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 Synpcc7942_0626 Synpcc7942_0626 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__SynE:Synpcc7942_0626 Length = 619 Score = 258 bits (659), Expect = 5e-73 Identities = 186/554 (33%), Positives = 280/554 (50%), Gaps = 66/554 (11%) Query: 44 RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASEN-TFRPTAMMY- 101 +P+I + N+++ P + HL++L + V + AGG E + + M+Y Sbjct: 34 KPIIAVANSFTQFVPGHVHLKDLGQLVAREIERAGGVAKEFNTIAVDDGIAMGHGGMLYS 93 Query: 102 ---RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYF 158 R+L A +VE + D V + CDK TP +LM A ++P++ V+GGPM G Sbjct: 94 LPSRDLIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPAVFVSGGPMEAG-- 151 Query: 159 RGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSS----GTCNTMGTASTMASMAE 214 + G HL MV A + +++ E A++ RS+ G+C+ M TA++M + E Sbjct: 152 KVILNGEERHLDLVDAMVVAADDRESD--EDVATIERSACPTCGSCSGMFTANSMNCLTE 209 Query: 215 ALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVK-------DDLKPSEIMTKQAFENAI 267 ALG++L GN ++ RK + GR V++ K + + P I + +AFENAI Sbjct: 210 ALGLSLPGNGSLLATHGDRKELFLEAGRLAVKLAKQYYEQDDESVLPRSIASFKAFENAI 269 Query: 268 RTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPS-GKYLMEEFFYA 326 + A+GGSTN V+HLLA A G+D ++ D DR R +P + + PS KY ME+ A Sbjct: 270 CLDIAMGGSTNTVLHLLAAAHEAGVDFTMKDIDRLSRKIPNLCKVAPSTQKYHMEDVHRA 329 Query: 327 GGLPVVLKRLGEAGLLHKDALTV--------------SGETVWDEVKD------------ 360 GG+ +L L AGLLH++ TV + ET +E K Sbjct: 330 GGVIAILGELDRAGLLHREVPTVHSPSLGAALDQWDINRETATEEAKSRYLAAPGGVPTQ 389 Query: 361 ------------VVNWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVH 408 ++ I E A + GG+ VL GNLA +G ++K + ++LV Sbjct: 390 EAFSQSKRWTALDLDRENGCIRDIEHAYSQDGGLAVLYGNLAEQGCIVKTAGVDENILVF 449 Query: 409 KGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLK-KG 467 G AVV E D+ I N + E +++++ GP+G PGM E M P LK KG Sbjct: 450 SGPAVVCESQDEAVNWIL--NGRVKEGDVVLIRYEGPRGGPGMQE---MLYPTSYLKSKG 504 Query: 468 I-LDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDE 526 + I+D R SG G + H SPEAA GG +A+V+ GD IE+D+PNRR+HL +S+E Sbjct: 505 LGKACALITDGRFSGGTSGLSIGHVSPEAAEGGLIALVEQGDRIEIDIPNRRIHLAVSEE 564 Query: 527 ELARRLAEWQPNHD 540 ELA R A + D Sbjct: 565 ELAHRRAAMEARGD 578 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: 957 Number of extensions: 52 Number of successful extensions: 8 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 2 Length of query: 579 Length of database: 619 Length adjustment: 37 Effective length of query: 542 Effective length of database: 582 Effective search space: 315444 Effective search space used: 315444 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