct: 189 LPSDTPESELKYKVVAYDYGVKRNILRMLVDRGCDVTVVPAQTPAAEVLAMNPDGIFLSN 248

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDP PCDYAI AIQ FL+TDIP+FGICLGHQLLALASGAKT+KMKFGHHG NHPV ++
Sbjct: 249 GPGDPEPCDYAIEAIQAFLKTDIPLFGICLGHQLLALASGAKTLKMKFGHHGANHPVSNL 308

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
           EK  VMIT+QNHGFA DE +LPAN++VTHKSLFDG+LQGIH TDKPAFSFQGHPEASPGP
Sbjct: 309 EKGNVMITSQNHGFAADETSLPANVKVTHKSLFDGSLQGIHLTDKPAFSFQGHPEASPGP 368

Query: 361 HDAAPLFDHFIELIEQYRKTAK 382
           HDAAPLFDHFIELIE+YR  AK
Sbjct: 369 HDAAPLFDHFIELIEEYRHNAK 390


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: 539
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: 390
Length adjustment: 30
Effective length of query: 352
Effective length of database: 360
Effective search space:   126720
Effective search space used:   126720
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 5210398 Shew_2839 (carbamoyl phosphate synthase small subunit (RefSeq))
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.13955.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.13955.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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