Query 019595
Match_columns 338
No_of_seqs 377 out of 1542
Neff 5.8
Searched_HMMs 46136
Date Fri Mar 29 03:01:07 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019595.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019595hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1843 Uncharacterized conser 100.0 1.4E-40 3E-45 323.3 4.9 289 29-336 57-346 (473)
2 COG2930 Uncharacterized conser 99.9 3.8E-22 8.3E-27 178.7 4.9 98 240-337 10-109 (227)
3 PF01363 FYVE: FYVE zinc finge 99.8 6.1E-20 1.3E-24 140.0 1.3 67 142-209 1-68 (69)
4 smart00064 FYVE Protein presen 99.7 2.2E-17 4.8E-22 125.5 3.2 66 142-209 2-67 (68)
5 KOG1729 FYVE finger containing 99.6 2.1E-16 4.6E-21 151.4 0.1 71 137-210 155-226 (288)
6 PTZ00303 phosphatidylinositol 99.6 1.4E-15 3E-20 157.9 4.6 72 138-209 447-530 (1374)
7 KOG1818 Membrane trafficking a 99.5 2.9E-15 6.3E-20 154.8 3.7 84 123-211 137-224 (634)
8 KOG1819 FYVE finger-containing 99.5 6.2E-15 1.3E-19 147.8 2.6 70 139-210 890-964 (990)
9 cd00065 FYVE FYVE domain; Zinc 99.4 1.5E-13 3.3E-18 100.6 2.9 55 150-206 2-56 (57)
10 KOG1843 Uncharacterized conser 99.2 2.3E-12 5E-17 126.8 0.6 97 241-337 4-101 (473)
11 KOG1842 FYVE finger-containing 99.2 1.8E-12 3.9E-17 128.6 -2.7 74 135-209 165-259 (505)
12 KOG1841 Smad anchor for recept 99.1 5.1E-11 1.1E-15 128.4 3.3 65 137-204 544-608 (1287)
13 KOG1409 Uncharacterized conser 98.8 7.8E-10 1.7E-14 107.5 0.1 94 116-213 249-354 (404)
14 KOG4424 Predicted Rho/Rac guan 98.6 9.6E-09 2.1E-13 105.3 -0.1 113 142-260 409-538 (623)
15 KOG1811 Predicted Zn2+-binding 97.9 1.2E-06 2.6E-11 90.8 -2.1 69 137-207 309-382 (1141)
16 KOG0230 Phosphatidylinositol-4 97.1 0.00027 5.9E-09 79.6 3.4 51 149-212 4-54 (1598)
17 PF02318 FYVE_2: FYVE-type zin 97.0 0.00042 9.1E-09 58.4 2.1 52 149-208 53-104 (118)
18 KOG0230 Phosphatidylinositol-4 96.2 0.0017 3.7E-08 73.4 1.3 34 145-181 92-125 (1598)
19 KOG1729 FYVE finger containing 93.1 0.02 4.4E-07 55.5 -0.7 67 140-207 10-81 (288)
20 KOG1841 Smad anchor for recept 91.8 0.097 2.1E-06 58.4 2.3 55 140-209 647-701 (1287)
21 KOG0320 Predicted E3 ubiquitin 87.6 0.067 1.4E-06 48.5 -2.6 50 150-211 131-180 (187)
22 TIGR00622 ssl1 transcription f 85.5 0.71 1.5E-05 38.9 2.7 40 144-183 49-97 (112)
23 PF09538 FYDLN_acid: Protein o 84.5 0.72 1.6E-05 38.6 2.3 34 141-177 3-36 (108)
24 PRK00464 nrdR transcriptional 83.7 0.59 1.3E-05 41.5 1.5 26 152-177 2-38 (154)
25 TIGR02300 FYDLN_acid conserved 81.5 1 2.2E-05 38.8 2.1 27 151-177 10-36 (129)
26 PF07975 C1_4: TFIIH C1-like d 79.5 0.34 7.4E-06 35.3 -1.2 31 152-182 1-36 (51)
27 COG3874 Uncharacterized conser 76.7 4.4 9.6E-05 35.0 4.5 50 248-304 6-55 (138)
28 KOG0993 Rab5 GTPase effector R 76.1 0.042 9E-07 55.4 -9.1 66 142-211 460-527 (542)
29 KOG2164 Predicted E3 ubiquitin 74.6 5.4 0.00012 41.6 5.3 52 150-210 186-237 (513)
30 PF13717 zinc_ribbon_4: zinc-r 74.4 1.8 3.9E-05 29.1 1.2 26 152-177 4-35 (36)
31 KOG0317 Predicted E3 ubiquitin 73.3 0.77 1.7E-05 44.5 -1.1 49 150-212 239-287 (293)
32 KOG1314 DHHC-type Zn-finger pr 72.1 1.3 2.8E-05 44.3 0.1 35 139-176 75-114 (414)
33 PF13719 zinc_ribbon_5: zinc-r 71.3 2.4 5.3E-05 28.5 1.3 26 152-177 4-35 (37)
34 PRK00432 30S ribosomal protein 68.6 3.8 8.1E-05 29.6 1.9 28 150-177 20-47 (50)
35 smart00154 ZnF_AN1 AN1-like Zi 68.2 3.3 7.2E-05 28.3 1.5 26 153-181 1-26 (39)
36 KOG3576 Ovo and related transc 67.1 1.1 2.3E-05 41.8 -1.4 34 146-179 113-157 (267)
37 TIGR01562 FdhE formate dehydro 67.1 5.7 0.00012 39.1 3.5 62 150-211 184-265 (305)
38 KOG4275 Predicted E3 ubiquitin 66.5 0.67 1.5E-05 45.1 -3.0 49 148-207 42-90 (350)
39 PF06577 DUF1134: Protein of u 66.4 8.6 0.00019 34.3 4.1 39 293-336 48-86 (160)
40 PF01485 IBR: IBR domain; Int 66.3 5.5 0.00012 28.7 2.5 35 150-184 18-57 (64)
41 PF14634 zf-RING_5: zinc-RING 66.1 1.2 2.5E-05 30.8 -1.1 32 152-185 1-32 (44)
42 PF12773 DZR: Double zinc ribb 65.2 4.8 0.0001 28.2 1.9 28 148-175 10-37 (50)
43 PF00415 RCC1: Regulator of ch 62.7 2 4.4E-05 29.7 -0.4 30 94-124 1-31 (51)
44 PRK00420 hypothetical protein; 61.7 5.9 0.00013 33.4 2.1 26 150-183 23-48 (112)
45 PF07282 OrfB_Zn_ribbon: Putat 61.6 7.3 0.00016 29.1 2.4 29 149-177 27-56 (69)
46 KOG3799 Rab3 effector RIM1 and 60.8 3.6 7.7E-05 36.0 0.6 52 149-207 64-116 (169)
47 KOG0978 E3 ubiquitin ligase in 58.4 1 2.2E-05 48.6 -3.7 46 150-208 643-688 (698)
48 PLN03208 E3 ubiquitin-protein 57.4 2.8 6E-05 38.6 -0.6 59 149-212 17-82 (193)
49 smart00647 IBR In Between Ring 55.9 10 0.00022 27.3 2.4 35 150-184 18-57 (64)
50 PRK03564 formate dehydrogenase 53.9 13 0.00028 36.7 3.3 62 150-211 187-265 (309)
51 PHA02768 hypothetical protein; 52.8 8.4 0.00018 28.5 1.4 26 152-177 7-41 (55)
52 PF01529 zf-DHHC: DHHC palmito 52.5 9.3 0.0002 33.2 1.9 27 147-176 45-71 (174)
53 COG1773 Rubredoxin [Energy pro 51.4 12 0.00026 27.8 2.0 41 166-206 2-44 (55)
54 TIGR00570 cdk7 CDK-activating 51.1 5.1 0.00011 39.5 0.0 49 151-209 4-54 (309)
55 PRK00398 rpoP DNA-directed RNA 51.0 9.1 0.0002 26.6 1.3 23 152-175 5-29 (46)
56 KOG0823 Predicted E3 ubiquitin 51.0 4.4 9.6E-05 38.2 -0.4 36 171-212 63-98 (230)
57 PF07191 zinc-ribbons_6: zinc- 50.7 9.6 0.00021 29.6 1.5 44 151-213 2-45 (70)
58 cd00162 RING RING-finger (Real 50.6 2.3 4.9E-05 27.8 -1.8 30 152-185 1-30 (45)
59 PF03604 DNA_RNApol_7kD: DNA d 50.5 12 0.00026 24.6 1.7 24 152-175 2-25 (32)
60 PF15135 UPF0515: Uncharacteri 50.4 10 0.00022 36.4 1.9 33 145-177 127-165 (278)
61 PF13923 zf-C3HC4_2: Zinc fing 49.4 4.9 0.00011 26.8 -0.3 29 153-185 1-29 (39)
62 PRK04023 DNA polymerase II lar 48.0 15 0.00033 41.5 3.0 50 148-213 624-678 (1121)
63 PF10367 Vps39_2: Vacuolar sor 47.3 16 0.00035 29.0 2.4 32 149-183 77-108 (109)
64 COG5574 PEX10 RING-finger-cont 47.0 5.2 0.00011 38.5 -0.6 48 151-210 216-263 (271)
65 PF10571 UPF0547: Uncharacteri 46.1 14 0.00029 23.2 1.4 23 152-177 2-24 (26)
66 smart00659 RPOLCX RNA polymera 44.8 13 0.00028 26.2 1.2 23 152-174 4-26 (44)
67 PF13639 zf-RING_2: Ring finge 44.2 4.9 0.00011 27.4 -0.9 32 152-185 2-33 (44)
68 PF04216 FdhE: Protein involve 43.7 12 0.00025 36.1 1.2 63 150-212 172-252 (290)
69 PRK14559 putative protein seri 43.6 14 0.0003 40.0 1.9 32 148-184 13-50 (645)
70 COG0675 Transposase and inacti 43.1 16 0.00036 34.4 2.2 26 148-177 307-332 (364)
71 PF13901 DUF4206: Domain of un 43.1 7.1 0.00015 35.9 -0.3 45 169-213 2-50 (202)
72 TIGR02098 MJ0042_CXXC MJ0042 f 42.2 15 0.00032 24.3 1.2 10 152-161 4-13 (38)
73 PF14353 CpXC: CpXC protein 42.1 15 0.00032 30.9 1.5 10 152-161 3-12 (128)
74 KOG2879 Predicted E3 ubiquitin 41.7 16 0.00034 35.6 1.7 54 149-213 238-291 (298)
75 PF10497 zf-4CXXC_R1: Zinc-fin 40.7 9.8 0.00021 31.6 0.2 58 149-209 6-72 (105)
76 KOG1814 Predicted E3 ubiquitin 40.7 12 0.00026 38.3 0.8 42 142-184 361-403 (445)
77 PF06750 DiS_P_DiS: Bacterial 40.5 20 0.00044 28.9 2.0 10 151-160 34-43 (92)
78 KOG1829 Uncharacterized conser 40.2 14 0.0003 39.4 1.3 61 151-211 341-406 (580)
79 PRK04136 rpl40e 50S ribosomal 39.3 18 0.00039 26.1 1.3 22 151-175 15-36 (48)
80 KOG3173 Predicted Zn-finger pr 39.0 16 0.00034 32.9 1.2 29 149-181 104-132 (167)
81 KOG1311 DHHC-type Zn-finger pr 38.9 14 0.0003 35.5 1.0 24 150-176 113-136 (299)
82 PF09297 zf-NADH-PPase: NADH p 38.8 26 0.00056 22.5 1.9 25 177-206 5-29 (32)
83 PF15616 TerY-C: TerY-C metal 38.1 22 0.00047 30.9 1.9 39 151-209 78-116 (131)
84 PF09889 DUF2116: Uncharacteri 37.8 5.9 0.00013 29.7 -1.4 31 167-214 3-34 (59)
85 COG5151 SSL1 RNA polymerase II 36.7 16 0.00034 36.3 0.9 39 144-182 356-403 (421)
86 TIGR00100 hypA hydrogenase nic 36.2 17 0.00037 30.4 1.0 25 150-175 70-94 (115)
87 PF13117 Cag12: Cag pathogenic 36.0 43 0.00093 28.3 3.3 37 2-38 1-45 (113)
88 TIGR02874 spore_ytfJ sporulati 35.5 82 0.0018 27.1 5.0 51 248-304 4-54 (125)
89 KOG1813 Predicted E3 ubiquitin 35.3 27 0.00058 34.3 2.2 28 152-184 243-270 (313)
90 TIGR02605 CxxC_CxxC_SSSS putat 35.1 18 0.00039 25.5 0.8 11 152-162 7-17 (52)
91 PF14803 Nudix_N_2: Nudix N-te 34.7 28 0.0006 23.2 1.6 28 177-206 2-30 (34)
92 PF01155 HypA: Hydrogenase exp 33.9 12 0.00025 31.3 -0.4 24 151-175 71-94 (113)
93 PF03107 C1_2: C1 domain; Int 33.6 40 0.00086 21.4 2.2 29 152-182 2-30 (30)
94 PRK00564 hypA hydrogenase nick 33.4 22 0.00048 29.9 1.2 25 150-175 71-96 (117)
95 PF04438 zf-HIT: HIT zinc fing 33.0 22 0.00048 22.9 0.9 23 151-179 3-25 (30)
96 PRK05978 hypothetical protein; 33.0 25 0.00054 31.1 1.5 26 151-176 34-61 (148)
97 KOG1315 Predicted DHHC-type Zn 33.0 20 0.00043 35.4 1.0 28 145-175 104-131 (307)
98 COG5273 Uncharacterized protei 32.4 22 0.00048 34.9 1.2 27 147-176 106-132 (309)
99 PF14445 Prok-RING_2: Prokaryo 32.4 7.6 0.00016 28.4 -1.5 45 151-209 8-52 (57)
100 PF13445 zf-RING_UBOX: RING-ty 32.2 14 0.0003 25.8 -0.2 31 153-185 1-31 (43)
101 COG1996 RPC10 DNA-directed RNA 32.1 22 0.00048 25.7 0.8 24 152-175 8-32 (49)
102 TIGR00599 rad18 DNA repair pro 31.8 24 0.00052 36.0 1.3 47 149-209 25-71 (397)
103 KOG3795 Uncharacterized conser 31.0 22 0.00047 32.6 0.8 23 160-183 9-34 (230)
104 PF01286 XPA_N: XPA protein N- 30.8 33 0.00072 22.9 1.5 10 197-206 23-32 (34)
105 smart00834 CxxC_CXXC_SSSS Puta 30.6 26 0.00056 23.2 1.0 10 152-161 7-16 (41)
106 PF14835 zf-RING_6: zf-RING of 30.1 36 0.00077 26.1 1.7 29 151-184 8-37 (65)
107 PHA02942 putative transposase; 30.0 42 0.00091 33.9 2.8 27 150-176 325-351 (383)
108 PF01927 Mut7-C: Mut7-C RNAse 30.0 39 0.00084 29.3 2.2 19 144-162 85-103 (147)
109 PRK12380 hydrogenase nickel in 29.5 25 0.00054 29.4 0.9 24 151-175 71-94 (113)
110 cd02341 ZZ_ZZZ3 Zinc finger, Z 29.4 24 0.00051 25.3 0.6 28 152-182 2-33 (48)
111 PF11781 RRN7: RNA polymerase 29.3 24 0.00053 23.7 0.6 25 152-176 10-34 (36)
112 COG1645 Uncharacterized Zn-fin 28.9 27 0.00059 30.3 1.0 24 151-183 29-52 (131)
113 KOG1313 DHHC-type Zn-finger pr 28.6 17 0.00038 35.3 -0.2 24 150-176 102-125 (309)
114 COG1198 PriA Primosomal protei 28.5 37 0.00079 37.4 2.2 10 198-207 475-484 (730)
115 PHA02929 N1R/p28-like protein; 28.3 18 0.0004 34.3 -0.1 52 149-209 173-227 (238)
116 KOG2593 Transcription initiati 27.5 27 0.00058 36.0 0.8 34 150-183 128-169 (436)
117 COG1327 Predicted transcriptio 27.3 32 0.00069 30.7 1.2 26 250-278 82-107 (156)
118 PF08271 TF_Zn_Ribbon: TFIIB z 27.1 35 0.00076 23.3 1.2 15 196-210 17-31 (43)
119 TIGR00311 aIF-2beta translatio 26.5 33 0.00072 29.7 1.2 26 151-176 98-127 (133)
120 PF15227 zf-C3HC4_4: zinc fing 26.5 21 0.00046 24.4 -0.1 28 153-185 1-28 (42)
121 PF00097 zf-C3HC4: Zinc finger 26.2 21 0.00045 23.6 -0.2 29 153-185 1-29 (41)
122 PF05191 ADK_lid: Adenylate ki 26.2 31 0.00068 23.1 0.7 14 196-209 19-32 (36)
123 PHA02926 zinc finger-like prot 25.7 19 0.00042 34.1 -0.5 54 151-209 171-230 (242)
124 PRK12496 hypothetical protein; 25.4 45 0.00099 29.7 1.8 24 151-175 128-151 (164)
125 PF09579 Spore_YtfJ: Sporulati 25.4 95 0.0021 24.6 3.5 22 284-305 5-26 (83)
126 PF13912 zf-C2H2_6: C2H2-type 24.8 18 0.00039 21.7 -0.6 11 152-162 3-13 (27)
127 KOG4739 Uncharacterized protei 24.8 32 0.00069 32.7 0.8 44 152-209 5-48 (233)
128 PF15616 TerY-C: TerY-C metal 24.8 39 0.00084 29.3 1.2 16 4-19 7-22 (131)
129 PF09723 Zn-ribbon_8: Zinc rib 24.7 34 0.00073 23.5 0.7 10 197-206 25-34 (42)
130 cd02340 ZZ_NBR1_like Zinc fing 24.1 37 0.00081 23.5 0.8 30 152-184 2-32 (43)
131 PF06221 zf-C2HC5: Putative zi 24.0 41 0.00089 25.1 1.1 28 167-208 18-45 (57)
132 PF09862 DUF2089: Protein of u 24.0 44 0.00096 28.3 1.4 25 153-180 1-25 (113)
133 PRK14559 putative protein seri 23.6 61 0.0013 35.2 2.7 54 151-216 2-59 (645)
134 PRK03824 hypA hydrogenase nick 23.4 40 0.00086 29.1 1.1 10 152-161 72-81 (135)
135 PRK03681 hypA hydrogenase nick 23.1 40 0.00086 28.2 1.0 25 151-175 71-95 (114)
136 COG4530 Uncharacterized protei 23.1 45 0.00097 28.3 1.2 27 151-177 10-36 (129)
137 KOG2807 RNA polymerase II tran 22.4 56 0.0012 32.7 2.0 51 144-205 324-374 (378)
138 cd02342 ZZ_UBA_plant Zinc fing 21.8 40 0.00087 23.8 0.6 28 152-181 2-30 (43)
139 smart00291 ZnF_ZZ Zinc-binding 21.8 54 0.0012 22.6 1.3 28 151-181 5-33 (44)
140 smart00661 RPOL9 RNA polymeras 21.7 75 0.0016 22.0 2.0 12 197-208 19-30 (52)
141 PF01428 zf-AN1: AN1-like Zinc 21.6 52 0.0011 22.6 1.2 16 167-182 13-28 (43)
142 PF12760 Zn_Tnp_IS1595: Transp 21.4 69 0.0015 22.2 1.8 30 143-175 14-45 (46)
143 TIGR01031 rpmF_bact ribosomal 21.3 64 0.0014 23.7 1.6 26 145-174 21-46 (55)
144 PRK14873 primosome assembly pr 21.2 53 0.0011 35.7 1.7 34 151-185 393-432 (665)
145 PF02150 RNA_POL_M_15KD: RNA p 20.7 49 0.0011 21.9 0.8 8 176-183 2-9 (35)
146 PF07503 zf-HYPF: HypF finger; 20.5 17 0.00038 24.3 -1.4 7 153-159 2-8 (35)
147 COG1198 PriA Primosomal protei 20.4 65 0.0014 35.5 2.1 35 151-185 445-485 (730)
148 cd00202 ZnF_GATA Zinc finger D 20.3 42 0.0009 24.5 0.5 13 153-165 2-14 (54)
149 smart00504 Ubox Modified RING 20.3 47 0.001 23.7 0.8 43 152-208 3-45 (63)
150 PRK11595 DNA utilization prote 20.2 25 0.00055 32.6 -0.9 30 151-183 21-56 (227)
No 1
>KOG1843 consensus Uncharacterized conserved protein [Function unknown]
Probab=100.00 E-value=1.4e-40 Score=323.30 Aligned_cols=289 Identities=34% Similarity=0.416 Sum_probs=260.4
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCcccccccCCCCCccchhhhhhcceeeecCCCCCCCCccccccCCCceeecccCCCCCc
Q 019595 29 YMYPFPLESDDVIDGGYDSSDDQCTDILRNNMPPEVNLKNVLSGIFAIITGQNKTPSDCMNQQESSSNVSFFGSGKNGDT 108 (338)
Q Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~g~~~~~~~~~~~~~~~~~v~~~g~~~nG~~ 108 (338)
-.|.|.+.....++.+|+.+.+ |..+..-.+.++.++++|.-+|..++++.|....+ +..++..+.|+|++
T Consensus 57 egflfsgr~Gsgviv~~l~dGt-wsapsa~~~~g~g~g~~Vgveltd~V~ilNs~~av---~~f~~~G~itLGgn----- 127 (473)
T KOG1843|consen 57 EGFLFSGRAGSGVIVGYLKDGT-WSAPSAIAEAGEGAGGMVGVELTDFVIILNSALAV---QSFARFGTITLGGN----- 127 (473)
T ss_pred ccccccccccCceeeeecCCCC-cCcchhhhhccccchhhhHHHHHHHHHhhcchHhh---hhhhhcCeeeecCc-----
Confidence 3566779999999999987766 56777888899999999999999988888866544 33446677777744
Q ss_pred ccCCCCCCCCCCCcccCCCccchhhhhhcccCCCCccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCCceeec
Q 019595 109 YLHSSVYIPSAPPLLEPDGVRYIAYKEVLEAEPPEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLL 188 (338)
Q Consensus 109 ~~~~s~~~~~~p~l~~~~~~~~~~~~~~~~~~~p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~l 188 (338)
...+++||.+. ++...+..++.++|.|.+++....|++|..+|+.+..||||||.|+.+||..|+..+.++
T Consensus 128 ------~svsAgPLgr~---aea~a~asl~~~ap~f~yskskglfagvSvegsaI~erR~anR~~yg~~cra~~ilsg~v 198 (473)
T KOG1843|consen 128 ------LSVSAGPLGRN---AEAAASASLGGEAPVFLYSKSKGLFAGVSVEGSAIIERREANRKFYGIFCRAKSILSGLV 198 (473)
T ss_pred ------ceeccCccccc---chhhhhhhhcCcCccccccccccceeeeecccceeeecchhhhhhcCccchhhhhhccCC
Confidence 55677888754 667788889999999999999999999999999999999999999999999999999999
Q ss_pred CccCCCCcceeecccccccccccccchhcccchhhhhccccccccccccccccCCcccchhHHHHHHHHHHHHh-hhccc
Q 019595 189 PVRFRERNPQRVCDACYDRLDPLQGVLINTISNAVQVAKHDVVDWTCTRGWLNLPVGLSMEYEIYKASNTLRSY-CQVAE 267 (338)
Q Consensus 189 P~~~~~~~p~RVC~~C~~~l~~~~~~l~~~~s~a~q~~~~d~~d~~~~r~wlnlPvglsmeeeI~kAa~iL~~~-~~~~~ 267 (338)
|.++....++|||+.|+..|...|..+.+.++++.|.++||..||+..|.|.|.|.+.+|+.++++++++|+.+ ++...
