Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate PP_4481 PP_4481 Succinylornithine transaminase/acetylornithine aminotransferase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Putida:PP_4481 Length = 406 Score = 223 bits (569), Expect = 6e-63 Identities = 149/399 (37%), Positives = 209/399 (52%), Gaps = 48/399 (12%) Query: 30 RAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAYEPYIE 89 R E S VWD GRE IDFAGGIAV GH HP ++ A+ EQ L H V EP + Sbjct: 30 RGEGSRVWDQSGRELIDFAGGIAVNALGHCHPALVKALTEQANTLWHVS-NVFTNEPALR 88 Query: 90 LAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIAR-AATGRAG-----VIAFTGAYHGRT 143 LA ++ V F + SG+E+ E A K+AR A R G +IA ++HGRT Sbjct: 89 LAHKL---VDATFADRAFFCNSGAESNEAAFKLARRVAHDRFGPQKHEIIATVNSFHGRT 145 Query: 144 MMTLGLTGKVVPYSAGMGLMPGGIFRALAPCELHGVSEDDSIASIERIFKND-----AQP 198 + T+ + G+ YS G G I I + ND AQ Sbjct: 146 LFTVSVGGQP-KYSDGFG---------------------PKITGISHVPYNDLEALKAQI 183 Query: 199 QD-IAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGTFFATEQ 257 D A++IEP+QGE G K++++ R LCD+H LLI DEVQTG GRTG+ +A + Sbjct: 184 SDKTCAVVIEPIQGESGVVPADKAYLEGARKLCDEHNALLIFDEVQTGVGRTGSLYAYQH 243 Query: 258 LGIVPDLTTFAKSVGGGFPISGVAGKAEIMDAIAPGGLGGTYAGSPIACAAALAVLKVFE 317 G++PD+ T AKS+GGGFPI + E+ +A G G TY G+P+ CA A AVL V Sbjct: 244 YGVIPDILTSAKSLGGGFPIGAMLTTTELAKHLAVGTHGTTYGGNPLGCAVACAVLDVVN 303 Query: 318 EEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGDTHKPAAELVSKI 377 + L +A ER K L +I ++ + VRG+G ++ L E A + +K Sbjct: 304 TPETLAGIKAKHERFKTRLEQIGQQYNLFSQVRGVGLLLGCVLTE-------AWKGKAKD 356 Query: 378 VVRAREK-GLILLSCGTYYNVIRFLMPVTIPDAQLEKGL 415 V+ A EK G+++L G +V+RF + + DA +++GL Sbjct: 357 VLNAAEKEGVMVLQAGP--DVVRFAPSLVVEDADIDEGL 393 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: 381 Number of extensions: 17 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: 406 Length adjustment: 31 Effective length of query: 395 Effective length of database: 375 Effective search space: 148125 Effective search space used: 148125 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