Align Phosphogluconate dehydratase; EC 4.2.1.12; 6-phosphogluconate dehydratase (uncharacterized)
to candidate AZOBR_RS15015 AZOBR_RS15015 dihydroxy-acid dehydratase
Query= curated2:P31961 (608 letters) >FitnessBrowser__azobra:AZOBR_RS15015 Length = 621 Score = 216 bits (551), Expect = 2e-60 Identities = 164/537 (30%), Positives = 256/537 (47%), Gaps = 44/537 (8%) Query: 68 VAIVSAYNDMLSAHQPFERFPGLIKQALHEIGSVGQFAGGVPAMCDGVTQGEPGMELSLA 127 +AI +++ + H + L+ + + + G V + + A+ DG+ G GM SL Sbjct: 37 IAIANSFTQFVPGHVHLKDLGQLVAREIEKAGGVAKEFNTI-AVDDGIAMGHDGMLYSLP 95 Query: 128 SRDVIAMSTAIALSHNMFDAALCLGVCDKIVPGLLIGSLRFGHLPTVFVPAGPMPTGISN 187 SR++IA + ++ + DA +C+ CDKI PG+L+ ++R ++P VFV GPM G N Sbjct: 96 SRELIADAVEYMVNAHCADALVCISNCDKITPGMLMAAMRL-NIPAVFVSGGPMEAGKVN 154 Query: 188 ---KEKAA----VRQLFAEGKATREELLASEMASYHAPGTCTFYGTANTNQLLVEVMGLH 240 K KA A+ + EE E S G+C+ TAN+ L E +GL Sbjct: 155 WRGKTKAVDLIDAMVAAADPTVSDEEAAVMERGSCPTCGSCSGMFTANSMNCLTEALGLS 214 Query: 241 LPGASFVNPNTPLRDELTREAARQASRL-----TPENGNYVPMAEIVDEKAIVNSVVALL 295 LPG + R EL A R A L E+ +P I +A N++ + Sbjct: 215 LPGNGTILATHADRKELFLAAGRMAVELCRRWYQEEDATALPRG-IATFEAFENAMTLDI 273 Query: 296 ATGGSTNHTLHLLAIAQAAGIQLTWQDMSELSHVVPTLARIYPN-GQADINHFQAAGGMS 354 A GGSTN LHLLA AQ + T D+ LS VP + ++ P I AGG+ Sbjct: 274 AMGGSTNTVLHLLAAAQEGQVPFTMADIDRLSRRVPNVCKVAPAVSDVHIEDVHKAGGIF 333 Query: 355 FLIRQLLDGGLLHEDVQTV----AGPGLRRYTREPFLEDG-RLVWREGP----------- 398 ++ +L GGLL+ DV TV G L R+ + ++G +++ P Sbjct: 334 GILGELDRGGLLNRDVATVHAKTLGDALDRWDVKRTQDEGVHTMFKAAPGGIPTTIAFSQ 393 Query: 399 -------ERSLDEAILRPLDKPFSAEGGLRLMEGNLGRG--VMKVSAVAPEHQVVEAPVR 449 + D+ ++R +D FS +GGL ++ GN+ ++K + V + V P R Sbjct: 394 EKRWPELDLDRDKGVIRSVDSAFSKDGGLAVLFGNIAEKGCIVKTAGVDASNLVFAGPAR 453 Query: 450 IFHDQASLAAAFKAGELERDLVAVVRFQGPRAN-GMPELHKLTPFLGVLQDRGFKVALVT 508 +F Q + A ++ V V+R++GPR GM E+ T +L + G ALVT Sbjct: 454 VFESQDAAVEAILGDTVKAGDVVVIRYEGPRGGPGMQEMLYPTSYL-KSKGLGKACALVT 512 Query: 509 DGRMSGASGKVPAAIHVSPEAIAGGPLARLRDGDRVRVDGVNGELRVLVDDAEWQAR 565 DGR SG + + H SPEA GG + ++DGDR+ +D N ++ + + D E Q R Sbjct: 513 DGRFSGGTSGLSIG-HASPEAAQGGAIGLVQDGDRIEIDIPNRKINLALSDEELQRR 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: 888 Number of extensions: 52 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 608 Length of database: 621 Length adjustment: 37 Effective length of query: 571 Effective length of database: 584 Effective search space: 333464 Effective search space used: 333464 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