Align D-xylonate dehydratase YagF; EC 4.2.1.82 (characterized)
to candidate HSERO_RS05520 HSERO_RS05520 phosphogluconate dehydratase
Query= SwissProt::P77596 (655 letters) >FitnessBrowser__HerbieS:HSERO_RS05520 Length = 623 Score = 164 bits (416), Expect = 9e-45 Identities = 153/504 (30%), Positives = 228/504 (45%), Gaps = 53/504 (10%) Query: 101 KEITRNGGI--PFAAFVSDPCDGRSQGTHGMFDSLPYRNDAAIVFRRLIRSLPTRRAVIG 158 K+ R G FA CDG +QG GM SL + DA + + S A + Sbjct: 94 KDAAREAGAVAQFAGGSPAMCDGVTQGQAGMELSL-FSRDAIAMATAIALSHNMFDAALY 152 Query: 159 VATCDKGLPATMIALAAMHDLPTILVPGGATLPPTVGEDAGKVQTIGARFANHELSLQEA 218 + CDK +P +I LP + VP G D K++ + L EA Sbjct: 153 LGVCDKIVPGLLIGALHFGHLPAVFVPAGPMTSGMSNSDKVKIRQLYTAGKIGRAELLEA 212 Query: 219 AELGCRACASPGGGCQFLGTAGTSQVVAEALGLALPHSAL----APSGQAVWLEIARQSA 274 G C F GTA ++Q++ EA+GL LP +A P A+ A+Q+A Sbjct: 213 ESKSYHGA----GTCTFYGTANSNQMLMEAMGLHLPGAAFITPNTPLRDALTAAAAKQAA 268 Query: 275 RAVSELDSRGITTRDILSDKAIENAMVIHAAFGGSTNLLLHIPAIAHAAGCTIPDVEHWT 334 + +++L ++ ++ +K+I NA+V A GGSTN LH+ AIA AAG I D + + Sbjct: 269 K-ITDLGTQYTPVGRMIDEKSIVNAIVALHATGGSTNHTLHLVAIAKAAGIVI-DWDDFD 326 Query: 335 RINRKVPRLVSVLPNGPDYHPTVRAF-LAGGVPEVMLHLRDLGLLHLDAMTVTGQTVGEN 393 +++ VP + + PNG V F AGG V+ L D GL+H D T+ GQ + Sbjct: 327 KLSAVVPLITKIYPNGT---ADVNHFHAAGGTGFVLRELIDAGLMHDDVTTILGQGL--- 380 Query: 394 LEWWQASERRARFRQCLREQDGVEPDDVIL--PPEKAKAKGLTSTVCFP----------T 441 + + E + P V P ++ +G+ TV P Sbjct: 381 -------RQHCKEPMLAAEGENGRPGIVTWHDAPAQSGDEGVLGTVAKPFAADGGLKLLQ 433 Query: 442 GNIAPEGSVIKATAIDPS--VVGEDGVYHHTGRVRVFVSEAQAIKAIKREEIVQGDIMVV 499 GN+ +VIK +A+ P VV V VF S+ + A K ++ + + V+ Sbjct: 434 GNLG--RAVIKISAVKPEHRVVEAPAV--------VFHSQEAFMAAFKAGQLDRDFVAVI 483 Query: 500 IGGGPSGTGMEETYQLTSALKHI-SWGKTVSLITDARFSGVSTGACFG-HVSPEALAGGP 557 GP GM E + LT AL + G+ V+L+TD R SG S HV+PE L GGP Sbjct: 484 TFQGPRANGMPELHALTPALGILQDKGRHVALVTDGRMSGASGKVPAAIHVTPEVLGGGP 543 Query: 558 IGKLRDNDIIEIAVDRLTLTGSVN 581 +G++RD DII + + TL V+ Sbjct: 544 LGRVRDGDIIRLDAEAGTLEAKVD 567 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: 1013 Number of extensions: 56 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: 623 Length adjustment: 38 Effective length of query: 617 Effective length of database: 585 Effective search space: 360945 Effective search space used: 360945 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