Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate HSERO_RS05205 HSERO_RS05205 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__HerbieS:HSERO_RS05205 Length = 585 Score = 431 bits (1109), Expect = e-125 Identities = 255/603 (42%), Positives = 347/603 (57%), Gaps = 42/603 (6%) Query: 7 RRLRSEQWFNDPAHADMTALYVERYM-NYGMTREELQSGRPIIGIAQTGSDLTPCNRHHL 65 R LRS WF AD +M N G+ E Q G+P+IGI T S+LTPCN H Sbjct: 10 RTLRSAGWFGT---ADKNGFMYRSWMKNQGIPDHEFQ-GKPVIGICNTWSELTPCNAHFR 65 Query: 66 ELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVVLT 125 ++A+ V+ GI +AGG P+EFPV E + RPTA L RNLA + + E + G P+D VVL Sbjct: 66 KIAEHVRRGIIEAGGFPVEFPVFSNGESNLRPTAMLTRNLASMDVEESIRGNPIDAVVLL 125 Query: 126 TGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEIDYE 185 TGCDKTTPA LM AA+ D+PAIV++GGPML+G H+G IGSGTV+W + AGEI Sbjct: 126 TGCDKTTPALLMGAASCDVPAIVVTGGPMLNGKHQGRDIGSGTVVWQLSEQVKAGEITIH 185 Query: 186 GFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGKRI 245 FM S S G CNTMGTA +M +AE+LG+SLP A+IPA R +A+ +G RI Sbjct: 186 DFMAAEAGMSRSAGTCNTMGTASTMACMAESLGVSLPHNAAIPAVDARRYVLAHLSGMRI 245 Query: 246 CELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQRIGE 305 ++V + + S+I+TR+AFENAI +A+G S+N HL AIA +GV+L L+DW RIG Sbjct: 246 VDMVWEGLTLSKILTRKAFENAIRTNAAIGGSTNAVIHLKAIAGRIGVDLELEDWTRIGR 305 Query: 306 DVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRL-HEDCATVSGRTIGEIVSSSLT 364 P +V+ P+G+YL E F+ AGG+P+V+ L +A L H+D TV+G+T+ + V + Sbjct: 306 GTPTIVDLQPSGRYLMEEFYYAGGLPAVLRRLGEADLLPHKDALTVNGQTMWDNVKDAPI 365 Query: 365 SNADVIHPFDTPLKHRAGFIVLSGNFFD-SAIMKMSVVGEAFRKTYLSEPGAENSFEARA 423 N +V+ P PL G +L GN A++K S K RA Sbjct: 366 YNDEVVRPLAKPLIEDGGICILRGNLAPRGAVLKPSAATPELMK-----------HRGRA 414 Query: 424 IVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDSLP 483 +VFE Y RI+DP LD+D C+LV++ VG GYPG AEV NM P ++ G+ + Sbjct: 415 VVFEDFNHYKERINDPDLDVDASCVLVMKNVGPKGYPGMAEVGNMGLPPKVLATGVKDMV 474 Query: 484 CLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMARRR 543 + D R SGT+ IL+++PEAA GG L ++Q D +++D + L I +EEM +RR Sbjct: 475 RISDARMSGTAYGTVILHVAPEAAAGGPLGIVQDGDFIELDAYAGKLQLDISEEEM-KRR 533 Query: 544 LEWTPNIPPSQTP-----WQELYRQLVGQLSTG-------GCLEPATLHLRVIARSGEPR 591 LE + + P +Q LY V Q G GC A P+ Sbjct: 534 LEARAKVLAERKPEMVGGYQSLYVDRVLQADEGCDFDFLVGCRGAAV-----------PK 582 Query: 592 HSH 594 HSH Sbjct: 583 HSH 585 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: 954 Number of extensions: 65 Number of successful extensions: 3 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: 585 Length adjustment: 37 Effective length of query: 557 Effective length of database: 548 Effective search space: 305236 Effective search space used: 305236 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