Align Aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78 (characterized)
to candidate WP_055435649.1 ASC41_RS05550 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::Q8KDS8 (400 letters) >NCBI__GCF_001418085.1:WP_055435649.1 Length = 395 Score = 363 bits (932), Expect = e-105 Identities = 183/390 (46%), Positives = 260/390 (66%), Gaps = 1/390 (0%) Query: 10 LSRRVLSMQESQTMKITGLAKKMQAEGKDVVSLSAGEPDFPTPENVCEAGIEAIRKGFTR 69 LS R+ +M S T+ + A++++AEGKD++ LS GEPDF TP+ + EA I+A+ + Sbjct: 4 LSERITNMSTSATLAMAAKARELRAEGKDIIGLSLGEPDFNTPDFIKEAAIQAVNDNYNS 63 Query: 70 YTANSGIPELKKAIIRKLQRDNGLEYAEDEIIVSNGGKQALANTFLALCDEGDEVIVPAP 129 Y+ G +LK+A+I K +RDN L Y +I+VS G KQ+L N + ++GDEVI+P P Sbjct: 64 YSPVDGYVDLKEAVITKFKRDNNLTYTLPQIVVSTGAKQSLYNIAQVMLNKGDEVILPCP 123 Query: 130 YWVSFPEMARLAEATPVIVETSIETGYKMTPEQLAAAITPKTRILVLNSPSNPSGAVYNE 189 YWVS+ ++ ++AE PV V+TSIE +KMT QL AAITPKT++L +SP NPSG++Y++ Sbjct: 124 YWVSYSDIVKVAEGVPVEVKTSIENDFKMTASQLEAAITPKTKMLWFSSPCNPSGSLYSK 183 Query: 190 AEVRALMQV-IEGKEIFVLSDEMYDMICYGGVRPFSPARIPEMKPWVIVSNGTSKSYSMT 248 E+ AL V ++ I+V+SDE+Y+ I Y G S A I M I NG SK+++MT Sbjct: 184 EELEALASVLVKYPNIYVVSDEIYEHINYTGKPHASMAGIDGMFNNTITVNGVSKAFAMT 243 Query: 249 GWRIGYLAAPKWIINACDKIQSQTTSNANSIAQKAAVAALDGDQSIVEQRRAEFEKRRDF 308 GWR+G++ AP WI AC+K+Q Q TS N IAQ+A + AL+ D S+V+ EF+ RRD Sbjct: 244 GWRVGFIGAPDWIARACNKMQGQVTSGTNCIAQRAVITALNADPSVVDYMIDEFKVRRDM 303 Query: 309 MFRELNTISGIECTLPEGAFYIFPSIKGLLGKTFGGKVMKDSTDVAEYLLTEHYVATVPG 368 + L I G + PEGAFY+FP + GKT GK + ++TD + YLL E VATV G Sbjct: 304 VLNLLEGIEGFKTNTPEGAFYVFPDVTYFFGKTLRGKTINNATDFSLYLLEEALVATVTG 363 Query: 369 DAFGAPENLRLSYAASIEELAEAVNRIRKA 398 DAFG P+ +R+SYAAS +++ EAV RI+ A Sbjct: 364 DAFGNPDCIRISYAASQDQIKEAVKRIKAA 393 Lambda K H 0.316 0.132 0.376 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: 372 Number of extensions: 9 Number of successful extensions: 2 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: 400 Length of database: 395 Length adjustment: 31 Effective length of query: 369 Effective length of database: 364 Effective search space: 134316 Effective search space used: 134316 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: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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