Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_004314496.1 C665_RS13470 4-aminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_000310185.1:WP_004314496.1 Length = 433 Score = 523 bits (1346), Expect = e-153 Identities = 250/422 (59%), Positives = 320/422 (75%) Query: 5 NESLLKRRQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVI 64 N + RR AA+PRGVGQ HP+ A +A N+ VWDVEGR +IDF GIAV+NTGH HP+V+ Sbjct: 12 NADFMARRAAALPRGVGQAHPLFATKALNAEVWDVEGRRFIDFVAGIAVVNTGHCHPRVV 71 Query: 65 AAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR 124 AA Q QL SHTCFQV+AY+ Y+ LAE + PGD KKT+LV++G+EAVENAVKIAR Sbjct: 72 AAAQAQLTHFSHTCFQVVAYDGYLRLAERLNALAPGDAAKKTMLVSTGAEAVENAVKIAR 131 Query: 125 AATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDS 184 A TGR GVIAF GA+HGRT++ LGLTGKV PY G+G PG I+ A PC LHG+S +D+ Sbjct: 132 AFTGRPGVIAFNGAFHGRTLLALGLTGKVDPYKLGVGPFPGEIYHAPYPCALHGISVEDA 191 Query: 185 IASIERIFKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQT 244 I IE +FKND + + +AA I+EPVQGEGG+Y F+QRLRAL D+HGILLIADE+Q+ Sbjct: 192 IHGIELLFKNDIEARRVAAFIVEPVQGEGGYYPAPAEFLQRLRALADKHGILLIADEIQS 251 Query: 245 GAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPI 304 G GR G FA E G++PD+ T AK +GGGFP++ V G+AE+MDA+APGGLG TYAG+P+ Sbjct: 252 GIGRCGKMFAVEHSGVMPDIITLAKGLGGGFPVAAVVGRAEVMDALAPGGLGSTYAGAPM 311 Query: 305 ACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGG 364 ACAAALAVL V EEEKL ER+ A+GE ++ LR++ +HK IGDVRGLG+MVA+E F G Sbjct: 312 ACAAALAVLDVMEEEKLCERALAIGEHMQRRLRDLAVRHKCIGDVRGLGAMVAVEFFHDG 371 Query: 365 DTHKPAAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDE 424 D +PA E+ ++ A ++GL+LLSCG+Y NV+R ++P+TI A L++GL +LA D Sbjct: 372 DHARPAPEIAKAVIAAALQRGLLLLSCGSYGNVLRLMVPLTIEQAVLDEGLDLLAAAMDA 431 Query: 425 LA 426 A Sbjct: 432 AA 433 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: 561 Number of extensions: 19 Number of successful extensions: 1 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: 433 Length adjustment: 32 Effective length of query: 394 Effective length of database: 401 Effective search space: 157994 Effective search space used: 157994 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