Query psy4518
Match_columns 376
No_of_seqs 254 out of 1270
Neff 6.6
Searched_HMMs 46136
Date Fri Aug 16 19:12:15 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4518.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4518hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG1842|consensus 100.0 4.7E-79 1E-83 596.2 29.5 363 1-371 118-502 (505)
2 PF11464 Rbsn: Rabenosyn Rab b 99.7 1.5E-17 3.3E-22 114.0 5.6 42 322-363 1-42 (42)
3 PF01363 FYVE: FYVE zinc finge 99.7 2.2E-18 4.8E-23 132.4 1.3 67 53-128 1-68 (69)
4 smart00064 FYVE Protein presen 99.6 3E-16 6.6E-21 120.1 3.5 65 53-128 2-67 (68)
5 KOG1729|consensus 99.5 1.8E-14 3.9E-19 138.8 3.9 72 46-129 153-226 (288)
6 PTZ00303 phosphatidylinositol 99.4 1.6E-13 3.4E-18 143.0 5.3 73 52-127 450-529 (1374)
7 KOG1818|consensus 99.4 8.2E-14 1.8E-18 144.9 3.0 67 51-131 158-225 (634)
8 KOG1819|consensus 99.4 1.1E-13 2.4E-18 138.7 1.5 64 52-126 892-961 (990)
9 cd00065 FYVE FYVE domain; Zinc 99.3 9.2E-13 2E-17 97.2 2.2 54 61-125 2-56 (57)
10 KOG1841|consensus 98.8 1E-09 2.2E-14 119.0 1.6 47 48-94 544-590 (1287)
11 KOG1843|consensus 98.4 6.2E-08 1.3E-12 96.0 1.0 71 45-127 144-218 (473)
12 KOG1409|consensus 98.2 2.6E-07 5.6E-12 90.1 -0.1 65 50-128 274-350 (404)
13 KOG4424|consensus 98.1 5.5E-07 1.2E-11 92.8 -0.5 62 54-128 410-472 (623)
14 KOG1811|consensus 97.2 3.6E-05 7.9E-10 80.1 -2.1 67 52-128 313-384 (1141)
15 KOG0230|consensus 97.1 0.00024 5.3E-09 80.4 2.4 49 60-129 4-52 (1598)
16 PF02318 FYVE_2: FYVE-type zin 97.1 0.00031 6.8E-09 59.6 2.5 51 61-128 54-105 (118)
17 KOG0230|consensus 96.1 0.0021 4.6E-08 73.1 1.3 34 56-91 92-125 (1598)
18 KOG1729|consensus 94.6 0.0064 1.4E-07 59.3 -1.2 75 51-129 10-85 (288)
19 KOG0993|consensus 92.3 0.01 2.2E-07 59.6 -4.0 64 53-129 460-526 (542)
20 PRK00464 nrdR transcriptional 92.0 0.071 1.5E-06 47.4 1.2 25 63-87 2-38 (154)
21 TIGR00622 ssl1 transcription f 89.5 0.29 6.2E-06 41.2 2.6 43 53-95 47-99 (112)
22 PF09538 FYDLN_acid: Protein o 89.0 0.21 4.6E-06 41.8 1.5 25 63-87 11-36 (108)
23 PRK03564 formate dehydrogenase 88.7 0.3 6.5E-06 48.2 2.5 63 61-129 187-264 (309)
24 KOG1841|consensus 88.3 0.26 5.6E-06 55.4 2.0 36 50-87 646-681 (1287)
25 TIGR02300 FYDLN_acid conserved 87.2 0.33 7.1E-06 41.6 1.5 26 62-87 10-36 (129)
26 KOG2164|consensus 86.4 0.19 4.1E-06 52.1 -0.4 50 62-129 187-237 (513)
27 KOG4275|consensus 85.8 0.16 3.5E-06 49.2 -1.1 49 59-126 42-90 (350)
28 TIGR01562 FdhE formate dehydro 85.3 0.54 1.2E-05 46.4 2.2 63 61-129 184-264 (305)
29 PF07975 C1_4: TFIIH C1-like d 84.6 0.26 5.6E-06 35.7 -0.3 33 63-95 1-39 (51)
30 PF13719 zinc_ribbon_5: zinc-r 84.3 0.5 1.1E-05 31.7 1.0 25 63-87 4-35 (37)
