Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate BPHYT_RS33915 BPHYT_RS33915 isopropylmalate isomerase
Query= curated2:O27668 (428 letters) >FitnessBrowser__BFirm:BPHYT_RS33915 Length = 469 Score = 194 bits (492), Expect = 6e-54 Identities = 143/440 (32%), Positives = 210/440 (47%), Gaps = 60/440 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANTIGAAEFQRVTR- 88 +D + H+ TSP + +A R VW + V DHNVP V++ Sbjct: 27 IDRHLLHEVTSPQAFEGLK-LAERP----VWRISANLAVSDHNVPTTDRSHGIADPVSKL 81 Query: 89 ------EFAREQGIVNIFQN--AAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAFA 140 GI N GI H + PE+G PGM IV DSHT T+GAFGA A Sbjct: 82 QVDTLDSNCDAYGITQFKMNDLRQGIVHIIGPEQGATLPGMTIVCGDSHTSTHGAFGALA 141 Query: 141 TGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATYRSV 200 G+G +++ V AT + M ++V G AKD++L IIG+IG G T ++ Sbjct: 142 HGIGTSEVEHVLATQTLLQKKSKNMLVKVEGALPRGCTAKDIVLAIIGKIGTAGGTGYAI 201 Query: 201 EFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRAR----TGRE------- 249 EF G TI ++ + GRMT+CNMA+E GA+ G++ + T++Y++ R G E Sbjct: 202 EFGGSTIRALSMEGRMTVCNMAIEAGARAGMVAVDDTTIEYLKGRPFSPEGVEWDHAVEY 261 Query: 250 FRVYSSDEDSQYLEDHHFDVSDLEPQVA--------------CPDDVDNVYPVHR----- 290 ++ + +DE + + + +++ PQV PD PV R Sbjct: 262 WKQFKTDEGAHFDRVVELNAAEIVPQVTWGTSPEMVTAVDGRVPDPDREKDPVKRDAMER 321 Query: 291 ------------VEGTHIDEAFLGSCTNGRYEDLKIAAEVIG--DRRVHEDVRF-IVSPA 335 +E D+ F+GSCTN R ED++ AA V+ RRV ++R +V P Sbjct: 322 ALKYMALEPNAPIESIKPDKIFIGSCTNARIEDIRAAAYVVKKLGRRVAPNIRLAMVVPG 381 Query: 336 SREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGD 395 S + +A +G+ + F AG PGC CL + L PGE +T+NRNF GR G Sbjct: 382 SGLVKAQAEREGLDKVFTDAGFEWREPGCSMCLAMNADRLDPGERCASTSNRNFEGRQG- 440 Query: 396 PASSVYLANPAVVAESAIEG 415 +L +PA+ A +AIEG Sbjct: 441 AGGRTHLVSPAMAAAAAIEG 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: 531 Number of extensions: 22 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: 469 Length adjustment: 33 Effective length of query: 395 Effective length of database: 436 Effective search space: 172220 Effective search space used: 172220 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