Query psy1990
Match_columns 382
No_of_seqs 161 out of 1344
Neff 3.5
Searched_HMMs 46136
Date Fri Aug 16 21:23:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1990.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1990hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4715|consensus 99.2 4.6E-11 9.9E-16 118.2 8.6 119 46-185 86-205 (410)
2 COG5648 NHP6B Chromatin-associ 99.1 1.1E-10 2.4E-15 109.6 6.1 90 1-90 101-209 (211)
3 PTZ00199 high mobility group p 99.0 5.2E-10 1.1E-14 92.0 5.8 47 47-93 45-93 (94)
4 cd01389 MATA_HMG-box MATA_HMG- 99.0 4E-10 8.8E-15 88.2 3.8 48 47-94 24-71 (77)
5 cd01388 SOX-TCF_HMG-box SOX-TC 99.0 4.3E-10 9.3E-15 87.2 3.8 47 47-93 24-70 (72)
6 PF00505 HMG_box: HMG (high mo 98.9 1.2E-09 2.7E-14 82.1 5.4 48 46-93 22-69 (69)
7 cd01390 HMGB-UBF_HMG-box HMGB- 98.9 2.7E-09 5.8E-14 79.4 5.1 44 47-90 23-66 (66)
8 smart00398 HMG high mobility g 98.9 2.9E-09 6.3E-14 79.3 5.2 47 47-93 24-70 (70)
9 PF09011 HMG_box_2: HMG-box do 98.9 3.3E-09 7.1E-14 82.5 5.2 44 50-93 30-73 (73)
10 KOG0381|consensus 98.6 4.2E-08 9.1E-13 78.8 5.2 50 46-95 44-94 (96)
11 cd00084 HMG-box High Mobility 98.6 7.4E-08 1.6E-12 70.9 5.1 43 47-89 23-65 (66)
12 KOG0527|consensus 98.5 2.5E-08 5.3E-13 99.2 1.6 52 46-101 84-135 (331)
13 PTZ00199 high mobility group p 98.4 3.3E-07 7.2E-12 75.4 4.4 39 1-39 55-93 (94)
14 COG5648 NHP6B Chromatin-associ 98.4 3E-07 6.5E-12 86.8 4.2 54 47-100 93-146 (211)
15 PF09011 HMG_box_2: HMG-box do 98.3 5.2E-07 1.1E-11 70.2 3.5 39 1-39 35-73 (73)
16 cd01389 MATA_HMG-box MATA_HMG- 98.2 1.1E-06 2.4E-11 68.9 3.1 39 1-39 32-70 (77)
17 PF00505 HMG_box: HMG (high mo 98.2 1.4E-06 3E-11 65.5 3.4 39 1-39 31-69 (69)
18 cd01390 HMGB-UBF_HMG-box HMGB- 98.2 1.7E-06 3.6E-11 64.4 3.5 36 1-36 31-66 (66)
19 cd01388 SOX-TCF_HMG-box SOX-TC 98.2 1.6E-06 3.5E-11 67.3 3.3 39 1-39 32-70 (72)
20 smart00398 HMG high mobility g 98.1 2.8E-06 6.1E-11 63.2 4.2 39 1-39 32-70 (70)
21 KOG0526|consensus 98.1 2.5E-06 5.4E-11 89.6 3.8 44 49-94 558-601 (615)
22 KOG0381|consensus 97.8 2.3E-05 4.9E-10 63.0 4.1 40 1-40 53-93 (96)
23 cd00084 HMG-box High Mobility 97.7 3.1E-05 6.8E-10 56.9 3.8 35 1-35 31-65 (66)
24 smart00451 ZnF_U1 U1-like zinc 97.3 5.4E-05 1.2E-09 50.8 0.3 32 165-196 3-34 (35)
25 KOG3248|consensus 97.3 0.00022 4.7E-09 72.2 4.3 57 52-108 219-275 (421)
26 KOG0527|consensus 97.1 0.00027 5.8E-09 70.9 2.2 39 1-39 93-131 (331)
27 PF14887 HMG_box_5: HMG (high 97.0 0.00065 1.4E-08 56.3 3.7 50 46-96 25-74 (85)
28 KOG4715|consensus 96.7 0.0019 4.2E-08 65.1 4.3 49 1-49 95-143 (410)
29 PF12874 zf-met: Zinc-finger o 96.6 0.00035 7.6E-09 44.0 -0.9 25 166-190 1-25 (25)
30 PF14887 HMG_box_5: HMG (high 96.4 0.0046 9.9E-08 51.4 4.2 38 3-40 35-72 (85)
31 PF12171 zf-C2H2_jaz: Zinc-fin 96.3 0.00081 1.7E-08 43.7 -0.4 26 166-191 2-27 (27)
32 KOG0528|consensus 95.6 0.0029 6.4E-08 66.3 -0.2 50 46-95 347-396 (511)
33 PF06220 zf-U1: U1 zinc finger 94.6 0.014 3E-07 41.7 0.9 32 166-197 4-37 (38)
34 KOG0717|consensus 92.6 0.034 7.3E-07 58.6 -0.0 37 161-197 288-324 (508)
35 PF13912 zf-C2H2_6: C2H2-type 90.0 0.057 1.2E-06 34.4 -0.9 19 167-185 3-21 (27)
36 KOG3408|consensus 88.6 0.3 6.5E-06 43.7 2.2 53 155-207 47-99 (129)
37 KOG3454|consensus 87.9 0.28 6.1E-06 45.5 1.7 33 166-198 4-38 (165)
38 KOG3248|consensus 86.2 0.48 1.1E-05 48.7 2.4 31 1-31 222-252 (421)
39 PF11304 DUF3106: Protein of u 84.8 4.2 9.1E-05 34.8 7.1 71 3-74 14-103 (107)
40 PF12756 zf-C2H2_2: C2H2 type 84.6 0.18 3.8E-06 39.4 -1.3 31 165-195 50-80 (100)
41 KOG2746|consensus 83.9 0.83 1.8E-05 50.1 3.0 43 46-88 205-247 (683)
42 PF00096 zf-C2H2: Zinc finger, 83.8 0.23 5E-06 30.4 -0.7 20 168-187 3-22 (23)
43 PF06382 DUF1074: Protein of u 82.0 1.1 2.4E-05 42.4 2.6 32 47-78 97-128 (183)
44 KOG0528|consensus 81.4 0.42 9E-06 50.8 -0.4 38 1-38 356-393 (511)
45 COG5112 UFD2 U1-like Zn-finger 79.8 0.79 1.7E-05 40.5 0.9 53 155-207 45-97 (126)
46 KOG2746|consensus 79.6 1.2 2.5E-05 49.1 2.2 34 1-34 214-247 (683)
47 TIGR03481 HpnM hopanoid biosyn 78.8 3.7 8E-05 38.3 5.0 48 47-94 61-110 (198)
48 PRK15117 ABC transporter perip 76.2 7.6 0.00016 36.6 6.3 47 47-93 65-113 (211)
49 KOG4727|consensus 76.0 0.88 1.9E-05 43.0 0.1 34 165-198 75-108 (193)
50 PF07535 zf-DBF: DBF zinc fing 70.8 1.8 4E-05 32.9 0.7 30 165-197 5-34 (49)
51 PF13894 zf-C2H2_4: C2H2-type 70.8 1 2.2E-05 26.8 -0.6 19 168-186 3-21 (24)
52 smart00586 ZnF_DBF Zinc finger 68.7 3 6.6E-05 31.8 1.5 33 162-197 2-34 (49)
53 PF03194 LUC7: LUC7 N_terminus 68.3 2.3 5.1E-05 41.3 1.0 28 166-193 191-221 (254)
54 PHA02768 hypothetical protein; 65.5 1.9 4.1E-05 33.6 -0.2 23 167-191 7-29 (55)
55 PF05494 Tol_Tol_Ttg2: Toluene 65.3 9 0.00019 34.1 4.0 48 47-94 35-84 (170)
56 COG5200 LUC7 U1 snRNP componen 64.8 3.2 6.9E-05 40.6 1.2 29 166-194 186-217 (258)
57 KOG2505|consensus 58.3 6 0.00013 42.8 1.9 37 162-198 63-99 (591)
58 TIGR03481 HpnM hopanoid biosyn 57.5 16 0.00035 34.1 4.4 37 4-40 73-110 (198)
59 COG5188 PRP9 Splicing factor 3 54.4 5.8 0.00013 41.4 1.0 36 164-199 237-272 (470)
60 PF12756 zf-C2H2_2: C2H2 type 49.5 5.5 0.00012 31.0 0.0 19 168-186 2-20 (100)
61 smart00355 ZnF_C2H2 zinc finge 47.9 5.7 0.00012 23.5 -0.1 20 167-186 2-21 (26)
62 KOG0796|consensus 47.3 11 0.00024 38.5 1.7 29 166-194 187-218 (319)
63 PF03480 SBP_bac_7: Bacterial 47.2 50 0.0011 31.3 6.0 69 6-84 213-281 (286)
64 COG5136 U1 snRNP-specific prot 46.8 14 0.0003 35.0 2.1 33 166-198 4-38 (188)
65 KOG2785|consensus 46.5 8.1 0.00017 40.3 0.6 36 161-196 64-99 (390)
66 PRK12751 cpxP periplasmic stre 45.0 1E+02 0.0023 28.5 7.5 78 10-94 55-151 (162)
67 PHA00616 hypothetical protein 41.5 13 0.00028 27.9 0.9 19 167-185 3-21 (44)
68 KOG1074|consensus 41.0 12 0.00027 42.6 1.0 26 161-186 903-928 (958)
69 PRK15117 ABC transporter perip 39.5 45 0.00098 31.5 4.4 38 3-40 76-114 (211)
70 PF05494 Tol_Tol_Ttg2: Toluene 39.1 42 0.0009 29.9 3.9 36 4-39 47-83 (170)
71 KOG3032|consensus 38.9 11 0.00023 37.5 0.1 36 161-197 31-66 (264)
72 PF09237 GAGA: GAGA factor; I 37.0 10 0.00023 29.7 -0.2 21 166-186 25-45 (54)
73 PF11304 DUF3106: Protein of u 36.3 86 0.0019 26.9 5.2 12 9-20 2-13 (107)
74 KOG0150|consensus 36.0 21 0.00045 36.7 1.6 34 164-197 9-43 (336)
75 PF06382 DUF1074: Protein of u 35.5 21 0.00046 33.9 1.6 25 2-26 106-130 (183)
76 PRK12750 cpxP periplasmic repr 35.1 3.2E+02 0.007 25.3 9.1 37 53-89 124-160 (170)
77 PF13909 zf-H2C2_5: C2H2-type 33.4 9.7 0.00021 23.6 -0.7 19 168-187 3-21 (24)
78 KOG3817|consensus 33.2 38 0.00082 35.8 3.0 93 72-174 320-415 (452)
79 PF12269 zf-CpG_bind_C: CpG bi 31.3 15 0.00032 36.1 -0.2 26 159-185 78-103 (236)
80 PF01352 KRAB: KRAB box; Inte 31.2 33 0.00072 24.9 1.6 27 51-77 2-29 (41)
81 KOG3214|consensus 29.1 16 0.00034 32.1 -0.4 19 163-181 45-63 (109)
82 KOG1074|consensus 28.5 19 0.00041 41.2 -0.0 24 166-189 634-657 (958)
83 PLN02748 tRNA dimethylallyltra 28.1 23 0.0005 37.7 0.5 31 167-197 420-451 (468)
84 KOG2462|consensus 27.8 20 0.00042 36.2 -0.1 21 167-187 217-237 (279)
85 PF14968 CCDC84: Coiled coil p 26.0 27 0.00058 35.9 0.5 28 167-197 1-28 (336)
86 PF12720 DUF3807: Protein of u 24.7 1E+02 0.0022 28.9 4.0 29 236-269 49-77 (172)
87 PF12907 zf-met2: Zinc-binding 24.6 35 0.00076 25.1 0.8 22 167-188 3-27 (40)
88 KOG3792|consensus 23.7 33 0.00073 38.7 0.8 29 165-193 359-387 (816)
89 PF11278 DUF3079: Protein of u 22.5 33 0.00072 26.7 0.3 13 336-348 6-18 (52)
90 PHA00732 hypothetical protein 21.9 26 0.00056 28.7 -0.4 21 167-187 3-23 (79)
91 PF08073 CHDNT: CHDNT (NUC034) 21.8 36 0.00077 26.8 0.4 23 46-68 30-52 (55)
92 PRK09706 transcriptional repre 21.4 1.6E+02 0.0036 25.2 4.4 41 54-94 87-127 (135)
No 1
>KOG4715|consensus
Probab=99.19 E-value=4.6e-11 Score=118.21 Aligned_cols=119 Identities=24% Similarity=0.409 Sum_probs=93.0
Q ss_pred hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHHHHH-HhhhhhhhccccccccccCCC
Q psy1990 46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLR-RKRVKKIQHHCLTAKVFSGTS 124 (382)
Q Consensus 46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~~~k-rk~~KK~k~~~~~~kv~s~ts 124 (382)
.+|.+..-||.|+||.+|..|.++||+.|.+..+.+|..|++-|++|..+++|.+|.- +-.++.. | .+
T Consensus 86 ~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp~y~ayinaKsra~a~--------l--e~- 154 (410)
T KOG4715|consen 86 SNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYLAYINAKSRAEAA--------L--EE- 154 (410)
T ss_pred cCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCchHHHHhhhhhhhhhh--------h--cc-
Confidence 3688999999999999999999999999999999999999999999999999999985 3333332 1 00
Q ss_pred CCCCCCCcccCCCccCCCCccccccccCCcccccccCCcchhhhhhhhhhhhhhhhhhhhh
Q psy1990 125 EGRDSGTYKTRGGLQANGTEESDIATDATDEIDEEEEDNEELYCRVCDQWFTTLHNKREHL 185 (382)
Q Consensus 125 ~~~~ng~~~~~gg~~~dg~~~~di~~d~~~~~d~~~~d~~~~~c~~c~q~fs~~hnk~eh~ 185 (382)
.....++..-.|+ -.| ++++|+|+||-|||.+-.|+++.+|-++|++---+
T Consensus 155 ~sr~~~sr~~~ge--------~~~--~IQPaeDeDD~ddg~stkhla~arf~rN~rLIsei 205 (410)
T KOG4715|consen 155 ESRQRQSRMEKGE--------PYM--SIQPAEDEDDYDDGFSTKHLATARFQRNHRLISEI 205 (410)
T ss_pred ccccccchhhcCC--------cce--ecccccCccccccccchhhhhhhhhhhhhHHHHHH
Confidence 0011112211122 125 78999999999999999999999999999875443
No 2
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=99.10 E-value=1.1e-10 Score=109.59 Aligned_cols=90 Identities=30% Similarity=0.493 Sum_probs=79.7
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcccc-------hhh------------hhhhhhHHHHhHHHHH
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD-------AYQ------------SYLILLFFQVTKLLGN 61 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~KD-------AY~------------lfPglSftEIsK~LGE 61 (382)
|+|++|++|++|+++||++|...|..++++|+.++..|.++. +|. ..|+.+..++++.+|.