31 PF13717 zinc_ribbon_4: zinc-r 83.9 0.56 1.2E-05 31.3 1.1 25 63-87 4-35 (36)
32 KOG3576|consensus 80.9 0.33 7.1E-06 45.0 -1.1 33 56-88 112-156 (267)
33 PRK00420 hypothetical protein; 80.8 0.95 2.1E-05 38.2 1.6 24 62-85 24-48 (112)
34 PRK00398 rpoP DNA-directed RNA 79.4 0.95 2.1E-05 31.7 1.0 24 63-86 5-30 (46)
35 COG3058 FdhE Uncharacterized p 78.8 0.92 2E-05 43.9 1.1 70 54-128 178-263 (308)
36 PF01485 IBR: IBR domain; Int 78.6 1.5 3.2E-05 32.0 2.0 35 60-94 17-57 (64)
37 TIGR00570 cdk7 CDK-activating 77.8 2 4.3E-05 42.4 3.0 30 63-94 5-37 (309)
38 PF04216 FdhE: Protein involve 77.4 1 2.2E-05 44.0 0.9 60 62-128 173-249 (290)
39 PHA02768 hypothetical protein; 76.7 1 2.2E-05 33.2 0.5 25 63-87 7-41 (55)
40 PRK00432 30S ribosomal protein 76.1 1.5 3.3E-05 31.5 1.3 27 61-87 20-47 (50)
41 TIGR02098 MJ0042_CXXC MJ0042 f 75.9 1.4 3E-05 29.3 1.0 24 63-86 4-34 (38)
42 KOG0320|consensus 75.4 0.52 1.1E-05 42.7 -1.5 49 61-129 131-179 (187)
43 PF10571 UPF0547: Uncharacteri 74.7 2 4.3E-05 26.7 1.4 23 63-87 2-24 (26)
44 smart00154 ZnF_AN1 AN1-like Zi 74.6 1.9 4.1E-05 29.3 1.4 25 64-90 1-25 (39)
45 PF15616 TerY-C: TerY-C metal 73.4 1.6 3.4E-05 37.8 1.0 24 61-89 77-100 (131)
46 KOG3173|consensus 72.7 1.8 3.9E-05 39.0 1.2 28 59-89 103-130 (167)
47 PF12773 DZR: Double zinc ribb 72.3 3.2 7E-05 29.2 2.2 29 58-86 9-38 (50)
48 PF07191 zinc-ribbons_6: zinc- 71.8 1.7 3.7E-05 33.5 0.7 56 63-130 3-63 (70)
49 COG5151 SSL1 RNA polymerase II 71.6 2 4.2E-05 42.3 1.2 43 53-95 354-406 (421)
50 TIGR00100 hypA hydrogenase nic 69.6 1.6 3.5E-05 36.8 0.2 33 54-86 63-95 (115)
51 PF08271 TF_Zn_Ribbon: TFIIB z 69.0 2.6 5.5E-05 29.0 1.1 25 63-87 2-29 (43)
52 KOG0317|consensus 68.9 2.1 4.6E-05 41.6 0.8 33 60-96 238-270 (293)
53 PF14353 CpXC: CpXC protein 68.7 2.2 4.7E-05 36.3 0.8 25 63-87 3-48 (128)
54 PF07282 OrfB_Zn_ribbon: Putat 67.6 3.2 6.9E-05 31.2 1.5 28 60-87 27-56 (69)
55 PF01155 HypA: Hydrogenase exp 65.9 1.8 4E-05 36.3 -0.2 28 59-86 68-95 (113)
56 PF01529 zf-DHHC: DHHC palmito 64.4 4.1 8.9E-05 35.9 1.8 30 57-88 44-73 (174)
57 PF10170 C6_DPF: Cysteine-rich 64.0 3.8 8.3E-05 33.6 1.3 36 73-128 45-82 (97)
58 TIGR02605 CxxC_CxxC_SSSS putat 63.8 3.1 6.8E-05 29.5 0.7 23 63-85 7-34 (52)
59 KOG4739|consensus 63.6 13 0.00027 35.4 4.9 44 63-128 5-48 (233)
60 PF06750 DiS_P_DiS: Bacterial 63.5 4.5 9.8E-05 32.8 1.7 25 62-86 34-67 (92)
61 KOG1814|consensus 63.3 5.3 0.00011 40.8 2.4 41 54-95 362-404 (445)
62 smart00647 IBR In Between Ring 63.3 5.6 0.00012 28.9 2.0 34 61-94 18-57 (64)
63 PRK12380 hydrogenase nickel in 62.9 3.6 7.8E-05 34.6 1.0 25 62-86 71-95 (113)
64 COG1997 RPL43A Ribosomal prote 61.0 5.1 0.00011 32.2 1.5 28 61-89 35-65 (89)
65 KOG2593|consensus 60.9 3.5 7.7E-05 42.2 0.8 32 62-93 129-169 (436)
