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_010529220.1 ON01_RS01390 aconitate hydratase
Query= curated2:O28084 (416 letters) >NCBI__GCF_000224785.1:WP_010529220.1 Length = 651 Score = 248 bits (634), Expect = 3e-70 Identities = 141/414 (34%), Positives = 222/414 (53%), Gaps = 2/414 (0%) Query: 1 MGKTIAEKILSEKSKS-DAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTH 59 M I +K++ + + + +G+ + +IDQ QD T L + +L + + + + Sbjct: 1 MPLNITQKLIKDHLVTGEMTSGEEIGLKIDQTLTQDATGTLVMLELEAMELDQAKTEVSA 60 Query: 60 FFVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADS 119 +VDH + +D F+ ++ G F+ PG G+ H + ++R KPG +G+DS Sbjct: 61 QYVDHNLIQEDSKNPDDHLFLQSATERFGLYFSRPGNGVSHPVHMQRLAKPGKTLLGSDS 120 Query: 120 HTCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIG 179 HTC G +G + G G DVA+AIA + ++P+ + V+L G LP V AKDVIL+L+ Sbjct: 121 HTCANGCMGMLAMGAGGIDVAMAIAGEPFYVKMPKVWGVKLTGKLPDWVSAKDVILELLR 180 Query: 180 DLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGRE 239 V G +E+ G EN++ +R IANM E GA +F SD+ ++FL RE Sbjct: 181 RHDVKGGVGSVIEYFGPGVENLSAMDRHVIANMGAELGATGTVFPSDKEVKRFLKAQDRE 240 Query: 240 GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNG 299 D+ E+ AD+ A Y+ +D+S L P+++KP + NV + E+ GT + Q Y+G+ N Sbjct: 241 DDWIELTADKGAAYDILEEVDLSELEPLIAKPSSPGNVVAVRELAGTPIYQSYVGSSANP 300 Query: 300 RLSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPC 359 D +AA I+ G + +GV + P SR++ + + I ++AG + GC C Sbjct: 301 GYRDFAIAAEIVNGMNIADGVSFDINPTSRQMLTDLVQESHIASLLQAGARMHQAGCNGC 360 Query: 360 VGIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPR 413 +G+ Q A G + T RNF GR G +FL SP TAAASA+ G I DPR Sbjct: 361 IGMGQA-PATGRNSLRTTPRNFPGRSGTREDSVFLCSPETAAASALTGQITDPR 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: 611 Number of extensions: 33 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: 651 Length adjustment: 35 Effective length of query: 381 Effective length of database: 616 Effective search space: 234696 Effective search space used: 234696 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