Query psy3162
Match_columns 91
No_of_seqs 140 out of 823
Neff 6.7
Searched_HMMs 46136
Date Fri Aug 16 17:58:31 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3162.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3162hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0944|consensus 99.9 1.6E-22 3.4E-27 161.6 5.0 86 5-91 470-562 (763)
2 cd02668 Peptidase_C19L A subfa 99.7 1.3E-17 2.9E-22 123.3 7.1 73 7-79 155-239 (324)
3 cd02667 Peptidase_C19K A subfa 99.7 2.6E-17 5.6E-22 119.7 6.3 71 5-78 108-189 (279)
4 cd02660 Peptidase_C19D A subfa 99.7 3.9E-17 8.4E-22 119.9 7.1 74 5-78 173-256 (328)
5 cd02663 Peptidase_C19G A subfa 99.7 9.3E-17 2E-21 117.7 7.2 70 7-76 146-227 (300)
6 KOG1865|consensus 99.7 3.5E-17 7.6E-22 128.9 3.6 65 15-85 284-348 (545)
7 cd02664 Peptidase_C19H A subfa 99.7 1.1E-16 2.4E-21 118.8 5.3 61 16-76 153-214 (327)
8 COG5560 UBP12 Ubiquitin C-term 99.6 1.3E-17 2.9E-22 133.4 -0.4 73 5-78 672-756 (823)
9 cd02671 Peptidase_C19O A subfa 99.6 5.2E-16 1.1E-20 116.4 6.5 71 7-77 179-265 (332)
10 cd02659 peptidase_C19C A subfa 99.6 3.1E-15 6.8E-20 110.0 7.4 74 7-80 150-235 (334)
11 cd02669 Peptidase_C19M A subfa 99.6 2E-15 4.4E-20 116.6 4.4 70 7-78 302-372 (440)
12 cd02657 Peptidase_C19A A subfa 99.6 7E-15 1.5E-19 107.2 6.2 71 7-77 159-236 (305)
13 cd02658 Peptidase_C19B A subfa 99.5 1.4E-14 3E-19 106.0 6.8 70 6-75 176-252 (311)
14 KOG1866|consensus 99.5 4.9E-16 1.1E-20 126.0 -2.3 67 15-81 264-331 (944)
15 KOG1870|consensus 99.5 2.4E-15 5.2E-20 124.1 0.9 76 4-80 692-779 (842)
16 cd02674 Peptidase_C19R A subfa 99.5 2.6E-14 5.7E-19 99.9 5.5 70 6-76 82-163 (230)
17 cd02661 Peptidase_C19E A subfa 99.5 3.2E-14 6.8E-19 102.5 5.8 69 8-79 162-241 (304)
18 cd02662 Peptidase_C19F A subfa 99.4 6.4E-13 1.4E-17 95.0 6.1 56 7-70 95-158 (240)
19 KOG4598|consensus 99.4 1.1E-13 2.4E-18 112.5 1.0 69 15-83 232-301 (1203)
20 cd02672 Peptidase_C19P A subfa 99.4 1.2E-12 2.6E-17 95.9 5.6 72 6-77 115-204 (268)
21 cd02670 Peptidase_C19N A subfa 99.3 9.4E-13 2E-17 95.6 4.4 61 6-79 78-138 (241)
22 COG5207 UBP14 Isopeptidase T [ 99.2 2.8E-12 6.1E-17 101.6 2.6 74 16-90 476-551 (749)
23 cd02257 Peptidase_C19 Peptidas 99.2 2.4E-11 5.2E-16 82.9 6.9 72 6-77 97-178 (255)
24 COG5533 UBP5 Ubiquitin C-termi 99.2 1.6E-11 3.4E-16 92.7 4.4 49 15-64 282-330 (415)
25 cd02665 Peptidase_C19I A subfa 99.1 1.1E-10 2.4E-15 84.2 3.4 67 8-75 93-164 (228)
26 KOG1868|consensus 99.0 7.5E-11 1.6E-15 95.5 -0.4 69 7-76 496-578 (653)
27 KOG1867|consensus 98.9 5.9E-10 1.3E-14 88.0 3.2 71 8-78 334-415 (492)
28 PF00443 UCH: Ubiquitin carbox 98.9 7.5E-10 1.6E-14 76.9 3.0 62 15-81 140-203 (269)
29 cd02673 Peptidase_C19Q A subfa 98.9 1.3E-09 2.9E-14 78.9 3.9 44 8-52 110-160 (245)
30 PF13423 UCH_1: Ubiquitin carb 98.7 2.9E-08 6.4E-13 72.7 5.3 79 2-81 157-243 (295)
31 KOG1864|consensus 98.6 1.6E-08 3.4E-13 81.4 2.2 68 15-82 439-507 (587)
32 KOG1873|consensus 98.6 2.5E-09 5.4E-14 87.5 -2.9 70 7-76 677-784 (877)
33 COG5077 Ubiquitin carboxyl-ter 98.5 2.3E-08 5E-13 82.5 -0.2 64 16-80 357-421 (1089)
34 KOG1863|consensus 98.4 8E-08 1.7E-12 81.7 1.3 61 18-78 338-399 (1093)
35 KOG2026|consensus 97.5 6.8E-05 1.5E-09 58.2 2.8 46 31-77 327-373 (442)
36 KOG1871|consensus 97.1 3.8E-05 8.3E-10 59.5 -2.5 59 16-74 280-338 (420)
37 KOG1872|consensus 96.4 0.00033 7.1E-09 55.3 -2.4 62 20-81 287-349 (473)
38 COG3478 Predicted nucleic-acid 92.3 0.18 3.8E-06 30.2 2.8 36 16-51 3-40 (68)
39 PF09855 DUF2082: Nucleic-acid 88.2 0.6 1.3E-05 27.7 2.7 34 18-51 1-36 (64)
40 cd02666 Peptidase_C19J A subfa 83.8 0.16 3.4E-06 38.7 -1.8 45 6-75 187-231 (343)
41 PF15499 Peptidase_C98: Ubiqui 80.5 0.6 1.3E-05 34.9 0.3 26 19-45 172-197 (275)
42 TIGR00373 conserved hypothetic 77.3 1.5 3.3E-05 29.9 1.5 24 3-26 114-137 (158)
43 KOG2463|consensus 72.4 5.5 0.00012 30.9 3.5 37 15-52 255-292 (376)
44 PF14690 zf-ISL3: zinc-finger 71.4 7.4 0.00016 20.6 3.1 34 18-51 3-44 (47)
45 KOG1275|consensus 70.5 1.7 3.6E-05 37.7 0.5 59 18-76 702-763 (1118)
46 PRK06266 transcription initiat 69.4 3.3 7.1E-05 28.9 1.7 23 5-27 124-146 (178)
47 TIGR00310 ZPR1_znf ZPR1 zinc f 67.9 5.8 0.00013 28.1 2.7 63 10-74 23-87 (192)
48 PF14205 Cys_rich_KTR: Cystein 67.5 3.6 7.7E-05 23.8 1.3 24 18-41 5-30 (55)
49 PF07754 DUF1610: Domain of un 66.5 2.8 6.2E-05 20.2 0.6 11 15-25 14-24 (24)
50 TIGR00340 zpr1_rel ZPR1-relate 60.6 8 0.00017 26.7 2.2 62 10-73 21-84 (163)
51 PF08772 NOB1_Zn_bind: Nin one 60.0 6.7 0.00015 23.7 1.6 33 15-48 22-54 (73)
52 COG1675 TFA1 Transcription ini 53.7 8.9 0.00019 26.9 1.6 24 5-28 120-143 (176)
53 COG1379 PHP family phosphoeste 48.7 8.6 0.00019 30.0 0.9 19 8-26 256-274 (403)
54 cd00730 rubredoxin Rubredoxin; 47.6 8.8 0.00019 21.5 0.6 15 14-28 31-45 (50)
55 PF10146 zf-C4H2: Zinc finger- 45.9 13 0.00029 27.0 1.6 27 3-29 190-220 (230)
56 cd00350 rubredoxin_like Rubred 45.1 10 0.00023 19.0 0.6 14 16-29 16-29 (33)
57 PF09723 Zn-ribbon_8: Zinc rib 44.5 15 0.00032 19.5 1.2 14 17-30 5-18 (42)
58 smart00440 ZnF_C2C2 C2C2 Zinc 44.4 26 0.00057 18.4 2.2 18 18-35 1-18 (40)
59 PF14353 CpXC: CpXC protein 44.4 17 0.00037 23.4 1.7 15 15-29 36-50 (128)
60 COG5533 UBP5 Ubiquitin C-termi 43.1 38 0.00082 26.5 3.6 64 15-78 233-334 (415)
61 PF12760 Zn_Tnp_IS1595: Transp 42.7 21 0.00046 19.1 1.7 12 15-26 16-27 (46)
62 PF00301 Rubredoxin: Rubredoxi 40.5 17 0.00036 20.1 1.1 14 14-27 31-44 (47)
63 PF12171 zf-C2H2_jaz: Zinc-fin 40.1 14 0.0003 17.4 0.6 10 17-26 1-10 (27)
64 PF04606 Ogr_Delta: Ogr/Delta- 37.9 20 0.00044 19.4 1.1 18 19-36 1-18 (47)
65 PF03367 zf-ZPR1: ZPR1 zinc-fi 37.7 51 0.0011 22.5 3.3 20 13-32 26-45 (161)
66 PF13894 zf-C2H2_4: C2H2-type 37.6 15 0.00031 15.9 0.4 10 18-27 1-10 (24)
67 TIGR00155 pqiA_fam integral me 37.3 19 0.00041 28.2 1.2 29 1-29 1-45 (403)
68 PF00096 zf-C2H2: Zinc finger, 37.1 11 0.00024 16.7 -0.1 9 18-26 1-9 (23)
69 PRK14890 putative Zn-ribbon RN 37.0 18 0.00038 21.2 0.8 12 15-26 46-57 (59)
70 cd04476 RPA1_DBD_C RPA1_DBD_C: 36.0 24 0.00051 23.6 1.5 12 16-27 50-61 (166)
71 PF13240 zinc_ribbon_2: zinc-r 35.1 19 0.00041 16.8 0.6 11 19-29 1-11 (23)
72 PF01096 TFIIS_C: Transcriptio 33.9 41 0.0009 17.5 1.9 16 18-33 1-16 (39)
73 COG2888 Predicted Zn-ribbon RN 33.5 21 0.00046 21.0 0.8 12 15-26 48-59 (61)
74 PF01780 Ribosomal_L37ae: Ribo 33.5 21 0.00047 22.5 0.9 22 15-36 33-54 (90)
75 TIGR03831 YgiT_finger YgiT-typ 33.0 20 0.00044 18.5 0.6 13 15-27 30-42 (46)
76 TIGR00280 L37a ribosomal prote 31.5 46 0.001 21.0 2.1 23 15-37 33-55 (91)
77 PF08271 TF_Zn_Ribbon: TFIIB z 31.3 24 0.00052 18.6 0.7 10 18-27 1-10 (43)
78 PRK03976 rpl37ae 50S ribosomal 31.0 49 0.0011 20.8 2.2 24 15-38 34-57 (90)
79 PF08646 Rep_fac-A_C: Replicat 31.0 23 0.00051 23.2 0.8 12 16-27 36-47 (146)
80 smart00834 CxxC_CXXC_SSSS Puta 30.6 34 0.00074 17.3 1.2 15 17-31 5-19 (41)
81 PF06397 Desulfoferrod_N: Desu 30.5 32 0.00069 18.0 1.1 16 16-31 5-20 (36)
82 PF04828 GFA: Glutathione-depe 30.0 54 0.0012 19.0 2.2 33 15-51 46-78 (92)
83 TIGR03071 couple_hipA HipA N-t 29.9 17 0.00037 22.3 -0.0 41 48-90 23-66 (101)
84 smart00709 Zpr1 Duplicated dom 29.6 95 0.002 21.3 3.6 23 10-32 22-44 (160)
85 PF09297 zf-NADH-PPase: NADH p 29.4 31 0.00067 17.0 0.9 13 17-29 3-15 (32)
86 PTZ00255 60S ribosomal protein 29.3 52 0.0011 20.7 2.1 23 15-37 34-56 (90)
87 smart00531 TFIIE Transcription 28.7 35 0.00076 22.7 1.3 11 17-27 99-109 (147)
88 PRK00398 rpoP DNA-directed RNA 28.4 34 0.00074 18.2 1.0 11 17-27 3-13 (46)
89 COG4830 RPS26B Ribosomal prote 28.3 47 0.001 21.5 1.8 21 18-38 21-44 (108)
90 KOG0402|consensus 27.4 17 0.00037 22.9 -0.4 23 15-37 34-56 (92)
91 PRK12366 replication factor A; 27.4 37 0.00079 28.1 1.5 11 16-26 547-557 (637)
92 TIGR02605 CxxC_CxxC_SSSS putat 26.5 42 0.00091 18.0 1.2 12 17-28 5-16 (52)
93 PF05605 zf-Di19: Drought indu 26.5 37 0.0008 18.6 0.9 10 16-25 1-10 (54)
94 PF04795 PAPA-1: PAPA-1-like c 26.2 53 0.0011 20.3 1.7 19 54-72 70-88 (89)
95 COG1997 RPL43A Ribosomal prote 25.8 53 0.0011 20.7 1.6 13 14-26 32-44 (89)
96 PRK08270 anaerobic ribonucleos 25.6 54 0.0012 27.4 2.1 25 8-32 624-654 (656)
97 PF13465 zf-H2C2_2: Zinc-finge 25.5 23 0.00049 16.7 -0.0 11 16-26 13-23 (26)
98 PF13248 zf-ribbon_3: zinc-rib 25.2 29 0.00064 16.4 0.3 11 16-26 15-25 (26)
99 TIGR00416 sms DNA repair prote 24.9 40 0.00087 26.7 1.2 29 1-29 1-33 (454)
100 smart00547 ZnF_RBZ Zinc finger 24.8 41 0.00088 15.5 0.8 13 16-28 1-13 (26)
101 PRK11823 DNA repair protein Ra 24.5 43 0.00093 26.4 1.3 31 1-31 1-35 (446)
102 cd00974 DSRD Desulforedoxin (D 23.9 58 0.0013 16.2 1.4 15 16-30 3-17 (34)
103 PF10825 DUF2752: Protein of u 23.6 30 0.00065 19.2 0.2 13 16-28 8-20 (52)
104 PHA02768 hypothetical protein; 23.6 34 0.00074 19.6 0.4 12 16-27 4-15 (55)
105 PF08792 A2L_zn_ribbon: A2L zi 23.4 47 0.001 16.9 0.9 14 16-29 2-15 (33)
106 COG5257 GCD11 Translation init 23.1 81 0.0018 24.9 2.5 26 15-40 70-95 (415)
107 TIGR00319 desulf_FeS4 desulfof 23.0 62 0.0013 16.1 1.3 15 16-30 6-20 (34)
108 PF04438 zf-HIT: HIT zinc fing 22.2 38 0.00082 16.8 0.4 11 16-26 12-22 (30)
109 PF03811 Zn_Tnp_IS1: InsA N-te 21.9 59 0.0013 16.9 1.1 15 17-31 5-19 (36)
110 PF10609 ParA: ParA/MinD ATPas 21.3 35 0.00076 20.9 0.2 13 15-27 63-75 (81)
111 KOG2324|consensus 21.1 1.1E+02 0.0024 24.4 2.9 49 18-76 248-300 (457)
112 PHA00616 hypothetical protein 20.8 31 0.00067 18.9 -0.1 9 18-26 2-10 (44)
113 smart00355 ZnF_C2H2 zinc finge 20.8 51 0.0011 14.0 0.7 9 18-26 1-9 (26)
114 TIGR00622 ssl1 transcription f 20.7 52 0.0011 21.5 0.9 35 17-51 1-36 (112)
115 PF03604 DNA_RNApol_7kD: DNA d 20.5 49 0.0011 16.7 0.6 11 18-28 1-11 (32)
116 PF08209 Sgf11: Sgf11 (transcr 20.2 42 0.00091 17.2 0.3 13 17-29 4-16 (33)
117 TIGR03830 CxxCG_CxxCG_HTH puta 20.0 48 0.001 20.8 0.7 12 15-26 29-40 (127)
No 1
>KOG0944|consensus
Probab=99.86 E-value=1.6e-22 Score=161.65 Aligned_cols=86 Identities=38% Similarity=0.674 Sum_probs=82.0
Q ss_pred CCCCchhhhh-------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCCCCC
Q psy3162 5 QPTKSFLGLY-------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPLRG 77 (91)
Q Consensus 5 ~~~~sl~~cl-------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~~~~ 77 (91)
|..|++..|+ .++|.|.+||+|..|+|+++|++||+|||||++||.+ .+|.++|++++|++|++|||+.|++
T Consensus 470 ~~~v~~~~cleaff~pq~~df~s~ac~~K~~a~kt~~~ksfP~yLiiqv~rf~~-~dw~pkKld~~iempe~ldls~~rs 548 (763)
T KOG0944|consen 470 REKVPISACLEAFFEPQVDDFWSTACGEKKGATKTTRFKSFPDYLIIQVGRFTL-QDWVPKKLDVSIEMPEELDLSSYRS 548 (763)
T ss_pred cccCCHHHHHHHhcCCcchhhhhHhhcCccccccccccccCCceEEEEeeEEEe-cCceeeeeccceecchhhchhhhhh
Confidence 5678899999 4699999999999999999999999999999999999 8999999999999999999999999
Q ss_pred CCCCCCCccCCCCC
Q psy3162 78 SGPQPGEEMLPEVA 91 (91)
Q Consensus 78 ~g~q~ge~~lpe~~ 91 (91)
.|+||||++||+++
T Consensus 549 ~g~~p~ee~lpde~ 562 (763)
T KOG0944|consen 549 KGLQPGEEALPDEA 562 (763)
T ss_pred cCCCCcccccCCcC
Confidence 99999999999975
No 2
>cd02668 Peptidase_C19L A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.72 E-value=1.3e-17 Score=123.25 Aligned_cols=73 Identities=18% Similarity=0.296 Sum_probs=65.3
Q ss_pred CCchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECC-CCeeeecceEEecCCCCCCCC
Q psy3162 7 TKSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKE-DWTLAKLDVEVEMPDTIDLTP 74 (91)
Q Consensus 7 ~~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~-~~~~~Kl~~~V~~P~~LDls~ 74 (91)
..||++|+ .+.|.|++|++++.|.|+..|.++|++|+||||||.++. .+...|+++.|+||+.|||++
T Consensus 155 ~~sl~~~L~~~~~~e~l~g~~~~~C~~C~~~~~a~k~~~i~~lP~iLii~LkRf~~d~~~~~~~Ki~~~v~fp~~Ldl~~ 234 (324)
T cd02668 155 HKTLEECIDEFLKEEQLTGDNQYFCESCNSKTDATRRIRLTTLPPTLNFQLLRFVFDRKTGAKKKLNASISFPEILDMGE 234 (324)
T ss_pred cCCHHHHHHHhhCceecCCCccccCCCCCceeeeEEEEEecCCCCeEEEEEEcceeecccCcceeCCcEEECCCeEechh
Confidence 46889998 245999999999999999999999999999999999974 477899999999999999999
Q ss_pred CCCCC
Q psy3162 75 LRGSG 79 (91)
Q Consensus 75 ~~~~g 79 (91)
|+..+
T Consensus 235 ~~~~~ 239 (324)
T cd02668 235 YLAES 239 (324)
T ss_pred hcccc
Confidence 97543
No 3
>cd02667 Peptidase_C19K A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.70 E-value=2.6e-17 Score=119.70 Aligned_cols=71 Identities=21% Similarity=0.318 Sum_probs=64.5
Q ss_pred CCCCchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCC
Q psy3162 5 QPTKSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLT 73 (91)
Q Consensus 5 ~~~~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls 73 (91)
...+||++|+ .+.|.|++|++ |+|+..|.++|++|+||||||.++.+|...|+++.|+||+.|||+
T Consensus 108 ~~~~sL~~~L~~~~~~E~l~~~~~~~C~~C~~---a~k~~~i~~~P~~Lii~LkRF~~~~~~~~~Ki~~~v~fP~~Ldl~ 184 (279)
T cd02667 108 KSECSIESCLKQFTEVEILEGNNKFACENCTK---AKKQYLISKLPPVLVIHLKRFQQPRSANLRKVSRHVSFPEILDLA 184 (279)
T ss_pred CCCCCHHHHHHhhcCeeEecCCCcccCCccCc---eeeEeEhhhCCCeEEEEEeccccCcccCceecCceEeCCCccchh
Confidence 4568999999 25699999998 899999999999999999999997777889999999999999999
Q ss_pred CCCCC
Q psy3162 74 PLRGS 78 (91)
Q Consensus 74 ~~~~~ 78 (91)
+|+..
