Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011308059.1 MBAR_RS16595 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000195895.1:WP_011308059.1 Length = 370 Score = 190 bits (483), Expect = 5e-53 Identities = 118/348 (33%), Positives = 188/348 (54%), Gaps = 13/348 (3%) Query: 32 DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91 D +NL GQP PE ++AAA A++ GY+V GIPELR+A+++ ++ +G +V P Sbjct: 28 DAINLGLGQPDFDTPEHIKAAAIKAINEGFTGYTVGPGIPELREALSSKFKEENGFSVSP 87 Query: 92 DAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQ 151 + +++T+G+S +A A + GD V +++PG+ Y + L + V +P + Sbjct: 88 EEIIVTSGASEALAIALAALLNHGDEVLISNPGFVSYNALTEILSGKAVGVPLAEDLTMK 147 Query: 152 PTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVYQ 211 P A +L +I P R +V SP+NPTGTV ++ A+A D ++ +ISDEVY VY+ Sbjct: 148 PEA-VLEKITPKTRAIVFNSPSNPTGTVASRADIKALAEIADDYNITIISDEVYEYFVYE 206 Query: 212 GAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPVLS 271 G + ++ S N + VN+ SK YAMTGWRLG++ + + F C ++ Sbjct: 207 GEHVSPASY--SDNVITVNATSKSYAMTGWRLGYVAARKDYIGQMLKVHQYFQACANSIA 264 Query: 272 QIAAVSAFT-PEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSDFT 330 Q AA +A P+ + +A + R +L+ GL +G++ P GAFY + V + T Sbjct: 265 QKAAYAAVAGPKDSIKA--MREEFRKRRDVLVKGLNDLGMECALP-KGAFYAFPKVPNST 321 Query: 331 SDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEAL 378 + F S GV + PG F + G +RIS+A DIE+AL Sbjct: 322 EVASKFIS-----NGVIVTPGTAFG-SEGDGHIRISYAASMKDIEKAL 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: 352 Number of extensions: 19 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