Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_027457779.1 K420_RS0109050 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000519045.1:WP_027457779.1 Length = 385 Score = 169 bits (427), Expect = 2e-46 Identities = 117/357 (32%), Positives = 178/357 (49%), Gaps = 15/357 (4%) Query: 34 VALTAGEPDFDTPEHVKEAARRALAQGKTKYAPPAGIPELREALAEKFRRENGLSVTPE- 92 V L+ G PDF + +A R + G+ +YAP G+PELR+A+ +K G E Sbjct: 32 VNLSQGFPDFQAEPALFDAVHRHMLAGRNQYAPMGGLPELRQAIVDKVATLYGPRFDVES 91 Query: 93 ETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWVSYPEMVRFAGGVVVEVETLPEEGFVP 152 E VT G QA+F A + PGDEVIV P + SY + GG V + L + P Sbjct: 92 EVTVTAGATQAIFTAIAAFVRPGDEVIVFEPVYDSYVPAIETVGGQAVFAQ-LRFPDYAP 150 Query: 153 DPERVRRAITPRTKALVVNSPNNPTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLYE 212 D ++VR I RT+ ++VNSP+NPTG++ L+ LA L D ++SDE+YEH++++ Sbjct: 151 DWDQVRGLINERTRMIIVNSPHNPTGSLLTAADLDRLAGLVRGTDIVILSDEVYEHIVFD 210 Query: 213 GEHFSPGRVAPE---HTLTVNGAAKAFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPDT 269 GE + E ++ V+ K + +TGW+IGY GP ++ V + + Sbjct: 211 GERHASLCAHAELAVRSIVVSSFGKTYHITGWKIGYVVGPAALMAEFRKVHQFNVFTVHA 270 Query: 270 IAQWATLEALTNQEASRAFVEMAREAYRRRRDLLLEGLTALGLKAVRPSGAFYVLMDTSP 329 +Q A E + Q+ASR A Y+ +RD + + A + G ++ L + Sbjct: 271 PSQLAIAEYM--QDASRHLGLAA--FYQAKRDHFRQLMAATPFTLLPCRGTYFQLARYAG 326 Query: 330 IA--PDEVRAAERLLEAGVAVVPGTDFAAFGH----VRLSYATSEENLRKALERFAR 380 ++ PD A E GVAV+P + F A G VR +A E L A+ER + Sbjct: 327 MSDLPDRAFAEWLTREVGVAVIPVSVFNADGRDDQVVRFCFAKREATLEAAVERLCK 383 Lambda K H 0.317 0.133 0.379 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: 335 Number of extensions: 19 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: 385 Length of database: 385 Length adjustment: 30 Effective length of query: 355 Effective length of database: 355 Effective search space: 126025 Effective search space used: 126025 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