Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_026127587.1 D471_RS0110175 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000341125.1:WP_026127587.1 Length = 402 Score = 149 bits (375), Expect = 2e-40 Identities = 115/375 (30%), Positives = 171/375 (45%), Gaps = 19/375 (5%) Query: 22 AAAERQRTHG-DLVNLSAGQPSAGAPEP-VRAAAAAALHLNQLGYSVALGIPELRDAIAA 79 A A+ + G ++ AG+P P+ V AA AA Y+ A G+PEL+ AIA Sbjct: 24 AKAKAMKAEGRPVIGFGAGEPDFPTPDYIVEAAVEAAREPRFHRYTPAGGLPELKKAIAE 83 Query: 80 DYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEV 139 R G VEP V++T G AF A D GD V + +P + Y + G Sbjct: 84 KTARDSGYRVEPSQVLVTNGGKQAIYEAFAALLDPGDEVIVVAPYWTTYPESIKLAGGVP 143 Query: 140 VEIPCGPQTRFQPTAQML-AEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVR 198 V + T + + L A + +V SP+NPTG V P E++ AI W D+ Sbjct: 144 VFVTTDESTGYMAGVEQLEAARTERTKILVFVSPSNPTGAVYPREQVRAIGRWALEHDLW 203 Query: 199 LISDEVYHGLVYQGAPQTSCAWQTSRNA---VVVNSFSKYYAMTGWRLGWLLVPTVLRRA 255 +++DE+Y LVY A S + A V+VN +K YAMTGWR+GW++ P + +A Sbjct: 204 VLTDEIYQHLVYGDAEFASIPVEVPELADRTVIVNGVAKTYAMTGWRVGWIIGPEDVVKA 263 Query: 256 VDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAP 315 L + T +SQ AA++A + + +A D S+ R ++ L I Sbjct: 264 AGNLQSHATSNVANVSQAAAIAAVSGDLSA-VDTMRESFDRRRRTIVRMLNEIDGVVCPE 322 Query: 316 TDGAFYVYADVSDF---------TSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRIS 366 GAFY Y V S S +L + VA+ PG F T ++R+S Sbjct: 323 PQGAFYAYPSVKGVLGKEIRGRRPSTSTELAELILEEAEVAVVPGEAFGTP---GYLRLS 379 Query: 367 FAGPSGDIEEALRRI 381 +A D+ E + R+ Sbjct: 380 YALSDEDLVEGVSRV 394 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: 414 Number of extensions: 19 Number of successful extensions: 3 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: 402 Length adjustment: 31 Effective length of query: 357 Effective length of database: 371 Effective search space: 132447 Effective search space used: 132447 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