Align 3-isopropylmalate dehydratase large subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate BPHYT_RS23060 BPHYT_RS23060 3-isopropylmalate dehydratase large subunit
Query= curated2:Q8TVF2 (418 letters) >FitnessBrowser__BFirm:BPHYT_RS23060 Length = 655 Score = 216 bits (549), Expect = 2e-60 Identities = 160/442 (36%), Positives = 220/442 (49%), Gaps = 35/442 (7%) Query: 3 KTMAEKILSR---ASGEDAEAGDIVVANIDVAMVHD-ITGPITVQRLEEMGVER-VWDPS 57 KT+ EKI+ R + A+ GD V D HD TG G + P Sbjct: 207 KTLVEKIIERHLHPASVGAQRGDGVFIAADWRFSHDYFTGMCAHLMHRAFGKPAPLHAPD 266 Query: 58 KIVVLFDHQVPADS-------------VEAAENH-KIMREF-VEEQGIEHFYDVREGVCH 102 I+ DH V A E H R++ V G EG+CH Sbjct: 267 HIIAFQDHLVLASQSIPHVRDGLLPGVANLMEGHTSFSRDYPVRSHGALDGMPGSEGICH 326 Query: 103 QVLPEKGHVRPGDVIVGADSHTCTHGALGAFATGIGSTDMAAVFATGKLWFRVPETYRVE 162 ++ E+ + PG V G DSHT GALG A G G+T++A + TG + +VPET R+E Sbjct: 327 ALMAEQ-YALPGQVACGTDSHTPHSGALGCLAFGAGATEIANSWVTGYVRCKVPETLRIE 385 Query: 163 ITGELPEGVYAKDVVLKV--TGEIGADGATYMAIEYHGEVVREMSVSDRMCLCNMAIEMG 220 I+G+L +GV AKDVVL + I + GA + EY G VR MS+ +R L NM E+G Sbjct: 386 ISGQLRDGVTAKDVVLHLLQMDAIRSGGAIGLVFEYGGSAVRAMSIDERATLTNMVAELG 445 Query: 221 AKTGMVPPDEKTLEYVKKRAG---TEGRPVEPDPDARYEAELTLDVSDLEPQVAKPFSPD 277 TG+V PDE+T+ ++K+R G T ++ D A Y +++D S ++P +A+P P Sbjct: 446 GFTGIVEPDERTVAFLKERRGVDFTLENWMKSDAGATYRDTISIDASAIQPMLARPGDPG 505 Query: 278 NVVPVGEVE-GIAIDQVFIGSCTNGRYEDLKVAAEVL-----EGEEVHDDVRLIVIPASR 331 N VP ++E +AID + GSCT G+ ED EVL +G V + RL + + Sbjct: 506 NGVPALQLEQDVAIDIAYGGSCTAGKREDFDFYHEVLHWGVEQGLRVPEGTRLYLQFGTM 565 Query: 332 EVYHRTLKDGVLEVLHEAGALICPPNCGPCLGGHMGVLAE-GERCVATSNRNFPGRMGHR 390 V + G L V AG + P CG C G AE E ++ NRNFPGR G Sbjct: 566 AVRAYCEERGYLPVFERAGVTLVMPGCGSCANCGPGQSAEANEVTISAINRNFPGRSG-- 623 Query: 391 ESEVYLASPATAAASAIEGEIT 412 V+LASP T AASA+ G+IT Sbjct: 624 PGNVWLASPYTVAASALAGKIT 645 Lambda K H 0.317 0.136 0.401 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: 634 Number of extensions: 36 Number of successful extensions: 6 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: 418 Length of database: 655 Length adjustment: 35 Effective length of query: 383 Effective length of database: 620 Effective search space: 237460 Effective search space used: 237460 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 (21.6 bits) S2: 52 (24.6 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