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PR00674

Identifier
LIGHTHARVSTB  [View Relations]  [View Alignment]  
Accession
PR00674
No. of Motifs
2
Creation Date
06-APR-1997  (UPDATE 19-JUN-1999)
Title
Light harvesting protein B chain signature
Database References

PROSITE; PS00969 ANTENNA_COMP_BETA
BLOCKS; BL00969
INTERPRO; IPR002362
Literature References
1. WAGNER-HUBER, R., BRUNISHOLZ, R.A., BISSIG, I., FRANK, G., SUTER, F.
AND ZUBER, H.
The primary structure of the antenna polypeptides of Ectothiorhodospira
halochloris and Ectothiorhodospira halophila - 4 core-type antenna
polypeptides in E.halochloris and E.halophila.
EUR.J.BIOCHEMISTRY 205 917-925 (1992).
 
2. BRUNISHOLZ, R.A. AND ZUBER, H.
Structure, function and organization of antenna polypeptides and antenna
complexes from the 3 families of Rhodospirillaneae.
J.PHOTOCHEM.PHOTOBIOL. B15 113-140 (1992).

Documentation
The antenna complexes of photosynthetic bacteria function as light-
harvesting systems that absorb light and transfer the excitation energy
to the reaction centers. The antenna complexes usually comprise 2
polypeptides (alpha- and beta-chains), 2-3 bacteriochlorophyll molecules
and some carotenoids [1,2].
 
The alpha- and beta-chains are small proteins of 40-70 residues. Each has 
an N-terminal hydrophilic cytoplasmic domain, a single transmembrane (TM)
region, and a small C-terminal hydrophilic periplasmic domain. In both
chains, the TM domain houses a conserved His residue, presumed to be
involved in binding the magnesium atom of a bacteriochlorophyll group.
The beta-chains are characterised by a further histidine at the C-terminal
extremity of the cytoplasmic domain, which is also thought to be involved
in bacteriochlorophyll binding.
 
LIGHTHARVSTB is a 2-element fingerprint that provides a signature for 
light harvesting protein B chains. The fingerprint was derived from an
initial alignment of 15 sequences: the motifs span the full alignment
length - motif 1 was drawn from the cytoplasmic domain and includes the
first conserved His; and motif 2 spans the TM domain and includes the
second His (cf. PROSITE pattern ANTENNA_COMP_BETA (PS00969)). Two iterations
on OWL29.1 were required to reach convergence, at which point a true set
comprising 35 sequences was identified.
 
