Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_005460356.1 SACCYDRAFT_RS24455 aspartate aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000244975.1:WP_005460356.1 Length = 393 Score = 469 bits (1207), Expect = e-137 Identities = 232/381 (60%), Positives = 283/381 (74%), Gaps = 3/381 (0%) Query: 8 RAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVA 67 R+ V PF+VM+V AA ERQRTHGD++ L AGQP++GAP PV AA AL N LGY+ Sbjct: 13 RSDVAPFHVMEVLSAAKERQRTHGDVIALCAGQPTSGAPRPVLEAAQRALRDNDLGYTPQ 72 Query: 68 LGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPC 127 LGIPELR+AIA Y R +G+ V PD V++TTGSSGGFLL+FLA FDAG R+AMA PGYP Sbjct: 73 LGIPELREAIAGHYARWYGLAVSPDDVIVTTGSSGGFLLSFLAAFDAGARIAMARPGYPA 132 Query: 128 YRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAA 187 YRN+LS+LGCEVVE TRFQPT ++L + L GV+VASP+NPTGTV+P +EL A Sbjct: 133 YRNLLSSLGCEVVEFDTDVSTRFQPTTELLDGLGE-LHGVIVASPSNPTGTVLPADELVA 191 Query: 188 IASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLL 247 IA WCD V+L+SDE+YHG+ Y+ Q AWQTS AVV+ SFSKY+ MTGWRLGW L Sbjct: 192 IARWCDERGVQLVSDEIYHGISYEA--QVGSAWQTSTEAVVLGSFSKYFGMTGWRLGWAL 249 Query: 248 VPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRR 307 VP L RAVD LTGN+ IC P L+Q AAV+AFT ++ AE D N+A Y NR LLL+GL Sbjct: 250 VPQRLHRAVDVLTGNYNICAPALAQQAAVAAFTDDSYAELDANVARYRANRDLLLEGLAD 309 Query: 308 IGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISF 367 IG+ ++AP DGAFY Y DVS+ T DSLA+C +LL DTGVAI PG+DFD GG FVR+SF Sbjct: 310 IGLGKVAPVDGAFYAYVDVSEHTDDSLAWCRRLLDDTGVAITPGVDFDPVHGGRFVRLSF 369 Query: 368 AGPSGDIEEALRRIGSWLPSQ 388 A ++ +A++RIG WL Q Sbjct: 370 ACSRAELAQAVQRIGGWLSRQ 390 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: 529 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: 393 Length adjustment: 31 Effective length of query: 357 Effective length of database: 362 Effective search space: 129234 Effective search space used: 129234 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 10 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