T Consensus 101 ~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~~~~~~~~e~~~~~r~~~~~~~~~~~~~e~~k~~~~ 180 (211)
T COG5648 101 VGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSPDKALVEETKIISK 180 (211)
T ss_pred HHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCCCCCchhhhccHHhccccCCCCcchhhhHHhhhhhh
Confidence 578999999999999999999999999999999999998752 232 2456678899999999
Q ss_pred HhcCCCcchhhhhHHHHHHHHHHHHHHHH
Q psy1990 62 EWSKLSLPEKKVYLDRAEVDKKRYREELK 90 (382)
Q Consensus 62 rWK~LSdEEKqpYedkAekdKeRYekEMk 90 (382)
.|++|++.-|.+|++.+.+++..|...++
T Consensus 181 ~w~el~~skK~~~~~~~Kk~k~~~~~~~~ 209 (211)
T COG5648 181 AWSELDESKKKKYIDKYKKLKEEYDSFYP 209 (211)
T ss_pred hhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence 99999999999999999999999987654
No 3
>PTZ00199 high mobility group protein; Provisional
Probab=99.01 E-value=5.2e-10 Score=91.97 Aligned_cols=47 Identities=38% Similarity=0.529 Sum_probs=44.2
Q ss_pred hhhhh--HHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990 47 YLILL--FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93 (382)
Q Consensus 47 fPglS--ftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk 93 (382)
+|+++ +++|+++||++|+.||+++|++|.++|+.++++|..+|.+|.
T Consensus 45 ~P~~~~~~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~ 93 (94)
T PTZ00199 45 NPELAKDVAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA 93 (94)
T ss_pred CcCCcccHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46765 899999999999999999999999999999999999999995
No 4
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=98.97 E-value=4e-10 Score=88.22 Aligned_cols=48 Identities=25% Similarity=0.324 Sum_probs=45.7
Q ss_pred hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990 47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 94 (382)
Q Consensus 47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk 94 (382)
+|++++.+|+++||++|+.||+++|++|.++|+.++++|.+++.+|+-
T Consensus 24 ~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky 71 (77)
T cd01389 24 NPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKY 71 (77)
T ss_pred CCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCcc
Confidence 578999999999999999999999999999999999999999999963
No 5
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=98.97 E-value=4.3e-10 Score=87.22 Aligned_cols=47 Identities=28% Similarity=0.400 Sum_probs=45.3
Q ss_pred hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990 47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93 (382)
Q Consensus 47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk 93 (382)
+|++++++|++.||++|+.||+++|++|.++|+.++++|.+++.+|+
T Consensus 24 ~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~ 70 (72)
T cd01388 24 YPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK 70 (72)
T ss_pred CCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence 68999999999999999999999999999999999999999999885
No 6
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=98.95 E-value=1.2e-09 Score=82.09 Aligned_cols=48 Identities=33% Similarity=0.520 Sum_probs=45.8
Q ss_pred hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990 46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93 (382)
Q Consensus 46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk 93 (382)
.+|++++.+|++.||++|++||+++|++|.+.|..++.+|.++|.+|+
T Consensus 22 ~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~ 69 (69)
T PF00505_consen 22 ENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK 69 (69)
T ss_dssp HSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 368999999999999999999999999999999999999999999995
No 7
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=98.88 E-value=2.7e-09 Score=79.43 Aligned_cols=44 Identities=45% Similarity=0.664 Sum_probs=41.6
Q ss_pred hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHH
Q psy1990 47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 90 (382)
Q Consensus 47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMk 90 (382)
+|++++.+|++.||++|++||+++|++|.++|+.++++|..+|.
T Consensus 23 ~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~~ 66 (66)
T cd01390 23 NPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 66 (66)
T ss_pred CcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 57889999999999999999999999999999999999999873
No 8
>smart00398 HMG high mobility group.
Probab=98.88 E-value=2.9e-09 Score=79.27 Aligned_cols=47 Identities=38% Similarity=0.570 Sum_probs=44.8
Q ss_pred hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990 47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93 (382)
Q Consensus 47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk 93 (382)
+|++++++|++.||.+|+.||+++|++|.++|+.++++|.+++..|+
T Consensus 24 ~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~ 70 (70)
T smart00398 24 NPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70 (70)
T ss_pred CcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 57889999999999999999999999999999999999999999884
No 9
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=98.86 E-value=3.3e-09 Score=82.49 Aligned_cols=44 Identities=39% Similarity=0.619 Sum_probs=40.5
Q ss_pred hhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHH
Q psy1990 50 LLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 93 (382)
Q Consensus 50 lSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYk 93 (382)
.++.|+++.||.+|++||++||.+|.++|+.++++|+.+|..|.
T Consensus 30 ~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~ 73 (73)
T PF09011_consen 30 QSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN 73 (73)
T ss_dssp SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred CCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 46889999999999999999999999999999999999999984
No 10
>KOG0381|consensus
Probab=98.64 E-value=4.2e-08 Score=78.82 Aligned_cols=50 Identities=34% Similarity=0.473 Sum_probs=46.8
Q ss_pred hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHH-HHHhh
Q psy1990 46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK-VYRKS 95 (382)
Q Consensus 46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMk-eYkks 95 (382)
.+|++++.+|++.+|++|++|++++|++|...|..++++|..+|. .|+.+
T Consensus 44 ~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~ 94 (96)
T KOG0381|consen 44 ENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKAS 94 (96)
T ss_pred hCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 368899999999999999999999999999999999999999999 88764
No 11
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=98.59 E-value=7.4e-08 Score=70.94 Aligned_cols=43 Identities=42% Similarity=0.623 Sum_probs=40.7
Q ss_pred hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHH
Q psy1990 47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 89 (382)
Q Consensus 47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEM 89 (382)
+|++++.+|++.||.+|+.|++++|++|.+.|+.++.+|.+++
T Consensus 23 ~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~ 65 (66)
T cd00084 23 NPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM 65 (66)
T ss_pred CcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 5788999999999999999999999999999999999999875
No 12
>KOG0527|consensus
Probab=98.54 E-value=2.5e-08 Score=99.24 Aligned_cols=52 Identities=29% Similarity=0.418 Sum_probs=48.8
Q ss_pred hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHHH
Q psy1990 46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSY 101 (382)
Q Consensus 46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~~ 101 (382)
.+|+|-+.||+|.||.+||.|+++||.||+++|++.|..+.+|..+|+ |+.-
T Consensus 84 qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYK----YRPR 135 (331)
T KOG0527|consen 84 QNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYK----YRPR 135 (331)
T ss_pred hCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcc----cccc
Confidence 378999999999999999999999999999999999999999999994 7773
No 13
>PTZ00199 high mobility group protein; Provisional
Probab=98.39 E-value=3.3e-07 Score=75.44 Aligned_cols=39 Identities=44% Similarity=0.688 Sum_probs=37.3
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk 39 (382)
|+++||++|+.||+++|.+|+++|..++.+|..+|..|.
T Consensus 55 vsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~ 93 (94)
T PTZ00199 55 VGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA 93 (94)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 578999999999999999999999999999999999985
No 14
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=98.37 E-value=3e-07 Score=86.77 Aligned_cols=54 Identities=33% Similarity=0.512 Sum_probs=50.2
Q ss_pred hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHH
Q psy1990 47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS 100 (382)
Q Consensus 47 fPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~ 100 (382)
+|.++|.+|++.+|++|++|+++||++|...|..++++|..++..|..+..+..
T Consensus 93 ~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~~ 146 (211)
T COG5648 93 NPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKA 146 (211)
T ss_pred CCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCCC
Confidence 468899999999999999999999999999999999999999999998876554
No 15
>PF09011 HMG_box_2: HMG-box domain; InterPro: IPR015101 This domain is predominantly found in Maelstrom homologue proteins. It has no known function. ; GO: 0005634 nucleus; PDB: 2EQZ_A 1V64_A 2CTO_A 1H5P_A 3TQ6_A 3FGH_A 3TMM_A 1J3X_A 2YRQ_A 1AAB_A ....
Probab=98.31 E-value=5.2e-07 Score=70.18 Aligned_cols=39 Identities=41% Similarity=0.682 Sum_probs=35.3
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk 39 (382)
|++.||..|++||++||.+|+++|+.++++|..+|..|.
T Consensus 35 ~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~ 73 (73)
T PF09011_consen 35 VMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN 73 (73)
T ss_dssp HHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 468899999999999999999999999999999999873
No 16
>cd01389 MATA_HMG-box MATA_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include the fungal mating type gene products MC, MATA1 and Ste11.
