GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltL in Pseudomonas fluorescens FW300-N1B4

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 Pf1N1B4_3435 Arginine/ornithine ABC transporter, ATP-binding protein AotP

Query= TCDB::Q9CES4
         (247 letters)



>lcl|FitnessBrowser__pseudo1_N1B4:Pf1N1B4_3435 Arginine/ornithine
           ABC transporter, ATP-binding protein AotP
          Length = 254

 Score =  254 bits (650), Expect = 9e-73
 Identities = 135/248 (54%), Positives = 173/248 (69%), Gaps = 11/248 (4%)

Query: 6   QIEVTDLHKSFGKNEVLKGITTKFEKGDVVCIIGPSGSGKSTFLRALNGLETATSGDIII 65
           ++EV DLHK +G +EVLKG++ K   GDV+ IIG SGSGKSTFLR +N LE   +G I++
Sbjct: 3   KLEVQDLHKRYGSHEVLKGVSLKAAAGDVISIIGSSGSGKSTFLRCINLLEQPHAGKILL 62

Query: 66  -----------DGFNLTDKNTNLNLVRQNVGMVFQHFNLFPNMTVMQNITYAPVELKKMS 114
                      DG         L  +R  + MVFQHFNL+ +MT M+NI  APV +  MS
Sbjct: 63  NNEELKLVANKDGALKAADPKQLQRMRSRLSMVFQHFNLWSHMTAMENIMEAPVHVLGMS 122

Query: 115 KDDADKKAIQLLETVGLLDKKDAMPEMLSGGQKQRVAIARALAMNPDVMLFDEPTSALDP 174
           K +A +KA   L  VG+  +KDA P  +SGG++QRVAIARALAM P+VMLFDEPTSALDP
Sbjct: 123 KTEAREKAEHYLNKVGVAHRKDAYPGHMSGGEQQRVAIARALAMEPEVMLFDEPTSALDP 182

Query: 175 EMVGDVLAVMQKLAEEGMTMLIVTHEMGFARKVANRVIFTDGGVILEDGTPEELFDSPKH 234
           E+VGDVL VMQ LA+EG TM++VTHEMGFAR+V+N+++F   GV+ E G P E+  +P+ 
Sbjct: 183 ELVGDVLKVMQALAQEGRTMVVVTHEMGFAREVSNQLVFLHKGVVEESGNPREVLVNPQS 242

Query: 235 PRLQDFLS 242
            RLQ FLS
Sbjct: 243 ERLQQFLS 250


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: 192
Number of extensions: 4
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: 254
Length adjustment: 24
Effective length of query: 223
Effective length of database: 230
Effective search space:    51290
Effective search space used:    51290
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 (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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 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