Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_041565154.1 NPUN_RS02975 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000020025.1:WP_041565154.1 Length = 388 Score = 147 bits (370), Expect = 7e-40 Identities = 99/308 (32%), Positives = 152/308 (49%), Gaps = 9/308 (2%) Query: 64 YSVALGIPELRDAIAADYQRRHGITVEPD-AVVITTGSSGGFLLAFLACFDAGDRVAMAS 122 Y GIP L AIA Q +GI + + +V+T GS+ GF+ A LA + GD + + + Sbjct: 61 YKSVEGIPPLLTAIAGKLQAFNGIEINGENCIVVTAGSNMGFMNAILAITNPGDEIILNT 120 Query: 123 PGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPP 182 P Y + ++ GC V + + +P A A I P R +V SP NPTG V Sbjct: 121 PYYFNHEMAIAIAGCRAVLVATDENYQLRPEAIAQA-ITPKTRAIVTISPNNPTGVVYSE 179 Query: 183 EELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSC-AWQTSRNAVVVNSFSKYYAMTGW 241 L + CD + ISDE Y Y G S A+ S+ + + S SK Y W Sbjct: 180 AALRQVNQICDTHRIYHISDEAYQYFTYNGVKHVSPGAFGKSKYTISLFSLSKAYGFASW 239 Query: 242 RLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAE-ADGNLASYAINRSL 300 R+G++++P L A+ + ICPPV+SQ AA+ A +A E N+ + R L Sbjct: 240 RIGYMVIPKHLFVAIKKVQDTILICPPVISQYAALGAL--QAKEEYLQSNIGAIFQVRQL 297 Query: 301 LLDGLRRI-GIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARG 359 +LD L R+ G+ + P +GAFY + V+ D+ +L+ + VA+ PG F Sbjct: 298 VLDSLNRLEGLCSITPANGAFYFFLKVNT-QMDAFELVKRLIQEHKVAVIPGTTFG-MDD 355 Query: 360 GSFVRISF 367 G ++R+++ Sbjct: 356 GCYLRVAY 363 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: 324 Number of extensions: 11 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: 388 Length adjustment: 30 Effective length of query: 358 Effective length of database: 358 Effective search space: 128164 Effective search space used: 128164 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