Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate Echvi_2531 Echvi_2531 aconitate hydratase, mitochondrial
Query= curated2:O28084 (416 letters) >FitnessBrowser__Cola:Echvi_2531 Length = 757 Score = 191 bits (485), Expect = 6e-53 Identities = 143/450 (31%), Positives = 217/450 (48%), Gaps = 49/450 (10%) Query: 4 TIAEKIL------SEKSKSDAYAGDIVVAEIDQIALQDGTAPLAIRQLMELGTEVRAADR 57 T+AEKIL + +++ V D++A+QD TA +A+ Q M+ G E A Sbjct: 31 TLAEKILYAHLWGGDATQAFERGKSYVDFAPDRVAMQDATAQMALLQFMQAGKEKVAVPS 90 Query: 58 THFFVDH-------AAPSPRRELSNDQK---FIYEFAKKVGADFNPPGEGIIHQIMVERY 107 T DH A R L+ + F+ + K G F PG GIIHQ+++E Y Sbjct: 91 TAH-CDHLILAQKGAEEDLRSSLTASGEVFNFLESVSNKYGIGFWKPGAGIIHQVVLENY 149 Query: 108 VKPGDLAVGADSHTCTYGGIGAFSTGMGSTDVAVAIALGKNW-FRVPESFRVQLDGSLPK 166 PG + +G DSHT GG+G + G+G D AV + G W + P+ V+L G + Sbjct: 150 AFPGGMMIGTDSHTVNAGGLGMVAIGVGGAD-AVDVMAGMPWELKFPKLIGVKLTGKMNG 208 Query: 167 GVFAKDVILKLIGDLGVDGATYKALEFHGECAENMTVEERLTIANMAVECGAKAGIFESD 226 AKDVILK+ G L V G T +E+ GE A++++ + TI NM E GA F D Sbjct: 209 WTSAKDVILKVAGILTVKGGTGCIVEYFGEGAKSLSATGKGTICNMGAEIGATTSTFGYD 268 Query: 227 ENTRKFL--------AELGRE------GDFREVKADEDAEYEKEIYMDVSSLVPVVSKPH 272 E+ ++L A+L E GD EV A+ + +++ I +D+S+L P ++ P Sbjct: 269 ESMERYLRSTDRADVADLANEVKEHLTGD-DEVYANPEQYFDQVIEIDLSTLEPHINGPF 327 Query: 273 NVDNVAEISEVEG--------TEVNQVYIGTCTNGRLSDLEVAARILK---GRKVKEGVR 321 D +S++ T+V IG+CTN DL A+ I + +++K Sbjct: 328 TPDRATPVSQIRAEAEKNGWPTKVEWGLIGSCTNSSYEDLSRASSIAQQAVDKQLKTKAD 387 Query: 322 LIVVPASRRVYLQALDKGLIRVFVEAGGMVLNPGCGPCVGIHQGILADGE---VCISTQN 378 + P S +V A G++++F + + CGPC+G AD + + + N Sbjct: 388 FGINPGSEQVRFTAERDGMLKIFEDLDATIFTNACGPCIGQWARTGADKQEKNTIVHSFN 447 Query: 379 RNFKGRM-GNPNAEIFLASPATAAASAVKG 407 RNF R GNPN F+ SP AA A+ G Sbjct: 448 RNFSKRADGNPNTHAFVTSPEMVAAIAISG 477 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: 720 Number of extensions: 44 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: 757 Length adjustment: 36 Effective length of query: 380 Effective length of database: 721 Effective search space: 273980 Effective search space used: 273980 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 09 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