Query psy12215
Match_columns 155
No_of_seqs 174 out of 1418
Neff 9.0
Searched_HMMs 46136
Date Fri Aug 16 21:45:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy12215.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/12215hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4577|consensus 99.9 5.1E-29 1.1E-33 184.3 1.1 146 1-155 51-203 (383)
2 KOG1701|consensus 99.9 8.6E-29 1.9E-33 191.5 -3.8 141 1-153 293-438 (468)
3 KOG2272|consensus 99.9 2E-24 4.4E-29 157.5 -2.3 131 2-143 32-162 (332)
4 KOG1701|consensus 99.8 5.1E-21 1.1E-25 148.6 4.6 104 1-108 351-463 (468)
5 KOG1044|consensus 99.8 5.2E-21 1.1E-25 153.1 3.4 135 1-149 82-223 (670)
6 KOG1703|consensus 99.8 4E-20 8.7E-25 150.4 2.5 130 1-144 321-450 (479)
7 KOG2272|consensus 99.8 3.5E-20 7.6E-25 135.4 0.2 125 3-144 156-280 (332)
8 KOG1044|consensus 99.7 2E-18 4.4E-23 138.4 1.2 98 1-105 151-248 (670)
9 KOG1703|consensus 99.6 4.3E-17 9.3E-22 132.7 0.8 99 1-104 380-478 (479)
10 PF00412 LIM: LIM domain; Int 99.6 7.3E-15 1.6E-19 86.5 5.4 58 50-108 1-58 (58)
11 KOG4577|consensus 99.3 1.6E-13 3.5E-18 102.4 -2.3 95 49-153 35-131 (383)
12 PF00412 LIM: LIM domain; Int 99.3 1.9E-12 4E-17 76.1 2.2 42 1-44 17-58 (58)
13 KOG1700|consensus 99.1 1.3E-11 2.7E-16 90.0 0.5 103 2-108 26-167 (200)
14 smart00132 LIM Zinc-binding do 98.7 1.4E-08 3E-13 54.4 2.5 37 49-85 1-37 (39)
15 KOG0490|consensus 97.9 1.9E-06 4.2E-11 63.9 -1.0 101 3-107 16-119 (235)
16 smart00132 LIM Zinc-binding do 97.8 1E-05 2.2E-10 42.9 1.0 20 1-20 18-37 (39)
17 KOG1702|consensus 97.4 9.6E-06 2.1E-10 58.5 -2.7 58 49-108 6-63 (264)
18 KOG1700|consensus 97.3 5.9E-05 1.3E-09 55.1 -0.2 58 49-108 9-66 (200)
19 KOG1702|consensus 96.1 0.0008 1.7E-08 48.8 -1.2 42 2-45 23-64 (264)
20 KOG0490|consensus 93.5 0.027 5.9E-07 41.6 0.6 66 53-123 2-69 (235)
21 PF06677 Auto_anti-p27: Sjogre 87.8 0.39 8.5E-06 25.9 1.5 22 12-39 19-40 (41)
22 PF11781 RRN7: RNA polymerase 86.7 0.49 1.1E-05 24.7 1.5 24 12-41 10-33 (36)
23 smart00504 Ubox Modified RING 86.7 0.43 9.4E-06 27.6 1.5 46 11-59 2-47 (63)
24 PF08394 Arc_trans_TRASH: Arch 86.4 0.42 9.1E-06 25.1 1.1 24 50-73 1-24 (37)
25 PF07191 zinc-ribbons_6: zinc- 84.4 2.1 4.6E-05 25.8 3.6 58 12-85 3-60 (70)
26 PF06906 DUF1272: Protein of u 83.4 1 2.3E-05 25.8 1.9 46 12-59 7-53 (57)
27 COG1645 Uncharacterized Zn-fin 83.4 0.78 1.7E-05 31.2 1.6 23 12-41 30-52 (131)
28 KOG1813|consensus 83.3 1.2 2.6E-05 34.4 2.7 50 76-129 242-291 (313)
29 PF14835 zf-RING_6: zf-RING of 82.4 1.5 3.2E-05 26.1 2.3 47 11-61 8-54 (65)
30 PF14446 Prok-RING_1: Prokaryo 82.3 0.72 1.6E-05 26.4 1.0 28 49-76 7-36 (54)
31 COG5152 Uncharacterized conser 82.2 0.88 1.9E-05 33.2 1.6 48 76-127 197-244 (259)
32 PF10367 Vps39_2: Vacuolar sor 81.2 1.2 2.5E-05 28.6 1.9 28 49-76 80-107 (109)
33 PF14634 zf-RING_5: zinc-RING 81.1 1.9 4E-05 23.2 2.4 41 78-120 2-43 (44)
34 PF14835 zf-RING_6: zf-RING of 80.1 1 2.2E-05 26.7 1.2 43 76-124 8-51 (65)
35 PF04570 DUF581: Protein of un 79.5 1.4 3E-05 25.6 1.5 27 12-38 18-44 (58)
36 KOG0320|consensus 78.3 1.3 2.8E-05 31.7 1.4 50 73-124 129-178 (187)
37 PF14471 DUF4428: Domain of un 76.6 2.4 5.2E-05 23.9 2.0 30 77-107 1-30 (51)
38 PF10235 Cript: Microtubule-as 75.4 1.5 3.3E-05 27.8 1.0 36 12-59 46-81 (90)
39 PF10367 Vps39_2: Vacuolar sor 74.0 3.1 6.7E-05 26.6 2.3 28 12-41 80-108 (109)
40 PF09943 DUF2175: Uncharacteri 73.6 1.3 2.8E-05 28.8 0.3 33 76-108 3-35 (101)
41 PF13920 zf-C3HC4_3: Zinc fing 73.5 6.1 0.00013 21.7 3.1 44 77-124 4-48 (50)
42 PF13240 zinc_ribbon_2: zinc-r 73.0 1.6 3.5E-05 20.3 0.5 8 13-20 2-9 (23)
43 PRK00420 hypothetical protein; 71.0 2.5 5.5E-05 28.0 1.3 25 11-41 24-48 (112)
44 PF13923 zf-C3HC4_2: Zinc fing 69.8 3.3 7.2E-05 21.5 1.4 38 13-52 1-38 (39)
45 KOG1813|consensus 68.7 2.7 5.8E-05 32.5 1.2 46 11-59 242-287 (313)
46 COG2191 Formylmethanofuran deh 68.5 1.7 3.6E-05 31.8 0.1 32 76-108 173-204 (206)
47 PRK14890 putative Zn-ribbon RN 67.2 3.5 7.5E-05 24.0 1.2 36 12-55 9-44 (59)
48 KOG4739|consensus 64.0 4.9 0.00011 30.1 1.8 42 78-124 6-48 (233)
49 PF06689 zf-C4_ClpX: ClpX C4-t 63.8 8.2 0.00018 20.6 2.2 31 12-42 3-33 (41)
50 PF13834 DUF4193: Domain of un 63.5 2.5 5.3E-05 27.3 0.1 29 10-39 70-98 (99)
51 COG1645 Uncharacterized Zn-fin 62.1 4.7 0.0001 27.5 1.3 21 78-104 31-51 (131)
52 PF13639 zf-RING_2: Ring finge 62.1 5.7 0.00012 21.1 1.4 32 13-44 3-34 (44)
53 PF12773 DZR: Double zinc ribb 62.0 3.8 8.2E-05 22.5 0.7 38 13-59 1-41 (50)
54 KOG0320|consensus 61.8 2.9 6.3E-05 30.0 0.2 51 8-59 129-179 (187)
55 PRK00807 50S ribosomal protein 61.2 8.8 0.00019 21.7 2.1 24 12-35 3-27 (52)
56 PF09943 DUF2175: Uncharacteri 61.2 8.9 0.00019 24.9 2.4 32 49-80 4-35 (101)
57 PF14570 zf-RING_4: RING/Ubox 60.2 4.4 9.5E-05 22.6 0.7 43 14-56 2-46 (48)
58 PF01258 zf-dskA_traR: Prokary 59.7 1.4 2.9E-05 22.8 -1.3 27 78-105 6-32 (36)
59 COG5152 Uncharacterized conser 57.5 2.6 5.6E-05 30.8 -0.6 46 11-59 197-242 (259)
60 cd02249 ZZ Zinc finger, ZZ typ 57.0 10 0.00022 20.5 1.9 10 97-106 23-32 (46)
61 cd00162 RING RING-finger (Real 56.9 5.9 0.00013 20.3 0.9 41 13-55 2-43 (45)
62 COG4847 Uncharacterized protei 55.4 11 0.00024 24.1 2.0 31 76-106 7-37 (103)
63 PF02069 Metallothio_Pro: Prok 55.4 6.5 0.00014 22.3 0.9 27 13-41 10-37 (52)
64 PRK14873 primosome assembly pr 54.6 9.5 0.00021 33.1 2.2 39 11-56 393-431 (665)
65 PF13248 zf-ribbon_3: zinc-rib 53.5 5.9 0.00013 18.8 0.5 7 13-19 5-11 (26)
66 PF00645 zf-PARP: Poly(ADP-rib 53.2 5.6 0.00012 24.4 0.4 13 49-61 9-21 (82)
67 PF12674 Zn_ribbon_2: Putative 52.6 4.6 9.9E-05 25.1 -0.0 30 12-43 2-36 (81)
68 PF08792 A2L_zn_ribbon: A2L zi 52.4 16 0.00035 18.5 2.0 24 12-40 5-28 (33)
69 PF12156 ATPase-cat_bd: Putati 51.6 12 0.00027 23.5 1.9 25 12-36 2-28 (88)
70 COG2075 RPL24A Ribosomal prote 50.8 17 0.00038 21.6 2.2 24 12-35 5-29 (66)
71 COG1198 PriA Primosomal protei 49.8 13 0.00028 32.7 2.2 40 11-56 445-484 (730)
72 smart00291 ZnF_ZZ Zinc-binding 48.8 19 0.00042 19.3 2.1 10 97-106 27-36 (44)
73 PF11571 Med27: Mediator compl 46.7 5.4 0.00012 25.2 -0.4 16 40-57 49-64 (90)
74 PF00097 zf-C3HC4: Zinc finger 46.6 24 0.00053 18.1 2.3 29 78-108 1-30 (41)
75 KOG0978|consensus 45.6 3.7 8.1E-05 35.6 -1.6 48 11-61 644-692 (698)
76 TIGR00595 priA primosomal prot 45.2 17 0.00037 30.4 2.2 40 11-56 223-262 (505)
77 PF15227 zf-C3HC4_4: zinc fing 45.0 36 0.00078 18.0 2.8 29 78-108 1-29 (42)
78 smart00547 ZnF_RBZ Zinc finger 43.7 11 0.00023 17.6 0.5 20 36-55 5-24 (26)
79 PF00569 ZZ: Zinc finger, ZZ t 41.6 38 0.00083 18.3 2.6 10 97-106 28-37 (46)
80 PRK14559 putative protein seri 40.9 20 0.00044 31.1 2.1 37 12-59 3-39 (645)
81 KOG2462|consensus 40.8 14 0.00031 28.4 1.0 69 9-85 129-197 (279)
82 PF03854 zf-P11: P-11 zinc fin 40.2 41 0.00089 18.7 2.5 28 95-124 19-46 (50)
83 COG2888 Predicted Zn-ribbon RN 39.7 14 0.00031 21.5 0.7 10 12-21 11-20 (61)
84 cd02336 ZZ_RSC8 Zinc finger, Z 37.0 40 0.00087 18.4 2.2 30 77-107 2-33 (45)
85 PF04981 NMD3: NMD3 family ; 36.9 24 0.00053 26.3 1.8 40 13-60 1-48 (236)
86 PF10122 Mu-like_Com: Mu-like 36.6 21 0.00045 20.1 1.0 12 11-22 5-16 (51)
87 PF10886 DUF2685: Protein of u 36.2 31 0.00068 19.7 1.7 24 49-73 3-26 (54)
88 COG3813 Uncharacterized protei 35.8 34 0.00074 20.8 1.9 45 13-59 8-53 (84)
89 PF00641 zf-RanBP: Zn-finger i 33.7 27 0.00059 16.9 1.1 24 33-56 4-27 (30)
90 smart00659 RPOLCX RNA polymera 33.7 26 0.00056 19.0 1.1 11 11-21 3-13 (44)
91 cd02340 ZZ_NBR1_like Zinc fing 33.7 38 0.00083 18.1 1.8 11 49-59 2-12 (43)
92 PF10764 Gin: Inhibitor of sig 33.3 35 0.00075 18.7 1.6 28 12-43 1-28 (46)
93 cd00472 Ribosomal_L24e_L24 Rib 33.3 42 0.00092 19.1 2.0 24 12-35 5-29 (54)
94 PF08271 TF_Zn_Ribbon: TFIIB z 33.2 29 0.00062 18.4 1.2 10 49-58 21-30 (43)
95 PRK12495 hypothetical protein; 33.1 21 0.00044 26.6 0.8 26 8-40 40-65 (226)
96 PF04564 U-box: U-box domain; 32.5 63 0.0014 19.2 2.8 48 9-59 3-51 (73)
97 PF06827 zf-FPG_IleRS: Zinc fi 32.3 26 0.00057 16.9 0.9 10 49-58 3-12 (30)
98 PF07754 DUF1610: Domain of un 31.7 32 0.00069 16.2 1.1 9 51-59 2-10 (24)
99 PRK00398 rpoP DNA-directed RNA 31.6 26 0.00057 18.9 0.9 11 11-21 4-14 (46)
100 PF04810 zf-Sec23_Sec24: Sec23 31.4 40 0.00086 17.7 1.6 29 49-83 4-32 (40)
101 PF01286 XPA_N: XPA protein N- 31.4 16 0.00034 18.8 -0.0 10 12-21 5-14 (34)
102 cd02335 ZZ_ADA2 Zinc finger, Z 30.2 49 0.0011 18.1 1.9 10 98-107 25-34 (49)
103 PRK14891 50S ribosomal protein 30.1 45 0.00097 22.7 2.0 24 12-35 6-30 (131)
104 PF10083 DUF2321: Uncharacteri 30.1 5.7 0.00012 27.8 -2.3 34 97-135 28-61 (158)
105 PF00096 zf-C2H2: Zinc finger, 29.9 20 0.00043 15.8 0.2 10 11-20 1-10 (23)
106 PRK05580 primosome assembly pr 29.6 43 0.00093 29.2 2.3 39 12-56 392-430 (679)
107 PRK04136 rpl40e 50S ribosomal 28.7 27 0.0006 19.4 0.6 24 32-55 13-36 (48)
108 TIGR00570 cdk7 CDK-activating 28.6 52 0.0011 25.9 2.4 28 96-124 27-54 (309)
109 PLN03208 E3 ubiquitin-protein 28.1 56 0.0012 23.8 2.3 48 75-124 18-79 (193)
110 PF14445 Prok-RING_2: Prokaryo 28.0 4.5 9.7E-05 22.7 -2.5 44 11-57 8-51 (57)
111 cd02341 ZZ_ZZZ3 Zinc finger, Z 28.0 64 0.0014 17.8 2.1 10 97-106 26-35 (48)
112 KOG3002|consensus 27.5 40 0.00087 26.3 1.6 43 11-58 49-91 (299)
113 PRK11595 DNA utilization prote 27.4 37 0.00079 25.1 1.4 38 13-58 8-45 (227)
114 cd02338 ZZ_PCMF_like Zinc fing 27.2 56 0.0012 17.9 1.8 11 97-107 24-34 (49)
115 PF13717 zinc_ribbon_4: zinc-r 27.0 21 0.00046 18.4 0.0 7 77-83 27-33 (36)
116 TIGR02098 MJ0042_CXXC MJ0042 f 26.7 20 0.00044 18.3 -0.1 9 49-57 27-35 (38)
117 PF09723 Zn-ribbon_8: Zinc rib 26.7 24 0.00052 18.8 0.2 11 11-21 6-16 (42)
118 PF13894 zf-C2H2_4: C2H2-type 26.4 30 0.00065 14.9 0.5 10 11-20 1-10 (24)
119 smart00834 CxxC_CXXC_SSSS Puta 25.7 26 0.00056 18.0 0.2 10 11-20 6-15 (41)
120 TIGR00270 conserved hypothetic 25.6 68 0.0015 22.4 2.4 28 12-40 2-31 (154)
121 KOG2893|consensus 24.9 29 0.00063 26.3 0.4 48 49-105 12-59 (341)
122 PF02591 DUF164: Putative zinc 23.5 14 0.00031 20.9 -1.2 11 49-59 24-34 (56)
123 PF05920 Homeobox_KN: Homeobox 23.4 63 0.0014 17.0 1.5 17 138-154 5-21 (40)
124 TIGR02605 CxxC_CxxC_SSSS putat 23.3 32 0.00069 18.9 0.3 10 11-20 6-15 (52)
125 PF00320 GATA: GATA zinc finge 22.6 79 0.0017 16.1 1.7 28 13-42 1-29 (36)
126 PRK00085 recO DNA repair prote 22.5 51 0.0011 24.4 1.4 31 8-40 147-177 (247)
127 COG4416 Com Mu-like prophage p 21.3 27 0.0006 19.9 -0.2 14 11-24 5-18 (60)
128 COG0266 Nei Formamidopyrimidin 21.1 60 0.0013 25.1 1.5 25 49-75 247-271 (273)
129 KOG4443|consensus 21.0 43 0.00093 29.0 0.7 19 67-85 107-125 (694)
130 PF10080 DUF2318: Predicted me 21.0 88 0.0019 20.3 2.0 17 26-42 45-61 (102)
131 PF13912 zf-C2H2_6: C2H2-type 21.0 42 0.00091 15.4 0.4 10 11-20 2-11 (27)
132 PF02428 Prot_inhib_II: Potato 20.9 1.2E+02 0.0026 17.1 2.3 15 23-37 37-51 (52)
133 cd02345 ZZ_dah Zinc finger, ZZ 20.7 75 0.0016 17.5 1.5 10 98-107 25-34 (49)
134 PF01246 Ribosomal_L24e: Ribos 20.6 68 0.0015 19.4 1.4 24 12-35 5-29 (71)
135 PF10170 C6_DPF: Cysteine-rich 20.4 81 0.0018 20.3 1.7 31 77-107 51-81 (97)
136 KOG3476|consensus 20.1 24 0.00052 22.2 -0.7 26 30-59 66-91 (100)
137 PF07649 C1_3: C1-like domain; 20.0 70 0.0015 15.4 1.1 11 11-21 1-11 (30)
No 1
>KOG4577|consensus
Probab=99.95 E-value=5.1e-29 Score=184.34 Aligned_cols=146 Identities=35% Similarity=0.729 Sum_probs=123.9
Q ss_pred CCCccccccCcccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCceEEeccCcccccccccccc
Q psy12215 1 ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQ 80 (155)
Q Consensus 1 A~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 80 (155)
++++.||..|++|++|..+|.+ .+|.++|.+||++++.++|+. +|..|...|.+...+..+.+..||..||.|..
T Consensus 51 vl~R~wHs~CLkCs~C~~qL~d---rCFsR~~s~yCkedFfKrfGT--KCsaC~~GIpPtqVVRkAqd~VYHl~CF~C~i 125 (383)
T KOG4577|consen 51 VLDRHWHSSCLKCSDCHDQLAD---RCFSREGSVYCKEDFFKRFGT--KCSACQEGIPPTQVVRKAQDFVYHLHCFACFI 125 (383)
T ss_pred HHhhhhhhhhcchhhhhhHHHH---HHhhcCCceeehHHHHHHhCC--cchhhcCCCChHHHHHHhhcceeehhhhhhHh
Confidence 4689999999999999999953 689999999999999999999 99999999999766777889999999999999
Q ss_pred CCcccccCCeEEe-eCCeeecHHhHHhhhcccCCCeee----ecCCeecchhhHHHHHHHHhhcCC--CCchHHHhhhhh
Q psy12215 81 CNHRFCVGDRFYL-CDNKILCEYDYEERQVFCVGDRFY----LCDNKILCEYDYEERQVFANIAYN--PSSLAHLRRQVT 153 (155)
Q Consensus 81 C~~~l~~~~~~~~-~~~~~~C~~c~~~~~~~~~~~~c~----~c~~~i~c~~~~~~~~~~~~~~~h--p~~~~~~~~~~~ 153 (155)
|++.|..+..|+. .|+++.|+.+|+... ...|. -=.++-+.++...++++..+.+|. |+|+||||||||
T Consensus 126 C~R~L~TGdEFYLmeD~rLvCK~DYE~Ak----~k~~~~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLs 201 (383)
T KOG4577|consen 126 CKRQLATGDEFYLMEDARLVCKDDYETAK----QKHCNELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLS 201 (383)
T ss_pred hhcccccCCeeEEeccceeehhhhHHHHH----hccccccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhh
Confidence 9999998999885 569999999999876 34432 222333334455899999999898 899999999998
Q ss_pred cC
Q psy12215 154 LQ 155 (155)
Q Consensus 154 ~~ 155 (155)
-+
T Consensus 202 se 203 (383)
T KOG4577|consen 202 SE 203 (383)
T ss_pred hc
Confidence 53
No 2
>KOG1701|consensus
Probab=99.93 E-value=8.6e-29 Score=191.48 Aligned_cols=141 Identities=26% Similarity=0.540 Sum_probs=123.5
Q ss_pred CCCccccccCcccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCceEEeccCcccccccccccc
Q psy12215 1 ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQ 80 (155)
Q Consensus 1 A~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 80 (155)
||++.||..||+|..|++.| .++.||..|+++||+.||..... +|..|++.|. |+++.+.|+.||+.||+|..
