Align aromatic-amino-acid transaminase (EC 2.6.1.57) (characterized)
to candidate WP_005452968.1 SACCYDRAFT_RS01550 putative succinyldiaminopimelate transaminase DapC
Query= BRENDA::O59096 (389 letters) >NCBI__GCF_000244975.1:WP_005452968.1 Length = 386 Score = 206 bits (525), Expect = 7e-58 Identities = 128/356 (35%), Positives = 193/356 (54%), Gaps = 8/356 (2%) Query: 29 ISLGIGEPDFDTPQHIKEYAKEALDKGLTHYGPNIGLLELREAIAEKLKKQNGIEADPKT 88 ++LG G PD D P+ + E A+ AL G Y P G ELREAIA + + G E DP Sbjct: 31 VNLGQGFPDTDGPEGMLEAARNALFGGANQYPPGPGRPELREAIAAH-RARYGTEYDPDG 89 Query: 89 EIMVLLGANQAFLMGLSAFLKDGEEVLIPTPAFVSYAPAVILAGGKPVEVPTYEE-DEFR 147 EI+V GA +A L A G+EV++ P + SYA AV +AG V + D F Sbjct: 90 EILVTAGATEAIAASLLALTGPGDEVIVIEPYYDSYAAAVAMAGATRRVVSLVPDGDRFA 149 Query: 148 LNVDELKKYVTDKTRALIINSPCNPTGAVLTKKDLEEIADFVVEHDLIVISDEVYEHFIY 207 L++D ++ V TRA+++NSP NPTG VLT+ +L +A+ VE DL+ I+DEVYEH ++ Sbjct: 150 LDLDAVRAAVNPNTRAILVNSPHNPTGTVLTRTELAGLAELCVERDLLAITDEVYEHLVF 209 Query: 208 DDARHYSIASLDGMFERTITVNGFSKTFAMTGWRLGFVAAPSWIIERMVKFQMYNATCPV 267 DDA H +A+ GM RT++++ KTF TGW++G+V AP + + + + Sbjct: 210 DDAEHLPLATFPGMSSRTVSISSAGKTFNCTGWKIGWVCAPRELTAAVRAAKQFLTFVSG 269 Query: 268 TFIQYAAAKALKDERSWKAVEEMRKEYDRRRKLVWKRLNEMGLPTVKPKGAFYIFPRIRD 327 +Q A A AL+ E W VE +R+ +R + L + G G +++ +R Sbjct: 270 GPLQPAVAHALRHELPW--VESLRESLQAKRDRLCAGLADAGFAVRPGAGTYFVCADVRP 327 Query: 328 TGLTSKKFSELMLKEA-RVAVVPGSAFGKAGEGY---VRISYATAYEKLEEAMDRM 379 G T+ + L E+ VA VP S F E + +R ++ E L+EA++R+ Sbjct: 328 LGFTNAEELAWRLPESIGVAAVPVSVFTDHPEEWQHLLRFAFCKREEVLDEAIERL 383 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: 357 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: 386 Length adjustment: 30 Effective length of query: 359 Effective length of database: 356 Effective search space: 127804 Effective search space used: 127804 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 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