Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 15560 b1439 fused predicted DNA-binding transcriptional regulator/predicted amino transferase (NCBI)
Query= BRENDA::Q72LL6 (397 letters) >FitnessBrowser__Keio:15560 Length = 468 Score = 156 bits (395), Expect = 1e-42 Identities = 113/379 (29%), Positives = 189/379 (49%), Gaps = 15/379 (3%) Query: 22 IRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRA 81 I ++L+ ++ P ++ FA P P LFP ++ + A++ + +++ + G A LR Sbjct: 93 IFDMLQASRDPSVVPFASAFPDPRLFPLQQLNRSLAQVSKTATAMSVIENLPPGNAELRQ 152 Query: 82 FVA-----EWIGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQG 136 +A + I + P+E++IT G+ +AL+L + + G V++E P + GA+QA Sbjct: 153 AIARRYALQGITISPDEIVITAGALEALNLSLQAVTEPGDWVIVENPCFYGALQALERLR 212 Query: 137 PRFLTVPAG-EEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMER 195 + L+V +EG DL ALE L+ + +L+ + QNP G + +L+ ++ + Sbjct: 213 LKALSVATDVKEGIDLQALELALQEYPVKACWLMTNSQNPLGFTLTPQKKAQLVALLNQY 272 Query: 196 GLVVVEDDAYRELYFG-EARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVA--H 252 + ++EDD Y ELYFG E LP+ + GV++ SFSK L PG R+ + A H Sbjct: 273 NVTLIEDDVYSELYFGREKPLPA----KAWDRHDGVLHCSSFSKCLVPGFRIGWVAAGKH 328 Query: 253 PEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSERLERVRRVYREKAQAMLHALDREV 312 +Q+L Q +PM LV L + L R+RR E+ Q AL R + Sbjct: 329 ARKIQRL-QLMSTLSTSSPM-QLALVDYLSTRRYDAHLRRLRRQLAERKQRAWQALLRYL 386 Query: 313 PKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRLSYA 372 P EV+ G F+W+ELP+ L A L AL +++ PG F R + A Sbjct: 387 PAEVKIHHNDSGYFLWLELPEPLDAGELSLAALTHHISIAPGKMFSTGENWSRFFRFNTA 446 Query: 373 TLDREGIAEGVRRLGRALK 391 E + V++LG+ ++ Sbjct: 447 WQWGEREEQAVKQLGKLIQ 465 Lambda K H 0.320 0.139 0.403 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: 421 Number of extensions: 25 Number of successful extensions: 5 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: 397 Length of database: 468 Length adjustment: 32 Effective length of query: 365 Effective length of database: 436 Effective search space: 159140 Effective search space used: 159140 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: 51 (24.3 bits)
This GapMind analysis is from Sep 17 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