Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate Pf6N2E2_63 3-isopropylmalate dehydratase large subunit (EC 4.2.1.33)
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_63 Length = 472 Score = 234 bits (596), Expect = 5e-66 Identities = 153/445 (34%), Positives = 219/445 (49%), Gaps = 59/445 (13%) Query: 5 VDYAMAHDGTSILAVNAFKEMEMERVWDPSRIVIPFDHIAPANTETSATLQKEIREWVR- 63 +D + H+ TS A + + + W + DH P E ++ + + R Sbjct: 28 IDRHIIHEVTSPQAFEGLR-LAGRKPWRIDANIATPDHNVPTTPERKGGIEAIVDQVSRL 86 Query: 64 ----------EQSIPNFY--EIGEGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFA 111 E I F ++ +GI H + PE G LPG +V DSH+ T+GAFGA A Sbjct: 87 QVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFGALA 146 Query: 112 TGVGATDMAEIFATGKLWFKVPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAV 171 G+G +++ + AT L K ++ + VEG L V AKD+ L +IGK G AG A+ Sbjct: 147 HGIGTSEVEHVLATQCLVAKKMKNMLVRVEGKLPFGVTAKDIVLAVIGKIGTAGGNGHAI 206 Query: 172 EFYGQAISELSVAGRMTLCNMAIEMGAKTGIVPPDEKTFDFLKNRAVAP----------- 220 EF G AI +LSV GRMT+CNM+IE GA+ G+V D+KT +++K R AP Sbjct: 207 EFAGSAIRDLSVEGRMTICNMSIEAGARVGLVAADKKTVEYVKGRPFAPKGAEWDMAVEA 266 Query: 221 YEPVYSDPDASYLKEFVYDAGDIEPQVACPHQVDNVKPVGE------------------- 261 ++ + SD DA + DA I+PQV+ + V V + Sbjct: 267 WKDLVSDADAKFDTVVELDATQIKPQVSWGTSPEMVLAVDQNVPDPAKEMDLVKRDSIVR 326 Query: 262 ------------VEGTHVDQVFIGTCTNGRLEDLEVAASVLKGKKVT---VRTIIIPASR 306 + +D+VFIG+CTN R+EDL AA + KG+KV + I++P S Sbjct: 327 ALKYMGLSANQAITDIQLDRVFIGSCTNSRIEDLRAAAVIAKGRKVASTIKQAIVVPGSG 386 Query: 307 STLLAAIKNGTMEILLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDG 366 A G +I L+AG PGC CL + L GE C ST+NRNF+GR G G Sbjct: 387 LVKAQAEAEGLDKIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQGAGG 446 Query: 367 FIYLASPATAAASALTGEITDPRKI 391 +L SPA AAA+A+ G D R++ Sbjct: 447 RTHLVSPAMAAAAAVNGRFVDVREL 471 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: 425 Number of extensions: 17 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: 391 Length of database: 472 Length adjustment: 32 Effective length of query: 359 Effective length of database: 440 Effective search space: 157960 Effective search space used: 157960 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