Query psy3924
Match_columns 131
No_of_seqs 147 out of 1056
Neff 7.3
Searched_HMMs 46136
Date Fri Aug 16 20:51:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3924.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3924hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1244|consensus 99.6 8.4E-17 1.8E-21 124.2 0.4 76 6-84 254-329 (336)
2 KOG4443|consensus 99.5 2.9E-15 6.3E-20 126.5 2.7 117 6-127 43-161 (694)
3 KOG1512|consensus 99.4 3.1E-14 6.8E-19 110.9 1.1 71 6-81 287-357 (381)
4 KOG1244|consensus 99.0 3.9E-11 8.6E-16 93.0 -0.1 77 46-124 241-335 (336)
5 PF00628 PHD: PHD-finger; Int 99.0 5.7E-11 1.2E-15 70.3 -0.6 48 38-85 1-50 (51)
6 smart00249 PHD PHD zinc finger 98.8 6.4E-09 1.4E-13 59.4 3.7 46 38-83 1-47 (47)
7 KOG0825|consensus 98.7 7.2E-09 1.6E-13 89.9 2.0 48 38-85 217-265 (1134)
8 KOG0383|consensus 98.6 3.4E-08 7.4E-13 85.5 2.8 69 6-83 4-91 (696)
9 KOG4299|consensus 98.5 3E-08 6.4E-13 84.1 1.7 49 37-85 254-304 (613)
10 cd04718 BAH_plant_2 BAH, or Br 98.3 3E-07 6.5E-12 66.0 2.4 26 60-85 1-26 (148)
11 KOG4443|consensus 98.3 1.9E-07 4.1E-12 79.8 0.5 97 30-128 12-125 (694)
12 KOG0957|consensus 97.9 3.3E-06 7.2E-11 70.7 1.2 47 38-84 546-596 (707)
13 KOG1973|consensus 97.8 9.7E-06 2.1E-10 63.6 1.5 37 47-85 228-267 (274)
14 KOG1245|consensus 97.7 4.7E-06 1E-10 77.3 -0.8 48 38-85 1110-1157(1404)
15 KOG0955|consensus 97.6 6.7E-05 1.5E-09 67.9 4.0 47 37-85 220-268 (1051)
16 cd04718 BAH_plant_2 BAH, or Br 97.6 4.2E-05 9.1E-10 55.0 2.1 26 7-38 1-26 (148)
17 KOG0954|consensus 97.4 9.4E-05 2E-09 64.5 1.9 52 37-90 272-330 (893)
18 COG5141 PHD zinc finger-contai 97.3 9.5E-05 2.1E-09 62.0 1.8 54 36-91 193-255 (669)
19 KOG1512|consensus 97.3 9.2E-05 2E-09 58.4 1.3 63 47-113 275-354 (381)
20 PF13831 PHD_2: PHD-finger; PD 97.2 2.6E-05 5.5E-10 43.2 -1.9 34 49-84 2-36 (36)
21 KOG4323|consensus 97.1 0.00025 5.4E-09 59.2 2.3 47 39-85 171-223 (464)
22 KOG0956|consensus 97.0 0.00038 8.2E-09 60.5 2.1 51 39-91 8-70 (900)
23 COG5034 TNG2 Chromatin remodel 96.9 0.00042 9E-09 53.8 1.8 42 41-85 225-269 (271)
24 PF00628 PHD: PHD-finger; Int 96.1 0.0014 3E-08 38.2 -0.0 29 6-38 22-50 (51)
25 KOG0825|consensus 95.5 0.0062 1.3E-07 54.0 1.5 30 2-37 235-264 (1134)
26 KOG0383|consensus 95.3 0.011 2.3E-07 52.0 2.2 53 56-109 1-84 (696)
27 PF15446 zf-PHD-like: PHD/FYVE 95.0 0.054 1.2E-06 39.8 4.7 32 39-70 2-36 (175)
28 KOG4299|consensus 94.0 0.021 4.5E-07 49.3 0.9 28 6-37 276-303 (613)
29 KOG1473|consensus 93.9 0.037 8E-07 50.8 2.3 50 39-91 347-396 (1414)
30 PF14446 Prok-RING_1: Prokaryo 93.8 0.027 5.9E-07 33.8 0.9 31 38-68 7-38 (54)
31 PF15446 zf-PHD-like: PHD/FYVE 93.4 0.073 1.6E-06 39.1 2.6 20 50-69 123-142 (175)
32 KOG0956|consensus 93.3 0.035 7.6E-07 48.7 1.0 30 39-68 120-156 (900)
33 smart00249 PHD PHD zinc finger 92.5 0.078 1.7E-06 29.3 1.4 26 6-36 22-47 (47)
34 PF12861 zf-Apc11: Anaphase-pr 92.1 0.038 8.2E-07 36.2 -0.2 52 32-85 23-79 (85)
35 KOG0957|consensus 91.2 0.27 5.9E-06 42.0 3.8 60 27-91 115-190 (707)
36 KOG1246|consensus 91.1 0.21 4.5E-06 45.3 3.3 47 38-85 157-203 (904)
37 KOG1473|consensus 87.1 0.1 2.2E-06 48.1 -1.6 70 7-85 365-478 (1414)
38 PF13901 DUF4206: Domain of un 86.7 0.45 9.8E-06 35.7 1.9 45 32-85 144-197 (202)
39 KOG0955|consensus 86.3 0.36 7.7E-06 44.5 1.4 24 6-37 244-267 (1051)
40 PF13832 zf-HC5HC2H_2: PHD-zin 86.2 0.37 8E-06 32.3 1.1 29 37-67 56-86 (110)
41 PF07649 C1_3: C1-like domain; 83.8 0.32 7E-06 25.2 -0.0 28 38-65 2-29 (30)
42 PF00641 zf-RanBP: Zn-finger i 82.8 1.1 2.5E-05 23.0 1.9 17 75-91 2-26 (30)
43 COG5141 PHD zinc finger-contai 81.3 0.54 1.2E-05 40.1 0.3 24 6-37 218-241 (669)
44 KOG1245|consensus 79.0 0.61 1.3E-05 44.4 -0.1 27 6-38 1131-1157(1404)
45 PF13639 zf-RING_2: Ring finge 78.5 0.049 1.1E-06 30.7 -4.8 42 38-83 2-43 (44)
46 PF11793 FANCL_C: FANCL C-term 74.8 1.7 3.7E-05 27.1 1.2 47 39-85 5-63 (70)
47 PF13771 zf-HC5HC2H: PHD-like 73.8 1.8 3.9E-05 27.7 1.1 30 37-68 37-68 (90)
48 PF00130 C1_1: Phorbol esters/ 70.5 3.7 8E-05 23.6 1.8 30 38-67 13-44 (53)
49 smart00547 ZnF_RBZ Zinc finger 65.9 4.2 9.1E-05 20.0 1.2 9 76-84 1-9 (26)
50 KOG4628|consensus 63.7 4.6 9.9E-05 33.0 1.7 46 37-85 230-275 (348)
51 PF12773 DZR: Double zinc ribb 62.3 7.5 0.00016 22.1 2.0 10 50-59 11-20 (50)
52 PF03107 C1_2: C1 domain; Int 60.9 8.8 0.00019 19.8 2.0 28 39-66 3-30 (30)
53 cd00029 C1 Protein kinase C co 54.4 6.8 0.00015 21.8 0.9 30 38-67 13-44 (50)
54 KOG3612|consensus 50.6 20 0.00043 31.1 3.4 51 27-86 57-108 (588)
55 KOG1311|consensus 48.3 22 0.00047 27.9 3.2 48 49-115 111-158 (299)
56 cd00162 RING RING-finger (Real 48.0 3.2 6.9E-05 22.0 -1.2 41 39-84 2-42 (45)
57 PF05191 ADK_lid: Adenylate ki 47.3 15 0.00032 20.0 1.5 15 52-66 2-16 (36)
58 PF12678 zf-rbx1: RING-H2 zinc 47.1 2.8 6.1E-05 26.2 -1.6 30 51-84 44-73 (73)
59 smart00109 C1 Protein kinase C 46.7 6.7 0.00015 21.6 0.1 30 38-67 13-43 (49)
60 PF08746 zf-RING-like: RING-li 45.3 3.9 8.5E-05 23.1 -1.1 41 39-83 1-43 (43)
61 PF00301 Rubredoxin: Rubredoxi 45.1 9.2 0.0002 22.1 0.5 11 28-38 32-42 (47)
62 PF10497 zf-4CXXC_R1: Zinc-fin 44.0 9.3 0.0002 25.8 0.4 12 73-84 57-68 (105)
63 PF10080 DUF2318: Predicted me 43.0 12 0.00027 25.2 0.9 28 38-65 37-66 (102)
64 KOG0954|consensus 42.2 10 0.00022 34.1 0.5 28 39-68 383-412 (893)
65 PF07227 DUF1423: Protein of u 38.5 23 0.0005 29.9 2.0 56 28-84 121-190 (446)
66 KOG2272|consensus 35.9 16 0.00035 28.9 0.7 55 6-61 160-231 (332)
67 PF10367 Vps39_2: Vacuolar sor 35.2 30 0.00065 22.3 1.9 29 38-67 80-108 (109)
68 KOG1632|consensus 34.8 25 0.00055 28.6 1.7 36 50-85 74-112 (345)
69 COG1773 Rubredoxin [Energy pro 34.3 32 0.0007 20.6 1.7 11 28-38 34-44 (55)
70 KOG1829|consensus 32.2 10 0.00022 33.1 -1.0 46 33-85 504-558 (580)
71 cd00730 rubredoxin Rubredoxin; 31.9 26 0.00057 20.4 1.0 11 27-37 31-41 (50)
72 PF14787 zf-CCHC_5: GAG-polypr 31.7 25 0.00055 19.2 0.8 12 53-64 4-15 (36)
73 cd00350 rubredoxin_like Rubred 31.3 39 0.00084 17.6 1.5 10 76-85 16-25 (33)
74 KOG3362|consensus 30.4 27 0.00058 25.2 1.0 37 6-61 103-139 (156)
75 COG0143 MetG Methionyl-tRNA sy 29.4 31 0.00067 30.1 1.4 40 28-69 124-173 (558)
76 KOG4198|consensus 28.5 39 0.00084 26.9 1.7 21 26-46 136-164 (280)
77 KOG1701|consensus 28.1 50 0.0011 28.0 2.4 30 38-67 396-429 (468)
78 PF13240 zinc_ribbon_2: zinc-r 28.1 43 0.00094 16.2 1.3 11 49-59 11-21 (23)
79 PF07496 zf-CW: CW-type Zinc F 27.2 32 0.0007 19.8 0.8 31 51-82 3-34 (50)
80 PRK14559 putative protein seri 26.5 81 0.0018 28.0 3.5 14 48-61 12-25 (645)
81 KOG1493|consensus 26.4 4.5 9.8E-05 26.1 -3.1 45 39-85 34-78 (84)
82 PF04810 zf-Sec23_Sec24: Sec23 26.4 36 0.00077 18.6 0.9 31 51-85 2-32 (40)
83 smart00184 RING Ring finger. E 25.5 9.2 0.0002 19.3 -1.7 16 53-68 12-27 (39)
84 PF09297 zf-NADH-PPase: NADH p 24.7 70 0.0015 16.4 1.8 22 38-59 5-29 (32)
85 PF00412 LIM: LIM domain; Int 22.4 56 0.0012 18.5 1.3 12 80-91 23-34 (58)
86 PF13248 zf-ribbon_3: zinc-rib 20.4 64 0.0014 15.8 1.1 9 50-58 15-23 (26)
No 1
>KOG1244|consensus
Probab=99.61 E-value=8.4e-17 Score=124.21 Aligned_cols=76 Identities=29% Similarity=0.937 Sum_probs=67.8
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCcccccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCC
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCTVCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCA 84 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~ 84 (131)
.+-|++||+-... ++..++.+.|+|.+|+.|.+|+-.++.++||+||.|+++|||+||.||+...|+|.|.|.-|.
