GapMind for catabolism of small carbon sources

 

Aligments for a candidate for rocD in Burkholderia phytofirmans PsJN

Align Ornithine aminotransferase; Orn-AT; Lysine aminotransferase; Lys-AT; EC 2.6.1.13; EC 2.6.1.36 (characterized)
to candidate BPHYT_RS10155 BPHYT_RS10155 2,2-dialkylglycine decarboxylase

Query= SwissProt::Q5JEW1
         (445 letters)



>lcl|FitnessBrowser__BFirm:BPHYT_RS10155 BPHYT_RS10155
           2,2-dialkylglycine decarboxylase
          Length = 433

 Score =  216 bits (550), Expect = 1e-60
 Identities = 144/417 (34%), Positives = 218/417 (52%), Gaps = 18/417 (4%)

Query: 37  PIVIERGEGIRVYDVDGNVFYDFASGVGVINVGHSHPRVVEAIKKQAEKFTHYSLTDFFY 96
           P++IER +G  VYD DG    DF SG     +GHSHP +V  I + A K  H   +    
Sbjct: 26  PMIIERAQGSFVYDADGRAILDFTSGQMSAVLGHSHPEIVSVINEYAGKLDHL-FSGMLS 84

Query: 97  ENAIILAEKLIELAPGDIERKVVYGNSGAEANEAAMKLVKYGTGRKQFLAFYHAFHGRTQ 156
              + LA +L E+ P  ++R ++  ++GAE+NEAA+++ K  TG+ + + F  ++HG T 
Sbjct: 85  RPVVDLATRLAEITPDGLDRALLL-STGAESNEAAIRMAKLVTGKYEIVGFAQSWHGMTA 143

Query: 157 AVLSLTASKWVQQDGFFPTMPGVTHIPYPNPYRNTWGIDGYEEPDELTNRVLDFIEEYVF 216
           A  S T S    + G  P   G   IP P  YR  +   G  + D L    LD+  + + 
Sbjct: 144 AAASATYS--AGRKGVGPAAVGSFAIPAPFLYRPRFERHG--DYDYLAE--LDYAFDLID 197

Query: 217 RHVPPHEIGAIFFEPIQGEGGYVVPPKGFFKALKKFADEYGILLADDEVQMGIGRTGKFW 276
           R    + + A   EPI   GG +  P+G+  ALK+  +E G+LL  DE Q G+GRTG  +
Sbjct: 198 RQSSGN-LAAFIAEPILSSGGIIELPEGYMTALKRKCEERGMLLILDEAQTGVGRTGTMF 256

Query: 277 AIEHFGVEPDLIQFGKAIGGGLPLAGVIHRADI---TFDKPGRHATTFGGNPVAIAAGIE 333
           A +  GV PD++   K +G GLPLA V+  A I     +      TT   +P+  A G+ 
Sbjct: 257 ACQRDGVTPDILTLSKTLGAGLPLAAVVTSAQIEERAHELGYLFYTTHVSDPLPAAVGLR 316

Query: 334 VVEIVKE--LLPHVQEVGDYLHKYLEEFKEKYEVIGDARGLGLAQAVEIVKSKETKEKYP 391
           V+E+V+   L+     +G  L + L +  E+++ IGD RG GL   +EIVK + TKE   
Sbjct: 317 VLEVVERDGLVARANLMGARLKRGLLDLMERFDCIGDIRGRGLLLGMEIVKDRRTKEPAD 376

Query: 392 ELRDRIVKESAKRGL----VLLGCGDNSIRFIPPLIVTKEEIDVAMEIFEEALKAAL 444
            L  +I +E    GL    V L       R  PPL V ++EID+ +++  +A++ +L
Sbjct: 377 GLGAKITRECMNLGLSMNIVQLPGMGGVFRIAPPLTVHEDEIDLGLDLLGQAIERSL 433


Lambda     K      H
   0.320    0.141    0.418 

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: 486
Number of extensions: 28
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: 445
Length of database: 433
Length adjustment: 32
Effective length of query: 413
Effective length of database: 401
Effective search space:   165613
Effective search space used:   165613
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 (21.7 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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