Query 027871
Match_columns 217
No_of_seqs 138 out of 198
Neff 4.6
Searched_HMMs 46136
Date Fri Mar 29 02:43:20 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/027871.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/027871hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03208 E3 ubiquitin-protein 100.0 1.2E-53 2.6E-58 365.2 8.3 164 3-217 16-193 (193)
2 KOG0823 Predicted E3 ubiquitin 100.0 3.8E-48 8.3E-53 337.8 6.3 180 2-217 44-230 (230)
3 smart00504 Ubox Modified RING 97.9 2E-06 4.3E-11 59.6 -1.1 48 6-60 2-54 (63)
4 TIGR00599 rad18 DNA repair pro 97.5 1.5E-05 3.3E-10 75.6 -1.1 48 4-58 25-77 (397)
5 KOG2164 Predicted E3 ubiquitin 97.4 4E-05 8.6E-10 74.5 -0.3 58 5-64 186-248 (513)
6 PF13920 zf-C3HC4_3: Zinc fing 97.3 1.3E-05 2.9E-10 54.1 -3.0 42 5-53 2-49 (50)
7 PF13923 zf-C3HC4_2: Zinc fing 97.1 2.7E-05 5.8E-10 50.2 -3.4 33 8-47 1-39 (39)
8 cd00162 RING RING-finger (Real 97.0 6.4E-05 1.4E-09 47.2 -1.9 39 7-51 1-45 (45)
9 PF04564 U-box: U-box domain; 96.8 0.00015 3.3E-09 52.8 -1.4 51 4-60 3-58 (73)
10 PF13639 zf-RING_2: Ring finge 96.8 4.9E-05 1.1E-09 49.9 -4.0 35 7-48 2-44 (44)
11 PHA02926 zinc finger-like prot 96.6 0.00027 5.9E-09 63.0 -1.8 47 5-52 170-230 (242)
12 KOG4628 Predicted E3 ubiquitin 96.5 0.0012 2.6E-08 62.0 1.6 44 6-55 230-281 (348)
13 PF14835 zf-RING_6: zf-RING of 96.4 0.0015 3.3E-08 47.9 1.5 40 5-53 7-52 (65)
14 PF14634 zf-RING_5: zinc-RING 96.3 0.0008 1.7E-08 44.5 -0.5 35 7-48 1-43 (44)
15 smart00184 RING Ring finger. E 95.8 0.00096 2.1E-08 40.2 -1.9 34 8-47 1-39 (39)
16 PF15227 zf-C3HC4_4: zinc fing 95.5 0.0014 3E-08 43.5 -2.1 37 8-47 1-42 (42)
17 PF00097 zf-C3HC4: Zinc finger 94.9 0.0012 2.5E-08 42.3 -3.8 35 8-47 1-41 (41)
18 PF05290 Baculo_IE-1: Baculovi 94.3 0.015 3.3E-07 48.2 0.6 41 2-53 77-133 (140)
19 KOG2177 Predicted E3 ubiquitin 93.9 0.0058 1.3E-07 50.3 -2.6 56 2-64 10-77 (386)
20 KOG1785 Tyrosine kinase negati 93.8 0.026 5.7E-07 54.5 1.1 61 1-66 365-433 (563)
21 KOG0287 Postreplication repair 93.7 0.0056 1.2E-07 57.8 -3.3 44 6-56 24-72 (442)
22 KOG4159 Predicted E3 ubiquitin 93.3 0.013 2.7E-07 56.0 -1.8 44 3-53 82-130 (398)
23 KOG4172 Predicted E3 ubiquitin 92.6 0.0053 1.2E-07 44.2 -4.1 42 5-53 7-55 (62)
24 COG5432 RAD18 RING-finger-cont 91.9 0.026 5.5E-07 52.6 -1.7 44 5-55 25-73 (391)
25 PF11793 FANCL_C: FANCL C-term 91.7 0.013 2.7E-07 42.8 -3.2 49 6-54 3-68 (70)
26 KOG1002 Nucleotide excision re 91.4 0.018 3.9E-07 57.2 -3.4 48 4-54 535-588 (791)
27 PHA02929 N1R/p28-like protein; 90.2 0.21 4.4E-06 44.8 2.4 13 40-52 215-227 (238)
28 KOG4362 Transcriptional regula 89.8 0.09 2E-06 53.3 -0.2 43 4-53 20-70 (684)
29 PF12678 zf-rbx1: RING-H2 zinc 87.2 0.06 1.3E-06 39.4 -2.5 35 7-48 21-73 (73)
30 PF12861 zf-Apc11: Anaphase-pr 86.7 0.16 3.5E-06 39.1 -0.6 45 4-52 29-82 (85)
31 COG5574 PEX10 RING-finger-cont 85.8 0.15 3.3E-06 46.5 -1.3 51 4-57 214-267 (271)
32 smart00744 RINGv The RING-vari 84.6 0.12 2.5E-06 35.4 -2.0 36 8-48 2-49 (49)
33 KOG0824 Predicted E3 ubiquitin 82.4 0.62 1.3E-05 43.5 1.1 44 5-54 7-55 (324)
34 TIGR01294 P_lamban phospholamb 80.2 2.5 5.4E-05 29.4 3.2 25 184-216 20-44 (52)
35 KOG0320 Predicted E3 ubiquitin 80.1 0.35 7.6E-06 42.0 -1.2 57 3-60 129-186 (187)
36 PF04641 Rtf2: Rtf2 RING-finge 78.2 1.3 2.7E-05 39.6 1.7 61 3-64 111-173 (260)
37 PF04272 Phospholamban: Phosph 74.1 5 0.00011 27.9 3.4 13 204-216 32-44 (52)
38 KOG1813 Predicted E3 ubiquitin 74.0 1.8 3.9E-05 40.4 1.5 40 5-51 241-285 (313)
39 KOG1039 Predicted E3 ubiquitin 72.9 1.3 2.9E-05 41.7 0.4 49 4-52 160-221 (344)
40 TIGR00570 cdk7 CDK-activating 72.4 1.3 2.8E-05 41.4 0.2 48 1-56 1-58 (309)
41 KOG0297 TNF receptor-associate 69.5 3.2 7E-05 39.4 2.2 48 4-58 20-73 (391)
42 KOG1001 Helicase-like transcri 69.0 0.93 2E-05 46.1 -1.6 46 6-57 455-505 (674)
43 KOG1645 RING-finger-containing 67.5 0.49 1.1E-05 45.8 -3.7 51 7-62 6-66 (463)
44 KOG3113 Uncharacterized conser 67.4 2 4.3E-05 39.5 0.3 39 22-63 129-169 (293)
45 COG5243 HRD1 HRD ubiquitin lig 67.3 0.83 1.8E-05 44.1 -2.2 39 7-52 289-345 (491)
46 COG5152 Uncharacterized conser 64.7 1.1 2.3E-05 40.1 -1.8 41 4-51 195-240 (259)
47 PF06750 DiS_P_DiS: Bacterial 63.0 4 8.6E-05 31.3 1.2 26 40-65 32-61 (92)
48 KOG0802 E3 ubiquitin ligase [P 62.3 0.79 1.7E-05 45.0 -3.5 48 6-60 292-349 (543)
49 PHA02862 5L protein; Provision 60.4 1.6 3.4E-05 37.1 -1.5 45 7-60 4-58 (156)
50 PRK11827 hypothetical protein; 56.4 5 0.00011 29.0 0.7 15 40-54 7-21 (60)
51 PF04423 Rad50_zn_hook: Rad50 55.1 3.5 7.5E-05 28.2 -0.3 13 43-55 22-34 (54)
52 PRK15178 Vi polysaccharide exp 54.3 13 0.00029 36.1 3.4 27 189-215 71-97 (434)
53 KOG0804 Cytoplasmic Zn-finger 54.0 4.5 9.7E-05 39.8 0.2 39 5-52 175-222 (493)
54 cd00350 rubredoxin_like Rubred 53.8 7.8 0.00017 24.2 1.2 11 40-50 16-26 (33)
55 PF03119 DNA_ligase_ZBD: NAD-d 53.0 5.8 0.00012 24.3 0.5 11 43-53 1-11 (28)
56 KOG0317 Predicted E3 ubiquitin 51.7 8.2 0.00018 35.9 1.5 21 40-60 272-292 (293)
57 smart00834 CxxC_CXXC_SSSS Puta 51.5 9.5 0.00021 24.0 1.4 30 22-51 7-36 (41)
58 PF07800 DUF1644: Protein of u 51.1 12 0.00027 32.0 2.3 18 40-57 79-96 (162)
59 PF03908 Sec20: Sec20; InterP 50.0 26 0.00057 26.3 3.8 27 189-216 63-89 (92)
60 PF14169 YdjO: Cold-inducible 49.0 11 0.00024 27.2 1.5 38 21-59 16-58 (59)
61 smart00734 ZnF_Rad18 Rad18-lik 48.9 6.2 0.00013 23.7 0.1 14 42-55 2-15 (26)
62 KOG4265 Predicted E3 ubiquitin 48.4 9.5 0.00021 36.3 1.4 56 3-64 288-346 (349)
63 PF10571 UPF0547: Uncharacteri 48.0 9 0.0002 23.2 0.8 13 42-54 1-13 (26)
64 KOG0311 Predicted E3 ubiquitin 45.5 1 2.2E-05 42.9 -5.5 41 4-50 42-88 (381)
65 KOG1734 Predicted RING-contain 43.2 6.4 0.00014 36.7 -0.6 46 7-57 226-286 (328)
66 COG4068 Uncharacterized protei 42.9 12 0.00025 27.5 0.8 17 40-56 7-23 (64)
67 PHA02610 uvsY.-2 hypothetical 41.8 11 0.00023 26.8 0.5 16 42-57 2-17 (53)
68 PF10146 zf-C4H2: Zinc finger- 41.7 11 0.00024 33.6 0.7 12 39-50 206-217 (230)
69 COG5175 MOT2 Transcriptional r 41.5 7.2 0.00016 37.5 -0.5 48 2-59 12-73 (480)
70 PHA03096 p28-like protein; Pro 40.9 3 6.4E-05 38.3 -3.1 45 6-51 179-236 (284)
71 PF11789 zf-Nse: Zinc-finger o 40.6 4.1 8.8E-05 28.7 -1.8 40 4-48 10-57 (57)
72 PF06716 DUF1201: Protein of u 40.5 18 0.00038 25.4 1.4 14 204-217 14-27 (54)
73 PF08525 OapA_N: Opacity-assoc 39.0 40 0.00086 20.9 2.7 19 199-217 9-27 (30)
74 KOG4451 Uncharacterized conser 37.9 11 0.00025 34.3 0.2 13 38-50 260-272 (286)
75 PF10886 DUF2685: Protein of u 36.6 14 0.00031 26.3 0.5 14 42-55 2-15 (54)
76 KOG1493 Anaphase-promoting com 36.6 9.1 0.0002 29.4 -0.6 25 23-51 56-80 (84)
77 PF13445 zf-RING_UBOX: RING-ty 36.4 17 0.00036 24.3 0.8 15 44-59 1-15 (43)
78 KOG4739 Uncharacterized protei 36.1 21 0.00046 32.2 1.6 44 6-58 4-54 (233)
79 PF05399 EVI2A: Ectropic viral 36.0 24 0.00053 31.7 1.9 17 201-217 132-148 (227)
80 KOG3970 Predicted E3 ubiquitin 35.9 13 0.00029 33.9 0.3 32 22-53 74-106 (299)
81 PF14255 Cys_rich_CPXG: Cystei 34.1 9.3 0.0002 26.8 -0.8 33 22-54 5-37 (52)
82 PF09986 DUF2225: Uncharacteri 34.1 19 0.00041 31.4 0.9 24 39-62 3-26 (214)
83 KOG0978 E3 ubiquitin ligase in 33.4 9.3 0.0002 39.4 -1.3 54 6-60 644-697 (698)
84 PF10215 Ost4: Oligosaccaryltr 33.2 31 0.00067 22.5 1.6 23 195-217 3-25 (35)
85 PF05883 Baculo_RING: Baculovi 33.1 4.9 0.00011 33.4 -2.7 27 4-30 25-65 (134)
86 COG2835 Uncharacterized conser 33.0 18 0.0004 26.2 0.6 13 40-52 7-19 (60)
87 COG1259 Uncharacterized conser 32.7 8.5 0.00018 32.6 -1.4 44 41-87 18-61 (151)
88 KOG0827 Predicted E3 ubiquitin 32.6 8 0.00017 37.6 -1.8 46 6-57 5-61 (465)
89 CHL00038 psbL photosystem II p 32.6 46 0.001 22.1 2.3 18 197-214 11-28 (38)
90 TIGR01562 FdhE formate dehydro 32.1 32 0.00069 32.0 2.1 37 7-50 186-233 (305)
91 smart00746 TRASH metallochaper 31.8 33 0.00072 19.0 1.5 9 44-52 1-9 (39)
92 cd00729 rubredoxin_SM Rubredox 31.6 22 0.00048 22.5 0.7 9 42-50 19-27 (34)
93 TIGR03831 YgiT_finger YgiT-typ 31.3 30 0.00066 21.9 1.3 13 44-56 1-13 (46)
94 PF09237 GAGA: GAGA factor; I 30.8 15 0.00032 26.2 -0.2 14 40-53 23-36 (54)
95 PHA02825 LAP/PHD finger-like p 30.0 12 0.00025 32.2 -1.1 44 4-53 7-60 (162)
96 PF13453 zf-TFIIB: Transcripti 29.7 25 0.00053 22.7 0.7 14 43-56 1-14 (41)
97 PF15012 DUF4519: Domain of un 29.1 44 0.00096 24.0 1.9 32 186-217 16-48 (56)
98 KOG3039 Uncharacterized conser 28.8 19 0.00042 33.2 0.1 50 4-60 220-278 (303)
99 PRK10299 PhoPQ regulatory prot 28.7 34 0.00074 23.8 1.3 14 203-216 6-19 (47)
100 PF14205 Cys_rich_KTR: Cystein 28.3 29 0.00063 24.9 0.9 19 43-61 6-31 (55)
101 KOG3002 Zn finger protein [Gen 28.0 33 0.00071 31.8 1.4 39 4-52 47-91 (299)
102 PF04216 FdhE: Protein involve 27.1 20 0.00043 32.2 -0.1 37 7-50 174-220 (290)
103 COG5222 Uncharacterized conser 27.1 13 0.00028 35.3 -1.4 51 6-62 275-332 (427)
104 PF05605 zf-Di19: Drought indu 26.9 19 0.00042 24.4 -0.2 17 42-58 3-19 (54)
105 PRK12380 hydrogenase nickel in 26.6 33 0.00071 27.1 1.0 31 15-50 65-95 (113)
106 PHA02975 hypothetical protein; 26.6 47 0.001 24.8 1.8 21 197-217 40-60 (69)
107 PF13240 zinc_ribbon_2: zinc-r 26.2 33 0.00073 20.0 0.8 10 44-53 2-11 (23)
108 PF05715 zf-piccolo: Piccolo Z 25.7 35 0.00076 24.9 0.9 11 42-52 3-13 (61)
109 PF10297 Hap4_Hap_bind: Minima 25.5 41 0.0009 18.8 1.0 11 78-88 5-15 (17)
110 smart00037 CNX Connexin homolo 25.1 29 0.00062 22.6 0.4 14 2-15 6-27 (34)
111 COG5151 SSL1 RNA polymerase II 25.0 28 0.0006 33.3 0.4 13 41-53 308-320 (421)
112 PHA02844 putative transmembran 24.8 55 0.0012 24.8 1.9 18 199-216 46-63 (75)
113 PF15221 LEP503: Lens epitheli 24.4 71 0.0015 23.1 2.3 18 195-212 39-56 (61)
114 PLN02195 cellulose synthase A 24.1 56 0.0012 35.1 2.5 46 1-52 2-59 (977)
115 KOG4692 Predicted E3 ubiquitin 23.9 11 0.00025 36.4 -2.4 40 7-53 424-468 (489)
116 TIGR01206 lysW lysine biosynth 23.2 38 0.00083 23.9 0.7 15 42-56 3-17 (54)
117 PF07092 DUF1356: Protein of u 23.0 15 0.00033 33.2 -1.7 16 201-216 73-88 (238)
118 KOG0825 PHD Zn-finger protein 22.5 9.7 0.00021 40.2 -3.3 33 22-61 148-180 (1134)
119 PRK06870 secG preprotein trans 22.4 94 0.002 22.7 2.7 19 195-213 48-66 (76)
120 PF10559 Plug_translocon: Plug 22.1 52 0.0011 21.1 1.1 7 56-62 8-14 (35)
121 PF09862 DUF2089: Protein of u 21.9 39 0.00085 27.2 0.7 13 44-56 1-13 (113)
122 KOG3053 Uncharacterized conser 21.7 9.7 0.00021 35.2 -3.2 43 8-52 23-82 (293)
123 PHA02849 putative transmembran 21.6 69 0.0015 24.6 1.9 16 201-216 19-34 (82)
124 KOG1952 Transcription factor N 21.4 25 0.00055 37.2 -0.6 63 2-64 188-259 (950)
125 PF13465 zf-H2C2_2: Zinc-finge 21.3 35 0.00075 20.0 0.2 12 2-13 11-22 (26)
126 COG4469 CoiA Competence protei 20.5 40 0.00086 32.1 0.5 22 42-63 26-50 (342)
127 PRK03681 hypA hydrogenase nick 20.1 54 0.0012 25.9 1.1 35 12-50 62-96 (114)
No 1
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=100.00 E-value=1.2e-53 Score=365.24 Aligned_cols=164 Identities=34% Similarity=0.640 Sum_probs=136.2
Q ss_pred CCCCccccccCCCCCcceE-----eeCCCCCCCCCCCCCC---------CcCCCCCCCccccccccceeeeecCCCCCCC
Q 027871 3 QNLFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKD---------DEQQQNCPVCKANISVASLVPLYGRGGISSA 68 (217)
Q Consensus 3 ~s~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~---------~~~~~~CPVCKa~Vs~~~viPLYGRG~~~~~ 68 (217)
++.|+|+||+|..+||||| |||.||..|+...++. ..+...|||||+.|+.+++|||||||...
