Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate 7023422 Shewana3_0652 aspartate kinase III (RefSeq)
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >FitnessBrowser__ANA3:7023422 Length = 451 Score = 206 bits (524), Expect = 2e-57 Identities = 153/453 (33%), Positives = 235/453 (51%), Gaps = 19/453 (4%) Query: 2 KFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQE--DKGKRVE 59 KFGGTSVA ++V R LVVVSA +G+T+ L ++ + D G R++ Sbjct: 7 KFGGTSVADYGAMNRCADIVLGN--PDCR-LVVVSASSGVTNLLVELTQESMNDDG-RLQ 62 Query: 60 AARAIAQRHYDLLDHMQLA--VPATLAERLSELAMLAEDGPGAMGELAWAALVQAHGELM 117 + IAQ Y +LD + V A L + LS +A+L+E + L+ GE Sbjct: 63 RLKQIAQIQYAILDKLGRPNDVAAALDKLLSRMAVLSEALASQRSKATMDELLSL-GEQC 121 Query: 118 SSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNE-RTKLLSAMVEARPDPALNARLAEL 176 SSAL AA L G + D R L + + E + + ++ + P L+ Sbjct: 122 SSALFAAVLREKGANSSAFDVRRVLRTDSHFGRAEPQVEQIAILSREHLLPLLSE----- 176 Query: 177 GEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANPRQVP 236 +V +TQGFI + G+T LGRGGSD SA+ LKA VEIWTDVAG++T +PR P Sbjct: 177 -QVIVTQGFIGSDEAGQTTTLGRGGSDYSAALLAEALKASAVEIWTDVAGIYTTDPRLAP 235 Query: 237 GARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGPEVRE 296 A + + + EA E+A+ GAKVLHP + P ++ + + + PE GT I +V E Sbjct: 236 NAHPIAEISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSKEPEKGGTWIRHQV-E 294 Query: 297 HAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVTVSLD 356 AP +A++ R+ TL+++ S+ M GFLA+ FA +H +SVDLI ++E NV+++LD Sbjct: 295 DAPVFRAVALRRDQTLLNLHSLQMLHAQGFLAETFATLARHKISVDLITTSEVNVSLTLD 354 Query: 357 PTENLLDSDAI--AALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEFGQIR 414 T + + AL +L++ CRV+V A + ++G + + V Sbjct: 355 KTGSDSSGQGLLSEALLQELSQHCRVRVEDGLALVAIIGNRIATTAGICRRVFEVLEPHN 414 Query: 415 VHLISQSSNNLNLTFVVDENVVDDLLPHLHELL 447 V +I Q ++ NL +V E+ ++ LHE L Sbjct: 415 VRMICQGASPHNLCVLVAESEAAQVVKALHENL 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: 771 Number of extensions: 35 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: 451 Length adjustment: 37 Effective length of query: 816 Effective length of database: 414 Effective search space: 337824 Effective search space used: 337824 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