Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate 350403 BT0875 beta-ureidopropionase (NCBI ptt file)
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170 (264 letters) >FitnessBrowser__Btheta:350403 Length = 294 Score = 97.8 bits (242), Expect = 2e-25 Identities = 86/276 (31%), Positives = 127/276 (46%), Gaps = 27/276 (9%) Query: 14 DVAGNLQRLQQL--ALEAKGADLLVLPEMFLTGYNIGVDAVSV--LAEVYNGESAQQVAR 69 D+ NL L + A A GA L+VL E+ + Y + ++ LAE G S + Sbjct: 16 DIRVNLMNLAKSIEACAAHGAQLIVLQELHNSLYFCQTENTNLFDLAEPIPGPSTGFYSE 75 Query: 70 IAKAAGIAILYGYPERTEDGQIYNAVQLIDSDGERVCNYRKTHLFGD---LDHSMFSAGS 126 +A A + ++ E+ G +N + D DG YRK H+ D + F+ G Sbjct: 76 LAAANKVVLVASLFEKRAPGLYHNTAVVFDRDGSIAGKYRKMHIPDDPAYYEKFYFTPGD 135 Query: 127 DEFPIVELNGWKLGFLICYDLEFPENARRLALAGAELILVPTANMIPFDFVAD------- 179 F ++ + KLG L+C+D +PE AR +AL GAEL++ PTA D Sbjct: 136 IGFEPIQTSLGKLGVLVCWDQWYPEAARLMALKGAELLIYPTAIGWESSDTDDEKARQLN 195 Query: 180 ---VTVRARAFENQCYVAYANYCGHEGD-------IHYCGQSSIAAPDGSRIAQAGLD-- 227 ++ RA A N V N GHE D I + G S +A P G +AQA D Sbjct: 196 AWIISQRAHAVANGLPVISVNRVGHEPDPSGQTNGIQFWGNSFVAGPQGEFLAQASNDHP 255 Query: 228 ESLIVGELDRQLMVDSRAANRYLLDRRPELYGELNK 263 E+++V E+D + + R +L DRR + Y L K Sbjct: 256 ENMVV-EIDMERSENVRRWWPFLRDRRIDEYDGLTK 290 Lambda K H 0.321 0.139 0.411 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: 157 Number of extensions: 11 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: 264 Length of database: 294 Length adjustment: 25 Effective length of query: 239 Effective length of database: 269 Effective search space: 64291 Effective search space used: 64291 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