66 PRK14559 putative protein seri 60.7 5 0.00011 43.7 1.9 32 59-94 13-50 (645)
67 smart00834 CxxC_CXXC_SSSS Puta 60.3 4.1 8.9E-05 27.2 0.8 13 63-75 7-19 (41)
68 PF12760 Zn_Tnp_IS1595: Transp 59.5 6.2 0.00013 27.5 1.6 29 54-85 14-45 (46)
69 COG2126 RPL37A Ribosomal prote 59.3 4.3 9.3E-05 30.1 0.7 17 70-86 7-25 (61)
70 KOG0978|consensus 58.5 1.6 3.4E-05 47.5 -2.3 42 61-125 643-686 (698)
71 PF13639 zf-RING_2: Ring finge 58.2 2.7 5.9E-05 28.7 -0.4 32 63-95 2-33 (44)
72 KOG1311|consensus 57.7 4.5 9.7E-05 39.4 0.9 26 61-88 113-138 (299)
73 COG1327 Predicted transcriptio 57.5 5.4 0.00012 35.4 1.2 26 63-88 2-39 (156)
74 PRK03824 hypA hydrogenase nick 57.4 5.2 0.00011 34.7 1.1 14 61-74 70-83 (135)
75 PF09986 DUF2225: Uncharacteri 57.2 5.8 0.00013 37.1 1.5 14 115-128 46-59 (214)
76 PRK00564 hypA hydrogenase nick 57.0 5.2 0.00011 33.8 1.0 28 59-86 69-97 (117)
77 PF09862 DUF2089: Protein of u 56.2 5 0.00011 33.9 0.8 24 64-89 1-24 (113)
78 KOG2807|consensus 55.5 5.2 0.00011 39.7 0.9 41 54-95 323-363 (378)
79 smart00531 TFIIE Transcription 54.8 4.9 0.00011 35.2 0.5 14 60-73 98-111 (147)
80 PF07776 zf-AD: Zinc-finger as 54.2 22 0.00047 26.0 4.0 21 114-134 42-62 (75)
81 PTZ00255 60S ribosomal protein 54.0 6.7 0.00015 31.8 1.1 31 61-91 36-68 (90)
82 PF13445 zf-RING_UBOX: RING-ty 54.0 4 8.6E-05 28.4 -0.1 31 64-95 1-31 (43)
83 COG5574 PEX10 RING-finger-cont 53.6 4.3 9.4E-05 39.0 -0.0 37 52-93 207-243 (271)
84 PRK03681 hypA hydrogenase nick 52.9 6.6 0.00014 33.0 1.0 25 62-86 71-96 (114)
85 PF10955 DUF2757: Protein of u 52.7 5.7 0.00012 31.2 0.5 16 114-129 48-64 (76)
86 PLN03208 E3 ubiquitin-protein 52.3 7.1 0.00015 36.0 1.2 68 55-128 12-79 (193)
87 TIGR00280 L37a ribosomal prote 52.0 6.3 0.00014 32.0 0.7 31 61-91 35-67 (91)
88 PRK06266 transcription initiat 51.7 6.8 0.00015 35.6 0.9 26 61-86 117-145 (178)
89 PRK03976 rpl37ae 50S ribosomal 51.6 6.4 0.00014 31.9 0.7 30 62-91 37-68 (90)
90 PRK14559 putative protein seri 51.6 11 0.00024 41.1 2.6 47 63-129 3-53 (645)
91 TIGR00244 transcriptional regu 51.1 8.6 0.00019 33.9 1.4 26 63-88 2-39 (147)
92 KOG1314|consensus 51.1 5.8 0.00013 39.8 0.4 33 53-87 78-115 (414)
93 TIGR00373 conserved hypothetic 51.0 6.6 0.00014 34.9 0.7 25 62-86 110-137 (158)
94 PF08274 PhnA_Zn_Ribbon: PhnA 50.7 5.9 0.00013 25.5 0.3 12 62-73 3-14 (30)
95 PF09889 DUF2116: Uncharacteri 50.3 14 0.0003 27.6 2.2 17 116-132 16-33 (59)
96 PRK04023 DNA polymerase II lar 50.1 12 0.00026 42.5 2.6 30 60-93 625-659 (1121)
97 PRK12496 hypothetical protein; 50.1 9 0.0002 34.3 1.5 23 63-85 129-151 (164)
98 COG5222 Uncharacterized conser 49.6 11 0.00023 37.1 1.9 82 62-177 275-356 (427)
