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_004139355.1 Mesci_0132 Dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >NCBI__GCF_000185905.1:YP_004139355.1 Length = 601 Score = 461 bits (1185), Expect = e-134 Identities = 249/545 (45%), Positives = 348/545 (63%), Gaps = 16/545 (2%) Query: 9 RKLRSQEWYGGTSRD---VIYHRGWLKNQGYPHDLFDGRPVIGILNTWSDMTPCNGHLRE 65 +K RSQEW+ +Y +L +L G+P+IGI T SD++PCN H E Sbjct: 9 KKFRSQEWFDNPDNPGMTALYLERYLNYGLTRAELMSGKPLIGIAQTGSDLSPCNRHHIE 68 Query: 66 LAEKVKAGVWEAGGFPLEVPVFSASENTFRPTAMMYRNLAALAVEEAIRGQPMDGCVLLV 125 LA++V+ G+ GG P E P E RPTA + RNLA L++ E + G P+DG VL + Sbjct: 69 LAKRVREGIVSMGGIPFEFPCHPIQETGKRPTAALDRNLAYLSLVEVLYGYPLDGVVLTI 128 Query: 126 GCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYFRGERVGSGTHLWKFSEMVKAGEMTQAE 185 GCDKTTP+LLM AA+ ++P+I ++ GPMLNG+ +G+R GSGT +W+ + + AGE+ E Sbjct: 129 GCDKTTPALLMAAATVNIPAIALSVGPMLNGWHKGKRTGSGTIVWESRQRLSAGEIDYDE 188 Query: 186 FLEAEASMSRSSGTCNTMGTASTMASMAEALGMALSGNAAIPGVDSRRKVMAQLTGRRIV 245 F++ AS + S+G CNTMGTA+TM S+AEALGM L G+AAIP R ++ TG+RIV Sbjct: 189 FMDIVASSAPSTGYCNTMGTATTMNSLAEALGMQLPGSAAIPAPYRERGQISYETGKRIV 248 Query: 246 QMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRD 305 +MV +DLKPS+IMT++AFENAI N+AIGGSTNA IHL AIA +G+ L DDW G + Sbjct: 249 EMVHEDLKPSDIMTREAFENAIVVNSAIGGSTNAPIHLNAIARHLGVKLDNDDWQTVGLN 308 Query: 306 VPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGEAGLL-HKDALTVSGETVWDEVKDVVNW 364 VP +VNL P+G+YL E++ +AGG+P V+ L + LL H A TV+G+++ + + V N Sbjct: 309 VPLLVNLQPTGEYLGEDYHHAGGVPAVIAELMKGDLLPHPGARTVNGKSIGENSEGVANE 368 Query: 365 NEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLL-----------VHKGRAV 413 N DVI K L ++ G + LRGNL A++K S SP +G A+ Sbjct: 369 NPDVIRSVAKPLKANAGFINLRGNLF-DSAIMKTSGISPEFRERYLSNPRDPEAFEGNAM 427 Query: 414 VFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLKKGILDMVR 473 VF+ +DY A+I+D IDE+ I+ M+ GP GYPG AEV NM P ++KKGI + Sbjct: 428 VFDGPEDYHARIDDPAQGIDEHTILFMRGAGPVGYPGGAEVVNMQPPAYLIKKGIHALAC 487 Query: 474 ISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEELARRLA 533 I D R SGT+ +L+ SPEAA+GG LA++K GD + +D+ + ++D+E+ RR A Sbjct: 488 IGDGRQSGTSGSPSILNASPEAAIGGGLALLKTGDRVRIDLRKGTADILVTDDEITRRRA 547 Query: 534 EWQPN 538 E Q N Sbjct: 548 ELQNN 552 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: 992 Number of extensions: 64 Number of successful extensions: 3 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: 601 Length adjustment: 37 Effective length of query: 542 Effective length of database: 564 Effective search space: 305688 Effective search space used: 305688 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