Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_084143905.1 METAC_RS0104560 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000427445.1:WP_084143905.1 Length = 370 Score = 342 bits (876), Expect = 1e-98 Identities = 183/371 (49%), Positives = 239/371 (64%), Gaps = 6/371 (1%) Query: 17 MDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDA 76 +DV + A R++ D+++L G+P+A P VR AA AAL ++GY+ ALG P LR Sbjct: 3 LDVMVGARRREQEGHDVIHLEIGEPAASPPRAVREAALAALDGRRIGYTEALGRPSLRAR 62 Query: 77 IAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALG 136 IA Y+ +G+ + P+ + +TTGSSGGF+LAFLA FD G RVA+A+PGYP YRNIL LG Sbjct: 63 IARHYRETYGVEIAPERIAVTTGSSGGFILAFLALFDVGARVAIAAPGYPAYRNILETLG 122 Query: 137 CEVVEIPCGPQTRFQPTAQML--AEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDA 194 E V + + F TA M+ A + L GV++ SPANPTG++ + L I C Sbjct: 123 IETVTLEAPEENGFIVTAAMIEAAHAEKALDGVLLMSPANPTGSMTSGDALREICEACAR 182 Query: 195 SDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRR 254 + LISDEVYHGL Y+ Q A Q S +AVVVNSFSKY+ MTGWR+GWL++P L R Sbjct: 183 LRIALISDEVYHGLTYEA--QAQSALQFSSDAVVVNSFSKYFCMTGWRIGWLVLPDALIR 240 Query: 255 AVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLA 314 ++ L + I P LSQ+ A +AF EA AE +A+YA NR++LL+ L +G+ R Sbjct: 241 PIERLQQSLAISVPFLSQLGAEAAF--EAKAELASVVAAYARNRAILLNELPAMGLGRFP 298 Query: 315 PTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDI 374 DGAFYVY DVS FT DSL FC ++L D GVA PG+DFD RG VR SFAGP D+ Sbjct: 299 RPDGAFYVYVDVSRFTDDSLDFCGRMLKDIGVAATPGLDFDRCRGHCAVRFSFAGPEKDL 358 Query: 375 EEALRRIGSWL 385 EA+ R+ SWL Sbjct: 359 IEAMLRLKSWL 369 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: 423 Number of extensions: 23 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: 370 Length adjustment: 30 Effective length of query: 358 Effective length of database: 340 Effective search space: 121720 Effective search space used: 121720 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