Query psy1729
Match_columns 170
No_of_seqs 142 out of 1413
Neff 5.3
Searched_HMMs 46136
Date Fri Aug 16 18:11:51 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1729.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1729hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 COG5648 NHP6B Chromatin-associ 99.4 1.1E-12 2.3E-17 108.9 7.3 85 3-87 88-209 (211)
2 KOG4715|consensus 99.1 3E-10 6.5E-15 99.7 8.2 106 51-156 94-207 (410)
3 PTZ00199 high mobility group p 98.9 1.8E-09 4E-14 79.0 5.9 40 51-90 54-93 (94)
4 cd01390 HMGB-UBF_HMG-box HMGB- 98.9 2E-09 4.4E-14 71.9 5.4 47 4-50 19-65 (66)
5 cd01388 SOX-TCF_HMG-box SOX-TC 98.9 2.3E-09 5E-14 74.2 5.3 47 4-50 20-66 (72)
6 cd01389 MATA_HMG-box MATA_HMG- 98.9 3.5E-09 7.5E-14 74.1 5.3 47 4-50 20-66 (77)
7 PF00505 HMG_box: HMG (high mo 98.8 8.6E-09 1.9E-13 69.6 5.4 48 4-51 19-66 (69)
8 PTZ00199 high mobility group p 98.8 1.9E-08 4.1E-13 73.6 7.5 41 13-53 52-92 (94)
9 PF09011 HMG_box_2: HMG-box do 98.8 7.2E-09 1.6E-13 71.9 4.7 40 51-90 34-73 (73)
10 KOG0381|consensus 98.7 2E-08 4.4E-13 72.3 5.6 48 4-51 41-88 (96)
11 smart00398 HMG high mobility g 98.7 2.9E-08 6.3E-13 66.5 5.6 47 4-50 20-66 (70)
12 cd01388 SOX-TCF_HMG-box SOX-TC 98.7 2.6E-08 5.6E-13 69.0 5.4 57 34-90 8-70 (72)
13 PF00505 HMG_box: HMG (high mo 98.7 5.8E-08 1.3E-12 65.5 7.0 57 34-90 7-69 (69)
14 cd01390 HMGB-UBF_HMG-box HMGB- 98.7 1.1E-07 2.3E-12 63.5 6.8 54 34-87 7-66 (66)
15 cd01389 MATA_HMG-box MATA_HMG- 98.6 5.7E-08 1.2E-12 68.0 5.2 42 51-92 31-72 (77)
16 cd00084 HMG-box High Mobility 98.6 7.9E-08 1.7E-12 63.6 5.4 47 4-50 19-65 (66)
17 smart00398 HMG high mobility g 98.6 2E-07 4.2E-12 62.4 6.8 57 34-90 8-70 (70)
18 PF09011 HMG_box_2: HMG-box do 98.6 7.9E-08 1.7E-12 66.7 5.0 45 8-52 27-71 (73)
19 KOG0527|consensus 98.5 8.2E-08 1.8E-12 84.9 2.7 60 34-97 69-134 (331)
20 KOG0381|consensus 98.4 6.9E-07 1.5E-11 64.3 5.2 42 51-92 52-94 (96)
21 cd00084 HMG-box High Mobility 98.3 4E-06 8.6E-11 55.4 6.7 53 34-86 7-65 (66)
22 PF14887 HMG_box_5: HMG (high 98.2 4.6E-06 1E-10 60.0 5.6 44 52-95 33-76 (85)
23 KOG0527|consensus 98.1 2.5E-06 5.4E-11 75.6 4.2 46 5-50 82-127 (331)
24 COG5648 NHP6B Chromatin-associ 98.0 1.2E-05 2.6E-10 67.2 6.4 63 34-96 77-145 (211)
25 KOG0526|consensus 97.7 3.7E-05 8E-10 71.8 5.0 38 51-90 563-600 (615)
26 KOG3248|consensus 97.7 4.4E-05 9.5E-10 68.0 4.7 46 51-96 221-266 (421)
27 smart00451 ZnF_U1 U1-like zinc 97.7 6.8E-06 1.5E-10 48.9 -0.5 32 134-165 3-34 (35)
28 KOG0526|consensus 97.5 7E-05 1.5E-09 69.9 3.6 43 10-54 558-600 (615)
29 PF12874 zf-met: Zinc-finger o 97.2 3E-05 6.5E-10 43.1 -2.1 25 135-159 1-25 (25)
30 KOG4715|consensus 97.1 0.0006 1.3E-08 60.5 4.5 48 3-50 82-129 (410)
31 PF12171 zf-C2H2_jaz: Zinc-fin 96.9 9E-05 2E-09 42.3 -1.7 26 135-160 2-27 (27)
32 PF14887 HMG_box_5: HMG (high 96.2 0.01 2.2E-07 42.9 4.5 44 7-51 25-68 (85)
33 KOG0717|consensus 95.4 0.022 4.7E-07 52.9 4.6 41 124-164 282-322 (508)
34 KOG0528|consensus 95.4 0.0045 9.7E-08 57.4 0.1 60 34-93 332-397 (511)
35 PF06220 zf-U1: U1 zinc finger 95.1 0.0051 1.1E-07 38.3 -0.3 31 135-165 4-36 (38)
36 PF13912 zf-C2H2_6: C2H2-type 93.6 0.0088 1.9E-07 33.5 -1.5 19 136-154 3-21 (27)
37 KOG3248|consensus 93.5 0.095 2.1E-06 47.2 4.0 34 13-46 219-252 (421)
38 KOG3408|consensus 93.3 0.063 1.4E-06 41.8 2.4 40 124-163 47-86 (129)
39 PF06382 DUF1074: Protein of u 92.2 0.16 3.6E-06 41.8 3.4 39 5-43 94-132 (183)
40 PF11304 DUF3106: Protein of u 92.0 1 2.3E-05 33.7 7.4 60 14-73 10-69 (107)
41 KOG0528|consensus 90.8 0.082 1.8E-06 49.3 0.4 37 8-44 348-384 (511)
42 PF12756 zf-C2H2_2: C2H2 type 90.8 0.033 7.2E-07 38.9 -1.7 31 134-164 50-80 (100)
43 KOG2746|consensus 90.6 0.31 6.8E-06 47.0 4.1 54 4-66 202-255 (683)
44 PF00096 zf-C2H2: Zinc finger, 89.1 0.049 1.1E-06 29.2 -1.5 20 137-156 3-22 (23)
45 COG5112 UFD2 U1-like Zn-finger 87.9 0.2 4.2E-06 38.5 0.5 56 108-163 22-84 (126)
46 PF11304 DUF3106: Protein of u 83.3 3.9 8.5E-05 30.6 5.6 50 24-73 2-51 (107)
47 PF07535 zf-DBF: DBF zinc fing 83.0 0.38 8.2E-06 31.6 0.0 29 133-164 4-32 (49)
48 smart00586 ZnF_DBF Zinc finger 82.4 0.61 1.3E-05 30.7 0.8 32 131-165 2-33 (49)
49 KOG4727|consensus 81.7 0.35 7.6E-06 39.8 -0.6 32 132-163 73-104 (193)
50 PF03194 LUC7: LUC7 N_terminus 81.3 0.71 1.5E-05 39.5 1.1 31 134-164 190-223 (254)
51 PF13894 zf-C2H2_4: C2H2-type 80.2 0.27 5.8E-06 25.7 -1.2 19 137-155 3-21 (24)
52 TIGR03481 HpnM hopanoid biosyn 80.2 8.5 0.00018 31.6 7.0 39 54-92 72-111 (198)
53 PHA02768 hypothetical protein; 79.2 0.54 1.2E-05 31.7 -0.3 26 136-163 7-32 (55)
54 COG5188 PRP9 Splicing factor 3 78.6 0.97 2.1E-05 41.2 1.1 35 132-166 236-270 (470)
55 KOG2785|consensus 78.5 1.1 2.3E-05 40.9 1.3 37 129-165 63-99 (390)
56 PF05494 Tol_Tol_Ttg2: Toluene 76.9 9.8 0.00021 29.8 6.3 39 53-91 45-84 (170)
57 COG5200 LUC7 U1 snRNP componen 74.4 1.6 3.5E-05 37.2 1.3 30 134-163 185-217 (258)
58 PF06382 DUF1074: Protein of u 73.6 4.6 9.9E-05 33.4 3.7 26 51-76 104-129 (183)
59 PRK15117 ABC transporter perip 72.5 6.2 0.00013 32.7 4.3 40 53-92 75-115 (211)
60 TIGR03481 HpnM hopanoid biosyn 72.1 8.3 0.00018 31.6 4.9 42 9-50 62-105 (198)
61 PF03480 SBP_bac_7: Bacterial 71.0 9.9 0.00021 31.9 5.3 60 22-81 214-281 (286)
62 PF12756 zf-C2H2_2: C2H2 type 69.6 1.5 3.2E-05 30.3 0.0 21 137-157 2-22 (100)
63 PRK12751 cpxP periplasmic stre 68.7 18 0.00039 29.2 6.1 34 51-91 118-151 (162)
64 PRK15117 ABC transporter perip 66.9 9.1 0.0002 31.7 4.1 45 6-50 63-109 (211)
65 KOG2746|consensus 65.1 5.9 0.00013 38.6 3.0 35 51-85 213-247 (683)
66 PHA00616 hypothetical protein 63.3 3.8 8.3E-05 26.4 1.0 18 137-154 4-21 (44)
67 COG4735 Uncharacterized protei 62.2 13 0.00029 31.3 4.2 65 10-74 36-101 (211)
68 smart00355 ZnF_C2H2 zinc finge 61.7 1.8 4E-05 22.4 -0.6 19 137-155 3-21 (26)
69 PF09237 GAGA: GAGA factor; I 59.6 2.2 4.8E-05 28.6 -0.6 21 135-155 25-45 (54)
70 PF07303 Occludin_ELL: Occludi 59.4 70 0.0015 23.7 7.6 65 28-97 6-77 (101)
71 PF01352 KRAB: KRAB box; Inte 59.2 7.3 0.00016 24.4 1.7 30 12-41 2-32 (41)
72 PF13909 zf-H2C2_5: C2H2-type 57.6 1.7 3.7E-05 23.4 -1.2 19 137-156 3-21 (24)
73 KOG0796|consensus 57.2 4.9 0.00011 35.9 0.9 30 135-164 187-219 (319)
74 PF12269 zf-CpG_bind_C: CpG bi 57.2 8.8 0.00019 32.9 2.4 28 126-154 76-103 (236)
75 KOG2505|consensus 56.1 3 6.6E-05 39.5 -0.6 35 131-165 63-97 (591)
76 PF07757 AdoMet_MTase: Predict 53.6 30 0.00066 26.5 4.6 41 31-77 3-43 (112)
77 PF12907 zf-met2: Zinc-binding 52.5 7.8 0.00017 24.5 1.0 22 136-157 3-27 (40)
78 PF08073 CHDNT: CHDNT (NUC034) 50.7 13 0.00029 25.0 2.0 24 4-27 27-50 (55)
79 KOG2785|consensus 47.5 3.6 7.7E-05 37.6 -1.5 29 136-164 219-250 (390)
80 PF05494 Tol_Tol_Ttg2: Toluene 47.5 14 0.00031 28.9 2.1 42 8-49 35-78 (170)
81 PRK10236 hypothetical protein; 47.4 17 0.00038 31.2 2.7 46 32-77 90-143 (237)
82 COG2854 Ttg2D ABC-type transpo 46.8 89 0.0019 26.2 6.8 42 52-93 76-118 (202)
83 KOG1074|consensus 43.4 11 0.00024 37.8 1.0 26 130-155 903-928 (958)
84 KOG3032|consensus 42.1 5 0.00011 34.6 -1.4 34 130-164 31-64 (264)
85 PRK10363 cpxP periplasmic repr 41.1 1.1E+02 0.0024 24.9 6.3 32 51-82 112-143 (166)
86 PRK12750 cpxP periplasmic repr 38.0 2.1E+02 0.0046 23.0 8.0 35 52-86 126-160 (170)
87 PF12881 NUT_N: NUT protein N 34.1 61 0.0013 29.1 4.0 48 7-54 246-294 (328)
88 TIGR02664 nitr_red_assoc conse 33.0 77 0.0017 25.4 4.1 27 22-48 33-62 (145)
89 KOG3214|consensus 32.3 10 0.00023 28.7 -0.8 20 131-150 44-63 (109)
90 KOG3817|consensus 32.1 50 0.0011 30.5 3.3 74 70-143 321-415 (452)
91 PTZ00448 hypothetical protein; 31.7 14 0.0003 33.7 -0.3 32 135-166 315-346 (373)
92 KOG2462|consensus 31.3 15 0.00032 32.4 -0.2 29 136-164 217-245 (279)
93 PLN02748 tRNA dimethylallyltra 31.3 13 0.00027 34.8 -0.7 30 136-165 420-450 (468)
94 PF06945 DUF1289: Protein of u 31.2 39 0.00084 21.9 1.8 16 59-74 29-44 (51)
95 PF12650 DUF3784: Domain of un 30.8 32 0.0007 24.6 1.6 15 59-73 25-39 (97)
96 PHA00732 hypothetical protein 30.0 11 0.00023 26.8 -1.1 20 137-156 4-23 (79)
97 KOG0227|consensus 29.6 18 0.00039 30.5 0.0 34 133-166 52-85 (222)
98 PRK09706 transcriptional repre 29.5 1.3E+02 0.0027 22.6 4.7 37 54-90 90-126 (135)
99 PRK10455 periplasmic protein; 28.2 2.1E+02 0.0046 22.8 6.0 24 51-74 118-141 (161)
100 KOG4722|consensus 28.0 28 0.0006 32.9 0.9 29 135-163 494-522 (672)
101 PRK10236 hypothetical protein; 26.8 63 0.0014 27.8 2.8 26 16-41 118-143 (237)
102 PF09655 Nitr_red_assoc: Conse 26.2 84 0.0018 25.1 3.3 29 22-50 33-64 (144)
103 KOG4323|consensus 25.8 17 0.00038 34.0 -0.8 19 129-147 180-198 (464)
104 KOG1074|consensus 25.0 22 0.00047 35.9 -0.3 24 135-158 634-657 (958)
105 PF06518 DUF1104: Protein of u 23.6 3E+02 0.0066 20.2 6.5 52 12-76 22-73 (93)
106 cd08317 Death_ank Death domain 21.8 42 0.00091 23.5 0.7 21 8-28 2-22 (84)
107 PF05605 zf-Di19: Drought indu 21.4 29 0.00062 22.3 -0.2 24 131-156 28-51 (54)
108 PF04423 Rad50_zn_hook: Rad50 21.1 28 0.00061 22.4 -0.3 19 136-156 22-40 (54)
109 cd07081 ALDH_F20_ACDH_EutE-lik 21.0 2.4E+02 0.0051 25.9 5.6 32 58-89 13-44 (439)
110 PF02892 zf-BED: BED zinc fing 20.8 18 0.00038 22.1 -1.2 25 130-154 12-40 (45)
111 PF15581 Imm35: Immunity prote 20.7 1.5E+02 0.0033 21.9 3.5 23 11-33 30-52 (93)
112 PF05914 RIB43A: RIB43A; Inte 20.5 3.5E+02 0.0076 24.6 6.5 91 7-97 255-350 (379)
No 1
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=99.38 E-value=1.1e-12 Score=108.87 Aligned_cols=85 Identities=31% Similarity=0.447 Sum_probs=79.0
Q ss_pred cccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH--------------------------------
Q psy1729 3 IESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL-------------------------------- 50 (170)
Q Consensus 3 ~~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em-------------------------------- 50 (170)
++...+|.+++++|++.+|++|++|+++||++|...|..++++|+++.