T Consensus 293 Am~~~fHv~CFtC~~C~r~L--~Gq~FY~v~~k~~CE~cyq~tle---kC~~Cg~~I~--d~iLrA~GkayHp~CF~Cv~ 365 (468)
T KOG1701|consen 293 AMDQLFHVQCFTCRTCRRQL--AGQSFYQVDGKPYCEGCYQDTLE---KCNKCGEPIM--DRILRALGKAYHPGCFTCVV 365 (468)
T ss_pred HhhhhhcccceehHhhhhhh--ccccccccCCcccchHHHHHHHH---HHhhhhhHHH--HHHHHhcccccCCCceEEEE
Confidence 79999999999999999999 78899999999999999998765 7999999997 48999999999999999999
Q ss_pred CCcccccCCeEEee-CCeeecHHhHHhhhcccCCCeeeecCCeecchhhHHH--HHHHHhhcCCCCc--hHHHhhhhh
Q psy12215 81 CNHRFCVGDRFYLC-DNKILCEYDYEERQVFCVGDRFYLCDNKILCEYDYEE--RQVFANIAYNPSS--LAHLRRQVT 153 (155)
Q Consensus 81 C~~~l~~~~~~~~~-~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~c~~~~~~--~~~~~~~~~hp~~--~~~~~~~~~ 153 (155)
|.+.| .+..|++. ++++||-.+|.++| +++|.+|.++|+...--++ +|+.+++.||=++ +.-.+-+||
T Consensus 366 C~r~l-dgipFtvd~~n~v~Cv~dfh~kf----APrCs~C~~PI~P~~G~~etvRvvamdr~fHv~CY~CEDCg~~LS 438 (468)
T KOG1701|consen 366 CARCL-DGIPFTVDSQNNVYCVPDFHKKF----APRCSVCGNPILPRDGKDETVRVVAMDRDFHVNCYKCEDCGLLLS 438 (468)
T ss_pred ecccc-CCccccccCCCceeeehhhhhhc----CcchhhccCCccCCCCCcceEEEEEccccccccceehhhcCcccc
Confidence 99999 88888764 59999999999999 9999999999986554333 3556778999764 666666666
No 3
>KOG2272|consensus
Probab=99.87 E-value=2e-24 Score=157.47 Aligned_cols=131 Identities=27% Similarity=0.627 Sum_probs=112.8
Q ss_pred CCccccccCcccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCceEEeccCccccccccccccC
Q psy12215 2 LDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQC 81 (155)
Q Consensus 2 ~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C 81 (155)
.|..||.+||.|+.|-.|++ +..|+..+|+.||+.|+..+|+| .|..|++.|.+ ++|.+.+.+||+.||+|..|
T Consensus 32 ~ge~wH~~CFvCAQCf~pf~--~g~~~efEgRkYCEhDF~~LfaP--cC~kC~EFiiG--rVikamnnSwHp~CF~Cd~C 105 (332)
T KOG2272|consen 32 NGELWHEQCFVCAQCFRPFP--DGIFYEFEGRKYCEHDFHVLFAP--CCGKCGEFIIG--RVIKAMNNSWHPACFRCDLC 105 (332)
T ss_pred CchhhHHHHHHHHHhcCcCC--CceeEEecCcccccccchhhhch--hhcccccchhh--HHHHhhccccCcccchhHHH
Confidence 46799999999999999995 56899999999999999999999 99999999987 78899999999999999999
Q ss_pred CcccccCCeEEeeCCeeecHHhHHhhhcccCCCeeeecCCeecchhhHHHHHHHHhhcCCCC
Q psy12215 82 NHRFCVGDRFYLCDNKILCEYDYEERQVFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPS 143 (155)
Q Consensus 82 ~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~c~~~~~~~~~~~~~~~hp~ 143 (155)
++.| .+..|+...|+.+|..|..+.. +.+..-+.|++... -++ ++.+.++|++|||.
T Consensus 106 n~~L-ad~gf~rnqgr~LC~~Cn~k~K--a~~~g~YvC~KCh~-~iD-~~~l~fr~d~yH~y 162 (332)
T KOG2272|consen 106 NKHL-ADQGFYRNQGRALCRECNQKEK--AKGRGRYVCQKCHA-HID-EQPLTFRGDPYHPY 162 (332)
T ss_pred HHHH-hhhhhHhhcchHHhhhhhhhhc--ccccceeehhhhhh-hcc-cccccccCCCCCcc
Confidence 9999 6777777779999999988754 33555677777333 222 68899999999995
No 4
>KOG1701|consensus
Probab=99.82 E-value=5.1e-21 Score=148.57 Aligned_cols=104 Identities=25% Similarity=0.560 Sum_probs=91.3
Q ss_pred CCCccccccCcccccCCcccccCCCeEEE-eCCeeecccchhccccccccccccccccccCce-----EEeccCcccccc
Q psy12215 1 ALDLFWHEDCLKCGCCDCRLGEVGSTLYQ-KANLILCKRDYLRLFGTTGYCAACTKVIPAFEM-----VMRAKNNVYHLE 74 (155)
Q Consensus 1 A~~~~~H~~Cf~C~~C~~~l~~~~~~~~~-~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~-----~~~~~~~~~H~~ 74 (155)
|+|+.||+.||+|..|++.|+ +-.|.+ .++++||-+||+++|++ +|+.|+++|++.+- -|.+.++.||.+
T Consensus 351 A~GkayHp~CF~Cv~C~r~ld--gipFtvd~~n~v~Cv~dfh~kfAP--rCs~C~~PI~P~~G~~etvRvvamdr~fHv~ 426 (468)
T KOG1701|consen 351 ALGKAYHPGCFTCVVCARCLD--GIPFTVDSQNNVYCVPDFHKKFAP--RCSVCGNPILPRDGKDETVRVVAMDRDFHVN 426 (468)
T ss_pred hcccccCCCceEEEEeccccC--CccccccCCCceeeehhhhhhcCc--chhhccCCccCCCCCcceEEEEEcccccccc
Confidence 799999999999999999995 456774 77889999999999999 99999999986431 466889999999
Q ss_pred ccccccCCcccc---cCCeEEeeCCeeecHHhHHhhh
Q psy12215 75 CFACQQCNHRFC---VGDRFYLCDNKILCEYDYEERQ 108 (155)
Q Consensus 75 Cf~C~~C~~~l~---~~~~~~~~~~~~~C~~c~~~~~ 108 (155)
|++|..|+..|+ ++..++..||.++|+.|..++.
T Consensus 427 CY~CEDCg~~LS~e~e~qgCyPld~HllCk~Ch~~Rl 463 (468)
T KOG1701|consen 427 CYKCEDCGLLLSSEEEGQGCYPLDGHLLCKTCHLKRL 463 (468)
T ss_pred ceehhhcCccccccCCCCcceeccCceeechhhhhhh
Confidence 999999999995 4556899999999999988765
No 5
>KOG1044|consensus
Probab=99.82 E-value=5.2e-21 Score=153.08 Aligned_cols=135 Identities=20% Similarity=0.459 Sum_probs=116.5
Q ss_pred CCCccccccCcccccCCcccccCCCeEEEeCCeeecccchhccc-------cccccccccccccccCceEEeccCccccc
Q psy12215 1 ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF-------GTTGYCAACTKVIPAFEMVMRAKNNVYHL 73 (155)
Q Consensus 1 A~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~-------~~~~~C~~C~~~I~~~~~~~~~~~~~~H~ 73 (155)
|+|++||+.||.|+.|..++.++ ...........|+.|..-.. ++ ..|++|++.|.. ..++.++++.||.
T Consensus 82 a~gktyh~~cf~cs~ck~pf~~g-~~vt~~gk~~~c~~c~~~~~~~p~~~~~p-s~cagc~~~lk~-gq~llald~qwhv 158 (670)
T KOG1044|consen 82 TLGKTYHPKCFSCSTCKSPFKSG-DKVTFSGKECLCQTCSQPMPVSPAESYGP-STCAGCGEELKN-GQALLALDKQWHV 158 (670)
T ss_pred cccceeccccceecccCCCCCCC-CeeeecchhhhhhhhcCcccCCcccccCC-ccccchhhhhhc-cceeeeeccceee
Confidence 68999999999999999999864 35566666788888874321 22 269999999986 4677899999999
Q ss_pred cccccccCCcccccCCeEEeeCCeeecHHhHHhhhcccCCCeeeecCCeecchhhHHHHHHHHhhcCCCCchHHHh
Q psy12215 74 ECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSSLAHLR 149 (155)
Q Consensus 74 ~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~c~~~~~~~~~~~~~~~hp~~~~~~~ 149 (155)
.||+|..|...| ...|+..+|.+||..+|...| |.+|..|.+-|. ++.++..|++|||.++|.+|
T Consensus 159 ~cfkc~~c~~vL--~gey~skdg~pyce~dy~~~f----gvkc~~c~~fis-----gkvLqag~kh~HPtCARCsR 223 (670)
T KOG1044|consen 159 SCFKCKSCSAVL--NGEYMSKDGVPYCEKDYQAKF----GVKCEECEKFIS-----GKVLQAGDKHFHPTCARCSR 223 (670)
T ss_pred eeeehhhhcccc--cceeeccCCCcchhhhhhhhc----CeehHHhhhhhh-----hhhhhccCcccCcchhhhhh
Confidence 999999999999 667999999999999999999 999999999888 88999999999999998876
No 6
>KOG1703|consensus
Probab=99.78 E-value=4e-20 Score=150.36 Aligned_cols=130 Identities=20% Similarity=0.416 Sum_probs=116.0
Q ss_pred CCCccccccCcccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCceEEeccCcccccccccccc
Q psy12215 1 ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQ 80 (155)
Q Consensus 1 A~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 80 (155)
|+++.||+.+|.|..|...+.. ..+...+|++||.+|+...+.+ .|.+|.++|.+ ..|.+.+..||++||.|..
T Consensus 321 ~~~~~~h~~~~~c~~~~~~~~~--~~~~~~~g~~~c~~~~~~~~~p--~C~~C~~~i~~--~~v~a~~~~wH~~cf~C~~ 394 (479)
T KOG1703|consen 321 ALGKEWHPEHFSCEVCAIVILD--GGPRELDGKILCHECFHAPFRP--NCKRCLLPILE--EGVCALGRLWHPECFVCAD 394 (479)
T ss_pred eccccccccceeeccccccccC--CCccccCCCccHHHHHHHhhCc--cccccCCchHH--hHhhhccCeechhceeeec
Confidence 6889999999999999999954 4578999999999999999999 99999999986 6778889999999999999
Q ss_pred CCcccccCCeEEeeCCeeecHHhHHhhhcccCCCeeeecCCeecchhhHHHHHHHHhhcCCCCc
Q psy12215 81 CNHRFCVGDRFYLCDNKILCEYDYEERQVFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSS 144 (155)
Q Consensus 81 C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~c~~~~~~~~~~~~~~~hp~~ 144 (155)
|.+++ .+..|+..++.+||..||.+++ +.+|..|..++. ..+..+...|..||+..
T Consensus 395 C~~~~-~~~~~~~~~~~pyce~~~~~~~----~~~~~~~~~p~~---~~~~~ie~~~~~~h~~~ 450 (479)
T KOG1703|consen 395 CGKPL-KNSSFFESDGEPYCEDHYKKLF----TTKCDYCKKPVE---FGSRQIEADGSPFHGDC 450 (479)
T ss_pred ccCCC-CCCcccccCCccchhhhHhhhc----cccchhccchhH---hhhhHhhccCccccccc
Confidence 99999 8888999999999999999999 788999988654 33677888888999874
No 7
>KOG2272|consensus
Probab=99.77 E-value=3.5e-20 Score=135.43 Aligned_cols=125 Identities=25% Similarity=0.438 Sum_probs=113.0
Q ss_pred CccccccCcccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCceEEeccCccccccccccccCC
Q psy12215 3 DLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCN 82 (155)
Q Consensus 3 ~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~ 82 (155)
|..||+-+|+|+.|++.|++. -....|.+||..|+.+.--| .|..|.++|. ++++.+.|+.||.++|+|..|.
T Consensus 156 ~d~yH~yHFkCt~C~keL~sd---aRevk~eLyClrChD~mgip--iCgaC~rpIe--ervi~amgKhWHveHFvCa~Ce 228 (332)
T KOG2272|consen 156 GDPYHPYHFKCTTCGKELTSD---AREVKGELYCLRCHDKMGIP--ICGACRRPIE--ERVIFAMGKHWHVEHFVCAKCE 228 (332)
T ss_pred CCCCCccceecccccccccch---hhhhccceeccccccccCCc--ccccccCchH--HHHHHHhccccchhheeehhcC
Confidence 678999999999999999643 34677899999999988777 8999999996 5788999999999999999999
Q ss_pred cccccCCeEEeeCCeeecHHhHHhhhcccCCCeeeecCCeecchhhHHHHHHHHhhcCCCCc
Q psy12215 83 HRFCVGDRFYLCDNKILCEYDYEERQVFCVGDRFYLCDNKILCEYDYEERQVFANIAYNPSS 144 (155)
Q Consensus 83 ~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~c~~~~~~~~~~~~~~~hp~~ 144 (155)
+++ -|-+-+.+.|..||+.+|.+++ |..|++|+..|- ++.+.+.+++|-|+.
T Consensus 229 kPF-lGHrHYEkkGlaYCe~h~~qLf----G~~CF~C~~~i~-----G~vv~al~KawCv~c 280 (332)
T KOG2272|consen 229 KPF-LGHRHYEKKGLAYCETHYHQLF----GNLCFICNRVIG-----GDVVSALNKAWCVEC 280 (332)
T ss_pred Ccc-cchhhhhhcCchhHHHHHHHHh----hhhheecCCccC-----ccHHHHhhhhhcccc
Confidence 999 8888999999999999999999 999999999998 788888888888763
No 8
>KOG1044|consensus
Probab=99.70 E-value=2e-18 Score=138.35 Aligned_cols=98 Identities=32% Similarity=0.707 Sum_probs=91.1
Q ss_pred CCCccccccCcccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCceEEeccCcccccccccccc
Q psy12215 1 ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQ 80 (155)
Q Consensus 1 A~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 80 (155)
|+++.||..||+|..|+..|. ..|..+||.+||+.||...|+. +|..|.+.|.+ .++.+.+++||+.|-+|+.
T Consensus 151 ald~qwhv~cfkc~~c~~vL~---gey~skdg~pyce~dy~~~fgv--kc~~c~~fisg--kvLqag~kh~HPtCARCsR 223 (670)
T KOG1044|consen 151 ALDKQWHVSCFKCKSCSAVLN---GEYMSKDGVPYCEKDYQAKFGV--KCEECEKFISG--KVLQAGDKHFHPTCARCSR 223 (670)
T ss_pred eeccceeeeeeehhhhccccc---ceeeccCCCcchhhhhhhhcCe--ehHHhhhhhhh--hhhhccCcccCcchhhhhh
Confidence 789999999999999999994 3599999999999999999999 99999999987 7889999999999999999
Q ss_pred CCcccccCCeEEeeCCeeecHHhHH
Q psy12215 81 CNHRFCVGDRFYLCDNKILCEYDYE 105 (155)
Q Consensus 81 C~~~l~~~~~~~~~~~~~~C~~c~~ 105 (155)
|+..+..|+..++.++.++-..|-.
T Consensus 224 CgqmF~eGEEMYlQGs~iWHP~C~q 248 (670)
T KOG1044|consen 224 CGQMFGEGEEMYLQGSEIWHPDCKQ 248 (670)
T ss_pred hccccccchheeeccccccCCcccc
Confidence 9999999999999999999777743
No 9
>KOG1703|consensus
Probab=99.63 E-value=4.3e-17 Score=132.72 Aligned_cols=99 Identities=27% Similarity=0.672 Sum_probs=90.8
Q ss_pred CCCccccccCcccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCceEEeccCcccccccccccc
Q psy12215 1 ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQ 80 (155)
Q Consensus 1 A~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 80 (155)
|++..||+.||+|..|.++| ....|+..+|.+||+.||.+++.+ +|..|..++...+..+.+.+..||..||+|..
T Consensus 380 a~~~~wH~~cf~C~~C~~~~--~~~~~~~~~~~pyce~~~~~~~~~--~~~~~~~p~~~~~~~ie~~~~~~h~~~F~c~~ 455 (479)
T KOG1703|consen 380 ALGRLWHPECFVCADCGKPL--KNSSFFESDGEPYCEDHYKKLFTT--KCDYCKKPVEFGSRQIEADGSPFHGDCFRCAN 455 (479)
T ss_pred hccCeechhceeeecccCCC--CCCcccccCCccchhhhHhhhccc--cchhccchhHhhhhHhhccCccccccceehhh
Confidence 67899999999999999999 556799999999999999999997 89999999875567889999999999999999
Q ss_pred CCcccccCCeEEeeCCeeecHHhH
Q psy12215 81 CNHRFCVGDRFYLCDNKILCEYDY 104 (155)
Q Consensus 81 C~~~l~~~~~~~~~~~~~~C~~c~ 104 (155)
|...| .+..|+...++++|..|+
T Consensus 456 c~~~l-~~~~~~~~~~~p~c~~~~ 478 (479)
T KOG1703|consen 456 CMKKL-TKKTFFETLDKPLCQKHF 478 (479)
T ss_pred hhccc-cCCceeecCCccccccCC
Confidence 99999 888999999999998875
No 10
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.56 E-value=7.3e-15 Score=86.51 Aligned_cols=58 Identities=36% Similarity=0.745 Sum_probs=52.2
Q ss_pred ccccccccccCceEEeccCccccccccccccCCcccccCCeEEeeCCeeecHHhHHhhh
Q psy12215 50 CAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 108 (155)
Q Consensus 50 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 108 (155)
|.+|+++|.+.+.++.+.++.||++||+|..|+++| .+..++..++++||..||.++|
T Consensus 1 C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l-~~~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 1 CARCGKPIYGTEIVIKAMGKFWHPECFKCSKCGKPL-NDGDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp BTTTSSBESSSSEEEEETTEEEETTTSBETTTTCBT-TTSSEEEETTEEEEHHHHHHHT
T ss_pred CCCCCCCccCcEEEEEeCCcEEEccccccCCCCCcc-CCCeeEeECCEEECHHHHhhhC
Confidence 789999999877777899999999999999999999 5555999999999999999875
No 11
>KOG4577|consensus
Probab=99.29 E-value=1.6e-13 Score=102.36 Aligned_cols=95 Identities=20% Similarity=0.517 Sum_probs=78.4
Q ss_pred cccccccccccCceEEeccCccccccccccccCCcccccCCeEEeeCCeeecHHhHHhhhcccCCCeeeecCCeecchhh
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFCVGDRFYLCDNKILCEYD 128 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~c~~~ 128 (155)
.|++|.+.|.+ ..++.++++.||..|++|+.|..+| +.+++.+++.+||+.+|.++| |.+|..|+.-|...+.
T Consensus 35 ~CagC~q~IlD-rFilKvl~R~wHs~CLkCs~C~~qL--~drCFsR~~s~yCkedFfKrf----GTKCsaC~~GIpPtqV 107 (383)
T KOG4577|consen 35 ICAGCDQHILD-RFILKVLDRHWHSSCLKCSDCHDQL--ADRCFSREGSVYCKEDFFKRF----GTKCSACQEGIPPTQV 107 (383)
T ss_pred cccchHHHHHH-HHHHHHHhhhhhhhhcchhhhhhHH--HHHHhhcCCceeehHHHHHHh----CCcchhhcCCCChHHH
Confidence 79999999986 5688899999999999999999999 788999999999999999999 9999999999984443
Q ss_pred HHHHHHHHhhcCCCCc--hHHHhhhhh
Q psy12215 129 YEERQVFANIAYNPSS--LAHLRRQVT 153 (155)
Q Consensus 129 ~~~~~~~~~~~~hp~~--~~~~~~~~~ 153 (155)
..+. ...+||=.+ +-..+++|.