Probab=98.19 E-value=1.1e-06 Score=68.86 Aligned_cols=39 Identities=28% Similarity=0.502 Sum_probs=37.3
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk 39 (382)
|+++||++|+.||+++|++|.++|+.++++|..++..|+
T Consensus 32 isk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yk 70 (77)
T cd01389 32 ISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYK 70 (77)
T ss_pred HHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCc
Confidence 689999999999999999999999999999999999885
No 17
>PF00505 HMG_box: HMG (high mobility group) box; InterPro: IPR000910 High mobility group (HMG or HMGB) proteins are a family of relatively low molecular weight non-histone components in chromatin. HMG1 (also called HMG-T in fish) and HMG2 are two highly related proteins that bind single-stranded DNA preferentially and unwind double-stranded DNA. Although they have no sequence specificity, they have a high affinity for bent or distorted DNA, and bend linear DNA. HMG1 and HMG2 contain two DNA-binding HMG-box domains (A and B) that show structural and functional differences, and have a long acidic C-terminal domain rich in aspartic and glutamic acid residues. The acidic tail modulates the affinity of the tandem HMG boxes in HMG1 and 2 for a variety of DNA targets. HMG1 and 2 appear to play important architectural roles in the assembly of nucleoprotein complexes in a variety of biological processes, for example V(D)J recombination, the initiation of transcription, and DNA repair []. The profile in this entry describing the HMG-domains is much more general than the signature. In addition to the HMG1 and HMG2 proteins, HMG-domains occur in single or multiple copies in the following protein classes; the SOX family of transcription factors; SRY sex determining region Y protein and related proteins []; LEF1 lymphoid enhancer binding factor 1 []; SSRP recombination signal recognition protein; MTF1 mitochondrial transcription factor 1; UBF1/2 nucleolar transcription factors; Abf2 yeast ARS-binding factor []; and Saccharomyces cerevisiae transcription factors Ixr1, Rox1, Nhp6a, Nhp6b and Spp41.; GO: 0003677 DNA binding; PDB: 1I11_A 1J3C_A 1J3D_A 1WZ6_A 1WGF_A 2D7L_A 1GT0_D 3U2B_C 2CRJ_A 2CS1_A ....
Probab=98.18 E-value=1.4e-06 Score=65.52 Aligned_cols=39 Identities=38% Similarity=0.726 Sum_probs=37.1
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk 39 (382)
|+++||++|++||+++|++|.+.|.+++.+|.++|..|+
T Consensus 31 i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~ 69 (69)
T PF00505_consen 31 ISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK 69 (69)
T ss_dssp HHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred chhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 578999999999999999999999999999999999884
No 18
>cd01390 HMGB-UBF_HMG-box HMGB-UBF_HMG-box, class II and III members of the HMG-box superfamily of DNA-binding proteins. These proteins bind the minor groove of DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III members include nucleolar and mitochondrial transcription factors, UBF and mtTF1, which bind four-way DNA junctions.
Probab=98.17 E-value=1.7e-06 Score=64.41 Aligned_cols=36 Identities=56% Similarity=0.914 Sum_probs=33.9
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHH
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 36 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMe 36 (382)
|++.||++|+.||+++|++|.++|.+++++|.++|.
T Consensus 31 i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~~ 66 (66)
T cd01390 31 VTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 66 (66)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 578999999999999999999999999999999873
No 19
>cd01388 SOX-TCF_HMG-box SOX-TCF_HMG-box, class I member of the HMG-box superfamily of DNA-binding proteins. These proteins contain a single HMG box, and bind the minor groove of DNA in a highly sequence-specific manner. Members include SRY and its homologs in insects and vertebrates, and transcription factor-like proteins, TCF-1, -3, -4, and LEF-1. They appear to bind the minor groove of the A/T C A A A G/C-motif.
Probab=98.15 E-value=1.6e-06 Score=67.29 Aligned_cols=39 Identities=31% Similarity=0.508 Sum_probs=36.8
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk 39 (382)
|+|+||++|+.||+++|++|.++|..++++|.+++-.|+
T Consensus 32 isk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~ 70 (72)
T cd01388 32 ISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK 70 (72)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence 578999999999999999999999999999999998874
No 20
>smart00398 HMG high mobility group.
Probab=98.14 E-value=2.8e-06 Score=63.18 Aligned_cols=39 Identities=44% Similarity=0.766 Sum_probs=36.8
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk 39 (382)
|+++||.+|+.||+++|++|.++|..++++|.++|..|+
T Consensus 32 i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~ 70 (70)
T smart00398 32 ISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70 (70)
T ss_pred HHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 578999999999999999999999999999999999874
No 21
>KOG0526|consensus
Probab=98.07 E-value=2.5e-06 Score=89.56 Aligned_cols=44 Identities=36% Similarity=0.646 Sum_probs=42.1
Q ss_pred hhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990 49 ILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 94 (382)
Q Consensus 49 glSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk 94 (382)
|.+++||+|.+|++|+.||. |.+|+++|+.+|.+|+.||++|+.
T Consensus 558 gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk~ 601 (615)
T KOG0526|consen 558 GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYKN 601 (615)
T ss_pred CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhcC
Confidence 67899999999999999999 999999999999999999999983
No 22
>KOG0381|consensus
Probab=97.80 E-value=2.3e-05 Score=63.04 Aligned_cols=40 Identities=38% Similarity=0.651 Sum_probs=37.5
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHH-hhcc
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK-VYRK 40 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMe-eYk~ 40 (382)
|+|++|++|++|++++|.+|+..+..++++|..+|. .|+.
T Consensus 53 v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~ 93 (96)
T KOG0381|consen 53 VAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKA 93 (96)
T ss_pred HHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 578999999999999999999999999999999999 8754
No 23
>cd00084 HMG-box High Mobility Group (HMG)-box is found in a variety of eukaryotic chromosomal proteins and transcription factors. HMGs bind to the minor groove of DNA and have been classified by DNA binding preferences. Two phylogenically distinct groups of Class I proteins bind DNA in a sequence specific fashion and contain a single HMG box. One group (SOX-TCF) includes transcription factors, TCF-1, -3, -4; and also SRY and LEF-1, which bind four-way DNA junctions and duplex DNA targets. The second group (MATA) includes fungal mating type gene products MC, MATA1 and Ste11. Class II and III proteins (HMGB-UBF) bind DNA in a non-sequence specific fashion and contain two or more tandem HMG boxes. Class II members include non-histone chromosomal proteins, HMG1 and HMG2, which bind to bent or distorted DNA such as four-way DNA junctions, synthetic DNA cruciforms, kinked cisplatin-modified DNA, DNA bulges, cross-overs in supercoiled DNA, and can cause looping of linear DNA. Class III member
Probab=97.75 E-value=3.1e-05 Score=56.92 Aligned_cols=35 Identities=49% Similarity=0.857 Sum_probs=32.9
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHH
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 35 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEM 35 (382)
|++.||++|+.||+++|++|.+.|+.++..|.+++
T Consensus 31 i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~ 65 (66)
T cd00084 31 ISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM 65 (66)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 57899999999999999999999999999998875
No 24
>smart00451 ZnF_U1 U1-like zinc finger. Family of C2H2-type zinc fingers, present in matrin, U1 small nuclear ribonucleoprotein C and other RNA-binding proteins.
Probab=97.33 E-value=5.4e-05 Score=50.81 Aligned_cols=32 Identities=31% Similarity=0.723 Sum_probs=29.4
Q ss_pred hhhhhhhhhhhhhhhhhhhhhchhhhHHhhhh
Q psy1990 165 ELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQ 196 (382)
Q Consensus 165 ~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~ 196 (382)
-.||.+|+.+|.+.+..+.|+.|++|..++..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 46899999999999999999999999998863
No 25
>KOG3248|consensus
Probab=97.31 E-value=0.00022 Score=72.16 Aligned_cols=57 Identities=25% Similarity=0.388 Sum_probs=50.3
Q ss_pred HHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHhhhh
Q psy1990 52 FFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVK 108 (382)
Q Consensus 52 ftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~aYk~~~krk~~K 108 (382)
..+|.++||++|.+||-+|..+|.++|.++++-+.+....|-+..+|-...+|+++|
T Consensus 219 SAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdNYgKKkKrkReK 275 (421)
T KOG3248|consen 219 SAAINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYGKKKKRKREK 275 (421)
T ss_pred HHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhhhhhhhhhhhhc
Confidence 457999999999999999999999999999999999999999988888555555554
No 26
>KOG0527|consensus
Probab=97.08 E-value=0.00027 Score=70.88 Aligned_cols=39 Identities=36% Similarity=0.565 Sum_probs=36.4
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhc
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 39 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk 39 (382)
|+|.||++||.|+++||.+|++.|++.|....++.=+||
T Consensus 93 ISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYK 131 (331)
T KOG0527|consen 93 ISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYK 131 (331)
T ss_pred HHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcc
Confidence 799999999999999999999999999999988887774
No 27
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=97.03 E-value=0.00065 Score=56.32 Aligned_cols=50 Identities=26% Similarity=0.396 Sum_probs=43.1
Q ss_pred hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhhh
Q psy1990 46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD 96 (382)
Q Consensus 46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks~ 96 (382)
.|+.....+ .+.+...|++|++.+|-+|+.+|.++.++|+.+|.+|+..+
T Consensus 25 ~~~~dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~ 74 (85)
T PF14887_consen 25 KFRNDRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAP 74 (85)
T ss_dssp HTTSTHHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CC
T ss_pred HhhHhHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCC
Confidence 567666665 56999999999999999999999999999999999997654
No 28
>KOG4715|consensus
Probab=96.65 E-value=0.0019 Score=65.07 Aligned_cols=49 Identities=37% Similarity=0.687 Sum_probs=46.0
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhhh
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLI 49 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~KDAY~lfPg 49 (382)
|.|+||.+|+.|+++||+.|...++.+|..|.+.|+.|..+-+|+.|.+
T Consensus 95 iGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp~y~ayin 143 (410)
T KOG4715|consen 95 IGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYLAYIN 143 (410)
T ss_pred HHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCchHHHHhh
Confidence 6799999999999999999999999999999999999998888887765
No 29
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=96.59 E-value=0.00035 Score=44.00 Aligned_cols=25 Identities=32% Similarity=0.939 Sum_probs=23.7
Q ss_pred hhhhhhhhhhhhhhhhhhhhchhhh
Q psy1990 166 LYCRVCDQWFTTLHNKREHLNGRQH 190 (382)
Q Consensus 166 ~~c~~c~q~fs~~hnk~eh~~~~~h 190 (382)
.+|.+|+..|++.-..+.||.|+.|
T Consensus 1 ~~C~~C~~~f~s~~~~~~H~~s~~H 25 (25)
T PF12874_consen 1 FYCDICNKSFSSENSLRQHLRSKKH 25 (25)
T ss_dssp EEETTTTEEESSHHHHHHHHTTHHH
T ss_pred CCCCCCCCCcCCHHHHHHHHCcCCC
Confidence 3799999999999999999999998
No 30
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=96.37 E-value=0.0046 Score=51.41 Aligned_cols=38 Identities=34% Similarity=0.640 Sum_probs=34.9
Q ss_pred chHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcc
Q psy1990 3 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 40 (382)
Q Consensus 3 KiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~ 40 (382)
+.+...|++|++.+|-+|...|.+|.++|+.+|.+|+.
T Consensus 35 kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~ 72 (85)
T PF14887_consen 35 KAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRS 72 (85)
T ss_dssp HHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-
T ss_pred HHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhc
Confidence 45788999999999999999999999999999999975
No 31
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=96.33 E-value=0.00081 Score=43.71 Aligned_cols=26 Identities=27% Similarity=0.912 Sum_probs=24.4
Q ss_pred hhhhhhhhhhhhhhhhhhhhchhhhH
Q psy1990 166 LYCRVCDQWFTTLHNKREHLNGRQHF 191 (382)
Q Consensus 166 ~~c~~c~q~fs~~hnk~eh~~~~~h~ 191 (382)
.||.+|+.+|++....+.||.|+.|.
