Align methanogen homoaconitase (EC 4.2.1.114) (characterized)
to candidate WP_012970815.1 ALVIN_RS07970 3-isopropylmalate dehydratase large subunit
Query= BRENDA::Q58409 (420 letters) >NCBI__GCF_000025485.1:WP_012970815.1 Length = 467 Score = 227 bits (579), Expect = 5e-64 Identities = 158/462 (34%), Positives = 236/462 (51%), Gaps = 49/462 (10%) Query: 2 TLVEKILSKKVGYEVCAGDSIEVEVDLAMTHDGTTPLAYKALKEMSDSVWNPDKIVVAFD 61 TL +K+ + V G ++ + +D + H+ T+P A++ L+ W + D Sbjct: 5 TLYDKLWDEHVVRVDDTGTAL-LYIDRQLIHEVTSPQAFEGLRLAGRQPWRVSANLAVPD 63 Query: 62 HNVPPNTVKAA----EMQKLALEFV----KRFGIKNFHKGG--EGICHQILAEN-YVLPN 110 HNVP T +AA + +L +E + + FGI G +G+ H + E + LP Sbjct: 64 HNVP-TTDRAAGIADPVSRLQVETLGTNCQTFGITELSMGDKRQGVVHVVGPEQGFTLPG 122 Query: 111 MFVAGGDSHTCTHGAFGAFATGFGATDMAYIYATGETWIKVPKTIRVDIVGK-NENVSAK 169 V GDSHT THGAFGA A G G +++ ++ AT + K++ + + G+ V+AK Sbjct: 123 ATVVCGDSHTATHGAFGALAFGIGTSEVEHVLATQTLIQRKSKSMLISVDGQLGAGVTAK 182 Query: 170 DIVLRVCKEIGRRGATYMAIEYGGEVVKNMDMDGRLTLCNMAIEMGGKTGVIEADEITYD 229 DIVL + EIG G T IE+GGE ++ + M+GR+T+CNMAIE G + G+I DE T D Sbjct: 183 DIVLAIIGEIGTAGGTGFVIEFGGEAIRALSMEGRMTVCNMAIEAGARAGLIGVDEKTVD 242 Query: 230 YLKKERGLSDEDIAKLKKE--RITVNRDEANYYKEIEIDITDMEEQVAVPHHPDNVKPIS 287 Y++ + ++ + R V+ A + + + ID ++ QV P+ V+P+ Sbjct: 243 YMRGRPLAPEGELFERAAAHWRTLVSDAGAQFDRVLHIDAASLKPQVTWGTSPEMVQPVD 302 Query: 288 D--------------------------VEGTEINQ-----VFIGSCTNGRLSDLREAAKY 316 GT I++ VFIGSCTN R+ DLR AA+ Sbjct: 303 GRVPDPAAESDPVKANGIRRALDYMGLTAGTPISEIRPDKVFIGSCTNSRIEDLRAAAEI 362 Query: 317 LKGREVHKDVKL-IVIPASKKVFLQALKEGIIDIFVKAGAMICTPGCGPCLGAHQGVLAE 375 KGR+V +KL +V+P S V QA EG+ IFV AG PGC CL + L Sbjct: 363 AKGRKVADSIKLAMVVPGSGLVKEQAEAEGLDKIFVAAGFEWREPGCSMCLAMNADRLEP 422 Query: 376 GEICLSTTNRNFKGRMGHINSYIYLASPKIAAISAVKGYITN 417 GE C ST+NRNF+GR G +L SP +AA +AV G+ + Sbjct: 423 GERCASTSNRNFEGRQGQ-GGRTHLVSPAMAAAAAVTGHFVD 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: 435 Number of extensions: 17 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 420 Length of database: 467 Length adjustment: 32 Effective length of query: 388 Effective length of database: 435 Effective search space: 168780 Effective search space used: 168780 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