Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate WP_014026152.1 PYRFU_RS02975 pyridoxal phosphate-dependent aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000223395.1:WP_014026152.1 Length = 401 Score = 167 bits (423), Expect = 5e-46 Identities = 124/401 (30%), Positives = 193/401 (48%), Gaps = 19/401 (4%) Query: 1 MRGLSRRV--QAMKPSATVAVNAKALELRRQGVDLVALTAGEPDFDTPEHVKEA-ARRAL 57 M +SRR + + T+A A E +R+ V + LT G+PD P+ + E A A Sbjct: 1 MARVSRRFLEDSSSGATTMAFAQLASEAKRKPV--IDLTLGQPDVTPPQTLVELLATEAR 58 Query: 58 AQGKTKYAPPAGIPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDE 117 G ++Y PP G+ E REA+A R G+ PE + G K + ++ D GD Sbjct: 59 GVGASRYPPPQGLAEYREAVASYMRDFYGVDAEPERVVALAGAKPGIAAAIYSVCDHGDA 118 Query: 118 VIVLSPYWVSYPEMVRFAGGVVVEVETLPEEG-FVPDPERVRRAITPRTKALV-VNSPNN 175 ++VL+P++ +Y R G V + G D + V++A LV VN+P+N Sbjct: 119 MLVLTPHFYAYVNAARMLGVKPVMARLRWDGGRLFIDEDEVKKAFEEHKPCLVIVNTPHN 178 Query: 176 PTGAVYPKEVLEALARLAVEHDFYLVSDEIYEHLLYEGEHFSPGR-VAPEHTLTVNGAAK 234 PTG +E L+ + LA EH+ ++SDE+Y L++ GEH R + E + + +K Sbjct: 179 PTGLHLDRETLKLIGDLASEHNTLVLSDEVYSWLVFRGEHVPLLRLLGEERVIHLESFSK 238 Query: 235 AFAMTGWRIGYACGPKEVIKAMASVSSQSTTSPDTIAQWATLEALT-NQEASRAFVEMAR 293 A+ GWR+G+ P+EV+KA +S T Q A + +T +E +VE R Sbjct: 239 TLAIPGWRVGFLYAPREVVKATVFFNSNVYTGIPRFIQLAVAKYITAYREDMVEYVERVR 298 Query: 294 EAYRRRRDLLLEGLTALG--LKAVRPSGAFYVLMDTSPIAPD-EVRAAERLL-----EAG 345 + Y RR + E L+ L + P+ F++ + V +AERL+ E G Sbjct: 299 KLYGRRARVFTEALSQLEDLIDVYEPAAGFFLFPRVERLIEKLGVGSAERLVELMAREVG 358 Query: 346 VAVVPGTDFAA--FGHVRLSYATSEENLRKALERFARVLGR 384 V VPGT F G++R+S E LR+A R + R Sbjct: 359 VLAVPGTVFGEEWRGYIRVSLTAPESRLREAAARIGELATR 399 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: 372 Number of extensions: 13 Number of successful extensions: 4 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: 401 Length adjustment: 31 Effective length of query: 354 Effective length of database: 370 Effective search space: 130980 Effective search space used: 130980 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