Query 027884
Match_columns 217
No_of_seqs 272 out of 1129
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:55:35 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027884.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027884hhsearch_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 1.3E-71 2.8E-76 447.6 6.0 100 15-114 30-131 (137)
2 KOG1632 Uncharacterized PHD Zn 100.0 3.1E-34 6.8E-39 263.5 -1.0 203 10-212 62-294 (345)
3 KOG1973 Chromatin remodeling p 99.2 3.2E-11 6.9E-16 108.1 5.6 54 156-215 214-270 (274)
4 PF00628 PHD: PHD-finger; Int 99.1 2E-11 4.2E-16 82.5 -0.4 50 163-213 1-51 (51)
5 smart00249 PHD PHD zinc finger 99.0 6E-10 1.3E-14 71.8 3.7 47 163-210 1-47 (47)
6 COG5034 TNG2 Chromatin remodel 98.9 1.9E-09 4.1E-14 96.4 5.3 54 154-213 214-270 (271)
7 KOG4323 Polycomb-like PHD Zn-f 97.8 9.3E-06 2E-10 78.2 2.0 50 166-216 175-227 (464)
8 KOG1632 Uncharacterized PHD Zn 97.5 4E-05 8.6E-10 71.3 1.1 50 163-213 62-113 (345)
9 KOG1844 PHD Zn-finger proteins 97.2 0.00043 9.2E-09 65.9 5.4 53 158-213 83-135 (508)
10 KOG0825 PHD Zn-finger protein 96.7 0.00086 1.9E-08 68.5 2.6 55 156-212 210-265 (1134)
11 PF13831 PHD_2: PHD-finger; PD 96.2 0.0011 2.3E-08 43.0 -0.2 35 175-211 2-36 (36)
12 KOG1512 PHD Zn-finger protein 96.2 0.0019 4.1E-08 59.7 1.3 45 163-211 316-361 (381)
13 KOG0955 PHD finger protein BR1 95.9 0.0074 1.6E-07 63.5 4.1 58 156-216 214-272 (1051)
14 KOG2752 Uncharacterized conser 95.4 0.008 1.7E-07 55.9 2.0 34 159-193 126-165 (345)
15 KOG0383 Predicted helicase [Ge 95.2 0.0098 2.1E-07 60.3 1.8 51 157-212 43-93 (696)
16 PF07227 DUF1423: Protein of u 94.8 0.033 7.1E-07 53.9 4.0 54 160-213 127-192 (446)
17 KOG0954 PHD finger protein [Ge 94.7 0.016 3.4E-07 59.1 1.8 50 160-212 270-320 (893)
18 KOG4299 PHD Zn-finger protein 94.6 0.015 3.2E-07 58.0 1.2 51 161-213 253-305 (613)
19 KOG1245 Chromatin remodeling c 94.5 0.0064 1.4E-07 65.7 -1.5 54 159-214 1106-1159(1404)
20 PF07496 zf-CW: CW-type Zinc F 94.4 0.024 5.2E-07 38.9 1.7 33 176-209 2-34 (50)
21 KOG0957 PHD finger protein [Ge 94.0 0.062 1.3E-06 53.1 4.1 51 162-212 120-178 (707)
22 KOG4443 Putative transcription 93.6 0.0089 1.9E-07 60.0 -2.4 52 161-212 145-201 (694)
23 KOG1244 Predicted transcriptio 93.5 0.042 9.2E-07 50.6 2.0 48 163-212 283-330 (336)
24 PF13639 zf-RING_2: Ring finge 92.2 0.037 8E-07 36.1 -0.2 43 163-211 2-44 (44)
25 KOG0957 PHD finger protein [Ge 91.7 0.078 1.7E-06 52.4 1.3 52 159-211 542-596 (707)
26 PF14446 Prok-RING_1: Prokaryo 90.7 0.2 4.3E-06 35.5 2.2 33 160-192 4-36 (54)
27 KOG1473 Nucleosome remodeling 88.1 0.16 3.4E-06 54.2 0.2 59 156-214 1117-1175(1414)
28 PF13832 zf-HC5HC2H_2: PHD-zin 86.8 0.35 7.7E-06 37.0 1.4 32 159-193 53-86 (110)
29 PF13901 DUF4206: Domain of un 86.7 0.5 1.1E-05 40.8 2.4 45 161-216 152-201 (202)
30 PF07649 C1_3: C1-like domain; 86.5 0.31 6.7E-06 29.7 0.7 29 163-192 2-30 (30)
31 PF13771 zf-HC5HC2H: PHD-like 81.1 1.1 2.4E-05 32.9 1.9 35 158-195 33-69 (90)
32 COG5141 PHD zinc finger-contai 80.4 0.71 1.5E-05 45.8 0.9 51 159-212 191-242 (669)
33 KOG0956 PHD finger protein AF1 80.2 0.98 2.1E-05 46.4 1.8 45 164-212 8-56 (900)
34 KOG1829 Uncharacterized conser 79.1 0.37 8E-06 48.2 -1.6 49 160-216 510-562 (580)
35 KOG1512 PHD Zn-finger protein 76.3 0.65 1.4E-05 43.3 -0.7 53 159-211 256-315 (381)
36 PF10367 Vps39_2: Vacuolar sor 72.2 3.4 7.4E-05 30.7 2.5 31 161-193 78-108 (109)
37 KOG4443 Putative transcription 71.9 1.1 2.3E-05 45.6 -0.5 54 159-212 16-70 (694)
38 PF12678 zf-rbx1: RING-H2 zinc 70.6 3.1 6.8E-05 30.2 1.9 41 164-211 22-73 (73)
39 PF11793 FANCL_C: FANCL C-term 67.9 4.4 9.6E-05 29.4 2.2 52 162-213 3-64 (70)
40 PF12861 zf-Apc11: Anaphase-pr 67.4 3.3 7.1E-05 31.9 1.5 47 163-213 23-80 (85)
41 KOG4628 Predicted E3 ubiquitin 66.0 5.1 0.00011 37.9 2.8 45 162-213 230-276 (348)
42 cd04714 BAH_BAHCC1 BAH, or Bro 63.7 4.3 9.4E-05 32.1 1.6 21 159-180 101-121 (121)
43 PF00130 C1_1: Phorbol esters/ 56.6 18 0.00039 23.9 3.5 38 160-197 10-48 (53)
44 TIGR01562 FdhE formate dehydro 52.7 13 0.00028 34.5 2.9 29 161-189 184-222 (305)
45 cd00162 RING RING-finger (Real 52.3 4.7 0.0001 24.5 0.0 42 164-212 2-43 (45)
46 PF03107 C1_2: C1 domain; Int 51.6 16 0.00035 22.2 2.3 28 163-192 2-30 (30)
47 KOG1941 Acetylcholine receptor 51.3 2.1 4.5E-05 41.6 -2.5 51 159-213 363-414 (518)
48 PLN03208 E3 ubiquitin-protein 49.5 12 0.00026 32.8 2.1 51 159-213 16-77 (193)
49 PF13717 zinc_ribbon_4: zinc-r 48.4 16 0.00035 23.3 2.1 10 175-184 23-32 (36)
50 PF14634 zf-RING_5: zinc-RING 47.6 8.8 0.00019 24.9 0.8 42 164-212 2-44 (44)
51 PRK03564 formate dehydrogenase 45.6 20 0.00044 33.4 3.0 53 160-212 186-260 (309)
52 KOG2626 Histone H3 (Lys4) meth 44.7 23 0.00051 35.4 3.5 54 159-213 18-76 (544)
53 KOG4218 Nuclear hormone recept 43.3 10 0.00023 36.4 0.8 52 161-212 15-75 (475)
54 PF02318 FYVE_2: FYVE-type zin 41.6 11 0.00023 29.8 0.5 51 160-214 53-104 (118)
55 PF13719 zinc_ribbon_5: zinc-r 39.8 30 0.00066 22.0 2.3 25 163-187 4-35 (37)
56 smart00109 C1 Protein kinase C 39.0 13 0.00029 23.5 0.6 36 160-195 10-45 (49)
57 PF09416 UPF1_Zn_bind: RNA hel 39.0 19 0.00042 30.4 1.7 24 164-189 3-26 (152)
58 PF10497 zf-4CXXC_R1: Zinc-fin 37.9 27 0.00059 27.4 2.3 52 159-212 5-69 (105)
59 KOG4299 PHD Zn-finger protein 37.4 34 0.00073 34.9 3.3 49 160-212 46-94 (613)
60 KOG2752 Uncharacterized conser 37.0 20 0.00044 33.8 1.7 52 160-215 52-103 (345)
61 PF13111 DUF3962: Protein of u 34.8 13 0.00028 33.0 -0.0 44 47-103 13-56 (216)
62 PF11351 DUF3154: Protein of u 34.8 20 0.00044 28.7 1.1 13 76-88 100-114 (123)
63 COG5574 PEX10 RING-finger-cont 33.8 24 0.00051 32.5 1.5 46 161-214 215-261 (271)
64 KOG1952 Transcription factor N 33.7 35 0.00077 36.1 2.9 54 159-212 189-244 (950)
65 PF06452 DUF1083: Domain of un 33.2 14 0.00031 29.7 0.0 44 33-77 123-171 (185)
66 KOG3799 Rab3 effector RIM1 and 32.2 20 0.00043 30.3 0.7 52 161-213 65-116 (169)
67 PF13341 RAG2_PHD: RAG2 PHD do 31.5 21 0.00046 26.9 0.7 36 174-209 27-67 (78)
68 KOG0320 Predicted E3 ubiquitin 31.2 48 0.001 29.0 2.9 47 160-213 130-176 (187)
69 PF08274 PhnA_Zn_Ribbon: PhnA 30.0 25 0.00054 22.0 0.7 10 163-172 4-13 (30)
70 PF05207 zf-CSL: CSL zinc fing 29.9 19 0.00041 25.1 0.2 32 157-189 14-52 (55)
71 cd00350 rubredoxin_like Rubred 29.2 42 0.00092 20.8 1.7 12 203-214 16-27 (33)
72 PF09065 Haemadin: Haemadin; 28.6 23 0.0005 21.4 0.4 10 21-30 4-13 (27)
73 cd00029 C1 Protein kinase C co 28.2 34 0.00075 21.8 1.2 36 160-195 10-46 (50)
74 TIGR00311 aIF-2beta translatio 27.8 37 0.0008 27.9 1.6 24 162-185 98-126 (133)
75 smart00653 eIF2B_5 domain pres 25.9 42 0.00092 26.6 1.6 24 162-185 81-109 (110)
76 PF09297 zf-NADH-PPase: NADH p 25.3 33 0.00072 21.0 0.7 24 162-185 4-29 (32)
77 PRK03988 translation initiatio 25.2 44 0.00096 27.6 1.6 26 161-186 102-132 (138)
78 PF04810 zf-Sec23_Sec24: Sec23 25.0 46 0.001 21.5 1.4 32 178-214 3-34 (40)
79 PF15643 Tox-PL-2: Papain fold 24.1 28 0.00061 27.6 0.2 14 55-68 83-96 (100)
80 PF07191 zinc-ribbons_6: zinc- 23.8 41 0.00088 25.1 1.0 51 162-212 2-58 (70)
81 PF13923 zf-C3HC4_2: Zinc fing 23.8 34 0.00073 21.4 0.5 39 164-210 1-39 (39)
82 PF03966 Trm112p: Trm112p-like 23.8 53 0.0011 23.3 1.6 13 175-187 51-63 (68)
83 PF08040 NADH_oxidored: MNLL s 23.7 43 0.00093 24.2 1.1 33 69-101 4-39 (59)
84 PF12773 DZR: Double zinc ribb 23.6 54 0.0012 21.5 1.5 25 161-185 12-37 (50)
85 KOG1493 Anaphase-promoting com 23.5 9.8 0.00021 29.1 -2.3 49 163-213 22-79 (84)
86 PHA02862 5L protein; Provision 23.1 37 0.00081 28.8 0.8 45 163-212 4-50 (156)
87 TIGR00686 phnA alkylphosphonat 23.1 47 0.001 26.8 1.3 28 162-189 3-32 (109)
88 PTZ00211 ribonucleoside-diphos 23.0 42 0.00091 30.9 1.2 36 70-108 111-146 (330)
89 PRK10220 hypothetical protein; 22.5 57 0.0012 26.4 1.7 29 162-190 4-34 (111)
90 PHA02929 N1R/p28-like protein; 22.3 43 0.00092 30.1 1.0 48 161-213 174-225 (238)
91 KOG1886 BAH domain proteins [T 22.2 52 0.0011 32.5 1.6 44 164-211 173-216 (464)
92 PF07282 OrfB_Zn_ribbon: Putat 21.9 1E+02 0.0022 21.5 2.7 32 160-191 27-60 (69)
93 PF12172 DUF35_N: Rubredoxin-l 21.6 63 0.0014 20.2 1.5 15 174-188 7-22 (37)
94 COG3896 Chloramphenicol 3-O-ph 21.4 34 0.00074 30.0 0.3 38 39-78 59-96 (205)
95 cd07168 NR_DBD_DHR4_like DNA-b 21.3 55 0.0012 24.8 1.4 34 158-191 3-37 (90)
96 PRK12775 putative trifunctiona 20.8 1E+02 0.0022 32.9 3.6 55 157-213 792-847 (1006)
97 PF01873 eIF-5_eIF-2B: Domain 20.7 57 0.0012 26.4 1.4 24 162-185 94-122 (125)
98 PF13913 zf-C2HC_2: zinc-finge 20.6 49 0.0011 19.4 0.7 13 177-189 2-14 (25)
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=1.3e-71 Score=447.55 Aligned_cols=100 Identities=81% Similarity=1.357 Sum_probs=98.3
Q ss_pred EeecCCCcceeeeccCCCceeEeCCCCCCCCCCCCCcccccccCCCCCcccchhheehccchHHHHHHHHhhcc--cChh
Q 027884 15 AFRALDKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFARDGMNRKDWLSLVAVHTDSWLLSVAFYLGAR--LNRN 92 (217)
