Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Ac3H11_4115 Aromatic-amino-acid aminotransferase (EC 2.6.1.57)
Query= BRENDA::W0PFQ7 (399 letters) >FitnessBrowser__acidovorax_3H11:Ac3H11_4115 Length = 398 Score = 520 bits (1340), Expect = e-152 Identities = 251/397 (63%), Positives = 309/397 (77%) Query: 3 TLFNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVEA 62 +LF AVE+APRDPILGLNEQ+NADT KVNLGVGVY+DDNGK+PLL+ VQ AE+ + Sbjct: 2 SLFTAVEMAPRDPILGLNEQFNADTNPNKVNLGVGVYFDDNGKLPLLQCVQAAEKTMMST 61 Query: 63 HAARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQP 122 ARGYLPI+GI Y+ + L+FG DS+ +T GR T QA+GGTG LKIGADFLK++ P Sbjct: 62 PTARGYLPIDGIVAYDNAVKSLVFGADSEPVTSGRVATVQAIGGTGGLKIGADFLKKVSP 121 Query: 123 DSTVYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLHA 182 + V ISDPSWENHRALF AGF+V+TY+YYDA G+NF+GF AS+ A G+I+VLHA Sbjct: 122 SAKVLISDPSWENHRALFTNAGFEVDTYAYYDAEKRGVNFEGFLASLNAAAPGTIVVLHA 181 Query: 183 CCHNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSMF 242 CCHNPTG D + QW Q+ VK + L PFLD+AYQGFG G+ ED AV+ F G++ F Sbjct: 182 CCHNPTGYDITAAQWDQVIAAVKAKGLTPFLDMAYQGFGHGIAEDGAVIGKFVAAGLNFF 241 Query: 243 ISSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQILN 302 +S+SFSKSFSLYGERVG L+V+ + +EASRVLSQ+K VIRTNYSNPP HGG VVA +LN Sbjct: 242 VSTSFSKSFSLYGERVGGLSVLCADKEEASRVLSQLKIVIRTNYSNPPIHGGAVVAAVLN 301 Query: 303 TPELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQVE 362 PEL A WE ELA+MR RI+ MR++L D L AAGVKQD +F+ Q GMFSYSGL+K+Q+ Sbjct: 302 NPELRAMWEQELAEMRVRIKAMRQKLVDGLKAAGVKQDMSFITTQIGMFSYSGLSKDQMV 361 Query: 363 RLRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAVL 399 RLR E G+Y ++GR+CVAALNS+NID V +AIA V+ Sbjct: 362 RLRNEFGVYGTDTGRMCVAALNSKNIDYVCQAIAKVV 398 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: 502 Number of extensions: 15 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: 398 Length adjustment: 31 Effective length of query: 368 Effective length of database: 367 Effective search space: 135056 Effective search space used: 135056 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 09 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