T Consensus 2 ~~C~~C~k~f~~~~~~~~H~~sk~Hk 27 (27)
T PF12171_consen 2 FYCDACDKYFSSENQLKQHMKSKKHK 27 (27)
T ss_dssp CBBTTTTBBBSSHHHHHCCTTSHHHH
T ss_pred CCcccCCCCcCCHHHHHHHHccCCCC
Confidence 48999999999999999999999994
No 32
>KOG0528|consensus
Probab=95.61 E-value=0.0029 Score=66.34 Aligned_cols=50 Identities=24% Similarity=0.361 Sum_probs=46.0
Q ss_pred hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHhh
Q psy1990 46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 95 (382)
Q Consensus 46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkks 95 (382)
.|||+-...|+|+||.+||.||..||+||.++-.+.-+.+.+....|+=+
T Consensus 347 A~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYk 396 (511)
T KOG0528|consen 347 AFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYK 396 (511)
T ss_pred cCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccC
Confidence 38999999999999999999999999999999999988999988888755
No 33
>PF06220 zf-U1: U1 zinc finger; InterPro: IPR013085 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. C2H2-type (classical) zinc fingers (Znf) were the first class to be characterised. They contain a short beta hairpin and an alpha helix (beta/beta/alpha structure), where a single zinc atom is held in place by Cys(2)His(2) (C2H2) residues in a tetrahedral array. C2H2 Znf's can be divided into three groups based on the number and pattern of fingers: triple-C2H2 (binds single ligand), multiple-adjacent-C2H2 (binds multiple ligands), and separated paired-C2H2 []. C2H2 Znf's are the most common DNA-binding motifs found in eukaryotic transcription factors, and have also been identified in prokaryotes []. Transcription factors usually contain several Znf's (each with a conserved beta/beta/alpha structure) capable of making multiple contacts along the DNA, where the C2H2 Znf motifs recognise DNA sequences by binding to the major groove of DNA via a short alpha-helix in the Znf, the Znf spanning 3-4 bases of the DNA []. C2H2 Znf's can also bind to RNA and protein targets []. This entry represents a C2H2-type zinc finger motif found in several U1 small nuclear ribonucleoprotein C (U1-C) proteins. Some proteins contain multiple copies of this motif. The U1 small nuclear ribonucleoprotein (U1 snRNP) binds to the pre-mRNA 5' splice site at early stages of spliceosome assembly. Recruitment of U1 to a class of weak 5' splice site is promoted by binding of the protein TIA-1 to uridine-rich sequences immediately downstream from the 5' splice site. Binding of TIA-1 in the vicinity of a 5' splice site helps to stabilise U1 snRNP recruitment, at least in part, via a direct interaction with U1-C, thus providing one molecular mechanism for the function of this splicing regulator []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2VRD_A.
Probab=94.62 E-value=0.014 Score=41.75 Aligned_cols=32 Identities=22% Similarity=0.616 Sum_probs=20.2
Q ss_pred hhhhhhhhhh--hhhhhhhhhhchhhhHHhhhhc
Q psy1990 166 LYCRVCDQWF--TTLHNKREHLNGRQHFQAVEQS 197 (382)
Q Consensus 166 ~~c~~c~q~f--s~~hnk~eh~~~~~h~~~~~~~ 197 (382)
-||-.|+.|| .+....+-|..|.+|..+++..
T Consensus 4 yyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~~ 37 (38)
T PF06220_consen 4 YYCDYCKKYLTHDSPSIRKQHERGWKHKENVKRY 37 (38)
T ss_dssp -B-TTT--B-S--SHHHHHHHT--THHHHHHHHH
T ss_pred eecccccceecCCChHHHHHhhccHHHHHHHHHh
Confidence 3899999999 3445669999999999999764
No 34
>KOG0717|consensus
Probab=92.61 E-value=0.034 Score=58.57 Aligned_cols=37 Identities=30% Similarity=0.627 Sum_probs=32.2
Q ss_pred CCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhc
Q psy1990 161 EDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQS 197 (382)
Q Consensus 161 ~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~ 197 (382)
.+++.|||-+|+..|-|---+.-|-.+++|.-||+.-
T Consensus 288 ~~ge~lyC~vCnKsFKseKq~kNHEnSKKHkenv~eL 324 (508)
T KOG0717|consen 288 NEGEVLYCVVCNKSFKSEKQLKNHENSKKHKENVAEL 324 (508)
T ss_pred hcCCceEEeeccccccchHHHHhhHHHHHHHHHHHHH
Confidence 3344499999999999999999999999999998753
No 35
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=90.00 E-value=0.057 Score=34.41 Aligned_cols=19 Identities=37% Similarity=0.698 Sum_probs=18.2
Q ss_pred hhhhhhhhhhhhhhhhhhh
Q psy1990 167 YCRVCDQWFTTLHNKREHL 185 (382)
Q Consensus 167 ~c~~c~q~fs~~hnk~eh~ 185 (382)
.|.+|++.|++..+.++|+
T Consensus 3 ~C~~C~~~F~~~~~l~~H~ 21 (27)
T PF13912_consen 3 ECDECGKTFSSLSALREHK 21 (27)
T ss_dssp EETTTTEEESSHHHHHHHH
T ss_pred CCCccCCccCChhHHHHHh
Confidence 5999999999999999999
No 36
>KOG3408|consensus
Probab=88.64 E-value=0.3 Score=43.69 Aligned_cols=53 Identities=19% Similarity=0.468 Sum_probs=44.5
Q ss_pred ccccccCCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhccccccccccc
Q psy1990 155 EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAVNESNS 207 (382)
Q Consensus 155 ~~d~~~~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~~l~~~~~~~ 207 (382)
+||.|=|-.|--||-.|..||.+--++..|.-|+-|..-|-.--+.+-.+++.
T Consensus 47 ~~D~dlPG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRvK~l~~~PySQeeA 99 (129)
T KOG3408|consen 47 EIDPDLPGGGQFYCIECARYFIDAKALKTHFKTKVHKRRVKELREVPYSQEEA 99 (129)
T ss_pred cCCCCCCCCceeehhhhhhhhcchHHHHHHHhccHHHHHHHhcccCCccHHHH
Confidence 56888899999999999999999999999999999998887655555554443
No 37
>KOG3454|consensus
Probab=87.93 E-value=0.28 Score=45.55 Aligned_cols=33 Identities=33% Similarity=0.724 Sum_probs=29.5
Q ss_pred hhhhhhhhhhh--hhhhhhhhhchhhhHHhhhhcc
Q psy1990 166 LYCRVCDQWFT--TLHNKREHLNGRQHFQAVEQSG 198 (382)
Q Consensus 166 ~~c~~c~q~fs--~~hnk~eh~~~~~h~~~~~~~~ 198 (382)
-||--|+-|-+ |+|+-+-|+.||+|++|+.-+.
T Consensus 4 YyCDYCdt~LthDslsvRK~H~~GrkH~~nvk~YY 38 (165)
T KOG3454|consen 4 YYCDYCDTYLTHDSLSVRKTHCGGRKHKDNVKDYY 38 (165)
T ss_pred chhhhhhhhhhcccHHHHHhhhhhHHHHHHHHHHH
Confidence 48999998875 7999999999999999998775
No 38
>KOG3248|consensus
Probab=86.17 E-value=0.48 Score=48.69 Aligned_cols=31 Identities=26% Similarity=0.551 Sum_probs=28.6
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHH
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRY 31 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRY 31 (382)
|-++||.+|-.||-+|..+|.++|.++|+-.
T Consensus 222 iNqiLGrRWH~LSrEEQAKYyElArKerqlH 252 (421)
T KOG3248|consen 222 INQILGRRWHALSREEQAKYYELARKERQLH 252 (421)
T ss_pred HHHHHhHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 4689999999999999999999999998776
No 39
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=84.79 E-value=4.2 Score=34.79 Aligned_cols=71 Identities=24% Similarity=0.440 Sum_probs=44.9
Q ss_pred chHHHHhcCCChHHHHHHHHHHH-------HHHHHHHHHHHhhccc---------chhhhhhhhhHHHHhHHHHHHh---
Q psy1990 3 KLLGNEWSKLSLPEKKVYLDRAE-------VDKKRYREELKVYRKS---------DAYQSYLILLFFQVTKLLGNEW--- 63 (382)
Q Consensus 3 KiLGEkWK~LSdeEKqkYedkAk-------eDKeRYeeEMeeYk~K---------DAY~lfPglSftEIsK~LGErW--- 63 (382)
.-+...|..|++..|.++...+. +++.++..-|..|..= ..|..|..++..+.. .|...|
T Consensus 14 ~pl~~~W~~l~~~qr~k~l~~a~r~~~mspeqq~r~~~rm~~W~~LspeqR~~~R~~~~~~~~Lpp~qR~-~lr~~w~~y 92 (107)
T PF11304_consen 14 APLAERWNSLPPEQRRKWLQIAERWPSMSPEQQQRLRERMRRWAALSPEQRQQARENYQRFKQLPPEQRQ-ALRARWEAY 92 (107)
T ss_pred HHHHHHHhcCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHcCCHHHHH-HHHHHHHHH
Confidence 45788999999999987766654 4666677777766431 134445555544433 456666
Q ss_pred cCCCcchhhhh
Q psy1990 64 SKLSLPEKKVY 74 (382)
Q Consensus 64 K~LSdEEKqpY 74 (382)
..||+++|+..
T Consensus 93 q~l~~eeR~~l 103 (107)
T PF11304_consen 93 QQLPPEERQAL 103 (107)
T ss_pred HcCCHHHHHHH
Confidence 67777776543
No 40
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=84.57 E-value=0.18 Score=39.43 Aligned_cols=31 Identities=19% Similarity=0.493 Sum_probs=26.3
Q ss_pred hhhhhhhhhhhhhhhhhhhhhchhhhHHhhh
Q psy1990 165 ELYCRVCDQWFTTLHNKREHLNGRQHFQAVE 195 (382)
Q Consensus 165 ~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~ 195 (382)
...|.+|++.|.+...+++||.+..|.+...
T Consensus 50 ~~~C~~C~~~f~s~~~l~~Hm~~~~H~~~~~ 80 (100)
T PF12756_consen 50 SFRCPYCNKTFRSREALQEHMRSKHHKKRNS 80 (100)
T ss_dssp SEEBSSSS-EESSHHHHHHHHHHTTTTC-S-
T ss_pred CCCCCccCCCCcCHHHHHHHHcCccCCCccc
Confidence 5899999999999999999999999988754
No 41
>KOG2746|consensus
Probab=83.94 E-value=0.83 Score=50.13 Aligned_cols=43 Identities=26% Similarity=0.162 Sum_probs=39.3
Q ss_pred hhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHH
Q psy1990 46 SYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 88 (382)
Q Consensus 46 lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekE 88 (382)
.||+..+.-|+|+||+.|-.|.+.||++|.++|.+.|+.+-+.
T Consensus 205 ~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka 247 (683)
T KOG2746|consen 205 RHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA 247 (683)
T ss_pred cCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence 3678888999999999999999999999999999999888775
No 42
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=83.78 E-value=0.23 Score=30.44 Aligned_cols=20 Identities=25% Similarity=0.735 Sum_probs=18.5
Q ss_pred hhhhhhhhhhhhhhhhhhch
Q psy1990 168 CRVCDQWFTTLHNKREHLNG 187 (382)
Q Consensus 168 c~~c~q~fs~~hnk~eh~~~ 187 (382)
|..|+..|++..+++.||.-
T Consensus 3 C~~C~~~f~~~~~l~~H~~~ 22 (23)
T PF00096_consen 3 CPICGKSFSSKSNLKRHMRR 22 (23)
T ss_dssp ETTTTEEESSHHHHHHHHHH
T ss_pred CCCCCCccCCHHHHHHHHhH
Confidence 89999999999999999864
No 43
>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta. The function of this family is unknown.
