GapMind for catabolism of small carbon sources

 

Aligments for a candidate for HSERO_RS17020 in Pedobacter sp. GW460-11-11-14-LB5

Align ABC-type sugar transport system, ATPase component protein (characterized, see rationale)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

Query= uniprot:D8IPI1
         (406 letters)



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

 Score =  129 bits (323), Expect = 1e-34
 Identities = 80/221 (36%), Positives = 121/221 (54%), Gaps = 15/221 (6%)

Query: 4   IHCQALAKHYAGGPPVLHPL---DLHIGDGEFVVLLGPSGCGKSTMLRMIAGLEDISGGT 60
           I  + + + Y  G  V+H L    L I  GEFV L+GPSG GKST++ ++  L+  S GT
Sbjct: 6   ITIKEIGRKYVIGSEVIHALKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGT 65

Query: 61  LRIGGTVVNDLP------ARERNVAMVFQNYALYPHMSVYDNIAFGLRRLKRPAAEIDRR 114
             + GT V+ +        R + +  VFQ + L P  +  DN+A  L  +    ++ DR 
Sbjct: 66  YVLNGTNVSHMSDDALAEVRNQEIGFVFQTFNLLPRSTSLDNVALPL--IYAGTSKKDRD 123

Query: 115 VREVAALLN--LEALLERKPRAMSGGQQQRAAIARAIIKTPSVFLFDEPLSNLDAKLRAQ 172
            R   AL N  L   ++ KP  +SGGQ+QR A+ARA+I  PS+ L DEP  NLD K   +
Sbjct: 124 ARAARALENVGLGNRMDHKPNELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIE 183

Query: 173 LRGDIKRLHQRLRTTTVYVTHDQLEAMTLADRVILMQDGRI 213
           + G ++ +H +   T + VTH++ +    A R++ M+DG I
Sbjct: 184 IMGLLEEIHSK-GNTIILVTHEE-DIAQHAHRIVRMRDGLI 222


Lambda     K      H
   0.321    0.137    0.403 

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: 201
Number of extensions: 6
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: 406
Length of database: 252
Length adjustment: 28
Effective length of query: 378
Effective length of database: 224
Effective search space:    84672
Effective search space used:    84672
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: 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 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