Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate H281DRAFT_05564 H281DRAFT_05564 Aspartate/methionine/tyrosine aminotransferase
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__Burk376:H281DRAFT_05564 Length = 392 Score = 285 bits (730), Expect = 1e-81 Identities = 156/378 (41%), Positives = 215/378 (56%), Gaps = 7/378 (1%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF+ M+ AA + ++ LS G+P GAP V AA A+ L Y+ ALGI Sbjct: 10 ISPFFAMEFGKRAAALEAQGHHIIKLSIGEPDFGAPPAVSLAAREAMDGRSLAYTSALGI 69 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 P LR+AIA Y+ H + V +V+T G+S LL A D GD V + P YPC R Sbjct: 70 PALREAIAGFYREVHDVEVHSSRIVVTAGASAALLLVTAALVDPGDEVIVGDPSYPCNRQ 129 Query: 131 ILSALGCEVVEIPCGPQTRFQ-PTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIA 189 L++ G +V +P TRFQ A + A RG+++A+P+NPTGT IPP EL AI Sbjct: 130 FLASFGAQVKLVPTDANTRFQLDAAAVRANWTEKTRGLMIATPSNPTGTSIPPHELEAIC 189 Query: 190 SWCDASDVRLISDEVYHGL----VYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGW 245 SW + I DE+Y L + APQT ++ +A+V+NSFSKY+ MTGWRLGW Sbjct: 190 SWAHQHNAWRIVDEIYLNLGDHDAHGRAPQTVLSFDP--DAIVINSFSKYFGMTGWRLGW 247 Query: 246 LLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGL 305 +VP L ++ L N+ ICP +SQ AA++ FT E+ A + +A R+L+L GL Sbjct: 248 CVVPDALVPTMERLAQNYYICPSTISQHAALACFTRESLALCEARRQQFAERRALVLAGL 307 Query: 306 RRIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRI 365 RIG+ P DGAFYVY DV S FC + L + VA+ PG DF + +FVR+ Sbjct: 308 ERIGLPVPVPPDGAFYVYFDVGHTGLTSWEFCERALEEAHVALTPGKDFGSCGAETFVRL 367 Query: 366 SFAGPSGDIEEALRRIGS 383 S+A + D+ EA+ R+GS Sbjct: 368 SYAASTSDLAEAIERLGS 385 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: 448 Number of extensions: 19 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: 392 Length adjustment: 31 Effective length of query: 357 Effective length of database: 361 Effective search space: 128877 Effective search space used: 128877 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