Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_092991566.1 BLP65_RS00600 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900102855.1:WP_092991566.1 Length = 393 Score = 265 bits (677), Expect = 2e-75 Identities = 153/378 (40%), Positives = 208/378 (55%), Gaps = 4/378 (1%) Query: 9 AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVAL 68 A + PF+VM++ A E + D+V++ G+P G PEP+ A AL Y+ AL Sbjct: 14 ADIEPFHVMELLGRARELEAAGHDIVHMEIGEPDFGTPEPIIERARQALTDGHTHYTPAL 73 Query: 69 GIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY 128 G+P LR+AIA Y+ R+G+ ++P VVIT G+SG LLA D D + +A PGYPC Sbjct: 74 GLPALREAIAGHYRDRYGVEIDPGRVVITPGASGALLLALGVLLDRDDELLLADPGYPCN 133 Query: 129 RNILSALGCEVVEIPCGPQTRFQPTAQML-AEIDPPLRGVVVASPANPTGTVIPPEELAA 187 R+ + + +P TR+Q A+ L A + +VASP+NPTGT++ ELAA Sbjct: 134 RHFARFVEGQARGVPVDATTRYQLDAERLSAHWNERCVAALVASPSNPTGTLLERSELAA 193 Query: 188 IASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLL 247 +A RLI DE+YHGL Y +T A A VVNSFSKY+ MTGWRLGWL+ Sbjct: 194 LAESVRVRSGRLIVDEIYHGLTYGIEAETVLA--VDHGAFVVNSFSKYFCMTGWRLGWLV 251 Query: 248 VPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRR 307 P +R V+ L N I P L+Q AA++AF PE + A + R LL LR Sbjct: 252 APEEYQREVEKLMQNLFIAAPTLAQHAALAAFEPETRKILESRRAEFERRRDFLLPALRE 311 Query: 308 IGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISF 367 +G + GAFY+YAD S F DS S LL GVA+ PG+DF R +R ++ Sbjct: 312 LGFEIPVEPRGAFYLYADCSRF-GDSKQLASDLLEKAGVAVTPGLDFGNYRPEQHLRFAY 370 Query: 368 AGPSGDIEEALRRIGSWL 385 +EE +RRI +L Sbjct: 371 TTSMERLEEGVRRIAGFL 388 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: 437 Number of extensions: 17 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: 393 Length adjustment: 31 Effective length of query: 357 Effective length of database: 362 Effective search space: 129234 Effective search space used: 129234 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