Query 041048
Match_columns 335
No_of_seqs 167 out of 898
Neff 7.8
Searched_HMMs 46136
Date Fri Mar 29 03:16:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041048.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041048hhsearch_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 1.7E-22 3.8E-27 159.5 10.9 95 233-327 1-99 (100)
2 PF02362 B3: B3 DNA binding do 99.8 1.5E-20 3.2E-25 148.4 10.2 93 8-100 1-100 (100)
3 PF03754 DUF313: Domain of unk 94.8 0.16 3.5E-06 40.9 7.5 67 233-299 24-114 (114)
4 PF03754 DUF313: Domain of unk 94.7 0.16 3.4E-06 41.0 7.3 66 8-73 24-114 (114)
5 PLN03148 Blue copper-like prot 64.6 7.1 0.00015 33.6 3.1 21 69-89 39-59 (167)
6 PF04014 Antitoxin-MazE: Antid 63.6 18 0.00038 23.9 4.4 26 68-93 13-38 (47)
7 PF04014 Antitoxin-MazE: Antid 63.3 15 0.00032 24.3 3.9 23 294-316 13-35 (47)
8 PLN03148 Blue copper-like prot 63.3 9.7 0.00021 32.8 3.7 28 295-322 39-66 (167)
9 PF08922 DUF1905: Domain of un 60.4 64 0.0014 24.0 7.4 65 246-312 13-80 (80)
10 TIGR01439 lp_hng_hel_AbrB loop 52.4 29 0.00062 22.0 3.8 29 19-47 6-35 (43)
11 PF02298 Cu_bind_like: Plastoc 48.1 13 0.00028 28.1 1.8 19 71-89 14-32 (85)
12 PF02298 Cu_bind_like: Plastoc 47.0 15 0.00033 27.8 2.1 27 296-322 13-39 (85)
13 smart00536 AXH domain in Ataxi 46.8 11 0.00024 30.3 1.4 24 287-310 79-112 (116)
14 PF12195 End_beta_barrel: Beta 29.7 29 0.00062 25.7 1.1 29 72-100 24-57 (83)
15 PRK09798 antitoxin MazE; Provi 29.5 60 0.0013 24.4 2.9 29 20-48 13-41 (82)
16 PRK13610 photosystem II reacti 25.3 1.3E+02 0.0029 24.0 4.2 50 23-73 42-102 (113)
17 PF09147 DUF1933: Domain of un 23.9 71 0.0015 27.8 2.6 19 299-317 94-112 (201)
18 PF11976 Rad60-SLD: Ubiquitin- 23.9 80 0.0017 22.3 2.6 48 39-89 2-49 (72)
19 PF08922 DUF1905: Domain of un 21.2 3.5E+02 0.0075 20.0 8.4 65 19-86 12-80 (80)
20 PF08916 Phe_ZIP: Phenylalanin 20.9 49 0.0011 23.3 0.9 7 66-72 2-8 (59)
21 PF11604 CusF_Ec: Copper bindi 20.4 1.9E+02 0.004 20.8 3.9 24 300-323 41-64 (70)
22 PF06071 YchF-GTPase_C: Protei 20.3 61 0.0013 24.6 1.4 15 72-86 69-83 (84)
23 cd06555 ASCH_PF0470_like ASC-1 20.0 2.1E+02 0.0045 22.8 4.4 31 300-331 30-60 (109)
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=99.88 E-value=1.7e-22 Score=159.50 Aligned_cols=95 Identities=40% Similarity=0.730 Sum_probs=72.5
Q ss_pred EEEEccCcccCCCceeecCHHHHHhhcCC--CCeeEEEEeCCCCeEEEEEEEe--CCeeeeccChhHhhhhcCCCCCCEE
Q 041048 233 FRVILRPSYVYRTLLLHVPTSFARKYLNG--IKGYITIIDSNGKQWPVRCIFK--NGGAKFSKGWPEFVWENNLDESDVC 308 (335)
Q Consensus 233 F~~~m~~s~v~~~~~L~iP~~F~~~~l~~--~~~~i~L~~~~G~~W~v~~~~~--~~~~~l~~GW~~F~~~n~L~~GD~c 308 (335)
|+++|+++++...+.|.||++|++.|... ...+|+|+|++|+.|+|++.+. .++.+|++||.+||++|+|++||+|
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 78999999988877899999999999643 5679999999999999999643 4578899999999999999999999
Q ss_pred EEEEecCCCcEEEEEEEee
Q 041048 309 VFELIKSNDVTLKATIFRV 327 (335)
Q Consensus 309 vFel~~~~~~~~~V~Ifr~ 327 (335)
+|+++++....+.|+|||.
