Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate BWI76_RS26375 BWI76_RS26375 aspartate aminotransferase family protein
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Koxy:BWI76_RS26375 Length = 421 Score = 199 bits (507), Expect = 1e-55 Identities = 128/341 (37%), Positives = 189/341 (55%), Gaps = 23/341 (6%) Query: 75 TLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLDPLRAM--LAKT 132 TL D +G E ID G + N GHR+P +++AV+ QL + H+ + P + LA+ Sbjct: 33 TLWDIEGNEVIDFAAGIAVLNTGHRHPKIIAAVEQQL-QAFTHTAYQIVPYESYVTLAER 91 Query: 133 LAALTP--GKLKYSFFCNSGTESVEAALKLAKAYQSPRGKFTFIATSGAFHGKSLGALSA 190 + AL P G K +FF +G E+VE A+K+A+AY G TF G FHG++ ++ Sbjct: 92 INALAPIDGPAKTAFF-TTGAEAVENAVKIARAYTGRPGLITF---GGGFHGRTFMTMAL 147 Query: 191 TAK-STFRKPFMPLLPGFRHVPFGNIEAMRTALNECKK---------TGDDVAAVILEPI 240 T K + ++ F P H + N T + K D VAA++LEPI Sbjct: 148 TGKVAPYKIGFGPFPGSVYHAVYPNAAHGITTADAMKSLDRIFKADIAADQVAAIVLEPI 207 Query: 241 QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAK 300 QGEGG + PP ++ A+R LCD G L+I DEVQTG RTGK+FA +H +V+PD++ +AK Sbjct: 208 QGEGGFNVAPPEFMQALRALCDTHGILLIADEVQTGFARTGKLFAMQHYDVKPDLMTMAK 267 Query: 301 ALGGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAE 360 +L GG P+ + EV P T+ GNPLA AAA A ++V+ E+ L +AE Sbjct: 268 SLAGG-FPLSGVVGRAEVMDA--PAPGGLGGTYAGNPLAVAAAHAVLDVIEEEQLCQRAE 324 Query: 361 QKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIG 401 + G L + Q AR+ + + RG+G ++A+EF D + G Sbjct: 325 RLGSHLKEVLNQ-ARQSCPAIADVRGQGSMVAVEFNDPQTG 364 Lambda K H 0.320 0.135 0.393 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: 427 Number of extensions: 21 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: 459 Length of database: 421 Length adjustment: 32 Effective length of query: 427 Effective length of database: 389 Effective search space: 166103 Effective search space used: 166103 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 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