T Consensus 199 p~p~a~d~l~RVldS~~~nl~~~q~~~~d~~~da~qy~d~d~~Di~~s~sstn~~~~~~~e~s~~rra~slrg~r~~~~d 278 (473)
T KOG1843|consen 199 PVPFAADPLQRVLDSCAFNLESVQGSLDDQYSDAAQYADHDYTDIPTSRSSTNFPSGRSMERSIYRRANSLRGYRSRVDD 278 (473)
T ss_pred CCCcccCCHHHHHhhHhhccCCCccccccccCcccccCcccccccccccccccCcccCcchHHHHHhhhhcccceeeccc
Confidence 98899999999999999999989999999999999999999999999999999999999999999999999888 55566
Q ss_pred CCCCcCcchhhhcCCcceEEEEEEeeeEEEEEecCceEEEEEcCCCccccceeEEEecceEEEEeeEEe
Q 019595 268 SNPERSIPLAVLNGAKGLAILTVAKAGVLVSYKLGTGLVVARRSDGSWSAPSAILSVGLGWGAQVNSHV 336 (338)
Q Consensus 268 ~~p~~~ip~~~l~~a~Gi~i~~v~k~g~~~g~~~G~G~vvaR~~~g~WS~P~~i~~~g~s~G~q~G~e~ 336 (338)
.++|..| ...+.+|||++++|+.++|.+.+.+.|+|++++|+++|+||+|++|+..|++||.|+|.|.
T Consensus 279 ddded~~-~a~~srakgLa~~t~~~~g~l~~yk~~s~~~~srR~~Gs~s~~s~~s~~glgWgaq~ggey 346 (473)
T KOG1843|consen 279 DDDEDSI-DAGLSRAKGLAPITVARSGVLDTYKLGSSLVVSRRNDGSWSPRSAISRFGLGWGAQAGGEY 346 (473)
T ss_pred Cchhhhh-hhhhhhcccCCcccccccccccccccccccceecccCCCCCCcchhcccccccchhccccc
Confidence 7788889 8899999999999999999999999999999999999999999999999999999999985
No 2
>COG2930 Uncharacterized conserved protein [Function unknown]
Probab=99.85 E-value=3.8e-22 Score=178.73 Aligned_cols=98 Identities=34% Similarity=0.524 Sum_probs=87.8
Q ss_pred ccCCcccchhHHHHHHHHHHHHhhhcc-cCCCCcCcchhhhcCCcceEEEE-EEeeeEEEEEecCceEEEEEcCCCcccc
Q 019595 240 LNLPVGLSMEYEIYKASNTLRSYCQVA-ESNPERSIPLAVLNGAKGLAILT-VAKAGVLVSYKLGTGLVVARRSDGSWSA 317 (338)
Q Consensus 240 lnlPvglsmeeeI~kAa~iL~~~~~~~-~~~p~~~ip~~~l~~a~Gi~i~~-v~k~g~~~g~~~G~G~vvaR~~~g~WS~ 317 (338)
+++|.+.++..+..++..++..|.... +..|+..||+++|++||||+||| |+|+||++||++|+||+++|+++++||+
T Consensus 10 i~~a~~~s~~s~~~k~~~~~s~~v~~~~~~~~~~~ip~~lL~rAkGi~Iip~vLkaGFvigGr~GqGvl~~r~~~nTWs~ 89 (227)
T COG2930 10 IPNAQGSSFASETNKAAKTNSSFVLTEQRLGPDQVIPPSLLERAKGIVIIPSVLKAGFVIGGRYGQGVLVARLPDNTWSA 89 (227)
T ss_pred CCCccchhhcchhhhhhhhhhhhcchhhhhCCcccCCHHHHhhcCeeEEehhhccccEEEeccccceEEEecCCCCCccc
Confidence 456777888888888887777665432 45799999999999999999999 9999999999999999999999999999
Q ss_pred ceeEEEecceEEEEeeEEee
Q 019595 318 PSAILSVGLGWGAQVNSHVF 337 (338)
Q Consensus 318 P~~i~~~g~s~G~q~G~e~t 337 (338)
|+||+++|+|+|+|+|+|+|
T Consensus 90 p~~v~~~g~siG~q~G~qs~ 109 (227)
T COG2930 90 PSFVKMAGASIGGQAGVQST 109 (227)
T ss_pred chhhhhhcccccccccceee
Confidence 99999999999999999987
No 3
>PF01363 FYVE: FYVE zinc finger; InterPro: IPR000306 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 FYVE zinc finger is named after four proteins that it has been found in: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two zinc ions []. The FYVE finger has eight potential zinc coordinating cysteine positions. Many members of this family also include two histidines in a motif R+HHC+XCG, where + represents a charged residue and X any residue. FYVE-type domains are divided into two known classes: FYVE domains that specifically bind to phosphatidylinositol 3-phosphate in lipid bilayers and FYVE-related domains of undetermined function []. Those that bind to phosphatidylinositol 3-phosphate are often found in proteins targeted to lipid membranes that are involved in regulating membrane traffic [, , ]. Most FYVE domains target proteins to endosomes by binding specifically to phosphatidylinositol-3-phosphate at the membrane surface. By contrast, the CARP2 FYVE-like domain is not optimized to bind to phosphoinositides or insert into lipid bilayers. FYVE domains are distinguished from other zinc fingers by three signature sequences: an N-terminal WxxD motif, a basic R(R/K)HHCR patch, and a C-terminal RVC motif. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0046872 metal ion binding; PDB: 1HYI_A 1JOC_B 1HYJ_A 1DVP_A 3ZYQ_A 4AVX_A 1VFY_A 3T7L_A 1X4U_A 1WFK_A ....
Probab=99.77 E-value=6.1e-20 Score=140.01 Aligned_cols=67 Identities=48% Similarity=1.064 Sum_probs=47.3
Q ss_pred CCccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCCceeecC-ccCCCCcceeeccccccccc
Q 019595 142 PEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLP-VRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 142 p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP-~~~~~~~p~RVC~~C~~~l~ 209 (338)
|.|+||+++..|+.|+++|+ |++||||||.||++||+.|+.++..+| ......+++|||+.|+..|+
T Consensus 1 ~~W~~d~~~~~C~~C~~~F~-~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~~~~~~~~RvC~~C~~~~~ 68 (69)
T PF01363_consen 1 PHWVPDSEASNCMICGKKFS-LFRRRHHCRNCGRVVCSSCSSQRIPLPTPSSGSGEPVRVCDSCYSKLQ 68 (69)
T ss_dssp --SSSGGG-SB-TTT--B-B-SSS-EEE-TTT--EEECCCS-EEEEET--GGTESEEEEE-HHHHHHHH
T ss_pred CCcCCCCCCCcCcCcCCcCC-CceeeEccCCCCCEECCchhCCEEcccccccCCCCcCEECHHHHHHhc
Confidence 78999999999999999998 678999999999999999999998876 23455789999999998774
No 4
>smart00064 FYVE Protein present in Fab1, YOTB, Vac1, and EEA1. The FYVE zinc finger is named after four proteins where it was first found: Fab1, YOTB/ZK632.12, Vac1, and EEA1. The FYVE finger has been shown to bind two Zn2+ ions. The FYVE finger has eight potential zinc coordinating cysteine positions. The FYVE finger is structurally related to the KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=99.58 E-value=2.1e-16 Score=151.35 Aligned_cols=71 Identities=45% Similarity=1.014 Sum_probs=63.1
Q ss_pred cccCCCCccCCCCCCccCCCCc-CCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccccccccc
Q 019595 137 LEAEPPEWLPDSSTTVCMQCTA-PFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDP 210 (338)
Q Consensus 137 ~~~~~p~W~pd~~~~~C~~C~~-~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~ 210 (338)
.....+.|+||++++.|+.|.. .|+ ++.||||||+||.|||..|+..+..+| +...++.|||+.||+.|.+
T Consensus 155 ~~~~~~~W~PD~ea~~C~~C~~~~Ft-l~~RRHHCR~CG~ivC~~Cs~n~~~l~--~~~~k~~rvC~~CF~el~~ 226 (288)
T KOG1729|consen 155 SNNSAAVWLPDSEATECMVCGCTEFT-LSERRHHCRNCGDIVCAPCSRNRFLLP--NLSTKPIRVCDICFEELEK 226 (288)
T ss_pred CCCcCCcccCcccceecccCCCcccc-HHHHHHHHHhcchHhhhhhhcCccccc--ccCCCCceecHHHHHHHhc
Confidence 3445789999999999999999 999 678999999999999999999987776 4557899999999999976
No 6
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=99.57 E-value=1.4e-15 Score=157.92 Aligned_cols=72 Identities=31% Similarity=0.701 Sum_probs=57.0
Q ss_pred ccCCCCccCCCCC-CccCCCCcCCccc----cccccccccCCceEeCCCCCceeecC-------ccCCCCcceeeccccc
Q 019595 138 EAEPPEWLPDSST-TVCMQCTAPFTAL----TRGRHHCRFCGGVFCRICTKGRCLLP-------VRFRERNPQRVCDACY 205 (338)
Q Consensus 138 ~~~~p~W~pd~~~-~~C~~C~~~F~~l----~rRrHHCR~CG~vfC~~Cs~~~~~lP-------~~~~~~~p~RVC~~C~ 205 (338)
....|.|++|+++ ..|+.|++.|+++ ..||||||+||++||..||+++..+| .......+.|||+.||
T Consensus 447 ~LhAPvWqpDDEaSdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs~yp~aKLpKPgsseE~ppRRVCD~CY 526 (1374)
T PTZ00303 447 LLHNPSWQKDDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRAHYSFAKLAKPGSSDEAEERLVCDTCY 526 (1374)
T ss_pred hccCCCCCCCcccCCcccCcCCcccccccccccccccccCCccccCccccCCcccCcccccCCCCCcccccccchhHHHH
Confidence 3568999999984 7899999999854 35899999999999999999886433 1122335779999999
Q ss_pred cccc
Q 019595 206 DRLD 209 (338)
Q Consensus 206 ~~l~ 209 (338)
+.++
T Consensus 527 dq~E 530 (1374)
T PTZ00303 527 KEYE 530 (1374)
T ss_pred HHHH
Confidence 7665
No 7
>KOG1818 consensus Membrane trafficking and cell signaling protein HRS, contains VHS and FYVE domains [Signal transduction mechanisms; Intracellular trafficking, secretion, and vesicular transport]
Probab=99.53 E-value=2.9e-15 Score=154.85 Aligned_cols=84 Identities=36% Similarity=0.858 Sum_probs=68.1
Q ss_pred ccCCCccchhhhhh---c-ccCCCCccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcce
Q 019595 123 LEPDGVRYIAYKEV---L-EAEPPEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQ 198 (338)
Q Consensus 123 ~~~~~~~~~~~~~~---~-~~~~p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~ 198 (338)
+...++.|+...+. + ...+|.|+.. ..|+.|...|+ ++.|+||||+||+|||..|+++.+.+| .++..+++
T Consensus 137 lk~~g~~Fpe~~e~d~mf~~~~~pdW~D~---~~C~rCr~~F~-~~~rkHHCr~CG~vFC~qcss~s~~lP-~~Gi~~~V 211 (634)
T KOG1818|consen 137 LKGGGHVFPELDENDAMFDAETAPDWIDS---EECLRCRVKFG-LTNRKHHCRNCGQVFCGQCSSKSLTLP-KLGIEKPV 211 (634)
T ss_pred HhcCCccccccccchhhhcccCCcccccc---cccceeeeeee-eccccccccccchhhccCccccccCcc-cccccccc
Confidence 44455566554432 1 3358899854 68999999999 667999999999999999999999998 67888999
Q ss_pred eeccccccccccc
Q 019595 199 RVCDACYDRLDPL 211 (338)
Q Consensus 199 RVC~~C~~~l~~~ 211 (338)
|||+.||+.+...
T Consensus 212 RVCd~C~E~l~~~ 224 (634)
T KOG1818|consen 212 RVCDSCYELLTRA 224 (634)
T ss_pred eehhhhHHHhhhc
Confidence 9999999988754
No 8
>KOG1819 consensus FYVE finger-containing proteins [General function prediction only]
Probab=99.50 E-value=6.2e-15 Score=147.75 Aligned_cols=70 Identities=41% Similarity=1.010 Sum_probs=62.7
Q ss_pred cCCCCccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecc-----cccccccc
Q 019595 139 AEPPEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCD-----ACYDRLDP 210 (338)
Q Consensus 139 ~~~p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~-----~C~~~l~~ 210 (338)
..+|.|+||.++..||.|+.+|+ ++|||||||+||.|||..|+...+.+| +++..+..|||. .||.+-+.
T Consensus 890 lsppawipd~~a~~cmacq~pf~-afrrrhhcrncggifcg~cs~asapip-~~gl~ka~rvcrpqsnldc~~rqdq 964 (990)
T KOG1819|consen 890 LSPPAWIPDEDAEQCMACQMPFN-AFRRRHHCRNCGGIFCGKCSCASAPIP-EHGLDKAPRVCRPQSNLDCLTRQDQ 964 (990)
T ss_pred cCCcccCCCCcchhhhhccCcHH-HHHHhhhhcccCceeecccccCCCCCc-ccccccCceecCCcccccceeeccc
Confidence 45889999999999999999999 678999999999999999999999998 567789999999 88876543
No 9
>cd00065 FYVE FYVE domain; Zinc-binding domain; targets proteins to membrane lipids via interaction with phosphatidylinositol-3-phosphate, PI3P; present in Fab1, YOTB, Vac1, and EEA1;
Probab=99.39 E-value=1.5e-13 Score=100.65 Aligned_cols=55 Identities=53% Similarity=1.178 Sum_probs=48.4
Q ss_pred CCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccccc
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYD 206 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~ 206 (338)
+..|+.|++.|+ ++.||||||.||++||.+|+.++..+|.. ...+|+|||+.||+
T Consensus 2 ~~~C~~C~~~F~-~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~-~~~~~~rvC~~C~~ 56 (57)
T cd00065 2 ASSCMGCGKPFT-LTRRRHHCRNCGRIFCSKCSSNRIPLPSM-GGGKPVRVCDSCYE 56 (57)
T ss_pred cCcCcccCcccc-CCccccccCcCcCCcChHHcCCeeecCcc-cCCCccEeChHHhC
Confidence 468999999999 56789999999999999999999888742 45689999999986
No 10
>KOG1843 consensus Uncharacterized conserved protein [Function unknown]
Probab=99.21 E-value=2.3e-12 Score=126.80 Aligned_cols=97 Identities=37% Similarity=0.560 Sum_probs=86.9
Q ss_pred cCCcccchhHHHHHHHHHHHHhhhcc-cCCCCcCcchhhhcCCcceEEEEEEeeeEEEEEecCceEEEEEcCCCccccce
Q 019595 241 NLPVGLSMEYEIYKASNTLRSYCQVA-ESNPERSIPLAVLNGAKGLAILTVAKAGVLVSYKLGTGLVVARRSDGSWSAPS 319 (338)
Q Consensus 241 nlPvglsmeeeI~kAa~iL~~~~~~~-~~~p~~~ip~~~l~~a~Gi~i~~v~k~g~~~g~~~G~G~vvaR~~~g~WS~P~ 319 (338)
|+|+.-++..|..++..++..|.++. ....+..||+.+|++|+|++|+|++|+||++.++.|.||+++|++||+||+|+
T Consensus 4 ~npipaSlkse~~~~~k~~~~fv~p~q~~Gs~e~ipPyvl~da~gl~~i~~lkegflfsgr~Gsgviv~~l~dGtwsaps 83 (473)
T KOG1843|consen 4 NNPIPASLKSETNKAVKSLSSFVDPNQDFGSDEGIPPYVLKDAPGLVSIPVLKEGFLFSGRAGSGVIVGYLKDGTWSAPS 83 (473)
T ss_pred CCcCccCccchhcccceeeccccChhhccCCccccCcceeccCCcceEeeeecccccccccccCceeeeecCCCCcCcch
Confidence 55777788888899999999987642 12356789999999999999999999999999999999999999999999999
Q ss_pred eEEEecceEEEEeeEEee
Q 019595 320 AILSVGLGWGAQVNSHVF 337 (338)
Q Consensus 320 ~i~~~g~s~G~q~G~e~t 337 (338)
+|...|.+.|.++|.|+|
T Consensus 84 a~~~~g~g~g~~Vgvelt 101 (473)
T KOG1843|consen 84 AIAEAGEGAGGMVGVELT 101 (473)
T ss_pred hhhhccccchhhhHHHHH
Confidence 999999999999999875
No 11
>KOG1842 consensus FYVE finger-containing protein [General function prediction only]
Probab=99.16 E-value=1.8e-12 Score=128.62 Aligned_cols=74 Identities=43% Similarity=0.838 Sum_probs=57.5
Q ss_pred hhcccCCCCccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCCceee-------------cCcc--------CC
Q 019595 135 EVLEAEPPEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCL-------------LPVR--------FR 193 (338)
Q Consensus 135 ~~~~~~~p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~-------------lP~~--------~~ 193 (338)
..++.....|+.|.++..|..|..+|+ ++|||||||.||+|+|..|+..-.. .+.. ..
T Consensus 165 k~~EqsvVpW~DDs~V~~CP~Ca~~F~-l~rRrHHCRLCG~VmC~~C~k~iSle~a~~ltsss~~dt~~e~~qq~~~lH~ 243 (505)
T KOG1842|consen 165 KRLEQSVVPWLDDSSVQFCPECANSFG-LTRRRHHCRLCGRVMCRDCSKFISLEIAIGLTSSSASDTHFEPNQQKDDLHQ 243 (505)
T ss_pred HHHHhccccccCCCcccccccccchhh-hHHHhhhhhhcchHHHHHHHHhcChHHHHHHhhccCCCCCcCcccCcccccC
Confidence 335566778999999999999999999 8999999999999999999875420 0000 11
Q ss_pred CCcceeeccccccccc
Q 019595 194 ERNPQRVCDACYDRLD 209 (338)
Q Consensus 194 ~~~p~RVC~~C~~~l~ 209 (338)
...+.|+|..|...|.
