Query 013795
Match_columns 436
No_of_seqs 192 out of 667
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 07:28:32 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/013795.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/013795hhsearch_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 1.3E-88 2.9E-93 664.0 19.3 336 2-430 3-345 (345)
2 smart00396 ZnF_UBR1 Putative z 99.2 3.7E-11 7.9E-16 96.7 4.8 64 42-123 2-69 (71)
3 PF02207 zf-UBR: Putative zinc 99.1 2.7E-11 5.9E-16 97.2 3.3 65 42-123 2-69 (71)
4 KOG1777 Putative Zn-finger pro 98.4 2.2E-07 4.8E-12 96.5 3.5 84 20-127 530-616 (625)
5 PF00628 PHD: PHD-finger; Int 98.3 5.7E-08 1.2E-12 72.3 -1.6 50 144-206 1-51 (51)
6 KOG1973 Chromatin remodeling p 98.2 7.6E-07 1.6E-11 88.7 3.2 56 133-206 210-268 (274)
7 smart00249 PHD PHD zinc finger 98.2 1.5E-06 3.2E-11 61.9 3.2 46 144-203 1-47 (47)
8 KOG2752 Uncharacterized conser 98.1 1.4E-06 3.1E-11 87.2 1.5 94 103-209 14-107 (345)
9 COG5034 TNG2 Chromatin remodel 97.9 5.8E-06 1.3E-10 80.9 3.0 47 141-205 220-269 (271)
10 KOG4323 Polycomb-like PHD Zn-f 97.9 1.5E-05 3.3E-10 84.2 5.2 75 130-215 159-233 (464)
11 KOG1776 Zn-binding protein Pus 97.1 0.00012 2.5E-09 80.0 0.4 59 42-118 766-828 (1110)
12 KOG1632 Uncharacterized PHD Zn 97.1 0.00019 4.1E-09 74.0 1.0 59 142-213 60-120 (345)
13 KOG0943 Predicted ubiquitin-pr 96.4 0.00087 1.9E-08 76.8 0.3 40 42-82 1242-1284(3015)
14 KOG0825 PHD Zn-finger protein 88.5 0.26 5.6E-06 55.5 2.2 52 140-206 213-266 (1134)
15 KOG4443 Putative transcription 85.3 0.19 4.1E-06 55.5 -1.0 54 142-204 145-200 (694)
16 KOG1844 PHD Zn-finger proteins 80.4 1.3 2.9E-05 47.4 3.0 64 129-207 71-136 (508)
17 PF13831 PHD_2: PHD-finger; PD 68.9 0.76 1.6E-05 32.4 -1.6 34 160-203 2-35 (36)
18 KOG1632 Uncharacterized PHD Zn 68.8 0.87 1.9E-05 47.3 -1.9 57 140-205 237-294 (345)
19 PF00643 zf-B_box: B-box zinc 68.1 4 8.6E-05 28.8 2.0 25 54-82 14-38 (42)
20 KOG1512 PHD Zn-finger protein 60.7 4.6 9.9E-05 41.1 1.5 98 52-206 255-363 (381)
21 cd04714 BAH_BAHCC1 BAH, or Bro 56.2 6.5 0.00014 34.6 1.5 20 141-165 102-121 (121)
22 KOG0957 PHD finger protein [Ge 54.4 7.3 0.00016 42.5 1.8 49 144-203 546-595 (707)
23 PF02881 SRP54_N: SRP54-type p 54.0 21 0.00046 28.1 4.1 31 400-431 1-32 (75)
24 KOG2626 Histone H3 (Lys4) meth 52.8 14 0.00031 40.4 3.7 58 139-206 17-76 (544)
25 PF13832 zf-HC5HC2H_2: PHD-zin 48.0 8.4 0.00018 32.7 0.9 35 135-177 49-85 (110)
26 KOG0383 Predicted helicase [Ge 43.4 11 0.00024 42.7 1.2 37 160-205 57-93 (696)
27 PF14071 YlbD_coat: Putative c 40.5 66 0.0014 29.0 5.4 74 339-417 26-110 (124)
28 PF13495 Phage_int_SAM_4: Phag 40.4 31 0.00068 27.2 3.1 41 391-432 16-56 (85)
29 KOG0957 PHD finger protein [Ge 39.1 29 0.00063 38.0 3.4 58 143-205 121-178 (707)
30 PF13405 EF-hand_6: EF-hand do 38.9 31 0.00067 22.6 2.4 25 403-427 1-27 (31)
31 PF08671 SinI: Anti-repressor 37.8 28 0.00061 23.8 2.0 13 417-429 17-29 (30)
32 cd00730 rubredoxin Rubredoxin; 37.7 23 0.00049 26.9 1.7 43 163-207 2-44 (50)
33 smart00336 BBOX B-Box-type zin 36.6 29 0.00063 23.9 2.1 27 52-82 12-38 (42)
34 KOG4299 PHD Zn-finger protein 36.4 14 0.0003 41.2 0.5 50 143-206 254-305 (613)
35 KOG3878 Protein involved in ma 35.6 43 0.00093 35.0 3.8 50 380-432 96-146 (469)
36 PF09416 UPF1_Zn_bind: RNA hel 33.1 27 0.0006 32.4 1.8 48 160-213 12-76 (152)
37 KOG0954 PHD finger protein [Ge 30.2 31 0.00066 39.5 1.9 37 141-181 270-307 (893)
38 PF09082 DUF1922: Domain of un 29.4 20 0.00044 29.0 0.3 9 107-115 4-12 (68)
39 PLN00035 histone H4; Provision 29.1 52 0.0011 28.7 2.8 29 396-424 51-89 (103)
40 smart00417 H4 Histone H4. 26.8 66 0.0014 26.4 2.9 28 396-423 35-72 (74)
41 cd00076 H4 Histone H4, one of 26.4 78 0.0017 26.6 3.3 29 396-424 35-73 (85)
42 PTZ00015 histone H4; Provision 26.1 75 0.0016 27.7 3.2 29 396-424 52-90 (102)
43 cd04718 BAH_plant_2 BAH, or Br 26.0 52 0.0011 30.5 2.3 27 172-207 2-28 (148)
44 PF07061 Swi5: Swi5; InterPro 25.8 68 0.0015 26.8 2.8 36 389-424 40-75 (83)
45 PF14659 Phage_int_SAM_3: Phag 24.3 1.1E+02 0.0023 22.2 3.4 30 399-429 28-57 (58)
46 TIGR02925 cis_trans_EpsD pepti 24.1 1.3E+02 0.0029 28.5 4.9 40 392-431 89-131 (232)
47 PF08164 TRAUB: Apoptosis-anta 23.8 79 0.0017 26.4 2.8 28 401-429 55-82 (83)
48 PF10776 DUF2600: Protein of u 23.1 1.5E+02 0.0032 31.0 5.2 53 375-431 38-92 (330)
49 cd00021 BBOX B-Box-type zinc f 23.1 62 0.0014 21.8 1.8 26 53-82 10-35 (39)
50 KOG0031 Myosin regulatory ligh 23.0 2E+02 0.0044 27.2 5.6 47 380-428 21-76 (171)
51 PF07106 TBPIP: Tat binding pr 23.0 4.2E+02 0.0091 24.2 7.9 48 383-430 107-155 (169)
52 cd05029 S-100A6 S-100A6: S-100 22.9 1E+02 0.0022 25.5 3.3 40 391-430 13-61 (88)
53 COG5100 NPL4 Nuclear pore prot 22.8 32 0.00068 36.9 0.4 23 48-74 126-148 (571)
54 PF00301 Rubredoxin: Rubredoxi 22.3 34 0.00073 25.7 0.3 12 195-206 32-43 (47)
55 PF07496 zf-CW: CW-type Zinc F 22.1 38 0.00083 25.3 0.6 15 161-175 2-16 (50)
56 PF07227 DUF1423: Protein of u 21.8 82 0.0018 34.1 3.2 62 144-208 131-194 (446)
57 KOG0955 PHD finger protein BR1 21.7 84 0.0018 37.5 3.5 53 140-207 218-270 (1051)
58 KOG1886 BAH domain proteins [T 20.9 73 0.0016 34.7 2.6 36 140-180 169-204 (464)
59 smart00054 EFh EF-hand, calciu 20.7 88 0.0019 18.0 2.0 25 404-428 2-28 (29)
60 PF14048 MBD_C: C-terminal dom 20.5 75 0.0016 27.3 2.1 29 407-435 63-91 (96)
61 KOG1245 Chromatin remodeling c 20.3 24 0.00052 43.2 -1.2 53 141-208 1107-1160(1404)
62 PF10752 DUF2533: Protein of u 20.1 2E+02 0.0043 24.3 4.4 35 394-428 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=1.3e-88 Score=663.97 Aligned_cols=336 Identities=44% Similarity=0.849 Sum_probs=269.8
Q ss_pred CCCCccchhhcccccHHHHHhhHHHHHHHHHHhcCCCCCCCcccccccccccceEeecCCCCCC-CceEecccchhhccC
Q 013795 2 SGELDDDVEAEQTISINEYLNDVEEKELEADLVLGGDEGKECTYSKGYMKRQAIFSCLSCAPEG-NAGVCTACSLTCHDG 80 (436)
Q Consensus 2 ~~~~~~~~e~e~~vT~~e~l~~q~eLE~eA~~vl~~~~~~~ct~~~~~~~~q~~~~c~~c~~~~-~~~~c~~c~~~ch~~ 80 (436)
+|-|++ +|...+||+.+|++++.+||.+|++|||+++++.|||++||++||++|+|+||.|+. .||||++|++.||+|
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 334459999999999999999999999999999999999999999999999999985 899999999999999
Q ss_pred CCccchhhhcccccceeEEEeecccccccccCCCCCCccceeecCCCCcccccccCCCCCcceEEeeCCCCCCCCccccc
Q 013795 81 HESWWWHCIVMSSSVCKIVELWTKRNFRCDCGNSKFGEFFCKLFPSKDVENAENSYNHNFKGVYCTCNRPYPDPDVEEQV 160 (436)
Q Consensus 81 h~~~~~~~~~~~~~~~~~~e~~~~r~f~cdcg~~~~~~~~C~l~~~k~~~n~~N~Yn~Nf~g~yC~C~rpYpDp~~e~~~ 160 (436)
|+ ||||||||||||||||++|+..+|+|.++++.+|+.|.|||||+|+||+|.+|||||..++.+
T Consensus 82 H~---------------lveL~tKR~FrCDCg~sk~g~~sc~l~~~~~~~n~~N~YNhNfqG~~C~Cd~~Ypdp~~~~e~ 146 (345)
T KOG2752|consen 82 HE---------------LVELYTKRNFRCDCGNSKFGRCSCNLLEDKDAENSENLYNHNFQGLFCKCDTPYPDPVRTEEG 146 (345)
T ss_pred ce---------------eeeccccCCcccccccccccccccccccccccccchhhhhhhhcceeEEecCCCCCccccccc
Confidence 99 999999999999999999999999999999999999999999999999999999999988899
Q ss_pred ceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccCCccccccccchhccccccCCCCCcCCCCCccccC
Q 013795 161 EMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVCSFLSTYPQTIWAAGLRRNAGCNTNKDKDVLEEI 240 (436)
Q Consensus 161 ~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~~pfL~~y~~~~~~~~~~~~~~~~~~~~k~~~~~~ 240 (436)
.|+||.+|||||| |..|++..+|+..||..... ++. +..