Probab=82.00 E-value=1.1 Score=42.36 Aligned_cols=32 Identities=25% Similarity=0.216 Sum_probs=29.4
Q ss_pred hhhhhHHHHhHHHHHHhcCCCcchhhhhHHHH
Q psy1990 47 YLILLFFQVTKLLGNEWSKLSLPEKKVYLDRA 78 (382)
Q Consensus 47 fPglSftEIsK~LGErWK~LSdEEKqpYedkA 78 (382)
|.+|+..|+....+..|..||+.||..|..++
T Consensus 97 h~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~ 128 (183)
T PF06382_consen 97 HCGLSPQDLIQRAARAWCRLSEAEKNRYRRMA 128 (183)
T ss_pred ccCCCHHHHHHHHHHHHHhCCHHHHHHHHhhc
Confidence 46899999999999999999999999998864
No 44
>KOG0528|consensus
Probab=81.35 E-value=0.42 Score=50.78 Aligned_cols=38 Identities=29% Similarity=0.488 Sum_probs=29.6
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhh
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 38 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeY 38 (382)
|+|+||-+||.||-.||++|.+.-..--+...+..-.|
T Consensus 356 ISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdY 393 (511)
T KOG0528|consen 356 ISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDY 393 (511)
T ss_pred hhHHhcccccccccccccchHHHHHHHHHhhhccCccc
Confidence 78999999999999999999877666555444444444
No 45
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=79.79 E-value=0.79 Score=40.54 Aligned_cols=53 Identities=21% Similarity=0.382 Sum_probs=45.8
Q ss_pred ccccccCCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhccccccccccc
Q psy1990 155 EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGHLAVNESNS 207 (382)
Q Consensus 155 ~~d~~~~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~~l~~~~~~~ 207 (382)
.+|.|-|--|--||-.|..||-+---+.||.-|+-|...+..--+.+-.+++.
T Consensus 45 p~Dp~lPGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~KelRevpytQe~a 97 (126)
T COG5112 45 PYDPELPGLGQHYCIECARYFITEKALMEHKKGKVHKRRAKELREVPYTQEDA 97 (126)
T ss_pred CCCCCCCCCceeeeehhHHHHHHHHHHHHHhccchhHHHHHHHhcCcchhHHH
Confidence 34677788899999999999999999999999999999888777777776665
No 46
>KOG2746|consensus
Probab=79.64 E-value=1.2 Score=49.06 Aligned_cols=34 Identities=32% Similarity=0.394 Sum_probs=31.1
Q ss_pred CcchHHHHhcCCChHHHHHHHHHHHHHHHHHHHH
Q psy1990 1 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 34 (382)
Q Consensus 1 ISKiLGEkWK~LSdeEKqkYedkAkeDKeRYeeE 34 (382)
|+|+||++|-.|.+.||++|.++|.+.|+.+-+.
T Consensus 214 IskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka 247 (683)
T KOG2746|consen 214 ISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA 247 (683)
T ss_pred HHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence 7899999999999999999999999999877554
No 47
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.
Probab=78.80 E-value=3.7 Score=38.32 Aligned_cols=48 Identities=17% Similarity=0.355 Sum_probs=39.1
Q ss_pred hhhhhHHHHhH-HHHHHhcCCCcchhhhhHHHHHH-HHHHHHHHHHHHHh
Q psy1990 47 YLILLFFQVTK-LLGNEWSKLSLPEKKVYLDRAEV-DKKRYREELKVYRK 94 (382)
Q Consensus 47 fPglSftEIsK-~LGErWK~LSdEEKqpYedkAek-dKeRYekEMkeYkk 94 (382)
-|...+..|++ .||..|+.+|++||+.|.+.... ....|-..+..|..
T Consensus 61 ~~~~Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~ 110 (198)
T TIGR03481 61 REAFDLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAG 110 (198)
T ss_pred HHhCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 34567788877 78999999999999999998887 67778887777743
No 48
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=76.24 E-value=7.6 Score=36.60 Aligned_cols=47 Identities=15% Similarity=0.263 Sum_probs=38.4
Q ss_pred hhhhhHHHHhH-HHHHHhcCCCcchhhhhHHHHHH-HHHHHHHHHHHHH
Q psy1990 47 YLILLFFQVTK-LLGNEWSKLSLPEKKVYLDRAEV-DKKRYREELKVYR 93 (382)
Q Consensus 47 fPglSftEIsK-~LGErWK~LSdEEKqpYedkAek-dKeRYekEMkeYk 93 (382)
-|...|..+++ .||..|+.+|++||+.|.+.... ...-|-..+..|.
T Consensus 65 ~p~~Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~ 113 (211)
T PRK15117 65 LPYVQVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYH 113 (211)
T ss_pred cccCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 45667777766 78999999999999999998776 5667888888875
No 49
>KOG4727|consensus
Probab=76.02 E-value=0.88 Score=42.99 Aligned_cols=34 Identities=32% Similarity=0.554 Sum_probs=30.4
Q ss_pred hhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhcc
Q psy1990 165 ELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSG 198 (382)
Q Consensus 165 ~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~ 198 (382)
--||.||+--|----|.-.|++|+.|.-++.-.+
T Consensus 75 GyyCdVCdcvvKDSinflDHiNgKkHqrnlgmsm 108 (193)
T KOG4727|consen 75 GYYCDVCDCVVKDSINFLDHINGKKHQRNLGMSM 108 (193)
T ss_pred ceeeeecceeehhhHHHHHHhccHHHHHHHhhhh
Confidence 3599999999999999999999999999886554
No 50
>PF07535 zf-DBF: DBF zinc finger; InterPro: IPR006572 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. In eukaryotes, initiation of DNA replication requires the assembly of pre-replication complexes (pre-RCs) on chromatin during the G1 phase. In the S phase, pre-RCs are activated by two protein kinases, Cdk2 and Cdc7, which results in the loading of replication factors and the unwinding of replication origins by the MCM helicase complex []. Cdc7 is a serine/threonine kinase that is conserved from yeast to human. It is regulated by its association with a regulatory subunit, the Dbf4 protein. This complex is often referred to as DDK (Dbf4-dependent kinase) []. DBF4 contains an N-terminal BRCT domain and a C-terminal conserved region that could potentially coordinate one zinc atom, the DBF4-type zinc finger. This entry represents the zinc finger, which is important for the interaction with Cdc7 [, ]. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding
Probab=70.76 E-value=1.8 Score=32.86 Aligned_cols=30 Identities=23% Similarity=0.495 Sum_probs=25.1
Q ss_pred hhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhc
Q psy1990 165 ELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQS 197 (382)
Q Consensus 165 ~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~ 197 (382)
.-||-.|...|.. +.+|+.+++|+.-+...
T Consensus 5 ~GYCE~C~~ky~~---l~~Hi~s~~Hr~FA~~~ 34 (49)
T PF07535_consen 5 PGYCENCRVKYDD---LEEHIQSEKHRKFAEND 34 (49)
T ss_pred CccCccccchhhh---HHHHhCCHHHHHHHcCc
Confidence 4599999999985 67999999999876544
No 51
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=70.76 E-value=1 Score=26.84 Aligned_cols=19 Identities=26% Similarity=0.768 Sum_probs=15.9
Q ss_pred hhhhhhhhhhhhhhhhhhc
Q psy1990 168 CRVCDQWFTTLHNKREHLN 186 (382)
Q Consensus 168 c~~c~q~fs~~hnk~eh~~ 186 (382)
|.+|+..|.+.-.++.||.
T Consensus 3 C~~C~~~~~~~~~l~~H~~ 21 (24)
T PF13894_consen 3 CPICGKSFRSKSELRQHMR 21 (24)
T ss_dssp -SSTS-EESSHHHHHHHHH
T ss_pred CcCCCCcCCcHHHHHHHHH
Confidence 8999999999999999985
No 52
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=68.69 E-value=3 Score=31.82 Aligned_cols=33 Identities=21% Similarity=0.472 Sum_probs=26.6
Q ss_pred CcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhc
Q psy1990 162 DNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQS 197 (382)
Q Consensus 162 d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~ 197 (382)
|....||-.|...|.. ..+|+.|++|+.-+...
T Consensus 2 ~~k~GYCE~Cr~kfd~---l~~Hi~s~~Hr~FA~~~ 34 (49)
T smart00586 2 EKKPGYCENCREKYDD---LETHLLSEKHRRFAENN 34 (49)
T ss_pred CCCCcccccHhHHHhh---HHHHhccHHHHHHHcCc
Confidence 3455699999999985 56899999999876654
No 53
>PF03194 LUC7: LUC7 N_terminus; InterPro: IPR004882 This family consists of several LUC7 protein homologues that are restricted to eukaryotes. LUC7 has been shown to be a U1 snRNA associated protein [] with a role in splice site recognition []. The entry contains human and mouse LUC7 like (LUC7L) proteins [] and human cisplatin resistance-associated overexpressed protein (CROP) [].
Probab=68.32 E-value=2.3 Score=41.31 Aligned_cols=28 Identities=25% Similarity=0.612 Sum_probs=23.3
Q ss_pred hhhhhhhhhhhhhh---hhhhhhchhhhHHh
Q psy1990 166 LYCRVCDQWFTTLH---NKREHLNGRQHFQA 193 (382)
Q Consensus 166 ~~c~~c~q~fs~~h---nk~eh~~~~~h~~~ 193 (382)
-.|-||+.+-|.+- +.-.|+.||+|+-.
T Consensus 191 ~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy 221 (254)
T PF03194_consen 191 EVCEVCGAFLSVGDNDRRLADHFGGKQHLGY 221 (254)
T ss_pred cchhhhhhHHhccchHHHHHHHhccchhhhH
Confidence 46999999998775 55699999999854
No 54
>PHA02768 hypothetical protein; Provisional
Probab=65.47 E-value=1.9 Score=33.63 Aligned_cols=23 Identities=22% Similarity=0.502 Sum_probs=20.5
Q ss_pred hhhhhhhhhhhhhhhhhhhchhhhH
Q psy1990 167 YCRVCDQWFTTLHNKREHLNGRQHF 191 (382)
Q Consensus 167 ~c~~c~q~fs~~hnk~eh~~~~~h~ 191 (382)
-|..|+..|++..++..||.- |.
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~--H~ 29 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRK--HN 29 (55)
T ss_pred CcchhCCeeccHHHHHHHHHh--cC
Confidence 599999999999999999954 65
No 55
>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []. Many proteins are involved in these processes. This family is a transporter which shows similarity to ABC transporters [].; PDB: 2QGU_A.
Probab=65.30 E-value=9 Score=34.08 Aligned_cols=48 Identities=19% Similarity=0.369 Sum_probs=35.0
Q ss_pred hhhhhHHHHhH-HHHHHhcCCCcchhhhhHHHHHH-HHHHHHHHHHHHHh
Q psy1990 47 YLILLFFQVTK-LLGNEWSKLSLPEKKVYLDRAEV-DKKRYREELKVYRK 94 (382)
Q Consensus 47 fPglSftEIsK-~LGErWK~LSdEEKqpYedkAek-dKeRYekEMkeYkk 94 (382)
-|...+..+++ .||.-|+.||++|++.|.+.... ....|-..+..|..
