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))
# hmmsearch :: search profile(s) against a sequence database # HMMER 3.3.1 (Jul 2020); http://hmmer.org/ # Copyright (C) 2020 Howard Hughes Medical Institute. # Freely distributed under the BSD open source license. # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - # query HMM file: ../tmp/path.carbon/TIGR03381.hmm # target sequence database: /tmp/gapView.24674.genome.faa # - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - Query: TIGR03381 [M=279] Accession: TIGR03381 Description: agmatine_aguB: N-carbamoylputrescine amidase Scores for complete sequences (score includes all domains): --- full sequence --- --- best 1 domain --- -#dom- E-value score bias E-value score bias exp N Sequence Description ------- ------ ----- ------- ------ ----- ---- -- -------- ----------- 6.8e-148 477.4 0.0 7.8e-148 477.2 0.0 1.0 1 lcl|FitnessBrowser__azobra:AZOBR_RS08170 AZOBR_RS08170 carbon-nitrogen fa Domain annotation for each sequence (and alignments): >> lcl|FitnessBrowser__azobra:AZOBR_RS08170 AZOBR_RS08170 carbon-nitrogen family hydrolase # score bias c-Evalue i-Evalue hmmfrom hmm to alifrom ali to envfrom env to acc --- ------ ----- --------- --------- ------- ------- ------- ------- ------- ------- ---- 1 ! 477.2 0.0 7.8e-148 7.8e-148 1 278 [. 9 286 .. 9 287 .. 0.99 Alignments for each domain: == domain 1 score: 477.2 bits; conditional E-value: 7.8e-148 TIGR03381 1 vkvaavqlalsedveeniekaeklvreaaakGaqiillpelfeapyfckeqeeeyfelakpveehplik 69 v+vaa+q+a+ +d ++n++ +e+lvr+aaa+Gaqiil++elfe+pyfck+q+++ f+la+pve+hp+i+ lcl|FitnessBrowser__azobra:AZOBR_RS08170 9 VTVAATQMACGWDRDANVNGVERLVRDAAARGAQIILPQELFETPYFCKDQKQDLFALAHPVEDHPVIA 77 79******************************************************************* PP TIGR03381 70 rlqklakelevvlpvsffekagnalynslavidadGevlgvyrkshiPdgpgyeekfyfkpGdtGfkvw 138 r+++la+el vv+p+sffe+a na+ynsla+idadG+vlgvyrkshiPdgpgy+ek+yf+pGdtGf+v+ lcl|FitnessBrowser__azobra:AZOBR_RS08170 78 RMSALARELSVVIPTSFFERARNAYYNSLAMIDADGTVLGVYRKSHIPDGPGYQEKYYFNPGDTGFQVY 146 ********************************************************************* PP TIGR03381 139 dtryakiGvgicWdqWfpeaaralalkGaevllyPtaiGsePadaeldskehWqramqGhaaanvvpvv 207 +trya iG +icWdqWfpe+ara+alkGae+l+yPtaiGseP+d +lds++hW+r+mqGha an++p+v lcl|FitnessBrowser__azobra:AZOBR_RS08170 147 KTRYAAIGCAICWDQWFPESARAMALKGAEILFYPTAIGSEPQDGALDSQAHWTRVMQGHAGANLMPLV 215 ********************************************************************* PP TIGR03381 208 aanrigkeveaeleltfyGssfiadetGelvaeadrseeavlvaefdldeiakeraawGlfrdrrpely 276 a+nrig+e+ +++ +tfyGssfia tGelva+adr+ e+vl+a+fdld+ia++ra+wG+frdrrpely lcl|FitnessBrowser__azobra:AZOBR_RS08170 216 ASNRIGREEGDTCGITFYGSSFIAGPTGELVAQADRDSETVLTASFDLDRIAAQRASWGIFRDRRPELY 284 ********************************************************************* PP TIGR03381 277 ek 278 lcl|FitnessBrowser__azobra:AZOBR_RS08170 285 GP 286 86 PP Internal pipeline statistics summary: ------------------------------------- Query model(s): 1 (279 nodes) Target sequences: 1 (298 residues searched) Passed MSV filter: 1 (1); expected 0.0 (0.02) Passed bias filter: 1 (1); expected 0.0 (0.02) Passed Vit filter: 1 (1); expected 0.0 (0.001) Passed Fwd filter: 1 (1); expected 0.0 (1e-05) Initial search space (Z): 1 [actual number of targets] Domain search space (domZ): 1 [number of targets reported over threshold] # CPU time: 0.01u 0.01s 00:00:00.02 Elapsed: 00:00:00.00 # Mc/sec: 8.56 // [ok]
This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.
Each pathway is defined by a set of rules based on individual steps or genes. Candidates for each step are identified by using ublast (a fast alternative to protein BLAST) against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer with enzyme models (usually from TIGRFam). Ublast hits may be split across two different proteins.
A candidate for a step is "high confidence" if either:
Otherwise, a candidate is "medium confidence" if either:
Other blast hits with at least 50% coverage are "low confidence."
Steps with no high- or medium-confidence candidates may be considered "gaps." For the typical bacterium that can make all 20 amino acids, there are 1-2 gaps in amino acid biosynthesis pathways. For diverse bacteria and archaea that can utilize a carbon source, there is a complete high-confidence catabolic pathway (including a transporter) just 38% of the time, and there is a complete medium-confidence pathway 63% of the time. Gaps may be due to:
GapMind relies on the predicted proteins in the genome and does not search the six-frame translation. In most cases, you can search the six-frame translation by clicking on links to Curated BLAST for each step definition (in the per-step page).
For more information, see:
If you notice any errors or omissions in the step descriptions, or any questionable results, please let us know
by Morgan Price, Arkin group, Lawrence Berkeley National Laboratory