Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012974929.1 AZL_RS12610 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000010725.1:WP_012974929.1 Length = 387 Score = 409 bits (1050), Expect = e-119 Identities = 209/382 (54%), Positives = 275/382 (71%), Gaps = 5/382 (1%) Query: 4 RVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPV-RAAAAAALHLNQL 62 +V+ R +PPF+VM+V AAAER+ +++++ GQPS+GAP+ V +AAA A + + L Sbjct: 6 KVSKRGAIPPFFVMEVMRAAAEREAAGLEVLHMEVGQPSSGAPKGVVQAAATAVVGSDPL 65 Query: 63 GYSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMAS 122 GY+ ALGIP LR AIA Y+ R+G+ V VV+TTGSSG F L FLA FD GDRVAMAS Sbjct: 66 GYTGALGIPPLRAAIAKWYKDRYGVEVPERRVVVTTGSSGAFQLGFLAAFDPGDRVAMAS 125 Query: 123 PGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPP 182 P YP YR+ L+A G VE+P GP+ RFQPT +L +D P++G++VASPANPTGT++ Sbjct: 126 PSYPAYRHTLTAAGVIPVELPTGPEHRFQPTVALLEALDEPVQGLIVASPANPTGTMLSR 185 Query: 183 EELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWR 242 EEL A++ WC A+ VR++SDE+YHGL Y G + A + + A+VVNSFSKY++MTGWR Sbjct: 186 EELTALSDWCRANGVRMVSDEIYHGLTY-GTDAVTAA-EVNDQALVVNSFSKYFSMTGWR 243 Query: 243 LGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLL 302 LGW++VP L R+V+CL N I P LSQ++AV+AF + T E DG++A YA NR+LLL Sbjct: 244 LGWMIVPDDLLRSVECLAQNLFISAPTLSQVSAVAAF--DCTEELDGHVARYARNRALLL 301 Query: 303 DGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSF 362 + L + G +LAP DGAFY+YADVSD T DS A +LL +TG+A PGIDFDTARG F Sbjct: 302 EELPKAGFAKLAPADGAFYIYADVSDLTDDSEALAKRLLEETGIACTPGIDFDTARGRRF 361 Query: 363 VRISFAGPSGDIEEALRRIGSW 384 +R SFAG I EA RR+ +W Sbjct: 362 LRFSFAGSEETIAEAARRLIAW 383 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: 477 Number of extensions: 16 Number of successful extensions: 5 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: 387 Length adjustment: 30 Effective length of query: 358 Effective length of database: 357 Effective search space: 127806 Effective search space used: 127806 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