Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate NP_347015.1 CA_C0375 aminotransferase
Query= BRENDA::Q9RAT0 (391 letters) >NCBI__GCF_000008765.1:NP_347015.1 Length = 386 Score = 342 bits (878), Expect = 8e-99 Identities = 176/381 (46%), Positives = 255/381 (66%), Gaps = 7/381 (1%) Query: 8 NPNLDKIEISLIRQFDQQVSSIPDIIKLTLGEPDFYTPEHVKQAGIAAIENNQSHYTGMA 67 NP + KIE+S IR+ D I LT+G+PDF TPEH+K + AI+NN + YT + Sbjct: 6 NPLVKKIELSPIREISDAALKYSDAINLTVGQPDFTTPEHIKLSAKKAIDNNHTSYTANS 65 Query: 68 GLLELRQAASEFLLKKYGLSYAAEDEILVTVGVTEAISSVLLSILVAGDEVLIPAPAYPG 127 G+ ELR+AAS F+ KKY L+Y ++ EI+VT G TEAI L +IL DEVL+PAP Y G Sbjct: 66 GICELRKAASNFINKKYNLNYNSDKEIIVTNGATEAIDISLRTILEKDDEVLLPAPIYVG 125 Query: 128 YEPLITLAGGSLVEIDTRANDFVLTPEMLDQAIIEREGKVKAVILNYPANPTGVTYNREQ 187 YEP+I G V +DT +N+F+L E+L++ + K K +IL YP NPTG ++ Sbjct: 126 YEPVINFCGAKPVYMDTSSNNFILNAEILEKYLTP---KTKCLILCYPCNPTGSAMDKNA 182 Query: 188 IKDLAEVLKKHEVFVIADEVYSELNYTDQPHVSIA--EYAPEQTIVLNGLSKSHAMTGWR 245 + ++ +LK ++FVI+DE+YSEL + + H SIA E +TI+LNG+SKSH+MTGWR Sbjct: 183 LTEIVNLLKNKDIFVISDEIYSELTFKKR-HFSIAGFEDMRNKTILLNGVSKSHSMTGWR 241 Query: 246 IGLIFAARELVAQIIKTHQYLVTSASTQSQFAAIEALKNGADDALPMKKEYLKRRDYIIE 305 IG IFA L ++I K HQY T + + SQ+AA+EAL NG +D+ MKKEY+KRRD+I + Sbjct: 242 IGFIFAPEYLTSEIFKLHQYGSTCSCSISQYAALEALTNGFNDSEYMKKEYIKRRDFIYK 301 Query: 306 KMSALGFKIIEPDGAFYIFAKIPADLEQDSFKFAVDFAKENAVAIIPGIAFGQYGEGFVR 365 ++ ++ F +++P+GAFYIF I S F++ ++ +A++PG AF YGEG++R Sbjct: 302 ELVSMDFDVVKPEGAFYIFPSI-KKFNMTSLNFSLKLLEKEHLAVVPGSAFSHYGEGYIR 360 Query: 366 LSYAASMDVIEQAMARLTDYV 386 +SYAASM +++ M RL ++ Sbjct: 361 ISYAASMKDLKEGMIRLRRFI 381 Lambda K H 0.318 0.135 0.375 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: 461 Number of extensions: 21 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: 391 Length of database: 386 Length adjustment: 30 Effective length of query: 361 Effective length of database: 356 Effective search space: 128516 Effective search space used: 128516 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