T Consensus 108 VRkA---qd~VYHl~CF~C~iC~R~L~ 131 (383)
T KOG4577|consen 108 VRKA---QDFVYHLHCFACFICKRQLA 131 (383)
T ss_pred HHHh---hcceeehhhhhhHhhhcccc
Confidence 3222 223788643 555566654
No 12
>PF00412 LIM: LIM domain; InterPro: IPR001781 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 LIM-type zinc finger (Znf) domains. LIM domains coordinate one or more zinc atoms, and are named after the three proteins (LIN-11, Isl1 and MEC-3) in which they were first found. They consist of two zinc-binding motifs that resemble GATA-like Znf's, however the residues holding the zinc atom(s) are variable, involving Cys, His, Asp or Glu residues. LIM domains are involved in proteins with differing functions, including gene expression, and cytoskeleton organisation and development [, ]. Protein containing LIM Znf domains include: Caenorhabditis elegans mec-3; a protein required for the differentiation of the set of six touch receptor neurons in this nematode. C. elegans. lin-11; a protein required for the asymmetric division of vulval blast cells. Vertebrate insulin gene enhancer binding protein isl-1. Isl-1 binds to one of the two cis-acting protein-binding domains of the insulin gene. Vertebrate homeobox proteins lim-1, lim-2 (lim-5) and lim3. Vertebrate lmx-1, which acts as a transcriptional activator by binding to the FLAT element; a beta-cell-specific transcriptional enhancer found in the insulin gene. Mammalian LH-2, a transcriptional regulatory protein involved in the control of cell differentiation in developing lymphoid and neural cell types. Drosophila melanogaster (Fruit fly) protein apterous, required for the normal development of the wing and halter imaginal discs. Vertebrate protein kinases LIMK-1 and LIMK-2. Mammalian rhombotins. Rhombotin 1 (RBTN1 or TTG-1) and rhombotin-2 (RBTN2 or TTG-2) are proteins of about 160 amino acids whose genes are disrupted by chromosomal translocations in T-cell leukemia. Mammalian and avian cysteine-rich protein (CRP), a 192 amino-acid protein of unknown function. Seems to interact with zyxin. Mammalian cysteine-rich intestinal protein (CRIP), a small protein which seems to have a role in zinc absorption and may function as an intracellular zinc transport protein. Vertebrate paxillin, a cytoskeletal focal adhesion protein. Mus musculus (Mouse) testin which should not be confused with rat testin which is a thiol protease homologue (see IPR000169 from INTERPRO). Helianthus annuus (Common sunflower) pollen specific protein SF3. Chicken zyxin. Zyxin is a low-abundance adhesion plaque protein which has been shown to interact with CRP. Yeast protein LRG1 which is involved in sporulation []. Saccharomyces cerevisiae (Baker's yeast) rho-type GTPase activating protein RGA1/DBM1. C. elegans homeobox protein ceh-14. C. elegans homeobox protein unc-97. S. cerevisiae hypothetical protein YKR090w. C. elegans hypothetical proteins C28H8.6. These proteins generally contain two tandem copies of the LIM domain in their N-terminal section. Zyxin and paxillin are exceptions in that they contain respectively three and four LIM domains at their C-terminal extremity. In apterous, isl-1, LH-2, lin-11, lim-1 to lim-3, lmx-1 and ceh-14 and mec-3 there is a homeobox domain some 50 to 95 amino acids after the LIM domains. LIM domains contain seven conserved cysteine residues and a histidine. The arrangement followed by these conserved residues is: C-x(2)-C-x(16,23)-H-x(2)-[CH]-x(2)-C-x(2)-C-x(16,21)-C-x(2,3)-[CHD] LIM domains bind two zinc ions []. LIM does not bind DNA, rather it seems to act as an interface for protein-protein interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CO8_A 2EGQ_A 2CUR_A 3IXE_B 1CTL_A 1B8T_A 1X62_A 2DFY_C 1IML_A 2CUQ_A ....
Probab=99.27 E-value=1.9e-12 Score=76.12 Aligned_cols=42 Identities=36% Similarity=0.863 Sum_probs=37.5
Q ss_pred CCCccccccCcccccCCcccccCCCeEEEeCCeeecccchhccc
Q psy12215 1 ALDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 44 (155)
Q Consensus 1 A~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~ 44 (155)
|+|+.||++||+|+.|+++|.+ ..|+..+|++||++||.++|
T Consensus 17 ~~~~~~H~~Cf~C~~C~~~l~~--~~~~~~~~~~~C~~c~~~~f 58 (58)
T PF00412_consen 17 AMGKFWHPECFKCSKCGKPLND--GDFYEKDGKPYCKDCYQKRF 58 (58)
T ss_dssp ETTEEEETTTSBETTTTCBTTT--SSEEEETTEEEEHHHHHHHT
T ss_pred eCCcEEEccccccCCCCCccCC--CeeEeECCEEECHHHHhhhC
Confidence 5789999999999999999964 44999999999999998865
No 13
>KOG1700|consensus
Probab=99.11 E-value=1.3e-11 Score=89.97 Aligned_cols=103 Identities=23% Similarity=0.564 Sum_probs=85.2
Q ss_pred CCccccccCcccccCCcccccCCCeEEEeCCeeecccchhccccccc---------------------------------
Q psy12215 2 LDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTG--------------------------------- 48 (155)
Q Consensus 2 ~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~--------------------------------- 48 (155)
.|..||..||.|..|.+.|.. ..+...++.+||+.+|...+++.+
T Consensus 26 ~g~~~hk~c~~c~~~~k~l~~--~~~~~~e~~~yc~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 103 (200)
T KOG1700|consen 26 DGVDFHKECFKCEKCKKTLTL--SGYSEHEGVPYCKNCHVAQFGPKGGGFGKGFQKAGGLGKDGKSLNESKPNQSAKFQV 103 (200)
T ss_pred cCcchhhhHHhcccccccccc--ccccccccccccccchHhhhCcccccccccccccCCCCcccccccccccccchhHHh
Confidence 478999999999999999964 457889999999998755554421
Q ss_pred ------cccccccccccCceEEeccCccccccccccccCCcccccCCeEEeeCCeeecHHhHHhhh
Q psy12215 49 ------YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 108 (155)
Q Consensus 49 ------~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 108 (155)
.|..|++.+++.+.+ ...+..||..||+|..|+..| ....+....+.++|..++...+
T Consensus 104 ~~g~~~~c~~c~k~vy~~Ek~-~~~~~~~hk~cfrc~~~~~~l-s~~~~~~~~g~l~~~~~~~~~~ 167 (200)
T KOG1700|consen 104 FAGEKEKCARCQKTVYPLEKV-TGNGLEFHKSCFRCTHCGKKL-SPKNYAALEGVLYCKHHFAQLF 167 (200)
T ss_pred hhccccccccccceeeehHHH-hhhhhhhhhhheeeccccccc-CCcchhhcCCccccchhhheee
Confidence 299999999986655 677999999999999999999 6777888888999988876654
No 14
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=98.68 E-value=1.4e-08 Score=54.38 Aligned_cols=37 Identities=43% Similarity=0.909 Sum_probs=33.3
Q ss_pred cccccccccccCceEEeccCccccccccccccCCccc
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 85 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 85 (155)
+|.+|+++|.+.+..+.+.+..||+.||+|..|+++|
T Consensus 1 ~C~~C~~~i~~~~~~~~~~~~~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 1 KCAGCGKPIRGGELVLRALGKVWHPECFKCSKCGKPL 37 (39)
T ss_pred CccccCCcccCCcEEEEeCCccccccCCCCcccCCcC
Confidence 4889999998855778889999999999999999988
No 15
>KOG0490|consensus
Probab=97.87 E-value=1.9e-06 Score=63.86 Aligned_cols=101 Identities=40% Similarity=0.738 Sum_probs=82.5
Q ss_pred CccccccCcccccCCcccccCCCeEEEeCCeeecccchhc--cccccccccccccccccCceEEeccCcccccccccccc
Q psy12215 3 DLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLR--LFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQ 80 (155)
Q Consensus 3 ~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~--~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 80 (155)
+..||..|..|..|..+|.... ..+..+|..||..+|.. .+.. +|.+|...+...+.+..+..+. |..||.|..
T Consensus 16 ~~~~~~~~~~~~~~~~~~~~~~-~~~~~~g~~~~~~d~~~~~~~~~--rr~rt~~~~~ql~~ler~f~~~-h~Pd~~~r~ 91 (235)
T KOG0490|consen 16 DRYWHASCLKCAECDNPLGVGD-TCFSKDGSIYCKRDYQREFKFSK--RCARCKFTISQLDELERAFEKV-HLPCFACRE 91 (235)
T ss_pred cHHHHHHHHhhhhhcchhccCC-CcccCCCcccccccchhhhhccc--cccCCCCCcCHHHHHHHhhcCC-CcCccchHH
Confidence 5789999999999999996333 34544999999999998 5554 8999999997667777777777 999999999
Q ss_pred CCcccccCCeEEeeCC-eeecHHhHHhh
Q psy12215 81 CNHRFCVGDRFYLCDN-KILCEYDYEER 107 (155)
Q Consensus 81 C~~~l~~~~~~~~~~~-~~~C~~c~~~~ 107 (155)
|...+..+..+.+... +..|...+...
T Consensus 92 ~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 92 CLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred HHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 9998767777877775 88898887554
No 16
>smart00132 LIM Zinc-binding domain present in Lin-11, Isl-1, Mec-3. Zinc-binding domain family. Some LIM domains bind protein partners via tyrosine-containing motifs. LIM domains are found in many key regulators of developmental pathways.
Probab=97.76 E-value=1e-05 Score=42.93 Aligned_cols=20 Identities=45% Similarity=1.076 Sum_probs=18.4
Q ss_pred CCCccccccCcccccCCccc
Q psy12215 1 ALDLFWHEDCLKCGCCDCRL 20 (155)
Q Consensus 1 A~~~~~H~~Cf~C~~C~~~l 20 (155)
++++.||+.||+|..|+.+|
T Consensus 18 ~~~~~~H~~Cf~C~~C~~~L 37 (39)
T smart00132 18 ALGKVWHPECFKCSKCGKPL 37 (39)
T ss_pred eCCccccccCCCCcccCCcC
Confidence 46889999999999999998
No 17
>KOG1702|consensus
Probab=97.42 E-value=9.6e-06 Score=58.52 Aligned_cols=58 Identities=24% Similarity=0.529 Sum_probs=48.8
Q ss_pred cccccccccccCceEEeccCccccccccccccCCcccccCCeEEeeCCeeecHHhHHhhh
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 108 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 108 (155)
-|..|++.+++.+.+ ..+++.||..||+|..|+..| .-..+-..+.++||..+|.+..
T Consensus 6 n~~~cgk~vYPvE~v-~cldk~whk~cfkce~c~mtl-nmKnyKgy~kkpycn~hYpkq~ 63 (264)
T KOG1702|consen 6 NREDCGKTVYPVEEV-KCLDKVWHKQCFKCEVCGMTL-NMKNYKGYDKKPYCNPHYPKQV 63 (264)
T ss_pred hhhhhccccccHHHH-hhHHHHHHHHhheeeeccCCh-hhhhccccccCCCcCcccccce
Confidence 477889988886544 788999999999999999999 6666777889999999998654
No 18
>KOG1700|consensus
Probab=97.26 E-value=5.9e-05 Score=55.11 Aligned_cols=58 Identities=22% Similarity=0.469 Sum_probs=48.5
Q ss_pred cccccccccccCceEEeccCccccccccccccCCcccccCCeEEeeCCeeecHHhHHhhh
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 108 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 108 (155)
+|..|++.++..+++ ...+..||..||+|..|.+.| ....+...++.+||+.++...+
T Consensus 9 kc~~c~k~vy~~e~~-~~~g~~~hk~c~~c~~~~k~l-~~~~~~~~e~~~yc~~~~~~~~ 66 (200)
T KOG1700|consen 9 KCNACGKTVYFVEKV-QKDGVDFHKECFKCEKCKKTL-TLSGYSEHEGVPYCKNCHVAQF 66 (200)
T ss_pred hhhhccCcchHHHHH-hccCcchhhhHHhcccccccc-ccccccccccccccccchHhhh
Confidence 799999999876555 477999999999999999999 6666777899999999665544
No 19
>KOG1702|consensus
Probab=96.13 E-value=0.0008 Score=48.77 Aligned_cols=42 Identities=26% Similarity=0.631 Sum_probs=35.8
Q ss_pred CCccccccCcccccCCcccccCCCeEEEeCCeeecccchhcccc
Q psy12215 2 LDLFWHEDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFG 45 (155)
Q Consensus 2 ~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~ 45 (155)
+++.||..||+|..|+-+|+. ..|-..+.++||...|.+..+
T Consensus 23 ldk~whk~cfkce~c~mtlnm--KnyKgy~kkpycn~hYpkq~a 64 (264)
T KOG1702|consen 23 LDKVWHKQCFKCEVCGMTLNM--KNYKGYDKKPYCNPHYPKQVA 64 (264)
T ss_pred HHHHHHHHhheeeeccCChhh--hhccccccCCCcCccccccee
Confidence 468899999999999999964 457788999999999987654
No 20
>KOG0490|consensus
Probab=93.48 E-value=0.027 Score=41.55 Aligned_cols=66 Identities=27% Similarity=0.673 Sum_probs=48.2
Q ss_pred cccccccCceEEeccCccccccccccccCCcccccCCeEEeeCCeeecHHhHHh--hhcccCCCeeeecCCee
Q psy12215 53 CTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYEE--RQVFCVGDRFYLCDNKI 123 (155)
Q Consensus 53 C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~--~~~~~~~~~c~~c~~~i 123 (155)
|+..|.+ ...+.+.+..||..|..|..|...+......+..+|.++|...|.+ .+ ..+|..|...+
T Consensus 2 ~~~~~~~-~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~d~~~~~~~----~~rr~rt~~~~ 69 (235)
T KOG0490|consen 2 CGRQILD-RYLLRVLDRYWHASCLKCAECDNPLGVGDTCFSKDGSIYCKRDYQREFKF----SKRCARCKFTI 69 (235)
T ss_pred CCccccc-hHHhhcccHHHHHHHHhhhhhcchhccCCCcccCCCcccccccchhhhhc----cccccCCCCCc
Confidence 4556654 3445566899999999999999999433444444999999999987 44 66777766654
No 21
>PF06677 Auto_anti-p27: Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27); InterPro: IPR009563 The proteins in this entry are functionally uncharacterised and include several proteins that characterise Sjogren's syndrome/scleroderma autoantigen 1 (Autoantigen p27). It is thought that the potential association of anti-p27 with anti-centromere antibodies suggests that autoantigen p27 might play a role in mitosis [].
Probab=87.80 E-value=0.39 Score=25.87 Aligned_cols=22 Identities=27% Similarity=0.531 Sum_probs=16.4
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccc
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRD 39 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c 39 (155)
.|..|+.|| +-.++|++||..|
T Consensus 19 ~Cp~C~~PL------~~~k~g~~~Cv~C 40 (41)
T PF06677_consen 19 HCPDCGTPL------MRDKDGKIYCVSC 40 (41)
T ss_pred ccCCCCCee------EEecCCCEECCCC
Confidence 577788888 3467888988765
No 22
>PF11781 RRN7: RNA polymerase I-specific transcription initiation factor Rrn7; InterPro: IPR021752 Rrn7 is a transcription binding factor that associates strongly with both Rrn6 and Rrn11 to form a complex which itself binds the TATA-binding protein and is required for transcription by the core domain of the RNA PolI promoter [],[].
Probab=86.75 E-value=0.49 Score=24.72 Aligned_cols=24 Identities=25% Similarity=0.580 Sum_probs=18.1
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccchh
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDYL 41 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~ 41 (155)
.|..|+.. .|...||..||..|..
T Consensus 10 ~C~~C~~~------~~~~~dG~~yC~~cG~ 33 (36)
T PF11781_consen 10 PCPVCGSR------WFYSDDGFYYCDRCGH 33 (36)
T ss_pred cCCCCCCe------EeEccCCEEEhhhCce
Confidence 47777554 4789999999987754
No 23
>smart00504 Ubox Modified RING finger domain. Modified RING finger domain, without the full complement of Zn2+-binding ligands. Probable involvement in E2-dependent ubiquitination.
Probab=86.70 E-value=0.43 Score=27.59 Aligned_cols=46 Identities=7% Similarity=0.046 Sum_probs=35.0
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhcccccccccccccccccc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 59 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~ 59 (155)
|.|..|+..+.+ ......|..||++|..+.+...+.|..|++++..
T Consensus 2 ~~Cpi~~~~~~~---Pv~~~~G~v~~~~~i~~~~~~~~~cP~~~~~~~~ 47 (63)
T smart00504 2 FLCPISLEVMKD---PVILPSGQTYERRAIEKWLLSHGTDPVTGQPLTH 47 (63)
T ss_pred cCCcCCCCcCCC---CEECCCCCEEeHHHHHHHHHHCCCCCCCcCCCCh
Confidence 678899998853 4667889999999988765434479888888854
No 24
>PF08394 Arc_trans_TRASH: Archaeal TRASH domain; InterPro: IPR013603 This region is found in the C terminus of a number of archaeal transcriptional regulators. It is thought to function as a metal-sensing regulatory module [].
Probab=86.40 E-value=0.42 Score=25.15 Aligned_cols=24 Identities=29% Similarity=0.563 Sum_probs=15.6
Q ss_pred ccccccccccCceEEeccCccccc
Q psy12215 50 CAACTKVIPAFEMVMRAKNNVYHL 73 (155)
Q Consensus 50 C~~C~~~I~~~~~~~~~~~~~~H~ 73 (155)
|.-|+.+|.+.-.++...++.|+.
T Consensus 1 Cd~CG~~I~~eP~~~k~~~~~y~f 24 (37)
T PF08394_consen 1 CDYCGGEITGEPIVVKIGNKVYYF 24 (37)
T ss_pred CCccCCcccCCEEEEEECCeEEEE
Confidence 566777777644455666777763
No 25
>PF07191 zinc-ribbons_6: zinc-ribbons; InterPro: IPR010807 This family consists of several short, hypothetical bacterial proteins of around 70 residues in length. Members of this family 8 highly conserved cysteine residues. The function of the family is unknown.; PDB: 2JRP_A 2JNE_A.
Probab=84.44 E-value=2.1 Score=25.82 Aligned_cols=58 Identities=19% Similarity=0.450 Sum_probs=30.4
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCceEEeccCccccccccccccCCccc
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 85 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 85 (155)
.|..|..+|.. .++..+|..|...... ...|+.|++++ .++.+-|..= |.|..|+..+
T Consensus 3 ~CP~C~~~L~~-------~~~~~~C~~C~~~~~~-~a~CPdC~~~L----e~LkACGAvd----YFC~~c~gLi 60 (70)
T PF07191_consen 3 TCPKCQQELEW-------QGGHYHCEACQKDYKK-EAFCPDCGQPL----EVLKACGAVD----YFCNHCHGLI 60 (70)
T ss_dssp B-SSS-SBEEE-------ETTEEEETTT--EEEE-EEE-TTT-SB-----EEEEETTEEE----EE-TTTT-EE
T ss_pred cCCCCCCccEE-------eCCEEECcccccccee-cccCCCcccHH----HHHHHhcccc----eeeccCCcee
Confidence 57788888843 3367788887765321 22799999999 3445555321 4677777766
No 26
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=83.39 E-value=1 Score=25.84 Aligned_cols=46 Identities=17% Similarity=0.410 Sum_probs=32.6
Q ss_pred ccccCCcccccCC-CeEEEeCCeeecccchhcccccccccccccccccc
Q psy12215 12 KCGCCDCRLGEVG-STLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 59 (155)
Q Consensus 12 ~C~~C~~~l~~~~-~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~ 59 (155)
.|..|++.|...+ ..++-.-.=.||.+|....+.. +|..|+..+..
T Consensus 7 nCE~C~~dLp~~s~~A~ICSfECTFC~~C~e~~l~~--~CPNCgGelv~ 53 (57)
T PF06906_consen 7 NCECCDKDLPPDSPEAYICSFECTFCADCAETMLNG--VCPNCGGELVR 53 (57)
T ss_pred CccccCCCCCCCCCcceEEeEeCcccHHHHHHHhcC--cCcCCCCcccc
Confidence 3667888887433 3455444557899999988655 89999887753
No 27
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=83.38 E-value=0.78 Score=31.18 Aligned_cols=23 Identities=22% Similarity=0.427 Sum_probs=18.0
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccchh
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDYL 41 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~ 41 (155)
.|..|+.|| |- ++|.+||.-|-.
T Consensus 30 hCp~Cg~PL------F~-KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL------FR-KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc------ee-eCCeEECCCCCc
Confidence 478889988 44 999999877654
No 28
>KOG1813|consensus
Probab=83.27 E-value=1.2 Score=34.41 Aligned_cols=50 Identities=18% Similarity=0.382 Sum_probs=38.6
Q ss_pred cccccCCcccccCCeEEeeCCeeecHHhHHhhhcccCCCeeeecCCeecchhhH
Q psy12215 76 FACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFCVGDRFYLCDNKILCEYDY 129 (155)
Q Consensus 76 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~c~~~~ 129 (155)
|.|..|.+.+ -......-+..+|..|..+.+ ..++.|++|++.+......
T Consensus 242 f~c~icr~~f--~~pVvt~c~h~fc~~ca~~~~--qk~~~c~vC~~~t~g~~~~ 291 (313)
T KOG1813|consen 242 FKCFICRKYF--YRPVVTKCGHYFCEVCALKPY--QKGEKCYVCSQQTHGSFNV 291 (313)
T ss_pred cccccccccc--ccchhhcCCceeehhhhcccc--ccCCcceecccccccccch
Confidence 7788888888 445556668899999987765 5689999999988755544
No 29
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=82.36 E-value=1.5 Score=26.07 Aligned_cols=47 Identities=21% Similarity=0.358 Sum_probs=23.4
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFE 61 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~ 61 (155)
++|+.|..-|.+. .....=..+||..|....++. .|+.|..+.+..|
T Consensus 8 LrCs~C~~~l~~p--v~l~~CeH~fCs~Ci~~~~~~--~CPvC~~Paw~qD 54 (65)
T PF14835_consen 8 LRCSICFDILKEP--VCLGGCEHIFCSSCIRDCIGS--ECPVCHTPAWIQD 54 (65)
T ss_dssp TS-SSS-S--SS---B---SSS--B-TTTGGGGTTT--B-SSS--B-S-SS
T ss_pred cCCcHHHHHhcCC--ceeccCccHHHHHHhHHhcCC--CCCCcCChHHHHH
Confidence 6789998888532 223445578999999888887 7999999886533
No 30
>PF14446 Prok-RING_1: Prokaryotic RING finger family 1
Probab=82.32 E-value=0.72 Score=26.39 Aligned_cols=28 Identities=21% Similarity=0.529 Sum_probs=19.7
Q ss_pred cccccccccccCceEEec--cCcccccccc
Q psy12215 49 YCAACTKVIPAFEMVMRA--KNNVYHLECF 76 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~--~~~~~H~~Cf 76 (155)
+|..|++.|.+.+.++.- -+..||.+|+
T Consensus 7 ~C~~Cg~~~~~~dDiVvCp~CgapyHR~C~ 36 (54)
T PF14446_consen 7 KCPVCGKKFKDGDDIVVCPECGAPYHRDCW 36 (54)
T ss_pred cChhhCCcccCCCCEEECCCCCCcccHHHH
Confidence 799999999644445442 3677888887
No 31
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=82.18 E-value=0.88 Score=33.15 Aligned_cols=48 Identities=15% Similarity=0.335 Sum_probs=38.2
Q ss_pred cccccCCcccccCCeEEeeCCeeecHHhHHhhhcccCCCeeeecCCeecchh
Q psy12215 76 FACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFCVGDRFYLCDNKILCEY 127 (155)
Q Consensus 76 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~c~~ 127 (155)
|.|..|.+.. ....+..-|..||..|+.+.+ ..|+.|.+|+....+..
