Align Probable methanogen homoaconitase large subunit; HACN; EC 4.2.1.114; Homoaconitate hydratase (uncharacterized)
to candidate 8501056 DvMF_1792 3-isopropylmalate dehydratase large subunit (RefSeq)
Query= curated2:O27668 (428 letters) >FitnessBrowser__Miya:8501056 Length = 418 Score = 390 bits (1003), Expect = e-113 Identities = 205/416 (49%), Positives = 275/416 (66%), Gaps = 6/416 (1%) Query: 6 MTEKILAEAAGLREVTPGEIIEARVDLAMTHDGTSPPTIRTFRDIASRGGPARVWDPERI 65 + +KIL G+I+ RV LA+ +D T+P I++FR + G +V+D +++ Sbjct: 5 LAQKILQAHTDEAITAAGQIVRCRVSLALANDITAPLAIKSFRAM----GAKKVFDRDKV 60 Query: 66 VMVFDHNVPANTIGAAEFQRVTREFAREQGIVNIFQNA-AGICHQVLPERGFVRPGMVIV 124 +V DH P I +A+ ++TREFARE G+ + ++ G+ H +LPE G V PG V+V Sbjct: 61 ALVMDHFTPQKDIASAQQVKLTREFAREMGVTHYYEGGDCGVEHALLPELGLVGPGDVVV 120 Query: 125 GADSHTCTYGAFGAFATGMGATDMAMVFATGKTWFMVPEAMRIEVTGEPEGHVYAKDVIL 184 GADSHTCTYG GAFATG G+TD+A A G+TWF VP +R TG V AKD+IL Sbjct: 121 GADSHTCTYGGLGAFATGFGSTDVAGAMALGETWFKVPPTIRATFTGTLPKWVGAKDLIL 180 Query: 185 HIIGEIGVDGATYRSVEFTGDTIESMDVSGRMTICNMAVEMGAKNGIMEPNRQTLDYVRA 244 +IGEIGVDGA YR++EF G IE++ V GRMTI NMA+E G K G+ + +TL Y A Sbjct: 181 RLIGEIGVDGALYRALEFDGAAIEALSVEGRMTIANMAIEAGGKAGLFAADAKTLAYTAA 240 Query: 245 RTGREFRVYSSDEDSQYLEDHHFDVSDLEPQVACPDDVDNVYPVHRVEGTHIDEAFLGSC 304 R GR+ S+D + Y + FDVS +EP VACP +NV PV V G +D+ +GSC Sbjct: 241 R-GRKDAPLSADPGATYERELTFDVSGMEPLVACPHLPENVKPVGEVRGVTLDQVVIGSC 299 Query: 305 TNGRYEDLKIAAEVIGDRRVHEDVRFIVSPASREIYLKALEDGIIETFIRAGAIVCNPGC 364 TNGR D++ AAEV+ R+V + VR IV PA+ ++ +AL++G+IETF+ +G IV C Sbjct: 300 TNGRISDMREAAEVLKGRKVAKGVRCIVLPATPGVWKEALKEGLIETFMESGCIVGPATC 359 Query: 365 GPCLGAHMGVLAPGEVSIATTNRNFRGRMGDPASSVYLANPAVVAESAIEGVISAP 420 GPCLG HMG+LA GE +IATTNRNFRGRMG S VYLA+PAV A SA+ G+I+ P Sbjct: 360 GPCLGGHMGILADGERAIATTNRNFRGRMGSLESEVYLASPAVAAASAVAGIIAHP 415 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: 530 Number of extensions: 26 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: 418 Length adjustment: 32 Effective length of query: 396 Effective length of database: 386 Effective search space: 152856 Effective search space used: 152856 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: 50 (23.9 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