Align Beta-ketoadipate enol-lactone hydrolase (EC 3.1.1.24) (characterized)
to candidate N515DRAFT_2628 N515DRAFT_2628 non-heme chloroperoxidase
Query= reanno::pseudo3_N2E3:AO353_17230 (266 letters) >FitnessBrowser__Dyella79:N515DRAFT_2628 Length = 275 Score = 60.1 bits (144), Expect = 5e-14 Identities = 67/224 (29%), Positives = 92/224 (41%), Gaps = 14/224 (6%) Query: 8 DGELKYQLDGPEHAPVLVLSNSLGTNLHMWDVQIPAFTKH-FRVLRFDTRGHGRSLVTPG 66 DG + D + PV V S+ + WD Q+ F H +RV+ D RGHGRS T Sbjct: 9 DGVEIFYKDWGKGQPV-VFSHGWPLSSDDWDAQMLFFLDHGYRVIAHDRRGHGRSTQTDT 67 Query: 67 PYSIEQLGRDVLALLDALNIERAHFCGLSM-GGLIGQWLGINAGERLHKLVVCNTAAKIG 125 +E D+ AL +AL++ A G S GG + ++ + +R K+V+ I Sbjct: 68 GNDMEHYAADLAALTEALDLRDAIHIGHSTGGGEVAAYVARHGQKRTAKIVLIGAVPPIM 127 Query: 126 DPSVWNP---RIETVLRDGPAAMVALRDASIARWFTPDFAQANPAVAKQITDMLAATSPQ 182 + NP IE V D +VA R T F N AK ++ Q Sbjct: 128 VKNANNPGGTPIE-VFDDFRKQLVANRAQFFLDIPTGPFYGFNRPGAKLSEGIVRNWWRQ 186 Query: 183 GYAANCAAVRD-------ADFREQLASITVPTLVIAGTEDAVTP 219 G A D DF E L I P LV+ G +D V P Sbjct: 187 GMMGGTKAHYDCIKAFSETDFTEDLKKIEQPALVLHGDDDQVVP 230 Lambda K H 0.321 0.136 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: 195 Number of extensions: 11 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: 266 Length of database: 275 Length adjustment: 25 Effective length of query: 241 Effective length of database: 250 Effective search space: 60250 Effective search space used: 60250 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 (21.9 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