Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate WP_011973392.1 MAEO_RS03365 aspartate kinase
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >NCBI__GCF_000017185.1:WP_011973392.1 Length = 468 Score = 170 bits (430), Expect = 2e-46 Identities = 144/466 (30%), Positives = 236/466 (50%), Gaps = 33/466 (7%) Query: 1 MKFGGTSVATLPRWQNIRELVASR-RAEGARVLVVVSALTGITDALKQMCAQ----EDKG 55 MKFGGTSV R +N+ +++ + E ++VV SA++ IT+AL M Q D Sbjct: 5 MKFGGTSVGDGQRIRNVAKIIVDKSNKENTDIVVVTSAMSQITNALVNMSKQALNVRDIA 64 Query: 56 KRVEAARAIAQRHYDLLDH------MQLAVPATLAERLSELAMLAEDGPGAMGELAWAA- 108 K + ++H +D ++ V + + EL + G +GEL + Sbjct: 65 KINNFVEELKEKHAIAIDEAVKNDDIRTEVRHVINSSIDELGKVLV-GVSYLGELTPKSK 123 Query: 109 -LVQAHGELMSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDP 167 + + GE +S+ + + + G + +L + A + + + ++ + +P Sbjct: 124 DYILSFGERLSAPILSGAVRDLGKNSLFLLGGE--AGLITDENYGCARPIKIKIKEKVNP 181 Query: 168 ALNARLAELGEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGM 227 L + + I GF+A G GRGGSD SA+ GA L A VEIWTDV+G+ Sbjct: 182 LLEENI-----IPIITGFVAGTENGDITTFGRGGSDYSAALVGAGLDADTVEIWTDVSGI 236 Query: 228 FTANPRQVPGARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEG 287 T++PR V + + ++ Y EA E+A GAKVLHPR + PL E +P+ IK+T PE EG Sbjct: 237 LTSDPRIVKNVKRIPKMSYIEAMELAYFGAKVLHPRTVEPLMEKNIPLRIKNTFEPENEG 296 Query: 288 TVIGPEVREHAPSV-KAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLI-- 344 T I +E + SV KA+SA + + L+++ GM G A +F+ + +V LI Sbjct: 297 TFI-TNCKELSNSVMKAVSAIRDVFLINIFGAGMVGVSGTAARIFSALGRADANVLLITQ 355 Query: 345 GSAETNVTVSLDPTENLLDSDAIAALASDLAKVCRVKVIA---PCAAITLVGRGM---RS 398 GS+ETNV+V + E + ++ + L + VK I+ A I+ VG GM + Sbjct: 356 GSSETNVSVVIYGDE-VDANNCMKELRKEFKNSNLVKDISIDENVAVISAVGVGMKGSKG 414 Query: 399 MLHTLSGVLAEFGQIRVHLISQSSNNLNLTFVVDENVVDDLLPHLH 444 + L G +AE G + +I+Q S+ +N++FV+ E +++ L LH Sbjct: 415 IAGKLFGAVAESG-ANIKMIAQGSSEVNISFVIGEEELENCLRILH 459 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: 768 Number of extensions: 36 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: 853 Length of database: 468 Length adjustment: 38 Effective length of query: 815 Effective length of database: 430 Effective search space: 350450 Effective search space used: 350450 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: 54 (25.4 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