GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cebG in Phaeobacter inhibens BS107

Align CBP protein aka CebG, component of The cellobiose/cellotriose (and possibly higher cellooligosaccharides), CebEFGMsiK [MsiK functions to energize several ABC transporters including those for maltose/maltotriose and trehalose] (characterized)
to candidate GFF3033 PGA1_c30820 putative ABC transporter permease protein

Query= TCDB::Q9X9R5
         (276 letters)



>lcl|FitnessBrowser__Phaeo:GFF3033 PGA1_c30820 putative ABC
           transporter permease protein
          Length = 320

 Score =  122 bits (305), Expect = 1e-32
 Identities = 73/223 (32%), Positives = 115/223 (51%), Gaps = 8/223 (3%)

Query: 58  NLEAAWEQAGLGTAMLNSVIVAGTITVSTVLFSTLAGFAFAKLRFRFSGLLLLLTIGTMM 117
           N   A+ +A L   +LN +IV G+I +  V+ +  A +A AKL+F     +  L +  ++
Sbjct: 101 NYSKAFTEAPLLRYLLNGIIVTGSIFLIQVVVALPAAYALAKLKFWGREAVFGLVLFCLL 160

Query: 118 IPPQLAVVPLYLWMSDLGWSNQLHTVILPSLVTAFGTFFMRQYLVQALPTELIEAARVDG 177
           IP     +PLY+ ++ LG +N    +++P  ++ FG F MRQ+ +  +P +LI+AAR+DG
Sbjct: 161 IPVHAIALPLYIMLAKLGLTNTYAALVVPWTISVFGIFLMRQFFM-TVPDDLIDAARMDG 219

Query: 178 ASSLRIVWHVVFPAARPAMAVLGLLTFVFAWNDFLWPIIALNQQNPTVQVGPELARHRVL 237
                IVW V+ P A PA+    + + V  WND+ WP I +          P L      
Sbjct: 220 MGEFSIVWRVMLPTAIPALLAFAIFSIVAHWNDYFWPRIVVTGNRDLFT--PPLGLREFK 277

Query: 238 PDQ-----AVIMAGALLGTLPLLVAFLLFGKQIVGGIMQGAIK 275
            D        +MA A +   PL+VAFLL  K+ + GI    +K
Sbjct: 278 GDGDGSYFGPMMATATVIVTPLIVAFLLAQKRFIEGITLSGMK 320


Lambda     K      H
   0.327    0.140    0.434 

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: 229
Number of extensions: 7
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: 276
Length of database: 320
Length adjustment: 26
Effective length of query: 250
Effective length of database: 294
Effective search space:    73500
Effective search space used:    73500
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 (21.7 bits)
S2: 48 (23.1 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 the paper from 2019 on GapMind for amino acid biosynthesis, the preprint on GapMind for carbon sources, 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