T Consensus 147 ~m~QC~iCEDWFH--------------------------ce~c~~~~~~~~~yp~~~~~-----D~e----------~~k 185 (345)
T KOG2752|consen 147 EMLQCVICEDWFH--------------------------CEGCMQAKTFLEDYPEQGKD-----DAE----------EVK 185 (345)
T ss_pred eeeeEEeccchhc--------------------------ccccCcccchhhcccccccc-----ccc----------cCC
Confidence 9999999999999 44566677888888842110 000 000
Q ss_pred CCCCCCCCCCCCccCCCCCCccccccccccccccCCCCcCCCCccccccc-cccccCCCCCcccccCCCcc----cCCCC
Q 013795 241 PSAGGSGKLENGICSNGSPREDNAIANTSAESVTGGKGVTGESSKKIFDL-VQCMNDGGAHIACLFGDNIV----VDGSI 315 (436)
Q Consensus 241 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~Ckl~~~~~----~~~~~ 315 (436)
+.+ +++ ... ++.++..+... ....-+..+++.|++. .+. .+.+
T Consensus 186 ~e~-~se---~~a--------------------------~~~c~~~i~~~~~~e~~~~e~~~~~~~~-~~e~~~k~~~~- 233 (345)
T KOG2752|consen 186 PEQ-NSE---KCA--------------------------GSSCSEDIQDVPKNESLNDESESGCKLQ-LLENFRKQLKK- 233 (345)
T ss_pred ccc-cCc---ccc--------------------------ccccHHHHHhcccCCCCccccccCCcHH-HHHhhHhhccc-
Confidence 000 000 000 00000000000 0000112233456664 221 1122
Q ss_pred CCCcceecCcchhhhcccchhhHhhhhhcCcCcccCCCcchhhhhhhhHhhhhhhhhhhhchHHHHHhhCChHHHHHHHH
Q 013795 316 SLTKPLFLSKNWRATLCRCKKCLSMYEQKRVPYLIDEEDSIAEYERTAKQKREEKLQQQEGAELTFLNKLGHVEKMEILN 395 (436)
Q Consensus 316 ~~~~s~Fl~~~wR~~LC~C~~Cl~~y~~~~~~FLlDeEDtv~~YE~~~~~~~~~s~~~d~g~~~~aL~sL~RvqaIE~l~ 395 (436)
..+..||.. +||+.||+|.+|+.||+++.|.||||+||||.+||..++...+.+ ..+.+|+ +|++|+|+|||+.|.
T Consensus 234 ~d~~~~~~~-~wR~~LC~Ce~Cl~mY~d~dv~fLlD~EDti~tyE~k~k~~~~~~-t~e~~~~--~L~~l~r~q~ve~i~ 309 (345)
T KOG2752|consen 234 KDGAAFWTN-NWRSKLCTCEDCLEMYEDLDVEFLLDEEDTILTYENKGKIAEENK-TSEDLME--ALDSLNRVQQVELIC 309 (345)
T ss_pred CCcccchhh-hHHHhhcchHHhhhhhhhhchheeecccchhhhhhhhhhhhhhcc-ccchHHH--HHHhccchhhHHHHH
Confidence 345556666 999999999999999999999999999999999999999555555 8888899 999999999999999
Q ss_pred HHHHHHHHHHHhhhcc-CCCCccCHHHHHHHHHHHH
Q 013795 396 GIADMKDEFHNFLQSF-DPSKAITSDDVHQIFENLA 430 (436)
Q Consensus 396 gYn~mKdkL~eFLk~F-e~gkVVTeEDIk~FFe~L~ 430 (436)
+||+||++|++||++| ++|+|||+|||++||++++
T Consensus 310 eyn~lK~~L~d~L~~fA~~~~vv~reDI~~FF~~~~ 345 (345)
T KOG2752|consen 310 EYNRLKDELKDYLKRFADEGTVVTREDIQQFFEEFQ 345 (345)
T ss_pred HHHhHHHHHHHHHHHhhhcCeEeeHHHHHHHHHhhC
Confidence 9999999999999999 9999999999999999874
No 2
>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=99.15 E-value=3.7e-11 Score=96.72 Aligned_cols=64 Identities=33% Similarity=0.713 Sum_probs=55.7
Q ss_pred CcccccccccccceEeecCCCCCCCceEecccch-hhccCCCccchhhhcccccceeEEEeecccc-cccccCCC--CCC
Q 013795 42 ECTYSKGYMKRQAIFSCLSCAPEGNAGVCTACSL-TCHDGHESWWWHCIVMSSSVCKIVELWTKRN-FRCDCGNS--KFG 117 (436)
Q Consensus 42 ~ct~~~~~~~~q~~~~c~~c~~~~~~~~c~~c~~-~ch~~h~~~~~~~~~~~~~~~~~~e~~~~r~-f~cdcg~~--~~~ 117 (436)
.|+|..++. +.+|.|+||...+..+||..|.. .||.||+ |.+++.++ |+||||+. ..+
T Consensus 2 ~C~~~~~~~--~~~y~C~tC~~~~~~~iC~~Cf~~~~H~gH~----------------~~~~~~~~~~~CDCG~~~~~~~ 63 (71)
T smart00396 2 VCTYKFTGG--EVIYRCKTCGLDPTCVLCSDCFRSNCHKGHD----------------YSLKTSRGSGICDCGDKEAWNE 63 (71)
T ss_pred CCCCccCCC--CEEEECcCCCCCCCEeEChHHCCCCCCCCCC----------------EEEEEecCCEEECCCChhccCC
Confidence 599998887 56699999999899999999999 9999999 78999998 99999998 344
Q ss_pred ccceee
Q 013795 118 EFFCKL 123 (436)
Q Consensus 118 ~~~C~l 123 (436)
+..|++
T Consensus 64 ~~~C~~ 69 (71)
T smart00396 64 DLKCKA 69 (71)
T ss_pred Cccccc
Confidence 556765
No 3
>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=99.13 E-value=2.7e-11 Score=97.19 Aligned_cols=65 Identities=34% Similarity=0.822 Sum_probs=46.6
Q ss_pred CcccccccccccceEeecCCCCCCCceEeccc-chhhccCCCccchhhhcccccceeEEEeecccccccccCCCCCCc--
Q 013795 42 ECTYSKGYMKRQAIFSCLSCAPEGNAGVCTAC-SLTCHDGHESWWWHCIVMSSSVCKIVELWTKRNFRCDCGNSKFGE-- 118 (436)
Q Consensus 42 ~ct~~~~~~~~q~~~~c~~c~~~~~~~~c~~c-~~~ch~~h~~~~~~~~~~~~~~~~~~e~~~~r~f~cdcg~~~~~~-- 118 (436)
.|+|..+.. |.+|.|+||......+||..| +..||.||+ ++.+...++|+||||+.....