T Consensus 88 ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~~~~~~~~e~~~~~r~~~~~~~~ 167 (211)
T COG5648 88 EIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNKAPIGPFIENEPKIRPKVEGPSP 167 (211)
T ss_pred HHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCCCCCchhhhccHHhccccCCCCc
Confidence 456789999999999999999999999999999999999999998865
Q ss_pred -----hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHH
Q psy1729 51 -----KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 87 (170)
Q Consensus 51 -----Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~ 87 (170)
+.++.+|..|+.|+++-|.+|++.+.+++..|...++
T Consensus 168 ~~~~~e~~k~~~~~w~el~~skK~~~~~~~Kk~k~~~~~~~~ 209 (211)
T COG5648 168 DKALVEETKIISKAWSELDESKKKKYIDKYKKLKEEYDSFYP 209 (211)
T ss_pred chhhhHHhhhhhhhhhhhChhhhhHHHHHHHHHHHHHhhhcc
Confidence 7899999999999999999999999999999987653
No 2
>KOG4715|consensus
Probab=99.09 E-value=3e-10 Score=99.68 Aligned_cols=106 Identities=25% Similarity=0.406 Sum_probs=86.3
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhHHHHHHh-hhhh-hhh-CCCCc--c---ccccccc
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQSYLRRK-RVKS-LQA-NGTEE--S---DIATDAT 122 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~~~~~~k-~~k~-~~~-~~~~~--~---~~~~d~~ 122 (170)
+|.|+||.+|.-|+++||+-|+...+..|..|++-|++|+.+++|.++.-.| +++- +-+ .++.. + ....+++
T Consensus 94 eiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~smkayh~sp~y~ayinaKsra~a~le~~sr~~~sr~~~ge~~~~IQ 173 (410)
T KOG4715|consen 94 EIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESMKAYHNSPAYLAYINAKSRAEAALEEESRQRQSRMEKGEPYMSIQ 173 (410)
T ss_pred HHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHHHHhhCCchHHHHhhhhhhhhhhhccccccccchhhcCCcceecc
Confidence 8999999999999999999999999999999999999999999999996533 3331 101 11111 1 2224889
Q ss_pred ccccccccCchhHHHHHHHHHhhhhhhhhhhhch
Q psy1729 123 DEIDEEEEDNEELYCRVCDQWFTTLHNKREHLNG 156 (170)
Q Consensus 123 ~~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~ 156 (170)
+++|+||-|||.+-.|+.+.+|-++|++---+++
T Consensus 174 PaeDeDD~ddg~stkhla~arf~rN~rLIsei~S 207 (410)
T KOG4715|consen 174 PAEDEDDYDDGFSTKHLATARFQRNHRLISEILS 207 (410)
T ss_pred cccCccccccccchhhhhhhhhhhhhHHHHHHhc
Confidence 9999999999999999999999999998655443
No 3
>PTZ00199 high mobility group protein; Provisional
Probab=98.94 E-value=1.8e-09 Score=79.02 Aligned_cols=40 Identities=43% Similarity=0.668 Sum_probs=21.5
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk 90 (170)
+|++.||++|++||+++|.+|+++|+.++.+|..+|.+|.
T Consensus 54 evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y~ 93 (94)
T PTZ00199 54 AVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEYA 93 (94)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4455555555555555555555555555555555555553
No 4
>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=98.93 E-value=2e-09 Score=71.95 Aligned_cols=47 Identities=40% Similarity=0.620 Sum_probs=42.7
Q ss_pred ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729 4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 50 (170)
Q Consensus 4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em 50 (170)
.+.++|++++++|++.||..|+.||+++|.+|.+.|..++.+|..+|
T Consensus 19 ~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~ 65 (66)
T cd01390 19 LKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEM 65 (66)
T ss_pred HHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 46788999999999999999999999999999999999999998875
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=98.91 E-value=2.3e-09 Score=74.24 Aligned_cols=47 Identities=23% Similarity=0.312 Sum_probs=40.9
Q ss_pred ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729 4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 50 (170)
Q Consensus 4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em 50 (170)
.+.++|++++++|++.||+.|+.||+++|++|.+.|..++++|..++
T Consensus 20 ~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~ 66 (72)
T cd01388 20 VLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLY 66 (72)
T ss_pred HHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHC
Confidence 35688999999999999999999999999999999999999887754
No 6
>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=98.88 E-value=3.5e-09 Score=74.14 Aligned_cols=47 Identities=23% Similarity=0.298 Sum_probs=35.3
Q ss_pred ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729 4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 50 (170)
Q Consensus 4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em 50 (170)
.++++|++++++|+++||++|+.||+++|++|.++|..++++|..++
T Consensus 20 ~~~~~p~~~~~eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~ 66 (77)
T cd01389 20 LKTENPGLTNNEISRIIGRMWRSESPEVKAYYKELAEEEKERHAREY 66 (77)
T ss_pred HHHHCCCCCHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHC
Confidence 35677777788888877777777777777777777777777776654
No 7
>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=98.81 E-value=8.6e-09 Score=69.56 Aligned_cols=48 Identities=31% Similarity=0.488 Sum_probs=37.0
Q ss_pred ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729 4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51 (170)
Q Consensus 4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE 51 (170)
.+.++|++++++|++.||..|+.||+++|++|.+.|..++..|..++.
T Consensus 19 ~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~ 66 (69)
T PF00505_consen 19 LKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMP 66 (69)
T ss_dssp HHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456778888888888888888888888888888888888877776653
No 8
>PTZ00199 high mobility group protein; Provisional
Probab=98.81 E-value=1.9e-08 Score=73.64 Aligned_cols=41 Identities=39% Similarity=0.548 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhh
Q psy1729 13 KLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVT 53 (170)
Q Consensus 13 ~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~ 53 (170)
+++|++.||++|+.||+++|.+|++.|..++.+|..++..+
T Consensus 52 ~~evsk~ige~Wk~ls~eeK~~y~~~A~~dk~rY~~e~~~Y 92 (94)
T PTZ00199 52 VAAVGKMVGEAWNKLSEEEKAPYEKKAQEDKVRYEKEKAEY 92 (94)
T ss_pred HHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78999999999999999999999999999999999988655
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=98.80 E-value=7.2e-09 Score=71.93 Aligned_cols=40 Identities=40% Similarity=0.675 Sum_probs=35.7
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk 90 (170)
++++.||..|++||++||.+|+++|+.++.+|..+|..|+
T Consensus 34 e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~~~ 73 (73)
T PF09011_consen 34 EVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKEWN 73 (73)
T ss_dssp HHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 7889999999999999999999999999999999999885
No 10
>KOG0381|consensus
Probab=98.74 E-value=2e-08 Score=72.31 Aligned_cols=48 Identities=29% Similarity=0.386 Sum_probs=42.0
Q ss_pred ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729 4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51 (170)
Q Consensus 4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE 51 (170)
+++++|++++.+|++.+|++|++|++++|.+|...+..++++|..+|.
T Consensus 41 ~k~~~p~~~~~~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~ 88 (96)
T KOG0381|consen 41 IKAENPGLSVGEVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELA 88 (96)
T ss_pred HHHhCCCCCHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578889999999999999999999988888888888888888888776
No 11
>smart00398 HMG high mobility group.
Probab=98.72 E-value=2.9e-08 Score=66.49 Aligned_cols=47 Identities=34% Similarity=0.518 Sum_probs=35.3
Q ss_pred ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729 4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 50 (170)
Q Consensus 4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em 50 (170)
.+.++|++++++|++.||..|+.||+++|.+|.+.|..++++|..++
T Consensus 20 ~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~ 66 (70)
T smart00398 20 IKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEM 66 (70)
T ss_pred HHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567777777777777777777777777777777777777776654
No 12
>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=98.72 E-value=2.6e-08 Score=68.97 Aligned_cols=57 Identities=23% Similarity=0.401 Sum_probs=47.7
Q ss_pred hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729 34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90 (170)
Q Consensus 34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk 90 (170)
.|.-...+.+.....+ .++++.||+.|+.||+++|++|.++|+.++++|.+++.+|+
T Consensus 8 af~~F~~~~r~~~~~~~p~~~~~eisk~l~~~Wk~ls~~eK~~y~~~a~~~k~~y~~~~p~y~ 70 (72)
T cd01388 8 AFMLFSKRHRRKVLQEYPLKENRAISKILGDRWKALSNEEKQPYYEEAKKLKELHMKLYPDYK 70 (72)
T ss_pred HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHCcCCC
Confidence 4555555556555443 38999999999999999999999999999999999999886
No 13
>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=98.72 E-value=5.8e-08 Score=65.47 Aligned_cols=57 Identities=30% Similarity=0.585 Sum_probs=47.6
Q ss_pred hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729 34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90 (170)
Q Consensus 34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk 90 (170)
+|.-.....+..+..+ .+|++.||++|++||+++|.+|.+.|.+++.+|..++.+|+
T Consensus 7 af~lf~~~~~~~~k~~~p~~~~~~i~~~~~~~W~~l~~~eK~~y~~~a~~~~~~y~~~~~~y~ 69 (69)
T PF00505_consen 7 AFMLFCKEKRAKLKEENPDLSNKEISKILAQMWKNLSEEEKAPYKEEAEEEKERYEKEMPEYK 69 (69)
T ss_dssp HHHHHHHHHHHHHHHHSTTSTHHHHHHHHHHHHHCSHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhcccccccchhhHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4555555555555443 28999999999999999999999999999999999999985
No 14
>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=98.65 E-value=1.1e-07 Score=63.54 Aligned_cols=54 Identities=41% Similarity=0.713 Sum_probs=45.2
Q ss_pred hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHH
Q psy1729 34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 87 (170)
Q Consensus 34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~ 87 (170)
+|.-.+...+..+..+ .++++.||+.|++||+++|++|.+.|.+++.+|..+|.
T Consensus 7 af~~f~~~~r~~~~~~~p~~~~~~i~~~~~~~W~~ls~~eK~~y~~~a~~~~~~y~~e~~ 66 (66)
T cd01390 7 AYFLFSQEQRPKLKKENPDASVTEVTKILGEKWKELSEEEKKKYEEKAEKDKERYEKEMK 66 (66)
T ss_pred HHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhhC
Confidence 5566666666666543 38999999999999999999999999999999999873
No 15
>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=98.64 E-value=5.7e-08 Score=67.95 Aligned_cols=42 Identities=26% Similarity=0.471 Sum_probs=40.1
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcc
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKS 92 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~ 92 (170)
+|++.||++|+.||+++|++|.++|+.++++|..++.+|+-.
T Consensus 31 eisk~~g~~Wk~ls~eeK~~y~~~A~~~k~~~~~~~p~Yky~ 72 (77)
T cd01389 31 EISRIIGRMWRSESPEVKAYYKELAEEEKERHAREYPDYKYT 72 (77)
T ss_pred HHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHCCCCccc
Confidence 899999999999999999999999999999999999999843
No 16
>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=98.62 E-value=7.9e-08 Score=63.64 Aligned_cols=47 Identities=36% Similarity=0.542 Sum_probs=41.5
Q ss_pred ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729 4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 50 (170)
Q Consensus 4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em 50 (170)
.+.++|++++.+|++.||..|+.||+++|.+|.+.|..++..|..++
T Consensus 19 ~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~ 65 (66)
T cd00084 19 VKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM 65 (66)
T ss_pred HHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 45678999999999999999999999999999999999999997653
No 17
>smart00398 HMG high mobility group.
Probab=98.60 E-value=2e-07 Score=62.41 Aligned_cols=57 Identities=32% Similarity=0.609 Sum_probs=46.3
Q ss_pred hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729 34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90 (170)
Q Consensus 34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk 90 (170)
+|.-.....+..+..+ .++++.||.+|+.||+++|++|.+.|..++.+|..++..|+
T Consensus 8 ~y~~f~~~~r~~~~~~~~~~~~~~i~~~~~~~W~~l~~~ek~~y~~~a~~~~~~y~~~~~~y~ 70 (70)
T smart00398 8 AFMLFSQENRAKIKAENPDLSNAEISKKLGERWKLLSEEEKAPYEEKAKKDKERYEEEMPEYK 70 (70)
T ss_pred HHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4444555555554432 37899999999999999999999999999999999999884
No 18
>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=98.60 E-value=7.9e-08 Score=66.66 Aligned_cols=45 Identities=36% Similarity=0.470 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhh
Q psy1729 8 MISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKV 52 (170)
Q Consensus 8 ~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi 52 (170)
.+..++.++++.||..|++||++||.+|.+.|+.++++|..++..
