GapMind for catabolism of small carbon sources

 

Aligments for a candidate for thuK in Pedobacter sp. GW460-11-11-14-LB5

Align ThuK aka RB0314 aka SMB20328, component of Trehalose/maltose/sucrose porter (trehalose inducible) (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

Query= TCDB::Q9R9Q4
         (342 letters)



>lcl|FitnessBrowser__Pedo557:CA265_RS07485 CA265_RS07485 macrolide
           ABC transporter ATP-binding protein
          Length = 252

 Score =  129 bits (323), Expect = 1e-34
 Identities = 77/204 (37%), Positives = 115/204 (56%), Gaps = 13/204 (6%)

Query: 19  IKGVSMEIKPGEFMVFVGPSGCGKSTLLRLIAGLEEITSGTLAFDGQIVNQLTPS----- 73
           +K VS++I  GEF+  +GPSG GKSTL+ ++  L+  +SGT   +G  V+ ++       
Sbjct: 25  LKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAEV 84

Query: 74  -RRGIAMVFQSYALYPHMTVYENMAFGMQLAGKDKQQCRKRVEAAAEMLQLTPYLERLPR 132
             + I  VFQ++ L P  T  +N+A  +  AG  K+    R   A E + L   ++  P 
Sbjct: 85  RNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGNRMDHKPN 144

Query: 133 QLSGGQRQRVAIGRAIVRDPKVFLFDEPLSNLDAALRVATRLEIAKLHRSMHK--TTMIY 190
           +LSGGQRQRVA+ RA++ +P + L DEP  NLD      T +EI  L   +H    T+I 
Sbjct: 145 ELSGGQRQRVAVARALINNPSIILADEPTGNLD----TKTSIEIMGLLEEIHSKGNTIIL 200

Query: 191 VTHDQVEAMTLADRICVLRDGLVE 214
           VTH++ +    A RI  +RDGL+E
Sbjct: 201 VTHEE-DIAQHAHRIVRMRDGLIE 223


Lambda     K      H
   0.321    0.138    0.396 

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: 191
Number of extensions: 8
Number of successful extensions: 3
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: 342
Length of database: 252
Length adjustment: 26
Effective length of query: 316
Effective length of database: 226
Effective search space:    71416
Effective search space used:    71416
Neighboring words threshold: 11
Window for multiple hits: 40
X1: 16 ( 7.4 bits)
X2: 38 (14.6 bits)
X3: 64 (24.7 bits)
S1: 41 (21.9 bits)
S2: 48 (23.1 bits)

This GapMind analysis is from Sep 17 2021. The underlying query database was built on Sep 17 2021.

Links

Downloads

Related tools

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 against a database of manually-curated proteins (most of which are experimentally characterized) or by using HMMer. 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. 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 preprint 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