T Consensus 16 ~~~~~CpICld~~~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~LvPiygrg~~~-- 93 (193)
T PLN03208 16 GGDFDCNICLDQVRDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEATLVPIYGRGQKA-- 93 (193)
T ss_pred CCccCCccCCCcCCCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhcEEEeeccCCCC--
Confidence 5679999999999999999 9999999997643211 23457999999999999999999999843
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCcccccCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCCccccccCCCcchhhc
Q 027871 69 SDSKKPNLGEVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAALASSSLGGMATISF 148 (217)
Q Consensus 69 ~~~k~~~~g~~IPpRP~~~R~es~~~~~~~~~~~~~~q~~~n~~~~~~~p~~~~~~~~~~y~~~~~~p~~~~gg~~~~~~ 148 (217)
.+.+.+||+||+++|.++ ++..++++ ++ ++|+|+ + ++
T Consensus 94 -----~~~~~~iP~rp~~~~~~~---------~~~~~~~~------~~---~~~~~~-------------------~-~~ 130 (193)
T PLN03208 94 -----PQSGSNVPSRPSGPVYDL---------RGVGQRLG------EG---ESQRYM-------------------Y-RM 130 (193)
T ss_pred -----CCCCCCCCcCCCCCccCC---------CCcccccc------cc---ccceee-------------------e-cc
Confidence 345678999999998773 23334441 11 233332 1 37
Q ss_pred ccccccccccceeccccCCCCCCCCCCCCCCCCCCCChhhhhhhhHHHHhhhhHHHHHHHHHHHHHhhC
Q 027871 149 FNPLMGMLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF 217 (217)
Q Consensus 149 ~~~~~Gmfgemv~~rvFG~~~~~~~~~p~~~~~g~~spR~Rrq~mq~d~sL~ri~~Fl~ccvvLCLllF 217 (217)
+.|++||||||||+||||++.+|+|+|||+ +||||||+||+|||||||+|||||||+||||||
T Consensus 131 ~~p~~g~~~~~~~~r~fg~~~~~~~~~~~~------~~r~r~~~~q~~~sl~r~~~f~~c~~~~~~~~f 193 (193)
T PLN03208 131 PDPVMGVVCEMVYRRLFGESSSNMAPYRDM------NVRSRRRAMQAEESLSRVYLFLLCFMFMCLFLF 193 (193)
T ss_pred CCccccchhhhhhhhhhCCccccccccccC------chHHHHHHHHHhhhhhHHHHHHHHHHHHHHHhC
Confidence 889999999999999999999999999996 899999999999999999999999999999998
No 2
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=100.00 E-value=3.8e-48 Score=337.77 Aligned_cols=180 Identities=27% Similarity=0.408 Sum_probs=132.2
Q ss_pred CCCCCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeeecCCCCCCCCCCCCCCC
Q 027871 2 EQNLFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLYGRGGISSASDSKKPNL 76 (217)
Q Consensus 2 ~~s~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLYGRG~~~~~~~~k~~~~ 76 (217)
++++||||||||+|+||||| |||+|||+|+... .+.++|||||++|++++||||||||.....+++|+.
T Consensus 44 ~~~~FdCNICLd~akdPVvTlCGHLFCWpClyqWl~~~----~~~~~cPVCK~~Vs~~~vvPlYGrG~~~~~~~~~~~-- 117 (230)
T KOG0823|consen 44 DGGFFDCNICLDLAKDPVVTLCGHLFCWPCLYQWLQTR----PNSKECPVCKAEVSIDTVVPLYGRGSKKPSDPRKKD-- 117 (230)
T ss_pred CCCceeeeeeccccCCCEEeecccceehHHHHHHHhhc----CCCeeCCccccccccceEEeeeccCCCCCCCccccc--
Confidence 57899999999999999999 9999999999864 577999999999999999999999996555544432
Q ss_pred CCCCCCCCCCCCCCcccccCCCccccccccccccccCCCCCCCCCCCCCCCCCCCCCcc--ccccCCCcchhhccccccc
Q 027871 77 GEVVPSRPHPSALNTSVTSSSTSTRHQTQQLHSDFFQSQAPAFHNPQYFPHHYGSHAAL--ASSSLGGMATISFFNPLMG 154 (217)
Q Consensus 77 g~~IPpRP~~~R~es~~~~~~~~~~~~~~q~~~n~~~~~~~p~~~~~~~~~~y~~~~~~--p~~~~gg~~~~~~~~~~~G 154 (217)
||+||+|+|.|+++.+. +. .+.|.-.+... ..+...+ -|...|.... -.+|+|
T Consensus 118 ---vP~RP~~~R~e~~~p~~---------~~---------~~~~g~r~~g~-~~~~~~~~~f~~s~~i~~~---~~~v~~ 172 (230)
T KOG0823|consen 118 ---VPPRPAGQRYESKRPTP---------QN---------RGNHGFRFFGF-RLGEESSNRFMYSFGIGLF---GDPVMG 172 (230)
T ss_pred ---CCCCCCCccccccCCCC---------cc---------ccccccccccc-cccccCCcceeEEeecccC---CCceee
Confidence 99999999999875442 11 00000011100 0010111 1222332222 158899
Q ss_pred ccccceeccccCCCCCCCCCCCCCCCCCCCChhhhhhhhHHHHhhhhHHHHHHHHHHHHHhhC
Q 027871 155 MLGGMTLERIFGGSTTSLFTYPSQSLLVSNNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLLF 217 (217)
Q Consensus 155 mfgemv~~rvFG~~~~~~~~~p~~~~~g~~spR~Rrq~mq~d~sL~ri~~Fl~ccvvLCLllF 217 (217)
||++|+++++||..++.. + .++ +-..+|.++++||.|++|+|+.+|+.|++++||+++
T Consensus 173 ~~p~~~~~~lf~~~~~~~-~--~~~--~~~~~~~~~r~~q~e~~ls~~f~~~~~~~~~~l~~~ 230 (230)
T KOG0823|consen 173 LFPFGLYTRLFGTDETFP-A--DTP--RPSPARPLGRQMQRENSLSRVFLFLACFFVSWLLVI 230 (230)
T ss_pred eccccceeeecCCCCCcc-c--cCC--CCCCCccccccchhhcccccchhhhhhhheeeeeeC
Confidence 999999999999998755 2 111 224578888889999999999999999999999875
No 3
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=97.86 E-value=2e-06 Score=59.55 Aligned_cols=48 Identities=13% Similarity=0.090 Sum_probs=43.1
Q ss_pred CccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeee
Q 027871 6 FEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLY 60 (217)
Q Consensus 6 FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLY 60 (217)
|-|.||++.-+|||++ ||..||..|+. .+..||+|+..++.+.++|++
T Consensus 2 ~~Cpi~~~~~~~Pv~~~~G~v~~~~~i~~~~~-------~~~~cP~~~~~~~~~~l~~~~ 54 (63)
T smart00504 2 FLCPISLEVMKDPVILPSGQTYERRAIEKWLL-------SHGTDPVTGQPLTHEDLIPNL 54 (63)
T ss_pred cCCcCCCCcCCCCEECCCCCEEeHHHHHHHHH-------HCCCCCCCcCCCChhhceeCH
Confidence 7899999999999997 99999999864 257899999999999999975
No 4
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=97.50 E-value=1.5e-05 Score=75.59 Aligned_cols=48 Identities=15% Similarity=0.085 Sum_probs=40.7
Q ss_pred CCCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceee
Q 027871 4 NLFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVP 58 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viP 58 (217)
..+.|.||+|.-++||++ ||+.||..|+. ....||+|+..+..+++.+
T Consensus 25 ~~l~C~IC~d~~~~PvitpCgH~FCs~CI~~~l~-------~~~~CP~Cr~~~~~~~Lr~ 77 (397)
T TIGR00599 25 TSLRCHICKDFFDVPVLTSCSHTFCSLCIRRCLS-------NQPKCPLCRAEDQESKLRS 77 (397)
T ss_pred cccCCCcCchhhhCccCCCCCCchhHHHHHHHHh-------CCCCCCCCCCccccccCcc
Confidence 568999999999999998 99999999864 2358999999998765543
No 5
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=97.35 E-value=4e-05 Score=74.47 Aligned_cols=58 Identities=12% Similarity=0.145 Sum_probs=49.8
Q ss_pred CCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeeecCCC
Q 027871 5 LFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLYGRGG 64 (217)
Q Consensus 5 ~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLYGRG~ 64 (217)
...|-|||+.+.-|+.| |||+||.+..+.. .......||.|...|....|-|+|.+-.
T Consensus 186 ~~~CPICL~~~~~p~~t~CGHiFC~~CiLqy~~~s--~~~~~~~CPiC~s~I~~kdl~pv~~e~~ 248 (513)
T KOG2164|consen 186 DMQCPICLEPPSVPVRTNCGHIFCGPCILQYWNYS--AIKGPCSCPICRSTITLKDLLPVFIEDD 248 (513)
T ss_pred CCcCCcccCCCCcccccccCceeeHHHHHHHHhhh--cccCCccCCchhhhccccceeeeeeccc
Confidence 67899999999999999 9999998854322 3557799999999999999999999654
No 6
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=97.31 E-value=1.3e-05 Score=54.13 Aligned_cols=42 Identities=17% Similarity=0.234 Sum_probs=34.3
Q ss_pred CCccccccCCCCCcceE------eeCCCCCCCCCCCCCCCcCCCCCCCccccccc
Q 027871 5 LFEPETGYATEEDASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISV 53 (217)
Q Consensus 5 ~FeCnICld~A~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~ 53 (217)
.++|.||+|...++++. +|..|+..|.. ....||+|++.|++
T Consensus 2 ~~~C~iC~~~~~~~~~~pCgH~~~C~~C~~~~~~-------~~~~CP~Cr~~i~~ 49 (50)
T PF13920_consen 2 DEECPICFENPRDVVLLPCGHLCFCEECAERLLK-------RKKKCPICRQPIES 49 (50)
T ss_dssp HSB-TTTSSSBSSEEEETTCEEEEEHHHHHHHHH-------TTSBBTTTTBB-SE
T ss_pred cCCCccCCccCCceEEeCCCChHHHHHHhHHhcc-------cCCCCCcCChhhcC
Confidence 47899999999999887 89999998753 66899999999874
No 7
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=97.06 E-value=2.7e-05 Score=50.22 Aligned_cols=33 Identities=15% Similarity=0.180 Sum_probs=26.2
Q ss_pred cccccCCCCCcc-eE-----eeCCCCCCCCCCCCCCCcCCCCCCCc
Q 027871 8 PETGYATEEDAS-LK-----QKWSPTSAPTNVPEKDDEQQQNCPVC 47 (217)
Q Consensus 8 CnICld~A~dpV-VT-----ycW~ci~~w~~~~~~~~~~~~~CPVC 47 (217)
|.||+|...+|| ++ ||+.|+.+|+. ....||+|
T Consensus 1 C~iC~~~~~~~~~~~~CGH~fC~~C~~~~~~-------~~~~CP~C 39 (39)
T PF13923_consen 1 CPICLDELRDPVVVTPCGHSFCKECIEKYLE-------KNPKCPVC 39 (39)
T ss_dssp ETTTTSB-SSEEEECTTSEEEEHHHHHHHHH-------CTSB-TTT
T ss_pred CCCCCCcccCcCEECCCCCchhHHHHHHHHH-------CcCCCcCC
Confidence 789999999995 44 99999999864 24899998
No 8
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=97.01 E-value=6.4e-05 Score=47.15 Aligned_cols=39 Identities=15% Similarity=0.182 Sum_probs=31.3
Q ss_pred ccccccCCCCCcceE------eeCCCCCCCCCCCCCCCcCCCCCCCccccc
Q 027871 7 EPETGYATEEDASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCKANI 51 (217)
Q Consensus 7 eCnICld~A~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~V 51 (217)
+|.||++.-.++++. ||+.|+..|... ....||+||..+
T Consensus 1 ~C~iC~~~~~~~~~~~~C~H~~c~~C~~~~~~~------~~~~Cp~C~~~~ 45 (45)
T cd00162 1 ECPICLEEFREPVVLLPCGHVFCRSCIDKWLKS------GKNTCPLCRTPI 45 (45)
T ss_pred CCCcCchhhhCceEecCCCChhcHHHHHHHHHh------CcCCCCCCCCcC
Confidence 699999998777765 899999998641 457899999864
No 9
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=96.83 E-value=0.00015 Score=52.83 Aligned_cols=51 Identities=14% Similarity=0.055 Sum_probs=39.1
Q ss_pred CCCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeee
Q 027871 4 NLFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLY 60 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLY 60 (217)
..|-|.|+++.-+|||++ |+=.+|.+|+.. ....||+|+..++.+.+||-+
T Consensus 3 ~~f~CpIt~~lM~dPVi~~~G~tyer~~I~~~l~~------~~~~~P~t~~~l~~~~l~pn~ 58 (73)
T PF04564_consen 3 DEFLCPITGELMRDPVILPSGHTYERSAIERWLEQ------NGGTDPFTRQPLSESDLIPNR 58 (73)
T ss_dssp GGGB-TTTSSB-SSEEEETTSEEEEHHHHHHHHCT------TSSB-TTT-SB-SGGGSEE-H
T ss_pred cccCCcCcCcHhhCceeCCcCCEEcHHHHHHHHHc------CCCCCCCCCCcCCcccceECH
Confidence 468999999999999997 888888888752 578999999999999999954
No 10
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=96.77 E-value=4.9e-05 Score=49.92 Aligned_cols=35 Identities=20% Similarity=0.277 Sum_probs=26.6
Q ss_pred ccccccCCC--CCcceE------eeCCCCCCCCCCCCCCCcCCCCCCCcc
Q 027871 7 EPETGYATE--EDASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCK 48 (217)
Q Consensus 7 eCnICld~A--~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCK 48 (217)
+|.||+|.- ++.++. |++.||..|+. .+..||+||
T Consensus 2 ~C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~~-------~~~~CP~CR 44 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLPCGHVFHRSCIKEWLK-------RNNSCPVCR 44 (44)
T ss_dssp CETTTTCBHHTTSCEEEETTSEEEEHHHHHHHHH-------HSSB-TTTH
T ss_pred CCcCCChhhcCCCeEEEccCCCeeCHHHHHHHHH-------hCCcCCccC
Confidence 699999965 345554 99999999975 346999996
No 11
>PHA02926 zinc finger-like protein; Provisional
Probab=96.59 E-value=0.00027 Score=62.97 Aligned_cols=47 Identities=15% Similarity=0.213 Sum_probs=33.5
Q ss_pred CCccccccCCCCC---------cceE-----eeCCCCCCCCCCCCCCCcCCCCCCCcccccc
Q 027871 5 LFEPETGYATEED---------ASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANIS 52 (217)
Q Consensus 5 ~FeCnICld~A~d---------pVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs 52 (217)
.-+|.||+|..-+ +++. |||.||..|.... .+......||+|+....
T Consensus 170 E~eCgICmE~I~eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r-~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 170 EKECGICYEVVYSKRLENDRYFGLLDSCNHIFCITCINIWHRTR-RETGASDNCPICRTRFR 230 (242)
T ss_pred CCCCccCccccccccccccccccccCCCCchHHHHHHHHHHHhc-cccCcCCcCCCCcceee
Confidence 4689999998533 4554 9999999996521 11223467999998766
No 12
>KOG4628 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=96.49 E-value=0.0012 Score=61.96 Aligned_cols=44 Identities=18% Similarity=0.126 Sum_probs=33.2
Q ss_pred CccccccCCC--CCcceE------eeCCCCCCCCCCCCCCCcCCCCCCCccccccccc
Q 027871 6 FEPETGYATE--EDASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVAS 55 (217)
Q Consensus 6 FeCnICld~A--~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~ 55 (217)
+.|.||+|.= .|-+.- |-=.||..|+. +.+.-|||||-.|-.++
T Consensus 230 ~~CaIClEdY~~GdklRiLPC~H~FH~~CIDpWL~------~~r~~CPvCK~di~~~~ 281 (348)
T KOG4628|consen 230 DTCAICLEDYEKGDKLRILPCSHKFHVNCIDPWLT------QTRTFCPVCKRDIRTDS 281 (348)
T ss_pred ceEEEeecccccCCeeeEecCCCchhhccchhhHh------hcCccCCCCCCcCCCCC
Confidence 6899999953 344432 78899999997 25677999999776554
No 13
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=96.43 E-value=0.0015 Score=47.88 Aligned_cols=40 Identities=15% Similarity=0.188 Sum_probs=21.1
Q ss_pred CCccccccCCCCCcceE------eeCCCCCCCCCCCCCCCcCCCCCCCccccccc
Q 027871 5 LFEPETGYATEEDASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISV 53 (217)
Q Consensus 5 ~FeCnICld~A~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~ 53 (217)
.-.|++|.+.-++||-+ |||.||..-+. .+||||+-...+
T Consensus 7 lLrCs~C~~~l~~pv~l~~CeH~fCs~Ci~~~~~---------~~CPvC~~Paw~ 52 (65)
T PF14835_consen 7 LLRCSICFDILKEPVCLGGCEHIFCSSCIRDCIG---------SECPVCHTPAWI 52 (65)
T ss_dssp TTS-SSS-S--SS-B---SSS--B-TTTGGGGTT---------TB-SSS--B-S-
T ss_pred hcCCcHHHHHhcCCceeccCccHHHHHHhHHhcC---------CCCCCcCChHHH
Confidence 45799999999999964 99999987322 469999866543
No 14
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=96.31 E-value=0.0008 Score=44.51 Aligned_cols=35 Identities=11% Similarity=0.216 Sum_probs=28.7
Q ss_pred ccccccCCC---CCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCcc
Q 027871 7 EPETGYATE---EDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCK 48 (217)
Q Consensus 7 eCnICld~A---~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCK 48 (217)
+||||++.- +.|+|| ||+.|+..+. .....||+|+
T Consensus 1 ~C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~-------~~~~~CP~C~ 43 (44)
T PF14634_consen 1 HCNICFEKYSEERRPRLTSCGHIFCEKCLKKLK-------GKSVKCPICR 43 (44)
T ss_pred CCcCcCccccCCCCeEEcccCCHHHHHHHHhhc-------CCCCCCcCCC
Confidence 699999977 457777 8999999964 3568999997
No 15
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=95.77 E-value=0.00096 Score=40.19 Aligned_cols=34 Identities=15% Similarity=0.159 Sum_probs=28.2
Q ss_pred cccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCc
Q 027871 8 PETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVC 47 (217)
Q Consensus 8 CnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVC 47 (217)
|.||++..++++++ ||+.|+..|.. .....||+|
T Consensus 1 C~iC~~~~~~~~~~~C~H~~c~~C~~~~~~------~~~~~CP~C 39 (39)
T smart00184 1 CPICLEELKDPVVLPCGHTFCRSCIRKWLK------SGNNTCPIC 39 (39)
T ss_pred CCcCccCCCCcEEecCCChHHHHHHHHHHH------hCcCCCCCC
Confidence 78999998888887 89999999864 245679998
No 16
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=95.47 E-value=0.0014 Score=43.49 Aligned_cols=37 Identities=16% Similarity=0.059 Sum_probs=25.0
Q ss_pred cccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCc
Q 027871 8 PETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVC 47 (217)
Q Consensus 8 CnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVC 47 (217)
|.||+|.-+|||.. ||-.||.+|.... ......||+|
T Consensus 1 CpiC~~~~~~Pv~l~CGH~FC~~Cl~~~~~~~---~~~~~~CP~C 42 (42)
T PF15227_consen 1 CPICLDLFKDPVSLPCGHSFCRSCLERLWKEP---SGSGFSCPEC 42 (42)
T ss_dssp ETTTTSB-SSEEE-SSSSEEEHHHHHHHHCCS---SSST---SSS
T ss_pred CCccchhhCCccccCCcCHHHHHHHHHHHHcc---CCcCCCCcCC
Confidence 78999999999987 9999999985422 2222689998
No 17
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 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 C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=94.88 E-value=0.0012 Score=42.35 Aligned_cols=35 Identities=17% Similarity=0.112 Sum_probs=29.2
Q ss_pred cccccCCCCCcc-eE-----eeCCCCCCCCCCCCCCCcCCCCCCCc
Q 027871 8 PETGYATEEDAS-LK-----QKWSPTSAPTNVPEKDDEQQQNCPVC 47 (217)
Q Consensus 8 CnICld~A~dpV-VT-----ycW~ci~~w~~~~~~~~~~~~~CPVC 47 (217)
|.||++..++++ ++ ||..||.+|... +....||+|
T Consensus 1 C~iC~~~~~~~~~~~~C~H~fC~~C~~~~~~~-----~~~~~CP~C 41 (41)
T PF00097_consen 1 CPICLEPFEDPVILLPCGHSFCRDCLRKWLEN-----SGSVKCPLC 41 (41)
T ss_dssp ETTTSSBCSSEEEETTTSEEEEHHHHHHHHHH-----TSSSBTTTT
T ss_pred CCcCCccccCCCEEecCCCcchHHHHHHHHHh-----cCCccCCcC
Confidence 789999999999 43 999999998642 466789998
No 18
>PF05290 Baculo_IE-1: Baculovirus immediate-early protein (IE-0); InterPro: IPR007954 This entry contains the Baculovirus immediate-early protein IE-0.
