Align aspartate-prephenate aminotransferase (EC 2.6.1.78) (characterized)
to candidate YP_001325861.1 Smed_0167 aspartate aminotransferase
Query= BRENDA::Q56232 (385 letters) >NCBI__GCF_000017145.1:YP_001325861.1 Length = 388 Score = 172 bits (436), Expect = 1e-47 Identities = 119/383 (31%), Positives = 189/383 (49%), Gaps = 13/383 (3%) Query: 10 AMKPSATVAVNAKALEL---RRQGVDLVALTAGEPDFDTPEHVKEAARRALAQGKTKYAP 66 ++ P AT A + +E+ R L+ L GE D TP+ V AA AL G+T Y Sbjct: 6 SLSPRATAAPESGIVEVVNYARGREGLIPLWVGEGDLPTPDFVSRAAADALMGGETFYTW 65 Query: 67 PAGIPELREALAEKFRRENGLSVTPEETIVTVGGKQALFNLFQAILDPGDEVIVLSPYWV 126 GIP LREALA ++R +++PE VT G QA+ +++ PGDE+++L+P W Sbjct: 66 QRGIPPLREALARYYQRRFQKTLSPENFYVTGSGMQAIKLAIESVASPGDEMVLLTPAWP 125 Query: 127 SYPEMVRFAGGVVVEVETLPEEG-FVPDPERVRRAITPRTKALVVNSPNNPTGAVYPKEV 185 ++ +G V V E G + D R+ AI RT+AL +N+P+NPTG + Sbjct: 126 NFAAAADLSGVRPVAVPLRFEAGKWQLDLTRLEAAIGERTRALFINTPSNPTGWTATLDD 185 Query: 186 LEALARLAVEHDFYLVSDEIYEHLLYEG---EHFSPGRVAPEHTLTVNGAAKAFAMTGWR 242 L+++ LA +H ++V+DEIY Y G F + L VN +K ++MTGWR Sbjct: 186 LKSILALARKHGLWIVADEIYALYHYLGGRAPSFLDVMEEEDRILFVNSFSKNWSMTGWR 245 Query: 243 IGYACGPKEVIKAMASVSSQSTTSPDTIAQWATLEALTNQEASRAFVEMAREAYRRRRDL 302 +G+ P + + + ++ ST+ +AQ+ A E FV+ +R RD Sbjct: 246 VGWIVAPPAMGQVLENLIQYSTSG---VAQFMQRGAAVALEEGDGFVDANIAKAKRNRDT 302 Query: 303 LLEGLTALG-LKAVRPSGAFYVLMDTSPIAPDEVRAAERLLEAGVAVVPGTDFAAFG--H 359 L + L A ++ ++P GA Y + +A A + + GV + PGT F G Sbjct: 303 LCDALIATNRVETLKPDGALYAFLKIDGVADSRAAAIDIVDRTGVGLAPGTAFGEGGALF 362 Query: 360 VRLSYATSEENLRKALERFARVL 382 +R + + + +A ER R + Sbjct: 363 MRACFLRDPDQIAEAAERLQRYI 385 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: 368 Number of extensions: 17 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: 388 Length adjustment: 30 Effective length of query: 355 Effective length of database: 358 Effective search space: 127090 Effective search space used: 127090 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