T Consensus 185 ~~~~~ 189 (279)
T cd02667 185 PFCDP 189 (279)
T ss_pred hccCc
Confidence 99865
No 4
>cd02660 Peptidase_C19D A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.70 E-value=3.9e-17 Score=119.87 Aligned_cols=74 Identities=20% Similarity=0.248 Sum_probs=66.4
Q ss_pred CCCCchhhhh--------c--CCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCC
Q psy3162 5 QPTKSFLGLY--------C--GKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTP 74 (91)
Q Consensus 5 ~~~~sl~~cl--------~--~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~ 74 (91)
.+..||++|+ + +.|+|++|+.++.+.|++.|.++|++|+||||||.++..|...|++..|.||.+|||++
T Consensus 173 ~~~~sl~~~L~~~~~~e~~~~~~~~C~~C~~~~~~~~~~~i~~lP~~Lii~lkRf~~~~~~~~~K~~~~v~fp~~Ldl~~ 252 (328)
T cd02660 173 SGTPTLSDCLDRFTRPEKLGDFAYKCSGCGSTQEATKQLSIKKLPPVLCFQLKRFEHSLNKTSRKIDTYVQFPLELNMTP 252 (328)
T ss_pred CCCCCHHHHHHHhcCccccCCCCccCCCCCCccceEEEEEecCCCceeEEEEEeEEecCCCCCcCCCcEEeCCCEechhh
Confidence 3458999998 1 23899999999999999999999999999999999965588899999999999999999
Q ss_pred CCCC
Q psy3162 75 LRGS 78 (91)
Q Consensus 75 ~~~~ 78 (91)
|+..
T Consensus 253 ~~~~ 256 (328)
T cd02660 253 YTSS 256 (328)
T ss_pred hccc
Confidence 9875
No 5
>cd02663 Peptidase_C19G A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.68 E-value=9.3e-17 Score=117.67 Aligned_cols=70 Identities=20% Similarity=0.220 Sum_probs=62.9
Q ss_pred CCchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCC-CeeeecceEEecCCCCCCCC
Q psy3162 7 TKSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKED-WTLAKLDVEVEMPDTIDLTP 74 (91)
Q Consensus 7 ~~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~-~~~~Kl~~~V~~P~~LDls~ 74 (91)
..||++|+ .+.|+|++|+.++.|+|++.|.++|++|+||||||.++.. +...|++..|.||.+|||..
T Consensus 146 ~~sl~~~L~~~~~~E~l~~~~~~~C~~C~~~~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fp~~L~~~~ 225 (300)
T cd02663 146 NTSITSCLRQFSATETLCGRNKFYCDECCSLQEAEKRMKIKKLPKILALHLKRFKYDEQLNRYIKLFYRVVFPLELRLFN 225 (300)
T ss_pred cCCHHHHHHHhhcccccCCCCcEECCCCCCceeEEEEEEeccCCceeEEEEEeEEeecccCCceecCceEecCcEEeccc
Confidence 56899998 2579999999999999999999999999999999999754 36789999999999999988
Q ss_pred CC
Q psy3162 75 LR 76 (91)
Q Consensus 75 ~~ 76 (91)
+.
T Consensus 226 ~~ 227 (300)
T cd02663 226 TT 227 (300)
T ss_pred cc
Confidence 74
No 6
>KOG1865|consensus
Probab=99.66 E-value=3.5e-17 Score=128.86 Aligned_cols=65 Identities=26% Similarity=0.358 Sum_probs=59.8
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCCCCCCCCCCCCc
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPLRGSGPQPGEE 85 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~~~~~g~q~ge~ 85 (91)
.|.|+|++|++++.|.|+++|.+.|.||+||||||+. ++..||+..|.||+.|||.+|++ |++|.
T Consensus 284 en~Y~C~~Ck~~v~A~K~lti~raPnVLTi~LKRF~~---~~~gKI~K~I~fPE~LDl~PyMS---~~~e~ 348 (545)
T KOG1865|consen 284 ENAYHCGRCKQKVPASKQLTIHRAPNVLTLHLKRFSN---GTGGKISKPVSFPETLDLQPYMS---QPNEG 348 (545)
T ss_pred ccccccchhhhhCcccceeeeecCCceEEEeeehhcc---CcccccccccCCccccccccccc---CCCCC
Confidence 5899999999999999999999999999999999997 45679999999999999999998 45554
No 7
>cd02664 Peptidase_C19H A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.66 E-value=1.1e-16 Score=118.83 Aligned_cols=61 Identities=13% Similarity=0.250 Sum_probs=56.5
Q ss_pred CCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCC-CeeeecceEEecCCCCCCCCCC
Q psy3162 16 GKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKED-WTLAKLDVEVEMPDTIDLTPLR 76 (91)
Q Consensus 16 ~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~-~~~~Kl~~~V~~P~~LDls~~~ 76 (91)
+.|+|++|++++.|.|++.|.++|+||+||||||.++.. +...|++..|.||..|||..|.
T Consensus 153 n~~~C~~C~~~~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fp~~ldl~~~~ 214 (327)
T cd02664 153 NQYYCEKCASLQDAEKEMKVTGAPEYLILTLLRFSYDQKTHVREKIMDNVSINEVLSLPVRV 214 (327)
T ss_pred CceeCCccCCccceeEEEEcccCChhhEEEeeeeEEccccCcceecCceEecCCEEecCccc
Confidence 459999999999999999999999999999999999754 6778999999999999999886
No 8
>COG5560 UBP12 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=99.65 E-value=1.3e-17 Score=133.43 Aligned_cols=73 Identities=22% Similarity=0.226 Sum_probs=67.6
Q ss_pred CCCCchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecC-CCCCC
Q psy3162 5 QPTKSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP-DTIDL 72 (91)
Q Consensus 5 ~~~~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P-~~LDl 72 (91)
..++||.+|+ .+.|+|+.|++++.|+|++.|+++|.+||||||||.. .+..+.|+++-|.|| ++|||
T Consensus 672 ~rtiTL~dCl~eFskpEqLgl~DswyCpgCkefrqasKqmelwrlP~iLiihLkRFss-~rsfrdKiddlVeyPiddldL 750 (823)
T COG5560 672 ERTITLQDCLNEFSKPEQLGLSDSWYCPGCKEFRQASKQMELWRLPMILIIHLKRFSS-VRSFRDKIDDLVEYPIDDLDL 750 (823)
T ss_pred cCCCcHHHHHHHhccHhhcCCcccccCCchHhhhhhhhhhhhhcCChheeeehhhhhh-cccchhhhhhhhccccccccc
Confidence 3689999999 5899999999999999999999999999999999998 677889999999999 99999
Q ss_pred CCCCCC
Q psy3162 73 TPLRGS 78 (91)
Q Consensus 73 s~~~~~ 78 (91)
+.+.+.
T Consensus 751 s~~~~~ 756 (823)
T COG5560 751 SGVEYM 756 (823)
T ss_pred cceEEe
Confidence 987654
No 9
>cd02671 Peptidase_C19O A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.63 E-value=5.2e-16 Score=116.37 Aligned_cols=71 Identities=17% Similarity=0.191 Sum_probs=62.3
Q ss_pred CCchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCC-----CeeeecceEEecCCCC
Q psy3162 7 TKSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKED-----WTLAKLDVEVEMPDTI 70 (91)
Q Consensus 7 ~~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~-----~~~~Kl~~~V~~P~~L 70 (91)
..||++|+ .|+|+|++|+.++.|+|++.|.++|++|+||||||.++.. +...|++..|.||..|
T Consensus 179 ~~tL~~~L~~f~~~E~l~g~n~y~C~~C~~~~~a~k~~~~~~~P~vL~i~LkRF~~~~~~~~~~~~~~Ki~~~v~fp~~L 258 (332)
T cd02671 179 MKTLKWAISQFASVERIVGEDKYFCENCHHYTEAERSLLFDKLPEVITIHLKCFAANGSEFDCYGGLSKVNTPLLTPLKL 258 (332)
T ss_pred cCCHHHHHHHhCCcceecCCCCeeCCCCCCceeEEEEEEEecCCCEEEEEeeeeccccccccccCCceecCccccCcccc
Confidence 36899998 2579999999999999999999999999999999998532 2468999999999999
Q ss_pred CCCCCCC
Q psy3162 71 DLTPLRG 77 (91)
Q Consensus 71 Dls~~~~ 77 (91)
||.++..
T Consensus 259 ~~~~~~~ 265 (332)
T cd02671 259 SLEEWST 265 (332)
T ss_pred ccccccC
Confidence 9998764
No 10
>cd02659 peptidase_C19C A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.59 E-value=3.1e-15 Score=110.00 Aligned_cols=74 Identities=18% Similarity=0.243 Sum_probs=64.7
Q ss_pred CCchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECC-CCeeeecceEEecCCCCCCCC
Q psy3162 7 TKSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKE-DWTLAKLDVEVEMPDTIDLTP 74 (91)
Q Consensus 7 ~~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~-~~~~~Kl~~~V~~P~~LDls~ 74 (91)
..++++|+ .+.|+|++|++++.|.|+..|.++|++|+|||+||.++. .+...|++..|+||..|||++
T Consensus 150 ~~~l~~~l~~~~~~e~l~~~~~~~C~~C~~~~~~~k~~~i~~lP~vLii~l~Rf~~~~~~~~~~K~~~~v~fp~~Ldl~~ 229 (334)
T cd02659 150 KKNLEESLDAYVQGETLEGDNKYFCEKCGKKVDAEKGVCFKKLPPVLTLQLKRFEFDFETMMRIKINDRFEFPLELDMEP 229 (334)
T ss_pred CCCHHHHHHHhcCeeEecCCccEecCcCCCcccEEEEEEeecCCCEEEEEeeeeEEccccCcceeCCceEeCCceecCcc
Confidence 45677887 245999999999999999999999999999999999963 366789999999999999999
Q ss_pred CCCCCC
Q psy3162 75 LRGSGP 80 (91)
Q Consensus 75 ~~~~g~ 80 (91)
|+..+.
T Consensus 230 ~~~~~~ 235 (334)
T cd02659 230 YTEKGL 235 (334)
T ss_pred cccccc
Confidence 987654
No 11
>cd02669 Peptidase_C19M A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.57 E-value=2e-15 Score=116.58 Aligned_cols=70 Identities=21% Similarity=0.312 Sum_probs=63.1
Q ss_pred CCchhhhhcCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCC-CCCCCCCCC
Q psy3162 7 TKSFLGLYCGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDT-IDLTPLRGS 78 (91)
Q Consensus 7 ~~sl~~cl~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~-LDls~~~~~ 78 (91)
.+++++|+ ++|.|+.|.....|+|+++|+++|+||+||||||.++ .+...|+++.|+||.. |||++|...
T Consensus 302 ~~~l~e~L-~ky~~~~c~~~~~a~k~~~I~~LP~vLiihLKRF~~~-~~~~~K~~t~V~FP~~~LDm~~y~~~ 372 (440)
T cd02669 302 QVPLKQLL-KKYDGKTETELKDSLKRYLISRLPKYLIFHIKRFSKN-NFFKEKNPTIVNFPIKNLDLSDYVHF 372 (440)
T ss_pred cccHHHHH-HhcCCccceecccceEEEEEeeCCcEEEEEEecccCC-CCccccCCCEEECCCCccchhhhhCc
Confidence 47888887 5899999999999999999999999999999999995 4677899999999975 899999863
No 12
>cd02657 Peptidase_C19A A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.56 E-value=7e-15 Score=107.15 Aligned_cols=71 Identities=23% Similarity=0.221 Sum_probs=62.0
Q ss_pred CCchhhhhc------CCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCC-CeeeecceEEecCCCCCCCCCCC
Q psy3162 7 TKSFLGLYC------GKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKED-WTLAKLDVEVEMPDTIDLTPLRG 77 (91)
Q Consensus 7 ~~sl~~cl~------~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~-~~~~Kl~~~V~~P~~LDls~~~~ 77 (91)
..+|++|+. ....|+.|+....++|+..|.++|++|+||||||.++.. +...|+++.|.||.+|||++|+.
T Consensus 159 ~~~l~~~L~~~~~~~~~~~~~~~~~~~~~~k~~~i~~lP~vLii~LkRF~~~~~~~~~~Ki~~~v~fP~~Ldl~~~~~ 236 (305)
T cd02657 159 VNYLQDGLKKGLEEEIEKHSPTLGRDAIYTKTSRISRLPKYLTVQFVRFFWKRDIQKKAKILRKVKFPFELDLYELCT 236 (305)
T ss_pred cccHHHHHHHhhhhhhhhcCcccCCCceEEEEEEeccCCcEEEEEEECCccccccCceeecCcEEECCceEecccccC
Confidence 457888883 345799999999999999999999999999999999644 45789999999999999999874
No 13
>cd02658 Peptidase_C19B A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.54 E-value=1.4e-14 Score=105.98 Aligned_cols=70 Identities=23% Similarity=0.440 Sum_probs=61.6
Q ss_pred CCCchhhhh-------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCCC
Q psy3162 6 PTKSFLGLY-------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPL 75 (91)
Q Consensus 6 ~~~sl~~cl-------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~~ 75 (91)
+.+||++|+ .-.++|+.|++++.|+|+.+|.++|++|+|||+||.++.+|.+.|++..|.||..|.-..|
T Consensus 176 ~~~sl~~~L~~~~~~e~i~~~C~~C~~~~~a~k~~~i~~lP~vLii~LkRF~~~~~~~~~Ki~~~v~~p~~l~~~~Y 252 (311)
T cd02658 176 EPVPLEDCLKAYFAPETIEDFCSTCKEKTTATKTTGFKTFPDYLVINMKRFQLLENWVPKKLDVPIDVPEELGPGKY 252 (311)
T ss_pred CCCCHHHHHHHHcCcccccccccCCCCcccEEEEEEeecCCceEEEEeEEEEecCCCceEeeccccccCCcCCCCcE
Confidence 467999999 2357899999999999999999999999999999999778999999999999987744444
No 14
>KOG1866|consensus
Probab=99.52 E-value=4.9e-16 Score=125.95 Aligned_cols=67 Identities=22% Similarity=0.319 Sum_probs=62.8
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEEC-CCCeeeecceEEecCCCCCCCCCCCCCCC
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMK-EDWTLAKLDVEVEMPDTIDLTPLRGSGPQ 81 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~-~~~~~~Kl~~~V~~P~~LDls~~~~~g~q 81 (91)
.|.|+|++|++|+...|++.|++||.||+||||||.|| ++....|.|..+.||.+|||++|..+|..
