Align L-arabonate dehydratase; L-arabinonate dehydratase; EC 4.2.1.25 (characterized)
to candidate WP_012172053.1 AZC_RS18155 dihydroxy-acid dehydratase
Query= SwissProt::Q1JUQ1 (583 letters) >NCBI__GCF_000010525.1:WP_012172053.1 Length = 617 Score = 234 bits (598), Expect = 6e-66 Identities = 180/570 (31%), Positives = 283/570 (49%), Gaps = 66/570 (11%) Query: 16 TNDKNGFMYRSWMKNQGIPDHEFDGRPIIGICNTWSELTPCNAHFRKLAEHVKRGISEAG 75 T+ +N R + G+ D +F G+PII + N++++ P + H + L + V R I +AG Sbjct: 10 THGRNMAGARGLWRATGMKDGDF-GKPIIAVVNSFTQFVPGHVHLKDLGQLVAREIEKAG 68 Query: 76 GFPVEFPVFSNGES-NLRPSAML----TRNLASMDVEEAIRGNPIDAVVLLAGCDKTTPA 130 G EF + + + ML +R + + VE + + DA+V ++ CDK TP Sbjct: 69 GVAKEFNTIAVDDGIAMGHDGMLYSLPSREIIADSVEYMVNAHCADAMVCISNCDKITPG 128 Query: 131 LLMGAASCDVPAIVVSGGPMLNGKLEGKNIGSGTAVWQLHEALKAGEIDVHHFLSAEAGM 190 +LM A ++PA+ VSGGPM GK+ + +G L +A+ A D + M Sbjct: 129 MLMAAMRLNIPAVFVSGGPMEAGKV---LLSTGEKKVDLIDAMIAAADDRVSDEDVKV-M 184 Query: 191 SRSA----GTCNTMGTASTMACMAEALGVALPHNAAIPAVDSRRYVLAHMSGIRIVEMAL 246 RSA G+C+ M TA++M C+ EALG+ALP N ++ A + R L +G +V++A Sbjct: 185 ERSACPTCGSCSGMFTANSMNCLTEALGLALPGNGSVLATHADRERLFVEAGHLVVDLAR 244 Query: 247 E-------GLVLSKILTRAAFENAIRANAAIGGSTNAVIHLKAIAGRIGVPLELEDWMRI 299 G++ I + AFENA+ + ++GGSTN V+HL A A VP + D R+ Sbjct: 245 RYYEQDDAGVLPRTIASFKAFENAMTLDISMGGSTNTVLHLLAAANEGEVPFTMADIDRL 304 Query: 300 GRDTPTIVDLMPS-GRFPMEEFYYAGGLPAVLRRLGEGGLLPNPDALTVNGKSL------ 352 R P + + P+ ME+ + AGG+ +L L GL+ + D TV+ S+ Sbjct: 305 SRKVPVLCKVAPAVANIHMEDVHRAGGIMGILGELDRAGLI-HTDLPTVHAPSMKDALER 363 Query: 353 WDNVR------------------------EAPNYDE-------EVIRPLDRPLIADGGIR 381 WD R ++ +D+ VIR + DGG+ Sbjct: 364 WDVTRTKAESVTTFYRAAPGGVPTQVAFSQSRRWDDLDTDRASGVIRDFEHAYSKDGGLA 423 Query: 382 ILRGNLAPRGAVLKPSAASPELLKHRGRAVVFENLDHYKATINDEALDIDASSVMVLKNC 441 +L GN+A G ++K + +LK G A +FE+ D I I A +++++ Sbjct: 424 VLFGNIAEDGCIVKTAGVDASILKFTGPARIFESQDAAVEAILANG-KIKAGDIVLIRYE 482 Query: 442 GPRGYPGMAEVGNMGLPPKLLR-QGV-KDMVRISDARMSGTAYGTVVLHVAPEAAAGGPL 499 GPRG PGM E M P L+ +G+ K ++D R SG + G + HV+PEAA GG + Sbjct: 483 GPRGGPGMQE---MLYPTSYLKSKGLGKACALVTDGRFSGGSSGLSIGHVSPEAAEGGAI 539 Query: 500 AAVRNGDWIELDCEAGTLHLDITDDELHRR 529 V GD IE+D +HL I+D+E+ RR Sbjct: 540 GLVEEGDTIEIDIPNRRIHLAISDEEMARR 569 Lambda K H 0.319 0.136 0.412 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: 856 Number of extensions: 46 Number of successful extensions: 9 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 3 Number of HSP's successfully gapped: 2 Length of query: 583 Length of database: 617 Length adjustment: 37 Effective length of query: 546 Effective length of database: 580 Effective search space: 316680 Effective search space used: 316680 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 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 24 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