Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate HSERO_RS05520 HSERO_RS05520 phosphogluconate dehydratase
Query= curated2:B7GUP9 (620 letters) >FitnessBrowser__HerbieS:HSERO_RS05520 Length = 623 Score = 221 bits (564), Expect = 6e-62 Identities = 168/537 (31%), Positives = 258/537 (48%), Gaps = 44/537 (8%) Query: 34 KKPIIAIANSFDEFLPGHVHLNKVGRIVSEAIKEAGGIPR-EFNTMAVDDGIAMGHTGML 92 K P +AI +++++ L H + +I+ +A +EAG + + + A+ DG+ G GM Sbjct: 66 KAPSLAIVSAYNDMLSAHQPFERFPQIIKDAAREAGAVAQFAGGSPAMCDGVTQGQAGME 125 Query: 93 YSLPSRDIIADTVEYQCNAHCADALICIPNCDKVVPGMLMAALRL-NIPTVFVSGGPMEA 151 SL SRD IA + + DA + + CDK+VPG+L+ AL ++P VFV GPM + Sbjct: 126 LSLFSRDAIAMATAIALSHNMFDAALYLGVCDKIVPGLLIGALHFGHLPAVFVPAGPMTS 185 Query: 152 GTTVLADGTVKSTDLIDVMYATADDSVSDEELLNYEKTVCPTCGSCAGMFTANSMNCLTE 211 G + ++D + + + ELL E G+C TANS L E Sbjct: 186 G--------MSNSDKVKIRQLYTAGKIGRAELLEAESKSYHGAGTCTFYGTANSNQMLME 237 Query: 212 AIGLALPGNGTILASHSYRKDLFERAAKQVVKIAHQYYDDSDDSVLPRS-IATKEAFENA 270 A+GL LPG I + R L AAKQ KI D P + +++ NA Sbjct: 238 AMGLHLPGAAFITPNTPLRDALTAAAAKQAAKIT-----DLGTQYTPVGRMIDEKSIVNA 292 Query: 271 MTMDVAMGGSTNTVLHILAMAQSADVDFTLDDIERISHTVPCICKASPSGKWEISDVHRA 330 + A GGSTN LH++A+A++A + DD +++S VP I K P+G +++ H A Sbjct: 293 IVALHATGGSTNHTLHLVAIAKAAGIVIDWDDFDKLSAVVPLITKIYPNGTADVNHFHAA 352 Query: 331 GGITGILGELDRAGKLHTNVHSIDYPTLEAKLADWDIMRPTCTEE--AQQMYKAAPGHII 388 GG +L EL AG +H +V +I L R C E A + PG + Sbjct: 353 GGTGFVLRELIDAGLMHDDVTTILGQGL----------RQHCKEPMLAAEGENGRPGIV- 401 Query: 389 SPEPWTHTTLFDSLDRDRTNGAIHDIDHPEIHEGGLAVLRGNLAPDGCVVKTAGVPPEIW 448 T D+ + G + + P +GGL +L+GNL V+K + V PE Sbjct: 402 --------TWHDAPAQSGDEGVLGTVAKPFAADGGLKLLQGNLG--RAVIKISAVKPEHR 451 Query: 449 KFRGPALVVDSQEQAIEVILNDTLKPGMALVIRYEGPK--GGPGMQEMLYPTSFVKGKGI 506 PA+V SQE + L VI ++GP+ G P + + ++ K Sbjct: 452 VVEAPAVVFHSQEAFMAAFKAGQLDRDFVAVITFQGPRANGMPELHALTPALGILQDK-- 509 Query: 507 GKQVAMLTDGRYSGGSSGL-AIGHMAPEAANKGPVALIRNGDIIDIDIEARSVNVEL 562 G+ VA++TDGR SG S + A H+ PE GP+ +R+GDII +D EA ++ ++ Sbjct: 510 GRHVALVTDGRMSGASGKVPAAIHVTPEVLGGGPLGRVRDGDIIRLDAEAGTLEAKV 566 Lambda K H 0.318 0.135 0.398 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: 927 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: 620 Length of database: 623 Length adjustment: 37 Effective length of query: 583 Effective length of database: 586 Effective search space: 341638 Effective search space used: 341638 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: 54 (25.4 bits)
This GapMind analysis is from Apr 09 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