Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate AO356_21400 AO356_21400 isopropylmalate isomerase
Query= BRENDA::Q58409 (420 letters) >FitnessBrowser__pseudo5_N2C3_1:AO356_21400 Length = 472 Score = 218 bits (556), Expect = 2e-61 Identities = 153/463 (33%), Positives = 235/463 (50%), Gaps = 55/463 (11%) Query: 2 TLVEKILSKKVGYEVCAGDSIEVEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFD 61 TL +K+ + + G ++ + +D + H+ T+P A++ L+ W D + D Sbjct: 5 TLYDKLWDSHLVKQRDDGSAL-IYIDRHIIHEVTSPQAFEGLRLAGRKPWRIDANIATPD 63 Query: 62 HNVPPNTVKAAEMQKLALEFVK-----------RFGIKNFHKGG--EGICHQILAEN-YV 107 HNVP + ++ +A + + +GI F +GI H I E Sbjct: 64 HNVPTTPERKGGIEAIADQVSRLQVQTLDDNCDEYGIVEFKMNDVRQGIVHVIGPEQGAT 123 Query: 108 LPNMFVAGGDSHTCTHGAFGAFATGFGATDMAYIYATGETWIKVPKTIRVDIVGKNE-NV 166 LP M V GDSHT THGAFGA A G G +++ ++ AT K K + V + GK V Sbjct: 124 LPGMTVVCGDSHTSTHGAFGALAHGIGTSEVEHVLATQCLVAKKMKNMLVRVEGKLPFGV 183 Query: 167 SAKDIVLRVCKEIGRRGATYMAIEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEI 226 +AKDIVL V +IG G AIE+ G ++++ ++GR+T+CNM+IE G + G++ ADE Sbjct: 184 TAKDIVLAVIGKIGTAGGNGHAIEFAGSAIRDLSVEGRMTICNMSIEAGARVGLVAADEK 243 Query: 227 TYDYLK----KERGLSDEDIAKLKKERITVNRDEANYYKEIEIDITDMEEQVAVPHHPDN 282 T +Y+K +G ++ D+A ++ + V+ +A + +E+D T ++ QV+ P+ Sbjct: 244 TVEYVKGRPFSPKG-AEWDMA-VEAWKDLVSDADAKFDTVVELDATQIKPQVSWGTSPEM 301 Query: 283 VKPISD-------------------------------VEGTEINQVFIGSCTNGRLSDLR 311 V + + ++++VFIGSCTN R+ DLR Sbjct: 302 VLAVDQNVPDPAKEMDLVKRDSIVRALKYMGLSANQAITDIQLDRVFIGSCTNSRIEDLR 361 Query: 312 EAAKYLKGREVHKDVK-LIVIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQ 370 AA KGR+V +K IV+P S V QA EG+ IF++AG PGC CL + Sbjct: 362 AAAVIAKGRKVASTIKQAIVVPGSGLVKAQAEAEGLDKIFLEAGFEWREPGCSMCLAMNP 421 Query: 371 GVLAEGEICLSTTNRNFKGRMGHINSYIYLASPKIAAISAVKG 413 L GE C ST+NRNF+GR G +L SP +AA +AV G Sbjct: 422 DRLESGEHCASTSNRNFEGRQG-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: 516 Number of extensions: 14 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 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