Query 042542
Match_columns 359
No_of_seqs 165 out of 781
Neff 7.3
Searched_HMMs 46136
Date Fri Mar 29 07:11:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/042542.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/042542hhsearch_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 2.6E-21 5.6E-26 155.8 9.9 92 268-359 1-99 (100)
2 PF02362 B3: B3 DNA binding do 99.8 7.1E-21 1.5E-25 153.3 10.3 93 22-114 1-100 (100)
3 PF03754 DUF313: Domain of unk 94.3 0.15 3.3E-06 42.1 6.5 65 267-331 23-114 (114)
4 PF03754 DUF313: Domain of unk 92.4 0.66 1.4E-05 38.3 7.4 70 18-87 18-114 (114)
5 PF08922 DUF1905: Domain of un 63.2 36 0.00077 26.0 6.6 60 281-344 14-80 (80)
6 PF04014 Antitoxin-MazE: Antid 60.1 22 0.00047 24.1 4.4 26 82-107 13-38 (47)
7 PLN03148 Blue copper-like prot 57.3 10 0.00022 33.5 2.9 26 83-108 39-66 (167)
8 PF04014 Antitoxin-MazE: Antid 55.5 20 0.00042 24.3 3.5 25 326-350 13-37 (47)
9 smart00536 AXH domain in Ataxi 54.7 6 0.00013 32.7 1.0 24 319-342 79-112 (116)
10 PLN03148 Blue copper-like prot 49.4 20 0.00044 31.6 3.5 28 327-354 39-66 (167)
11 PF08517 AXH: Ataxin-1 and HBP 43.9 6.7 0.00015 32.4 -0.3 23 319-341 78-110 (115)
12 PF02298 Cu_bind_like: Plastoc 43.2 15 0.00032 28.5 1.6 19 85-103 14-32 (85)
13 TIGR01439 lp_hng_hel_AbrB loop 39.1 54 0.0012 21.2 3.6 24 326-349 13-36 (43)
14 PF11976 Rad60-SLD: Ubiquitin- 32.0 50 0.0011 24.0 2.9 48 53-103 2-49 (72)
15 PF02298 Cu_bind_like: Plastoc 31.6 36 0.00078 26.3 2.0 26 329-354 14-39 (85)
16 KOG4146 Ubiquitin-like protein 29.7 32 0.0007 27.3 1.4 44 39-100 53-96 (101)
17 PF08922 DUF1905: Domain of un 27.8 2.7E+02 0.0059 21.1 7.4 64 34-100 13-80 (80)
18 COG5131 URM1 Ubiquitin-like pr 23.8 46 0.00099 26.2 1.3 37 46-100 55-91 (96)
19 PF12195 End_beta_barrel: Beta 23.4 44 0.00095 25.5 1.1 17 85-101 23-39 (83)
20 PF11976 Rad60-SLD: Ubiquitin- 22.0 1.6E+02 0.0034 21.3 3.9 43 298-342 2-45 (72)
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=99.85 E-value=2.6e-21 Score=155.84 Aligned_cols=92 Identities=36% Similarity=0.632 Sum_probs=69.2
Q ss_pred EEEEccCcccccCc-eEcCHHHHHhhCCC--CC-eEEEEeCCCCEEEEEEEecc---ccccccchhhhhcccCCCCCCEE
Q 042542 268 FLVFLRASNMQLNC-VYVPNSFARKYFNG--EE-CVTIQDSDGRKLAVKVKVSC---SKCLLTRWGKFFKKTNVKEGDIL 340 (359)
Q Consensus 268 f~~~m~~s~v~~~~-l~iP~~F~~~~l~~--~~-~i~L~~~~G~~W~v~l~~~~---~~~l~~GW~~F~~~n~L~~GD~c 340 (359)
|+++|.++++...+ |.||++|+++|... .. +|+|++++|+.|.|.+.++. .+.|++||.+||++|+|++||+|
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 77888888887665 99999999999643 45 99999999999999995432 25899999999999999999999
Q ss_pred EEEEEecceeEEEEEEEeC
Q 042542 341 FFEMIQMKNILLKVSVFNA 359 (359)
