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 AZOBR_RS15015 AZOBR_RS15015 dihydroxy-acid dehydratase
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__azobra:AZOBR_RS15015 Length = 621 Score = 242 bits (617), Expect = 4e-68 Identities = 181/545 (33%), Positives = 268/545 (49%), Gaps = 65/545 (11%) Query: 43 GRPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASEN-TFRPTAMMY 101 G+P+I I N+++ P + HL++L + V + +AGG E + + M+Y Sbjct: 33 GKPIIAIANSFTQFVPGHVHLKDLGQLVAREIEKAGGVAKEFNTIAVDDGIAMGHDGMLY 92 Query: 102 ----RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGY 157 R L A AVE + D V + CDK TP +LM A ++P++ V+GGPM G Sbjct: 93 SLPSRELIADAVEYMVNAHCADALVCISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGK 152 Query: 158 FRGERVGSGTHLWKFSEMVKAGEMTQAEFLEAEASMSRSS----GTCNTMGTASTMASMA 213 L MV A + T ++ E A M R S G+C+ M TA++M + Sbjct: 153 VNWRGKTKAVDL--IDAMVAAADPTVSD--EEAAVMERGSCPTCGSCSGMFTANSMNCLT 208 Query: 214 EALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVK-----DDLK--PSEIMTKQAFENA 266 EALG++L GN I + RK + GR V++ + +D P I T +AFENA Sbjct: 209 EALGLSLPGNGTILATHADRKELFLAAGRMAVELCRRWYQEEDATALPRGIATFEAFENA 268 Query: 267 IRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMPS-GKYLMEEFFY 325 + + A+GGSTN V+HLLA A + ++ D DR R VP + + P+ +E+ Sbjct: 269 MTLDIAMGGSTNTVLHLLAAAQEGQVPFTMADIDRLSRRVPNVCKVAPAVSDVHIEDVHK 328 Query: 326 AGGLPVVLKRLGEAGLLHKDALTVSGETVWD-----EVKDVVN----------------- 363 AGG+ +L L GLL++D TV +T+ D +VK + Sbjct: 329 AGGIFGILGELDRGGLLNRDVATVHAKTLGDALDRWDVKRTQDEGVHTMFKAAPGGIPTT 388 Query: 364 --------WNE-------DVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLVH 408 W E VI + A + GG+ VL GN+A KG ++K + LV Sbjct: 389 IAFSQEKRWPELDLDRDKGVIRSVDSAFSKDGGLAVLFGNIAEKGCIVKTAGVDASNLVF 448 Query: 409 KGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLK-KG 467 G A VFE D I D + + ++V++ GP+G PGM E M P LK KG Sbjct: 449 AGPARVFESQDAAVEAILGDTVKAGD--VVVIRYEGPRGGPGMQE---MLYPTSYLKSKG 503 Query: 468 I-LDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISDE 526 + ++D R SG G + H SPEAA GG + +V++GD IE+D+PNR+++L +SDE Sbjct: 504 LGKACALVTDGRFSGGTSGLSIGHASPEAAQGGAIGLVQDGDRIEIDIPNRKINLALSDE 563 Query: 527 ELARR 531 EL RR Sbjct: 564 ELQRR 568 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: 928 Number of extensions: 46 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: 621 Length adjustment: 37 Effective length of query: 542 Effective length of database: 584 Effective search space: 316528 Effective search space used: 316528 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