T Consensus 35 ~~~~D~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~ 84 (170)
T PF05494_consen 35 DPYFDFERMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG 84 (170)
T ss_dssp GGGB-HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred HHhCCHHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 45666766666 67889999999999999987766 56667777777763
No 56
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=64.79 E-value=3.2 Score=40.63 Aligned_cols=29 Identities=28% Similarity=0.788 Sum_probs=25.2
Q ss_pred hhhhhhhhhhhhhhhhh---hhhchhhhHHhh
Q psy1990 166 LYCRVCDQWFTTLHNKR---EHLNGRQHFQAV 194 (382)
Q Consensus 166 ~~c~~c~q~fs~~hnk~---eh~~~~~h~~~~ 194 (382)
--|.+|+.|.|++-++| .|++||-||--|
T Consensus 186 qvC~iCgayLsrlDtdrrladHf~GklHlGy~ 217 (258)
T COG5200 186 QVCGICGAYLSRLDTDRRLADHFNGKLHLGYL 217 (258)
T ss_pred hhhhhhhhHHHhcchhhHHHHHhccchhhhHH
Confidence 36999999999999988 699999998543
No 57
>KOG2505|consensus
Probab=58.34 E-value=6 Score=42.80 Aligned_cols=37 Identities=19% Similarity=0.278 Sum_probs=32.8
Q ss_pred CcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhcc
Q psy1990 162 DNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSG 198 (382)
Q Consensus 162 d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~ 198 (382)
..+-++|.||.+-|.++---|||...-=|+-|+-...
T Consensus 63 ~sd~~~CstCq~~F~s~~eqr~HyksD~HR~N~Krkl 99 (591)
T KOG2505|consen 63 ISDSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKRKL 99 (591)
T ss_pred hcccccccccCCccccHHHHHHHHHHHHHHHHHHHHh
Confidence 3467899999999999999999999999998877655
No 58
>TIGR03481 HpnM hopanoid biosynthesis associated membrane protein HpnM. The genomes containing members of this family share the machinery for the biosynthesis of hopanoid lipids. Furthermore, the genes of this family are usually located proximal to other components of this biological process. The proteins are members of the pfam05494 family of putative transporters known as "toluene tolerance protein Ttg2D", although it is unlikely that the members included here have anything to do with toluene per-se.
Probab=57.45 E-value=16 Score=34.07 Aligned_cols=37 Identities=22% Similarity=0.501 Sum_probs=32.8
Q ss_pred hHHHHhcCCChHHHHHHHHHHHH-HHHHHHHHHHhhcc
Q psy1990 4 LLGNEWSKLSLPEKKVYLDRAEV-DKKRYREELKVYRK 40 (382)
Q Consensus 4 iLGEkWK~LSdeEKqkYedkAke-DKeRYeeEMeeYk~ 40 (382)
.||..|+.+|+++|+.|.+.... -...|-..+..|..
T Consensus 73 vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~ 110 (198)
T TIGR03481 73 TLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAG 110 (198)
T ss_pred HhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 68999999999999999999998 66789999988853
No 59
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=54.41 E-value=5.8 Score=41.42 Aligned_cols=36 Identities=22% Similarity=0.477 Sum_probs=31.3
Q ss_pred chhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhccc
Q psy1990 164 EELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQSGH 199 (382)
Q Consensus 164 ~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~~~ 199 (382)
.-.||-+|..+|++..-.+-|+-|+.|-.+..+--+
T Consensus 237 ~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~~~ 272 (470)
T COG5188 237 PKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGKEE 272 (470)
T ss_pred cceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhhhH
Confidence 457999999999999999999999999988776543
No 60
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=49.47 E-value=5.5 Score=30.96 Aligned_cols=19 Identities=26% Similarity=0.796 Sum_probs=0.0
Q ss_pred hhhhhhhhhhhhhhhhhhc
Q psy1990 168 CRVCDQWFTTLHNKREHLN 186 (382)
Q Consensus 168 c~~c~q~fs~~hnk~eh~~ 186 (382)
|..|++.|++.-..++||.
T Consensus 2 C~~C~~~f~~~~~l~~H~~ 20 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMK 20 (100)
T ss_dssp -------------------
T ss_pred ccccccccccccccccccc
Confidence 9999999999999999995
No 61
>smart00355 ZnF_C2H2 zinc finger.
Probab=47.91 E-value=5.7 Score=23.47 Aligned_cols=20 Identities=25% Similarity=0.612 Sum_probs=17.9
Q ss_pred hhhhhhhhhhhhhhhhhhhc
Q psy1990 167 YCRVCDQWFTTLHNKREHLN 186 (382)
Q Consensus 167 ~c~~c~q~fs~~hnk~eh~~ 186 (382)
-|..|...|++.-+...||.
T Consensus 2 ~C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 2 RCPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCCcchhCCHHHHHHHHH
Confidence 38899999999999999986
No 62
>KOG0796|consensus
Probab=47.29 E-value=11 Score=38.47 Aligned_cols=29 Identities=28% Similarity=0.688 Sum_probs=24.4
Q ss_pred hhhhhhhhhhhhhhhhh---hhhchhhhHHhh
Q psy1990 166 LYCRVCDQWFTTLHNKR---EHLNGRQHFQAV 194 (382)
Q Consensus 166 ~~c~~c~q~fs~~hnk~---eh~~~~~h~~~~ 194 (382)
--|-||+.+-+-+-|.+ .|+.|+.|+-.+
T Consensus 187 ~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~ 218 (319)
T KOG0796|consen 187 RVCEVCGAFLSVNDADRRLADHFGGKLHLGYV 218 (319)
T ss_pred hHHHhhhHHHhccchHHHHHHhhcchHHHHHH
Confidence 36999999999887755 899999998654
No 63
>PF03480 SBP_bac_7: Bacterial extracellular solute-binding protein, family 7; InterPro: IPR018389 This family of proteins are involved in binding extracellular solutes for transport across the bacterial cytoplasmic membrane. This family includes a C4-dicarboxylate-binding protein DctP [, ] and the sialic acid-binding protein SiaP. The structure of the SiaP receptor has revealed an overall topology similar to ATP binding cassette ESR (extracytoplasmic solute receptors) proteins []. Upon binding of sialic acid, SiaP undergoes domain closure about a hinge region and kinking of an alpha-helix hinge component [].; GO: 0006810 transport, 0030288 outer membrane-bounded periplasmic space; PDB: 2HZK_C 2HZL_B 2HPG_C 2XWI_A 2XWK_A 2WX9_A 2CEY_A 2WYP_A 3B50_A 2CEX_B ....
Probab=47.22 E-value=50 Score=31.33 Aligned_cols=69 Identities=17% Similarity=0.080 Sum_probs=45.0
Q ss_pred HHHhcCCChHHHHHHHHHHHHHHHHHHHHHHhhcccchhhhhhhhhHHHHhHHHHHHhcCCCcchhhhhHHHHHHHHHH
Q psy1990 6 GNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLILLFFQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKR 84 (382)
Q Consensus 6 GEkWK~LSdeEKqkYedkAkeDKeRYeeEMeeYk~KDAY~lfPglSftEIsK~LGErWK~LSdEEKqpYedkAekdKeR 84 (382)
.+.|..||++.|+...+.+.+--..+...+... .....+....-|-....+++++++.|.+.+....++
T Consensus 213 ~~~w~~L~~e~q~~l~~~~~~~~~~~~~~~~~~----------~~~~~~~~~~~G~~v~~~s~~~~~~~~~~~~~~~~e 281 (286)
T PF03480_consen 213 KDWWDSLPDEDQEALDDAADEAEARAREYYEAE----------DEEALKELEENGVTVVELSDEELAAWREAAAPVWEE 281 (286)
T ss_dssp HHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHTT-EEEEGCHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHCcCEEeCCCHHHHHHHHHHHHHHHHH
Confidence 468999999999999888876554443333322 111222333356677778999999999888877776
No 64
>COG5136 U1 snRNP-specific protein C [RNA processing and modification]
Probab=46.80 E-value=14 Score=35.00 Aligned_cols=33 Identities=21% Similarity=0.450 Sum_probs=28.6
Q ss_pred hhhhhhhhhhh--hhhhhhhhhchhhhHHhhhhcc
Q psy1990 166 LYCRVCDQWFT--TLHNKREHLNGRQHFQAVEQSG 198 (382)
Q Consensus 166 ~~c~~c~q~fs--~~hnk~eh~~~~~h~~~~~~~~ 198 (382)
-||--|+.|.+ ++.--+-|.-|+.|++|.+.+.
T Consensus 4 Y~CeyC~~~LthD~lsvRk~H~~G~~H~~~~~dYY 38 (188)
T COG5136 4 YFCEYCNKMLTHDRLSVRKMHCGGAKHGLMRKDYY 38 (188)
T ss_pred hHHHHHHHHHhccHHHHHHHhhhhHHHHHHHHHHH
Confidence 48999999986 5677789999999999988766
No 65
>KOG2785|consensus
Probab=46.55 E-value=8.1 Score=40.34 Aligned_cols=36 Identities=22% Similarity=0.654 Sum_probs=33.0
Q ss_pred CCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhh
Q psy1990 161 EDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQ 196 (382)
Q Consensus 161 ~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~ 196 (382)
.-....+|.+|++.|-+.-+...||..|.|.-++..
T Consensus 64 ~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~ 99 (390)
T KOG2785|consen 64 EAESVVYCEACNKSFASPKAHENHLKSKKHVENLSN 99 (390)
T ss_pred hcccceehHHhhccccChhhHHHHHHHhhcchhhhh
Confidence 566788999999999999999999999999988876
No 66
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=45.03 E-value=1e+02 Score=28.49 Aligned_cols=78 Identities=13% Similarity=0.192 Sum_probs=47.3
Q ss_pred cCCChHHHHHHHHHHHHHHHHH-------HHHHHhhcccchhh------hhh------hhhHHHHhHHHHHHhcCCCcch
Q psy1990 10 SKLSLPEKKVYLDRAEVDKKRY-------REELKVYRKSDAYQ------SYL------ILLFFQVTKLLGNEWSKLSLPE 70 (382)
Q Consensus 10 K~LSdeEKqkYedkAkeDKeRY-------eeEMeeYk~KDAY~------lfP------glSftEIsK~LGErWK~LSdEE 70 (382)
-+|++++|+...+.....+... .++|......++|- +.- ..-..+..+..-++++.|+++|
T Consensus 55 l~LTd~QR~qmr~im~~~r~~~~~~~~~~~~~m~~Li~Ad~FDeaAvra~~~kma~~~~e~~v~~~~~~~qmy~lLTPEQ 134 (162)
T PRK12751 55 INLTEQQRQQMRDLMRQSHQSQPRLDLEDREAMHKLITADKFDEAAVRAQAEKMSQNQIERHVEMAKVRNQMYNLLTPEQ 134 (162)
T ss_pred CCCCHHHHHHHHHHHHHhhhcccchhHHHHHHHHHHHhcCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCHHH
Confidence 3689999998888877665532 11122222234441 111 1112456778888999999999
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990 71 KKVYLDRAEVDKKRYREELKVYRK 94 (382)
Q Consensus 71 KqpYedkAekdKeRYekEMkeYkk 94 (382)
|..|.+ +|++.|..++.
T Consensus 135 ra~l~~-------~~e~r~~~~~~ 151 (162)
T PRK12751 135 KEALNK-------KHQERIEKLQQ 151 (162)
T ss_pred HHHHHH-------HHHHHHHHHHh
Confidence 999987 45555555543
No 67
>PHA00616 hypothetical protein
Probab=41.51 E-value=13 Score=27.91 Aligned_cols=19 Identities=32% Similarity=0.530 Sum_probs=17.6
Q ss_pred hhhhhhhhhhhhhhhhhhh
Q psy1990 167 YCRVCDQWFTTLHNKREHL 185 (382)
Q Consensus 167 ~c~~c~q~fs~~hnk~eh~ 185 (382)
-|..|+..|...-+...||
T Consensus 3 qC~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 3 QCLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred ccchhhHHHhhHHHHHHHH
Confidence 3999999999999999998
No 68
>KOG1074|consensus
Probab=41.02 E-value=12 Score=42.61 Aligned_cols=26 Identities=27% Similarity=0.661 Sum_probs=22.9
Q ss_pred CCcchhhhhhhhhhhhhhhhhhhhhc
Q psy1990 161 EDNEELYCRVCDQWFTTLHNKREHLN 186 (382)
Q Consensus 161 ~d~~~~~c~~c~q~fs~~hnk~eh~~ 186 (382)
+-+..-||++|.+-|+++-|+++||.
