Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_027456455.1 K420_RS0101285 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000519045.1:WP_027456455.1 Length = 387 Score = 267 bits (683), Expect = 3e-76 Identities = 148/386 (38%), Positives = 212/386 (54%), Gaps = 4/386 (1%) Query: 1 MTDRVALR-AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHL 59 MT R A R A + PF+V+++ A + + D++++ G+P PEP+ AA AA+ Sbjct: 1 MTYRPARRLADIEPFHVVELLTRARQLEAEGRDIIHMEVGEPDFPTPEPIAEAAIAAIQR 60 Query: 60 NQLGYSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVA 119 + Y+ ALG+PELR AIA Y+ R+G+ V + IT G+SG LAF A + GD Sbjct: 61 GKTLYTQALGLPELRAAIADFYRERYGVVVPASRIAITNGASGALNLAFAALANPGDEWL 120 Query: 120 MASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGT 178 +A PGYPC R+IL IP GP++ FQPT ML + G++VASPANPTGT Sbjct: 121 LADPGYPCNRHILRTYEGVPRSIPVGPESNFQPTPAMLRQHWTEQTAGLLVASPANPTGT 180 Query: 179 VIPPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAM 238 ++ E+ A+A+ C + DE+YHGL Y+ + T+CA + V+NSFSKY+ M Sbjct: 181 LLTLAEIEALAAVCREKGGHFMVDEIYHGLTYEISAPTACA--AGDDIWVINSFSKYFQM 238 Query: 239 TGWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINR 298 TGWRLGWL+VP R ++ L N +CP +Q AA++AF P + A + R Sbjct: 239 TGWRLGWLVVPEAYGRDIEKLAQNLVLCPSTPAQYAALAAFEPHTIDILEARRAEFRRRR 298 Query: 299 SLLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTAR 358 L L IG A +GAFY+Y D S DS LL GVA PG+DF + Sbjct: 299 DFLAPALEAIGFRITARPEGAFYLYCDCSALADDSFMLARDLLEKAGVAATPGLDFGSNA 358 Query: 359 GGSFVRISFAGPSGDIEEALRRIGSW 384 +R ++ + EA+ R+ ++ Sbjct: 359 PEKHIRFAYTTGIPRLAEAIERLSAY 384 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: 474 Number of extensions: 27 Number of successful extensions: 3 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