Query 014619
Match_columns 421
No_of_seqs 199 out of 689
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 06:54:08 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014619.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014619hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2752 Uncharacterized conser 100.0 1.5E-90 3.4E-95 672.6 18.8 338 2-415 3-345 (345)
2 PF02207 zf-UBR: Putative zinc 99.4 2.4E-13 5.1E-18 108.4 3.2 66 42-109 2-70 (71)
3 smart00396 ZnF_UBR1 Putative z 99.3 3.4E-12 7.4E-17 101.9 5.1 65 42-109 2-70 (71)
4 KOG1777 Putative Zn-finger pro 98.7 6.2E-09 1.3E-13 107.0 3.0 69 42-112 545-616 (625)
5 PF00628 PHD: PHD-finger; Int 98.4 2.9E-08 6.3E-13 73.4 -1.5 50 129-191 1-51 (51)
6 KOG2752 Uncharacterized conser 98.4 8.7E-08 1.9E-12 95.0 1.0 107 67-194 1-107 (345)
7 KOG1973 Chromatin remodeling p 98.3 2.7E-07 5.8E-12 91.5 3.6 56 119-192 211-269 (274)
8 smart00249 PHD PHD zinc finger 98.3 7.1E-07 1.5E-11 63.3 3.2 46 129-188 1-47 (47)
9 COG5034 TNG2 Chromatin remodel 98.0 2.5E-06 5.4E-11 82.8 2.8 47 126-190 220-269 (271)
10 KOG1776 Zn-binding protein Pus 97.5 2.6E-05 5.7E-10 84.3 0.6 60 41-103 765-828 (1110)
11 KOG4323 Polycomb-like PHD Zn-f 97.4 6.3E-05 1.4E-09 79.1 2.3 66 124-200 168-233 (464)
12 KOG1632 Uncharacterized PHD Zn 97.1 0.00017 3.6E-09 73.9 1.0 59 127-198 60-120 (345)
13 KOG0943 Predicted ubiquitin-pr 97.0 0.00022 4.7E-09 80.9 0.7 58 41-99 1241-1301(3015)
14 KOG4443 Putative transcription 89.7 0.062 1.3E-06 58.7 -1.6 55 127-190 145-201 (694)
15 PF00643 zf-B_box: B-box zinc 87.3 0.44 9.6E-06 33.5 2.1 29 54-86 14-42 (42)
16 KOG0825 PHD Zn-finger protein 86.1 0.46 9.9E-06 53.2 2.3 52 126-192 214-267 (1134)
17 KOG1844 PHD Zn-finger proteins 86.0 0.8 1.7E-05 48.9 4.1 62 116-192 73-136 (508)
18 PF13831 PHD_2: PHD-finger; PD 84.4 0.22 4.9E-06 34.7 -0.7 34 145-188 2-35 (36)
19 KOG1512 PHD Zn-finger protein 75.9 1.3 2.8E-05 44.5 1.2 47 129-192 316-364 (381)
20 cd04714 BAH_BAHCC1 BAH, or Bro 75.8 1.8 4E-05 37.8 2.0 63 81-150 58-121 (121)
21 smart00336 BBOX B-Box-type zin 74.1 2.5 5.4E-05 29.2 2.0 31 52-86 12-42 (42)
22 KOG1632 Uncharacterized PHD Zn 70.1 0.72 1.6E-05 47.6 -2.2 57 125-190 237-294 (345)
23 cd00021 BBOX B-Box-type zinc f 60.9 5.9 0.00013 26.8 1.7 30 53-86 10-39 (39)
24 KOG0957 PHD finger protein [Ge 59.5 5.7 0.00012 42.9 2.0 49 129-188 546-595 (707)
25 KOG0957 PHD finger protein [Ge 58.9 8.9 0.00019 41.5 3.3 58 128-190 121-178 (707)
26 PF13832 zf-HC5HC2H_2: PHD-zin 57.5 5.2 0.00011 33.8 1.1 36 119-162 48-85 (110)
27 PF02881 SRP54_N: SRP54-type p 55.2 22 0.00047 27.8 4.3 31 385-416 1-32 (75)
28 KOG0954 PHD finger protein [Ge 49.6 9.6 0.00021 42.9 1.8 49 126-189 270-319 (893)
29 KOG2626 Histone H3 (Lys4) meth 49.3 17 0.00036 39.6 3.5 59 124-192 17-77 (544)
30 cd00730 rubredoxin Rubredoxin; 48.1 16 0.00035 27.4 2.3 42 148-191 2-43 (50)
31 PF14071 YlbD_coat: Putative c 47.7 45 0.00097 29.8 5.4 74 324-402 26-110 (124)
32 PF13405 EF-hand_6: EF-hand do 42.5 26 0.00057 22.7 2.5 25 388-412 1-27 (31)
33 PF13495 Phage_int_SAM_4: Phag 40.6 31 0.00067 27.0 3.1 40 376-416 16-55 (85)
34 KOG0955 PHD finger protein BR1 40.4 26 0.00056 41.4 3.5 53 125-192 218-270 (1051)
35 PF07061 Swi5: Swi5; InterPro 40.3 29 0.00063 28.7 2.9 36 374-409 40-75 (83)
36 cd02340 ZZ_NBR1_like Zinc fing 40.2 26 0.00057 25.2 2.3 33 49-85 9-42 (43)
37 KOG0383 Predicted helicase [Ge 39.6 14 0.0003 41.7 1.2 37 144-189 56-92 (696)
38 PF09082 DUF1922: Domain of un 37.9 15 0.00032 29.5 0.7 11 92-102 4-14 (68)
39 KOG4299 PHD Zn-finger protein 37.6 14 0.00031 40.7 0.9 52 127-192 253-306 (613)
40 PF08671 SinI: Anti-repressor 36.9 30 0.00065 23.4 2.0 13 402-414 17-29 (30)
41 KOG3878 Protein involved in ma 35.0 46 0.001 34.5 3.9 51 365-418 96-147 (469)
42 PF09416 UPF1_Zn_bind: RNA hel 32.9 34 0.00074 31.5 2.4 56 128-198 4-76 (152)
43 PLN00035 histone H4; Provision 30.5 50 0.0011 28.5 2.9 29 381-409 51-89 (103)
44 smart00417 H4 Histone H4. 29.8 57 0.0012 26.5 2.9 28 381-408 35-72 (74)
45 cd04718 BAH_plant_2 BAH, or Br 29.0 41 0.00089 30.9 2.3 27 157-192 2-28 (148)
46 PF14659 Phage_int_SAM_3: Phag 28.9 81 0.0018 22.7 3.5 30 384-414 28-57 (58)
47 PF00301 Rubredoxin: Rubredoxi 28.4 25 0.00055 26.0 0.7 11 180-190 32-42 (47)
48 PF07227 DUF1423: Protein of u 28.4 55 0.0012 35.1 3.3 63 129-194 131-195 (446)
49 cd00076 H4 Histone H4, one of 28.0 74 0.0016 26.5 3.4 28 381-408 35-72 (85)
50 PTZ00015 histone H4; Provision 27.6 71 0.0015 27.6 3.3 29 381-409 52-90 (102)
51 PF07496 zf-CW: CW-type Zinc F 26.3 31 0.00066 25.6 0.8 15 146-160 2-16 (50)
52 cd05029 S-100A6 S-100A6: S-100 25.6 87 0.0019 25.7 3.4 40 376-415 13-61 (88)
53 TIGR02925 cis_trans_EpsD pepti 25.5 1.3E+02 0.0027 28.6 5.0 40 377-416 89-131 (232)
54 KOG1244 Predicted transcriptio 25.3 40 0.00087 34.0 1.6 51 125-190 279-330 (336)
55 cd02339 ZZ_Mind_bomb Zinc fing 25.1 56 0.0012 23.9 1.9 34 48-85 9-44 (45)
56 KOG1245 Chromatin remodeling c 24.3 18 0.00039 44.0 -1.2 53 126-193 1107-1160(1404)
57 KOG0031 Myosin regulatory ligh 23.7 2E+02 0.0043 26.9 5.6 46 366-413 22-76 (171)
58 smart00054 EFh EF-hand, calciu 23.6 74 0.0016 18.2 2.1 25 389-413 2-28 (29)
59 PF13771 zf-HC5HC2H: PHD-like 22.9 42 0.00091 27.0 1.1 31 126-164 36-68 (90)
60 PF07106 TBPIP: Tat binding pr 22.8 4.3E+02 0.0094 24.0 7.8 50 366-415 105-155 (169)
61 PF02885 Glycos_trans_3N: Glyc 22.7 67 0.0015 24.8 2.1 27 389-415 2-28 (66)
62 PF07649 C1_3: C1-like domain; 21.9 24 0.00052 23.1 -0.5 18 145-162 13-30 (30)
63 PF08164 TRAUB: Apoptosis-anta 21.2 96 0.0021 25.7 2.8 27 387-414 56-82 (83)
64 PF14047 DCR: Dppa2/4 conserve 20.9 45 0.00098 26.6 0.8 13 180-192 53-65 (66)
65 PF07191 zinc-ribbons_6: zinc- 20.6 61 0.0013 26.2 1.5 18 67-84 40-60 (70)
66 PF14048 MBD_C: C-terminal dom 20.2 81 0.0017 26.8 2.2 29 392-420 63-91 (96)
No 1
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=100.00 E-value=1.5e-90 Score=672.64 Aligned_cols=338 Identities=43% Similarity=0.822 Sum_probs=271.5
Q ss_pred CCCCCccchhccCccHHHHHHhHHHHHHHHHHhcCCCCCCCcccccccccccceEeecCCCCC-CCceEeccchhhhcCC
Q 014619 2 SGELDDDVEAEQTISINEYLNDVEEKELEADLVLGGDEGKECTYSKGYMKRQAIFSCLSCAPE-GNAGVCTACSLTCHDG 80 (421)
Q Consensus 2 ~~~~~~~~e~e~~vT~~d~le~q~eLE~eA~~vl~~~~~~~Cty~~g~~~rQ~~y~C~tC~~~-~~~gvC~~Cs~~CH~~ 80 (421)
+|-|++ +|...+||+.+|++++.+||.+|++|||++++++|||++||++||++|+|+||+|. +.+||||+|++.||+|
T Consensus 3 ~~~~e~-ee~~~tiT~~e~vE~~~~lE~~a~~vL~~~~~~~CTy~~Gy~~rQ~l~sClTC~P~~~~agvC~~C~~~CH~~ 81 (345)
T KOG2752|consen 3 DGVEET-EEIAPTITLGEYVEQIDELEDEADVVLGTQNPDVCTYAKGYKKRQALFSCLTCTPAPEMAGVCYACSLSCHDG 81 (345)
T ss_pred cchhcc-hhccccccHHHHHHhHHHHHHHHHhhcCCCCCcccccccCcccccceeEeecccCChhhceeEEEeeeeecCC
Confidence 455555 34445999999999999999999999999999999999999999999999999998 4899999999999999
Q ss_pred CceeEeecccceeeccCCCCCCCcceeecCCCCCCCccCcCCCCCCcceEEeCCCCCCCCcccccceeeccccCceeccc
Q 014619 81 HEIVELWTKRNFRCDCGNSKFGEFFCKLFPSKDVENAENSYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEE 160 (421)
Q Consensus 81 H~l~el~~kr~f~CDCG~~~~~~~~C~l~~~k~~~n~~N~Yn~Nf~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~ 160 (421)
|+||||||||||||||||++|+..+|+|.+.|+.+|++|.|||||+|+||+|.+|||||..++.+.|+||.+||||||
T Consensus 82 H~lveL~tKR~FrCDCg~sk~g~~sc~l~~~~~~~n~~N~YNhNfqG~~C~Cd~~Ypdp~~~~e~~m~QC~iCEDWFH-- 159 (345)
T KOG2752|consen 82 HELVELYTKRNFRCDCGNSKFGRCSCNLLEDKDAENSENLYNHNFQGLFCKCDTPYPDPVRTEEGEMLQCVICEDWFH-- 159 (345)
