Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate 8501474 DvMF_2204 aminotransferase class I and II (RefSeq)
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__Miya:8501474 Length = 390 Score = 148 bits (374), Expect = 2e-40 Identities = 113/384 (29%), Positives = 179/384 (46%), Gaps = 14/384 (3%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + P + V A E + +V+L+ G+P PE VR AA A+ Y+ GI Sbjct: 10 IKPSATLAVNAKALELKAKGVQVVSLAVGEPDFPTPEHVREAAKTAIDQGFTRYTQVPGI 69 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 PELR A+ + R +G+ +A V+T G F + GD V + +P + Y Sbjct: 70 PELRQAVCGYFARFYGVEAPMEATVVTNGGKQALYNLFQCLLNPGDEVLVPAPYWVSYPA 129 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQML-AEIDPPLRGVVVASPANPTGTVIPPEELAAIA 189 ++ G V + + F+ T + L + P R +++ SP+NPTG E AI Sbjct: 130 LVELAGGVPVFVASPAERGFKVTPEELDRAVTPKTRVLLLNSPSNPTGACYSRAETDAIM 189 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTS-CAW--QTSRNAVVVNSFSKYYAMTGWRLGWL 246 W A D+ ++SDE+Y LVY+ A S C W + N VVN +K +AMTGWR+G+ Sbjct: 190 EWAIARDLFVVSDEIYDRLVYEPAEAVSVCDWWERHPENVAVVNGLAKTFAMTGWRVGYA 249 Query: 247 LVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLR 306 L L +A+ + G T ++Q AA++A T +A + R L G+ Sbjct: 250 LAHPDLIKAMTKIQGQSTSNICSVAQKAALAALT--GPYDAVEEMKKSFRRRRDLAHGIV 307 Query: 307 RIGIDRLAP-TDGAFYVYADV----SDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGS 361 + P DGAFY++AD+ + DS + C+ ++ VA+ PG F + Sbjct: 308 SSWPGVICPKPDGAFYLFADMRALFTPALPDSASLCTYIMEQANVALVPGAAFG---DDA 364 Query: 362 FVRISFAGPSGDIEEALRRIGSWL 385 +R S+A + AL ++ L Sbjct: 365 CLRFSYAVSDDTLMIALDKVAKVL 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: 407 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: 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