Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_084544820.1 H566_RS0102945 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000482785.1:WP_084544820.1 Length = 387 Score = 207 bits (527), Expect = 4e-58 Identities = 135/393 (34%), Positives = 202/393 (51%), Gaps = 34/393 (8%) Query: 25 PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84 P+ R E +WD +GR+Y+D GIAV GH HPK++AA+ +Q+GKL HT + Sbjct: 8 PITLARGEGVWLWDEQGRKYLDGLAGIAVNGLGHAHPKLVAALTDQIGKLIHTS-NIYGV 66 Query: 85 EPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAG-----VIAFTGAY 139 +LA+ I R ++ +SG+EA ENA+K+AR + G + A+ Sbjct: 67 RGQEDLADAICAR---SGMEEVFFCSSGAEANENAIKLARFYGYKQGKDFIKTVVMENAW 123 Query: 140 HGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQ 199 HGRT+ TL T A G P E +++A+I + + + + Sbjct: 124 HGRTIATLAATDSP---KARKGFEP-------MQDECFVRVPHNNLAAIIEVAETNPE-- 171 Query: 200 DIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLG 259 I ++++E +QGEGG + S ++Q LR LCD+ G LLI DEVQ G GRTGT+F + G Sbjct: 172 -INSVMLEVLQGEGGINLASVEYLQGLRKLCDERGWLLILDEVQCGVGRTGTWFGYQHAG 230 Query: 260 IVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEEE 319 I PD T AK +G G PI +A + I PG G T+ G+P+A A L+ EE+ Sbjct: 231 IEPDAITLAKGLGSGVPIGALAVRGSAAKLIGPGNFGTTFGGNPLAMRAGTCTLQTLEED 290 Query: 320 KLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVV 379 LL+ + +G+ ++AG R + D+RG G M+ IEL +P IV Sbjct: 291 GLLQHAVVIGDHIRAGFRAALEGVAGVTDIRGQGLMIGIEL------DRPC----GVIVT 340 Query: 380 RAREKGLILLSCGTYYNVIRFLMPVTIPDAQLE 412 RA E G ++ T V+R L P+ + A+ + Sbjct: 341 RALEAGFLINV--TRDKVVRLLPPLIMTTAEAD 371 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: 381 Number of extensions: 22 Number of successful extensions: 4 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: 387 Length adjustment: 31 Effective length of query: 395 Effective length of database: 356 Effective search space: 140620 Effective search space used: 140620 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 Sep 24 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