Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_028312237.1 H566_RS0116110 glutamate-1-semialdehyde-2,1-aminomutase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000482785.1:WP_028312237.1 Length = 426 Score = 184 bits (468), Expect = 3e-51 Identities = 136/407 (33%), Positives = 192/407 (47%), Gaps = 41/407 (10%) Query: 5 NESLLKRRQAAVPRGVGQIHPVVA-----------ERAENSTVWDVEGREYIDFAGGIAV 53 N+ L R Q ++P GV PV A ER + +WD +GREYID+ G Sbjct: 4 NDELFARAQRSIPGGVNS--PVRAFRQVGGTPRFFERGAGARLWDADGREYIDYVGSWGP 61 Query: 54 LNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGS 113 + GH HP V+AAVQ+ +H E I +AEE+ K +P +K V+SG+ Sbjct: 62 MILGHAHPTVVAAVQD---AAAHGLGYGAPTEAEIVIAEEVMKLMPS--LEKIRFVSSGT 116 Query: 114 EAVENAVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMP-GGIFRALA 172 EA +A+++AR ATGR ++ F G YHG L AG GL+ G A Sbjct: 117 EAAMSAIRLARGATGRTRIVKFDGCYHGHADSLL--------VKAGSGLLTFGNPTSAGV 168 Query: 173 PCELHG---VSEDDSIASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRAL 229 P + V + + IA I+ F+ +IA +I+EP+ G F + + RLR L Sbjct: 169 PADFAAHTIVLDYNDIAEIDACFEKFG--HEIACVIVEPIAGNMNFVRGTPEWHARLREL 226 Query: 230 CDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDA 289 C QHG +LI DEV TG R A GI PDLT K +GGG P++ G AE+M Sbjct: 227 CTQHGSVLIWDEVMTGF-RVALGGAQSLYGIRPDLTVLGKVIGGGMPVAAFGGSAEVMKF 285 Query: 290 IAPGG---LGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVI 346 +AP G GT +G+P+A AA LA L++ +E +R +L AG + + Sbjct: 286 LAPEGPVYQAGTLSGNPVAVAAGLATLRLIQEPGFHDRLGEQTAKLMAGFQAAAESAGLP 345 Query: 347 GDVRGLGSMVAIELFEG-----GDTHKPAAELVSKIVVRAREKGLIL 388 V +G M EG + H E K ++G+ L Sbjct: 346 LAVDSVGGMFGFYFREGLPGTLSEVHTADVERFKKFFHAMLDRGVYL 392 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: 488 Number of extensions: 23 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: 426 Length adjustment: 32 Effective length of query: 394 Effective length of database: 394 Effective search space: 155236 Effective search space used: 155236 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 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