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PR00251

Identifier
BACTRLOPSIN  [View Relations]  [View Alignment]  
Accession
PR00251
No. of Motifs
7
Creation Date
11-NOV-1993  (UPDATE 06-JUN-1999)
Title
Bacterial opsin signature
Database References
PRINTS; PR90007 7TM
PROSITE; PS00950 BACTERIAL_OPSIN_1; PS00327 BACTERIAL_OPSIN_RET
BLOCKS; BL00327
PFAM; PF01036 Bac_rhodopsin
INTERPRO; IPR001425
PDB; 1BRD
SCOP; 1BRD
Literature References
1. OESTERHELT, D. AND TITTOR, J.
Two pumps, one principle - Light-driven ion-transport in halobacteria.
TRENDS BIOCHEM.SCI. 14(2) 57-61 (1989).
 
2. BLANCK, A., OESTERHELT, D., FERRANDO, E., SCHEGK, E.S. AND LOTTSPEICH, F.
Primary structure of sensory rhodopsin-I, a prokaryotic photoreceptor.
EMBO J. 8(13) 3963-3971 (1989).
 
3. OTOMO, J., TOMIOKA, H. AND SASABE,H. 
Properties and the primary structure of a new halorhodopsin from 
halobacterial strain mex.
BIOCHIM.BIOPHYS.ACTA 1112 7-13 (1991).

Documentation
The bacterial opsins are retinal-binding proteins that provide light-
dependent ion transport and sensory functions to a family of halophilic 
bacteria [1,2]. They are integral membrane proteins believed to contain
7 transmembrane (TM) domains, the last of which contains the attachment
point for retinal (a conserved lysine). There are several classes of these
bacterial proteins: they include bacteriorhodopsin and archaerhodopsin,
which are light-driven proton pumps; halorhodopsin, a light-driven 
chloride pump; and sensory rhodopsin, which mediates both photoattractant
(in the red) and photophobic (in the UV) responses.
   
BACTRLOPSIN is a 7-element fingerprint that provides a signature for the
bacterial opsins. The fingerprint was derived from an initial alignment
of 5 sequences: the motifs were drawn from the 7 putative membrane-
spanning domains - motif 3 includes the region encoded by PROSITE pattern
BACTERIAL_OPSIN_1 (PS00950), which contains a functionally important Arg
residue, and motif 7 encompasses the region encoded by PROSITE pattern
BACTERIAL_OPSIN_RET (PS00327), which contains the retinal-binding lysine.
Two iterations on OWL21.2 were required to reach convergence, at which
point a true set comprising 8 sequences was identified. A single partial
match was also found, a halorhodopsin fragment [3] lacking the first and
the seventh TM domains.
 
