GapMind for catabolism of small carbon sources

 

Alignments for a candidate for msiK in Thiothrix lacustris DSM 21227

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_028488909.1 Q394_RS0108480 spermidine/putrescine ABC transporter ATP-binding protein PotA

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_000621325.1:WP_028488909.1
          Length = 369

 Score =  228 bits (580), Expect = 3e-64
 Identities = 112/238 (47%), Positives = 160/238 (67%), Gaps = 7/238 (2%)

Query: 16  SDKPAVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPK 75
           + +  +   ++ I+DGEF  ++GPSGCGK+T LR++AG E  N G I +   D+  +P +
Sbjct: 17  ASQEVLSDFNLTIQDGEFFTILGPSGCGKTTVLRLIAGFEQPNEGQILLNGDDIARIPAE 76

Query: 76  DRDIAMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKA 135
            R    VFQ+YAL+PH+TV DN+ F LK+AGV   +I  +V +A  I+ L+++  RKP  
Sbjct: 77  KRPFNTVFQSYALFPHLTVFDNVAFGLKMAGVDVQDIAVRVADALAIVRLSEFATRKPHQ 136

Query: 136 LSGGQRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHD 195
           LSGGQ+QRVA+ RA+V  P++ L+DE LS LD KLR   + ++  LQR+LGIT VYVTHD
Sbjct: 137 LSGGQKQRVAIARAVVNRPKILLLDESLSALDYKLRQQMQLELKQLQRQLGITFVYVTHD 196

Query: 196 QVEAMTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGV 253
           Q EA++M DR+ V+ +G  QQV +PR +Y+ P NLFVA FIG       E+ + DG +
Sbjct: 197 QEEALSMSDRILVMHNGQAQQVGTPREIYESPRNLFVAQFIG-------EINVFDGEI 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: 333
Number of extensions: 13
Number of successful extensions: 2
Number of sequences better than 1.0e-02: 1
Number of HSP's gapped: 2
Number of HSP's successfully gapped: 1
Length of query: 377
Length of database: 369
Length adjustment: 30
Effective length of query: 347
Effective length of database: 339
Effective search space:   117633
Effective search space used:   117633
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: 50 (23.9 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