Probab=94.30 E-value=0.015 Score=48.24 Aligned_cols=41 Identities=27% Similarity=0.502 Sum_probs=28.9
Q ss_pred CCCCCccccccCCCCCcc-eE------e---------eCCCCCCCCCCCCCCCcCCCCCCCccccccc
Q 027871 2 EQNLFEPETGYATEEDAS-LK------Q---------KWSPTSAPTNVPEKDDEQQQNCPVCKANISV 53 (217)
Q Consensus 2 ~~s~FeCnICld~A~dpV-VT------y---------cW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~ 53 (217)
|...||||||-|+-.|.- ++ | -|..- .-++.|||||-....
T Consensus 77 d~~lYeCnIC~etS~ee~FLKPneCCgY~iCn~Cya~LWK~~-----------~~ypvCPvCkTSFKs 133 (140)
T PF05290_consen 77 DPKLYECNICKETSAEERFLKPNECCGYSICNACYANLWKFC-----------NLYPVCPVCKTSFKS 133 (140)
T ss_pred CCCceeccCcccccchhhcCCcccccchHHHHHHHHHHHHHc-----------ccCCCCCcccccccc
Confidence 567899999999877654 33 2 25522 356899999976543
No 19
>KOG2177 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.94 E-value=0.0058 Score=50.26 Aligned_cols=56 Identities=18% Similarity=0.153 Sum_probs=42.1
Q ss_pred CCCCCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCcc-------ccccccceeeeecCCC
Q 027871 2 EQNLFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCK-------ANISVASLVPLYGRGG 64 (217)
Q Consensus 2 ~~s~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCK-------a~Vs~~~viPLYGRG~ 64 (217)
.+..+.|-||++.-++|++. ||..|+..+.. ..-.||+|+ ..+...+++..+-...
T Consensus 10 ~~~~~~C~iC~~~~~~p~~l~C~H~~c~~C~~~~~~-------~~~~Cp~cr~~~~~~~~n~~l~~~~~~~~~~~ 77 (386)
T KOG2177|consen 10 LQEELTCPICLEYFREPVLLPCGHNFCRACLTRSWE-------GPLSCPVCRPPSRNLRPNVLLANLVERLRQLR 77 (386)
T ss_pred ccccccChhhHHHhhcCccccccchHhHHHHHHhcC-------CCcCCcccCCchhccCccHHHHHHHHHHHhcC
Confidence 35678999999999999664 89999999743 447999999 4555555566655443
No 20
>KOG1785 consensus Tyrosine kinase negative regulator CBL [Defense mechanisms]
Probab=93.78 E-value=0.026 Score=54.49 Aligned_cols=61 Identities=20% Similarity=0.236 Sum_probs=46.3
Q ss_pred CCCCCCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccc---eeeeecCCCCC
Q 027871 1 MEQNLFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVAS---LVPLYGRGGIS 66 (217)
Q Consensus 1 m~~s~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~---viPLYGRG~~~ 66 (217)
|+..|-=|.||-|..+|.-+. .|=.|+.+|.. +++-+.||-|..+|.-.. |=|.|+|+...
T Consensus 365 MgsTFeLCKICaendKdvkIEPCGHLlCt~CLa~WQ~-----sd~gq~CPFCRcEIKGte~viid~F~pr~~~s 433 (563)
T KOG1785|consen 365 MGSTFELCKICAENDKDVKIEPCGHLLCTSCLAAWQD-----SDEGQTCPFCRCEIKGTEPVIIDPFDPRPVGS 433 (563)
T ss_pred ccchHHHHHHhhccCCCcccccccchHHHHHHHhhcc-----cCCCCCCCceeeEeccccceeeeccCCCccch
Confidence 333444499999999998875 79999999854 345799999999997654 44777877643
No 21
>KOG0287 consensus Postreplication repair protein RAD18 [Replication, recombination and repair]
Probab=93.74 E-value=0.0056 Score=57.83 Aligned_cols=44 Identities=9% Similarity=0.092 Sum_probs=39.0
Q ss_pred CccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccce
Q 027871 6 FEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASL 56 (217)
Q Consensus 6 FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~v 56 (217)
-.|-||+|--+.|++| ||=.||...+. ++++||.|-..+.|..+
T Consensus 24 LRC~IC~eyf~ip~itpCsHtfCSlCIR~~L~-------~~p~CP~C~~~~~Es~L 72 (442)
T KOG0287|consen 24 LRCGICFEYFNIPMITPCSHTFCSLCIRKFLS-------YKPQCPTCCVTVTESDL 72 (442)
T ss_pred HHHhHHHHHhcCceeccccchHHHHHHHHHhc-------cCCCCCceecccchhhh
Confidence 4799999999999998 99999999764 88999999999988543
No 22
>KOG4159 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=93.34 E-value=0.013 Score=56.03 Aligned_cols=44 Identities=14% Similarity=0.203 Sum_probs=37.1
Q ss_pred CCCCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccc
Q 027871 3 QNLFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISV 53 (217)
Q Consensus 3 ~s~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~ 53 (217)
.+.|||+||+++.-+||+| +|=.||.+- + +...+||-|+.++.+
T Consensus 82 ~sef~c~vc~~~l~~pv~tpcghs~c~~Cl~r~---l----d~~~~cp~Cr~~l~e 130 (398)
T KOG4159|consen 82 RSEFECCVCSRALYPPVVTPCGHSFCLECLDRS---L----DQETECPLCRDELVE 130 (398)
T ss_pred cchhhhhhhHhhcCCCccccccccccHHHHHHH---h----ccCCCCccccccccc
Confidence 4679999999999999999 777788772 2 377899999999875
No 23
>KOG4172 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=92.60 E-value=0.0053 Score=44.17 Aligned_cols=42 Identities=21% Similarity=0.263 Sum_probs=30.3
Q ss_pred CCccccccCCCCCcceE------eeCCCCCC-CCCCCCCCCcCCCCCCCccccccc
Q 027871 5 LFEPETGYATEEDASLK------QKWSPTSA-PTNVPEKDDEQQQNCPVCKANISV 53 (217)
Q Consensus 5 ~FeCnICld~A~dpVVT------ycW~ci~~-w~~~~~~~~~~~~~CPVCKa~Vs~ 53 (217)
.=||.||+|.+-|-|+- .|..|-.. |. .-+-+||.|++.|..
T Consensus 7 ~dECTICye~pvdsVlYtCGHMCmCy~Cg~rl~~-------~~~g~CPiCRapi~d 55 (62)
T KOG4172|consen 7 SDECTICYEHPVDSVLYTCGHMCMCYACGLRLKK-------ALHGCCPICRAPIKD 55 (62)
T ss_pred ccceeeeccCcchHHHHHcchHHhHHHHHHHHHH-------ccCCcCcchhhHHHH
Confidence 35999999999999983 56655333 21 145699999998753
No 24
>COG5432 RAD18 RING-finger-containing E3 ubiquitin ligase [Signal transduction mechanisms]
Probab=91.92 E-value=0.026 Score=52.62 Aligned_cols=44 Identities=11% Similarity=0.050 Sum_probs=38.0
Q ss_pred CCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccc
Q 027871 5 LFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVAS 55 (217)
Q Consensus 5 ~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~ 55 (217)
.-.|-||-+.-+.|++| ||-.||..-++ +++-||||.++-.+.-
T Consensus 25 ~lrC~IC~~~i~ip~~TtCgHtFCslCIR~hL~-------~qp~CP~Cr~~~~esr 73 (391)
T COG5432 25 MLRCRICDCRISIPCETTCGHTFCSLCIRRHLG-------TQPFCPVCREDPCESR 73 (391)
T ss_pred HHHhhhhhheeecceecccccchhHHHHHHHhc-------CCCCCccccccHHhhh
Confidence 34699999999999998 99999999765 7899999999876644
No 25
>PF11793 FANCL_C: FANCL C-terminal domain; PDB: 3K1L_A.
Probab=91.66 E-value=0.013 Score=42.84 Aligned_cols=49 Identities=20% Similarity=0.131 Sum_probs=23.7
Q ss_pred CccccccCCCC----CcceE---------eeCCCCCCCCCCCCCCCc----CCCCCCCcccccccc
Q 027871 6 FEPETGYATEE----DASLK---------QKWSPTSAPTNVPEKDDE----QQQNCPVCKANISVA 54 (217)
Q Consensus 6 FeCnICld~A~----dpVVT---------ycW~ci~~w~~~~~~~~~----~~~~CPVCKa~Vs~~ 54 (217)
-||.||++... .|++. |-=.||++|+...++... -.-+||.||..|+-.
T Consensus 3 ~~C~IC~~~~~~~~~~p~~~C~n~~C~~~fH~~CL~~wf~~~~~~~~~~~~~~G~CP~C~~~i~~~ 68 (70)
T PF11793_consen 3 LECGICYSYRLDDGEIPDVVCPNPSCGKKFHLLCLSEWFLSLEKSRQSFIPIFGECPYCSSPISWS 68 (70)
T ss_dssp -S-SSS--SS-TT-----B--S-TT----B-SGGGHHHHHHHHSSS-TTT--EEE-TTT-SEEEGG
T ss_pred CCCCcCCcEecCCCCcCceEcCCcccCCHHHHHHHHHHHHHcccCCeeecccccCCcCCCCeeeEe
Confidence 58999998643 34443 667899999764322111 113699999998753
No 26
>KOG1002 consensus Nucleotide excision repair protein RAD16 [Replication, recombination and repair]
Probab=91.42 E-value=0.018 Score=57.23 Aligned_cols=48 Identities=19% Similarity=0.154 Sum_probs=37.7
Q ss_pred CCCccccccCCCCCcceE-----eeCCCCCCCCCC-CCCCCcCCCCCCCcccccccc
Q 027871 4 NLFEPETGYATEEDASLK-----QKWSPTSAPTNV-PEKDDEQQQNCPVCKANISVA 54 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT-----ycW~ci~~w~~~-~~~~~~~~~~CPVCKa~Vs~~ 54 (217)
+--||-+|.|.|+|+++| ||=.||-..... ++ .+...||||--+++.|
T Consensus 535 ~~~~C~lc~d~aed~i~s~ChH~FCrlCi~eyv~~f~~---~~nvtCP~C~i~LsiD 588 (791)
T KOG1002|consen 535 GEVECGLCHDPAEDYIESSCHHKFCRLCIKEYVESFME---NNNVTCPVCHIGLSID 588 (791)
T ss_pred CceeecccCChhhhhHhhhhhHHHHHHHHHHHHHhhhc---ccCCCCcccccccccc
Confidence 446899999999999998 999999433221 22 3458999999999988
No 27
>PHA02929 N1R/p28-like protein; Provisional
Probab=90.24 E-value=0.21 Score=44.82 Aligned_cols=13 Identities=31% Similarity=1.025 Sum_probs=11.0
Q ss_pred CCCCCCCcccccc
Q 027871 40 QQQNCPVCKANIS 52 (217)
Q Consensus 40 ~~~~CPVCKa~Vs 52 (217)
.+..||+|+..+.
T Consensus 215 ~~~tCPlCR~~~~ 227 (238)
T PHA02929 215 EKNTCPVCRTPFI 227 (238)
T ss_pred cCCCCCCCCCEee
Confidence 4679999999876
No 28
>KOG4362 consensus Transcriptional regulator BRCA1 [Replication, recombination and repair; Transcription]
Probab=89.82 E-value=0.09 Score=53.34 Aligned_cols=43 Identities=16% Similarity=0.278 Sum_probs=35.6
Q ss_pred CCCccccccCCCCCcceE--------eeCCCCCCCCCCCCCCCcCCCCCCCccccccc
Q 027871 4 NLFEPETGYATEEDASLK--------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISV 53 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT--------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~ 53 (217)
..-||.||+....+|+.+ +||.+...|.. ...+|||||+.+++
T Consensus 20 k~lEc~ic~~~~~~p~~~kc~~~~l~~~~n~~f~~~~-------~~~~~~lc~~~~eK 70 (684)
T KOG4362|consen 20 KILECPICLEHVKEPSLLKCDHIFLKFCLNKLFESKK-------GPKQCALCKSDIEK 70 (684)
T ss_pred hhccCCceeEEeeccchhhhhHHHHhhhhhceeeccC-------ccccchhhhhhhhh
Confidence 456999999999999665 79999998754 36899999977765
No 29
>PF12678 zf-rbx1: RING-H2 zinc finger; InterPro: IPR024766 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This domain constitutes a conserved region found in proteins that participate in diverse functions relevant to chromosome metabolism and cell cycle control [].The domain contains 8 cysteine/ histidine residues which are proposed to be the conserved residues involved in zinc binding.; PDB: 4A0C_D 4A0L_I 4A0K_B 2ECL_A 1LDK_C 3RTR_F 3DQV_Y 1U6G_B 1LDJ_B 2HYE_D ....
Probab=87.23 E-value=0.06 Score=39.38 Aligned_cols=35 Identities=20% Similarity=0.308 Sum_probs=24.7
Q ss_pred ccccccCCCCCcceE------------------eeCCCCCCCCCCCCCCCcCCCCCCCcc
Q 027871 7 EPETGYATEEDASLK------------------QKWSPTSAPTNVPEKDDEQQQNCPVCK 48 (217)
Q Consensus 7 eCnICld~A~dpVVT------------------ycW~ci~~w~~~~~~~~~~~~~CPVCK 48 (217)
+|-||++.-.++.+. |-=.||.+|+. .+..||+|+
T Consensus 21 ~C~IC~~~l~~~~~~~~~~~~~~~i~~~~C~H~FH~~Ci~~Wl~-------~~~~CP~CR 73 (73)
T PF12678_consen 21 NCAICREPLEDPCPECQAPQDECPIVWGPCGHIFHFHCISQWLK-------QNNTCPLCR 73 (73)
T ss_dssp BETTTTSBTTSTTCCHHHCTTTS-EEEETTSEEEEHHHHHHHHT-------TSSB-TTSS
T ss_pred cccccChhhhChhhhhcCCccccceEecccCCCEEHHHHHHHHh-------cCCcCCCCC
Confidence 499999987555432 56678888875 445999996
No 30
>PF12861 zf-Apc11: Anaphase-promoting complex subunit 11 RING-H2 finger
Probab=86.69 E-value=0.16 Score=39.10 Aligned_cols=45 Identities=11% Similarity=0.129 Sum_probs=33.2
Q ss_pred CCCc--cccccCCCCC-cceE------eeCCCCCCCCCCCCCCCcCCCCCCCcccccc
Q 027871 4 NLFE--PETGYATEED-ASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCKANIS 52 (217)
Q Consensus 4 s~Fe--CnICld~A~d-pVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs 52 (217)
..|| |..|.--..| |+|. |-..||.+|+..+ +.+++||-|.....
