Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_028313919.1 G491_RS0105965 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000429905.1:WP_028313919.1 Length = 384 Score = 154 bits (389), Expect = 4e-42 Identities = 111/357 (31%), Positives = 164/357 (45%), Gaps = 8/357 (2%) Query: 34 VNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPDA 93 +NL+ G P+ V A A A+ Y+ G+PELR AIA +G +P+ Sbjct: 28 INLAQGVCDIKVPDEVIAGAKKAMDEGYNVYTPNHGLPELRQAIAGKTAAFYGRRPDPET 87 Query: 94 -VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQT-RFQ 151 +V + G++G F A +A + GD V + P Y + + L A+G V +P P T + Sbjct: 88 EIVASLGATGVFYCAAMALLNPGDEVILFEPYYGYHASTLEAVGAVPVFVPTKPGTWEIE 147 Query: 152 PTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVYQ 211 P A A + P +G+V+ +P NP+G V+ E+ IA D+ + SDE+Y +Y Sbjct: 148 PDALAKA-VTPRTKGIVLCTPGNPSGHVMTAGEIDLIAEAAQKHDLVIFSDEIYEHFLYD 206 Query: 212 GAPQTSCAWQ--TSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPV 269 G V ++ SK YA+TGWRLG+ + P + A+ L +C P Sbjct: 207 GRTHLCPGLHPGLEGRTVTMSGASKTYAITGWRLGYCICPADVTEAITHLNDLVYVCAPA 266 Query: 270 LSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSDF 329 Q+ + +G + R L D + + G+ P +GA+YV ADVS Sbjct: 267 PLQMGVAAGMNMLGRDYYEGLARDHQKKRDLFCDTIEKAGMKPYRP-EGAYYVLADVSGV 325 Query: 330 TS-DSLAFCSKLLADTGVAIAPG-IDFDTARGGSFVRISFAGPSGDIEEALRRIGSW 384 DS +L TGV+ PG F G S VR FA +EEA RI SW Sbjct: 326 PGHDSFTRAMHILEKTGVSSVPGRAFFHDDSGDSLVRFCFAKEFPVLEEACERIASW 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: 407 Number of extensions: 24 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: 384 Length adjustment: 30 Effective length of query: 358 Effective length of database: 354 Effective search space: 126732 Effective search space used: 126732 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