Align Valine--pyruvate aminotransferase; Alanine--valine transaminase; EC 2.6.1.66 (characterized)
to candidate WP_007474288.1 CMTB2_RS04230 aminotransferase
Query= SwissProt::P96847 (388 letters) >NCBI__GCF_000170735.1:WP_007474288.1 Length = 358 Score = 220 bits (560), Expect = 6e-62 Identities = 131/375 (34%), Positives = 212/375 (56%), Gaps = 24/375 (6%) Query: 13 PFYVMDVWLAAAERQRTHGDLVNLSAGQPSAGAPEPVRAAAAAALHLNQLGYSVALGIPE 72 PF VMD+ + +T D+++L G+P V+ A+ A+ N+ Y+ + G+ Sbjct: 3 PFIVMDI----VSKAKTIDDVIHLEIGEPDTLPSPKVKKASIKAIEENKFFYTESKGLKN 58 Query: 73 LRDAIAADYQRRHGITVEPDAVVITTGSSGGFLLAFLACFDAGDRVAMASPGYPCYRNIL 132 LR+ IA Y+ + + V+PD ++ITTG+S FL+AF ++A PGYPCY+N Sbjct: 59 LREKIAKHYKIFYDVEVKPDNIIITTGTSTAFLIAFYFA----KKIATPIPGYPCYKNFA 114 Query: 133 SALGCEVVEIPCGPQTRFQPTAQMLAEIDPPLR--GVVVASPANPTGTVIPPEELAAIAS 190 E V+IP T F P Q+ E L+ ++++SP NPTGTVI E L I Sbjct: 115 ELENKEFVKIP----TSF-PDYQLTIEDLKKLKFDTLMISSPNNPTGTVIDKENLRKICE 169 Query: 191 WCDASDVRLISDEVYHGLVYQGAPQTSCAWQTSRNAVVVNSFSKYYAMTGWRLGWLLVPT 250 +C ++ LISDE+YHGLVY+ + + A + ++NA+++N FSK+++M G+R+GW+++P Sbjct: 170 FCKLNNKLLISDELYHGLVYE--KEYTTALKYNKNAIIINGFSKFFSMPGFRIGWIILPD 227 Query: 251 VLRRAVDCLTGNFTICPPVLSQIAAVSAFTPEATAEADGNLASYAINRSLLLDGLRRIGI 310 L R + + N I P +SQ AA+ AF ++ R L L+ I Sbjct: 228 NLVRDAEVIAQNILISAPTISQYAAIEAFD---YGHLQNIQKTFKKRRDFLYKELK--DI 282 Query: 311 DRLAPTDGAFYVYADVSDFTSDSLAFCSKLLADTGVAIAPGIDFDTARGGSFVRISFAGP 370 +A DGAFY++ ++S ++ DSL+FC +LL + VA PGIDF + +F+RI++ Sbjct: 283 FEIAKPDGAFYLWCNISKYSDDSLSFCDELLTKSKVATTPGIDFGDYK--NFIRIAYTKD 340 Query: 371 SGDIEEALRRIGSWL 385 + EA++RI ++ Sbjct: 341 ISILNEAVKRIKKFI 355 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: 301 Number of extensions: 12 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: 358 Length adjustment: 30 Effective length of query: 358 Effective length of database: 328 Effective search space: 117424 Effective search space used: 117424 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