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 5207771 Shew_0292 dihydroxy-acid dehydratase (RefSeq)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__PV4:5207771 Length = 616 Score = 237 bits (605), Expect = 9e-67 Identities = 187/588 (31%), Positives = 279/588 (47%), Gaps = 70/588 (11%) Query: 43 GRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASEN-TFRPTAMMY 101 G+P++ I N+++ P + HL+++ V + EAGG E + + M+Y Sbjct: 33 GKPIVAIANSFTQFVPGHVHLKDMGSLVAGAIEEAGGIAKEFNTIAVDDGIAMGHGGMLY 92 Query: 102 ----RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGY 157 R L A +VE + D V + CDK TP +LM A ++P + V+GGPM G Sbjct: 93 SLPSRELIADSVEYMVNAHCADALVCISNCDKITPGMLMAALRLNIPVVFVSGGPMEAG- 151 Query: 158 FRGERVGSGTHLWKFSEMVKAGE--MTQAEFLEAEASMSRSSGTCNTMGTASTMASMAEA 215 + + L MV A + ++ + + E S + G+C+ M TA++M + EA Sbjct: 152 -KTKLSDKLIKLDLVDAMVAAADDRVSDEDSEKIERSACPTCGSCSGMFTANSMNCLTEA 210 Query: 216 LGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMV----KDDLK---PSEIMTKQAFENAIR 268 LG++L GN ++ S R+ + GRR++ + +DD + P I + +AFENA+ Sbjct: 211 LGLSLPGNGSLLATHSDRRELFLEAGRRVMALANRYYRDDDESALPRNIASFKAFENAMA 270 Query: 269 TNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPS-GKYLMEEFFYAG 327 + A+GGS+N V+HLLA A +D ++ D DR R VP + + PS KY ME+ AG Sbjct: 271 LDIAMGGSSNTVLHLLAAAQEAKVDFTMADIDRLSRQVPHLCKVAPSTPKYHMEDVHRAG 330 Query: 328 GLPVVLKRLGEAGLLHKDALTVSGETV------WDEVKDV-------------------- 361 G+ +L L AGLLH D V+GE + +D V+ Sbjct: 331 GVMGILGELDRAGLLHTDVSHVAGENLKAVLVQYDLVQTQDEAVQQFYAAGPAGIPTTKA 390 Query: 362 -----------VNWNEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVHKG 410 V+ E I E A + GG+ VL GN+A G ++K + G Sbjct: 391 FSQSCRWPSLDVDRQEGCIRTREFAFSQEGGLAVLSGNIAADGCIVKTAGVDEANHTFVG 450 Query: 411 RAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLK-KGI- 468 A V+E DD A I ++ ++V++ GPKG PGM E M P LK KG+ Sbjct: 451 HARVYESQDDAVAGILGG--EVVAGDVVVIRYEGPKGGPGMQE---MLYPTSYLKSKGLG 505 Query: 469 LDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDEEL 528 I+D R SG G + H SPEAA GG +A+V+ GD IE+D+P R + L +SDE L Sbjct: 506 TSCALITDGRFSGGTSGLSIGHVSPEAAAGGTIALVETGDRIEIDIPARSITLAVSDEVL 565 Query: 529 --------ARRLAEWQP-NHDLPTSGYAFLHQQHVEGADTGADLDFLK 567 AR W+P N + S + AD GA D K Sbjct: 566 ETRRQAMQARGKQAWKPVNRERSVSLALKAYAMLATSADKGAVRDVSK 613 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: 916 Number of extensions: 45 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: 616 Length adjustment: 37 Effective length of query: 542 Effective length of database: 579 Effective search space: 313818 Effective search space used: 313818 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