Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate CA265_RS15830 CA265_RS15830 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >FitnessBrowser__Pedo557:CA265_RS15830 Length = 470 Score = 221 bits (562), Expect = 5e-62 Identities = 147/442 (33%), Positives = 225/442 (50%), Gaps = 62/442 (14%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPA--------NTIGAA 81 +D + H+ TSP + F + RG P V+ P++ V DHNVP + Sbjct: 27 IDTHLIHEVTSP---QAFDGLRKRGLP--VFRPKQTVATADHNVPTLNQLLPIKEELSRY 81 Query: 82 EFQRVTR---EFARE-QGIVNIFQNAAGICHQVLPERGFVRPGMVIVGADSHTCTYGAFG 137 + +T+ EF E G+ + FQ GI H + PE G PG +V DSHT T+GAFG Sbjct: 82 QVDMLTKNCAEFGVELYGLGHPFQ---GIVHVIGPELGITLPGKTMVCGDSHTSTHGAFG 138 Query: 138 AFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATY 197 A A G+G + + VFAT P+ M+IEV GE V AKD+IL+II +I G T Sbjct: 139 AIAFGIGTSQVEQVFATQCLLQSKPKTMKIEVNGELGKGVGAKDIILYIIAKISAAGGTG 198 Query: 198 RSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRAR----TGRE---- 249 +E+ G IE++ + RMTICNM++EMGA+ G++ P++ T DY++ R G E Sbjct: 199 YFIEYAGSAIEALSMEARMTICNMSIEMGARGGLIAPDQTTFDYIKGREFAPAGEEWDKA 258 Query: 250 ---FRVYSSDEDSQYLEDHHFDVSDLEPQV--------------------ACPDDVDNVY 286 ++ SD D+++ FD +D+ P + A P+ Y Sbjct: 259 LAYWKTLYSDADAKFDSVLTFDAADIAPMITYGTNPGMGMGIQEHIPATGAQPEKEKLSY 318 Query: 287 PV----------HRVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPAS 336 + G +D F+GSCTN R EDL+ A+ + D+R ++V + P S Sbjct: 319 QKALDYMGFDDDSSLIGKPVDYVFIGSCTNSRIEDLREVADFVKDKRKADNVTVWIVPGS 378 Query: 337 REIYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDP 396 +++ +A +G+ + F AG + PGC CLG + + G+ ++T+NRNF GR G Sbjct: 379 KQVEQQAKNEGLDKIFEAAGFQLREPGCSACLGMNEDKIPAGKYCVSTSNRNFEGRQGQN 438 Query: 397 ASSVYLANPAVVAESAIEGVIS 418 A ++ LA+P A +A+ G I+ Sbjct: 439 ARTL-LASPLTAAAAAVTGKIT 459 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: 506 Number of extensions: 29 Number of successful extensions: 3 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: 470 Length adjustment: 33 Effective length of query: 395 Effective length of database: 437 Effective search space: 172615 Effective search space used: 172615 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