Query 026373
Match_columns 239
No_of_seqs 294 out of 1160
Neff 4.9
Searched_HMMs 46136
Date Fri Mar 29 07:11:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026373.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026373hhsearch_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 2.5E-88 5.5E-93 549.2 10.0 129 8-136 1-131 (137)
2 KOG1632 Uncharacterized PHD Zn 100.0 6.1E-41 1.3E-45 312.3 -1.8 230 5-234 35-294 (345)
3 KOG1973 Chromatin remodeling p 99.1 6.5E-11 1.4E-15 107.7 6.2 51 180-236 216-269 (274)
4 PF00628 PHD: PHD-finger; Int 99.1 2.3E-11 5.1E-16 83.3 0.1 50 185-235 1-51 (51)
5 COG5034 TNG2 Chromatin remodel 99.0 4.4E-10 9.5E-15 101.5 4.8 50 181-235 218-270 (271)
6 smart00249 PHD PHD zinc finger 98.9 8E-10 1.7E-14 72.3 3.6 47 185-232 1-47 (47)
7 KOG4323 Polycomb-like PHD Zn-f 97.7 1.6E-05 3.5E-10 77.5 1.9 51 186-237 171-226 (464)
8 KOG1632 Uncharacterized PHD Zn 97.3 7.5E-05 1.6E-09 70.5 1.1 50 185-235 62-113 (345)
9 KOG1844 PHD Zn-finger proteins 97.2 0.00025 5.4E-09 68.7 3.0 52 181-235 84-135 (508)
10 PF13831 PHD_2: PHD-finger; PD 96.7 0.00033 7.2E-09 45.8 -0.3 35 197-233 2-36 (36)
11 KOG0825 PHD Zn-finger protein 96.6 0.0013 2.8E-08 68.0 2.6 53 180-234 212-265 (1134)
12 KOG1512 PHD Zn-finger protein 96.4 0.0014 3E-08 61.1 1.2 45 185-233 316-361 (381)
13 KOG0955 PHD finger protein BR1 96.2 0.0032 7E-08 67.0 3.3 58 179-239 215-273 (1051)
14 KOG2752 Uncharacterized conser 95.7 0.0056 1.2E-07 57.5 2.0 34 182-216 127-166 (345)
15 KOG0383 Predicted helicase [Ge 95.6 0.0056 1.2E-07 62.8 1.7 51 178-233 42-92 (696)
16 KOG4299 PHD Zn-finger protein 95.5 0.0051 1.1E-07 61.9 0.9 51 183-235 253-305 (613)
17 KOG0954 PHD finger protein [Ge 95.3 0.0087 1.9E-07 61.6 1.8 50 182-234 270-320 (893)
18 KOG1244 Predicted transcriptio 95.2 0.01 2.2E-07 55.1 1.8 48 185-234 283-330 (336)
19 KOG0957 PHD finger protein [Ge 95.1 0.02 4.4E-07 56.9 3.8 50 184-233 120-177 (707)
20 PF07227 DUF1423: Protein of u 95.1 0.021 4.5E-07 55.9 3.6 54 182-235 127-192 (446)
21 PF07496 zf-CW: CW-type Zinc F 94.7 0.016 3.5E-07 40.2 1.4 33 198-231 2-34 (50)
22 KOG1245 Chromatin remodeling c 94.1 0.0096 2.1E-07 65.3 -1.3 54 181-236 1106-1159(1404)
23 KOG0957 PHD finger protein [Ge 93.9 0.051 1.1E-06 54.2 3.5 51 182-233 543-596 (707)
24 KOG4443 Putative transcription 93.6 0.0098 2.1E-07 60.4 -2.0 51 183-233 145-200 (694)
25 PF13639 zf-RING_2: Ring finge 91.4 0.05 1.1E-06 35.9 -0.3 43 185-233 2-44 (44)
26 PF14446 Prok-RING_1: Prokaryo 91.3 0.16 3.5E-06 36.3 2.2 34 182-215 4-37 (54)
27 KOG1512 PHD Zn-finger protein 89.4 0.13 2.8E-06 48.3 0.5 53 181-233 256-315 (381)
28 COG5141 PHD zinc finger-contai 86.8 0.27 5.8E-06 49.2 0.9 49 182-233 192-241 (669)
29 PF13832 zf-HC5HC2H_2: PHD-zin 86.2 0.41 8.8E-06 37.3 1.5 32 182-216 54-87 (110)
30 KOG0956 PHD finger protein AF1 85.6 0.44 9.5E-06 49.3 1.7 47 185-234 7-56 (900)
31 PF07649 C1_3: C1-like domain; 85.5 0.36 7.8E-06 29.8 0.7 29 185-214 2-30 (30)
32 PF13901 DUF4206: Domain of un 84.2 0.78 1.7E-05 40.2 2.5 46 183-239 152-202 (202)
33 KOG1473 Nucleosome remodeling 83.0 0.39 8.4E-06 52.0 0.1 59 179-237 1118-1176(1414)
34 KOG1829 Uncharacterized conser 79.4 0.37 8.1E-06 48.8 -1.4 49 182-238 510-562 (580)
35 KOG4443 Putative transcription 79.3 0.57 1.2E-05 48.1 -0.2 54 181-234 16-70 (694)
36 PF12861 zf-Apc11: Anaphase-pr 78.2 1.2 2.5E-05 34.7 1.3 47 185-235 23-80 (85)
37 PF13771 zf-HC5HC2H: PHD-like 77.7 1.6 3.6E-05 32.5 2.0 35 181-218 34-70 (90)
38 PF12678 zf-rbx1: RING-H2 zinc 71.8 2.6 5.6E-05 31.1 1.7 43 186-233 22-73 (73)
39 PF10367 Vps39_2: Vacuolar sor 70.2 3.8 8.3E-05 30.9 2.4 31 183-215 78-108 (109)
40 KOG4628 Predicted E3 ubiquitin 69.3 4 8.6E-05 39.2 2.8 46 184-234 230-275 (348)
41 PF13880 Acetyltransf_13: ESCO 59.9 2 4.4E-05 32.1 -0.9 52 18-89 16-68 (70)
42 KOG4218 Nuclear hormone recept 59.5 4 8.7E-05 39.5 0.8 52 182-233 14-74 (475)
43 PF07775 PaRep2b: PaRep2b prot 59.3 13 0.00029 37.2 4.4 74 18-132 119-197 (512)
44 PF11793 FANCL_C: FANCL C-term 55.8 8.4 0.00018 28.3 1.8 52 184-235 3-64 (70)
45 KOG2626 Histone H3 (Lys4) meth 55.6 12 0.00026 37.8 3.4 53 182-235 19-76 (544)
46 cd04714 BAH_BAHCC1 BAH, or Bro 53.4 7.7 0.00017 31.2 1.4 21 181-202 101-121 (121)
47 PF03107 C1_2: C1 domain; Int 53.2 14 0.0003 22.7 2.3 28 185-214 2-30 (30)
48 KOG1941 Acetylcholine receptor 52.7 1.7 3.7E-05 42.5 -2.8 52 181-236 363-415 (518)
49 PF02318 FYVE_2: FYVE-type zin 52.0 6.6 0.00014 31.4 0.8 49 183-235 54-103 (118)
50 PF00130 C1_1: Phorbol esters/ 50.9 24 0.00051 23.7 3.4 38 182-219 10-48 (53)
51 KOG4299 PHD Zn-finger protein 47.7 15 0.00032 37.8 2.7 49 182-234 46-94 (613)
52 cd00162 RING RING-finger (Real 47.5 6.3 0.00014 24.3 0.0 42 186-234 2-43 (45)
53 PF13717 zinc_ribbon_4: zinc-r 47.5 16 0.00035 23.6 2.0 23 185-207 4-33 (36)
54 PF06783 UPF0239: Uncharacteri 45.4 62 0.0013 25.3 5.2 37 65-132 8-44 (85)
55 smart00109 C1 Protein kinase C 43.3 11 0.00024 24.3 0.7 36 182-217 10-45 (49)
56 PF09416 UPF1_Zn_bind: RNA hel 43.1 15 0.00032 31.5 1.6 26 186-213 3-28 (152)
57 PLN03208 E3 ubiquitin-protein 42.9 17 0.00038 32.2 2.1 51 181-235 16-77 (193)
58 TIGR01562 FdhE formate dehydro 41.9 24 0.00051 33.3 2.9 29 183-211 184-222 (305)
59 KOG3799 Rab3 effector RIM1 and 41.7 11 0.00025 32.0 0.7 53 182-235 64-116 (169)
60 PF09483 HpaP: Type III secret 41.0 23 0.00051 31.2 2.6 71 23-104 95-171 (185)
61 PF14634 zf-RING_5: zinc-RING 40.0 13 0.00029 24.4 0.7 42 186-234 2-44 (44)
62 PF13719 zinc_ribbon_5: zinc-r 39.8 28 0.00061 22.4 2.2 26 184-209 3-35 (37)
63 PF13341 RAG2_PHD: RAG2 PHD do 39.8 15 0.00032 27.9 1.0 35 197-231 28-67 (78)
64 COG5574 PEX10 RING-finger-cont 38.7 22 0.00047 33.1 2.1 45 184-236 216-261 (271)
65 cd00350 rubredoxin_like Rubred 38.5 24 0.00052 22.2 1.7 12 225-236 16-27 (33)
66 PF05402 PqqD: Coenzyme PQQ sy 35.7 39 0.00085 23.6 2.6 33 6-38 28-60 (68)
67 PRK03564 formate dehydrogenase 35.7 38 0.00083 32.0 3.3 52 183-234 187-260 (309)
68 KOG1493 Anaphase-promoting com 35.0 4.8 0.00011 31.0 -2.3 48 185-234 22-78 (84)
69 PRK12775 putative trifunctiona 34.2 38 0.00083 36.6 3.4 54 180-235 793-847 (1006)
70 COG3405 CelA Endoglucanase Y [ 33.7 21 0.00045 34.3 1.1 71 24-124 63-143 (360)
71 COG1773 Rubredoxin [Energy pro 33.6 27 0.00059 25.1 1.5 41 184-234 4-44 (55)
72 PF13111 DUF3962: Protein of u 32.8 31 0.00068 31.0 2.0 34 86-126 24-57 (216)
73 smart00744 RINGv The RING-vari 32.6 18 0.0004 24.7 0.5 45 186-233 2-49 (49)
74 PHA02929 N1R/p28-like protein; 32.3 24 0.00052 32.1 1.3 47 183-234 174-224 (238)
75 TIGR00311 aIF-2beta translatio 32.3 26 0.00057 29.1 1.4 27 182-208 96-127 (133)
76 cd04120 Rab12 Rab12 subfamily. 32.0 25 0.00054 30.3 1.3 14 61-74 184-197 (202)
77 PF10497 zf-4CXXC_R1: Zinc-fin 31.9 42 0.00092 26.6 2.5 52 181-234 5-69 (105)
78 PF08274 PhnA_Zn_Ribbon: PhnA 30.6 24 0.00052 22.3 0.7 10 185-194 4-13 (30)
79 PF09297 zf-NADH-PPase: NADH p 30.5 27 0.00058 21.6 0.9 25 183-207 3-29 (32)
80 smart00653 eIF2B_5 domain pres 30.4 30 0.00064 27.8 1.4 26 182-207 79-109 (110)
81 PRK03988 translation initiatio 30.4 30 0.00064 29.0 1.5 27 182-208 101-132 (138)
82 PF00301 Rubredoxin: Rubredoxi 30.4 45 0.00096 23.0 2.1 13 224-236 32-44 (47)
83 PHA02862 5L protein; Provision 30.2 25 0.00053 30.2 0.9 47 185-234 4-50 (156)
84 PF05180 zf-DNL: DNL zinc fing 30.1 15 0.00034 27.2 -0.2 24 185-208 6-38 (66)
85 PHA03099 epidermal growth fact 29.4 21 0.00045 30.1 0.4 23 27-50 34-56 (139)
86 cd00029 C1 Protein kinase C co 29.1 34 0.00074 22.2 1.3 36 182-217 10-46 (50)
87 PF04810 zf-Sec23_Sec24: Sec23 29.1 34 0.00075 22.4 1.3 32 200-236 3-34 (40)
88 KOG2752 Uncharacterized conser 29.1 33 0.00071 32.9 1.6 52 183-238 53-104 (345)
89 KOG1952 Transcription factor N 27.8 47 0.001 35.7 2.7 54 181-234 189-244 (950)
90 KOG0320 Predicted E3 ubiquitin 27.5 69 0.0015 28.4 3.3 47 182-235 130-176 (187)
91 KOG3277 Uncharacterized conser 26.5 38 0.00081 29.4 1.4 32 184-215 80-129 (165)
92 PRK04023 DNA polymerase II lar 26.3 52 0.0011 36.1 2.7 46 179-235 622-672 (1121)
93 PF01873 eIF-5_eIF-2B: Domain 26.1 38 0.00083 27.8 1.4 24 184-207 94-122 (125)
94 PF09065 Haemadin: Haemadin; 26.0 30 0.00066 21.1 0.6 8 44-51 5-12 (27)
95 PF07282 OrfB_Zn_ribbon: Putat 25.2 76 0.0016 22.4 2.7 32 182-213 27-60 (69)
96 COG2888 Predicted Zn-ribbon RN 24.8 78 0.0017 23.3 2.6 49 183-235 9-59 (61)
97 smart00432 MADS MADS domain. 24.6 87 0.0019 22.4 2.8 37 16-57 19-55 (59)
98 KOG2879 Predicted E3 ubiquitin 24.2 56 0.0012 30.8 2.2 47 182-234 238-284 (298)
99 PF07191 zinc-ribbons_6: zinc- 24.1 39 0.00085 25.4 1.0 51 184-234 2-58 (70)
100 PRK12336 translation initiatio 23.6 44 0.00096 29.3 1.4 28 182-209 97-129 (201)
101 KOG1886 BAH domain proteins [T 23.3 48 0.001 33.1 1.7 44 186-233 173-216 (464)
102 cd00730 rubredoxin Rubredoxin; 23.1 37 0.0008 23.7 0.7 13 224-236 32-44 (50)
103 cd07168 NR_DBD_DHR4_like DNA-b 22.7 53 0.0012 25.2 1.5 32 182-213 5-37 (90)
104 PF13913 zf-C2HC_2: zinc-finge 22.6 43 0.00093 19.8 0.8 13 199-211 2-14 (25)
105 PF08040 NADH_oxidored: MNLL s 22.5 67 0.0015 23.5 1.9 29 91-119 4-35 (59)
106 COG2835 Uncharacterized conser 22.2 67 0.0015 23.5 1.9 29 183-211 8-38 (60)
107 PF05876 Terminase_GpA: Phage 21.4 58 0.0013 32.8 1.9 39 196-234 197-237 (557)
108 PF12773 DZR: Double zinc ribb 21.3 65 0.0014 21.3 1.6 25 183-207 12-37 (50)
109 PF12172 DUF35_N: Rubredoxin-l 21.0 62 0.0013 20.5 1.3 15 196-210 7-22 (37)
110 TIGR00686 phnA alkylphosphonat 21.0 55 0.0012 26.7 1.3 28 184-211 3-32 (109)
