Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_013707121.1 DESAC_RS10860 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000195295.1:WP_013707121.1 Length = 390 Score = 219 bits (557), Expect = 1e-61 Identities = 130/376 (34%), Positives = 196/376 (52%), Gaps = 9/376 (2%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PF VMD+ A E +R +++L GQP P+ V+ AA AA+ + Y+ ++G+ Sbjct: 13 ITPFLVMDILERAQELERQGISVIHLEVGQPDWDTPQVVKEAAFAAMQRGETQYTHSMGL 72 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 ELR AI Y ++G+ + PD V++T+G+S LL F A D GD + + P Y CY N Sbjct: 73 LELRQAICQHYAEKYGVRLTPDRVIVTSGTSPAMLLIFAALLDPGDEIILTDPHYACYPN 132 Query: 131 ILSALGCEVVEIPCGPQTRFQPTAQMLAE-IDPPLRGVVVASPANPTGTVIPPEELAAIA 189 + + P FQ + A + + +++ SPANPTGTV+ + + IA Sbjct: 133 FVRLVDAVPRYAPIRETDGFQVHQEDFARYLTARTKALLINSPANPTGTVLTRKHMEEIA 192 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 +ISDE+YHGL+Y+G + + + A V+N FSK YAMTGWRLG+L+ P Sbjct: 193 ----GLGPYVISDEIYHGLIYEGREHS--ILEFTDRAFVINGFSKAYAMTGWRLGYLIAP 246 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 R + L NF I Q A ++A T A AE + Y+ R L+DGL+++G Sbjct: 247 PEFMRPLQKLMQNFFISANAFVQQAGIAALT-LAGAEVEQMRQIYSQRRRFLVDGLKKLG 305 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 GAFYV+ + + DS +L V + PG+DF + G F+R S+A Sbjct: 306 FAIPVEPTGAFYVFVNAGHLSGDSYQLAFDILEQAHVGVTPGVDFG-SNGEGFLRFSYAN 364 Query: 370 PSGDIEEALRRIGSWL 385 +I EAL R+ +L Sbjct: 365 SLDNIGEALGRLEQYL 380 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: 366 Number of extensions: 16 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: 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 09 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