GapMind for catabolism of small carbon sources

 

Aligments for a candidate for gltK in Pseudomonas fluorescens GW456-L13

Align Amino acid ABC transporter membrane protein, component of Amino acid transporter, AatJMQP. Probably transports L-glutamic acid, D-glutamine acid, L-glutamine and N-acetyl L-glutamic acid (Johnson et al. 2008). Very similar to 3.A.1.3.19 of P. putida (characterized)
to candidate PfGW456L13_1700 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)

Query= TCDB::Q9I404
         (222 letters)



>lcl|FitnessBrowser__pseudo13_GW456_L13:PfGW456L13_1700 Glutamate
           Aspartate transport system permease protein GltK (TC
           3.A.1.3.4)
          Length = 365

 Score =  136 bits (342), Expect = 6e-37
 Identities = 77/218 (35%), Positives = 122/218 (55%), Gaps = 7/218 (3%)

Query: 6   GIVPALPSLWEGMLMTLKLMVLGVLGGVALGTVLALMRLSHSKLLSNIAGFYVNYFRSIP 65
           G+     S W G+++TL +  +G+ G + LG VLAL R S+   +  +   ++ ++R +P
Sbjct: 146 GLDAVATSQWGGLMLTLVIATVGIAGALPLGIVLALGRRSNMPAIRVVCVTFIEFWRGVP 205

Query: 66  LLLVITWFYFAVPFILRWITGEDTPVGAFTSCLVAFMMFEAAYYCEIVRAGIQAIPKGQM 125
           L+ V+      +P  L     E          L+  ++F++AY  E+VR G+QAIPKGQ 
Sbjct: 206 LITVLFMSSVMLPLFLP----EGMNFDKLLRALIGVILFQSAYVAEVVRGGLQAIPKGQY 261

Query: 126 GAAQALGMTYGQTMRLVILPQAFRKMTPLLLQQSIILFQDTSLVYTVGLMDFLNSARSRG 185
            AA A+G+ Y ++M LVILPQA + + P ++   I LF+DTSLV  +GL D LNS +   
Sbjct: 262 EAAAAMGLGYWRSMGLVILPQALKLVIPGIVNTFIALFKDTSLVIIIGLFDLLNSVKQAA 321

Query: 186 ---DIIGQANEFLIFAGLVYFVVSFTASFAVKRLQKRL 220
                +G A E  +FA LV+++  F  S     L+++L
Sbjct: 322 ADPKWLGMATEGYVFAALVFWIFCFGMSRYSMHLERKL 359


Lambda     K      H
   0.331    0.143    0.426 

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: 224
Number of extensions: 11
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 222
Length of database: 365
Length adjustment: 26
Effective length of query: 196
Effective length of database: 339
Effective search space:    66444
Effective search space used:    66444
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.9 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 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