Query 014983
Match_columns 415
No_of_seqs 162 out of 417
Neff 6.4
Searched_HMMs 46136
Date Fri Mar 29 01:58:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014983.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014983hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2061 Uncharacterized MYND Z 100.0 6.1E-89 1.3E-93 670.1 22.8 334 50-410 5-361 (362)
2 PF04194 PDCD2_C: Programmed c 100.0 6.8E-48 1.5E-52 350.4 13.5 156 253-410 1-163 (164)
3 PF09234 DUF1963: Domain of un 97.0 0.0013 2.8E-08 62.2 6.1 53 74-132 1-56 (224)
4 PF01753 zf-MYND: MYND finger; 96.9 0.00017 3.8E-09 49.4 -0.3 37 189-227 1-37 (37)
5 PF04194 PDCD2_C: Programmed c 95.5 0.0093 2E-07 54.5 2.6 61 75-136 78-147 (164)
6 KOG1710 MYND Zn-finger and ank 93.7 0.019 4.1E-07 56.6 0.0 43 187-230 320-362 (396)
7 COG3878 Uncharacterized protei 90.7 0.29 6.3E-06 47.2 4.0 65 50-129 19-87 (261)
8 KOG2061 Uncharacterized MYND Z 80.8 0.98 2.1E-05 46.1 2.0 59 329-395 31-90 (362)
9 smart00440 ZnF_C2C2 C2C2 Zinc 66.1 11 0.00024 26.2 3.8 34 349-395 2-35 (40)
10 PF01096 TFIIS_C: Transcriptio 60.7 12 0.00027 25.8 3.2 34 349-395 2-35 (39)
11 PF09234 DUF1963: Domain of un 58.2 10 0.00022 35.5 3.4 35 72-112 154-188 (224)
12 PF08394 Arc_trans_TRASH: Arch 57.3 5.4 0.00012 27.5 0.9 28 96-135 1-30 (37)
13 PF09151 DUF1936: Domain of un 54.3 19 0.00042 23.8 3.1 31 95-135 3-33 (36)
14 TIGR01384 TFS_arch transcripti 49.3 24 0.00053 29.2 3.9 35 348-395 63-97 (104)
15 PF14353 CpXC: CpXC protein 47.8 15 0.00032 31.8 2.4 39 94-136 2-46 (128)
16 PF14353 CpXC: CpXC protein 44.8 29 0.00064 29.8 3.8 44 349-396 3-46 (128)
17 PF14169 YdjO: Cold-inducible 43.0 15 0.00033 28.0 1.5 23 345-367 37-59 (59)
18 PF09855 DUF2082: Nucleic-acid 31.1 55 0.0012 25.3 2.9 39 95-135 2-43 (64)
19 PF14475 Mso1_Sec1_bdg: Sec1-b 28.5 11 0.00023 26.7 -1.3 18 66-83 24-41 (41)
20 KOG2906 RNA polymerase III sub 24.3 55 0.0012 27.6 2.0 17 348-364 66-82 (105)
21 PF08421 Methyltransf_13: Puta 22.8 1.2E+02 0.0026 22.9 3.5 44 350-395 1-47 (62)
22 PF11331 DUF3133: Protein of u 21.7 64 0.0014 23.4 1.6 15 93-107 31-45 (46)
23 PF07295 DUF1451: Protein of u 21.2 55 0.0012 29.4 1.5 44 307-356 88-139 (146)
24 TIGR00686 phnA alkylphosphonat 20.5 64 0.0014 27.6 1.6 17 347-363 2-18 (109)
No 1
>KOG2061 consensus Uncharacterized MYND Zn-finger protein [General function prediction only]
Probab=100.00 E-value=6.1e-89 Score=670.10 Aligned_cols=334 Identities=41% Similarity=0.796 Sum_probs=272.8
Q ss_pred ccceEEEeecCCCCccccccCCCC-ccccCCCCCCCCCCCCCCCccccCccCCCceeEEEEeecCCCCCCCcccEEEEEe
Q 014983 50 QKPVTLGFLEKPKNRWSLLRHLFP-SKAGGPPAWLDPINLPTGRSCLCDMCGEPLQFVLQVYAPIIEKESTFHRTLFLFM 128 (415)
Q Consensus 50 ~~~V~LGF~d~~~~~~~l~~~~fp-SKiGG~P~WL~p~~lP~~~~l~C~~C~~pm~fLlQvYAPl~~~~~~fhRtLYVF~ 128 (415)
.++|+|||++ +...+.+.+..|+ |||||.|+||++.++|....++|..|+++|.||||+|||+.+.+++|||+||||+
T Consensus 5 ~~~V~LGf~d-~~~~~~~~~~~~~~skiGG~P~wl~~~~~p~~~~l~C~~C~~~~~lllQ~YAP~~~~~~~fhR~LyvF~ 83 (362)
T KOG2061|consen 5 MEPVLLGFAD-PVPAKELDSLDFPTSKIGGRPAWLGPDPLPNPEALLCELCGNPLSLLLQVYAPLPDIPSAFHRSLYVFG 83 (362)
T ss_pred ccceeeccCC-cccccccccccccccccCCccccCCcccCCCcccccchhhcChHhhhhhhhccCCCCCCccceEEEEEE
Confidence 4689999999 3344555555556 9999999999999999999999999999999999999998888899999999999
Q ss_pred CCCCccCCccccccccCCCccCCCceeeeeecCCCCCCCCCCCCCCCCCCCCC--------CCCCCCcccccCCCCCCCc
Q 014983 129 CPSMACLRRDQHEQWKRPPEKASRSVKVFRCQLPRSNPYYSSEPPKCNGTDKP--------SGPGVSLCNWCGTWKGDKV 200 (415)
Q Consensus 129 C~~~~C~~~~~~~~~k~~~~~~~~s~kvfR~Qlp~~N~fy~~e~~~~~~~~~~--------~~~~~~~c~~cg~w~~~~~ 200 (415)
|++++|++ +.++|+|||+|+||.|+||+.+.++......+ ...++.+|++||.| +++.