T Consensus 244 ~~~~iRlC~hCl~~L~ 259 (505)
T KOG1842|consen 244 HPQPIRLCMHCLDNLF 259 (505)
T ss_pred ChhHhHHHHHHHHHHH
Confidence 2356899999987664
No 12
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=99.08 E-value=5.1e-11 Score=128.42 Aligned_cols=65 Identities=37% Similarity=0.862 Sum_probs=53.5
Q ss_pred cccCCCCccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccc
Q 019595 137 LEAEPPEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDAC 204 (338)
Q Consensus 137 ~~~~~p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C 204 (338)
++...|.|+||.++..||.|.+.|+ +.+||||||+||+|+|..|+..+..+- |-....-|||..|
T Consensus 544 lgkkqP~wvpdse~pncm~clqkft-~ikrrhhcRacgkVlcgvccnek~~le--yl~e~~~rv~nV~ 608 (1287)
T KOG1841|consen 544 LGKKQPSWVPDSEAPNCMDCLQKFT-PIKRRHHCRACGKVLCGVCCNEKSALE--YLSESEGRVSNVD 608 (1287)
T ss_pred cCCCCCccCccccCchHHHHHhhcc-cccccccchhccceeehhhcchhhhhh--hcCcccccccccc
Confidence 5667899999999999999999999 567899999999999999999987763 3333445555544
No 13
>KOG1409 consensus Uncharacterized conserved protein, contains WD40 repeats and FYVE domains [Function unknown]
Probab=98.81 E-value=7.8e-10 Score=107.47 Aligned_cols=94 Identities=30% Similarity=0.596 Sum_probs=70.2
Q ss_pred CCCCCCcccCCCccchhhhhh--cccCCCCccCCCCCCccCCCCcCCcc----------ccccccccccCCceEeCCCCC
Q 019595 116 IPSAPPLLEPDGVRYIAYKEV--LEAEPPEWLPDSSTTVCMQCTAPFTA----------LTRGRHHCRFCGGVFCRICTK 183 (338)
Q Consensus 116 ~~~~p~l~~~~~~~~~~~~~~--~~~~~p~W~pd~~~~~C~~C~~~F~~----------l~rRrHHCR~CG~vfC~~Cs~ 183 (338)
...+.++.+.+.....+.++. ...+.|.|+.+ ..|..|+++|.. +..|.||||.||..+|..|++
T Consensus 249 ~~~t~~l~S~~edg~i~~w~mn~~r~etpewl~s---~~cQ~c~qpffwn~~~m~~~k~~glr~h~crkcg~avc~~c~s 325 (404)
T KOG1409|consen 249 AQHTRQLISCGEDGGIVVWNMNVKRVETPEWLDS---DSCQKCNQPFFWNFRQMWDRKQLGLRQHHCRKCGKAVCGKCSS 325 (404)
T ss_pred hhhheeeeeccCCCeEEEEeccceeecCcccccc---chhhhhCchHHHHHHHHHhhhhhhhhhhhhhhhhhhcCccccc
Confidence 344555655555544444333 35578999976 689999999853 235799999999999999999
Q ss_pred ceeecCccCCCCcceeeccccccccccccc
Q 019595 184 GRCLLPVRFRERNPQRVCDACYDRLDPLQG 213 (338)
Q Consensus 184 ~~~~lP~~~~~~~p~RVC~~C~~~l~~~~~ 213 (338)
++...|.. +..-.+|+|+.||..+....+
T Consensus 326 ~~~~~p~m-g~e~~vR~~~~c~~~i~~~~~ 354 (404)
T KOG1409|consen 326 NRSSYPTM-GFEFSVRVCDSCYPTIKDEER 354 (404)
T ss_pred Cccccccc-cceeEEEEecccchhhhcCCC
Confidence 99888742 345789999999999987655
No 14
>KOG4424 consensus Predicted Rho/Rac guanine nucleotide exchange factor/faciogenital dysplasia protein 3 [Signal transduction mechanisms]
Probab=98.58 E-value=9.6e-09 Score=105.28 Aligned_cols=113 Identities=23% Similarity=0.408 Sum_probs=81.7
Q ss_pred CCccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccccccc------ch
Q 019595 142 PEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPLQG------VL 215 (338)
Q Consensus 142 p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~~~------~l 215 (338)
|+| +++...|+.|+.+|+..+.|||||+.||.++|+.|+..+..+. +......|||..||........ ..
T Consensus 409 ~r~--~~k~~~c~~c~e~~~s~t~~R~~~k~~~~vlc~~cs~~~~~l~--~~~s~ssrv~~~~~~~~~~a~~s~~~rr~~ 484 (623)
T KOG4424|consen 409 PRR--DNKVTSCDSCEETFNSITFRRHRCKAKGAVLCDKCSDFMAKLS--YDNSRSSRVCMDRYLTPSGAPGSPPKRRQS 484 (623)
T ss_pred ccc--ccccccchhhcCchhhHHHhhhhhhhccceeeccccchhhhhc--ccccchhhhhhhhccCCCCCCCCchhcccc
Confidence 366 7788999999999999999999999999999999999988774 4556789999999987753211 11
Q ss_pred --hcc---------cchhhhhccccccccccccccccCCcccchhHHHHHHHHHHH
Q 019595 216 --INT---------ISNAVQVAKHDVVDWTCTRGWLNLPVGLSMEYEIYKASNTLR 260 (338)
Q Consensus 216 --~~~---------~s~a~q~~~~d~~d~~~~r~wlnlPvglsmeeeI~kAa~iL~ 260 (338)
..+ ++...+. -+....++...|.+.|..-++....+.+.+.++
T Consensus 485 ~l~~~~a~~s~~~~~~s~l~~--~~~~~~~g~~a~~~vP~~d~~~~~~Yg~~qDv~ 538 (623)
T KOG4424|consen 485 ILEIELATVSKENVICSHLKY--MEAAGKTGILAWSVVPKSDPLVDYSYGSPQDVR 538 (623)
T ss_pred cccccccccCCCceehhhHHH--HhhcCccceeeeeeccCCCCccccccCCccccc
Confidence 111 1111111 111234568899999998888777776666544
No 15
>KOG1811 consensus Predicted Zn2+-binding protein, contains FYVE domain [General function prediction only]
Probab=97.90 E-value=1.2e-06 Score=90.77 Aligned_cols=69 Identities=29% Similarity=0.672 Sum_probs=52.3
Q ss_pred cccCCCCccCCC----CCCccCC-CCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccc
Q 019595 137 LEAEPPEWLPDS----STTVCMQ-CTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDR 207 (338)
Q Consensus 137 ~~~~~p~W~pd~----~~~~C~~-C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~ 207 (338)
+....+.|+||. .-.-|+. |+..|. .++||||||.||...|..|...+.... .-+...|.++|+.|+..
T Consensus 309 f~~al~nfq~darrafs~a~~~a~~R~~~k-d~~Rk~~~~g~Ga~e~aa~ea~kgiqE-d~gse~~Adg~Dq~psv 382 (1141)
T KOG1811|consen 309 FPPALHNFQPDARRAFSEAICMACCREHFK-DFNRKHHCRGCGALECAACEAKKGIQE-DCGSENPADGCDQCPSV 382 (1141)
T ss_pred CCchhhhcChhhhhhhhhhHHHHHHHHHHH-HHHHhhhccccchHHHhHHHHhhhhhh-cccccCcccccccccch
Confidence 333456899997 4567885 555777 567899999999999999998775443 33446799999999954
No 16
>KOG0230 consensus Phosphatidylinositol-4-phosphate 5-kinase and related FYVE finger-containing proteins [Signal transduction mechanisms]
Probab=97.15 E-value=0.00027 Score=79.58 Aligned_cols=51 Identities=37% Similarity=0.937 Sum_probs=39.8
Q ss_pred CCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccccccccccc
Q 019595 149 STTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPLQ 212 (338)
Q Consensus 149 ~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~~ 212 (338)
....|..|... .+||||||.||++||++|... . .+..|||..|+.......
T Consensus 4 s~~~~~~~~t~----~~~~~~~~~~g~~~~~~~~~~------~---~~~i~~~~~~~~~~~~~~ 54 (1598)
T KOG0230|consen 4 SSNVCYDCDTS----VNRRHHCRVCGRVFCSKCQDS------P---ETSIRVCNECRGQWEQGN 54 (1598)
T ss_pred cccchhccccc----cccCCCCcccCceeccccCCC------C---ccceeehhhhhhhccccC
Confidence 45789999943 358999999999999999832 1 238999999998776543
No 17
>PF02318 FYVE_2: FYVE-type zinc finger; InterPro: IPR003315 This entry represents the zinc-binding domain found in rabphilin Rab3A. The small G protein Rab3A plays an important role in the regulation of neurotransmitter release. The crystal structure of the small G protein Rab3A complexed with the effector domain of rabphilin-3A shows that the effector domain of rabphilin-3A contacts Rab3A in two distinct areas. The first interface involves the Rab3A switch I and switch II regions, which are sensitive to the nucleotide-binding state of Rab3A. The second interface consists of a deep pocket in Rab3A that interacts with a SGAWFF structural element of rabphilin-3A. Sequence and structure analysis, and biochemical data suggest that this pocket, or Rab complementarity-determining region (RabCDR), establishes a specific interaction between each Rab protein and its effectors. It has been suggested that RabCDRs could be major determinants of effector specificity during vesicle trafficking and fusion [].; GO: 0008270 zinc ion binding, 0017137 Rab GTPase binding, 0006886 intracellular protein transport; PDB: 2CSZ_A 2ZET_C 1ZBD_B 3BC1_B 2CJS_C 2A20_A.
Probab=96.96 E-value=0.00042 Score=58.43 Aligned_cols=52 Identities=23% Similarity=0.586 Sum_probs=42.0
Q ss_pred CCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccccccc
Q 019595 149 STTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRL 208 (338)
Q Consensus 149 ~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l 208 (338)
....|..|+++|+++..+.+.|..|.+-||.+|... ....+.-+|..|+..-
T Consensus 53 ~~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~--------~~~~~~WlC~vC~k~r 104 (118)
T PF02318_consen 53 GERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVY--------SKKEPIWLCKVCQKQR 104 (118)
T ss_dssp CCSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEE--------TSSSCCEEEHHHHHHH
T ss_pred CCcchhhhCCcccccCCCCCcCCcCCccccCccCCc--------CCCCCCEEChhhHHHH
Confidence 346999999999988889999999999999999854 2246789999998643
No 18
>KOG0230 consensus Phosphatidylinositol-4-phosphate 5-kinase and related FYVE finger-containing proteins [Signal transduction mechanisms]
Probab=96.23 E-value=0.0017 Score=73.42 Aligned_cols=34 Identities=47% Similarity=1.228 Sum_probs=32.1
Q ss_pred cCCCCCCccCCCCcCCccccccccccccCCceEeCCC
Q 019595 145 LPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRIC 181 (338)
Q Consensus 145 ~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~C 181 (338)
+||.....|..|.+.|.. +||+||| ||++||.+|
T Consensus 92 m~d~s~~ec~~~~~~~~t-~Rr~~~~--~gqi~~ss~ 125 (1598)
T KOG0230|consen 92 MPDSSSKECYDCEQKFET-FRRKHHC--CGQIFCSSC 125 (1598)
T ss_pred CCccccchhhhhccchhh-hhccccc--CccccCCcc
Confidence 889999999999999995 6899999 999999999
No 19
>KOG1729 consensus FYVE finger containing protein [General function prediction only]
Probab=93.14 E-value=0.02 Score=55.54 Aligned_cols=67 Identities=28% Similarity=0.564 Sum_probs=51.4
Q ss_pred CCCCccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCC-ceeecCcc----CCCCcceeeccccccc
Q 019595 140 EPPEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTK-GRCLLPVR----FRERNPQRVCDACYDR 207 (338)
Q Consensus 140 ~~p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~-~~~~lP~~----~~~~~p~RVC~~C~~~ 207 (338)
..+.|+.+.++..|..|...|. |.+|+|||+.||+++|..|+. +....+.+ +-.....+.|..|+..
T Consensus 10 ~~~~~~~~~e~~s~~~~~~e~~-~~~r~~~~~~~grv~~~q~~~~k~~rk~~q~r~~~l~~D~~~~~~~~~~~ 81 (288)
T KOG1729|consen 10 NMVDWQANSEANSCRNCKVEFC-FGRRGHPCRECGRVLCRQGTLVKRCRKKLQSRSFFLFNDILVYGNIVSDN 81 (288)
T ss_pred hhHHHHHhccchhhhhhcccch-hhhccCcccccchhhhhhhhhHHHHhcccccccccccccchhhcccccCH
Confidence 3567999999999999999999 678899999999999999987 22222111 2234567888888876
No 20
>KOG1841 consensus Smad anchor for receptor activation [Defense mechanisms]
Probab=91.80 E-value=0.097 Score=58.40 Aligned_cols=55 Identities=27% Similarity=0.450 Sum_probs=45.6
Q ss_pred CCCCccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccc
Q 019595 140 EPPEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 140 ~~p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~ 209 (338)
..+.|.+|..+..|+.|.+.|. ++.+||||| |.++ . .+...+..|+|..|.+.+.
T Consensus 647 ~ksVw~aDg~aPng~la~t~~~-~~~e~~hsr--~~ls---------~---~~~s~~~~~~~n~t~s~~r 701 (1287)
T KOG1841|consen 647 VKSVWFADGIAPNGELAETRFT-FTGERHHSR--GKLS---------L---LYSSRKEARPCNITHSVLR 701 (1287)
T ss_pred ecceeccCCcCCCceeccccee-eeccccccc--cccc---------c---cccccccCCCCcccCccch
Confidence 3678999999999999999999 678999999 8876 1 2344577899999998764
No 21
>KOG0320 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=87.57 E-value=0.067 Score=48.46 Aligned_cols=50 Identities=24% Similarity=0.528 Sum_probs=36.6
Q ss_pred CCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccccc
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPL 211 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~ 211 (338)
.-.|.+|=..|. .+-----+||+|||..|.+.. .+..++|-.|..+++..
T Consensus 131 ~~~CPiCl~~~s---ek~~vsTkCGHvFC~~Cik~a---------lk~~~~CP~C~kkIt~k 180 (187)
T KOG0320|consen 131 TYKCPICLDSVS---EKVPVSTKCGHVFCSQCIKDA---------LKNTNKCPTCRKKITHK 180 (187)
T ss_pred ccCCCceecchh---hccccccccchhHHHHHHHHH---------HHhCCCCCCcccccchh
Confidence 357888877766 233355789999999998643 24678999999888654
No 22
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=85.54 E-value=0.71 Score=38.94 Aligned_cols=40 Identities=28% Similarity=0.655 Sum_probs=29.3
Q ss_pred ccCCCCCCccCCCCcCCccc---------cccccccccCCceEeCCCCC
Q 019595 144 WLPDSSTTVCMQCTAPFTAL---------TRGRHHCRFCGGVFCRICTK 183 (338)
Q Consensus 144 W~pd~~~~~C~~C~~~F~~l---------~rRrHHCR~CG~vfC~~Cs~ 183 (338)
|........|..|+++|... ...|..|..|.++||..|=.
T Consensus 49 ~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~ 97 (112)
T TIGR00622 49 LEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDV 97 (112)
T ss_pred ccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccch
Confidence 43333445799999999731 23468899999999999954
No 23
>PF09538 FYDLN_acid: Protein of unknown function (FYDLN_acid); InterPro: IPR012644 Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=84.51 E-value=0.72 Score=38.61 Aligned_cols=34 Identities=32% Similarity=0.622 Sum_probs=26.4
Q ss_pred CCCccCCCCCCccCCCCcCCccccccccccccCCceE
Q 019595 141 PPEWLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVF 177 (338)
Q Consensus 141 ~p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vf 177 (338)
.|.|-- -..|..|+++|-=|.|+--+|..||..|
T Consensus 3 kpelGt---KR~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 3 KPELGT---KRTCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred ccccCC---cccCCCCcchhccCCCCCccCCCCCCcc
Confidence 345543 2689999999988887777799998876
No 24
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=83.69 E-value=0.59 Score=41.49 Aligned_cols=26 Identities=38% Similarity=0.718 Sum_probs=19.1
Q ss_pred ccCCCCcCCc-----------cccccccccccCCceE
Q 019595 152 VCMQCTAPFT-----------ALTRGRHHCRFCGGVF 177 (338)
Q Consensus 152 ~C~~C~~~F~-----------~l~rRrHHCR~CG~vf 177 (338)
.|+.|+.+++ ...+|+++|.+||.-|
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 5888888772 1345679999998876
No 25
>TIGR02300 FYDLN_acid conserved hypothetical protein TIGR02300. Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=81.48 E-value=1 Score=38.80 Aligned_cols=27 Identities=22% Similarity=0.445 Sum_probs=24.2
Q ss_pred CccCCCCcCCccccccccccccCCceE
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGVF 177 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~vf 177 (338)
..|+.|+++|-=|.|+--+|..||..+
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCcc
Confidence 689999999988888889999999875
No 26
>PF07975 C1_4: TFIIH C1-like domain; InterPro: IPR004595 All proteins in this domain for which functions are known are components of the TFIIH complex which is involved in the initiation of transcription and nucleotide excision repair. It includes the yeast transcription factor Ssl1 (Suppressor of stem-loop protein 1) that is essential for translation initiation and affects UV resistance. The C-terminal region is essential for transcription activity. This regions binds three zinc atoms through two independent domain. The first contains a C4 zinc finger motif, whereas the second is characterised by a CX(2)CX(2-4)FCADCD motif. The solution structure of the second C-terminal domain revealed homology with the regulatory domain of protein kinase C [].; GO: 0006281 DNA repair, 0005634 nucleus; PDB: 1Z60_A.
Probab=79.49 E-value=0.34 Score=35.30 Aligned_cols=31 Identities=32% Similarity=0.810 Sum_probs=18.8
Q ss_pred ccCCCCcCCcccc-----ccccccccCCceEeCCCC
Q 019595 152 VCMQCTAPFTALT-----RGRHHCRFCGGVFCRICT 182 (338)
Q Consensus 152 ~C~~C~~~F~~l~-----rRrHHCR~CG~vfC~~Cs 182 (338)
.|.+|.++|.... ..+..|..|++.||..|=
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD 36 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCD 36 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B-HHHH
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccccCcC
Confidence 4889999998431 247999999999999884
No 27
>COG3874 Uncharacterized conserved protein [Function unknown]
Probab=76.66 E-value=4.4 Score=35.02 Aligned_cols=50 Identities=22% Similarity=0.261 Sum_probs=35.8
Q ss_pred hhHHHHHHHHHHHHhhhcccCCCCcCcchhhhcCCcceEEEEEEeeeEEEEEecCce
Q 019595 248 MEYEIYKASNTLRSYCQVAESNPERSIPLAVLNGAKGLAILTVAKAGVLVSYKLGTG 304 (338)
Q Consensus 248 meeeI~kAa~iL~~~~~~~~~~p~~~ip~~~l~~a~Gi~i~~v~k~g~~~g~~~G~G 304 (338)
.++.+..+..-|+.|..+.. |--+-++ +.|-.|+||.|++|.|++.+|.|
T Consensus 6 Iee~mkt~~e~Lk~m~dv~T------iVGdPIe-~dgs~iiPvsKv~fGFgaGGgEg 55 (138)
T COG3874 6 IEELMKTTMENLKKMLDVNT------IVGDPIE-PDGSTIIPVSKVGFGFGAGGGEG 55 (138)
T ss_pred hhHHHHHHHHHHHHHhhhcc------cccCccc-CCCcEEEEEEEEeeeeccCCccc
Confidence 45566667777888765421 2122244 78889999999999999988888
No 28
>KOG0993 consensus Rab5 GTPase effector Rabaptin-5 [Intracellular trafficking, secretion, and vesicular transport]
Probab=76.12 E-value=0.042 Score=55.41 Aligned_cols=66 Identities=27% Similarity=0.616 Sum_probs=52.0
Q ss_pred CCccCCCCCCccCCCCcCCcccccccccccc--CCceEeCCCCCceeecCccCCCCcceeeccccccccccc
Q 019595 142 PEWLPDSSTTVCMQCTAPFTALTRGRHHCRF--CGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPL 211 (338)
Q Consensus 142 p~W~pd~~~~~C~~C~~~F~~l~rRrHHCR~--CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~ 211 (338)
-.|.=+.+...|..|-.+|..+ +-.-||-+ |+++||-.|++. .+|. .....|.+||+-|...+..-
T Consensus 460 le~ql~~~ve~c~~~~aS~~sl-k~e~erl~qq~eqi~~~~~~Ka--tvp~-l~~e~~akv~rlq~eL~~se 527 (542)
T KOG0993|consen 460 LEWQLDDDVEQCSNCDASFASL-KVEPERLHQQCEQIFCMNCLKA--TVPS-LPNERPAKVCRLQHELLNSE 527 (542)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH-hccHHHHHHHHHHHHHHhHHHh--hccc-ccccchHHHHHHHHHHhhhc
Confidence 3587788889999999999976 44778877 999999999864 4552 23357899999999887643
No 29
>KOG2164 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=74.60 E-value=5.4 Score=41.61 Aligned_cols=52 Identities=19% Similarity=0.431 Sum_probs=37.9
Q ss_pred CCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccccccccc
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDP 210 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~ 210 (338)
-..|.+|=.++. +-.| - +||++||..|.-+....+ ..+..+-|--|+..+..
T Consensus 186 ~~~CPICL~~~~-~p~~-t---~CGHiFC~~CiLqy~~~s----~~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 186 DMQCPICLEPPS-VPVR-T---NCGHIFCGPCILQYWNYS----AIKGPCSCPICRSTITL 237 (513)
T ss_pred CCcCCcccCCCC-cccc-c---ccCceeeHHHHHHHHhhh----cccCCccCCchhhhccc
Confidence 368999999887 3332 2 399999999976554433 23567889999998765
No 30
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=74.39 E-value=1.8 Score=29.05 Aligned_cols=26 Identities=31% Similarity=0.741 Sum_probs=16.9
Q ss_pred ccCCCCcCCccc------cccccccccCCceE
Q 019595 152 VCMQCTAPFTAL------TRGRHHCRFCGGVF 177 (338)
Q Consensus 152 ~C~~C~~~F~~l------~rRrHHCR~CG~vf 177 (338)
.|..|++.|..= ..++-.|.+||++|
T Consensus 4 ~Cp~C~~~y~i~d~~ip~~g~~v~C~~C~~~f 35 (36)
T PF13717_consen 4 TCPNCQAKYEIDDEKIPPKGRKVRCSKCGHVF 35 (36)
T ss_pred ECCCCCCEEeCCHHHCCCCCcEEECCCCCCEe
Confidence 578888888620 22466777777765
No 31
>KOG0317 consensus Predicted E3 ubiquitin ligase, integral peroxisomal membrane protein [Posttranslational modification, protein turnover, chaperones]
Probab=73.29 E-value=0.77 Score=44.54 Aligned_cols=49 Identities=27% Similarity=0.719 Sum_probs=34.3
Q ss_pred CCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccccccccccc
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPLQ 212 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~~ 212 (338)
...|..|=. .++---|-.||++||++|...+..- ++. |.-|....++.+
T Consensus 239 ~~kC~LCLe-----~~~~pSaTpCGHiFCWsCI~~w~~e-------k~e--CPlCR~~~~psk 287 (293)
T KOG0317|consen 239 TRKCSLCLE-----NRSNPSATPCGHIFCWSCILEWCSE-------KAE--CPLCREKFQPSK 287 (293)
T ss_pred CCceEEEec-----CCCCCCcCcCcchHHHHHHHHHHcc-------ccC--CCcccccCCCcc
Confidence 368888844 2345679999999999997654321 122 999988887654
No 32
>KOG1314 consensus DHHC-type Zn-finger protein [General function prediction only]
Probab=72.12 E-value=1.3 Score=44.30 Aligned_cols=35 Identities=29% Similarity=0.831 Sum_probs=25.6
Q ss_pred cCCCCccCCCCC-----CccCCCCcCCccccccccccccCCce
Q 019595 139 AEPPEWLPDSST-----TVCMQCTAPFTALTRGRHHCRFCGGV 176 (338)
Q Consensus 139 ~~~p~W~pd~~~-----~~C~~C~~~F~~l~rRrHHCR~CG~v 176 (338)
..|+.|.|.... +.|..|+. |. .-|-||||.|.+.
