Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate 5209193 Shew_1671 enoyl-CoA hydratase/isomerase (RefSeq)
Query= reanno::pseudo1_N1B4:Pf1N1B4_4790 (356 letters) >FitnessBrowser__PV4:5209193 Length = 376 Score = 246 bits (629), Expect = 5e-70 Identities = 147/349 (42%), Positives = 198/349 (56%), Gaps = 14/349 (4%) Query: 16 IGHLTLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEKAFCAGGDIRSLYD 75 +G TLN LNA+ ++MVR+L QL AWA D + VVL GAGEKAFCAGGD+R+LY Sbjct: 21 VGVATLNMEKALNALNMEMVRALTTQLTAWADDDAIAMVVLDGAGEKAFCAGGDVRALYQ 80 Query: 76 SFKS--GDT--LHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTE 131 + + G+ + +DFF EY LD +H + KPVL DG V+GGG+GL+ GA RVVTE Sbjct: 81 AARELPGEIPEVTQDFFTREYFLDHLLHTFDKPVLVWGDGIVMGGGLGLMAGASHRVVTE 140 Query: 132 RSRLAMPEVAIGYFPDVGGSHFLPRVPGELGIYLGVSGVQIRAADALYCGLADWYLESNK 191 RSR+AMPEV IG +PDVGGS+FL R+PG +G +LG++ + ADA Y GL + YL S+ Sbjct: 141 RSRIAMPEVTIGLYPDVGGSYFLNRMPGHMGRFLGMTAYNMDGADAFYVGLGNHYLNSSD 200 Query: 192 LGTLDEQLDQLQW------HETPLKDLQGLLAKLAVQQLPAAPLAALRPAIDHFFALPDV 245 L + L + W + L L ++ Q + + L + ID AL D Sbjct: 201 KQPLFDALSSIDWENDVCANHGKLNALLEAMSSRCAQPMGESILEQHQAQID---ALMDG 257 Query: 246 PSMVEQLRAVTVADSHEWATATADLLESRSPLAMGVTLEMLRRGRHLSLEQCFALELHLD 305 R V D+ W + + + SPL++ + + G LSL Q F LEL L Sbjct: 258 ELNEIMTRVKAVEDAEPWLSRALSTMLAGSPLSLHLVYQQSLLGTELSLSQVFQLELGLS 317 Query: 306 RQWFERGDLIEGVRALLIDKDKNPRWSPPTLQALDAGHVASFFTG-FDP 353 GD EGVRALLIDKD+ P+W T++A+ V S T +DP Sbjct: 318 CNCCSIGDFAEGVRALLIDKDRQPQWLYETVEAVPQEMVKSLMTSPWDP 366 Lambda K H 0.322 0.138 0.422 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: 382 Number of extensions: 24 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: 356 Length of database: 376 Length adjustment: 30 Effective length of query: 326 Effective length of database: 346 Effective search space: 112796 Effective search space used: 112796 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