Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate PP_1412 PP_1412 3-hydroxyisobutyryl-CoA hydrolase
Query= reanno::pseudo1_N1B4:Pf1N1B4_4790 (356 letters) >FitnessBrowser__Putida:PP_1412 Length = 368 Score = 245 bits (625), Expect = 2e-69 Identities = 151/350 (43%), Positives = 194/350 (55%), Gaps = 9/350 (2%) Query: 7 EVLAEVRN-HIGHLTLNRPAGLNAITLDMVRSLQQQLDAWAQDPQVHAVVLRGAGEKAFC 65 EVL V IG TL+ P LNA+ L M+ L +QL AWA+DP + V+LRG G KAFC Sbjct: 6 EVLTGVDGARIGIATLDAPKALNALNLPMIEVLGEQLHAWARDPGIVCVLLRGNGAKAFC 65 Query: 66 AGGDIRSLYDSFK----SGDTLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLV 121 AGGD+R+L + + S L FF EY LD A+H Y KP+L G VLGGGMGL+ Sbjct: 66 AGGDVRALAQACRDHPGSVPPLAASFFAAEYRLDFALHTYPKPLLCWGHGHVLGGGMGLL 125 Query: 122 QGADLRVVTERSRLAMPEVAIGYFPDVGGSHFLPRVPGELGIYLGVSGVQIRAADALYCG 181 QGA++R+VT SRLAMPE++IG +PDVG S FL R+PG+LG++ G++G I A DAL G Sbjct: 126 QGANVRIVTPSSRLAMPEISIGLYPDVGASWFLARLPGKLGLFFGLTGAPINARDALDLG 185 Query: 182 LADWYLESNKLGTLDEQLDQLQWHETPLKDLQGLL---AKLAVQQLPAAPLAALRPAIDH 238 LAD +L ++ L E+L QL W E L LL A +LP A R ID Sbjct: 186 LADRFLGEHQQEALIEELLQLNWQEQTAIQLNSLLKAEQHRACAELPDAQWLPRRHEIDQ 245 Query: 239 FFALPDVPSMVEQLRAVTVADSHEWATATADLLESRSPLAMGVTLEMLRRGRHLSLEQCF 298 + D S L + D A A L E PL + E +RR R+LSL Q F Sbjct: 246 LLDVADAASAWRALERLKQHDDPLLADAGHRLHEG-CPLTAHLVWEQIRRARYLSLAQVF 304 Query: 299 ALELHLDRQWFERGDLIEGVRALLIDKDKNPRWSPPTLQALDAGHVASFF 348 +E + + EGVRA L+DKD PRW P + + V + F Sbjct: 305 QMEYSMSLNCCRHPEFSEGVRARLLDKDNQPRWHWPDVAQVPTAVVEAHF 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: 411 Number of extensions: 21 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: 368 Length adjustment: 29 Effective length of query: 327 Effective length of database: 339 Effective search space: 110853 Effective search space used: 110853 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