Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_013722122.1 ALIDE2_RS11230 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000204645.1:WP_013722122.1 Length = 394 Score = 234 bits (597), Expect = 3e-66 Identities = 145/381 (38%), Positives = 201/381 (52%), Gaps = 11/381 (2%) Query: 11 VPPFYVMDVWLAAAERQR----THGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSV 66 + PFYVM+V AA R T ++ L+ G+P AP VR AA A+ Y+ Sbjct: 10 IEPFYVMEVAKAAQGLAREVAGTREPMIFLNIGEPDFTAPPLVRQAADRAVRDGLTQYTN 69 Query: 67 ALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYP 126 ALG+ ELR+ I+ Y R G+ V +V+T G+S LA LA DAGD + M P YP Sbjct: 70 ALGLDELRERISGWYAARFGVNVPARRIVVTAGASAALQLACLALIDAGDEILMPDPSYP 129 Query: 127 CYRNILSALGCEVVEIPCGPQTRFQ-PTAQMLAEIDPPLRGVVVASPANPTGTVIPPEEL 185 C R+ +SA V +P + RFQ A++ A RGV++ASP+NPTGT I P+EL Sbjct: 130 CNRHFVSAADGRAVLVPTTAEERFQLSAAKVEAAWGARTRGVLLASPSNPTGTSIAPDEL 189 Query: 186 AAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGW 245 I A + DE+Y GL Y+ A + A + + +NSFSKY+ MTGWRLGW Sbjct: 190 RRIHEAVRARGGITVIDEIYLGLSYEEAFGHT-ALALGEDVISINSFSKYFNMTGWRLGW 248 Query: 246 LLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGL 305 ++VP + V+ L N IC +SQ AA++ F E+ AE + A + R + L Sbjct: 249 MVVPEAMVSVVERLAQNLFICASTISQHAALACFEAESIAEYERRRAEFKARRDFFIPAL 308 Query: 306 RRIGIDRLAPTDGAFYVYADVSDF-----TSDSLAFCSKLLADTGVAIAPGIDFDTARGG 360 R+G+ P DGAFY +AD + S F +L+ +AI PG DF TA Sbjct: 309 NRLGLTVPVPPDGAFYAWADCGEAARRLGVQGSWDFAFELMRRAHLAITPGRDFGTADTA 368 Query: 361 SFVRISFAGPSGDIEEALRRI 381 FVR S A ++EA+ R+ Sbjct: 369 RFVRFSTANSMAQLQEAVARM 389 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: 407 Number of extensions: 21 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: 394 Length adjustment: 31 Effective length of query: 357 Effective length of database: 363 Effective search space: 129591 Effective search space used: 129591 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