Query 025377
Match_columns 253
No_of_seqs 283 out of 1220
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 05:12:03 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025377.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025377hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF12165 DUF3594: Domain of un 100.0 8.6E-94 1.9E-98 587.8 9.4 137 10-146 1-137 (137)
2 KOG1632 Uncharacterized PHD Zn 100.0 1.7E-43 3.7E-48 332.2 0.1 242 7-248 35-294 (345)
3 KOG1973 Chromatin remodeling p 99.1 8.9E-11 1.9E-15 107.8 5.2 53 193-251 215-270 (274)
4 PF00628 PHD: PHD-finger; Int 99.0 4.8E-11 1E-15 82.4 -0.4 50 199-249 1-51 (51)
5 smart00249 PHD PHD zinc finger 98.9 1.3E-09 2.9E-14 71.7 3.6 47 199-246 1-47 (47)
6 COG5034 TNG2 Chromatin remodel 98.9 1.4E-09 3E-14 99.4 4.4 50 195-249 218-270 (271)
7 KOG4323 Polycomb-like PHD Zn-f 97.8 1E-05 2.2E-10 79.7 1.9 49 202-251 175-226 (464)
8 KOG1632 Uncharacterized PHD Zn 97.4 6E-05 1.3E-09 71.8 1.1 49 199-248 62-112 (345)
9 KOG1844 PHD Zn-finger proteins 97.3 0.00025 5.4E-09 69.2 5.0 53 194-249 83-135 (508)
10 KOG0825 PHD Zn-finger protein 96.9 0.00055 1.2E-08 71.3 2.4 55 192-248 210-265 (1134)
11 PF13831 PHD_2: PHD-finger; PD 96.5 0.00049 1.1E-08 45.6 -0.5 35 211-247 2-36 (36)
12 KOG0955 PHD finger protein BR1 96.4 0.0025 5.4E-08 68.4 3.9 58 192-252 214-272 (1051)
13 KOG1512 PHD Zn-finger protein 96.1 0.0024 5.3E-08 60.2 1.3 48 196-247 313-361 (381)
14 KOG0383 Predicted helicase [Ge 95.7 0.004 8.6E-08 64.5 1.2 52 192-248 42-93 (696)
15 KOG2752 Uncharacterized conser 95.7 0.0055 1.2E-07 58.2 1.9 35 196-231 127-167 (345)
16 KOG0957 PHD finger protein [Ge 95.4 0.017 3.6E-07 58.2 4.3 49 199-247 121-177 (707)
17 KOG0954 PHD finger protein [Ge 95.3 0.0078 1.7E-07 62.6 1.7 50 196-248 270-320 (893)
18 KOG4299 PHD Zn-finger protein 95.1 0.0073 1.6E-07 61.5 0.8 51 197-249 253-305 (613)
19 KOG0957 PHD finger protein [Ge 94.3 0.029 6.3E-07 56.5 2.6 50 197-247 544-596 (707)
20 PF07227 DUF1423: Protein of u 94.2 0.046 1E-06 54.1 3.9 53 196-249 127-192 (446)
21 KOG1244 Predicted transcriptio 94.1 0.025 5.4E-07 53.2 1.7 49 198-248 282-330 (336)
22 KOG4443 Putative transcription 93.7 0.0091 2E-07 61.3 -2.2 51 197-247 145-200 (694)
23 PF07496 zf-CW: CW-type Zinc F 93.7 0.035 7.6E-07 38.9 1.4 33 212-245 2-34 (50)
24 KOG1245 Chromatin remodeling c 93.0 0.018 4E-07 63.8 -1.4 56 193-250 1104-1159(1404)
25 PF13639 zf-RING_2: Ring finge 91.1 0.064 1.4E-06 35.8 -0.0 43 199-247 2-44 (44)
26 PF14446 Prok-RING_1: Prokaryo 89.6 0.26 5.5E-06 35.8 2.0 33 196-228 4-36 (54)
27 KOG0956 PHD finger protein AF1 88.8 0.21 4.6E-06 52.1 1.6 47 199-248 7-56 (900)
28 COG5141 PHD zinc finger-contai 87.9 0.2 4.4E-06 50.5 0.8 51 195-248 191-242 (669)
29 KOG1512 PHD Zn-finger protein 87.6 0.13 2.9E-06 48.8 -0.6 53 195-247 256-315 (381)
30 KOG1473 Nucleosome remodeling 85.8 0.25 5.5E-06 53.9 0.2 59 193-251 1118-1176(1414)
31 PF13832 zf-HC5HC2H_2: PHD-zin 84.5 0.54 1.2E-05 36.9 1.5 32 196-230 54-87 (110)
32 PF07649 C1_3: C1-like domain; 83.3 0.51 1.1E-05 29.5 0.7 29 199-228 2-30 (30)
33 PF13901 DUF4206: Domain of un 81.5 1 2.2E-05 39.8 2.2 44 198-252 153-201 (202)
34 PF13771 zf-HC5HC2H: PHD-like 76.6 1.9 4E-05 32.5 2.0 35 195-232 34-70 (90)
35 KOG4443 Putative transcription 74.3 0.9 2E-05 47.2 -0.3 54 195-248 16-70 (694)
36 KOG4628 Predicted E3 ubiquitin 74.2 2.5 5.5E-05 40.9 2.7 47 198-249 230-276 (348)
37 KOG1829 Uncharacterized conser 71.8 0.69 1.5E-05 47.4 -1.8 49 196-252 510-562 (580)
38 KOG2626 Histone H3 (Lys4) meth 69.7 5 0.00011 40.9 3.7 54 195-249 18-76 (544)
39 PF12678 zf-rbx1: RING-H2 zinc 67.4 3.9 8.5E-05 30.5 1.9 43 200-247 22-73 (73)
40 PF10367 Vps39_2: Vacuolar sor 66.1 5.1 0.00011 30.5 2.3 30 198-229 79-108 (109)
41 COG5574 PEX10 RING-finger-cont 65.2 3.5 7.6E-05 38.7 1.5 44 198-249 216-260 (271)
42 PF02318 FYVE_2: FYVE-type zin 58.6 3.3 7.1E-05 33.5 0.1 50 196-249 53-103 (118)
43 cd04714 BAH_BAHCC1 BAH, or Bro 58.0 5.5 0.00012 32.4 1.3 21 195-216 101-121 (121)
44 PF11793 FANCL_C: FANCL C-term 58.0 8 0.00017 28.7 2.0 52 198-249 3-64 (70)
45 PF12861 zf-Apc11: Anaphase-pr 56.7 4.5 9.7E-05 31.9 0.5 47 198-248 22-79 (85)
46 PLN03208 E3 ubiquitin-protein 54.7 7.4 0.00016 34.9 1.6 51 195-249 16-77 (193)
47 PF00130 C1_1: Phorbol esters/ 52.0 25 0.00055 23.8 3.7 38 196-233 10-48 (53)
48 PF03107 C1_2: C1 domain; Int 50.9 16 0.00035 22.8 2.3 28 199-228 2-30 (30)
49 KOG3799 Rab3 effector RIM1 and 49.6 7.2 0.00016 33.7 0.7 53 196-249 64-116 (169)
50 COG1993 PII-like signaling pro 49.0 8.5 0.00018 31.7 1.0 29 113-141 47-78 (109)
51 TIGR01562 FdhE formate dehydro 46.4 19 0.0004 34.3 3.0 53 196-248 183-260 (305)
52 PF13341 RAG2_PHD: RAG2 PHD do 45.0 10 0.00022 29.3 0.8 35 212-246 29-68 (78)
53 cd00162 RING RING-finger (Real 43.7 7.9 0.00017 24.0 0.1 42 200-248 2-43 (45)
54 PF00319 SRF-TF: SRF-type tran 43.2 30 0.00065 24.5 3.0 35 18-58 12-46 (51)
55 COG1773 Rubredoxin [Energy pro 43.1 17 0.00037 26.5 1.7 41 198-248 4-44 (55)
56 PF09416 UPF1_Zn_bind: RNA hel 42.8 15 0.00033 31.8 1.7 26 200-227 3-28 (152)
57 PF05402 PqqD: Coenzyme PQQ sy 42.6 38 0.00082 23.9 3.5 32 9-40 29-60 (68)
58 smart00109 C1 Protein kinase C 42.5 10 0.00023 24.6 0.5 36 196-231 10-45 (49)
59 PF13717 zinc_ribbon_4: zinc-r 42.0 24 0.00052 23.1 2.2 23 199-221 4-33 (36)
60 KOG4218 Nuclear hormone recept 40.5 12 0.00026 36.8 0.8 51 198-248 16-75 (475)
61 PF13023 HD_3: HD domain; PDB: 39.8 16 0.00035 31.1 1.4 40 94-139 23-65 (165)
62 PRK03564 formate dehydrogenase 39.3 32 0.00069 32.9 3.4 52 197-248 187-260 (309)
63 PF10497 zf-4CXXC_R1: Zinc-fin 38.6 26 0.00056 28.2 2.3 52 195-248 5-69 (105)
64 KOG2752 Uncharacterized conser 36.9 21 0.00045 34.6 1.7 52 197-252 53-104 (345)
65 KOG0913 Thiol-disulfide isomer 36.3 11 0.00024 35.0 -0.1 49 79-146 63-111 (248)
66 PF14634 zf-RING_5: zinc-RING 35.9 17 0.00037 24.2 0.7 42 200-248 2-44 (44)
67 KOG1493 Anaphase-promoting com 35.4 4.6 9.9E-05 31.6 -2.4 48 199-248 22-78 (84)
68 KOG4299 PHD Zn-finger protein 34.8 25 0.00055 36.5 2.1 48 197-248 47-94 (613)
69 KOG0320 Predicted E3 ubiquitin 34.4 35 0.00075 30.6 2.6 46 197-249 131-176 (187)
70 PF05715 zf-piccolo: Piccolo Z 32.7 22 0.00047 26.5 0.9 53 198-251 3-60 (61)
71 PF13719 zinc_ribbon_5: zinc-r 31.7 35 0.00076 22.3 1.7 25 199-223 4-35 (37)
72 PF13922 PHD_3: PHD domain of 31.4 13 0.00029 28.2 -0.4 31 196-232 32-62 (69)
73 cd00350 rubredoxin_like Rubred 30.9 25 0.00055 22.3 0.9 12 239-250 16-27 (33)
74 cd04120 Rab12 Rab12 subfamily. 30.7 27 0.00059 30.4 1.3 14 63-76 184-197 (202)
75 KOG1941 Acetylcholine receptor 30.7 5.7 0.00012 39.5 -3.1 52 195-250 363-415 (518)
76 KOG1952 Transcription factor N 29.4 41 0.00088 36.5 2.6 54 195-248 189-244 (950)
77 cd00029 C1 Protein kinase C co 29.4 32 0.00069 22.5 1.2 36 196-231 10-46 (50)
78 PF11351 DUF3154: Protein of u 29.4 25 0.00055 28.9 0.9 13 100-112 100-114 (123)
79 PF06452 DUF1083: Domain of un 29.0 16 0.00034 30.3 -0.4 44 57-101 123-171 (185)
80 PHA02929 N1R/p28-like protein; 28.4 33 0.00071 31.6 1.5 46 198-248 175-224 (238)
81 PF00301 Rubredoxin: Rubredoxi 27.7 57 0.0012 22.8 2.3 13 238-250 32-44 (47)
82 KOG3277 Uncharacterized conser 27.4 35 0.00077 29.9 1.4 33 197-229 79-129 (165)
83 PF13111 DUF3962: Protein of u 27.0 31 0.00068 31.4 1.1 34 88-130 24-57 (216)
84 smart00432 MADS MADS domain. 26.3 84 0.0018 22.8 3.1 38 18-60 19-56 (59)
85 PHA03099 epidermal growth fact 24.9 19 0.00042 30.7 -0.6 23 29-52 34-56 (139)
86 TIGR03859 PQQ_PqqD coenzyme PQ 24.7 86 0.0019 23.6 3.0 31 9-40 43-73 (81)
87 cd07168 NR_DBD_DHR4_like DNA-b 24.4 43 0.00092 26.1 1.3 33 195-227 4-37 (90)
88 PF05180 zf-DNL: DNL zinc fing 24.0 30 0.00066 26.0 0.4 17 206-222 22-38 (66)
89 smart00064 FYVE Protein presen 23.8 40 0.00086 24.0 1.0 53 197-249 10-65 (68)
90 KOG2932 E3 ubiquitin ligase in 23.5 28 0.0006 33.9 0.1 42 199-250 92-133 (389)
91 PF08274 PhnA_Zn_Ribbon: PhnA 22.9 41 0.0009 21.5 0.8 10 199-208 4-13 (30)
92 CHL00174 accD acetyl-CoA carbo 22.8 35 0.00075 32.5 0.6 32 209-248 34-65 (296)
93 KOG1886 BAH domain proteins [T 22.2 51 0.0011 33.3 1.7 44 200-247 173-216 (464)
94 PF03966 Trm112p: Trm112p-like 22.2 78 0.0017 23.0 2.3 13 211-223 51-63 (68)
95 smart00744 RINGv The RING-vari 21.8 37 0.0008 23.5 0.4 45 200-247 2-49 (49)
96 PF13880 Acetyltransf_13: ESCO 21.6 35 0.00076 25.9 0.3 52 20-91 16-68 (70)
97 PF09297 zf-NADH-PPase: NADH p 21.5 54 0.0012 20.5 1.1 25 197-221 3-29 (32)
98 PF04810 zf-Sec23_Sec24: Sec23 20.7 69 0.0015 21.2 1.6 32 214-250 3-34 (40)
99 PF05207 zf-CSL: CSL zinc fing 20.6 70 0.0015 22.8 1.7 30 195-225 16-52 (55)
100 KOG1473 Nucleosome remodeling 20.3 73 0.0016 35.9 2.4 48 195-247 342-389 (1414)
101 PRK04023 DNA polymerase II lar 20.3 83 0.0018 35.0 2.9 48 192-250 621-673 (1121)
102 PF08479 POTRA_2: POTRA domain 20.3 1.3E+02 0.0027 21.9 3.1 35 6-40 13-49 (76)
No 1
>PF12165 DUF3594: Domain of unknown function (DUF3594); InterPro: IPR021998 This presumed domain is functionally uncharacterised.This domain family is found in eukaryotes, and is approximately 140 amino acids in length. The family is found in association with PF00628 from PFAM.
