Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012335129.1 M446_RS26220 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000019365.1:WP_012335129.1 Length = 387 Score = 340 bits (872), Expect = 4e-98 Identities = 184/379 (48%), Positives = 246/379 (64%), Gaps = 6/379 (1%) Query: 9 AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVAL 68 A V PF MDV AAA ++R +V++ GQPSA AP P AA AAL ++ Y+ AL Sbjct: 12 ARVAPFLAMDVLAAAAVKERRGEAVVHMEVGQPSAPAPRPAILAAQAALAQGRIPYTEAL 71 Query: 69 GIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY 128 GI LR+ IA Y +G++V P+ VV+TTGSS GF+LAFLA FDAG RVA+ +PGYP Y Sbjct: 72 GIAPLRERIARHYAETYGVSVPPERVVVTTGSSAGFVLAFLALFDAGGRVAITAPGYPAY 131 Query: 129 RNILSALGCEVVEIPCGPQTRFQPTAQMLAEID--PPLRGVVVASPANPTGTVIPPEELA 186 R+IL AL V + + F PTA M+ E PL G++V SPANP+GT+I P LA Sbjct: 132 RSILEALDLAPVALRLRAEDGFVPTAAMVREAHAAQPLSGLLVMSPANPSGTMIDPVHLA 191 Query: 187 AIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWL 246 + C A + +SDE+YHGL Y G P + A ++ +AV++NSFSKYY MTGWR+GW+ Sbjct: 192 ELGRTCRALGLAFVSDEIYHGLTY-GVP-AATALRSDPDAVIINSFSKYYCMTGWRIGWM 249 Query: 247 LVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLR 306 +VP L R ++ L N I P LSQ+AA++AF +AT E + A YA R+LLL+ L Sbjct: 250 VVPDALVRPIERLAQNLYISAPYLSQVAALAAF--DATEELEAVKADYARARALLLNELP 307 Query: 307 RIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRIS 366 +G+ P DGAFY+YADV+ T+D+ AFC ++L GVA PG+DFD A G ++R S Sbjct: 308 GLGLGDAHPADGAFYLYADVARLTNDAGAFCRRMLDQAGVAATPGLDFDPAEGHHYLRFS 367 Query: 367 FAGPSGDIEEALRRIGSWL 385 FAG + EA+RR+ +WL Sbjct: 368 FAGGEREAHEAVRRLRAWL 386 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: 445 Number of extensions: 21 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: 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