Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate AO353_01655 AO353_01655 GntR family transcriptional regulator
Query= BRENDA::Q72LL6 (397 letters) >FitnessBrowser__pseudo3_N2E3:AO353_01655 Length = 468 Score = 132 bits (332), Expect = 2e-35 Identities = 98/327 (29%), Positives = 148/327 (45%), Gaps = 17/327 (5%) Query: 39 GGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPLRAFVAEW-----IGVRPEE 93 GGLP ++ + A ++ R YSP+ G LR + + I V + Sbjct: 115 GGLPE-SWRESDDLSYAIRQVSRTDMAGLFNYSPSYGLPVLRQQILKRLQQMSITVDENQ 173 Query: 94 VLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRLQGPRFLTVPAGEEGPDLDA 153 VL TTG+ LDL+ + L G V++E+P Y + +L G R L VP GPD++ Sbjct: 174 VLTTTGATHGLDLIVRTLLKPGDCVVVESPGYSNLFKLLKLHGVRLLEVPRTSRGPDIEV 233 Query: 154 LEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQMVMERGLVVVEDDAYRELYFGEA 213 LE +L PR L++ F NPTG +R+LQ+ L++VEDD Y + + G A Sbjct: 234 LEALLSANNPRALFINSLFHNPTGSSLAPAVAQRILQLAKRHELIIVEDDVYAD-FQGSA 292 Query: 214 RLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAVAHPEALQKLVQAKQGADLHTPML 273 LA V+Y+GSFSK LS LRV + VA + +L K L Sbjct: 293 GT----RLAAMDAGQSVVYVGSFSKTLSSSLRVGYVVASAAIIARLADMKMITSLGASRF 348 Query: 274 NQMLVHELLKEGFSERLERVRRVYREKAQAMLHALDREVPKEVRYTRPKGGMFVWMELPK 333 + ++ LL G +L + +R ++ A + + EV + +P GG+++W + Sbjct: 349 CESVLSSLLANGAYRKLVQRQRQRLKRDMAATLLVLEDAGWEV-FGKPAGGLYIWARPRE 407 Query: 334 GLSA-----EGLFRRALEENVAFVPGG 355 SA F L AF P G Sbjct: 408 HESAWVRTLAHSFGIVLSSRTAFSPSG 434 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: 476 Number of extensions: 25 Number of successful extensions: 2 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 Apr 09 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