T Consensus 75 ~vp~~wkPe~~~D~~~lqfCk~Cqg-YK--apRSHHCrkCnrC 114 (414)
T KOG1314|consen 75 FVPLGWKPENPKDEMFLQFCKKCQG-YK--APRSHHCRKCNRC 114 (414)
T ss_pred CCCCCCCCCCChhHHHHHHHhhccC-cC--CCccccchHHHHH
Confidence 357889985544 47888876 44 3589999999774
No 33
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=71.26 E-value=2.4 Score=28.48 Aligned_cols=26 Identities=31% Similarity=0.746 Sum_probs=17.6
Q ss_pred ccCCCCcCCccc------cccccccccCCceE
Q 019595 152 VCMQCTAPFTAL------TRGRHHCRFCGGVF 177 (338)
Q Consensus 152 ~C~~C~~~F~~l------~rRrHHCR~CG~vf 177 (338)
.|..|+..|..- ..++..|-.|+++|
T Consensus 4 ~CP~C~~~f~v~~~~l~~~~~~vrC~~C~~~f 35 (37)
T PF13719_consen 4 TCPNCQTRFRVPDDKLPAGGRKVRCPKCGHVF 35 (37)
T ss_pred ECCCCCceEEcCHHHcccCCcEEECCCCCcEe
Confidence 688888888621 23467777777765
No 34
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=68.59 E-value=3.8 Score=29.61 Aligned_cols=28 Identities=32% Similarity=0.621 Sum_probs=19.5
Q ss_pred CCccCCCCcCCccccccccccccCCceE
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGVF 177 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~vf 177 (338)
...|..|+..|-.....|++|..||..+
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCCEE
Confidence 3589999886443344578888888764
No 35
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=68.21 E-value=3.3 Score=28.28 Aligned_cols=26 Identities=38% Similarity=0.933 Sum_probs=19.7
Q ss_pred cCCCCcCCccccccccccccCCceEeCCC
Q 019595 153 CMQCTAPFTALTRGRHHCRFCGGVFCRIC 181 (338)
Q Consensus 153 C~~C~~~F~~l~rRrHHCR~CG~vfC~~C 181 (338)
|..|++.-. |+ ...|+.|+++||...
T Consensus 1 C~~C~~~~~-l~--~f~C~~C~~~FC~~H 26 (39)
T smart00154 1 CHFCRKKVG-LT--GFKCRHCGNLFCGEH 26 (39)
T ss_pred CcccCCccc-cc--CeECCccCCcccccc
Confidence 667887655 33 578999999998864
No 36
>KOG3576 consensus Ovo and related transcription factors [Transcription]
Probab=67.14 E-value=1.1 Score=41.84 Aligned_cols=34 Identities=35% Similarity=0.731 Sum_probs=24.1
Q ss_pred CCCCCCccCCCCcCCcc---cc--------ccccccccCCceEeC
Q 019595 146 PDSSTTVCMQCTAPFTA---LT--------RGRHHCRFCGGVFCR 179 (338)
Q Consensus 146 pd~~~~~C~~C~~~F~~---l~--------rRrHHCR~CG~vfC~ 179 (338)
+|.+.-.|..|++.|+. |. .|||-|+.||+-|=.
T Consensus 113 sd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfnd 157 (267)
T KOG3576|consen 113 SDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFND 157 (267)
T ss_pred CCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCcccc
Confidence 45566789999999973 11 248889999887644
No 37
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE. The only sequence scoring between trusted and noise is that from Aquifex aeolicus, which shows certain structural differences from the proteobacterial forms in the alignment. However it is notable that A. aeolicus also has a sequence scoring above trusted to the alpha subunit of formate dehydrogenase (TIGR01553).
Probab=67.14 E-value=5.7 Score=39.06 Aligned_cols=62 Identities=27% Similarity=0.631 Sum_probs=37.2
Q ss_pred CCccCCCCcCC--ccc-------cccccccccCCc------eEeCCCCCceee--cCccCC-CCccee--eccccccccc
Q 019595 150 TTVCMQCTAPF--TAL-------TRGRHHCRFCGG------VFCRICTKGRCL--LPVRFR-ERNPQR--VCDACYDRLD 209 (338)
Q Consensus 150 ~~~C~~C~~~F--~~l-------~rRrHHCR~CG~------vfC~~Cs~~~~~--lP~~~~-~~~p~R--VC~~C~~~l~ 209 (338)
...|..|+..= +.+ ..|..||-.|+. +-|..|-+.+.+ ...... ....+| +|+.|..-++
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~e~~~~~~~~r~e~C~~C~~YlK 263 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLSLEHDAEKAVLKAETCDSCQGYLK 263 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEeecCCCCCcceEEeeccccccchh
Confidence 46899998842 111 236788988874 578888765421 111110 123455 9999998876
Q ss_pred cc
Q 019595 210 PL 211 (338)
Q Consensus 210 ~~ 211 (338)
..
T Consensus 264 ~~ 265 (305)
T TIGR01562 264 IL 265 (305)
T ss_pred hh
Confidence 54
No 38
>KOG4275 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=66.54 E-value=0.67 Score=45.14 Aligned_cols=49 Identities=24% Similarity=0.628 Sum_probs=39.2
Q ss_pred CCCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccc
Q 019595 148 SSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDR 207 (338)
Q Consensus 148 ~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~ 207 (338)
..+..|..|+..|. -++|||-|--|-+-||..||.. . ...|.|..|...
T Consensus 42 ~~~p~ckacg~~f~-~~~~k~~c~dckk~fc~tcs~v--~--------~~lr~c~~c~r~ 90 (350)
T KOG4275|consen 42 SQAPHCKACGEEFE-DAQSKSDCEDCKKEFCATCSRV--S--------ISLRTCTSCRRV 90 (350)
T ss_pred cccchhhhhchhHh-hhhhhhhhhhhhHHHHHHHHHh--c--------ccchhhhHHHHH
Confidence 34458999999999 5789999999999999999921 1 346788888753
No 39
>PF06577 DUF1134: Protein of unknown function (DUF1134); InterPro: IPR008325 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=66.36 E-value=8.6 Score=34.30 Aligned_cols=39 Identities=13% Similarity=0.261 Sum_probs=29.5
Q ss_pred eeEEEEEecCceEEEEEcCCCccccceeEEEecceEEEEeeEEe
Q 019595 293 AGVLVSYKLGTGLVVARRSDGSWSAPSAILSVGLGWGAQVNSHV 336 (338)
Q Consensus 293 ~g~~~g~~~G~G~vvaR~~~g~WS~P~~i~~~g~s~G~q~G~e~ 336 (338)
++|++|.++|+|.|.-|...- --+-|-|-|+|+.+|++-
T Consensus 48 GA~~~GlrYGeG~L~~k~~g~-----~~vyWqGPSiG~D~G~~~ 86 (160)
T PF06577_consen 48 GAFVVGLRYGEGTLYTKNAGQ-----HKVYWQGPSIGFDFGGNG 86 (160)
T ss_pred ccEEEEEEecccEEEEcCCCe-----eEEEEeCCceeEeecCCc
Confidence 456889999999999987432 345666778888888764
No 40
>PF01485 IBR: IBR domain; InterPro: IPR002867 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 cysteine-rich (C6HC) zinc finger domain that is present in Triad1, and which is conserved in other proteins encoded by various eukaryotes. The C6HC consensus pattern is: C-x(4)-C-x(14-30)-C-x(1-4)-C-x(4)-C-x(2)-C-x(4)-H-x(4)-C The C6HC zinc finger motif is the fourth family member of the zinc-binding RING, LIM, and LAP/PHD fingers. Strikingly, in most of the proteins the C6HC domain is flanked by two RING finger structures IPR001841 from INTERPRO. The novel C6HC motif has been called DRIL (double RING finger linked). The strong conservation of the larger tripartite TRIAD (twoRING fingers and DRIL) structure indicates that the three subdomains are functionally linked and identifies a novel class of proteins []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 2CT7_A 1WD2_A 2JMO_A 1WIM_A.
Probab=66.29 E-value=5.5 Score=28.70 Aligned_cols=35 Identities=23% Similarity=0.457 Sum_probs=20.4
Q ss_pred CCccCC--CCcCCcccccc---ccccccCCceEeCCCCCc
Q 019595 150 TTVCMQ--CTAPFTALTRG---RHHCRFCGGVFCRICTKG 184 (338)
Q Consensus 150 ~~~C~~--C~~~F~~l~rR---rHHCR~CG~vfC~~Cs~~ 184 (338)
...|.. |+..|..-... .-.|..||..||..|...
T Consensus 18 ~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 18 IRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSE
T ss_pred ccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcc
Confidence 357866 99877632111 257999999999999753
No 41
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=66.13 E-value=1.2 Score=30.78 Aligned_cols=32 Identities=28% Similarity=0.692 Sum_probs=23.8
Q ss_pred ccCCCCcCCccccccccccccCCceEeCCCCCce
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGR 185 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~ 185 (338)
.|..|.+.|+ .+++-.=-.||++||..|....
T Consensus 1 ~C~~C~~~~~--~~~~~~l~~CgH~~C~~C~~~~ 32 (44)
T PF14634_consen 1 HCNICFEKYS--EERRPRLTSCGHIFCEKCLKKL 32 (44)
T ss_pred CCcCcCcccc--CCCCeEEcccCCHHHHHHHHhh
Confidence 4788888884 1344555689999999998654
No 42
>PF12773 DZR: Double zinc ribbon
Probab=65.18 E-value=4.8 Score=28.23 Aligned_cols=28 Identities=21% Similarity=0.713 Sum_probs=17.3
Q ss_pred CCCCccCCCCcCCccccccccccccCCc
Q 019595 148 SSTTVCMQCTAPFTALTRGRHHCRFCGG 175 (338)
Q Consensus 148 ~~~~~C~~C~~~F~~l~rRrHHCR~CG~ 175 (338)
.++..|..|+.+...-......|..||.
T Consensus 10 ~~~~fC~~CG~~l~~~~~~~~~C~~Cg~ 37 (50)
T PF12773_consen 10 DDAKFCPHCGTPLPPPDQSKKICPNCGA 37 (50)
T ss_pred ccccCChhhcCChhhccCCCCCCcCCcC
Confidence 3467788888876622233566777766
No 43
>PF00415 RCC1: Regulator of chromosome condensation (RCC1) repeat; InterPro: IPR000408 The regulator of chromosome condensation (RCC1) [] is a eukaryotic protein which binds to chromatin and interacts with ran, a nuclear GTP-binding protein IPR002041 from INTERPRO, to promote the loss of bound GDP and the uptake of fresh GTP, thus acting as a guanine-nucleotide dissociation stimulator (GDS). The interaction of RCC1 with ran probably plays an important role in the regulation of gene expression. RCC1, known as PRP20 or SRM1 in yeast, pim1 in fission yeast and BJ1 in Drosophila, is a protein that contains seven tandem repeats of a domain of about 50 to 60 amino acids. As shown in the following schematic representation, the repeats make up the major part of the length of the protein. Outside the repeat region, there is just a small N-terminal domain of about 40 to 50 residues and, in the Drosophila protein only, a C-terminal domain of about 130 residues. +----+-------+-------+-------+-------+-------+-------+-------+-------------+ |N-t.|Rpt. 1 |Rpt. 2 |Rpt. 3 |Rpt. 4 |Rpt. 5 |Rpt. 6 |Rpt. 7 | C-terminal | +----+-------+-------+-------+-------+-------+-------+-------+-------------+ The RCC1-type of repeat is also found in the X-linked retinitis pigmentosa GTPase regulator []. The RCC repeats form a beta-propeller structure.; PDB: 3MVD_L 3OF7_A 1I2M_D 1A12_B 3KCI_A 4DNV_B 4DNU_A 4D9S_B 4DNW_A.
Probab=62.74 E-value=2 Score=29.73 Aligned_cols=30 Identities=20% Similarity=0.151 Sum_probs=21.7
Q ss_pred CCceeecccCCCCCccc-CCCCCCCCCCCccc
Q 019595 94 SSNVSFFGSGKNGDTYL-HSSVYIPSAPPLLE 124 (338)
Q Consensus 94 ~~~v~~~g~~~nG~~~~-~~s~~~~~~p~l~~ 124 (338)
.++||+||.+.+|++ + ..+......|..++
T Consensus 1 dG~vy~wG~n~~GqL-G~~~~~~~~~~P~~v~ 31 (51)
T PF00415_consen 1 DGRVYSWGSNDYGQL-GSGGDNKNVSVPTKVP 31 (51)
T ss_dssp TSEEEEEEEETTSTT-SSSSSSSEEEEEEEEG
T ss_pred CCcEEEEECCCCCCC-CCCCCCCceeEEEEEC
Confidence 368999999999998 5 55555555555543
No 44
>PRK00420 hypothetical protein; Validated
Probab=61.70 E-value=5.9 Score=33.44 Aligned_cols=26 Identities=31% Similarity=0.659 Sum_probs=16.6
Q ss_pred CCccCCCCcCCccccccccccccCCceEeCCCCC
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTK 183 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~ 183 (338)
...|..|+.+|.-+.. |++||..|..
T Consensus 23 ~~~CP~Cg~pLf~lk~--------g~~~Cp~Cg~ 48 (112)
T PRK00420 23 SKHCPVCGLPLFELKD--------GEVVCPVHGK 48 (112)
T ss_pred cCCCCCCCCcceecCC--------CceECCCCCC
Confidence 3689999987764433 4555555543
No 45
>PF07282 OrfB_Zn_ribbon: Putative transposase DNA-binding domain; InterPro: IPR010095 This entry represents a region of a sequence similarity between a family of putative transposases of Thermoanaerobacter tengcongensis, smaller related proteins from Bacillus anthracis, putative transposes described by IPR001959 from INTERPRO, and other proteins. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=61.61 E-value=7.3 Score=29.11 Aligned_cols=29 Identities=17% Similarity=0.391 Sum_probs=22.3
Q ss_pred CCCccCCCCcCCcc-ccccccccccCCceE
Q 019595 149 STTVCMQCTAPFTA-LTRGRHHCRFCGGVF 177 (338)
Q Consensus 149 ~~~~C~~C~~~F~~-l~rRrHHCR~CG~vf 177 (338)
....|..|+..-.. ...|.++|..||..+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEE
Confidence 35789999986653 466789999999864
No 46
>KOG3799 consensus Rab3 effector RIM1 and related proteins, contain Rab3a binding domain [Intracellular trafficking, secretion, and vesicular transport]
Probab=60.83 E-value=3.6 Score=35.99 Aligned_cols=52 Identities=27% Similarity=0.645 Sum_probs=38.6
Q ss_pred CCCccCCCCc-CCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccc
Q 019595 149 STTVCMQCTA-PFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDR 207 (338)
Q Consensus 149 ~~~~C~~C~~-~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~ 207 (338)
+...|.+|.+ +|. -.. -|.|..|---||..|--.. .+ +.++-.-||.-|-..
T Consensus 64 ddatC~IC~KTKFA-DG~-GH~C~YCq~r~CARCGGrv-~l----rsNKv~wvcnlc~k~ 116 (169)
T KOG3799|consen 64 DDATCGICHKTKFA-DGC-GHNCSYCQTRFCARCGGRV-SL----RSNKVMWVCNLCRKQ 116 (169)
T ss_pred cCcchhhhhhcccc-ccc-CcccchhhhhHHHhcCCee-ee----ccCceEEeccCCcHH
Confidence 3468999988 565 233 6999999999999998643 22 345778899999753
No 47
>KOG0978 consensus E3 ubiquitin ligase involved in syntaxin degradation [Posttranslational modification, protein turnover, chaperones]
Probab=58.36 E-value=1 Score=48.62 Aligned_cols=46 Identities=28% Similarity=0.665 Sum_probs=33.3
Q ss_pred CCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccccccc
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRL 208 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l 208 (338)
.-.|..|...|-- ----.||++||..|...+. ...+|-|..|-.-.
T Consensus 643 ~LkCs~Cn~R~Kd-----~vI~kC~H~FC~~Cvq~r~--------etRqRKCP~Cn~aF 688 (698)
T KOG0978|consen 643 LLKCSVCNTRWKD-----AVITKCGHVFCEECVQTRY--------ETRQRKCPKCNAAF 688 (698)
T ss_pred ceeCCCccCchhh-----HHHHhcchHHHHHHHHHHH--------HHhcCCCCCCCCCC
Confidence 3589999875532 1224799999999986542 35799999997654
No 48
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=57.36 E-value=2.8 Score=38.62 Aligned_cols=59 Identities=15% Similarity=0.433 Sum_probs=37.8
Q ss_pred CCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCc-------cCCCCcceeecccccccccccc
Q 019595 149 STTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPV-------RFRERNPQRVCDACYDRLDPLQ 212 (338)
Q Consensus 149 ~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~-------~~~~~~p~RVC~~C~~~l~~~~ 212 (338)
+.-.|.+|...+.- . .--.||++||..|......... .....+....|-.|...+....
T Consensus 17 ~~~~CpICld~~~d----P-VvT~CGH~FC~~CI~~wl~~s~~s~~~~~~~~~~k~~~~CPvCR~~Is~~~ 82 (193)
T PLN03208 17 GDFDCNICLDQVRD----P-VVTLCGHLFCWPCIHKWTYASNNSRQRVDQYDHKREPPKCPVCKSDVSEAT 82 (193)
T ss_pred CccCCccCCCcCCC----c-EEcCCCchhHHHHHHHHHHhccccccccccccccCCCCcCCCCCCcCChhc
Confidence 34689999987752 1 2257999999999875422110 0111234568999999887543
No 49
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=55.86 E-value=10 Score=27.26 Aligned_cols=35 Identities=29% Similarity=0.581 Sum_probs=25.1
Q ss_pred CCccC--CCCcCCccc---cccccccccCCceEeCCCCCc
Q 019595 150 TTVCM--QCTAPFTAL---TRGRHHCRFCGGVFCRICTKG 184 (338)
Q Consensus 150 ~~~C~--~C~~~F~~l---~rRrHHCR~CG~vfC~~Cs~~ 184 (338)
...|. .|+...... ...+-.|..||..||..|...
T Consensus 18 ~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 18 LKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred ccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCc
Confidence 34677 787655422 345788999999999999754
No 50
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=53.90 E-value=13 Score=36.71 Aligned_cols=62 Identities=21% Similarity=0.423 Sum_probs=37.4
Q ss_pred CCccCCCCcC--Cccc------cccccccccCCc------eEeCCCCCceeec--CccCC-CCcceeeccccccccccc
Q 019595 150 TTVCMQCTAP--FTAL------TRGRHHCRFCGG------VFCRICTKGRCLL--PVRFR-ERNPQRVCDACYDRLDPL 211 (338)
Q Consensus 150 ~~~C~~C~~~--F~~l------~rRrHHCR~CG~------vfC~~Cs~~~~~l--P~~~~-~~~p~RVC~~C~~~l~~~ 211 (338)
...|..|+.. .+.+ ..|..||-.|+. +-|..|-+.+.+- ..... ....+-+|+.|..-++..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~~~~~~~~~r~e~C~~C~~YlK~~ 265 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWSLDSEQAAVKAESCGDCGTYLKIL 265 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeeeecCCCcceEeeecccccccceec
Confidence 4789999885 2211 246788888874 5788887643211 00111 123456999999887654
No 51
>PHA02768 hypothetical protein; Provisional
Probab=52.84 E-value=8.4 Score=28.53 Aligned_cols=26 Identities=12% Similarity=0.195 Sum_probs=17.1
Q ss_pred ccCCCCcCCccc---c--cc----ccccccCCceE
Q 019595 152 VCMQCTAPFTAL---T--RG----RHHCRFCGGVF 177 (338)
Q Consensus 152 ~C~~C~~~F~~l---~--rR----rHHCR~CG~vf 177 (338)
.|..|++.|+.. . .| .+.|-.||++|
T Consensus 7 ~C~~CGK~Fs~~~~L~~H~r~H~k~~kc~~C~k~f 41 (55)
T PHA02768 7 ECPICGEIYIKRKSMITHLRKHNTNLKLSNCKRIS 41 (55)
T ss_pred CcchhCCeeccHHHHHHHHHhcCCcccCCccccee
Confidence 799999999741 0 12 44577777765
No 52
>PF01529 zf-DHHC: DHHC palmitoyltransferase; InterPro: IPR001594 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 DHHC-type zinc finger domain, which is also known as NEW1 []. The DHHC Zn-finger was first isolated in the Drosophila putative transcription factor DNZ1 and was named after a conserved sequence motif []. This domain has palmitoyltransferase activity; this post-translational modification attaches the C16 saturated fatty acid palmitate via a thioester linkage, predominantly to cysteine residues []. This domain is found in the DHHC proteins which are palmitoyl transferases []; the DHHC motif is found within a cysteine-rich domain which is thought to contain the catalytic site. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding
Probab=52.46 E-value=9.3 Score=33.19 Aligned_cols=27 Identities=26% Similarity=0.651 Sum_probs=19.8
Q ss_pred CCCCCccCCCCcCCccccccccccccCCce
Q 019595 147 DSSTTVCMQCTAPFTALTRGRHHCRFCGGV 176 (338)
Q Consensus 147 d~~~~~C~~C~~~F~~l~rRrHHCR~CG~v 176 (338)
......|..|...=- .|-|||+.|++.
