Query 014692
Match_columns 420
No_of_seqs 194 out of 700
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 07:35:53 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/014692.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/014692hhsearch_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 6.7E-89 1.5E-93 661.2 18.6 336 2-414 3-345 (345)
2 PF02207 zf-UBR: Putative zinc 99.4 2.8E-13 6.2E-18 107.9 3.2 66 41-108 2-70 (71)
3 smart00396 ZnF_UBR1 Putative z 99.3 5.9E-12 1.3E-16 100.6 5.1 65 41-108 2-70 (71)
4 KOG1777 Putative Zn-finger pro 98.6 1.6E-08 3.4E-13 104.1 3.8 84 20-111 530-616 (625)
5 PF00628 PHD: PHD-finger; Int 98.3 4.8E-08 1E-12 72.2 -1.5 50 128-190 1-51 (51)
6 KOG2752 Uncharacterized conser 98.3 1.4E-07 3.1E-12 93.6 1.0 106 67-193 2-107 (345)
7 KOG1973 Chromatin remodeling p 98.2 6.4E-07 1.4E-11 88.8 3.6 56 118-191 211-269 (274)
8 smart00249 PHD PHD zinc finger 98.2 9.3E-07 2E-11 62.7 3.2 46 128-187 1-47 (47)
9 COG5034 TNG2 Chromatin remodel 97.9 6E-06 1.3E-10 80.2 2.8 47 125-189 220-269 (271)
10 KOG1776 Zn-binding protein Pus 97.4 4.6E-05 9.9E-10 82.5 0.5 59 41-102 766-828 (1110)
11 KOG4323 Polycomb-like PHD Zn-f 97.3 0.00012 2.7E-09 76.9 2.3 66 122-198 167-232 (464)
12 KOG0943 Predicted ubiquitin-pr 97.1 0.00018 3.8E-09 81.6 0.7 57 40-97 1241-1300(3015)
13 KOG1632 Uncharacterized PHD Zn 97.0 0.00024 5.3E-09 72.8 1.0 59 126-197 60-120 (345)
14 PF00643 zf-B_box: B-box zinc 87.8 0.42 9E-06 33.6 2.1 29 53-85 14-42 (42)
15 KOG4443 Putative transcription 87.1 0.27 5.8E-06 54.0 1.2 54 126-188 145-200 (694)
16 KOG1844 PHD Zn-finger proteins 85.0 0.94 2E-05 48.3 4.0 63 114-191 72-136 (508)
17 KOG0825 PHD Zn-finger protein 85.0 0.55 1.2E-05 52.7 2.3 51 126-191 215-267 (1134)
18 cd04714 BAH_BAHCC1 BAH, or Bro 82.4 0.87 1.9E-05 39.8 2.1 63 80-149 58-121 (121)
19 PF13831 PHD_2: PHD-finger; PD 82.0 0.32 7E-06 34.0 -0.6 34 144-187 2-35 (36)
20 smart00336 BBOX B-Box-type zin 75.1 2.2 4.8E-05 29.4 2.0 31 51-85 12-42 (42)
21 cd00021 BBOX B-Box-type zinc f 63.6 4.9 0.00011 27.2 1.6 30 52-85 10-39 (39)
22 KOG1512 PHD Zn-finger protein 63.4 3.5 7.7E-05 41.5 1.2 45 130-191 319-364 (381)
23 KOG1632 Uncharacterized PHD Zn 60.2 1.4 3.1E-05 45.4 -2.3 42 144-189 253-294 (345)
24 KOG0957 PHD finger protein [Ge 59.7 5.6 0.00012 42.9 2.0 47 130-187 549-595 (707)
25 PF13832 zf-HC5HC2H_2: PHD-zin 58.0 5 0.00011 33.9 1.1 37 117-161 47-85 (110)
26 PF02881 SRP54_N: SRP54-type p 56.5 20 0.00044 28.0 4.3 31 384-415 1-32 (75)
27 KOG2626 Histone H3 (Lys4) meth 50.5 16 0.00035 39.7 3.6 59 123-191 17-77 (544)
28 KOG0957 PHD finger protein [Ge 46.7 18 0.0004 39.2 3.3 58 127-189 121-178 (707)
29 cd00730 rubredoxin Rubredoxin; 45.8 19 0.0004 27.1 2.3 42 147-190 2-43 (50)
30 PF14071 YlbD_coat: Putative c 45.8 50 0.0011 29.5 5.4 74 323-401 26-110 (124)
31 PF13405 EF-hand_6: EF-hand do 43.2 26 0.00055 22.8 2.5 25 387-411 1-27 (31)
32 PF13495 Phage_int_SAM_4: Phag 42.3 28 0.0006 27.3 3.1 40 375-415 16-55 (85)
33 cd02340 ZZ_NBR1_like Zinc fing 39.3 27 0.00058 25.2 2.3 33 48-84 9-42 (43)
34 PF08671 SinI: Anti-repressor 37.9 28 0.00061 23.5 2.0 13 401-413 17-29 (30)
35 PF07061 Swi5: Swi5; InterPro 37.8 34 0.00073 28.3 2.9 36 373-408 40-75 (83)
36 PF09416 UPF1_Zn_bind: RNA hel 36.0 28 0.00061 32.1 2.4 56 127-197 4-76 (152)
37 KOG0383 Predicted helicase [Ge 34.6 19 0.0004 40.7 1.2 37 143-188 56-92 (696)
38 KOG3878 Protein involved in ma 33.2 51 0.0011 34.2 3.9 51 364-417 96-147 (469)
39 KOG0955 PHD finger protein BR1 33.1 41 0.00088 39.8 3.6 53 124-191 218-270 (1051)
40 PF09082 DUF1922: Domain of un 32.0 21 0.00045 28.7 0.7 11 91-101 4-14 (68)
41 PLN00035 histone H4; Provision 31.7 46 0.001 28.7 2.9 29 380-408 51-89 (103)
42 smart00417 H4 Histone H4. 31.2 52 0.0011 26.7 2.9 28 380-407 35-72 (74)
43 PF14659 Phage_int_SAM_3: Phag 30.1 75 0.0016 22.9 3.5 29 384-413 29-57 (58)
44 KOG4299 PHD Zn-finger protein 29.7 23 0.00051 39.2 0.9 51 127-191 254-306 (613)
45 cd00076 H4 Histone H4, one of 29.3 68 0.0015 26.7 3.4 28 380-407 35-72 (85)
46 PTZ00015 histone H4; Provision 28.9 65 0.0014 27.8 3.3 29 380-408 52-90 (102)
47 TIGR02925 cis_trans_EpsD pepti 27.3 1.1E+02 0.0024 28.9 5.0 40 376-415 89-131 (232)
48 PF00301 Rubredoxin: Rubredoxi 26.4 29 0.00063 25.7 0.7 11 179-189 32-42 (47)
49 cd04718 BAH_plant_2 BAH, or Br 26.1 50 0.0011 30.3 2.3 27 156-191 2-28 (148)
50 cd05029 S-100A6 S-100A6: S-100 25.6 87 0.0019 25.7 3.4 40 375-414 13-61 (88)
51 PF07496 zf-CW: CW-type Zinc F 24.8 34 0.00073 25.3 0.8 15 145-159 2-16 (50)
52 PF07227 DUF1423: Protein of u 24.6 71 0.0015 34.3 3.4 64 128-194 131-196 (446)
53 cd02339 ZZ_Mind_bomb Zinc fing 24.1 59 0.0013 23.7 1.9 34 47-84 9-44 (45)
54 PF13771 zf-HC5HC2H: PHD-like 23.7 40 0.00087 27.2 1.1 36 120-163 31-68 (90)
55 smart00054 EFh EF-hand, calciu 23.6 74 0.0016 18.2 2.1 25 388-412 2-28 (29)
56 KOG0031 Myosin regulatory ligh 23.5 2E+02 0.0044 26.9 5.6 46 365-412 22-76 (171)
57 PF08164 TRAUB: Apoptosis-anta 22.9 84 0.0018 26.0 2.8 27 386-413 56-82 (83)
58 PF02885 Glycos_trans_3N: Glyc 22.1 70 0.0015 24.7 2.1 27 388-414 2-28 (66)
59 PF09332 Mcm10: Mcm10 replicat 22.1 81 0.0018 32.8 3.2 41 53-98 251-294 (344)
60 KOG0954 PHD finger protein [Ge 22.0 40 0.00086 38.3 0.9 49 125-188 270-319 (893)
61 PF07106 TBPIP: Tat binding pr 21.9 5.1E+02 0.011 23.5 8.1 49 366-414 106-155 (169)
62 PF03726 PNPase: Polyribonucle 20.6 1.1E+02 0.0024 24.5 3.1 40 378-417 27-67 (83)
63 KOG1245 Chromatin remodeling c 20.6 23 0.00051 43.0 -1.3 52 126-192 1108-1160(1404)