T ss_pred ceeeeccccCCcccccccccccccccccccccccccchhhhhhhhcceeEEecCCCCCccccccceeeeEEeccchhc--
Confidence 999999999999999999999999999999999999999999999999999999999999888999999999999999
Q ss_pred CCCCCCCCCCCCCCCCCCccCeeeccCccCCCcccccccccccccccccCCCcccCCCCCccccCCCCCCCCCCCCCCCC
Q 014619 161 HIGLEPSDEIPRDDEGEPVYEDFICKACSAVCSFLSTYPQTIWAAGLRRNAGCNTNKDKDVLEEIPSAGGSGKLENGICS 240 (421)
Q Consensus 161 Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~~fL~~y~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 240 (421)
|..|++..+|+..|+..... .... ..+.+++. +...+
T Consensus 160 ------------------------ce~c~~~~~~~~~yp~~~~~----D~e~-----------~k~e~~se----~~a~~ 196 (345)
T KOG2752|consen 160 ------------------------CEGCMQAKTFLEDYPEQGKD----DAEE-----------VKPEQNSE----KCAGS 196 (345)
T ss_pred ------------------------ccccCcccchhhcccccccc----cccc-----------CCccccCc----ccccc
Confidence 44566677888888732110 0000 00000000 00000
Q ss_pred CCCCCccccccccccccccCCCCccCCCcccccccccccCCCCCCcccccCCCcc---cCCCCCCCcceecCcchhhhcc
Q 014619 241 NGSPREDNAIANTSAESVTGGKGVTGESSKKIFDLVQCMNDGGAHIACLFGDNIV---VDGSISLTKPLFLSKNWRATLC 317 (421)
Q Consensus 241 ~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ckl~~~~~---~~~~~~~~~~~fl~~~wR~~LC 317 (421)
.. +.-+++ . +. .+ .-...+++.|++. .+. .......++.||.. +||+.||
T Consensus 197 ~c----------~~~i~~----~-----~~-----~e-~~~~e~~~~~~~~-~~e~~~k~~~~~d~~~~~~~-~wR~~LC 249 (345)
T KOG2752|consen 197 SC----------SEDIQD----V-----PK-----NE-SLNDESESGCKLQ-LLENFRKQLKKKDGAAFWTN-NWRSKLC 249 (345)
T ss_pred cc----------HHHHHh----c-----cc-----CC-CCccccccCCcHH-HHHhhHhhcccCCcccchhh-hHHHhhc
Confidence 00 000000 0 00 00 0011223456665 221 11122466778877 9999999
Q ss_pred cchhhhhhhhhcCCCcccCCCcchHHhhhhhHhhhhhhhhhhhchHHHHHhhCChHHHHHHHHHHHHHHHHHHHhhhhc-
Q 014619 318 RCKKCLSMYEQKRVPYLIDEEDSIAEYERTAKQKREEKLQQQEGAELTFLNKLGHVEKMEILNGIADMKDEFHNFLQSF- 396 (421)
Q Consensus 318 ~C~~C~~~y~~~~~~FLldeeDtv~~YE~~~~~~~~~s~~~d~g~~~~aL~sl~RvqaIE~i~gYn~mKdkL~~fLk~F- 396 (421)
+|.+|+.||+.+.|.||||+||||.+||.+++...+.+ +.+.+|+ +|++|+|||||++|.+||+||++|++||++|
T Consensus 250 ~Ce~Cl~mY~d~dv~fLlD~EDti~tyE~k~k~~~~~~-t~e~~~~--~L~~l~r~q~ve~i~eyn~lK~~L~d~L~~fA 326 (345)
T KOG2752|consen 250 TCEDCLEMYEDLDVEFLLDEEDTILTYENKGKIAEENK-TSEDLME--ALDSLNRVQQVELICEYNRLKDELKDYLKRFA 326 (345)
T ss_pred chHHhhhhhhhhchheeecccchhhhhhhhhhhhhhcc-ccchHHH--HHHhccchhhHHHHHHHHhHHHHHHHHHHHhh
Confidence 99999999999999999999999999999999656655 8888999 9999999999999999999999999999999
Q ss_pred CCCCccCHHHHHHHHHHHH
Q 014619 397 DPSKAITSDDVHQIFENLA 415 (421)
Q Consensus 397 e~gkvVt~EDIk~FFe~l~ 415 (421)
++|+|||+|||++||++++
T Consensus 327 ~~~~vv~reDI~~FF~~~~ 345 (345)
T KOG2752|consen 327 DEGTVVTREDIQQFFEEFQ 345 (345)
T ss_pred hcCeEeeHHHHHHHHHhhC
Confidence 9999999999999999874
No 2
>PF02207 zf-UBR: Putative zinc finger in N-recognin (UBR box); InterPro: IPR003126 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. The N-end rule-based degradation signal, which targets a protein for ubiquitin-dependent proteolysis, comprises a destabilising amino-terminal residue and a specific internal lysine residue. This entry describes a putative zinc finger in N-recognin, a recognition component of the N-end rule pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0004842 ubiquitin-protein ligase activity, 0008270 zinc ion binding; PDB: 3NY1_B 3NIS_F 3NIM_A 3NIK_A 3NII_A 3NIH_A 3NIL_D 3NIN_B 3NIJ_A 3NIT_A ....
Probab=99.37 E-value=2.4e-13 Score=108.39 Aligned_cols=66 Identities=33% Similarity=0.809 Sum_probs=48.1
Q ss_pred CcccccccccccceEeecCCCCCCCceEeccc-hhhhcCCCceeEeecccceeeccCCCCCCC--cceeec
Q 014619 42 ECTYSKGYMKRQAIFSCLSCAPEGNAGVCTAC-SLTCHDGHEIVELWTKRNFRCDCGNSKFGE--FFCKLF 109 (421)
Q Consensus 42 ~Cty~~g~~~rQ~~y~C~tC~~~~~~gvC~~C-s~~CH~~H~l~el~~kr~f~CDCG~~~~~~--~~C~l~ 109 (421)
.|+|..+.. |.+|.|+||......+||..| +..||.||+++.+++.++|+||||+..... ..|+++
T Consensus 2 ~C~~~~~~~--q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~~~~~~~~~~~~CDCG~~~~~k~~~~C~~H 70 (71)
T PF02207_consen 2 KCTYVWTSG--QIFYRCLTCSLDESSGICEECFANSCHEGHRVVYYRSSSGGCCDCGDPEAWKKEGFCKKH 70 (71)
T ss_dssp SS--B--TT---EEEEETTTBSSTT-BBEHHHHCTSGGGGSSEEEEE--SCEBB-TT-GGGBSS--S-TTT
T ss_pred cCCCCCcCC--CEEEECccCCCCCCEEEchhhCCCCCcCCCcEEEEEeCCCeEEeCCCCccccCCCCCCCC
Confidence 588876554 999999999998899999999 999999999999999889999999998863 347664
No 3
>smart00396 ZnF_UBR1 Putative zinc finger in N-recognin, a recognition component of the N-end rule pathway. Domain is involved in recognition of N-end rule substrates in yeast Ubr1p
Probab=99.29 E-value=3.4e-12 Score=101.93 Aligned_cols=65 Identities=32% Similarity=0.713 Sum_probs=55.5
Q ss_pred CcccccccccccceEeecCCCCCCCceEeccchh-hhcCCCceeEeecccc-eeeccCCCCCC--Ccceeec
Q 014619 42 ECTYSKGYMKRQAIFSCLSCAPEGNAGVCTACSL-TCHDGHEIVELWTKRN-FRCDCGNSKFG--EFFCKLF 109 (421)
Q Consensus 42 ~Cty~~g~~~rQ~~y~C~tC~~~~~~gvC~~Cs~-~CH~~H~l~el~~kr~-f~CDCG~~~~~--~~~C~l~ 109 (421)
.|+|..++. +.+|.|+||......+||..|.. .||.||+ |.++++++ |+||||+...+ ++.|+++
T Consensus 2 ~C~~~~~~~--~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~-~~~~~~~~~~~CDCG~~~~~~~~~~C~~h 70 (71)
T smart00396 2 VCTYKFTGG--EVIYRCKTCGLDPTCVLCSDCFRSNCHKGHD-YSLKTSRGSGICDCGDKEAWNEDLKCKAH 70 (71)
T ss_pred CCCCccCCC--CEEEECcCCCCCCCEeEChHHCCCCCCCCCC-EEEEEecCCEEECCCChhccCCCcccccc
Confidence 599998877 56699999998888999999999 9999999 57999998 99999998543 4567654
No 4
>KOG1777 consensus Putative Zn-finger protein [General function prediction only]
Probab=98.71 E-value=6.2e-09 Score=107.04 Aligned_cols=69 Identities=25% Similarity=0.780 Sum_probs=59.5
Q ss_pred Ccccc---cccccccceEeecCCCCCCCceEeccchhhhcCCCceeEeecccceeeccCCCCCCCcceeecCCC
Q 014619 42 ECTYS---KGYMKRQAIFSCLSCAPEGNAGVCTACSLTCHDGHEIVELWTKRNFRCDCGNSKFGEFFCKLFPSK 112 (421)
Q Consensus 42 ~Cty~---~g~~~rQ~~y~C~tC~~~~~~gvC~~Cs~~CH~~H~l~el~~kr~f~CDCG~~~~~~~~C~l~~~k 112 (421)
.|.|. ..+.+...+|.|.||+.....+||..|...||+||+| |+..-..|+||||+..... .|.|...+
T Consensus 545 qCLfkvSs~~syPMHnFYRC~TCNttdRNAIC~nCI~~CH~GH~V-efir~Drffcdcgagtl~~-~c~lq~ep 616 (625)
T KOG1777|consen 545 QCLFKVSSYTSYPMHNFYRCITCNTTDRNAICVNCIKRCHEGHDV-EFIRHDRFFCDCGAGTLSN-VCDLQGEP 616 (625)
T ss_pred ceEEEecCCCcccccceeEeeecCCccccHHHHHHHHHhcCCCce-EEEeeceEEEecCCceecc-eeeccCCc
Confidence 59995 3455699999999999999999999999999999999 5666678999999998774 79998765
No 5
>PF00628 PHD: PHD-finger; InterPro: IPR019787 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 the PHD (homeodomain) zinc finger domain [,], which is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in chromatin-mediated transcriptional regulation. The PHD finger motif is reminiscent of, but distinct from the C3HC4 type RING finger. The function of this domain is not yet known but in analogy with the LIM domain it could be involved in protein-protein interaction and be important for the assembly or activity of multicomponent complexes involved in transcriptional activation or repression. Alternatively, the interactions could be intra-molecular and be important in maintaining the structural integrity of the protein. In similarity to the RING finger and the LIM domain, the PHD finger is thought to bind two zinc ions. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0005515 protein binding; PDB: 3ZVY_A 2LGG_A 3SOW_A 3SOU_B 3ASL_A 3ASK_A 3ZVZ_B 3T6R_A 2LGK_A 3SOX_B ....