Q Consensus 15 ~~~~~~~~~l~lyg~~~~~w~v~~p~~~~p~~~pep~~gin~~rd~m~~~~wl~~va~h~d~wl~~~a~~~~~~--~~~~ 92 (217)
.+|||+||||||||+|||+|||+||+||||||||||+||||||||||+|+|||||||||||||||||||||||| ||++
T Consensus 30 ~~CDP~kenLCLYG~p~~~WeV~lP~eevPpeLPEPaLGINfaRDgM~r~dWLslVAvHsDsWLlsvAfy~gar~~~~~~ 109 (137)
T PF12165_consen 30 QQCDPEKENLCLYGHPDGTWEVNLPAEEVPPELPEPALGINFARDGMQRKDWLSLVAVHSDSWLLSVAFYFGARFGFDKN 109 (137)
T ss_pred HhcCccccceEEecCCCCCeEEeCChHhCCCCCCCcccCcccccCCccHHHHHHHHHHhccHHHHHHHHHHHHhhccChH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999 7999
Q ss_pred hhhhhhhhccCCCchhhhhhcc
Q 027884 93 ERKRLFSLINDQPTVFEVVTER 114 (217)
Q Consensus 93 ~r~rLf~mIndLPTVfEvVtg~ 114 (217)
+|+|||+|||+||||||||||+
T Consensus 110 ~R~rLF~mIN~lpTv~Evv~g~ 131 (137)
T PF12165_consen 110 ERKRLFSMINDLPTVFEVVTGR 131 (137)
T ss_pred HHHHHHHHHhcCchHHHHHhcc
Confidence 9999999999999999999994
No 2
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=99.97 E-value=3.1e-34 Score=263.49 Aligned_cols=203 Identities=38% Similarity=0.583 Sum_probs=168.0
Q ss_pred ceEEEEeecC----CCcceeeeccCCCceeEeCCCCCCCCCCCCCcccccccCCCCCcccchhheehccchHHHHHHHHh
Q 027884 10 GICCVAFRAL----DKENLCLYGHPNESWEVTLPAEEVPPELPEPALGINFARDGMNRKDWLSLVAVHTDSWLLSVAFYL 85 (217)
Q Consensus 10 ~~~~~~~~~~----~~~~l~lyg~~~~~w~v~~p~~~~p~~~pep~~gin~~rd~m~~~~wl~~va~h~d~wl~~~a~~~ 85 (217)
...|--+||| .++++|+|+++++.|+|++|++++|++++++++||||++|||+.+|||+++++|+|+|+++++|||
T Consensus 62 ~~~~~~~~~p~~~~~~cd~C~~~~~~ec~~v~~~~~e~p~~~~~~c~~c~~~~~~~~~~~~l~~~~~~~~~~~~s~s~~~ 141 (345)
T KOG1632|consen 62 YCKCYKPCDPDDLMEQCDLCEDWYHGECWEVGTAEKEAPKEDPKVCDECKEAQDGMSESDGLSCVCRQDDSELLSPSFYF 141 (345)
T ss_pred hhhcccccCchhhhhccccccccccccccccCchhhcCCccccccccccchhhhhhhhhccceeeccccccccccccccc
Confidence 3456778999 899999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hccc-------ChhhhhhhhhhccCCCchhhhhhcc----CCCCCCCCCCCCCCcCCCCCC--CCCCCCCCCCCC--CC-
Q 027884 86 GARL-------NRNERKRLFSLINDQPTVFEVVTER----KPIKDKPSVDSSSKSRGSTKR--SNDGQVKSNPKL--AD- 149 (217)
Q Consensus 86 ~~~~-------~~~~r~rLf~mIndLPTVfEvVtg~----kq~k~k~s~~ss~~~kssskr--~~e~~~k~~k~~--~d- 149 (217)
|+++ .+.+|+|+|.++|++||||++++|. ...|.++++++++.+..+.++ ..+...+..+.. ++
T Consensus 142 ~~~~~~~~~~~~~~~~~r~~~~~~~~~t~~~~~~~~~~~~~~~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 221 (345)
T KOG1632|consen 142 GKRGCQFWVKLQKLGRVRLEAEKNDDPTVFEVVSGTATGELPSKDKSSNDRGSKSKTRKKRNRESELEEKKRKHFSNEEL 221 (345)
T ss_pred CCccccccccchhhhhhhhhhhhcccchhhhcccccccccccccccccccccceecccCcccccchhhhhhhhhccCccc
Confidence 9995 8999999999999999999999993 245666666666555555443 222222212111 11
Q ss_pred -C-----CCCCCCcccCCceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCe----EEcCCCCC
Q 027884 150 -E-----SFDDEEDEHSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQ----YKCPSCSM 212 (217)
Q Consensus 150 -e-----~~eeedee~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~----y~Cp~C~~ 212 (217)
+ ....+..+.....|..|+.++....|||.|+.|+.|||+.|+.++++....+.. |+|+.|..
T Consensus 222 ~~~~~~~~~~~~~~~~~~~~~~~cg~~~~~~~~~~~~~~~e~w~~~~~v~~~~a~~~~~~~~~~~~~c~~~~~ 294 (345)
T KOG1632|consen 222 TEPAREPVDESEAPDYSKLICDPCGLSDANKKFEICCDLCESWFHGDCVQIFEARKRLNEIRNEVYKCPHCTV 294 (345)
T ss_pred ccccccCCCcccccccccccccccCcchHHHHHHHHHHHHHHHhcccccccccchhhhhhhhccceecCceee
Confidence 1 233445667778898999998767999999999999999999999998888888 99999986
No 3
>KOG1973 consensus Chromatin remodeling protein, contains PHD Zn-finger [Chromatin structure and dynamics]
Probab=99.16 E-value=3.2e-11 Score=108.13 Aligned_cols=54 Identities=31% Similarity=0.724 Sum_probs=42.6
Q ss_pred CcccCCceeCccCCCCCCCCceEeccC--CC-CeeeccccccCccccCCCCeEEcCCCCCcCC
Q 027884 156 EDEHSETLCGSCGGNYNADEFWIGCDI--CE-RWFHGKCVKITPAKAENIKQYKCPSCSMKRG 215 (217)
Q Consensus 156 dee~~~~~C~iC~~py~~d~~mIqCD~--Ce-~WfH~~CVgIt~~~a~~~d~y~Cp~C~~kr~ 215 (217)
.+....++| +|.+.. .+.||+||. |. .|||+.||||+.+. .++|||+.|.....
T Consensus 214 ~d~~e~~yC-~Cnqvs--yg~Mi~CDn~~C~~eWFH~~CVGL~~~P---kgkWyC~~C~~~~~ 270 (274)
T KOG1973|consen 214 VDPDEPTYC-ICNQVS--YGKMIGCDNPGCPIEWFHFTCVGLKTKP---KGKWYCPRCKAENK 270 (274)
T ss_pred cCCCCCEEE-Eecccc--cccccccCCCCCCcceEEEeccccccCC---CCcccchhhhhhhh
Confidence 344566777 999543 679999996 99 99999999999653 35799999987553
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=2e-11 Score=82.47 Aligned_cols=50 Identities=36% Similarity=0.834 Sum_probs=40.3
Q ss_pred eeCccCCCCCCCCceEeccCCCCeeeccccccCccccCC-CCeEEcCCCCCc
Q 027884 163 LCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAEN-IKQYKCPSCSMK 213 (217)
Q Consensus 163 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~-~d~y~Cp~C~~k 213 (217)
+|.+|++.. +++.||+||.|+.|||..|+++....... ...|+|+.|..|
T Consensus 1 ~C~vC~~~~-~~~~~i~C~~C~~~~H~~C~~~~~~~~~~~~~~w~C~~C~~~ 51 (51)
T PF00628_consen 1 YCPVCGQSD-DDGDMIQCDSCNRWYHQECVGPPEKAEEIPSGDWYCPNCRPK 51 (51)
T ss_dssp EBTTTTSSC-TTSSEEEBSTTSCEEETTTSTSSHSHHSHHSSSBSSHHHHHC
T ss_pred eCcCCCCcC-CCCCeEEcCCCChhhCcccCCCChhhccCCCCcEECcCCcCc
Confidence 578999954 48899999999999999999988663322 238999999764
No 5
>smart00249 PHD PHD zinc finger. The plant homeodomain (PHD) finger is a C4HC3 zinc-finger-like motif found in nuclear proteins thought to be involved in epigenetics and chromatin-mediated transcriptional regulation. The PHD finger binds two zinc ions using the so-called 'cross-brace' motif and is thus structurally related to the COG5034 TNG2 Chromatin remodeling protein, contains PhD zinc finger [Chromatin structure and dynamics]
Probab=98.89 E-value=1.9e-09 Score=96.39 Aligned_cols=54 Identities=28% Similarity=0.727 Sum_probs=42.0
Q ss_pred CCCcccCCceeCccCCCCCCCCceEecc--CCC-CeeeccccccCccccCCCCeEEcCCCCCc
Q 027884 154 DEEDEHSETLCGSCGGNYNADEFWIGCD--ICE-RWFHGKCVKITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 154 eedee~~~~~C~iC~~py~~d~~mIqCD--~Ce-~WfH~~CVgIt~~~a~~~d~y~Cp~C~~k 213 (217)
++.++..+.+| .|++.. -+.||.|| .|+ .|||..|||+.... -..|+|+.|...
T Consensus 214 ~d~se~e~lYC-fCqqvS--yGqMVaCDn~nCkrEWFH~~CVGLk~pP---KG~WYC~eCk~~ 270 (271)
T COG5034 214 EDNSEGEELYC-FCQQVS--YGQMVACDNANCKREWFHLECVGLKEPP---KGKWYCPECKKA 270 (271)
T ss_pred cccccCceeEE-Eecccc--cccceecCCCCCchhheeccccccCCCC---CCcEeCHHhHhc
Confidence 33344555666 999864 46999999 898 99999999998753 358999999754
No 7
>KOG4323 consensus Polycomb-like PHD Zn-finger protein [General function prediction only]
Probab=97.79 E-value=9.3e-06 Score=78.16 Aligned_cols=50 Identities=26% Similarity=0.678 Sum_probs=37.4
Q ss_pred ccCCCCCCCCceEeccCCCCeeeccccc--cCccccCCC-CeEEcCCCCCcCCC
Q 027884 166 SCGGNYNADEFWIGCDICERWFHGKCVK--ITPAKAENI-KQYKCPSCSMKRGR 216 (217)
Q Consensus 166 iC~~py~~d~~mIqCD~Ce~WfH~~CVg--It~~~a~~~-d~y~Cp~C~~kr~r 216 (217)
.|+.+-. ...||||+.|..|||..|.. +++..+.+. -.|+|..|.+++.+
T Consensus 175 ~~g~~~~-~NrmlqC~~C~~~fHq~Chqp~i~~~l~~D~~~~w~C~~C~~~~~~ 227 (464)
T KOG4323|consen 175 YCGGPGA-GNRMLQCDKCRQWYHQACHQPLIKDELAGDPFYEWFCDVCNRGPKK 227 (464)
T ss_pred ecCCcCc-cceeeeecccccHHHHHhccCCCCHhhccCccceEeehhhccchhh
Confidence 5556654 44999999999999999997 455544443 37999999986643
No 8
>KOG1632 consensus Uncharacterized PHD Zn-finger protein [General function prediction only]
Probab=97.46 E-value=4e-05 Score=71.34 Aligned_cols=50 Identities=30% Similarity=0.810 Sum_probs=45.8
Q ss_pred eeCccCCCCCCCCceEeccCCCCeeeccc--cccCccccCCCCeEEcCCCCCc
Q 027884 163 LCGSCGGNYNADEFWIGCDICERWFHGKC--VKITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 163 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~C--VgIt~~~a~~~d~y~Cp~C~~k 213 (217)
+| .|..+++++.+|++||.|..|||+.| |++....+..++.|+|..|..-
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 56 89999987779999999999999999 9999999999999999999753
No 9
>KOG1844 consensus PHD Zn-finger proteins [General function prediction only]
Probab=97.25 E-value=0.00043 Score=65.89 Aligned_cols=53 Identities=26% Similarity=0.676 Sum_probs=44.5
Q ss_pred ccCCceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 027884 158 EHSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 158 e~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~k 213 (217)
......| .|+..++.+++||||+.|..|.|..|+|+..... ++.|.|..|..+
T Consensus 83 ~~~~~~c-~c~~~~~~~g~~i~c~~c~~Wqh~~C~g~~~~~~--p~~y~c~~c~~~ 135 (508)
T KOG1844|consen 83 AREISRC-DCGLEDDMEGLMIQCDWCGRWQHKICCGSFKSTK--PDKYVCEICTPR 135 (508)
T ss_pred cCccccc-ccccccCCCceeeCCcccCcccCceeeeecCCCC--chhceeeeeccc
Confidence 3566778 9998876578999999999999999999887543 579999999864
No 10
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.73 E-value=0.00086 Score=68.47 Aligned_cols=55 Identities=20% Similarity=0.588 Sum_probs=44.0
Q ss_pred CcccCCceeCccCCCCCCCCceEeccCCCCe-eeccccccCccccCCCCeEEcCCCCC
Q 027884 156 EDEHSETLCGSCGGNYNADEFWIGCDICERW-FHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 156 dee~~~~~C~iC~~py~~d~~mIqCD~Ce~W-fH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
++....+.|-+|..++. .+.||.||.|+.- ||..|+.....++. +..|+|+.|..
