Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_086508765.1 BZY95_RS04400 3-isopropylmalate dehydratase large subunit
Query= curated2:Q8PZT3 (391 letters) >NCBI__GCF_002151265.1:WP_086508765.1 Length = 481 Score = 235 bits (600), Expect = 2e-66 Identities = 143/360 (39%), Positives = 194/360 (53%), Gaps = 45/360 (12%) Query: 75 EGICHQVLPENGFALPGKLLVGADSHSCTYGAFGAFATGVGATDMAEIFATGKLWFKVPE 134 +GI H V PE G LPG +V DSH+ T+GAF A A G+G +++ + AT L + + Sbjct: 111 QGIVHVVGPEQGATLPGMTVVCGDSHTATHGAFAALAHGIGTSEVEHVLATQCLLAQKMK 170 Query: 135 SFRMTVEGSLDKHVYAKDLTLYLIGKTGIAGATYKAVEFYGQAISELSVAGRMTLCNMAI 194 + ++ VEG L V AKD+ L +IGK G AG T A+EF G AI +LS+ GRMT+CNMAI Sbjct: 171 NMQVRVEGKLGTGVTAKDVVLAIIGKIGTAGGTGYAIEFAGSAIRDLSMEGRMTVCNMAI 230 Query: 195 EMGAKTGIVPPDEKTFDFLKNR-----------AVAPYEPVYSDPDASYLKEFVYDAGDI 243 E GA+ G++ D+ T ++L R AVA + + SD DA + K DA +I Sbjct: 231 EAGARVGLIAVDDTTIEYLAERPFAPRGEQWQAAVADWRNLVSDADARFDKVVTLDAAEI 290 Query: 244 EPQVA---CPHQV---------------DNVK-------------PVGEVEGTHVDQVFI 272 EPQV+ P V D VK P ++ +D+VFI Sbjct: 291 EPQVSWGTSPEMVTGISGEVPDPAEQNDDTVKRGYTRALEYMGLAPKQKITEIKLDKVFI 350 Query: 273 GTCTNGRLEDLEVAASVLKGKKVT---VRTIIIPASRSTLLAAIKNGTMEILLKAGVTLA 329 G+CTN R+EDL AA V +GKKV +++P S A G ++ ++AG Sbjct: 351 GSCTNSRIEDLREAAKVARGKKVADSIKLAMVVPGSGLVKRQAEAEGLDKVFIEAGFEWR 410 Query: 330 TPGCGPCLGAHQGVLGEGEVCVSTANRNFKGRMGKDGFIYLASPATAAASALTGEITDPR 389 PGC CL + LG GE C ST+NRNF+GR G G +L SPA AAA+A+ G D R Sbjct: 411 EPGCSMCLAMNADKLGAGEHCASTSNRNFEGRQGYGGRTHLVSPAMAAAAAIAGHFVDVR 470 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: 438 Number of extensions: 24 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 391 Length of database: 481 Length adjustment: 32 Effective length of query: 359 Effective length of database: 449 Effective search space: 161191 Effective search space used: 161191 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: 51 (24.3 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