Align 3-isopropylmalate dehydratase large subunit 2; EC 4.2.1.33; Alpha-IPM isomerase 2; IPMI 2; Isopropylmalate isomerase 2 (uncharacterized)
to candidate Dsui_2347 Dsui_2347 aconitate hydratase 1
Query= curated2:Q9WZ24 (417 letters) >FitnessBrowser__PS:Dsui_2347 Length = 898 Score = 132 bits (333), Expect = 3e-35 Identities = 129/440 (29%), Positives = 197/440 (44%), Gaps = 85/440 (19%) Query: 55 DRVVLVPDHFTPNKDIKSAMQVKMMREFAREQ----GIEKF--FEI--GRMGIEHVLLPE 106 D V V ++ TP ++ M+++ R R Q G++ F F++ +GI H + E Sbjct: 129 DHSVQVDEYGTPTA-LRRNMELEFQRNAERYQFMKWGMQAFDTFKVVPPGIGIVHQVNLE 187 Query: 107 ---EGIVKSGDLV-----VGADSHTCTYGALGAFATGVGSTDIAGFYLIGKVWFRVPESI 158 G+ + G+L+ VG DSHT +G GVG + L V+F P+ + Sbjct: 188 YLFRGVRRQGELLFPDTLVGTDSHTTMINGVGVVGWGVGGIEAEAAMLGQPVYFLTPDVV 247 Query: 159 KVTLRGKFKDLVTAKDLVLKLISILGVDGANYKAIEFSGPGVKEISMDGRFTISNMAIEA 218 V LRG+ + VTA DLVL + +L + K +EF GPG +S+ R TI+NMA E Sbjct: 248 GVELRGRLNEGVTATDLVLTVTELLRREKVVGKFVEFFGPGSTSLSLTDRATIANMAPEY 307 Query: 219 GGKTGLFPVDEITIAYERERG-----IEVEEMY----------PDEDAKYVREVEMDLSE 263 G G FPVDE T+ Y R+ G +E E Y D Y ++ +DL+ Sbjct: 308 GATLGFFPVDEKTVDYLRQTGRNEAEVEAFEAYFRAQGLFGAPRAGDIDYSTQLSLDLAT 367 Query: 264 LEPQVAYPFLPSNAKDVSEAEKE----------------------------RIKIDQ--- 292 + P +A P P + D+S+ + R +D Sbjct: 368 IVPSLAGPKRPQDRIDLSDMGRSFDTLFSQPTSANGFGKPAEQLPQRQPTARAGVDLGHG 427 Query: 293 ----AVIGSCTNGRIEDLRLAAQIL------KGRTVSPDVRCIIIPGSQKVYKQALKEGL 342 A I SCTN + +AA +L KG +V P ++ + PGS+ V K GL Sbjct: 428 DVLIAAITSCTNTSNPAVLIAAGLLAKKAVDKGLSVQPHIKTSLAPGSRVVTDYLEKAGL 487 Query: 343 IDIFIDAGCAVSTPTCGPCLG--GHMG-----VLAEGEV---AISTTNRNFVGRMGHPNS 392 + G A++ C C+G G + +AE ++ A+ + NRNF R+ HP Sbjct: 488 LAPLARLGFALAGYGCTTCIGNAGDLAPEFNQAIAERDLVVAAVLSGNRNFEARI-HPAI 546 Query: 393 KV-FLASPAVAAASAIKGYI 411 + +LASP + A AI G + Sbjct: 547 RANYLASPPLVVAFAIAGRV 566 Lambda K H 0.318 0.138 0.395 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: 776 Number of extensions: 55 Number of successful extensions: 3 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: 417 Length of database: 898 Length adjustment: 37 Effective length of query: 380 Effective length of database: 861 Effective search space: 327180 Effective search space used: 327180 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