Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011157996.1 TX73_RS12470 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000195775.1:WP_011157996.1 Length = 396 Score = 345 bits (884), Expect = 2e-99 Identities = 187/380 (49%), Positives = 246/380 (64%), Gaps = 6/380 (1%) Query: 8 RAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVA 67 R+ VPPF VMDV AA + G ++++ GQP A AP AAA AAL +++ Y+ A Sbjct: 19 RSDVPPFMVMDVMAAADRIEAAGGHVIHMEVGQPWAPAPRAALAAAHAALDSSRIDYTSA 78 Query: 68 LGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPC 127 LGIP LR IA Y+ + V+PD +V+TTGSSG F+L+FLA F+ GDRVA+ PGYP Sbjct: 79 LGIPSLRARIAKHYRETYRCDVDPDRIVVTTGSSGAFILSFLALFEPGDRVAVTVPGYPP 138 Query: 128 YRNILSALGCEVVEIPCGPQTRFQPTAQML--AEIDPPLRGVVVASPANPTGTVIPPEEL 185 YR+IL+ALGC V I +TR T + L A PL+GV+V SPANPTGT++ E L Sbjct: 139 YRHILNALGCVPVPIETHSETRHALTGEALLAAHRKAPLKGVLVGSPANPTGTMMTREAL 198 Query: 186 AAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGW 245 + + ++ +R ISDE+YHGL Y T A + S NAVV+NSFSKY+ MTGWR+GW Sbjct: 199 TELIAVAESEGIRFISDEIYHGLDYAFPAVT--AAELSPNAVVINSFSKYFCMTGWRVGW 256 Query: 246 LLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGL 305 +++P L R V+ L N I P LSQIAA +AF + AE + Y NR++L++GL Sbjct: 257 MVLPESLVRPVERLQQNLAISVPTLSQIAAEAAF--DGRAEMEAVKRGYEENRAILIEGL 314 Query: 306 RRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRI 365 + G+ P DGAFY+YADVS FTSDS F ++L + VA PGIDFD RG SFVR Sbjct: 315 PKAGLTEFLPADGAFYLYADVSAFTSDSYDFTKRMLEEARVAATPGIDFDPVRGKSFVRF 374 Query: 366 SFAGPSGDIEEALRRIGSWL 385 S+A + D+ EA+RRI +WL Sbjct: 375 SYARSADDMREAVRRITAWL 394 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: 456 Number of extensions: 19 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: 396 Length adjustment: 31 Effective length of query: 357 Effective length of database: 365 Effective search space: 130305 Effective search space used: 130305 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