Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_014449573.1 LFE_RS07250 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000284315.1:WP_014449573.1 Length = 401 Score = 184 bits (468), Expect = 3e-51 Identities = 124/372 (33%), Positives = 190/372 (51%), Gaps = 18/372 (4%) Query: 24 AERQRTHG-DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQ 82 A + +G D+ + + G+P PEP++ AA AAL Y+ GIPEL+ AI ++ Sbjct: 26 AREMKANGIDVRDFTGGEPDFDTPEPIKDAAIAALKSGFTKYTAVGGIPELKSAIIEKFE 85 Query: 83 RRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEI 142 R GI +P +V+++G+ F A + GD V + +P + Y + + G V+ + Sbjct: 86 RDQGIVYKPSEIVVSSGAKHSLFQIFQALVNPGDHVLLPTPAWVSYPDQILLNGGVVIGV 145 Query: 143 PCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLIS 201 PC P F+ Q L E I P R +V+ SP NP+G +IP E+L IA ++ +IS Sbjct: 146 PCLPSDGFRLRPQALLEAITPRSRVLVLNSPNNPSGAIIPKEDLLRIAEIVKKHNLIVIS 205 Query: 202 DEVYHGLVYQGAPQTSCAW---QTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDC 258 DE+Y +V+ G +S A + V+VN SK YAMTGWR+G+ P + AV+ Sbjct: 206 DEIYEKIVFDGQETSSIASLVPEIRDRTVIVNGVSKTYAMTGWRIGYAAGPAPIIEAVET 265 Query: 259 LTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDG 318 + P ++Q AAV A LA Y R++LL+ L I R++P DG Sbjct: 266 IQSQTASNPTSIAQKAAVVAIR-SGEIYFKPMLAEYTRRRAMLLESLNAIDGIRMSPPDG 324 Query: 319 AFYVYADVS--------DFTSDSLAFCSK-LLADTGVAIAPGIDFDTARGGSFVRISFAG 369 AFY + DVS D ++ S+ LA+ VA+ PG F + +R+SFA Sbjct: 325 AFYAFPDVSGLLGKRFGDMEIRTVTDLSEFFLAEARVALVPGSAFGS---DHHMRMSFAT 381 Query: 370 PSGDIEEALRRI 381 ++EE +RR+ Sbjct: 382 SPENLEEGVRRL 393 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: 424 Number of extensions: 21 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: 401 Length adjustment: 31 Effective length of query: 357 Effective length of database: 370 Effective search space: 132090 Effective search space used: 132090 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