Probab=100.00 E-value=8.6e-94 Score=587.80 Aligned_cols=137 Identities=84% Similarity=1.432 Sum_probs=135.2
Q ss_pred CCHHHHHhhhhhhhhHHHHHhhHHHHHHHhhcCCCCcceeeecCCCCceeeeCCCCCCCCCCCCCccCccccCCCccccc
Q 025377 10 RTVEEVFGDFKGRRAGMIKALTTEVEEFYHQCDPEKENLCLYGFPSEQWEVNLPAEEVPPELPEPALGINFARDGMQEKD 89 (253)
Q Consensus 10 ~~~~~~f~d~~~rr~~~~~alt~d~~~f~~~c~p~~~~l~lyg~~~~~w~v~~p~~~~p~~~pep~~gin~~rd~~~~~~ 89 (253)
||||+||+||++||+|||||||+||++||+||||+||||||||+|||+|||+||+||||||||||+||||||||||+|+|
T Consensus 1 rtve~if~df~~RR~g~v~ALT~dve~Fy~~CDP~kenLCLYG~p~~~WeV~lP~eevPpeLPEPaLGINfaRDgM~r~d 80 (137)
T PF12165_consen 1 RTVEEIFRDFSGRRAGIVRALTTDVEEFYQQCDPEKENLCLYGHPDGTWEVNLPAEEVPPELPEPALGINFARDGMQRKD 80 (137)
T ss_pred CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccccceEEecCCCCCeEEeCChHhCCCCCCCcccCcccccCCccHHH
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred chhhhhhhhhhHHHHHhhhhccccccChhhhHHHHHhhhcCCceeeeeccccccccc
Q 025377 90 WLSLVAVHSDAWLLSVAFYFGARFGFDKSDRKRLFNMINELPTIFEVVTGTTKKQAK 146 (253)
Q Consensus 90 wl~~va~h~d~wl~~~~~~~~~~~~f~~~~r~~lf~min~LPTv~EvVtg~~kkq~k 146 (253)
|||||||||||||||||||||||||||+++|+|||+|||+||||||||+|+++||.|
T Consensus 81 WLslVAvHsDsWLlsvAfy~gar~~~~~~~R~rLF~mIN~lpTv~Evv~g~~~~q~k 137 (137)
T PF12165_consen 81 WLSLVAVHSDSWLLSVAFYFGARFGFDKNERKRLFSMINDLPTVFEVVTGRAKKQSK 137 (137)
T ss_pred HHHHHHHhccHHHHHHHHHHHHhhccChHHHHHHHHHHhcCchHHHHHhccccccCC
Confidence 999999999999999999999999999999999999999999999999999988854
No 2
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=100.00 E-value=1.7e-43 Score=332.16 Aligned_cols=242 Identities=41% Similarity=0.660 Sum_probs=201.0
Q ss_pred CCCCCHHHHHhhhhhhhhHHHHHhhHHHHHHHhhcCC----CCcceeeecCCCCceeeeCCCCCCCCCCCCCccCccccC
Q 025377 7 YNPRTVEEVFGDFKGRRAGMIKALTTEVEEFYHQCDP----EKENLCLYGFPSEQWEVNLPAEEVPPELPEPALGINFAR 82 (253)
Q Consensus 7 ~~~~~~~~~f~d~~~rr~~~~~alt~d~~~f~~~c~p----~~~~l~lyg~~~~~w~v~~p~~~~p~~~pep~~gin~~r 82 (253)
+.+++|+++|.+|++||++++.||+.++..||.+||| .++|||+|+++++.|+|++|++++|++++++++|||+|+
T Consensus 35 ~~~~~~~~~~~~~k~~~~~~~~a~~~~~~~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~ 114 (345)
T KOG1632|consen 35 PIERPVPDVFRGRKGRRGGLLKALTQRYCKCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQ 114 (345)
T ss_pred CCCCCCcccccccccccccccHhhhhchhhcccccCchhhhhccccccccccccccccCchhhcCCccccccccccchhh
Confidence 7899999999999999999999999999999999999 789999999999999999999999999999999999999
Q ss_pred CCcccccchhhhhhhhhhHHHHHhhhhcccc-----ccChhhhHHHHHhhhcCCceeeeecccccccccccCCCCCCCCC
Q 025377 83 DGMQEKDWLSLVAVHSDAWLLSVAFYFGARF-----GFDKSDRKRLFNMINELPTIFEVVTGTTKKQAKEKSSVSNHSSS 157 (253)
Q Consensus 83 d~~~~~~wl~~va~h~d~wl~~~~~~~~~~~-----~f~~~~r~~lf~min~LPTv~EvVtg~~kkq~kekss~s~~s~s 157 (253)
|||+.+|||++|++|+|+|+++++||||+++ ++.+.+|+|++.++|++|||++++++.+......+....+.+.+
T Consensus 115 ~~~~~~~~l~~~~~~~~~~~~s~s~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~t~~~~~~~~~~~~~~~k~~~~~~~~~ 194 (345)
T KOG1632|consen 115 DGMSESDGLSCVCRQDDSELLSPSFYFGKRGCQFWVKLQKLGRVRLEAEKNDDPTVFEVVSGTATGELPSKDKSSNDRGS 194 (345)
T ss_pred hhhhhhccceeecccccccccccccccCCccccccccchhhhhhhhhhhhcccchhhhcccccccccccccccccccccc
Confidence 9999999999999999999999999999998 89999999999999999999999999876543333333334445
Q ss_pred CCCCCCCCCCCccccccccc-CCcccccc----CCccccccccCcceecccCCcccCCCceEEccCCCCeeeccccccCc
Q 025377 158 KSKSNSKRGSETQAKFSKAV-QSKDEEDE----GLEEEDEEEHGETLCGACGENYAADEFWICCDVCEKWFHGKCVKITP 232 (253)
Q Consensus 158 ks~ss~Kr~~s~~~K~~k~~-~~~~dEeE----~~eeedeEd~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~ 232 (253)
++.++.++...+.....+.. ..+.+..+ ...+.+..+.+...|..||.++..+.+||.|+.|+.|||+.|+.+++
T Consensus 195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~ 274 (345)
T KOG1632|consen 195 KSKTRKKRNRESELEEKKRKHFSNEELTEPAREPVDESEAPDYSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFE 274 (345)
T ss_pred eecccCcccccchhhhhhhhhccCcccccccccCCCcccccccccccccccCcchHHHHHHHHHHHHHHHhccccccccc
Confidence 55444443332222221111 11111111 13455666778889999999887678999999999999999999999
Q ss_pred cccCCCCe----EEcCCCCC
Q 025377 233 ARAEHIKQ----YKCPSCSN 248 (253)
Q Consensus 233 ~~a~~id~----y~Cp~C~~ 248 (253)
+....+.. |+|+.|..
T Consensus 275 a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 275 ARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred chhhhhhhhccceecCceee
Confidence 98877777 99999986
No 3
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=99.09 E-value=8.9e-11 Score=107.76 Aligned_cols=53 Identities=28% Similarity=0.743 Sum_probs=42.1
Q ss_pred cccCcceecccCCcccCCCceEEccC--CC-CeeeccccccCccccCCCCeEEcCCCCCcCC
Q 025377 193 EEHGETLCGACGENYAADEFWICCDV--CE-KWFHGKCVKITPARAEHIKQYKCPSCSNKRA 251 (253)
Q Consensus 193 Ed~~~t~C~iC~~py~~d~~mIqCD~--Ce-~WfH~~CVgit~~~a~~id~y~Cp~C~~Kr~ 251 (253)
+.++.++| +|.+. ..+.||.||. |. .|||+.||||+..+. ++|+|+.|.....
T Consensus 215 d~~e~~yC-~Cnqv--syg~Mi~CDn~~C~~eWFH~~CVGL~~~Pk---gkWyC~~C~~~~~ 270 (274)
T KOG1973|consen 215 DPDEPTYC-ICNQV--SYGKMIGCDNPGCPIEWFHFTCVGLKTKPK---GKWYCPRCKAENK 270 (274)
T ss_pred CCCCCEEE-Eeccc--ccccccccCCCCCCcceEEEeccccccCCC---Ccccchhhhhhhh
Confidence 34455666 99965 5789999996 99 999999999996543 5699999997543
No 4
>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=99.00 E-value=4.8e-11 Score=82.42 Aligned_cols=50 Identities=34% Similarity=0.866 Sum_probs=40.5
Q ss_pred eecccCCcccCCCceEEccCCCCeeeccccccCccccCCC-CeEEcCCCCCc
Q 025377 199 LCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHI-KQYKCPSCSNK 249 (253)
Q Consensus 199 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~i-d~y~Cp~C~~K 249 (253)
+|.+|++. ++++.||+||.|..|||..|++++....... ..|+|+.|..|
T Consensus 1 ~C~vC~~~-~~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~~ 51 (51)
T PF00628_consen 1 YCPVCGQS-DDDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRPK 51 (51)
T ss_dssp EBTTTTSS-CTTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHHC
T ss_pred eCcCCCCc-CCCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcCc
Confidence 57899994 4588999999999999999999987643322 37999999754
No 5
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.89 E-value=1.4e-09 Score=99.42 Aligned_cols=50 Identities=30% Similarity=0.787 Sum_probs=40.2
Q ss_pred cCcceecccCCcccCCCceEEcc--CCC-CeeeccccccCccccCCCCeEEcCCCCCc
Q 025377 195 HGETLCGACGENYAADEFWICCD--VCE-KWFHGKCVKITPARAEHIKQYKCPSCSNK 249 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d~~mIqCD--~Ce-~WfH~~CVgit~~~a~~id~y~Cp~C~~K 249 (253)
+++.++|.|++. ..+.||.|| .|+ .|||..|||+...+- ..|+|+.|..+
T Consensus 218 e~e~lYCfCqqv--SyGqMVaCDn~nCkrEWFH~~CVGLk~pPK---G~WYC~eCk~~ 270 (271)
T COG5034 218 EGEELYCFCQQV--SYGQMVACDNANCKREWFHLECVGLKEPPK---GKWYCPECKKA 270 (271)
T ss_pred cCceeEEEeccc--ccccceecCCCCCchhheeccccccCCCCC---CcEeCHHhHhc
Confidence 333444499997 468999999 898 999999999987642 57999999754
No 7
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.77 E-value=1e-05 Score=79.70 Aligned_cols=49 Identities=24% Similarity=0.593 Sum_probs=36.2
Q ss_pred ccCCcccCCCceEEccCCCCeeecccccc--CccccCCC-CeEEcCCCCCcCC
Q 025377 202 ACGENYAADEFWICCDVCEKWFHGKCVKI--TPARAEHI-KQYKCPSCSNKRA 251 (253)
Q Consensus 202 iC~~py~~d~~mIqCD~Ce~WfH~~CVgi--t~~~a~~i-d~y~Cp~C~~Kr~ 251 (253)
.|+++-. ...||||+.|..|||..|..- ++..+.+. -.|+|..|..+..
T Consensus 175 ~~g~~~~-~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 175 YCGGPGA-GNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred ecCCcCc-cceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 5566654 349999999999999999974 33334333 4899999997654
No 8
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.37 E-value=6e-05 Score=71.82 Aligned_cols=49 Identities=31% Similarity=0.826 Sum_probs=45.4
Q ss_pred eecccCCcccCCCceEEccCCCCeeeccc--cccCccccCCCCeEEcCCCCC
Q 025377 199 LCGACGENYAADEFWICCDVCEKWFHGKC--VKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 199 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~C--Vgit~~~a~~id~y~Cp~C~~ 248 (253)
+| .|..+++.+.+||+|+.|..|||+.| ||+....+..++.|+|..|..
T Consensus 62 ~~-~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~ 112 (345)
T KOG1632|consen 62 YC-KCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKE 112 (345)
T ss_pred hh-hcccccCchhhhhccccccccccccccccCchhhcCCccccccccccch
Confidence 56 89999887789999999999999999 999999999999999999985
No 9
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=97.34 E-value=0.00025 Score=69.19 Aligned_cols=53 Identities=25% Similarity=0.640 Sum_probs=44.6
Q ss_pred ccCcceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 025377 194 EHGETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNK 249 (253)
Q Consensus 194 d~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~K 249 (253)
....+.| +|+..++.+++||||+.|..|.|.-|+|+..... ++.|.|..|..+
T Consensus 83 ~~~~~~c-~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~--p~~y~c~~c~~~ 135 (508)
T KOG1844|consen 83 AREISRC-DCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK--PDKYVCEICTPR 135 (508)
T ss_pred cCccccc-ccccccCCCceeeCCcccCcccCceeeeecCCCC--chhceeeeeccc
Confidence 3466778 9999875589999999999999999999987653 578999999854
No 10
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.87 E-value=0.00055 Score=71.35 Aligned_cols=55 Identities=22% Similarity=0.596 Sum_probs=43.7
Q ss_pred ccccCcceecccCCcccCCCceEEccCCCCe-eeccccccCccccCCCCeEEcCCCCC
Q 025377 192 EEEHGETLCGACGENYAADEFWICCDVCEKW-FHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 192 eEd~~~t~C~iC~~py~~d~~mIqCD~Ce~W-fH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
....+.+.|-+|..++. .+.||.||.|..- ||..|+.....+.. +..|+|++|..
