Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate 203315 SO4234 3-isopropylmalate dehydratase, large subunit (NCBI ptt file)
Query= BRENDA::Q58409 (420 letters) >FitnessBrowser__MR1:203315 Length = 474 Score = 244 bits (624), Expect = 3e-69 Identities = 162/470 (34%), Positives = 240/470 (51%), Gaps = 54/470 (11%) Query: 1 MTLVEKILSKKVGYEVC---------AGDSIEVEVDLAMTHDGTTPLAYKALKEMSDSVW 51 MT+ K ++ K Y+ G++ + VD + H+ T+P A+ LK + Sbjct: 1 MTVPSKTIAPKTLYQKVWDAHIVATPEGEAPIIYVDRHLVHEVTSPQAFSGLKVAGRQLR 60 Query: 52 NPDKIVVAFDHNVPPNTVKAAEMQKLA-------LEFVKRFGIK--NFHKGGEGICHQIL 102 P+K DHN + + +A + K FG+ + H +GI H + Sbjct: 61 APEKTFATMDHNTSTRSASLDALSPMARIQVETLAQNCKDFGVLLYDIHHPNQGIVHVMG 120 Query: 103 AE-NYVLPNMFVAGGDSHTCTHGAFGAFATGFGATDMAYIYATGETWIKVPKTIRVDIVG 161 E LP + GDSHT THGAFGA A G G +++ ++ AT KT+++++ G Sbjct: 121 PELGITLPGTVIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLRQLKAKTMKIEVRG 180 Query: 162 K-NENVSAKDIVLRVCKEIGRRGATYMAIEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGV 220 + + V+AKDIVL + +IG G T +E+ GE ++ + M+GR+T+CNMAIEMG K G+ Sbjct: 181 QVTDGVTAKDIVLAIIGKIGMDGGTGYVVEFCGEAIEALSMEGRMTVCNMAIEMGAKAGM 240 Query: 221 IEADEITYDYLK-KERGLSDEDIAKLKKERITVNRDE-ANYYKEIEIDITDMEEQVA--- 275 + D+ T+DYL+ +E ED A+ E T+ D A + + +D D+ Q+ Sbjct: 241 VAPDQTTFDYLEGREFAPKGEDWAQAVAEWKTLKTDVGAEFDATVVLDAADIAPQLTWGT 300 Query: 276 -----------VPHHPDNVKP------------ISDVEGTE-----INQVFIGSCTNGRL 307 VP+ D V P I GT IN+VFIGSCTN R+ Sbjct: 301 NPGQVVAIDAPVPNPADEVNPTIRSSMEKALDYIGLTAGTPMTEVAINKVFIGSCTNSRI 360 Query: 308 SDLREAAKYLKGREVHKDVKLIVIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLG 367 DLR AAK+ KGR+V V IV+P S +V QA EG+ IF++AG PGC CL Sbjct: 361 EDLRSAAKHAKGRKVAAGVTAIVVPGSGQVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLA 420 Query: 368 AHQGVLAEGEICLSTTNRNFKGRMGHINSYIYLASPKIAAISAVKGYITN 417 + L G+ C ST+NRNF+GR G S +L SP +AA +A+ G+ + Sbjct: 421 MNDDRLEAGDRCASTSNRNFEGRQGR-GSRTHLVSPAMAAAAAIAGHFVD 469 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: 474 Number of extensions: 24 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: 420 Length of database: 474 Length adjustment: 33 Effective length of query: 387 Effective length of database: 441 Effective search space: 170667 Effective search space used: 170667 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: 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