Align phosphogluconate dehydratase (EC 4.2.1.12) (characterized)
to candidate Dsui_1122 Dsui_1122 dihydroxy-acid dehydratase
Query= BRENDA::Q1PAG1 (608 letters) >FitnessBrowser__PS:Dsui_1122 Length = 619 Score = 207 bits (526), Expect = 1e-57 Identities = 166/549 (30%), Positives = 252/549 (45%), Gaps = 55/549 (10%) Query: 68 VAIVSSYNDMLSAHQPYEHFPEQIKKALREMGSVGQFAGGTPAMCDGVTQGEAGMELSLP 127 +A+V+S+ + H + + + + + G + + T A+ DG+ G GM SLP Sbjct: 37 IAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGIAK-EFNTIAIDDGIAMGHDGMLYSLP 95 Query: 128 SREVIALSTAVALSHNMFDAALMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMPSGISN 187 SR++IA S ++ + DA + + CDKI PG++M A+R ++PTIFV GGPM +G Sbjct: 96 SRDLIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRV-NIPTIFVSGGPMEAGKVK 154 Query: 188 KE-------KADVRQRYAEGKATREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 E D + + + E+ E E + + G+C+ TAN+ L E +GL Sbjct: 155 WEGKTIAVDLIDAMIKAGDSNCSDAEVEEFERSACPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPYTPLRDALTHEAAQQVTRLTKQ-----SGNFTPIGEIVDERSLVNSIVALH 295 LPG + R L EA +++ RL ++ + P I ++++ N+ Sbjct: 215 LPGNGTLVATHADRKGLFLEAGRRIVRLAQRWYEENDASVLP-RSIANQKAFENAFALDV 273 Query: 296 ATGGSTNHTLHMPAIAQAAGIQLTWQDMADLSEVVPTLSHVYP-NGKADINHFQAAGGMA 354 A GGSTN LH+ A AQ AG+ T D+ +S VP L V P I AGG+ Sbjct: 274 AMGGSTNTVLHLLATAQEAGVTFTMADIDAISRKVPCLCKVAPATQDYHIEDVHRAGGIM 333 Query: 355 FLIRELLEAGLLHEDVNTV----AGRGLSRY----------------------TQEPFLD 388 ++ EL GL+H D TV G + Y TQ F Sbjct: 334 AILGELSRGGLIHRDTPTVHCHTLGEAIDTYDVQRAGSQRTLEFFRAAPGGIPTQTAFSQ 393 Query: 389 NGKLVWRDGPIESLDENILRPVARAFSPEGGLRVMEGNLGRGVMKVSAVALQHQI--VEA 446 + + D + +R VA A+S EGGL V+ GN+ V + I Sbjct: 394 DRRYTELD---QDRSNGCIRNVAHAYSKEGGLAVLHGNIALDGCIVKTAGVDESIWKFTG 450 Query: 447 PAVVFQDQQDLADAFKAGELEKDFVAVMRFQGPRSNGMPELHKMTPFLGVLQDRGF--KV 504 A V++ Q A GE+ V V+R++GP+ G P + +M L+ RG + Sbjct: 451 KAKVYESQDSAVTAILGGEVVAGDVVVIRYEGPK--GGPGMQEMLYPTSYLKSRGLGKEC 508 Query: 505 ALVTDGRMSGASGKIPAAIHVSPEAQVGGALARVRDGDIIRVDGVKGTLELKV---DADE 561 AL+TDGR SG + + H SPEA GGA+ VR GD I +D + L V + ++ Sbjct: 509 ALLTDGRFSGGTSGLSIG-HASPEAAEGGAIGLVRTGDTIEIDIPGRRIHLAVSDAELEK 567 Query: 562 FAAREPAKG 570 A E AKG Sbjct: 568 RRAEENAKG 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: 940 Number of extensions: 51 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: 1 Length of query: 608 Length of database: 619 Length adjustment: 37 Effective length of query: 571 Effective length of database: 582 Effective search space: 332322 Effective search space used: 332322 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