WORKLIST ENTRIES (1):
LIGHTHARVSTA View alignment View Structure Light harvesting protein A chain signature
Type of fingerprint: COMPOUND with 3 elements
Links:
PRINTS; PR00674 LIGHTHARVSTB
INTERPRO; IPR002361
PROSITE; PS00968 ANTENNA_COMP_ALPHA
Creation date 07-APR-1997; UPDATE 19-JUN-1999
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.BIOCHEM. 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. 15 113-140 (1992).
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.
LIGHTHARVSTA is a 3-element fingerprint that provides a signature for
light harvesting protein A chains. The fingerprint was derived from an
initial alignment of 26 sequences: the motifs span the full alignment
length - motif 1 was drawn from the cytoplasmic domain; motif 2 spans
the TM domain and includes the conserved His (cf. PROSITE pattern
ANTENNA_COMP_ALPHA (PS00968)); and motif 3 lies in the C-terminal
periplasmic domain. Two iterations on OWL29.2 were required to reach
convergence, at which point a true set comprising 34 sequences was
identified. Three partial matches were also found, all of which are family
members that fail to make significant matches with either motif 1 or 3.
An update on SPTR37_9f identified a true set of 31 sequences, and 5
partial matches.
SUMMARY INFORMATION
31 codes involving 3 elements
5 codes involving 2 elements
COMPOSITE FINGERPRINT INDEX
3| 31 31 31
2| 5 4 1
--+----------------
| 1 2 3
True positives..
LHA3_RHOAC Q52654 LHA1_RHOPA LHA2_RHOAC
LHA5_RHOPA LHA_RHOMA Q52652 LHA4_RHOAC
LHA2_RHOPA Q52648 Q52650 O32410
LHA_RHORU LHA1_RHOCA LHA6_RHOAC O30842
O66385 O70086 LHA7_RHOAC O82944
LHA4_RHOPA LHA1_RHOAC LHA_RHOVI LHA2_RHOCA
LHA3_RHOPA LHA1_RHOTE LHA2_RHOTE LHA1_RHOSH
P95615 LHA1_RHOGE LHA_RHOMO
Subfamily: Codes involving 2 elements
Subfamily True positives..
LHA2_RHOSH LHA_ERYSP LHA_RHOTE P77799
LHA2_RHOSU
PROTEIN TITLES
LHA3_RHOAC LIGHT-HARVESTING PROTEIN B-800/850, ALPHA CHAIN (ANTENNA PIG
Q52654 PUC4A - RHODOPSEUDOMONAS ACIDOPHILA.
LHA1_RHOPA LIGHT-HARVESTING PROTEIN B-800-850, ALPHA CHAIN A (ANTENNA P
LHA2_RHOAC LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN (ANTENNA PIG
LHA5_RHOPA LIGHT-HARVESTING PROTEIN B-800-850, ALPHA CHAIN E (ANTENNA P
LHA_RHOMA LIGHT-HARVESTING PROTEIN B-880, ALPHA CHAIN (ANTENNA PIGMENT
Q52652 PUC3A - RHODOPSEUDOMONAS ACIDOPHILA.
LHA4_RHOAC LIGHT-HARVESTING PROTEIN B-800/850, ALPHA CHAIN (ANTENNA PIG
LHA2_RHOPA LIGHT-HARVESTING PROTEIN B-800-850, ALPHA CHAIN B (ANTENNA P
Q52648 PUC1A - RHODOPSEUDOMONAS ACIDOPHILA.
Q52650 PUC2A - RHODOPSEUDOMONAS ACIDOPHILA.
