Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_015932463.1 MNOD_RS28595 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000022085.1:WP_015932463.1 Length = 390 Score = 337 bits (863), Expect = 4e-97 Identities = 182/379 (48%), Positives = 243/379 (64%), Gaps = 6/379 (1%) Query: 9 AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVAL 68 A V PF MDV AAA R+R +V++ GQP+A AP AAA AL ++ Y+ AL Sbjct: 15 ARVAPFLAMDVLSAAAARERRGDSVVHMEVGQPAAPAPRAAIAAAQGALAAGRIPYTEAL 74 Query: 69 GIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY 128 GI LR+ IA Y +GI V P+ +V+TTGSS GF+LAFLA FDAG RVA+A PGYP Y Sbjct: 75 GITPLRERIARHYAETYGIAVSPERIVVTTGSSAGFVLAFLALFDAGGRVAIAEPGYPAY 134 Query: 129 RNILSALGCEVVEIPCGPQTRFQPTAQML--AEIDPPLRGVVVASPANPTGTVIPPEELA 186 R+IL AL E V + + F PTA + A + PL G++V SPANP+GT+I P LA Sbjct: 135 RSILQALDLEPVPLRLRAEDGFVPTAAAVRAAHAERPLSGLLVMSPANPSGTMIDPVGLA 194 Query: 187 AIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWL 246 + C A + +SDE+YHGL Y G P + A Q+ +AV++NSFSKYY MTGWR+GW+ Sbjct: 195 ELGRTCRALRLSFVSDEIYHGLTY-GVP-AATALQSDPDAVIINSFSKYYCMTGWRIGWM 252 Query: 247 LVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLR 306 +VP L R ++ L N I P LSQ+AA++AF +AT E + A YA R++LL+ L Sbjct: 253 VVPEELVRPIERLAQNLYISAPYLSQVAALAAF--DATQELEAVKADYARARAVLLNELP 310 Query: 307 RIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRIS 366 +G+ + P DGAFY+YADV+ T+D+ FC ++L + GVA PG+DFD G +R S Sbjct: 311 GLGLGDVHPADGAFYLYADVARLTNDASGFCRRMLDEAGVAATPGLDFDPTEGNHHLRFS 370 Query: 367 FAGPSGDIEEALRRIGSWL 385 FAG + EA+RR+ WL Sbjct: 371 FAGGEREAHEAVRRLRIWL 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: 461 Number of extensions: 25 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: 390 Length adjustment: 30 Effective length of query: 358 Effective length of database: 360 Effective search space: 128880 Effective search space used: 128880 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 09 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