Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_336884956.1 NPUN_RS00030 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= curated2:O33822 (383 letters) >NCBI__GCF_000020025.1:WP_336884956.1 Length = 314 Score = 168 bits (426), Expect = 2e-46 Identities = 110/312 (35%), Positives = 169/312 (54%), Gaps = 15/312 (4%) Query: 77 VAEKFRRENGLEVTPEETI-VTVGGKQALFNLFQAILDPGDEVIVLAPYWVSYPEMVRFA 135 +A K R GL++ PE I VT G +A+ ++ A +DPGDEVIV PY+ +Y A Sbjct: 1 MASKVRWYLGLDIDPETQITVTCGSTEAMASVMLATVDPGDEVIVFEPYYENYGPDAILA 60 Query: 136 GGVPVEVPTLPEEGFVPDPERVRRAITPRTKALVVNSPNNPTGVVYPEEVLRALAEMALQ 195 G P V TL + D ++ +A TKA+++N+P+NPTG V+ E L +AE+ + Sbjct: 61 GATPRYV-TLHPPHWTFDEAQLHQAFNANTKAIIINTPHNPTGKVFTREELTLIAELCQK 119 Query: 196 HDFYLVSDEIYEHLIYEGA-HFSPGTL--APEHTITVNGAAKAFAMTGWRIGYACGPKAV 252 D +DEIYEH++Y+G H + TL E TIT+NG +K +++TGWR+GY A+ Sbjct: 120 WDVLAFTDEIYEHILYDGTQHIALATLPGMEERTITINGLSKTYSVTGWRVGYILANPAL 179 Query: 253 IKAMADVSSQSTTSPDTIAQWATLEALTNREASMAFIAMAREAYRKRRDLLLEGLSRIGL 312 A+ V T Q A + A+ + ++ + Y ++RD +L+ L +G+ Sbjct: 180 TGAIRKVHDFLTVGAPAPLQRAGVTAM---QLPPSYYEELGKLYHQKRDSILQILDGVGI 236 Query: 313 EAVRPSGAFYVLMDTSPFA-PNEVEAAERLLM-AGVAVVPGTEFAA---FGH--VRLSYA 365 P GA+YVL D S F ++E L+ GVAVVPG+ F + GH +R ++ Sbjct: 237 PYFLPQGAYYVLADISKFGYKTDIEFTYHLIKNIGVAVVPGSSFFSQPEKGHSLIRFCFS 296 Query: 366 TGEENLKKALER 377 E L+ A +R Sbjct: 297 KTPETLQAASDR 308 Lambda K H 0.317 0.133 0.382 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: 315 Number of extensions: 14 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: 383 Length of database: 314 Length adjustment: 29 Effective length of query: 354 Effective length of database: 285 Effective search space: 100890 Effective search space used: 100890 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 (21.7 bits) S2: 49 (23.5 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