GapMind for catabolism of small carbon sources

 

Aligments for a candidate for natG in Pseudomonas stutzeri RCH2

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate GFF3103 Psest_3162 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q8YPM8
         (308 letters)



>lcl|FitnessBrowser__psRCH2:GFF3103 Psest_3162 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          Length = 394

 Score =  157 bits (398), Expect = 3e-43
 Identities = 115/305 (37%), Positives = 159/305 (52%), Gaps = 24/305 (7%)

Query: 21  LIALFLAAFVVAIL-LGNLNRN-----LQRLGIQFGFDFLKQQASFDIGETLIAYKPTDT 74
           +I +FLA  +  IL +G L+ N     L  L I+   +       F +   +I+  P   
Sbjct: 97  VIGIFLATVMGFILGVGRLSSNWLIRQLATLYIEIFRNIPPLLLIFFVYFAVISPLPGPR 156

Query: 75  YSLALW-VGLINSLRI---------AFVGIILTTIVGILAGIARLSDNWLVRNISLVYVE 124
            SL+LW V  +N+  +          F    L  +V ++A +         R+ +     
Sbjct: 157 NSLSLWDVVFVNNRGVQMPAPSAGDGFWAFWLALLVALVAVVVLNRWARARRHATGRMFP 216

Query: 125 IFRNTPLLLQLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGL 184
           +F  +P L   + W      G P       L  F       +   W    PE  ++++ L
Sbjct: 217 VFWTSPGLFLAIPWLMTFIAGAPFTWEVPELQRF------NIRGGWVVI-PELVSIVVAL 269

Query: 185 IFYTGAFIAEIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLN 244
             YT AFI E VR GIQSVS GQ EA  SLGL P  ++RLVI PQALRVI+PPLTSQYLN
Sbjct: 270 SVYTAAFIGETVRSGIQSVSHGQTEAAASLGLRPGQVLRLVIVPQALRVIVPPLTSQYLN 329

Query: 245 LTKNSSLAIAIGYPD-IYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNRTV 303
           L KNSSLA AIGYPD +   A T  NQTG+A+E M + M  YL++S++ISL+MN +N+ +
Sbjct: 330 LAKNSSLAAAIGYPDMVSLFAGTVLNQTGQAIETMAITMSVYLAISISISLLMNWYNKRI 389

Query: 304 QIKER 308
            + ER
Sbjct: 390 ALIER 394



 Score =  127 bits (320), Expect = 3e-34
 Identities = 68/177 (38%), Positives = 99/177 (55%), Gaps = 3/177 (1%)

Query: 20  QLIALFLAAFVVAILLGNLNRNLQRLGIQFGFDFLKQQASFDIGETLIAYKPTDTYSLAL 79
           Q++A+         L  N   NL   GI  GF FL   A F I + LI Y  +DTY    
Sbjct: 26  QVLAVLAVVAFGWYLFHNTQTNLAHRGITSGFGFLNNAAGFGISQHLIDYSESDTYGRVF 85

Query: 80  WVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLLQLLFWY 139
           WVGL+N+L ++ +GI L T++G + G+ RLS NWL+R ++ +Y+EIFRN P LL + F Y
Sbjct: 86  WVGLLNTLLVSVIGIFLATVMGFILGVGRLSSNWLIRQLATLYIEIFRNIPPLLLIFFVY 145

Query: 140 FAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIAEIV 196
           FAV   LP   N +SL   + ++  G+++P  +    F A  L L+    A +A +V
Sbjct: 146 FAVISPLPGPRNSLSLWDVVFVNNRGVQMPAPSAGDGFWAFWLALLV---ALVAVVV 199


Lambda     K      H
   0.328    0.143    0.430 

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: 350
Number of extensions: 19
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: 2
Length of query: 308
Length of database: 394
Length adjustment: 29
Effective length of query: 279
Effective length of database: 365
Effective search space:   101835
Effective search space used:   101835
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.1 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.7 bits)
S2: 49 (23.5 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, 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