Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate CCNA_03139 CCNA_03139 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >FitnessBrowser__Caulo:CCNA_03139 Length = 617 Score = 201 bits (510), Expect = 1e-55 Identities = 162/540 (30%), Positives = 252/540 (46%), Gaps = 50/540 (9%) Query: 68 VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127 +A+ +++ + H + L+ + + G V + + A+ DG+ G GM SL Sbjct: 37 IAVANSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTI-AVDDGIAMGHGGMLYSLP 95 Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTG-IS 186 SRD+IA S ++ + DA +C+ CDKI PG+L+ ++R ++P VFV GPM G ++ Sbjct: 96 SRDLIADSVEYMVNAHCADAIVCISNCDKITPGMLMAAMRL-NIPVVFVSGGPMEAGKVT 154 Query: 187 NKEKAAVRQLF------AEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLH 240 K K L A+ + EE+ A E A+ G+C+ TAN+ L E +GL Sbjct: 155 VKGKIRALDLVDAMVVAADDSYSDEEVEAIEKAACPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPNTPLRDELTREAARQASRLTP-----ENGNYVPMAEIVDEKAIVNSVVALL 295 LPG V R+ L +EA R L E+ +P I A N++ + Sbjct: 215 LPGNGSVLATHADREALFKEAGRVVVDLCQRWYEQEDATALPRG-IATRAAFENAMSLDI 273 Query: 296 ATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYP-NGQADINHFQAAGGMS 354 A GGSTN LHLLA A GI + D+ LS VP L+++ P + AGG+ Sbjct: 274 AMGGSTNTVLHLLAAAHEGGIDFSMADIDRLSRHVPCLSKVAPAKSDVHMEDVHRAGGVM 333 Query: 355 FLIRQLLDGGLLHEDVQTVAGP----GLRRY----------------------TREPFLE 388 ++ +L GGL+ TV P L R+ T+ F + Sbjct: 334 AILGELERGGLIDASQPTVHAPTMGEALARWDIGRTNSQIAHEFFKAAPGGKPTQVAFSQ 393 Query: 389 DGRLVWREGPERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVVEA 446 R W E + + ++R ++ PFS +GGL ++ GNL ++K + V Sbjct: 394 AAR--WEE-LDLDRENGVIRSVEHPFSKDGGLAVLFGNLAPEGCIVKTAGVDESILTFRG 450 Query: 447 PVRIFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFKVA 505 R+F Q + + G+++ V V+R++GP+ GM E+ T +L + G A Sbjct: 451 TARVFESQDAAVSGILGGQVKAGEVVVIRYEGPKGGPGMQEMLYPTTYLKS-KGLGAACA 509 Query: 506 LVTDGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQAR 565 LVTDGR SG + + HVSPEA GG +A + GD + +D + + V DA AR Sbjct: 510 LVTDGRFSGGTSGLSIG-HVSPEAGEGGLIALVETGDPILIDIPTRGITLEVSDAVLAAR 568 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: 940 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: 1 Length of query: 608 Length of database: 617 Length adjustment: 37 Effective length of query: 571 Effective length of database: 580 Effective search space: 331180 Effective search space used: 331180 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