T Consensus 81 ~F~~~~~~~~~~~v~i~~~ 99 (100)
T PF02362_consen 81 VFELIGNSNFTLKVHIFRK 99 (100)
T ss_dssp EEEE-SSSCE-EEEEEE--
T ss_pred EEEEecCCCceEEEEEEEC
Confidence 9999987767789999986
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=99.84 E-value=1.5e-20 Score=148.42 Aligned_cols=93 Identities=33% Similarity=0.657 Sum_probs=70.0
Q ss_pred EEEEcccCcc-cCceEecchHHHHhhCCC--CCceEEEEcCCCCEEEEEE--EEeCCeEEEcccHHHHHhHcCCCCCcEE
Q 041048 8 FYKLIVPSIL-QDKKLRIPDKFVQKFGDE--LSSIAKFTIPSGRMWFVEL--KKCNKQLWFDIGWHEFIEHCSIHSGYFL 82 (335)
Q Consensus 8 Ffk~~~~~~~-~~~~l~IP~~F~~~~~~~--~~~~v~L~~~~g~~W~V~l--~~~~~~~~~~~GW~~F~~~~~L~~Gd~l 82 (335)
|+|++++++. ....|.||..|++.|+.. .+..|+|.+++|+.|.|.+ .+..+.++|++||++||++|+|++||+|
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 8999987655 336799999999999754 5779999999999999999 4556789999999999999999999999
Q ss_pred EEEEcccceE--EEEEEeCC
Q 041048 83 IFKYQGNSNF--NVYIFDLA 100 (335)
Q Consensus 83 vF~~~g~~~F--~V~if~~~ 100 (335)
+|++++++.| .|.||+.+
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 9999998777 99999753
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=94.77 E-value=0.16 Score=40.87 Aligned_cols=67 Identities=18% Similarity=0.198 Sum_probs=47.9
Q ss_pred EEEEccCcccCCC-ceeecCHHHHHhh--cC----------------CCCeeEEEEeCCCCeEEEEEEEeCC-----eee
Q 041048 233 FRVILRPSYVYRT-LLLHVPTSFARKY--LN----------------GIKGYITIIDSNGKQWPVRCIFKNG-----GAK 288 (335)
Q Consensus 233 F~~~m~~s~v~~~-~~L~iP~~F~~~~--l~----------------~~~~~i~L~~~~G~~W~v~~~~~~~-----~~~ 288 (335)
+.+.|..+++... .+|.||-.=+..+ |. ...-.|+|.|+.++.|.+++.+-.. .+.
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 4468888888754 4789987755222 21 1234689999999999999875322 578
Q ss_pred eccChhHhhhh
Q 041048 289 FSKGWPEFVWE 299 (335)
Q Consensus 289 l~~GW~~F~~~ 299 (335)
|..||..++.+
T Consensus 104 L~~gWn~VV~~ 114 (114)
T PF03754_consen 104 LNSGWNKVVED 114 (114)
T ss_pred EEcChHhhccC
Confidence 99999998864
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=94.72 E-value=0.16 Score=40.95 Aligned_cols=66 Identities=23% Similarity=0.410 Sum_probs=48.9
Q ss_pred EEEEcccCccc--CceEecchHHHHh--h----------------CCCCCceEEEEcCCCCEEEEEEEEeCC-----eEE
Q 041048 8 FYKLIVPSILQ--DKKLRIPDKFVQK--F----------------GDELSSIAKFTIPSGRMWFVELKKCNK-----QLW 62 (335)
Q Consensus 8 Ffk~~~~~~~~--~~~l~IP~~F~~~--~----------------~~~~~~~v~L~~~~g~~W~V~l~~~~~-----~~~ 62 (335)
+-|.++.+++. ..+|.||..=+.. | .....-.|+|.+|+++.|.+.|.+..- .+.