T Consensus 210 ~~~~E~~~C~IC~~~Dp-EdVLLLCDsCN~~~YH~YCLDPdl~eiP-~~eWYC~NC~d 265 (1134)
T KOG0825|consen 210 GLSQEEVKCDICTVHDP-EDVLLLCDSCNKVYYHVYCLDPDLSESP-VNEWYCTNCSL 265 (1134)
T ss_pred CcccccccceeeccCCh-HHhheeecccccceeeccccCccccccc-ccceecCcchh
Confidence 34556678999999864 6899999999977 99999988664433 36799999974
No 11
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.52 E-value=0.00049 Score=45.60 Aligned_cols=35 Identities=20% Similarity=0.590 Sum_probs=19.9
Q ss_pred CceEEccCCCCeeeccccccCccccCCCCeEEcCCCC
Q 025377 211 EFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCS 247 (253)
Q Consensus 211 ~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~ 247 (253)
..||+|+.|...+|.+|.|+...... +.|+|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~~--~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPDG--DDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--SS-------HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCCC--CcEECCcCC
Confidence 47999999999999999999987543 459998774
No 12
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.44 E-value=0.0025 Score=68.43 Aligned_cols=58 Identities=21% Similarity=0.456 Sum_probs=46.4
Q ss_pred ccccCcceecccCCcccC-CCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCcCCC
Q 025377 192 EEEHGETLCGACGENYAA-DEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNKRAR 252 (253)
Q Consensus 192 eEd~~~t~C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~Kr~R 252 (253)
-+.+.+.+|++|...... ....++||.|..-+|..|+|+..... .+|.|-.|.....|
T Consensus 214 ~~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ipe---g~WlCr~Cl~s~~~ 272 (1051)
T KOG0955|consen 214 ALLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIPE---GQWLCRRCLQSPQR 272 (1051)
T ss_pred cccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCCC---CcEeehhhccCcCc
Confidence 455677899999886542 26889999999999999999776542 57999999987765
No 13
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.07 E-value=0.0024 Score=60.20 Aligned_cols=48 Identities=25% Similarity=0.583 Sum_probs=38.8
Q ss_pred CcceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcC-CCC
Q 025377 196 GETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCP-SCS 247 (253)
Q Consensus 196 ~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp-~C~ 247 (253)
+-.+|-+|++|.- .+.|+.||.|++=||.-|||+..-.. ..|+|. .|.
T Consensus 313 ~C~lC~IC~~P~~-E~E~~FCD~CDRG~HT~CVGL~~lP~---G~WICD~~C~ 361 (381)
T KOG1512|consen 313 SCELCRICLGPVI-ESEHLFCDVCDRGPHTLCVGLQDLPR---GEWICDMRCR 361 (381)
T ss_pred ccHhhhccCCccc-chheeccccccCCCCccccccccccC---ccchhhhHHH
Confidence 3446888999975 57899999999999999999987543 469998 454
No 14
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=95.71 E-value=0.004 Score=64.47 Aligned_cols=52 Identities=21% Similarity=0.586 Sum_probs=42.0
Q ss_pred ccccCcceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 192 EEEHGETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 192 eEd~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
.++...-.|++|+.. +..|.||.|..|||..|.+.+-.+.+... |+|+.|.-
T Consensus 42 ~~~~~~e~c~ic~~~----g~~l~c~tC~~s~h~~cl~~pl~~~p~~~-~~c~Rc~~ 93 (696)
T KOG0383|consen 42 WDDAEQEACRICADG----GELLWCDTCPASFHASCLGPPLTPQPNGE-FICPRCFC 93 (696)
T ss_pred cchhhhhhhhhhcCC----CcEEEeccccHHHHHHccCCCCCcCCccc-eeeeeecc
Confidence 445666679999864 67888999999999999998777666556 99999953
No 15
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=95.69 E-value=0.0055 Score=58.25 Aligned_cols=35 Identities=29% Similarity=0.879 Sum_probs=28.0
Q ss_pred CcceecccCCcccC-----CCceEEccCCCCeee-ccccccC
Q 025377 196 GETLCGACGENYAA-----DEFWICCDVCEKWFH-GKCVKIT 231 (253)
Q Consensus 196 ~~t~C~iC~~py~~-----d~~mIqCD~Ce~WfH-~~CVgit 231 (253)
...+| .|..+|++ ++.|+||.+|+.||| ..|...+
T Consensus 127 qG~~C-~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~~ 167 (345)
T KOG2752|consen 127 QGLFC-KCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQAK 167 (345)
T ss_pred cceeE-EecCCCCCccccccceeeeEEeccchhcccccCccc
Confidence 34556 99999986 578999999999999 6776443
No 16
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.43 E-value=0.017 Score=58.20 Aligned_cols=49 Identities=18% Similarity=0.451 Sum_probs=36.2
Q ss_pred eecccCC-cccCCCceEEccCCCCeeeccccccCccc-----cC--CCCeEEcCCCC
Q 025377 199 LCGACGE-NYAADEFWICCDVCEKWFHGKCVKITPAR-----AE--HIKQYKCPSCS 247 (253)
Q Consensus 199 ~C~iC~~-py~~d~~mIqCD~Ce~WfH~~CVgit~~~-----a~--~id~y~Cp~C~ 247 (253)
+||+|-. ...+-+..||||.|+--.|..|.|+.... +. ....|+|..|.
T Consensus 121 iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~ 177 (707)
T KOG0957|consen 121 ICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACL 177 (707)
T ss_pred EEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHh
Confidence 8999954 33334789999999999999999987321 11 12579998886
No 17
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=95.35 E-value=0.0078 Score=62.60 Aligned_cols=50 Identities=20% Similarity=0.561 Sum_probs=42.1
Q ss_pred CcceecccCCcccC-CCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 196 GETLCGACGENYAA-DEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 196 ~~t~C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
++.+|-+|..++.+ ...||.||.|..=.|..|.||..... ..|.|..|.-
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p~---gpWlCr~Cal 320 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVPE---GPWLCRTCAL 320 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecCC---CCeeehhccc
Confidence 56789999998655 46899999999999999999997653 5699999863
No 18
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.14 E-value=0.0073 Score=61.49 Aligned_cols=51 Identities=33% Similarity=0.765 Sum_probs=38.4
Q ss_pred cceecccCCcccCCCceEEccCCCCeeeccccccC--ccccCCCCeEEcCCCCCc
Q 025377 197 ETLCGACGENYAADEFWICCDVCEKWFHGKCVKIT--PARAEHIKQYKCPSCSNK 249 (253)
Q Consensus 197 ~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit--~~~a~~id~y~Cp~C~~K 249 (253)
+.+|..|++...- ...|+||.|..-||..|+.-+ .+..+ .+.|+|+.|.-+
T Consensus 253 ~~fCsaCn~~~~F-~~~i~CD~Cp~sFH~~CLePPl~~eniP-~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLF-NDIICCDGCPRSFHQTCLEPPLEPENIP-PGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCcccc-ccceeecCCchHHHHhhcCCCCCcccCC-CCccccCCCeee
Confidence 4499999997432 345999999999999999865 32222 268999999753
No 19
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=94.26 E-value=0.029 Score=56.50 Aligned_cols=50 Identities=22% Similarity=0.602 Sum_probs=38.9
Q ss_pred cceecccCCcccCCCceEEccCCCCeeeccccccCccccCC---CCeEEcCCCC
Q 025377 197 ETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEH---IKQYKCPSCS 247 (253)
Q Consensus 197 ~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~---id~y~Cp~C~ 247 (253)
...|++|.+..+ ....++||.|..-||.-|+.-+-.+.+. .--|.|..|-
T Consensus 544 ~ysCgiCkks~d-QHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 544 NYSCGICKKSTD-QHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred ceeeeeeccchh-hHHHhhcchhhceeeccccCCccccCcccccCcceeecccc
Confidence 356999999864 6788999999999999999865544322 2369999993
No 20
>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=94.24 E-value=0.046 Score=54.08 Aligned_cols=53 Identities=26% Similarity=0.725 Sum_probs=35.9
Q ss_pred CcceecccCCcccC---CCceEEccCCCCeeecccc--------ccCccc-cC-CCCeEEcCCCCCc
Q 025377 196 GETLCGACGENYAA---DEFWICCDVCEKWFHGKCV--------KITPAR-AE-HIKQYKCPSCSNK 249 (253)
Q Consensus 196 ~~t~C~iC~~py~~---d~~mIqCD~Ce~WfH~~CV--------git~~~-a~-~id~y~Cp~C~~K 249 (253)
...-|++|.+ ++. .-.||.||.|..|-|..|. |.+... .. .--.|+|-.|..+
T Consensus 127 ~~C~C~iC~k-fD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 127 RRCMCCICSK-FDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred ccCCccccCC-cccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 4456888987 433 3569999999999999995 222111 11 1138999999864
No 21
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=94.14 E-value=0.025 Score=53.20 Aligned_cols=49 Identities=22% Similarity=0.653 Sum_probs=38.3
Q ss_pred ceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 198 TLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 198 t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
.+|.+|+...+ ++.++.||.|++=||.-|+.-+-...+. ..|.|..|..
T Consensus 282 k~csicgtsen-ddqllfcddcdrgyhmyclsppm~eppe-gswsc~KOG~ 330 (336)
T KOG1244|consen 282 KYCSICGTSEN-DDQLLFCDDCDRGYHMYCLSPPMVEPPE-GSWSCHLCLE 330 (336)
T ss_pred ceeccccCcCC-CceeEeecccCCceeeEecCCCcCCCCC-CchhHHHHHH
Confidence 36888998876 5788999999999999999755443322 5799999974
No 22
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=93.71 E-value=0.0091 Score=61.29 Aligned_cols=51 Identities=33% Similarity=0.912 Sum_probs=40.4
Q ss_pred cceecccCCcccCCC--ceEEccCCCCeeeccccccCccccCC--CC-eEEcCCCC
Q 025377 197 ETLCGACGENYAADE--FWICCDVCEKWFHGKCVKITPARAEH--IK-QYKCPSCS 247 (253)
Q Consensus 197 ~t~C~iC~~py~~d~--~mIqCD~Ce~WfH~~CVgit~~~a~~--id-~y~Cp~C~ 247 (253)
-.+|++|...|...+ .|++|++|.+|.|+.|.++....... ++ .|.|..|+
T Consensus 145 ~~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR 200 (694)
T KOG4443|consen 145 LSYCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCR 200 (694)
T ss_pred cccCchHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceee
Confidence 467888988887654 46999999999999999998664221 24 89999997
No 23
>PF07496 zf-CW: CW-type Zinc Finger; InterPro: IPR011124 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a CW-type zinc finger motif, named for its conserved cysteine and tryptophan residues. It is predicted to be a highly specialised mononuclear four-cysteine (C4) zinc finger that plays a role in DNA binding and/or promoting protein-protein interactions in complicated eukaryotic processes including chromatin methylation status and early embryonic development. Weak homology to members of IPR001965 from INTERPRO further evidences these predictions. The domain is found exclusively in vertebrates, vertebrate-infecting parasites and higher plants []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2RR4_A 2E61_A 2L7P_A.
Probab=93.69 E-value=0.035 Score=38.95 Aligned_cols=33 Identities=30% Similarity=0.803 Sum_probs=17.3
Q ss_pred ceEEccCCCCeeeccccccCccccCCCCeEEcCC
Q 025377 212 FWICCDVCEKWFHGKCVKITPARAEHIKQYKCPS 245 (253)
Q Consensus 212 ~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~ 245 (253)
.|||||.|.+|=... .++........+.|+|..
T Consensus 2 ~WVQCd~C~KWR~lp-~~~~~~~~~~~d~W~C~~ 34 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP-EEVDPIREELPDPWYCSM 34 (50)
T ss_dssp EEEE-TTT--EEEE--CCHHCTSCCSSTT--GGG
T ss_pred eEEECCCCCceeeCC-hhhCcccccCCCeEEcCC
Confidence 699999999998876 444332122235899987
No 24
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=92.98 E-value=0.018 Score=63.77 Aligned_cols=56 Identities=27% Similarity=0.598 Sum_probs=45.9
Q ss_pred cccCcceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCcC
Q 025377 193 EEHGETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNKR 250 (253)
Q Consensus 193 Ed~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~Kr 250 (253)
-......|-+|..-.+ ...|+-|+.|..|||.-|.......+.. ..|.|+.|+..+
T Consensus 1104 ~s~~~~~c~~cr~k~~-~~~m~lc~~c~~~~h~~C~rp~~~~~~~-~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1104 RSAVNALCKVCRRKKQ-DEKMLLCDECLSGFHLFCLRPALSSVPP-GDWMCPSCRKEH 1159 (1404)
T ss_pred cccchhhhhhhhhccc-chhhhhhHhhhhhHHHHhhhhhhccCCc-CCccCCccchhh
Confidence 3456778999998653 5799999999999999999987766543 679999999755
No 25
>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=91.10 E-value=0.064 Score=35.80 Aligned_cols=43 Identities=30% Similarity=0.634 Sum_probs=32.3
Q ss_pred eecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCC
Q 025377 199 LCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCS 247 (253)
Q Consensus 199 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~ 247 (253)
.|++|...+..++.++... |+..||..|+.--... ...||.|+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~~~~-----~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEWLKR-----NNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHHHHH-----SSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHHHHh-----CCcCCccC
Confidence 3899999987777788777 9999999998643322 24899884
No 26
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=89.60 E-value=0.26 Score=35.79 Aligned_cols=33 Identities=21% Similarity=0.643 Sum_probs=29.5
Q ss_pred CcceecccCCcccCCCceEEccCCCCeeecccc
Q 025377 196 GETLCGACGENYAADEFWICCDVCEKWFHGKCV 228 (253)
Q Consensus 196 ~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CV 228 (253)
....|.+|+++..+++..+.|..|..-||..|.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 456799999998778899999999999999997
No 27
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=88.82 E-value=0.21 Score=52.10 Aligned_cols=47 Identities=23% Similarity=0.569 Sum_probs=37.1
Q ss_pred eecccCCcc-cCCCceEEcc--CCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 199 LCGACGENY-AADEFWICCD--VCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 199 ~C~iC~~py-~~d~~mIqCD--~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
-||+|...- -.+..+|-|| .|..-.|..|.||..... ..|+|-.|..
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPt---GpWfCrKCes 56 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPT---GPWFCRKCES 56 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCC---Cchhhhhhhh
Confidence 388996521 1256899999 899999999999987653 4699999985
No 28
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=87.95 E-value=0.2 Score=50.54 Aligned_cols=51 Identities=22% Similarity=0.494 Sum_probs=40.0
Q ss_pred cCcceecccCCcccCC-CceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 195 HGETLCGACGENYAAD-EFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d-~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
+-+..|.+|...++++ ...|.||.|+.-.|..|.||.--.. .+|.|..|.-
T Consensus 191 ~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~pe---G~WlCrkCi~ 242 (669)
T COG5141 191 EFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPE---GFWLCRKCIY 242 (669)
T ss_pred hhhhhhHhccccccCCcceEEEecCcchhhhhhcccceecCc---chhhhhhhcc
Confidence 4456788898887654 5678899999999999999986432 4699998863
No 29
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=87.65 E-value=0.13 Score=48.76 Aligned_cols=53 Identities=25% Similarity=0.489 Sum_probs=40.3
Q ss_pred cCcceecccCCccc-----CCCceEEccCCCCeeeccccccCccccCCCC--eEEcCCCC
Q 025377 195 HGETLCGACGENYA-----ADEFWICCDVCEKWFHGKCVKITPARAEHIK--QYKCPSCS 247 (253)
Q Consensus 195 ~~~t~C~iC~~py~-----~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id--~y~Cp~C~ 247 (253)
.-...|++|-.... .-+.||.|..|..-+|..|+.+++..+..++ .|.|..|.