99 PRK11595 DNA utilization prote 49.5 5.2 0.00011 37.5 -0.2 21 63-85 22-42 (227)
100 PF14803 Nudix_N_2: Nudix N-te 49.5 6.5 0.00014 26.0 0.3 24 63-86 2-31 (34)
101 PF01166 TSC22: TSC-22/dip/bun 49.4 24 0.00052 26.3 3.3 25 343-367 14-38 (59)
102 COG0675 Transposase and inacti 49.3 9.9 0.00021 36.6 1.7 27 59-88 307-333 (364)
103 KOG3576|consensus 49.0 4.2 9.1E-05 37.9 -0.8 64 62-127 146-222 (267)
104 COG1198 PriA Primosomal protei 48.4 12 0.00026 41.4 2.3 36 59-94 442-484 (730)
105 PF09723 Zn-ribbon_8: Zinc rib 47.6 8.2 0.00018 26.5 0.6 23 63-85 7-34 (42)
106 smart00659 RPOLCX RNA polymera 47.3 11 0.00023 26.4 1.2 12 63-74 4-15 (44)
107 PF01927 Mut7-C: Mut7-C RNAse 47.2 12 0.00027 32.6 1.9 18 54-71 84-101 (147)
108 PF01780 Ribosomal_L37ae: Ribo 46.8 7.1 0.00015 31.6 0.2 29 62-90 36-66 (90)
109 smart00661 RPOL9 RNA polymeras 46.6 12 0.00027 26.2 1.5 24 63-86 2-29 (52)
110 PF11023 DUF2614: Protein of u 46.5 8.7 0.00019 32.3 0.7 25 63-87 71-95 (114)
111 PRK05978 hypothetical protein; 46.5 10 0.00023 33.5 1.3 26 62-87 34-62 (148)
112 PF03604 DNA_RNApol_7kD: DNA d 46.5 13 0.00028 24.3 1.3 23 63-85 2-25 (32)
113 PF01286 XPA_N: XPA protein N- 46.4 9.6 0.00021 25.3 0.8 19 62-80 4-24 (34)
114 PF09332 Mcm10: Mcm10 replicat 46.4 8.3 0.00018 38.7 0.7 37 50-86 273-312 (344)
115 TIGR00599 rad18 DNA repair pro 46.2 4.1 8.8E-05 41.7 -1.5 29 62-94 27-55 (397)
116 PF10367 Vps39_2: Vacuolar sor 46.1 13 0.00027 30.0 1.6 30 62-93 79-108 (109)
117 PRK14714 DNA polymerase II lar 45.9 14 0.0003 42.9 2.4 49 62-129 668-721 (1337)
118 TIGR01384 TFS_arch transcripti 45.9 11 0.00025 30.6 1.3 26 63-88 2-27 (104)
119 PF13913 zf-C2HC_2: zinc-finge 45.7 5 0.00011 24.5 -0.6 10 63-72 4-13 (25)
120 PF04216 FdhE: Protein involve 45.6 7 0.00015 38.1 0.0 36 59-96 195-249 (290)
121 PF07503 zf-HYPF: HypF finger; 45.0 5.9 0.00013 26.4 -0.4 16 64-79 2-18 (35)
122 PF14634 zf-RING_5: zinc-RING 44.9 8 0.00017 26.5 0.2 32 63-95 1-32 (44)
123 PF09947 DUF2180: Uncharacteri 44.7 11 0.00023 29.0 0.9 45 78-127 17-66 (68)
124 KOG1315|consensus 44.7 10 0.00022 37.5 1.1 29 56-86 104-132 (307)
125 cd00162 RING RING-finger (Real 43.9 8.1 0.00018 25.2 0.1 29 63-94 1-29 (45)
126 PF13923 zf-C3HC4_2: Zinc fing 43.7 7 0.00015 26.0 -0.2 28 64-94 1-28 (39)
127 KOG3795|consensus 43.5 11 0.00025 34.1 1.1 24 70-93 8-34 (230)
128 TIGR00595 priA primosomal prot 43.2 16 0.00034 38.6 2.2 24 63-86 224-249 (505)
129 COG2051 RPS27A Ribosomal prote 43.1 11 0.00024 28.8 0.7 27 63-89 21-50 (67)
130 PF02150 RNA_POL_M_15KD: RNA p 42.8 11 0.00023 25.0 0.5 7 63-69 3-9 (35)
131 KOG1818|consensus 42.7 6 0.00013 42.6 -1.0 31 63-93 56-87 (634)
132 KOG0823|consensus 41.7 5.9 0.00013 37.4 -1.1 51 59-128 45-95 (230)