T Consensus 210 ~~~~E~~~C~IC~~~Dp-EdVLLLCDsCN~~~YH~YCLDPdl~eiP-~~eWYC~NC~d 265 (1134)
T KOG0825|consen 210 GLSQEEVKCDICTVHDP-EDVLLLCDSCNKVYYHVYCLDPDLSESP-VNEWYCTNCSL 265 (1134)
T ss_pred CcccccccceeeccCCh-HHhheeecccccceeeccccCccccccc-ccceecCcchh
Confidence 34566678999999865 7899999999966 99999987654443 46799999974
No 11
>PF13831 PHD_2: PHD-finger; PDB: 2L43_A 2KU3_A.
Probab=96.22 E-value=0.0011 Score=42.96 Aligned_cols=35 Identities=20% Similarity=0.507 Sum_probs=19.7
Q ss_pred CceEeccCCCCeeeccccccCccccCCCCeEEcCCCC
Q 027884 175 EFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 211 (217)
Q Consensus 175 ~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~ 211 (217)
..+|+|+.|...+|.+|-|+..... .+.|+|..|.
T Consensus 2 n~ll~C~~C~v~VH~~CYGv~~~~~--~~~W~C~~C~ 36 (36)
T PF13831_consen 2 NPLLFCDNCNVAVHQSCYGVSEVPD--GDDWLCDRCE 36 (36)
T ss_dssp CEEEE-SSS--EEEHHHHT-SS--S--S-----HHH-
T ss_pred CceEEeCCCCCcCChhhCCcccCCC--CCcEECCcCC
Confidence 3689999999999999999987643 3459998874
No 12
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=96.22 E-value=0.0019 Score=59.66 Aligned_cols=45 Identities=29% Similarity=0.643 Sum_probs=36.6
Q ss_pred eeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcC-CCC
Q 027884 163 LCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCP-SCS 211 (217)
Q Consensus 163 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp-~C~ 211 (217)
+|-+|++|.- .+.|+.||.|++=||.-|||+..-. ...|+|. .|.
T Consensus 316 lC~IC~~P~~-E~E~~FCD~CDRG~HT~CVGL~~lP---~G~WICD~~C~ 361 (381)
T KOG1512|consen 316 LCRICLGPVI-ESEHLFCDVCDRGPHTLCVGLQDLP---RGEWICDMRCR 361 (381)
T ss_pred hhhccCCccc-chheeccccccCCCCcccccccccc---CccchhhhHHH
Confidence 3667888876 7789999999999999999998642 3679998 454
No 13
>KOG0955 consensus PHD finger protein BR140/LIN-49 [General function prediction only]
Probab=95.91 E-value=0.0074 Score=63.46 Aligned_cols=58 Identities=21% Similarity=0.359 Sum_probs=46.2
Q ss_pred CcccCCceeCccCCCCCC-CCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCcCCC
Q 027884 156 EDEHSETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKRGR 216 (217)
Q Consensus 156 dee~~~~~C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~kr~r 216 (217)
.+.+++..|++|..-... ...-++||.|+.-+|..|.|+... ...+|.|-.|..+.+|
T Consensus 214 ~~~~~D~~C~iC~~~~~~n~n~ivfCD~Cnl~VHq~Cygi~~i---peg~WlCr~Cl~s~~~ 272 (1051)
T KOG0955|consen 214 ALLEEDAVCCICLDGECQNSNVIVFCDGCNLAVHQECYGIPFI---PEGQWLCRRCLQSPQR 272 (1051)
T ss_pred cccCCCccceeecccccCCCceEEEcCCCcchhhhhccCCCCC---CCCcEeehhhccCcCc
Confidence 455677889999876542 368999999999999999997653 2368999999987765
No 14
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=95.44 E-value=0.008 Score=55.90 Aligned_cols=34 Identities=32% Similarity=0.920 Sum_probs=28.1
Q ss_pred cCCceeCccCCCCCC-----CCceEeccCCCCeee-ccccc
Q 027884 159 HSETLCGSCGGNYNA-----DEFWIGCDICERWFH-GKCVK 193 (217)
Q Consensus 159 ~~~~~C~iC~~py~~-----d~~mIqCD~Ce~WfH-~~CVg 193 (217)
....+| .|..+|++ ++.|+||-.|+.||| -.|..
T Consensus 126 fqG~~C-~Cd~~Ypdp~~~~e~~m~QC~iCEDWFHce~c~~ 165 (345)
T KOG2752|consen 126 FQGLFC-KCDTPYPDPVRTEEGEMLQCVICEDWFHCEGCMQ 165 (345)
T ss_pred hcceeE-EecCCCCCccccccceeeeEEeccchhcccccCc
Confidence 356677 99999986 688999999999999 56653
No 15
>KOG0383 consensus Predicted helicase [General function prediction only]
Probab=95.16 E-value=0.0098 Score=60.26 Aligned_cols=51 Identities=25% Similarity=0.619 Sum_probs=39.8
Q ss_pred cccCCceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 027884 157 DEHSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 157 ee~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
++.....|++|.. ++..|.||.|..|||..|.+..-...+..+ |+|++|..
T Consensus 43 ~~~~~e~c~ic~~----~g~~l~c~tC~~s~h~~cl~~pl~~~p~~~-~~c~Rc~~ 93 (696)
T KOG0383|consen 43 DDAEQEACRICAD----GGELLWCDTCPASFHASCLGPPLTPQPNGE-FICPRCFC 93 (696)
T ss_pred chhhhhhhhhhcC----CCcEEEeccccHHHHHHccCCCCCcCCccc-eeeeeecc
Confidence 4455667989985 456788999999999999987666555555 99999953
No 16
>PF07227 DUF1423: Protein of unknown function (DUF1423); InterPro: IPR004082 A total of 715 potential protein-coding genes have been identified in the nucleotide sequence of Arabidopsis thaliana chromosome 5, with an average gene density of 1 gene per 4001 bp []. Amongst the gene products is a well-conserved family of 130.7kDa proteins that share no sequence similarity with any other known proteins, other than in plants. The sequences are characterised by an N-terminal domain of variable length, a central cysteine-rich region and a relatively acidic C-terminal domain. The sequences may possess a PHD finger.
Probab=94.75 E-value=0.033 Score=53.88 Aligned_cols=54 Identities=26% Similarity=0.690 Sum_probs=36.7
Q ss_pred CCceeCccCCCCCC--CCceEeccCCCCeeecccc--------ccCcccc--CCCCeEEcCCCCCc
Q 027884 160 SETLCGSCGGNYNA--DEFWIGCDICERWFHGKCV--------KITPAKA--ENIKQYKCPSCSMK 213 (217)
Q Consensus 160 ~~~~C~iC~~py~~--d~~mIqCD~Ce~WfH~~CV--------gIt~~~a--~~~d~y~Cp~C~~k 213 (217)
....|++|.+-+.. .-.||.||.|..|=|..|. |.+.... .....|+|..|..+
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 45668899873222 4679999999999999996 2221110 11238999999865
No 17
>KOG0954 consensus PHD finger protein [General function prediction only]
Probab=94.72 E-value=0.016 Score=59.15 Aligned_cols=50 Identities=20% Similarity=0.549 Sum_probs=41.8
Q ss_pred CCceeCccCCCCCC-CCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 027884 160 SETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 160 ~~~~C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
++.+|-+|+.++.+ ...||.||.|+.=.|..|.||..-. ...|.|..|.-
T Consensus 270 edviCDvCrspD~e~~neMVfCd~Cn~cVHqaCyGIle~p---~gpWlCr~Cal 320 (893)
T KOG0954|consen 270 EDVICDVCRSPDSEEANEMVFCDKCNICVHQACYGILEVP---EGPWLCRTCAL 320 (893)
T ss_pred ccceeceecCCCccccceeEEeccchhHHHHhhhceeecC---CCCeeehhccc
Confidence 56789999998754 5789999999999999999998742 26799999864
No 18
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=94.57 E-value=0.015 Score=58.03 Aligned_cols=51 Identities=33% Similarity=0.748 Sum_probs=39.0
Q ss_pred CceeCccCCCCCCCCceEeccCCCCeeeccccccC--ccccCCCCeEEcCCCCCc
Q 027884 161 ETLCGSCGGNYNADEFWIGCDICERWFHGKCVKIT--PAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 161 ~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt--~~~a~~~d~y~Cp~C~~k 213 (217)
+.+|..|+++..- ...|+||.|..=||..|+.-. .+..+ .+.|+|+.|.-+
T Consensus 253 ~~fCsaCn~~~~F-~~~i~CD~Cp~sFH~~CLePPl~~eniP-~g~W~C~ec~~k 305 (613)
T KOG4299|consen 253 EDFCSACNGSGLF-NDIICCDGCPRSFHQTCLEPPLEPENIP-PGSWFCPECKIK 305 (613)
T ss_pred HHHHHHhCCcccc-ccceeecCCchHHHHhhcCCCCCcccCC-CCccccCCCeee
Confidence 4589999987541 346999999999999999743 44333 368999999754
No 19
>KOG1245 consensus Chromatin remodeling complex WSTF-ISWI, large subunit (contains heterochromatin localization, PHD and BROMO domains) [Chromatin structure and dynamics]
Probab=94.53 E-value=0.0064 Score=65.68 Aligned_cols=54 Identities=28% Similarity=0.575 Sum_probs=45.2
Q ss_pred cCCceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCcC
Q 027884 159 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKR 214 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~kr 214 (217)
....+|.+|++..+ ...|+-||.|..|||.-|+......+. +..|+|+.|+..+
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 45677999998765 679999999999999999998776664 4679999999765
No 20
>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=94.42 E-value=0.024 Score=38.85 Aligned_cols=33 Identities=24% Similarity=0.773 Sum_probs=17.4
Q ss_pred ceEeccCCCCeeeccccccCccccCCCCeEEcCC
Q 027884 176 FWIGCDICERWFHGKCVKITPAKAENIKQYKCPS 209 (217)
Q Consensus 176 ~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~ 209 (217)
.|||||.|.+|=... .++........+.|+|..
