Query 016655
Match_columns 385
No_of_seqs 209 out of 770
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 08:48:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/016655.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/016655hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02362 B3: B3 DNA binding do 99.9 1.4E-21 3.1E-26 160.3 10.5 96 250-376 1-100 (100)
2 PF02362 B3: B3 DNA binding do 99.8 3.6E-20 7.9E-25 151.9 10.4 93 6-98 1-100 (100)
3 PF03754 DUF313: Domain of unk 91.9 0.76 1.6E-05 39.1 7.3 66 6-71 24-114 (114)
4 PF03754 DUF313: Domain of unk 91.5 0.3 6.6E-06 41.4 4.5 38 310-347 72-114 (114)
5 PF04014 Antitoxin-MazE: Antid 58.3 22 0.00049 24.8 4.3 25 342-366 13-37 (47)
6 PLN03148 Blue copper-like prot 53.3 15 0.00033 33.2 3.5 28 343-370 39-66 (167)
7 PF04014 Antitoxin-MazE: Antid 50.9 38 0.00082 23.6 4.5 27 66-92 13-39 (47)
8 PLN03148 Blue copper-like prot 47.7 16 0.00035 33.1 2.7 26 67-92 39-66 (167)
9 PF08922 DUF1905: Domain of un 46.9 1.4E+02 0.003 23.4 7.9 60 297-360 16-80 (80)
10 smart00536 AXH domain in Ataxi 41.7 14 0.00031 31.4 1.3 24 335-358 79-112 (116)
11 TIGR01439 lp_hng_hel_AbrB loop 40.7 55 0.0012 21.8 4.0 29 17-45 6-35 (43)
12 TIGR01439 lp_hng_hel_AbrB loop 39.2 67 0.0014 21.3 4.2 30 333-365 7-36 (43)
13 PF02298 Cu_bind_like: Plastoc 34.7 24 0.00053 28.0 1.6 24 69-92 14-39 (85)
14 PF02298 Cu_bind_like: Plastoc 34.0 29 0.00063 27.6 1.9 27 344-370 13-39 (85)
15 TIGR02219 phage_NlpC_fam putat 20.1 1.1E+02 0.0025 26.1 3.3 30 70-99 73-103 (134)
No 1
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.86 E-value=1.4e-21 Score=160.25 Aligned_cols=96 Identities=42% Similarity=0.763 Sum_probs=72.3
Q ss_pred EEEEccccccCCCeEEeeecccccccccccccccchhhhhhhhccCcccCHHHHHhcCCC--CceeEEEEeCCCCeEEEE
Q 016655 250 CRVVLRPSYLYKGCIMVSCRISITLHCFSVSHDNMLDVRCIYFLLLQYLPSCFAEKHLNG--VCGFIKLQLSDGKQWPVR 327 (385)
Q Consensus 250 f~~vm~~s~v~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~IP~~Fa~~~lp~--~~~~i~L~~~~Gr~W~v~ 327 (385)
|+++|.++++...+.| .||++|+++|... ...+|+|+|++|+.|.|+
T Consensus 1 F~K~l~~s~~~~~~~l-------------------------------~iP~~f~~~~~~~~~~~~~v~l~~~~g~~W~v~ 49 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRL-------------------------------IIPKEFAKKHGGNKRKSREVTLKDPDGRSWPVK 49 (100)
T ss_dssp EEEE--TTCCCCTT-E-------------------------------EE-HHHHTTTS--SS--CEEEEEETTTEEEEEE
T ss_pred CEEEEEccCcCCCCEE-------------------------------EeCHHHHHHhCCCcCCCeEEEEEeCCCCEEEEE
Confidence 6889999988887667 8999999999633 567999999999999999
Q ss_pred EEEe--CCeeEeccChHHHhhHcCCCCCCEEEEEEecCceeEEEEEEEeec
Q 016655 328 CLYR--GGRAKFSQGWYEFTVENRLGEGDVCVFEVLRAREFVLKVTVFRVS 376 (385)
Q Consensus 328 ~~~~--~~~~~ls~GW~~F~~dN~L~~GDvcvFel~~~~~~~~~V~Ifr~~ 376 (385)
+.+. .++++|++||.+||+||+|++||+|+|+++++..+.+.|+|||+.
