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_068175562.1 HTA01S_RS22650 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_001592305.1:WP_068175562.1 Length = 568 Score = 303 bits (777), Expect = 9e-87 Identities = 183/530 (34%), Positives = 300/530 (56%), Gaps = 16/530 (3%) Query: 44 RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPT-----A 98 +P++G+ N S +TPCN L++LA+ AG+ EAGG + S+ T + Sbjct: 44 KPMVGVANGHSTITPCNSGLQKLADAAIAGIEEAGGNAQVFGTPTISDGMAMGTEGMKYS 103 Query: 99 MMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYF 158 ++ R + + VE ++GQ MDG V++ GCDK P LMG ++P+I V GG +L G + Sbjct: 104 LVSREVISDCVETCVQGQWMDGVVVIGGCDKNMPGGLMGMLRANVPAIYVYGGTILPGRY 163 Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGM 218 + + + +++ AG+++ + E E +G+C M TA+TM+S EALG+ Sbjct: 164 KDQDLNI-VSVFEAVGQNAAGKLSDHDLHEIEQRAIPGTGSCGGMYTANTMSSAFEALGI 222 Query: 219 ALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTN 278 +L ++ + + A+ + + +++ ++ D+KP +I+T+++ ENA+ A GGSTN Sbjct: 223 SLPYSSTMANPHDEKTNSARESAKVLIEAIRKDIKPRDIVTRKSIENAVAVIMATGGSTN 282 Query: 279 AVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGE 338 AV+H LAIA G++ ++DD++R + +P + +L PSGKYL + AGG+P V+K L Sbjct: 283 AVLHFLAIAHAAGVEWTIDDFERVRQKIPVLCDLKPSGKYLAVDLHRAGGIPQVMKMLLH 342 Query: 339 AGLLHKDALTVSGETVWDEVKDVVN---WNEDVILPAEKALTSSGGIVVLRGNLAPKGAV 395 AGLLH D LT++G+T+ + +KDV + ++DVI P ++ L G + +L+GNL+P+G V Sbjct: 343 AGLLHADCLTITGQTIAEVLKDVPDAPRADQDVIRPFDRPLYEHGHLAILKGNLSPEGCV 402 Query: 396 LKPSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVG 455 K + ++ G A VF+D I D ++ + +MV++ GPKG PGM E+ Sbjct: 403 AKITGLKNPVMT--GPARVFDDEQSALQAILDGHIVAGD--VMVLRYLGPKGGPGMPEM- 457 Query: 456 NMGLPPKVLKKGILDMV-RISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDV 514 + ++ G+ + V I+D R SG +G VV H +PEAAVGG + +V+ GD I +D Sbjct: 458 -LAPTGALIGAGLGESVGLITDGRFSGGTWGMVVGHVAPEAAVGGTIGLVQEGDRITIDA 516 Query: 515 PNRRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQQHVEGADTGADLD 564 L L + D E+A+R A W T G + A GA LD Sbjct: 517 HRLLLELHVPDAEIAKRRAAWMAPAPRYTRGVQAKFAFNASSASQGAVLD 566 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: 953 Number of extensions: 67 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: 568 Length adjustment: 36 Effective length of query: 543 Effective length of database: 532 Effective search space: 288876 Effective search space used: 288876 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