Query 041992
Match_columns 473
No_of_seqs 240 out of 831
Neff 4.1
Searched_HMMs 46136
Date Fri Mar 29 12:53:46 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/041992.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/041992hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 smart00719 Plus3 Short conserv 99.1 7.7E-11 1.7E-15 102.7 6.2 59 337-395 51-109 (109)
2 PF03126 Plus-3: Plus-3 domain 98.9 1.3E-09 2.9E-14 94.2 4.7 60 337-396 48-107 (108)
3 KOG1244 Predicted transcriptio 98.4 4.6E-08 1E-12 97.9 0.2 93 121-216 223-332 (336)
4 COG5034 TNG2 Chromatin remodel 98.4 1.3E-07 2.9E-12 93.8 3.2 47 119-169 218-267 (271)
5 KOG1512 PHD Zn-finger protein 98.4 7E-08 1.5E-12 97.2 1.3 87 122-213 258-361 (381)
6 KOG4443 Putative transcription 98.4 7.1E-08 1.5E-12 105.2 0.8 94 119-215 15-118 (694)
7 KOG4299 PHD Zn-finger protein 98.2 3.1E-07 6.7E-12 99.9 1.2 49 122-172 253-305 (613)
8 KOG4299 PHD Zn-finger protein 98.2 1.9E-06 4.2E-11 93.8 6.4 54 170-223 255-313 (613)
9 KOG1973 Chromatin remodeling p 98.2 6.4E-07 1.4E-11 89.5 1.6 48 119-169 216-265 (274)
10 smart00249 PHD PHD zinc finger 98.2 1.8E-06 3.8E-11 61.6 3.3 44 124-169 1-47 (47)
11 KOG0383 Predicted helicase [Ge 98.0 2.9E-06 6.2E-11 94.3 2.9 74 141-216 1-95 (696)
12 PF00628 PHD: PHD-finger; Int 97.9 2.7E-06 5.9E-11 63.7 0.2 44 124-169 1-48 (51)
13 KOG1081 Transcription factor N 97.7 8.7E-05 1.9E-09 79.5 7.3 141 115-274 82-230 (463)
14 KOG0383 Predicted helicase [Ge 97.6 1.5E-05 3.3E-10 88.7 1.0 53 118-173 43-95 (696)
15 KOG2402 Paf1/RNA polymerase II 97.6 0.00034 7.4E-09 75.8 9.7 112 336-447 263-395 (525)
16 PF15446 zf-PHD-like: PHD/FYVE 97.4 0.00016 3.4E-09 68.6 4.3 72 124-197 1-142 (175)
17 KOG1473 Nucleosome remodeling 97.4 3E-05 6.4E-10 89.2 -0.8 116 116-235 338-498 (1414)
18 KOG0956 PHD finger protein AF1 97.3 8.1E-05 1.8E-09 82.4 1.8 95 124-221 7-186 (900)
19 COG5296 Transcription factor i 97.3 0.0016 3.5E-08 68.8 10.8 107 337-443 256-383 (521)
20 KOG1244 Predicted transcriptio 96.9 0.00036 7.8E-09 70.6 1.3 42 123-167 282-326 (336)
21 smart00249 PHD PHD zinc finger 96.9 0.0011 2.3E-08 47.1 3.3 43 170-212 1-47 (47)
22 KOG4443 Putative transcription 96.8 0.00054 1.2E-08 75.7 2.0 71 123-196 69-154 (694)
23 KOG0825 PHD Zn-finger protein 96.6 0.0011 2.4E-08 74.6 2.1 46 121-169 214-263 (1134)
24 KOG0954 PHD finger protein [Ge 96.5 0.0011 2.3E-08 74.3 1.3 46 119-169 268-318 (893)
25 KOG0955 PHD finger protein BR1 96.4 0.0029 6.2E-08 73.7 4.4 66 118-191 215-285 (1051)
26 PF00628 PHD: PHD-finger; Int 96.2 0.0016 3.4E-08 48.7 0.5 44 170-213 1-49 (51)
27 COG5141 PHD zinc finger-contai 96.0 0.0026 5.5E-08 68.8 1.3 47 118-169 189-240 (669)
28 KOG1512 PHD Zn-finger protein 95.8 0.0044 9.5E-08 63.4 1.6 39 124-167 316-357 (381)
29 cd04718 BAH_plant_2 BAH, or Br 95.7 0.0066 1.4E-07 56.7 2.4 32 145-177 1-32 (148)
30 KOG0825 PHD Zn-finger protein 95.2 0.01 2.2E-07 67.2 2.3 46 169-215 216-266 (1134)
31 KOG4323 Polycomb-like PHD Zn-f 94.8 0.035 7.6E-07 60.0 5.0 41 125-167 171-219 (464)
32 KOG1946 RNA polymerase I trans 94.7 0.019 4.2E-07 57.3 2.5 43 236-278 2-44 (240)
33 PF13771 zf-HC5HC2H: PHD-like 94.3 0.017 3.6E-07 47.8 0.8 49 121-169 35-89 (90)
34 KOG4323 Polycomb-like PHD Zn-f 93.5 0.041 8.9E-07 59.5 2.2 96 121-221 82-230 (464)
35 KOG1245 Chromatin remodeling c 93.0 0.023 5E-07 68.4 -0.7 48 119-169 1105-1155(1404)
36 KOG0957 PHD finger protein [Ge 92.6 0.052 1.1E-06 59.2 1.3 44 170-214 546-597 (707)
37 KOG0957 PHD finger protein [Ge 92.2 0.13 2.8E-06 56.3 3.7 45 121-167 543-593 (707)
38 KOG1973 Chromatin remodeling p 91.8 0.12 2.5E-06 52.2 2.7 50 159-215 215-268 (274)
39 KOG0955 PHD finger protein BR1 91.4 0.11 2.4E-06 61.0 2.3 42 170-214 221-268 (1051)
40 cd04718 BAH_plant_2 BAH, or Br 90.2 0.16 3.5E-06 47.6 1.8 27 188-215 1-27 (148)
41 PF13832 zf-HC5HC2H_2: PHD-zin 86.5 0.35 7.5E-06 41.6 1.4 34 121-154 54-88 (110)
42 KOG3362 Predicted BBOX Zn-fing 85.5 0.33 7.2E-06 45.6 0.8 44 143-195 102-146 (156)
43 COG5141 PHD zinc finger-contai 82.1 0.53 1.1E-05 51.7 0.7 42 170-214 195-242 (669)
44 KOG1245 Chromatin remodeling c 81.4 0.37 8E-06 58.5 -0.8 45 170-215 1110-1158(1404)
45 KOG0956 PHD finger protein AF1 79.6 0.78 1.7E-05 52.1 0.9 33 179-214 22-56 (900)
46 PF13832 zf-HC5HC2H_2: PHD-zin 79.0 1.7 3.8E-05 37.2 2.7 72 124-197 2-88 (110)
47 KOG3612 PHD Zn-finger protein 78.7 2.3 5E-05 47.2 4.1 56 117-176 55-110 (588)
48 PF13831 PHD_2: PHD-finger; PD 77.0 0.47 1E-05 34.4 -1.1 31 179-212 4-35 (36)
49 PF13831 PHD_2: PHD-finger; PD 75.7 0.52 1.1E-05 34.2 -1.2 34 132-169 2-35 (36)
50 KOG0954 PHD finger protein [Ge 75.3 1.3 2.7E-05 50.8 1.1 43 170-215 273-321 (893)
51 KOG4628 Predicted E3 ubiquitin 73.0 1.8 3.9E-05 45.7 1.4 44 123-177 230-276 (348)
52 PF10497 zf-4CXXC_R1: Zinc-fin 66.8 2.4 5.2E-05 37.4 0.7 45 170-214 9-69 (105)
53 COG5034 TNG2 Chromatin remodel 66.0 3.6 7.9E-05 41.9 1.9 40 173-215 225-270 (271)
54 PF11793 FANCL_C: FANCL C-term 61.1 4.5 9.8E-05 33.0 1.3 34 122-155 2-41 (70)
55 PF14446 Prok-RING_1: Prokaryo 58.4 5.4 0.00012 31.8 1.2 30 123-154 6-39 (54)
56 PF02178 AT_hook: AT hook moti 57.7 4.6 0.0001 23.7 0.6 11 92-102 1-11 (13)
57 PF04438 zf-HIT: HIT zinc fing 57.4 3.9 8.5E-05 28.7 0.3 25 167-191 1-25 (30)
58 PF13901 DUF4206: Domain of un 55.2 6.6 0.00014 38.1 1.5 27 179-215 172-198 (202)
59 smart00384 AT_hook DNA binding 54.4 8.2 0.00018 26.7 1.4 12 92-103 1-12 (26)
60 PF06524 NOA36: NOA36 protein; 49.3 13 0.00029 38.3 2.6 46 170-215 173-218 (314)
61 KOG1428 Inhibitor of type V ad 48.1 3.7 7.9E-05 50.5 -1.7 54 118-176 3482-3541(3738)
62 KOG1473 Nucleosome remodeling 47.5 11 0.00023 45.5 1.8 43 170-213 346-389 (1414)
63 PF11793 FANCL_C: FANCL C-term 44.4 13 0.00028 30.3 1.4 38 179-216 20-65 (70)
64 PF05565 Sipho_Gp157: Siphovir 42.8 92 0.002 29.2 7.0 56 375-439 15-75 (162)
65 COG5082 AIR1 Arginine methyltr 41.1 21 0.00046 35.0 2.5 50 119-178 57-107 (190)
66 PF14446 Prok-RING_1: Prokaryo 41.0 15 0.00032 29.4 1.2 27 169-195 6-37 (54)
67 PF07649 C1_3: C1-like domain; 40.7 12 0.00025 25.7 0.5 25 170-194 2-30 (30)
68 PF15446 zf-PHD-like: PHD/FYVE 40.6 14 0.0003 35.8 1.2 26 171-196 2-34 (175)
69 smart00064 FYVE Protein presen 39.6 13 0.00028 29.3 0.7 46 170-215 12-65 (68)
70 PF05502 Dynactin_p62: Dynacti 37.8 36 0.00078 37.4 3.9 29 133-169 4-32 (483)
71 PRK14714 DNA polymerase II lar 36.8 47 0.001 40.8 4.9 37 170-216 681-719 (1337)
72 PRK14559 putative protein seri 36.7 21 0.00045 40.7 2.0 12 203-214 38-49 (645)
73 PF07227 DUF1423: Protein of u 36.4 34 0.00074 37.5 3.4 52 165-216 125-193 (446)
74 PF13771 zf-HC5HC2H: PHD-like 35.5 23 0.00051 29.1 1.6 31 168-198 36-70 (90)
75 PF00641 zf-RanBP: Zn-finger i 34.4 24 0.00053 24.0 1.3 9 161-169 2-10 (30)
76 PF13901 DUF4206: Domain of un 34.4 26 0.00057 33.9 2.0 28 124-153 154-189 (202)
77 KOG2807 RNA polymerase II tran 34.3 26 0.00056 37.3 2.1 39 170-213 332-374 (378)
78 PRK04023 DNA polymerase II lar 34.0 63 0.0014 39.0 5.3 29 244-277 683-711 (1121)
79 PLN02915 cellulose synthase A 33.3 34 0.00073 41.1 3.0 52 165-220 12-71 (1044)
80 KOG1701 Focal adhesion adaptor 33.3 36 0.00077 37.4 2.9 74 141-214 351-460 (468)
81 PF07749 ERp29: Endoplasmic re 31.1 40 0.00086 29.0 2.4 16 420-435 58-73 (95)
82 PF13639 zf-RING_2: Ring finge 30.4 10 0.00022 27.5 -1.1 31 123-156 1-35 (44)
83 PLN02436 cellulose synthase A 30.0 43 0.00093 40.4 3.1 68 166-237 34-109 (1094)
84 PF03833 PolC_DP2: DNA polymer 29.3 18 0.00039 42.5 0.0 40 161-215 653-701 (900)
85 PF12861 zf-Apc11: Anaphase-pr 28.7 20 0.00044 31.0 0.2 33 121-156 20-66 (85)
86 PF11629 Mst1_SARAH: C termina 28.7 1.2E+02 0.0027 24.0 4.4 33 396-433 2-34 (49)
87 PLN02189 cellulose synthase 28.6 43 0.00094 40.2 2.9 68 166-237 32-107 (1040)
88 PF03107 C1_2: C1 domain; Int 28.2 49 0.0011 22.8 2.0 25 170-194 2-30 (30)
89 KOG2932 E3 ubiquitin ligase in 27.6 20 0.00043 37.9 -0.1 55 123-189 91-157 (389)
90 PF02318 FYVE_2: FYVE-type zin 27.6 17 0.00036 32.3 -0.6 45 168-216 54-104 (118)
91 KOG3576 Ovo and related transc 27.4 12 0.00025 37.6 -1.6 70 132-215 115-221 (267)
92 KOG1734 Predicted RING-contain 27.2 15 0.00033 38.1 -0.9 45 169-216 225-280 (328)
93 KOG0804 Cytoplasmic Zn-finger 26.9 33 0.00071 37.8 1.4 33 120-155 173-210 (493)
94 KOG1246 DNA-binding protein ju 26.3 53 0.0012 38.6 3.0 54 119-175 152-207 (904)
95 PF10497 zf-4CXXC_R1: Zinc-fin 26.2 30 0.00064 30.6 0.8 35 143-177 37-79 (105)
96 cd00065 FYVE FYVE domain; Zinc 25.9 45 0.00098 25.1 1.7 44 171-214 5-56 (57)
97 PF10367 Vps39_2: Vacuolar sor 25.8 40 0.00086 28.1 1.4 32 119-152 75-108 (109)
98 smart00547 ZnF_RBZ Zinc finger 25.3 38 0.00082 22.1 1.0 8 162-169 1-8 (26)
99 PLN02638 cellulose synthase A 25.1 53 0.0011 39.7 2.7 50 168-221 17-74 (1079)
100 PF08746 zf-RING-like: RING-li 24.6 22 0.00048 26.6 -0.3 39 171-212 1-43 (43)
101 PLN02400 cellulose synthase 23.5 63 0.0014 39.1 3.0 66 167-236 35-108 (1085)
102 TIGR01562 FdhE formate dehydro 23.4 1E+02 0.0022 32.2 4.2 13 207-219 253-265 (305)
103 COG1645 Uncharacterized Zn-fin 23.4 41 0.00089 31.3 1.2 53 198-253 37-89 (131)
104 KOG1671 Ubiquinol cytochrome c 23.3 43 0.00092 33.4 1.3 20 147-168 155-174 (210)
105 cd00238 ERp29c ERp29 and ERp38 23.3 62 0.0013 28.0 2.2 16 420-435 56-71 (93)
106 TIGR00570 cdk7 CDK-activating 23.1 35 0.00076 35.8 0.7 43 170-216 5-53 (309)
107 PF07191 zinc-ribbons_6: zinc- 23.0 54 0.0012 27.6 1.7 36 179-216 17-60 (70)
108 KOG1701 Focal adhesion adaptor 21.8 61 0.0013 35.6 2.2 111 122-238 274-422 (468)
109 COG5432 RAD18 RING-finger-cont 21.8 22 0.00048 37.3 -1.0 41 170-215 27-68 (391)
110 PRK03564 formate dehydrogenase 21.7 98 0.0021 32.5 3.7 13 207-219 253-265 (309)
111 PF00130 C1_1: Phorbol esters/ 21.6 67 0.0015 23.9 1.9 28 170-197 13-46 (53)
112 PRK05467 Fe(II)-dependent oxyg 21.3 88 0.0019 31.3 3.1 28 380-407 7-36 (226)
113 COG2888 Predicted Zn-ribbon RN 21.3 43 0.00093 27.5 0.8 25 162-186 26-57 (61)
114 PF03285 Paralemmin: Paralemmi 20.6 94 0.002 32.2 3.2 26 405-432 6-31 (278)
115 PHA02696 hypothetical protein; 20.5 59 0.0013 27.5 1.4 22 373-394 40-61 (79)
116 cd00162 RING RING-finger (Real 20.4 32 0.0007 23.3 -0.1 40 171-214 2-43 (45)
No 1
>smart00719 Plus3 Short conserved domain in transcriptional regulators. Plus3 domains occur in the Saccharomyces cerevisiae Rtf1p protein, which interacts with Spt6p, and in parsley CIP, which interacts with the bZIP protein CPRF1.
Probab=99.13 E-value=7.7e-11 Score=102.66 Aligned_cols=59 Identities=41% Similarity=0.717 Sum_probs=56.3
Q ss_pred ceeeeeeeecCcccccCCcccceEEEeeCCCccceeeeecccCCCCCHHHHHHHHHHhh
Q 041992 337 MPLIKGTSKVGKPYKIGDRTADVILEIRNLQKKEVVAIDAISNQEFSEDECSRLRQSIK 395 (473)
Q Consensus 337 l~qV~G~~k~~e~yk~~~~~~~i~L~i~nl~k~~~i~i~~ls~~df~eeEC~~lrq~ik 395 (473)
|+||+|+.+..++|++++++|++.|.+.+-...++++|++|||++|||+||++++|.++
T Consensus 51 l~qI~gv~~~~k~Y~~~~~~t~~~L~v~~g~~~~~~~i~~iSn~~fte~E~~~w~~~~~ 109 (109)
T smart00719 51 LVQVTGVKEADKPYELGGKTTNVLLEVLNGDSEKVVQINFISNQDFTEEEFQRWKQAIK 109 (109)
T ss_pred EEEEeeEEecCcceecCCceeeEEEEEecCCceEEEEEEEecCCCCCHHHHHHHHHHhC
Confidence 99999999999999999999999999988777889999999999999999999999875
No 2
>PF03126 Plus-3: Plus-3 domain; InterPro: IPR004343 The yeast Paf1 complex consists of Pfa1, Rtf1, Cdc73, Ctr9, and Leo1. The complex regulates histone H2B ubiquitination, histone H3 methylation, RNA polymerase II carboxy-terminal domain (CTD) Ser2 phosphorylation, and RNA 3' end processing. The conservation of Paf1 complex function in higher eukaryotes has been confirmed in human cells, Drosophila and Arabidopsis. The Plus3 domain spans the most conserved regions of the Rtf1 protein and is surrounded by regions of low complexity and coiled-coil propensity []. It contains only a limited number of highly conserved amino acids, among which are three positively charged residues that gave the Plus3 domain its name. The capacity to bind single-stranded DNA is at least one function of the Plus3 domain []. The plus-3 domain is about 90 residues in length and is often found associated with the GYF domain (IPR003169 from INTERPRO). The Plus3 domain structure consists of six alpha helices intervened by a sequence of six beta strands in a mixed alpha/beta topology. Beta strands 1, 2, 5, and 6 compose a four-stranded antiparallel beta sheet with a beta-hairpin insertion formed by strands 3 and 4. The N-terminal helices alpha1-alpha3 and C-terminal helix alpha6 pack together to form an alpha subdomain, while the beta strands and the small 3(10) helix alpha 4 form a beta subdomain. The two subdomains pack together to form a compact, globular protein [].; GO: 0003677 DNA binding, 0006352 transcription initiation, DNA-dependent, 0016570 histone modification, 0005634 nucleus; PDB: 2BZE_A 3U1U_B 2DB9_A.