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 56777777663 3788888764411 1 124567899999999999999998753 577
Q ss_pred EcccHHHHHhH
Q 041048 63 FDIGWHEFIEH 73 (335)
Q Consensus 63 ~~~GW~~F~~~ 73 (335)
|..||..+|++
T Consensus 104 L~~gWn~VV~~ 114 (114)
T PF03754_consen 104 LNSGWNKVVED 114 (114)
T ss_pred EEcChHhhccC
Confidence 99999999863
No 5
>PLN03148 Blue copper-like protein; Provisional
Probab=64.61 E-value=7.1 Score=33.63 Aligned_cols=21 Identities=19% Similarity=0.404 Sum_probs=17.8
Q ss_pred HHHhHcCCCCCcEEEEEEccc
Q 041048 69 EFIEHCSIHSGYFLIFKYQGN 89 (335)
Q Consensus 69 ~F~~~~~L~~Gd~lvF~~~g~ 89 (335)
.-+..+..+.||.|+|+|..+
T Consensus 39 ~WA~~k~F~VGD~LvF~Y~~~ 59 (167)
T PLN03148 39 LWANNQTFYVGDLISFRYQKT 59 (167)
T ss_pred HhhcCCCCccCCEEEEEecCC
Confidence 446778899999999999865
No 6
>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=63.58 E-value=18 Score=23.90 Aligned_cols=26 Identities=15% Similarity=0.262 Sum_probs=22.3
Q ss_pred HHHHhHcCCCCCcEEEEEEcccceEE
Q 041048 68 HEFIEHCSIHSGYFLIFKYQGNSNFN 93 (335)
Q Consensus 68 ~~F~~~~~L~~Gd~lvF~~~g~~~F~ 93 (335)
++|++.++|+.||.+.+.+.++....
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~g~i~ 38 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGDGKIV 38 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETTSEEE
T ss_pred HHHHHHcCCCCCCEEEEEEeCCCEEE
Confidence 57889999999999999999987443
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=63.29 E-value=15 Score=24.27 Aligned_cols=23 Identities=17% Similarity=0.076 Sum_probs=20.2
Q ss_pred hHhhhhcCCCCCCEEEEEEecCC
Q 041048 294 PEFVWENNLDESDVCVFELIKSN 316 (335)
Q Consensus 294 ~~F~~~n~L~~GD~cvFel~~~~ 316 (335)
++|++..+|++||.+.+....++
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~g 35 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGDG 35 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETTS
T ss_pred HHHHHHcCCCCCCEEEEEEeCCC
Confidence 47888999999999999998875
No 8
>PLN03148 Blue copper-like protein; Provisional
Probab=63.26 E-value=9.7 Score=32.79 Aligned_cols=28 Identities=11% Similarity=0.130 Sum_probs=20.7
Q ss_pred HhhhhcCCCCCCEEEEEEecCCCcEEEE
Q 041048 295 EFVWENNLDESDVCVFELIKSNDVTLKA 322 (335)
Q Consensus 295 ~F~~~n~L~~GD~cvFel~~~~~~~~~V 322 (335)
.-+..+...+||.++|.+.....-++.|
T Consensus 39 ~WA~~k~F~VGD~LvF~Y~~~~hnV~~V 66 (167)
T PLN03148 39 LWANNQTFYVGDLISFRYQKTQYNVFEV 66 (167)
T ss_pred HhhcCCCCccCCEEEEEecCCCceEEEE
Confidence 3367889999999999998754334444
No 9
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=60.41 E-value=64 Score=23.99 Aligned_cols=65 Identities=15% Similarity=0.141 Sum_probs=37.7
Q ss_pred ceeecCHHHHHhhcCC--CCeeEEEEeCCCCeEEEEEEEeC-CeeeeccChhHhhhhcCCCCCCEEEEEE
Q 041048 246 LLLHVPTSFARKYLNG--IKGYITIIDSNGKQWPVRCIFKN-GGAKFSKGWPEFVWENNLDESDVCVFEL 312 (335)
Q Consensus 246 ~~L~iP~~F~~~~l~~--~~~~i~L~~~~G~~W~v~~~~~~-~~~~l~~GW~~F~~~n~L~~GD~cvFel 312 (335)
