Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011973901.1 MAEO_RS06050 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000017185.1:WP_011973901.1 Length = 375 Score = 153 bits (386), Expect = 9e-42 Identities = 103/359 (28%), Positives = 182/359 (50%), Gaps = 17/359 (4%) Query: 32 DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91 D +NL G+P P+ + A AL + Y+ GIPELR+AI+ + + + V+ Sbjct: 24 DSINLGIGEPDFDTPQHIVEGAKKALDEGKTHYTPNNGIPELREAISHKLKIDNNLDVDA 83 Query: 92 DAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQ 151 + ++ T G+S +L+ + + GD V +++PG+ Y ++ CE IP +F Sbjct: 84 NNIITTCGASEALMLSLMTLVNKGDEVLISNPGFVSYNSLTQL--CEGNIIPMKLDEKFN 141 Query: 152 -PTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVY 210 ++ I + +++ SPANPTG V+ E+ AI + +++ +ISDE+Y ++Y Sbjct: 142 IDIEEVKNSITNKTKCIMLNSPANPTGKVMDKSEIKAICDIAEDNNIIIISDEIYEKIIY 201 Query: 211 QGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTI----- 265 + + + N +++N FSK +AMTGWR+G++ + L + D + I Sbjct: 202 D--KKHYSPMEFTDNCILINGFSKSHAMTGWRIGYIGINENLNKKYDLIENMTKIHQYGF 259 Query: 266 -CPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYA 324 C +Q A+ A T + L + R L+++GL+ +L DGAFYV+ Sbjct: 260 ACATSFAQYGALEALTGSQNC-VNEMLNEFRRRRDLMVNGLK--NTFKLTVPDGAFYVFP 316 Query: 325 DVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRIGS 383 +V ++ D+ S+ L + + PGI F + G ++VR S+A DIE+AL I + Sbjct: 317 NVEEY--DNGMEISQKLIENNILCVPGIAFGSG-GENYVRFSYATKYEDIEKALEIINN 372 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: 282 Number of extensions: 14 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: 375 Length adjustment: 30 Effective length of query: 358 Effective length of database: 345 Effective search space: 123510 Effective search space used: 123510 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