Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate BWI76_RS01790 BWI76_RS01790 lysine-sensitive aspartokinase 3
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >FitnessBrowser__Koxy:BWI76_RS01790 Length = 449 Score = 213 bits (543), Expect = 1e-59 Identities = 144/453 (31%), Positives = 235/453 (51%), Gaps = 20/453 (4%) Query: 2 KFGGTSVA---TLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRV 58 KFGGTSVA + R ++ L A+ R +VV+SA G+T+ L + + G+R Sbjct: 8 KFGGTSVADFDAMNRSVDVALLDANTR------VVVLSASAGVTNLLVALAEGLEPGERF 61 Query: 59 EAARAIAQRHYDLLDHMQL--AVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGEL 116 A+ Q +++L+ ++ + + L + LAE A LV +HGEL Sbjct: 62 AKLDAMRQIQFNILERLRYPNVIRDEIERLLENITTLAEAASLASSTALTDELV-SHGEL 120 Query: 117 MSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAEL 176 MS+ L L G+ +W D R + ++ R + A + L RLAE Sbjct: 121 MSTLLFVEILRERGIAAQWFDVRKIMRT---NDRFGRAEPDIAALSELTQQQLTPRLAE- 176 Query: 177 GEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVP 236 + ITQGFI EA+GRT LGRGGSD +A+ G L A RV+IWTDV G++T +PR P Sbjct: 177 -GLVITQGFIGSEAKGRTTTLGRGGSDYTAALLGEALNATRVDIWTDVPGIYTTDPRVAP 235 Query: 237 GARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVRE 296 A+ + + +EEA E+A+ GAKVLHP L P +P+ + + P+ GT++ + Sbjct: 236 AAKRIDVIAFEEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKEPKAGGTLVCKNTK- 294 Query: 297 HAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLD 356 + P +A++ R+ TL+++ S+ M GFLA+VF+ +H +SVDLI ++E +V +++D Sbjct: 295 NPPLFRALALRRKQTLLTLHSLNMLHSRGFLAEVFSILARHSISVDLITTSEVSVALTMD 354 Query: 357 PTENLLDSDAI--AALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIR 414 T + D + L ++L+ +CRV+V A + ++G + V Sbjct: 355 TTGSTSAGDTLLTQGLLTELSSLCRVEVEQDLALVAIIGNELSKACGVGKEVFGVLDPFN 414 Query: 415 VHLISQSSNNLNLTFVVDENVVDDLLPHLHELL 447 + +I +++ NL F+V + ++ LH L Sbjct: 415 IRMICYGASSHNLCFLVPGADAEKVVQKLHHNL 447 Lambda K H 0.319 0.135 0.398 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: 784 Number of extensions: 34 Number of successful extensions: 5 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: 853 Length of database: 449 Length adjustment: 37 Effective length of query: 816 Effective length of database: 412 Effective search space: 336192 Effective search space used: 336192 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 (21.8 bits) S2: 53 (25.0 bits)
This GapMind analysis is from Apr 09 2024. The underlying query database was built on Apr 09 2024.
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