Align putrescine-2-oxoglutarate transaminase (EC 2.6.1.82) (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= BRENDA::P42588 (459 letters) >FitnessBrowser__Dyella79:N515DRAFT_1751 Length = 467 Score = 187 bits (474), Expect = 8e-52 Identities = 133/405 (32%), Positives = 213/405 (52%), Gaps = 40/405 (9%) Query: 76 LVDTQGQEFIDCLGGFGIFNVGHRNPVVVSAVQNQL--AKQPLHSQELLDPLRAMLAKTL 133 LVD G+ ++D + + GH NP + +A++ QL + + + +P LA+ L Sbjct: 58 LVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFTHEPA-IELAERL 116 Query: 134 AALTPGKLKYSFFCNSGTESVEAALKLAKAYQSPRG---KFTFIATSGAFHGKSLGALSA 190 A +TP L+ F ++G+ ++E ALK++ Y +G K FIA +G++HG++LGALS Sbjct: 117 AQITPAGLERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGSYHGETLGALSV 176 Query: 191 TAKSTFRKPFMPLL---------PGFRHVPFGNIEAMRTA-LNECK----KTGDDVAAVI 236 + + +RK + PLL + P + EA L E + + + AVI Sbjct: 177 SDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLLEQHAHETCAVI 236 Query: 237 LEP-IQGEGGVILPPPGYLTAVRKLCDEFGALMILDEVQTGMGRTGKMFACEHENVQPDI 295 +EP +Q GG+ + P YLT +R LCDEFG I DE+ G GRTG +FACE V PD Sbjct: 237 VEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGTLFACEQAGVSPDF 296 Query: 296 LCLAKALGGGVMPIGATIATEEVFSVLF-----DNPFLHTTTFGGNPLACAAALATINVL 350 +CL+K L GG +P+ A + T V+ + FLH+ ++ GNPLAC AALAT+++ Sbjct: 297 MCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNPLACRAALATLDIF 356 Query: 351 LEQNLPAQAEQKGDMLLDGFRQLA--REYPDLVQEARGKGMLMAIEFV-DNEIGYNFASE 407 ++ + E+ ++ R+LA RE+P V + R GM+ A+E V D + SE Sbjct: 357 RDEPV---LERNRELAAHLARRLAPLREHPQ-VADVRQTGMIAAVELVRDKATRAPYPSE 412 Query: 408 MFR-QRVLVAGTLNNA------KTIRIEPPLTLTIEQCELVIKAA 445 R RV + G + A + PP ++ ++ + ++ A Sbjct: 413 ERRGLRVYLHGLEHGALLRPLGNVVYFMPPYVVSTDELDHLVDVA 457 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: 505 Number of extensions: 37 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: 467 Length adjustment: 33 Effective length of query: 426 Effective length of database: 434 Effective search space: 184884 Effective search space used: 184884 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