Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate RR42_RS21085 RR42_RS21085 3-isopropylmalate dehydratase
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__Cup4G11:RR42_RS21085 Length = 435 Score = 308 bits (788), Expect = 3e-88 Identities = 168/395 (42%), Positives = 231/395 (58%), Gaps = 11/395 (2%) Query: 5 VDYAMAHDGTSILAVNAFKEMEMERVWDPSRIVIPFDHIAPANTETSATLQKEIREWVRE 64 VD AM+HD + V +VWDP R V+ DH PA + + + R+WVRE Sbjct: 38 VDLAMSHDSSGPRRVAPLLRELGAKVWDPERYVVVTDHYLPAADPEAQAIVRFTRDWVRE 97 Query: 65 QSIPNFYEIGEGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATGVGATDMAEIFA 124 +P+F + GEGICH VLPE+G LPG+ +VG DSHS T GAFGA+ G+GAT+MA + A Sbjct: 98 ARLPHFID-GEGICHLVLPEHGHVLPGRFIVGGDSHSPTGGAFGAYMFGIGATEMAGVLA 156 Query: 125 TGKLWFKVPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEFYGQAISELSVA 184 TG++W +VP + R+ +G L V AKD+ L+L G+ G+ G Y+A+E+ G+A++ L + Sbjct: 157 TGEIWLRVPHTIRLQWDGKLSAGVCAKDIMLFLCGRLGLDGGRYEAIEYTGEAVTALPMQ 216 Query: 185 GRMTLCNMAIEMGAKTGIVPPDEKTFDFLKNRAV--APYEPV-----YSDPDASYLKEFV 237 RMTL NM+ E+GA+TG++ PD T +L V A + + S+P A L Sbjct: 217 ERMTLTNMSAELGAQTGLIAPDATTRAWLAQAGVPAAKLDAIALSHWRSEPGAPVLASHR 276 Query: 238 YDAGDIEPQVACPHQVDNVKPVGEVEGTHVDQVFIGTCTNGRLEDLEVAASVLKGKKVT- 296 +DA + PQVA PH N PV + G VD ++G CT +LEDL +AASVL+G++V Sbjct: 277 FDAAALAPQVAAPHSPANTGPVDQAAGQRVDIAYLGACTGAKLEDLRMAASVLRGRRVAP 336 Query: 297 -VRTIIIPASRSTLLAAIKNGTMEILLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTAN 355 V + PAS A GT+ ILL AG L C C G +++ Sbjct: 337 GVTLQVAPASLRDQRQAESEGTLAILLDAGAQLLPNACNACAGYGPSRFPANSRAIASTA 396 Query: 356 RNFKGRMGKDG-FIYLASPATAAASALTGEITDPR 389 RNF GRMG+ G ++LASP T AA A+TG ITDPR Sbjct: 397 RNFAGRMGESGSAVWLASPLTVAACAVTGSITDPR 431 Lambda K H 0.318 0.135 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: 436 Number of extensions: 23 Number of successful extensions: 5 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: 391 Length of database: 435 Length adjustment: 31 Effective length of query: 360 Effective length of database: 404 Effective search space: 145440 Effective search space used: 145440 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: 50 (23.9 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