Q Consensus 341 vFeli~~~~~~~~VhIfr~ 359 (359)
+|+++++....+.|+|||+
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 9999987677889999986
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=7.1e-21 Score=153.26 Aligned_cols=93 Identities=28% Similarity=0.600 Sum_probs=70.8
Q ss_pred eEEEccCCccc-cceeeCchHHHHhhCCC--CCceEEEECCCCCEEEEEE--EEECCeeEEcccHHHHHhHcCCCCCCEE
Q 042542 22 FFQVILAVTIE-DKKMKIPQNFVGRFGDE--LSYVATLTNPKGYVVRIGI--TKKEGKIWFDDGWNEFVQYHSIGVGYFV 96 (359)
Q Consensus 22 F~k~i~~~~l~-~~~l~IP~~F~~~~~~~--~~~~i~L~~~~g~~W~V~l--~~~~~~~~~~~GW~~F~~~~~l~~Gd~l 96 (359)
|+|+|++++.. .+.|.||..|++.|+.. .+..|+|.+++|+.|.|.+ .+.++.++|+.||++||++|+|++||+|
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 89999887654 46899999999999865 5779999999999999999 5566789999999999999999999999
Q ss_pred EEEEeecceE--EEEEEccC
Q 042542 97 VFQYRKNSKF--QVFVFNTT 114 (359)
Q Consensus 97 vF~~~g~s~F--~V~if~~s 114 (359)
+|++++++.| .|+||+.+
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 9999987776 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=94.31 E-value=0.15 Score=42.06 Aligned_cols=65 Identities=15% Similarity=0.187 Sum_probs=47.8
Q ss_pred eEEEEccCcccccCc--eEcCHHHHHh--h--------C--------CCCC-eEEEEeCCCCEEEEEEEecc------cc
Q 042542 267 SFLVFLRASNMQLNC--VYVPNSFARK--Y--------F--------NGEE-CVTIQDSDGRKLAVKVKVSC------SK 319 (359)
Q Consensus 267 ~f~~~m~~s~v~~~~--l~iP~~F~~~--~--------l--------~~~~-~i~L~~~~G~~W~v~l~~~~------~~ 319 (359)
.+.+.+..++|..+. |.||..=... + + .... .++|.|+.++.|.+.|..+. .|
T Consensus 23 i~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~~~~~Y 102 (114)
T PF03754_consen 23 IIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGNGTSNY 102 (114)
T ss_pred EEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccCCceEE
Confidence 467788999997764 9999763311 1 1 1223 88999999999999987542 36
Q ss_pred ccccchhhhhcc
Q 042542 320 CLLTRWGKFFKK 331 (359)
Q Consensus 320 ~l~~GW~~F~~~ 331 (359)
.|..||.++|.+
T Consensus 103 vL~~gWn~VV~~ 114 (114)
T PF03754_consen 103 VLNSGWNKVVED 114 (114)
T ss_pred EEEcChHhhccC
Confidence 899999999864
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=92.43 E-value=0.66 Score=38.34 Aligned_cols=70 Identities=13% Similarity=0.251 Sum_probs=49.1
Q ss_pred CCCc--eEEEccCCccc--cceeeCchHHHHhh------------------CCCCCceEEEECCCCCEEEEEEEEE-C--
Q 042542 18 TNSL--FFQVILAVTIE--DKKMKIPQNFVGRF------------------GDELSYVATLTNPKGYVVRIGITKK-E-- 72 (359)
Q Consensus 18 ~~p~--F~k~i~~~~l~--~~~l~IP~~F~~~~------------------~~~~~~~i~L~~~~g~~W~V~l~~~-~-- 72 (359)
..|. +-|.+..+++. ..+|.||-.=+... .....-.|+|.+|+++.|.+.|++- .
