Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate GFF1262 Psest_1295 Aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::W0PFQ7 (399 letters) >FitnessBrowser__psRCH2:GFF1262 Length = 398 Score = 541 bits (1393), Expect = e-158 Identities = 262/397 (65%), Positives = 321/397 (80%) Query: 3 TLFNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVEA 62 +LF+AVE+APRDPILGLNE +NADTR KVNLGVGVYY++ G+IPLL+AV EAE R+ A Sbjct: 2 SLFSAVEMAPRDPILGLNEAFNADTRPNKVNLGVGVYYNEEGRIPLLRAVVEAEHARIAA 61 Query: 63 HAARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQP 122 +A RGYLPIEGI Y+ Q+LLFG DS +I +GR +T QALGGTGALK+GADFLK+L P Sbjct: 62 NAPRGYLPIEGIAAYDAAVQKLLFGNDSSLIAEGRVVTTQALGGTGALKVGADFLKRLLP 121 Query: 123 DSTVYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLHA 182 D+ V IS+PSWENHRALFE AGF V+ YSYYDA+ HG++ G +K +P SI+VLHA Sbjct: 122 DAVVAISNPSWENHRALFESAGFPVQNYSYYDASNHGIDRAGLLQDLKNLPPRSIVVLHA 181 Query: 183 CCHNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSMF 242 CCHNPTGVD + E W+QI +++ ++ VPF+DIAYQGFG ++EDAA VRLFA+ GM+ F Sbjct: 182 CCHNPTGVDLNLEDWKQILEVLRAQDHVPFIDIAYQGFGDSIEEDAAAVRLFAESGMTFF 241 Query: 243 ISSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQILN 302 +SSSFSKSFSLYGERVGAL++VT S +E++RVLSQ+KRVIRTNYSNPPTHG +VA +LN Sbjct: 242 VSSSFSKSFSLYGERVGALSMVTQSREESARVLSQVKRVIRTNYSNPPTHGATIVASVLN 301 Query: 303 TPELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQVE 362 +PEL A WE+EL +MR RIRE+R + ++L A G K DF+FV AQRGMFSYSGLT EQVE Sbjct: 302 SPELRAMWEAELGEMRSRIRELRLSMVEQLTAKGAKTDFSFVAAQRGMFSYSGLTAEQVE 361 Query: 363 RLRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAVL 399 RLR E G+YA+++GRIC AALN NI V AI VL Sbjct: 362 RLRVEFGVYAISTGRICAAALNRSNIGHVTDAIVQVL 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: 475 Number of extensions: 13 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