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PR00156

Identifier
COPPERBLUE  [View Relations]  [View Alignment]  
Accession
PR00156
No. of Motifs
3
Creation Date
06-FEB-1995  (UPDATE 14-JUN-1999)
Title
Type I copper blue protein signature
Database References
PRINTS; PR00155 AMICYANIN; PR00157 PLASTOCYANIN; PR00158 RUSTICYANIN

PROSITE; PS00196 COPPER_BLUE
BLOCKS; BL00196
INTERPRO; IPR001235
PDB; 9PCY
SCOP; 9PCY
CATH; 9PCY
Literature References
1. KALVERDA, A.P., WYMENGA, S.S., LOMMEN, A., VAN DE VEN, F.J.M.,
HILBERS, C.W. AND CANTERS, G.W.
Solution structure of the type 1 blue copper protein amicyanin from
Thiobacillus versutus.
J.MOL.BIOL. 240 358-371 (1994).
 
2. RYDEN, L.G. AND HUNT, L.T.
Evolution of protein complexity - the blue copper-containing oxidases
and related proteins.
J.MOL.EVOL. 36 41-66 (1993).

Documentation
Type I blue copper proteins are found in methylothropic bacteria, where
they appear to function as the electron acceptor to methylamine dehydro-
genase [1]. They bind a single copper atom and are characterised by an
intense electronic absorption band near 600nm [2]. Several classes of blue
copper protein have been identified, including amicyanins, azurins,
pseudoazurins, plastocyanins and rusticyanins. Based on their primary
sequences, amicyanins appear to be most closely related to the plant
plastocyanins, and are also highly similar to the pseudoazurins. By
contrast, the rusticyanins fall into a distinct subclass.
 
The fold of type I blue copper proteins is a beta-sandwich, built from
9 beta-strands. The copper atom is located between 3 loops on one end of
the molecule. Two of these loops contribute the copper ligands. The other
3 ligands are located on the loop between strands 8 and 9.
 
COPPERBLUE is a 3-element fingerprint that provides a signature for the
type I copper blue protein family. The fingerprint was derived from an 
initial alignment of 11 sequences: the motifs were drawn from conserved 
regions spanning the full alignment length, motif 3 including the Cys and
His residues involved in copper binding (cf. PROSITE pattern COPPER_BLUE
(PS00196)). Three iterations on OWL25.1 were required to reach convergence,
at which point a true set comprising 59 sequences was identified. 
 
