GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glpF in Escherichia coli BW25113

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 15000 b0875 aquaporin Z (NCBI)

Query= TCDB::P08995
         (271 letters)



>lcl|FitnessBrowser__Keio:15000 b0875 aquaporin Z (NCBI)
          Length = 231

 Score =  146 bits (369), Expect = 3e-40
 Identities = 90/222 (40%), Positives = 124/222 (55%), Gaps = 16/222 (7%)

Query: 38  QKLVAEAVGTYFLIFAGCASLVVNENYYNM-ITFPGIAIVWGLVLTVLVYTVGHISGGHF 96
           +KL AE  GT++L+F GC S V+   +  + I F G+A+ +GL +  + + VGHISGGHF
Sbjct: 3   RKLAAECFGTFWLVFGGCGSAVLAAGFPELGIGFAGVALAFGLTVLTMAFAVGHISGGHF 62

Query: 97  NPAVTIAFASTRRFPLIQVPAYVVAQLLGSILASGTLRLLFMGN---HDQFSGTVPNG-- 151
           NPAVTI   +  RFP  +V  YV+AQ++G I+A+  L L+  G        SG   NG  
Sbjct: 63  NPAVTIGLWAGGRFPAKEVVGYVIAQVVGGIVAAALLYLIASGKTGFDAAASGFASNGYG 122

Query: 152 -------TNLQAFVFEFIMTFFLMFVICGVATDNRAVGEFAGIAIGSTLLLNVIIGGPVT 204
                  + L A V E +++   + VI G ATD  A   FA IAIG  L L  +I  PVT
Sbjct: 123 EHSPGGYSMLSALVVELVLSAGFLLVIHG-ATDKFAPAGFAPIAIGLALTLIHLISIPVT 181

Query: 205 GASMNPARSLGPAFVHGEY--EGIWIYLLAPVVGAIAGAWVY 244
             S+NPARS   A   G +  E +W + + P+VG I G  +Y
Sbjct: 182 NTSVNPARSTAVAIFQGGWALEQLWFFWVVPIVGGIIGGLIY 223


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: 197
Number of extensions: 21
Number of successful extensions: 4
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: 231
Length adjustment: 24
Effective length of query: 247
Effective length of database: 207
Effective search space:    51129
Effective search space used:    51129
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: 46 (22.3 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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, or view the source code.

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