..+.||...+..+... ..-.|..+- +|..|+..+...+ +.++|. ==++..++-++..||.+.++|
T Consensus 13 ~fv~vP~~v~~~l~~~~~g~v~V~~tI-~g~~~~~sl~p~g~G~~~Lp-v~~~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 13 TFVEVPFDVAEELGEGGWGRVPVRGTI-DGHPWRTSLFPMGNGGYILP-VKAAVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp EEEE--S-HHHHH--S--S-EEEEEEE-TTEEEEEEEEESSTT-EEEE-E-HHHHHHHT--TTSEEEEEE
T ss_pred EEEEeCHHHHHHhccccCCceEEEEEE-CCEEEEEEEEECCCCCEEEE-EcHHHHHHcCCCCCCEEEEEC
Confidence 4689999988887665 444454443 5799999877633 333321 114777888999999998875
No 10
>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=52.38 E-value=29 Score=21.96 Aligned_cols=29 Identities=17% Similarity=0.342 Sum_probs=23.9
Q ss_pred CceEecchHHHHhhCCCCCceEEEE-cCCC
Q 041048 19 DKKLRIPDKFVQKFGDELSSIAKFT-IPSG 47 (335)
Q Consensus 19 ~~~l~IP~~F~~~~~~~~~~~v~L~-~~~g 47 (335)
+.++.||..|.+.++......+.+. .++|
T Consensus 6 kgri~iP~~~r~~l~~~~gd~~~i~~~~~~ 35 (43)
T TIGR01439 6 KGQIVIPKEIREKLGLKEGDRLEVIRVEDG 35 (43)
T ss_pred CCeEEecHHHHHHcCcCCCCEEEEEEeCCC
Confidence 3689999999999988888888887 5555
No 11
>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=48.07 E-value=13 Score=28.13 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=13.3
Q ss_pred HhHcCCCCCcEEEEEEccc
Q 041048 71 IEHCSIHSGYFLIFKYQGN 89 (335)
Q Consensus 71 ~~~~~L~~Gd~lvF~~~g~ 89 (335)
+....+..||.|+|.|...
T Consensus 14 a~~~~F~vGD~LvF~y~~~ 32 (85)
T PF02298_consen 14 ASGKTFRVGDTLVFNYDSG 32 (85)
T ss_dssp HCTS-BETTEEEEEE--TT
T ss_pred hcCCcEeCCCEEEEEecCC
Confidence 4566788999999999975
No 12
>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=47.05 E-value=15 Score=27.77 Aligned_cols=27 Identities=11% Similarity=0.193 Sum_probs=16.7
Q ss_pred hhhhcCCCCCCEEEEEEecCCCcEEEE
Q 041048 296 FVWENNLDESDVCVFELIKSNDVTLKA 322 (335)
Q Consensus 296 F~~~n~L~~GD~cvFel~~~~~~~~~V 322 (335)
-+..+.+.+||+++|.+.....-++.|
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 356778899999999998763334544
No 13
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=46.83 E-value=11 Score=30.31 Aligned_cols=24 Identities=29% Similarity=0.447 Sum_probs=18.1
Q ss_pred eeeccChhHhhhh----------cCCCCCCEEEE
Q 041048 287 AKFSKGWPEFVWE----------NNLDESDVCVF 310 (335)
Q Consensus 287 ~~l~~GW~~F~~~----------n~L~~GD~cvF 310 (335)
.+.+.||..|.=. ..|++||+|+-
T Consensus 79 FV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~ 112 (116)
T smart00536 79 FVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLS 112 (116)
T ss_pred EEcCccccccChhhhhhhcCCcceecccCCEEec
Confidence 3457899998643 46789999974
No 14
>PF12195 End_beta_barrel: Beta barrel domain of bacteriophage endosialidase; InterPro: IPR024427 This entry represents the beta barrel domain of endosialidases which is nested in a beta propeller domain. This beta barrel domain is approximately 80 amino acids in length and represents one of the two sialic acid binding sites of the enzyme [].; PDB: 1V0E_B 1V0F_E 3JU4_A 3GVL_A 3GVK_B 3GVJ_A.
