GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglF in Jannaschia aquimarina GSW-M26

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate WP_043916933.1 jaqu_RS00200 sugar ABC transporter permease

Query= uniprot:A8LLL5
         (334 letters)



>NCBI__GCF_000877395.1:WP_043916933.1
          Length = 329

 Score =  413 bits (1062), Expect = e-120
 Identities = 206/333 (61%), Positives = 258/333 (77%), Gaps = 10/333 (3%)

Query: 3   PAFQGLITIIIGVGGCVGYFYFANQFLDKVLYPAKGPKAGRNINRANQIRPWIFLFPALF 62
           P  QG++TI++GVGGC+GYF+ +N  LDKV++PAKG  AG+NINRAN +RPW+F+FPA  
Sbjct: 6   PILQGVLTIVLGVGGCIGYFWASNIVLDKVIFPAKGANAGKNINRANMVRPWLFIFPAFA 65

Query: 63  VLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAMRNNMFWLIVVPA 122
            L LYL YPVV +   SL +R    G  ++G  NYA +  + +F +A+ NN+ W +VVPA
Sbjct: 66  ALGLYLAYPVVGSFIRSLYDR---SGDTFIGFGNYAWLMQDSEFQQAVFNNILWALVVPA 122

Query: 123 LSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGRPIEQEQIGILNA 182
            ST FGL+AAQLTDR+ WGN+AKS+IFMPMAISFVGAS+IWK VY         IGI+NA
Sbjct: 123 GSTFFGLVAAQLTDRLSWGNIAKSLIFMPMAISFVGASLIWKFVY----ANDADIGIVNA 178

Query: 183 IIVGL-GGDPVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAIIDGA 241
               + G D V  L + FWNNFFLM +L+W+QTGFAMVILSAALRGIPEET+EAAI+DGA
Sbjct: 179 FREWVFGADSVDPLQVSFWNNFFLMFILIWIQTGFAMVILSAALRGIPEETVEAAIVDGA 238

Query: 242 SPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWETQVLANYMFDKLFRA 301
           SPLQ+FFKIKVPQIM T+VVVWTTIT++VLKVFDIV+ MT G + TQ+L +YMF+ +FR 
Sbjct: 239 SPLQVFFKIKVPQIMGTIVVVWTTITILVLKVFDIVYTMTGGNFGTQILPSYMFEFMFR- 297

Query: 302 NDWGVGSASAMVIMLLVTPILIWNIHSARKEMR 334
            D G  +A A VIML+VTP+++WNI  ARKEMR
Sbjct: 298 -DDGRATAVAFVIMLIVTPVMVWNIIQARKEMR 329


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: 390
Number of extensions: 17
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: 329
Length adjustment: 28
Effective length of query: 306
Effective length of database: 301
Effective search space:    92106
Effective search space used:    92106
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: 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