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 Ac3H11_954 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_954 Length = 567 Score = 306 bits (783), Expect = 2e-87 Identities = 189/530 (35%), Positives = 296/530 (55%), Gaps = 16/530 (3%) Query: 44 RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPT-----A 98 +P++G+ N S +TPCN L++LA+ AG+ EAGG + S+ T + Sbjct: 43 KPMVGVANGHSTITPCNSGLQKLADAAIAGIEEAGGNAQVFGTPTISDGMAMGTEGMKYS 102 Query: 99 MMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYF 158 ++ R + + +E + GQ MDG +++ GCDK P LMG ++P+I V GG +L G++ Sbjct: 103 LVSREVISDCIETCVGGQWMDGVLVVGGCDKNMPGGLMGMLRANVPAIYVYGGTILPGHY 162 Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGM 218 +G+ + + E AG+++ + E E +G+C M TA+TM+S EALG+ Sbjct: 163 QGKDLNIVSVFEAVGENA-AGKLSDFDLKEIEKRAIPGTGSCGGMYTANTMSSAFEALGI 221 Query: 219 ALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTN 278 +L ++ + + A+ + + +++ +K D+KP +I+TK++ ENA+ A GGSTN Sbjct: 222 SLPYSSTMANPHDEKMNSAKESAKVLIEAIKKDIKPRDIVTKKSIENAVAVIMATGGSTN 281 Query: 279 AVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGE 338 AV+H LAIA G++ S+DD++R P + +L PSGKYL + AGG+P V+K L Sbjct: 282 AVLHFLAIAHAAGVEWSIDDFERVRVKTPVLCDLKPSGKYLAVDLHRAGGIPQVMKVLLN 341 Query: 339 AGLLHKDALTVSGETVWDEVKDVVNW---NEDVILPAEKALTSSGGIVVLRGNLAPKGAV 395 AGLLH D LT+ G+TV + +KDV + ++DVI P + + G + +L+GNL+P+GAV Sbjct: 342 AGLLHGDCLTIEGKTVAEVLKDVPDQPRADQDVIRPINNPMYAQGHLAILKGNLSPEGAV 401 Query: 396 LKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVG 455 K + ++ G A VFED I + + +MV++ GPKG PGM E+ Sbjct: 402 AKITGLKNPVIT--GPARVFEDEQSALEAILAGKIKAGD--VMVLRYLGPKGGPGMPEM- 456 Query: 456 NMGLPPKVLKKGILDMV-RISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDV 514 + ++ G+ + V I+D R SG +G VV H +PEAA GG +A V GD I +D Sbjct: 457 -LAPTGALIGAGLGESVGLITDGRFSGGTWGMVVGHVAPEAAAGGTIAFVHEGDSITIDA 515 Query: 515 PNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQQHVEGADTGADLD 564 L L++S+EE+ARR A W T G + A GA LD Sbjct: 516 RQLLLELNVSEEEIARRRAAWTAPAPRYTRGVQAKFAFNASSASKGAVLD 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: 938 Number of extensions: 62 Number of successful extensions: 6 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: 567 Length adjustment: 36 Effective length of query: 543 Effective length of database: 531 Effective search space: 288333 Effective search space used: 288333 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