GapMind for catabolism of small carbon sources

 

Alignments for a candidate for dsdA in Phaeobacter inhibens BS107

Align L-serine ammonia-lyase (EC 4.3.1.17); D-Serine ammonia-lyase (EC 4.3.1.18) (characterized)
to candidate GFF3319 PGA1_c33720 D-cysteine desulfhydrase 2

Query= BRENDA::O57809
         (325 letters)



>FitnessBrowser__Phaeo:GFF3319
          Length = 337

 Score =  209 bits (532), Expect = 8e-59
 Identities = 128/324 (39%), Positives = 181/324 (55%), Gaps = 17/324 (5%)

Query: 9   LAKFPRVELIPWETPIQYLPNISREIGADVYIKRDDLTGLGIGGNKIRKLEYLLGDALSK 68
           LA+FPRV L    TP++ +  +S+E+G +++IKRDD TG+  GGNK RKLE+L+ +AL +
Sbjct: 3   LARFPRVHLAHLSTPLEPMERLSKELGVELWIKRDDCTGMSTGGNKTRKLEFLMAEALEQ 62

Query: 69  GADVVITVGAVHSNHAFVTGLAAKKLGLDAILVLRGKE-------ELKGNYLLDKIMGIE 121
           GAD+V+T GA  +NH   T   A KLGL   ++L  +           GN LLD + G  
Sbjct: 63  GADMVMTQGATQTNHGRQTAAFAAKLGLKCHILLEDRTGYQDSNYNTNGNVLLDHLHGAT 122

Query: 122 TRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYVRAVGEIATQSE-- 179
           T  +      ++    E+ AE+++ +G K YVIP GG++P G LGYV A  E+ +Q+   
Sbjct: 123 TEKFPG--GHDMPGEMEKAAEKMRAKGHKVYVIPGGGSNPTGALGYVNAAFELVSQANDR 180

Query: 180 -VKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPVGIAVGRFGEVMTSKLDNLIKEAAELL 238
            +K D +V A GS GT AGL  G+  +N  I  +GI            + +L  + AE L
Sbjct: 181 GLKIDRLVHATGSSGTQAGLVTGMCAMNAQIPVLGIGTRAPQPKQEQMIFDLACKTAEKL 240

Query: 239 G----VKVEVRPELYDYSFGEYGKITGEVAQIIRKVGTREGIILDPVYTGKAFYGLVDLA 294
           G    VK E      DY    YG  T    + I+     EGI+LDP Y+ K   GL+DLA
Sbjct: 241 GCAGIVKREDVMANTDYVGEGYGLPTQSGIEAIQMFAELEGILLDPCYSAKGGAGLIDLA 300

Query: 295 RKGEL-GEKILFIHTGGISGTFHY 317
           RKGE  GE+++F+HTGG +    Y
Sbjct: 301 RKGEFAGERVVFLHTGGAAALGGY 324


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: 298
Number of extensions: 17
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: 337
Length adjustment: 28
Effective length of query: 297
Effective length of database: 309
Effective search space:    91773
Effective search space used:    91773
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: 49 (23.5 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