Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate AO353_10500 AO353_10500 acetylornithine aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__pseudo3_N2E3:AO353_10500 Length = 390 Score = 233 bits (594), Expect = 8e-66 Identities = 138/388 (35%), Positives = 219/388 (56%), Gaps = 17/388 (4%) Query: 66 VEWQAGSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQPLHSQELLD-P 124 V + G +L D G E++D + G + ++GH NP + +A+ Q A Q LH+ + Sbjct: 17 VSFSRGQGASLWDKHGVEYLDAIAGVAVTSLGHANPEIAAAIAEQ-AGQLLHTSNMFHIE 75 Query: 125 LRAMLAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPR--GKFTFIATSGAFHG 182 + L++ L AL+ ++ +FFCNSG E+ EAALKLA+ + + R + + +FHG Sbjct: 76 WQEQLSERLCALSG--MQRAFFCNSGAEANEAALKLARLHANARHVAQPQVLVMENSFHG 133 Query: 183 KSLGALSATAKSTFRKPFMPLLPGFRHVPFGNIEAMRTALNECKKTGDDVAAVILEPIQG 242 ++L L+AT ++ F PL+PGF VP+ NIE +R + D+ AV++EP+QG Sbjct: 134 RTLATLAATGNPAVQRGFEPLMPGFLRVPYDNIEEIRKVAAQ----SPDIVAVLVEPVQG 189 Query: 243 EGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDILCLAKAL 302 EGGV GYL A+R+LCDE LM++DEVQTGMGRTG F +H + PD++ LAKAL Sbjct: 190 EGGVHAASAGYLQALRQLCDEHDWLMMVDEVQTGMGRTGAWFGYQHAGIVPDVITLAKAL 249 Query: 303 GGGVMPIGATIATEEVFSVLFDNPFLHTTTFGGNPLACAAALATINVLLEQNLPAQAEQK 362 G G PIGA +A + + +P H +TFGGNPLAC ++++ ++P +A Sbjct: 250 GNG-FPIGACLARGKAAELF--SPGHHASTFGGNPLACRVGCTVLDIMERDHIPQRAATS 306 Query: 363 GDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQRVLVAGTLNNA 422 G LL ++ + ++V RG G+++ IE ++ + + QR+L+ T+ Sbjct: 307 GRRLLAALQEALGNHSEVV-SIRGLGLMVGIE-LNRQCAELVGRALDEQRLLI--TVTRG 362 Query: 423 KTIRIEPPLTLTIEQCELVIKAARKALA 450 T+R+ PPL Q + + + L+ Sbjct: 363 TTLRLLPPLICEDSQIDDIAARVSRLLS 390 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: 428 Number of extensions: 16 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: 459 Length of database: 390 Length adjustment: 32 Effective length of query: 427 Effective length of database: 358 Effective search space: 152866 Effective search space used: 152866 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 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