Align [LysW]-L-2-aminoadipate 6-kinase monomer (EC 2.7.2.17) (characterized)
to candidate SMc01726 SMc01726 acetylglutamate kinase
Query= metacyc::MONOMER-6801 (269 letters) >FitnessBrowser__Smeli:SMc01726 Length = 295 Score = 127 bits (318), Expect = 4e-34 Identities = 90/274 (32%), Positives = 141/274 (51%), Gaps = 15/274 (5%) Query: 2 IVVKVGGAEGINYE---AVAKDAASLWKEGVKLLLVHGGSAETNKVAEALGHPPRFLTHP 58 IVVK GG N E A A D A L + GV ++VHGG + + +G +F Sbjct: 28 IVVKYGGHAMGNAELGRAFASDIALLKQSGVNPIVVHGGGPQIGAMLNRMGIESKF---E 84 Query: 59 GGQVSRLTDRKTLEIFEMVYCGLVNKRLVELLQKEGANAIGLSGLDGRL-FVGRRKTAVK 117 GG R+TD KT+EI EMV G +NK +V L+ + G AIGL G DG + F + K ++ Sbjct: 85 GGL--RVTDEKTVEIVEMVLAGSINKEIVALINQTGEWAIGLCGKDGNMVFAEKAKKTIR 142 Query: 118 YVENGKVKVHRGDYTGTVEEVNKALLDLLLQAGYLPVLTPPALSYENEAINTDGDQIAAL 177 ++ +V + G V EV++ LLDLL ++ +PV+ P A + N + D A Sbjct: 143 DPDSNIERVLDLGFVGDVVEVDRTLLDLLARSEMIPVIAPVAPGRDGHTYNINADTFAGA 202 Query: 178 LATLYGAEALVYLSNVPGLLARYPDEASLVREIPVERIEDPEYLALAQGRMKRKVMGAVE 237 +A A L++L++VPG+L + + L++++ V G M KV +E Sbjct: 203 IAGALNATRLLFLTDVPGVLNK---KGELIKQLSVAEARALIADGTISGGMIPKVETCIE 259 Query: 238 AVKGGVKRVVFADGRVENPIRRAL---SGEGTVV 268 A+K GV+ VV +G+ + + + G GT++ Sbjct: 260 AIKAGVQGVVILNGKTAHSVLLEIFTEHGAGTLI 293 Lambda K H 0.317 0.137 0.385 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: 213 Number of extensions: 16 Number of successful extensions: 4 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: 269 Length of database: 295 Length adjustment: 26 Effective length of query: 243 Effective length of database: 269 Effective search space: 65367 Effective search space used: 65367 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.6 bits) S2: 47 (22.7 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