Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_086509386.1 BZY95_RS07830 phosphogluconate dehydratase
Query= curated2:A7GVT2 (557 letters) >NCBI__GCF_002151265.1:WP_086509386.1 Length = 628 Score = 211 bits (538), Expect = 5e-59 Identities = 158/511 (30%), Positives = 257/511 (50%), Gaps = 34/511 (6%) Query: 34 IGVANSFIEIIPGHFFLNKYAEILKDEIRKNGCVP-FEFNTIGVDDGIAMGHGGMLYSLP 92 + + +S+ +++ H Y E++K R G F + DG+ G GM SL Sbjct: 75 LAIVSSYNDMLSAHRPFESYPEVIKQAARGMGSTAQFAGGVPAMCDGVTQGMPGMELSLF 134 Query: 93 SREIIANSIETVMNAHALDALVCMPNCDKIVPGMVMGALRV-NVPTIFVSGGPMRKGYTK 151 SR++IA + ++ + DA + + CDKIVPG+ +GA R ++P +FV GGPM Sbjct: 135 SRDVIAMATAVALSHNMFDAALYLGICDKIVPGLFIGAARFGHLPAVFVPGGPM-----P 189 Query: 152 SGQPIDLATAFEAVGKFETKEISEEELKEIECNACPSGGSCSGMFTANSMNTLCEAMGIA 211 SG P D + + ++ EEL E E + S G+C+ TANS + E MG+ Sbjct: 190 SGLPNDEKARIRQL--YAEGKVGREELLEAESRSYHSPGTCTFYGTANSNQLMMEMMGLH 247 Query: 212 LSGNGTILALTKEREELIRRAGR---RICEIALDERFKIRNILNEKAVRNALVVDMAMGG 268 L G + T RE L R A R E + + R R I +E+A+ NA+V +A GG Sbjct: 248 LPGASFVNPGTPLREALTRYATEQAIRNTEQSGNYRPFYRQI-DERAIVNAMVGLLASGG 306 Query: 269 SSNTVLHMLAISREAGVNLQISQLNKISQNIAHIAKISPSLPNVHMEDIGRAGGMNAVIK 328 S+N LH++A++ AG+ + + N +S + + +I P+ + + AGGM+ +I+ Sbjct: 307 STNHTLHLVAMAAAAGITIDWNDFNDLSAAVPSLTRIYPN-GSADVNHFQAAGGMSLLIR 365 Query: 329 EISRRDNGMLHLENLTVSGETLGE--------------RVGLSEIKDESVIHKVENAYSK 374 E+ D G++H + TV G L R G +E D V+ V N ++ Sbjct: 366 EL--LDAGLIHGDIPTVFGTDLTAYTQEPFLEDGKLTWREGPTESLDSDVLRPVSNPFAA 423 Query: 375 VGGLAILFGNLAEQGCVIKTAGIVGERKFSGKAVCFNSQDEAIAGISSGKVGKGDVVVIR 434 GGL ++ GNL +G + +A R F+ Q++ A SG++ + VVV+R Sbjct: 424 TGGLVVMEGNLG-RGVIKISAVKQANRVVEAPVRIFDDQNQVKAAFESGELDRDVVVVVR 482 Query: 435 YEGPRGGPGMQEMLSPTSLI-MGRGLGADVALITDGRFSGATRGLSIG-HISPEAAEGGM 492 ++GP+ GM E+ T + + + G VAL+TDGR SGA+ + H++PEA + G Sbjct: 483 FQGPKAN-GMPELHKLTPFLGVLQDRGYKVALVTDGRMSGASGKVPAAIHVTPEAVDRGP 541 Query: 493 IGLLRDGDIIDIDVDTYSINVRLSEAETLKR 523 + LRDGD++ +D + + + AE R Sbjct: 542 LARLRDGDVVRVDAERGELTALVDAAEFASR 572 Lambda K H 0.318 0.136 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: 755 Number of extensions: 43 Number of successful extensions: 8 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: 557 Length of database: 628 Length adjustment: 37 Effective length of query: 520 Effective length of database: 591 Effective search space: 307320 Effective search space used: 307320 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