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Table 2 Annotations for IS element rich regions

From: Comprehensive de novo structure prediction in a systems-biology context for the archaea Halobacterium sp. NRC-1

Name

IS-element

Method

Annotation

IS-element rich region 1

VNG5101H/6098H

ISH2

Pfam

PF01402 CopG ribbon helix, regulates plasmid copy number

VNG5102H/6099H

-

TMHMM

Membrane protein, unknown function

VNG5104H/6101H

-

-

-

VNG5105H/6102H

-

Meta-Server

Hit to 1dhx, Coper binding protein

VNG5106H/6103H

-

TMHMM

Membrane protein, unknown function

VNG5108H/6105H

-

Rosetta

Hit to 1d1A2, capsid protein/transcription factor

VNG5109H/6106H

ISH8

Pfam

PF01609, transposase DDE domain

VNG5112H/6109H

-

Rosetta

Hit to 1dt9A1, translation initiation factor

VNG5114H/6111H

ISH3

-

-

VNG5115H/6112H

-

Pfam

PF00589, phage integrase family

VNG5116H/6113H

-

Meta-Server

Hit to 1d1qA, phosphotyrosine protein phosphatase

VNG5118H/6115H

-

Rosetta

1he8A3, serine/threonine protein phosphatase

VNG5119H/6116H

-

Meta-Server

1smtA, winged helix (DNA binding) in domain 1

VNG5120H/6117H

-

Rosetta

small protein, 2 hits to 1asu00 phage integrase (weak hits)

VNG5122H/6119H

ISH7

Pfam

PF01609

VNG5123H/6120H

ISH7

TMHMM

membrane protein, unknown function

VNG5124H/6121H

-

-

-

IS-element rich region 2

VNG5040H

ISH8

Pfam

PF01609

VNG5041H/5256H

-

Rosetta

-

VNG5042H/5255H Domain 1

ISH9

Rosetta

Hit to 1ez3A0, 2 long helices, no function annotation (domain 1)

VNG5042H/5255H Domain 2

ISH9

Pfam

PF01609 (domain 2)

VNG5044H/5253H

ISH5

Pfam

PF01609

VNG5045H/5252H

ISH11 (in ISH5)

Pfam

PF01609

VNG5047H/5250H

-

Rosetta

Hit to 1am3 (HIV capsid protein), 1.10.1200.30

VNG5048H/5249H

-

Rosetta

Hit to 1ais (cyclin-like fold/TBP fragment), 1.10.472.10

VNG5049H/5248H

-

Rosetta

Hit to 2ezh (transposase/transcription factor), 1.10.10.60

VNG5050H/5247H

-

Pfam

PF03551, PadR repressor

tbpB

-

known

tata-box binding protein B