T Consensus 29 ~~fdg~Cp~Ck~Pgd~Cplv~g~C~H~FH~hCI~kWl~~~----~~~~~CPmCR~~w~ 82 (85)
T PF12861_consen 29 MPFDGCCPDCKFPGDDCPLVWGKCSHNFHMHCILKWLSTQ----SSKGQCPMCRQPWK 82 (85)
T ss_pred cccccCCCCccCCCCCCceeeccCccHHHHHHHHHHHccc----cCCCCCCCcCCeee
Confidence 3466 7788777666 7775 7789999998743 34689999987643
No 31
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=85.77 E-value=0.15 Score=46.53 Aligned_cols=51 Identities=12% Similarity=0.124 Sum_probs=31.7
Q ss_pred CCCccccccCCCCCcceEeeCCCCCC--CCCCCCCCCcCCCC-CCCcccccccccee
Q 027871 4 NLFEPETGYATEEDASLKQKWSPTSA--PTNVPEKDDEQQQN-CPVCKANISVASLV 57 (217)
Q Consensus 4 s~FeCnICld~A~dpVVTycW~ci~~--w~~~~~~~~~~~~~-CPVCKa~Vs~~~vi 57 (217)
..|+|-||+|.+.+|+-|-|=- |.- =+.-+ --....+ ||+|.+.+...+||
T Consensus 214 ~d~kC~lC~e~~~~ps~t~CgH-lFC~~Cl~~~--~t~~k~~~CplCRak~~pk~vi 267 (271)
T COG5574 214 ADYKCFLCLEEPEVPSCTPCGH-LFCLSCLLIS--WTKKKYEFCPLCRAKVYPKKVI 267 (271)
T ss_pred cccceeeeecccCCcccccccc-hhhHHHHHHH--HHhhccccCchhhhhccchhhh
Confidence 4799999999999999980000 000 00000 0014445 99999999988875
No 32
>smart00744 RINGv The RING-variant domain is a C4HC3 zinc-finger like motif found in a number of cellular and viral proteins. Some of these proteins have been shown both in vivo and in vitro to have ubiquitin E3 ligase activity. The RING-variant domain is reminiscent of both the RING and the PHD domains and may represent an evolutionary intermediate. To describe this domain the term PHD/LAP domain has been used in the past. Extended description: The RING-variant (RINGv) domain contains a C4HC3 zinc-finger-like motif similar to the PHD domain, while some of the spacing between the Cys/His residues follow a pattern somewhat closer to that found in the RING domain. The RINGv domain, similar to the RING, PHD and LIM domains, is thought to bind two zinc ions co-ordinated by the highly conserved Cys and His residues. RING variant domain: C-x (2) -C-x(10-45)-C-x (1) -C-x (7) -H-x(2)-C-x(11-25)-C-x(2)-C As opposed to a PHD: C-x(1-2) -C-x (7-13)-C-x(2-4)-C-x(4-5)-H-x(2)-C-x(10-21)-C-x(2)-C Class
Probab=84.60 E-value=0.12 Score=35.39 Aligned_cols=36 Identities=17% Similarity=0.157 Sum_probs=25.9
Q ss_pred cccccC--CCCCcceEee----------CCCCCCCCCCCCCCCcCCCCCCCcc
Q 027871 8 PETGYA--TEEDASLKQK----------WSPTSAPTNVPEKDDEQQQNCPVCK 48 (217)
Q Consensus 8 CnICld--~A~dpVVTyc----------W~ci~~w~~~~~~~~~~~~~CPVCK 48 (217)
|-||++ .+.++.++.| =.|+.+|+... ....||+||
T Consensus 2 CrIC~~~~~~~~~l~~PC~C~G~~~~vH~~Cl~~W~~~~-----~~~~C~iC~ 49 (49)
T smart00744 2 CRICHDEGDEGDPLVSPCRCKGSLKYVHQECLERWINES-----GNKTCEICK 49 (49)
T ss_pred ccCCCCCCCCCCeeEeccccCCchhHHHHHHHHHHHHHc-----CCCcCCCCC
Confidence 889997 7778888743 25677887532 446999997
No 33
>KOG0824 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=82.36 E-value=0.62 Score=43.50 Aligned_cols=44 Identities=16% Similarity=0.131 Sum_probs=34.0
Q ss_pred CCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCcccccccc
Q 027871 5 LFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVA 54 (217)
Q Consensus 5 ~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~ 54 (217)
.=||-||+-+-.-||.- ||..||---. + .+...|+||..+|.++
T Consensus 7 ~~eC~IC~nt~n~Pv~l~C~HkFCyiCiKGsy-~-----ndk~~CavCR~pids~ 55 (324)
T KOG0824|consen 7 KKECLICYNTGNCPVNLYCFHKFCYICIKGSY-K-----NDKKTCAVCRFPIDST 55 (324)
T ss_pred CCcceeeeccCCcCccccccchhhhhhhcchh-h-----cCCCCCceecCCCCcc
Confidence 45899999999999764 8999997521 1 2557899998888764
No 34
>TIGR01294 P_lamban phospholamban. This model represents the short (52 residue) transmembrane phosphoprotein phospholamban. Phospholamban, in its unphosphorylated form, inhibits SERCA2, the cardiac sarcoplasmic reticulum Ca-ATPase.
Probab=80.19 E-value=2.5 Score=29.42 Aligned_cols=25 Identities=28% Similarity=0.630 Sum_probs=12.2
Q ss_pred CChhhhhhhhHHHHhhhhHHHHHHHHHHHHHhh
Q 027871 184 NNPRIRRQEMELDKSLNRVSLFLFCCLVLCLLL 216 (217)
Q Consensus 184 ~spR~Rrq~mq~d~sL~ri~~Fl~ccvvLCLll 216 (217)
.+|..||..++ +|.=||++++||||
T Consensus 20 ~~~qar~~lq~--------lfvnf~liliclll 44 (52)
T TIGR01294 20 MPQQARQNLQN--------LFINFCLILICLLL 44 (52)
T ss_pred CCHHHHHHHHH--------HHHHHHHHHHHHHH
Confidence 55665555432 23344555555543
No 35
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=80.11 E-value=0.35 Score=42.04 Aligned_cols=57 Identities=11% Similarity=0.293 Sum_probs=34.9
Q ss_pred CCCCccccccCCCCCcc-eEeeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeee
Q 027871 3 QNLFEPETGYATEEDAS-LKQKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLY 60 (217)
Q Consensus 3 ~s~FeCnICld~A~dpV-VTycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLY 60 (217)
+..|.|-||+|...+-| |.=+-.|+.= ..=..++-+....||+|.-.|++.-+++||
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC-~~Cik~alk~~~~CP~C~kkIt~k~~~rI~ 186 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFC-SQCIKDALKNTNKCPTCRKKITHKQFHRIY 186 (187)
T ss_pred ccccCCCceecchhhccccccccchhHH-HHHHHHHHHhCCCCCCcccccchhhheecc
Confidence 56799999999776655 4100000000 000000124668999999999999999998
No 36
>PF04641 Rtf2: Rtf2 RING-finger
Probab=78.21 E-value=1.3 Score=39.57 Aligned_cols=61 Identities=15% Similarity=0.179 Sum_probs=40.2
Q ss_pred CCCCccccccCCCCCcceE--eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeeecCCC
Q 027871 3 QNLFEPETGYATEEDASLK--QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLYGRGG 64 (217)
Q Consensus 3 ~s~FeCnICld~A~dpVVT--ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLYGRG~ 64 (217)
...|-|-|.+..- ..-.. |-|+|=+..+..--++-.....||||-...+++.||||-+-+.
T Consensus 111 ~~~~~CPvt~~~~-~~~~~fv~l~~cG~V~s~~alke~k~~~~Cp~c~~~f~~~DiI~Lnp~~e 173 (260)
T PF04641_consen 111 EGRFICPVTGKEF-NGKHKFVYLRPCGCVFSEKALKELKKSKKCPVCGKPFTEEDIIPLNPPEE 173 (260)
T ss_pred CceeECCCCCccc-CCceeEEEEcCCCCEeeHHHHHhhcccccccccCCccccCCEEEecCCcc
Confidence 4567788876554 22222 7799887743211000112347999999999999999999776
No 37
>PF04272 Phospholamban: Phospholamban; InterPro: IPR005984 Phospholamban (PLB) is a small protein (52 amino acids) that regulates the affinity of the cardiac sarcoplasmic reticulum Ca2+-ATPase (SERCA2a) for calcium. PLB is present in cardiac myocytes, in slow-twitch and smooth muscle and is expressed also in aorta endothelial cells in which it could play a role in tissue relaxation. The phosphorylation/dephosphorylation of phospholamban removes and restores, respectively, its inhibitory activity on SERCA2a. It has in fact been shown that phospholamban, in its non-phosphorylated form, binds to SERCA2a and inhibits this pump by lowering its affinity for Ca2+, whereas the phosphorylated form does not exert the inhibition. PLB is phosphorylated at two sites, namely at Ser-16 for a cAMP-dependent phosphokinase and at Thr-17 for a Ca2+/calmodulin-dependent phosphokinase, phosphorylation at Ser-16 being a prerequisite for the phosphorylation at Thr-17. The structure of a 36-amino-acid-long N-terminal fragment of human phospholamban phosphorylated at Ser-16 and Thr-17 and Cys36Ser mutated was determined from nuclear magnetic resonance data. The peptide assumes a conformation characterised by two alpha-helices connected by an irregular strand, which comprises the amino acids from Arg-13 to Pro-21. The proline is in a trans conformation. The two phosphate groups on Ser-16 and Thr-17 are shown to interact preferably with the side chains of Arg-14 and Arg-13, respectively [].; GO: 0005246 calcium channel regulator activity, 0042030 ATPase inhibitor activity, 0006816 calcium ion transport, 0016020 membrane; PDB: 1N7L_A 1FJP_A 1FJK_A 2HYN_C 1ZLL_D 1PLP_A 3O7L_I.
Probab=74.11 E-value=5 Score=27.95 Aligned_cols=13 Identities=46% Similarity=1.203 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHhh
Q 027871 204 LFLFCCLVLCLLL 216 (217)
Q Consensus 204 ~Fl~ccvvLCLll 216 (217)
|.=||++++||||
T Consensus 32 fvnfcliliclll 44 (52)
T PF04272_consen 32 FVNFCLILICLLL 44 (52)
T ss_dssp HHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH
Confidence 4445666666654
No 38
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.00 E-value=1.8 Score=40.37 Aligned_cols=40 Identities=13% Similarity=0.032 Sum_probs=33.2
Q ss_pred CCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccc
Q 027871 5 LFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANI 51 (217)
Q Consensus 5 ~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~V 51 (217)
.|.|-||-..=.+|||| ||=.|-.+- +.....|.||-..+
T Consensus 241 Pf~c~icr~~f~~pVvt~c~h~fc~~ca~~~-------~qk~~~c~vC~~~t 285 (313)
T KOG1813|consen 241 PFKCFICRKYFYRPVVTKCGHYFCEVCALKP-------YQKGEKCYVCSQQT 285 (313)
T ss_pred CccccccccccccchhhcCCceeehhhhccc-------cccCCcceeccccc
Confidence 69999999999999998 888887773 34558999997654
No 39
>KOG1039 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=72.85 E-value=1.3 Score=41.74 Aligned_cols=49 Identities=12% Similarity=0.160 Sum_probs=34.9
Q ss_pred CCCccccccCCCCCcc-----e------E--eeCCCCCCCCCCCCCCCcCCCCCCCcccccc
Q 027871 4 NLFEPETGYATEEDAS-----L------K--QKWSPTSAPTNVPEKDDEQQQNCPVCKANIS 52 (217)
Q Consensus 4 s~FeCnICld~A~dpV-----V------T--ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs 52 (217)
+..+|-||+|.-.+.+ . + ||=.||..|-...-.+..-.+-||-|+...+
T Consensus 160 ~~k~CGICme~i~ek~~~~~rfgilpnC~H~~Cl~Cir~wr~~~q~~~~~sksCP~CRv~s~ 221 (344)
T KOG1039|consen 160 SEKECGICMETINEKAASERRFGILPNCNHSFCLNCIRKWRQATQFESKTSKSCPFCRVPSS 221 (344)
T ss_pred ccccceehhhhccccchhhhhcccCCCcchhhhhcHhHhhhhhhccccccccCCCcccCccc
Confidence 4789999999999988 2 1 8999999996432112223588999985543
No 40
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=72.45 E-value=1.3 Score=41.36 Aligned_cols=48 Identities=13% Similarity=0.095 Sum_probs=32.6
Q ss_pred CCCCCCccccccCC---CCCcc--e--E---eeCCCCCCCCCCCCCCCcCCCCCCCccccccccce
Q 027871 1 MEQNLFEPETGYAT---EEDAS--L--K---QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASL 56 (217)
Q Consensus 1 m~~s~FeCnICld~---A~dpV--V--T---ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~v 56 (217)
||+ ..|-||... ..+-. | | ||=.||..... .....||+|+..+...++
T Consensus 1 md~--~~CP~Ck~~~y~np~~kl~i~~CGH~~C~sCv~~l~~------~~~~~CP~C~~~lrk~~f 58 (309)
T TIGR00570 1 MDD--QGCPRCKTTKYRNPSLKLMVNVCGHTLCESCVDLLFV------RGSGSCPECDTPLRKNNF 58 (309)
T ss_pred CCC--CCCCcCCCCCccCcccccccCCCCCcccHHHHHHHhc------CCCCCCCCCCCccchhhc
Confidence 444 689999984 44422 2 2 88888888321 134689999998888773
No 41
>KOG0297 consensus TNF receptor-associated factor [Signal transduction mechanisms]
Probab=69.49 E-value=3.2 Score=39.36 Aligned_cols=48 Identities=17% Similarity=0.221 Sum_probs=40.8
Q ss_pred CCCccccccCCCCCcceE------eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceee
Q 027871 4 NLFEPETGYATEEDASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVP 58 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viP 58 (217)
....|-||-.+-.||+-| ||=.|+..|+. .++.||||-.++.....+|
T Consensus 20 ~~l~C~~C~~vl~~p~~~~~cgh~fC~~C~~~~~~-------~~~~cp~~~~~~~~~~~~~ 73 (391)
T KOG0297|consen 20 ENLLCPICMSVLRDPVQTTTCGHRFCAGCLLESLS-------NHQKCPVCRQELTQAEELP 73 (391)
T ss_pred ccccCccccccccCCCCCCCCCCcccccccchhhc-------cCcCCcccccccchhhccC
Confidence 357899999999999994 99999999975 4899999987777777766
No 42
>KOG1001 consensus Helicase-like transcription factor HLTF/DNA helicase RAD5, DEAD-box superfamily [Transcription; Replication, recombination and repair]
Probab=68.97 E-value=0.93 Score=46.12 Aligned_cols=46 Identities=9% Similarity=0.109 Sum_probs=33.9
Q ss_pred CccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCcccccccccee
Q 027871 6 FEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLV 57 (217)
Q Consensus 6 FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~vi 57 (217)
++|.||.| ...+|+| +|=.|+..-..- ++...||.|++.+.+++++
T Consensus 455 ~~c~ic~~-~~~~~it~c~h~~c~~c~~~~i~~-----~~~~~~~~cr~~l~~~~l~ 505 (674)
T KOG1001|consen 455 HWCHICCD-LDSFFITRCGHDFCVECLKKSIQQ-----SENAPCPLCRNVLKEKKLL 505 (674)
T ss_pred cccccccc-cccceeecccchHHHHHHHhcccc-----ccCCCCcHHHHHHHHHHHh
Confidence 89999999 8888888 454444443222 2334999999999998864
No 43
>KOG1645 consensus RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=67.50 E-value=0.49 Score=45.81 Aligned_cols=51 Identities=12% Similarity=0.152 Sum_probs=40.6
Q ss_pred ccccccCCCCCcceE----------eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeeecC
Q 027871 7 EPETGYATEEDASLK----------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLYGR 62 (217)
Q Consensus 7 eCnICld~A~dpVVT----------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLYGR 62 (217)
-|.||||.-.-|+=+ |==.||-.|+. .....+||-||++-.+..|-|+|--
T Consensus 6 tcpiclds~~~~g~hr~vsl~cghlFgs~cie~wl~-----k~~~~~cp~c~~katkr~i~~e~al 66 (463)
T KOG1645|consen 6 TCPICLDSYTTAGNHRIVSLQCGHLFGSQCIEKWLG-----KKTKMQCPLCSGKATKRQIRPEYAL 66 (463)
T ss_pred cCceeeeeeeecCceEEeeecccccccHHHHHHHHh-----hhhhhhCcccCChhHHHHHHHHHHH
Confidence 499999976666533 55677888874 2467899999999999999999984
No 44
>KOG3113 consensus Uncharacterized conserved protein [Function unknown]
Probab=67.36 E-value=2 Score=39.49 Aligned_cols=39 Identities=15% Similarity=0.218 Sum_probs=29.3
Q ss_pred eeCCCCCCCCCCCCCCCcC--CCCCCCccccccccceeeeecCC
Q 027871 22 QKWSPTSAPTNVPEKDDEQ--QQNCPVCKANISVASLVPLYGRG 63 (217)
Q Consensus 22 ycW~ci~~w~~~~~~~~~~--~~~CPVCKa~Vs~~~viPLYGRG 63 (217)
+.|.|-+..+. ++-.+ ...|+||-|.++++.||+|-|.-
T Consensus 129 ~l~~CGcV~Se---rAlKeikas~C~~C~a~y~~~dvIvlNg~~ 169 (293)
T KOG3113|consen 129 ALRCCGCVFSE---RALKEIKASVCHVCGAAYQEDDVIVLNGTE 169 (293)
T ss_pred EEeccceeccH---HHHHHhhhccccccCCcccccCeEeeCCCH
Confidence 57999887543 22222 37899999999999999998843
No 45
>COG5243 HRD1 HRD ubiquitin ligase complex, ER membrane component [Posttranslational modification, protein turnover, chaperones]
Probab=67.33 E-value=0.83 Score=44.08 Aligned_cols=39 Identities=13% Similarity=0.255 Sum_probs=25.6
Q ss_pred ccccccCC----CCCcceE--------------eeCCCCCCCCCCCCCCCcCCCCCCCcccccc
Q 027871 7 EPETGYAT----EEDASLK--------------QKWSPTSAPTNVPEKDDEQQQNCPVCKANIS 52 (217)
Q Consensus 7 eCnICld~----A~dpVVT--------------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs 52 (217)
-|-||.|. ..+|.-. +--.|+-.|.. .+|.||.||..|-
T Consensus 289 ~C~ICmde~~h~~~~~~~~~~~~~pKrLpCGHilHl~CLknW~E-------RqQTCPICr~p~i 345 (491)
T COG5243 289 TCTICMDEMFHPDHEPLPRGLDMTPKRLPCGHILHLHCLKNWLE-------RQQTCPICRRPVI 345 (491)
T ss_pred eEEEecccccCCCCccCcccccCCcccccccceeeHHHHHHHHH-------hccCCCcccCccc
Confidence 48999886 2233322 34556667754 5699999998753
No 46
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=64.74 E-value=1.1 Score=40.07 Aligned_cols=41 Identities=12% Similarity=0.011 Sum_probs=34.3
Q ss_pred CCCccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccc
Q 027871 4 NLFEPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANI 51 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~V 51 (217)
=.|-|-||-+.-+.|||| ||=+|... .+..-.+|-||-++.
