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_084691817.1 Q366_RS12560 aconitate hydratase AcnA
Query= curated2:Q9WZ24 (417 letters) >NCBI__GCF_000745975.1:WP_084691817.1 Length = 897 Score = 109 bits (272), Expect = 4e-28 Identities = 104/354 (29%), Positives = 148/354 (41%), Gaps = 56/354 (15%) Query: 114 DLVVGADSHTCTYGALGAFATGVGSTDIAGFYLIGKVWFRVPESIKVTLRGKFKDLVTAK 173 D +VG DSHT ++G GVG + L + +P+ I V L G+ VTA Sbjct: 214 DTLVGTDSHTPMINSIGVLGWGVGGIEAEAVMLGQPYFMPLPQVIGVELTGRLNPGVTAT 273 Query: 174 DLVLKLISILGVDGANYKAIEFSGPGVKEISMDGRFTISNMAIEAGGKTGLFPVDEITIA 233 D+VL + + L K +EF G G+K + + R TI+NM+ E G G FP+DE TI Sbjct: 274 DMVLTVTNRLRQMNVVEKFVEFYGSGLKNLKVPDRATIANMSPEYGATMGFFPIDEQTID 333 Query: 234 YER-----ERGIEVEE-------MYPDED-AKYVREVEMDLSELEPQVAYPFLP------ 274 Y R E+G VE D D ++ +++DL+E+ P +A P P Sbjct: 334 YFRITNRGEQGEVVEAWAKACGLFRNDGDIPEFSDSLKIDLTEIVPCLAGPARPQDLVKL 393 Query: 275 -------SNAKDVSEAEKERIKIDQ--------------AVIGSCTNGRIEDLRLAAQIL 313 S D + E ++I I A I SCTN + L A +L Sbjct: 394 GDLKTNFSGLLDATAPENKQINIRLNDTPAQIGNGSVVIAAITSCTNTSNPYVLLGAGLL 453 Query: 314 ------KGRTVSPDVRCIIIPGSQKVYKQALKEGLIDIFIDAGCAVSTPTCGPCLGGHMG 367 KG P V+ PGS+ V GL+ G V+ C C+G Sbjct: 454 ARNAVKKGIFPKPHVKTSFAPGSKVVVDYLSDAGLMPYLESLGFHVAAFGCTTCIGNSGP 513 Query: 368 VLAEGE----------VAISTTNRNFVGRMGHPNSKVFLASPAVAAASAIKGYI 411 + E E A+ + NRNF R+ FLASP + A A+ G + Sbjct: 514 LHPEIEKQIKEKDLAVAAVLSGNRNFEARIHQLTKANFLASPMLVVAFALCGRV 567 Lambda K H 0.318 0.138 0.395 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: 771 Number of extensions: 42 Number of successful extensions: 2 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: 417 Length of database: 897 Length adjustment: 37 Effective length of query: 380 Effective length of database: 860 Effective search space: 326800 Effective search space used: 326800 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 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