Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012048726.1 SWIT_RS12735 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000016765.1:WP_012048726.1 Length = 374 Score = 326 bits (835), Expect = 8e-94 Identities = 176/377 (46%), Positives = 241/377 (63%), Gaps = 9/377 (2%) Query: 11 VPPFYVMDVWLAAAERQRTHG-DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALG 69 V PF +++ A R T G ++++ GQPS G P V A AA+ +++GY + Sbjct: 5 VQPFRAIEI-SGLARRLATEGRSVLHMEFGQPSMGPPRKVLDVARAAIDNDRMGYWES-- 61 Query: 70 IPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYR 129 P L++ +AA Y R+G+ ++P ++T G+S +LA CF AG R+AMA PGY YR Sbjct: 62 -PALKERLAALYADRYGVAIDPSRFLLTCGASPALVLALSICFPAGARIAMARPGYVAYR 120 Query: 130 NILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIA 189 N + AL VE+PCG ++RFQ TA+ LA I+P GV++ASPANPTGT+I +EL AIA Sbjct: 121 NTVRALNMVPVELPCGAESRFQLTAEALAAIEPAPDGVIIASPANPTGTIIGGDELRAIA 180 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 C +R++SDE+YH L Y G P S A + +AV+++SFSKYY M GWRLGWLLVP Sbjct: 181 EVCRRRGIRILSDEIYHALSY-GEPCRSMA-EYDPDAVIISSFSKYYCMPGWRLGWLLVP 238 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 L G + PP LSQ AA++A +AT E D N+A YA NR+ LL+ L ++G Sbjct: 239 PDLVERAWSYLGCLFLTPPTLSQHAALAAL--DATEELDANVAVYAGNRARLLEALPQMG 296 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 + R+AP DGAFY+YAD+ T DS+ FC KLL DTG+A PGID D G F R+SFA Sbjct: 297 LRRIAPPDGAFYIYADIGHLTDDSMGFCRKLLLDTGLATGPGIDHDPVDGHRFFRLSFAI 356 Query: 370 PSGDIEEALRRIGSWLP 386 + ++E+AL+R+ WLP Sbjct: 357 SAEEVEKALQRLADWLP 373 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: 479 Number of extensions: 26 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: 374 Length adjustment: 30 Effective length of query: 358 Effective length of database: 344 Effective search space: 123152 Effective search space used: 123152 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