Align phosphogluconate dehydratase (characterized)
to candidate WP_066605615.1 V473_RS11950 dihydroxy-acid dehydratase family protein
Query= CharProtDB::CH_024239 (603 letters) >NCBI__GCF_001046645.1:WP_066605615.1 Length = 600 Score = 175 bits (443), Expect = 6e-48 Identities = 144/458 (31%), Positives = 217/458 (47%), Gaps = 49/458 (10%) Query: 136 AAVGLSHNMF----DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV 191 A +GL M+ DG + CDK P L MAA + ++PA+ + GPM +G E+ Sbjct: 108 AYLGLVEAMYGYPLDGVILTTGCDKTTPALLMAAATV-NIPAIALSVGPMLNGWFKGERT 166 Query: 192 -------RIRQLYAEGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGS 244 + R+L A GK+D ++ A+S + G C GTA+T + E +GM LPGS Sbjct: 167 GSGTIVWKGRELLAAGKIDDEGFIKLVASSAPSTGYCNTMGTASTMNSLAEALGMMLPGS 226 Query: 245 SFVHPDSPLRDALTAA--AARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTN 302 + + +P RD A +++ M E + ++ N IV A GGSTN Sbjct: 227 AAI--PAPYRDRQEVAYLTGKRIVDMVA---EDLKPSDIMTLDAFHNAIVVNSAIGGSTN 281 Query: 303 HTMHLVAMARAAGIQINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLK 362 +HL A+AR G+ + D+ + VPL+ L P G + AGGVP +V +L+ Sbjct: 282 APIHLSAIARHMGVDLPLKDWETVGHKVPLLVNLQPAGEYLGEDYYRAGGVPAVVSQLID 341 Query: 363 AGLLHEDVNTVAGFGLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKV 422 GL+ TV G T+ E++ D VI F+QP G V Sbjct: 342 QGLIRTSAMTVNG-----KTMGENCKGVEIE---------DEKVIRPFDQPLVTDAGFLV 387 Query: 423 LSGNL-GRAVMKTSAVPVE-----------NQVIEAPAVVFESQHDVMPAFE--AGLLDR 468 LSGNL AVMKTS + VE + E PAVVF+ D + A + Sbjct: 388 LSGNLFDAAVMKTSVISVEFRDRYLSNPDDPEAFEGPAVVFDGPEDYHHRIDDPATGITA 447 Query: 469 DCVVVVRHQGPKA-NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTP 527 + ++ +R GP G E+ + PP ++ + + + DGR SG SG PS ++ +P Sbjct: 448 NSLMFMRGAGPIGYPGAAEVVNMRPPAYLITEGVSALPCIGDGRQSGTSGS-PSILNASP 506 Query: 528 EAYDGGLLAKVRDGDIIRVNGQTGELTLLVDEAELAAR 565 EA G LA + GD +R++ + G + +L+ + ELA R Sbjct: 507 EAAAMGGLALLETGDRVRMDLKAGTVNVLISDEELAER 544 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: 847 Number of extensions: 55 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: 603 Length of database: 600 Length adjustment: 37 Effective length of query: 566 Effective length of database: 563 Effective search space: 318658 Effective search space used: 318658 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