T Consensus 195 IPF~C~iCKkdy~spvvt~CGH~FC~~Cai~-------~y~kg~~C~~Cgk~t 240 (259)
T COG5152 195 IPFLCGICKKDYESPVVTECGHSFCSLCAIR-------KYQKGDECGVCGKAT 240 (259)
T ss_pred CceeehhchhhccchhhhhcchhHHHHHHHH-------HhccCCcceecchhh
Confidence 479999999999999999 88888776 345678999997653
No 47
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=63.05 E-value=4 Score=31.32 Aligned_cols=26 Identities=31% Similarity=0.704 Sum_probs=23.0
Q ss_pred CCCCCCCccccccccceeeeec----CCCC
Q 027871 40 QQQNCPVCKANISVASLVPLYG----RGGI 65 (217)
Q Consensus 40 ~~~~CPVCKa~Vs~~~viPLYG----RG~~ 65 (217)
.+..||.|+..+.--.+|||.| ||+.
T Consensus 32 ~rS~C~~C~~~L~~~~lIPi~S~l~lrGrC 61 (92)
T PF06750_consen 32 PRSHCPHCGHPLSWWDLIPILSYLLLRGRC 61 (92)
T ss_pred CCCcCcCCCCcCcccccchHHHHHHhCCCC
Confidence 5689999999999999999987 6765
No 48
>KOG0802 consensus E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=62.28 E-value=0.79 Score=44.95 Aligned_cols=48 Identities=17% Similarity=0.048 Sum_probs=35.2
Q ss_pred CccccccCCCCC------cceE----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeee
Q 027871 6 FEPETGYATEED------ASLK----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLY 60 (217)
Q Consensus 6 FeCnICld~A~d------pVVT----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLY 60 (217)
=.|-||.|.=.. +.+. |+=.|+.+|+. ..+.||.|+..+....++=+.
T Consensus 292 ~~C~IC~e~l~~~~~~~~~rL~C~Hifh~~CL~~W~e-------r~qtCP~CR~~~~~~~~~~~~ 349 (543)
T KOG0802|consen 292 ELCIICLEELHSGHNITPKRLPCGHIFHDSCLRSWFE-------RQQTCPTCRTVLYDYVLWQIA 349 (543)
T ss_pred CeeeeechhhccccccccceeecccchHHHHHHHHHH-------HhCcCCcchhhhhcccccccc
Confidence 369999996555 3444 88889999875 468999999977666554333
No 49
>PHA02862 5L protein; Provisional
Probab=60.35 E-value=1.6 Score=37.05 Aligned_cols=45 Identities=13% Similarity=0.163 Sum_probs=33.3
Q ss_pred ccccccCCCCCcceE-------eeC---CCCCCCCCCCCCCCcCCCCCCCccccccccceeeee
Q 027871 7 EPETGYATEEDASLK-------QKW---SPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLY 60 (217)
Q Consensus 7 eCnICld~A~dpVVT-------ycW---~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLY 60 (217)
.|=||++.++|.+ . ..| .|+.+|++. +....|+-||.+-. +.+.|
T Consensus 4 iCWIC~~~~~e~~-~PC~C~GS~K~VHq~CL~~WIn~-----S~k~~CeLCkteY~---Ik~~y 58 (156)
T PHA02862 4 ICWICNDVCDERN-NFCGCNEEYKVVHIKCMQLWINY-----SKKKECNLCKTKYN---IKKTY 58 (156)
T ss_pred EEEEecCcCCCCc-ccccccCcchhHHHHHHHHHHhc-----CCCcCccCCCCeEE---EEEcc
Confidence 5899999987763 4 335 578889863 57899999998764 44444
No 50
>PRK11827 hypothetical protein; Provisional
Probab=56.43 E-value=5 Score=28.99 Aligned_cols=15 Identities=27% Similarity=0.707 Sum_probs=11.9
Q ss_pred CCCCCCCcccccccc
Q 027871 40 QQQNCPVCKANISVA 54 (217)
Q Consensus 40 ~~~~CPVCKa~Vs~~ 54 (217)
+--.||+||+.+..+
T Consensus 7 eILaCP~ckg~L~~~ 21 (60)
T PRK11827 7 EIIACPVCNGKLWYN 21 (60)
T ss_pred hheECCCCCCcCeEc
Confidence 456899999988654
No 51
>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=55.09 E-value=3.5 Score=28.23 Aligned_cols=13 Identities=23% Similarity=0.749 Sum_probs=7.3
Q ss_pred CCCCccccccccc
Q 027871 43 NCPVCKANISVAS 55 (217)
Q Consensus 43 ~CPVCKa~Vs~~~ 55 (217)
.||||...++++.
T Consensus 22 ~CPlC~r~l~~e~ 34 (54)
T PF04423_consen 22 CCPLCGRPLDEEH 34 (54)
T ss_dssp E-TTT--EE-HHH
T ss_pred cCCCCCCCCCHHH
Confidence 8999999988753
No 52
>PRK15178 Vi polysaccharide export inner membrane protein VexD; Provisional
Probab=54.26 E-value=13 Score=36.15 Aligned_cols=27 Identities=26% Similarity=0.429 Sum_probs=21.3
Q ss_pred hhhhhHHHHhhhhHHHHHHHHHHHHHh
Q 027871 189 RRQEMELDKSLNRVSLFLFCCLVLCLL 215 (217)
Q Consensus 189 Rrq~mq~d~sL~ri~~Fl~ccvvLCLl 215 (217)
-|+.+|++++|+|+++|+++-.++..+
T Consensus 71 ~~~~~~~~~~~~rl~~~VllPtlla~~ 97 (434)
T PRK15178 71 ERRVQQAKQSLRRLFLYIALPLLVIML 97 (434)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999998887777776654
No 53
>KOG0804 consensus Cytoplasmic Zn-finger protein BRAP2 (BRCA1 associated protein) [General function prediction only]
Probab=54.01 E-value=4.5 Score=39.78 Aligned_cols=39 Identities=21% Similarity=0.156 Sum_probs=27.0
Q ss_pred CCccccccCCCCCcc---eE-eeC-----CCCCCCCCCCCCCCcCCCCCCCcccccc
Q 027871 5 LFEPETGYATEEDAS---LK-QKW-----SPTSAPTNVPEKDDEQQQNCPVCKANIS 52 (217)
Q Consensus 5 ~FeCnICld~A~dpV---VT-ycW-----~ci~~w~~~~~~~~~~~~~CPVCKa~Vs 52 (217)
.--|-+|||.-.+-| || .|| .|+..|.. ..||||.=--+
T Consensus 175 LPTCpVCLERMD~s~~gi~t~~c~Hsfh~~cl~~w~~---------~scpvcR~~q~ 222 (493)
T KOG0804|consen 175 LPTCPVCLERMDSSTTGILTILCNHSFHCSCLMKWWD---------SSCPVCRYCQS 222 (493)
T ss_pred CCCcchhHhhcCccccceeeeecccccchHHHhhccc---------CcChhhhhhcC
Confidence 346999998766555 77 555 67778743 58999975444
No 54
>cd00350 rubredoxin_like Rubredoxin_like; nonheme iron binding domain containing a [Fe(SCys)4] center. The family includes rubredoxins, a small electron transfer protein, and a slightly smaller modular rubredoxin domain present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=53.80 E-value=7.8 Score=24.21 Aligned_cols=11 Identities=45% Similarity=0.881 Sum_probs=8.4
Q ss_pred CCCCCCCcccc
Q 027871 40 QQQNCPVCKAN 50 (217)
Q Consensus 40 ~~~~CPVCKa~ 50 (217)
....||+|++.
T Consensus 16 ~~~~CP~Cg~~ 26 (33)
T cd00350 16 APWVCPVCGAP 26 (33)
T ss_pred CCCcCcCCCCc
Confidence 34599999874
No 55
>PF03119 DNA_ligase_ZBD: NAD-dependent DNA ligase C4 zinc finger domain; InterPro: IPR004149 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in NAD-dependent DNA ligases. DNA ligases catalyse the crucial step of joining the breaks in duplex DNA during DNA replication, repair and recombination, utilizing either ATP or NAD(+) as a cofactor []. This domain is a small zinc binding motif that is presumably DNA binding. It is found only in NAD-dependent DNA ligases. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair; PDB: 1DGS_A 1V9P_B 2OWO_A.
Probab=52.97 E-value=5.8 Score=24.29 Aligned_cols=11 Identities=36% Similarity=1.063 Sum_probs=6.3
Q ss_pred CCCCccccccc
Q 027871 43 NCPVCKANISV 53 (217)
Q Consensus 43 ~CPVCKa~Vs~ 53 (217)
.||||.+.+.+
T Consensus 1 ~CP~C~s~l~~ 11 (28)
T PF03119_consen 1 TCPVCGSKLVR 11 (28)
T ss_dssp B-TTT--BEEE
T ss_pred CcCCCCCEeEc
Confidence 59999998873
No 56
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=51.72 E-value=8.2 Score=35.86 Aligned_cols=21 Identities=19% Similarity=0.705 Sum_probs=19.0
Q ss_pred CCCCCCCccccccccceeeee
Q 027871 40 QQQNCPVCKANISVASLVPLY 60 (217)
Q Consensus 40 ~~~~CPVCKa~Vs~~~viPLY 60 (217)
+..+||+|...+...+||=||
T Consensus 272 ek~eCPlCR~~~~pskvi~Lr 292 (293)
T KOG0317|consen 272 EKAECPLCREKFQPSKVICLR 292 (293)
T ss_pred cccCCCcccccCCCcceeeec
Confidence 779999999999999999765
No 57
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=51.51 E-value=9.5 Score=23.96 Aligned_cols=30 Identities=13% Similarity=0.285 Sum_probs=17.7
Q ss_pred eeCCCCCCCCCCCCCCCcCCCCCCCccccc
Q 027871 22 QKWSPTSAPTNVPEKDDEQQQNCPVCKANI 51 (217)
Q Consensus 22 ycW~ci~~w~~~~~~~~~~~~~CPVCKa~V 51 (217)
.|+.|=..|..+..........||.|.+++
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~~~ 36 (41)
T smart00834 7 RCEDCGHTFEVLQKISDDPLATCPECGGDV 36 (41)
T ss_pred EcCCCCCEEEEEEecCCCCCCCCCCCCCcc
Confidence 366666654433222224667899999865
No 58
>PF07800 DUF1644: Protein of unknown function (DUF1644); InterPro: IPR012866 This family consists of sequences found in a number of hypothetical plant proteins of unknown function. The region of interest contains nine highly conserved cysteine residues and is approximately 160 amino acids in length, which probably represent a zinc-binding domain.
Probab=51.14 E-value=12 Score=32.00 Aligned_cols=18 Identities=22% Similarity=0.724 Sum_probs=15.7
Q ss_pred CCCCCCCcccccccccee
Q 027871 40 QQQNCPVCKANISVASLV 57 (217)
Q Consensus 40 ~~~~CPVCKa~Vs~~~vi 57 (217)
....||-|.|+|..-+||
T Consensus 79 ~~L~CPLCRG~V~GWtvv 96 (162)
T PF07800_consen 79 PELACPLCRGEVKGWTVV 96 (162)
T ss_pred ccccCccccCceeceEEc
Confidence 468999999999988876
No 59
>PF03908 Sec20: Sec20; InterPro: IPR005606 Sec20 is a membrane glycoprotein associated with secretory pathway.
Probab=50.01 E-value=26 Score=26.33 Aligned_cols=27 Identities=26% Similarity=0.448 Sum_probs=18.5
Q ss_pred hhhhhHHHHhhhhHHHHHHHHHHHHHhh
Q 027871 189 RRQEMELDKSLNRVSLFLFCCLVLCLLL 216 (217)
Q Consensus 189 Rrq~mq~d~sL~ri~~Fl~ccvvLCLll 216 (217)
.|++. .||-+=.+.|++|+|+++-+|+
T Consensus 63 ~r~~~-~D~~li~~~~~~f~~~v~yI~~ 89 (92)
T PF03908_consen 63 ERRDK-TDRILIFFAFLFFLLVVLYILW 89 (92)
T ss_pred HHHHH-HhHHHHHHHHHHHHHHHHHHhh
Confidence 44433 5888877888888888776653
No 60
>PF14169 YdjO: Cold-inducible protein YdjO
Probab=48.99 E-value=11 Score=27.22 Aligned_cols=38 Identities=24% Similarity=0.516 Sum_probs=24.2
Q ss_pred EeeCCCCCC----CCCCCCCCCcCCCCCCCcccccccc-ceeee
Q 027871 21 KQKWSPTSA----PTNVPEKDDEQQQNCPVCKANISVA-SLVPL 59 (217)
Q Consensus 21 TycW~ci~~----w~~~~~~~~~~~~~CPVCKa~Vs~~-~viPL 59 (217)
|--|.|... |-- -+-..++.+.||-||+....+ +++|+
T Consensus 16 t~VW~Ct~e~C~gWmR-~nFs~~~~p~CPlC~s~M~~~~r~Lp~ 58 (59)
T PF14169_consen 16 TKVWECTSEDCNGWMR-DNFSFEEEPVCPLCKSPMVSGTRMLPV 58 (59)
T ss_pred eeeEEeCCCCCCcccc-cccccCCCccCCCcCCccccceeeccc
Confidence 467887763 321 133445779999999997663 46553
No 61
>smart00734 ZnF_Rad18 Rad18-like CCHC zinc finger. Yeast Rad18p functions with Rad5p in error-free post-replicative DNA repair. This zinc finger is likely to bind nucleic-acids.
Probab=48.88 E-value=6.2 Score=23.70 Aligned_cols=14 Identities=29% Similarity=0.700 Sum_probs=10.2
Q ss_pred CCCCCccccccccc
Q 027871 42 QNCPVCKANISVAS 55 (217)
Q Consensus 42 ~~CPVCKa~Vs~~~ 55 (217)
-+||||-..|++..
T Consensus 2 v~CPiC~~~v~~~~ 15 (26)
T smart00734 2 VQCPVCFREVPENL 15 (26)
T ss_pred CcCCCCcCcccHHH
Confidence 37999988875543
No 62
>KOG4265 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=48.40 E-value=9.5 Score=36.27 Aligned_cols=56 Identities=18% Similarity=0.234 Sum_probs=34.1
Q ss_pred CCCCccccccCCCCCcceEee-CCCCCCCCC--CCCCCCcCCCCCCCccccccccceeeeecCCC
Q 027871 3 QNLFEPETGYATEEDASLKQK-WSPTSAPTN--VPEKDDEQQQNCPVCKANISVASLVPLYGRGG 64 (217)
Q Consensus 3 ~s~FeCnICld~A~dpVVTyc-W~ci~~w~~--~~~~~~~~~~~CPVCKa~Vs~~~viPLYGRG~ 64 (217)
++.=||=||++..+|-||-=| =.|+-+-=. .+ -++..||+|...|.+ ++=||..+.
T Consensus 288 ~~gkeCVIClse~rdt~vLPCRHLCLCs~Ca~~Lr----~q~n~CPICRqpi~~--ll~i~~~~~ 346 (349)
T KOG4265|consen 288 ESGKECVICLSESRDTVVLPCRHLCLCSGCAKSLR----YQTNNCPICRQPIEE--LLEIYVNKE 346 (349)
T ss_pred cCCCeeEEEecCCcceEEecchhhehhHhHHHHHH----HhhcCCCccccchHh--hheeccccc
Confidence 567799999999999999611 111111000 00 134679999999876 344555443
No 63
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=47.98 E-value=9 Score=23.17 Aligned_cols=13 Identities=31% Similarity=0.912 Sum_probs=9.4
Q ss_pred CCCCCcccccccc
Q 027871 42 QNCPVCKANISVA 54 (217)
Q Consensus 42 ~~CPVCKa~Vs~~ 54 (217)
+.||.|.+.|..+
T Consensus 1 K~CP~C~~~V~~~ 13 (26)
T PF10571_consen 1 KTCPECGAEVPES 13 (26)
T ss_pred CcCCCCcCCchhh
Confidence 4688888888654
No 64
>KOG0311 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=45.48 E-value=1 Score=42.93 Aligned_cols=41 Identities=7% Similarity=0.078 Sum_probs=31.8
Q ss_pred CCCccccccCCCCCcceE------eeCCCCCCCCCCCCCCCcCCCCCCCcccc
Q 027871 4 NLFEPETGYATEEDASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCKAN 50 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~ 50 (217)
..|-|.|||++-+...-| ||-.||..-+- ....+||-||-.
T Consensus 42 ~~v~c~icl~llk~tmttkeClhrfc~~ci~~a~r------~gn~ecptcRk~ 88 (381)
T KOG0311|consen 42 IQVICPICLSLLKKTMTTKECLHRFCFDCIWKALR------SGNNECPTCRKK 88 (381)
T ss_pred hhhccHHHHHHHHhhcccHHHHHHHHHHHHHHHHH------hcCCCCchHHhh
Confidence 357899999998887776 89999976432 356899999754
No 65
>KOG1734 consensus Predicted RING-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=43.23 E-value=6.4 Score=36.67 Aligned_cols=46 Identities=20% Similarity=0.304 Sum_probs=28.8
Q ss_pred ccccccC-----CCCCcceE--eeCC--------CCCCCCCCCCCCCcCCCCCCCcccccccccee
Q 027871 7 EPETGYA-----TEEDASLK--QKWS--------PTSAPTNVPEKDDEQQQNCPVCKANISVASLV 57 (217)
Q Consensus 7 eCnICld-----~A~dpVVT--ycW~--------ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~vi 57 (217)
-|.||.. ..+|.|+. |.-. ||.-|--.- ..|.||.||..|+..++.
T Consensus 226 vCaVCg~~~~~s~~eegvienty~LsCnHvFHEfCIrGWcivG-----KkqtCPYCKekVdl~rmf 286 (328)
T KOG1734|consen 226 VCAVCGQQIDVSVDEEGVIENTYKLSCNHVFHEFCIRGWCIVG-----KKQTCPYCKEKVDLKRMF 286 (328)
T ss_pred hhHhhcchheeecchhhhhhhheeeecccchHHHhhhhheeec-----CCCCCchHHHHhhHhhhc
Confidence 3777753 34456653 5444 444554432 568999999999876653
No 66
>COG4068 Uncharacterized protein containing a Zn-ribbon [Function unknown]
Probab=42.87 E-value=12 Score=27.46 Aligned_cols=17 Identities=24% Similarity=0.538 Sum_probs=11.6
Q ss_pred CCCCCCCccccccccce
Q 027871 40 QQQNCPVCKANISVASL 56 (217)
Q Consensus 40 ~~~~CPVCKa~Vs~~~v 56 (217)
.|+.|+||-+.|.+|..
