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 3608367 Dshi_1769 6-phosphogluconate dehydratase (RefSeq)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Dino:3608367 Length = 601 Score = 186 bits (471), Expect = 3e-51 Identities = 151/498 (30%), Positives = 237/498 (47%), Gaps = 49/498 (9%) Query: 47 IGILNTWSDMTPCNGHLRELAEKVK-------AGVWEAGGFPLEVPVFSASENTFRPTAM 99 IGI+ ++DM + ++ +K+K A AGG P + + ++ Sbjct: 69 IGIVTAYNDMLSAHQPFKDYPDKIKEAARRAGATAQVAGGVPAMCDGVTQGQVGME-LSL 127 Query: 100 MYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD-LPSIVVTGGPMLNGYF 158 R++ ALA A+ D L CDK P L++ AA+ LP + V GPM++G Sbjct: 128 FSRDVIALATGVALSHNTFDAAAYLGVCDKIVPGLVIAAATFGYLPGVFVPAGPMVSGLP 187 Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGM 218 ++ K + AGE+ + + +EAE + GTC GTA++ + E +G+ Sbjct: 188 NDQKA-------KVRQQFAAGEIGRDKLMEAEMASYHGPGTCTFYGTANSNQMLMEFMGL 240 Query: 219 ALSGNAAI-PGVDSRRKVMAQLTGR--RIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGG 275 L G + + PG R + A R I Q+ + +I+ +AF N I A GG Sbjct: 241 HLPGASFVNPGTPLREALTAAAAERLAAITQLGNEYRPVCDILDAKAFVNGIVGLMATGG 300 Query: 276 STNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKR 335 STN VIHL A+A G+ L L D+ P + + P+G + F AGGL ++ Sbjct: 301 STNLVIHLPAMARAAGVILDLQDFADISEATPLMARVYPNGLADVNHFHAAGGLAYMIGE 360 Query: 336 LGEAGLLHKDALTVSGETVWDEVKD------VVNW--------NEDVILPAEKALTSSGG 381 L GLLH D T++G+ + D ++ V+ W N ++ PA SGG Sbjct: 361 LLSEGLLHPDTKTIAGDGLADYAREPKLIDGVLRWEDGPRRSLNAKILRPASDGFAPSGG 420 Query: 382 IVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFED----IDDYKAKINDDNLDIDENCI 437 + L+GNL V+K SA +P V + RA VFED D +KA + E+ + Sbjct: 421 LKELKGNLG--RGVMKVSAVAPERHVIEARARVFEDQGAVKDAFKAG------EFTEDTV 472 Query: 438 MVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV--VLHTSPEA 495 ++++ GPK GM E+ + VL+ L + ++D RMSG A G V +H +PEA Sbjct: 473 VIVRFQGPKA-NGMPELHALTPVLAVLQDRGLKVALVTDGRMSG-ASGKVPAAIHVAPEA 530 Query: 496 AVGGPLAVVKNGDMIELD 513 GG +A V+ GD++ +D Sbjct: 531 LDGGLMAKVRTGDLVRVD 548 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: 834 Number of extensions: 46 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: 601 Length adjustment: 37 Effective length of query: 542 Effective length of database: 564 Effective search space: 305688 Effective search space used: 305688 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