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 201628 SO2487 6-phosphogluconate dehydratase (NCBI ptt file)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__MR1:201628 Length = 608 Score = 202 bits (513), Expect = 4e-56 Identities = 156/515 (30%), Positives = 255/515 (49%), Gaps = 43/515 (8%) Query: 47 IGILNTWSDMTPCNGH-------LRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAM 99 IGI+ ++DM + L++ ++V + AGG P + + ++ Sbjct: 68 IGIITAFNDMLSAHQPYETYPDLLKKACQEVGSVAQVAGGVPAMCDGVTQGQPGME-LSL 126 Query: 100 MYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCD-LPSIVVTGGPMLNGYF 158 + R + A+A + DG +LL CDK P LL+GA S LP + V GPM +G Sbjct: 127 LSREVIAMATAVGLSHNMFDGALLLGICDKIVPGLLIGALSFGHLPMLFVPAGPMKSGIP 186 Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGM 218 E+ + + G++ +A+ LEAEA S+GTC GTA++ M E +G+ Sbjct: 187 NKEKA-------RIRQQFAQGKVDRAQLLEAEAQSYHSAGTCTFYGTANSNQLMLEVMGL 239 Query: 219 ALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPS---EIMTKQAFENAIRTNAAIGG 275 L G++ + D R+ + ++ +++ ++ + + S E++ +++ N I A GG Sbjct: 240 QLPGSSFVNPDDPLREALNKMAAKQVCRLTELGTQYSPIGEVVNEKSIVNGIVALLATGG 299 Query: 276 STNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKR 335 STN +H++A A GI ++ DD+ VP + + P+G + F AGG+ ++K Sbjct: 300 STNLTMHIVAAARAAGIIVNWDDFSELSDAVPLLARVYPNGHADINHFHAAGGMAFLIKE 359 Query: 336 LGEAGLLHKDALTVS---------------GETVWDEVKDVVNWNEDVILPAEKALTSSG 380 L +AGLLH+D TV+ GE W + V+ + +V+ ++G Sbjct: 360 LLDAGLLHEDVNTVAGYGLRRYTQEPKLLDGELRWVD-GPTVSLDTEVLTSVATPFQNNG 418 Query: 381 GIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVM 440 G+ +L+GNL AV+K SA P V + AVV +D + A LD D C++V+ Sbjct: 419 GLKLLKGNLG--RAVIKVSAVQPQHRVVEAPAVVIDDQNKLDALFKSGALDRD--CVVVV 474 Query: 441 KNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTAYGTV--VLHTSPEAAVG 498 K GPK GM E+ + L+ + ++D RMSG A G V +H +PEA G Sbjct: 475 KGQGPKA-NGMPELHKLTPLLGSLQDKGFKVALMTDGRMSG-ASGKVPAAIHLTPEAIDG 532 Query: 499 GPLAVVKNGDMIELDVPNRRLHLDISDEELARRLA 533 G +A V++GD+I +D L L +SD ELA R A Sbjct: 533 GLIAKVQDGDLIRVDALTGELSLLVSDTELATRTA 567 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: 784 Number of extensions: 42 Number of successful extensions: 8 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