An update on SPTR57.15_40.15f identified a true set of 179 sequences and
85 partial matches.
Summary Information
50 codes involving  3 elements
0 codes involving 2 elements
Composite Feature Index
3505050
2000
123
True Positives
AMCY_METEX    AMCY_PARDE    AMCY_PARVE    AZUP_ACHCY    
AZUP_ALCFA AZUP_METEX AZUP_PARDE AZUP_PARDT
AZUP_RHILV D112_ARATH O22646 O24185
O52830 PLAS_ANASP PLAS_ANASQ PLAS_ANAVA
PLAS_ARATH PLAS_CAPBU PLAS_CHLFU PLAS_CHLRE
PLAS_CUCPE PLAS_CUCSA PLAS_DAUCA PLAS_ENTPR
PLAS_HORVU PLAS_LACSA PLAS_LYCES PLAS_MERPE
PLAS_ORYSA PLAS_PEA PLAS_PETCR PLAS_PHAVU
PLAS_PHOLA PLAS_POPNI PLAS_PROHO PLAS_RUMOB
PLAS_SAMNI PLAS_SCEOB PLAS_SILPR PLAS_SOLCR
PLAS_SOLTU PLAS_SPIOL PLAS_SYNP7 PLAS_SYNY3
PLAS_TOBAC PLAS_ULVAR PLAS_ULVPE PLAS_VICFA
PLAT_POPNI PLAT_TOBAC
Sequence Titles
AMCY_METEX  AMICYANIN-ALPHA PRECURSOR - METHYLOBACTERIUM EXTORQUENS. 
AMCY_PARDE AMICYANIN PRECURSOR - PARACOCCUS DENITRIFICANS.
AMCY_PARVE AMICYANIN PRECURSOR - PARACOCCUS VERSUTUS (THIOBACILLUS VERSUTUS).
AZUP_ACHCY PSEUDOAZURIN PRECURSOR (BLUE COPPER PROTEIN) - ACHROMOBACTER CYCLOCLASTES.
AZUP_ALCFA PSEUDOAZURIN PRECURSOR (CUPREDOXIN) (BLUE COPPER PROTEIN) - ALCALIGENES FAECALIS.
AZUP_METEX PSEUDOAZURIN - METHYLOBACTERIUM EXTORQUENS.
AZUP_PARDE PSEUDOAZURIN - PARACOCCUS DENITRIFICANS.
AZUP_PARDT PSEUDOAZURIN PRECURSOR - PARACOCCUS DENITRIFICANS (SUBSP. THIOSPHAERA PANTOTROPHA).
AZUP_RHILV PUTATIVE PSEUDOAZURIN PRECURSOR (BLUE COPPER PROTEIN) - RHIZOBIUM LEGUMINOSARUM (BIOVAR VICIAE).
D112_ARATH DNA-DAMAGE-REPAIR/TOLERATION PROTEIN DRT112 PRECURSOR - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
O22646 PLASTOCYANIN - FRITILLARIA AGRESTIS.
O24185 PLASTOCYANIN PRECURSOR - ORYZA SATIVA (RICE).
O52830 CYTOCHROME C6 - ANABAENA SP. (STRAIN PCC 7119).
PLAS_ANASP PLASTOCYANIN PRECURSOR - ANABAENA SP. (STRAIN PCC 7120).
PLAS_ANASQ PLASTOCYANIN PRECURSOR - ANABAENA SP. (STRAIN PCC 7937).
PLAS_ANAVA PLASTOCYANIN - ANABAENA VARIABILIS.
PLAS_ARATH PLASTOCYANIN PRECURSOR - ARABIDOPSIS THALIANA (MOUSE-EAR CRESS).
PLAS_CAPBU PLASTOCYANIN - CAPSELLA BURSA-PASTORIS (SHEPHERD'S PURSE).
PLAS_CHLFU PLASTOCYANIN - CHLORELLA FUSCA.
PLAS_CHLRE PLASTOCYANIN PRECURSOR (PC6-2) - CHLAMYDOMONAS REINHARDTII.
PLAS_CUCPE PLASTOCYANIN - CUCURBITA PEPO (VEGETABLE MARROW) (SUMMER SQUASH).
PLAS_CUCSA PLASTOCYANIN - CUCUMIS SATIVUS (CUCUMBER).
