Align Putative [LysW]-aminoadipate/[LysW]-glutamate kinase; EC 2.7.2.17; EC 2.7.2.19 (uncharacterized)
to candidate Echvi_3850 Echvi_3850 acetylglutamate kinase
Query= curated2:A9A1K7 (267 letters) >FitnessBrowser__Cola:Echvi_3850 Length = 266 Score = 111 bits (278), Expect = 1e-29 Identities = 89/273 (32%), Positives = 141/273 (51%), Gaps = 30/273 (10%) Query: 4 IKIGGSVVDDLHPSTIADIKKI-AESEGV-ILVHGGGKEVTKVCEQLGKEPKFVTSPSGI 61 +KIGG+V+DD P+ + + + A EG ILVHGGG +K +QLG EPK V Sbjct: 6 VKIGGNVIDD--PAKLQEFLMLFARLEGKKILVHGGGVMASKFGQQLGIEPKMVDG---- 59 Query: 62 KSRYTDKETAEIFTMVMSGRINKTIVQMLQKNGINAIGLSGVDAKVIEADRKKKLLIVNE 121 R TD+ T ++ TMV +G INK IV LQ+ NA+G +G D +I + ++ Sbjct: 60 -RRITDEATLDVVTMVYAGMINKKIVAKLQQLEQNAMGFTGADGNLIRSAKRP------- 111 Query: 122 KGRKQAIDGGYTGKIREVNASFIKSLLDQGLTPVISPIAISEESEFLNVDGDRAAAYVAG 181 + ID G+ G ++EV+ ++ LL++ + PV S I + LN + D A+ +A Sbjct: 112 ---VKDIDYGFVGDVKEVDTELMEVLLEKDVVPVFSAITHDRKGNLLNTNADTIASEIAT 168 Query: 182 KVG---SDKVLFITNVDGLLM----DDKVVPKLTLAEAKEIRPK--IGPGMEKKILASTE 232 + + ++ F N G+L+ DD +VPK+ E++ I GM K+ + Sbjct: 169 AMAVKHTVRLYFCFNKAGVLIDEHNDDSLVPKINEDIYDELKRDNVIHSGMIPKLDNAFS 228 Query: 233 ALDMGVTTALIANGQKENPISSAISHDNCTVIE 265 AL GV+ + G+ EN I ++ + T IE Sbjct: 229 ALHKGVSNVWL--GKAENLILASKGKKSGTNIE 259 Lambda K H 0.313 0.133 0.360 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: 183 Number of extensions: 10 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: 267 Length of database: 266 Length adjustment: 25 Effective length of query: 242 Effective length of database: 241 Effective search space: 58322 Effective search space used: 58322 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.2 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 42 (21.9 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