GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Pseudomonas fluorescens GW456-L13

Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate PfGW456L13_443 D-cysteine desulfhydrase (EC 4.4.1.15)

Query= BRENDA::O57809
         (325 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_443
          Length = 330

 Score =  216 bits (549), Expect = 8e-61
 Identities = 130/327 (39%), Positives = 194/327 (59%), Gaps = 16/327 (4%)

Query: 9   LAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSK 68
           LA+F R++L+   T ++ L  +S  +G D+Y+KRDDLT L +GGNK+RKLEYL  DAL++
Sbjct: 6   LARFNRLDLLGQPTALEKLERLSTWLGRDLYVKRDDLTPLAMGGNKLRKLEYLAADALAQ 65

Query: 69  GADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLR---GKEEL----KGNYLLDKIMGIE 121
           GAD +IT GA+ SNH   T   A KLGL  + +L    G ++      GN LL  +   +
Sbjct: 66  GADTLITAGALQSNHVRQTAAIAAKLGLGCVALLENPLGTDDSNYTGNGNRLLLDLFDAK 125

Query: 122 TRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQ---S 178
             + +  D+ +  +  + +A  L   G+KPY++P GG++ +G LGYVRA  E+A Q   +
Sbjct: 126 VELVENLDNAD--EQLQALANRLCSNGKKPYLVPIGGSNALGALGYVRAGLELAEQIKDT 183

Query: 179 EVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELL 238
            +KF ++V+A+GS GT +GL+L LS    D+  +G+ V R  E    K+  L +  AELL
Sbjct: 184 GLKFAAVVLASGSAGTHSGLALALSEALPDLPVIGVTVSRSDEDQRPKVQGLAERTAELL 243

Query: 239 GVKV--EVRPELYDYSFG-EYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLAR 295
           GV +    + EL+D  F   YG+        ++ + ++EG++LDPVYTGKA  GL+D   
Sbjct: 244 GVSLPEAFKVELWDEYFAPRYGEPNAGTLAAVKLLASQEGLLLDPVYTGKAMAGLLDGIG 303

Query: 296 KGELGE-KILFIHTGGISGTFHYGDKL 321
           +    E  I+F+HTGG    F Y D L
Sbjct: 304 RQRFNEGPIIFLHTGGAPALFAYKDFL 330


Lambda     K      H
   0.319    0.142    0.402 

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: 292
Number of extensions: 18
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: 325
Length of database: 330
Length adjustment: 28
Effective length of query: 297
Effective length of database: 302
Effective search space:    89694
Effective search space used:    89694
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: 48 (23.1 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