Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_085773856.1 B1812_RS19415 1-aminocyclopropane-1-carboxylate deaminase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_002117405.1:WP_085773856.1 Length = 380 Score = 334 bits (856), Expect = 3e-96 Identities = 176/372 (47%), Positives = 237/372 (63%), Gaps = 8/372 (2%) Query: 17 MDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDA 76 MDV A +R +V++ G+P A P + AA AL GY A G P LR Sbjct: 3 MDVLREARRLEREGRRIVHMELGEPGAPTPRRILDAAQRALAAGAPGYGEAAGDPALRTR 62 Query: 77 IAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALG 136 IA YQ +G+ + P+ V+ITTGSSG FLLAFL+ FD G R+ + +PGYP Y NIL ALG Sbjct: 63 IARHYQEYYGVALSPERVMITTGSSGAFLLAFLSAFDIGARIGVTAPGYPAYLNILEALG 122 Query: 137 CEVVEIPCGPQTRFQPTAQML--AEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDA 194 I G +TRF PTA ++ A L G+++ SPANPTGT+I ELA IA++C+ Sbjct: 123 LVPAPIEIGEETRFAPTAALIEAAHRKERLDGLLLMSPANPTGTMIASGELARIAAFCEE 182 Query: 195 SDVRLISDEVYHGLVY-QGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLR 253 + V L++DE+YHGL Y + AP W R+A++VNSFSKYYAMTGWRLGW++ P L Sbjct: 183 AGVTLVADEIYHGLEYEERAPTALRFW---RDAIIVNSFSKYYAMTGWRLGWIVAPENLA 239 Query: 254 RAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRL 313 R ++ L + IC P L+Q A+ AF EA E + A YA +R+LL++ L +IG+ R Sbjct: 240 RPIERLQQSLAICAPTLAQRVALEAF--EAREELEAIKAGYAKSRALLIERLPKIGLPRF 297 Query: 314 APTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGD 373 AP DGAFY+YADV+ T DS A C+++LA+ GVA PG+DFD ARGG +R+S+AG + Sbjct: 298 APPDGAFYIYADVTHLTRDSAALCARMLAEAGVAATPGVDFDRARGGRTLRLSYAGGEAE 357 Query: 374 IEEALRRIGSWL 385 + + L R+ WL Sbjct: 358 VAQGLDRLADWL 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: 470 Number of extensions: 20 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: 380 Length adjustment: 30 Effective length of query: 358 Effective length of database: 350 Effective search space: 125300 Effective search space used: 125300 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