Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_068174275.1 HTA01S_RS18800 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_001592305.1:WP_068174275.1 Length = 406 Score = 230 bits (586), Expect = 6e-65 Identities = 144/401 (35%), Positives = 206/401 (51%), Gaps = 23/401 (5%) Query: 4 RVALRAG-VPPFYVMDVWLAAAERQRTHGD----LVNLSAGQPSAGAPEPVRAAAAAALH 58 ++A RA V PFYVM++ AA+ G ++ L+ G+P AP V+AAA A+H Sbjct: 2 KIAQRAQRVEPFYVMELAKAASAMAAKAGPGDRPMLYLNIGEPDFTAPPLVQAAAERAVH 61 Query: 59 LNQLGYSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRV 118 + Y+ A G+P LR+AI+ Y R G+ ++P +V+T G+S LA LA +AGD V Sbjct: 62 AGRSQYTPATGLPALREAISGWYASRFGLHIDPGRIVVTAGASAALQLACLALIEAGDEV 121 Query: 119 AMASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTG 177 M P YPC R + A V IPCGP RFQ +A + E P RGV++ASP+NPTG Sbjct: 122 LMPDPSYPCNRQFVQAAEGRAVLIPCGPGQRFQLSAAQVEEHWRPATRGVLLASPSNPTG 181 Query: 178 TVIPPEELAAIASWCDASDVRLISDEVYHGLVYQ---GAPQTSCAWQTSRNAVVVNSFSK 234 T I +EL IA + + DE+Y GL + G + +NSFSK Sbjct: 182 TSIARDELEHIARFVRRQGGVTLVDEIYLGLSFDADYGHSALGLPDGLGDEVISINSFSK 241 Query: 235 YYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASY 294 Y+ MTGWRLGWL++P L V+ L N IC ++Q AA++ F P++ AE + + Sbjct: 242 YFNMTGWRLGWLVLPPALVPVVERLAQNLFICASTIAQHAALACFEPDSLAEYERRRGEF 301 Query: 295 AINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSDF--------------TSDSLAFCSKL 340 R + + L R+G+ DGAFY +ADV+ S A +L Sbjct: 302 QARRDVFIPELNRLGLTVPVMPDGAFYAWADVAPLCERWGIPLRGEHPGDGGSWALAFEL 361 Query: 341 LADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRI 381 + +A PG DF A ++R S A + EA+ R+ Sbjct: 362 MRRCQIATTPGRDFGNADPWRYLRFSTANSMAQLREAVVRL 402 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: 460 Number of extensions: 23 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: 406 Length adjustment: 31 Effective length of query: 357 Effective length of database: 375 Effective search space: 133875 Effective search space used: 133875 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