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_012383914.1 BIND_RS04615 aconitate hydratase
Query= curated2:O28084 (416 letters) >NCBI__GCF_000019845.1:WP_012383914.1 Length = 668 Score = 233 bits (593), Expect = 2e-65 Identities = 139/414 (33%), Positives = 215/414 (51%), Gaps = 2/414 (0%) Query: 1 MGKTIAEKILSEKSKSDAY-AGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTH 59 M + +++K++ G + IDQ QD T L + L + + + + Sbjct: 1 MAQNVSQKLIGSHLVDGVMNPGAPITLRIDQTLTQDATGTLVMLTLEAMELDHVKTEVSV 60 Query: 60 FFVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADS 119 +VDH ++D F+ ++ G ++ PG GI H + +ER+ +PG +G+DS Sbjct: 61 QYVDHNLLQIDNLNADDHLFLESACRRFGIWYSRPGNGISHVVHMERFGRPGKSLLGSDS 120 Query: 120 HTCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIG 179 HT G + + G G DVA+A+A +P F V+L G+LP V AKDVIL+++ Sbjct: 121 HTPAAGSLSMLAIGAGGLDVALAMAGEPYPTAMPRIFGVELKGALPDWVSAKDVILEMLR 180 Query: 180 DLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGRE 239 GV G K +E++G + ++ +R IANM E GA +F SDE T+KFL GR Sbjct: 181 RHGVSGGVGKIIEYYGPGLDCLSAMDRHVIANMGAELGATTTVFPSDEETKKFLEARGRG 240 Query: 240 GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNG 299 D+ + AD EY+ +D+S L P++++P + NV + ++EG ++ Q YIG+ N Sbjct: 241 RDWCAIAADPGCEYDDHDEIDLSKLEPLIAQPSSPGNVVAVKDIEGEDIYQAYIGSSANP 300 Query: 300 RLSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPC 359 D VAA I++G+ + V V P SR+ + G + + AG + GC C Sbjct: 301 GWRDFAVAAEIVRGKSIPAHVSFDVNPTSRQGLEILVADGHLNDLLVAGARIHQTGCNGC 360 Query: 360 VGIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPR 413 +G+ Q A G+ + T RNF GR G +FL SP TAAASA+ G I DPR Sbjct: 361 IGMGQA-PAIGKNSLRTTPRNFPGRSGTEEDAVFLCSPETAAASALTGKITDPR 413 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: 656 Number of extensions: 30 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: 416 Length of database: 668 Length adjustment: 35 Effective length of query: 381 Effective length of database: 633 Effective search space: 241173 Effective search space used: 241173 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: 52 (24.6 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