Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate Synpcc7942_1898 Synpcc7942_1898 isopropylmalate isomerase large subunit
Query= curated2:O27668 (428 letters) >FitnessBrowser__SynE:Synpcc7942_1898 Length = 468 Score = 221 bits (563), Expect = 4e-62 Identities = 154/442 (34%), Positives = 219/442 (49%), Gaps = 61/442 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANTIGA------AEF 83 + L + H+ TSP RD RG + P R V DH VP AE Sbjct: 28 IGLHLIHEVTSPQAFSMLRD---RGLTVKF--PGRTVATVDHIVPTENQARPFADSLAEE 82 Query: 84 QRVTREF-AREQGI--VNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAFA 140 VT E RE GI NI + GI H + PE+G +PGM I DSHT T+GAFGA A Sbjct: 83 MIVTLERNCRENGIRFYNIGSGSQGIVHVIAPEQGLTQPGMTIACGDSHTSTHGAFGAIA 142 Query: 141 TGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATYRSV 200 G+G + + V A+ + +IEV GE + VYAKDVILHII ++GV G + Sbjct: 143 FGIGTSQVRDVLASQTLALSKLKVRKIEVNGELQPGVYAKDVILHIIRKLGVKGGVGYAY 202 Query: 201 EFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRARTGREF---------- 250 EF G T +M + RMT+CNMA+E GA+ G + P++ T DY++ GREF Sbjct: 203 EFAGSTFAAMSMEERMTVCNMAIEGGARCGYVNPDQITYDYLQ---GREFAPQGEAWDRA 259 Query: 251 ----RVYSSDEDSQYLEDHHFDVSDLEPQVA----------------CPD---DVD---- 283 S+ D++Y + FD +++ P V PD D D Sbjct: 260 IAWWESLRSEADAEYDDVVVFDAAEIAPTVTWGITPGQGIGITETIPTPDSLLDEDRAVA 319 Query: 284 -------NVYPVHRVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPAS 336 ++ P ++GT +D F+GSCTNGR DL+ AA+V R+V ++ V P S Sbjct: 320 AEAYSYMDLEPGAPLQGTKVDVCFIGSCTNGRLSDLREAAKVAQGRKVAAGIKAFVVPGS 379 Query: 337 REIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDP 396 + +A +G+ + F AG GC CL + L ++S +++NRNF+GR G Sbjct: 380 ERVKQQAEAEGLDQIFTAAGFEWRQAGCSMCLAMNPDKLEGRQISASSSNRNFKGRQGSA 439 Query: 397 ASSVYLANPAVVAESAIEGVIS 418 + L +PA+VA +AI G ++ Sbjct: 440 SGRTLLMSPAMVAAAAIAGEVT 461 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: 535 Number of extensions: 25 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: 468 Length adjustment: 33 Effective length of query: 395 Effective length of database: 435 Effective search space: 171825 Effective search space used: 171825 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