Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_051180794.1 G579_RS15645 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_000423825.1:WP_051180794.1 Length = 480 Score = 221 bits (564), Expect = 3e-62 Identities = 152/448 (33%), Positives = 217/448 (48%), Gaps = 60/448 (13%) Query: 21 TPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVP------ 74 T G+ +D + H+ TSP R +A R + W + V V DHNVP Sbjct: 18 TEGDATLLYIDRQLIHEVTSPQAFEGLR-VAGR----KPWRVDANVAVPDHNVPTIGREQ 72 Query: 75 --ANTIGAAEFQRVTREFAREQGIVNIFQNAA--GICHQVLPERGFVRPGMVIVGADSHT 130 A+ + + + + R A E GI GI H + PE+G PGM +V DSHT Sbjct: 73 GIADPVSRLQVETLDRNCA-EFGIEEFAMGDVRQGIVHVIAPEQGLTLPGMTVVCGDSHT 131 Query: 131 CTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEI 190 T+GA GA A G+G +++ V AT W ++MRI V GE AKD++L +IG+I Sbjct: 132 ATHGALGALAFGIGTSEVEHVLATQCLWTQKTKSMRIRVEGELPAGCTAKDIVLAVIGKI 191 Query: 191 GVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRAR----- 245 G G T ++EF G IE++ + GRMT+CNMA+E GA+ G++ + +T+DYV+ R Sbjct: 192 GTAGGTGYTIEFAGPAIEALSIEGRMTVCNMAIEAGARAGMVAVDDKTIDYVKGRPFAPQ 251 Query: 246 ------TGREFRVYSSDEDSQYLEDHHFDVSDLEPQVA--------------CPDDVDNV 285 +R SD D+ + + D ++++PQV PD Sbjct: 252 GALWEQAVAAWRELRSDPDAVFDREVVLDAAEIQPQVTWGTSPEMVVGINDRVPDPAREP 311 Query: 286 YPVHR-----------------VEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDV 328 PV R + ID+ F+GSCTN R EDL+ AA V +V V Sbjct: 312 DPVRRHAMEQALAYMGLEANTPMTAIAIDKVFIGSCTNARIEDLRAAAAVAKGHKVAPHV 371 Query: 329 R-FIVSPASREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNR 387 + +V P S + +A +G+ F AG +PGC CL + L PGE AT+NR Sbjct: 372 KQALVVPGSGLVKRQAEAEGLDRIFKEAGFEWRDPGCSMCLAMNADRLEPGERCAATSNR 431 Query: 388 NFRGRMGDPASSVYLANPAVVAESAIEG 415 NF GR G +L +PAV A +AI G Sbjct: 432 NFEGRQG-KGGRTHLVSPAVAAAAAIAG 458 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: 564 Number of extensions: 32 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: 480 Length adjustment: 33 Effective length of query: 395 Effective length of database: 447 Effective search space: 176565 Effective search space used: 176565 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