Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012115472.1 XAUT_RS17635 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000017645.1:WP_012115472.1 Length = 393 Score = 344 bits (882), Expect = 3e-99 Identities = 190/380 (50%), Positives = 248/380 (65%), Gaps = 6/380 (1%) Query: 8 RAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVA 67 R+ V PF VMDV AA + G +++L GQP+A AP R AAAAAL Q+GY+ A Sbjct: 15 RSAVEPFIVMDVMEHAARIEAGGGHVIHLEVGQPAAPAPTVARRAAAAALEAGQVGYTAA 74 Query: 68 LGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPC 127 LGIP LR IA Y HG+ V+P+ VV+T GSSGGF+LAFLA F+ GDRVA+A+PGYP Sbjct: 75 LGIPALRARIARHYGEIHGVAVDPERVVVTHGSSGGFVLAFLALFEPGDRVAIAAPGYPP 134 Query: 128 YRNILSALGCEVVEIPCGPQTRFQPTAQMLAEI--DPPLRGVVVASPANPTGTVIPPEEL 185 YR++L ALGCE V I + R T + L E PL+GV+VASPANPTGT++ L Sbjct: 135 YRHVLHALGCEPVLIETRAEDRHALTPERLLEAHRKAPLKGVLVASPANPTGTMMDRAAL 194 Query: 186 AAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGW 245 A+ + ++ ISDE+YHGL Y P S A + + V+NSFSKY+ MTGWR+GW Sbjct: 195 TALHACARDLNLAFISDEIYHGLDY-AFPAVS-AVEIGEDVTVINSFSKYFCMTGWRVGW 252 Query: 246 LLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGL 305 ++VP + R ++ L N +I P LSQIAA +AF E AE D A+Y NR +L +GL Sbjct: 253 MVVPPGVSRTMERLQQNLSISVPTLSQIAADAAF--EGRAEMDLVKATYVENRRILTEGL 310 Query: 306 RRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRI 365 + G+ R P DGAFY+YADVS+FT DS AF ++L VA PG+DFD G F+RI Sbjct: 311 PQAGLKRFLPADGAFYLYADVSEFTDDSAAFARRMLDAAHVATTPGVDFDPFHGHQFLRI 370 Query: 366 SFAGPSGDIEEALRRIGSWL 385 S+AG + D+ EA+ RIG++L Sbjct: 371 SYAGSAPDMAEAVARIGAFL 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: 487 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: 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