O32410 LIGHT HARVESTING 1 ALPHA SUBUNIT - RHODOSPIRILLUM MOLISCHIAN
LHA_RHORU LIGHT-HARVESTING PROTEIN B-870, ALPHA CHAIN PRECURSOR (LH-1)
LHA1_RHOCA LIGHT-HARVESTING PROTEIN B-870, ALPHA CHAIN (LH-1) (ANTENNA
LHA6_RHOAC LIGHT-HARVESTING PROTEIN B-880, ALPHA CHAIN (ANTENNA PIGMENT
O30842 B880 ANTENNA ALPHA-SUBUNIT - ECTOTHIORHODOSPIRA SHAPOSHNIKOV
O66385 ALPHA SUBUNIT OF LIGHT-HARVESTING 1 COMPLEX - ACIDIPHILIUM A
O70086 ALPHA SUBUNIT OF LIGHT-HARVESTING 1 COMPLEX - ACIDIPHILIUM A
LHA7_RHOAC LIGHT-HARVESTING PROTEIN B-880, ALPHA CHAIN (ANTENNA PIGMENT
O82944 ALPHA SUBUNIT OF LIGHT-HARVESTING 1 COMPLEX - CHROMATIUM VIN
LHA4_RHOPA LIGHT-HARVESTING PROTEIN B-800-850, ALPHA CHAIN D (ANTENNA P
LHA1_RHOAC LIGHT-HARVESTING PROTEIN B-800/820, ALPHA CHAIN (ANTENNA PIG
LHA_RHOVI LIGHT-HARVESTING PROTEIN B-1015, ALPHA CHAIN PRECURSOR (ANTE
LHA2_RHOCA LIGHT-HARVESTING PROTEIN B-800/850, ALPHA CHAIN (LH-2) (ANTE
LHA3_RHOPA LIGHT-HARVESTING PROTEIN B-800-850, ALPHA CHAIN C (ANTENNA P
LHA1_RHOTE LIGHT-HARVESTING POLYPEPTIDE B-885, ALPHA-1 CHAIN (LH-1) (AN
LHA2_RHOTE LIGHT-HARVESTING POLYPEPTIDE B-885, ALPHA-2 CHAIN (LH-1) (AN
LHA1_RHOSH LIGHT-HARVESTING PROTEIN B-875, ALPHA CHAIN (LH-1) (ANTENNA
P95615 LHI COMPLEX ALPHA SUBUNIT - RHODOCYCLUS GELATINOSUS (RHODOPS
LHA1_RHOGE LIGHT-HARVESTING PROTEIN B-870, ALPHA CHAIN (ANTENNA PIGMENT
LHA_RHOMO LIGHT-HARVESTING PROTEIN B-800/850, ALPHA CHAIN (ANTENNA PIG
LHA2_RHOSH LIGHT-HARVESTING PROTEIN B-800/850, ALPHA CHAIN (LH-2) (ANTE
LHA_ERYSP LIGHT-HARVESTING PROTEIN B-870, ALPHA CHAIN (ANTENNA PIGMENT
LHA_RHOTE LIGHT-HARVESTING POLYPEPTIDE B-800/860, ALPHA CHAIN (LH-2) (
P77799 LIGHT-HARVESTING B800-850 ALPHA POLYPEPTIDE - RHODOCYCLUS GE
LHA2_RHOSU LIGHT-HARVESTING PROTEIN B-800/850, ALPHA CHAIN (LH-2) (ANTE
SCAN HISTORY
OWL29_2 2 200 NSINGLE
SPTR37_9f 3 100 NSINGLE
INITIAL MOTIF SETS
LIGHTHARVSTA1 Length of motif = 8 Motif number = 1
Light harvesting protein A chain motif I - 1