T Consensus 27 ~~~~~~~e~~k~~~~~Wk~Ls~~EK~~Y~~~A~~~k~~y~~e~~~ 71 (73)
T PF09011_consen 27 GQKQSFREVMKEISERWKSLSEEEKEPYEERAKEDKERYEREMKE 71 (73)
T ss_dssp -T-SSHHHHHHHHHHHHHHS-HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred ccCCCHHHHHHHHHHHHHhcCHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 567889999999999999999999999999999999999998743
No 19
>KOG0527|consensus
Probab=98.46 E-value=8.2e-08 Score=84.92 Aligned_cols=60 Identities=25% Similarity=0.491 Sum_probs=50.6
Q ss_pred hHHHHHHHHHHHHHHHH------hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhHH
Q psy1729 34 VYLDRAEVDKKRYREEL------KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS 97 (170)
Q Consensus 34 ~Ye~~Ak~dKerY~~Em------Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~~ 97 (170)
-|.-.+...|.+-.++- ||+|.||.+||.|+++||.||++.|++++..++++..+|+ |+.
T Consensus 69 AFMVWSq~~RRkma~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~HmkehPdYK----YRP 134 (331)
T KOG0527|consen 69 AFMVWSQGQRRKLAKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEYPDYK----YRP 134 (331)
T ss_pred hhhhhhHHHHHHHHHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhCCCcc----ccc
Confidence 45556666665554432 9999999999999999999999999999999999999999 666
No 20
>KOG0381|consensus
Probab=98.37 E-value=6.9e-07 Score=64.28 Aligned_cols=42 Identities=38% Similarity=0.647 Sum_probs=39.7
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHH-HHHcc
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK-VYRKS 92 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~-~yk~~ 92 (170)
++.+.+|++|++|++++|.+|+..|..++++|..+|. .|+..
T Consensus 52 ~v~k~~g~~W~~l~~~~k~~y~~ka~~~k~~Y~~~~~~~~~~~ 94 (96)
T KOG0381|consen 52 EVAKALGEMWKNLAEEEKQPYEEKASKLKEKYEKELAGEYKAS 94 (96)
T ss_pred HHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 8999999999999999999999999999999999999 87754
No 21
>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=98.27 E-value=4e-06 Score=55.36 Aligned_cols=53 Identities=36% Similarity=0.621 Sum_probs=43.4
Q ss_pred hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHH
Q psy1729 34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 86 (170)
Q Consensus 34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em 86 (170)
+|.-.....+..+..+ .+|++.+|.+|+.||+++|.+|.+.|..++.+|..++
T Consensus 7 af~~f~~~~~~~~~~~~~~~~~~~i~~~~~~~W~~l~~~~k~~y~~~a~~~~~~y~~~~ 65 (66)
T cd00084 7 AYFLFSQEHRAEVKAENPGLSVGEISKILGEMWKSLSEEEKKKYEEKAEKDKERYEKEM 65 (66)
T ss_pred HHHHHHHHHHHHHHHHCcCCCHHHHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHhh
Confidence 4555555555555443 3899999999999999999999999999999999875
No 22
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=98.17 E-value=4.6e-06 Score=60.03 Aligned_cols=44 Identities=32% Similarity=0.544 Sum_probs=39.0
Q ss_pred hhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhh
Q psy1729 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAY 95 (170)
Q Consensus 52 i~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~ 95 (170)
..+.+...|++|++.+|.+|+.+|.++..+|+.+|.+|+...+.
T Consensus 33 ~~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~e~r~~~~~ 76 (85)
T PF14887_consen 33 ALKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELREMRSAPAD 76 (85)
T ss_dssp HHHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHHCCS-CCCT
T ss_pred HHHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHHHHhcCCCC
Confidence 35689999999999999999999999999999999999876653
No 23
>KOG0527|consensus
Probab=98.12 E-value=2.5e-06 Score=75.59 Aligned_cols=46 Identities=28% Similarity=0.386 Sum_probs=42.1
Q ss_pred cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729 5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 50 (170)
Q Consensus 5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em 50 (170)
-.++|.|...||+|.||.+||.|+++||.+|++.|++.|....++-
T Consensus 82 a~qnP~mHNSEISK~LG~~WK~Lse~EKrPFi~EAeRLR~~Hmkeh 127 (331)
T KOG0527|consen 82 AKQNPKMHNSEISKRLGAEWKLLSEEEKRPFVDEAERLRAQHMKEY 127 (331)
T ss_pred HHhCcchhhHHHHHHHHHHHhhcCHhhhccHHHHHHHHHHHHHHhC
Confidence 3579999999999999999999999999999999999999876653
No 24
>COG5648 NHP6B Chromatin-associated proteins containing the HMG domain [Chromatin structure and dynamics]
Probab=98.03 E-value=1.2e-05 Score=67.19 Aligned_cols=63 Identities=30% Similarity=0.509 Sum_probs=51.8
Q ss_pred hHHHHHHHHHHHHHHH------HhhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhH
Q psy1729 34 VYLDRAEVDKKRYREE------LKVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 96 (170)
Q Consensus 34 ~Ye~~Ak~dKerY~~E------mEi~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~ 96 (170)
.|.-.++..|.....+ .++.+.+|++|++|+++||+||...|..++++|..++..|..+..+.
T Consensus 77 ayf~y~~~~R~ei~~~~p~l~~~e~~k~~~e~WK~Ltd~eke~y~k~~~~~~erYq~ek~~y~~k~~~~ 145 (211)
T COG5648 77 AYFLYSAENRDEIRKENPKLTFGEVGKLLSEKWKELTDEEKEPYYKEANSDRERYQREKEEYNKKLPNK 145 (211)
T ss_pred HHHHHHHHHHHHHHHhCCCCChHHHHHHHHHHHHhccHhhhhhHHHHHhhHHHHHHHHHHhhhcccCCC
Confidence 4555555555554442 38999999999999999999999999999999999999999875544
No 25
>KOG0526|consensus
Probab=97.74 E-value=3.7e-05 Score=71.78 Aligned_cols=38 Identities=42% Similarity=0.815 Sum_probs=37.3
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk 90 (170)
++.|.+|++|+.||. |.+|+++|+.+++||+.+|++|+
T Consensus 563 dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk 600 (615)
T KOG0526|consen 563 DVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYK 600 (615)
T ss_pred HHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhc
Confidence 899999999999999 99999999999999999999999
No 26
>KOG3248|consensus
Probab=97.70 E-value=4.4e-05 Score=68.03 Aligned_cols=46 Identities=22% Similarity=0.426 Sum_probs=43.6
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhH
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQ 96 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~ 96 (170)
+|.++||++|.+||-+|..+|.++|.++++-+.+-...|-....|-
T Consensus 221 aiNqiLGrRWH~LSrEEQAKYyElArKerqlH~qlYP~WSARdNYg 266 (421)
T KOG3248|consen 221 AINQILGRRWHALSREEQAKYYELARKERQLHMQLYPGWSARDNYG 266 (421)
T ss_pred HHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHHHHhcCCcchhhhhh
Confidence 7899999999999999999999999999999999999998888776
No 27
>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=97.69 E-value=6.8e-06 Score=48.95 Aligned_cols=32 Identities=28% Similarity=0.700 Sum_probs=29.1
Q ss_pred hHHHHHHHHHhhhhhhhhhhhchhhhhhhhcc
Q psy1729 134 ELYCRVCDQWFTTLHNKREHLNGRQHFQRFDR 165 (170)
Q Consensus 134 ~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~ 165 (170)
-.||.+|+.+|.+.+..+.|+.|++|.+++..
T Consensus 3 ~~~C~~C~~~~~~~~~~~~H~~gk~H~~~~~~ 34 (35)
T smart00451 3 GFYCKLCNVTFTDEISVEAHLKGKKHKKNVKK 34 (35)
T ss_pred CeEccccCCccCCHHHHHHHHChHHHHHHHHc
Confidence 36899999999999999999999999998753
No 28
>KOG0526|consensus
Probab=97.53 E-value=7e-05 Score=69.95 Aligned_cols=43 Identities=37% Similarity=0.577 Sum_probs=41.1
Q ss_pred CCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhh
Q psy1729 10 STTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTK 54 (170)
Q Consensus 10 ~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K 54 (170)
+.++++|+|.+|++|+.||. |.+|++.|+.+|.+|+.+|.-++
T Consensus 558 gi~~~dv~kk~g~~wk~ms~--k~~we~ka~~dk~ry~~em~~yk 600 (615)
T KOG0526|consen 558 GISVGDVAKKAGEKWKQMSA--KEEWEDKAAVDKQRYEDEMKEYK 600 (615)
T ss_pred CchHHHHHHHHhHHHhhhcc--cchhhHHHHHHHHHHHHHHHhhc
Confidence 89999999999999999999 99999999999999999997666
No 29
>PF12874 zf-met: Zinc-finger of C2H2 type; PDB: 1ZU1_A 2KVG_A.
Probab=97.16 E-value=3e-05 Score=43.06 Aligned_cols=25 Identities=32% Similarity=0.939 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhhhhhhhhhhchhhh
Q psy1729 135 LYCRVCDQWFTTLHNKREHLNGRQH 159 (170)
Q Consensus 135 ~~~~~~~~~f~~~h~~~~~~~~~~~ 159 (170)
.+|.+|+..|++.-..+.||.|+.|
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
>KOG4715|consensus
Probab=97.11 E-value=0.0006 Score=60.54 Aligned_cols=48 Identities=25% Similarity=0.380 Sum_probs=45.5
Q ss_pred cccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHH
Q psy1729 3 IESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 50 (170)
Q Consensus 3 ~~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~Em 50 (170)
--|++||.+.+=+|.|+||.+|..|++.||+.|...+...|..|.+.|
T Consensus 82 ~VkA~nPe~kLWeiGK~Ig~mW~dLpd~EK~ey~~EYeaEKieY~~sm 129 (410)
T KOG4715|consen 82 QVKASNPELKLWEIGKIIGGMWLDLPDEEKQEYLNEYEAEKIEYNESM 129 (410)
T ss_pred hhhccCcchHHHHHHHHHHHHHhhCcchHHHHHHHHHHHHHHHHHHHH
Confidence 358999999999999999999999999999999999999999998877
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=96.89 E-value=9e-05 Score=42.28 Aligned_cols=26 Identities=27% Similarity=0.912 Sum_probs=24.3
Q ss_pred HHHHHHHHHhhhhhhhhhhhchhhhh
Q psy1729 135 LYCRVCDQWFTTLHNKREHLNGRQHF 160 (170)
Q Consensus 135 ~~~~~~~~~f~~~h~~~~~~~~~~~~ 160 (170)
.||.+|+-+|++....+.||.|+.|.
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 47999999999999999999999994
No 32
>PF14887 HMG_box_5: HMG (high mobility group) box 5; PDB: 1L8Y_A 1L8Z_A 2HDZ_A.
Probab=96.15 E-value=0.01 Score=42.93 Aligned_cols=44 Identities=32% Similarity=0.545 Sum_probs=36.8
Q ss_pred cCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHh
Q psy1729 7 KMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELK 51 (170)
Q Consensus 7 ~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmE 51 (170)
.+++-...+ -+.+...|++|+..+|-+|...|.++..+|+++|-
T Consensus 25 ~~~~dr~K~-~kam~~~W~~me~Kekl~WIkKA~EdqKrYE~el~ 68 (85)
T PF14887_consen 25 KFRNDRKKA-LKAMEAQWSQMEKKEKLKWIKKAAEDQKRYERELR 68 (85)
T ss_dssp HTTSTHHHH-HHHHHHHHHTTGGGHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhHhHHHH-HHHHHHHHHHhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 344444555 45899999999999999999999999999999873
No 33
>KOG0717|consensus
Probab=95.39 E-value=0.022 Score=52.94 Aligned_cols=41 Identities=32% Similarity=0.649 Sum_probs=33.6
Q ss_pred cccccccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729 124 EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFD 164 (170)
Q Consensus 124 ~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~ 164 (170)
+.|+-+.+++.|||.+|+..|-|---+.-|-.+++|.-||.
T Consensus 282 e~de~d~~ge~lyC~vCnKsFKseKq~kNHEnSKKHkenv~ 322 (508)
T KOG0717|consen 282 ESDEADNEGEVLYCVVCNKSFKSEKQLKNHENSKKHKENVA 322 (508)
T ss_pred hhhhhhhcCCceEEeeccccccchHHHHhhHHHHHHHHHHH
Confidence 33443444555999999999999999999999999998874
No 34
>KOG0528|consensus
Probab=95.36 E-value=0.0045 Score=57.44 Aligned_cols=60 Identities=22% Similarity=0.417 Sum_probs=48.4
Q ss_pred hHHHHHHHHHHHHHHH---H---hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcch
Q psy1729 34 VYLDRAEVDKKRYREE---L---KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSD 93 (170)
Q Consensus 34 ~Ye~~Ak~dKerY~~E---m---Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~ 93 (170)
.|.-.|+..|..-... | .|+|.||.+||.||..||+||.+.-+++-..+.+....|+-++
T Consensus 332 AFMVWAkDERRKILqA~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk~HlEk~PdYrYkP 397 (511)
T KOG0528|consen 332 AFMVWAKDERRKILQAFPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSKLHLEKYPDYRYKP 397 (511)
T ss_pred hhhcccchhhhhhhhcCccccccchhHHhcccccccccccccchHHHHHHHHHhhhccCcccccCC
Confidence 4555666666554332 2 7999999999999999999999999999999999999998653
No 35
>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=95.06 E-value=0.0051 Score=38.29 Aligned_cols=31 Identities=23% Similarity=0.654 Sum_probs=19.1
Q ss_pred HHHHHHHHHh--hhhhhhhhhhchhhhhhhhcc
Q psy1729 135 LYCRVCDQWF--TTLHNKREHLNGRQHFQRFDR 165 (170)
Q Consensus 135 ~~~~~~~~~f--~~~h~~~~~~~~~~~~~~~~~ 165 (170)
-||-.|+-|| .+...-+-|..|.+|..++..
T Consensus 4 yyCdyC~~~~~~d~~~~Rk~H~~G~kH~~nv~~ 36 (38)
T PF06220_consen 4 YYCDYCKKYLTHDSPSIRKQHERGWKHKENVKR 36 (38)
T ss_dssp -B-TTT--B-S--SHHHHHHHT--THHHHHHHH
T ss_pred eecccccceecCCChHHHHHhhccHHHHHHHHH
Confidence 3899999999 344566999999999998864
No 36
>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=93.60 E-value=0.0088 Score=33.46 Aligned_cols=19 Identities=37% Similarity=0.698 Sum_probs=18.0
Q ss_pred HHHHHHHHhhhhhhhhhhh
Q psy1729 136 YCRVCDQWFTTLHNKREHL 154 (170)
Q Consensus 136 ~~~~~~~~f~~~h~~~~~~ 154 (170)
.|.+|++.|+++.++++|+
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 4899999999999999999
No 37
>KOG3248|consensus
Probab=93.46 E-value=0.095 Score=47.22 Aligned_cols=34 Identities=24% Similarity=0.480 Sum_probs=31.2
Q ss_pred HHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHH
Q psy1729 13 KLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRY 46 (170)
Q Consensus 13 ~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY 46 (170)
-++|.++||.+|-.||-+|..+|+++|.++|+..
