Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate 8500245 DvMF_1002 adenosylmethionine-8-amino-7-oxononanoate aminotransferase (RefSeq)
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__Miya:8500245 Length = 491 Score = 188 bits (478), Expect = 3e-52 Identities = 135/417 (32%), Positives = 208/417 (49%), Gaps = 36/417 (8%) Query: 25 PVVAERAENSTVWDVEGREYIDFAGGIAVLNTGHLHPKVIAAVQEQLGKLSHTCFQVLAY 84 P+V AE + + D +G Y+D + GH HP++ AA++ QL K++HT L Sbjct: 50 PLVIGAAEGNRLTDTDGVSYLDGVSSLWTNVHGHRHPRLDAAIRAQLDKVAHTTLLGLGS 109 Query: 85 EPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVENAVKIA----RAATGRAG-------VI 133 EP IELA +A P + SGS +VE A+KIA R A G + Sbjct: 110 EPSIELAARLAAIAPQGLTR-VFYSDSGSTSVEVALKIAFQFHRQAPAHLGGDARRTRFL 168 Query: 134 AFTGAYHGRTMMTLGLTGKVVPYSAGMGLMPGGIFRALAPC------ELHGVSEDDSIAS 187 + AYHG T+ + L G + +S L+ + C G E + I Sbjct: 169 SLRNAYHGDTVGAVALGGMALFHSIYAPLLFDTVKAESPYCYRCPFGRQAGSCERECITH 228 Query: 188 IERIFKNDAQPQDIAAIIIEP-VQGEGGFYVNSKSFMQRLRALCDQHGILLIADEVQTGA 246 +E +F ++ A ++EP VQG G + +++R+R LCD+HG+ L+ADEV G Sbjct: 229 METLFARHGH--ELCAAVVEPLVQGAAGMLLQPPGWLRRVRELCDEHGVFLVADEVAVGF 286 Query: 247 GRTGTFFATEQLGIVPDLTTFAKSVGGGF-PISGVAGKAEIMDA-------IAPGGLGGT 298 G+TGT FA EQ G+ PD AK + GG+ P++ + D + G T Sbjct: 287 GKTGTLFACEQEGVTPDFLCLAKGISGGYLPLAATLTTERVHDGFLARHEELRTFFHGHT 346 Query: 299 YAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKVIGDVRGLGSMVAI 358 Y G+P+ACAAA+A L VFEEE+++ER Q RL A L ++ V GD+R G M I Sbjct: 347 YTGNPLACAAAIASLDVFEEERVMERLQPKIARLAARLDTLRDLPHV-GDIRQRGVMTGI 405 Query: 359 ELFEGGDTHKP---AAELVSKIVVRAREKGLILLSCGTYYNVIRFLMPVTIPDAQLE 412 E+ T + A + ++ + AR +G+I+ G +V+ + P++I D +++ Sbjct: 406 EMVRNRATKEAYDLALRVGHRVTLEARRRGVIIRPLG---DVMVLMPPLSITDDEID 459 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: 503 Number of extensions: 26 Number of successful extensions: 4 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: 491 Length adjustment: 33 Effective length of query: 393 Effective length of database: 458 Effective search space: 179994 Effective search space used: 179994 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