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 YP_001313211.1 Smed_4478 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_000017145.1:YP_001313211.1 Length = 581 Score = 892 bits (2306), Expect = 0.0 Identities = 429/581 (73%), Positives = 507/581 (87%), Gaps = 2/581 (0%) Query: 1 MKKKAEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCN 60 MKKKAEWPRKLRSQ+W+GGT ++ I HR W+KNQG P D FDGRP+IGI NTWS++TPCN Sbjct: 1 MKKKAEWPRKLRSQDWFGGTGKNAIMHRSWMKNQGLPADTFDGRPIIGICNTWSELTPCN 60 Query: 61 GHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDG 120 HLR+LAE+VK GV+EAGGFP+E PVFS E+T RPTAMM+RNLAA+ VEE+IRG P+DG Sbjct: 61 AHLRDLAERVKRGVYEAGGFPVEFPVFSTGESTLRPTAMMFRNLAAMDVEESIRGNPIDG 120 Query: 121 CVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGE 180 VLL GCDKTTPSLLMGAAS D+P+IVV+GGPMLNG +RG+ VGSGT +W+FSEMVK+GE Sbjct: 121 VVLLGGCDKTTPSLLMGAASVDIPAIVVSGGPMLNGKWRGKDVGSGTAIWQFSEMVKSGE 180 Query: 181 MTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLT 240 MT EF++AE M+RS+G+C TMGTASTMASMAEALGM LSGNAAIP VD+RR+V++QLT Sbjct: 181 MTLEEFMDAEQGMARSAGSCMTMGTASTMASMAEALGMTLSGNAAIPAVDARRRVISQLT 240 Query: 241 GRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWD 300 GRRIV+MVK+DLKPS+I+TK+AFENAIR N A+GGSTNAV+HLLA+AGRVG+DLSLDDWD Sbjct: 241 GRRIVEMVKEDLKPSDILTKEAFENAIRVNGAVGGSTNAVLHLLALAGRVGVDLSLDDWD 300 Query: 301 RCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKD 360 R GRDVPTIVNL PSGKYLMEEF+YAGGLPVV+K + E GLLH DA+TVSG+T+W++VK Sbjct: 301 RLGRDVPTIVNLQPSGKYLMEEFYYAGGLPVVIKAVAEMGLLHNDAITVSGDTIWNDVKG 360 Query: 361 VVNWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDD 420 VVN+N+DVILP E+ALT SGGI VLRGNLAP+GAVLKPSAASP+L+ HKGRAVVFE I+D Sbjct: 361 VVNYNDDVILPRERALTKSGGIAVLRGNLAPRGAVLKPSAASPNLMQHKGRAVVFESIED 420 Query: 421 YKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMS 480 Y A+IN ++LDIDE CIMV+K CGPKGYPGMAEVGNMGLPPKVLKKG+ DM+RISDARMS Sbjct: 421 YHARINREDLDIDETCIMVLKYCGPKGYPGMAEVGNMGLPPKVLKKGVTDMIRISDARMS 480 Query: 481 GTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHD 540 GTAYGTV+LHT+PEAA GGPLA+V+NGD+IE+D+PNR LHL +SDEELARR A W Sbjct: 481 GTAYGTVILHTAPEAAEGGPLALVENGDLIEVDIPNRTLHLHVSDEELARRRAAWVSPVK 540 Query: 541 LPTSGYAFLHQQHVEGADTGADLDFLKGCRGNAV--GKDSH 579 + GY L+ + V AD GADLDFL G RG+ + +DSH Sbjct: 541 PLSGGYGSLYMKTVMQADAGADLDFLVGPRGDRIPMDRDSH 581 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: 1276 Number of extensions: 60 Number of successful extensions: 1 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: 581 Length adjustment: 36 Effective length of query: 543 Effective length of database: 545 Effective search space: 295935 Effective search space used: 295935 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