Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate CA265_RS18530 CA265_RS18530 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Pedo557:CA265_RS18530 Length = 382 Score = 204 bits (520), Expect = 3e-57 Identities = 129/342 (37%), Positives = 199/342 (58%), Gaps = 30/342 (8%) Query: 23 IHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVL 82 ++ + +A S VWD ++Y+D GG AV++ GH +P + + +QL K+ V Sbjct: 9 LNDIEITKAAGSNVWDANDQQYLDLYGGHAVISIGHTNPHYVNRLTDQLNKVGFYSNSV- 67 Query: 83 AYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYHGR 142 ++LAE++ + V G + L SG+EA ENA+K+A GR VIAFTGA+HGR Sbjct: 68 KIPLQVQLAEKLGE-VSGKKDFQLFLCNSGAEANENALKLASFYNGRKKVIAFTGAFHGR 126 Query: 143 TMMTLGLTG--KVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQPQD 200 T + + +T K+V A + IF ++ ++E FK AQ + Sbjct: 127 TSLAVAVTDNPKIV---APVNQTENVIFLPF-----------NNEIALEETFK--AQGNE 170 Query: 201 IAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQLGI 260 I+A+IIE +QG GG SKSF+Q++R+LCD++ + IAD VQ G GRTG+F++ + G+ Sbjct: 171 ISAVIIEGIQGVGGIKEASKSFLQKIRSLCDEYNAVYIADSVQCGYGRTGSFYSHDYSGV 230 Query: 261 VPDLTTFAKSVGGGFPISGVAGKAEIMDAIAP--GGLGGTYAGSPIACAAALAVLKVFEE 318 D+ T AK +G GFP++G++ I P G LG T+ G+ +ACAAALAVL+V E+ Sbjct: 231 EADVYTMAKGMGNGFPVAGIS----IASKFKPWHGELGTTFGGNHLACAAALAVLEVMEK 286 Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIEL 360 + L++ ++ VG L A L+ K + + +VRG G M+ IEL Sbjct: 287 DNLIKNAEEVGNYLIAELK----KFEQVVEVRGRGLMIGIEL 324 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: 384 Number of extensions: 24 Number of successful extensions: 5 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: 382 Length adjustment: 31 Effective length of query: 395 Effective length of database: 351 Effective search space: 138645 Effective search space used: 138645 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 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