111 KOG1473 Nucleosome remodeling 20.9 72 0.0016 35.5 2.5 53 176-233 337-389 (1414)
112 PRK11788 tetratricopeptide rep 20.8 74 0.0016 28.7 2.3 25 182-208 353-377 (389)
113 PF08429 PLU-1: PLU-1-like pro 20.4 57 0.0012 29.9 1.5 69 63-131 243-335 (335)
114 CHL00174 accD acetyl-CoA carbo 20.3 41 0.00088 31.7 0.5 32 195-234 34-65 (296)
115 PF09447 Cnl2_NKP2: Cnl2/NKP2 20.3 1.4E+02 0.0031 22.1 3.3 29 9-37 38-66 (67)
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=2.5e-88 Score=549.24 Aligned_cols=129 Identities=82% Similarity=1.410 Sum_probs=127.9
Q ss_pred CCHHHHHHHHhhhHHHHHHHhhhcHHHhhhcCCcCCCceeeccCCCCceeeeCCCccCCCCCCCcccCccccccccccch
Q 026373 8 RTVEEIYKDFCARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFARDGMNRKD 87 (239)
Q Consensus 8 ~~~~~~~~~~~~rr~~~~~alt~~~~~~~~~c~~~~~~l~lyg~~~~~w~v~~~~~~~p~~lpep~lgin~~rd~m~~~~ 87 (239)
||||+||+||++||+|||||||+|||+||+||||+||||||||+|||+|||+||+||||||||||+||||||||||+|+|
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 hhhhhhhhhcHHHHHHHHHHhhc--cChHHHHHHHHhhhcCCceeeeeccc
Q 026373 88 WLSLVAVHTDSWLLSVAFYLGAR--LNRNERKRLFSLINDQPTVFEVVTER 136 (239)
Q Consensus 88 wl~~vavh~d~wl~~~a~~~~a~--~~~~~r~rlf~miNdlPTv~Evvtgk 136 (239)
||||||||||+|||+|||||||| |++++|+|||+|||+||||||||+|+
T Consensus 81 WLslVAvHsDsWLlsvAfy~gar~~~~~~~R~rLF~mIN~lpTv~Evv~g~ 131 (137)
T PF12165_consen 81 WLSLVAVHSDSWLLSVAFYFGARFGFDKNERKRLFSMINDLPTVFEVVTGR 131 (137)
T ss_pred HHHHHHHhccHHHHHHHHHHHHhhccChHHHHHHHHHHhcCchHHHHHhcc
Confidence 99999999999999999999999 79999999999999999999999994
No 2
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=100.00 E-value=6.1e-41 Score=312.33 Aligned_cols=230 Identities=38% Similarity=0.633 Sum_probs=195.7
Q ss_pred CCCCCHHHHHHHHhhhHHHHHHHhhhcHHHhhhcCCc----CCCceeeccCCCCceeeeCCCccCCCCCCCcccCccccc
Q 026373 5 SSPRTVEEIYKDFCARRAGVVRALTNDVDEFYGLCDP----DKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFAR 80 (239)
Q Consensus 5 ~~~~~~~~~~~~~~~rr~~~~~alt~~~~~~~~~c~~----~~~~l~lyg~~~~~w~v~~~~~~~p~~lpep~lgin~~r 80 (239)
+.+++|+++|.+|++||++++.||+.++..||.+||| .++|+|+|+++++.|+|++|++++|+++|++.+|||+|+
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 6789999999999999999999999999999999999 789999999999999999999999999999999999999
Q ss_pred cccccchhhhhhhhhhcHHHHHHHHHHhhcc-------ChHHHHHHHHhhhcCCceeeeeccc----CCCCCCCCCCCCC
Q 026373 81 DGMNRKDWLSLVAVHTDSWLLSVAFYLGARL-------NRNERKRLFSLINDQPTVFEVVTER----KPIKDKPSVDSSS 149 (239)
Q Consensus 81 d~m~~~~wl~~vavh~d~wl~~~a~~~~a~~-------~~~~r~rlf~miNdlPTv~Evvtgk----Kq~k~k~s~~sss 149 (239)
|+|+.+|||+++++|+++|+++++||||+++ .+..|+|+|.++|++|||++++++. ...+.++++++++
T Consensus 115 ~~~~~~~~l~~~~~~~~~~~~s~s~~~~~~~~~~~~~~~~~~~~r~~~~~~~~~t~~~~~~~~~~~~~~~k~~~~~~~~~ 194 (345)
T KOG1632|consen 115 DGMSESDGLSCVCRQDDSELLSPSFYFGKRGCQFWVKLQKLGRVRLEAEKNDDPTVFEVVSGTATGELPSKDKSSNDRGS 194 (345)
T ss_pred hhhhhhccceeecccccccccccccccCCccccccccchhhhhhhhhhhhcccchhhhcccccccccccccccccccccc
Confidence 9999999999999999999999999999995 8899999999999999999999993 2455566666665
Q ss_pred CCCCCCCCCCCCCCC--CCCCCC----CC-----CCCCCcccCCCceecccCCCCCCCCCeEeccCCCCeeeccccccCc
Q 026373 150 KSRGSTKRSNDGQVK--SNPKLA----DE-----SFDDEEDEHSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITP 218 (239)
Q Consensus 150 ksksssKr~s~~~~k--~~k~~~----eE-----~~eeeeee~~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~ 218 (239)
++.++.++....... ..+-.. .+ ..+.+..+.+...|..||..+..+.+||.|+.|..|||+.|+.+++
T Consensus 195 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~ 274 (345)
T KOG1632|consen 195 KSKTRKKRNRESELEEKKRKHFSNEELTEPAREPVDESEAPDYSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFE 274 (345)
T ss_pred eecccCcccccchhhhhhhhhccCcccccccccCCCcccccccccccccccCcchHHHHHHHHHHHHHHHhccccccccc
Confidence 555554432222111 111111 11 2234455677788989999887678999999999999999999999
Q ss_pred cccCCCCc----EEcCCCcc
Q 026373 219 AKAENIKQ----YKCPSCSM 234 (239)
Q Consensus 219 ~~a~~i~~----y~Cp~C~~ 234 (239)
+....+.. |+|+.|..
T Consensus 275 a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 275 ARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred chhhhhhhhccceecCceee
Confidence 98888888 99999985
No 3
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=99.13 E-value=6.5e-11 Score=107.73 Aligned_cols=51 Identities=31% Similarity=0.767 Sum_probs=40.0
Q ss_pred cCCCceecccCCCCCCCCCeEeccC--CC-CeeeccccccCccccCCCCcEEcCCCcccc
Q 026373 180 EHSETLCGSCGGNYNADEFWIGCDI--CE-RWFHGKCVKITPAKAENIKQYKCPSCSMKR 236 (239)
Q Consensus 180 e~~~~~C~~C~~~~~~d~~mIqCD~--C~-~WfH~~CVgit~~~a~~i~~y~Cp~C~~Kr 236 (239)
.++.++| +|.+.. .+.||.||. |. .|||+.||||+.++. ++|+|+.|....
T Consensus 216 ~~e~~yC-~Cnqvs--yg~Mi~CDn~~C~~eWFH~~CVGL~~~Pk---gkWyC~~C~~~~ 269 (274)
T KOG1973|consen 216 PDEPTYC-ICNQVS--YGKMIGCDNPGCPIEWFHFTCVGLKTKPK---GKWYCPRCKAEN 269 (274)
T ss_pred CCCCEEE-Eecccc--cccccccCCCCCCcceEEEeccccccCCC---Ccccchhhhhhh
Confidence 3445555 998553 679999996 99 999999999996543 569999998654
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=99.06 E-value=2.3e-11 Score=83.26 Aligned_cols=50 Identities=36% Similarity=0.862 Sum_probs=40.1
Q ss_pred eecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCC-CcEEcCCCccc
Q 026373 185 LCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENI-KQYKCPSCSMK 235 (239)
Q Consensus 185 ~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i-~~y~Cp~C~~K 235 (239)
+|.+|++. .+++.||+||.|+.|||..|++++....... ..|+|+.|..|
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 4588999999999999999999986533221 37999999764
No 5
>COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.98 E-value=4.4e-10 Score=101.54 Aligned_cols=50 Identities=28% Similarity=0.682 Sum_probs=39.8
Q ss_pred CCCceecccCCCCCCCCCeEecc--CCC-CeeeccccccCccccCCCCcEEcCCCccc
Q 026373 181 HSETLCGSCGGNYNADEFWIGCD--ICE-RWFHGKCVKITPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~d~~mIqCD--~C~-~WfH~~CVgit~~~a~~i~~y~Cp~C~~K 235 (239)
.++.++|.|++.. -+.||.|| .|+ .|||..|||+..++. ..|+|+.|...
T Consensus 218 e~e~lYCfCqqvS--yGqMVaCDn~nCkrEWFH~~CVGLk~pPK---G~WYC~eCk~~ 270 (271)
T COG5034 218 EGEELYCFCQQVS--YGQMVACDNANCKREWFHLECVGLKEPPK---GKWYCPECKKA 270 (271)
T ss_pred cCceeEEEecccc--cccceecCCCCCchhheeccccccCCCCC---CcEeCHHhHhc
Confidence 4444555999975 46999999 898 999999999976532 57999999753
No 6
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.69 E-value=1.6e-05 Score=77.49 Aligned_cols=51 Identities=27% Similarity=0.730 Sum_probs=37.0
Q ss_pred eccc--CCCCCCCCCeEeccCCCCeeeccccc--cCccccCCC-CcEEcCCCccccC
Q 026373 186 CGSC--GGNYNADEFWIGCDICERWFHGKCVK--ITPAKAENI-KQYKCPSCSMKRG 237 (239)
Q Consensus 186 C~~C--~~~~~~d~~mIqCD~C~~WfH~~CVg--it~~~a~~i-~~y~Cp~C~~Kr~ 237 (239)
|++| +.+.. ...||||+.|..|||..|.. ++...+.+. -.|+|..|..+..
T Consensus 171 c~vC~~g~~~~-~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~ 226 (464)
T KOG4323|consen 171 CSVCYCGGPGA-GNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPK 226 (464)
T ss_pred eeeeecCCcCc-cceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchh
Confidence 5555 45543 44899999999999999988 344444433 3799999997543
No 8
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.32 E-value=7.5e-05 Score=70.53 Aligned_cols=50 Identities=30% Similarity=0.810 Sum_probs=45.2
Q ss_pred eecccCCCCCCCCCeEeccCCCCeeeccc--cccCccccCCCCcEEcCCCccc
Q 026373 185 LCGSCGGNYNADEFWIGCDICERWFHGKC--VKITPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 185 ~C~~C~~~~~~d~~mIqCD~C~~WfH~~C--Vgit~~~a~~i~~y~Cp~C~~K 235 (239)
+| .|..+++++.+|++||.|..|||+.| ||+....+..+..|+|..|..-
T Consensus 62 ~~-~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~ 113 (345)
T KOG1632|consen 62 YC-KCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEA 113 (345)
T ss_pred hh-hcccccCchhhhhccccccccccccccccCchhhcCCccccccccccchh
Confidence 45 89998887779999999999999999 9999998999999999999753
No 9
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=97.17 E-value=0.00025 Score=68.67 Aligned_cols=52 Identities=27% Similarity=0.689 Sum_probs=43.0
Q ss_pred CCCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCccc
Q 026373 181 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~K 235 (239)
.....| .|+..++.+++||||+.|..|.|.-|+|+..... ++.|.|..|..+
T Consensus 84 ~~~~~c-~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~--p~~y~c~~c~~~ 135 (508)
T KOG1844|consen 84 REISRC-DCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK--PDKYVCEICTPR 135 (508)
T ss_pred Cccccc-ccccccCCCceeeCCcccCcccCceeeeecCCCC--chhceeeeeccc
Confidence 355667 9998875478999999999999999999876543 578999999854
No 10
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.72 E-value=0.00033 Score=45.82 Aligned_cols=35 Identities=20% Similarity=0.543 Sum_probs=19.7
Q ss_pred CCeEeccCCCCeeeccccccCccccCCCCcEEcCCCc
Q 026373 197 EFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 233 (239)
Q Consensus 197 ~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~ 233 (239)
..+|+|+.|...+|.+|-|+...... +.|+|..|.
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 47999999999999999999876433 459998874
No 11
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.59 E-value=0.0013 Score=68.00 Aligned_cols=53 Identities=21% Similarity=0.640 Sum_probs=42.2
Q ss_pred cCCCceecccCCCCCCCCCeEeccCCCCe-eeccccccCccccCCCCcEEcCCCcc
Q 026373 180 EHSETLCGSCGGNYNADEFWIGCDICERW-FHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 180 e~~~~~C~~C~~~~~~d~~mIqCD~C~~W-fH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
....+.|-+|..++. .+.||.||.|..- ||..|+....-+.. +..|+|+.|..