Probab=98.90 E-value=1.3e-09 Score=94.20 Aligned_cols=60 Identities=32% Similarity=0.493 Sum_probs=53.1
Q ss_pred ceeeeeeeecCcccccCCcccceEEEeeCCCccceeeeecccCCCCCHHHHHHHHHHhhh
Q 041992 337 MPLIKGTSKVGKPYKIGDRTADVILEIRNLQKKEVVAIDAISNQEFSEDECSRLRQSIKC 396 (473)
Q Consensus 337 l~qV~G~~k~~e~yk~~~~~~~i~L~i~nl~k~~~i~i~~ls~~df~eeEC~~lrq~ik~ 396 (473)
|+||+|+.....+|++++..|+..|.+.+-....++.|++|||++|||+||++++|.+++
T Consensus 48 l~qI~~v~~~~k~Y~~~~~~t~~~L~l~~g~~~r~~~i~~vSn~~~te~E~~~w~~~~~~ 107 (108)
T PF03126_consen 48 LCQIVGVKEGKKPYKLGSKKTNKYLVLRHGNSERDFPIDMVSNSPFTEEEFERWKQSCEK 107 (108)
T ss_dssp EEEEEEEEEEEEEEEETTEEEEEEEEEEETTEEEEEEGGGBBSS---HHHHHHHHHHH--
T ss_pred EEEEEEEecccccEecCCeEEEEEEEEEECCceeEEEeEeeECCCCCHHHHHHHHHHhcc
Confidence 999999999999999999999999999987778899999999999999999999999875
No 3
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=98.42 E-value=4.6e-08 Score=97.91 Aligned_cols=93 Identities=23% Similarity=0.589 Sum_probs=76.7
Q ss_pred ccccccccccc-------C---ceeecCCCCCCCcccccccCcccc--cCCCCCceeecCc-ccccccCCc----eeecc
Q 041992 121 EEDVCFICFDG-------G---SLVLCDRKGCPKAYHPACIKREES--FFRSKAKWNCGWH-ICSICEKAS----YYMCY 183 (473)
Q Consensus 121 ned~CfVC~dG-------G---eLv~CD~~gCPraYH~~CL~p~~~--~~~p~g~W~CP~H-~C~vC~k~s----l~~C~ 183 (473)
-..+|..|-.+ | +||.|. .|.|+-|++||..... ......+|.|-.| .|.+||-+. +++|+
T Consensus 223 Pn~YCDFclgdsr~nkkt~~peelvscs--dcgrsghpsclqft~nm~~avk~yrwqcieck~csicgtsenddqllfcd 300 (336)
T KOG1244|consen 223 PNPYCDFCLGDSRENKKTGMPEELVSCS--DCGRSGHPSCLQFTANMIAAVKTYRWQCIECKYCSICGTSENDDQLLFCD 300 (336)
T ss_pred CCcccceeccccccccccCCchhhcchh--hcCCCCCcchhhhhHHHHHHHHhheeeeeecceeccccCcCCCceeEeec
Confidence 45689999532 2 899999 8999999999986532 1124678999998 699999874 89999
Q ss_pred CCCccccccccCCCccccccCCeeecCCCCcch
Q 041992 184 TCTYSLCKGCTKGADYYSLRGNKGFCGICMRTI 216 (473)
Q Consensus 184 ~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~ 216 (473)
.|.+.||-.||. +++.+.|.+.|-|..|++.+
T Consensus 301 dcdrgyhmycls-ppm~eppegswsc~KOG~~~ 332 (336)
T KOG1244|consen 301 DCDRGYHMYCLS-PPMVEPPEGSWSCHLCLEEL 332 (336)
T ss_pred ccCCceeeEecC-CCcCCCCCCchhHHHHHHHH
Confidence 999999999998 56889999999999998753
No 4
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.42 E-value=1.3e-07 Score=93.78 Aligned_cols=47 Identities=36% Similarity=0.796 Sum_probs=41.0
Q ss_pred cccccccccccc--cCceeecCCCCCCC-cccccccCcccccCCCCCceeecCc
Q 041992 119 TEEEDVCFICFD--GGSLVLCDRKGCPK-AYHPACIKREESFFRSKAKWNCGWH 169 (473)
Q Consensus 119 ~~ned~CfVC~d--GGeLv~CD~~gCPr-aYH~~CL~p~~~~~~p~g~W~CP~H 169 (473)
..++-||| |.+ .|+||-||+.+|.+ +||+.|||... +|+|.||||.|
T Consensus 218 e~e~lYCf-CqqvSyGqMVaCDn~nCkrEWFH~~CVGLk~---pPKG~WYC~eC 267 (271)
T COG5034 218 EGEELYCF-CQQVSYGQMVACDNANCKREWFHLECVGLKE---PPKGKWYCPEC 267 (271)
T ss_pred cCceeEEE-ecccccccceecCCCCCchhheeccccccCC---CCCCcEeCHHh
Confidence 44667899 986 58999999999998 99999999986 68999999854
No 5
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.42 E-value=7e-08 Score=97.25 Aligned_cols=87 Identities=21% Similarity=0.432 Sum_probs=73.1
Q ss_pred ccccccccccC---------ceeecCCCCCCCcccccccCcccc--cCCCCCceeecCc-ccccccCCc----eeeccCC
Q 041992 122 EDVCFICFDGG---------SLVLCDRKGCPKAYHPACIKREES--FFRSKAKWNCGWH-ICSICEKAS----YYMCYTC 185 (473)
Q Consensus 122 ed~CfVC~dGG---------eLv~CD~~gCPraYH~~CL~p~~~--~~~p~g~W~CP~H-~C~vC~k~s----l~~C~~C 185 (473)
...|.+|.+|- .+++|. .|-.+|||.|+..+.. .+.....|.|-.| .|.+|+++. ++.|+.|
T Consensus 258 ~~~~~~~~~~~~~~~~~r~~S~I~C~--~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~lC~IC~~P~~E~E~~FCD~C 335 (381)
T KOG1512|consen 258 RNERKHFWDIQTNIIQSRRNSWIVCK--PCATRPHPYCVAMIPELVGQYKTYFWKCSSCELCRICLGPVIESEHLFCDVC 335 (381)
T ss_pred hhhhhhhhcchhhhhhhhhccceeec--ccccCCCCcchhcCHHHHhHHhhcchhhcccHhhhccCCcccchheeccccc
Confidence 45699997653 699999 7999999999998753 2345678999998 799999985 7999999
Q ss_pred CccccccccCCCccccccCCeeecC-CCC
Q 041992 186 TYSLCKGCTKGADYYSLRGNKGFCG-ICM 213 (473)
Q Consensus 186 p~AyH~~CL~~~~~~sv~~~kwfC~-~C~ 213 (473)
.+.||..|+. +..+|.+.|.|. .|.
T Consensus 336 DRG~HT~CVG---L~~lP~G~WICD~~C~ 361 (381)
T KOG1512|consen 336 DRGPHTLCVG---LQDLPRGEWICDMRCR 361 (381)
T ss_pred cCCCCccccc---cccccCccchhhhHHH
Confidence 9999999998 678899999998 454
No 6
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=98.39 E-value=7.1e-08 Score=105.22 Aligned_cols=94 Identities=23% Similarity=0.581 Sum_probs=75.4
Q ss_pred cccccccccccccC-----ceeecCCCCCCCcccccccCcccccCCCCCceeecCc-ccccccCCc----eeeccCCCcc
Q 041992 119 TEEEDVCFICFDGG-----SLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH-ICSICEKAS----YYMCYTCTYS 188 (473)
Q Consensus 119 ~~ned~CfVC~dGG-----eLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H-~C~vC~k~s----l~~C~~Cp~A 188 (473)
......|++|+..| .|+.|. .|...||+.||........-.+.|.||.| .|..|+..+ ++.|..|.-+
T Consensus 15 ~~~~~mc~l~~s~G~~~ag~m~ac~--~c~~~yH~~cvt~~~~~~~l~~gWrC~~crvCe~c~~~gD~~kf~~Ck~cDvs 92 (694)
T KOG4443|consen 15 IIVCLMCPLCGSSGKGRAGRLLACS--DCGQKYHPYCVTSWAQHAVLSGGWRCPSCRVCEACGTTGDPKKFLLCKRCDVS 92 (694)
T ss_pred hhhhhhhhhhccccccccCcchhhh--hhcccCCcchhhHHHhHHHhcCCcccCCceeeeeccccCCccccccccccccc
Confidence 34566799997654 689999 79999999999965432223456999999 699999655 7899999999
Q ss_pred ccccccCCCccccccCCeeecCCCCcc
Q 041992 189 LCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 189 yH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
||.+|+. ++...++.+.|+|..|.+.
T Consensus 93 yh~yc~~-P~~~~v~sg~~~ckk~~~c 118 (694)
T KOG4443|consen 93 YHCYCQK-PPNDKVPSGPWLCKKCTRC 118 (694)
T ss_pred ccccccC-CccccccCcccccHHHHhh
Confidence 9999998 4578899999999866553
No 7
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.24 E-value=3.1e-07 Score=99.87 Aligned_cols=49 Identities=29% Similarity=0.717 Sum_probs=42.4
Q ss_pred ccccccccccCce---eecCCCCCCCcccccccCcccc-cCCCCCceeecCcccc
Q 041992 122 EDVCFICFDGGSL---VLCDRKGCPKAYHPACIKREES-FFRSKAKWNCGWHICS 172 (473)
Q Consensus 122 ed~CfVC~dGGeL---v~CD~~gCPraYH~~CL~p~~~-~~~p~g~W~CP~H~C~ 172 (473)
++||+.|...|.. +||| +||++||+.||.|+.. ..+|.|.|+||.|.|.
T Consensus 253 ~~fCsaCn~~~~F~~~i~CD--~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLFNDIICCD--GCPRSFHQTCLEPPLEPENIPPGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCccccccceeec--CCchHHHHhhcCCCCCcccCCCCccccCCCeee
Confidence 5699999998866 9999 7999999999999953 3368999999987765
No 8
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=98.20 E-value=1.9e-06 Score=93.84 Aligned_cols=54 Identities=19% Similarity=0.402 Sum_probs=45.1
Q ss_pred ccccccCCce----eeccCCCccccccccCCCc-cccccCCeeecCCCCcchhhhhccC
Q 041992 170 ICSICEKASY----YMCYTCTYSLCKGCTKGAD-YYSLRGNKGFCGICMRTIMLIENCA 223 (473)
Q Consensus 170 ~C~vC~k~sl----~~C~~Cp~AyH~~CL~~~~-~~sv~~~kwfC~~C~~~~~~iE~~~ 223 (473)
+|..|++.+. ++|+.||++||..||.++. ...+|.+.|||..|...+...+...
T Consensus 255 fCsaCn~~~~F~~~i~CD~Cp~sFH~~CLePPl~~eniP~g~W~C~ec~~k~~in~~~~ 313 (613)
T KOG4299|consen 255 FCSACNGSGLFNDIICCDGCPRSFHQTCLEPPLEPENIPPGSWFCPECKIKSVINPKME 313 (613)
T ss_pred HHHHhCCccccccceeecCCchHHHHhhcCCCCCcccCCCCccccCCCeeeeecccchh
Confidence 7999999873 6899999999999999752 4578999999999998776666654
No 9
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=98.16 E-value=6.4e-07 Score=89.52 Aligned_cols=48 Identities=29% Similarity=0.753 Sum_probs=38.9
Q ss_pred cccccccccc-cccCceeecCCCCCC-CcccccccCcccccCCCCCceeecCc
Q 041992 119 TEEEDVCFIC-FDGGSLVLCDRKGCP-KAYHPACIKREESFFRSKAKWNCGWH 169 (473)
Q Consensus 119 ~~ned~CfVC-~dGGeLv~CD~~gCP-raYH~~CL~p~~~~~~p~g~W~CP~H 169 (473)
.++..||+.. ...|+||-||+.+|| .+||+.|||+.. .|.|.||||.|
T Consensus 216 ~~e~~yC~Cnqvsyg~Mi~CDn~~C~~eWFH~~CVGL~~---~PkgkWyC~~C 265 (274)
T KOG1973|consen 216 PDEPTYCICNQVSYGKMIGCDNPGCPIEWFHFTCVGLKT---KPKGKWYCPRC 265 (274)
T ss_pred CCCCEEEEecccccccccccCCCCCCcceEEEecccccc---CCCCcccchhh
Confidence 3455667633 358999999988999 899999999985 58999999954
No 10
>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 KOG0383 consensus Predicted helicase [General function prediction only]
Probab=98.01 E-value=2.9e-06 Score=94.34 Aligned_cols=74 Identities=23% Similarity=0.513 Sum_probs=61.2
Q ss_pred CCCCcccccccCcccccCCCCCceeecCc--------------------ccccccCCc-eeeccCCCccccccccCCCcc
Q 041992 141 GCPKAYHPACIKREESFFRSKAKWNCGWH--------------------ICSICEKAS-YYMCYTCTYSLCKGCTKGADY 199 (473)
Q Consensus 141 gCPraYH~~CL~p~~~~~~p~g~W~CP~H--------------------~C~vC~k~s-l~~C~~Cp~AyH~~CL~~~~~ 199 (473)
.|||+||..|+.|.... .+.++|.||.| .|.+|+.++ +++|+.||.+||..|+.. +.
T Consensus 1 ~~~r~~~~~~~~p~~~~-~~~~~~k~~~~e~~~~~~~~~~~~~~~~~~e~c~ic~~~g~~l~c~tC~~s~h~~cl~~-pl 78 (696)
T KOG0383|consen 1 TCPRAYHRVCLDPKLKE-EPEMDPKCPGCESSSAQVEAKDDDWDDAEQEACRICADGGELLWCDTCPASFHASCLGP-PL 78 (696)
T ss_pred CCCcccCcCCCCccccc-CCcCCccCcchhhcccccccccCCcchhhhhhhhhhcCCCcEEEeccccHHHHHHccCC-CC
Confidence 39999999999987643 46899999975 699999987 788999999999999974 45
Q ss_pred ccccCCeeecCCCCcch
Q 041992 200 YSLRGNKGFCGICMRTI 216 (473)
Q Consensus 200 ~sv~~~kwfC~~C~~~~ 216 (473)
...+.+.|.|..|..+.
T Consensus 79 ~~~p~~~~~c~Rc~~p~ 95 (696)
T KOG0383|consen 79 TPQPNGEFICPRCFCPK 95 (696)
T ss_pred CcCCccceeeeeeccCC
Confidence 66666669999885543
No 12
>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=97.89 E-value=2.7e-06 Score=63.69 Aligned_cols=44 Identities=27% Similarity=0.718 Sum_probs=35.1
Q ss_pred ccccccc---cCceeecCCCCCCCcccccccCcccccC-CCCCceeecCc
Q 041992 124 VCFICFD---GGSLVLCDRKGCPKAYHPACIKREESFF-RSKAKWNCGWH 169 (473)
Q Consensus 124 ~CfVC~d---GGeLv~CD~~gCPraYH~~CL~p~~~~~-~p~g~W~CP~H 169 (473)
+|.+|+. .+++|.|+ .|.++||..|++++.... .+.+.|+||.|
T Consensus 1 ~C~vC~~~~~~~~~i~C~--~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C 48 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCD--SCNRWYHQECVGPPEKAEEIPSGDWYCPNC 48 (51)
T ss_dssp EBTTTTSSCTTSSEEEBS--TTSCEEETTTSTSSHSHHSHHSSSBSSHHH
T ss_pred eCcCCCCcCCCCCeEEcC--CCChhhCcccCCCChhhccCCCCcEECcCC
Confidence 5888887 67999999 799999999999986421 23459999854
No 13
>KOG1081 consensus Transcription factor NSD1 and related SET domain proteins [Transcription]
Probab=97.67 E-value=8.7e-05 Score=79.53 Aligned_cols=141 Identities=17% Similarity=0.111 Sum_probs=90.4
Q ss_pred CCCccccccccccccccCceeecC------CCCCCCcccccccCc--ccccCCCCCceeecCcccccccCCceeeccCCC
Q 041992 115 GRRKTEEEDVCFICFDGGSLVLCD------RKGCPKAYHPACIKR--EESFFRSKAKWNCGWHICSICEKASYYMCYTCT 186 (473)
Q Consensus 115 ~~~~~~ned~CfVC~dGGeLv~CD------~~gCPraYH~~CL~p--~~~~~~p~g~W~CP~H~C~vC~k~sl~~C~~Cp 186 (473)
+.....+.++||+|.+||.++.|+ .+.|+.+||+.|+.. ...++.....|.|-|+.|..|....-+.|..
T Consensus 82 ~~~~~~~~~~c~vc~~ggs~v~~~s~~~~~~r~c~~~~~~~c~~~~~d~~~~~~~~~~~~vw~~vg~~~~~~c~vc~~-- 159 (463)
T KOG1081|consen 82 RRHPKIEPSECFVCFKGGSLVTCKSRIQAPHRKCKPAQLEKCSKRCTDCRAFKKREVGDLVWSKVGEYPWWPCMVCHD-- 159 (463)
T ss_pred hhccCCCcchhccccCCCccceeccccccccccCcCccCcccccCCcceeeeccccceeEEeEEcCcccccccceecC--
Confidence 455678899999999999999999 999999999999998 4444456678999888777666544222211
Q ss_pred ccccccccCCCccccccCCeeecCCCCcchhhhhccCCCCCCceeeecCCCCccchhhHHHHHHhhhccCCChhhhhhcC
Q 041992 187 YSLCKGCTKGADYYSLRGNKGFCGICMRTIMLIENCAPGNQEKVVVDFDDKTSWEYLFKVYWIFLKEKLSLTLDELTGAK 266 (473)
Q Consensus 187 ~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~~~iE~~~~~dseg~~VDf~D~~~~e~lfK~Yw~~iK~~~~Lt~~~l~~a~ 266 (473)
..++ +... .. ...+..| .....+...... ..+|.+... ++|+.||..-+.....+..-...+.
T Consensus 160 ~~~~---~~~~-----~~-~~~f~~~-~~~~~~~~~~~~-----~g~~~~~l~--~~~~~~s~~~~~~~~~~~r~~~~~~ 222 (463)
T KOG1081|consen 160 PLLP---KGMK-----HD-HVNFFGC-YAWTHEKRVFPY-----EGQSSKLIP--HSKKPASTMSEKIKEAKARFGKLKA 222 (463)
T ss_pred cccc---hhhc-----cc-cceeccc-hhhHHHhhhhhc-----cchHHHhhh--hccccchhhhhhhhcccchhhhccc
Confidence 2222 1111 00 1222334 333333332222 344554334 8888888888888777776666666
Q ss_pred CCCCCCCC
Q 041992 267 NPWKEPAI 274 (473)
Q Consensus 267 ~~~k~~~~ 274 (473)
.++++...
T Consensus 223 q~~~~~~~ 230 (463)
T KOG1081|consen 223 QWEAGIKQ 230 (463)
T ss_pred chhhccch
Confidence 66666655
No 14
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=97.63 E-value=1.5e-05 Score=88.68 Aligned_cols=53 Identities=30% Similarity=0.820 Sum_probs=45.1
Q ss_pred ccccccccccccccCceeecCCCCCCCcccccccCcccccCCCCCceeecCccccc
Q 041992 118 KTEEEDVCFICFDGGSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWHICSI 173 (473)
Q Consensus 118 ~~~ned~CfVC~dGGeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H~C~v 173 (473)
...+...|.+|+++|++++|+ .||.+||..|++++... .|.+.|.|++|.|..
