GapMind for catabolism of small carbon sources

 

Alignments for a candidate for gltK in Pseudomonas fluorescens FW300-N2E2

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 Pf6N2E2_5404 Glutamate Aspartate transport system permease protein GltK (TC 3.A.1.3.4)

Query= TCDB::Q9I404
         (222 letters)



>FitnessBrowser__pseudo6_N2E2:Pf6N2E2_5404
          Length = 365

 Score =  137 bits (344), Expect = 4e-37
 Identities = 77/218 (35%), Positives = 123/218 (56%), Gaps = 7/218 (3%)

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

Query: 66  LLLVITWFYFAVPFILRWITGEDTPVGAFTSCLVAFMMFEAAYYCEIVRAGIQAIPKGQM 125
           L+ V+      +P  L     E          L+  ++F++AY  E+VR G+QAIPKGQ 
Sbjct: 206 LITVLFMSSVMLPLFLP----EGMNFDKLLRALIGVILFQSAYIAEVVRGGLQAIPKGQY 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: 215
Number of extensions: 10
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: 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:

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