Align Probable aspartate/prephenate aminotransferase; AspAT / PAT; EC 2.6.1.1; EC 2.6.1.78; Transaminase A (uncharacterized)
to candidate WP_011885513.1 aminotransferase
Query= curated2:O33822 (383 letters) >NCBI__GCF_000016205.1:WP_011885513.1 Length = 390 Score = 177 bits (450), Expect = 3e-49 Identities = 119/357 (33%), Positives = 177/357 (49%), Gaps = 15/357 (4%) Query: 34 VALTAGEPDFDTPEHVKEAGRRALAQGKTKYAPPAGIPELREAVAEKFRRENGLEV-TPE 92 V L G PDFD + +A A+ G +Y P AG+ LR+A+A+K G Sbjct: 38 VNLGQGFPDFDCDPRIVDAVAAAMRNGHNQYPPMAGVASLRDAIADKIEHLYGRRYDAAT 97 Query: 93 ETIVTVGGKQALFNLFQAILDPGDEVIVLAPYWVSYPEMVRFAGGVPVEVPTLPEEGFVP 152 E VT G QAL + PGDEVIV+ P + SY + AGG PV V TL + Sbjct: 98 EITVTAGATQALLTAILCAVHPGDEVIVIEPTYDSYLPSIELAGGKPVFV-TLDAPDYAI 156 Query: 153 DPERVRRAITPRTKALVVNSPNNPTGVVYPEEVLRALAEMALQHDFYLVSDEIYEHLIYE 212 +R+ AITP+T+ +++N+P+NPTG V+ E LR L E+ + ++SDE+YEH++Y+ Sbjct: 157 PFDRLAAAITPKTRMILINTPHNPTGTVWREADLRRLEEIVRGTNVLILSDEVYEHMVYD 216 Query: 213 GAHFSPGTLAPE---HTITVNGAAKAFAMTGWRIGYACGPKAVIKAMADVSSQSTTSPDT 269 GA PE + V+ K F +TGW+IGY P A+ V + + +T Sbjct: 217 GARHESVARYPELAARSFIVSSFGKTFHVTGWKIGYVAAPAALTAEFRKVHQFNVFTVNT 276 Query: 270 IAQWATLEALTNREASMAFIAMAREAYRKRRDLLLEGLSRIGLEAVRPSGAFYVLMDTSP 329 Q + L + + + Y+K+RD GL R + + +G ++ +D S Sbjct: 277 PMQVGIADYLRDPAPYLTL----PDFYQKKRDFFRAGLERTRFKLLPCTGTYFQCVDYSA 332 Query: 330 FAP-NEVEAAERLLM-AGVAVVPGTEFAAFGH----VRLSYATGEENLKKALERFAQ 380 + +E E A+ L GVA +P + F H VR +A E L ALER A+ Sbjct: 333 ISDVSEAEFAKWLTAEIGVAAIPVSAFYHAPHESGVVRFCFAKQESTLASALERLAR 389 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: 356 Number of extensions: 18 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: 390 Length adjustment: 30 Effective length of query: 353 Effective length of database: 360 Effective search space: 127080 Effective search space used: 127080 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