T Consensus 43 ~~~~~e~c~ic~~~g~~l~c~--tC~~s~h~~cl~~pl~~-~p~~~~~c~Rc~~p~ 95 (696)
T KOG0383|consen 43 DDAEQEACRICADGGELLWCD--TCPASFHASCLGPPLTP-QPNGEFICPRCFCPK 95 (696)
T ss_pred chhhhhhhhhhcCCCcEEEec--cccHHHHHHccCCCCCc-CCccceeeeeeccCC
Confidence 456778899999999999999 89999999999998765 466779999776553
No 15
>KOG2402 consensus Paf1/RNA polymerase II complex, RTF1 component (involved in regulation of TATA box-binding protein) [Transcription]
Probab=97.55 E-value=0.00034 Score=75.84 Aligned_cols=112 Identities=26% Similarity=0.281 Sum_probs=94.9
Q ss_pred cceeeeeeeecCcccccCCcccceEEEeeCCCccceeeeecccCCCCCHHHHHHHHHHhhhcccccchHHHHHHHHHHHH
Q 041992 336 GMPLIKGTSKVGKPYKIGDRTADVILEIRNLQKKEVVAIDAISNQEFSEDECSRLRQSIKCGFIKHLTVGEIQEKAMSLQ 415 (473)
Q Consensus 336 ~l~qV~G~~k~~e~yk~~~~~~~i~L~i~nl~k~~~i~i~~ls~~df~eeEC~~lrq~ik~gl~kr~tv~~~eeka~~l~ 415 (473)
.+++|+||-.+..+|+++.+.|+..|.+++=....+-.|.+|||++|+|+|-++++..++.--+.-|||-.|.+|-..|.
T Consensus 263 Rv~~I~gV~es~k~Y~l~~~~Tnk~l~~~~G~s~r~f~m~~iSn~~f~e~Efq~w~~~~~~s~~~~PT~~~i~~K~~~i~ 342 (525)
T KOG2402|consen 263 RVAEIVGVLESDKPYKLEGVKTNKYLRVRHGRSERVFRMNFISNGEFTEEEFQDWLRACKNSHGIMPTVDLISRKKLDIV 342 (525)
T ss_pred eEEEEeeecccCccccccceeecceeeeecCcchhhcchhhhcCCcccHHHHHHHHHHHHhhcCCCchHHHHHHHHHHHH
Confidence 38999999999999999999999999999644456899999999999999999999999999999999999999987776
Q ss_pred HH------------HHHH---------HHHHHHHHHHhhHhhhhhcccccccc
Q 041992 416 AL------------RVND---------LLESEILRLNNLRDRASEKGHRKEYP 447 (473)
Q Consensus 416 ~~------------~~~~---------wi~~e~~rl~~l~dra~ekg~r~e~p 447 (473)
.. ||++ =++-|..+|..-+|.|.+.|--+..+
T Consensus 343 ~a~~~~~sd~~v~~~v~~k~~~~~~p~N~ameK~~l~k~r~~A~~~~d~~~a~ 395 (525)
T KOG2402|consen 343 KALNYRLSDKEVDQMVAEKFEASPRPRNVAMEKTGLRKERDLAQLLGDAKSAE 395 (525)
T ss_pred HHhcCccCcccHHHHHHhhhhcCcCcchHHHHHHhHHHHHHHHHhcccHhHHH
Confidence 43 4554 35667788888888888877655444
No 16
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=97.40 E-value=0.00016 Score=68.59 Aligned_cols=72 Identities=25% Similarity=0.625 Sum_probs=52.9
Q ss_pred ccccccc------cCceeecCCCCCCCcccccccCcccc--c---CCCCCce--eecCc---------------cccccc
Q 041992 124 VCFICFD------GGSLVLCDRKGCPKAYHPACIKREES--F---FRSKAKW--NCGWH---------------ICSICE 175 (473)
Q Consensus 124 ~CfVC~d------GGeLv~CD~~gCPraYH~~CL~p~~~--~---~~p~g~W--~CP~H---------------~C~vC~ 175 (473)
.|.+|+. -|.||.|. ||..+||..||++... . ....+.| .|-+| .|..|+
T Consensus 1 ~C~~C~~~g~~~~kG~Lv~CQ--GCs~sYHk~CLG~Rs~ReHlVTKVg~d~FVLQCr~Cig~~~kKD~~aP~~~~C~~C~ 78 (175)
T PF15446_consen 1 TCDTCGYEGDDRNKGPLVYCQ--GCSSSYHKACLGPRSQREHLVTKVGDDDFVLQCRRCIGIAHKKDPRAPHHGMCQQCK 78 (175)
T ss_pred CcccccCCCCCccCCCeEEcC--ccChHHHhhhcCCccccceeeEEEcCCceEEechhhcChhhcccCCCCCCCcccccC
Confidence 3777843 36899999 8999999999998642 1 0122333 35544 688888
Q ss_pred CCc------------------------------------------eeeccCCCccccccccCCC
Q 041992 176 KAS------------------------------------------YYMCYTCTYSLCKGCTKGA 197 (473)
Q Consensus 176 k~s------------------------------------------l~~C~~Cp~AyH~~CL~~~ 197 (473)
..+ +|+|..|.++||..+|+..
T Consensus 79 ~~G~~c~pfr~r~T~kQEe~~ReeNgG~DPit~Vd~~lvnN~~nVLFRC~~C~RawH~~HLP~~ 142 (175)
T PF15446_consen 79 KPGPSCKPFRPRKTPKQEEKLREENGGVDPITPVDPELVNNPDNVLFRCTSCHRAWHFEHLPPP 142 (175)
T ss_pred CCCCCCcccCCCCCcHHHHHHHHHcCCCCCCccCCHHHccChhheEEecCCccceeehhhCCCC
Confidence 641 7999999999999999864
No 17
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=97.39 E-value=3e-05 Score=89.16 Aligned_cols=116 Identities=22% Similarity=0.322 Sum_probs=80.0
Q ss_pred CCccccccccccccccCceeecCCCCCCCcccccccCcccccCCCCCceeecCc--------------------------
Q 041992 116 RRKTEEEDVCFICFDGGSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH-------------------------- 169 (473)
Q Consensus 116 ~~~~~ned~CfVC~dGGeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H-------------------------- 169 (473)
+.+..-+|.|-+|.+.|+++||. +||++||++|+.++.-. .+...|-|--|
T Consensus 338 e~~~~~ddhcrf~~d~~~~lc~E--t~prvvhlEcv~hP~~~-~~s~~~e~evc~~hkvngvvd~vl~~~K~~~~iR~~~ 414 (1414)
T KOG1473|consen 338 EGEIEYDDHCRFCHDLGDLLCCE--TCPRVVHLECVFHPRFA-VPSAFWECEVCNIHKVNGVVDCVLPPSKNVDSIRHTP 414 (1414)
T ss_pred ccceeecccccccCcccceeecc--cCCceEEeeecCCcccc-CCCccchhhhhhhhccCcccccccChhhcccceeccC
Confidence 33455678999999999999999 89999999999998644 57888998743
Q ss_pred ---------------ccccccCCc-eeeccC-CCccccc-cccCCCcc-ccccCCeeecCCCCcchhhhhccCCCCCCce
Q 041992 170 ---------------ICSICEKAS-YYMCYT-CTYSLCK-GCTKGADY-YSLRGNKGFCGICMRTIMLIENCAPGNQEKV 230 (473)
Q Consensus 170 ---------------~C~vC~k~s-l~~C~~-Cp~AyH~-~CL~~~~~-~sv~~~kwfC~~C~~~~~~iE~~~~~dseg~ 230 (473)
.|.+|+... ++.|+. ||.+||. .||...-+ ..++.+-|+|..|.---|.|-. +..++.-+
T Consensus 415 iG~dr~gr~ywfi~rrl~Ie~~det~l~yysT~pqly~ll~cLd~~~~e~~L~d~i~~~~ee~~rqM~lT~-~ltne~R~ 493 (1414)
T KOG1473|consen 415 IGRDRYGRKYWFISRRLRIEGMDETLLWYYSTCPQLYHLLRCLDRTYVEMYLCDGIWERREEIIRQMGLTE-ELTNELRG 493 (1414)
T ss_pred CCcCccccchhceeeeeEEecCCCcEEEEecCcHHHHHHHHHhchHHHHHhhccchhhhHHHHHHhccchh-hhhhhhhc
Confidence 466666554 455654 9999998 99974222 1346778999877543333321 12223335
Q ss_pred eeecC
Q 041992 231 VVDFD 235 (473)
Q Consensus 231 ~VDf~ 235 (473)
.|||-
T Consensus 494 ~~~f~ 498 (1414)
T KOG1473|consen 494 AVDFG 498 (1414)
T ss_pred ccccc
Confidence 56664
No 18
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=97.34 E-value=8.1e-05 Score=82.35 Aligned_cols=95 Identities=27% Similarity=0.671 Sum_probs=70.5
Q ss_pred cccccccc-C----ceeecCCCCCCCcccccccCcccccCCCCCceeecCc-----------------------------
Q 041992 124 VCFICFDG-G----SLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH----------------------------- 169 (473)
Q Consensus 124 ~CfVC~dG-G----eLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H----------------------------- 169 (473)
=|.||-|. | .||.||..+|--+-|..|-++.. .|.|.|||..|
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvq---VPtGpWfCrKCesqeraarvrCeLCP~kdGALKkTDn~GW 83 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQ---VPTGPWFCRKCESQERAARVRCELCPHKDGALKKTDNGGW 83 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcceeEe---cCCCchhhhhhhhhhhhccceeecccCcccceecccCCCc
Confidence 38999873 3 79999999999999999999986 68999999843
Q ss_pred -----------------------------------ccccccCCc---------eeec--cCCCccccccccCCCccc---
Q 041992 170 -----------------------------------ICSICEKAS---------YYMC--YTCTYSLCKGCTKGADYY--- 200 (473)
Q Consensus 170 -----------------------------------~C~vC~k~s---------l~~C--~~Cp~AyH~~CL~~~~~~--- 200 (473)
.|.+|...+ -|.| ..|-.+||..|....-+-
T Consensus 84 AHVVCALYIPEVrFgNV~TMEPIiLq~VP~dRfnKtCYIC~E~GrpnkA~~GACMtCNKs~CkqaFHVTCAQ~~GLLCEE 163 (900)
T KOG0956|consen 84 AHVVCALYIPEVRFGNVHTMEPIILQDVPHDRFNKTCYICNEEGRPNKAAKGACMTCNKSGCKQAFHVTCAQRAGLLCEE 163 (900)
T ss_pred eEEEEEeeccceeecccccccceeeccCchhhhcceeeeecccCCccccccccceecccccchhhhhhhHhhhhccceec
Confidence 577777642 2455 467778999997654322
Q ss_pred --cccCCeeecCCCCcchhhhhc
Q 041992 201 --SLRGNKGFCGICMRTIMLIEN 221 (473)
Q Consensus 201 --sv~~~kwfC~~C~~~~~~iE~ 221 (473)
.+-.|.-+|+.|...+..+.+
T Consensus 164 ~gn~~dNVKYCGYCk~HfsKlkk 186 (900)
T KOG0956|consen 164 EGNISDNVKYCGYCKYHFSKLKK 186 (900)
T ss_pred cccccccceechhHHHHHHHhhc
Confidence 223567889999877665555
No 19
>COG5296 Transcription factor involved in TATA site selection and in elongation by RNA polymerase II [Transcription]
Probab=97.31 E-value=0.0016 Score=68.77 Aligned_cols=107 Identities=24% Similarity=0.281 Sum_probs=92.5
Q ss_pred ceeeeeeeecCcccccCCcccceEEEeeCCCccceeeeecccCCCCCHHHHHHHHHHhhhcccccchHHHHHHHHHHHHH
Q 041992 337 MPLIKGTSKVGKPYKIGDRTADVILEIRNLQKKEVVAIDAISNQEFSEDECSRLRQSIKCGFIKHLTVGEIQEKAMSLQA 416 (473)
Q Consensus 337 l~qV~G~~k~~e~yk~~~~~~~i~L~i~nl~k~~~i~i~~ls~~df~eeEC~~lrq~ik~gl~kr~tv~~~eeka~~l~~ 416 (473)
||||-|+...+.+|-+++.-|+.-|.++.=-..++..|.-|||.-|.++|-+|+..+++.|-+..|.+.-+.+|-.-|-.
T Consensus 256 iv~V~~~~~~~kpy~~~~v~Tn~yl~v~~Gr~~kvF~in~~Sn~pf~~~eyQr~~r~~~~~kl~~PS~~~v~~k~~~l~d 335 (521)
T COG5296 256 IVGVGKGSTYSKPYGRKEVKTNRYLDVSTGRTYKVFRINNISNSPFLREEYQRVWRSFKVGKLSMPSIAKVKEKYDKLVD 335 (521)
T ss_pred EEEeccceeccccccccceeeeeeEeeecCcceeeeEeecccCCcccHHHHHHHHHHHhccccccchHHHHHHHHHHHHH
Confidence 88999999999999999999999999995444579999999999999999999999999999999999999999876642
Q ss_pred ------------HHHHH---------HHHHHHHHHHhhHhhhhhcccc
Q 041992 417 ------------LRVND---------LLESEILRLNNLRDRASEKGHR 443 (473)
Q Consensus 417 ------------~~~~~---------wi~~e~~rl~~l~dra~ekg~r 443 (473)
+||+| =+..|..+|...+++|.|.|=.
T Consensus 336 ~~~~~LSdkeis~~V~~k~e~~~k~sNvi~eKt~Lrqkrq~A~e~~n~ 383 (521)
T COG5296 336 TMGRRLSDKEISKMVACKDEVHPKRSNVIHEKTELRQKRQRAIELKNK 383 (521)
T ss_pred HhCCcCchhHHHHHHHHHHhcCccchhHHHHHHHHHHHHHHHHHccCH
Confidence 44554 4567888888889999887654
No 20
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=96.90 E-value=0.00036 Score=70.57 Aligned_cols=42 Identities=29% Similarity=0.786 Sum_probs=35.1
Q ss_pred ccccccccc---CceeecCCCCCCCcccccccCcccccCCCCCceeec
Q 041992 123 DVCFICFDG---GSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCG 167 (473)
Q Consensus 123 d~CfVC~dG---GeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP 167 (473)
-+|.+|+.. .+|+.|| .|.|.||..||.|+... +|.|.|.|-
T Consensus 282 k~csicgtsenddqllfcd--dcdrgyhmyclsppm~e-ppegswsc~ 326 (336)
T KOG1244|consen 282 KYCSICGTSENDDQLLFCD--DCDRGYHMYCLSPPMVE-PPEGSWSCH 326 (336)
T ss_pred ceeccccCcCCCceeEeec--ccCCceeeEecCCCcCC-CCCCchhHH
Confidence 457777643 3899999 89999999999999865 689999884
No 21
>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 KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=96.82 E-value=0.00054 Score=75.70 Aligned_cols=71 Identities=30% Similarity=0.680 Sum_probs=57.7
Q ss_pred cccccccccC---ceeecCCCCCCCcccccccCcccccCCCCCceeecCc-ccccccCCc----------eeeccCCCc-
Q 041992 123 DVCFICFDGG---SLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH-ICSICEKAS----------YYMCYTCTY- 187 (473)
Q Consensus 123 d~CfVC~dGG---eLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H-~C~vC~k~s----------l~~C~~Cp~- 187 (473)
.+|..|+.+| .++.|+ .|.-+||-.|..|+... ++.+.|+|+|| .|..|.... ...|+.|.+
T Consensus 69 rvCe~c~~~gD~~kf~~Ck--~cDvsyh~yc~~P~~~~-v~sg~~~ckk~~~c~qc~~~lpg~s~~~~~~~~~~~~c~s~ 145 (694)
T KOG4443|consen 69 RVCEACGTTGDPKKFLLCK--RCDVSYHCYCQKPPNDK-VPSGPWLCKKCTRCRQCDSTLPGLSLDLQEGYLQCAPCASL 145 (694)
T ss_pred eeeeeccccCCcccccccc--cccccccccccCCcccc-ccCcccccHHHHhhhhccccccccchhhhccCccccccccc
Confidence 3466666544 789999 79999999999999765 68999999999 588888742 457899998
Q ss_pred cccccccCC
Q 041992 188 SLCKGCTKG 196 (473)
Q Consensus 188 AyH~~CL~~ 196 (473)
+||..|+..
T Consensus 146 ~~cPvc~~~ 154 (694)
T KOG4443|consen 146 SYCPVCLIV 154 (694)
T ss_pred ccCchHHHh
Confidence 899988874
No 23
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.55 E-value=0.0011 Score=74.56 Aligned_cols=46 Identities=37% Similarity=0.707 Sum_probs=37.5
Q ss_pred cccccccccccC---ceeecCCCCCCCc-ccccccCcccccCCCCCceeecCc
Q 041992 121 EEDVCFICFDGG---SLVLCDRKGCPKA-YHPACIKREESFFRSKAKWNCGWH 169 (473)
Q Consensus 121 ned~CfVC~dGG---eLv~CD~~gCPra-YH~~CL~p~~~~~~p~g~W~CP~H 169 (473)
...-|.+|.-.. -||.|| +|..+ ||..||+|++.. .|.+.|||+.|
T Consensus 214 E~~~C~IC~~~DpEdVLLLCD--sCN~~~YH~YCLDPdl~e-iP~~eWYC~NC 263 (1134)
T KOG0825|consen 214 EEVKCDICTVHDPEDVLLLCD--SCNKVYYHVYCLDPDLSE-SPVNEWYCTNC 263 (1134)
T ss_pred ccccceeeccCChHHhheeec--ccccceeeccccCccccc-ccccceecCcc
Confidence 344599997543 589999 89998 999999998755 58899999975
No 24
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=96.47 E-value=0.0011 Score=74.29 Aligned_cols=46 Identities=28% Similarity=0.646 Sum_probs=39.4
Q ss_pred ccccccccccccc-----CceeecCCCCCCCcccccccCcccccCCCCCceeecCc
Q 041992 119 TEEEDVCFICFDG-----GSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH 169 (473)
Q Consensus 119 ~~ned~CfVC~dG-----GeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H 169 (473)
..++..|.+|..+ .+||.|| .|-..-|..|-|+.. .|.+.|.|.+|
T Consensus 268 ~dedviCDvCrspD~e~~neMVfCd--~Cn~cVHqaCyGIle---~p~gpWlCr~C 318 (893)
T KOG0954|consen 268 YDEDVICDVCRSPDSEEANEMVFCD--KCNICVHQACYGILE---VPEGPWLCRTC 318 (893)
T ss_pred ccccceeceecCCCccccceeEEec--cchhHHHHhhhceee---cCCCCeeehhc
Confidence 3477789999865 3899999 799999999999986 57899999976
No 25
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.41 E-value=0.0029 Score=73.74 Aligned_cols=66 Identities=32% Similarity=0.625 Sum_probs=49.3
Q ss_pred ccccccccccccccC-----ceeecCCCCCCCcccccccCcccccCCCCCceeecCcccccccCCceeeccCCCccccc
Q 041992 118 KTEEEDVCFICFDGG-----SLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWHICSICEKASYYMCYTCTYSLCK 191 (473)
Q Consensus 118 ~~~ned~CfVC~dGG-----eLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H~C~vC~k~sl~~C~~Cp~AyH~ 191 (473)
....+.+|.||.++- ..|.|| +|..++|..|.+.+. +|.|.|.|..|.=.. .....|..||.+-+.
