Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate WP_086509434.1 BZY95_RS08080 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >NCBI__GCF_002151265.1:WP_086509434.1 Length = 614 Score = 218 bits (556), Expect = 5e-61 Identities = 174/547 (31%), Positives = 257/547 (46%), Gaps = 48/547 (8%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +A+ +S+ + H + + + + + + G V + T A+ DG+ G GM SLP Sbjct: 37 IAVANSFTQFVPGHVHLKDMGQLVAREIEKAGGVAK-EFNTIAVDDGIAMGHDGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGIS- 186 SR++IA S ++ + DA + + CDKI PG++M A+R ++P IFV GGPM +G + Sbjct: 96 SRDIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRL-NIPVIFVSGGPMEAGKTK 154 Query: 187 ----NKEKADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLHLP 242 + D A+ E L E E + + G+C+ TAN+ L E +GL LP Sbjct: 155 LLDHGLDLVDAMVMAADDSVDDETLAEVERSACPTCGSCSGMFTANSMNCLTEALGLALP 214 Query: 243 GASFVNPYTPLRDALTHEAAQQVTRLTKQ-----SGNFTPIGEIVDERSLVNSIVALHAT 297 G V R L A ++ L K+ + P I + + N++ A Sbjct: 215 GNGTVLATHADRRRLFETAGHRIVELAKRYYEGDEAHLLP-RAIGSKAAFKNAMTLDIAM 273 Query: 298 GGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPN-GKADINHFQAAGGMAFL 356 GGSTN LH+ A AQ A I T D+ LS VP L V PN K I AGG+ + Sbjct: 274 GGSTNTILHLLAAAQEAEIDFTMADIDRLSREVPQLCKVAPNTQKYHIEDVHRAGGIMAI 333 Query: 357 IRELLEAGLLHEDVNTVAGRGLSRY--------------------------TQEPFLDNG 390 + EL AG+L V TV G L TQ F + Sbjct: 334 LGELDRAGVLDTRVPTVYGDSLKEALDEWDIMRNPSPEVVEFFKAGPGGVPTQVAFSQSA 393 Query: 391 KLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRG--VMKVSAVALQHQIVEAPA 448 + DG +R + AFS EGGL V+ GN+ V+K + V + E PA Sbjct: 394 RWPTLDG---DRANGCIRDLEHAFSREGGLAVLYGNIAVDGCVVKTAGVDDSILVFEGPA 450 Query: 449 VVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALV 507 V + Q + AG++++ V V+R++GP+ GM E+ T +L + G AL+ Sbjct: 451 HVVESQDQAVEHILAGQVKEGEVVVIRYEGPKGGPGMQEMLYPTSYL-KSKGLGKACALL 509 Query: 508 TDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAREP 567 TDGR SG + + HVSPEA GGA+ VR GDIIR+D +++K+ E AAR Sbjct: 510 TDGRFSGGTSGLSIG-HVSPEAAAGGAIGLVRSGDIIRIDIPNRRIDVKLSDSELAARRE 568 Query: 568 AKGLLGN 574 A+ G+ Sbjct: 569 AEEARGS 575 Lambda K H 0.318 0.134 0.386 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: 900 Number of extensions: 53 Number of successful extensions: 10 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 608 Length of database: 614 Length adjustment: 37 Effective length of query: 571 Effective length of database: 577 Effective search space: 329467 Effective search space used: 329467 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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