GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpF in Pseudomonas simiae WCS417

Align Nodulin-26 aquaporin and glycerol facilitator, NIP (de Paula Santos Martins et al. 2015). Transports NH3 5-fold better than water in Hg2+-sensitive fashion (characterized)
to candidate GFF3160 PS417_16175 porin

Query= TCDB::P08995
         (271 letters)



>FitnessBrowser__WCS417:GFF3160
          Length = 251

 Score =  141 bits (355), Expect = 2e-38
 Identities = 92/228 (40%), Positives = 127/228 (55%), Gaps = 14/228 (6%)

Query: 38  QKLVAEAVGTYFLIFAGCASLVVNENYYNM-ITFPGIAIVWGLVLTVLVYTVGHISGGHF 96
           ++L AE +GT++L F GC S ++   +  + I F G+++ +GL +  + Y VG ISGGHF
Sbjct: 3   KRLTAEFIGTFWLTFGGCGSAILAAAFPELGIGFVGVSLAFGLTVLTMAYAVGGISGGHF 62

Query: 97  NPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGNHD-QFSGTVPNGTN-- 153
           NPAVT+   + RR    +V  Y+ AQ+ G+I AS  L L+  G  D    G   NG    
Sbjct: 63  NPAVTLGLWAGRRVAAGEVLPYIAAQVAGAIGASAALYLIANGQPDFAIGGFAANGYGPL 122

Query: 154 -------LQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVTGA 206
                    A + E I TFF +F+I  V T + AV  FA IAIG  L L  ++  PVT  
Sbjct: 123 SPGLFDMKAALLAECIATFFFLFIIMRV-TSSGAVPGFAPIAIGLALTLIHLVLIPVTNT 181

Query: 207 SMNPARSLGPA-FVHGEY-EGIWIYLLAPVVGAIAGAWVYNIVRYTDK 252
           S+NPARS GPA F  GEY   +W++ LAP+VG + GA     +   DK
Sbjct: 182 SVNPARSTGPALFAGGEYLAQLWLFWLAPMVGGVMGALAARSLGERDK 229


Lambda     K      H
   0.323    0.138    0.407 

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: 220
Number of extensions: 25
Number of successful extensions: 7
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: 271
Length of database: 251
Length adjustment: 25
Effective length of query: 246
Effective length of database: 226
Effective search space:    55596
Effective search space used:    55596
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.5 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (22.0 bits)
S2: 47 (22.7 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