T Consensus 2 ~C~~~~~~~--q~~y~C~tC~~~~~~~iC~~CF~~~~H~gH~---------------~~~~~~~~~~~CDCG~~~~~k~~ 64 (71)
T PF02207_consen 2 KCTYVWTSG--QIFYRCLTCSLDESSGICEECFANSCHEGHR---------------VVYYRSSSGGCCDCGDPEAWKKE 64 (71)
T ss_dssp SS--B--TT---EEEEETTTBSSTT-BBEHHHHCTSGGGGSS---------------EEEEE--SCEBB-TT-GGGBSS-
T ss_pred cCCCCCcCC--CEEEECccCCCCCCEEEchhhCCCCCcCCCc---------------EEEEEeCCCeEEeCCCCccccCC
Confidence 588876554 999999999999999999999 999999999 988888889999999988743
Q ss_pred cceee
Q 013795 119 FFCKL 123 (436)
Q Consensus 119 ~~C~l 123 (436)
..|++
T Consensus 65 ~~C~~ 69 (71)
T PF02207_consen 65 GFCKK 69 (71)
T ss_dssp -S-TT
T ss_pred CCCCC
Confidence 34654
No 4
>KOG1777 consensus Putative Zn-finger protein [General function prediction only]
Probab=98.36 E-value=2.2e-07 Score=96.54 Aligned_cols=84 Identities=24% Similarity=0.705 Sum_probs=67.7
Q ss_pred HHhhHHHHHHHHHHhcCCCCCCCcccc---cccccccceEeecCCCCCCCceEecccchhhccCCCccchhhhcccccce
Q 013795 20 YLNDVEEKELEADLVLGGDEGKECTYS---KGYMKRQAIFSCLSCAPEGNAGVCTACSLTCHDGHESWWWHCIVMSSSVC 96 (436)
Q Consensus 20 ~l~~q~eLE~eA~~vl~~~~~~~ct~~---~~~~~~q~~~~c~~c~~~~~~~~c~~c~~~ch~~h~~~~~~~~~~~~~~~ 96 (436)
+.+.++..|+.-. .+ .|.|+ +.+.|...+|.|.||+.....+||..|...||.||+
T Consensus 530 iydN~D~vekAik------~G-qCLfkvSs~~syPMHnFYRC~TCNttdRNAIC~nCI~~CH~GH~-------------- 588 (625)
T KOG1777|consen 530 IYDNLDHVEKAIK------KG-QCLFKVSSYTSYPMHNFYRCITCNTTDRNAICVNCIKRCHEGHD-------------- 588 (625)
T ss_pred cccchHHHHHHhh------cC-ceEEEecCCCcccccceeEeeecCCccccHHHHHHHHHhcCCCc--------------
Confidence 3444555554432 23 49994 456668999999999999999999999999999999
Q ss_pred eEEEeecccccccccCCCCCCccceeecCCC
Q 013795 97 KIVELWTKRNFRCDCGNSKFGEFFCKLFPSK 127 (436)
Q Consensus 97 ~~~e~~~~r~f~cdcg~~~~~~~~C~l~~~k 127 (436)
||+.....|+||||+..... .|.|..++
T Consensus 589 --Vefir~Drffcdcgagtl~~-~c~lq~ep 616 (625)
T KOG1777|consen 589 --VEFIRHDRFFCDCGAGTLSN-VCDLQGEP 616 (625)
T ss_pred --eEEEeeceEEEecCCceecc-eeeccCCc
Confidence 89998899999999988764 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=98.31 E-value=5.7e-08 Score=72.27 Aligned_cols=50 Identities=30% Similarity=0.798 Sum_probs=36.7
Q ss_pred EE-eeCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccC
Q 013795 144 YC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAV 206 (436)
Q Consensus 144 yC-~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~ 206 (436)
|| +|+++. + .+.||||+.|..|||..|++++.. +.... ...|+|+.|..+
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 68 899843 2 489999999999999999998532 11111 238999999753
No 6
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.21 E-value=7.6e-07 Score=88.72 Aligned_cols=56 Identities=30% Similarity=0.663 Sum_probs=43.4
Q ss_pred cccCCCCCcceEEeeCCCCCCCCcccccceeeccc--cc-ccccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccC
Q 013795 133 ENSYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCI--CE-DWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAV 206 (436)
Q Consensus 133 ~N~Yn~Nf~g~yC~C~rpYpDp~~e~~~~MiQC~~--CE-DWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~ 206 (436)
...+...-.-.||+|++.- .+.||.|+. |. +|||..||||.. .| .+.|+|+.|...
T Consensus 210 ~~~~~d~~e~~yC~Cnqvs-------yg~Mi~CDn~~C~~eWFH~~CVGL~~---~P--------kgkWyC~~C~~~ 268 (274)
T KOG1973|consen 210 SEEAVDPDEPTYCICNQVS-------YGKMIGCDNPGCPIEWFHFTCVGLKT---KP--------KGKWYCPRCKAE 268 (274)
T ss_pred cccccCCCCCEEEEecccc-------cccccccCCCCCCcceEEEecccccc---CC--------CCcccchhhhhh
Confidence 3444444568999999652 589999998 98 999999999963 23 457999999754
No 7
>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 KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=98.05 E-value=1.4e-06 Score=87.23 Aligned_cols=94 Identities=12% Similarity=0.058 Sum_probs=77.1
Q ss_pred cccccccccCCCCCCccceeecCCCCcccccccCCCCCcceEEeeCCCCCCCCcccccceeecccccccccCCCCCCCCC
Q 013795 103 TKRNFRCDCGNSKFGEFFCKLFPSKDVENAENSYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPS 182 (436)
Q Consensus 103 ~~r~f~cdcg~~~~~~~~C~l~~~k~~~n~~N~Yn~Nf~g~yC~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~ 182 (436)
|++.++|+++...+.+..+.|.+...+.+-++.|+.++++.+|+|-+++|+| +.|.+|..|..|+|+.|+.+.
T Consensus 14 tiT~~e~vE~~~~lE~~a~~vL~~~~~~~CTy~~Gy~~rQ~l~sClTC~P~~-----~~agvC~~C~~~CH~~H~lve-- 86 (345)
T KOG2752|consen 14 TITLGEYVEQIDELEDEADVVLGTQNPDVCTYAKGYKKRQALFSCLTCTPAP-----EMAGVCYACSLSCHDGHELVE-- 86 (345)
T ss_pred cccHHHHHHhHHHHHHHHHhhcCCCCCcccccccCcccccceeEeecccCCh-----hhceeEEEeeeeecCCceeee--
Confidence 7899999999999999899999999999999999999999999999999865 489999999999999998773
Q ss_pred CCCCCCCCCCCccCeeecCCcccCCcc
Q 013795 183 DEIPRDDEGEPVYEDFICKACSAVCSF 209 (436)
Q Consensus 183 ~~~p~~~~~e~~~~~fIC~~C~~~~pf 209 (436)
.+.-.. |.-..|-.|+.+.++
T Consensus 87 --L~tKR~----FrCDCg~sk~g~~sc 107 (345)
T KOG2752|consen 87 --LYTKRN----FRCDCGNSKFGRCSC 107 (345)
T ss_pred --ccccCC----ccccccccccccccc
Confidence 233223 444444555555454
No 9
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=97.92 E-value=5.8e-06 Score=80.93 Aligned_cols=47 Identities=34% Similarity=0.894 Sum_probs=39.3
Q ss_pred cceEEeeCCCCCCCCcccccceeeccc--c-cccccCCCCCCCCCCCCCCCCCCCCccCeeecCCccc
Q 013795 141 KGVYCTCNRPYPDPDVEEQVEMIQCCI--C-EDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 205 (436)
Q Consensus 141 ~g~yC~C~rpYpDp~~e~~~~MiQC~~--C-EDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~ 205 (436)
..+||.|+++- .+.||.|+. | .+|||..||||. ++| -..|+|+.|-.
T Consensus 220 e~lYCfCqqvS-------yGqMVaCDn~nCkrEWFH~~CVGLk---~pP--------KG~WYC~eCk~ 269 (271)
T COG5034 220 EELYCFCQQVS-------YGQMVACDNANCKREWFHLECVGLK---EPP--------KGKWYCPECKK 269 (271)
T ss_pred ceeEEEecccc-------cccceecCCCCCchhheeccccccC---CCC--------CCcEeCHHhHh
Confidence 57899999984 489999995 9 899999999995 234 36899999964
No 10
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.87 E-value=1.5e-05 Score=84.17 Aligned_cols=75 Identities=17% Similarity=0.405 Sum_probs=53.6
Q ss_pred ccccccCCCCCcceEEeeCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccCCcc
Q 013795 130 ENAENSYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVCSF 209 (436)
Q Consensus 130 ~n~~N~Yn~Nf~g~yC~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~~pf 209 (436)
..+.-.+--|-.-.||.|..|-. ..-||||..|..|||..|....-. ..-..|. |.+|+|..|.....+
T Consensus 159 l~wD~~~~~n~qc~vC~~g~~~~------~NrmlqC~~C~~~fHq~Chqp~i~-~~l~~D~----~~~w~C~~C~~~~~~ 227 (464)
T KOG4323|consen 159 LDWDSGHKVNLQCSVCYCGGPGA------GNRMLQCDKCRQWYHQACHQPLIK-DELAGDP----FYEWFCDVCNRGPKK 227 (464)
T ss_pred cccCccccccceeeeeecCCcCc------cceeeeecccccHHHHHhccCCCC-HhhccCc----cceEeehhhccchhh
Confidence 33455555666677888888853 349999999999999999865322 1122334 899999999988777
Q ss_pred cccccc
Q 013795 210 LSTYPQ 215 (436)
Q Consensus 210 L~~y~~ 215 (436)
+.+..+
T Consensus 228 ~~r~t~ 233 (464)
T KOG4323|consen 228 VPRLTL 233 (464)
T ss_pred cccccc
Confidence 776544
No 11
>KOG1776 consensus Zn-binding protein Push [Signal transduction mechanisms]
Probab=97.14 E-value=0.00012 Score=80.04 Aligned_cols=59 Identities=20% Similarity=0.095 Sum_probs=51.7
Q ss_pred Cccccc---ccccccceEeecCCCCC-CCceEecccchhhccCCCccchhhhcccccceeEEEeecccccccccCCCCCC
Q 013795 42 ECTYSK---GYMKRQAIFSCLSCAPE-GNAGVCTACSLTCHDGHESWWWHCIVMSSSVCKIVELWTKRNFRCDCGNSKFG 117 (436)
Q Consensus 42 ~ct~~~---~~~~~q~~~~c~~c~~~-~~~~~c~~c~~~ch~~h~~~~~~~~~~~~~~~~~~e~~~~r~f~cdcg~~~~~ 117 (436)
.|||.+ -|| -|.+|.|.+|... +..|+|..||++||.+|+ |. +.+..|.|+||-++.+
T Consensus 766 ~~T~Kkk~q~~m-~n~~~q~~k~~M~~~~gG~~kV~s~t~H~~~~---------------i~--~S~~~~~C~C~Es~~~ 827 (1110)
T KOG1776|consen 766 DETEKKKKQMAM-LNREKQLTKMRMKVGTGGQIKVSSRTLHNEPS---------------ID--DSDSLPCCICRESVIS 827 (1110)
T ss_pred HHHHhhhhhHHH-HHHHhhhhhheeeeccCceEEEeeecccCCCC---------------cc--ccCCCceeeccccccc
Confidence 599953 788 9999999999987 666999999999999999 64 5599999999999887
Q ss_pred c
Q 013795 118 E 118 (436)
Q Consensus 118 ~ 118 (436)
.