PCODE ST INT
KIWTVVNP LHA2_RHOAC 5 5
KIWTVVNP LHA3_RHOAC 5 5
KIWTVVNP LHA4_RHOAC 5 5
KIWTVVKP LHA2_RHOCA 5 5
KIWLVFDP LHA1_RHOCA 6 6
KIWLVVKP LHA2_RHOSH 5 5
KIWTVVPP LHA1_RHOAC 5 5
RIWTVVNP LHA2_RHOPA 5 5
RIWTVVKP LHA1_RHOPA 5 5
RIWTVVKP LHA4_RHOPA 5 5
RIWTVVKP LHA5_RHOPA 5 5
RIWLVVKP LHA3_ECTHA 5 5
RIWTVVSP LHA3_RHOPA 5 5
KIWLIFDP LHA_ERYSP 6 6
RIWKVFDP LHA1_ECTHL 3 3
KLWLVMDP LHA1_RHOTE 7 7
KLWLVMDP LHA2_RHOTE 7 7
KIWMIFDP LHA1_RHOSH 6 6
KLWLLFDP LHA6_RHOAC 3 3
KLWLLFDP LHA7_RHOAC 3 3
RIWRLFDP LHA_RHOGE 3 3
KVWLLFDP LHA_RHOMA 3 3
RIWQLFDP LHA_RHORU 3 3
KLWLILDP LHA_RHOVI 10 10
RLWKLYDP LHA1_ECTHA 3 3
KLWKFVDF LHA2_ECTHL 3 3
LIGHTHARVSTA2 Length of motif = 20 Motif number = 2
Light harvesting protein A chain motif II - 1
PCODE ST INT
PAVGLPLLLGSVAITALLVH LHA2_RHOAC 12 -1
PSVGLPLLLGSVTVIAILVH LHA3_RHOAC 12 -1
PAIGIPALLGSVTVIAILVH LHA4_RHOAC 12 -1
PSTGIPLILGAVAVAALIVH LHA2_RHOCA 12 -1
PRRVFVAQGVFLFLLAVLIH LHA1_RHOCA 13 -1
PTVGVPLFLSAAVIASVVIH LHA2_RHOSH 12 -1
PAFGLPLMLGAVAITALLVH LHA1_RHOAC 12 -1
PGVGLPLLLGSVTVIAILVH LHA2_RHOPA 12 -1
PTVGLPLLLGSVTVIAILVH LHA1_RHOPA 12 -1
PTVGLPLLLGSVAIMVFLVH LHA4_RHOPA 12 -1
PTVGLPLLLGSVTVIAILVH LHA5_RHOPA 12 -1
PSVGLPLLLGVVLLIALLVH LHA3_ECTHA 12 -1
PTVGLPLLLGSVAAIAFAVH LHA3_RHOPA 12 -1
PRRVFVAQGVFLFLLAAMIH LHA_ERYSP 13 -1
PRRILIATAIWLIIIALTIH LHA1_ECTHL 10 -1
PRTVMIGTAAWLGVLALLIH LHA1_RHOTE 14 -1
PRTVMIGTAAWLGVLALLIH LHA2_RHOTE 14 -1
PRRVFVAQGVFLFLLAVMIH LHA1_RHOSH 13 -1
PRRALVALSAFLFVLALIIH LHA6_RHOAC 10 -1
PRRTLVALSAFLFVLGLIIH LHA7_RHOAC 10 -1
PMRAMVAQAVFLLGLAVLIH LHA_RHOGE 10 -1
PRRTLVALFTFLFVLALLIH LHA_RHOMA 10 -1
PRQALVGLATFLFVLALLIH LHA_RHORU 10 -1
PRRVLTALFVYLTVIALLIH LHA_RHOVI 17 -1
PRRVLIGIFSWLAVLALVIH LHA1_ECTHA 10 -1
FRMTAVGFHIFFALIAFAVH LHA2_ECTHL 10 -1
LIGHTHARVSTA3 Length of motif = 12 Motif number = 3
Light harvesting protein A chain motif III - 1
PCODE ST INT
HLAVLTHTTWFP LHA2_RHOAC 31 -1
HAAVLSHTTWFP LHA3_RHOAC 31 -1
