Align homoserine dehydrogenase (EC 1.1.1.3); aspartate kinase (EC 2.7.2.4) (characterized)
to candidate N515DRAFT_4002 N515DRAFT_4002 aspartate kinase
Query= BRENDA::P00561 (820 letters) >FitnessBrowser__Dyella79:N515DRAFT_4002 Length = 853 Score = 174 bits (442), Expect = 1e-47 Identities = 147/470 (31%), Positives = 226/470 (48%), Gaps = 37/470 (7%) Query: 4 LKFGGTSVANAERFLRVADILESNARQG-QVATVLSAPAKITNHLVAMIEKTISGQDALP 62 +KFGGTSVA R+ + +++ S +G +V V+SA IT+ L M + G+ Sbjct: 1 MKFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDALKQMCAQEDKGKRVEA 60 Query: 63 NISDAERIFAELLTGLAAAQPGFPLAQLKTFVDQEFAQIKHVLHGISLLGQCPDSINAAL 122 + A+R + +LL + A P +L E A + G +G+ + A + Sbjct: 61 ARAIAQRHY-DLLDHMQLAVPATLAERLS-----ELAMLAE--DGPGAMGELAWA--ALV 110 Query: 123 ICRGEKMSIAIMAGVLEARGHNVTVIDPVEKLLAVG-------HYLESTVDIAESTRRIA 175 GE MS A+ A L G +D + L AV L S + A + Sbjct: 111 QAHGELMSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALN 170 Query: 176 ASRIPADHMVLMAGFTAGNEKGELVVLGRNGSDYSAAVLAACLRADCCEIWTDVDGVYTC 235 A + + GF A +G V+LGR GSD SA+ A L+A EIWTDV G++T Sbjct: 171 ARLAELGEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTA 230 Query: 236 DPRQVPDARLLKSMSYQEAMELSYFGAKVLHPRTITPIAQFQIPCLIKNTGNPQAPGTLI 295 +PRQVP ARLL+ + Y+EA E++ GAKVLHPR ++P+ + ++P LIK+T P+ GT+I Sbjct: 231 NPRQVPGARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVI 290 Query: 296 GASRDEDELPVKGISNLNNMAMFSVSGPGMKGMVGMAARVFAAMSRARISVVLITQSSSE 355 G E VK IS + + S+ GM VG A VFA + +SV LI + + Sbjct: 291 GPEVREHAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLIGSAETN 350 Query: 356 YSISFCVPQSDCVRAERAMQEEFYLELKEGLLE--PLAVTERLAIISVVGDGMR----TL 409 ++S E + + L L + + V A I++VG GMR TL Sbjct: 351 VTVSL-------DPTENLLDSDAIAALASDLAKVCRVKVIAPCAAITLVGRGMRSMLHTL 403 Query: 410 RGISAKFFAALARANINIVAIAQGSSERSISVVVNNDDATTGVRVTHQML 459 G+ A+F I + I+Q S+ +++ VV+ + + H++L Sbjct: 404 SGVLAEF------GQIRVHLISQSSNNLNLTFVVDENVVDDLLPHLHELL 447 Lambda K H 0.319 0.135 0.384 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: 1365 Number of extensions: 60 Number of successful extensions: 3 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: 820 Length of database: 853 Length adjustment: 42 Effective length of query: 778 Effective length of database: 811 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