Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_017549848.1 C792_RS0112765 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q9RAT0 (391 letters) >NCBI__GCF_000330705.1:WP_017549848.1 Length = 387 Score = 328 bits (840), Expect = 2e-94 Identities = 169/385 (43%), Positives = 243/385 (63%), Gaps = 7/385 (1%) Query: 4 LKKFNPNLDKIEISLIRQFDQQVSSIPDIIKLTLGEPDFYTPEHVKQAGIAAIENNQSHY 63 + K N + IE+ RQF +V P + LTLG+PDF T + +++A I AI Y Sbjct: 1 MPKANRRMQYIEVPGTRQFANRVEEFPGCVDLTLGQPDFETSQPIREAAIDAINTQSMKY 60 Query: 64 TGMAGLLELRQAASEFLLKKYGLSYAAEDEILVTVGVTEAISSVLLSILVAGDEVLIPAP 123 + GL LR+A S + ++G Y E+LVTVG +E I VL +IL GDEV++PAP Sbjct: 61 SHNTGLYVLREAISNYYKDRHGAHYDPNGEVLVTVGGSEGIDGVLRAILDPGDEVIVPAP 120 Query: 124 AYPGYEPLITLAGGSLVEIDTRANDFVLTPEMLDQAIIEREGKVKAVILNYPANPTGVTY 183 Y GYEP+I L+GG +DT + TPE++++ I E K KAV+LNYP NPTGVTY Sbjct: 121 TYLGYEPIIELSGGITKFVDTTDTGLIATPELIERNITE---KTKAVLLNYPTNPTGVTY 177 Query: 184 NREQIKDLAEVLKKHEVFVIADEVYSELNYTDQPHVSIAEY--APEQTIVLNGLSKSHAM 241 +EQ+ L EV +K+++FVI DE+Y E N + H+S+A Y E+ +V+NGLSKSH M Sbjct: 178 TKEQMDRLVEVFRKYDIFVITDEIYGE-NTLEGDHISLAGYPEIKEKVLVINGLSKSHGM 236 Query: 242 TGWRIGLIFAARELVAQIIKTHQYLVTSASTQSQFAAIEALKNGADDALPMKKEYLKRRD 301 TGWRIG + R+++ ++ H Y AS SQ+AAIEALK+ M KEY++RRD Sbjct: 237 TGWRIGYVTGHRQIMEEVTAVHLYNTICASLPSQYAAIEALKHQLHVPGEMNKEYIRRRD 296 Query: 302 YIIEKMSALGFKIIEPDGAFYIFAKIPADLEQDSFKFAVDFAKENAVAIIPGIAFGQYGE 361 YI ++++ +G ++ +P GAFYIF + E DSFKF + + +A++PG +F ++GE Sbjct: 297 YIYDRLTGMGLEVKKPTGAFYIFPSV-EKYEHDSFKFCTELLETVQLAVVPGRSFSEFGE 355 Query: 362 GFVRLSYAASMDVIEQAMARLTDYV 386 G +RLS+A SM +E+A RL Y+ Sbjct: 356 GHIRLSFACSMHELEEAADRLEKYL 380 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: 440 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: 387 Length adjustment: 30 Effective length of query: 361 Effective length of database: 357 Effective search space: 128877 Effective search space used: 128877 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 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