Align 2-aminoadipate transaminase (EC 2.6.1.39) (characterized)
to candidate WP_092481894.1 BM299_RS02515 putrescine aminotransferase
Query= reanno::Putida:PP_4108 (416 letters) >NCBI__GCF_900115975.1:WP_092481894.1 Length = 453 Score = 189 bits (481), Expect = 1e-52 Identities = 136/396 (34%), Positives = 206/396 (52%), Gaps = 27/396 (6%) Query: 25 EVWDTDGKRYIDFVGGIGVLNLGHCNPAVVEAIQAQATRLT-HYAFNAAPHGPYLALMEQ 83 ++W GK +ID +GG G+ N+GH +P V++A+ Q R H P +LA + Sbjct: 73 DIW---GKEFIDCLGGYGIYNVGHRHPKVLKAVMDQLQRQALHSQELLDPLRAFLAKL-- 127 Query: 84 LSQFVPVSYPLAGMLTNSGAEAAENALKVARGATGKRAIIAFDGGFHGRTLATLNLNGKV 143 L P A NSG E+ E +K A+ TG+R+ I+ FHG++L +L+ K Sbjct: 128 LGSITPGDLQYA-FFVNSGTESVEAGIKFAKMYTGRRSFISTTRAFHGKSLGSLSATAKG 186 Query: 144 APYKQRVGELPGPVYHLPYPSADTGVTCEQALKAMDRLFSVELAVEDVAAFIFEPVQGEG 203 K + +PG +H+PY +A+ A++ M L S EDVAA I EPVQGEG Sbjct: 187 VFRKPFLPLIPG-FHHVPYGNAE-------AVEMM--LESCAFVGEDVAAVIVEPVQGEG 236 Query: 204 GFLALDPAFAQALRRFCDERGILIIIDEIQSGFGRTGQRFAFPRLGIEPDLLLLAKSIAG 263 G + + LR CD+ G L+I+DE+Q+G GRTG+ FA + PD+L LAK+ G Sbjct: 237 GVIIPPEDYLPKLRELCDKYGALLILDEVQTGMGRTGKMFACEHSNVVPDILCLAKAFGG 296 Query: 264 G-MPLGAVVGRKELMAALPKGGL--GGTYSGNPISCAAALASLAQMTDENLATWGERQEQ 320 G MP+GA V RK + L + T+ GNP+ CAAA+A++ + +ENL Sbjct: 297 GIMPIGATVARKPMWEKLVENPFLHTTTFGGNPVCCAAAIANINVLLEENLPQRSAESGV 356 Query: 321 AIVSRYERWKASGLSPYIGRLTGVGAMRGIEFANADGSPAPAQLAKVMEAARARGLLLMP 380 ++ + R A + + G G M GIEF N + +V + ARG+L+ Sbjct: 357 YMLGKL-RELAEKYPAVVQEVRGKGLMIGIEFFNDELG------YEVAKGLFARGVLVAG 409 Query: 381 SGKARHIIRLLAPLTIEAEVLEEGLDILEQCLAELN 416 + IR+ PLTI E ++ ++ L+ LAE++ Sbjct: 410 TLINAKSIRIEPPLTISREQQDQVIERLDNTLAEVD 445 Lambda K H 0.320 0.137 0.402 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: 467 Number of extensions: 23 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: 416 Length of database: 453 Length adjustment: 32 Effective length of query: 384 Effective length of database: 421 Effective search space: 161664 Effective search space used: 161664 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 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