T Consensus 256 ~~~~~~~~~~~~~~~~~~~r~~S~I~C~~C~~~~HP~Ci~M~~elv~~~KTY~W~C~~C~ 315 (381)
T KOG1512|consen 256 QRRNERKHFWDIQTNIIQSRRNSWIVCKPCATRPHPYCVAMIPELVGQYKTYFWKCSSCE 315 (381)
T ss_pred cchhhhhhhhcchhhhhhhhhccceeecccccCCCCcchhcCHHHHhHHhhcchhhcccH
Confidence 45567888865322 1368999999999999999999988766554 57787775
No 30
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=85.82 E-value=0.25 Score=53.88 Aligned_cols=59 Identities=25% Similarity=0.578 Sum_probs=50.1
Q ss_pred cccCcceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCcCC
Q 025377 193 EEHGETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNKRA 251 (253)
Q Consensus 193 Ed~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~Kr~ 251 (253)
.-....+|.+|..||+++...|.|-.|..|+|..-|.+........-.+.|-.|+..+.
T Consensus 1118 kp~~~p~~~i~~~p~~pg~~~i~~~~~~~~~~~~~v~ln~s~~p~~~~~k~~~~~ri~~ 1176 (1414)
T KOG1473|consen 1118 KPTLSPVCFICTLPYNPGLTYIHCTVCMTWGHKEAVKLNSSPIPEVVGFKCCQCRRIRS 1176 (1414)
T ss_pred CCCCCccccceeeccCCCCCcceEEEeeccCcceeEecCCCcchHHhhhhHHhhhccCC
Confidence 34567789999999999999999999999999999999887665556789988887653
No 31
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=84.50 E-value=0.54 Score=36.91 Aligned_cols=32 Identities=28% Similarity=0.656 Sum_probs=27.2
Q ss_pred CcceecccCCcccCCCceEEccC--CCCeeecccccc
Q 025377 196 GETLCGACGENYAADEFWICCDV--CEKWFHGKCVKI 230 (253)
Q Consensus 196 ~~t~C~iC~~py~~d~~mIqCD~--Ce~WfH~~CVgi 230 (253)
....|.+|++. .+..|+|.. |..+||..|...
T Consensus 54 ~~~~C~iC~~~---~G~~i~C~~~~C~~~fH~~CA~~ 87 (110)
T PF13832_consen 54 FKLKCSICGKS---GGACIKCSHPGCSTAFHPTCARK 87 (110)
T ss_pred cCCcCcCCCCC---CceeEEcCCCCCCcCCCHHHHHH
Confidence 45679999997 578999997 999999999743
No 32
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=83.31 E-value=0.51 Score=29.48 Aligned_cols=29 Identities=28% Similarity=0.793 Sum_probs=12.6
Q ss_pred eecccCCcccCCCceEEccCCCCeeecccc
Q 025377 199 LCGACGENYAADEFWICCDVCEKWFHGKCV 228 (253)
Q Consensus 199 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CV 228 (253)
.|.+|+++-.. ..+-.|..|+-..|..|+
T Consensus 2 ~C~~C~~~~~~-~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPIDG-GWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS----S---EEE-TTT-----HHHH
T ss_pred cCCcCCCcCCC-CceEECccCCCccChhcC
Confidence 47889998543 478889999999999985
No 33
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=81.47 E-value=1 Score=39.82 Aligned_cols=44 Identities=25% Similarity=0.802 Sum_probs=32.7
Q ss_pred ceecccCCc-----ccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCcCCC
Q 025377 198 TLCGACGEN-----YAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNKRAR 252 (253)
Q Consensus 198 t~C~iC~~p-----y~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~Kr~R 252 (253)
-+|.+|+.+ ++ .+.-++|..|..-||-.|..- -.||.|.+.+.|
T Consensus 153 fiCe~C~~~~~IfPF~-~~~~~~C~~C~~v~H~~C~~~----------~~CpkC~R~~~r 201 (202)
T PF13901_consen 153 FICEICNSDDIIFPFQ-IDTTVRCPKCKSVFHKSCFRK----------KSCPKCARRQKR 201 (202)
T ss_pred CCCccCCCCCCCCCCC-CCCeeeCCcCccccchhhcCC----------CCCCCcHhHhcc
Confidence 357777653 22 246789999999999999972 129999987776
No 34
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=76.62 E-value=1.9 Score=32.50 Aligned_cols=35 Identities=23% Similarity=0.562 Sum_probs=28.1
Q ss_pred cCcceecccCCcccCCCceEEcc--CCCCeeeccccccCc
Q 025377 195 HGETLCGACGENYAADEFWICCD--VCEKWFHGKCVKITP 232 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d~~mIqCD--~Ce~WfH~~CVgit~ 232 (253)
.....|.+|+++ .+-.|+|. .|...||..|.....
T Consensus 34 ~~~~~C~~C~~~---~Ga~i~C~~~~C~~~fH~~CA~~~~ 70 (90)
T PF13771_consen 34 RRKLKCSICKKK---GGACIGCSHPGCSRSFHVPCARKAG 70 (90)
T ss_pred HhCCCCcCCCCC---CCeEEEEeCCCCCcEEChHHHccCC
Confidence 455679999987 46899998 699999999986543
No 35
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=74.26 E-value=0.9 Score=47.16 Aligned_cols=54 Identities=24% Similarity=0.512 Sum_probs=40.2
Q ss_pred cCcceecccCCcccC-CCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 195 HGETLCGACGENYAA-DEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 195 ~~~t~C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
.....|.+|+..... .+.|..|..|..-||..||.+-...+....-|.|+.|+.
T Consensus 16 ~~~~mc~l~~s~G~~~ag~m~ac~~c~~~yH~~cvt~~~~~~~l~~gWrC~~crv 70 (694)
T KOG4443|consen 16 IVCLMCPLCGSSGKGRAGRLLACSDCGQKYHPYCVTSWAQHAVLSGGWRCPSCRV 70 (694)
T ss_pred hhhhhhhhhccccccccCcchhhhhhcccCCcchhhHHHhHHHhcCCcccCCcee
Confidence 445567778654332 467999999999999999997665554455699999873
No 36
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.21 E-value=2.5 Score=40.94 Aligned_cols=47 Identities=23% Similarity=0.532 Sum_probs=32.7
Q ss_pred ceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 025377 198 TLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNK 249 (253)
Q Consensus 198 t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~K 249 (253)
..|+||-..|..++.. .==-|..-||..|+.-=-.. ..-.||-|...
T Consensus 230 ~~CaIClEdY~~Gdkl-RiLPC~H~FH~~CIDpWL~~----~r~~CPvCK~d 276 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKL-RILPCSHKFHVNCIDPWLTQ----TRTFCPVCKRD 276 (348)
T ss_pred ceEEEeecccccCCee-eEecCCCchhhccchhhHhh----cCccCCCCCCc
Confidence 5799999999765433 32678889999999632211 12479999863
No 37
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=71.80 E-value=0.69 Score=47.42 Aligned_cols=49 Identities=27% Similarity=0.620 Sum_probs=33.7
Q ss_pred CcceecccCCcc---cC-CCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCcCCC
Q 025377 196 GETLCGACGENY---AA-DEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNKRAR 252 (253)
Q Consensus 196 ~~t~C~iC~~py---~~-d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~Kr~R 252 (253)
...+|.+|..+. .- .+.-..|+.|..|||-+|...... .||.|.+.+.|
T Consensus 510 ~gfiCe~Cq~~~iiyPF~~~~~~rC~~C~avfH~~C~~r~s~--------~CPrC~R~q~r 562 (580)
T KOG1829|consen 510 KGFICELCQHNDIIYPFETRNTRRCSTCLAVFHKKCLRRKSP--------CCPRCERRQKR 562 (580)
T ss_pred CeeeeeeccCCCcccccccccceeHHHHHHHHHHHHHhccCC--------CCCchHHHHHH
Confidence 344666774421 11 344588999999999999976643 29999976655
No 38
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=69.65 E-value=5 Score=40.91 Aligned_cols=54 Identities=20% Similarity=0.495 Sum_probs=37.3
Q ss_pred cCcceecccCCcccCCCceEEccCCCCeeeccccccCcc---ccCC--CCeEEcCCCCCc
Q 025377 195 HGETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPA---RAEH--IKQYKCPSCSNK 249 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~---~a~~--id~y~Cp~C~~K 249 (253)
...++| +|+...+....-+||..|.+|||..|.-.... ..+. -..|.|..|...
T Consensus 18 ~~~~~~-y~e~~r~l~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 18 KQATVC-YCEGERNLGIVELQCSTCLKWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPS 76 (544)
T ss_pred cCcccc-ccccccccCceeeEeeecccccccccccccccccccCCcccceeEEeccccCc
Confidence 344566 99987776778899999999999855432221 1111 147999999864
No 39
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=67.44 E-value=3.9 Score=30.49 Aligned_cols=43 Identities=30% Similarity=0.633 Sum_probs=27.3
Q ss_pred ecccCCcccC---------CCceEEccCCCCeeeccccccCccccCCCCeEEcCCCC
Q 025377 200 CGACGENYAA---------DEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCS 247 (253)
Q Consensus 200 C~iC~~py~~---------d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~ 247 (253)
|++|..++.+ ++-.|.=..|+.-||..|+.-=-.. .-.||.|+
T Consensus 22 C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~-----~~~CP~CR 73 (73)
T PF12678_consen 22 CAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQ-----NNTCPLCR 73 (73)
T ss_dssp ETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTT-----SSB-TTSS
T ss_pred ccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhc-----CCcCCCCC
Confidence 9999987732 2344544579999999999621111 12899985
No 40
>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=66.15 E-value=5.1 Score=30.51 Aligned_cols=30 Identities=27% Similarity=0.525 Sum_probs=22.5
Q ss_pred ceecccCCcccCCCceEEccCCCCeeeccccc
Q 025377 198 TLCGACGENYAADEFWICCDVCEKWFHGKCVK 229 (253)
Q Consensus 198 t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVg 229 (253)
..|.+|+++-....|.+..+ +.-||..|..
T Consensus 79 ~~C~vC~k~l~~~~f~~~p~--~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGNSVFVVFPC--GHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCCceEEEeCC--CeEEeccccc
Confidence 46999999876655666644 4889999974
No 41
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=65.21 E-value=3.5 Score=38.67 Aligned_cols=44 Identities=32% Similarity=0.589 Sum_probs=30.3
Q ss_pred ceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeE-EcCCCCCc
Q 025377 198 TLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQY-KCPSCSNK 249 (253)
Q Consensus 198 t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y-~Cp~C~~K 249 (253)
..|.+|-.+- .--.|-.|..-|-..|+-+.-.. .+| +||.|+.|
T Consensus 216 ~kC~lC~e~~----~~ps~t~CgHlFC~~Cl~~~~t~----~k~~~CplCRak 260 (271)
T COG5574 216 YKCFLCLEEP----EVPSCTPCGHLFCLSCLLISWTK----KKYEFCPLCRAK 260 (271)
T ss_pred cceeeeeccc----CCcccccccchhhHHHHHHHHHh----hccccCchhhhh
Confidence 3499998742 22368889999999998773221 234 49999975
No 42
>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=58.62 E-value=3.3 Score=33.53 Aligned_cols=50 Identities=22% Similarity=0.510 Sum_probs=35.1
Q ss_pred CcceecccCCcccC-CCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 025377 196 GETLCGACGENYAA-DEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNK 249 (253)
Q Consensus 196 ~~t~C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~K 249 (253)
+...|..|+.+..- ...-..|..|...+-.+|....... ..|+|..|.+.
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~----~~WlC~vC~k~ 103 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKE----PIWLCKVCQKQ 103 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSS----CCEEEHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCC----CCEEChhhHHH
Confidence 34469899987532 2345899999999999998874332 46999999754
No 43
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=58.03 E-value=5.5 Score=32.36 Aligned_cols=21 Identities=24% Similarity=0.537 Sum_probs=18.1
Q ss_pred cCcceecccCCcccCCCceEEc
Q 025377 195 HGETLCGACGENYAADEFWICC 216 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d~~mIqC 216 (253)
.+..+| +|..+|+++..||+|
T Consensus 101 ~~~d~~-~Ce~~yn~~~~~~~c 121 (121)
T cd04714 101 DGVDFY-YCAGTYNPDTGMLKC 121 (121)
T ss_pred cCCCEE-EEeccCCCCcCcccC
Confidence 455568 999999999999998
No 44
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=58.02 E-value=8 Score=28.73 Aligned_cols=52 Identities=25% Similarity=0.427 Sum_probs=19.4
Q ss_pred ceecccCCccc--CCCceEEcc--CCCCeeecccccc-----Ccc-ccCCCCeEEcCCCCCc
Q 025377 198 TLCGACGENYA--ADEFWICCD--VCEKWFHGKCVKI-----TPA-RAEHIKQYKCPSCSNK 249 (253)
Q Consensus 198 t~C~iC~~py~--~d~~mIqCD--~Ce~WfH~~CVgi-----t~~-~a~~id~y~Cp~C~~K 249 (253)
..|+||-.... +...-+.|+ .|..-||..|+-- ... ..-.+....||.|...