T Consensus 212 ~~E~~~C~IC~~~Dp-EdVLLLCDsCN~~~YH~YCLDPdl~eiP-~~eWYC~NC~d 265 (1134)
T KOG0825|consen 212 SQEEVKCDICTVHDP-EDVLLLCDSCNKVYYHVYCLDPDLSESP-VNEWYCTNCSL 265 (1134)
T ss_pred ccccccceeeccCCh-HHhheeecccccceeeccccCccccccc-ccceecCcchh
Confidence 345677999998864 7899999999976 99999998654333 35699999974
No 12
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.36 E-value=0.0014 Score=61.14 Aligned_cols=45 Identities=29% Similarity=0.657 Sum_probs=36.4
Q ss_pred eecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcC-CCc
Q 026373 185 LCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCP-SCS 233 (239)
Q Consensus 185 ~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp-~C~ 233 (239)
+|-+|++|.- .+.|+.||.|++-||.-|||+..-+. ..|+|. .|.
T Consensus 316 lC~IC~~P~~-E~E~~FCD~CDRG~HT~CVGL~~lP~---G~WICD~~C~ 361 (381)
T KOG1512|consen 316 LCRICLGPVI-ESEHLFCDVCDRGPHTLCVGLQDLPR---GEWICDMRCR 361 (381)
T ss_pred hhhccCCccc-chheeccccccCCCCccccccccccC---ccchhhhHHH
Confidence 4778899876 67899999999999999999975432 569998 354
No 13
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=96.24 E-value=0.0032 Score=66.97 Aligned_cols=58 Identities=21% Similarity=0.359 Sum_probs=45.4
Q ss_pred ccCCCceecccCCCCCC-CCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCccccCCC
Q 026373 179 DEHSETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKRGRQ 239 (239)
Q Consensus 179 ee~~~~~C~~C~~~~~~-d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~Kr~r~ 239 (239)
+.+.+..|++|...... ...-|.||.|+.-+|..|+|+.... -..|.|-.|....+|.
T Consensus 215 ~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~ip---eg~WlCr~Cl~s~~~~ 273 (1051)
T KOG0955|consen 215 LLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFIP---EGQWLCRRCLQSPQRP 273 (1051)
T ss_pred ccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCCC---CCcEeehhhccCcCcc
Confidence 33566789999875432 3689999999999999999976542 2579999999887763
No 14
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=95.71 E-value=0.0056 Score=57.54 Aligned_cols=34 Identities=32% Similarity=0.913 Sum_probs=28.0
Q ss_pred CCceecccCCCCCC-----CCCeEeccCCCCeee-cccccc
Q 026373 182 SETLCGSCGGNYNA-----DEFWIGCDICERWFH-GKCVKI 216 (239)
Q Consensus 182 ~~~~C~~C~~~~~~-----d~~mIqCD~C~~WfH-~~CVgi 216 (239)
...+| .|..+|++ ++.|+||-+|+.||| -.|...
T Consensus 127 qG~~C-~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~~ 166 (345)
T KOG2752|consen 127 QGLFC-KCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQA 166 (345)
T ss_pred cceeE-EecCCCCCccccccceeeeEEeccchhcccccCcc
Confidence 45566 99999976 688999999999999 677643
No 15
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=95.60 E-value=0.0056 Score=62.81 Aligned_cols=51 Identities=25% Similarity=0.599 Sum_probs=40.0
Q ss_pred cccCCCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCc
Q 026373 178 EDEHSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 233 (239)
Q Consensus 178 eee~~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~ 233 (239)
.++...-.|++|+.. +..|.||.|..|||..|.+......+... |+|+.|.
T Consensus 42 ~~~~~~e~c~ic~~~----g~~l~c~tC~~s~h~~cl~~pl~~~p~~~-~~c~Rc~ 92 (696)
T KOG0383|consen 42 WDDAEQEACRICADG----GELLWCDTCPASFHASCLGPPLTPQPNGE-FICPRCF 92 (696)
T ss_pred cchhhhhhhhhhcCC----CcEEEeccccHHHHHHccCCCCCcCCccc-eeeeeec
Confidence 345566679999764 46778999999999999998766555545 9999995
No 16
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=95.47 E-value=0.0051 Score=61.93 Aligned_cols=51 Identities=33% Similarity=0.734 Sum_probs=39.1
Q ss_pred CceecccCCCCCCCCCeEeccCCCCeeeccccccC--ccccCCCCcEEcCCCccc
Q 026373 183 ETLCGSCGGNYNADEFWIGCDICERWFHGKCVKIT--PAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 183 ~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit--~~~a~~i~~y~Cp~C~~K 235 (239)
+.+|..|++... -...|+||.|..-||..|+.-. ....+ .+.|+|+.|.-+
T Consensus 253 ~~fCsaCn~~~~-F~~~i~CD~Cp~sFH~~CLePPl~~eniP-~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGL-FNDIICCDGCPRSFHQTCLEPPLEPENIP-PGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCccc-cccceeecCCchHHHHhhcCCCCCcccCC-CCccccCCCeee
Confidence 559999999854 1335999999999999999865 33333 257999999754
No 17
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=95.28 E-value=0.0087 Score=61.59 Aligned_cols=50 Identities=20% Similarity=0.567 Sum_probs=41.8
Q ss_pred CCceecccCCCCCC-CCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 182 SETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 182 ~~~~C~~C~~~~~~-d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
++.+|-+|..++.+ ...||.||.|..=.|..|.||..... +.|.|..|..
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 66789999988654 56899999999999999999986532 5699999874
No 18
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=95.20 E-value=0.01 Score=55.11 Aligned_cols=48 Identities=27% Similarity=0.647 Sum_probs=37.2
Q ss_pred eecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 185 LCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 185 ~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
.|.+||...+ ++..+.||.|++-||.-|+..+-...+. ..|.|..|..
T Consensus 283 ~csicgtsen-ddqllfcddcdrgyhmyclsppm~eppe-gswsc~KOG~ 330 (336)
T KOG1244|consen 283 YCSICGTSEN-DDQLLFCDDCDRGYHMYCLSPPMVEPPE-GSWSCHLCLE 330 (336)
T ss_pred eeccccCcCC-CceeEeecccCCceeeEecCCCcCCCCC-CchhHHHHHH
Confidence 4668888776 6789999999999999999854432222 5799999974
No 19
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=95.11 E-value=0.02 Score=56.93 Aligned_cols=50 Identities=18% Similarity=0.436 Sum_probs=36.6
Q ss_pred ceecccC-CCCCCCCCeEeccCCCCeeeccccccCcc-----ccC--CCCcEEcCCCc
Q 026373 184 TLCGSCG-GNYNADEFWIGCDICERWFHGKCVKITPA-----KAE--NIKQYKCPSCS 233 (239)
Q Consensus 184 ~~C~~C~-~~~~~d~~mIqCD~C~~WfH~~CVgit~~-----~a~--~i~~y~Cp~C~ 233 (239)
.+||+|- +...+-+..||||.|+-=.|-.|.|+... ... ....|+|..|.
T Consensus 120 ~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~ 177 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACL 177 (707)
T ss_pred eEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHh
Confidence 4899994 44444578999999999999999998722 111 12579998886
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=95.07 E-value=0.021 Score=55.87 Aligned_cols=54 Identities=26% Similarity=0.686 Sum_probs=36.5
Q ss_pred CCceecccCCCCCC--CCCeEeccCCCCeeecccc--------ccCccc--cCCCCcEEcCCCccc
Q 026373 182 SETLCGSCGGNYNA--DEFWIGCDICERWFHGKCV--------KITPAK--AENIKQYKCPSCSMK 235 (239)
Q Consensus 182 ~~~~C~~C~~~~~~--d~~mIqCD~C~~WfH~~CV--------git~~~--a~~i~~y~Cp~C~~K 235 (239)
..+-|++|++-+.. .-.||.||.|+.|=|..|. |.+... ......|+|..|.++
T Consensus 127 ~~C~C~iC~kfD~~~n~~~Wi~Cd~CgH~cH~dCALr~~~i~~G~s~~g~~g~~d~~f~C~~C~~~ 192 (446)
T PF07227_consen 127 RRCMCCICSKFDDNKNTCSWIGCDVCGHWCHLDCALRHELIGTGPSVKGSIGTLDMQFHCRACGKT 192 (446)
T ss_pred ccCCccccCCcccCCCCeeEEeccCCCceehhhhhcccccccCCccCCCCCccCceEEEccCCCCh
Confidence 45668889874322 4569999999999999994 222111 011237999999865
No 21
>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=94.71 E-value=0.016 Score=40.20 Aligned_cols=33 Identities=24% Similarity=0.773 Sum_probs=17.2
Q ss_pred CeEeccCCCCeeeccccccCccccCCCCcEEcCC
Q 026373 198 FWIGCDICERWFHGKCVKITPAKAENIKQYKCPS 231 (239)
Q Consensus 198 ~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~ 231 (239)
.|||||.|.+|-... .++........+.|+|..
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 699999999998887 444331122234799987
No 22
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=94.06 E-value=0.0096 Score=65.29 Aligned_cols=54 Identities=28% Similarity=0.575 Sum_probs=44.3
Q ss_pred CCCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcccc
Q 026373 181 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKR 236 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~Kr 236 (239)
....+|-+|..... ...|+-||.|..|||.-|.......++ +..|+|+.|+..+
T Consensus 1106 ~~~~~c~~cr~k~~-~~~m~lc~~c~~~~h~~C~rp~~~~~~-~~dW~C~~c~~e~ 1159 (1404)
T KOG1245|consen 1106 AVNALCKVCRRKKQ-DEKMLLCDECLSGFHLFCLRPALSSVP-PGDWMCPSCRKEH 1159 (1404)
T ss_pred cchhhhhhhhhccc-chhhhhhHhhhhhHHHHhhhhhhccCC-cCCccCCccchhh
Confidence 45678999987754 578999999999999999997766554 4679999999755
No 23
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=93.93 E-value=0.051 Score=54.21 Aligned_cols=51 Identities=20% Similarity=0.569 Sum_probs=39.0
Q ss_pred CCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCC---CCcEEcCCCc
Q 026373 182 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAEN---IKQYKCPSCS 233 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~---i~~y~Cp~C~ 233 (239)
-...|++|.+..+ ....++||.|..-||..|+...-.+.+. .--|.|..|.
T Consensus 543 ~~ysCgiCkks~d-QHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 543 MNYSCGICKKSTD-QHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred cceeeeeeccchh-hHHHhhcchhhceeeccccCCccccCcccccCcceeecccc
Confidence 3456999998764 7889999999999999999854433322 1359999993
No 24
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=93.65 E-value=0.0098 Score=60.41 Aligned_cols=51 Identities=37% Similarity=0.830 Sum_probs=39.5
Q ss_pred CceecccCCCCCCCC--CeEeccCCCCeeeccccccCccccC--CCC-cEEcCCCc
Q 026373 183 ETLCGSCGGNYNADE--FWIGCDICERWFHGKCVKITPAKAE--NIK-QYKCPSCS 233 (239)
Q Consensus 183 ~~~C~~C~~~~~~d~--~mIqCD~C~~WfH~~CVgit~~~a~--~i~-~y~Cp~C~ 233 (239)
..+|++|...|...+ .|++|+.|.+|.|+.|.++...... .++ .|.|..|+
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 467889988887644 4699999999999999998654221 123 79999997
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=91.37 E-value=0.05 Score=35.91 Aligned_cols=43 Identities=26% Similarity=0.597 Sum_probs=32.4
Q ss_pred eecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCc
Q 026373 185 LCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 233 (239)
Q Consensus 185 ~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~ 233 (239)
.|++|...+..+..++... |+..||..|+.--... ...||.|+
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 4899999887667777777 9999999998754332 24899985
No 26
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=91.30 E-value=0.16 Score=36.33 Aligned_cols=34 Identities=21% Similarity=0.582 Sum_probs=30.0
Q ss_pred CCceecccCCCCCCCCCeEeccCCCCeeeccccc
Q 026373 182 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVK 215 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVg 215 (239)
....|.+|+++..+++.-|.|..|+.=||..|..
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~~ 37 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCWE 37 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHHh
Confidence 4568999999987788999999999999999973
No 27
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=89.42 E-value=0.13 Score=48.33 Aligned_cols=53 Identities=25% Similarity=0.453 Sum_probs=39.8
Q ss_pred CCCceecccCCCCCC-----CCCeEeccCCCCeeeccccccCccccCCCC--cEEcCCCc
Q 026373 181 HSETLCGSCGGNYNA-----DEFWIGCDICERWFHGKCVKITPAKAENIK--QYKCPSCS 233 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~-----d~~mIqCD~C~~WfH~~CVgit~~~a~~i~--~y~Cp~C~ 233 (239)
.....|++|-..... .+.||.|..|..-+|..|+.+++..+..++ .|.|..|.
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 456678888543211 468999999999999999999988766554 46777775
No 28
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=86.81 E-value=0.27 Score=49.19 Aligned_cols=49 Identities=24% Similarity=0.531 Sum_probs=38.3
Q ss_pred CCceecccCCCCCCC-CCeEeccCCCCeeeccccccCccccCCCCcEEcCCCc
Q 026373 182 SETLCGSCGGNYNAD-EFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 233 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d-~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~ 233 (239)
-+.+|.+|....+++ .-.|-||+|+.-.|..|.||.--+. ..|+|-.|.
T Consensus 192 ~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~pe---G~WlCrkCi 241 (669)
T COG5141 192 FDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLPE---GFWLCRKCI 241 (669)
T ss_pred hhhhhHhccccccCCcceEEEecCcchhhhhhcccceecCc---chhhhhhhc
Confidence 445788898877653 5688999999999999999975421 469998886
No 29
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=86.21 E-value=0.41 Score=37.27 Aligned_cols=32 Identities=28% Similarity=0.660 Sum_probs=27.3
Q ss_pred CCceecccCCCCCCCCCeEeccC--CCCeeecccccc
Q 026373 182 SETLCGSCGGNYNADEFWIGCDI--CERWFHGKCVKI 216 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~--C~~WfH~~CVgi 216 (239)
....|.+|++. .+..|+|.. |..+||..|...
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 56789999987 568999997 999999999743
No 30
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=85.56 E-value=0.44 Score=49.32 Aligned_cols=47 Identities=23% Similarity=0.498 Sum_probs=35.9
Q ss_pred eecccCCCC-CCCCCeEecc--CCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 185 LCGSCGGNY-NADEFWIGCD--ICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 185 ~C~~C~~~~-~~d~~mIqCD--~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
-||+|...- =.+...|-|| .|..-.|..|.||...+. ..|||..|..
