Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate AZOBR_RS03545 AZOBR_RS03545 isopropylmalate isomerase
Query= curated2:O27668 (428 letters) >FitnessBrowser__azobra:AZOBR_RS03545 Length = 467 Score = 226 bits (575), Expect = 1e-63 Identities = 149/437 (34%), Positives = 214/437 (48%), Gaps = 57/437 (13%) Query: 30 VDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERIVMVFDHNVPANTIGAAEFQRVTR- 88 +D + H+ TSP + F + G P R PE + V DHNVP + +R Sbjct: 29 IDRHLVHEVTSP---QAFEGLRLAGRPVR--RPEATLAVPDHNVPTTDRSKGIVEEESRI 83 Query: 89 ------EFAREQGIVNIFQNAA--GICHQVLPERGFVRPGMVIVGADSHTCTYGAFGAFA 140 + AR+ G+ + GI H V PE+GF PG IV DSHT T+GAFGA A Sbjct: 84 QVETLDKNARDFGVRYFPMDDVRQGIVHIVGPEQGFTLPGATIVCGDSHTATHGAFGALA 143 Query: 141 TGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVILHIIGEIGVDGATYRSV 200 G+G +++ V AT + M + V GE V AKD++L IIG IG G T + Sbjct: 144 FGIGTSEVEHVLATQTLLQKPAKNMLVRVDGELPAGVTAKDIVLAIIGRIGTAGGTGHVI 203 Query: 201 EFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRAR-----------TGRE 249 EF GD I + + GRMT+CNMA+E GA+ G++ P+ +T +YV+ R Sbjct: 204 EFAGDAIRGLSMEGRMTVCNMAIEGGARAGLIAPDEKTFEYVKGRALAPKAGAWEQAVEY 263 Query: 250 FRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPV--------------------- 288 ++ SDE + Y + +D+ PQV ++V P+ Sbjct: 264 WKTLPSDEGAVYDTTVVLNAADIVPQVTWGTSPEDVLPITATVPNPADVADAGKRAAVER 323 Query: 289 ----------HRVEGTHIDEAFLGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASRE 338 ++ +D F+GSCTNGR EDL+ AA + R+V E VR +V P S Sbjct: 324 SLAYMGLEPGQKLTDVKVDTVFIGSCTNGRIEDLRAAAVIAQGRKVAEGVRALVVPGSGL 383 Query: 339 IYLKALEDGIIETFIRAGAIVCNPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPAS 398 + +A E+G+ + F AG PGC CL + L+PGE S +T+NRNF GR G Sbjct: 384 VKDQAEEEGLDKIFTEAGFEWREPGCSMCLAMNADRLSPGERSASTSNRNFEGRQG-RGG 442 Query: 399 SVYLANPAVVAESAIEG 415 +L +PA+ A +A+ G Sbjct: 443 RTHLLSPAMAAAAAVTG 459 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: 571 Number of extensions: 27 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: 467 Length adjustment: 33 Effective length of query: 395 Effective length of database: 434 Effective search space: 171430 Effective search space used: 171430 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: 51 (24.3 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