GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aatM in Pseudomonas stutzeri RCH2

Align ABC transporter for L-Asparagine and possibly other L-amino acids, permease component 2 (characterized)
to candidate GFF18 Psest_0018 ectoine/hydroxyectoine ABC transporter, permease protein EhuC

Query= reanno::pseudo13_GW456_L13:PfGW456L13_4772
         (223 letters)



>FitnessBrowser__psRCH2:GFF18
          Length = 219

 Score = 88.2 bits (217), Expect = 1e-22
 Identities = 66/215 (30%), Positives = 104/215 (48%), Gaps = 5/215 (2%)

Query: 8   IIPSLPGLWNGMIMTLKLMAMGVIGGIILGTILALMRLSHNKVLSNIAGAYVNYFRSIPL 67
           +I  LP L  G  +T+K+   G +  I    I AL RLS    L  +A  Y+  FR   L
Sbjct: 1   MIELLPLLLQGAWVTVKVTFFGSLLAIACALIAALARLSPVAPLRWLAITYIEVFRGSSL 60

Query: 68  LLVITWFYLAVPFVLRWITGEDTPIGAFASCIVAFMMFEAAYFCEIVRAGVQSIPKGQMG 127
           L+ + W Y  +P     +   +  + AFA  +V   +   AY  E++R  ++S+ +GQ  
Sbjct: 61  LVQLFWLYFVLP-----MPPFNIEMSAFAVAVVGLGLNIGAYGAEVLRGAIRSVHRGQHE 115

Query: 128 AAQALGMSYGQMMRLIILPQAFRKMTPLLLQQSIILFQDTSLVYAVGLVDFLNASRASGD 187
           A QAL M+    MR IILPQA     P      I L ++TSLV  + L D    +R    
Sbjct: 116 ACQALNMTPLTRMRRIILPQALLAAIPPGTNLLIELLKNTSLVSLITLSDLAFRARQLDQ 175

Query: 188 IIGRSNEFLIFAGLVYFIISFAASQLVKRLQKRFA 222
               + E    A ++YF+++   +  +++L++R A
Sbjct: 176 ATLMTMEIFGLALVIYFVLAQTINFGMRQLERRLA 210


Lambda     K      H
   0.332    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: 110
Number of extensions: 6
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: 223
Length of database: 219
Length adjustment: 22
Effective length of query: 201
Effective length of database: 197
Effective search space:    39597
Effective search space used:    39597
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: 45 (21.9 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