T Consensus 264 ~nAYhCeKCdeK~~TvkRt~ik~LPsvl~IqLkRF~yD~e~~~~iK~n~~frFP~~ldMePYtvsg~a 331 (944)
T KOG1866|consen 264 ANAYHCEKCDEKVDTVKRTCIKKLPSVLAIQLKRFDYDWERECAIKFNDYFRFPRELDMEPYTVSGVA 331 (944)
T ss_pred cchhhhhhhhhhhHhHHHHHHhhCChhheehhhhccchhhhccccccchhcccchhhcCCceeehhhh
Confidence 59999999999999999999999999999999999997 56678899999999999999999988865
No 15
>KOG1870|consensus
Probab=99.51 E-value=2.4e-15 Score=124.08 Aligned_cols=76 Identities=18% Similarity=0.271 Sum_probs=68.9
Q ss_pred CCCCCchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecC-CCCC
Q psy3162 4 PQPTKSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP-DTID 71 (91)
Q Consensus 4 ~~~~~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P-~~LD 71 (91)
..+.+||+.|+ .+.|+|+.|++++.|+|++.++++|++||||||||.+ .++...|+++.|+|| ..||
T Consensus 692 ~~~~~sL~~cl~~F~~~E~L~~~~~w~C~~Cke~~~A~Kk~~lwrlPeiLiihLKrF~~-~r~~~~k~~~~v~fPi~~ld 770 (842)
T KOG1870|consen 692 SPAPNSLESCLELFSEPETLGKDDRWYCPQCKELRQATKKLDLWRLPEILIIHLKRFQY-SRESSSKVKTKVEFPLGSLD 770 (842)
T ss_pred CCCcccHHHHHHhhcchhcCCccccccChHHHHHHHHhhhhhhhhCCceEEEEeeccee-echhhhhhCccccCCCcCCC
Confidence 44589999999 4899999999999999999999999999999999999 555569999999999 8999
Q ss_pred CCCCCCCCC
Q psy3162 72 LTPLRGSGP 80 (91)
Q Consensus 72 ls~~~~~g~ 80 (91)
+++|...+-
T Consensus 771 ~s~~~~~~~ 779 (842)
T KOG1870|consen 771 LSEFVVNKE 779 (842)
T ss_pred cchhhccCc
Confidence 999987653
No 16
>cd02674 Peptidase_C19R A subfamily of peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.51 E-value=2.6e-14 Score=99.85 Aligned_cols=70 Identities=21% Similarity=0.328 Sum_probs=63.0
Q ss_pred CCCchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecC-CCCCCC
Q psy3162 6 PTKSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP-DTIDLT 73 (91)
Q Consensus 6 ~~~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P-~~LDls 73 (91)
+..||.+|+ .+.+.|++|+.++.+.++..|.++|++|+|||+||.++ ++...|++..|.|| +.|||+
T Consensus 82 ~~~sl~~~L~~~~~~e~~~~~~~~~C~~C~~~~~~~~~~~i~~lP~iLii~l~R~~~~-~~~~~K~~~~v~~~~~~l~l~ 160 (230)
T cd02674 82 PKVTLEDCLRLFTKEETLDGDNAWKCPKCKKKRKATKKLTISRLPKVLIIHLKRFSFS-RGSTRKLTTPVTFPLNDLDLT 160 (230)
T ss_pred CCCCHHHHHHHhcCccccCCCCceeCCCCCCccceEEEEEEecCChhhEeEhhheecC-CCCcccCCceEeccccccccc
Confidence 568999998 24699999999999999999999999999999999994 47788999999999 679999
Q ss_pred CCC
Q psy3162 74 PLR 76 (91)
Q Consensus 74 ~~~ 76 (91)
+|.
T Consensus 161 ~~~ 163 (230)
T cd02674 161 PYV 163 (230)
T ss_pred ccc
Confidence 884
No 17
>cd02661 Peptidase_C19E A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.50 E-value=3.2e-14 Score=102.55 Aligned_cols=69 Identities=20% Similarity=0.297 Sum_probs=61.1
Q ss_pred Cchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCCCC
Q psy3162 8 KSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPLR 76 (91)
Q Consensus 8 ~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~~~ 76 (91)
.+|.+|+ .+.|+|++|++++.+.++..|.++|++|+|||+||.++ ...|++..|.||++|||++|.
T Consensus 162 ~~l~~~l~~~~~~e~~~~~~~~~C~~C~~~~~~~~~~~i~~~P~iL~i~l~Rf~~~---~~~Ki~~~v~f~~~L~l~~~~ 238 (304)
T cd02661 162 DSLEDALEQFTKPEQLDGENKYKCERCKKKVKASKQLTIHRAPNVLTIHLKRFSNF---RGGKINKQISFPETLDLSPYM 238 (304)
T ss_pred CcHHHHHHHhcCceeeCCCCCeeCCCCCCccceEEEEEEecCCcEEEEEEeccccC---CccccCCeEecCCeechhhcc
Confidence 4677777 23489999999999999999999999999999999994 567999999999999999988
Q ss_pred CCC
Q psy3162 77 GSG 79 (91)
Q Consensus 77 ~~g 79 (91)
..+
T Consensus 239 ~~~ 241 (304)
T cd02661 239 SQP 241 (304)
T ss_pred ccC
Confidence 653
No 18
>cd02662 Peptidase_C19F A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.39 E-value=6.4e-13 Score=95.04 Aligned_cols=56 Identities=16% Similarity=0.197 Sum_probs=50.8
Q ss_pred CCchhhhh--------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCC
Q psy3162 7 TKSFLGLY--------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTI 70 (91)
Q Consensus 7 ~~sl~~cl--------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~L 70 (91)
..|+++|+ +++|.|++| +..|.++|++|+||||||.++..|...|+++.|.||+.|
T Consensus 95 ~~sl~~~L~~~~~~E~l~~~~C~~C--------~~~i~~lP~vLii~LkRF~~~~~~~~~K~~~~v~fp~~l 158 (240)
T cd02662 95 GTTLEHCLDDFLSTEIIDDYKCDRC--------QTVIVRLPQILCIHLSRSVFDGRGTSTKNSCKVSFPERL 158 (240)
T ss_pred CCCHHHHHHHhcCcccccCcCCCCC--------eEEeecCCcEEEEEEEEEEEcCCCceeeeccEEECCCcc
Confidence 67899999 468999999 678999999999999999997558999999999999988
No 19
>KOG4598|consensus
Probab=99.37 E-value=1.1e-13 Score=112.50 Aligned_cols=69 Identities=19% Similarity=0.304 Sum_probs=61.9
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECC-CCeeeecceEEecCCCCCCCCCCCCCCCCC
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKE-DWTLAKLDVEVEMPDTIDLTPLRGSGPQPG 83 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~-~~~~~Kl~~~V~~P~~LDls~~~~~g~q~g 83 (91)
.|+|.|++|+++..|.|-++|++||-+|.||||||.+|- .....|||..++||+.|||..|....-..|
T Consensus 232 ~nqy~ce~ck~k~dahkgl~~~~fpy~lt~~lkrfdfdy~tmhriklnd~~tfp~~l~ln~~in~~~~s~ 301 (1203)
T KOG4598|consen 232 SNQYMCENCKSKQDAHKGLRITQFPYLLTIQLKRFDFDYNTMHRIKLNDKMTFPDVLDLNDYVNKEKRST 301 (1203)
T ss_pred ccHHHHhhhhhhhhhhcCceeeccceeeEEeeecccccchheeeeeecccccCcccccHHHhhhhccCCc
Confidence 589999999999999999999999999999999999973 488999999999999999999985443333
No 20
>cd02672 Peptidase_C19P A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.35 E-value=1.2e-12 Score=95.93 Aligned_cols=72 Identities=17% Similarity=0.074 Sum_probs=60.8
Q ss_pred CCCchhhhh--------cCCcccCCCCCcceeEEEeecccCCC----eeEEEeeceEECCC------CeeeecceEEecC
Q psy3162 6 PTKSFLGLY--------CGKVLTYALDFVLSTLRTTRLASFPD----YLMFHLKKFTMKED------WTLAKLDVEVEMP 67 (91)
Q Consensus 6 ~~~sl~~cl--------~~~~~C~~C~~~~~a~k~~~~~~lP~----vLiihlkRF~~~~~------~~~~Kl~~~V~~P 67 (91)
+.+||.+|+ .++|.|++|++++.|+|+++|++||+ ||+||||||..... ....|++..|.+|
T Consensus 115 ~~~sl~~cL~~~~~~E~~~~~~C~~C~~~~~a~k~~~i~~lP~~L~~VL~i~lkrf~~~~~~~~~~~~~~~~~~~~v~f~ 194 (268)
T cd02672 115 KESTFLQLLKRSLDLEKVTKAWCDTCCKYQPLEQTTSIRHLPDILLLVLVINLSVTNGEFDDINVVLPSGKVMQNKVSPK 194 (268)
T ss_pred cCCCHHHHHHHHhhhhhcccccccccCcccccEEEEEeecCCCcccceEEEEEeccChhhcccCcceeEEEecCCeeccc
Confidence 568999999 57899999999999999999999999 99999999997311 1346888999999
Q ss_pred CCCCCCCCCC
Q psy3162 68 DTIDLTPLRG 77 (91)
Q Consensus 68 ~~LDls~~~~ 77 (91)
..+|+..+..
T Consensus 195 ~~~~~~~~~~ 204 (268)
T cd02672 195 AIDHDKLVKN 204 (268)
T ss_pred ccccchhhhc
Confidence 8887766543
No 21
>cd02670 Peptidase_C19N A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.34 E-value=9.4e-13 Score=95.61 Aligned_cols=61 Identities=18% Similarity=0.209 Sum_probs=51.3
Q ss_pred CCCchhhhhcCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCCCCCCC
Q psy3162 6 PTKSFLGLYCGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPLRGSG 79 (91)
Q Consensus 6 ~~~sl~~cl~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~~~~~g 79 (91)
..+||++|+..-+.-+. |+++|++|+||||||.++. |...|+++.|.||..|||++|....
T Consensus 78 ~~~tLedcLe~~~~~e~------------i~~lP~vLiIhLKRF~~~~-~~~~Kl~~~I~fP~~Ldl~~~~~~~ 138 (241)
T cd02670 78 GGITLEQCLEQYFNNSV------------FAKAPSCLIICLKRYGKTE-GKAQKMFKKILIPDEIDIPDFVADD 138 (241)
T ss_pred CcCCHHHHHHHHhchhh------------hhhCCCeEEEEEEccccCC-CcceeCCcEECCCCcCCchhhcccc
Confidence 57999999943332222 9999999999999999965 7889999999999999999998654
No 22
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=99.25 E-value=2.8e-12 Score=101.58 Aligned_cols=74 Identities=20% Similarity=0.331 Sum_probs=68.5
Q ss_pred CCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecC--CCCCCCCCCCCCCCCCCccCCCC
Q psy3162 16 GKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP--DTIDLTPLRGSGPQPGEEMLPEV 90 (91)
Q Consensus 16 ~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P--~~LDls~~~~~g~q~ge~~lpe~ 90 (91)
-.|.|++|+.+..|+++..|++||+|||+|..||.+ .+|...||..+|.+- +-+|+++|++.-....|..|||+
T Consensus 476 iE~~CenCk~K~~a~~k~~~kslPk~LIlq~~R~~l-qny~v~kls~pi~~~~D~m~~~~s~msk~~PqtEn~LPde 551 (749)
T COG5207 476 IEWSCENCKGKKKASRKPFIKSLPKYLILQVGRYSL-QNYKVEKLSDPIEMRSDDMIKLGSFMSKFDPQTENLLPDE 551 (749)
T ss_pred eeeehhhhcCcccccccchhhccCceeEEecceeec-cceeehhccCceEEccccccchhhHhhccCCcccccCCcc
Confidence 489999999999999999999999999999999999 799999999999997 45999999999666699999986
No 23
>cd02257 Peptidase_C19 Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyse bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.25 E-value=2.4e-11 Score=82.88 Aligned_cols=72 Identities=26% Similarity=0.413 Sum_probs=64.2
Q ss_pred CCCchhhhh--------cCCcccCCCC--CcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCCC
Q psy3162 6 PTKSFLGLY--------CGKVLTYALD--FVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPL 75 (91)
Q Consensus 6 ~~~sl~~cl--------~~~~~C~~C~--~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~~ 75 (91)
...+|.+|+ .....|..|+ +.+.+.++..|.++|++|+||++||.++..|...|++..|.+|++|++..+
T Consensus 97 ~~~~l~~~l~~~~~~e~~~~~~~~~c~~~~~~~~~~~~~i~~lP~~L~i~l~R~~~~~~~~~~k~~~~v~~~~~l~~~~~ 176 (255)
T cd02257 97 PQVSLEDCLEKFFKEEILEGDNCYKCEKKKKQEATKRLKIKKLPPVLIIHLKRFSFNEDGTKEKLNTKVSFPLELDLSPY 176 (255)
T ss_pred CCCcHHHHHHHhhhhhccCCCCcccCCCCcccceeEEEecccCCceeEEEeeceeeccccccccCCCeEeCCCcccCccc
Confidence 367899998 4778899998 688899999999999999999999999544889999999999999999888
Q ss_pred CC
Q psy3162 76 RG 77 (91)
Q Consensus 76 ~~ 77 (91)
..
T Consensus 177 ~~ 178 (255)
T cd02257 177 LS 178 (255)
T ss_pred cc
Confidence 64
No 24
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=99.20 E-value=1.6e-11 Score=92.72 Aligned_cols=49 Identities=16% Similarity=0.186 Sum_probs=40.9
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEE
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEV 64 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V 64 (91)
.++|+|++|+.+..++|++.|.++|++||||++||.... ..++|+|++-
T Consensus 282 ~d~W~CpkC~~k~ss~K~~~I~~lP~~LII~i~RF~i~V-~~~~kiD~p~ 330 (415)
T COG5533 282 KDAWRCPKCGRKESSRKRMEILVLPDVLIIHISRFHISV-MGRKKIDTPQ 330 (415)
T ss_pred cccccCchhcccccchheEEEEecCceEEEEeeeeeEEe-ecccccCCCc
Confidence 489999999999999999999999999999999999632 2345555543
No 25
>cd02665 Peptidase_C19I A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=99.06 E-value=1.1e-10 Score=84.21 Aligned_cols=67 Identities=19% Similarity=0.326 Sum_probs=50.0
Q ss_pred Cchhhhhc-----CCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCCC
Q psy3162 8 KSFLGLYC-----GKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPL 75 (91)
Q Consensus 8 ~sl~~cl~-----~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~~ 75 (91)
-+|++|+. +.-....|.....+.|+..|.++|+||+||||||.++. ....|+++.|+||..|+-..|
T Consensus 93 ~~L~e~L~~~~~ee~l~~~~~~~~~~~~~~~~i~~lP~vL~i~LkRF~~~~-~~~~Ki~~~v~FP~~l~~~~Y 164 (228)
T cd02665 93 GNLHECLEAAMFEGEVELLPSDHSVKSGQERWFTELPPVLTFELSRFEFNQ-GRPEKIHDKLEFPQIIQQVPY 164 (228)
T ss_pred CCHHHHHHHhhhhcccccccccchhhhhhhhhhhhCChhhEEEeEeeEEcC-CccEECCEEEEeeCccCCcee
Confidence 57888881 11122344445567788899999999999999999954 678899999999988744334
No 26
>KOG1868|consensus
Probab=98.97 E-value=7.5e-11 Score=95.52 Aligned_cols=69 Identities=23% Similarity=0.308 Sum_probs=59.5
Q ss_pred CCchhhhh-----------cCCcccCCCCCcceeE--EEeecccCCCeeEEEeeceEECCCCeeeecceEEecC-CCCCC
Q psy3162 7 TKSFLGLY-----------CGKVLTYALDFVLSTL--RTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP-DTIDL 72 (91)
Q Consensus 7 ~~sl~~cl-----------~~~~~C~~C~~~~~a~--k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P-~~LDl 72 (91)
.++|.+|+ .+.|.|++|+++..+. |++.|.+||++|+|||+||..+.+| ..|+...|+|| ..+|+
T Consensus 496 ~~~L~~C~~~ft~~ekle~~~~w~Cp~c~~~~~~~~lK~~~i~~lp~iLiihL~Rf~~~~~~-~~k~~~~v~~~~~~~~~ 574 (653)
T KOG1868|consen 496 KVSLEDCLSLFTKEEKLEGDEAWLCPRCKHKESSKTLKKLTILRLPKILIIHLKRFSSDGNS-FNKLSTGVDFPLREADL 574 (653)
T ss_pred ccchHhhhccccchhhcccccccCCccccCcccccccceeeeecCCHHHHHHHHHhccCccc-ccccceeeccchHhhhh
Confidence 47799999 3679999999999885 9999999999999999999996555 56999999999 67777
Q ss_pred CCCC
Q psy3162 73 TPLR 76 (91)
Q Consensus 73 s~~~ 76 (91)
.++.