T Consensus 18 ~d~kli~~K~L~~tDv~~~qsRLsmP~~qi~~~dFLt~eE~~~i~~~~~~~~~~~Gv~V~lvdp~~~~~~m~lkkW~mg~ 97 (114)
T PF03754_consen 18 EDPKLIIEKTLFKTDVDPHQSRLSMPFNQIIDNDFLTEEEKRIIKEEKKNNDKKKGVEVILVDPSLRKWTMRLKKWNMGN 97 (114)
T ss_pred CCCeEEEeeeecccCCCCCCceeeccHHHhcccccCCHHHHHHHHHhhccCcccCCceEEEECCcCcEEEEEEEEecccC
Confidence 4553 56777777775 36888886644111 1123456999999999999999873 2
Q ss_pred --CeeEEcccHHHHHhH
Q 042542 73 --GKIWFDDGWNEFVQY 87 (359)
Q Consensus 73 --~~~~~~~GW~~F~~~ 87 (359)
..+.|..||.++|++
T Consensus 98 ~~~~YvL~~gWn~VV~~ 114 (114)
T PF03754_consen 98 GTSNYVLNSGWNKVVED 114 (114)
T ss_pred CceEEEEEcChHhhccC
Confidence 267899999999864
No 5
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=63.24 E-value=36 Score=26.05 Aligned_cols=60 Identities=18% Similarity=0.085 Sum_probs=36.3
Q ss_pred ceEcCHHHHHhhCCC--CC-eEEEEeCCCCEEEEEEEecc-c-c--ccccchhhhhcccCCCCCCEEEEEE
Q 042542 281 CVYVPNSFARKYFNG--EE-CVTIQDSDGRKLAVKVKVSC-S-K--CLLTRWGKFFKKTNVKEGDILFFEM 344 (359)
Q Consensus 281 ~l~iP~~F~~~~l~~--~~-~i~L~~~~G~~W~v~l~~~~-~-~--~l~~GW~~F~~~n~L~~GD~cvFel 344 (359)
++.||..-+...... .. .+.... +|..|...|.... . + .+. ++.-++-++.+||.+.++|
T Consensus 14 fv~vP~~v~~~l~~~~~g~v~V~~tI-~g~~~~~sl~p~g~G~~~Lpv~---~~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 14 FVEVPFDVAEELGEGGWGRVPVRGTI-DGHPWRTSLFPMGNGGYILPVK---AAVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp EEE--S-HHHHH--S--S-EEEEEEE-TTEEEEEEEEESSTT-EEEEE----HHHHHHHT--TTSEEEEEE
T ss_pred EEEeCHHHHHHhccccCCceEEEEEE-CCEEEEEEEEECCCCCEEEEEc---HHHHHHcCCCCCCEEEEEC
Confidence 599999888887766 55 665554 5789999886522 1 2 122 5677788999999998876
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=60.06 E-value=22 Score=24.09 Aligned_cols=26 Identities=15% Similarity=0.118 Sum_probs=22.2
Q ss_pred HHHHhHcCCCCCCEEEEEEeecceEE
Q 042542 82 NEFVQYHSIGVGYFVVFQYRKNSKFQ 107 (359)
Q Consensus 82 ~~F~~~~~l~~Gd~lvF~~~g~s~F~ 107 (359)
++|++.++|+.||-+.+.+.++....