T Consensus 7 PH~HC~VCg~aIp~de~ 23 (64)
T COG4068 7 PHRHCVVCGKAIPPDEQ 23 (64)
T ss_pred CCccccccCCcCCCccc
Confidence 45678888777766543
No 67
>PHA02610 uvsY.-2 hypothetical protein; Provisional
Probab=41.82 E-value=11 Score=26.84 Aligned_cols=16 Identities=44% Similarity=0.696 Sum_probs=11.8
Q ss_pred CCCCCcccccccccee
Q 027871 42 QNCPVCKANISVASLV 57 (217)
Q Consensus 42 ~~CPVCKa~Vs~~~vi 57 (217)
..|.|||-.|.....|
T Consensus 2 ~iCvvCK~Pi~~al~v 17 (53)
T PHA02610 2 KICVVCKQPIEKALVV 17 (53)
T ss_pred ceeeeeCCchhhceEE
Confidence 4699999999655433
No 68
>PF10146 zf-C4H2: Zinc finger-containing protein ; InterPro: IPR018482 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a family of proteins which appears to have a highly conserved zinc finger domain at the C-terminal end, described as -C-X2-CH-X3-H-X5-C-X2-C-. The structure is predicted to contain a coiled coil. Members of this family are annotated as being tumour-associated antigen HCA127 in humans, but this could not be confirmed.
Probab=41.70 E-value=11 Score=33.56 Aligned_cols=12 Identities=42% Similarity=1.018 Sum_probs=10.0
Q ss_pred cCCCCCCCcccc
Q 027871 39 EQQQNCPVCKAN 50 (217)
Q Consensus 39 ~~~~~CPVCKa~ 50 (217)
-+.+-||+||+.
T Consensus 206 RNAPiCPlCK~K 217 (230)
T PF10146_consen 206 RNAPICPLCKAK 217 (230)
T ss_pred cCCCCCcccccc
Confidence 367999999984
No 69
>COG5175 MOT2 Transcriptional repressor [Transcription]
Probab=41.55 E-value=7.2 Score=37.50 Aligned_cols=48 Identities=13% Similarity=0.216 Sum_probs=33.5
Q ss_pred CCCCCccccccCCCC----CcceE--------eeCCCCCCCCCCCCCCCcCCCCCCCccccccccce--eee
Q 027871 2 EQNLFEPETGYATEE----DASLK--------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASL--VPL 59 (217)
Q Consensus 2 ~~s~FeCnICld~A~----dpVVT--------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~v--iPL 59 (217)
|+..+ |-.|.|.-+ +..-+ |||..|.+=++ -.||.|.-.-++++| +||
T Consensus 12 deed~-cplcie~mditdknf~pc~cgy~ic~fc~~~irq~ln---------grcpacrr~y~denv~~~~~ 73 (480)
T COG5175 12 DEEDY-CPLCIEPMDITDKNFFPCPCGYQICQFCYNNIRQNLN---------GRCPACRRKYDDENVRYVTL 73 (480)
T ss_pred ccccc-CcccccccccccCCcccCCcccHHHHHHHHHHHhhcc---------CCChHhhhhccccceeEEec
Confidence 45556 888887432 22222 89999998443 589999999999886 454
No 70
>PHA03096 p28-like protein; Provisional
Probab=40.92 E-value=3 Score=38.35 Aligned_cols=45 Identities=4% Similarity=-0.255 Sum_probs=31.3
Q ss_pred CccccccCCCCCcceE-------------eeCCCCCCCCCCCCCCCcCCCCCCCccccc
Q 027871 6 FEPETGYATEEDASLK-------------QKWSPTSAPTNVPEKDDEQQQNCPVCKANI 51 (217)
Q Consensus 6 FeCnICld~A~dpVVT-------------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~V 51 (217)
=+|.||+|...+--+. ||=.|+..|-.... ...-.++||+|..-+
T Consensus 179 k~c~ic~e~~~~k~~~~~~fgil~~c~h~fc~~ci~~wr~~~~-~~e~~~~c~~~~~~~ 236 (284)
T PHA03096 179 KICGICLENIKAKYIIKKYYGILSEIKHEFNIFCIKIWMTESL-YKETEPENRRLNTVI 236 (284)
T ss_pred hhcccchhhhhhhccccccccccccCCcHHHHHHHHHHHHhhh-hcccCccccchhhHH
Confidence 3799999976643222 89999999866431 233458899998776
No 71
>PF11789 zf-Nse: Zinc-finger of the MIZ type in Nse subunit; PDB: 2YU4_A 3HTK_C.
Probab=40.65 E-value=4.1 Score=28.73 Aligned_cols=40 Identities=15% Similarity=0.174 Sum_probs=22.7
Q ss_pred CCCccccccCCCCCcceE------eeCCCCCCCCCCCCCCCcCCCCCCC--cc
Q 027871 4 NLFEPETGYATEEDASLK------QKWSPTSAPTNVPEKDDEQQQNCPV--CK 48 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPV--CK 48 (217)
-.+-|-|.+..-+|||.+ |.=..|.+|+. .....+||| |.
T Consensus 10 ~~~~CPiT~~~~~~PV~s~~C~H~fek~aI~~~i~-----~~~~~~CPv~GC~ 57 (57)
T PF11789_consen 10 ISLKCPITLQPFEDPVKSKKCGHTFEKEAILQYIQ-----RNGSKRCPVAGCN 57 (57)
T ss_dssp --SB-TTTSSB-SSEEEESSS--EEEHHHHHHHCT-----TTS-EE-SCCC-S
T ss_pred eccCCCCcCChhhCCcCcCCCCCeecHHHHHHHHH-----hcCCCCCCCCCCC
Confidence 357899999999999997 43334444442 236689999 73
No 72
>PF06716 DUF1201: Protein of unknown function (DUF1201); InterPro: IPR009591 This entry consists of several Beet yellows virus (BYV) putative membrane-binding proteins of around 54 residues in length. The function of this currently unknown.
Probab=40.50 E-value=18 Score=25.43 Aligned_cols=14 Identities=43% Similarity=1.177 Sum_probs=8.2
Q ss_pred HHHHHHHHHHHhhC
Q 027871 204 LFLFCCLVLCLLLF 217 (217)
Q Consensus 204 ~Fl~ccvvLCLllF 217 (217)
-||.|+++.||..|
T Consensus 14 ~~lIC~Fl~~~~~F 27 (54)
T PF06716_consen 14 GFLICLFLFCLVVF 27 (54)
T ss_pred HHHHHHHHHHHHHH
Confidence 35666666666543
No 73
>PF08525 OapA_N: Opacity-associated protein A N-terminal motif; InterPro: IPR013731 This domain is found in the Haemophilus influenzae opacity-associated protein (OapA). It is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation [, ]. This motif occurs at the N terminus of these proteins. It contains a conserved histidine followed by a run of hydrophobic residues. Many of the proteins in this entry are unassigned peptidases belonging to MEROPS peptidase family M23B.
Probab=38.97 E-value=40 Score=20.90 Aligned_cols=19 Identities=42% Similarity=0.705 Sum_probs=13.0
Q ss_pred hhhHHHHHHHHHHHHHhhC
Q 027871 199 LNRVSLFLFCCLVLCLLLF 217 (217)
Q Consensus 199 L~ri~~Fl~ccvvLCLllF 217 (217)
+||+.+.++..+++-++++
T Consensus 9 ~Hr~~l~~l~~v~l~ll~~ 27 (30)
T PF08525_consen 9 LHRRALIALSAVVLVLLLW 27 (30)
T ss_pred HHHHHHHHHHHHHHHHHhc
Confidence 5677777777777666654
No 74
>KOG4451 consensus Uncharacterized conserved protein (tumor-associated antigen HCA127 in humans) [Function unknown]
Probab=37.87 E-value=11 Score=34.29 Aligned_cols=13 Identities=38% Similarity=0.951 Sum_probs=10.6
Q ss_pred CcCCCCCCCcccc
Q 027871 38 DEQQQNCPVCKAN 50 (217)
Q Consensus 38 ~~~~~~CPVCKa~ 50 (217)
+.+.+.|||||+.
T Consensus 260 HRNAPiCPlCKaK 272 (286)
T KOG4451|consen 260 HRNAPICPLCKAK 272 (286)
T ss_pred hcCCCCCcchhhc
Confidence 4477999999985
No 75
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=36.65 E-value=14 Score=26.30 Aligned_cols=14 Identities=43% Similarity=0.655 Sum_probs=11.5
Q ss_pred CCCCCccccccccc
Q 027871 42 QNCPVCKANISVAS 55 (217)
Q Consensus 42 ~~CPVCKa~Vs~~~ 55 (217)
.-|.|||-.|....
T Consensus 2 ~~CvVCKqpi~~a~ 15 (54)
T PF10886_consen 2 EICVVCKQPIDDAL 15 (54)
T ss_pred CeeeeeCCccCcce
Confidence 46999999998853
No 76
>KOG1493 consensus Anaphase-promoting complex (APC), subunit 11 [Cell cycle control, cell division, chromosome partitioning; Posttranslational modification, protein turnover, chaperones]
Probab=36.58 E-value=9.1 Score=29.40 Aligned_cols=25 Identities=24% Similarity=0.422 Sum_probs=18.4
Q ss_pred eCCCCCCCCCCCCCCCcCCCCCCCccccc
Q 027871 23 KWSPTSAPTNVPEKDDEQQQNCPVCKANI 51 (217)
Q Consensus 23 cW~ci~~w~~~~~~~~~~~~~CPVCKa~V 51 (217)
-=.||..|++.. .++.+||-|+-+-
T Consensus 56 h~hCI~~wl~~~----tsq~~CPmcRq~~ 80 (84)
T KOG1493|consen 56 HAHCILKWLNTP----TSQGQCPMCRQTW 80 (84)
T ss_pred HHHHHHHHhcCc----cccccCCcchhee
Confidence 346788888753 5679999998653
No 77
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=36.43 E-value=17 Score=24.28 Aligned_cols=15 Identities=40% Similarity=1.019 Sum_probs=5.8
Q ss_pred CCCccccccccceeee
Q 027871 44 CPVCKANISVASLVPL 59 (217)
Q Consensus 44 CPVCKa~Vs~~~viPL 59 (217)
|||||. .+.+.-.|.
T Consensus 1 CpIc~e-~~~~~n~P~ 15 (43)
T PF13445_consen 1 CPICKE-FSTEENPPM 15 (43)
T ss_dssp -TTT-----TTSS-EE
T ss_pred CCcccc-ccCCCCCCE
Confidence 899999 666444454
No 78
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=36.13 E-value=21 Score=32.15 Aligned_cols=44 Identities=18% Similarity=0.213 Sum_probs=30.3
Q ss_pred CccccccCCCC--CcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceee
Q 027871 6 FEPETGYATEE--DASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVP 58 (217)
Q Consensus 6 FeCnICld~A~--dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viP 58 (217)
-.||-|+-.-+ .-.+| ||=.|.-+- ...+||-||-.|...++.+
T Consensus 4 VhCn~C~~~~~~~~f~LTaC~HvfC~~C~k~~---------~~~~C~lCkk~ir~i~l~~ 54 (233)
T KOG4739|consen 4 VHCNKCFRFPSQDPFFLTACRHVFCEPCLKAS---------SPDVCPLCKKSIRIIQLNR 54 (233)
T ss_pred EEeccccccCCCCceeeeechhhhhhhhcccC---------Cccccccccceeeeeeccc
Confidence 36999986544 23366 899998872 2239999998877666543
No 79
>PF05399 EVI2A: Ectropic viral integration site 2A protein (EVI2A); InterPro: IPR008608 This family contains several mammalian ectropic viral integration site 2A (EVI2A) proteins. The function of this protein is unknown although it is thought to be a membrane protein and may function as an oncogene in retrovirus induced myeloid tumours [, ].; GO: 0016021 integral to membrane
Probab=36.00 E-value=24 Score=31.67 Aligned_cols=17 Identities=24% Similarity=0.590 Sum_probs=13.2
Q ss_pred hHHHHHHHHHHHHHhhC
Q 027871 201 RVSLFLFCCLVLCLLLF 217 (217)
Q Consensus 201 ri~~Fl~ccvvLCLllF 217 (217)
-.+|.+.++|++|-|||
T Consensus 132 IClIIIAVLfLICT~Lf 148 (227)
T PF05399_consen 132 ICLIIIAVLFLICTLLF 148 (227)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34566788999999887
No 80
>KOG3970 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.86 E-value=13 Score=33.88 Aligned_cols=32 Identities=16% Similarity=0.338 Sum_probs=22.8
Q ss_pred eeCCCCCCCCCCC-CCCCcCCCCCCCccccccc
Q 027871 22 QKWSPTSAPTNVP-EKDDEQQQNCPVCKANISV 53 (217)
Q Consensus 22 ycW~ci~~w~~~~-~~~~~~~~~CPVCKa~Vs~ 53 (217)
|-|.|+..|.... -|....--+||-|..+|-.
T Consensus 74 fHW~ClneraA~lPanTAPaGyqCP~Cs~eiFP 106 (299)
T KOG3970|consen 74 FHWKCLNERAANLPANTAPAGYQCPCCSQEIFP 106 (299)
T ss_pred HHHHHhhHHHhhCCCcCCCCcccCCCCCCccCC
Confidence 7899999986533 1222234799999999865
No 81
>PF14255 Cys_rich_CPXG: Cysteine-rich CPXCG
Probab=34.12 E-value=9.3 Score=26.77 Aligned_cols=33 Identities=24% Similarity=0.342 Sum_probs=23.4
Q ss_pred eeCCCCCCCCCCCCCCCcCCCCCCCcccccccc
Q 027871 22 QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVA 54 (217)
Q Consensus 22 ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~ 54 (217)
|||..+..+.-.+....+....|+||...|.-.
T Consensus 5 yCge~~~~~iD~s~~~Q~yiEDC~vCC~PI~~~ 37 (52)
T PF14255_consen 5 YCGEPIEILIDPSAGDQEYIEDCQVCCRPIEVQ 37 (52)
T ss_pred CCCCeeEEEEecCCCCeeEEeehhhcCCccEEE
Confidence 788877776665544344558999999988654
No 82
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=34.08 E-value=19 Score=31.39 Aligned_cols=24 Identities=21% Similarity=0.451 Sum_probs=18.4
Q ss_pred cCCCCCCCccccccccceeeeecC
Q 027871 39 EQQQNCPVCKANISVASLVPLYGR 62 (217)
Q Consensus 39 ~~~~~CPVCKa~Vs~~~viPLYGR 62 (217)
+..-.||||+.+....+|-.=-+|
T Consensus 3 ~k~~~CPvC~~~F~~~~vrs~~~r 26 (214)
T PF09986_consen 3 DKKITCPVCGKEFKTKKVRSGKIR 26 (214)
T ss_pred CCceECCCCCCeeeeeEEEcCCce
Confidence 355789999999999888764444
No 83
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=33.36 E-value=9.3 Score=39.37 Aligned_cols=54 Identities=15% Similarity=0.236 Sum_probs=34.9
Q ss_pred CccccccCCCCCcceEeeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeee
Q 027871 6 FEPETGYATEEDASLKQKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLY 60 (217)
Q Consensus 6 FeCnICld~A~dpVVTycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLY 60 (217)
--|..|.+.-+|.|++-|-=++..-= ......-.++-||-|-+......|.|||
T Consensus 644 LkCs~Cn~R~Kd~vI~kC~H~FC~~C-vq~r~etRqRKCP~Cn~aFganDv~~I~ 697 (698)
T KOG0978|consen 644 LKCSVCNTRWKDAVITKCGHVFCEEC-VQTRYETRQRKCPKCNAAFGANDVHRIH 697 (698)
T ss_pred eeCCCccCchhhHHHHhcchHHHHHH-HHHHHHHhcCCCCCCCCCCCcccccccC
Confidence 35999999999999970000000000 0000112568999999999999999998
No 84
>PF10215 Ost4: Oligosaccaryltransferase ; InterPro: IPR018943 Ost4 is a very short, approximately 30 residues, enzyme found from fungi to vertebrates. It is a member of the ER oligosaccaryltansferase complex, 2.4.1.119 from EC, that catalyses the asparagine-linked glycosylation of proteins. It appears to be an integral membrane protein that mediates the en bloc transfer of a pre-assembled high-mannose oligosaccharide onto asparagine residues of nascent polypeptides as they enter the lumen of the rough endoplasmic reticulum. ; PDB: 1RKL_A 2LAT_A.
Probab=33.21 E-value=31 Score=22.46 Aligned_cols=23 Identities=22% Similarity=0.350 Sum_probs=18.8
Q ss_pred HHHhhhhHHHHHHHHHHHHHhhC
Q 027871 195 LDKSLNRVSLFLFCCLVLCLLLF 217 (217)
Q Consensus 195 ~d~sL~ri~~Fl~ccvvLCLllF 217 (217)
-|.-|+++.+||+++.++..++|
T Consensus 3 sD~qL~~lan~lG~~~~~LIVlY 25 (35)
T PF10215_consen 3 SDVQLYTLANFLGVAAMVLIVLY 25 (35)
T ss_dssp SSHHHHHHHHHHHHHHHHHHHHH
T ss_pred cHHHHHHHHHHHHHHHHHHHHHH
Confidence 37789999999999988876653
No 85
>PF05883 Baculo_RING: Baculovirus U-box/Ring-like domain; InterPro: IPR008573 This family consists of several Baculovirus proteins of around 130 residues in length. The function of this family is unknown, but it appears to be related to the U-box and ring finger domain by profile-profile comparison.
Probab=33.11 E-value=4.9 Score=33.42 Aligned_cols=27 Identities=4% Similarity=-0.149 Sum_probs=21.0
Q ss_pred CCCccccccCCCCC--cce--E----------eeCCCCCCC
Q 027871 4 NLFEPETGYATEED--ASL--K----------QKWSPTSAP 30 (217)
Q Consensus 4 s~FeCnICld~A~d--pVV--T----------ycW~ci~~w 30 (217)
...||-||||.-.+ -|| | ||=.|+-.|
T Consensus 25 ~~~EC~IC~~~I~~~~GvV~vt~~g~lnLEkmfc~~C~~rw 65 (134)
T PF05883_consen 25 CTVECQICFDRIDNNDGVVYVTDGGTLNLEKMFCADCDKRW 65 (134)
T ss_pred cCeeehhhhhhhhcCCCEEEEecCCeehHHHHHHHHHHHHH
Confidence 47899999997766 555 4 787888887
No 86
>COG2835 Uncharacterized conserved protein [Function unknown]
Probab=33.02 E-value=18 Score=26.24 Aligned_cols=13 Identities=38% Similarity=0.935 Sum_probs=10.0
Q ss_pred CCCCCCCcccccc
Q 027871 40 QQQNCPVCKANIS 52 (217)
Q Consensus 40 ~~~~CPVCKa~Vs 52 (217)
+--.||+||+...
