Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate Pf6N2E2_4564 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_4564 Length = 613 Score = 199 bits (507), Expect = 2e-55 Identities = 156/493 (31%), Positives = 234/493 (47%), Gaps = 53/493 (10%) Query: 120 DGRTQGTTGMFDSLPYRNDASMVMRRLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNI 179 DG G GM SLP R + + ++ + A A++ +++CDK P +MA A + NI Sbjct: 81 DGIAMGHDGMLYSLPSREIIADSVEYMVNA-HCADAIVCISNCDKITPGMLMA-ALRLNI 138 Query: 180 ATVLVPGGA-----TLPAKDGEDNGKVQTIGARFANGELSLQDARRAGCKACASSGGGCQ 234 + V GG T A G D I A + + + + R+ C C G C Sbjct: 139 PVIFVSGGPMEAGKTKLASHGLDLVDAMVIAADSSASDEKVAEYERSACPTC----GSCS 194 Query: 235 FLGTAGTSQVVAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQK-------GITT 287 + TA + + E LGLA+P + + ++ + R + L ++ + Sbjct: 195 GMFTANSMNCLTEALGLALPGNGSTLATHSDREQLFLQAGRTIVELCKRYYGENDESVLP 254 Query: 288 REILTDKAIENAMTVHAAFGGSTNLLLHIPAIAHQAGCHIPTVDDWIRINKRVPRLVSVL 347 R I KA ENAMT+ A GGSTN +LH+ A A +A + D R+++ VP+L V Sbjct: 255 RNIANFKAFENAMTLDIAMGGSTNTILHLLAAAQEAEIDF-DLRDIDRLSRHVPQLCKVA 313 Query: 348 PNGPVYHPTVNAFMAGGVPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWEHSER----- 402 PN YH + AGG+ ++ L GLLH D+ TV T+ E + W+ ++ Sbjct: 314 PNIQKYH-MEDVHRAGGIFSILGSLARGGLLHTDLPTVHSKTMAEAIAKWDITQTTDEAV 372 Query: 403 -----------------RQRFKQLLLDQEQINADEVIMSPQQAKARGLTSTITFPVGNIA 445 Q + LD ++ N + +K GL GNIA Sbjct: 373 HHFFKAGPAGIPTQTAFSQSTRWETLDDDRENGCIRSVEHAYSKEGGLAVL----YGNIA 428 Query: 446 PEGSVIKSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAGDILVIIGVGP- 504 +G V+K+ +D S I+ +G AK++ S+ SA+ I D++KAGDI++I GP Sbjct: 429 LDGCVVKTAGVDES------IHVFEGNAKIFESQDSAVRGILADEVKAGDIVIIRYEGPK 482 Query: 505 SGTGMEETYQVTSALKHLSYGKHVSLITDARFSGVSTGACIGHVGPEALAGGPIGKLRTG 564 G GM+E TS LK GK +L+TD RFSG ++G IGH PEA AGG IG +R G Sbjct: 483 GGPGMQEMLYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHASPEAAAGGAIGLVRDG 542 Query: 565 DLIEIKIDCRELH 577 D + I I R ++ Sbjct: 543 DKVLIDIPNRSIN 555 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: 895 Number of extensions: 47 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