GapMind for catabolism of small carbon sources

 

Aligments for a candidate for AO353_03050 in Pseudomonas stutzeri RCH2

Align ABC transporter for L-Arginine and L-Citrulline, permease component 1 (characterized)
to candidate GFF18 Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC

Query= reanno::pseudo1_N1B4:Pf1N1B4_3432
         (229 letters)



>lcl|FitnessBrowser__psRCH2:GFF18 Psest_0018 ectoine/hydroxyectoine
           ABC transporter, permease protein EhuC
          Length = 219

 Score =  114 bits (284), Expect = 2e-30
 Identities = 70/216 (32%), Positives = 110/216 (50%), Gaps = 10/216 (4%)

Query: 8   VILDGVWLTLQLALSSMVLAIVLGLIGVALRLSPIRWLAWLGDLYSTVIRGIPDLVLILL 67
           ++L G W+T+++     +LAI   LI    RLSP+  L WL   Y  V RG   LV +  
Sbjct: 7   LLLQGAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSLLVQLFW 66

Query: 68  IFYGGQDLLNRVAPMFGYDDYIDLNPLAAGIGTLGFIFGAYLSETFRGAFMAIPKGQAEA 127
           +++        V PM  ++  I+++  A  +  LG   GAY +E  RGA  ++ +GQ EA
Sbjct: 67  LYF--------VLPMPPFN--IEMSAFAVAVVGLGLNIGAYGAEVLRGAIRSVHRGQHEA 116

Query: 128 GMAYGMSSFQVFFRVLVPQMIRLAIPGFTNNWLVLTKATALISVVGLQDMMFKAKQAADA 187
             A  M+      R+++PQ +  AIP  TN  + L K T+L+S++ L D+ F+A+Q   A
Sbjct: 117 CQALNMTPLTRMRRIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDLAFRARQLDQA 176

Query: 188 TREPFTFFLAVAAMYLVITSVSLLALRHLEKRYSVG 223
           T      F     +Y V+       +R LE+R + G
Sbjct: 177 TLMTMEIFGLALVIYFVLAQTINFGMRQLERRLARG 212


Lambda     K      H
   0.329    0.144    0.428 

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: 158
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: 229
Length of database: 219
Length adjustment: 22
Effective length of query: 207
Effective length of database: 197
Effective search space:    40779
Effective search space used:    40779
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 (21.8 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 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