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 7023120 Shewana3_0358 dihydroxy-acid dehydratase (RefSeq)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__ANA3:7023120 Length = 619 Score = 241 bits (614), Expect = 8e-68 Identities = 181/548 (33%), Positives = 265/548 (48%), Gaps = 68/548 (12%) Query: 43 GRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASEN-TFRPTAMMY 101 G+P+I I N+++ P + HL+++ V + EAGG E + + M+Y Sbjct: 33 GKPIIAIANSFTQFVPGHVHLKDMGSLVADAIEEAGGIAKEFNTIAVDDGIAMGHGGMLY 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 FRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSS----GTCNTMGTASTMASMA 213 + + L MV A + + ++ E A + RS+ G+C+ M TA++M + Sbjct: 152 -KTKLSDKLIKLDLVDAMVAAADSSVSD--EDSAKIERSACPTCGSCSGMFTANSMNCLT 208 Query: 214 EALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVK-----DDLK--PSEIMTKQAFENA 266 EALG++L GN ++ + R+ + GRR++ + K DD P I + +AFENA Sbjct: 209 EALGLSLPGNGSMLATHADRRELFLEAGRRVMALTKRYYEQDDASALPRNIASFKAFENA 268 Query: 267 IRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPS-GKYLMEEFFY 325 + + A+GGS+N V+HLLA A + ++DD DR R VP + + PS KY ME+ Sbjct: 269 MALDIAMGGSSNTVLHLLAAAQEADVAFTMDDIDRMSRQVPHLCKVAPSTAKYHMEDVHR 328 Query: 326 AGGLPVVLKRLGEAGLLHKDALTVSG----------------ETVWDEVKDV-------- 361 AGG+ +L L AGLLH D V+ +T D+VK Sbjct: 329 AGGVMGILGELDRAGLLHTDVPHVAADAGGNLKSVLAKYDVMQTQDDKVKQFFMAGPAGI 388 Query: 362 ---------VNW-------NEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHL 405 W E I E A + GG+ VL GNLA G ++K + Sbjct: 389 PTTKAFSQDCRWPSLDDDRREGCIRSREFAFSQEGGLAVLSGNLADNGCIVKTAGVDESN 448 Query: 406 LVHKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLK 465 L G A V+E DD A I ++ ++V++ GPKG PGM E M P LK Sbjct: 449 LTFIGSARVYESQDDAVAGILGG--EVVAGDVVVIRYEGPKGGPGMQE---MLYPTSYLK 503 Query: 466 KGILD--MVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDI 523 L I+D R SG G + H SPEAA GG +A+++NGD IE+D+P R + L + Sbjct: 504 SRGLGKACALITDGRFSGGTSGLSIGHVSPEAAAGGTIALIENGDRIEIDIPKRSIKLAV 563 Query: 524 SDEELARR 531 SD ELA R Sbjct: 564 SDAELAAR 571 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: 910 Number of extensions: 43 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