An update on SPTR37_9f identified a true set of 36 sequences.
Summary Information
36 codes involving  2 elements
Composite Feature Index
23636
12
True Positives
LHB1_RHOAC    LHB1_RHOCA    LHB1_RHOGE    LHB1_RHOMO    
LHB1_RHOPA LHB1_RHOSH LHB1_RHOTE LHB2_ECTHL
LHB2_RHOAC LHB2_RHOCA LHB2_RHOMO LHB2_RHOPA
LHB2_RHOSH LHB2_RHOSU LHB2_RHOTE LHB3_RHOAC
LHB3_RHOGE LHB3_RHOPA LHB4_RHOAC LHB4_RHOPA
LHB5_RHOAC LHB6_RHOAC LHB7_RHOAC LHB_ERYSP
LHB_RHOMA LHB_RHORU LHB_RHOTE LHB_RHOVI
O30841 O32409 O70094 O82943
O82948 Q52649 Q52651 Q52653
Sequence Titles
LHB1_RHOAC  LIGHT-HARVESTING PROTEIN B-800/820, BETA CHAIN (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOPSEUDOMONAS ACIDOPHILA. 
LHB1_RHOCA LIGHT-HARVESTING PROTEIN B-870, BETA CHAIN (LH-2) (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
LHB1_RHOGE LIGHT-HARVESTING PROTEIN B-870, BETA CHAIN (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOCYCLUS GELATINOSUS (RHODOPSEUDOMONAS GELATINOSA).
LHB1_RHOMO LIGHT-HARVESTING PROTEIN B-800/850, BETA 1 CHAIN (ANTENNA PIGMENT PROTEIN, BETA 1 CHAIN) - RHODOSPIRILLUM MOLISCHIANUM.
LHB1_RHOPA LIGHT-HARVESTING PROTEIN B-800-850, BETA CHAIN A (ANTENNA PIGMENT PROTEIN, BETA CHAIN A) (LH II-A BETA) - RHODOPSEUDOMONAS PALUSTRIS.
LHB1_RHOSH LIGHT-HARVESTING PROTEIN B-875, BETA CHAIN (LH-3A) (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
LHB1_RHOTE LIGHT-HARVESTING POLYPEPTIDE B-885, BETA-1 CHAIN (LH-1) (ANTENNA PIGMENT POLYPEPTIDE, BETA-1 CHAIN) - RHODOCYCLUS TENUIS (RHODOSPIRILLUM TENUE).
LHB2_ECTHL LIGHT-HARVESTING PROTEIN B800/830/1020, BETA-2 CHAIN (EHS-BETA-2) (ANTENNA PIGMENT PROTEIN, BETA-2 CHAIN) - ECTOTHIORHODOSPIRA HALOCHLORIS.
LHB2_RHOAC LIGHT-HARVESTING PROTEIN B-800/820, BETA-1 CHAIN (ANTENNA PIGMENT PROTEIN, BETA-1 CHAIN) - RHODOPSEUDOMONAS ACIDOPHILA.
LHB2_RHOCA LIGHT-HARVESTING PROTEIN B-800/850, BETA CHAIN (LH-3B) (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOBACTER CAPSULATUS (RHODOPSEUDOMONAS CAPSULATA).
LHB2_RHOMO LIGHT-HARVESTING PROTEIN B-800/850, BETA 2 CHAIN (ANTENNA PIGMENT PROTEIN, BETA 2 CHAIN) - RHODOSPIRILLUM MOLISCHIANUM.
LHB2_RHOPA LIGHT-HARVESTING PROTEIN B-800-850, BETA CHAIN B (ANTENNA PIGMENT PROTEIN, BETA CHAIN B) (LH II-B BETA) - RHODOPSEUDOMONAS PALUSTRIS.
LHB2_RHOSH LIGHT-HARVESTING PROTEIN B-800/850, BETA CHAIN (LH-3B) (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOBACTER SPHAEROIDES (RHODOPSEUDOMONAS SPHAEROIDES).
LHB2_RHOSU LIGHT-HARVESTING PROTEIN B-800/850, BETA CHAIN (LH-3B) (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOVULUM SULFIDOPHILUM (RHODOBACTER SULFIDOPHILUS).
LHB2_RHOTE LIGHT-HARVESTING POLYPEPTIDE B-885, BETA-2 CHAIN (LH-1) (ANTENNA PIGMENT POLYPEPTIDE, BETA-2 CHAIN) - RHODOCYCLUS TENUIS (RHODOSPIRILLUM TENUE).
LHB3_RHOAC LIGHT-HARVESTING PROTEIN B-800/820, BETA-2 CHAIN (ANTENNA PIGMENT PROTEIN, BETA-2 CHAIN) - RHODOPSEUDOMONAS ACIDOPHILA.
