Conserved positions in expansin homologues (ICPSR doi:10.18419/darus-735)

View:

Part 1: Document Description
Part 2: Study Description
Part 3: Data Files Description
Part 4: Variable Description
Entire Codebook

Document Description

Citation

Title:

Conserved positions in expansin homologues

Identification Number:

doi:10.18419/darus-735

Distributor:

DaRUS

Date of Distribution:

2020-04-09

Version:

1

Bibliographic Citation:

Lohoff, Caroline, 2020, "Conserved positions in expansin homologues", https://doi.org/10.18419/darus-735, DaRUS, V1, UNF:6:HemykMznkJ0tyrf89mswkg== [fileUNF]

Study Description

Citation

Title:

Conserved positions in expansin homologues

Identification Number:

doi:10.18419/darus-735

Authoring Entity:

Lohoff, Caroline (Universität Stuttgart)

Distributor:

DaRUS

Access Authority:

Pleiss, Jürgen

Depositor:

Buchholz, Patrick

Date of Deposit:

2020-03-10

Study Scope

Keywords:

Medicine, Health and Life Sciences, conservation analysis

Abstract:

Conserved positions in the N- and C-terminal expansin domains of different groups from the Expansin Engineering Database (occurring in at least 70% of the annotated sequence entries). The expansin domains were annotated using hmmscan (from the HMMER software suite) against all sequence entries in the Expansin Engineering Database.

Methodology and Processing

Sources Statement

Data Sources:

Expansin Engineering Database (<a href="https://exed.biocatnet.de/">https://exed.biocatnet.de/</a>)

<br> PDB (<a href="https://doi.org/10.2210/pdb4FER/pdb">doi: 10.2210/pdb4FER/pdb</a>)

<br> Georgelis N, Tabuchi A, Nikolaidis N, Cosgrove DJ. Structure-function analysis of the bacterial expansin EXLX1. J Biol Chem. 2011;286:16814-16823. <a href="https://doi.org/10.1074/jbc.M111.225037">doi:10.1074/jbc.M111.225037</a>

<br> Yennawar NH, Li AC, Dudzinski DM, Tabuchi A, Cosgrove DJ. Crystal structure and activities of EXPB1 (Zea m 1), a β-expansin and group-1 pollen allergen from maize. Proc Natl Acad Sci U S A. 2006;103:14664-14671. <a href="https://doi.org/10.1073/pnas.0605979103">doi:10.1073/pnas.0605979103</a>

Data Access

Notes:

CC BY Waiver

Other Study Description Materials

Related Studies

Lohoff, Caroline, 2020, "Profile hidden Markov models of the ExED", <a href="https://doi.org/10.18419/darus-623">doi:10.18419/darus-623</a>, DaRUS

Related Publications

Citation

Bibliographic Citation:

Lohoff C, Buchholz PCF, Le Roes-Hill M, Pleiss J (2020) The Expansin Engineering Database: a navigation and classification tool for expansins and homologues (submitted)

File Description--f2785

File: Conserved_amino_acids_in_C-terminal_domain.tab

  • Number of cases: 85

  • No. of variables per record: 8

  • Type of File: text/tab-separated-values

Notes:

UNF:6:CE90w0ai1+p+rVxLddj0OA==

File Description--f2786

File: Conserved_amino_acids_in_N-terminal_domain.tab

  • Number of cases: 123

  • No. of variables per record: 8

  • Type of File: text/tab-separated-values

Notes:

UNF:6:ztPrC1aaxgvhz6A2pKE7oA==

Variable Description

List of Variables:

Variables

Standard Position

f2785 Location:

Summary Statistics: Valid 85.0; Mean 151.5423529411765; StDev 21.733304355465208; Min. 114.0; Max. 186.0

Variable Format: numeric

Notes: UNF:6:FiLhp1HoXjQcPJhMHeU33g==

Bacteria

f2785 Location:

Variable Format: character

Notes: UNF:6:H53KNu0oXii9+B23LypWTQ==

Fungi

f2785 Location:

Variable Format: character

Notes: UNF:6:nQ9hI0zfA6j2J+X8F+rtHQ==

EXPA

f2785 Location:

Variable Format: character

Notes: UNF:6:c3gyMMJa/sr3rXKH4yS/XA==

EXPB

f2785 Location:

Variable Format: character

Notes: UNF:6:w1j4qfH3f1s2QEjmV9zX1g==

EXLA

f2785 Location:

Variable Format: character

Notes: UNF:6:VSiM3cY8pSER8yjbAj1njQ==

EXLB

f2785 Location:

Variable Format: character

Notes: UNF:6:qSup5mynUsx0U+vOksAtdg==

Function

f2785 Location:

Variable Format: character

Notes: UNF:6:1lceCvJEnlQ/8WCZJ65KTQ==

Standard Position

f2786 Location:

Summary Statistics: Min. 11.0; Valid 123.0; Max. 105.0; StDev 27.51324128406087; Mean 58.96178861788616;

Variable Format: numeric

Notes: UNF:6:2d+fOWxIK+1op4PNWxTExw==

Bacteria

f2786 Location:

Variable Format: character

Notes: UNF:6:ohsZmXjl8LdREENAlUhAgA==

Fungi

f2786 Location:

Variable Format: character

Notes: UNF:6:15utZQYFN2zx2TIlVbmF7w==

EXPA

f2786 Location:

Variable Format: character

Notes: UNF:6:OteMKkYuXrxPynmgs5UomA==

EXPB

f2786 Location:

Variable Format: character

Notes: UNF:6:8sDN2/dYTyh/XIFYVX8FJw==

EXLA

f2786 Location:

Variable Format: character

Notes: UNF:6:XWNQgJmggT9fKteFkdRTKw==

EXLB

f2786 Location:

Variable Format: character

Notes: UNF:6:luP+tC2dJyfEerMUC+3qxQ==

Function and motif

f2786 Location:

Variable Format: character

Notes: UNF:6:Jh6IIsU713G1CIS9knvGig==