Align D-xylonate dehydratase YagF; EC 4.2.1.82 (characterized)
to candidate WP_039951110.1 BUB52_RS01630 dihydroxy-acid dehydratase
Query= SwissProt::P77596 (655 letters) >NCBI__GCF_900129655.1:WP_039951110.1 Length = 600 Score = 198 bits (503), Expect = 7e-55 Identities = 169/553 (30%), Positives = 262/553 (47%), Gaps = 61/553 (11%) Query: 86 HTGHWEIGMQMQAAAKEITRNG--GIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIVF 143 H EIG ++A EI + G F D DG + G GM SLP R+ A Sbjct: 51 HVHLHEIGQFVKA---EIEKQGCFAAEFNTIAID--DGIAMGHDGMLYSLPSRDIIADSV 105 Query: 144 RRLIRSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGATLPPTVGEDAGK-VQ 202 ++ + A++ ++ CDK P ++A ++ +PT+ V GG P GE G+ + Sbjct: 106 EYMVNAHKAD-AMVCISNCDKITPGMLMAAMRLN-IPTVFVSGG---PMEAGEWNGQHLD 160 Query: 203 TIGA--RFANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQVVAEALGLALPHSALAP 260 I A + A+ +S E A++ AC + G C + TA + + EA+GLALP + Sbjct: 161 LIDAMIKSADESVSDNEVAKIEQHACPTCGC-CSGMFTANSMNCLNEAIGLALPGNGTIV 219 Query: 261 SGQAVWLEIARQSARAVSEL-------DSRGITTRDILSDKAIENAMVIHAAFGGSTNLL 313 + E+ + +A+ + E + R I + +A NAM + A GGSTN + Sbjct: 220 ATHKNRKELFKDAAKLIVENAYKYYEEGDESVLPRSIATREAFLNAMTLDIAMGGSTNTV 279 Query: 314 LHIPAIAHAAGC--TIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFLAGGVPEVMLH 371 LH+ A+AH AG T+ D++ ++RK P L V PN YH AGG+ +M Sbjct: 280 LHLLAVAHEAGADFTMDDID---MLSRKTPCLCKVAPNTQKYH-VQDVNRAGGIVAIMGE 335 Query: 372 LRDLGLLHLDAMTVTGQTVGENLEWW--------------QASERRARFRQCLREQDGVE 417 L GL+ + V G T+ E ++ + +S +F L QD Sbjct: 336 LAKGGLVDTNVRRVDGMTLAEEIDRYCITDPNVCKEAIKKYSSAAAGKFNLVLGSQDAYY 395 Query: 418 PDDVILPPEKAK--------AKGLTSTVCFPTGNIAPEGSVIKATAIDPSVVGEDGVYHH 469 + L ++A+ A + GNIA +G V+K +D S+ + Sbjct: 396 KE---LDTDRAEGCIRDLQHAYSKDGGLAVLKGNIAQDGCVVKTAGVDESI------WKF 446 Query: 470 TGRVRVFVSEAQAIKAIKREEIVQGDIMVVIGGGPSG-TGMEETYQLTSALKHISWGKTV 528 TG +VF S+ A I ++V GD++V+ GP G GM+E TS +K GK Sbjct: 447 TGPAKVFDSQEAACDGILGGKVVSGDVVVITHEGPKGGPGMQEMLYPTSYIKSRHLGKEC 506 Query: 529 SLITDARFSGVSTGACFGHVSPEALAGGPIGKLRDNDIIEIAVDRLTLTGSVNFIGTADN 588 +LITD RFSG ++G GH+SPEA AGG IGK++D DIIEI + ++ + A Sbjct: 507 ALITDGRFSGGTSGLSIGHISPEAAAGGNIGKIQDGDIIEIDIPNRSINVKLTDEELAAR 566 Query: 589 PLTPEEGARELAR 601 P+TP R++++ Sbjct: 567 PMTPVTRDRQVSK 579 Lambda K H 0.319 0.136 0.411 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: 941 Number of extensions: 40 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: 600 Length adjustment: 38 Effective length of query: 617 Effective length of database: 562 Effective search space: 346754 Effective search space used: 346754 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 24 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