133 PF05191 ADK_lid: Adenylate ki 41.2 14 0.0003 24.7 0.9 12 63-74 3-14 (36)
134 KOG4797|consensus 41.1 1.1E+02 0.0024 25.7 6.3 45 319-367 47-91 (123)
135 PF13248 zf-ribbon_3: zinc-rib 40.8 15 0.00033 22.5 1.0 21 63-85 4-24 (26)
136 PRK14892 putative transcriptio 40.7 12 0.00027 30.8 0.8 32 60-94 20-51 (99)
137 PF06221 zf-C2HC5: Putative zi 40.7 11 0.00023 28.0 0.4 13 77-89 18-30 (57)
138 COG5273 Uncharacterized protei 40.6 14 0.0003 36.6 1.3 29 57-87 105-133 (309)
139 KOG2462|consensus 40.5 12 0.00025 36.4 0.7 31 57-87 157-197 (279)
140 smart00778 Prim_Zn_Ribbon Zinc 40.4 16 0.00035 24.6 1.2 22 63-84 5-32 (37)
141 PF08996 zf-DNA_Pol: DNA Polym 39.9 1.1E+02 0.0023 27.9 6.9 11 63-73 20-30 (188)
142 PF13453 zf-TFIIB: Transcripti 39.4 15 0.00033 24.9 0.9 9 63-71 1-9 (41)
143 PF13912 zf-C2H2_6: C2H2-type 39.4 8.2 0.00018 23.3 -0.4 10 63-72 3-12 (27)
144 KOG3799|consensus 38.2 26 0.00055 30.6 2.3 55 53-125 60-115 (169)
145 PF14445 Prok-RING_2: Prokaryo 38.0 6.4 0.00014 28.4 -1.1 30 63-93 9-38 (57)
146 TIGR01031 rpmF_bact ribosomal 37.9 20 0.00044 26.2 1.5 27 55-84 19-46 (55)
147 smart00291 ZnF_ZZ Zinc-binding 37.5 20 0.00044 24.7 1.4 29 61-91 4-33 (44)
148 PRK14873 primosome assembly pr 37.3 18 0.0004 39.6 1.6 33 61-93 392-430 (665)
149 COG4530 Uncharacterized protei 36.8 18 0.00039 30.4 1.2 25 62-86 10-35 (129)
150 PF03833 PolC_DP2: DNA polymer 36.7 12 0.00025 41.8 0.0 28 62-93 656-688 (900)
151 PRK05580 primosome assembly pr 36.7 22 0.00048 39.0 2.1 24 63-86 392-417 (679)
152 KOG2199|consensus 36.2 1.3E+02 0.0028 31.0 7.2 56 137-204 313-368 (462)
153 COG1996 RPC10 DNA-directed RNA 36.0 17 0.00038 26.1 0.8 23 63-85 8-32 (49)
154 PRK14714 DNA polymerase II lar 35.7 20 0.00044 41.7 1.7 28 63-93 681-717 (1337)
155 PF10263 SprT-like: SprT-like 35.4 17 0.00036 31.6 0.8 28 59-86 121-152 (157)
156 COG1645 Uncharacterized Zn-fin 35.4 18 0.00038 31.4 0.9 23 63-93 30-52 (131)
157 PF11781 RRN7: RNA polymerase 35.2 21 0.00046 23.8 1.1 24 63-86 10-34 (36)
158 cd02342 ZZ_UBA_plant Zinc fing 35.0 19 0.00041 25.2 0.9 30 63-93 2-32 (43)
159 PRK00415 rps27e 30S ribosomal 35.0 19 0.00042 26.8 1.0 26 63-88 13-41 (59)
160 COG1439 Predicted nucleic acid 34.7 18 0.00038 33.0 0.8 22 63-86 141-162 (177)
161 PF10892 DUF2688: Protein of u 34.6 13 0.00028 27.5 -0.0 10 78-87 11-20 (60)
162 PF14835 zf-RING_6: zf-RING of 34.2 24 0.00052 26.8 1.4 27 63-93 9-36 (65)
163 PF03107 C1_2: C1 domain; Int 33.7 29 0.00062 21.9 1.5 28 63-91 2-29 (30)
164 PF00096 zf-C2H2: Zinc finger, 33.6 15 0.00032 21.1 0.1 10 63-72 2-11 (23)
165 PF15227 zf-C3HC4_4: zinc fing 33.5 13 0.00028 25.5 -0.2 27 64-94 1-27 (42)