64 PF14048 MBD_C: C-terminal dom 20.3 80 0.0017 26.9 2.2 28 392-419 64-91 (96)
65 PF10752 DUF2533: Protein of u 20.1 2E+02 0.0043 24.0 4.4 35 378-412 47-83 (84)
No 1
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=100.00 E-value=6.7e-89 Score=661.24 Aligned_cols=336 Identities=42% Similarity=0.828 Sum_probs=269.1
Q ss_pred CCCCcccchhccCcCHHHHHHhHHHHHH-HHhhcCCCCCCCcccccccccccceEeecCCCCCC-CceEeccchhhhcCC
Q 014692 2 SGELDDDVEAEQTISINEYLNDVEEKEL-ADLVLGGDEGKECTYSKGYMKRQAIFSCLSCAPEG-NAGVCTACSLTCHDG 79 (420)
Q Consensus 2 ~~~~~~~~e~e~~vT~~e~le~q~eLE~-a~~~l~~~~~~~Cty~~g~~~rQ~~y~C~tC~~~~-~~giC~~Cs~~CH~~ 79 (420)
+|-+++ +|.-.+||+.+|++++.+||. |++|||++++++|||++||++||++|+|+||+|.. .+||||+|++.||+|
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 455665 333459999999999999999 99999999999999999999999999999999974 899999999999999
Q ss_pred CceeEeecccceeeccCCCCCCccceeecCCCCCCCccCcCCCCCCcceEEeCCCCCCCCcccccceeeccccCceeccc
Q 014692 80 HEIVELWTKRNFRCDCGNSKFGEFFCKLFPSKDVENAENSYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEE 159 (420)
Q Consensus 80 H~l~el~~kr~f~CDCG~~~~~~~~C~l~~~k~~~n~~N~Yn~Nf~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~ 159 (420)
|+||||||||||||||||++++..+|+|.+.|+.+|++|.|||||+|+||+|++|||||..++.+.|+||.+||||||
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 014692 160 HIGLEPSDEIPRDDEGEPVYEDFICKACSAVCSFLSTYPQTIWAAGLRRNAGCNTNKDKDVLEEIPSAGGSGKLENGICS 239 (420)
Q Consensus 160 Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~~fL~~y~~~~~~~~~~~~~~~~~~~~~~~~e~~~~~~~~~~~~~~~~~ 239 (420)
|..|++..+|+..|+..... .......+.. +++. ..+
T Consensus 160 ------------------------ce~c~~~~~~~~~yp~~~~~----D~e~~k~e~~-----se~~----------a~~ 196 (345)
T KOG2752|consen 160 ------------------------CEGCMQAKTFLEDYPEQGKD----DAEEVKPEQN-----SEKC----------AGS 196 (345)
T ss_pred ------------------------ccccCcccchhhcccccccc----ccccCCcccc-----Cccc----------ccc
Confidence 44566666788888732110 0000000000 0000 000
Q ss_pred CCCCCccccccccccccccCCCCccCCCcccccccccccCCCCCCcccccCCCc----ccCCCCCCCcceecCcchhhhc
Q 014692 240 NGSPREDNAIANTSAESVTGGKGVTGESSKKIFDLVQCMNDGGAHIACLFGDNI----VVDGSISLTKPLFLSKNWRATL 315 (420)
Q Consensus 240 ~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~Ckl~~~~----~~~~~~~~~~~~fl~~~wR~~L 315 (420)
.. +.-+++ .+.+ + .-+..+++.|++. .+ +++.+ ..++.||.. +||+.|
T Consensus 197 ~c----------~~~i~~---------~~~~-----e-~~~~e~~~~~~~~-~~e~~~k~~~~-~d~~~~~~~-~wR~~L 248 (345)
T KOG2752|consen 197 SC----------SEDIQD---------VPKN-----E-SLNDESESGCKLQ-LLENFRKQLKK-KDGAAFWTN-NWRSKL 248 (345)
T ss_pred cc----------HHHHHh---------cccC-----C-CCccccccCCcHH-HHHhhHhhccc-CCcccchhh-hHHHhh
Confidence 00 000000 0000 0 0011223456655 22 12222 456677776 999999
Q ss_pred ccchhhhhhhhhcCCCcccCCCcchHHhhhhhHhhhhhhhhhhhchHHHHHhhCChHHHHHHHHHHHHHHHHHHHhhhhc
Q 014692 316 CRCKKCLSMYEQKRVPYLIDEEDSIAEYERTAKQKREEKLQQQEGAELTFLNKLGHVEKMEILNGIADMKDEFHNFLQSF 395 (420)
Q Consensus 316 C~C~~C~~~y~~~~~~FLldeeDtv~~YE~~~~~~~~~s~~~d~g~~~~aL~sl~RvqaiE~i~~Yn~mKdkL~~fLk~F 395 (420)
|+|.+|+.||+.+.|.||||+||||.+||.+++...+.+ +.+.+|+ +|++|+|||||++|.+||+||++|++||++|
T Consensus 249 C~Ce~Cl~mY~d~dv~fLlD~EDti~tyE~k~k~~~~~~-t~e~~~~--~L~~l~r~q~ve~i~eyn~lK~~L~d~L~~f 325 (345)
T KOG2752|consen 249 CTCEDCLEMYEDLDVEFLLDEEDTILTYENKGKIAEENK-TSEDLME--ALDSLNRVQQVELICEYNRLKDELKDYLKRF 325 (345)
T ss_pred cchHHhhhhhhhhchheeecccchhhhhhhhhhhhhhcc-ccchHHH--HHHhccchhhHHHHHHHHhHHHHHHHHHHHh
Confidence 999999999999999999999999999999999555555 8889999 9999999999999999999999999999999
Q ss_pred -CCCCccCHHHHHHHHHHHH
Q 014692 396 -DPSKAITSDDVHQIFENLA 414 (420)
Q Consensus 396 -e~gkvVt~EDIk~FFe~l~ 414 (420)
++|+|||+|||++||++++
T Consensus 326 A~~~~vv~reDI~~FF~~~~ 345 (345)
T KOG2752|consen 326 ADEGTVVTREDIQQFFEEFQ 345 (345)
T ss_pred hhcCeEeeHHHHHHHHHhhC
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=2.8e-13 Score=107.91 Aligned_cols=66 Identities=33% Similarity=0.809 Sum_probs=48.1
Q ss_pred CcccccccccccceEeecCCCCCCCceEeccc-hhhhcCCCceeEeecccceeeccCCCCCCc--cceeec
Q 014692 41 ECTYSKGYMKRQAIFSCLSCAPEGNAGVCTAC-SLTCHDGHEIVELWTKRNFRCDCGNSKFGE--FFCKLF 108 (420)
Q Consensus 41 ~Cty~~g~~~rQ~~y~C~tC~~~~~~giC~~C-s~~CH~~H~l~el~~kr~f~CDCG~~~~~~--~~C~l~ 108 (420)
.|+|..+.. |.+|.|+||......+||..| +..||.||+++.+++.++|+||||+...+. ..|+++
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 999999999998889999999 999999999999999999999999988863 347654
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=99.26 E-value=5.9e-12 Score=100.57 Aligned_cols=65 Identities=32% Similarity=0.713 Sum_probs=55.3
Q ss_pred CcccccccccccceEeecCCCCCCCceEeccchh-hhcCCCceeEeecccc-eeeccCCCCCC--ccceeec
Q 014692 41 ECTYSKGYMKRQAIFSCLSCAPEGNAGVCTACSL-TCHDGHEIVELWTKRN-FRCDCGNSKFG--EFFCKLF 108 (420)
Q Consensus 41 ~Cty~~g~~~rQ~~y~C~tC~~~~~~giC~~Cs~-~CH~~H~l~el~~kr~-f~CDCG~~~~~--~~~C~l~ 108 (420)
.|+|..++. +.+|.|+||......+||..|.. .||.||+ |.++++++ |+||||+...+ ++.|+++
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 45699999998888999999999 9999999 57888988 99999998644 3467654
No 4
>KOG1777 consensus Putative Zn-finger protein [General function prediction only]
Probab=98.65 E-value=1.6e-08 Score=104.13 Aligned_cols=84 Identities=24% Similarity=0.695 Sum_probs=66.1
Q ss_pred HHHhHHHHHHHHhhcCCCCCCCccccc---ccccccceEeecCCCCCCCceEeccchhhhcCCCceeEeecccceeeccC
Q 014692 20 YLNDVEEKELADLVLGGDEGKECTYSK---GYMKRQAIFSCLSCAPEGNAGVCTACSLTCHDGHEIVELWTKRNFRCDCG 96 (420)
Q Consensus 20 ~le~q~eLE~a~~~l~~~~~~~Cty~~---g~~~rQ~~y~C~tC~~~~~~giC~~Cs~~CH~~H~l~el~~kr~f~CDCG 96 (420)