T Consensus 828 g 828 (1110)
T KOG1776|consen 828 G 828 (1110)
T ss_pred c
Confidence 4
No 12
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.06 E-value=0.00019 Score=73.99 Aligned_cols=59 Identities=37% Similarity=0.819 Sum_probs=46.0
Q ss_pred ceEEeeCCCCCCCCcccccceeecccccccccCCC--CCCCCCCCCCCCCCCCCccCeeecCCcccCCcccccc
Q 013795 142 GVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEH--IGLEPSDEIPRDDEGEPVYEDFICKACSAVCSFLSTY 213 (436)
Q Consensus 142 g~yC~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~C--l~~~~~~~~p~~~~~e~~~~~fIC~~C~~~~pfL~~y 213 (436)
..||.|..++ ||+ ..|+||++|++|||+.| +|++.. ..| ..+.++|..|.....-+..+
T Consensus 60 ~~~~~~~~~~-~p~----~~~~~cd~C~~~~~~ec~~v~~~~~-e~p-------~~~~~~c~~c~~~~~~~~~~ 120 (345)
T KOG1632|consen 60 QRYCKCYKPC-DPD----DLMEQCDLCEDWYHGECWEVGTAEK-EAP-------KEDPKVCDECKEAQDGMSES 120 (345)
T ss_pred hchhhccccc-Cch----hhhhccccccccccccccccCchhh-cCC-------ccccccccccchhhhhhhhh
Confidence 4599999998 675 59999999999999999 998754 233 26789999998765444443
No 13
>KOG0943 consensus Predicted ubiquitin-protein ligase/hyperplastic discs protein, HECT superfamily [Posttranslational modification, protein turnover, chaperones]
Probab=96.41 E-value=0.00087 Score=76.81 Aligned_cols=40 Identities=35% Similarity=0.945 Sum_probs=36.1
Q ss_pred Ccccc---cccccccceEeecCCCCCCCceEecccchhhccCCC
Q 013795 42 ECTYS---KGYMKRQAIFSCLSCAPEGNAGVCTACSLTCHDGHE 82 (436)
Q Consensus 42 ~ct~~---~~~~~~q~~~~c~~c~~~~~~~~c~~c~~~ch~~h~ 82 (436)
.|+|. ...| .|-||.|.||...+.-..|.-|+++||.||+
T Consensus 1242 tCSFTWTGadHI-NQDIfECkTCGL~~SLCCCsECAltCHk~HD 1284 (3015)
T KOG0943|consen 1242 TCSFTWTGADHI-NQDIFECKTCGLLESLCCCSECALTCHKGHD 1284 (3015)
T ss_pred ccceeecchhhc-cchhhhhcccccchhhhhhHHHHHHhccCCc
Confidence 58775 3678 9999999999988889999999999999999
No 14
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=88.53 E-value=0.26 Score=55.52 Aligned_cols=52 Identities=27% Similarity=0.633 Sum_probs=38.9
Q ss_pred CcceEE-eeCCCCCCCCcccccceeeccccccc-ccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccC
Q 013795 140 FKGVYC-TCNRPYPDPDVEEQVEMIQCCICEDW-FHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAV 206 (436)
Q Consensus 140 f~g~yC-~C~rpYpDp~~e~~~~MiQC~~CEDW-fH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~ 206 (436)
....-| +|..+ ||+ +.||-|+.|.+= ||-.||..+-. .+| ...|+|..|+..
T Consensus 213 ~E~~~C~IC~~~--DpE----dVLLLCDsCN~~~YH~YCLDPdl~-eiP--------~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 213 QEEVKCDICTVH--DPE----DVLLLCDSCNKVYYHVYCLDPDLS-ESP--------VNEWYCTNCSLL 266 (1134)
T ss_pred cccccceeeccC--ChH----HhheeecccccceeeccccCcccc-ccc--------ccceecCcchhh
Confidence 345556 78877 664 799999999766 99999986432 233 578999999854
No 15
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=85.34 E-value=0.19 Score=55.53 Aligned_cols=54 Identities=26% Similarity=0.720 Sum_probs=39.4
Q ss_pred ceEE-eeCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccC-eeecCCcc
Q 013795 142 GVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYE-DFICKACS 204 (436)
Q Consensus 142 g~yC-~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~-~fIC~~C~ 204 (436)
+.|| +|.+.|-+-+ ...|++|.+|.-|-|..|.++.....+. ...+ .|-|..|.
T Consensus 145 ~~~cPvc~~~Y~~~e---~~~~~~c~~c~rwsh~~c~~~sdd~~~q------~~vD~~~~CS~CR 200 (694)
T KOG4443|consen 145 LSYCPVCLIVYQDSE---SLPMVCCSICQRWSHGGCDGISDDKYMQ------AQVDLQYKCSTCR 200 (694)
T ss_pred cccCchHHHhhhhcc---chhhHHHHHhcccccCCCCccchHHHHH------Hhhhhhcccceee
Confidence 6788 6889996433 6789999999999999999985321111 0123 78899997
No 16
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=80.38 E-value=1.3 Score=47.36 Aligned_cols=64 Identities=23% Similarity=0.414 Sum_probs=47.7
Q ss_pred cccccccCCCCC--cceEEeeCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccC
Q 013795 129 VENAENSYNHNF--KGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAV 206 (436)
Q Consensus 129 ~~n~~N~Yn~Nf--~g~yC~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~ 206 (436)
..+....|+-+. ...-|+|+... ++ .+.||||..|.-|=|.-|+|.... .. -+.|.|..|..+
T Consensus 71 ~~~~~~~~~~~~~~~~~~c~c~~~~-~~----~g~~i~c~~c~~Wqh~~C~g~~~~------~~----p~~y~c~~c~~~ 135 (508)
T KOG1844|consen 71 LLSLNGSEAGSEAREISRCDCGLED-DM----EGLMIQCDWCGRWQHKICCGSFKS------TK----PDKYVCEICTPR 135 (508)
T ss_pred cccccccccccCcCccccccccccc-CC----CceeeCCcccCcccCceeeeecCC------CC----chhceeeeeccc
Confidence 344456666665 67789999885 22 389999999999999999987432 11 368999999765
Q ss_pred C
Q 013795 207 C 207 (436)
Q Consensus 207 ~ 207 (436)
.
T Consensus 136 ~ 136 (508)
T KOG1844|consen 136 N 136 (508)
T ss_pred c
Confidence 4
No 17
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=68.94 E-value=0.76 Score=32.44 Aligned_cols=34 Identities=24% Similarity=0.636 Sum_probs=18.6
Q ss_pred cceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCc
Q 013795 160 VEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKAC 203 (436)
Q Consensus 160 ~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C 203 (436)
..||+|..|.-..|..|-|+... |. .+.|+|..|
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~---~~-------~~~W~C~~C 35 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEV---PD-------GDDWLCDRC 35 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS-----S-------S-----HHH
T ss_pred CceEEeCCCCCcCChhhCCcccC---CC-------CCcEECCcC
Confidence 47999999999999999998532 22 235888776
No 18
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=68.84 E-value=0.87 Score=47.29 Aligned_cols=57 Identities=25% Similarity=0.600 Sum_probs=37.0
Q ss_pred CcceEEe-eCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCccc
Q 013795 140 FKGVYCT-CNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 205 (436)
Q Consensus 140 f~g~yC~-C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~ 205 (436)
..+.+|. |+..|- . ..+||-|.+|+.|||+.|+.+.+. ...... --...|+|+.|..
T Consensus 237 ~~~~~~~~cg~~~~--~---~~~~~~~~~~e~w~~~~~v~~~~a--~~~~~~--~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 237 YSKLICDPCGLSDA--N---KKFEICCDLCESWFHGDCVQIFEA--RKRLNE--IRNEVYKCPHCTV 294 (345)
T ss_pred cccccccccCcchH--H---HHHHHHHHHHHHHhcccccccccc--hhhhhh--hhccceecCceee
Confidence 4466774 454442 1 378999999999999999998653 111111 0014599999975
No 19
>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=68.13 E-value=4 Score=28.79 Aligned_cols=25 Identities=28% Similarity=0.858 Sum_probs=22.7
Q ss_pred ceEeecCCCCCCCceEecccchhhccCCC
Q 013795 54 AIFSCLSCAPEGNAGVCTACSLTCHDGHE 82 (436)
Q Consensus 54 ~~~~c~~c~~~~~~~~c~~c~~~ch~~h~ 82 (436)
+.|-|.+|. ..||..|...=|.+|.