T Consensus 7 GCCVCSDErGWaeNPLVYCDG~nCsVAVHQaCYGIvqVPt---GpWfCrKCes 56 (900)
T KOG0956|consen 7 GCCVCSDERGWAENPLVYCDGHNCSVAVHQACYGIVQVPT---GPWFCRKCES 56 (900)
T ss_pred ceeeecCcCCCccCceeeecCCCceeeeehhcceeEecCC---Cchhhhhhhh
Confidence 388996421 1156899999 899999999999976432 5699999973
No 31
>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=85.46 E-value=0.36 Score=29.77 Aligned_cols=29 Identities=24% Similarity=0.786 Sum_probs=12.6
Q ss_pred eecccCCCCCCCCCeEeccCCCCeeecccc
Q 026373 185 LCGSCGGNYNADEFWIGCDICERWFHGKCV 214 (239)
Q Consensus 185 ~C~~C~~~~~~d~~mIqCD~C~~WfH~~CV 214 (239)
.|.+|+++... ..+-.|..|+...|..|+
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 47889988753 577889999999999985
No 32
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=84.16 E-value=0.78 Score=40.20 Aligned_cols=46 Identities=24% Similarity=0.769 Sum_probs=34.5
Q ss_pred CceecccCCC-----CCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCccccCCC
Q 026373 183 ETLCGSCGGN-----YNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKRGRQ 239 (239)
Q Consensus 183 ~~~C~~C~~~-----~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~Kr~r~ 239 (239)
+-+|.+|+.+ .+ ...-++|+.|..-||..|..- . .||.|.+.+.|.
T Consensus 152 GfiCe~C~~~~~IfPF~-~~~~~~C~~C~~v~H~~C~~~--~--------~CpkC~R~~~r~ 202 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQ-IDTTVRCPKCKSVFHKSCFRK--K--------SCPKCARRQKRK 202 (202)
T ss_pred CCCCccCCCCCCCCCCC-CCCeeeCCcCccccchhhcCC--C--------CCCCcHhHhccC
Confidence 4567778753 21 346789999999999999982 1 399999888763
No 33
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=83.00 E-value=0.39 Score=51.95 Aligned_cols=59 Identities=25% Similarity=0.581 Sum_probs=49.8
Q ss_pred ccCCCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCccccC
Q 026373 179 DEHSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKRG 237 (239)
Q Consensus 179 ee~~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~Kr~ 237 (239)
-.....+|.+|..||+++...|-|-.|..|+|..-|.+........-.+.|-.|++-++
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 34567889999999999999999999999999999999877666656788988886543
No 34
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=79.39 E-value=0.37 Score=48.82 Aligned_cols=49 Identities=27% Similarity=0.584 Sum_probs=34.6
Q ss_pred CCceecccCCCCCC----CCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCccccCC
Q 026373 182 SETLCGSCGGNYNA----DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKRGR 238 (239)
Q Consensus 182 ~~~~C~~C~~~~~~----d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~Kr~r 238 (239)
...+|.+|..+.-- .+.-..|+.|..|||.+|...... .||.|.+.+.|
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 45567777443210 344588999999999999887643 29999987655
No 35
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=79.32 E-value=0.57 Score=48.06 Aligned_cols=54 Identities=24% Similarity=0.540 Sum_probs=40.2
Q ss_pred CCCceecccCCCCCC-CCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 181 HSETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~-d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
.....|.+|+....+ .+.|..|..|..-||.-||.+-...+....-|.|+.|+.
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 344567788765433 467999999999999999997555454456699999873
No 36
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=78.24 E-value=1.2 Score=34.69 Aligned_cols=47 Identities=23% Similarity=0.627 Sum_probs=28.4
Q ss_pred eecccCCCCCC---------CCCeEeccCCCCeeecccccc--CccccCCCCcEEcCCCccc
Q 026373 185 LCGSCGGNYNA---------DEFWIGCDICERWFHGKCVKI--TPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 185 ~C~~C~~~~~~---------d~~mIqCD~C~~WfH~~CVgi--t~~~a~~i~~y~Cp~C~~K 235 (239)
.|++|+.++++ ++--|--..|..=||..|+-- ....+ +=.||.|++.
T Consensus 23 ~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~~----~~~CPmCR~~ 80 (85)
T PF12861_consen 23 VCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQSS----KGQCPMCRQP 80 (85)
T ss_pred ceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccccC----CCCCCCcCCe
Confidence 47777666543 111222235999999999873 32222 2489999863
No 37
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=77.75 E-value=1.6 Score=32.47 Aligned_cols=35 Identities=29% Similarity=0.628 Sum_probs=28.2
Q ss_pred CCCceecccCCCCCCCCCeEecc--CCCCeeeccccccCc
Q 026373 181 HSETLCGSCGGNYNADEFWIGCD--ICERWFHGKCVKITP 218 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~d~~mIqCD--~C~~WfH~~CVgit~ 218 (239)
.....|.+|+++ .+-.|+|. .|...||..|.....
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 456689999987 35899998 599999999976543
No 38
>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=71.77 E-value=2.6 Score=31.10 Aligned_cols=43 Identities=28% Similarity=0.559 Sum_probs=27.6
Q ss_pred ecccCCCCCC---------CCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCc
Q 026373 186 CGSCGGNYNA---------DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 233 (239)
Q Consensus 186 C~~C~~~~~~---------d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~ 233 (239)
|++|..+..+ ++..|.=..|+.-||..|+.--.... -.||.|+
T Consensus 22 C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~~~-----~~CP~CR 73 (73)
T PF12678_consen 22 CAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLKQN-----NTCPLCR 73 (73)
T ss_dssp ETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHTTS-----SB-TTSS
T ss_pred ccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHhcC-----CcCCCCC
Confidence 9999887732 23444445799999999997322211 2899985
No 39
>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=70.24 E-value=3.8 Score=30.91 Aligned_cols=31 Identities=26% Similarity=0.426 Sum_probs=23.1
Q ss_pred CceecccCCCCCCCCCeEeccCCCCeeeccccc
Q 026373 183 ETLCGSCGGNYNADEFWIGCDICERWFHGKCVK 215 (239)
Q Consensus 183 ~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVg 215 (239)
+..|.+|+++-....|.+..+ +.-||..|..
T Consensus 78 ~~~C~vC~k~l~~~~f~~~p~--~~v~H~~C~~ 108 (109)
T PF10367_consen 78 STKCSVCGKPLGNSVFVVFPC--GHVVHYSCIK 108 (109)
T ss_pred CCCccCcCCcCCCceEEEeCC--CeEEeccccc
Confidence 346999999887666666644 4889999974
No 40
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=69.34 E-value=4 Score=39.16 Aligned_cols=46 Identities=22% Similarity=0.463 Sum_probs=33.3
Q ss_pred ceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 184 TLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 184 ~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
..|++|-..|..+ .-+.==-|..-||..|+..--.... -+||.|..
T Consensus 230 ~~CaIClEdY~~G-dklRiLPC~H~FH~~CIDpWL~~~r----~~CPvCK~ 275 (348)
T KOG4628|consen 230 DTCAICLEDYEKG-DKLRILPCSHKFHVNCIDPWLTQTR----TFCPVCKR 275 (348)
T ss_pred ceEEEeecccccC-CeeeEecCCCchhhccchhhHhhcC----ccCCCCCC
Confidence 5799999999754 3334377888999999985332211 37999986
No 41
>PF13880 Acetyltransf_13: ESCO1/2 acetyl-transferase
Probab=59.85 E-value=2 Score=32.13 Aligned_cols=52 Identities=29% Similarity=0.523 Sum_probs=40.2
Q ss_pred hhhHHHHHHHhhhcHHHhhhcCCcCCCceeeccCCCCceeeeCCCccCCCCCCCcc-cCccccccccccchhh
Q 026373 18 CARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEVTLPAEEVPPELPEPA-LGINFARDGMNRKDWL 89 (239)
Q Consensus 18 ~~rr~~~~~alt~~~~~~~~~c~~~~~~l~lyg~~~~~w~v~~~~~~~p~~lpep~-lgin~~rd~m~~~~wl 89 (239)
+-||.||...|..=+-+ | -+||..-...+|.. -+|+ -|..||+.+.+..+||
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 46999999999874332 2 36888777777764 4577 8999999999998886
No 42
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=59.53 E-value=4 Score=39.52 Aligned_cols=52 Identities=23% Similarity=0.655 Sum_probs=31.2
Q ss_pred CCceecccCCCCCC-CCCeEeccCCCCee--------eccccccCccccCCCCcEEcCCCc
Q 026373 182 SETLCGSCGGNYNA-DEFWIGCDICERWF--------HGKCVKITPAKAENIKQYKCPSCS 233 (239)
Q Consensus 182 ~~~~C~~C~~~~~~-d~~mIqCD~C~~Wf--------H~~CVgit~~~a~~i~~y~Cp~C~ 233 (239)
.+-.|++||..-.+ --..+.|++|+-.| |..|..-..-..+....-.||.|+
T Consensus 14 l~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CR 74 (475)
T KOG4218|consen 14 LGELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCR 74 (475)
T ss_pred cccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchh
Confidence 33479999975432 12467899998766 455654333323222335788886
No 43
>PF07775 PaRep2b: PaRep2b protein; InterPro: IPR011689 This is a group of proteins, expressed in the crenarchaeon Pyrobaculum aerophilum, whose members are variable in length and level of conservation. The presence of numerous frameshifts and internal stop codons in multiple alignments are thought to indicate that most family members are no longer functional [].
Probab=59.34 E-value=13 Score=37.23 Aligned_cols=74 Identities=28% Similarity=0.583 Sum_probs=57.4
Q ss_pred hhhHHHHHHHhhhcHHHhhhcCCcCCCceeeccCCCCceeeeCCCccCCCCCCCcccCccccccccccchhhhhhhhhhc
Q 026373 18 CARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFARDGMNRKDWLSLVAVHTD 97 (239)
Q Consensus 18 ~~rr~~~~~alt~~~~~~~~~c~~~~~~l~lyg~~~~~w~v~~~~~~~p~~lpep~lgin~~rd~m~~~~wl~~vavh~d 97 (239)
..|++.||+||--++|. |+ | ++.|-|.|-.. +|.|+-.+
T Consensus 119 AErlAsILrAlG~~aEv--------k~----~---g~~W~V~l~Td--------------------------~IaAirh~ 157 (512)
T PF07775_consen 119 AERLASILRALGAEAEV--------KK----Y---GGEWRVVLTTD--------------------------SIAAIRHP 157 (512)
T ss_pred HHHHHHHHHhcCCeeEE--------EE----c---CCeEEEEEEeC--------------------------cchhcccH
Confidence 45899999999877652 11 1 67899997663 34677788
Q ss_pred HHHHHHHHHHhhc-----cChHHHHHHHHhhhcCCceeee
Q 026373 98 SWLLSVAFYLGAR-----LNRNERKRLFSLINDQPTVFEV 132 (239)
Q Consensus 98 ~wl~~~a~~~~a~-----~~~~~r~rlf~miNdlPTv~Ev 132 (239)
.||-+|.-|...- ++.+.+.+|..-|..-|++-|+
T Consensus 158 ewl~AV~~fVeel~~~G~I~~~~~~~L~~~ieaGPN~ve~ 197 (512)
T PF07775_consen 158 EWLEAVRAFVEELHEKGVISEEQYERLLKKIEAGPNVVEI 197 (512)
T ss_pred HHHHHHHHHHHHHhhcccccHHHHHHHHHHHhcCCCCCcc
Confidence 9998887766543 5999999999999999988764
No 44
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=55.77 E-value=8.4 Score=28.26 Aligned_cols=52 Identities=23% Similarity=0.310 Sum_probs=19.3
Q ss_pred ceecccCCCCC--CCCCeEecc--CCCCeeeccccccCc------cccCCCCcEEcCCCccc
Q 026373 184 TLCGSCGGNYN--ADEFWIGCD--ICERWFHGKCVKITP------AKAENIKQYKCPSCSMK 235 (239)
Q Consensus 184 ~~C~~C~~~~~--~d~~mIqCD--~C~~WfH~~CVgit~------~~a~~i~~y~Cp~C~~K 235 (239)
..|++|-.... +...-+-|+ .|..=||..|..--- ...-.+....||.|...
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 234467898 999999999985211 11112235689999863
No 45
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=55.63 E-value=12 Score=37.83 Aligned_cols=53 Identities=23% Similarity=0.558 Sum_probs=36.2
Q ss_pred CCceecccCCCCCCCCCeEeccCCCCeeeccccccCcc---ccCC--CCcEEcCCCccc
Q 026373 182 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPA---KAEN--IKQYKCPSCSMK 235 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~---~a~~--i~~y~Cp~C~~K 235 (239)
..++| .|+...+....-+||-.|.+|||..|.-.... .+.. --.|.|..|...
T Consensus 19 ~~~~~-y~e~~r~l~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 19 QATVC-YCEGERNLGIVELQCSTCLKWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPS 76 (544)
T ss_pred Ccccc-ccccccccCceeeEeeecccccccccccccccccccCCcccceeEEeccccCc
Confidence 44456 89888777778899999999999855433221 1111 136899999854
No 46
>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=53.39 E-value=7.7 Score=31.16 Aligned_cols=21 Identities=29% Similarity=0.653 Sum_probs=18.1
Q ss_pred CCCceecccCCCCCCCCCeEec
Q 026373 181 HSETLCGSCGGNYNADEFWIGC 202 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~d~~mIqC 202 (239)
.+..+| +|..+|+++..||||
T Consensus 101 ~~~d~~-~Ce~~yn~~~~~~~c 121 (121)
T cd04714 101 DGVDFY-YCAGTYNPDTGMLKC 121 (121)
T ss_pred cCCCEE-EEeccCCCCcCcccC
Confidence 355668 999999999999998
No 47
>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=53.20 E-value=14 Score=22.74 Aligned_cols=28 Identities=25% Similarity=0.708 Sum_probs=21.9
Q ss_pred eecccCCCCCCCCC-eEeccCCCCeeecccc
Q 026373 185 LCGSCGGNYNADEF-WIGCDICERWFHGKCV 214 (239)
Q Consensus 185 ~C~~C~~~~~~d~~-mIqCD~C~~WfH~~CV 214 (239)
.|.+|++.-+ ++ .=.|+.|..-.|.+|+
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 3788988764 34 7788999988898885
No 48
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=52.71 E-value=1.7 Score=42.55 Aligned_cols=52 Identities=27% Similarity=0.636 Sum_probs=39.0
Q ss_pred CCCceecccCCCCCCCCCeEeccCCCCeeeccccc-cCccccCCCCcEEcCCCcccc
Q 026373 181 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVK-ITPAKAENIKQYKCPSCSMKR 236 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVg-it~~~a~~i~~y~Cp~C~~Kr 236 (239)
..+.+|+.||+.+.....-+|-=-|..-||.+|.. +-.... .-.||.|++-+
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n~----~rsCP~Crklr 415 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENNG----TRSCPNCRKLR 415 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhCC----CCCCccHHHHH
Confidence 45678999999887666677878899999999987 332222 24899998543
No 49
>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=52.02 E-value=6.6 Score=31.41 Aligned_cols=49 Identities=20% Similarity=0.424 Sum_probs=34.0
Q ss_pred CceecccCCCCCC-CCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCccc
Q 026373 183 ETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 183 ~~~C~~C~~~~~~-d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~K 235 (239)
+..|..|+.+..- ...-..|-.|..-+=.+|....... ..|+|..|.+.