+.+.++..|+| +-.| .|.|.. -+.|...+|.|.||+.....+||..|...||+||+| |+..-..|+||||
T Consensus 530 iydN~D~vekA--ik~G----qCLfkvSs~~syPMHnFYRC~TCNttdRNAIC~nCI~~CH~GH~V-efir~Drffcdcg 602 (625)
T KOG1777|consen 530 IYDNLDHVEKA--IKKG----QCLFKVSSYTSYPMHNFYRCITCNTTDRNAICVNCIKRCHEGHDV-EFIRHDRFFCDCG 602 (625)
T ss_pred cccchHHHHHH--hhcC----ceEEEecCCCcccccceeEeeecCCccccHHHHHHHHHhcCCCce-EEEeeceEEEecC
Confidence 44555566653 3333 599963 345599999999999998999999999999999999 5555677999999
Q ss_pred CCCCCccceeecCCC
Q 014692 97 NSKFGEFFCKLFPSK 111 (420)
Q Consensus 97 ~~~~~~~~C~l~~~k 111 (420)
..... ..|.|...+
T Consensus 603 agtl~-~~c~lq~ep 616 (625)
T KOG1777|consen 603 AGTLS-NVCDLQGEP 616 (625)
T ss_pred Cceec-ceeeccCCc
Confidence 98877 479998765
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=98.34 E-value=4.8e-08 Score=72.22 Aligned_cols=50 Identities=30% Similarity=0.798 Sum_probs=36.3
Q ss_pred eE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCC
Q 014692 128 YC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAV 190 (420)
Q Consensus 128 yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~ 190 (420)
|| +|+++. + .+.||||+.|..|||..|++++.. +.... ...|+|+.|..+
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 888842 2 589999999999999999998532 11111 238999999753
No 6
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=98.33 E-value=1.4e-07 Score=93.57 Aligned_cols=106 Identities=10% Similarity=0.014 Sum_probs=88.8
Q ss_pred eEeccchhhhcCCCceeEeecccceeeccCCCCCCccceeecCCCCCCCccCcCCCCCCcceEEeCCCCCCCCcccccce
Q 014692 67 GVCTACSLTCHDGHEIVELWTKRNFRCDCGNSKFGEFFCKLFPSKDVENAENSYNHNFKGVYCTCNRPYPDPDVEEQVEM 146 (420)
Q Consensus 67 giC~~Cs~~CH~~H~l~el~~kr~f~CDCG~~~~~~~~C~l~~~k~~~n~~N~Yn~Nf~g~yC~C~rpypdp~~e~~~~M 146 (420)
++|.+|+..||. |.+.++|+++...+....|.|.+.++..+-.+.|+.++++.+|+|-+++|+| +.|
T Consensus 2 ~~~~~e~ee~~~--------tiT~~e~vE~~~~lE~~a~~vL~~~~~~~CTy~~Gy~~rQ~l~sClTC~P~~-----~~a 68 (345)
T KOG2752|consen 2 DDGVEETEEIAP--------TITLGEYVEQIDELEDEADVVLGTQNPDVCTYAKGYKKRQALFSCLTCTPAP-----EMA 68 (345)
T ss_pred Ccchhcchhccc--------cccHHHHHHhHHHHHHHHHhhcCCCCCcccccccCcccccceeEeecccCCh-----hhc
Confidence 677888888886 8899999999999998899999999999999999999999999999999865 489
Q ss_pred eeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCCcc
Q 014692 147 IQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVCSF 193 (420)
Q Consensus 147 iQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~~f 193 (420)
.+|..|..|+|..|+.+. ++.-.. |....|-.|+.+.++
T Consensus 69 gvC~~C~~~CH~~H~lve----L~tKR~----FrCDCg~sk~g~~sc 107 (345)
T KOG2752|consen 69 GVCYACSLSCHDGHELVE----LYTKRN----FRCDCGNSKFGRCSC 107 (345)
T ss_pred eeEEEeeeeecCCceeee----ccccCC----ccccccccccccccc
Confidence 999999999999999873 333334 555556666666555
No 7
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.25 E-value=6.4e-07 Score=88.78 Aligned_cols=56 Identities=30% Similarity=0.651 Sum_probs=42.8
Q ss_pred CcCCCCCCcceEEeCCCCCCCCcccccceeeccc--cC-ceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014692 118 NSYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCI--CE-DWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 191 (420)
Q Consensus 118 N~Yn~Nf~g~yC~C~rpypdp~~e~~~~MiQC~~--CE-DWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 191 (420)
..+...-.-.||+|++.- .+.||.|+. |. +|||..||||.. .| ...|.|+.|....
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 334444468899999652 589999997 98 999999999963 22 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=97.91 E-value=6e-06 Score=80.19 Aligned_cols=47 Identities=32% Similarity=0.865 Sum_probs=38.7
Q ss_pred CcceEEeCCCCCCCCcccccceeeccc--c-CceecccCCCCCCCCCCCCCCCCCCccCeeeccCccC
Q 014692 125 KGVYCTCNRPYPDPDVEEQVEMIQCCI--C-EDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 189 (420)
Q Consensus 125 ~g~yC~C~rpypdp~~e~~~~MiQC~~--C-EDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~ 189 (420)
..+||.|+++- -|.||-|+. | .+|||..||||.. .| -..|.|+.|-.
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 46899999984 489999994 9 8999999999952 33 25799999964
No 10
>KOG1776 consensus Zn-binding protein Push [Signal transduction mechanisms]
Probab=97.38 E-value=4.6e-05 Score=82.50 Aligned_cols=59 Identities=20% Similarity=0.108 Sum_probs=51.7
Q ss_pred Cccccc-c--cccccceEeecCCCCC-CCceEeccchhhhcCCCceeEeecccceeeccCCCCCCc
Q 014692 41 ECTYSK-G--YMKRQAIFSCLSCAPE-GNAGVCTACSLTCHDGHEIVELWTKRNFRCDCGNSKFGE 102 (420)
Q Consensus 41 ~Cty~~-g--~~~rQ~~y~C~tC~~~-~~~giC~~Cs~~CH~~H~l~el~~kr~f~CDCG~~~~~~ 102 (420)
.|||.+ | |+ -|.+|.|.||... +..|+|..||+.||.||++- |.+..|.||||-+..++
T Consensus 766 ~~T~Kkk~q~~m-~n~~~q~~k~~M~~~~gG~~kV~s~t~H~~~~i~--~S~~~~~C~C~Es~~~g 828 (1110)
T KOG1776|consen 766 DETEKKKKQMAM-LNREKQLTKMRMKVGTGGQIKVSSRTLHNEPSID--DSDSLPCCICRESVISG 828 (1110)
T ss_pred HHHHhhhhhHHH-HHHHhhhhhheeeeccCceEEEeeecccCCCCcc--ccCCCceeecccccccc
Confidence 599963 4 99 9999999999997 45699999999999999996 67999999999887663
No 11
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.28 E-value=0.00012 Score=76.91 Aligned_cols=66 Identities=20% Similarity=0.476 Sum_probs=46.9
Q ss_pred CCCCcceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCCccccccc
Q 014692 122 HNFKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVCSFLSTYP 198 (420)
Q Consensus 122 ~Nf~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~~fL~~y~ 198 (420)
-|-+-.||.|..|.. ..-||||..|..|||..|..-.-. ..-..|. |.+|+|..|.....++.+-.