T Consensus 14 ~~~~C~~C~----~~~C~~C~~~~H~~H~ 38 (42)
T PF00643_consen 14 LSLFCEDCN----EPLCSECTVSGHKGHK 38 (42)
T ss_dssp EEEEETTTT----EEEEHHHHHTSTTTSE
T ss_pred eEEEecCCC----CccCccCCCCCCCCCE
Confidence 789999995 4899999988899999
No 20
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=60.73 E-value=4.6 Score=41.13 Aligned_cols=98 Identities=23% Similarity=0.508 Sum_probs=64.8
Q ss_pred ccceEeecCCCCC---------CCceEecccchhhccCCCccchhhhcccccceeEEEeecccccccccCCCCCCcccee
Q 013795 52 RQAIFSCLSCAPE---------GNAGVCTACSLTCHDGHESWWWHCIVMSSSVCKIVELWTKRNFRCDCGNSKFGEFFCK 122 (436)
Q Consensus 52 ~q~~~~c~~c~~~---------~~~~~c~~c~~~ch~~h~~~~~~~~~~~~~~~~~~e~~~~r~f~cdcg~~~~~~~~C~ 122 (436)
-|+--.|..|... +...+|..|.+. +|. .||-|--..+++|.-|.- .| ..|+
T Consensus 255 ~~~~~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~---~HP----~Ci~M~~elv~~~KTY~W---~C---------~~C~ 315 (381)
T KOG1512|consen 255 NQRRNERKHFWDIQTNIIQSRRNSWIVCKPCATR---PHP----YCVAMIPELVGQYKTYFW---KC---------SSCE 315 (381)
T ss_pred CcchhhhhhhhcchhhhhhhhhccceeecccccC---CCC----cchhcCHHHHhHHhhcch---hh---------cccH
Confidence 4666667777543 345677777764 666 688887776666543310 11 0233
Q ss_pred ecCCCCcccccccCCCCCcceEE-eeCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecC
Q 013795 123 LFPSKDVENAENSYNHNFKGVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICK 201 (436)
Q Consensus 123 l~~~k~~~n~~N~Yn~Nf~g~yC-~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~ 201 (436)
| | +|.+|.- ..+|+-|+.|..=||.-|||+. .+| -..|||.
T Consensus 316 l---------------------C~IC~~P~~------E~E~~FCD~CDRG~HT~CVGL~---~lP--------~G~WICD 357 (381)
T KOG1512|consen 316 L---------------------CRICLGPVI------ESEHLFCDVCDRGPHTLCVGLQ---DLP--------RGEWICD 357 (381)
T ss_pred h---------------------hhccCCccc------chheeccccccCCCCccccccc---ccc--------Cccchhh
Confidence 2 3 7888852 4789999999999999999995 355 3589998
Q ss_pred -CcccC
Q 013795 202 -ACSAV 206 (436)
Q Consensus 202 -~C~~~ 206 (436)
.|...
T Consensus 358 ~~C~~~ 363 (381)
T KOG1512|consen 358 MRCREA 363 (381)
T ss_pred hHHHHh
Confidence 35443
No 21
>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=56.23 E-value=6.5 Score=34.60 Aligned_cols=20 Identities=30% Similarity=0.788 Sum_probs=17.1
Q ss_pred cceEEeeCCCCCCCCcccccceeec
Q 013795 141 KGVYCTCNRPYPDPDVEEQVEMIQC 165 (436)
Q Consensus 141 ~g~yC~C~rpYpDp~~e~~~~MiQC 165 (436)
...+|+|..+| ||+ ..||||
T Consensus 102 ~~d~~~Ce~~y-n~~----~~~~~c 121 (121)
T cd04714 102 GVDFYYCAGTY-NPD----TGMLKC 121 (121)
T ss_pred CCCEEEEeccC-CCC----cCcccC
Confidence 46799999999 675 789998
No 22
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=54.39 E-value=7.3 Score=42.45 Aligned_cols=49 Identities=22% Similarity=0.596 Sum_probs=38.8
Q ss_pred EE-eeCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCc
Q 013795 144 YC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKAC 203 (436)
Q Consensus 144 yC-~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C 203 (436)
-| +|++.. | +-..+||+.|.--||..||+-+-. .+|.-.. ...|+|..|
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 46 899886 2 678999999999999999976543 4565444 578999999
No 23
>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=53.99 E-value=21 Score=28.06 Aligned_cols=31 Identities=16% Similarity=0.393 Sum_probs=26.8
Q ss_pred HHHHHHHhhhcc-CCCCccCHHHHHHHHHHHHH
Q 013795 400 MKDEFHNFLQSF-DPSKAITSDDVHQIFENLAK 431 (436)
Q Consensus 400 mKdkL~eFLk~F-e~gkVVTeEDIk~FFe~L~~ 431 (436)
||..|...++.| .+ .++++++|.+|+++|+.
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 77799999999999874
No 24
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=52.83 E-value=14 Score=40.39 Aligned_cols=58 Identities=22% Similarity=0.505 Sum_probs=40.5
Q ss_pred CCcceEEeeCCCCCCCCcccccceeecccccccccCCCCCCCCCC--CCCCCCCCCCccCeeecCCcccC
Q 013795 139 NFKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSD--EIPRDDEGEPVYEDFICKACSAV 206 (436)
Q Consensus 139 Nf~g~yC~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~--~~p~~~~~e~~~~~fIC~~C~~~ 206 (436)
+-.+.+|+|+..-+ + ...-+||-.|-.|||..++-..+.. .+|.. . ...|+|..|...
T Consensus 17 ~~~~~~~y~e~~r~-l----~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~-t----~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 17 MKQATVCYCEGERN-L----GIVELQCSTCLKWFHLPTLEAFHLIKSSLPFM-T----SYEFVCKECTPS 76 (544)
T ss_pred ccCccccccccccc-c----CceeeEeeecccccccccccccccccccCCcc-c----ceeEEeccccCc
Confidence 44578999987752 3 3667999999999998776443211 23322 1 589999999876
No 25
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=48.03 E-value=8.4 Score=32.75 Aligned_cols=35 Identities=23% Similarity=0.387 Sum_probs=27.5
Q ss_pred cCCCCCcceEEeeCCCCCCCCcccccceeeccc--ccccccCCCC
Q 013795 135 SYNHNFKGVYCTCNRPYPDPDVEEQVEMIQCCI--CEDWFHEEHI 177 (436)
Q Consensus 135 ~Yn~Nf~g~yC~C~rpYpDp~~e~~~~MiQC~~--CEDWfH~~Cl 177 (436)
....++...-.+|++. .+..|||.. |..+||..|.
T Consensus 49 i~~~~~~~~C~iC~~~--------~G~~i~C~~~~C~~~fH~~CA 85 (110)
T PF13832_consen 49 IPPSRFKLKCSICGKS--------GGACIKCSHPGCSTAFHPTCA 85 (110)
T ss_pred ecchhcCCcCcCCCCC--------CceeEEcCCCCCCcCCCHHHH
Confidence 3333456666699987 378999998 9999999996
No 26
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=43.38 E-value=11 Score=42.68 Aligned_cols=37 Identities=30% Similarity=0.661 Sum_probs=27.3
Q ss_pred cceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCccc
Q 013795 160 VEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 205 (436)
Q Consensus 160 ~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~ 205 (436)
+..|-|+.|-.|||..|++.+- .+.. ..+|+|+.|..
T Consensus 57 g~~l~c~tC~~s~h~~cl~~pl---~~~p------~~~~~c~Rc~~ 93 (696)
T KOG0383|consen 57 GELLWCDTCPASFHASCLGPPL---TPQP------NGEFICPRCFC 93 (696)
T ss_pred CcEEEeccccHHHHHHccCCCC---CcCC------ccceeeeeecc
Confidence 6777899999999999998742 2221 23399999943
No 27
>PF14071 YlbD_coat: Putative coat protein
Probab=40.53 E-value=66 Score=29.01 Aligned_cols=74 Identities=19% Similarity=0.308 Sum_probs=49.5
Q ss_pred hhhhhcCcCcccCCCc-chhhhhhhhHh--------hhhhh-hhhhhchHHHHHhhCChHHHHHHHHHHHHHHHHHHHhh
Q 013795 339 SMYEQKRVPYLIDEED-SIAEYERTAKQ--------KREEK-LQQQEGAELTFLNKLGHVEKMEILNGIADMKDEFHNFL 408 (436)
Q Consensus 339 ~~y~~~~~~FLlDeED-tv~~YE~~~~~--------~~~~s-~~~d~g~~~~aL~sL~RvqaIE~l~gYn~mKdkL~eFL 408 (436)
.+|+. =+||-|+| -+.+|-+.+.. +.+.+ ......+. +|.+||-.+.-.-|..++..=..|..+|
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 46764 36776555 56777621111 01111 13334445 8999999999999999999999999999
Q ss_pred hcc-CCCCcc
Q 013795 409 QSF-DPSKAI 417 (436)
Q Consensus 409 k~F-e~gkVV 417 (436)
..| .++.-.
T Consensus 101 ~qFq~~~~~~ 110 (124)
T PF14071_consen 101 SQFQGNGQKQ 110 (124)
T ss_pred HHhcCCCCCC
Confidence 999 665543
No 28
>PF13495 Phage_int_SAM_4: Phage integrase, N-terminal SAM-like domain; PDB: 2A3V_A.
