Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_027456324.1 K420_RS0100520 3-isopropylmalate dehydratase large subunit
Query= curated2:Q8PZT3 (391 letters) >NCBI__GCF_000519045.1:WP_027456324.1 Length = 468 Score = 239 bits (609), Expect = 2e-67 Identities = 163/443 (36%), Positives = 217/443 (48%), Gaps = 58/443 (13%) Query: 5 VDYAMAHDGTSILAVNAFKEMEMERVWDPSRIVIPFDHIAPAN-----------TETSAT 53 +D + H+ TS A K + + W S IV DH P + + T Sbjct: 27 IDRHLVHEVTSPQAFEGLK-LAGRKPWRVSSIVATPDHNTPTDHWEEGIKDPISRQQVET 85 Query: 54 LQKEIREWVREQSIPNFYEIGEGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATG 113 L IRE P F + GI H V PENG LPG +V DSH+ T+GAF A G Sbjct: 86 LDANIREVGALAYFP-FKDQRMGILHVVGPENGATLPGMTVVCGDSHTSTHGAFACMAHG 144 Query: 114 VGATDMAEIFATGKLWFKVPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEF 173 +G +++ + AT L K ++ + VEG L K V AKD+ L +IG G AG T A+E+ Sbjct: 145 IGTSEVEHVLATQCLLQKKSKTMLIAVEGKLGKGVTAKDVALAIIGAIGTAGGTGYAIEY 204 Query: 174 YGQAISELSVAGRMTLCNMAIEMGAKTGIVPPDEKTFDFLKNR-----------AVAPYE 222 G AI LS+ GRMTLCNMAIE GA+ G V D+ T ++LK R AVA + Sbjct: 205 GGSAIRSLSMEGRMTLCNMAIEGGARLGFVAVDDTTINYLKGRPFSPTGENWDKAVAYWR 264 Query: 223 PVYSDPDASYLKEFVYDAGDIEPQVACPHQVDNVKPVGEV-------------EGTH--- 266 ++SDP A + + A DI PQV + V PV V EG Sbjct: 265 TLHSDPGAQFDRVVTLKAEDIRPQVTWGTSPEMVVPVDAVVPDPAREADPVKREGMERAL 324 Query: 267 ---------------VDQVFIGTCTNGRLEDLEVAASVLKGKKVTVR---TIIIPASRST 308 +D+VFIG+CTN R+EDL AA+VLKG+++ + +P S Sbjct: 325 QYMGLNPNTPIKDIAIDKVFIGSCTNSRIEDLREAAAVLKGRRIAANVKLALAVPGSGLV 384 Query: 309 LLAAIKNGTMEILLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDGFI 368 A G +I + AG PGC CL + L GE C ST+NRNF+GR G G Sbjct: 385 KRQAEAEGLDKIFVAAGFEWREPGCSMCLAMNADRLEPGERCASTSNRNFEGRQGPGGRT 444 Query: 369 YLASPATAAASALTGEITDPRKI 391 +L SPA AAA+A+ G D R++ Sbjct: 445 HLVSPAMAAAAAVAGHFADVREV 467 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: 20 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: 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 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