PLAS_DAUCA PLASTOCYANIN - DAUCUS CAROTA (CARROT).
PLAS_ENTPR PLASTOCYANIN - ENTEROMORPHA PROLIFERA.
PLAS_HORVU PLASTOCYANIN PRECURSOR - HORDEUM VULGARE (BARLEY).
PLAS_LACSA PLASTOCYANIN - LACTUCA SATIVA (GARDEN LETTUCE).
PLAS_LYCES PLASTOCYANIN PRECURSOR - LYCOPERSICON ESCULENTUM (TOMATO).
PLAS_MERPE PLASTOCYANIN - MERCURIALIS PERENNIS (DOG'S MERCURY).
PLAS_ORYSA PLASTOCYANIN - ORYZA SATIVA (RICE).
PLAS_PEA PLASTOCYANIN PRECURSOR - PISUM SATIVUM (GARDEN PEA).
PLAS_PETCR PLASTOCYANINS A AND B - PETROSELINUM CRISPUM (PARSLEY) (PETROSELINUM HORTENSE).
PLAS_PHAVU PLASTOCYANIN - PHASEOLUS VULGARIS (KIDNEY BEAN) (FRENCH BEAN).
PLAS_PHOLA PLASTOCYANIN PRECURSOR - PHORMIDIUM LAMINOSUM.
PLAS_POPNI PLASTOCYANIN A PRECURSOR - POPULUS NIGRA (LOMBARDY POPLAR).
PLAS_PROHO PLASTOCYANIN PRECURSOR - PROCHLOROTHRIX HOLLANDICA.
PLAS_RUMOB PLASTOCYANIN - RUMEX OBTUSIFOLIUS (BITTER DOCK).
PLAS_SAMNI PLASTOCYANIN - SAMBUCUS NIGRA (EUROPEAN ELDER).
PLAS_SCEOB PLASTOCYANIN - SCENEDESMUS OBLIQUUS.
PLAS_SILPR PLASTOCYANIN PRECURSOR - SILENE PRATENSIS (WHITE CAMPION) (LYCHNIS ALBA).
PLAS_SOLCR PLASTOCYANIN - SOLANUM CRISPUM (CHILEAN POTATO-TREE).
PLAS_SOLTU PLASTOCYANIN - SOLANUM TUBEROSUM (POTATO).
PLAS_SPIOL PLASTOCYANIN PRECURSOR - SPINACIA OLERACEA (SPINACH).
PLAS_SYNP7 PLASTOCYANIN PRECURSOR - SYNECHOCOCCUS SP. (STRAIN PCC 7942) (ANACYSTIS NIDULANS R2).
PLAS_SYNY3 PLASTOCYANIN PRECURSOR - SYNECHOCYSTIS SP. (STRAIN PCC 6803).
PLAS_TOBAC PLASTOCYANIN A'/A'' - NICOTIANA TABACUM (COMMON TOBACCO).
PLAS_ULVAR PLASTOCYANIN - ULVA ARASAKII (SEA LETTUCE).
PLAS_ULVPE PLASTOCYANIN - ULVA PERTUSA (SEA LETTUCE).
PLAS_VICFA PLASTOCYANIN - VICIA FABA (BROAD BEAN).
PLAT_POPNI PLASTOCYANIN B PRECURSOR - POPULUS NIGRA (LOMBARDY POPLAR).
PLAT_TOBAC PLASTOCYANIN B'/B'' - NICOTIANA TABACUM (COMMON TOBACCO).
Scan History
OWL25_1    3  200  NSINGLE    
SPTR37_9f 3 200 NSINGLE
Initial Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
TIKAGETVYWVNGE AMCY_THIVE 37 37 -
HVKVGDTVTWINRE NRL_1AAJ 36 36 -
HVKVGDTVTWINRE NRL_1AAN 36 36 -
HVKVGDTVTWINRE NRL_2MTAA 36 36 -
KANPGDTVTFIPVD NRL_1PAZ 24 24 -
SVSAGEKITFKNNA PLAS_LYCES 91 91 -
SISPGEKIVFKNNA PLAS_POPNI 20 20 -
TIKPGDTVEFLNNK PLAS_ANASQ 56 56 -
HVKVGDTVTWINRE AMCY_PARDE 62 62 -
KANPGDTVTFIPVD AZUP_ALCFA 47 47 -
RIKAGSAVTWTNTE AMCY_METEX 50 50 -

