Align 2-methylisocitrate dehydratase (EC 4.2.1.99) (characterized)
to candidate Ac3H11_1140 Aconitate hydratase (EC 4.2.1.3) @ 2-methylisocitrate dehydratase (EC 4.2.1.99)
Query= reanno::acidovorax_3H11:Ac3H11_1140 (980 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_1140 Length = 980 Score = 1951 bits (5055), Expect = 0.0 Identities = 980/980 (100%), Positives = 980/980 (100%) Query: 1 MATSRKSSPQPARHAFANTLKSFRTASGKDGQFYSLPALAKQFPEIKRLPVSIRIVLESV 60 MATSRKSSPQPARHAFANTLKSFRTASGKDGQFYSLPALAKQFPEIKRLPVSIRIVLESV Sbjct: 1 MATSRKSSPQPARHAFANTLKSFRTASGKDGQFYSLPALAKQFPEIKRLPVSIRIVLESV 60 Query: 61 LRNCDGRKVTPEHVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPLLADLAAMRSVAAK 120 LRNCDGRKVTPEHVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPLLADLAAMRSVAAK Sbjct: 61 LRNCDGRKVTPEHVEQLARWAPNAERKDEIPFVVSRVVLQDFTGVPLLADLAAMRSVAAK 120 Query: 121 LGKNPKKIEPLVPVDLVVDHSIMIDHYGKKNSLDLNMKLEFQRNRERYEFMKWGMQAFDT 180 LGKNPKKIEPLVPVDLVVDHSIMIDHYGKKNSLDLNMKLEFQRNRERYEFMKWGMQAFDT Sbjct: 121 LGKNPKKIEPLVPVDLVVDHSIMIDHYGKKNSLDLNMKLEFQRNRERYEFMKWGMQAFDT 180 Query: 181 FGVVPPGFGIVHQVNLEYLARGVHKRKDGVFYPDTLVGTDSHTTMINGIGVVGWGVGGIE 240 FGVVPPGFGIVHQVNLEYLARGVHKRKDGVFYPDTLVGTDSHTTMINGIGVVGWGVGGIE Sbjct: 181 FGVVPPGFGIVHQVNLEYLARGVHKRKDGVFYPDTLVGTDSHTTMINGIGVVGWGVGGIE 240 Query: 241 AEAAMLGQPVYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGT 300 AEAAMLGQPVYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGT Sbjct: 241 AEAAMLGQPVYFLTPDVVGFEMTGRLREGVTATDLVLTVTELLRKHKVVGKFVEFFGEGT 300 Query: 301 RTLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIEAFEAYFKAQGLFGV 360 RTLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIEAFEAYFKAQGLFGV Sbjct: 301 RTLALPDRATIGNMAPEYGATMGFFPVDEKTIDYFQGTGRTKAEIEAFEAYFKAQGLFGV 360 Query: 361 PLAGEVDYSQVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLFSQPAAHNGFNRPAE 420 PLAGEVDYSQVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLFSQPAAHNGFNRPAE Sbjct: 361 PLAGEVDYSQVVTLDLGSVTPSLAGPKRPQDRIELGQVSRQFADLFSQPAAHNGFNRPAE 420 Query: 421 LLHTRFHIHRAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATAHAEARSATLPARGA 480 LLHTRFHIHRAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATAHAEARSATLPARGA Sbjct: 421 LLHTRFHIHRAAEVVADVTPDGKPTPAGAPRSVVEMEANKPALATAHAEARSATLPARGA 480 Query: 481 DPTVGNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTE 540 DPTVGNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTE Sbjct: 481 DPTVGNGDVLIAAITSCTNTSNPSVLLAAGLLAKKAVEAGLKVQPHIKTSLAPGSRIVTE 540 Query: 541 YLSETGLLPYLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDLVCAAVLSGNRNFEA 600 YLSETGLLPYLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDLVCAAVLSGNRNFEA Sbjct: 541 YLSETGLLPYLEKLGFSIAGYGCTTCIGNAGDLTPELNEAITQNDLVCAAVLSGNRNFEA 600 Query: 601 RIHPNLKANFLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYLGDIWPSSDEVHALL 660 RIHPNLKANFLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYLGDIWPSSDEVHALL Sbjct: 601 RIHPNLKANFLASPPLVVAYAIAGTVLKDLMTEPVGQGKGGKDIYLGDIWPSSDEVHALL 660 Query: 661 KFAMKGKAFRDNYAKVATDPGKLWEKIQGVSGTAYTWPASTYIAEPPFFAQFALEKGANK 720 KFAMKGKAFRDNYAKVATDPGKLWEKIQGVSGTAYTWPASTYIAEPPFFAQFALEKGANK Sbjct: 661 KFAMKGKAFRDNYAKVATDPGKLWEKIQGVSGTAYTWPASTYIAEPPFFAQFALEKGANK 720 Query: 721 ASGTRGEGQKDAQLPSVMGARIMALFGDSITTDHISPAGSIKESSPAGQWLLQHGVQKAD 780 ASGTRGEGQKDAQLPSVMGARIMALFGDSITTDHISPAGSIKESSPAGQWLLQHGVQKAD Sbjct: 721 ASGTRGEGQKDAQLPSVMGARIMALFGDSITTDHISPAGSIKESSPAGQWLLQHGVQKAD 780 Query: 781 FNSYGARRGNHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVFQNEGALQGEKMFIFD 840 FNSYGARRGNHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVFQNEGALQGEKMFIFD Sbjct: 781 FNSYGARRGNHDVMVRGTFANVRIKNLMIPPTADGSREEGGVTVFQNEGALQGEKMFIFD 840 Query: 841 AAMQYMAQGTPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVL 900 AAMQYMAQGTPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVL Sbjct: 841 AAMQYMAQGTPTVVFAGEEYGTGSSRDWAAKGTQLLGIKAVVARSFERIHRSNLVGMGVL 900 Query: 901 PLQFKAGDSWETLGLTGNEVIDVLPDPALTPQSDARLVIRRADGTVREVVVTLRIDTPIE 960 PLQFKAGDSWETLGLTGNEVIDVLPDPALTPQSDARLVIRRADGTVREVVVTLRIDTPIE Sbjct: 901 PLQFKAGDSWETLGLTGNEVIDVLPDPALTPQSDARLVIRRADGTVREVVVTLRIDTPIE 960 Query: 961 VDYYRAGGILPFVLRQLLEG 980 VDYYRAGGILPFVLRQLLEG Sbjct: 961 VDYYRAGGILPFVLRQLLEG 980 Lambda K H 0.318 0.136 0.399 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: 3089 Number of extensions: 89 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: 980 Length of database: 980 Length adjustment: 44 Effective length of query: 936 Effective length of database: 936 Effective search space: 876096 Effective search space used: 876096 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 bits) S2: 57 (26.6 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