Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_013537316.1 THEAM_RS02845 aminotransferase class I and II
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000185805.1:WP_013537316.1 Length = 369 Score = 264 bits (675), Expect = 3e-75 Identities = 148/375 (39%), Positives = 210/375 (56%), Gaps = 12/375 (3%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PFYVM V A E ++ ++++L G+P PE V+ AA L +L Y+ A GI Sbjct: 6 IEPFYVMQVLERAKELEKRGREVIHLEIGEPDLPVPERVKRKAAELLTETELKYTPATGI 65 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P+L++AIA Y R+ + VEP+ VV+T GSS G + A ++ PGYPCY+N Sbjct: 66 PKLKEAIAEFYYSRYRVVVEPEQVVVTPGSSPGLVAALKTVSRLVGEISFTDPGYPCYKN 125 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIAS 190 IL LG E V +P GP+ F+ +++ P ++V SPANP+G V EL ++ Sbjct: 126 ILKVLGEEGVALPVGPENSFKVRP---FQVNTP--ALIVNSPANPSGAVYTKRELEKLSK 180 Query: 191 WCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPT 250 LISDE+YHGL Y + A + +RN +VVN FSK++ MTGWR+GWL+ Sbjct: 181 -----RAFLISDEIYHGLTY--GEEAPSALEVTRNCIVVNGFSKFFLMTGWRVGWLIASP 233 Query: 251 VLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGI 310 + ++ + N I PP LSQ+AAV F+ E +E N+ + + +LL+GL+ IG Sbjct: 234 DMVEPINAILQNTVIAPPTLSQLAAVECFSEEVLSELQENVKVFRKRKEILLNGLKEIGF 293 Query: 311 DRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGP 370 GAFY++AD S FT DS F +LL T VA+ PG DF FVR SF Sbjct: 294 KVPVEPKGAFYIWADASPFTEDSFKFAFELLERTSVAVTPGRDFGYNGTEKFVRFSFCTE 353 Query: 371 SGDIEEALRRIGSWL 385 + I EAL R+ S+L Sbjct: 354 TEKILEALERLYSYL 368 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: 375 Number of extensions: 10 Number of successful extensions: 4 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: 369 Length adjustment: 30 Effective length of query: 358 Effective length of database: 339 Effective search space: 121362 Effective search space used: 121362 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