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~~----~~WlC~vC~k~ 103 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKKE----PIWLCKVCQKQ 103 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSSS----CCEEEHHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCCC----CCEEChhhHHH
Confidence 3469899886422 3345899999999888988874322 45999999864
No 50
>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=50.91 E-value=24 Score=23.67 Aligned_cols=38 Identities=26% Similarity=0.498 Sum_probs=27.8
Q ss_pred CCceecccCCCCC-CCCCeEeccCCCCeeeccccccCcc
Q 026373 182 SETLCGSCGGNYN-ADEFWIGCDICERWFHGKCVKITPA 219 (239)
Q Consensus 182 ~~~~C~~C~~~~~-~d~~mIqCD~C~~WfH~~CVgit~~ 219 (239)
..+.|.+|++.-- ....-..|..|+.-.|.+|...-+.
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 4567999998762 2456789999999999999986543
No 51
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=47.74 E-value=15 Score=37.76 Aligned_cols=49 Identities=27% Similarity=0.551 Sum_probs=35.5
Q ss_pred CCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 182 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
..+.|++|.+. +...+|+.|..-||..|.+...........+.|..|..
T Consensus 46 ~~ts~~~~~~~----gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~ 94 (613)
T KOG4299|consen 46 AATSCGICKSG----GNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPK 94 (613)
T ss_pred hhhhcchhhhc----CCccccccCccccchhccCcccCcccccccccccCCCc
Confidence 36679889764 35679999999999999997655333334567776664
No 52
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=47.49 E-value=6.3 Score=24.28 Aligned_cols=42 Identities=19% Similarity=0.404 Sum_probs=27.2
Q ss_pred ecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 186 CGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 186 C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
|.+|..... ..+.-..|+.-||..|+...... ....||.|..
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 678877652 22333458888999998743322 2357999975
No 53
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=47.47 E-value=16 Score=23.55 Aligned_cols=23 Identities=22% Similarity=0.660 Sum_probs=11.9
Q ss_pred eecccCCCCCC-------CCCeEeccCCCC
Q 026373 185 LCGSCGGNYNA-------DEFWIGCDICER 207 (239)
Q Consensus 185 ~C~~C~~~~~~-------d~~mIqCD~C~~ 207 (239)
.|+.|+..|.- .+..++|-.|+.
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 45666554421 345666666653
No 54
>PF06783 UPF0239: Uncharacterised protein family (UPF0239); InterPro: IPR009621 This is a group of transmembrane proteins of unknown function.; GO: 0016021 integral to membrane
Probab=45.43 E-value=62 Score=25.27 Aligned_cols=37 Identities=32% Similarity=0.703 Sum_probs=26.3
Q ss_pred CCCCCCCcccCccccccccccchhhhhhhhhhcHHHHHHHHHHhhccChHHHHHHHHhhhcCCceeee
Q 026373 65 VPPELPEPALGINFARDGMNRKDWLSLVAVHTDSWLLSVAFYLGARLNRNERKRLFSLINDQPTVFEV 132 (239)
Q Consensus 65 ~p~~lpep~lgin~~rd~m~~~~wl~~vavh~d~wl~~~a~~~~a~~~~~~r~rlf~miNdlPTv~Ev 132 (239)
-||+.|||. ++.+ ||--.+|+|| +|++|==|--|+-+
T Consensus 8 sp~ei~Eet--------------~~e~--------llRYGLf~GA---------IFQliCilAiI~~~ 44 (85)
T PF06783_consen 8 SPPEIPEET--------------FFEN--------LLRYGLFVGA---------IFQLICILAIILPI 44 (85)
T ss_pred CCccCCcch--------------HHHH--------HHHHHHHHHH---------HHHHHHHHheeeec
Confidence 488888886 3433 3566789998 78888777777743
No 55
>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=43.34 E-value=11 Score=24.27 Aligned_cols=36 Identities=22% Similarity=0.392 Sum_probs=26.8
Q ss_pred CCceecccCCCCCCCCCeEeccCCCCeeeccccccC
Q 026373 182 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKIT 217 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit 217 (239)
..++|.+|++........+.|..|+.-.|.+|...-
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~v 45 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEKV 45 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCchHHHHHHhhc
Confidence 346799998875422137889999999999998753
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=43.10 E-value=15 Score=31.47 Aligned_cols=26 Identities=27% Similarity=0.838 Sum_probs=16.0
Q ss_pred ecccCCCCCCCCCeEeccCCCCeeeccc
Q 026373 186 CGSCGGNYNADEFWIGCDICERWFHGKC 213 (239)
Q Consensus 186 C~~C~~~~~~d~~mIqCD~C~~WfH~~C 213 (239)
|..||-.. -.-.++|..|++||=..=
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 77788543 358999999999996543
No 57
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=42.85 E-value=17 Score=32.17 Aligned_cols=51 Identities=18% Similarity=0.423 Sum_probs=31.7
Q ss_pred CCCceecccCCCCCCCCCeEeccCCCCeeeccccccCc-------ccc----CCCCcEEcCCCccc
Q 026373 181 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITP-------AKA----ENIKQYKCPSCSMK 235 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~-------~~a----~~i~~y~Cp~C~~K 235 (239)
.++..|++|.....+ ..+ -.|+..|+..|+.--. ... .......||.|+..
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 355779999887642 333 3688899999985210 000 01135689999853
No 58
>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=41.87 E-value=24 Score=33.28 Aligned_cols=29 Identities=28% Similarity=0.721 Sum_probs=19.3
Q ss_pred CceecccCCCC----------CCCCCeEeccCCCCeeec
Q 026373 183 ETLCGSCGGNY----------NADEFWIGCDICERWFHG 211 (239)
Q Consensus 183 ~~~C~~C~~~~----------~~d~~mIqCD~C~~WfH~ 211 (239)
..+|++||..- .++.-+..|-.|+.-+|.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~ 222 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHY 222 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccc
Confidence 44799998642 124568889999855555
No 59
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=41.67 E-value=11 Score=32.02 Aligned_cols=53 Identities=21% Similarity=0.525 Sum_probs=39.7
Q ss_pred CCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCccc
Q 026373 182 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~K 235 (239)
.+.+|.+|.+....|+.---|..|..=|-..|-|--..+... ..|.|..|.+.
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 345799999987667777789999988889998854433322 46999999853
No 60
>PF09483 HpaP: Type III secretion protein (HpaP); InterPro: IPR013390 This entry represents proteins encoded by genes which are always found in type III secretion operons, although their function in the processes of secretion and virulence is unclear []. Hpa stands for Hrp-associated gene, where Hrp stands for hypersensitivity response and virulence.
Probab=41.05 E-value=23 Score=31.16 Aligned_cols=71 Identities=21% Similarity=0.370 Sum_probs=46.9
Q ss_pred HHHHHhhhcHHHhhhcCCcCCCceeeccCCCCceeeeCCCccCCCCCCCcccCccccccccc------cchhhhhhhhhh
Q 026373 23 GVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFARDGMN------RKDWLSLVAVHT 96 (239)
Q Consensus 23 ~~~~alt~~~~~~~~~c~~~~~~l~lyg~~~~~w~v~~~~~~~p~~lpep~lgin~~rd~m~------~~~wl~~vavh~ 96 (239)
.+|..|+..|-.|...=.= ...|+|||.||.. |.-||+-+|.+...+.+|. .-+-=.|+--|+
T Consensus 95 ~~~~~la~eIA~FC~~~aI---------~~aG~We~~l~LD--paiLp~TtL~L~LS~f~LsLRFdt~d~~tr~LL~~h~ 163 (185)
T PF09483_consen 95 RVAEHLAREIAAFCADPAI---------REAGNWEAQLPLD--PAILPETTLNLRLSPFQLSLRFDTRDPETRELLSTHR 163 (185)
T ss_pred HHHHHHHHHHHHHhCCccc---------ccCCcceEeeeCC--hhhccCceEEEEeccceEEEEeeCCChHHHHHHHhhh
Confidence 4678888888888653210 1368899999874 7899999999988877542 111222366676
Q ss_pred cHHHHHHH
Q 026373 97 DSWLLSVA 104 (239)
Q Consensus 97 d~wl~~~a 104 (239)
|..--.+.
T Consensus 164 ~~L~~~L~ 171 (185)
T PF09483_consen 164 DMLRRELE 171 (185)
T ss_pred HHHHHHHH
Confidence 66544443
No 61
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=40.00 E-value=13 Score=24.39 Aligned_cols=42 Identities=31% Similarity=0.619 Sum_probs=28.6
Q ss_pred ecccCCCCCC-CCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 186 CGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 186 C~~C~~~~~~-d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
|.+|.+.|++ ..++|- .|+..|...|+.-.. .....||.|++
T Consensus 2 C~~C~~~~~~~~~~~l~--~CgH~~C~~C~~~~~-----~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLT--SCGHIFCEKCLKKLK-----GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEEc--ccCCHHHHHHHHhhc-----CCCCCCcCCCC
Confidence 7889888833 233433 678888888887654 13468999974
No 62
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=39.83 E-value=28 Score=22.44 Aligned_cols=26 Identities=19% Similarity=0.555 Sum_probs=14.1
Q ss_pred ceecccCCCCCC-------CCCeEeccCCCCee
Q 026373 184 TLCGSCGGNYNA-------DEFWIGCDICERWF 209 (239)
Q Consensus 184 ~~C~~C~~~~~~-------d~~mIqCD~C~~Wf 209 (239)
..|+.|+..|.- .+.++.|-.|+.-|
T Consensus 3 i~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 3 ITCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred EECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 346667654422 34466666666444
No 63
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=39.80 E-value=15 Score=27.93 Aligned_cols=35 Identities=20% Similarity=0.544 Sum_probs=19.0
Q ss_pred CCeEeccC-CCCeeeccccccCcccc----CCCCcEEcCC
Q 026373 197 EFWIGCDI-CERWFHGKCVKITPAKA----ENIKQYKCPS 231 (239)
Q Consensus 197 ~~mIqCD~-C~~WfH~~CVgit~~~a----~~i~~y~Cp~ 231 (239)
--||-|.. =+.|.|..|+.+++... +...+|+|..
T Consensus 28 PAMI~cs~~~GHWvhaqCm~LsE~~L~~LSq~n~KYfC~d 67 (78)
T PF13341_consen 28 PAMIFCSRGGGHWVHAQCMDLSETMLIQLSQENTKYFCND 67 (78)
T ss_dssp --EEEE-STT-EEEETGGGT--HHHHHHHHHSSS-B--TT
T ss_pred ceEEEEeCCCceEeEeecccchHHHHHHHccCCceEEEhh
Confidence 35999984 35999999999887532 2335799865
No 64
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=38.68 E-value=22 Score=33.10 Aligned_cols=45 Identities=31% Similarity=0.555 Sum_probs=29.6
Q ss_pred ceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcE-EcCCCcccc
Q 026373 184 TLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQY-KCPSCSMKR 236 (239)
Q Consensus 184 ~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y-~Cp~C~~Kr 236 (239)
-.|.+|-..-. ---|-.|+.-|-..|+-+.-.. ++| +||.|+.|-
T Consensus 216 ~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t~----~k~~~CplCRak~ 261 (271)
T COG5574 216 YKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWTK----KKYEFCPLCRAKV 261 (271)
T ss_pred cceeeeecccC----CcccccccchhhHHHHHHHHHh----hccccCchhhhhc
Confidence 45989976431 2257788888999998773211 223 699999763
No 65
>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=38.50 E-value=24 Score=22.15 Aligned_cols=12 Identities=25% Similarity=0.922 Sum_probs=8.8
Q ss_pred CcEEcCCCcccc
Q 026373 225 KQYKCPSCSMKR 236 (239)
Q Consensus 225 ~~y~Cp~C~~Kr 236 (239)
..|.||.|...+
T Consensus 16 ~~~~CP~Cg~~~ 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCcCcCCCCcH
Confidence 348999997644
No 66
>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=35.74 E-value=39 Score=23.57 Aligned_cols=33 Identities=33% Similarity=0.412 Sum_probs=23.5
Q ss_pred CCCCHHHHHHHHhhhHHHHHHHhhhcHHHhhhc
Q 026373 6 SPRTVEEIYKDFCARRAGVVRALTNDVDEFYGL 38 (239)
Q Consensus 6 ~~~~~~~~~~~~~~rr~~~~~alt~~~~~~~~~ 38 (239)
.++|+++|-+.+..+=..=...+..||.+|.++
T Consensus 28 g~~t~~ei~~~l~~~y~~~~~~~~~dv~~fl~~ 60 (68)
T PF05402_consen 28 GPRTVEEIVDALAEEYDVDPEEAEEDVEEFLEQ 60 (68)
T ss_dssp SSS-HHHHHHHHHHHTT--HHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 479999999988877655455578899998764
No 67
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.71 E-value=38 Score=32.00 Aligned_cols=52 Identities=23% Similarity=0.624 Sum_probs=28.5
Q ss_pred CceecccCCCC---------CCCCCeEeccCCCCeeec---cccccCcc--------c--cCCCCcEEcCCCcc
Q 026373 183 ETLCGSCGGNY---------NADEFWIGCDICERWFHG---KCVKITPA--------K--AENIKQYKCPSCSM 234 (239)
Q Consensus 183 ~~~C~~C~~~~---------~~d~~mIqCD~C~~WfH~---~CVgit~~--------~--a~~i~~y~Cp~C~~ 234 (239)
..+|++||..- .++.-+..|-.|+.-+|. .|..-... . ...+....|..|..