Probab=98.39 E-value=2.9e-08 Score=73.39 Aligned_cols=50 Identities=30% Similarity=0.798 Sum_probs=36.5
Q ss_pred eE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCC
Q 014619 129 YC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAV 191 (421)
Q Consensus 129 yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~ 191 (421)
|| +|+++. + .+.||||+.|..|||..|++++.. +.... ...|+|+.|..+
T Consensus 1 ~C~vC~~~~--~----~~~~i~C~~C~~~~H~~C~~~~~~---~~~~~----~~~w~C~~C~~~ 51 (51)
T PF00628_consen 1 YCPVCGQSD--D----DGDMIQCDSCNRWYHQECVGPPEK---AEEIP----SGDWYCPNCRPK 51 (51)
T ss_dssp EBTTTTSSC--T----TSSEEEBSTTSCEEETTTSTSSHS---HHSHH----SSSBSSHHHHHC
T ss_pred eCcCCCCcC--C----CCCeEEcCCCChhhCcccCCCChh---hccCC----CCcEECcCCcCc
Confidence 67 899843 2 589999999999999999998542 11111 238999999753
No 6
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=98.38 E-value=8.7e-08 Score=95.05 Aligned_cols=107 Identities=10% Similarity=0.012 Sum_probs=89.6
Q ss_pred ceEeccchhhhcCCCceeEeecccceeeccCCCCCCCcceeecCCCCCCCccCcCCCCCCcceEEeCCCCCCCCcccccc
Q 014619 67 AGVCTACSLTCHDGHEIVELWTKRNFRCDCGNSKFGEFFCKLFPSKDVENAENSYNHNFKGVYCTCNRPYPDPDVEEQVE 146 (421)
Q Consensus 67 ~gvC~~Cs~~CH~~H~l~el~~kr~f~CDCG~~~~~~~~C~l~~~k~~~n~~N~Yn~Nf~g~yC~C~rpypdp~~e~~~~ 146 (421)
+++|.+|+..||. |++.++|+++...+.+..|.|.+.++..+-.+.|+.++++.+|+|-+++|+| +.
T Consensus 1 ~~~~~~e~ee~~~--------tiT~~e~vE~~~~lE~~a~~vL~~~~~~~CTy~~Gy~~rQ~l~sClTC~P~~-----~~ 67 (345)
T KOG2752|consen 1 MDDGVEETEEIAP--------TITLGEYVEQIDELEDEADVVLGTQNPDVCTYAKGYKKRQALFSCLTCTPAP-----EM 67 (345)
T ss_pred CCcchhcchhccc--------cccHHHHHHhHHHHHHHHHhhcCCCCCcccccccCcccccceeEeecccCCh-----hh
Confidence 3677888888886 7899999999999999899999999999999999999999999999999865 48
Q ss_pred eeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCCcc
Q 014619 147 MIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVCSF 194 (421)
Q Consensus 147 MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~~f 194 (421)
|++|..|..|+|..|+.+. ++.-.+ |.-..|-.|+.+.++
T Consensus 68 agvC~~C~~~CH~~H~lve----L~tKR~----FrCDCg~sk~g~~sc 107 (345)
T KOG2752|consen 68 AGVCYACSLSCHDGHELVE----LYTKRN----FRCDCGNSKFGRCSC 107 (345)
T ss_pred ceeEEEeeeeecCCceeee----ccccCC----ccccccccccccccc
Confidence 9999999999999999873 333334 555566666666665
No 7
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.35 E-value=2.7e-07 Score=91.45 Aligned_cols=56 Identities=30% Similarity=0.651 Sum_probs=43.1
Q ss_pred CcCCCCCCcceEEeCCCCCCCCcccccceeeccc--cC-ceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014619 119 NSYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCI--CE-DWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 192 (421)
Q Consensus 119 N~Yn~Nf~g~yC~C~rpypdp~~e~~~~MiQC~~--CE-DWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 192 (421)
......-.-.||+|.+.- .+.||.|+. |. +|||..||||.. .| ...|+|+.|....
T Consensus 211 ~~~~d~~e~~yC~Cnqvs-------yg~Mi~CDn~~C~~eWFH~~CVGL~~---~P--------kgkWyC~~C~~~~ 269 (274)
T KOG1973|consen 211 EEAVDPDEPTYCICNQVS-------YGKMIGCDNPGCPIEWFHFTCVGLKT---KP--------KGKWYCPRCKAEN 269 (274)
T ss_pred ccccCCCCCEEEEecccc-------cccccccCCCCCCcceEEEecccccc---CC--------CCcccchhhhhhh
Confidence 334444468899999653 589999997 98 999999999963 12 4569999997543
No 8
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.04 E-value=2.5e-06 Score=82.80 Aligned_cols=47 Identities=32% Similarity=0.865 Sum_probs=38.9
Q ss_pred CcceEEeCCCCCCCCcccccceeecc--cc-CceecccCCCCCCCCCCCCCCCCCCccCeeeccCccC
Q 014619 126 KGVYCTCNRPYPDPDVEEQVEMIQCC--IC-EDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 190 (421)
Q Consensus 126 ~g~yC~C~rpypdp~~e~~~~MiQC~--~C-EDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~ 190 (421)
..+||.|+++- -|.||.|+ .| .+|||..||||.. .| -..|+|+.|-.
T Consensus 220 e~lYCfCqqvS-------yGqMVaCDn~nCkrEWFH~~CVGLk~---pP--------KG~WYC~eCk~ 269 (271)
T COG5034 220 EELYCFCQQVS-------YGQMVACDNANCKREWFHLECVGLKE---PP--------KGKWYCPECKK 269 (271)
T ss_pred ceeEEEecccc-------cccceecCCCCCchhheeccccccCC---CC--------CCcEeCHHhHh
Confidence 47899999984 48999999 49 8999999999953 33 25799999964
No 10
>KOG1776 consensus Zn-binding protein Push [Signal transduction mechanisms]
Probab=97.51 E-value=2.6e-05 Score=84.31 Aligned_cols=60 Identities=20% Similarity=0.102 Sum_probs=52.6
Q ss_pred CCccccc---ccccccceEeecCCCCC-CCceEeccchhhhcCCCceeEeecccceeeccCCCCCCC
Q 014619 41 KECTYSK---GYMKRQAIFSCLSCAPE-GNAGVCTACSLTCHDGHEIVELWTKRNFRCDCGNSKFGE 103 (421)
Q Consensus 41 ~~Cty~~---g~~~rQ~~y~C~tC~~~-~~~gvC~~Cs~~CH~~H~l~el~~kr~f~CDCG~~~~~~ 103 (421)
..|||.+ -|+ -|.+|.|.||+.. +..|+|..||+.||.||++ -|.+..|.||||-+..++
T Consensus 765 ~~~T~Kkk~q~~m-~n~~~q~~k~~M~~~~gG~~kV~s~t~H~~~~i--~~S~~~~~C~C~Es~~~g 828 (1110)
T KOG1776|consen 765 RDETEKKKKQMAM-LNREKQLTKMRMKVGTGGQIKVSSRTLHNEPSI--DDSDSLPCCICRESVISG 828 (1110)
T ss_pred HHHHHhhhhhHHH-HHHHhhhhhheeeeccCceEEEeeecccCCCCc--cccCCCceeecccccccc
Confidence 3599963 599 9999999999987 5569999999999999999 577999999999988763
No 11
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.43 E-value=6.3e-05 Score=79.06 Aligned_cols=66 Identities=20% Similarity=0.478 Sum_probs=46.5
Q ss_pred CCCcceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCCcccccccc
Q 014619 124 NFKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVCSFLSTYPQ 200 (421)
Q Consensus 124 Nf~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~~fL~~y~~ 200 (421)
|-.=.||.|..|-. ..-||||..|..|||..|..-.-. ..-..|. |.+|+|..|..+..++.+-.+
T Consensus 168 n~qc~vC~~g~~~~------~NrmlqC~~C~~~fHq~Chqp~i~-~~l~~D~----~~~w~C~~C~~~~~~~~r~t~ 233 (464)
T KOG4323|consen 168 NLQCSVCYCGGPGA------GNRMLQCDKCRQWYHQACHQPLIK-DELAGDP----FYEWFCDVCNRGPKKVPRLTL 233 (464)
T ss_pred cceeeeeecCCcCc------cceeeeecccccHHHHHhccCCCC-HhhccCc----cceEeehhhccchhhcccccc
Confidence 44456788887742 348999999999999999854221 1122234 899999999988877766443
No 12
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.10 E-value=0.00017 Score=73.94 Aligned_cols=59 Identities=37% Similarity=0.835 Sum_probs=45.8
Q ss_pred cceEEeCCCCCCCCcccccceeeccccCceecccC--CCCCCCCCCCCCCCCCCccCeeeccCccCCCcccccc
Q 014619 127 GVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEH--IGLEPSDEIPRDDEGEPVYEDFICKACSAVCSFLSTY 198 (421)
Q Consensus 127 g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~C--lgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~~fL~~y 198 (421)
..||.|..++ ||+ ..|+||+.|++|||+.| ||++.. ..| . .+.++|..|.....-+..+
T Consensus 60 ~~~~~~~~~~-~p~----~~~~~cd~C~~~~~~ec~~v~~~~~-e~p---~----~~~~~c~~c~~~~~~~~~~ 120 (345)
T KOG1632|consen 60 QRYCKCYKPC-DPD----DLMEQCDLCEDWYHGECWEVGTAEK-EAP---K----EDPKVCDECKEAQDGMSES 120 (345)
T ss_pred hchhhccccc-Cch----hhhhccccccccccccccccCchhh-cCC---c----cccccccccchhhhhhhhh
Confidence 3599999998 674 59999999999999999 998653 233 2 6789999998766444443
No 13
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=96.99 E-value=0.00022 Score=80.93 Aligned_cols=58 Identities=31% Similarity=0.733 Sum_probs=48.6
Q ss_pred CCcccc---cccccccceEeecCCCCCCCceEeccchhhhcCCCceeEeecccceeeccCCC
Q 014619 41 KECTYS---KGYMKRQAIFSCLSCAPEGNAGVCTACSLTCHDGHEIVELWTKRNFRCDCGNS 99 (421)
Q Consensus 41 ~~Cty~---~g~~~rQ~~y~C~tC~~~~~~gvC~~Cs~~CH~~H~l~el~~kr~f~CDCG~~ 99 (421)
+.|+|+ ...| .|.+|.|+||...+.-..|.-|+..||.||+-.=-.|.---+|||=-.
