Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_020174243.1 A3OQ_RS0104875 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000385335.1:WP_020174243.1 Length = 413 Score = 163 bits (412), Expect = 9e-45 Identities = 121/375 (32%), Positives = 175/375 (46%), Gaps = 23/375 (6%) Query: 28 RTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGI 87 R L+ L G+ AP V A ++ + Y+ GIPELR+AIA R H Sbjct: 41 RGRDGLIPLWVGEGDLPAPGFVVEAMIGSIEAGETFYTHQRGIPELREAIARYMARIHSK 100 Query: 88 TVE-------PDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVV 140 P +T G +A AGD V + +P +P + L G ++ Sbjct: 101 PFANSAEPFTPKRFFVTVGGMHAVQIAIRLLAGAGDDVLVLTPAWPNFEGALKVSGARLI 160 Query: 141 EIPCGPQTRFQPTA---------QMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASW 191 EIP QT+ T Q+ A + P + +VV SP+NPTG V E+L+A+ ++ Sbjct: 161 EIPL--QTKMDSTGRQIWSLDLDQLTAAVTPAAKVLVVNSPSNPTGWVATREDLSALLAF 218 Query: 192 CDASDVRLISDEVYHGLVYQG--APQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 D+ +I+DE+Y + + G AP + + SFSK +AMTG R+GWL P Sbjct: 219 ARRHDLWIIADEIYGRISFDGGRAPSFHDVMDEEDRVLFIQSFSKNWAMTGLRIGWLEAP 278 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 ++ L T V Q AA++A E A L A +R++L DGLRRI Sbjct: 279 PCFGEIIENLIQYSTSGVAVPLQRAAIAAL-EEGEAFFQNQLKRLAESRAILCDGLRRID 337 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 R A GAFY++ + T D+ + + + GV +APG F A G +VRI FA Sbjct: 338 RVRFAEPQGAFYLFCTIEGVT-DTRELAFRWVDEAGVGVAPGTAFG-AGGRDYVRICFAR 395 Query: 370 PSGDIEEALRRIGSW 384 I EA+RRI +W Sbjct: 396 DPARIAEAVRRIETW 410 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: 429 Number of extensions: 24 Number of successful extensions: 7 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: 413 Length adjustment: 31 Effective length of query: 357 Effective length of database: 382 Effective search space: 136374 Effective search space used: 136374 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