Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate AO353_17555 AO353_17555 enoyl-CoA hydratase
Query= reanno::pseudo1_N1B4:Pf1N1B4_4790 (356 letters) >lcl|FitnessBrowser__pseudo3_N2E3:AO353_17555 AO353_17555 enoyl-CoA hydratase Length = 370 Score = 242 bits (617), Expect = 1e-68 Identities = 141/342 (41%), Positives = 198/342 (57%), Gaps = 12/342 (3%) Query: 16 IGHLTLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEKAFCAGGDIRSLYD 75 IG +L+ LNA++L M+R+L QL+AWA++PQ+ V+LRG G KAFCAGG++R+L + Sbjct: 16 IGIASLDAEKSLNALSLPMIRALSDQLEAWAKEPQIVCVLLRGNGAKAFCAGGEVRNLVE 75 Query: 76 SFKS--GDT--LHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQGADLRVVTE 131 + ++ G+ L FF EY LD +H Y KP++ G+VLGGG+GL+QGA +R+VT Sbjct: 76 ACRAHPGEVPPLAAQFFSAEYRLDFRLHTYPKPLICWGHGYVLGGGLGLLQGASIRIVTP 135 Query: 132 RSRLAMPEVAIGYFPDVGGSHFLPRVPGELGIYLGVSGVQIRAADALYCGLADWYLESNK 191 SRLAMPE++IG +PDVG S FL R+PG+LG++LG++G Q+ A DA+ LAD +L + Sbjct: 136 SSRLAMPEISIGLYPDVGASWFLSRLPGKLGLFLGLTGAQMNARDAIDLDLADRFLLDEQ 195 Query: 192 LGTLDEQLDQLQWHETPLKDLQGLLAKL---AVQQLPAAPLAALRPAIDHFFALPDVPSM 248 L E L QL W E L LL L AV ++P A R ID + DV Sbjct: 196 QEELIEGLLQLNWQEQTPMQLNSLLKALQQEAVGKMPEAQWLPRRQQIDELLDVSDVRC- 254 Query: 249 VEQLRAVTVADSHE--WATATADLLESRSPLAMGVTLEMLRRGRHLSLEQCFALELHLDR 306 RA+++ H A L PL + E ++R RHLSL + F +E + Sbjct: 255 --AWRAISLLRDHRDLLLARAAKNLHEGCPLTAHLVWEQIQRARHLSLAEVFQMEYTMSL 312 Query: 307 QWFERGDLIEGVRALLIDKDKNPRWSPPTLQALDAGHVASFF 348 + EGVRA LIDKD+ P W P + A+ V + F Sbjct: 313 NCCRHPEFSEGVRARLIDKDQKPHWHWPDINAIPEAVVQAHF 354 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: 397 Number of extensions: 15 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: 370 Length adjustment: 29 Effective length of query: 327 Effective length of database: 341 Effective search space: 111507 Effective search space used: 111507 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.
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