T Consensus 45 ~~~~~~C~~C~~~kp---~Rs~HC~~C~~C 71 (174)
T PF01529_consen 45 NGELKYCSTCKIIKP---PRSHHCRVCNRC 71 (174)
T ss_pred CCCCEECcccCCcCC---Ccceeccccccc
Confidence 345578999987533 378999999775
No 53
>COG1773 Rubredoxin [Energy production and conversion]
Probab=51.38 E-value=12 Score=27.78 Aligned_cols=41 Identities=27% Similarity=0.521 Sum_probs=23.5
Q ss_pred cccccccCCceEeCCCCCceeecC--ccCCCCcceeecccccc
Q 019595 166 GRHHCRFCGGVFCRICTKGRCLLP--VRFRERNPQRVCDACYD 206 (338)
Q Consensus 166 RrHHCR~CG~vfC~~Cs~~~~~lP--~~~~~~~p~RVC~~C~~ 206 (338)
+++.|+.||.|+=..=-..+.-++ .+|.......+|..|-.
T Consensus 2 ~~~~C~~CG~vYd~e~Gdp~~gi~pgT~fedlPd~w~CP~Cg~ 44 (55)
T COG1773 2 KRWRCSVCGYVYDPEKGDPRCGIAPGTPFEDLPDDWVCPECGV 44 (55)
T ss_pred CceEecCCceEeccccCCccCCCCCCCchhhCCCccCCCCCCC
Confidence 479999999997443222222222 12333445678888863
No 54
>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=51.07 E-value=5.1 Score=39.46 Aligned_cols=49 Identities=18% Similarity=0.437 Sum_probs=30.7
Q ss_pred CccCCCCcC--CccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccc
Q 019595 151 TVCMQCTAP--FTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 151 ~~C~~C~~~--F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~ 209 (338)
..|..|... +++-.+=-.+ .||+.||.+|...-.. .....|..|...+.
T Consensus 4 ~~CP~Ck~~~y~np~~kl~i~--~CGH~~C~sCv~~l~~--------~~~~~CP~C~~~lr 54 (309)
T TIGR00570 4 QGCPRCKTTKYRNPSLKLMVN--VCGHTLCESCVDLLFV--------RGSGSCPECDTPLR 54 (309)
T ss_pred CCCCcCCCCCccCcccccccC--CCCCcccHHHHHHHhc--------CCCCCCCCCCCccc
Confidence 579999984 4421111233 8999999999875321 11236888876554
No 55
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=51.01 E-value=9.1 Score=26.64 Aligned_cols=23 Identities=26% Similarity=0.691 Sum_probs=13.8
Q ss_pred ccCCCCcCCcccccc--ccccccCCc
Q 019595 152 VCMQCTAPFTALTRG--RHHCRFCGG 175 (338)
Q Consensus 152 ~C~~C~~~F~~l~rR--rHHCR~CG~ 175 (338)
.|..|+..|. +... ..+|..||.
T Consensus 5 ~C~~CG~~~~-~~~~~~~~~Cp~CG~ 29 (46)
T PRK00398 5 KCARCGREVE-LDEYGTGVRCPYCGY 29 (46)
T ss_pred ECCCCCCEEE-ECCCCCceECCCCCC
Confidence 5777888776 2222 356666665
No 56
>KOG0823 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=50.97 E-value=4.4 Score=38.21 Aligned_cols=36 Identities=22% Similarity=0.517 Sum_probs=25.7
Q ss_pred ccCCceEeCCCCCceeecCccCCCCcceeecccccccccccc
Q 019595 171 RFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPLQ 212 (338)
Q Consensus 171 R~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~~ 212 (338)
-.||++||+-|.-++... ....+.|-.|...++...
T Consensus 63 TlCGHLFCWpClyqWl~~------~~~~~~cPVCK~~Vs~~~ 98 (230)
T KOG0823|consen 63 TLCGHLFCWPCLYQWLQT------RPNSKECPVCKAEVSIDT 98 (230)
T ss_pred eecccceehHHHHHHHhh------cCCCeeCCccccccccce
Confidence 489999999999877443 234567788877776433
No 57
>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=50.74 E-value=9.6 Score=29.60 Aligned_cols=44 Identities=23% Similarity=0.641 Sum_probs=21.6
Q ss_pred CccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccccccc
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPLQG 213 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~~~ 213 (338)
..|..|+.+.. ....+.||-.|..-| ..+-.|..|...|+.++.
T Consensus 2 ~~CP~C~~~L~-~~~~~~~C~~C~~~~------------------~~~a~CPdC~~~Le~LkA 45 (70)
T PF07191_consen 2 NTCPKCQQELE-WQGGHYHCEACQKDY------------------KKEAFCPDCGQPLEVLKA 45 (70)
T ss_dssp -B-SSS-SBEE-EETTEEEETTT--EE------------------EEEEE-TTT-SB-EEEEE
T ss_pred CcCCCCCCccE-EeCCEEECccccccc------------------eecccCCCcccHHHHHHH
Confidence 36899999876 334466666665531 245566666666655543
No 58
>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=50.63 E-value=2.3 Score=27.80 Aligned_cols=30 Identities=33% Similarity=0.654 Sum_probs=21.1
Q ss_pred ccCCCCcCCccccccccccccCCceEeCCCCCce
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGR 185 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~ 185 (338)
.|..|...+. ....-..||+.||..|....
T Consensus 1 ~C~iC~~~~~----~~~~~~~C~H~~c~~C~~~~ 30 (45)
T cd00162 1 ECPICLEEFR----EPVVLLPCGHVFCRSCIDKW 30 (45)
T ss_pred CCCcCchhhh----CceEecCCCChhcHHHHHHH
Confidence 3778887763 23445569999999997643
No 59
>PF03604 DNA_RNApol_7kD: DNA directed RNA polymerase, 7 kDa subunit; InterPro: IPR006591 DNA-dependent RNA polymerase catalyzes the transcription of DNA into RNA using the four ribonucleoside triphosphates as substrates. Each class of RNA polymerase is assembled from 9 to 15 different polypeptides. Rbp10 (RNA polymerase CX) is a domain found in RNA polymerase subunit 10; present in RNA polymerase I, II and III.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 2PMZ_Z 3HKZ_X 2NVX_L 3S1Q_L 2JA6_L 3S17_L 3HOW_L 3HOV_L 3PO2_L 3HOZ_L ....
Probab=50.48 E-value=12 Score=24.64 Aligned_cols=24 Identities=25% Similarity=0.582 Sum_probs=14.3
Q ss_pred ccCCCCcCCccccccccccccCCc
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGG 175 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~ 175 (338)
.|..|+..|..-..-.-.|+.||.
T Consensus 2 ~C~~Cg~~~~~~~~~~irC~~CG~ 25 (32)
T PF03604_consen 2 ICGECGAEVELKPGDPIRCPECGH 25 (32)
T ss_dssp BESSSSSSE-BSTSSTSSBSSSS-
T ss_pred CCCcCCCeeEcCCCCcEECCcCCC
Confidence 478888888732223457777775
No 60
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=50.40 E-value=10 Score=36.40 Aligned_cols=33 Identities=18% Similarity=0.506 Sum_probs=26.5
Q ss_pred cCCCCCCccCCCCcCCccc------cccccccccCCceE
Q 019595 145 LPDSSTTVCMQCTAPFTAL------TRGRHHCRFCGGVF 177 (338)
Q Consensus 145 ~pd~~~~~C~~C~~~F~~l------~rRrHHCR~CG~vf 177 (338)
-.-++++.|..|++.|.++ ..-..||..|++.|
T Consensus 127 p~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F 165 (278)
T PF15135_consen 127 PQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNF 165 (278)
T ss_pred CcccccccccccccccCCCccccccceeeeecccccccc
Confidence 4557889999999998764 22378999999987
No 61
>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=49.37 E-value=4.9 Score=26.77 Aligned_cols=29 Identities=24% Similarity=0.610 Sum_probs=20.1
Q ss_pred cCCCCcCCccccccccccccCCceEeCCCCCce
Q 019595 153 CMQCTAPFTALTRGRHHCRFCGGVFCRICTKGR 185 (338)
Q Consensus 153 C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~ 185 (338)
|..|...+. .....-.||++||..|....
T Consensus 1 C~iC~~~~~----~~~~~~~CGH~fC~~C~~~~ 29 (39)
T PF13923_consen 1 CPICLDELR----DPVVVTPCGHSFCKECIEKY 29 (39)
T ss_dssp ETTTTSB-S----SEEEECTTSEEEEHHHHHHH
T ss_pred CCCCCCccc----CcCEECCCCCchhHHHHHHH
Confidence 566765433 34567899999999997543
No 62
>PRK04023 DNA polymerase II large subunit; Validated
Probab=48.05 E-value=15 Score=41.51 Aligned_cols=50 Identities=22% Similarity=0.522 Sum_probs=35.3
Q ss_pred CCCCccCCCCcCCccccccccccccCCce-----EeCCCCCceeecCccCCCCcceeeccccccccccccc
Q 019595 148 SSTTVCMQCTAPFTALTRGRHHCRFCGGV-----FCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPLQG 213 (338)
Q Consensus 148 ~~~~~C~~C~~~F~~l~rRrHHCR~CG~v-----fC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~~~ 213 (338)
.....|..|+.... ...|..||.. ||..|-... ..-.|..|-..+...+.
T Consensus 624 Vg~RfCpsCG~~t~-----~frCP~CG~~Te~i~fCP~CG~~~-----------~~y~CPKCG~El~~~s~ 678 (1121)
T PRK04023 624 IGRRKCPSCGKETF-----YRRCPFCGTHTEPVYRCPRCGIEV-----------EEDECEKCGREPTPYSK 678 (1121)
T ss_pred ccCccCCCCCCcCC-----cccCCCCCCCCCcceeCccccCcC-----------CCCcCCCCCCCCCccce
Confidence 34579999999743 3689999964 999994321 11349999888776544
No 63
>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=47.35 E-value=16 Score=28.99 Aligned_cols=32 Identities=28% Similarity=0.501 Sum_probs=24.9
Q ss_pred CCCccCCCCcCCccccccccccccCCceEeCCCCC
Q 019595 149 STTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTK 183 (338)
Q Consensus 149 ~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~ 183 (338)
+...|..|+++|.. ..-.-..||.+|-..|..
T Consensus 77 ~~~~C~vC~k~l~~---~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 77 ESTKCSVCGKPLGN---SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCCCccCcCCcCCC---ceEEEeCCCeEEeccccc
Confidence 34679999999872 456667889999999864
No 64
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=46.97 E-value=5.2 Score=38.49 Aligned_cols=48 Identities=23% Similarity=0.574 Sum_probs=32.1
Q ss_pred CccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccccccccc
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDP 210 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~ 210 (338)
-.|..|-..=. .--|+.||++||..|.-.. ...+..--|.-|..+..+
T Consensus 216 ~kC~lC~e~~~-----~ps~t~CgHlFC~~Cl~~~-------~t~~k~~~CplCRak~~p 263 (271)
T COG5574 216 YKCFLCLEEPE-----VPSCTPCGHLFCLSCLLIS-------WTKKKYEFCPLCRAKVYP 263 (271)
T ss_pred cceeeeecccC-----CcccccccchhhHHHHHHH-------HHhhccccCchhhhhccc
Confidence 57888866333 4679999999999997431 112334458888776654
No 65
>PF10571 UPF0547: Uncharacterised protein family UPF0547; InterPro: IPR018886 This domain may well be a type of zinc-finger as it carries two pairs of highly conserved cysteine residues though with no accompanying histidines. Several members are annotated as putative helicases.
Probab=46.07 E-value=14 Score=23.18 Aligned_cols=23 Identities=30% Similarity=0.733 Sum_probs=14.2
Q ss_pred ccCCCCcCCccccccccccccCCceE
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGVF 177 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~vf 177 (338)
.|..|++.-. .. -.-|.+||..|
T Consensus 2 ~CP~C~~~V~-~~--~~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVP-ES--AKFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCch-hh--cCcCCCCCCCC
Confidence 4777777665 22 35677777765
No 66
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=44.78 E-value=13 Score=26.15 Aligned_cols=23 Identities=26% Similarity=0.686 Sum_probs=13.1
Q ss_pred ccCCCCcCCccccccccccccCC
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCG 174 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG 174 (338)
.|..|+..|..-..-.-.|+.||
T Consensus 4 ~C~~Cg~~~~~~~~~~irC~~CG 26 (44)
T smart00659 4 ICGECGRENEIKSKDVVRCRECG 26 (44)
T ss_pred ECCCCCCEeecCCCCceECCCCC
Confidence 58889998883212233444444
No 67
>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=44.20 E-value=4.9 Score=27.38 Aligned_cols=32 Identities=31% Similarity=0.534 Sum_probs=23.1
Q ss_pred ccCCCCcCCccccccccccccCCceEeCCCCCce
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGR 185 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~ 185 (338)
.|.+|...|.. .. .-.--.||++||..|....
T Consensus 2 ~C~IC~~~~~~-~~-~~~~l~C~H~fh~~Ci~~~ 33 (44)
T PF13639_consen 2 ECPICLEEFED-GE-KVVKLPCGHVFHRSCIKEW 33 (44)
T ss_dssp CETTTTCBHHT-TS-CEEEETTSEEEEHHHHHHH
T ss_pred CCcCCChhhcC-CC-eEEEccCCCeeCHHHHHHH
Confidence 68999999863 22 3333449999999997654
No 68
>PF04216 FdhE: Protein involved in formate dehydrogenase formation; InterPro: IPR006452 This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex []. The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. ; GO: 0005737 cytoplasm; PDB: 2FIY_B.
Probab=43.67 E-value=12 Score=36.14 Aligned_cols=63 Identities=25% Similarity=0.548 Sum_probs=31.2
Q ss_pred CCccCCCCcCCc--cc------cccccccccCCc------eEeCCCCCceee-cC---ccCCCCcceeeccccccccccc
Q 019595 150 TTVCMQCTAPFT--AL------TRGRHHCRFCGG------VFCRICTKGRCL-LP---VRFRERNPQRVCDACYDRLDPL 211 (338)
Q Consensus 150 ~~~C~~C~~~F~--~l------~rRrHHCR~CG~------vfC~~Cs~~~~~-lP---~~~~~~~p~RVC~~C~~~l~~~ 211 (338)
...|..|+..=. .+ .+|..||-.||. +-|..|-+.... +- ........+-||+.|..-++..
T Consensus 172 ~g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK~v 251 (290)
T PF04216_consen 172 RGYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLKTV 251 (290)
T ss_dssp -SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEEEE
T ss_pred CCcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHHHH
Confidence 369999998521 11 247889999985 479999765421 11 1112234567999999887655
Q ss_pred c
Q 019595 212 Q 212 (338)
Q Consensus 212 ~ 212 (338)
.
T Consensus 252 d 252 (290)
T PF04216_consen 252 D 252 (290)
T ss_dssp E
T ss_pred h
Confidence 4
No 69
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=43.57 E-value=14 Score=40.01 Aligned_cols=32 Identities=25% Similarity=0.717 Sum_probs=23.5
Q ss_pred CCCCccCCCCcCCccccccccccccCCce------EeCCCCCc
Q 019595 148 SSTTVCMQCTAPFTALTRGRHHCRFCGGV------FCRICTKG 184 (338)
Q Consensus 148 ~~~~~C~~C~~~F~~l~rRrHHCR~CG~v------fC~~Cs~~ 184 (338)
..+..|..|+.++.. ..|..||.. ||..|-..
T Consensus 13 ~~akFC~~CG~~l~~-----~~Cp~CG~~~~~~~~fC~~CG~~ 50 (645)
T PRK14559 13 NNNRFCQKCGTSLTH-----KPCPQCGTEVPVDEAHCPNCGAE 50 (645)
T ss_pred CCCccccccCCCCCC-----CcCCCCCCCCCcccccccccCCc
Confidence 356789999887761 368888887 88888653
No 70
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.12 E-value=16 Score=34.36 Aligned_cols=26 Identities=27% Similarity=0.550 Sum_probs=19.8
Q ss_pred CCCCccCCCCcCCccccccccccccCCceE
Q 019595 148 SSTTVCMQCTAPFTALTRGRHHCRFCGGVF 177 (338)
Q Consensus 148 ~~~~~C~~C~~~F~~l~rRrHHCR~CG~vf 177 (338)
..+..|..|+. +..|.+.|..||..+
T Consensus 307 ~tS~~C~~cg~----~~~r~~~C~~cg~~~ 332 (364)
T COG0675 307 YTSKTCPCCGH----LSGRLFKCPRCGFVH 332 (364)
T ss_pred CCcccccccCC----ccceeEECCCCCCee
Confidence 44578999999 335778899888864
No 71
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=43.08 E-value=7.1 Score=35.90 Aligned_cols=45 Identities=22% Similarity=0.488 Sum_probs=34.6
Q ss_pred ccccCCceEeCCCCCc-eeecCcc---CCCCcceeeccccccccccccc
Q 019595 169 HCRFCGGVFCRICTKG-RCLLPVR---FRERNPQRVCDACYDRLDPLQG 213 (338)
Q Consensus 169 HCR~CG~vfC~~Cs~~-~~~lP~~---~~~~~p~RVC~~C~~~l~~~~~ 213 (338)
.|...|+.||..|-.. ...+|.+ ...-++..||+..++.|.....
T Consensus 2 ~C~Y~G~yyC~~CH~~~~~vIParil~~WDf~~~pVs~~a~~~L~~~~~ 50 (202)
T PF13901_consen 2 FCDYTGKYYCSSCHWNDTSVIPARILHNWDFRPYPVSRFAKQFLDQIWS 50 (202)
T ss_pred ccCCCCCcCCCCCCCCCceeccHHHHHhcCCCccHHHHHHHHHHHHhcc
Confidence 5999999999999765 5667743 2345789999999998875443
No 72
>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=42.16 E-value=15 Score=24.33 Aligned_cols=10 Identities=30% Similarity=0.923 Sum_probs=5.7
Q ss_pred ccCCCCcCCc
Q 019595 152 VCMQCTAPFT 161 (338)
Q Consensus 152 ~C~~C~~~F~ 161 (338)
.|..|++.|.
T Consensus 4 ~CP~C~~~~~ 13 (38)
T TIGR02098 4 QCPNCKTSFR 13 (38)
T ss_pred ECCCCCCEEE
Confidence 4566666554
No 73
>PF14353 CpXC: CpXC protein
Probab=42.13 E-value=15 Score=30.92 Aligned_cols=10 Identities=30% Similarity=0.876 Sum_probs=7.7
Q ss_pred ccCCCCcCCc
Q 019595 152 VCMQCTAPFT 161 (338)
Q Consensus 152 ~C~~C~~~F~ 161 (338)
.|..|+..|.
T Consensus 3 tCP~C~~~~~ 12 (128)
T PF14353_consen 3 TCPHCGHEFE 12 (128)
T ss_pred CCCCCCCeeE
Confidence 5888888874
No 74
>KOG2879 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=41.69 E-value=16 Score=35.61 Aligned_cols=54 Identities=31% Similarity=0.683 Sum_probs=40.4
Q ss_pred CCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccccccc
Q 019595 149 STTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPLQG 213 (338)
Q Consensus 149 ~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~~~ 213 (338)
...+|..|+..=+ + -||--.||+++|-.|......- ...-.|..|-+-..+.|+
T Consensus 238 ~~~~C~~Cg~~Pt-i---P~~~~~C~HiyCY~Ci~ts~~~-------~asf~Cp~Cg~~~~~lq~ 291 (298)
T KOG2879|consen 238 SDTECPVCGEPPT-I---PHVIGKCGHIYCYYCIATSRLW-------DASFTCPLCGENVEPLQA 291 (298)
T ss_pred CCceeeccCCCCC-C---Ceeeccccceeehhhhhhhhcc-------hhhcccCccCCCCcchhh
Confidence 3478999999555 2 6999999999999998654322 234579999988776663
No 75
>PF10497 zf-4CXXC_R1: Zinc-finger domain of monoamine-oxidase A repressor R1; InterPro: IPR018866 R1 is a transcription factor repressor that inhibits monoamine oxidase A gene expression. This domain is a four-CXXC zinc finger putative DNA-binding domain found at the C-terminal end of R1. The domain carries 12 cysteines of which four pairs are of the CXXC type [].
Probab=40.74 E-value=9.8 Score=31.56 Aligned_cols=58 Identities=24% Similarity=0.472 Sum_probs=35.6
Q ss_pred CCCccCCCCcCCcccccccccc------ccC---CceEeCCCCCceeecCccCCCCcceeeccccccccc
Q 019595 149 STTVCMQCTAPFTALTRGRHHC------RFC---GGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 149 ~~~~C~~C~~~F~~l~rRrHHC------R~C---G~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~ 209 (338)
.-..|..|+++-. ..+..| ..| ...||..|...+.-.-...-...+..+|..|...-+
T Consensus 6 ~g~~CHqCrqKt~---~~~~~C~~~~~~~~C~~~~~~fC~~CL~~ryge~~~ev~~~~~W~CP~CrgiCn 72 (105)
T PF10497_consen 6 NGKTCHQCRQKTL---DFKTICTGHWKNSSCRGCRGKFCGGCLRNRYGENVEEVLEDPNWKCPKCRGICN 72 (105)
T ss_pred CCCCchhhcCCCC---CCceEcCCCCCCCCCccCcceehHhHHHHHHhhhHHHHhcCCceECCCCCCeeC
Confidence 3467899988543 122334 666 999999998765321100111356789999988654
No 76
>KOG1814 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=40.69 E-value=12 Score=38.29 Aligned_cols=42 Identities=31% Similarity=0.785 Sum_probs=32.0
Q ss_pred CCccCCCCCCccCCCCcCCcccc-ccccccccCCceEeCCCCCc
Q 019595 142 PEWLPDSSTTVCMQCTAPFTALT-RGRHHCRFCGGVFCRICTKG 184 (338)
Q Consensus 142 p~W~pd~~~~~C~~C~~~F~~l~-rRrHHCR~CG~vfC~~Cs~~ 184 (338)
-.|+. +....|..|...-...- .-|+||-.||..||.-|+..