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 35688887642 124567788888844454 45321110 0 01234578999974
No 68
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=34.96 E-value=4.8 Score=31.04 Aligned_cols=48 Identities=25% Similarity=0.509 Sum_probs=27.6
Q ss_pred eecccCCCCCCCCC-----eEecc----CCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 185 LCGSCGGNYNADEF-----WIGCD----ICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 185 ~C~~C~~~~~~d~~-----mIqCD----~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
.|++|+.++++--. --.|- .|..-||..|+---.. ++ ..+-.||.|++
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~-~~-tsq~~CPmcRq 78 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLN-TP-TSQGQCPMCRQ 78 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhc-Cc-cccccCCcchh
Confidence 79999888764000 00111 4566799999853221 11 13468999986
No 69
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=34.20 E-value=38 Score=36.57 Aligned_cols=54 Identities=28% Similarity=0.565 Sum_probs=39.9
Q ss_pred cCCCceecccCCCCCCCCCeEeccCCC-CeeeccccccCccccCCCCcEEcCCCccc
Q 026373 180 EHSETLCGSCGGNYNADEFWIGCDICE-RWFHGKCVKITPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 180 e~~~~~C~~C~~~~~~d~~mIqCD~C~-~WfH~~CVgit~~~a~~i~~y~Cp~C~~K 235 (239)
+.....|+.|.+|-.+++.+|+|-.-+ .|--..|-.++..-+-. --.||.|..|
T Consensus 793 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 847 (1006)
T PRK12775 793 ETGVATCPKCHRPLEGDEEYVCCATSELQWRCDDCGKVSEGFAFP--YGMCPACGGK 847 (1006)
T ss_pred cCCCccCcccCCCCCCCceeEEecCcceeeehhhhccccccccCC--cCcCcccccc
Confidence 567788999999998889999997554 77777777766543321 1389999864
No 70
>COG3405 CelA Endoglucanase Y [Carbohydrate transport and metabolism]
Probab=33.70 E-value=21 Score=34.27 Aligned_cols=71 Identities=30% Similarity=0.396 Sum_probs=52.2
Q ss_pred HHHHhhhcHHHhhhcCCcCCCceeec----cC------CCCceeeeCCCccCCCCCCCcccCccccccccccchhhhhhh
Q 026373 24 VVRALTNDVDEFYGLCDPDKENLCLY----GH------PNESWEVTLPAEEVPPELPEPALGINFARDGMNRKDWLSLVA 93 (239)
Q Consensus 24 ~~~alt~~~~~~~~~c~~~~~~l~ly----g~------~~~~w~v~~~~~~~p~~lpep~lgin~~rd~m~~~~wl~~va 93 (239)
++-+|..|-+.|++.=+=-++||-.= |+ |+++|+|+ -+|=|-||
T Consensus 63 ~~Av~addk~~F~rIwnwT~~nL~~~~~~dgl~AWlw~p~~~~~v~---------------d~nnAtDG----------- 116 (360)
T COG3405 63 FFAVLADDKDAFDRIWNWTQNNLAQGSLKDGLFAWLWGPKEKGHVL---------------DSNNATDG----------- 116 (360)
T ss_pred HHHHHhCCHHHHHHHHHHHHHHHhhhhhhcCcceeeecCCCCCccc---------------cCCCCCch-----------
Confidence 45667889999999887777777542 22 34455554 57777776
Q ss_pred hhhcHHHHHHHHHHhhccChHHHHHHHHhhh
Q 026373 94 VHTDSWLLSVAFYLGARLNRNERKRLFSLIN 124 (239)
Q Consensus 94 vh~d~wl~~~a~~~~a~~~~~~r~rlf~miN 124 (239)
|.| ++.|.++++++|++++...|+---
T Consensus 117 ---Di~-iA~ALl~As~~Wkd~dyt~~s~A~ 143 (360)
T COG3405 117 ---DIW-IAYALLEASRLWKDQDYTEFSYAL 143 (360)
T ss_pred ---hHH-HHHHHHHHhhhhcccccchhhHHH
Confidence 777 899999999999998888876543
No 71
>COG1773 Rubredoxin [Energy production and conversion]
Probab=33.61 E-value=27 Score=25.11 Aligned_cols=41 Identities=22% Similarity=0.485 Sum_probs=23.5
Q ss_pred ceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 184 TLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 184 ~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
..|.+|+-.|++..-.=.|++| -|..-+.. .+.|.||.|.-
T Consensus 4 ~~C~~CG~vYd~e~Gdp~~gi~--------pgT~fedl--Pd~w~CP~Cg~ 44 (55)
T COG1773 4 WRCSVCGYVYDPEKGDPRCGIA--------PGTPFEDL--PDDWVCPECGV 44 (55)
T ss_pred eEecCCceEeccccCCccCCCC--------CCCchhhC--CCccCCCCCCC
Confidence 3577788777664333333333 23222333 36799999984
No 72
>PF13111 DUF3962: Protein of unknown function (DUF3962)
Probab=32.77 E-value=31 Score=30.99 Aligned_cols=34 Identities=26% Similarity=0.701 Sum_probs=26.5
Q ss_pred chhhhhhhhhhcHHHHHHHHHHhhccChHHHHHHHHhhhcC
Q 026373 86 KDWLSLVAVHTDSWLLSVAFYLGARLNRNERKRLFSLINDQ 126 (239)
Q Consensus 86 ~~wl~~vavh~d~wl~~~a~~~~a~~~~~~r~rlf~miNdl 126 (239)
++|+.||-.|.|.|++-+-+ +.-+.||+.|..|.
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 57999999999999987765 33457788887654
No 73
>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=32.63 E-value=18 Score=24.73 Aligned_cols=45 Identities=16% Similarity=0.443 Sum_probs=25.3
Q ss_pred ecccCCCCCCCCCeEeccCC---CCeeeccccccCccccCCCCcEEcCCCc
Q 026373 186 CGSCGGNYNADEFWIGCDIC---ERWFHGKCVKITPAKAENIKQYKCPSCS 233 (239)
Q Consensus 186 C~~C~~~~~~d~~mIqCD~C---~~WfH~~CVgit~~~a~~i~~y~Cp~C~ 233 (239)
|-+|.....+++.+|.==.| -.|+|..|+.--..... .-.|+.|.
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 56776633335556552123 37999999984322221 12788874
No 74
>PHA02929 N1R/p28-like protein; Provisional
Probab=32.30 E-value=24 Score=32.10 Aligned_cols=47 Identities=21% Similarity=0.518 Sum_probs=29.5
Q ss_pred CceecccCCCCCCCC----CeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 183 ETLCGSCGGNYNADE----FWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 183 ~~~C~~C~~~~~~d~----~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
+..|++|.....+.. ....=-.|+.-||..|+..-... +=.||.|+.
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~~-----~~tCPlCR~ 224 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKKE-----KNTCPVCRT 224 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHhc-----CCCCCCCCC
Confidence 346999987643221 11122368889999999753321 237999985
No 75
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=32.29 E-value=26 Score=29.11 Aligned_cols=27 Identities=15% Similarity=0.421 Sum_probs=18.4
Q ss_pred CCceecccCCCCCC-----CCCeEeccCCCCe
Q 026373 182 SETLCGSCGGNYNA-----DEFWIGCDICERW 208 (239)
Q Consensus 182 ~~~~C~~C~~~~~~-----d~~mIqCD~C~~W 208 (239)
.-++|..|+.|+.. ...++.|+.|+..
T Consensus 96 ~yVlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 96 KYVICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred heEECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 34679999998743 2335678888753
No 76
>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=31.95 E-value=25 Score=30.30 Aligned_cols=14 Identities=57% Similarity=1.151 Sum_probs=12.0
Q ss_pred CCccCCCCCCCccc
Q 026373 61 PAEEVPPELPEPAL 74 (239)
Q Consensus 61 ~~~~~p~~lpep~l 74 (239)
|..|+|||||.|-.
T Consensus 184 ~~~~~~~~~~~~~~ 197 (202)
T cd04120 184 PEPEIPPELPPPRP 197 (202)
T ss_pred CCCCCCcCCCCCCC
Confidence 77899999999864
No 77
>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=31.92 E-value=42 Score=26.64 Aligned_cols=52 Identities=23% Similarity=0.542 Sum_probs=31.2
Q ss_pred CCCceecccCCCCCCCCCeEec------cCC---CCeeeccccc----cCccccCCCCcEEcCCCcc
Q 026373 181 HSETLCGSCGGNYNADEFWIGC------DIC---ERWFHGKCVK----ITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~d~~mIqC------D~C---~~WfH~~CVg----it~~~a~~i~~y~Cp~C~~ 234 (239)
.....|=.|++.-. ++.+.| ..| ..=|=+.|+- ....++-....|.||.|+.
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 34566777877543 244456 566 6667777853 2222222335799999975
No 78
>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=30.55 E-value=24 Score=22.27 Aligned_cols=10 Identities=40% Similarity=1.112 Sum_probs=2.2
Q ss_pred eecccCCCCC
Q 026373 185 LCGSCGGNYN 194 (239)
Q Consensus 185 ~C~~C~~~~~ 194 (239)
-|+.|+..|.
T Consensus 4 ~Cp~C~se~~ 13 (30)
T PF08274_consen 4 KCPLCGSEYT 13 (30)
T ss_dssp --TTT-----
T ss_pred CCCCCCCcce
Confidence 4777776553
No 79
>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=30.48 E-value=27 Score=21.63 Aligned_cols=25 Identities=24% Similarity=0.709 Sum_probs=13.8
Q ss_pred CceecccCCCCC--CCCCeEeccCCCC
Q 026373 183 ETLCGSCGGNYN--ADEFWIGCDICER 207 (239)
Q Consensus 183 ~~~C~~C~~~~~--~d~~mIqCD~C~~ 207 (239)
..+|+.||.+-. .++...+|..|+.
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 458999987642 2567788888864
No 80
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=30.40 E-value=30 Score=27.85 Aligned_cols=26 Identities=27% Similarity=0.764 Sum_probs=18.4
Q ss_pred CCceecccCCCCCC-----CCCeEeccCCCC
Q 026373 182 SETLCGSCGGNYNA-----DEFWIGCDICER 207 (239)
Q Consensus 182 ~~~~C~~C~~~~~~-----d~~mIqCD~C~~ 207 (239)
.-++|..|+.|+.. ...++.|+.|+.
T Consensus 79 ~yVlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 79 EYVLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred hcEECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 34789999998643 344667888874
No 81
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=30.40 E-value=30 Score=28.97 Aligned_cols=27 Identities=19% Similarity=0.546 Sum_probs=19.3
Q ss_pred CCceecccCCCCCC-----CCCeEeccCCCCe
Q 026373 182 SETLCGSCGGNYNA-----DEFWIGCDICERW 208 (239)
Q Consensus 182 ~~~~C~~C~~~~~~-----d~~mIqCD~C~~W 208 (239)
.-.+|..|+.|+.. ...++.|+.|+..
T Consensus 101 ~yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 101 EYVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred hcEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 34789999998743 3356778888754
No 82
>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=30.36 E-value=45 Score=23.01 Aligned_cols=13 Identities=23% Similarity=0.836 Sum_probs=8.0
Q ss_pred CCcEEcCCCcccc
Q 026373 224 IKQYKCPSCSMKR 236 (239)
Q Consensus 224 i~~y~Cp~C~~Kr 236 (239)
.+.|.||.|...+
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 4679999998654
No 83
>PHA02862 5L protein; Provisional
Probab=30.20 E-value=25 Score=30.23 Aligned_cols=47 Identities=21% Similarity=0.498 Sum_probs=27.3
Q ss_pred eecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 185 LCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 185 ~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
.|-+|...++++..-=.|-+--+|.|..|+.---... ..=.|+.|..
T Consensus 4 iCWIC~~~~~e~~~PC~C~GS~K~VHq~CL~~WIn~S---~k~~CeLCkt 50 (156)
T PHA02862 4 ICWICNDVCDERNNFCGCNEEYKVVHIKCMQLWINYS---KKKECNLCKT 50 (156)
T ss_pred EEEEecCcCCCCcccccccCcchhHHHHHHHHHHhcC---CCcCccCCCC
Confidence 4666666554333333355556899999987322211 2347888874
No 84
>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=30.13 E-value=15 Score=27.20 Aligned_cols=24 Identities=25% Similarity=0.727 Sum_probs=15.0
Q ss_pred eecccCC---------CCCCCCCeEeccCCCCe
Q 026373 185 LCGSCGG---------NYNADEFWIGCDICERW 208 (239)
Q Consensus 185 ~C~~C~~---------~~~~d~~mIqCD~C~~W 208 (239)
.|..|+. .|..+.-.|+|+.|+.|
T Consensus 6 TC~~C~~Rs~~~~sk~aY~~GvViv~C~gC~~~ 38 (66)
T PF05180_consen 6 TCNKCGTRSAKMFSKQAYHKGVVIVQCPGCKNR 38 (66)
T ss_dssp EETTTTEEEEEEEEHHHHHTSEEEEE-TTS--E
T ss_pred EcCCCCCccceeeCHHHHhCCeEEEECCCCcce
Confidence 4667764 44447789999999886
No 85
>PHA03099 epidermal growth factor-like protein (EGF-like protein); Provisional
Probab=29.44 E-value=21 Score=30.10 Aligned_cols=23 Identities=35% Similarity=0.793 Sum_probs=20.3
Q ss_pred HhhhcHHHhhhcCCcCCCceeecc
Q 026373 27 ALTNDVDEFYGLCDPDKENLCLYG 50 (239)
Q Consensus 27 alt~~~~~~~~~c~~~~~~l~lyg 50 (239)
--|+|+-+ ++.|.+++.+.||+|
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
>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=29.07 E-value=34 Score=22.16 Aligned_cols=36 Identities=22% Similarity=0.444 Sum_probs=26.8
Q ss_pred CCceecccCCCCCC-CCCeEeccCCCCeeeccccccC
Q 026373 182 SETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKIT 217 (239)
Q Consensus 182 ~~~~C~~C~~~~~~-d~~mIqCD~C~~WfH~~CVgit 217 (239)
..+.|..|++..-. ......|+.|+.-.|.+|...-
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~v 46 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADKV 46 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCchhhhhhccC
Confidence 34578899876542 1466789999999999998753
No 87
>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=29.06 E-value=34 Score=22.37 Aligned_cols=32 Identities=22% Similarity=0.534 Sum_probs=13.7
Q ss_pred EeccCCCCeeeccccccCccccCCCCcEEcCCCcccc
Q 026373 200 IGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKR 236 (239)
Q Consensus 200 IqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~Kr 236 (239)
|.|..|..-.-.-|.-.. ....|.|+.|..+.
