GapMind for catabolism of small carbon sources

 

Alignments for a candidate for glpF in Pedobacter sp. GW460-11-11-14-LB5

Align Glycerol uptake facilitator protein 3 (characterized)
to candidate CA265_RS07865 CA265_RS07865 aquaporin

Query= SwissProt::F9UTW9
         (240 letters)



>FitnessBrowser__Pedo557:CA265_RS07865
          Length = 246

 Score =  229 bits (583), Expect = 5e-65
 Identities = 115/237 (48%), Positives = 146/237 (61%), Gaps = 11/237 (4%)

Query: 11  LGEFLGTFILILLGDGVVAGVTLNKSKAQNAGWVAITLGWGFAVTMGVYASSFMSPAHLN 70
           L EF+GT ++ILLG+GVVA V L  +K  N+GW+ IT  W  AV +GV  +   S AHLN
Sbjct: 5   LAEFIGTALMILLGNGVVANVVLKGTKGNNSGWIVITTAWALAVFVGVVVAGPYSGAHLN 64

Query: 71  PAVSLGMAVAGKFPWAYVIPYSAAQIAGGVIGGLVVWLHYYPHWQATKDAGAILGIFATG 130
           P V+LG+A+   F WA    Y  AQ+AG + G  +VWL Y  H+ AT D G     FAT 
Sbjct: 65  PIVTLGLAIGKGFSWALAPFYIIAQLAGAMTGSFLVWLIYKDHFDATDDQGLKAAPFATA 124

Query: 131 PGIRRYFWNFISEVIGTFVLVFGLLAFTKGQF-----------TAGLNPIVVGILIIAIG 179
           P IR    N +SE+IGTFVL+F +  FT                  +  I V  L+  IG
Sbjct: 125 PAIRNISSNLLSEIIGTFVLIFVIFYFTDASMGTKETVTTPIGLGSMGAIPVAFLVWVIG 184

Query: 180 LSLGGTTGYAINPARDLGPRIAHAVLPIANKGTSDWAYSWVPIAGPLVGGALGALLF 236
           L+LGGTTGYAINPARDLGPRI H ++P+  KG SDW+Y+WVPI GP++G  L A+ F
Sbjct: 185 LALGGTTGYAINPARDLGPRIIHFLIPMKGKGGSDWSYAWVPIVGPIIGSVLAAVAF 241



 Score = 23.5 bits (49), Expect = 0.004
 Identities = 26/114 (22%), Positives = 40/114 (35%), Gaps = 11/114 (9%)

Query: 6   LALQLLGEFLGTFILILL-------GDGVVAGVTLNKSKAQNAGWVAITLGWGFAVTMGV 58
           ++  LL E +GTF+LI +         G    VT               L W   + +G 
Sbjct: 130 ISSNLLSEIIGTFVLIFVIFYFTDASMGTKETVTTPIGLGSMGAIPVAFLVWVIGLALGG 189

Query: 59  YASSFMSPAH-LNPAV---SLGMAVAGKFPWAYVIPYSAAQIAGGVIGGLVVWL 108
                ++PA  L P +    + M   G   W+Y        I G V+  +   L
Sbjct: 190 TTGYAINPARDLGPRIIHFLIPMKGKGGSDWSYAWVPIVGPIIGSVLAAVAFLL 243


Lambda     K      H
   0.325    0.143    0.459 

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: 260
Number of extensions: 16
Number of successful extensions: 3
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 2
Length of query: 240
Length of database: 246
Length adjustment: 23
Effective length of query: 217
Effective length of database: 223
Effective search space:    48391
Effective search space used:    48391
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 (21.6 bits)
S2: 46 (22.3 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