Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate BPHYT_RS04815 BPHYT_RS04815 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__BFirm:BPHYT_RS04815 Length = 557 Score = 249 bits (636), Expect = 2e-70 Identities = 173/529 (32%), Positives = 274/529 (51%), Gaps = 32/529 (6%) Query: 30 RYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHP 89 R M Y + E+ +P+IGIA S +TPCN LA A I+ A P F Sbjct: 20 RSMYYALGYEKADFDKPMIGIANGHSTITPCNAGLQRLADAAVAAIKGADANPQIFGTPT 79 Query: 90 IAEQSRRPTAALDRNLAYLGLVE-----ILHGYPLDGVVLTTGCDKTTPACLMAAATTDL 144 I++ T + +L ++ + G +DGVV+ GCDK P ++ T++ Sbjct: 80 ISDGMSMGTEGMKYSLVSREVISDCIETCVQGQWMDGVVVIGGCDKNMPGGMIGMLRTNV 139 Query: 145 PAIVLSGGPMLDGHHKGELIGSGTVL--WHARNLMAAGEIDYEGFMEMTTAASPSVGHCN 202 P+I + GG + G+ KG + T++ + A AG + E F + A PS G C Sbjct: 140 PSIYVYGGTIRPGNWKGTDL---TIVSSFEAVGEFTAGRMSQEDFDGIEQNACPSTGSCG 196 Query: 203 TMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICELVLQDIRPSQIMTRQ 262 M TA +M++ EALGMSL +++ P +E+ A + + + E V +D++P I+T++ Sbjct: 197 GMYTANTMSSSFEALGMSLLYSSTMANPDQEKVDSAAESARVLVESVKKDLKPRDIVTKK 256 Query: 263 AFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGEDVPLLVNCMPAGKYLGE 322 + ENA+AV A G S+N H +AIA VE S+DD++R+ + VP++ N P+G+++ Sbjct: 257 SIENAVAVIMATGGSTNAVLHFLAIAHAAEVEWSIDDFERMRKKVPVICNLKPSGQFVAT 316 Query: 323 GFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGE---IVSSSLTSNADVIHPFDTPLKH 379 H+AGG+P VM L AG LH DC T++GRTI E V ++ VI P D L Sbjct: 317 DLHKAGGIPQVMKILLDAGLLHGDCITITGRTIAEELKDVPGKPRADQQVIFPIDQALYK 376 Query: 380 RAGFIVLSGNFFDSAIMKMSVVGEAFRKTYLSEPGAENSFEARAIVFEGPED-YHARIDD 438 +L GN ++V G + T L P A VF+ + A + D Sbjct: 377 EGHLAILKGN--------LAVDGAVAKITGLKNP----VITGPARVFDDEQSALEAILAD 424 Query: 439 PALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASP 497 + D ++V+R +G G PG E+ +AP +A+I +G+ +S+ + DGR SG + Sbjct: 425 KIVAGD---VVVLRYLGPKGGPGMPEM--LAPTSAIIGKGLGESVGLITDGRFSGGTWGM 479 Query: 498 SILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRRLEW 546 + +++PEA VGG +A +Q D + +D + + L ID+ E+ RRR W Sbjct: 480 VVGHVAPEAFVGGTIAFVQEGDSITIDAHKLLLQLNIDNAELERRRAAW 528 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: 806 Number of extensions: 42 Number of successful extensions: 4 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: 557 Length adjustment: 36 Effective length of query: 558 Effective length of database: 521 Effective search space: 290718 Effective search space used: 290718 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