Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011446155.1 SARO_RS12655 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000013325.1:WP_011446155.1 Length = 385 Score = 333 bits (853), Expect = 6e-96 Identities = 177/380 (46%), Positives = 240/380 (63%), Gaps = 7/380 (1%) Query: 9 AGVPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVAL 68 A V PF+ + + A + + ++++ GQPS GAP A A L +GY ++ Sbjct: 3 AQVEPFHAIAISRLAHDLEAAGQSVIHMEFGQPSTGAPAEAIALAHEVLDNEAMGYWESV 62 Query: 69 GIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY 128 L++ IA Y HG+ VE + V++T G+S F++A F G R+A+A PGY Y Sbjct: 63 ---PLKERIARSYAENHGVKVEREQVILTCGASPAFVMALSCLFRPGARIALARPGYVAY 119 Query: 129 RNILSALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAI 188 RN L A+ E VE+ CGP RFQ TA + +DP G++VASPANPTGT+I P ELAAI Sbjct: 120 RNSLKAMYLEPVEMECGPAERFQVTAAAVDALDPVPDGLIVASPANPTGTIIEPGELAAI 179 Query: 189 ASWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLV 248 A C +R+ISDE+YHGL Y A + + +AV+VNSFSKY++M GWRLGWL+V Sbjct: 180 AEVCCRKGIRVISDEIYHGLSYGKAAASMLEYLP--DAVIVNSFSKYFSMAGWRLGWLVV 237 Query: 249 PTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRI 308 P L A G+ + PPVL+Q A + AF + AE DG++ +YA NR++LL+ L ++ Sbjct: 238 PPSLIDAARARMGSLFLTPPVLAQKAGLKAF--DCRAELDGHVETYARNRAILLEALPQM 295 Query: 309 GIDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFA 368 G+ R+AP DGAFY+YAD S+FT DSLA C LL DTGVA APG+DFD G F+R SFA Sbjct: 296 GLGRIAPPDGAFYIYADASEFTDDSLALCEALLRDTGVATAPGLDFDPVNGKRFIRFSFA 355 Query: 369 GPSGDIEEALRRIGSWLPSQ 388 + IEEA+RRIG W ++ Sbjct: 356 VSTPLIEEAVRRIGPWFAAR 375 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: 456 Number of extensions: 16 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