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 556666544333332222 22579999998654
No 88
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=29.06 E-value=33 Score=32.86 Aligned_cols=52 Identities=23% Similarity=0.290 Sum_probs=38.7
Q ss_pred CceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCccccCC
Q 026373 183 ETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKRGR 238 (239)
Q Consensus 183 ~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~Kr~r 238 (239)
..+| +|-..+...+.+++|=.|.-|+|..-..+..-. -.+|.|.-|..|-+|
T Consensus 53 Q~l~-sClTC~P~~~~agvC~~C~~~CH~~H~lveL~t---KR~FrCDCg~sk~g~ 104 (345)
T KOG2752|consen 53 QALF-SCLTCTPAPEMAGVCYACSLSCHDGHELVELYT---KRNFRCDCGNSKFGR 104 (345)
T ss_pred ccee-EeecccCChhhceeEEEeeeeecCCceeeeccc---cCCcccccccccccc
Confidence 4566 787777656699999999999999988876432 256888877665443
No 89
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=27.77 E-value=47 Score=35.66 Aligned_cols=54 Identities=20% Similarity=0.503 Sum_probs=38.3
Q ss_pred CCCceecccCCCCCCCCCeEeccCCCCeeeccccccCc--cccCCCCcEEcCCCcc
Q 026373 181 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITP--AKAENIKQYKCPSCSM 234 (239)
Q Consensus 181 ~~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~--~~a~~i~~y~Cp~C~~ 234 (239)
....-|-+|-..-.....+-.|-.|-.-||..|+.--. ......+.|.||.|..
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 44556888866554455667899999999999987422 2233336899999984
No 90
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=27.53 E-value=69 Score=28.37 Aligned_cols=47 Identities=23% Similarity=0.448 Sum_probs=30.7
Q ss_pred CCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCccc
Q 026373 182 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~K 235 (239)
.-.-|++|-..+.. ..+-=-.|+.-|-..|+.-.-. ..-.||.|.+|
T Consensus 130 ~~~~CPiCl~~~se--k~~vsTkCGHvFC~~Cik~alk-----~~~~CP~C~kk 176 (187)
T KOG0320|consen 130 GTYKCPICLDSVSE--KVPVSTKCGHVFCSQCIKDALK-----NTNKCPTCRKK 176 (187)
T ss_pred cccCCCceecchhh--ccccccccchhHHHHHHHHHHH-----hCCCCCCcccc
Confidence 44669999877642 2222247888888888875432 12589999864
No 91
>KOG3277 consensus Uncharacterized conserved protein [Function unknown]
Probab=26.45 E-value=38 Score=29.37 Aligned_cols=32 Identities=28% Similarity=0.666 Sum_probs=23.1
Q ss_pred ceecccCC---------CCCCCCCeEeccCCC---------Ceeeccccc
Q 026373 184 TLCGSCGG---------NYNADEFWIGCDICE---------RWFHGKCVK 215 (239)
Q Consensus 184 ~~C~~C~~---------~~~~d~~mIqCD~C~---------~WfH~~CVg 215 (239)
-.|-+|+. .|..+...|||++|. .|||..=+.
T Consensus 80 yTCkvCntRs~ktisk~AY~~GvVivqC~gC~~~HliaDnL~~F~d~~~~ 129 (165)
T KOG3277|consen 80 YTCKVCNTRSTKTISKQAYEKGVVIVQCPGCKNHHLIADNLGWFHDLKGK 129 (165)
T ss_pred EEeeccCCccccccChhhhhCceEEEECCCCccceeehhhhccccccccc
Confidence 45888975 455577899999995 588775544
No 92
>PRK04023 DNA polymerase II large subunit; Validated
Probab=26.35 E-value=52 Score=36.08 Aligned_cols=46 Identities=24% Similarity=0.602 Sum_probs=30.1
Q ss_pred ccCCCceecccCCCCCCCCCeEeccCCCC-----eeeccccccCccccCCCCcEEcCCCccc
Q 026373 179 DEHSETLCGSCGGNYNADEFWIGCDICER-----WFHGKCVKITPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 179 ee~~~~~C~~C~~~~~~d~~mIqCD~C~~-----WfH~~CVgit~~~a~~i~~y~Cp~C~~K 235 (239)
-+....+|+.||... .+..|..|+. +|-..|-... ..+.||.|..+
T Consensus 622 VEVg~RfCpsCG~~t----~~frCP~CG~~Te~i~fCP~CG~~~-------~~y~CPKCG~E 672 (1121)
T PRK04023 622 VEIGRRKCPSCGKET----FYRRCPFCGTHTEPVYRCPRCGIEV-------EEDECEKCGRE 672 (1121)
T ss_pred ecccCccCCCCCCcC----CcccCCCCCCCCCcceeCccccCcC-------CCCcCCCCCCC
Confidence 345677899999873 6789999985 4445551111 22678888754
No 93
>PF01873 eIF-5_eIF-2B: Domain found in IF2B/IF5; InterPro: IPR002735 The beta subunit of archaeal and eukaryotic translation initiation factor 2 (IF2beta) and the N-terminal domain of translation initiation factor 5 (IF5) show significant sequence homology []. Archaeal IF2beta contains two independent structural domains: an N-terminal mixed alpha/beta core domain (topological similarity to the common core of ribosomal proteins L23 and L15e), and a C-terminal domain consisting of a zinc-binding C4 finger []. Archaeal IF2beta is a ribosome-dependent GTPase that stimulates the binding of initiator Met-tRNA(i)(Met) to the ribosomes, even in the absence of other factors []. The C-terminal domain of eukaryotic IF5 is involved in the formation of the multi-factor complex (MFC), an important intermediate for the 43S pre-initiation complex assembly []. IF5 interacts directly with IF1, IF2beta and IF3c, which together with IF2-bound Met-tRNA(i)(Met) form the MFC. This entry represents both the N-terminal and zinc-binding domains of IF2, as well as a domain in IF5.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 2DCU_B 2D74_B 2E9H_A 2G2K_A 1NEE_A 3CW2_L 2QMU_C 3V11_C 2NXU_A 2QN6_C ....
Probab=26.06 E-value=38 Score=27.77 Aligned_cols=24 Identities=25% Similarity=0.749 Sum_probs=17.5
Q ss_pred ceecccCCCCCC-----CCCeEeccCCCC
Q 026373 184 TLCGSCGGNYNA-----DEFWIGCDICER 207 (239)
Q Consensus 184 ~~C~~C~~~~~~-----d~~mIqCD~C~~ 207 (239)
++|+.|+.|+.. ....+.|+.|+.
T Consensus 94 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 122 (125)
T PF01873_consen 94 VLCPECGSPDTELIKEGRLIFLKCKACGA 122 (125)
T ss_dssp SSCTSTSSSSEEEEEETTCCEEEETTTSC
T ss_pred EEcCCCCCCccEEEEcCCEEEEEecccCC
Confidence 679999988643 455677888863
No 94
>PF09065 Haemadin: Haemadin; InterPro: IPR015150 Members of this family adopt a secondary structure consisting of five short beta-strands (beta1-beta5), which are arranged in two antiparallel distorted sheets formed by strands beta1-beta4-beta5 and beta2-beta3 facing each other. This beta-sandwich is stabilised by six enclosed cysteines arranged in a [1-2, 3-5, 4-6] disulphide pairing resulting in a disulphide-rich hydrophobic core that is largely inaccessible to bulk solvent. The close proximity of disulphide bonds [3-5] and [4-6] organises haemadin into four distinct loops. The N-terminal segment of this domain binds to the active site of thrombin, inhibiting it []. ; PDB: 1E0F_K.
Probab=26.00 E-value=30 Score=21.07 Aligned_cols=8 Identities=63% Similarity=1.593 Sum_probs=5.6
Q ss_pred CceeeccC
Q 026373 44 ENLCLYGH 51 (239)
Q Consensus 44 ~~l~lyg~ 51 (239)
|.+||||.
T Consensus 5 ekiclygq 12 (27)
T PF09065_consen 5 EKICLYGQ 12 (27)
T ss_dssp SSEE-TTE
T ss_pred ceeeEecc
Confidence 56899996
No 95
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=25.21 E-value=76 Score=22.41 Aligned_cols=32 Identities=16% Similarity=0.341 Sum_probs=20.5
Q ss_pred CCceecccCCCCCC--CCCeEeccCCCCeeeccc
Q 026373 182 SETLCGSCGGNYNA--DEFWIGCDICERWFHGKC 213 (239)
Q Consensus 182 ~~~~C~~C~~~~~~--d~~mIqCD~C~~WfH~~C 213 (239)
....|+.|+..... ...+..|..|+..+|..-
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~ 60 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRDV 60 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEECcHH
Confidence 44568889876543 445666777776666543
No 96
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=24.79 E-value=78 Score=23.27 Aligned_cols=49 Identities=27% Similarity=0.613 Sum_probs=28.7
Q ss_pred CceecccCCCCCCCCC--eEeccCCCCeeeccccccCccccCCCCcEEcCCCccc
Q 026373 183 ETLCGSCGGNYNADEF--WIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMK 235 (239)
Q Consensus 183 ~~~C~~C~~~~~~d~~--mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~K 235 (239)
...|-.|+..-..++. -.-|-.|++-.-+.|..-... -..|.||.|.-+
T Consensus 9 ~~~CtSCg~~i~p~e~~v~F~CPnCGe~~I~Rc~~CRk~----g~~Y~Cp~CGF~ 59 (61)
T COG2888 9 PPVCTSCGREIAPGETAVKFPCPNCGEVEIYRCAKCRKL----GNPYRCPKCGFE 59 (61)
T ss_pred CceeccCCCEeccCCceeEeeCCCCCceeeehhhhHHHc----CCceECCCcCcc
Confidence 4567778775533322 334777776556666554322 134999999643
No 97
>smart00432 MADS MADS domain.
Probab=24.61 E-value=87 Score=22.42 Aligned_cols=37 Identities=27% Similarity=0.578 Sum_probs=23.4
Q ss_pred HHhhhHHHHHHHhhhcHHHhhhcCCcCCCceeeccCCCCcee
Q 026373 16 DFCARRAGVVRALTNDVDEFYGLCDPDKENLCLYGHPNESWE 57 (239)
Q Consensus 16 ~~~~rr~~~~~alt~~~~~~~~~c~~~~~~l~lyg~~~~~w~ 57 (239)
-|+.||.||.+-- .++.-+||-+-- |-+|+..+..++
T Consensus 19 tf~kRk~gl~kKa----~Els~Lc~~~v~-~iv~sp~g~~~~ 55 (59)
T smart00432 19 TFSKRRNGLFKKA----HELSVLCDAEVA-LIVFSPTGKLYE 55 (59)
T ss_pred hhHhhhhhHHHHH----HHHhhccCCeEE-EEEECCCCCeee
Confidence 3899999999865 557778986432 223544443333
No 98
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=24.22 E-value=56 Score=30.78 Aligned_cols=47 Identities=26% Similarity=0.523 Sum_probs=29.0
Q ss_pred CCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 182 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
..+.|++|+.+.. --.-|+ .|+.-|-.-|+.-.-.- ...|.||.|..
T Consensus 238 ~~~~C~~Cg~~Pt-iP~~~~--~C~HiyCY~Ci~ts~~~---~asf~Cp~Cg~ 284 (298)
T KOG2879|consen 238 SDTECPVCGEPPT-IPHVIG--KCGHIYCYYCIATSRLW---DASFTCPLCGE 284 (298)
T ss_pred CCceeeccCCCCC-CCeeec--cccceeehhhhhhhhcc---hhhcccCccCC
Confidence 3456999998753 223344 25556777777654321 13489999975
No 99
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=24.10 E-value=39 Score=25.40 Aligned_cols=51 Identities=20% Similarity=0.447 Sum_probs=22.5
Q ss_pred ceecccCCCCCCCCCeEeccCCCCeeec--cccc----cCccccCCCCcEEcCCCcc
Q 026373 184 TLCGSCGGNYNADEFWIGCDICERWFHG--KCVK----ITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 184 ~~C~~C~~~~~~d~~mIqCD~C~~WfH~--~CVg----it~~~a~~i~~y~Cp~C~~ 234 (239)
..|+.|+.+-...+.-..|+.|+.=|-. -|=. +..-.+=....|+|..|..
T Consensus 2 ~~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACGAvdYFC~~c~g 58 (70)
T PF07191_consen 2 NTCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACGAVDYFCNHCHG 58 (70)
T ss_dssp -B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETTEEEEE-TTTT-
T ss_pred CcCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhcccceeeccCCc
Confidence 3577887765444456678887764432 2311 1111111123599999974
No 100
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=23.59 E-value=44 Score=29.35 Aligned_cols=28 Identities=21% Similarity=0.529 Sum_probs=20.1
Q ss_pred CCceecccCCCCCC-----CCCeEeccCCCCee
Q 026373 182 SETLCGSCGGNYNA-----DEFWIGCDICERWF 209 (239)
Q Consensus 182 ~~~~C~~C~~~~~~-----d~~mIqCD~C~~Wf 209 (239)
.-.+|..|+.|+.. ...++.|+.|+...
