Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 5209582 Shew_2046 phosphogluconate dehydratase (RefSeq)
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__PV4:5209582 Length = 608 Score = 166 bits (421), Expect = 2e-45 Identities = 156/524 (29%), Positives = 242/524 (46%), Gaps = 68/524 (12%) Query: 83 LALHQGHYELDIQMKAAAEVIKANHALPYAVYVSDPCDGRTQGTTGMFDSLPYRNDASMV 142 L+ HQ + +K A + + A V CDG TQG GM SL R +M Sbjct: 78 LSAHQPYEHYPQLLKDACHEVGS--VAQVAAGVPAMCDGVTQGQPGMELSLLSREVIAMS 135 Query: 143 MR-RLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGATLPAKDGEDNGKV 201 L ++ D ++G+ CDK +P ++ + ++ + VP G P K G N + Sbjct: 136 TAVGLSHNMFDGALLLGI--CDKIVPGLLIGALSFGHLPMLFVPAG---PMKSGIPNKEK 190 Query: 202 QTIGARFANGELSLQDARRAGCKACASSGGGCQFLGTAGTSQVVAEGLGLAIPHSALAPS 261 + +FA G++ A K+ S+G C F GTA ++Q++ E +GL +P S+ Sbjct: 191 ARVRQKFAQGQVDRAALLEAESKSYHSAGT-CTFYGTANSNQLMLEVMGLQLPGSSFVNP 249 Query: 262 GEPVWREIARASARAALNLSQKG---ITTREILTDKAIENAMTVHAAFGGSTNLLLHIPA 318 +P+ + + +A+ L++ G E++ +K++ N + A GGSTNL +HI A Sbjct: 250 DDPLREALNKMAAKQVCRLTEMGTQYTPIGEVVNEKSVVNGIVALLATGGSTNLTMHIVA 309 Query: 319 IAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAF-MAGGVPEVMLHLRSLGL 377 A AG I DD+ ++ VP L V PNG H +N F AGG+ ++ L GL Sbjct: 310 AARAAGI-IVNWDDFSELSDAVPLLARVYPNG---HADINHFHAAGGMAFLIKELLDAGL 365 Query: 378 LHEDVMTVTGSTLK----------ENLDWWEHSERRQRFKQLLLDQEQINADEVIMSPQQ 427 LHEDV+TV G L+ L W E LD+E + A + SP Q Sbjct: 366 LHEDVLTVAGPGLRRYTQEPRLIDNELVWVEGPNES-------LDKEVLTA---VASPFQ 415 Query: 428 AKA-----RGLTSTITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSA 482 A +G V +A +++ A+ +ID+Q ++ Sbjct: 416 ANGGLKLLKGNLGRAVIKVSAVAESHRFVEAPAV---VIDDQ-------------NKLEG 459 Query: 483 IYDIKHDKIKAGDILVIIGVGPSGTGMEETYQVTSALKHL-SYGKHVSLITDARFSGVS- 540 ++ K ++ ++V+ G GP GM E +++T L L G V+L+TD R SG S Sbjct: 460 LF--KAGELDRDCVVVVKGQGPKANGMPELHKLTPILGSLQDKGFKVALLTDGRMSGASG 517 Query: 541 -TGACIGHVGPEALAGGPIGKLRTGDLIEIKIDCRELHGEVNFL 583 A I H+ PEAL GG I K+ GDLI + + GEV+ L Sbjct: 518 KVPAAI-HLTPEALDGGLIAKVENGDLIRVDANT----GEVSLL 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: 872 Number of extensions: 51 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: 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