Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_034996772.1 DL88_RS12710 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000745425.1:WP_034996772.1 Length = 389 Score = 355 bits (910), Expect = e-102 Identities = 184/386 (47%), Positives = 247/386 (63%), Gaps = 6/386 (1%) Query: 4 RVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLG 63 R + R+ + PF +D+ A +R+R ++V++ G+P A P VR A L ++G Sbjct: 8 RSSSRSAMAPFLALDILNQATQREREGQNIVHMEVGEPGAATPALVREAVQEELARGRIG 67 Query: 64 YSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASP 123 Y+ ALG P LR IA Y+ +G+ V P+ V +T GSSGGF+LAFLA FDAG R+ + SP Sbjct: 68 YTEALGRPSLRARIARHYRETYGVEVPPERVAVTIGSSGGFMLAFLAGFDAGARIGVQSP 127 Query: 124 GYPCYRNILSALGCEVVEIPCGPQTRFQPTAQML--AEIDPPLRGVVVASPANPTGTVIP 181 GYP YRNI ALG E V I +R TA M+ + PL G+++ SPANPTGT++ Sbjct: 128 GYPAYRNIFDALGLEAVVIETNGASRHVVTAAMIEATHAEKPLDGLLLMSPANPTGTMMS 187 Query: 182 PEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGW 241 PE+L A+ + CD + +SDEVYHGL Y +T A + S +V NSFSKYY MTGW Sbjct: 188 PEDLQAVCAVCDRLGITFVSDEVYHGLTYGEPAET--ALKFSDRVIVANSFSKYYCMTGW 245 Query: 242 RLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLL 301 R+GWL+VP R ++ L N I P LSQ+AA +AF +A E A YA NR+ L Sbjct: 246 RVGWLIVPEEFVRPIERLQQNLAISVPYLSQVAAEAAF--DARDELQLIKAGYAANRNFL 303 Query: 302 LDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGS 361 L+ L +IG+ P DGAFY+YADVS FT+DSL F ++L +TG+A+ PG+DFD RG S Sbjct: 304 LNSLPQIGLSEFHPVDGAFYIYADVSRFTNDSLDFSRRMLDETGIAVTPGLDFDRNRGNS 363 Query: 362 FVRISFAGPSGDIEEALRRIGSWLPS 387 F+R+SFAGP D+ EA+ R+G WLPS Sbjct: 364 FIRLSFAGPERDMVEAVSRLGLWLPS 389 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: 452 Number of extensions: 19 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: 389 Length adjustment: 30 Effective length of query: 358 Effective length of database: 359 Effective search space: 128522 Effective search space used: 128522 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