GapMind for catabolism of small carbon sources

 

Aligments for a candidate for cebF in Escherichia coli BW25113

Align CBP protein aka CebF, 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 17513 b3452 glycerol-3-phosphate transporter subunit (NCBI)

Query= TCDB::Q9X9R6
         (306 letters)



>lcl|FitnessBrowser__Keio:17513 b3452 glycerol-3-phosphate
           transporter subunit (NCBI)
          Length = 295

 Score =  122 bits (305), Expect = 1e-32
 Identities = 84/274 (30%), Positives = 138/274 (50%), Gaps = 10/274 (3%)

Query: 19  PYAFVAPFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSDFFWNAL 78
           PY  VAP  ++   F + P     WYSL +V       + + GLDN+  L    ++ ++ 
Sbjct: 14  PYLLVAPQLIITVIFFIWPAGEALWYSLQSVDPFGFSSQ-FVGLDNFVTLFHDSYYLDSF 72

Query: 79  KNTLTIGIISTVPQLLAALALAHLLNYKLRGSTAWRVVMLTPYATSVAAATLVFTLLYSW 138
             T+      TV  LL +L  A L+ Y +RGS  ++ +ML PYA + A A +++  L++ 
Sbjct: 73  WTTIKFSTFVTVSGLLVSLFFAALVEYIVRGSRFYQTLMLLPYAVAPAVAAVLWIFLFNP 132

Query: 139 DGGMVNWILDFFGVDPVNWRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQAIPADLYES 198
             G++   L  FG D  N  ++   + F V    +W+   YN L + AA+Q+IP  L E+
Sbjct: 133 GRGLITHFLAEFGYD-WNHAQNSGQAMFLVVFASVWKQISYNFLFFYAALQSIPRSLIEA 191

Query: 199 AALDGANRWQQFRHVTVPQLRPTILFTVVVSTIGATQLFGE-PLLFGGVSGSKGGSEHQY 257
           AA+DGA   ++F  + +P + P   F +VV+ + A   F   P++    S   GG     
Sbjct: 192 AAIDGAGPIRRFFKIALPLIAPVSFFLLVVNLVYA--FFDTFPVIDAATS---GGPVQAT 246

Query: 258 QTLGLYMYDQGWIIGNLGKASAIAWSMFLILLIV 291
            TL   +Y +G+    L  AS+ A S+ L+ L++
Sbjct: 247 TTLIYKIYREGFT--GLDLASSAAQSVVLMFLVI 278


Lambda     K      H
   0.324    0.137    0.441 

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: 234
Number of extensions: 16
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: 306
Length of database: 295
Length adjustment: 27
Effective length of query: 279
Effective length of database: 268
Effective search space:    74772
Effective search space used:    74772
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: 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