Align phosphogluconate dehydratase (characterized)
to candidate WP_002968570.1 BIBO1_RS18925 dihydroxy-acid dehydratase family protein
Query= CharProtDB::CH_024239 (603 letters) >NCBI__GCF_000182725.1:WP_002968570.1 Length = 601 Score = 189 bits (480), Expect = 3e-52 Identities = 143/447 (31%), Positives = 217/447 (48%), Gaps = 51/447 (11%) Query: 146 DGALFLGVCDKIVPGLTMAALSFGHLPAVFVPSGPMASGLPNKEKV-------RIRQLYA 198 DG + CDK P MAA + ++PA+ + GPM +G E+ + R+L A Sbjct: 123 DGVVLTIGCDKTTPACLMAAATV-NIPAIALSVGPMLNGWFRGERTGSGTIVWKARELLA 181 Query: 199 EGKVDRMALLESEAASYHAPGTCTFYGTANTNQMVVEFMGMQLPGSSFVHPDSPLRDALT 258 +G++D ++ A+S + G C GTA T + E +GMQLPGS+ + +P RD Sbjct: 182 KGEIDYQGFVKLVASSAPSTGYCNTMGTATTMNSLAEALGMQLPGSAAI--PAPYRDRQE 239 Query: 259 AA--AARQVTRMTGNGNEWMPIGKMIDEKVVVNGIVALLATGGSTNHTMHLVAMARAAGI 316 A R++ M +E + ++ ++ +N I A GGSTN +HL A+AR G+ Sbjct: 240 VAYLTGRRIVEMV---HEDLKPSDILTKEAFINAIRVNSAIGGSTNAPIHLNALARHIGV 296 Query: 317 QINWDDFSDLSDVVPLMARLYPNGPADINHFQAAGGVPVLVRELLKAGLLHEDVNTVAGF 376 ++ DD+ + +PL+ L P G + AGGVP +V +L+ GL+HED TV G Sbjct: 297 ELTVDDWQKYGEEIPLLVNLQPAGEYLGEDYYHAGGVPAVVNQLMGQGLIHEDAITVNG- 355 Query: 377 GLSRYTLEPWLNNGELDWREGAEKSLDSNVIASFEQPFSHHGGTKVLSGNL-GRAVMKTS 435 T+ N ++ D NVI +++QP H G +VL GNL A+MK S Sbjct: 356 ----KTIGENCKNATIE---------DGNVIKTYDQPLKKHAGFRVLRGNLFSSAIMKLS 402 Query: 436 AVPVE-----------NQVIEAPAVVFESQHDVM-----PAFEAGLLDRDCVVVVRHQGP 479 + E E AVVF+ D PA E +D V+ +R GP Sbjct: 403 VISDEFRNRYLSDAKDPNAFEGKAVVFDGPEDYHHRIDDPALE---IDEHTVLFMRGAGP 459 Query: 480 KA-NGMPELHKLMPPLGVLLDRCFKIALVTDGRLSGASGKVPSAIHVTPEAYDGGLLAKV 538 G E+ + P +L + + DGR SG SG PS ++ +PEA GG LA + Sbjct: 460 IGYPGAAEVVNMRAPDYLLKKGITSLPCIGDGRQSGTSGS-PSILNASPEAAAGGGLAIL 518 Query: 539 RDGDIIRVNGQTGELTLLVDEAELAAR 565 + GD +R++ G +L+ + ELA R Sbjct: 519 KTGDRVRIDLGRGTADILISDEELAER 545 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: 848 Number of extensions: 40 Number of successful extensions: 5 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: 601 Length adjustment: 37 Effective length of query: 566 Effective length of database: 564 Effective search space: 319224 Effective search space used: 319224 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