Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_092993282.1 BLP65_RS04675 aspartate aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900102855.1:WP_092993282.1 Length = 368 Score = 133 bits (335), Expect = 7e-36 Identities = 109/364 (29%), Positives = 162/364 (44%), Gaps = 8/364 (2%) Query: 29 THGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGIT 88 T D+++LS GQP P + A AL GY++ G+PEL + A Y R+G Sbjct: 7 TMDDVIHLSIGQPDFPTPPHIVEAHIQALRDGHTGYTMDAGLPELVTELVAYYSERYGRQ 66 Query: 89 VEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQT 148 ++ D ++TTG++ LA A G + P +P Y ++ G EV I Sbjct: 67 LKEDNFLVTTGATEALYLALSATAAPGREFLIPEPTFPLYAPLVRMNGGEVKSIETSADR 126 Query: 149 RFQPTAQ-MLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHG 207 +Q Q ++ I +V+ SP NPTG V P E + AI V++ISDEVY Sbjct: 127 GYQLDPQEVIDAIGMSTYAIVLNSPNNPTGVVYPRETVEAIVQEAAYRGVKVISDEVYDH 186 Query: 208 LVYQGAPQ---TSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFT 264 LV SCA + +VV+SFSK ++M G R+GW++ + + T Sbjct: 187 LVLDDIEYPSIISCAADIDQ-TMVVSSFSKTFSMPGMRIGWIIASEAAIKTLRRYHMFTT 245 Query: 265 ICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYA 324 Q A V+A T D +A Y R ++ + GAFY+ Sbjct: 246 TVANTPGQWAGVAALT-GGRGFLDEMIAEYRRRRDKVVQLVGDAPHLTGYWPQGAFYILP 304 Query: 325 DVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRIGSW 384 + +D + ++L +TGV PG F + +F RISF+ IEEA R+ W Sbjct: 305 SL-PANADGSSVALRMLEETGVCTVPGETFGESTTNTF-RISFSTSLEKIEEAFSRMIPW 362 Query: 385 LPSQ 388 L Q Sbjct: 363 LEKQ 366 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: 363 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: 368 Length adjustment: 30 Effective length of query: 358 Effective length of database: 338 Effective search space: 121004 Effective search space used: 121004 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