Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate NP_348995.1 CA_C2380 PLP-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000008765.1:NP_348995.1 Length = 395 Score = 153 bits (386), Expect = 9e-42 Identities = 107/359 (29%), Positives = 173/359 (48%), Gaps = 10/359 (2%) Query: 34 VNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAADYQRRHGITVEPDA 93 ++L+ GQP P+ V+ A A+ N+ Y+ GI ELR+ I+ Y +R I D Sbjct: 40 ISLTLGQPDFPVPDKVKRAMVRAIEDNKTVYTSNAGIDELRNEISK-YLKRFNINYSKDE 98 Query: 94 VVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVVEIPC-GPQ--TRF 150 + IT G + G L F A + GD+V + P +P Y + L EV+ G + F Sbjct: 99 ICITAGGTEGILDIFQALLNKGDKVLVPDPSFPAYASCTKLLEGEVITYGLYGSEFSIDF 158 Query: 151 QPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIASWCDASDVRLISDEVYHGLVY 210 + P + +V++ P+NPTGTVI E+ + +D+ ++DE+Y L Y Sbjct: 159 NELENKIKNEKP--KFMVLSYPSNPTGTVISKEDNEKLHKIIKDNDIIAVTDEMYSALCY 216 Query: 211 QGAPQTSCAWQTSR-NAVVVNSFSKYYAMTGWRLGWLLVPTVLRRAVDCLTGNFTICPPV 269 + + ++ R +VV+ FSK ++MTG R+G++ + ++ + T C P Sbjct: 217 EDDYYSVSQYEDIREKVIVVSGFSKTFSMTGLRIGYVCAESSFMSSILKVHQYTTTCAPS 276 Query: 270 LSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAPTDGAFYVYADVSDF 329 +SQ A+ + + R + L+ +G + P GAFY++ D+S F Sbjct: 277 ISQYGALEGL-KNCDEDVQYMKNEFKKRRDYVYKRLKDMGFEVRLP-KGAFYIFPDISRF 334 Query: 330 TSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGPSGDIEEALRRIGSWLPSQ 388 S FC KLL + VAI PG F +G F RIS+A ++EE + RI W+ Q Sbjct: 335 GMTSEQFCEKLLNEAKVAIVPGSAFG-EKGEGFARISYAYSKKELEECMNRIEKWVEVQ 392 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: 288 Number of extensions: 11 Number of successful extensions: 6 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: 395 Length adjustment: 31 Effective length of query: 357 Effective length of database: 364 Effective search space: 129948 Effective search space used: 129948 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