GapMind for catabolism of small carbon sources

 

Alignments for a candidate for aglG in Sinorhizobium meliloti 1021

Align ABC transporter for D-Maltose and D-Trehalose, permease component 2 (characterized)
to candidate SMc03063 SMc03063 alpha-glucoside ABC transporter permease

Query= reanno::Smeli:SMc03063
         (380 letters)



>FitnessBrowser__Smeli:SMc03063
          Length = 380

 Score =  741 bits (1914), Expect = 0.0
 Identities = 380/380 (100%), Positives = 380/380 (100%)

Query: 1   MNPSRRSPLTWAVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSRNAVV 60
           MNPSRRSPLTWAVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSRNAVV
Sbjct: 1   MNPSRRSPLTWAVHLSVLLLVLLWTLPTAGLLISSLRDKDQLAVSGWWTALSSSSRNAVV 60

Query: 61  RAPSAEDQVERDGKFVISGNLLEGRGEVSAFGFSSREPTKFKPGETAELNDGERLTVQSD 120
           RAPSAEDQVERDGKFVISGNLLEGRGEVSAFGFSSREPTKFKPGETAELNDGERLTVQSD
Sbjct: 61  RAPSAEDQVERDGKFVISGNLLEGRGEVSAFGFSSREPTKFKPGETAELNDGERLTVQSD 120

Query: 121 GSFEIVSDQRMEGSRGQRIFFTATTPPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVI 180
           GSFEIVSDQRMEGSRGQRIFFTATTPPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVI
Sbjct: 121 GSFEIVSDQRMEGSRGQRIFFTATTPPRFTLDNYAEVLSAAGIGRSFLNSLTVAVPSTVI 180

Query: 181 PILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTY 240
           PILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTY
Sbjct: 181 PILIAAFAAYALAWMPFPGRAVLLAVVVGLLVVPLQMSLIPLLQLYNGVGAFFGVSAKTY 240

Query: 241 MGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASF 300
           MGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASF
Sbjct: 241 MGIWLAHTGFGLPLAIYLLRNYMAGLPREIMESARVDGASDFDIFVKIILPLSFPALASF 300

Query: 301 AIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIV 360
           AIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIV
Sbjct: 301 AIFQFLWTWNDLLVAIVFLGAGDDKLVLTGRLVNLLGSRGGNWEILTASAFITIVVPLIV 360

Query: 361 FFALQRYLVRGLLAGSVKGG 380
           FFALQRYLVRGLLAGSVKGG
Sbjct: 361 FFALQRYLVRGLLAGSVKGG 380


Lambda     K      H
   0.324    0.139    0.418 

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: 627
Number of extensions: 17
Number of successful extensions: 1
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: 380
Length of database: 380
Length adjustment: 30
Effective length of query: 350
Effective length of database: 350
Effective search space:   122500
Effective search space used:   122500
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 15 ( 7.0 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 40 (21.5 bits)
S2: 50 (23.9 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