HLAILSHTTWFP LHA4_RHOAC 31 -1
HAGLLTNTTWFA LHA2_RHOCA 31 -1
HLILLSTPAFNW LHA1_RHOCA 32 -1
HAAVLTTTTWLP LHA2_RHOSH 31 -1
HAAVLTHTTWYA LHA1_RHOAC 31 -1
HYAVLSNTTWFP LHA2_RHOPA 31 -1
HFAVLSHTTWFS LHA1_RHOPA 31 -1
HFAVLTHTTWVA LHA4_RHOPA 31 -1
HFAVLSNTTWFS LHA5_RHOPA 31 -1
HGAILTNTSWYP LHA3_ECTHA 31 -1
HFAVLENTSWVA LHA3_RHOPA 31 -1
HLVVLSSGLNWF LHA_ERYSP 32 -1
HVILMTTERFNW LHA1_ECTHL 29 -1
HFLLLGTERFNW LHA1_RHOTE 33 -1
HFLLLGTERFNW LHA2_RHOTE 33 -1
HLILLSTPSYNW LHA1_RHOSH 32 -1
HFIALSTDRFNW LHA6_RHOAC 29 -1
HFISLSTDRFNW LHA7_RHOAC 29 -1
HLMLLGTNKYNW LHA_RHOGE 29 -1
HFILLSTDRFNW LHA_RHOMA 29 -1
HFILLSTERFNW LHA_RHORU 29 -1
HFGLLSTDRLNW LHA_RHOVI 36 -1
HFILLSTDRFNW LHA1_ECTHA 29 -1
HFACISSERFNW LHA2_ECTHL 29 -1
FINAL MOTIF SETS
LIGHTHARVSTA1 Length of motif = 8 Motif number = 1
Light harvesting protein A chain motif I - 3
PCODE ST INT
KIWTVVNP LHA3_RHOAC 5 5
KIWTVVNP Q52654 5 5
RIWTVVKP LHA1_RHOPA 5 5
KIWTVVNP LHA2_RHOAC 5 5
RIWTVVKP LHA5_RHOPA 5 5
KVWLLFDP LHA_RHOMA 3 3
KIWTVVNP Q52652 5 5
KIWTVVNP LHA4_RHOAC 5 5
RIWTVVNP LHA2_RHOPA 5 5
KIWTVVDP Q52648 5 5
KIWTVVNP Q52650 5 5
KIWTLYDP O32410 3 3
RIWQLFDP LHA_RHORU 3 3
KIWLVFDP LHA1_RHOCA 6 6
KLWLLFDP LHA6_RHOAC 3 3
RVWLLFDP O30842 3 3
RMWLLFDP O66385 3 3
RMWLLFDP O70086 3 3
KLWLLFDP LHA7_RHOAC 3 3
KIWLLVDP O82944 7 7
RIWTVVKP LHA4_RHOPA 5 5
KIWTVVPP LHA1_RHOAC 5 5
KLWLILDP LHA_RHOVI 10 10
KIWTVVKP LHA2_RHOCA 5 5
RIWTVVSP LHA3_RHOPA 5 5
KLWLVMDP LHA1_RHOTE 7 7
KLWLVMDP LHA2_RHOTE 7 7
KIWMIFDP LHA1_RHOSH 6 6
RIWRLFDP P95615 3 3
RIWRLFDP LHA1_RHOGE 3 3
KIWLVINP LHA_RHOMO 8 8
LIGHTHARVSTA2 Length of motif = 20 Motif number = 2
Light harvesting protein A chain motif II - 3
PCODE ST INT
PSVGLPLLLGSVTVIAILVH LHA3_RHOAC 12 -1
PSVGLPLLLGSVTVIAILVH Q52654 12 -1
PTVGLPLLLGSVTVIAILVH LHA1_RHOPA 12 -1
PAVGLPLLLGSVAITALLVH LHA2_RHOAC 12 -1
PTVGLPLLLGSVTVIAILVH LHA5_RHOPA 12 -1
PRRTLVALFTFLFVLALLIH LHA_RHOMA 10 -1
PAIGLPLLLGSVAITALLVH Q52652 12 -1