T Consensus 254 rsghpsclqft~n---m~~avk~yrwqcieck~csicgtsenddqllfcddcdrgyhmyclsppm~eppegswsc~KOG 329 (336)
T KOG1244|consen 254 RSGHPSCLQFTAN---MIAAVKTYRWQCIECKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPPEGSWSCHLCL 329 (336)
T ss_pred CCCCcchhhhhHH---HHHHHHhheeeeeecceeccccCcCCCceeEeecccCCceeeEecCCCcCCCCCCchhHHHHH
Confidence 4679999986654 344567899999999999999999999999999999999999999999999999999998774
No 2
>KOG4443|consensus
Probab=99.53 E-value=2.9e-15 Score=126.46 Aligned_cols=117 Identities=33% Similarity=0.748 Sum_probs=96.9
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCcccccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCTVCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
.-||.+|+...+.. +.....|+|+.|++|..|+..+++..+++|+.|+.+||.+|..|++..++.++|+|+.|..
T Consensus 43 ~~yH~~cvt~~~~~-----~~l~~gWrC~~crvCe~c~~~gD~~kf~~Ck~cDvsyh~yc~~P~~~~v~sg~~~ckk~~~ 117 (694)
T KOG4443|consen 43 QKYHPYCVTSWAQH-----AVLSGGWRCPSCRVCEACGTTGDPKKFLLCKRCDVSYHCYCQKPPNDKVPSGPWLCKKCTR 117 (694)
T ss_pred ccCCcchhhHHHhH-----HHhcCCcccCCceeeeeccccCCcccccccccccccccccccCCccccccCcccccHHHHh
Confidence 56999999876433 3334579999999999999999999999999999999999999999999999999999999
Q ss_pred cccCCCcccccccCCC--CCCCccccCCCCcccccchhhhhhHh
Q psy3924 86 CLTCGATGYHIYCTDP--PLDHIIFVQDKIRPKRLTTYKADAAT 127 (131)
Q Consensus 86 c~~Cg~~~~~~~c~~p--pl~~~~~~~~~~~~~~~~~~~~~~~~ 127 (131)
|+.|+....+...--+ -+...+++.+.++|++.+.|++++..
T Consensus 118 c~qc~~~lpg~s~~~~~~~~~~~~c~s~~~cPvc~~~Y~~~e~~ 161 (694)
T KOG4443|consen 118 CRQCDSTLPGLSLDLQEGYLQCAPCASLSYCPVCLIVYQDSESL 161 (694)
T ss_pred hhhccccccccchhhhccCcccccccccccCchHHHhhhhccch
Confidence 9999865554211111 23456778899999999999998764
No 3
>KOG1512|consensus
Probab=99.42 E-value=3.1e-14 Score=110.86 Aligned_cols=71 Identities=27% Similarity=0.644 Sum_probs=64.4
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCcccccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeecc
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCTVCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCK 81 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~ 81 (131)
+++|++|+++..+.+. .+.-+.|.|.+|+.|.+|++...++++++||.|+++||.+|+. |..+|.|.|+|.
T Consensus 287 ~~~HP~Ci~M~~elv~---~~KTY~W~C~~C~lC~IC~~P~~E~E~~FCD~CDRG~HT~CVG--L~~lP~G~WICD 357 (381)
T KOG1512|consen 287 TRPHPYCVAMIPELVG---QYKTYFWKCSSCELCRICLGPVIESEHLFCDVCDRGPHTLCVG--LQDLPRGEWICD 357 (381)
T ss_pred cCCCCcchhcCHHHHh---HHhhcchhhcccHhhhccCCcccchheeccccccCCCCccccc--cccccCccchhh
Confidence 6899999998876443 3468899999999999999999899999999999999999995 999999999997
No 4
>KOG1244|consensus
Probab=99.02 E-value=3.9e-11 Score=93.01 Aligned_cols=77 Identities=27% Similarity=0.588 Sum_probs=64.6
Q ss_pred CCCCCceeeCcCCCcccCCCCCCCC---CCCCCCCeeccCCCccccCCC--------------cccccccCCCCCCCccc
Q psy3924 46 HDEGRLILCDECDISYHIYCTDPPL---DHIPRGTWKCKWCAQCLTCGA--------------TGYHIYCTDPPLDHIIF 108 (131)
Q Consensus 46 ~~~~~ll~Cd~C~~~~H~~Cl~p~l---~~~p~~~W~C~~C~~c~~Cg~--------------~~~~~~c~~ppl~~~~~ 108 (131)
+-+++||.|..|+++-|++||+=.. ..+....|.|.+|+.|..||+ +.||+|||.|||-+.|
T Consensus 241 ~~peelvscsdcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsenddqllfcddcdrgyhmyclsppm~epp- 319 (336)
T KOG1244|consen 241 GMPEELVSCSDCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSENDDQLLFCDDCDRGYHMYCLSPPMVEPP- 319 (336)
T ss_pred CCchhhcchhhcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCCceeEeecccCCceeeEecCCCcCCCC-
Confidence 3478999999999999999998322 245667999999998888876 3699999999999999
Q ss_pred cCCCCcc-cccchhhhh
Q psy3924 109 VQDKIRP-KRLTTYKAD 124 (131)
Q Consensus 109 ~~~~~~~-~~~~~~~~~ 124 (131)
.|.|.. +|+..++++
T Consensus 320 -egswsc~KOG~~~~e~ 335 (336)
T KOG1244|consen 320 -EGSWSCHLCLEELKEK 335 (336)
T ss_pred -CCchhHHHHHHHHhhc
Confidence 999987 688877765
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=98.98 E-value=5.7e-11 Score=70.35 Aligned_cols=48 Identities=42% Similarity=1.020 Sum_probs=40.5
Q ss_pred ccccccccCCCCCceeeCcCCCcccCCCCCCCCC--CCCCCCeeccCCCc
Q psy3924 38 VCEGCAQRHDEGRLILCDECDISYHIYCTDPPLD--HIPRGTWKCKWCAQ 85 (131)
Q Consensus 38 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~--~~p~~~W~C~~C~~ 85 (131)
+|.+|++.++.+.+|.|+.|++.||+.|+++++. ..+.+.|+|+.|..
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRP 50 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcC
Confidence 4778888888999999999999999999998876 34445899998864
No 6
>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 KOG0825|consensus
Probab=98.68 E-value=7.2e-09 Score=89.86 Aligned_cols=48 Identities=40% Similarity=1.006 Sum_probs=45.3
Q ss_pred ccccccccCCCCCceeeCcCCCc-ccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 38 VCEGCAQRHDEGRLILCDECDIS-YHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 38 ~C~~C~~~~~~~~ll~Cd~C~~~-~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
.|.+|...+.++.||+||.|+.+ ||++||+|++.++|-++|+|+.|..
T Consensus 217 ~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDPdl~eiP~~eWYC~NC~d 265 (1134)
T KOG0825|consen 217 KCDICTVHDPEDVLLLCDSCNKVYYHVYCLDPDLSESPVNEWYCTNCSL 265 (1134)
T ss_pred cceeeccCChHHhheeecccccceeeccccCcccccccccceecCcchh
Confidence 48999999889999999999999 9999999999999999999999983
No 8
>KOG0383|consensus
Probab=98.56 E-value=3.4e-08 Score=85.52 Aligned_cols=69 Identities=41% Similarity=0.912 Sum_probs=60.3
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCc-------------------ccccccccCCCCCceeeCcCCCcccCCCC
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCT-------------------VCEGCAQRHDEGRLILCDECDISYHIYCT 66 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~-------------------~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl 66 (131)
.+||..|+++.+..-+ ..+|.|+.|. .|.+|+. ++.+|+|+.|..+||.+|+
T Consensus 4 r~~~~~~~~p~~~~~~------~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~---~g~~l~c~tC~~s~h~~cl 74 (696)
T KOG0383|consen 4 RAYHRVCLDPKLKEEP------EMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICAD---GGELLWCDTCPASFHASCL 74 (696)
T ss_pred cccCcCCCCcccccCC------cCCccCcchhhcccccccccCCcchhhhhhhhhhcC---CCcEEEeccccHHHHHHcc
Confidence 4799999998876554 4499999886 3778875 8999999999999999999
Q ss_pred CCCCCCCCCCCeeccCC
Q psy3924 67 DPPLDHIPRGTWKCKWC 83 (131)
Q Consensus 67 ~p~l~~~p~~~W~C~~C 83 (131)
++++...|.+.|.|+.|
T Consensus 75 ~~pl~~~p~~~~~c~Rc 91 (696)
T KOG0383|consen 75 GPPLTPQPNGEFICPRC 91 (696)
T ss_pred CCCCCcCCccceeeeee
Confidence 99999999999999988
No 9
>KOG4299|consensus
Probab=98.53 E-value=3e-08 Score=84.14 Aligned_cols=49 Identities=37% Similarity=0.906 Sum_probs=43.1
Q ss_pred cccccccccCCCCCceeeCcCCCcccCCCCCCCC--CCCCCCCeeccCCCc
Q psy3924 37 TVCEGCAQRHDEGRLILCDECDISYHIYCTDPPL--DHIPRGTWKCKWCAQ 85 (131)
Q Consensus 37 ~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l--~~~p~~~W~C~~C~~ 85 (131)
++|..|++.+.-..+++||+|+++||+.||+||+ ..+|.|.|+|++|..
T Consensus 254 ~fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~ 304 (613)
T KOG4299|consen 254 DFCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKI 304 (613)
T ss_pred HHHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCee
Confidence 3799999976666779999999999999999995 468999999999984
No 10
>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=98.32 E-value=3e-07 Score=65.95 Aligned_cols=26 Identities=38% Similarity=1.256 Sum_probs=25.0
Q ss_pred cccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 60 SYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 60 ~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
+||++||+|||..+|+|+|+|+.|..
