Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_048038594.1 MM_RS12280 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000007065.1:WP_048038594.1 Length = 370 Score = 182 bits (462), Expect = 1e-50 Identities = 113/346 (32%), Positives = 186/346 (53%), Gaps = 13/346 (3%) Query: 34 VNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPDA 93 +NL GQP P+ ++AAA A++ GY+ GIPELR+A++ ++ + +V P Sbjct: 30 INLGLGQPDFDTPDHIKAAAIKAINEGFTGYTAGPGIPELREALSQKFKEENCFSVSPQE 89 Query: 94 VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQPT 153 +++T+G+S +A A + GD V +++PG+ Y + L +VV +P G +P Sbjct: 90 IIVTSGASEALTIALTALLNRGDEVLISNPGFVSYNALTEMLYGKVVNVPLGEDLTMKP- 148 Query: 154 AQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVYQGA 213 +L I P + +++ SP+NPTG V ++ A+A D + +ISDEVY +Y+G Sbjct: 149 EDVLERITPKTKAIILNSPSNPTGAVSSRADIKALAEIADDHRITIISDEVYEYFIYEGE 208 Query: 214 PQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQI 273 + ++ S N V VN+ SK YAMTGWRLG+L + + C ++Q Sbjct: 209 HVSPASY--SDNVVTVNATSKSYAMTGWRLGYLAARNEYISQMLKVHQYIQACANSIAQK 266 Query: 274 AAVSAFT-PEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSD 332 AA +A T P+ + A + R +L+ GL +G++ P GAFY + V S+ Sbjct: 267 AAYAAVTGPKDSVSA--MREEFRKRRDVLVKGLNDLGMECALP-KGAFYAFPRV----SN 319 Query: 333 SLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEAL 378 S SK++++ GV + PG F + G ++RIS+A DIE++L Sbjct: 320 SAEVASKMISN-GVVVVPGTAFG-SEGDGYIRISYAASMKDIEKSL 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: 333 Number of extensions: 17 Number of successful extensions: 4 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: 370 Length adjustment: 30 Effective length of query: 358 Effective length of database: 340 Effective search space: 121720 Effective search space used: 121720 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