Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate WP_027489558.1 LRK54_RS06590 acetylornithine/succinylornithine family transaminase
Query= BRENDA::Q9I6M4 (426 letters) >NCBI__GCF_021560695.1:WP_027489558.1 Length = 408 Score = 232 bits (591), Expect = 2e-65 Identities = 149/408 (36%), Positives = 219/408 (53%), Gaps = 33/408 (8%) Query: 26 VVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYE 85 +V + + + VWD EGR+Y+DF GIAV GH P ++AA+ Q KL H+ V E Sbjct: 25 LVLDHGKGARVWDTEGRDYVDFGAGIAVNALGHQDPDLLAALAAQAHKLWHSS-NVFYTE 83 Query: 86 PYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR---AATGRAG----VIAFTGA 138 P + LAEE+ F ++ L SG+EA E A+K+ R AA GRA ++ F G+ Sbjct: 84 PPLRLAEELVHA--SGFAERVFLCNSGAEANEAAIKLVRKWAAAQGRAPERRVIVTFNGS 141 Query: 139 YHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKNDAQP 198 +HGRT+ T+ T + Y G +P G FR L + + ++E F Sbjct: 142 FHGRTLATVTATAQA-KYQQGYEPLPEG-FRYL---------DFNDAEALEATFAAG--- 187 Query: 199 QDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQL 258 D+AA+++EPVQGEGG + F++R+R LCDQH LL+ DE+Q G GRTGT FA Sbjct: 188 -DVAAVMLEPVQGEGGVLPAAPGFLKRVRELCDQHDALLVLDEIQCGMGRTGTLFAHVHD 246 Query: 259 GIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFEE 318 +VPD+ T AK++GGGFPI + ++ + + G G T+ G+P+A A A L Sbjct: 247 HVVPDIVTLAKALGGGFPIGAMLAGPKVAEVMQYGAHGTTFGGNPMAAAVARVALAKLSS 306 Query: 319 EKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKIV 378 +L + L+AGL I + ++ +VRG G M+ L D +K A ++ Sbjct: 307 PAVLMNVERQANDLRAGLARINHELQLFAEVRGRGLMIGAVL---ADAYKGKA---GAVL 360 Query: 379 VRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDELA 426 A +GL+LL G +V+RF+ P+TI D +L GLA L + A Sbjct: 361 DHAATRGLLLLQAGP--DVLRFVPPLTITDEELADGLARLHAALSDFA 406 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: 424 Number of extensions: 14 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: 408 Length adjustment: 31 Effective length of query: 395 Effective length of database: 377 Effective search space: 148915 Effective search space used: 148915 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 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