Align D-xylonate dehydratase YagF; EC 4.2.1.82 (characterized)
to candidate Ga0059261_0354 Ga0059261_0354 6-phosphogluconate dehydratase (EC 4.2.1.12)
Query= SwissProt::P77596 (655 letters) >FitnessBrowser__Korea:Ga0059261_0354 Length = 608 Score = 169 bits (427), Expect = 4e-46 Identities = 164/540 (30%), Positives = 244/540 (45%), Gaps = 56/540 (10%) Query: 83 LGYHTGHWEIGMQMQAAAKEITRNGGIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIV 142 L H ++ QM+ A E + A V CDG +QG GM SL + D + Sbjct: 81 LSAHAPYYRYPEQMKIWALEAGATAQV--AGGVPAMCDGVTQGYAGMELSL-FSRDTIAM 137 Query: 143 FRRLIRSLPTRRAVIGVATCDKGLPATMIALAAMHDLPTILVPGGATLPPTVGEDAGKVQ 202 + S T + CDK +P ++ LP +L+PGGA ++ +V+ Sbjct: 138 STAVALSHNTFEGAALLGICDKIVPGLLMGALRFGHLPMVLIPGGAMPTGIANKEKARVR 197 Query: 203 TIGARFANHELSLQEAAELGCRACASPGGGCQFLGTAGTSQVVAEALGLALPHSALAPSG 262 + +A + S +E + A G C F GTA ++Q++ EA+GL +P +A G Sbjct: 198 EL---YAEGKASREELLDSEIAAYHGKGT-CTFYGTANSNQMMVEAMGLHMPGAAFIHPG 253 Query: 263 QAVWLEIARQSARAVSEL-----DSRGITTRDILSDKAIENAMVIHAAFGGSTNLLLHIP 317 + + R + + + E+ D R I +I+ ++AI NA V+ A GGSTN L+H+P Sbjct: 254 TKLRQALTRAAVQRLPEIGWDSNDYRPI--GEIVDERAIVNAAVVLLATGGSTNHLIHLP 311 Query: 318 AIAHAAGCTIPDVEHWTRINRKVPRLVSVLPNGPDYHPTVRAFL-AGGVPEVMLHLRDLG 376 AIA AG I D + + R++R VP L V PNG V F AGG V+ L G Sbjct: 312 AIARCAGVLI-DWDDFDRLSRVVPLLARVYPNG---SADVNGFEDAGGPTFVIRELIKGG 367 Query: 377 LLHLDAMTVTGQTVGENLEWWQASERRARFRQCLREQDGVEPDDVILPPEKAKAKGLTST 436 +LH D +TV G ++ + + RR V DD ++ + G S Sbjct: 368 VLHGDTLTVAGDSLADYV-------RRP-----------VLEDDTLVWKDHGAKSGDDSI 409 Query: 437 VCFPTGNIAPEGSV------IKATAIDPSVVGEDGVYHHTGRVRVFVSEAQAIKAIKREE 490 + + EG + I S V D + RVF ++ + A K E Sbjct: 410 LRTIDAPFSEEGGFRILSGNLGRACIKVSAVERDR-WTIEAPCRVFATQQEVQDAFKAGE 468 Query: 491 IVQGDIMVVIGGGPSGTGMEETYQLTSALKHI-SWGKTVSLITDARFSGVSTGACFG-HV 548 + + ++VV GP GM E ++LT L + + G V+L+TD R SG S H+ Sbjct: 469 LDRDVVVVVRFQGPRANGMPELHKLTPPLGVLQNKGFRVALVTDGRMSGASGKVPAAIHL 528 Query: 549 SPEALAGGPIGKLRDNDIIEIAVDRLTLTGSVNFIGTADNPLTPEEGARELARRQTHPDL 608 SPEA+ GGPIGKLRD D++ + + L V E ARELA PDL Sbjct: 529 SPEAIGGGPIGKLRDGDVVRLCAEEGILQALVE---------PAEWEARELAAAPP-PDL 578 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: 976 Number of extensions: 57 Number of successful extensions: 7 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: 608 Length adjustment: 38 Effective length of query: 617 Effective length of database: 570 Effective search space: 351690 Effective search space used: 351690 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 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