T Consensus 50 ~~~~~~~~~~~l~~GW~~Fv~~n~L~~GD~~~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 50 LKYRKNSGRYYLTGGWKKFVRDNGLKEGDVCVFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp EEEECCTTEEEEETTHHHHHHHCT--TT-EEEEEE-SSSCE-EEEEEE---
T ss_pred EEEEccCCeEEECCCHHHHHHHcCCCCCCEEEEEEecCCCceEEEEEEECc
Confidence 9654 357899999999999999999999999999877788999999963
No 2
>PF02362 B3: B3 DNA binding domain; InterPro: IPR003340 Two DNA binding proteins, RAV1 and RAV2 from Arabidopsis thaliana contain two distinct amino acid sequence domains found only in higher plant species. The N-terminal regions of RAV1 and RAV2 are homologous to the AP2 DNA-binding domain (see IPR001471 from INTERPRO) present in a family of transcription factors, while the C-terminal region exhibits homology to the highly conserved C-terminal domain, designated B3, of VP1/ABI3 transcription factors []. The AP2 and B3-like domains of RAV1 bind autonomously to the CAACA and CACCTG motifs, respectively, and together achieve a high affinity and specificity of binding. It has been suggested that the AP2 and B3-like domains of RAV1 are connected by a highly flexible structure enabling the two domains to bind to the CAACA and CACCTG motifs in various spacings and orientations [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1WID_A 1YEL_A.
Probab=99.83 E-value=3.6e-20 Score=151.88 Aligned_cols=93 Identities=31% Similarity=0.521 Sum_probs=70.6
Q ss_pred eEEEccCCccC-CCeeecCHHHHHhccCC--CCceEEEEcCCCCEEEEEE--EEeCCeEEeccCHHHHHhHhCCCCCcEE
Q 016655 6 FHKLILASTIR-DKRLRIPENFVRNFKDD--LSAAATLIVPNGMVSRVGL--RRLDNKVWFYDGWQEFMERYFIRIGYFL 80 (385)
Q Consensus 6 F~kv~~~~~l~-~~~L~IP~~F~~~~~~~--~~~~v~L~~p~G~~W~V~l--~~~~~~~~~~~GW~~Fv~~~~L~~Gd~l 80 (385)
|+|+|++++.. ...|.||..|++.|+.. .+..|+|++++|+.|.|++ .+.++.++|+.||++||++|+|++||+|
T Consensus 1 F~K~l~~s~~~~~~~l~iP~~f~~~~~~~~~~~~~v~l~~~~g~~W~v~~~~~~~~~~~~l~~GW~~Fv~~n~L~~GD~~ 80 (100)
T PF02362_consen 1 FFKVLKPSDVSSSCRLIIPKEFAKKHGGNKRKSREVTLKDPDGRSWPVKLKYRKNSGRYYLTGGWKKFVRDNGLKEGDVC 80 (100)
T ss_dssp EEEE--TTCCCCTT-EEE-HHHHTTTS--SS--CEEEEEETTTEEEEEEEEEECCTTEEEEETTHHHHHHHCT--TT-EE
T ss_pred CEEEEEccCcCCCCEEEeCHHHHHHhCCCcCCCeEEEEEeCCCCEEEEEEEEEccCCeEEECCCHHHHHHHcCCCCCCEE
Confidence 89999988764 35799999999999754 5779999999999999999 4557789999999999999999999999
Q ss_pred EEEEeecceE--EEEEEcCC
Q 016655 81 VFRYEGNSAF--NVYIFNLP 98 (385)
Q Consensus 81 vF~~~g~s~F--~V~If~~s 98 (385)
+|++++++.| .|.||+.+
T Consensus 81 ~F~~~~~~~~~~~v~i~~~~ 100 (100)
T PF02362_consen 81 VFELIGNSNFTLKVHIFRKS 100 (100)
T ss_dssp EEEE-SSSCE-EEEEEE---
T ss_pred EEEEecCCCceEEEEEEECc
Confidence 9999987766 99999864
No 3
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=91.89 E-value=0.76 Score=39.06 Aligned_cols=66 Identities=18% Similarity=0.368 Sum_probs=47.2
Q ss_pred eEEEccCCccC--CCeeecCHHHHHh--c----------------cCCCCceEEEEcCCCCEEEEEEEEe-C----CeEE
Q 016655 6 FHKLILASTIR--DKRLRIPENFVRN--F----------------KDDLSAAATLIVPNGMVSRVGLRRL-D----NKVW 60 (385)
Q Consensus 6 F~kv~~~~~l~--~~~L~IP~~F~~~--~----------------~~~~~~~v~L~~p~G~~W~V~l~~~-~----~~~~ 60 (385)
+-|.+..+++. ..+|.||-.=+.. | .....-.|+|.+|.++.|.+.|++- . ..+.
