Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_084056111.1 B9A12_RS02895 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_900176285.1:WP_084056111.1 Length = 398 Score = 155 bits (392), Expect = 2e-42 Identities = 112/375 (29%), Positives = 181/375 (48%), Gaps = 19/375 (5%) Query: 22 AAAERQRTHGD-LVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPELRDAIAAD 80 A A+ R G +++ G+P P + AA A+ Q Y+ GIPEL++AI Sbjct: 20 AKAKALRAQGKKVISFGVGEPDFDTPHHIGQAAIQAVQRGQTRYTAVQGIPELKEAIIDV 79 Query: 81 YQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNILSALGCEVV 140 + +G+ P+ V+++ G F A D GD+V + +P + Y +++ G E V Sbjct: 80 VRADYGLDYSPEEVLVSCGGKHSLYNLFQAVLDPGDQVIIPAPYWVSYPDMVRLAGAEPV 139 Query: 141 EIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIAS-WCDASDVR 198 + C T F+ Q L E I R +++ SP+NPTG PEEL +A D V Sbjct: 140 IVDCPMSTSFKLEPQALREAITERTRMLILNSPSNPTGVHYTPEELRGLAQVLLDHEQVV 199 Query: 199 LISDEVYHGLVYQGAPQTSCAWQTSR---NAVVVNSFSKYYAMTGWRLGWLLVPTVLRRA 255 ++SD++Y+ L+Y+GA + A R +VN SK YAMTGWR+G+LL + +A Sbjct: 200 IVSDDIYYRLLYKGAQWANMAMVEPRLKDRTFIVNGVSKTYAMTGWRIGYLLGDADVIKA 259 Query: 256 VDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGIDRLAP 315 + T P ++Q AAV+A + + ++A R +++ L R+ Sbjct: 260 AGKIQSQSTSNPCSVAQWAAVAALR-GSQEDVQTMRQAFARRREYVMERLGRLPGVTCPD 318 Query: 316 TDGAFYVYADVSDF---------TSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRIS 366 +GAFYV+ +VS + SL L+ + +A+ PG F R +R+S Sbjct: 319 PNGAFYVFPNVSAYYGKKAGERSIQGSLDLSDYLMEEAHLAVVPGAAFGEDR---CIRLS 375 Query: 367 FAGPSGDIEEALRRI 381 FA ++EE R+ Sbjct: 376 FALSMEELEEGFDRL 390 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: 380 Number of extensions: 23 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: 398 Length adjustment: 31 Effective length of query: 357 Effective length of database: 367 Effective search space: 131019 Effective search space used: 131019 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