Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate GFF2541 Psest_2591 3-isopropylmalate dehydratase, large subunit
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__psRCH2:GFF2541 Length = 475 Score = 235 bits (599), Expect = 2e-66 Identities = 142/368 (38%), Positives = 202/368 (54%), Gaps = 51/368 (13%) Query: 72 EIGEGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATGVGATDMAEIFATGKLWFK 131 ++ +GI H + PE G LPG +V DSH+ T+GAFGA A G+G +++ + AT L K Sbjct: 108 DVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAK 167 Query: 132 VPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEFYGQAISELSVAGRMTLCN 191 ++ ++ VEG L V AKD+ L +IGK G AG A+EF G AI +LS+ GRMT+CN Sbjct: 168 KMKNMQVRVEGKLPFGVTAKDIVLAVIGKIGTAGGNGHALEFAGSAIRDLSMEGRMTICN 227 Query: 192 MAIEMGAKTGIVPPDEKTFDFLKNRAVAP-----------YEPVYSDPDASYLKEFVYDA 240 M+IE GA+ G+V DEKT +++ R AP ++ + SD DA + A Sbjct: 228 MSIEAGARVGMVAVDEKTIAYVEGRPFAPKGDDWDKAVELWQGLVSDDDAVFDTVVELKA 287 Query: 241 GDIEPQV----------------------ACPHQVDNV------------KPVGEVEGTH 266 DI+PQV A P + D++ +P+ E++ Sbjct: 288 EDIKPQVSWGTSPEMVLAVDQKVPDPAVEADPVKRDSIMRALKYMGLNANQPITEIK--- 344 Query: 267 VDQVFIGTCTNGRLEDLEVAASVLKGKKVTV---RTIIIPASRSTLLAAIKNGTMEILLK 323 +D+VFIG+CTN R+EDL AA V KG+KV + +++P S A G +I ++ Sbjct: 345 LDRVFIGSCTNSRIEDLRAAAEVAKGRKVAANVKQALVVPGSGLVKQQAEAEGLDKIFVE 404 Query: 324 AGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDGFIYLASPATAAASALTG 383 AG PGC CL + LG GE C ST+NRNF+GR G G +L SPA AAA+A+TG Sbjct: 405 AGFEWREPGCSMCLAMNPDKLGSGEHCASTSNRNFEGRQGAGGRTHLVSPAMAAAAAVTG 464 Query: 384 EITDPRKI 391 D R++ Sbjct: 465 HFIDVREL 472 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: 410 Number of extensions: 15 Number of successful extensions: 4 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: 475 Length adjustment: 32 Effective length of query: 359 Effective length of database: 443 Effective search space: 159037 Effective search space used: 159037 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: 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