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 N515DRAFT_0569 N515DRAFT_0569 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__Dyella79:N515DRAFT_0569 Length = 568 Score = 273 bits (697), Expect = 2e-77 Identities = 172/526 (32%), Positives = 280/526 (53%), Gaps = 18/526 (3%) Query: 44 RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASENTFRPT-----A 98 +P++ +++TWS+++PCN +LRELAE+V G+ AGG P+E + ++ T + Sbjct: 31 KPLVAVVHTWSNVSPCNLNLRELAEQVAEGIRAAGGTPIEFNTIAVTDGIAMGTPGMRAS 90 Query: 99 MMYRNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYF 158 ++ R + ++E A+ G +D V+L GCDKT P+ M A D+P++ + GG + +G Sbjct: 91 LISREVITDSIELAVDGHCLDAMVVLCGCDKTIPAAAMAMARLDIPAVALYGGTIAHGTH 150 Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEALGM 218 + + +++ AG++ AE E +G C TA+TMA + LG+ Sbjct: 151 DAHPI-TIQQVFEAVGAHGAGKIDDAELAAVERDACPGAGACGGQFTANTMAMVLTTLGL 209 Query: 219 ALSGNAAIPGVDSRRKVMAQLTGRRIVQMVKDDLKPSEIMTKQAFENAIRTNAAIGGSTN 278 + G IP + A+ G ++ +++ P ++ + + NA R AA GSTN Sbjct: 210 SPMGFNDIPATHPAKAAAARRCGELVMDCLREQRTPRALINRTSLRNAARMVAATAGSTN 269 Query: 279 AVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPSGKYLMEEFFYAGGLPVVLKRLGE 338 AV+HLLAIA G +L+D++ + P I +L+P G+Y E F AGG V + L Sbjct: 270 AVLHLLAIAREAGAPWTLEDFEPASKHTPVIADLLPGGRYTAVEMFGAGGAARVAQELIA 329 Query: 339 AGLLHKDALTVSGETVWDEVKDVVN-WNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLK 397 AG+L D TV+G ++++E +DVILP + L GG +L GNLAP+G +LK Sbjct: 330 AGML-DDVPTVTGRSLFEEAAAAPRAEQQDVILPVGQPLKPRGGYSILYGNLAPEGCILK 388 Query: 398 PSAASPHLLVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNM 457 A +G A VFE + A + I + ++V++N GP G PGM E+ + Sbjct: 389 --LAGKGATHFEGTARVFESEEQAFAAVQQGR--IAKGDVIVIRNEGPAGGPGMREM--L 442 Query: 458 GLPPKVLKKGILDMVR-ISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPN 516 G+ ++ +G+ D V I+D R SG +G +V H +PEA GGP+A++++GD I +D Sbjct: 443 GVTAALIGRGLGDDVALITDGRFSGATHGFMVGHMAPEAVRGGPIALLRDGDRIRIDAGL 502 Query: 517 RRLHLDISDEELARRLAEWQPNHDLPTSGYAFLHQQHVEGADTGAD 562 R + +D +LA R W P T+G + + V A GA+ Sbjct: 503 REI---ATDADLAERRQHWTPPAPKVTTGALAKYARLVGSASDGAN 545 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: 842 Number of extensions: 41 Number of successful extensions: 7 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 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