Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_036257785.1 DL86_RS02895 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000746085.1:WP_036257785.1 Length = 396 Score = 340 bits (872), Expect = 4e-98 Identities = 181/384 (47%), Positives = 243/384 (63%), Gaps = 6/384 (1%) Query: 4 RVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLG 63 +++ R+ V PF +DV A R+ D+++L G+P + P VR AA AAL ++G Sbjct: 16 QISRRSNVAPFMALDVLANARRREAQGQDIIHLEIGEPGSPPPRAVREAAMAALDGRRIG 75 Query: 64 YSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASP 123 Y+ ALG P LR+ IA Y+ +G+ V P+ +V+T GSSGGFLLAFL+ FDAG RVA+A+P Sbjct: 76 YTEALGRPSLRERIARHYRDAYGLAVAPEHIVVTNGSSGGFLLAFLSLFDAGARVAIAAP 135 Query: 124 GYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLR--GVVVASPANPTGTVIP 181 GYP YRNIL ALG E V I TRF T M+ + R G+++ SPANP+GT++ Sbjct: 136 GYPAYRNILEALGIETVTIEVSEATRFVVTPSMIEAVHAKTRLDGILLMSPANPSGTMMS 195 Query: 182 PEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGW 241 E L + + C+ V ISDEVYHGL Y +T A + S +V NSFSKY+ MTGW Sbjct: 196 AEALRDVCAACERLGVAFISDEVYHGLTYGQPART--ALEFSSEVIVANSFSKYFCMTGW 253 Query: 242 RLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLL 301 R+GWL++P + R V+ L N + +LSQI A + F +A + L+ YA NR++L Sbjct: 254 RIGWLVLPGHMVRTVERLQQNLAVSVGLLSQIGAEAVF--DAQEDLQRVLSGYARNRAIL 311 Query: 302 LDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGS 361 L+ L +G+ P DGAFY+Y DVS T DS FC+K+L + GVA PG+DFD RG Sbjct: 312 LNELPDMGLGGFHPVDGAFYIYVDVSRLTDDSGHFCAKMLDEIGVAATPGLDFDRTRGRG 371 Query: 362 FVRISFAGPSGDIEEALRRIGSWL 385 VR SFAGP GDI EA+RR+ SWL Sbjct: 372 AVRFSFAGPEGDIVEAMRRLKSWL 395 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: 469 Number of extensions: 26 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