Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate BWI76_RS04670 BWI76_RS04670 3-isopropylmalate dehydratase large subunit
Query= BRENDA::Q58409 (420 letters) >FitnessBrowser__Koxy:BWI76_RS04670 Length = 466 Score = 237 bits (604), Expect = 6e-67 Identities = 156/462 (33%), Positives = 236/462 (51%), Gaps = 50/462 (10%) Query: 2 TLVEKILSKKVGYEVCAGDSIEVEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFD 61 TL EK+ V YE ++ + +D + H+ T+P A+ L+ V P K D Sbjct: 4 TLYEKLFDAHVVYEA-QNETPLLYIDRHLVHEVTSPQAFDGLRAHKRPVRQPGKTFATMD 62 Query: 62 HNVPPNTVK---AAEMQKLALEFV----KRFGIK--NFHKGGEGICHQILAENYV-LPNM 111 HNV T + EM ++ ++ + K FG++ + + +GI H + E V LP M Sbjct: 63 HNVSTQTKDINASGEMARIQMQELIKNCKEFGVELYDLNHPFQGIVHVMGPEQGVTLPGM 122 Query: 112 FVAGGDSHTCTHGAFGAFATGFGATDMAYIYATGETWIKVPKTIRVDIVGKNE-NVSAKD 170 + GDSHT THGAFGA A G G +++ ++ AT KT+++++ GK ++AKD Sbjct: 123 TIVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLKQGRAKTMKIEVKGKAAPGITAKD 182 Query: 171 IVLRVCKEIGRRGATYMAIEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYDY 230 IVL + + G G T +E+ GE ++++ M+GR+TLCNMAIEMG K G++ D+ T+DY Sbjct: 183 IVLAIIGKTGSAGGTGHVVEFCGEAIRDLSMEGRMTLCNMAIEMGAKAGLVAPDQTTFDY 242 Query: 231 LKKE----RGLSDEDIAKLKKERITVNRDEANYYKEIEIDITDMEEQVAVPHHPDNVKPI 286 +K +G+ D K T D A + + + ++ QV +P V + Sbjct: 243 VKGRLHAPKGVDFADAVAYWKTLTT--DDGATFDSVVTLQAEEIAPQVTWGTNPGQVISV 300 Query: 287 SDV-------------------------------EGTEINQVFIGSCTNGRLSDLREAAK 315 +D+ I++VFIGSCTN R+ DLR AA+ Sbjct: 301 TDIIPDPASFSDPVERASAEKALAYMGLKSGVPLTEVAIDKVFIGSCTNSRIEDLRAAAE 360 Query: 316 YLKGREVHKDVKLIVIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAE 375 KGR+V V+ +V+P S V QA EG+ IF++AG PGC CL + L Sbjct: 361 IAKGRKVAPGVQALVVPGSGPVKAQAEAEGLDKIFIEAGFEWRLPGCSMCLAMNNDRLNP 420 Query: 376 GEICLSTTNRNFKGRMGHINSYIYLASPKIAAISAVKGYITN 417 GE C ST+NRNF+GR G +L SP +AA +AV G+ + Sbjct: 421 GERCASTSNRNFEGRQGR-GGRTHLVSPAMAAAAAVTGHFAD 461 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: 488 Number of extensions: 22 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: 466 Length adjustment: 32 Effective length of query: 388 Effective length of database: 434 Effective search space: 168392 Effective search space used: 168392 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