Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_050465852.1 AKL27_RS26210 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::W0PFQ7 (399 letters) >NCBI__GCF_001189915.1:WP_050465852.1 Length = 403 Score = 449 bits (1155), Expect = e-131 Identities = 217/397 (54%), Positives = 286/397 (72%), Gaps = 1/397 (0%) Query: 3 TLFNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVEA 62 +L A+ +APRDPILG+ E YN T K+NLGVGVYYDD GK+PLL+ V++AE ++ Sbjct: 8 SLLAAITMAPRDPILGITEAYNRSTHPAKINLGVGVYYDDQGKVPLLQCVRQAEADLLQH 67 Query: 63 HAARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQP 122 YLPIEG+ YN + LF + + R +T Q GGTGALK+GADFL++ P Sbjct: 68 PKPHTYLPIEGLAAYNNAVRRQLFD-GTRAFDEQRVITLQTAGGTGALKVGADFLQRFFP 126 Query: 123 DSTVYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLHA 182 D+ V+ISDPSWENH ALFE AGF V Y YYDAA + LNF A+++ +P G I++LHA Sbjct: 127 DAQVWISDPSWENHAALFEAAGFTVNAYPYYDAARNDLNFPAMLATLEQIPAGDIVLLHA 186 Query: 183 CCHNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSMF 242 CCHNPTG+D QWQQ+ ++ R L+PFLD+AYQGFG L ED VV+ FAD G+++F Sbjct: 187 CCHNPTGLDLDDSQWQQVLEIITRRRLIPFLDMAYQGFGGSLAEDGKVVQRFADSGLTVF 246 Query: 243 ISSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQILN 302 +SS+FSKSFSLY ER+GAL+VV++S DEA+R+LSQ+KR IRTNYS+PP HG +VA +L Sbjct: 247 VSSTFSKSFSLYSERIGALSVVSASPDEAARLLSQLKRTIRTNYSSPPGHGAAIVAAVLG 306 Query: 303 TPELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQVE 362 + +L A WE ELAQMR+RI MR+QL +L +DF+F+ Q G+FSY+GL EQV Sbjct: 307 SDQLRALWEQELAQMRERITGMRQQLRARLQQHLPARDFSFLTRQAGLFSYTGLQPEQVT 366 Query: 363 RLRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAVL 399 RLR E I+ + +GRICVAA+NS N+D++ A+A V+ Sbjct: 367 RLREEFEIHTLGTGRICVAAVNSGNLDTIATALARVM 403 Lambda K H 0.318 0.134 0.385 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: 450 Number of extensions: 15 Number of successful extensions: 2 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: 399 Length of database: 403 Length adjustment: 31 Effective length of query: 368 Effective length of database: 372 Effective search space: 136896 Effective search space used: 136896 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