Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 201628 SO2487 6-phosphogluconate dehydratase (NCBI ptt file)
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__MR1:201628 Length = 608 Score = 164 bits (414), Expect = 1e-44 Identities = 156/518 (30%), Positives = 245/518 (47%), Gaps = 56/518 (10%) Query: 83 LALHQGHYEL-DIQMKAAAEVIKANHALPYAVYVSDPCDGRTQGTTGMFDSLPYRNDASM 141 L+ HQ + D+ KA EV A V CDG TQG GM SL R +M Sbjct: 78 LSAHQPYETYPDLLKKACQEV---GSVAQVAGGVPAMCDGVTQGQPGMELSLLSREVIAM 134 Query: 142 VMR-RLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGATLPAKDGEDNGK 200 L ++ D ++G+ CDK +P ++ + ++ + VP G P K G N + Sbjct: 135 ATAVGLSHNMFDGALLLGI--CDKIVPGLLIGALSFGHLPMLFVPAG---PMKSGIPNKE 189 Query: 201 VQTIGARFANGELSLQDARRAGCKACASSGGGCQFLGTAGTSQVVAEGLGLAIPHSALAP 260 I +FA G++ A ++ S+G C F GTA ++Q++ E +GL +P S+ Sbjct: 190 KARIRQQFAQGKVDRAQLLEAEAQSYHSAGT-CTFYGTANSNQLMLEVMGLQLPGSSFVN 248 Query: 261 SGEPVWREIARASARAALNLSQKGI---TTREILTDKAIENAMTVHAAFGGSTNLLLHIP 317 +P+ + + +A+ L++ G E++ +K+I N + A GGSTNL +HI Sbjct: 249 PDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSIVNGIVALLATGGSTNLTMHIV 308 Query: 318 AIAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAF-MAGGVPEVMLHLRSLG 376 A A AG I DD+ ++ VP L V PNG H +N F AGG+ ++ L G Sbjct: 309 AAARAAGI-IVNWDDFSELSDAVPLLARVYPNG---HADINHFHAAGGMAFLIKELLDAG 364 Query: 377 LLHEDVMTVTGSTLKENLDWWEHSERRQRF---KQLLLDQEQINADEVIMSPQQAKA--- 430 LLHEDV TV G L+ + + R+ + LD E + + + +P Q Sbjct: 365 LLHEDVNTVAGYGLRRYTQEPKLLDGELRWVDGPTVSLDTEVLTS---VATPFQNNGGLK 421 Query: 431 --RGLTSTITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKH 488 +G V + P+ V+++ A+ +ID+Q ++ A++ K Sbjct: 422 LLKGNLGRAVIKVSAVQPQHRVVEAPAV---VIDDQ-------------NKLDALF--KS 463 Query: 489 DKIKAGDILVIIGVGPSGTGMEETYQVTSALKHL-SYGKHVSLITDARFSGVS--TGACI 545 + ++V+ G GP GM E +++T L L G V+L+TD R SG S A I Sbjct: 464 GALDRDCVVVVKGQGPKANGMPELHKLTPLLGSLQDKGFKVALMTDGRMSGASGKVPAAI 523 Query: 546 GHVGPEALAGGPIGKLRTGDLIEIKIDCRELHGEVNFL 583 H+ PEA+ GG I K++ GDLI + L GE++ L Sbjct: 524 -HLTPEAIDGGLIAKVQDGDLIRVD----ALTGELSLL 556 Lambda K H 0.317 0.135 0.400 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: 859 Number of extensions: 50 Number of successful extensions: 8 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: 655 Length of database: 608 Length adjustment: 38 Effective length of query: 617 Effective length of database: 570 Effective search space: 351690 Effective search space used: 351690 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: 54 (25.4 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