Probab=40.43 E-value=31 Score=27.19 Aligned_cols=41 Identities=22% Similarity=0.395 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHHHHHHhhhccCCCCccCHHHHHHHHHHHHHh
Q 013795 391 MEILNGIADMKDEFHNFLQSFDPSKAITSDDVHQIFENLAKK 432 (436)
Q Consensus 391 IE~l~gYn~mKdkL~eFLk~Fe~gkVVTeEDIk~FFe~L~~~ 432 (436)
-.-+..|-..=..+..|+.. ..-.-||.+||++|+..|..+
T Consensus 16 ~~Ti~~Y~~~l~~f~~~~~~-~~~~~it~~~i~~y~~~l~~~ 56 (85)
T PF13495_consen 16 EKTIKNYRYHLKRFLRFLGN-KPPDEITPEDIEQYLNYLQNE 56 (85)
T ss_dssp HHHHHHHHHHHHHHHTTSSS---GGG--HHHHHHHHHHHHTT
T ss_pred HHHHHHHHHHHHHHHHHccc-CccchhHHHHHHHHHHHHHHh
Confidence 44555665444444444431 233678999999999999833
No 29
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=39.06 E-value=29 Score=38.05 Aligned_cols=58 Identities=26% Similarity=0.496 Sum_probs=40.2
Q ss_pred eEEeeCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCccc
Q 013795 143 VYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSA 205 (436)
Q Consensus 143 ~yC~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~ 205 (436)
..|+|-..--+ ..++.|||+.|.-=.|+.|-|+..+..+|...+ .-..+-|+|..|.-
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 77899544212 158899999999999999999886656664332 11236778877753
No 30
>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=38.85 E-value=31 Score=22.61 Aligned_cols=25 Identities=16% Similarity=0.349 Sum_probs=21.9
Q ss_pred HHHHhhhcc--CCCCccCHHHHHHHHH
Q 013795 403 EFHNFLQSF--DPSKAITSDDVHQIFE 427 (436)
Q Consensus 403 kL~eFLk~F--e~gkVVTeEDIk~FFe 427 (436)
+|+.+|+.| +..-.|+.+|++.++.
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 31
>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=37.76 E-value=28 Score=23.83 Aligned_cols=13 Identities=8% Similarity=0.404 Sum_probs=9.3
Q ss_pred cCHHHHHHHHHHH
Q 013795 417 ITSDDVHQIFENL 429 (436)
Q Consensus 417 VTeEDIk~FFe~L 429 (436)
||.||||+|++..
T Consensus 17 ls~eeir~FL~~~ 29 (30)
T PF08671_consen 17 LSKEEIREFLEFN 29 (30)
T ss_dssp --HHHHHHHHHHH
T ss_pred CCHHHHHHHHHhC
Confidence 7899999999754
No 32
>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=37.67 E-value=23 Score=26.90 Aligned_cols=43 Identities=26% Similarity=0.523 Sum_probs=21.2
Q ss_pred eecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccCC
Q 013795 163 IQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 207 (436)
Q Consensus 163 iQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~~ 207 (436)
.+|.+|. |-+..-.|-+.. ++|..-.-+.+-+.|.||.|-...
T Consensus 2 y~C~~Cg-yiYd~~~Gd~~~-~i~pGt~f~~Lp~~w~CP~C~a~K 44 (50)
T cd00730 2 YECRICG-YIYDPAEGDPDE-GIPPGTPFEDLPDDWVCPVCGAGK 44 (50)
T ss_pred cCCCCCC-eEECCCCCCccc-CcCCCCCHhHCCCCCCCCCCCCcH
Confidence 4566666 444443333221 222211111236799999997543
No 33
>smart00336 BBOX B-Box-type zinc finger.
Probab=36.63 E-value=29 Score=23.87 Aligned_cols=27 Identities=37% Similarity=0.762 Sum_probs=22.0
Q ss_pred ccceEeecCCCCCCCceEecccchhhccCCC
Q 013795 52 RQAIFSCLSCAPEGNAGVCTACSLTCHDGHE 82 (436)
Q Consensus 52 ~q~~~~c~~c~~~~~~~~c~~c~~~ch~~h~ 82 (436)
....|-|.+|. ..||..|...=|.+|.
T Consensus 12 ~~~~~~C~~c~----~~iC~~C~~~~H~~H~ 38 (42)
T smart00336 12 EPAEFFCEECG----ALLCRTCDEAEHRGHT 38 (42)
T ss_pred CceEEECCCCC----cccccccChhhcCCCc
Confidence 34467798885 4899999988999998
No 34
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=36.42 E-value=14 Score=41.17 Aligned_cols=50 Identities=24% Similarity=0.552 Sum_probs=35.6
Q ss_pred eEE-eeCCCCCCCCcccccceeecccccccccCCCCCCCCC-CCCCCCCCCCCccCeeecCCcccC
Q 013795 143 VYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPS-DEIPRDDEGEPVYEDFICKACSAV 206 (436)
Q Consensus 143 ~yC-~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~-~~~p~~~~~e~~~~~fIC~~C~~~ 206 (436)
.|| .|+++.. -...|+|+.|--=||..||.-+-. ..+| -..|.|+.|.-+
T Consensus 254 ~fCsaCn~~~~------F~~~i~CD~Cp~sFH~~CLePPl~~eniP--------~g~W~C~ec~~k 305 (613)
T KOG4299|consen 254 DFCSACNGSGL------FNDIICCDGCPRSFHQTCLEPPLEPENIP--------PGSWFCPECKIK 305 (613)
T ss_pred HHHHHhCCccc------cccceeecCCchHHHHhhcCCCCCcccCC--------CCccccCCCeee
Confidence 388 7888742 234599999999999999965411 1344 358999999644
No 35
>KOG3878 consensus Protein involved in maintenance of Golgi structure and ER-Golgi transport [Intracellular trafficking, secretion, and vesicular transport]
Probab=35.57 E-value=43 Score=35.05 Aligned_cols=50 Identities=14% Similarity=0.245 Sum_probs=42.4
Q ss_pred HHHhhCChHHHHHHHHHHHHHHHHHHHhhhcc-CCCCccCHHHHHHHHHHHHHh
Q 013795 380 TFLNKLGHVEKMEILNGIADMKDEFHNFLQSF-DPSKAITSDDVHQIFENLAKK 432 (436)
Q Consensus 380 ~aL~sL~RvqaIE~l~gYn~mKdkL~eFLk~F-e~gkVVTeEDIk~FFe~L~~~ 432 (436)
++|.+|.|++|+++ |-+|-+.+-.-|++| ...|..+.|..|+|=..+++.
T Consensus 96 ~~LG~~sre~AM~~---FV~Lldr~C~~F~~yia~~k~~kde~lkE~e~r~~ee 146 (469)
T KOG3878|consen 96 QLLGEISREQAMEG---FVDLLDRMCSAFRPYIAAVKQDKDETLKEKELRLMEE 146 (469)
T ss_pred HHHhcccHHHHHHH---HHHHHHhcchhhhhHHHHhhhhhhhHHHHHHHHHHHh
Confidence 48999999999874 668888888899999 999999999999887766643
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=33.08 E-value=27 Score=32.45 Aligned_cols=48 Identities=21% Similarity=0.484 Sum_probs=23.6
Q ss_pred cceeecccccccccCCCCCCCCC-----------------CCCCCCCCCCCccCeeecCCcccCCcccccc
Q 013795 160 VEMIQCCICEDWFHEEHIGLEPS-----------------DEIPRDDEGEPVYEDFICKACSAVCSFLSTY 213 (436)
Q Consensus 160 ~~MiQC~~CEDWfH~~Cl~~~~~-----------------~~~p~~~~~e~~~~~fIC~~C~~~~pfL~~y 213 (436)
.-.++|..|..||=..=-+.+.+ +..|-. -..+-|..|-.++-|+.-|
T Consensus 12 ~~vv~C~~c~kWFCNg~~~~s~SHIv~HLv~srh~ev~LH~~s~lg------dt~leCy~Cg~~NvF~LGF 76 (152)
T PF09416_consen 12 SCVVKCNTCNKWFCNGRGNTSGSHIVNHLVRSRHKEVSLHPDSPLG------DTVLECYNCGSRNVFLLGF 76 (152)
T ss_dssp CCEEEETTTTEEEES--TTSSS-HHHHHHHHHT---EEE-TTSTT-------S-B---TTT----TTTEEE
T ss_pred ccEeEcCCCCcEeecCCCCCcccHHHHHHHHccCCceeeCCCCCCC------CcEEEEEecCCCceeeEEE
Confidence 46899999999996654322111 112221 2578899999999998844
No 37
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=30.16 E-value=31 Score=39.47 Aligned_cols=37 Identities=32% Similarity=0.701 Sum_probs=30.8
Q ss_pred cceEE-eeCCCCCCCCcccccceeecccccccccCCCCCCCC
Q 013795 141 KGVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEP 181 (436)
Q Consensus 141 ~g~yC-~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~ 181 (436)
..+.| +|+.| |-+ +..+||-|+.|.--.|-.|-|+..
T Consensus 270 edviCDvCrsp--D~e--~~neMVfCd~Cn~cVHqaCyGIle 307 (893)
T KOG0954|consen 270 EDVICDVCRSP--DSE--EANEMVFCDKCNICVHQACYGILE 307 (893)
T ss_pred ccceeceecCC--Ccc--ccceeEEeccchhHHHHhhhceee
Confidence 46788 89877 433 478999999999999999999964
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=29.42 E-value=20 Score=29.04 Aligned_cols=9 Identities=67% Similarity=1.564 Sum_probs=4.6
Q ss_pred cccccCCCC
Q 013795 107 FRCDCGNSK 115 (436)
Q Consensus 107 f~cdcg~~~ 115 (436)
||||||+--
T Consensus 4 frC~Cgr~l 12 (68)
T PF09082_consen 4 FRCDCGRYL 12 (68)
T ss_dssp EEETTS--E
T ss_pred EEecCCCEE
Confidence 677777643
No 39
>PLN00035 histone H4; Provisional
Probab=29.05 E-value=52 Score=28.71 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=23.3
Q ss_pred HHHHHHHHHHHhhhcc----------CCCCccCHHHHHH
Q 013795 396 GIADMKDEFHNFLQSF----------DPSKAITSDDVHQ 424 (436)
Q Consensus 396 gYn~mKdkL~eFLk~F----------e~gkVVTeEDIk~ 424 (436)
+|..|...|.+||... ..-|+||++||.-
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 4789999999964
No 40
>smart00417 H4 Histone H4.
