Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 7024978 Shewana3_2149 phosphogluconate dehydratase (RefSeq)
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__ANA3:7024978 Length = 608 Score = 160 bits (404), Expect = 2e-43 Identities = 148/495 (29%), Positives = 238/495 (48%), Gaps = 54/495 (10%) Query: 119 CDGRTQGTTGMFDSLPYRNDASMVMR-RLIRSLPDAKAVIGVASCDKGLPATMMALAAQH 177 CDG TQG GM SL R +M L ++ D ++G+ CDK +P ++ + Sbjct: 112 CDGVTQGQPGMELSLLSREVIAMATAVGLSHNMFDGALLLGI--CDKIVPGLLIGALSFG 169 Query: 178 NIATVLVPGGATLPAKDGEDNGKVQTIGARFANGELSLQDARRAGCKACASSGGGCQFLG 237 ++ + VP G P K G N + I +FA G++ A ++ S+G C F G Sbjct: 170 HLPMLFVPAG---PMKSGIPNKEKARIRQQFAQGKVDRAQLLEAEAQSYHSAGT-CTFYG 225 Query: 238 TAGTSQVVAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQKGI---TTREILTDK 294 TA ++Q++ E +GL +P S+ +P+ + + +A+ L++ G E++ +K Sbjct: 226 TANSNQLMLEVMGLQLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEK 285 Query: 295 AIENAMTVHAAFGGSTNLLLHIPAIAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYH 354 ++ N + A GGSTNL +HI A A AG I DD+ ++ VP L V PNG H Sbjct: 286 SVVNGIVALLATGGSTNLTMHIVAAARAAGI-IVNWDDFSELSDAVPLLARVYPNG---H 341 Query: 355 PTVNAF-MAGGVPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWEHSERRQRF---KQLL 410 +N F AGG+ ++ L GLLHEDV TV G L+ + + R+ + Sbjct: 342 ADINHFHAAGGMAFLIKELLDAGLLHEDVNTVAGFGLRRYTQEPKLLDGELRWVDGPTVS 401 Query: 411 LDQEQINADEVIMSPQQAKA-----RGLTSTITFPVGNIAPEGSVIKSTAIDPSMIDEQG 465 LD E + + + +P Q +G V + + V+++ A+ +ID+Q Sbjct: 402 LDTEVLTS---VATPFQNNGGLKLLKGNLGRAVIKVSAVQEKHRVVEAPAV---VIDDQ- 454 Query: 466 IYYHKGVAKVYLSEKSAIYDIKHDKIKAGDILVIIGVGPSGTGMEETYQVTSALKHL-SY 524 ++ A++ K + ++V+ G GP GM E +++T L L Sbjct: 455 ------------NKLDALF--KSGALDRDCVVVVKGQGPKANGMPELHKLTPLLGSLQDK 500 Query: 525 GKHVSLITDARFSGVS--TGACIGHVGPEALAGGPIGKLRTGDLIEIKIDCRELHGEVNF 582 G V+L+TD R SG S A I H+ PEA+ GG I K++ GDLI + L GE++ Sbjct: 501 GFKVALMTDGRMSGASGKVPAAI-HLTPEAIDGGLIAKVQDGDLIRVD----ALTGELSL 555 Query: 583 LGTRSDEQLPSQEEA 597 L SD +L ++ A Sbjct: 556 L--VSDAELAARTAA 568 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: 863 Number of extensions: 50 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 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