Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_013135865.1 ARNIT_RS10285 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000092245.1:WP_013135865.1 Length = 390 Score = 170 bits (431), Expect = 6e-47 Identities = 115/375 (30%), Positives = 181/375 (48%), Gaps = 10/375 (2%) Query: 13 PFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPE 72 P M + E + D+++ SAG+P P+ V+ AA A+ Y+ GI E Sbjct: 12 PSVTMAITALGRELKAQGKDILSFSAGEPDFDTPDIVKQAAIKAIQDGHTKYTAVEGITE 71 Query: 73 LRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNIL 132 + AI ++ HG+ D ++I+ G+ F + GD V + +P + Y + Sbjct: 72 TKKAIITKLKKDHGLNYNLDEIIISNGAKHSLFNLFQVLIEEGDEVIIPAPYWVTYPEQV 131 Query: 133 SALGCEVVEIPCGPQTRFQPTAQML-AEIDPPLRGVVVASPANPTGTVIPPEELAAIASW 191 V I T F+ TA+ + A I P + +++ +P+NPTG + EEL AI Sbjct: 132 KFSDGVPVFIETDDTTGFKVTAEQIKAAITPKTKVLLLNTPSNPTGAIYTKEELTAIGKV 191 Query: 192 CDASDVRLISDEVYHGLVYQGAPQTSCAWQTS---RNAVVVNSFSKYYAMTGWRLGWLLV 248 + +D+ + SDE+Y ++Y G + A + + V +N SK AMTGWR G+L Sbjct: 192 LEGTDILVFSDEMYEKIIYDGKKFCTAAEVSDDMFQRTVTINGLSKAVAMTGWRFGYLAT 251 Query: 249 PTV-LRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRR 307 P L +A+ L G T ++Q AA+ A EA A + + R + ++ Sbjct: 252 PQKNLVKAMTKLQGQVTSNVNSITQYAAIPALEGEADATIEIMRKEFEKRRDISVEKFNA 311 Query: 308 I-GIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRIS 366 I GI L P DGAFY++ ++ + T DS+ FCS LL GVA+ PG+ F T + R S Sbjct: 312 IKGISCLKP-DGAFYLFVNIKELTFDSMKFCSDLLELKGVAVVPGLAFGTE---GYFRFS 367 Query: 367 FAGPSGDIEEALRRI 381 FA I + + RI Sbjct: 368 FATDLDSILKGIARI 382 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: 286 Number of extensions: 10 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: 390 Length adjustment: 30 Effective length of query: 358 Effective length of database: 360 Effective search space: 128880 Effective search space used: 128880 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