Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate YP_001326057.1 Smed_0365 aconitate hydratase
Query= curated2:Q9WZ24 (417 letters) >NCBI__GCF_000017145.1:YP_001326057.1 Length = 872 Score = 134 bits (338), Expect = 8e-36 Identities = 111/348 (31%), Positives = 156/348 (44%), Gaps = 52/348 (14%) Query: 114 DLVVGADSHTCTYGALGAFATGVGSTDIAGFYLIGKVWFRVPESIKVTLRGKFKDLVTAK 173 D ++G DSHT +G A GVG + + V RVP+ + V L G+ D V A Sbjct: 196 DTLIGTDSHTPMINGIGVLAWGVGGLEAESVFFGMPVSLRVPDVVGVRLTGRLGDGVLAT 255 Query: 174 DLVLKLISILGVDGANYKAIEFSGPGVKEISMDGRFTISNMAIEAGGKTGLFPVDEITIA 233 DL L + IL K +EF GPGV ++ R ++NM E GG +G FPVD T+ Sbjct: 256 DLALTVTHILRKIDLQDKYVEFYGPGVSLLTAGDRSVVANMTPEFGGNSGYFPVDGRTLD 315 Query: 234 YERERG-----IEVEEMY---------PDEDAKYVREVEMDLSELEPQVAYPFLPSNAKD 279 Y R G +E+ E + PDE +Y VE+DLS +EP +A P P + Sbjct: 316 YLRTTGRTSEQVELVEAFTKRVGLWFDPDEKPRYTHVVEIDLSAIEPSLAGPTRPHDRIS 375 Query: 280 VSE------------------AEKERIKIDQAVIGSCTNGRIEDLRLAAQIL--KGRTV- 318 V E +E + A I SCTN L +AA +L K R + Sbjct: 376 VGETSAAISSMKRDAVVSAHTSEPNDGAVAIAAITSCTNTSDPRLVIAAGLLARKARALG 435 Query: 319 ---SPDVRCIIIPGSQKVYKQALKEGLIDIFIDAGCAVSTPTCGPCLGGHMGVLAEG--- 372 +P V+ + PGS + + GL+ G + C C+ G+ G L E Sbjct: 436 LHPAPWVKTSLAPGSPTAERYLRRSGLLQDLEAVGFGIVGYGCTTCI-GNSGPLTEPIAV 494 Query: 373 --------EVAISTTNRNFVGRMGHPNSKV-FLASPAVAAASAIKGYI 411 VA+ + NRNF GR+ HP + FLASP + A A+ G + Sbjct: 495 AMKDRGILPVAVLSGNRNFPGRV-HPQLEAGFLASPPLVVAFALAGTV 541 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: 736 Number of extensions: 47 Number of successful extensions: 4 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: 872 Length adjustment: 37 Effective length of query: 380 Effective length of database: 835 Effective search space: 317300 Effective search space used: 317300 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