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 GFF3102 Psest_3161 amine acid ABC transporter, permease protein, 3-TM region, His/Glu/Gln/Arg/opine family

Query= TCDB::Q8YPM8
         (308 letters)



>lcl|FitnessBrowser__psRCH2:GFF3102 Psest_3161 amine acid ABC
           transporter, permease protein, 3-TM region,
           His/Glu/Gln/Arg/opine family
          Length = 365

 Score = 94.4 bits (233), Expect = 4e-24
 Identities = 62/186 (33%), Positives = 98/186 (52%), Gaps = 22/186 (11%)

Query: 74  TYSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLL 133
           T   + W GL+ ++ IA VGI     +GIL  + R SD   +R + + ++E +R  PL+ 
Sbjct: 149 TVPTSQWGGLMLTVVIAAVGIAGALPLGILLALGRRSDMPAIRVLCVTFIEFWRGVPLIT 208

Query: 134 QLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIA 193
            L      + L LP   N   L                       A+L+ ++F+  A+IA
Sbjct: 209 VLFMSSVMLPLFLPEGMNLDKL---------------------LRAMLM-VVFFEAAYIA 246

Query: 194 EIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAI 253
           E+VRGG+Q++ KGQ+EA  ++GL       LVI PQAL+++IP + + ++ L K++SL I
Sbjct: 247 EVVRGGLQAIPKGQYEAAAAMGLGYWRSTLLVILPQALKLVIPGIVNTFIALFKDTSLVI 306

Query: 254 AIGYPD 259
            IG  D
Sbjct: 307 IIGLFD 312


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: 341
Number of extensions: 19
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: 308
Length of database: 365
Length adjustment: 28
Effective length of query: 280
Effective length of database: 337
Effective search space:    94360
Effective search space used:    94360
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, 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