Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate RR42_RS16210 RR42_RS16210 dihydroxy-acid dehydratase
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__Cup4G11:RR42_RS16210 Length = 557 Score = 219 bits (559), Expect = 2e-61 Identities = 177/507 (34%), Positives = 254/507 (50%), Gaps = 46/507 (9%) Query: 98 AAAEVIKANHALPYAVYVSDPCDGRTQGTTGMFDSLPYRNDASMVMRRLIRSLPDAK--- 154 AA IKA+ A P DG + GT GM SL R V+ I + + Sbjct: 60 AAVAAIKASDANPQIFGTPTISDGMSMGTEGMKYSLISRE----VIADCIETATQGQWMD 115 Query: 155 AVIGVASCDKGLPATMMALAAQHNIATVLVPGGATLPAK-DGEDNGKVQTIGA--RFANG 211 V+ + CDK +P M+ALA + N+ + V GG P G+D V + A F G Sbjct: 116 GVVVIGGCDKNMPGGMIALA-RTNVPGIYVYGGTIKPGNWKGKDLTIVSSFEAVGEFTAG 174 Query: 212 ELSLQDARRAGCKACASSGGGCQFLGTAGTSQVVAEGLGLAIPHSALAPSGEPVWREIAR 271 LS +D AC SSG C + TA T E LG+++ +S+ + + + A Sbjct: 175 RLSQEDFEGVEKNACPSSGS-CGGMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAA 233 Query: 272 ASARAALNLSQKGITTREILTDKAIENAMTVHAAFGGSTNLLLHIPAIAHQAGCHIPTVD 331 SAR + +K I R+I+T K+IENA+ + A GGSTN +LH AIAH A ++D Sbjct: 234 ESARVLVEAIKKDIKPRDIITRKSIENAVALIMATGGSTNAVLHYLAIAHSAEVEW-SID 292 Query: 332 DWIRINKRVPRLVSVLPNGPVYHPTVNAFMAGGVPEVMLHLRSLGLLHEDVMTVTGSTLK 391 D+ RI ++VP + ++ P+G + + AGG+P+VM L GL+H D +T+TG TL Sbjct: 293 DFERIRRKVPVICNLKPSG--QYVATDLHRAGGIPQVMKILLKAGLMHGDCLTITGRTLA 350 Query: 392 ENLDWWEHSERRQRFKQLLLDQEQINADEVIMSPQQAKARGLTSTITFPVGNIAPEGSVI 451 E L+ + R AD+ ++ P + KA + GN+A EG+V Sbjct: 351 EELENVPDTPR---------------ADQDVIMPIE-KALYKEGHLAILKGNLAQEGAVA 394 Query: 452 KSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAGDILVIIGVGP-SGTGME 510 K T + +I G A+V+ E+SA+ I DKI AGDILV+ +GP G GM Sbjct: 395 KITGLKNPVI--------TGPARVFEDEQSAMDAILADKINAGDILVLRYLGPKGGPGMP 446 Query: 511 ETYQVTSALKHLSYGKHVSLITDARFSGVSTGACIGHVGPEALAGGPIGKLRTGDLIEIK 570 E TSA+ G+ V ITD RFSG + G +GHV PEA GG I ++ GD + Sbjct: 447 EMLAPTSAIIGKGLGESVGFITDGRFSGGTWGMVVGHVAPEAHVGGNIALVQEGD--SVT 504 Query: 571 IDCRELHGEVNFLGTRSDEQLPSQEEA 597 ID +L E+N S+E+L + A Sbjct: 505 IDAHKLLLELNV----SEEELAKRRAA 527 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: 806 Number of extensions: 43 Number of successful extensions: 8 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: 557 Length adjustment: 37 Effective length of query: 618 Effective length of database: 520 Effective search space: 321360 Effective search space used: 321360 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: 53 (25.0 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