Query 043499
Match_columns 396
No_of_seqs 170 out of 800
Neff 6.9
Searched_HMMs 46136
Date Fri Mar 29 05:40:05 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/043499.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/043499hhsearch_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 99.8 7.6E-21 1.6E-25 156.2 9.4 93 303-395 1-100 (100)
2 PF02362 B3: B3 DNA binding do 99.8 1.6E-20 3.5E-25 154.2 10.7 93 73-165 1-100 (100)
3 PF03754 DUF313: Domain of unk 93.4 0.36 7.9E-06 40.8 7.3 67 72-138 23-114 (114)
4 PF03754 DUF313: Domain of unk 92.5 0.46 1E-05 40.2 6.7 65 302-366 23-114 (114)
5 smart00536 AXH domain in Ataxi 60.7 4.9 0.00011 34.0 1.5 24 354-377 79-112 (116)
6 PLN03148 Blue copper-like prot 60.4 7.7 0.00017 35.1 2.8 26 134-159 39-66 (167)
7 PF08922 DUF1905: Domain of un 57.3 52 0.0011 25.8 6.7 64 314-379 13-80 (80)
8 PLN03148 Blue copper-like prot 55.4 15 0.00032 33.2 3.7 27 363-389 40-66 (167)
9 PF04014 Antitoxin-MazE: Antid 54.6 18 0.00039 25.1 3.3 24 361-384 13-36 (47)
10 PF04014 Antitoxin-MazE: Antid 53.4 32 0.0007 23.9 4.5 28 133-160 13-40 (47)
11 PF08517 AXH: Ataxin-1 and HBP 52.1 4.5 9.8E-05 34.3 -0.1 23 354-376 78-110 (115)
12 PF02298 Cu_bind_like: Plastoc 43.0 16 0.00034 29.1 1.7 20 135-154 13-32 (85)
13 PF02298 Cu_bind_like: Plastoc 41.4 20 0.00044 28.4 2.1 26 364-389 14-39 (85)
14 TIGR01439 lp_hng_hel_AbrB loop 38.0 49 0.0011 21.9 3.4 23 361-383 13-35 (43)
15 PF11598 COMP: Cartilage oligo 36.4 42 0.0009 23.7 2.7 19 2-20 21-39 (45)
16 KOG2357 Uncharacterized conser 27.9 46 0.001 34.2 2.6 28 6-34 238-265 (440)
17 PF04692 PDGF_N: Platelet-deri 24.8 63 0.0014 25.5 2.3 24 1-24 5-33 (78)
18 KOG0260 RNA polymerase II, lar 24.0 1.3E+02 0.0028 35.3 5.3 80 70-153 338-440 (1605)
19 KOG2880 SMAD6 interacting prot 22.5 59 0.0013 32.9 2.1 59 44-117 325-386 (424)
20 PF12195 End_beta_barrel: Beta 22.5 45 0.00097 26.1 1.0 29 137-165 24-57 (83)
21 PF08922 DUF1905: Domain of un 22.1 3.8E+02 0.0083 20.8 7.7 64 85-151 13-80 (80)
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=99.84 E-value=7.6e-21 Score=156.16 Aligned_cols=93 Identities=37% Similarity=0.732 Sum_probs=68.8
Q ss_pred EEEEcccccce--eEEEeCHHHHHhhcCC--CCeeEEEEcCCCCEEEEEEEee---cceEeCcCchhhhcccCCCCCCEE
Q 043499 303 FVDILRSKKRY--SYMYVPSKFSKKHLIR--GTRSIKLQDSDGKEWPAQLTWS---SGCGIKGGWPAFSKYKNLKQGHVC 375 (396)
Q Consensus 303 F~~~m~~s~v~--~~L~IP~~F~~~~l~~--~~~~i~L~~~~G~~W~v~l~~~---~~~~~~~GW~~F~~~N~L~~GD~c 375 (396)
|+++|.++++. +.|.||++|+++|... .+.+|+|+|++|+.|+|++... ..+.|++||.+||++|+|++||+|
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 78888888776 7899999999999633 5679999999999999999532 247899999999999999999999
Q ss_pred EEEEeeCcccEEEEEEEecC
Q 043499 376 VFELIKAKDILLKVSIHASS 395 (396)
Q Consensus 376 vFeli~~~~~~~~VhI~r~~ 395 (396)
+|+++++....+.|||||+.
