Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate YP_002825650.1 NGR_c11110 aspartate transaminase protein
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000018545.1:YP_002825650.1 Length = 385 Score = 343 bits (879), Expect = 6e-99 Identities = 181/386 (46%), Positives = 246/386 (63%), Gaps = 8/386 (2%) Query: 4 RVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLG 63 +++ R+ V PF+ MDV A R+ +++++ GQP+ AP+ R AA AL +LG Sbjct: 3 QMSKRSAVEPFHAMDVLAEATRRRDAGHPVISMAVGQPAHPAPKAAREAARRALEHGRLG 62 Query: 64 YSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASP 123 Y+ ALG L+ AIAA YQ RHGI ++P + +TTGSS GF LAFLA FD GD VA+A P Sbjct: 63 YTDALGTLSLKRAIAAHYQSRHGIALDPQRIAVTTGSSAGFNLAFLALFDPGDCVAIARP 122 Query: 124 GYPCYRNILSALGCEVVEIPCGPQTRFQPTAQML----AEIDPPLRGVVVASPANPTGTV 179 GYP YRNI++ALG VVEI +T F T + L A+ PL+GV++ASPANPTGTV Sbjct: 123 GYPAYRNIMAALGLSVVEIEANAETGFTLTPESLERAAAQAGKPLKGVLLASPANPTGTV 182 Query: 180 IPPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMT 239 L A+A +C A + ISDE+YHGL + G + + A + + +A+V+NSFSKYY MT Sbjct: 183 TGRARLKALADYCRAQSIAFISDEIYHGLTFAG--EETSALEIADDAIVINSFSKYYCMT 240 Query: 240 GWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRS 299 GWR+GW+++P R + + + I PP LSQIAA +A A E DG +YA NR Sbjct: 241 GWRIGWMVLPEDQIRVFERIAQSLYISPPELSQIAAEAAL--GAQEELDGYKRAYAANRD 298 Query: 300 LLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARG 359 LL+ L +G+ +P DGAFY Y D S FT+DS+AF ++LA+ VA PG DFD G Sbjct: 299 LLMRRLPELGLSIASPMDGAFYAYVDASRFTNDSMAFARRMLAEINVAATPGFDFDPLEG 358 Query: 360 GSFVRISFAGPSGDIEEALRRIGSWL 385 +R S+AG + D+ EA+ RI +WL Sbjct: 359 HRTMRFSYAGSAADMAEAMDRIANWL 384 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: 466 Number of extensions: 21 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: 385 Length adjustment: 30 Effective length of query: 358 Effective length of database: 355 Effective search space: 127090 Effective search space used: 127090 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