GapMind for catabolism of small carbon sources

 

Alignments for a candidate for lat 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)



>FitnessBrowser__BFirm:BPHYT_RS10155
          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:

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