T Consensus 197 F~C~iCKkdy--~spvvt~CGH~FC~~Cai~~y--~kg~~C~~Cgk~t~G~f 244 (259)
T COG5152 197 FLCGICKKDY--ESPVVTECGHSFCSLCAIRKY--QKGDECGVCGKATYGRF 244 (259)
T ss_pred eeehhchhhc--cchhhhhcchhHHHHHHHHHh--ccCCcceecchhhccce
Confidence 7899999887 444555568999999998876 66999999998776544
No 32
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=81.18 E-value=1.2 Score=28.63 Aligned_cols=28 Identities=25% Similarity=0.502 Sum_probs=16.9
Q ss_pred cccccccccccCceEEeccCcccccccc
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHLECF 76 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf 76 (155)
.|..|+++|.....++-..|..+|..|+
T Consensus 80 ~C~vC~k~l~~~~f~~~p~~~v~H~~C~ 107 (109)
T PF10367_consen 80 KCSVCGKPLGNSVFVVFPCGHVVHYSCI 107 (109)
T ss_pred CccCcCCcCCCceEEEeCCCeEEecccc
Confidence 5777777776533334444566676664
No 33
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=81.11 E-value=1.9 Score=23.25 Aligned_cols=41 Identities=20% Similarity=0.425 Sum_probs=25.3
Q ss_pred cccCCcccccCCeEEeeC-CeeecHHhHHhhhcccCCCeeeecC
Q psy12215 78 CQQCNHRFCVGDRFYLCD-NKILCEYDYEERQVFCVGDRFYLCD 120 (155)
Q Consensus 78 C~~C~~~l~~~~~~~~~~-~~~~C~~c~~~~~~~~~~~~c~~c~ 120 (155)
|..|...+.....+.+.. |.++|..|..+.. .....|.+|.
T Consensus 2 C~~C~~~~~~~~~~~l~~CgH~~C~~C~~~~~--~~~~~CP~C~ 43 (44)
T PF14634_consen 2 CNICFEKYSEERRPRLTSCGHIFCEKCLKKLK--GKSVKCPICR 43 (44)
T ss_pred CcCcCccccCCCCeEEcccCCHHHHHHHHhhc--CCCCCCcCCC
Confidence 455666663344455555 8899999987764 3445555554
No 34
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=80.14 E-value=1 Score=26.72 Aligned_cols=43 Identities=16% Similarity=0.390 Sum_probs=19.5
Q ss_pred cccccCCcccccCCeEEeeC-CeeecHHhHHhhhcccCCCeeeecCCeec
Q psy12215 76 FACQQCNHRFCVGDRFYLCD-NKILCEYDYEERQVFCVGDRFYLCDNKIL 124 (155)
Q Consensus 76 f~C~~C~~~l~~~~~~~~~~-~~~~C~~c~~~~~~~~~~~~c~~c~~~i~ 124 (155)
.+|+.|...| .+.+...+ +.+||..|-.+.. |..|..|..|-.
T Consensus 8 LrCs~C~~~l--~~pv~l~~CeH~fCs~Ci~~~~----~~~CPvC~~Paw 51 (65)
T PF14835_consen 8 LRCSICFDIL--KEPVCLGGCEHIFCSSCIRDCI----GSECPVCHTPAW 51 (65)
T ss_dssp TS-SSS-S----SS-B---SSS--B-TTTGGGGT----TTB-SSS--B-S
T ss_pred cCCcHHHHHh--cCCceeccCccHHHHHHhHHhc----CCCCCCcCChHH
Confidence 5677777776 44443333 6788888887766 777888876654
No 35
>PF04570 DUF581: Protein of unknown function (DUF581); InterPro: IPR007650 This is a family of uncharacterised proteins.
Probab=79.48 E-value=1.4 Score=25.64 Aligned_cols=27 Identities=15% Similarity=0.351 Sum_probs=21.3
Q ss_pred ccccCCcccccCCCeEEEeCCeeeccc
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKR 38 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~ 38 (155)
.|..|+++|.++.-.|..+..+.||..
T Consensus 18 ~C~~C~k~L~~~~DiymYrGd~aFCS~ 44 (58)
T PF04570_consen 18 FCYLCKKKLDPGKDIYMYRGDKAFCSE 44 (58)
T ss_pred HHHccCCCCCCCCCeeeeccccccccH
Confidence 478899999865557778888999963
No 36
>KOG0320|consensus
Probab=78.27 E-value=1.3 Score=31.69 Aligned_cols=50 Identities=12% Similarity=0.191 Sum_probs=37.2
Q ss_pred ccccccccCCcccccCCeEEeeCCeeecHHhHHhhhcccCCCeeeecCCeec
Q psy12215 73 LECFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQVFCVGDRFYLCDNKIL 124 (155)
Q Consensus 73 ~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~ 124 (155)
..++.|-.|-........+...=|.+||+.|-.... ..+..|..|.++|.
T Consensus 129 ~~~~~CPiCl~~~sek~~vsTkCGHvFC~~Cik~al--k~~~~CP~C~kkIt 178 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEKVPVSTKCGHVFCSQCIKDAL--KNTNKCPTCRKKIT 178 (187)
T ss_pred ccccCCCceecchhhccccccccchhHHHHHHHHHH--HhCCCCCCcccccc
Confidence 457888888777733333445669999999987654 55788999998777
No 37
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=76.62 E-value=2.4 Score=23.89 Aligned_cols=30 Identities=20% Similarity=0.490 Sum_probs=22.4
Q ss_pred ccccCCcccccCCeEEeeCCeeecHHhHHhh
Q psy12215 77 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER 107 (155)
Q Consensus 77 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 107 (155)
.|..|+..++.-..+-..|| ..|..|+.+.
T Consensus 1 ~C~iCg~kigl~~~~k~~DG-~iC~~C~~Kl 30 (51)
T PF14471_consen 1 KCAICGKKIGLFKRFKIKDG-YICKDCLKKL 30 (51)
T ss_pred CCCccccccccccceeccCc-cchHHHHHHh
Confidence 37788888854444667788 6999999876
No 38
>PF10235 Cript: Microtubule-associated protein CRIPT; InterPro: IPR019367 The CRIPT protein is a cytoskeletal protein involved in microtubule production. This C-terminal domain is essential for binding to the PDZ3 domain of the SAP90 protein, one of a super-family of PDZ-containing proteins that play an important role in coupling the membrane ion channels with their signalling partners [].
Probab=75.44 E-value=1.5 Score=27.82 Aligned_cols=36 Identities=28% Similarity=0.617 Sum_probs=23.5
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccchhcccccccccccccccccc
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 59 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~ 59 (155)
+|..|...+.. .|.-||..|..+. +.|+-|++.|.+
T Consensus 46 ~C~~CK~~v~q--------~g~~YCq~CAYkk----GiCamCGKki~d 81 (90)
T PF10235_consen 46 KCKICKTKVHQ--------PGAKYCQTCAYKK----GICAMCGKKILD 81 (90)
T ss_pred ccccccccccc--------CCCccChhhhccc----CcccccCCeecc
Confidence 45666555531 2457888887663 368888888854
No 39
>PF10367 Vps39_2: Vacuolar sorting protein 39 domain 2; InterPro: IPR019453 This entry represents a domain found in the vacuolar sorting protein Vps39 and transforming growth factor beta receptor-associated protein Trap1. Vps39, a component of the C-Vps complex, is thought to be required for the fusion of endosomes and other types of transport intermediates with the vacuole [, ]. In Saccharomyces cerevisiae (Baker's yeast), Vps39 has been shown to stimulate nucleotide exchange []. Trap1 plays a role in the TGF-beta/activin signaling pathway. It associates with inactive heteromeric TGF-beta and activin receptor complexes, mainly through the type II receptor, and is released upon activation of signaling [, ]. The precise function of this domain has not been characterised In Vps39 this domain is involved in localisation and in mediating the interactions with Vps11 [].
Probab=74.02 E-value=3.1 Score=26.61 Aligned_cols=28 Identities=21% Similarity=0.343 Sum_probs=20.5
Q ss_pred ccccCCcccccCCCeEE-EeCCeeecccchh
Q psy12215 12 KCGCCDCRLGEVGSTLY-QKANLILCKRDYL 41 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~-~~~~~~~C~~c~~ 41 (155)
.|..|+++|.. ..|. ..+|.+++..|..
T Consensus 80 ~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 80 KCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 59999999953 4555 4667888877764
No 40
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=73.58 E-value=1.3 Score=28.76 Aligned_cols=33 Identities=15% Similarity=0.348 Sum_probs=21.2
Q ss_pred cccccCCcccccCCeEEeeCCeeecHHhHHhhh
Q psy12215 76 FACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 108 (155)
Q Consensus 76 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 108 (155)
++|..|+..+..|+.|++..+.+.--.||.+..
T Consensus 3 WkC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 3 WKCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred eEEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 356677777666666766665666666666544
No 41
>PF13920 zf-C3HC4_3: Zinc finger, C3HC4 type (RING finger); PDB: 2YHN_B 2YHO_G 3T6P_A 2CSY_A 2VJE_B 2VJF_B 2HDP_B 2EA5_A 2ECG_A 3EB5_A ....
Probab=73.48 E-value=6.1 Score=21.71 Aligned_cols=44 Identities=20% Similarity=0.282 Sum_probs=28.3
Q ss_pred ccccCCcccccCCeEEeeCCee-ecHHhHHhhhcccCCCeeeecCCeec
Q psy12215 77 ACQQCNHRFCVGDRFYLCDNKI-LCEYDYEERQVFCVGDRFYLCDNKIL 124 (155)
Q Consensus 77 ~C~~C~~~l~~~~~~~~~~~~~-~C~~c~~~~~~~~~~~~c~~c~~~i~ 124 (155)
.|..|.... .......=|.. +|..|+.+... ....|.+|..+|.
T Consensus 4 ~C~iC~~~~--~~~~~~pCgH~~~C~~C~~~~~~--~~~~CP~Cr~~i~ 48 (50)
T PF13920_consen 4 ECPICFENP--RDVVLLPCGHLCFCEECAERLLK--RKKKCPICRQPIE 48 (50)
T ss_dssp B-TTTSSSB--SSEEEETTCEEEEEHHHHHHHHH--TTSBBTTTTBB-S
T ss_pred CCccCCccC--CceEEeCCCChHHHHHHhHHhcc--cCCCCCcCChhhc
Confidence 456666654 23333444777 99999988752 5788888888764
No 42
>PF13240 zinc_ribbon_2: zinc-ribbon domain
Probab=73.03 E-value=1.6 Score=20.28 Aligned_cols=8 Identities=25% Similarity=0.974 Sum_probs=3.7
Q ss_pred cccCCccc
Q psy12215 13 CGCCDCRL 20 (155)
Q Consensus 13 C~~C~~~l 20 (155)
|..|+..+
T Consensus 2 Cp~CG~~~ 9 (23)
T PF13240_consen 2 CPNCGAEI 9 (23)
T ss_pred CcccCCCC
Confidence 44444444
No 43
>PRK00420 hypothetical protein; Validated
Probab=70.99 E-value=2.5 Score=27.98 Aligned_cols=25 Identities=20% Similarity=0.373 Sum_probs=16.2
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchh
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYL 41 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~ 41 (155)
-.|..|+.+| |-.++|+.||..|-.
T Consensus 24 ~~CP~Cg~pL------f~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPL------FELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcc------eecCCCceECCCCCC
Confidence 3577788877 334788887655443
No 44
>PF13923 zf-C3HC4_2: Zinc finger, C3HC4 type (RING finger); PDB: 3HCU_A 2ECI_A 2JMD_A 3HCS_B 3HCT_A 3ZTG_A 2YUR_A 3L11_A.
Probab=69.78 E-value=3.3 Score=21.52 Aligned_cols=38 Identities=16% Similarity=0.329 Sum_probs=21.5
Q ss_pred cccCCcccccCCCeEEEeCCeeecccchhccccccccccc
Q psy12215 13 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAA 52 (155)
Q Consensus 13 C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~ 52 (155)
|..|...+. +......=|..||.+|..+......+|..
T Consensus 1 C~iC~~~~~--~~~~~~~CGH~fC~~C~~~~~~~~~~CP~ 38 (39)
T PF13923_consen 1 CPICLDELR--DPVVVTPCGHSFCKECIEKYLEKNPKCPV 38 (39)
T ss_dssp ETTTTSB-S--SEEEECTTSEEEEHHHHHHHHHCTSB-TT
T ss_pred CCCCCCccc--CcCEECCCCCchhHHHHHHHHHCcCCCcC
Confidence 455655552 22245677889999998775543224544
No 45
>KOG1813|consensus
Probab=68.66 E-value=2.7 Score=32.52 Aligned_cols=46 Identities=17% Similarity=0.369 Sum_probs=34.7
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhcccccccccccccccccc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 59 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~ 59 (155)
|.|..|.+...+ ..+..-+.-||+.|..+.+....+|..|++.+.+
T Consensus 242 f~c~icr~~f~~---pVvt~c~h~fc~~ca~~~~qk~~~c~vC~~~t~g 287 (313)
T KOG1813|consen 242 FKCFICRKYFYR---PVVTKCGHYFCEVCALKPYQKGEKCYVCSQQTHG 287 (313)
T ss_pred cccccccccccc---chhhcCCceeehhhhccccccCCcceeccccccc
Confidence 678888887742 3556677788999998887554589999998875
No 46
>COG2191 Formylmethanofuran dehydrogenase subunit E [Energy production and conversion]
Probab=68.55 E-value=1.7 Score=31.81 Aligned_cols=32 Identities=22% Similarity=0.485 Sum_probs=26.0
Q ss_pred cccccCCcccccCCeEEeeCCeeecHHhHHhhh
Q psy12215 76 FACQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 108 (155)
Q Consensus 76 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 108 (155)
-+|+.|+..+ ....-...+|+++|..||.+.+
T Consensus 173 v~C~kCGE~~-~e~~~~~~ng~~vC~~C~~~~~ 204 (206)
T COG2191 173 VRCSKCGELF-MEPRAVVLNGKPVCKPCAEKKY 204 (206)
T ss_pred eeccccCccc-ccchhhhcCCceeccccccccc
Confidence 5799999988 5666677899999999987643
No 47
>PRK14890 putative Zn-ribbon RNA-binding protein; Provisional
Probab=67.19 E-value=3.5 Score=24.01 Aligned_cols=36 Identities=28% Similarity=0.498 Sum_probs=18.9
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccchhcccccccccccccc
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTK 55 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~ 55 (155)
+|+.|+..|.+.+ +.-...|..|-..... +|..|.+
T Consensus 9 ~CtSCg~~i~~~~-----~~~~F~CPnCG~~~I~---RC~~CRk 44 (59)
T PRK14890 9 KCTSCGIEIAPRE-----KAVKFLCPNCGEVIIY---RCEKCRK 44 (59)
T ss_pred cccCCCCcccCCC-----ccCEeeCCCCCCeeEe---echhHHh
Confidence 5888888885432 1123455555443222 3555544
No 48
>KOG4739|consensus
Probab=64.00 E-value=4.9 Score=30.10 Aligned_cols=42 Identities=26% Similarity=0.514 Sum_probs=30.8
Q ss_pred cccCCcccccCCeEEeeC-CeeecHHhHHhhhcccCCCeeeecCCeec
Q psy12215 78 CQQCNHRFCVGDRFYLCD-NKILCEYDYEERQVFCVGDRFYLCDNKIL 124 (155)
Q Consensus 78 C~~C~~~l~~~~~~~~~~-~~~~C~~c~~~~~~~~~~~~c~~c~~~i~ 124 (155)
|..|...- ....|++.. ..++|..|..-.. ++.|..|.+.|.
T Consensus 6 Cn~C~~~~-~~~~f~LTaC~HvfC~~C~k~~~----~~~C~lCkk~ir 48 (233)
T KOG4739|consen 6 CNKCFRFP-SQDPFFLTACRHVFCEPCLKASS----PDVCPLCKKSIR 48 (233)
T ss_pred eccccccC-CCCceeeeechhhhhhhhcccCC----ccccccccceee
Confidence 44555554 366677766 8899999976655 779999998875
No 49
>PF06689 zf-C4_ClpX: ClpX C4-type zinc finger; InterPro: IPR010603 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 ClpX heat shock protein of Escherichia coli is a member of the universally conserved Hsp100 family of proteins, and possesses a putative zinc finger motif of the C4 type []. This presumed zinc binding domain (ZBD) is found at the N terminus of the ClpX protein. ClpX is an ATPase which functions both as a substrate specificity component of the ClpXP protease and as a molecular chaperone. ZBD is a member of the treble clef zinc finger family, a motif known to facilitate protein-ligand, protein-DNA, and protein-protein interactions and forms a constitutive dimer that is essential for the degradation of some, but not all, ClpX substrates []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0016887 ATPase activity, 0046983 protein dimerization activity, 0006200 ATP catabolic process, 0019538 protein metabolic process; PDB: 2DS8_B 2DS6_B 2DS5_A 1OVX_A 2DS7_A.
Probab=63.75 E-value=8.2 Score=20.56 Aligned_cols=31 Identities=19% Similarity=0.421 Sum_probs=18.7
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccchhc
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDYLR 42 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~ 42 (155)
.|+-|+++-++.+......++...|.+|...
T Consensus 3 ~CSFCgr~~~~v~~li~g~~~~~IC~~Cv~~ 33 (41)
T PF06689_consen 3 RCSFCGRPESEVGRLISGPNGAYICDECVEQ 33 (41)
T ss_dssp B-TTT--BTTTSSSEEEES-SEEEEHHHHHH
T ss_pred CccCCCCCHHHHhceecCCCCcEECHHHHHH
Confidence 5888999987665544445467778888754
No 50
>PF13834 DUF4193: Domain of unknown function (DUF4193)
Probab=63.55 E-value=2.5 Score=27.30 Aligned_cols=29 Identities=14% Similarity=0.230 Sum_probs=16.5
Q ss_pred CcccccCCcccccCCCeEEEeCCeeecccc
Q psy12215 10 CLKCGCCDCRLGEVGSTLYQKANLILCKRD 39 (155)
Q Consensus 10 Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c 39 (155)
=|+|+.|.---. .++.-...+|.++|.+|
T Consensus 70 EFTCssCFLV~H-RSqLa~~~~g~~iC~DC 98 (99)
T PF13834_consen 70 EFTCSSCFLVHH-RSQLAREKDGQPICRDC 98 (99)
T ss_pred ceeeeeeeeEec-hhhhccccCCCEecccc
Confidence 478887744322 11122356678888776
No 51
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=62.13 E-value=4.7 Score=27.46 Aligned_cols=21 Identities=24% Similarity=0.667 Sum_probs=16.5
Q ss_pred cccCCcccccCCeEEeeCCeeecHHhH
Q psy12215 78 CQQCNHRFCVGDRFYLCDNKILCEYDY 104 (155)
Q Consensus 78 C~~C~~~l~~~~~~~~~~~~~~C~~c~ 104 (155)
|..|+.+| |- .+|.+||..|=
T Consensus 31 Cp~Cg~PL-----F~-KdG~v~CPvC~ 51 (131)
T COG1645 31 CPKCGTPL-----FR-KDGEVFCPVCG 51 (131)
T ss_pred CcccCCcc-----ee-eCCeEECCCCC
Confidence 67788888 44 78999998884
No 52
>PF13639 zf-RING_2: Ring finger domain; PDB: 2KIZ_A 4EPO_C 1IYM_A 2EP4_A 2ECT_A 2JRJ_A 2ECN_A 2ECM_A 3NG2_A 2EA6_A ....
Probab=62.09 E-value=5.7 Score=21.12 Aligned_cols=32 Identities=6% Similarity=0.128 Sum_probs=15.7
Q ss_pred cccCCcccccCCCeEEEeCCeeecccchhccc
Q psy12215 13 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLF 44 (155)
Q Consensus 13 C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~ 44 (155)
|..|-..+.+........=+..||.+|..+.+
T Consensus 3 C~IC~~~~~~~~~~~~l~C~H~fh~~Ci~~~~ 34 (44)
T PF13639_consen 3 CPICLEEFEDGEKVVKLPCGHVFHRSCIKEWL 34 (44)
T ss_dssp ETTTTCBHHTTSCEEEETTSEEEEHHHHHHHH
T ss_pred CcCCChhhcCCCeEEEccCCCeeCHHHHHHHH
Confidence 55555555433333334445566666655443
No 53
>PF12773 DZR: Double zinc ribbon
Probab=61.96 E-value=3.8 Score=22.54 Aligned_cols=38 Identities=18% Similarity=0.384 Sum_probs=22.4
Q ss_pred cccCCcccccCCCeEEEeCCeeecccchhccc---ccccccccccccccc
Q psy12215 13 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLF---GTTGYCAACTKVIPA 59 (155)
Q Consensus 13 C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~---~~~~~C~~C~~~I~~ 59 (155)
|..|+.++++ +..||..|-..+. .....|..|+..+..
