Align Dihydroxy-acid dehydratase ilvC, mitochondrial; DHAD ilvC; EC 4.2.1.9 (characterized)
to candidate YP_004139355.1 Mesci_0132 Dihydroxy-acid dehydratase
Query= SwissProt::Q4X099 (606 letters) >NCBI__GCF_000185905.1:YP_004139355.1 Length = 601 Score = 270 bits (689), Expect = 2e-76 Identities = 177/523 (33%), Positives = 283/523 (54%), Gaps = 29/523 (5%) Query: 61 GLTEEDM--NKAQVGISSVWYNGNPCNMHLLDLSNRVREGVQKAGLVGFQFNTVGVSDAI 118 GLT ++ K +GI+ + +PCN H ++L+ RVREG+ G + F+F + + Sbjct: 37 GLTRAELMSGKPLIGIAQTGSDLSPCNRHHIELAKRVREGIVSMGGIPFEFPCHPIQETG 96 Query: 119 SMGTKGMRYSLQSRDLIADSIETVMGGQWYDANISIPGCDKNMPGVLMAMGRVNRPSLMV 178 T + R+L S+ V+ G D + GCDK P +LMA VN P++ + Sbjct: 97 KRPTAAL-----DRNLAYLSLVEVLYGYPLDGVVLTIGCDKTTPALLMAAATVNIPAIAL 151 Query: 179 YGGTIKPGCARTQNNADIDIVSAFQAYGQFLTGEITENQRFDIIRNACPGGGACGGMYTA 238 G + G + + IV +++ + GEI ++ DI+ ++ P G C M TA Sbjct: 152 SVGPMLNGWHKGKRTGSGTIV--WESRQRLSAGEIDYDEFMDIVASSAPSTGYCNTMGTA 209 Query: 239 NTMATAIEVMGMTLPGSSSNPAESKAKDLECLAAGEAIKRLLKEDIRPSDILTRQAFENA 298 TM + E +GM LPGS++ PA + + G+ I ++ ED++PSDI+TR+AFENA Sbjct: 210 TTMNSLAEALGMQLPGSAAIPAPYRERGQISYETGKRIVEMVHEDLKPSDIMTREAFENA 269 Query: 299 MIVVNITGGSTNAVLHLIAIADSVGIKLDIEDFQKVSDRTPFLADLKPSGKYVMADLHNI 358 ++V + GGSTNA +HL AIA +G+KLD +D+Q V P L +L+P+G+Y+ D H+ Sbjct: 270 IVVNSAIGGSTNAPIHLNAIARHLGVKLDNDDWQTVGLNVPLLVNLQPTGEYLGEDYHHA 329 Query: 359 GGTPSLLKFLLKEGVIDGSG-MTVTGETLAKNLEKVPDFPADQKIIRPLSNPIKKTGHIQ 417 GG P+++ L+K ++ G TV G+++ +N E V + D +IR ++ P+K Sbjct: 330 GGVPAVIAELMKGDLLPHPGARTVNGKSIGENSEGVANENPD--VIRSVAKPLKANAGFI 387 Query: 418 ILRGSLAPGGSVGKITG-------------KEGTRFVGKARVFDDEDDFIAALERNEIKK 464 LRG+L ++ K +G ++ F G A VFD +D+ A ++ Sbjct: 388 NLRGNLF-DSAIMKTSGISPEFRERYLSNPRDPEAFEGNAMVFDGPEDYHARIDDPAQGI 446 Query: 465 EEKTVVVIRYTGPKGGPGMPEM--LKPSSALMGAGLGSSCALITDGRFSGGSHGFLIGHI 522 +E T++ +R GP G PG E+ ++P + L+ G+ + A I DGR SG S I + Sbjct: 447 DEHTILFMRGAGPVGYPGGAEVVNMQPPAYLIKKGI-HALACIGDGRQSGTSGSPSILNA 505 Query: 523 VPEAAVGGPIGLVKDGDTITIDAEKRLLDLDVDETELARRRKE 565 PEAA+GG + L+K GD + ID K D+ V + E+ RRR E Sbjct: 506 SPEAAIGGGLALLKTGDRVRIDLRKGTADILVTDDEITRRRAE 548 Lambda K H 0.316 0.135 0.387 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: 900 Number of extensions: 45 Number of successful extensions: 5 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: 606 Length of database: 601 Length adjustment: 37 Effective length of query: 569 Effective length of database: 564 Effective search space: 320916 Effective search space used: 320916 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: 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