Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 206498 DVU1064 aconitate hydratase, putative
Query= curated2:O27668 (428 letters) >MicrobesOnline__882:206498 Length = 642 Score = 224 bits (570), Expect = 8e-63 Identities = 147/419 (35%), Positives = 207/419 (49%), Gaps = 11/419 (2%) Query: 4 MNMTEKILAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPE 63 +N T+KI+ ++ PG I R+D +T D T F + G RV + Sbjct: 3 LNQTQKIIKAHLVHGDMAPGAPIALRIDQTLTQDATGTMAYLQFEAM----GVDRV-RTD 57 Query: 64 RIVMVFDHNVPANTIGAAEFQRVTREFAREQGIVNIFQNAAGICHQVLPERGFVRPGMVI 123 V DHN A+ R R A GIV GICHQ+ E F RPG + Sbjct: 58 LSVSYVDHNTLQMGFRNADDHRFLRTVAARHGIV-FSAPGNGICHQLHLEN-FGRPGATL 115 Query: 124 VGADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVI 183 VG+DSHT T G GA A G G +A+ A +P+ + + + G G AKDVI Sbjct: 116 VGSDSHTPTAGGIGALAMGAGGLSVALSMAGEPYTITMPKVVNVRLEGRLTGWAAAKDVI 175 Query: 184 LHIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVR 243 LH++G + V G R E+TG + ++ V R TI NM E+GA I + T ++ Sbjct: 176 LHLLGLLTVKGGVGRVFEYTGPGVATLSVPERATITNMGAELGATTSIFPSDESTRAFL- 234 Query: 244 ARTGRE--FRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVHRVEGTHIDEAFL 301 A GRE ++ ++D + Y E+ D+S LEP VA P D V V + G +D+ + Sbjct: 235 AAMGREADWQPLAADAGAVYDEEVVIDLSQLEPLVATPHMPDRVVTVASLAGLKVDQVAI 294 Query: 302 GSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREIYLKALEDGIIETFIRAGAIVCN 361 GSCTN Y DLK A+V+ RRV ++SP S+++ +G++E + AG + Sbjct: 295 GSCTNSSYADLKSVAQVVAGRRVDSTTDCMISPGSKQVLRMLATEGLLEPLLDAGIRMLE 354 Query: 362 PGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAP 420 CGPC+G G G VS+ T NRNF GR G + VYLA+P A A+ G + P Sbjct: 355 CTCGPCIGMG-GSPVSGGVSVRTFNRNFEGRSGTKDAGVYLASPLTAAMVALHGGFTDP 412 Lambda K H 0.320 0.137 0.408 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: 665 Number of extensions: 40 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: 428 Length of database: 642 Length adjustment: 35 Effective length of query: 393 Effective length of database: 607 Effective search space: 238551 Effective search space used: 238551 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.8 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