Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate WP_012536129.1 AFE_RS01995 aconitate hydratase
Query= SwissProt::Q9ZNE0 (418 letters) >NCBI__GCF_000021485.1:WP_012536129.1 Length = 645 Score = 235 bits (599), Expect = 3e-66 Identities = 156/428 (36%), Positives = 219/428 (51%), Gaps = 18/428 (4%) Query: 1 MGQTLAEKILS-HKVGRPVRAGELVVVEVDQVMVVDSIAGSFFKRLEYLEATPRYPERVS 59 M + +KIL+ H V + AG + + +DQ + D+ + + E L PR +S Sbjct: 1 MAMNVTQKILAAHLVSGTLEAGSPIAIRIDQTLTQDATGTMAYLQFEAL-GLPRVRTELS 59 Query: 60 I-VIDHVAPAANLEVAKAQKEIREWGKRHGIRVFDVGRGVCHQVLIEEGLAQPGWVVVGS 118 + +DH + E A + ++ + ++G+ G G+CHQV +E ++PG ++GS Sbjct: 60 VSYVDHNMLQSGFENADDHRFLQSFAAKYGVHFSRPGNGICHQVHLER-FSRPGGTLLGS 118 Query: 119 DSHSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRGRLPKGVTAKDAALEM 178 DSH+ T G G G G DIALA L +P+ V V GRL V+AKD LE+ Sbjct: 119 DSHTPTSGGAGMLAIGAGGLDIALAMGGLPFNLNMPQVVGVKLTGRLQPFVSAKDIILEV 178 Query: 179 VRLLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAGLVVPSGEILEMYRVP 238 +R T +G E + G L+ ER T+ N+ E GA V PS + Y Sbjct: 179 LRHKTVKGGVGKVFE-YFGPGVAHLSVPERATITNMGAELGATTS-VFPSDAVTRRYLAA 236 Query: 239 --------DWLYPDPDARYAKEVEIDLSALTPRVSVPFYVDNVHEVAQVKGKRVDQVFIG 290 +W+ D DA Y + +EIDL L P ++ P DNV +V +V G V QV IG Sbjct: 237 QGRDAFWSEWV-ADADADYDEVLEIDLDQLEPLIACPHSPDNVRKVREVAGTPVAQVAIG 295 Query: 291 TCTNGRIEDLRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTP 350 +CTN DL A +L+G+ VA V L V P S QV+E RDG LL + AG+ I Sbjct: 296 SCTNSSYTDLMTVASMLKGKVVADGVSLGVSPGSRQVMEMVTRDGGLLDFIGAGSRILES 355 Query: 351 GCGPCMGRHMGVLAPGE-VCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYLTTPE 409 CGPC+G MG P E V V + NRNF GR G +A +YLASP AA A+ G +T P Sbjct: 356 ACGPCIG--MGFAPPTEGVSVRSFNRNFYGRSGTKNAAVYLASPETCAACALTGVITDPR 413 Query: 410 ELEEEEVH 417 +L +H Sbjct: 414 DLGLAPIH 421 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: 585 Number of extensions: 30 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: 645 Length adjustment: 35 Effective length of query: 383 Effective length of database: 610 Effective search space: 233630 Effective search space used: 233630 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