Probab=29.66 E-value=29 Score=25.71 Aligned_cols=29 Identities=21% Similarity=0.345 Sum_probs=14.9
Q ss_pred hHcCCCCCcEEEEEEccc----ceEEEE-EEeCC
Q 041048 72 EHCSIHSGYFLIFKYQGN----SNFNVY-IFDLA 100 (335)
Q Consensus 72 ~~~~L~~Gd~lvF~~~g~----~~F~V~-if~~~ 100 (335)
.+|+|..||++.|.-.+- +.+.|. |.|.+
T Consensus 24 ~~HGl~vGD~VnFsnsa~tGvSG~mTVatVid~n 57 (83)
T PF12195_consen 24 TDHGLFVGDFVNFSNSAVTGVSGNMTVATVIDAN 57 (83)
T ss_dssp TT----TT-EEEEES-SSTT--EEEEEEEEEETT
T ss_pred ccCceeecceEEEeccccccccccEEEEEEecCC
Confidence 579999999999987652 345554 44444
No 15
>PRK09798 antitoxin MazE; Provisional
Probab=29.50 E-value=60 Score=24.42 Aligned_cols=29 Identities=21% Similarity=0.441 Sum_probs=24.7
Q ss_pred ceEecchHHHHhhCCCCCceEEEEcCCCC
Q 041048 20 KKLRIPDKFVQKFGDELSSIAKFTIPSGR 48 (335)
Q Consensus 20 ~~l~IP~~F~~~~~~~~~~~v~L~~~~g~ 48 (335)
.-++||..|++.++......|.|...+|+
T Consensus 13 ~~vRIPk~~l~~l~l~~g~~vei~v~~~~ 41 (82)
T PRK09798 13 PAVRIPATLMQALNLNIDDEVKIDLVDGK 41 (82)
T ss_pred ceEEcCHHHHHHcCCCCCCEEEEEEECCE
Confidence 47899999999999888888888876665
No 16
>PRK13610 photosystem II reaction center protein Psb28; Provisional
Probab=25.34 E-value=1.3e+02 Score=24.00 Aligned_cols=50 Identities=8% Similarity=0.162 Sum_probs=37.1
Q ss_pred ecchHHHHhhCCCCCceEEEEcCCC--CEEEEEEEEeCCe------EE-E--cccHHHHHhH
Q 041048 23 RIPDKFVQKFGDELSSIAKFTIPSG--RMWFVELKKCNKQ------LW-F--DIGWHEFIEH 73 (335)
Q Consensus 23 ~IP~~F~~~~~~~~~~~v~L~~~~g--~~W~V~l~~~~~~------~~-~--~~GW~~F~~~ 73 (335)
.=|..|...+.+++.+ +.|.|..| .++.|..+..+|. .| + ..-|..|.++
T Consensus 42 ~~p~~l~~~~~~~ItG-M~LiDeEGei~tr~v~aKFvnGkp~~iEa~y~m~s~~~WdRFMRF 102 (113)
T PRK13610 42 YKPKTITLTNYKSVQR-MFLIDSEGVLSTKKIDLSISEDHVKEVKSTYNWNSEEAFERFMRF 102 (113)
T ss_pred CCchhcccccccceee-eEEEccCceEEEEeeeEEEEcCCccEEEEEEEECCHHHHHHHHHH
Confidence 3477777777778887 99999999 6788888877653 33 2 5589888765
No 17
>PF09147 DUF1933: Domain of unknown function (DUF1933); InterPro: IPR015230 This domain is predominantly found in carbapenam synthetase, and is composed of two antiparallel six-stranded beta-sheets that form a sandwich, flanked on each side by two alpha-helices. Their exact function has not, as yet, been determined []. ; PDB: 1Q19_A 1Q15_D.