T Consensus 1241 DtCSFTWTGadHI-NQDIfECkTCGL~~SLCCCsECAltCHk~HDCkLKRTSPTAYCDCWEK 1301 (3015)
T KOG0943|consen 1241 DTCSFTWTGADHI-NQDIFECKTCGLLESLCCCSECALTCHKGHDCKLKRTSPTAYCDCWEK 1301 (3015)
T ss_pred Cccceeecchhhc-cchhhhhcccccchhhhhhHHHHHHhccCCccceeccCCcceeehhhc
Confidence 358886 3589 999999999998888899999999999999986455556779999544
No 14
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=89.65 E-value=0.062 Score=58.74 Aligned_cols=55 Identities=25% Similarity=0.685 Sum_probs=39.8
Q ss_pred cceE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccC-eeeccCccC
Q 014619 127 GVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYE-DFICKACSA 190 (421)
Q Consensus 127 g~yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~-~fiC~~C~~ 190 (421)
+.|| +|.+-|-+.| ...|++|.+|.-|-|..|.++... .......+ .|-|..|.-
T Consensus 145 ~~~cPvc~~~Y~~~e---~~~~~~c~~c~rwsh~~c~~~sdd------~~~q~~vD~~~~CS~CR~ 201 (694)
T KOG4443|consen 145 LSYCPVCLIVYQDSE---SLPMVCCSICQRWSHGGCDGISDD------KYMQAQVDLQYKCSTCRG 201 (694)
T ss_pred cccCchHHHhhhhcc---chhhHHHHHhcccccCCCCccchH------HHHHHhhhhhcccceeeh
Confidence 6778 6888896543 678999999999999999998531 11011133 788999983
No 15
>PF00643 zf-B_box: B-box zinc finger; InterPro: IPR000315 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 B-box-type zinc finger domains, which are around 40 residues in length. B-box zinc fingers can be divided into two groups, where types 1 and 2 B-box domains differ in their consensus sequence and in the spacing of the 7-8 zinc-binding residues. Several proteins contain both types 1 and 2 B-boxes, suggesting some level of cooperativity between these two domains. B-box domains are found in over 1500 proteins from a variety of organisms. They are found in TRIM (tripartite motif) proteins that consist of an N-terminal RING finger (originally called an A-box), followed by 1-2 B-box domains and a coiled-coil domain (also called RBCC for Ring, B-box, Coiled-Coil). TRIM proteins contain a type 2 B-box domain, and may also contain a type 1 B-box. In proteins that do not contain RING or coiled-coil domains, the B-box domain is primarily type 2. Many type 2 B-box proteins are involved in ubiquitinylation. Proteins containing a B-box zinc finger domain include transcription factors, ribonucleoproteins and proto-oncoproteins; for example, MID1, MID2, TRIM9, TNL, TRIM36, TRIM63, TRIFIC, NCL1 and CONSTANS-like proteins []. The microtubule-associated E3 ligase MID1 (6.3.2 from EC) contains a type 1 B-box zinc finger domain. MID1 specifically binds Alpha-4, which in turn recruits the catalytic subunit of phosphatase 2A (PP2Ac). This complex is required for targeting of PP2Ac for proteasome-mediated degradation. The MID1 B-box coordinates two zinc ions and adopts a beta/beta/alpha cross-brace structure similar to that of ZZ, PHD, RING and FYVE zinc fingers [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 3DDT_B 2D8U_A 3Q1D_A 2EGM_A 2YVR_B 2DJA_A 2DQ5_A 2JUN_A 2YRG_A 2DID_A ....
Probab=87.35 E-value=0.44 Score=33.47 Aligned_cols=29 Identities=31% Similarity=0.851 Sum_probs=25.9
Q ss_pred ceEeecCCCCCCCceEeccchhhhcCCCceeEe
Q 014619 54 AIFSCLSCAPEGNAGVCTACSLTCHDGHEIVEL 86 (421)
Q Consensus 54 ~~y~C~tC~~~~~~gvC~~Cs~~CH~~H~l~el 86 (421)
..|-|.+|. ..||..|...=|.+|.++.|
T Consensus 14 ~~~~C~~C~----~~~C~~C~~~~H~~H~~~~i 42 (42)
T PF00643_consen 14 LSLFCEDCN----EPLCSECTVSGHKGHKIVPI 42 (42)
T ss_dssp EEEEETTTT----EEEEHHHHHTSTTTSEEEEC
T ss_pred eEEEecCCC----CccCccCCCCCCCCCEEeEC
Confidence 789999995 48999999999999999865
No 16
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=86.09 E-value=0.46 Score=53.23 Aligned_cols=52 Identities=27% Similarity=0.624 Sum_probs=38.1
Q ss_pred CcceE-EeCCCCCCCCcccccceeeccccCce-ecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014619 126 KGVYC-TCNRPYPDPDVEEQVEMIQCCICEDW-FHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 192 (421)
Q Consensus 126 ~g~yC-~C~rpypdp~~e~~~~MiQC~~CEDW-fH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 192 (421)
...-| +|..+ || .+.||-|+.|.+- ||.-||..+-. .+| ...|+|..|+...
T Consensus 214 E~~~C~IC~~~--Dp----EdVLLLCDsCN~~~YH~YCLDPdl~-eiP--------~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 214 EEVKCDICTVH--DP----EDVLLLCDSCNKVYYHVYCLDPDLS-ESP--------VNEWYCTNCSLLE 267 (1134)
T ss_pred ccccceeeccC--Ch----HHhheeecccccceeeccccCcccc-ccc--------ccceecCcchhhh
Confidence 34455 77777 56 4799999999776 99999986432 233 5789999998543
No 17
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=85.99 E-value=0.8 Score=48.88 Aligned_cols=62 Identities=24% Similarity=0.432 Sum_probs=46.8
Q ss_pred CccCcCCCCC--CcceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014619 116 NAENSYNHNF--KGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 192 (421)
Q Consensus 116 n~~N~Yn~Nf--~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 192 (421)
+....++-++ ...-|+|+.-+ +. .+.||||..|.-|-|.-|+|.... .. .+.|.|..|..+.
T Consensus 73 ~~~~~~~~~~~~~~~~c~c~~~~-~~----~g~~i~c~~c~~Wqh~~C~g~~~~------~~----p~~y~c~~c~~~~ 136 (508)
T KOG1844|consen 73 SLNGSEAGSEAREISRCDCGLED-DM----EGLMIQCDWCGRWQHKICCGSFKS------TK----PDKYVCEICTPRN 136 (508)
T ss_pred cccccccccCcCccccccccccc-CC----CceeeCCcccCcccCceeeeecCC------CC----chhceeeeecccc
Confidence 4455566666 66789999875 22 489999999999999999987432 12 3689999998766
No 18
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=84.41 E-value=0.22 Score=34.73 Aligned_cols=34 Identities=24% Similarity=0.676 Sum_probs=18.6
Q ss_pred cceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCc
Q 014619 145 VEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKAC 188 (421)
Q Consensus 145 ~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C 188 (421)
..||+|..|.-+.|..|-|+.. .|. .+.|+|..|
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~---~~~-------~~~W~C~~C 35 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSE---VPD-------GDDWLCDRC 35 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS-----S-------S-----HHH
T ss_pred CceEEeCCCCCcCChhhCCccc---CCC-------CCcEECCcC
Confidence 4699999999999999999854 222 235888776
No 19
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=75.93 E-value=1.3 Score=44.50 Aligned_cols=47 Identities=28% Similarity=0.709 Sum_probs=36.3
Q ss_pred eE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeecc-CccCCC
Q 014619 129 YC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICK-ACSAVC 192 (421)
Q Consensus 129 yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~-~C~~~~ 192 (421)
.| +|.+|.- ..+|+-|+.|..=||.-||||.. +| -..|||. .|....
T Consensus 316 lC~IC~~P~~------E~E~~FCD~CDRG~HT~CVGL~~---lP--------~G~WICD~~C~~~~ 364 (381)
T KOG1512|consen 316 LCRICLGPVI------ESEHLFCDVCDRGPHTLCVGLQD---LP--------RGEWICDMRCREAT 364 (381)
T ss_pred hhhccCCccc------chheeccccccCCCCcccccccc---cc--------CccchhhhHHHHhc
Confidence 44 7888852 47899999999999999999953 55 3579998 365444
No 20
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=75.78 E-value=1.8 Score=37.79 Aligned_cols=63 Identities=17% Similarity=0.313 Sum_probs=39.6
Q ss_pred CceeEeecccceeeccCCCCCCCcceeecCCCCCCCccCcC-CCCCCcceEEeCCCCCCCCcccccceeec
Q 014619 81 HEIVELWTKRNFRCDCGNSKFGEFFCKLFPSKDVENAENSY-NHNFKGVYCTCNRPYPDPDVEEQVEMIQC 150 (421)
Q Consensus 81 H~l~el~~kr~f~CDCG~~~~~~~~C~l~~~k~~~n~~N~Y-n~Nf~g~yC~C~rpypdp~~e~~~~MiQC 150 (421)
|.--|||...++ =++...... ++|++...++.....+.= ..+-...+|+|..+| ||+ ..||||
T Consensus 58 ~~~~EvF~S~~~-d~~~~~~I~-gkc~V~~~~ey~~~~~~~~~~~~~~d~~~Ce~~y-n~~----~~~~~c 121 (121)
T cd04714 58 HGEKELFASDHQ-DENSVQTIE-HKCYVLTFAEYERLARVKKKPQDGVDFYYCAGTY-NPD----TGMLKC 121 (121)
T ss_pred CCCCceEecCCc-ccccHHHhC-cccEEEehhHheecccccCCCCcCCCEEEEeccC-CCC----cCcccC
Confidence 566678866554 344444433 489988766654433321 112246799999999 574 789998
No 21
>smart00336 BBOX B-Box-type zinc finger.
Probab=74.07 E-value=2.5 Score=29.18 Aligned_cols=31 Identities=39% Similarity=0.746 Sum_probs=24.9
Q ss_pred ccceEeecCCCCCCCceEeccchhhhcCCCceeEe
Q 014619 52 RQAIFSCLSCAPEGNAGVCTACSLTCHDGHEIVEL 86 (421)
Q Consensus 52 rQ~~y~C~tC~~~~~~gvC~~Cs~~CH~~H~l~el 86 (421)
....|-|.+|. ..||..|...=|.+|.++.|
T Consensus 12 ~~~~~~C~~c~----~~iC~~C~~~~H~~H~~~~l 42 (42)
T smart00336 12 EPAEFFCEECG----ALLCRTCDEAEHRGHTVVLL 42 (42)
T ss_pred CceEEECCCCC----cccccccChhhcCCCceecC
Confidence 34467799985 48999999999999998653
No 22
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=70.08 E-value=0.72 Score=47.56 Aligned_cols=57 Identities=25% Similarity=0.583 Sum_probs=36.6
Q ss_pred CCcceEE-eCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccC
Q 014619 125 FKGVYCT-CNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 190 (421)
Q Consensus 125 f~g~yC~-C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~ 190 (421)
+.+.+|. |+..|- . ..+||-|.+|+.|||+.||.+.++. ...... -...|+|+.|..
T Consensus 237 ~~~~~~~~cg~~~~-~----~~~~~~~~~~e~w~~~~~v~~~~a~--~~~~~~--~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 237 YSKLICDPCGLSDA-N----KKFEICCDLCESWFHGDCVQIFEAR--KRLNEI--RNEVYKCPHCTV 294 (345)
T ss_pred cccccccccCcchH-H----HHHHHHHHHHHHHhcccccccccch--hhhhhh--hccceecCceee
Confidence 3466774 444431 1 3789999999999999999986531 111110 014599999975
No 23
>cd00021 BBOX B-Box-type zinc finger; zinc binding domain (CHC3H2); often present in combination with other motifs, like RING zinc finger, NHL motif, coiled-coil or RFP domain in functionally unrelated proteins, most likely mediating protein-protein interaction.
