GapMind for Amino acid biosynthesis

 

Alignments for a candidate for gatB in Caulobacter crescentus NA1000

Align Aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B; Asp/Glu-ADT subunit B; EC 6.3.5.- (characterized)
to candidate CCNA_02518 CCNA_02518 aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B

Query= SwissProt::Q9RF06
         (475 letters)



>FitnessBrowser__Caulo:CCNA_02518
          Length = 498

 Score =  425 bits (1092), Expect = e-123
 Identities = 221/483 (45%), Positives = 328/483 (67%), Gaps = 15/483 (3%)

Query: 3   FETVIGLEVHVELKTDSKMFSPSPAHFGAEPNSNTNVIDLAYPGVLPVVNKRAVDWAMRA 62
           +E V+GLEVH ++ + SK+FS +   FGA PN   +++D A PG+LPV+N+  V+ A++ 
Sbjct: 15  WEMVLGLEVHAQVASKSKLFSGAAVGFGAGPNEQVSLVDAAMPGMLPVLNRFCVEQAVKT 74

Query: 63  AMALNMEIATESKFDRKNYFYPDNPKAYQISQFDQPIGENGYIDIEVD-GETKRIGITRL 121
            + L  +I  +S+FDRKNYFYPD P+ YQISQFDQPI   G + +E D G T  + I RL
Sbjct: 75  GLGLRAQINLKSRFDRKNYFYPDLPQGYQISQFDQPIVGEGVVSVERDDGTTFDVRIERL 134

Query: 122 HMEEDAGKSTHKGE--YSLVDLNRQGTPLIEIVSEPDIRSPKEAYAYLEKLRSIIQYTGV 179
           H+E+DAGKS H  +   + VDLNR GT L+EIVS+PD+R+ +EA AY++KLR+I+ Y G 
Sbjct: 135 HLEQDAGKSLHDQDPNATYVDLNRAGTALMEIVSKPDMRTSEEAAAYVKKLRTILVYLGT 194

Query: 180 SDVKMEEGSLRCDANISL-RPYGQEKF---------GTKAELKNLNSFNYVRKGLEYEEK 229
            D  ME+G+LR D N+S+ RP   EKF         GT+ E+KN+NS+ Y+++ +EYE +
Sbjct: 195 CDGDMEKGNLRADVNVSVCRPGDYEKFRATGDFKHLGTRCEIKNVNSYRYIQQAIEYEAR 254

Query: 230 RQEEELLSGGEIGQETRRFDESTGKTILMRVKEGSDDYRYFPEPDIVPLYIDDAWKERVR 289
           RQ E L  GG++ QETR FD + G+T  MR KE + DYRYFP+PD++PL +D AW + + 
Sbjct: 255 RQIEILEDGGKVDQETRLFDPTKGETRSMRSKEEAHDYRYFPDPDLLPLVLDPAWVKSIE 314

Query: 290 QTIPELPDERKAKYVNELGLPAYDAHVLTLTKEMSDFFESTIEHGADVKLTSNWLMGGVN 349
           +T+PELPD +KA+  ++ GL AYDA VL +  + +D+FE+  + G D KL +NW+   + 
Sbjct: 315 ETLPELPDAKKARLQSQYGLSAYDAGVLIIDADRADYFEAAAK-GRDAKLVANWVTNELL 373

Query: 350 EYLNKNQVELLDTKLTPENLAGMIKLIEDGTMSSKIAKKVFPELAAKGGNAKQIMEDNGL 409
             L+    E  ++ L   ++A +++LIE+GT+SSKIAK+VF  + A  G   +I+E  GL
Sbjct: 374 AKLSAAGTEFTNSPLPHTDIAQLVELIENGTISSKIAKEVFEHMWAGEGRPAEIVEKRGL 433

Query: 410 VQISDEATLLKFVNEALDNNEQSVEDYKNGKGKAMGFLVGQIMKASKGQANPQLVNQLLK 469
           VQI+D   + K +++ +  N    E  K+ K +A+G+ VGQ+MKA+ G+ANP  VN+LL+
Sbjct: 434 VQINDTGAIEKAIDDLIAGNPDKAEAVKD-KPQALGWFVGQVMKATGGKANPGTVNELLR 492

Query: 470 QEL 472
           ++L
Sbjct: 493 KKL 495


Lambda     K      H
   0.313    0.133    0.373 

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: 646
Number of extensions: 32
Number of successful extensions: 6
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: 475
Length of database: 498
Length adjustment: 34
Effective length of query: 441
Effective length of database: 464
Effective search space:   204624
Effective search space used:   204624
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 bits)
S2: 52 (24.6 bits)

Align candidate CCNA_02518 CCNA_02518 (aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase subunit B)
to HMM TIGR00133 (gatB: aspartyl/glutamyl-tRNA(Asn/Gln) amidotransferase, B subunit (EC 6.3.5.-))

Software error:

../bin/blast/fastacmd -i /tmp/list.2633.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.2633.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.