Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_084687626.1 OLEAN_RS17845 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000967895.1:WP_084687626.1 Length = 401 Score = 249 bits (637), Expect = 7e-71 Identities = 147/394 (37%), Positives = 204/394 (51%), Gaps = 9/394 (2%) Query: 1 MTDRVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLN 60 MT + + PF VM + A D+++L G+P PEP+ A AL Sbjct: 1 MTGFASRTEEIAPFQVMAILQQAQALAAKGIDVIHLEVGEPDFATPEPIVQAGINALSEG 60 Query: 61 QLGYSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAM 120 + Y+ ALG+PELR IA YQ R+G+ V D + IT G+SG LL A +AGD + M Sbjct: 61 KTHYTPALGLPELRRKIADFYQSRYGVEVSADRIAITPGASGALLLLMAARLEAGDELLM 120 Query: 121 ASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEI--DPPLRGVVVASPANPTGT 178 A PGYPC R+ IP + FQ T + + + + V++ASPANPTG Sbjct: 121 ADPGYPCNRHFARVFEAHGRLIPTTASSGFQLTPEHVKQHWNKGASKAVLMASPANPTGA 180 Query: 179 VIPPEELAAIASWCDASDVRLISDEVYHGLVY-------QGAPQTSCAWQTSRNAVVVNS 231 VIP E+L IA+ L DE+YHGL Y Q + + A + VV+NS Sbjct: 181 VIPHEDLEKIAAQTRLLKGELWVDEIYHGLTYHDVGESDQQSKRPKTALALGDDVVVINS 240 Query: 232 FSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNL 291 FSKY+ MTGWRLGW++VP ++ L N + P +Q A++AF EA A + Sbjct: 241 FSKYFGMTGWRLGWMVVPEHYIPVIERLAQNLFLAPSTPAQYGALAAFGEEALAIMEARR 300 Query: 292 ASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPG 351 R LL L ++G DGAFY+YAD S+ T D+ FC +LL DTGVA+ PG Sbjct: 301 LELKQRRDYLLAELPKLGFKIPVIPDGAFYIYADASELTQDTQKFCEQLLQDTGVALTPG 360 Query: 352 IDFDTARGGSFVRISFAGPSGDIEEALRRIGSWL 385 DF +VR ++ +++A+ RI +WL Sbjct: 361 FDFGEQNAHLYVRFAYTTNIDRLQQAVVRIQTWL 394 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: 431 Number of extensions: 15 Number of successful extensions: 3 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: 401 Length adjustment: 31 Effective length of query: 357 Effective length of database: 370 Effective search space: 132090 Effective search space used: 132090 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