GapMind for Amino acid biosynthesis

 

Alignments for a candidate for carA in Caulobacter crescentus NA1000

Align Carbamoyl-phosphate synthase small chain, chloroplastic; Carbamoyl-phosphate synthetase glutamine chain; Protein VENOSA 6; EC 6.3.5.5 (characterized)
to candidate CCNA_02925 CCNA_02925 carbamoyl-phosphate synthase small chain

Query= SwissProt::Q9LVW7
         (430 letters)



>FitnessBrowser__Caulo:CCNA_02925
          Length = 388

 Score =  300 bits (768), Expect = 5e-86
 Identities = 162/377 (42%), Positives = 227/377 (60%), Gaps = 10/377 (2%)

Query: 60  LVLEDGSIWPAKSFGAPGTRIAELVFNTSLTGYQEILTDPSYAGQFVLMTNPQIGNTGVN 119
           L L DG+I      GA G  + E+ FNT++TGYQEILTDPSY  Q V  T P +GN GVN
Sbjct: 13  LALADGAILQGVGCGAVGDAVGEVCFNTAMTGYQEILTDPSYMAQIVAFTFPHVGNVGVN 72

Query: 120 PDDEES----GQCFLTGLVIRNLSISTSNWRCTKTLADYLTERDIMGVYDLDTRAITRRL 175
            +D E      +    G + R++    +NWR       ++  R ++G+  +DTRA+TR++
Sbjct: 73  GEDVEQITGVAETAARGALFRDVPTVQANWRADGDFDAWMKARGVVGLAGVDTRALTRKI 132

Query: 176 REDGSLIGVLSTEQSKTDD--ELLQMSRSW-DIVGIDLISDVSCKSPYEWVDKTNAEWDF 232
           RE G   GV++       D   L+  +++W  + G+DL  D S    + W D+    W  
Sbjct: 133 RETGMPHGVIAHSPDGQFDLAALVAKAKAWAGLEGLDLAKDASTTQTFTW-DEGLWSWPE 191

Query: 233 NTNSRDGKSYKVIAYDFGIKQNILRRLSSYGCQITVVPSTFPAAEALKMNPDGILFSNGP 292
                D   Y+V+  D+G+K+NILR L+  G + TVVP++  A + L  NPDG++ SNGP
Sbjct: 192 GYAKLDKPKYEVVVIDYGVKRNILRALAHVGARATVVPASTSAEDILARNPDGVMLSNGP 251

Query: 293 GDPSAV-PYAVETVKELLGK-VPVYGICMGHQLLGQALGGKTFKMKFGHHGGNHPVRNNR 350
           GDP+A   YAV  +++L+    PV+GIC+GHQ+L  ALG KT KM+ GHHG NHPV++  
Sbjct: 252 GDPAATGQYAVPEIQKLVASGKPVFGICLGHQMLALALGAKTVKMEQGHHGANHPVKDLT 311

Query: 351 TGQVEISAQNHNYAVDPASLPGGVEVTHVNLNDGSCAGLSFPEMNVMSLQYHPEASPGPH 410
           TG+VEI + NH + VD ASLP  V+ THV+L DG+ AG++     V S+Q+HPEASPGP 
Sbjct: 312 TGKVEIVSMNHGFTVDTASLPAPVKETHVSLFDGTNAGIALDGKPVFSVQHHPEASPGPT 371

Query: 411 DSDNAFREFIELMKRSK 427
           DS   F  F  LM  +K
Sbjct: 372 DSLYLFERFAGLMDAAK 388


Lambda     K      H
   0.316    0.134    0.403 

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: 480
Number of extensions: 27
Number of successful extensions: 4
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: 430
Length of database: 388
Length adjustment: 31
Effective length of query: 399
Effective length of database: 357
Effective search space:   142443
Effective search space used:   142443
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 (21.6 bits)
S2: 50 (23.9 bits)

Align candidate CCNA_02925 CCNA_02925 (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.14608.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.14608.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.