Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_018123429.1 B149_RS0101705 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_000375485.1:WP_018123429.1 Length = 419 Score = 391 bits (1004), Expect = e-113 Identities = 198/420 (47%), Positives = 276/420 (65%), Gaps = 5/420 (1%) Query: 2 VKMNMTEKILAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWD 61 + + EKIL + PG+I++ RV + +D T+P I+ FR++ G +V+D Sbjct: 1 MSQTLAEKILQQHTDETVEGPGQIVQCRVSGVLANDITAPLAIKAFREM----GAKKVFD 56 Query: 62 PERIVMVFDHNVPANTIGAAEFQRVTREFAREQGIVNIFQ-NAAGICHQVLPERGFVRPG 120 +R+ +V DH P I +AE +V REFA E G+ N ++ G+ H +LPE+G V PG Sbjct: 57 QDRVFLVCDHFTPNRDIDSAEQVKVVREFAEEMGVTNYYECGDVGVEHALLPEKGLVGPG 116 Query: 121 MVIVGADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAK 180 +++GADSHTCTYG GAFATGMG+TD+ A G+TWF VP +R++VTG+ +V AK Sbjct: 117 DIVIGADSHTCTYGGLGAFATGMGSTDIGAAMALGETWFKVPPTIRVQVTGKASQYVGAK 176 Query: 181 DVILHIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLD 240 DV+L++IG IGV GA Y+++EF G+TI M V GRMTI NMA+E G K G+ + +T+D Sbjct: 177 DVMLNLIGRIGVAGALYKALEFGGETIADMTVEGRMTIANMAIEAGGKVGLFAADGKTID 236 Query: 241 YVRARTGREFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVHRVEGTHIDEAF 300 YV + + + D D+QY DV+ +EPQVACP DNV PV G I +A Sbjct: 237 YVVEAGRKNAEMLAPDPDAQYERVVDIDVNGMEPQVACPHLPDNVKPVDETAGLKIHQAV 296 Query: 301 LGSCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREIYLKALEDGIIETFIRAGAIVC 360 +GSCTNGR ED++ AA ++ +R+V + VR IV PA+ +I+ L +G++E F++AG IV Sbjct: 297 IGSCTNGRIEDMREAAAILKNRKVDKSVRCIVLPATPKIWQDCLSEGLMEIFMQAGCIVG 356 Query: 361 NPGCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAP 420 P CGPCLG HMG+LA GE +IATTNRNF+GRMG S V+L+NP+V A SA+ G I P Sbjct: 357 PPTCGPCLGGHMGILAGGERAIATTNRNFKGRMGSLESEVFLSNPSVAAASAVAGEIIHP 416 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: 524 Number of extensions: 25 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: 428 Length of database: 419 Length adjustment: 32 Effective length of query: 396 Effective length of database: 387 Effective search space: 153252 Effective search space used: 153252 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 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