T Consensus 219 SAaiNqiLGrRWH~LSrEEQAKYyElArKerqlH 252 (421)
T KOG3248|consen 219 SAAINQILGRRWHALSREEQAKYYELARKERQLH 252 (421)
T ss_pred HHHHHHHHhHHHhhhhHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999999998764
No 38
>KOG3408|consensus
Probab=93.35 E-value=0.063 Score=41.77 Aligned_cols=40 Identities=25% Similarity=0.586 Sum_probs=35.5
Q ss_pred cccccccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhh
Q psy1729 124 EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRF 163 (170)
Q Consensus 124 ~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~ 163 (170)
++|.|=+-.+.-||..|..||++--++..|.-|+-|-..|
T Consensus 47 ~~D~dlPG~GqfyCi~CaRyFi~~~~l~~H~ktK~HKrRv 86 (129)
T KOG3408|consen 47 EIDPDLPGGGQFYCIECARYFIDAKALKTHFKTKVHKRRV 86 (129)
T ss_pred cCCCCCCCCceeehhhhhhhhcchHHHHHHHhccHHHHHH
Confidence 4577777788899999999999999999999999998765
No 39
>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=92.15 E-value=0.16 Score=41.75 Aligned_cols=39 Identities=21% Similarity=0.225 Sum_probs=33.2
Q ss_pred cccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHH
Q psy1729 5 SEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDK 43 (170)
Q Consensus 5 k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dK 43 (170)
+.+|.++++.|++...+..|..||+.+|..|...+....
T Consensus 94 Rrkh~~L~p~dlI~~AAraW~rLSe~eK~rYrr~~~~~~ 132 (183)
T PF06382_consen 94 RRKHCGLSPQDLIQRAARAWCRLSEAEKNRYRRMAPSVR 132 (183)
T ss_pred HHHccCCCHHHHHHHHHHHHHhCCHHHHHHHHhhcchhh
Confidence 457889999999999999999999999999998765444
No 40
>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=92.04 E-value=1 Score=33.71 Aligned_cols=60 Identities=17% Similarity=0.219 Sum_probs=39.2
Q ss_pred HHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChhhhhhhHH
Q psy1729 14 LLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLD 73 (170)
Q Consensus 14 ~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~EK~~Y~~ 73 (170)
.++..-++..|..|++..+..+...+..-..--..+-+-+..--..|.+||++++..-..
T Consensus 10 q~~L~pl~~~W~~l~~~qr~k~l~~a~r~~~mspeqq~r~~~rm~~W~~LspeqR~~~R~ 69 (107)
T PF11304_consen 10 QQALAPLAERWNSLPPEQRRKWLQIAERWPSMSPEQQQRLRERMRRWAALSPEQRQQARE 69 (107)
T ss_pred HHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHhCCHHHHHHHHH
Confidence 456788999999999999999988776521111112233333335788888888765444
No 41
>KOG0528|consensus
Probab=90.82 E-value=0.082 Score=49.29 Aligned_cols=37 Identities=24% Similarity=0.427 Sum_probs=32.3
Q ss_pred CCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHH
Q psy1729 8 MISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKK 44 (170)
Q Consensus 8 ~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKe 44 (170)
.|+|....|+|+||.+|+.|+..||++|++.-...-.
T Consensus 348 ~PDMHNSnISKILGSRWKaMSN~eKQPYYEEQaRLSk 384 (511)
T KOG0528|consen 348 FPDMHNSNISKILGSRWKAMSNTEKQPYYEEQARLSK 384 (511)
T ss_pred CccccccchhHHhcccccccccccccchHHHHHHHHH
Confidence 5889999999999999999999999999986655443
No 42
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=90.80 E-value=0.033 Score=38.90 Aligned_cols=31 Identities=23% Similarity=0.544 Sum_probs=26.3
Q ss_pred hHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729 134 ELYCRVCDQWFTTLHNKREHLNGRQHFQRFD 164 (170)
Q Consensus 134 ~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~ 164 (170)
...|.+|++.|++...+++||.+..|.++..
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 5889999999999999999999999988653
No 43
>KOG2746|consensus
Probab=90.65 E-value=0.31 Score=47.03 Aligned_cols=54 Identities=28% Similarity=0.331 Sum_probs=45.2
Q ss_pred ccccCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChh
Q psy1729 4 ESEKMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLP 66 (170)
Q Consensus 4 ~k~~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~ 66 (170)
-...+|+....-|+++||+.|-+|.+.||+.|.++|.+.++.+.+. .|+..+..
T Consensus 202 vhq~~pn~DNrtIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka---------e~~k~sk~ 255 (683)
T KOG2746|consen 202 VHQRHPNQDNRTISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA---------EWKKDSKE 255 (683)
T ss_pred hhccCccccchhHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh---------hcccccch
Confidence 3457889999999999999999999999999999999988876442 77777654
No 44
>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=89.08 E-value=0.049 Score=29.18 Aligned_cols=20 Identities=25% Similarity=0.735 Sum_probs=18.4
Q ss_pred HHHHHHHhhhhhhhhhhhch
Q psy1729 137 CRVCDQWFTTLHNKREHLNG 156 (170)
Q Consensus 137 ~~~~~~~f~~~h~~~~~~~~ 156 (170)
|..|+..|++..+++.||..
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 88999999999999999864
No 45
>COG5112 UFD2 U1-like Zn-finger-containing protein [General function prediction only]
Probab=87.91 E-value=0.2 Score=38.46 Aligned_cols=56 Identities=27% Similarity=0.421 Sum_probs=42.5
Q ss_pred hhCCCCcccccccccc-------cccccccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhh
Q psy1729 108 QANGTEESDIATDATD-------EIDEEEEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRF 163 (170)
Q Consensus 108 ~~~~~~~~~~~~d~~~-------~~d~~~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~ 163 (170)
+-+|-..+.|-+|... .+|.+-+--|.-||.-|..||-+---+-||.-|+-|...+
T Consensus 22 r~~grDlDqi~nDls~~Es~~Klp~Dp~lPGlGqhYCieCaryf~t~~aL~~HkkgkvHkRR~ 84 (126)
T COG5112 22 RLFGRDLDQIKNDLSTKESQKKLPYDPELPGLGQHYCIECARYFITEKALMEHKKGKVHKRRA 84 (126)
T ss_pred HHhcccHHHHHHhcchhhhhccCCCCCCCCCCceeeeehhHHHHHHHHHHHHHhccchhHHHH
Confidence 3345445667677621 2366666678899999999999999999999999997665
No 46
>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=83.35 E-value=3.9 Score=30.59 Aligned_cols=50 Identities=18% Similarity=0.245 Sum_probs=23.6
Q ss_pred hcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChhhhhhhHH
Q psy1729 24 WSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLD 73 (170)
Q Consensus 24 Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~EK~~Y~~ 73 (170)
|..||+.++..+.-++..=..--...-.-...++..|..||++++..+..
T Consensus 2 W~~L~~~Qq~~L~pl~~~W~~l~~~qr~k~l~~a~r~~~mspeqq~r~~~ 51 (107)
T PF11304_consen 2 WSSLSPAQQQALAPLAERWNSLPPEQRRKWLQIAERWPSMSPEQQQRLRE 51 (107)
T ss_pred hhhCCHHHHHHHHHHHHHHhcCCHHHHHHHHHHHHHHhcCCHHHHHHHHH
Confidence 77777777766543333211000011123334555666666665554433
No 47
>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=83.00 E-value=0.38 Score=31.64 Aligned_cols=29 Identities=21% Similarity=0.464 Sum_probs=24.1
Q ss_pred hhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729 133 EELYCRVCDQWFTTLHNKREHLNGRQHFQRFD 164 (170)
Q Consensus 133 ~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~ 164 (170)
-.-||-.|...|.+ +.+|+.+++|+.-++
T Consensus 4 k~GYCE~C~~ky~~---l~~Hi~s~~Hr~FA~ 32 (49)
T PF07535_consen 4 KPGYCENCRVKYDD---LEEHIQSEKHRKFAE 32 (49)
T ss_pred CCccCccccchhhh---HHHHhCCHHHHHHHc
Confidence 34599999999985 579999999987653
No 48
>smart00586 ZnF_DBF Zinc finger in DBF-like proteins.
Probab=82.42 E-value=0.61 Score=30.75 Aligned_cols=32 Identities=19% Similarity=0.429 Sum_probs=25.7
Q ss_pred CchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhcc
Q psy1729 131 DNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFDR 165 (170)
Q Consensus 131 ~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~ 165 (170)
|+-.-||-.|...|.. +.+|+.|++|+.-+..
T Consensus 2 ~~k~GYCE~Cr~kfd~---l~~Hi~s~~Hr~FA~~ 33 (49)
T smart00586 2 EKKPGYCENCREKYDD---LETHLLSEKHRRFAEN 33 (49)
T ss_pred CCCCcccccHhHHHhh---HHHHhccHHHHHHHcC
Confidence 4456799999999985 5689999999876543
No 49
>KOG4727|consensus
Probab=81.70 E-value=0.35 Score=39.82 Aligned_cols=32 Identities=31% Similarity=0.629 Sum_probs=29.0
Q ss_pred chhHHHHHHHHHhhhhhhhhhhhchhhhhhhh
Q psy1729 132 NEELYCRVCDQWFTTLHNKREHLNGRQHFQRF 163 (170)
Q Consensus 132 ~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~ 163 (170)
-+--||.||+--|----|.-.|++|+.|..+|
T Consensus 73 ~~GyyCdVCdcvvKDSinflDHiNgKkHqrnl 104 (193)
T KOG4727|consen 73 KGGYYCDVCDCVVKDSINFLDHINGKKHQRNL 104 (193)
T ss_pred cCceeeeecceeehhhHHHHHHhccHHHHHHH
Confidence 35679999999999999999999999998776
No 50
>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=81.34 E-value=0.71 Score=39.54 Aligned_cols=31 Identities=23% Similarity=0.508 Sum_probs=25.3
Q ss_pred hHHHHHHHHHhhhhh---hhhhhhchhhhhhhhc
Q psy1729 134 ELYCRVCDQWFTTLH---NKREHLNGRQHFQRFD 164 (170)
Q Consensus 134 ~~~~~~~~~~f~~~h---~~~~~~~~~~~~~~~~ 164 (170)
--.|-||+.+-|++- +.-.|+.|++|+-.+.
T Consensus 190 l~VCeVCGA~Ls~~D~d~RladH~~GK~HlGy~~ 223 (254)
T PF03194_consen 190 LEVCEVCGAFLSVGDNDRRLADHFGGKQHLGYAK 223 (254)
T ss_pred ccchhhhhhHHhccchHHHHHHHhccchhhhHHH
Confidence 367999999998875 5669999999986543
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=80.21 E-value=0.27 Score=25.68 Aligned_cols=19 Identities=26% Similarity=0.768 Sum_probs=15.8
Q ss_pred HHHHHHHhhhhhhhhhhhc
Q psy1729 137 CRVCDQWFTTLHNKREHLN 155 (170)
Q Consensus 137 ~~~~~~~f~~~h~~~~~~~ 155 (170)
|..|+..|++.-.++.||.
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 8899999999999999985
No 52
>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=80.19 E-value=8.5 Score=31.59 Aligned_cols=39 Identities=21% Similarity=0.459 Sum_probs=34.8
Q ss_pred hhHHHHhhCCChhhhhhhHHHHHH-HHHHHHHHHHHHHcc
Q psy1729 54 KLLGNEWSKLSLPEKKVYLDRAEV-DKKRYREELKVYRKS 92 (170)
Q Consensus 54 K~lg~~Wk~LS~~EK~~Y~~~A~~-dk~rY~~em~~yk~~ 92 (170)
..||.-|+.+|+++++.|.+.... ....|-..+..|...
T Consensus 72 ~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l~~y~~~ 111 (198)
T TIGR03481 72 LTLGSSWTSLSPEQRRRFIGAFRELSIATYASQFKSYAGE 111 (198)
T ss_pred HHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhcCc
Confidence 479999999999999999999888 888999999998743
No 53
>PHA02768 hypothetical protein; Provisional
Probab=79.23 E-value=0.54 Score=31.71 Aligned_cols=26 Identities=19% Similarity=0.474 Sum_probs=21.8
Q ss_pred HHHHHHHHhhhhhhhhhhhchhhhhhhh
Q psy1729 136 YCRVCDQWFTTLHNKREHLNGRQHFQRF 163 (170)
Q Consensus 136 ~~~~~~~~f~~~h~~~~~~~~~~~~~~~ 163 (170)
-|..|+..||+..++..||.- |....
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~--H~k~~ 32 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRK--HNTNL 32 (55)
T ss_pred CcchhCCeeccHHHHHHHHHh--cCCcc
Confidence 599999999999999999954 76433
No 54
>COG5188 PRP9 Splicing factor 3a, subunit 3 [RNA processing and modification]
Probab=78.61 E-value=0.97 Score=41.22 Aligned_cols=35 Identities=23% Similarity=0.468 Sum_probs=31.3
Q ss_pred chhHHHHHHHHHhhhhhhhhhhhchhhhhhhhccc
Q psy1729 132 NEELYCRVCDQWFTTLHNKREHLNGRQHFQRFDRR 166 (170)
Q Consensus 132 ~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~~ 166 (170)
-.-.||.+|..+|++..-.+-|+-|+.|-.+.+|+
T Consensus 236 ~~~~YC~~C~r~f~~~~VFe~Hl~gK~H~k~~~~~ 270 (470)
T COG5188 236 FPKVYCVKCGREFSRSKVFEYHLEGKRHCKEGQGK 270 (470)
T ss_pred ccceeeHhhhhHhhhhHHHHHHHhhhhhhhhhhhh
Confidence 34579999999999999999999999999888775
No 55
>KOG2785|consensus
Probab=78.54 E-value=1.1 Score=40.94 Aligned_cols=37 Identities=24% Similarity=0.675 Sum_probs=33.0
Q ss_pred ccCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhcc
Q psy1729 129 EEDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFDR 165 (170)
Q Consensus 129 ~~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~ 165 (170)
+.-+...+|.+|++.|-|.-..-.||.+|.|.-+++.
