Align 3-hydroxy-isobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate 6937209 Sama_1379 enoyl-CoA hydratase/isomerase family protein (RefSeq)
Query= reanno::pseudo3_N2E3:AO353_25665 (368 letters) >FitnessBrowser__SB2B:6937209 Length = 368 Score = 249 bits (635), Expect = 1e-70 Identities = 142/339 (41%), Positives = 198/339 (58%), Gaps = 6/339 (1%) Query: 28 IGHLTLNRPAGLNAITLDMVRSLHRQLDAWSKDPHIHAVVLRGAGEKAFCAGGDIRSLYD 87 IG TLN A LNA+ LDMVR+L QL AW D +I V+L GAG+KAFCAGGD+R+LY Sbjct: 18 IGVATLNVEAALNALDLDMVRALSAQLKAWQADSNIAMVLLDGAGDKAFCAGGDVRALYQ 77 Query: 88 SFK----SGGTLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTE 143 + K S TL + FF EEY LD IH + KP + DG V+GGG+GL+ GA R+ TE Sbjct: 78 ASKDAPGSTETLAKTFFEEEYRLDYFIHEFGKPFMVWGDGIVMGGGLGLMAGASHRIATE 137 Query: 144 RSRLAMPEVAIGYFPDVGGSYFLPRIPGELGIYLGVSGVQIRAADALYCGLADWYLESQK 203 RSR+AMPE+ IG +PDVGG++FL +P + G++LG++ Q+ ADALY G A++ LES Sbjct: 138 RSRIAMPEITIGLYPDVGGTFFLAHMPEKTGVFLGLTAFQMNGADALYAGTANFLLESDD 197 Query: 204 LAELDQHLDSLEWHDTPLKDLQGLLAKLALQQLPD-APLQALRPTIDHFFALPDVPSIVE 262 L L + W D + Q L L + +P+ A + D+ +++E Sbjct: 198 KEPLLDALAEVAWDDHSEANHQRLSDVLGTRAVPEQASFLKDNAELISELCSGDLDTVIE 257 Query: 263 QLRTVTVADSHDWAMTTADLLDSRSPLAMGVTLEMLRRGRQLSLENCFALELHLDRQWFE 322 + + + DSH + D L + SPL+ + G +LSL +CF EL + Sbjct: 258 RFKALP-DDSHKSLLRARDTLLAGSPLSAHLVWHQAIIGEELSLNDCFRWELGVSINCCA 316 Query: 323 RGDLIEGVRALLIDKDKSPRWNPPTVQALDAKHVASFFS 361 GD +EGVRALLIDKD++P W V ++ A+ + S S Sbjct: 317 HGDFVEGVRALLIDKDRNPTWQYADVASVPAEAIGSLLS 355 Lambda K H 0.321 0.138 0.418 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: 387 Number of extensions: 17 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: 368 Length of database: 368 Length adjustment: 30 Effective length of query: 338 Effective length of database: 338 Effective search space: 114244 Effective search space used: 114244 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: 49 (23.5 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