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 99999877678899999974
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=1.6e-20 Score=154.20 Aligned_cols=93 Identities=39% Similarity=0.720 Sum_probs=70.4
Q ss_pred EEEEccCCCCcc-ceeecChHHHHHhCCC--CCceEEEEcCCCCEEEEEE--EEECCeEEecccHHHHHhHcCCCCCCEE
Q 043499 73 FFKVILPSTVQE-KKLRIPRKFVKRFGDE--LSAVATLNVPNGRVWQVGL--RKDGRKIWLQDGWDNFAEYHSIAVGYFL 147 (396)
Q Consensus 73 F~kv~~~~~~~~-~~L~IP~~F~~~~~~~--~~~~v~L~~p~G~~W~V~l--~~~~~~~~~~~GW~~F~~~~~L~~GD~l 147 (396)
|+|+|++++... ..|.||..|++.|... .+..|+|++++|+.|.|.+ .+.++.++|++||++||++|+|++||+|
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 899998876544 6899999999999754 5779999999999999999 4556788999999999999999999999
Q ss_pred EEEEccCceE--EEEEEcCC
Q 043499 148 VFKYAKNSTF--DVLVFDMT 165 (396)
Q Consensus 148 vF~~~g~~~F--~V~If~~s 165 (396)
+|++++++.| .|+||+.|
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 9999997766 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=93.39 E-value=0.36 Score=40.83 Aligned_cols=67 Identities=21% Similarity=0.328 Sum_probs=45.6
Q ss_pred cEEEEccCCCCcc--ceeecChHHHHH--------------h----CCCCCceEEEEcCCCCEEEEEEEEECC-----eE
Q 043499 72 HFFKVILPSTVQE--KKLRIPRKFVKR--------------F----GDELSAVATLNVPNGRVWQVGLRKDGR-----KI 126 (396)
Q Consensus 72 ~F~kv~~~~~~~~--~~L~IP~~F~~~--------------~----~~~~~~~v~L~~p~G~~W~V~l~~~~~-----~~ 126 (396)
.+-|.+..+.+.. .+|.||-.=+.. . .....-.|+|.+|+++.|.+.+++..- .+
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 4555566655533 567777553311 0 123345799999999999999998643 56
Q ss_pred EecccHHHHHhH
Q 043499 127 WLQDGWDNFAEY 138 (396)
Q Consensus 127 ~~~~GW~~F~~~ 138 (396)
.|..||.++|.+
T Consensus 103 vL~~gWn~VV~~ 114 (114)
T PF03754_consen 103 VLNSGWNKVVED 114 (114)
T ss_pred EEEcChHhhccC
Confidence 799999999864
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=92.48 E-value=0.46 Score=40.19 Aligned_cols=65 Identities=17% Similarity=0.303 Sum_probs=47.2
Q ss_pred EEEEEcccccce---eEEEeCHHHHHhh--cC----------------CCCeeEEEEcCCCCEEEEEEE-eec-----ce
Q 043499 302 SFVDILRSKKRY---SYMYVPSKFSKKH--LI----------------RGTRSIKLQDSDGKEWPAQLT-WSS-----GC 354 (396)
Q Consensus 302 ~F~~~m~~s~v~---~~L~IP~~F~~~~--l~----------------~~~~~i~L~~~~G~~W~v~l~-~~~-----~~ 354 (396)
.+.+.|.+|+|. .+|.||-.=+..+ |. ...-.++|.|+.++.|.+++. |.. .|