T Consensus 84 C~~p~C~~-------------~~~~~~vfr~qlpr~~d~~s~~~pk~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-a~~~ 149 (362)
T KOG2061|consen 84 CRNPSCST-------------ANRSWKVFRVQLPRANDFYSEKAPKTGEPDPQTGSWCEGADKDGADLCGSCGCS-APAA 149 (362)
T ss_pred cCCCcccc-------------cccceeEeeeccccCCccccccccccCCCccccCCccccccCcccchhccCccc-Cccc
Confidence 99999985 25789999999999999999887764421111 23467899999997 9999
Q ss_pred CCcccccccchhhhhcccccccchhhhhhhccCCCCCCCCccCCCCccCCCCCCCCceeeeccCCCCcccccccccchhh
Q 014983 201 CSSCRRAHYCQQKHQVTHWRSGHKVECQQLNLSSPSSDSNLADAGTTSVASNSLWPEYEMINEDESEYDTEMSEVNGQTN 280 (415)
Q Consensus 201 cs~c~~~~ycs~~hq~~~~~~ghk~~c~~~~~~~~~~~~~~~~~~~~~~~~~~~fpe~~i~ve~E~~~~~~~~~~~~~~~ 280 (415)
|+.|+.++|||+.||.+||..+|+..|.+......+.+ .......+||||||+|++|........ ..+.+
T Consensus 150 ~~~~~~a~~~S~~~q~~d~~~~~~~a~aq~~~~~~~~~--------~~p~~~~~~pef~i~vd~E~~~~e~~~--~~~~~ 219 (362)
T KOG2061|consen 150 CSPCKAAAYCSKKHQSLDWPKGHKDACAQPSTLGEIHD--------LGPDHNKVFPEFYIYVDTETFNGEDLT--EVHEK 219 (362)
T ss_pred ccccchhhhcCchhhcccccccccccccCccccccccc--------cCCCCceeceeEEEEEeecccccccch--hhhhh
Confidence 99999999999999999999999999976654332110 123557899999999999966443221 12222
Q ss_pred Hh---hhc---cCC---chhhhhHhhhhcCC--cccHHHHHHHHHHHhCCCceEEeeccCCCeeecccCCCCCCCCCCCC
Q 014983 281 AL---VSK---TGV---DDTMKSLLDSFEGD--SDRRSWATFQEHLAKAPEQVLRYCRSAGAKALWPTSSGQLSKADIPK 349 (415)
Q Consensus 281 ~~---~~~---~~~---~~~~~~~~e~~e~~--~~D~~F~kF~~ri~~~P~QVLRY~~~~gG~PLw~s~~~~~~~~~iP~ 349 (415)
.+ +.+ ++. .+.+..++++||+. ..|++|+||++||++||+|||||.| ||+|||++....+....||+
T Consensus 220 ~~~~e~~~~~~~~~~~~~e~~~~~~deyek~~~~~d~tF~kF~k~i~~nP~QilRY~r--gg~PLl~t~~~~~~~~~~p~ 297 (362)
T KOG2061|consen 220 SLLSEYDKRDGNGDGESAESSEADMDEYEKSLKADDKTFLKFQKRIAANPEQILRYSR--GGKPLLATGTTEPIESLIPK 297 (362)
T ss_pred hhhhhhhhhcccCCccccccchhhhhhhhccccccchHHHHHHHHHhcCchheEEeec--CCcceeeccCCCcccccCCC
Confidence 22 111 111 12223456678875 7999999999999999999999999 89999999887776667899
Q ss_pred CCCCCCCceeeEeechhhhhhcccCC-CCCcceeeEEEEEecCCCCCCC--CCceeeEEEEecC
Q 014983 350 CSYCGGPRCFEFQILPQLLFYFGVSN-DVDSLDWATMVVYTCESSCEAN--VSYKEEFVWVQHS 410 (415)
Q Consensus 350 C~~CG~~R~FEfQlmP~ll~~L~~~~-~~~~ldwGTi~VYTCs~sC~~~--~~y~eE~v~vQ~~ 410 (415)
|.+||++|+||||||||||++|+++. ...+||||||+||||++||+.. ++|+|||||||+.