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~ 64 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSP 64 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SE
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCe
Confidence 35999976432 234567898 9999999999842 111 1112345789999863
No 45
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=56.73 E-value=4.5 Score=31.88 Aligned_cols=47 Identities=23% Similarity=0.660 Sum_probs=29.2
Q ss_pred ceecccCCcccC---------CCceEEccCCCCeeecccccc--CccccCCCCeEEcCCCCC
Q 025377 198 TLCGACGENYAA---------DEFWICCDVCEKWFHGKCVKI--TPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 198 t~C~iC~~py~~---------d~~mIqCD~Ce~WfH~~CVgi--t~~~a~~id~y~Cp~C~~ 248 (253)
..|+||+.+++. ++--|.-..|..=||..|+-- .... .+=.||.|++
T Consensus 22 d~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~----~~~~CPmCR~ 79 (85)
T PF12861_consen 22 DVCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQS----SKGQCPMCRQ 79 (85)
T ss_pred CceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHcccc----CCCCCCCcCC
Confidence 358888876653 111222236999999999852 3221 2358999986
No 46
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=54.66 E-value=7.4 Score=34.91 Aligned_cols=51 Identities=22% Similarity=0.495 Sum_probs=31.5
Q ss_pred cCcceecccCCcccCCCceEEccCCCCeeeccccccC-------cccc----CCCCeEEcCCCCCc
Q 025377 195 HGETLCGACGENYAADEFWICCDVCEKWFHGKCVKIT-------PARA----EHIKQYKCPSCSNK 249 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit-------~~~a----~~id~y~Cp~C~~K 249 (253)
.++..|.+|.....+ ..+ -.|+..|+..|+.-- .... .......||.|+..
T Consensus 16 ~~~~~CpICld~~~d--PVv--T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~ 77 (193)
T PLN03208 16 GGDFDCNICLDQVRD--PVV--TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSD 77 (193)
T ss_pred CCccCCccCCCcCCC--cEE--cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCc
Confidence 345679999987542 233 468889999998421 0000 01235789999863
No 47
>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=52.00 E-value=25 Score=23.81 Aligned_cols=38 Identities=26% Similarity=0.501 Sum_probs=27.7
Q ss_pred CcceecccCCccc-CCCceEEccCCCCeeeccccccCcc
Q 025377 196 GETLCGACGENYA-ADEFWICCDVCEKWFHGKCVKITPA 233 (253)
Q Consensus 196 ~~t~C~iC~~py~-~d~~mIqCD~Ce~WfH~~CVgit~~ 233 (253)
..+.|.+|++.-- ....-..|..|..-.|.+|...-+.
T Consensus 10 ~~~~C~~C~~~i~g~~~~g~~C~~C~~~~H~~C~~~~~~ 48 (53)
T PF00130_consen 10 KPTYCDVCGKFIWGLGKQGYRCSWCGLVCHKKCLSKVPP 48 (53)
T ss_dssp STEB-TTSSSBECSSSSCEEEETTTT-EEETTGGCTSSS
T ss_pred CCCCCcccCcccCCCCCCeEEECCCCChHhhhhhhhcCC
Confidence 4578999998752 2456789999999999999976543
No 48
>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=50.94 E-value=16 Score=22.78 Aligned_cols=28 Identities=25% Similarity=0.718 Sum_probs=22.1
Q ss_pred eecccCCcccCCCc-eEEccCCCCeeecccc
Q 025377 199 LCGACGENYAADEF-WICCDVCEKWFHGKCV 228 (253)
Q Consensus 199 ~C~iC~~py~~d~~-mIqCD~Ce~WfH~~CV 228 (253)
.|.+|++.-+ ++ .-.|+.|..-.|..|+
T Consensus 2 ~C~~C~~~~~--~~~~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKID--GFYFYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcC--CCEeEEeCCCCCeEcCccC
Confidence 4888988743 45 7889999988898885
No 49
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=49.63 E-value=7.2 Score=33.68 Aligned_cols=53 Identities=23% Similarity=0.559 Sum_probs=39.2
Q ss_pred CcceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 025377 196 GETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNK 249 (253)
Q Consensus 196 ~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~K 249 (253)
.+..|.||.+..-.|+-=--|.-|..-|...|-|--..+... -.|.|..|.+.
T Consensus 64 ddatC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsNK-v~wvcnlc~k~ 116 (169)
T KOG3799|consen 64 DDATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSNK-VMWVCNLCRKQ 116 (169)
T ss_pred cCcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccCc-eEEeccCCcHH
Confidence 346799999876566666678899988888998755444322 57999999853
No 50
>COG1993 PII-like signaling protein [Signal transduction mechanisms]
Probab=49.02 E-value=8.5 Score=31.70 Aligned_cols=29 Identities=31% Similarity=0.638 Sum_probs=23.5
Q ss_pred cccChhh---hHHHHHhhhcCCceeeeecccc
Q 025377 113 FGFDKSD---RKRLFNMINELPTIFEVVTGTT 141 (253)
Q Consensus 113 ~~f~~~~---r~~lf~min~LPTv~EvVtg~~ 141 (253)
.||.+.. .-++|.+-++||.|.|||-...
T Consensus 47 ~GfG~~~~~h~~~if~Ls~~LPVviEvVD~ee 78 (109)
T COG1993 47 AGFGKDGKIHGSKIFRLSTDLPVVVEVVDEEE 78 (109)
T ss_pred eccCCCCcccccchhhccCCCCEEEEEeCCHH
Confidence 4666665 5689999999999999997743
No 51
>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=46.35 E-value=19 Score=34.34 Aligned_cols=53 Identities=28% Similarity=0.658 Sum_probs=32.7
Q ss_pred CcceecccCCcc----------cCCCceEEccCCCCeeec---cccccCccc------------cCCCCeEEcCCCCC
Q 025377 196 GETLCGACGENY----------AADEFWICCDVCEKWFHG---KCVKITPAR------------AEHIKQYKCPSCSN 248 (253)
Q Consensus 196 ~~t~C~iC~~py----------~~d~~mIqCD~Ce~WfH~---~CVgit~~~------------a~~id~y~Cp~C~~ 248 (253)
...+|++||..- ..+..+..|..|+.-+|. .|..-...+ ........|..|..
T Consensus 183 ~~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~ 260 (305)
T TIGR01562 183 SRTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQG 260 (305)
T ss_pred CCCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEeecCCCCCcceEEeecccccc
Confidence 345899998632 234579999999955565 564322211 11235678999974
No 52
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=44.97 E-value=10 Score=29.26 Aligned_cols=35 Identities=20% Similarity=0.597 Sum_probs=19.6
Q ss_pred ceEEccCC-CCeeeccccccCccc----cCCCCeEEcCCC
Q 025377 212 FWICCDVC-EKWFHGKCVKITPAR----AEHIKQYKCPSC 246 (253)
Q Consensus 212 ~mIqCD~C-e~WfH~~CVgit~~~----a~~id~y~Cp~C 246 (253)
-||.|..= +.|.|..|+.+++.. .+...+|+|..=
T Consensus 29 AMI~cs~~~GHWvhaqCm~LsE~~L~~LSq~n~KYfC~dH 68 (78)
T PF13341_consen 29 AMIFCSRGGGHWVHAQCMDLSETMLIQLSQENTKYFCNDH 68 (78)
T ss_dssp -EEEE-STT-EEEETGGGT--HHHHHHHHHSSS-B--TTT
T ss_pred eEEEEeCCCceEeEeecccchHHHHHHHccCCceEEEhhh
Confidence 59999844 499999999998754 223367999753
No 53
>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=43.73 E-value=7.9 Score=24.05 Aligned_cols=42 Identities=21% Similarity=0.478 Sum_probs=27.1
Q ss_pred ecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 200 CGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 200 C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
|.+|..... ..+.-..|+.-||..|+..-... ....||.|..
T Consensus 2 C~iC~~~~~---~~~~~~~C~H~~c~~C~~~~~~~----~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFR---EPVVLLPCGHVFCRSCIDKWLKS----GKNTCPLCRT 43 (45)
T ss_pred CCcCchhhh---CceEecCCCChhcHHHHHHHHHh----CcCCCCCCCC
Confidence 778877652 23333458888999998643321 2467999975
No 54
>PF00319 SRF-TF: SRF-type transcription factor (DNA-binding and dimerisation domain); InterPro: IPR002100 Human serum response factor (SRF) is a ubiquitous nuclear protein important for cell proliferation and differentiation. SRF function is essential for transcriptional regulation of numerous growth-factor-inducible genes, such as c-fos oncogene and muscle-specific actin genes. A core domain of around 90 amino acids is sufficient for the activities of DNA-binding, dimerisation and interaction with accessory factors. Within the core is a DNA-binding region, designated the MADS box [], that is highly similar to many eukaryotic regulatory proteins: among these are MCM1, the regulator of cell type-specific genes in fission yeast; DSRF, a Drosophila trachea development factor; the MEF2 family of myocyte-specific enhancer factors; and the Agamous and Deficiens families of plant homeotic proteins. In SRF, the MADS box has been shown to be involved in DNA-binding and dimerisation []. Proteins belonging to the MADS family function as dimers, the primary DNA-binding element of which is an anti-parallel coiled coil of two amphipathic alpha-helices, one from each subunit. The DNA wraps around the coiled coil allowing the basic N-termini of the helices to fit into the DNA major groove. The chain extending from the helix N-termini reaches over the DNA backbone and penetrates into the minor groove. A 4-stranded, anti-parallel beta-sheet packs against the coiled-coil face opposite the DNA and is the central element of the dimerisation interface. The MADS-box domain is commonly found associated with K-box region see IPR002487 from INTERPRO ; GO: 0003677 DNA binding, 0046983 protein dimerization activity; PDB: 1MNM_B 1N6J_A 1TQE_S 3MU6_D 3P57_I 1EGW_A 1C7U_B 3KOV_A 1HBX_A 1K6O_C ....
Probab=43.24 E-value=30 Score=24.53 Aligned_cols=35 Identities=23% Similarity=0.547 Sum_probs=25.1
Q ss_pred hhhhhhhHHHHHhhHHHHHHHhhcCCCCcceeeecCCCCce
Q 025377 18 DFKGRRAGMIKALTTEVEEFYHQCDPEKENLCLYGFPSEQW 58 (253)
Q Consensus 18 d~~~rr~~~~~alt~d~~~f~~~c~p~~~~l~lyg~~~~~w 58 (253)
-|+.||.||.|= +.++--+||-+-- |-+|| |+|..
T Consensus 12 tf~KRk~gL~KK----a~ELs~LC~~~v~-~iv~~-~~g~~ 46 (51)
T PF00319_consen 12 TFSKRKKGLFKK----ASELSTLCGVDVA-LIVFS-PDGKL 46 (51)
T ss_dssp HHHHHHHHHHHH----HHHHHHHHT-EEE-EEEEE-TTSEE
T ss_pred HHHHHHhhhhhc----cceeeeecCCeEE-EEEEC-CCCCE
Confidence 488999998874 5688999988765 44477 66654
No 55
>COG1773 Rubredoxin [Energy production and conversion]
Probab=43.14 E-value=17 Score=26.49 Aligned_cols=41 Identities=20% Similarity=0.459 Sum_probs=24.7
Q ss_pred ceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 198 TLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 198 t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
..|.+|+-.|++..-.=.|++|. |-.=+ +..+.|.||.|..
T Consensus 4 ~~C~~CG~vYd~e~Gdp~~gi~p--------gT~fe--dlPd~w~CP~Cg~ 44 (55)
T COG1773 4 WRCSVCGYVYDPEKGDPRCGIAP--------GTPFE--DLPDDWVCPECGV 44 (55)
T ss_pred eEecCCceEeccccCCccCCCCC--------CCchh--hCCCccCCCCCCC
Confidence 35778888887654444444443 22212 2347899999984
No 56
>PF09416 UPF1_Zn_bind: RNA helicase (UPF2 interacting domain); InterPro: IPR018999 UPF1 (or regulator of nonsense transcripts 1 homologue) is an essential RNA helicase that detects mRNAs containing premature stop codons and triggers their degradation. This domain contains 3 zinc binding motifs and forms interactions with another protein (UPF2) that is also involved nonsense-mediated mRNA decay (NMD) []. ; GO: 0003677 DNA binding, 0004386 helicase activity, 0005524 ATP binding, 0008270 zinc ion binding, 0000184 nuclear-transcribed mRNA catabolic process, nonsense-mediated decay, 0005737 cytoplasm; PDB: 2IYK_B 2WJY_A 2WJV_A 2XZL_A.
Probab=42.82 E-value=15 Score=31.79 Aligned_cols=26 Identities=31% Similarity=0.850 Sum_probs=16.6
Q ss_pred ecccCCcccCCCceEEccCCCCeeeccc
Q 025377 200 CGACGENYAADEFWICCDVCEKWFHGKC 227 (253)
Q Consensus 200 C~iC~~py~~d~~mIqCD~Ce~WfH~~C 227 (253)
|.+||... ..-.++|..|.+||-..=
T Consensus 3 C~YCG~~~--p~~vv~C~~c~kWFCNg~ 28 (152)
T PF09416_consen 3 CAYCGIHD--PSCVVKCNTCNKWFCNGR 28 (152)
T ss_dssp -TTT------CCCEEEETTTTEEEES--
T ss_pred ccccCCCC--cccEeEcCCCCcEeecCC
Confidence 77888652 468999999999997644
No 57
>PF05402 PqqD: Coenzyme PQQ synthesis protein D (PqqD); InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; PDB: 3G2B_A.
Probab=42.59 E-value=38 Score=23.90 Aligned_cols=32 Identities=34% Similarity=0.437 Sum_probs=23.3
Q ss_pred CCCHHHHHhhhhhhhhHHHHHhhHHHHHHHhh
Q 025377 9 PRTVEEVFGDFKGRRAGMIKALTTEVEEFYHQ 40 (253)
Q Consensus 9 ~~~~~~~f~d~~~rr~~~~~alt~d~~~f~~~ 40 (253)
++|+++|-+.+..+=..=...+..||.+|.++
T Consensus 29 ~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~ 60 (68)
T PF05402_consen 29 PRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQ 60 (68)
T ss_dssp SS-HHHHHHHHHHHTT--HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 69999999888877655555578899999864
No 58
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=42.53 E-value=10 Score=24.64 Aligned_cols=36 Identities=22% Similarity=0.397 Sum_probs=26.8
Q ss_pred CcceecccCCcccCCCceEEccCCCCeeeccccccC
Q 025377 196 GETLCGACGENYAADEFWICCDVCEKWFHGKCVKIT 231 (253)
Q Consensus 196 ~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit 231 (253)
..+.|.+|++.-......+.|..|..-.|..|...-
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~v 45 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEKV 45 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCchHHHHHHhhc
Confidence 356799998865422137889999999999998643
No 59
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=42.03 E-value=24 Score=23.06 Aligned_cols=23 Identities=22% Similarity=0.611 Sum_probs=11.7
Q ss_pred eecccCCcccC-------CCceEEccCCCC
Q 025377 199 LCGACGENYAA-------DEFWICCDVCEK 221 (253)
Q Consensus 199 ~C~iC~~py~~-------d~~mIqCD~Ce~ 221 (253)
.|+.|+..|.- .+..++|..|+.