An update on SPTR37_9f identified a true set of 15 sequences, and 5
partial matches.
Summary Information
  15 codes involving  7 elements
1 codes involving 6 elements
1 codes involving 5 elements
1 codes involving 4 elements
2 codes involving 3 elements
0 codes involving 2 elements
Composite Feature Index
715151515151515
60111111
50110111
40110011
30022011
20000000
1234567
True Positives
BAC1_HALS1    BAC2_HALS2    BAC3_HALSD    BACH_HALHP    
BACH_HALHS BACH_HALSP BACH_HALSS BACH_HALVA
BACH_NATPH BACR_HALAR BACR_HALHA BACR_HALSR
BACR_HALVA BACS_HALHA BACS_HALSS
True Positive Partials
Codes involving 6 elements
BAC3_HALVA
Codes involving 5 elements
BACT_NATPH
Codes involving 4 elements
BACT_HALVA
Codes involving 3 elements
BACT_HALSA O74631
Sequence Titles
BAC1_HALS1  ARCHAERHODOPSIN 1 PRECURSOR (AR 1) - HALOBACTERIUM SP. (STRAIN AUS-1), AND HALOBACTERIUM SP. (STRAIN SG1). 
BAC2_HALS2 ARCHAERHODOPSIN 2 PRECURSOR (AR 2) - HALOBACTERIUM SP. (STRAIN AUS-2).
BAC3_HALSD ARCHAERHODOPSIN 3 PRECURSOR (AR 3) - HALORUBRUM SODOMENSE.
BACH_HALHP HALORHODOPSIN PRECURSOR (HR) - HALOBACTERIUM HALOBIUM (STRAIN PORT).
BACH_HALHS HALORHODOPSIN PRECURSOR (HR) - HALOBACTERIUM HALOBIUM (STRAIN SHARK).
BACH_HALSP HALORHODOPSIN PRECURSOR (HR) - HALOBACTERIUM SP.
BACH_HALSS HALORHODOPSIN (HR) - HALOBACTERIUM SP. (STRAIN SG1).
BACH_HALVA CRUXHALORHODOPSIN-3 PRECURSOR (CHR-3) - HALOARCULA VALLISMORTIS.
BACH_NATPH HALORHODOPSIN (HR) - NATRONOMONAS PHARAONIS (NATRONOBACTERIUM PHARAONIS).
BACR_HALAR CRUXRHODOPSIN-1 (COP-1) (CR-1) - HALOARCULA ARGENTINOS (HALOARCULA STRAIN ARG-1).
BACR_HALHA BACTERIORHODOPSIN PRECURSOR (BR) - HALOBACTERIUM HALOBIUM.
BACR_HALSR CRUXRHODOPSIN-2 (COP-2) (CR-2) - HALOARCULA SP. (STRAIN ARG-2 / ANDES HEIGHTS).
BACR_HALVA CRUXRHODOPSIN-3 (COP-3) (CR-3) - HALOARCULA VALLISMORTIS.
BACS_HALHA SENSORY RHODOPSIN I (SR-I) - HALOBACTERIUM HALOBIUM.
BACS_HALSS SENSORY RHODOPSIN I (SR-I) - HALOBACTERIUM SP. (STRAIN SG1).

BAC3_HALVA BACTERIAL RHODOPSIN CSR3 - HALOARCULA VALLISMORTIS.

BACT_NATPH SENSORY RHODOPSIN II (SR-II) - NATRONOMONAS PHARAONIS (NATRONOBACTERIUM PHARAONIS).

BACT_HALVA SENSORY RHODOPSIN II (SR-II) - HALOARCULA VALLISMORTIS.

BACT_HALSA SENSORY RHODOPSIN II (SR-II) - HALOBACTERIUM SALINARIUM.
O74631 HEAT SHOCK PROTEIN - CORIOLUS VERSICOLOR.
Scan History
OWL21_2    2  50   NSINGLE    
OWL26_0 1 100 NSINGLE
SPTR37_9f 2 92 NSINGLE
Initial Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
LYINIALAGLSILLFVFMTR BACH_NATPH 37 37 -
LWLGIGTLLMLIGTFYFIVK BAC1_HALS1 22 22 -
LWVNVALAGIAILVFVYMGR BACH_HALSP 32 32 -
IWLALGTALMGLGTLYFLVK BACR_HALHA 23 23 -
AYLGGAVALIVGVAFVWLLY BACS_HALHA 6 6 -

Motif 2 width=21
Element Seqn Id St Int Rpt
IAVSTILVPVVSIASYTGLAS BACH_NATPH 66 9 -
YYSITILVPGIASAAYLSMFF BAC1_HALS1 53 11 -
IWGATLMIPLVSISSYLGLLS BACH_HALSP 61 9 -
FYAITTLVPAIAFTMYLSMLL BACR_HALHA 54 11 -
ALAPLAIIPVFAGLSYVGMAY BACS_HALHA 36 10 -