Probab=26.83 E-value=66 Score=26.41 Aligned_cols=28 Identities=21% Similarity=0.347 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHhhhcc----------CCCCccCHHHHH
Q 013795 396 GIADMKDEFHNFLQSF----------DPSKAITSDDVH 423 (436)
Q Consensus 396 gYn~mKdkL~eFLk~F----------e~gkVVTeEDIk 423 (436)
+|..+..-|++||..- ..-|+||.+||.
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 478999999984
No 41
>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=26.43 E-value=78 Score=26.61 Aligned_cols=29 Identities=17% Similarity=0.331 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHhhhcc----------CCCCccCHHHHHH
Q 013795 396 GIADMKDEFHNFLQSF----------DPSKAITSDDVHQ 424 (436)
Q Consensus 396 gYn~mKdkL~eFLk~F----------e~gkVVTeEDIk~ 424 (436)
+|..+..-|++||... ..-|+||++||.-
T Consensus 35 ~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~ 73 (85)
T cd00076 35 VYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVY 73 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHH
Confidence 7888888888888763 4789999999953
No 42
>PTZ00015 histone H4; Provisional
Probab=26.12 E-value=75 Score=27.69 Aligned_cols=29 Identities=21% Similarity=0.306 Sum_probs=23.0
Q ss_pred HHHHHHHHHHHhhhcc----------CCCCccCHHHHHH
Q 013795 396 GIADMKDEFHNFLQSF----------DPSKAITSDDVHQ 424 (436)
Q Consensus 396 gYn~mKdkL~eFLk~F----------e~gkVVTeEDIk~ 424 (436)
+|..++.-|++||..- ..-|+||.+||.-
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 6788888888888752 4789999999953
No 43
>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=26.04 E-value=52 Score=30.53 Aligned_cols=27 Identities=30% Similarity=0.551 Sum_probs=19.0
Q ss_pred ccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccCC
Q 013795 172 FHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 207 (436)
Q Consensus 172 fH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~~ 207 (436)
||..||.-+-. .+|+ ..++||.|..+.
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 89999965432 3442 579999998664
No 44
>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=25.83 E-value=68 Score=26.78 Aligned_cols=36 Identities=17% Similarity=0.330 Sum_probs=25.4
Q ss_pred HHHHHHHHHHHHHHHHHHhhhccCCCCccCHHHHHH
Q 013795 389 EKMEILNGIADMKDEFHNFLQSFDPSKAITSDDVHQ 424 (436)
Q Consensus 389 qaIE~l~gYn~mKdkL~eFLk~Fe~gkVVTeEDIk~ 424 (436)
+-|..||.||.+||-=...+.....-+=||--||.+
T Consensus 40 ~hI~lLheYNeiKD~gQ~Lig~iA~~rgvt~~~v~~ 75 (83)
T PF07061_consen 40 RHIKLLHEYNEIKDIGQGLIGLIADQRGVTVKDVYE 75 (83)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHcCCcHHHHHH
Confidence 458899999999998777777762234455555543
No 45
>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=24.27 E-value=1.1e+02 Score=22.23 Aligned_cols=30 Identities=20% Similarity=0.346 Sum_probs=17.2
Q ss_pred HHHHHHHHhhhccCCCCccCHHHHHHHHHHH
Q 013795 399 DMKDEFHNFLQSFDPSKAITSDDVHQIFENL 429 (436)
Q Consensus 399 ~mKdkL~eFLk~Fe~gkVVTeEDIk~FFe~L 429 (436)
.++..+..+|... .=+-||..||+.|+.+|
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 3343444444333 33458999999999887
No 46
>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=24.12 E-value=1.3e+02 Score=28.54 Aligned_cols=40 Identities=10% Similarity=0.360 Sum_probs=27.1
Q ss_pred HHHHHHHHHHHHH--HHhhhcc-CCCCccCHHHHHHHHHHHHH
Q 013795 392 EILNGIADMKDEF--HNFLQSF-DPSKAITSDDVHQIFENLAK 431 (436)
Q Consensus 392 E~l~gYn~mKdkL--~eFLk~F-e~gkVVTeEDIk~FFe~L~~ 431 (436)
+...+++.+|+.| ..|++.. .+.-.||++||++||++..+
T Consensus 89 ~~~~~~~~~r~~ll~~~~~~~~v~~~~~vse~ev~~~Y~~~~~ 131 (232)
T TIGR02925 89 DVVMALEAAKREILARAYLRQLAGAQSKPSPEEAKSYFQEHPQ 131 (232)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhccCCCCCHHHHHHHHHhCHH
Confidence 4445556666653 3455655 55568999999999997654
No 47
>PF08164 TRAUB: Apoptosis-antagonizing transcription factor, C-terminal; InterPro: IPR012617 This C-terminal domain is found in traube proteins [].; GO: 0005634 nucleus
Probab=23.83 E-value=79 Score=26.43 Aligned_cols=28 Identities=14% Similarity=0.522 Sum_probs=22.5
Q ss_pred HHHHHHhhhccCCCCccCHHHHHHHHHHH
Q 013795 401 KDEFHNFLQSFDPSKAITSDDVHQIFENL 429 (436)
Q Consensus 401 KdkL~eFLk~Fe~gkVVTeEDIk~FFe~L 429 (436)
-.||..|..| ...-..+++.|.+||+.|
T Consensus 55 heKL~NFmaP-~~~~~w~~~~~delf~sL 82 (83)
T PF08164_consen 55 HEKLVNFMAP-EDRPTWSDEQIDELFASL 82 (83)
T ss_pred HHHHhhhcCC-CCCCCCCHHHHHHHHHHc
Confidence 3678888877 566778899999999876
No 48
>PF10776 DUF2600: Protein of unknown function (DUF2600); InterPro: IPR019712 This is a bacterial family of proteins. Some members in the family are annotated as YtpB, however no function is currently known.
Probab=23.14 E-value=1.5e+02 Score=31.04 Aligned_cols=53 Identities=17% Similarity=0.390 Sum_probs=43.2
Q ss_pred hchHH-HHHhhCChHHHHHHHHHHHHHHHHHHHhhhcc-CCCCccCHHHHHHHHHHHHH
Q 013795 375 EGAEL-TFLNKLGHVEKMEILNGIADMKDEFHNFLQSF-DPSKAITSDDVHQIFENLAK 431 (436)
Q Consensus 375 ~g~~~-~aL~sL~RvqaIE~l~gYn~mKdkL~eFLk~F-e~gkVVTeEDIk~FFe~L~~ 431 (436)
+|... .++....|...|+.|-||+.| .+||--. +...++.+.|+++.+..|..
T Consensus 38 eGgsi~al~~~~~~~~~i~fIVAyQTI----sDYLDNLcDrs~~~d~~~Fr~LH~am~d 92 (330)
T PF10776_consen 38 EGGSIYALLPGENRDELIRFIVAYQTI----SDYLDNLCDRSTSLDPKDFRQLHQAMLD 92 (330)
T ss_pred cchhhhhhcCCccHhhHHHHHHHHHHH----HHHHHhhhhccCCCChHHHHHHHHHHHH
Confidence 44442 244667788999999999987 5688888 99999999999999999974
No 49
>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=23.12 E-value=62 Score=21.83 Aligned_cols=26 Identities=31% Similarity=0.646 Sum_probs=20.7
Q ss_pred cceEeecCCCCCCCceEecccchhhccCCC
Q 013795 53 QAIFSCLSCAPEGNAGVCTACSLTCHDGHE 82 (436)
Q Consensus 53 q~~~~c~~c~~~~~~~~c~~c~~~ch~~h~ 82 (436)
...|-|.+|. ..||..|...=|.+|.