T Consensus 1 Cp~Cg~~~~~---------~~~fC~~CG~~l~~~~~~~~~C~~Cg~~~~~ 41 (50)
T PF12773_consen 1 CPHCGTPNPD---------DAKFCPHCGTPLPPPDQSKKICPNCGAENPP 41 (50)
T ss_pred CCCcCCcCCc---------cccCChhhcCChhhccCCCCCCcCCcCCCcC
Confidence 4566666642 2457777776655 111258888887654
No 54
>KOG0320|consensus
Probab=61.80 E-value=2.9 Score=29.97 Aligned_cols=51 Identities=24% Similarity=0.432 Sum_probs=34.7
Q ss_pred ccCcccccCCcccccCCCeEEEeCCeeecccchhcccccccccccccccccc
Q psy12215 8 EDCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 59 (155)
Q Consensus 8 ~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~ 59 (155)
..+++|-.|=....+. ..+..+=|.+||+.|.........+|..|++.|.-
T Consensus 129 ~~~~~CPiCl~~~sek-~~vsTkCGHvFC~~Cik~alk~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 129 EGTYKCPICLDSVSEK-VPVSTKCGHVFCSQCIKDALKNTNKCPTCRKKITH 179 (187)
T ss_pred ccccCCCceecchhhc-cccccccchhHHHHHHHHHHHhCCCCCCcccccch
Confidence 3567777774444221 23446778899999998876555589999998853
No 55
>PRK00807 50S ribosomal protein L24e; Validated
Probab=61.24 E-value=8.8 Score=21.67 Aligned_cols=24 Identities=25% Similarity=0.534 Sum_probs=14.7
Q ss_pred ccccCCccccc-CCCeEEEeCCeee
Q psy12215 12 KCGCCDCRLGE-VGSTLYQKANLIL 35 (155)
Q Consensus 12 ~C~~C~~~l~~-~~~~~~~~~~~~~ 35 (155)
.|+.|+..+.+ .+..|+..||++|
T Consensus 3 ~C~fcG~~I~pg~G~~~vr~Dgkv~ 27 (52)
T PRK00807 3 TCSFCGKEIEPGTGKMYVKKDGTIL 27 (52)
T ss_pred ccCCCCCeEcCCCCeEEEEeCCcEE
Confidence 46777777763 3444556777755
No 56
>PF09943 DUF2175: Uncharacterized protein conserved in archaea (DUF2175); InterPro: IPR018686 This family of various hypothetical archaeal proteins has no known function.
Probab=61.21 E-value=8.9 Score=24.90 Aligned_cols=32 Identities=28% Similarity=0.445 Sum_probs=23.2
Q ss_pred cccccccccccCceEEeccCcccccccccccc
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQ 80 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~ 80 (155)
+|..|+++|..++...-..+..-|-.||+=..
T Consensus 4 kC~iCg~~I~~gqlFTF~~kG~VH~~C~~~~~ 35 (101)
T PF09943_consen 4 KCYICGKPIYEGQLFTFTKKGPVHYECFREKA 35 (101)
T ss_pred EEEecCCeeeecceEEEecCCcEeHHHHHHHH
Confidence 69999999987655444445667888887544
No 57
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=60.15 E-value=4.4 Score=22.60 Aligned_cols=43 Identities=23% Similarity=0.597 Sum_probs=16.8
Q ss_pred ccCCcccccCCCeEEE-eCCeeecccchhcccc-ccccccccccc
Q psy12215 14 GCCDCRLGEVGSTLYQ-KANLILCKRDYLRLFG-TTGYCAACTKV 56 (155)
Q Consensus 14 ~~C~~~l~~~~~~~~~-~~~~~~C~~c~~~~~~-~~~~C~~C~~~ 56 (155)
..|...|+..+..|.. .=|--+|..||.+... ..++|.+|.++
T Consensus 2 p~C~e~~d~~d~~~~PC~Cgf~IC~~C~~~i~~~~~g~CPgCr~~ 46 (48)
T PF14570_consen 2 PLCDEELDETDKDFYPCECGFQICRFCYHDILENEGGRCPGCREP 46 (48)
T ss_dssp TTTS-B--CCCTT--SSTTS----HHHHHHHTTSS-SB-TTT--B
T ss_pred CCcccccccCCCccccCcCCCcHHHHHHHHHHhccCCCCCCCCCC
Confidence 3455556544444442 2233467888876552 34578888764
No 58
>PF01258 zf-dskA_traR: Prokaryotic dksA/traR C4-type zinc finger; InterPro: IPR000962 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 domains identified in zinc finger-containing members of the DksA/TraR family. DksA is a critical component of the rRNA transcription initiation machinery that potentiates the regulation of rRNA promoters by ppGpp and the initiating NTP. In delta-dksA mutants, rRNA promoters are unresponsive to changes in amino acid availability, growth rate, or growth phase. In vitro, DksA binds to RNAP, reduces open complex lifetime, inhibits rRNA promoter activity, and amplifies effects of ppGpp and the initiating NTP on rRNA transcription [, ]. The dksA gene product suppresses the temperature-sensitive growth and filamentation of a dnaK deletion mutant of Escherichia coli. Gene knockout [] and deletion [] experiments have shown the gene to be non-essential, mutations causing a mild sensitivity to UV light, but not affecting DNA recombination []. In Pseudomonas aeruginosa, dksA is a novel regulator involved in the post-transcriptional control of extracellular virulence factor production []. The proteins contain a C-terminal region thought to fold into a 4-cysteine zinc finger. Other proteins found to contain a similar zinc finger domain include: the traR gene products encoded on the E. coli F and R100 plasmids [, ] the traR gene products encoded on Salmonella spp. plasmids pED208 and pSLT the dnaK suppressor hypothetical proteins from bacteria and bacteriophage FHL4, LIM proteins from Homo sapiens (Human) and Mus musculus (Mouse) [] More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2GVI_A 2KQ9_A 2KGO_A 1TJL_I.
Probab=59.71 E-value=1.4 Score=22.80 Aligned_cols=27 Identities=22% Similarity=0.486 Sum_probs=10.1
Q ss_pred cccCCcccccCCeEEeeCCeeecHHhHH
Q psy12215 78 CQQCNHRFCVGDRFYLCDNKILCEYDYE 105 (155)
Q Consensus 78 C~~C~~~l~~~~~~~~~~~~~~C~~c~~ 105 (155)
|..|+..+ ...+....++..+|..|..
T Consensus 6 C~~CGe~I-~~~Rl~~~p~~~~C~~C~~ 32 (36)
T PF01258_consen 6 CEDCGEPI-PEERLVAVPGATLCVECQE 32 (36)
T ss_dssp -TTTSSBE-EHHHHHHCTTECS-HHHHH
T ss_pred ccccCChH-HHHHHHhCCCcEECHHHhC
Confidence 34444444 2222333344455555543
No 59
>COG5152 Uncharacterized conserved protein, contains RING and CCCH-type Zn-fingers [General function prediction only]
Probab=57.49 E-value=2.6 Score=30.81 Aligned_cols=46 Identities=17% Similarity=0.428 Sum_probs=34.0
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhcccccccccccccccccc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 59 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~ 59 (155)
|.|..|.+...+ +.+..=|.-||..|+++.+.....|..|++...+
T Consensus 197 F~C~iCKkdy~s---pvvt~CGH~FC~~Cai~~y~kg~~C~~Cgk~t~G 242 (259)
T COG5152 197 FLCGICKKDYES---PVVTECGHSFCSLCAIRKYQKGDECGVCGKATYG 242 (259)
T ss_pred eeehhchhhccc---hhhhhcchhHHHHHHHHHhccCCcceecchhhcc
Confidence 778888877642 3455667788999998877544489999888776
No 60
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=56.97 E-value=10 Score=20.54 Aligned_cols=10 Identities=30% Similarity=0.418 Sum_probs=6.3
Q ss_pred eeecHHhHHh
Q psy12215 97 KILCEYDYEE 106 (155)
Q Consensus 97 ~~~C~~c~~~ 106 (155)
--+|..||..
T Consensus 23 ~dLC~~Cf~~ 32 (46)
T cd02249 23 FDLCSSCYAK 32 (46)
T ss_pred CcCHHHHHCc
Confidence 4467777764
No 61
>cd00162 RING RING-finger (Really Interesting New Gene) domain, a specialized type of Zn-finger of 40 to 60 residues that binds two atoms of zinc; defined by the 'cross-brace' motif C-X2-C-X(9-39)-C-X(1-3)- H-X(2-3)-(N/C/H)-X2-C-X(4-48)C-X2-C; probably involved in mediating protein-protein interactions; identified in a proteins with a wide range of functions such as viral replication, signal transduction, and development; has two variants, the C3HC4-type and a C3H2C3-type (RING-H2 finger), which have different cysteine/histidine pattern; a subset of RINGs are associated with B-Boxes (C-X2-H-X7-C-X7-C-X2-C-H-X2-H)
Probab=56.87 E-value=5.9 Score=20.32 Aligned_cols=41 Identities=12% Similarity=0.400 Sum_probs=19.9
Q ss_pred cccCCcccccCCCeEEEeCCeeecccchhccccc-ccccccccc
Q psy12215 13 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT-TGYCAACTK 55 (155)
Q Consensus 13 C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~-~~~C~~C~~ 55 (155)
|..|...+. .......=|..||.+|....+.. ..+|..|..
T Consensus 2 C~iC~~~~~--~~~~~~~C~H~~c~~C~~~~~~~~~~~Cp~C~~ 43 (45)
T cd00162 2 CPICLEEFR--EPVVLLPCGHVFCRSCIDKWLKSGKNTCPLCRT 43 (45)
T ss_pred CCcCchhhh--CceEecCCCChhcHHHHHHHHHhCcCCCCCCCC
Confidence 555655552 11222225566777776544321 124666554
No 62
>COG4847 Uncharacterized protein conserved in archaea [Function unknown]
Probab=55.44 E-value=11 Score=24.12 Aligned_cols=31 Identities=16% Similarity=0.329 Sum_probs=20.4
Q ss_pred cccccCCcccccCCeEEeeCCeeecHHhHHh
Q psy12215 76 FACQQCNHRFCVGDRFYLCDNKILCEYDYEE 106 (155)
Q Consensus 76 f~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~ 106 (155)
|+|..|+.++..|+.|++....+.--.|+..
T Consensus 7 wkC~VCg~~iieGqkFTF~~kGsVH~eCl~~ 37 (103)
T COG4847 7 WKCYVCGGTIIEGQKFTFTKKGSVHYECLAE 37 (103)
T ss_pred eeEeeeCCEeeeccEEEEeeCCcchHHHHHH
Confidence 5677788777777777665544555556543
No 63
>PF02069 Metallothio_Pro: Prokaryotic metallothionein; InterPro: IPR000518 Metallothioneins (MT) are small proteins that bind heavy metals, such as zinc, copper, cadmium and nickel. They have a high content of cysteine residues that bind the metal ions through clusters of thiolate bonds [, , ]. An empirical classification into three classes was proposed by Kojima [], with class III MTs including atypical polypeptides composed of gamma-glutamylcysteinyl units. Class I and class II MTs (the proteinaceous sequences) have now been grouped into families of phylogenetically-related and thus alignable sequences. The MT superfamily is subdivided into families, subfamilies, subgroups, and isolated isoforms and alleles. The metallothionein superfamily comprises all polypeptides that resemble equine renal metallothionein in several respects [], e.g., low molecular weight; high metal content; amino acid composition with high Cys and low aromatic residue content; unique sequence with characteristic distribution of cysteines, and spectroscopic manifestations indicative of metal thiolate clusters. A MT family subsumes MTs that share particular sequence-specific features and are thought to be evolutionarily related. Fifteen MT families have been characterised, each family being identified by its number and its taxonomic range. Family 14 consists of prokaryota MTs. Its members are recognised by the sequence pattern K-C-A-C-x(2)-C-L-C.The taxonomic range of the members extends to cyanobacteria. Known characteristics are: 53 to 56 AAs; 9 conserved Cys; one conserved tyrosine residue; one conserved histidine residue; contain other unusual residues. ; GO: 0046872 metal ion binding; PDB: 1JJD_A.
Probab=55.41 E-value=6.5 Score=22.30 Aligned_cols=27 Identities=26% Similarity=0.511 Sum_probs=14.1
Q ss_pred cccCCcccccCCCeEEEeCCeeecc-cchh
Q psy12215 13 CGCCDCRLGEVGSTLYQKANLILCK-RDYL 41 (155)
Q Consensus 13 C~~C~~~l~~~~~~~~~~~~~~~C~-~c~~ 41 (155)
|..|...+++ ..-+.+||+.||. .|..
T Consensus 10 C~~C~C~V~~--~~Ai~~dGk~YCS~aCA~ 37 (52)
T PF02069_consen 10 CPSCSCVVSE--EEAIQKDGKYYCSEACAN 37 (52)
T ss_dssp STT----B-T--TTSEESSS-EESSHHHHH
T ss_pred CCCCEeEECc--hHhHHhCCEeeecHHHhc
Confidence 5677777753 3468999999985 4443
No 64
>PRK14873 primosome assembly protein PriA; Provisional
Probab=54.58 E-value=9.5 Score=33.13 Aligned_cols=39 Identities=18% Similarity=0.249 Sum_probs=28.2
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKV 56 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~ 56 (155)
++|..|+-+| +|...++.+.|..|-...... .|..|+..
T Consensus 393 ~~C~~C~~~L-----~~h~~~~~l~Ch~CG~~~~p~--~Cp~Cgs~ 431 (665)
T PRK14873 393 ARCRHCTGPL-----GLPSAGGTPRCRWCGRAAPDW--RCPRCGSD 431 (665)
T ss_pred eECCCCCCce-----eEecCCCeeECCCCcCCCcCc--cCCCCcCC
Confidence 4566677666 355566788899998766443 89999875
No 65
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=53.54 E-value=5.9 Score=18.79 Aligned_cols=7 Identities=29% Similarity=0.980 Sum_probs=2.7
Q ss_pred cccCCcc
Q psy12215 13 CGCCDCR 19 (155)
Q Consensus 13 C~~C~~~ 19 (155)
|..|+..
T Consensus 5 Cp~Cg~~ 11 (26)
T PF13248_consen 5 CPNCGAE 11 (26)
T ss_pred CcccCCc
Confidence 3334443
No 66
>PF00645 zf-PARP: Poly(ADP-ribose) polymerase and DNA-Ligase Zn-finger region; InterPro: IPR001510 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 PARP (Poly(ADP) polymerase) type zinc finger domains. NAD(+) ADP-ribosyltransferase(2.4.2.30 from EC) [, ] is a eukaryotic enzyme that catalyses the covalent attachment of ADP-ribose units from NAD(+) to various nuclear acceptor proteins. This post-translational modification of nuclear proteins is dependent on DNA. It appears to be involved in the regulation of various important cellular processes such as differentiation, proliferation and tumour transformation as well as in the regulation of the molecular events involved in the recovery of the cell from DNA damage. Structurally, NAD(+) ADP-ribosyltransferase consists of three distinct domains: an N-terminal zinc-dependent DNA-binding domain, a central automodification domain and a C-terminal NAD-binding domain. The DNA-binding region contains a pair of PARP-type zinc finger domains which have been shown to bind DNA in a zinc-dependent manner. The PARP-type zinc finger domains seem to bind specifically to single-stranded DNA and to act as a DNA nick sensor. DNA ligase III [] contains, in its N-terminal section, a single copy of a zinc finger highly similar to those of PARP. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003677 DNA binding, 0008270 zinc ion binding; PDB: 1UW0_A 3OD8_D 3ODA_A 4AV1_A 2DMJ_A 4DQY_D 2L30_A 2CS2_A 2L31_A 3ODE_B ....
Probab=53.18 E-value=5.6 Score=24.39 Aligned_cols=13 Identities=38% Similarity=0.639 Sum_probs=8.9
Q ss_pred cccccccccccCc
Q psy12215 49 YCAACTKVIPAFE 61 (155)
Q Consensus 49 ~C~~C~~~I~~~~ 61 (155)
+|..|+..|.-++
T Consensus 9 ~Ck~C~~~I~kg~ 21 (82)
T PF00645_consen 9 KCKGCKKKIAKGE 21 (82)
T ss_dssp BETTTSCBE-TTS
T ss_pred cCcccCCcCCCCC
Confidence 6888888886544
No 67
>PF12674 Zn_ribbon_2: Putative zinc ribbon domain
Probab=52.60 E-value=4.6 Score=25.11 Aligned_cols=30 Identities=17% Similarity=0.264 Sum_probs=19.4
Q ss_pred ccccCCcccccCCCeEE--EeCC---eeecccchhcc
Q psy12215 12 KCGCCDCRLGEVGSTLY--QKAN---LILCKRDYLRL 43 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~--~~~~---~~~C~~c~~~~ 43 (155)
.|+.|+-||.... .+ ..|| .-||..||..-
T Consensus 2 ~CQSCGMPl~~~~--~~Gte~dGs~s~~YC~yCy~~G 36 (81)
T PF12674_consen 2 FCQSCGMPLSKDE--DFGTEADGSKSEDYCSYCYQNG 36 (81)
T ss_pred cCCcCcCccCCcc--ccccccCCCCchhHHHHHhcCC
Confidence 4889999996432 22 2233 36999998753
No 68
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=52.38 E-value=16 Score=18.52 Aligned_cols=24 Identities=17% Similarity=0.283 Sum_probs=15.8
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccch
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDY 40 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~ 40 (155)
.|..|+.++ .+...++..+|..|-
T Consensus 5 ~C~~C~~~~-----i~~~~~~~~~C~~Cg 28 (33)
T PF08792_consen 5 KCSKCGGNG-----IVNKEDDYEVCIFCG 28 (33)
T ss_pred EcCCCCCCe-----EEEecCCeEEcccCC
Confidence 477777765 244677777777664
No 69
>PF12156 ATPase-cat_bd: Putative metal-binding domain of cation transport ATPase; InterPro: IPR021993 This domain is found in bacteria, and is approximately 90 amino acids in length. It is found associated with PF00403 from PFAM, PF00122 from PFAM, PF00702 from PFAM. The cysteine-rich nature and composition suggest this might be a cation-binding domain; most members are annotated as being cation transport ATPases.
Probab=51.64 E-value=12 Score=23.47 Aligned_cols=25 Identities=20% Similarity=0.336 Sum_probs=12.6
Q ss_pred ccccCCcccccCCCeEEEeCC--eeec
Q psy12215 12 KCGCCDCRLGEVGSTLYQKAN--LILC 36 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~--~~~C 36 (155)
.|..|+.++++....-...+| +.||
T Consensus 2 ~C~HCg~~~p~~~~~~~~~~g~~~~FC 28 (88)
T PF12156_consen 2 KCYHCGLPVPEGAKITVEIDGEERPFC 28 (88)
T ss_pred CCCCCCCCCCCCCCeeeeeCCCccccc
Confidence 466677777533222223444 4554
No 70
>COG2075 RPL24A Ribosomal protein L24E [Translation, ribosomal structure and biogenesis]
Probab=50.77 E-value=17 Score=21.58 Aligned_cols=24 Identities=17% Similarity=0.498 Sum_probs=15.8
Q ss_pred ccccCCcccccCCCeEE-EeCCeee
Q psy12215 12 KCGCCDCRLGEVGSTLY-QKANLIL 35 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~-~~~~~~~ 35 (155)
+|+-|+..+.++....+ ..||.++
T Consensus 5 ~CsFcG~~I~PGtG~m~Vr~Dg~v~ 29 (66)
T COG2075 5 VCSFCGKKIEPGTGIMYVRNDGKVL 29 (66)
T ss_pred EecCcCCccCCCceEEEEecCCeEE
Confidence 57888888876544444 4666654
No 71
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=49.76 E-value=13 Score=32.68 Aligned_cols=40 Identities=23% Similarity=0.368 Sum_probs=30.8
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKV 56 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~ 56 (155)
++|..|+.+| +|....+.+.|..|-.....| ..|..|+..
T Consensus 445 ~~Cp~Cd~~l-----t~H~~~~~L~CH~Cg~~~~~p-~~Cp~Cgs~ 484 (730)
T COG1198 445 AECPNCDSPL-----TLHKATGQLRCHYCGYQEPIP-QSCPECGSE 484 (730)
T ss_pred ccCCCCCcce-----EEecCCCeeEeCCCCCCCCCC-CCCCCCCCC
Confidence 6777888777 477778899999998874333 379999876
No 72
>smart00291 ZnF_ZZ Zinc-binding domain, present in Dystrophin, CREB-binding protein. Putative zinc-binding domain present in dystrophin-like proteins, and CREB-binding protein/p300 homologues. The ZZ in dystrophin appears to bind calmodulin. A missense mutation of one of the conserved cysteines in dystrophin results in a patient with Duchenne muscular dystrophy [3].