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 355688888887 8899997755222 11 122478999999999999986 322 37
Q ss_pred EeCcCchhhhcc
Q 043499 355 GIKGGWPAFSKY 366 (396)
Q Consensus 355 ~~~~GW~~F~~~ 366 (396)
.|..||.+++.+
T Consensus 103 vL~~gWn~VV~~ 114 (114)
T PF03754_consen 103 VLNSGWNKVVED 114 (114)
T ss_pred EEEcChHhhccC
Confidence 899999998864
No 5
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=60.70 E-value=4.9 Score=34.01 Aligned_cols=24 Identities=25% Similarity=0.461 Sum_probs=18.8
Q ss_pred eEeCcCchhhhc----------ccCCCCCCEEEE
Q 043499 354 CGIKGGWPAFSK----------YKNLKQGHVCVF 377 (396)
Q Consensus 354 ~~~~~GW~~F~~----------~N~L~~GD~cvF 377 (396)
+++++||..|+= -..|++||+|+-
T Consensus 79 FV~gqGWsSc~P~lT~~~ygL~C~~L~vGDVCl~ 112 (116)
T smart00536 79 FVKGKGWSSCYPSLTVQLYGLPCCELQVGDVCLS 112 (116)
T ss_pred EEcCccccccChhhhhhhcCCcceecccCCEEec
Confidence 567889999963 356889999974
No 6
>PLN03148 Blue copper-like protein; Provisional
Probab=60.41 E-value=7.7 Score=35.05 Aligned_cols=26 Identities=31% Similarity=0.641 Sum_probs=20.1
Q ss_pred HHHhHcCCCCCCEEEEEEccC--ceEEE
Q 043499 134 NFAEYHSIAVGYFLVFKYAKN--STFDV 159 (396)
Q Consensus 134 ~F~~~~~L~~GD~lvF~~~g~--~~F~V 159 (396)
.-+..+..+.||.|+|+|..+ ++.+|
T Consensus 39 ~WA~~k~F~VGD~LvF~Y~~~~hnV~~V 66 (167)
T PLN03148 39 LWANNQTFYVGDLISFRYQKTQYNVFEV 66 (167)
T ss_pred HhhcCCCCccCCEEEEEecCCCceEEEE
Confidence 446778999999999999875 34444
No 7
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=57.29 E-value=52 Score=25.77 Aligned_cols=64 Identities=19% Similarity=0.219 Sum_probs=36.8
Q ss_pred eEEEeCHHHHHhhcCC--CCeeEEEEcCCCCEEEEEEEe-ecc-eEeCcCchhhhcccCCCCCCEEEEEE
Q 043499 314 SYMYVPSKFSKKHLIR--GTRSIKLQDSDGKEWPAQLTW-SSG-CGIKGGWPAFSKYKNLKQGHVCVFEL 379 (396)
Q Consensus 314 ~~L~IP~~F~~~~l~~--~~~~i~L~~~~G~~W~v~l~~-~~~-~~~~~GW~~F~~~N~L~~GD~cvFel 379 (396)
..+.||..-+..+... ..-.|... =+|..|...+.. ..+ +.+ .==++..+.-++.+||.+.++|
T Consensus 13 ~fv~vP~~v~~~l~~~~~g~v~V~~t-I~g~~~~~sl~p~g~G~~~L-pv~~~vRk~~g~~~Gd~V~v~l 80 (80)
T PF08922_consen 13 TFVEVPFDVAEELGEGGWGRVPVRGT-IDGHPWRTSLFPMGNGGYIL-PVKAAVRKAIGKEAGDTVEVTL 80 (80)
T ss_dssp EEEE--S-HHHHH--S--S-EEEEEE-ETTEEEEEEEEESSTT-EEE-EE-HHHHHHHT--TTSEEEEEE
T ss_pred EEEEeCHHHHHHhccccCCceEEEEE-ECCEEEEEEEEECCCCCEEE-EEcHHHHHHcCCCCCCEEEEEC
Confidence 5688999998888766 44444444 466899998866 333 221 0014566788999999998876