T Consensus 63 e~~~~~~~c~~c~k~~~s~~a~~~hl~Sk~h~~~~~~ 99 (390)
T KOG2785|consen 63 EEAESVVYCEACNKSFASPKAHENHLKSKKHVENLSN 99 (390)
T ss_pred hhcccceehHHhhccccChhhHHHHHHHhhcchhhhh
Confidence 4667789999999999999999999999999887754
No 56
>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=76.95 E-value=9.8 Score=29.82 Aligned_cols=39 Identities=21% Similarity=0.460 Sum_probs=32.1
Q ss_pred hhhHHHHhhCCChhhhhhhHHHHHH-HHHHHHHHHHHHHc
Q psy1729 53 TKLLGNEWSKLSLPEKKVYLDRAEV-DKKRYREELKVYRK 91 (170)
Q Consensus 53 ~K~lg~~Wk~LS~~EK~~Y~~~A~~-dk~rY~~em~~yk~ 91 (170)
-..||.-|+.||+++++.|.+.... ....|-..+..|..
T Consensus 45 r~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~l~~y~~ 84 (170)
T PF05494_consen 45 RRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKRLDEYSG 84 (170)
T ss_dssp HHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHHHHT-SS
T ss_pred HHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHHHHhhCC
Confidence 3568999999999999999999777 77889999999985
No 57
>COG5200 LUC7 U1 snRNP component, mediates U1 snRNP association with cap-binding complex [RNA processing and modification]
Probab=74.37 E-value=1.6 Score=37.21 Aligned_cols=30 Identities=27% Similarity=0.738 Sum_probs=25.8
Q ss_pred hHHHHHHHHHhhhhhhhh---hhhchhhhhhhh
Q psy1729 134 ELYCRVCDQWFTTLHNKR---EHLNGRQHFQRF 163 (170)
Q Consensus 134 ~~~~~~~~~~f~~~h~~~---~~~~~~~~~~~~ 163 (170)
---|-+|+.|.|+|-+.| .|++|+-||--+
T Consensus 185 lqvC~iCgayLsrlDtdrrladHf~GklHlGy~ 217 (258)
T COG5200 185 LQVCGICGAYLSRLDTDRRLADHFNGKLHLGYL 217 (258)
T ss_pred hhhhhhhhhHHHhcchhhHHHHHhccchhhhHH
Confidence 347999999999999987 699999998644
No 58
>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=73.59 E-value=4.6 Score=33.39 Aligned_cols=26 Identities=27% Similarity=0.417 Sum_probs=23.5
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHH
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAE 76 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~ 76 (170)
+++...+..|..||+.+|.+|..++.
T Consensus 104 dlI~~AAraW~rLSe~eK~rYrr~~~ 129 (183)
T PF06382_consen 104 DLIQRAARAWCRLSEAEKNRYRRMAP 129 (183)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHhhcc
Confidence 88999999999999999999988654
No 59
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=72.55 E-value=6.2 Score=32.72 Aligned_cols=40 Identities=18% Similarity=0.365 Sum_probs=35.1
Q ss_pred hhhHHHHhhCCChhhhhhhHHHHHH-HHHHHHHHHHHHHcc
Q psy1729 53 TKLLGNEWSKLSLPEKKVYLDRAEV-DKKRYREELKVYRKS 92 (170)
Q Consensus 53 ~K~lg~~Wk~LS~~EK~~Y~~~A~~-dk~rY~~em~~yk~~ 92 (170)
-..||.-|+.+|++++..|.+.... ...-|...+..|...
T Consensus 75 ~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l~~y~~q 115 (211)
T PRK15117 75 ALVLGRYYKDATPAQREAYFAAFREYLKQAYGQALAMYHGQ 115 (211)
T ss_pred HHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHHHHhCCc
Confidence 3579999999999999999999777 778899999999743
No 60
>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=72.11 E-value=8.3 Score=31.64 Aligned_cols=42 Identities=14% Similarity=0.340 Sum_probs=32.9
Q ss_pred CCCCHHHHHH-HHHHHhcCCChHHHHhHHHHHHH-HHHHHHHHH
Q psy1729 9 ISTTKLLVTK-LLGNEWSKLSLPEKKVYLDRAEV-DKKRYREEL 50 (170)
Q Consensus 9 p~~s~~evsK-~lge~Wk~Lse~EK~~Ye~~Ak~-dKerY~~Em 50 (170)
|...+..+++ .||..|+.+|+++++.|.+.+.. ....|...+
T Consensus 62 ~~~Df~~mar~vLG~~W~~~s~~Qr~~F~~~F~~~l~~tY~~~l 105 (198)
T TIGR03481 62 EAFDLPAMARLTLGSSWTSLSPEQRRRFIGAFRELSIATYASQF 105 (198)
T ss_pred HhCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466777776 78999999999999999999988 445565533
No 61
>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=71.00 E-value=9.9 Score=31.94 Aligned_cols=60 Identities=23% Similarity=0.182 Sum_probs=43.1
Q ss_pred HHhcCCChHHHHhHHHHHHHHHHHHHH----HH----hhhhhHHHHhhCCChhhhhhhHHHHHHHHHH
Q psy1729 22 NEWSKLSLPEKKVYLDRAEVDKKRYRE----EL----KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKR 81 (170)
Q Consensus 22 e~Wk~Lse~EK~~Ye~~Ak~dKerY~~----Em----Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~r 81 (170)
+.|..||++.|+.+.+.+.+--..+.. .. ..+..-|-....+|++++..|.+.++...++
T Consensus 214 ~~w~~L~~e~q~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~G~~v~~~s~~~~~~~~~~~~~~~~e 281 (286)
T PF03480_consen 214 DWWDSLPDEDQEALDDAADEAEARAREYYEAEDEEALKELEENGVTVVELSDEELAAWREAAAPVWEE 281 (286)
T ss_dssp HHHHHS-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-EEEEGCHHHHHHHHHHHHHHHHH
T ss_pred HHHhcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCcCEEeCCCHHHHHHHHHHHHHHHHH
Confidence 579999999999999988776544322 11 2333344567788999999999998887776
No 62
>PF12756 zf-C2H2_2: C2H2 type zinc-finger (2 copies); PDB: 2DMI_A.
Probab=69.62 E-value=1.5 Score=30.34 Aligned_cols=21 Identities=24% Similarity=0.746 Sum_probs=0.0
Q ss_pred HHHHHHHhhhhhhhhhhhchh
Q psy1729 137 CRVCDQWFTTLHNKREHLNGR 157 (170)
Q Consensus 137 ~~~~~~~f~~~h~~~~~~~~~ 157 (170)
|..|++.|++.-.+++||.-.
T Consensus 2 C~~C~~~f~~~~~l~~H~~~~ 22 (100)
T PF12756_consen 2 CLFCDESFSSVDDLLQHMKKK 22 (100)
T ss_dssp ---------------------
T ss_pred ccccccccccccccccccccc
Confidence 899999999999999999643
No 63
>PRK12751 cpxP periplasmic stress adaptor protein CpxP; Reviewed
Probab=68.71 E-value=18 Score=29.16 Aligned_cols=34 Identities=12% Similarity=0.256 Sum_probs=25.5
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHc
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRK 91 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~ 91 (170)
+..+...+.++-|++++|..|.+ +|++.+..+..
T Consensus 118 ~~~~~~~qmy~lLTPEQra~l~~-------~~e~r~~~~~~ 151 (162)
T PRK12751 118 EMAKVRNQMYNLLTPEQKEALNK-------KHQERIEKLQQ 151 (162)
T ss_pred HHHHHHHHHHHcCCHHHHHHHHH-------HHHHHHHHHHh
Confidence 45566778899999999999988 55555555544
No 64
>PRK15117 ABC transporter periplasmic binding protein MlaC; Provisional
Probab=66.90 E-value=9.1 Score=31.72 Aligned_cols=45 Identities=16% Similarity=0.214 Sum_probs=35.4
Q ss_pred ccCCCCCHHHHHH-HHHHHhcCCChHHHHhHHHHHHHHHH-HHHHHH
Q psy1729 6 EKMISTTKLLVTK-LLGNEWSKLSLPEKKVYLDRAEVDKK-RYREEL 50 (170)
Q Consensus 6 ~~~p~~s~~evsK-~lge~Wk~Lse~EK~~Ye~~Ak~dKe-rY~~Em 50 (170)
.=.|...+..+++ .||.-|+.+|+++++.|.+.+..--. .|...+
T Consensus 63 ~l~p~~Df~~~s~~vLG~~wr~as~eQr~~F~~~F~~~Lv~tYa~~l 109 (211)
T PRK15117 63 ELLPYVQVKYAGALVLGRYYKDATPAQREAYFAAFREYLKQAYGQAL 109 (211)
T ss_pred HccccCCHHHHHHHHhhhhhhhCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3457778888877 78999999999999999998888554 365543
No 65
>KOG2746|consensus
Probab=65.15 E-value=5.9 Score=38.57 Aligned_cols=35 Identities=31% Similarity=0.384 Sum_probs=32.4
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHH
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREE 85 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~e 85 (170)
-|+++||+.|-.|.+.||+.|.+.|.+.++.+-+.
T Consensus 213 tIskiLgewWytL~~~Ekq~yhdLa~Qvk~Ahfka 247 (683)
T KOG2746|consen 213 TISKILGEWWYTLGPNEKQKYHDLAFQVKEAHFKA 247 (683)
T ss_pred hHHHHHhhhHhhhCchhhhhHHHHHHHHHHHHhhh
Confidence 69999999999999999999999999988887765
No 66
>PHA00616 hypothetical protein
Probab=63.32 E-value=3.8 Score=26.38 Aligned_cols=18 Identities=33% Similarity=0.591 Sum_probs=17.3
Q ss_pred HHHHHHHhhhhhhhhhhh
Q psy1729 137 CRVCDQWFTTLHNKREHL 154 (170)
Q Consensus 137 ~~~~~~~f~~~h~~~~~~ 154 (170)
|..|+..|...-+...||
T Consensus 4 C~~CG~~F~~~s~l~~H~ 21 (44)
T PHA00616 4 CLRCGGIFRKKKEVIEHL 21 (44)
T ss_pred cchhhHHHhhHHHHHHHH
Confidence 899999999999999999
No 67
>COG4735 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.19 E-value=13 Score=31.31 Aligned_cols=65 Identities=17% Similarity=0.108 Sum_probs=52.1
Q ss_pred CCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHH-HHhhhhhHHHHhhCCChhhhhhhHHH
Q psy1729 10 STTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYRE-ELKVTKLLGNEWSKLSLPEKKVYLDR 74 (170)
Q Consensus 10 ~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~-EmEi~K~lg~~Wk~LS~~EK~~Y~~~ 74 (170)
+.++.-+.+..|..|+.++.++++.+.-.+.+.-....- |.=.++.+..-|..|+..+++.+.+.
T Consensus 36 g~s~anflr~~G~lyk~il~d~~~~Lk~k~~k~~~tt~Iee~ll~~il~~~l~km~~~~~~e~~~~ 101 (211)
T COG4735 36 GLSAANFLRDLGQLYKKILCDEKDKLKVKVQKELGTTEIEEPLLLQILRNPLEKMLKGGKAEAVDS 101 (211)
T ss_pred cHHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHhhccccccchhHHHHHHhHHHHHhHHHHHHHHHH
Confidence 467788889999999999999999988877766555532 33456788899999999999887764
No 68
>smart00355 ZnF_C2H2 zinc finger.
Probab=61.71 E-value=1.8 Score=22.42 Aligned_cols=19 Identities=26% Similarity=0.676 Sum_probs=17.3
Q ss_pred HHHHHHHhhhhhhhhhhhc
Q psy1729 137 CRVCDQWFTTLHNKREHLN 155 (170)
Q Consensus 137 ~~~~~~~f~~~h~~~~~~~ 155 (170)
|..|...|++.-.+..|+.
T Consensus 3 C~~C~~~f~~~~~l~~H~~ 21 (26)
T smart00355 3 CPECGKVFKSKSALKEHMR 21 (26)
T ss_pred CCCCcchhCCHHHHHHHHH
Confidence 7889999999999999986
No 69
>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=59.65 E-value=2.2 Score=28.65 Aligned_cols=21 Identities=29% Similarity=0.578 Sum_probs=16.0
Q ss_pred HHHHHHHHHhhhhhhhhhhhc
Q psy1729 135 LYCRVCDQWFTTLHNKREHLN 155 (170)
Q Consensus 135 ~~~~~~~~~f~~~h~~~~~~~ 155 (170)
--|.+|+.-+++.-|+|-||-
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 459999999999999999984
No 70
>PF07303 Occludin_ELL: Occludin homology domain; InterPro: IPR010844 This represents a conserved region approximately 100 residues long within eukaryotic occludin proteins and the RNA polymerase II elongation factor ELL. Occludin is an integral membrane protein that localises to tight junctions [], while ELL is an elongation factor that can increase the catalytic rate of RNA polymerase II transcription by suppressing transient pausing by polymerase at multiple sites along the DNA []. This shared domain is thought to mediate protein interactions [].; PDB: 1WPA_A 3G7C_A 1XAW_A.
Probab=59.40 E-value=70 Score=23.67 Aligned_cols=65 Identities=22% Similarity=0.309 Sum_probs=45.6
Q ss_pred ChHHHHhHHHHHHHHHHHHHH---HH----hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHHcchhhHH
Q psy1729 28 SLPEKKVYLDRAEVDKKRYRE---EL----KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYRKSDAYQS 97 (170)
Q Consensus 28 se~EK~~Ye~~Ak~dKerY~~---Em----Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk~~~~~~~ 97 (170)
|.++++.|...+..+-..|.. ++ ..+..|+..++.|++. =..|...+ .-..+|.+-. +..+.|..
