Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_089300381.1 CHB84_RS05330 putative succinyldiaminopimelate transaminase DapC
Query= BRENDA::O59096 (389 letters) >NCBI__GCF_900188115.1:WP_089300381.1 Length = 391 Score = 207 bits (528), Expect = 3e-58 Identities = 130/378 (34%), Positives = 195/378 (51%), Gaps = 10/378 (2%) Query: 12 ASEIRKLFDIAAGMKDVISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPNIGLLELREA 71 AS I A ++LG G PD D P + + +A+D G Y P G ELR A Sbjct: 14 ASTIFAEMTALATRTSAVNLGQGFPDTDGPAGMLDAVHDAIDNGANQYPPGPGRPELRAA 73 Query: 72 IAEKLKKQNGIEADPKTEIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFVSYAPAVILA 131 ++E +K+ G+E DP TE++V GA +A L A G++VL+ P + SY AV +A Sbjct: 74 VSEH-RKRFGVEYDPDTEVLVTTGATEAIAASLLALTSRGDDVLVIEPYYDSYVAAVAMA 132 Query: 132 GGKPVEVPTYEEDE---FRLNVDELKKYVTDKTRALIINSPCNPTGAVLTKKDLEEIADF 188 G + VP + ++ F L+V L+ +TD TRA+I+NSP NPTG V T +L +A+ Sbjct: 133 GARRRVVPLHLDENSGRFELDVAALEAAITDSTRAIIVNSPHNPTGTVFTHAELAALAEL 192 Query: 189 VVEHDLIVISDEVYEHFIYDDARHYSIASLDGMFERTITVNGFSKTFAMTGWRLGFVAAP 248 V HDLI ISDEVYEH ++DD H +A+L GM RT+T++ K F TGW++G+ Sbjct: 193 CVRHDLIAISDEVYEHLVFDDTEHVPVATLPGMAGRTVTISSAGKIFNCTGWKIGWACGN 252 Query: 249 SWIIERMVKFQMYNATCPVTFIQYAAAKALKDERSWKAVEEMRKEYDRRRKLVWKRLNEM 308 +I + + + Q A A AL+ E W VE+ R +R + L E Sbjct: 253 RDLIAAVRAAKQFLTFVSGGPFQPAVAHALRAELDW--VEQSRAALGDKRDRLSAGLAEA 310 Query: 309 GLPTVKPKGAFYIFPRIRDTGLTSKKFSELMLKE-ARVAVVPGSAFGKAGEG---YVRIS 364 G + G +++ +R G + L E VA VP S F + G G +R + Sbjct: 311 GFSVLPCSGTYFVCADVRPLGYSDATDLAWALPERVGVAAVPVSVFTENGAGNTHLLRFA 370 Query: 365 YATAYEKLEEAMDRMERV 382 + + L+ A++R+ R+ Sbjct: 371 FCKRDDVLDTAIERLHRL 388 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: 319 Number of extensions: 13 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: 389 Length of database: 391 Length adjustment: 31 Effective length of query: 358 Effective length of database: 360 Effective search space: 128880 Effective search space used: 128880 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 Sep 24 2021. The underlying query database was built on Sep 17 2021.
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