Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate Dsui_3201 Dsui_3201 3-isopropylmalate dehydratase, large subunit
Query= BRENDA::Q58409 (420 letters) >FitnessBrowser__PS:Dsui_3201 Length = 468 Score = 224 bits (572), Expect = 3e-63 Identities = 156/466 (33%), Positives = 229/466 (49%), Gaps = 50/466 (10%) Query: 2 TLVEKILSKKVGYEVCAGDSIEVEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFD 61 TL +K+ V +E G ++ + +D + H+ T+P A++ LK W IV D Sbjct: 4 TLYDKLWQNHVVHEEADGTAL-IYIDRHLVHEVTSPQAFEGLKLAGRKPWRVSSIVATAD 62 Query: 62 HNVP----------PNTVKAAEMQKLALEFVKRFGIKNFHKGGEGICHQILAEN-YVLPN 110 HN P P + + E + V F +GI H + EN LP Sbjct: 63 HNTPTDHWEEGIKDPISRQQVETLDANIREVGALAYWPFKDMRQGIVHVVGPENGATLPG 122 Query: 111 MFVAGGDSHTCTHGAFGAFATGFGATDMAYIYATGETWIKVPKTIRVDIVGK-NENVSAK 169 M V GDSHT THGAF A G G +++ ++ AT K K++ + + GK + V+ K Sbjct: 123 MTVVCGDSHTSTHGAFACMAHGIGTSEVEHVMATQCLIQKKSKSMLIRVEGKLGKGVTGK 182 Query: 170 DIVLRVCKEIGRRGATYMAIEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYD 229 D+ L + +IG G T AIE+GG ++ + M+GR+TLCNMAIE G + G + D+ T + Sbjct: 183 DVALAIIGKIGTAGGTGYAIEFGGSAIRGLSMEGRMTLCNMAIEAGARMGFVAVDDTTIN 242 Query: 230 YLKKERGLS--DEDIAKLKKERITVNRDE-ANYYKEIEIDITDMEEQVAVPHHPDNVKPI 286 YL K+R S E K T+ DE A + +++ +++ QV P+ V PI Sbjct: 243 YL-KDRPFSPKGETWDKAVAYWRTLKSDEGARFDCTVDLKAEEIQPQVTWGTSPEMVVPI 301 Query: 287 S-------------------------------DVEGTEINQVFIGSCTNGRLSDLREAAK 315 +++ I++VFIGSCTN R+ DLREAA Sbjct: 302 GATVPDPAKEADPVKREGMERALQYMGLTPNLEIKKIAIDKVFIGSCTNSRIEDLREAAA 361 Query: 316 YLKGREVHKDVKL-IVIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLA 374 ++GR+ +VKL +V+P S V QA EG+ IFV AG PGC CL + L Sbjct: 362 VVRGRQKAANVKLALVVPGSGLVKRQAEAEGLDKIFVAAGFEWREPGCSMCLAMNADRLE 421 Query: 375 EGEICLSTTNRNFKGRMGHINSYIYLASPKIAAISAVKGYITNKLD 420 GE C ST+NRNF+GR G +L SP +AA + + G+ + D Sbjct: 422 PGERCASTSNRNFEGRQGP-GGRTHLVSPAMAAAAGIAGHFADVRD 466 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: 489 Number of extensions: 20 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: 468 Length adjustment: 32 Effective length of query: 388 Effective length of database: 436 Effective search space: 169168 Effective search space used: 169168 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