T Consensus 167 ~n~qc~vC~~g~~~~------~NrmlqC~~C~~~fHq~Chqp~i~-~~l~~D~----~~~w~C~~C~~~~~~~~r~t 232 (464)
T KOG4323|consen 167 VNLQCSVCYCGGPGA------GNRMLQCDKCRQWYHQACHQPLIK-DELAGDP----FYEWFCDVCNRGPKKVPRLT 232 (464)
T ss_pred ccceeeeeecCCcCc------cceeeeecccccHHHHHhccCCCC-HhhccCc----cceEeehhhccchhhccccc
Confidence 344466888888742 348999999999999999854321 1122334 89999999998887766544
No 12
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=97.05 E-value=0.00018 Score=81.63 Aligned_cols=57 Identities=33% Similarity=0.765 Sum_probs=48.3
Q ss_pred CCccccc-c--cccccceEeecCCCCCCCceEeccchhhhcCCCceeEeecccceeeccCC
Q 014692 40 KECTYSK-G--YMKRQAIFSCLSCAPEGNAGVCTACSLTCHDGHEIVELWTKRNFRCDCGN 97 (420)
Q Consensus 40 ~~Cty~~-g--~~~rQ~~y~C~tC~~~~~~giC~~Cs~~CH~~H~l~el~~kr~f~CDCG~ 97 (420)
+.|+|.- | .| .|.+|.|+||...+.-.+|.-|+.+||.||+-.=-.|.-.-+|||=-
T Consensus 1241 DtCSFTWTGadHI-NQDIfECkTCGL~~SLCCCsECAltCHk~HDCkLKRTSPTAYCDCWE 1300 (3015)
T KOG0943|consen 1241 DTCSFTWTGADHI-NQDIFECKTCGLLESLCCCSECALTCHKGHDCKLKRTSPTAYCDCWE 1300 (3015)
T ss_pred Cccceeecchhhc-cchhhhhcccccchhhhhhHHHHHHhccCCccceeccCCcceeehhh
Confidence 3588873 4 88 99999999999988899999999999999998655566677999954
No 13
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=96.99 E-value=0.00024 Score=72.75 Aligned_cols=59 Identities=37% Similarity=0.844 Sum_probs=45.4
Q ss_pred cceEEeCCCCCCCCcccccceeeccccCceecccC--CCCCCCCCCCCCCCCCCccCeeeccCccCCCcccccc
Q 014692 126 GVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEH--IGLEPSDEIPRDDEGEPVYEDFICKACSAVCSFLSTY 197 (420)
Q Consensus 126 g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~C--lg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~~fL~~y 197 (420)
..||.|..++ ||+ .+|+||+.|++|||+.| +|++.. ..|. .+.++|..|.....-+..+
T Consensus 60 ~~~~~~~~~~-~p~----~~~~~cd~C~~~~~~ec~~v~~~~~-e~p~-------~~~~~c~~c~~~~~~~~~~ 120 (345)
T KOG1632|consen 60 QRYCKCYKPC-DPD----DLMEQCDLCEDWYHGECWEVGTAEK-EAPK-------EDPKVCDECKEAQDGMSES 120 (345)
T ss_pred hchhhccccc-Cch----hhhhccccccccccccccccCchhh-cCCc-------cccccccccchhhhhhhhh
Confidence 3499999998 674 59999999999999999 998643 2332 6788999998666444433
No 14
>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=87.76 E-value=0.42 Score=33.61 Aligned_cols=29 Identities=31% Similarity=0.851 Sum_probs=26.0
Q ss_pred ceEeecCCCCCCCceEeccchhhhcCCCceeEe
Q 014692 53 AIFSCLSCAPEGNAGVCTACSLTCHDGHEIVEL 85 (420)
Q Consensus 53 ~~y~C~tC~~~~~~giC~~Cs~~CH~~H~l~el 85 (420)
..|-|.+|. ..||..|...=|.+|.++.|
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 15
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=87.11 E-value=0.27 Score=54.01 Aligned_cols=54 Identities=26% Similarity=0.695 Sum_probs=39.1
Q ss_pred cceE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccC-eeeccCcc
Q 014692 126 GVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYE-DFICKACS 188 (420)
Q Consensus 126 g~yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~-~fiC~~C~ 188 (420)
+.|| +|.+.|-+-+ .-.|++|.+|.-|-|..|.++... .......+ .|-|..|.
T Consensus 145 ~~~cPvc~~~Y~~~e---~~~~~~c~~c~rwsh~~c~~~sdd------~~~q~~vD~~~~CS~CR 200 (694)
T KOG4443|consen 145 LSYCPVCLIVYQDSE---SLPMVCCSICQRWSHGGCDGISDD------KYMQAQVDLQYKCSTCR 200 (694)
T ss_pred cccCchHHHhhhhcc---chhhHHHHHhcccccCCCCccchH------HHHHHhhhhhcccceee
Confidence 5677 5888897543 678999999999999999998531 11011123 78899998
No 16
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=85.03 E-value=0.94 Score=48.32 Aligned_cols=63 Identities=24% Similarity=0.411 Sum_probs=47.4
Q ss_pred CCccCcCCCCC--CcceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014692 114 ENAENSYNHNF--KGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 191 (420)
Q Consensus 114 ~n~~N~Yn~Nf--~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 191 (420)
.+....|+-++ ...-|.|..-+ ++ .+.||||..|.-|-|.-|+|.... .. -+.|.|..|..+.
T Consensus 72 ~~~~~~~~~~~~~~~~~c~c~~~~-~~----~g~~i~c~~c~~Wqh~~C~g~~~~------~~----p~~y~c~~c~~~~ 136 (508)
T KOG1844|consen 72 LSLNGSEAGSEAREISRCDCGLED-DM----EGLMIQCDWCGRWQHKICCGSFKS------TK----PDKYVCEICTPRN 136 (508)
T ss_pred ccccccccccCcCccccccccccc-CC----CceeeCCcccCcccCceeeeecCC------CC----chhceeeeecccc
Confidence 34555677666 66789999875 22 489999999999999999987432 11 3589999998665
No 17
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=85.01 E-value=0.55 Score=52.66 Aligned_cols=51 Identities=27% Similarity=0.628 Sum_probs=37.0
Q ss_pred cceE-EeCCCCCCCCcccccceeeccccCce-ecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014692 126 GVYC-TCNRPYPDPDVEEQVEMIQCCICEDW-FHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 191 (420)
Q Consensus 126 g~yC-~C~rpypdp~~e~~~~MiQC~~CEDW-fH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 191 (420)
..-| +|..+ || .+.||-|+.|.+= ||--||..+-. .+| ...|+|..|+...
T Consensus 215 ~~~C~IC~~~--Dp----EdVLLLCDsCN~~~YH~YCLDPdl~-eiP--------~~eWYC~NC~dL~ 267 (1134)
T KOG0825|consen 215 EVKCDICTVH--DP----EDVLLLCDSCNKVYYHVYCLDPDLS-ESP--------VNEWYCTNCSLLE 267 (1134)
T ss_pred cccceeeccC--Ch----HHhheeecccccceeeccccCcccc-ccc--------ccceecCcchhhh
Confidence 3344 67776 55 3799999999776 99999986432 233 5789999998543
No 18
>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=82.38 E-value=0.87 Score=39.80 Aligned_cols=63 Identities=19% Similarity=0.336 Sum_probs=39.9
Q ss_pred CceeEeecccceeeccCCCCCCccceeecCCCCCCCccCcC-CCCCCcceEEeCCCCCCCCcccccceeec
Q 014692 80 HEIVELWTKRNFRCDCGNSKFGEFFCKLFPSKDVENAENSY-NHNFKGVYCTCNRPYPDPDVEEQVEMIQC 149 (420)
Q Consensus 80 H~l~el~~kr~f~CDCG~~~~~~~~C~l~~~k~~~n~~N~Y-n~Nf~g~yC~C~rpypdp~~e~~~~MiQC 149 (420)
|.--|||...++ =++..... .++|.+...++.....+.= +.+-...+|+|..+| ||+ ..||||
T Consensus 58 ~~~~EvF~S~~~-d~~~~~~I-~gkc~V~~~~ey~~~~~~~~~~~~~~d~~~Ce~~y-n~~----~~~~~c 121 (121)
T cd04714 58 HGEKELFASDHQ-DENSVQTI-EHKCYVLTFAEYERLARVKKKPQDGVDFYYCAGTY-NPD----TGMLKC 121 (121)
T ss_pred CCCCceEecCCc-ccccHHHh-CcccEEEehhHheecccccCCCCcCCCEEEEeccC-CCC----cCcccC
Confidence 666688877665 23333333 3589998776655433321 112246699999999 574 789998
No 19
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=82.00 E-value=0.32 Score=33.95 Aligned_cols=34 Identities=24% Similarity=0.676 Sum_probs=18.5
Q ss_pred cceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCc
Q 014692 144 VEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKAC 187 (420)
Q Consensus 144 ~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C 187 (420)
..||+|..|.-++|..|-|+.. .|. ...|+|..|
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 4699999999999999999853 222 234888776
No 20
>smart00336 BBOX B-Box-type zinc finger.
Probab=75.08 E-value=2.2 Score=29.41 Aligned_cols=31 Identities=39% Similarity=0.746 Sum_probs=25.0
Q ss_pred ccceEeecCCCCCCCceEeccchhhhcCCCceeEe
Q 014692 51 RQAIFSCLSCAPEGNAGVCTACSLTCHDGHEIVEL 85 (420)
Q Consensus 51 rQ~~y~C~tC~~~~~~giC~~Cs~~CH~~H~l~el 85 (420)
....|-|.+|. ..||..|...=|.+|.++.|
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 34477799995 48999999989999998653
No 21
>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=63.61 E-value=4.9 Score=27.25 Aligned_cols=30 Identities=33% Similarity=0.610 Sum_probs=23.9
Q ss_pred cceEeecCCCCCCCceEeccchhhhcCCCceeEe
Q 014692 52 QAIFSCLSCAPEGNAGVCTACSLTCHDGHEIVEL 85 (420)
Q Consensus 52 Q~~y~C~tC~~~~~~giC~~Cs~~CH~~H~l~el 85 (420)
...|-|.+|. ..||..|...=|.+|..+.|
T Consensus 10 ~~~~fC~~~~----~~iC~~C~~~~H~~H~~~~i 39 (39)
T cd00021 10 PLSLFCETDR----ALLCVDCDLSVHSGHRRVPL 39 (39)
T ss_pred ceEEEeCccC----hhhhhhcChhhcCCCCEeeC
Confidence 3478899985 48999998666999998754
No 22
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=63.43 E-value=3.5 Score=41.51 Aligned_cols=45 Identities=27% Similarity=0.680 Sum_probs=35.0
Q ss_pred EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeecc-CccCCC
Q 014692 130 TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICK-ACSAVC 191 (420)
Q Consensus 130 ~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~-~C~~~~ 191 (420)
+|..|.- ..+|+=|+.|..=||.-|||+. .+| -..|||. .|....
