Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011372764.1 SUDEN_RS05945 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000012965.1:WP_011372764.1 Length = 387 Score = 176 bits (447), Expect = 8e-49 Identities = 109/370 (29%), Positives = 188/370 (50%), Gaps = 7/370 (1%) Query: 23 AAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQ 82 A E + + D+++ SAG+P P+ ++ AA AA++ Y+ GIP L+ AIA + Sbjct: 21 AGELKASGKDILSFSAGEPDFDTPQVIKDAAIAAINEGFTKYTAVEGIPTLKAAIANKLK 80 Query: 83 RRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEI 142 R +G+T P+ ++ G+ F A GD V + +P + Y ++ G VVEI Sbjct: 81 RDNGLTYAPNQIITNNGAKHSLFNLFAAVIQKGDEVIIPAPYWVTYPELVLYHGGTVVEI 140 Query: 143 PCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLIS 201 ++ F+ T Q L + P + +V+ SP+NPTG+V +EL A+ + +DV + S Sbjct: 141 ETNDESSFKITPQQLKNALTPKTKMIVLTSPSNPTGSVYSKDELTALGKVLEGTDVLVAS 200 Query: 202 DEVYHGLVYQGAPQTSCAWQTS--RNAVVVNSFSKYYAMTGWRLGWLLV-PTVLRRAVDC 258 DE+Y L+Y G ++ A + + +N SK AMTGWR G++ T + +A Sbjct: 201 DEMYEKLIYDGEFTSAAAVSDDMYKRTITINGLSKSVAMTGWRFGYMAAHQTEIIQATKK 260 Query: 259 LTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDG 318 L T ++Q AA+ EA A+ + ++ R + + I + DG Sbjct: 261 LQSQSTSNINSITQKAAIVGLNGEADADIEKMRIAFKERRDEAVKLINAIDGLSVYKPDG 320 Query: 319 AFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEAL 378 AFY++ ++ + DS+ FC +LL + GVA+ PG+ F + + R SFA I + + Sbjct: 321 AFYLFINIKKVSKDSMKFCKELLEEKGVALVPGVGFGSE---GYARFSFATDIESIRKGI 377 Query: 379 RRIGSWLPSQ 388 +RI ++ ++ Sbjct: 378 KRIEEFVSAR 387 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: 336 Number of extensions: 23 Number of successful extensions: 5 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