T Consensus 215 ~~~~D~~C~iC~~~~~~n~n~ivfCD--~Cnl~VHq~Cygi~~---ipeg~WlCr~Cl~s~---~~~v~c~~cp~~~gA 285 (1051)
T KOG0955|consen 215 LLEEDAVCCICLDGECQNSNVIVFCD--GCNLAVHQECYGIPF---IPEGQWLCRRCLQSP---QRPVRCLLCPSKGGA 285 (1051)
T ss_pred ccCCCccceeecccccCCCceEEEcC--CCcchhhhhccCCCC---CCCCcEeehhhccCc---CcccceEeccCCCCc
Confidence 456778999999864 689999 899999999999653 799999997543221 114677777765544
No 26
>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=96.18 E-value=0.0016 Score=48.73 Aligned_cols=44 Identities=16% Similarity=0.543 Sum_probs=33.6
Q ss_pred ccccccCCc----eeeccCCCccccccccCCCccc-cccCCeeecCCCC
Q 041992 170 ICSICEKAS----YYMCYTCTYSLCKGCTKGADYY-SLRGNKGFCGICM 213 (473)
Q Consensus 170 ~C~vC~k~s----l~~C~~Cp~AyH~~CL~~~~~~-sv~~~kwfC~~C~ 213 (473)
+|.+|+... ++.|..|...||..|+..+... .++.+.|+|+.|.
T Consensus 1 ~C~vC~~~~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~ 49 (51)
T PF00628_consen 1 YCPVCGQSDDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCR 49 (51)
T ss_dssp EBTTTTSSCTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHH
T ss_pred eCcCCCCcCCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCc
Confidence 367888743 8899999999999999965431 3345599999885
No 27
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=96.01 E-value=0.0026 Score=68.80 Aligned_cols=47 Identities=28% Similarity=0.644 Sum_probs=38.6
Q ss_pred ccccccccccccccC-----ceeecCCCCCCCcccccccCcccccCCCCCceeecCc
Q 041992 118 KTEEEDVCFICFDGG-----SLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH 169 (473)
Q Consensus 118 ~~~ned~CfVC~dGG-----eLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H 169 (473)
.+.-++.|.+|.... .+|.|| +|..+-|..|-|... .|.|.|.|..|
T Consensus 189 ~d~~d~~C~~c~~t~~eN~naiVfCd--gC~i~VHq~CYGI~f---~peG~WlCrkC 240 (669)
T COG5141 189 SDEFDDICTKCTSTHNENSNAIVFCD--GCEICVHQSCYGIQF---LPEGFWLCRKC 240 (669)
T ss_pred chhhhhhhHhccccccCCcceEEEec--Ccchhhhhhccccee---cCcchhhhhhh
Confidence 445677888887543 689999 899999999999985 68999999865
No 28
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.76 E-value=0.0044 Score=63.39 Aligned_cols=39 Identities=26% Similarity=0.842 Sum_probs=33.0
Q ss_pred cccccccc---CceeecCCCCCCCcccccccCcccccCCCCCceeec
Q 041992 124 VCFICFDG---GSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCG 167 (473)
Q Consensus 124 ~CfVC~dG---GeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP 167 (473)
.|.+|+.+ .+++.|| -|.|.||..|++... .|.|.|+|-
T Consensus 316 lC~IC~~P~~E~E~~FCD--~CDRG~HT~CVGL~~---lP~G~WICD 357 (381)
T KOG1512|consen 316 LCRICLGPVIESEHLFCD--VCDRGPHTLCVGLQD---LPRGEWICD 357 (381)
T ss_pred hhhccCCcccchheeccc--cccCCCCcccccccc---ccCccchhh
Confidence 47777654 3899999 699999999999986 589999996
No 29
>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=95.69 E-value=0.0066 Score=56.67 Aligned_cols=32 Identities=13% Similarity=0.421 Sum_probs=26.1
Q ss_pred cccccccCcccccCCCCCceeecCcccccccCC
Q 041992 145 AYHPACIKREESFFRSKAKWNCGWHICSICEKA 177 (473)
Q Consensus 145 aYH~~CL~p~~~~~~p~g~W~CP~H~C~vC~k~ 177 (473)
.||..||.|++.. +|.|+|+||.|.....++.
T Consensus 1 g~H~~CL~Ppl~~-~P~g~W~Cp~C~~~~~~~~ 32 (148)
T cd04718 1 GFHLCCLRPPLKE-VPEGDWICPFCEVEKSGQS 32 (148)
T ss_pred CcccccCCCCCCC-CCCCCcCCCCCcCCCCCCc
Confidence 3899999999875 6899999998776655554
No 30
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.22 E-value=0.01 Score=67.23 Aligned_cols=46 Identities=22% Similarity=0.452 Sum_probs=40.7
Q ss_pred cccccccCCc----eeeccCCCcc-ccccccCCCccccccCCeeecCCCCcc
Q 041992 169 HICSICEKAS----YYMCYTCTYS-LCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 169 H~C~vC~k~s----l~~C~~Cp~A-yH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
+.|.+|+... +++|+.|..+ ||.+||.+ ++..++.+.|+|..|.-+
T Consensus 216 ~~C~IC~~~DpEdVLLLCDsCN~~~YH~YCLDP-dl~eiP~~eWYC~NC~dL 266 (1134)
T KOG0825|consen 216 VKCDICTVHDPEDVLLLCDSCNKVYYHVYCLDP-DLSESPVNEWYCTNCSLL 266 (1134)
T ss_pred ccceeeccCChHHhheeecccccceeeccccCc-ccccccccceecCcchhh
Confidence 5799999975 8999999999 99999984 567889999999999865
No 31
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=94.84 E-value=0.035 Score=59.97 Aligned_cols=41 Identities=32% Similarity=0.783 Sum_probs=33.0
Q ss_pred cccccccC-----ceeecCCCCCCCcccccccCcccc---cCCCCCceeec
Q 041992 125 CFICFDGG-----SLVLCDRKGCPKAYHPACIKREES---FFRSKAKWNCG 167 (473)
Q Consensus 125 CfVC~dGG-----eLv~CD~~gCPraYH~~CL~p~~~---~~~p~g~W~CP 167 (473)
|.+|..|| .||-|+ .|-.+||..|..+... .-.+...|+|-
T Consensus 171 c~vC~~g~~~~~NrmlqC~--~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~ 219 (464)
T KOG4323|consen 171 CSVCYCGGPGAGNRMLQCD--KCRQWYHQACHQPLIKDELAGDPFYEWFCD 219 (464)
T ss_pred eeeeecCCcCccceeeeec--ccccHHHHHhccCCCCHhhccCccceEeeh
Confidence 88998655 899999 7999999999998753 22467889885
No 32
>KOG1946 consensus RNA polymerase I transcription factor UAF [Transcription]
Probab=94.71 E-value=0.019 Score=57.27 Aligned_cols=43 Identities=44% Similarity=0.607 Sum_probs=38.6
Q ss_pred CCCccchhhHHHHHHhhhccCCChhhhhhcCCCCCCCCCCCCC
Q 041992 236 DKTSWEYLFKVYWIFLKEKLSLTLDELTGAKNPWKEPAITAPK 278 (473)
Q Consensus 236 D~~~~e~lfK~Yw~~iK~~~~Lt~~~l~~a~~~~k~~~~~~~~ 278 (473)
|..+|+|+|++||+..+.+++||.++|..|.++|.+....+.+
T Consensus 2 ~~~~~~~~~~~~~l~~~~~~~lt~~~vr~~~~~~~~v~~~~~k 44 (240)
T KOG1946|consen 2 DSLSWEYLFKDYILSLKDQETLTPDDVRRAMAPRSGVDGTAQK 44 (240)
T ss_pred cchhhhhhhhHHHhcccccccCCHHHHHHHhccccCCCCcchh
Confidence 4579999999999999999999999999999999988775544
No 33
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=94.28 E-value=0.017 Score=47.81 Aligned_cols=49 Identities=27% Similarity=0.683 Sum_probs=37.3
Q ss_pred ccccccccccc-CceeecCCCCCCCcccccccCcccccCC-----CCCceeecCc
Q 041992 121 EEDVCFICFDG-GSLVLCDRKGCPKAYHPACIKREESFFR-----SKAKWNCGWH 169 (473)
Q Consensus 121 ned~CfVC~dG-GeLv~CD~~gCPraYH~~CL~p~~~~~~-----p~g~W~CP~H 169 (473)
....|.+|+.. |-.+-|..++|.++||+.|.-.....+. ..-..+||.|
T Consensus 35 ~~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~~~~~~~~~~~~~~~~~~C~~H 89 (90)
T PF13771_consen 35 RKLKCSICKKKGGACIGCSHPGCSRSFHVPCARKAGCFIEFDEDNGKFRIFCPKH 89 (90)
T ss_pred hCCCCcCCCCCCCeEEEEeCCCCCcEEChHHHccCCeEEEEccCCCceEEEChhc
Confidence 44579999998 9999999999999999999986542111 1245677776
No 34
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=93.54 E-value=0.041 Score=59.49 Aligned_cols=96 Identities=20% Similarity=0.290 Sum_probs=65.8
Q ss_pred cccccccccc-----cCceeecCCCCCCCcccccccCcccccCCCCCceeecC---------------------------
Q 041992 121 EEDVCFICFD-----GGSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGW--------------------------- 168 (473)
Q Consensus 121 ned~CfVC~d-----GGeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~--------------------------- 168 (473)
.+-.|-+|.. +.+++.|+ -|-+.||..|..+.. ...+.|.+..
T Consensus 82 ~e~~~nv~~s~~~~p~~e~~~~~--r~~~~~~q~~~i~~~---~~~~~~~~~~c~~~~~~~~g~a~K~g~~a~~~l~y~~ 156 (464)
T KOG4323|consen 82 SELNPNVLTSETVLPENEKVICG--RCKSGYHQGCNIPRF---PSLDIGESTECVFPIFSQEGGALKKGRLARPSLPYPE 156 (464)
T ss_pred cccCCcccccccccCchhhhhhh--hhccCcccccCccCc---CcCCccccccccccccccccccccccccccccccCcc
Confidence 3444666643 34688899 499999999987764 2234444441
Q ss_pred ------------cccccccCCc------eeeccCCCccccccccCCCccccc---cCCeeecCCCCcchhhhhc
Q 041992 169 ------------HICSICEKAS------YYMCYTCTYSLCKGCTKGADYYSL---RGNKGFCGICMRTIMLIEN 221 (473)
Q Consensus 169 ------------H~C~vC~k~s------l~~C~~Cp~AyH~~CL~~~~~~sv---~~~kwfC~~C~~~~~~iE~ 221 (473)
-.|.+|.... ++.|..|..=||..|..+..-... +...|||..|.+..-.+..
T Consensus 157 ~~l~wD~~~~~n~qc~vC~~g~~~~~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~~~r 230 (464)
T KOG4323|consen 157 ASLDWDSGHKVNLQCSVCYCGGPGAGNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKKVPR 230 (464)
T ss_pred cccccCccccccceeeeeecCCcCccceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhhccc
Confidence 1588888643 789999999999999986432222 4458999999986544444
No 35
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=92.95 E-value=0.023 Score=68.37 Aligned_cols=48 Identities=23% Similarity=0.614 Sum_probs=40.3
Q ss_pred cccccccccccccC---ceeecCCCCCCCcccccccCcccccCCCCCceeecCc
Q 041992 119 TEEEDVCFICFDGG---SLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH 169 (473)
Q Consensus 119 ~~ned~CfVC~dGG---eLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H 169 (473)
......|.+|...+ .++.|+ .|-..||..|+.|.... .+.++|+||+|
T Consensus 1105 s~~~~~c~~cr~k~~~~~m~lc~--~c~~~~h~~C~rp~~~~-~~~~dW~C~~c 1155 (1404)
T KOG1245|consen 1105 SAVNALCKVCRRKKQDEKMLLCD--ECLSGFHLFCLRPALSS-VPPGDWMCPSC 1155 (1404)
T ss_pred ccchhhhhhhhhcccchhhhhhH--hhhhhHHHHhhhhhhcc-CCcCCccCCcc
Confidence 45566799997654 689999 89999999999998765 57899999975
No 36
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=92.58 E-value=0.052 Score=59.23 Aligned_cols=44 Identities=27% Similarity=0.551 Sum_probs=35.5
Q ss_pred ccccccCCc----eeeccCCCccccccccCCCccccccC----CeeecCCCCc
Q 041992 170 ICSICEKAS----YYMCYTCTYSLCKGCTKGADYYSLRG----NKGFCGICMR 214 (473)
Q Consensus 170 ~C~vC~k~s----l~~C~~Cp~AyH~~CL~~~~~~sv~~----~kwfC~~C~~ 214 (473)
.|.+|+++. +..|++|...||.+||.+ ++..+|. -.|.|..|-+
T Consensus 546 sCgiCkks~dQHll~~CDtC~lhYHlGCL~P-PLTR~Pkk~kn~gWqCsECdk 597 (707)
T KOG0957|consen 546 SCGICKKSTDQHLLTQCDTCHLHYHLGCLSP-PLTRLPKKNKNFGWQCSECDK 597 (707)
T ss_pred eeeeeccchhhHHHhhcchhhceeeccccCC-ccccCcccccCcceeeccccc
Confidence 578999986 689999999999999985 4555654 2599999943
No 37
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=92.17 E-value=0.13 Score=56.26 Aligned_cols=45 Identities=27% Similarity=0.609 Sum_probs=34.3
Q ss_pred cccccccccccC---ceeecCCCCCCCcccccccCcccccCCC---CCceeec
Q 041992 121 EEDVCFICFDGG---SLVLCDRKGCPKAYHPACIKREESFFRS---KAKWNCG 167 (473)
Q Consensus 121 ned~CfVC~dGG---eLv~CD~~gCPraYH~~CL~p~~~~~~p---~g~W~CP 167 (473)
-...|.||+..- -|+.|| .|...||+.||.|++.-++. ...|.|-
T Consensus 543 ~~ysCgiCkks~dQHll~~CD--tC~lhYHlGCL~PPLTR~Pkk~kn~gWqCs 593 (707)
T KOG0957|consen 543 MNYSCGICKKSTDQHLLTQCD--TCHLHYHLGCLSPPLTRLPKKNKNFGWQCS 593 (707)
T ss_pred cceeeeeeccchhhHHHhhcc--hhhceeeccccCCccccCcccccCcceeec
Confidence 345699998643 588999 89999999999999864221 3469885
No 38
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=91.81 E-value=0.12 Score=52.21 Aligned_cols=50 Identities=16% Similarity=0.285 Sum_probs=38.1
Q ss_pred CCCCceeecCcccccccCCc-eeeccC--CC-ccccccccCCCccccccCCeeecCCCCcc
Q 041992 159 RSKAKWNCGWHICSICEKAS-YYMCYT--CT-YSLCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 159 ~p~g~W~CP~H~C~vC~k~s-l~~C~~--Cp-~AyH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
.+...|||. |. |-..+ ..-|+. || .=||..|+. +...|.++|||+.|..-
T Consensus 215 d~~e~~yC~---Cn-qvsyg~Mi~CDn~~C~~eWFH~~CVG---L~~~PkgkWyC~~C~~~ 268 (274)
T KOG1973|consen 215 DPDEPTYCI---CN-QVSYGKMIGCDNPGCPIEWFHFTCVG---LKTKPKGKWYCPRCKAE 268 (274)
T ss_pred CCCCCEEEE---ec-ccccccccccCCCCCCcceEEEeccc---cccCCCCcccchhhhhh
Confidence 456778884 44 44444 678877 99 789999998 66778899999999763
No 39
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=91.37 E-value=0.11 Score=61.01 Aligned_cols=42 Identities=19% Similarity=0.612 Sum_probs=36.2
Q ss_pred ccccccCCc------eeeccCCCccccccccCCCccccccCCeeecCCCCc
Q 041992 170 ICSICEKAS------YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMR 214 (473)
Q Consensus 170 ~C~vC~k~s------l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~ 214 (473)
.|.+|.+.. ++.|+.|..++|.+|.. .+-+|.+.|+|.+|.-
T Consensus 221 ~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cyg---i~~ipeg~WlCr~Cl~ 268 (1051)
T KOG0955|consen 221 VCCICLDGECQNSNVIVFCDGCNLAVHQECYG---IPFIPEGQWLCRRCLQ 268 (1051)
T ss_pred cceeecccccCCCceEEEcCCCcchhhhhccC---CCCCCCCcEeehhhcc
Confidence 688888753 78999999999999997 4567899999999984
No 40
>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=90.24 E-value=0.16 Score=47.61 Aligned_cols=27 Identities=11% Similarity=0.297 Sum_probs=23.7
Q ss_pred cccccccCCCccccccCCeeecCCCCcc
Q 041992 188 SLCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 188 AyH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
.||..||. +++..+|.+.|+|+.|...
T Consensus 1 g~H~~CL~-Ppl~~~P~g~W~Cp~C~~~ 27 (148)
T cd04718 1 GFHLCCLR-PPLKEVPEGDWICPFCEVE 27 (148)
T ss_pred CcccccCC-CCCCCCCCCCcCCCCCcCC
Confidence 48999998 5678999999999999864
No 41
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=86.55 E-value=0.35 Score=41.58 Aligned_cols=34 Identities=35% Similarity=0.914 Sum_probs=29.4
Q ss_pred cccccccccc-cCceeecCCCCCCCcccccccCcc
Q 041992 121 EEDVCFICFD-GGSLVLCDRKGCPKAYHPACIKRE 154 (473)
Q Consensus 121 ned~CfVC~d-GGeLv~CD~~gCPraYH~~CL~p~ 154 (473)
....|.+|+. +|-.+.|..++|..+||+.|....
T Consensus 54 ~~~~C~iC~~~~G~~i~C~~~~C~~~fH~~CA~~~ 88 (110)
T PF13832_consen 54 FKLKCSICGKSGGACIKCSHPGCSTAFHPTCARKA 88 (110)
T ss_pred cCCcCcCCCCCCceeEEcCCCCCCcCCCHHHHHHC
Confidence 4667999997 688999998889999999998654
No 42
>KOG3362 consensus Predicted BBOX Zn-finger protein [General function prediction only]
Probab=85.49 E-value=0.33 Score=45.58 Aligned_cols=44 Identities=30% Similarity=0.576 Sum_probs=35.4
Q ss_pred CCcccccccCcccccCCCCCceeecCcccccccCCceeeccCCCcccc-ccccC
Q 041992 143 PKAYHPACIKREESFFRSKAKWNCGWHICSICEKASYYMCYTCTYSLC-KGCTK 195 (473)
Q Consensus 143 PraYH~~CL~p~~~~~~p~g~W~CP~H~C~vC~k~sl~~C~~Cp~AyH-~~CL~ 195 (473)
...||..|..|+..+ +.++|.+||--+.+.|..|+..|| ..|+.
