Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate GFF2902 PGA1_c29490 dihydroxy-acid dehydratase LivD
Query= reanno::pseudo6_N2E2:Pf6N2E2_1668 (594 letters) >FitnessBrowser__Phaeo:GFF2902 Length = 614 Score = 211 bits (536), Expect = 9e-59 Identities = 171/562 (30%), Positives = 263/562 (46%), Gaps = 70/562 (12%) Query: 35 GMTREELQSGRPIIGIAQTGSDLTPCNRHHLELAQRVKAGIRDAGGIPMEFPVHPIAEQS 94 GMT ++ G+PII I + + P + H +L Q V + AGG+ EF + + Sbjct: 26 GMTDDDF--GKPIIAIVNSFTQFVPGHVHLKDLGQMVAREVEAAGGVAKEFNTIAVDDGI 83 Query: 95 RRPTAAL-----DRNLAYLGLVEILHGYPLDGVVLTTGCDKTTPACLMAAATTDLPAIVL 149 + R + + +++ + D +V + CDK TP LMAA ++PAI + Sbjct: 84 AMGHDGMLYSLPSREVIADSVEYMVNAHCADAMVCISNCDKITPGMLMAAMRLNIPAIFV 143 Query: 150 SGGPMLDGHHK-GELIGSGTVLWHARNLMAAGEIDYEGFMEMTTAASPSVGHCNTMGTAL 208 SGGPM G +L L A A+ + E + A P+ G C+ M TA Sbjct: 144 SGGPMEAGKIDIADLDMKKIDLVDAMVAAASDTMTDEQVQHIEENACPTCGSCSGMFTAN 203 Query: 209 SMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRICDLVR-------QDIRPSQIMTR 261 SMN LAEALG++LPG S A + +R + G++I D+ + + + P +I T Sbjct: 204 SMNCLAEALGLALPGNGSTLATHADRKHLFLEAGRKIVDITKRHYVGEEKGLLPREIATF 263 Query: 262 QAFENAIAVASALGASSNCPPHLIAIARHMGVELSLEDWQRIGEDVPLLVNCMPAGKYLG 321 AFENA+++ A+G S+N HL+AIA V+ ++ D R+ VP L P + + Sbjct: 264 DAFENAMSLDIAMGGSTNTVLHLLAIANEGKVDFTMTDMDRLSRKVPCLCKVAPNIENVH 323 Query: 322 -EGFHRAGGVPSVMHELQKAGRLHEDCATVSGKTIGEIVSN---SLTSNTD--------- 368 E HRAGG+ S++ EL +AG LH +C+TV T+GE ++ + +N D Sbjct: 324 MEDVHRAGGIFSILGELSRAGLLHNECSTVHSSTMGEAIAKWDIKVANNPDAEALFKAAP 383 Query: 369 -------------------------VIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVG 402 VI D G VL GN D I+K + V Sbjct: 384 GGVRTTEAFSQSNRYKELDTDREGGVIRSKDHAFSQDGGLAVLFGNIARDGCIVKTAGVD 443 Query: 403 EAFRKTYLSEPGAENSFEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGS 462 + K F A V E + A D + E ++VIR G G PG Sbjct: 444 DNILK-----------FTGSAYVCESQD--QAVNDILTSKVKEGDVVVIRYEGPRGGPGM 490 Query: 463 AEVVNMAPPAALIKQGI-DSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLKTNDRL 521 E+ + P + L +G+ + L DGR SG ++ SI ++SPEAA GG + L++ D + Sbjct: 491 QEM--LYPTSYLKSKGLGKACALLTDGRFSGGTSGLSIGHVSPEAAEGGTIGLVQQGDTI 548 Query: 522 KVDLNTRTVNLLIDDAEMAQRR 543 ++D+ RT++L + D E+A RR Sbjct: 549 EIDIPNRTIHLAVSDEELAARR 570 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: 830 Number of extensions: 37 Number of successful extensions: 6 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: 594 Length of database: 614 Length adjustment: 37 Effective length of query: 557 Effective length of database: 577 Effective search space: 321389 Effective search space used: 321389 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