T Consensus 361 ekwl~-~N~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~ 403 (445)
T KOG1814|consen 361 EKWLE-SNSKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAEL 403 (445)
T ss_pred HHHHH-hcCCCCCcccceeecCCCccceeeccccccceeehhhh
Confidence 37885 45789999998654221 23899999999999999864
No 77
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=40.53 E-value=20 Score=28.90 Aligned_cols=10 Identities=30% Similarity=0.966 Sum_probs=5.7
Q ss_pred CccCCCCcCC
Q 019595 151 TVCMQCTAPF 160 (338)
Q Consensus 151 ~~C~~C~~~F 160 (338)
+.|..|+++.
T Consensus 34 S~C~~C~~~L 43 (92)
T PF06750_consen 34 SHCPHCGHPL 43 (92)
T ss_pred CcCcCCCCcC
Confidence 5566666554
No 78
>KOG1829 consensus Uncharacterized conserved protein, contains C1, PH and RUN domains [Signal transduction mechanisms]
Probab=40.20 E-value=14 Score=39.44 Aligned_cols=61 Identities=23% Similarity=0.482 Sum_probs=44.3
Q ss_pred CccCCCCcCCc-cccccccccccCCceEeCCCCCcee-ecCcc---CCCCcceeeccccccccccc
Q 019595 151 TVCMQCTAPFT-ALTRGRHHCRFCGGVFCRICTKGRC-LLPVR---FRERNPQRVCDACYDRLDPL 211 (338)
Q Consensus 151 ~~C~~C~~~F~-~l~rRrHHCR~CG~vfC~~Cs~~~~-~lP~~---~~~~~p~RVC~~C~~~l~~~ 211 (338)
-.|.+|++.+. .+..|---|+.+|+-||..|-.... .+|.+ ...-++..||+.=...|...
T Consensus 341 ~~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~~~svIPARVl~~WDf~~y~Vs~~a~~~L~~i 406 (580)
T KOG1829|consen 341 FRCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQNDKSVIPARVLHNWDFTKYPVSNFAKQFLDEI 406 (580)
T ss_pred ceecccCCCcccccccchhHhhhhhhhhCchhcccCcccccccceecccCcccccchhHHHHHHHH
Confidence 48999999998 5566778899999999999976543 34643 12236788887766666543
No 79
>PRK04136 rpl40e 50S ribosomal protein L40e; Provisional
Probab=39.30 E-value=18 Score=26.11 Aligned_cols=22 Identities=36% Similarity=0.835 Sum_probs=17.6
Q ss_pred CccCCCCcCCccccccccccccCCc
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGG 175 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~ 175 (338)
..|+.|...-. -|-.+||.||.
T Consensus 15 ~ICrkC~ARnp---~~A~~CRKCg~ 36 (48)
T PRK04136 15 KICMRCNARNP---WRATKCRKCGY 36 (48)
T ss_pred cchhcccCCCC---ccccccccCCC
Confidence 57999988766 36899999886
No 80
>KOG3173 consensus Predicted Zn-finger protein [General function prediction only]
Probab=38.98 E-value=16 Score=32.89 Aligned_cols=29 Identities=38% Similarity=0.989 Sum_probs=22.9
Q ss_pred CCCccCCCCcCCccccccccccccCCceEeCCC
Q 019595 149 STTVCMQCTAPFTALTRGRHHCRFCGGVFCRIC 181 (338)
Q Consensus 149 ~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~C 181 (338)
....|..|++.-. ++ . .||| ||.+||...
T Consensus 104 ~~~rC~~C~kk~g-lt-g-f~Cr-CG~~fC~~H 132 (167)
T KOG3173|consen 104 KKKRCFKCRKKVG-LT-G-FKCR-CGNTFCGTH 132 (167)
T ss_pred cchhhhhhhhhhc-cc-c-cccc-cCCcccccc
Confidence 3456999998888 55 3 8997 999999864
No 81
>KOG1311 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=38.94 E-value=14 Score=35.54 Aligned_cols=24 Identities=21% Similarity=0.535 Sum_probs=17.9
Q ss_pred CCccCCCCcCCccccccccccccCCce
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGV 176 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~v 176 (338)
...|..|+.. . -.|-|||+.|++.
T Consensus 113 ~~~C~~C~~~-r--PpRs~HCsvC~~C 136 (299)
T KOG1311|consen 113 WKYCDTCQLY-R--PPRSSHCSVCNNC 136 (299)
T ss_pred eEEcCcCccc-C--CCCcccchhhccc
Confidence 4689999874 2 2578999988764
No 82
>PF09297 zf-NADH-PPase: NADH pyrophosphatase zinc ribbon domain; InterPro: IPR015376 This domain has a zinc ribbon structure and is often found between two NUDIX domains.; GO: 0016787 hydrolase activity, 0046872 metal ion binding; PDB: 1VK6_A 2GB5_A.
Probab=38.76 E-value=26 Score=22.51 Aligned_cols=25 Identities=28% Similarity=0.551 Sum_probs=13.1
Q ss_pred EeCCCCCceeecCccCCCCcceeecccccc
Q 019595 177 FCRICTKGRCLLPVRFRERNPQRVCDACYD 206 (338)
Q Consensus 177 fC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~ 206 (338)
||..|-......+ ..-.|+|..|-.
T Consensus 5 fC~~CG~~t~~~~-----~g~~r~C~~Cg~ 29 (32)
T PF09297_consen 5 FCGRCGAPTKPAP-----GGWARRCPSCGH 29 (32)
T ss_dssp B-TTT--BEEE-S-----SSS-EEESSSS-
T ss_pred ccCcCCccccCCC-----CcCEeECCCCcC
Confidence 6777776554443 357899999864
No 83
>PF15616 TerY-C: TerY-C metal binding domain
Probab=38.10 E-value=22 Score=30.86 Aligned_cols=39 Identities=23% Similarity=0.608 Sum_probs=27.9
Q ss_pred CccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccc
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~ 209 (338)
..|..|+..|. |. -| .||+++|..= ...-+|.-|-....
T Consensus 78 PgCP~CGn~~~-fa----~C-~CGkl~Ci~g--------------~~~~~CPwCg~~g~ 116 (131)
T PF15616_consen 78 PGCPHCGNQYA-FA----VC-GCGKLFCIDG--------------EGEVTCPWCGNEGS 116 (131)
T ss_pred CCCCCCcChhc-EE----Ee-cCCCEEEeCC--------------CCCEECCCCCCeee
Confidence 68999999999 43 36 7999999642 12557777766543
No 84
>PF09889 DUF2116: Uncharacterized protein containing a Zn-ribbon (DUF2116); InterPro: IPR019216 This entry contains various hypothetical prokaryotic proteins whose functions are unknown. They contain a conserved zinc ribbon motif in the N-terminal part and a predicted transmembrane segment in the C-terminal part.
Probab=37.77 E-value=5.9 Score=29.71 Aligned_cols=31 Identities=26% Similarity=0.680 Sum_probs=21.8
Q ss_pred ccccccCCceEeCCCCCceeecCccCCCCcceeec-ccccccccccccc
Q 019595 167 RHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVC-DACYDRLDPLQGV 214 (338)
Q Consensus 167 rHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC-~~C~~~l~~~~~~ 214 (338)
..||..||.- +| ...+.| +.|.+.+...|+.
T Consensus 3 HkHC~~CG~~-----------Ip------~~~~fCS~~C~~~~~k~qk~ 34 (59)
T PF09889_consen 3 HKHCPVCGKP-----------IP------PDESFCSPKCREEYRKRQKR 34 (59)
T ss_pred CCcCCcCCCc-----------CC------cchhhhCHHHHHHHHHHHHH
Confidence 4799999873 33 247899 4898888765543
No 85
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=36.70 E-value=16 Score=36.28 Aligned_cols=39 Identities=31% Similarity=0.812 Sum_probs=29.9
Q ss_pred ccCCCCCCccCCCCcCCcc---------ccccccccccCCceEeCCCC
Q 019595 144 WLPDSSTTVCMQCTAPFTA---------LTRGRHHCRFCGGVFCRICT 182 (338)
Q Consensus 144 W~pd~~~~~C~~C~~~F~~---------l~rRrHHCR~CG~vfC~~Cs 182 (338)
|-..-....|..|+.+|-. +...|..|..|-.-||..|-
T Consensus 356 ~~~~~ks~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCd 403 (421)
T COG5151 356 EGTNPKSTHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCD 403 (421)
T ss_pred CCCCCCCccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhH
Confidence 4444456789999998842 23568999999999999995
No 86
>TIGR00100 hypA hydrogenase nickel insertion protein HypA. In Hpylori, hypA mutant abolished hydrogenase activity and decrease in urease activity. Nickel supplementation in media restored urease activity and partial hydrogenase activity. HypA probably involved in inserting Ni in enzymes.
Probab=36.24 E-value=17 Score=30.44 Aligned_cols=25 Identities=20% Similarity=0.501 Sum_probs=15.2
Q ss_pred CCccCCCCcCCccccccccccccCCc
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGG 175 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~ 175 (338)
.-.|..|+..|. +.....+|..||.
T Consensus 70 ~~~C~~Cg~~~~-~~~~~~~CP~Cgs 94 (115)
T TIGR00100 70 ECECEDCSEEVS-PEIDLYRCPKCHG 94 (115)
T ss_pred EEEcccCCCEEe-cCCcCccCcCCcC
Confidence 367889998887 3333344555553
No 87
>PF13117 Cag12: Cag pathogenicity island protein Cag12
Probab=36.00 E-value=43 Score=28.33 Aligned_cols=37 Identities=30% Similarity=0.454 Sum_probs=22.3
Q ss_pred eEEEEEeccccccCCCCCCCCCC--------CCCCCCCCCCCCCC
Q 019595 2 MIIVILFGGCQKAKKPYPTVSNS--------TKEDYMYPFPLESD 38 (338)
Q Consensus 2 ~~~~~~~~~~~~~~~~~~~~~~~--------~~~~~~~~~~~~~~ 38 (338)
||+++++.||....+|-|---+. -.+.+++.+++.++
T Consensus 1 ~~~~~~L~gCSSpP~P~~v~~~k~~~~iN~~l~~~~~~~~V~~s~ 45 (113)
T PF13117_consen 1 MILALMLSGCSSPPEPPPVDWNKPAVPINTSLPEWKPNSFVPKSD 45 (113)
T ss_pred CchheeehhcCCCCCCCCcCCCCCcceecccccccccCcCcCCCc
Confidence 68899999997776664432221 14445555555554
No 88
>TIGR02874 spore_ytfJ sporulation protein YtfJ. Members of this protein family, exemplified by YtfJ of Bacillus subtilis, are encoded by bacterial genomes if and only if the species is capable of endospore formation. YtfJ was confirmed in spores of Bacillus subtilis; it appears to be expressed in the forespore under control of SigF (see PubMed:12480901).
Probab=35.53 E-value=82 Score=27.11 Aligned_cols=51 Identities=12% Similarity=0.098 Sum_probs=34.2
Q ss_pred hhHHHHHHHHHHHHhhhcccCCCCcCcchhhhcCCcceEEEEEEeeeEEEEEecCce
Q 019595 248 MEYEIYKASNTLRSYCQVAESNPERSIPLAVLNGAKGLAILTVAKAGVLVSYKLGTG 304 (338)
Q Consensus 248 meeeI~kAa~iL~~~~~~~~~~p~~~ip~~~l~~a~Gi~i~~v~k~g~~~g~~~G~G 304 (338)
.+..+..+.+-|++|.... .+-=+-++-.-|-.|+||.|++|.||+.+|.+
T Consensus 4 ie~lm~t~~e~ik~~i~v~------tVvGdPI~~~dgt~IIPvs~VsfGfgaGg~~~ 54 (125)
T TIGR02874 4 IENLMKTTMENIKEMIDVN------TIVGDPVETPDGSVIIPISKVSFGFAAGGSEF 54 (125)
T ss_pred HHHHHHHHHHHHHHheeec------eEEecCEEcCCCeEEEEEEEEEEeeeeccCcc
Confidence 3455666777788886532 12222244556789999999999998777664
No 89
>KOG1813 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=35.26 E-value=27 Score=34.31 Aligned_cols=28 Identities=29% Similarity=0.744 Sum_probs=21.9
Q ss_pred ccCCCCcCCccccccccccccCCceEeCCCCCc
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGVFCRICTKG 184 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~ 184 (338)
.|.+|++.|-.-. =-.||+-||..|+..
T Consensus 243 ~c~icr~~f~~pV-----vt~c~h~fc~~ca~~ 270 (313)
T KOG1813|consen 243 KCFICRKYFYRPV-----VTKCGHYFCEVCALK 270 (313)
T ss_pred cccccccccccch-----hhcCCceeehhhhcc
Confidence 5999999886322 247999999999865
No 90
>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=35.11 E-value=18 Score=25.49 Aligned_cols=11 Identities=27% Similarity=0.739 Sum_probs=7.3
Q ss_pred ccCCCCcCCcc
Q 019595 152 VCMQCTAPFTA 162 (338)
Q Consensus 152 ~C~~C~~~F~~ 162 (338)
.|..|+..|..
T Consensus 7 ~C~~Cg~~fe~ 17 (52)
T TIGR02605 7 RCTACGHRFEV 17 (52)
T ss_pred EeCCCCCEeEE
Confidence 46777777763
No 91
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=34.74 E-value=28 Score=23.18 Aligned_cols=28 Identities=29% Similarity=0.517 Sum_probs=12.5
Q ss_pred EeCCCCCce-eecCccCCCCcceeecccccc
Q 019595 177 FCRICTKGR-CLLPVRFRERNPQRVCDACYD 206 (338)
Q Consensus 177 fC~~Cs~~~-~~lP~~~~~~~p~RVC~~C~~ 206 (338)
||..|...- ..+| .+.+++-.||..|-.
T Consensus 2 fC~~CG~~l~~~ip--~gd~r~R~vC~~Cg~ 30 (34)
T PF14803_consen 2 FCPQCGGPLERRIP--EGDDRERLVCPACGF 30 (34)
T ss_dssp B-TTT--B-EEE----TT-SS-EEEETTTTE
T ss_pred ccccccChhhhhcC--CCCCccceECCCCCC
Confidence 455554332 2334 234678889999964
No 92
>PF01155 HypA: Hydrogenase expression/synthesis hypA family; InterPro: IPR000688 Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions []. One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanocaldococcus jannaschii (Methanococcus jannaschii).; GO: 0016151 nickel ion binding, 0006464 protein modification process; PDB: 2KDX_A 3A44_D 3A43_B.
Probab=33.91 E-value=12 Score=31.27 Aligned_cols=24 Identities=25% Similarity=0.605 Sum_probs=14.0
Q ss_pred CccCCCCcCCccccccccccccCCc
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGG 175 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~ 175 (338)
-.|..|+..|. +......|..||.
T Consensus 71 ~~C~~Cg~~~~-~~~~~~~CP~Cgs 94 (113)
T PF01155_consen 71 ARCRDCGHEFE-PDEFDFSCPRCGS 94 (113)
T ss_dssp EEETTTS-EEE-CHHCCHH-SSSSS
T ss_pred EECCCCCCEEe-cCCCCCCCcCCcC
Confidence 57889999888 3333345555554
No 93
>PF03107 C1_2: C1 domain; InterPro: IPR004146 This short domain is rich in cysteines and histidines. The pattern of conservation is similar to that found in DAG_PE-bind (IPR002219 from INTERPRO), therefore we have termed this domain DC1 for divergent C1 domain. This domain probably also binds to two zinc ions. The function of proteins with this domain is uncertain, however this domain may bind to molecules such as diacylglycerol. This family are found in plant proteins.
Probab=33.60 E-value=40 Score=21.39 Aligned_cols=29 Identities=21% Similarity=0.424 Sum_probs=22.4
Q ss_pred ccCCCCcCCccccccccccccCCceEeCCCC
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGVFCRICT 182 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs 182 (338)
.|..|++..+.+. ..+|..|+..+-..|.
T Consensus 2 ~C~~C~~~~~~~~--~Y~C~~c~f~lh~~Ca 30 (30)
T PF03107_consen 2 WCDVCRRKIDGFY--FYHCSECCFTLHVRCA 30 (30)
T ss_pred CCCCCCCCcCCCE--eEEeCCCCCeEcCccC
Confidence 5889999888553 6899999877776663
No 94
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=33.36 E-value=22 Score=29.90 Aligned_cols=25 Identities=20% Similarity=0.441 Sum_probs=14.9
Q ss_pred CCccCCCCcCCcccccccc-ccccCCc
Q 019595 150 TTVCMQCTAPFTALTRGRH-HCRFCGG 175 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrH-HCR~CG~ 175 (338)
.-.|..|+..|. +..... +|..||.
T Consensus 71 ~~~C~~Cg~~~~-~~~~~~~~CP~Cgs 96 (117)
T PRK00564 71 ELECKDCSHVFK-PNALDYGVCEKCHS 96 (117)
T ss_pred EEEhhhCCCccc-cCCccCCcCcCCCC
Confidence 357888988887 322222 3666654
No 95
>PF04438 zf-HIT: HIT zinc finger; InterPro: IPR007529 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents the HIT-type zinc finger, which contains 7 conserved cysteines and one histidine that can potentially coordinate two zinc atoms. It has been named after the first protein that originally defined the domain: the yeast HIT1 protein (P46973 from SWISSPROT) []. The HIT-type zinc finger displays some sequence similarities to the MYND-type zinc finger. The function of this domain is unknown but it is mainly found in nuclear proteins involved in gene regulation and chromatin remodeling. This domain is also found in the thyroid receptor interacting protein 3 (TRIP-3) Q15649 from SWISSPROT, that specifically interacts with the ligand binding domain of the thyroid receptor. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; PDB: 2YQP_A 2YQQ_A 1X4S_A.
Probab=33.01 E-value=22 Score=22.89 Aligned_cols=23 Identities=26% Similarity=0.852 Sum_probs=15.3
Q ss_pred CccCCCCcCCccccccccccccCCceEeC
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGVFCR 179 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~vfC~ 179 (338)
..|..|+. + .++.|..||..+|+
T Consensus 3 ~~C~vC~~-~-----~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 3 KLCSVCGN-P-----AKYRCPRCGARYCS 25 (30)
T ss_dssp EEETSSSS-E-----ESEE-TTT--EESS
T ss_pred CCCccCcC-C-----CEEECCCcCCceeC
Confidence 46888887 2 26889999999886
No 96
>PRK05978 hypothetical protein; Provisional
Probab=32.95 E-value=25 Score=31.09 Aligned_cols=26 Identities=31% Similarity=0.671 Sum_probs=16.1
Q ss_pred CccCCCCc--CCccccccccccccCCce
Q 019595 151 TVCMQCTA--PFTALTRGRHHCRFCGGV 176 (338)
Q Consensus 151 ~~C~~C~~--~F~~l~rRrHHCR~CG~v 176 (338)
..|..|++ -|..+.+=+.+|..||.-
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~ 61 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGED 61 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCc
Confidence 56777776 354444446777777764
No 97
>KOG1315 consensus Predicted DHHC-type Zn-finger protein [General function prediction only]
Probab=32.95 E-value=20 Score=35.36 Aligned_cols=28 Identities=25% Similarity=0.711 Sum_probs=18.4
Q ss_pred cCCCCCCccCCCCcCCccccccccccccCCc
Q 019595 145 LPDSSTTVCMQCTAPFTALTRGRHHCRFCGG 175 (338)
Q Consensus 145 ~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~ 175 (338)
.++.....|..|+. .. --|-|||+-|++
T Consensus 104 ~~~g~~R~C~kC~~-iK--PdRaHHCsvC~r 131 (307)
T KOG1315|consen 104 TSDGAVRYCDKCKC-IK--PDRAHHCSVCNR 131 (307)
T ss_pred cCCCCceeeccccc-cc--CCccccchhhhh
Confidence 34556678888876 22 147899988743
No 98
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=32.42 E-value=22 Score=34.90 Aligned_cols=27 Identities=22% Similarity=0.568 Sum_probs=17.6
Q ss_pred CCCCCccCCCCcCCccccccccccccCCce
Q 019595 147 DSSTTVCMQCTAPFTALTRGRHHCRFCGGV 176 (338)
Q Consensus 147 d~~~~~C~~C~~~F~~l~rRrHHCR~CG~v 176 (338)
+.....|..|+.-=- -|-|||+.|++.
T Consensus 106 ~~~~~~C~~C~~~KP---~RS~HC~~Cn~C 132 (309)
T COG5273 106 FGTENFCSTCNIYKP---PRSHHCSICNRC 132 (309)
T ss_pred cccceeccccccccC---CCCccchhhcch
Confidence 334467888876222 368999888764
No 99
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=32.38 E-value=7.6 Score=28.43 Aligned_cols=45 Identities=20% Similarity=0.623 Sum_probs=34.2
Q ss_pred CccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccc
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~ 209 (338)
-.|..|+..|. + ..-..|-.||+--|++|-.. ..-.|+.|-..++
T Consensus 8 y~CDLCn~~~p-~-~~LRQCvlCGRWaC~sCW~d------------eYY~CksC~Gii~ 52 (57)
T PF14445_consen 8 YSCDLCNSSHP-I-SELRQCVLCGRWACNSCWQD------------EYYTCKSCNGIIN 52 (57)
T ss_pred HhHHhhcccCc-H-HHHHHHhhhchhhhhhhhhh------------hHhHHHhhhchhh
Confidence 36889999998 4 34678999999999999743 3556888876553
No 100
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=32.19 E-value=14 Score=25.81 Aligned_cols=31 Identities=29% Similarity=0.667 Sum_probs=14.1
Q ss_pred cCCCCcCCccccccccccccCCceEeCCCCCce
Q 019595 153 CMQCTAPFTALTRGRHHCRFCGGVFCRICTKGR 185 (338)
Q Consensus 153 C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~ 185 (338)
|.+|.. |+.-. ..--=-.||++||..|..+.