T Consensus 102 ~~~Y~~~~a~p~~KP---------~r~fCaVCG~~S~ysC~~CG~kyCsv~C~~ 146 (156)
T KOG3362|consen 102 NPNYHTAYAKPSFKP---------LRKFCAVCGYDSKYSCVNCGTKYCSVRCLK 146 (156)
T ss_pred ccchhhcccCCCCCC---------cchhhhhcCCCchhHHHhcCCceeechhhh
Confidence 347999888887532 357899999889999999999999 47765
No 43
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=82.09 E-value=0.53 Score=51.65 Aligned_cols=42 Identities=21% Similarity=0.556 Sum_probs=33.9
Q ss_pred ccccccCC------ceeeccCCCccccccccCCCccccccCCeeecCCCCc
Q 041992 170 ICSICEKA------SYYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMR 214 (473)
Q Consensus 170 ~C~vC~k~------sl~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~ 214 (473)
.|.+|..+ ++..|+-|..+.|..|.. ..-+|.+.|+|..|+=
T Consensus 195 ~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYG---I~f~peG~WlCrkCi~ 242 (669)
T COG5141 195 ICTKCTSTHNENSNAIVFCDGCEICVHQSCYG---IQFLPEGFWLCRKCIY 242 (669)
T ss_pred hhHhccccccCCcceEEEecCcchhhhhhccc---ceecCcchhhhhhhcc
Confidence 45555543 388999999999999987 4567899999999974
No 44
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=81.42 E-value=0.37 Score=58.52 Aligned_cols=45 Identities=18% Similarity=0.568 Sum_probs=39.8
Q ss_pred ccccccCCc----eeeccCCCccccccccCCCccccccCCeeecCCCCcc
Q 041992 170 ICSICEKAS----YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 170 ~C~vC~k~s----l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
.|.+|.+.+ +.+|..|-..||..|++ +.+.+++.+.|+|+.|..-
T Consensus 1110 ~c~~cr~k~~~~~m~lc~~c~~~~h~~C~r-p~~~~~~~~dW~C~~c~~e 1158 (1404)
T KOG1245|consen 1110 LCKVCRRKKQDEKMLLCDECLSGFHLFCLR-PALSSVPPGDWMCPSCRKE 1158 (1404)
T ss_pred hhhhhhhcccchhhhhhHhhhhhHHHHhhh-hhhccCCcCCccCCccchh
Confidence 688999875 78999999999999999 4578899999999999874
No 45
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=79.61 E-value=0.78 Score=52.09 Aligned_cols=33 Identities=18% Similarity=0.518 Sum_probs=28.3
Q ss_pred eeec--cCCCccccccccCCCccccccCCeeecCCCCc
Q 041992 179 YYMC--YTCTYSLCKGCTKGADYYSLRGNKGFCGICMR 214 (473)
Q Consensus 179 l~~C--~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~ 214 (473)
++.| .-|..|+|..|.. +.+||.+.|||..|..
T Consensus 22 LVYCDG~nCsVAVHQaCYG---IvqVPtGpWfCrKCes 56 (900)
T KOG0956|consen 22 LVYCDGHNCSVAVHQACYG---IVQVPTGPWFCRKCES 56 (900)
T ss_pred eeeecCCCceeeeehhcce---eEecCCCchhhhhhhh
Confidence 6667 5788999999987 7899999999999964
No 46
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=78.96 E-value=1.7 Score=37.24 Aligned_cols=72 Identities=21% Similarity=0.395 Sum_probs=44.0
Q ss_pred ccccccccCceeecCCCCCCCcccccccCcccc-cCCC---CCcee----ec---CcccccccCCc--eeeccC--CCcc
Q 041992 124 VCFICFDGGSLVLCDRKGCPKAYHPACIKREES-FFRS---KAKWN----CG---WHICSICEKAS--YYMCYT--CTYS 188 (473)
Q Consensus 124 ~CfVC~dGGeLv~CD~~gCPraYH~~CL~p~~~-~~~p---~g~W~----CP---~H~C~vC~k~s--l~~C~~--Cp~A 188 (473)
.|.+|...|.++.-. .-..+.|..|.--... .+.. ...+. =+ .-.|.+|+... .+.|.. |..+
T Consensus 2 ~C~lC~~~~Galk~t--~~~~WvHv~Cal~~~~~~~~~~~~~~~v~~~~i~~~~~~~~C~iC~~~~G~~i~C~~~~C~~~ 79 (110)
T PF13832_consen 2 SCVLCPKRGGALKRT--SDGQWVHVLCALWIPEVIFNNGESMEPVDISNIPPSRFKLKCSICGKSGGACIKCSHPGCSTA 79 (110)
T ss_pred ccEeCCCCCCcccCc--cCCcEEEeEccceeCccEEeechhcCcccceeecchhcCCcCcCCCCCCceeEEcCCCCCCcC
Confidence 488887654344333 2467889988764221 0000 00011 01 24799999964 789987 9999
Q ss_pred ccccccCCC
Q 041992 189 LCKGCTKGA 197 (473)
Q Consensus 189 yH~~CL~~~ 197 (473)
||..|....
T Consensus 80 fH~~CA~~~ 88 (110)
T PF13832_consen 80 FHPTCARKA 88 (110)
T ss_pred CCHHHHHHC
Confidence 999998653
No 47
>KOG3612 consensus PHD Zn-finger protein [General function prediction only]
Probab=78.69 E-value=2.3 Score=47.20 Aligned_cols=56 Identities=14% Similarity=0.282 Sum_probs=43.3
Q ss_pred CccccccccccccccCceeecCCCCCCCcccccccCcccccCCCCCceeecCcccccccC
Q 041992 117 RKTEEEDVCFICFDGGSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWHICSICEK 176 (473)
Q Consensus 117 ~~~~ned~CfVC~dGGeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H~C~vC~k 176 (473)
...+.+-+||.|.-.|..+.|+ .|-++||..|+.+..........|.||. |..|+.
T Consensus 55 ~~~N~d~~cfechlpg~vl~c~--vc~Rs~h~~c~sp~~q~r~~s~p~~~p~--p~s~k~ 110 (588)
T KOG3612|consen 55 PSSNIDPFCFECHLPGAVLKCI--VCHRSFHENCQSPDPQKRNYSVPSDKPQ--PYSFKV 110 (588)
T ss_pred cccCCCcccccccCCcceeeee--hhhccccccccCcchhhccccccccCCc--ccccCC
Confidence 3456778999999999999999 7999999999998764323456799985 344443
No 48
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=77.02 E-value=0.47 Score=34.38 Aligned_cols=31 Identities=16% Similarity=0.531 Sum_probs=16.7
Q ss_pred eeeccCCCccccccccCCCccccccCC-eeecCCC
Q 041992 179 YYMCYTCTYSLCKGCTKGADYYSLRGN-KGFCGIC 212 (473)
Q Consensus 179 l~~C~~Cp~AyH~~CL~~~~~~sv~~~-kwfC~~C 212 (473)
++.|..|..++|..|..- ..++.+ .|+|..|
T Consensus 4 ll~C~~C~v~VH~~CYGv---~~~~~~~~W~C~~C 35 (36)
T PF13831_consen 4 LLFCDNCNVAVHQSCYGV---SEVPDGDDWLCDRC 35 (36)
T ss_dssp EEE-SSS--EEEHHHHT----SS--SS-----HHH
T ss_pred eEEeCCCCCcCChhhCCc---ccCCCCCcEECCcC
Confidence 688999999999999973 334433 6999876
No 49
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=75.68 E-value=0.52 Score=34.19 Aligned_cols=34 Identities=29% Similarity=0.672 Sum_probs=17.9
Q ss_pred CceeecCCCCCCCcccccccCcccccCCCCCceeecCc
Q 041992 132 GSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH 169 (473)
Q Consensus 132 GeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H 169 (473)
..|+.|+ +|.-+.|..|-+....+ ....|+|-.|
T Consensus 2 n~ll~C~--~C~v~VH~~CYGv~~~~--~~~~W~C~~C 35 (36)
T PF13831_consen 2 NPLLFCD--NCNVAVHQSCYGVSEVP--DGDDWLCDRC 35 (36)
T ss_dssp CEEEE-S--SS--EEEHHHHT-SS----SS-----HHH
T ss_pred CceEEeC--CCCCcCChhhCCcccCC--CCCcEECCcC
Confidence 3689999 79999999999988632 2336999643
No 50
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=75.34 E-value=1.3 Score=50.76 Aligned_cols=43 Identities=19% Similarity=0.607 Sum_probs=37.6
Q ss_pred ccccccCCc------eeeccCCCccccccccCCCccccccCCeeecCCCCcc
Q 041992 170 ICSICEKAS------YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 170 ~C~vC~k~s------l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
.|.+|..+. +..|+.|-..+|..|.. +-.+|++.|+|.+|.-.
T Consensus 273 iCDvCrspD~e~~neMVfCd~Cn~cVHqaCyG---Ile~p~gpWlCr~Calg 321 (893)
T KOG0954|consen 273 ICDVCRSPDSEEANEMVFCDKCNICVHQACYG---ILEVPEGPWLCRTCALG 321 (893)
T ss_pred eeceecCCCccccceeEEeccchhHHHHhhhc---eeecCCCCeeehhcccc
Confidence 799999872 78999999999999987 67789999999999854
No 51
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.99 E-value=1.8 Score=45.73 Aligned_cols=44 Identities=25% Similarity=0.641 Sum_probs=30.8
Q ss_pred cccccccc---cCceeecCCCCCCCcccccccCcccccCCCCCceeecCcccccccCC
Q 041992 123 DVCFICFD---GGSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWHICSICEKA 177 (473)
Q Consensus 123 d~CfVC~d---GGeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H~C~vC~k~ 177 (473)
+.|.||-+ .|+-+.== .|.-.||..|+++.... | +++|++|+..
T Consensus 230 ~~CaIClEdY~~GdklRiL--PC~H~FH~~CIDpWL~~------~---r~~CPvCK~d 276 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRIL--PCSHKFHVNCIDPWLTQ------T---RTFCPVCKRD 276 (348)
T ss_pred ceEEEeecccccCCeeeEe--cCCCchhhccchhhHhh------c---CccCCCCCCc
Confidence 58999975 34433223 57789999999998632 3 5677888864
No 52
>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=66.83 E-value=2.4 Score=37.42 Aligned_cols=45 Identities=22% Similarity=0.566 Sum_probs=28.4
Q ss_pred ccccccCCc---eeec------cCC---CccccccccCCC----ccccccCCeeecCCCCc
Q 041992 170 ICSICEKAS---YYMC------YTC---TYSLCKGCTKGA----DYYSLRGNKGFCGICMR 214 (473)
Q Consensus 170 ~C~vC~k~s---l~~C------~~C---p~AyH~~CL~~~----~~~sv~~~kwfC~~C~~ 214 (473)
.|+.|++.. .+.| ..| ...||..||... ....+....|.|+.|..
T Consensus 9 ~CHqCrqKt~~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 9 TCHQCRQKTLDFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CchhhcCCCCCCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 355666543 3444 555 889999998752 11123467899998876
No 53
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=66.01 E-value=3.6 Score=41.95 Aligned_cols=40 Identities=20% Similarity=0.497 Sum_probs=30.8
Q ss_pred cccCCc---eeec--cCCCc-cccccccCCCccccccCCeeecCCCCcc
Q 041992 173 ICEKAS---YYMC--YTCTY-SLCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 173 vC~k~s---l~~C--~~Cp~-AyH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
.|.+.+ ..-| ..|++ =||..|+. +...|.++|+|..|...
T Consensus 225 fCqqvSyGqMVaCDn~nCkrEWFH~~CVG---Lk~pPKG~WYC~eCk~~ 270 (271)
T COG5034 225 FCQQVSYGQMVACDNANCKREWFHLECVG---LKEPPKGKWYCPECKKA 270 (271)
T ss_pred EecccccccceecCCCCCchhheeccccc---cCCCCCCcEeCHHhHhc
Confidence 466654 5667 46775 58999998 78889999999999753
No 54
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=61.05 E-value=4.5 Score=33.01 Aligned_cols=34 Identities=32% Similarity=0.698 Sum_probs=14.6
Q ss_pred ccccccccc----cC--ceeecCCCCCCCcccccccCccc
Q 041992 122 EDVCFICFD----GG--SLVLCDRKGCPKAYHPACIKREE 155 (473)
Q Consensus 122 ed~CfVC~d----GG--eLv~CD~~gCPraYH~~CL~p~~ 155 (473)
+..|.||.. .+ ..+.|++..|...||..||....
T Consensus 2 ~~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf 41 (70)
T PF11793_consen 2 ELECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWF 41 (70)
T ss_dssp --S-SSS--SS-TT-----B--S-TT----B-SGGGHHHH
T ss_pred CCCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHH
Confidence 356999964 23 35889988999999999998653
No 55
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=58.41 E-value=5.4 Score=31.84 Aligned_cols=30 Identities=30% Similarity=0.821 Sum_probs=25.4
Q ss_pred cccccccc----cCceeecCCCCCCCcccccccCcc
Q 041992 123 DVCFICFD----GGSLVLCDRKGCPKAYHPACIKRE 154 (473)
Q Consensus 123 d~CfVC~d----GGeLv~CD~~gCPraYH~~CL~p~ 154 (473)
..|.+|++ ++++|.|. .|...||-.|-...
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp--~CgapyHR~C~~~~ 39 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCP--ECGAPYHRDCWEKA 39 (54)
T ss_pred ccChhhCCcccCCCCEEECC--CCCCcccHHHHhhC
Confidence 45999975 67999999 79999999998654
No 56
>PF02178 AT_hook: AT hook motif; InterPro: IPR017956 AT hooks are DNA-binding motifs with a preference for A/T rich regions. These motifs are found in a variety of proteins, including the high mobility group (HMG) proteins [], in DNA-binding proteins from plants [] and in hBRG1 protein, a central ATPase of the human switching/sucrose non-fermenting (SWI/SNF) remodeling complex []. High mobility group (HMG) proteins are a family of relatively low molecular weight non-histone components in chromatin []. HMG-I and HMG-Y (HMGA) are proteins of about 100 amino acid residues which are produced by the alternative splicing of a single gene. HMG-I/Y proteins bind preferentially to the minor groove of AT-rich regions in double-stranded DNA in a non-sequence specific manner [, ]. It is suggested that these proteins could function in nucleosome phasing and in the 3' end processing of mRNA transcripts. They are also involved in the transcription regulation of genes containing, or in close proximity to, AT-rich regions. ; GO: 0003677 DNA binding; PDB: 2EZE_A 2EZD_A 2EZF_A 2EZG_A.
Probab=57.68 E-value=4.6 Score=23.71 Aligned_cols=11 Identities=36% Similarity=0.516 Sum_probs=4.1
Q ss_pred cccCCCCCCCC
Q 041992 92 KQKAGRRPPRG 102 (473)
Q Consensus 92 KrKrGrppk~~ 102 (473)
+++||||++..
T Consensus 1 ~r~RGRP~k~~ 11 (13)
T PF02178_consen 1 KRKRGRPRKNA 11 (13)
T ss_dssp S--SS--TT--
T ss_pred CCcCCCCcccc
Confidence 57899998853
No 57
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=57.39 E-value=3.9 Score=28.68 Aligned_cols=25 Identities=28% Similarity=0.822 Sum_probs=17.2
Q ss_pred cCcccccccCCceeeccCCCccccc
Q 041992 167 GWHICSICEKASYYMCYTCTYSLCK 191 (473)
Q Consensus 167 P~H~C~vC~k~sl~~C~~Cp~AyH~ 191 (473)
|.+.|.+|+..+.+.|..|...||.
T Consensus 1 ~~~~C~vC~~~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 1 PRKLCSVCGNPAKYRCPRCGARYCS 25 (30)
T ss_dssp --EEETSSSSEESEE-TTT--EESS
T ss_pred CcCCCccCcCCCEEECCCcCCceeC
Confidence 4567999999778999999988874
No 58
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=55.24 E-value=6.6 Score=38.05 Aligned_cols=27 Identities=26% Similarity=0.579 Sum_probs=22.4
Q ss_pred eeeccCCCccccccccCCCccccccCCeeecCCCCcc
Q 041992 179 YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 179 l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
..+|..|..-||..|... .-|+.|.+.
T Consensus 172 ~~~C~~C~~v~H~~C~~~----------~~CpkC~R~ 198 (202)
T PF13901_consen 172 TVRCPKCKSVFHKSCFRK----------KSCPKCARR 198 (202)
T ss_pred eeeCCcCccccchhhcCC----------CCCCCcHhH
Confidence 689999999999999872 239999875
No 59
>smart00384 AT_hook DNA binding domain with preference for A/T rich regions. Small DNA-binding motif first described in the high mobility group non-histone chromosomal protein HMG-I(Y).
Probab=54.36 E-value=8.2 Score=26.72 Aligned_cols=12 Identities=33% Similarity=0.360 Sum_probs=9.8
Q ss_pred cccCCCCCCCCC
Q 041992 92 KQKAGRRPPRGG 103 (473)
Q Consensus 92 KrKrGrppk~~~ 103 (473)
+||||||+|...
T Consensus 1 kRkRGRPrK~~~ 12 (26)
T smart00384 1 KRKRGRPRKAPK 12 (26)
T ss_pred CCCCCCCCCCCC
Confidence 589999999753
No 60
>PF06524 NOA36: NOA36 protein; InterPro: IPR010531 This family consists of several NOA36 proteins which contain 29 highly conserved cysteine residues. The function of this protein is unknown.; GO: 0008270 zinc ion binding, 0005634 nucleus
Probab=49.33 E-value=13 Score=38.34 Aligned_cols=46 Identities=20% Similarity=0.556 Sum_probs=38.1
Q ss_pred ccccccCCceeeccCCCccccccccCCCccccccCCeeecCCCCcc
Q 041992 170 ICSICEKASYYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 170 ~C~vC~k~sl~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
.|..|.+-+.+.|.+|...||...++...+....+....|+.|.-.
T Consensus 173 KC~SCNrlGq~sCLRCK~cfCddHvrrKg~ky~k~k~~PCPKCg~e 218 (314)
T PF06524_consen 173 KCQSCNRLGQYSCLRCKICFCDDHVRRKGFKYEKGKPIPCPKCGYE 218 (314)
T ss_pred cccccccccchhhhheeeeehhhhhhhcccccccCCCCCCCCCCCc
Confidence 4778999899999999999999998865566666777889999764
No 61
>KOG1428 consensus Inhibitor of type V adenylyl cyclases/Neuronal presynaptic protein Highwire/PAM/RPM-1 [Signal transduction mechanisms]
Probab=48.08 E-value=3.7 Score=50.52 Aligned_cols=54 Identities=28% Similarity=0.701 Sum_probs=36.5
Q ss_pred ccccccccccccccC-ceeecCCCCCCCcccccccCcccccCCCCCceeecCc-----ccccccC
Q 041992 118 KTEEEDVCFICFDGG-SLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH-----ICSICEK 176 (473)
Q Consensus 118 ~~~ned~CfVC~dGG-eLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H-----~C~vC~k 176 (473)
+.+.+|.|.+|.... ..--|-+-+|.-.||+.|...-+ ..+|.=|+- .|.+|+.