T Consensus 1 g~H~~CL~Ppl~~~P~g~W~Cp~C~~ 26 (148)
T cd04718 1 GFHLCCLRPPLKEVPEGDWICPFCEV 26 (148)
T ss_pred CcccccCCCCCCCCCCCCcCCCCCcC
Confidence 69999999999999999999999986
No 11
>KOG4443|consensus
Probab=98.27 E-value=1.9e-07 Score=79.75 Aligned_cols=97 Identities=32% Similarity=0.748 Sum_probs=73.6
Q ss_pred CccCccCcccccccccCC--CCCceeeCcCCCcccCCCCCCCCCCC-CCCCeeccCCCccccCCC--------------c
Q psy3924 30 GWRCLDCTVCEGCAQRHD--EGRLILCDECDISYHIYCTDPPLDHI-PRGTWKCKWCAQCLTCGA--------------T 92 (131)
Q Consensus 30 ~W~C~~C~~C~~C~~~~~--~~~ll~Cd~C~~~~H~~Cl~p~l~~~-p~~~W~C~~C~~c~~Cg~--------------~ 92 (131)
+-.+.-|..|.+|...+. .+.|+.|..|...||.+|+..-+... -.+.|.|+.|+.|+.||+ .
T Consensus 12 ~~~~~~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~gD~~kf~~Ck~cDv 91 (694)
T KOG4443|consen 12 DKAIIVCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTGDPKKFLLCKRCDV 91 (694)
T ss_pred chhhhhhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccCCcccccccccccc
Confidence 445667778888887654 68899999999999999997554443 234599999999988873 3
Q ss_pred ccccccCCCCCCCccccCCCCcccccchhhhhhHhh
Q psy3924 93 GYHIYCTDPPLDHIIFVQDKIRPKRLTTYKADAATL 128 (131)
Q Consensus 93 ~~~~~c~~ppl~~~~~~~~~~~~~~~~~~~~~~~~~ 128 (131)
+||.||..|++..|+ .|.|...+...-+..+..+
T Consensus 92 syh~yc~~P~~~~v~--sg~~~ckk~~~c~qc~~~l 125 (694)
T KOG4443|consen 92 SYHCYCQKPPNDKVP--SGPWLCKKCTRCRQCDSTL 125 (694)
T ss_pred cccccccCCcccccc--CcccccHHHHhhhhccccc
Confidence 799999999999999 7777776555444443333
No 12
>KOG0957|consensus
Probab=97.92 E-value=3.3e-06 Score=70.69 Aligned_cols=47 Identities=36% Similarity=0.997 Sum_probs=42.9
Q ss_pred ccccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCC----CeeccCCC
Q psy3924 38 VCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRG----TWKCKWCA 84 (131)
Q Consensus 38 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~----~W~C~~C~ 84 (131)
.|.+|++..+...+++||.|...||+-||+|||+..|+. .|.|.+|.
T Consensus 546 sCgiCkks~dQHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 546 SCGICKKSTDQHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred eeeeeccchhhHHHhhcchhhceeeccccCCccccCcccccCcceeecccc
Confidence 588999988899999999999999999999999998875 59999994
No 13
>KOG1973|consensus
Probab=97.77 E-value=9.7e-06 Score=63.65 Aligned_cols=37 Identities=35% Similarity=0.942 Sum_probs=33.8
Q ss_pred CCCCceeeCc--CC-CcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 47 DEGRLILCDE--CD-ISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 47 ~~~~ll~Cd~--C~-~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
..+.|+-||. |+ .+||+.|++ |...|.|.|||+.|+.
T Consensus 228 syg~Mi~CDn~~C~~eWFH~~CVG--L~~~PkgkWyC~~C~~ 267 (274)
T KOG1973|consen 228 SYGKMIGCDNPGCPIEWFHFTCVG--LKTKPKGKWYCPRCKA 267 (274)
T ss_pred ccccccccCCCCCCcceEEEeccc--cccCCCCcccchhhhh
Confidence 4899999997 99 999999996 8899999999999975
No 14
>KOG1245|consensus
Probab=97.74 E-value=4.7e-06 Score=77.26 Aligned_cols=48 Identities=33% Similarity=1.097 Sum_probs=45.0
Q ss_pred ccccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 38 VCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 38 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
.|.+|++.+....|++|+.|..+||++|+.|.+..++.++|+|+.|+.
T Consensus 1110 ~c~~cr~k~~~~~m~lc~~c~~~~h~~C~rp~~~~~~~~dW~C~~c~~ 1157 (1404)
T KOG1245|consen 1110 LCKVCRRKKQDEKMLLCDECLSGFHLFCLRPALSSVPPGDWMCPSCRK 1157 (1404)
T ss_pred hhhhhhhcccchhhhhhHhhhhhHHHHhhhhhhccCCcCCccCCccch
Confidence 488899888889999999999999999999999999999999999984
No 15
>KOG0955|consensus
Probab=97.57 E-value=6.7e-05 Score=67.87 Aligned_cols=47 Identities=32% Similarity=0.873 Sum_probs=40.3
Q ss_pred cccccccccCC--CCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 37 TVCEGCAQRHD--EGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 37 ~~C~~C~~~~~--~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
.+|.+|....- .+.+|+||.|+.++|++|++ ...+|+|.|.|..|.+
T Consensus 220 ~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cyg--i~~ipeg~WlCr~Cl~ 268 (1051)
T KOG0955|consen 220 AVCCICLDGECQNSNVIVFCDGCNLAVHQECYG--IPFIPEGQWLCRRCLQ 268 (1051)
T ss_pred ccceeecccccCCCceEEEcCCCcchhhhhccC--CCCCCCCcEeehhhcc
Confidence 57888887654 48999999999999999998 5568999999999974
No 16
>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=97.57 E-value=4.2e-05 Score=54.96 Aligned_cols=26 Identities=27% Similarity=0.699 Sum_probs=23.3
Q ss_pred eeccccCCCCCCCCCccccccCCCccCccCcc
Q psy3924 7 AYGSVCRDVKLHDLPISKVILSKGWRCLDCTV 38 (131)
Q Consensus 7 ~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~~ 38 (131)
.||++||+|++..+|++ +|.||.|..
T Consensus 1 g~H~~CL~Ppl~~~P~g------~W~Cp~C~~ 26 (148)
T cd04718 1 GFHLCCLRPPLKEVPEG------DWICPFCEV 26 (148)
T ss_pred CcccccCCCCCCCCCCC------CcCCCCCcC
Confidence 49999999999999887 999999954
No 17
>KOG0954|consensus
Probab=97.35 E-value=9.4e-05 Score=64.46 Aligned_cols=52 Identities=31% Similarity=1.006 Sum_probs=43.2
Q ss_pred cccccccccC--CCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCC-----ccccCC
Q psy3924 37 TVCEGCAQRH--DEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCA-----QCLTCG 90 (131)
Q Consensus 37 ~~C~~C~~~~--~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~-----~c~~Cg 90 (131)
..|.+|+..+ ..++||+||.|....|+.|+. +.++|.+.|.|..|. .|.-|+
T Consensus 272 viCDvCrspD~e~~neMVfCd~Cn~cVHqaCyG--Ile~p~gpWlCr~Calg~~ppCvLCP 330 (893)
T KOG0954|consen 272 VICDVCRSPDSEEANEMVFCDKCNICVHQACYG--ILEVPEGPWLCRTCALGIEPPCVLCP 330 (893)
T ss_pred ceeceecCCCccccceeEEeccchhHHHHhhhc--eeecCCCCeeehhccccCCCCeeecc
Confidence 3577777753 368999999999999999995 889999999999997 366664
No 18
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=97.34 E-value=9.5e-05 Score=62.03 Aligned_cols=54 Identities=30% Similarity=0.936 Sum_probs=43.5
Q ss_pred CcccccccccC--CCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc-------cccCCC
Q psy3924 36 CTVCEGCAQRH--DEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ-------CLTCGA 91 (131)
Q Consensus 36 C~~C~~C~~~~--~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~-------c~~Cg~ 91 (131)
++.|.+|.++. +.+.+++||+|+.+.|..|++ +.-+|+|.|+|..|.. |..|++
T Consensus 193 d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYG--I~f~peG~WlCrkCi~~~~~i~~C~fCps 255 (669)
T COG5141 193 DDICTKCTSTHNENSNAIVFCDGCEICVHQSCYG--IQFLPEGFWLCRKCIYGEYQIRCCSFCPS 255 (669)
T ss_pred hhhhHhccccccCCcceEEEecCcchhhhhhccc--ceecCcchhhhhhhcccccceeEEEeccC
Confidence 45566666654 368899999999999999996 6788999999999972 677754
No 19
>KOG1512|consensus
Probab=97.31 E-value=9.2e-05 Score=58.43 Aligned_cols=63 Identities=25% Similarity=0.586 Sum_probs=45.9
Q ss_pred CCCCceeeCcCCCcccCCCCCCCCC---CCCCCCeeccCCCccccCCC--------------cccccccCCCCCCCcccc
Q psy3924 47 DEGRLILCDECDISYHIYCTDPPLD---HIPRGTWKCKWCAQCLTCGA--------------TGYHIYCTDPPLDHIIFV 109 (131)
Q Consensus 47 ~~~~ll~Cd~C~~~~H~~Cl~p~l~---~~p~~~W~C~~C~~c~~Cg~--------------~~~~~~c~~ppl~~~~~~ 109 (131)
..+.++.|..|..++|++|+.-+.. .+....|.|..|+.|..|+. ++||.+| -.|..+|
T Consensus 275 r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~E~E~~FCD~CDRG~HT~C--VGL~~lP-- 350 (381)
T KOG1512|consen 275 RRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVIESEHLFCDVCDRGPHTLC--VGLQDLP-- 350 (381)
T ss_pred hhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCcccchheeccccccCCCCccc--ccccccc--
Confidence 4578999999999999999974432 24557899999985544432 4678777 4556777
Q ss_pred CCCC
Q psy3924 110 QDKI 113 (131)
Q Consensus 110 ~~~~ 113 (131)
+|.|
T Consensus 351 ~G~W 354 (381)
T KOG1512|consen 351 RGEW 354 (381)
T ss_pred Cccc
Confidence 5555
No 20
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=97.22 E-value=2.6e-05 Score=43.20 Aligned_cols=34 Identities=32% Similarity=1.056 Sum_probs=19.2
Q ss_pred CCceeeCcCCCcccCCCCCCCCCCCCCC-CeeccCCC
Q psy3924 49 GRLILCDECDISYHIYCTDPPLDHIPRG-TWKCKWCA 84 (131)
Q Consensus 49 ~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~-~W~C~~C~ 84 (131)
+.||.|++|....|.+|+. +..++.+ +|+|..|+
T Consensus 2 n~ll~C~~C~v~VH~~CYG--v~~~~~~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYG--VSEVPDGDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT---SS--SS-----HHH-
T ss_pred CceEEeCCCCCcCChhhCC--cccCCCCCcEECCcCC
Confidence 5789999999999999996 5555555 79998763
No 21
>KOG4323|consensus
Probab=97.15 E-value=0.00025 Score=59.21 Aligned_cols=47 Identities=30% Similarity=0.752 Sum_probs=37.4
Q ss_pred ccccc--ccCCCCCceeeCcCCCcccCCCCCCCCCC----CCCCCeeccCCCc
Q psy3924 39 CEGCA--QRHDEGRLILCDECDISYHIYCTDPPLDH----IPRGTWKCKWCAQ 85 (131)
Q Consensus 39 C~~C~--~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~----~p~~~W~C~~C~~ 85 (131)
|-+|. +.+....||+|++|...||..|.+|.++. .+...|+|..|..
