Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_012506055.1 PAES_RS07515 aminotransferase class I/II-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::O59096 (389 letters) >NCBI__GCF_000020625.1:WP_012506055.1 Length = 388 Score = 196 bits (499), Expect = 7e-55 Identities = 133/390 (34%), Positives = 205/390 (52%), Gaps = 11/390 (2%) Query: 1 MALSDRLELVSASEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEALDKGLTHYG 60 + S+R V S+IR + + I+L G D P + E A AL + Y Sbjct: 3 LGTSERCRSVLQSDIR-MMSVECHRLGGINLSQGVCDTPVPGVVLEGASHALSQRQNSYT 61 Query: 61 PNIGLLELREAIAEKLKKQNGIEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPA 120 G+ LREA+AEK + GI+ DP+ EI+V GA A A L G+EV++ P Sbjct: 62 HYAGIGGLREALAEKYRTMYGIDVDPQQEIVVSAGATGAMYCAFQALLNPGDEVIVFEPY 121 Query: 121 FVSYAPAVILAGGKPVEVPTYEEDEFRLNVDELKKYVTDKTRALIINSPCNPTGAVLTKK 180 + + + PV + D + + +L+ V+ +TRA++IN+P NP+G V T Sbjct: 122 YGYHISTLNALQAVPVFLSLTSPD-WTFSEADLEAAVSSRTRAILINTPGNPSGKVFTLA 180 Query: 181 DLEEIADFVVEHDLIVISDEVYEHFIYDDARHYSIASLDGMFERTITVNGFSKTFAMTGW 240 +L+ IADF EHDL V +DE+YEHF+YD RH+S +L GM +RT+ ++GFSKTF++TGW Sbjct: 181 ELQRIADFAEEHDLFVFTDEIYEHFLYDGRRHHSPFALPGMRKRTVLISGFSKTFSVTGW 240 Query: 241 RLGFVAAPSWIIERMVKFQMYNATCPVTFIQ--YAAAKALKDERSWKAVEEMRKEYDRRR 298 R+G+ + + + + F C + +Q AA A D + + + EY +R Sbjct: 241 RIGYAISDARWAQAIGYFNDLVYVCAPSALQPGVAAGLATLDTSYYLS---LSAEYGFKR 297 Query: 299 KLVWKRLNEMGLPTVKPKGAFYIFPRIRD-TGLTSKKFSELMLKEARVAVVPGSAF--GK 355 + L E GL V P+GA+Y+ + G T++ + +L+ VA VPGSAF + Sbjct: 298 NRFCRALGEAGLNAVLPQGAYYVLADVSHLPGSTTRDKAMHILRTTGVASVPGSAFFRNE 357 Query: 356 AGEGYVRISYATAYEKLEEAMDRMERVLKE 385 + VR YA L+ A +R+ + LKE Sbjct: 358 NDQHLVRFCYAKDDVVLDAACERLMK-LKE 386 Lambda K H 0.319 0.136 0.391 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: 326 Number of extensions: 19 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: 389 Length of database: 388 Length adjustment: 30 Effective length of query: 359 Effective length of database: 358 Effective search space: 128522 Effective search space used: 128522 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 (21.8 bits) S2: 50 (23.9 bits)
This GapMind analysis is from Jul 25 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