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 AO353_03420 AO353_03420 phosphogluconate dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__pseudo3_N2E3:AO353_03420 Length = 608 Score = 197 bits (500), Expect = 1e-54 Identities = 156/516 (30%), Positives = 250/516 (48%), Gaps = 49/516 (9%) Query: 47 IGILNTWSDMTPCNGHLRELAEKVKAGVWEAGG---FPLEVPVFSASENTFRP---TAMM 100 + I+++++DM + E++K + E G F VP P + Sbjct: 68 VAIVSSYNDMLSAHQPYEHYPEQIKHALREIGSVGQFAGGVPAMCDGVTQGEPGMELGIA 127 Query: 101 YRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD-LPSIVVTGGPMLNGYFR 159 R + A++ A+ D ++L CDK P L+MGA LP+I V GGPM++G Sbjct: 128 SREVIAMSTAVALSHNMFDAAMMLGICDKIVPGLMMGALRFGHLPTIFVPGGPMVSGISN 187 Query: 160 GERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMA 219 E+ + G+ ++ E LE+E S GTC GTA+T + E +G+ Sbjct: 188 KEKAD-------VRQRYAEGKASREELLESEMKSYHSPGTCTFYGTANTNQLLMEVMGLH 240 Query: 220 LSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDD---LKPSEIMTKQAFENAIRTNAAIGGS 276 L G + + R + + +I ++ K + EI+ +++ N+I A GGS Sbjct: 241 LPGASFVNPNTPLRDALTREAAHQITRLTKQSGNFMPIGEIVDERSLVNSIVALHATGGS 300 Query: 277 TNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRL 336 TN +H+ AIA GI L+ D VPT+ ++ P+GK + F AGG+ +++ L Sbjct: 301 TNHTLHMPAIAMAAGIQLTWQDMADLSEVVPTLSHVYPNGKADINHFQAAGGMSFLIREL 360 Query: 337 GEAGLLHKDALTV---------------SGETVWDEVKDVVNWNEDVILPAEKALTSSGG 381 EAGLLH+D TV +GE VW E + + +E+++ P +A + GG Sbjct: 361 LEAGLLHEDVNTVAGHGLSRYTQEPFLENGELVWRE-GPIESLDENILRPVARAFSPEGG 419 Query: 382 IVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFED----IDDYKAKINDDNLDIDENCI 437 + V+ GNL V+K SA +P V + A+VF+D D +KA + ++++ + Sbjct: 420 LRVMEGNLG--RGVMKVSAVAPEHQVVEAPAMVFQDQQDLADAFKAGL------LEKDFV 471 Query: 438 MVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV--VLHTSPEA 495 VM+ GP+ GM E+ M VL+ + ++D RMSG A G + +H SPEA Sbjct: 472 AVMRFQGPRS-NGMPELHKMTPFLGVLQDRGFKVALVTDGRMSG-ASGKIPAAIHVSPEA 529 Query: 496 AVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARR 531 VGG LA V+ GD+I +D L L + +E A R Sbjct: 530 FVGGALARVQEGDIIRVDGVKGTLQLLVDADEFAAR 565 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: 773 Number of extensions: 40 Number of successful extensions: 8 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: 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