Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate GFF1850 PS417_09410 isopropylmalate isomerase
Query= curated2:O27668 (428 letters) >FitnessBrowser__WCS417:GFF1850 Length = 472 Score = 218 bits (555), Expect = 3e-61 Identities = 147/438 (33%), Positives = 212/438 (48%), Gaps = 58/438 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANT--------IGAA 81 +D + ++ TSP R+ VW P + V DH P G A Sbjct: 29 IDRQVINEYTSPQAFSGLREAGRN-----VWRPGTALAVVDHVNPTTPKRIAAMPDAGGA 83 Query: 82 EFQRVTREFAREQGI--VNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAF 139 E R+ GI ++I GI H + PE+GF+ PGMVI DSHT TYGA GAF Sbjct: 84 RQVSYLAENCRDFGIELLDILDKRQGIEHVIAPEQGFILPGMVIAAGDSHTTTYGALGAF 143 Query: 140 ATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATYRS 199 G+G +++ + A+ + + M + V G+ + +KDVI+ +IG+IG GAT + Sbjct: 144 GFGIGTSEIEHLLASQTLVYKRLKTMCVSVDGDLAPGLTSKDVIMALIGKIGASGATGYA 203 Query: 200 VEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYV----RARTGR------- 248 +EF G T++++ V RMTICNMAVE GA+ M P+ + Y+ RA G Sbjct: 204 IEFRGSTLDALSVEARMTICNMAVEAGARGAFMAPDEKVFAYLKGKPRAPQGELWDQALA 263 Query: 249 EFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPV-------------------- 288 +R+ SD + + ++ D + LEP V D P+ Sbjct: 264 GWRLLHSDVGAVFDQEVQLDATTLEPMVTWGTSPDQAAPIGARVPDPQDVSDLILRQDMR 323 Query: 289 -----------HRVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASR 337 R+ I AF+GSCTN R EDL+ AA V+ + V E VR ++ P S Sbjct: 324 RALNYMGLEAGMRLSDIVISHAFIGSCTNARIEDLRDAASVVRGKHVAEHVRAMIVPGST 383 Query: 338 EIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPA 397 E+ +A +G+ FI AG GC CL + VLAPG+ ++TNRNF GR G A Sbjct: 384 EVRDQAEAEGLAAIFIDAGFEWRQSGCSMCLAMNDDVLAPGDRCASSTNRNFEGRQGAGA 443 Query: 398 SSVYLANPAVVAESAIEG 415 + +L +PA+VA +AI G Sbjct: 444 RT-HLMSPAMVAAAAITG 460 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: 525 Number of extensions: 22 Number of successful extensions: 2 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 428 Length of database: 472 Length adjustment: 33 Effective length of query: 395 Effective length of database: 439 Effective search space: 173405 Effective search space used: 173405 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