Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate 8501445 DvMF_2175 transcriptional regulator, GntR family with aminotransferase domain (RefSeq)
Query= BRENDA::Q72LL6 (397 letters) >FitnessBrowser__Miya:8501445 Length = 498 Score = 160 bits (405), Expect = 8e-44 Identities = 117/379 (30%), Positives = 181/379 (47%), Gaps = 13/379 (3%) Query: 18 QASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYA 77 +A I +L+ ++ F P L P + ++R + A Y+ G Sbjct: 113 RARLISTVLEAVGNRDLVPFGVLCPDETLLPGRALGRILSEVMRSRAGEAAAYATIPGDL 172 Query: 78 PLRAFVAEW------IGVRPEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQA 131 LR +A W +G P+++LIT G+ +AL + + G V++++P+Y +Q Sbjct: 173 ELRRQIA-WRHRECGVGAGPDDILITNGAVEALYIALRCLTRPGDIVMIQSPTYYCFLQL 231 Query: 132 FRLQGPRFLTVPAGEE-GPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLPARKRLLQ 190 G R + VP+ E G D + +L R R P+F NP G LTP A++ +L Sbjct: 232 IESLGLRAIEVPSTPEAGVDPRDVRHILDRHRVAACAFSPNFNNPDGSLTPDDAKREILD 291 Query: 191 MVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPGLRVAFAV 250 M+ ERG+ ++EDD +L++G +R PS F G V SFSK ++PG R+ + V Sbjct: 292 MLAERGIHLIEDDVSTDLHYGPSR-PSTFLQWDVHGL--VTLCSSFSKTVAPGFRMGWMV 348 Query: 251 AHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSER-LERVRRVYREKAQAMLHALD 309 ++ + K ++ L Q + E L++G ER L R+R + + QAM L Sbjct: 349 TGRIG-ERAREIKATTNVCGATLTQFAMAEYLRQGLFERQLRRLRTAFSRQMQAMRMHLA 407 Query: 310 REVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLRL 369 P TRP+GG +W+ELP G LF RA + ++ PG F N LRL Sbjct: 408 DCFPSGTGVTRPEGGGVLWLELPPGTDGVELFFRARQAGISVAPGAVFSTQEKFANYLRL 467 Query: 370 SYATLDREGIAEGVRRLGR 388 L E +AEG+R LGR Sbjct: 468 GCNGLWNERMAEGLRTLGR 486 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: 520 Number of extensions: 34 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: 397 Length of database: 498 Length adjustment: 32 Effective length of query: 365 Effective length of database: 466 Effective search space: 170090 Effective search space used: 170090 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 Aug 03 2021. The underlying query database was built on Aug 03 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