Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate 6937660 Sama_1810 phosphogluconate dehydratase (RefSeq)
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__SB2B:6937660 Length = 608 Score = 175 bits (443), Expect = 6e-48 Identities = 158/505 (31%), Positives = 242/505 (47%), Gaps = 40/505 (7%) Query: 83 LALHQGHYELDIQMKAAAEVIKANHALPYAVYVSDPCDGRTQGTTGMFDSLPYRNDASMV 142 L+ HQ + +KAA + + A V CDG TQG GM SL R +M Sbjct: 78 LSAHQPYEHYPELLKAACNEVGS--VAQVAGGVPAMCDGVTQGQPGMELSLLSREVIAMA 135 Query: 143 MR-RLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGATLPAKDGEDNGKV 201 L ++ D ++GV CDK +P ++ + ++ + VP G P + G N + Sbjct: 136 TAVGLSHNMFDGALLLGV--CDKIVPGLLIGAMSFGHLPMLFVPAG---PMRSGIPNKEK 190 Query: 202 QTIGARFANGELSLQDARRAGCKACASS---GGGCQFLGTAGTSQVVAEGLGLAIPHSAL 258 + +FA G++ R A +A ASS G C F GTA ++Q+V E +GL +P S+ Sbjct: 191 ARVRQKFAEGKVD----REALLEAEASSYHSAGTCTFYGTANSNQLVLEVMGLQLPGSSF 246 Query: 259 APSGEPVWREIARASARAALNLSQKGI---TTREILTDKAIENAMTVHAAFGGSTNLLLH 315 +P+ E+++ +A+ L++ G+ EI+ +K++ N + A GGSTNL +H Sbjct: 247 VNPDDPLRTELSKMAAKQVCRLTENGLQYSPIGEIVNEKSVVNGIVALLATGGSTNLTMH 306 Query: 316 IPAIAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAF-MAGGVPEVMLHLRS 374 I A A AG I DD+ ++ VP L V PNG H +N F AGG+ +M L Sbjct: 307 IVAAARAAGI-IINWDDFSELSDAVPLLARVYPNG---HADINHFHAAGGMAFLMKELLD 362 Query: 375 LGLLHEDVMTVTGSTLKENLDWWEHSERRQRFKQLLLDQEQINADEVIMSPQQAKARGLT 434 GL+HEDV TV G L RR + L+D + D + S Q RG+ Sbjct: 363 AGLIHEDVNTVAGYGL-----------RRYTQEPRLIDGQLTWVDGPVTSLDQEVLRGVA 411 Query: 435 STITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAG 494 G +G++ ++ ++ ++ I V ++ A++ K ++ Sbjct: 412 EPFQSNGGLKLMKGNLGRAVIKVSAVQEQHRIVEAPAVVIDDQNKLDALF--KAGELDRD 469 Query: 495 DILVIIGVGPSGTGMEETYQVTSALKHL-SYGKHVSLITDARFSGVS--TGACIGHVGPE 551 ++V+ G GP GM E +++T L L G V+L+TD R SG S A I H+ PE Sbjct: 470 CVVVVKGQGPKANGMPELHKLTPILGTLQDRGFKVALMTDGRMSGASGKVPAAI-HLTPE 528 Query: 552 ALAGGPIGKLRTGDLIEIKIDCREL 576 AL GG I K++ GDLI I EL Sbjct: 529 ALDGGLIAKVQDGDLIRINAITGEL 553 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: 891 Number of extensions: 52 Number of successful extensions: 7 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