T Consensus 575 ~~~~ 578 (653)
T KOG1868|consen 575 SPRF 578 (653)
T ss_pred chhc
Confidence 7644
No 27
>KOG1867|consensus
Probab=98.93 E-value=5.9e-10 Score=87.99 Aligned_cols=71 Identities=20% Similarity=0.271 Sum_probs=63.2
Q ss_pred Cchhhhh-----------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCCCC
Q psy3162 8 KSFLGLY-----------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPLR 76 (91)
Q Consensus 8 ~sl~~cl-----------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~~~ 76 (91)
-++.+|+ ..++.|..|+.++.++|++.+..+|.+|.+|+|||.+.......|+++.|.||..|+|.+|+
T Consensus 334 ~~~~~cl~~~~~~~~~~~~~~~~c~~c~~~~~~~kql~~~~lP~~l~~~lkRfe~~~~~~~~ki~~~v~fp~~l~m~p~~ 413 (492)
T KOG1867|consen 334 LTLLDCLDRFTRSEQLGKDSKYKCSSCKSKQESTKQLTIRKLPAVLCLHLKRFEHSATGAREKIDSYVSFPVLLNMKPYC 413 (492)
T ss_pred hhhhhhhhhhhhhhhcCcccccccCCcccccccccccccccCCceeeeeeccccccccccccccCcccccchhhcCCccc
Confidence 4467777 47899999999999999999999999999999999996554445999999999999999999
Q ss_pred CC
Q psy3162 77 GS 78 (91)
Q Consensus 77 ~~ 78 (91)
+.
T Consensus 414 ~~ 415 (492)
T KOG1867|consen 414 SS 415 (492)
T ss_pred cc
Confidence 86
No 28
>PF00443 UCH: Ubiquitin carboxyl-terminal hydrolase; InterPro: IPR001394 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. Cysteine peptidases have characteristic molecular topologies, which can be seen not only in their three-dimensional structures, but commonly also in the two-dimensional structures. These are peptidases in which the nucleophile is the sulphydryl group of a cysteine residue. Cysteine proteases are divided into clans (proteins which are evolutionary related), and further sub-divided into families, on the basis of the architecture of their catalytic dyad or triad []. This group of cysteine peptidases belong to the MEROPS peptidase family C19 (ubiquitin-specific protease family, clan CA). Families within the CA clan are loosely termed papain-like as protein fold of the peptidase unit resembles that of papain, the type example for clan CA. Predicted active site residues for members of this family and family C1 occur in the same order in the sequence: N/Q, C, H. The type example is human ubiquitin-specific protease 14. Ubiquitin is highly conserved, commonly found conjugated to proteins in eukaryotic cells, where it may act as a marker for rapid degradation, or it may have a chaperone function in protein assembly []. The ubiquitin is released by cleavage from the bound protein by a protease []. A number of deubiquitinising proteases are known: all are activated by thiol compounds [, ], and inhibited by thiol-blocking agents and ubiquitin aldehyde [, ], and as such have the properties of cysteine proteases []. The deubiquitinsing proteases can be split into 2 size ranges (20-30 kDa, IPR001578 from INTERPRO, and 100-200 kDa) []: this family are the 100-200 kDa peptides which includes the Ubp1 ubiquitin peptidase from yeast. Only one conserved cysteine can be identified, along with two conserved histidines. The spacing between the cysteine and the second histidine is thought to be more representative of the cysteine/histidine spacing of a cysteine protease catalytic dyad [].; GO: 0004221 ubiquitin thiolesterase activity, 0006511 ubiquitin-dependent protein catabolic process; PDB: 2LBC_A 3MHH_A 3MHS_A 3M99_A 2Y6E_D 2VHF_A 2HD5_A 3NHE_A 2IBI_A 1NBF_B ....
Probab=98.92 E-value=7.5e-10 Score=76.85 Aligned_cols=62 Identities=21% Similarity=0.388 Sum_probs=49.0
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECC-CCeeeecceEEecC-CCCCCCCCCCCCCC
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKE-DWTLAKLDVEVEMP-DTIDLTPLRGSGPQ 81 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~-~~~~~Kl~~~V~~P-~~LDls~~~~~g~q 81 (91)
.+...|..|+.. +..|.++|++|+||++||.++. .+...|+...|.|| ++|||++|...+..
T Consensus 140 ~~~~~c~~c~~~-----~~~~~~~P~~L~i~l~R~~~~~~~~~~~K~~~~v~~~~~~l~l~~~~~~~~~ 203 (269)
T PF00443_consen 140 ESSIKCSSCKNS-----QSSISSLPPILIIQLKRFEFDQETGRSKKINNPVEFPLEELDLSPYLEKNNS 203 (269)
T ss_dssp EEEEEETTTTCE-----EEEEEEBBSEEEEEEE-EEEESTSSEEEE--CEEB--SSEEEGGGGBSSCCC
T ss_pred cccccccccccc-----ccccccccceeeeccccceeccccccccccccccccCchhhhhhhhhccccc
Confidence 467899999988 6678999999999999998763 47799999999999 89999999876654
No 29
>cd02673 Peptidase_C19Q A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=98.90 E-value=1.3e-09 Score=78.94 Aligned_cols=44 Identities=18% Similarity=0.233 Sum_probs=37.1
Q ss_pred Cchhhhh-------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEEC
Q psy3162 8 KSFLGLY-------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMK 52 (91)
Q Consensus 8 ~sl~~cl-------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~ 52 (91)
.++++|+ ..+|+|++|+.+ .|.|+.+|.++|++|+||||||.+.
T Consensus 110 ~~le~l~~~~~~~~~~e~~C~~C~~~-~a~k~~~i~~~P~vL~i~lkRf~~~ 160 (245)
T cd02673 110 DIDELLISNFKTWSPIEKDCSSCKCE-SAISSERIMTFPECLSINLKRYKLR 160 (245)
T ss_pred chHHHHHHHhhcccccCccCCCCCCc-cceeechhhhCChhhEEeeEeeeec
Confidence 3455665 457899999986 7889999999999999999999874
No 30
>PF13423 UCH_1: Ubiquitin carboxyl-terminal hydrolase
Probab=98.69 E-value=2.9e-08 Score=72.68 Aligned_cols=79 Identities=18% Similarity=0.283 Sum_probs=68.0
Q ss_pred CCCCCCCchhhhh--------cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCC
Q psy3162 2 PKPQPTKSFLGLY--------CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLT 73 (91)
Q Consensus 2 ~~~~~~~sl~~cl--------~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls 73 (91)
|.....++|.+++ .....|++|++.+.+..+..|.++|+||.|.++|+..+..| ..|+...+.+|..+++.
T Consensus 157 p~~~~~~tf~~~Le~sl~~e~~~~a~C~~C~~~~~~~~~r~i~~LPpVL~In~~~~~~~~~w-~~~~~~~~~ip~~i~~~ 235 (295)
T PF13423_consen 157 PPSNSNVTFSQVLEHSLNREQQTRAWCEKCNKYQPTEQRRTIRSLPPVLSINLNRYSEEEFW-PKKNWLKIWIPPSINLP 235 (295)
T ss_pred CCCCccchHHHHHHHHHhhcccccccccccccccceeeeeeccCCCcEEEEEccCCCccccc-ccccCCceecceeeecc
Confidence 4445678999999 35689999999998888899999999999999999996568 88999999999999999
Q ss_pred CCCCCCCC
Q psy3162 74 PLRGSGPQ 81 (91)
Q Consensus 74 ~~~~~g~q 81 (91)
.+.+...+
T Consensus 236 ~~~~~~~~ 243 (295)
T PF13423_consen 236 HFIADDSQ 243 (295)
T ss_pred cccccccc
Confidence 88766543
No 31
>KOG1864|consensus
Probab=98.62 E-value=1.6e-08 Score=81.43 Aligned_cols=68 Identities=22% Similarity=0.231 Sum_probs=59.3
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECC-CCeeeecceEEecCCCCCCCCCCCCCCCC
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKE-DWTLAKLDVEVEMPDTIDLTPLRGSGPQP 82 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~-~~~~~Kl~~~V~~P~~LDls~~~~~g~q~ 82 (91)
-+.|+|++|...+.|.|++.++.+|.+|+||||||.++. .....|+...|.+|.+|++......+..+
T Consensus 439 ~nky~c~~c~s~qeae~~l~~k~lp~~L~l~Lkrfk~~~~~~~~~kl~~~v~~plel~l~~~~~~~~~~ 507 (587)
T KOG1864|consen 439 ENKYSCENCCSLQEAERRLKIKKLPYVLTLHLKRFKYSEQQNRYTKLLYRVVFPLELRLKDTLKDDNNP 507 (587)
T ss_pred CCcccccccCchhhHHHhccccCCcceeeeehhccccccccccccccccccccccceeeccccccccCc
Confidence 489999999999999999999999999999999999973 34567999999999999988766555543
No 32
>KOG1873|consensus
Probab=98.60 E-value=2.5e-09 Score=87.50 Aligned_cols=70 Identities=20% Similarity=0.118 Sum_probs=60.2
Q ss_pred CCchhhhh-----------cCCcccCCCCC------c---------------------ceeEEEeecccCCCeeEEEeec
Q psy3162 7 TKSFLGLY-----------CGKVLTYALDF------V---------------------LSTLRTTRLASFPDYLMFHLKK 48 (91)
Q Consensus 7 ~~sl~~cl-----------~~~~~C~~C~~------~---------------------~~a~k~~~~~~lP~vLiihlkR 48 (91)
.+|+..|| .|.|.|+.|-+ . +.|.|++-|...|+||+|||||
T Consensus 677 p~Svq~CL~nFT~~E~Ls~~N~~~CEnCtk~~n~~~r~k~~~n~~~sk~s~~es~~~~t~akk~~li~~aPpVltihlKr 756 (877)
T KOG1873|consen 677 PCSVQRCLKNFTKVEILSGDNKWACENCTKNLNLQRREKRGLNEDNSKYSFNESEYRNTYAKKKVLINKAPPVLTIHLKR 756 (877)
T ss_pred CccHHHHHHhhhhhhhcccccchhhhhhhccccccchhhccCCCCcccccccchhhhhhhhheeeecccCCceeeehHhh
Confidence 57899999 49999999977 1 1257889999999999999999
Q ss_pred eEECCCCeeeecceEEecCCCCCCCCCC
Q psy3162 49 FTMKEDWTLAKLDVEVEMPDTIDLTPLR 76 (91)
Q Consensus 49 F~~~~~~~~~Kl~~~V~~P~~LDls~~~ 76 (91)
|..+..+...|++.+|+|++-+||..|+
T Consensus 757 f~q~~~~~~~k~~~h~~f~E~~dL~~~~ 784 (877)
T KOG1873|consen 757 FFQDIRGRLSKLNKHVDFKEFEDLLDYM 784 (877)
T ss_pred hhhhhhchhhcccccchHHHHHHHHHHh
Confidence 9997667789999999999888888876
No 33
>COG5077 Ubiquitin carboxyl-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=98.48 E-value=2.3e-08 Score=82.46 Aligned_cols=64 Identities=20% Similarity=0.280 Sum_probs=54.4
Q ss_pred CCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECC-CCeeeecceEEecCCCCCCCCCCCCCC
Q psy3162 16 GKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKE-DWTLAKLDVEVEMPDTIDLTPLRGSGP 80 (91)
Q Consensus 16 ~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~-~~~~~Kl~~~V~~P~~LDls~~~~~g~ 80 (91)
|.|.|+.=| -+.|.|-.-|.+||+||-+|||||.+|. .....|+|...+||+++||.+|.+..-
T Consensus 357 N~Y~ae~~G-lqdAkKGViFeSlPpVlhlqLKRFeyDfe~d~mvKINDryEFP~eiDl~pfld~da 421 (1089)
T COG5077 357 NRYNAEKHG-LQDAKKGVIFESLPPVLHLQLKRFEYDFERDMMVKINDRYEFPLEIDLLPFLDRDA 421 (1089)
T ss_pred ccccccccc-chhhccceeeccCchHHHHHHHHhccccccCceeeecccccCcchhccccccCchh
Confidence 566666544 3579999999999999999999999984 467889999999999999999987643
No 34
>KOG1863|consensus
Probab=98.41 E-value=8e-08 Score=81.72 Aligned_cols=61 Identities=16% Similarity=0.205 Sum_probs=56.7
Q ss_pred cccCCCCCcceeEEEeecccCCCeeEEEeeceEEC-CCCeeeecceEEecCCCCCCCCCCCC
Q psy3162 18 VLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMK-EDWTLAKLDVEVEMPDTIDLTPLRGS 78 (91)
Q Consensus 18 ~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~-~~~~~~Kl~~~V~~P~~LDls~~~~~ 78 (91)
-+|+.|...+.|.|.+.|.+||+||.|||+||.++ ......|++....||..|||.+|.+.
T Consensus 338 ~~~~~~~~~~~a~k~~~f~~lPpvl~~qL~Rf~~~~~~~~~~Ki~d~~~fp~~i~~d~~~~~ 399 (1093)
T KOG1863|consen 338 KYDAECHGLQDAKKGVLFDSLPPVLFIQLMRFEYDFSTGQKIKINDKFEFPLIIDMDRYLSR 399 (1093)
T ss_pred cccccccchhhhhcceeeccCCchhhhhhhheeeeccCCceeehhhccCCccccccchhccc
Confidence 38999999999999999999999999999999997 34789999999999999999999764
No 35
>KOG2026|consensus
Probab=97.52 E-value=6.8e-05 Score=58.21 Aligned_cols=46 Identities=30% Similarity=0.579 Sum_probs=41.7
Q ss_pred EEeecccCCCeeEEEeeceEECCCCeeeecceEEecC-CCCCCCCCCC
Q psy3162 31 RTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMP-DTIDLTPLRG 77 (91)
Q Consensus 31 k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P-~~LDls~~~~ 77 (91)
++..+.++|++||+|++||.- .+|...|+-+.|+|| ..+|+.++..
T Consensus 327 ~rf~l~k~P~ylifh~~rF~k-Nn~f~ekNpTl~~f~~~~~~~~~~~~ 373 (442)
T KOG2026|consen 327 MRFRLTKLPRYLIFHMKRFKK-NNFFKEKNPTLVEFPYSEVDILHVLD 373 (442)
T ss_pred hheeeecCCceEEEEeeeccc-cCcccccCCceeeccCCccchhhhhh
Confidence 788999999999999999998 679999999999999 7888887653
No 36
>KOG1871|consensus
Probab=97.11 E-value=3.8e-05 Score=59.50 Aligned_cols=59 Identities=22% Similarity=0.289 Sum_probs=50.8
Q ss_pred CCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCC
Q psy3162 16 GKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTP 74 (91)
Q Consensus 16 ~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~ 74 (91)
..++..+-+..+.|.+++.+..||.+|++|+|||.|-..+...|+...|+||-.|.++.
T Consensus 280 lp~~st~s~~eV~~s~q~~leklp~vlilhlkrF~ye~tgg~~k~~K~i~~~~~l~i~~ 338 (420)
T KOG1871|consen 280 LPGYSTKSGQEVEASSQTTLEKLPPVLILHLKRFVYEKTGGARKLGKKIEYPWTLKISK 338 (420)
T ss_pred ccceecCCCCeechhhhhhHhhcchhhhhhhhHHHHHhccchhhhchhhhccceeeech
Confidence 44555557778889999999999999999999999944688999999999998888876
No 37
>KOG1872|consensus
Probab=96.36 E-value=0.00033 Score=55.34 Aligned_cols=62 Identities=19% Similarity=0.271 Sum_probs=51.1
Q ss_pred cCCCCCcceeEEEeecccCCCeeEEEeeceEECCC-CeeeecceEEecCCCCCCCCCCCCCCC
Q psy3162 20 TYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKED-WTLAKLDVEVEMPDTIDLTPLRGSGPQ 81 (91)
Q Consensus 20 C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~-~~~~Kl~~~V~~P~~LDls~~~~~g~q 81 (91)
.+..|..-.-.|.+.|.+||++|.|+.-||.+... ....|+-..|.||..||.-.++++.++
T Consensus 287 s~~lgr~a~y~k~~~isrlP~ylTvq~vrf~~k~k~~~~akil~~V~fP~~ld~~d~ct~el~ 349 (473)
T KOG1872|consen 287 SSILGRPAAYQKVMYISRLPEYLTVQEVRFFSKAKIMVVAKILNAVNFPKDLDQQDLCTPELK 349 (473)
T ss_pred CcccCCChHHHHHhHhhcCcccceEEEEEEEeccccchHHHHHHhccChhhhhHHHhhCHHhh
Confidence 45556555567889999999999999999999643 666788889999999999999887654
No 38
>COG3478 Predicted nucleic-acid-binding protein containing a Zn-ribbon domain [General function prediction only]
Probab=92.34 E-value=0.18 Score=30.20 Aligned_cols=36 Identities=6% Similarity=-0.049 Sum_probs=29.8
Q ss_pred CCcccCCCCCcceeEEEeecc--cCCCeeEEEeeceEE
Q psy3162 16 GKVLTYALDFVLSTLRTTRLA--SFPDYLMFHLKKFTM 51 (91)
Q Consensus 16 ~~~~C~~C~~~~~a~k~~~~~--~lP~vLiihlkRF~~ 51 (91)
+.|.|++||...-..|.+... .+-+++=||.++|..
T Consensus 3 ~~~kCpKCgn~~~~ekei~~tg~~lskifdvq~n~f~~ 40 (68)
T COG3478 3 NAFKCPKCGNTNYEEKEIAATGGGLSKIFDVQNNKFIV 40 (68)
T ss_pred ccccCCCcCCcchhhceeeccCCCcceeEEecccEEEE
Confidence 567899999988777777664 678999999999986
No 39
>PF09855 DUF2082: Nucleic-acid-binding protein containing Zn-ribbon domain (DUF2082); InterPro: IPR018652 This family of proteins contains various hypothetical prokaryotic proteins as well as some Zn-ribbon nucleic-acid-binding proteins.