Probab=48.80 E-value=19 Score=19.27 Aligned_cols=10 Identities=20% Similarity=0.418 Sum_probs=7.0
Q ss_pred eeecHHhHHh
Q psy12215 97 KILCEYDYEE 106 (155)
Q Consensus 97 ~~~C~~c~~~ 106 (155)
.-+|..||.+
T Consensus 27 ~dlC~~Cf~~ 36 (44)
T smart00291 27 YDLCQSCFAK 36 (44)
T ss_pred ccchHHHHhC
Confidence 4578888765
No 73
>PF11571 Med27: Mediator complex subunit 27; InterPro: IPR021627 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Mediator exists in two major forms in human cells: a smaller form that interacts strongly with pol II and activates transcription, and a large form that does not interact strongly with pol II and does not directly activate transcription. The ubiquitous expression of Med27 mRNA suggests a universal requirement for Med27 in transcriptional initiation. Loss of Crsp34/Med27 decreases amacrine cell number, but increases the number of rod photoreceptor cells [].
Probab=46.70 E-value=5.4 Score=25.19 Aligned_cols=16 Identities=44% Similarity=0.949 Sum_probs=12.3
Q ss_pred hhcccccccccccccccc
Q psy12215 40 YLRLFGTTGYCAACTKVI 57 (155)
Q Consensus 40 ~~~~~~~~~~C~~C~~~I 57 (155)
|...|.. +|.+|++.+
T Consensus 49 Y~~lfs~--pC~~C~klL 64 (90)
T PF11571_consen 49 YRNLFST--PCKKCGKLL 64 (90)
T ss_pred Hhhhccc--hhhHHHhHh
Confidence 4556666 799999988
No 74
>PF00097 zf-C3HC4: Zinc finger, C3HC4 type (RING finger); InterPro: IPR018957 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C3HC4 type zinc-finger (RING finger) is a cysteine-rich domain of 40 to 60 residues that coordinates two zinc ions, and has the consensus sequence: C-X2-C-X(9-39)-C-X(1-3)-H-X(2-3)-C-X2-C-X(4-48)-C-X2-C where X is any amino acid []. Many proteins containing a RING finger play a key role in the ubiquitination pathway []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 1CHC_A 2ECW_A 2Y43_B 1V87_A 2DJB_A 2H0D_B 3RPG_C 3KNV_A 2CKL_B 1JM7_A ....
Probab=46.56 E-value=24 Score=18.08 Aligned_cols=29 Identities=21% Similarity=0.393 Sum_probs=17.6
Q ss_pred cccCCcccccCCeEEeeC-CeeecHHhHHhhh
Q psy12215 78 CQQCNHRFCVGDRFYLCD-NKILCEYDYEERQ 108 (155)
Q Consensus 78 C~~C~~~l~~~~~~~~~~-~~~~C~~c~~~~~ 108 (155)
|..|...+ .......+ |..||..|..+..
T Consensus 1 C~iC~~~~--~~~~~~~~C~H~fC~~C~~~~~ 30 (41)
T PF00097_consen 1 CPICLEPF--EDPVILLPCGHSFCRDCLRKWL 30 (41)
T ss_dssp ETTTSSBC--SSEEEETTTSEEEEHHHHHHHH
T ss_pred CCcCCccc--cCCCEEecCCCcchHHHHHHHH
Confidence 44555555 23333444 8889999987665
No 75
>KOG0978|consensus
Probab=45.58 E-value=3.7 Score=35.55 Aligned_cols=48 Identities=23% Similarity=0.555 Sum_probs=31.1
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhccccc-cccccccccccccCc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT-TGYCAACTKVIPAFE 61 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~-~~~C~~C~~~I~~~~ 61 (155)
++|+.|+....+ .....=+.+||..|...++.. .-+|+.|+.+..++|
T Consensus 644 LkCs~Cn~R~Kd---~vI~kC~H~FC~~Cvq~r~etRqRKCP~Cn~aFganD 692 (698)
T KOG0978|consen 644 LKCSVCNTRWKD---AVITKCGHVFCEECVQTRYETRQRKCPKCNAAFGAND 692 (698)
T ss_pred eeCCCccCchhh---HHHHhcchHHHHHHHHHHHHHhcCCCCCCCCCCCccc
Confidence 578888866532 234455567888888776522 116888888876644
No 76
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=45.17 E-value=17 Score=30.44 Aligned_cols=40 Identities=25% Similarity=0.368 Sum_probs=28.3
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKV 56 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~ 56 (155)
.+|..|+.+| +|...++.+.|..|-...-.+ ..|..|+..
T Consensus 223 ~~C~~C~~~l-----~~h~~~~~l~Ch~Cg~~~~~~-~~Cp~C~s~ 262 (505)
T TIGR00595 223 LCCPNCDVSL-----TYHKKEGKLRCHYCGYQEPIP-KTCPQCGSE 262 (505)
T ss_pred cCCCCCCCce-----EEecCCCeEEcCCCcCcCCCC-CCCCCCCCC
Confidence 3455666665 577778889999998776433 289999874
No 77
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=44.96 E-value=36 Score=18.02 Aligned_cols=29 Identities=24% Similarity=0.332 Sum_probs=19.1
Q ss_pred cccCCcccccCCeEEeeCCeeecHHhHHhhh
Q psy12215 78 CQQCNHRFCVGDRFYLCDNKILCEYDYEERQ 108 (155)
Q Consensus 78 C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~ 108 (155)
|..|...| .+.....=|..||..|..+..
T Consensus 1 CpiC~~~~--~~Pv~l~CGH~FC~~Cl~~~~ 29 (42)
T PF15227_consen 1 CPICLDLF--KDPVSLPCGHSFCRSCLERLW 29 (42)
T ss_dssp ETTTTSB---SSEEE-SSSSEEEHHHHHHHH
T ss_pred CCccchhh--CCccccCCcCHHHHHHHHHHH
Confidence 45566666 556666668999999987765
No 78
>smart00547 ZnF_RBZ Zinc finger domain. Zinc finger domain in Ran-binding proteins (RanBPs), and other proteins. In RanBPs, this domain binds RanGDP.
Probab=43.69 E-value=11 Score=17.55 Aligned_cols=20 Identities=25% Similarity=0.512 Sum_probs=10.4
Q ss_pred cccchhcccccccccccccc
Q psy12215 36 CKRDYLRLFGTTGYCAACTK 55 (155)
Q Consensus 36 C~~c~~~~~~~~~~C~~C~~ 55 (155)
|..|....+.....|..|+.
T Consensus 5 C~~C~~~N~~~~~~C~~C~~ 24 (26)
T smart00547 5 CPACTFLNFASRSKCFACGA 24 (26)
T ss_pred CCCCCCcChhhhccccccCC
Confidence 45555555444445666654
No 79
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 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 ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=41.55 E-value=38 Score=18.29 Aligned_cols=10 Identities=30% Similarity=0.458 Sum_probs=7.2
Q ss_pred eeecHHhHHh
Q psy12215 97 KILCEYDYEE 106 (155)
Q Consensus 97 ~~~C~~c~~~ 106 (155)
--+|..||.+
T Consensus 28 ~dLC~~C~~~ 37 (46)
T PF00569_consen 28 YDLCEDCFSK 37 (46)
T ss_dssp -EEEHHHHHH
T ss_pred CchhhHHHhC
Confidence 4578888876
No 80
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=40.92 E-value=20 Score=31.08 Aligned_cols=37 Identities=22% Similarity=0.447 Sum_probs=21.7
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccchhcccccccccccccccccc
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 59 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~ 59 (155)
.|..|+....+ +..||..|-.+.-.. .|..|+..+..
T Consensus 3 ~Cp~Cg~~n~~---------~akFC~~CG~~l~~~--~Cp~CG~~~~~ 39 (645)
T PRK14559 3 ICPQCQFENPN---------NNRFCQKCGTSLTHK--PCPQCGTEVPV 39 (645)
T ss_pred cCCCCCCcCCC---------CCccccccCCCCCCC--cCCCCCCCCCc
Confidence 56677666532 244677776654333 57777766543
No 81
>KOG2462|consensus
Probab=40.80 E-value=14 Score=28.35 Aligned_cols=69 Identities=20% Similarity=0.293 Sum_probs=39.6
Q ss_pred cCcccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccccCceEEeccCccccccccccccCCccc
Q psy12215 9 DCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRF 85 (155)
Q Consensus 9 ~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l 85 (155)
..++|.+|++.+.. ..=..+..+.-|..+-.+.+ .|..|++.-.... . ...-..-|.-=+.|..|++.+
T Consensus 129 ~r~~c~eCgk~ysT--~snLsrHkQ~H~~~~s~ka~----~C~~C~K~YvSmp-A-LkMHirTH~l~c~C~iCGKaF 197 (279)
T KOG2462|consen 129 PRYKCPECGKSYST--SSNLSRHKQTHRSLDSKKAF----SCKYCGKVYVSMP-A-LKMHIRTHTLPCECGICGKAF 197 (279)
T ss_pred Cceecccccccccc--ccccchhhcccccccccccc----cCCCCCceeeehH-H-HhhHhhccCCCcccccccccc
Confidence 45789999998842 12234555566655553333 5888887554311 1 111122355456888999988
No 82
>PF03854 zf-P11: P-11 zinc finger; InterPro: IPR003224 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 RING-finger is a specialised type of Zn-finger of 40 to 60 residues that binds two atoms of zinc, and is probably involved in mediating protein-protein interactions [, , ]. There are two different variants, the C3HC4-type and a C3H2C3-type, which is clearly related despite the different cysteine/histidine pattern. The latter type is sometimes referred to as 'RING-H2 finger'. The RING domain is a protein interaction domain which has been implicated in a range of diverse biological processes. Several 3D-structures for RING-fingers are known [, ]. The 3D structure of the zinc ligation system is unique to the RING domain and is referred to as the 'cross-brace' motif. The spacing of the cysteines in such a domain is: C-x(2)-C-x(9 to 39)-C-x(1 to 3)-H-x(2 to 3)-C-x(2)-C-x(4 to 48)-C-x(2)-C Metal ligand pairs one and three co-ordinate to bind one zinc ion, whilst pairs two and four bind the second. This entry represents RING finger protein Z, a small polypeptide found in some negative-strand RNA viruses including Lassa fever virus, which plays a crucial role in virion assembly and budding. RING finger Z has been shown to interact with several host proteins, including promyelocytic leukemia protein and the eukaryotic translation initiation factor 4E [, ]. It is sufficient in the absence of any other viral proteins to release virus-like particles from the infected cell []. This protein is also responsible for arenavirus superinfection exclusion; expression of this protein in a host cell strongly and specifically inhibits areanavirus transcription and replication []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003723 RNA binding, 0008270 zinc ion binding; PDB: 2KO5_A.
Probab=40.18 E-value=41 Score=18.73 Aligned_cols=28 Identities=18% Similarity=0.364 Sum_probs=17.3
Q ss_pred CCeeecHHhHHhhhcccCCCeeeecCCeec
Q psy12215 95 DNKILCEYDYEERQVFCVGDRFYLCDNKIL 124 (155)
Q Consensus 95 ~~~~~C~~c~~~~~~~~~~~~c~~c~~~i~ 124 (155)
.+..+|..|... ++..++.|.+|..+++
T Consensus 19 ~dHYLCl~CLt~--ml~~s~~C~iC~~~LP 46 (50)
T PF03854_consen 19 SDHYLCLNCLTL--MLSRSDRCPICGKPLP 46 (50)
T ss_dssp SS-EEEHHHHHH--T-SSSSEETTTTEE--
T ss_pred cchhHHHHHHHH--HhccccCCCcccCcCc
Confidence 345556666554 3477899999998887
No 83
>COG2888 Predicted Zn-ribbon RNA-binding protein with a function in translation [Translation, ribosomal structure and biogenesis]
Probab=39.68 E-value=14 Score=21.52 Aligned_cols=10 Identities=20% Similarity=0.730 Sum_probs=6.8
Q ss_pred ccccCCcccc
Q psy12215 12 KCGCCDCRLG 21 (155)
Q Consensus 12 ~C~~C~~~l~ 21 (155)
+|+.|+..|.
T Consensus 11 ~CtSCg~~i~ 20 (61)
T COG2888 11 VCTSCGREIA 20 (61)
T ss_pred eeccCCCEec
Confidence 5677777774
No 84
>cd02336 ZZ_RSC8 Zinc finger, ZZ type. Zinc finger present in RSC8 and related proteins. RSC8 is a component of the RSC complex, which is closely related to the SWI/SNF complex and is involved in remodeling chromatin structure. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=37.00 E-value=40 Score=18.37 Aligned_cols=30 Identities=23% Similarity=0.409 Sum_probs=18.0
Q ss_pred ccccCCcccccCCeEEee--CCeeecHHhHHhh
Q psy12215 77 ACQQCNHRFCVGDRFYLC--DNKILCEYDYEER 107 (155)
Q Consensus 77 ~C~~C~~~l~~~~~~~~~--~~~~~C~~c~~~~ 107 (155)
.|..|+..+ ...+|.-. .+..+|..||.+-
T Consensus 2 ~C~~Cg~D~-t~vryh~~~~~~~dLC~~CF~~G 33 (45)
T cd02336 2 HCFTCGNDC-TRVRYHNLKAKKYDLCPSCYQEG 33 (45)
T ss_pred cccCCCCcc-CceEEEecCCCccccChHHHhCc
Confidence 466677776 33344321 2467899998763
No 85
>PF04981 NMD3: NMD3 family ; InterPro: IPR007064 The NMD3 protein is involved in nonsense mediated mRNA decay. This N-terminal region contains four conserved CXXC motifs that could be metal binding. NMD3 is involved in export of the 60S ribosomal subunit is mediated by the adapter protein Nmd3p in a Crm1p-dependent pathway [].
Probab=36.87 E-value=24 Score=26.32 Aligned_cols=40 Identities=23% Similarity=0.434 Sum_probs=25.5
Q ss_pred cccCCcccccCCCeEEEeCCeeecccchhccccccc--------cccccccccccC
Q psy12215 13 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTG--------YCAACTKVIPAF 60 (155)
Q Consensus 13 C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~--------~C~~C~~~I~~~ 60 (155)
|-.||.+.++. . .-+|.+||.+.+.... .|..|+....++
T Consensus 1 C~~CG~~~~~~------~--~~lC~~C~~~~~~i~ei~~~i~v~~C~~Cg~~~~~~ 48 (236)
T PF04981_consen 1 CPRCGREIEPL------I--DGLCPDCYLKRFDIIEIPDRIEVTICPKCGRYRIGG 48 (236)
T ss_pred CCCCCCCCCCc------c--cccChHHhcccCCeeecCCccCceECCCCCCEECCC
Confidence 56788876421 1 1389999988764321 488887776653
No 86
>PF10122 Mu-like_Com: Mu-like prophage protein Com; InterPro: IPR019294 Members of this entry belong to the Com family of proteins that act as translational regulators of mom [, ].
Probab=36.57 E-value=21 Score=20.12 Aligned_cols=12 Identities=33% Similarity=1.019 Sum_probs=9.6
Q ss_pred cccccCCccccc
Q psy12215 11 LKCGCCDCRLGE 22 (155)
Q Consensus 11 f~C~~C~~~l~~ 22 (155)
++|..|++.|..
T Consensus 5 iRC~~CnklLa~ 16 (51)
T PF10122_consen 5 IRCGHCNKLLAK 16 (51)
T ss_pred eeccchhHHHhh
Confidence 678889998854
No 87
>PF10886 DUF2685: Protein of unknown function (DUF2685); InterPro: IPR024362 This is a family of uncharacterised bacteriophage proteins. Their function in unknown.
Probab=36.18 E-value=31 Score=19.67 Aligned_cols=24 Identities=21% Similarity=0.488 Sum_probs=13.7
Q ss_pred cccccccccccCceEEeccCccccc
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHL 73 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~ 73 (155)
+|..|+++|.+. ..+...+..-|+
T Consensus 3 ~CvVCKqpi~~a-~~v~T~~G~VH~ 26 (54)
T PF10886_consen 3 ICVVCKQPIDDA-LVVETESGPVHP 26 (54)
T ss_pred eeeeeCCccCcc-eEEEcCCCccCc
Confidence 577777777654 344444445554
No 88
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.80 E-value=34 Score=20.79 Aligned_cols=45 Identities=20% Similarity=0.395 Sum_probs=28.5
Q ss_pred cccCCcccccCCC-eEEEeCCeeecccchhcccccccccccccccccc
Q psy12215 13 CGCCDCRLGEVGS-TLYQKANLILCKRDYLRLFGTTGYCAACTKVIPA 59 (155)
Q Consensus 13 C~~C~~~l~~~~~-~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~ 59 (155)
|.-|++.|+..+. ..+-.-.-.||.+|...++.. .|..|+..+..
T Consensus 8 CECCDrDLpp~s~dA~ICtfEcTFCadCae~~l~g--~CPnCGGelv~ 53 (84)
T COG3813 8 CECCDRDLPPDSTDARICTFECTFCADCAENRLHG--LCPNCGGELVA 53 (84)
T ss_pred CcccCCCCCCCCCceeEEEEeeehhHhHHHHhhcC--cCCCCCchhhc
Confidence 4446777763221 222222346899999977765 79999987753
No 89
>PF00641 zf-RanBP: Zn-finger in Ran binding protein and others; InterPro: IPR001876 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the zinc finger domain found in RanBP2 proteins. Ran is an evolutionary conserved member of the Ras superfamily that regulates all receptor-mediated transport between the nucleus and the cytoplasm. Ran binding protein 2 (RanBP2) is a 358kDa nucleoporin located on the cytoplasmic side of the nuclear pore complex which plays a role in nuclear protein import []. RanBP2 contains multiple zinc fingers which mediate binding to RanGDP []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9G_A 2EBR_A 2WX0_C 2WX1_C 2WWZ_C 3GJ6_B 2LK0_A 2LK1_A 3GJ5_B 3GJ8_B ....
Probab=33.75 E-value=27 Score=16.86 Aligned_cols=24 Identities=17% Similarity=0.189 Sum_probs=12.2
Q ss_pred eeecccchhccccccccccccccc
Q psy12215 33 LILCKRDYLRLFGTTGYCAACTKV 56 (155)
Q Consensus 33 ~~~C~~c~~~~~~~~~~C~~C~~~ 56 (155)
.=.|..|...++....+|..|+.+
T Consensus 4 ~W~C~~C~~~N~~~~~~C~~C~~~ 27 (30)
T PF00641_consen 4 DWKCPSCTFMNPASRSKCVACGAP 27 (30)
T ss_dssp SEEETTTTEEEESSSSB-TTT--B
T ss_pred CccCCCCcCCchHHhhhhhCcCCC
Confidence 344666666665554467777654
No 90
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=33.74 E-value=26 Score=19.01 Aligned_cols=11 Identities=27% Similarity=0.576 Sum_probs=8.2
Q ss_pred cccccCCcccc
Q psy12215 11 LKCGCCDCRLG 21 (155)
Q Consensus 11 f~C~~C~~~l~ 21 (155)
+.|..|+..+.
T Consensus 3 Y~C~~Cg~~~~ 13 (44)
T smart00659 3 YICGECGRENE 13 (44)
T ss_pred EECCCCCCEee
Confidence 57888888763
No 91
>cd02340 ZZ_NBR1_like Zinc finger, ZZ type. Zinc finger present in Drosophila ref(2)P, NBR1, Human sequestosome 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Drosophila ref(2)P appears to control the multiplication of sigma rhabdovirus. NBR1 (Next to BRCA1 gene 1 protein) interacts with fasciculation and elongation protein zeta-1 (FEZ1) and calcium and integrin binding protein (CIB), and may function in cell signalling pathways. Sequestosome 1 is a phosphotyrosine independent ligand for the Lck SH2 domain and binds noncovalently to ubiquitin via its UBA domain.
Probab=33.68 E-value=38 Score=18.12 Aligned_cols=11 Identities=27% Similarity=0.676 Sum_probs=6.0
Q ss_pred ccccccccccc
Q psy12215 49 YCAACTKVIPA 59 (155)
Q Consensus 49 ~C~~C~~~I~~ 59 (155)
.|..|+++|.+
T Consensus 2 ~Cd~C~~~i~G 12 (43)
T cd02340 2 ICDGCQGPIVG 12 (43)
T ss_pred CCCCCCCcCcC
Confidence 36666665543
No 92
>PF10764 Gin: Inhibitor of sigma-G Gin; InterPro: IPR019700 Gin allows sigma-F to delay late forespore transcription by preventing sigma-G to take over before the cell has reached a critical stage of development. Gin is also known as CsfB [].
Probab=33.27 E-value=35 Score=18.74 Aligned_cols=28 Identities=21% Similarity=0.363 Sum_probs=16.4
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccchhcc
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRL 43 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~ 43 (155)
+|..|+++..+ | ....|+..|.+|-.+.
