Align D-xylonate dehydratase YagF; EC 4.2.1.82 (characterized)
to candidate GFF2757 PGA1_c28000 phosphogluconate dehydratase Edd
Query= SwissProt::P77596 (655 letters) >FitnessBrowser__Phaeo:GFF2757 Length = 607 Score = 164 bits (415), Expect = 1e-44 Identities = 154/487 (31%), Positives = 221/487 (45%), Gaps = 35/487 (7%) Query: 107 GGIPFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIVFRRLIRSLPTRRAVIGVATCDKGL 166 GG+P CDG +QG GM SL + D + + S A + + CDK + Sbjct: 107 GGVPAM------CDGVTQGEAGMELSL-FSRDTIAMATGIALSHNVFDATVYLGVCDKIV 159 Query: 167 PATMIALAAMHDLPTILVPGGATLPPTVGEDAGKVQTIGARFANHELSLQEAAELGCRAC 226 P +I LP + +P G +D KV+ +FA E+ E + A Sbjct: 160 PGLVIGAQVFGHLPAVFLPAGPMTSGISNDDKAKVRQ---KFAAGEIGRDELLKSEMAAY 216 Query: 227 ASPGGGCQFLGTAGTSQVVAEALGLALPHSALAPSGQAVWLEIARQSAR---AVSELDSR 283 PG C F GTA T+Q++ E +GL LP S+ G + + + AR A+S L + Sbjct: 217 HGPGT-CTFYGTANTNQMLMEFMGLHLPGSSFVNPGTDMRAALTEEGARRALALSALGND 275 Query: 284 GITTRDILSDKAIENAMVIHAAFGGSTNLLLHIPAIAHAAGCTIPDVEHWTRINRKVPRL 343 DIL ++A N +V GGSTNLL+H+ A+A A G I D + ++ ++ VP L Sbjct: 276 YTPVCDILDERAYVNGIVGLMTTGGSTNLLIHLIAMARAGG-IILDWQDFSELSDVVPLL 334 Query: 344 VSVLPNGPDYHPTVRAFLAGGVPEVMLHLRDLGLLHLDAMTVTGQTVGENLEWWQASERR 403 V PNG AGG+ V+ L + G LH D TV G LE + A Sbjct: 335 ARVYPNG--LADVNHFHAAGGLGYVIGQLLNSGHLHSDTRTV----AGSGLESYTAEPFL 388 Query: 404 ARFRQCLREQDGVEPDDVILPPEKAKAKGLTSTVCFPTGNIAPEGSVIKATAIDPSVVGE 463 + + +D I+ P A + T + +GN+ I A A + +V Sbjct: 389 SDDGLVWKPGAAESLNDKIIRPASAPFQP-TGGLARLSGNLGTGVMKISAVAPEHRMV-- 445 Query: 464 DGVYHHTGRVRVFVSEAQAIKAIKREEIVQGDIMVVIG-GGPSGTGMEETYQLTSALKHI 522 RVF + + A K E+ +GD+++V+ GP GM E + +T L + Sbjct: 446 ------EAPARVFHDQEEVKAAFKAGELDKGDMIIVVRFQGPKANGMPELHSMTPFLGIM 499 Query: 523 SW-GKTVSLITDARFSGVSTGACFG-HVSPEALAGGPIGKLRDNDIIEIAVDRLTLTGSV 580 G+ V+L+TD R SG S HV PEAL GGPI KLRD D++ VD LT T V Sbjct: 500 QGRGQKVALVTDGRMSGASGKIPSAIHVVPEALDGGPISKLRDGDMVR--VDALTGTLEV 557 Query: 581 NFIGTAD 587 G D Sbjct: 558 KAEGFDD 564 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: 1017 Number of extensions: 67 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: 1 Length of query: 655 Length of database: 607 Length adjustment: 38 Effective length of query: 617 Effective length of database: 569 Effective search space: 351073 Effective search space used: 351073 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