GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglE' in Phaeobacter inhibens BS107

Align Putative bacterial solute-binding protein 1 family (characterized, see rationale)
to candidate GFF772 PGA1_c07860 alpha-glucosides-binding periplasmic protein AglE

Query= uniprot:A8LLL6
         (452 letters)



>FitnessBrowser__Phaeo:GFF772
          Length = 450

 Score =  634 bits (1636), Expect = 0.0
 Identities = 299/452 (66%), Positives = 361/452 (79%), Gaps = 2/452 (0%)

Query: 1   MRHTLHASAAALALSAGMAGAGGHLAFTPGEGEFNWDSYQAFAEATDLSGQDLSIFGPWL 60
           M+ +L A+A  LALSAG+A A G L F  GEGEFNW+S++A  +ATDLSG+ +++FGPWL
Sbjct: 1   MKRSLLAAAGVLALSAGLAQAEGALTFPVGEGEFNWESFEAL-KATDLSGEQVTVFGPWL 59

Query: 61  AGEADAFSNLVAFFNEATGANATYVGSDSLEQQIVIDAEAGSAPDLTVFPQPGLATTMAA 120
             + +    ++A+F EATGA+  Y GSDS EQQIV+DAEAGSAP++ VFPQPGL + MAA
Sbjct: 60  GPDQELVEKVLAYFAEATGADVRYTGSDSFEQQIVVDAEAGSAPNVAVFPQPGLVSDMAA 119

Query: 121 RGFLTPLPDGTDDWLRENYAAGQSWIDLGTYADGSGNDQLYGFFFNVNVKSLVWYIPENF 180
           RGF+ PL   T DW+RENYAAG SW+DL T+    GN+ ++G F+ V+VKSLVWY+PE F
Sbjct: 120 RGFIAPLGSETADWVRENYAAGDSWVDLSTFTGPDGNEDVFGLFYKVDVKSLVWYVPETF 179

Query: 181 EDFDYEVPETMEEFKALMDQMVEDGQTPLCVGLGSGGATGWPATDWVEDLMLRTQPPEVY 240
           EDF Y++P++MEE KAL DQMV DG TP C+GLGSGGATGWPATDWVED+MLRTQ P VY
Sbjct: 180 EDFGYDIPQSMEELKALTDQMVADGNTPWCIGLGSGGATGWPATDWVEDMMLRTQDPGVY 239

Query: 241 DAWVSNEMPFDDPRVVAAIEEYGSFTRNDDYVVGNANDTASVDFRESPLGLFASPPACMM 300
           D WVSNE+PF DPRVV AIEE+G F RNDDYV G A   AS DFR+SP GLFASPP C+M
Sbjct: 240 DQWVSNEIPFTDPRVVNAIEEFGYFARNDDYVSGGAGAVASTDFRDSPKGLFASPPQCLM 299

Query: 301 HRQASFIPAYFPEGTELGEDADFFYFPAFEEKDLGRPVLGAGTLFAITNENPAASAFIEF 360
           HRQASFIPA+FPEGTE+G DADFFYFPA+ EKDLG PVLGAGTL++ITN++  A A +EF
Sbjct: 300 HRQASFIPAFFPEGTEVGLDADFFYFPAYAEKDLGSPVLGAGTLWSITNDSKGARALMEF 359

Query: 361 LKTPFAHEIMMAQDGFLTPFKGANPAAYASDTLRGQGEILTNATTFRFDGSDLMPGGVGA 420
           LK+P  HE+ MAQ GFLTP KG N   YA+DTL+  GEIL +A TFRFD SDLMPGGVGA
Sbjct: 360 LKSPIGHEVWMAQQGFLTPHKGVNTDVYATDTLKKMGEILLSADTFRFDASDLMPGGVGA 419

Query: 421 GTFWTGMVDYSSGAKSAADVASEIQASWESLK 452
           G+FWTGMV Y+ G   A +VA+EIQ+SW++LK
Sbjct: 420 GSFWTGMVGYAGGT-PAEEVAAEIQSSWDALK 450


Lambda     K      H
   0.317    0.134    0.413 

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: 854
Number of extensions: 42
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: 452
Length of database: 450
Length adjustment: 33
Effective length of query: 419
Effective length of database: 417
Effective search space:   174723
Effective search space used:   174723
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 51 (24.3 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 (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