Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_004298659.1 C665_RS01920 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000310185.1:WP_004298659.1 Length = 391 Score = 193 bits (491), Expect = 7e-54 Identities = 133/402 (33%), Positives = 195/402 (48%), Gaps = 39/402 (9%) Query: 25 PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTC--FQVL 82 PV E ++D G+ Y+D GIAV G+ HP+++ A+ +Q ++ HT +++ Sbjct: 12 PVAFTHGEGVWLYDETGKRYLDALSGIAVNTLGYKHPRLVKAIADQAERVLHTSNLYRIP 71 Query: 83 AYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAGV-----IAFTG 137 E +L++ IA+ D + SG EA E A+K+AR G+ I Sbjct: 72 LQE---QLSDRIAEAAGMD---EVFFCNSGCEANEAAIKLARMYGHNKGIELPHIIVMEN 125 Query: 138 AYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQ 197 A+HGRTM TL TG AG + G R IE I K Sbjct: 126 AFHGRTMATLSATGNRKA-QAGFEPLVQGFIRV-------------PYKDIEAIRKIAEH 171 Query: 198 PQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQ 257 + A+++E +QGEGG V ++F + LRALCD G L+I DEVQ G GRTG +F + Sbjct: 172 NHTVVAVMLEMIQGEGGVNVADEAFQRDLRALCDDRGWLMICDEVQCGMGRTGKWFGWQH 231 Query: 258 LGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFE 317 G PD+ T AK + G PI PG G T+ G+P+ACAA LA Sbjct: 232 AGTRPDVMTLAKGLASGVPIGACVTSGLAKGLFGPGNHGSTFGGNPLACAAGLATFDAIV 291 Query: 318 EEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKI 377 E++L++ + AVG ++ G+ E A + D+RG G M+ IEL +P L++ Sbjct: 292 EDELMDNAVAVGAAIRKGMAEALAGEAGVVDIRGRGLMIGIEL------DRPCGVLMA-- 343 Query: 378 VVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILA 419 RA E GL+L T V+R L +T A + +++LA Sbjct: 344 --RAAENGLLL--SVTSERVVRLLPALTFTTADAQTLVSMLA 381 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: 396 Number of extensions: 19 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: 391 Length adjustment: 31 Effective length of query: 395 Effective length of database: 360 Effective search space: 142200 Effective search space used: 142200 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