Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate GFF612 HP15_595 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >FitnessBrowser__Marino:GFF612 Length = 597 Score = 216 bits (551), Expect = 2e-60 Identities = 172/586 (29%), Positives = 281/586 (47%), Gaps = 59/586 (10%) Query: 68 VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127 +A+ +++ + H + L+ + + G V + + A+ DG+ G GM SL Sbjct: 23 IAVANSFTQFVPGHVHLKDLGQLVCREIESAGGVAKEFNTI-AVDDGIAMGHDGMLYSLP 81 Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISN 187 SR++IA S ++ + DA +C+ CDKI PG+L+ ++R ++PT+FV GPM G Sbjct: 82 SREIIADSVEYMVNAHCADALVCISNCDKITPGMLMAAMRL-NIPTIFVSGGPMEAG--- 137 Query: 188 KEKAAVRQL--------FAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGL 239 K K + +L A+ A+ E++ E + G+C+ TAN+ L E +GL Sbjct: 138 KTKLSEHKLDLVDAMVIAADPNASDEQVEEYERNACPTCGSCSGMFTANSMNCLTEAIGL 197 Query: 240 HLPGASFVNPNTPLRDELTREAARQ----ASRLTPENGNYVPMAEIVDEKAIVNSVVALL 295 LPG + R++L +A RQ A R E+ V I A N++V + Sbjct: 198 ALPGNGSLLATHADREQLFLKAGRQIVENARRYYEEDDASVLPLSIASMAAFENAMVMDI 257 Query: 296 ATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPNG-QADINHFQAAGGMS 354 A GGSTN LHLLA AQ G+ T ++ +LS VP L ++ PN + + AGG+ Sbjct: 258 AMGGSTNTILHLLAAAQEGGVPFTLNEIDQLSRRVPQLCKVAPNSPKYHMEDVHRAGGIM 317 Query: 355 FLIRQLLDGGLLHEDVQTVAGPGLRR------YTREPFLEDGRLVWREGP---------- 398 ++ +L GGL++ D+ TV +R R P E ++ GP Sbjct: 318 GILGELERGGLINTDLPTVHSKTMREALETWDIMRSPPTEVVEF-YKAGPAGIPTQTAFS 376 Query: 399 --------ERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVVEAPV 448 + + +R ++ +S+EGGL ++ GN+ V+K + V V E Sbjct: 377 QSTRWPTLDGDRETGCIRSVENAYSSEGGLAVLYGNIALDGCVVKTAGVDESIFVFEGKA 436 Query: 449 RIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFKVALV 507 R+F Q S A + E++ V ++R++GPR GM E+ T +L + G AL+ Sbjct: 437 RVFESQDSAVAGILSDEVKPGEVVIIRYEGPRGGPGMQEMLYPTSYL-KSKGLGKDCALL 495 Query: 508 TDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEW----- 562 TDGR SG + + H SPEA AGG + + +GD +R+D N + V +D E Sbjct: 496 TDGRFSGGTSGLSIG-HASPEAAAGGAIGLIENGDTIRIDIPNRSINVELDQHELDRRRE 554 Query: 563 --QARSLEP-APQDGNLGCGRELFAFMRNAMSSAEEGACSFTESLN 605 A+ +P P+D + + +A + +SA++GA E L+ Sbjct: 555 ARDAKGWKPELPRDRKVSAALKAYALL---ATSADKGAVRDLEKLD 597 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: 870 Number of extensions: 49 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: 597 Length adjustment: 37 Effective length of query: 571 Effective length of database: 560 Effective search space: 319760 Effective search space used: 319760 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