Probab=23.95 E-value=71 Score=27.85 Aligned_cols=19 Identities=32% Similarity=0.473 Sum_probs=13.0
Q ss_pred hcCCCCCCEEEEEEecCCC
Q 041048 299 ENNLDESDVCVFELIKSND 317 (335)
Q Consensus 299 ~n~L~~GD~cvFel~~~~~ 317 (335)
+=.|.+||+|.|-=.++++
T Consensus 94 aLsLAEGdfcffiE~kng~ 112 (201)
T PF09147_consen 94 ALSLAEGDFCFFIEDKNGE 112 (201)
T ss_dssp GGGG--SSEEEEEEETTSE
T ss_pred hhhhhcCceEEEEecCCCc
Confidence 3468899999997777763
No 18
>PF11976 Rad60-SLD: Ubiquitin-2 like Rad60 SUMO-like; InterPro: IPR022617 This entry includes small ubiquitin-related modifier (SUMO) proteins. SUMOs are small proteins that are covalently attached to lysines as post-translational modifications and are used to control multiple cellular process including signal transduction, nuclear transport and DNA replication and repair []. Unlike ubiquitin, they are not involved in protein degradation. This entry also contains the C-terminal Rad60 DNA repair protein SUMO-like domain.; PDB: 3RD2_A 2JXX_A 3RCZ_A 3GOE_A 3A4S_D 3A4R_B 2IO1_D 1U4A_A 2K1F_A 1WZ0_A ....
Probab=23.92 E-value=80 Score=22.35 Aligned_cols=48 Identities=13% Similarity=0.097 Sum_probs=36.6
Q ss_pred eEEEEcCCCCEEEEEEEEeCCeEEEcccHHHHHhHcCCCCCcEEEEEEccc
Q 041048 39 IAKFTIPSGRMWFVELKKCNKQLWFDIGWHEFIEHCSIHSGYFLIFKYQGN 89 (335)
Q Consensus 39 ~v~L~~~~g~~W~V~l~~~~~~~~~~~GW~~F~~~~~L~~Gd~lvF~~~g~ 89 (335)
+++|++.+|+.-.+.+.. ..-|..=...|++.+++..-.-+.|.|+|.
T Consensus 2 ~i~v~~~~~~~~~~~v~~---~~~~~~l~~~~~~~~~i~~~~~~~l~fdG~ 49 (72)
T PF11976_consen 2 TIKVRSQDGKEIKFKVKP---TTTVSKLIEKYCEKKGIPPEESIRLIFDGK 49 (72)
T ss_dssp EEEEEETTSEEEEEEEET---TSCCHHHHHHHHHHHTTTT-TTEEEEETTE
T ss_pred EEEEEeCCCCEEEEEECC---CCcHHHHHHHHHHhhCCCccceEEEEECCE
Confidence 578899999977777654 345667778999999999966777888775
No 19
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=21.22 E-value=3.5e+02 Score=19.98 Aligned_cols=65 Identities=12% Similarity=0.068 Sum_probs=39.4
Q ss_pred CceEecchHHHHhhCCC--CCceEEEEcCCCCEEEEEEEEe-CCeEEE-cccHHHHHhHcCCCCCcEEEEEE
Q 041048 19 DKKLRIPDKFVQKFGDE--LSSIAKFTIPSGRMWFVELKKC-NKQLWF-DIGWHEFIEHCSIHSGYFLIFKY 86 (335)
Q Consensus 19 ~~~l~IP~~F~~~~~~~--~~~~v~L~~~~g~~W~V~l~~~-~~~~~~-~~GW~~F~~~~~L~~Gd~lvF~~ 86 (335)
...+.||..-++.++.. -.-.|.-. -+|..|+-.|-.. ++.++| -+ ++..+.-++..||.+.+++
T Consensus 12 ~~fv~vP~~v~~~l~~~~~g~v~V~~t-I~g~~~~~sl~p~g~G~~~Lpv~--~~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 12 WTFVEVPFDVAEELGEGGWGRVPVRGT-IDGHPWRTSLFPMGNGGYILPVK--AAVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp -EEEE--S-HHHHH--S--S-EEEEEE-ETTEEEEEEEEESSTT-EEEEE---HHHHHHHT--TTSEEEEEE
T ss_pred eEEEEeCHHHHHHhccccCCceEEEEE-ECCEEEEEEEEECCCCCEEEEEc--HHHHHHcCCCCCCEEEEEC
Confidence 35788999999988865 33333333 4678999988773 455554 33 6889999999999998764
No 20
>PF08916 Phe_ZIP: Phenylalanine zipper; InterPro: IPR015012 The phenylalanine zipper consists of aromatic side chains from ten phenylalanine residues that are stacked within a hydrophobic core. This zipper mediates dimerisation of various proteins, such as APS, SH2-B and Lnk []. ; GO: 0004871 signal transducer activity, 0035556 intracellular signal transduction; PDB: 1Q2H_B.
