Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate WP_011386009.1 AMB_RS18485 aconitate hydratase AcnA
Query= curated2:O28084 (416 letters) >NCBI__GCF_000009985.1:WP_011386009.1 Length = 903 Score = 115 bits (288), Expect = 5e-30 Identities = 112/395 (28%), Positives = 156/395 (39%), Gaps = 78/395 (19%) Query: 93 PPGEGIIHQIMVERYV-----KPG----DLAVGADSHTCTYGGIGAFSTGMGSTDVAVAI 143 PPG GI+HQ+ +E K G D VG DSHT +G G+G + + Sbjct: 175 PPGIGIVHQVNLEFLARGVLEKDGITYPDTLVGTDSHTTMINALGVAGWGVGGIEAEAGM 234 Query: 144 ALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIGDLGVDGATYKALEFHGECAENMTV 203 F P+ V L G LP+G A D++L L L K +EF GE ++ V Sbjct: 235 LGQPLVFLTPDVVGVHLHGRLPEGATATDLVLFLTERLRRAKVVGKFVEFFGEGTRSLAV 294 Query: 204 EERLTIANMAVECGAKAGIFESDENTRKFLAELGREGDFREV-------------KADED 250 +R TIANMA E GA G F D+ T ++L GR EV D Sbjct: 295 PDRATIANMAPEYGATMGFFPVDKETVRYLEATGRTDSEIEVFRAYYSAQGLFGMPMPGD 354 Query: 251 AEYEKEIYMDVSSLVPVVSKP--------------------------------------- 271 +Y + I D+ S+ P ++ P Sbjct: 355 IDYSEVIEFDLGSVQPSIAGPKRPQDRLNLSDMRRAFTSLFSAPAKDDGYGRPAEALGRR 414 Query: 272 HNVDNVAEISEVEGTEVNQVYIGTCTNGRLSDLEVAARILK------GRKVKEGVRLIVV 325 H V+ A +++ +V I +CTN + +AA +L G KV V+ + Sbjct: 415 HRVETTA-AADIGHGDVLIAAITSCTNTSNPGVMLAAGLLARKAVALGLKVGPRVKTSLA 473 Query: 326 PASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPCVG--------IHQGILADGEVC--IS 375 P SR V GL+ G V+ GC C+G + Q I AD VC + Sbjct: 474 PGSRVVTEYLAKAGLLGDLESLGFGVVAYGCTTCIGNSGPLMPDLEQAIAADDLVCAAVL 533 Query: 376 TQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIA 410 + NRNF+ R+ FL SP A A+ G IA Sbjct: 534 SGNRNFEARIHPAIKANFLMSPPLVVAFAIAGRIA 568 Lambda K H 0.318 0.136 0.391 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: 828 Number of extensions: 42 Number of successful extensions: 3 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: 416 Length of database: 903 Length adjustment: 37 Effective length of query: 379 Effective length of database: 866 Effective search space: 328214 Effective search space used: 328214 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: 53 (25.0 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