T Consensus 298 C~~Cg~~R~FE~QLMP~LI~~L~~d~~~~~sldWgtilVyTCs~SC~~~~~~gy~eE~v~vQ~~ 361 (362)
T KOG2061|consen 298 CPNCGGQRIFEFQLMPQLISFLNEDASVDESLDWGTILVYTCSKSCWPANNVGYAEEFVWVQDE 361 (362)
T ss_pred CcCCCCceEEEEeecHHHHHHhhhhccccccccceeEEEEEehhhcCCccccceeeeEEEEeec
Confidence 99999999999999999999999765 4678999999999999999955 4999999999986
No 2
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=100.00 E-value=6.8e-48 Score=350.43 Aligned_cols=156 Identities=44% Similarity=0.855 Sum_probs=119.1
Q ss_pred CCCCceeeeccCCCCccccccccc--chhhHhhhccCCchhhhhHhhhh--cCCcccHHHHHHHHHHHhCCCceEEeecc
Q 014983 253 SLWPEYEMINEDESEYDTEMSEVN--GQTNALVSKTGVDDTMKSLLDSF--EGDSDRRSWATFQEHLAKAPEQVLRYCRS 328 (415)
Q Consensus 253 ~~fpe~~i~ve~E~~~~~~~~~~~--~~~~~~~~~~~~~~~~~~~~e~~--e~~~~D~~F~kF~~ri~~~P~QVLRY~~~ 328 (415)
++||+|+|+|++|+........+. ..+.............+...+.+ .....|++|+||++||+++|+|||||+|
T Consensus 1 ~~fpe~~i~ve~E~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~e~~e~~~~~~D~~f~~F~~rl~~~P~QvlRY~~- 79 (164)
T PF04194_consen 1 PSFPEFEIVVEEEPEEEEELDEEYEEEEIVEFEDDEDESDGGASDEESYESEEDEVDKAFLKFQKRLSRNPEQVLRYCR- 79 (164)
T ss_pred CCCCCEEEEEEECCCCCCcccccchHHHhhhhhhhccccCccccchhhhhhcccccCHHHHHHHHHHhcCCCeEEEECC-
Confidence 369999999999987653321111 11111111111111101122233 3467999999999999999999999999
Q ss_pred CCCeeecccCCCCCCCCCCCCCCCCCCCceeeEeechhhhhhcccCCCC-CcceeeEEEEEecCCCCC--CCCCceeeEE
Q 014983 329 AGAKALWPTSSGQLSKADIPKCSYCGGPRCFEFQILPQLLFYFGVSNDV-DSLDWATMVVYTCESSCE--ANVSYKEEFV 405 (415)
Q Consensus 329 ~gG~PLw~s~~~~~~~~~iP~C~~CG~~R~FEfQlmP~ll~~L~~~~~~-~~ldwGTi~VYTCs~sC~--~~~~y~eE~v 405 (415)
||+|||+++.+.+....||+|++||++|+|||||||+||++|++++.. .+||||||+||||++||+ .+.+|+||||
T Consensus 80 -gG~PLw~s~~~~~~~~~ip~C~~Cg~~R~FEfQlmP~li~~L~~~~~~~~~~dwgtv~VyTCs~sC~~~~~~~y~eE~v 158 (164)
T PF04194_consen 80 -GGKPLWISSTPIPPESDIPKCENCGSPRVFEFQLMPQLIYYLEVDDEGSDSMDWGTVLVYTCSASCWPNDSVGYVEEFV 158 (164)
T ss_pred -CCeEEEecCCCCCccccCCCCccCCCccEEEEEechHHHHHhhccccCCCCceeeEEEEEEehHHcCCCCCCceEEEEE
Confidence 899999998777655569999999999999999999999999998653 589999999999999995 5689999999
Q ss_pred EEecC
Q 014983 406 WVQHS 410 (415)
Q Consensus 406 ~vQ~~ 410 (415)
|||+.
T Consensus 159 ~vQ~e 163 (164)
T PF04194_consen 159 WVQDE 163 (164)
T ss_pred EEEcC
Confidence 99986
No 3
>PF09234 DUF1963: Domain of unknown function (DUF1963); InterPro: IPR015315 This entry is a set of hypothetical bacterial proteins. Their function has not, as yet, been described. ; PDB: 1PV5_A.