PAIGIPALLGSVTVIAILVH LHA4_RHOAC 12 -1
PGVGLPLLLGSVTVIAILVH LHA2_RHOPA 12 -1
PAVGIPLLLGSVAVTALLVH Q52648 12 -1
PAVGFPLLLGSVAITALLVH Q52650 12 -1
PRRTLTALFTFLTVLGLLIH O32410 10 -1
PRQALVGLATFLFVLALLIH LHA_RHORU 10 -1
PRRVFVAQGVFLFLLAVLIH LHA1_RHOCA 13 -1
PRRALVALSAFLFVLALIIH LHA6_RHOAC 10 -1
PRRALVALFTVPGVLALLIH O30842 10 -1
PRRVLTALGVFLFALAILIH O66385 10 -1
PRRVLTALGVFLFALAILIH O70086 10 -1
PRRTLVALSAFLFVLGLIIH LHA7_RHOAC 10 -1
PRRILIAVFAFLTVLGLAIH O82944 14 -1
PTVGLPLLLGSVAIMVFLVH LHA4_RHOPA 12 -1
PAFGLPLMLGAVAITALLVH LHA1_RHOAC 12 -1
PRRVLTALFVYLTVIALLIH LHA_RHOVI 17 -1
PSTGIPLILGAVAVAALIVH LHA2_RHOCA 12 -1
PTVGLPLLLGSVAAIAFAVH LHA3_RHOPA 12 -1
PRTVMIGTAAWLGVLALLIH LHA1_RHOTE 14 -1
PRTVMIGTAAWLGVLALLIH LHA2_RHOTE 14 -1
PRRVFVAQGVFLFLLAVMIH LHA1_RHOSH 13 -1
PMRAMVAQAVFLLGLAVLIH P95615 10 -1
PMRAMVAQAVFLLGLAVLIH LHA1_RHOGE 10 -1
PSTWLPVIWIVATVVAIAVH LHA_RHOMO 15 -1
LIGHTHARVSTA3 Length of motif = 12 Motif number = 3
Light harvesting protein A chain motif III - 3
PCODE ST INT
HAAVLSHTTWFP LHA3_RHOAC 31 -1
HLAVLSNTKWFP Q52654 31 -1
HFAVLSHTTWFS LHA1_RHOPA 31 -1
HLAVLTHTTWFP LHA2_RHOAC 31 -1
HFAVLSNTTWFS LHA5_RHOPA 31 -1
HFILLSTDRFNW LHA_RHOMA 29 -1
HLAVLTHTTWFP Q52652 31 -1
HLAILSHTTWFP LHA4_RHOAC 31 -1
HYAVLSNTTWFP LHA2_RHOPA 31 -1
HLAILQNTTWFP Q52648 31 -1
HLAVLTHTTWFP Q52650 31 -1
HFLLLSTDRFNW O32410 29 -1
HFILLSTERFNW LHA_RHORU 29 -1
HLILLSTPAFNW LHA1_RHOCA 32 -1
HFIALSTDRFNW LHA6_RHOAC 29 -1
HFILLSTERFNW O30842 29 -1
HFILLSTPRFDW O66385 29 -1
HFILLSTPRFDW O70086 29 -1
HFISLSTDRFNW LHA7_RHOAC 29 -1
HMILLSTAEFNW O82944 33 -1
HFAVLTHTTWVA LHA4_RHOPA 31 -1
HAAVLTHTTWYA LHA1_RHOAC 31 -1
HFGLLSTDRLNW LHA_RHOVI 36 -1
HAGLLTNTTWFA LHA2_RHOCA 31 -1
HFAVLENTSWVA LHA3_RHOPA 31 -1
HFLLLGTERFNW LHA1_RHOTE 33 -1
HFLLLGTERFNW LHA2_RHOTE 33 -1
HLILLSTPSYNW LHA1_RHOSH 32 -1
HLMLLGTNKYNW P95615 29 -1
HLMLLGTNKYNW LHA1_RHOGE 29 -1
HAAVLAAPGFNW LHA_RHOMO 34 -1
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