Align isopropylmalate/citramalate isomerase large subunit LeuC (EC 4.2.1.33; EC 4.2.1.35) (characterized)
to candidate RR42_RS21085 RR42_RS21085 3-isopropylmalate dehydratase
Query= reanno::DvH:208495 (419 letters) >FitnessBrowser__Cup4G11:RR42_RS21085 Length = 435 Score = 296 bits (758), Expect = 8e-85 Identities = 175/424 (41%), Positives = 239/424 (56%), Gaps = 11/424 (2%) Query: 4 TLAQKILQRHTDEAITDAGQIVRCRVSMVLANDITAPLAIKSF-RAMGAKRVFDKDRVAL 62 TLAQK++ R G IV CRV + +++D + P + R +GAK V+D +R + Sbjct: 13 TLAQKLVARAAGLERVTPGTIVTCRVDLAMSHDSSGPRRVAPLLRELGAK-VWDPERYVV 71 Query: 63 VMDHFTPQKDIEAAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVVGA 122 V DH+ P D EA V+ TR++ RE + H+ +G G+ H +LPE G V PG +VG Sbjct: 72 VTDHYLPAADPEAQAIVRFTRDWVREARLPHFIDGE--GICHLVLPEHGHVLPGRFIVGG 129 Query: 123 DSHTCTYGGLGAFATGLGSTDVAGAMALGETWFKVPPTIRATFTGTLPAYVGAKDLILTL 182 DSH+ T G GA+ G+G+T++AG +A GE W +VP TIR + G L A V AKD++L L Sbjct: 130 DSHSPTGGAFGAYMFGIGATEMAGVLATGEIWLRVPHTIRLQWDGKLSAGVCAKDIMLFL 189 Query: 183 IGAIGVDGALYRALEFDGAAIEALDVEGRMTMANMAIEAGGKAGLFAADAKTLTYCTTAG 242 G +G+DG Y A+E+ G A+ AL ++ RMT+ NM+ E G + GL A DA T + AG Sbjct: 190 CGRLGLDGGRYEAIEYTGEAVTALPMQERMTLTNMSAELGAQTGLIAPDATTRAWLAQAG 249 Query: 243 ----RTGDTAFS---ADAGAVYERELSFDVTGMTPVVACPHLPDNVKPVSEVKDVTVQQV 295 + A S ++ GA FD + P VA PH P N PV + V Sbjct: 250 VPAAKLDAIALSHWRSEPGAPVLASHRFDAAALAPQVAAPHSPANTGPVDQAAGQRVDIA 309 Query: 296 VIGSCTNGRIGDLREAAAVLRGRKVSRDVRCIVLPATPGIWRQALREGLIETFMEAGCIV 355 +G+CT ++ DLR AA+VLRGR+V+ V V PA+ RQA EG + ++AG + Sbjct: 310 YLGACTGAKLEDLRMAASVLRGRRVAPGVTLQVAPASLRDQRQAESEGTLAILLDAGAQL 369 Query: 356 GPATCGPCLGGHMGILADGERAIATTNRNFKGRMGSLESEVYLSGPATAAASAVTGVITD 415 P C C G RAIA+T RNF GRMG S V+L+ P T AA AVTG ITD Sbjct: 370 LPNACNACAGYGPSRFPANSRAIASTARNFAGRMGESGSAVWLASPLTVAACAVTGSITD 429 Query: 416 PSTL 419 P L Sbjct: 430 PRGL 433 Lambda K H 0.320 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: 519 Number of extensions: 17 Number of successful extensions: 3 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: 419 Length of database: 435 Length adjustment: 32 Effective length of query: 387 Effective length of database: 403 Effective search space: 155961 Effective search space used: 155961 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 (21.8 bits) S2: 51 (24.3 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