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~ 33 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGH 33 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCC
Confidence 45556554431 344566666653
No 60
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=40.49 E-value=12 Score=36.79 Aligned_cols=51 Identities=24% Similarity=0.696 Sum_probs=29.3
Q ss_pred ceecccCCcccC-CCceEEccCCCCeee--------ccccccCccccCCCCeEEcCCCCC
Q 025377 198 TLCGACGENYAA-DEFWICCDVCEKWFH--------GKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 198 t~C~iC~~py~~-d~~mIqCD~Ce~WfH--------~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
..|++||..-.. .--.+-|++|.-.|- ..|.--..-..+..-.-.||.|+-
T Consensus 16 ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRF 75 (475)
T KOG4218|consen 16 ELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRF 75 (475)
T ss_pred cccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhH
Confidence 479999975432 234788999997773 345432222222222346777763
No 61
>PF13023 HD_3: HD domain; PDB: 1XX7_D 2GZ4_B 4DMB_B.
Probab=39.79 E-value=16 Score=31.07 Aligned_cols=40 Identities=30% Similarity=0.629 Sum_probs=24.7
Q ss_pred hhhhhhhHHHHHh-hhhccccc--cChhhhHHHHHhhhcCCceeeeecc
Q 025377 94 VAVHSDAWLLSVA-FYFGARFG--FDKSDRKRLFNMINELPTIFEVVTG 139 (253)
Q Consensus 94 va~h~d~wl~~~~-~~~~~~~~--f~~~~r~~lf~min~LPTv~EvVtg 139 (253)
||=|| |.+|+. +.++..+| +|.. |--...++-|+| |+++|
T Consensus 23 VAeHS--~~vA~~a~~la~~~~~~~d~~-k~~~~aL~HDl~---E~~~G 65 (165)
T PF13023_consen 23 VAEHS--WRVALIALLLAEEAGPDLDIE-KVVKMALFHDLP---EAITG 65 (165)
T ss_dssp HHHHH--HHHHHHHHHHHHHHH-HC-HH-HHHHHHHHTTTT---HHHH-
T ss_pred HHHHH--HHHHHHHHHHhHHhcccCCHH-HHHHHHhhccch---hhhcC
Confidence 66674 887754 34444454 4555 444555899998 88998
No 62
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=39.31 E-value=32 Score=32.90 Aligned_cols=52 Identities=23% Similarity=0.620 Sum_probs=32.0
Q ss_pred cceecccCCcc---------cCCCceEEccCCCCeeec---cccccCccc----------cCCCCeEEcCCCCC
Q 025377 197 ETLCGACGENY---------AADEFWICCDVCEKWFHG---KCVKITPAR----------AEHIKQYKCPSCSN 248 (253)
Q Consensus 197 ~t~C~iC~~py---------~~d~~mIqCD~Ce~WfH~---~CVgit~~~----------a~~id~y~Cp~C~~ 248 (253)
..+|++||..- ..+..+..|..|+.-+|. .|..-.... ........|..|..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~ 260 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGT 260 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeeeecCCCcceEeeecccccc
Confidence 45799998641 235678899999855555 554322211 01235688999974
No 63
>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=38.58 E-value=26 Score=28.22 Aligned_cols=52 Identities=23% Similarity=0.608 Sum_probs=32.1
Q ss_pred cCcceecccCCcccCCCceEEc------cCC---CCeeeccccc----cCccccCCCCeEEcCCCCC
Q 025377 195 HGETLCGACGENYAADEFWICC------DVC---EKWFHGKCVK----ITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d~~mIqC------D~C---e~WfH~~CVg----it~~~a~~id~y~Cp~C~~ 248 (253)
.....|-.|.+... +..+.| ..| ..=|-+.|+- ....++-....|.||.|+.
T Consensus 5 ~~g~~CHqCrqKt~--~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~Crg 69 (105)
T PF10497_consen 5 VNGKTCHQCRQKTL--DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRG 69 (105)
T ss_pred CCCCCchhhcCCCC--CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCC
Confidence 34556777887533 344556 566 7778888863 2222222335799999985
No 64
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=36.88 E-value=21 Score=34.59 Aligned_cols=52 Identities=19% Similarity=0.309 Sum_probs=39.3
Q ss_pred cceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCcCCC
Q 025377 197 ETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNKRAR 252 (253)
Q Consensus 197 ~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~Kr~R 252 (253)
.++| +|...+.+.+.++.|-.|.-|+|..-..+..-.. ..|.|.=|..+-+|
T Consensus 53 Q~l~-sClTC~P~~~~agvC~~C~~~CH~~H~lveL~tK---R~FrCDCg~sk~g~ 104 (345)
T KOG2752|consen 53 QALF-SCLTCTPAPEMAGVCYACSLSCHDGHELVELYTK---RNFRCDCGNSKFGR 104 (345)
T ss_pred ccee-EeecccCChhhceeEEEeeeeecCCceeeecccc---CCcccccccccccc
Confidence 4566 8888777777999999999999999888765432 46888776655443
No 65
>KOG0913 consensus Thiol-disulfide isomerase and thioredoxin [Posttranslational modification, protein turnover, chaperones; Energy production and conversion]
Probab=36.26 E-value=11 Score=34.97 Aligned_cols=49 Identities=27% Similarity=0.390 Sum_probs=36.9
Q ss_pred cccCCCcccccchhhhhhhhhhHHHHHhhhhccccccChhhhHHHHHhhhcCCceeeeeccccccccc
Q 025377 79 NFARDGMQEKDWLSLVAVHSDAWLLSVAFYFGARFGFDKSDRKRLFNMINELPTIFEVVTGTTKKQAK 146 (253)
Q Consensus 79 n~~rd~~~~~~wl~~va~h~d~wl~~~~~~~~~~~~f~~~~r~~lf~min~LPTv~EvVtg~~kkq~k 146 (253)
|||+=+|.---|++-|-|- +++-.-.|| |+.-|||||+|+-|.=++-+.
T Consensus 63 ~~a~~s~dL~v~va~VDvt-------~npgLsGRF------------~vtaLptIYHvkDGeFrrysg 111 (248)
T KOG0913|consen 63 NFATVSLDLGVKVAKVDVT-------TNPGLSGRF------------LVTALPTIYHVKDGEFRRYSG 111 (248)
T ss_pred ccCCccCCCceeEEEEEEE-------eccccceee------------EEEecceEEEeeccccccccC
Confidence 6777777777778877764 445556788 999999999999997665533
No 66
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=35.90 E-value=17 Score=24.17 Aligned_cols=42 Identities=33% Similarity=0.720 Sum_probs=28.6
Q ss_pred ecccCCcccCC-CceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 200 CGACGENYAAD-EFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 200 C~iC~~py~~d-~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
|.+|...|++. .++| -.|...|...|+.-.. .....||.|.+
T Consensus 2 C~~C~~~~~~~~~~~l--~~CgH~~C~~C~~~~~-----~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRL--TSCGHIFCEKCLKKLK-----GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEE--cccCCHHHHHHHHhhc-----CCCCCCcCCCC
Confidence 78899988432 3333 3777788888987554 23478999863
No 67
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=35.41 E-value=4.6 Score=31.62 Aligned_cols=48 Identities=25% Similarity=0.486 Sum_probs=28.5
Q ss_pred eecccCCcccCCCc-----eEEcc----CCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 199 LCGACGENYAADEF-----WICCD----VCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 199 ~C~iC~~py~~d~~-----mIqCD----~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
.|++|+++++.-=. =-.|- .|..-||..|+----.. ...+-.||.|++
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~--~tsq~~CPmcRq 78 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNT--PTSQGQCPMCRQ 78 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcC--ccccccCCcchh
Confidence 79999998864100 00121 56677999997422111 124578999985
No 68
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=34.78 E-value=25 Score=36.54 Aligned_cols=48 Identities=29% Similarity=0.668 Sum_probs=36.1
Q ss_pred cceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 197 ETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 197 ~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
.+.|++|.+. +...+|+.|..-||..|.+...........+.|..|..
T Consensus 47 ~ts~~~~~~~----gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~ 94 (613)
T KOG4299|consen 47 ATSCGICKSG----GNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPK 94 (613)
T ss_pred hhhcchhhhc----CCccccccCccccchhccCcccCcccccccccccCCCc
Confidence 6779999874 56789999999999999998766433334566666654
No 69
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=34.44 E-value=35 Score=30.57 Aligned_cols=46 Identities=26% Similarity=0.551 Sum_probs=31.7
Q ss_pred cceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 025377 197 ETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNK 249 (253)
Q Consensus 197 ~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~K 249 (253)
-.-|++|-..+. +..+-=-.|+.-|--.|+.-.-. ..-.||.|.+|
T Consensus 131 ~~~CPiCl~~~s--ek~~vsTkCGHvFC~~Cik~alk-----~~~~CP~C~kk 176 (187)
T KOG0320|consen 131 TYKCPICLDSVS--EKVPVSTKCGHVFCSQCIKDALK-----NTNKCPTCRKK 176 (187)
T ss_pred ccCCCceecchh--hccccccccchhHHHHHHHHHHH-----hCCCCCCcccc
Confidence 366999988764 33333468888898899864433 24689999864
No 70
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 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 (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=32.65 E-value=22 Score=26.52 Aligned_cols=53 Identities=23% Similarity=0.603 Sum_probs=32.1
Q ss_pred ceecccCCcccC----CCceEEccCCCCeeeccccccCc-cccCCCCeEEcCCCCCcCC
Q 025377 198 TLCGACGENYAA----DEFWICCDVCEKWFHGKCVKITP-ARAEHIKQYKCPSCSNKRA 251 (253)
Q Consensus 198 t~C~iC~~py~~----d~~mIqCD~Ce~WfH~~CVgit~-~~a~~id~y~Cp~C~~Kr~ 251 (253)
..|++|....+- .-.+-.|-.|..-.-..| |+.+ ........|.|-.|..+|+
T Consensus 3 ~~CPlCkt~~n~gsk~~pNyntCT~Ck~~VCnlC-GFNP~Phl~E~~eWLCLnCQ~qRa 60 (61)
T PF05715_consen 3 SLCPLCKTTLNVGSKDPPNYNTCTECKSQVCNLC-GFNPTPHLTEVKEWLCLNCQMQRA 60 (61)
T ss_pred ccCCcccchhhcCCCCCCCccHHHHHhhhhhccc-CCCCCccccccceeeeecchhhhc
Confidence 468888753321 124556777776555555 4443 2233357899999998875
No 71
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=31.68 E-value=35 Score=22.30 Aligned_cols=25 Identities=20% Similarity=0.559 Sum_probs=13.1
Q ss_pred eecccCCcccC-------CCceEEccCCCCee
Q 025377 199 LCGACGENYAA-------DEFWICCDVCEKWF 223 (253)
Q Consensus 199 ~C~iC~~py~~-------d~~mIqCD~Ce~Wf 223 (253)
.|+.|+..|.- .+.++.|-.|+.-|
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 46666654431 24466666665443
No 72
>PF13922 PHD_3: PHD domain of transcriptional enhancer, Asx
Probab=31.42 E-value=13 Score=28.19 Aligned_cols=31 Identities=26% Similarity=0.664 Sum_probs=25.2
Q ss_pred CcceecccCCcccCCCceEEccCCCCeeeccccccCc
Q 025377 196 GETLCGACGENYAADEFWICCDVCEKWFHGKCVKITP 232 (253)
Q Consensus 196 ~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~ 232 (253)
-..-| .|... -||-|..|+..-|-.|+|-+.
T Consensus 32 ~~~~C-~C~Lk-----AMi~Cq~CGAFCHDDCIgpsk 62 (69)
T PF13922_consen 32 TSNKC-ACSLK-----AMIMCQGCGAFCHDDCIGPSK 62 (69)
T ss_pred ccccc-ccchH-----HHHHHhhccchhccccccHHH
Confidence 33447 88874 799999999999999998653
No 73
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=30.93 E-value=25 Score=22.35 Aligned_cols=12 Identities=25% Similarity=0.933 Sum_probs=8.8
Q ss_pred CeEEcCCCCCcC
Q 025377 239 KQYKCPSCSNKR 250 (253)
Q Consensus 239 d~y~Cp~C~~Kr 250 (253)
..|.||.|...+
T Consensus 16 ~~~~CP~Cg~~~ 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCcCcCCCCcH
Confidence 458999997644
No 74
>cd04120 Rab12 Rab12 subfamily. Rab12 was first identified in canine cells, where it was localized to the Golgi complex. The specific function of Rab12 remains unknown, and inconsistent results about its cellular localization have been reported. More recent studies have identified Rab12 associated with post-Golgi vesicles, or with other small vesicle-like structures but not with the Golgi complex. Most Rab GTPases contain a lipid modification site at the C-terminus, with sequence motifs CC, CXC, or CCX. Lipid binding is essential for membrane attachment, a key feature of most Rab proteins. GTPase activating proteins (GAPs) interact with GTP-bound Rab and accelerate the hydrolysis of GTP to GDP. Guanine nucleotide exchange factors (GEFs) interact with GDP-bound Rabs to promote the formation of the GTP-bound state. Rabs are further regulated by guanine nucleotide dissociation inhibitors (GDIs), which facilitate Rab recycling by masking C-terminal lipid binding and promoting cytosolic
Probab=30.75 E-value=27 Score=30.36 Aligned_cols=14 Identities=57% Similarity=1.151 Sum_probs=12.1
Q ss_pred CCCCCCCCCCCCcc
Q 025377 63 PAEEVPPELPEPAL 76 (253)
Q Consensus 63 p~~~~p~~~pep~~ 76 (253)
|..|+|||||.|-.
