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_066324960.1 BLR17_RS07090 aconitate hydratase
Query= curated2:O28084 (416 letters) >NCBI__GCF_900100165.1:WP_066324960.1 Length = 753 Score = 183 bits (465), Expect = 1e-50 Identities = 136/418 (32%), Positives = 196/418 (46%), Gaps = 41/418 (9%) Query: 29 DQIALQDGTAPLAIRQLMELGTEVRAADRT----HFFVDHAAPSPRRELSNDQK-----F 79 D++A QD TA +A+ Q M G A T H S ++N Q F Sbjct: 62 DRVACQDATAQMALLQFMHAGKSKVAVPTTVHCDHLIQAKVGASTDLAVANTQSKEVFDF 121 Query: 80 IYEFAKKVGADFNPPGEGIIHQIMVERYVKPGDLAVGADSHTCTYGGIGAFSTGMGSTDV 139 + + K G F PG GIIHQI++E Y PG + +G DSHT GG+G + G+G D Sbjct: 122 LSSVSNKYGIGFWKPGSGIIHQIVLENYAFPGGMMIGTDSHTVNAGGLGMLAIGVGGAD- 180 Query: 140 AVAIALGKNW-FRVPESFRVQLDGSLPKGVFAKDVILKLIGDLGVDGATYKALEFHGECA 198 AV + G +W + P+ V+L G L KDVILK+ L V G T +E+ GE A Sbjct: 181 AVDVMSGMSWELKFPKLIGVKLTGKLSGWTAPKDVILKVADILTVKGGTGAIVEYFGEGA 240 Query: 199 ENMTVEERLTIANMAVECGAKAGIFESDENTRKFLAELGREGDF-------------REV 245 NM+ + TI NM E GA F D++ R++L GR+ EV Sbjct: 241 TNMSCTGKGTICNMGAEIGATTSTFGYDDSMRRYLTATGRQDVVDAADKVAAYLTADSEV 300 Query: 246 KADEDAEYEKEIYMDVSSLVPVVSKPHNVDNVAEISEVEG--------TEVNQVYIGTCT 297 A+ + +++ I +++S L P ++ P D +S+++ +V IG+CT Sbjct: 301 YANPEQYFDQLIEINLSELEPHINGPFTPDRGTPVSQMKAEAEANGWPLKVEWGLIGSCT 360 Query: 298 NGRLSDLEVAARILKGRKVKEGV----RLIVVPASRRVYLQALDKGLIRVFVEAGGMVLN 353 N D+ AA I++ + V GV + P S ++ G+I F + G V Sbjct: 361 NSSYEDMSRAASIVR-QAVALGVTPKAEFGINPGSEQIRYTIERDGIIADFEKMGTKVFT 419 Query: 354 PGCGPCVGIHQGILAD-GE--VCISTQNRNFKGRM-GNPNAEIFLASPATAAASAVKG 407 CGPC+G AD GE + + NRNF R GNPN F+ SP AA A+ G Sbjct: 420 NACGPCIGQWDRAGADKGEKNTIVHSFNRNFSKRADGNPNTHAFVTSPEMVAALAISG 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: 731 Number of extensions: 46 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: 753 Length adjustment: 36 Effective length of query: 380 Effective length of database: 717 Effective search space: 272460 Effective search space used: 272460 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 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