T Consensus 171 c~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~ 223 (464)
T KOG4323|consen 171 CSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNR 223 (464)
T ss_pred eeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhcc
Confidence 55544 44566799999999999999999987653 3567899999974
No 22
>KOG0956|consensus
Probab=96.99 E-value=0.00038 Score=60.46 Aligned_cols=51 Identities=31% Similarity=0.920 Sum_probs=41.1
Q ss_pred ccccccc-C-CCCCceeeC--cCCCcccCCCCCCCCCCCCCCCeeccCCC--------ccccCCC
Q psy3924 39 CEGCAQR-H-DEGRLILCD--ECDISYHIYCTDPPLDHIPRGTWKCKWCA--------QCLTCGA 91 (131)
Q Consensus 39 C~~C~~~-~-~~~~ll~Cd--~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~--------~c~~Cg~ 91 (131)
|-||... + .+..||.|| .|.-+.|..|+. +..+|.|+|||.+|. .|+.|+.
T Consensus 8 CCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYG--IvqVPtGpWfCrKCesqeraarvrCeLCP~ 70 (900)
T KOG0956|consen 8 CCVCSDERGWAENPLVYCDGHNCSVAVHQACYG--IVQVPTGPWFCRKCESQERAARVRCELCPH 70 (900)
T ss_pred eeeecCcCCCccCceeeecCCCceeeeehhcce--eEecCCCchhhhhhhhhhhhccceeecccC
Confidence 4455532 2 268999998 899999999995 889999999999996 5788864
No 23
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=96.95 E-value=0.00042 Score=53.75 Aligned_cols=42 Identities=33% Similarity=0.906 Sum_probs=33.8
Q ss_pred cccccCCCCCceeeC--cCCC-cccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 41 GCAQRHDEGRLILCD--ECDI-SYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 41 ~C~~~~~~~~ll~Cd--~C~~-~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
.|++ ..-|+||-|| .|.+ +||+.|++ |...|+|.|+|+.|+.
T Consensus 225 fCqq-vSyGqMVaCDn~nCkrEWFH~~CVG--Lk~pPKG~WYC~eCk~ 269 (271)
T COG5034 225 FCQQ-VSYGQMVACDNANCKREWFHLECVG--LKEPPKGKWYCPECKK 269 (271)
T ss_pred Eecc-cccccceecCCCCCchhheeccccc--cCCCCCCcEeCHHhHh
Confidence 3554 2368999998 6775 59999995 8899999999999973
No 24
>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=96.12 E-value=0.0014 Score=38.21 Aligned_cols=29 Identities=24% Similarity=0.418 Sum_probs=21.3
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCcc
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCTV 38 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~~ 38 (131)
..||..|++++..... +....|.|+.|+.
T Consensus 22 ~~~H~~C~~~~~~~~~----~~~~~w~C~~C~~ 50 (51)
T PF00628_consen 22 RWYHQECVGPPEKAEE----IPSGDWYCPNCRP 50 (51)
T ss_dssp CEEETTTSTSSHSHHS----HHSSSBSSHHHHH
T ss_pred hhhCcccCCCChhhcc----CCCCcEECcCCcC
Confidence 7999999999864222 2234999999864
No 25
>KOG0825|consensus
Probab=95.54 E-value=0.0062 Score=53.98 Aligned_cols=30 Identities=30% Similarity=0.930 Sum_probs=26.3
Q ss_pred CccceeeccccCCCCCCCCCccccccCCCccCccCc
Q psy3924 2 NCDVIAYGSVCRDVKLHDLPISKVILSKGWRCLDCT 37 (131)
Q Consensus 2 ~~~~~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~ 37 (131)
.||..-||.+||+|++.++|+. .|+|++|.
T Consensus 235 sCN~~~YH~YCLDPdl~eiP~~------eWYC~NC~ 264 (1134)
T KOG0825|consen 235 SCNKVYYHVYCLDPDLSESPVN------EWYCTNCS 264 (1134)
T ss_pred ccccceeeccccCccccccccc------ceecCcch
Confidence 3777889999999999888877 99999996
No 26
>KOG0383|consensus
Probab=95.30 E-value=0.011 Score=52.01 Aligned_cols=53 Identities=36% Similarity=0.686 Sum_probs=45.3
Q ss_pred cCCCcccCCCCCCCCCCCCCCCeeccCCC-------------------------------ccccCCCcccccccCCCCCC
Q psy3924 56 ECDISYHIYCTDPPLDHIPRGTWKCKWCA-------------------------------QCLTCGATGYHIYCTDPPLD 104 (131)
Q Consensus 56 ~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~-------------------------------~c~~Cg~~~~~~~c~~ppl~ 104 (131)
.|.+.||..|++|.+...++++|.|+.|. -|++|. .+||++|+++|+.
T Consensus 1 ~~~r~~~~~~~~p~~~~~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~g~~l~c~tC~-~s~h~~cl~~pl~ 79 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKEEPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADGGELLWCDTCP-ASFHASCLGPPLT 79 (696)
T ss_pred CCCcccCcCCCCcccccCCcCCccCcchhhcccccccccCCcchhhhhhhhhhcCCCcEEEecccc-HHHHHHccCCCCC
Confidence 47899999999999988888999999986 156664 5899999999998
Q ss_pred Ccccc
Q psy3924 105 HIIFV 109 (131)
Q Consensus 105 ~~~~~ 109 (131)
.++.+
T Consensus 80 ~~p~~ 84 (696)
T KOG0383|consen 80 PQPNG 84 (696)
T ss_pred cCCcc
Confidence 88866
No 27
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=94.96 E-value=0.054 Score=39.81 Aligned_cols=32 Identities=34% Similarity=0.946 Sum_probs=25.8
Q ss_pred ccccc---ccCCCCCceeeCcCCCcccCCCCCCCC
Q psy3924 39 CEGCA---QRHDEGRLILCDECDISYHIYCTDPPL 70 (131)
Q Consensus 39 C~~C~---~~~~~~~ll~Cd~C~~~~H~~Cl~p~l 70 (131)
|.+|+ ...+-|.||.|.+|..+||..||.+..
T Consensus 2 C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~Rs 36 (175)
T PF15446_consen 2 CDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGPRS 36 (175)
T ss_pred cccccCCCCCccCCCeEEcCccChHHHhhhcCCcc
Confidence 55664 444578999999999999999999754
No 28
>KOG4299|consensus
Probab=94.02 E-value=0.021 Score=49.26 Aligned_cols=28 Identities=21% Similarity=0.618 Sum_probs=21.1
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCc
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCT 37 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~ 37 (131)
.+||+.||+|+++ .+.+....|+|+.|+
T Consensus 276 ~sFH~~CLePPl~----~eniP~g~W~C~ec~ 303 (613)
T KOG4299|consen 276 RSFHQTCLEPPLE----PENIPPGSWFCPECK 303 (613)
T ss_pred hHHHHhhcCCCCC----cccCCCCccccCCCe
Confidence 5899999999942 222344599999997
No 29
>KOG1473|consensus
Probab=93.94 E-value=0.037 Score=50.84 Aligned_cols=50 Identities=30% Similarity=0.723 Sum_probs=43.3
Q ss_pred cccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCccccCCC
Q psy3924 39 CEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQCLTCGA 91 (131)
Q Consensus 39 C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~c~~Cg~ 91 (131)
|.+|. +.+.+++|..|++.||..|..+|+..+++..|.|--|.+++.=|.
T Consensus 347 crf~~---d~~~~lc~Et~prvvhlEcv~hP~~~~~s~~~e~evc~~hkvngv 396 (1414)
T KOG1473|consen 347 CRFCH---DLGDLLCCETCPRVVHLECVFHPRFAVPSAFWECEVCNIHKVNGV 396 (1414)
T ss_pred ccccC---cccceeecccCCceEEeeecCCccccCCCccchhhhhhhhccCcc
Confidence 55555 488999999999999999999999999999999999998766553
No 30
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=93.84 E-value=0.027 Score=33.81 Aligned_cols=31 Identities=29% Similarity=0.836 Sum_probs=26.4
Q ss_pred ccccccccC-CCCCceeeCcCCCcccCCCCCC
Q psy3924 38 VCEGCAQRH-DEGRLILCDECDISYHIYCTDP 68 (131)
Q Consensus 38 ~C~~C~~~~-~~~~ll~Cd~C~~~~H~~Cl~p 68 (131)
.|.+|+..- +++++|.|..|+..||-.|+..
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~~ 38 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCWEK 38 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHHhh
Confidence 577888765 3899999999999999999963
No 31
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=93.38 E-value=0.073 Score=39.13 Aligned_cols=20 Identities=30% Similarity=0.723 Sum_probs=15.2
Q ss_pred CceeeCcCCCcccCCCCCCC
Q psy3924 50 RLILCDECDISYHIYCTDPP 69 (131)
Q Consensus 50 ~ll~Cd~C~~~~H~~Cl~p~ 69 (131)
.|.-|..|.++||+.-|.++
T Consensus 123 VLFRC~~C~RawH~~HLP~~ 142 (175)
T PF15446_consen 123 VLFRCTSCHRAWHFEHLPPP 142 (175)
T ss_pred eEEecCCccceeehhhCCCC
Confidence 45668889999998888654
No 32
>KOG0956|consensus
Probab=93.27 E-value=0.035 Score=48.68 Aligned_cols=30 Identities=23% Similarity=0.773 Sum_probs=23.0
Q ss_pred cccccccCCC-----CCceeeC--cCCCcccCCCCCC
Q psy3924 39 CEGCAQRHDE-----GRLILCD--ECDISYHIYCTDP 68 (131)
Q Consensus 39 C~~C~~~~~~-----~~ll~Cd--~C~~~~H~~Cl~p 68 (131)
|.+|.+.+.+ +.-+.|. .|.++||..|.+-
T Consensus 120 CYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~ 156 (900)
T KOG0956|consen 120 CYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQR 156 (900)
T ss_pred eeeecccCCccccccccceecccccchhhhhhhHhhh
Confidence 9999987643 4556674 7889999999973
No 33
>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 PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=92.14 E-value=0.038 Score=36.23 Aligned_cols=52 Identities=25% Similarity=0.568 Sum_probs=34.6
Q ss_pred cCccCcc-----cccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 32 RCLDCTV-----CEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 32 ~C~~C~~-----C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
.|..|+. |..|...++.-.+++.. |...||+.|+..-+.+.. ..=.||-|+.