Probab=97.01 E-value=0.0013 Score=62.16 Aligned_cols=53 Identities=26% Similarity=0.208 Sum_probs=28.2
Q ss_pred ccccCCCCCCCCCCCCCCCccccCccCCCceeEEEEeecC-CCCCC--CcccEEEEEeCCCC
Q 014983 74 SKAGGPPAWLDPINLPTGRSCLCDMCGEPLQFVLQVYAPI-IEKES--TFHRTLFLFMCPSM 132 (415)
Q Consensus 74 SKiGG~P~WL~p~~lP~~~~l~C~~C~~pm~fLlQvYAPl-~~~~~--~fhRtLYVF~C~~~ 132 (415)
||+||.|.|......| ++ ..|.||.||+||++.- ..... +-+=.||+|+...-
T Consensus 1 Sk~GG~P~LP~~~~wP-----~~-~~g~pl~flaQinl~elp~~~~~~P~~GlL~fF~~~~~ 56 (224)
T PF09234_consen 1 SKFGGLPDLPPGEEWP-----TD-EDGEPLSFLAQINLAELPPFLPGFPKEGLLQFFIDLDD 56 (224)
T ss_dssp -EESS----BTTS--------B--TTS-B-EEEEEEEGGGS----TTS-SS-EEEEEE-SSS
T ss_pred CCcCCcCCCCCCCCCC-----cC-CCCCcceeEEEEEhhhcccchhcCCCceEEEEEEECCc
Confidence 8999999998777666 34 7789999999999862 21112 23579999998664
No 4
>PF01753 zf-MYND: MYND finger; InterPro: IPR002893 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents MYND-type zinc finger domains. The MYND domain (myeloid, Nervy, and DEAF-1) is present in a large group of proteins that includes RP-8 (PDCD2), Nervy, and predicted proteins from Drosophila, mammals, Caenorhabditis elegans, yeast, and plants [, , ]. The MYND domain consists of a cluster of cysteine and histidine residues, arranged with an invariant spacing to form a potential zinc-binding motif []. Mutating conserved cysteine residues in the DEAF-1 MYND domain does not abolish DNA binding, which suggests that the MYND domain might be involved in protein-protein interactions []. Indeed, the MYND domain of ETO/MTG8 interacts directly with the N-CoR and SMRT co-repressors [, ]. Aberrant recruitment of co-repressor complexes and inappropriate transcriptional repression is believed to be a general mechanism of leukemogenesis caused by the t(8;21) translocations that fuse ETO with the acute myelogenous leukemia 1 (AML1) protein. ETO has been shown to be a co-repressor recruited by the promyelocytic leukemia zinc finger (PLZF) protein []. A divergent MYND domain present in the adenovirus E1A binding protein BS69 was also shown to interact with N-CoR and mediate transcriptional repression []. The current evidence suggests that the MYND motif in mammalian proteins constitutes a protein-protein interaction domain that functions as a co-repressor-recruiting interface. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3QWW_A 3QWV_A 3TG5_A 3S7F_A 3RIB_B 3TG4_A 3S7J_A 3S7D_A 3S7B_A 3RU0_A ....
Probab=96.94 E-value=0.00017 Score=49.38 Aligned_cols=37 Identities=41% Similarity=0.964 Sum_probs=29.4
Q ss_pred ccccCCCCCCCcCCcccccccchhhhhcccccccchhhh
Q 014983 189 CNWCGTWKGDKVCSSCRRAHYCQQKHQVTHWRSGHKVEC 227 (415)
Q Consensus 189 c~~cg~w~~~~~cs~c~~~~ycs~~hq~~~~~~ghk~~c 227 (415)
|..|+. .+...|++|+.+.|||+.+|..+| ..|+..|
T Consensus 1 C~~C~~-~~~~~C~~C~~~~YCs~~Cq~~~w-~~Hk~~C 37 (37)
T PF01753_consen 1 CAVCGK-PALKRCSRCKSVYYCSEECQRADW-PYHKFEC 37 (37)
T ss_dssp -TTTSS-CSSEEETTTSSSEESSHHHHHHHH-HHHCCTH
T ss_pred CcCCCC-CcCCcCCCCCCEEecCHHHHHHHH-HHHhhhC
Confidence 455665 344589999999999999999999 7788665
No 5
>PF04194 PDCD2_C: Programmed cell death protein 2, C-terminal putative domain ; InterPro: IPR007320 PDCD2 is localized predominantly in the cytosol of cells situated at the opposite pole of the germinal centre from the centroblasts as well as in cells in the mantle zone. It has been shown to interact with BCL6, an evolutionarily conserved Kruppel-type zinc finger protein that functions as a strong transcriptional repressor and is required for germinal centre development. The rat homologue, Rp8, is associated with programmed cell death in thymocytes.; GO: 0005737 cytoplasm
Probab=95.48 E-value=0.0093 Score=54.47 Aligned_cols=61 Identities=26% Similarity=0.639 Sum_probs=46.0
Q ss_pred cccCCCCCCCCCCCCCCC-ccccCccCCCceeEEEEeecCCCC--------CCCcccEEEEEeCCCCccCC
Q 014983 75 KAGGPPAWLDPINLPTGR-SCLCDMCGEPLQFVLQVYAPIIEK--------ESTFHRTLFLFMCPSMACLR 136 (415)
Q Consensus 75 KiGG~P~WL~p~~lP~~~-~l~C~~C~~pm~fLlQvYAPl~~~--------~~~fhRtLYVF~C~~~~C~~ 136 (415)
-.||.|-|+.....+... .+.|..||.+..|=+||--+|=.. .+---=||.||.|.+ +|+.
T Consensus 78 ~~gG~PLw~s~~~~~~~~~ip~C~~Cg~~R~FEfQlmP~li~~L~~~~~~~~~~dwgtv~VyTCs~-sC~~ 147 (164)
T PF04194_consen 78 CRGGKPLWISSTPIPPESDIPKCENCGSPRVFEFQLMPQLIYYLEVDDEGSDSMDWGTVLVYTCSA-SCWP 147 (164)
T ss_pred CCCCeEEEecCCCCCccccCCCCccCCCccEEEEEechHHHHHhhccccCCCCceeeEEEEEEehH-HcCC
Confidence 469999999987666433 689999999999999998875311 012345999999986 5863
No 6
>KOG1710 consensus MYND Zn-finger and ankyrin repeat protein [General function prediction only]
Probab=93.68 E-value=0.019 Score=56.65 Aligned_cols=43 Identities=40% Similarity=0.831 Sum_probs=38.0
Q ss_pred CcccccCCCCCCCcCCcccccccchhhhhcccccccchhhhhhh
Q 014983 187 SLCNWCGTWKGDKVCSSCRRAHYCQQKHQVTHWRSGHKVECQQL 230 (415)
Q Consensus 187 ~~c~~cg~w~~~~~cs~c~~~~ycs~~hq~~~~~~ghk~~c~~~ 230 (415)
..|..||-.+++|.|+.|+.+.||+..-|++||-. ||..|...