T Consensus 6 s~eqR~~Yk~eF~~~y~EYk~L~~~v~~v~~~f~~L~~~l~~l~~~-s~ey~~i~-~I~~eY~k~K---k~~p~y~~ 77 (101)
T PF07303_consen 6 SSEQRQRYKAEFNDDYDEYKELHAEVDAVSRRFQELDSELKRLPPG-SQEYKRIA-QILQEYNKKK---KRDPNYQE 77 (101)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHS-TT-SHHHHHHH----HHHHHHH---HTSHHHHH
T ss_pred CHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCC-CcHHHHHH-HHHHHHHHHH---hcCccHHH
Confidence 678999999999999999876 33 4567788889999994 45788777 7788887754 44555554
No 71
>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=59.19 E-value=7.3 Score=24.41 Aligned_cols=30 Identities=27% Similarity=0.297 Sum_probs=14.8
Q ss_pred CHHHHHHHHHH-HhcCCChHHHHhHHHHHHH
Q psy1729 12 TKLLVTKLLGN-EWSKLSLPEKKVYLDRAEV 41 (170)
Q Consensus 12 s~~evsK~lge-~Wk~Lse~EK~~Ye~~Ak~ 41 (170)
++.||+--++. .|..|.+.+|.-|.+...+
T Consensus 2 tf~Dvav~fs~eEW~~L~~~Qk~ly~dvm~E 32 (41)
T PF01352_consen 2 TFEDVAVYFSQEEWELLDPAQKNLYRDVMLE 32 (41)
T ss_dssp -----TT---HHHHHTS-HHHHHHHHHHHHH
T ss_pred eEEEEEEEcChhhcccccceecccchhHHHH
Confidence 44555555555 4888888888888776544
No 72
>PF13909 zf-H2C2_5: C2H2-type zinc-finger domain; PDB: 1X5W_A.
Probab=57.56 E-value=1.7 Score=23.39 Aligned_cols=19 Identities=32% Similarity=0.670 Sum_probs=12.6
Q ss_pred HHHHHHHhhhhhhhhhhhch
Q psy1729 137 CRVCDQWFTTLHNKREHLNG 156 (170)
Q Consensus 137 ~~~~~~~f~~~h~~~~~~~~ 156 (170)
|..|+ |.++..++++||.-
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 77888 55557888888753
No 73
>KOG0796|consensus
Probab=57.21 E-value=4.9 Score=35.87 Aligned_cols=30 Identities=23% Similarity=0.588 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhhhhhhh---hhhchhhhhhhhc
Q psy1729 135 LYCRVCDQWFTTLHNKR---EHLNGRQHFQRFD 164 (170)
Q Consensus 135 ~~~~~~~~~f~~~h~~~---~~~~~~~~~~~~~ 164 (170)
--|-||+.+.+-+-|.+ .|+.|+.|+-.+.
T Consensus 187 ~VCeVCGa~L~~~D~d~RlaDHf~GKlHlGy~~ 219 (319)
T KOG0796|consen 187 RVCEVCGAFLSVNDADRRLADHFGGKLHLGYVL 219 (319)
T ss_pred hHHHhhhHHHhccchHHHHHHhhcchHHHHHHH
Confidence 47999999999887654 8999999997654
No 74
>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=57.19 E-value=8.8 Score=32.93 Aligned_cols=28 Identities=29% Similarity=0.690 Sum_probs=21.8
Q ss_pred cccccCchhHHHHHHHHHhhhhhhhhhhh
Q psy1729 126 DEEEEDNEELYCRVCDQWFTTLHNKREHL 154 (170)
Q Consensus 126 d~~~~~~~~~~~~~~~~~f~~~h~~~~~~ 154 (170)
++.++++...||.||+.-+++.+-.| ||
T Consensus 76 ~e~~D~~~~~~Cv~Cg~~i~~~~a~k-Hm 103 (236)
T PF12269_consen 76 DESEDDDLSIYCVTCGHEIPSKKALK-HM 103 (236)
T ss_pred ccccccceeeeeeeCCCcCCHHHHHH-HH
Confidence 34456788999999999998887665 44
No 75
>KOG2505|consensus
Probab=56.14 E-value=3 Score=39.55 Aligned_cols=35 Identities=23% Similarity=0.343 Sum_probs=30.8
Q ss_pred CchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhcc
Q psy1729 131 DNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFDR 165 (170)
Q Consensus 131 ~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~ 165 (170)
..+.++|.||.+-|.|+---|||...-=|+-|+-+
T Consensus 63 ~sd~~~CstCq~~F~s~~eqr~HyksD~HR~N~Kr 97 (591)
T KOG2505|consen 63 ISDSDQCSTCQIPFGSRQEQREHYKSDWHRFNTKR 97 (591)
T ss_pred hcccccccccCCccccHHHHHHHHHHHHHHHHHHH
Confidence 44678999999999999999999999999877654
No 76
>PF07757 AdoMet_MTase: Predicted AdoMet-dependent methyltransferase; InterPro: IPR011671 tRNA (uracil-O(2)-)-methyltransferase catalyses the formation of O(2)-methyl-uracil at position 44 (m2U44) in tRNA(Ser) [].; GO: 0008168 methyltransferase activity
Probab=53.63 E-value=30 Score=26.52 Aligned_cols=41 Identities=29% Similarity=0.458 Sum_probs=34.6
Q ss_pred HHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChhhhhhhHHHHHH
Q psy1729 31 EKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRAEV 77 (170)
Q Consensus 31 EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~EK~~Y~~~A~~ 77 (170)
.+..|.+.+...|.+|.+ .|-+.|..-++-.|..|++.|-.
T Consensus 3 ~~~~yq~~Y~~LK~kYa~------~lv~~W~E~TdP~K~VfEDlaIA 43 (112)
T PF07757_consen 3 PKERYQDTYQRLKEKYAR------WLVDNWPESTDPQKHVFEDLAIA 43 (112)
T ss_pred CHHHHHHHHHHHHHHHHH------HHHHhCcccCCchhhHHHHHHHH
Confidence 367899999999999965 56788999999999999998755
No 77
>PF12907 zf-met2: Zinc-binding
Probab=52.53 E-value=7.8 Score=24.46 Aligned_cols=22 Identities=32% Similarity=0.736 Sum_probs=17.9
Q ss_pred HHHHHHHHhhhhhh---hhhhhchh
Q psy1729 136 YCRVCDQWFTTLHN---KREHLNGR 157 (170)
Q Consensus 136 ~~~~~~~~f~~~h~---~~~~~~~~ 157 (170)
-|.+|-|-|...-+ ++||...|
T Consensus 3 ~C~iC~qtF~~t~~~~~L~eH~enK 27 (40)
T PF12907_consen 3 ICKICRQTFMQTTNEPQLKEHAENK 27 (40)
T ss_pred CcHHhhHHHHhcCCHHHHHHHHHcc
Confidence 49999999988766 88887654
No 78
>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=50.72 E-value=13 Score=25.03 Aligned_cols=24 Identities=13% Similarity=0.202 Sum_probs=21.0
Q ss_pred ccccCCCCCHHHHHHHHHHHhcCC
Q psy1729 4 ESEKMISTTKLLVTKLLGNEWSKL 27 (170)
Q Consensus 4 ~k~~~p~~s~~evsK~lge~Wk~L 27 (170)
+-+.||+..++.+...++.+|+.-
T Consensus 27 l~~~NPk~~~sKl~~l~~AKwrEF 50 (55)
T PF08073_consen 27 LAKANPKAPMSKLMMLLQAKWREF 50 (55)
T ss_pred HHHHCCCCcHHHHHHHHHHHHHHH
Confidence 346899999999999999999854
No 79
>KOG2785|consensus
Probab=47.53 E-value=3.6 Score=37.62 Aligned_cols=29 Identities=24% Similarity=0.516 Sum_probs=26.1
Q ss_pred HHHHHH---HHhhhhhhhhhhhchhhhhhhhc
Q psy1729 136 YCRVCD---QWFTTLHNKREHLNGRQHFQRFD 164 (170)
Q Consensus 136 ~~~~~~---~~f~~~h~~~~~~~~~~~~~~~~ 164 (170)
-|..|| ..|+||---|-||..++|-++..
T Consensus 219 ~CL~CN~~~~~f~sleavr~HM~~K~HCkl~y 250 (390)
T KOG2785|consen 219 ICLFCNELGRPFSSLEAVRAHMRDKGHCKLPY 250 (390)
T ss_pred eEEEeccccCcccccHHHHHHHhhccCcccCC
Confidence 388999 99999999999999999987654
No 80
>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=47.50 E-value=14 Score=28.86 Aligned_cols=42 Identities=17% Similarity=0.233 Sum_probs=29.5
Q ss_pred CCCCCHHHHHH-HHHHHhcCCChHHHHhHHHHHHHHHHH-HHHH
Q psy1729 8 MISTTKLLVTK-LLGNEWSKLSLPEKKVYLDRAEVDKKR-YREE 49 (170)
Q Consensus 8 ~p~~s~~evsK-~lge~Wk~Lse~EK~~Ye~~Ak~dKer-Y~~E 49 (170)
.|...+..+++ .||.-|+.+|+++++.|.+.+..--.+ |...
T Consensus 35 ~~~~D~~~~ar~~LG~~w~~~s~~q~~~F~~~f~~~l~~~Y~~~ 78 (170)
T PF05494_consen 35 DPYFDFERMARRVLGRYWRKASPAQRQRFVEAFKQLLVRTYAKR 78 (170)
T ss_dssp GGGB-HHHHHHHHHGGGTTTS-HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhCCHHHHHHHHHHHhHhhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 35566666666 467799999999999999988885543 5443
No 81
>PRK10236 hypothetical protein; Provisional
Probab=47.44 E-value=17 Score=31.20 Aligned_cols=46 Identities=22% Similarity=0.427 Sum_probs=30.9
Q ss_pred HHhHHHHHHHHHHHHHHH-------Hh-hhhhHHHHhhCCChhhhhhhHHHHHH
Q psy1729 32 KKVYLDRAEVDKKRYREE-------LK-VTKLLGNEWSKLSLPEKKVYLDRAEV 77 (170)
Q Consensus 32 K~~Ye~~Ak~dKerY~~E-------mE-i~K~lg~~Wk~LS~~EK~~Y~~~A~~ 77 (170)
|+...+.+...+-.|... .+ +++.+++.|+.||++|++.+-+.-..
T Consensus 90 reIL~DVc~~LKV~y~~~~st~~iE~~il~kll~~a~~kms~eE~~~L~~~l~~ 143 (237)
T PRK10236 90 RAILLDVSKRLKLKADKEMSTFEIEQQLLEQFLRNTWKKMDEEHKQEFLHAVDA 143 (237)
T ss_pred HHHHHHHHHHcCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHhh
Confidence 444445555555555442 23 57889999999999999888765444
No 82
>COG2854 Ttg2D ABC-type transport system involved in resistance to organic solvents, auxiliary component [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=46.83 E-value=89 Score=26.25 Aligned_cols=42 Identities=14% Similarity=0.301 Sum_probs=36.0
Q ss_pred hhhhHHHHhhCCChhhhhhhHHHHHH-HHHHHHHHHHHHHcch
Q psy1729 52 VTKLLGNEWSKLSLPEKKVYLDRAEV-DKKRYREELKVYRKSD 93 (170)
Q Consensus 52 i~K~lg~~Wk~LS~~EK~~Y~~~A~~-dk~rY~~em~~yk~~~ 93 (170)
....||.=|+.+|+++++.|.+.... ....|-..|..|+.+.
T Consensus 76 a~~vLGk~~k~aspeQ~~~F~~aF~~yl~q~Y~~aL~~Y~~q~ 118 (202)
T COG2854 76 AKLVLGKYYKTASPEQRQAFFKAFRTYLEQTYGQALLDYKGQT 118 (202)
T ss_pred HHHHhccccccCCHHHHHHHHHHHHHHHHHHHHHHHHHccCCC
Confidence 45678999999999999999998776 7788999999998543
No 83
>KOG1074|consensus
Probab=43.40 E-value=11 Score=37.83 Aligned_cols=26 Identities=27% Similarity=0.661 Sum_probs=22.6
Q ss_pred cCchhHHHHHHHHHhhhhhhhhhhhc
Q psy1729 130 EDNEELYCRVCDQWFTTLHNKREHLN 155 (170)
Q Consensus 130 ~~~~~~~~~~~~~~f~~~h~~~~~~~ 155 (170)
+-+..-||+.|.+-|...-|++.||.
T Consensus 903 tg~KPF~C~fC~~aFttrgnLKvHMg 928 (958)
T KOG1074|consen 903 TGPKPFFCHFCEEAFTTRGNLKVHMG 928 (958)
T ss_pred CCCCCccchhhhhhhhhhhhhhhhhc
Confidence 44556899999999999999999997
No 84
>KOG3032|consensus
Probab=42.12 E-value=5 Score=34.63 Aligned_cols=34 Identities=26% Similarity=0.499 Sum_probs=26.6
Q ss_pred cCchhHHHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729 130 EDNEELYCRVCDQWFTTLHNKREHLNGRQHFQRFD 164 (170)
Q Consensus 130 ~~~~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~ 164 (170)
..+|-|-|+||+--.- -.--.=|..|+||...+.
T Consensus 31 n~sgql~C~vCn~piK-p~lW~vHvnsKkHre~id 64 (264)
T KOG3032|consen 31 NESGQLVCRVCNVPIK-PSLWDVHVNSKKHREAID 64 (264)
T ss_pred CCCCCeeEEEecCccc-HHHHHHHhccHHHHHHHH
Confidence 5678899999998766 334467999999987664
No 85
>PRK10363 cpxP periplasmic repressor CpxP; Reviewed
Probab=41.11 E-value=1.1e+02 Score=24.90 Aligned_cols=32 Identities=9% Similarity=0.198 Sum_probs=24.5
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHHHHHHHHHH
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRY 82 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY 82 (170)
+.++.-.+..+-|++++|..|.+..++-...+
T Consensus 112 em~k~~nqmy~lLTPEQKaq~~~~~~~rm~~~ 143 (166)
T PRK10363 112 EMAKVRNQMYRLLTPEQQAVLNEKHQQRMEQL 143 (166)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHHHHHHHHHH
Confidence 67777888899999999999987544444444
No 86
>PRK12750 cpxP periplasmic repressor CpxP; Reviewed
Probab=38.05 E-value=2.1e+02 Score=22.98 Aligned_cols=35 Identities=9% Similarity=0.106 Sum_probs=26.3
Q ss_pred hhhhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHH
Q psy1729 52 VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREEL 86 (170)
Q Consensus 52 i~K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em 86 (170)
..+...+.+.-|++++|..|.+.-.+-..++...+
T Consensus 126 ~~~~~~~~~~vLTpEQRak~~e~~~~r~~~~~~~~ 160 (170)
T PRK12750 126 MLEKRHQMLSILTPEQKAKFQELQQERMQECQDKM 160 (170)
T ss_pred HHHHHHHHHHhCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44556667999999999999987666666665554
No 87
>PF12881 NUT_N: NUT protein N terminus; InterPro: IPR024309 This domain is found in the N-terminal region of Nuclear Testis (NUT) proteins. It is also found in FAM22, which are a family of uncharacterised mammalian proteins.
