Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_028315364.1 G491_RS0116380 aconitate hydratase
Query= SwissProt::Q9ZNE0 (418 letters) >NCBI__GCF_000429905.1:WP_028315364.1 Length = 640 Score = 235 bits (600), Expect = 3e-66 Identities = 153/415 (36%), Positives = 212/415 (51%), Gaps = 12/415 (2%) Query: 5 LAEKILSHKVGRPV-RAGELVVVEVDQVMVVDSIAGSFFKRLEYLEATPRYPERVSIVID 63 L EKILSH P+ G + + +DQ + D+ + E L + +D Sbjct: 3 LFEKILSHHGIDPIPEPGTPIRLPIDQTLTQDATGTMACLQFEALGIDKVKADLSVSYVD 62 Query: 64 HVAPAANLEVAKAQKEIREWGKRHGIRVFDVGRGVCHQVLIEEGLAQPGWVVVGSDSHST 123 H + + +R ++G+ + G G+CHQ+ +E PG ++GSDSH+ Sbjct: 63 HNTLQSGFYNFDDHRFLRTIAAKYGMVFSEPGNGICHQLNLER-FGVPGRTLLGSDSHTP 121 Query: 124 TYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRGRLPKGVTAKDAALEMVRLLT 183 T G +G G G D+A+A A L +PE V V G+LP V AKD LE++R T Sbjct: 122 TGGGIGMVAIGAGGLDVAMAMAGEPFTLPMPEVVSVHLTGQLPAWVAAKDVILEVLRRET 181 Query: 184 AEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAGLVVPSGEILEMYRVPD---- 239 +G E + GA L+ ER T+ N+ E GA L L R Sbjct: 182 VKGGVGKVYE-YTGPGAATLSVTERATITNMGAELGATTSLFSSDDNTLAFLRAQGREDV 240 Query: 240 W--LYPDPDARYAKEVEIDLSALTPRVSVPFYVDNVHEVAQVKGKRVDQVFIGTCTNGRI 297 W L PD DA+Y++ +EIDLS L P + P D V EV +++G +VDQV IG+CTN Sbjct: 241 WTRLEPDADAKYSRVIEIDLSKLVPLAACPHMPDLVKEVRELEGTQVDQVVIGSCTNSSY 300 Query: 298 EDLRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPGCGPCMG 357 +DL A ++RG+++ P V L++ P S QVL A G L++AGA I CGPC+G Sbjct: 301 KDLATVAAMVRGKRIPPEVSLVIAPGSRQVLTMLADSGEFTDLIKAGARIMECACGPCIG 360 Query: 358 RHMGVLAP-GEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYLTTPEEL 411 MG P G V V T NRNF+GR G DA YL SP AAA+A+AG P +L Sbjct: 361 --MGQAPPSGGVTVRTMNRNFKGRCGTKDAGAYLVSPETAAATALAGKFADPRDL 413 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: 567 Number of extensions: 29 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: 640 Length adjustment: 35 Effective length of query: 383 Effective length of database: 605 Effective search space: 231715 Effective search space used: 231715 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: 52 (24.6 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