Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate BPHYT_RS21270 BPHYT_RS21270 dihydroxy-acid dehydratase
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__BFirm:BPHYT_RS21270 Length = 586 Score = 375 bits (963), Expect = e-108 Identities = 223/573 (38%), Positives = 317/573 (55%), Gaps = 35/573 (6%) Query: 9 LRSEQWF--NDP---AHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNRH 63 LRS +W+ ND H TA G REE +G+P+I I T S++ C+ H Sbjct: 10 LRSHRWYGVNDLRSFGHRSRTA-------QMGYDREEY-AGKPVIAILNTWSEINACHTH 61 Query: 64 HLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGVV 123 + + VK GI AGG P+E PV ++E ++PT L RN + E L YP DGVV Sbjct: 62 FKQRVEEVKRGIWQAGGFPVELPVQTLSEPFQKPTTMLYRNFLAMEAEETLRSYPADGVV 121 Query: 124 LTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEID 183 L GCDKTTP LM A + DLPAI L GPML G+ G +GSG+ +W + AG I Sbjct: 122 LMGGCDKTTPGLLMGAISMDLPAIFLPAGPMLRGNWNGVTLGSGSDVWKYWAELRAGTIT 181 Query: 184 YEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATGK 243 + + + + S GHC TMGTA +M + AEALG +LPG ASIPA QMA TGK Sbjct: 182 QDDWQGIEGGIARSPGHCMTMGTASTMTSAAEALGFTLPGFASIPAADSRHAQMAAKTGK 241 Query: 244 RICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQRI 303 RI E+V +D++PS ++T + +NA+ AL S+N H+IA+AR G+EL+LD + I Sbjct: 242 RIVEMVWEDLKPSDLITAGSVDNAVTTCLALSGSTNAIVHMIALARRAGIELTLDRYDDI 301 Query: 304 GEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIVSSSL 363 P+L N P G YL E F AGG+ +++ EL + + TV+GRT+GE + + Sbjct: 302 ARRTPVLANVRPTGAYLMEDFFYAGGLRALLAELGEL--IDRSQKTVNGRTLGENLEGAE 359 Query: 364 TSNADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENS---- 418 N DVI D PL +G VL GN D A++K PGA Sbjct: 360 IFNDDVIRRRDKPLLPNSGLAVLRGNIAPDGAVIK---------------PGAAEPHLLV 404 Query: 419 FEARAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQG 478 RA+VF+ D ARIDD LDIDE ++V++ G VG PG E + P L+++G Sbjct: 405 HTGRAVVFKDYNDMAARIDDDTLDIDENSLIVLQHAGPVGAPGMPEWGQLPIPRKLLQKG 464 Query: 479 IDSLPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEE 538 + + + D R SGTS +L+++PE+ +GG AL+++ D +++D+ R +NLL+ D+E Sbjct: 465 VRDMVRISDARMSGTSYGACVLHVAPESFIGGPFALVESGDMIELDVPRRKLNLLVTDDE 524 Query: 539 MARRRLEWTPNIPPSQTPWQELYRQLVGQLSTG 571 +ARR+ W P + +++ V Q + G Sbjct: 525 LARRKAAWVRPAPRFTRGYGAMHQVHVMQANQG 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: 962 Number of extensions: 66 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: 586 Length adjustment: 37 Effective length of query: 557 Effective length of database: 549 Effective search space: 305793 Effective search space used: 305793 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