Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_073036174.1 BUB04_RS01205 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900129305.1:WP_073036174.1 Length = 389 Score = 151 bits (382), Expect = 3e-41 Identities = 108/356 (30%), Positives = 162/356 (45%), Gaps = 12/356 (3%) Query: 34 VNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPDA 93 +NLS G PEPVR A A+ Y+ G+ ELR+AIA +++ +G+ V+P+ Sbjct: 30 INLSQGVCDLEIPEPVRRGAQQAIDEGYNVYTRYDGLQELREAIAHKHKQFNGLEVDPEG 89 Query: 94 -VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQP 152 V+++ G++G F A LA + GD V + P Y + + L A + P Sbjct: 90 EVIVSAGTTGAFYCACLALLEPGDEVIVFEPYYGYHISTLLATQARPAYVRLHPPGWTFT 149 Query: 153 TAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVYQG 212 + A + RG++V +PANP+G V EEL AI + D+ + +DE+Y VY G Sbjct: 150 EEDLEAAVTSRTRGILVNTPANPSGKVFTREELEAIGRFATRHDLFIFTDEIYEYFVYDG 209 Query: 213 APQT--SCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPVL 270 + + ++ SK +++TGWR+G+ + R + +C P Sbjct: 210 RRHVPPAAIEGIGERTITISGLSKTFSITGWRIGYCICDRKWARPIGWFNDLVYVCAPAP 269 Query: 271 SQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVS--- 327 QI Y R + D L R G+D + P GA+YV AD+S Sbjct: 270 LQIGVARGLLQLDAGYYQQIAREYQEKRDRICDALTRAGLDPVVP-QGAYYVLADISRLP 328 Query: 328 -DFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGS-FVRISFAGPSGDIEEALRRI 381 D + D F LL +TGVA PG F GS R FA ++EA RRI Sbjct: 329 GDASKDKAMF---LLQETGVAAVPGEAFYHDEAGSQLARFCFAKRDQVLDEACRRI 381 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: 419 Number of extensions: 33 Number of successful extensions: 6 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