Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate WP_012709627.1 NGR_RS26830 3-isopropylmalate dehydratase large subunit
Query= BRENDA::Q58409 (420 letters) >NCBI__GCF_000018545.1:WP_012709627.1 Length = 469 Score = 233 bits (595), Expect = 7e-66 Identities = 152/437 (34%), Positives = 228/437 (52%), Gaps = 46/437 (10%) Query: 26 VDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFDHNVPPNTVKAA----EMQKLALEF 81 +D + H+ T+P A++ L+ V P+K + DHNVP + + E ++ +E Sbjct: 29 IDRHLVHEVTSPQAFEGLRMAGRKVRAPEKTLAVVDHNVPTSPDRHLGIKNEESRIQVEA 88 Query: 82 VKR----FGIKNFHKGG--EGICHQILAEN-YVLPNMFVAGGDSHTCTHGAFGAFATGFG 134 + R FG++ + + +GI H + E + LP M + GDSHT THGAFGA A G G Sbjct: 89 LARNAADFGVEYYSENDKRQGIVHIVGPEQGFTLPGMTIVCGDSHTSTHGAFGALAHGIG 148 Query: 135 ATDMAYIYATGETWIKVPKTIRVDIVGK-NENVSAKDIVLRVCKEIGRRGATYMAIEYGG 193 +++ ++ AT K K + V + G+ V+AKDI+L + EIG G T IE+ G Sbjct: 149 TSEVEHVLATQTLIQKKAKNMLVRVDGQLPPGVTAKDIILAIIGEIGTAGGTGHVIEFAG 208 Query: 194 EVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYDYLK-KERGLSDEDIAKLKKERITV 252 E ++++ M+GR+T+CNM IE G + G+I DE T+DY+K K R + T+ Sbjct: 209 EAIRSLSMEGRMTICNMTIEGGARAGLIAPDETTFDYIKDKPRAPKGKAWDMALDYWKTL 268 Query: 253 NRDEANYYKEIEI-DITDMEE--------------QVAVPHHPD---------------- 281 + DE +Y I + D D+ Q AVP+ D Sbjct: 269 HTDEGAHYDRIVVLDAADLPPIVSWGSSPEDVISVQGAVPNPDDIQEETKRASKWRALDY 328 Query: 282 -NVKPISDVEGTEINQVFIGSCTNGRLSDLREAAKYLKGREVHKDVKLIVIPASKKVFLQ 340 +KP + + +++VFIGSCTNGR+ DLR AK ++GR+V V +++P S V Q Sbjct: 329 MGLKPGTKITDIAVDRVFIGSCTNGRIEDLRAVAKVVEGRKVASTVSAMIVPGSGLVKEQ 388 Query: 341 ALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAEGEICLSTTNRNFKGRMGHINSYIYL 400 A EG+ IF +AG PGC CL + L GE C ST+NRNF+GR G +L Sbjct: 389 AEAEGLDKIFKEAGFDWREPGCSMCLAMNDDRLKPGERCASTSNRNFEGRQG-FKGRTHL 447 Query: 401 ASPKIAAISAVKGYITN 417 SP +AA +AV G+ + Sbjct: 448 VSPAMAAAAAVAGHFVD 464 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: 19 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: 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 Jul 25 2024. The underlying query database was built on Jul 25 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