Probab=60.87 E-value=5.9 Score=26.81 Aligned_cols=30 Identities=33% Similarity=0.610 Sum_probs=23.8
Q ss_pred cceEeecCCCCCCCceEeccchhhhcCCCceeEe
Q 014619 53 QAIFSCLSCAPEGNAGVCTACSLTCHDGHEIVEL 86 (421)
Q Consensus 53 Q~~y~C~tC~~~~~~gvC~~Cs~~CH~~H~l~el 86 (421)
...|-|.+|. ..||..|...=|.+|..+.|
T Consensus 10 ~~~~fC~~~~----~~iC~~C~~~~H~~H~~~~i 39 (39)
T cd00021 10 PLSLFCETDR----ALLCVDCDLSVHSGHRRVPL 39 (39)
T ss_pred ceEEEeCccC----hhhhhhcChhhcCCCCEeeC
Confidence 3477899985 48999998766999998754
No 24
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=59.50 E-value=5.7 Score=42.86 Aligned_cols=49 Identities=22% Similarity=0.596 Sum_probs=37.9
Q ss_pred eE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCc
Q 014619 129 YC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKAC 188 (421)
Q Consensus 129 yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C 188 (421)
-| +|++.. | +-..+||+.|.--||..||+-+-. .+|.-.. ...|+|..|
T Consensus 546 sCgiCkks~-d-----QHll~~CDtC~lhYHlGCL~PPLT-R~Pkk~k----n~gWqCsEC 595 (707)
T KOG0957|consen 546 SCGICKKST-D-----QHLLTQCDTCHLHYHLGCLSPPLT-RLPKKNK----NFGWQCSEC 595 (707)
T ss_pred eeeeeccch-h-----hHHHhhcchhhceeeccccCCccc-cCccccc----Ccceeeccc
Confidence 45 788875 2 678999999999999999976543 3554443 578999999
No 25
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=58.94 E-value=8.9 Score=41.46 Aligned_cols=58 Identities=26% Similarity=0.496 Sum_probs=40.3
Q ss_pred ceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccC
Q 014619 128 VYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 190 (421)
Q Consensus 128 ~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~ 190 (421)
..|+|-..--+ ..++.|||+.|.-=.|+.|-|+.....+|...+ .-....|+|..|.-
T Consensus 121 iCcVClg~rs~----da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s-~~stepWfCeaC~~ 178 (707)
T KOG0957|consen 121 ICCVCLGQRSV----DAGEILQCDKCGINVHEGCYGVLDNVSIPSGSS-DCSTEPWFCEACLY 178 (707)
T ss_pred EEEEeecCccc----cccceeeccccCceecccccccccccccCCCCc-cCCCCchhhhhHhc
Confidence 77888543211 168899999999999999999976555554222 11257788888863
No 26
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=57.53 E-value=5.2 Score=33.83 Aligned_cols=36 Identities=25% Similarity=0.411 Sum_probs=28.8
Q ss_pred CcCCCCCCcceEEeCCCCCCCCcccccceeeccc--cCceecccCC
Q 014619 119 NSYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCI--CEDWFHEEHI 162 (421)
Q Consensus 119 N~Yn~Nf~g~yC~C~rpypdp~~e~~~~MiQC~~--CEDWfH~~Cl 162 (421)
+....++...-.+|++. .+..|||.. |..+||..|.
T Consensus 48 ~i~~~~~~~~C~iC~~~--------~G~~i~C~~~~C~~~fH~~CA 85 (110)
T PF13832_consen 48 NIPPSRFKLKCSICGKS--------GGACIKCSHPGCSTAFHPTCA 85 (110)
T ss_pred eecchhcCCcCcCCCCC--------CceeEEcCCCCCCcCCCHHHH
Confidence 44444566777799987 488999998 9999999996
No 27
>PF02881 SRP54_N: SRP54-type protein, helical bundle domain; InterPro: IPR013822 The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes [, ]. SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. Eukaryotic SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor []. In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane. In archaea, the SRP complex contains 7S RNA like its eukaryotic counterpart, yet only includes two of the six protein subunits found in the eukarytic complex: SRP19 and SRP54 []. This entry represents the N-terminal helical bundle domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homologue of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0006614 SRP-dependent cotranslational protein targeting to membrane; PDB: 1J8M_F 1J8Y_F 2J37_W 2OG2_A 3B9Q_A 2V3C_C 3NDB_B 1ZU5_B 1ZU4_A 1WGW_A ....
Probab=55.21 E-value=22 Score=27.81 Aligned_cols=31 Identities=16% Similarity=0.393 Sum_probs=26.9
Q ss_pred HHHHHHHhhhhc-CCCCccCHHHHHHHHHHHHH
Q 014619 385 MKDEFHNFLQSF-DPSKAITSDDVHQIFENLAK 416 (421)
Q Consensus 385 mKdkL~~fLk~F-e~gkvVt~EDIk~FFe~l~~ 416 (421)
||..|...++.| .+ .++++++|.+|+++|..
T Consensus 1 L~~~l~kt~~~l~~~-~~~~~~~i~~~l~ele~ 32 (75)
T PF02881_consen 1 LKKGLSKTFKKLSGS-IFLTEKDIEEFLEELEE 32 (75)
T ss_dssp HHHHHHHHHHHHHCC-SSCTHHHHHHHHHHHHH
T ss_pred ChHHHHHHHHHHhCc-ccccHHhHHHHHHHHHH
Confidence 688899999999 55 77899999999999874
No 28
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=49.63 E-value=9.6 Score=42.93 Aligned_cols=49 Identities=31% Similarity=0.824 Sum_probs=37.2
Q ss_pred CcceE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCcc
Q 014619 126 KGVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACS 189 (421)
Q Consensus 126 ~g~yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~ 189 (421)
..+.| +|+-| |-| +..+||-|+.|.--.|-.|-||.+ +|. ..|.|..|.
T Consensus 270 edviCDvCrsp--D~e--~~neMVfCd~Cn~cVHqaCyGIle---~p~--------gpWlCr~Ca 319 (893)
T KOG0954|consen 270 EDVICDVCRSP--DSE--EANEMVFCDKCNICVHQACYGILE---VPE--------GPWLCRTCA 319 (893)
T ss_pred ccceeceecCC--Ccc--ccceeEEeccchhHHHHhhhceee---cCC--------CCeeehhcc
Confidence 46788 88877 443 478999999999999999999965 342 356666665
No 29
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=49.29 E-value=17 Score=39.61 Aligned_cols=59 Identities=22% Similarity=0.510 Sum_probs=40.4
Q ss_pred CCCcceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCC--CCCCCCCCCCCccCeeeccCccCCC
Q 014619 124 NFKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPS--DEIPRDDEGEPVYEDFICKACSAVC 192 (421)
Q Consensus 124 Nf~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~--~~~p~~~~~~~~~~~fiC~~C~~~~ 192 (421)
+-.+.+|+|+..-+ + ...-+||-.|-.|||..++-..+. +.+|.. ....|+|..|....
T Consensus 17 ~~~~~~~y~e~~r~-l----~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~-----t~y~fvc~~c~~~~ 77 (544)
T KOG2626|consen 17 MKQATVCYCEGERN-L----GIVELQCSTCLKWFHLPTLEAFHLIKSSLPFM-----TSYEFVCKECTPSG 77 (544)
T ss_pred ccCccccccccccc-c----CceeeEeeecccccccccccccccccccCCcc-----cceeEEeccccCcc
Confidence 44578999987642 2 456799999999999877643321 022221 15789999998764
No 30
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=48.09 E-value=16 Score=27.37 Aligned_cols=42 Identities=26% Similarity=0.558 Sum_probs=22.2
Q ss_pred eeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCC
Q 014619 148 IQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAV 191 (421)
Q Consensus 148 iQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~ 191 (421)
.+|.+|. |-+..-.|-+.. +++..-.=+.+-+.|.||.|...
T Consensus 2 y~C~~Cg-yiYd~~~Gd~~~-~i~pGt~f~~Lp~~w~CP~C~a~ 43 (50)
T cd00730 2 YECRICG-YIYDPAEGDPDE-GIPPGTPFEDLPDDWVCPVCGAG 43 (50)
T ss_pred cCCCCCC-eEECCCCCCccc-CcCCCCCHhHCCCCCCCCCCCCc
Confidence 4677777 544444443321 22221111123678999999644
No 31
>PF14071 YlbD_coat: Putative coat protein
Probab=47.65 E-value=45 Score=29.76 Aligned_cols=74 Identities=19% Similarity=0.313 Sum_probs=50.8
Q ss_pred hhhhhcCCCcccCCCcc-hHHhhhhhHhh------h--hhh-hhhhhchHHHHHhhCChHHHHHHHHHHHHHHHHHHHhh
Q 014619 324 SMYEQKRVPYLIDEEDS-IAEYERTAKQK------R--EEK-LQQQEGAELTFLNKLGHVEKMEILNGIADMKDEFHNFL 393 (421)
Q Consensus 324 ~~y~~~~~~FLldeeDt-v~~YE~~~~~~------~--~~s-~~~d~g~~~~aL~sl~RvqaIE~i~gYn~mKdkL~~fL 393 (421)
.+|+. =+||-|+|. +.+|-+.+... . +.+ ......|. +|.+||-.+--.-|..++..=..|..+|
T Consensus 26 ~~YEe---W~LlGEdD~~W~~Yk~~~~~~~~~~~~~~~~~~~d~~~ql~~--~vKkmD~nq~q~hl~~~sqai~~vQ~~l 100 (124)
T PF14071_consen 26 QFYEE---WYLLGEDDPIWDPYKEDSEPSNSAEKKSETEKKNDWMSQLLS--MVKKMDVNQMQKHLNNVSQAIGSVQQVL 100 (124)
T ss_pred HHHHH---HHHhCCCcchHHHhhccccccccccccccccchhHHHHHHHH--HHHHCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 56775 467766665 78887221111 1 111 13344455 9999999999999999999999999999
Q ss_pred hhc-CCCCcc
Q 014619 394 QSF-DPSKAI 402 (421)
Q Consensus 394 k~F-e~gkvV 402 (421)
..| ..+.-.
T Consensus 101 ~qFq~~~~~~ 110 (124)
T PF14071_consen 101 SQFQGNGQKQ 110 (124)
T ss_pred HHhcCCCCCC
Confidence 999 665543
No 32
>PF13405 EF-hand_6: EF-hand domain; PDB: 2AMI_A 3QRX_A 1W7J_B 1OE9_B 1W7I_B 1KFU_S 1KFX_S 2BL0_B 1Y1X_B 3MSE_B ....
Probab=42.54 E-value=26 Score=22.70 Aligned_cols=25 Identities=16% Similarity=0.349 Sum_probs=21.9
Q ss_pred HHHHhhhhc--CCCCccCHHHHHHHHH
Q 014619 388 EFHNFLQSF--DPSKAITSDDVHQIFE 412 (421)
Q Consensus 388 kL~~fLk~F--e~gkvVt~EDIk~FFe 412 (421)
+|+.+|+.| +..-.|+.+|++.++.
T Consensus 1 ~l~~~F~~~D~d~dG~I~~~el~~~l~ 27 (31)
T PF13405_consen 1 RLREAFKMFDKDGDGFIDFEELRAILR 27 (31)
T ss_dssp HHHHHHHHH-TTSSSEEEHHHHHHHHH
T ss_pred CHHHHHHHHCCCCCCcCcHHHHHHHHH
Confidence 478889999 7788999999999987
No 33
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=40.56 E-value=31 Score=27.04 Aligned_cols=40 Identities=23% Similarity=0.395 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCccCHHHHHHHHHHHHH
Q 014619 376 MEILNGIADMKDEFHNFLQSFDPSKAITSDDVHQIFENLAK 416 (421)
Q Consensus 376 IE~i~gYn~mKdkL~~fLk~Fe~gkvVt~EDIk~FFe~l~~ 416 (421)
-.-|..|-..=..+..|+.. ..-.-||.+||++|+..|..
