Align xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate BWI76_RS18100 BWI76_RS18100 phosphogluconate dehydratase
Query= BRENDA::Q9A9Z2 (595 letters) >FitnessBrowser__Koxy:BWI76_RS18100 Length = 603 Score = 174 bits (442), Expect = 7e-48 Identities = 143/438 (32%), Positives = 210/438 (47%), Gaps = 48/438 (10%) Query: 132 CDKTTPAGIMAATTV-NIPAIVLSGGPMLDGWHENELVGSGTVIWRSRRKLAAGEITEEE 190 CDK P MAA + ++P+I + GPM G E V R R+ A G++ Sbjct: 154 CDKIVPGLAMAALSFGHLPSIFIPSGPMASGLANKEKV-------RIRQLYAEGKVDRMA 206 Query: 191 FIDRAASSAPSAGHCNTMGTASTMNAVAEALGLSLTGCAAI--PAPYRERGQMAYKTGQR 248 ++ A+S + G C GTA+T V E +G+ L G + + AP RE A Sbjct: 207 LLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDAPLREALTAAAARQVT 266 Query: 249 IVDLAYDDVKPLD-ILTKQAFENAIALVAAAGGSTNAQPHIVAMARHAGVEITADDWRAA 307 + ++ PL + ++ N I + A GGSTN H+VAMAR AG+ I DD+ Sbjct: 267 RLTGNGNEWMPLGKMFDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGIIINWDDFSDL 326 Query: 308 YDI-PLIVNMQPAGKYLGERFHRAGGAPAVLWELLQQGRLHGDVLTVTGKTMSE------ 360 D+ PL+ + P G F AGG P ++ ELL+ G LH DV TV G +S Sbjct: 327 SDVVPLLARLYPNGPADINHFQAAGGVPVLVRELLKGGLLHEDVHTVAGFGLSRYTMEPW 386 Query: 361 ----NLQGRETS----DREVIFPYHEPLAEKAGFLVLKGNLFDFAIMKSSVIGEEFRKRY 412 L RE + D VI + +P + G VL GNL A+MK+S + Sbjct: 387 LNNGELDWREGAAAPLDEAVIATFDKPFSRHGGTKVLSGNL-GRAVMKTSAV-------- 437 Query: 413 LSQPGQEGVFEARAIVFDGSDDYHKRINDPALE---IDERCILVIRGAGPIGWPGSAEVV 469 P + + EA A+VF+ D PA E +D+ C++V+R GP G E+ Sbjct: 438 ---PVENQIIEAPAVVFESQHDVL-----PAFEAGLLDKDCVVVVRHQGPKA-NGMPELH 488 Query: 470 NMQPPDHLLKKGIMSLPTLGDGRQSGTADS-PSILNASPESAIGGGLSWLRTGDTIRIDL 528 + PP +L + + DGR SG + PS ++ +PE+ GG L+ +R GD IR++ Sbjct: 489 KLMPPLGVLLDRRFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKVRDGDIIRVNG 548 Query: 529 NTGRCDALVDEATIAARK 546 TG VD+A +AAR+ Sbjct: 549 QTGELTLRVDDAELAARQ 566 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: 879 Number of extensions: 50 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: 595 Length of database: 603 Length adjustment: 37 Effective length of query: 558 Effective length of database: 566 Effective search space: 315828 Effective search space used: 315828 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: 53 (25.0 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