Align 2-keto-4-pentenoate hydratase 2; EC 4.2.1.80; 2-hydroxypentadienoic acid hydratase 2 (uncharacterized)
to candidate HSERO_RS13395 HSERO_RS13395 hydratase
Query= curated2:Q49KF9 (270 letters) >FitnessBrowser__HerbieS:HSERO_RS13395 Length = 262 Score = 90.1 bits (222), Expect = 4e-23 Identities = 76/242 (31%), Positives = 113/242 (46%), Gaps = 13/242 (5%) Query: 25 VGPLRDVIGATNVEHAYAIQRLNQAYAIANGRRLVGRKIGLTNPKVQAQLGVDQPDFGCL 84 +G L + + + AY IQ +A + A L G KIG T P Q L VD P G L Sbjct: 24 IGQLPPPLQPADRQQAYDIQARLEARSFAP---LAGWKIGATGPGGQQLLNVDGPMAGRL 80 Query: 85 FADMAYGDNEVIPFERVLQPKIEAEIALILERDLPSASTTFA--DVIAATGWVVPALEVV 142 A+ + + + L IEAE+ + LP + ++ +V+ A G V P +E+ Sbjct: 81 LAERMHRNGAHVTLGDNLMSVIEAEVVFRMRSALPPRTQPYSQEEVMEAVGSVHPGIEIP 140 Query: 143 GSRIEGWN-IKFADTVADNASSGCFVLGGPA----RRIDGLDLRGATMRMSKNGEVVSSG 197 +R + + + +ADN + FVLG P R +D L AT + GE SG Sbjct: 141 DTRYQQFREVGAYQLIADNCCADQFVLGAPTSMDWRHLDLAAL--ATSAFIEGGEQ-RSG 197 Query: 198 SGGECLGNPLNAAVWLARTMAEFGEPLKAGDIILTGALGPMVGVSAGDHFEAEIEGLGRV 257 SG + LG+P A WL + + G L AG ++ TG+ + V AG A++ LG V Sbjct: 198 SGAQVLGDPRIALTWLVNELRQHGLTLAAGQLVATGSTIVPMPVQAGQTVRADLGVLGSV 257 Query: 258 GV 259 V Sbjct: 258 TV 259 Lambda K H 0.317 0.136 0.395 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: 166 Number of extensions: 10 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: 270 Length of database: 262 Length adjustment: 25 Effective length of query: 245 Effective length of database: 237 Effective search space: 58065 Effective search space used: 58065 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 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