Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_059153645.1 V474_RS23740 dihydroxy-acid dehydratase family protein
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_001046635.1:WP_059153645.1 Length = 598 Score = 298 bits (762), Expect = 5e-85 Identities = 190/521 (36%), Positives = 288/521 (55%), Gaps = 24/521 (4%) Query: 23 GLIDEELR--RPLIGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTIAVCDGI 80 GL EELR +P+IG+A + +++ P + H +AE ++ GIR GG LEF + + Sbjct: 35 GLSLEELRSGKPIIGIAQTGSDLSPCNRHHLVLAERIREGIREQGGIALEFPVHPIQETG 94 Query: 81 AMGHEGMRYSLPSREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARLEVPVILI 140 G+ +L ++ + + LD VV+ T CDK TP L+AAA + +P I + Sbjct: 95 KRPTAGLDRNLAYLALVE-----AIYGYPLDGVVLTTGCDKTTPALLMAAATVNIPAIAL 149 Query: 141 NGGPMMPGVYGKERIDFKDLMERMNVLIKEGRTEE--LRKLEESALPGPGSCAGLFTANT 198 + GPM+ G + ER ++ + ++ G + KL S+ P G C + TA T Sbjct: 150 SVGPMLNGWHKGERTGSGTIVWKGRQMMAAGELDADGFIKLVASSAPSTGYCNTMGTATT 209 Query: 199 MNMLSEAMGLMLPGASTVPAVEARRLWYAKLTGMRIVKMVEEGLTPDKILTRKALENAIA 258 MN L+EA+G+MLPG++ +PA R A TG RIV MV E L P ILT A NAI Sbjct: 210 MNSLAEALGMMLPGSAAIPAPYRDRQECAWRTGKRIVDMVHEDLKPSDILTLDAFHNAIV 269 Query: 259 VDMALGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGG 318 V+ A+GGSTN+ +HL A+A +G+DLPL+ ++ + KVP + ++ P+G + D RAGG Sbjct: 270 VNAAIGGSTNAPIHLAAIARHIGVDLPLKDWERLGHKVPLLVNLQPAGEYLGEDYYRAGG 329 Query: 319 IPAVLKELGEAGLIHKDALTVTGKTVWENVKDAAVLDREVIRPLDNPYSPFGGLAILKGS 378 +PAV+ +L GLI + A+TV G T+ +N +DA + D +VI+ D P G +L G+ Sbjct: 330 VPAVVAQLIGQGLIAESAMTVNGLTIGDNCRDATIEDDKVIKTFDQPLVEEAGFLVLSGN 389 Query: 379 LAPNGAVVKASAVKREL-----------WKFKGVARVFDREEDAVKAIRGGE--IEPGTV 425 L + A++K S + E F+G A VFD ED I I P T+ Sbjct: 390 LF-DAAIMKTSVISDEFRARYLSNPDDPEAFEGPAVVFDGPEDYHHRIDDPSVGITPETL 448 Query: 426 IVIRYEGPRGGPGMREMLTATAAVMALGLG-DKVALVTDGRFSGATRGPAIGHVSPEAAA 484 + +R GP G PG E++ + G + + DGR SG + P+I + SPEAAA Sbjct: 449 MFMRGAGPIGYPGAAEVVNMRPPSYLITEGVSALPCIGDGRQSGTSGSPSILNASPEAAA 508 Query: 485 GGPIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPK 525 G +AL+Q GD + +D++K +D+L+ ++EL RRA + K Sbjct: 509 MGGLALLQTGDRVRMDLKKGTVDVLISDEELAARRADLEAK 549 Lambda K H 0.319 0.138 0.401 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: 842 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: 552 Length of database: 598 Length adjustment: 36 Effective length of query: 516 Effective length of database: 562 Effective search space: 289992 Effective search space used: 289992 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 (21.7 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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