Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate Synpcc7942_0903 Synpcc7942_0903 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:Q8PZT3 (391 letters) >FitnessBrowser__SynE:Synpcc7942_0903 Length = 861 Score = 97.1 bits (240), Expect = 2e-24 Identities = 96/356 (26%), Positives = 139/356 (39%), Gaps = 55/356 (15%) Query: 74 GEGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATGVGATDMAEIFATGKLWFKVP 133 G+GI H L N LP + G DSH+ + +F G G A A G + +P Sbjct: 465 GDGIIHSWL--NRMLLPDTVGTGGDSHT-RFPLGISFPAGSGLVAFAA--AIGAMPLDMP 519 Query: 134 ESFRMTVEGSLDKHVYAKD--------------LTLYLIGKTGIAGATYKAVEFYGQAIS 179 ES + GSL + +D LT+ K + +E + Sbjct: 520 ESVLVRFTGSLQPGITLRDVVNAIPYQAIQQGLLTVSKENKVNVFSGRIMEIE----GLP 575 Query: 180 ELSVAGRMTLCNMAIEMGAKTGIVPPDEKTFD--------FLKNRAVAPYEP-------- 223 +L + L + E + E T +KN YE Sbjct: 576 DLKLEQAFELTDATAERSCAGSTIKLSEDTVAEYLRSNVALMKNMIARGYEDSRTLARRI 635 Query: 224 ------------VYSDPDASYLKEFVYDAGDI-EPQVACPHQVDNVKPVGEVEGTHVDQV 270 + +D DA Y + ++ EP +ACP+ DNVK + EV G + ++ Sbjct: 636 RQMEDWLANPQLLSADEDAEYAAVIEINLDELTEPILACPNDPDNVKKLSEVAGDPIHEI 695 Query: 271 FIGTCTNGRLEDLEVAASVLKGK-KVTVRTIIIPASRSTLLAAIKNGTMEILLKAGVTLA 329 FIG+C + AA VL+G+ +V R I P +R + G AG L Sbjct: 696 FIGSCMT-NIGHYRAAAKVLEGEGQVGGRLWICPPTRMDEDRLKEEGYYSTFAAAGARLE 754 Query: 330 TPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDGFIYLASPATAAASALTGEI 385 PGC C+G +Q + + ST+ RNF RMGK +YL S AA AL G I Sbjct: 755 VPGCSLCMG-NQARVADNTTVFSTSTRNFNNRMGKGAQVYLGSAELAAVCALLGRI 809 Lambda K H 0.318 0.135 0.401 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: 696 Number of extensions: 29 Number of successful extensions: 3 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: 391 Length of database: 861 Length adjustment: 36 Effective length of query: 355 Effective length of database: 825 Effective search space: 292875 Effective search space used: 292875 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: 53 (25.0 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