GapMind for catabolism of small carbon sources

 

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

Align glycine betaine/l-proline transport atp-binding protein prov (characterized)
to candidate CA265_RS07485 CA265_RS07485 macrolide ABC transporter ATP-binding protein

Query= CharProtDB::CH_001555
         (400 letters)



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

 Score =  141 bits (356), Expect = 2e-38
 Identities = 87/225 (38%), Positives = 126/225 (56%), Gaps = 15/225 (6%)

Query: 44  VKDASLAIEEGEIFVIMGLSGSGKSTMVRLLNRLIEPTRGQVLIDGVDIAKISDAELREV 103
           +K  SL I +GE   +MG SGSGKST++ +L  L  P+ G  +++G +++ +SD  L EV
Sbjct: 25  LKSVSLDINKGEFVALMGPSGSGKSTLMNILGCLDTPSSGTYVLNGTNVSHMSDDALAEV 84

Query: 104 RRKKIAMVFQSFALMPHMTVLDNTAFGMELAGINAEERREKALDALRQVGLENYAHSYPD 163
           R ++I  VFQ+F L+P  T LDN A  +  AG + ++R  +A  AL  VGL N     P+
Sbjct: 85  RNQEIGFVFQTFNLLPRSTSLDNVALPLIYAGTSKKDRDARAARALENVGLGNRMDHKPN 144

Query: 164 ELSGGMRQRVGLARALAINPDILLMDEAFSALDPLIRTEMQDELVKLQAKHQRTIVFISH 223
           ELSGG RQRV +ARAL  NP I+L DE    LD     E+   L ++ +K   TI+ ++H
Sbjct: 145 ELSGGQRQRVAVARALINNPSIILADEPTGNLDTKTSIEIMGLLEEIHSK-GNTIILVTH 203

Query: 224 DLDEAMRIGDRIAIMQNGEVVQVGTPDEILNNPANDYVRTFFRGV 268
           + D A     RI  M++G +              NDY+ T  + V
Sbjct: 204 EEDIAQH-AHRIVRMRDGLI-------------ENDYLNTDIKNV 234


Lambda     K      H
   0.319    0.137    0.378 

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: 222
Number of extensions: 12
Number of successful extensions: 1
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: 400
Length of database: 252
Length adjustment: 27
Effective length of query: 373
Effective length of database: 225
Effective search space:    83925
Effective search space used:    83925
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 (21.7 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