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_017548203.1 C792_RS0104225 aconitate hydratase
Query= curated2:O28084 (416 letters) >NCBI__GCF_000330705.1:WP_017548203.1 Length = 644 Score = 260 bits (664), Expect = 1e-73 Identities = 144/415 (34%), Positives = 231/415 (55%), Gaps = 2/415 (0%) Query: 1 MGKTIAEKILSEKSKS-DAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTH 59 M +A+K++ E S + G+ + +IDQ QD T + + +L + + + + Sbjct: 1 MQLNVAQKLIKEHLLSGEMTPGEEIGLKIDQTLTQDATGTMVMLELEAMDLDRVKTEVSA 60 Query: 60 FFVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADS 119 +VDH +D F+ A+K G ++ PG G+ H + ++ PG +G+DS Sbjct: 61 QYVDHNLIQDDYRNPDDHIFLRSAARKFGVHYSRPGNGVSHPVHMQELAIPGKTLLGSDS 120 Query: 120 HTCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIG 179 HTC G +G + G G DVA+A+A +P V+L G LP+ V AKDVIL+++ Sbjct: 121 HTCANGCMGMLAMGAGGIDVAMAMAGEAYHVEMPRVMGVKLTGELPEWVSAKDVILEMLR 180 Query: 180 DLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGRE 239 V G + +E++G +N++ +R IANM E GA A +F SD+ ++F+A+ GR Sbjct: 181 RHSVKGGVGRIIEYYGPGLDNLSAMDRHVIANMGAELGATATVFPSDDEVKRFMAQEGRG 240 Query: 240 GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNG 299 ++ E+KADE AEY+ +++S LVP+++KP + DNV ++E+EG + Q YIG+ N Sbjct: 241 DEWVELKADEGAEYDDHDEINLSELVPLIAKPTSPDNVVPVTEIEGEPIYQSYIGSSANP 300 Query: 300 RLSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPC 359 D +A+ I++GR + G+ + P SR++ Q ++ G I + AGG + GC C Sbjct: 301 GYRDFAIASLIVQGRYIANGISFDINPTSRQLLQQLVENGHIANLLGAGGRMHQAGCNGC 360 Query: 360 VGIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPRE 414 +G+ Q A G+ + T RNF GR G +FL SP AAASA+ G I DPR+ Sbjct: 361 IGMGQA-PATGQNSLRTTPRNFPGRSGTKEDSVFLCSPEIAAASALYGVITDPRK 414 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: 637 Number of extensions: 34 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: 416 Length of database: 644 Length adjustment: 35 Effective length of query: 381 Effective length of database: 609 Effective search space: 232029 Effective search space used: 232029 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 Jul 26 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