Probab=34.08 E-value=61 Score=29.14 Aligned_cols=48 Identities=19% Similarity=0.095 Sum_probs=37.7
Q ss_pred cCCCCCHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHH-HHHHhhhh
Q psy1729 7 KMISTTKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRY-REELKVTK 54 (170)
Q Consensus 7 ~~p~~s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY-~~EmEi~K 54 (170)
-.|.|++.|-....-.+|...|.-+|..|+++|++--+-= ++||++.+
T Consensus 246 ~kPtMtlEeGl~ra~qEW~~~SnfdRmifyemaekFmEFEaeEEmq~q~ 294 (328)
T PF12881_consen 246 LKPTMTLEEGLWRAVQEWQHTSNFDRMIFYEMAEKFMEFEAEEEMQIQK 294 (328)
T ss_pred cCCCccHHHHHHHHHHHhhccccccHHHHHHHHHHHccCCcHHHHHHHH
Confidence 3688999999999999999999999999999998744321 24555544
No 88
>TIGR02664 nitr_red_assoc conserved hypothetical protein. Most members of this protein family are found in the Cyanobacteria, and these mostly near nitrate reductase genes and molybdopterin biosynthesis genes. We note that molybdopterin guanine dinucleotide is a cofactor for nitrate reductase. This protein is sometimes annotated as nitrate reductase-associated protein. Its function is unknown.
Probab=33.03 E-value=77 Score=25.36 Aligned_cols=27 Identities=22% Similarity=0.401 Sum_probs=20.5
Q ss_pred HHhcCCChHHHHhHHHHHH---HHHHHHHH
Q psy1729 22 NEWSKLSLPEKKVYLDRAE---VDKKRYRE 48 (170)
Q Consensus 22 e~Wk~Lse~EK~~Ye~~Ak---~dKerY~~ 48 (170)
..|..||.+||+.+.+... .+...|..
T Consensus 33 ~hW~~ls~~eRq~Lv~~pc~t~~e~~~yr~ 62 (145)
T TIGR02664 33 EHWQQLTQAEREELVRLPCDTAEVIDPYRE 62 (145)
T ss_pred HHHhhCCHHHHHHHHhCccCCHHHHHHHHH
Confidence 5799999999999988763 23345655
No 89
>KOG3214|consensus
Probab=32.26 E-value=10 Score=28.71 Aligned_cols=20 Identities=25% Similarity=0.579 Sum_probs=16.5
Q ss_pred CchhHHHHHHHHHhhhhhhh
Q psy1729 131 DNEELYCRVCDQWFTTLHNK 150 (170)
Q Consensus 131 ~~~~~~~~~~~~~f~~~h~~ 150 (170)
--|.+.|++|.|.|+++-|.
T Consensus 44 ~iG~~sC~iC~esFqt~it~ 63 (109)
T KOG3214|consen 44 NIGKASCRICEESFQTTITA 63 (109)
T ss_pred CcceeeeeehhhhhccchHh
Confidence 34788999999999987664
No 90
>KOG3817|consensus
Probab=32.13 E-value=50 Score=30.52 Aligned_cols=74 Identities=24% Similarity=0.303 Sum_probs=53.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHcchhhHHHHHH---hhhhhhhhC--CC----------------Cccccccccccccccc
Q psy1729 70 VYLDRAEVDKKRYREELKVYRKSDAYQSYLRR---KRVKSLQAN--GT----------------EESDIATDATDEIDEE 128 (170)
Q Consensus 70 ~Y~~~A~~dk~rY~~em~~yk~~~~~~~~~~~---k~~k~~~~~--~~----------------~~~~~~~d~~~~~d~~ 128 (170)
.|++.|+..-.+=..++.+|=.++...+++.- +..+++... |. ..++++-|.++++|..
T Consensus 321 EYeeQaeveT~kaLaeLReycnkpd~~~Wkvvgrlrsp~rfA~F~eG~~Hlt~~Ei~~He~t~~~~~~~a~dee~~E~~~ 400 (452)
T KOG3817|consen 321 EYEEQAEVETSKALAELREYCNKPDCKQWKVVGRLRSPLRFASFAEGAPHLTDEEIEDHERTIEESMDAAPDEESVEEPE 400 (452)
T ss_pred HHHHHHHHHHHHHHHHHHHHhCCCCCchhhhhhhccCHHHHHHHhcCCCCCCHHHHHHHHhhhhhhcccccchhcccccc
Confidence 59999999999999999999999999988643 233333332 21 1246666777777777
Q ss_pred ccCchhHHHHHHHHH
Q psy1729 129 EEDNEELYCRVCDQW 143 (170)
Q Consensus 129 ~~~~~~~~~~~~~~~ 143 (170)
++.|+++-|+-.-|+
T Consensus 401 Ee~d~~~~~~~~sq~ 415 (452)
T KOG3817|consen 401 EEKDAELLPLPNSQF 415 (452)
T ss_pred cccCccccCCcchhh
Confidence 888889989877664
No 91
>PTZ00448 hypothetical protein; Provisional
Probab=31.73 E-value=14 Score=33.72 Aligned_cols=32 Identities=22% Similarity=0.433 Sum_probs=29.0
Q ss_pred HHHHHHHHHhhhhhhhhhhhchhhhhhhhccc
Q psy1729 135 LYCRVCDQWFTTLHNKREHLNGRQHFQRFDRR 166 (170)
Q Consensus 135 ~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~~ 166 (170)
.-|.+|+--|.+..-.|+|+-+-=|+-||.++
T Consensus 315 ~tC~~C~v~F~~~~~qR~H~KSDwHrYNLKRk 346 (373)
T PTZ00448 315 LLCRKCNIQLMDHNAFKQHYRSEWHIFNTKRN 346 (373)
T ss_pred ccccccccccCCHHHHHHHhhhhHHHHHHHHH
Confidence 45999999999999999999999999998765
No 92
>KOG2462|consensus
Probab=31.33 E-value=15 Score=32.37 Aligned_cols=29 Identities=21% Similarity=0.489 Sum_probs=21.5
Q ss_pred HHHHHHHHhhhhhhhhhhhchhhhhhhhc
Q psy1729 136 YCRVCDQWFTTLHNKREHLNGRQHFQRFD 164 (170)
Q Consensus 136 ~~~~~~~~f~~~h~~~~~~~~~~~~~~~~ 164 (170)
-|-.|+..|.-..|+|-||+---+...++
T Consensus 217 ~C~hC~kAFADRSNLRAHmQTHS~~K~~q 245 (279)
T KOG2462|consen 217 SCPHCGKAFADRSNLRAHMQTHSDVKKHQ 245 (279)
T ss_pred cCCcccchhcchHHHHHHHHhhcCCcccc
Confidence 48888999999999999987544444433
No 93
>PLN02748 tRNA dimethylallyltransferase
Probab=31.29 E-value=13 Score=34.81 Aligned_cols=30 Identities=30% Similarity=0.614 Sum_probs=27.0
Q ss_pred HHHHHHH-Hhhhhhhhhhhhchhhhhhhhcc
Q psy1729 136 YCRVCDQ-WFTTLHNKREHLNGRQHFQRFDR 165 (170)
Q Consensus 136 ~~~~~~~-~f~~~h~~~~~~~~~~~~~~~~~ 165 (170)
.|-+|+- -|-.-|+-.-|+.||+|..++.+
T Consensus 420 ~Ce~C~~~~~~G~~eW~~Hlksr~Hk~~~~~ 450 (468)
T PLN02748 420 VCEACGNKVLRGAHEWEQHKQGRGHRKRVQR 450 (468)
T ss_pred cccCCCCcccCCHHHHHHHhcchHHHHHHhH
Confidence 5999997 79999999999999999988764
No 94
>PF06945 DUF1289: Protein of unknown function (DUF1289); InterPro: IPR010710 This family consists of a number of hypothetical bacterial proteins. The aligned region spans around 56 residues and contains 4 highly conserved cysteine residues towards the N terminus. The function of this family is unknown.
Probab=31.18 E-value=39 Score=21.90 Aligned_cols=16 Identities=31% Similarity=0.713 Sum_probs=9.0
Q ss_pred HhhCCChhhhhhhHHH
Q psy1729 59 EWSKLSLPEKKVYLDR 74 (170)
Q Consensus 59 ~Wk~LS~~EK~~Y~~~ 74 (170)
.|+.||+++|......
T Consensus 29 ~W~~~s~~er~~i~~~ 44 (51)
T PF06945_consen 29 DWKSMSDDERRAILAR 44 (51)
T ss_pred HHhhCCHHHHHHHHHH
Confidence 3666666666554443
No 95
>PF12650 DUF3784: Domain of unknown function (DUF3784); InterPro: IPR017259 This group represents an uncharacterised conserved protein.
Probab=30.83 E-value=32 Score=24.60 Aligned_cols=15 Identities=27% Similarity=0.386 Sum_probs=11.7
Q ss_pred HhhCCChhhhhhhHH
Q psy1729 59 EWSKLSLPEKKVYLD 73 (170)
Q Consensus 59 ~Wk~LS~~EK~~Y~~ 73 (170)
-|+.||++||++|..
T Consensus 25 Gyntms~eEk~~~D~ 39 (97)
T PF12650_consen 25 GYNTMSKEEKEKYDK 39 (97)
T ss_pred hcccCCHHHHHHhhH
Confidence 478888888888854
No 96
>PHA00732 hypothetical protein
Probab=30.02 E-value=11 Score=26.84 Aligned_cols=20 Identities=25% Similarity=0.493 Sum_probs=18.2
Q ss_pred HHHHHHHhhhhhhhhhhhch
Q psy1729 137 CRVCDQWFTTLHNKREHLNG 156 (170)
Q Consensus 137 ~~~~~~~f~~~h~~~~~~~~ 156 (170)
|..|+..|++..+++.||..
T Consensus 4 C~~Cgk~F~s~s~Lk~H~r~ 23 (79)
T PHA00732 4 CPICGFTTVTLFALKQHARR 23 (79)
T ss_pred CCCCCCccCCHHHHHHHhhc
Confidence 88999999999999999863
No 97
>KOG0227|consensus
Probab=29.62 E-value=18 Score=30.49 Aligned_cols=34 Identities=21% Similarity=0.440 Sum_probs=25.4
Q ss_pred hhHHHHHHHHHhhhhhhhhhhhchhhhhhhhccc
Q psy1729 133 EELYCRVCDQWFTTLHNKREHLNGRQHFQRFDRR 166 (170)
Q Consensus 133 ~~~~~~~~~~~f~~~h~~~~~~~~~~~~~~~~~~ 166 (170)
|.+-|..|+----+--+---|.+|+.|--||-+|
T Consensus 52 G~yeCkLClT~H~ne~Syl~HtqGKKHq~Nlarr 85 (222)
T KOG0227|consen 52 GKYECKLCLTLHNNEGSYLAHTQGKKHQTNLARR 85 (222)
T ss_pred cceeehhhhhhhcchhhhhhhhccchhhHHHHHH
Confidence 4556999985444444456799999999998876
No 98
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=29.53 E-value=1.3e+02 Score=22.64 Aligned_cols=37 Identities=14% Similarity=0.136 Sum_probs=32.8
Q ss_pred hhHHHHhhCCChhhhhhhHHHHHHHHHHHHHHHHHHH
Q psy1729 54 KLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVYR 90 (170)
Q Consensus 54 K~lg~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~yk 90 (170)
+.|-..|+.||++++......+...++-|++-+++|-
T Consensus 90 ~~ll~~~~~L~~~~~~~~l~~l~~~~~~~~~~~~~~~ 126 (135)
T PRK09706 90 KELLELFDALPESEQDAQLSEMRARVENFNKLFEELL 126 (135)
T ss_pred HHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5677889999999999999999999999998888875
No 99
>PRK10455 periplasmic protein; Reviewed
Probab=28.23 E-value=2.1e+02 Score=22.82 Aligned_cols=24 Identities=13% Similarity=0.120 Sum_probs=17.7
Q ss_pred hhhhhHHHHhhCCChhhhhhhHHH
Q psy1729 51 KVTKLLGNEWSKLSLPEKKVYLDR 74 (170)
Q Consensus 51 Ei~K~lg~~Wk~LS~~EK~~Y~~~ 74 (170)
..++.-...+.-|++++|+.|.+.
T Consensus 118 ~~~~~~~qiy~vLTPEQr~q~~~~ 141 (161)
T PRK10455 118 AHMETQNKIYNVLTPEQKKQFNAN 141 (161)
T ss_pred HHHHHHHHHHHhCCHHHHHHHHHH
Confidence 345555667889999999888773
No 100
>KOG4722|consensus
Probab=28.03 E-value=28 Score=32.90 Aligned_cols=29 Identities=24% Similarity=0.488 Sum_probs=26.6
Q ss_pred HHHHHHHHHhhhhhhhhhhhchhhhhhhh
Q psy1729 135 LYCRVCDQWFTTLHNKREHLNGRQHFQRF 163 (170)
Q Consensus 135 ~~~~~~~~~f~~~h~~~~~~~~~~~~~~~ 163 (170)
--|..||--.||---+=-|.-||.|.|.|
T Consensus 494 kqcslcnvlissevylfshvkgrkhqqal 522 (672)
T KOG4722|consen 494 KQCSLCNVLISSEVYLFSHVKGRKHQQAL 522 (672)
T ss_pred hccchhhhhhhhhhhhhhhhcchhHHHHH
Confidence 46999999999999999999999999876
No 101
>PRK10236 hypothetical protein; Provisional
Probab=26.84 E-value=63 Score=27.82 Aligned_cols=26 Identities=23% Similarity=0.570 Sum_probs=21.4
Q ss_pred HHHHHHHHhcCCChHHHHhHHHHHHH
Q psy1729 16 VTKLLGNEWSKLSLPEKKVYLDRAEV 41 (170)
Q Consensus 16 vsK~lge~Wk~Lse~EK~~Ye~~Ak~ 41 (170)
+.+.++..|..||++|++.+.+.-..
