Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate N515DRAFT_1536 N515DRAFT_1536 N-carbamoylputrescine amidase
Query= reanno::pseudo5_N2C3_1:AO356_14225 (264 letters) >FitnessBrowser__Dyella79:N515DRAFT_1536 Length = 296 Score = 101 bits (252), Expect = 2e-26 Identities = 81/258 (31%), Positives = 124/258 (48%), Gaps = 23/258 (8%) Query: 29 ARGADVLVLPEMFMTGYNIGVDAVNVL--AEVYNGEWAQQIGRIAKAANLAIVYGYPERG 86 A GA++++L E+ Y ++V AE G ++IG++A+ L +V E+ Sbjct: 35 AAGAELVLLQELHNGPYFCQHESVGEFDHAETIPGPGTERIGKLAEELKLVVVASLFEKR 94 Query: 87 EDGQIYNAVQLIDAQGERLANYRKSHLFGD---LDHAMFSAGDSALPIVELNGWKLGLLI 143 G +N + D + YRK H+ D + F+ GD ++ +LG+L+ Sbjct: 95 ATGLYHNTAVVFDRSAKIAGKYRKMHIPDDPAFYEKFYFTPGDLGFDPIDTAVGRLGVLV 154 Query: 144 CYDLEFPENARRLALAGAELILVPTA-NMQPYEFIAD--------VTV-RARAIENQCFV 193 C+D +PE AR +ALAGAEL+L PTA P + A+ VTV R A+ N + Sbjct: 155 CWDQWYPEAARLMALAGAELLLYPTAIGWDPNDEQAEKDRQREAWVTVQRGHAVANGLPL 214 Query: 194 AYANYCGHE-------AELQYCGQSSIAAPNGSRPALAGLD-EALIVGELDRQLLDDSRA 245 N G+E A +Q+ G S +A P G AG D L+V E+D + R Sbjct: 215 LACNRTGYEPDPSGVGAGIQFWGTSFVAGPQGEFLGQAGTDGRQLLVVEIDMARSEHVRR 274 Query: 246 AYNYLHDRRPELYDDLHK 263 + +L DRR + Y DL K Sbjct: 275 IWPFLRDRRIDAYGDLLK 292 Lambda K H 0.321 0.139 0.419 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: 11 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 264 Length of database: 296 Length adjustment: 26 Effective length of query: 238 Effective length of database: 270 Effective search space: 64260 Effective search space used: 64260 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: 47 (22.7 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