T Consensus 319 IC~~P~~------E~E~~FCD~CDRG~HT~CVGL~---~lP--------~G~WICD~~C~~~~ 364 (381)
T KOG1512|consen 319 ICLGPVI------ESEHLFCDVCDRGPHTLCVGLQ---DLP--------RGEWICDMRCREAT 364 (381)
T ss_pred ccCCccc------chheeccccccCCCCccccccc---ccc--------CccchhhhHHHHhc
Confidence 7888852 4789999999999999999995 355 3579998 365444
No 23
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=60.18 E-value=1.4 Score=45.44 Aligned_cols=42 Identities=29% Similarity=0.593 Sum_probs=29.5
Q ss_pred cceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccC
Q 014692 144 VEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 189 (420)
Q Consensus 144 ~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~ 189 (420)
.+||-|.+|+.|||+.||.+.+.. ...... -...|+|+.|..
T Consensus 253 ~~~~~~~~~e~w~~~~~v~~~~a~--~~~~~~--~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 253 KFEICCDLCESWFHGDCVQIFEAR--KRLNEI--RNEVYKCPHCTV 294 (345)
T ss_pred HHHHHHHHHHHHhcccccccccch--hhhhhh--hccceecCceee
Confidence 789999999999999999986531 111110 014599999975
No 24
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=59.74 E-value=5.6 Score=42.92 Aligned_cols=47 Identities=21% Similarity=0.554 Sum_probs=36.9
Q ss_pred EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCc
Q 014692 130 TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKAC 187 (420)
Q Consensus 130 ~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C 187 (420)
+|++.. | +-..+||+.|.--||..||+-+-. .+|.-.. ...|+|..|
T Consensus 549 iCkks~-d-----QHll~~CDtC~lhYHlGCL~PPLT-R~Pkk~k----n~gWqCsEC 595 (707)
T KOG0957|consen 549 ICKKST-D-----QHLLTQCDTCHLHYHLGCLSPPLT-RLPKKNK----NFGWQCSEC 595 (707)
T ss_pred eeccch-h-----hHHHhhcchhhceeeccccCCccc-cCccccc----Ccceeeccc
Confidence 788875 2 678999999999999999976543 3555444 578999999
No 25
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=57.99 E-value=5 Score=33.88 Aligned_cols=37 Identities=24% Similarity=0.402 Sum_probs=29.7
Q ss_pred cCcCCCCCCcceEEeCCCCCCCCcccccceeeccc--cCceecccCC
Q 014692 117 ENSYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCI--CEDWFHEEHI 161 (420)
Q Consensus 117 ~N~Yn~Nf~g~yC~C~rpypdp~~e~~~~MiQC~~--CEDWfH~~Cl 161 (420)
.+....++...-.+|++. .|..|||.. |..+||..|.
T Consensus 47 ~~i~~~~~~~~C~iC~~~--------~G~~i~C~~~~C~~~fH~~CA 85 (110)
T PF13832_consen 47 SNIPPSRFKLKCSICGKS--------GGACIKCSHPGCSTAFHPTCA 85 (110)
T ss_pred eeecchhcCCcCcCCCCC--------CceeEEcCCCCCCcCCCHHHH
Confidence 344444577778899987 488999998 9999999996
No 26
>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=56.47 E-value=20 Score=28.00 Aligned_cols=31 Identities=16% Similarity=0.393 Sum_probs=26.9
Q ss_pred HHHHHHHhhhhc-CCCCccCHHHHHHHHHHHHH
Q 014692 384 MKDEFHNFLQSF-DPSKAITSDDVHQIFENLAK 415 (420)
Q Consensus 384 mKdkL~~fLk~F-e~gkvVt~EDIk~FFe~l~~ 415 (420)
||..|...++.| .+ .++++++|.+|+++|..
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 27
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=50.48 E-value=16 Score=39.69 Aligned_cols=59 Identities=22% Similarity=0.486 Sum_probs=40.5
Q ss_pred CCCcceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCCC--CCCCCCCCCCccCeeeccCccCCC
Q 014692 123 NFKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSD--EIPRDDEGEPVYEDFICKACSAVC 191 (420)
Q Consensus 123 Nf~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~--~~p~~~~~~~~~~~fiC~~C~~~~ 191 (420)
+-.+.+|+|+..-+ + .-.-+||-.|-.|||..++-..+.. .+|.. ....|+|..|....
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 45678999987643 2 4567999999999998776433210 22221 25799999998764
No 28
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=46.65 E-value=18 Score=39.15 Aligned_cols=58 Identities=26% Similarity=0.496 Sum_probs=39.8
Q ss_pred ceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccC
Q 014692 127 VYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 189 (420)
Q Consensus 127 ~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~ 189 (420)
..|+|-..--+ ..++.|||+.|.-=.|+.|-|+.....+|...+ .-..+.|+|..|.-
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 68888543211 158899999999999999999875555664322 11246788887753
No 29
>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=45.83 E-value=19 Score=27.07 Aligned_cols=42 Identities=26% Similarity=0.558 Sum_probs=22.1
Q ss_pred eeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCC
Q 014692 147 IQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAV 190 (420)
Q Consensus 147 iQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~ 190 (420)
.+|.+|. |-+..-.|-+.. ++|..-.=+.+-+.|.||.|-..
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 5788887 544444443221 22221111113678999999643
No 30
>PF14071 YlbD_coat: Putative coat protein
Probab=45.83 E-value=50 Score=29.49 Aligned_cols=74 Identities=19% Similarity=0.313 Sum_probs=50.7
Q ss_pred hhhhhcCCCcccCCCcc-hHHhhhhhHhh------h--hhh-hhhhhchHHHHHhhCChHHHHHHHHHHHHHHHHHHHhh
Q 014692 323 SMYEQKRVPYLIDEEDS-IAEYERTAKQK------R--EEK-LQQQEGAELTFLNKLGHVEKMEILNGIADMKDEFHNFL 392 (420)
Q Consensus 323 ~~y~~~~~~FLldeeDt-v~~YE~~~~~~------~--~~s-~~~d~g~~~~aL~sl~RvqaiE~i~~Yn~mKdkL~~fL 392 (420)
.+|+. =+||-|+|. +.+|-+.+... . +.+ ......|. +|.+||-.+.-.-|...+..=..|..+|
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 367766665 78887211111 1 111 13344455 9999999999999999999999999999
Q ss_pred hhc-CCCCcc
Q 014692 393 QSF-DPSKAI 401 (420)
Q Consensus 393 k~F-e~gkvV 401 (420)
..| ..+.-.
T Consensus 101 ~qFq~~~~~~ 110 (124)
T PF14071_consen 101 SQFQGNGQKQ 110 (124)
T ss_pred HHhcCCCCCC
Confidence 999 665543
No 31
>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=43.18 E-value=26 Score=22.79 Aligned_cols=25 Identities=16% Similarity=0.349 Sum_probs=22.0
Q ss_pred HHHHhhhhc--CCCCccCHHHHHHHHH
Q 014692 387 EFHNFLQSF--DPSKAITSDDVHQIFE 411 (420)
Q Consensus 387 kL~~fLk~F--e~gkvVt~EDIk~FFe 411 (420)
+|+.+|+.| +..-.|+.+|++.++.
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 7778999999999987
No 32
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=42.31 E-value=28 Score=27.29 Aligned_cols=40 Identities=23% Similarity=0.395 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhcCCCCccCHHHHHHHHHHHHH
Q 014692 375 MEILNGIADMKDEFHNFLQSFDPSKAITSDDVHQIFENLAK 415 (420)
Q Consensus 375 iE~i~~Yn~mKdkL~~fLk~Fe~gkvVt~EDIk~FFe~l~~ 415 (420)
-.-|..|-..=..+..|+.. ..-.-||.+||++|+..|..
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 44555665444444444431 23367899999999999983
No 33
>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=39.32 E-value=27 Score=25.17 Aligned_cols=33 Identities=21% Similarity=0.673 Sum_probs=25.0
Q ss_pred cccccceEeecCCCCCCCceEeccchhh-hcCCCceeE
Q 014692 48 YMKRQAIFSCLSCAPEGNAGVCTACSLT-CHDGHEIVE 84 (420)
Q Consensus 48 ~~~rQ~~y~C~tC~~~~~~giC~~Cs~~-CH~~H~l~e 84 (420)
+| .-..|.|.+|. ..-+|..|... -|..|+.+.
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 677887763
No 34
>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=37.91 E-value=28 Score=23.52 Aligned_cols=13 Identities=8% Similarity=0.404 Sum_probs=9.2
Q ss_pred cCHHHHHHHHHHH
Q 014692 401 ITSDDVHQIFENL 413 (420)
Q Consensus 401 Vt~EDIk~FFe~l 413 (420)
||.+|||+|++..
