GapMind for catabolism of small carbon sources

 

Alignments for a candidate for thuK in Dyella japonica UNC79MFTsu3.2

Align ABC transporter (characterized, see rationale)
to candidate N515DRAFT_1085 N515DRAFT_1085 D-methionine transport system ATP-binding protein

Query= uniprot:A0A166QFW2
         (381 letters)



>FitnessBrowser__Dyella79:N515DRAFT_1085
          Length = 336

 Score =  135 bits (339), Expect = 2e-36
 Identities = 85/242 (35%), Positives = 130/242 (53%), Gaps = 10/242 (4%)

Query: 19  LRDVSLEIAAGEFVVFVGPSGCGKSTLLRLIAGLDSICGGDLLIDGRRVNDL-----EPR 73
           L+  SL+IA GE    +G SG GKSTL+RLI  L+   GG +LIDG  +  L       +
Sbjct: 21  LQPFSLDIADGEVFGIIGHSGAGKSTLIRLINLLERPSGGSILIDGTEMTALGDAALRAQ 80

Query: 74  ERGVGMVFQSYALYPHMSVYDNISFGLKLA-KTDKTSLRERVLKTAQILQLDKLLQRKPK 132
            R +GM+FQ + L    +V DNI+F L+LA +TD   ++ RV +  + + L+    + P 
Sbjct: 81  RRRIGMIFQHFNLLSSQTVADNIAFPLRLAGETDAGKIKARVDELLRRVGLEAHASKYPA 140

Query: 133 ELSGGQRQRVAMGRAMAREPDILLFDEPLSNLDASLRVQMRNEIARLHDRLGSTMIYVTH 192
           +LSGGQ+QRV + RA+A  P ILL DE  S LD      +   +A ++  L  T++ +TH
Sbjct: 141 QLSGGQKQRVGIARALANRPSILLCDEATSALDPQTTASVLELLAEINRELKLTIVLITH 200

Query: 193 DQVEAMTLADKIVVLNGGRVEQVGSPRELYERP----ASRFVAGFLGSPRMNFLSARLQT 248
           +      + D++ VL+ GR+ + G+  +++  P      RFV   L       L+     
Sbjct: 201 EMDVVRRVCDRVAVLDAGRIVEHGAVADVFLHPRHPTTRRFVNEALPEEAAGELAPYTHV 260

Query: 249 PG 250
           PG
Sbjct: 261 PG 262


Lambda     K      H
   0.320    0.137    0.394 

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: 262
Number of extensions: 13
Number of successful extensions: 4
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: 381
Length of database: 336
Length adjustment: 29
Effective length of query: 352
Effective length of database: 307
Effective search space:   108064
Effective search space used:   108064
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 (21.8 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:

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