T Consensus 24 ~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~~Yv 103 (114)
T PF03754_consen 24 IEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGTSNYV 103 (114)
T ss_pred EeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCceEEE
Confidence 45777777764 3678888664411 1 1234568999999999999999985 3 1566
Q ss_pred eccCHHHHHhH
Q 016655 61 FYDGWQEFMER 71 (385)
Q Consensus 61 ~~~GW~~Fv~~ 71 (385)
|..||.++|.+
T Consensus 104 L~~gWn~VV~~ 114 (114)
T PF03754_consen 104 LNSGWNKVVED 114 (114)
T ss_pred EEcChHhhccC
Confidence 89999998864
No 4
>PF03754 DUF313: Domain of unknown function (DUF313) ; InterPro: IPR005508 This is a family of proteins from Arabidopsis thaliana (Mouse-ear cress) with uncharacterised function.
Probab=91.47 E-value=0.3 Score=41.45 Aligned_cols=38 Identities=13% Similarity=0.182 Sum_probs=31.3
Q ss_pred CceeEEEEeCCCCeEEEEEEEeCC-----eeEeccChHHHhhH
Q 016655 310 VCGFIKLQLSDGKQWPVRCLYRGG-----RAKFSQGWYEFTVE 347 (385)
Q Consensus 310 ~~~~i~L~~~~Gr~W~v~~~~~~~-----~~~ls~GW~~F~~d 347 (385)
..-.++|.||.++.|.+.+.+..- .|.|..||.++|.+
T Consensus 72 ~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 72 KGVEVILVDPSLRKWTMRLKKWNMGNGTSNYVLNSGWNKVVED 114 (114)
T ss_pred CCceEEEECCcCcEEEEEEEEecccCCceEEEEEcChHhhccC
Confidence 345799999999999999887643 58899999999864
No 5
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=58.32 E-value=22 Score=24.78 Aligned_cols=25 Identities=24% Similarity=0.170 Sum_probs=20.8
Q ss_pred HHHhhHcCCCCCCEEEEEEecCcee
Q 016655 342 YEFTVENRLGEGDVCVFEVLRAREF 366 (385)
Q Consensus 342 ~~F~~dN~L~~GDvcvFel~~~~~~ 366 (385)
++|++..+|++||.+.++..++..+
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~g~i 37 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGDGKI 37 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETTSEE
T ss_pred HHHHHHcCCCCCCEEEEEEeCCCEE
Confidence 3788899999999999999976433
No 6
>PLN03148 Blue copper-like protein; Provisional
Probab=53.27 E-value=15 Score=33.24 Aligned_cols=28 Identities=18% Similarity=0.256 Sum_probs=21.2
Q ss_pred HHhhHcCCCCCCEEEEEEecCceeEEEE
Q 016655 343 EFTVENRLGEGDVCVFEVLRAREFVLKV 370 (385)
Q Consensus 343 ~F~~dN~L~~GDvcvFel~~~~~~~~~V 370 (385)
+-+..+...+||.++|.+..+..-+++|
T Consensus 39 ~WA~~k~F~VGD~LvF~Y~~~~hnV~~V 66 (167)
T PLN03148 39 LWANNQTFYVGDLISFRYQKTQYNVFEV 66 (167)
T ss_pred HhhcCCCCccCCEEEEEecCCCceEEEE
Confidence 3467789999999999998764444555
No 7
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=50.93 E-value=38 Score=23.60 Aligned_cols=27 Identities=19% Similarity=0.283 Sum_probs=23.0
Q ss_pred HHHHhHhCCCCCcEEEEEEeecceEEE
Q 016655 66 QEFMERYFIRIGYFLVFRYEGNSAFNV 92 (385)
