Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate PfGW456L13_973 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_973 Length = 613 Score = 191 bits (485), Expect = 8e-53 Identities = 164/544 (30%), Positives = 257/544 (47%), Gaps = 63/544 (11%) Query: 88 GHYEL-DIQMKAAAEVIKANH-ALPYAVYVSDPCDGRTQGTTGMFDSLPYRNDASMVMRR 145 GH L D+ A E+ +A A + D DG G GM SLP R + + Sbjct: 49 GHVHLKDLGQLVAREIERAGGVAKEFNTIAVD--DGIAMGHDGMLYSLPSREIIADSVEY 106 Query: 146 LIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLVPGGA-----TLPAKDGEDNGK 200 ++ + A A++ +++CDK P +MA + + NI + V GG T A G D Sbjct: 107 MVNA-HCADAIVCISNCDKITPGMLMA-SLRLNIPVIFVSGGPMEAGKTKLASHGLDLVD 164 Query: 201 VQTIGARFANGELSLQDARRAGCKACASSGGGCQFLGTAGTSQVVAEGLGLAIPHSALAP 260 I A + + + + R+ C C G C + TA + + E LGLA+P + Sbjct: 165 AMVIAADSSASDEKVAEYERSACPTC----GSCSGMFTANSMNCLVEALGLALPGNGSTL 220 Query: 261 SGEPVWREIARASARAALNLSQK-------GITTREILTDKAIENAMTVHAAFGGSTNLL 313 + ++ + R + L ++ + R I +A ENAMT+ A GGSTN + Sbjct: 221 ATHSDREQLFLQAGRTIVELCKRYYGENDQSVLPRNIANFQAFENAMTLDIAMGGSTNTI 280 Query: 314 LHIPAIAHQAGCHIPTVDDWIRINKRVPRLVSVLPNGPVYHPTVNAFMAGGVPEVMLHLR 373 LH+ A A +A + D R+++ VP+L V PN YH + AGG+ ++ L Sbjct: 281 LHLLAAAQEAEIDF-DLRDIDRLSRNVPQLCKVAPNIQKYH-MEDVHRAGGIFSILGSLA 338 Query: 374 SLGLLHEDVMTVTGSTLKENLDWWEHSERR----------------------QRFKQLLL 411 GLLH + TV +++E + W+ ++ Q + L Sbjct: 339 RGGLLHTQLPTVHSRSMEEAIAKWDITQTNDEAVHHFFKAGPAGIPTQTAFSQSTRWETL 398 Query: 412 DQEQINADEVIMSPQQAKARGLTSTITFPVGNIAPEGSVIKSTAIDPSMIDEQGIYYHKG 471 D ++ N I S + A ++ + + GNIA +G V+K+ +D S I+ +G Sbjct: 399 DDDRENG--CIRSVEHAYSQEGGLAVLY--GNIALDGCVVKTAGVDES------IHVFEG 448 Query: 472 VAKVYLSEKSAIYDIKHDKIKAGDILVIIGVGP-SGTGMEETYQVTSALKHLSYGKHVSL 530 AK++ S+ SA+ I D++K GDI++I GP G GM+E TS LK GK +L Sbjct: 449 NAKIFESQDSAVRGILADEVKEGDIVIIRYEGPKGGPGMQEMLYPTSYLKSKGLGKACAL 508 Query: 531 ITDARFSGVSTGACIGHVGPEALAGGPIGKLRTGDLIEIKIDCRELHGEVNFLGTRSDEQ 590 +TD RFSG ++G IGH PEA AGG IG ++ GD + I I R ++ V SDE+ Sbjct: 509 LTDGRFSGGTSGLSIGHASPEAAAGGAIGLVQDGDKVLIDIPNRSINLLV------SDEE 562 Query: 591 LPSQ 594 L ++ Sbjct: 563 LAAR 566 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: 885 Number of extensions: 45 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: 2 Length of query: 655 Length of database: 613 Length adjustment: 38 Effective length of query: 617 Effective length of database: 575 Effective search space: 354775 Effective search space used: 354775 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