T Consensus 3482 kQD~DDmCmICFTE~L~AAP~IqL~C~HiFHlqC~R~vL-----E~RW~GPRItF~FisCPiC~n 3541 (3738)
T KOG1428|consen 3482 KQDADDMCMICFTEALSAAPAIQLDCSHIFHLQCCRRVL-----ENRWLGPRITFGFISCPICKN 3541 (3738)
T ss_pred hcccCceEEEEehhhhCCCcceecCCccchhHHHHHHHH-----HhcccCCeeEEeeeecccccc
Confidence 567788899997421 12234445699999999998765 345766653 5777775
No 62
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=47.52 E-value=11 Score=45.54 Aligned_cols=43 Identities=19% Similarity=0.481 Sum_probs=37.3
Q ss_pred ccccccCCc-eeeccCCCccccccccCCCccccccCCeeecCCCC
Q 041992 170 ICSICEKAS-YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICM 213 (473)
Q Consensus 170 ~C~vC~k~s-l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~ 213 (473)
.|.+|.+.+ +.+|..||+-||..|+.. +...++...|-|..|.
T Consensus 346 hcrf~~d~~~~lc~Et~prvvhlEcv~h-P~~~~~s~~~e~evc~ 389 (1414)
T KOG1473|consen 346 HCRFCHDLGDLLCCETCPRVVHLECVFH-PRFAVPSAFWECEVCN 389 (1414)
T ss_pred cccccCcccceeecccCCceEEeeecCC-ccccCCCccchhhhhh
Confidence 799999876 889999999999999985 4667888889888876
No 63
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=44.36 E-value=13 Score=30.31 Aligned_cols=38 Identities=21% Similarity=0.264 Sum_probs=16.3
Q ss_pred eeecc--CCCccccccccCCCcc------ccccCCeeecCCCCcch
Q 041992 179 YYMCY--TCTYSLCKGCTKGADY------YSLRGNKGFCGICMRTI 216 (473)
Q Consensus 179 l~~C~--~Cp~AyH~~CL~~~~~------~sv~~~kwfC~~C~~~~ 216 (473)
...|. .|...||..||..--. .......|-|+.|...+
T Consensus 20 ~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i 65 (70)
T PF11793_consen 20 DVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPI 65 (70)
T ss_dssp -B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEE
T ss_pred ceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCee
Confidence 46675 8999999999975211 11122358899999864
No 64
>PF05565 Sipho_Gp157: Siphovirus Gp157; InterPro: IPR008840 This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophage. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage [].
Probab=42.76 E-value=92 Score=29.21 Aligned_cols=56 Identities=23% Similarity=0.388 Sum_probs=42.7
Q ss_pred ecccCCCCCHHHHHHHHHHhhhcccccchHHHHHHHHHHHHHHHHH-----HHHHHHHHHHHhhHhhhhh
Q 041992 375 DAISNQEFSEDECSRLRQSIKCGFIKHLTVGEIQEKAMSLQALRVN-----DLLESEILRLNNLRDRASE 439 (473)
Q Consensus 375 ~~ls~~df~eeEC~~lrq~ik~gl~kr~tv~~~eeka~~l~~~~~~-----~wi~~e~~rl~~l~dra~e 439 (473)
+++.+.+..+|...|.-+++. .++++||..+=..|-+ .++..|+.||+.+...+..
T Consensus 15 ~~~e~~~~d~e~~~dtLe~i~---------~~~~~K~~~~~~~Ik~~ea~~e~~k~E~krL~~rkk~~e~ 75 (162)
T PF05565_consen 15 ELLEEGDLDEEAIADTLESIE---------DEIEEKADNIAKVIKNLEADIEAIKAEIKRLQERKKSIEN 75 (162)
T ss_pred HHHhcCCCCHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666788888888888865 7899999876655544 3999999999988866544
No 65
>COG5082 AIR1 Arginine methyltransferase-interacting protein, contains RING Zn-finger [Posttranslational modification, protein turnover, chaperones / Intracellular trafficking and secretion]
Probab=41.07 E-value=21 Score=35.04 Aligned_cols=50 Identities=28% Similarity=0.615 Sum_probs=30.5
Q ss_pred cccccccccccccCceeecCCCCCCCcccccccCcccccCCCCCceeecCc-ccccccCCc
Q 041992 119 TEEEDVCFICFDGGSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH-ICSICEKAS 178 (473)
Q Consensus 119 ~~ned~CfVC~dGGeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H-~C~vC~k~s 178 (473)
....-.|+.|+..|.+. +.||.+--..| ..+.. ..=.||+. .|..||..+
T Consensus 57 ~~~~~~C~nCg~~GH~~----~DCP~~iC~~C-~~~~H-----~s~~C~~~~~C~~Cg~~G 107 (190)
T COG5082 57 REENPVCFNCGQNGHLR----RDCPHSICYNC-SWDGH-----RSNHCPKPKKCYNCGETG 107 (190)
T ss_pred cccccccchhcccCccc----ccCChhHhhhc-CCCCc-----ccccCCcccccccccccC
Confidence 34556799999999876 26883333344 22221 11247776 677887765
No 66
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=41.04 E-value=15 Score=29.42 Aligned_cols=27 Identities=22% Similarity=0.614 Sum_probs=22.9
Q ss_pred cccccccCCc-----eeeccCCCccccccccC
Q 041992 169 HICSICEKAS-----YYMCYTCTYSLCKGCTK 195 (473)
Q Consensus 169 H~C~vC~k~s-----l~~C~~Cp~AyH~~CL~ 195 (473)
..|..|++.- +..|..|..-||..|-.
T Consensus 6 ~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~ 37 (54)
T PF14446_consen 6 CKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE 37 (54)
T ss_pred ccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence 4688999863 78999999999999974
No 67
>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=40.67 E-value=12 Score=25.67 Aligned_cols=25 Identities=32% Similarity=0.988 Sum_probs=11.5
Q ss_pred ccccccCCc----eeeccCCCcccccccc
Q 041992 170 ICSICEKAS----YYMCYTCTYSLCKGCT 194 (473)
Q Consensus 170 ~C~vC~k~s----l~~C~~Cp~AyH~~CL 194 (473)
.|..|++.. .+.|..|....|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDGGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCCCceEECccCCCccChhcC
Confidence 477888864 6899999999998873
No 68
>PF15446 zf-PHD-like: PHD/FYVE-zinc-finger like domain
Probab=40.65 E-value=14 Score=35.85 Aligned_cols=26 Identities=27% Similarity=0.654 Sum_probs=21.2
Q ss_pred cccccCC-------ceeeccCCCccccccccCC
Q 041992 171 CSICEKA-------SYYMCYTCTYSLCKGCTKG 196 (473)
Q Consensus 171 C~vC~k~-------sl~~C~~Cp~AyH~~CL~~ 196 (473)
|.+|+.. .++.|.-|..|||..||..
T Consensus 2 C~~C~~~g~~~~kG~Lv~CQGCs~sYHk~CLG~ 34 (175)
T PF15446_consen 2 CDTCGYEGDDRNKGPLVYCQGCSSSYHKACLGP 34 (175)
T ss_pred cccccCCCCCccCCCeEEcCccChHHHhhhcCC
Confidence 6777432 2899999999999999986
No 69
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the PF05502 Dynactin_p62: Dynactin p62 family; InterPro: IPR008603 Dynactin is a multi-subunit complex and a required cofactor for most, or all, o f the cellular processes powered by the microtubule-based motor cytoplasmic dyn ein. p62 binds directly to the Arp1 subunit of dynactin [, ].
Probab=37.83 E-value=36 Score=37.43 Aligned_cols=29 Identities=28% Similarity=0.668 Sum_probs=19.9
Q ss_pred ceeecCCCCCCCcccccccCcccccCCCCCceeecCc
Q 041992 133 SLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH 169 (473)
Q Consensus 133 eLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H 169 (473)
+|..|. .|-..=.+.|+.... ..||||.|
T Consensus 4 ~L~fC~--~C~~irc~~c~~~Ei------~~~yCp~C 32 (483)
T PF05502_consen 4 ELYFCE--HCHKIRCPRCVSEEI------DSYYCPNC 32 (483)
T ss_pred cceecc--cccccCChhhccccc------ceeECccc
Confidence 466777 577666677776543 45899976
No 71
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=36.80 E-value=47 Score=40.81 Aligned_cols=37 Identities=19% Similarity=0.450 Sum_probs=22.5
Q ss_pred ccccccCCc--eeeccCCCccccccccCCCccccccCCeeecCCCCcch
Q 041992 170 ICSICEKAS--YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRTI 216 (473)
Q Consensus 170 ~C~vC~k~s--l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~ 216 (473)
+|..||... .+.|..|...... -+.+..+|+.|...+
T Consensus 681 fCP~CGs~te~vy~CPsCGaev~~----------des~a~~CP~CGtpl 719 (1337)
T PRK14714 681 RCPDCGTHTEPVYVCPDCGAEVPP----------DESGRVECPRCDVEL 719 (1337)
T ss_pred cCcccCCcCCCceeCccCCCccCC----------CccccccCCCCCCcc
Confidence 566788765 5677777654321 011145899998764
No 72
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=36.71 E-value=21 Score=40.73 Aligned_cols=12 Identities=17% Similarity=0.393 Sum_probs=6.2
Q ss_pred cCCeeecCCCCc
Q 041992 203 RGNKGFCGICMR 214 (473)
Q Consensus 203 ~~~kwfC~~C~~ 214 (473)
+.+.-||+.|-.
T Consensus 38 ~~~~~fC~~CG~ 49 (645)
T PRK14559 38 PVDEAHCPNCGA 49 (645)
T ss_pred CcccccccccCC
Confidence 344456665554
No 73
>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=36.38 E-value=34 Score=37.50 Aligned_cols=52 Identities=23% Similarity=0.491 Sum_probs=37.0
Q ss_pred eecCcccccccCCc-------eeeccCCCccccccccCCCccc----ccc------CCeeecCCCCcch
Q 041992 165 NCGWHICSICEKAS-------YYMCYTCTYSLCKGCTKGADYY----SLR------GNKGFCGICMRTI 216 (473)
Q Consensus 165 ~CP~H~C~vC~k~s-------l~~C~~Cp~AyH~~CL~~~~~~----sv~------~~kwfC~~C~~~~ 216 (473)
||..|.|.+|.+-. ++.|+.|...-|.+|-=...+. ++. .....|..|.+..
T Consensus 125 FC~~C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~s 193 (446)
T PF07227_consen 125 FCRRCMCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKTS 193 (446)
T ss_pred ccccCCccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCChh
Confidence 79999999998842 7899999999999996432221 111 1246788998863
No 74
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=35.45 E-value=23 Score=29.07 Aligned_cols=31 Identities=32% Similarity=0.612 Sum_probs=24.7
Q ss_pred CcccccccCC-c-eeecc--CCCccccccccCCCc
Q 041992 168 WHICSICEKA-S-YYMCY--TCTYSLCKGCTKGAD 198 (473)
Q Consensus 168 ~H~C~vC~k~-s-l~~C~--~Cp~AyH~~CL~~~~ 198 (473)
.-.|..|++. + .+.|. .|..+||..|.....
T Consensus 36 ~~~C~~C~~~~Ga~i~C~~~~C~~~fH~~CA~~~~ 70 (90)
T PF13771_consen 36 KLKCSICKKKGGACIGCSHPGCSRSFHVPCARKAG 70 (90)
T ss_pred CCCCcCCCCCCCeEEEEeCCCCCcEEChHHHccCC
Confidence 3479999998 5 67774 699999999987643
No 75
>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=34.42 E-value=24 Score=24.00 Aligned_cols=9 Identities=22% Similarity=0.833 Sum_probs=6.8
Q ss_pred CCceeecCc
Q 041992 161 KAKWNCGWH 169 (473)
Q Consensus 161 ~g~W~CP~H 169 (473)
.|.|.|+.|
T Consensus 2 ~g~W~C~~C 10 (30)
T PF00641_consen 2 EGDWKCPSC 10 (30)
T ss_dssp SSSEEETTT
T ss_pred CcCccCCCC
Confidence 478999854
No 76
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=34.42 E-value=26 Score=33.95 Aligned_cols=28 Identities=29% Similarity=0.898 Sum_probs=20.2
Q ss_pred ccccccccC--------ceeecCCCCCCCcccccccCc
Q 041992 124 VCFICFDGG--------SLVLCDRKGCPKAYHPACIKR 153 (473)
Q Consensus 124 ~CfVC~dGG--------eLv~CD~~gCPraYH~~CL~p 153 (473)
.|.+|.+.+ ..+.|. .|..+||..|...
T Consensus 154 iCe~C~~~~~IfPF~~~~~~~C~--~C~~v~H~~C~~~ 189 (202)
T PF13901_consen 154 ICEICNSDDIIFPFQIDTTVRCP--KCKSVFHKSCFRK 189 (202)
T ss_pred CCccCCCCCCCCCCCCCCeeeCC--cCccccchhhcCC
Confidence 466665432 567888 6999999999874
No 77
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=34.31 E-value=26 Score=37.25 Aligned_cols=39 Identities=23% Similarity=0.713 Sum_probs=25.5
Q ss_pred ccccccCC----ceeeccCCCccccccccCCCccccccCCeeecCCCC
Q 041992 170 ICSICEKA----SYYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICM 213 (473)
Q Consensus 170 ~C~vC~k~----sl~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~ 213 (473)
.|+.|+.. ..++|..|..-||.+|-- | +-....+|+.|.
T Consensus 332 ~Cf~C~~~~~~~~~y~C~~Ck~~FCldCDv---~--iHesLh~CpgCe 374 (378)
T KOG2807|consen 332 FCFACQGELLSSGRYRCESCKNVFCLDCDV---F--IHESLHNCPGCE 374 (378)
T ss_pred ceeeeccccCCCCcEEchhccceeeccchH---H--HHhhhhcCCCcC
Confidence 38888332 368888888888888842 1 233457788776
No 78
>PRK04023 DNA polymerase II large subunit; Validated
Probab=34.05 E-value=63 Score=38.97 Aligned_cols=29 Identities=14% Similarity=-0.064 Sum_probs=16.0
Q ss_pred hHHHHHHhhhccCCChhhhhhcCCCCCCCCCCCC
Q 041992 244 FKVYWIFLKEKLSLTLDELTGAKNPWKEPAITAP 277 (473)
Q Consensus 244 fK~Yw~~iK~~~~Lt~~~l~~a~~~~k~~~~~~~ 277 (473)
.++||..--+++++.-. ...+||.+...+
T Consensus 683 l~~~~~~A~~~lg~~~~-----~~~~KGVkgl~S 711 (1121)
T PRK04023 683 LKELYDRALENLGERKN-----FDEVKGVKGLTS 711 (1121)
T ss_pred HHHHHHHHHHHhCCcCC-----ccccccceeccc
Confidence 45677777677666432 144555554433
No 79
>PLN02915 cellulose synthase A [UDP-forming], catalytic subunit
Probab=33.28 E-value=34 Score=41.13 Aligned_cols=52 Identities=19% Similarity=0.593 Sum_probs=41.1
Q ss_pred eecCcccccccCCc--------eeeccCCCccccccccCCCccccccCCeeecCCCCcchhhhh
Q 041992 165 NCGWHICSICEKAS--------YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRTIMLIE 220 (473)
Q Consensus 165 ~CP~H~C~vC~k~s--------l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~~~iE 220 (473)
.|+...|.+||..- ..-|..|....|..|.. + +...+.--|++|...+-...
T Consensus 12 ~~~~~~c~iCGd~vg~~~~Ge~FVAC~eC~fpvCr~cye---y-e~~~g~~~cp~c~t~y~~~~ 71 (1044)
T PLN02915 12 SADAKTCRVCGDEVGVKEDGQPFVACHVCGFPVCKPCYE---Y-ERSEGNQCCPQCNTRYKRHK 71 (1044)
T ss_pred CCCcchhhccccccCcCCCCCEEEEeccCCCccccchhh---h-hhhcCCccCCccCCchhhhc
Confidence 57888999999862 57999999999999984 2 34567788999998776443
No 80
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=33.27 E-value=36 Score=37.35 Aligned_cols=74 Identities=20% Similarity=0.297 Sum_probs=40.5
Q ss_pred CCCCcccccccCcc-----c--cc--CCCCCceeecCc-------ccccccCCc--------eeeccCCCccccccccCC
Q 041992 141 GCPKAYHPACIKRE-----E--SF--FRSKAKWNCGWH-------ICSICEKAS--------YYMCYTCTYSLCKGCTKG 196 (473)
Q Consensus 141 gCPraYH~~CL~p~-----~--~~--~~p~g~W~CP~H-------~C~vC~k~s--------l~~C~~Cp~AyH~~CL~~ 196 (473)
.|.++||+.|..=. + .. ......-+|-.+ .|.+|+..- .++=..-.+.||..|..-
T Consensus 351 A~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~C 430 (468)
T KOG1701|consen 351 ALGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKC 430 (468)
T ss_pred hcccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCCCcceEEEEEccccccccceeh
Confidence 36789999765311 1 11 124556778764 699999852 233333355666555432
Q ss_pred C----ccc-------ccc-CCeeecCCCCc
Q 041992 197 A----DYY-------SLR-GNKGFCGICMR 214 (473)
Q Consensus 197 ~----~~~-------sv~-~~kwfC~~C~~ 214 (473)
- .+. ..+ .|..||.+|+-
T Consensus 431 EDCg~~LS~e~e~qgCyPld~HllCk~Ch~ 460 (468)
T KOG1701|consen 431 EDCGLLLSSEEEGQGCYPLDGHLLCKTCHL 460 (468)
T ss_pred hhcCccccccCCCCcceeccCceeechhhh
Confidence 1 011 111 35678988874
No 81
>PF07749 ERp29: Endoplasmic reticulum protein ERp29, C-terminal domain; InterPro: IPR011679 ERp29 is a ubiquitously expressed endoplasmic reticulum protein found in mammals []. This protein is found associated with an N-terminal thioredoxin-like domain (IPR006662 from INTERPRO), which is homologous to the domain of human protein disulphide isomerase (PDI). ERp29 may help mediate the chaperone function of PDI. The C-terminal Erp29 domain has a 5-helical bundle fold. ERp29 is thought to form part of the thyroglobulin folding complex []. ; GO: 0005783 endoplasmic reticulum; PDB: 2QC7_B 1G7D_A 2C0G_B 1OVN_A 2C0F_A 2C0E_A 2C1Y_A.
Probab=31.09 E-value=40 Score=29.04 Aligned_cols=16 Identities=31% Similarity=0.590 Sum_probs=14.6
Q ss_pred HHHHHHHHHHHHhhHh
Q 041992 420 NDLLESEILRLNNLRD 435 (473)
Q Consensus 420 ~~wi~~e~~rl~~l~d 435 (473)
.+|+++|+.||++++.
T Consensus 58 ~~fv~~E~~RL~~lL~ 73 (95)
T PF07749_consen 58 EEFVAKEIARLERLLE 73 (95)
T ss_dssp THHHHHHHHHHHHHHH
T ss_pred chHHHHHHHHHHHHHh
Confidence 3699999999999997
No 82
>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=30.39 E-value=10 Score=27.49 Aligned_cols=31 Identities=35% Similarity=0.759 Sum_probs=21.5
Q ss_pred ccccccccc---C-ceeecCCCCCCCcccccccCcccc
Q 041992 123 DVCFICFDG---G-SLVLCDRKGCPKAYHPACIKREES 156 (473)
Q Consensus 123 d~CfVC~dG---G-eLv~CD~~gCPraYH~~CL~p~~~ 156 (473)
|.|.||.+. + .++.. .|.-.||..|+.....
