Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate PP_5128 PP_5128 Dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >FitnessBrowser__Putida:PP_5128 Length = 613 Score = 215 bits (548), Expect = 4e-60 Identities = 169/545 (31%), Positives = 258/545 (47%), Gaps = 56/545 (10%) Query: 68 VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127 +AI +++ + H + L+ + + G V + + A+ DG+ G GM SL Sbjct: 37 IAIANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTI-AVDDGIAMGHDGMLYSLP 95 Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISN 187 SR++IA + ++ + DA +C+ CDKI PG+L+ +LR ++P +FV GPM G Sbjct: 96 SREIIADAVEYMVNAHCADAIVCISNCDKITPGMLMAALRL-NIPVIFVSGGPMEAG--- 151 Query: 188 KEKAAVRQL--------FAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGL 239 K K A L A+ A+ E++ E ++ G+C+ TAN+ L E +GL Sbjct: 152 KTKLASHGLDLVDAMVIAADSTASDEKVAEYERSACPTCGSCSGMFTANSMNCLTEALGL 211 Query: 240 HLPGASFVNPNTPLRDELTREAARQ----ASRLTPENGNYVPMAEIVDEKAIVNSVVALL 295 LPG R++L A R R EN V I + KA N+++ + Sbjct: 212 ALPGNGSTLATHSDREQLFLTAGRTIVELCKRYYGENDESVLPRSIANFKAFENAMMLDI 271 Query: 296 ATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNGQA-DINHFQAAGGMS 354 A GGSTN LHLLA AQ + +D+ LS VP L ++ PN Q + AGG+ Sbjct: 272 AMGGSTNTILHLLAAAQEGEVAFDLRDIDRLSRKVPQLCKVAPNIQKYHMEDVHRAGGIF 331 Query: 355 FLIRQLLDGGLLHEDVQTV---------------------------AGP-GLRRYTREPF 386 ++ L GGLLH D+ TV AGP G+ T+ F Sbjct: 332 SILGSLARGGLLHTDLPTVHSRSMEEAIAKWDITQTDDEAVHTFFKAGPAGIP--TQTAF 389 Query: 387 LEDGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVV 444 + R W E + + +R + +S EGGL ++ GN+ V+K + V V Sbjct: 390 SQSTR--W-ETLDDDRENGCIRSFEHAYSQEGGLAVLYGNIALDGCVVKTAGVDESIHVF 446 Query: 445 EAPVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFK 503 E +IF Q S A E++ + ++R++GP+ GM E+ T +L + G Sbjct: 447 EGTAKIFESQDSAVRGILADEVKAGDIVIIRYEGPKGGPGMQEMLYPTSYL-KSKGLGKA 505 Query: 504 VALVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQ 563 AL+TDGR SG + + H SPEA AGG + +RDGD+V +D N + +LV D E Sbjct: 506 CALLTDGRFSGGTSGLSIG-HASPEAAAGGAIGLVRDGDKVLIDIPNRSINLLVSDEELA 564 Query: 564 ARSLE 568 R +E Sbjct: 565 QRRVE 569 Lambda K H 0.319 0.135 0.397 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: 856 Number of extensions: 52 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: 613 Length adjustment: 37 Effective length of query: 571 Effective length of database: 576 Effective search space: 328896 Effective search space used: 328896 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 (21.8 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