T Consensus 903 tg~KPF~C~fC~~aFttrgnLKvHMg 928 (958)
T KOG1074|consen 903 TGPKPFFCHFCEEAFTTRGNLKVHMG 928 (958)
T ss_pred CCCCCccchhhhhhhhhhhhhhhhhc
Confidence 44566999999999999999999996
No 69
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=39.53 E-value=45 Score=31.46 Aligned_cols=38 Identities=18% Similarity=0.356 Sum_probs=32.1
Q ss_pred chHHHHhcCCChHHHHHHHHHHHHHHH-HHHHHHHhhcc
Q psy1990 3 KLLGNEWSKLSLPEKKVYLDRAEVDKK-RYREELKVYRK 40 (382)
Q Consensus 3 KiLGEkWK~LSdeEKqkYedkAkeDKe-RYeeEMeeYk~ 40 (382)
..||.-|+++|+++|+.|.+....--. .|-..+..|..
T Consensus 76 ~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~ 114 (211)
T PRK15117 76 LVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHG 114 (211)
T ss_pred HHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCC
Confidence 368999999999999999998887554 68888888864
No 70
>PF05494 Tol_Tol_Ttg2: Toluene tolerance, Ttg2 ; InterPro: IPR008869 Toluene tolerance is mediated by increased cell membrane rigidity resulting from changes in fatty acid and phospholipid compositions, exclusion of toluene from the cell membrane, and removal of intracellular toluene by degradation []. Many proteins are involved in these processes. This family is a transporter which shows similarity to ABC transporters [].; PDB: 2QGU_A.
Probab=39.07 E-value=42 Score=29.85 Aligned_cols=36 Identities=22% Similarity=0.441 Sum_probs=28.2
Q ss_pred hHHHHhcCCChHHHHHHHHHHHHHHH-HHHHHHHhhc
Q psy1990 4 LLGNEWSKLSLPEKKVYLDRAEVDKK-RYREELKVYR 39 (382)
Q Consensus 4 iLGEkWK~LSdeEKqkYedkAkeDKe-RYeeEMeeYk 39 (382)
.||.-|++||+++++.|.+....--. .|-..+..|.
T Consensus 47 ~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~ 83 (170)
T PF05494_consen 47 VLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYS 83 (170)
T ss_dssp HHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-S
T ss_pred HHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 58899999999999999998887554 4777778775
No 71
>KOG3032|consensus
Probab=38.87 E-value=11 Score=37.47 Aligned_cols=36 Identities=25% Similarity=0.482 Sum_probs=27.6
Q ss_pred CCcchhhhhhhhhhhhhhhhhhhhhchhhhHHhhhhc
Q psy1990 161 EDNEELYCRVCDQWFTTLHNKREHLNGRQHFQAVEQS 197 (382)
Q Consensus 161 ~d~~~~~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~ 197 (382)
...|-+-|+||+.--- -.--.=|..||||..++..-
T Consensus 31 n~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id~l 66 (264)
T KOG3032|consen 31 NESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAIDSL 66 (264)
T ss_pred CCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHHHH
Confidence 4567799999998765 33346799999999888653
No 72
>PF09237 GAGA: GAGA factor; InterPro: IPR015318 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. Members of this entry bind to a 5'-GAGAG-3' DNA consensus binding site, and contain a Cys2-His2 zinc finger core as well as an N-terminal extension containing two highly basic regions. The zinc finger core binds in the DNA major groove and recognises the first three GAG bases of the consensus in a manner similar to that seen in other classical zinc finger-DNA complexes. The second basic region forms a helix that interacts in the major groove recognising the last G of the consensus, while the first basic region wraps around the DNA in the minor groove and recognises the A in the fourth position of the consensus sequence []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1YUI_A 1YUJ_A.
Probab=37.05 E-value=10 Score=29.67 Aligned_cols=21 Identities=29% Similarity=0.578 Sum_probs=15.9
Q ss_pred hhhhhhhhhhhhhhhhhhhhc
Q psy1990 166 LYCRVCDQWFTTLHNKREHLN 186 (382)
Q Consensus 166 ~~c~~c~q~fs~~hnk~eh~~ 186 (382)
--|.+|+.-+++.-|+|-||-
T Consensus 25 atCP~C~a~~~~srnLrRHle 45 (54)
T PF09237_consen 25 ATCPICGAVIRQSRNLRRHLE 45 (54)
T ss_dssp EE-TTT--EESSHHHHHHHHH
T ss_pred CCCCcchhhccchhhHHHHHH
Confidence 359999999999999999984
No 73
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=36.33 E-value=86 Score=26.86 Aligned_cols=12 Identities=33% Similarity=0.708 Sum_probs=8.1
Q ss_pred hcCCChHHHHHH
Q psy1990 9 WSKLSLPEKKVY 20 (382)
Q Consensus 9 WK~LSdeEKqkY 20 (382)
|..||+.++...
T Consensus 2 W~~L~~~Qq~~L 13 (107)
T PF11304_consen 2 WSSLSPAQQQAL 13 (107)
T ss_pred hhhCCHHHHHHH
Confidence 667777776655
No 74
>KOG0150|consensus
Probab=36.04 E-value=21 Score=36.69 Aligned_cols=34 Identities=24% Similarity=0.571 Sum_probs=28.1
Q ss_pred chhhhhhhhhhhhhhh-hhhhhhchhhhHHhhhhc
Q psy1990 164 EELYCRVCDQWFTTLH-NKREHLNGRQHFQAVEQS 197 (382)
Q Consensus 164 ~~~~c~~c~q~fs~~h-nk~eh~~~~~h~~~~~~~ 197 (382)
+--||..|.-||..+- .-|=|=+|++|..||+.-
T Consensus 9 ~kkfCdyCKiWi~dN~~Sv~~He~GkrHke~V~Kr 43 (336)
T KOG0150|consen 9 PKKFCDYCKIWIKDNPASVRFHERGKRHKENVAKR 43 (336)
T ss_pred cchhhhhhhhhhcCChHHHHhHhhhhHHHHHHHHH
Confidence 4569999999998764 456789999999999864
No 75
>PF06382 DUF1074: Protein of unknown function (DUF1074); InterPro: IPR024460 This family consists of several proteins which appear to be specific to Insecta. The function of this family is unknown.
Probab=35.53 E-value=21 Score=33.93 Aligned_cols=25 Identities=28% Similarity=0.389 Sum_probs=20.8
Q ss_pred cchHHHHhcCCChHHHHHHHHHHHH
Q psy1990 2 TKLLGNEWSKLSLPEKKVYLDRAEV 26 (382)
Q Consensus 2 SKiLGEkWK~LSdeEKqkYedkAke 26 (382)
+...+..|..||+.+|..|..++..
T Consensus 106 I~~AAraW~rLSe~eK~rYrr~~~~ 130 (183)
T PF06382_consen 106 IQRAARAWCRLSEAEKNRYRRMAPS 130 (183)
T ss_pred HHHHHHHHHhCCHHHHHHHHhhcch
Confidence 4567899999999999999886553
No 76
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=35.15 E-value=3.2e+02 Score=25.26 Aligned_cols=37 Identities=8% Similarity=0.115 Sum_probs=26.7
Q ss_pred HHHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHH
Q psy1990 53 FQVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 89 (382)
Q Consensus 53 tEIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEM 89 (382)
.+..+..-+.+..|+++||..|.+.-++-..+|...+
T Consensus 124 v~~~~~~~~~~~vLTpEQRak~~e~~~~r~~~~~~~~ 160 (170)
T PRK12750 124 VKMLEKRHQMLSILTPEQKAKFQELQQERMQECQDKM 160 (170)
T ss_pred HHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456666778999999999999887655555554443
No 77
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=33.41 E-value=9.7 Score=23.62 Aligned_cols=19 Identities=32% Similarity=0.670 Sum_probs=12.6
Q ss_pred hhhhhhhhhhhhhhhhhhch
Q psy1990 168 CRVCDQWFTTLHNKREHLNG 187 (382)
Q Consensus 168 c~~c~q~fs~~hnk~eh~~~ 187 (382)
|..|+ |.++..++++||.-
T Consensus 3 C~~C~-y~t~~~~l~~H~~~ 21 (24)
T PF13909_consen 3 CPHCS-YSTSKSNLKRHLKR 21 (24)
T ss_dssp -SSSS--EESHHHHHHHHHH
T ss_pred CCCCC-CcCCHHHHHHHHHh
Confidence 88898 44457888888753
No 78
>KOG3817|consensus
Probab=33.16 E-value=38 Score=35.77 Aligned_cols=93 Identities=22% Similarity=0.237 Sum_probs=57.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHhhhhhHHHHHHhhhhhhhccccccccccCCCCCCCC---CCcccCCCccCCCCccccc
Q psy1990 72 KVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRKRVKKIQHHCLTAKVFSGTSEGRDS---GTYKTRGGLQANGTEESDI 148 (382)
Q Consensus 72 qpYedkAekdKeRYekEMkeYkks~aYk~~~krk~~KK~k~~~~~~kv~s~ts~~~~n---g~~~~~gg~~~dg~~~~di 148 (382)
+.|+++|+..-.+=..++.+|-.++..++|+--.+-.-.++.+ .+..|.++--.+ .|- -++| ...|+
T Consensus 320 eEYeeQaeveT~kaLaeLReycnkpd~~~Wkvvgrlrsp~rfA---~F~eG~~Hlt~~Ei~~He-~t~~------~~~~~ 389 (452)
T KOG3817|consen 320 EEYEEQAEVETSKALAELREYCNKPDCKQWKVVGRLRSPLRFA---SFAEGAPHLTDEEIEDHE-RTIE------ESMDA 389 (452)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCCchhhhhhhccCHHHHH---HHhcCCCCCCHHHHHHHH-hhhh------hhccc
Confidence 3699999999999999999999999988886322221111111 111222210011 111 1122 23567
Q ss_pred cccCCcccccccCCcchhhhhhhhhh
Q psy1990 149 ATDATDEIDEEEEDNEELYCRVCDQW 174 (382)
Q Consensus 149 ~~d~~~~~d~~~~d~~~~~c~~c~q~ 174 (382)
+.|..+++|.+|+.|+++-|+-..|+
T Consensus 390 a~dee~~E~~~Ee~d~~~~~~~~sq~ 415 (452)
T KOG3817|consen 390 APDEESVEEPEEEKDAELLPLPNSQF 415 (452)
T ss_pred ccchhcccccccccCccccCCcchhh
Confidence 77777778888889999999877663
No 79
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=31.27 E-value=15 Score=36.08 Aligned_cols=26 Identities=23% Similarity=0.636 Sum_probs=21.4
Q ss_pred ccCCcchhhhhhhhhhhhhhhhhhhhh
Q psy1990 159 EEEDNEELYCRVCDQWFTTLHNKREHL 185 (382)
Q Consensus 159 ~~~d~~~~~c~~c~q~fs~~hnk~eh~ 185 (382)
++|++...||-||+.-++..+-.| ||
T Consensus 78 ~~D~~~~~~Cv~Cg~~i~~~~a~k-Hm 103 (236)
T PF12269_consen 78 SEDDDLSIYCVTCGHEIPSKKALK-HM 103 (236)
T ss_pred ccccceeeeeeeCCCcCCHHHHHH-HH
Confidence 456789999999999999887766 55
No 80
>PF01352 KRAB: KRAB box; InterPro: IPR001909 The Krueppel-associated box (KRAB) is a domain of around 75 amino acids that is found in the N-terminal part of about one third of eukaryotic Krueppel-type C2H2 zinc finger proteins (ZFPs) []. It is enriched in charged amino acids and can be divided into subregions A and B, which are predicted to fold into two amphipathic alpha-helices. The KRAB A and B boxes can be separated by variable spacer segments and many KRAB proteins contain only the A box []. The functions currently known for members of the KRAB-containing protein family include transcriptional repression of RNA polymerase I, II, and III promoters, binding and splicing of RNA, and control of nucleolus function. The KRAB domain functions as a transcriptional repressor when tethered to the template DNA by a DNA-binding domain. A sequence of 45 amino acids in the KRAB A subdomain has been shown to be necessary and sufficient for transcriptional repression. The B box does not repress by itself but does potentiate the repression exerted by the KRAB A subdomain [, ]. Gene silencing requires the binding of the KRAB domain to the RING-B box-coiled coil (RBCC) domain of the KAP-1/TIF1-beta corepressor. As KAP-1 binds to the heterochromatin proteins HP1, it has been proposed that the KRAB-ZFP-bound target gene could be silenced following recruitment to heterochromatin [, ]. KRAB-ZFPs probably constitute the single largest class of transcription factors within the human genome []. Although the function of KRAB-ZFPs is largely unknown, they appear to play important roles during cell differentiation and development. The KRAB domain is generally encoded by two exons. The regions coded by the two exons are known as KRAB-A and KRAB-B.; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1V65_A.