No 8
>PLN03148 Blue copper-like protein; Provisional
Probab=55.39 E-value=15 Score=33.21 Aligned_cols=27 Identities=15% Similarity=0.308 Sum_probs=21.3
Q ss_pred hhcccCCCCCCEEEEEEeeCcccEEEE
Q 043499 363 FSKYKNLKQGHVCVFELIKAKDILLKV 389 (396)
Q Consensus 363 F~~~N~L~~GD~cvFeli~~~~~~~~V 389 (396)
-+..+...+||.++|.+.....-|++|
T Consensus 40 WA~~k~F~VGD~LvF~Y~~~~hnV~~V 66 (167)
T PLN03148 40 WANNQTFYVGDLISFRYQKTQYNVFEV 66 (167)
T ss_pred hhcCCCCccCCEEEEEecCCCceEEEE
Confidence 357788999999999998875546665
No 9
>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=54.57 E-value=18 Score=25.15 Aligned_cols=24 Identities=17% Similarity=0.134 Sum_probs=20.2
Q ss_pred hhhhcccCCCCCCEEEEEEeeCcc
Q 043499 361 PAFSKYKNLKQGHVCVFELIKAKD 384 (396)
Q Consensus 361 ~~F~~~N~L~~GD~cvFeli~~~~ 384 (396)
++|.+..+|++||.+.++..+++.
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~g~ 36 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGDGK 36 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETTSE
T ss_pred HHHHHHcCCCCCCEEEEEEeCCCE
Confidence 467788899999999999998753
No 10
>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=53.43 E-value=32 Score=23.86 Aligned_cols=28 Identities=7% Similarity=0.049 Sum_probs=23.3
Q ss_pred HHHHhHcCCCCCCEEEEEEccCceEEEE
Q 043499 133 DNFAEYHSIAVGYFLVFKYAKNSTFDVL 160 (396)
Q Consensus 133 ~~F~~~~~L~~GD~lvF~~~g~~~F~V~ 160 (396)
++|+..++|+.||.+.+.+.++....+.
T Consensus 13 k~~~~~l~l~~Gd~v~i~~~~~g~i~i~ 40 (47)
T PF04014_consen 13 KEIREKLGLKPGDEVEIEVEGDGKIVIR 40 (47)
T ss_dssp HHHHHHTTSSTTTEEEEEEETTSEEEEE
T ss_pred HHHHHHcCCCCCCEEEEEEeCCCEEEEE
Confidence 5788999999999999999998744443
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=52.07 E-value=4.5 Score=34.27 Aligned_cols=23 Identities=26% Similarity=0.638 Sum_probs=14.3
Q ss_pred eEeCcCchhhh----------cccCCCCCCEEE
Q 043499 354 CGIKGGWPAFS----------KYKNLKQGHVCV 376 (396)
Q Consensus 354 ~~~~~GW~~F~----------~~N~L~~GD~cv 376 (396)
+++++||..|. .-..|++||+|+
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 45678998885 345789999997
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=43.03 E-value=16 Score=29.08 Aligned_cols=20 Identities=35% Similarity=0.549 Sum_probs=13.8
Q ss_pred HHhHcCCCCCCEEEEEEccC
Q 043499 135 FAEYHSIAVGYFLVFKYAKN 154 (396)
Q Consensus 135 F~~~~~L~~GD~lvF~~~g~ 154 (396)
=+....+..||.|+|.|...