T Consensus 2 ~WVQCd~C~KWR~lp-~~~~~~~~~~~d~W~C~~ 34 (50)
T PF07496_consen 2 YWVQCDSCLKWRRLP-EEVDPIREELPDPWYCSM 34 (50)
T ss_dssp EEEE-TTT--EEEE--CCHHCTSCCSSTT--GGG
T ss_pred eEEECCCCCceeeCC-hhhCcccccCCCeEEcCC
Confidence 699999999998876 444432122345899976
No 21
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=93.95 E-value=0.062 Score=53.10 Aligned_cols=51 Identities=18% Similarity=0.430 Sum_probs=36.4
Q ss_pred ceeCccC-CCCCCCCceEeccCCCCeeeccccccCccc-----cCC--CCeEEcCCCCC
Q 027884 162 TLCGSCG-GNYNADEFWIGCDICERWFHGKCVKITPAK-----AEN--IKQYKCPSCSM 212 (217)
Q Consensus 162 ~~C~iC~-~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~-----a~~--~d~y~Cp~C~~ 212 (217)
.+||+|- +...+-+..||||.|+-=.|-.|.|+.... ... ...|+|..|.-
T Consensus 120 ~iCcVClg~rs~da~ei~qCd~CGi~VHEgCYGv~dn~si~s~~s~~stepWfCeaC~~ 178 (707)
T KOG0957|consen 120 VICCVCLGQRSVDAGEILQCDKCGINVHEGCYGVLDNVSIPSGSSDCSTEPWFCEACLY 178 (707)
T ss_pred eEEEEeecCccccccceeeccccCceecccccccccccccCCCCccCCCCchhhhhHhc
Confidence 3799994 333335788999999999999999987321 111 25699988863
No 22
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=93.59 E-value=0.0089 Score=60.00 Aligned_cols=52 Identities=37% Similarity=0.792 Sum_probs=40.5
Q ss_pred CceeCccCCCCCCCC--ceEeccCCCCeeeccccccCccccCC--CC-eEEcCCCCC
Q 027884 161 ETLCGSCGGNYNADE--FWIGCDICERWFHGKCVKITPAKAEN--IK-QYKCPSCSM 212 (217)
Q Consensus 161 ~~~C~iC~~py~~d~--~mIqCD~Ce~WfH~~CVgIt~~~a~~--~d-~y~Cp~C~~ 212 (217)
..+|++|...|...+ .|++|+.|.+|.|+.|.++....... ++ .|.|..|+-
T Consensus 145 ~~~cPvc~~~Y~~~e~~~~~~c~~c~rwsh~~c~~~sdd~~~q~~vD~~~~CS~CR~ 201 (694)
T KOG4443|consen 145 LSYCPVCLIVYQDSESLPMVCCSICQRWSHGGCDGISDDKYMQAQVDLQYKCSTCRG 201 (694)
T ss_pred cccCchHHHhhhhccchhhHHHHHhcccccCCCCccchHHHHHHhhhhhcccceeeh
Confidence 468999998886543 46999999999999999987653221 34 799999973
No 23
>KOG1244 consensus Predicted transcription factor Requiem/NEURO-D4 [Transcription]
Probab=93.50 E-value=0.042 Score=50.57 Aligned_cols=48 Identities=27% Similarity=0.622 Sum_probs=36.4
Q ss_pred eeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 027884 163 LCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 163 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
+|.+|+-..+ ++..+.||.|++=||.-|+.-.-...+ ...|-|..|..
T Consensus 283 ~csicgtsen-ddqllfcddcdrgyhmyclsppm~epp-egswsc~KOG~ 330 (336)
T KOG1244|consen 283 YCSICGTSEN-DDQLLFCDDCDRGYHMYCLSPPMVEPP-EGSWSCHLCLE 330 (336)
T ss_pred eeccccCcCC-CceeEeecccCCceeeEecCCCcCCCC-CCchhHHHHHH
Confidence 3668888877 778999999999999999854332222 25799998864
No 24
>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=92.23 E-value=0.037 Score=36.09 Aligned_cols=43 Identities=26% Similarity=0.597 Sum_probs=32.1
Q ss_pred eeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCC
Q 027884 163 LCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 211 (217)
Q Consensus 163 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~ 211 (217)
.|++|...+..+..++... |+..||.+|+.---.. ...||.|+
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 4899999987677788777 9999999998743321 24899885
No 25
>KOG0957 consensus PHD finger protein [General function prediction only]
Probab=91.73 E-value=0.078 Score=52.42 Aligned_cols=52 Identities=19% Similarity=0.553 Sum_probs=40.1
Q ss_pred cCCceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCC---CCeEEcCCCC
Q 027884 159 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAEN---IKQYKCPSCS 211 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~---~d~y~Cp~C~ 211 (217)
.-...|++|++..+ ....++||.|..-||.-|+.-.-.+.+. .--|.|..|.
T Consensus 542 a~~ysCgiCkks~d-QHll~~CDtC~lhYHlGCL~PPLTR~Pkk~kn~gWqCsECd 596 (707)
T KOG0957|consen 542 AMNYSCGICKKSTD-QHLLTQCDTCHLHYHLGCLSPPLTRLPKKNKNFGWQCSECD 596 (707)
T ss_pred ccceeeeeeccchh-hHHHhhcchhhceeeccccCCccccCcccccCcceeecccc
Confidence 34567999999876 7889999999999999999754333322 2359999993
No 26
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=90.67 E-value=0.2 Score=35.50 Aligned_cols=33 Identities=21% Similarity=0.587 Sum_probs=29.8
Q ss_pred CCceeCccCCCCCCCCceEeccCCCCeeecccc
Q 027884 160 SETLCGSCGGNYNADEFWIGCDICERWFHGKCV 192 (217)
Q Consensus 160 ~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CV 192 (217)
....|.+|+++..+++.-|.|..|..=||..|.
T Consensus 4 ~~~~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 4 EGCKCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred cCccChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 456799999999778899999999999999997
No 27
>KOG1473 consensus Nucleosome remodeling factor, subunit NURF301/BPTF [Chromatin structure and dynamics; Transcription]
Probab=88.09 E-value=0.16 Score=54.17 Aligned_cols=59 Identities=25% Similarity=0.594 Sum_probs=50.2
Q ss_pred CcccCCceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCcC
Q 027884 156 EDEHSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKR 214 (217)
Q Consensus 156 dee~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~kr 214 (217)
+-...+.+|++|..||+++...|.|-.|..|+|..-|.+........-.|+|-.|++-+
T Consensus 1117 ~kp~~~p~~~i~~~p~~pg~~~i~~~~~~~~~~~~~v~ln~s~~p~~~~~k~~~~~ri~ 1175 (1414)
T KOG1473|consen 1117 DKPTLSPVCFICTLPYNPGLTYIHCTVCMTWGHKEAVKLNSSPIPEVVGFKCCQCRRIR 1175 (1414)
T ss_pred CCCCCCccccceeeccCCCCCcceEEEeeccCcceeEecCCCcchHHhhhhHHhhhccC
Confidence 34456778999999999999999999999999999999988766665678998888654
No 28
>PF13832 zf-HC5HC2H_2: PHD-zinc-finger like domain
Probab=86.79 E-value=0.35 Score=37.04 Aligned_cols=32 Identities=28% Similarity=0.688 Sum_probs=27.3
Q ss_pred cCCceeCccCCCCCCCCceEeccC--CCCeeeccccc
Q 027884 159 HSETLCGSCGGNYNADEFWIGCDI--CERWFHGKCVK 193 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d~~mIqCD~--Ce~WfH~~CVg 193 (217)
.....|.+|++. .+..|+|.. |..+||..|..
T Consensus 53 ~~~~~C~iC~~~---~G~~i~C~~~~C~~~fH~~CA~ 86 (110)
T PF13832_consen 53 RFKLKCSICGKS---GGACIKCSHPGCSTAFHPTCAR 86 (110)
T ss_pred hcCCcCcCCCCC---CceeEEcCCCCCCcCCCHHHHH
Confidence 356789999987 458999997 99999999974
No 29
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=86.69 E-value=0.5 Score=40.82 Aligned_cols=45 Identities=24% Similarity=0.775 Sum_probs=34.1
Q ss_pred CceeCccCCC-----CCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCcCCC
Q 027884 161 ETLCGSCGGN-----YNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKRGR 216 (217)
Q Consensus 161 ~~~C~iC~~p-----y~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~kr~r 216 (217)
+.+|.+|+.+ ++ .+.-++|+.|..-||..|..- . .||.|.+.+.|
T Consensus 152 GfiCe~C~~~~~IfPF~-~~~~~~C~~C~~v~H~~C~~~--~--------~CpkC~R~~~r 201 (202)
T PF13901_consen 152 GFICEICNSDDIIFPFQ-IDTTVRCPKCKSVFHKSCFRK--K--------SCPKCARRQKR 201 (202)
T ss_pred CCCCccCCCCCCCCCCC-CCCeeeCCcCccccchhhcCC--C--------CCCCcHhHhcc
Confidence 4567778753 32 347889999999999999972 1 19999998776
No 30
>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=86.45 E-value=0.31 Score=29.74 Aligned_cols=29 Identities=24% Similarity=0.782 Sum_probs=12.6
Q ss_pred eeCccCCCCCCCCceEeccCCCCeeecccc
Q 027884 163 LCGSCGGNYNADEFWIGCDICERWFHGKCV 192 (217)
Q Consensus 163 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CV 192 (217)
.|.+|+++.. +...-.|..|+..+|..|+
T Consensus 2 ~C~~C~~~~~-~~~~Y~C~~Cdf~lH~~Ca 30 (30)
T PF07649_consen 2 RCDACGKPID-GGWFYRCSECDFDLHEECA 30 (30)
T ss_dssp --TTTS-----S--EEE-TTT-----HHHH
T ss_pred cCCcCCCcCC-CCceEECccCCCccChhcC
Confidence 4788998875 3577889999999999985
No 31
>PF13771 zf-HC5HC2H: PHD-like zinc-binding domain
Probab=81.09 E-value=1.1 Score=32.89 Aligned_cols=35 Identities=29% Similarity=0.608 Sum_probs=28.1
Q ss_pred ccCCceeCccCCCCCCCCceEecc--CCCCeeeccccccC
Q 027884 158 EHSETLCGSCGGNYNADEFWIGCD--ICERWFHGKCVKIT 195 (217)
Q Consensus 158 e~~~~~C~iC~~py~~d~~mIqCD--~Ce~WfH~~CVgIt 195 (217)
......|.+|++++ +-.|+|. .|...||..|....
T Consensus 33 ~~~~~~C~~C~~~~---Ga~i~C~~~~C~~~fH~~CA~~~ 69 (90)
T PF13771_consen 33 RRRKLKCSICKKKG---GACIGCSHPGCSRSFHVPCARKA 69 (90)
T ss_pred HHhCCCCcCCCCCC---CeEEEEeCCCCCcEEChHHHccC
Confidence 34667899999873 4889998 69999999998543
No 32
>COG5141 PHD zinc finger-containing protein [General function prediction only]
Probab=80.40 E-value=0.71 Score=45.80 Aligned_cols=51 Identities=24% Similarity=0.494 Sum_probs=39.0
Q ss_pred cCCceeCccCCCCCCC-CceEeccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 027884 159 HSETLCGSCGGNYNAD-EFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d-~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
.-+..|.+|...++++ ...|.||+|+.=.|..|-||.--. ...|.|-.|.-
T Consensus 191 ~~d~~C~~c~~t~~eN~naiVfCdgC~i~VHq~CYGI~f~p---eG~WlCrkCi~ 242 (669)
T COG5141 191 EFDDICTKCTSTHNENSNAIVFCDGCEICVHQSCYGIQFLP---EGFWLCRKCIY 242 (669)
T ss_pred hhhhhhHhccccccCCcceEEEecCcchhhhhhcccceecC---cchhhhhhhcc
Confidence 3445688898877653 567899999999999999987531 24799988863
No 33
>KOG0956 consensus PHD finger protein AF10 [General function prediction only]
Probab=80.17 E-value=0.98 Score=46.37 Aligned_cols=45 Identities=22% Similarity=0.590 Sum_probs=35.5
Q ss_pred eCccCC--CCCCCCceEecc--CCCCeeeccccccCccccCCCCeEEcCCCCC
Q 027884 164 CGSCGG--NYNADEFWIGCD--ICERWFHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 164 C~iC~~--py~~d~~mIqCD--~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
||+|.- -+. +...|-|| .|..-.|..|.||..-. ...|||-.|..
T Consensus 8 CCVCSDErGWa-eNPLVYCDG~nCsVAVHQaCYGIvqVP---tGpWfCrKCes 56 (900)
T KOG0956|consen 8 CCVCSDERGWA-ENPLVYCDGHNCSVAVHQACYGIVQVP---TGPWFCRKCES 56 (900)
T ss_pred eeeecCcCCCc-cCceeeecCCCceeeeehhcceeEecC---CCchhhhhhhh
Confidence 779953 333 56889999 89999999999997642 35799999975
No 34
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=79.11 E-value=0.37 Score=48.23 Aligned_cols=49 Identities=27% Similarity=0.584 Sum_probs=34.5
Q ss_pred CCceeCccCCCCCC----CCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCcCCC
Q 027884 160 SETLCGSCGGNYNA----DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKRGR 216 (217)
Q Consensus 160 ~~~~C~iC~~py~~----d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~kr~r 216 (217)
...+|.+|..+.-. .+.-..|+.|..|||.+|...... .||.|.+.+.|
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 44567777442110 445688999999999999976643 19999987655
No 35
>KOG1512 consensus PHD Zn-finger protein [General function prediction only]
Probab=76.26 E-value=0.65 Score=43.34 Aligned_cols=53 Identities=25% Similarity=0.453 Sum_probs=39.7
Q ss_pred cCCceeCccCCCCCC-----CCceEeccCCCCeeeccccccCccccCCCC--eEEcCCCC
Q 027884 159 HSETLCGSCGGNYNA-----DEFWIGCDICERWFHGKCVKITPAKAENIK--QYKCPSCS 211 (217)
Q Consensus 159 ~~~~~C~iC~~py~~-----d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d--~y~Cp~C~ 211 (217)
.....|++|-..... ...||.|..|..=+|..|+.+++..+..++ .|.|..|.