T Consensus 7 eiLaCP~~kg~L~ 19 (60)
T COG2835 7 EILACPVCKGPLV 19 (60)
T ss_pred eeeeccCcCCcce
Confidence 4468999999853
No 87
>COG1259 Uncharacterized conserved protein [Function unknown]
Probab=32.65 E-value=8.5 Score=32.57 Aligned_cols=44 Identities=23% Similarity=0.248 Sum_probs=30.4
Q ss_pred CCCCCCccccccccceeeeecCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 027871 41 QQNCPVCKANISVASLVPLYGRGGISSASDSKKPNLGEVVPSRPHPS 87 (217)
Q Consensus 41 ~~~CPVCKa~Vs~~~viPLYGRG~~~~~~~~k~~~~g~~IPpRP~~~ 87 (217)
...|+||.-.-.++.++|||+ |.+...+-.|+ ....-||||-.+
T Consensus 18 ~~~~~v~~~~~~~~~~lPI~I-g~~ea~si~~~--l~~~~p~RP~tH 61 (151)
T COG1259 18 SFPTVVLLLEGGDNRVLPIYI-GASEALAIAKA--LEGVEPPRPLTH 61 (151)
T ss_pred CCceEEEEEEcCCCeEEEEEE-eHHHHHHHHHh--hccCCCCCCcHH
Confidence 356799999999999999999 44433222222 334457799876
No 88
>KOG0827 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=32.63 E-value=8 Score=37.63 Aligned_cols=46 Identities=11% Similarity=0.139 Sum_probs=28.7
Q ss_pred CccccccCCCCCcceE-----------eeCCCCCCCCCCCCCCCcCCCCCCCcccccccccee
Q 027871 6 FEPETGYATEEDASLK-----------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLV 57 (217)
Q Consensus 6 FeCnICld~A~dpVVT-----------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~vi 57 (217)
=+|.||-|. -|++- |-=.|+-+|... .. ..+.||.||-.+.+-.|+
T Consensus 5 A~C~Ic~d~--~p~~~~l~~i~~cGhifh~~cl~qwfe~---~P-s~R~cpic~ik~~~r~~~ 61 (465)
T KOG0827|consen 5 AECHICIDG--RPNDHELGPIGTCGHIFHTTCLTQWFEG---DP-SNRGCPICQIKLQERHVA 61 (465)
T ss_pred ceeeEeccC--CccccccccccchhhHHHHHHHHHHHcc---CC-ccCCCCceeecccceeee
Confidence 479999543 23332 666777887642 12 237999999655555555
No 89
>CHL00038 psbL photosystem II protein L
Probab=32.63 E-value=46 Score=22.13 Aligned_cols=18 Identities=39% Similarity=0.491 Sum_probs=12.3
Q ss_pred HhhhhHHHHHHHHHHHHH
Q 027871 197 KSLNRVSLFLFCCLVLCL 214 (217)
Q Consensus 197 ~sL~ri~~Fl~ccvvLCL 214 (217)
.-|||-+++++.+.|++|
T Consensus 11 VELNRTSLy~GLLlifvl 28 (38)
T CHL00038 11 VELNRTSLYWGLLLIFVL 28 (38)
T ss_pred cchhhhhHHHHHHHHHHH
Confidence 348888888776665554
No 90
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=32.06 E-value=32 Score=32.02 Aligned_cols=37 Identities=5% Similarity=-0.016 Sum_probs=29.4
Q ss_pred ccccccCCCCCcceE-----------eeCCCCCCCCCCCCCCCcCCCCCCCcccc
Q 027871 7 EPETGYATEEDASLK-----------QKWSPTSAPTNVPEKDDEQQQNCPVCKAN 50 (217)
Q Consensus 7 eCnICld~A~dpVVT-----------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~ 50 (217)
.|-+|.....--+|. +|..|=..|-. .+-.||.|...
T Consensus 186 ~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~-------~R~~C~~Cg~~ 233 (305)
T TIGR01562 186 LCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHY-------VRVKCSHCEES 233 (305)
T ss_pred cCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccc-------cCccCCCCCCC
Confidence 699999877555442 79999999954 67899999874
No 91
>smart00746 TRASH metallochaperone-like domain.
Probab=31.81 E-value=33 Score=19.04 Aligned_cols=9 Identities=33% Similarity=0.973 Sum_probs=8.0
Q ss_pred CCCcccccc
Q 027871 44 CPVCKANIS 52 (217)
Q Consensus 44 CPVCKa~Vs 52 (217)
||||+..|.
T Consensus 1 c~~C~~~~~ 9 (39)
T smart00746 1 CSFCGKDIY 9 (39)
T ss_pred CCCCCCCcc
Confidence 899999886
No 92
>cd00729 rubredoxin_SM Rubredoxin, Small Modular nonheme iron binding domain containing a [Fe(SCys)4] center, present in rubrerythrin and nigerythrin and detected either N- or C-terminal to such proteins as flavin reductase, NAD(P)H-nitrite reductase, and ferredoxin-thioredoxin reductase. In rubredoxin, the iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), and believed to be involved in electron transfer. Rubrerythrins and nigerythrins are small homodimeric proteins, generally consisting of 2 domains: a rubredoxin domain C-terminal to a non-sulfur, oxo-bridged diiron site in the N-terminal rubrerythrin domain. Rubrerythrins and nigerythrins have putative peroxide activity.
Probab=31.57 E-value=22 Score=22.46 Aligned_cols=9 Identities=44% Similarity=1.353 Sum_probs=7.8
Q ss_pred CCCCCcccc
Q 027871 42 QNCPVCKAN 50 (217)
Q Consensus 42 ~~CPVCKa~ 50 (217)
..||||++.
T Consensus 19 ~~CP~Cg~~ 27 (34)
T cd00729 19 EKCPICGAP 27 (34)
T ss_pred CcCcCCCCc
Confidence 599999985
No 93
>TIGR03831 YgiT_finger YgiT-type zinc finger domain. This domain model describes a small domain with two copies of a putative zinc-binding motif CXXC (usually CXXCG). Most member proteins consist largely of this domain or else carry an additional C-terminal helix-turn-helix domain, resembling that of the phage protein Cro and modeled by pfam01381.
Probab=31.27 E-value=30 Score=21.90 Aligned_cols=13 Identities=23% Similarity=0.682 Sum_probs=9.5
Q ss_pred CCCccccccccce
Q 027871 44 CPVCKANISVASL 56 (217)
Q Consensus 44 CPVCKa~Vs~~~v 56 (217)
||+|++..-+.++
T Consensus 1 C~~C~~~~~~~~~ 13 (46)
T TIGR03831 1 CPICGGEELEGKT 13 (46)
T ss_pred CCCCCCceecceE
Confidence 9999876666554
No 94
>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=30.82 E-value=15 Score=26.19 Aligned_cols=14 Identities=43% Similarity=0.902 Sum_probs=7.7
Q ss_pred CCCCCCCccccccc
Q 027871 40 QQQNCPVCKANISV 53 (217)
Q Consensus 40 ~~~~CPVCKa~Vs~ 53 (217)
....||+|.+.|+.
T Consensus 23 ~PatCP~C~a~~~~ 36 (54)
T PF09237_consen 23 QPATCPICGAVIRQ 36 (54)
T ss_dssp --EE-TTT--EESS
T ss_pred CCCCCCcchhhccc
Confidence 44799999999875
No 95
>PHA02825 LAP/PHD finger-like protein; Provisional
Probab=29.96 E-value=12 Score=32.17 Aligned_cols=44 Identities=9% Similarity=-0.009 Sum_probs=30.7
Q ss_pred CCCccccccCCCCCcceEe-------eC---CCCCCCCCCCCCCCcCCCCCCCccccccc
Q 027871 4 NLFEPETGYATEEDASLKQ-------KW---SPTSAPTNVPEKDDEQQQNCPVCKANISV 53 (217)
Q Consensus 4 s~FeCnICld~A~dpVVTy-------cW---~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~ 53 (217)
..-+|=||+|.+.+ .+.. .| .|+..|+.. +....|+.|+..-.-
T Consensus 7 ~~~~CRIC~~~~~~-~~~PC~CkGs~k~VH~sCL~rWi~~-----s~~~~CeiC~~~Y~i 60 (162)
T PHA02825 7 MDKCCWICKDEYDV-VTNYCNCKNENKIVHKECLEEWINT-----SKNKSCKICNGPYNI 60 (162)
T ss_pred CCCeeEecCCCCCC-ccCCcccCCCchHHHHHHHHHHHhc-----CCCCcccccCCeEEE
Confidence 45689999999753 3332 23 467778763 367899999987643
No 96
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=29.68 E-value=25 Score=22.73 Aligned_cols=14 Identities=29% Similarity=0.831 Sum_probs=10.4
Q ss_pred CCCCccccccccce
Q 027871 43 NCPVCKANISVASL 56 (217)
Q Consensus 43 ~CPVCKa~Vs~~~v 56 (217)
.||.|+..+.+..+
T Consensus 1 ~CP~C~~~l~~~~~ 14 (41)
T PF13453_consen 1 KCPRCGTELEPVRL 14 (41)
T ss_pred CcCCCCcccceEEE
Confidence 59999997765444
No 97
>PF15012 DUF4519: Domain of unknown function (DUF4519)
Probab=29.08 E-value=44 Score=24.00 Aligned_cols=32 Identities=22% Similarity=0.423 Sum_probs=18.3
Q ss_pred hhhhhhhhH-HHHhhhhHHHHHHHHHHHHHhhC
Q 027871 186 PRIRRQEME-LDKSLNRVSLFLFCCLVLCLLLF 217 (217)
Q Consensus 186 pR~Rrq~mq-~d~sL~ri~~Fl~ccvvLCLllF 217 (217)
-+.||++|+ +..-+..|-+=.+..|+||+.+|
T Consensus 16 K~ERk~~~~e~~~kv~tVVlP~l~~~~~~Ivv~ 48 (56)
T PF15012_consen 16 KKERKKEMQEAQQKVFTVVLPTLAAVFLFIVVF 48 (56)
T ss_pred HHHHHHHHHHHHHhheeEehhHHHHHHHHHhhe
Confidence 345888854 44456666555555555555544
No 98
>KOG3039 consensus Uncharacterized conserved protein [Function unknown]
Probab=28.77 E-value=19 Score=33.20 Aligned_cols=50 Identities=8% Similarity=-0.033 Sum_probs=39.5
Q ss_pred CCCccccccCCCCCcceE---------eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeee
Q 027871 4 NLFEPETGYATEEDASLK---------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLY 60 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT---------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLY 60 (217)
..|-|.||.|+-.+.+-+ +|-.|+-...- .-..||||-..+++.+||+|=
T Consensus 220 ~ryiCpvtrd~LtNt~~ca~Lr~sg~Vv~~ecvEklir-------~D~v~pv~d~plkdrdiI~Lq 278 (303)
T KOG3039|consen 220 KRYICPVTRDTLTNTTPCAVLRPSGHVVTKECVEKLIR-------KDMVDPVTDKPLKDRDIIGLQ 278 (303)
T ss_pred cceecccchhhhcCccceEEeccCCcEeeHHHHHHhcc-------ccccccCCCCcCcccceEeee
Confidence 578999999987776644 56777666432 347999999999999999996
No 99
>PRK10299 PhoPQ regulatory protein; Provisional
Probab=28.74 E-value=34 Score=23.77 Aligned_cols=14 Identities=36% Similarity=0.681 Sum_probs=8.5
Q ss_pred HHHHHHHHHHHHhh
Q 027871 203 SLFLFCCLVLCLLL 216 (217)
Q Consensus 203 ~~Fl~ccvvLCLll 216 (217)
|+.+.+.++.||+|
T Consensus 6 wiili~iv~~Cl~l 19 (47)
T PRK10299 6 WVVLVVVVLACLLL 19 (47)
T ss_pred ehHHHHHHHHHHHH
Confidence 45556666666665
No 100
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=28.34 E-value=29 Score=24.86 Aligned_cols=19 Identities=37% Similarity=0.920 Sum_probs=11.5
Q ss_pred CCCCccc----cccccce---eeeec
Q 027871 43 NCPVCKA----NISVASL---VPLYG 61 (217)
Q Consensus 43 ~CPVCKa----~Vs~~~v---iPLYG 61 (217)
.||+|++ .|-+|++ .|||-
T Consensus 6 ~CP~CgnKTR~kir~DT~LkNfPlyC 31 (55)
T PF14205_consen 6 LCPICGNKTRLKIREDTVLKNFPLYC 31 (55)
T ss_pred ECCCCCCccceeeecCceeccccccC
Confidence 5888874 3445554 36665
No 101
>KOG3002 consensus Zn finger protein [General function prediction only]
Probab=27.98 E-value=33 Score=31.84 Aligned_cols=39 Identities=15% Similarity=0.330 Sum_probs=29.5
Q ss_pred CCCccccccCCCCCcceE------eeCCCCCCCCCCCCCCCcCCCCCCCcccccc
Q 027871 4 NLFEPETGYATEEDASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCKANIS 52 (217)
Q Consensus 4 s~FeCnICld~A~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs 52 (217)
..+||.||++.-+-|+.. -|=.|=.. -...||+|...|.
T Consensus 47 ~lleCPvC~~~l~~Pi~QC~nGHlaCssC~~~----------~~~~CP~Cr~~~g 91 (299)
T KOG3002|consen 47 DLLDCPVCFNPLSPPIFQCDNGHLACSSCRTK----------VSNKCPTCRLPIG 91 (299)
T ss_pred hhccCchhhccCcccceecCCCcEehhhhhhh----------hcccCCccccccc
Confidence 468999999999988875 34444433 4469999998877
No 102
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=27.11 E-value=20 Score=32.24 Aligned_cols=37 Identities=11% Similarity=-0.008 Sum_probs=19.9
Q ss_pred ccccccCCCCCcceE----------eeCCCCCCCCCCCCCCCcCCCCCCCcccc
Q 027871 7 EPETGYATEEDASLK----------QKWSPTSAPTNVPEKDDEQQQNCPVCKAN 50 (217)
Q Consensus 7 eCnICld~A~dpVVT----------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~ 50 (217)
-|-||.....-.+|. +|-.|=+.|-. .+-.||.|-..
T Consensus 174 ~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~-------~R~~Cp~Cg~~ 220 (290)
T PF04216_consen 174 YCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRF-------VRIKCPYCGNT 220 (290)
T ss_dssp S-TTT---EEEEEEE------EEEEEETTT--EEE---------TTS-TTT---
T ss_pred cCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeee-------cCCCCcCCCCC
Confidence 689998876655554 79999999954 66899999665
No 103
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=27.11 E-value=13 Score=35.32 Aligned_cols=51 Identities=10% Similarity=0.081 Sum_probs=41.2
Q ss_pred CccccccCCCCCcceE------eeCCCCCCCCCCCCCCCcCCCCCCCccc-cccccceeeeecC
Q 027871 6 FEPETGYATEEDASLK------QKWSPTSAPTNVPEKDDEQQQNCPVCKA-NISVASLVPLYGR 62 (217)
Q Consensus 6 FeCnICld~A~dpVVT------ycW~ci~~w~~~~~~~~~~~~~CPVCKa-~Vs~~~viPLYGR 62 (217)
-.|-.|..++..|+-| ||=.||-..+.- .--+||+|.- .|-.|.++|=|-.
T Consensus 275 LkCplc~~Llrnp~kT~cC~~~fc~eci~~al~d------sDf~CpnC~rkdvlld~l~pD~dk 332 (427)
T COG5222 275 LKCPLCHCLLRNPMKTPCCGHTFCDECIGTALLD------SDFKCPNCSRKDVLLDGLTPDIDK 332 (427)
T ss_pred ccCcchhhhhhCcccCccccchHHHHHHhhhhhh------ccccCCCcccccchhhccCccHHH
Confidence 5799999999999987 888898875542 3479999975 7888899997754
No 104
>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=26.87 E-value=19 Score=24.44 Aligned_cols=17 Identities=41% Similarity=0.741 Sum_probs=13.0
Q ss_pred CCCCCccccccccceee
Q 027871 42 QNCPVCKANISVASLVP 58 (217)
Q Consensus 42 ~~CPVCKa~Vs~~~viP 58 (217)
-.||.|..++++..|+-
T Consensus 3 f~CP~C~~~~~~~~L~~ 19 (54)
T PF05605_consen 3 FTCPYCGKGFSESSLVE 19 (54)
T ss_pred cCCCCCCCccCHHHHHH
Confidence 47999999888776653
No 105
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=26.62 E-value=33 Score=27.10 Aligned_cols=31 Identities=13% Similarity=0.339 Sum_probs=20.3
Q ss_pred CCCcceEeeCCCCCCCCCCCCCCCcCCCCCCCcccc
Q 027871 15 EEDASLKQKWSPTSAPTNVPEKDDEQQQNCPVCKAN 50 (217)
Q Consensus 15 A~dpVVTycW~ci~~w~~~~~~~~~~~~~CPVCKa~ 50 (217)
...|++-+|..|=+.|... ...-.||.|++.
