Alignments for a candidate for carA in Caulobacter crescentus NA1000

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate CCNA_02925 CCNA_02925 carbamoyl-phosphate synthase small chain

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Caulo:CCNA_02925
          Length = 388

 Score =  376 bits (966), Expect = e-109
 Identities = 195/379 (51%), Positives = 248/379 (65%), Gaps = 10/379 (2%)

Query: 4   SALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGNV 63
           + +L L DG    G   GA G AVGEV FNT+MTGYQEILTDPSY  QIV  T+PH+GNV
Sbjct: 10  TGVLALADGAILQGVGCGAVGDAVGEVCFNTAMTGYQEILTDPSYMAQIVAFTFPHVGNV 69

Query: 64  GTNDADEES----SQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLT 119
           G N  D E     ++  A+G + RD+P + +N+R   D  +++K   +V +A +DTR LT
Sbjct: 70  GVNGEDVEQITGVAETAARGALFRDVPTVQANWRADGDFDAWMKARGVVGLAGVDTRALT 129

Query: 120 RLLREKGAQNGCIIAGDNP--DAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTL 177
           R +RE G  +G I    +   D A  + KA+A+ GL G+DLAK+ +T + ++W +G W+ 
Sbjct: 130 RKIRETGMPHGVIAHSPDGQFDLAALVAKAKAWAGLEGLDLAKDASTTQTFTWDEGLWSW 189

Query: 178 TGGLPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIF 237
             G     K D+  + VV  D+G KRNILR L   G R T+VPA TSAED+L  NPDG+ 
Sbjct: 190 PEGYA---KLDKPKYEVVVIDYGVKRNILRALAHVGARATVVPASTSAEDILARNPDGVM 246

Query: 238 LSNGPGDPAPC-DYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHP 296
           LSNGPGDPA    YA+  IQK + +  PVFGICLGHQ+LALA GAKTVKM+ GHHG NHP
Sbjct: 247 LSNGPGDPAATGQYAVPEIQKLVASGKPVFGICLGHQMLALALGAKTVKMEQGHHGANHP 306

Query: 297 VKDVEKNVVMITAQNHGFAVDEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEA 356
           VKD+    V I + NHGF VD A+LPA ++ TH SLFDGT  GI    KP FS Q HPEA
Sbjct: 307 VKDLTTGKVEIVSMNHGFTVDTASLPAPVKETHVSLFDGTNAGIALDGKPVFSVQHHPEA 366

Query: 357 SPGPHDAAPLFDHFIELIE 375
           SPGP D+  LF+ F  L++
Sbjct: 367 SPGPTDSLYLFERFAGLMD 385


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: 490
Number of extensions: 23
Number of successful extensions: 5
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: 388
Length adjustment: 30
Effective length of query: 352
Effective length of database: 358
Effective search space:   126016
Effective search space used:   126016
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 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.9770.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.9770.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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