Align Transaminase BacF; Transaminase A; EC 2.6.1.- (characterized)
to candidate WP_017548713.1 C792_RS0106810 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= SwissProt::P39643 (399 letters) >NCBI__GCF_000330705.1:WP_017548713.1 Length = 384 Score = 260 bits (664), Expect = 5e-74 Identities = 134/354 (37%), Positives = 207/354 (58%), Gaps = 3/354 (0%) Query: 34 IINLGQGNPDLPTPPHIVEALREASLNPSFHGYGPFRGYPFLKEAIAAFYKREYGVTINP 93 ++NL G PD TP I +A+ ++ P YG FRG K+AI YK+ Y VT++ Sbjct: 29 LLNLAVGIPDGETPDVIKKAVADSVYLPENQRYGVFRGKRSFKDAIIRLYKKHYDVTLHE 88 Query: 94 ETEVALFGGGKAGLYVLTQCLLNPGDIALVPNPGYPEYLSGITMARAELYEMPLYEENGY 153 E +AL G K+GL + PG+ +PNPGYP+Y++G+ +AR E+Y++PL N + Sbjct: 89 EN-IALLYGTKSGLVQFPMTFIEPGEGVYLPNPGYPDYMAGVKLARGEIYDLPLLAGNDF 147 Query: 154 LPDFEKIDPAVLEKAKLMFLNYPNNPTGAVADAAFYAKAAAFAKEHNIHLIHDFAYGAFE 213 LPDF+ +D L A+L++LNYP+NP GAVA F+ + + ++HDFAY AF Sbjct: 148 LPDFDSLDKDELSNARLIYLNYPSNPLGAVATKEFFDETVERFRGTRTRIVHDFAYAAFS 207 Query: 214 FDQKPASFLEAEDAKTVGAELYSFSKTFNMAGWRMAFAVGNEKIIQAVNEFQDHVFVGMF 273 FD+K S L ++ + E+YS SK FNM+G+R+ FAVGN+++++++N +QDH GM+ Sbjct: 208 FDEKHPSILSSDPSLECCMEIYSLSKGFNMSGFRVGFAVGNKEMVESINLYQDHTQTGMW 267 Query: 274 GGLQQAASAALSGDPEHTESLKRIYKERIDFFTALCEKELGWKMEKPKGTFYVWAEIPNT 333 G LQ A+ AAL + E +++R DFF E G + KG + W +P Sbjct: 268 GVLQDASVAALEHEEEILSMQHVKFQKRRDFFEK-AVIESGIPLNPLKGGIFGWIAVPKG 326 Query: 334 FETSHQFSDYLLEHAHVVVTPGEIFGSNGKRHVRISMVSKQEDLREFVTRIQKL 387 ++ F+D+L+ ++VTPG FGS GK ++RIS+ L + R+ + Sbjct: 327 YD-GESFADFLIREKSILVTPGRPFGSRGKNYIRISLAVDDAVLDAVIERLDTI 379 Lambda K H 0.319 0.137 0.407 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: 458 Number of extensions: 19 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: 399 Length of database: 384 Length adjustment: 31 Effective length of query: 368 Effective length of database: 353 Effective search space: 129904 Effective search space used: 129904 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 (21.7 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 26 2024. The underlying query database was built on Jul 25 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