Alignments for a candidate for carA in Pseudomonas putida KT2440

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate PP_4724 PP_4724 Carbamoyl-phosphate synthase small chain

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Putida:PP_4724
          Length = 378

 Score =  539 bits (1389), Expect = e-158
 Identities = 264/378 (69%), Positives = 301/378 (79%)

Query: 1   MIKSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHI 60
           M K A+L L DG+ F G AIGA G  VGEVVFNT+MTGYQEILTDPSY++QIVTLTYPHI
Sbjct: 1   MTKPAILALADGSIFRGEAIGADGQTVGEVVFNTAMTGYQEILTDPSYAQQIVTLTYPHI 60

Query: 61  GNVGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTR 120
           GN GT   D ESS+V + GLVIRDLPL+ASN+RNT+ L  YLK +N+VAIA IDTR+LTR
Sbjct: 61  GNTGTTPEDAESSRVWSAGLVIRDLPLLASNWRNTQSLPEYLKANNVVAIAGIDTRRLTR 120

Query: 121 LLREKGAQNGCIIAGDNPDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           +LREKGAQNGCI+AGDN     A+  AR FPGL GMDLAK V+T E Y W    W L   
Sbjct: 121 ILREKGAQNGCILAGDNISEEAAIAAARGFPGLKGMDLAKVVSTKERYEWRSSVWELKTD 180

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
                   +LP+HVVA+D+G K NILRMLV RGCR+T+VPAQT A +VL +NPDG+FLSN
Sbjct: 181 SHPTIDAADLPYHVVAFDYGVKLNILRMLVARGCRVTVVPAQTPASEVLALNPDGVFLSN 240

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDP PCDYAI AI++ LET+IPVFGICLGHQLLALASGAKTVKM  GHHG NHPV+D+
Sbjct: 241 GPGDPEPCDYAIQAIKEILETEIPVFGICLGHQLLALASGAKTVKMGHGHHGANHPVQDL 300

Query: 301 EKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASPGP 360
           +  VVMIT+QNHGFAVDEATLP N+R  HKSLFDGTLQGI RTDK AFSFQGHPEASPGP
Sbjct: 301 DTGVVMITSQNHGFAVDEATLPGNVRAIHKSLFDGTLQGIERTDKSAFSFQGHPEASPGP 360

Query: 361 HDAAPLFDHFIELIEQYR 378
            D APLFD F + + + R
Sbjct: 361 TDVAPLFDRFTDAMAKRR 378


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: 514
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: 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 PP_4724 PP_4724 (Carbamoyl-phosphate synthase small chain)
to HMM TIGR01368 (carA: carbamoyl-phosphate synthase, small subunit (EC 6.3.5.5))

Software error:

../bin/blast/fastacmd -i /tmp/list.21581.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.21581.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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