Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate 6936415 Sama_0603 aspartate kinase III (RefSeq)
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >FitnessBrowser__SB2B:6936415 Length = 452 Score = 209 bits (532), Expect = 3e-58 Identities = 152/462 (32%), Positives = 238/462 (51%), Gaps = 27/462 (5%) Query: 2 KFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMC-AQEDKGKRVEA 60 KFGGTSVA +V A A LVVVSA +G+T+ L ++ A +R++ Sbjct: 7 KFGGTSVADFNAMSRCAAIVL---ANSATRLVVVSASSGVTNLLVELTQATVTDERRLQL 63 Query: 61 ARAIAQRHYDLLDHMQLA--VPATLAERLSELAMLAED-----GPGAMGELAWAALVQAH 113 + IAQ Y +LD ++ V A L LS +++L+E M EL + Sbjct: 64 LKQIAQIQYAILDKLERPQDVAAALDALLSRISVLSESLILNRSKAIMDELL------SM 117 Query: 114 GELMSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNE-RTKLLSAMVEARPDPALNAR 172 GE S+ L +A L G + D R + + + E + + ++A+ P L Sbjct: 118 GEQCSALLFSAVLRQQGAKSSSFDVRQVMRTDSHFGRAEPQIEDIAALARDFLQPLLER- 176 Query: 173 LAELGEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTANP 232 ++ +TQGFI +A+GRT LGRGGSD SA+ L+A VEIWTDVAG++T +P Sbjct: 177 -----DIVVTQGFIGADAEGRTTTLGRGGSDYSAALLAEALRADAVEIWTDVAGIYTTDP 231 Query: 233 RQVPGARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIGP 292 R P AR + + + EA E+A+ GAKVLHP + P ++ + + + PE GT I Sbjct: 232 RLAPNARPIAEISFNEAAEMATFGAKVLHPATILPAVRQQIQVFVGSSREPEKGGTWIRH 291 Query: 293 EVREHAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETNVT 352 +V ++ P +A++ R+ TL+++ S+ M GFLA+ FA +H +SVDLI ++E NV+ Sbjct: 292 QV-DNPPIYRAVAVRRDQTLLNLHSLQMLHARGFLAETFATLARHKISVDLITTSEVNVS 350 Query: 353 VSLDPTENLLDSDAI--AALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTLSGVLAEF 410 ++LD T + + AL +L++ CRV+V A + ++G + S V Sbjct: 351 LTLDKTGSDSTGSGLLSEALLQELSQHCRVRVEDNLALVAIIGNRIASTPGICRQVFTVL 410 Query: 411 GQIRVHLISQSSNNLNLTFVVDENVVDDLLPHLHELLIAAGA 452 V +I Q ++ NL +V E+ ++ LHE L A Sbjct: 411 ENHNVRMICQGASPHNLCVLVAESEAAQVVKALHENLFEGQA 452 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: 732 Number of extensions: 26 Number of successful extensions: 5 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