T Consensus 1 d~C~IC~~~~~~~~~~~~l---~C~H~fh~~Ci~~~~~ 35 (44)
T PF13639_consen 1 DECPICLEEFEDGEKVVKL---PCGHVFHRSCIKEWLK 35 (44)
T ss_dssp -CETTTTCBHHTTSCEEEE---TTSEEEEHHHHHHHHH
T ss_pred CCCcCCChhhcCCCeEEEc---cCCCeeCHHHHHHHHH
Confidence 468888752 3 44444 3999999999988653
No 83
>PLN02436 cellulose synthase A
Probab=29.98 E-value=43 Score=40.45 Aligned_cols=68 Identities=22% Similarity=0.538 Sum_probs=45.4
Q ss_pred ecCcccccccCCc--------eeeccCCCccccccccCCCccccccCCeeecCCCCcchhhhhccCCCCCCceeeecCCC
Q 041992 166 CGWHICSICEKAS--------YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRTIMLIENCAPGNQEKVVVDFDDK 237 (473)
Q Consensus 166 CP~H~C~vC~k~s--------l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~~~iE~~~~~dseg~~VDf~D~ 237 (473)
...+.|.+||..- ..-|..|..-.|..|.. + +...+.--|++|...+-.......+..|.+..|++|-
T Consensus 34 ~~~~iCqICGD~Vg~t~dGe~FVACn~C~fpvCr~Cye---y-er~eg~~~Cpqckt~Y~r~kgs~~~~~d~ee~~~dd~ 109 (1094)
T PLN02436 34 LSGQTCQICGDEIELTVDGEPFVACNECAFPVCRPCYE---Y-ERREGNQACPQCKTRYKRIKGSPRVEGDEEEDDIDDL 109 (1094)
T ss_pred cCCccccccccccCcCCCCCEEEeeccCCCccccchhh---h-hhhcCCccCcccCCchhhccCCCCcCCccccccchhh
Confidence 4556899999852 57899999999999984 2 3446677899999877644433333322234455543
No 84
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=29.31 E-value=18 Score=42.47 Aligned_cols=40 Identities=23% Similarity=0.586 Sum_probs=0.0
Q ss_pred CCceeecCc-------ccccccCCc--eeeccCCCccccccccCCCccccccCCeeecCCCCcc
Q 041992 161 KAKWNCGWH-------ICSICEKAS--YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 161 ~g~W~CP~H-------~C~vC~k~s--l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
-+...||.| .|..||..+ ++.|..|...+ +...|+.|...
T Consensus 653 i~~r~Cp~Cg~~t~~~~Cp~CG~~T~~~~~Cp~C~~~~---------------~~~~C~~C~~~ 701 (900)
T PF03833_consen 653 IGRRRCPKCGKETFYNRCPECGSHTEPVYVCPDCGIEV---------------EEDECPKCGRE 701 (900)
T ss_dssp ----------------------------------------------------------------
T ss_pred eecccCcccCCcchhhcCcccCCccccceecccccccc---------------Ccccccccccc
Confidence 345566644 566676654 45666654332 12278888764
No 85
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=28.72 E-value=20 Score=30.98 Aligned_cols=33 Identities=39% Similarity=0.699 Sum_probs=23.3
Q ss_pred cccccccccc-----------cC---ceeecCCCCCCCcccccccCcccc
Q 041992 121 EEDVCFICFD-----------GG---SLVLCDRKGCPKAYHPACIKREES 156 (473)
Q Consensus 121 ned~CfVC~d-----------GG---eLv~CD~~gCPraYH~~CL~p~~~ 156 (473)
+++.|.+|.. +| .++.+. |...||..|+.....
T Consensus 20 ~dd~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~---C~H~FH~hCI~kWl~ 66 (85)
T PF12861_consen 20 NDDVCGICRMPFDGCCPDCKFPGDDCPLVWGK---CSHNFHMHCILKWLS 66 (85)
T ss_pred CCCceeeEecccccCCCCccCCCCCCceeecc---CccHHHHHHHHHHHc
Confidence 4777777742 33 355554 999999999987764
No 86
>PF11629 Mst1_SARAH: C terminal SARAH domain of Mst1; InterPro: IPR024205 The SARAH (Sav/Rassf/Hpo) domain is found at the C terminus in three classes of eukaryotic tumour suppressors that give the domain its name. In the Sav (Salvador) and Hpo (Hippo) families, the SARAH domain mediates signal transduction from Hpo via the Sav scaffolding protein to the downstream component Wts (Warts); the phosphorylation of Wts by Hpo triggers cell cycle arrest and apoptosis by down-regulating cyclin E, Diap 1 and other targets []. The SARAH domain is also involved in dimerisation, as in the human Hpo orthologue, Mst1, which homodimerises via its C-terminal SARAH domain. The SARAH domain is found associated with other domains, such as protein kinase domains, WW/rsp5/WWP domain (IPR001202 from INTERPRO), C1 domain (IPR002219 from INTERPRO), LIM domain (IPR001781 from INTERPRO), or the Ras-associating (RA) domain (IPR000159 from INTERPRO).; GO: 0004674 protein serine/threonine kinase activity; PDB: 2JO8_A.
Probab=28.69 E-value=1.2e+02 Score=23.96 Aligned_cols=33 Identities=33% Similarity=0.417 Sum_probs=25.2
Q ss_pred hcccccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 041992 396 CGFIKHLTVGEIQEKAMSLQALRVNDLLESEILRLNNL 433 (473)
Q Consensus 396 ~gl~kr~tv~~~eeka~~l~~~~~~~wi~~e~~rl~~l 433 (473)
.+++|.+++.||++.-.+|-..| ++||..|..+
T Consensus 2 ~~fLk~ls~~eL~~rl~~LD~~M-----E~Eieelr~R 34 (49)
T PF11629_consen 2 FEFLKFLSYEELQQRLASLDPEM-----EQEIEELRQR 34 (49)
T ss_dssp -GGGGGS-HHHHHHHHHHHHHHH-----HHHHHHHHHH
T ss_pred hHHHhhCCHHHHHHHHHhCCHHH-----HHHHHHHHHH
Confidence 47899999999999999987665 7777766543
No 87
>PLN02189 cellulose synthase
Probab=28.62 E-value=43 Score=40.25 Aligned_cols=68 Identities=21% Similarity=0.530 Sum_probs=45.4
Q ss_pred ecCcccccccCCc--------eeeccCCCccccccccCCCccccccCCeeecCCCCcchhhhhccCCCCCCceeeecCCC
Q 041992 166 CGWHICSICEKAS--------YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRTIMLIENCAPGNQEKVVVDFDDK 237 (473)
Q Consensus 166 CP~H~C~vC~k~s--------l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~~~iE~~~~~dseg~~VDf~D~ 237 (473)
...+.|.+||..- ..-|..|..-.|..|.. + +...+.--|++|...+-.......+..|.+..|++|-
T Consensus 32 ~~~~~C~iCgd~vg~~~~g~~fvaC~~C~fpvCr~Cye---y-er~eg~q~CpqCkt~Y~r~kgs~~v~gd~ee~~~dd~ 107 (1040)
T PLN02189 32 LDGQVCEICGDEIGLTVDGDLFVACNECGFPVCRPCYE---Y-ERREGTQNCPQCKTRYKRLKGSPRVEGDDDEEDIDDI 107 (1040)
T ss_pred ccCccccccccccCcCCCCCEEEeeccCCCccccchhh---h-hhhcCCccCcccCCchhhccCCCCcCCccccccchhh
Confidence 4456888999851 57899999999999984 2 3456778899999887655433333333344455553
No 88
>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=28.16 E-value=49 Score=22.79 Aligned_cols=25 Identities=28% Similarity=1.019 Sum_probs=19.6
Q ss_pred ccccccCCc----eeeccCCCcccccccc
Q 041992 170 ICSICEKAS----YYMCYTCTYSLCKGCT 194 (473)
Q Consensus 170 ~C~vC~k~s----l~~C~~Cp~AyH~~CL 194 (473)
.|.+|++.. .+.|..|....|..|.
T Consensus 2 ~C~~C~~~~~~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCEeEEeCCCCCeEcCccC
Confidence 577888753 6789999988888873
No 89
>KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=27.60 E-value=20 Score=37.94 Aligned_cols=55 Identities=22% Similarity=0.422 Sum_probs=0.0
Q ss_pred cccccccc----cCceeecCCCCCCCcccccccCcccccCCCCCceeecCc-----ccccccCCceeec---cCCCccc
Q 041992 123 DVCFICFD----GGSLVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWH-----ICSICEKASYYMC---YTCTYSL 189 (473)
Q Consensus 123 d~CfVC~d----GGeLv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H-----~C~vC~k~sl~~C---~~Cp~Ay 189 (473)
++|..|.- .|.|+-|+ |.+|+.-. .....=.||.| .=-.|...++|+| .-|-+.|
T Consensus 91 HfCd~Cd~PI~IYGRmIPCk--------HvFCl~CA----r~~~dK~Cp~C~d~VqrIeq~~~g~iFmC~~~~GC~RTy 157 (389)
T KOG2932|consen 91 HFCDRCDFPIAIYGRMIPCK--------HVFCLECA----RSDSDKICPLCDDRVQRIEQIMMGGIFMCAAPHGCLRTY 157 (389)
T ss_pred EeecccCCcceeeecccccc--------hhhhhhhh----hcCccccCcCcccHHHHHHHhcccceEEeecchhHHHHH
No 90
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=27.55 E-value=17 Score=32.30 Aligned_cols=45 Identities=24% Similarity=0.557 Sum_probs=29.7
Q ss_pred CcccccccCC------ceeeccCCCccccccccCCCccccccCCeeecCCCCcch
Q 041992 168 WHICSICEKA------SYYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRTI 216 (473)
Q Consensus 168 ~H~C~vC~k~------sl~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~ 216 (473)
.+.|..|+.. .-..|..|...+|..|-.. ......|+|..|.+..
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~----~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY----SKKEPIWLCKVCQKQR 104 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE----TSSSCCEEEHHHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCc----CCCCCCEEChhhHHHH
Confidence 3456666653 1467888888888888652 2346789999998743
No 91
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=27.41 E-value=12 Score=37.64 Aligned_cols=70 Identities=24% Similarity=0.541 Sum_probs=45.3
Q ss_pred CceeecCCCCCCCcc--------cccccCcccccCCCCCceeecCcccccccCCc-----------------eeeccCCC
Q 041992 132 GSLVLCDRKGCPKAY--------HPACIKREESFFRSKAKWNCGWHICSICEKAS-----------------YYMCYTCT 186 (473)
Q Consensus 132 GeLv~CD~~gCPraY--------H~~CL~p~~~~~~p~g~W~CP~H~C~vC~k~s-----------------l~~C~~Cp 186 (473)
++++.|+ .|.+.| |..|..... +|.|..||++- -+.|..|.
T Consensus 115 ~d~ftCr--vCgK~F~lQRmlnrh~kch~~vk------------r~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~ 180 (267)
T KOG3576|consen 115 QDSFTCR--VCGKKFGLQRMLNRHLKCHSDVK------------RHLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCE 180 (267)
T ss_pred CCeeeee--hhhhhhhHHHHHHHHhhhccHHH------------HHHHhhccCcccchhhhhhhhccccCccccchhhhh
Confidence 4566666 466665 556665432 46788899851 48999999
Q ss_pred ccccccccCCCccc------------cccCCeeecCCCCcc
Q 041992 187 YSLCKGCTKGADYY------------SLRGNKGFCGICMRT 215 (473)
Q Consensus 187 ~AyH~~CL~~~~~~------------sv~~~kwfC~~C~~~ 215 (473)
+||-..|--...+. +-+....+|..|--.
T Consensus 181 kaftqrcsleshl~kvhgv~~~yaykerr~kl~vcedcg~t 221 (267)
T KOG3576|consen 181 KAFTQRCSLESHLKKVHGVQHQYAYKERRAKLYVCEDCGYT 221 (267)
T ss_pred HHHHhhccHHHHHHHHcCchHHHHHHHhhhheeeecccCCC
Confidence 99988885432222 223456888888754
No 92
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.20 E-value=15 Score=38.08 Aligned_cols=45 Identities=20% Similarity=0.630 Sum_probs=34.4
Q ss_pred cccccccCCc-----------eeeccCCCccccccccCCCccccccCCeeecCCCCcch
Q 041992 169 HICSICEKAS-----------YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRTI 216 (473)
Q Consensus 169 H~C~vC~k~s-----------l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~ 216 (473)
..|.+|++.- ...=..|...||..|++. -.+-+.+-+|+.|.+.+
T Consensus 225 ~vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrG---WcivGKkqtCPYCKekV 280 (328)
T KOG1734|consen 225 SVCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRG---WCIVGKKQTCPYCKEKV 280 (328)
T ss_pred chhHhhcchheeecchhhhhhhheeeecccchHHHhhhh---heeecCCCCCchHHHHh
Confidence 3688999852 123356899999999985 56778899999998754
No 93
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=26.93 E-value=33 Score=37.84 Aligned_cols=33 Identities=18% Similarity=0.494 Sum_probs=21.5
Q ss_pred cccccccccccc-----CceeecCCCCCCCcccccccCccc
Q 041992 120 EEEDVCFICFDG-----GSLVLCDRKGCPKAYHPACIKREE 155 (473)
Q Consensus 120 ~ned~CfVC~dG-----GeLv~CD~~gCPraYH~~CL~p~~ 155 (473)
..--.|-||-.. +.++- - -|--+||-.|+....
T Consensus 173 tELPTCpVCLERMD~s~~gi~t-~--~c~Hsfh~~cl~~w~ 210 (493)
T KOG0804|consen 173 TELPTCPVCLERMDSSTTGILT-I--LCNHSFHCSCLMKWW 210 (493)
T ss_pred ccCCCcchhHhhcCccccceee-e--ecccccchHHHhhcc
Confidence 455679999642 12221 1 366799999998875
No 94
>KOG1246 consensus DNA-binding protein jumonji/RBP2/SMCY, contains JmjC domain [General function prediction only]
Probab=26.26 E-value=53 Score=38.57 Aligned_cols=54 Identities=26% Similarity=0.579 Sum_probs=41.2
Q ss_pred cccccccccccccCc--eeecCCCCCCCcccccccCcccccCCCCCceeecCccccccc
Q 041992 119 TEEEDVCFICFDGGS--LVLCDRKGCPKAYHPACIKREESFFRSKAKWNCGWHICSICE 175 (473)
Q Consensus 119 ~~ned~CfVC~dGGe--Lv~CD~~gCPraYH~~CL~p~~~~~~p~g~W~CP~H~C~vC~ 175 (473)
......|..|..+.. ++.|+ +|-+.||..|+.++... .+++.|.|+.|....|.
T Consensus 152 ~~~~~~~~~~~k~~~~~~~~~~--~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~~~~~~ 207 (904)
T KOG1246|consen 152 FIDYPQCNTCSKGKEEKLLLCD--SCDDSYHTYCLRPPLTR-VPDGDWRCPKCIPTPES 207 (904)
T ss_pred cccchhhhccccCCCccceecc--cccCcccccccCCCCCc-CCcCcccCCcccccccC
Confidence 344556999987662 33888 79999999999998765 68999999877666444
No 95
>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=26.21 E-value=30 Score=30.61 Aligned_cols=35 Identities=17% Similarity=0.550 Sum_probs=23.4
Q ss_pred CCcccccccCcccc----cCCCCCceeecCc----ccccccCC
Q 041992 143 PKAYHPACIKREES----FFRSKAKWNCGWH----ICSICEKA 177 (473)
Q Consensus 143 PraYH~~CL~p~~~----~~~p~g~W~CP~H----~C~vC~k~ 177 (473)
...|=-.||...-. .......|.||.| .|..|.+.
T Consensus 37 ~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiCnCs~Crrk 79 (105)
T PF10497_consen 37 RGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGICNCSFCRRK 79 (105)
T ss_pred cceehHhHHHHHHhhhHHHHhcCCceECCCCCCeeCCHhhhcc
Confidence 77787888764321 1135788999975 67777664
No 96
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=25.90 E-value=45 Score=25.12 Aligned_cols=44 Identities=20% Similarity=0.486 Sum_probs=26.2
Q ss_pred cccccCC-----ceeeccCCCccccccccCCCccccc---cCCeeecCCCCc
Q 041992 171 CSICEKA-----SYYMCYTCTYSLCKGCTKGADYYSL---RGNKGFCGICMR 214 (473)
Q Consensus 171 C~vC~k~-----sl~~C~~Cp~AyH~~CL~~~~~~sv---~~~kwfC~~C~~ 214 (473)
|..|++. ....|..|+..||..|......... .....+|..|..
T Consensus 5 C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~~~~~~~rvC~~C~~ 56 (57)
T cd00065 5 CMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSMGGGKPVRVCDSCYE 56 (57)
T ss_pred CcccCccccCCccccccCcCcCCcChHHcCCeeecCcccCCCccEeChHHhC
Confidence 5556553 1467888888999999875322111 123466776653
No 97
>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=25.77 E-value=40 Score=28.05 Aligned_cols=32 Identities=31% Similarity=0.615 Sum_probs=20.9
Q ss_pred cccccccccccc--cCceeecCCCCCCCcccccccC
Q 041992 119 TEEEDVCFICFD--GGSLVLCDRKGCPKAYHPACIK 152 (473)
Q Consensus 119 ~~ned~CfVC~d--GGeLv~CD~~gCPraYH~~CL~ 152 (473)
...+..|.+|+. |...+.-- .|..+||..|..
T Consensus 75 i~~~~~C~vC~k~l~~~~f~~~--p~~~v~H~~C~~ 108 (109)
T PF10367_consen 75 ITESTKCSVCGKPLGNSVFVVF--PCGHVVHYSCIK 108 (109)
T ss_pred ECCCCCccCcCCcCCCceEEEe--CCCeEEeccccc
Confidence 345667999986 22333222 366899999975
No 98
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=25.34 E-value=38 Score=22.09 Aligned_cols=8 Identities=25% Similarity=0.879 Sum_probs=5.6
Q ss_pred CceeecCc
Q 041992 162 AKWNCGWH 169 (473)
Q Consensus 162 g~W~CP~H 169 (473)
+.|.|+.|
T Consensus 1 g~W~C~~C 8 (26)
T smart00547 1 GDWECPAC 8 (26)
T ss_pred CcccCCCC
Confidence 46888854
No 99
>PLN02638 cellulose synthase A (UDP-forming), catalytic subunit
Probab=25.10 E-value=53 Score=39.73 Aligned_cols=50 Identities=20% Similarity=0.665 Sum_probs=38.5
Q ss_pred CcccccccCCc--------eeeccCCCccccccccCCCccccccCCeeecCCCCcchhhhhc
Q 041992 168 WHICSICEKAS--------YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRTIMLIEN 221 (473)
Q Consensus 168 ~H~C~vC~k~s--------l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~~~iE~ 221 (473)
.+.|.+||..- ..-|..|..-.|.-|.. + +...+.--|++|...+-....
