Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate WP_019866607.1 METMI_RS0112345 3-isopropylmalate dehydratase large subunit
Query= BRENDA::Q58409 (420 letters) >NCBI__GCF_000384075.1:WP_019866607.1 Length = 469 Score = 230 bits (586), Expect = 8e-65 Identities = 159/462 (34%), Positives = 235/462 (50%), Gaps = 49/462 (10%) Query: 2 TLVEKILSKKVGYEVCAGDSIEVEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFD 61 TL +K+ V Y G S+ + +D + H+ T+P A++ L+ W D+ + D Sbjct: 5 TLYDKLWEDHVVYTEDDGSSL-IYIDRHLVHEVTSPQAFEGLRLAGRKPWRADRNLAVAD 63 Query: 62 HNVPPNTVK---AAEMQKLALEFVK----RFGIKNF--HKGGEGICHQILAEN-YVLPNM 111 HNVP A + +L +E + FGI F + G +GI H I E LP M Sbjct: 64 HNVPTTDRDKGIADPVSRLQVETLDSNCAEFGITEFAMNDGRQGIVHVIGPEQGATLPGM 123 Query: 112 FVAGGDSHTCTHGAFGAFATGFGATDMAYIYATGETWIKVPKTIRVDIVGK-NENVSAKD 170 V GDSHT THGA GA A G G +++ ++ AT K K + + + G+ V+AKD Sbjct: 124 TVVCGDSHTSTHGASGALAFGIGTSEVEHVLATQCLVQKKAKNLLIKVNGQVGLGVTAKD 183 Query: 171 IVLRVCKEIGRRGATYMAIEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYDY 230 IVL + IG G IE+ GE ++ + M+GR+T+CNMAIE G + G+I D++T DY Sbjct: 184 IVLAIIGTIGTAGGNGHTIEFAGEAIRALSMEGRMTVCNMAIEAGARAGLIAVDDVTIDY 243 Query: 231 LKKERGLSDEDIAKLKKERITVNRD---EANYYKEIEIDITDMEEQV------------- 274 ++R S ++ ER+ N +A + K +EID + + QV Sbjct: 244 Y-RDRPYSPKNGDWYMAERLWRNLHSDADATFDKVVEIDASMIVPQVTWGTSPELVVAVD 302 Query: 275 -AVPHHPDNVKPISD-----------------VEGTEINQVFIGSCTNGRLSDLREAAKY 316 VP + P+ + I++VFIGSCTN R+ DLR AA Sbjct: 303 GCVPDPALEINPVKQQSMVRALQYMGLSAGQAITDISIDKVFIGSCTNSRIEDLRAAANV 362 Query: 317 LKGREVHKDVKL-IVIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAE 375 KG+++ ++KL +V+P S V QA EG+ IF+ AG PGC CL + L E Sbjct: 363 AKGKKIANNIKLALVVPGSGLVKRQAETEGLDKIFLDAGFEWREPGCSMCLAMNADRLEE 422 Query: 376 GEICLSTTNRNFKGRMGHINSYIYLASPKIAAISAVKGYITN 417 GE C ST+NRNF+GR G+ +L SP +AA +A+ G+ + Sbjct: 423 GERCASTSNRNFEGRQGY-GGRTHLVSPSMAAAAAIAGHFVD 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: 476 Number of extensions: 16 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: 469 Length adjustment: 32 Effective length of query: 388 Effective length of database: 437 Effective search space: 169556 Effective search space used: 169556 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 10 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