Align L-arabinonate dehydratase; ArDHT; D-fuconate dehydratase; Galactonate dehydratase; L-arabonate dehydratase; EC 4.2.1.25; EC 4.2.1.67; EC 4.2.1.6 (characterized)
to candidate 5209582 Shew_2046 phosphogluconate dehydratase (RefSeq)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__PV4:5209582 Length = 608 Score = 192 bits (487), Expect = 4e-53 Identities = 151/515 (29%), Positives = 247/515 (47%), Gaps = 41/515 (7%) Query: 47 IGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFP---LEVPVFSASENTFRP---TAMM 100 IGI+ ++DM + + +K E G VP +P +++ Sbjct: 68 IGIVTAFNDMLSAHQPYEHYPQLLKDACHEVGSVAQVAAGVPAMCDGVTQGQPGMELSLL 127 Query: 101 YRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD-LPSIVVTGGPMLNGYFR 159 R + A++ + DG +LL CDK P LL+GA S LP + V GPM +G Sbjct: 128 SREVIAMSTAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGPMKSGIPN 187 Query: 160 GERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMA 219 E+ + + G++ +A LEAE+ S+GTC GTA++ M E +G+ Sbjct: 188 KEKA-------RVRQKFAQGQVDRAALLEAESKSYHSAGTCTFYGTANSNQLMLEVMGLQ 240 Query: 220 LSGNAAIPGVDSRRKVMAQLTGR---RIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGS 276 L G++ + D R+ + ++ + R+ +M E++ +++ N I A GGS Sbjct: 241 LPGSSFVNPDDPLREALNKMAAKQVCRLTEMGTQYTPIGEVVNEKSVVNGIVALLATGGS 300 Query: 277 TNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRL 336 TN +H++A A GI ++ DD+ VP + + P+G + F AGG+ ++K L Sbjct: 301 TNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKEL 360 Query: 337 GEAGLLHKDALTVSG---------------ETVWDEVKDVVNWNEDVILPAEKALTSSGG 381 +AGLLH+D LTV+G E VW E + + +++V+ ++GG Sbjct: 361 LDAGLLHEDVLTVAGPGLRRYTQEPRLIDNELVWVEGPN-ESLDKEVLTAVASPFQANGG 419 Query: 382 IVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMK 441 + +L+GNL AV+K SA + + AVV +D + + LD D C++V+K Sbjct: 420 LKLLKGNLG--RAVIKVSAVAESHRFVEAPAVVIDDQNKLEGLFKAGELDRD--CVVVVK 475 Query: 442 NCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV--VLHTSPEAAVGG 499 GPK GM E+ + L+ + ++D RMSG A G V +H +PEA GG Sbjct: 476 GQGPKA-NGMPELHKLTPILGSLQDKGFKVALLTDGRMSG-ASGKVPAAIHLTPEALDGG 533 Query: 500 PLAVVKNGDMIELDVPNRRLHLDISDEELARRLAE 534 +A V+NGD+I +D + L + + LA R E Sbjct: 534 LIAKVENGDLIRVDANTGEVSLLVDEAVLASREVE 568 Lambda K H 0.318 0.135 0.408 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: 791 Number of extensions: 38 Number of successful extensions: 7 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 579 Length of database: 608 Length adjustment: 37 Effective length of query: 542 Effective length of database: 571 Effective search space: 309482 Effective search space used: 309482 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 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