Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate WP_028313822.1 G491_RS0105155 3-isopropylmalate dehydratase large subunit
Query= curated2:O27668 (428 letters) >NCBI__GCF_000429905.1:WP_028313822.1 Length = 419 Score = 404 bits (1037), Expect = e-117 Identities = 198/418 (47%), Positives = 287/418 (68%), Gaps = 5/418 (1%) Query: 4 MNMTEKILAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPE 63 M + EKILA AG E +PG++I A+VD+A+ +D T+P I+ FR + G A+V+D + Sbjct: 3 MTIAEKILAAHAGQEEASPGDLINAKVDIALGNDITAPIAIKLFR----QSGAAKVFDKD 58 Query: 64 RIVMVFDHNVPANTIGAAEFQRVTREFAREQGIVNIFQNA-AGICHQVLPERGFVRPGMV 122 R+V+V DH P I +A ++ R+FAREQ + + ++ +G+ H +LPE+G V PG + Sbjct: 59 RVVLVPDHFTPTKDINSAMQVKMVRDFAREQELSHWYEGGDSGVEHALLPEKGIVGPGDL 118 Query: 123 IVGADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDV 182 ++GADSHTCTYG GAFATG+G+TD+A TG+ W VPE+++ G+ HV KD+ Sbjct: 119 VIGADSHTCTYGGLGAFATGVGSTDLAAAMITGEVWLKVPESIKFVYKGKLRPHVEGKDL 178 Query: 183 ILHIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYV 242 ILH IG+IGVDGA Y ++EFTG+ I+++ ++ R+T+ NMA+E G K GI+ P+ T +Y Sbjct: 179 ILHTIGDIGVDGALYMAMEFTGEVIDALPMAERLTMANMAIEAGGKAGIIAPDATTKEYA 238 Query: 243 RARTGREFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVHRVEGTHIDEAFLG 302 R R+ Y+SD D++Y + +DV+DLEPQVA P +N P+ +V I + +G Sbjct: 239 DGRVIRKPVFYASDPDAKYAKVIEYDVTDLEPQVAFPHLPENTRPISQVGDVPIHQVIIG 298 Query: 303 SCTNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREIYLKALEDGIIETFIRAGAIVCNP 362 SCTNGR ED++ AA ++ + ++VR I+ PA+ +IY +A+E+G+ +TF+ AGA++ P Sbjct: 299 SCTNGRIEDMRSAARILTGNKADKNVRLIIIPATPQIYRQAMEEGLFDTFLSAGAVISPP 358 Query: 363 GCGPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAP 420 CGPCLG HMG+LA GE ++ATTNRNF GRMG S VYLANPAV A SAI G I+ P Sbjct: 359 TCGPCLGGHMGILAAGERAVATTNRNFVGRMGHVESEVYLANPAVAAASAIAGKIAGP 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: 525 Number of extensions: 27 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