166 PRK03564 formate dehydrogenase 33.4 25 0.00055 34.8 1.8 28 57-86 208-235 (309)
167 KOG1538|consensus 33.4 14 0.0003 40.2 -0.0 29 56-84 1039-1073(1081)
168 PRK12366 replication factor A; 32.9 20 0.00043 39.1 1.0 26 61-86 532-557 (637)
169 cd02341 ZZ_ZZZ3 Zinc finger, Z 32.8 22 0.00047 25.3 0.9 29 63-92 2-33 (48)
170 PF01667 Ribosomal_S27e: Ribos 32.6 20 0.00044 26.3 0.7 26 63-88 9-37 (55)
171 PF14369 zf-RING_3: zinc-finge 32.4 26 0.00057 23.2 1.2 9 63-71 23-31 (35)
172 PF05605 zf-Di19: Drought indu 31.8 21 0.00046 25.6 0.7 31 63-93 4-39 (54)
173 KOG1313|consensus 31.8 16 0.00034 35.6 0.1 27 60-88 101-127 (309)
174 PF12172 DUF35_N: Rubredoxin-l 31.6 14 0.00031 24.3 -0.2 20 63-84 13-32 (37)
175 PF15135 UPF0515: Uncharacteri 31.1 29 0.00063 33.3 1.7 35 54-88 125-166 (278)
176 cd07178 terB_like_YebE telluri 30.5 38 0.00082 27.4 2.1 28 328-355 2-31 (95)
177 COG1405 SUA7 Transcription ini 30.4 27 0.00058 34.3 1.4 27 62-88 2-31 (285)
178 PRK02935 hypothetical protein; 30.3 26 0.00055 29.3 1.0 25 63-87 72-96 (110)
179 smart00504 Ubox Modified RING 30.3 20 0.00044 25.9 0.4 28 63-94 3-30 (63)
180 PF02151 UVR: UvrB/uvrC motif; 30.2 1.6E+02 0.0035 19.3 5.4 35 324-358 2-36 (36)
181 cd02340 ZZ_NBR1_like Zinc fing 30.1 27 0.00059 24.1 1.0 29 63-93 2-31 (43)
182 PF00097 zf-C3HC4: Zinc finger 29.9 16 0.00034 24.2 -0.2 28 64-94 1-28 (41)
183 PHA00732 hypothetical protein 29.8 34 0.00073 26.9 1.6 10 63-72 3-12 (79)
184 PHA02942 putative transposase; 29.5 34 0.00073 34.9 2.0 28 60-87 324-352 (383)
185 PF02403 Seryl_tRNA_N: Seryl-t 29.4 1E+02 0.0022 25.1 4.5 44 319-364 45-88 (108)
186 PF14447 Prok-RING_4: Prokaryo 29.4 26 0.00056 25.8 0.8 17 57-73 35-51 (55)
187 TIGR00311 aIF-2beta translatio 29.4 24 0.00053 30.6 0.8 24 63-86 99-127 (133)
188 PRK09678 DNA-binding transcrip 29.2 29 0.00062 27.0 1.1 26 62-87 2-39 (72)
189 PF00569 ZZ: Zinc finger, ZZ t 28.9 18 0.00039 25.2 -0.1 22 62-84 5-26 (46)
190 KOG0810|consensus 28.8 5.8E+02 0.013 25.2 15.4 27 338-364 201-227 (297)
191 PF04423 Rad50_zn_hook: Rad50 28.7 20 0.00044 25.7 0.2 10 63-72 22-31 (54)
192 PF13005 zf-IS66: zinc-finger 28.7 35 0.00075 23.5 1.4 10 63-72 4-13 (47)
193 cd02249 ZZ Zinc finger, ZZ typ 28.6 27 0.00058 24.2 0.8 29 63-93 2-31 (46)
194 TIGR00595 priA primosomal prot 28.4 33 0.00071 36.2 1.7 22 73-94 204-231 (505)
195 PLN00209 ribosomal protein S27 28.3 28 0.0006 28.0 0.9 27 63-89 38-67 (86)
196 COG1773 Rubredoxin [Energy pro 28.3 23 0.00049 26.1 0.4 12 76-87 2-13 (55)
197 cd04476 RPA1_DBD_C RPA1_DBD_C: 28.0 29 0.00064 30.6 1.1 28 60-87 33-61 (166)
198 PRK09720 cybC cytochrome b562; 28.0 98 0.0021 25.6 4.1 43 315-361 55-97 (100)