Q Consensus 66 ~~Fv~~~~L~~Gd~lvF~~~g~s~F~V 92 (385)
++|+..++|+.||-+.+.+.++....+
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~g~i~i 39 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGDGKIVI 39 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETTSEEEE
T ss_pred HHHHHHcCCCCCCEEEEEEeCCCEEEE
Confidence 688999999999999999998874433
No 8
>PLN03148 Blue copper-like protein; Provisional
Probab=47.71 E-value=16 Score=33.14 Aligned_cols=26 Identities=23% Similarity=0.516 Sum_probs=19.9
Q ss_pred HHHhHhCCCCCcEEEEEEeec--ceEEE
Q 016655 67 EFMERYFIRIGYFLVFRYEGN--SAFNV 92 (385)
Q Consensus 67 ~Fv~~~~L~~Gd~lvF~~~g~--s~F~V 92 (385)
.-+..+....||.|+|+|..+ +..+|
T Consensus 39 ~WA~~k~F~VGD~LvF~Y~~~~hnV~~V 66 (167)
T PLN03148 39 LWANNQTFYVGDLISFRYQKTQYNVFEV 66 (167)
T ss_pred HhhcCCCCccCCEEEEEecCCCceEEEE
Confidence 335778899999999999854 45555
No 9
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=46.93 E-value=1.4e+02 Score=23.40 Aligned_cols=60 Identities=18% Similarity=0.179 Sum_probs=36.3
Q ss_pred ccCHHHHHhcCCC--CceeEEEEeCCCCeEEEEEEEeC-CeeE--eccChHHHhhHcCCCCCCEEEEEE
Q 016655 297 YLPSCFAEKHLNG--VCGFIKLQLSDGKQWPVRCLYRG-GRAK--FSQGWYEFTVENRLGEGDVCVFEV 360 (385)
Q Consensus 297 ~IP~~Fa~~~lp~--~~~~i~L~~~~Gr~W~v~~~~~~-~~~~--ls~GW~~F~~dN~L~~GDvcvFel 360 (385)
.||.+-++..... ..-.|...- +|..|...+...+ +.+. +.. +.-++-++.+||.+.++|
T Consensus 16 ~vP~~v~~~l~~~~~g~v~V~~tI-~g~~~~~sl~p~g~G~~~Lpv~~---~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 16 EVPFDVAEELGEGGWGRVPVRGTI-DGHPWRTSLFPMGNGGYILPVKA---AVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp E--S-HHHHH--S--S-EEEEEEE-TTEEEEEEEEESSTT-EEEEE-H---HHHHHHT--TTSEEEEEE
T ss_pred EeCHHHHHHhccccCCceEEEEEE-CCEEEEEEEEECCCCCEEEEEcH---HHHHHcCCCCCCEEEEEC
Confidence 7998888876655 555555555 5789999877633 4433 443 777889999999998876
No 10
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=41.72 E-value=14 Score=31.41 Aligned_cols=24 Identities=29% Similarity=0.477 Sum_probs=18.0
Q ss_pred eEeccChHHHhhH----------cCCCCCCEEEE
Q 016655 335 AKFSQGWYEFTVE----------NRLGEGDVCVF 358 (385)
Q Consensus 335 ~~ls~GW~~F~~d----------N~L~~GDvcvF 358 (385)
+....||..|.=. ..|++||+|+-
T Consensus 79 FV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~ 112 (116)
T smart00536 79 FVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLS 112 (116)
T ss_pred EEcCccccccChhhhhhhcCCcceecccCCEEec
Confidence 4467899988643 46789999974
No 11
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=40.70 E-value=55 Score=21.78 Aligned_cols=29 Identities=17% Similarity=0.299 Sum_probs=23.3
Q ss_pred CCeeecCHHHHHhccCCCCceEEEE-cCCC
Q 016655 17 DKRLRIPENFVRNFKDDLSAAATLI-VPNG 45 (385)
