Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate AZOBR_RS02985 AZOBR_RS02985 aconitate hydratase
Query= curated2:Q9WYC7 (418 letters) >FitnessBrowser__azobra:AZOBR_RS02985 Length = 896 Score = 123 bits (308), Expect = 3e-32 Identities = 132/476 (27%), Positives = 200/476 (42%), Gaps = 105/476 (22%) Query: 25 LARVDIAMAQDGTGPLMINEFRELGFKEVKVPKAFLFIDHA-------SPSPRK---ELS 74 LA + AMA G P IN VP L IDH+ +PS + EL Sbjct: 104 LAAMREAMAALGGDPKKINPL---------VP-VDLVIDHSVMVDYFGNPSAFEKNVELE 153 Query: 75 NSQKMMREFGKEMGVKVFD------AGDGISHQILAE--------------KYVKPGDLV 114 + + R G K FD G GI HQ+ E K V D + Sbjct: 154 FERNLERYAFLRWGQKAFDNFRVVPPGTGICHQVNVEYLAQGVWTDTDPAGKLVAYPDTL 213 Query: 115 AGADSHTCTAGGLGAFGTGMGSTDVAIIFGLGQNW-FKVPETIKVVVNGKLQDGVYAKDI 173 G DSHT GLG G G+G + LGQ +PE + + G+L++G A D+ Sbjct: 214 VGTDSHTTMVNGLGVLGWGVGGIEAEAAM-LGQPISMLIPEVVGFKLTGRLKEGTTATDL 272 Query: 174 ILEIARILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFL 233 +L + ++L G K +EF+G ++++ + DR TI NMA E GA G+ P D +T +L Sbjct: 273 VLTVTQMLRKKGVVGKFVEFYGPGLDHLTLADRATIGNMAPEYGATCGIFPIDAETIRYL 332 Query: 234 KKMGREED--------------FRELKADPDAVYETEIEIDATTLEPLVSLPHYVDNVRK 279 GR+ D +R+ PD V+ +E+D TT+EP ++ P + Sbjct: 333 TFTGRDADRVAMVEAYARAQGMWRD-AGTPDPVFTDALELDMTTVEPSLAGPKRPQDRVP 391 Query: 280 VSEVEKE-----------------------KIKIDQ-----VFIGTCTNGRLQDLEIALK 311 +S+ + +DQ I +CTN + +A Sbjct: 392 LSQAAQSFGTDLVGAFKAEDADRSVPVKGCGYNLDQGAVVIAAITSCTNTSNPAVLVAAG 451 Query: 312 ILEKHG------KHPDVRLIVGPASRKVYMDALEKGIIKKFV-ELGAAVIPPGCGPCVGI 364 +L + P V+ + P S +V D L K ++ ++ +LG ++ GC C+G Sbjct: 452 LLARKAVEKGLKSKPWVKTSLAPGS-QVVTDYLAKAGLQPYLDQLGFNIVGYGCTTCIG- 509 Query: 365 HMGVLGD--------GERVLS---TQNRNFKGRMGNPNAEIYLASPATAAATAVTG 409 + G L D G V++ + NRNF+GR+ YLASP A A+ G Sbjct: 510 NSGPLPDPIAAAVEEGNLVVAAVLSGNRNFEGRVNPHTRANYLASPPLCVAYALAG 565 Lambda K H 0.318 0.137 0.395 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: 810 Number of extensions: 47 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 4 Number of HSP's successfully gapped: 2 Length of query: 418 Length of database: 896 Length adjustment: 37 Effective length of query: 381 Effective length of database: 859 Effective search space: 327279 Effective search space used: 327279 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: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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