Probab=88.21 E-value=0.6 Score=27.65 Aligned_cols=34 Identities=15% Similarity=-0.020 Sum_probs=24.6
Q ss_pred cccCCCCCcceeEEEeecc--cCCCeeEEEeeceEE
Q psy3162 18 VLTYALDFVLSTLRTTRLA--SFPDYLMFHLKKFTM 51 (91)
Q Consensus 18 ~~C~~C~~~~~a~k~~~~~--~lP~vLiihlkRF~~ 51 (91)
|.|++||...-..++++.. -+-.++=|+.+||..
T Consensus 1 y~C~KCg~~~~e~~~v~~tgg~~skiFdvq~~~f~~ 36 (64)
T PF09855_consen 1 YKCPKCGNEEYESGEVRATGGGLSKIFDVQNKKFTT 36 (64)
T ss_pred CCCCCCCCcceecceEEccCCeeEEEEEecCcEEEE
Confidence 7899999987555555443 345677888888886
No 40
>cd02666 Peptidase_C19J A subfamily of Peptidase C19. Peptidase C19 contains ubiquitinyl hydrolases. They are intracellular peptidases that remove ubiquitin molecules from polyubiquinated peptides by cleavage of isopeptide bonds. They hydrolyze bonds involving the carboxyl group of the C-terminal Gly residue of ubiquitin. The purpose of the de-ubiquitination is thought to be editing of the ubiquitin conjugates, which could rescue them from degradation, as well as recycling of the ubiquitin. The ubiquitin/proteasome system is responsible for most protein turnover in the mammalian cell, and with over 50 members, family C19 is one of the largest families of peptidases in the human genome.
Probab=83.84 E-value=0.16 Score=38.73 Aligned_cols=45 Identities=9% Similarity=0.013 Sum_probs=31.8
Q ss_pred CCCchhhhhcCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceEEecCCCCCCCCC
Q psy3162 6 PTKSFLGLYCGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVEVEMPDTIDLTPL 75 (91)
Q Consensus 6 ~~~sl~~cl~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~V~~P~~LDls~~ 75 (91)
...+|.+|+..-+.=+. |.+||++|.|||| +.++.|++.++|.+|
T Consensus 187 ~~~~L~d~L~~~~~~e~------------~~~~P~vl~~qlq-------------~~~~~~~~~~~~dry 231 (343)
T cd02666 187 EPKDLYDALDRYFDYDS------------LTKLPQRSQVQAQ-------------LAQPLQRELISMDRY 231 (343)
T ss_pred CCCCHHHHHHHhcChhh------------hccCCHHHHHHHh-------------hcccccchheeeccc
Confidence 35678888843332222 9999999999999 445566777777777
No 41
>PF15499 Peptidase_C98: Ubiquitin-specific peptidase-like, SUMO isopeptidase
Probab=80.50 E-value=0.6 Score=34.90 Aligned_cols=26 Identities=19% Similarity=0.200 Sum_probs=23.0
Q ss_pred ccCCCCCcceeEEEeecccCCCeeEEE
Q psy3162 19 LTYALDFVLSTLRTTRLASFPDYLMFH 45 (91)
Q Consensus 19 ~C~~C~~~~~a~k~~~~~~lP~vLiih 45 (91)
-|.+|+.+.. .++|.+.+.|+++.+|
T Consensus 172 pCn~C~~ksQ-~rkMvlekv~~vfmLH 197 (275)
T PF15499_consen 172 PCNSCNSKSQ-RRKMVLEKVPPVFMLH 197 (275)
T ss_pred CCcccCChHH-hHhhhhhcCchhhhhh
Confidence 5889998875 5889999999999999
No 42
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=77.29 E-value=1.5 Score=29.86 Aligned_cols=24 Identities=4% Similarity=-0.276 Sum_probs=19.2
Q ss_pred CCCCCCchhhhhcCCcccCCCCCc
Q psy3162 3 KPQPTKSFLGLYCGKVLTYALDFV 26 (91)
Q Consensus 3 ~~~~~~sl~~cl~~~~~C~~C~~~ 26 (91)
.-..+.||.+-+.++|.|+.||..
T Consensus 114 ~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 114 NMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred CCCcEeeHHHHHHcCCcCCCCCCE
Confidence 345677888888889999999976
No 43
>KOG2463|consensus
Probab=72.37 E-value=5.5 Score=30.94 Aligned_cols=37 Identities=14% Similarity=-0.013 Sum_probs=25.4
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEee-ceEEC
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLK-KFTMK 52 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlk-RF~~~ 52 (91)
+..-+|++||.++-..-..++..= --+..|+| ||.++
T Consensus 255 m~k~FCp~CG~~TL~K~aVsv~~d-G~~~~h~k~r~~~n 292 (376)
T KOG2463|consen 255 MPKDFCPSCGHKTLTKCAVSVDED-GNGQTHFKKRFQWN 292 (376)
T ss_pred cchhcccccCCCeeeEEEEEecCC-CceeEEeecccccc
Confidence 467899999999543333344433 45888998 98874
No 44
>PF14690 zf-ISL3: zinc-finger of transposase IS204/IS1001/IS1096/IS1165
Probab=71.42 E-value=7.4 Score=20.57 Aligned_cols=34 Identities=12% Similarity=0.115 Sum_probs=22.7
Q ss_pred cccCCCCCcce--------eEEEeecccCCCeeEEEeeceEE
Q psy3162 18 VLTYALDFVLS--------TLRTTRLASFPDYLMFHLKKFTM 51 (91)
Q Consensus 18 ~~C~~C~~~~~--------a~k~~~~~~lP~vLiihlkRF~~ 51 (91)
..|+.||.... ..+.+.+...|-+|.|...||.-
T Consensus 3 ~~Cp~Cg~~~~~~~g~~~r~i~~l~~~~~~~~L~i~~~R~~C 44 (47)
T PF14690_consen 3 PRCPHCGSPSVHRHGYKTRRIRHLPIGGRPVYLRIRKRRYRC 44 (47)
T ss_pred ccCCCcCCCceECCceEEEEEeecccCCEEEEEEEEeEEEEC
Confidence 46899997652 22334455667788888888864
No 45
>KOG1275|consensus
Probab=70.46 E-value=1.7 Score=37.73 Aligned_cols=59 Identities=17% Similarity=0.105 Sum_probs=44.4
Q ss_pred cccCCCCCcceeEEEeecccCCCeeEEEeeceEEC-CCCeee--ecceEEecCCCCCCCCCC
Q psy3162 18 VLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMK-EDWTLA--KLDVEVEMPDTIDLTPLR 76 (91)
Q Consensus 18 ~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~-~~~~~~--Kl~~~V~~P~~LDls~~~ 76 (91)
-.|+.|++......+..++++|++|.|...-+... .+|... |+-..|-+|..+-|..-.
T Consensus 702 ~~C~~C~k~ep~~q~~~vr~LPd~L~in~~~~~~~~~~~~a~q~~~~~~vWLP~~~~~~~~k 763 (1118)
T KOG1275|consen 702 AWCETCTKPEPTSQKKNVRSLPDCLSINTCLNVHELVDFWARQNKLLEDVWLPEWFHMIISK 763 (1118)
T ss_pred cccccccCCCCcccccccccCcceeeeeeeccchhhhhhHHHhhccccccccchheeEEEec
Confidence 67999999999999999999999999998877763 344333 445566777766655433
No 46
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=69.39 E-value=3.3 Score=28.88 Aligned_cols=23 Identities=9% Similarity=-0.233 Sum_probs=17.7
Q ss_pred CCCCchhhhhcCCcccCCCCCcc
Q psy3162 5 QPTKSFLGLYCGKVLTYALDFVL 27 (91)
Q Consensus 5 ~~~~sl~~cl~~~~~C~~C~~~~ 27 (91)
..+.||.+-+..+|.|+.||..-
T Consensus 124 ~~rytf~eA~~~~F~Cp~Cg~~L 146 (178)
T PRK06266 124 HIRFTFDEAMEYGFRCPQCGEML 146 (178)
T ss_pred CcEEeHHHHhhcCCcCCCCCCCC
Confidence 45677777778889999998753
No 47
>TIGR00310 ZPR1_znf ZPR1 zinc finger domain.
Probab=67.87 E-value=5.8 Score=28.11 Aligned_cols=63 Identities=10% Similarity=0.202 Sum_probs=34.4
Q ss_pred hhhhhcCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECCC-CeeeecceEEecC-CCCCCCC
Q psy3162 10 FLGLYCGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKED-WTLAKLDVEVEMP-DTIDLTP 74 (91)
Q Consensus 10 l~~cl~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~-~~~~Kl~~~V~~P-~~LDls~ 74 (91)
|-.+++-.+.|+.||-+..-++...-.. |.-+.+++.-=. |-+ ...+.-...|.+| .+|.|.+
T Consensus 23 F~evii~sf~C~~CGyr~~ev~~~g~~~-p~r~~l~V~~~~-DL~r~VvkS~tati~IPEl~lei~p 87 (192)
T TIGR00310 23 FGEVLETSTICEHCGYRSNDVKTLGAKE-PKRYILKIDDEA-DLNRRVVKSESATIRIPELGLDIEP 87 (192)
T ss_pred cceEEEEEEECCCCCCccceeEECCCCC-CEEEEEEECChh-cccceEEEcCCcEEEccceEEEECC
Confidence 4555667888888888877666544322 333333322111 111 3344555677888 4566654
No 48
>PF14205 Cys_rich_KTR: Cysteine-rich KTR
Probab=67.55 E-value=3.6 Score=23.75 Aligned_cols=24 Identities=25% Similarity=0.224 Sum_probs=17.5
Q ss_pred cccCCCCCcce--eEEEeecccCCCe
Q psy3162 18 VLTYALDFVLS--TLRTTRLASFPDY 41 (91)
Q Consensus 18 ~~C~~C~~~~~--a~k~~~~~~lP~v 41 (91)
..|+.||.+++ ....+.+..||-+
T Consensus 5 i~CP~CgnKTR~kir~DT~LkNfPly 30 (55)
T PF14205_consen 5 ILCPICGNKTRLKIREDTVLKNFPLY 30 (55)
T ss_pred EECCCCCCccceeeecCceecccccc
Confidence 37999998763 4566778888854
No 49
>PF07754 DUF1610: Domain of unknown function (DUF1610); InterPro: IPR011668 This domain is found in archaeal species. It is likely to bind zinc via its four well-conserved cysteine residues.
Probab=66.45 E-value=2.8 Score=20.19 Aligned_cols=11 Identities=9% Similarity=-0.115 Sum_probs=9.2
Q ss_pred cCCcccCCCCC
Q psy3162 15 CGKVLTYALDF 25 (91)
Q Consensus 15 ~~~~~C~~C~~ 25 (91)
...|.|++||+
T Consensus 14 ~v~f~CPnCG~ 24 (24)
T PF07754_consen 14 AVPFPCPNCGF 24 (24)
T ss_pred CceEeCCCCCC
Confidence 46899999985
No 50
>TIGR00340 zpr1_rel ZPR1-related zinc finger protein. A model ZPR1_znf (TIGR00310) has been created to describe the domain shared by this protein and ZPR1.
Probab=60.61 E-value=8 Score=26.75 Aligned_cols=62 Identities=6% Similarity=0.128 Sum_probs=33.2
Q ss_pred hhhhhcCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEECC-CCeeeecceEEecCC-CCCCC
Q psy3162 10 FLGLYCGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKE-DWTLAKLDVEVEMPD-TIDLT 73 (91)
Q Consensus 10 l~~cl~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~-~~~~~Kl~~~V~~P~-~LDls 73 (91)
|.++++-.+.|+.||-+.+-++...-.. |.-+.+++.-=. |- ....+--...|.+|+ +|.|.
T Consensus 21 F~evii~sf~C~~CGyr~~ev~~~~~~~-p~r~~l~V~~~~-DL~r~VvkS~ta~i~IPEl~lei~ 84 (163)
T TIGR00340 21 FGKIMLSTYICEKCGYRSTDVYQLEEKE-PVRYIIKIENED-DLFTLVYRSRSATIRIPELGIKIE 84 (163)
T ss_pred cceEEEEEEECCCCCCchhheeEcCCcC-CEEEEEEECChh-hccceEEEcCCcEEEccceeEEec
Confidence 4455567889999998877666544322 233333322110 11 123445556788884 45554
No 51
>PF08772 NOB1_Zn_bind: Nin one binding (NOB1) Zn-ribbon like; InterPro: IPR014881 This entry corresponds to a zinc ribbon and is found on the RNA binding protein NOB1. ; PDB: 2CON_A.
Probab=59.97 E-value=6.7 Score=23.74 Aligned_cols=33 Identities=15% Similarity=0.021 Sum_probs=8.8
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEeec
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKK 48 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkR 48 (91)
+...+|++||..+--.-...+. ---.+.+|+++
T Consensus 22 ~~k~FCp~CGn~TL~rvsvsv~-~~G~~~~~~~~ 54 (73)
T PF08772_consen 22 MTKQFCPKCGNATLKRVSVSVD-EDGKIKLHLKK 54 (73)
T ss_dssp SS--S-SSS--S--EEEE-B---SS---B-----
T ss_pred CCceeCcccCCCcceEEEEEEC-CCCCEEEEecC
Confidence 5789999999986432222333 22345566654
No 52
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=53.72 E-value=8.9 Score=26.94 Aligned_cols=24 Identities=13% Similarity=-0.237 Sum_probs=18.9
Q ss_pred CCCCchhhhhcCCcccCCCCCcce
Q psy3162 5 QPTKSFLGLYCGKVLTYALDFVLS 28 (91)
Q Consensus 5 ~~~~sl~~cl~~~~~C~~C~~~~~ 28 (91)
-..+||.+-...+|.|+.||+.-.
T Consensus 120 ~~r~sfdeA~~~~F~Cp~Cg~~L~ 143 (176)
T COG1675 120 HVKYSFDEAMELGFTCPKCGEDLE 143 (176)
T ss_pred CCcccHHHHHHhCCCCCCCCchhh
Confidence 456777777778899999998754
No 53
>COG1379 PHP family phosphoesterase with a Zn ribbon [General function prediction only]
Probab=48.72 E-value=8.6 Score=30.00 Aligned_cols=19 Identities=5% Similarity=-0.408 Sum_probs=13.8
Q ss_pred CchhhhhcCCcccCCCCCc
Q psy3162 8 KSFLGLYCGKVLTYALDFV 26 (91)
Q Consensus 8 ~sl~~cl~~~~~C~~C~~~ 26 (91)
.||++-....|.|++||.+
T Consensus 256 y~le~A~~~~wrCpkCGg~ 274 (403)
T COG1379 256 YSLEEAKSLRWRCPKCGGK 274 (403)
T ss_pred cCcchhhhhcccCcccccc
Confidence 3444444688999999984
No 54
>cd00730 rubredoxin Rubredoxin; nonheme iron binding domains containing a [Fe(SCys)4] center. Rubredoxins are small nonheme iron proteins. The iron atom is coordinated by four cysteine residues (Fe(S-Cys)4), but iron can also be replaced by cobalt, nickel or zinc. They are believed to be involved in electron transfer.
Probab=47.56 E-value=8.8 Score=21.49 Aligned_cols=15 Identities=0% Similarity=-0.339 Sum_probs=12.3
Q ss_pred hcCCcccCCCCCcce
Q psy3162 14 YCGKVLTYALDFVLS 28 (91)
Q Consensus 14 l~~~~~C~~C~~~~~ 28 (91)
|-++|.|+.|+....
T Consensus 31 Lp~~w~CP~C~a~K~ 45 (50)
T cd00730 31 LPDDWVCPVCGAGKD 45 (50)
T ss_pred CCCCCCCCCCCCcHH
Confidence 568999999998654
No 55
>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=45.95 E-value=13 Score=26.97 Aligned_cols=27 Identities=11% Similarity=0.041 Sum_probs=22.9
Q ss_pred CCCCCCchhhhh----cCCcccCCCCCccee
Q psy3162 3 KPQPTKSFLGLY----CGKVLTYALDFVLST 29 (91)
Q Consensus 3 ~~~~~~sl~~cl----~~~~~C~~C~~~~~a 29 (91)
+++|+.+...|. .|.--|+-|+.+++.
T Consensus 190 Q~PPMK~C~sC~qqIHRNAPiCPlCK~KsRS 220 (230)
T PF10146_consen 190 QPPPMKTCQSCHQQIHRNAPICPLCKAKSRS 220 (230)
T ss_pred cCCCcchhHhHHHHHhcCCCCCccccccccc
Confidence 467888899998 699999999998764
No 56
>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=45.10 E-value=10 Score=19.04 Aligned_cols=14 Identities=0% Similarity=-0.268 Sum_probs=10.6
Q ss_pred CCcccCCCCCccee
Q psy3162 16 GKVLTYALDFVLST 29 (91)
Q Consensus 16 ~~~~C~~C~~~~~a 29 (91)
..|.|+.||.....
T Consensus 16 ~~~~CP~Cg~~~~~ 29 (33)
T cd00350 16 APWVCPVCGAPKDK 29 (33)
T ss_pred CCCcCcCCCCcHHH
Confidence 57899999986543
No 57
>PF09723 Zn-ribbon_8: Zinc ribbon domain; InterPro: IPR013429 This entry 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=44.51 E-value=15 Score=19.49 Aligned_cols=14 Identities=7% Similarity=-0.057 Sum_probs=9.8
Q ss_pred CcccCCCCCcceeE
Q psy3162 17 KVLTYALDFVLSTL 30 (91)
Q Consensus 17 ~~~C~~C~~~~~a~ 30 (91)
+|+|++||..-...
