Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_077243460.1 B1A74_RS00520 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_001995255.1:WP_077243460.1 Length = 469 Score = 225 bits (573), Expect = 3e-63 Identities = 159/467 (34%), Positives = 232/467 (49%), Gaps = 59/467 (12%) Query: 11 LAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFD 70 L EA +RE G + +D + H+ TSP R +A R + W + ++ V D Sbjct: 10 LWEAHVVREEPDGSTL-LYIDRHLVHEVTSPQAFEGLR-LAGR----KPWRGDSVLAVPD 63 Query: 71 HNVPANTIGAAEFQRVTREFAR--EQGI----VNIFQNA---AGICHQVLPERGFVRPGM 121 HNVP A V+R E + + F A GI H + PE+G PGM Sbjct: 64 HNVPTTNRDAGIEDPVSRTQVETLESNVSGFGLKFFPMADVRQGIVHVIGPEQGATLPGM 123 Query: 122 VIVGADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKD 181 +V DSHT T+GA GA A G+G +++ V AT W +AM+I V GE V AKD Sbjct: 124 TVVCGDSHTSTHGALGALAFGIGTSEVEHVLATQCLWQKKTKAMQIRVEGELRPGVTAKD 183 Query: 182 VILHIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDY 241 ++L IIG IG G T ++EF G I S+ + GRM+ICNM++E GA+ G++ + +T++Y Sbjct: 184 IVLAIIGRIGTAGGTGYAIEFAGSAIRSLSIEGRMSICNMSIEAGARAGMVAVDEKTIEY 243 Query: 242 VRAR----TGREF-------RVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVH- 289 VR + TG F R SD D+++ D +++ PQV+ + V P+ Sbjct: 244 VRGKPQAPTGEMFERAAEYWRTLVSDPDAEFDAVVELDAAEIAPQVSWGTSPEMVAPIDG 303 Query: 290 ------------RVEG----------------THI--DEAFLGSCTNGRYEDLKIAAEVI 319 R EG T I D+ F+GSCTN R EDL+ AAEV+ Sbjct: 304 RVPDPAAESDPVRAEGMQRALEYMDLKANTPMTEIRPDKVFIGSCTNSRIEDLRAAAEVV 363 Query: 320 GDRRVHEDVRF-IVSPASREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPG 378 RR ++++ +V P S + +A ++G+ F+ AG PGC CL + L PG Sbjct: 364 KGRRKADNIKLAMVVPGSGLVKQQAEQEGLDRIFLDAGFEWREPGCSMCLAMNADRLEPG 423 Query: 379 EVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAPQQEAG 425 E +T+NRNF GR G +L +PA+ A +A+ G P + G Sbjct: 424 ERCASTSNRNFEGRQGQ-GGRTHLVSPALAAAAAVAGHFIEPSELEG 469 Lambda K H 0.320 0.137 0.408 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: 558 Number of extensions: 33 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 428 Length of database: 469 Length adjustment: 33 Effective length of query: 395 Effective length of database: 436 Effective search space: 172220 Effective search space used: 172220 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 10 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