Motif 2 width=16
Element Seqn Id St Int Rpt
FPHNIVFDEDSIPSGV PLAS_POPNI 35 1 -
PPHNVVFDATLNPAKS PLAS_ANASQ 71 1 -
MPHNVHFVAGVLGEAA AMCY_PARDE 77 1 -
KGHNVESIKDMIPEGA AZUP_ALCFA 61 0 -
LPHNVHFKSGPGVEKD AMCY_METEX 65 1 -
MPHNVAFKKGIVGEDA AMCY_THIVE 52 1 -
MPHNVHFVAGVLGEAA NRL_1AAJ 51 1 -
MPHNVHFVAGVLGEAA NRL_1AAN 51 1 -
MPHNVHFVAGVLGEAA NRL_2MTAA 51 1 -
KGHNVESIKDMIPEGA NRL_1PAZ 38 0 -
FPHNVVFDEDEIPAGV PLAS_LYCES 106 1 -

Motif 3 width=15
Element Seqn Id St Int Rpt
EAGSYDYFCTPHPFM AMCY_THIVE 85 17 -
EAGTYDYHCTPHPFM NRL_1AAN 84 17 -
EAGTYDYHCTPHPFM NRL_2MTAA 84 17 -
QPGAYLVKCTPHYAM NRL_1PAZ 70 16 -
EKGTYTFYCAPHQGA PLAS_LYCES 147 25 -
NKGEYSFYCSPHQGA PLAS_POPNI 76 25 -
PAGDYSFYCEPHRGA PLAS_ANASQ 115 28 -
EAGTYDYHCTPHPFM AMCY_PARDE 110 17 -
QPGAYLVKCTPHYAM AZUP_ALCFA 93 16 -
APGTYDYICTPHPFM AMCY_METEX 98 17 -
EAGTYDYHCTPHPFM NRL_1AAJ 84 17 -
Final Motifs
Motif 1  width=14
Element Seqn Id St Int Rpt
SVSAGEKITFKNNA PLAT_TOBAC 20 20 -
SVSAGEKITFKNNA PLAS_TOBAC 20 20 -
SVSAGEKITFKNNA PLAS_SOLTU 20 20 -
SVSAGEKITFKNNA PLAS_LYCES 91 91 -
SISAGEKITFKNNA PLAS_SOLCR 20 20 -
SVASGEKIVFKNNA PLAS_LACSA 20 20 -
SVAAGEKIVFKNNA PLAS_CUCPE 20 20 -
TVAAGEKIVFKNNA PLAS_RUMOB 20 20 -
TVAAGEKITFKNNA PLAS_PETCR 20 20 -
SVASGEEIVFKNNA PLAS_SPIOL 89 89 -
SVPSGEKIVFKNNA PLAS_PHAVU 20 20 -
SIASGEKITFKNNA PLAS_SILPR 86 86 -
SVPSGEKITFKNNA PLAS_MERPE 20 20 -
SIAKGEKIVFKNNA PLAS_CAPBU 20 20 -
SVPSGEKITFKNNA PLAS_SAMNI 20 20 -
EVSAGETIVFKNNA PLAS_PEA 89 89 -
TVAKGEKIVFKNNA PLAS_ARATH 92 92 -
TVASGEKITFKNNA PLAS_CUCSA 20 20 -
TVKSGETITFKNNA PLAS_ORYSA 20 20 -
SIAKGEKIVFKNNA D112_ARATH 88 88 -
SVKAGETITFKNNA PLAS_HORVU 78 78 -
EVSAGDTIVFKNNA PLAS_VICFA 20 20 -
TVKSGETITFKNNA O24185 77 77 -
SVAKGEGISFKNNA PLAS_DAUCA 20 20 -
SVPAGEKIVFKNNA PLAT_POPNI 89 89 -
EVAAGETVVFKNNA O22646 87 87 -
SISPGEKIVFKNNA PLAS_POPNI 20 20 -
SVAAGEAIEFVNNA PLAS_ULVPE 21 21 -
SVAAGEAIEFVNNA PLAS_ULVAR 21 21 -
TVGAGESIEFINNA PLAS_ENTPR 21 21 -
TIKSGETVNFVNNA PLAS_CHLRE 68 68 -
TIKAGETVTWVNNA PLAS_CHLFU 21 21 -
TIKAGDSVTWTNNA PLAS_SCEOB 20 20 -
TIKPGDTVEFLNNK O52830 56 56 -
TIKPGDTVEFLNNK PLAS_ANASP 56 56 -
TIKPGDTVEFLNNK PLAS_ANAVA 22 22 -
TIKPGDTVEFLNNK PLAS_ANASQ 56 56 -
TIKAGEEVKWVNNK PLAS_SYNY3 50 50 -
SISAGDTVEFVMNK PLAS_PROHO 56 56 -
TVHPGDTVKWVNNK PLAS_PHOLA 56 56 -
EIQAGDTVQWVNNK PLAS_SYNP7 56 56 -
KVAPGDTVTFIPTD AZUP_ACHCY 52 52 -
KIAPGDTVTFIPTD AZUP_RHILV 47 47 -
TIKAGETVYWVNGE AMCY_PARVE 63 63 -
RAEPGDVINFVPTD AZUP_PARDT 46 46 -
RAEPGDVINFIPTD AZUP_PARDE 24 24 -
HVKVGDTVTWINRE AMCY_PARDE 62 62 -
KANPGDTVTFIPVD AZUP_ALCFA 47 47 -
RLKPGDSIKFLPTD AZUP_METEX 24 24 -
RIKAGSAVTWTNTE AMCY_METEX 50 50 -

