Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_092344251.1 BLU87_RS01970 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900107645.1:WP_092344251.1 Length = 384 Score = 218 bits (555), Expect = 2e-61 Identities = 132/376 (35%), Positives = 191/376 (50%), Gaps = 9/376 (2%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 V PF M++ A E + D++ L G+P P + AA AL Y+ +LG+ Sbjct: 12 VEPFLAMELMERAKELETAGQDVIYLCLGEPDFNTPAAILAATGQALAEGATSYTHSLGL 71 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 ELR I Y +G+ + PD V++++G+S LL F D GD + + PGY CY Sbjct: 72 LELRQEICRHYLNYYGVKIVPDQVIVSSGTSPLMLLLFSTLLDQGDELILTDPGYACYPG 131 Query: 131 ILSALGCEVVEIPCGPQTRFQPTA-QMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIA 189 + G V + + FQP Q+ A + RG+++ SP+NP G+V+ EE+ A+A Sbjct: 132 FVKFSGGAPVLLKTAAKDGFQPKVDQVKALMTEKTRGLLINSPSNPAGSVLSGEEMQALA 191 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 + +ISDE+YHGL Y G + C + + NA V+ FSK YAMTGWRLG+L+ P Sbjct: 192 Q----LPIPIISDEIYHGLTYHG--EERCILEFTENAFVLGGFSKAYAMTGWRLGFLISP 245 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 R + L NF IC Q ++A + E D + Y R L+ GLR +G Sbjct: 246 LSCIRTLQTLHQNFLICANHFVQRGGIAAL-QQCDDEVDAMRSVYDKRRIALVAGLRELG 304 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 GAFYV AD +S +L TGVA+ PG+DF G F+R S+ Sbjct: 305 FGVHFEPQGAFYVLADARHIDGNSQRLALDILEKTGVAVTPGVDFGQGAEG-FLRFSYTR 363 Query: 370 PSGDIEEALRRIGSWL 385 P +I AL+R+G +L Sbjct: 364 PLTEITVALQRLGVYL 379 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: 365 Number of extensions: 23 Number of successful extensions: 6 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