Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 6936140 Sama_0337 isopropylmalate isomerase large subunit (RefSeq)
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__SB2B:6936140 Length = 470 Score = 238 bits (606), Expect = 3e-67 Identities = 142/359 (39%), Positives = 195/359 (54%), Gaps = 44/359 (12%) Query: 75 EGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATGVGATDMAEIFATGKLWFKVPE 134 +GI H + PE G LPG ++V DSH+ T+GAFGA A G+G +++ + AT L + Sbjct: 105 QGIVHVMGPELGITLPGTVIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLRQLKAK 164 Query: 135 SFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEFYGQAISELSVAGRMTLCNMAI 194 + ++ V G + + AKD+ L +IGK G+ G T VEF G+AI +LS+ GRMTLCNMAI Sbjct: 165 TMKIEVRGKVADGITAKDIVLAIIGKIGMDGGTGYVVEFCGEAIRDLSMEGRMTLCNMAI 224 Query: 195 EMGAKTGIVPPDEKTFDFLKNRAVAP-----------YEPVYSDPDASYLKEFVYDAGDI 243 EMGAK G+V PDE TF +L+ R AP + +++D DA + E V +A I Sbjct: 225 EMGAKAGMVAPDETTFAYLEGREFAPKGDAWQQALADWRELHTDADAVFDAEVVLEAAAI 284 Query: 244 EPQV--------------ACPHQVDNVKPVGEVE------------GT-----HVDQVFI 272 PQ+ P+ D PV GT +++VFI Sbjct: 285 APQLTWGTNPGQVVAIDGVVPNPADETNPVVRTSMEKALAYVDLTPGTPMTDIAINKVFI 344 Query: 273 GTCTNGRLEDLEVAASVLKGKKVT--VRTIIIPASRSTLLAAIKNGTMEILLKAGVTLAT 330 G+CTN R+EDL AA+ KG+KV V I++P S L A G +I L+AG Sbjct: 345 GSCTNSRIEDLRAAAAQAKGRKVASGVTAIVVPGSGQVKLQAEAEGLDKIFLEAGFEWRL 404 Query: 331 PGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDGFIYLASPATAAASALTGEITDPR 389 PGC CL + L G+ C ST+NRNF+GR G+ +L SPA AAA+A+ G D R Sbjct: 405 PGCSMCLAMNDDRLEAGDRCASTSNRNFEGRQGRGSRTHLVSPAMAAAAAVAGHFVDIR 463 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: 425 Number of extensions: 19 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: 470 Length adjustment: 32 Effective length of query: 359 Effective length of database: 438 Effective search space: 157242 Effective search space used: 157242 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