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 Ac3H11_955 Dihydroxy-acid dehydratase (EC 4.2.1.9)
Query= SwissProt::B5ZZ34 (579 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_955 Length = 619 Score = 253 bits (645), Expect = 2e-71 Identities = 191/591 (32%), Positives = 288/591 (48%), Gaps = 73/591 (12%) Query: 44 RPVIGILNTWSDMTPCNGHLRELAEKVKAGVWEAGGFPLEVPVFSASEN-TFRPTAMMY- 101 +P+I ++N+++ P + HL++L + V + AGG E + + M+Y Sbjct: 34 KPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEAAGGVAKEFNTIAVDDGIAMGHDGMLYS 93 Query: 102 ---RNLAALAVEEAIRGQPMDGCVLLVGCDKTTPSLLMGAASCDLPSIVVTGGPMLNGYF 158 R++ A +VE + D V + CDK TP +LM A ++P I V+GGPM G Sbjct: 94 LPSRDIIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPVIFVSGGPMEAGKT 153 Query: 159 RGERVGSGTHLWKFSEMVKA------GEMTQAEFLEAEASMSRSSGTCNTMGTASTMASM 212 R + +K ++V A + A+ E E S + G+C+ M TA++M + Sbjct: 154 RLANPVTKVMEFKKLDLVDAMVIAADSNYSDADVAEVERSACPTCGSCSGMFTANSMNCL 213 Query: 213 AEALGMALSGNAAIPGVDSRRKVMAQLTGRRIVQMVK-----DDLK--PSEIMTKQAFEN 265 EALG++L GN + + R+ + + GRRIV + K DD + P + K AFEN Sbjct: 214 TEALGLSLPGNGTVVATHADREQLFKRAGRRIVDLAKQYYEQDDERVLPRSVGFK-AFEN 272 Query: 266 AIRTNAAIGGSTNAVIHLLAIAGRVGIDLSLDDWDRCGRDVPTIVNLMP-SGKYLMEEFF 324 A+ + A+GGSTN ++HLLAIA I ++ D DR R VP + + P + KY +E+ Sbjct: 273 AMTLDIAMGGSTNTILHLLAIASEAEIPFTMADIDRLSRVVPQLCKVAPNTNKYHIEDVH 332 Query: 325 YAGGLPVVLKRLGEAGLLHKDALTVSGETV------WDEVK------------------- 359 AGG+ +L L AG LH D TV T+ WD V+ Sbjct: 333 RAGGIMAILGELDRAGKLHTDVPTVHTATLKDALDQWDIVRTQDEAVRTFYMAGPAGVPT 392 Query: 360 -----DVVNW-------NEDVILPAEKALTSSGGIVVLRGNLAPKGAVLKPSAASPHLLV 407 W E I + A + GG+ VL GN+A G V+K + +LV Sbjct: 393 QVAFSQATRWPSLDLDRAEGCIRSYDHAFSKEGGLAVLTGNIAVDGCVVKSAGVDESILV 452 Query: 408 HKGRAVVFEDIDDYKAKINDDNLDIDENCIMVMKNCGPKGYPGMAEVGNMGLPPKVLK-K 466 +G A V E D+ A I D + + +++++ GPKG PGM E M P +K K Sbjct: 453 FEGTAHVTESQDEAVANILADKVQAGD--VVIVRYEGPKGGPGMQE---MLYPTSYIKSK 507 Query: 467 GI-LDMVRISDARMSGTAYGTVVLHTSPEAAVGGPLAVVKNGDMIELDVPNRRLHLDISD 525 G+ ++D R SG G + H SPEAA GG + +V+NGD I +D+PNR +++ +SD Sbjct: 508 GLGKACALLTDGRFSGGTSGLSIGHCSPEAAAGGAIGLVQNGDRIRIDIPNRTINVLVSD 567 Query: 526 EELARR-----LAEWQPNHDLPTSGYAFL--HQQHVEGADTGA--DLDFLK 567 EELA+R W+P P A L + + V AD GA DL L+ Sbjct: 568 EELAKRREAQNAKGWKPAQPRPRKVSAALKAYAKLVMSADKGAVRDLSLLE 618 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: 48 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