Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate Dsui_1122 Dsui_1122 dihydroxy-acid dehydratase
Query= BRENDA::P39358 (655 letters) >FitnessBrowser__PS:Dsui_1122 Length = 619 Score = 204 bits (518), Expect = 1e-56 Identities = 172/547 (31%), Positives = 255/547 (46%), Gaps = 56/547 (10%) Query: 72 GLRGAD-GKPVALALHQ------GHYELDIQMKAAAEVIKANHALPYAVYVSDPCDGRTQ 124 G++ D GKP+ ++ GH L + A I+A + DG Sbjct: 26 GMKDGDFGKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGIAKEFNTIAIDDGIAM 85 Query: 125 GTTGMFDSLPYRNDASMVMRRLIRSLPDAKAVIGVASCDKGLPATMMALAAQHNIATVLV 184 G GM SLP R+ + + ++ + A A++ +++CDK P +MA A + NI T+ V Sbjct: 86 GHDGMLYSLPSRDLIADSVEYMVNA-HCADAMVCISNCDKITPGMLMA-AMRVNIPTIFV 143 Query: 185 PGGATLPAKDGEDNGK---VQTIGARFANGELSLQDAR-----RAGCKACASSGGGCQFL 236 GG + A + GK V I A G+ + DA R+ C C G C + Sbjct: 144 SGGP-MEAGKVKWEGKTIAVDLIDAMIKAGDSNCSDAEVEEFERSACPTC----GSCSGM 198 Query: 237 GTAGTSQVVAEGLGLAIPHSALAPSGEPVWREIARASARAALNLSQK-------GITTRE 289 TA + + E LGL++P + + + + + R + L+Q+ + R Sbjct: 199 FTANSMNCLTEALGLSLPGNGTLVATHADRKGLFLEAGRRIVRLAQRWYEENDASVLPRS 258 Query: 290 ILTDKAIENAMTVHAAFGGSTNLLLHIPAIAHQAGCHIPTVDDWIRINKRVPRLVSVLPN 349 I KA ENA + A GGSTN +LH+ A A +AG T+ D I+++VP L V P Sbjct: 259 IANQKAFENAFALDVAMGGSTNTVLHLLATAQEAGVTF-TMADIDAISRKVPCLCKVAPA 317 Query: 350 GPVYHPTVNAFMAGGVPEVMLHLRSLGLLHEDVMTVTGSTLKENLDWWE----HSERRQR 405 YH + AGG+ ++ L GL+H D TV TL E +D ++ S+R Sbjct: 318 TQDYH-IEDVHRAGGIMAILGELSRGGLIHRDTPTVHCHTLGEAIDTYDVQRAGSQRTLE 376 Query: 406 FKQL----LLDQEQINADEVIMSPQQAKARGLTSTITFPV----------GNIAPEGSVI 451 F + + Q + D Q ++ G + GNIA +G ++ Sbjct: 377 FFRAAPGGIPTQTAFSQDRRYTELDQDRSNGCIRNVAHAYSKEGGLAVLHGNIALDGCIV 436 Query: 452 KSTAIDPSMIDEQGIYYHKGVAKVYLSEKSAIYDIKHDKIKAGDILVIIGVGPSG-TGME 510 K+ +D S I+ G AKVY S+ SA+ I ++ AGD++VI GP G GM+ Sbjct: 437 KTAGVDES------IWKFTGKAKVYESQDSAVTAILGGEVVAGDVVVIRYEGPKGGPGMQ 490 Query: 511 ETYQVTSALKHLSYGKHVSLITDARFSGVSTGACIGHVGPEALAGGPIGKLRTGDLIEIK 570 E TS LK GK +L+TD RFSG ++G IGH PEA GG IG +RTGD IEI Sbjct: 491 EMLYPTSYLKSRGLGKECALLTDGRFSGGTSGLSIGHASPEAAEGGAIGLVRTGDTIEID 550 Query: 571 IDCRELH 577 I R +H Sbjct: 551 IPGRRIH 557 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: 905 Number of extensions: 33 Number of successful extensions: 6 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: 619 Length adjustment: 38 Effective length of query: 617 Effective length of database: 581 Effective search space: 358477 Effective search space used: 358477 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