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 455678888542211 468999999999999999999988776554 46777775
No 36
>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=72.24 E-value=3.4 Score=30.67 Aligned_cols=31 Identities=26% Similarity=0.426 Sum_probs=23.9
Q ss_pred CceeCccCCCCCCCCceEeccCCCCeeeccccc
Q 027884 161 ETLCGSCGGNYNADEFWIGCDICERWFHGKCVK 193 (217)
Q Consensus 161 ~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVg 193 (217)
...|.+|+++-..+.|.+..+ +.-||..|..
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 346999999987667777654 4889999974
No 37
>KOG4443 consensus Putative transcription factor HALR/MLL3, involved in embryonic development [General function prediction only]
Probab=71.89 E-value=1.1 Score=45.63 Aligned_cols=54 Identities=24% Similarity=0.540 Sum_probs=40.4
Q ss_pred cCCceeCccCCCCCC-CCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 027884 159 HSETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 159 ~~~~~C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
.....|.+|+..... .+.|..|..|..-||.-||.+-...+....-|.|+.|+.
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 345568788765433 467999999999999999996555554556699999874
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=70.62 E-value=3.1 Score=30.25 Aligned_cols=41 Identities=29% Similarity=0.661 Sum_probs=27.4
Q ss_pred eCccCCCCCC---------CCceEeccCCCCeeeccccc--cCccccCCCCeEEcCCCC
Q 027884 164 CGSCGGNYNA---------DEFWIGCDICERWFHGKCVK--ITPAKAENIKQYKCPSCS 211 (217)
Q Consensus 164 C~iC~~py~~---------d~~mIqCD~Ce~WfH~~CVg--It~~~a~~~d~y~Cp~C~ 211 (217)
|++|..++.+ ++..|.=..|+.-||..|+. +... -.||.|+
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 9999988732 23444445799999999997 3322 2799885
No 39
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=67.85 E-value=4.4 Score=29.37 Aligned_cols=52 Identities=23% Similarity=0.352 Sum_probs=19.5
Q ss_pred ceeCccCCCCC--CCCceEecc--CCCCeeecccccc-----Cc-cccCCCCeEEcCCCCCc
Q 027884 162 TLCGSCGGNYN--ADEFWIGCD--ICERWFHGKCVKI-----TP-AKAENIKQYKCPSCSMK 213 (217)
Q Consensus 162 ~~C~iC~~py~--~d~~mIqCD--~Ce~WfH~~CVgI-----t~-~~a~~~d~y~Cp~C~~k 213 (217)
..|++|..... +...-+.|+ .|..=||..|+.- .. ...-.+....||.|...
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 45999986533 234467898 9999999999841 11 11112345789999863
No 40
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=67.37 E-value=3.3 Score=31.87 Aligned_cols=47 Identities=23% Similarity=0.654 Sum_probs=28.2
Q ss_pred eeCccCCCCCC---------CCceEeccCCCCeeeccccc--cCccccCCCCeEEcCCCCCc
Q 027884 163 LCGSCGGNYNA---------DEFWIGCDICERWFHGKCVK--ITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 163 ~C~iC~~py~~---------d~~mIqCD~Ce~WfH~~CVg--It~~~a~~~d~y~Cp~C~~k 213 (217)
.|++|+.+++. ++--|---.|..=||..|+- +.... .+=.||.|++.
T Consensus 23 ~CgICr~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~~----~~~~CPmCR~~ 80 (85)
T PF12861_consen 23 VCGICRMPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQS----SKGQCPMCRQP 80 (85)
T ss_pred ceeeEecccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHcccc----CCCCCCCcCCe
Confidence 47777766552 11112223699999999986 33321 23479999863
No 41
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.04 E-value=5.1 Score=37.94 Aligned_cols=45 Identities=24% Similarity=0.623 Sum_probs=33.2
Q ss_pred ceeCccCCCCCCCCceEeccCCCCeeeccccc--cCccccCCCCeEEcCCCCCc
Q 027884 162 TLCGSCGGNYNADEFWIGCDICERWFHGKCVK--ITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 162 ~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVg--It~~~a~~~d~y~Cp~C~~k 213 (217)
..|++|-..|..|+ -+.==-|..=||..|+. ++.. .-+||-|.+.
T Consensus 230 ~~CaIClEdY~~Gd-klRiLPC~H~FH~~CIDpWL~~~------r~~CPvCK~d 276 (348)
T KOG4628|consen 230 DTCAICLEDYEKGD-KLRILPCSHKFHVNCIDPWLTQT------RTFCPVCKRD 276 (348)
T ss_pred ceEEEeecccccCC-eeeEecCCCchhhccchhhHhhc------CccCCCCCCc
Confidence 67999999998543 33437888899999997 3432 3569999863
No 42
>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=63.71 E-value=4.3 Score=32.15 Aligned_cols=21 Identities=29% Similarity=0.653 Sum_probs=18.5
Q ss_pred cCCceeCccCCCCCCCCceEec
Q 027884 159 HSETLCGSCGGNYNADEFWIGC 180 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d~~mIqC 180 (217)
.+..+| +|..+|+++..||||
T Consensus 101 ~~~d~~-~Ce~~yn~~~~~~~c 121 (121)
T cd04714 101 DGVDFY-YCAGTYNPDTGMLKC 121 (121)
T ss_pred cCCCEE-EEeccCCCCcCcccC
Confidence 455678 999999999999998
No 43
>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=56.60 E-value=18 Score=23.92 Aligned_cols=38 Identities=26% Similarity=0.533 Sum_probs=28.1
Q ss_pred CCceeCccCCCC-CCCCceEeccCCCCeeeccccccCcc
Q 027884 160 SETLCGSCGGNY-NADEFWIGCDICERWFHGKCVKITPA 197 (217)
Q Consensus 160 ~~~~C~iC~~py-~~d~~mIqCD~Ce~WfH~~CVgIt~~ 197 (217)
..+.|.+|++.- .....-..|..|+.-.|.+|....+.
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 456899999876 22556789999999999999976543
No 44
>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=52.67 E-value=13 Score=34.53 Aligned_cols=29 Identities=28% Similarity=0.721 Sum_probs=20.3
Q ss_pred CceeCccCCCC----------CCCCceEeccCCCCeeec
Q 027884 161 ETLCGSCGGNY----------NADEFWIGCDICERWFHG 189 (217)
Q Consensus 161 ~~~C~iC~~py----------~~d~~mIqCD~Ce~WfH~ 189 (217)
..+|++||..- ..+..+..|..|+.-+|.
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~ 222 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHY 222 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccc
Confidence 45799998642 235679999999854465
No 45
>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=52.34 E-value=4.7 Score=24.48 Aligned_cols=42 Identities=19% Similarity=0.404 Sum_probs=27.3
Q ss_pred eCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 027884 164 CGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 164 C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
|.+|..... ..+.-..|+.-||..|+...... ....||.|+.
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 678877662 22333458888999998643321 3466999975
No 46
>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=51.55 E-value=16 Score=22.19 Aligned_cols=28 Identities=25% Similarity=0.708 Sum_probs=21.8
Q ss_pred eeCccCCCCCCCCc-eEeccCCCCeeecccc
Q 027884 163 LCGSCGGNYNADEF-WIGCDICERWFHGKCV 192 (217)
Q Consensus 163 ~C~iC~~py~~d~~-mIqCD~Ce~WfH~~CV 192 (217)
.|.+|++.-+ ++ .=.|+.|..=+|.+|+
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 4788988764 34 6778999988898885
No 47
>KOG1941 consensus Acetylcholine receptor-associated protein of the synapse (rapsyn) [Extracellular structures]
Probab=51.25 E-value=2.1 Score=41.61 Aligned_cols=51 Identities=25% Similarity=0.607 Sum_probs=38.8
Q ss_pred cCCceeCccCCCCCCCCceEeccCCCCeeeccccc-cCccccCCCCeEEcCCCCCc
Q 027884 159 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVK-ITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVg-It~~~a~~~d~y~Cp~C~~k 213 (217)
.-+.+|+.|++.+.....-.|-=-|..-||.+|.. |-... ..--||.|++-
T Consensus 363 e~~L~Cg~CGe~~Glk~e~LqALpCsHIfH~rCl~e~L~~n----~~rsCP~Crkl 414 (518)
T KOG1941|consen 363 ETELYCGLCGESIGLKNERLQALPCSHIFHLRCLQEILENN----GTRSCPNCRKL 414 (518)
T ss_pred HHhhhhhhhhhhhcCCcccccccchhHHHHHHHHHHHHHhC----CCCCCccHHHH
Confidence 45678999999987766778888899999999997 33222 23569999853
No 48
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=49.48 E-value=12 Score=32.79 Aligned_cols=51 Identities=20% Similarity=0.468 Sum_probs=32.1
Q ss_pred cCCceeCccCCCCCCCCceEeccCCCCeeecccccc--Cc-----ccc----CCCCeEEcCCCCCc
Q 027884 159 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKI--TP-----AKA----ENIKQYKCPSCSMK 213 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgI--t~-----~~a----~~~d~y~Cp~C~~k 213 (217)
.++..|++|..... + ..+ -.|+..|+..|+.- .. ... .......||.|+..
T Consensus 16 ~~~~~CpICld~~~-d-PVv--T~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~ 77 (193)
T PLN03208 16 GGDFDCNICLDQVR-D-PVV--TLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSD 77 (193)
T ss_pred CCccCCccCCCcCC-C-cEE--cCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCc
Confidence 45677999998765 2 222 36888999999852 10 000 01235789999863
No 49
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=48.36 E-value=16 Score=23.28 Aligned_cols=10 Identities=20% Similarity=0.508 Sum_probs=5.0
Q ss_pred CceEeccCCC
Q 027884 175 EFWIGCDICE 184 (217)
Q Consensus 175 ~~mIqCD~Ce 184 (217)
+..++|..|+
T Consensus 23 g~~v~C~~C~ 32 (36)
T PF13717_consen 23 GRKVRCSKCG 32 (36)
T ss_pred CcEEECCCCC
Confidence 3455555554
No 50
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=47.64 E-value=8.8 Score=24.94 Aligned_cols=42 Identities=31% Similarity=0.628 Sum_probs=28.8
Q ss_pred eCccCCCCCC-CCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 027884 164 CGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 164 C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
|.+|.+.|++ ..+++ -.|...|...|+.-.. .....||.|++
T Consensus 2 C~~C~~~~~~~~~~~l--~~CgH~~C~~C~~~~~-----~~~~~CP~C~k 44 (44)
T PF14634_consen 2 CNICFEKYSEERRPRL--TSCGHIFCEKCLKKLK-----GKSVKCPICRK 44 (44)
T ss_pred CcCcCccccCCCCeEE--cccCCHHHHHHHHhhc-----CCCCCCcCCCC
Confidence 7889998842 33333 3778888888887554 23577999874
No 51
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=45.60 E-value=20 Score=33.39 Aligned_cols=53 Identities=23% Similarity=0.597 Sum_probs=31.2
Q ss_pred CCceeCccCCCC---------CCCCceEeccCCCCeeec---cccccCccc------c----CCCCeEEcCCCCC
Q 027884 160 SETLCGSCGGNY---------NADEFWIGCDICERWFHG---KCVKITPAK------A----ENIKQYKCPSCSM 212 (217)
Q Consensus 160 ~~~~C~iC~~py---------~~d~~mIqCD~Ce~WfH~---~CVgIt~~~------a----~~~d~y~Cp~C~~ 212 (217)
...+|++||..- ..+..+..|..|+.-.|. .|..-.... . .......|..|..
T Consensus 186 ~~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~ 260 (309)
T PRK03564 186 QRQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGT 260 (309)
T ss_pred CCCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeeeecCCCcceEeeecccccc
Confidence 346799998642 236678899999844455 454211110 0 1234578999975
No 52
>KOG2626 consensus Histone H3 (Lys4) methyltransferase complex, subunit CPS60/ASH2/BRE2 [Chromatin structure and dynamics; Transcription]
Probab=44.66 E-value=23 Score=35.41 Aligned_cols=54 Identities=22% Similarity=0.551 Sum_probs=37.0
Q ss_pred cCCceeCccCCCCCCCCceEeccCCCCeeeccccccCcc---ccCC--CCeEEcCCCCCc
Q 027884 159 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPA---KAEN--IKQYKCPSCSMK 213 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~---~a~~--~d~y~Cp~C~~k 213 (217)
...++| .|+...+.+..-+||-.|.+|||..+...+.. .+.. -..|.|..|...
