GapMind for catabolism of small carbon sources

 

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

Align ABC transporter for D-Maltose and D-Trehalose, permease component 1 (characterized)
to candidate WP_049991587.1 LT39_RS16410 sugar ABC transporter permease

Query= reanno::Smeli:SMc03062
         (336 letters)



>NCBI__GCF_000784335.1:WP_049991587.1
          Length = 319

 Score =  111 bits (278), Expect = 2e-29
 Identities = 84/287 (29%), Positives = 141/287 (49%), Gaps = 25/287 (8%)

Query: 45  RNLRIANSIRPWLFLAPALLALTLYLVYPVVQSVWLSLHGRGG------QNFVGLSNYSW 98
           R      SI  WL   P  L + L++   +  +V +SL G  G       NF  L  Y  
Sbjct: 36  RRSDFVESIPFWL---PPTLLVLLFVYGAIGWNVVISLTGWSGLGQPEYTNF-SLEMYRQ 91

Query: 99  MINDGEFRQSIFNNFLWLLVVPALSTFFGLIIAALTDR-IWWGNIAKTLIFMPMAISFVG 157
           +  D  FR ++ N    L+    +S   GL +A L DR I + N  +T+  +PMA+SFV 
Sbjct: 92  LPADQNFRAALRNTVALLVGFTGVSLLVGLGLALLVDRKIRFENTFRTIYLLPMALSFVV 151

Query: 158 AAVIWKFIYDYRAAGSEQIGLLNAIVVALGGEPQAWITLPFWNNFFLMVILIWIQTGFAM 217
            A+ W ++Y          GL+NA++         W+  P      ++  L+W  +G+ M
Sbjct: 152 TAIFWSWMYASN-------GLINAVLPI----SPDWLGNPRLKLAAVIFALVWQFSGYCM 200

Query: 218 VILSAALRGIPEETIEAAVIDGANGWQIFFKIMVPQIWGTIAVVWTTITILVLKVFDIVL 277
           ++  A LR IP++  EAA IDGA+  ++++++++PQ+  +       + +  LK FD + 
Sbjct: 201 IVYLAGLRSIPDDHYEAARIDGASTLKLYWRVIIPQLRSSTVGATVVLMVFALKAFDFIY 260

Query: 278 AM--TNGQWQSQVLANLMFDWMFRGGGDFGRGAAIAVVIMILVVPIM 322
            M  TN      +LA +M+   F    ++  GAA+AVV+ +L + I+
Sbjct: 261 VMFGTNPGRSVDILAVMMYREAF-SAAEWAYGAAVAVVLFLLALTII 306


Lambda     K      H
   0.330    0.142    0.466 

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: 308
Number of extensions: 11
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: 336
Length of database: 319
Length adjustment: 28
Effective length of query: 308
Effective length of database: 291
Effective search space:    89628
Effective search space used:    89628
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