Probab=20.86 E-value=49 Score=23.34 Aligned_cols=7 Identities=71% Similarity=1.640 Sum_probs=2.6
Q ss_pred cHHHHHh
Q 041048 66 GWHEFIE 72 (335)
Q Consensus 66 GW~~F~~ 72 (335)
||.+||+
T Consensus 2 ~W~EFCE 8 (59)
T PF08916_consen 2 GWREFCE 8 (59)
T ss_dssp -HHHHHH
T ss_pred CHHHHHH
Confidence 4444443
No 21
>PF11604 CusF_Ec: Copper binding periplasmic protein CusF; InterPro: IPR021647 CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein []. ; PDB: 2L55_A 2VB3_X 1ZEQ_X 2QCP_X 3E6Z_X 2VB2_X.
Probab=20.36 E-value=1.9e+02 Score=20.85 Aligned_cols=24 Identities=21% Similarity=0.293 Sum_probs=16.1
Q ss_pred cCCCCCCEEEEEEecCCCcEEEEE
Q 041048 300 NNLDESDVCVFELIKSNDVTLKAT 323 (335)
Q Consensus 300 n~L~~GD~cvFel~~~~~~~~~V~ 323 (335)
..|++||.+.|.+....+..+.|.
T Consensus 41 ~~l~~Gd~V~F~~~~~~~~~~~I~ 64 (70)
T PF11604_consen 41 AGLKPGDKVRFTFERTDDGSYVIT 64 (70)
T ss_dssp SS-STT-EEEEEEEEETTCEEEEE
T ss_pred hcCCCCCEEEEEEEECCCCcEEEE
Confidence 679999999999998654334433
No 22
>PF06071 YchF-GTPase_C: Protein of unknown function (DUF933); InterPro: IPR013029 This domain is found at the C terminus of family of conserved hypothetical proteins found in both prokaryotes and eukaryotes. While the function of these proteins is not known, the crystal structure of P44681 from SWISSPROT from Haemophilus influenzae has been determined []. This protein consists of three domains: an N-terminal domain which has a mononucleotide binding fold typical for the P-loop NTPases, a central domain which forms an alpha-helical coiled coil, and this C-terminal domain which is composed of a six-stranded half-barrel curved around an alpha helix. The central domain and this domain are topologically similar to RNA-binding proteins, while the N-terminal region contains the features typical of GTP-dependent molecular switches. The purified protein was capable of binding both double-stranded nucleic acid and GTP. It was suggested, therefore, that this protein might be part of a nucleoprotein complex and could function as a GTP-dependent translation factor.; PDB: 1NI3_A 1JAL_A 2DWQ_B 2DBY_A 2OHF_A.
Probab=20.27 E-value=61 Score=24.59 Aligned_cols=15 Identities=13% Similarity=0.541 Sum_probs=10.3
Q ss_pred hHcCCCCCcEEEEEE
Q 041048 72 EHCSIHSGYFLIFKY 86 (335)
Q Consensus 72 ~~~~L~~Gd~lvF~~ 86 (335)
++|-++.||++.|++
T Consensus 69 K~YivqDGDIi~f~f 83 (84)
T PF06071_consen 69 KDYIVQDGDIIHFRF 83 (84)
T ss_dssp TT-B--TTEEEEEEE
T ss_pred CceeEeCCCEEEEEc
Confidence 468889999999986
No 23
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=20.03 E-value=2.1e+02 Score=22.79 Aligned_cols=31 Identities=10% Similarity=0.201 Sum_probs=21.0
Q ss_pred cCCCCCCEEEEEEecCCCcEEEEEEEeeCCCC
Q 041048 300 NNLDESDVCVFELIKSNDVTLKATIFRVLEDA 331 (335)
Q Consensus 300 n~L~~GD~cvFel~~~~~~~~~V~Ifr~~~~~ 331 (335)
.++++||.++|.-..++ -.+.|.|.....+.
T Consensus 30 ~~ikvGD~I~f~~~~~~-~~l~v~V~~i~~Y~ 60 (109)
T cd06555 30 QQIKVGDKILFNDLDTG-QQLLVKVVDIRKYD 60 (109)
T ss_pred hcCCCCCEEEEEEcCCC-cEEEEEEEEEEecC
Confidence 56899999999766543 25666666655543
Done!