Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_011386418.1 AMB_RS20560 3-isopropylmalate dehydratase large subunit
Query= curated2:Q8PZT3 (391 letters) >NCBI__GCF_000009985.1:WP_011386418.1 Length = 467 Score = 248 bits (632), Expect = 3e-70 Identities = 157/440 (35%), Positives = 227/440 (51%), Gaps = 54/440 (12%) Query: 5 VDYAMAHDGTSILAVNAFKEMEMERVWDPSRIVIPFDHIAPANTETSATLQKEIREWVR- 63 +D M H+ TS A EM +V P + DH P + +E R V Sbjct: 29 IDRHMVHEVTSPQAFEGL-EMSGRKVRHPELTLAVADHNVPTTDRSKGIENEESRIQVET 87 Query: 64 -EQSIPNFY-------EIGEGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATGVG 115 E + F +I +G+ H V PE GF LPG +V DSH+ T+GAFG+ A G+G Sbjct: 88 LEANAKKFGVEYLRMDDIRQGVVHIVGPEQGFTLPGTTIVCGDSHTATHGAFGSLAFGIG 147 Query: 116 ATDMAEIFATGKLWFKVPESFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEFYG 175 +++ + AT L K ++ R+TV G V AKD+ L +IGK G AG T VEF G Sbjct: 148 TSEVEHVLATQTLVQKPAKNMRITVTGKPGPGVTAKDIVLAIIGKIGTAGGTGYVVEFAG 207 Query: 176 QAISELSVAGRMTLCNMAIEMGAKTGIVPPDEKTFDFLKNR-----------AVAPYEPV 224 +AI +LS+ GRMT+CNM IE GA+ G+V PDEKTF ++ + AV+ ++ + Sbjct: 208 EAIRDLSMEGRMTVCNMTIEAGARAGLVAPDEKTFAYIAGKPRSPKGAAFEAAVSYWKTL 267 Query: 225 YSDPDASYLKEFVYDAGDIEPQV-----------------------------ACPHQVDN 255 ++D A + E DA + PQ+ A +D Sbjct: 268 FTDEGAHFDAEVTLDASTLVPQITWGTSPEDVIAITGTVPNPADIKDEAKRKAVERSLDY 327 Query: 256 VKPVGEVEGTH--VDQVFIGTCTNGRLEDLEVAASVLKGKKV--TVRTIIIPASRSTLLA 311 + ++ T +D VFIG+CTNGR+ED AA + KG+KV +V+ +I+P S Sbjct: 328 MGLTAGMKATDIAIDVVFIGSCTNGRIEDFRAAAEIFKGRKVAASVQALIVPGSGLVKEQ 387 Query: 312 AIKNGTMEILLKAGVTLATPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDGFIYLA 371 A + G +I ++AG PGC CL + L G+ ST+NRNF+GR G+ G +L Sbjct: 388 AEQEGLDKIFIEAGAEWREPGCSMCLAMNADQLKPGQRSASTSNRNFEGRQGRGGRTHLV 447 Query: 372 SPATAAASALTGEITDPRKI 391 SPA AAA+A+TG++TD R + Sbjct: 448 SPAMAAAAAITGKLTDVRSL 467 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: 438 Number of extensions: 15 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: 391 Length of database: 467 Length adjustment: 32 Effective length of query: 359 Effective length of database: 435 Effective search space: 156165 Effective search space used: 156165 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