Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate 18052 b4024 aspartate kinase III (NCBI)
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >FitnessBrowser__Keio:18052 Length = 449 Score = 211 bits (537), Expect = 7e-59 Identities = 146/452 (32%), Positives = 227/452 (50%), Gaps = 18/452 (3%) Query: 2 KFGGTSVATLPRWQNIRELVASRRAEGARV-LVVVSALTGITDALKQMCAQEDKGKRVEA 60 KFGGTSVA ++V S A V LVV+SA GIT+ L + + G+R E Sbjct: 8 KFGGTSVADFDAMNRSADIVLS----DANVRLVVLSASAGITNLLVALAEGLEPGERFEK 63 Query: 61 ARAIAQRHYDLLDHMQL--AVPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELMS 118 AI + +L+ ++ + + L + +LAE A LV +HGELMS Sbjct: 64 LDAIRNIQFAILERLRYPNVIREEIERLLENITVLAEAAALATSPALTDELV-SHGELMS 122 Query: 119 SALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAELGE 178 + L L + +W D R + N+R + A + A L L E Sbjct: 123 TLLFVEILRERDVQAQWFDVRKVMRT------NDRFGRAEPDIAALAELAALQLLPRLNE 176 Query: 179 -VFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVPG 237 + ITQGFI E +GRT LGRGGSD +A+ L A RV+IWTDV G++T +PR V Sbjct: 177 GLVITQGFIGSENKGRTTTLGRGGSDYTAALLAEALHASRVDIWTDVPGIYTTDPRVVSA 236 Query: 238 ARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVREH 297 A+ + + + EA E+A+ GAKVLHP L P +P+ + + P GT++ + E+ Sbjct: 237 AKRIDEIAFAEAAEMATFGAKVLHPATLLPAVRSDIPVFVGSSKDPRAGGTLVCNKT-EN 295 Query: 298 APSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLDP 357 P +A++ R+ TL+++ S+ M GFLA+VF +H +SVDLI ++E +V ++LD Sbjct: 296 PPLFRALALRRNQTLLTLHSLNMLHSRGFLAEVFGILARHNISVDLITTSEVSVALTLDT 355 Query: 358 TENLLDSDAI--AALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIRV 415 T + D + +L +L+ +CRV+V A + L+G + V + Sbjct: 356 TGSTSTGDTLLTQSLLMELSALCRVEVEEGLALVALIGNDLSKACGVGKEVFGVLEPFNI 415 Query: 416 HLISQSSNNLNLTFVVDENVVDDLLPHLHELL 447 +I +++ NL F+V + ++ LH L Sbjct: 416 RMICYGASSHNLCFLVPGEDAEQVVQKLHSNL 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: 794 Number of extensions: 32 Number of successful extensions: 6 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