Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate AZOBR_RS15565 AZOBR_RS15565 isopropylmalate isomerase
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__azobra:AZOBR_RS15565 Length = 468 Score = 251 bits (642), Expect = 2e-71 Identities = 146/402 (36%), Positives = 214/402 (53%), Gaps = 51/402 (12%) Query: 41 DHIAPANTETSATLQKEIREWV-------REQSIPNF--YEIGEGICHQVLPENGFALPG 91 DH P+++ EI V + +F ++ +GI H + PE G LPG Sbjct: 64 DHYVPSHSRAKPIADPEIANMVTMLEANAERHGLRHFGLHDPAQGIVHVLAPEQGLTLPG 123 Query: 92 KLLVGADSHSCTYGAFGAFATGVGATDMAEIFATGKLWFKVPESFRMTVEGSLDKHVYAK 151 +V DSH+ T+GAFGA A G+GAT+++ + AT LW + P++ R+ ++G L HV AK Sbjct: 124 LTIVCGDSHTSTHGAFGALAFGIGATEVSHVLATQTLWQRRPKTMRIIIDGELGAHVTAK 183 Query: 152 DLTLYLIGKTGIAGATYKAVEFYGQAISELSVAGRMTLCNMAIEMGAKTGIVPPDEKTFD 211 DL L +IG G GA +E+ G AI LS+ GR+T+CNM+IE GA+ G++ PD+ TF Sbjct: 184 DLILAVIGFIGADGAAGHVIEYAGSAIRALSMEGRLTVCNMSIEAGARAGMIAPDDITFS 243 Query: 212 FLK-----------NRAVAPYEPVYSDPDASYLKEFVYDAGDIEPQVACPHQVDNVKPV- 259 +++ +RAVA + + SDP+A++ +E DA I P V + PV Sbjct: 244 WIEGRNYAPKGDLFDRAVAHWRTLPSDPEAAFDREVSLDAAAIAPLVTWGTSPETAVPVT 303 Query: 260 -------------------------GEVEGTH-----VDQVFIGTCTNGRLEDLEVAASV 289 G GT +D+VFIG+CTN RLEDL AA+V Sbjct: 304 GTVPDPGAESDPVRAGQMRKMLDYMGLTPGTRLEEVGIDRVFIGSCTNARLEDLRAAAAV 363 Query: 290 LKGKKVTVRTIIIPASRSTLLAAIKNGTMEILLKAGVTLATPGCGPCLGAHQGVLGEGEV 349 L+G++ V +++ S A G + + AG+ PGC C+G + ++ GE Sbjct: 364 LRGRRAVVPGLVVAGSVPVRRQAEAEGLDRVFIGAGLEWGEPGCSMCVGINGDLVPAGER 423 Query: 350 CVSTANRNFKGRMGKDGFIYLASPATAAASALTGEITDPRKI 391 C ST NRNF GR G + +L SPA AAA+A+TG +TD RK+ Sbjct: 424 CASTTNRNFPGRQGPNARTHLMSPAMAAAAAVTGRLTDVRKL 465 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: 466 Number of extensions: 18 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: 391 Length of database: 468 Length adjustment: 32 Effective length of query: 359 Effective length of database: 436 Effective search space: 156524 Effective search space used: 156524 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