T Consensus 17 ~qiCqICGD~vg~~~~Ge~FVAC~eC~FPVCrpCYE---Y-Er~eG~q~CPqCktrYkr~kg 74 (1079)
T PLN02638 17 GQVCQICGDNVGKTVDGEPFVACDVCAFPVCRPCYE---Y-ERKDGNQSCPQCKTKYKRHKG 74 (1079)
T ss_pred CceeeecccccCcCCCCCEEEEeccCCCccccchhh---h-hhhcCCccCCccCCchhhhcC
Confidence 35799999852 57899999999999984 2 345677889999988765553
No 100
>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=24.62 E-value=22 Score=26.63 Aligned_cols=39 Identities=31% Similarity=0.726 Sum_probs=18.6
Q ss_pred cccccCCc--eeecc--CCCccccccccCCCccccccCCeeecCCC
Q 041992 171 CSICEKAS--YYMCY--TCTYSLCKGCTKGADYYSLRGNKGFCGIC 212 (473)
Q Consensus 171 C~vC~k~s--l~~C~--~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C 212 (473)
|.+|+.-. -.+|. .|+..+|..|+.. +.....+. .|+.|
T Consensus 1 C~~C~~iv~~G~~C~~~~C~~r~H~~C~~~--y~r~~~~~-~CP~C 43 (43)
T PF08746_consen 1 CEACKEIVTQGQRCSNRDCNVRLHDDCFKK--YFRHRSNP-KCPNC 43 (43)
T ss_dssp -TTT-SB-SSSEE-SS--S--EE-HHHHHH--HTTT-SS--B-TTT
T ss_pred CcccchhHeeeccCCCCccCchHHHHHHHH--HHhcCCCC-CCcCC
Confidence 56777754 46887 6999999999973 33332333 67766
No 101
>PLN02400 cellulose synthase
Probab=23.54 E-value=63 Score=39.13 Aligned_cols=66 Identities=21% Similarity=0.554 Sum_probs=43.9
Q ss_pred cCcccccccCCc--------eeeccCCCccccccccCCCccccccCCeeecCCCCcchhhhhccCCCCCCceeeecCC
Q 041992 167 GWHICSICEKAS--------YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRTIMLIENCAPGNQEKVVVDFDD 236 (473)
Q Consensus 167 P~H~C~vC~k~s--------l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~~~iE~~~~~dseg~~VDf~D 236 (473)
..+.|.+||..- ..-|..|..-.|.-|.. + +...+.--|++|...+-.....-.+..|.+.-|++|
T Consensus 35 ~gqiCqICGD~VG~t~dGe~FVAC~eCaFPVCRpCYE---Y-ERkeGnq~CPQCkTrYkR~KgsprV~GDeeedd~DD 108 (1085)
T PLN02400 35 NGQICQICGDDVGVTETGDVFVACNECAFPVCRPCYE---Y-ERKDGTQCCPQCKTRYRRHKGSPRVEGDEDEDDVDD 108 (1085)
T ss_pred CCceeeecccccCcCCCCCEEEEEccCCCccccchhh---e-ecccCCccCcccCCccccccCCCCCCcccccccchh
Confidence 345899999852 57899999999999984 2 345677889999987765543333322223344444
No 102
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=23.36 E-value=1e+02 Score=32.23 Aligned_cols=13 Identities=15% Similarity=0.549 Sum_probs=8.7
Q ss_pred eecCCCCcchhhh
Q 041992 207 GFCGICMRTIMLI 219 (473)
Q Consensus 207 wfC~~C~~~~~~i 219 (473)
-.|..|...+-.+
T Consensus 253 e~C~~C~~YlK~~ 265 (305)
T TIGR01562 253 ETCDSCQGYLKIL 265 (305)
T ss_pred eeccccccchhhh
Confidence 4688888765444
No 103
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=23.35 E-value=41 Score=31.30 Aligned_cols=53 Identities=17% Similarity=0.194 Sum_probs=28.7
Q ss_pred ccccccCCeeecCCCCcchhhhhccCCCCCCceeeecCCCCccchhhHHHHHHhhh
Q 041992 198 DYYSLRGNKGFCGICMRTIMLIENCAPGNQEKVVVDFDDKTSWEYLFKVYWIFLKE 253 (473)
Q Consensus 198 ~~~sv~~~kwfC~~C~~~~~~iE~~~~~dseg~~VDf~D~~~~e~lfK~Yw~~iK~ 253 (473)
|++. ..+..||+.|.......+.-.....+.+++-+. .+-.-+++.+|+..+.
T Consensus 37 PLF~-KdG~v~CPvC~~~~~~v~~e~~~~~~~~~~~~~--~~~~~~~~~~~~~~~~ 89 (131)
T COG1645 37 PLFR-KDGEVFCPVCGYREVVVEEEEEEVEAEVQEQLR--RSRPELPDDSDELKKE 89 (131)
T ss_pred ccee-eCCeEECCCCCceEEEeecccccchhhhhcchh--hcccccccchhhhhcc
Confidence 3444 678999999997655555544433333333332 2333445555555444
No 104
>KOG1671 consensus Ubiquinol cytochrome c reductase, subunit RIP1 [Energy production and conversion]
Probab=23.27 E-value=43 Score=33.39 Aligned_cols=20 Identities=15% Similarity=0.438 Sum_probs=15.7
Q ss_pred cccccCcccccCCCCCceeecC
Q 041992 147 HPACIKREESFFRSKAKWNCGW 168 (473)
Q Consensus 147 H~~CL~p~~~~~~p~g~W~CP~ 168 (473)
|+.|+.+... ...|.|+||.
T Consensus 155 hLGCVp~~~A--Gd~gg~~CPC 174 (210)
T KOG1671|consen 155 HLGCVPIANA--GDYGGYYCPC 174 (210)
T ss_pred cccccccccc--cccCceeccc
Confidence 9999988653 3568999994
No 105
>cd00238 ERp29c ERp29 and ERp38, C-terminal domain; composed of the protein disulfide isomerase (PDI)-like proteins ERp29 and ERp38. ERp29 (also called ERp28) is a ubiquitous endoplasmic reticulum (ER)-resident protein expressed in high levels in secretory cells. It contains a redox inactive TRX-like domain at the N-terminus. The expression profile of ERp29 suggests a role in secretory protein production, distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex and is essential in regulating the secretion of thyroglobulin. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase. ERp38 is a P5-like protein, first isolated from alfalfa (the cDNA clone was named G1), which contains two redox active TRX domains at the N-terminus, like human P5.
Probab=23.26 E-value=62 Score=27.99 Aligned_cols=16 Identities=38% Similarity=0.640 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHhhHh
Q 041992 420 NDLLESEILRLNNLRD 435 (473)
Q Consensus 420 ~~wi~~e~~rl~~l~d 435 (473)
.+|+++|+.||+++++
T Consensus 56 ~~yv~~E~~RL~~iL~ 71 (93)
T cd00238 56 EDYVEKELARLERLLE 71 (93)
T ss_pred hhHHHHHHHHHHHHHh
No 106
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=23.05 E-value=35 Score=35.80 Aligned_cols=43 Identities=23% Similarity=0.600 Sum_probs=26.6
Q ss_pred ccccccCCc------eeeccCCCccccccccCCCccccccCCeeecCCCCcch
Q 041992 170 ICSICEKAS------YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMRTI 216 (473)
Q Consensus 170 ~C~vC~k~s------l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~~ 216 (473)
.|++|+... .++=..|+..||..|+... + ..+...|+.|...+
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l-~---~~~~~~CP~C~~~l 53 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLL-F---VRGSGSCPECDTPL 53 (309)
T ss_pred CCCcCCCCCccCcccccccCCCCCcccHHHHHHH-h---cCCCCCCCCCCCcc
Confidence 355677632 1222278999999998731 2 23456899997653
No 107
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=23.01 E-value=54 Score=27.56 Aligned_cols=36 Identities=31% Similarity=0.741 Sum_probs=17.2
Q ss_pred eeeccCCCc-----cccccccCCCcccccc--C-CeeecCCCCcch
Q 041992 179 YYMCYTCTY-----SLCKGCTKGADYYSLR--G-NKGFCGICMRTI 216 (473)
Q Consensus 179 l~~C~~Cp~-----AyH~~CL~~~~~~sv~--~-~kwfC~~C~~~~ 216 (473)
.++|..|.. +||.+|-.+ +..+. + -..||.+|+.++
T Consensus 17 ~~~C~~C~~~~~~~a~CPdC~~~--Le~LkACGAvdYFC~~c~gLi 60 (70)
T PF07191_consen 17 HYHCEACQKDYKKEAFCPDCGQP--LEVLKACGAVDYFCNHCHGLI 60 (70)
T ss_dssp EEEETTT--EEEEEEE-TTT-SB---EEEEETTEEEEE-TTTT-EE
T ss_pred EEECccccccceecccCCCcccH--HHHHHHhcccceeeccCCcee
Confidence 456666653 556666542 33332 1 368999999875
No 108
>KOG1701 consensus Focal adhesion adaptor protein Paxillin and related LIM proteins [Signal transduction mechanisms]
Probab=21.81 E-value=61 Score=35.64 Aligned_cols=111 Identities=19% Similarity=0.377 Sum_probs=60.5
Q ss_pred cccccccccc--CceeecCCCCCCCcccccccCcc--------cccCCCCCceeecCc------ccccccCCce-eeccC
Q 041992 122 EDVCFICFDG--GSLVLCDRKGCPKAYHPACIKRE--------ESFFRSKAKWNCGWH------ICSICEKASY-YMCYT 184 (473)
Q Consensus 122 ed~CfVC~dG--GeLv~CD~~gCPraYH~~CL~p~--------~~~~~p~g~W~CP~H------~C~vC~k~sl-~~C~~ 184 (473)
-..|.-|+++ |+-.-|. .=.+.||..|..=. ..|..-+++-+|-.| .|..|++.-+ .+=..
T Consensus 274 ~~iC~~C~K~V~g~~~ac~--Am~~~fHv~CFtC~~C~r~L~Gq~FY~v~~k~~CE~cyq~tlekC~~Cg~~I~d~iLrA 351 (468)
T KOG1701|consen 274 FGICAFCHKTVSGQGLAVE--AMDQLFHVQCFTCRTCRRQLAGQSFYQVDGKPYCEGCYQDTLEKCNKCGEPIMDRILRA 351 (468)
T ss_pred hhhhhhcCCcccCcchHHH--HhhhhhcccceehHhhhhhhccccccccCCcccchHHHHHHHHHHhhhhhHHHHHHHHh
Confidence 3478888763 5555565 24578998886521 124445678888877 5999998530 01123
Q ss_pred CCccccc---------cccCCCccccccCCe------------eecCCCCcchhhhhccCCCCCCceeeecCCCC
Q 041992 185 CTYSLCK---------GCTKGADYYSLRGNK------------GFCGICMRTIMLIENCAPGNQEKVVVDFDDKT 238 (473)
Q Consensus 185 Cp~AyH~---------~CL~~~~~~sv~~~k------------wfC~~C~~~~~~iE~~~~~dseg~~VDf~D~~ 238 (473)
|+++||. .||..-+|.--..|. -.|..|.+.|+--+. .+|-++|---|++
T Consensus 352 ~GkayHp~CF~Cv~C~r~ldgipFtvd~~n~v~Cv~dfh~kfAPrCs~C~~PI~P~~G----~~etvRvvamdr~ 422 (468)
T KOG1701|consen 352 LGKAYHPGCFTCVVCARCLDGIPFTVDSQNNVYCVPDFHKKFAPRCSVCGNPILPRDG----KDETVRVVAMDRD 422 (468)
T ss_pred cccccCCCceEEEEeccccCCccccccCCCceeeehhhhhhcCcchhhccCCccCCCC----CcceEEEEEcccc
Confidence 3444444 444443332112333 346777777644333 3344566555554
No 109
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=21.76 E-value=22 Score=37.34 Aligned_cols=41 Identities=29% Similarity=0.770 Sum_probs=30.6
Q ss_pred ccccccCCceeec-cCCCccccccccCCCccccccCCeeecCCCCcc
Q 041992 170 ICSICEKASYYMC-YTCTYSLCKGCTKGADYYSLRGNKGFCGICMRT 215 (473)
Q Consensus 170 ~C~vC~k~sl~~C-~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~~ 215 (473)
.|.+|...-...| ..|+..||..|++.. -++..||+.|...
T Consensus 27 rC~IC~~~i~ip~~TtCgHtFCslCIR~h-----L~~qp~CP~Cr~~ 68 (391)
T COG5432 27 RCRICDCRISIPCETTCGHTFCSLCIRRH-----LGTQPFCPVCRED 68 (391)
T ss_pred HhhhhhheeecceecccccchhHHHHHHH-----hcCCCCCcccccc
Confidence 5777777655666 679999999998743 2567899999864
No 110
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=21.75 E-value=98 Score=32.47 Aligned_cols=13 Identities=23% Similarity=0.605 Sum_probs=9.1
Q ss_pred eecCCCCcchhhh
Q 041992 207 GFCGICMRTIMLI 219 (473)
Q Consensus 207 wfC~~C~~~~~~i 219 (473)
-.|.+|...+-.+
T Consensus 253 e~C~~C~~YlK~~ 265 (309)
T PRK03564 253 ESCGDCGTYLKIL 265 (309)
T ss_pred eecccccccceec
Confidence 5688888765554
No 111
>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=21.58 E-value=67 Score=23.93 Aligned_cols=28 Identities=29% Similarity=0.600 Sum_probs=21.0
Q ss_pred ccccccCCc------eeeccCCCccccccccCCC
Q 041992 170 ICSICEKAS------YYMCYTCTYSLCKGCTKGA 197 (473)
Q Consensus 170 ~C~vC~k~s------l~~C~~Cp~AyH~~CL~~~ 197 (473)
.|..|++.- -++|..|....|..|+...
T Consensus 13 ~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~ 46 (53)
T PF00130_consen 13 YCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKV 46 (53)
T ss_dssp B-TTSSSBECSSSSCEEEETTTT-EEETTGGCTS
T ss_pred CCcccCcccCCCCCCeEEECCCCChHhhhhhhhc
Confidence 577787752 6899999999999999754
No 112
>PRK05467 Fe(II)-dependent oxygenase superfamily protein; Provisional
Probab=21.33 E-value=88 Score=31.26 Aligned_cols=28 Identities=18% Similarity=0.442 Sum_probs=19.9
Q ss_pred CCCCHHHHHHHHHHhhh-ccc-ccchHHHH
Q 041992 380 QEFSEDECSRLRQSIKC-GFI-KHLTVGEI 407 (473)
Q Consensus 380 ~df~eeEC~~lrq~ik~-gl~-kr~tv~~~ 407 (473)
+=||+|||+.+++.+.. |+. -+.|.+..
T Consensus 7 ~vLs~eec~~~~~~le~~~~~dg~~taG~~ 36 (226)
T PRK05467 7 DVLSPEEVAQIRELLDAAEWVDGRVTAGAQ 36 (226)
T ss_pred ccCCHHHHHHHHHHHHhcCCccCCcCcCcc
Confidence 34899999999999875 443 45566544
No 113
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=21.27 E-value=43 Score=27.51 Aligned_cols=25 Identities=32% Similarity=0.737 Sum_probs=13.7
Q ss_pred CceeecCc------ccccccCCc-eeeccCCC
Q 041992 162 AKWNCGWH------ICSICEKAS-YYMCYTCT 186 (473)
Q Consensus 162 g~W~CP~H------~C~vC~k~s-l~~C~~Cp 186 (473)
-.|.||.| .|..|++-+ .+.|..|+
T Consensus 26 v~F~CPnCGe~~I~Rc~~CRk~g~~Y~Cp~CG 57 (61)
T COG2888 26 VKFPCPNCGEVEIYRCAKCRKLGNPYRCPKCG 57 (61)
T ss_pred eEeeCCCCCceeeehhhhHHHcCCceECCCcC
Confidence 45777765 355555544 45555553
No 114
>PF03285 Paralemmin: Paralemmin; InterPro: IPR004965 Paralemmin was identified in the chicken lens as a protein with a molecular weight of 65 kDa (isoform 1) and a splice variant of 60 kDa (isoform 2). Isoform 2 is predominant during infancy and levels of isoform 1 increase with age. Paralemmin is localised to the plasma membrane of fibre cells, and was not detected in the annular pad cells. Its localisation to the short side of the fibre cell and the sites of fibre cell interlocking suggests that paralemmin may play a role in the development of such interdigitating processes []. Palmitoylation is important for localising these proteins to the filopodia of dendritic cells where they have been implicated in the regulation of membrane dynamics and process outgrowth. ; GO: 0008360 regulation of cell shape, 0016020 membrane
Probab=20.62 E-value=94 Score=32.25 Aligned_cols=26 Identities=38% Similarity=0.342 Sum_probs=22.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 041992 405 GEIQEKAMSLQALRVNDLLESEILRLNN 432 (473)
Q Consensus 405 ~~~eeka~~l~~~~~~~wi~~e~~rl~~ 432 (473)
-+=|+|+|.|.+.|.. |++||..|++
T Consensus 6 qEDEqKtR~LEesI~R--LEkEIe~LE~ 31 (278)
T PF03285_consen 6 QEDEQKTRSLEESIHR--LEKEIEALEN 31 (278)
T ss_pred hHHHHHHHHHHHHHHH--HHHHHHHhcc
Confidence 3458999999999977 9999999954
No 115
>PHA02696 hypothetical protein; Provisional
Probab=20.53 E-value=59 Score=27.49 Aligned_cols=22 Identities=23% Similarity=0.400 Sum_probs=18.4
Q ss_pred eeecccCCCCCHHHHHHHHHHh
Q 041992 373 AIDAISNQEFSEDECSRLRQSI 394 (473)
Q Consensus 373 ~i~~ls~~df~eeEC~~lrq~i 394 (473)
-|..-.|+.|||||-.|-.|.+
T Consensus 40 ViQtCdDDYFTEeEFdDgkQvV 61 (79)
T PHA02696 40 VIQTCDDDYFTEEEFDDGKQVV 61 (79)
T ss_pred eeeecccccccHhhcccHHHHH
Confidence 3566679999999999998876
No 116
>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=20.37 E-value=32 Score=23.35 Aligned_cols=40 Identities=25% Similarity=0.673 Sum_probs=23.6
Q ss_pred cccccCCc--eeeccCCCccccccccCCCccccccCCeeecCCCCc
Q 041992 171 CSICEKAS--YYMCYTCTYSLCKGCTKGADYYSLRGNKGFCGICMR 214 (473)
Q Consensus 171 C~vC~k~s--l~~C~~Cp~AyH~~CL~~~~~~sv~~~kwfC~~C~~ 214 (473)
|.+|...- .+.-..|...||..|+... ...+...|+.|..
T Consensus 2 C~iC~~~~~~~~~~~~C~H~~c~~C~~~~----~~~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFREPVVLLPCGHVFCRSCIDKW----LKSGKNTCPLCRT 43 (45)
T ss_pred CCcCchhhhCceEecCCCChhcHHHHHHH----HHhCcCCCCCCCC
Confidence 44555432 2333458888999998632 1124566888765
Done!