Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate YP_427510.1 Rru_A2423 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000013085.1:YP_427510.1 Length = 395 Score = 407 bits (1046), Expect = e-118 Identities = 204/384 (53%), Positives = 261/384 (67%), Gaps = 4/384 (1%) Query: 1 MTDRVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLN 60 M +VA R +PPF VMDV AAAER+ T ++++L GQPS G PE A LH Sbjct: 11 MALKVARRGLIPPFIVMDVMRAAAEREATGAEVMHLEVGQPSTGLPEQALDEVARRLHSG 70 Query: 61 QLGYSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAM 120 +GY+VALG+ LR+AIA YQR G+ V+P +++TTGSS GF+LAFLA F+AGDRV + Sbjct: 71 PMGYTVALGLDALREAIALHYQRTQGVAVDPGRIIVTTGSSAGFILAFLAAFEAGDRVGL 130 Query: 121 ASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVI 180 A+PGYP YR+IL ALGCE V +P GP+TR+QPT +L E L G++VASPANPTGTV+ Sbjct: 131 AAPGYPAYRHILKALGCEPVILPTGPETRYQPTVAVLEEAGMDLDGLIVASPANPTGTVM 190 Query: 181 PPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTG 240 P +L A+ ++C +RLISDE+YHG+ Y A ++ + + VVVNSFSKY+ MTG Sbjct: 191 PAADLKALVAYCGERGIRLISDEIYHGITYGEAALSTVG--LAEHPVVVNSFSKYFCMTG 248 Query: 241 WRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSL 300 WRLGWL++P L R V+CLT N I PP LSQ A ++A E N+ YA NR + Sbjct: 249 WRLGWLVLPPDLLRPVECLTQNLFISPPALSQYAGLAALRHHGAFEE--NIRRYARNRQI 306 Query: 301 LLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGG 360 LLD L G AP DGAFY+Y DVS T DSL FC+++LA+TGVA PG+DFD ARG Sbjct: 307 LLDALPAAGFGAFAPADGAFYLYGDVSGLTDDSLGFCARMLAETGVAATPGLDFDDARGA 366 Query: 361 SFVRISFAGPSGDIEEALRRIGSW 384 FVR SF+G + IE+A RR+ W Sbjct: 367 HFVRFSFSGATETIEKAARRLLEW 390 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: 515 Number of extensions: 20 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: 395 Length adjustment: 31 Effective length of query: 357 Effective length of database: 364 Effective search space: 129948 Effective search space used: 129948 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