Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate 351943 BT2415 aspartate aminotransferase (NCBI ptt file)
Query= SwissProt::P96847 (388 letters) >FitnessBrowser__Btheta:351943 Length = 397 Score = 147 bits (370), Expect = 7e-40 Identities = 112/366 (30%), Positives = 176/366 (48%), Gaps = 24/366 (6%) Query: 32 DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91 D++NLS G+P P+ ++ AA A+ N YS G P LR+AI ++ +G+ Sbjct: 32 DVINLSVGEPDFNTPDHIKEAAKKAIDDNFSRYSPVPGYPALRNAIVEKLKKENGLEYTA 91 Query: 92 DAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTRFQ 151 + G+ A L + GD V + +P + Y ++ V + G + F+ Sbjct: 92 AQISCANGAKQSVCNAILVLVNPGDEVIVPAPYWVSYPEMVKMAEGTPVIVSAGIEQDFK 151 Query: 152 PTAQML-AEIDPPLRGVVVASPANPTGTVIPPEELAAIAS-WCDASDVRLISDEVYHGLV 209 T + L A I P + +++ SP+NPTG+V EELA +A+ V +I+DE+Y + Sbjct: 152 ITPKQLEAAITPKTKALILCSPSNPTGSVYSKEELAGLAAVLAKYPQVVVIADEIYEHIN 211 Query: 210 YQGAPQTSCAW-QTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPP 268 Y GA Q+ + + V+VN SK YAMTGWR+G++ P + +A + L G +T P Sbjct: 212 YIGAHQSIAQFPEMKERTVIVNGVSKAYAMTGWRIGFIAGPEWIVKACNKLQGQYTSGPC 271 Query: 269 VLSQIAAVSAF--TPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADV 326 +SQ AA +A+ T E E ++ R L++ + + + GAFY++ Sbjct: 272 SVSQKAAEAAYVGTQEPVKEMQ---KAFERRRDLIVKLAKEVPGFEVNVPQGAFYLFPKC 328 Query: 327 SDF-----------TSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIE 375 S F SD LA LL D VA G F +R+S+A +I Sbjct: 329 SYFFGKSNGERKIENSDDLAM--YLLEDAHVACVGGTSFGAP---ECIRMSYATSDENIV 383 Query: 376 EALRRI 381 EA+RRI Sbjct: 384 EAIRRI 389 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: 364 Number of extensions: 22 Number of successful extensions: 5 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: 397 Length adjustment: 31 Effective length of query: 357 Effective length of database: 366 Effective search space: 130662 Effective search space used: 130662 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