GapMind for catabolism of small carbon sources

 

Alignments for a candidate for bmpA in Lactobacillus delbrueckii ZN7a-9

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 WP_002878343.1 B506_RS03315 BMP family ABC transporter substrate-binding protein

Query= TCDB::D2BKA1
         (350 letters)



>NCBI__GCF_000387565.1:WP_002878343.1
          Length = 365

 Score =  317 bits (812), Expect = 3e-91
 Identities = 158/351 (45%), Positives = 229/351 (65%), Gaps = 6/351 (1%)

Query: 3   KRVIAVSALALASVAVLAGCRSHDAAGSGKAKTDLKA-AIVTDTGGVNDRSFNQSAWEGL 61
           K++  ++  A++   +L  C+   ++ S   KT   + A++TD   ++D SFN++AW G 
Sbjct: 7   KKLATIATAAVSVSVLLTACQGKKSSSSTGTKTTKHSIALITDNNAIDDHSFNEAAWNGF 66

Query: 62  QSWGKENNLKKGTG-YTYFQSNSASDYTTNYNSAEQQGYKLLFGIGFSLQDATSAAAKNN 120
           +++GK++ LK+G G Y YF+S+SA+D+T N N A   G++ +FG+G+ L  A  +AAK N
Sbjct: 67  KAFGKKHGLKQGKGGYQYFESSSAADFTPNANEAASSGFETIFGVGYQLTSAIKSAAKKN 126

Query: 121 PKSNFVIVDSVIKDQKNVASATFADNESAYLAGVAAAKATKTNKIGFIGGMQSDVITRFE 180
           PK NFVI+D VI  QKNVAS TF  N+++YLAG+AAA  TKTN +G+IGG +S  +  FE
Sbjct: 127 PKKNFVIIDDVISGQKNVASVTFESNQASYLAGIAAAYTTKTNHVGYIGGAKSATLELFE 186

Query: 181 KGY----EAGAKSVNPDIKVDVQYAGSFSDAAKGKTIAAAMYGAGDDVVYQCAGGVGTGV 236
            G+    EAGAK++   IK+D QY G+F+   K K+IA +MY +G D++Y  AG  G GV
Sbjct: 187 AGFKQGVEAGAKALGKKIKIDDQYIGNFTSTDKAKSIAQSMYASGADIIYHAAGNAGNGV 246

Query: 237 FSEAKALNSTKNEADKVWVIGVDQDQEYLGKYKSKDGKDSNFVLVSTIKEVGNVVKDIAD 296
           F+EAK +N  +  + KVWVIGVD DQ  LG Y SKDGK SNFVL S +K +   V+ IA+
Sbjct: 247 FTEAKDINKNRKASKKVWVIGVDVDQSSLGSYTSKDGKKSNFVLTSVLKGLDVAVERIAE 306

Query: 297 KTKDGKFPGGTIVTYDLKNGGVNLGLDSANSEIKDAVAKAKADIIDGKITV 347
           K   GKFPGG    Y L+  GV++   + +S+    V  A+  I++GK+ V
Sbjct: 307 KAYQGKFPGGKHFVYTLEGNGVSVTKGNIDSKTWSKVQAARKQILNGKVKV 357


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: 417
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 350
Length of database: 365
Length adjustment: 29
Effective length of query: 321
Effective length of database: 336
Effective search space:   107856
Effective search space used:   107856
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 24 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