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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