T Consensus 5 ey~C~~Cg~~fe~~ 18 (42)
T PF09723_consen 5 EYRCEECGHEFEVL 18 (42)
T ss_pred EEEeCCCCCEEEEE
Confidence 57888888765543
No 58
>smart00440 ZnF_C2C2 C2C2 Zinc finger. Nucleic-acid-binding motif in transcriptional elongation factor TFIIS and RNA polymerases.
Probab=44.40 E-value=26 Score=18.40 Aligned_cols=18 Identities=6% Similarity=-0.260 Sum_probs=11.7
Q ss_pred cccCCCCCcceeEEEeec
Q psy3162 18 VLTYALDFVLSTLRTTRL 35 (91)
Q Consensus 18 ~~C~~C~~~~~a~k~~~~ 35 (91)
+.|++||......-++..
T Consensus 1 ~~Cp~C~~~~a~~~q~Q~ 18 (40)
T smart00440 1 APCPKCGNREATFFQLQT 18 (40)
T ss_pred CcCCCCCCCeEEEEEEcc
Confidence 469999977665444433
No 59
>PF14353 CpXC: CpXC protein
Probab=44.39 E-value=17 Score=23.40 Aligned_cols=15 Identities=0% Similarity=-0.286 Sum_probs=11.9
Q ss_pred cCCcccCCCCCccee
Q psy3162 15 CGKVLTYALDFVLST 29 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a 29 (91)
.+.+.|++||.....
T Consensus 36 l~~~~CP~Cg~~~~~ 50 (128)
T PF14353_consen 36 LFSFTCPSCGHKFRL 50 (128)
T ss_pred cCEEECCCCCCceec
Confidence 478899999988754
No 60
>COG5533 UBP5 Ubiquitin C-terminal hydrolase [Posttranslational modification, protein turnover, chaperones]
Probab=43.10 E-value=38 Score=26.49 Aligned_cols=64 Identities=17% Similarity=0.272 Sum_probs=43.2
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEee------ceEE------CCCCee-------------------------
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLK------KFTM------KEDWTL------------------------- 57 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlk------RF~~------~~~~~~------------------------- 57 (91)
.....|+.|+..++.......-..|.+=++|+. ||+- ++.|+-
T Consensus 233 ~srlqC~~C~~TStT~a~fs~l~vp~~~v~~~~l~eC~~~f~~~e~L~g~d~W~CpkC~~k~ss~K~~~I~~lP~~LII~ 312 (415)
T COG5533 233 KSRLQCEACNYTSTTIAMFSTLLVPPYEVVQLGLQECIDRFYEEEKLEGKDAWRCPKCGRKESSRKRMEILVLPDVLIIH 312 (415)
T ss_pred hhhhhhhhcCCceeEEeccceeeeccchheeecHHHHHHHhhhHHhhcCcccccCchhcccccchheEEEEecCceEEEE
Confidence 456789999999887777777777877777755 6653 344751
Q ss_pred -eecceEEecCCCCCCCCCCCC
Q psy3162 58 -AKLDVEVEMPDTIDLTPLRGS 78 (91)
Q Consensus 58 -~Kl~~~V~~P~~LDls~~~~~ 78 (91)
+..++.|-.|..||+.++.+.
T Consensus 313 i~RF~i~V~~~~kiD~p~gw~~ 334 (415)
T COG5533 313 ISRFHISVMGRKKIDTPQGWKN 334 (415)
T ss_pred eeeeeEEeecccccCCCcchhc
Confidence 122345566778888877643
No 61
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=42.73 E-value=21 Score=19.09 Aligned_cols=12 Identities=0% Similarity=-0.297 Sum_probs=10.5
Q ss_pred cCCcccCCCCCc
Q psy3162 15 CGKVLTYALDFV 26 (91)
Q Consensus 15 ~~~~~C~~C~~~ 26 (91)
-+++.|+.||..
T Consensus 16 ~~g~~CP~Cg~~ 27 (46)
T PF12760_consen 16 PDGFVCPHCGST 27 (46)
T ss_pred CCCCCCCCCCCe
Confidence 478999999987
No 62
>PF00301 Rubredoxin: Rubredoxin; InterPro: IPR004039 Rubredoxin is a low molecular weight iron-containing bacterial protein involved in electron transfer [, ], sometimes replacing ferredoxin as an electron carrier []. The 3-D structures of a number of rubredoxins have been solved [, ]. The fold belongs to the alpha+beta class, with 2 alpha-helices and 2-3 beta-strands. Its active site contains an iron ion which is co-ordinated by the sulphurs of four conserved cysteine residues forming an almost regular tetrahedron. The conserved cysteines reside on two loops, which are the most conserved regions of the protein. In addition, a ring of acidic residues in the proximity of the [Fe(Cys)4] centre is also well-conserved []. ; GO: 0009055 electron carrier activity, 0046872 metal ion binding; PDB: 2RDV_C 1RDV_A 1S24_A 1T9O_B 1B2J_A 1SMW_A 2PVE_B 1BFY_A 1T9P_C 1C09_C ....
Probab=40.53 E-value=17 Score=20.09 Aligned_cols=14 Identities=0% Similarity=-0.339 Sum_probs=8.8
Q ss_pred hcCCcccCCCCCcc
Q psy3162 14 YCGKVLTYALDFVL 27 (91)
Q Consensus 14 l~~~~~C~~C~~~~ 27 (91)
|-++|.|+.|+...
T Consensus 31 Lp~~w~CP~C~a~K 44 (47)
T PF00301_consen 31 LPDDWVCPVCGAPK 44 (47)
T ss_dssp S-TT-B-TTTSSBG
T ss_pred CCCCCcCcCCCCcc
Confidence 46889999999764
No 63
>PF12171 zf-C2H2_jaz: Zinc-finger double-stranded RNA-binding; InterPro: IPR022755 This zinc finger is found in archaea and eukaryotes, and is approximately 30 amino acids in length. The mammalian members of this group occur multiple times along the protein, joined by flexible linkers, and are referred to as JAZ - dsRNA-binding ZF protein - zinc-fingers. The JAZ proteins are expressed in all tissues tested and localise in the nucleus, particularly the nucleolus []. JAZ preferentially binds to double-stranded (ds) RNA or RNA/DNA hybrids rather than DNA. In addition to binding double-stranded RNA, these zinc-fingers are required for nucleolar localisation. This entry represents the multiple-adjacent-C2H2 zinc finger, JAZ. ; PDB: 4DGW_A 1ZR9_A.
Probab=40.10 E-value=14 Score=17.37 Aligned_cols=10 Identities=20% Similarity=-0.014 Sum_probs=7.3
Q ss_pred CcccCCCCCc
Q psy3162 17 KVLTYALDFV 26 (91)
Q Consensus 17 ~~~C~~C~~~ 26 (91)
.|+|+.|++.
T Consensus 1 q~~C~~C~k~ 10 (27)
T PF12171_consen 1 QFYCDACDKY 10 (27)
T ss_dssp -CBBTTTTBB
T ss_pred CCCcccCCCC
Confidence 4789999864
No 64
>PF04606 Ogr_Delta: Ogr/Delta-like zinc finger; InterPro: IPR007684 This entry is represented by Bacteriophage P2, Ogr. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes []. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F [].; GO: 0006355 regulation of transcription, DNA-dependent
Probab=37.86 E-value=20 Score=19.36 Aligned_cols=18 Identities=6% Similarity=-0.164 Sum_probs=12.8
Q ss_pred ccCCCCCcceeEEEeecc
Q psy3162 19 LTYALDFVLSTLRTTRLA 36 (91)
Q Consensus 19 ~C~~C~~~~~a~k~~~~~ 36 (91)
+|+.||.+-...++..+.
T Consensus 1 ~CP~Cg~~a~ir~S~~~s 18 (47)
T PF04606_consen 1 RCPHCGSKARIRTSRQLS 18 (47)
T ss_pred CcCCCCCeeEEEEchhhC
Confidence 599999987665554443
No 65
>PF03367 zf-ZPR1: ZPR1 zinc-finger domain; InterPro: IPR004457 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 ZPR1-type zinc finger domains. An orthologous protein found once in each of the completed archaeal genomes corresponds to a zinc finger-containing domain repeated as the N-terminal and C-terminal halves of the mouse protein ZPR1. ZPR1 is an experimentally proven zinc-binding protein that binds the tyrosine kinase domain of the epidermal growth factor receptor (EGFR); binding is inhibited by EGF stimulation and tyrosine phosphorylation, and activation by EGF is followed by some redistribution of ZPR1 to the nucleus. By analogy, other proteins with the ZPR1 zinc finger domain may be regulatory proteins that sense protein phosphorylation state and/or participate in signal transduction (see also IPR004470 from INTERPRO). Deficiencies in ZPR1 may contribute to neurodegenerative disorders. ZPR1 appears to be down-regulated in patients with spinal muscular atrophy (SMA), a disease characterised by degeneration of the alpha-motor neurons in the spinal cord that can arise from mutations affecting the expression of Survival Motor Neurons (SMN) []. ZPR1 interacts with complexes formed by SMN [], and may act as a modifier that effects the severity of SMA. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2QKD_A.
Probab=37.68 E-value=51 Score=22.53 Aligned_cols=20 Identities=0% Similarity=-0.069 Sum_probs=9.8
Q ss_pred hhcCCcccCCCCCcceeEEE
Q psy3162 13 LYCGKVLTYALDFVLSTLRT 32 (91)
Q Consensus 13 cl~~~~~C~~C~~~~~a~k~ 32 (91)
+++-.+.|++||-+..-.+.
T Consensus 26 vii~sf~C~~CGyk~~ev~~ 45 (161)
T PF03367_consen 26 VIIMSFECEHCGYKNNEVKS 45 (161)
T ss_dssp EEEEEEE-TTT--EEEEEEE
T ss_pred EEEEEeECCCCCCEeeeEEE
Confidence 33456677777766655554
No 66
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=37.56 E-value=15 Score=15.89 Aligned_cols=10 Identities=0% Similarity=-0.317 Sum_probs=5.8
Q ss_pred cccCCCCCcc
Q psy3162 18 VLTYALDFVL 27 (91)
Q Consensus 18 ~~C~~C~~~~ 27 (91)
|.|+.|+..-
T Consensus 1 ~~C~~C~~~~ 10 (24)
T PF13894_consen 1 FQCPICGKSF 10 (24)
T ss_dssp EE-SSTS-EE
T ss_pred CCCcCCCCcC
Confidence 6788888753
No 67
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=37.29 E-value=19 Score=28.18 Aligned_cols=29 Identities=17% Similarity=-0.067 Sum_probs=18.9
Q ss_pred CCCCCC------CCchhhhh----------cCCcccCCCCCccee
Q psy3162 1 MPKPQP------TKSFLGLY----------CGKVLTYALDFVLST 29 (91)
Q Consensus 1 ~~~~~~------~~sl~~cl----------~~~~~C~~C~~~~~a 29 (91)
|||... .+...+|- .+..+|++||.+-..
T Consensus 1 ~~~~~~~~~~~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~ 45 (403)
T TIGR00155 1 MPKMCEHHPAAKHILCSQCDMLVALPRIESGQKAACPRCGTTLTV 45 (403)
T ss_pred CccccccCCCCCeeeCCCCCCcccccCCCCCCeeECCCCCCCCcC
Confidence 788777 34455555 245679999987543
No 68
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=37.09 E-value=11 Score=16.74 Aligned_cols=9 Identities=0% Similarity=-0.489 Sum_probs=6.6
Q ss_pred cccCCCCCc
Q psy3162 18 VLTYALDFV 26 (91)
Q Consensus 18 ~~C~~C~~~ 26 (91)
|.|+.|++.
T Consensus 1 y~C~~C~~~ 9 (23)
T PF00096_consen 1 YKCPICGKS 9 (23)
T ss_dssp EEETTTTEE
T ss_pred CCCCCCCCc
Confidence 578888864
No 69
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=37.04 E-value=18 Score=21.17 Aligned_cols=12 Identities=8% Similarity=-0.075 Sum_probs=9.5
Q ss_pred cCCcccCCCCCc
Q psy3162 15 CGKVLTYALDFV 26 (91)
Q Consensus 15 ~~~~~C~~C~~~ 26 (91)
.+.|.|++||-.
T Consensus 46 ~~~Y~CP~CGF~ 57 (59)
T PRK14890 46 SNPYTCPKCGFE 57 (59)
T ss_pred CCceECCCCCCc
Confidence 588899998854
No 70
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=36.01 E-value=24 Score=23.63 Aligned_cols=12 Identities=8% Similarity=-0.053 Sum_probs=10.1
Q ss_pred CCcccCCCCCcc
Q psy3162 16 GKVLTYALDFVL 27 (91)
Q Consensus 16 ~~~~C~~C~~~~ 27 (91)
..|+|++|+...
T Consensus 50 ~~~~C~~C~~~~ 61 (166)
T cd04476 50 GTYRCEKCNKSV 61 (166)
T ss_pred CcEECCCCCCcC
Confidence 479999999875
No 71
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=35.09 E-value=19 Score=16.82 Aligned_cols=11 Identities=0% Similarity=-0.194 Sum_probs=7.7
Q ss_pred ccCCCCCccee
Q psy3162 19 LTYALDFVLST 29 (91)
Q Consensus 19 ~C~~C~~~~~a 29 (91)
+|++||.....
T Consensus 1 ~Cp~CG~~~~~ 11 (23)
T PF13240_consen 1 YCPNCGAEIED 11 (23)
T ss_pred CCcccCCCCCC
Confidence 58888877543
No 72
>PF01096 TFIIS_C: Transcription factor S-II (TFIIS); InterPro: IPR001222 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 zinc finger motif found in transcription factor IIs (TFIIS). In eukaryotes the initiation of transcription of protein encoding genes by polymerase II (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least eight different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, -IIH and -IIS []. During mRNA elongation, Pol II can encounter DNA sequences that cause reverse movement of the enzyme. Such backtracking involves extrusion of the RNA 3'-end into the pore, and can lead to transcriptional arrest. Escape from arrest requires cleavage of the extruded RNA with the help of TFIIS, which induces mRNA cleavage by enhancing the intrinsic nuclease activity of RNA polymerase (Pol) II, past template-encoded pause sites []. TFIIS extends from the polymerase surface via a pore to the internal active site. Two essential and invariant acidic residues in a TFIIS loop complement the Pol II active site and could position a metal ion and a water molecule for hydrolytic RNA cleavage. TFIIS also induces extensive structural changes in Pol II that would realign nucleic acids in the active centre. TFIIS is a protein of about 300 amino acids. It contains three regions: a variable N-terminal domain not required for TFIIS activity; a conserved central domain required for Pol II binding; and a conserved C-terminal C4-type zinc finger essential for RNA cleavage. The zinc finger folds in a conformation termed a zinc ribbon [] characterised by a three-stranded antiparallel beta-sheet and two beta-hairpins. A backbone model for Pol II-TFIIS complex was obtained from X-ray analysis. It shows that a beta hairpin protrudes from the zinc finger and complements the pol II active site []. Some viral proteins also contain the TFIIS zinc ribbon C-terminal domain. The Vaccinia virus protein, unlike its eukaryotic homologue, is an integral RNA polymerase subunit rather than a readily separable transcription factor []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003676 nucleic acid binding, 0008270 zinc ion binding, 0006351 transcription, DNA-dependent; PDB: 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I 3I4M_I ....
Probab=33.91 E-value=41 Score=17.49 Aligned_cols=16 Identities=0% Similarity=-0.209 Sum_probs=8.6
Q ss_pred cccCCCCCcceeEEEe
Q psy3162 18 VLTYALDFVLSTLRTT 33 (91)
Q Consensus 18 ~~C~~C~~~~~a~k~~ 33 (91)
..|++||......-+.
T Consensus 1 ~~Cp~Cg~~~a~~~~~ 16 (39)
T PF01096_consen 1 IKCPKCGHNEAVFFQI 16 (39)
T ss_dssp S--SSS-SSEEEEEEE
T ss_pred CCCcCCCCCeEEEEEe
Confidence 3699999987654433
No 73
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=33.54 E-value=21 Score=20.97 Aligned_cols=12 Identities=8% Similarity=-0.158 Sum_probs=9.5
Q ss_pred cCCcccCCCCCc
Q psy3162 15 CGKVLTYALDFV 26 (91)
Q Consensus 15 ~~~~~C~~C~~~ 26 (91)
.+-|.|++||-.
T Consensus 48 g~~Y~Cp~CGF~ 59 (61)
T COG2888 48 GNPYRCPKCGFE 59 (61)
T ss_pred CCceECCCcCcc
Confidence 588999999854
No 74
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=33.52 E-value=21 Score=22.47 Aligned_cols=22 Identities=9% Similarity=-0.247 Sum_probs=13.4
Q ss_pred cCCcccCCCCCcceeEEEeecc
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLA 36 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~ 36 (91)
-..|.|+.|++..--.....||
T Consensus 33 ~~ky~Cp~Cgk~~vkR~a~GIW 54 (90)
T PF01780_consen 33 HAKYTCPFCGKTSVKRVATGIW 54 (90)
T ss_dssp HS-BEESSSSSSEEEEEETTEE
T ss_pred hCCCcCCCCCCceeEEeeeEEe
Confidence 3678999999887433333333
No 75
>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=32.98 E-value=20 Score=18.46 Aligned_cols=13 Identities=0% Similarity=-0.238 Sum_probs=10.0
Q ss_pred cCCcccCCCCCcc
Q psy3162 15 CGKVLTYALDFVL 27 (91)
Q Consensus 15 ~~~~~C~~C~~~~ 27 (91)
.-.|.|+.||+..