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 57888999999999999999887433
No 7
>PLN03148 Blue copper-like protein; Provisional
Probab=57.32 E-value=10 Score=33.54 Aligned_cols=26 Identities=27% Similarity=0.565 Sum_probs=19.6
Q ss_pred HHHhHcCCCCCCEEEEEEeec--ceEEE
Q 042542 83 EFVQYHSIGVGYFVVFQYRKN--SKFQV 108 (359)
Q Consensus 83 ~F~~~~~l~~Gd~lvF~~~g~--s~F~V 108 (359)
.-+..+....||.|+|+|..+ ++..|
T Consensus 39 ~WA~~k~F~VGD~LvF~Y~~~~hnV~~V 66 (167)
T PLN03148 39 LWANNQTFYVGDLISFRYQKTQYNVFEV 66 (167)
T ss_pred HhhcCCCCccCCEEEEEecCCCceEEEE
Confidence 345778899999999999854 44444
No 8
>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=55.47 E-value=20 Score=24.33 Aligned_cols=25 Identities=24% Similarity=0.210 Sum_probs=19.4
Q ss_pred hhhhcccCCCCCCEEEEEEEeccee
Q 042542 326 GKFFKKTNVKEGDILFFEMIQMKNI 350 (359)
Q Consensus 326 ~~F~~~n~L~~GD~cvFeli~~~~~ 350 (359)
++|.+..+|++||.+.+....++.+
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 4677788999999999999765433
No 9
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=54.69 E-value=6 Score=32.67 Aligned_cols=24 Identities=13% Similarity=0.303 Sum_probs=18.7
Q ss_pred cccccchhhhhcc----------cCCCCCCEEEE
Q 042542 319 KCLLTRWGKFFKK----------TNVKEGDILFF 342 (359)
Q Consensus 319 ~~l~~GW~~F~~~----------n~L~~GD~cvF 342 (359)
++.++||..|.=. ..|++||+|+-
T Consensus 79 FV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~ 112 (116)
T smart00536 79 FVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLS 112 (116)
T ss_pred EEcCccccccChhhhhhhcCCcceecccCCEEec
Confidence 4789999998643 46789999973
No 10
>PLN03148 Blue copper-like protein; Provisional
Probab=49.44 E-value=20 Score=31.63 Aligned_cols=28 Identities=14% Similarity=0.280 Sum_probs=21.2
Q ss_pred hhhcccCCCCCCEEEEEEEecceeEEEE
Q 042542 327 KFFKKTNVKEGDILFFEMIQMKNILLKV 354 (359)
Q Consensus 327 ~F~~~n~L~~GD~cvFeli~~~~~~~~V 354 (359)
+-+..+..++||.++|.+-....-+++|
T Consensus 39 ~WA~~k~F~VGD~LvF~Y~~~~hnV~~V 66 (167)
T PLN03148 39 LWANNQTFYVGDLISFRYQKTQYNVFEV 66 (167)
T ss_pred HhhcCCCCccCCEEEEEecCCCceEEEE
Confidence 3457789999999999997654456655
No 11
>PF08517 AXH: Ataxin-1 and HBP1 module (AXH); InterPro: IPR013723 AXH is a protein-protein and RNA binding motif found in Ataxin-1 (ATX1)[]. ATX1 is responsible for the autosomal-dominant neurodegenerative disorder Spinocerebellar ataxia type-1 (SCA1) in humans. The AXH module has also been identified in the apparently unrelated transcription factor HBP1 which is thought to be involved in the architectural regulation of chromatin and in specific gene expression []. ; GO: 0005488 binding; PDB: 1OA8_C 3QVE_C 1V06_A.
Probab=43.93 E-value=6.7 Score=32.42 Aligned_cols=23 Identities=13% Similarity=0.239 Sum_probs=15.1
Q ss_pred cccccchhhhhcc----------cCCCCCCEEE
Q 042542 319 KCLLTRWGKFFKK----------TNVKEGDILF 341 (359)
Q Consensus 319 ~~l~~GW~~F~~~----------n~L~~GD~cv 341 (359)
++.++||..|.=+ ..|++||+|+
T Consensus 78 FV~gkGWsS~~P~~T~~~ygL~C~~L~vGDvCl 110 (115)
T PF08517_consen 78 FVKGKGWSSCNPSLTVQLYGLPCRQLQVGDVCL 110 (115)
T ss_dssp EETTTEEEESSHHHHHHHHTS--EE--TT-EEE
T ss_pred EEeCCcccccCcchhceecCCcccccccCCEEe
Confidence 3679999888532 4678999997
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=43.24 E-value=15 Score=28.50 Aligned_cols=19 Identities=26% Similarity=0.427 Sum_probs=13.1
Q ss_pred HhHcCCCCCCEEEEEEeec
Q 042542 85 VQYHSIGVGYFVVFQYRKN 103 (359)
Q Consensus 85 ~~~~~l~~Gd~lvF~~~g~ 103 (359)
+....+..||.|+|.|...
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 4566788999999999864
No 13
>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=39.06 E-value=54 Score=21.16 Aligned_cols=24 Identities=25% Similarity=0.228 Sum_probs=18.4
Q ss_pred hhhhcccCCCCCCEEEEEEEecce
Q 042542 326 GKFFKKTNVKEGDILFFEMIQMKN 349 (359)
Q Consensus 326 ~~F~~~n~L~~GD~cvFeli~~~~ 349 (359)
++|....+++.||.+.++....+.
