Align aspartate transaminase (EC 2.6.1.1) (characterized)
to candidate Dsui_2433 Dsui_2433 aspartate/tyrosine/aromatic aminotransferase
Query= BRENDA::W0PFQ7 (399 letters) >FitnessBrowser__PS:Dsui_2433 Length = 402 Score = 544 bits (1401), Expect = e-159 Identities = 267/398 (67%), Positives = 318/398 (79%) Query: 2 TTLFNAVELAPRDPILGLNEQYNADTRDTKVNLGVGVYYDDNGKIPLLKAVQEAERQRVE 61 +++F +VE+APRDPILGL E +NADTR TKVNLGVGVYYDDNGKIPLL AV+ AE+ R+E Sbjct: 3 SSIFASVEMAPRDPILGLTEAFNADTRATKVNLGVGVYYDDNGKIPLLAAVKAAEKARLE 62 Query: 62 AHAARGYLPIEGIGNYNKGAQELLFGKDSDVITQGRALTFQALGGTGALKIGADFLKQLQ 121 RGY PIEG+ YN+ Q LLFG S+++ GR +T +ALGGTGALKIGADFLK++ Sbjct: 63 TMPPRGYQPIEGLNAYNQAVQNLLFGAGSELLAAGRVITAEALGGTGALKIGADFLKRIS 122 Query: 122 PDSTVYISDPSWENHRALFERAGFKVETYSYYDAATHGLNFDGFAASVKAMPEGSIIVLH 181 P++ VYISDPSWENHRALFE AGF VE Y YYDAAT G+NF G + ++ + GSII+LH Sbjct: 123 PNAKVYISDPSWENHRALFESAGFVVENYPYYDAATRGVNFAGMKSFLEGLAAGSIIILH 182 Query: 182 ACCHNPTGVDPSPEQWQQIATLVKERNLVPFLDIAYQGFGAGLQEDAAVVRLFADLGMSM 241 ACCHNPTG D S QWQ++ + K + LVPFLD+AYQGF G+ DA VR F+ G+ Sbjct: 183 ACCHNPTGADLSDAQWQEVVDVCKAKGLVPFLDMAYQGFADGIDADAVAVRAFSASGLQF 242 Query: 242 FISSSFSKSFSLYGERVGALTVVTSSTDEASRVLSQIKRVIRTNYSNPPTHGGMVVAQIL 301 F+SSSFSKSFSLYGERVGAL+VVT+S +E++RVLSQ+KRVIRTNYSNPPTHGG VVA +L Sbjct: 243 FVSSSFSKSFSLYGERVGALSVVTASKEESARVLSQVKRVIRTNYSNPPTHGGAVVAAVL 302 Query: 302 NTPELFAQWESELAQMRDRIREMRKQLTDKLNAAGVKQDFNFVMAQRGMFSYSGLTKEQV 361 +TPEL WE ELA MRDRIR MR L DKL A GV QDF+FV+ QRGMFSY+GLT QV Sbjct: 303 STPELRQMWEDELAGMRDRIRAMRVALVDKLKAKGVAQDFSFVVKQRGMFSYTGLTSAQV 362 Query: 362 ERLRTEHGIYAVNSGRICVAALNSRNIDSVVKAIAAVL 399 + LR E GIYAV +GRIC+AALNS+NID+VV AIAAVL Sbjct: 363 DVLRNEFGIYAVGTGRICLAALNSKNIDAVVDAIAAVL 400 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: 478 Number of extensions: 14 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: 402 Length adjustment: 31 Effective length of query: 368 Effective length of database: 371 Effective search space: 136528 Effective search space used: 136528 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