Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 3606654 Dshi_0085 3-isopropylmalate dehydratase, large subunit (RefSeq)
Query= curated2:Q8TLF1 (424 letters) >FitnessBrowser__Dino:3606654 Length = 467 Score = 270 bits (689), Expect = 9e-77 Identities = 172/463 (37%), Positives = 248/463 (53%), Gaps = 57/463 (12%) Query: 14 TISEKIFSRAAGTEAKANDFVLADVDYAMAHDGTSVLAVNAFKEMEMEKVWDPSRIVVPF 73 T+ +KI+ EA+ +L +D + H+ TS A + M V P + + Sbjct: 5 TLYDKIWDAHLAHEAEDGTCLLY-IDRHLVHEVTSPQAFEGLR-MAGRTVRAPDKTIAVP 62 Query: 74 DHIAPAN---------NETSATLQREIREWVKEQGIPNFYEVGE---GICHQVLPENGFA 121 DH P E S + + K+ GI ++Y V + GI H V PE G+ Sbjct: 63 DHNVPTTLGRENPDQMTEDSRIQVEALDKNAKDFGI-HYYPVSDIRQGIVHIVGPEQGWT 121 Query: 122 LPGKLVVGADSHSCTYGAFGAFATGVGATDMAEIFATGKLWFKVPESFRMTVEGSLRKGV 181 LPG VV DSH+ T+GAFGA A G+G +++ + AT L K ++ ++ + G LR GV Sbjct: 122 LPGMTVVCGDSHTATHGAFGALAHGIGTSEVEHVLATQTLIQKKSKNMKVEITGKLRPGV 181 Query: 182 YAKDLTLYLIGKTGIAGATYKAVEFYGQAIRELTVAGRMTLCNMAIEMGAKTGIVPPDEK 241 AKD+TL +IG TG AG T +E+ G+AIR+L++ GRMT+CNMAIE GA+ G++ PDEK Sbjct: 182 TAKDITLSVIGATGTAGGTGYVIEYCGEAIRDLSMEGRMTVCNMAIEGGARAGLIAPDEK 241 Query: 242 TFEFLKNR-----------AAATYEPVYADPDAVYLEEFTYDADDIEPQVACPHQVDNVK 290 T+E+++ R A A ++ +Y+D DA + + T +DI P V ++V Sbjct: 242 TYEYVQGRPHAPKGAQWEAALAWWKTLYSDDDAHWDKVVTIKGEDIAPVVTWGTSPEDVL 301 Query: 291 PV------------GEVEGT------------------HVDQVFIGTCTNGRLEDLEVAA 320 P+ G+V+ +D VFIG+CTNGR+EDL AA Sbjct: 302 PISAMVPAPEDFTGGKVDAARRSLDYMGLTPGTPLSEIEIDTVFIGSCTNGRIEDLRAAA 361 Query: 321 AVLKGKQVAV-RTIVIPASRTTLLAAIENGTMETLLKAGVTLATPGCGPCLGAHQGVLGE 379 +LKGK++AV R +V+P S A E G + +AG GC CL + L E Sbjct: 362 EILKGKKIAVKRAMVVPGSGLVRAQAEEEGLADIFKQAGFEWRMAGCSMCLAMNPDQLSE 421 Query: 380 GEVCVSTANRNFKGRMGKGGFIYLASPATAAASALTGEITDPR 422 GE C ST+NRNF+GR G G +L SPA AAA+A+TG++TD R Sbjct: 422 GERCASTSNRNFEGRQGYKGRTHLVSPAMAAAAAVTGKLTDVR 464 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: 545 Number of extensions: 20 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: 424 Length of database: 467 Length adjustment: 32 Effective length of query: 392 Effective length of database: 435 Effective search space: 170520 Effective search space used: 170520 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