Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_083509522.1 APY04_RS05760 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_001541235.1:WP_083509522.1 Length = 413 Score = 333 bits (855), Expect = 4e-96 Identities = 179/386 (46%), Positives = 237/386 (61%), Gaps = 11/386 (2%) Query: 6 ALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYS 65 +LR+ VP F VMDV AA E + ++++ GQP AP R AA AL + LGY+ Sbjct: 27 SLRSDVPSFIVMDVMRAALEAENAGRHIIHMEVGQPGTPAPRVARDVAARALQNDTLGYT 86 Query: 66 VALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGY 125 +ALG LR IA Y +HG+ V P+ + +T GSS F+L FL+ FDAGD VA+ SPGY Sbjct: 87 MALGNDALRARIARHYADQHGLNVAPERIAVTAGSSAAFVLTFLSLFDAGDTVALPSPGY 146 Query: 126 PCYRNILSALGCEVVEIPCGPQTRFQPTAQ--MLAEIDPPLRGVVVASPANPTGTVIPPE 183 PCYR+ILSALG V + GP + P + A ++G+++ASPANPTGT+I E Sbjct: 147 PCYRHILSALGQRSVLLETGPSNDWMPDPDDVLRAITRDGIKGLLIASPANPTGTMISRE 206 Query: 184 ELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRL 243 L A+ C VR ISDE+YHGL Y T+ A S + +V+NSFSKY++MTGWR+ Sbjct: 207 RLRALTDVCQQHGVRFISDEIYHGLTYTRPADTALA--CSDDTIVINSFSKYFSMTGWRI 264 Query: 244 GWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLD 303 GW++VP L RAV+ LT N I PP ++Q AA+ AF +A E + N YA NR LLL Sbjct: 265 GWMVVPQRLIRAVERLTQNLYISPPSIAQAAALGAF--DARVELEANRGVYAANRELLLA 322 Query: 304 GLRRIGIDRLAPTDGAFYVYADVSDF-----TSDSLAFCSKLLADTGVAIAPGIDFDTAR 358 L + G + AP DGAFY+Y +V +F D+ A LL + GVA+ PG DFD R Sbjct: 323 ELPKAGFTQFAPADGAFYLYCNVGEFLRDTGPQDAAALARTLLDEAGVALTPGNDFDAQR 382 Query: 359 GGSFVRISFAGPSGDIEEALRRIGSW 384 GG F+R S+AG + D+ EA RR+ W Sbjct: 383 GGQFLRFSYAGTTADMAEAARRLQVW 408 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: 465 Number of extensions: 34 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: 413 Length adjustment: 31 Effective length of query: 357 Effective length of database: 382 Effective search space: 136374 Effective search space used: 136374 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