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 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=37.83 E-value=34 Score=28.31 Aligned_cols=36 Identities=17% Similarity=0.330 Sum_probs=25.7
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhcCCCCccCHHHHHH
Q 014692 373 EKMEILNGIADMKDEFHNFLQSFDPSKAITSDDVHQ 408 (420)
Q Consensus 373 qaiE~i~~Yn~mKdkL~~fLk~Fe~gkvVt~EDIk~ 408 (420)
+-|..||.||++||-=...+.....-+=||--||.+
T Consensus 40 ~hI~lLheYNeiKD~gQ~Lig~iA~~rgvt~~~v~~ 75 (83)
T PF07061_consen 40 RHIKLLHEYNEIKDIGQGLIGLIADQRGVTVKDVYE 75 (83)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHcCCcHHHHHH
Confidence 468999999999998887777762334455555543
No 36
>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=36.05 E-value=28 Score=32.08 Aligned_cols=56 Identities=23% Similarity=0.568 Sum_probs=25.6
Q ss_pred ceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCC-----------------CCCCCCCCCCCccCeeeccCccC
Q 014692 127 VYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPS-----------------DEIPRDDEGEPVYEDFICKACSA 189 (420)
Q Consensus 127 ~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~-----------------~~~p~~~~~~~~~~~fiC~~C~~ 189 (420)
.||.|+.| .-.++|..|..||=..=-+.+.+ +..|-. -..+-|..|-.
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 37777754 46899999999996553322111 011211 24678999999
Q ss_pred CCcccccc
Q 014692 190 VCSFLSTY 197 (420)
Q Consensus 190 ~~~fL~~y 197 (420)
++.|+.-|
T Consensus 69 ~NvF~LGF 76 (152)
T PF09416_consen 69 RNVFLLGF 76 (152)
T ss_dssp --TTTEEE
T ss_pred CceeeEEE
Confidence 99988755
No 37
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=34.61 E-value=19 Score=40.69 Aligned_cols=37 Identities=30% Similarity=0.647 Sum_probs=27.3
Q ss_pred ccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCcc
Q 014692 143 QVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACS 188 (420)
Q Consensus 143 ~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~ 188 (420)
.+.-|-|+.|-.|||..|++.+- .+.+ ..+|+|+.|.
T Consensus 56 ~g~~l~c~tC~~s~h~~cl~~pl---~~~p------~~~~~c~Rc~ 92 (696)
T KOG0383|consen 56 GGELLWCDTCPASFHASCLGPPL---TPQP------NGEFICPRCF 92 (696)
T ss_pred CCcEEEeccccHHHHHHccCCCC---CcCC------ccceeeeeec
Confidence 36677799999999999998742 2221 2339999994
No 38
>KOG3878 consensus Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=33.23 E-value=51 Score=34.20 Aligned_cols=51 Identities=14% Similarity=0.258 Sum_probs=42.6
Q ss_pred HHHhhCChHHHHHHHHHHHHHHHHHHHhhhhc-CCCCccCHHHHHHHHHHHHHhh
Q 014692 364 TFLNKLGHVEKMEILNGIADMKDEFHNFLQSF-DPSKAITSDDVHQIFENLAKKR 417 (420)
Q Consensus 364 ~aL~sl~RvqaiE~i~~Yn~mKdkL~~fLk~F-e~gkvVt~EDIk~FFe~l~~~~ 417 (420)
.+|.+|.|++|+++ |-+|-+.+-.-|++| ...|..+.|..|+|=..+++.+
T Consensus 96 ~~LG~~sre~AM~~---FV~Lldr~C~~F~~yia~~k~~kde~lkE~e~r~~ee~ 147 (469)
T KOG3878|consen 96 QLLGEISREQAMEG---FVDLLDRMCSAFRPYIAAVKQDKDETLKEKELRLMEEK 147 (469)
T ss_pred HHHhcccHHHHHHH---HHHHHHhcchhhhhHHHHhhhhhhhHHHHHHHHHHHhh
Confidence 38999999999874 667888888889999 9999999999998877666443
No 39
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=33.05 E-value=41 Score=39.79 Aligned_cols=53 Identities=25% Similarity=0.538 Sum_probs=39.3
Q ss_pred CCcceEEeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014692 124 FKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 191 (420)
Q Consensus 124 f~g~yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 191 (420)
-.+..|+|... +.+....-|+|+.|.--+|-.|.|++. +| + ..|.|..|..+.
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 1 368999998554
No 40
>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=31.98 E-value=21 Score=28.65 Aligned_cols=11 Identities=55% Similarity=1.449 Sum_probs=6.4
Q ss_pred eeeccCCCCCC
Q 014692 91 FRCDCGNSKFG 101 (420)
Q Consensus 91 f~CDCG~~~~~ 101 (420)
||||||..-..
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 78888875443
No 41
>PLN00035 histone H4; Provisional
Probab=31.67 E-value=46 Score=28.74 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHhhhhc----------CCCCccCHHHHHH
Q 014692 380 GIADMKDEFHNFLQSF----------DPSKAITSDDVHQ 408 (420)
Q Consensus 380 ~Yn~mKdkL~~fLk~F----------e~gkvVt~EDIk~ 408 (420)
+|..|+..|.+||... ..-|+||++||.-
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 42
>smart00417 H4 Histone H4.
Probab=31.16 E-value=52 Score=26.71 Aligned_cols=28 Identities=21% Similarity=0.406 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHhhhh-------c---CCCCccCHHHHH
Q 014692 380 GIADMKDEFHNFLQS-------F---DPSKAITSDDVH 407 (420)
Q Consensus 380 ~Yn~mKdkL~~fLk~-------F---e~gkvVt~EDIk 407 (420)
+|..|+.-|++||.. | ...|+||.+||.
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 788888888888876 2 578999999984
No 43
>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=30.13 E-value=75 Score=22.86 Aligned_cols=29 Identities=21% Similarity=0.401 Sum_probs=16.7
Q ss_pred HHHHHHHhhhhcCCCCccCHHHHHHHHHHH
Q 014692 384 MKDEFHNFLQSFDPSKAITSDDVHQIFENL 413 (420)
Q Consensus 384 mKdkL~~fLk~Fe~gkvVt~EDIk~FFe~l 413 (420)
++..+..+|... .=+-||..||+.|+.+|
T Consensus 29 ~~~~i~p~~g~~-~i~~It~~~i~~~~~~l 57 (58)
T PF14659_consen 29 IKNHILPYFGNK-KIKDITPRDIQNFINEL 57 (58)
T ss_dssp HHHHHHHHTTSS-BGGG--HHHHHHHHHHH
T ss_pred HHHHHHHHHCcC-cHHHCCHHHHHHHHHHc
Confidence 333344444332 33458999999999987
No 44
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=29.73 E-value=23 Score=39.15 Aligned_cols=51 Identities=24% Similarity=0.542 Sum_probs=35.7
Q ss_pred ceE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCC-CCCCCCCCCCCccCeeeccCccCCC
Q 014692 127 VYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPS-DEIPRDDEGEPVYEDFICKACSAVC 191 (420)
Q Consensus 127 ~yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~-~~~p~~~~~~~~~~~fiC~~C~~~~ 191 (420)
.|| .|+++.. -...|+|+.|--=||-.||.-+-. ..+| -..|.|+.|.-+-
T Consensus 254 ~fCsaCn~~~~------F~~~i~CD~Cp~sFH~~CLePPl~~eniP--------~g~W~C~ec~~k~ 306 (613)
T KOG4299|consen 254 DFCSACNGSGL------FNDIICCDGCPRSFHQTCLEPPLEPENIP--------PGSWFCPECKIKS 306 (613)
T ss_pred HHHHHhCCccc------cccceeecCCchHHHHhhcCCCCCcccCC--------CCccccCCCeeee
Confidence 388 7888742 123599999999999999965411 1344 3589999996543
No 45
>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=29.31 E-value=68 Score=26.71 Aligned_cols=28 Identities=18% Similarity=0.363 Sum_probs=23.7
Q ss_pred HHHHHHHHHHHhhhhc----------CCCCccCHHHHH
Q 014692 380 GIADMKDEFHNFLQSF----------DPSKAITSDDVH 407 (420)
Q Consensus 380 ~Yn~mKdkL~~fLk~F----------e~gkvVt~EDIk 407 (420)
+|..+..-|++||... ..-|+||++||.