T Consensus 18 ~~~~~~-y~e~~r~l~~~elqcs~clk~~~~~~~~~~~~~~s~~pf~t~y~fvc~~c~~~ 76 (544)
T KOG2626|consen 18 KQATVC-YCEGERNLGIVELQCSTCLKWFHLPTLEAFHLIKSSLPFMTSYEFVCKECTPS 76 (544)
T ss_pred cCcccc-ccccccccCceeeEeeecccccccccccccccccccCCcccceeEEeccccCc
Confidence 344567 99988777778899999999999755432211 1111 247899999864
No 53
>KOG4218 consensus Nuclear hormone receptor betaFTZ-F1 [Transcription]
Probab=43.32 E-value=10 Score=36.42 Aligned_cols=52 Identities=23% Similarity=0.679 Sum_probs=30.3
Q ss_pred CceeCccCCCCCC-CCceEeccCCCCee--------eccccccCccccCCCCeEEcCCCCC
Q 027884 161 ETLCGSCGGNYNA-DEFWIGCDICERWF--------HGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 161 ~~~C~iC~~py~~-d~~mIqCD~Ce~Wf--------H~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
+-.|++||-.-.. ---..-|++|.-.| |..|..-..-.++..-.-.||.|+-
T Consensus 15 ~ElCPVCGDkVSGYHYGLLTCESCKGFFKRTVQNnK~YtC~e~qnC~iDkTqRKRCP~CRF 75 (475)
T KOG4218|consen 15 GELCPVCGDKVSGYHYGLLTCESCKGFFKRTVQNNKQYTCSEEQNCHIDKTQRKRCPSCRF 75 (475)
T ss_pred ccccccccCccccceeeeeehhhhhhHHHHHhhcCcceecccccccccchHhhccCCchhH
Confidence 3469999864432 12357899999877 4455543332222223456888864
No 54
>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=41.62 E-value=11 Score=29.79 Aligned_cols=51 Identities=22% Similarity=0.415 Sum_probs=35.1
Q ss_pred CCceeCccCCCCCC-CCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCcC
Q 027884 160 SETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKR 214 (217)
Q Consensus 160 ~~~~C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~kr 214 (217)
++..|..|+.+..- ...-..|..|..-+=.+|-..... ...|+|..|.+.+
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~~----~~~WlC~vC~k~r 104 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSKK----EPIWLCKVCQKQR 104 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETSS----SCCEEEHHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCcCCC----CCCEEChhhHHHH
Confidence 33469899887532 334589999999888888877432 2479999997643
No 55
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=39.81 E-value=30 Score=22.04 Aligned_cols=25 Identities=20% Similarity=0.585 Sum_probs=12.3
Q ss_pred eeCccCCCCCC-------CCceEeccCCCCee
Q 027884 163 LCGSCGGNYNA-------DEFWIGCDICERWF 187 (217)
Q Consensus 163 ~C~iC~~py~~-------d~~mIqCD~Ce~Wf 187 (217)
.|+.|+..|.- .+.++.|-.|+.-|
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 46666554422 23355566655433
No 56
>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=39.04 E-value=13 Score=23.52 Aligned_cols=36 Identities=22% Similarity=0.392 Sum_probs=26.9
Q ss_pred CCceeCccCCCCCCCCceEeccCCCCeeeccccccC
Q 027884 160 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKIT 195 (217)
Q Consensus 160 ~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt 195 (217)
..++|.+|++..........|..|+.=.|.+|...-
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~v 45 (49)
T smart00109 10 KPTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEKV 45 (49)
T ss_pred CCCCccccccccCcCCCCcCCCCCCchHHHHHHhhc
Confidence 356798998876522137889999999999998654
No 57
>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=39.02 E-value=19 Score=30.42 Aligned_cols=24 Identities=29% Similarity=0.953 Sum_probs=15.7
Q ss_pred eCccCCCCCCCCceEeccCCCCeeec
Q 027884 164 CGSCGGNYNADEFWIGCDICERWFHG 189 (217)
Q Consensus 164 C~iC~~py~~d~~mIqCD~Ce~WfH~ 189 (217)
|.+|+-.. -.-.++|..|++||=-
T Consensus 3 C~YCG~~~--p~~vv~C~~c~kWFCN 26 (152)
T PF09416_consen 3 CAYCGIHD--PSCVVKCNTCNKWFCN 26 (152)
T ss_dssp -TTT------CCCEEEETTTTEEEES
T ss_pred ccccCCCC--cccEeEcCCCCcEeec
Confidence 67787543 4578999999999954
No 58
>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=37.85 E-value=27 Score=27.38 Aligned_cols=52 Identities=23% Similarity=0.542 Sum_probs=31.6
Q ss_pred cCCceeCccCCCCCCCCceEec------cCC---CCeeeccccc----cCccccCCCCeEEcCCCCC
Q 027884 159 HSETLCGSCGGNYNADEFWIGC------DIC---ERWFHGKCVK----ITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d~~mIqC------D~C---e~WfH~~CVg----It~~~a~~~d~y~Cp~C~~ 212 (217)
.....|-.|++... ++.+.| ..| ..=|=+.|+- ....++.....|.||.|+.
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 34456878887543 344556 566 6667777763 2222233345799999985
No 59
>KOG4299 consensus PHD Zn-finger protein [General function prediction only]
Probab=37.38 E-value=34 Score=34.85 Aligned_cols=49 Identities=27% Similarity=0.551 Sum_probs=34.7
Q ss_pred CCceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCC
Q 027884 160 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 160 ~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~ 212 (217)
.-+.|++|.+. +.-.+|+.|..=||..|.+...........+.|..|..
T Consensus 46 ~~ts~~~~~~~----gn~~~~~~~~~s~h~~~~~~~~sp~~~~~~~~~~~~~~ 94 (613)
T KOG4299|consen 46 AATSCGICKSG----GNLLCCDHCPASFHLECDKPPLSPDLKGSEINCSRCPK 94 (613)
T ss_pred hhhhcchhhhc----CCccccccCccccchhccCcccCcccccccccccCCCc
Confidence 46779899864 45679999999999999997655332334566666654
No 60
>KOG2752 consensus Uncharacterized conserved protein, contains N-recognin-type Zn-finger [General function prediction only]
Probab=37.04 E-value=20 Score=33.84 Aligned_cols=52 Identities=21% Similarity=0.259 Sum_probs=39.3
Q ss_pred CCceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCcCC
Q 027884 160 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKRG 215 (217)
Q Consensus 160 ~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~kr~ 215 (217)
.+.+| +|-..+...+.++.|-.|.-|+|..-..+..-. -.+|.|.-|..+-+
T Consensus 52 rQ~l~-sClTC~P~~~~agvC~~C~~~CH~~H~lveL~t---KR~FrCDCg~sk~g 103 (345)
T KOG2752|consen 52 RQALF-SCLTCTPAPEMAGVCYACSLSCHDGHELVELYT---KRNFRCDCGNSKFG 103 (345)
T ss_pred cccee-EeecccCChhhceeEEEeeeeecCCceeeeccc---cCCccccccccccc
Confidence 35667 888777666799999999999999888766542 35788877766544
No 61
>PF13111 DUF3962: Protein of unknown function (DUF3962)
Probab=34.85 E-value=13 Score=33.04 Aligned_cols=44 Identities=30% Similarity=0.646 Sum_probs=30.6
Q ss_pred CCCCcccccccCCCCCcccchhheehccchHHHHHHHHhhcccChhhhhhhhhhccC
Q 027884 47 LPEPALGINFARDGMNRKDWLSLVAVHTDSWLLSVAFYLGARLNRNERKRLFSLIND 103 (217)
Q Consensus 47 ~pep~~gin~~rd~m~~~~wl~~va~h~d~wl~~~a~~~~~~~~~~~r~rLf~mInd 103 (217)
+-||+-=|-|. .+|+.||-.|-|-|++.+-+ +.-++||+.|..|
T Consensus 13 ~~e~v~~~~fP------~~W~~ll~~~~~~~~l~~Kl-------~~l~erL~~mFsd 56 (216)
T PF13111_consen 13 PNEPVSYIYFP------IEWLDLLEIHYKTFLLTSKL-------KRLNERLYDMFSD 56 (216)
T ss_pred ccCceEEEEcc------HHHHHHHHHhccccccHHHH-------HHHHHHHHHHHHH
Confidence 33444444443 68999999999999998765 3345777777544
No 62
>PF11351 DUF3154: Protein of unknown function (DUF3154); InterPro: IPR021497 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=34.76 E-value=20 Score=28.72 Aligned_cols=13 Identities=62% Similarity=1.019 Sum_probs=11.3
Q ss_pred hHHH--HHHHHhhcc
Q 027884 76 SWLL--SVAFYLGAR 88 (217)
Q Consensus 76 ~wl~--~~a~~~~~~ 88 (217)
-||| .|.||||+|
T Consensus 100 w~Llg~~vlgy~~~R 114 (123)
T PF11351_consen 100 WWLLGAGVLGYFGAR 114 (123)
T ss_pred HHHHHHHHhhhHHHh
Confidence 4777 899999998
No 63
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=33.83 E-value=24 Score=32.53 Aligned_cols=46 Identities=28% Similarity=0.524 Sum_probs=30.4
Q ss_pred CceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeE-EcCCCCCcC
Q 027884 161 ETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQY-KCPSCSMKR 214 (217)
Q Consensus 161 ~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y-~Cp~C~~kr 214 (217)
+..|.+|-..-. --.|-.|+.-|-..|+-+.-. ..+| +||.|+.|-
T Consensus 215 d~kC~lC~e~~~----~ps~t~CgHlFC~~Cl~~~~t----~~k~~~CplCRak~ 261 (271)
T COG5574 215 DYKCFLCLEEPE----VPSCTPCGHLFCLSCLLISWT----KKKYEFCPLCRAKV 261 (271)
T ss_pred ccceeeeecccC----CcccccccchhhHHHHHHHHH----hhccccCchhhhhc
Confidence 345989976432 235778888999999876311 1334 499999763
No 64
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=33.73 E-value=35 Score=36.15 Aligned_cols=54 Identities=20% Similarity=0.524 Sum_probs=39.4
Q ss_pred cCCceeCccCCCCCCCCceEeccCCCCeeecccccc--CccccCCCCeEEcCCCCC
Q 027884 159 HSETLCGSCGGNYNADEFWIGCDICERWFHGKCVKI--TPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 159 ~~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgI--t~~~a~~~d~y~Cp~C~~ 212 (217)
....-|-+|-..-.....+-.|-.|-.-||..|+.- ...+....+.|.||.|+.
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 445568888766555667889999999999999863 112233347899999994
No 65
>PF06452 DUF1083: Domain of unknown function (DUF1083); InterPro: IPR010502 This entry represents the family 9 carbohydrate-binding module (CBD9), which exhibit an immunoglobulin-like beta-sandwich fold, with an additional beta-strand at the N terminus []. Bacterial extracellular cellulases and hemicellulases are involved in the hydrolysis of the major structural polysaccharides of plant cell walls. These are usually modular enzymes that contain catalytic and non-catalytic domains. The CBD9 domain binds to cellulose, xylan, as well as to a range of soluble di- and mono-saccharides, and is found in cellulose- and xylan-degrading enzymes, such as endo-1,4-beta-xylanase (3.2.1.8 from EC) [].; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0030246 carbohydrate binding, 0016052 carbohydrate catabolic process; PDB: 1I82_A 1I8A_A 1I8U_A.
Probab=33.18 E-value=14 Score=29.69 Aligned_cols=44 Identities=32% Similarity=0.655 Sum_probs=26.3
Q ss_pred ceeEeCCCCCC-CCCCCCCccccccc----CCCCCcccchhheehccchH
Q 027884 33 SWEVTLPAEEV-PPELPEPALGINFA----RDGMNRKDWLSLVAVHTDSW 77 (217)
Q Consensus 33 ~w~v~~p~~~~-p~~~pep~~gin~~----rd~m~~~~wl~~va~h~d~w 77 (217)
+.|+.+|-..+ +|+.... +|+||. +++=.|..|++......+.|
T Consensus 123 ~~E~~IP~~~l~~~~~g~~-~g~~~~~~d~~~~~~r~~~~~w~~~~~~~~ 171 (185)
T PF06452_consen 123 TVEIAIPWSALFPPQPGDK-FGFNFAVNDNDDGGKREGWISWSDPSGPSF 171 (185)
T ss_dssp EEEEEEE-SS-----TTEE-EEEEEEEEEE-TTS-EEEEEESS-SSS-TT
T ss_pred EEEEEechHHcCCCCCCCE-EEEEEEEEECCCCCcceEEEEEcCCCCcCc
Confidence 67999999998 4444333 888888 45566888988877766664
No 66
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=32.20 E-value=20 Score=30.34 Aligned_cols=52 Identities=21% Similarity=0.514 Sum_probs=38.0
Q ss_pred CceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 027884 161 ETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 161 ~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~k 213 (217)
+..|++|.+..-.++----|..|..=|-..|-|-...+.. .-.|.|..|.+.
T Consensus 65 datC~IC~KTKFADG~GH~C~YCq~r~CARCGGrv~lrsN-Kv~wvcnlc~k~ 116 (169)
T KOG3799|consen 65 DATCGICHKTKFADGCGHNCSYCQTRFCARCGGRVSLRSN-KVMWVCNLCRKQ 116 (169)
T ss_pred CcchhhhhhcccccccCcccchhhhhHHHhcCCeeeeccC-ceEEeccCCcHH
Confidence 3579999987765666667889998888889874443332 247999999864
No 67
>PF13341 RAG2_PHD: RAG2 PHD domain; PDB: 2JWO_A 2V86_B 2V85_B 2V87_A 2V83_C 2V89_A 2V88_A.