T Consensus 16 ~~Ti~~Y~~~l~~f~~~~~~-~~~~~it~~~i~~y~~~l~~ 55 (85)
T PF13495_consen 16 EKTIKNYRYHLKRFLRFLGN-KPPDEITPEDIEQYLNYLQN 55 (85)
T ss_dssp HHHHHHHHHHHHHHHTTSSS---GGG--HHHHHHHHHHHHT
T ss_pred HHHHHHHHHHHHHHHHHccc-CccchhHHHHHHHHHHHHHH
Confidence 34555665444444444431 23367899999999999983
No 34
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=40.44 E-value=26 Score=41.36 Aligned_cols=53 Identities=25% Similarity=0.538 Sum_probs=39.6
Q ss_pred CCcceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014619 125 FKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 192 (421)
Q Consensus 125 f~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 192 (421)
-.+..|+|... +.+...+-|+|+.|.--+|-.|.|++. +| + ..|.|..|..+.
T Consensus 218 ~D~~C~iC~~~----~~~n~n~ivfCD~Cnl~VHq~Cygi~~---ip---e-----g~WlCr~Cl~s~ 270 (1051)
T KOG0955|consen 218 EDAVCCICLDG----ECQNSNVIVFCDGCNLAVHQECYGIPF---IP---E-----GQWLCRRCLQSP 270 (1051)
T ss_pred CCccceeeccc----ccCCCceEEEcCCCcchhhhhccCCCC---CC---C-----CcEeehhhccCc
Confidence 44678899865 222357899999999999999999743 33 2 368999998654
No 35
>PF07061 Swi5: Swi5; InterPro: IPR010760 This entry represents Swi5 and is involved in meiotic DNA repair synthesis and meiotic joint molecule formation []. It is known to interact with Swi2, Rhp51 and Swi6 [].
Probab=40.28 E-value=29 Score=28.67 Aligned_cols=36 Identities=17% Similarity=0.330 Sum_probs=26.1
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCccCHHHHHH
Q 014619 374 EKMEILNGIADMKDEFHNFLQSFDPSKAITSDDVHQ 409 (421)
Q Consensus 374 qaIE~i~gYn~mKdkL~~fLk~Fe~gkvVt~EDIk~ 409 (421)
+-|..||.||++||-=...+.....-+=||--||.+
T Consensus 40 ~hI~lLheYNeiKD~gQ~Lig~iA~~rgvt~~~v~~ 75 (83)
T PF07061_consen 40 RHIKLLHEYNEIKDIGQGLIGLIADQRGVTVKDVYE 75 (83)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHcCCcHHHHHH
Confidence 468999999999998887777763334556555544
No 36
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=40.22 E-value=26 Score=25.23 Aligned_cols=33 Identities=21% Similarity=0.673 Sum_probs=25.1
Q ss_pred cccccceEeecCCCCCCCceEeccchhh-hcCCCceeE
Q 014619 49 YMKRQAIFSCLSCAPEGNAGVCTACSLT-CHDGHEIVE 85 (421)
Q Consensus 49 ~~~rQ~~y~C~tC~~~~~~gvC~~Cs~~-CH~~H~l~e 85 (421)
+| .-..|.|.+|. ..-+|..|... -|..|+.+.
T Consensus 9 ~i-~G~ry~C~~C~---d~dLC~~C~~~~~H~~H~f~~ 42 (43)
T cd02340 9 PI-VGVRYKCLVCP---DYDLCESCEAKGVHPEHAMLK 42 (43)
T ss_pred cC-cCCeEECCCCC---CccchHHhhCcCCCCCCCEEe
Confidence 66 77889999994 56788888544 677888763
No 37
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=39.56 E-value=14 Score=41.67 Aligned_cols=37 Identities=30% Similarity=0.666 Sum_probs=27.4
Q ss_pred ccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCcc
Q 014619 144 QVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACS 189 (421)
Q Consensus 144 ~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~ 189 (421)
.+..|-|+.|-.|||..|++.+-. +.+ ..+|+|+.|.
T Consensus 56 ~g~~l~c~tC~~s~h~~cl~~pl~---~~p------~~~~~c~Rc~ 92 (696)
T KOG0383|consen 56 GGELLWCDTCPASFHASCLGPPLT---PQP------NGEFICPRCF 92 (696)
T ss_pred CCcEEEeccccHHHHHHccCCCCC---cCC------ccceeeeeec
Confidence 367788999999999999987431 211 2339999994
No 38
>PF09082 DUF1922: Domain of unknown function (DUF1922); InterPro: IPR015166 Members of this family consist of a beta-sheet region followed by an alpha-helix and an unstructured C terminus. The beta-sheet region contains a CXCX...XCXC sequence with Cys residues located in two proximal loops and pointing towards each other. This precise function of this set of bacterial proteins is, as yet, unknown []. ; PDB: 1GH9_A.
Probab=37.86 E-value=15 Score=29.51 Aligned_cols=11 Identities=55% Similarity=1.449 Sum_probs=6.6
Q ss_pred eeeccCCCCCC
Q 014619 92 FRCDCGNSKFG 102 (421)
Q Consensus 92 f~CDCG~~~~~ 102 (421)
||||||.--..
T Consensus 4 frC~Cgr~lya 14 (68)
T PF09082_consen 4 FRCDCGRYLYA 14 (68)
T ss_dssp EEETTS--EEE
T ss_pred EEecCCCEEEe
Confidence 78888876543
No 39
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=37.57 E-value=14 Score=40.71 Aligned_cols=52 Identities=23% Similarity=0.526 Sum_probs=36.1
Q ss_pred cceE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCC-CCCCCCCCCCCccCeeeccCccCCC
Q 014619 127 GVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPS-DEIPRDDEGEPVYEDFICKACSAVC 192 (421)
Q Consensus 127 g~yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~-~~~p~~~~~~~~~~~fiC~~C~~~~ 192 (421)
..|| .|+++.. --..|+|+.|--=||..||.-+-. ..+| -..|.|+.|.-+-
T Consensus 253 ~~fCsaCn~~~~------F~~~i~CD~Cp~sFH~~CLePPl~~eniP--------~g~W~C~ec~~k~ 306 (613)
T KOG4299|consen 253 EDFCSACNGSGL------FNDIICCDGCPRSFHQTCLEPPLEPENIP--------PGSWFCPECKIKS 306 (613)
T ss_pred HHHHHHhCCccc------cccceeecCCchHHHHhhcCCCCCcccCC--------CCccccCCCeeee
Confidence 3488 8988732 123599999999999999965411 1233 3589999996543
No 40
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=36.90 E-value=30 Score=23.38 Aligned_cols=13 Identities=8% Similarity=0.404 Sum_probs=9.2
Q ss_pred cCHHHHHHHHHHH
Q 014619 402 ITSDDVHQIFENL 414 (421)
Q Consensus 402 Vt~EDIk~FFe~l 414 (421)
||.+|||+|++-.
T Consensus 17 ls~eeir~FL~~~ 29 (30)
T PF08671_consen 17 LSKEEIREFLEFN 29 (30)
T ss_dssp --HHHHHHHHHHH
T ss_pred CCHHHHHHHHHhC
Confidence 7899999998754
No 41
>KOG3878 consensus Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=34.96 E-value=46 Score=34.51 Aligned_cols=51 Identities=16% Similarity=0.330 Sum_probs=42.9
Q ss_pred HHHhhCChHHHHHHHHHHHHHHHHHHHhhhhc-CCCCccCHHHHHHHHHHHHHhh
Q 014619 365 TFLNKLGHVEKMEILNGIADMKDEFHNFLQSF-DPSKAITSDDVHQIFENLAKKR 418 (421)
Q Consensus 365 ~aL~sl~RvqaIE~i~gYn~mKdkL~~fLk~F-e~gkvVt~EDIk~FFe~l~~~k 418 (421)
.+|.+|.|++|++ +|-+|-+.+-.-|++| ...|..+.|..|+|=..+++.+
T Consensus 96 ~~LG~~sre~AM~---~FV~Lldr~C~~F~~yia~~k~~kde~lkE~e~r~~ee~ 147 (469)
T KOG3878|consen 96 QLLGEISREQAME---GFVDLLDRMCSAFRPYIAAVKQDKDETLKEKELRLMEEK 147 (469)
T ss_pred HHHhcccHHHHHH---HHHHHHHhcchhhhhHHHHhhhhhhhHHHHHHHHHHHhh
Confidence 3899999999987 4678888888899999 9999999999998877666443
No 42
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=32.86 E-value=34 Score=31.55 Aligned_cols=56 Identities=23% Similarity=0.568 Sum_probs=25.4
Q ss_pred ceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCC-----------------CCCCCCCCCCCccCeeeccCccC
Q 014619 128 VYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPS-----------------DEIPRDDEGEPVYEDFICKACSA 190 (421)
Q Consensus 128 ~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~-----------------~~~p~~~~~~~~~~~fiC~~C~~ 190 (421)
.||.|+.| .-.++|..|..||=..=-+.+.+ +..|-. -..+-|..|-.
T Consensus 4 ~YCG~~~p---------~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lg------dt~leCy~Cg~ 68 (152)
T PF09416_consen 4 AYCGIHDP---------SCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLG------DTVLECYNCGS 68 (152)
T ss_dssp TTT----C---------CCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-------S-B---TTT--
T ss_pred cccCCCCc---------ccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCC------CcEEEEEecCC
Confidence 36777654 46899999999996553222110 011211 24678999999
Q ss_pred CCcccccc
Q 014619 191 VCSFLSTY 198 (421)
Q Consensus 191 ~~~fL~~y 198 (421)
++-|+.-|
T Consensus 69 ~NvF~LGF 76 (152)
T PF09416_consen 69 RNVFLLGF 76 (152)
T ss_dssp --TTTEEE
T ss_pred CceeeEEE
Confidence 99888755
No 43
>PLN00035 histone H4; Provisional
Probab=30.46 E-value=50 Score=28.54 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHhhhhc----------CCCCccCHHHHHH
Q 014619 381 GIADMKDEFHNFLQSF----------DPSKAITSDDVHQ 409 (421)
Q Consensus 381 gYn~mKdkL~~fLk~F----------e~gkvVt~EDIk~ 409 (421)
+|..|...|.+||... ..-|+||++||.-
T Consensus 51 ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~ 89 (103)
T PLN00035 51 IYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVY 89 (103)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHH
Confidence 6888888888888763 4789999999953
No 44
>smart00417 H4 Histone H4.
Probab=29.77 E-value=57 Score=26.49 Aligned_cols=28 Identities=21% Similarity=0.347 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhhhhc----------CCCCccCHHHHH
Q 014619 381 GIADMKDEFHNFLQSF----------DPSKAITSDDVH 408 (421)
Q Consensus 381 gYn~mKdkL~~fLk~F----------e~gkvVt~EDIk 408 (421)
+|..|+.-|++||..- ...|+||.+||.
