Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate SMc01340 SMc01340 aminotransferase
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__Smeli:SMc01340 Length = 385 Score = 349 bits (896), Expect = e-101 Identities = 187/386 (48%), Positives = 249/386 (64%), Gaps = 8/386 (2%) Query: 4 RVALRAGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLG 63 +++ R+ V PF+ MDV A R+ + +++++ GQP+ AP+ AA AL +LG Sbjct: 3 QMSKRSAVEPFHAMDVLAEATRRRDSGHPVISMAVGQPAHPAPKAALDAARRALDHGRLG 62 Query: 64 YSVALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASP 123 Y+ ALG L+ AIAA Y RHGIT++P + +TTGSS GF LAFLA FD GDRVA+A P Sbjct: 63 YTDALGTHSLKRAIAAHYHSRHGITLDPQRIAVTTGSSAGFNLAFLALFDPGDRVAIARP 122 Query: 124 GYPCYRNILSALGCEVVEIPCGPQTRFQPTAQML----AEIDPPLRGVVVASPANPTGTV 179 GYP YRNI++ALG EVVEI + F T L A PL+GV++ASPANPTGTV Sbjct: 123 GYPAYRNIMAALGLEVVEIEANAEAGFTLTPDSLEGAAARAGKPLKGVLLASPANPTGTV 182 Query: 180 IPPEELAAIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMT 239 +L A+A +C + ISDE+YHGL + G T A + + +AVV+NSFSKYY MT Sbjct: 183 TGKAQLKALADYCRDHSIAFISDEIYHGLTFAGEETT--ALEVADDAVVINSFSKYYCMT 240 Query: 240 GWRLGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRS 299 GWR+GW+++P RA + + + I PP LSQIAA +A A E DG +YA NR+ Sbjct: 241 GWRIGWMVLPEARVRAFERIAQSLYISPPELSQIAAEAAL--GAHEELDGYKRAYAANRA 298 Query: 300 LLLDGLRRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARG 359 LLL+ L +IG +P DGAFY YADVS FT+DS+AF ++LA+ VA PG DFD G Sbjct: 299 LLLERLPQIGFSIASPMDGAFYAYADVSRFTNDSMAFARRMLAEIDVAATPGFDFDPLEG 358 Query: 360 GSFVRISFAGPSGDIEEALRRIGSWL 385 +R S+AG + ++EEA+ RI WL Sbjct: 359 HRTMRFSYAGAATEMEEAMNRIARWL 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: 468 Number of extensions: 24 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 Jul 25 2024. The underlying query database was built on Jul 25 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