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 7888888888888863 488999999995
No 46
>PTZ00015 histone H4; Provisional
Probab=28.90 E-value=65 Score=27.78 Aligned_cols=29 Identities=21% Similarity=0.306 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHhhhhc----------CCCCccCHHHHHH
Q 014692 380 GIADMKDEFHNFLQSF----------DPSKAITSDDVHQ 408 (420)
Q Consensus 380 ~Yn~mKdkL~~fLk~F----------e~gkvVt~EDIk~ 408 (420)
+|..++.-|++||..- ..-|+||.+||.-
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 47
>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=27.26 E-value=1.1e+02 Score=28.91 Aligned_cols=40 Identities=10% Similarity=0.360 Sum_probs=27.2
Q ss_pred HHHHHHHHHHHHH--HHhhhhc-CCCCccCHHHHHHHHHHHHH
Q 014692 376 EILNGIADMKDEF--HNFLQSF-DPSKAITSDDVHQIFENLAK 415 (420)
Q Consensus 376 E~i~~Yn~mKdkL--~~fLk~F-e~gkvVt~EDIk~FFe~l~~ 415 (420)
+....++.+|+.| ..|++.. .+.-.||++||++||++.++
T Consensus 89 ~~~~~~~~~r~~ll~~~~~~~~v~~~~~vse~ev~~~Y~~~~~ 131 (232)
T TIGR02925 89 DVVMALEAAKREILARAYLRQLAGAQSKPSPEEAKSYFQEHPQ 131 (232)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHhCHH
Confidence 3445556666653 3455655 55578999999999998654
No 48
>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=26.41 E-value=29 Score=25.70 Aligned_cols=11 Identities=36% Similarity=1.099 Sum_probs=6.5
Q ss_pred cCeeeccCccC
Q 014692 179 YEDFICKACSA 189 (420)
Q Consensus 179 ~~~fiC~~C~~ 189 (420)
-+.|+|+.|-.
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 56899999964
No 49
>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=26.13 E-value=50 Score=30.34 Aligned_cols=27 Identities=30% Similarity=0.551 Sum_probs=19.0
Q ss_pred ecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCC
Q 014692 156 FHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 191 (420)
Q Consensus 156 fH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~ 191 (420)
||..||.-+-. .+|+ ..|+|+.|..+.
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 3442 469999998664
No 50
>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=28.4
Q ss_pred HHHHHHHHH--------HHHHHHHhhhhc-CCCCccCHHHHHHHHHHHH
Q 014692 375 MEILNGIAD--------MKDEFHNFLQSF-DPSKAITSDDVHQIFENLA 414 (420)
Q Consensus 375 iE~i~~Yn~--------mKdkL~~fLk~F-e~gkvVt~EDIk~FFe~l~ 414 (420)
|+..+.|.. =+++|+.+|+.+ .-|..+|+++|.+.|..+.
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 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=24.84 E-value=34 Score=25.33 Aligned_cols=15 Identities=27% Similarity=0.581 Sum_probs=9.1
Q ss_pred ceeeccccCceeccc
Q 014692 145 EMIQCCICEDWFHEE 159 (420)
Q Consensus 145 ~MiQC~~CEDWfH~~ 159 (420)
.-|||+.|..|=...
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 469999999998765
No 52
>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=24.62 E-value=71 Score=34.27 Aligned_cols=64 Identities=22% Similarity=0.534 Sum_probs=37.3
Q ss_pred eEEeCCCCCCCCcccccceeeccccCceecccCC-CCCCCC-CCCCCCCCCCccCeeeccCccCCCccc
Q 014692 128 YCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHI-GLEPSD-EIPRDDEGEPVYEDFICKACSAVCSFL 194 (420)
Q Consensus 128 yC~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Cl-g~~~~~-~~p~~~~~~~~~~~fiC~~C~~~~~fL 194 (420)
.|+|.+ | |-+-+ +-..|-|++|.-|=|..|- .-.... +.-.......+--.|.|..|-.....|
T Consensus 131 C~iC~k-f-D~~~n-~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~seLl 196 (446)
T PF07227_consen 131 CCICSK-F-DDNKN-TCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSELL 196 (446)
T ss_pred ccccCC-c-ccCCC-CeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhhHH
Confidence 557877 4 33322 5779999999999999993 211000 000000000123589999998877433
No 53
>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=24.11 E-value=59 Score=23.75 Aligned_cols=34 Identities=21% Similarity=0.430 Sum_probs=23.7
Q ss_pred ccccccceEeecCCCCCCCceEeccchh--hhcCCCceeE
Q 014692 47 GYMKRQAIFSCLSCAPEGNAGVCTACSL--TCHDGHEIVE 84 (420)
Q Consensus 47 g~~~rQ~~y~C~tC~~~~~~giC~~Cs~--~CH~~H~l~e 84 (420)
..| +-.-|.|++|. ..-+|..|.. .-+.+|+.++
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 5679999954 2235777653
No 54
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=23.65 E-value=40 Score=27.15 Aligned_cols=36 Identities=19% Similarity=0.242 Sum_probs=26.5
Q ss_pred CCCCCCcceEEeCCCCCCCCcccccceeeccc--cCceecccCCCC
Q 014692 120 YNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCI--CEDWFHEEHIGL 163 (420)
Q Consensus 120 Yn~Nf~g~yC~C~rpypdp~~e~~~~MiQC~~--CEDWfH~~Clg~ 163 (420)
....+.-.-.+|++++ |..|+|.. |..+||..|.-.
T Consensus 31 ~~~~~~~~C~~C~~~~--------Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 31 IKRRRKLKCSICKKKG--------GACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred HHHHhCCCCcCCCCCC--------CeEEEEeCCCCCcEEChHHHcc
Confidence 3334444555888773 78999996 999999999643
No 55
>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=23.62 E-value=74 Score=18.17 Aligned_cols=25 Identities=12% Similarity=0.343 Sum_probs=17.5
Q ss_pred HHHhhhhc--CCCCccCHHHHHHHHHH
Q 014692 388 FHNFLQSF--DPSKAITSDDVHQIFEN 412 (420)
Q Consensus 388 L~~fLk~F--e~gkvVt~EDIk~FFe~ 412 (420)
|+..|+.+ ..+..|+..++..++..
T Consensus 2 ~~~~f~~~d~~~~g~i~~~e~~~~~~~ 28 (29)
T smart00054 2 LKEAFRLFDKDGDGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHHCCCCCCcEeHHHHHHHHHh
Confidence 45566666 44457999998888764
No 56
>KOG0031 consensus Myosin regulatory light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=23.49 E-value=2e+02 Score=26.89 Aligned_cols=46 Identities=13% Similarity=0.341 Sum_probs=38.2
Q ss_pred HHhhCChHHHHHHHHHHHHH---------HHHHHHhhhhcCCCCccCHHHHHHHHHH
Q 014692 365 FLNKLGHVEKMEILNGIADM---------KDEFHNFLQSFDPSKAITSDDVHQIFEN 412 (420)
Q Consensus 365 aL~sl~RvqaiE~i~~Yn~m---------KdkL~~fLk~Fe~gkvVt~EDIk~FFe~ 412 (420)
.++.++.-|-.|.=.|||-| |..|+++|.+. ||+|+++.|.+.+.+
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 67778888888998999988 77888888775 788999999887764
No 57
>PF08164 TRAUB: Apoptosis-antagonizing transcription factor, C-terminal; InterPro: IPR012617 This C-terminal domain is found in traube proteins [].; GO: 0005634 nucleus
Probab=22.88 E-value=84 Score=25.99 Aligned_cols=27 Identities=15% Similarity=0.534 Sum_probs=21.8
Q ss_pred HHHHHhhhhcCCCCccCHHHHHHHHHHH
Q 014692 386 DEFHNFLQSFDPSKAITSDDVHQIFENL 413 (420)
Q Consensus 386 dkL~~fLk~Fe~gkvVt~EDIk~FFe~l 413 (420)
.||..|..| ...-..+.+.|.+||+.|
T Consensus 56 eKL~NFmaP-~~~~~w~~~~~delf~sL 82 (83)
T PF08164_consen 56 EKLVNFMAP-EDRPTWSDEQIDELFASL 82 (83)
T ss_pred HHHhhhcCC-CCCCCCCHHHHHHHHHHc
Confidence 678888877 566677899999999876
No 58
>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=22.14 E-value=70 Score=24.68 Aligned_cols=27 Identities=7% Similarity=0.391 Sum_probs=17.0
Q ss_pred HHHhhhhcCCCCccCHHHHHHHHHHHH
Q 014692 388 FHNFLQSFDPSKAITSDDVHQIFENLA 414 (420)
Q Consensus 388 L~~fLk~Fe~gkvVt~EDIk~FFe~l~ 414 (420)
++++|+..-.|+..|.++++++|..+-
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 466777765568888888888888765
No 59
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=22.11 E-value=81 Score=32.78 Aligned_cols=41 Identities=32% Similarity=0.621 Sum_probs=20.7
Q ss_pred ceEeecCCCCCCCceEeccchhhhc-CCCceeEe-ecccceeec-cCCC
Q 014692 53 AIFSCLSCAPEGNAGVCTACSLTCH-DGHEIVEL-WTKRNFRCD-CGNS 98 (420)
Q Consensus 53 ~~y~C~tC~~~~~~giC~~Cs~~CH-~~H~l~el-~~kr~f~CD-CG~~ 98 (420)
.+|.|.+|. .....=+..|= .+|+|.-. -.||-|.|. ||+.
