GapMind for catabolism of small carbon sources

 

Alignments for a candidate for cebF in Sinorhizobium meliloti 1021

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 SMc02472 SMc02472 ABC transporter permease

Query= TCDB::Q9X9R6
         (306 letters)



>FitnessBrowser__Smeli:SMc02472
          Length = 312

 Score =  144 bits (364), Expect = 2e-39
 Identities = 86/271 (31%), Positives = 149/271 (54%), Gaps = 6/271 (2%)

Query: 22  FVAPFFLLFGAFSLVPLLYTAWYSLHNVQLSALDHKTWAGLDNYENLLSSDFFWNALKNT 81
           F+ P  LLF  F ++P+   AWYSL+         + + GL N+E L ++  F  AL N 
Sbjct: 37  FLPPALLLFTVFVILPMGEAAWYSLYRWNGYGTPTQ-FVGLRNFEVLFNNAAFSRALINN 95

Query: 82  LTIGIISTVPQLLAALALAHLLNYKLRGSTAWRVVMLTPYATSVAAATLVFTLLYSWDGG 141
             I ++S + Q+  AL LA +L +++ G  A+R++   PY  +  AA L++  +Y  D G
Sbjct: 96  GIIILVSVLLQIPLALWLAMMLAHRIAGVVAFRLIFFLPYVLADVAAGLIWRFVYDGDYG 155

Query: 142 MVNWILDFFGVDPVNWRESDWGSQFAVSSIVIWRWTGYNALIYLAAMQAIPADLYESAAL 201
           +V  I  FFGV           + +AV +++IW++ G++ ++++A +QA+   + E+A +
Sbjct: 156 LVAAIAGFFGVATPYVLADRSLAIYAVLAVIIWKYFGFHMMLFIAGLQAVDRSVLEAAEI 215

Query: 202 DGANRWQQFRHVTVPQLRPTILFTVVVSTIGATQLFGEPLLFGGVSGSKGGSEHQYQTLG 261
           DGA  WQ+FR+VT+P L  T+  ++  + IG+ QLF   +   G     GG  +  QT+ 
Sbjct: 216 DGATGWQKFRYVTLPLLGSTVRLSIFFAVIGSLQLFDLVMPLTG-----GGPSNSTQTMV 270

Query: 262 LYMYDQGWIIGNLGKASAIAWSMFLILLIVA 292
            ++Y  G     +G  SA+   +F+I + +A
Sbjct: 271 TFLYTYGVTRMQVGLGSAVGVVLFVICVTLA 301


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: 265
Number of extensions: 17
Number of successful extensions: 4
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: 312
Length adjustment: 27
Effective length of query: 279
Effective length of database: 285
Effective search space:    79515
Effective search space used:    79515
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