T Consensus 30 vp~~~C~~CGE~~ 42 (46)
T TIGR03831 30 VPALVCPQCGEEY 42 (46)
T ss_pred CCccccccCCCEe
Confidence 3578999999853
No 76
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=31.46 E-value=46 Score=21.01 Aligned_cols=23 Identities=9% Similarity=-0.177 Sum_probs=14.9
Q ss_pred cCCcccCCCCCcceeEEEeeccc
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLAS 37 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~ 37 (91)
-..|.|+.|++..--.....||.
T Consensus 33 ~a~y~CpfCgk~~vkR~a~GIW~ 55 (91)
T TIGR00280 33 KAKYVCPFCGKKTVKRGSTGIWT 55 (91)
T ss_pred hcCccCCCCCCCceEEEeeEEEE
Confidence 46889999987654444444554
No 77
>PF08271 TF_Zn_Ribbon: TFIIB zinc-binding; InterPro: IPR013137 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 zinc finger motif found in transcription factor IIB (TFIIB). In eukaryotes the initiation of transcription of protein encoding genes by the polymerase II complexe (Pol II) is modulated by general and specific transcription factors. The general transcription factors operate through common promoters elements (such as the TATA box). At least seven different proteins associate to form the general transcription factors: TFIIA, -IIB, -IID, -IIE, -IIF, -IIG, and -IIH []. TFIIB and TFIID are responsible for promoter recognition and interaction with pol II; together with Pol II, they form a minimal initiation complex capable of transcription under certain conditions. The TATA box of a Pol II promoter is bound in the initiation complex by the TBP subunit of TFIID, which bends the DNA around the C-terminal domain of TFIIB whereas the N-terminal zinc finger of TFIIB interacts with Pol II [, ]. The TFIIB zinc finger adopts a zinc ribbon fold characterised by two beta-hairpins forming two structurally similar zinc-binding sub-sites []. The zinc finger contacts the rbp1 subunit of Pol II through its dock domain, a conserved region of about 70 amino acids located close to the polymerase active site []. In the Pol II complex this surface is located near the RNA exit groove. Interestingly this sequence is best conserved in the three polymerases that utilise a TFIIB-like general transcription factor (Pol II, Pol III, and archaeal RNA polymerase) but not in Pol I []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1VD4_A 1PFT_A 3K1F_M 3K7A_M 1RO4_A 1RLY_A 1DL6_A.
Probab=31.34 E-value=24 Score=18.56 Aligned_cols=10 Identities=0% Similarity=-0.433 Sum_probs=7.6
Q ss_pred cccCCCCCcc
Q psy3162 18 VLTYALDFVL 27 (91)
Q Consensus 18 ~~C~~C~~~~ 27 (91)
|+|+.|+...
T Consensus 1 m~Cp~Cg~~~ 10 (43)
T PF08271_consen 1 MKCPNCGSKE 10 (43)
T ss_dssp ESBTTTSSSE
T ss_pred CCCcCCcCCc
Confidence 5788888865
No 78
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=31.04 E-value=49 Score=20.83 Aligned_cols=24 Identities=8% Similarity=-0.230 Sum_probs=15.9
Q ss_pred cCCcccCCCCCcceeEEEeecccC
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASF 38 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~l 38 (91)
-..|.|+.|++..--.....||.-
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~C 57 (90)
T PRK03976 34 RAKHVCPVCGRPKVKRVGTGIWEC 57 (90)
T ss_pred hcCccCCCCCCCceEEEEEEEEEc
Confidence 468899999876554455555554
No 79
>PF08646 Rep_fac-A_C: Replication factor-A C terminal domain; InterPro: IPR013955 Replication factor A (RP-A) binds and subsequently stabilises single-stranded DNA intermediates and thus prevents complementary DNA from reannealing. It also plays an essential role in several cellular processes in DNA metabolism including replication, recombination and repair of DNA []. Replication factor-A protein is also known as Replication protein A 70 kDa DNA-binding subunit. This entry is found at the C terminus of Replication factor A.; PDB: 1L1O_F 3U50_C.
Probab=31.00 E-value=23 Score=23.17 Aligned_cols=12 Identities=8% Similarity=-0.025 Sum_probs=9.8
Q ss_pred CCcccCCCCCcc
Q psy3162 16 GKVLTYALDFVL 27 (91)
Q Consensus 16 ~~~~C~~C~~~~ 27 (91)
+.|.|++|++..
T Consensus 36 ~~y~C~~C~~~~ 47 (146)
T PF08646_consen 36 GSYRCEKCNKTV 47 (146)
T ss_dssp TEEEETTTTEEE
T ss_pred cEEECCCCCCcC
Confidence 469999999875
No 80
>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=30.58 E-value=34 Score=17.25 Aligned_cols=15 Identities=7% Similarity=0.016 Sum_probs=9.7
Q ss_pred CcccCCCCCcceeEE
Q psy3162 17 KVLTYALDFVLSTLR 31 (91)
Q Consensus 17 ~~~C~~C~~~~~a~k 31 (91)
.|+|..||..-....
T Consensus 5 ~y~C~~Cg~~fe~~~ 19 (41)
T smart00834 5 EYRCEDCGHTFEVLQ 19 (41)
T ss_pred EEEcCCCCCEEEEEE
Confidence 467888887655443
No 81
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=30.55 E-value=32 Score=18.02 Aligned_cols=16 Identities=0% Similarity=-0.170 Sum_probs=8.9
Q ss_pred CCcccCCCCCcceeEE
Q psy3162 16 GKVLTYALDFVLSTLR 31 (91)
Q Consensus 16 ~~~~C~~C~~~~~a~k 31 (91)
+-|+|..||.......
T Consensus 5 ~~YkC~~CGniVev~~ 20 (36)
T PF06397_consen 5 EFYKCEHCGNIVEVVH 20 (36)
T ss_dssp EEEE-TTT--EEEEEE
T ss_pred cEEEccCCCCEEEEEE
Confidence 3589999998775443
No 82
>PF04828 GFA: Glutathione-dependent formaldehyde-activating enzyme; InterPro: IPR006913 The GFA family consists mainly of glutathione-dependent formaldehyde-activating enzymes, but also includes centromere protein V and a fission yeast protein described as uncharacterised lyase. Glutathione-dependent formaldehyde-activating enzyme catalyse the condensation of formaldehyde and glutathione to S-hydroxymethylglutathione. All known members of this family contain 5 strongly conserved cysteine residues.; GO: 0016846 carbon-sulfur lyase activity, 0008152 metabolic process; PDB: 3FAC_B 1XA8_A 1X6M_B.
Probab=29.96 E-value=54 Score=18.96 Aligned_cols=33 Identities=9% Similarity=-0.061 Sum_probs=24.0
Q ss_pred cCCcccCCCCCcceeEEEeecccCCCeeEEEeeceEE
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTM 51 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~ 51 (91)
...++|..||...-+. ....|+.+.|.+-=|.-
T Consensus 46 ~~r~FC~~CGs~l~~~----~~~~~~~~~V~~g~ld~ 78 (92)
T PF04828_consen 46 VERYFCPTCGSPLFSE----DERDPDLVGVNAGTLDD 78 (92)
T ss_dssp CEEEEETTT--EEEEE----ESSTTTEEEEEGGGBTT
T ss_pred CcCcccCCCCCeeecc----cCCCCCEEEEEeEeeCC
Confidence 3568999999987654 67899999998876654
No 83
>TIGR03071 couple_hipA HipA N-terminal domain. Although Pfam models pfam07805 and pfam07804 currently are called HipA-like N-terminal domain and HipA-like C-terminal domain, respectively, those models hit the central and C-terminal regions of E. coli HipA but not the N-terminal region. This model hits the N-terminal region of HipA and its homologs, and also identifies proteins that lack match regions for pfam07804 and pfam07805.
Probab=29.95 E-value=17 Score=22.33 Aligned_cols=41 Identities=20% Similarity=0.336 Sum_probs=20.8
Q ss_pred ceEECCCCeeee--cceEEecCCCCCCCCCCCCCCCC-CCccCCCC
Q psy3162 48 KFTMKEDWTLAK--LDVEVEMPDTIDLTPLRGSGPQP-GEEMLPEV 90 (91)
Q Consensus 48 RF~~~~~~~~~K--l~~~V~~P~~LDls~~~~~g~q~-ge~~lpe~ 90 (91)
+|.|+.+|.... ....+.+|. +-..|.+.++.+ -+..|||.
T Consensus 23 ~F~Y~~~~l~~~~~~~lS~~lPl--~~~~~~~~~l~~~f~~lLPEg 66 (101)
T TIGR03071 23 SFRYDDDYLGSPSAPPLSLSLPL--QAEEFRSGVVPPFFDGLLPEG 66 (101)
T ss_pred EEEEcHHHHhCCCCCceEeeccC--CCCCCCCccHHHHHhhcCCCH
Confidence 588977786543 233344442 223344333333 45666663
No 84
>smart00709 Zpr1 Duplicated domain in the epidermal growth factor- and elongation factor-1alpha-binding protein Zpr1. Also present in archaeal proteins.
Probab=29.58 E-value=95 Score=21.26 Aligned_cols=23 Identities=4% Similarity=-0.006 Sum_probs=13.8
Q ss_pred hhhhhcCCcccCCCCCcceeEEE
Q psy3162 10 FLGLYCGKVLTYALDFVLSTLRT 32 (91)
Q Consensus 10 l~~cl~~~~~C~~C~~~~~a~k~ 32 (91)
|.++++-.+.|+.||-+..-.+.
T Consensus 22 F~evii~sf~C~~CGyk~~ev~~ 44 (160)
T smart00709 22 FREVIIMSFECEHCGYRNNEVKS 44 (160)
T ss_pred cceEEEEEEECCCCCCccceEEE
Confidence 33444556777777777655554
No 85
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=29.36 E-value=31 Score=17.01 Aligned_cols=13 Identities=0% Similarity=-0.281 Sum_probs=6.9
Q ss_pred CcccCCCCCccee
Q psy3162 17 KVLTYALDFVLST 29 (91)
Q Consensus 17 ~~~C~~C~~~~~a 29 (91)
.-+|++||..+..
T Consensus 3 ~rfC~~CG~~t~~ 15 (32)
T PF09297_consen 3 HRFCGRCGAPTKP 15 (32)
T ss_dssp TSB-TTT--BEEE
T ss_pred CcccCcCCccccC
Confidence 4579999987653
No 86
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=29.25 E-value=52 Score=20.72 Aligned_cols=23 Identities=4% Similarity=-0.193 Sum_probs=14.2
Q ss_pred cCCcccCCCCCcceeEEEeeccc
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLAS 37 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~ 37 (91)
-..|.|+.|++..--.....||.
T Consensus 34 ~a~y~CpfCgk~~vkR~a~GIW~ 56 (90)
T PTZ00255 34 HAKYFCPFCGKHAVKRQAVGIWR 56 (90)
T ss_pred hCCccCCCCCCCceeeeeeEEEE
Confidence 46889999986553333334443
No 87
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=28.70 E-value=35 Score=22.71 Aligned_cols=11 Identities=0% Similarity=-0.429 Sum_probs=6.0
Q ss_pred CcccCCCCCcc
Q psy3162 17 KVLTYALDFVL 27 (91)
Q Consensus 17 ~~~C~~C~~~~ 27 (91)
.|.|+.|+.+-
T Consensus 99 ~Y~Cp~C~~~y 109 (147)
T smart00531 99 YYKCPNCQSKY 109 (147)
T ss_pred EEECcCCCCEe
Confidence 45566665443
No 88
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=28.37 E-value=34 Score=18.18 Aligned_cols=11 Identities=0% Similarity=-0.300 Sum_probs=6.3
Q ss_pred CcccCCCCCcc
Q psy3162 17 KVLTYALDFVL 27 (91)
Q Consensus 17 ~~~C~~C~~~~ 27 (91)
.|.|++||...
T Consensus 3 ~y~C~~CG~~~ 13 (46)
T PRK00398 3 EYKCARCGREV 13 (46)
T ss_pred EEECCCCCCEE
Confidence 45666666544
No 89
>COG4830 RPS26B Ribosomal protein S26 [Translation, ribosomal structure and biogenesis]
Probab=28.33 E-value=47 Score=21.51 Aligned_cols=21 Identities=14% Similarity=0.055 Sum_probs=16.5
Q ss_pred cccCCCCCcc---eeEEEeecccC
Q psy3162 18 VLTYALDFVL---STLRTTRLASF 38 (91)
Q Consensus 18 ~~C~~C~~~~---~a~k~~~~~~l 38 (91)
..|.+||+.. .|.|++.+.++
T Consensus 21 v~CdnCg~~vPkdKAikr~~i~s~ 44 (108)
T COG4830 21 VRCDNCGKAVPKDKAIKRTAIRSP 44 (108)
T ss_pred eeeccccccCCccceeeEeeccCc
Confidence 5899999854 58888888765
No 90
>KOG0402|consensus
Probab=27.45 E-value=17 Score=22.86 Aligned_cols=23 Identities=4% Similarity=-0.198 Sum_probs=15.1
Q ss_pred cCCcccCCCCCcceeEEEeeccc
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLAS 37 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~ 37 (91)
-..|.|+.||+.+--.+-..||.
T Consensus 34 haky~CsfCGK~~vKR~AvGiW~ 56 (92)
T KOG0402|consen 34 HAKYTCSFCGKKTVKRKAVGIWK 56 (92)
T ss_pred hhhhhhhhcchhhhhhhceeEEe
Confidence 36789999998765444444443
No 91
>PRK12366 replication factor A; Reviewed
Probab=27.42 E-value=37 Score=28.14 Aligned_cols=11 Identities=18% Similarity=0.066 Sum_probs=9.1
Q ss_pred CCcccCCCCCc
Q psy3162 16 GKVLTYALDFV 26 (91)
Q Consensus 16 ~~~~C~~C~~~ 26 (91)
..|+|++|++.
T Consensus 547 g~~~C~~c~~~ 557 (637)
T PRK12366 547 GEYICEFCGEV 557 (637)
T ss_pred CcEECCCCCCC
Confidence 46899999977
No 92
>TIGR02605 CxxC_CxxC_SSSS putative regulatory protein, FmdB family. This model represents a region of about 50 amino acids found in a number of small proteins in a wide range of bacteria. The region begins usually with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One member of this family is has been noted as a putative regulatory protein, designated FmdB (PubMed:8841393). Most members of this family have a C-terminal region containing highly degenerate sequence, such as SSTSESTKSSGSSGSSGSSESKASGSTEKSTSSTTAAAAV in Mycobacterium tuberculosis and VAVGGSAPAPSPAPRAGGGGGGCCGGGCCG in Streptomyces avermitilis. These low complexity regions, which are not included in the model, resemble low-complexity C-terminal regions of some heterocycle-containing bacteriocin precursors.
Probab=26.49 E-value=42 Score=18.04 Aligned_cols=12 Identities=8% Similarity=-0.092 Sum_probs=6.8
Q ss_pred CcccCCCCCcce
Q psy3162 17 KVLTYALDFVLS 28 (91)
Q Consensus 17 ~~~C~~C~~~~~ 28 (91)
+|+|..||..-+
T Consensus 5 ey~C~~Cg~~fe 16 (52)
T TIGR02605 5 EYRCTACGHRFE 16 (52)
T ss_pred EEEeCCCCCEeE
Confidence 456666665443
No 93
>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=26.47 E-value=37 Score=18.64 Aligned_cols=10 Identities=0% Similarity=-0.380 Sum_probs=7.3
Q ss_pred CCcccCCCCC
Q psy3162 16 GKVLTYALDF 25 (91)
Q Consensus 16 ~~~~C~~C~~ 25 (91)
+.|.|+-|++
T Consensus 1 ~~f~CP~C~~ 10 (54)
T PF05605_consen 1 DSFTCPYCGK 10 (54)
T ss_pred CCcCCCCCCC
Confidence 4677888877
No 94
>PF04795 PAPA-1: PAPA-1-like conserved region; InterPro: IPR006880 This is a group of proteins with a conserved C-terminal region which is found in PAPA-1, a PAP-1 binding protein, Q9C086 from SWISSPROT.
Probab=26.18 E-value=53 Score=20.30 Aligned_cols=19 Identities=26% Similarity=0.583 Sum_probs=14.5
Q ss_pred CCeeeecceEEecCCCCCC
Q psy3162 54 DWTLAKLDVEVEMPDTIDL 72 (91)
Q Consensus 54 ~~~~~Kl~~~V~~P~~LDl 72 (91)
.|...+..+.|.||+++++
T Consensus 70 R~v~~~~G~~vs~P~~~~~ 88 (89)
T PF04795_consen 70 RWVSNKNGSRVSVPEEMGL 88 (89)
T ss_pred EEEECCCceEEEecCCCCC
Confidence 3566678889999988764
No 95
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=25.78 E-value=53 Score=20.71 Aligned_cols=13 Identities=8% Similarity=-0.276 Sum_probs=11.0
Q ss_pred hcCCcccCCCCCc
Q psy3162 14 YCGKVLTYALDFV 26 (91)
Q Consensus 14 l~~~~~C~~C~~~ 26 (91)
....|.|+.|+++
T Consensus 32 ~~~~~~Cp~C~~~ 44 (89)
T COG1997 32 QRAKHVCPFCGRT 44 (89)
T ss_pred HhcCCcCCCCCCc
Confidence 3578999999998
No 96
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.63 E-value=54 Score=27.38 Aligned_cols=25 Identities=4% Similarity=-0.238 Sum_probs=16.0
Q ss_pred Cchhhhh------cCCcccCCCCCcceeEEE
Q psy3162 8 KSFLGLY------CGKVLTYALDFVLSTLRT 32 (91)
Q Consensus 8 ~sl~~cl------~~~~~C~~C~~~~~a~k~ 32 (91)
..+.-|. ...+.||.||+......|
T Consensus 624 ~~~~~C~~CG~~~g~~~~CP~CG~~~~v~sR 654 (656)
T PRK08270 624 PTFSICPKHGYLSGEHEFCPKCGEETEVYSR 654 (656)
T ss_pred CCCcccCCCCCcCCCCCCCcCCcCccceEEe
Confidence 3455565 256799999977554433
No 97
>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=25.54 E-value=23 Score=16.67 Aligned_cols=11 Identities=0% Similarity=-0.493 Sum_probs=8.5
Q ss_pred CCcccCCCCCc
Q psy3162 16 GKVLTYALDFV 26 (91)
Q Consensus 16 ~~~~C~~C~~~ 26 (91)
..|.|+.|++.
