Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_052669770.1 NITAL_RS17580 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000969705.1:WP_052669770.1 Length = 387 Score = 165 bits (417), Expect = 2e-45 Identities = 126/385 (32%), Positives = 184/385 (47%), Gaps = 31/385 (8%) Query: 22 AAAERQRTHGD-LVNLSAGQPSAGAPEPV-----RAAAAAALHLNQLGYSVALGIPELRD 75 A A+ + G+ ++ AG+P P + RAAA A H YS A G+P LR+ Sbjct: 11 AKAKALKAAGEPVIGFGAGEPDFPTPANIVEAAQRAAADPATHR----YSPAAGLPALRE 66 Query: 76 AIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCY-RNILSA 134 AIAA R G V PD V +T G F A D GD V + +P + Y +L A Sbjct: 67 AIAAKTLRDTGFEVAPDQVTVTNGGKHALYNVFQALVDPGDEVLIPAPYWVSYPAQVLLA 126 Query: 135 LGCEVVEIPCGPQTRFQPTAQMLAEIDPPLRGVVV-ASPANPTGTVIPPEELAAIASWCD 193 G V +P +T F+ + + L E ++V SP+NPTG V P +E+AAI +W Sbjct: 127 DGVPVA-VPTTKETGFRTSVEQLEEHRTDRTKILVFVSPSNPTGAVYPADEVAAIGAWAA 185 Query: 194 ASDVRLISDEVYHGLVYQGAPQTS---CAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPT 250 + +I+DE+Y L+Y A TS A Q + +VVN +K YAMTGWR+GW + P Sbjct: 186 EHGIWVITDEIYEHLIYGDATMTSLPVIAPQAAPRTIVVNGVAKTYAMTGWRVGWSICPL 245 Query: 251 VLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRI-G 309 + + ++ L T ++Q AA+ A A A+ A++ R L + L I G Sbjct: 246 EIAKGINKLQSQITSNVANVAQFAALEALGGSQDAVAEMR-AAFDRRRKLAVAELSAIDG 304 Query: 310 IDRLAPTDGAFYVYADVSDF---------TSDSLAFCSKLLADTGVAIAPGIDFDTARGG 360 +D + P +GAFYV+ S +L LL VA+ PG F Sbjct: 305 VDVVEP-EGAFYVFPSFEGVLGREIAGRTVSSTLELAEVLLEQVNVALVPGEAFGAP--- 360 Query: 361 SFVRISFAGPSGDIEEALRRIGSWL 385 + R+S+A D+ E + RI +L Sbjct: 361 GYARLSYALGDDDLAEGIARIAGFL 385 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: 436 Number of extensions: 23 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: 387 Length adjustment: 30 Effective length of query: 358 Effective length of database: 357 Effective search space: 127806 Effective search space used: 127806 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