Align 5-aminovalerate transaminase (EC 2.6.1.48) (characterized)
to candidate BPHYT_RS10155 BPHYT_RS10155 2,2-dialkylglycine decarboxylase
Query= BRENDA::Q9I6M4 (426 letters) >FitnessBrowser__BFirm:BPHYT_RS10155 Length = 433 Score = 219 bits (558), Expect = 1e-61 Identities = 143/440 (32%), Positives = 234/440 (53%), Gaps = 27/440 (6%) Query: 1 MSKTNESLLKR--RQAAVPRGVGQIHPVVAERAENSTVWDVEGREYIDFAGGIAVLNTGH 58 MS+ N+++ R +Q + G G P++ ERA+ S V+D +GR +DF G GH Sbjct: 1 MSRNNDAVFWRNAKQHLIRYG-GTFEPMIIERAQGSFVYDADGRAILDFTSGQMSAVLGH 59 Query: 59 LHPKVIAAVQEQLGKLSHTCFQVLAYEPYIELAEEIAKRVPGDFPKKTLLVTSGSEAVEN 118 HP++++ + E GKL H F + P ++LA +A+ P D + LL+++G+E+ E Sbjct: 60 SHPEIVSVINEYAGKLDHL-FSGMLSRPVVDLATRLAEITP-DGLDRALLLSTGAESNEA 117 Query: 119 AVKIARAATGRAGVIAFTGAYHGRTMMTLGLTGKVVPYSAGM-GLMPG--GIFRALAPC- 174 A+++A+ TG+ ++ F ++HG T T YSAG G+ P G F AP Sbjct: 118 AIRMAKLVTGKYEIVGFAQSWHGMTAAAASAT-----YSAGRKGVGPAAVGSFAIPAPFL 172 Query: 175 -----ELHGVSEDDSIASIERIFKN-DAQPQ-DIAAIIIEPVQGEGGFYVNSKSFMQRLR 227 E HG + D +A ++ F D Q ++AA I EP+ GG + +M L+ Sbjct: 173 YRPRFERHG--DYDYLAELDYAFDLIDRQSSGNLAAFIAEPILSSGGIIELPEGYMTALK 230 Query: 228 ALCDQHGILLIADEVQTGAGRTGTFFATEQLGIVPDLTTFAKSVGGGFPISGVAGKAEIM 287 C++ G+LLI DE QTG GRTGT FA ++ G+ PD+ T +K++G G P++ V A+I Sbjct: 231 RKCEERGMLLILDEAQTGVGRTGTMFACQRDGVTPDILTLSKTLGAGLPLAAVVTSAQIE 290 Query: 288 DAIAPGG--LGGTYAGSPIACAAALAVLKVFEEEKLLERSQAVGERLKAGLREIQAKHKV 345 + G T+ P+ A L VL+V E + L+ R+ +G RLK GL ++ + Sbjct: 291 ERAHELGYLFYTTHVSDPLPAAVGLRVLEVVERDGLVARANLMGARLKRGLLDLMERFDC 350 Query: 346 IGDVRGLGSMVAIELFEGGDTHKPAAELVSKIVVRAREKGLI--LLSCGTYYNVIRFLMP 403 IGD+RG G ++ +E+ + T +PA L +KI GL ++ V R P Sbjct: 351 IGDIRGRGLLLGMEIVKDRRTKEPADGLGAKITRECMNLGLSMNIVQLPGMGGVFRIAPP 410 Query: 404 VTIPDAQLEKGLAILAECFD 423 +T+ + +++ GL +L + + Sbjct: 411 LTVHEDEIDLGLDLLGQAIE 430 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: 416 Number of extensions: 13 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: 433 Length adjustment: 32 Effective length of query: 394 Effective length of database: 401 Effective search space: 157994 Effective search space used: 157994 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