199 PRK12495 hypothetical protein; 27.8 68 0.0015 30.3 3.5 25 62-94 43-67 (226)
200 KOG3896|consensus 27.6 27 0.00058 35.0 0.8 29 65-94 13-41 (449)
201 PTZ00083 40S ribosomal protein 27.5 29 0.00063 27.8 0.9 27 63-89 37-66 (85)
202 PF13465 zf-H2C2_2: Zinc-finge 27.4 22 0.00048 21.6 0.2 11 62-72 15-25 (26)
203 COG1675 TFA1 Transcription ini 27.3 75 0.0016 28.9 3.6 25 63-87 115-142 (176)
204 PRK09263 anaerobic ribonucleos 27.3 39 0.00084 37.4 2.1 35 51-85 631-667 (711)
205 PRK04351 hypothetical protein; 27.1 31 0.00067 30.5 1.1 26 62-87 113-142 (149)
206 PF11593 Med3: Mediator comple 27.0 1.8E+02 0.0039 29.6 6.5 47 164-210 48-94 (379)
207 KOG1829|consensus 26.9 22 0.00047 38.2 0.1 32 63-94 342-375 (580)
208 PHA00733 hypothetical protein 26.9 35 0.00077 29.2 1.4 27 62-88 74-110 (128)
209 COG0375 HybF Zn finger protein 26.6 28 0.0006 29.5 0.7 27 60-86 69-95 (115)
210 PRK08271 anaerobic ribonucleos 26.5 41 0.00089 36.6 2.1 36 48-85 553-588 (623)
211 KOG2932|consensus 26.5 38 0.00083 33.5 1.7 35 56-93 85-119 (389)
212 PRK00762 hypA hydrogenase nick 26.5 31 0.00067 29.4 1.0 23 62-85 71-100 (124)
213 PF10013 DUF2256: Uncharacteri 26.2 21 0.00045 24.8 -0.1 15 62-76 9-23 (42)
214 COG0498 ThrC Threonine synthas 26.2 27 0.00058 36.0 0.6 26 62-87 6-31 (411)
215 KOG2177|consensus 25.8 19 0.00042 33.3 -0.5 29 61-93 13-41 (386)
216 PRK01343 zinc-binding protein; 25.8 36 0.00079 25.2 1.1 13 61-73 9-21 (57)
217 PF13894 zf-C2H2_4: C2H2-type 25.4 28 0.0006 19.5 0.3 10 63-72 2-11 (24)
218 COG1779 C4-type Zn-finger prot 25.3 32 0.0007 31.9 0.9 31 63-93 16-51 (201)
219 PLN02195 cellulose synthase A 25.2 32 0.0007 39.1 1.0 22 80-125 9-41 (977)
220 PF04438 zf-HIT: HIT zinc fing 24.9 32 0.0007 22.0 0.6 22 63-89 4-25 (30)
221 COG1998 RPS31 Ribosomal protei 24.8 38 0.00083 24.4 1.0 24 62-85 20-45 (51)
222 PF05615 THOC7: Tho complex su 24.8 2.5E+02 0.0055 23.9 6.4 19 191-209 111-129 (139)
223 PRK03988 translation initiatio 24.7 33 0.00071 30.0 0.8 24 63-86 104-132 (138)
224 COG0353 RecR Recombinational D 24.6 36 0.00079 31.5 1.1 18 76-93 53-74 (198)
225 COG4338 Uncharacterized protei 24.5 12 0.00027 26.7 -1.5 14 63-76 14-27 (54)
226 KOG2824|consensus 24.5 51 0.0011 32.1 2.1 9 31-39 217-225 (281)
227 PF02945 Endonuclease_7: Recom 24.4 25 0.00054 27.9 -0.0 24 63-86 24-50 (81)
228 COG1592 Rubrerythrin [Energy p 24.3 1.1E+02 0.0024 27.6 4.1 21 63-84 136-156 (166)
229 PF03833 PolC_DP2: DNA polymer 24.2 26 0.00055 39.2 0.0 57 196-252 783-849 (900)
230 COG0333 RpmF Ribosomal protein 23.8 41 0.0009 24.9 1.0 21 61-84 27-47 (57)
231 KOG4317|consensus 23.8 43 0.00094 33.2 1.5 27 59-89 5-31 (383)
232 PF14471 DUF4428: Domain of un 23.8 28 0.00061 25.0 0.2 10 118-127 21-30 (51)
