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_028489030.1 Q394_RS0109195 ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>NCBI__GCF_000621325.1:WP_028489030.1
          Length = 348

 Score =  308 bits (788), Expect = 2e-88
 Identities = 180/364 (49%), Positives = 228/364 (62%), Gaps = 48/364 (13%)

Query: 20  AVDQLDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDI 79
           A+ Q+ + I+ GEF+V VGPSGCGKST LRM+AGLE +NGG + +  RD+T +PP  RD+
Sbjct: 18  AIKQVSLEIQSGEFIVFVGPSGCGKSTLLRMIAGLEVINGGQLILDGRDITEVPPSQRDL 77

Query: 80  AMVFQNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGG 139
           AMVFQ+YALYPHMTV +NM FAL++A V  A I++KV+ AA  L+LT YL R PKALSGG
Sbjct: 78  AMVFQSYALYPHMTVEENMSFALRLAKVDPAIIQEKVKMAADKLNLTAYLQRTPKALSGG 137

Query: 140 QRQRVAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEA 199
           QRQRVA+GR+IVR P+VFL DEPLSNLDA LR +TR +IASL R LG TTVYVTHDQVEA
Sbjct: 138 QRQRVAIGRSIVRSPKVFLFDEPLSNLDAALRGNTRVEIASLHRELGATTVYVTHDQVEA 197

Query: 200 MTMGDRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPITDGGVKFGNSV 259
           MT+ DRV VL+DG+++QV +P  +YD+P N FVA FIG P MN+    +      FG   
Sbjct: 198 MTLADRVVVLRDGIIEQVGTPLELYDQPINRFVARFIGMPQMNVAPASL------FGQFP 251

Query: 260 VPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAVSVNVVEE 319
             V                VG+RPEH  +V     +              LA  V +VE 
Sbjct: 252 AQV--------------AEVGIRPEHLQMVSPEDGL--------------LAGKVVLVEA 283

Query: 320 LGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPG-------ETHVFSTSTG 372
           LG +  V+   +     + L+VR+ GR      +T+HV  R G         H F T  G
Sbjct: 284 LGNETLVHVRPDKVQLEEPLIVRLYGR------TTVHVGDRVGLKWDDSKHIHYFDTK-G 336

Query: 373 ERLS 376
            RL+
Sbjct: 337 MRLT 340


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: 409
Number of extensions: 14
Number of successful extensions: 2
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: 348
Length adjustment: 29
Effective length of query: 348
Effective length of database: 319
Effective search space:   111012
Effective search space used:   111012
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: 49 (23.5 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