Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate GFF3491 HP15_3433 aconitate hydratase 1
Query= curated2:Q9WYC7 (418 letters) >FitnessBrowser__Marino:GFF3491 Length = 919 Score = 114 bits (286), Expect = 9e-30 Identities = 128/496 (25%), Positives = 199/496 (40%), Gaps = 111/496 (22%) Query: 21 GEIVLARVDIAMAQDGTGPLMINEFRELGF---KEVKVPKAFLFIDHASPSPRKELSNSQ 77 G + LA + A+ G P MIN + V V K F D +S + + Sbjct: 100 GVVDLAAMREAVQAAGKDPAMINPLSPVDLVIDHSVMVDK---FGDASSFKDNVAIEMER 156 Query: 78 KMMREFGKEMGVKVFD------AGDGISHQILAE-------------KYVKPGDLVAGAD 118 R G + FD G GI HQ+ E K + D + G D Sbjct: 157 NQERYEFLRWGQQAFDNFRVVPPGTGICHQVNLEYLGKTVWQKDQDGKTIAYPDTLVGTD 216 Query: 119 SHTCTAGGLGAFGTGMGSTDVAIIFGLGQNW-FKVPETIKVVVNGKLQDGVYAKDIILEI 177 SHT GLG G G+G + LGQ +PE + + GKL++G+ A D++L + Sbjct: 217 SHTTMINGLGILGWGVGGIEAEAAM-LGQPVSMLIPEVVGFKITGKLREGITATDLVLTV 275 Query: 178 ARILGSDGATYKALEFHGSCIENMNVEDRLTISNMAVEVGAKAGLMPSDEKTREFLKKMG 237 +L G K +EF+G +++M V DR TI+NMA E GA G P DE+T ++++ G Sbjct: 276 TEMLRKKGVVGKFVEFYGDGLKDMPVADRATIANMAPEYGATCGFFPVDEQTIKYMRLTG 335 Query: 238 REEDFREL------------KADPDAVYETEIEIDATTLEPLVSLP-------------- 271 REE+ EL + + VY +E+D +E ++ P Sbjct: 336 REEEQLELVEAYAKAQGLWREPGHEPVYTDNLELDMGEVEASLAGPKRPQDRVALKNMKS 395 Query: 272 ---------------------------------HYVDNVRKVSEVEKEKIKIDQ-----V 293 Y + + E+ EK ++D Sbjct: 396 SFELLMETAEGPAENREANLESEGGQTAVGVDDSYKHHASQPLEMNGEKSRLDPGAVVIA 455 Query: 294 FIGTCTNGRLQDLEIALKILEKH------GKHPDVRLIVGPASRKVYMDALEKGIIKKFV 347 I +CTN + +A ++ + P V+ + P S KV D L+ G + + Sbjct: 456 AITSCTNTSNPSVMMAAGLIAQKAVQKGLSTKPWVKTSLAPGS-KVVTDYLKVGGFQDDL 514 Query: 348 E-LGAAVIPPGCGPCVGIHMGVLGDG-ERVLS----------TQNRNFKGRMGNPNAEIY 395 + LG ++ GC C+G + G L D E+ +S + NRNF+GR+ + Sbjct: 515 DKLGFNLVGYGCTTCIG-NSGPLPDAVEKAISDGDLTVASVLSGNRNFEGRVHPLVKTNW 573 Query: 396 LASPATAAATAVTGYI 411 LASP A A+ G + Sbjct: 574 LASPPLVVAYALAGNV 589 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: 858 Number of extensions: 44 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 418 Length of database: 919 Length adjustment: 37 Effective length of query: 381 Effective length of database: 882 Effective search space: 336042 Effective search space used: 336042 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