Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_041230373.1 DACET_RS11845 bifunctional aconitate hydratase 2/2-methylisocitrate dehydratase
Query= curated2:B2V844 (431 letters) >NCBI__GCF_000025725.1:WP_041230373.1 Length = 848 Score = 118 bits (296), Expect = 6e-31 Identities = 122/470 (25%), Positives = 199/470 (42%), Gaps = 57/470 (12%) Query: 2 GMTITEKIIAAHAGRDYVEPGELVTVKVDLAIANDITAPLAIKQLEKYGIDKVHDPNKIA 61 G T+ +KII AG D V PG K+ + D T P+ ++++ + P + Sbjct: 367 GYTLAQKIIGKAAGVDGVLPGTACEPKMTTVGSQDTTGPMTRDEIKELACLEFQSPMFMQ 426 Query: 62 LVMDHFFPPKDIMSAQQIKISRDFAKKMGIKNYFEGQDSGVMHTLLPEKGFVVPGDLVIG 121 PK + + +++ G+ GV+H+ L ++P L G Sbjct: 427 SFCHTAAYPKKADVDMHKSLPQFVSERKGVSLR---PGDGVIHSWLNR--LLLPDTLGTG 481 Query: 122 ADSHTCTYGGIGAFSTGVGSTDIAYIWATGETWLRVPESMKFVFYNKPQKWVGGKDFV-- 179 DSHT G+ S GS +A+ A G L VPES+ F + +D V Sbjct: 482 GDSHTRFPMGL---SLPAGSGLVAFAGALGFMPLDVPESVLVKFKGDFNPGITLRDAVNA 538 Query: 180 ----------LTVIGKIGVDGALYKAMEYQGEAIRALDIDNRLTIANMAIEAGGKSGIIE 229 LTV K + ++ + E + L ++ + + E G I+ Sbjct: 539 IPYWAIKQGLLTVPKKNKKN--IFNGRILEMEGLPNLTVEQAFELTDATAERSAAGGTIK 596 Query: 230 PDEKTV----------------------DWVRKRTN------REFKLYKSDPDAKYCCEY 261 E++V + ++KR KL + D +A+Y Sbjct: 597 LSEESVANYLKSNIALMKKMIEAGYQHAETLKKRIEDCEAWLANPKLLERDENAEYAAVI 656 Query: 262 EFDASKI-EPVVACPSLPSNVKPVSEVAGTHIDQVFIGSCTNGRLSDLRIAAAILKSKKV 320 E D ++I EP++ACP+ P +VK +S++AGT ID+ FIGSC + R A I + + Sbjct: 657 EIDLAEITEPILACPNDPDDVKLLSDIAGTKIDETFIGSCMT-NIGHFRAAGKIWEG-EA 714 Query: 321 HPEVRCIVIPASDQIYKQALHEGIIEILADAGCLISTSTCGPCLGGHMGILAEGEVCLST 380 +P+ R + P + Q + EG I + G C C+ G+ G +A LST Sbjct: 715 YPKTRMWMTPPTRMDEMQLMEEGYYSIFSSVGARTEIPGCSLCM-GNQGRVAPKAFVLST 773 Query: 381 SNRNFVGRMGHPKSQVYLSSPAVAAASAVLGRIAHPDEVAKYEEVETLIT 430 S RNF R+G +SQV+L S + A +A+ G + P + +E E +T Sbjct: 774 STRNFPNRIG-DESQVFLGSAELTAITALCGEL--PTKEKYFELFEKKVT 820 Lambda K H 0.319 0.137 0.407 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: 901 Number of extensions: 47 Number of successful extensions: 4 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 431 Length of database: 848 Length adjustment: 37 Effective length of query: 394 Effective length of database: 811 Effective search space: 319534 Effective search space used: 319534 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