Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_066919925.1 ACG33_RS07200 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_001579945.1:WP_066919925.1 Length = 397 Score = 140 bits (354), Expect = 5e-38 Identities = 108/365 (29%), Positives = 170/365 (46%), Gaps = 16/365 (4%) Query: 32 DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91 D+++L AG+P P + AA A+ Y+ G E+++A+ A ++R + + + Sbjct: 33 DIISLGAGEPDFDTPAHLAAAGIQAIREGHTRYTPVDGTVEMKNAVIAKFRRDNRLEYQR 92 Query: 92 DAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN-ILSALGCEVVEIPCGPQTRF 150 +++++G+ +A D GD + +P + Y + ++ A G V + Q Sbjct: 93 QQILVSSGAKQILFNLIMALIDPGDEAVIPAPYWVSYPDMVMLAEGVPVTPLAGRDQGYK 152 Query: 151 QPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLI--SDEVYHGL 208 AQ+ A I P R ++ SP NPTG EL A+ + A R+I +D++Y + Sbjct: 153 ITPAQLEAAITPHTRLFILNSPNNPTGAAYTAAELRALGAVL-ARHPRIIICTDDIYEHI 211 Query: 209 VYQGAPQTSCAW---QTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTI 265 + P S A + V VN SK YAMTGWR+G+ P L A+ + G T Sbjct: 212 YWAREPFISLAQACPELYERIVTVNGVSKAYAMTGWRIGYCGGPAALITAMATIQGQSTS 271 Query: 266 CPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYAD 325 P ++Q AA +A + + N + LL+ GL R+ G FY +A+ Sbjct: 272 NPSSIAQKAAAAALNGDQACVREMN-RHFRERHDLLVAGLNRLPGVSCLEGAGTFYAFAN 330 Query: 326 VSDF-----TSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRR 380 V +D AF LLA +GVA+ PG F VR+SFA +EEALRR Sbjct: 331 VERAIEMIGVADDTAFAEHLLATSGVAVVPGSGFGAP---GHVRLSFACSMQTLEEALRR 387 Query: 381 IGSWL 385 +G L Sbjct: 388 MGKTL 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: 364 Number of extensions: 18 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: 397 Length adjustment: 31 Effective length of query: 357 Effective length of database: 366 Effective search space: 130662 Effective search space used: 130662 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