Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_042441707.1 TX73_RS22075 pyridoxal phosphate-dependent aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000195775.1:WP_042441707.1 Length = 400 Score = 147 bits (371), Expect = 5e-40 Identities = 115/389 (29%), Positives = 187/389 (48%), Gaps = 25/389 (6%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 V P + V A E + +++ L +G+P P ++ AA A+ + Y+ GI Sbjct: 11 VKPSATIAVTDKARELKAAGRNVIGLGSGEPDFDTPANIKLAAIHAVEAGKTKYTAVDGI 70 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 PEL+ AI ++R +G+T +P+ +++ TG A +A + GD V + +P + Y Sbjct: 71 PELKQAIIDKFKRENGLTYKPNQIIVGTGGKQVLYNALMATINPGDEVIIPAPYWVSYPE 130 Query: 131 ILSALGCEVVEIPCGPQTRF--QPTAQMLAEIDPPLRGVVVASPANPTGTVIPPEELAAI 188 +++ G E V + C + F QP A + A I P + +++ SP+NPTG EL A+ Sbjct: 131 MVALAGGESVPVVCTAEFGFKLQPAA-LEAAITPKTKWIILNSPSNPTGAAYSRAELKAL 189 Query: 189 AS-WCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSR---NAVVVNSFSKYYAMTGWRLG 244 V +++D++Y LVY T+ A + + VN SK Y MTGWR+G Sbjct: 190 TDVLVKHPHVWVMTDDMYEHLVYDDFEFTTPAQIEPKLFDRTLTVNGVSKSYCMTGWRIG 249 Query: 245 WLLVPTVLRRAVDCLTGNFTICPPVLSQIAAVSAFT-PEATAEADGNLASYAINRSLLLD 303 + P L +A+ + T P ++Q AAV A P+ +A + + R L++ Sbjct: 250 YAGGPAELIKAMSTIQSQSTSNPCSIAQWAAVEALNGPQDFIDAHNKV--FKERRDLVVS 307 Query: 304 GLRR-IGIDRLAPTDGAFYVYADVSDFTSDSLA----------FCSKLLADTGVAIAPGI 352 L + GID P +GAFYVY + + F ++LL GVA+ G Sbjct: 308 MLNQATGIDCPRP-EGAFYVYPSCAGTIGKTAPSGKKIETDQDFVTELLEAEGVAVVQGS 366 Query: 353 DFDTARGGSFVRISFAGPSGDIEEALRRI 381 F G RIS+A + D+E+A +RI Sbjct: 367 AFGL---GPAFRISYATKTSDLEDACKRI 392 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: 367 Number of extensions: 20 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: 400 Length adjustment: 31 Effective length of query: 357 Effective length of database: 369 Effective search space: 131733 Effective search space used: 131733 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