T Consensus 97 ~yV~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~ 129 (201)
T PRK12336 97 EYVICSECGLPDTRLVKEDRVLMLRCDACGAHR 129 (201)
T ss_pred heEECCCCCCCCcEEEEcCCeEEEEcccCCCCc
Confidence 34789999998743 34466899998653
No 101
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=23.28 E-value=48 Score=33.13 Aligned_cols=44 Identities=11% Similarity=-0.228 Sum_probs=36.3
Q ss_pred ecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCc
Q 026373 186 CGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 233 (239)
Q Consensus 186 C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~ 233 (239)
|+.|++.+.+...+.+|..|+.|+|..|++.+.. ++..+|..|+
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 5589999888888999999999999999998873 2446777773
No 102
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=23.12 E-value=37 Score=23.67 Aligned_cols=13 Identities=23% Similarity=0.823 Sum_probs=10.2
Q ss_pred CCcEEcCCCcccc
Q 026373 224 IKQYKCPSCSMKR 236 (239)
Q Consensus 224 i~~y~Cp~C~~Kr 236 (239)
++.|.||.|...+
T Consensus 32 p~~w~CP~C~a~K 44 (50)
T cd00730 32 PDDWVCPVCGAGK 44 (50)
T ss_pred CCCCCCCCCCCcH
Confidence 4679999998644
No 103
>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=22.70 E-value=53 Score=25.23 Aligned_cols=32 Identities=25% Similarity=0.525 Sum_probs=20.4
Q ss_pred CCceecccCCCCCCCC-CeEeccCCCCeeeccc
Q 026373 182 SETLCGSCGGNYNADE-FWIGCDICERWFHGKC 213 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~-~mIqCD~C~~WfH~~C 213 (239)
....|-+|+.+..+-. .-+.|..|...|...-
T Consensus 5 ~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v 37 (90)
T cd07168 5 SPKLCSICEDKATGLHYGIITCEGCKGFFKRTV 37 (90)
T ss_pred cCCCCcccCCcCcceEECceehhhhhHhhhhhh
Confidence 4446999987654321 1467999987775533
No 104
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=22.56 E-value=43 Score=19.83 Aligned_cols=13 Identities=38% Similarity=0.874 Sum_probs=10.0
Q ss_pred eEeccCCCCeeec
Q 026373 199 WIGCDICERWFHG 211 (239)
Q Consensus 199 mIqCD~C~~WfH~ 211 (239)
|++|..|++.|..
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 6788888888753
No 105
>PF08040 NADH_oxidored: MNLL subunit; InterPro: IPR012575 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. This family consists of the MNLL subunits of NADH:ubiquinone oxidoreductase complex []. MNLL subunit is one of the many subunits found in the complex and it contains a mitochondrial import sequence. However, the role of MNLL subunit is unclear [].; GO: 0003954 NADH dehydrogenase activity, 0005739 mitochondrion
Probab=22.48 E-value=67 Score=23.47 Aligned_cols=29 Identities=34% Similarity=0.771 Sum_probs=22.4
Q ss_pred hhhhhhcHHHHH---HHHHHhhccChHHHHHH
Q 026373 91 LVAVHTDSWLLS---VAFYLGARLNRNERKRL 119 (239)
Q Consensus 91 ~vavh~d~wl~~---~a~~~~a~~~~~~r~rl 119 (239)
++.++.|.|+.+ +.|++|-.||+.+-.||
T Consensus 4 ~~~~vr~~~~~~~vPlgf~iG~yLDr~~~erl 35 (59)
T PF08040_consen 4 LIQIVRDHWVWILVPLGFVIGCYLDRKETERL 35 (59)
T ss_pred HHHHHHHHHHHHHHhhHhhheeeecccchHHH
Confidence 466777777644 47899999999888887
No 106
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=22.25 E-value=67 Score=23.52 Aligned_cols=29 Identities=21% Similarity=0.460 Sum_probs=20.5
Q ss_pred CceecccCCC--CCCCCCeEeccCCCCeeec
Q 026373 183 ETLCGSCGGN--YNADEFWIGCDICERWFHG 211 (239)
Q Consensus 183 ~~~C~~C~~~--~~~d~~mIqCD~C~~WfH~ 211 (239)
...|+.|+.+ +......+-|..|+.||-.
T Consensus 8 iLaCP~~kg~L~~~~~~~~L~c~~~~~aYpI 38 (60)
T COG2835 8 ILACPVCKGPLVYDEEKQELICPRCKLAYPI 38 (60)
T ss_pred eeeccCcCCcceEeccCCEEEecccCceeec
Confidence 3468888875 3335667889999998853
No 107
>PF05876 Terminase_GpA: Phage terminase large subunit (GpA); InterPro: IPR008866 This entry is represented by Bacteriophage lambda, GpA. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry consists of several phage terminase large subunit proteins as well as related sequences from several bacterial species. The DNA packaging enzyme of bacteriophage lambda, terminase, is a heteromultimer composed of a small subunit, gpNu1, and a large subunit, gpA, products of the Nu1 and A genes, respectively. Terminase is involved in the site-specific binding and cutting of the DNA in the initial stages of packaging. It is now known that gpA is actively involved in late stages of packaging, including DNA translocation, and that this enzyme contains separate functional domains for its early and late packaging activities [].
Probab=21.38 E-value=58 Score=32.81 Aligned_cols=39 Identities=18% Similarity=0.509 Sum_probs=26.2
Q ss_pred CCCeEeccCCCCeeecccccc--CccccCCCCcEEcCCCcc
Q 026373 196 DEFWIGCDICERWFHGKCVKI--TPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 196 d~~mIqCD~C~~WfH~~CVgi--t~~~a~~i~~y~Cp~C~~ 234 (239)
..++|.|-.|+.||...=-++ +.........|.|+.|..
T Consensus 197 r~~~vpCPhCg~~~~l~~~~l~w~~~~~~~~a~y~C~~Cg~ 237 (557)
T PF05876_consen 197 RRYYVPCPHCGEEQVLEWENLKWDKGEAPETARYVCPHCGC 237 (557)
T ss_pred eEEEccCCCCCCCccccccceeecCCCCccceEEECCCCcC
Confidence 367899999998887653333 221134446799999974
No 108
>PF12773 DZR: Double zinc ribbon
Probab=21.26 E-value=65 Score=21.35 Aligned_cols=25 Identities=24% Similarity=0.519 Sum_probs=13.6
Q ss_pred CceecccCCCCC-CCCCeEeccCCCC
Q 026373 183 ETLCGSCGGNYN-ADEFWIGCDICER 207 (239)
Q Consensus 183 ~~~C~~C~~~~~-~d~~mIqCD~C~~ 207 (239)
..+|..|+.+-. .....+.|-.|+.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcC
Confidence 456777766543 1334555666654
No 109
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=21.03 E-value=62 Score=20.45 Aligned_cols=15 Identities=20% Similarity=0.308 Sum_probs=7.8
Q ss_pred CCCeEe-ccCCCCeee
Q 026373 196 DEFWIG-CDICERWFH 210 (239)
Q Consensus 196 d~~mIq-CD~C~~WfH 210 (239)
+.+++| |..|+.|+|
T Consensus 7 ~~l~~~rC~~Cg~~~~ 22 (37)
T PF12172_consen 7 GRLLGQRCRDCGRVQF 22 (37)
T ss_dssp T-EEEEE-TTT--EEE
T ss_pred CEEEEEEcCCCCCEec
Confidence 345555 999999876
No 110
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=20.95 E-value=55 Score=26.67 Aligned_cols=28 Identities=25% Similarity=0.648 Sum_probs=19.9
Q ss_pred ceecccCCCCCC-CCCeEeccCCC-Ceeec
Q 026373 184 TLCGSCGGNYNA-DEFWIGCDICE-RWFHG 211 (239)
Q Consensus 184 ~~C~~C~~~~~~-d~~mIqCD~C~-~WfH~ 211 (239)
..|+.|+..|.- ++.+.-|..|. .|-..
T Consensus 3 p~CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcceEecCCeeECcccccccccc
Confidence 458999886533 56677899997 77544
No 111
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=20.90 E-value=72 Score=35.50 Aligned_cols=53 Identities=21% Similarity=0.437 Sum_probs=36.6
Q ss_pred CCcccCCCceecccCCCCCCCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCc
Q 026373 176 DEEDEHSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 233 (239)
Q Consensus 176 eeeee~~~~~C~~C~~~~~~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~ 233 (239)
.+++-+-+..|-+|.. .+..++|+.|.+-||..||........ ...|-|..|.
T Consensus 337 se~~~~~ddhcrf~~d----~~~~lc~Et~prvvhlEcv~hP~~~~~-s~~~e~evc~ 389 (1414)
T KOG1473|consen 337 SEGEIEYDDHCRFCHD----LGDLLCCETCPRVVHLECVFHPRFAVP-SAFWECEVCN 389 (1414)
T ss_pred cccceeecccccccCc----ccceeecccCCceEEeeecCCccccCC-Cccchhhhhh
Confidence 3333345556777765 357899999999999999986654332 2458787776
No 112
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=20.78 E-value=74 Score=28.73 Aligned_cols=25 Identities=24% Similarity=0.761 Sum_probs=17.9
Q ss_pred CCceecccCCCCCCCCCeEeccCCCCe
Q 026373 182 SETLCGSCGGNYNADEFWIGCDICERW 208 (239)
Q Consensus 182 ~~~~C~~C~~~~~~d~~mIqCD~C~~W 208 (239)
.+.+|..||... ....-.|..|+.|
T Consensus 353 p~~~c~~cg~~~--~~~~~~c~~c~~~ 377 (389)
T PRK11788 353 PRYRCRNCGFTA--RTLYWHCPSCKAW 377 (389)
T ss_pred CCEECCCCCCCC--ccceeECcCCCCc
Confidence 446688888765 3466778888887
No 113
>PF08429 PLU-1: PLU-1-like protein; InterPro: IPR013637 This domain is found in the central region of lysine-specific demethylases, which are nuclear proteins that may have a role in DNA-binding and transcription, and are associated with malignant cancer phenotypes []. The domain is also found in various other Jumonji/ARID domain-containing proteins (see IPR013129 from INTERPRO, IPR001606 from INTERPRO). ; GO: 0016706 oxidoreductase activity, acting on paired donors, with incorporation or reduction of molecular oxygen, 2-oxoglutarate as one donor, and incorporation of one atom each of oxygen into both donors, 0055114 oxidation-reduction process
Probab=20.42 E-value=57 Score=29.93 Aligned_cols=69 Identities=20% Similarity=0.182 Sum_probs=52.4
Q ss_pred ccCCCCCCCcc-cC--ccccccccccchhh--h-------------------hhhhhhcHHHHHHHHHHhhccChHHHHH
Q 026373 63 EEVPPELPEPA-LG--INFARDGMNRKDWL--S-------------------LVAVHTDSWLLSVAFYLGARLNRNERKR 118 (239)
Q Consensus 63 ~~~p~~lpep~-lg--in~~rd~m~~~~wl--~-------------------~vavh~d~wl~~~a~~~~a~~~~~~r~r 118 (239)
+.||..+|.=. |- ++.||++.....=| + -++|+.|........+-.+..|.+.-++
T Consensus 243 ~~ipv~~~~~~~L~~~l~kak~w~~~i~~ll~~~~~~~p~~~el~~l~~~~~~L~~~~~~~~~Le~~~~~~~~W~~~~~k 322 (335)
T PF08429_consen 243 ENIPVSLPSLDKLKDALQKAKEWLRQIEELLEQNGSKRPTLDELEELVAESEELPVKLEELSDLEKQLKRAEDWMEKAKK 322 (335)
T ss_pred hcCCCchHHHHHHHHHHHHHHHHHHHHHHHhcccCCCCCcHHHHHHHHHHHhcCCCCCchHHHHHHHHHHHHHHHHHHHH
Confidence 34666666522 22 67777765554444 1 1789999999999999999999999999
Q ss_pred HHHhhhcCCceee
Q 026373 119 LFSLINDQPTVFE 131 (239)
Q Consensus 119 lf~miNdlPTv~E 131 (239)
||...|..-||+|
T Consensus 323 ~F~k~ns~~~ll~ 335 (335)
T PF08429_consen 323 LFLKKNSPLHLLE 335 (335)
T ss_pred HhcccCchhhhhC
Confidence 9999999999886
No 114
>CHL00174 accD acetyl-CoA carboxylase beta subunit; Reviewed
Probab=20.34 E-value=41 Score=31.67 Aligned_cols=32 Identities=22% Similarity=0.537 Sum_probs=20.4
Q ss_pred CCCCeEeccCCCCeeeccccccCccccCCCCcEEcCCCcc
Q 026373 195 ADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 234 (239)
Q Consensus 195 ~d~~mIqCD~C~~WfH~~CVgit~~~a~~i~~y~Cp~C~~ 234 (239)
+++.|+.|+.|..-.+.+ ..+. ..|.||.|..
T Consensus 34 p~~lw~kc~~C~~~~~~~-------~l~~-~~~vcp~c~~ 65 (296)
T CHL00174 34 YKHLWVQCENCYGLNYKK-------FLKS-KMNICEQCGY 65 (296)
T ss_pred CCCCeeECCCccchhhHH-------HHHH-cCCCCCCCCC
Confidence 467899999998533221 1111 2479999973
No 115
>PF09447 Cnl2_NKP2: Cnl2/NKP2 family protein; InterPro: IPR018565 This entry includes the Cnl2 kinetochore protein [].
Probab=20.34 E-value=1.4e+02 Score=22.13 Aligned_cols=29 Identities=21% Similarity=0.549 Sum_probs=26.4
Q ss_pred CHHHHHHHHhhhHHHHHHHhhhcHHHhhh
Q 026373 9 TVEEIYKDFCARRAGVVRALTNDVDEFYG 37 (239)
Q Consensus 9 ~~~~~~~~~~~rr~~~~~alt~~~~~~~~ 37 (239)
.|..+|++....|+..+-++...++.+++
T Consensus 38 ~ir~LYr~Lq~qR~~~~d~V~~nI~~e~~ 66 (67)
T PF09447_consen 38 QIRSLYRDLQAQREQVLDKVRENIDQEFK 66 (67)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 57999999999999999999999988874
Done!