LHB3_RHOGE LIGHT-HARVESTING PROTEIN B-800/850, BETA CHAIN (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOCYCLUS GELATINOSUS (RHODOPSEUDOMONAS GELATINOSA).
LHB3_RHOPA LIGHT-HARVESTING PROTEIN B-800-850, BETA CHAIN C (ANTENNA PIGMENT PROTEIN, BETA CHAIN C) (LH II-C BETA) - RHODOPSEUDOMONAS PALUSTRIS.
LHB4_RHOAC LIGHT-HARVESTING PROTEIN B-800-850, BETA CHAIN (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOPSEUDOMONAS ACIDOPHILA.
LHB4_RHOPA LIGHT-HARVESTING PROTEIN B-800-850, BETA CHAIN D (ANTENNA PIGMENT PROTEIN, BETA CHAIN D) (LH II-D BETA) - RHODOPSEUDOMONAS PALUSTRIS.
LHB5_RHOAC LIGHT-HARVESTING PROTEIN B-800/850, BETA CHAIN (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOPSEUDOMONAS ACIDOPHILA.
LHB6_RHOAC LIGHT-HARVESTING PROTEIN B-880, BETA CHAIN (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOPSEUDOMONAS ACIDOPHILA.
LHB7_RHOAC LIGHT-HARVESTING PROTEIN B-880, BETA CHAIN (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOPSEUDOMONAS ACIDOPHILA.
LHB_ERYSP LIGHT-HARVESTING PROTEIN B-870, BETA CHAIN (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - ERYTHROBACTER SP. (STRAIN OCH 114).
LHB_RHOMA LIGHT-HARVESTING PROTEIN B-880, BETA CHAIN (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOPSEUDOMONAS MARINA (RHODOBIUM MARINUM).
LHB_RHORU LIGHT-HARVESTING PROTEIN B-870, BETA CHAIN PRECURSOR (LH-1) (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOSPIRILLUM RUBRUM.
LHB_RHOTE LIGHT-HARVESTING POLYPEPTIDE B-800/860, BETA CHAIN (LH-2) (ANTENNA PIGMENT POLYPEPTIDE, BETA CHAIN) - RHODOCYCLUS TENUIS (RHODOSPIRILLUM TENUE).
LHB_RHOVI LIGHT-HARVESTING PROTEIN B-1015, BETA CHAIN PRECURSOR (ANTENNA PIGMENT PROTEIN, BETA CHAIN) - RHODOPSEUDOMONAS VIRIDIS.
O30841 B880 ANTENNA BETA-SUBUNIT - ECTOTHIORHODOSPIRA SHAPOSHNIKOVII.
O32409 LIGHT HARVESTING 1 BETA SUBUNIT - RHODOSPIRILLUM MOLISCHIANUM.
O70094 BETA SUBUNIT OF LIGHT-HARVESTING 1 COMPLEX - ACIDIPHILIUM ANGUSTUM, AND ACIDIPHILIUM RUBRUM.
O82943 BETA SUBUNIT OF LIGHT-HARVESTING 1 COMPLEX - CHROMATIUM VINOSUM.
O82948 2ND BETA SUBUNIT OF LIGHT-HARVESTING 1 COMPLEX - CHROMATIUM VINOSUM.
Q52649 PUC2B - RHODOPSEUDOMONAS ACIDOPHILA.
Q52651 PUC3B - RHODOPSEUDOMONAS ACIDOPHILA.
Q52653 PUC4B - RHODOPSEUDOMONAS ACIDOPHILA.
Scan History
OWL29_1    2  100  NSINGLE    
SPTR37_9f 3 70 NSINGLE
Initial Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
GLSDEEAKEFHSIFMQSFLIF LHB1_ECTHA 8 8 -
GLTVEESEELHKHVIDGTRIF LHB1_RHOPA 7 7 -
GLTIAESEELHKHVIDGTRIF LHB2_RHOPA 11 11 -
GLTIAESEELHKHVIDGSRIF LHB4_RHOPA 12 12 -
GLTAAESEELHKHVIDGTRVF LHB4_RHOAC 9 9 -
GLTIAESEEIHKHVIDGARIF LHB3_RHOPA 12 12 -
VLTSEQAEELHKHVIDGTRVF LHB1_RHOAC 3 3 -
TLTAEQSEELHKYVIDGTRVF LHB5_RHOAC 2 2 -
PLTADQAEELHKYVIDGARAF LHB2_RHOAC 4 4 -
VLSPEQSEELHKYVIDGARAF LHB3_RHOAC 2 2 -
GVSDAEAKEFHALFVSSFTAF LHB7_RHOAC 9 9 -
GITEGEAKEFHKIFTSSILVF LHB_RHORU 11 11 -
GLTDEQAQELHSVYMSGLWLF LHB1_RHOSH 10 10 -
GLTDEQAQELHSVYMSGLFLF LHB_ERYSP 10 10 -
GLTDEQAQELHAVYMSGLSAF LHB1_RHOCA 10 10 -

