Align N-carbamoylputrescine amidase; Nitrilase-like protein 1; EC 3.5.1.53 (characterized)
to candidate 350332 BT0804 putative carbon-nitrogen hydrolase (NCBI ptt file)
Query= SwissProt::Q8VYF5 (299 letters) >FitnessBrowser__Btheta:350332 Length = 512 Score = 63.2 bits (152), Expect = 1e-14 Identities = 58/193 (30%), Positives = 88/193 (45%), Gaps = 16/193 (8%) Query: 104 YNSIAIIDADGTDLGIYRKSHI-PDGPGYQEKFYFNPGDTGFKVFQTKFAKIGVAICWDQ 162 YN + DGT +Y K H+ PD + K + G + F T AK+GV IC+D Sbjct: 327 YNVGFLCRRDGT-YEMYEKMHVTPD----EIKSWGLSGGKLLQTFDTDCAKVGVLICYDV 381 Query: 163 WFPEAARAMVLQGAEILFYPTAIGSEPQDQGLDSRDHWRRVMQGHAGANVVPLVASNRIG 222 FPE +R M QG +ILF P ++ ++ R Q A N +V + +G Sbjct: 382 EFPELSRLMADQGMQILFVPFLTDTQ------NAYSRVRVCAQARAIENECFVVIAGCVG 435 Query: 223 K--EIIETEHGPSQITFYGTSFIAGPTGEIVAEADDKSEAVLVAQFDLDMIKSKRQSWGV 280 + + +Q + A PT AEA +E +LV+ DLD++ + V Sbjct: 436 NLPRVHNMDIQYAQSGVFTPCDFAFPTDGKRAEATPNTEMILVSDVDLDLLNALHTYGSV 495 Query: 281 --FRDRRPDLYKV 291 +DRR D+Y+V Sbjct: 496 RNLKDRRNDVYEV 508 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: 308 Number of extensions: 15 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: 512 Length adjustment: 31 Effective length of query: 268 Effective length of database: 481 Effective search space: 128908 Effective search space used: 128908 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: 50 (23.9 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