Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate BWI76_RS04245 BWI76_RS04245 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >FitnessBrowser__Koxy:BWI76_RS04245 Length = 820 Score = 174 bits (441), Expect = 2e-47 Identities = 144/475 (30%), Positives = 231/475 (48%), Gaps = 47/475 (9%) Query: 1 MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA 60 +KFGGTSVA R+ + +++ S +G +V V+SA IT+ L M + G+ Sbjct: 4 LKFGGTSVANAERFLRVADILESNARQG-QVATVLSAPAKITNHLVAMIEKTIGGQDALT 62 Query: 61 ARAIAQRHY-DLLDHMQLAVPATLAERLS-----ELAMLAE--DGPGAMGELAWA--ALV 110 A A+R + +LL + A P +L E A + G +G+ + A + Sbjct: 63 NIADAERIFAELLQGLADAQPGFPLAQLKAFVEQEFAQIKHVLHGISLLGQCPDSVNASL 122 Query: 111 QAHGELMSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALN 170 GE +S A+ A L G V + N E+ + +E+ D A + Sbjct: 123 ICRGEKLSIAIMAGLLEARG------------HNVTVINPVEKLLAVGHYLESTVDIAES 170 Query: 171 ARLAELGEV-----FITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVA 225 R ++ + GF A +G V+LGR GSD SA+ A L+A EIWTDV Sbjct: 171 TRRIAASQIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVD 230 Query: 226 GMFTANPRQVPGARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPEL 285 G++T +PRQVP ARLL+ + Y+EA E++ GAKVLHPR ++P+ + ++P LIK+T P+ Sbjct: 231 GVYTCDPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTIAPIAQFQIPCLIKNTGNPQA 290 Query: 286 EGTVIGPEVREHAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIG 345 GT+IG E VK IS + + ++ GM VG A VFA + G+SV LI Sbjct: 291 PGTLIGASRDEDDLPVKGISNLNNMAMFNVSGPGMKGMVGMAARVFATMSRAGISVVLIT 350 Query: 346 SAETNVTVSL-------DPTENLLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRS 398 + + ++S + +++ + L L + + ++ A I++VG GMR Sbjct: 351 QSSSEYSISFCVPQSDCARAKRVMEDEFYLELKEGLLE--PLSIMERLAIISVVGDGMR- 407 Query: 399 MLHTLSGVLAEF------GQIRVHLISQSSNNLNLTFVVDENVVDDLLPHLHELL 447 TL G+ A+F I + I+Q S+ +++ VV + + H++L Sbjct: 408 ---TLRGISAKFFAALARANINIVAIAQGSSERSISVVVSNDDATTGVRVTHQML 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: 1360 Number of extensions: 53 Number of successful extensions: 6 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 853 Length of database: 820 Length adjustment: 42 Effective length of query: 811 Effective length of database: 778 Effective search space: 630958 Effective search space used: 630958 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: 56 (26.2 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