T Consensus 35 ~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~ 72 (74)
T smart00417 35 IYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVV 72 (74)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhe
Confidence 7888888888888762 578999999984
No 45
>cd04718 BAH_plant_2 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=29.03 E-value=41 Score=30.86 Aligned_cols=27 Identities=30% Similarity=0.551 Sum_probs=19.0
Q ss_pred ecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014619 157 FHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 192 (421)
Q Consensus 157 fH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 192 (421)
||..||.-+-. .+|+ ..|+|+.|..+.
T Consensus 2 ~H~~CL~Ppl~-~~P~--------g~W~Cp~C~~~~ 28 (148)
T cd04718 2 FHLCCLRPPLK-EVPE--------GDWICPFCEVEK 28 (148)
T ss_pred cccccCCCCCC-CCCC--------CCcCCCCCcCCC
Confidence 89999975432 2442 469999998664
No 46
>PF14659 Phage_int_SAM_3: Phage integrase, N-terminal SAM-like domain; PDB: 2KD1_A 2KOB_A 2KHQ_A 3LYS_E 2KIW_A 2KKP_A.
Probab=28.87 E-value=81 Score=22.68 Aligned_cols=30 Identities=20% Similarity=0.346 Sum_probs=17.1
Q ss_pred HHHHHHHHhhhhcCCCCccCHHHHHHHHHHH
Q 014619 384 DMKDEFHNFLQSFDPSKAITSDDVHQIFENL 414 (421)
Q Consensus 384 ~mKdkL~~fLk~Fe~gkvVt~EDIk~FFe~l 414 (421)
.++..+..+|... .=+-||..||+.|+.+|
T Consensus 28 ~~~~~i~p~~g~~-~i~~It~~~i~~~~~~l 57 (58)
T PF14659_consen 28 IIKNHILPYFGNK-KIKDITPRDIQNFINEL 57 (58)
T ss_dssp HHHHHHHHHTTSS-BGGG--HHHHHHHHHHH
T ss_pred HHHHHHHHHHCcC-cHHHCCHHHHHHHHHHc
Confidence 3333344444332 33458999999999987
No 47
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=28.41 E-value=25 Score=26.01 Aligned_cols=11 Identities=36% Similarity=1.099 Sum_probs=6.5
Q ss_pred cCeeeccCccC
Q 014619 180 YEDFICKACSA 190 (421)
Q Consensus 180 ~~~fiC~~C~~ 190 (421)
-+.|.||.|-.
T Consensus 32 p~~w~CP~C~a 42 (47)
T PF00301_consen 32 PDDWVCPVCGA 42 (47)
T ss_dssp -TT-B-TTTSS
T ss_pred CCCCcCcCCCC
Confidence 57899999964
No 48
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=28.35 E-value=55 Score=35.07 Aligned_cols=63 Identities=21% Similarity=0.520 Sum_probs=37.1
Q ss_pred eEEeCCCCCCCCcccccceeeccccCceecccCC-CCCCC-CCCCCCCCCCCccCeeeccCccCCCcc
Q 014619 129 YCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHI-GLEPS-DEIPRDDEGEPVYEDFICKACSAVCSF 194 (421)
Q Consensus 129 yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Cl-gl~~~-~~~p~~~~~~~~~~~fiC~~C~~~~~f 194 (421)
-|+|.+ | |-+-. +--+|-|++|.-|=|..|- .-... .+.........+--.|.|..|-.....
T Consensus 131 C~iC~k-f-D~~~n-~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seL 195 (446)
T PF07227_consen 131 CCICSK-F-DDNKN-TCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSEL 195 (446)
T ss_pred ccccCC-c-ccCCC-CeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhhH
Confidence 558877 4 33322 5779999999999999994 21100 000000000012358999999887743
No 49
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=27.99 E-value=74 Score=26.49 Aligned_cols=28 Identities=18% Similarity=0.363 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhhhhc----------CCCCccCHHHHH
Q 014619 381 GIADMKDEFHNFLQSF----------DPSKAITSDDVH 408 (421)
Q Consensus 381 gYn~mKdkL~~fLk~F----------e~gkvVt~EDIk 408 (421)
+|..+..-|+.||... ..-|+||++||.
T Consensus 35 ~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~ 72 (85)
T cd00076 35 VYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVV 72 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHH
Confidence 7888888888888763 588999999995
No 50
>PTZ00015 histone H4; Provisional
Probab=27.62 E-value=71 Score=27.55 Aligned_cols=29 Identities=21% Similarity=0.306 Sum_probs=23.1
Q ss_pred HHHHHHHHHHHhhhhc----------CCCCccCHHHHHH
Q 014619 381 GIADMKDEFHNFLQSF----------DPSKAITSDDVHQ 409 (421)
Q Consensus 381 gYn~mKdkL~~fLk~F----------e~gkvVt~EDIk~ 409 (421)
+|..++.-|++||..- ..-|+||.+||.-
T Consensus 52 ~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~ 90 (102)
T PTZ00015 52 IYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVY 90 (102)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHH
Confidence 6888888888888762 4789999999953
No 51
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 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 CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=26.29 E-value=31 Score=25.57 Aligned_cols=15 Identities=27% Similarity=0.581 Sum_probs=9.2
Q ss_pred ceeeccccCceeccc
Q 014619 146 EMIQCCICEDWFHEE 160 (421)
Q Consensus 146 ~MiQC~~CEDWfH~~ 160 (421)
..|||+.|..|=...
T Consensus 2 ~WVQCd~C~KWR~lp 16 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP 16 (50)
T ss_dssp EEEE-TTT--EEEE-
T ss_pred eEEECCCCCceeeCC
Confidence 469999999998766
No 52
>cd05029 S-100A6 S-100A6: S-100A6 domain found in proteins similar to S100A6. S100A6 is a member of the S100 domain family within EF-hand Ca2+-binding proteins superfamily. Note that the S-100 hierarchy, to which this S-100A6 group belongs, contains only S-100 EF-hand domains, other EF-hands have been modeled separately. S100 proteins exhibit unique patterns of tissue- and cell type-specific expression and have been implicated in the Ca2+-dependent regulation of diverse physiological processes, including cell cycle regulation, differentiation, growth, and metabolic control . S100A6 is normally expressed in the G1 phase of the cell cycle in neuronal cells. The function of S100A6 remains unclear, but evidence suggests that it is involved in cell cycle regulation and exocytosis. S100A6 may also be involved in tumorigenesis; the protein is overexpressed in several tumors. Ca2+ binding to S100A6 leads to a conformational change in the protein, which exposes a hydrophobic surface for interact
Probab=25.58 E-value=87 Score=25.69 Aligned_cols=40 Identities=15% Similarity=0.353 Sum_probs=28.5
Q ss_pred HHHHHHHHH--------HHHHHHHhhhhc-CCCCccCHHHHHHHHHHHH
Q 014619 376 MEILNGIAD--------MKDEFHNFLQSF-DPSKAITSDDVHQIFENLA 415 (421)
Q Consensus 376 IE~i~gYn~--------mKdkL~~fLk~F-e~gkvVt~EDIk~FFe~l~ 415 (421)
|++.+.|.. =+++|+.+|+.+ .-|..+|.++|.+.|..+.
T Consensus 13 i~~F~~y~~~~~~~g~Is~~EL~~~l~~~~~lg~k~t~~ev~~m~~~~D 61 (88)
T cd05029 13 VAIFHKYSGREGDKNTLSKKELKELIQKELTIGSKLQDAEIAKLMEDLD 61 (88)
T ss_pred HHHHHHHHccCCCCCEECHHHHHHHHHHHHhcCCCCCHHHHHHHHHHhc
Confidence 555566654 245688888765 5677789999999998764
No 53
>TIGR02925 cis_trans_EpsD peptidyl-prolyl cis-trans isomerase, EpsD family. Members of this family belong to the peptidyl-prolyl cis-trans isomerase family and are found in loci associated with exopolysaccharide biosynthesis. All members are encoded near a homolog of EpsH, as detected by TIGR02602.
Probab=25.47 E-value=1.3e+02 Score=28.56 Aligned_cols=40 Identities=10% Similarity=0.360 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHH--HHhhhhc-CCCCccCHHHHHHHHHHHHH
Q 014619 377 EILNGIADMKDEF--HNFLQSF-DPSKAITSDDVHQIFENLAK 416 (421)
Q Consensus 377 E~i~gYn~mKdkL--~~fLk~F-e~gkvVt~EDIk~FFe~l~~ 416 (421)
+....++.+|+.| ..|++.. .+.-.||++||++||++..+
T Consensus 89 ~~~~~~~~~r~~ll~~~~~~~~v~~~~~vse~ev~~~Y~~~~~ 131 (232)
T TIGR02925 89 DVVMALEAAKREILARAYLRQLAGAQSKPSPEEAKSYFQEHPQ 131 (232)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHhCHH
Confidence 4445556666653 3455655 55568999999999998654
No 54
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=25.27 E-value=40 Score=34.03 Aligned_cols=51 Identities=22% Similarity=0.511 Sum_probs=36.7
Q ss_pred CCcceE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccC
Q 014619 125 FKGVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 190 (421)
Q Consensus 125 f~g~yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~ 190 (421)
-.-+|| +|+...+| .-.+-|+.|..=||.-||.-+-. -|. + ..|-|-.|+.
T Consensus 279 ieck~csicgtsend------dqllfcddcdrgyhmyclsppm~--epp--e-----gswsc~KOG~ 330 (336)
T KOG1244|consen 279 IECKYCSICGTSEND------DQLLFCDDCDRGYHMYCLSPPMV--EPP--E-----GSWSCHLCLE 330 (336)
T ss_pred eecceeccccCcCCC------ceeEeecccCCceeeEecCCCcC--CCC--C-----CchhHHHHHH
Confidence 445688 89988653 56899999999999999975432 122 2 3678888874
No 55
>cd02339 ZZ_Mind_bomb Zinc finger, ZZ type. Zinc finger present in Drosophila Mind bomb (D-mib) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Mind bomb is an E3 ubiqitin ligase that has been shown to regulate signaling by the Notch ligand Delta in Drosophila melanogaster.
Probab=25.11 E-value=56 Score=23.88 Aligned_cols=34 Identities=21% Similarity=0.430 Sum_probs=23.9
Q ss_pred ccccccceEeecCCCCCCCceEeccchh--hhcCCCceeE
Q 014619 48 GYMKRQAIFSCLSCAPEGNAGVCTACSL--TCHDGHEIVE 85 (421)
Q Consensus 48 g~~~rQ~~y~C~tC~~~~~~gvC~~Cs~--~CH~~H~l~e 85 (421)
..| +-.-|.|++|. ..-+|..|.. .-+.+|+.++
T Consensus 9 ~~i-~G~RykC~~C~---dyDLC~~C~~~~~H~~~H~f~r 44 (45)
T cd02339 9 QGI-IGIRWKCAECP---NYDLCTTCYHGDKHDLEHRFYR 44 (45)
T ss_pred CCc-ccCeEECCCCC---CccchHHHhCCCCCCCCCCEEe
Confidence 455 67789999994 5679999953 3246777654
No 56
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=24.28 E-value=18 Score=44.02 Aligned_cols=53 Identities=25% Similarity=0.524 Sum_probs=39.0
Q ss_pred CcceE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCCc
Q 014619 126 KGVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVCS 193 (421)
Q Consensus 126 ~g~yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clgl~~~~~~p~~~~~~~~~~~fiC~~C~~~~~ 193 (421)
....| +|++.- + ...|+-|+.|..|||.-|+...-. .+| +..|.|+.|...+.
