Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_011802293.1 PNAP_RS14575 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000015505.1:WP_011802293.1 Length = 398 Score = 237 bits (605), Expect = 4e-67 Identities = 142/384 (36%), Positives = 206/384 (53%), Gaps = 13/384 (3%) Query: 11 VPPFYVMDVWLAAAERQR----THGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSV 66 + PFYVM+V AA+ + T ++ L+ G+P AP V+ AA+ A+ Y+ Sbjct: 10 IEPFYVMEVAKAASALAQQVADTDSPMIFLNIGEPDFTAPPLVQQAASRAIAQGNTQYTP 69 Query: 67 ALGIPELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYP 126 ALG+P LR+ I+ Y R G V P +VIT G+S LA LA +AGD + M P YP Sbjct: 70 ALGLPALRERISGWYASRFGADVAPGRIVITAGASAALQLACLALIEAGDEILMPDPSYP 129 Query: 127 CYRNILSALGCEVVEIPCGPQTRFQPTAQMLAEI-DPPLRGVVVASPANPTGTVIPPEEL 185 C R+ +SA V IP + RFQ T + +A + RGV++ASP+NPTGT I PEEL Sbjct: 130 CNRHFVSAAEGTSVLIPTTAEERFQLTREKVAAAWNDKTRGVLLASPSNPTGTSIAPEEL 189 Query: 186 AAIASWCDASDVRLISDEVYHGLVYQ---GAPQTSCAWQTSRNAVVVNSFSKYYAMTGWR 242 I + + + DE+Y GL Y+ G + + + ++ + +NSFSKY++MTGWR Sbjct: 190 QGIHEFVHSRGGITLVDEIYLGLSYEEHFGHSALALSGELGQSVISINSFSKYFSMTGWR 249 Query: 243 LGWLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLL 302 LGWL+VP L ++ + N IC ++Q AA++ F PE E + A + R + Sbjct: 250 LGWLVVPEALTPVIERIAQNLFICASTVAQHAALACFEPETLLEYERRRAEFKARRDYFI 309 Query: 303 DGLRRIGIDRLAPTDGAFYVYADVSDF-----TSDSLAFCSKLLADTGVAIAPGIDFDTA 357 L R+G++ DGAFY YAD + S S F +L+ +A+ PG DF A Sbjct: 310 PELDRLGLNVPVMPDGAFYAYADCTSAAARLGVSGSWDFAFELMKRAHLAVTPGRDFGHA 369 Query: 358 RGGSFVRISFAGPSGDIEEALRRI 381 FVR S A + EA+ R+ Sbjct: 370 APERFVRFSTANSMAQLHEAVARL 393 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: 401 Number of extensions: 19 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