Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_086511325.1 BZY95_RS18280 diaminobutyrate--2-oxoglutarate transaminase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_002151265.1:WP_086511325.1 Length = 421 Score = 211 bits (537), Expect = 3e-59 Identities = 150/426 (35%), Positives = 224/426 (52%), Gaps = 21/426 (4%) Query: 9 LKRRQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQ 68 L+R ++ V R + PVV +A N+ + D GREYIDF G LN GH +P + A+ Sbjct: 6 LERLESNV-RTYSRSFPVVFTKARNARLTDESGREYIDFLAGAGTLNYGHNNPHLKQALL 64 Query: 69 EQL---GKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARA 125 + L G + F A Y+E EE+ + G K L +G+ AVE A+++AR Sbjct: 65 DYLDSDGIVHGLDFWTAAKRDYLETLEEVILKPRGLDYKVHLPGPTGTNAVEAAIRLARV 124 Query: 126 ATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSI 185 A GR +++FT +HG TM +L TG A G+ G A P + + DS+ Sbjct: 125 AQGRHNIVSFTNGFHGVTMGSLATTGNRKFREATGGIPLQG--SAFMPYDGYLGEHTDSL 182 Query: 186 ASIERIFKNDAQPQDI-AAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQT 244 E++ +++ D+ AA+I+E VQGEGG V ++QRL +C + ILLI D++Q Sbjct: 183 DYFEKLLGDNSSGLDLPAAVIVETVQGEGGINVAGLEWLQRLERICRDNDILLIVDDIQA 242 Query: 245 GAGRTGTFFATEQLGIVPDLTTFAKSVGG-GFPISGVAGKAEIMDAIAPGGLGGTYAGSP 303 G GRTG FF+ E GI PD+ T +KS+ G G P + V + E +D PG GT+ G Sbjct: 243 GCGRTGKFFSFEHAGITPDIVTNSKSLSGFGLPFAHVLMRPE-LDKWKPGQYNGTFRGFN 301 Query: 304 IACAAALAVLKVFEEEKLLERS-QAVGERLKAGLREIQA---KHKVIGDVRGLGSMVAIE 359 +A A A A ++ + ++ ER Q G ++ ++I A ++ V RG G M I+ Sbjct: 302 LAFATAAAAMRQYWQDDTFERDVQRKGRVVEDRFQKIAALIGEYGVKATERGRGLMRGID 361 Query: 360 LFEGGDTHKPAAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILA 419 + G EL KI +A EKGL++ + G V++ L P+TIPD L +GL IL Sbjct: 362 VGSG--------ELADKITAKAFEKGLVIETSGQAGEVVKCLCPLTIPDEDLLEGLDILE 413 Query: 420 ECFDEL 425 E+ Sbjct: 414 ASVKEV 419 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: 406 Number of extensions: 20 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: 421 Length adjustment: 32 Effective length of query: 394 Effective length of database: 389 Effective search space: 153266 Effective search space used: 153266 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 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