Q Consensus 17 ~~~L~IP~~F~~~~~~~~~~~v~L~-~p~G 45 (385)
.+.+.||..|.+.++-.....+.+. .++|
T Consensus 6 kgri~iP~~~r~~l~~~~gd~~~i~~~~~~ 35 (43)
T TIGR01439 6 KGQIVIPKEIREKLGLKEGDRLEVIRVEDG 35 (43)
T ss_pred CCeEEecHHHHHHcCcCCCCEEEEEEeCCC
Confidence 3789999999999987777778777 5554
No 12
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=39.22 E-value=67 Score=21.34 Aligned_cols=30 Identities=23% Similarity=0.230 Sum_probs=22.3
Q ss_pred CeeEeccChHHHhhHcCCCCCCEEEEEEecCce
Q 016655 333 GRAKFSQGWYEFTVENRLGEGDVCVFEVLRARE 365 (385)
Q Consensus 333 ~~~~ls~GW~~F~~dN~L~~GDvcvFel~~~~~ 365 (385)
++..|-. +|.+..+++.||.++++...+..
T Consensus 7 gri~iP~---~~r~~l~~~~gd~~~i~~~~~~~ 36 (43)
T TIGR01439 7 GQIVIPK---EIREKLGLKEGDRLEVIRVEDGE 36 (43)
T ss_pred CeEEecH---HHHHHcCcCCCCEEEEEEeCCCE
Confidence 3444543 78889999999999999765443
No 13
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=34.72 E-value=24 Score=28.05 Aligned_cols=24 Identities=33% Similarity=0.519 Sum_probs=15.0
Q ss_pred HhHhCCCCCcEEEEEEeec--ceEEE
Q 016655 69 MERYFIRIGYFLVFRYEGN--SAFNV 92 (385)
Q Consensus 69 v~~~~L~~Gd~lvF~~~g~--s~F~V 92 (385)
+....+..||.|+|+|... +...|
T Consensus 14 a~~~~F~vGD~LvF~y~~~~h~V~~V 39 (85)
T PF02298_consen 14 ASGKTFRVGDTLVFNYDSGQHSVVEV 39 (85)
T ss_dssp HCTS-BETTEEEEEE--TTTB-EEEE
T ss_pred hcCCcEeCCCEEEEEecCCCCeEEec
Confidence 4566788999999999864 44444
No 14
>PF02298 Cu_bind_like: Plastocyanin-like domain; InterPro: IPR003245 Blue (type 1) copper proteins are small proteins which bind a single copper atom and which are characterised by an intense electronic absorption band near 600 nm [, ]. The most well known members of this class of proteins are the plant chloroplastic plastocyanins, which exchange electrons with cytochrome c6, and the distantly related bacterial azurins, which exchange electrons with cytochrome c551. This family of proteins also includes amicyanin from bacteria such as Methylobacterium extorquens or Paracoccus versutus (Thiobacillus versutus) that can grow on methylamine; auracyanins A and B from Chloroflexus aurantiacus []; blue copper protein from Alcaligenes faecalis; cupredoxin (CPC) from Cucumis sativus (Cucumber) peelings []; cusacyanin (basic blue protein; plantacyanin, CBP) from cucumber; halocyanin from Natronomonas pharaonis (Natronobacterium pharaonis) [], a membrane associated copper-binding protein; pseudoazurin from Pseudomonas; rusticyanin from Thiobacillus ferrooxidans []; stellacyanin from Rhus vernicifera (Japanese lacquer tree); umecyanin from the roots of Armoracia rusticana (Horseradish); and allergen Ra3 from ragweed. Although there is an appreciable amount of divergence in the sequences of all these