Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 5208501 Shew_1012 glutamate-1-semialdehyde-2,1-aminomutase (RefSeq)
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__PV4:5208501 Length = 428 Score = 169 bits (427), Expect = 2e-46 Identities = 119/363 (32%), Positives = 181/363 (49%), Gaps = 24/363 (6%) Query: 5 NESLLKRRQAAVPRGVGQI---------HPVVAERAENSTVWDVEGREYIDFAGGIAVLN 55 +E+L ++ + +P GV P E+A+ + ++D +G+ YID+ G + Sbjct: 4 SETLFEQAKKTIPGGVNSPVRAFNGVGGSPRFIEKADGAYIYDADGKAYIDYVGSWGPMI 63 Query: 56 TGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEA 115 GH HPK+ AV L + + E + +AE++ + VP ++ +V+SG+EA Sbjct: 64 LGHNHPKIRQAV---LDAVENGLSFGAPTELEVRMAEKVIEMVPS--MEQVRMVSSGTEA 118 Query: 116 VENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCE 175 +A+++AR T R ++ F G YHG L G + G PG I A Sbjct: 119 TMSAIRLARGFTNRDKILKFEGCYHGHADCLLVKAGSGA-LTLGQPSSPG-IPEDFAKHT 176 Query: 176 LHGVSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGI 235 L V + + S++ +F+ P++IA II+EPV G F++ LRALCDQ+G Sbjct: 177 LTAVYNE--LESVKTLFEQ--YPEEIACIILEPVAGNMNCIPPIPGFLEGLRALCDQYGA 232 Query: 236 LLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGG- 294 LLI DEV TG R A GI PDLTT K +GGG P+ G+ E+M IAP G Sbjct: 233 LLIIDEVMTGF-RVSKSGAQGHYGITPDLTTLGKVIGGGMPVGAFGGRKEVMQFIAPTGP 291 Query: 295 --LGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGL 352 GT +G+PIA +A LA ++ E L E A +R+ G + KH + + + Sbjct: 292 VYQAGTLSGNPIAMSAGLAQMEELCAEGLYEELAAKTKRIAEGFKAAANKHGIPLSINYV 351 Query: 353 GSM 355 G M Sbjct: 352 GGM 354 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: 475 Number of extensions: 21 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: 428 Length adjustment: 32 Effective length of query: 394 Effective length of database: 396 Effective search space: 156024 Effective search space used: 156024 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