T Consensus 1 ~CiiC~~~~~~-G---I~I~~~fIC~~CE~~i 28 (46)
T PF10764_consen 1 KCIICGKEKEE-G---IHIYGKFICSDCEKEI 28 (46)
T ss_pred CeEeCCCcCCC-C---EEEECeEehHHHHHHh
Confidence 46677887754 2 4445566666655443
No 93
>cd00472 Ribosomal_L24e_L24 Ribosomal protein L24e/L24 is a ribosomal protein found in eukaryotes (L24) and in archaea (L24e, distinct from archaeal L24). L24e/L24 is located on the surface of the large subunit, adjacent to proteins L14 and L3, and near the translation factor binding site. L24e/L24 appears to play a role in the kinetics of peptide synthesis, and may be involved in interactions between the large and small subunits, either directly or through other factors. In mouse, a deletion mutation in L24 has been identified as the cause for the belly spot and tail (Bst) mutation that results in disrupted pigmentation, somitogenesis and retinal cell fate determination. L24 may be an important protein in eukaryotic reproduction: in shrimp, L24 expression is elevated in the ovary, suggesting a role in oogenesis, and in Arabidopsis, L24 has been proposed to have a specific function in gynoecium development. No protein with sequence or structural homology to L24e/L24 has been identifi
Probab=33.25 E-value=42 Score=19.10 Aligned_cols=24 Identities=17% Similarity=0.484 Sum_probs=14.8
Q ss_pred ccccCCccccc-CCCeEEEeCCeee
Q psy12215 12 KCGCCDCRLGE-VGSTLYQKANLIL 35 (155)
Q Consensus 12 ~C~~C~~~l~~-~~~~~~~~~~~~~ 35 (155)
.|+-|+..+.+ .+..|+..||+++
T Consensus 5 ~C~f~g~~I~PG~G~~~Vr~Dgkv~ 29 (54)
T cd00472 5 KCSFCGYKIYPGHGKMYVRNDGKVF 29 (54)
T ss_pred EecCcCCeecCCCccEEEecCCCEE
Confidence 46777777754 3445666777654
No 94
>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=33.19 E-value=29 Score=18.41 Aligned_cols=10 Identities=30% Similarity=0.813 Sum_probs=5.4
Q ss_pred cccccccccc
Q psy12215 49 YCAACTKVIP 58 (155)
Q Consensus 49 ~C~~C~~~I~ 58 (155)
.|..|+..|.
T Consensus 21 vC~~CG~Vl~ 30 (43)
T PF08271_consen 21 VCPNCGLVLE 30 (43)
T ss_dssp EETTT-BBEE
T ss_pred ECCCCCCEee
Confidence 4666666664
No 95
>PRK12495 hypothetical protein; Provisional
Probab=33.11 E-value=21 Score=26.61 Aligned_cols=26 Identities=12% Similarity=0.194 Sum_probs=17.0
Q ss_pred ccCcccccCCcccccCCCeEEEeCCeeecccch
Q psy12215 8 EDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 40 (155)
Q Consensus 8 ~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~ 40 (155)
+.-+.|..|+.||. ...|..+|..|-
T Consensus 40 msa~hC~~CG~PIp-------a~pG~~~Cp~CQ 65 (226)
T PRK12495 40 MTNAHCDECGDPIF-------RHDGQEFCPTCQ 65 (226)
T ss_pred cchhhcccccCccc-------CCCCeeECCCCC
Confidence 34467888999983 336777665554
No 96
>PF04564 U-box: U-box domain; InterPro: IPR003613 Quality control of intracellular proteins is essential for cellular homeostasis. Molecular chaperones recognise and contribute to the refolding of misfolded or unfolded proteins, whereas the ubiquitin-proteasome system mediates the degradation of such abnormal proteins. Ubiquitin-protein ligases (E3s) determine the substrate specificity for ubiquitylation and have been classified into HECT and RING-finger families. More recently, however, U-box proteins, which contain a domain (the U box) of about 70 amino acids that is conserved from yeast to humans, have been identified as a new type of E3 []. Members of the U-box family of proteins constitute a class of ubiquitin-protein ligases (E3s) distinct from the HECT-type and RING finger-containing E3 families []. Using yeast two-hybrid technology, all mammalian U-box proteins have been reported to interact with molecular chaperones or co-chaperones, including Hsp90, Hsp70, DnaJc7, EKN1, CRN, and VCP. This suggests that the function of U box-type E3s is to mediate the degradation of unfolded or misfolded proteins in conjunction with molecular chaperones as receptors that recognise such abnormal proteins [, ]. Unlike the RING finger domain, IPR001841 from INTERPRO, that is stabilised by Zn2+ ions coordinated by the cysteines and a histidine, the U-box scaffold is probably stabilised by a system of salt-bridges and hydrogen bonds. The charged and polar residues that participate in this network of bonds are more strongly conserved in the U-box proteins than in classic RING fingers, which supports their role in maintaining the stability of the U box. Thus, the U box appears to have evolved from a RING finger domain by appropriation of a new set of residues required to stabilise its structure, concomitant with the loss of the original, metal-chelating residues [].; GO: 0004842 ubiquitin-protein ligase activity, 0016567 protein ubiquitination, 0000151 ubiquitin ligase complex; PDB: 1T1H_A 2C2L_D 2C2V_V 1WGM_A 2KR4_A 3L1Z_B 3L1X_A 2KRE_A 3M63_A 2QIZ_A ....
Probab=32.54 E-value=63 Score=19.23 Aligned_cols=48 Identities=8% Similarity=0.048 Sum_probs=31.2
Q ss_pred cCcccccCCcccccCCCeEEEeCCeeecccchhccccc-ccccccccccccc
Q psy12215 9 DCLKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGT-TGYCAACTKVIPA 59 (155)
Q Consensus 9 ~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~-~~~C~~C~~~I~~ 59 (155)
.=|.|..++..+. ......+|..|...+..+-+.. ...|..++.++..
T Consensus 3 ~~f~CpIt~~lM~---dPVi~~~G~tyer~~I~~~l~~~~~~~P~t~~~l~~ 51 (73)
T PF04564_consen 3 DEFLCPITGELMR---DPVILPSGHTYERSAIERWLEQNGGTDPFTRQPLSE 51 (73)
T ss_dssp GGGB-TTTSSB-S---SEEEETTSEEEEHHHHHHHHCTTSSB-TTT-SB-SG
T ss_pred cccCCcCcCcHhh---CceeCCcCCEEcHHHHHHHHHcCCCCCCCCCCcCCc
Confidence 4588888888774 3578889999998877665433 3378888888865
No 97
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 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 domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=32.34 E-value=26 Score=16.92 Aligned_cols=10 Identities=30% Similarity=0.677 Sum_probs=4.9
Q ss_pred cccccccccc
Q psy12215 49 YCAACTKVIP 58 (155)
Q Consensus 49 ~C~~C~~~I~ 58 (155)
+|.+|...|.
T Consensus 3 ~C~rC~~~~~ 12 (30)
T PF06827_consen 3 KCPRCWNYIE 12 (30)
T ss_dssp B-TTT--BBE
T ss_pred cCccCCCcce
Confidence 5777777774
No 98
>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=31.73 E-value=32 Score=16.16 Aligned_cols=9 Identities=22% Similarity=0.652 Sum_probs=4.1
Q ss_pred ccccccccc
Q psy12215 51 AACTKVIPA 59 (155)
Q Consensus 51 ~~C~~~I~~ 59 (155)
..|+..|.+
T Consensus 2 ~sC~~~i~~ 10 (24)
T PF07754_consen 2 TSCGRPIAP 10 (24)
T ss_pred ccCCCcccC
Confidence 344444443
No 99
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=31.62 E-value=26 Score=18.87 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=8.4
Q ss_pred cccccCCcccc
Q psy12215 11 LKCGCCDCRLG 21 (155)
Q Consensus 11 f~C~~C~~~l~ 21 (155)
|+|..|+..+.
T Consensus 4 y~C~~CG~~~~ 14 (46)
T PRK00398 4 YKCARCGREVE 14 (46)
T ss_pred EECCCCCCEEE
Confidence 67888888773
No 100
>PF04810 zf-Sec23_Sec24: Sec23/Sec24 zinc finger; InterPro: IPR006895 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. COPII (coat protein complex II)-coated vesicles carry proteins from the endoplasmic reticulum (ER) to the Golgi complex []. COPII-coated vesicles form on the ER by the stepwise recruitment of three cytosolic components: Sar1-GTP to initiate coat formation, Sec23/24 heterodimer to select SNARE and cargo molecules, and Sec13/31 to induce coat polymerisation and membrane deformation []. Sec23 p and Sec24p are structurally related, folding into five distinct domains: a beta-barrel, a zinc-finger, an alpha/beta trunk domain (IPR006896 from INTERPRO), an all-helical region (IPR006900 from INTERPRO), and a C-terminal gelsolin-like domain (IPR007123 from INTERPRO). This entry describes an approximately 55-residue Sec23/24 zinc-binding domain, which lies against the beta-barrel at the periphery of the complex. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0006886 intracellular protein transport, 0006888 ER to Golgi vesicle-mediated transport, 0030127 COPII vesicle coat; PDB: 3EFO_B 3EG9_B 3EGD_A 2YRC_A 2NUP_A 2YRD_A 3EGX_A 2NUT_A 3EH1_A 1PD0_A ....
Probab=31.41 E-value=40 Score=17.67 Aligned_cols=29 Identities=17% Similarity=0.583 Sum_probs=12.5
Q ss_pred cccccccccccCceEEeccCccccccccccccCCc
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNH 83 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~ 83 (155)
+|..|+..|.+- ..+...++.| .|..|+.
T Consensus 4 rC~~C~aylNp~-~~~~~~~~~w-----~C~~C~~ 32 (40)
T PF04810_consen 4 RCRRCRAYLNPF-CQFDDGGKTW-----ICNFCGT 32 (40)
T ss_dssp B-TTT--BS-TT-SEEETTTTEE-----EETTT--
T ss_pred ccCCCCCEECCc-ceEcCCCCEE-----ECcCCCC
Confidence 677787777662 2333434443 6666654
No 101
>PF01286 XPA_N: XPA protein N-terminal; InterPro: IPR022652 Xeroderma pigmentosum (XP) [] is a human autosomal recessive disease, characterised by a high incidence of sunlight-induced skin cancer. Skin cells of individual's with this condition are hypersensitive to ultraviolet light, due to defects in the incision step of DNA excision repair. There are a minimum of seven genetic complementation groups involved in this pathway: XP-A to XP-G. XP-A is the most severe form of the disease and is due to defects in a 30 kDa nuclear protein called XPA (or XPAC) []. The sequence of the XPA protein is conserved from higher eukaryotes [] to yeast (gene RAD14) []. XPA is a hydrophilic protein of 247 to 296 amino-acid residues which has a C4-type zinc finger motif in its central section. This entry contains the zinc-finger containing region in the XPA protein. It is found N-terminal to PF05181 from PFAM ; PDB: 1D4U_A 1XPA_A.
Probab=31.38 E-value=16 Score=18.78 Aligned_cols=10 Identities=30% Similarity=0.607 Sum_probs=4.5
Q ss_pred ccccCCcccc
Q psy12215 12 KCGCCDCRLG 21 (155)
Q Consensus 12 ~C~~C~~~l~ 21 (155)
.|..|++++.
T Consensus 5 ~C~eC~~~f~ 14 (34)
T PF01286_consen 5 KCDECGKPFM 14 (34)
T ss_dssp E-TTT--EES
T ss_pred hHhHhCCHHH
Confidence 4667777773
No 102
>cd02335 ZZ_ADA2 Zinc finger, ZZ type. Zinc finger present in ADA2, a putative transcriptional adaptor, and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=30.24 E-value=49 Score=18.12 Aligned_cols=10 Identities=20% Similarity=0.245 Sum_probs=6.5
Q ss_pred eecHHhHHhh
Q psy12215 98 ILCEYDYEER 107 (155)
Q Consensus 98 ~~C~~c~~~~ 107 (155)
-+|..||...
T Consensus 25 dLC~~Cf~~g 34 (49)
T cd02335 25 DLCLECFSAG 34 (49)
T ss_pred chhHHhhhCc
Confidence 4677777653
No 103
>PRK14891 50S ribosomal protein L24e/unknown domain fusion protein; Provisional
Probab=30.08 E-value=45 Score=22.65 Aligned_cols=24 Identities=17% Similarity=0.400 Sum_probs=14.5
Q ss_pred ccccCCccccc-CCCeEEEeCCeee
Q psy12215 12 KCGCCDCRLGE-VGSTLYQKANLIL 35 (155)
Q Consensus 12 ~C~~C~~~l~~-~~~~~~~~~~~~~ 35 (155)
+|+-|+.+|.+ .|..|+..||++|
T Consensus 6 ~CsFcG~kIyPG~G~~fVR~DGkvf 30 (131)
T PRK14891 6 TCDYTGEEIEPGTGTMFVRKDGTVL 30 (131)
T ss_pred eecCcCCcccCCCCcEEEecCCCEE
Confidence 47777777753 3445556666654
No 104
>PF10083 DUF2321: Uncharacterized protein conserved in bacteria (DUF2321); InterPro: IPR016891 This entry is represented by Bacteriophage 'Lactobacillus prophage Lj928', Orf-Ljo1454. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=30.05 E-value=5.7 Score=27.81 Aligned_cols=34 Identities=15% Similarity=0.138 Sum_probs=20.4
Q ss_pred eeecHHhHHhhhcccCCCeeeecCCeecchhhHHHHHHH
Q psy12215 97 KILCEYDYEERQVFCVGDRFYLCDNKILCEYDYEERQVF 135 (155)
Q Consensus 97 ~~~C~~c~~~~~~~~~~~~c~~c~~~i~c~~~~~~~~~~ 135 (155)
.-||..|=.+.. ..|..|+.+|.+..+.++.+.+
T Consensus 28 ~~fC~kCG~~tI-----~~Cp~C~~~IrG~y~v~gv~~~ 61 (158)
T PF10083_consen 28 EKFCSKCGAKTI-----TSCPNCSTPIRGDYHVEGVFGL 61 (158)
T ss_pred HHHHHHhhHHHH-----HHCcCCCCCCCCceecCCeeee
Confidence 346666655543 5666677777666665555555
No 105
>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=29.94 E-value=20 Score=15.79 Aligned_cols=10 Identities=30% Similarity=0.753 Sum_probs=6.1
Q ss_pred cccccCCccc
Q psy12215 11 LKCGCCDCRL 20 (155)
Q Consensus 11 f~C~~C~~~l 20 (155)
|+|..|++.+
T Consensus 1 y~C~~C~~~f 10 (23)
T PF00096_consen 1 YKCPICGKSF 10 (23)
T ss_dssp EEETTTTEEE
T ss_pred CCCCCCCCcc
Confidence 4566666655
No 106
>PRK05580 primosome assembly protein PriA; Validated
Probab=29.60 E-value=43 Score=29.20 Aligned_cols=39 Identities=23% Similarity=0.397 Sum_probs=25.9
Q ss_pred ccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccc
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKV 56 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~ 56 (155)
+|..|+.+| +|....+.+.|..|-.....+ ..|..|+..
T Consensus 392 ~C~~C~~~l-----~~h~~~~~l~Ch~Cg~~~~~~-~~Cp~Cg~~ 430 (679)
T PRK05580 392 ECPHCDASL-----TLHRFQRRLRCHHCGYQEPIP-KACPECGST 430 (679)
T ss_pred CCCCCCCce-----eEECCCCeEECCCCcCCCCCC-CCCCCCcCC
Confidence 445555555 455667788899998775322 279999775
No 107
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=28.66 E-value=27 Score=19.37 Aligned_cols=24 Identities=25% Similarity=0.297 Sum_probs=16.4
Q ss_pred Ceeecccchhcccccccccccccc
Q psy12215 32 NLILCKRDYLRLFGTTGYCAACTK 55 (155)
Q Consensus 32 ~~~~C~~c~~~~~~~~~~C~~C~~ 55 (155)
++..|-.||.++...+..|..|+-
T Consensus 13 ~k~ICrkC~ARnp~~A~~CRKCg~ 36 (48)
T PRK04136 13 NKKICMRCNARNPWRATKCRKCGY 36 (48)
T ss_pred cccchhcccCCCCccccccccCCC
Confidence 355688888877655557877764
No 108
>TIGR00570 cdk7 CDK-activating kinase assembly factor MAT1. All proteins in this family for which functions are known are cyclin dependent protein kinases that are components of TFIIH, a complex that is involved in nucleotide excision repair and transcription initiation. Also known as MAT1 (menage a trois 1). This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.63 E-value=52 Score=25.86 Aligned_cols=28 Identities=21% Similarity=0.203 Sum_probs=16.0
Q ss_pred CeeecHHhHHhhhcccCCCeeeecCCeec
Q psy12215 96 NKILCEYDYEERQVFCVGDRFYLCDNKIL 124 (155)
Q Consensus 96 ~~~~C~~c~~~~~~~~~~~~c~~c~~~i~ 124 (155)
|..+|..|....+... ...|..|...+.
T Consensus 27 GH~~C~sCv~~l~~~~-~~~CP~C~~~lr 54 (309)
T TIGR00570 27 GHTLCESCVDLLFVRG-SGSCPECDTPLR 54 (309)
T ss_pred CCcccHHHHHHHhcCC-CCCCCCCCCccc
Confidence 6667777776654221 225666665543
No 109
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=28.15 E-value=56 Score=23.85 Aligned_cols=48 Identities=13% Similarity=0.212 Sum_probs=28.5
Q ss_pred ccccccCCcccccCCeEEeeCCeeecHHhHHhhhc--------------ccCCCeeeecCCeec
Q psy12215 75 CFACQQCNHRFCVGDRFYLCDNKILCEYDYEERQV--------------FCVGDRFYLCDNKIL 124 (155)
Q Consensus 75 Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~~~--------------~~~~~~c~~c~~~i~ 124 (155)
-|.|.+|...+ .......=|..||..|..+... ......|..|...|.
T Consensus 18 ~~~CpICld~~--~dPVvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 18 DFDCNICLDQV--RDPVVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred ccCCccCCCcC--CCcEEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCC
Confidence 36677777665 3334444577888888754321 112357888877775
No 110
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=27.97 E-value=4.5 Score=22.75 Aligned_cols=44 Identities=16% Similarity=0.347 Sum_probs=24.1
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhcccccccccccccccc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVI 57 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I 57 (155)
|+|..|+...+-.+..=-+.=|+--|..|+...+-. |..|+..|
T Consensus 8 y~CDLCn~~~p~~~LRQCvlCGRWaC~sCW~deYY~---CksC~Gii 51 (57)
T PF14445_consen 8 YSCDLCNSSHPISELRQCVLCGRWACNSCWQDEYYT---CKSCNGII 51 (57)
T ss_pred HhHHhhcccCcHHHHHHHhhhchhhhhhhhhhhHhH---HHhhhchh
Confidence 567777664432221111233445567777766653 77777666
No 111
>cd02341 ZZ_ZZZ3 Zinc finger, ZZ type. Zinc finger present in ZZZ3 (ZZ finger containing 3) and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding.
Probab=27.95 E-value=64 Score=17.80 Aligned_cols=10 Identities=20% Similarity=0.079 Sum_probs=6.5
Q ss_pred eeecHHhHHh
Q psy12215 97 KILCEYDYEE 106 (155)
Q Consensus 97 ~~~C~~c~~~ 106 (155)
--+|..||..
T Consensus 26 ~DlC~~C~~~ 35 (48)
T cd02341 26 FDLCQDCVVK 35 (48)
T ss_pred CccCHHHHhC
Confidence 3467777764
No 112
>KOG3002|consensus
Probab=27.49 E-value=40 Score=26.33 Aligned_cols=43 Identities=19% Similarity=0.364 Sum_probs=33.4
Q ss_pred cccccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccc
Q psy12215 11 LKCGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 58 (155)
Q Consensus 11 f~C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~ 58 (155)
+.|-.|.-.|. ...|.=.+|.+.|..|-.++.. +|+.|..+|.
T Consensus 49 leCPvC~~~l~--~Pi~QC~nGHlaCssC~~~~~~---~CP~Cr~~~g 91 (299)
T KOG3002|consen 49 LDCPVCFNPLS--PPIFQCDNGHLACSSCRTKVSN---KCPTCRLPIG 91 (299)
T ss_pred ccCchhhccCc--ccceecCCCcEehhhhhhhhcc---cCCccccccc
Confidence 56777777774 3457778899999999976655 6999999886
No 113
>PRK11595 DNA utilization protein GntX; Provisional
Probab=27.43 E-value=37 Score=25.14 Aligned_cols=38 Identities=18% Similarity=0.273 Sum_probs=23.2
Q ss_pred cccCCcccccCCCeEEEeCCeeecccchhccccccccccccccccc
Q psy12215 13 CGCCDCRLGEVGSTLYQKANLILCKRDYLRLFGTTGYCAACTKVIP 58 (155)
Q Consensus 13 C~~C~~~l~~~~~~~~~~~~~~~C~~c~~~~~~~~~~C~~C~~~I~ 58 (155)
|..|+.++... ...+|..|..........|..|+.++.
T Consensus 8 C~~C~~~~~~~--------~~~lC~~C~~~l~~~~~~C~~Cg~~~~ 45 (227)
T PRK11595 8 CWLCRMPLALS--------HWGICSVCSRALRTLKTCCPQCGLPAT 45 (227)
T ss_pred CccCCCccCCC--------CCcccHHHHhhCCcccCcCccCCCcCC
Confidence 56667777321 124799887765322227999987653
No 114
>cd02338 ZZ_PCMF_like Zinc finger, ZZ type. Zinc finger present in potassium channel modulatory factor (PCMF) 1 and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Human potassium channel modulatory factor 1 or FIGC has been shown to possess intrinsic E3 ubiquitin ligase activity and to promote ubiquitination.
Probab=27.19 E-value=56 Score=17.95 Aligned_cols=11 Identities=27% Similarity=0.404 Sum_probs=7.2
Q ss_pred eeecHHhHHhh
Q psy12215 97 KILCEYDYEER 107 (155)
Q Consensus 97 ~~~C~~c~~~~ 107 (155)
--+|..||...
