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_078427497.1 BK574_RS03330 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_002019605.1:WP_078427497.1 Length = 556 Score = 319 bits (818), Expect = 2e-91 Identities = 191/519 (36%), Positives = 294/519 (56%), Gaps = 17/519 (3%) Query: 27 HRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPV 86 +R ++ G + F+ +P +GI +TWS++TPCN H+ ELA K K G +AGG P Sbjct: 21 NRAMIRAMGIKDEDFN-KPFVGIASTWSEVTPCNMHIDELARKAKKGALDAGGTPFIFNT 79 Query: 87 FSASENTFRPTAMMY-----RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASC 141 + S+ T M R + A ++E + Q DG V + GCDK P ++ Sbjct: 80 ITVSDGISMGTEGMRFSLPSREVIADSIETVVGAQNYDGVVAIGGCDKNMPGCMIAIGRL 139 Query: 142 DLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCN 201 +LP++ V GG + G G+ + ++ G++ + E + E +G+C Sbjct: 140 NLPAVFVYGGTIRPGNVDGKDIDI-VSAFEAVGKYNNGDIDRDELHKIECHACPGAGSCG 198 Query: 202 TMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQ 261 M TA+TMAS EA+GM+L G+++ P + G+ ++ ++ + P +IMTK+ Sbjct: 199 GMYTANTMASAIEAMGMSLPGSSSNPAETEEKLEDCIKAGKAVMNLLNKGITPKDIMTKK 258 Query: 262 AFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLME 321 AFENAI A+GGSTNAV+HLLA+A V +DL+LDD++R + VP I +L PSG+Y+ME Sbjct: 259 AFENAITVVMALGGSTNAVLHLLALAHTVDVDLNLDDFERIRKKVPHIADLKPSGRYVME 318 Query: 322 EFFYAGGLPVVLKRLGEAGLLHKDALTVSGETVWDEVKDVVNWNE-DVILPAEKALTSSG 380 GG+P V+K L + GLLH D LTV+ T+ + ++ E I+ E +G Sbjct: 319 NLSEIGGVPAVMKLLLDKGLLHGDCLTVTSNTIEQNLSEIQPLKEGQEIISFENPKRETG 378 Query: 381 GIVVLRGNLAPKGAVLKPSAASPHLLVHKGRAVVFE-DIDDYKAKINDDNLDIDENCIMV 439 +V+L+GNLAP GA+ K S + G A VF+ + D A +N+ +++ ++V Sbjct: 379 PLVILKGNLAPDGALAKMSGLKIKKIT--GPARVFDSETDATNAVLNN---EVNPGDVIV 433 Query: 440 MKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMV-RISDARMSGTAYGTVVLHTSPEAAVG 498 ++ GPKG PGMAE+ + + V+ KG + V I+D R SG +G VV H SPEA VG Sbjct: 434 IRYVGPKGGPGMAEM--LSITAIVVGKGFGEKVGLITDGRFSGGTHGLVVGHISPEAQVG 491 Query: 499 GPLAVVKNGDMIELDVPNRRLHLDISDEELARRLAEWQP 537 GP+A++K GDMI +D + L +D+S E+L RL +W P Sbjct: 492 GPIALIKEGDMITIDSELQELAVDVSPEDLNERLKDWSP 530 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: 902 Number of extensions: 48 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: 556 Length adjustment: 36 Effective length of query: 543 Effective length of database: 520 Effective search space: 282360 Effective search space used: 282360 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 Apr 09 2024. 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