T Consensus 23 ~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~-C~H~FH~hCI~kWl~~~~-~~~~CPmCR~ 79 (85)
T PF12861_consen 23 VCGICRMPFDGCCPDCKFPGDDCPLVWGK-CSHNFHMHCILKWLSTQS-SKGQCPMCRQ 79 (85)
T ss_pred ceeeEecccccCCCCccCCCCCCceeecc-CccHHHHHHHHHHHcccc-CCCCCCCcCC
Confidence 4666653 66677766666666555 999999999976555432 2237887774
No 35
>KOG0957|consensus
Probab=91.22 E-value=0.27 Score=41.96 Aligned_cols=60 Identities=30% Similarity=0.638 Sum_probs=40.8
Q ss_pred cCCCccCccCcccccccc--cCCCCCceeeCcCCCcccCCCCCCC-CCCCC-------CCCeeccCCCc------cccCC
Q psy3924 27 LSKGWRCLDCTVCEGCAQ--RHDEGRLILCDECDISYHIYCTDPP-LDHIP-------RGTWKCKWCAQ------CLTCG 90 (131)
Q Consensus 27 ~~~~W~C~~C~~C~~C~~--~~~~~~ll~Cd~C~~~~H~~Cl~p~-l~~~p-------~~~W~C~~C~~------c~~Cg 90 (131)
...+|. .|-||-. ..+.+++|.||.|+-..|-.|+... ..+++ ..+|||-.|+. |..|+
T Consensus 115 apkk~~-----iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~Gvs~P~CElCP 189 (707)
T KOG0957|consen 115 APKKAV-----ICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLYGVSLPHCELCP 189 (707)
T ss_pred ccccce-----EEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhcCCCCCccccCC
Confidence 345673 4556654 3457899999999999999999743 11122 24799999873 66665
Q ss_pred C
Q psy3924 91 A 91 (131)
Q Consensus 91 ~ 91 (131)
.
T Consensus 190 n 190 (707)
T KOG0957|consen 190 N 190 (707)
T ss_pred C
Confidence 3
No 36
>KOG1246|consensus
Probab=91.11 E-value=0.21 Score=45.29 Aligned_cols=47 Identities=47% Similarity=1.252 Sum_probs=40.1
Q ss_pred ccccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 38 VCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 38 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
.|..|.+...+ .+++|+.|...||.+|..+++..+++++|.|+.|..
T Consensus 157 ~~~~~~k~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 203 (904)
T KOG1246|consen 157 QCNTCSKGKEE-KLLLCDSCDDSYHTYCLRPPLTRVPDGDWRCPKCIP 203 (904)
T ss_pred hhhccccCCCc-cceecccccCcccccccCCCCCcCCcCcccCCcccc
Confidence 36677776556 445999999999999999999999999999999875
No 37
>KOG1473|consensus
Probab=87.12 E-value=0.1 Score=48.12 Aligned_cols=70 Identities=19% Similarity=0.320 Sum_probs=53.6
Q ss_pred eeccccCCCCCCCCCccccccCCCccCccCcc----------------------------------------cccccccC
Q psy3924 7 AYGSVCRDVKLHDLPISKVILSKGWRCLDCTV----------------------------------------CEGCAQRH 46 (131)
Q Consensus 7 ~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~~----------------------------------------C~~C~~~~ 46 (131)
-||..|+.+++...|.. .|.|.-|.+ |.+|+.
T Consensus 365 vvhlEcv~hP~~~~~s~------~~e~evc~~hkvngvvd~vl~~~K~~~~iR~~~iG~dr~gr~ywfi~rrl~Ie~~-- 436 (1414)
T KOG1473|consen 365 VVHLECVFHPRFAVPSA------FWECEVCNIHKVNGVVDCVLPPSKNVDSIRHTPIGRDRYGRKYWFISRRLRIEGM-- 436 (1414)
T ss_pred eEEeeecCCccccCCCc------cchhhhhhhhccCcccccccChhhcccceeccCCCcCccccchhceeeeeEEecC--
Confidence 36999999998777654 899988874 334443
Q ss_pred CCCCceeeCc-CCCcccC-CCCCCC--CCCCCCCCeeccCCCc
Q psy3924 47 DEGRLILCDE-CDISYHI-YCTDPP--LDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 47 ~~~~ll~Cd~-C~~~~H~-~Cl~p~--l~~~p~~~W~C~~C~~ 85 (131)
.+.+|+|.. |...||+ .||+.. -..++++.|+|++|..
T Consensus 437 -det~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~ 478 (1414)
T KOG1473|consen 437 -DETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERREEII 478 (1414)
T ss_pred -CCcEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHHHHH
Confidence 567888876 9999999 999833 2357889999999974
No 38
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=86.67 E-value=0.45 Score=35.73 Aligned_cols=45 Identities=27% Similarity=0.734 Sum_probs=33.5
Q ss_pred cCccCc----ccccccccC-----CCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 32 RCLDCT----VCEGCAQRH-----DEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 32 ~C~~C~----~C~~C~~~~-----~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
.|+.|+ +|++|...+ +.+....|..|...||..|... . .||.|..
T Consensus 144 ~C~lC~~kGfiCe~C~~~~~IfPF~~~~~~~C~~C~~v~H~~C~~~---~------~CpkC~R 197 (202)
T PF13901_consen 144 SCELCQQKGFICEICNSDDIIFPFQIDTTVRCPKCKSVFHKSCFRK---K------SCPKCAR 197 (202)
T ss_pred HhHHHHhCCCCCccCCCCCCCCCCCCCCeeeCCcCccccchhhcCC---C------CCCCcHh
Confidence 366666 588898754 3467899999999999999962 1 2887753
No 39
>KOG0955|consensus
Probab=86.32 E-value=0.36 Score=44.50 Aligned_cols=24 Identities=25% Similarity=0.654 Sum_probs=19.2
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCc
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCT 37 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~ 37 (131)
+++|..|.+.+ ..|++ .|.|..|-
T Consensus 244 l~VHq~Cygi~--~ipeg------~WlCr~Cl 267 (1051)
T KOG0955|consen 244 LAVHQECYGIP--FIPEG------QWLCRRCL 267 (1051)
T ss_pred chhhhhccCCC--CCCCC------cEeehhhc
Confidence 68999999966 34555 99999887
No 40
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=86.18 E-value=0.37 Score=32.27 Aligned_cols=29 Identities=28% Similarity=0.763 Sum_probs=24.7
Q ss_pred cccccccccCCCCCceeeCc--CCCcccCCCCC
Q psy3924 37 TVCEGCAQRHDEGRLILCDE--CDISYHIYCTD 67 (131)
Q Consensus 37 ~~C~~C~~~~~~~~ll~Cd~--C~~~~H~~Cl~ 67 (131)
..|.+|++. .|..+.|.. |...||+.|..
T Consensus 56 ~~C~iC~~~--~G~~i~C~~~~C~~~fH~~CA~ 86 (110)
T PF13832_consen 56 LKCSICGKS--GGACIKCSHPGCSTAFHPTCAR 86 (110)
T ss_pred CcCcCCCCC--CceeEEcCCCCCCcCCCHHHHH
Confidence 468888874 788999987 99999999985
No 41
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=83.84 E-value=0.32 Score=25.24 Aligned_cols=28 Identities=36% Similarity=0.910 Sum_probs=11.6
Q ss_pred ccccccccCCCCCceeeCcCCCcccCCC
Q psy3924 38 VCEGCAQRHDEGRLILCDECDISYHIYC 65 (131)
Q Consensus 38 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~C 65 (131)
.|.+|++...++..-.|..|+-..|..|
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~C 29 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEEC 29 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhc
Confidence 5778888766667888999999888776
No 42
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 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 zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=82.78 E-value=1.1 Score=23.05 Aligned_cols=17 Identities=53% Similarity=1.566 Sum_probs=11.2
Q ss_pred CCCeeccCCC--------ccccCCC
Q psy3924 75 RGTWKCKWCA--------QCLTCGA 91 (131)
Q Consensus 75 ~~~W~C~~C~--------~c~~Cg~ 91 (131)
.++|.|+.|. .|..|++
T Consensus 2 ~g~W~C~~C~~~N~~~~~~C~~C~~ 26 (30)
T PF00641_consen 2 EGDWKCPSCTFMNPASRSKCVACGA 26 (30)
T ss_dssp SSSEEETTTTEEEESSSSB-TTT--
T ss_pred CcCccCCCCcCCchHHhhhhhCcCC
Confidence 4689999997 4777765
No 43
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=81.28 E-value=0.54 Score=40.11 Aligned_cols=24 Identities=29% Similarity=0.665 Sum_probs=20.0
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCc
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCT 37 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~ 37 (131)
++-|..|-.++ -+|++ .|.|..|.
T Consensus 218 i~VHq~CYGI~--f~peG------~WlCrkCi 241 (669)
T COG5141 218 ICVHQSCYGIQ--FLPEG------FWLCRKCI 241 (669)
T ss_pred hhhhhhcccce--ecCcc------hhhhhhhc
Confidence 67899999988 46766 89999987
No 44
>KOG1245|consensus
Probab=79.00 E-value=0.61 Score=44.35 Aligned_cols=27 Identities=22% Similarity=0.625 Sum_probs=24.2
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCcc
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCTV 38 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~~ 38 (131)
..||.+|+++.+..+|.+ +|+|+.|+.
T Consensus 1131 ~~~h~~C~rp~~~~~~~~------dW~C~~c~~ 1157 (1404)
T KOG1245|consen 1131 SGFHLFCLRPALSSVPPG------DWMCPSCRK 1157 (1404)
T ss_pred hhHHHHhhhhhhccCCcC------CccCCccch
Confidence 679999999999888877 899999984
No 45
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=78.52 E-value=0.049 Score=30.66 Aligned_cols=42 Identities=21% Similarity=0.513 Sum_probs=25.2
Q ss_pred ccccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCC
Q psy3924 38 VCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWC 83 (131)
Q Consensus 38 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C 83 (131)
.|.+|...-..+..+.--.|+..||..|+..-+... -.||.|
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~~~----~~CP~C 43 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLKRN----NSCPVC 43 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHHHS----SB-TTT
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHHhC----CcCCcc
Confidence 466777654333444444499999999997544332 256665
No 46
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=74.77 E-value=1.7 Score=27.08 Aligned_cols=47 Identities=19% Similarity=0.476 Sum_probs=16.7
Q ss_pred cccccccC---CCCCceeeC--cCCCcccCCCCCCCCCC-------CCCCCeeccCCCc
Q psy3924 39 CEGCAQRH---DEGRLILCD--ECDISYHIYCTDPPLDH-------IPRGTWKCKWCAQ 85 (131)
Q Consensus 39 C~~C~~~~---~~~~ll~Cd--~C~~~~H~~Cl~p~l~~-------~p~~~W~C~~C~~ 85 (131)
|.+|.+.. +....+.|+ .|...||..||..-+.. ...-...||.|..