T Consensus 184 ~~~~~~~~~~~~~~ 197 (202)
T cd04120 184 PEPEIPPELPPPRP 197 (202)
T ss_pred CCCCCCcCCCCCCC
Confidence 78899999998864
No 75
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=30.74 E-value=5.7 Score=39.53 Aligned_cols=52 Identities=27% Similarity=0.608 Sum_probs=38.5
Q ss_pred cCcceecccCCcccCCCceEEccCCCCeeecccccc-CccccCCCCeEEcCCCCCcC
Q 025377 195 HGETLCGACGENYAADEFWICCDVCEKWFHGKCVKI-TPARAEHIKQYKCPSCSNKR 250 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgi-t~~~a~~id~y~Cp~C~~Kr 250 (253)
+-+.+|+.||+.+.-...-+|---|..-||..|..- -... ..-.||.|++-|
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n----~~rsCP~Crklr 415 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN----GTRSCPNCRKLR 415 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC----CCCCCccHHHHH
Confidence 456789999998876566778788999999999972 2222 336799998544
No 76
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=29.40 E-value=41 Score=36.54 Aligned_cols=54 Identities=22% Similarity=0.525 Sum_probs=38.8
Q ss_pred cCcceecccCCcccCCCceEEccCCCCeeeccccccC--ccccCCCCeEEcCCCCC
Q 025377 195 HGETLCGACGENYAADEFWICCDVCEKWFHGKCVKIT--PARAEHIKQYKCPSCSN 248 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit--~~~a~~id~y~Cp~C~~ 248 (253)
.....|-||-..-+....+-.|..|-..||..|+.-= ..+....+.|.||.|..
T Consensus 189 ~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqs 244 (950)
T KOG1952|consen 189 NRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQS 244 (950)
T ss_pred cCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccc
Confidence 4556788886654445678899999999999998531 12223347899999984
No 77
>cd00029 C1 Protein kinase C conserved region 1 (C1) . Cysteine-rich zinc binding domain. Some members of this domain family bind phorbol esters and diacylglycerol, some are reported to bind RasGTP. May occur in tandem arrangement. Diacylglycerol (DAG) is a second messenger, released by activation of Phospholipase D. Phorbol Esters (PE) can act as analogues of DAG and mimic its downstream effects in, for example, tumor promotion. Protein Kinases C are activated by DAG/PE, this activation is mediated by their N-terminal conserved region (C1). DAG/PE binding may be phospholipid dependent. C1 domains may also mediate DAG/PE signals in chimaerins (a family of Rac GTPase activating proteins), RasGRPs (exchange factors for Ras/Rap1), and Munc13 isoforms (scaffolding proteins involved in exocytosis).
Probab=29.39 E-value=32 Score=22.55 Aligned_cols=36 Identities=22% Similarity=0.453 Sum_probs=26.8
Q ss_pred CcceecccCCcccCC-CceEEccCCCCeeeccccccC
Q 025377 196 GETLCGACGENYAAD-EFWICCDVCEKWFHGKCVKIT 231 (253)
Q Consensus 196 ~~t~C~iC~~py~~d-~~mIqCD~Ce~WfH~~CVgit 231 (253)
..+.|.+|++..... .....|+.|..-.|..|...-
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~v 46 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADKV 46 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCchhhhhhccC
Confidence 356798998865321 466789999999999998644
No 78
>PF11351 DUF3154: Protein of unknown function (DUF3154); InterPro: IPR021497 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=29.38 E-value=25 Score=28.86 Aligned_cols=13 Identities=69% Similarity=1.140 Sum_probs=11.2
Q ss_pred hHHH--HHhhhhccc
Q 025377 100 AWLL--SVAFYFGAR 112 (253)
Q Consensus 100 ~wl~--~~~~~~~~~ 112 (253)
-||| .|.||||+|
T Consensus 100 w~Llg~~vlgy~~~R 114 (123)
T PF11351_consen 100 WWLLGAGVLGYFGAR 114 (123)
T ss_pred HHHHHHHHhhhHHHh
Confidence 4777 899999999
No 79
>PF06452 DUF1083: Domain of unknown function (DUF1083); InterPro: IPR010502 This entry represents the family 9 carbohydrate-binding module (CBD9), which exhibit an immunoglobulin-like beta-sandwich fold, with an additional beta-strand at the N terminus []. Bacterial extracellular cellulases and hemicellulases are involved in the hydrolysis of the major structural polysaccharides of plant cell walls. These are usually modular enzymes that contain catalytic and non-catalytic domains. The CBD9 domain binds to cellulose, xylan, as well as to a range of soluble di- and mono-saccharides, and is found in cellulose- and xylan-degrading enzymes, such as endo-1,4-beta-xylanase (3.2.1.8 from EC) [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0016052 carbohydrate catabolic process; PDB: 1I82_A 1I8A_A 1I8U_A.
Probab=28.99 E-value=16 Score=30.26 Aligned_cols=44 Identities=27% Similarity=0.613 Sum_probs=26.5
Q ss_pred ceeeeCCCCCC-CCCCCCCccCcccc----CCCcccccchhhhhhhhhhH
Q 025377 57 QWEVNLPAEEV-PPELPEPALGINFA----RDGMQEKDWLSLVAVHSDAW 101 (253)
Q Consensus 57 ~w~v~~p~~~~-p~~~pep~~gin~~----rd~~~~~~wl~~va~h~d~w 101 (253)
++|+.+|-..+ +|+.... +|+||. .++=.|..|++...+..+.|
T Consensus 123 ~~E~~IP~~~l~~~~~g~~-~g~~~~~~d~~~~~~r~~~~~w~~~~~~~~ 171 (185)
T PF06452_consen 123 TVEIAIPWSALFPPQPGDK-FGFNFAVNDNDDGGKREGWISWSDPSGPSF 171 (185)
T ss_dssp EEEEEEE-SS-----TTEE-EEEEEEEEEE-TTS-EEEEEESS-SSS-TT
T ss_pred EEEEEechHHcCCCCCCCE-EEEEEEEEECCCCCcceEEEEEcCCCCcCc
Confidence 57999999998 4444433 888888 45566888998877776664
No 80
>PHA02929 N1R/p28-like protein; Provisional
Probab=28.42 E-value=33 Score=31.63 Aligned_cols=46 Identities=24% Similarity=0.580 Sum_probs=29.1
Q ss_pred ceecccCCcccCCC----ceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 198 TLCGACGENYAADE----FWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 198 t~C~iC~~py~~d~----~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
..|++|.....+.. ....=..|..-||..|+..-.. ..-.||.|+.
T Consensus 175 ~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-----~~~tCPlCR~ 224 (238)
T PHA02929 175 KECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-----EKNTCPVCRT 224 (238)
T ss_pred CCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-----cCCCCCCCCC
Confidence 46999988643221 1122247888999999964322 1237999985
No 81
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=27.68 E-value=57 Score=22.79 Aligned_cols=13 Identities=23% Similarity=0.846 Sum_probs=8.1
Q ss_pred CCeEEcCCCCCcC
Q 025377 238 IKQYKCPSCSNKR 250 (253)
Q Consensus 238 id~y~Cp~C~~Kr 250 (253)
.+.|.||.|...+
T Consensus 32 p~~w~CP~C~a~K 44 (47)
T PF00301_consen 32 PDDWVCPVCGAPK 44 (47)
T ss_dssp -TT-B-TTTSSBG
T ss_pred CCCCcCcCCCCcc
Confidence 4689999998654
No 82
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=27.41 E-value=35 Score=29.92 Aligned_cols=33 Identities=27% Similarity=0.655 Sum_probs=23.9
Q ss_pred cceecccCC---------cccCCCceEEccCCC---------Ceeeccccc
Q 025377 197 ETLCGACGE---------NYAADEFWICCDVCE---------KWFHGKCVK 229 (253)
Q Consensus 197 ~t~C~iC~~---------py~~d~~mIqCD~Ce---------~WfH~~CVg 229 (253)
.-.|-+|+. .|..+...|||++|. .|||..=+.
T Consensus 79 ~yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~HliaDnL~~F~d~~~~ 129 (165)
T KOG3277|consen 79 AYTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLIADNLGWFHDLKGK 129 (165)
T ss_pred EEEeeccCCccccccChhhhhCceEEEECCCCccceeehhhhccccccccc
Confidence 345888975 455577899999997 588875544
No 83
>PF13111 DUF3962: Protein of unknown function (DUF3962)
Probab=26.99 E-value=31 Score=31.38 Aligned_cols=34 Identities=29% Similarity=0.738 Sum_probs=26.5
Q ss_pred ccchhhhhhhhhhHHHHHhhhhccccccChhhhHHHHHhhhcC
Q 025377 88 KDWLSLVAVHSDAWLLSVAFYFGARFGFDKSDRKRLFNMINEL 130 (253)
Q Consensus 88 ~~wl~~va~h~d~wl~~~~~~~~~~~~f~~~~r~~lf~min~L 130 (253)
.+|+.||-.|-|.|++-+-+ +.-++||+.|.-+.
T Consensus 24 ~~W~~ll~~~~~~~~l~~Kl---------~~l~erL~~mFsdI 57 (216)
T PF13111_consen 24 IEWLDLLEIHYKTFLLTSKL---------KRLNERLYDMFSDI 57 (216)
T ss_pred HHHHHHHHHhccccccHHHH---------HHHHHHHHHHHHHH
Confidence 68999999999999998754 23367888876554
No 84
>smart00432 MADS MADS domain.
Probab=26.25 E-value=84 Score=22.80 Aligned_cols=38 Identities=29% Similarity=0.530 Sum_probs=24.9
Q ss_pred hhhhhhhHHHHHhhHHHHHHHhhcCCCCcceeeecCCCCceee
Q 025377 18 DFKGRRAGMIKALTTEVEEFYHQCDPEKENLCLYGFPSEQWEV 60 (253)
Q Consensus 18 d~~~rr~~~~~alt~d~~~f~~~c~p~~~~l~lyg~~~~~w~v 60 (253)
-|+.||+||.+-- .++.-+||-+-- |-+|+..+..+.+
T Consensus 19 tf~kRk~gl~kKa----~Els~Lc~~~v~-~iv~sp~g~~~~~ 56 (59)
T smart00432 19 TFSKRRNGLFKKA----HELSVLCDAEVA-LIVFSPTGKLYEF 56 (59)
T ss_pred hhHhhhhhHHHHH----HHHhhccCCeEE-EEEECCCCCeeec
Confidence 3899999999864 567789996543 3335554444443
No 85
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=24.95 E-value=19 Score=30.68 Aligned_cols=23 Identities=35% Similarity=0.751 Sum_probs=20.2
Q ss_pred HhhHHHHHHHhhcCCCCcceeeec
Q 025377 29 ALTTEVEEFYHQCDPEKENLCLYG 52 (253)
Q Consensus 29 alt~d~~~f~~~c~p~~~~l~lyg 52 (253)
--|+|+-+ ++.|.+++.++||+|
T Consensus 34 ~~~~~~~~-i~~Cp~ey~~YClHG 56 (139)
T PHA03099 34 NATTDIPA-IRLCGPEGDGYCLHG 56 (139)
T ss_pred cCccCCcc-cccCChhhCCEeECC
Confidence 34778888 899999999999998
No 86
>TIGR03859 PQQ_PqqD coenzyme PQQ biosynthesis protein PqqD. This model identifies PqqD, a protein involved in the final steps of the biosynthesis of pyrroloquinoline quinone, coenzyme PQQ.
Probab=24.65 E-value=86 Score=23.63 Aligned_cols=31 Identities=16% Similarity=0.334 Sum_probs=23.9
Q ss_pred CCCHHHHHhhhhhhhhHHHHHhhHHHHHHHhh
Q 025377 9 PRTVEEVFGDFKGRRAGMIKALTTEVEEFYHQ 40 (253)
Q Consensus 9 ~~~~~~~f~d~~~rr~~~~~alt~d~~~f~~~ 40 (253)
++||++|-.....+=.. -.-+..||..|.++
T Consensus 43 ~~tv~eI~~~L~~~Y~~-~e~~~~dV~~fL~~ 73 (81)
T TIGR03859 43 KRSLAEIIQELAQRFPA-AEEIEDDVIAFLAV 73 (81)
T ss_pred CCcHHHHHHHHHHHcCC-hhhHHHHHHHHHHH
Confidence 68999998887766666 55567899998764
No 87
>cd07168 NR_DBD_DHR4_like DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. DNA-binding domain of ecdysone-induced DHR4 orphan nuclear receptor is composed of two C4-type zinc fingers. Each zinc finger contains a group of four Cys residues which coordinates a single zinc atom. This domain interacts with specific DNA sites upstream of the target gene and modulates the rate of transcriptional initiation. Ecdysone-induced orphan receptor DHR4 is a member of the nuclear receptor family. DHR4 is expressed during the early Drosophila larval development and is induced by ecdysone. DHR4 coordinates growth and maturation in Drosophila by mediating endocrine response to the attainment of proper body size during larval development. Mutations in DHR4 result in shorter larval development which translates into smaller and lighter flies. Like other members of the nuclear receptor (NR) superfamily of ligand-activated transcription factors, DHR4
Probab=24.37 E-value=43 Score=26.10 Aligned_cols=33 Identities=21% Similarity=0.518 Sum_probs=21.4
Q ss_pred cCcceecccCCcccCC-CceEEccCCCCeeeccc
Q 025377 195 HGETLCGACGENYAAD-EFWICCDVCEKWFHGKC 227 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d-~~mIqCD~Ce~WfH~~C 227 (253)
.....|-+|+.+...- -.-+.|..|...|...-
T Consensus 4 ~~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v 37 (90)
T cd07168 4 ESPKLCSICEDKATGLHYGIITCEGCKGFFKRTV 37 (90)
T ss_pred ccCCCCcccCCcCcceEECceehhhhhHhhhhhh
Confidence 4455799999864321 12478999998776543
No 88
>PF05180 zf-DNL: DNL zinc finger; InterPro: IPR007853 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The DNL-type zinc finger is found in Tim15, a zinc finger protein essential for protein import into mitochondria. Mitochondrial functions rely on the correct transport of resident proteins synthesized in the cytosol to mitochondria. Protein import into mitochondria is mediated by membrane protein complexes, protein translocators, in the outer and inner mitochondrial membranes, in cooperation with their assistant proteins in the cytosol, intermembrane space and matrix. Proteins destined to the mitochondrial matrix cross the outer membrane with the aid of the outer membrane translocator, the tOM40 complex, and then the inner membrane with the aid of the inner membrane translocator, the TIM23 complex, and mitochondrial motor and chaperone (MMC) proteins including mitochondrial heat- shock protein 70 (mtHsp70), and translocase in the inner mitochondrial membrane (Tim)15. Tim15 is also known as zinc finger motif (Zim)17 or mtHsp70 escort protein (Hep)1. Tim15 contains a zinc-finger motif (CXXC and CXXC) of ~100 residues, which has been named DNL after a short C-terminal motif of D(N/H)L [, , ]. The DNL-type zinc finger is an L-shaped molecule. The two CXXC motifs are located at the end of the L, and are sandwiched by two- stranded antiparallel beta-sheets. Two short alpha-helices constitute another leg of the L. The outer (convex) face of the L has a large acidic groove, which is lined with five acidic residues, whereas the inner (concave) face of the L has two positively charged residues, next to the CXXC motifs []. This entry represents the DNL-type zinc finger.; GO: 0008270 zinc ion binding; PDB: 2E2Z_A.
