Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate BPHYT_RS00250 BPHYT_RS00250 hydratase
Query= SwissProt::Q8VYF5 (299 letters) >FitnessBrowser__BFirm:BPHYT_RS00250 Length = 283 Score = 102 bits (255), Expect = 8e-27 Identities = 90/295 (30%), Positives = 133/295 (45%), Gaps = 19/295 (6%) Query: 7 RREVVVSSLQFACS-DDISTNVAAAERLVREAHAKGANIILIQELFE-GYYFCQAQREDF 64 R+ V ++ +Q A + NV A V A GA ++++ EL GY F R + Sbjct: 5 RKNVQIACVQMAPRIGEKDLNVRRAIDFVTRAADLGAELVVLPELANTGYVF--DSRAEA 62 Query: 65 FKRAKPYKNHPTIARMQKLAKELGVVIPVSFFEEANTAHYNSIAIIDADGTDLGIYRKSH 124 A+P + T A ++A LGV I E+A+ A YNS ++ DG LG YRK+H Sbjct: 63 ESLAEPVPDGSTTAAWSEVASALGVYIVAGIAEKADGALYNSAVLLGPDGY-LGSYRKTH 121 Query: 125 IPDGPGYQEKFYFNPGDTGFKVFQTKFAKIGVAICWDQWFPEAARAMVLQGAEILFYPTA 184 + EK F GD ++ T +I +AIC+D WFPE R L GA+I+ PT Sbjct: 122 LWG----DEKKLFASGDRPSPIYDTPLGRIAIAICYDLWFPELFRLYALGGAQIVCVPTN 177 Query: 185 IGSEPQDQGLDSRDHWRRVMQGHAGANVVPLVASNRIGKEIIETEHGPSQITFYGTSFIA 244 P +Q D + A N + + ++R+G E G F G S + Sbjct: 178 WVPMP-NQSADRPAMANTLAMAAAHTNGLVVACADRVG-----VERGQ---PFEGQSLVV 228 Query: 245 GPTGEIVAEADDKS-EAVLVAQFDLDMIKSKRQSWGVFRDRRPDLYKVLLTMDGN 298 +G V + +S E ++ A LD S V DRR D+Y + DG+ Sbjct: 229 DQSGWPVGDVASRSLEEIVSASITLDARTSVGTHNDVLADRRADIYGRIPAFDGH 283 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: 202 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: 299 Length of database: 283 Length adjustment: 26 Effective length of query: 273 Effective length of database: 257 Effective search space: 70161 Effective search space used: 70161 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)
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