T Consensus 320 ~fCstCG~~ga~KrCs~CKav~YCdqeCQk~hWf~-HKK~C~~L 362 (396)
T KOG1710|consen 320 QFCSTCGHPGAKKRCSQCKAVAYCDQECQKFHWFI-HKKVCSFL 362 (396)
T ss_pred ccccccCCCCccchhhhhHHHHHHHHHHHHhhhHH-HHHHHHHH
Confidence 46888998889999999999999999999999976 88888655
No 7
>COG3878 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=90.70 E-value=0.29 Score=47.24 Aligned_cols=65 Identities=23% Similarity=0.291 Sum_probs=43.9
Q ss_pred ccceEEEeecCCCCccccccCCCCccccCCCCCCCCCCCCCCCccccCccCCCceeEEEEee----cCCCCCCCcccEEE
Q 014983 50 QKPVTLGFLEKPKNRWSLLRHLFPSKAGGPPAWLDPINLPTGRSCLCDMCGEPLQFVLQVYA----PIIEKESTFHRTLF 125 (415)
Q Consensus 50 ~~~V~LGF~d~~~~~~~l~~~~fpSKiGG~P~WL~p~~lP~~~~l~C~~C~~pm~fLlQvYA----Pl~~~~~~fhRtLY 125 (415)
...++|-|.......+ -|||||+|--.--...|..+ =|.||.||+||+= +|++.| -.-.|+
T Consensus 19 k~~iel~~k~~~~~~~-------~SKiGG~pYlpk~e~yP~de------~g~Pl~fLAQINf~elp~le~yP--~~GILq 83 (261)
T COG3878 19 KPCIELDFKMGEETLS-------QSKIGGRPYLPKFETYPLDE------NGVPLVFLAQINFEELPQLEEYP--VEGILQ 83 (261)
T ss_pred hheeEEeeccCCcccc-------ccccCCCcccccccccCccC------CCCceeeeeecChhhCcchhcCC--ccceEE
Confidence 3457888885433332 59999999866666777533 2679999999973 344433 366788
Q ss_pred EEeC
Q 014983 126 LFMC 129 (415)
Q Consensus 126 VF~C 129 (415)
.|+=
T Consensus 84 Fyi~ 87 (261)
T COG3878 84 FYIS 87 (261)
T ss_pred EEEe
Confidence 7775
No 8
>KOG2061 consensus Uncharacterized MYND Zn-finger protein [General function prediction only]
Probab=80.80 E-value=0.98 Score=46.09 Aligned_cols=59 Identities=20% Similarity=0.465 Sum_probs=43.8
Q ss_pred CCCeeecccCCCCCCCCCCCCCCCCCCCceeeEeechhhhhhcccCCCCCcceeeEEEEEecCCC-CC
Q 014983 329 AGAKALWPTSSGQLSKADIPKCSYCGGPRCFEFQILPQLLFYFGVSNDVDSLDWATMVVYTCESS-CE 395 (415)
Q Consensus 329 ~gG~PLw~s~~~~~~~~~iP~C~~CG~~R~FEfQlmP~ll~~L~~~~~~~~ldwGTi~VYTCs~s-C~ 395 (415)
-||.|-|+.....+. ..++.|..||.++.|=+|+--.|..- .+..=-+|.||-|.+. |.
T Consensus 31 iGG~P~wl~~~~~p~-~~~l~C~~C~~~~~lllQ~YAP~~~~-------~~~fhR~LyvF~C~~p~C~ 90 (362)
T KOG2061|consen 31 IGGRPAWLGPDPLPN-PEALLCELCGNPLSLLLQVYAPLPDI-------PSAFHRSLYVFGCRNPSCS 90 (362)
T ss_pred cCCccccCCcccCCC-cccccchhhcChHhhhhhhhccCCCC-------CCccceEEEEEEcCCCccc
Confidence 389999976666665 47899999999999999987752221 1223378999999764 65
No 9
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=66.05 E-value=11 Score=26.24 Aligned_cols=34 Identities=26% Similarity=0.656 Sum_probs=23.2
Q ss_pred CCCCCCCCceeeEeechhhhhhcccCCCCCcceeeEEEEEecCCCCC
Q 014983 349 KCSYCGGPRCFEFQILPQLLFYFGVSNDVDSLDWATMVVYTCESSCE 395 (415)
Q Consensus 349 ~C~~CG~~R~FEfQlmP~ll~~L~~~~~~~~ldwGTi~VYTCs~sC~ 395 (415)
.|+.||....+=||+- +...++ +..++|+|.+ |.
