Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BWI76_RS07600 BWI76_RS07600 aspartate aminotransferase family protein
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Koxy:BWI76_RS07600 Length = 445 Score = 218 bits (555), Expect = 3e-61 Identities = 154/422 (36%), Positives = 226/422 (53%), Gaps = 28/422 (6%) Query: 21 GQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQ 80 G +HP+V A+ +WD EG Y+DF+ + +N G+ HP+V+AA++ QL L T Sbjct: 32 GNLHPLVIAGAKGCELWDYEGNTYLDFSSQLVNVNIGYQHPRVLAAMKAQLEALV-TIAP 90 Query: 81 VLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIARAATGRAGVIAFTGAYH 140 A E A+ I + P F K +G++A ENA+++AR TGR V++ +YH Sbjct: 91 ATANLARGEAAKRIVELAPEGF-SKVFFTNAGADANENAIRMARLYTGRDKVLSAYRSYH 149 Query: 141 GRTMMTLGLTG--KVVP--YSAG-MGLMPGGIFRALAPCELHGVSEDD----SIASIERI 191 G T + TG + VP YS G + ++R+ E + +E++ ++A + R+ Sbjct: 150 GNTGSAIAATGDWRRVPNEYSRGHVHFFNPYLYRS----EFNATTEEEECQRALAHLRRM 205 Query: 192 FKNDAQPQDIAAIIIEPVQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGAGRTGT 251 + + P IAAI++E + G G V + +MQ +RAL D+ GI+LI DEV G GRTG+ Sbjct: 206 IECEG-PNAIAAILLESIPGTAGILVPPEGYMQGVRALADEFGIILILDEVMAGFGRTGS 264 Query: 252 FFATEQLGIVPDLTTFAKSVGGGF-PISGVAGKAEIM----DAIAPGGLGGTYAGSPIAC 306 +FA EQ G+VPDL TFAK V G+ P GV I D GGL TY+G P+A Sbjct: 265 WFAFEQDGVVPDLVTFAKGVNAGYVPAGGVLISEPIARYFDDHFFAGGL--TYSGHPLAM 322 Query: 307 AAALAVLKVFEEEKLLERSQAVG-ERLKAGLREIQAKHKVIGDVRGLGSMVAIELFEGGD 365 AA +A + +EEK++E + +G E L+ GL + KH +IG+VRG G A+EL + Sbjct: 323 AAIVATIDAMKEEKVVENAATIGNEVLRPGLEALAEKHAIIGNVRGRGLFQALELVSSRE 382 Query: 366 THKP-AAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLEKGLAILAECFDE 424 P A ++ I E GL+ N I + P TI Q+ KGLAI F Sbjct: 383 HKTPLGAADMAAIKGALTEAGLLAF---VVENRIHVVPPCTISAEQVAKGLAIFDAVFAR 439 Query: 425 LA 426 A Sbjct: 440 FA 441 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: 445 Number of extensions: 22 Number of successful extensions: 6 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: 445 Length adjustment: 32 Effective length of query: 394 Effective length of database: 413 Effective search space: 162722 Effective search space used: 162722 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 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