T Consensus 118 l~kll~~a~~kms~eE~~~L~~~l~~ 143 (237)
T PRK10236 118 LEQFLRNTWKKMDEEHKQEFLHAVDA 143 (237)
T ss_pred HHHHHHHHHHHCCHHHHHHHHHHHhh
Confidence 57889999999999999887764443
No 102
>PF09655 Nitr_red_assoc: Conserved nitrate reductase-associated protein (Nitr_red_assoc); InterPro: IPR013481 Proteins in this entry are found in the Cyanobacteria, and are mostly encoded near nitrate reductase and molybdopterin biosynthesis genes. Molybdopterin guanine dinucleotide is a cofactor for nitrate reductase. These proteins are sometimes annotated as nitrate reductase-associated proteins, though their function is unknown.
Probab=26.24 E-value=84 Score=25.11 Aligned_cols=29 Identities=31% Similarity=0.557 Sum_probs=22.3
Q ss_pred HHhcCCChHHHHhHHHHH---HHHHHHHHHHH
Q psy1729 22 NEWSKLSLPEKKVYLDRA---EVDKKRYREEL 50 (170)
Q Consensus 22 e~Wk~Lse~EK~~Ye~~A---k~dKerY~~Em 50 (170)
..|..||..||+.+.+.. ..+.+.|...+
T Consensus 33 ~~W~~l~~~eRq~Lv~~pc~t~~ei~~yr~~L 64 (144)
T PF09655_consen 33 SHWQQLSQEERQQLVDLPCDTPEEIQNYREFL 64 (144)
T ss_pred HHHhcCCHHHHHHHHcCCCCCHHHHHHHHHHH
Confidence 579999999999999876 34556676633
No 103
>KOG4323|consensus
Probab=25.76 E-value=17 Score=34.04 Aligned_cols=19 Identities=32% Similarity=0.789 Sum_probs=15.5
Q ss_pred ccCchhHHHHHHHHHhhhh
Q psy1729 129 EEDNEELYCRVCDQWFTTL 147 (170)
Q Consensus 129 ~~~~~~~~~~~~~~~f~~~ 147 (170)
+.-|--|+|..|+|||+.+
T Consensus 180 ~~~NrmlqC~~C~~~fHq~ 198 (464)
T KOG4323|consen 180 GAGNRMLQCDKCRQWYHQA 198 (464)
T ss_pred CccceeeeecccccHHHHH
Confidence 4556779999999999875
No 104
>KOG1074|consensus
Probab=24.96 E-value=22 Score=35.89 Aligned_cols=24 Identities=29% Similarity=0.668 Sum_probs=21.4
Q ss_pred HHHHHHHHHhhhhhhhhhhhchhh
Q psy1729 135 LYCRVCDQWFTTLHNKREHLNGRQ 158 (170)
Q Consensus 135 ~~~~~~~~~f~~~h~~~~~~~~~~ 158 (170)
.-|.+|+.-|++.-|+|-||.+-+
T Consensus 634 FkCKiCgRAFtTkGNLkaH~~vHk 657 (958)
T KOG1074|consen 634 FKCKICGRAFTTKGNLKAHMSVHK 657 (958)
T ss_pred cccccccchhccccchhhcccccc
Confidence 469999999999999999999843
No 105
>PF06518 DUF1104: Protein of unknown function (DUF1104); InterPro: IPR009488 This family consists of several hypothetical proteins of unknown function which appear to be found exclusively in Helicobacter pylori.; PDB: 2XRH_A.
Probab=23.55 E-value=3e+02 Score=20.17 Aligned_cols=52 Identities=15% Similarity=0.090 Sum_probs=28.5
Q ss_pred CHHHHHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChhhhhhhHHHHH
Q psy1729 12 TKLLVTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKVYLDRAE 76 (170)
Q Consensus 12 s~~evsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~EK~~Y~~~A~ 76 (170)
.+.|+.-.|..+-+.|++.++..|...... .+...-.+||.++...|.+...
T Consensus 22 ~~~dy~~Ei~KR~~~m~~~~~k~f~~~~~~-------------~~~kn~~~ms~~e~~k~~~ev~ 73 (93)
T PF06518_consen 22 DVPDYKMEIHKRLKKMKEKEAKDFKKQFKE-------------AARKNLSKMSVEERKKRREEVR 73 (93)
T ss_dssp GHHHHHHHHHHHHHHS-HHHHHHHHHHHHH-------------HHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHhCCHHHHHHHHHHHHH-------------HHHHHHHHCCHHHHHHHHHHHH
Confidence 455556666666666666666655554433 3444556666666666655433
No 106
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=21.80 E-value=42 Score=23.47 Aligned_cols=21 Identities=24% Similarity=0.552 Sum_probs=17.6
Q ss_pred CCCCCHHHHHHHHHHHhcCCC
Q psy1729 8 MISTTKLLVTKLLGNEWSKLS 28 (170)
Q Consensus 8 ~p~~s~~evsK~lge~Wk~Ls 28 (170)
.|.+.+..|++.||..|+.|-
T Consensus 2 ~~~~~l~~ia~~lG~dW~~LA 22 (84)
T cd08317 2 RADIRLADISNLLGSDWPQLA 22 (84)
T ss_pred cccchHHHHHHHHhhHHHHHH
Confidence 467888999999999999883
No 107
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=21.43 E-value=29 Score=22.35 Aligned_cols=24 Identities=29% Similarity=0.656 Sum_probs=18.6
Q ss_pred CchhHHHHHHHHHhhhhhhhhhhhch
Q psy1729 131 DNEELYCRVCDQWFTTLHNKREHLNG 156 (170)
Q Consensus 131 ~~~~~~~~~~~~~f~~~h~~~~~~~~ 156 (170)
+.....|.+|...|++ |+..||..
T Consensus 28 ~~~~v~CPiC~~~~~~--~l~~Hl~~ 51 (54)
T PF05605_consen 28 ESKNVVCPICSSRVTD--NLIRHLNS 51 (54)
T ss_pred CCCCccCCCchhhhhh--HHHHHHHH
Confidence 3446889999998876 88888864
No 108
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=21.14 E-value=28 Score=22.43 Aligned_cols=19 Identities=21% Similarity=0.485 Sum_probs=11.4
Q ss_pred HHHHHHHHhhhhhhhhhhhch
Q psy1729 136 YCRVCDQWFTTLHNKREHLNG 156 (170)
Q Consensus 136 ~~~~~~~~f~~~h~~~~~~~~ 156 (170)
-|.||..-|+.-|. +.+..
T Consensus 22 ~CPlC~r~l~~e~~--~~li~ 40 (54)
T PF04423_consen 22 CCPLCGRPLDEEHR--QELIK 40 (54)
T ss_dssp E-TTT--EE-HHHH--HHHHH
T ss_pred cCCCCCCCCCHHHH--HHHHH
Confidence 79999999999887 44444
No 109
>cd07081 ALDH_F20_ACDH_EutE-like Coenzyme A acylating aldehyde dehydrogenase (ACDH), Ethanolamine utilization protein EutE, and related proteins. Coenzyme A acylating aldehyde dehydrogenase (ACDH), an NAD+ and CoA-dependent acetaldehyde dehydrogenase, acetylating (EC=1.2.1.10), functions as a single enzyme (such as the Ethanolamine utilization protein, EutE, in Salmonella typhimurium) or as part of a multifunctional enzyme to convert acetaldehyde into acetyl-CoA. The E. coli aldehyde-alcohol dehydrogenase includes the functional domains, alcohol dehydrogenase (ADH), ACDH, and pyruvate-formate-lyase deactivase; and the Entamoeba histolytica aldehyde-alcohol dehydrogenase 2 (ALDH20A1) includes the functional domains ADH and ACDH, and may be critical enzymes in the fermentative pathway.
Probab=21.03 E-value=2.4e+02 Score=25.88 Aligned_cols=32 Identities=16% Similarity=0.010 Sum_probs=16.8
Q ss_pred HHhhCCChhhhhhhHHHHHHHHHHHHHHHHHH
Q psy1729 58 NEWSKLSLPEKKVYLDRAEVDKKRYREELKVY 89 (170)
Q Consensus 58 ~~Wk~LS~~EK~~Y~~~A~~dk~rY~~em~~y 89 (170)
..|+.+|..+|..+..++++..+++..++...
T Consensus 13 ~~W~~~~~~~R~~iL~~~a~~l~~~~~ela~~ 44 (439)
T cd07081 13 QGLSCKSQEMVDLIFRAAAEAAEDARIDLAKL 44 (439)
T ss_pred HHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555555555555555555444
No 110
>PF02892 zf-BED: BED zinc finger; InterPro: IPR003656 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 predicted BED-type zinc finger domains. The BED finger which was named after the Drosophila proteins BEAF and DREF, is found in one or more copies in cellular regulatory factors and transposases from plants, animals and fungi. The BED finger is an about 50 to 60 amino acid residues domain that contains a characteristic motif with two highly conserved aromatic positions, as well as a shared pattern of cysteines and histidines that is predicted to form a zinc finger. As diverse BED fingers are able to bind DNA, it has been suggested that DNA-binding is the general function of this domain []. Some proteins known to contain a BED domain include animal, plant and fungi AC1 and Hobo-like transposases; Caenorhabditis elegans Dpy-20 protein, a predicted cuticular gene transcriptional regulator; Drosophila BEAF (boundary element-associated factor), thought to be involved in chromatin insulation; Drosophila DREF, a transcriptional regulator for S-phase genes; and tobacco 3AF1 and tomato E4/E8-BP1, light- and ethylene-regulated DNA binding proteins that contain two BED fingers. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding; PDB: 2DJR_A 2CT5_A.
Probab=20.83 E-value=18 Score=22.10 Aligned_cols=25 Identities=24% Similarity=0.522 Sum_probs=16.5
Q ss_pred cCchhHHHHHHHHHhhhh----hhhhhhh
Q psy1729 130 EDNEELYCRVCDQWFTTL----HNKREHL 154 (170)
Q Consensus 130 ~~~~~~~~~~~~~~f~~~----h~~~~~~ 154 (170)
.+.....|..|++-|+.. .|++.||
T Consensus 12 ~~~~~a~C~~C~~~~~~~~~~ts~l~~HL 40 (45)
T PF02892_consen 12 GDKKKAKCKYCGKVIKYSSGGTSNLKRHL 40 (45)
T ss_dssp GCSS-EEETTTTEE-----SSTHHHHHHH
T ss_pred CCcCeEEeCCCCeEEeeCCCcHHHHHHhh
Confidence 456678899999999875 6888888
No 111
>PF15581 Imm35: Immunity protein 35
Probab=20.66 E-value=1.5e+02 Score=21.93 Aligned_cols=23 Identities=22% Similarity=0.284 Sum_probs=17.9
Q ss_pred CCHHHHHHHHHHHhcCCChHHHH
Q psy1729 11 TTKLLVTKLLGNEWSKLSLPEKK 33 (170)
Q Consensus 11 ~s~~evsK~lge~Wk~Lse~EK~ 33 (170)
-++.-+...|...|+.||+.+=.
T Consensus 30 ~~i~~l~~lIe~eWRGl~~~qV~ 52 (93)
T PF15581_consen 30 RTIRNLESLIEHEWRGLPEEQVL 52 (93)
T ss_pred HHHHHHHHHHHHHHcCCCHHHHH
Confidence 45667788899999999887754
No 112
>PF05914 RIB43A: RIB43A; InterPro: IPR008805 This family consists of several RIB43A-like eukaryotic proteins. Ciliary and flagellar microtubules contain a specialised set of protofilaments, termed ribbons, that are composed of tubulin and several associated proteins. RIB43A was first characterised in the unicellular biflagellate, Chlamydomonas reinhardtii although highly related sequences are present in several higher eukaryotes including humans. The function of this protein is unknown although the structure of RIB43A and its association with the specialised protofilament ribbons and with basal bodies is relevant to the proposed role of ribbons in forming and stabilising doublet and triplet microtubules and in organising their three-dimensional structure. Human RIB43A homologues could represent a structural requirement in centriole replication in dividing cells [].
Probab=20.55 E-value=3.5e+02 Score=24.61 Aligned_cols=91 Identities=10% Similarity=0.176 Sum_probs=47.0
Q ss_pred cCCCCCHHH--HHHHHHHHhcCCChHHHHhHHHHHHHHHHHHHHHHhhhhhHHHHhhCCChhhhhh---hHHHHHHHHHH
Q psy1729 7 KMISTTKLL--VTKLLGNEWSKLSLPEKKVYLDRAEVDKKRYREELKVTKLLGNEWSKLSLPEKKV---YLDRAEVDKKR 81 (170)
Q Consensus 7 ~~p~~s~~e--vsK~lge~Wk~Lse~EK~~Ye~~Ak~dKerY~~EmEi~K~lg~~Wk~LS~~EK~~---Y~~~A~~dk~r 81 (170)
++|..+... --+.+...||.||+++...+...-......-..--+.-+.....|-.....--.- ++.........
T Consensus 255 Enp~~a~s~~gp~Rv~~d~wKGMs~eQl~~i~~~Q~~Q~~Ek~r~r~~E~~~e~~w~~~~~~~~ra~~~~Erq~~r~~~e 334 (379)
T PF05914_consen 255 ENPQVAQSSFGPHRVIPDRWKGMSPEQLEEIRKEQEQQREEKQRRREEEKEREAEWDRQRIQMARAALLLERQQQRQRRE 334 (379)
T ss_pred CCchhccccCCCCCCCCcccCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456543222 2466778999999999998887555444333322223333444454333222111 22333344455
Q ss_pred HHHHHHHHHcchhhHH
Q psy1729 82 YREELKVYRKSDAYQS 97 (170)
Q Consensus 82 Y~~em~~yk~~~~~~~ 97 (170)
-...+..++..-+...
T Consensus 335 ~r~~l~~~N~~LA~eQ 350 (379)
T PF05914_consen 335 LRRQLDEENQQLAEEQ 350 (379)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 5566666664444333
Done!