Motif 2 width=16
Element Seqn Id St Int Rpt
FPHNVVFDEDEIPAGV PLAT_TOBAC 35 1 -
FPHNVVFDEDEIPAGV PLAS_TOBAC 35 1 -
FPHNVVFDEDEIPAGV PLAS_SOLTU 35 1 -
FPHNVVFDEDEIPAGV PLAS_LYCES 106 1 -
FPHNVVFDEDEIPAGV PLAS_SOLCR 35 1 -
FPHNVVFDEDEIPAGV PLAS_LACSA 35 1 -
FPHNVVFDEDEIPSGV PLAS_CUCPE 35 1 -
FPHNIVFDEDEVPAGV PLAS_RUMOB 35 1 -
FPHNIVFDEDEVPAGV PLAS_PETCR 35 1 -
FPHNVVFDEDEIPSGV PLAS_SPIOL 104 1 -
FPHNVVFDEDEIPAGV PLAS_PHAVU 35 1 -
FPHNVVFDEDEVPAGV PLAS_SILPR 101 1 -
FPHNVVFDEDEIPSGV PLAS_MERPE 35 1 -
FPHNVVFDEDEIPSGV PLAS_CAPBU 35 1 -
FPHNVVFDEDEVPSGV PLAS_SAMNI 35 1 -
FPHNVVFDEDEIPAGV PLAS_PEA 104 1 -
FPHNVVFDEDEIPSGV PLAS_ARATH 107 1 -
FPHNVVFDEDEIPSGV PLAS_CUCSA 35 1 -
FPHNVVFDEDAVPSGV PLAS_ORYSA 35 1 -
YPHNVVFDEDEIPSGV D112_ARATH 103 1 -
YPHNVVFDEDAVPSGV PLAS_HORVU 93 1 -
FPHNVVFDEDEIPSGV PLAS_VICFA 35 1 -
FPHNVVFDKDAVPSGV O24185 92 1 -
FPHNIVFDEDEVPAGV PLAS_DAUCA 35 1 -
FPHNVLFDEDAVPSGV PLAT_POPNI 104 1 -
FPHNVLFDEDEVPKGV O22646 102 1 -
FPHNIVFDEDSIPSGV PLAS_POPNI 35 1 -
FPHNIVFDEDAVPAGV PLAS_ULVPE 36 1 -
FPHNIVFDEDAVPAGV PLAS_ULVAR 36 1 -
FPHNIVFDEDAVPAGV PLAS_ENTPR 36 1 -
FPHNIVFDEDAIPSGV PLAS_CHLRE 83 1 -
FPHNIVFDEDEVPSGA PLAS_CHLFU 36 1 -
FPHNIVFDEDAVPAGV PLAS_SCEOB 35 1 -
PPHNVVFDAALNPAKS O52830 71 1 -
PPHNVVFDAALNPAKS PLAS_ANASP 71 1 -
PPHNVVFDAALNPAKS PLAS_ANAVA 37 1 -
PPHNVVFDATLNPAKS PLAS_ANASQ 71 1 -
SPHNIVFAADGVDADT PLAS_SYNY3 65 1 -
GPHNVIFDKVPAGESA PLAS_PROHO 71 1 -
PPHNILFDDKQVPGAS PLAS_PHOLA 71 1 -
APHNVVVEGQPELSHK PLAS_SYNP7 71 1 -
KGHNVETIKGMIPDGA AZUP_ACHCY 66 0 -
KSHNVETFKGLIPDGV AZUP_RHILV 61 0 -
MPHNVAFKKGIVGEDA AMCY_PARVE 78 1 -
KSHNVEAIKEILPEGV AZUP_PARDT 60 0 -
KSHNVEAIKEILPEGV AZUP_PARDE 38 0 -
MPHNVHFVAGVLGEAA AMCY_PARDE 77 1 -
KGHNVESIKDMIPEGA AZUP_ALCFA 61 0 -
KGHNVETIKGMAPDGA AZUP_METEX 38 0 -
LPHNVHFKSGPGVEKD AMCY_METEX 65 1 -

