GapMind for catabolism of small carbon sources

 

Aligments for a candidate for bmpA in Phaeobacter inhibens BS107

Align Basic membrane lipoprotein, component of General nucleoside uptake porter, NupABC/BmpA (transports all common nucleosides as well as 5-fluorocytidine, inosine, deoxyuridine and xanthosine) (Martinussen et al., 2010) (Most similar to 3.A.1.2.12). NupA is 506aas with two ABC (C) domains. NupB has 8 predicted TMSs, NupC has 9 or 10 predicted TMSs in a 4 + 1 (or 2) + 4 arrangement (characterized)
to candidate GFF386 PGA1_c03970 putative lipoprotein

Query= TCDB::D2BKA1
         (350 letters)



>lcl|FitnessBrowser__Phaeo:GFF386 PGA1_c03970 putative lipoprotein
          Length = 331

 Score =  152 bits (384), Expect = 1e-41
 Identities = 116/357 (32%), Positives = 164/357 (45%), Gaps = 53/357 (14%)

Query: 1   MKKRVIAVSALALASVAVLAGCRSHDAAGSGKAKTDLKAAIVTDTGGVNDRSFNQSAWEG 60
           MK  + A +A+AL + A +A                 + A++ D GG  D+SFN++A+ G
Sbjct: 4   MKSLMSAAAAVALTAGAAMA-----------------EPALIFDLGGKFDKSFNEAAFAG 46

Query: 61  LQSWGKENNLKKGTGYTYFQSNSASDYTTNYNSAEQQGYKLLFGIGFSLQDATSAAAKNN 120
            Q W +E     G  +   +  S +          + G   +   GF+  DA    A + 
Sbjct: 47  AQRWAEET----GESFREIELQSEAQREQALRRFAEAGANPIVMAGFAFADALGQVAADY 102

Query: 121 PKSNFVIVDSVIKDQKNVASATFADNESAYLAGVAAAKATKTNKIGFIGGMQSDVITRFE 180
           P + FVI+D V+ D  NV S  F ++E +YL G+ AAKA+K+  +GFIGGM   +I +F 
Sbjct: 103 PDTKFVIIDMVV-DAPNVRSVVFNEHEGSYLVGMLAAKASKSGTVGFIGGMDIPLIRKFA 161

Query: 181 KGYEAGAKSVNPDIKVDVQYAG----SFSDAAKGKTIAAAMYGAGDDVVYQCAGGVGTGV 236
            GY  G K+ NPD  V     G    +++D  KG  +  A    G DVVY  AGG G GV
Sbjct: 162 CGYAEGVKAANPDATVIANMTGTTPAAWNDPVKGSELTKAQISQGADVVYAAAGGTGVGV 221

Query: 237 FSEAKALNSTKNEADK-VWVIGVDQDQEYLGKYKSKDGKDSNFVLVSTIKEVGNVVKDIA 295
              A         AD+ +  IGVD +Q +L   K         VL S +K V N V    
Sbjct: 222 LQTA---------ADEGILSIGVDSNQNHLHPGK---------VLTSMMKRVDNAV---F 260

Query: 296 DKTKDGKFPGGTIVTYDLKNGGVNLGLDSANS-----EIKDAVAKAKADIIDGKITV 347
           +   DG           L NGGV   +D  N+     E+  A  +A A I  G+ITV
Sbjct: 261 EAFSDGTELETGFSVMGLSNGGVGFAVDDNNASLITEEMTAATDEAAAKIATGEITV 317


Lambda     K      H
   0.310    0.128    0.353 

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: 290
Number of extensions: 19
Number of successful extensions: 4
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: 350
Length of database: 331
Length adjustment: 28
Effective length of query: 322
Effective length of database: 303
Effective search space:    97566
Effective search space used:    97566
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 (21.8 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 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, 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