Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_038071183.1 N745_RS0107275 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_000526715.1:WP_038071183.1 Length = 473 Score = 202 bits (515), Expect = 1e-56 Identities = 148/443 (33%), Positives = 219/443 (49%), Gaps = 66/443 (14%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANTIGAAE-----FQ 84 +D + H+ TSP R +A R + W E + DHNVP + E Sbjct: 27 IDRQLLHEVTSPQAFEGLR-MAGR----KPWRIEANIATPDHNVPTTDYSSVEDIKDPIS 81 Query: 85 RV--------TREFA-REQGIVNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGA 135 R+ T+ F E GI ++ Q GI H V PE G PGM +V DSHT T+GA Sbjct: 82 RIQVQTLGANTKYFGITEFGIGDMRQ---GIVHVVGPEEGVTLPGMTLVCGDSHTATHGA 138 Query: 136 FGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGA 195 GA A G+G +++ V AT + M I+V G+ V KDVIL IIG+IG G Sbjct: 139 LGALAHGVGTSEVEHVLATQCLLQKKMKNMLIKVNGQLRPGVTPKDVILAIIGKIGTAGG 198 Query: 196 TYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRART--------G 247 ++EF G E M V GRMT+CNMA+E GA+ G++ + +T++YV+ R Sbjct: 199 NGHAIEFGGQVFEDMSVEGRMTVCNMAIEAGARVGMVAVDEKTIEYVKGRPYSPKGEDWD 258 Query: 248 REFRVYS---SDEDSQYLEDHHFDVSDLEPQVA---CPD---DVDNVYPVHRVEGTH--- 295 + + +S SD+D+ + + SD+EPQV+ P+ D++ P +EG Sbjct: 259 KAVQAWSSLHSDDDAVFDTVVEMEGSDIEPQVSWGTSPEMVTDINGKVPDPDMEGDEVKA 318 Query: 296 ----------------------IDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDV-RFIV 332 +D F+GSCTN R ED++ AA+V+ R+V +V + ++ Sbjct: 319 GGIRRALDYMGLDAGMSITDIPVDYVFIGSCTNSRIEDIRAAAQVLKGRKVASNVEQALI 378 Query: 333 SPASREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGR 392 P S + +A E+G+ + FI AG NPGC CL + L G+ +T+NRNF GR Sbjct: 379 VPGSGLVKKQAEEEGLDKIFIEAGFEWRNPGCSMCLAMNADRLPSGKHCASTSNRNFEGR 438 Query: 393 MGDPASSVYLANPAVVAESAIEG 415 G +L +P + A +A+ G Sbjct: 439 QG-AGGRTHLVSPEMAAAAAVAG 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: 540 Number of extensions: 33 Number of successful extensions: 5 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: 473 Length adjustment: 33 Effective length of query: 395 Effective length of database: 440 Effective search space: 173800 Effective search space used: 173800 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