Align Dihydroxy-acid dehydratase; DAD; EC 4.2.1.9 (uncharacterized)
to candidate WP_011445545.1 SARO_RS09490 phosphogluconate dehydratase
Query= curated2:A8AB39 (552 letters) >NCBI__GCF_000013325.1:WP_011445545.1 Length = 606 Score = 263 bits (673), Expect = 1e-74 Identities = 182/544 (33%), Positives = 281/544 (51%), Gaps = 42/544 (7%) Query: 34 IGVANSWNEIVPGHVHLDKVAEAVKAGIRMAGGTPLEFGTI-AVCDGIAMGHEGMRYSLP 92 IG+ ++N+++ H + E +K R G T G + A+CDG+ G + M SL Sbjct: 69 IGIVTAYNDMLSAHQPYGRYPEQIKIFAREVGATAQVAGGVPAMCDGVTQGQDSMELSLF 128 Query: 93 SREVIADTVEIMVEAHRLDAVVMVTNCDKITPGFLLAAARL-EVPVILINGGPMMPGVYG 151 SR+VIA + + + +++ CDKI PG L+ + R +P IL+ GPM G+ Sbjct: 129 SRDVIAMATTVGLSHAMFEGALLLGICDKIVPGLLIGSLRFGHLPTILVPAGPMPTGLPN 188 Query: 152 KERIDFKDLMERMNVLIKEGRT--EELRKLEESALPGPGSCAGLFTANTMNMLSEAMGLM 209 KE++ R+ L EG+ +EL + E ++ G+C TAN+ M+ E MGL Sbjct: 189 KEKV-------RIRQLYAEGKVGRDELLESESASYHSAGTCTFYGTANSNQMMMEMMGLH 241 Query: 210 LPGASTV-PAVEARRLWYAKLTGMRIVKMVEEGLTPD------KILTRKALENAIAVDMA 262 +PG+S V P + R+ +LT ++ + G D + + KA+ NAI +A Sbjct: 242 MPGSSFVLPGTKIRQ----ELTRAATHRIAQIGWDGDDYRPLGRCVDEKAIVNAIVGLLA 297 Query: 263 LGGSTNSVLHLEALAYELGIDLPLEVFDEISRKVPHIASISPSGRHFVVDLDRAGGIPAV 322 GGSTN V+HL A+A GI + D++SR VP IAS+ P+G V AGG+P V Sbjct: 298 TGGSTNHVIHLPAIARAAGIQIDWNDMDDLSRVVPLIASVYPNGAGDVNYFAAAGGMPYV 357 Query: 323 LKELGEAGLIHKDALTVTGKTVWENVKDAAVL--------------DREVIRPLDNPYSP 368 ++EL +GL H D LTV G+++ E + + D ++RP+ P+ P Sbjct: 358 IRELIGSGLAHPDILTVYGQSLEEGAQQPVMEGDNLRWDPAPEVSGDDSMLRPVSAPFQP 417 Query: 369 FGGLAILKGSLAPNGAVVKASAVKRELWKFKGVARVFDREEDAVKAIRGGEIEPGTVIVI 428 GG +LKG+L +K SAV W + RVF+ + + A + GE+E ++V+ Sbjct: 418 EGGFRLLKGNL--GRGTIKVSAVDPSRWTIEAPCRVFEDQNAVLDAFKAGELERDVIVVV 475 Query: 429 RYEGPRGGPGMREMLTATAAVMAL-GLGDKVALVTDGRFSGAT-RGPAIGHVSPEAAAGG 486 R++GP GM E+ T + L G KVALVTDGR SGA+ + PA HVSPEA GG Sbjct: 476 RFQGPAAN-GMPELHKLTPPLGVLQDRGFKVALVTDGRMSGASGKVPAAIHVSPEAKLGG 534 Query: 487 PIALVQDGDEIVIDIEKRRLDLLVDEKELEERRARWKPKVKP-LRRGILRRYAKMALSAD 545 P+A ++DGD + + L +V +E R P P + R + + + A+ Sbjct: 535 PLARLRDGDVVRVCANSGELVAVVPAEEWSAREEAVAPASAPGVGRELFALMRQHSDPAE 594 Query: 546 KGGA 549 +GG+ Sbjct: 595 RGGS 598 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: 849 Number of extensions: 52 Number of successful extensions: 9 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: 606 Length adjustment: 36 Effective length of query: 516 Effective length of database: 570 Effective search space: 294120 Effective search space used: 294120 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 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