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~~~~ 36 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVEDGE 36 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeCCCE
Confidence 467788899999999998764443
No 14
>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=32.02 E-value=50 Score=24.00 Aligned_cols=48 Identities=4% Similarity=0.084 Sum_probs=35.7
Q ss_pred eEEEECCCCCEEEEEEEEECCeeEEcccHHHHHhHcCCCCCCEEEEEEeec
Q 042542 53 VATLTNPKGYVVRIGITKKEGKIWFDDGWNEFVQYHSIGVGYFVVFQYRKN 103 (359)
Q Consensus 53 ~i~L~~~~g~~W~V~l~~~~~~~~~~~GW~~F~~~~~l~~Gd~lvF~~~g~ 103 (359)
+|+|++.+|+.-.+.+... .-|..=...|++..++..-.-+.|.|+|.
T Consensus 2 ~i~v~~~~~~~~~~~v~~~---~~~~~l~~~~~~~~~i~~~~~~~l~fdG~ 49 (72)
T PF11976_consen 2 TIKVRSQDGKEIKFKVKPT---TTVSKLIEKYCEKKGIPPEESIRLIFDGK 49 (72)
T ss_dssp EEEEEETTSEEEEEEEETT---SCCHHHHHHHHHHHTTTT-TTEEEEETTE
T ss_pred EEEEEeCCCCEEEEEECCC---CcHHHHHHHHHHhhCCCccceEEEEECCE
Confidence 5788998888777777643 34677779999999999955666777664
No 15
>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=31.62 E-value=36 Score=26.33 Aligned_cols=26 Identities=19% Similarity=0.293 Sum_probs=16.9
Q ss_pred hcccCCCCCCEEEEEEEecceeEEEE
Q 042542 329 FKKTNVKEGDILFFEMIQMKNILLKV 354 (359)
Q Consensus 329 ~~~n~L~~GD~cvFeli~~~~~~~~V 354 (359)
+..+.+.+||.++|.......-+++|
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 46678899999999997654556665
No 16
>KOG4146 consensus Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=29.69 E-value=32 Score=27.26 Aligned_cols=44 Identities=14% Similarity=0.064 Sum_probs=30.4
Q ss_pred chHHHHhhCCCCCceEEEECCCCCEEEEEEEEECCeeEEcccHHHHHhHcCCCCCCEEEEEE
Q 042542 39 PQNFVGRFGDELSYVATLTNPKGYVVRIGITKKEGKIWFDDGWNEFVQYHSIGVGYFVVFQY 100 (359)
Q Consensus 39 P~~F~~~~~~~~~~~i~L~~~~g~~W~V~l~~~~~~~~~~~GW~~F~~~~~l~~Gd~lvF~~ 100 (359)
|..|.-+++.-.++.|+|.+ ..-|++.=+ .+|.|++||.+||.-
T Consensus 53 r~~lFi~~gsvrpGii~lIN--d~DWEllek----------------edy~ledgD~ivfiS 96 (101)
T KOG4146|consen 53 RDSLFIHHGSVRPGIIVLIN--DMDWELLEK----------------EDYPLEDGDHIVFIS 96 (101)
T ss_pred CcceEeeCCcCcCcEEEEEe--ccchhhhcc----------------cccCcccCCEEEEEE
Confidence 44444455556678888875 466776543 478999999999964
No 17
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=27.78 E-value=2.7e+02 Score=21.09 Aligned_cols=64 Identities=13% Similarity=0.058 Sum_probs=38.2
Q ss_pred ceeeCchHHHHhhCCC--CCceEEEECCCCCEEEEEEEEE-CCeeEE-cccHHHHHhHcCCCCCCEEEEEE
Q 042542 34 KKMKIPQNFVGRFGDE--LSYVATLTNPKGYVVRIGITKK-EGKIWF-DDGWNEFVQYHSIGVGYFVVFQY 100 (359)
