GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glnQ in Pseudomonas stutzeri RCH2

Align Glutamine ABC transporter ATP-binding protein, component of Glutamine transporter, GlnQP. Takes up glutamine, asparagine and glutamate which compete for each other for binding both substrate and the transmembrane protein constituent of the system (Fulyani et al. 2015). Tandem substrate binding domains (SBDs) differ in substrate specificity and affinity, allowing cells to efficiently accumulate different amino acids via a single ABC transporter. Analysis revealed the roles of individual residues in determining the substrate affinity (characterized)
to candidate GFF139 Psest_0139 ABC-type histidine transport system, ATPase component

Query= TCDB::Q9CES4
         (247 letters)



>lcl|FitnessBrowser__psRCH2:GFF139 Psest_0139 ABC-type histidine
           transport system, ATPase component
          Length = 257

 Score =  241 bits (614), Expect = 1e-68
 Identities = 126/247 (51%), Positives = 168/247 (68%), Gaps = 11/247 (4%)

Query: 7   IEVTDLHKSFGKNEVLKGITTKFEKGDVVCIIGPSGSGKSTFLRALNGLETATSGDIIID 66
           +E+ +LHK +G  EVLKGI+     GDV+ I+G SGSGKSTFLR +N LE    G+I++ 
Sbjct: 8   LEIRNLHKRYGDLEVLKGISLTARDGDVISILGSSGSGKSTFLRCINLLENPHEGEILVA 67

Query: 67  GFNLTDKNTN-----------LNLVRQNVGMVFQHFNLFPNMTVMQNITYAPVELKKMSK 115
           G  L  K              LN +R  +G VFQ+FNL+P+MT++ NI  AP  +   SK
Sbjct: 68  GEQLKLKRDKQGDLVAADGKQLNRIRSELGFVFQNFNLWPHMTILDNIIEAPRRVLGQSK 127

Query: 116 DDADKKAIQLLETVGLLDKKDAMPEMLSGGQKQRVAIARALAMNPDVMLFDEPTSALDPE 175
            +A + A  LL  VG+ DK+   P  LSGGQ+QR AIAR LAM P V+LFDEPTSALDPE
Sbjct: 128 AEATEVAEALLAKVGIADKRHVYPNQLSGGQQQRAAIARTLAMQPKVILFDEPTSALDPE 187

Query: 176 MVGDVLAVMQKLAEEGMTMLIVTHEMGFARKVANRVIFTDGGVILEDGTPEELFDSPKHP 235
           MV +VLAV++ LAEEG TML+VTHEM FA++V++ V+F   G++ E GTPE++FD+P+  
Sbjct: 188 MVQEVLAVIRSLAEEGRTMLLVTHEMNFAKQVSSEVVFLHQGLVEEQGTPEQVFDNPQSA 247

Query: 236 RLQDFLS 242
           R + F+S
Sbjct: 248 RCKQFMS 254


Lambda     K      H
   0.318    0.136    0.378 

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: 199
Number of extensions: 6
Number of successful extensions: 2
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: 247
Length of database: 257
Length adjustment: 24
Effective length of query: 223
Effective length of database: 233
Effective search space:    51959
Effective search space used:    51959
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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