Align 3-isopropylmalate dehydratase small subunit 1; EC 4.2.1.33; Alpha-IPM isomerase 1; IPMI 1; Isopropylmalate isomerase 1 (uncharacterized)
to candidate 8502313 DvMF_3021 aconitate hydratase (RefSeq)
Query= curated2:Q8TX94 (170 letters) >FitnessBrowser__Miya:8502313 Length = 641 Score = 77.0 bits (188), Expect = 6e-19 Identities = 63/173 (36%), Positives = 87/173 (50%), Gaps = 35/173 (20%) Query: 13 GDDIDTDQIIP-GRYLTT--QDPEELAKHVMEGADPEFPEKVREGD--VIVAGKNFGCGS 67 GDDI TD I+P G +T+ + +A+HV D +F + R VIVAG N+G GS Sbjct: 475 GDDITTDHIMPAGAEITSLRSNVPAIAQHVFGRVDADFVARARAAGIGVIVAGDNYGQGS 534 Query: 68 SREHAPIALKAAGIACVVTRSFARIFYRNAINLG-LPLVVCPGVD--------------D 112 SREHA +A + GI V+ RS ARI N +N G LPL++C D Sbjct: 535 SREHAALAPRHLGIRAVIVRSLARIHRANLVNFGILPLILCDRTDYDKLAVGGTVAIPAS 594 Query: 113 AFEDGQGIEVNLREGY----VRNLDTGEELEAKPLPDFMMRILEAGGLVELIK 161 A G ++V + EG VRN T +EL+ I+ AGGL+ ++ Sbjct: 595 AITAGGEVDVQV-EGVGAIRVRNDLTQKELD----------IIRAGGLLNHVR 636 Lambda K H 0.321 0.143 0.428 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: 286 Number of extensions: 24 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: 170 Length of database: 641 Length adjustment: 28 Effective length of query: 142 Effective length of database: 613 Effective search space: 87046 Effective search space used: 87046 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 (21.8 bits) S2: 48 (23.1 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