GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS00900 in Dyella japonica UNC79MFTsu3.2

Align ABC transporter ATP-binding protein (characterized, see rationale)
to candidate N515DRAFT_3950 N515DRAFT_3950 lipopolysaccharide export system ATP-binding protein

Query= uniprot:A0A165KC78
         (242 letters)



>lcl|FitnessBrowser__Dyella79:N515DRAFT_3950 N515DRAFT_3950
           lipopolysaccharide export system ATP-binding protein
          Length = 239

 Score =  133 bits (335), Expect = 3e-36
 Identities = 77/238 (32%), Positives = 124/238 (52%), Gaps = 9/238 (3%)

Query: 9   LLQVKGLKVAYGGIQAVKGVDFEVREGELVSLIGSNGAGKTTTMKAITGTLSMNDGNIEY 68
           +L  +GL+  +   Q V+   F +REGE+V L+G NGAGKTT    + G +  + G I+ 
Sbjct: 1   MLSAEGLQKRFRTRQVVRDFAFSIREGEVVGLLGPNGAGKTTCFYMVVGLIEADAGTIKL 60

Query: 69  LGKSIKGKGAWDLVKEGLVMVPEGRGVFARMTITENLQMGAYIR-----KDKAGILADIE 123
               I G       K G+  +P+   VF R+T+ +N+     +R     K +AG L  + 
Sbjct: 61  DKYDITGLPMHARAKLGIGYLPQEPSVFRRLTVADNIMAVLELRENLSAKQRAGELESLL 120

Query: 124 KMFTIFPRLRERKDQLAGTMSGGEQQMLAMGRALMSQPKVLLLDEPSMGLSPIMVDKIFE 183
                  ++    DQ   ++SGGE++ + + RAL ++P+ +LLDEP  G+ PI V +I  
Sbjct: 121 DEL----KIAHIADQRGISLSGGERRRVEIARALAAEPRYMLLDEPFAGVDPISVGEIQR 176

Query: 184 VVRDVYALGVTIVLVEQNASRALAIADRGYVMESGLITMTGPGQQLLNDPKVRAAYLG 241
           +VR +   G+ +++ + N    L I DR Y++  G +   G    +L D KVR  YLG
Sbjct: 177 IVRHLKERGIGVLITDHNVRETLGICDRAYILNDGEVLSRGTPAHILADEKVREVYLG 234


Lambda     K      H
   0.317    0.136    0.373 

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: 161
Number of extensions: 9
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: 242
Length of database: 239
Length adjustment: 23
Effective length of query: 219
Effective length of database: 216
Effective search space:    47304
Effective search space used:    47304
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.7 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