T Consensus 10 ~~~~fC~~~~----~~iC~~C~~~~H~~H~ 35 (39)
T cd00021 10 PLSLFCETDR----ALLCVDCDLSVHSGHR 35 (39)
T ss_pred ceEEEeCccC----hhhhhhcChhhcCCCC
Confidence 3467788885 4899999866699999
No 50
>KOG0031 consensus Myosin regulatory light chain, EF-Hand protein superfamily [Cytoskeleton]
Probab=23.03 E-value=2e+02 Score=27.20 Aligned_cols=47 Identities=13% Similarity=0.337 Sum_probs=38.9
Q ss_pred HHHhhCChHHHHHHHHHHHHH---------HHHHHHhhhccCCCCccCHHHHHHHHHH
Q 013795 380 TFLNKLGHVEKMEILNGIADM---------KDEFHNFLQSFDPSKAITSDDVHQIFEN 428 (436)
Q Consensus 380 ~aL~sL~RvqaIE~l~gYn~m---------KdkL~eFLk~Fe~gkVVTeEDIk~FFe~ 428 (436)
+.++.++--|-.|.=.|||-| |..|+++|.+. ||+|+++.|.+.+.+
T Consensus 21 nvFamf~q~QIqEfKEAF~~mDqnrDG~IdkeDL~d~~aSl--Gk~~~d~elDaM~~E 76 (171)
T KOG0031|consen 21 NVFAMFDQSQIQEFKEAFNLMDQNRDGFIDKEDLRDMLASL--GKIASDEELDAMMKE 76 (171)
T ss_pred hHHHHhhHHHHHHHHHHHHHHhccCCCcccHHHHHHHHHHc--CCCCCHHHHHHHHHh
Confidence 366778888888999999988 78899988776 788999999887764
No 51
>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=23.02 E-value=4.2e+02 Score=24.22 Aligned_cols=48 Identities=13% Similarity=0.230 Sum_probs=35.8
Q ss_pred hhCChHHHHHHHHHHHHHHHHHHHhhhcc-CCCCccCHHHHHHHHHHHH
Q 013795 383 NKLGHVEKMEILNGIADMKDEFHNFLQSF-DPSKAITSDDVHQIFENLA 430 (436)
Q Consensus 383 ~sL~RvqaIE~l~gYn~mKdkL~eFLk~F-e~gkVVTeEDIk~FFe~L~ 430 (436)
+.+.=.+....|.....=...|.+=|.++ +++..|+++|+...=...+
T Consensus 107 ~~~t~~el~~~i~~l~~e~~~l~~kL~~l~~~~~~vs~ee~~~~~~~~~ 155 (169)
T PF07106_consen 107 SEPTNEELREEIEELEEEIEELEEKLEKLRSGSKPVSPEEKEKLEKEYK 155 (169)
T ss_pred cCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHHHHHH
Confidence 55666666777777777777788888888 8889999999887644433
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=22.85 E-value=1e+02 Score=25.53 Aligned_cols=40 Identities=15% Similarity=0.353 Sum_probs=28.6
Q ss_pred HHHHHHHHH--------HHHHHHHhhhcc-CCCCccCHHHHHHHHHHHH
Q 013795 391 MEILNGIAD--------MKDEFHNFLQSF-DPSKAITSDDVHQIFENLA 430 (436)
Q Consensus 391 IE~l~gYn~--------mKdkL~eFLk~F-e~gkVVTeEDIk~FFe~L~ 430 (436)
|+..+.|.. =+++|+.+|+.+ .-|..+|+++|.+.|..+.
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
>COG5100 NPL4 Nuclear pore protein [Nuclear structure]
Probab=22.80 E-value=32 Score=36.86 Aligned_cols=23 Identities=35% Similarity=0.934 Sum_probs=18.0
Q ss_pred ccccccceEeecCCCCCCCceEecccc
Q 013795 48 GYMKRQAIFSCLSCAPEGNAGVCTACS 74 (436)
Q Consensus 48 ~~~~~q~~~~c~~c~~~~~~~~c~~c~ 74 (436)
|-|+||.-.-|.- +..|.|..||
T Consensus 126 gli~rs~t~lC~H----g~~gMC~yCs 148 (571)
T COG5100 126 GLIRRSMTMLCQH----GSNGMCSYCS 148 (571)
T ss_pred ccchhhhhHHhhc----CCCcccccCC
Confidence 7788888777754 7788888887
No 54
>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=22.28 E-value=34 Score=25.66 Aligned_cols=12 Identities=33% Similarity=0.958 Sum_probs=7.0
Q ss_pred cCeeecCCcccC
Q 013795 195 YEDFICKACSAV 206 (436)
Q Consensus 195 ~~~fIC~~C~~~ 206 (436)
-+.|.||.|-..
T Consensus 32 p~~w~CP~C~a~ 43 (47)
T PF00301_consen 32 PDDWVCPVCGAP 43 (47)
T ss_dssp -TT-B-TTTSSB
T ss_pred CCCCcCcCCCCc
Confidence 578999999643
No 55
>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=22.14 E-value=38 Score=25.31 Aligned_cols=15 Identities=27% Similarity=0.581 Sum_probs=9.1
Q ss_pred ceeecccccccccCC
Q 013795 161 EMIQCCICEDWFHEE 175 (436)
Q Consensus 161 ~MiQC~~CEDWfH~~ 175 (436)
..|||+.|..|=.-.
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 56
>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=21.82 E-value=82 Score=34.10 Aligned_cols=62 Identities=21% Similarity=0.537 Sum_probs=37.2
Q ss_pred EEeeCCCCCCCCcccccceeecccccccccCCC-CCCCCC-CCCCCCCCCCCccCeeecCCcccCCc
Q 013795 144 YCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEH-IGLEPS-DEIPRDDEGEPVYEDFICKACSAVCS 208 (436)
Q Consensus 144 yC~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~C-l~~~~~-~~~p~~~~~e~~~~~fIC~~C~~~~p 208 (436)
-|+|.+ | |-+.. .-.+|-|++|.-|=|-.| |.-... .|.-.......+-..|.|..|-.+..
T Consensus 131 C~iC~k-f-D~~~n-~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~se 194 (446)
T PF07227_consen 131 CCICSK-F-DDNKN-TCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTSE 194 (446)
T ss_pred ccccCC-c-ccCCC-CeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChhh
Confidence 458877 4 44432 578999999999999999 421100 01000010001246899999987753
No 57
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=21.66 E-value=84 Score=37.54 Aligned_cols=53 Identities=23% Similarity=0.464 Sum_probs=39.0
Q ss_pred CcceEEeeCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccCC
Q 013795 140 FKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVC 207 (436)
Q Consensus 140 f~g~yC~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~~ 207 (436)
-.+.-|+|..-- .+...+-|+|+.|.--+|-.|.|+.. +| -..|.|..|..+.
T Consensus 218 ~D~~C~iC~~~~----~~n~n~ivfCD~Cnl~VHq~Cygi~~---ip--------eg~WlCr~Cl~s~ 270 (1051)
T KOG0955|consen 218 EDAVCCICLDGE----CQNSNVIVFCDGCNLAVHQECYGIPF---IP--------EGQWLCRRCLQSP 270 (1051)
T ss_pred CCccceeecccc----cCCCceEEEcCCCcchhhhhccCCCC---CC--------CCcEeehhhccCc
Confidence 346678998652 11247899999999999999999743 33 2478999998653
No 58
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=20.92 E-value=73 Score=34.67 Aligned_cols=36 Identities=6% Similarity=-0.166 Sum_probs=31.5
Q ss_pred CcceEEeeCCCCCCCCcccccceeecccccccccCCCCCCC
Q 013795 140 FKGVYCTCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLE 180 (436)
Q Consensus 140 f~g~yC~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~ 180 (436)
..+.||.|.+.|+| ...|.||..|.+|+|..+++.+
T Consensus 169 ~~~~~~~~~k~e~d-----~~~~kt~~~~~~~~~p~~~~t~ 204 (464)
T KOG1886|consen 169 RDGDFGDGQKLEID-----MLVPKTGPRRGTLPDPKKVQTL 204 (464)
T ss_pred cccchhcccccCCc-----cchhhhcccCCCCCCccccccc
Confidence 55889999999963 4789999999999999999875
No 59
>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=20.71 E-value=88 Score=17.97 Aligned_cols=25 Identities=12% Similarity=0.343 Sum_probs=17.2
Q ss_pred HHHhhhcc--CCCCccCHHHHHHHHHH
Q 013795 404 FHNFLQSF--DPSKAITSDDVHQIFEN 428 (436)
Q Consensus 404 L~eFLk~F--e~gkVVTeEDIk~FFe~ 428 (436)
|+..|+.| ..+..|+..++..++..
T Consensus 2 ~~~~f~~~d~~~~g~i~~~e~~~~~~~ 28 (29)
T smart00054 2 LKEAFRLFDKDGDGKIDFEEFKDLLKA 28 (29)
T ss_pred HHHHHHHHCCCCCCcEeHHHHHHHHHh
Confidence 45566666 44457999988888764
No 60
>PF14048 MBD_C: C-terminal domain of methyl-CpG binding protein 2 and 3; PDB: 2L2L_B.
Probab=20.51 E-value=75 Score=27.31 Aligned_cols=29 Identities=21% Similarity=0.252 Sum_probs=13.7
Q ss_pred hhhccCCCCccCHHHHHHHHHHHHHhhhc
Q 013795 407 FLQSFDPSKAITSDDVHQIFENLAKKRRR 435 (436)
Q Consensus 407 FLk~Fe~gkVVTeEDIk~FFe~L~~~~r~ 435 (436)
-.+|+=..-+||++||+.==++.++.|+|
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
No 61
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=20.28 E-value=24 Score=43.20 Aligned_cols=53 Identities=25% Similarity=0.524 Sum_probs=39.2
Q ss_pred cceEE-eeCCCCCCCCcccccceeecccccccccCCCCCCCCCCCCCCCCCCCCccCeeecCCcccCCc
Q 013795 141 KGVYC-TCNRPYPDPDVEEQVEMIQCCICEDWFHEEHIGLEPSDEIPRDDEGEPVYEDFICKACSAVCS 208 (436)
Q Consensus 141 ~g~yC-~C~rpYpDp~~e~~~~MiQC~~CEDWfH~~Cl~~~~~~~~p~~~~~e~~~~~fIC~~C~~~~p 208 (436)
....| +|++.- + ...|+-|+.|..|||.-|+...-. ..| +..|.|+.|.....
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 35567 788774 2 368999999999999999865322 222 56799999987663
No 62
>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=20.09 E-value=2e+02 Score=24.28 Aligned_cols=35 Identities=14% Similarity=0.222 Sum_probs=30.1
Q ss_pred HHHHHHHHHHHHHhhhcc--CCCCccCHHHHHHHHHH
Q 013795 394 LNGIADMKDEFHNFLQSF--DPSKAITSDDVHQIFEN 428 (436)
Q Consensus 394 l~gYn~mKdkL~eFLk~F--e~gkVVTeEDIk~FFe~ 428 (436)
+-++|.+-.++.+.-+.+ -.-|.||.|=|++|-++
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 457888999999999988 88899999999999764
Done!