Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate H281DRAFT_02541 H281DRAFT_02541 3-isopropylmalate dehydratase, large subunit (EC 4.2.1.33)
Query= curated2:O27668 (428 letters) >FitnessBrowser__Burk376:H281DRAFT_02541 Length = 465 Score = 202 bits (513), Expect = 2e-56 Identities = 142/445 (31%), Positives = 215/445 (48%), Gaps = 59/445 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPA--------NTIGAA 81 +D + HD + P T +A+R P V P+ DH V + N GA Sbjct: 27 IDRHLLHDLSGPGGFET---LAARELP--VSRPDLSFATADHAVSSAPHRTGETNPAGAK 81 Query: 82 EFQRVTREFAREQGI--VNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAF 139 + + R F + ++ + GI H + PE G PG IV DSHTCT+G GA Sbjct: 82 LYASL-RRFCDSASVPFYDLGKAGQGIVHVMAPEMGLTLPGTTIVCGDSHTCTHGGLGAL 140 Query: 140 ATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATYRS 199 A G+G++++A V AT P MRI TG V+AKD+ LH+I ++G + Sbjct: 141 AFGIGSSELAHVLATQTVRQKKPRQMRITYTGVLAKGVFAKDLALHVIAKLGCSAGVGYA 200 Query: 200 VEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVR----ARTGREF----- 250 +E G ++ + V R+T+CNM+VE+G+K P+ T D++R A G EF Sbjct: 201 IEHCGPALKRLSVEERLTLCNMSVELGSKIAFCPPDDVTFDFLRGLPYAPAGDEFEHAVS 260 Query: 251 --RVYSSDEDSQYLEDHHFDVSDLEPQV--------------ACPDDVDNVYPVHR---- 290 R SD+++ + + D+SD+EP V A PD D+ R Sbjct: 261 EWRKLRSDDNAHFDVEVSIDLSDVEPMVTWGTTPEHALAVTSAVPDPTDSTDAERRKGVE 320 Query: 291 -------------VEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASR 337 + GT +D F+GSC N R DL+ AA ++ + V +V+ V P S+ Sbjct: 321 AALEYMGLCGGQSLAGTSVDWVFIGSCANSRISDLREAASIVRGKHVAPNVQAWVVPGSQ 380 Query: 338 EIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPA 397 + A +G+ + F AG PGC C+ A+ V+ PG+ ++T+NRNF GR G P Sbjct: 381 LVKEIAEAEGLADVFRSAGFEWREPGCSMCVAANGDVVPPGQRIVSTSNRNFIGRQG-PG 439 Query: 398 SSVYLANPAVVAESAIEGVISAPQQ 422 + +LA+PA A +AI G I P++ Sbjct: 440 ARTHLASPATAAAAAIAGAIVDPRR 464 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: 539 Number of extensions: 23 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: 428 Length of database: 465 Length adjustment: 32 Effective length of query: 396 Effective length of database: 433 Effective search space: 171468 Effective search space used: 171468 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 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