Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate 5208267 Shew_0779 aspartate kinase III (RefSeq)
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >FitnessBrowser__PV4:5208267 Length = 452 Score = 205 bits (521), Expect = 5e-57 Identities = 157/458 (34%), Positives = 236/458 (51%), Gaps = 29/458 (6%) Query: 2 KFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQE-DKGKRVEA 60 KFGGTSVA ++V A +VVVSA +G+T+ L ++ + D +R + Sbjct: 7 KFGGTSVADYEAMNRCADIVL---ANPETRVVVVSASSGVTNLLVELTQEHVDFERRQQL 63 Query: 61 ARAIAQRHYDLLDHMQLAVPATLAERL----SELAMLAEDGPGAMGELAWAALVQAHGEL 116 +AIA Y +LD +L P +A RL S++A L+E + L+ A GE Sbjct: 64 LKAIASIQYKILD--ELGQPHDVAARLDAILSKIASLSESLSQNRNKATTDELL-AQGEQ 120 Query: 117 MSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNARLAEL 176 SS L AA L G D R + + + E +EA L L Sbjct: 121 CSSVLFAAVLREKGERASAFDVRQVMRTDSHFGRAE------PQIEAVKQLCTEHLLPLL 174 Query: 177 GEV-FITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQV 235 E +TQGFI + QG T LGRGGSD SA+ L A VEIWTDV G+FT +PR Sbjct: 175 SEQRIVTQGFIGADEQGATTTLGRGGSDYSAALLAEALDASAVEIWTDVPGIFTTDPRLA 234 Query: 236 PGARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVR 295 P AR + + + EA E+A+ GAKVLHP + P ++ + + + PEL GT I +V Sbjct: 235 PNARPIPEISFNEAAEMATFGAKVLHPATILPAVRHKIQVFVGSSKAPELGGTWIRHQVN 294 Query: 296 EHAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSL 355 + P +A++ R+ TL+++ S+ M GFLA+ FA +H +SVDLI ++E NV+++L Sbjct: 295 DE-PIYRAVAVRRDQTLLNLHSLQMLHAQGFLAETFATLARHKISVDLITTSEVNVSLTL 353 Query: 356 DPT--ENLLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQI 413 D T ++ +S AL +L++ CRV+V A + +VG + + T SGV ++ Sbjct: 354 DKTGSDSAGNSLLSEALLQELSQHCRVRVEDGLALVAIVG----NKIATTSGVCRRVFEV 409 Query: 414 ----RVHLISQSSNNLNLTFVVDENVVDDLLPHLHELL 447 V +I Q ++ NL +V E+ ++ LH+ L Sbjct: 410 LEPHNVRMICQGASPHNLCVLVAESEAAQVVSALHQNL 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: 740 Number of extensions: 34 Number of successful extensions: 4 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: 452 Length adjustment: 37 Effective length of query: 816 Effective length of database: 415 Effective search space: 338640 Effective search space used: 338640 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