Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011318914.1 AVA_RS10755 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000204075.1:WP_011318914.1 Length = 388 Score = 187 bits (476), Expect = 3e-52 Identities = 119/372 (31%), Positives = 193/372 (51%), Gaps = 9/372 (2%) Query: 22 AAAERQRTHG-DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAAD 80 A A+ + G D+ + SAG+P P ++AAAA AL + Y A G P+LR+AIA Sbjct: 20 AKAKAMKAEGIDVCSFSAGEPDFDTPAHIKAAAAKALDEGKTKYGAAAGEPKLREAIAHK 79 Query: 81 YQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVV 140 Q+ + + +P+ V++T G +A D GD V + +P + Y +++ +G + V Sbjct: 80 LQKDNHLDYKPENVIVTNGGKHSLYNLIVALIDPGDEVIIPAPYWLSYPEMVTLVGGKSV 139 Query: 141 EIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRL 199 +P T ++ T + L + I P + V+ SP+NPTG V PEE+ A+A +D+ + Sbjct: 140 IVPTDASTGYKITPEQLRKAITPKTKLFVLNSPSNPTGMVYTPEEIKALAQVVVDADIYV 199 Query: 200 ISDEVYHGLVYQGAPQT---SCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAV 256 +SDE+Y ++Y GA S + ++ N F+K Y+MTGWRLG+L P + +A Sbjct: 200 VSDEIYEKILYDGAQHISIGSLGKEIFNRTLISNGFAKAYSMTGWRLGYLAGPVDIIKAA 259 Query: 257 DCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPT 316 + G+ T +Q A++A + A +A R ++LD L I A Sbjct: 260 SSIQGHSTSNVCTFAQYGAIAALEDSQDCVEEMRQA-FAKRRQVMLDRLNAIPGLSTAKP 318 Query: 317 DGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEE 376 DGAFY++ D+S SL FC L+ + VA+ PGI F +R+S+A IE+ Sbjct: 319 DGAFYLFPDISKTGLKSLEFCDALIEEHKVAVIPGIAFG---ADDNIRLSYATDLATIEK 375 Query: 377 ALRRIGSWLPSQ 388 L R+ ++ S+ Sbjct: 376 GLDRLEKFVRSR 387 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: 367 Number of extensions: 17 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: 388 Length adjustment: 30 Effective length of query: 358 Effective length of database: 358 Effective search space: 128164 Effective search space used: 128164 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 09 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