Align Probable 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_012469942.1 GLOV_RS09360 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:O27439 (419 letters) >NCBI__GCF_000020385.1:WP_012469942.1 Length = 843 Score = 102 bits (254), Expect = 4e-26 Identities = 113/455 (24%), Positives = 189/455 (41%), Gaps = 57/455 (12%) Query: 4 TVSEKILARASGKDRVEAGEIVMADIDVAMTHDLTGPLSVESFRAIGEDRVWDPEKIVVI 63 ++++K++ +A G + G + + D TGP++ + + + + P + Sbjct: 372 SLAQKMVGKACGVAGILPGTACEPKMTTVGSQDTTGPMTADELKELACLKFLSP-MFMQS 430 Query: 64 FDHQVPADSIEAAQNHMIMRDFVEEQGIRNFYDVREGVCHQVLPEKGHVVPGEVVVGTDS 123 F H + H + F+ E+G +GV H L ++P V G DS Sbjct: 431 FCHTAAYPKPADVKMHKTLPAFIAERG-GVALKPGDGVIHSWLNRL--LLPDTVGTGGDS 487 Query: 124 HTCTHGALGAFATGI----GSTDMAMVFATGKLWFRVPETLRFDVRGKLREHVYAKDVIL 179 HT F GI GS +A A G + +PE++ +G + +D + Sbjct: 488 HT-------RFPIGISFPAGSGLVAFAGAMGFMPLDMPESVLVRFKGTFNPGITLRDAVN 540 Query: 180 NIIGRVGADGATYMACE-----FAG-----ETVAEMSVSDRMVLSNMAIEMGGKTGIVE- 228 I G + + F G E + E++V L++ A E G ++ Sbjct: 541 AIPYWAIKQGLLTVPKKNKVNIFNGRILEMEGLPELTVEQGFELTDAAAERSAAAGCIQL 600 Query: 229 PDEKTLNYVRRRSG---------------------------KPWRVFKTDPDAPSLSVME 261 E Y+R K ++ + D +A +V+E Sbjct: 601 SKESVATYLRSNVALMKKMIADGYQDPQTLQNRIDAVNEWLKNPQLLEADKNAEYAAVIE 660 Query: 262 VDVSDL-EPQVACPHNVDNVKPVTEVEGTEIDQVFLGSCTNGRLSDLRDAAAILKNRKVS 320 +D++++ EP +ACP++ D+VK ++EV GT I VF+GSC + R AA I K K + Sbjct: 661 IDLAEITEPILACPNDPDDVKLLSEVAGTPIQDVFIGSCMT-NIGHFRAAAEIWKGEKFN 719 Query: 321 DSVRMLVIPASREVYRRALDEGLIEIFVDAGALVCNPCCGPCLGGHVGLVGPGEVSLSTS 380 +VR + P +R DE + I+ GA + C C+G V G STS Sbjct: 720 PNVRTWITPPTRMDSDLLKDEAVFSIYSAFGARIEIAGCSLCMGNQ-ARVPDGVNMFSTS 778 Query: 381 NRNFRGRQGSPEAEVYLSSAAVAAASAVKGSITHP 415 RNF R G+ A+V+L SA + A +A G + P Sbjct: 779 TRNFDDRIGN-GAKVFLGSAELGAVAAKMGKLPTP 812 Lambda K H 0.318 0.135 0.396 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: 749 Number of extensions: 39 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: 419 Length of database: 843 Length adjustment: 37 Effective length of query: 382 Effective length of database: 806 Effective search space: 307892 Effective search space used: 307892 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 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