Probab=31.52 E-value=21 Score=26.91 Aligned_cols=36 Identities=19% Similarity=0.534 Sum_probs=19.2
Q ss_pred CCceEeccCC-CCeeeccccccCcccc----CCCCeEEcCC
Q 027884 174 DEFWIGCDIC-ERWFHGKCVKITPAKA----ENIKQYKCPS 209 (217)
Q Consensus 174 d~~mIqCD~C-e~WfH~~CVgIt~~~a----~~~d~y~Cp~ 209 (217)
.--||.|..= +.|.|..|..+++... +...+|+|..
T Consensus 27 kPAMI~cs~~~GHWvhaqCm~LsE~~L~~LSq~n~KYfC~d 67 (78)
T PF13341_consen 27 KPAMIFCSRGGGHWVHAQCMDLSETMLIQLSQENTKYFCND 67 (78)
T ss_dssp S--EEEE-STT-EEEETGGGT--HHHHHHHHHSSS-B--TT
T ss_pred CceEEEEeCCCceEeEeecccchHHHHHHHccCCceEEEhh
Confidence 3469999844 4999999998877533 2235799864
No 68
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.18 E-value=48 Score=29.04 Aligned_cols=47 Identities=23% Similarity=0.448 Sum_probs=31.4
Q ss_pred CCceeCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 027884 160 SETLCGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 160 ~~~~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~k 213 (217)
.-.-|++|--++.. ..+-=-.|+.-|-..|++-.-. ..-.||.|.+|
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 34679999888752 2222357888888888864332 24679999864
No 69
>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=29.97 E-value=25 Score=21.99 Aligned_cols=10 Identities=40% Similarity=1.112 Sum_probs=2.1
Q ss_pred eeCccCCCCC
Q 027884 163 LCGSCGGNYN 172 (217)
Q Consensus 163 ~C~iC~~py~ 172 (217)
.|+.|+..|.
T Consensus 4 ~Cp~C~se~~ 13 (30)
T PF08274_consen 4 KCPLCGSEYT 13 (30)
T ss_dssp --TTT-----
T ss_pred CCCCCCCcce
Confidence 3667776554
No 70
>PF05207 zf-CSL: CSL zinc finger; InterPro: IPR007872 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a probable zinc binding motif that contains four cysteines and may chelate zinc, known as the DPH-type after the diphthamide (DPH) biosynthesis protein in which it was first characterised, including the proteins DPH3 and DPH4. This domain is also found associated with N-terminal domain of heat shock protein DnaJ IPR001623 from INTERPRO domain. Diphthamide is a unique post-translationally modified histidine residue found only in translation elongation factor 2 (eEF-2). It is conserved from archaea to humans and serves as the target for diphteria toxin and Pseudomonas exotoxin A. These two toxins catalyse the transfer of ADP-ribose to diphtamide on eEF-2, thus inactivating eEF-2, halting cellular protein synthesis, and causing cell death []. The biosynthesis of diphtamide is dependent on at least five proteins, DPH1 to -5, and a still unidentified amidating enzyme. DPH3 and DPH4 share a conserved region, which encode a putative zinc finger, the DPH-type or CSL-type (after the conserved motif of the final cysteine) zinc finger [, ]. The function of this motif is unknown. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2L6L_A 1WGE_A 2JR7_A 1YOP_A 1YWS_A.
Probab=29.90 E-value=19 Score=25.07 Aligned_cols=32 Identities=28% Similarity=0.798 Sum_probs=20.5
Q ss_pred cccCCceeCccCCCCCC-------CCceEeccCCCCeeec
Q 027884 157 DEHSETLCGSCGGNYNA-------DEFWIGCDICERWFHG 189 (217)
Q Consensus 157 ee~~~~~C~iC~~py~~-------d~~mIqCD~Ce~WfH~ 189 (217)
++.....| -||..|.- +...|+|+.|.-|.+.
T Consensus 14 ~~~~~y~C-RCG~~f~i~e~~l~~~~~iv~C~sCSL~I~V 52 (55)
T PF05207_consen 14 EGVYSYPC-RCGGEFEISEEDLEEGEVIVQCDSCSLWIRV 52 (55)
T ss_dssp TTEEEEEE-TTSSEEEEEHHHHHCT--EEEETTTTEEEEE
T ss_pred CCEEEEcC-CCCCEEEEcchhccCcCEEEECCCCccEEEE
Confidence 33455567 88865421 4578999999998753
No 71
>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=29.20 E-value=42 Score=20.77 Aligned_cols=12 Identities=25% Similarity=0.922 Sum_probs=9.0
Q ss_pred CeEEcCCCCCcC
Q 027884 203 KQYKCPSCSMKR 214 (217)
Q Consensus 203 d~y~Cp~C~~kr 214 (217)
+.|.||.|...+
T Consensus 16 ~~~~CP~Cg~~~ 27 (33)
T cd00350 16 APWVCPVCGAPK 27 (33)
T ss_pred CCCcCcCCCCcH
Confidence 458999997654
No 72
>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=28.65 E-value=23 Score=21.44 Aligned_cols=10 Identities=50% Similarity=1.252 Sum_probs=6.6
Q ss_pred CcceeeeccC
Q 027884 21 KENLCLYGHP 30 (217)
Q Consensus 21 ~~~l~lyg~~ 30 (217)
.|.+||||..
T Consensus 4 gekiclygqs 13 (27)
T PF09065_consen 4 GEKICLYGQS 13 (27)
T ss_dssp SSSEE-TTEE
T ss_pred cceeeEeccc
Confidence 4679999964
No 73
>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=28.21 E-value=34 Score=21.82 Aligned_cols=36 Identities=22% Similarity=0.444 Sum_probs=26.8
Q ss_pred CCceeCccCCCCCC-CCceEeccCCCCeeeccccccC
Q 027884 160 SETLCGSCGGNYNA-DEFWIGCDICERWFHGKCVKIT 195 (217)
Q Consensus 160 ~~~~C~iC~~py~~-d~~mIqCD~Ce~WfH~~CVgIt 195 (217)
..++|..|++..-. ......|+.|+.=.|.+|...-
T Consensus 10 ~~~~C~~C~~~i~~~~~~~~~C~~C~~~~H~~C~~~v 46 (50)
T cd00029 10 KPTFCDVCRKSIWGLFKQGLRCSWCKVKCHKKCADKV 46 (50)
T ss_pred CCCChhhcchhhhccccceeEcCCCCCchhhhhhccC
Confidence 34678889876642 1466789999999999998644
No 74
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=27.80 E-value=37 Score=27.88 Aligned_cols=24 Identities=17% Similarity=0.558 Sum_probs=16.1
Q ss_pred ceeCccCCCCCC-----CCceEeccCCCC
Q 027884 162 TLCGSCGGNYNA-----DEFWIGCDICER 185 (217)
Q Consensus 162 ~~C~iC~~py~~-----d~~mIqCD~Ce~ 185 (217)
.+|..|+.|+.. ...++.|+.|+.
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa 126 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGA 126 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCC
Confidence 579999988753 233456777764
No 75
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=25.92 E-value=42 Score=26.62 Aligned_cols=24 Identities=29% Similarity=0.862 Sum_probs=17.4
Q ss_pred ceeCccCCCCCC-----CCceEeccCCCC
Q 027884 162 TLCGSCGGNYNA-----DEFWIGCDICER 185 (217)
Q Consensus 162 ~~C~iC~~py~~-----d~~mIqCD~Ce~ 185 (217)
.+|..|+.|+.. ...++.|+.|+.
T Consensus 81 VlC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 81 VLCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred EECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 679999998753 344566888863
No 76
>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=25.28 E-value=33 Score=20.95 Aligned_cols=24 Identities=25% Similarity=0.733 Sum_probs=13.1
Q ss_pred ceeCccCCCCC--CCCceEeccCCCC
Q 027884 162 TLCGSCGGNYN--ADEFWIGCDICER 185 (217)
Q Consensus 162 ~~C~iC~~py~--~d~~mIqCD~Ce~ 185 (217)
.+|+.|+.+-. .++...+|..|+.
T Consensus 4 rfC~~CG~~t~~~~~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 4 RFCGRCGAPTKPAPGGWARRCPSCGH 29 (32)
T ss_dssp SB-TTT--BEEE-SSSS-EEESSSS-
T ss_pred cccCcCCccccCCCCcCEeECCCCcC
Confidence 47888987642 2567778888864
No 77
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=25.18 E-value=44 Score=27.56 Aligned_cols=26 Identities=19% Similarity=0.565 Sum_probs=18.1
Q ss_pred CceeCccCCCCCC-----CCceEeccCCCCe
Q 027884 161 ETLCGSCGGNYNA-----DEFWIGCDICERW 186 (217)
Q Consensus 161 ~~~C~iC~~py~~-----d~~mIqCD~Ce~W 186 (217)
=..|..|+.|+.. ...++.|+.|+..
T Consensus 102 yVlC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 102 YVICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred cEECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 3679999998754 3346678888754
No 78
>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=24.98 E-value=46 Score=21.49 Aligned_cols=32 Identities=22% Similarity=0.534 Sum_probs=14.6
Q ss_pred EeccCCCCeeeccccccCccccCCCCeEEcCCCCCcC
Q 027884 178 IGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMKR 214 (217)
Q Consensus 178 IqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~kr 214 (217)
+.|..|..-+-.-|.-.. ....|+|+.|..+.
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 566666654444333222 23589999998754
No 79
>PF15643 Tox-PL-2: Papain fold toxin 2
Probab=24.13 E-value=28 Score=27.61 Aligned_cols=14 Identities=50% Similarity=1.123 Sum_probs=12.9
Q ss_pred cccCCCCCcccchh
Q 027884 55 NFARDGMNRKDWLS 68 (217)
Q Consensus 55 n~~rd~m~~~~wl~ 68 (217)
|+-+.||.|.|||.
T Consensus 83 Nl~p~G~~r~dWl~ 96 (100)
T PF15643_consen 83 NLHPEGMSREDWLR 96 (100)
T ss_pred ccCcccCCHHHHHH
Confidence 88899999999986
No 80
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=23.82 E-value=41 Score=25.06 Aligned_cols=51 Identities=20% Similarity=0.422 Sum_probs=23.6
Q ss_pred ceeCccCCCCCCCCceEeccCCCCeeec--ccccc----CccccCCCCeEEcCCCCC
Q 027884 162 TLCGSCGGNYNADEFWIGCDICERWFHG--KCVKI----TPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 162 ~~C~iC~~py~~d~~mIqCD~Ce~WfH~--~CVgI----t~~~a~~~d~y~Cp~C~~ 212 (217)
..|+.|+.+-...+.-..|+.|+.=|-. .|=.- ..-.+=....|+|..|..
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 4588888776555566778888764433 23211 111111113699999875
No 81
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=23.77 E-value=34 Score=21.43 Aligned_cols=39 Identities=26% Similarity=0.523 Sum_probs=25.6
Q ss_pred eCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCC
Q 027884 164 CGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSC 210 (217)
Q Consensus 164 C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C 210 (217)
|++|..... ..+....|+..|...|+...-.. ...||.|
T Consensus 1 C~iC~~~~~---~~~~~~~CGH~fC~~C~~~~~~~-----~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELR---DPVVVTPCGHSFCKECIEKYLEK-----NPKCPVC 39 (39)
T ss_dssp ETTTTSB-S---SEEEECTTSEEEEHHHHHHHHHC-----TSB-TTT
T ss_pred CCCCCCccc---CcCEECCCCCchhHHHHHHHHHC-----cCCCcCC
Confidence 678877654 35567889999999998654331 2567766
No 82
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=23.75 E-value=53 Score=23.32 Aligned_cols=13 Identities=31% Similarity=0.430 Sum_probs=6.7
Q ss_pred CceEeccCCCCee
Q 027884 175 EFWIGCDICERWF 187 (217)
Q Consensus 175 ~~mIqCD~Ce~Wf 187 (217)
+....|..|++||
T Consensus 51 eg~L~Cp~c~r~Y 63 (68)
T PF03966_consen 51 EGELICPECGREY 63 (68)
T ss_dssp TTEEEETTTTEEE
T ss_pred CCEEEcCCCCCEE
Confidence 3445555555555
No 83
>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=23.70 E-value=43 Score=24.24 Aligned_cols=33 Identities=30% Similarity=0.663 Sum_probs=24.1
Q ss_pred heehccchHHHH---HHHHhhcccChhhhhhhhhhc
Q 027884 69 LVAVHTDSWLLS---VAFYLGARLNRNERKRLFSLI 101 (217)
Q Consensus 69 ~va~h~d~wl~~---~a~~~~~~~~~~~r~rLf~mI 101 (217)
++++|-|-|+.. +.|.+|-.||+.+-.||..-.
