Align L-leucine transaminase; L-isoleucine transaminase (EC 2.6.1.42) (characterized)
to candidate WP_019866951.1 METMI_RS0114165 PLP-dependent aminotransferase family protein
Query= reanno::acidovorax_3H11:Ac3H11_1358 (401 letters) >NCBI__GCF_000384075.1:WP_019866951.1 Length = 386 Score = 242 bits (617), Expect = 2e-68 Identities = 156/402 (38%), Positives = 214/402 (53%), Gaps = 26/402 (6%) Query: 3 LNDLPQNSTWTLARRAERMNPSVIREILKVTEKPGIISLAGGLPSPKTFPVSAFAAASAA 62 +NDL + R ++PS IREIL V +PG+IS AGGLP+ +FP + A Sbjct: 1 MNDLSPQHKPHFSARTRNLHPSPIREILSVINRPGMISFAGGLPAVDSFPQFSLDAMPQH 60 Query: 63 VLANDGPAALQYAASEGYAPLRQAIADFLPW---DVDADQILITTGSQQALDLIAKVLID 119 +L QY ASEG LRQ +A+ L A Q+LI +GSQQ +DL+AK+ ID Sbjct: 61 IL--------QYGASEGEGGLRQRVAEDLQGLGLQCTAGQVLILSGSQQGIDLVAKLFID 112 Query: 120 ENSRVLVETPTYLGALQAFTPMEPSVVA--VASDDEGVLIDDLKAKVGTGADKARFLYVL 177 + V VE+PTYL ALQ F VA S D G L+ +K F Y + Sbjct: 113 PGTPVAVESPTYLAALQVFRYFGARFVAYDAGSPDMGELL----------REKPAFAYAI 162 Query: 178 PNFQNPTGRTMTEARRAALVKAAAELNLPLVEDNPYGDLWFDNPPPAPLTARNPEG-CIY 236 P FQNP+G+ + A RAAL A +PL ED+PY DL +D P+ A + IY Sbjct: 163 PTFQNPSGQCLDAAGRAALAAACDAARIPLFEDDPYRDLAYDPCERTPVCALLKQAPWIY 222 Query: 237 MGSFSKVLAPGLRLGFVVAPKAVYPKLLQAKQAADLHTPGYNQRLVAEVMKGNFLDRHVP 296 GSFSK LAPGLRLG++ A + P L + KQAADLH+ +Q LV + + + + Sbjct: 223 QGSFSKSLAPGLRLGYLAASPDLLPYLTRLKQAADLHSNRVSQWLVLQQLNDPARSQQLD 282 Query: 297 TIRALYKQQCEAMLAALTQEMAGLGVEWNRPDGGMFLWVRLPEGMSAIELLPQAVERNVA 356 + Y+Q+ +A AAL + +GL W P GG+F W+ L + +LLP+A+E VA Sbjct: 283 KLAGAYRQRRDAFEAALRRHFSGL-ASWQTPPGGLFFWLTLNRRIDTRQLLPKAIEAGVA 341 Query: 357 FVPGAAFYADNADP-RTLRLSFVTSTVEQIATGIAALAAAIR 397 F+PG F + LRL+F + Q G+ LA +R Sbjct: 342 FMPGEPFLPMEVENCGQLRLNFSHADETQAELGLGKLAELVR 383 Lambda K H 0.318 0.134 0.392 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: 402 Number of extensions: 12 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: 401 Length of database: 386 Length adjustment: 31 Effective length of query: 370 Effective length of database: 355 Effective search space: 131350 Effective search space used: 131350 Neighboring words threshold: 11 Window for multiple hits: 40 X1: 16 ( 7.3 bits) X2: 38 (14.6 bits) X3: 64 (24.7 bits) S1: 41 (21.7 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