GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglF in Halopiger salifodinae KCY07-B2

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_049992209.1 LT39_RS19805 sugar ABC transporter permease

Query= uniprot:A8LLL5
         (334 letters)



>NCBI__GCF_000784335.1:WP_049992209.1
          Length = 317

 Score =  116 bits (291), Expect = 7e-31
 Identities = 72/234 (30%), Positives = 124/234 (52%), Gaps = 12/234 (5%)

Query: 94  LDNYAQMASEPKFWEAMRNNMFWLIVVPALSTAFGLLAAQLTDR-IKWGNVAKSIIFMPM 152
           L+ Y +  +   F EA  NN   LI    +S A GL  A L D  I++ +  ++I  +PM
Sbjct: 78  LEMYREALASEAFREAAFNNFVLLIAFTTISLALGLFLAILLDHGIRYKDKIQTIYLLPM 137

Query: 153 AISFVGASVIWKLVYDGRPIEQEQIGILNAIIVGLGGDPVTFLTIPFWNNFFLMIVLVWV 212
           A+SFV  + +W  +++       + G+L  I+  LG +P+ +L  P      ++  LVW 
Sbjct: 138 ALSFVVTAQLWLWMFN------PESGVLTVIVTTLGFEPIDWLGNPRLALPAVIFALVWQ 191

Query: 213 QTGFAMVILSAALRGIPEETIEAAIIDGASPLQIFFKIKVPQIMPTVVVVWTTITLVVLK 272
            +G+AMV+  A L+ IP +  EAA +DGAS ++ + +I VPQ+  + V     + +  LK
Sbjct: 192 FSGYAMVVYLAGLQSIPADQFEAANVDGASTIRTYLRIIVPQLKESSVSAAVVLMVFALK 251

Query: 273 VFDIVFAMTNGQWE----TQVLANYMFDKLFRANDWGVGSASAMVIMLLVTPIL 322
            F  ++++  GQ+     T +LA  M  + F+   W  G+A A +++LL   ++
Sbjct: 252 AFTFLYSLV-GQYRPPNGTDILATLMVRQAFKFGKWAYGAAIATMLLLLALSVI 304


Lambda     K      H
   0.329    0.143    0.455 

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: 241
Number of extensions: 14
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: 334
Length of database: 317
Length adjustment: 28
Effective length of query: 306
Effective length of database: 289
Effective search space:    88434
Effective search space used:    88434
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 (21.8 bits)
S2: 48 (23.1 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