YRC Public Data Repository - Protein Structure Prediction

Protein:	NIKR_PYRAB
Organism:	Pyrococcus abyssi GE5
Length:	138 amino acids
Reference:	Drew K, et al. (2011) The proteome folding project: Proteome-scale prediction of structure and function. Genome Res. 2011 Sep 16

[What does the above image mean?]

[Show Ginzu Version Information]

Top Sequence Alignment Hits

Listed below are up to the top 10 sequence alignment matches, by species, for the PSI-BLAST search against the protein sequence for NIKR_PYRAB.

Description	E-value	Query Range	Subject Range
NIKR_PYRHO - Putative nickel-responsive regulator OS=Pyrococcus horikoshii (strain ATCC 700860 / DSM 12428 / JCM ... NIKR_PYRHO - Putative nickel-responsive regulator OS=Pyrococcus horikoshii GN=PH0601 PE=1 SV=1	182.0	[0..1]	[138..1]
NIKR_DESAG - Putative nickel-responsive regulator OS=Desulfovibrio alaskensis (strain G20) GN=Dde_2956 PE=3 SV=1	180.0	[0..4]	[137..5]
NIKR_DESVV - Putative nickel-responsive regulator OS=Desulfovibrio vulgaris subsp. vulgaris (strain DP4) GN=Dvul_... gi\|241878338, gi... - gi\|241909299\|ref\|ZP_04793845.1\| putative transcriptional regulator, CopG family [Desulfovibrio vulga... NIKR_DESVH - Putative nickel-responsive regulator OS=Desulfovibrio vulgaris (strain Hildenborough / ATCC 29579 / ...	180.0	[0..4]	[137..5]
gi\|48840950, gi\|... - gi\|73668054\|ref\|YP_304069.1\| CopG family transcriptional regulator [Methanosarcina barkeri str. Fusa...	179.0	[0..2]	[137..4]
NIKR_METAR - Putative nickel-responsive regulator OS=Methanocella arvoryzae (strain DSM 22066 / NBRC 105507 / MRE...	179.0	[0..2]	[137..4]
NIKR_PYRFU - Putative nickel-responsive regulator OS=Pyrococcus furiosus (strain ATCC 43587 / DSM 3638 / JCM 8422... NIKR_PYRFU - Putative nickel-responsive regulator OS=Pyrococcus furiosus GN=PF0322 PE=3 SV=1	179.0	[0..1]	[138..1]
NIKR_PYRKO - Putative nickel-responsive regulator OS=Pyrococcus kodakaraensis GN=TK1439 PE=3 SV=1 NIKR_THEKO - Putative nickel-responsive regulator OS=Thermococcus kodakarensis (strain ATCC BAA-918 / JCM 12380 /...	179.0	[0..1]	[138..1]
gi\|20905255, gi\|... - gi\|21226944\|ref\|NP_632866.1\| hypothetical protein MM_0842 [Methanosarcina mazei Go1], gi\|20905255\|gb...	178.0	[0..2]	[137..31]
NIKR3_METAC - Putative nickel-responsive regulator 3 OS=Methanosarcina acetivorans (strain ATCC 35395 / DSM 2834 /... NIKR3_METAC, NIK... - Putative nickel-responsive regulator 3 OS=Methanosarcina acetivorans GN=MA_4075 PE=3 SV=1, (Q8TIR7) ...	178.0	[0..2]	[137..4]
NIKR_METBU - Putative nickel-responsive regulator OS=Methanococcoides burtonii (strain DSM 6242 / NBRC 107633 / O...	176.0	[0..2]	[137..4]

Back

Predicted Domain #1

Region A:
Residues: [1-138]

      1          11         21         31         41         51         
      |          |          |          |          |          |          
    1 MDLVRFSISI PAELLEKFDR IIEEIGYENR SEAIRDLIRD FIIRREWEVG NEEVAGTITI  60
   61 VYNHDEGDVV KELLDLQHEY LDEIISTLHV HMDEHNCLEV IVVKGKAKRI KMIASRLMSL 120
  121 KGVKHGKLVM TSTGKELL

[Run NCBI BLAST on this sequence.]

Detection Method:	PSI-BLAST
Confidence:	46.39794
Match:	2bj1A
Description:	NIKR IN OPEN CONFORMATION AND NICKEL BOUND TO HIGH-AFFINITY SITES
Matching Structure (courtesy of the PDB):

TMHMM	2.0c	PSIPRED	v2.61
SignalP	3.0	COILS	1999
DISOPRED	v0.1	NCBI nr	06/2007
PSI-BLAST	2.2.18	FFAS	ffas03
PDB	06/2007	Pfam	22
HMMER	2.3.2

View Structure Prediction Details

Top Sequence Alignment Hits