Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate RR42_RS31070 RR42_RS31070 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__Cup4G11:RR42_RS31070 Length = 576 Score = 347 bits (889), Expect = 1e-99 Identities = 206/529 (38%), Positives = 294/529 (55%), Gaps = 15/529 (2%) Query: 45 RPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRN 104 RP+IGI T S PC+ + +L + VK G+ AGG+P++FP + E PT+ RN Sbjct: 42 RPVIGIVNTNSSYNPCHGNAPQLVEAVKRGVMLAGGLPVDFPTISVHESFSAPTSMYLRN 101 Query: 105 LAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELI 164 L + E++ P+D VVL GCDKT PA LM AA+ +PAI L G ML G H+GE + Sbjct: 102 LMSMDTEEMIRAQPMDAVVLIGGCDKTVPAQLMGAASAGVPAIQLVTGSMLTGSHRGERV 161 Query: 165 GSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGC 224 G+ T A EID ++ SVG C+ MGTA +M L EALGM + G Sbjct: 162 GACTDCRRYWGRYRAEEIDAPEIADVNNQLVASVGTCSVMGTASTMACLTEALGMMVAGG 221 Query: 225 ASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHL 284 AS PA +R ++A TG + + P +I+T +A ENAI V A+G S+N HL Sbjct: 222 ASAPAVTADRVRVAERTGTTAVAMARSGLTPERILTGRAIENAIRVLLAIGGSTNGIVHL 281 Query: 285 IAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLH 344 AIA +G+ + L R+ + P+LV+ P+G++ E FH AGG+P+++ EL+ LH Sbjct: 282 TAIAGRLGIGIDLAGLDRMSRETPVLVDLKPSGQHYMEDFHAAGGMPALLRELRPL--LH 339 Query: 345 EDCATVSGRTIGEIVSSSLTSNA-DVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVG 402 D TVSGRT+GE + ++ A +VI PFD P+ G VL GN AI+K S Sbjct: 340 LDTLTVSGRTLGEELDAAPAPFAQEVIRPFDAPIYPVGGLAVLRGNLAPGGAIIKQSAAD 399 Query: 403 EAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGS 462 + E RA+VFE ED RIDD ALD+ ILV++ +G G PG Sbjct: 400 PVLME-----------HEGRAVVFEDAEDMALRIDDDALDVKADDILVLKRIGPTGAPGM 448 Query: 463 AEVVNMAPPAALIKQGIDSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLK 522 E M P L + G+ + + DGR SGT+A +L+++PEAA+GG LA ++ DR++ Sbjct: 449 PEAGYMPIPRKLARAGVKDMVRISDGRMSGTAAGTIVLHVTPEAAIGGPLAHVRNGDRIR 508 Query: 523 VDLNTRTVNLLIDDEEMARRRLEWTPNIPPSQTPWQELYRQLVGQLSTG 571 + + R ++LLIDD E+ARR E P ++ +++L+ V Q G Sbjct: 509 LSVARREISLLIDDAELARRAAEHEVVRPAAERGYRKLFLATVTQADQG 557 Lambda K H 0.319 0.135 0.407 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: 917 Number of extensions: 57 Number of successful extensions: 5 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 1 Number of HSP's successfully gapped: 1 Length of query: 594 Length of database: 576 Length adjustment: 37 Effective length of query: 557 Effective length of database: 539 Effective search space: 300223 Effective search space used: 300223 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 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