Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate Dsui_0132 Dsui_0132 aspartate/tyrosine/aromatic aminotransferase
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__PS:Dsui_0132 Length = 385 Score = 264 bits (674), Expect = 4e-75 Identities = 154/375 (41%), Positives = 206/375 (54%), Gaps = 5/375 (1%) Query: 9 AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVAL 68 A + PF+VM++ A E + D++++ G+P PEP+ AAA L ++ Y+ AL Sbjct: 9 ADIAPFHVMELLGRARELEAQGRDIIHMEVGEPDFPTPEPILAAAREFLQDGRVFYTPAL 68 Query: 69 GIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDA-GDRVAMASPGYPC 127 G+PELR+AI+ Y++R+GI V + IT G+SG LA LAC A G + PGYPC Sbjct: 69 GLPELREAISGFYRQRYGIAVPASRIAITAGASGALTLA-LACLAAPGSEWLLTDPGYPC 127 Query: 128 YRNILSALGCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGTVIPPEELA 186 R+ + A V IP G + FQPT L + + G + ASPANPTGT++ ELA Sbjct: 128 NRHFVRAFEGVPVSIPVGAASNFQPTRLDLEQHWNERTAGALFASPANPTGTMLDAAELA 187 Query: 187 AIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWL 246 IA + +LI DE+YHGL Y G T+ A N VV SFSKY+ MTGWRLGWL Sbjct: 188 DIADFVRQRQGQLIIDEIYHGLTYNGDAPTALA--AGDNIFVVQSFSKYFQMTGWRLGWL 245 Query: 247 LVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLR 306 ++P R V+ L N I +Q AA++AF PE A + A + R L L Sbjct: 246 VIPEPFVRDVEKLAQNLFISASTPAQHAALAAFQPETIALLEQRRAEFKARRDYLAPALE 305 Query: 307 RIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRIS 366 IG A +GAFY+YAD S T DS F +LL + GVAI PGIDF S VR + Sbjct: 306 AIGFRITAQPEGAFYLYADCSTLTDDSFGFARRLLEEAGVAITPGIDFGNHGASSHVRFA 365 Query: 367 FAGPSGDIEEALRRI 381 + + E + RI Sbjct: 366 YTNAQARLAEGVERI 380 Lambda K H 0.321 0.136 0.416 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: 430 Number of extensions: 22 Number of successful extensions: 3 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: 388 Length of database: 385 Length adjustment: 30 Effective length of query: 358 Effective length of database: 355 Effective search space: 127090 Effective search space used: 127090 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.4 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.9 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