Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate Pf6N2E2_5161 Valine--pyruvate aminotransferase (EC 2.6.1.66) ## AvtA
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5161 Length = 390 Score = 261 bits (667), Expect = 2e-74 Identities = 143/378 (37%), Positives = 205/378 (54%), Gaps = 3/378 (0%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF+VM + A E Q D+++L G+P EP+ A AAL + Y+ A GI Sbjct: 12 IEPFHVMALLARANELQAAGHDVIHLEIGEPDFTTAEPIIQAGQAALAAGKTRYTAARGI 71 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 PELR+AIA Y +R+G+ ++P +++T G SG LLA D G +A PGYPC R+ Sbjct: 72 PELREAIAGFYGQRYGVEIDPRRILVTPGGSGALLLASALLVDPGKHWLLADPGYPCNRH 131 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQML-AEIDPPLRGVVVASPANPTGTVIPPEELAAIA 189 L + +P GP+ R+Q T ++ D G +VASPANPTGT++ +ELA ++ Sbjct: 132 FLRLVEGAAQLVPVGPEVRYQLTPDLVNRHWDQDSVGALVASPANPTGTILTRDELAGLS 191 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 + L+ DE+YHGL Y + + +A V+NSFSKY+ MTGWRLGWL+ P Sbjct: 192 KVIKGHNGHLVVDEIYHGLTY--GTDAASVLEVDDDAFVLNSFSKYFGMTGWRLGWLVAP 249 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 + ++ L N I P ++Q AA++ F P + A +A R LL LR +G Sbjct: 250 SAAVGELEKLAQNLYISAPSMAQYAALACFEPATIEIFEQRRAEFARRRDFLLPALRELG 309 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 +GAFY+YAD+S F D+ AFC L VA PG+DF + G VR ++ Sbjct: 310 FGIAVEPEGAFYLYADISAFGGDAFAFCQHFLETEHVAFTPGLDFGRHQAGHHVRFAYTQ 369 Query: 370 PSGDIEEALRRIGSWLPS 387 +EEA+ RI L S Sbjct: 370 SLPRLEEAVARIERGLRS 387 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: 413 Number of extensions: 26 Number of successful extensions: 3 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: 390 Length adjustment: 30 Effective length of query: 358 Effective length of database: 360 Effective search space: 128880 Effective search space used: 128880 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