Align 3-isopropylmalate dehydratase large subunit; EC 4.2.1.33; Alpha-IPM isomerase; IPMI; Isopropylmalate isomerase (uncharacterized)
to candidate WP_013076481.1 BTUS_RS12735 aconitate hydratase AcnA
Query= curated2:Q97EE0 (422 letters) >NCBI__GCF_000092905.1:WP_013076481.1 Length = 903 Score = 137 bits (346), Expect = 1e-36 Identities = 108/368 (29%), Positives = 165/368 (44%), Gaps = 72/368 (19%) Query: 119 DVIIGADSHTCTYGALGVFSTGVGSTDMAVGMATGKAWFKVPEAIKFVLKGKPAKWVSGK 178 D ++G DSHT LGV GVG + GM +F +PE I F L G+ + + Sbjct: 207 DSLVGTDSHTTMINGLGVLGWGVGGIEAEAGMLGQPLYFLIPEVIGFRLTGRLPEGSTAT 266 Query: 179 DIILHIIGMIGVDGALYKSMEYTGDGLEYLSMDDRFTIANMAIEAGAKNGIFPVDEKTIE 238 D+ L + ++ G + K +E+ G GL +++ DR T+ANMA E GA G FPVDE+T++ Sbjct: 267 DLALTVTNLLRKKGVVGKFVEFFGPGLSSITVADRATVANMAPEYGATMGYFPVDERTLD 326 Query: 239 YMK--GRSDRELKKFDADEDAE------------YSRVIEIDLSTLKPTVAFPH------ 278 Y++ GR ++ +A A+ +S ++E+DLST+KPT+A P Sbjct: 327 YLRLTGRKAEDVALAEAYLKAQGLLHTEEAPEPVFSDIVELDLSTVKPTLAGPKRPQDKV 386 Query: 279 -LPENTKTIDQVGEVNVDQ---------------------------------VVIGSCTN 304 LP+ + ++ E VDQ I SCTN Sbjct: 387 PLPDLKASFEKAVESPVDQGGFGFGKEGLARTSDVKYPDGGRETLRTGAVVIAAITSCTN 446 Query: 305 GRMEDLRIAASILKGKKIKKG------IRLIVFPGTQNIYLEAMEEGLVRTFIEAGGIVS 358 + I A +L K ++KG ++ + PG++ + GL+ + G V Sbjct: 447 TSNPSVMIGAGLLAKKAVEKGLTKPRYVKSSLAPGSRVVTAYLKRAGLLPALEQLGFAVV 506 Query: 359 TPTCGPCLGGHMGILAEGERAIS----------TTNRNFVGRMGHPKSEV-YLASPAVAA 407 C C+G + E AI + NRNF GR+ HP YLASP + Sbjct: 507 GYGCTTCIGNSGPLDPEVAEAIQEKDMTVAAVLSGNRNFEGRI-HPLVRANYLASPPLVV 565 Query: 408 ASAIAGKI 415 A A+AG + Sbjct: 566 AYALAGTV 573 Lambda K H 0.317 0.136 0.390 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: 890 Number of extensions: 46 Number of successful extensions: 3 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: 422 Length of database: 903 Length adjustment: 37 Effective length of query: 385 Effective length of database: 866 Effective search space: 333410 Effective search space used: 333410 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 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