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_3549 pyridoxal phosphate-dependent deaminase, putative

Query= BRENDA::O57809
         (325 letters)



>FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_3549
          Length = 343

 Score =  179 bits (455), Expect = 7e-50
 Identities = 121/339 (35%), Positives = 180/339 (53%), Gaps = 24/339 (7%)

Query: 1   MHPKIFALLAKFPRVELIPWETPIQYLPNISREIGAD-----VYIKRDDLTGLGIGGNKI 55
           M  ++   L+ F R +L+   TPIQ    + + +G D     +++KRDD   +G GGNK+
Sbjct: 1   MQTQLDKSLSVFARADLLQGPTPIQRAARLEQLLGLDKQGIGLFLKRDDHMLIGAGGNKL 60

Query: 56  RKLEYLLGDALSKGADVVITVGAVHSNHAFVTGLAAKKLGLDAILVL-------RGKEEL 108
           RKLE+ +G AL  G D +ITVG + SNHA +T     +LG+   L+L           EL
Sbjct: 61  RKLEFHIGAALQAGIDTIITVGGIQSNHARLTAAVCARLGIACELLLTRAVAKAEVDYEL 120

Query: 109 KGNYLLDKIMGIETRVYDAKDSFELMKYAEEIAEELKREGRKPYVIPPGGASPIGTLGYV 168
            GN LLD++ G + +V+ A  +  L K AE  A  L+  G K  V+P GG++P+G+LGY 
Sbjct: 121 NGNVLLDQLFGAQMQVF-AGGTDSLAK-AEARAALLRDSGHKVMVLPTGGSTPLGSLGYA 178

Query: 169 RAVGEIATQS---EVKFDSIVVAAGSGGTLAGLSLGLSILNEDIRPV-GIAVGRFGEVMT 224
           R   EIA Q    ++ F+ +VV  GS GT AGL+ G  +L      V   +V    E   
Sbjct: 179 RCAAEIAQQEAELQLTFNQVVVPNGSAGTHAGLAAGFRLLGRGTSMVKSFSVLSDQESSI 238

Query: 225 SKLDNLIKEAAELLGVKVEVRPELYDYSFGE----YGKITGEVAQIIRKVGTREGIILDP 280
           ++   L +E   LL    +VR +       +    YG  T  +   +R +   EG+++DP
Sbjct: 239 ARTLQLTRETLALLDSNAQVRADELVVDGSQLGTGYGLPTAAMQDAVRLMARAEGLLVDP 298

Query: 281 VYTGKAFYGLVDLARKGEL--GEKILFIHTGGISGTFHY 317
           VY+GKAF GL+   ++G    G+ +LFI TGG  G + Y
Sbjct: 299 VYSGKAFAGLLADLQQGRFVPGDNVLFIMTGGTPGLYAY 337


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: 266
Number of extensions: 16
Number of successful extensions: 6
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: 343
Length adjustment: 28
Effective length of query: 297
Effective length of database: 315
Effective search space:    93555
Effective search space used:    93555
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