Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate H281DRAFT_01667 H281DRAFT_01667 DNA-binding transcriptional regulator, MocR family, contains an aminotransferase domain
Query= BRENDA::Q72LL6 (397 letters) >FitnessBrowser__Burk376:H281DRAFT_01667 Length = 409 Score = 234 bits (596), Expect = 4e-66 Identities = 145/387 (37%), Positives = 212/387 (54%), Gaps = 13/387 (3%) Query: 20 STIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVALQYSPTEGYAPL 79 S IREL K PG++SFAGG PA +LF + A A R R LQY PT+G L Sbjct: 14 SPIRELFKYLAEPGMISFAGGYPASDLFDVDGLASAQKRAYRNSNR-CLQYGPTDGLPEL 72 Query: 80 RAFVAEWIGVR-----PEEVLITTGSQQALDLVGKVFLDEGSPVLLEAPSYMGAIQAFRL 134 ++ + + R P E+L+TTGSQQ LDL+ +V + G V+ E P+Y +QA +L Sbjct: 73 KSELVNLMARRGVTCEPGELLVTTGSQQGLDLLLRVLVAPGDVVVTEQPAYPATLQALKL 132 Query: 135 QGPRFLTVPAGEEGPDLDALEEVLKR---ERPRFLYLIPSFQNPTGGLTPLPARKRLLQM 191 Q + +T G D++ L L+ RP+ LY +P+F NPTG R LL++ Sbjct: 133 QHAQIVTAQVDGHGIDVENLAAHLESGAVPRPKLLYTVPTFANPTGATITRERRIELLKL 192 Query: 192 VMERGLVVVEDDAYRELYFGEARLPSLFELAR--EAGYPGVIYLGSFSKVLSPGLRVAFA 249 ++ V+VEDD Y +L F +PS+ L E V++ S SK+++PG+RV ++ Sbjct: 193 AVKYRFVIVEDDPYGDLRFSGDTVPSILALTAEVEGSRDWVVHFASLSKIVAPGVRVGWS 252 Query: 250 VAHPEALQKLVQAKQGADLHTPMLNQMLVHELLKEGFSER-LERVRRVYREKAQAMLHAL 308 +A E ++ V AKQ DL + Q + E L +G ER L R+ YR K A+ + L Sbjct: 253 IAPAEITRRCVIAKQTVDLCSAPWTQAIAAEYLADGALERHLPRITTTYRRKCDALCNEL 312 Query: 309 DREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGGGENTLR 368 ++ +++ +P+GGMFVW + +G+ + L A+E V FVPG FFA+ +LR Sbjct: 313 RWQLDDAIQFHQPEGGMFVWARI-EGIDSSELLWHAIENKVIFVPGKAFFADKLDVASLR 371 Query: 369 LSYATLDREGIAEGVRRLGRALKGLLA 395 LS+A E I EG RRL RA + LA Sbjct: 372 LSFAAPGVEEIQEGARRLKRAYEAALA 398 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: 414 Number of extensions: 18 Number of successful extensions: 6 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: 409 Length adjustment: 31 Effective length of query: 366 Effective length of database: 378 Effective search space: 138348 Effective search space used: 138348 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 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