Align 5-aminopentanamidase (EC 3.5.1.30) (characterized)
to candidate WP_029132564.1 A3GO_RS0105545 amidohydrolase
Query= reanno::pseudo13_GW456_L13:PfGW456L13_1170 (264 letters) >NCBI__GCF_000428045.1:WP_029132564.1 Length = 255 Score = 95.9 bits (237), Expect = 7e-25 Identities = 71/232 (30%), Positives = 113/232 (48%), Gaps = 12/232 (5%) Query: 18 NLQRLQQLALEAKGADLLVLPEMFLTGYNIGVDAVSVLAEVYNGESAQQVARIAKAAGIA 77 N + + L +A +DL++LPEMF TG+++ LAE GES + R+A+ +G A Sbjct: 21 NREHFEVLISQAPASDLILLPEMFSTGFSL---ESFQLAETMTGESIHWMTRMARESG-A 76 Query: 78 ILYGYPERTEDGQIYNAVQLIDSDGERVCNYRKTHLFGDLDHSMFSAGSDEFPIVELNGW 137 ++ G + G +N + + +G Y K HLF + D +V LNGW Sbjct: 77 VIAGSLILEDAGHYFNRLIWMRPNGS-FAFYDKRHLFRMAEEHRHYKPGDARLVVTLNGW 135 Query: 138 KLGFLICYDLEFPENARRLALAGAELILV--PTANMIPFDFVADVTVRARAFENQCYVAY 195 ++ L+CYDL FP +R + L + P + + + + ARA EN CYVA Sbjct: 136 RICPLVCYDLRFPVWSRNNSSFDLLLYVANWPEKRRMHWQRL----LPARAIENLCYVAG 191 Query: 196 ANYCGHEG-DIHYCGQSSIAAPDGSRIAQAGLDESLIVGELDRQLMVDSRAA 246 N G +G +I Y G S + +P G + AG + L +L+ ++ R A Sbjct: 192 LNRVGEDGNNIAYSGDSVVISPQGEELLNAGSEAGLFTVQLNHAELMSYREA 243 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: 196 Number of extensions: 18 Number of successful extensions: 5 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: 255 Length adjustment: 24 Effective length of query: 240 Effective length of database: 231 Effective search space: 55440 Effective search space used: 55440 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 24 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