Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_027457779.1 K420_RS0109050 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000519045.1:WP_027457779.1 Length = 385 Score = 107 bits (267), Expect = 6e-28 Identities = 107/372 (28%), Positives = 168/372 (45%), Gaps = 30/372 (8%) Query: 26 RQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRH 85 R T VNLS G P A + A + + Y+ G+PELR AI + Sbjct: 24 RLATECGAVNLSQGFPDFQAEPALFDAVHRHMLAGRNQYAPMGGLPELRQAIVDKVATLY 83 Query: 86 GITVEPDA-VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPC 144 G + ++ V +T G++ A A GD V + P Y Y + +G + V Sbjct: 84 GPRFDVESEVTVTAGATQAIFTAIAAFVRPGDEVIVFEPVYDSYVPAIETVGGQAVFA-- 141 Query: 145 GPQTRFQPTA----QMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLI 200 Q RF A Q+ I+ R ++V SP NPTG+++ +L +A +D+ ++ Sbjct: 142 --QLRFPDYAPDWDQVRGLINERTRMIIVNSPHNPTGSLLTAADLDRLAGLVRGTDIVIL 199 Query: 201 SDEVYHGLVYQGAPQTS-CAW-QTSRNAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDC 258 SDEVY +V+ G S CA + + ++VV+SF K Y +TGW++G+++ P L Sbjct: 200 SDEVYEHIVFDGERHASLCAHAELAVRSIVVSSFGKTYHITGWKIGYVVGPAALMAEFRK 259 Query: 259 L--TGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGID---RL 313 + FT+ P SQ+ A++ + +A+ G A Y R D R++ L Sbjct: 260 VHQFNVFTVHAP--SQL-AIAEYMQDASRHL-GLAAFYQAKR----DHFRQLMAATPFTL 311 Query: 314 APTDGAFYV---YADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDT-ARGGSFVRISFAG 369 P G ++ YA +SD AF L + GVA+ P F+ R VR FA Sbjct: 312 LPCRGTYFQLARYAGMSDL--PDRAFAEWLTREVGVAVIPVSVFNADGRDDQVVRFCFAK 369 Query: 370 PSGDIEEALRRI 381 +E A+ R+ Sbjct: 370 REATLEAAVERL 381 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: 355 Number of extensions: 17 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: 385 Length adjustment: 30 Effective length of query: 358 Effective length of database: 355 Effective search space: 127090 Effective search space used: 127090 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