Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_057509011.1 ABB28_RS12960 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::W0PFQ7 (399 letters) >NCBI__GCF_001431535.1:WP_057509011.1 Length = 400 Score = 449 bits (1155), Expect = e-131 Identities = 215/397 (54%), Positives = 296/397 (74%), Gaps = 2/397 (0%) Query: 3 TLFNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVEA 62 + F VEL P DPILGL E YNAD+R TKVNLGVG+YYD++G+IPLL+AV++ E+Q Sbjct: 2 SFFANVELVPGDPILGLTEAYNADSRPTKVNLGVGIYYDESGRIPLLRAVKQIEQQLATE 61 Query: 63 HAARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQP 122 RGYLPI+G+ Y + +EL+FGKDS ++ GR T Q +GG+GAL++GA+ L +L P Sbjct: 62 AKPRGYLPIDGLPAYTQATRELVFGKDSPLLAAGRVATTQTVGGSGALRVGAELLNKLLP 121 Query: 123 DSTVYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLHA 182 +T+ IS+PSWENHRA+F AGF V YSY+DA THG++F A ++ + G++++LHA Sbjct: 122 HATIAISNPSWENHRAVFGAAGFDVVEYSYFDAQTHGVDFPAMLADLQKLQPGTVVLLHA 181 Query: 183 CCHNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSMF 242 CCHNPTG D + +QW+Q+A ++KE+ L PF+D+AYQGF G+++D A VR+ A+ G+ F Sbjct: 182 CCHNPTGADLTVDQWKQVAEVLKEQQLFPFIDMAYQGFDKGIEQDGAAVRIIAEAGIDSF 241 Query: 243 -ISSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQIL 301 +++S+SKSFSLYGERVGAL++V + EA V SQIKR+IRT YS+P HG +VA +L Sbjct: 242 VVANSYSKSFSLYGERVGALSIVAPNATEAKAVQSQIKRIIRTIYSSPSNHGAALVAGVL 301 Query: 302 NTPELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQV 361 N+PEL WE+EL +MR+RI +R L D+L A G +F F+ Q GMFSYSGL++ QV Sbjct: 302 NSPELRTLWEAELTEMRERIHALRHGLVDRLAALGA-PEFAFINDQAGMFSYSGLSRVQV 360 Query: 362 ERLRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAV 398 E+LR ++GIYAV +GRICVAAL+ N+D V +A+A V Sbjct: 361 EKLRDDYGIYAVGTGRICVAALSQSNLDYVAQAVANV 397 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: 448 Number of extensions: 15 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: 399 Length of database: 400 Length adjustment: 31 Effective length of query: 368 Effective length of database: 369 Effective search space: 135792 Effective search space used: 135792 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