GapMind for catabolism of small carbon sources

 

Aligments for a candidate for glnQ in Herbaspirillum seropedicae SmR1

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 HSERO_RS00320 HSERO_RS00320 peptide ABC transporter ATP-binding protein

Query= TCDB::Q9CES4
         (247 letters)



>lcl|FitnessBrowser__HerbieS:HSERO_RS00320 HSERO_RS00320 peptide ABC
           transporter ATP-binding protein
          Length = 240

 Score =  299 bits (765), Expect = 4e-86
 Identities = 147/239 (61%), Positives = 187/239 (78%)

Query: 7   IEVTDLHKSFGKNEVLKGITTKFEKGDVVCIIGPSGSGKSTFLRALNGLETATSGDIIID 66
           I+V  L K FG+  +L+GI  +    +VVC+IGPSGSGKSTFLR LNGLE  + GDI I+
Sbjct: 2   IKVNQLQKRFGQAHILRGIDCEIRAREVVCVIGPSGSGKSTFLRCLNGLEEVSDGDIFIE 61

Query: 67  GFNLTDKNTNLNLVRQNVGMVFQHFNLFPNMTVMQNITYAPVELKKMSKDDADKKAIQLL 126
           G  L D   NLN +R  +GMVFQ FNLFP+MTV++N+  AP+++KK+S+ +A   A +LL
Sbjct: 62  GVKLNDPKVNLNALRAELGMVFQRFNLFPHMTVLENLIMAPMQVKKLSRREAVLVAEKLL 121

Query: 127 ETVGLLDKKDAMPEMLSGGQKQRVAIARALAMNPDVMLFDEPTSALDPEMVGDVLAVMQK 186
           + VGLLDK DA P  LSGGQ+QRVAIARALAM P VMLFDEPTSALDPE+VG+VL VM++
Sbjct: 122 QKVGLLDKIDAFPNQLSGGQQQRVAIARALAMEPKVMLFDEPTSALDPELVGEVLTVMKQ 181

Query: 187 LAEEGMTMLIVTHEMGFARKVANRVIFTDGGVILEDGTPEELFDSPKHPRLQDFLSKVL 245
           LAEEGMTM++VTHEMGFAR+V++RV+F D GVI+E+G P+++   P H R +DFL KVL
Sbjct: 182 LAEEGMTMVVVTHEMGFAREVSDRVLFIDQGVIMEEGPPQQVLGDPHHERTRDFLRKVL 240


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: 196
Number of extensions: 5
Number of successful extensions: 1
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: 240
Length adjustment: 23
Effective length of query: 224
Effective length of database: 217
Effective search space:    48608
Effective search space used:    48608
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