GapMind for catabolism of small carbon sources

 

Aligments for a candidate for mglB in Escherichia coli BW25113

Align glucose transporter, periplasmic substrate-binding component (characterized)
to candidate 17627 b3566 D-xylose transporter subunit (NCBI)

Query= reanno::Phaeo:GFF3639
         (341 letters)



>lcl|FitnessBrowser__Keio:17627 b3566 D-xylose transporter subunit
           (NCBI)
          Length = 330

 Score =  242 bits (618), Expect = 8e-69
 Identities = 132/313 (42%), Positives = 192/313 (61%), Gaps = 8/313 (2%)

Query: 19  AFAEDVTVGVSWSNFQEERWKTDEAAIKAALEAKGATYVSADAQSSSAKQLSDIESLIAQ 78
           A A++V +G++  + + ERW+ D        E+ GA      A  +   Q+S IE++I +
Sbjct: 21  AHAKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINR 80

Query: 79  GVDALIVLAQDAQAIGPAVQAAADEGIPVVAYDRLIEDGRA-FYLTFDNVEVGRMQARAV 137
           GVD L+++  + Q +   V+ A  EGI V+AYDR+I D    FY++FDN +VG +QA+A+
Sbjct: 81  GVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKAL 140

Query: 138 LEAQPSGNYVMIKGSPTDPNADFLRGGQQEIIQAAIDSGDIKIVGEAYTDGWLPANAQRN 197
           ++  P GNY ++ GSP D NA   R GQ ++++  +DSG IK+VG+ + DGWLP NA + 
Sbjct: 141 VDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKI 200

Query: 198 MEQILTANDNKVDAVVASNDGTAGGVVAALTAQGMEG-IAVSGQDGDHAALNRVAKGTQT 256
           ME  LTAN+NK+DAVVASND TAGG + AL+AQG+ G +A+SGQD D A + R+A GTQT
Sbjct: 201 MENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQT 260

Query: 257 VSVWKDARDLGKAAANIAVEMAEGAVMGDVAGGAAWTSPAG-TELTARFLEPIPVTADNL 315
           ++V+K    L   AA IAVE+  G         A  T   G  ++ +R L PI V  +N+
Sbjct: 261 MTVYKPITLLANTAAEIAVELGNGQ-----EPKADTTLNNGLKDVPSRLLTPIDVNKNNI 315

Query: 316 SVVVDAGWITKEA 328
              V      KE+
Sbjct: 316 KDTVIKDGFHKES 328


Lambda     K      H
   0.313    0.128    0.362 

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: 227
Number of extensions: 10
Number of successful extensions: 3
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: 341
Length of database: 330
Length adjustment: 28
Effective length of query: 313
Effective length of database: 302
Effective search space:    94526
Effective search space used:    94526
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.2 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 42 (21.9 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 (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 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