GapMind for catabolism of small carbon sources

 

Aligments for a candidate for msiK in Pseudomonas simiae WCS417

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 GFF2490 PS417_12700 ABC transporter ATP-binding protein

Query= TCDB::P96483
         (377 letters)



>lcl|FitnessBrowser__WCS417:GFF2490 PS417_12700 ABC transporter
           ATP-binding protein
          Length = 367

 Score =  307 bits (786), Expect = 3e-88
 Identities = 167/357 (46%), Positives = 221/357 (61%), Gaps = 35/357 (9%)

Query: 24  LDIAIEDGEFLVLVGPSGCGKSTSLRMLAGLEDVNGGAIRIGDRDVTHLPPKDRDIAMVF 83
           +D+ + D EF+V VGPSGCGKST LR++AGLE+V+ G I +  RD+T + P  RD+AMVF
Sbjct: 22  IDLEVNDKEFVVFVGPSGCGKSTLLRLIAGLEEVSEGTIELDGRDITEVTPAKRDLAMVF 81

Query: 84  QNYALYPHMTVADNMGFALKIAGVPKAEIRQKVEEAAKILDLTQYLDRKPKALSGGQRQR 143
           Q YALYPHM+V  NM FAL +AGV K  +  KV EAA+IL+L   L+RKPK LSGGQRQR
Sbjct: 82  QTYALYPHMSVRKNMSFALDLAGVDKKLVESKVSEAARILELGPLLERKPKQLSGGQRQR 141

Query: 144 VAMGRAIVREPQVFLMDEPLSNLDAKLRVSTRTQIASLQRRLGITTVYVTHDQVEAMTMG 203
           VA+GRAIVR P++FL DEPLSNLDA LRV  R ++A L + L  T +YVTHDQVEAMT+ 
Sbjct: 142 VAIGRAIVRNPKIFLFDEPLSNLDAALRVQMRLELARLHKELQATMIYVTHDQVEAMTLA 201

Query: 204 DRVAVLKDGLLQQVDSPRNMYDKPANLFVAGFIGSPAMNLVEVPIT-----------DGG 252
           D+V VL  G ++QV SP  +Y +PANLFVAGF+G+P M  ++  +T           D G
Sbjct: 202 DKVVVLNSGRIEQVGSPLELYHQPANLFVAGFLGTPKMGFLKGKVTRVESQSCEVQLDAG 261

Query: 253 VKFGNSVVPVNREALSAADKGDRTVTVGVRPEHFDVVELGGAVAASLSKDSADAPAGLAV 312
                  +P++   LS        VT+G+RPEH ++   G                 L V
Sbjct: 262 TLIN---LPLSGATLSVGS----AVTLGIRPEHLEIASPGQTT--------------LTV 300

Query: 313 SVNVVEELGADGYVYGTAEVGGEVKDLVVRVNGRQVPEKGSTLHVVPRPGETHVFST 369
           + +V E LG+D + +     G   + L +R+ G    + G TLH+   P   H+F T
Sbjct: 301 TADVGERLGSDTFCHVITANG---EPLTMRIRGDMASQYGETLHLHLDPAHCHLFDT 354


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: 392
Number of extensions: 16
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: 367
Length adjustment: 30
Effective length of query: 347
Effective length of database: 337
Effective search space:   116939
Effective search space used:   116939
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 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 the paper from 2019 on GapMind for amino acid biosynthesis, the paper from 2022 on GapMind for carbon sources, or view the source code.

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