T Consensus 65 ~~vp~~~~C~~Cg~~~~~~-----~~~~~CP~Cgs~ 95 (113)
T PRK12380 65 VYKPAQAWCWDCSQVVEIH-----QHDAQCPHCHGE 95 (113)
T ss_pred EeeCcEEEcccCCCEEecC-----CcCccCcCCCCC
Confidence 3344455899999887531 233459999964
No 106
>PHA02975 hypothetical protein; Provisional
Probab=26.60 E-value=47 Score=24.80 Aligned_cols=21 Identities=29% Similarity=0.630 Sum_probs=14.6
Q ss_pred HhhhhHHHHHHHHHHHHHhhC
Q 027871 197 KSLNRVSLFLFCCLVLCLLLF 217 (217)
Q Consensus 197 ~sL~ri~~Fl~ccvvLCLllF 217 (217)
++...++++++.++++|+++|
T Consensus 40 ~~~~~~~~ii~i~~v~~~~~~ 60 (69)
T PHA02975 40 KSSLSIILIIFIIFITCIAVF 60 (69)
T ss_pred CCchHHHHHHHHHHHHHHHHH
Confidence 666777777777777777654
No 107
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=26.20 E-value=33 Score=19.97 Aligned_cols=10 Identities=50% Similarity=1.062 Sum_probs=4.6
Q ss_pred CCCccccccc
Q 027871 44 CPVCKANISV 53 (217)
Q Consensus 44 CPVCKa~Vs~ 53 (217)
||.|.++|.+
T Consensus 2 Cp~CG~~~~~ 11 (23)
T PF13240_consen 2 CPNCGAEIED 11 (23)
T ss_pred CcccCCCCCC
Confidence 4444444443
No 108
>PF05715 zf-piccolo: Piccolo Zn-finger; InterPro: IPR008899 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This (predicted) zinc finger is found in the bassoon and piccolo proteins, both of which are components of the presynaptic cytoskeletal matrix (PCM) assembled at the active zone of neurotransmitter release, where Piccolo plays a role in the trafficking of synaptic vesicles (SVs) [, , ]. The Piccolo zinc fingers were found to interact with the dual prenylated rab3A and VAMP2/Synaptobrevin II receptor PRA1. There are eight conserved cysteines in Piccolo-type zinc fingers, suggesting that they coordinates two zinc ligands. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding, 0045202 synapse
Probab=25.67 E-value=35 Score=24.90 Aligned_cols=11 Identities=36% Similarity=1.138 Sum_probs=9.1
Q ss_pred CCCCCcccccc
Q 027871 42 QNCPVCKANIS 52 (217)
Q Consensus 42 ~~CPVCKa~Vs 52 (217)
..||+||.+..
T Consensus 3 ~~CPlCkt~~n 13 (61)
T PF05715_consen 3 SLCPLCKTTLN 13 (61)
T ss_pred ccCCcccchhh
Confidence 57999998873
No 109
>PF10297 Hap4_Hap_bind: Minimal binding motif of Hap4 for binding to Hap2/3/5 ; InterPro: IPR018287 This entry represents an essential domain of the transcription activator Hap4 that allows it to associate with Hap2, Hap3 and Hap5 to form the Hap complex [, ]. In Saccharomyces cerevisiae (Baker's yeast), the haem-activated protein complex Hap2/3/4/5 plays a major role in the transcription of genes involved in respiration []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=25.46 E-value=41 Score=18.77 Aligned_cols=11 Identities=45% Similarity=0.885 Sum_probs=8.8
Q ss_pred CCCCCCCCCCC
Q 027871 78 EVVPSRPHPSA 88 (217)
Q Consensus 78 ~~IPpRP~~~R 88 (217)
-.||+||.+-|
T Consensus 5 WvlPprpkpgR 15 (17)
T PF10297_consen 5 WVLPPRPKPGR 15 (17)
T ss_pred cccCCCCCCCC
Confidence 35899998876
No 110
>smart00037 CNX Connexin homologues. Connexin channels participate in the regulation of signaling between developing and differentiated cell types.
Probab=25.09 E-value=29 Score=22.63 Aligned_cols=14 Identities=29% Similarity=0.278 Sum_probs=10.1
Q ss_pred CCCCCccc--------cccCCC
Q 027871 2 EQNLFEPE--------TGYATE 15 (217)
Q Consensus 2 ~~s~FeCn--------ICld~A 15 (217)
|++.|.|| +|+|.+
T Consensus 6 Eq~~FvCnT~QPGC~nvCyD~~ 27 (34)
T smart00037 6 EQSDFVCNTQQPGCENVCYDQA 27 (34)
T ss_pred chhhceecCCCCCccceecccc
Confidence 67888886 577654
No 111
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=25.01 E-value=28 Score=33.25 Aligned_cols=13 Identities=38% Similarity=0.999 Sum_probs=10.5
Q ss_pred CCCCCCccccccc
Q 027871 41 QQNCPVCKANISV 53 (217)
Q Consensus 41 ~~~CPVCKa~Vs~ 53 (217)
--+|||||+.|--
T Consensus 308 Gy~CP~CktkVCs 320 (421)
T COG5151 308 GYECPVCKTKVCS 320 (421)
T ss_pred ceeCCcccceeec
Confidence 3699999998853
No 112
>PHA02844 putative transmembrane protein; Provisional
Probab=24.80 E-value=55 Score=24.81 Aligned_cols=18 Identities=11% Similarity=0.019 Sum_probs=8.5
Q ss_pred hhhHHHHHHHHHHHHHhh
Q 027871 199 LNRVSLFLFCCLVLCLLL 216 (217)
Q Consensus 199 L~ri~~Fl~ccvvLCLll 216 (217)
..+++++++.++++|+++
T Consensus 46 ~~~~~~ii~i~~v~~~~~ 63 (75)
T PHA02844 46 SSTKIWILTIIFVVFATF 63 (75)
T ss_pred hhHHHHHHHHHHHHHHHH
Confidence 334444444555555544
No 113
>PF15221 LEP503: Lens epithelial cell protein LEP503
Probab=24.39 E-value=71 Score=23.11 Aligned_cols=18 Identities=33% Similarity=0.920 Sum_probs=15.3
Q ss_pred HHHhhhhHHHHHHHHHHH
Q 027871 195 LDKSLNRVSLFLFCCLVL 212 (217)
Q Consensus 195 ~d~sL~ri~~Fl~ccvvL 212 (217)
+.++|+.+..||+||--+
T Consensus 39 ~~~tLKe~aYilLCCWCI 56 (61)
T PF15221_consen 39 LQQTLKEVAYILLCCWCI 56 (61)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 578999999999999644
No 114
>PLN02195 cellulose synthase A
Probab=24.12 E-value=56 Score=35.11 Aligned_cols=46 Identities=15% Similarity=0.004 Sum_probs=33.3
Q ss_pred CCCCCCccccccCCC-----CCcceE-------eeCCCCCCCCCCCCCCCcCCCCCCCcccccc
Q 027871 1 MEQNLFEPETGYATE-----EDASLK-------QKWSPTSAPTNVPEKDDEQQQNCPVCKANIS 52 (217)
Q Consensus 1 m~~s~FeCnICld~A-----~dpVVT-------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs 52 (217)
||.+.--|.||.|.. .||.|- .|=+|.-= .+.+.++.||-||..-.
T Consensus 2 ~~~~~~~c~~cgd~~~~~~~g~~fvaC~eC~~pvCrpCyey------er~eg~q~CpqCkt~Yk 59 (977)
T PLN02195 2 MESGAPICATCGEEVGVDSNGEAFVACHECSYPLCKACLEY------EIKEGRKVCLRCGGPYD 59 (977)
T ss_pred CcCCCccceecccccCcCCCCCeEEEeccCCCccccchhhh------hhhcCCccCCccCCccc
Confidence 677777899999943 366664 47777632 13457799999998776
No 115
>KOG4692 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=23.95 E-value=11 Score=36.37 Aligned_cols=40 Identities=15% Similarity=0.159 Sum_probs=33.8
Q ss_pred ccccccCCCCCcceE-----eeCCCCCCCCCCCCCCCcCCCCCCCccccccc
Q 027871 7 EPETGYATEEDASLK-----QKWSPTSAPTNVPEKDDEQQQNCPVCKANISV 53 (217)
Q Consensus 7 eCnICld~A~dpVVT-----ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~ 53 (217)
-|-||+...-.+|.+ =|..||-+-+ | +.+.|=-||..|..
T Consensus 424 lCpICyA~pi~Avf~PC~H~SC~~CI~qHl--m-----N~k~CFfCktTv~~ 468 (489)
T KOG4692|consen 424 LCPICYAGPINAVFAPCSHRSCYGCITQHL--M-----NCKRCFFCKTTVID 468 (489)
T ss_pred cCcceecccchhhccCCCCchHHHHHHHHH--h-----cCCeeeEecceeee
Confidence 499999999999998 5889998833 3 67999999999986
No 116
>TIGR01206 lysW lysine biosynthesis protein LysW. This very small, poorly characterized protein has been shown essential in Thermus thermophilus for an unusual pathway of Lys biosynthesis from aspartate by way of alpha-aminoadipate (AAA) rather than diaminopimelate. It is found also in Deinococcus radiodurans and Pyrococcus horikoshii, which appear to share the AAA pathway.
Probab=23.17 E-value=38 Score=23.85 Aligned_cols=15 Identities=33% Similarity=0.729 Sum_probs=11.7
Q ss_pred CCCCCccccccccce
Q 027871 42 QNCPVCKANISVASL 56 (217)
Q Consensus 42 ~~CPVCKa~Vs~~~v 56 (217)
-+||+|.+.|.....
T Consensus 3 ~~CP~CG~~iev~~~ 17 (54)
T TIGR01206 3 FECPDCGAEIELENP 17 (54)
T ss_pred cCCCCCCCEEecCCC
Confidence 389999999876543
No 117
>PF07092 DUF1356: Protein of unknown function (DUF1356); InterPro: IPR009790 This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
Probab=22.98 E-value=15 Score=33.18 Aligned_cols=16 Identities=50% Similarity=1.090 Sum_probs=11.0
Q ss_pred hHHHHHHHHHHHHHhh
Q 027871 201 RVSLFLFCCLVLCLLL 216 (217)
Q Consensus 201 ri~~Fl~ccvvLCLll 216 (217)
|.++++++.|+||||+
T Consensus 73 RTklyV~~sV~~CLl~ 88 (238)
T PF07092_consen 73 RTKLYVFLSVLLCLLL 88 (238)
T ss_pred eeEEEeeHHHHHHHHH
Confidence 5566777777777765
No 118
>KOG0825 consensus PHD Zn-finger protein [General function prediction only]
Probab=22.53 E-value=9.7 Score=40.18 Aligned_cols=33 Identities=15% Similarity=0.155 Sum_probs=24.6
Q ss_pred eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeeec
Q 027871 22 QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLYG 61 (217)
Q Consensus 22 ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLYG 61 (217)
||=.||..|.- ..+.||+|..+..+..|.=-|+
T Consensus 148 FC~~Ci~sWsR-------~aqTCPiDR~EF~~v~V~eS~~ 180 (1134)
T KOG0825|consen 148 FCEECVGSWSR-------CAQTCPVDRGEFGEVKVLESTG 180 (1134)
T ss_pred cHHHHhhhhhh-------hcccCchhhhhhheeeeecccc
Confidence 67778888753 5689999999888766655555
No 119
>PRK06870 secG preprotein translocase subunit SecG; Reviewed
Probab=22.40 E-value=94 Score=22.72 Aligned_cols=19 Identities=16% Similarity=0.245 Sum_probs=13.7
Q ss_pred HHHhhhhHHHHHHHHHHHH
Q 027871 195 LDKSLNRVSLFLFCCLVLC 213 (217)
Q Consensus 195 ~d~sL~ri~~Fl~ccvvLC 213 (217)
.|+.|+|+-.++.+++++.
T Consensus 48 ~~~~L~k~T~il~~~F~i~ 66 (76)
T PRK06870 48 AENFLSRLTAVLAVLFFVL 66 (76)
T ss_pred HhHHHHHHHHHHHHHHHHH
Confidence 6999999987766555443
No 120
>PF10559 Plug_translocon: Plug domain of Sec61p; InterPro: IPR019561 The Sec61/SecY translocon mediates translocation of proteins across the membrane and integration of membrane proteins into the lipid bilayer. The structure of the translocon revealed a plug domain blocking the pore on the lumenal side. The plug is unlikely to be important for sealing the translocation pore in yeast but it plays a role in stabilising Sec61p during translocon formation. The domain runs from residues 52-74 []. ; PDB: 2YXR_A 1RHZ_A 3KCR_A 3DKN_A 2YXQ_A 1RH5_A 3BO1_A 3BO0_A 2WWA_A 2WW9_A ....
Probab=22.13 E-value=52 Score=21.10 Aligned_cols=7 Identities=57% Similarity=1.203 Sum_probs=5.0
Q ss_pred eeeeecC
Q 027871 56 LVPLYGR 62 (217)
Q Consensus 56 viPLYGR 62 (217)
-|||||-
T Consensus 8 ~ipLyG~ 14 (35)
T PF10559_consen 8 QIPLYGL 14 (35)
T ss_dssp HSB-STS
T ss_pred CCccccc
Confidence 4899997
No 121
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.91 E-value=39 Score=27.24 Aligned_cols=13 Identities=46% Similarity=1.124 Sum_probs=9.5
Q ss_pred CCCccccccccce
Q 027871 44 CPVCKANISVASL 56 (217)
Q Consensus 44 CPVCKa~Vs~~~v 56 (217)
||||.+.+..+.+
T Consensus 1 CPvCg~~l~vt~l 13 (113)
T PF09862_consen 1 CPVCGGELVVTRL 13 (113)
T ss_pred CCCCCCceEEEEE
Confidence 8999887765544
No 122
>KOG3053 consensus Uncharacterized conserved protein [Function unknown]
Probab=21.74 E-value=9.7 Score=35.19 Aligned_cols=43 Identities=35% Similarity=0.495 Sum_probs=29.5
Q ss_pred cccccCCCCCcceE-----------eeC---CCCCCCCCCCCCCC---cCCCCCCCcccccc
Q 027871 8 PETGYATEEDASLK-----------QKW---SPTSAPTNVPEKDD---EQQQNCPVCKANIS 52 (217)
Q Consensus 8 CnICld~A~dpVVT-----------ycW---~ci~~w~~~~~~~~---~~~~~CPVCKa~Vs 52 (217)
|-|||++.+|-=.. -+| .|++.|.. |+.- -+.-.||-|..+-.
T Consensus 23 CWiCF~TdeDn~~a~WV~PCrCRGt~KWVHqsCL~rWiD--EK~~~n~~q~V~C~QCqTEYi 82 (293)
T KOG3053|consen 23 CWICFATDEDNRLAAWVHPCRCRGTTKWVHQSCLSRWID--EKQRGNPLQTVSCPQCQTEYI 82 (293)
T ss_pred EEEEeccCcccchhhhcccccccCccHHHHHHHHHHHHh--HHhcCCCCceeechhhcchhe
Confidence 89999999986543 346 68888864 2221 23467999988754
No 123
>PHA02849 putative transmembrane protein; Provisional
Probab=21.61 E-value=69 Score=24.60 Aligned_cols=16 Identities=19% Similarity=0.455 Sum_probs=10.6
Q ss_pred hHHHHHHHHHHHHHhh
Q 027871 201 RVSLFLFCCLVLCLLL 216 (217)
Q Consensus 201 ri~~Fl~ccvvLCLll 216 (217)
-|++|+++.+++|.||
T Consensus 19 vi~v~v~vI~i~~flL 34 (82)
T PHA02849 19 VILVFVLVISFLAFML 34 (82)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3666777777777665
No 124
>KOG1952 consensus Transcription factor NF-X1, contains NFX-type Zn2+-binding and R3H domains [Transcription]
Probab=21.45 E-value=25 Score=37.24 Aligned_cols=63 Identities=13% Similarity=0.091 Sum_probs=43.6
Q ss_pred CCCCCccccccCCCC--CcceE-------eeCCCCCCCCCCCCCCCcCCCCCCCccccccccceeeeecCCC
Q 027871 2 EQNLFEPETGYATEE--DASLK-------QKWSPTSAPTNVPEKDDEQQQNCPVCKANISVASLVPLYGRGG 64 (217)
Q Consensus 2 ~~s~FeCnICld~A~--dpVVT-------ycW~ci~~w~~~~~~~~~~~~~CPVCKa~Vs~~~viPLYGRG~ 64 (217)
+++.|||-||+|.-+ +||-. |--.||-.|....++...+.--||-|...-.+..+..+-=-|+
T Consensus 188 ~~~~yeCmIC~e~I~~t~~~WSC~sCYhVFHl~CI~~WArs~ek~~~~~WrCP~Cqsv~~~~~~~y~C~CGk 259 (950)
T KOG1952|consen 188 SNRKYECMICTERIKRTAPVWSCKSCYHVFHLNCIKKWARSSEKTGQDGWRCPACQSVSKTVPKTYLCFCGK 259 (950)
T ss_pred hcCceEEEEeeeeccccCCceecchhhhhhhHHHHHHHHHHhhhccCccccCCcccchhccCCcccceecCc
Confidence 578999999999765 56653 4566888887655555557788999997666555544333344
No 125
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=21.29 E-value=35 Score=19.97 Aligned_cols=12 Identities=0% Similarity=-0.169 Sum_probs=8.2
Q ss_pred CCCCCccccccC
Q 027871 2 EQNLFEPETGYA 13 (217)
Q Consensus 2 ~~s~FeCnICld 13 (217)
.+..|+|.+|-.
T Consensus 11 ~~k~~~C~~C~k 22 (26)
T PF13465_consen 11 GEKPYKCPYCGK 22 (26)
T ss_dssp SSSSEEESSSSE
T ss_pred CCCCCCCCCCcC
Confidence 456778888754
No 126
>COG4469 CoiA Competence protein CoiA-like family, contains a predicted nuclease domain [General function prediction only]
Probab=20.48 E-value=40 Score=32.10 Aligned_cols=22 Identities=18% Similarity=0.566 Sum_probs=16.5
Q ss_pred CCCCCccccccc---cceeeeecCC
Q 027871 42 QNCPVCKANISV---ASLVPLYGRG 63 (217)
Q Consensus 42 ~~CPVCKa~Vs~---~~viPLYGRG 63 (217)
--|||||+.|-. ..++|=+..-
T Consensus 26 ffCPaC~~~l~lK~G~~k~pHFAHk 50 (342)
T COG4469 26 FFCPACGSQLILKQGLIKIPHFAHK 50 (342)
T ss_pred cccCCCCCeeeeecCccccchhhhh
Confidence 479999999876 4567766654
No 127
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=20.05 E-value=54 Score=25.89 Aligned_cols=35 Identities=17% Similarity=0.226 Sum_probs=21.5
Q ss_pred cCCCCCcceEeeCCCCCCCCCCCCCCCcCCCCCCCcccc
Q 027871 12 YATEEDASLKQKWSPTSAPTNVPEKDDEQQQNCPVCKAN 50 (217)
Q Consensus 12 ld~A~dpVVTycW~ci~~w~~~~~~~~~~~~~CPVCKa~ 50 (217)
|+....|++.+|..|=..+... ......||.|++.
T Consensus 62 L~i~~~p~~~~C~~Cg~~~~~~----~~~~~~CP~Cgs~ 96 (114)
T PRK03681 62 LHLEEQEAECWCETCQQYVTLL----TQRVRRCPQCHGD 96 (114)
T ss_pred EEEEeeCcEEEcccCCCeeecC----CccCCcCcCcCCC
Confidence 3444455566899998765431 1122569999964
Done!