Align L-2-aminoadipate aminotransferase monomer (EC 2.6.1.39) (characterized)
to candidate Pf6N2E2_5813 Transcriptional regulator, GntR family domain / Aspartate aminotransferase (EC 2.6.1.1)
Query= metacyc::MONOMER-6727 (397 letters) >FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5813 Length = 388 Score = 242 bits (617), Expect = 2e-68 Identities = 148/394 (37%), Positives = 217/394 (55%), Gaps = 18/394 (4%) Query: 9 AFGKSAGRIQASTIRELLKLTQRPGILSFAGGLPAPELFPKEEAAEAAARILREKGEVAL 68 AF + R+++S IRE+L QRP ++SFAGGLPA + PK E A + Sbjct: 2 AFSERVSRLKSSLIREILAAAQRPEVMSFAGGLPAEAMLPKVEWAAMPLSMG-------- 53 Query: 69 QYSPTEGYAPLR---AFVAEWIGVRPE--EVLITTGSQQALDLVGKVFLDEGSPVLLEAP 123 QY +EG LR A A +GV E +VL+ +GSQQ LDL K+ +D G+ V+LEAP Sbjct: 54 QYGMSEGEPALREALAAQARALGVACEASQVLVVSGSQQTLDLAAKLHIDVGTEVMLEAP 113 Query: 124 SYMGAIQAFRLQGPRFLTVPAGEEGPDLDALEEVLKRERPRFLYLIPSFQNPTGGLTPLP 183 +Y+ A+Q F+L G +TVP +GPDL AL L+R RP F+YLIP+FQNP+ Sbjct: 114 TYLAALQIFQLFGADCITVPLEADGPDLKALRARLERHRPAFIYLIPTFQNPSAVRYSEA 173 Query: 184 ARKRLLQMVMERGLVVVEDDAYRELYFGEARLPSLFELAREAGYPGVIYLGSFSKVLSPG 243 R + ++ E G+ ++ED+ YREL F + R+A + IY G+ SK L PG Sbjct: 174 KRDAVAALLDEFGVTLIEDEPYRELTFDGGSATPIVSRLRKASW---IYTGTVSKTLLPG 230 Query: 244 LRVAFAVAHPEALQKLVQAKQGADLHTPMLNQMLVHELL-KEGFSERLERVRRVYREKAQ 302 LRV + +A P+ L++ KQ ADLHT + Q + + E + L +R YR++ Sbjct: 231 LRVGYLIASPDLFPHLLRLKQSADLHTNRIGQWQALQWIGTEQYRRHLSELRDFYRDRRD 290 Query: 303 AMLHALDREVPKEVRYTRPKGGMFVWMELPKGLSAEGLFRRALEENVAFVPGGPFFANGG 362 AL++ + P+GG+F W+ L + L L AL +VAF+PG PFF Sbjct: 291 RFQAALEKHFTDLADWNIPQGGLFFWLTLKQPLDTRTLLAAALAADVAFMPGEPFFPEPD 350 Query: 363 GE-NTLRLSYATLDREGIAEGVRRLGRALKGLLA 395 LRL+++ +D + EG++RL ++ LA Sbjct: 351 QHPGHLRLNFSHIDPARLDEGLKRLAGVVREALA 384 Lambda K H 0.320 0.139 0.401 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: 403 Number of extensions: 19 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: 388 Length adjustment: 31 Effective length of query: 366 Effective length of database: 357 Effective search space: 130662 Effective search space used: 130662 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