T Consensus 5 C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~ 63 (70)
T PF11793_consen 5 CGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSS 63 (70)
T ss_dssp -SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-S
T ss_pred CCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCC
Confidence 55555432 233568898 99999999999632211 1112356888864
No 47
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=73.85 E-value=1.8 Score=27.66 Aligned_cols=30 Identities=30% Similarity=0.756 Sum_probs=24.0
Q ss_pred cccccccccCCCCCceeeC--cCCCcccCCCCCC
Q psy3924 37 TVCEGCAQRHDEGRLILCD--ECDISYHIYCTDP 68 (131)
Q Consensus 37 ~~C~~C~~~~~~~~ll~Cd--~C~~~~H~~Cl~p 68 (131)
..|.+|++. .|..+.|. .|.+.||+.|..-
T Consensus 37 ~~C~~C~~~--~Ga~i~C~~~~C~~~fH~~CA~~ 68 (90)
T PF13771_consen 37 LKCSICKKK--GGACIGCSHPGCSRSFHVPCARK 68 (90)
T ss_pred CCCcCCCCC--CCeEEEEeCCCCCcEEChHHHcc
Confidence 467888873 47889996 6999999999963
No 48
>PF00130 C1_1: Phorbol esters/diacylglycerol binding domain (C1 domain); InterPro: IPR002219 Diacylglycerol (DAG) is an important second messenger. Phorbol esters (PE) are analogues of DAG and potent tumour promoters that cause a variety of physiological changes when administered to both cells and tissues. DAG activates a family of serine/threonine protein kinases, collectively known as protein kinase C (PKC) []. Phorbol esters can directly stimulate PKC. The N-terminal region of PKC, known as C1, has been shown [] to bind PE and DAG in a phospholipid and zinc-dependent fashion. The C1 region contains one or two copies (depending on the isozyme of PKC) of a cysteine-rich domain, which is about 50 amino-acid residues long, and which is essential for DAG/PE-binding. The DAG/PE-binding domain binds two zinc ions; the ligands of these metal ions are probably the six cysteines and two histidines that are conserved in this domain.; GO: 0035556 intracellular signal transduction; PDB: 1RFH_A 2FNF_X 3PFQ_A 1PTQ_A 1PTR_A 2VRW_B 1XA6_A 2ENN_A 1TBN_A 1TBO_A ....
Probab=70.45 E-value=3.7 Score=23.58 Aligned_cols=30 Identities=20% Similarity=0.438 Sum_probs=21.9
Q ss_pred ccccccccC--CCCCceeeCcCCCcccCCCCC
Q psy3924 38 VCEGCAQRH--DEGRLILCDECDISYHIYCTD 67 (131)
Q Consensus 38 ~C~~C~~~~--~~~~ll~Cd~C~~~~H~~Cl~ 67 (131)
.|.+|++.- ....-+.|..|....|..|+.
T Consensus 13 ~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~ 44 (53)
T PF00130_consen 13 YCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLS 44 (53)
T ss_dssp B-TTSSSBECSSSSCEEEETTTT-EEETTGGC
T ss_pred CCcccCcccCCCCCCeEEECCCCChHhhhhhh
Confidence 466666543 467789999999999999996
No 49
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=65.87 E-value=4.2 Score=19.96 Aligned_cols=9 Identities=44% Similarity=1.531 Sum_probs=7.3
Q ss_pred CCeeccCCC
Q psy3924 76 GTWKCKWCA 84 (131)
Q Consensus 76 ~~W~C~~C~ 84 (131)
++|.|+.|.
T Consensus 1 g~W~C~~C~ 9 (26)
T smart00547 1 GDWECPACT 9 (26)
T ss_pred CcccCCCCC
Confidence 479999985
No 50
>KOG4628|consensus
Probab=63.65 E-value=4.6 Score=33.03 Aligned_cols=46 Identities=24% Similarity=0.573 Sum_probs=35.9
Q ss_pred cccccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 37 TVCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 37 ~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
..|.+|.+.-..|+.|.=--|...||..|.+|.|.+. .=+||-|+.
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~~~---r~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLTQT---RTFCPVCKR 275 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHhhc---CccCCCCCC
Confidence 4788898765566666668999999999999987754 236888874
No 51
>PF12773 DZR: Double zinc ribbon
Probab=62.27 E-value=7.5 Score=22.07 Aligned_cols=10 Identities=20% Similarity=0.687 Sum_probs=5.2
Q ss_pred CceeeCcCCC
Q psy3924 50 RLILCDECDI 59 (131)
Q Consensus 50 ~ll~Cd~C~~ 59 (131)
...+|..|+.
T Consensus 11 ~~~fC~~CG~ 20 (50)
T PF12773_consen 11 DAKFCPHCGT 20 (50)
T ss_pred cccCChhhcC
Confidence 3445555554
No 52
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=60.92 E-value=8.8 Score=19.75 Aligned_cols=28 Identities=29% Similarity=0.784 Sum_probs=19.4
Q ss_pred cccccccCCCCCceeeCcCCCcccCCCC
Q psy3924 39 CEGCAQRHDEGRLILCDECDISYHIYCT 66 (131)
Q Consensus 39 C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl 66 (131)
|.+|++..++...=.|+.|.-..|..|.
T Consensus 3 C~~C~~~~~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 3 CDVCRRKIDGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCcCCCEeEEeCCCCCeEcCccC
Confidence 6777765443327778999888887763
No 53
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=54.41 E-value=6.8 Score=21.81 Aligned_cols=30 Identities=23% Similarity=0.585 Sum_probs=21.8
Q ss_pred ccccccccCCC--CCceeeCcCCCcccCCCCC
Q psy3924 38 VCEGCAQRHDE--GRLILCDECDISYHIYCTD 67 (131)
Q Consensus 38 ~C~~C~~~~~~--~~ll~Cd~C~~~~H~~Cl~ 67 (131)
+|.+|++.-.+ ..-+.|..|....|..|..
T Consensus 13 ~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~ 44 (50)
T cd00029 13 FCDVCRKSIWGLFKQGLRCSWCKVKCHKKCAD 44 (50)
T ss_pred ChhhcchhhhccccceeEcCCCCCchhhhhhc
Confidence 46666654332 4678899999999999985
No 54
>KOG3612|consensus
Probab=50.63 E-value=20 Score=31.15 Aligned_cols=51 Identities=18% Similarity=0.282 Sum_probs=37.0
Q ss_pred cCCCccCccCcccccccccCCCCCceeeCcCCCcccCCCCCCCCCCCC-CCCeeccCCCcc
Q psy3924 27 LSKGWRCLDCTVCEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIP-RGTWKCKWCAQC 86 (131)
Q Consensus 27 ~~~~W~C~~C~~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p-~~~W~C~~C~~c 86 (131)
...+|+|-.| .. ++..|.|+.|-+.||..|..|.-.... ...|.++.+..+
T Consensus 57 ~N~d~~cfec------hl---pg~vl~c~vc~Rs~h~~c~sp~~q~r~~s~p~~~p~p~s~ 108 (588)
T KOG3612|consen 57 SNIDPFCFEC------HL---PGAVLKCIVCHRSFHENCQSPDPQKRNYSVPSDKPQPYSF 108 (588)
T ss_pred cCCCcccccc------cC---CcceeeeehhhccccccccCcchhhccccccccCCccccc
Confidence 3456765554 33 888999999999999999987644332 347999988754
No 55
>KOG1311|consensus
Probab=48.29 E-value=22 Score=27.86 Aligned_cols=48 Identities=21% Similarity=0.452 Sum_probs=30.0
Q ss_pred CCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCccccCCCcccccccCCCCCCCccccCCCCcc
Q psy3924 49 GRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQCLTCGATGYHIYCTDPPLDHIIFVQDKIRP 115 (131)
Q Consensus 49 ~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~c~~Cg~~~~~~~c~~ppl~~~~~~~~~~~~ 115 (131)
.+...|+.|.. .+|.+.|.|+.|..| ......|| |. -+-.-|++|++-
T Consensus 111 ~~~~~C~~C~~------------~rPpRs~HCsvC~~C----V~rfDHHC--~W-vnnCVG~rNyr~ 158 (299)
T KOG1311|consen 111 VEWKYCDTCQL------------YRPPRSSHCSVCNNC----VLRFDHHC--PW-LNNCIGERNYRY 158 (299)
T ss_pred cceEEcCcCcc------------cCCCCcccchhhccc----ccccCCCC--CC-ccceECCCchHH
Confidence 35788888843 256677888888777 55566677 32 233345666653
No 56
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=47.96 E-value=3.2 Score=22.03 Aligned_cols=41 Identities=22% Similarity=0.499 Sum_probs=23.6
Q ss_pred cccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCC
Q psy3924 39 CEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCA 84 (131)
Q Consensus 39 C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~ 84 (131)
|.+|...- ...+.-..|+..||..|+...+.. +...||.|+
T Consensus 2 C~iC~~~~--~~~~~~~~C~H~~c~~C~~~~~~~---~~~~Cp~C~ 42 (45)
T cd00162 2 CPICLEEF--REPVVLLPCGHVFCRSCIDKWLKS---GKNTCPLCR 42 (45)
T ss_pred CCcCchhh--hCceEecCCCChhcHHHHHHHHHh---CcCCCCCCC
Confidence 45555432 234445568888999998644332 234576665
No 57
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=47.30 E-value=15 Score=19.98 Aligned_cols=15 Identities=33% Similarity=0.769 Sum_probs=10.5
Q ss_pred eeeCcCCCcccCCCC
Q psy3924 52 ILCDECDISYHIYCT 66 (131)
Q Consensus 52 l~Cd~C~~~~H~~Cl 66 (131)
..|..|++.||..=.
T Consensus 2 r~C~~Cg~~Yh~~~~ 16 (36)
T PF05191_consen 2 RICPKCGRIYHIEFN 16 (36)
T ss_dssp EEETTTTEEEETTTB
T ss_pred cCcCCCCCccccccC
Confidence 357888888885443
No 58
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 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 domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=47.11 E-value=2.8 Score=26.25 Aligned_cols=30 Identities=23% Similarity=0.515 Sum_probs=18.2
Q ss_pred ceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCC
Q psy3924 51 LILCDECDISYHIYCTDPPLDHIPRGTWKCKWCA 84 (131)
Q Consensus 51 ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~ 84 (131)
.+.=..|+..||..|+..-+... ..||-|+
T Consensus 44 ~i~~~~C~H~FH~~Ci~~Wl~~~----~~CP~CR 73 (73)
T PF12678_consen 44 PIVWGPCGHIFHFHCISQWLKQN----NTCPLCR 73 (73)
T ss_dssp -EEEETTSEEEEHHHHHHHHTTS----SB-TTSS
T ss_pred ceEecccCCCEEHHHHHHHHhcC----CcCCCCC
Confidence 33445799999999996443322 2677664
No 59
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=46.72 E-value=6.7 Score=21.58 Aligned_cols=30 Identities=20% Similarity=0.497 Sum_probs=21.2
Q ss_pred ccccccccCCCC-CceeeCcCCCcccCCCCC
Q psy3924 38 VCEGCAQRHDEG-RLILCDECDISYHIYCTD 67 (131)
Q Consensus 38 ~C~~C~~~~~~~-~ll~Cd~C~~~~H~~Cl~ 67 (131)
+|.+|++.-... ..+.|..|....|..|..
