GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aguB in Azospirillum brasilense Sp245

Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate AZOBR_RS08170 AZOBR_RS08170 carbon-nitrogen family hydrolase

Query= SwissProt::Q8VYF5
         (299 letters)



>FitnessBrowser__azobra:AZOBR_RS08170
          Length = 298

 Score =  405 bits (1041), Expect = e-118
 Identities = 198/290 (68%), Positives = 232/290 (80%), Gaps = 4/290 (1%)

Query: 8   REVVVSSLQFACSDDISTNVAAAERLVREAHAKGANIILIQELFEGYYFCQAQREDFFKR 67
           R V V++ Q AC  D   NV   ERLVR+A A+GA IIL QELFE  YFC+ Q++D F  
Sbjct: 7   RTVTVAATQMACGWDRDANVNGVERLVRDAAARGAQIILPQELFETPYFCKDQKQDLFAL 66

Query: 68  AKPYKNHPTIARMQKLAKELGVVIPVSFFEEANTAHYNSIAIIDADGTDLGIYRKSHIPD 127
           A P ++HP IARM  LA+EL VVIP SFFE A  A+YNS+A+IDADGT LG+YRKSHIPD
Sbjct: 67  AHPVEDHPVIARMSALARELSVVIPTSFFERARNAYYNSLAMIDADGTVLGVYRKSHIPD 126

Query: 128 GPGYQEKFYFNPGDTGFKVFQTKFAKIGVAICWDQWFPEAARAMVLQGAEILFYPTAIGS 187
           GPGYQEK+YFNPGDTGF+V++T++A IG AICWDQWFPE+ARAM L+GAEILFYPTAIGS
Sbjct: 127 GPGYQEKYYFNPGDTGFQVYKTRYAAIGCAICWDQWFPESARAMALKGAEILFYPTAIGS 186

Query: 188 EPQDQGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGPSQITFYGTSFIAGPT 247
           EPQD  LDS+ HW RVMQGHAGAN++PLVASNRIG+E    E     ITFYG+SFIAGPT
Sbjct: 187 EPQDGALDSQAHWTRVMQGHAGANLMPLVASNRIGRE----EGDTCGITFYGSSFIAGPT 242

Query: 248 GEIVAEADDKSEAVLVAQFDLDMIKSKRQSWGVFRDRRPDLYKVLLTMDG 297
           GE+VA+AD  SE VL A FDLD I ++R SWG+FRDRRP+LY  LLT+DG
Sbjct: 243 GELVAQADRDSETVLTASFDLDRIAAQRASWGIFRDRRPELYGPLLTLDG 292


Lambda     K      H
   0.321    0.137    0.410 

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: 340
Number of extensions: 8
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: 299
Length of database: 298
Length adjustment: 27
Effective length of query: 272
Effective length of database: 271
Effective search space:    73712
Effective search space used:    73712
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.8 bits)
S2: 48 (23.1 bits)

Align candidate AZOBR_RS08170 AZOBR_RS08170 (carbon-nitrogen family hydrolase)
to HMM TIGR03381 (aguB: N-carbamoylputrescine amidase (EC 3.5.1.53))

Software error:

../bin/blast/fastacmd -i /tmp/list.6824.in -d ../tmp/orgsFit/orgs.faa -p T > /tmp/gapView.6824.genome.faa failed: Inappropriate ioctl for device at ../lib/pbutils.pm line 379.

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