Motif 2 width=18
Element Seqn Id St Int Rpt
FIAVAVLAHLAVMIWRPW LHB1_RHOCA 30 -1 -
FTAVAVVAHFLAWAWRPW LHB1_ECTHA 28 -1 -
FGAIAIVAHFLAYVYSPW LHB1_RHOPA 27 -1 -
FGAIAIVAHFLAYVYSPW LHB2_RHOPA 31 -1 -
FVAIAIVAHFLAYVYSPW LHB4_RHOPA 32 -1 -
FFVIAIFAHVLAFAFSPW LHB4_RHOAC 29 -1 -
FVAIAIVAHFLAYVYSPW LHB3_RHOPA 32 -1 -
FLVIAAIAHFLAFTLTPW LHB1_RHOAC 23 -1 -
FLGLALVAHFLAFSATPW LHB5_RHOAC 22 -1 -
FVAIAAFAHVLAYSLTPW LHB2_RHOAC 24 -1 -
FLGIALVAHFLAFSATPW LHB3_RHOAC 22 -1 -
FIVIAVLAHVLAWAWRPW LHB7_RHOAC 29 -1 -
FFGVAAFAHLLVWIWRPW LHB_RHORU 31 -1 -
FSAVAIVAHLAVYIWRPW LHB1_RHOSH 30 -1 -
FAAVAVVAHLATYIWRPW LHB_ERYSP 30 -1 -
Final Motifs
Motif 1  width=21
Element Seqn Id St Int Rpt
GLTVEESEELHKHVIDGTRIF LHB1_RHOPA 7 7 -
GLTAAEAEELHKYVIDGTRVF Q52653 9 9 -
GLTIAESEELHKHVIDGTRIF LHB2_RHOPA 11 11 -
GLTIAESEELHKHVIDGSRIF LHB4_RHOPA 12 12 -
GLTLAEAEEVHKQLIDGTRVF LHB2_RHOSU 11 11 -
GLTAAESEELHKHVIDGTRVF LHB4_RHOAC 9 9 -
GLTIAESEEIHKHVIDGARIF LHB3_RHOPA 12 12 -
GLTVAEAEELHTYVTNGFRVF LHB_RHOTE 10 10 -
GLTDDEAQEFHKFWVQGFVGF LHB1_RHOGE 10 10 -
GLTEGEAREFHGVFMTSFMVF LHB_RHOMA 11 11 -
VLTSEQAEELHKHVIDGTRVF LHB1_RHOAC 3 3 -
GLTVAEAEEVHKQLILGTRVF LHB2_RHOSH 11 11 -
GLTTAEAEELQKGLVDGTRVF LHB3_RHOGE 12 12 -
VLTPEQSEELHKYVIDGARVF Q52651 3 3 -
TLTAEQSEELHKYVIDGTRVF LHB5_RHOAC 2 2 -
GLTEDEAMEFHGVFMTSMMGF O30841 11 11 -
PLTADQAEELHKYVIDGARAF LHB2_RHOAC 4 4 -
VLSPEQSEELHKYVIDGARAF LHB3_RHOAC 2 2 -
VLSPEQSEELHKYVIDGARVF Q52649 3 3 -
GLTEREAKEFHSIFVMSFIGF O70094 14 14 -
GLTEDEAREFHGIFVSSFVVF O82948 10 10 -
GLSESEAQEFHGIFVTSFISF O32409 14 14 -
GLTEQEAQEFHGIFVQSMTAF O82943 8 8 -
GVSDAEAKEFHALFVSSFTAF LHB7_RHOAC 9 9 -
GLSLKEAEEIHSYLIDGTRVF LHB2_RHOCA 10 10 -
GITEGEAKEFHKIFTSSILVF LHB_RHORU 11 11 -
GLTDEQAQELHSVYMSGLWLF LHB1_RHOSH 10 10 -
GVSDAEAKEFHALFVSSFMGF LHB6_RHOAC 9 9 -
GLTDEQAQELHSVYMSGLFLF LHB_ERYSP 10 10 -
GLTDEQAQELHAVYMSGLSAF LHB1_RHOCA 10 10 -
GLTEEEAVAVHAQFQTTFSAF LHB2_RHOMO 7 7 -
GLTEEEAIAVHDQFKTTFSAF LHB1_RHOMO 7 7 -
GLTEQEAQEFGTLYTQGVAFV LHB1_RHOTE 9 9 -
GLTEQEAQEFGTLYTQGVAFV LHB2_RHOTE 9 9 -
GLTEEEAKEFHGIFVTSTVLY LHB_RHOVI 9 9 -
GLTDEECQEIHEMNMLGMHAY LHB2_ECTHL 6 6 -