proteins, the copper ligand sites are conserved. This domain is found in a variety of plant cyanins and pollern allergen. Some of the proteins in this family are allergens. Allergies are hypersensitivity reactions of the immune system to specific substances called allergens (such as pollen, stings, drugs, or food) that, in most people, result in no symptoms. A nomenclature system has been established for antigens (allergens) that cause IgE-mediated atopic allergies in humans [WHO/IUIS Allergen Nomenclature Subcommittee King T.P., Hoffmann D., Loewenstein H., Marsh D.G., Platts-Mills T.A.E., Thomas W. Bull. World Health Organ. 72:797-806(1994)]. This nomenclature system is defined by a designation that is composed of the first three letters of the genus; a space; the first letter of the species name; a space and an arabic number. In the event that two species names have identical designations, they are discriminated from one another by adding one or more letters (as necessary) to each species designation. The allergens in this family include allergens with the following designations: Amb a 3.; GO: 0005507 copper ion binding, 0009055 electron carrier activity; PDB: 1JER_A 1WS7_A 1WS8_D 1F56_B 1X9R_B 1X9U_A 2CBP_A.
Probab=34.00 E-value=29 Score=27.63 Aligned_cols=27 Identities=22% Similarity=0.338 Sum_probs=17.2
Q ss_pred HhhHcCCCCCCEEEEEEecCceeEEEE
Q 016655 344 FTVENRLGEGDVCVFEVLRAREFVLKV 370 (385)
Q Consensus 344 F~~dN~L~~GDvcvFel~~~~~~~~~V 370 (385)
-+..+.+.+||.++|.+.....-+++|
T Consensus 13 Wa~~~~F~vGD~LvF~y~~~~h~V~~V 39 (85)
T PF02298_consen 13 WASGKTFRVGDTLVFNYDSGQHSVVEV 39 (85)
T ss_dssp HHCTS-BETTEEEEEE--TTTB-EEEE
T ss_pred hhcCCcEeCCCEEEEEecCCCCeEEec
Confidence 356778899999999998764445555
No 15
>TIGR02219 phage_NlpC_fam putative phage cell wall peptidase, NlpC/P60 family. Members of this family show sequence similarity to members of the NlpC/P60 family described by Pfam model pfam00877 and by Anantharaman and Aravind (PubMed:12620121). The NlpC/P60 family includes a number of characterized bacterial cell wall hydrolases. Members of this related family are all found in prophage regions of bacterial genomes.
Probab=20.12 E-value=1.1e+02 Score=26.13 Aligned_cols=30 Identities=27% Similarity=0.272 Sum_probs=22.4
Q ss_pred hHhCCCCCcEEEEEEeec-ceEEEEEEcCCC
Q 016655 70 ERYFIRIGYFLVFRYEGN-SAFNVYIFNLPS 99 (385)
Q Consensus 70 ~~~~L~~Gd~lvF~~~g~-s~F~V~If~~s~ 99 (385)
....|+.||+|.|+..+. ..-+|=|+-.++
T Consensus 73 ~~~~~qpGDlvff~~~~~~~~~HvGIy~G~g 103 (134)
T TIGR02219 73 PCDAAQPGDVLVFRWRPGAAAKHAAIAASPT 103 (134)
T ss_pred chhcCCCCCEEEEeeCCCCCCcEEEEEeCCC
Confidence 346799999999997533 356888886555
Done!