T Consensus 1 CpIc~e-~~~~~-n~P~~L~CGH~~c~~cl~~l 31 (43)
T PF13445_consen 1 CPICKE-FSTEE-NPPMVLPCGHVFCKDCLQKL 31 (43)
T ss_dssp -TTT-----TTS-S-EEE-SSS-EEEHHHHHHH
T ss_pred CCcccc-ccCCC-CCCEEEeCccHHHHHHHHHH
Confidence 677777 75311 11222459999999997643
No 101
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=32.05 E-value=22 Score=25.74 Aligned_cols=24 Identities=21% Similarity=0.625 Sum_probs=14.5
Q ss_pred ccCCCCcCCccc-cccccccccCCc
Q 019595 152 VCMQCTAPFTAL-TRGRHHCRFCGG 175 (338)
Q Consensus 152 ~C~~C~~~F~~l-~rRrHHCR~CG~ 175 (338)
.|..|++.|..+ ..+.-.|..||.
T Consensus 8 ~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EhhhcCCeeehhhccCceeCCCCCc
Confidence 688999998743 223444555543
No 102
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=31.76 E-value=24 Score=36.04 Aligned_cols=47 Identities=21% Similarity=0.489 Sum_probs=32.0
Q ss_pred CCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccc
Q 019595 149 STTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 149 ~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~ 209 (338)
..-.|.+|...|.- .---.||+.||..|...... ....|-.|...+.
T Consensus 25 ~~l~C~IC~d~~~~-----PvitpCgH~FCs~CI~~~l~---------~~~~CP~Cr~~~~ 71 (397)
T TIGR00599 25 TSLRCHICKDFFDV-----PVLTSCSHTFCSLCIRRCLS---------NQPKCPLCRAEDQ 71 (397)
T ss_pred cccCCCcCchhhhC-----ccCCCCCCchhHHHHHHHHh---------CCCCCCCCCCccc
Confidence 44689999987752 23468999999999764311 1246888876654
No 103
>KOG3795 consensus Uncharacterized conserved protein [Function unknown]
Probab=30.96 E-value=22 Score=32.60 Aligned_cols=23 Identities=35% Similarity=0.870 Sum_probs=16.7
Q ss_pred CccccccccccccCCc---eEeCCCCC
Q 019595 160 FTALTRGRHHCRFCGG---VFCRICTK 183 (338)
Q Consensus 160 F~~l~rRrHHCR~CG~---vfC~~Cs~ 183 (338)
|..+ ..||.|+.|+. .||-.|.-
T Consensus 9 ~d~i-eGRs~C~~C~~SRkFfCY~C~V 34 (230)
T KOG3795|consen 9 FDPI-EGRSTCPGCKSSRKFFCYDCRV 34 (230)
T ss_pred cCcc-cccccCCCCCCcceEEEEeecc
Confidence 4433 46899999985 48999873
No 104
>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=30.84 E-value=33 Score=22.94 Aligned_cols=10 Identities=50% Similarity=1.012 Sum_probs=3.9
Q ss_pred ceeecccccc
Q 019595 197 PQRVCDACYD 206 (338)
Q Consensus 197 p~RVC~~C~~ 206 (338)
..+||+.|.+
T Consensus 23 ~~~VCD~CRD 32 (34)
T PF01286_consen 23 DLPVCDKCRD 32 (34)
T ss_dssp S-S--TTT-S
T ss_pred CccccccccC
Confidence 4677777754
No 105
>smart00834 CxxC_CXXC_SSSS Putative regulatory protein. CxxC_CXXC_SSSS represents a region of about 41 amino acids found in a number of small proteins in a wide range of bacteria. The region usually begins with the initiator Met and contains two CxxC motifs separated by 17 amino acids. One protein in this entry has been noted as a putative regulatory protein, designated FmdB. Most proteins in this entry have a C-terminal region containing highly degenerate sequence.
Probab=30.62 E-value=26 Score=23.16 Aligned_cols=10 Identities=30% Similarity=0.833 Sum_probs=6.2
Q ss_pred ccCCCCcCCc
Q 019595 152 VCMQCTAPFT 161 (338)
Q Consensus 152 ~C~~C~~~F~ 161 (338)
.|..|+..|.
T Consensus 7 ~C~~Cg~~fe 16 (41)
T smart00834 7 RCEDCGHTFE 16 (41)
T ss_pred EcCCCCCEEE
Confidence 4666666665
No 106
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=30.14 E-value=36 Score=26.11 Aligned_cols=29 Identities=24% Similarity=0.684 Sum_probs=13.7
Q ss_pred CccCCCCcCCcccccccccc-ccCCceEeCCCCCc
Q 019595 151 TVCMQCTAPFTALTRGRHHC-RFCGGVFCRICTKG 184 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHC-R~CG~vfC~~Cs~~ 184 (338)
-.|..|.. ++ |.-+| -.|.++||+.|.+.
T Consensus 8 LrCs~C~~----~l-~~pv~l~~CeH~fCs~Ci~~ 37 (65)
T PF14835_consen 8 LRCSICFD----IL-KEPVCLGGCEHIFCSSCIRD 37 (65)
T ss_dssp TS-SSS-S-------SS-B---SSS--B-TTTGGG
T ss_pred cCCcHHHH----Hh-cCCceeccCccHHHHHHhHH
Confidence 35666644 33 46667 79999999999854
No 107
>PHA02942 putative transposase; Provisional
Probab=30.01 E-value=42 Score=33.91 Aligned_cols=27 Identities=22% Similarity=0.603 Sum_probs=16.0
Q ss_pred CCccCCCCcCCccccccccccccCCce
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGV 176 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~v 176 (338)
+..|..|+..=..+..|.+.|..||..
T Consensus 325 Sq~Cs~CG~~~~~l~~r~f~C~~CG~~ 351 (383)
T PHA02942 325 SVSCPKCGHKMVEIAHRYFHCPSCGYE 351 (383)
T ss_pred CccCCCCCCccCcCCCCEEECCCCCCE
Confidence 456777775322233456777777765
No 108
>PF01927 Mut7-C: Mut7-C RNAse domain; InterPro: IPR002782 This prokaryotic family of proteins have no known function. The proteins contain four conserved cysteines that may be involved in metal binding or disulphide bridges.
Probab=29.96 E-value=39 Score=29.28 Aligned_cols=19 Identities=21% Similarity=0.495 Sum_probs=13.0
Q ss_pred ccCCCCCCccCCCCcCCcc
Q 019595 144 WLPDSSTTVCMQCTAPFTA 162 (338)
Q Consensus 144 W~pd~~~~~C~~C~~~F~~ 162 (338)
...+..-+.|..|+..+-.
T Consensus 85 ~~~~~~~sRC~~CN~~L~~ 103 (147)
T PF01927_consen 85 LRLDPIFSRCPKCNGPLRP 103 (147)
T ss_pred cccCCCCCccCCCCcEeee
Confidence 3444456899999986653
No 109
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=29.51 E-value=25 Score=29.38 Aligned_cols=24 Identities=21% Similarity=0.699 Sum_probs=15.0
Q ss_pred CccCCCCcCCccccccccccccCCc
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGG 175 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~ 175 (338)
-.|..|+..|. +..+..-|..||.
T Consensus 71 ~~C~~Cg~~~~-~~~~~~~CP~Cgs 94 (113)
T PRK12380 71 AWCWDCSQVVE-IHQHDAQCPHCHG 94 (113)
T ss_pred EEcccCCCEEe-cCCcCccCcCCCC
Confidence 57888888887 3323333666663
No 110
>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=29.44 E-value=24 Score=25.26 Aligned_cols=28 Identities=32% Similarity=0.777 Sum_probs=19.4
Q ss_pred ccCCCCc-CCccccccccccccCC---ceEeCCCC
Q 019595 152 VCMQCTA-PFTALTRGRHHCRFCG---GVFCRICT 182 (338)
Q Consensus 152 ~C~~C~~-~F~~l~rRrHHCR~CG---~vfC~~Cs 182 (338)
.|..|+. ++. -.|.||-.|. .-+|..|-
T Consensus 2 ~Cd~C~~~pI~---G~R~~C~~C~~~d~DlC~~C~ 33 (48)
T cd02341 2 KCDSCGIEPIP---GTRYHCSECDDGDFDLCQDCV 33 (48)
T ss_pred CCCCCCCCccc---cceEECCCCCCCCCccCHHHH
Confidence 4888987 443 4589999997 44566554
No 111
>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=29.28 E-value=24 Score=23.68 Aligned_cols=25 Identities=24% Similarity=0.473 Sum_probs=13.4
Q ss_pred ccCCCCcCCccccccccccccCCce
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGV 176 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~v 176 (338)
.|..|+..|......+.-|..||.+
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceE
Confidence 3777777644333445555555543
No 112
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=28.88 E-value=27 Score=30.30 Aligned_cols=24 Identities=42% Similarity=0.909 Sum_probs=16.9
Q ss_pred CccCCCCcCCccccccccccccCCceEeCCCCC
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGVFCRICTK 183 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~ 183 (338)
..|..|+.+ ||+ .=|.|||..|-.
T Consensus 29 ~hCp~Cg~P---LF~------KdG~v~CPvC~~ 52 (131)
T COG1645 29 KHCPKCGTP---LFR------KDGEVFCPVCGY 52 (131)
T ss_pred hhCcccCCc---cee------eCCeEECCCCCc
Confidence 578888884 443 348888888864
No 113
>KOG1313 consensus DHHC-type Zn-finger proteins [General function prediction only]
Probab=28.64 E-value=17 Score=35.35 Aligned_cols=24 Identities=29% Similarity=0.847 Sum_probs=19.1
Q ss_pred CCccCCCCcCCccccccccccccCCce
Q 019595 150 TTVCMQCTAPFTALTRGRHHCRFCGGV 176 (338)
Q Consensus 150 ~~~C~~C~~~F~~l~rRrHHCR~CG~v 176 (338)
.+.|..|..+=+ -|-|||+.|++.
T Consensus 102 ~SfC~KC~~pK~---prTHHCsiC~kC 125 (309)
T KOG1313|consen 102 DSFCNKCNYPKS---PRTHHCSICNKC 125 (309)
T ss_pred ccHHhhcCCCCC---CCcchhhHHhhH
Confidence 378999998777 368999988774
No 114
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=28.53 E-value=37 Score=37.39 Aligned_cols=10 Identities=20% Similarity=0.650 Sum_probs=6.3
Q ss_pred eeeccccccc
Q 019595 198 QRVCDACYDR 207 (338)
Q Consensus 198 ~RVC~~C~~~ 207 (338)
-..|..|-..
T Consensus 475 p~~Cp~Cgs~ 484 (730)
T COG1198 475 PQSCPECGSE 484 (730)
T ss_pred CCCCCCCCCC
Confidence 3467777665
No 115
>PHA02929 N1R/p28-like protein; Provisional
Probab=28.29 E-value=18 Score=34.33 Aligned_cols=52 Identities=17% Similarity=0.294 Sum_probs=32.3
Q ss_pred CCCccCCCCcCCcccc---ccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccc
Q 019595 149 STTVCMQCTAPFTALT---RGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 149 ~~~~C~~C~~~F~~l~---rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~ 209 (338)
....|..|...|..-- ++--.=-.||++||..|..... +....|..|...+.
T Consensus 173 ~~~eC~ICle~~~~~~~~~~~~~vl~~C~H~FC~~CI~~Wl---------~~~~tCPlCR~~~~ 227 (238)
T PHA02929 173 KDKECAICMEKVYDKEIKNMYFGILSNCNHVFCIECIDIWK---------KEKNTCPVCRTPFI 227 (238)
T ss_pred CCCCCccCCcccccCccccccceecCCCCCcccHHHHHHHH---------hcCCCCCCCCCEee
Confidence 4578999999765100 0001123799999999986542 12346888876654
No 116
>KOG2593 consensus Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=27.49 E-value=27 Score=35.96 Aligned_cols=34 Identities=35% Similarity=0.754 Sum_probs=26.8
Q ss_pred CCccCCCCcCCccc--------cccccccccCCceEeCCCCC
Q 019595 150 TTVCMQCTAPFTAL--------TRGRHHCRFCGGVFCRICTK 183 (338)
Q Consensus 150 ~~~C~~C~~~F~~l--------~rRrHHCR~CG~vfC~~Cs~ 183 (338)
.-.|+.|+++|+.| -.-..||-+||.-+=..|+.
T Consensus 128 ~Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~ 169 (436)
T KOG2593|consen 128 GYVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENK 169 (436)
T ss_pred cccCCccccchhhhHHHHhhcccCceEEEecCCCchhccccc
Confidence 35899999999753 13579999999988777765
No 117
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=27.31 E-value=32 Score=30.65 Aligned_cols=26 Identities=23% Similarity=0.258 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHhhhcccCCCCcCcchhh
Q 019595 250 YEIYKASNTLRSYCQVAESNPERSIPLAV 278 (338)
Q Consensus 250 eeI~kAa~iL~~~~~~~~~~p~~~ip~~~ 278 (338)
+.|+.+++-+..=. ....+.+||.+.
T Consensus 82 e~ie~~v~~ie~~L---r~~g~~EV~S~~ 107 (156)
T COG1327 82 EQIEEAVSHIERQL---RSSGEREVPSKE 107 (156)
T ss_pred HHHHHHHHHHHHHH---HhcCCCCCCHHH
Confidence 34555554333322 234556676653
No 118
>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=27.08 E-value=35 Score=23.30 Aligned_cols=15 Identities=27% Similarity=0.441 Sum_probs=7.6
Q ss_pred cceeecccccccccc
Q 019595 196 NPQRVCDACYDRLDP 210 (338)
Q Consensus 196 ~p~RVC~~C~~~l~~ 210 (338)
+-..||..|=.+|..
T Consensus 17 ~g~~vC~~CG~Vl~e 31 (43)
T PF08271_consen 17 RGELVCPNCGLVLEE 31 (43)
T ss_dssp TTEEEETTT-BBEE-
T ss_pred CCeEECCCCCCEeec
Confidence 345577777655543
No 119
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=26.52 E-value=33 Score=29.69 Aligned_cols=26 Identities=27% Similarity=0.745 Sum_probs=18.5
Q ss_pred CccCCCCcCCccccc--cc--cccccCCce
Q 019595 151 TVCMQCTAPFTALTR--GR--HHCRFCGGV 176 (338)
Q Consensus 151 ~~C~~C~~~F~~l~r--Rr--HHCR~CG~v 176 (338)
-.|..|+.+-+.|.+ |. .+|..||..
T Consensus 98 VlC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 98 VICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred EECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 479999999987654 32 467777654
No 120
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=26.46 E-value=21 Score=24.45 Aligned_cols=28 Identities=32% Similarity=0.689 Sum_probs=17.8
Q ss_pred cCCCCcCCccccccccccccCCceEeCCCCCce
Q 019595 153 CMQCTAPFTALTRGRHHCRFCGGVFCRICTKGR 185 (338)
Q Consensus 153 C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~ 185 (338)
|.+|..-|.- -.=-.||+.||..|....
T Consensus 1 CpiC~~~~~~-----Pv~l~CGH~FC~~Cl~~~ 28 (42)
T PF15227_consen 1 CPICLDLFKD-----PVSLPCGHSFCRSCLERL 28 (42)
T ss_dssp ETTTTSB-SS-----EEE-SSSSEEEHHHHHHH
T ss_pred CCccchhhCC-----ccccCCcCHHHHHHHHHH
Confidence 5667665541 222479999999997654
No 121
>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=26.16 E-value=21 Score=23.60 Aligned_cols=29 Identities=34% Similarity=0.723 Sum_probs=20.3
Q ss_pred cCCCCcCCccccccccccccCCceEeCCCCCce
Q 019595 153 CMQCTAPFTALTRGRHHCRFCGGVFCRICTKGR 185 (338)
Q Consensus 153 C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~ 185 (338)
|..|...|..- ..=..||+.||..|....
T Consensus 1 C~iC~~~~~~~----~~~~~C~H~fC~~C~~~~ 29 (41)
T PF00097_consen 1 CPICLEPFEDP----VILLPCGHSFCRDCLRKW 29 (41)
T ss_dssp ETTTSSBCSSE----EEETTTSEEEEHHHHHHH
T ss_pred CCcCCccccCC----CEEecCCCcchHHHHHHH
Confidence 56777766521 235689999999998654
No 122
>PF05191 ADK_lid: Adenylate kinase, active site lid; InterPro: IPR007862 Adenylate kinases (ADK; 2.7.4.3 from EC) are phosphotransferases that catalyse the Mg-dependent reversible conversion of ATP and AMP to two molecules of ADP, an essential reaction for many processes in living cells. In large variants of adenylate kinase, the AMP and ATP substrates are buried in a domain that undergoes conformational changes from an open to a closed state when bound to substrate; the ligand is then contained within a highly specific environment required for catalysis. Adenylate kinase is a 3-domain protein consisting of a large central CORE domain flanked by a LID domain on one side and the AMP-binding NMPbind domain on the other []. The LID domain binds ATP and covers the phosphates at the active site. The substrates first bind the CORE domain, followed by closure of the active site by the LID and NMPbind domains. Comparisons of adenylate kinases have revealed a particular divergence in the active site lid. In some organisms, particularly the Gram-positive bacteria, residues in the lid domain have been mutated to cysteines and these cysteine residues (two CX(n)C motifs) are responsible for the binding of a zinc ion. The bound zinc ion in the lid domain is clearly structurally homologous to Zinc-finger domains. However, it is unclear whether the adenylate kinase lid is a novel zinc-finger DNA/RNA binding domain, or that the lid bound zinc serves a purely structural function [].; GO: 0004017 adenylate kinase activity; PDB: 3BE4_A 2OSB_B 2ORI_A 2EU8_A 3DL0_A 1P3J_A 2QAJ_A 2OO7_A 2P3S_A 3DKV_A ....
Probab=26.16 E-value=31 Score=23.14 Aligned_cols=14 Identities=36% Similarity=0.669 Sum_probs=9.6
Q ss_pred cceeeccccccccc
Q 019595 196 NPQRVCDACYDRLD 209 (338)
Q Consensus 196 ~p~RVC~~C~~~l~ 209 (338)
+..-+|+.|-..|.
T Consensus 19 ~~~~~Cd~cg~~L~ 32 (36)
T PF05191_consen 19 KVEGVCDNCGGELV 32 (36)
T ss_dssp SSTTBCTTTTEBEB
T ss_pred CCCCccCCCCCeeE
Confidence 45568888877653
No 123
>PHA02926 zinc finger-like protein; Provisional
Probab=25.68 E-value=19 Score=34.08 Aligned_cols=54 Identities=22% Similarity=0.453 Sum_probs=33.7
Q ss_pred CccCCCCcCCccccccccccc------cCCceEeCCCCCceeecCccCCCCcceeeccccccccc
Q 019595 151 TVCMQCTAPFTALTRGRHHCR------FCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR------~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~ 209 (338)
..|..|-.... -++.-.+| .|+++||-.|-....... ....-.|.|.-|...+.
T Consensus 171 ~eCgICmE~I~--eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r---~~~~~~rsCPiCR~~f~ 230 (242)
T PHA02926 171 KECGICYEVVY--SKRLENDRYFGLLDSCNHIFCITCINIWHRTR---RETGASDNCPICRTRFR 230 (242)
T ss_pred CCCccCccccc--cccccccccccccCCCCchHHHHHHHHHHHhc---cccCcCCcCCCCcceee
Confidence 67888876432 11123343 899999999987664321 12234677888877654
No 124
>PRK12496 hypothetical protein; Provisional
Probab=25.39 E-value=45 Score=29.68 Aligned_cols=24 Identities=25% Similarity=0.757 Sum_probs=14.2
Q ss_pred CccCCCCcCCccccccccccccCCc
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGG 175 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~ 175 (338)
..|.+|++.|.. ..-+.-|..||.
T Consensus 128 ~~C~gC~~~~~~-~~~~~~C~~CG~ 151 (164)
T PRK12496 128 KVCKGCKKKYPE-DYPDDVCEICGS 151 (164)
T ss_pred EECCCCCccccC-CCCCCcCCCCCC
Confidence 468888877762 222345666665
No 125
>PF09579 Spore_YtfJ: Sporulation protein YtfJ (Spore_YtfJ); InterPro: IPR014229 Proteins in this entry, exemplified by YtfJ of Bacillus subtilis, are encoded by bacterial genomes if, and only if, the species is capable of endospore formation. YtfJ was confirmed in spores of B. subtilis; it appears to be expressed in the forespore under control of SigF [].
Probab=25.37 E-value=95 Score=24.64 Aligned_cols=22 Identities=23% Similarity=0.214 Sum_probs=18.1
Q ss_pred ceEEEEEEeeeEEEEEecCceE
Q 019595 284 GLAILTVAKAGVLVSYKLGTGL 305 (338)
Q Consensus 284 Gi~i~~v~k~g~~~g~~~G~G~ 305 (338)
...|+||.+++|.||+..|.+=
T Consensus 5 d~tiIPv~~VsfGfG~Gg~~~~ 26 (83)
T PF09579_consen 5 DTTIIPVSKVSFGFGAGGGEGK 26 (83)
T ss_pred CEEEEEEEEEEEEEEEeCCCCC
Confidence 3678999999999988877764
No 126
>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=24.83 E-value=18 Score=21.75 Aligned_cols=11 Identities=27% Similarity=0.848 Sum_probs=8.8
Q ss_pred ccCCCCcCCcc
Q 019595 152 VCMQCTAPFTA 162 (338)
Q Consensus 152 ~C~~C~~~F~~ 162 (338)
.|..|++.|..