Motif 3 width=15
Element Seqn Id St Int Rpt
EKGTYTFYCAPHQGA PLAT_TOBAC 76 25 -
EKGTYTFYCAPHQGA PLAS_TOBAC 76 25 -
EKGTYTFYCAPHQGA PLAS_SOLTU 76 25 -
EKGTYTFYCAPHQGA PLAS_LYCES 147 25 -
EKGTYSFYCSPHQGA PLAS_SOLCR 76 25 -
EKGTYSFYCAPHQGA PLAS_LACSA 76 25 -
EKGSYSFYCSPHQGA PLAS_CUCPE 76 25 -
EKGTYSFYCSPHQGA PLAS_RUMOB 76 25 -
EKGTYKFYCEPHAGA PLAS_PETCR 74 23 -
EKGTYKFYCSPHQGA PLAS_SPIOL 145 25 -
TKGTYSFYCSPHQGA PLAS_PHAVU 76 25 -
EKGTYKFYCAPHAGA PLAS_SILPR 142 25 -
EKGSYSFYCSPHQGA PLAS_MERPE 76 25 -
EAGTYSFYCAPHQGA PLAS_CAPBU 76 25 -
ESGTYKFYCSPHQGA PLAS_SAMNI 76 25 -
AKGTYKFYCSPHQGA PLAS_PEA 145 25 -
EPGSYGFYCAPHQGA PLAS_ARATH 148 25 -
ZKGSYSFYCSPHQGA PLAS_CUCSA 76 25 -
VPGTYGFYCEPHAGA PLAS_ORYSA 74 23 -
EPGTYSFYCAPHQGA D112_ARATH 144 25 -
VPGTYGFYCEPHAGA PLAS_HORVU 132 23 -
AKGTYKFYCSPHQGA PLAS_VICFA 76 25 -
VPGTYGFYCEPHAGA O24185 131 23 -
EKGTYKFYCEPHAGA PLAS_DAUCA 74 23 -
DKGEYTFYCSPHQGA PLAT_POPNI 145 25 -
EKGTYSIYCSPHQGA O22646 143 25 -
NKGEYSFYCSPHQGA PLAS_POPNI 76 25 -
TPGVYGVYCEPHAGA PLAS_ULVPE 75 23 -
TPGVYGVYCEPHAGA PLAS_ULVAR 75 23 -
TPGTYGVYCDPHSGA PLAS_ENTPR 75 23 -
AAGEYGYYCEPHQGA PLAS_CHLRE 122 23 -
TAGTYGYFCEPHQGA PLAS_CHLFU 75 23 -
TAGEYGYFCEPHQGA PLAS_SCEOB 74 23 -
PAGEYTFYCEPHRGA O52830 115 28 -
PAGEYTFYCEPHRGA PLAS_ANASP 115 28 -
PAGEYTFYCEPHRGA PLAS_ANAVA 81 28 -
PAGDYSFYCEPHRGA PLAS_ANASQ 115 28 -
EPGTYTYYCEPHRGA PLAS_SYNY3 103 22 -
TPGTYSFYCTPHRGA PLAS_PROHO 108 21 -
PAGTYTYYCAPHRGA PLAS_PHOLA 115 28 -
EPGTYTYYCEPHRGA PLAS_SYNP7 102 15 -
APGVYGVKCTPHYGM AZUP_ACHCY 98 16 -
IPGAYVLKCTPHVGM AZUP_RHILV 93 16 -
EAGSYDYFCTPHPFM AMCY_PARVE 111 17 -
EPGLYGVKCTPHFGM AZUP_PARDT 92 16 -
EPGLYGVKCTPHFGM AZUP_PARDE 70 16 -
EAGTYDYHCTPHPFM AMCY_PARDE 110 17 -
QPGAYLVKCTPHYAM AZUP_ALCFA 93 16 -
KEGVYGFKCAPHYMM AZUP_METEX 70 16 -
APGTYDYICTPHPFM AMCY_METEX 98 17 -