Probab=23.98 E-value=30 Score=26.01 Aligned_cols=17 Identities=18% Similarity=0.450 Sum_probs=11.1
Q ss_pred cccCCCceEEccCCCCe
Q 025377 206 NYAADEFWICCDVCEKW 222 (253)
Q Consensus 206 py~~d~~mIqCD~Ce~W 222 (253)
.|..+...|+|+.|..|
T Consensus 22 aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 22 AYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp HHHTSEEEEE-TTS--E
T ss_pred HHhCCeEEEECCCCcce
Confidence 45557789999999987
No 89
>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 KOG2932 consensus E3 ubiquitin ligase involved in ubiquitination of E-cadherin complex [Posttranslational modification, protein turnover, chaperones]
Probab=23.50 E-value=28 Score=33.87 Aligned_cols=42 Identities=24% Similarity=0.509 Sum_probs=28.4
Q ss_pred eecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCCcC
Q 025377 199 LCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNKR 250 (253)
Q Consensus 199 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~Kr 250 (253)
+|--|+.+-.-.+.||-|+. -|..+|....+. -+|+.|..+-
T Consensus 92 fCd~Cd~PI~IYGRmIPCkH---vFCl~CAr~~~d-------K~Cp~C~d~V 133 (389)
T KOG2932|consen 92 FCDRCDFPIAIYGRMIPCKH---VFCLECARSDSD-------KICPLCDDRV 133 (389)
T ss_pred eecccCCcceeeecccccch---hhhhhhhhcCcc-------ccCcCcccHH
Confidence 45558776555678888764 567777766652 4788888653
No 91
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=22.86 E-value=41 Score=21.52 Aligned_cols=10 Identities=40% Similarity=1.139 Sum_probs=2.1
Q ss_pred eecccCCccc
Q 025377 199 LCGACGENYA 208 (253)
Q Consensus 199 ~C~iC~~py~ 208 (253)
.|+.|+..|.
T Consensus 4 ~Cp~C~se~~ 13 (30)
T PF08274_consen 4 KCPLCGSEYT 13 (30)
T ss_dssp --TTT-----
T ss_pred CCCCCCCcce
Confidence 4667766543
No 92
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=22.75 E-value=35 Score=32.49 Aligned_cols=32 Identities=22% Similarity=0.530 Sum_probs=20.7
Q ss_pred CCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 025377 209 ADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSN 248 (253)
Q Consensus 209 ~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~ 248 (253)
+++.|+.|+.|..-.+.+= .+. ..|+||.|..
T Consensus 34 p~~lw~kc~~C~~~~~~~~-------l~~-~~~vcp~c~~ 65 (296)
T CHL00174 34 YKHLWVQCENCYGLNYKKF-------LKS-KMNICEQCGY 65 (296)
T ss_pred CCCCeeECCCccchhhHHH-------HHH-cCCCCCCCCC
Confidence 4678999999986433221 111 3589999974
No 93
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=22.24 E-value=51 Score=33.33 Aligned_cols=44 Identities=11% Similarity=-0.191 Sum_probs=36.7
Q ss_pred ecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCC
Q 025377 200 CGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCS 247 (253)
Q Consensus 200 C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~ 247 (253)
|+.|++.+.+...+.+|..|..|+|..|++.+.. ++..+|..|+
T Consensus 173 ~~~~~k~e~d~~~~kt~~~~~~~~~p~~~~t~~~----~~~~~~~~~s 216 (464)
T KOG1886|consen 173 FGDGQKLEIDMLVPKTGPRRGTLPDPKKVQTLNA----AASKRSQQKS 216 (464)
T ss_pred hhcccccCCccchhhhcccCCCCCCccccccccc----cccceecccc
Confidence 5589999988889999999999999999998873 3457777773
No 94
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=22.17 E-value=78 Score=23.02 Aligned_cols=13 Identities=23% Similarity=0.486 Sum_probs=7.5
Q ss_pred CceEEccCCCCee
Q 025377 211 EFWICCDVCEKWF 223 (253)
Q Consensus 211 ~~mIqCD~Ce~Wf 223 (253)
+..+.|..|++||
T Consensus 51 eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 51 EGELICPECGREY 63 (68)
T ss_dssp TTEEEETTTTEEE
T ss_pred CCEEEcCCCCCEE
Confidence 4455566666665
No 95
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=21.80 E-value=37 Score=23.53 Aligned_cols=45 Identities=18% Similarity=0.449 Sum_probs=24.2
Q ss_pred ecccCCcccCCCceEEccCC---CCeeeccccccCccccCCCCeEEcCCCC
Q 025377 200 CGACGENYAADEFWICCDVC---EKWFHGKCVKITPARAEHIKQYKCPSCS 247 (253)
Q Consensus 200 C~iC~~py~~d~~mIqCD~C---e~WfH~~CVgit~~~a~~id~y~Cp~C~ 247 (253)
|-+|....++++.+|.==.| -.|+|..|+.-=-.... .-.|+.|.
T Consensus 2 CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~~---~~~C~iC~ 49 (49)
T smart00744 2 CRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINESG---NKTCEICK 49 (49)
T ss_pred ccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHcC---CCcCCCCC
Confidence 56676633334555541123 37999999863221111 12787773
No 96
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=21.56 E-value=35 Score=25.85 Aligned_cols=52 Identities=29% Similarity=0.507 Sum_probs=35.9
Q ss_pred hhhhhHHHHHhhHHHHHHHhhcCCCCcceeeecCCCCceeeeCCCCCCCCCCCCCc-cCccccCCCcccccch
Q 025377 20 KGRRAGMIKALTTEVEEFYHQCDPEKENLCLYGFPSEQWEVNLPAEEVPPELPEPA-LGINFARDGMQEKDWL 91 (253)
Q Consensus 20 ~~rr~~~~~alt~d~~~f~~~c~p~~~~l~lyg~~~~~w~v~~p~~~~p~~~pep~-~gin~~rd~~~~~~wl 91 (253)
+-||.||+..|..=+-+ | .+||..-...+|.. -+|+ -|..||+.=....+||
T Consensus 16 ~~RR~GIAt~Lld~ar~----------~-~iyG~~l~~~~iAF---------SqPT~~G~~fA~~y~~~~~fl 68 (70)
T PF13880_consen 16 SHRRKGIATRLLDAARE----------N-FIYGCVLPKNEIAF---------SQPTESGKKFAKKYFGTDDFL 68 (70)
T ss_pred hhhhhhHHHHHHHHHHH----------h-ccCceEechhheEe---------cCCCHhHHHHHHHHcCCCCEE
Confidence 46999999999875533 2 46888766665553 2344 6888888777777665
No 97
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=21.50 E-value=54 Score=20.53 Aligned_cols=25 Identities=24% Similarity=0.676 Sum_probs=13.7
Q ss_pred cceecccCCccc--CCCceEEccCCCC
Q 025377 197 ETLCGACGENYA--ADEFWICCDVCEK 221 (253)
Q Consensus 197 ~t~C~iC~~py~--~d~~mIqCD~Ce~ 221 (253)
..+|+.|+.+-. .++...+|..|..
T Consensus 3 ~rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 3 HRFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp TSB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred CcccCcCCccccCCCCcCEeECCCCcC
Confidence 357999987543 2567788888874
No 98
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=20.74 E-value=69 Score=21.21 Aligned_cols=32 Identities=22% Similarity=0.520 Sum_probs=14.0
Q ss_pred EEccCCCCeeeccccccCccccCCCCeEEcCCCCCcC
Q 025377 214 ICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCSNKR 250 (253)
Q Consensus 214 IqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~~Kr 250 (253)
|.|..|..-.-.-|.-.. ....|+|+.|..+.
T Consensus 3 ~rC~~C~aylNp~~~~~~-----~~~~w~C~~C~~~N 34 (40)
T PF04810_consen 3 VRCRRCRAYLNPFCQFDD-----GGKTWICNFCGTKN 34 (40)
T ss_dssp -B-TTT--BS-TTSEEET-----TTTEEEETTT--EE
T ss_pred cccCCCCCEECCcceEcC-----CCCEEECcCCCCcC
Confidence 556666654433333222 22579999998643
No 99
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=20.62 E-value=70 Score=22.78 Aligned_cols=30 Identities=27% Similarity=0.714 Sum_probs=19.2
Q ss_pred cCcceecccCCccc-------CCCceEEccCCCCeeec
Q 025377 195 HGETLCGACGENYA-------ADEFWICCDVCEKWFHG 225 (253)
Q Consensus 195 ~~~t~C~iC~~py~-------~d~~mIqCD~Ce~WfH~ 225 (253)
.-...| -||..|. .....|+|+.|.-|.+.
T Consensus 16 ~~~y~C-RCG~~f~i~e~~l~~~~~iv~C~sCSL~I~V 52 (55)
T PF05207_consen 16 VYSYPC-RCGGEFEISEEDLEEGEVIVQCDSCSLWIRV 52 (55)
T ss_dssp EEEEEE-TTSSEEEEEHHHHHCT--EEEETTTTEEEEE
T ss_pred EEEEcC-CCCCEEEEcchhccCcCEEEECCCCccEEEE
Confidence 344456 7887543 24578999999988653
No 100
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=20.35 E-value=73 Score=35.88 Aligned_cols=48 Identities=21% Similarity=0.560 Sum_probs=34.2
Q ss_pred cCcceecccCCcccCCCceEEccCCCCeeeccccccCccccCCCCeEEcCCCC
Q 025377 195 HGETLCGACGENYAADEFWICCDVCEKWFHGKCVKITPARAEHIKQYKCPSCS 247 (253)
Q Consensus 195 ~~~t~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgit~~~a~~id~y~Cp~C~ 247 (253)
+-+..|-+|.. .+..++|+.|.+-||..||.-....... ..|-|--|.
T Consensus 342 ~~ddhcrf~~d----~~~~lc~Et~prvvhlEcv~hP~~~~~s-~~~e~evc~ 389 (1414)
T KOG1473|consen 342 EYDDHCRFCHD----LGDLLCCETCPRVVHLECVFHPRFAVPS-AFWECEVCN 389 (1414)
T ss_pred eecccccccCc----ccceeecccCCceEEeeecCCccccCCC-ccchhhhhh
Confidence 34445767764 4678999999999999999766544322 457777775
No 101
>PRK04023 DNA polymerase II large subunit; Validated
Probab=20.33 E-value=83 Score=34.96 Aligned_cols=48 Identities=25% Similarity=0.668 Sum_probs=32.6
Q ss_pred ccccCcceecccCCcccCCCceEEccCCCC-----eeeccccccCccccCCCCeEEcCCCCCcC
Q 025377 192 EEEHGETLCGACGENYAADEFWICCDVCEK-----WFHGKCVKITPARAEHIKQYKCPSCSNKR 250 (253)
Q Consensus 192 eEd~~~t~C~iC~~py~~d~~mIqCD~Ce~-----WfH~~CVgit~~~a~~id~y~Cp~C~~Kr 250 (253)
+-+.....|..|+.. ..+..|..|+. +|...|-... ..+.||.|..+.
T Consensus 621 eVEVg~RfCpsCG~~----t~~frCP~CG~~Te~i~fCP~CG~~~-------~~y~CPKCG~El 673 (1121)
T PRK04023 621 EVEIGRRKCPSCGKE----TFYRRCPFCGTHTEPVYRCPRCGIEV-------EEDECEKCGREP 673 (1121)
T ss_pred eecccCccCCCCCCc----CCcccCCCCCCCCCcceeCccccCcC-------CCCcCCCCCCCC
Confidence 345667789999986 36789999984 5666662111 237799997643
No 102
>PF08479 POTRA_2: POTRA domain, ShlB-type; InterPro: IPR013686 The POTRA domain (for polypeptide-transport-associated domain) is found towards the N terminus of ShlB family proteins (IPR005565 from INTERPRO). ShlB is important in the secretion and activation of the haemolysin ShlA. It has been postulated that the POTRA domain has a chaperone-like function over ShlA; it may fold back into the C-terminal beta-barrel channel []. ; PDB: 2X8X_X 2QDZ_A 3NJT_A 3MC8_A 3MC9_B.
Probab=20.29 E-value=1.3e+02 Score=21.92 Aligned_cols=35 Identities=11% Similarity=0.346 Sum_probs=28.2
Q ss_pred CCCCCCHHHHHhhhhhhhhH--HHHHhhHHHHHHHhh
Q 025377 6 GYNPRTVEEVFGDFKGRRAG--MIKALTTEVEEFYHQ 40 (253)
Q Consensus 6 ~~~~~~~~~~f~d~~~rr~~--~~~alt~d~~~f~~~ 40 (253)
..++..++.+++.|.||.-+ =+.+|+..+.++|..
T Consensus 13 ~~~~~~l~~~~~~~~g~~l~~~~l~~~~~~l~~~y~~ 49 (76)
T PF08479_consen 13 LLPEEELQAILAPYIGRCLTLADLQQLADALTNYYRE 49 (76)
T ss_dssp SSSCCHHHHHHGGGTTSBB-HHHHHHHHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHhcCCCcCHHHHHHHHHHHHHHHHH
Confidence 34567899999999999854 478899999999974
Done!