T Consensus 13 k~~~C~~C~k~ 23 (26)
T PF13465_consen 13 KPYKCPYCGKS 23 (26)
T ss_dssp SSEEESSSSEE
T ss_pred CCCCCCCCcCe
Confidence 45899999864
No 98
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=25.19 E-value=29 Score=16.38 Aligned_cols=11 Identities=0% Similarity=-0.278 Sum_probs=6.9
Q ss_pred CCcccCCCCCc
Q psy3162 16 GKVLTYALDFV 26 (91)
Q Consensus 16 ~~~~C~~C~~~ 26 (91)
+.-+|+.||.+
T Consensus 15 ~~~fC~~CG~~ 25 (26)
T PF13248_consen 15 DAKFCPNCGAK 25 (26)
T ss_pred ccccChhhCCC
Confidence 45567777753
No 99
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=24.89 E-value=40 Score=26.66 Aligned_cols=29 Identities=10% Similarity=-0.267 Sum_probs=19.3
Q ss_pred CCCCCCCCchhhhh----cCCcccCCCCCccee
Q psy3162 1 MPKPQPTKSFLGLY----CGKVLTYALDFVLST 29 (91)
Q Consensus 1 ~~~~~~~~sl~~cl----~~~~~C~~C~~~~~a 29 (91)
|.|.++..-...|= .-.|+|+.|++=.+.
T Consensus 1 m~~~~~~y~C~~Cg~~~~~~~g~Cp~C~~w~t~ 33 (454)
T TIGR00416 1 MAKAKSKFVCQHCGADSPKWQGKCPACHAWNTI 33 (454)
T ss_pred CCCCCCeEECCcCCCCCccccEECcCCCCcccc
Confidence 66666555555555 357899999985543
No 100
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=24.82 E-value=41 Score=15.46 Aligned_cols=13 Identities=23% Similarity=0.054 Sum_probs=9.1
Q ss_pred CCcccCCCCCcce
Q psy3162 16 GKVLTYALDFVLS 28 (91)
Q Consensus 16 ~~~~C~~C~~~~~ 28 (91)
.+|.|++|.-...
T Consensus 1 g~W~C~~C~~~N~ 13 (26)
T smart00547 1 GDWECPACTFLNF 13 (26)
T ss_pred CcccCCCCCCcCh
Confidence 3688999876543
No 101
>PRK11823 DNA repair protein RadA; Provisional
Probab=24.54 E-value=43 Score=26.38 Aligned_cols=31 Identities=6% Similarity=-0.290 Sum_probs=20.9
Q ss_pred CCCCCCCCchhhhh----cCCcccCCCCCcceeEE
Q psy3162 1 MPKPQPTKSFLGLY----CGKVLTYALDFVLSTLR 31 (91)
Q Consensus 1 ~~~~~~~~sl~~cl----~~~~~C~~C~~~~~a~k 31 (91)
|.|.++..-...|- .-.|+|+.|++-.+...
T Consensus 1 m~~~~~~y~C~~Cg~~~~~~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 1 MAKKKTAYVCQECGAESPKWLGRCPECGAWNTLVE 35 (446)
T ss_pred CCCCCCeEECCcCCCCCcccCeeCcCCCCccceee
Confidence 66666555566665 35779999998665443
No 102
>cd00974 DSRD Desulforedoxin (DSRD) domain; a small non-heme iron domain present in the desulforedoxin (rubredoxin oxidoreductase) and desulfoferrodoxin proteins of some archeael and bacterial methanogens and sulfate/sulfur reducers. Desulforedoxin is a small, single-domain homodimeric protein; each subunit contains an iron atom bound to four cysteinyl sulfur atoms, Fe(S-Cys)4, in a distorted tetrahedral coordination. Its metal center is similar to that found in rubredoxin type proteins. Desulforedoxin is regarded as a potential redox partner for rubredoxin. Desulfoferrodoxin forms a homodimeric protein, with each protomer comprised of two domains, the N-terminal DSRD domain and C-terminal superoxide reductase-like (SORL) domain. Each domain has a distinct iron center: the DSRD iron center I, Fe(S-Cys)4; and the SORL iron center II, Fe[His4Cys(Glu)].
Probab=23.91 E-value=58 Score=16.19 Aligned_cols=15 Identities=7% Similarity=-0.110 Sum_probs=11.1
Q ss_pred CCcccCCCCCcceeE
Q psy3162 16 GKVLTYALDFVLSTL 30 (91)
Q Consensus 16 ~~~~C~~C~~~~~a~ 30 (91)
+-|+|+.||......
T Consensus 3 ~~ykC~~CGniv~v~ 17 (34)
T cd00974 3 EVYKCEICGNIVEVL 17 (34)
T ss_pred cEEEcCCCCcEEEEE
Confidence 358899999877544
No 103
>PF10825 DUF2752: Protein of unknown function (DUF2752); InterPro: IPR021215 This family is conserved in bacteria. Many members are annotated as being putative membrane proteins.
Probab=23.64 E-value=30 Score=19.24 Aligned_cols=13 Identities=0% Similarity=-0.135 Sum_probs=10.4
Q ss_pred CCcccCCCCCcce
Q psy3162 16 GKVLTYALDFVLS 28 (91)
Q Consensus 16 ~~~~C~~C~~~~~ 28 (91)
-++.|+.||-.+.
T Consensus 8 tG~~CPgCG~tRa 20 (52)
T PF10825_consen 8 TGIPCPGCGMTRA 20 (52)
T ss_pred hCCCCCCCcHHHH
Confidence 4789999998764
No 104
>PHA02768 hypothetical protein; Provisional
Probab=23.60 E-value=34 Score=19.61 Aligned_cols=12 Identities=0% Similarity=-0.441 Sum_probs=9.5
Q ss_pred CCcccCCCCCcc
Q psy3162 16 GKVLTYALDFVL 27 (91)
Q Consensus 16 ~~~~C~~C~~~~ 27 (91)
-+|.|+.||+.=
T Consensus 4 ~~y~C~~CGK~F 15 (55)
T PHA02768 4 LGYECPICGEIY 15 (55)
T ss_pred cccCcchhCCee
Confidence 368999999853
No 105
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=23.38 E-value=47 Score=16.86 Aligned_cols=14 Identities=0% Similarity=-0.550 Sum_probs=10.1
Q ss_pred CCcccCCCCCccee
Q psy3162 16 GKVLTYALDFVLST 29 (91)
Q Consensus 16 ~~~~C~~C~~~~~a 29 (91)
+.+.|+.|+...-.
T Consensus 2 ~~~~C~~C~~~~i~ 15 (33)
T PF08792_consen 2 NLKKCSKCGGNGIV 15 (33)
T ss_pred CceEcCCCCCCeEE
Confidence 56788888876543
No 106
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=23.10 E-value=81 Score=24.91 Aligned_cols=26 Identities=8% Similarity=-0.024 Sum_probs=21.0
Q ss_pred cCCcccCCCCCcceeEEEeecccCCC
Q psy3162 15 CGKVLTYALDFVLSTLRTTRLASFPD 40 (91)
Q Consensus 15 ~~~~~C~~C~~~~~a~k~~~~~~lP~ 40 (91)
...-.|+.|+..+...++.+|-.-|-
T Consensus 70 ~~~~~C~~cg~~~~l~R~VSfVDaPG 95 (415)
T COG5257 70 TTEPKCPNCGAETELVRRVSFVDAPG 95 (415)
T ss_pred ccCCCCCCCCCCccEEEEEEEeeCCc
Confidence 45668999999988889888887773
No 107
>TIGR00319 desulf_FeS4 desulfoferrodoxin FeS4 iron-binding domain. Neelaredoxin, a monomeric blue non-heme iron protein, lacks this domain.
Probab=22.99 E-value=62 Score=16.06 Aligned_cols=15 Identities=7% Similarity=-0.095 Sum_probs=11.2
Q ss_pred CCcccCCCCCcceeE
Q psy3162 16 GKVLTYALDFVLSTL 30 (91)
Q Consensus 16 ~~~~C~~C~~~~~a~ 30 (91)
+-|+|+.||......
T Consensus 6 ~~ykC~~Cgniv~v~ 20 (34)
T TIGR00319 6 QVYKCEVCGNIVEVL 20 (34)
T ss_pred cEEEcCCCCcEEEEE
Confidence 458999999877543
No 108
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 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 HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=22.20 E-value=38 Score=16.80 Aligned_cols=11 Identities=9% Similarity=-0.285 Sum_probs=6.5
Q ss_pred CCcccCCCCCc
Q psy3162 16 GKVLTYALDFV 26 (91)
Q Consensus 16 ~~~~C~~C~~~ 26 (91)
..|.|++|+..
T Consensus 12 ~kY~Cp~C~~~ 22 (30)
T PF04438_consen 12 AKYRCPRCGAR 22 (30)
T ss_dssp ESEE-TTT--E
T ss_pred CEEECCCcCCc
Confidence 57899999875
No 109
>PF03811 Zn_Tnp_IS1: InsA N-terminal domain; InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. Protein InsA is absolutely required for transposition of insertion element 1. This entry represents a short zinc binding domain found in IS1 InsA family protein. It is found at the N terminus of the protein and may be a DNA-binding domain.; GO: 0006313 transposition, DNA-mediated
Probab=21.93 E-value=59 Score=16.85 Aligned_cols=15 Identities=7% Similarity=-0.161 Sum_probs=10.7
Q ss_pred CcccCCCCCcceeEE
Q psy3162 17 KVLTYALDFVLSTLR 31 (91)
Q Consensus 17 ~~~C~~C~~~~~a~k 31 (91)
..+|+.|++.....|
T Consensus 5 ~v~CP~C~s~~~v~k 19 (36)
T PF03811_consen 5 DVHCPRCQSTEGVKK 19 (36)
T ss_pred eeeCCCCCCCCccee
Confidence 568999998774433
No 110
>PF10609 ParA: ParA/MinD ATPase like; InterPro: IPR019591 This entry represents ATPases involved in plasmid partitioning []. It also contains cytosolic Fe-S cluster assembling factors, NBP35 and CFD1 which are required for biogenesis and export of both ribosomal subunits probably through assembling the ISCs in RLI1, a protein which performs rRNA processing and ribosome export [, , ].; PDB: 2PH1_A 3KB1_B.
Probab=21.32 E-value=35 Score=20.95 Aligned_cols=13 Identities=0% Similarity=-0.243 Sum_probs=7.4
Q ss_pred cCCcccCCCCCcc
Q psy3162 15 CGKVLTYALDFVL 27 (91)
Q Consensus 15 ~~~~~C~~C~~~~ 27 (91)
+..|.|+.|++..
T Consensus 63 Ms~~~Cp~Cg~~~ 75 (81)
T PF10609_consen 63 MSYFVCPHCGERI 75 (81)
T ss_dssp T-EEE-TTT--EE
T ss_pred CCccCCCCCCCee
Confidence 5789999999865
No 111
>KOG2324|consensus
Probab=21.12 E-value=1.1e+02 Score=24.41 Aligned_cols=49 Identities=14% Similarity=0.093 Sum_probs=28.5
Q ss_pred cccCCCCCcceeEEEeecccCCCeeEEEeeceEECCCCeeeecceE-Eec---CCCCCCCCCC
Q psy3162 18 VLTYALDFVLSTLRTTRLASFPDYLMFHLKKFTMKEDWTLAKLDVE-VEM---PDTIDLTPLR 76 (91)
Q Consensus 18 ~~C~~C~~~~~a~k~~~~~~lP~vLiihlkRF~~~~~~~~~Kl~~~-V~~---P~~LDls~~~ 76 (91)
-.|++|++- .+...+.+=|=|. |..+ +-.+++++.. |++ |+.|+|..|-
T Consensus 248 ~~Cp~C~~~-------~L~~~~~IEVgHt--F~LG-~kYS~~lna~f~~~~gKpe~l~MgCyG 300 (457)
T KOG2324|consen 248 ASCPKCNEG-------RLTKTKSIEVGHT--FLLG-TKYSKPLNAKFVNVEGKPEFLHMGCYG 300 (457)
T ss_pred ccCCcccCC-------CcccccceEEEEE--EEec-cccccccCceeeeecCCcceEEeccee
Confidence 568888874 2334444444443 4553 3345566665 666 5778888773
No 112
>PHA00616 hypothetical protein
Probab=20.80 E-value=31 Score=18.90 Aligned_cols=9 Identities=0% Similarity=-0.267 Sum_probs=7.0
Q ss_pred cccCCCCCc
Q psy3162 18 VLTYALDFV 26 (91)
Q Consensus 18 ~~C~~C~~~ 26 (91)
|.|+.||..
T Consensus 2 YqC~~CG~~ 10 (44)
T PHA00616 2 YQCLRCGGI 10 (44)
T ss_pred CccchhhHH
Confidence 678888864
No 113
>smart00355 ZnF_C2H2 zinc finger.
Probab=20.76 E-value=51 Score=14.02 Aligned_cols=9 Identities=11% Similarity=-0.300 Sum_probs=6.0
Q ss_pred cccCCCCCc
Q psy3162 18 VLTYALDFV 26 (91)
Q Consensus 18 ~~C~~C~~~ 26 (91)
|.|+.|+..
T Consensus 1 ~~C~~C~~~ 9 (26)
T smart00355 1 YRCPECGKV 9 (26)
T ss_pred CCCCCCcch
Confidence 467777754
No 114
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=20.72 E-value=52 Score=21.51 Aligned_cols=35 Identities=9% Similarity=-0.055 Sum_probs=23.5
Q ss_pred CcccCCCCCccee-EEEeecccCCCeeEEEeeceEE
Q psy3162 17 KVLTYALDFVLST-LRTTRLASFPDYLMFHLKKFTM 51 (91)
Q Consensus 17 ~~~C~~C~~~~~a-~k~~~~~~lP~vLiihlkRF~~ 51 (91)
+|.|++|+.+.-. --.-.+-.|.=|+--||.|=..
T Consensus 1 GY~CPrC~skvC~LP~~CpiCgLtLVss~HLARSyH 36 (112)
T TIGR00622 1 GYFCPQCRAKVCELPVECPICGLTLILSTHLARSYH 36 (112)
T ss_pred CccCCCCCCCccCCCCcCCcCCCEEeccchHHHhhh
Confidence 5899999998731 1233455666677778888654
No 115
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=20.47 E-value=49 Score=16.74 Aligned_cols=11 Identities=0% Similarity=-0.191 Sum_probs=6.8
Q ss_pred cccCCCCCcce
Q psy3162 18 VLTYALDFVLS 28 (91)
Q Consensus 18 ~~C~~C~~~~~ 28 (91)
|.|..||....
T Consensus 1 Y~C~~Cg~~~~ 11 (32)
T PF03604_consen 1 YICGECGAEVE 11 (32)
T ss_dssp EBESSSSSSE-
T ss_pred CCCCcCCCeeE
Confidence 56777776654
No 116
>PF08209 Sgf11: Sgf11 (transcriptional regulation protein); InterPro: IPR013246 The Sgf11 family is a SAGA complex subunit in Saccharomyces cerevisiae (Baker's yeast). The SAGA complex is a multisubunit protein complex involved in transcriptional regulation. SAGA combines proteins involved in interactions with DNA-bound activators and TATA-binding protein (TBP), as well as enzymes for histone acetylation and deubiquitylation [].; PDB: 3M99_B 2LO2_A 3MHH_C 3MHS_C.
Probab=20.17 E-value=42 Score=17.18 Aligned_cols=13 Identities=8% Similarity=-0.210 Sum_probs=9.0
Q ss_pred CcccCCCCCccee
Q psy3162 17 KVLTYALDFVLST 29 (91)
Q Consensus 17 ~~~C~~C~~~~~a 29 (91)
.+.|++|+....|
T Consensus 4 ~~~C~nC~R~v~a 16 (33)
T PF08209_consen 4 YVECPNCGRPVAA 16 (33)
T ss_dssp EEE-TTTSSEEEG
T ss_pred eEECCCCcCCcch
Confidence 4689999987654
No 117
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=20.04 E-value=48 Score=20.76 Aligned_cols=12 Identities=8% Similarity=-0.377 Sum_probs=10.2
Q ss_pred cCCcccCCCCCc
Q psy3162 15 CGKVLTYALDFV 26 (91)
Q Consensus 15 ~~~~~C~~C~~~ 26 (91)
.+.|.|+.||+.
T Consensus 29 ~~~~~C~~CGe~ 40 (127)
T TIGR03830 29 VPGWYCPACGEE 40 (127)
T ss_pred eeeeECCCCCCE
Confidence 578999999985
Done!