Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_018124551.1 B149_RS0107400 aconitate hydratase
Query= curated2:O27668 (428 letters) >NCBI__GCF_000375485.1:WP_018124551.1 Length = 640 Score = 225 bits (573), Expect = 4e-63 Identities = 142/418 (33%), Positives = 209/418 (50%), Gaps = 11/418 (2%) Query: 5 NMTEKILAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPER 64 N+T KI+ + PG I +D +T D T F I G RV E Sbjct: 4 NITRKIIERHLKSGSMEPGAEIGLEIDQTLTQDATGTMAYLQFEAI----GLDRV-KTEL 58 Query: 65 IVMVFDHNVPANTIGAAEFQRVTREFAREQGIVNIFQNAAGICHQVLPERGFVRPGMVIV 124 V DHN + R R A+ G++ GICHQ+ E F RPG ++ Sbjct: 59 SVSYVDHNTLQMGFRNPDDHRYLRTVAQRYGVI-FSPPGTGICHQLHLEN-FARPGRTLI 116 Query: 125 GADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVIL 184 G+DSHT T G G+ A G G +A+ A +P+ +++ +TG+ G AKDVIL Sbjct: 117 GSDSHTPTAGGIGSLAMGAGGLSVALAMAGEPYAISMPKVVKVNLTGKLTGWAAAKDVIL 176 Query: 185 HIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRA 244 H++G++ V G + E+ G +ES+ V R I NM E+GA I + +T D++ + Sbjct: 177 HLLGKLTVKGGVGKVFEYAGPGVESLSVPERACITNMGAELGATTSIFPSDERTRDFL-S 235 Query: 245 RTGRE--FRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVHRVEGTHIDEAFLG 302 + GRE + D D++Y + D+S LEP VA P D V PV + G ID+ +G Sbjct: 236 KMGREDDWEELLPDADAEYDKVIDIDLSALEPLVAQPHMPDLVVPVRELAGLKIDQCAIG 295 Query: 303 SCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREIYLKALEDGIIETFIRAGAIVCNP 362 SCTN Y DLK A V+ +R+ ++SP S+++ + +IE + AGA + Sbjct: 296 SCTNSSYSDLKTTALVLDGKRIPASTDVLISPGSKQVVKMLAAENLIEPMLDAGARMLEC 355 Query: 363 GCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAP 420 CGPC+G ++ G VS+ T NRNF GR G + +YLA+ A A+EG + P Sbjct: 356 TCGPCIGMGGSPVSAG-VSVRTFNRNFEGRSGTQDAQIYLASAETAARLALEGQFTDP 412 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: 673 Number of extensions: 36 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: 640 Length adjustment: 35 Effective length of query: 393 Effective length of database: 605 Effective search space: 237765 Effective search space used: 237765 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: 52 (24.6 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