Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate SMc04045 SMc04045 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__Smeli:SMc04045 Length = 612 Score = 212 bits (539), Expect = 4e-59 Identities = 173/545 (31%), Positives = 262/545 (48%), Gaps = 47/545 (8%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +A+V+S+ + H + + + + + G V + T A+ DG+ G GM SLP Sbjct: 37 IAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAK-EFNTIAVDDGIAMGHDGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSG--- 184 SRE+IA S ++ + DA + + CDKI PG++M ALR ++P +FV GGPM +G Sbjct: 96 SREIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAALRL-NIPAVFVSGGPMEAGKVV 154 Query: 185 ISNKEKA----DVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 + K A D A+ K + E++ E + + G+C+ TAN+ L E +GL Sbjct: 155 LHGKTHALDLVDAMVAAADDKVSDEDVQIIERSACPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTK----QSGNFTPIGEIVDERSLVNSIVALHA 296 LPG R L EA + L + Q I +++ N++ A Sbjct: 215 LPGNGSTLATHADRKRLFVEAGHLIVDLARRYYEQEDERVLPRNIATKQAFENAMALDIA 274 Query: 297 TGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYPNGKADIN--HFQAAGGMA 354 GGSTN LH+ A A I T D+ LS VP LS V P KAD++ AGG+ Sbjct: 275 MGGSTNTVLHILAAAYEGEIDFTMDDIDRLSRKVPCLSKVAP-AKADVHMEDVHRAGGIM 333 Query: 355 FLIRELLEAGLLHEDVNTV----AGRGLSRY-TQEPFLDNGKLVWRDGP----------- 398 ++ EL + GL++ D TV G + R+ D + +R P Sbjct: 334 SILGELDKGGLINRDCPTVHAETLGDAIDRWDITRTSSDTVRKFFRAAPGGIPTQVAFSQ 393 Query: 399 ------IESLDEN-ILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQIVE--APAV 449 +++ EN ++R V FS +GGL V++GN+ V + I++ PA Sbjct: 394 EARWDELDTDRENGVIRSVEHPFSKDGGLAVLKGNIALDGCIVKTAGVDESILKFSGPAR 453 Query: 450 VFQDQQDLADAFKAGELEKDFVAVMRFQGPRSN-GMPELHKMTPFLGVLQDRGFKVALVT 508 VF+ Q A E++ V V+R++GP+ GM E+ T +L + G AL+T Sbjct: 454 VFESQDAAVKGILANEIKAGDVVVIRYEGPKGGPGMQEMLYPTSYL-KSKGLGKACALIT 512 Query: 509 DGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKVDADEFAAR--- 565 DGR SG + + HVSPEA GG + VR+GD+I +D T+ L+VD E AAR Sbjct: 513 DGRFSGGTSGLSIG-HVSPEAANGGTIGLVREGDMIDIDIPNRTISLRVDEAELAARRTE 571 Query: 566 EPAKG 570 + AKG Sbjct: 572 QDAKG 576 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: 908 Number of extensions: 55 Number of successful extensions: 9 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: 608 Length of database: 612 Length adjustment: 37 Effective length of query: 571 Effective length of database: 575 Effective search space: 328325 Effective search space used: 328325 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 17 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