Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_041750777.1 BBTA_RS19685 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000015165.1:WP_041750777.1 Length = 399 Score = 345 bits (886), Expect = e-99 Identities = 184/380 (48%), Positives = 245/380 (64%), Gaps = 6/380 (1%) Query: 8 RAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVA 67 R+ VPPF VMDV AA + + G ++++ GQP+A AP AAA AAL ++ Y+ A Sbjct: 23 RSNVPPFMVMDVMAAAERIEASGGHVIHMEVGQPAAPAPRTALAAAHAALDQARIDYTSA 82 Query: 68 LGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPC 127 LG+P LR IA Y+ +G ++P +VITTGSS GF+LAFLA F+ GDRVA+ PGYP Sbjct: 83 LGLPSLRGRIARHYRETYGCDIDPGRIVITTGSSAGFILAFLAMFEPGDRVAVTVPGYPP 142 Query: 128 YRNILSALGCEVVEIPCGPQTRFQPTAQML--AEIDPPLRGVVVASPANPTGTVIPPEEL 185 YR+IL+ALGCE V I +TR T + L A PL+GV+VASPANPTGT++ L Sbjct: 143 YRHILTALGCEPVLIETTAETRHALTGEALLAAHRKTPLKGVLVASPANPTGTMMSRAAL 202 Query: 186 AAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGW 245 + + + +R ISDE+YHGL Y T A Q + +A+++NSFSKY+ MTGWR+GW Sbjct: 203 GDVIAAARDAGIRFISDEIYHGLDYAFPAVT--AAQLTADALIINSFSKYFCMTGWRVGW 260 Query: 246 LLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGL 305 ++VP L R ++ L N I P LSQIAA +AF + E DG Y NR +L++G Sbjct: 261 MVVPDALVRPIERLQQNLAISVPTLSQIAAEAAF--DGRPEMDGIKHGYQENRRILIEGF 318 Query: 306 RRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRI 365 + G+ R P DGAFY+YADVSDFT DSL F ++L +T VA PG+DFD G +FVR Sbjct: 319 PKAGLSRFLPADGAFYLYADVSDFTKDSLDFAKRMLEETHVAATPGVDFDPIHGRNFVRF 378 Query: 366 SFAGPSGDIEEALRRIGSWL 385 S+A + D+ EA+ RI WL Sbjct: 379 SYARSAEDMREAVARIARWL 398 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: 485 Number of extensions: 20 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: 399 Length adjustment: 31 Effective length of query: 357 Effective length of database: 368 Effective search space: 131376 Effective search space used: 131376 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