GapMind for catabolism of small carbon sources

 

Alignments for a candidate for natG in Pseudomonas simiae WCS417

Align NatG, component of Acidic and neutral amino acid uptake transporter NatFGH/BgtA. BgtA is shared with BgtAB (characterized)
to candidate GFF4253 PS417_21785 ABC transporter permease

Query= TCDB::Q8YPM8
         (308 letters)



>FitnessBrowser__WCS417:GFF4253
          Length = 292

 Score =  132 bits (331), Expect = 1e-35
 Identities = 76/228 (33%), Positives = 130/228 (57%), Gaps = 13/228 (5%)

Query: 74  TYSLALWVGLINSLRIAFVGIILTTIVGILAGIARLSDNWLVRNISLVYVEIFRNTPLLL 133
           T    LW GL+N++ ++ + + L  ++G++  I R+S N ++R +++ Y  +FR TPL+L
Sbjct: 68  TSEAILW-GLVNTIIMSVLAMALGVVIGVITAIMRMSANPILRYVAITYTWLFRGTPLIL 126

Query: 134 QLLFWYFAVFLGLPRADNKISLGGFIGLSQNGLELPWFTFSPEFSALLLGLIFYTGAFIA 193
           QLL W F + L  P     I++ G   +    L  P       F A LLGL    GA+ A
Sbjct: 127 QLLLW-FNLALIFP----VIAIPGLFSIDTVDLMTP-------FVAALLGLSINQGAYTA 174

Query: 194 EIVRGGIQSVSKGQWEAGRSLGLNPSLIMRLVIFPQALRVIIPPLTSQYLNLTKNSSLAI 253
           E+VR G+ SV  GQ+EA +S+G+     +R VI PQA+RVIIPP+ ++++++ K +SLA 
Sbjct: 175 EVVRAGLLSVDTGQYEAAKSIGMPSLQALRRVILPQAMRVIIPPVGNEFISMVKMTSLAS 234

Query: 254 AIGYPDIYFVASTTFNQTGKAVEVMLLLMLTYLSLSLTISLIMNAFNR 301
            I Y ++   A   +    + +E++++  + YL++   +S   +   R
Sbjct: 235 VIQYSELLHNAQNIYYANARVMELLIVAGIWYLAVVTVLSFGQSRLER 282


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: 221
Number of extensions: 14
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: 292
Length adjustment: 27
Effective length of query: 281
Effective length of database: 265
Effective search space:    74465
Effective search space used:    74465
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: 48 (23.1 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