T Consensus 2 ~Cp~C~~~~a~~~q~Q------~RsaDE------~mT~fy~C~~-C~ 35 (40)
T smart00440 2 PCPKCGNREATFFQLQ------TRSADE------PMTVFYVCTK-CG 35 (40)
T ss_pred cCCCCCCCeEEEEEEc------ccCCCC------CCeEEEEeCC-CC
Confidence 5999999887766642 222223 6679999975 75
No 10
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=60.67 E-value=12 Score=25.80 Aligned_cols=34 Identities=32% Similarity=0.630 Sum_probs=20.7
Q ss_pred CCCCCCCCceeeEeechhhhhhcccCCCCCcceeeEEEEEecCCCCC
Q 014983 349 KCSYCGGPRCFEFQILPQLLFYFGVSNDVDSLDWATMVVYTCESSCE 395 (415)
Q Consensus 349 ~C~~CG~~R~FEfQlmP~ll~~L~~~~~~~~ldwGTi~VYTCs~sC~ 395 (415)
.|+.||+...+=||+- .... |=+..++|+|. +|.
T Consensus 2 ~Cp~Cg~~~a~~~~~Q------~rsa------DE~~T~fy~C~-~C~ 35 (39)
T PF01096_consen 2 KCPKCGHNEAVFFQIQ------TRSA------DEPMTLFYVCC-NCG 35 (39)
T ss_dssp --SSS-SSEEEEEEES------SSSS------SSSSEEEEEES-SST
T ss_pred CCcCCCCCeEEEEEee------ccCC------CCCCeEEEEeC-CCC
Confidence 5999999988777542 1112 22678899997 674
No 11
>PF09234 DUF1963: Domain of unknown function (DUF1963); InterPro: IPR015315 This entry is a set of hypothetical bacterial proteins. Their function has not, as yet, been described. ; PDB: 1PV5_A.
Probab=58.24 E-value=10 Score=35.52 Aligned_cols=35 Identities=17% Similarity=0.149 Sum_probs=16.8
Q ss_pred CCccccCCCCCCCCCCCCCCCccccCccCCCceeEEEEeec
Q 014983 72 FPSKAGGPPAWLDPINLPTGRSCLCDMCGEPLQFVLQVYAP 112 (415)
Q Consensus 72 fpSKiGG~P~WL~p~~lP~~~~l~C~~C~~pm~fLlQvYAP 112 (415)
..+||||.|.|.....-.. .. -.+...|||||-+-
T Consensus 154 ~~~~lgG~p~~~Q~d~~~~---~~---~~~~~~lLlQidsd 188 (224)
T PF09234_consen 154 PIHKLGGYPDFIQEDPREE---EE---GADDWILLLQIDSD 188 (224)
T ss_dssp -SSEEES----SS--S-TT---TT----TT--EEEEEEE-B
T ss_pred ccceecccCCCccCChhhh---cc---cccCcEEEEEEEeC
Confidence 3489999999997421111 11 56789999999888
No 12
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=57.31 E-value=5.4 Score=27.54 Aligned_cols=28 Identities=36% Similarity=1.003 Sum_probs=19.6
Q ss_pred cCccCCCceeEEEEeecCCCCC--CCcccEEEEEeCCCCccC
Q 014983 96 CDMCGEPLQFVLQVYAPIIEKE--STFHRTLFLFMCPSMACL 135 (415)
Q Consensus 96 C~~C~~pm~fLlQvYAPl~~~~--~~fhRtLYVF~C~~~~C~ 135 (415)
|..||++ |.+.+ --+++-.|.|+|++ |.
T Consensus 1 Cd~CG~~----------I~~eP~~~k~~~~~y~fCC~t--C~ 30 (37)
T PF08394_consen 1 CDYCGGE----------ITGEPIVVKIGNKVYYFCCPT--CL 30 (37)
T ss_pred CCccCCc----------ccCCEEEEEECCeEEEEECHH--HH
Confidence 6777765 33332 24689999999998 75
No 13
>PF09151 DUF1936: Domain of unknown function (DUF1936); InterPro: IPR015234 This domain is found in a set of hypothetical archaeal proteins. Its exact function has not, as yet, been defined. ; PDB: 2QH1_B 1PVM_B.
Probab=54.33 E-value=19 Score=23.85 Aligned_cols=31 Identities=32% Similarity=0.666 Sum_probs=16.7
Q ss_pred ccCccCCCceeEEEEeecCCCCCCCcccEEEEEeCCCCccC
Q 014983 95 LCDMCGEPLQFVLQVYAPIIEKESTFHRTLFLFMCPSMACL 135 (415)
Q Consensus 95 ~C~~C~~pm~fLlQvYAPl~~~~~~fhRtLYVF~C~~~~C~ 135 (415)
.|+.||- -.|.-+|--- --|-||-|.+++|-
T Consensus 3 lcpkcgv--gvl~pvy~~k--------geikvfrcsnpacd 33 (36)
T PF09151_consen 3 LCPKCGV--GVLEPVYNQK--------GEIKVFRCSNPACD 33 (36)
T ss_dssp B-TTTSS--SBEEEEE-TT--------S-EEEEEES-TT--
T ss_pred cCCccCc--eEEEEeecCC--------CcEEEEEcCCCccc
Confidence 4778873 4556666432 35778888888884
No 14
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=49.27 E-value=24 Score=29.25 Aligned_cols=35 Identities=17% Similarity=0.576 Sum_probs=24.4
Q ss_pred CCCCCCCCCceeeEeechhhhhhcccCCCCCcceeeEEEEEecCCCCC
Q 014983 348 PKCSYCGGPRCFEFQILPQLLFYFGVSNDVDSLDWATMVVYTCESSCE 395 (415)
Q Consensus 348 P~C~~CG~~R~FEfQlmP~ll~~L~~~~~~~~ldwGTi~VYTCs~sC~ 395 (415)
-.|+.||+.+.+=+|+. +...++ |.-++|+|.+ |.