T Consensus 3 ~C~~C~~~F~~ 13 (27)
T PF13912_consen 3 ECDECGKTFSS 13 (27)
T ss_dssp EETTTTEEESS
T ss_pred CCCccCCccCC
Confidence 58888888875
No 127
>KOG4739 consensus Uncharacterized protein involved in synaptonemal complex formation [Cell cycle control, cell division, chromosome partitioning; General function prediction only]
Probab=24.81 E-value=32 Score=32.67 Aligned_cols=44 Identities=25% Similarity=0.554 Sum_probs=28.3
Q ss_pred ccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccccccc
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRLD 209 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~ 209 (338)
.|..|...=+ ....+=-.|++|||..|...- . -++|..|-..+.
T Consensus 5 hCn~C~~~~~---~~~f~LTaC~HvfC~~C~k~~--~---------~~~C~lCkk~ir 48 (233)
T KOG4739|consen 5 HCNKCFRFPS---QDPFFLTACRHVFCEPCLKAS--S---------PDVCPLCKKSIR 48 (233)
T ss_pred EeccccccCC---CCceeeeechhhhhhhhcccC--C---------ccccccccceee
Confidence 5777765222 234455589999999998532 1 129999987643
No 128
>PF15616 TerY-C: TerY-C metal binding domain
Probab=24.80 E-value=39 Score=29.33 Aligned_cols=16 Identities=56% Similarity=1.041 Sum_probs=14.1
Q ss_pred EEEEeccccccCCCCC
Q 019595 4 IVILFGGCQKAKKPYP 19 (338)
Q Consensus 4 ~~~~~~~~~~~~~~~~ 19 (338)
.|||.|=|||.||||=
T Consensus 7 ~vvl~gkCsktk~pYl 22 (131)
T PF15616_consen 7 CVVLVGKCSKTKKPYL 22 (131)
T ss_pred EEEEEEeccCCCCceE
Confidence 4889999999999983
No 129
>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=24.70 E-value=34 Score=23.48 Aligned_cols=10 Identities=20% Similarity=0.471 Sum_probs=5.3
Q ss_pred ceeecccccc
Q 019595 197 PQRVCDACYD 206 (338)
Q Consensus 197 p~RVC~~C~~ 206 (338)
+.-.|-.|-.
T Consensus 25 ~~~~CP~Cg~ 34 (42)
T PF09723_consen 25 DPVPCPECGS 34 (42)
T ss_pred CCCcCCCCCC
Confidence 4455555554
No 130
>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=24.09 E-value=37 Score=23.51 Aligned_cols=30 Identities=27% Similarity=0.734 Sum_probs=21.2
Q ss_pred ccCCCCcCCccccccccccccC-CceEeCCCCCc
Q 019595 152 VCMQCTAPFTALTRGRHHCRFC-GGVFCRICTKG 184 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~C-G~vfC~~Cs~~ 184 (338)
.|.+|+++. .-.|.+|..| ..-+|..|-..
T Consensus 2 ~Cd~C~~~i---~G~ry~C~~C~d~dLC~~C~~~ 32 (43)
T cd02340 2 ICDGCQGPI---VGVRYKCLVCPDYDLCESCEAK 32 (43)
T ss_pred CCCCCCCcC---cCCeEECCCCCCccchHHhhCc
Confidence 588999843 3458999999 45577777543
No 131
>PF06221 zf-C2HC5: Putative zinc finger motif, C2HC5-type; InterPro: IPR009349 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 zinc finger appears to be common in activating signal cointegrator 1/thyroid receptor interacting protein 4. 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, 0005634 nucleus
Probab=24.01 E-value=41 Score=25.06 Aligned_cols=28 Identities=29% Similarity=0.655 Sum_probs=19.4
Q ss_pred ccccccCCceEeCCCCCceeecCccCCCCcceeecccccccc
Q 019595 167 RHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRL 208 (338)
Q Consensus 167 rHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l 208 (338)
--+|-+||+|+|..=. |.-.|..|-..+
T Consensus 18 ~~NCl~CGkIiC~~Eg--------------~~~pC~fCg~~l 45 (57)
T PF06221_consen 18 APNCLNCGKIICEQEG--------------PLGPCPFCGTPL 45 (57)
T ss_pred cccccccChhhccccc--------------CcCcCCCCCCcc
Confidence 4689999999987521 245577776554
No 132
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=24.01 E-value=44 Score=28.26 Aligned_cols=25 Identities=28% Similarity=0.599 Sum_probs=19.6
Q ss_pred cCCCCcCCccccccccccccCCceEeCC
Q 019595 153 CMQCTAPFTALTRGRHHCRFCGGVFCRI 180 (338)
Q Consensus 153 C~~C~~~F~~l~rRrHHCR~CG~vfC~~ 180 (338)
|..|+.... ++ |-+|.+|+-.+-..
T Consensus 1 CPvCg~~l~-vt--~l~C~~C~t~i~G~ 25 (113)
T PF09862_consen 1 CPVCGGELV-VT--RLKCPSCGTEIEGE 25 (113)
T ss_pred CCCCCCceE-EE--EEEcCCCCCEEEee
Confidence 889999887 43 79999998876554
No 133
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.60 E-value=61 Score=35.22 Aligned_cols=54 Identities=22% Similarity=0.536 Sum_probs=37.9
Q ss_pred CccCCCCcCCccccccccccccCCce----EeCCCCCceeecCccCCCCcceeecccccccccccccchh
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGV----FCRICTKGRCLLPVRFRERNPQRVCDACYDRLDPLQGVLI 216 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~v----fC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l~~~~~~l~ 216 (338)
..|..|+..-. ..-.-|..||.. +|..|... +| ...+.|..|-..+...-..++
T Consensus 2 ~~Cp~Cg~~n~---~~akFC~~CG~~l~~~~Cp~CG~~---~~------~~~~fC~~CG~~~~~~~~~~~ 59 (645)
T PRK14559 2 LICPQCQFENP---NNNRFCQKCGTSLTHKPCPQCGTE---VP------VDEAHCPNCGAETGTIWWAII 59 (645)
T ss_pred CcCCCCCCcCC---CCCccccccCCCCCCCcCCCCCCC---CC------cccccccccCCcccchhhhhc
Confidence 47999998754 235679999987 58888753 23 357899999988765543333
No 134
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=23.43 E-value=40 Score=29.07 Aligned_cols=10 Identities=20% Similarity=0.783 Sum_probs=5.2
Q ss_pred ccCCCCcCCc
Q 019595 152 VCMQCTAPFT 161 (338)
Q Consensus 152 ~C~~C~~~F~ 161 (338)
.|..|+..|.
T Consensus 72 ~C~~CG~~~~ 81 (135)
T PRK03824 72 KCRNCGNEWS 81 (135)
T ss_pred ECCCCCCEEe
Confidence 4555555544
No 135
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=23.12 E-value=40 Score=28.21 Aligned_cols=25 Identities=32% Similarity=0.626 Sum_probs=13.8
Q ss_pred CccCCCCcCCccccccccccccCCc
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGG 175 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~ 175 (338)
-.|..|+..|.......-.|..||.
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs 95 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHG 95 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCC
Confidence 5788888877732111123666653
No 136
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.12 E-value=45 Score=28.30 Aligned_cols=27 Identities=15% Similarity=0.234 Sum_probs=22.2
Q ss_pred CccCCCCcCCccccccccccccCCceE
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGVF 177 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~vf 177 (338)
..|..|+++|--|.|+.--|..||+.|
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s~ 36 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKSY 36 (129)
T ss_pred ccCccccchhhccCCCccccCcccccc
Confidence 579999999988888878888888754
No 137
>KOG2807 consensus RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription; Replication, recombination and repair]
Probab=22.44 E-value=56 Score=32.67 Aligned_cols=51 Identities=24% Similarity=0.567 Sum_probs=32.7
Q ss_pred ccCCCCCCccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeeccccc
Q 019595 144 WLPDSSTTVCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACY 205 (338)
Q Consensus 144 W~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~ 205 (338)
|........|..|+..-. ...+..|+.|-.+||..|-..- ....-.|-.|.
T Consensus 324 ~~~~~~~~~Cf~C~~~~~--~~~~y~C~~Ck~~FCldCDv~i---------HesLh~CpgCe 374 (378)
T KOG2807|consen 324 ETEYNGSRFCFACQGELL--SSGRYRCESCKNVFCLDCDVFI---------HESLHNCPGCE 374 (378)
T ss_pred ccccCCCcceeeeccccC--CCCcEEchhccceeeccchHHH---------HhhhhcCCCcC
Confidence 333333456999954333 3458999999999999995321 13455666665
No 138
>cd02342 ZZ_UBA_plant Zinc finger, ZZ type. Zinc finger present in plant ubiquitin-associated (UBA) proteins. The ZZ motif coordinates a zinc ion and most likely participates in ligand binding or molecular scaffolding.
Probab=21.81 E-value=40 Score=23.78 Aligned_cols=28 Identities=25% Similarity=0.565 Sum_probs=16.8
Q ss_pred ccCCCCcCCccccccccccccCCce-EeCCC
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGV-FCRIC 181 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~v-fC~~C 181 (338)
.|-.|+.. ++.-+|++|..|-.- +|..|
T Consensus 2 ~CDgCg~~--PI~G~RykC~~C~dyDLC~~C 30 (43)
T cd02342 2 QCDGCGVL--PITGPRYKSKVKEDYDLCTIC 30 (43)
T ss_pred CCCCCCCC--cccccceEeCCCCCCccHHHH
Confidence 47888862 233468888877443 44444
No 139
>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=21.77 E-value=54 Score=22.57 Aligned_cols=28 Identities=32% Similarity=0.828 Sum_probs=18.3
Q ss_pred CccCCCCcCCccccccccccccCCc-eEeCCC
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGG-VFCRIC 181 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~-vfC~~C 181 (338)
..|..|++.+. ..|.||..|.. -+|..|
T Consensus 5 ~~C~~C~~~i~---g~ry~C~~C~d~dlC~~C 33 (44)
T smart00291 5 YSCDTCGKPIV---GVRYHCLVCPDYDLCQSC 33 (44)
T ss_pred cCCCCCCCCCc---CCEEECCCCCCccchHHH
Confidence 57999998544 45788888833 244444
No 140
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=21.65 E-value=75 Score=22.05 Aligned_cols=12 Identities=25% Similarity=0.387 Sum_probs=8.6
Q ss_pred ceeecccccccc
Q 019595 197 PQRVCDACYDRL 208 (338)
Q Consensus 197 p~RVC~~C~~~l 208 (338)
...||..|--..
T Consensus 19 ~~~vC~~Cg~~~ 30 (52)
T smart00661 19 RRFVCRKCGYEE 30 (52)
T ss_pred CEEECCcCCCeE
Confidence 477899887543
No 141
>PF01428 zf-AN1: AN1-like Zinc finger; InterPro: IPR000058 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 AN1-type zinc finger domain, which has a dimetal (zinc)-bound alpha/beta fold. This domain was first identified as a zinc finger at the C terminus of AN1 Q91889 from SWISSPROT, a ubiquitin-like protein in Xenopus laevis []. The AN1-type zinc finger contains six conserved cysteines and two histidines that could potentially coordinate 2 zinc atoms. Certain stress-associated proteins (SAP) contain AN1 domain, often in combination with A20 zinc finger domains (SAP8) or C2H2 domains (SAP16) []. For example, the human protein Znf216 has an A20 zinc-finger at the N terminus and an AN1 zinc-finger at the C terminus, acting to negatively regulate the NFkappaB activation pathway and to interact with components of the immune response like RIP, IKKgamma and TRAF6. The interact of Znf216 with IKK-gamma and RIP is mediated by the A20 zinc-finger domain, while its interaction with TRAF6 is mediated by the AN1 zinc-finger domain; therefore, both zinc-finger domains are involved in regulating the immune response []. The AN1 zinc finger domain is also found in proteins containing a ubiquitin-like domain, which are involved in the ubiquitination pathway []. Proteins containing an AN1-type zinc finger include: Ascidian posterior end mark 6 (pem-6) protein []. Human AWP1 protein (associated with PRK1), which is expressed during early embryogenesis []. Human immunoglobulin mu binding protein 2 (SMUBP-2), mutations in which cause muscular atrophy with respiratory distress type 1 []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1WFP_A 1WYS_A 1WG2_A 1WFH_A 1X4W_A 1WFE_A 1WFL_A 1X4V_A.
Probab=21.61 E-value=52 Score=22.57 Aligned_cols=16 Identities=31% Similarity=0.883 Sum_probs=10.1
Q ss_pred ccccccCCceEeCCCC
Q 019595 167 RHHCRFCGGVFCRICT 182 (338)
Q Consensus 167 rHHCR~CG~vfC~~Cs 182 (338)
...|+.|+..||...-
T Consensus 13 ~~~C~~C~~~FC~~Hr 28 (43)
T PF01428_consen 13 PFKCKHCGKSFCLKHR 28 (43)
T ss_dssp HEE-TTTS-EE-TTTH
T ss_pred CeECCCCCcccCcccc
Confidence 3679999999998753
No 142
>PF12760 Zn_Tnp_IS1595: Transposase zinc-ribbon domain; InterPro: IPR024442 This zinc binding domain is found in a range of transposase proteins such as ISSPO8, ISSOD11, ISRSSP2 etc. It may be a zinc-binding beta ribbon domain that could bind DNA.
Probab=21.37 E-value=69 Score=22.21 Aligned_cols=30 Identities=33% Similarity=0.800 Sum_probs=18.2
Q ss_pred CccCCCCCCccCCCCcC-Ccccc-ccccccccCCc
Q 019595 143 EWLPDSSTTVCMQCTAP-FTALT-RGRHHCRFCGG 175 (338)
Q Consensus 143 ~W~pd~~~~~C~~C~~~-F~~l~-rRrHHCR~CG~ 175 (338)
.|... -.|..|+.. ...+. +.++.|+.|++
T Consensus 14 RW~~g---~~CP~Cg~~~~~~~~~~~~~~C~~C~~ 45 (46)
T PF12760_consen 14 RWPDG---FVCPHCGSTKHYRLKTRGRYRCKACRK 45 (46)
T ss_pred cCCCC---CCCCCCCCeeeEEeCCCCeEECCCCCC
Confidence 56544 568888873 11132 35788888864
No 143
>TIGR01031 rpmF_bact ribosomal protein L32. This protein describes bacterial ribosomal protein L32. The noise cutoff is set low enough to include the equivalent protein from mitochondria and chloroplasts. No related proteins from the Archaea nor from the eukaryotic cytosol are detected by this model. This model is a fragment model; the putative L32 of some species shows similarity only toward the N-terminus.
Probab=21.34 E-value=64 Score=23.68 Aligned_cols=26 Identities=27% Similarity=0.659 Sum_probs=13.9
Q ss_pred cCCCCCCccCCCCcCCccccccccccccCC
Q 019595 145 LPDSSTTVCMQCTAPFTALTRGRHHCRFCG 174 (338)
Q Consensus 145 ~pd~~~~~C~~C~~~F~~l~rRrHHCR~CG 174 (338)
+.......|..|+. +.+.-|-|..||
T Consensus 21 l~~p~l~~C~~cG~----~~~~H~vc~~cG 46 (55)
T TIGR01031 21 LTAPTLVVCPNCGE----FKLPHRVCPSCG 46 (55)
T ss_pred ccCCcceECCCCCC----cccCeeECCccC
Confidence 33334466777776 333344455665
No 144
>PRK14873 primosome assembly protein PriA; Provisional
Probab=21.24 E-value=53 Score=35.75 Aligned_cols=34 Identities=38% Similarity=0.969 Sum_probs=19.4
Q ss_pred CccCCCCcCCcccc--ccccccccCCce----EeCCCCCce
Q 019595 151 TVCMQCTAPFTALT--RGRHHCRFCGGV----FCRICTKGR 185 (338)
Q Consensus 151 ~~C~~C~~~F~~l~--rRrHHCR~CG~v----fC~~Cs~~~ 185 (338)
..|..|..+.+ +. .++-.|+.||.. .|..|.+..
T Consensus 393 ~~C~~C~~~L~-~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs~~ 432 (665)
T PRK14873 393 ARCRHCTGPLG-LPSAGGTPRCRWCGRAAPDWRCPRCGSDR 432 (665)
T ss_pred eECCCCCCcee-EecCCCeeECCCCcCCCcCccCCCCcCCc
Confidence 45666666655 32 124557777764 466666543
No 145
>PF02150 RNA_POL_M_15KD: RNA polymerases M/15 Kd subunit; InterPro: IPR001529 DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length []. The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel. RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise: RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors. RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs. Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kDa, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits. In archaebacteria, there is generally a single form of RNA polymerase which also consist of an oligomeric assemblage of 10 to 13 polypeptides. It has recently been shown [], [] that small subunits of about 15 kDa, found in polymerase types I and II, are highly conserved. These proteins contain a probable zinc finger in their N-terminal region and a C-terminal zinc ribbon domain (see IPR001222 from INTERPRO).; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3H0G_I 3M4O_I 3S14_I 2E2J_I 4A3J_I 3HOZ_I 1TWA_I 3S1Q_I 3S1N_I 1TWG_I ....
Probab=20.69 E-value=49 Score=21.94 Aligned_cols=8 Identities=38% Similarity=1.003 Sum_probs=4.0
Q ss_pred eEeCCCCC
Q 019595 176 VFCRICTK 183 (338)
Q Consensus 176 vfC~~Cs~ 183 (338)
.||..|.+
T Consensus 2 ~FCp~C~n 9 (35)
T PF02150_consen 2 RFCPECGN 9 (35)
T ss_dssp -BETTTTS
T ss_pred eeCCCCCc
Confidence 35666654
No 146
>PF07503 zf-HYPF: HypF finger; InterPro: IPR011125 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. Proteins of the HypF family are involved in the maturation and regulation of hydrogenase []. In the N terminus they appear to have two zinc finger domains that are similar to those found in the DnaJ chaperone []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 3TTD_A 3TSQ_A 3TTC_A 3TSP_A 3TTF_A 3TSU_A.
Probab=20.47 E-value=17 Score=24.32 Aligned_cols=7 Identities=29% Similarity=0.890 Sum_probs=2.8
Q ss_pred cCCCCcC
Q 019595 153 CMQCTAP 159 (338)
Q Consensus 153 C~~C~~~ 159 (338)
|..|.+.
T Consensus 2 C~~C~~E 8 (35)
T PF07503_consen 2 CDDCLKE 8 (35)
T ss_dssp -HHHHHH
T ss_pred CHHHHHH
Confidence 4445444
No 147
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.35 E-value=65 Score=35.53 Aligned_cols=35 Identities=29% Similarity=0.784 Sum_probs=23.7
Q ss_pred CccCCCCcCCcc-ccccccccccCCce-----EeCCCCCce
Q 019595 151 TVCMQCTAPFTA-LTRGRHHCRFCGGV-----FCRICTKGR 185 (338)
Q Consensus 151 ~~C~~C~~~F~~-l~rRrHHCR~CG~v-----fC~~Cs~~~ 185 (338)
..|..|...++. -.++.-.|+.||+- .|..|.+..
T Consensus 445 ~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~~ 485 (730)
T COG1198 445 AECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSEH 485 (730)
T ss_pred ccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCCe
Confidence 467777776662 12345678888887 788888763
No 148
>cd00202 ZnF_GATA Zinc finger DNA binding domain; binds specifically to DNA consensus sequence [AT]GATA[AG] promoter elements; a subset of family members may also bind protein; zinc-finger consensus topology is C-X(2)-C-X(17)-C-X(2)-C
Probab=20.30 E-value=42 Score=24.48 Aligned_cols=13 Identities=38% Similarity=0.710 Sum_probs=7.9
Q ss_pred cCCCCcCCccccc
Q 019595 153 CMQCTAPFTALTR 165 (338)
Q Consensus 153 C~~C~~~F~~l~r 165 (338)
|..|+...+++.|
T Consensus 2 C~~C~~~~Tp~WR 14 (54)
T cd00202 2 CSNCGTTTTPLWR 14 (54)
T ss_pred CCCCCCCCCcccc
Confidence 6666666665553
No 149
>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=20.29 E-value=47 Score=23.72 Aligned_cols=43 Identities=12% Similarity=0.037 Sum_probs=27.4
Q ss_pred ccCCCCcCCccccccccccccCCceEeCCCCCceeecCccCCCCcceeecccccccc
Q 019595 152 VCMQCTAPFTALTRGRHHCRFCGGVFCRICTKGRCLLPVRFRERNPQRVCDACYDRL 208 (338)
Q Consensus 152 ~C~~C~~~F~~l~rRrHHCR~CG~vfC~~Cs~~~~~lP~~~~~~~p~RVC~~C~~~l 208 (338)
.|..|...+.- --...||++||..|...... ....|-.|-..+
T Consensus 3 ~Cpi~~~~~~~-----Pv~~~~G~v~~~~~i~~~~~---------~~~~cP~~~~~~ 45 (63)
T smart00504 3 LCPISLEVMKD-----PVILPSGQTYERRAIEKWLL---------SHGTDPVTGQPL 45 (63)
T ss_pred CCcCCCCcCCC-----CEECCCCCEEeHHHHHHHHH---------HCCCCCCCcCCC
Confidence 57788876652 24568899999998765421 023566666555
No 150
>PRK11595 DNA utilization protein GntX; Provisional
Probab=20.15 E-value=25 Score=32.58 Aligned_cols=30 Identities=23% Similarity=0.682 Sum_probs=21.7
Q ss_pred CccCCCCcCCccccccccccccCCce------EeCCCCC
Q 019595 151 TVCMQCTAPFTALTRGRHHCRFCGGV------FCRICTK 183 (338)
Q Consensus 151 ~~C~~C~~~F~~l~rRrHHCR~CG~v------fC~~Cs~ 183 (338)
..|..|...+.. . .++|..||.. +|..|..
T Consensus 21 ~lC~~C~~~l~~-~--~~~C~~Cg~~~~~~~~~C~~C~~ 56 (227)
T PRK11595 21 GICSVCSRALRT-L--KTCCPQCGLPATHPHLPCGRCLQ 56 (227)
T ss_pred cccHHHHhhCCc-c--cCcCccCCCcCCCCCCCcHHHHc
Confidence 468888888873 3 4789999974 3777754
Done!