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 WP_013092366.1 BC1002_RS22880 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_000092885.1:WP_013092366.1 Length = 578 Score = 574 bits (1480), Expect = e-168 Identities = 293/564 (51%), Positives = 381/564 (67%), Gaps = 3/564 (0%) Query: 4 KAEWPRKLRSQEWYGGTSRDVIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHL 63 K + +LRS WYG HR GY + + G+PVI ILNTWS++ PC+ H Sbjct: 3 KRKTAEELRSHRWYGANDLRSFGHRSRTAQMGYNREEYAGKPVIAILNTWSEINPCHTHF 62 Query: 64 RELAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVL 123 ++ E+VK G+W+AGGFP+E+PV + SE +PT M+YRN A+ EE +R P DG VL Sbjct: 63 KQRVEEVKRGIWQAGGFPIELPVQTLSEPFQKPTTMLYRNFLAMEAEEMLRSYPADGVVL 122 Query: 124 LVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQ 183 + GCDKTTP+LLMGA S DLP+I + GPML G + G +GSG+ W++ ++AG +T Sbjct: 123 MGGCDKTTPALLMGAISMDLPAIFLPAGPMLRGNWNGVTLGSGSDSWRYWAELRAGTLTP 182 Query: 184 AEFLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRR 243 ++ E S++RS G C TMGTASTM S AEALG L G A+IP DSR MA TG R Sbjct: 183 EDWQGVEGSIARSPGHCMTMGTASTMTSAAEALGFTLPGFASIPAADSRHAQMAAKTGMR 242 Query: 244 IVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCG 303 IV+MV +DLKPS+++T + +NA+ T A+ GSTN+V+H++A+A R GI L+LD +D+ Sbjct: 243 IVEMVWEDLKPSDLLTAASVDNAVTTCVALSGSTNSVVHMIALARRAGIALTLDRFDQIA 302 Query: 304 RDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVN 363 R P + N+ P+G YLME+FFYAGGL VL LGE L+ TV+G T+ + + Sbjct: 303 RRTPVLANIRPTGAYLMEDFFYAGGLRGVLAELGE--LIDGSQKTVNGRTLGENLAGAQI 360 Query: 364 WNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFEDIDDYKA 423 +N+DVI L + VLRGNLAP GAV+KP AA PHLLVH GRAVVF D D A Sbjct: 361 FNDDVIRRRTNPLLRDSSLAVLRGNLAPDGAVIKPGAAEPHLLVHTGRAVVFSDYTDMAA 420 Query: 424 KINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVRISDARMSGTA 483 +I+DD LDIDE+C++V+++ GP G GM E G + +P K+L+KG+ DMVRISDARMSGT+ Sbjct: 421 RIDDDALDIDESCVLVLQHAGPVG-AGMPEWGQLPIPRKLLQKGVRDMVRISDARMSGTS 479 Query: 484 YGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQPNHDLPT 543 YG VLH +PEA VGGPLA+V++GD+IELDVP RRL+L ISDEE ARR A W Sbjct: 480 YGACVLHVAPEAFVGGPLALVRSGDLIELDVPRRRLNLLISDEEFARRKAAWVKPAARFE 539 Query: 544 SGYAFLHQQHVEGADTGADLDFLK 567 GY LHQ HV AD G D DFL+ Sbjct: 540 RGYGALHQAHVMQADQGCDFDFLQ 563 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: 982 Number of extensions: 45 Number of successful extensions: 5 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: 578 Length adjustment: 36 Effective length of query: 543 Effective length of database: 542 Effective search space: 294306 Effective search space used: 294306 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