Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_092991562.1 BLP65_RS00590 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900102855.1:WP_092991562.1 Length = 399 Score = 155 bits (393), Expect = 1e-42 Identities = 116/355 (32%), Positives = 170/355 (47%), Gaps = 10/355 (2%) Query: 34 VNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPDA 93 +N++ G P V A AA+ + Y+ A G ELRDAIAA Q R+G++V+PDA Sbjct: 29 INMAQGVCDLAIPSSVIEGAKAAMDAGRNIYTPAEGFVELRDAIAAATQARYGLSVDPDA 88 Query: 94 -VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQP 152 ++I++G++G F A D GD V + P Y + L A+GC V + P Sbjct: 89 EIMISSGATGAFHSTAHALLDPGDEVILFEPYYGYHAASLKAMGCRVRYVRLEPPGWRVN 148 Query: 153 TAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVYQG 212 + I+ R VV+++P+NPTG V +EL +A + D+ + SDE+Y VY G Sbjct: 149 WEALGRTINSRTRAVVLSNPSNPTGKVFRRDELERLARFARQHDLVVFSDEIYEHFVYDG 208 Query: 213 ---APQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPV 269 P S R V ++ FSK +++TGWRLG+ + P + +A +CPP Sbjct: 209 LTHIPPASIDALRER-TVTISGFSKIFSITGWRLGYAIAPPEVIQAATQYNDLVYVCPPA 267 Query: 270 LSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSDF 329 Q+ A + + R LR+ G+ P +GA+YV AD+S Sbjct: 268 PLQLGAARGVLELGVEFYREVAREHRVKRDRFCAALRQAGLTPHRP-EGAYYVMADISGV 326 Query: 330 T-SDSLAFCSKLLADTGVAIAPGIDF--DTARGGSFVRISFAGPSGDIEEALRRI 381 +D +L TGVA PG F D A G + R FA S +EEA RI Sbjct: 327 PGADDRERALWILERTGVACVPGRAFYHDDA-GRNLARFCFAKKSEVLEEACDRI 380 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: 420 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: 399 Length adjustment: 31 Effective length of query: 357 Effective length of database: 368 Effective search space: 131376 Effective search space used: 131376 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