Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 3607280 Dshi_0695 3-isopropylmalate dehydratase, large subunit (RefSeq)
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__Dino:3607280 Length = 464 Score = 254 bits (648), Expect = 5e-72 Identities = 158/433 (36%), Positives = 224/433 (51%), Gaps = 50/433 (11%) Query: 5 VDYAMAHDGTSILAVNAFKEMEME--RVWDPSRIVIPFDHIAPANTETSATLQKEIREWV 62 VD + H+G+ +AF ++ V P++ DH AP + EIR + Sbjct: 29 VDRHLLHEGSH----HAFAKLAERGLSVAAPAQTFAVMDHYAPTRDRAAEGATPEIRAMI 84 Query: 63 ---REQS------IPNFYEIGEGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATG 113 RE + + + ++ +GI H + PE G LPG + DSH+ T+GAFGA A G Sbjct: 85 ARLRENAEIHQIRLFDLFDRDQGIVHVIGPEQGLTLPGLTINCGDSHTSTHGAFGALAFG 144 Query: 114 VGATDMAEIFATGKLWFKVPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEF 173 +GAT++A + AT +W P++ R+ +G L V AKDL L I G GA A+E+ Sbjct: 145 IGATEVAHVLATQTVWQTRPKTLRLRFDGRLGPGVGAKDLALAWIAALGSDGARGHAIEY 204 Query: 174 YGQAISELSVAGRMTLCNMAIEMGAKTGIVPPDEKTFDFLKNRAVAP-----------YE 222 G+A+ LS+ GRMTLCN++IE GAK G++ PDE TF +L+ R AP + Sbjct: 205 TGEAVRRLSMEGRMTLCNLSIEGGAKLGLIAPDETTFAYLRGRPHAPDGADWGRAVEDWA 264 Query: 223 PVYSDPDASYLKEFVYDAGDIEPQVACPHQVDNVKPVGE--------------------- 261 + SD DA + +E D I P V + D PV E Sbjct: 265 ALRSDEDAVFDREETLDCAAIAPVVTWGTRPDQAIPVTENLPRGEGSEVNSALTYMGLRA 324 Query: 262 ---VEGTHVDQVFIGTCTNGRLEDLEVAASVLKGKKVTVRTIIIPASRSTLLAAIKNGTM 318 + GT VDQVFIG+CTNGR+EDL AA+VL G++ V + P S A + G Sbjct: 325 GAPIAGTPVDQVFIGSCTNGRIEDLRAAAAVLAGRRARVPGQVTPGSARIKAQAEQEGLA 384 Query: 319 EILLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDGFIYLASPATAAA 378 EI + AG+ GC C+G + ++ G+ C S+ NRNF+GR G +L SPA AA Sbjct: 385 EIFIAAGLEWTEAGCAMCVGMNGDLVAPGKRCASSTNRNFRGRQGPGARTHLMSPAMVAA 444 Query: 379 SALTGEITDPRKI 391 +A+TGEITD R + Sbjct: 445 AAVTGEITDVRPL 457 Lambda K H 0.318 0.135 0.401 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: 428 Number of extensions: 18 Number of successful extensions: 3 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: 391 Length of database: 464 Length adjustment: 32 Effective length of query: 359 Effective length of database: 432 Effective search space: 155088 Effective search space used: 155088 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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