T Consensus 63 ~~Cp~Cg~~~a~f~~~Q------~RsadE------~~T~fy~C~~-C~ 97 (104)
T TIGR01384 63 VECPKCGHKEAYYWLLQ------TRRADE------PETRFYKCTK-CG 97 (104)
T ss_pred CCCCCCCCCeeEEEEec------cCCCCC------CcEEEEEeCC-CC
Confidence 48999999997666642 222233 6679999966 85
No 15
>PF14353 CpXC: CpXC protein
Probab=47.83 E-value=15 Score=31.77 Aligned_cols=39 Identities=38% Similarity=0.829 Sum_probs=26.8
Q ss_pred cccCccCCCceeEEEEeecCCC------CCCCcccEEEEEeCCCCccCC
Q 014983 94 CLCDMCGEPLQFVLQVYAPIIE------KESTFHRTLFLFMCPSMACLR 136 (415)
Q Consensus 94 l~C~~C~~pm~fLlQvYAPl~~------~~~~fhRtLYVF~C~~~~C~~ 136 (415)
++|+.|++...+- +|-=++. .+....-+||.|.||+ |..
T Consensus 2 itCP~C~~~~~~~--v~~~I~~~~~p~l~e~il~g~l~~~~CP~--Cg~ 46 (128)
T PF14353_consen 2 ITCPHCGHEFEFE--VWTSINADEDPELKEKILDGSLFSFTCPS--CGH 46 (128)
T ss_pred cCCCCCCCeeEEE--EEeEEcCcCCHHHHHHHHcCCcCEEECCC--CCC
Confidence 6899999975443 3433332 1245678999999999 874
No 16
>PF14353 CpXC: CpXC protein
Probab=44.81 E-value=29 Score=29.85 Aligned_cols=44 Identities=23% Similarity=0.468 Sum_probs=23.7
Q ss_pred CCCCCCCCceeeEeechhhhhhcccCCCCCcceeeEEEEEecCCCCCC
Q 014983 349 KCSYCGGPRCFEFQILPQLLFYFGVSNDVDSLDWATMVVYTCESSCEA 396 (415)
Q Consensus 349 ~C~~CG~~R~FEfQlmP~ll~~L~~~~~~~~ldwGTi~VYTCs~sC~~ 396 (415)
.|++||.. |++.+-. +|+.-........+==|++..|||++ |..
T Consensus 3 tCP~C~~~--~~~~v~~-~I~~~~~p~l~e~il~g~l~~~~CP~-Cg~ 46 (128)
T PF14353_consen 3 TCPHCGHE--FEFEVWT-SINADEDPELKEKILDGSLFSFTCPS-CGH 46 (128)
T ss_pred CCCCCCCe--eEEEEEe-EEcCcCCHHHHHHHHcCCcCEEECCC-CCC
Confidence 69999975 4444332 22211000001122239999999986 973
No 17
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=42.98 E-value=15 Score=28.02 Aligned_cols=23 Identities=30% Similarity=0.678 Sum_probs=19.7
Q ss_pred CCCCCCCCCCCCceeeEeechhh
Q 014983 345 ADIPKCSYCGGPRCFEFQILPQL 367 (415)
Q Consensus 345 ~~iP~C~~CG~~R~FEfQlmP~l 367 (415)
...|.|+.|+++-+=+.-++|.|
T Consensus 37 ~~~p~CPlC~s~M~~~~r~Lp~l 59 (59)
T PF14169_consen 37 EEEPVCPLCKSPMVSGTRMLPVL 59 (59)
T ss_pred CCCccCCCcCCccccceeecccC
Confidence 46799999999999888888864
No 18
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=31.11 E-value=55 Score=25.34 Aligned_cols=39 Identities=18% Similarity=0.179 Sum_probs=30.8
Q ss_pred ccCccCCCceeEEEEeecCCCC---CCCcccEEEEEeCCCCccC
Q 014983 95 LCDMCGEPLQFVLQVYAPIIEK---ESTFHRTLFLFMCPSMACL 135 (415)
Q Consensus 95 ~C~~C~~pm~fLlQvYAPl~~~---~~~fhRtLYVF~C~~~~C~ 135 (415)
.|..||..+.-.-||-++=... .+.-||..++-.|++ |.
T Consensus 2 ~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~v~C~~--CG 43 (64)
T PF09855_consen 2 KCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTTVSCTN--CG 43 (64)
T ss_pred CCCCCCCcceecceEEccCCeeEEEEEecCcEEEEEECCC--CC
Confidence 5999999999999998884321 233488999999999 85
No 19
>PF14475 Mso1_Sec1_bdg: Sec1-binding region of Mso1
Probab=28.47 E-value=11 Score=26.70 Aligned_cols=18 Identities=33% Similarity=0.739 Sum_probs=14.8
Q ss_pred ccccCCCCccccCCCCCC
Q 014983 66 SLLRHLFPSKAGGPPAWL 83 (415)
Q Consensus 66 ~l~~~~fpSKiGG~P~WL 83 (415)
.-++.||.+|..|.|.||
T Consensus 24 r~l~~yY~~k~~~~P~WL 41 (41)
T PF14475_consen 24 RVLRKYYTEKGRPFPGWL 41 (41)
T ss_pred HHHHHHHHHcCCCCCCcC
Confidence 345688899999999998
No 20
>KOG2906 consensus RNA polymerase III subunit C11 [Transcription]
Probab=24.32 E-value=55 Score=27.56 Aligned_cols=17 Identities=29% Similarity=0.755 Sum_probs=14.3
Q ss_pred CCCCCCCCCceeeEeec
Q 014983 348 PKCSYCGGPRCFEFQIL 364 (415)
Q Consensus 348 P~C~~CG~~R~FEfQlm 364 (415)
-.|+.||.+|.+=|||.
