Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_027721528.1 H589_RS0107920 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000425265.1:WP_027721528.1 Length = 386 Score = 215 bits (547), Expect = 2e-60 Identities = 132/384 (34%), Positives = 209/384 (54%), Gaps = 21/384 (5%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF VMDV A + +R ++++ G+P P+ ++ A A+ + Y+ +LGI Sbjct: 11 ITPFLVMDVLEKAQQMEREGRSIIHMEIGEPDFDTPDCIKKACCEAMDKGETHYTHSLGI 70 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 PELR+AI+ ++ R+ + V+PD V+IT G+S LL F D GD V ++ P Y CY N Sbjct: 71 PELREAISKYHKDRYNVDVDPDRVIITQGTSPAMLLLFTFILDKGDNVIVSDPCYACYSN 130 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPE---ELA 186 +S G E I + FQ + + + I+ + +++ SP+NPTGT++ PE E+A Sbjct: 131 FISFAGAEANRITTFEEDGFQYRPEAIKKAINTKTKAILINSPSNPTGTLLSPERMKEIA 190 Query: 187 AIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWL 246 + W +ISDE+YHGLVY G + S T +A V+N FSK +AMTGWRLG++ Sbjct: 191 GMGPW-------IISDEIYHGLVY-GEKEHSILEYTD-HAFVLNGFSKLFAMTGWRLGYI 241 Query: 247 LVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLR 306 + P R + L NF I ++Q A V+A T E+ + + +Y R +L LR Sbjct: 242 ISPEKYVRPLQKLCQNFFISANSMAQRAGVAALT-ESWDDVNRIKNTYDERRKYMLKRLR 300 Query: 307 RIGIDRLAPTDGAFYVYADV----SDFTSDSLAFCSKLLADTGVAIAPGIDF-DTARGGS 361 +G D GAFYV ++ + F SL +L G+ + PGIDF D A G Sbjct: 301 EMGFDIKVEPTGAFYVLVNMKHLAAKFDGSSLKLAFDILEQAGIGVTPGIDFGDGAEG-- 358 Query: 362 FVRISFAGPSGDIEEALRRIGSWL 385 ++R+S+A ++ E + R+ +++ Sbjct: 359 YIRLSYANSIENLAEGMDRLENYV 382 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: 381 Number of extensions: 20 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: 386 Length adjustment: 30 Effective length of query: 358 Effective length of database: 356 Effective search space: 127448 Effective search space used: 127448 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