Align Dihydroxy-acid dehydratase 2; DAD 2; EC 4.2.1.9 (uncharacterized)
to candidate WP_012758714.1 RLEG_RS16525 dihydroxy-acid dehydratase
Query= curated2:Q5YX61 (629 letters) >NCBI__GCF_000023185.1:WP_012758714.1 Length = 594 Score = 199 bits (506), Expect = 3e-55 Identities = 176/555 (31%), Positives = 250/555 (45%), Gaps = 76/555 (13%) Query: 35 KPVVAVANSFTEFVPGHTHLQPVGRIVGDAIRRAGGIPREFNTIAVDDGIAMGHQGMLYS 94 KPV+ +A S ++ P + + + V D IR AGGIP EF T + + + Sbjct: 47 KPVIGIAQSGSDLTPCNRVHVELAKRVRDGIRDAGGIPIEFPTHPIFENCKRPTAAL--- 103 Query: 95 LPSRDLIADSIEYMVQAHCADALVCISNCDKITPGMLLAAMRLDIPTVFVSGGPMEGG-- 152 R+L + ++ + D +V + CDK TP ++AA +DIP + +SGGPM G Sbjct: 104 --DRNLAYLGLVEILYGYPLDGVVLTTGCDKTTPSAIMAASTVDIPAIVLSGGPMLDGWH 161 Query: 153 RATLA-DGTVR-RLDLITAMSEAVNDATSDADLATIEENACPTCGSCAGMFTANSMNCLV 210 LA GTV R+ A E + A L ++ P+ G C M TA++MN L Sbjct: 162 EGELAGSGTVIWRMRRKYAAGEIDREEFLQAAL-----DSAPSVGHCNTMGTASTMNALA 216 Query: 211 EALGLALPGNGTTLATHTARRDLYEAAGATIMAITRRYYDRDDATVLPRAIASRAAFDNA 270 EALGL+L G G A + R + G RR + + P I +R AF NA Sbjct: 217 EALGLSLTGCGAIPAAYRERGQMAYRTG-------RRAVEIVFEDLKPSDILTREAFLNA 269 Query: 271 MALDLAMGGSTNTVLHLLAAAHEAGLDYTLADIEKRSRAVPCLCKVAPNGSHLMEDVHRA 330 + + A+GGSTN HL A A AG++ D + +P L V P G++L E HRA Sbjct: 270 IRTNSAIGGSTNAQPHLAAMAKHAGVELYPDDWQVHGFDIPLLANVQPAGAYLGERFHRA 329 Query: 331 GGIPAILGELRRGGHLHTTVRAVHSESLDGWLAEWDVRGPNPAQAAVDLFHAAPGGVRSA 390 GG PAI+ EL + G L R V ++ L + R Sbjct: 330 GGTPAIMWELLQAGKLAGNCRTVTGRTIAENLEGKEAR---------------------- 367 Query: 391 TAFSQSARWAALDLDAESGCIRDVAHAYSEDGGLAVLRGNLAVDGAVVKSAGVPADLH-- 448 + I+ A E G VL+GNL D A++K + V D Sbjct: 368 ----------------DREVIKPFAEPLKERAGFLVLKGNL-FDFAIMKMSVVSEDFRRR 410 Query: 449 ---------VFTGEAVVAESQEEAVTAVLSGR--VRPGTVLVIRYEGPRGGPGMQEM--L 495 VF G AVV + E+ + + T+L IR GP G PG E+ + Sbjct: 411 YLEEPGHEGVFEGRAVVFDGSEDYHKRINDPELGIDENTILAIRGAGPIGWPGSAEVVNM 470 Query: 496 YPTAYLKGRGLAGSVAVVTDGRFSGGSSGLSIGHVSPEAAAGGTIAAVTDGDPITIDIPS 555 P +L RG++ S+ + DGR SG + SI + SPE+AAGG +A + GD I ID Sbjct: 471 QPPDHLLKRGIS-SLPTIGDGRQSGTADSPSILNASPESAAGGGLAWLRTGDIIRIDFNH 529 Query: 556 RTLRLEVDDAEIARR 570 + V+DAEI RR Sbjct: 530 GRCDMLVEDAEIERR 544 Lambda K H 0.319 0.134 0.395 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: 955 Number of extensions: 51 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 629 Length of database: 594 Length adjustment: 37 Effective length of query: 592 Effective length of database: 557 Effective search space: 329744 Effective search space used: 329744 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