Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_077280099.1 B1C78_RS15630 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_002000365.1:WP_077280099.1 Length = 389 Score = 270 bits (690), Expect = 5e-77 Identities = 148/375 (39%), Positives = 211/375 (56%), Gaps = 5/375 (1%) Query: 9 AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVAL 68 A + PF+VMD+ A + +V+L G+P PEP+ A AL Y+ A+ Sbjct: 13 ADIEPFHVMDLLARARRLEAAGRSIVHLEIGEPDFPTPEPIMEAGRKALADGHTHYTPAV 72 Query: 69 GIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY 128 G+P LR+ IA Y+ RHG+ V P+ ++IT G+SG LL D GD+V MA PGYPC Sbjct: 73 GLPALRETIAGFYRDRHGVDVSPERIIITPGASGALLLVMAVLLDPGDQVLMADPGYPCN 132 Query: 129 RNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGV--VVASPANPTGTVIPPEELA 186 R+ + E V +P GP++ +Q TA+ L E R V +VASPANPTGT++ + + Sbjct: 133 RHFVRTFEGEAVSVPVGPESAYQLTAEHL-ESHWGERSVAAMVASPANPTGTLVSADTMK 191 Query: 187 AIASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWL 246 + ++ RLI DE+YHGLVY T+ A S + V+NSFSKY+ MTGWRLGW+ Sbjct: 192 RMLAFTAGRGGRLIVDEIYHGLVYDEEAITALAH--SPDVFVINSFSKYFGMTGWRLGWI 249 Query: 247 LVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLR 306 + P R++D L N + P +Q AA++AF PE D ++ R LL LR Sbjct: 250 VAPEDYVRSIDKLAQNLFLAAPTPAQHAALAAFQPETLQILDARREAFRERRDFLLPALR 309 Query: 307 RIGIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRIS 366 +G +GAFY+YAD + F SDS +LL + GVAI PG+DF R + VR + Sbjct: 310 DLGFGIPVTPEGAFYIYADSTAFDSDSQRLAERLLEEVGVAITPGLDFGHHRPQAHVRFA 369 Query: 367 FAGPSGDIEEALRRI 381 + ++EE + R+ Sbjct: 370 YTREIAELEEGVARL 384 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: 434 Number of extensions: 20 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: 389 Length adjustment: 30 Effective length of query: 358 Effective length of database: 359 Effective search space: 128522 Effective search space used: 128522 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