Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate N515DRAFT_1751 N515DRAFT_1751 adenosylmethionine-8-amino-7-oxononanoate aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Dyella79:N515DRAFT_1751 Length = 467 Score = 178 bits (452), Expect = 3e-49 Identities = 129/412 (31%), Positives = 199/412 (48%), Gaps = 33/412 (8%) Query: 25 PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84 P+V R E + D +GR Y+D GH +P++ AA+++QL L H F + Sbjct: 49 PIV--RGEGPWLVDADGRRYLDGISSWWTNLFGHANPRIGAALKQQLDTLEHVIFAGFTH 106 Query: 85 EPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIA------RAATGRAGVIAFTGA 138 EP IELAE +A+ P ++ L +GS A+E A+K++ + A + IA TG+ Sbjct: 107 EPAIELAERLAQITPAGL-ERVFLADNGSAAIEVALKMSFHYWLNQGAGQKTRFIALTGS 165 Query: 139 YHGRTMMTLGLTGKVV------PYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIF 192 YHG T+ L ++ + P L P P E + + + Sbjct: 166 YHGETLGALSVSDVALYRKTYAPLLLTPVLAPSPDAYEAEPGESAEACAARRLGELRVLL 225 Query: 193 KNDAQPQDIAAIIIEP-VQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGT 251 + A + A+I+EP VQ GG + S++ LRALCD+ G+ IADE+ G GRTGT Sbjct: 226 EQHAH--ETCAVIVEPLVQCAGGMRMYHPSYLTGLRALCDEFGVHFIADEIAVGFGRTGT 283 Query: 252 FFATEQLGIVPDLTTFAKSVGGGF-PISGVAGKAEIMDAIAPGGLGG-------TYAGSP 303 FA EQ G+ PD +K + GGF P+S V + +A G +Y G+P Sbjct: 284 LFACEQAGVSPDFMCLSKGLTGGFLPLSAVLTTTPVYEAFYAEYNAGKAFLHSHSYTGNP 343 Query: 304 IACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEG 363 +AC AALA L +F +E +LER++ + L L ++ +H + DVR G + A+EL Sbjct: 344 LACRAALATLDIFRDEPVLERNRELAAHLARRLAPLR-EHPQVADVRQTGMIAAVELVRD 402 Query: 364 GDTHKP---AAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLE 412 T P ++ + E G +L G NV+ F+ P + +L+ Sbjct: 403 KATRAPYPSEERRGLRVYLHGLEHGALLRPLG---NVVYFMPPYVVSTDELD 451 Lambda K H 0.319 0.137 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: 455 Number of extensions: 25 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: 426 Length of database: 467 Length adjustment: 32 Effective length of query: 394 Effective length of database: 435 Effective search space: 171390 Effective search space used: 171390 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