Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_028313919.1 G491_RS0105965 pyridoxal phosphate-dependent aminotransferase
Query= curated2:O33822 (383 letters) >NCBI__GCF_000429905.1:WP_028313919.1 Length = 384 Score = 189 bits (479), Expect = 1e-52 Identities = 122/357 (34%), Positives = 187/357 (52%), Gaps = 15/357 (4%) Query: 34 VALTAGEPDFDTPEHVKEAGRRALAQGKTKYAPPAGIPELREAVAEKFRRENGLEVTPE- 92 + L G D P+ V ++A+ +G Y P G+PELR+A+A K G PE Sbjct: 28 INLAQGVCDIKVPDEVIAGAKKAMDEGYNVYTPNHGLPELRQAIAGKTAAFYGRRPDPET 87 Query: 93 ETIVTVGGKQALFNLFQAILDPGDEVIVLAPYWVSYPEMVRFAGGVPVEVPTLPEEGFVP 152 E + ++G + A+L+PGDEVI+ PY+ + + G VPV VPT P + Sbjct: 88 EIVASLGATGVFYCAAMALLNPGDEVILFEPYYGYHASTLEAVGAVPVFVPTKPGTWEI- 146 Query: 153 DPERVRRAITPRTKALVVNSPNNPTGVVYPEEVLRALAEMALQHDFYLVSDEIYEHLIYE 212 +P+ + +A+TPRTK +V+ +P NP+G V + +AE A +HD + SDEIYEH +Y+ Sbjct: 147 EPDALAKAVTPRTKGIVLCTPGNPSGHVMTAGEIDLIAEAAQKHDLVIFSDEIYEHFLYD 206 Query: 213 G-AHFSPGTLAP---EHTITVNGAAKAFAMTGWRIGYACGPKAVIKAMADVSSQSTTSPD 268 G H PG L P T+T++GA+K +A+TGWR+GY P V +A+ ++ Sbjct: 207 GRTHLCPG-LHPGLEGRTVTMSGASKTYAITGWRLGYCICPADVTEAITHLNDLVYVCAP 265 Query: 269 TIAQWATLEALTNREASMAFIAMAREAYRKRRDLLLEGLSRIGLEAVRPSGAFYVLMDTS 328 Q + N + +AR+ ++K+RDL + + + G++ RP GA+YVL D S Sbjct: 266 APLQMGVAAGM-NMLGRDYYEGLARD-HQKKRDLFCDTIEKAGMKPYRPEGAYYVLADVS 323 Query: 329 --PFAPNEVEAAERLLMAGVAVVPGTEF----AAFGHVRLSYATGEENLKKALERFA 379 P + A L GV+ VPG F + VR +A L++A ER A Sbjct: 324 GVPGHDSFTRAMHILEKTGVSSVPGRAFFHDDSGDSLVRFCFAKEFPVLEEACERIA 380 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: 426 Number of extensions: 28 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: 384 Length adjustment: 30 Effective length of query: 353 Effective length of database: 354 Effective search space: 124962 Effective search space used: 124962 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: 50 (23.9 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