Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011879750.1 dihydroxy-acid dehydratase
Query= curated2:Q2FMZ1 (547 letters) >NCBI__GCF_000016205.1:WP_011879750.1 Length = 593 Score = 289 bits (739), Expect = 2e-82 Identities = 200/539 (37%), Positives = 284/539 (52%), Gaps = 40/539 (7%) Query: 25 DESEMHQPFIGIANSWNTIVPGHTHLRVLGERVREGITAGGGTPFEFNTIGICDGIAMGH 84 DE + +P IGIA + + + P + H L ERVR GI GG P EF + + Sbjct: 38 DELQSGRPIIGIAQTGSDLAPCNRHHLELAERVRAGIRDAGGIPMEFPVHPLAE------ 91 Query: 85 EGMRYSLPSRENIADSVELMIQAHKF--DGIVCICTCDKIVPGMLMAAGRCNIPAIVLTG 142 + R + N+A + L+ H F DG+V CDK P LMAA ++PAIVL+G Sbjct: 92 QSRRPTAALDRNLA-YLGLVEVLHGFPLDGVVLTTGCDKTTPACLMAAATVDMPAIVLSG 150 Query: 143 GNMLPGNLHGCEL-SLTDVFEGVGKVAGGTMTEEELTELETAAMPGCGSCQGLYTANTMA 201 G ML G G + S T ++ +A G + E L TAA P G C + TA +M Sbjct: 151 GPMLDGWHDGKRVGSGTVIWHARNLLAAGEIDYEGFMALTTAASPSIGHCNTMGTALSMN 210 Query: 202 CMTEALGMSLPGCAATPAVYADKIRLAYRTGKRIVDLVRKQILPRDIITPASLRNAIRVD 261 + EALGMSLPGCA+ PA Y ++ ++AY TGKR V+LVR + P I+T A+ NAI V Sbjct: 211 SLAEALGMSLPGCASIPAAYRERGQMAYATGKRAVELVRDDVRPSQIMTRAAFENAIVVA 270 Query: 262 MALGGSTNTVLHLMAIATEAGVPFDLQEFNRLSEQIPHIASMMPAGPHSMQALHHAGGIP 321 ALG STN HL+AIA GV L ++ R E +P + + MPAG + ++ H AGG+P Sbjct: 271 SALGASTNCPPHLIAIARHMGVELSLDDWQRFGEAVPLLVNCMPAGEYLGESFHRAGGVP 330 Query: 322 AVFRQIRSH---LENCQTVSGMDIYTIADSVKYVDESVIRPEQSPVHQSGGLMILTGSLA 378 AV RQ+ + +C TVSG I IAD+ D VIR +P+ G ++L+G+ Sbjct: 331 AVLRQLDAAGLLRRDCMTVSGRPIGAIADAAPPADRDVIRTPDAPLKHGAGFIVLSGNFF 390 Query: 379 PDGAVIKSGAVQDEM---------WKHTGPAR--VFDGEELAMKAI--LAREIKEGDIIV 425 D A++K V D ++T AR VFDG E I I E I+V Sbjct: 391 -DSAIMKMSVVGDAFRQTYLAEPGAENTFDARAIVFDGPEDYRARIDDPQLNIDERCILV 449 Query: 426 IRYEGPKGGPGMPEM--LSPTSALVGLGYSRVALITDGRFSGGTRGPCIGHVAPEAAAGG 483 IR G G PG E+ ++P +ALV G + + + DGR SG + P I +++PEAA GG Sbjct: 450 IRGCGTVGYPGSAEVVNMAPPAALVKRGVTSLPCMGDGRQSGTSASPSILNMSPEAAVGG 509 Query: 484 PIAFVKDGDQISIDLFTKTVNLNISADEIENRKK-----------GWKPLKRPLTGVLA 531 +A ++ D+I +DL +TV++ + E+ R++ W+ L R G L+ Sbjct: 510 GLALLRTDDRIRVDLNRRTVDVLVDEAELARRRETATFAAPPAQTPWQELYRRFVGQLS 568 Lambda K H 0.319 0.137 0.409 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: 828 Number of extensions: 47 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: 547 Length of database: 593 Length adjustment: 36 Effective length of query: 511 Effective length of database: 557 Effective search space: 284627 Effective search space used: 284627 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: 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