T Consensus 13 Wa~~~~F~vGD~LvF~y~~~ 32 (85)
T PF02298_consen 13 WASGKTFRVGDTLVFNYDSG 32 (85)
T ss_dssp HHCTS-BETTEEEEEE--TT
T ss_pred hhcCCcEeCCCEEEEEecCC
Confidence 35667789999999999875
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=41.45 E-value=20 Score=28.44 Aligned_cols=26 Identities=19% Similarity=0.335 Sum_probs=17.2
Q ss_pred hcccCCCCCCEEEEEEeeCcccEEEE
Q 043499 364 SKYKNLKQGHVCVFELIKAKDILLKV 389 (396)
Q Consensus 364 ~~~N~L~~GD~cvFeli~~~~~~~~V 389 (396)
+..+.+.+||+++|.+.....-|++|
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 45677889999999998875556666
No 14
>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=38.05 E-value=49 Score=21.94 Aligned_cols=23 Identities=13% Similarity=0.092 Sum_probs=19.0
Q ss_pred hhhhcccCCCCCCEEEEEEeeCc
Q 043499 361 PAFSKYKNLKQGHVCVFELIKAK 383 (396)
Q Consensus 361 ~~F~~~N~L~~GD~cvFeli~~~ 383 (396)
++|....+++.||.+.++....+
T Consensus 13 ~~~r~~l~~~~gd~~~i~~~~~~ 35 (43)
T TIGR01439 13 KEIREKLGLKEGDRLEVIRVEDG 35 (43)
T ss_pred HHHHHHcCcCCCCEEEEEEeCCC
Confidence 46788899999999999976554
No 15
>PF11598 COMP: Cartilage oligomeric matrix protein; InterPro: IPR024665 Thrombospondins are adhesive glycoproteins that mediate cell-to-cell and cell-to-matrix interactions. Cartilage oligomeric matrix protein may play a role in the structural integrity of cartilage via its interaction with other extracellular matrix proteins such as collagen and fibronectin [, ]. Thrombospondin 3 and 4 and cartilage oligomeric matrix proteins contain a five-stranded coiled-coil domain represented by this entry. This domain has a binding site between two internal rings formed by Leu37 and Thr40 [].; PDB: 1MZ9_D 1FBM_A 1VDF_E.
Probab=36.36 E-value=42 Score=23.65 Aligned_cols=19 Identities=37% Similarity=0.464 Sum_probs=16.1
Q ss_pred chhHHHhHHHHHHHHHHHH
Q 043499 2 PEDMHQQLDNFRMLRRLIK 20 (396)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~ 20 (396)
-++|.||.+|.+-||..+.
T Consensus 21 k~~l~~Q~kE~~~LRntI~ 39 (45)
T PF11598_consen 21 KELLRQQIKETRFLRNTIM 39 (45)
T ss_dssp HHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 4789999999999998764
No 16
>KOG2357 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.92 E-value=46 Score=34.22 Aligned_cols=28 Identities=18% Similarity=0.256 Sum_probs=23.4
Q ss_pred HHhHHHHHHHHHHHHhhcCCCCCCceeec
Q 043499 6 HQQLDNFRMLRRLIKIFNEPDPNNRWKLK 34 (396)
Q Consensus 6 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 34 (396)
..--++.|||+||.-|..+| +||.|.-.