Probab=31.22 E-value=33 Score=24.91 Aligned_cols=27 Identities=30% Similarity=0.523 Sum_probs=15.0
Q ss_pred hHHHHhHHHHHH-hcCCCcchhhhhHHH
Q psy1990 51 LFFQVTKLLGNE-WSKLSLPEKKVYLDR 77 (382)
Q Consensus 51 SftEIsK~LGEr-WK~LSdEEKqpYedk 77 (382)
+|.|++--++.. |..|.+.||.-|.+.
T Consensus 2 tf~Dvav~fs~eEW~~L~~~Qk~ly~dv 29 (41)
T PF01352_consen 2 TFEDVAVYFSQEEWELLDPAQKNLYRDV 29 (41)
T ss_dssp -----TT---HHHHHTS-HHHHHHHHHH
T ss_pred eEEEEEEEcChhhcccccceecccchhH
Confidence 456666665554 999999999999875
No 81
>KOG3214|consensus
Probab=29.06 E-value=16 Score=32.12 Aligned_cols=19 Identities=26% Similarity=0.571 Sum_probs=16.5
Q ss_pred cchhhhhhhhhhhhhhhhh
Q psy1990 163 NEELYCRVCDQWFTTLHNK 181 (382)
Q Consensus 163 ~~~~~c~~c~q~fs~~hnk 181 (382)
-|.+.|+||.+.|++.-|+
T Consensus 45 iG~~sC~iC~esFqt~it~ 63 (109)
T KOG3214|consen 45 IGKASCRICEESFQTTITA 63 (109)
T ss_pred cceeeeeehhhhhccchHh
Confidence 3778999999999998775
No 82
>KOG1074|consensus
Probab=28.52 E-value=19 Score=41.23 Aligned_cols=24 Identities=29% Similarity=0.668 Sum_probs=21.5
Q ss_pred hhhhhhhhhhhhhhhhhhhhchhh
Q psy1990 166 LYCRVCDQWFTTLHNKREHLNGRQ 189 (382)
Q Consensus 166 ~~c~~c~q~fs~~hnk~eh~~~~~ 189 (382)
.-|.||+.-|++.-|+|-||.+-+
T Consensus 634 FkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 634 FKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred cccccccchhccccchhhcccccc
Confidence 469999999999999999998853
No 83
>PLN02748 tRNA dimethylallyltransferase
Probab=28.06 E-value=23 Score=37.67 Aligned_cols=31 Identities=26% Similarity=0.524 Sum_probs=27.9
Q ss_pred hhhhhhh-hhhhhhhhhhhhchhhhHHhhhhc
Q psy1990 167 YCRVCDQ-WFTTLHNKREHLNGRQHFQAVEQS 197 (382)
Q Consensus 167 ~c~~c~q-~fs~~hnk~eh~~~~~h~~~~~~~ 197 (382)
.|-+|+- -|-.-|+-.-|+.||+|..++..-
T Consensus 420 ~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~~ 451 (468)
T PLN02748 420 VCEACGNKVLRGAHEWEQHKQGRGHRKRVQRL 451 (468)
T ss_pred cccCCCCcccCCHHHHHHHhcchHHHHHHhHH
Confidence 5999997 799999999999999999998743
No 84
>KOG2462|consensus
Probab=27.80 E-value=20 Score=36.15 Aligned_cols=21 Identities=29% Similarity=0.575 Sum_probs=18.9
Q ss_pred hhhhhhhhhhhhhhhhhhhch
Q psy1990 167 YCRVCDQWFTTLHNKREHLNG 187 (382)
Q Consensus 167 ~c~~c~q~fs~~hnk~eh~~~ 187 (382)
-|..|+..|.-+.|+|-||+-
T Consensus 217 ~C~hC~kAFADRSNLRAHmQT 237 (279)
T KOG2462|consen 217 SCPHCGKAFADRSNLRAHMQT 237 (279)
T ss_pred cCCcccchhcchHHHHHHHHh
Confidence 489999999999999999974
No 85
>PF14968 CCDC84: Coiled coil protein 84
Probab=26.02 E-value=27 Score=35.92 Aligned_cols=28 Identities=25% Similarity=0.578 Sum_probs=23.6
Q ss_pred hhhhhhhhhhhhhhhhhhhchhhhHHhhhhc
Q psy1990 167 YCRVCDQWFTTLHNKREHLNGRQHFQAVEQS 197 (382)
Q Consensus 167 ~c~~c~q~fs~~hnk~eh~~~~~h~~~~~~~ 197 (382)
||.+|.+.+-. =|-|.+++.|...|.+-
T Consensus 1 yC~vCr~~h~~---gr~H~Y~~~Hq~~L~~~ 28 (336)
T PF14968_consen 1 YCEVCRRNHDQ---GRRHVYSPKHQKSLSAF 28 (336)
T ss_pred CcchhhCcccc---cCCCccCHHHHHHHHHH
Confidence 89999987655 57799999999988875
No 86
>PF12720 DUF3807: Protein of unknown function (DUF3807); InterPro: IPR024526 This is a family of conserved fungal proteins of unknown function.
Probab=24.66 E-value=1e+02 Score=28.93 Aligned_cols=29 Identities=28% Similarity=0.388 Sum_probs=24.6
Q ss_pred chhHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Q psy1990 236 TMEDNIASVVRTMIDQNKEIQLLRSKMKSLQEKR 269 (382)
Q Consensus 236 ~~~~~~~~~~~~~~~~~~e~~~l~~~~~~~~~~~ 269 (382)
|++|-+..|| |--||+.|+|+-+..++..
T Consensus 49 TLTDEQI~IF-----RHSEI~aL~Rere~~~e~~ 77 (172)
T PF12720_consen 49 TLTDEQIEIF-----RHSEIQALRRERELREEAE 77 (172)
T ss_pred cccHHHHHHH-----HHHHHHHHHHHHHHHHHhh
Confidence 5999999999 8899999999966666654
No 87
>PF12907 zf-met2: Zinc-binding
Probab=24.61 E-value=35 Score=25.11 Aligned_cols=22 Identities=32% Similarity=0.736 Sum_probs=17.6
Q ss_pred hhhhhhhhhhhhhh---hhhhhchh
Q psy1990 167 YCRVCDQWFTTLHN---KREHLNGR 188 (382)
Q Consensus 167 ~c~~c~q~fs~~hn---k~eh~~~~ 188 (382)
-|.||-|.|-..-+ ++||-..|
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~enK 27 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAENK 27 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHHcc
Confidence 59999999987766 78887654
No 88
>KOG3792|consensus
Probab=23.68 E-value=33 Score=38.70 Aligned_cols=29 Identities=34% Similarity=0.676 Sum_probs=26.1
Q ss_pred hhhhhhhhhhhhhhhhhhhhhchhhhHHh
Q psy1990 165 ELYCRVCDQWFTTLHNKREHLNGRQHFQA 193 (382)
Q Consensus 165 ~~~c~~c~q~fs~~hnk~eh~~~~~h~~~ 193 (382)
...|..|+--|.-+-||-=||.||+|.-.
T Consensus 359 ~f~cKlcdckf~d~nak~mhl~grRhrLQ 387 (816)
T KOG3792|consen 359 RFHCKLCDCKFNDPNAKEMHLKGRRHRLQ 387 (816)
T ss_pred hhhhhhhcCCCCCcchHHhhhhcccccce
Confidence 45899999999999999999999999643
No 89
>PF11278 DUF3079: Protein of unknown function (DUF3079); InterPro: IPR021430 This family of proteins with unknown function appears to be restricted to Proteobacteria.
Probab=22.51 E-value=33 Score=26.69 Aligned_cols=13 Identities=46% Similarity=0.815 Sum_probs=10.6
Q ss_pred ccccCcchhhhhh
Q psy1990 336 KVHPVHLERACLV 348 (382)
Q Consensus 336 ~~~~~~~~~~~~~ 348 (382)
-.||.||||.|.-
T Consensus 6 PlhP~hPERiCWG 18 (52)
T PF11278_consen 6 PLHPKHPERICWG 18 (52)
T ss_pred CCCCCCccceeec
Confidence 3699999999853
No 90
>PHA00732 hypothetical protein
Probab=21.89 E-value=26 Score=28.68 Aligned_cols=21 Identities=24% Similarity=0.436 Sum_probs=18.9
Q ss_pred hhhhhhhhhhhhhhhhhhhch
Q psy1990 167 YCRVCDQWFTTLHNKREHLNG 187 (382)
Q Consensus 167 ~c~~c~q~fs~~hnk~eh~~~ 187 (382)
-|..|+..|++..+++.||..
T Consensus 3 ~C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 3 KCPICGFTTVTLFALKQHARR 23 (79)
T ss_pred cCCCCCCccCCHHHHHHHhhc
Confidence 399999999999999999863
No 91
>PF08073 CHDNT: CHDNT (NUC034) domain; InterPro: IPR012958 The CHD N-terminal domain is found in PHD/RING fingers and chromo domain-associated helicases [].; GO: 0003677 DNA binding, 0005524 ATP binding, 0008270 zinc ion binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=21.78 E-value=36 Score=26.76 Aligned_cols=23 Identities=13% Similarity=0.210 Sum_probs=20.0
Q ss_pred hhhhhhHHHHhHHHHHHhcCCCc
Q psy1990 46 SYLILLFFQVTKLLGNEWSKLSL 68 (382)
Q Consensus 46 lfPglSftEIsK~LGErWK~LSd 68 (382)
.+|++..+.++.+++.+|+..++
T Consensus 30 ~NPk~~~sKl~~l~~AKwrEF~~ 52 (55)
T PF08073_consen 30 ANPKAPMSKLMMLLQAKWREFQE 52 (55)
T ss_pred HCCCCcHHHHHHHHHHHHHHHHh
Confidence 47899999999999999997654
No 92
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=21.37 E-value=1.6e+02 Score=25.21 Aligned_cols=41 Identities=15% Similarity=0.139 Sum_probs=35.5
Q ss_pred HHhHHHHHHhcCCCcchhhhhHHHHHHHHHHHHHHHHHHHh
Q psy1990 54 QVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 94 (382)
Q Consensus 54 EIsK~LGErWK~LSdEEKqpYedkAekdKeRYekEMkeYkk 94 (382)
+--+.|-..|+.|++++++.....+...++.|.+-+++|-+
T Consensus 87 ~~~~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~~~~~~~ 127 (135)
T PRK09706 87 EDQKELLELFDALPESEQDAQLSEMRARVENFNKLFEELLK 127 (135)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34578899999999999999999999999999988887754
Done!