Motif 3 width=22
Element Seqn Id St Int Rpt
WGRYLTWALSTPMILLALGLLA BACH_NATPH 120 33 -
YARYADWLFTTPLLLLDLALLA BAC1_HALS1 91 17 -
WGRYLTWALSTPMILLALGLLA BACH_HALSP 105 23 -
WARYADWLFTTPLLLLDLALLV BACR_HALHA 92 17 -
GLRYIDWLVTTPILVGYVGYAA BACS_HALHA 70 13 -

Motif 4 width=20
Element Seqn Id St Int Rpt
LFTAITFDIAMCVTGLAAAL BACH_NATPH 148 6 -
IGTLVGVDALMIVTGLVGAL BAC1_HALS1 119 6 -
LFTVIAADIGMCVTGLAAAM BACH_HALSP 133 6 -
ILALVGADGIMIGTGLVGAL BACR_HALHA 120 6 -
IIGVMVADALMIAVGAGAVV BACS_HALHA 98 6 -

Motif 5 width=22
Element Seqn Id St Int Rpt
MRWFWYAISCACFLVVLYILLV BACH_NATPH 174 6 -
ARYTWWLFSTICMIVVLYFLAT BAC1_HALS1 144 5 -
FRWAFYAISCAFFVVVLSALVT BACH_HALSP 159 6 -
YRFVWWAISTAAMLYILYVLFF BACR_HALHA 145 5 -
LKWALFGVSSIFHLSLFAYLYV BACS_HALHA 122 4 -

Motif 6 width=19
Element Seqn Id St Int Rpt
LKLLTVVMWLGYPIVWALG BACH_NATPH 213 17 -
LTALVLVLWTAYPILWIIG BAC1_HALS1 185 19 -
LRVLTVVLWLGYPIVWAVG BACH_HALSP 198 17 -
LRNVTVVLWSAYPVVWLIG BACR_HALHA 186 19 -
LKNHIGLLWLAYPLVWLFG BACS_HALHA 162 18 -

Motif 7 width=19
Element Seqn Id St Int Rpt
WGYSFLDIVAKYIFAFLLL BACH_NATPH 245 13 -
LLFMVLDVTAKVGFGFILL BAC1_HALS1 217 13 -
WAYSVLDVFAKYVFAFILL BACH_HALSP 231 14 -
LLFMVLDVSAKVGFGLILL BACR_HALHA 218 13 -
LTYVFLDVLAKVPYVYFFY BACS_HALHA 194 13 -
Final Motifs
Motif 1  width=20
Element Seqn Id St Int Rpt
IWVNIALAGVVILLFVAMGR BACH_HALHP 33 33 -
IWVNIALAGVVILLFVAMGR BACH_HALHS 33 33 -
LWVNIALAGVVILLFVAMGR BACH_HALVA 33 33 -
LWLGIGTLLMLIGTFYFLVR BAC3_HALSD 21 21 -
LWLGIGTLLMLIGTFYFIAR BAC2_HALS2 21 21 -
LYINIALAGLSILLFVFMTR BACH_NATPH 37 37 -
LWINIALAGLSILLFVYMGR BACH_HALSS 38 38 -
LWLGIGTLLMLIGTFYFIVK BAC1_HALS1 22 22 -
IWLWLGTAGMFLGMLYFIAR BACR_HALAR 9 9 -
IWLWLGTAGMFLGMLYFIAR BACR_HALVA 9 9 -
LWVNVALAGIAILVFVYMGR BACH_HALSP 32 32 -
IFLWVGTAGMFLGMLYFIAR BACR_HALSR 16 16 -
IWLALGTALMGLGTLYFLVK BACR_HALHA 23 23 -
AYLGGAVALIVGVAFVWLLY BACS_HALHA 6 6 -
AYWIAAVAFLVGLGITAALY BACS_HALSS 8 8 -

