Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_019865509.1 METMI_RS0106730 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000384075.1:WP_019865509.1 Length = 388 Score = 240 bits (612), Expect = 6e-68 Identities = 140/372 (37%), Positives = 195/372 (52%), Gaps = 3/372 (0%) Query: 11 VPPFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGI 70 + PFYVM + A + + D++++ G+P P+ + A L ++ Y+ A G+ Sbjct: 12 ISPFYVMALLQRAKQLESEGRDVIHMEIGEPDFPTPKAIVEAGVRLLQTGEVKYTPAAGL 71 Query: 71 PELRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRN 130 ELR IA YQ ++G++V P+ + IT G+SG FLLA + G+ + MA P YPC N Sbjct: 72 LELRRKIARFYQSQYGVSVAPERIFITPGASGAFLLALGISLNPGEELLMADPCYPCNSN 131 Query: 131 ILSALGCEVVEIPCGPQTRFQPTA-QMLAEIDPPLRGVVVASPANPTGTVIPPEELAAIA 189 S G +P T +Q TA Q+ +GV+VASP+NPTGT+I PE L A+ Sbjct: 132 FASLFGATPRALPVDAGTSYQLTADQVKQHWHSHSKGVLVASPSNPTGTLISPEALQAVV 191 Query: 190 SWCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVP 249 +A SDE+YHGLVY + A Q S V+NSFSKY+ MTGWR+GWL+VP Sbjct: 192 QTTNALGGCFYSDEIYHGLVY--GQNATTALQYSDEVFVINSFSKYFGMTGWRIGWLVVP 249 Query: 250 TVLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIG 309 A + L N I SQ AA++AF E E + A A R L L +G Sbjct: 250 DGFISAAEKLAQNIFIATSTHSQYAALAAFDRETLVELERRRAELAARRDFLYAHLLDLG 309 Query: 310 IDRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAG 369 A +GAFY+YAD S FT DS F L VAI PG DF T +R ++ Sbjct: 310 FGIPAKPEGAFYIYADCSRFTDDSFQFALDFLEQEAVAITPGKDFGTYNAQHNLRFAYTT 369 Query: 370 PSGDIEEALRRI 381 + + A++R+ Sbjct: 370 TADKMAAAMQRL 381 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: 389 Number of extensions: 15 Number of successful extensions: 3 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: 388 Length adjustment: 30 Effective length of query: 358 Effective length of database: 358 Effective search space: 128164 Effective search space used: 128164 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