T Consensus 238 k~l~ke~~DLs~F~si~~~p-~~~~~lP~ 265 (440)
T KOG2357|consen 238 KKLFKEMRDLSRFASIVSSP-EGRYNLPE 265 (440)
T ss_pred HHHHHHHHHHHHHhccCCCc-ccccCCCc
Confidence 34568899999999999999 77877766
No 17
>PF04692 PDGF_N: Platelet-derived growth factor, N terminal region; InterPro: IPR006782 Platelet-derived growth factor (PDGF) [, ] is a potent mitogen for cells of mesenchymal origin, including smooth muscle cells and glial cells. In both mouse and human, the PDGF signalling network consists of four ligands, PDGFA-D, and two receptors, PDGFRalpha and PDGFRbeta. All PDGFs function as secreted, disulphide-linked homodimers, but only PDGFA and B can form functional heterodimers. PDGFRs also function as homo- and heterodimers. All known PDGFs have characteristic `PDGF domains', which include eight conserved cysteines that are involved in inter- and intramolecular bonds. Alternate splicing of the A chain transcript can give rise to two different forms that differ only in their C-terminal extremity. The transforming protein of Woolly monkey sarcoma virus (WMSV) (Simian sarcoma virus), encoded by the v-sis oncogene, is derived from the B chain of PDGF. PDGFs are mitogenic during early developmental stages, driving the proliferation of undifferentiated mesenchyme and some progenitor populations. During later maturation stages, PDGF signalling has been implicated in tissue remodelling and cellular differentiation, and in inductive events involved in patterning and morphogenesis. In addition to driving mesenchymal proliferation, PDGFs have been shown to direct the migration, differentiation and function of a variety of specialised mesenchymal and migratory cell types, both during development and in the adult animal []. PDGF is structurally related to a number of other growth factors which also form disulphide-linked homo- or heterodimers. This domain consists of the N-terminal regions of PGDF A and B.; GO: 0008083 growth factor activity, 0016020 membrane; PDB: 3MJK_Y 3MJG_A 1PDG_B.
Probab=24.75 E-value=63 Score=25.48 Aligned_cols=24 Identities=29% Similarity=0.558 Sum_probs=14.5
Q ss_pred CchhHHHhHH-----HHHHHHHHHHhhcC
Q 043499 1 MPEDMHQQLD-----NFRMLRRLIKIFNE 24 (396)
Q Consensus 1 ~~~~~~~~~~-----~~~~~~~~~~~~~~ 24 (396)
+|+++...|- -++|||||..|=+-
T Consensus 5 iP~eliErLs~S~I~SIsDLQrLL~iDSV 33 (78)
T PF04692_consen 5 IPEELIERLSNSEIRSISDLQRLLEIDSV 33 (78)
T ss_dssp S-HHHHHHHHTS---SHHHHHHHHT-SSS
T ss_pred ccHHHHHHHhcCCcccHHHHHHHHhcCCC
Confidence 3666655444 47888888887654
No 18
>KOG0260 consensus RNA polymerase II, large subunit [Transcription]
Probab=24.05 E-value=1.3e+02 Score=35.33 Aligned_cols=80 Identities=21% Similarity=0.248 Sum_probs=56.7
Q ss_pred CccEEEEccCC-CCccceeecChHHHHHhCC---------------------CCC-ceEEEEcCCCCEEEEEEEEECCeE
Q 043499 70 TSHFFKVILPS-TVQEKKLRIPRKFVKRFGD---------------------ELS-AVATLNVPNGRVWQVGLRKDGRKI 126 (396)
Q Consensus 70 ~p~F~kv~~~~-~~~~~~L~IP~~F~~~~~~---------------------~~~-~~v~L~~p~G~~W~V~l~~~~~~~ 126 (396)
