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_078717163.1 B5D49_RS07960 aconitate hydratase
Query= curated2:O28084 (416 letters) >NCBI__GCF_900167125.1:WP_078717163.1 Length = 641 Score = 288 bits (736), Expect = 4e-82 Identities = 157/416 (37%), Positives = 236/416 (56%), Gaps = 2/416 (0%) Query: 1 MGKTIAEKIL-SEKSKSDAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADRTH 59 MG+ I KI+ + + + G + IDQ QD T +A Q +G + + + Sbjct: 1 MGENITRKIIGAHRLSGEMTPGSEIGLRIDQTLTQDATGTMACLQFEAVGLDRVQTELSV 60 Query: 60 FFVDHAAPSPRRELSNDQKFIYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADS 119 +VDH +D +++ A + G F+PPG GI HQ+ +E + +PG +G+DS Sbjct: 61 SYVDHNTLQMGFRNPDDHRYLRTMAARYGIVFSPPGTGICHQLHLENFARPGKTLIGSDS 120 Query: 120 HTCTYGGIGAFSTGMGSTDVAVAIALGKNWFRVPESFRVQLDGSLPKGVFAKDVILKLIG 179 HT T GG+G+ + G G VA+A+A +P+ RVQL G L KDVIL+L+ Sbjct: 121 HTPTAGGVGSLAMGAGGLSVALAMAGEPYTISMPKVVRVQLTGRLSGWAAGKDVILELLR 180 Query: 180 DLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGRE 239 L V G K EF G ++TV ER TI NM E GA IF SDE TR+F +GRE Sbjct: 181 RLTVKGGVGKVFEFAGPGVASLTVPERATITNMGAELGATTSIFPSDERTREFFRIMGRE 240 Query: 240 GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEGTEVNQVYIGTCTNG 299 ++ E+ AD DAEY++ I +++S L P+V++PH D V + E+ G V+QV IG+CTN Sbjct: 241 DEWTELVADADAEYDETIEINLSDLEPLVAQPHMPDRVVPVRELAGLPVSQVAIGSCTNS 300 Query: 300 RLSDLEVAARILKGRKVKEGVRLIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPC 359 +DL+ ++L+GR++ L+V P S++V +GL+ ++AG +L CGPC Sbjct: 301 SYADLKTTVQVLQGRRLPPETDLLVSPGSKQVLKMLAAEGLVEPLLDAGARLLECSCGPC 360 Query: 360 VGIHQGILADGEVCISTQNRNFKGRMGNPNAEIFLASPATAAASAVKGYIADPREF 415 +G+ ++ G V + T NRNF+GR G +A+++LASP TA A+ G DP E+ Sbjct: 361 IGMGGSPVSQG-VSVRTFNRNFEGRSGTKDAQVYLASPQTAVNLALAGKFTDPAEW 415 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: 648 Number of extensions: 30 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: 416 Length of database: 641 Length adjustment: 35 Effective length of query: 381 Effective length of database: 606 Effective search space: 230886 Effective search space used: 230886 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