T Consensus 4 ~~~~vr~~~~~~~vPlgf~iG~yLDr~~~erlT~FR 39 (59)
T PF08040_consen 4 LIQIVRDHWVWILVPLGFVIGCYLDRKETERLTAFR 39 (59)
T ss_pred HHHHHHHHHHHHHHhhHhhheeeecccchHHHHhhc
Confidence 456677777643 589999999998877775433
No 84
>PF12773 DZR: Double zinc ribbon
Probab=23.58 E-value=54 Score=21.46 Aligned_cols=25 Identities=24% Similarity=0.519 Sum_probs=11.6
Q ss_pred CceeCccCCCCC-CCCceEeccCCCC
Q 027884 161 ETLCGSCGGNYN-ADEFWIGCDICER 185 (217)
Q Consensus 161 ~~~C~iC~~py~-~d~~mIqCD~Ce~ 185 (217)
..+|..|+.+-. .....+.|-.|+.
T Consensus 12 ~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 12 AKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred ccCChhhcCChhhccCCCCCCcCCcC
Confidence 345666665443 1233444555544
No 85
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=23.54 E-value=9.8 Score=29.13 Aligned_cols=49 Identities=24% Similarity=0.493 Sum_probs=28.2
Q ss_pred eeCccCCCCCCCCc-----eEecc----CCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 027884 163 LCGSCGGNYNADEF-----WIGCD----ICERWFHGKCVKITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 163 ~C~iC~~py~~d~~-----mIqCD----~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~k 213 (217)
.|++|+.+++.--. -=.|- .|..-||..|+----.. ...+-.||.|++.
T Consensus 22 ~CGiCRm~Fdg~Cp~Ck~PgDdCPLv~G~C~h~fh~hCI~~wl~~--~tsq~~CPmcRq~ 79 (84)
T KOG1493|consen 22 TCGICRMPFDGCCPDCKLPGDDCPLVWGYCLHAFHAHCILKWLNT--PTSQGQCPMCRQT 79 (84)
T ss_pred ccceEecccCCcCCCCcCCCCCCccHHHHHHHHHHHHHHHHHhcC--ccccccCCcchhe
Confidence 68899888863000 00121 45667999998422111 1245789999863
No 86
>PHA02862 5L protein; Provisional
Probab=23.14 E-value=37 Score=28.85 Aligned_cols=45 Identities=24% Similarity=0.572 Sum_probs=24.8
Q ss_pred eeCccCCCCCCCCceEeccCCCCeeeccccc--cCccccCCCCeEEcCCCCC
Q 027884 163 LCGSCGGNYNADEFWIGCDICERWFHGKCVK--ITPAKAENIKQYKCPSCSM 212 (217)
Q Consensus 163 ~C~iC~~py~~d~~mIqCD~Ce~WfH~~CVg--It~~~a~~~d~y~Cp~C~~ 212 (217)
.|-+|...++++..-=.|-+--+|.|.+|+. +... ..=.|+.|..
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 3555555443332233344445799999986 3322 2356888874
No 87
>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=23.10 E-value=47 Score=26.76 Aligned_cols=28 Identities=25% Similarity=0.648 Sum_probs=20.3
Q ss_pred ceeCccCCCCCC-CCceEeccCCC-Ceeec
Q 027884 162 TLCGSCGGNYNA-DEFWIGCDICE-RWFHG 189 (217)
Q Consensus 162 ~~C~iC~~py~~-d~~mIqCD~Ce-~WfH~ 189 (217)
..|+.|+..|.. ++.+.-|..|. .|-..
T Consensus 3 p~CP~C~seytY~dg~~~iCpeC~~EW~~~ 32 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQLICPSCLYEWNEN 32 (109)
T ss_pred CcCCcCCCcceEecCCeeECcccccccccc
Confidence 358899887644 56678899996 88544
No 88
>PTZ00211 ribonucleoside-diphosphate reductase small subunit; Provisional
Probab=22.95 E-value=42 Score=30.90 Aligned_cols=36 Identities=25% Similarity=0.575 Sum_probs=26.6
Q ss_pred eehccchHHHHHHHHhhcccChhhhhhhhhhccCCCchh
Q 027884 70 VAVHTDSWLLSVAFYLGARLNRNERKRLFSLINDQPTVF 108 (217)
Q Consensus 70 va~h~d~wl~~~a~~~~~~~~~~~r~rLf~mIndLPTVf 108 (217)
=+||+++.-.-+..|. .+..+|.++|..+.++|+|.
T Consensus 111 E~iHs~sYs~il~tl~---~~~~~~~~~f~~~~~~p~i~ 146 (330)
T PTZ00211 111 ENIHSETYSLLIDTYI---TDEEEKDRLFHAIETIPAIK 146 (330)
T ss_pred HHHHHHHHHHHHHHcC---CCHHHHHHHHHHHHhCHHHH
Confidence 3689998866554432 26788899999999999754
No 89
>PRK10220 hypothetical protein; Provisional
Probab=22.47 E-value=57 Score=26.38 Aligned_cols=29 Identities=24% Similarity=0.631 Sum_probs=20.8
Q ss_pred ceeCccCCCCCC-CCceEeccCCC-Ceeecc
Q 027884 162 TLCGSCGGNYNA-DEFWIGCDICE-RWFHGK 190 (217)
Q Consensus 162 ~~C~iC~~py~~-d~~mIqCD~Ce-~WfH~~ 190 (217)
..|+.|+..|.. ++.+.-|..|. +|-...
T Consensus 4 P~CP~C~seytY~d~~~~vCpeC~hEW~~~~ 34 (111)
T PRK10220 4 PHCPKCNSEYTYEDNGMYICPECAHEWNDAE 34 (111)
T ss_pred CcCCCCCCcceEcCCCeEECCcccCcCCccc
Confidence 358889886643 56677899996 886554
No 90
>PHA02929 N1R/p28-like protein; Provisional
Probab=22.35 E-value=43 Score=30.12 Aligned_cols=48 Identities=21% Similarity=0.504 Sum_probs=29.8
Q ss_pred CceeCccCCCCCCCC----ceEeccCCCCeeeccccccCccccCCCCeEEcCCCCCc
Q 027884 161 ETLCGSCGGNYNADE----FWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 161 ~~~C~iC~~py~~d~----~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~~k 213 (217)
+..|++|.....+.. ....=..|+.-||..|+..-.. ..-.||.|+..
T Consensus 174 ~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl~-----~~~tCPlCR~~ 225 (238)
T PHA02929 174 DKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWKK-----EKNTCPVCRTP 225 (238)
T ss_pred CCCCccCCcccccCccccccceecCCCCCcccHHHHHHHHh-----cCCCCCCCCCE
Confidence 356999988643221 1112247888999999964322 12369999863
No 91
>KOG1886 consensus BAH domain proteins [Transcription]
Probab=22.15 E-value=52 Score=32.52 Aligned_cols=44 Identities=11% Similarity=-0.228 Sum_probs=36.6
Q ss_pred eCccCCCCCCCCceEeccCCCCeeeccccccCccccCCCCeEEcCCCC
Q 027884 164 CGSCGGNYNADEFWIGCDICERWFHGKCVKITPAKAENIKQYKCPSCS 211 (217)
Q Consensus 164 C~iC~~py~~d~~mIqCD~Ce~WfH~~CVgIt~~~a~~~d~y~Cp~C~ 211 (217)
|+.|++.+.+...+.+|..|..|+|..|++.+.. ++.++|..|+
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 4489999988888999999999999999998873 3567777773
No 92
>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=21.86 E-value=1e+02 Score=21.45 Aligned_cols=32 Identities=16% Similarity=0.341 Sum_probs=20.0
Q ss_pred CCceeCccCCCCCC--CCceEeccCCCCeeeccc
Q 027884 160 SETLCGSCGGNYNA--DEFWIGCDICERWFHGKC 191 (217)
Q Consensus 160 ~~~~C~iC~~py~~--d~~mIqCD~Ce~WfH~~C 191 (217)
....|+.|+..... ...+..|..|+..+|.+-
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~~rD~ 60 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEMDRDV 60 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEECcHH
Confidence 44568888876543 455666777776666543
No 93
>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=21.61 E-value=63 Score=20.16 Aligned_cols=15 Identities=20% Similarity=0.308 Sum_probs=7.9
Q ss_pred CCceEe-ccCCCCeee
Q 027884 174 DEFWIG-CDICERWFH 188 (217)
Q Consensus 174 d~~mIq-CD~Ce~WfH 188 (217)
+.++++ |..|+.|+|
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 445655 999999876
No 94
>COG3896 Chloramphenicol 3-O-phosphotransferase [Defense mechanisms]
Probab=21.44 E-value=34 Score=29.96 Aligned_cols=38 Identities=34% Similarity=0.412 Sum_probs=32.0
Q ss_pred CCCCCCCCCCCCcccccccCCCCCcccchhheehccchHH
Q 027884 39 PAEEVPPELPEPALGINFARDGMNRKDWLSLVAVHTDSWL 78 (217)
Q Consensus 39 p~~~~p~~~pep~~gin~~rd~m~~~~wl~~va~h~d~wl 78 (217)
=-|.|||++--|+.| |-+|+-.+.|=+.+|.||--.=+
T Consensus 59 f~e~lpp~~~d~a~g--~~~~~~v~~dg~~~v~v~~gpi~ 96 (205)
T COG3896 59 FWEALPPEQLDLARG--YTWDSAVEADGLEWVTVHPGPIL 96 (205)
T ss_pred HHHhCCHHhhccccc--cccccccccCCceeeEeechhHH
Confidence 346799999888877 99999999999999999976654
No 95
>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=21.32 E-value=55 Score=24.82 Aligned_cols=34 Identities=24% Similarity=0.494 Sum_probs=21.1
Q ss_pred ccCCceeCccCCCCCCC-CceEeccCCCCeeeccc
Q 027884 158 EHSETLCGSCGGNYNAD-EFWIGCDICERWFHGKC 191 (217)
Q Consensus 158 e~~~~~C~iC~~py~~d-~~mIqCD~Ce~WfH~~C 191 (217)
+.....|-+|+.+...- -.-+.|..|...|...-
T Consensus 3 ~~~~~~C~VCg~~~~g~hyGv~sC~aCk~FFRR~v 37 (90)
T cd07168 3 DESPKLCSICEDKATGLHYGIITCEGCKGFFKRTV 37 (90)
T ss_pred cccCCCCcccCCcCcceEECceehhhhhHhhhhhh
Confidence 33445699998754321 11367999988776543
No 96
>PRK12775 putative trifunctional 2-polyprenylphenol hydroxylase/glutamate synthase subunit beta/ferritin domain-containing protein; Provisional
Probab=20.75 E-value=1e+02 Score=32.92 Aligned_cols=55 Identities=27% Similarity=0.553 Sum_probs=40.6
Q ss_pred cccCCceeCccCCCCCCCCceEeccCCC-CeeeccccccCccccCCCCeEEcCCCCCc
Q 027884 157 DEHSETLCGSCGGNYNADEFWIGCDICE-RWFHGKCVKITPAKAENIKQYKCPSCSMK 213 (217)
Q Consensus 157 ee~~~~~C~iC~~py~~d~~mIqCD~Ce-~WfH~~CVgIt~~~a~~~d~y~Cp~C~~k 213 (217)
-+.....|+.|.+|...++.+|+|-.=+ .|---.|-.++..-+-. --.||.|..+
T Consensus 792 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~ 847 (1006)
T PRK12775 792 AETGVATCPKCHRPLEGDEEYVCCATSELQWRCDDCGKVSEGFAFP--YGMCPACGGK 847 (1006)
T ss_pred ccCCCccCcccCCCCCCCceeEEecCcceeeehhhhccccccccCC--cCcCcccccc
Confidence 3566778999999998889999997554 77777787776653321 2379999864
No 97
>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=20.74 E-value=57 Score=26.43 Aligned_cols=24 Identities=25% Similarity=0.749 Sum_probs=16.7
Q ss_pred ceeCccCCCCCC-----CCceEeccCCCC
Q 027884 162 TLCGSCGGNYNA-----DEFWIGCDICER 185 (217)
Q Consensus 162 ~~C~iC~~py~~-----d~~mIqCD~Ce~ 185 (217)
.+|+.|+.|+.. ....+.|+.|+.
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 579999988643 455667777763
No 98
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=20.60 E-value=49 Score=19.39 Aligned_cols=13 Identities=38% Similarity=0.874 Sum_probs=9.9
Q ss_pred eEeccCCCCeeec
Q 027884 177 WIGCDICERWFHG 189 (217)
Q Consensus 177 mIqCD~Ce~WfH~ 189 (217)
|+.|..|++.|..
T Consensus 2 l~~C~~CgR~F~~ 14 (25)
T PF13913_consen 2 LVPCPICGRKFNP 14 (25)
T ss_pred CCcCCCCCCEECH
Confidence 6788888887754
Done!