GapMind for catabolism of small carbon sources

 

Alignments 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)



>FitnessBrowser__Pedo557:CA265_RS07485
          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.

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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