Motif 2 width=18
Element Seqn Id St Int Rpt
FGAIAIVAHFLAYVYSPW LHB1_RHOPA 27 -1 -
FFVIAIFAHVLAFAFSPW Q52653 29 -1 -
FGAIAIVAHFLAYVYSPW LHB2_RHOPA 31 -1 -
FVAIAIVAHFLAYVYSPW LHB4_RHOPA 32 -1 -
FGAIALFAHFLAAIATPW LHB2_RHOSU 31 -1 -
FFVIAIFAHVLAFAFSPW LHB4_RHOAC 29 -1 -
FVAIAIVAHFLAYVYSPW LHB3_RHOPA 32 -1 -
FVGIAVVAHVLVFAAHPW LHB_RHOTE 30 -1 -
FTAVAVVAHFLVWVWRPW LHB1_RHOGE 30 -1 -
FIAVAIVAHILAWMWRPW LHB_RHOMA 31 -1 -
FLVIAAIAHFLAFTLTPW LHB1_RHOAC 23 -1 -
FGGMALIAHFLAAAATPW LHB2_RHOSH 31 -1 -
FGVIAVLAHILAYAYTPW LHB3_RHOGE 32 -1 -
FLGVALVAHFLAFSATPW Q52651 23 -1 -
FLGLALVAHFLAFSATPW LHB5_RHOAC 22 -1 -
FLAVAAVAHVLAWMWRPW O30841 31 -1 -
FVAIAAFAHVLAYSLTPW LHB2_RHOAC 24 -1 -
FLGIALVAHFLAFSATPW LHB3_RHOAC 22 -1 -
FLGIALVAHFLAFSMTPW Q52649 23 -1 -
FVIIAVIAHFLVWQWRPW O70094 34 -1 -
FTGIVVVAHILVWLWRPW O82948 30 -1 -
FIVVAIDAHFLAWKWRPW O32409 34 -1 -
FFGIVVIAHILAWLWRPW O82943 28 -1 -
FIVIAVLAHVLAWAWRPW LHB7_RHOAC 29 -1 -
FGAMALVAHILSAIATPW LHB2_RHOCA 30 -1 -
FFGVAAFAHLLVWIWRPW LHB_RHORU 31 -1 -
FSAVAIVAHLAVYIWRPW LHB1_RHOSH 30 -1 -
FMVVAVLAHVLAWAWRPW LHB6_RHOAC 29 -1 -
FAAVAVVAHLATYIWRPW LHB_ERYSP 30 -1 -
FIAVAVLAHLAVMIWRPW LHB1_RHOCA 30 -1 -
FIVLAAVAHVLVWVWKPW LHB2_RHOMO 27 -1 -
FIILAAVAHVLVWVWKPW LHB1_RHOMO 27 -1 -
VAVIAVVAHALVWAWRPW LHB1_RHOTE 29 -1 -
VAVIAIVAHALVWAWRPW LHB2_RHOTE 29 -1 -
YLATAVIVHYLVWTARPW LHB_RHOVI 29 -1 -
YWSIGLIANALAYAWRPF LHB2_ECTHL 26 -1 -