Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate WP_028997539.1 H537_RS0108305 amino acid aminotransferase
Query= BRENDA::W0PFQ7 (399 letters) >NCBI__GCF_000430725.1:WP_028997539.1 Length = 399 Score = 523 bits (1347), Expect = e-153 Identities = 256/396 (64%), Positives = 308/396 (77%) Query: 3 TLFNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVEA 62 +LF AVE+APRDPILGLNEQ+ AD KVNLGVGVY+DD GK+PLLK V AE+Q +EA Sbjct: 2 SLFAAVEMAPRDPILGLNEQFAADPNPAKVNLGVGVYFDDEGKLPLLKCVAAAEQQLLEA 61 Query: 63 HAARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQP 122 RGYLPI+GI Y+K Q L+FG DSD + GR T QALGGTG LKIGADFLK++ P Sbjct: 62 KKPRGYLPIDGIAAYDKAVQGLVFGADSDAVKGGRVATVQALGGTGGLKIGADFLKRVNP 121 Query: 123 DSTVYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLHA 182 + V ISDPSWENHRALF AGF+V TY YYDA G+ FD A++++ +G+++VLHA Sbjct: 122 GAKVLISDPSWENHRALFTNAGFEVGTYPYYDADKRGVRFDDMVAALRSAAKGTVVVLHA 181 Query: 183 CCHNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSMF 242 CCHNPTG D +PEQW Q+ VK+ LV FLD+AYQGFG G+ ED AV++ F D G+ F Sbjct: 182 CCHNPTGYDITPEQWTQVVAAVKDAGLVAFLDMAYQGFGEGIAEDGAVIQQFLDAGIDFF 241 Query: 243 ISSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQILN 302 +S+SFSKSFSLYGERVGAL+VV S DEA+RVLSQ+K VIRTNYSNPPT G VVA +L Sbjct: 242 VSTSFSKSFSLYGERVGALSVVCDSADEAARVLSQLKIVIRTNYSNPPTFGAQVVATVLT 301 Query: 303 TPELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQVE 362 TP L AQWE ELA MR RI+ MR L +KL AAGVKQD ++++ Q+GMFSYSGL KEQ++ Sbjct: 302 TPSLRAQWEEELAGMRQRIKLMRSLLVEKLQAAGVKQDLSYIVRQKGMFSYSGLGKEQMQ 361 Query: 363 RLRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAV 398 RLR+E G+Y V+SGRICVAALNSRNID+V A+A V Sbjct: 362 RLRSEFGVYGVDSGRICVAALNSRNIDAVASAMAQV 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: 486 Number of extensions: 17 Number of successful extensions: 1 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: 399 Length adjustment: 31 Effective length of query: 368 Effective length of database: 368 Effective search space: 135424 Effective search space used: 135424 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 Jul 25 2024. The underlying query database was built on Jul 25 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