T Consensus 1107 ~~~~c~~cr~k~-~-----~~~m~lc~~c~~~~h~~C~rp~~~-~~~--------~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1107 VNALCKVCRRKK-Q-----DEKMLLCDECLSGFHLFCLRPALS-SVP--------PGDWMCPSCRKEHR 1160 (1404)
T ss_pred chhhhhhhhhcc-c-----chhhhhhHhhhhhHHHHhhhhhhc-cCC--------cCCccCCccchhhh
Confidence 34567 788774 2 368999999999999999965332 123 45699999997764
No 57
>KOG0031 consensus Myosin regulatory light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=23.72 E-value=2e+02 Score=26.93 Aligned_cols=46 Identities=13% Similarity=0.341 Sum_probs=38.2
Q ss_pred HHhhCChHHHHHHHHHHHHH---------HHHHHHhhhhcCCCCccCHHHHHHHHHH
Q 014619 366 FLNKLGHVEKMEILNGIADM---------KDEFHNFLQSFDPSKAITSDDVHQIFEN 413 (421)
Q Consensus 366 aL~sl~RvqaIE~i~gYn~m---------KdkL~~fLk~Fe~gkvVt~EDIk~FFe~ 413 (421)
.++.++--|=.|.=.|||-| |..|+++|.+. ||+|+++.|.+.+.+
T Consensus 22 vFamf~q~QIqEfKEAF~~mDqnrDG~IdkeDL~d~~aSl--Gk~~~d~elDaM~~E 76 (171)
T KOG0031|consen 22 VFAMFDQSQIQEFKEAFNLMDQNRDGFIDKEDLRDMLASL--GKIASDEELDAMMKE 76 (171)
T ss_pred HHHHhhHHHHHHHHHHHHHHhccCCCcccHHHHHHHHHHc--CCCCCHHHHHHHHHh
Confidence 67778888888888999888 77888888775 888999999888764
No 58
>smart00054 EFh EF-hand, calcium binding motif. EF-hands are calcium-binding motifs that occur at least in pairs. Links between disease states and genes encoding EF-hands, particularly the S100 subclass, are emerging. Each motif consists of a 12 residue loop flanked on either side by a 12 residue alpha-helix. EF-hands undergo a conformational change unpon binding calcium ions.
Probab=23.56 E-value=74 Score=18.16 Aligned_cols=25 Identities=12% Similarity=0.343 Sum_probs=17.5
Q ss_pred HHHhhhhc--CCCCccCHHHHHHHHHH
Q 014619 389 FHNFLQSF--DPSKAITSDDVHQIFEN 413 (421)
Q Consensus 389 L~~fLk~F--e~gkvVt~EDIk~FFe~ 413 (421)
|+..|+.+ ..+..|+..++..++..
T Consensus 2 ~~~~f~~~d~~~~g~i~~~e~~~~~~~ 28 (29)
T smart00054 2 LKEAFRLFDKDGDGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHHCCCCCCcEeHHHHHHHHHh
Confidence 45566666 44457999998888764
No 59
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=22.88 E-value=42 Score=27.02 Aligned_cols=31 Identities=23% Similarity=0.305 Sum_probs=24.2
Q ss_pred CcceEEeCCCCCCCCcccccceeeccc--cCceecccCCCC
Q 014619 126 KGVYCTCNRPYPDPDVEEQVEMIQCCI--CEDWFHEEHIGL 164 (421)
Q Consensus 126 ~g~yC~C~rpypdp~~e~~~~MiQC~~--CEDWfH~~Clgl 164 (421)
.-.-.+|++++ |..|+|.. |..+||..|.-.
T Consensus 36 ~~~C~~C~~~~--------Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 36 KLKCSICKKKG--------GACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCCcCCCCCC--------CeEEEEeCCCCCcEEChHHHcc
Confidence 34444888773 78999996 999999999643
No 60
>PF07106 TBPIP: Tat binding protein 1(TBP-1)-interacting protein (TBPIP); InterPro: IPR010776 This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation [].
Probab=22.80 E-value=4.3e+02 Score=23.97 Aligned_cols=50 Identities=12% Similarity=0.220 Sum_probs=35.8
Q ss_pred HHhhCChHHHHHHHHHHHHHHHHHHHhhhhc-CCCCccCHHHHHHHHHHHH
Q 014619 366 FLNKLGHVEKMEILNGIADMKDEFHNFLQSF-DPSKAITSDDVHQIFENLA 415 (421)
Q Consensus 366 aL~sl~RvqaIE~i~gYn~mKdkL~~fLk~F-e~gkvVt~EDIk~FFe~l~ 415 (421)
+.+.+.=.+....|.....=...|.+=|.++ +++..|+++|+...=...+
T Consensus 105 L~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~ 155 (169)
T PF07106_consen 105 LSSEPTNEELREEIEELEEEIEELEEKLEKLRSGSKPVSPEEKEKLEKEYK 155 (169)
T ss_pred HhcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence 3355556666666767766677777788888 8889999999887654443
No 61
>PF02885 Glycos_trans_3N: Glycosyl transferase family, helical bundle domain Prosite entry for Thymidine and pyrimidine-nucleoside phosphorylases; InterPro: IPR017459 The biosynthesis of disaccharides, oligosaccharides and polysaccharides involves the action of hundreds of different glycosyltransferases. These enzymes catalyse the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. A classification of glycosyltransferases using nucleotide diphospho-sugar, nucleotide monophospho-sugar and sugar phosphates (2.4.1.- from EC) and related proteins into distinct sequence based families has been described []. This classification is available on the CAZy (CArbohydrate-Active EnZymes) web site. The same three-dimensional fold is expected to occur within each of the families. Because 3-D structures are better conserved than sequences, several of the families defined on the basis of sequence similarities may have similar 3-D structures and therefore form 'clans'. The glycosyl transferase family includes anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase (2.4.2.2 from EC) catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism. This N-terminal domain is found in various family 3 glycosyl transferases, including anthranilate phosphoribosyltransferase (TrpD, 2.4.2.18 from EC) and thymidine phosphorylase (2.4.2.2 from EC). All these proteins can transfer a phosphorylated ribose substrate. Thymidine phosphorylase catalyses the reversible phosphorolysis of thymidine, deoxyuridine and their analogues to their respective bases and 2-deoxyribose 1-phosphate. This enzyme regulates the availability of thymidine and is therefore essential to nucleic acid metabolism.; PDB: 2DSJ_B 2ELC_B 2BPQ_A 1ZVW_B 3QR9_B 1V8G_B 2WK5_C 2J0F_C 2WK6_B 1UOU_A ....
Probab=22.75 E-value=67 Score=24.79 Aligned_cols=27 Identities=7% Similarity=0.391 Sum_probs=17.2
Q ss_pred HHHhhhhcCCCCccCHHHHHHHHHHHH
Q 014619 389 FHNFLQSFDPSKAITSDDVHQIFENLA 415 (421)
Q Consensus 389 L~~fLk~Fe~gkvVt~EDIk~FFe~l~ 415 (421)
++++|+..-.|+..|.++++++|..+-
T Consensus 2 ~~~~l~~l~~g~~Ls~~e~~~~~~~i~ 28 (66)
T PF02885_consen 2 IKEILKKLRDGEDLSREEAKAAFDAIL 28 (66)
T ss_dssp HHHHHHHHHTT----HHHHHHHHHHHH
T ss_pred HHHHHHHHHcCCCCCHHHHHHHHHHHH
Confidence 466777775668889999999888765
No 62
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=21.88 E-value=24 Score=23.13 Aligned_cols=18 Identities=28% Similarity=0.396 Sum_probs=8.7
Q ss_pred cceeeccccCceecccCC
Q 014619 145 VEMIQCCICEDWFHEEHI 162 (421)
Q Consensus 145 ~~MiQC~~CEDWfH~~Cl 162 (421)
..+..|..|.-++|..|+
T Consensus 13 ~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 13 GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --EEE-TTT-----HHHH
T ss_pred CceEECccCCCccChhcC
Confidence 378999999999999874
No 63
>PF08164 TRAUB: Apoptosis-antagonizing transcription factor, C-terminal; InterPro: IPR012617 This C-terminal domain is found in traube proteins [].; GO: 0005634 nucleus
Probab=21.16 E-value=96 Score=25.65 Aligned_cols=27 Identities=15% Similarity=0.534 Sum_probs=21.4
Q ss_pred HHHHHhhhhcCCCCccCHHHHHHHHHHH
Q 014619 387 DEFHNFLQSFDPSKAITSDDVHQIFENL 414 (421)
Q Consensus 387 dkL~~fLk~Fe~gkvVt~EDIk~FFe~l 414 (421)
.||..|..| ...-..+.+.|.+||..|
T Consensus 56 eKL~NFmaP-~~~~~w~~~~~delf~sL 82 (83)
T PF08164_consen 56 EKLVNFMAP-EDRPTWSDEQIDELFASL 82 (83)
T ss_pred HHHhhhcCC-CCCCCCCHHHHHHHHHHc
Confidence 578888877 566677899999999876
No 64
>PF14047 DCR: Dppa2/4 conserved region
Probab=20.93 E-value=45 Score=26.58 Aligned_cols=13 Identities=15% Similarity=0.611 Sum_probs=11.1
Q ss_pred cCeeeccCccCCC
Q 014619 180 YEDFICKACSAVC 192 (421)
Q Consensus 180 ~~~fiC~~C~~~~ 192 (421)
-|.|+|+.|++++
T Consensus 53 eDNmLCp~Cv~rN 65 (66)
T PF14047_consen 53 EDNMLCPECVKRN 65 (66)
T ss_pred cccccCHhHhhcc
Confidence 5789999999875
No 65
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=20.63 E-value=61 Score=26.15 Aligned_cols=18 Identities=28% Similarity=0.637 Sum_probs=10.6
Q ss_pred ceEeccc---hhhhcCCCcee
Q 014619 67 AGVCTAC---SLTCHDGHEIV 84 (421)
Q Consensus 67 ~gvC~~C---s~~CH~~H~l~ 84 (421)
--|.-|| .+.||.+|.|+
T Consensus 40 Le~LkACGAvdYFC~~c~gLi 60 (70)
T PF07191_consen 40 LEVLKACGAVDYFCNHCHGLI 60 (70)
T ss_dssp -EEEEETTEEEEE-TTTT-EE
T ss_pred HHHHHHhcccceeeccCCcee
Confidence 3455555 58899999885
No 66
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=20.23 E-value=81 Score=26.83 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=13.4
Q ss_pred hhhhcCCCCccCHHHHHHHHHHHHHhhhc
Q 014619 392 FLQSFDPSKAITSDDVHQIFENLAKKRRR 420 (421)
Q Consensus 392 fLk~Fe~gkvVt~EDIk~FFe~l~~~kr~ 420 (421)
-.+|+=..=+||++||+.==++.+..|+|
T Consensus 63 ~~QPLc~~~~VT~eDIr~QE~rVk~aR~R 91 (96)
T PF14048_consen 63 PPQPLCKQFVVTEEDIRRQERRVKKARKR 91 (96)
T ss_dssp ------T-----HHHHHHHHHHHHHHHHH
T ss_pred CCcccccCCccCHHHHHHHHHHHHHHHHH
Confidence 34555233459999999877777766654
Done!