Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate 350970 BT1442 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (NCBI ptt file)
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Btheta:350970 Length = 804 Score = 154 bits (389), Expect = 1e-41 Identities = 122/400 (30%), Positives = 189/400 (47%), Gaps = 26/400 (6%) Query: 71 GSLNTLVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQLAKQP--LHSQELLDPLRAM 128 G+ TL D G+ I+ + + G+ +PV+ A ++QL K + DP Sbjct: 413 GATITLED--GRTLIEGMSSWWCAVHGYNHPVLNQAAKDQLDKMSHVMFGGLTHDPA-IE 469 Query: 129 LAKTLAALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRGK---FTFIATSGAFHGKSL 185 L K L L P ++ F+ +SG+ +VE ALK+A Y GK F+ +HG + Sbjct: 470 LGKLLLPLVPPSMQKIFYADSGSVAVEVALKMAVQYWYAAGKPDKNNFVTIRSGYHGDTW 529 Query: 186 GALSATAKST-FRKPFMPLLPGFRHVPFG--------NIEAMRTALNECKKTGDDVAAVI 236 A+S T F LP VP N + + +K ++AA+I Sbjct: 530 NAMSVCDPVTGMHSLFGSSLPVRYFVPAPSSRFDGEWNPDEIIPLRETIEKHSKELAALI 589 Query: 237 LEPI-QGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDI 295 LEPI QG GG+ P YL KLC E L+I DE+ TG GRTGK+FA EH V+PDI Sbjct: 590 LEPIVQGAGGMWFYHPQYLREAEKLCKEHDILLIFDEIATGFGRTGKLFAWEHAGVEPDI 649 Query: 296 LCLAKALGGGVMPIGATIATEEVFSVLFDN---PFLHTTTFGGNPLACAAALATINVLLE 352 +C+ KAL GG M + A +A+ ++ + ++ F+H TF GNPLACA A A++ +LL+ Sbjct: 650 MCIGKALTGGYMTLSAVLASNQIADTISNHAPKAFMHGPTFMGNPLACAVACASVRLLLD 709 Query: 353 QNLPAQAEQKGDMLLDGFRQLAREYPDLVQEARGKGMLMAIEFVDNEIGYNFASEMFRQR 412 ++ L + AR++P V + R G + I+ + + + F + Sbjct: 710 SGWAENVKRIEAQLKEELAP-ARKFPQ-VADVRILGAIGVIQ-TERSVSMAYMQRRFVEE 766 Query: 413 VLVAGTLNNAKTIRIEPPLTLTIEQCELVIKAARKALAAM 452 + K + + PP ++ EQ + K + M Sbjct: 767 GIWVRPF--GKLVYLMPPFIISPEQLSKLTSGVLKIVREM 804 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: 741 Number of extensions: 32 Number of successful extensions: 3 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: 804 Length adjustment: 37 Effective length of query: 422 Effective length of database: 767 Effective search space: 323674 Effective search space used: 323674 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: 53 (25.0 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