Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate GFF2541 Psest_2591 3-isopropylmalate dehydratase, large subunit
Query= curated2:O27668 (428 letters) >FitnessBrowser__psRCH2:GFF2541 Length = 475 Score = 194 bits (493), Expect = 5e-54 Identities = 141/444 (31%), Positives = 212/444 (47%), Gaps = 65/444 (14%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANTIGAAE--FQRVT 87 +D + H+ TSP R +A+R + W + + DHNVP T G + + + Sbjct: 28 IDRHILHEVTSPQAFEGLR-LANR----KPWRIDANIATPDHNVPT-TKGERQGGLEAIA 81 Query: 88 REFAREQ-----------GIVNIFQNAA--GICHQVLPERGFVRPGMVIVGADSHTCTYG 134 E +R Q GI+ N GI H + PE+G PGM +V DSHT T+G Sbjct: 82 DEVSRIQVQTLDENCDDFGILEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHG 141 Query: 135 AFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDG 194 AFGA A G+G +++ V AT + M++ V G+ V AKD++L +IG+IG G Sbjct: 142 AFGALAHGIGTSEVEHVLATQCLVAKKMKNMQVRVEGKLPFGVTAKDIVLAVIGKIGTAG 201 Query: 195 ATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRAR--------- 245 ++EF G I + + GRMTICNM++E GA+ G++ + +T+ YV R Sbjct: 202 GNGHALEFAGSAIRDLSMEGRMTICNMSIEAGARVGMVAVDEKTIAYVEGRPFAPKGDDW 261 Query: 246 --TGREFRVYSSDEDSQYLEDHHFDVSDLEPQVA--------------CPDDVDNVYPVH 289 ++ SD+D+ + D++PQV+ PD PV Sbjct: 262 DKAVELWQGLVSDDDAVFDTVVELKAEDIKPQVSWGTSPEMVLAVDQKVPDPAVEADPVK 321 Query: 290 R-----------------VEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVR-FI 331 R + +D F+GSCTN R EDL+ AAEV R+V +V+ + Sbjct: 322 RDSIMRALKYMGLNANQPITEIKLDRVFIGSCTNSRIEDLRAAAEVAKGRKVAANVKQAL 381 Query: 332 VSPASREIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRG 391 V P S + +A +G+ + F+ AG PGC CL + L GE +T+NRNF G Sbjct: 382 VVPGSGLVKQQAEAEGLDKIFVEAGFEWREPGCSMCLAMNPDKLGSGEHCASTSNRNFEG 441 Query: 392 RMGDPASSVYLANPAVVAESAIEG 415 R G +L +PA+ A +A+ G Sbjct: 442 RQG-AGGRTHLVSPAMAAAAAVTG 464 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: 504 Number of extensions: 27 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: 475 Length adjustment: 33 Effective length of query: 395 Effective length of database: 442 Effective search space: 174590 Effective search space used: 174590 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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