Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate BPHYT_RS23060 BPHYT_RS23060 3-isopropylmalate dehydratase large subunit
Query= BRENDA::Q58409 (420 letters) >FitnessBrowser__BFirm:BPHYT_RS23060 Length = 655 Score = 194 bits (494), Expect = 5e-54 Identities = 148/448 (33%), Positives = 214/448 (47%), Gaps = 43/448 (9%) Query: 2 TLVEKILSK-----KVGYEVCAGDSIEVEVDLAMTHDGTTPLAYKALKEMSDS---VWNP 53 TLVEKI+ + VG + GD + + D +HD T + + + P Sbjct: 208 TLVEKIIERHLHPASVGAQ--RGDGVFIAADWRFSHDYFTGMCAHLMHRAFGKPAPLHAP 265 Query: 54 DKIVVAFDH------NVP-------PNTVKAAEMQ-KLALEF-VKRFGIKNFHKGGEGIC 98 D I+ DH ++P P E + ++ V+ G + G EGIC Sbjct: 266 DHIIAFQDHLVLASQSIPHVRDGLLPGVANLMEGHTSFSRDYPVRSHGALDGMPGSEGIC 325 Query: 99 HQILAENYVLPNMFVAGGDSHTCTHGAFGAFATGFGATDMAYIYATGETWIKVPKTIRVD 158 H ++AE Y LP G DSHT GA G A G GAT++A + TG KVP+T+R++ Sbjct: 326 HALMAEQYALPGQVACGTDSHTPHSGALGCLAFGAGATEIANSWVTGYVRCKVPETLRIE 385 Query: 159 IVGK-NENVSAKDIVLRVCK--EIGRRGATYMAIEYGGEVVKNMDMDGRLTLCNMAIEMG 215 I G+ + V+AKD+VL + + I GA + EYGG V+ M +D R TL NM E+G Sbjct: 386 ISGQLRDGVTAKDVVLHLLQMDAIRSGGAIGLVFEYGGSAVRAMSIDERATLTNMVAELG 445 Query: 216 GKTGVIEADEITYDYLKKERGLSDEDIAKLKKERITVNRDEANYYKEIEIDITDMEEQVA 275 G TG++E DE T +LK+ RG+ E + A Y I ID + ++ +A Sbjct: 446 GFTGIVEPDERTVAFLKERRGVD------FTLENWMKSDAGATYRDTISIDASAIQPMLA 499 Query: 276 VPHHPDNVKPISDVE-GTEINQVFIGSCTNGRLSDLREAAKYL-----KGREVHKDVKLI 329 P P N P +E I+ + GSCT G+ D + L +G V + +L Sbjct: 500 RPGDPGNGVPALQLEQDVAIDIAYGGSCTAGKREDFDFYHEVLHWGVEQGLRVPEGTRLY 559 Query: 330 VIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAE-GEICLSTTNRNFK 388 + + V + G + +F +AG + PGCG C G AE E+ +S NRNF Sbjct: 560 LQFGTMAVRAYCEERGYLPVFERAGVTLVMPGCGSCANCGPGQSAEANEVTISAINRNFP 619 Query: 389 GRMGHINSYIYLASPKIAAISAVKGYIT 416 GR G N ++LASP A SA+ G IT Sbjct: 620 GRSGPGN--VWLASPYTVAASALAGKIT 645 Lambda K H 0.318 0.136 0.399 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: 630 Number of extensions: 36 Number of successful extensions: 5 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: 420 Length of database: 655 Length adjustment: 35 Effective length of query: 385 Effective length of database: 620 Effective search space: 238700 Effective search space used: 238700 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: 52 (24.6 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