T Consensus 251 kav~C~~C~-----yt~~~~~~~C~~~~H~l~~~~a~KRFFkC~~C~~R 294 (344)
T PF09332_consen 251 KAVTCKQCK-----YTAFKPSDRCKEEGHPLKWHDAVKRFFKCKDCGNR 294 (344)
T ss_dssp EEEEETTT-------EESS--HHHHHTT--EEEEEEE-EEEE-T-TS-E
T ss_pred EEEEcCCCC-----CcccCcchhHHhcCCceEEeeeeeeeEECCCCCCe
Confidence 478899995 45555555663 56665422 135899998 9874
No 60
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=21.97 E-value=40 Score=38.28 Aligned_cols=49 Identities=33% Similarity=0.830 Sum_probs=36.6
Q ss_pred CcceE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCcc
Q 014692 125 KGVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACS 188 (420)
Q Consensus 125 ~g~yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~ 188 (420)
..+.| +|+-| |- |+..+||-|+.|.--.|-.|-||.. +|. ..|.|..|.
T Consensus 270 edviCDvCrsp--D~--e~~neMVfCd~Cn~cVHqaCyGIle---~p~--------gpWlCr~Ca 319 (893)
T KOG0954|consen 270 EDVICDVCRSP--DS--EEANEMVFCDKCNICVHQACYGILE---VPE--------GPWLCRTCA 319 (893)
T ss_pred ccceeceecCC--Cc--cccceeEEeccchhHHHHhhhceee---cCC--------CCeeehhcc
Confidence 46777 78876 43 3478999999999999999999964 342 246666665
No 61
>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=21.87 E-value=5.1e+02 Score=23.51 Aligned_cols=49 Identities=12% Similarity=0.211 Sum_probs=35.3
Q ss_pred HhhCChHHHHHHHHHHHHHHHHHHHhhhhc-CCCCccCHHHHHHHHHHHH
Q 014692 366 LNKLGHVEKMEILNGIADMKDEFHNFLQSF-DPSKAITSDDVHQIFENLA 414 (420)
Q Consensus 366 L~sl~RvqaiE~i~~Yn~mKdkL~~fLk~F-e~gkvVt~EDIk~FFe~l~ 414 (420)
.+.++=.+....|.....=...|.+=|.++ +++..|+++|+...=...+
T Consensus 106 ~~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~ 155 (169)
T PF07106_consen 106 SSEPTNEELREEIEELEEEIEELEEKLEKLRSGSKPVSPEEKEKLEKEYK 155 (169)
T ss_pred hcCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence 345556666666767666677777788888 8889999999886644433
No 62
>PF03726 PNPase: Polyribonucleotide nucleotidyltransferase, RNA binding domain; InterPro: IPR015848 The PH (phosphorolytic) domain is responsible for 3'-5' exoribonuclease activity, although in some proteins this domain has lost its catalytic function. An active PH domain uses inorganic phosphate as a nucleophile, adding it across the phosphodiester bond between the end two nucleotides in order to release ribonucleoside 5'-diphosphate (rNDP) from the 3' end of the RNA substrate. PH domains can be found in bacterial/organelle RNases and PNPases (polynucleotide phosphorylases) [], as well as in archaeal and eukaryotic RNA exosomes [, ], the later acting as nano-compartments for the degradation or processing of RNA (including mRNA, rRNA, snRNA and snoRNA). Bacterial/organelle PNPases share a common barrel structure with RNA exosomes, consisting of a hexameric ring of PH domains that act as a degradation chamber, and an S1-domain/KH-domain containing cap that binds the RNA substrate (and sometimes accessory proteins) in order to regulate and restrict entry into the degradation chamber []. Unstructured RNA substrates feed in through the pore made by the S1 domains, are degraded by the PH domain ring, and exit as nucleotides via the PH pore at the opposite end of the barrel [, ]. This entry represents an RNA-binding phosphorolytic (PH) domain found in bacterial and organelle PNPases, but not in exosomes. It usually occurs in combination with PH domain 1 (IPR001247 from INTERPRO) and PH domain 2 (IPR015847 from INTERPRO), both of which are found in PNPases and exosomes. The core structure of the RNA-binding PH domain consists of a DNA/RNA-binding 3-helical bundle. More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0000175 3'-5'-exoribonuclease activity, 0003723 RNA binding, 0006396 RNA processing; PDB: 1E3H_A 1E3P_A 3U1K_B 3GCM_A 3GLL_A 3GME_A 4AM3_B 4AID_C 4AIM_A 1WHU_A ....
Probab=20.64 E-value=1.1e+02 Score=24.46 Aligned_cols=40 Identities=20% Similarity=0.313 Sum_probs=29.2
Q ss_pred HHHHHHHHHHHHHhhhhc-CCCCccCHHHHHHHHHHHHHhh
Q 014692 378 LNGIADMKDEFHNFLQSF-DPSKAITSDDVHQIFENLAKKR 417 (420)
Q Consensus 378 i~~Yn~mKdkL~~fLk~F-e~gkvVt~EDIk~FFe~l~~~~ 417 (420)
-.+.+.+|+++.+-|.+- ++.....+.+|...|.+|.++-
T Consensus 27 ~~a~~~i~~~~~~~~~~~~~e~~~~~~~~i~~~~~~l~k~~ 67 (83)
T PF03726_consen 27 EEALDAIKEEVIEELEEEYEEEDEEDEKEIKEAFEELEKKI 67 (83)
T ss_dssp HHHHHHHHHHHHHHHHCCCHHSTTSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHHHHHHHH
Confidence 344566777777777653 4445889999999999998764
No 63
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=20.59 E-value=23 Score=43.05 Aligned_cols=52 Identities=25% Similarity=0.545 Sum_probs=37.8
Q ss_pred cceE-EeCCCCCCCCcccccceeeccccCceecccCCCCCCCCCCCCCCCCCCccCeeeccCccCCCc
Q 014692 126 GVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVCS 192 (420)
Q Consensus 126 g~yC-~C~rpypdp~~e~~~~MiQC~~CEDWfH~~Clg~~~~~~~p~~~~~~~~~~~fiC~~C~~~~~ 192 (420)
...| +|++.- + ...|+-|+.|..|||.-|+-..-. ..| +..|.|+.|...+.
T Consensus 1108 ~~~c~~cr~k~-~-----~~~m~lc~~c~~~~h~~C~rp~~~-~~~--------~~dW~C~~c~~e~~ 1160 (1404)
T KOG1245|consen 1108 NALCKVCRRKK-Q-----DEKMLLCDECLSGFHLFCLRPALS-SVP--------PGDWMCPSCRKEHR 1160 (1404)
T ss_pred hhhhhhhhhcc-c-----chhhhhhHhhhhhHHHHhhhhhhc-cCC--------cCCccCCccchhhh
Confidence 4456 777764 2 368999999999999999965322 122 45699999997664
No 64
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=20.33 E-value=80 Score=26.86 Aligned_cols=28 Identities=21% Similarity=0.306 Sum_probs=13.2
Q ss_pred hhhcCCCCccCHHHHHHHHHHHHHhhhc
Q 014692 392 LQSFDPSKAITSDDVHQIFENLAKKRRR 419 (420)
Q Consensus 392 Lk~Fe~gkvVt~EDIk~FFe~l~~~~r~ 419 (420)
.+|+=..=+||++|||.==++.++.|+|
T Consensus 64 ~QPLc~~~~VT~eDIr~QE~rVk~aR~R 91 (96)
T PF14048_consen 64 PQPLCKQFVVTEEDIRRQERRVKKARKR 91 (96)
T ss_dssp -----T-----HHHHHHHHHHHHHHHHH
T ss_pred CcccccCCccCHHHHHHHHHHHHHHHHH
Confidence 4555233459999999877777666654
No 65
>PF10752 DUF2533: Protein of unknown function (DUF2533) ; InterPro: IPR019688 This entry represents proteins with unknown function, and appear to be restricted to Bacillus spp.
Probab=20.11 E-value=2e+02 Score=23.97 Aligned_cols=35 Identities=14% Similarity=0.222 Sum_probs=29.8
Q ss_pred HHHHHHHHHHHHHhhhhc--CCCCccCHHHHHHHHHH
Q 014692 378 LNGIADMKDEFHNFLQSF--DPSKAITSDDVHQIFEN 412 (420)
Q Consensus 378 i~~Yn~mKdkL~~fLk~F--e~gkvVt~EDIk~FFe~ 412 (420)
+-++|.+-.++.+.-+.+ -.-+.||.|=|++|-++
T Consensus 47 ~d~IN~vT~~mN~LAk~givP~Rk~VT~eMV~EYv~r 83 (84)
T PF10752_consen 47 TDKINEVTKEMNELAKQGIVPTRKYVTVEMVKEYVSR 83 (84)
T ss_pred HHHHHHHHHHHHHHHHcCCCCcchhccHHHHHHHHhc
Confidence 357888888999988888 88899999999999764
Done!