GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Rhizorhabdus wittichii RW1

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_012048833.1 SWIT_RS13320 amino acid ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_000016765.1:WP_012048833.1
          Length = 241

 Score =  126 bits (316), Expect = 7e-34
 Identities = 74/222 (33%), Positives = 119/222 (53%), Gaps = 6/222 (2%)

Query: 20  AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTH----LPPK 75
           A+  + + +  GE +V+ GPSG GKST +R + GLE  + G IRIG+ +V      L   
Sbjct: 16  ALRNVSLDVARGERIVICGPSGSGKSTLIRCINGLETHDEGVIRIGEDEVRPDRRVLQRI 75

Query: 76  DRDIAMVFQNYALYPHMTVADNMGFA-LKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPK 134
              + MVFQ++ L+PH+T+ +N   A +K+ G+ +        E  + + +    D+ P 
Sbjct: 76  RARVGMVFQDFNLFPHLTILENCALAPMKVRGLARDAAEALARELLERVRIADQADKYPA 135

Query: 135 ALSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTH 194
            LSGGQ+QR A+ RA+  +P++ L DEP S LDA++ V     I       GIT + VTH
Sbjct: 136 QLSGGQQQRTAIARALAMQPEIILFDEPTSALDAEM-VKEVLDIMKALATEGITMLCVTH 194

Query: 195 DQVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFI 236
           +   A  + DR+  +  G + +  SPR+ +  P +     F+
Sbjct: 195 EMGFAREVADRIIFMDAGQIVETGSPRDFFTAPCHERTRAFL 236


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: 210
Number of extensions: 7
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: 377
Length of database: 241
Length adjustment: 27
Effective length of query: 350
Effective length of database: 214
Effective search space:    74900
Effective search space used:    74900
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 Apr 09 2024. 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