Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_014027416.1 PYRFU_RS09265 3-isopropylmalate dehydratase large subunit
Query= SwissProt::Q9ZNE0 (418 letters) >NCBI__GCF_000223395.1:WP_014027416.1 Length = 422 Score = 353 bits (905), Expect = e-102 Identities = 196/418 (46%), Positives = 261/418 (62%), Gaps = 9/418 (2%) Query: 2 GQTLAEKILSHKVGRPVRAGELVVVEVDQVMVVDSIAGSFFK--RLEYLEATPRYPERVS 59 GQT EK+ S + GR V GE+VVV+VD V D A + R E+ P+R Sbjct: 3 GQTFVEKLFSLRTGRRVSPGEIVVVDVDVVYAQDGTAPLAIRVMREEFGVERVAKPDRTL 62 Query: 60 IVIDHVAPAANLEVAKAQKEIREWGKRHGIRVFDVGRGVCHQVLIEEGLAQPGWVVVGSD 119 IDHV+P++N + + + +RE+ RHGIR++DVG G+ HQV+ EEG PG VVVG+D Sbjct: 63 FFIDHVSPSSNPDTSALHRLMREFAARHGIRLYDVGMGISHQVVFEEGWVVPGAVVVGAD 122 Query: 120 SHSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRGRLPKGVTAKDAALEMV 179 SH+ T GAVGAF TG+G+TD A A SGR W RVPE+++V RG L V KD AL+++ Sbjct: 123 SHTVTGGAVGAFATGVGSTDAAAAMVSGRLWFRVPEAIRVWLRGSLSGPVLGKDVALKLL 182 Query: 180 RLLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAGLVVPSGEILEMYR--- 236 +L + GA+Y ++E DG ++L+ R+T+AN++VE GAK P + E R Sbjct: 183 SILGSSGASYKSLEFWG-DGVKSLSLASRLTIANMSVEMGAKNAYFPPDERVFEHLRNVG 241 Query: 237 --VPDW-LYPDPDARYAKEVEIDLSALTPRVSVPFYVDNVHEVAQVKGKRVDQVFIGTCT 293 VP +YPDPDA Y+ E+E++L + P V++P N V +V+G VDQVFIG+CT Sbjct: 242 AKVPVRPIYPDPDAVYSDEIEVELDKVEPMVALPPNPSNAKPVTEVEGLEVDQVFIGSCT 301 Query: 294 NGRIEDLRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPGCG 353 NGR ED AAA VL+GRKV P VR + VPAS +V + G + L+EAG + CG Sbjct: 302 NGREEDFEAAARVLKGRKVHPRVRCIAVPASRRVYMNLLKRGIIDILVEAGCIVTHSTCG 361 Query: 354 PCMGRHMGVLAPGEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYLTTPEEL 411 PC+G H G+L P EV V T+NRNF GR G A+I LASP AAA+AV G L P L Sbjct: 362 PCVGAHFGLLGPEEVGVFTTNRNFPGRAGHRSAKIILASPYTAAAAAVTGKLVDPRSL 419 Lambda K H 0.318 0.135 0.393 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: 461 Number of extensions: 26 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: 418 Length of database: 422 Length adjustment: 32 Effective length of query: 386 Effective length of database: 390 Effective search space: 150540 Effective search space used: 150540 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: 50 (23.9 bits)
This GapMind analysis is from Apr 10 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