Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_010961297.1 MCA_RS10050 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000008325.1:WP_010961297.1 Length = 400 Score = 259 bits (661), Expect = 1e-73 Identities = 147/378 (38%), Positives = 206/378 (54%), Gaps = 7/378 (1%) Query: 7 LRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSV 66 L + PF+VM + A E + + +V+L G+P PEPV AAA L Q+ Y+ Sbjct: 21 LADAIRPFHVMAILARARELESSGRSIVHLEIGEPDFPTPEPVAAAATRFLAGGQVRYTP 80 Query: 67 ALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYP 126 A G+PELR+ IAA Y R+G+ V P + +T G+SG LA G RV +A PGYP Sbjct: 81 AAGLPELRERIAAYYAERYGVAVAPQRIFLTPGASGALSLALAVALSPGRRVMLADPGYP 140 Query: 127 CYRNILSALGCEVVEIPCGPQTRFQPTA---QMLAEIDPPLRGVVVASPANPTGTVIPPE 183 CY N + + +P G + FQ A +M D P+ + ASP+NPTGTV+ Sbjct: 141 CYSNFVRLYSGDPHAVPVGAEQDFQLNAALCRMHCGGDVPV--AISASPSNPTGTVMRTG 198 Query: 184 ELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRL 243 L + W +A LISDE+YHGL Y G + A + ++ VVNSFSKY+ MTGWRL Sbjct: 199 VLRELVEWFEAEGGILISDEIYHGLEYGG--RAVSALEFGQHTFVVNSFSKYFGMTGWRL 256 Query: 244 GWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLD 303 GW++VP AV+ + N I P LSQ AA++AF+ E+ AE + ++ R L Sbjct: 257 GWVVVPEAYAAAVERVAQNIFISAPTLSQYAALAAFSEESRAELERRRRAFEARRDFLWG 316 Query: 304 GLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFV 363 L ++G GAFY+YAD S F DS F ++LL GVA+ PG DF ++ Sbjct: 317 ELVKLGFGVPVAPSGAFYIYADCSAFAEDSAEFAARLLETAGVAVTPGKDFGAQSPERYL 376 Query: 364 RISFAGPSGDIEEALRRI 381 R ++ ++EA+ RI Sbjct: 377 RFAYTADIPVLQEAVGRI 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: 455 Number of extensions: 31 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: 400 Length adjustment: 31 Effective length of query: 357 Effective length of database: 369 Effective search space: 131733 Effective search space used: 131733 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