Align phosphogluconate dehydratase (characterized)
to candidate WP_086511017.1 BZY95_RS16650 dihydroxy-acid dehydratase
Query= CharProtDB::CH_024239 (603 letters) >NCBI__GCF_002151265.1:WP_086511017.1 Length = 599 Score = 189 bits (481), Expect = 2e-52 Identities = 158/527 (29%), Positives = 238/527 (45%), Gaps = 53/527 (10%) Query: 68 IAIITSYNDMLSAHQPYEHYPEIIRKALHEANAVGQVAGGVPAMCDGVTQGQDGMELSLL 127 I I S +D+ ++ H+ E++++ A AGGVP ++ + Sbjct: 50 IGICQSGSDLTPCNR---HHIELVKRVKEGIRA----AGGVPFEFPLHPIHENARRPTAA 102 Query: 128 SREVIAMSAAVGLSHNM-FDGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLP 186 +A V + H DG + CDK P MAA + ++PA+ + GPM +G Sbjct: 103 LDRNLAYLGLVEVLHGYPLDGVVLTTGCDKTTPASLMAAATV-NIPAIVLSGGPMLNGWR 161 Query: 187 NKEKV-------RIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGM 239 ++V +R+ A G +D L S + G C GTA+T + E +GM Sbjct: 162 GPDRVGSGTIIWELRKRLAAGDIDYAEFLARATDSAPSVGHCNTMGTASTMNSMAEALGM 221 Query: 240 QLPGSSFVHPDSPLRDALTAAAARQVTRMTGNGNEWMPI--GKMIDEKVVVNGIVALLAT 297 LPGS+ + R + ++ M W + ++ + N IV A Sbjct: 222 SLPGSAMIPAPYKERAMVAYDTGARIVDMV-----WQDLRPSDILTRQAFENAIVVCSAL 276 Query: 298 GGSTNHTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLV 357 GGS+N +H+ A+AR +G+++ DD+ L +PL+A + P G F AGGVP +V Sbjct: 277 GGSSNAPIHINAIARHSGVELTNDDWQALGHAIPLLANVMPAGAYLSEEFYRAGGVPAVV 336 Query: 358 RELLKAGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHH 417 ELL AG LH + TV G L+ D G E + D VI ++ P Sbjct: 337 NELLGAGKLHGEALTVNGRTLA-------------DNCAGRE-TQDPEVIRRYDNPLVEQ 382 Query: 418 GGTKVLSGNL-GRAVMKTSAV-----------PVENQVIEAPAVVFESQHDVMPAFEAGL 465 G L GNL A+MKTS + P + E VVF+ D + Sbjct: 383 AGFLNLKGNLFDSALMKTSVISADFRARFLSNPDDPNAFEGKVVVFDGSEDYHARIDDPA 442 Query: 466 LDRD--CVVVVRHQGPKAN-GMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSA 522 LD D ++V+R GP + G E+ + PP ++ + + DGR SG SG PS Sbjct: 443 LDIDEHTILVMRGAGPVGHPGGAEVVNMQPPEALIKRGIESLPCLGDGRQSGTSGS-PSI 501 Query: 523 IHVTPEAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAREPHI 569 ++ PEA GG LA + DGD +RV+ GE+ LLVD+AEL AR + Sbjct: 502 LNAAPEAATGGGLALLEDGDRLRVDLNRGEVRLLVDDAELQARRERL 548 Lambda K H 0.318 0.134 0.392 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: 898 Number of extensions: 44 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: 603 Length of database: 599 Length adjustment: 37 Effective length of query: 566 Effective length of database: 562 Effective search space: 318092 Effective search space used: 318092 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 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 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