Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_013518270.1 ALIDE2_RS17550 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000204645.1:WP_013518270.1 Length = 398 Score = 218 bits (554), Expect = 3e-61 Identities = 136/400 (34%), Positives = 215/400 (53%), Gaps = 37/400 (9%) Query: 25 PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84 P+ ER + VWDV G++Y+D GGIAV GH HP+++ A+QEQ+ KL HT Sbjct: 20 PIALERGQGVRVWDVNGKQYLDGLGGIAVNTLGHNHPRLVPALQEQIAKLIHTSNYY--- 76 Query: 85 EPYIELAEEIAKRVPGDFPK-KTLLVTSGSEAVENAVKIARAATGRAGV-----IAFTGA 138 ++ EE+A+ + G +G EA E A+KIAR G+ + + A Sbjct: 77 --HVPGQEELARLLTGRARMTNAFFCNTGLEANECAIKIARKYGVDKGIEKPEIVVYDHA 134 Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQP 198 +HGR++ T+ TG + G G + G R +AP ++ + E + P Sbjct: 135 FHGRSIATMTATGNPKVRN-GFGPLLEGFIR-VAPNDIEALQE-----------ATEGNP 181 Query: 199 QDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258 ++ A+++EP+QGEGG + ++Q++R LCD +G LL+ DEVQ G GRTG +FA + Sbjct: 182 -NVVAVLMEPIQGEGGLHPMRVEYLQQVRKLCDANGWLLMLDEVQAGMGRTGKWFAHQWA 240 Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318 GIVPD+ T AK +G G P+ V + + PG G T+ G+P+A A + +++ EE Sbjct: 241 GIVPDVMTLAKGLGSGVPVGAVLAHGAASEVLKPGNHGSTFGGNPLAMRAGVETIRIMEE 300 Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIV 378 E LL+ + VG LKAGL++ + +VRG G ++ +EL +P L+ Sbjct: 301 EGLLQNAADVGAHLKAGLQQALGSVPGVNEVRGQGLIIGVEL------DRPCGVLID--- 351 Query: 379 VRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAIL 418 RA + GL+L T VIR + +T+ A+ ++ +A+L Sbjct: 352 -RAAQAGLLL--SVTADRVIRLVPALTLTRAEADEIVALL 388 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: 414 Number of extensions: 20 Number of successful extensions: 3 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: 398 Length adjustment: 31 Effective length of query: 395 Effective length of database: 367 Effective search space: 144965 Effective search space used: 144965 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 Apr 09 2024. 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