Motif 2 width=21
Element Seqn Id St Int Rpt
IWVATMLVPLVSISSYAGLAS BACH_HALHP 62 9 -
IWVATMLVPLVSISSYAGLAS BACH_HALHS 62 9 -
IWVATMLVPLVSISSYAGLAS BACH_HALVA 62 9 -
YYAVTILVPGIASAAYLSMFF BAC3_HALSD 52 11 -
YYAITILVPGIASAAYLAMFF BAC2_HALS2 52 11 -
IAVSTILVPVVSIASYTGLAS BACH_NATPH 66 9 -
IFVATLMVPLVSISSYTGLVS BACH_HALSS 67 9 -
YYSITILVPGIASAAYLSMFF BAC1_HALS1 53 11 -
FYIATILITAIAFVNYLAMAL BACR_HALAR 40 11 -
FYIATILITAIAFVNYLAMAL BACR_HALVA 40 11 -
IWGATLMIPLVSISSYLGLLS BACH_HALSP 61 9 -
FYIATIMIAAIAFVNYLSMAL BACR_HALSR 47 11 -
FYAITTLVPAIAFTMYLSMLL BACR_HALHA 54 11 -
ALAPLAIIPVFAGLSYVGMAY BACS_HALHA 36 10 -
RLAALAVIPGFAGLAYAGMAL BACS_HALSS 38 10 -

Motif 3 width=22
Element Seqn Id St Int Rpt
WGRYLTWTFSTPMILLALGLLA BACH_HALHP 106 23 -
WGRYLTWTFSTPMILLALGLLA BACH_HALHS 106 23 -
WGRYLTWTFSTPMILLALGLLA BACH_HALVA 106 23 -
YARYADWLFTTPLLLLDLALLA BAC3_HALSD 90 17 -
YARYADWLFTTPLLLLDLALLA BAC2_HALS2 91 18 -
WGRYLTWALSTPMILLALGLLA BACH_NATPH 120 33 -
WGRYLTWALSTPMILIAVGLLA BACH_HALSS 111 23 -
YARYADWLFTTPLLLLDLALLA BAC1_HALS1 91 17 -
WARYSDWLFTTPLLLYDLGLLA BACR_HALAR 78 17 -
WARYSDWLFTTPLLLYDLGLLA BACR_HALVA 78 17 -
WGRYLTWALSTPMILLALGLLA BACH_HALSP 105 23 -
WARYTDWLFTTPLLLYDLALLA BACR_HALSR 85 17 -
WARYADWLFTTPLLLLDLALLV BACR_HALHA 92 17 -
GLRYIDWLVTTPILVGYVGYAA BACS_HALHA 70 13 -
GLRYVDWIVTTPLLVGFIGYVA BACS_HALSS 72 13 -

Motif 4 width=20
Element Seqn Id St Int Rpt
LFTAITMDIGMCVTGLAAAL BACH_HALHP 134 6 -
LFTAITMDIGMCVTGLAAAL BACH_HALHS 134 6 -
LFTAITMDIGMCITGLAAAL BACH_HALVA 134 6 -
IGTLVGVDALMIVTGLIGAL BAC3_HALSD 118 6 -
IGTLIGVDALMIVTGLIGAL BAC2_HALS2 119 6 -
LFTAITFDIAMCVTGLAAAL BACH_NATPH 148 6 -
LFTAVVADIGMCVTGLAAAL BACH_HALSS 139 6 -
IGTLVGVDALMIVTGLVGAL BAC1_HALS1 119 6 -
ITSLVSLDVLMIGTGLVATL BACR_HALAR 106 6 -
ISSLVSLDVLMIGTGLVATL BACR_HALVA 106 6 -
LFTVIAADIGMCVTGLAAAM BACH_HALSP 133 6 -
IYSLVGLDVLMIGTGALATL BACR_HALSR 113 6 -
ILALVGADGIMIGTGLVGAL BACR_HALHA 120 6 -
IIGVMVADALMIAVGAGAVV BACS_HALHA 98 6 -
IAGVMLADALMIAFGAGAVV BACS_HALSS 100 6 -

