Alignments for a candidate for carA in Echinicola vietnamensis KMM 6221, DSM 17526

Align Carbamoyl-phosphate synthase small chain; Carbamoyl-phosphate synthetase glutamine chain; EC 6.3.5.5 (characterized)
to candidate Echvi_0226 Echvi_0226 carbamoyl-phosphate synthase, small subunit

Query= SwissProt::P0A6F1
         (382 letters)



>FitnessBrowser__Cola:Echvi_0226
          Length = 364

 Score =  296 bits (759), Expect = 5e-85
 Identities = 168/376 (44%), Positives = 220/376 (58%), Gaps = 22/376 (5%)

Query: 3   KSALLVLEDGTQFHGRAIGATGSAVGEVVFNTSMTGYQEILTDPSYSRQIVTLTYPHIGN 62
           + A L+LEDGT F+G  IG  G+  GE+ FNT MTGYQEI TDPSY+ QIV  T  HIGN
Sbjct: 4   QKATLLLEDGTVFYGTLIGKHGTNGGEICFNTGMTGYQEIYTDPSYTGQIVVTTTSHIGN 63

Query: 63  VGTNDADEESSQVHAQGLVIRDLPLIASNFRNTEDLSSYLKRHNIVAIADIDTRKLTRLL 122
            G  D++ ES       +V+     I S    T+ L  +L+ + I  IAD+DTRKL R +
Sbjct: 64  YGVIDSEAESDGPTIASIVVNSFSEIYSRLDATQSLQEFLESNGITGIADVDTRKLVRHI 123

Query: 123 REKGAQNGCIIAG-DN-PDAALALEKARAFPGLNGMDLAKEVTTAEAYSWTQGSWTLTGG 180
           R KGA N  I +  DN  D    L+K    P + G++L+ +V T E Y     + T+   
Sbjct: 124 RSKGAMNAIISSEFDNLEDLQKELDKV---PDMAGLELSSKVCTKEPYYVGDENSTIK-- 178

Query: 181 LPEAKKEDELPFHVVAYDFGAKRNILRMLVDRGCRLTIVPAQTSAEDVLKMNPDGIFLSN 240
                        V   D+G KRNILR L  RG    + PA+T+  D+    P+  FLSN
Sbjct: 179 -------------VACVDYGIKRNILRNLAARGVYCKVFPAKTAVADMEAWQPNAYFLSN 225

Query: 241 GPGDPAPCDYAITAIQKFLETDIPVFGICLGHQLLALASGAKTVKMKFGHHGGNHPVKDV 300
           GPGDPA  DYA+  +++ L  + PVFGICLGHQLLA A G KT KM  GH G NHP+K++
Sbjct: 226 GPGDPAVMDYAVETVKEILALNKPVFGICLGHQLLAEAVGIKTYKMHHGHRGINHPIKNL 285

Query: 301 EKNVVMITAQNHGFAV--DEATLPANLRVTHKSLFDGTLQGIHRTDKPAFSFQGHPEASP 358
                 IT+QNHGF +  +++    ++ +TH  L D T+ GI   D+PAFS Q HPE++P
Sbjct: 286 NTGKSEITSQNHGFNIVREDSENHPDIEITHVHLNDNTVAGIKLKDRPAFSVQYHPESAP 345

Query: 359 GPHDAAPLFDHFIELI 374
           GPHD+  LFD FI LI
Sbjct: 346 GPHDSRYLFDDFISLI 361


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: 392
Number of extensions: 13
Number of successful extensions: 3
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: 364
Length adjustment: 30
Effective length of query: 352
Effective length of database: 334
Effective search space:   117568
Effective search space used:   117568
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 Echvi_0226 Echvi_0226 (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.3901.in -d ../tmp/orgsDef_201/orgs.faa -p T > /tmp/gapView.3901.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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