Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate H281DRAFT_06075 H281DRAFT_06075 3-isopropylmalate dehydratase, large subunit
Query= curated2:Q8TLF1 (424 letters) >FitnessBrowser__Burk376:H281DRAFT_06075 Length = 469 Score = 226 bits (576), Expect = 1e-63 Identities = 154/441 (34%), Positives = 212/441 (48%), Gaps = 57/441 (12%) Query: 38 VDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPFDHIAPANNETSATLQREIREWVKE 97 +D + H+ TS A K + VW S + DH P + + + V Sbjct: 27 IDRHLLHEVTSPQAFEGLK-LAQRPVWRISANLAVSDHNVPTTDRSHGIADPVSKLQVDT 85 Query: 98 -------QGIPNFY--EVGEGICHQVLPENGFALPGKLVVGADSHSCTYGAFGAFATGVG 148 GI F ++ +GI H + PE G LPG +V DSH+ T+GAFGA A G+G Sbjct: 86 LDSNCDAYGITQFKMNDLRQGIVHIIGPEQGATLPGMTIVCGDSHTSTHGAFGALAHGIG 145 Query: 149 ATDMAEIFATGKLWFKVPESFRMTVEGSLRKGVYAKDLTLYLIGKTGIAGATYKAVEFYG 208 +++ + AT L K ++ + VEG L +G AKD+ L +IGK G AG T A+EF G Sbjct: 146 TSEVEHVLATQTLLQKKSKNMLVKVEGPLPRGCTAKDIVLAIIGKIGTAGGTGYAIEFGG 205 Query: 209 QAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEKTFEFLKNR-----------AAATYEPV 257 IR L++ GRMT+CNMAIE GA+ G+V D+ T E+LK R A ++ Sbjct: 206 STIRSLSMEGRMTVCNMAIEAGARAGMVAVDDTTIEYLKGRPFSPQGAEWDHAVEYWKQF 265 Query: 258 YADPDAVYLEEFTYDADDIEPQV---ACPHQVDNV------------------------- 289 +D A + +A DI PQV P V V Sbjct: 266 KSDEGAQFDRVVELNAADIVPQVTWGTSPEMVTAVDGRVPDPEREKDPVKRDAMERALKY 325 Query: 290 ---KPVGEVEGTHVDQVFIGTCTNGRLEDLEVAAAVLK--GKQVAVR---TIVIPASRTT 341 +P +E D++FIG+CTN R+ED+ AA V+K G++VA +V+P S Sbjct: 326 MALEPNAPIESIKPDKIFIGSCTNARIEDIRAAAYVVKKLGRRVAPNIRLAMVVPGSGLV 385 Query: 342 LLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKGGFI 401 A G + AG PGC CL + L GE C ST+NRNF+GR G GG Sbjct: 386 KAQAEREGLDKVFTDAGFEWREPGCSMCLAMNADRLDPGERCASTSNRNFEGRQGAGGRT 445 Query: 402 YLASPATAAASALTGEITDPR 422 +L SPA AAA+A+ G D R Sbjct: 446 HLVSPAMAAAAAIEGHFVDIR 466 Lambda K H 0.318 0.135 0.400 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: 483 Number of extensions: 19 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: 424 Length of database: 469 Length adjustment: 32 Effective length of query: 392 Effective length of database: 437 Effective search space: 171304 Effective search space used: 171304 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 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