Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011020683.1 MA_RS03340 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000007345.1:WP_011020683.1 Length = 394 Score = 225 bits (573), Expect = 2e-63 Identities = 127/381 (33%), Positives = 208/381 (54%), Gaps = 9/381 (2%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 +PPFYVM+V +A E + +++L G+P + AA AA+ Y+ + G+ Sbjct: 17 IPPFYVMEVLESAKELEAQGRHIIHLEVGEPDFPTAPHICEAACAAIGKGLTKYTHSQGL 76 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P LR+AIA Y R+ G+ ++P+ V++T+G+S G L+ F+A + D V M++P Y CY N Sbjct: 77 PALREAIAESYYRKFGVDLDPNQVIVTSGTSPGLLMVFMALLEKRDEVIMSNPHYACYPN 136 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIA 189 + LG V + F + + + + P + +++ SP+NP G V+ P+ L +A Sbjct: 137 FVKYLGGTPVFVYTSEANGFALEPETVRQCLSPNTKAILINSPSNPGGHVMSPDTLQGLA 196 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 + D + ++SDE+Y GL+Y G + + ++NA V+N FSK YAMTGWRLG+++ P Sbjct: 197 AIADEKGIPVVSDEIYQGLIYSGEEHSILEY--TKNAFVLNGFSKLYAMTGWRLGYIICP 254 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAF--TPEATAEADGNLASYAINRSLLLDGLRR 307 RA+ + NF IC Q A ++A + E E + Y + R +L L Sbjct: 255 PGCVRAIQKIHQNFFICANSFVQEAGIAALKGSQEHVVEM---VQIYNMRRQYMLKRLLG 311 Query: 308 IGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISF 367 +G++ GAFYV AD F +DSL +L + GVA+ PG+DF G ++R S+ Sbjct: 312 MGLEVRKEPMGAFYVLADARKFGNDSLELSRSILNEAGVAVTPGVDFGNGAEG-YLRFSY 370 Query: 368 AGPSGDIEEALRRIGSWLPSQ 388 A +I E + R+ ++L + Sbjct: 371 ANSLENIAEGMDRLEAFLEKE 391 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: 378 Number of extensions: 12 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: 394 Length adjustment: 31 Effective length of query: 357 Effective length of database: 363 Effective search space: 129591 Effective search space used: 129591 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