Align aspartate kinase / diaminopimelate decarboxylase (EC 4.1.1.20; EC 2.7.2.4) (characterized)
to candidate WP_083491847.1 ABB28_RS00495 bifunctional aspartate kinase/homoserine dehydrogenase I
Query= reanno::Dyella79:N515DRAFT_4002 (853 letters) >NCBI__GCF_001431535.1:WP_083491847.1 Length = 837 Score = 164 bits (415), Expect = 2e-44 Identities = 147/448 (32%), Positives = 225/448 (50%), Gaps = 29/448 (6%) Query: 2 KFGGTSVATLPRWQNIRELVASRRAEGARVLVVVSALTGITDAL---KQMCAQEDKGKRV 58 KFGGTSVA ++++ L+ +R A + VVSA+ G+TDAL ++ A D R Sbjct: 27 KFGGTSVADADCYRHVARLLQARPE--ALQVTVVSAMKGVTDALIALARLAAAGDAQWR- 83 Query: 59 EAARAIAQRHY----DLLDHMQLAVPATLAERLSELAMLAEDGPGAMGELAWAAL--VQA 112 E + RH LL A L R ELA L +G L L VQ Sbjct: 84 EDWHDLRARHRGAAASLLGEHAGASVEWLDARFDELAELLA-ALAVIGGLPEEVLDRVQG 142 Query: 113 HGELMSSALGAAFLSHAGLPTEWLDARDCLAAVALPNQNERTKLLSAMVEARPDPALNA- 171 GE+ S+ L +G P LDAR+ L E +L + L+A Sbjct: 143 LGEVCSAHLLGQHFQASGEPCAVLDAREVLVV-------EHGELGVNVDWETSAQRLHAW 195 Query: 172 RLAELGEVFITQGFIAREAQGRTVLLGRGGSDTSASYFGALLKAQRVEIWTDVAGMFTAN 231 R A + + + GFIAR+ + R LGR GSD S + F AL A ++IWTDV G+ +A+ Sbjct: 196 RQANVQQRIVVTGFIARDRRDRITTLGRNGSDYSGAIFAALFNADELQIWTDVDGVLSAD 255 Query: 232 PRQVPGARLLQRLDYEEAQEIASTGAKVLHPRCLSPLREPRVPMLIKDTNRPELEGTVIG 291 PR VP A L+ L Y+EA E+A GAKV+HP+ +SP + +P+LI++T +PE GT I Sbjct: 256 PRLVPEAVQLEALSYDEACELAYFGAKVVHPQTMSPAIQRGLPILIRNTFQPEHPGTRIT 315 Query: 292 PEVREHAPSVKAISARKGITLVSMESVGMWQQVGFLADVFAQFKQHGLSVDLI--GSAET 349 E P +K ++ + ++++E G+ G VF+ +Q +SV +I GS+E Sbjct: 316 AERSVRGP-IKGLTLSAELAVLNLEGTGLIGVPGTAERVFSALRQAQVSVVMISQGSSEH 374 Query: 350 NVTVSLDPTENLLDSDA-IAALASDLA--KVCRVKVIAPCAAITLVGRGMRSMLHTLSGV 406 ++ + E+ DA + A A +LA +V RV++ + + VG GM + + Sbjct: 375 SICCVVRGNESERGRDALLQAFAHELAVGQVQRVQLRGGVSVLAAVGDGMAGQPGVAARL 434 Query: 407 LAEFGQIRVHL--ISQSSNNLNLTFVVD 432 G+ +V++ I+Q S+ N++ VD Sbjct: 435 FESLGRAQVNILAIAQGSSERNISVAVD 462 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: 1600 Number of extensions: 81 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: 837 Length adjustment: 42 Effective length of query: 811 Effective length of database: 795 Effective search space: 644745 Effective search space used: 644745 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 10 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