Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011734893.1 PPRO_RS04680 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000015045.1:WP_011734893.1 Length = 381 Score = 213 bits (542), Expect = 7e-60 Identities = 133/372 (35%), Positives = 196/372 (52%), Gaps = 15/372 (4%) Query: 14 FYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPEL 73 F VMDV A E +R D+++L G+P G PE V A + A+ Y+ +LG+ EL Sbjct: 12 FIVMDVLEKAQEMERAGIDVIHLEVGEPDFGVPECVSEAISRAVRDGHTHYTHSLGMVEL 71 Query: 74 RDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILS 133 R+AI Y + +G+ V PD VV+T+G+S L F GD V ++ P Y CY N + Sbjct: 72 REAICEHYGKNYGVAVHPDQVVVTSGTSPAMLSMFSTLLAKGDEVIISDPHYACYPNFIQ 131 Query: 134 ALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIAS-- 190 L +VV++P FQ + + + I R +++ SP+NPTGTV+ E + AIA Sbjct: 132 FLEGKVVKVPVCEDDGFQYRPEAIRDRITERTRAILINSPSNPTGTVLSAERMWAIAQLG 191 Query: 191 -WCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 +C ISDE+YHGL Y G+ T + + +A V+N FSK +AMTG RLG+L+ P Sbjct: 192 PYC-------ISDEIYHGLNYHGSEHT--ILEFTDHAFVLNGFSKIFAMTGLRLGYLIAP 242 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 R + L NF + P ++QI ++A EA A+ +Y R ++ LR IG Sbjct: 243 PCFIRPLQKLQQNFFLAPNSVAQIGGIAAL-KEADADVLRMRNTYDQRRRFMIQRLRDIG 301 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 GAFYV+A+ + DS A +L V + PGIDF G ++R ++A Sbjct: 302 FGIPVEPTGAFYVFANAKHLSGDSYALAYDILEKARVGVTPGIDFGQG-GEGYLRFTYAN 360 Query: 370 PSGDIEEALRRI 381 +I E L R+ Sbjct: 361 SLENIAEGLSRL 372 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: 392 Number of extensions: 14 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: 381 Length adjustment: 30 Effective length of query: 358 Effective length of database: 351 Effective search space: 125658 Effective search space used: 125658 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