Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate WP_012467305.1 CLIM_RS12130 lysine-sensitive aspartokinase 3
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >NCBI__GCF_000020465.1:WP_012467305.1 Length = 471 Score = 225 bits (573), Expect = 5e-63 Identities = 151/460 (32%), Positives = 243/460 (52%), Gaps = 28/460 (6%) Query: 1 MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA 60 MKFGGTSV Q +LV + GA LVV+SA +GIT+ L ++ + EA Sbjct: 4 MKFGGTSVGNARAMQQAIDLVVREKLNGAP-LVVLSACSGITNKLVRLAEASGRSALDEA 62 Query: 61 ---ARAIAQRHYDLL------DHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAA--L 109 A + Q H DL +Q + A + E ++ L MLA G +GEL + Sbjct: 63 LLLAGEVRQHHIDLTAELIQAPELQAELEAKVEEYVAGLEMLAR-GVDIVGELTERSKDT 121 Query: 110 VQAHGELMSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPAL 169 + GEL+S+ + AA + G EWLD R V + + N + A+ Sbjct: 122 FCSFGELLSTTIFAAAMKEQGHDAEWLDVR----RVMITDDNHGFARPLGDICRENAGAI 177 Query: 170 NARLAELGEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFT 229 + L + G + ITQG+I GRT LGRGGSD SA+ GA L A ++IWTDV G+ T Sbjct: 178 ISPLLDAGTIVITQGYIGAALNGRTTTLGRGGSDYSAALLGAWLNANAIQIWTDVDGVMT 237 Query: 230 ANPRQVPGARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTV 289 +PR VP AR ++ + + EA E+A GAKVLHP ++P E +P+ + +T P+ +GT+ Sbjct: 238 CDPRLVPEARSIRIMTFSEAAELAYLGAKVLHPDTIAPAVEKNIPVWVLNTWHPDAKGTL 297 Query: 290 IGPEVR-----EHAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLI 344 I + + VK+I+ +KG ++++ S M + GF+A++F F ++G+S+++I Sbjct: 298 ITDDTERLSGMSYGGLVKSIAVKKGQCIINVRSNRMLGRYGFMAELFGAFSRYGVSIEMI 357 Query: 345 GSAETNVTVSLDPTENLLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLS 404 S+E +V+V++D D+ L DL + +V + A +++VG +R Sbjct: 358 SSSEVSVSVTVD------DTCFSEELLQDLRVLGQVDIEHRVATVSVVGDNLRMSKGVAG 411 Query: 405 GVLAEFGQIRVHLISQSSNNLNLTFVVDENVVDDLLPHLH 444 + + + + +ISQ ++ +N+ FVV+EN V+ + LH Sbjct: 412 RIFSSLRDVNLRMISQGASEINVGFVVEENDVERAVNTLH 451 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: 774 Number of extensions: 33 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: 471 Length adjustment: 38 Effective length of query: 815 Effective length of database: 433 Effective search space: 352895 Effective search space used: 352895 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 10 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