--.|-+||+++ +++-+.+.||..-|+.+-- +-+ .+-++++ +|..-...+.+..+++
T Consensus 338 DFSaRTVItgDPnl~ldevGVP~sIAk~lTfpE~Vtp~NidrLqeLV~~g~~~~pgakyiird-~G~Ridlr~~~~~~d~ 416 (1605)
T KOG0260|consen 338 DFSARTVITGDPNLSLDEVGVPRSIAKRLTFPEHVTPFNIDRLQELVRRGLLEHPGAKYIIRD-NGDRIDLRYHKRAGDI 416 (1605)
T ss_pred CcceeeeecCCCCcchhcccCcHHHHhhccCcceeccccHHHHHHHhhCCCCCCCCcceeeec-CCcEEEEeecCCcccc
Confidence 34778889986 6665889999998887621 111 1223333 6777777777777888
Q ss_pred EecccHHHHHhHcCCCCCCEEEEEEcc
Q 043499 127 WLQDGWDNFAEYHSIAVGYFLVFKYAK 153 (396)
Q Consensus 127 ~~~~GW~~F~~~~~L~~GD~lvF~~~g 153 (396)
-|+-||+- +-+|+.||+++|.---
T Consensus 417 ~Lq~G~kV---eRhl~DGD~VlfNRqP 440 (1605)
T KOG0260|consen 417 HLQPGYKV---ERHLMDGDVVLFNRQP 440 (1605)
T ss_pred ccccccEE---EEeeccCCEEEEcCCC
Confidence 99999985 4579999999997543
No 19
>KOG2880 consensus SMAD6 interacting protein AMSH, contains JAB/MPN/Mov34 domain [Signal transduction mechanisms]
Probab=22.54 E-value=59 Score=32.90 Aligned_cols=59 Identities=14% Similarity=0.204 Sum_probs=35.7
Q ss_pred EeeccceeeeccCchhhhccCCCCCCCccEEEEcc-CCCCccceeecChHHHHHhCCC--CCceEEEEcCCCCEEEE
Q 043499 44 LIQKGLYTTVANNNVKQMAGGNRRAETSHFFKVIL-PSTVQEKKLRIPRKFVKRFGDE--LSAVATLNVPNGRVWQV 117 (396)
Q Consensus 44 ~~~~g~~~~~~~~~~~~ma~~~~~~~~p~F~kv~~-~~~~~~~~L~IP~~F~~~~~~~--~~~~v~L~~p~G~~W~V 117 (396)
|+..|||+. .+...+|...+- ..+. +..+++|.++|=-.-+. ..+...|.+|.|-.--.
T Consensus 325 L~tlGWIHT--------------HPTQt~FmSSVDlHTHc-SYQiMlPEAiAIV~aPk~~~tGiFrLt~~~Gm~~i~ 386 (424)
T KOG2880|consen 325 LLTLGWIHT--------------HPTQTCFMSSVDLHTHC-SYQIMLPEAIAIVCAPKSKTTGIFRLTDPGGMEVIR 386 (424)
T ss_pred ceeeeeeec--------------CCccchhheeccccccc-eeeeecchheeEEeccccCCcceEEecCCcchHHHh
Confidence 666899998 456668866542 2222 36789998886554442 34455666665544333
No 20
>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=22.46 E-value=45 Score=26.13 Aligned_cols=29 Identities=28% Similarity=0.410 Sum_probs=15.1
Q ss_pred hHcCCCCCCEEEEEEccC----ceEEEE-EEcCC
Q 043499 137 EYHSIAVGYFLVFKYAKN----STFDVL-VFDMT 165 (396)
Q Consensus 137 ~~~~L~~GD~lvF~~~g~----~~F~V~-If~~s 165 (396)
.+|+|..||++.|.-.+- ..+.|. |.|++
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 589999999999987763 255554 44443
No 21
>PF08922 DUF1905: Domain of unknown function (DUF1905); InterPro: IPR015018 This family consist of hypothetical bacterial proteins. ; PDB: 2D9R_A.
Probab=22.12 E-value=3.8e+02 Score=20.80 Aligned_cols=64 Identities=11% Similarity=0.153 Sum_probs=38.3
Q ss_pred ceeecChHHHHHhCCC--CCceEEEEcCCCCEEEEEEEEE-CCeEEec-ccHHHHHhHcCCCCCCEEEEEE
Q 043499 85 KKLRIPRKFVKRFGDE--LSAVATLNVPNGRVWQVGLRKD-GRKIWLQ-DGWDNFAEYHSIAVGYFLVFKY 151 (396)
Q Consensus 85 ~~L~IP~~F~~~~~~~--~~~~v~L~~p~G~~W~V~l~~~-~~~~~~~-~GW~~F~~~~~L~~GD~lvF~~ 151 (396)
..+.||..-+..+... -.-.|.-.- +|..|+-.+--. ++.++|- + ++..+.-++..||.+.+++
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 5789999999998866 333333333 678999988763 3544432 3 6888899999999988764
Done!