T Consensus 13 ~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~ 43 (49)
T smart00109 13 KCCVCRKSIWGSFQGLRCSWCKVKCHKKCAE 43 (49)
T ss_pred CccccccccCcCCCCcCCCCCCchHHHHHHh
Confidence 466666643322 467899999999998885
No 60
>PF08746 zf-RING-like: RING-like domain; InterPro: IPR014857 This is a zinc finger domain that is related to the C3HC4 RING finger domain (IPR001841 from INTERPRO). ; PDB: 3NW0_A 2CT0_A.
Probab=45.30 E-value=3.9 Score=23.07 Aligned_cols=41 Identities=27% Similarity=0.657 Sum_probs=17.4
Q ss_pred cccccccCCCCCceeeC--cCCCcccCCCCCCCCCCCCCCCeeccCC
Q psy3924 39 CEGCAQRHDEGRLILCD--ECDISYHIYCTDPPLDHIPRGTWKCKWC 83 (131)
Q Consensus 39 C~~C~~~~~~~~ll~Cd--~C~~~~H~~Cl~p~l~~~p~~~W~C~~C 83 (131)
|.+|++.. -.-+.|. .|...+|..|+.--+..... + .||.|
T Consensus 1 C~~C~~iv--~~G~~C~~~~C~~r~H~~C~~~y~r~~~~-~-~CP~C 43 (43)
T PF08746_consen 1 CEACKEIV--TQGQRCSNRDCNVRLHDDCFKKYFRHRSN-P-KCPNC 43 (43)
T ss_dssp -TTT-SB---SSSEE-SS--S--EE-HHHHHHHTTT-SS---B-TTT
T ss_pred CcccchhH--eeeccCCCCccCchHHHHHHHHHHhcCCC-C-CCcCC
Confidence 44555422 2235677 68899999999644433322 2 57765
No 61
>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=45.14 E-value=9.2 Score=22.13 Aligned_cols=11 Identities=27% Similarity=0.909 Sum_probs=6.1
Q ss_pred CCCccCccCcc
Q psy3924 28 SKGWRCLDCTV 38 (131)
Q Consensus 28 ~~~W~C~~C~~ 38 (131)
.++|.||.|..
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 56899999853
No 62
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=43.99 E-value=9.3 Score=25.79 Aligned_cols=12 Identities=33% Similarity=1.016 Sum_probs=9.7
Q ss_pred CCCCCeeccCCC
Q psy3924 73 IPRGTWKCKWCA 84 (131)
Q Consensus 73 ~p~~~W~C~~C~ 84 (131)
+.+..|.||.|+
T Consensus 57 ~~~~~W~CP~Cr 68 (105)
T PF10497_consen 57 LEDPNWKCPKCR 68 (105)
T ss_pred hcCCceECCCCC
Confidence 345689999998
No 63
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=43.01 E-value=12 Score=25.16 Aligned_cols=28 Identities=25% Similarity=0.839 Sum_probs=21.2
Q ss_pred ccccccccC--CCCCceeeCcCCCcccCCC
Q psy3924 38 VCEGCAQRH--DEGRLILCDECDISYHIYC 65 (131)
Q Consensus 38 ~C~~C~~~~--~~~~ll~Cd~C~~~~H~~C 65 (131)
.|++|+..+ ..+..|.|..|+..+++.=
T Consensus 37 aCeiC~~~GY~q~g~~lvC~~C~~~~~~~~ 66 (102)
T PF10080_consen 37 ACEICGPKGYYQEGDQLVCKNCGVRFNLPT 66 (102)
T ss_pred eccccCCCceEEECCEEEEecCCCEEehhh
Confidence 488887655 3577888999999887643
No 64
>KOG0954|consensus
Probab=42.17 E-value=10 Score=34.12 Aligned_cols=28 Identities=29% Similarity=0.812 Sum_probs=20.9
Q ss_pred cccccccCCCCCceeeC--cCCCcccCCCCCC
Q psy3924 39 CEGCAQRHDEGRLILCD--ECDISYHIYCTDP 68 (131)
Q Consensus 39 C~~C~~~~~~~~ll~Cd--~C~~~~H~~Cl~p 68 (131)
|.+|.. ..|.-+.|. .|..+||..|...
T Consensus 383 C~LCk~--k~GACIqCs~k~C~t~fHv~CA~~ 412 (893)
T KOG0954|consen 383 CNLCKV--KSGACIQCSNKTCRTAFHVTCAFE 412 (893)
T ss_pred HHHhcc--cCcceEEecccchhhhccchhhhh
Confidence 777775 366667774 8888999999864
No 65
>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=38.51 E-value=23 Score=29.95 Aligned_cols=56 Identities=23% Similarity=0.441 Sum_probs=39.6
Q ss_pred CCCccCccCcccccccccC---CCCCceeeCcCCCcccCCCCCCCC-------CCC----CCCCeeccCCC
Q psy3924 28 SKGWRCLDCTVCEGCAQRH---DEGRLILCDECDISYHIYCTDPPL-------DHI----PRGTWKCKWCA 84 (131)
Q Consensus 28 ~~~W~C~~C~~C~~C~~~~---~~~~ll~Cd~C~~~~H~~Cl~p~l-------~~~----p~~~W~C~~C~ 84 (131)
..+=+|..| .|-+|.+-+ ++-.-|.||.|+.+-|+.|.--.. ... .+..++|..|-
T Consensus 121 ~~~gFC~~C-~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~ 190 (446)
T PF07227_consen 121 SEPGFCRRC-MCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACG 190 (446)
T ss_pred CCCCccccC-CccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCC
Confidence 446678888 899998854 355668999999999999985211 111 23468888886
No 66
>KOG2272|consensus
Probab=35.89 E-value=16 Score=28.91 Aligned_cols=55 Identities=20% Similarity=0.562 Sum_probs=33.6
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCc------ccccccccCCCC-----------CceeeCcCCCcc
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCT------VCEGCAQRHDEG-----------RLILCDECDISY 61 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~------~C~~C~~~~~~~-----------~ll~Cd~C~~~~ 61 (131)
-+||+.|..=.- .+....+....+-+|+.|- +|..|++..++. +-..|..|.+.|
T Consensus 160 H~yHFkCt~C~k-eL~sdaRevk~eLyClrChD~mgipiCgaC~rpIeervi~amgKhWHveHFvCa~CekPF 231 (332)
T KOG2272|consen 160 HPYHFKCTTCGK-ELTSDAREVKGELYCLRCHDKMGIPICGACRRPIEERVIFAMGKHWHVEHFVCAKCEKPF 231 (332)
T ss_pred Cccceecccccc-cccchhhhhccceeccccccccCCcccccccCchHHHHHHHhccccchhheeehhcCCcc
Confidence 478888876442 3334444456788898886 477777654322 123577777654
No 67
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=35.21 E-value=30 Score=22.26 Aligned_cols=29 Identities=17% Similarity=0.466 Sum_probs=19.1
Q ss_pred ccccccccCCCCCceeeCcCCCcccCCCCC
Q psy3924 38 VCEGCAQRHDEGRLILCDECDISYHIYCTD 67 (131)
Q Consensus 38 ~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~ 67 (131)
.|.+|++.-..+ ...---++..+|..|..
T Consensus 80 ~C~vC~k~l~~~-~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGNS-VFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCCc-eEEEeCCCeEEeccccc
Confidence 588888765443 33334556889999874
No 68
>KOG1632|consensus
Probab=34.82 E-value=25 Score=28.61 Aligned_cols=36 Identities=25% Similarity=0.542 Sum_probs=29.7
Q ss_pred CceeeCcCCCcccCCC--CCCCCCCCCC-CCeeccCCCc
Q psy3924 50 RLILCDECDISYHIYC--TDPPLDHIPR-GTWKCKWCAQ 85 (131)
Q Consensus 50 ~ll~Cd~C~~~~H~~C--l~p~l~~~p~-~~W~C~~C~~ 85 (131)
.++.|+.|..+||..| ++.+....|. ..|+|..|..
T Consensus 74 ~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~ 112 (345)
T KOG1632|consen 74 LMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKE 112 (345)
T ss_pred hhhccccccccccccccccCchhhcCCccccccccccch
Confidence 7899999999999999 8766665554 4799999874
No 69
>COG1773 Rubredoxin [Energy production and conversion]
Probab=34.30 E-value=32 Score=20.64 Aligned_cols=11 Identities=36% Similarity=1.177 Sum_probs=8.5
Q ss_pred CCCccCccCcc
Q psy3924 28 SKGWRCLDCTV 38 (131)
Q Consensus 28 ~~~W~C~~C~~ 38 (131)
..+|.||.|.+
T Consensus 34 Pd~w~CP~Cg~ 44 (55)
T COG1773 34 PDDWVCPECGV 44 (55)
T ss_pred CCccCCCCCCC
Confidence 45899999865
No 70
>KOG1829|consensus
Probab=32.23 E-value=10 Score=33.09 Aligned_cols=46 Identities=28% Similarity=0.715 Sum_probs=29.6
Q ss_pred CccCc----ccccccccC-----CCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 33 CLDCT----VCEGCAQRH-----DEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 33 C~~C~----~C~~C~~~~-----~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
|..|. +|.+|...+ ..+....|+.|...||..|+... .+ .||.|..
T Consensus 504 C~lC~~~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~---s~----~CPrC~R 558 (580)
T KOG1829|consen 504 CDLCTGKGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRK---SP----CCPRCER 558 (580)
T ss_pred chhhccCeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhcc---CC----CCCchHH
Confidence 55554 466664432 24566789999999999999522 11 1888863
No 71
>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=31.94 E-value=26 Score=20.44 Aligned_cols=11 Identities=36% Similarity=1.026 Sum_probs=8.5
Q ss_pred cCCCccCccCc
Q psy3924 27 LSKGWRCLDCT 37 (131)
Q Consensus 27 ~~~~W~C~~C~ 37 (131)
..++|.||.|.
T Consensus 31 Lp~~w~CP~C~ 41 (50)
T cd00730 31 LPDDWVCPVCG 41 (50)
T ss_pred CCCCCCCCCCC
Confidence 35699999885
No 72
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=31.75 E-value=25 Score=19.24 Aligned_cols=12 Identities=33% Similarity=0.894 Sum_probs=8.3
Q ss_pred eeCcCCCcccCC
Q psy3924 53 LCDECDISYHIY 64 (131)
Q Consensus 53 ~Cd~C~~~~H~~ 64 (131)
+|-+|.++||..
