Align 3-hydroxyisobutyryl-CoA hydrolase (EC 3.1.2.4) (characterized)
to candidate PP_3491 PP_3491 Enoly-coenzyme A hydratase/isomerase family protein
Query= reanno::pseudo13_GW456_L13:PfGW456L13_2986 (356 letters) >FitnessBrowser__Putida:PP_3491 Length = 357 Score = 546 bits (1407), Expect = e-160 Identities = 266/346 (76%), Positives = 294/346 (84%) Query: 3 AMQNEVLAEVRNHIGHLTLNRPAGLNALTLDMVRNLHRQLDAWAQDSQVHAVVLRGAGEK 62 A + VLAEVRN IGHLTLNRPAGLNALTLDMVR+L + LD WA + QV AVVLRG G K Sbjct: 9 AATDHVLAEVRNQIGHLTLNRPAGLNALTLDMVRSLRQHLDQWADNPQVRAVVLRGEGPK 68 Query: 63 AFCAGGDIRSLHDSFKSGDTLHEDFFVEEYALDLAIHHYRKPVLALMDGFVLGGGMGLVQ 122 FCAGGDIRSL+DSFK+GDTLHE FFVEEYALDL IH YRKP+L +MDGF LGGGMGL Q Sbjct: 69 GFCAGGDIRSLYDSFKAGDTLHETFFVEEYALDLVIHRYRKPILVVMDGFTLGGGMGLAQ 128 Query: 123 GADLRVVTEKSRLAMPEVGIGYFPDVGGSYFLSRIPGELGIYLGVSGVQIRAADALYCGL 182 G DLRVVTE+SRL MPEVGIGYFPDVGGSYFLSR+PGELGIYLGVSG QI+AADALYCGL Sbjct: 129 GCDLRVVTERSRLGMPEVGIGYFPDVGGSYFLSRLPGELGIYLGVSGAQIQAADALYCGL 188 Query: 183 ADWYLESGKLGVLDEKLDQLEWHDTPLKDLQGLLAKFAVQQLPDAPLATLRPAIDHFFAQ 242 ADWYL S +L LD+ LDQL++ D PLKDLQ LLA+ Q L DAPL LRPAIDHFFA Sbjct: 189 ADWYLASDQLAALDQGLDQLDFSDHPLKDLQNLLARLGTQVLDDAPLEKLRPAIDHFFAL 248 Query: 243 PDVPSIVEQLRQVTVADSHEWAVTTADLLETRSPLAMAVTLEMLRRGRELPLEQCFALEL 302 PD+P+IVEQLR V++ DSH WAV TAD LETRSPLAMAVTLEMLRRGREL ++ CFA+EL Sbjct: 249 PDLPAIVEQLRAVSIGDSHAWAVATADQLETRSPLAMAVTLEMLRRGRELGIDDCFAMEL 308 Query: 303 HLDRQWFERGDLIEGVRALLIDKDKTPRWNPPTLQALDAEHVASFF 348 HLDRQWF+ GD+IEGVRAL+IDKDK PRWNPPTL AL ++ V FF Sbjct: 309 HLDRQWFQHGDIIEGVRALIIDKDKQPRWNPPTLAALQSQRVEQFF 354 Lambda K H 0.322 0.139 0.419 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: 563 Number of extensions: 17 Number of successful extensions: 1 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: 357 Length adjustment: 29 Effective length of query: 327 Effective length of database: 328 Effective search space: 107256 Effective search space used: 107256 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