Align Xylonate dehydratase (EC 4.2.1.82) (characterized)
to candidate H281DRAFT_03422 H281DRAFT_03422 dihydroxyacid dehydratase (EC 4.2.1.9)
Query= reanno::pseudo5_N2C3_1:AO356_28760 (594 letters) >FitnessBrowser__Burk376:H281DRAFT_03422 Length = 592 Score = 345 bits (885), Expect = 3e-99 Identities = 207/570 (36%), Positives = 314/570 (55%), Gaps = 27/570 (4%) Query: 8 RLRSEQWF--NDP---AHADMTALYVERYMNYGMTREELQSGRPIIGIAQTGSDLTPCNR 62 +LRS +W+ ND H TA +Y G+P+I + T S++ C+ Sbjct: 9 QLRSYRWYGVNDLRSFGHRSRTAQMGYHASDY--------MGKPVIAVVNTWSEINSCHT 60 Query: 63 HHLELAQRVKAGIRDAGGIPMEFPVHPIAEQSRRPTAALDRNLAYLGLVEILHGYPLDGV 122 H + + VK GI AGG P+E PV +AE ++PT L RN + EIL YP DG Sbjct: 61 HFKQRVEEVKRGIWQAGGFPVEMPVMTLAEPFQKPTTMLYRNFLAMETEEILKSYPFDGC 120 Query: 123 VLTTGCDKTTPACLMAAATTDLPAIVLSGGPMLDGHHKGELIGSGTVLWHARNLMAAGEI 182 VL GCDKTTP LM A + +LP+I L GPML G+ G +GSG+ W + AG+I Sbjct: 121 VLMGGCDKTTPGLLMGAISMNLPSIFLPAGPMLRGNWNGRTLGSGSDTWKYWAELRAGKI 180 Query: 183 DYEGFMEMTTAASPSVGHCNTMGTALSMNALAEALGMSLPGCASIPAPYRERGQMAYATG 242 + + + + + S GHC TMGTA +M + AEALG++LPG +SIPA Q A TG Sbjct: 181 TEDEWKGIESGIARSPGHCMTMGTASTMTSAAEALGLTLPGFSSIPAVDSRHAQFASLTG 240 Query: 243 KRICELVLQDIRPSQIMTRQAFENAIAVASALGASSNCPPHLIAIARHMGVELSLDDWQR 302 +RI E+V D++PS I+T ++F+NA+ A+ S+N HL+A+AR G++L+ + Sbjct: 241 QRIVEMVWTDVKPSDILTAKSFDNAVTTVLAMSGSTNAIVHLVAVARRAGIDLTTARFDE 300 Query: 303 IGEDVPLLVNCMPAGKYLGEGFHRAGGVPSVMHELQKAGRLHEDCATVSGRTIGEIVSSS 362 + P++ N P+G+YL E F AGG+ +++ EL + TV+G T+GE ++ + Sbjct: 301 LSRITPVIGNLRPSGQYLMEDFFYAGGLRALLLEL--GDLIDGSQMTVNGSTLGENIAGA 358 Query: 363 LTSNADVIHPFDTPLKHRAGFIVLSGNFF-DSAIMKMSVVGEAFRKTYLSEPGAENSFEA 421 N DVI P+ G VL+GN D A++K + A L+ G Sbjct: 359 EIFNDDVIRKRGNPVVASDGLAVLTGNLAPDGAVIKPA----AMEAHLLNHRG------- 407 Query: 422 RAIVFEGPEDYHARIDDPALDIDERCILVIRGVGTVGYPGSAEVVNMAPPAALIKQGIDS 481 RA+VF+ D ARID LDI ++V++ G VG PG E + P L+KQG+ Sbjct: 408 RAVVFKDYADMAARIDMEDLDITADSVIVLQHAGPVGAPGMPEWGQLPIPQKLLKQGVRD 467 Query: 482 LPCLGDGRQSGTSASPSILNMSPEAAVGGGLALLQTNDRLKVDLNTRTVNLLIDDEEMAR 541 + + D R SGTS +L+++PE+ VGG LAL++ D +++D+ R ++L + DEE++ Sbjct: 468 MVRISDARMSGTSYGACVLHVAPESFVGGPLALVKDGDMIQLDVAARRLHLEVSDEELSA 527 Query: 542 RRLEWTPNIPPSQTPWQELYRQLVGQLSTG 571 R+ W P P + + +++ V Q + G Sbjct: 528 RKAAWQPPKLPFERGFGVMHQLHVLQANKG 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: 914 Number of extensions: 62 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: 592 Length adjustment: 37 Effective length of query: 557 Effective length of database: 555 Effective search space: 309135 Effective search space used: 309135 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