Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_043743690.1 AMB_RS07030 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000009985.1:WP_043743690.1 Length = 384 Score = 399 bits (1026), Expect = e-116 Identities = 198/384 (51%), Positives = 266/384 (69%), Gaps = 2/384 (0%) Query: 1 MTDRVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLN 60 MT + A R + PF VMDV AA RQ D+++L GQPS AP V AAA A+ Sbjct: 1 MTFKAARRGAIAPFIVMDVMRDAAARQAAGADVIHLEVGQPSGQAPPKVLDAAARAVRTE 60 Query: 61 QLGYSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAM 120 LGY++ALG LR+ IA Y + +G++V P+ V +TTGSS FLLAFLA F+ GDRVA+ Sbjct: 61 PLGYTLALGRDSLRERIARHYHQAYGVSVVPERVCVTTGSSAAFLLAFLAAFEPGDRVAV 120 Query: 121 ASPGYPCYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVI 180 A+PGYP YRNIL +LG E V +P GP +R+Q TA++LA ++ L GVVVASP+NPTG+++ Sbjct: 121 AAPGYPAYRNILESLGVECVLVPVGPSSRWQITAEVLAGVEGRLDGVVVASPSNPTGSML 180 Query: 181 PPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTG 240 E+A +A WC+ +RLISDE+YHG+ Y A T+ + +AVV+NSFSKYYAMTG Sbjct: 181 SAHEVAELAGWCELHGIRLISDEIYHGITYGRAAATAAGMAAAPHAVVINSFSKYYAMTG 240 Query: 241 WRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSL 300 WRLGW+++P L R+V+CLT N I PP LSQ+AA S F + E + +A+Y NR + Sbjct: 241 WRLGWMVLPEDLARSVECLTQNLYISPPTLSQVAAESVF--DCIDELEARVAAYRANRDI 298 Query: 301 LLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGG 360 L+ L + G DRLAP+DGAFY+YADVS+ T+DS FC+++LA+TGVA PG+DFD G Sbjct: 299 LVAELPKAGFDRLAPSDGAFYLYADVSEMTNDSREFCARMLAETGVACTPGVDFDPIEGH 358 Query: 361 SFVRISFAGPSGDIEEALRRIGSW 384 +R S+AG + + EA RR+ +W Sbjct: 359 RTLRFSYAGSAEHMAEAARRLKAW 382 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: 479 Number of extensions: 22 Number of successful extensions: 2 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: 384 Length adjustment: 30 Effective length of query: 358 Effective length of database: 354 Effective search space: 126732 Effective search space used: 126732 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