GapMind for catabolism of small carbon sources

 

Aligments for a candidate for aglF in Phaeobacter inhibens BS107

Align Inner membrane ABC transporter permease protein (characterized, see rationale)
to candidate GFF773 PGA1_c07870 alpha-glucoside transport system permease protein AglF

Query= uniprot:A8LLL5
         (334 letters)



>lcl|FitnessBrowser__Phaeo:GFF773 PGA1_c07870 alpha-glucoside
           transport system permease protein AglF
          Length = 335

 Score =  543 bits (1398), Expect = e-159
 Identities = 259/335 (77%), Positives = 296/335 (88%), Gaps = 1/335 (0%)

Query: 1   MHPAFQGLITIIIGVGGCVGYFYFANQFLDKVLYPAKGPKAGRNINRANQIRPWIFLFPA 60
           MHPA QGL TI  GVGGCVGYFYF+N  LD+V++PA+G    RNI RAN IRPW+FLFPA
Sbjct: 1   MHPAIQGLFTIAFGVGGCVGYFYFSNLVLDRVIFPARGAHIARNIRRANMIRPWLFLFPA 60

Query: 61  LFVLLLYLGYPVVETLRLSLLERVPGGGYQWVGLDNYAQMASEPKFWEAMRNNMFWLIVV 120
           L  L LYL YPVVETLRLS+ ERVPGGG ++VGL NY QM +E KFWEA++NN  WL+VV
Sbjct: 61  LLALGLYLAYPVVETLRLSVTERVPGGGSEFVGLANYQQMLAEAKFWEALQNNFLWLLVV 120

Query: 121 PALSTAFGLLAAQLTDRIKWGNVAKSIIFMPMAISFVGASVIWKLVYDGRPIEQEQIGIL 180
           PA STAFGLLAAQLTDR+ WGN+AKS+IFMPMAISFVGA+VIWKLVYD RP   +QIG+L
Sbjct: 121 PAASTAFGLLAAQLTDRLAWGNIAKSLIFMPMAISFVGAAVIWKLVYDARPEGTDQIGVL 180

Query: 181 NAIIVGLGGD-PVTFLTIPFWNNFFLMIVLVWVQTGFAMVILSAALRGIPEETIEAAIID 239
           NA+ +  GGD P+ +LTIPFWN+FFLM+VL+W+QTGFAMVILSAALRGIPEET+EAAI+D
Sbjct: 181 NALYIYFGGDGPMQWLTIPFWNSFFLMMVLIWIQTGFAMVILSAALRGIPEETVEAAIVD 240

Query: 240 GASPLQIFFKIKVPQIMPTVVVVWTTITLVVLKVFDIVFAMTNGQWETQVLANYMFDKLF 299
           GA P QIFFKIKVPQIM T+VVVWTTIT+VVLKVFDIVFAMTNGQWETQVLANYM+DKLF
Sbjct: 241 GAGPFQIFFKIKVPQIMDTIVVVWTTITIVVLKVFDIVFAMTNGQWETQVLANYMYDKLF 300

Query: 300 RANDWGVGSASAMVIMLLVTPILIWNIHSARKEMR 334
           RANDWGVGSASAMVIMLLV PIL+WN+++AR+EMR
Sbjct: 301 RANDWGVGSASAMVIMLLVLPILVWNVYNARREMR 335


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: 458
Number of extensions: 12
Number of successful extensions: 2
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: 335
Length adjustment: 28
Effective length of query: 306
Effective length of database: 307
Effective search space:    93942
Effective search space used:    93942
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 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