GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Keio:17513
          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:

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