Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_018123199.1 B149_RS0100510 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000375485.1:WP_018123199.1 Length = 388 Score = 223 bits (568), Expect = 7e-63 Identities = 133/382 (34%), Positives = 198/382 (51%), Gaps = 9/382 (2%) Query: 9 AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVAL 68 A + PF VM+V A +R +V+L G+P P ++ AA AAL Y+ +L Sbjct: 8 AQMKPFMVMEVLEKAQRMEREGASVVHLEIGEPDFDTPASIKRAACAALDDGHTHYTHSL 67 Query: 69 GIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY 128 GI ELR+AI+ DY++R+G+ V+P ++IT G+S + F A G V ++P Y CY Sbjct: 68 GIRELREAISDDYRQRYGVEVDPGRIIITQGTSPAMFVLFSAILRQGQEVIASNPCYACY 127 Query: 129 RNILSALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAA 187 N + G EV +P Q +Q + E + R +++ SPANPTGT++ E + A Sbjct: 128 HNFIRFAGGEVNPVPVTEQDGWQYRVSAVREAVSDRTRALLINSPANPTGTLLSSERMKA 187 Query: 188 IASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLL 247 +A D + L+SDE+YHGLVY+G + + S +A V N FSK YAMTGWRLG+L+ Sbjct: 188 LAELADEKGLHLVSDEIYHGLVYEGREHS--VLEFSDDAFVFNGFSKLYAMTGWRLGYLI 245 Query: 248 VPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRR 307 P R + NF I ++Q A V+A EA + + A Y R +L L Sbjct: 246 APESFVRPLQIACQNFFISANSMAQWAGVAALR-EAGEDVEHMKAVYDDRRRYMLSRLEG 304 Query: 308 IGIDRLAPTDGAFYVYAD----VSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFV 363 +G+ P GAFY+ D F SL +L + + PG+DF G ++ Sbjct: 305 MGLSIPNPPTGAFYILVDFRKYAERFDGSSLKLAYDILEKAAIGVTPGVDFGPGAEG-YI 363 Query: 364 RISFAGPSGDIEEALRRIGSWL 385 R S+A +I E + R+ +L Sbjct: 364 RFSYANSLENIREGMDRLERYL 385 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: 380 Number of extensions: 16 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: 388 Length adjustment: 30 Effective length of query: 358 Effective length of database: 358 Effective search space: 128164 Effective search space used: 128164 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