Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_025763135.1 X939_RS0110060 aminotransferase class III-fold pyridoxal phosphate-dependent enzyme
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000566685.1:WP_025763135.1 Length = 384 Score = 195 bits (496), Expect = 2e-54 Identities = 142/407 (34%), Positives = 204/407 (50%), Gaps = 55/407 (13%) Query: 23 IHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVL 82 I PV +A+ S +WD G EY+D GG AV++ GH HP +A + EQL K+S V Sbjct: 13 IEPV---KAQGSYLWDQNGIEYLDMYGGHAVISVGHCHPDYVARLTEQLSKISFYSNSV- 68 Query: 83 AYEPYIELAEEIAKRVP--GDFPK-KTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAY 139 I EE+A ++ +P K L SG+EA ENA+K+A TGR V+AFT A+ Sbjct: 69 ----QIPQQEELATKLGTLSGYPDYKLFLCNSGAEANENALKLASFHTGRKKVVAFTKAF 124 Query: 140 HGRTMMTLGLTGKV-----VPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKN 194 HGRT + T V Y+ + +P AL G++E+ Sbjct: 125 HGRTAGAVAATDNPSIVAPVNYNEHVSFLPFNDIEALQA----GITEE------------ 168 Query: 195 DAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFA 254 +AA+I+E +QG GG V S F+Q LR CD+ G LI D VQ G GRTG FF+ Sbjct: 169 ------VAAVIVEGIQGVGGIQVCSDEFLQALRKRCDETGAALILDSVQCGYGRTGKFFS 222 Query: 255 TEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLK 314 + GI PD+ T AK +G GFPI+GV + + G LG T+ G+ +ACAA +AVL Sbjct: 223 HQFSGIHPDMMTMAKGMGNGFPIAGVLIAPQFKASF--GLLGTTFGGNHLACAAGIAVLD 280 Query: 315 VFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELV 374 + ++E+LL+ + +G L + E+ D+RG G M+ IE P EL Sbjct: 281 IMKDEQLLDNATKIGAYLFHEIEELGG----YKDLRGRGLMIGIEF------DFPVKELR 330 Query: 375 SKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAEC 421 +K++ E + G Y +R L + I + ++ L C Sbjct: 331 NKLLF---EHHIFTGVAGAY--TLRLLPSLAISQKEADQFLEAYRSC 372 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: 19 Number of successful extensions: 3 Number of sequences better than 1.0e-02: 1 Number of HSP's gapped: 2 Number of HSP's successfully gapped: 1 Length of query: 426 Length of database: 384 Length adjustment: 31 Effective length of query: 395 Effective length of database: 353 Effective search space: 139435 Effective search space used: 139435 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