GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Rhodanobacter denitrificans 2APBS1

Align MsiK protein, 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 WP_015448118.1 R2APBS1_RS12060 ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_000230695.2:WP_015448118.1
          Length = 255

 Score =  140 bits (354), Expect = 3e-38
 Identities = 80/222 (36%), Positives = 128/222 (57%), Gaps = 3/222 (1%)

Query: 20  AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDV--THLPPKDR 77
           A++Q+ +A   G    L+G SG GKST LR+L GLE  + G + +  R +  + + P  R
Sbjct: 26  ALEQVSLAFAAGTTTALIGSSGSGKSTVLRLLLGLEWPDHGHVEVDGRPLQRSDVLPLRR 85

Query: 78  DIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDL-TQYLDRKPKAL 136
            +  V Q+  L+PH+T   N+    +  G  +  IRQ+ E+ A +  L T  L+R P  L
Sbjct: 86  RVGYVIQDGGLFPHLTALGNLALLPRHLGWNRERIRQRAEQLAALTHLPTGVLERYPAEL 145

Query: 137 SGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQ 196
           SGGQRQRVA+ RA++ +P   L+DEPL  LD  +R   + ++  +  +LG T + VTHD 
Sbjct: 146 SGGQRQRVALMRALMADPDALLLDEPLGALDPVVRHELQDELKQIFDQLGKTVIVVTHDL 205

Query: 197 VEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGS 238
            EA    +R+ +L+ G + Q  + R++ ++PA+ FV  F+ +
Sbjct: 206 AEAAWFAERLVLLRQGAVLQDGTFRDLRERPADAFVNRFVAA 247


Lambda     K      H
   0.317    0.135    0.379 

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: 14
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: 377
Length of database: 255
Length adjustment: 27
Effective length of query: 350
Effective length of database: 228
Effective search space:    79800
Effective search space used:    79800
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.3 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.6 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 24 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