Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_014146819.1 MEALZ_RS01520 aconitate hydratase AcnA
Query= curated2:Q2G958 (478 letters) >NCBI__GCF_000968535.2:WP_014146819.1 Length = 899 Score = 125 bits (314), Expect = 6e-33 Identities = 107/359 (29%), Positives = 166/359 (46%), Gaps = 29/359 (8%) Query: 138 DSHTACHGGLGALAFGIGTSEVEHVLATQTLLLKQSKTMEVRVEGELTPGVTAKDVVLHI 197 DSHT GLG LA+G+G E E V+ Q + + + + +++ G+L PGVTA D+VL I Sbjct: 211 DSHTPMVNGLGVLAWGVGGIEAEAVILDQPIYMLEPDVVGIKLTGKLPPGVTATDLVLRI 270 Query: 198 TGVLGAAGGTGSVIEYTGSVIRDLSIEGRLTISNMAIEHGARAGLCAPDEKTFAYLKGRP 257 T + G G +E+ GS + LSI R TISNMA E G+ D+ Y++ Sbjct: 271 TELCRQFGVVGQFVEFYGSGLSQLSIPDRATISNMAPEQGSTVSFFPVDKAALNYMRLTG 330 Query: 258 YAPRGEDWDKAVAWWKSL-ATD--PGATYDKVVVIDAKDIAPSVTWGTSPEDVLPISGLV 314 +P + + A + L TD P + + + +D +I P++ P+D +P+S + Sbjct: 331 RSPEQIELTERYAKLQGLFRTDDAPEPEFTRTLEVDLGEIEPALAGPKRPQDRIPLSQVG 390 Query: 315 PA-PESFADP---SKQEAARASLEYMGLVPG----QRMEDVEVQNIFIGSCTNSRIEDMR 366 P ++ P A + L+ G+V + + V I SCTN+ + Sbjct: 391 PTYRQTLIAPVGIRGMGLAESDLDRCGVVSNKGACETITHGAVVIAAITSCTNTSNPSVM 450 Query: 367 AAA------AILKGRKKADNVKWAIVVPGSGLVKKQAEEEGLDRVFIEAGFEWREPGCSA 420 A A+ KG K + VK ++ PGS +V + ++ GL GF GC+ Sbjct: 451 LGAGLVAKKAVEKGLKVKNYVKTSL-APGSQVVTEYLKQSGLLPYLEALGFYLVGYGCTT 509 Query: 421 CLG-MNPDKVPAGERCAS---------TSNRNFVGRQGPGART-HLVSPAMAAAAAVTG 468 C+G P V E + NRNF GR P +T +L SP + A A+ G Sbjct: 510 CIGNSGPLDVAVEEAIVDNDLVVSAVLSGNRNFEGRVHPLTKTNYLASPPLVVAYALAG 568 Lambda K H 0.317 0.134 0.399 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: 1041 Number of extensions: 62 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: 478 Length of database: 899 Length adjustment: 38 Effective length of query: 440 Effective length of database: 861 Effective search space: 378840 Effective search space used: 378840 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 (21.6 bits) S2: 54 (25.4 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