Q Consensus 34 ~~l~IP~~F~~~~~~~--~~~~i~L~~~~g~~W~V~l~~~-~~~~~~-~~GW~~F~~~~~l~~Gd~lvF~~ 100 (359)
..+.||..-+..++.. -.-.|.-+- +|..|+-.|-.. +|.++| -+ ++..+.-++..||.+.+++
T Consensus 13 ~fv~vP~~v~~~l~~~~~g~v~V~~tI-~g~~~~~sl~p~g~G~~~Lpv~--~~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 13 TFVEVPFDVAEELGEGGWGRVPVRGTI-DGHPWRTSLFPMGNGGYILPVK--AAVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp EEEE--S-HHHHH--S--S-EEEEEEE-TTEEEEEEEEESSTT-EEEEE---HHHHHHHT--TTSEEEEEE
T ss_pred EEEEeCHHHHHHhccccCCceEEEEEE-CCEEEEEEEEECCCCCEEEEEc--HHHHHHcCCCCCCEEEEEC
Confidence 5678998888888866 344444433 679999988763 344433 22 6888999999999998764
No 18
>COG5131 URM1 Ubiquitin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=23.80 E-value=46 Score=26.24 Aligned_cols=37 Identities=16% Similarity=0.109 Sum_probs=26.1
Q ss_pred hCCCCCceEEEECCCCCEEEEEEEEECCeeEEcccHHHHHhHcCCCCCCEEEEEE
Q 042542 46 FGDELSYVATLTNPKGYVVRIGITKKEGKIWFDDGWNEFVQYHSIGVGYFVVFQY 100 (359)
Q Consensus 46 ~~~~~~~~i~L~~~~g~~W~V~l~~~~~~~~~~~GW~~F~~~~~l~~Gd~lvF~~ 100 (359)
++.-.++.|+|.+ +.-|++.=+ ++|.|++||.++|.-
T Consensus 55 ~g~lrpGiI~LIN--d~DWeLlek----------------e~y~ledgDiIvfis 91 (96)
T COG5131 55 HGELRPGIICLIN--DMDWELLEK----------------ERYPLEDGDIIVFIS 91 (96)
T ss_pred CCCCcccEEEEEc--CccHhhhhc----------------ccccCCCCCEEEEEe
Confidence 3444577788874 677776543 257899999999964
No 19
>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=23.43 E-value=44 Score=25.50 Aligned_cols=17 Identities=35% Similarity=0.471 Sum_probs=8.6
Q ss_pred HhHcCCCCCCEEEEEEe
Q 042542 85 VQYHSIGVGYFVVFQYR 101 (359)
Q Consensus 85 ~~~~~l~~Gd~lvF~~~ 101 (359)
..+|+|..||++.|--.
T Consensus 23 l~~HGl~vGD~VnFsns 39 (83)
T PF12195_consen 23 LTDHGLFVGDFVNFSNS 39 (83)
T ss_dssp -TT----TT-EEEEES-
T ss_pred EccCceeecceEEEecc
Confidence 35799999999999765
No 20
>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=21.98 E-value=1.6e+02 Score=21.30 Aligned_cols=43 Identities=19% Similarity=0.375 Sum_probs=31.0
Q ss_pred eEEEEeCCCCEEEEEEEeccccccccchhhhhcccCCCC-CCEEEE
Q 042542 298 CVTIQDSDGRKLAVKVKVSCSKCLLTRWGKFFKKTNVKE-GDILFF 342 (359)
Q Consensus 298 ~i~L~~~~G~~W~v~l~~~~~~~l~~GW~~F~~~n~L~~-GD~cvF 342 (359)
+|+|+..+|+. +.+.+.....++.=...|+..+++.. .++.++
T Consensus 2 ~i~v~~~~~~~--~~~~v~~~~~~~~l~~~~~~~~~i~~~~~~~l~ 45 (72)
T PF11976_consen 2 TIKVRSQDGKE--IKFKVKPTTTVSKLIEKYCEKKGIPPEESIRLI 45 (72)
T ss_dssp EEEEEETTSEE--EEEEEETTSCCHHHHHHHHHHHTTTT-TTEEEE
T ss_pred EEEEEeCCCCE--EEEEECCCCcHHHHHHHHHHhhCCCccceEEEE
Confidence 47888888884 44445555567777889999999998 655544
Done!