Align L-arabonate dehydratase (EC 4.2.1.25) (characterized)
to candidate WP_011339020.1 RSPH17029_RS19210 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_24585 (578 letters) >NCBI__GCF_000015985.1:WP_011339020.1 Length = 612 Score = 255 bits (652), Expect = 3e-72 Identities = 199/615 (32%), Positives = 305/615 (49%), Gaps = 72/615 (11%) Query: 6 PSLRSAQWFGTADKNGFMYRSWMKNQGIADHQFHGKPIIGICNTWSELTPCNAHFRQIAE 65 P+ RS T +N R + G+ D F GKPII I N++++ P + H + + + Sbjct: 2 PAFRSRT--STHGRNMAGARGLWRATGVKDSDF-GKPIIAIVNSFTQFVPGHVHLKDLGQ 58 Query: 66 HVKRGVIEAGGFPVEFPVFSNGES-NLRPTAML----TRNLASMDVEEAIRGNPIDGVVL 120 V R V AGG EF + + + ML +R L + VE + + D +V Sbjct: 59 LVAREVEAAGGIAKEFNTIAVDDGIAMGHDGMLYSLPSRELIADSVEYMVNAHCADAMVC 118 Query: 121 LTGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHKGQDIGSG-TVVWQLSEQVKAGT-- 177 ++ CDK TP +LM A ++PA+ V+GGPM GK +G G TV L + + A Sbjct: 119 ISNCDKITPGMLMAAMRLNIPAVFVSGGPMEAGK---VTLGDGRTVKMDLIDAMVAAADE 175 Query: 178 -ITIDDFLAAEGGMSRSAGTCNTMGTASTMACMAEALGTSLPHNAAIPAVDARRYVLAHM 236 ++ DD E + G+C+ M TA++M C+ EALG SLP N + A A R L Sbjct: 176 KVSDDDLTRIEQAACPTCGSCSGMFTANSMNCLTEALGLSLPGNGSTLATHAYRKELFLE 235 Query: 237 SGMRAVEMVR-------EDLKLSKILTKEAFENAIRVNAAIGGSTNAVIHLKAIAGRIGV 289 +G RAVE+ R E + I TKEAFENA+ ++ A+GGSTN V+H+ A A GV Sbjct: 236 AGRRAVELCRRYYEQEDEGVLPRAIATKEAFENAMALDIAMGGSTNTVLHILAAAQEGGV 295 Query: 290 QLDLDDWTRIGRGMPTIVDLQPSGRFL-MEEFYYAGGLPAVLRRLGEANLIPNPNALTVN 348 +DD + R +P + + P+ + +E+ + AGG+ ++L L L+ + + TV+ Sbjct: 296 DFTMDDIDALSRRVPCLCKVAPNKADVHIEDVHRAGGIMSILGELDRGGLL-HRDTRTVH 354 Query: 349 GKSLGE-------NTKDAP-----------------IYGQDE------------VIRTLD 372 +LG +AP + Q VIR++ Sbjct: 355 APTLGAAIDQWDIGRSNAPEARELFLAAPGGVPTQVAFSQSSTWDTLDTDRETGVIRSVA 414 Query: 373 NPIRADGGICVLRGNLAPLGAVLKPSAATAELMQHRGRAVVFENFDEYKARINDPELDVD 432 P DGG+ VL+GNLAP G ++K + ++ G A VFE+ D I + V Sbjct: 415 TPFSKDGGLAVLKGNLAPDGCIVKTAGVDESILVFAGPAKVFESQDAAVYGILNG--GVQ 472 Query: 433 ANSILVMKNCGPKGYPGMAEVGNMGLPAKLLAQGV-TDMVRISDARMSGTAYGTVVLHVA 491 A ++V++ GPKG PGM E+ + + L ++G+ I+D R SG G + H + Sbjct: 473 AGDVVVIRYEGPKGGPGMQEM--LYPTSYLKSKGLGKACALITDGRFSGGTSGLSIGHAS 530 Query: 492 PEAAAGGPLAAVKEGDWIELDCASGRLHLDIPDAELAARLADL-------APPQQLLVGG 544 PEAA+GGP+ V+EGD IE+D + + L +P+AELAAR A+ A P++ V Sbjct: 531 PEAASGGPIGLVREGDRIEIDIPNRTITLAVPEAELAARRAEQDAKGWKPAGPRKRKVSQ 590 Query: 545 YRQLYIDHVLQADQG 559 ++Y AD+G Sbjct: 591 ALKVYAQFASSADKG 605 Lambda K H 0.319 0.136 0.409 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: 821 Number of extensions: 36 Number of successful extensions: 7 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: 578 Length of database: 612 Length adjustment: 37 Effective length of query: 541 Effective length of database: 575 Effective search space: 311075 Effective search space used: 311075 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 Apr 10 2024. 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