GapMind for catabolism of small carbon sources

 

Alignments for a candidate for davT in Burkholderia phytofirmans PsJN

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.

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About GapMind

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:

where "other" refers to the best ublast hit to a sequence that is not annotated as performing this step (and is not "ignored").

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