T Consensus 24 ~dlC~~Cf~~~ 34 (49)
T cd02338 24 YDLCADCYDSG 34 (49)
T ss_pred CccchhHHhCC
Confidence 34788887754
No 115
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=26.97 E-value=21 Score=18.35 Aligned_cols=7 Identities=43% Similarity=1.450 Sum_probs=3.1
Q ss_pred ccccCCc
Q psy12215 77 ACQQCNH 83 (155)
Q Consensus 77 ~C~~C~~ 83 (155)
+|..|+.
T Consensus 27 ~C~~C~~ 33 (36)
T PF13717_consen 27 RCSKCGH 33 (36)
T ss_pred ECCCCCC
Confidence 4444443
No 116
>TIGR02098 MJ0042_CXXC MJ0042 family finger-like domain. This domain contains a CXXCX(19)CXXC motif suggestive of both zinc fingers and thioredoxin, usually found at the N-terminus of prokaryotic proteins. One partially characterized gene, agmX, is among a large set in Myxococcus whose interruption affects adventurous gliding motility.
Probab=26.71 E-value=20 Score=18.31 Aligned_cols=9 Identities=33% Similarity=0.829 Sum_probs=5.6
Q ss_pred ccccccccc
Q psy12215 49 YCAACTKVI 57 (155)
Q Consensus 49 ~C~~C~~~I 57 (155)
+|+.|+..+
T Consensus 27 ~C~~C~~~~ 35 (38)
T TIGR02098 27 RCGKCGHVW 35 (38)
T ss_pred ECCCCCCEE
Confidence 566666655
No 117
>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=26.65 E-value=24 Score=18.76 Aligned_cols=11 Identities=18% Similarity=0.676 Sum_probs=7.9
Q ss_pred cccccCCcccc
Q psy12215 11 LKCGCCDCRLG 21 (155)
Q Consensus 11 f~C~~C~~~l~ 21 (155)
|+|..|+..+.
T Consensus 6 y~C~~Cg~~fe 16 (42)
T PF09723_consen 6 YRCEECGHEFE 16 (42)
T ss_pred EEeCCCCCEEE
Confidence 67888877663
No 118
>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=26.44 E-value=30 Score=14.88 Aligned_cols=10 Identities=20% Similarity=0.763 Sum_probs=4.9
Q ss_pred cccccCCccc
Q psy12215 11 LKCGCCDCRL 20 (155)
Q Consensus 11 f~C~~C~~~l 20 (155)
|.|..|+..+
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 4566666655
No 119
>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=25.66 E-value=26 Score=18.03 Aligned_cols=10 Identities=20% Similarity=0.743 Sum_probs=7.3
Q ss_pred cccccCCccc
Q psy12215 11 LKCGCCDCRL 20 (155)
Q Consensus 11 f~C~~C~~~l 20 (155)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (41)
T smart00834 6 YRCEDCGHTF 15 (41)
T ss_pred EEcCCCCCEE
Confidence 5777887766
No 120
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=25.57 E-value=68 Score=22.41 Aligned_cols=28 Identities=14% Similarity=0.274 Sum_probs=19.0
Q ss_pred ccccCCcccccCCCeEEEeCCee--ecccch
Q psy12215 12 KCGCCDCRLGEVGSTLYQKANLI--LCKRDY 40 (155)
Q Consensus 12 ~C~~C~~~l~~~~~~~~~~~~~~--~C~~c~ 40 (155)
.|..||+++...+ .-+..+|.. .|.+|+
T Consensus 2 ~CEiCG~~i~~~~-~~v~iega~l~vC~~C~ 31 (154)
T TIGR00270 2 NCEICGRKIKGKG-FKIVIEGSEMTVCGECR 31 (154)
T ss_pred ccccCCCccCCCC-eEEEEcCeEEehhhhHH
Confidence 3899999995322 344667764 488888
No 121
>KOG2893|consensus
Probab=24.89 E-value=29 Score=26.28 Aligned_cols=48 Identities=19% Similarity=0.452 Sum_probs=29.2
Q ss_pred cccccccccccCceEEeccCccccccccccccCCcccccCCeEEeeCCeeecHHhHH
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHLECFACQQCNHRFCVGDRFYLCDNKILCEYDYE 105 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~~Cf~C~~C~~~l~~~~~~~~~~~~~~C~~c~~ 105 (155)
.|.-|++.+.+ |.++.... -..+|+|.+|.+.| |..-+-.+.|..-..
T Consensus 12 wcwycnrefdd-ekiliqhq---kakhfkchichkkl-----~sgpglsihcmqvhk 59 (341)
T KOG2893|consen 12 WCWYCNREFDD-EKILIQHQ---KAKHFKCHICHKKL-----FSGPGLSIHCMQVHK 59 (341)
T ss_pred eeeecccccch-hhhhhhhh---hhccceeeeehhhh-----ccCCCceeehhhhhh
Confidence 58888887754 44332212 24569999999988 333344567755443
No 122
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=23.48 E-value=14 Score=20.87 Aligned_cols=11 Identities=27% Similarity=0.902 Sum_probs=7.3
Q ss_pred ccccccccccc
Q psy12215 49 YCAACTKVIPA 59 (155)
Q Consensus 49 ~C~~C~~~I~~ 59 (155)
+|.+|...|.+
T Consensus 24 ~C~gC~~~l~~ 34 (56)
T PF02591_consen 24 TCSGCHMELPP 34 (56)
T ss_pred ccCCCCEEcCH
Confidence 57777776665
No 123
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=23.37 E-value=63 Score=16.98 Aligned_cols=17 Identities=12% Similarity=0.090 Sum_probs=11.3
Q ss_pred hcCCCCchHHHhhhhhc
Q psy12215 138 IAYNPSSLAHLRRQVTL 154 (155)
Q Consensus 138 ~~~hp~~~~~~~~~~~~ 154 (155)
...||.|+...++.|+-
T Consensus 5 h~~nPYPs~~ek~~L~~ 21 (40)
T PF05920_consen 5 HLHNPYPSKEEKEELAK 21 (40)
T ss_dssp TTTSGS--HHHHHHHHH
T ss_pred HCCCCCCCHHHHHHHHH
Confidence 45679999988888863
No 124
>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=23.33 E-value=32 Score=18.88 Aligned_cols=10 Identities=30% Similarity=1.019 Sum_probs=7.4
Q ss_pred cccccCCccc
Q psy12215 11 LKCGCCDCRL 20 (155)
Q Consensus 11 f~C~~C~~~l 20 (155)
|+|..|+..+
T Consensus 6 y~C~~Cg~~f 15 (52)
T TIGR02605 6 YRCTACGHRF 15 (52)
T ss_pred EEeCCCCCEe
Confidence 5788887766
No 125
>PF00320 GATA: GATA zinc finger; InterPro: IPR000679 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 GATA-type zinc fingers (Znf). A number of transcription factors (including erythroid-specific transcription factor and nitrogen regulatory proteins), specifically bind the DNA sequence (A/T)GATA(A/G) [] in the regulatory regions of genes. They are consequently termed GATA-binding transcription factors. The interactions occur via highly-conserved Znf domains in which the zinc ion is coordinated by 4 cysteine residues [, ]. NMR studies have shown the core of the Znf to comprise 2 irregular anti-parallel beta-sheets and an alpha-helix, followed by a long loop to the C-terminal end of the finger. The N-terminal part, which includes the helix, is similar in structure, but not sequence, to the N-terminal zinc module of the glucocorticoid receptor DNA-binding domain. The helix and the loop connecting the 2 beta-sheets interact with the major groove of the DNA, while the C-terminal tail wraps around into the minor groove. It is this tail that is the essential determinant of specific binding. Interactions between the Znf and DNA are mainly hydrophobic, explaining the preponderance of thymines in the binding site; a large number of interactions with the phosphate backbone have also been observed []. Two GATA zinc fingers are found in the GATA transcription factors. However there are several proteins which only contains a single copy of the domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0008270 zinc ion binding, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 3GAT_A 2GAT_A 1GAU_A 1GAT_A 1Y0J_A 1GNF_A 2L6Z_A 2L6Y_A 3DFV_D 3DFX_B ....
Probab=22.65 E-value=79 Score=16.08 Aligned_cols=28 Identities=18% Similarity=0.158 Sum_probs=14.6
Q ss_pred cccCCcccccCCCeEEEeCCee-ecccchhc
Q psy12215 13 CGCCDCRLGEVGSTLYQKANLI-LCKRDYLR 42 (155)
Q Consensus 13 C~~C~~~l~~~~~~~~~~~~~~-~C~~c~~~ 42 (155)
|+.|+..- ....-...+|.. +|..|...
T Consensus 1 C~~C~tt~--t~~WR~~~~g~~~LCn~Cg~~ 29 (36)
T PF00320_consen 1 CSNCGTTE--TPQWRRGPNGNRTLCNACGLY 29 (36)
T ss_dssp -TTT--ST---SSEEEETTSEE-EEHHHHHH
T ss_pred CcCCcCCC--CchhhcCCCCCCHHHHHHHHH
Confidence 45555544 333444556776 88888754
No 126
>PRK00085 recO DNA repair protein RecO; Reviewed
Probab=22.52 E-value=51 Score=24.41 Aligned_cols=31 Identities=16% Similarity=0.188 Sum_probs=22.8
Q ss_pred ccCcccccCCcccccCCCeEEEeCCeeecccch
Q psy12215 8 EDCLKCGCCDCRLGEVGSTLYQKANLILCKRDY 40 (155)
Q Consensus 8 ~~Cf~C~~C~~~l~~~~~~~~~~~~~~~C~~c~ 40 (155)
+.=..|..|+++++ ...|...+|-++|..|.
T Consensus 147 p~l~~C~~Cg~~~~--~~~f~~~~gg~~c~~c~ 177 (247)
T PRK00085 147 LDLDHCAVCGAPGD--HRYFSPKEGGAVCSECG 177 (247)
T ss_pred cchhhHhcCCCCCC--ceEEecccCCccccccc
Confidence 34457899999984 34566788888888875
No 127
>COG4416 Com Mu-like prophage protein Com [General function prediction only]
Probab=21.30 E-value=27 Score=19.90 Aligned_cols=14 Identities=29% Similarity=0.733 Sum_probs=10.7
Q ss_pred cccccCCcccccCC
Q psy12215 11 LKCGCCDCRLGEVG 24 (155)
Q Consensus 11 f~C~~C~~~l~~~~ 24 (155)
.+|..|++.|.+.+
T Consensus 5 iRC~~CnKlLa~a~ 18 (60)
T COG4416 5 IRCAKCNKLLAEAE 18 (60)
T ss_pred eehHHHhHHHHhcc
Confidence 57889999996543
No 128
>COG0266 Nei Formamidopyrimidine-DNA glycosylase [DNA replication, recombination, and repair]
Probab=21.10 E-value=60 Score=25.06 Aligned_cols=25 Identities=20% Similarity=0.535 Sum_probs=16.4
Q ss_pred cccccccccccCceEEeccCccccccc
Q psy12215 49 YCAACTKVIPAFEMVMRAKNNVYHLEC 75 (155)
Q Consensus 49 ~C~~C~~~I~~~~~~~~~~~~~~H~~C 75 (155)
.|..|+.+|.- ..+.-++..|-|.|
T Consensus 247 pC~~CGt~I~k--~~~~gR~t~~CP~C 271 (273)
T COG0266 247 PCRRCGTPIEK--IKLGGRSTFYCPVC 271 (273)
T ss_pred CCCccCCEeEE--EEEcCCcCEeCCCC
Confidence 59999999953 44555556565544
No 129
>KOG4443|consensus
Probab=21.00 E-value=43 Score=29.03 Aligned_cols=19 Identities=21% Similarity=0.606 Sum_probs=15.3
Q ss_pred cCccccccccccccCCccc
Q psy12215 67 KNNVYHLECFACQQCNHRF 85 (155)
Q Consensus 67 ~~~~~H~~Cf~C~~C~~~l 85 (155)
.+..+-++|++|..|+..+
T Consensus 107 sg~~~ckk~~~c~qc~~~l 125 (694)
T KOG4443|consen 107 SGPWLCKKCTRCRQCDSTL 125 (694)
T ss_pred CcccccHHHHhhhhccccc
Confidence 3566678899999999888
No 130
>PF10080 DUF2318: Predicted membrane protein (DUF2318); InterPro: IPR018758 This domain of unknown function is found in hypothetical bacterial membrane proteins with no known function.
Probab=20.99 E-value=88 Score=20.30 Aligned_cols=17 Identities=29% Similarity=0.600 Sum_probs=11.7
Q ss_pred eEEEeCCeeecccchhc
Q psy12215 26 TLYQKANLILCKRDYLR 42 (155)
Q Consensus 26 ~~~~~~~~~~C~~c~~~ 42 (155)
-|+..++.+.|..|-.+
T Consensus 45 GY~q~g~~lvC~~C~~~ 61 (102)
T PF10080_consen 45 GYYQEGDQLVCKNCGVR 61 (102)
T ss_pred ceEEECCEEEEecCCCE
Confidence 47788888876666544
No 131
>PF13912 zf-C2H2_6: C2H2-type zinc finger; PDB: 1JN7_A 1FU9_A 2L1O_A 1NJQ_A 2EN8_A 2EMM_A 1FV5_A 1Y0J_B 2L6Z_B.
Probab=20.96 E-value=42 Score=15.38 Aligned_cols=10 Identities=20% Similarity=0.747 Sum_probs=6.3
Q ss_pred cccccCCccc
Q psy12215 11 LKCGCCDCRL 20 (155)
Q Consensus 11 f~C~~C~~~l 20 (155)
|+|..|++.+
T Consensus 2 ~~C~~C~~~F 11 (27)
T PF13912_consen 2 FECDECGKTF 11 (27)
T ss_dssp EEETTTTEEE
T ss_pred CCCCccCCcc
Confidence 4566666655
No 132
>PF02428 Prot_inhib_II: Potato type II proteinase inhibitor family; InterPro: IPR003465 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. Members of the Pin2 family are proteinase inhibitors that belong to MEROPS inhibitor family I20, clan IA and are restricted to plants. They inhibit serine peptidases belonging to MEROPS peptidase family S1 [] (IPR001254 from INTERPRO). They have a multidomain structure [], which permits circular permutation of the sequences. It was been shown that some naturally occurring Pin2 proteins, have an `ancestral' circularly permuted structure []. Circular permutation/ rearrangements of sequences has also been observed between species, such as favin from Vicia faba and the lectin concanavalin A from Canavalia ensiformis [] or amongst members of the plant aspartyl proteinases and human lung surfactant proteins []. The Pin2 family of proteinase inhibitors are present in seeds, leaves and other organs. Perhaps the best known representatives are the wound-induced proteinase inhibitors [, ], which contain up to eight sequence-repeats (the `IP repeats'). The sequence of the IP repeats is quite variable, only the cysteines constituting the four disulphide bridges and a single proline residue are conserved throughout all the known repeat sequences. The structure of the proteinase inhibitor complex is known [].; GO: 0004867 serine-type endopeptidase inhibitor activity; PDB: 1PJU_C 1OYV_I 1QH2_B 1FYB_A 1CE3_A 2JZM_A 1YTP_A 2JYY_A 1TIH_A 4SGB_I ....
Probab=20.90 E-value=1.2e+02 Score=17.15 Aligned_cols=15 Identities=20% Similarity=0.631 Sum_probs=12.2
Q ss_pred CCCeEEEeCCeeecc
Q psy12215 23 VGSTLYQKANLILCK 37 (155)
Q Consensus 23 ~~~~~~~~~~~~~C~ 37 (155)
.+-.||..||...|+
T Consensus 37 KGC~yy~~dGtfiCe 51 (52)
T PF02428_consen 37 KGCNYYSADGTFICE 51 (52)
T ss_dssp TTSEEEETTTEEEEE
T ss_pred cccEEECCCCcEEeC
Confidence 567889999988886
No 133
>cd02345 ZZ_dah Zinc finger, ZZ type. Zinc finger present in Drosophila dah and related proteins. The ZZ motif coordinates two zinc ions and most likely participates in ligand binding or molecular scaffolding. Dah (discontinuous actin hexagon) is a membrane associated protein essential for cortical furrow formation in Drosophila.
Probab=20.67 E-value=75 Score=17.47 Aligned_cols=10 Identities=30% Similarity=0.388 Sum_probs=6.5
Q ss_pred eecHHhHHhh
Q psy12215 98 ILCEYDYEER 107 (155)
Q Consensus 98 ~~C~~c~~~~ 107 (155)
-+|..||...
T Consensus 25 dLC~~Cf~~~ 34 (49)
T cd02345 25 SLCLGCYTKG 34 (49)
T ss_pred CchHHHHhCC
Confidence 4677777643
No 134
>PF01246 Ribosomal_L24e: Ribosomal protein L24e; InterPro: IPR000988 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 [, ]. A number of eukaryotic and archaeabacterial ribosomal proteins can be grouped on the basis of sequence similarities. One of these families [] consists of mammalian ribosomal protein L24; yeast ribosomal protein L30A/B (Rp29) (YL21); Kluyveromyces lactis ribosomal protein L30; Arabidopsis thaliana ribosomal protein L24 homolog; Haloarcula marismortui ribosomal protein HL21/HL22; and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ1201. These proteins have 60 to 160 amino-acid residues. This entry represents proteins related to the L24e ribosomal proteins.; PDB: 2ZKR_u 1VQ9_U 1VQL_U 1KD1_V 1VQP_U 3CCM_U 3CD6_U 3CCL_U 3CCR_U 1Q86_V ....
Probab=20.64 E-value=68 Score=19.38 Aligned_cols=24 Identities=8% Similarity=0.198 Sum_probs=11.4
Q ss_pred ccccCCcccccCC-CeEEEeCCeee
Q psy12215 12 KCGCCDCRLGEVG-STLYQKANLIL 35 (155)
Q Consensus 12 ~C~~C~~~l~~~~-~~~~~~~~~~~ 35 (155)
.|+-|+..+.++. ..|+..||+++
T Consensus 5 ~C~Fsg~~I~PG~G~~~Vr~DG~v~ 29 (71)
T PF01246_consen 5 KCSFSGYKIYPGHGKMYVRNDGKVF 29 (71)
T ss_dssp E-TTT-SEE-SSSSEEEE-TTS-EE
T ss_pred EecccCCccCCCCCeEEEecCCCeE
Confidence 5777888776533 34445677654
No 135
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=20.36 E-value=81 Score=20.33 Aligned_cols=31 Identities=26% Similarity=0.518 Sum_probs=23.5
Q ss_pred ccccCCcccccCCeEEeeCCeeecHHhHHhh
Q psy12215 77 ACQQCNHRFCVGDRFYLCDNKILCEYDYEER 107 (155)
Q Consensus 77 ~C~~C~~~l~~~~~~~~~~~~~~C~~c~~~~ 107 (155)
.|+.|++..-.+..+.+.-.+-+|..|..+.
T Consensus 51 ~CS~C~~~VC~~~~CSlFYtkrFC~pC~~~~ 81 (97)
T PF10170_consen 51 PCSICGKPVCVGQDCSLFYTKRFCLPCVKRN 81 (97)
T ss_pred cccccCCceEcCCCccEEeeCceeHHHHHHH
Confidence 5888888886666776667778898887654
No 136
>KOG3476|consensus
Probab=20.09 E-value=24 Score=22.22 Aligned_cols=26 Identities=27% Similarity=0.492 Sum_probs=19.3
Q ss_pred eCCeeecccchhcccccccccccccccccc
Q psy12215 30 KANLILCKRDYLRLFGTTGYCAACTKVIPA 59 (155)
Q Consensus 30 ~~~~~~C~~c~~~~~~~~~~C~~C~~~I~~ 59 (155)
..|.-||..|..++ +.|+-|++.|..
T Consensus 66 Q~GshYC~tCAY~K----giCAMCGKki~n 91 (100)
T KOG3476|consen 66 QPGSHYCQTCAYKK----GICAMCGKKILN 91 (100)
T ss_pred CCcchhHhHhhhhh----hHHHHhhhHhhc
Confidence 34567898887764 369999998865
No 137
>PF07649 C1_3: C1-like domain; InterPro: IPR011424 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in IPR002219 from INTERPRO. C1 domains are protein kinase C-like zinc finger structures. Diacylglycerol (DAG) kinases (DGKs) have a two or three commonly conserved cysteine-rich C1 domains []. DGKs modulate the balance between the two signaling lipids, DAG and phosphatidic acid (PA), by phosphorylating DAG to yield PA []. The PKD (protein kinase D) family are novel DAG receptors. They have twin C1 domains, designated C1a and C1b, which bind DAG or phorbol esters. Individual C1 domains differ in ligand-binding activity and selectivity []. ; GO: 0047134 protein-disulfide reductase activity, 0055114 oxidation-reduction process; PDB: 1V5N_A.
Probab=20.05 E-value=70 Score=15.38 Aligned_cols=11 Identities=18% Similarity=0.836 Sum_probs=3.2
Q ss_pred cccccCCcccc
Q psy12215 11 LKCGCCDCRLG 21 (155)
Q Consensus 11 f~C~~C~~~l~ 21 (155)
|+|..|++++.
T Consensus 1 ~~C~~C~~~~~ 11 (30)
T PF07649_consen 1 FRCDACGKPID 11 (30)
T ss_dssp ---TTTS----
T ss_pred CcCCcCCCcCC
Confidence 56788887773
Done!