Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate 15396 b1276 aconitate hydratase (NCBI)
Query= curated2:Q9WZ24 (417 letters) >FitnessBrowser__Keio:15396 Length = 891 Score = 121 bits (304), Expect = 7e-32 Identities = 103/358 (28%), Positives = 155/358 (43%), Gaps = 63/358 (17%) Query: 114 DLVVGADSHTCTYGALGAFATGVGSTDIAGFYLIGKVWFRVPESIKVTLRGKFKDLVTAK 173 D +VG DSHT LG GVG + L V +P+ + L GK ++ +TA Sbjct: 206 DTLVGTDSHTTMINGLGVLGWGVGGIEAEAAMLGQPVSMLIPDVVGFKLTGKLREGITAT 265 Query: 174 DLVLKLISILGVDGANYKAIEFSGPGVKEISMDGRFTISNMAIEAGGKTGLFPVDEITIA 233 DLVL + +L G K +EF G G+ + + R TI+NM+ E G G FP+D +T+ Sbjct: 266 DLVLTVTQMLRKHGVVGKFVEFYGDGLDSLPLADRATIANMSPEYGATCGFFPIDAVTLD 325 Query: 234 YERERG-----IEVEEMY---------PDEDAKYVREVEMDLSELEPQVAYP-------- 271 Y R G +E+ E Y P ++ + +E+D++++E +A P Sbjct: 326 YMRLSGRSEDQVELVEKYAKAQGMWRNPGDEPIFTSTLELDMNDVEASLAGPKRPQDRVA 385 Query: 272 -------FLPSNAKDVSEAEKERIKIDQ----------------AVIGSCTNGRIEDLRL 308 F SN +V+ K+R +D A I SCTN + + Sbjct: 386 LPDVPKAFAASNELEVNATHKDRQPVDYVMNGHQYQLPDGAVVIAAITSCTNTSNPSVLM 445 Query: 309 AAQILKGRTVS------PDVRCIIIPGSQKVYKQALKEGLIDIFIDAGCAVSTPTCGPCL 362 AA +L + V+ P V+ + PGS+ V K L + G + C C+ Sbjct: 446 AAGLLAKKAVTLGLKRQPWVKASLAPGSKVVSDYLAKAKLTPYLDELGFNLVGYGCTTCI 505 Query: 363 GGHMGVLAEGEVAISTT----------NRNFVGRMGHPNSKV-FLASPAVAAASAIKG 409 G + E AI + NRNF GR+ HP K +LASP + A A+ G Sbjct: 506 GNSGPLPDPIETAIKKSDLTVGAVLSGNRNFEGRI-HPLVKTNWLASPPLVVAYALAG 562 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: 727 Number of extensions: 43 Number of successful extensions: 3 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: 891 Length adjustment: 37 Effective length of query: 380 Effective length of database: 854 Effective search space: 324520 Effective search space used: 324520 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 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