Motif 5 width=22
Element Seqn Id St Int Rpt
LRWVFYGISCAFFVAVLYVLLV BACH_HALHP 160 6 -
LRWVFYGISCAFFVAVLYVLLV BACH_HALHS 160 6 -
LRWVFYGISCAFFIAVLYVLLV BACH_HALVA 160 6 -
ARYSWWLFSTICMIVVLYFLAT BAC3_HALSD 143 5 -
ARYTWWLFSTIAFLFVLYYLLT BAC2_HALS2 144 5 -
MRWFWYAISCACFLVVLYILLV BACH_NATPH 174 6 -
LRWVWYAISCAFFVVVLYILLA BACH_HALSS 165 6 -
ARYTWWLFSTICMIVVLYFLAT BAC1_HALS1 144 5 -
ERLVWWGISTAFLLVLLYFLFS BACR_HALAR 137 11 -
ERLVWWGISTAFLLVLLYFLFS BACR_HALVA 137 11 -
FRWAFYAISCAFFVVVLSALVT BACH_HALSP 159 6 -
ERLVWWGISTGFLLVLLYFLFS BACR_HALSR 144 11 -
YRFVWWAISTAAMLYILYVLFF BACR_HALHA 145 5 -
LKWALFGVSSIFHLSLFAYLYV BACS_HALHA 122 4 -
LKWVLFGVSSIFHVTLFAYLYV BACS_HALSS 124 4 -

Motif 6 width=19
Element Seqn Id St Int Rpt
LKILTVVLWLGYPILWALG BACH_HALHP 199 17 -
LKILTVVLWLGYPILWALG BACH_HALHS 199 17 -
LKLLTVVLWLGYPILWALG BACH_HALVA 199 17 -
LTALVLVLWTAYPILWIIG BAC3_HALSD 184 19 -
LTALVAVLWTAYPILWIVG BAC2_HALS2 185 19 -
LKLLTVVMWLGYPIVWALG BACH_NATPH 213 17 -
LKVLTVVLWLGYPIFWALG BACH_HALSS 204 17 -
LTALVLVLWTAYPILWIIG BAC1_HALS1 185 19 -
LRNLVTVVWLVYPVWWLIG BACR_HALAR 178 19 -
LRNLVTVVWLVYPVWWLVG BACR_HALVA 178 19 -
LRVLTVVLWLGYPIVWAVG BACH_HALSP 198 17 -
LRNLVLVLWLVYPVLWLVG BACR_HALSR 185 19 -
LRNVTVVLWSAYPVVWLIG BACR_HALHA 186 19 -
LKNHIGLLWLAYPLVWLFG BACS_HALHA 162 18 -
LKNHVGLLWLAYPFVWLMG BACS_HALSS 164 18 -

Motif 7 width=19
Element Seqn Id St Int Rpt
WGYSGLDILAKYVFAFLLL BACH_HALHP 231 13 -
WGYSGLDILAKYVFAFLLL BACH_HALHS 231 13 -
WGYSGLDILAKYVFAFLLL BACH_HALVA 231 13 -
LLFMVLDVTAKVGFGFILL BAC3_HALSD 216 13 -
LAFMVLDVTAKVGFGFVLL BAC2_HALS2 217 13 -
WGYSFLDIVAKYIFAFLLL BACH_NATPH 245 13 -
WAYSGMDIVAKYLFAFLLL BACH_HALSS 236 13 -
LLFMVLDVTAKVGFGFILL BAC1_HALS1 217 13 -
AGFMVIDLTAKVGFGIILL BACR_HALAR 210 13 -
AGFMVIDLVAKVGFGIILL BACR_HALVA 210 13 -
WAYSVLDVFAKYVFAFILL BACH_HALSP 231 14 -
AAFMVLDLTAKIGFGIILL BACR_HALSR 217 13 -
LLFMVLDVSAKVGFGLILL BACR_HALHA 218 13 -
LTYVFLDVLAKVPYVYFFY BACS_HALHA 194 13 -
LTYAFLDVLAKVPYVYFFY BACS_HALSS 196 13 -