Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_029912413.1 P166_RS0110670 class I and II aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000711315.1:WP_029912413.1 Length = 396 Score = 234 bits (597), Expect = 3e-66 Identities = 134/379 (35%), Positives = 202/379 (53%), Gaps = 2/379 (0%) Query: 9 AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVAL 68 + V PF+VM + A + ++++L G+P + + V A A++ Y+ L Sbjct: 14 SAVEPFHVMKLLGEAKALEAEGREMIHLEIGEPDFPSLDCVHQAVTDAINHGNTHYTPTL 73 Query: 69 GIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY 128 G+P LR+ ++ Y + V +V+T G+SG L A + D+V M P YPC Sbjct: 74 GLPALREKLSRFYHDFYHADVAAQRIVMTPGASGALHLLLTALLNPSDKVMMCDPTYPCN 133 Query: 129 RNILSALGCEVVEIPCGPQTRFQPTAQMLA-EIDPPLRGVVVASPANPTGTVIPPEELAA 187 R ++ L EV+ +P T FQ TA+++ P ++ V+VASP+NPTGT+I EL A Sbjct: 134 REFVNLLHGEVLSVPVEASTGFQLTAELIELHWQPGIKAVMVASPSNPTGTLIEQPELLA 193 Query: 188 IASWCDASDVRLISDEVYHGLVYQGAPQTSCA-WQTSRNAVVVNSFSKYYAMTGWRLGWL 246 +A++ LI DE+Y GLVY+ A +T A N VV+NSFSK++ MTGWRLGW+ Sbjct: 194 MANFLSEQGAYLIVDEIYQGLVYERAAETILANANLPDNVVVINSFSKFFGMTGWRLGWI 253 Query: 247 LVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLR 306 + P L A+D L N + P SQ A+ +A A + + R+ L D + Sbjct: 254 VAPEFLIPALDKLAQNLYLAAPTPSQYGALRVLESDALAALEQRRQIFEQRRNRLYDAMM 313 Query: 307 RIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRIS 366 G GAFY+Y DVS+ T D+ AFC L+ TGV + PG DF R VRI+ Sbjct: 314 SAGFKIPCKPAGAFYLYWDVSELTDDAEAFCQTLMLHTGVVVTPGKDFGEYRSRQHVRIA 373 Query: 367 FAGPSGDIEEALRRIGSWL 385 + ++ EA+R+I S++ Sbjct: 374 YTTGDNELLEAVRKIQSFI 392 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: 389 Number of extensions: 15 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: 396 Length adjustment: 31 Effective length of query: 357 Effective length of database: 365 Effective search space: 130305 Effective search space used: 130305 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