Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate GFF3634 PS417_18600 isopropylmalate isomerase
Query= BRENDA::Q58409 (420 letters) >FitnessBrowser__WCS417:GFF3634 Length = 472 Score = 219 bits (557), Expect = 2e-61 Identities = 150/441 (34%), Positives = 226/441 (51%), Gaps = 54/441 (12%) Query: 24 VEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFDHNVPPNTVK-------AAEMQK 76 + +D + H+ T+P A++ L+ W D I+ DHNVP + A ++ + Sbjct: 26 IYIDRHIIHEVTSPQAFEGLRLAGRKPWRVDSIIATPDHNVPTTPERKGGIDAIADQVSR 85 Query: 77 LALE----FVKRFGIKNFHKGG--EGICHQILAEN-YVLPNMFVAGGDSHTCTHGAFGAF 129 L ++ + +GI F +GI H I E LP M V GDSHT THGAFGA Sbjct: 86 LQVQTLDDYCDEYGITEFKMNDVRQGIVHVIGPEQGATLPGMTVVCGDSHTSTHGAFGAL 145 Query: 130 ATGFGATDMAYIYATGETWIKVPKTIRVDIVGKNE-NVSAKDIVLRVCKEIGRRGATYMA 188 A G G +++ +++AT K K + V + G V+AKDIVL V +IG G A Sbjct: 146 AHGIGTSEVEHVFATQCLVAKKMKNMLVKVEGTLPFGVTAKDIVLAVIGKIGTAGGNGHA 205 Query: 189 IEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYDYLK----KERGLSDEDIAK 244 IE+ G ++++ ++GR+T+CNM+IE G + G++ ADE T +Y+K +G +D D A Sbjct: 206 IEFAGSAIRDLSIEGRMTICNMSIEAGARVGMVAADEKTVEYVKGRPFAPQG-ADWD-AA 263 Query: 245 LKKERITVNRDEANYYKEIEIDITDMEEQVAVPHHPDNVKPISD---------------- 288 ++ + V+ +A + +E+D ++ QV+ P+ V + Sbjct: 264 VEAWKDLVSDADAVFDTVVELDAAQIKPQVSWGTSPEMVLAVDQNVPDPAKETDLVKRGS 323 Query: 289 ---------------VEGTEINQVFIGSCTNGRLSDLREAAKYLKGREVHKDVK-LIVIP 332 + ++++VFIGSCTN R+ DLR AA KGR+V +K IV+P Sbjct: 324 IERALKYMGLQANQAITDIQLDRVFIGSCTNSRIEDLRAAAVIAKGRKVASTIKQAIVVP 383 Query: 333 ASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAEGEICLSTTNRNFKGRMG 392 S V QA EG+ IF++AG PGC CL + L GE C ST+NRNF+GR G Sbjct: 384 GSGLVKAQAEAEGLDKIFLEAGFEWREPGCSMCLAMNPDRLESGEHCASTSNRNFEGRQG 443 Query: 393 HINSYIYLASPKIAAISAVKG 413 +L SP +AA +AV G Sbjct: 444 -AGGRTHLVSPAMAAAAAVNG 463 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: 494 Number of extensions: 17 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: 472 Length adjustment: 32 Effective length of query: 388 Effective length of database: 440 Effective search space: 170720 Effective search space used: 170720 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 Aug 03 2021. The underlying query database was built on Aug 03 2021.
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