Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_012567061.1 RC1_RS09020 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000016185.1:WP_012567061.1 Length = 401 Score = 135 bits (340), Expect = 2e-36 Identities = 112/368 (30%), Positives = 172/368 (46%), Gaps = 24/368 (6%) Query: 32 DLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEP 91 D++ L AG+P P+ ++ AA A+ Y+ G PEL+ A+AA ++R +G+ +P Sbjct: 32 DVIGLGAGEPDFDTPDSIKDAAIEAIRRGFTKYTDVDGTPELKKAVAAKFRRDNGLEYDP 91 Query: 92 DAVVITTGSSGGFLL--AFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPCGPQTR 149 A IT G+ G +L A LA D GD V + +P + Y +++ V + C + Sbjct: 92 -ATQITVGTGGKQVLFNALLATLDPGDEVIVPAPYWVSYPDMVLLAEGTPVPVACPAEAG 150 Query: 150 FQPT-AQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIAS-WCDASDVRLISDEVYHG 207 F+ T A + A I P + +++ SP+NPTG EL A+ V ++SD++Y Sbjct: 151 FKLTPAALEAAITPRTKWLILNSPSNPTGAAYTAAELTALGEVLLRHPQVWVMSDDMYEH 210 Query: 208 LVYQGAPQTSCAWQTS---RNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFT 264 LVY G + A + VN SK Y+MTGWR+G+ P L +A+ + T Sbjct: 211 LVYDGFRFATIAQVVPGLLGRTLTVNGVSKAYSMTGWRIGFAGGPKELIKAMGVIQSQST 270 Query: 265 ICPPVLSQIAAVSAFT-PEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVY 323 P +SQ AA A P+ + +A R L++ L + +GAFYVY Sbjct: 271 SNPTSISQAAATEALNGPQDYIPRQAEV--FARRRDLVVSMLNQAKGLSCPNPEGAFYVY 328 Query: 324 ADVSDFTSDSLA----------FCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGD 373 + S F ++LL GVA+ G F + RIS+A Sbjct: 329 PSCAATLGLSTPGGRVIGSDEDFATELLEAEGVAVVHGAAFGLS---PHFRISYATSETV 385 Query: 374 IEEALRRI 381 +EEA RRI Sbjct: 386 LEEACRRI 393 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: 386 Number of extensions: 26 Number of successful extensions: 7 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: 401 Length adjustment: 31 Effective length of query: 357 Effective length of database: 370 Effective search space: 132090 Effective search space used: 132090 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