Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_078427541.1 BK574_RS03580 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_002019605.1:WP_078427541.1 Length = 470 Score = 205 bits (522), Expect = 2e-57 Identities = 141/437 (32%), Positives = 217/437 (49%), Gaps = 57/437 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPAN-------TIGAAE 82 +DL + H+ +SP R A+R V PE V DH VP + + Sbjct: 28 IDLHLLHEVSSPMAFSGLRK-ANR----TVRRPELTVGTMDHIVPTSGRQNPYLDPNTTK 82 Query: 83 FQRVTREFAREQGI--VNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAFA 140 + E +E GI N+ GI H + PE G PG IV DSHT T+GAFGA A Sbjct: 83 QIQALEENCKEFGIKLYNLESANQGIVHVIAPELGLSLPGQTIVCGDSHTSTHGAFGALA 142 Query: 141 TGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATYRSV 200 G+G +++ V AT + + I G V AKD+IL IG +G D AT + Sbjct: 143 FGIGTSEVEHVLATQCLQQYKSKTLEIRFNGRLAQGVTAKDLILSTIGTLGTDFATGYVI 202 Query: 201 EFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVR----ARTGREF------ 250 E+TG+ I+ + + RMT+CNM++E+GA+ G++ P+ T Y++ A G F Sbjct: 203 EYTGEVIKQLSMEERMTVCNMSIELGARAGLIAPDETTFAYIKDKRYAPKGEVFDKALEY 262 Query: 251 -RVYSSDEDSQYLEDHHFDVSDLEPQVA--------------CPDDVDNVYPVHR----- 290 + + +DED+ Y + D S +EPQV PD +D + R Sbjct: 263 WKKFYTDEDASYDKTVEIDASIIEPQVTWGTNPGMVVNVSSNVPDPMDMINKEERYYAEK 322 Query: 291 ------------VEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASRE 338 ++ I++ F+GSCTN R EDL++AA+++ +V DV+ +V P S+ Sbjct: 323 ALEYMGLNANTPIKNIKINKVFIGSCTNSRLEDLRLAAKMVKGYKVSPDVKALVVPGSQL 382 Query: 339 IYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPAS 398 + +A +G+ + FI AG + GC C+G + ++ PGE +T+NRNF GR G A Sbjct: 383 VKKEAEVEGLDKIFIEAGFEWRDSGCSMCVGMNPDIVEPGERCASTSNRNFEGRQGRNAR 442 Query: 399 SVYLANPAVVAESAIEG 415 + +L +P + A +A+ G Sbjct: 443 T-HLVSPPMAAVAALAG 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: 478 Number of extensions: 28 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: 428 Length of database: 470 Length adjustment: 33 Effective length of query: 395 Effective length of database: 437 Effective search space: 172615 Effective search space used: 172615 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