T Consensus 66 ~~Cp~Cgh~rayF~qlQ 82 (105)
T KOG2906|consen 66 ATCPTCGHERAYFMQLQ 82 (105)
T ss_pred CcCCCCCCCceEEEEee
Confidence 57999999999888763
No 21
>PF08421 Methyltransf_13: Putative zinc binding domain; InterPro: IPR013630 This domain is found at the N terminus of bacterial methyltransferases. ; PDB: 4E2X_A 3NDJ_A 3NDI_A 4E32_A 4E33_A 4E31_A 4E2Y_A 4E2W_A 4E2Z_A 4E30_A.
Probab=22.83 E-value=1.2e+02 Score=22.91 Aligned_cols=44 Identities=18% Similarity=0.439 Sum_probs=27.1
Q ss_pred CCCCCCC---ceeeEeechhhhhhcccCCCCCcceeeEEEEEecCCCCC
Q 014983 350 CSYCGGP---RCFEFQILPQLLFYFGVSNDVDSLDWATMVVYTCESSCE 395 (415)
Q Consensus 350 C~~CG~~---R~FEfQlmP~ll~~L~~~~~~~~ldwGTi~VYTCs~sC~ 395 (415)
|..||+. .++.|=-||-.-.|+.. +....-.+.-+-||.|. +|+
T Consensus 1 CR~Cgs~~l~~vldLG~~Pl~~~f~~~-~~~~~e~~~pL~l~~C~-~Cg 47 (62)
T PF08421_consen 1 CRICGSSDLKPVLDLGDQPLANSFLKP-ELDEPEPRYPLDLYVCE-DCG 47 (62)
T ss_dssp -TTTS-E-EEEEEEEEEEE-TT--B-T-TS-S---EEEEEEEEET-TT-
T ss_pred CCCCCCCccceEeecCCCCccccccCh-hhCCCceEECCEEEECC-CCC
Confidence 7889997 67788889988888876 44456789999999994 586
No 22
>PF11331 DUF3133: Protein of unknown function (DUF3133); InterPro: IPR021480 This eukaryotic family of proteins has no known function.
Probab=21.67 E-value=64 Score=23.39 Aligned_cols=15 Identities=40% Similarity=0.782 Sum_probs=11.3
Q ss_pred ccccCccCCCceeEE
Q 014983 93 SCLCDMCGEPLQFVL 107 (415)
Q Consensus 93 ~l~C~~C~~pm~fLl 107 (415)
.++|+.|++-+.|=+
T Consensus 31 klrCGaCs~vl~~s~ 45 (46)
T PF11331_consen 31 KLRCGACSEVLSFSL 45 (46)
T ss_pred EEeCCCCceeEEEec
Confidence 588888888777643
No 23
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=21.17 E-value=55 Score=29.42 Aligned_cols=44 Identities=23% Similarity=0.517 Sum_probs=24.2
Q ss_pred HHHHHHHHHHhCCCceEEeeccCCCee---ecc-cCCC----CCCCCCCCCCCCCCCC
Q 014983 307 SWATFQEHLAKAPEQVLRYCRSAGAKA---LWP-TSSG----QLSKADIPKCSYCGGP 356 (415)
Q Consensus 307 ~F~kF~~ri~~~P~QVLRY~~~~gG~P---Lw~-s~~~----~~~~~~iP~C~~CG~~ 356 (415)
-+..+.+.+.++. .|.- |-.+ .++ ...+ ...+..||+|+.||+.
T Consensus 88 Ew~el~~d~~h~g----~Y~s--GE~~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~ 139 (146)
T PF07295_consen 88 EWAELAQDLEHHG----VYHS--GEVVGPGTLVCENCGHEVELTHPERLPPCPKCGHT 139 (146)
T ss_pred HHHHHHHHHHhcC----Ceec--CcEecCceEecccCCCEEEecCCCcCCCCCCCCCC
Confidence 3777888888766 4542 2111 111 0000 0123579999999985
No 24
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=20.47 E-value=64 Score=27.63 Aligned_cols=17 Identities=18% Similarity=0.559 Sum_probs=14.7
Q ss_pred CCCCCCCCCCceeeEee
Q 014983 347 IPKCSYCGGPRCFEFQI 363 (415)
Q Consensus 347 iP~C~~CG~~R~FEfQl 363 (415)
.|+|+.|++.-+||.+-
T Consensus 2 lp~CP~C~seytY~dg~ 18 (109)
T TIGR00686 2 LPPCPKCNSEYTYHDGT 18 (109)
T ss_pred CCcCCcCCCcceEecCC
Confidence 68999999999999654
Done!