Align Homoaconitase large subunit; HACN; Homoaconitate hydratase; EC 4.2.1.36 (characterized)
to candidate 8502313 DvMF_3021 aconitate hydratase (RefSeq)
Query= SwissProt::Q9ZNE0 (418 letters) >FitnessBrowser__Miya:8502313 Length = 641 Score = 229 bits (583), Expect = 2e-64 Identities = 153/416 (36%), Positives = 207/416 (49%), Gaps = 12/416 (2%) Query: 1 MGQTLAEKILS-HKVGRPVRAGELVVVEVDQVMVVDSIAGSFFKRLEYLEATPRYPERVS 59 M L +KI++ H V + G + + +DQ + D+ + + E + + Sbjct: 1 MSMNLTQKIIAAHLVSGEMAPGAEIGLRIDQTLTQDATGTMAYLQFEAMGVDRVRTDLSV 60 Query: 60 IVIDHVAPAANLEVAKAQKEIREWGKRHGIRVFDVGRGVCHQVLIEEGLAQPGWVVVGSD 119 +DH + +R +HG+ G G+CHQ+ +E A PG +VGSD Sbjct: 61 SYVDHNTLQMGFRNPDDHRFLRTVAAKHGVIFSPPGTGICHQLHLEN-FALPGATLVGSD 119 Query: 120 SHSTTYGAVGAFGTGMGATDIALAAASGRTWLRVPESVKVVFRGRLPKGVTAKDAALEMV 179 SH+ T G +G+ G G +ALA A ++ +P V+V GRL +AKD L ++ Sbjct: 120 SHTPTAGGIGSLAMGAGGLSVALAMAGEPYFISMPRVVRVRLEGRLTGWASAKDVILHLL 179 Query: 180 RLLTAEGATYMAVEIHLLDGAEALTRGERMTLANLTVEAGAKAGLVVPSGE-----ILEM 234 LLT +G E G L+ ER + N+ E GA A L PS E + M Sbjct: 180 GLLTVKGGVGKVFEF-AGPGVATLSVPERAVITNMGAELGATASLF-PSDERTRAFLASM 237 Query: 235 YRVPDW--LYPDPDARYAKEVEIDLSALTPRVSVPFYVDNVHEVAQVKGKRVDQVFIGTC 292 R DW L D DA Y E+ IDLSAL P V+ P D V VA++ G VDQV IG+C Sbjct: 238 DREGDWKPLAADADATYDDEIVIDLSALVPLVAQPHMPDRVVPVAELAGLSVDQVAIGSC 297 Query: 293 TNGRIEDLRAAAEVLRGRKVAPWVRLLVVPASSQVLEEAARDGTLLTLLEAGATIGTPGC 352 TN D+R AEVLRGR V +V P S QVL+ A +G + LL+AG I C Sbjct: 298 TNSSYADMRMVAEVLRGRMVHVGTDTMVSPGSKQVLKMLAAEGLVEPLLDAGVRILECSC 357 Query: 353 GPCMGRHMGVLAPGEVCVSTSNRNFRGRMGAPDAEIYLASPRVAAASAVAGYLTTP 408 GPC+G G G V V T NRNF GR G DA++YL SP AA +A+ G T P Sbjct: 358 GPCIGMG-GSPVSGGVSVRTFNRNFEGRSGTKDAKVYLVSPLTAAMAALHGQFTDP 412 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: 603 Number of extensions: 33 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: 641 Length adjustment: 35 Effective length of query: 383 Effective length of database: 606 Effective search space: 232098 Effective search space used: 232098 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 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