T Consensus 4 ~CprC~kg~Hwa 15 (36)
T PF14787_consen 4 LCPRCGKGFHWA 15 (36)
T ss_dssp C-TTTSSSCS-T
T ss_pred cCcccCCCcchh
Confidence 588899999974
No 73
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.28 E-value=39 Score=17.64 Aligned_cols=10 Identities=30% Similarity=1.105 Sum_probs=7.0
Q ss_pred CCeeccCCCc
Q psy3924 76 GTWKCKWCAQ 85 (131)
Q Consensus 76 ~~W~C~~C~~ 85 (131)
.+|.||.|..
T Consensus 16 ~~~~CP~Cg~ 25 (33)
T cd00350 16 APWVCPVCGA 25 (33)
T ss_pred CCCcCcCCCC
Confidence 4688887753
No 74
>KOG3362|consensus
Probab=30.37 E-value=27 Score=25.23 Aligned_cols=37 Identities=19% Similarity=0.512 Sum_probs=24.6
Q ss_pred eeeccccCCCCCCCCCccccccCCCccCccCcccccccccCCCCCceeeCcCCCcc
Q psy3924 6 IAYGSVCRDVKLHDLPISKVILSKGWRCLDCTVCEGCAQRHDEGRLILCDECDISY 61 (131)
Q Consensus 6 ~~~H~~Cl~~~~~~~~~~~~~~~~~W~C~~C~~C~~C~~~~~~~~ll~Cd~C~~~~ 61 (131)
..||..+..+++- |.. .+|.||+ -...-.|..|+..|
T Consensus 103 ~~Y~~~~a~p~~K--P~r-------------~fCaVCG----~~S~ysC~~CG~ky 139 (156)
T KOG3362|consen 103 PNYHTAYAKPSFK--PLR-------------KFCAVCG----YDSKYSCVNCGTKY 139 (156)
T ss_pred cchhhcccCCCCC--Ccc-------------hhhhhcC----CCchhHHHhcCCce
Confidence 5688888887743 322 5788888 33445688887765
No 75
>COG0143 MetG Methionyl-tRNA synthetase [Translation, ribosomal structure and biogenesis]
Probab=29.36 E-value=31 Score=30.05 Aligned_cols=40 Identities=23% Similarity=0.600 Sum_probs=28.4
Q ss_pred CCCccCccCc----------ccccccccCCCCCceeeCcCCCcccCCCCCCC
Q psy3924 28 SKGWRCLDCT----------VCEGCAQRHDEGRLILCDECDISYHIYCTDPP 69 (131)
Q Consensus 28 ~~~W~C~~C~----------~C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~ 69 (131)
-..|+|+.|. .|.-|+.....| -.|+.|++.+.+..+.-|
T Consensus 124 ~~~~Yc~~~e~fl~dr~v~g~cp~cg~~~arG--D~Ce~Cg~~~~P~~l~~p 173 (558)
T COG0143 124 YEGLYCVSCERFLPDRYVEGTCPKCGGEDARG--DQCENCGRTLDPTELINP 173 (558)
T ss_pred eeeeEcccccccccchheeccCCCcCccccCc--chhhhccCcCCchhcCCC
Confidence 3489999998 477787543333 269999999998876433
No 76
>KOG4198|consensus
Probab=28.50 E-value=39 Score=26.92 Aligned_cols=21 Identities=29% Similarity=0.871 Sum_probs=15.4
Q ss_pred ccCCCccCccCcc--------cccccccC
Q psy3924 26 ILSKGWRCLDCTV--------CEGCAQRH 46 (131)
Q Consensus 26 ~~~~~W~C~~C~~--------C~~C~~~~ 46 (131)
.+..+|.||.|.+ |..|+...
T Consensus 136 ~~~GDW~Cp~C~fhNfarn~~C~rC~~~r 164 (280)
T KOG4198|consen 136 WRSGDWECPGCNFHNFARNSECFRCGAKR 164 (280)
T ss_pred ccccCcccCCCCceeccccchhhhcCCcC
Confidence 4677999998874 77776543
No 77
>KOG1701|consensus
Probab=28.14 E-value=50 Score=27.96 Aligned_cols=30 Identities=20% Similarity=0.489 Sum_probs=20.3
Q ss_pred ccccccccC---C-CCCceeeCcCCCcccCCCCC
Q psy3924 38 VCEGCAQRH---D-EGRLILCDECDISYHIYCTD 67 (131)
Q Consensus 38 ~C~~C~~~~---~-~~~ll~Cd~C~~~~H~~Cl~ 67 (131)
.|.+|+... + .++.+.-..=++.||+.|+.
T Consensus 396 rCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~ 429 (468)
T KOG1701|consen 396 RCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYK 429 (468)
T ss_pred chhhccCCccCCCCCcceEEEEEcccccccccee
Confidence 377777653 2 24467777778888888874
No 78
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=28.12 E-value=43 Score=16.17 Aligned_cols=11 Identities=18% Similarity=0.643 Sum_probs=5.3
Q ss_pred CCceeeCcCCC
Q psy3924 49 GRLILCDECDI 59 (131)
Q Consensus 49 ~~ll~Cd~C~~ 59 (131)
+...+|..|+.
T Consensus 11 ~~~~fC~~CG~ 21 (23)
T PF13240_consen 11 DDAKFCPNCGT 21 (23)
T ss_pred CcCcchhhhCC
Confidence 33445555543
No 79
>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=27.19 E-value=32 Score=19.80 Aligned_cols=31 Identities=26% Similarity=0.627 Sum_probs=13.3
Q ss_pred ceeeCcCCCcccCC-CCCCCCCCCCCCCeeccC
Q psy3924 51 LILCDECDISYHIY-CTDPPLDHIPRGTWKCKW 82 (131)
Q Consensus 51 ll~Cd~C~~~~H~~-Cl~p~l~~~p~~~W~C~~ 82 (131)
-|.|+.|.+.-.+. -+.+....+++ .|+|..
T Consensus 3 WVQCd~C~KWR~lp~~~~~~~~~~~d-~W~C~~ 34 (50)
T PF07496_consen 3 WVQCDSCLKWRRLPEEVDPIREELPD-PWYCSM 34 (50)
T ss_dssp EEE-TTT--EEEE-CCHHCTSCCSST-T--GGG
T ss_pred EEECCCCCceeeCChhhCcccccCCC-eEEcCC
Confidence 36788888775543 11111233455 899976
No 80
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=26.49 E-value=81 Score=28.00 Aligned_cols=14 Identities=21% Similarity=0.562 Sum_probs=8.3
Q ss_pred CCCceeeCcCCCcc
Q psy3924 48 EGRLILCDECDISY 61 (131)
Q Consensus 48 ~~~ll~Cd~C~~~~ 61 (131)
+....+|..|+...
T Consensus 12 ~~~akFC~~CG~~l 25 (645)
T PRK14559 12 PNNNRFCQKCGTSL 25 (645)
T ss_pred CCCCccccccCCCC
Confidence 44555677776653
No 81
>KOG1493|consensus
Probab=26.43 E-value=4.5 Score=26.08 Aligned_cols=45 Identities=27% Similarity=0.556 Sum_probs=29.2
Q ss_pred cccccccCCCCCceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 39 CEGCAQRHDEGRLILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 39 C~~C~~~~~~~~ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
|..|+..++.=.||+- .|...||..|...-+.. +...=.||-|++
T Consensus 34 Cp~Ck~PgDdCPLv~G-~C~h~fh~hCI~~wl~~-~tsq~~CPmcRq 78 (84)
T KOG1493|consen 34 CPDCKLPGDDCPLVWG-YCLHAFHAHCILKWLNT-PTSQGQCPMCRQ 78 (84)
T ss_pred CCCCcCCCCCCccHHH-HHHHHHHHHHHHHHhcC-ccccccCCcchh
Confidence 5566666665556554 88888999998754433 333456777764
No 82
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 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. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=26.40 E-value=36 Score=18.65 Aligned_cols=31 Identities=26% Similarity=0.743 Sum_probs=14.4
Q ss_pred ceeeCcCCCcccCCCCCCCCCCCCCCCeeccCCCc
Q psy3924 51 LILCDECDISYHIYCTDPPLDHIPRGTWKCKWCAQ 85 (131)
Q Consensus 51 ll~Cd~C~~~~H~~Cl~p~l~~~p~~~W~C~~C~~ 85 (131)
.+.|..|..-.-+++.. . .....|.|+.|..
T Consensus 2 p~rC~~C~aylNp~~~~---~-~~~~~w~C~~C~~ 32 (40)
T PF04810_consen 2 PVRCRRCRAYLNPFCQF---D-DGGKTWICNFCGT 32 (40)
T ss_dssp S-B-TTT--BS-TTSEE---E-TTTTEEEETTT--
T ss_pred ccccCCCCCEECCcceE---c-CCCCEEECcCCCC
Confidence 35677776655555542 1 1234799998864
No 83
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=25.46 E-value=9.2 Score=19.25 Aligned_cols=16 Identities=13% Similarity=0.370 Sum_probs=10.8
Q ss_pred eeCcCCCcccCCCCCC
Q psy3924 53 LCDECDISYHIYCTDP 68 (131)
Q Consensus 53 ~Cd~C~~~~H~~Cl~p 68 (131)
.-..|+..||..|+..
T Consensus 12 ~~~~C~H~~c~~C~~~ 27 (39)
T smart00184 12 VVLPCGHTFCRSCIRK 27 (39)
T ss_pred EEecCCChHHHHHHHH
Confidence 3346877788888753
No 84
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=24.71 E-value=70 Score=16.40 Aligned_cols=22 Identities=23% Similarity=0.584 Sum_probs=9.0
Q ss_pred ccccccccC---CCCCceeeCcCCC
Q psy3924 38 VCEGCAQRH---DEGRLILCDECDI 59 (131)
Q Consensus 38 ~C~~C~~~~---~~~~ll~Cd~C~~ 59 (131)
+|..|+... ..+..+.|..|+.
T Consensus 5 fC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--BEEE-SSSS-EEESSSS-
T ss_pred ccCcCCccccCCCCcCEeECCCCcC
Confidence 455555432 2455566666654
No 85
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=22.42 E-value=56 Score=18.48 Aligned_cols=12 Identities=33% Similarity=0.880 Sum_probs=7.6
Q ss_pred ccCCCccccCCC
Q psy3924 80 CKWCAQCLTCGA 91 (131)
Q Consensus 80 C~~C~~c~~Cg~ 91 (131)
-+.|..|..|+.
T Consensus 23 H~~Cf~C~~C~~ 34 (58)
T PF00412_consen 23 HPECFKCSKCGK 34 (58)
T ss_dssp ETTTSBETTTTC
T ss_pred EccccccCCCCC
Confidence 356667777764
No 86
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=20.44 E-value=64 Score=15.82 Aligned_cols=9 Identities=22% Similarity=0.803 Sum_probs=4.1
Q ss_pred CceeeCcCC
Q psy3924 50 RLILCDECD 58 (131)
Q Consensus 50 ~ll~Cd~C~ 58 (131)
...+|..|+
T Consensus 15 ~~~fC~~CG 23 (26)
T PF13248_consen 15 DAKFCPNCG 23 (26)
T ss_pred ccccChhhC
Confidence 334455544
Done!