233 PRK08402 replication factor A; 23.6 41 0.00089 34.0 1.3 30 58-87 209-240 (355)
234 PRK06260 threonine synthase; V 23.3 41 0.00089 34.2 1.3 24 63-86 5-28 (397)
235 KOG0153|consensus 23.2 18 0.0004 36.2 -1.2 20 58-77 38-57 (377)
236 TIGR03655 anti_R_Lar restricti 23.2 54 0.0012 23.5 1.5 8 63-70 3-10 (53)
237 PHA02926 zinc finger-like prot 22.8 27 0.00059 33.0 -0.1 53 62-127 171-229 (242)
238 PF09845 DUF2072: Zn-ribbon co 22.5 37 0.0008 29.4 0.7 24 62-85 2-27 (131)
239 PF05458 Siva: Cd27 binding pr 22.5 30 0.00064 31.5 0.1 13 80-92 142-154 (175)
240 COG4855 Uncharacterized protei 22.4 32 0.00068 26.4 0.2 61 63-128 9-74 (76)
241 KOG1356|consensus 22.4 47 0.001 37.1 1.6 107 52-166 218-328 (889)
242 PF07361 Cytochrom_B562: Cytoc 22.3 1.5E+02 0.0032 24.4 4.2 44 315-362 58-101 (103)
243 PRK12286 rpmF 50S ribosomal pr 22.1 49 0.0011 24.4 1.2 23 59-84 25-47 (57)
244 PF08273 Prim_Zn_Ribbon: Zinc- 22.1 42 0.00091 23.0 0.7 21 63-83 5-32 (40)
245 KOG2462|consensus 22.0 90 0.0019 30.4 3.2 27 61-87 130-171 (279)
246 PF14584 DUF4446: Protein of u 22.0 67 0.0014 28.5 2.2 37 340-376 50-86 (151)
247 smart00184 RING Ring finger. E 21.8 30 0.00065 21.4 -0.0 26 64-93 1-26 (39)
248 PF13901 DUF4206: Domain of un 21.8 52 0.0011 30.4 1.6 35 51-86 163-198 (202)
249 PF06397 Desulfoferrod_N: Desu 21.7 33 0.00071 23.0 0.2 11 77-87 6-16 (36)
250 PF06476 DUF1090: Protein of u 21.7 1.9E+02 0.0041 24.4 4.8 35 323-357 23-57 (115)
251 COG1545 Predicted nucleic-acid 21.7 42 0.00091 29.2 0.9 23 62-86 30-52 (140)
252 PF14257 DUF4349: Domain of un 21.6 2.4E+02 0.0051 26.8 6.1 43 321-366 143-185 (262)
253 KOG4343|consensus 21.6 1.6E+02 0.0034 31.5 5.1 48 321-368 279-327 (655)
254 TIGR00155 pqiA_fam integral me 21.5 64 0.0014 33.2 2.3 28 60-88 214-241 (403)
255 PRK07591 threonine synthase; V 21.4 47 0.001 34.2 1.3 25 62-87 19-43 (421)
256 TIGR03278 methan_mark_10 putat 21.4 65 0.0014 33.2 2.3 31 63-93 12-44 (404)
257 PHA02565 49 recombination endo 21.3 56 0.0012 29.2 1.6 19 63-81 22-43 (157)
258 PRK05580 primosome assembly pr 21.3 46 0.001 36.5 1.3 17 79-95 383-400 (679)
259 PF03966 Trm112p: Trm112p-like 21.2 45 0.00098 25.1 0.9 9 63-71 9-17 (68)
260 KOG1812|consensus 21.2 49 0.0011 33.8 1.4 51 31-91 285-337 (384)
261 smart00653 eIF2B_5 domain pres 21.1 42 0.0009 28.2 0.7 23 63-85 82-109 (110)
262 smart00109 C1 Protein kinase C 21.0 46 0.001 22.4 0.8 35 61-95 11-45 (49)
263 cd00202 ZnF_GATA Zinc finger D 21.0 44 0.00095 24.3 0.7 30 63-94 1-30 (54)
264 COG1198 PriA Primosomal protei 20.8 62 0.0013 35.9 2.1 17 225-241 606-622 (730)
265 PHA03158 hypothetical protein; 20.7 2E+02 0.0044 26.7 5.0 38 323-366 233-270 (273)
266 smart00731 SprT SprT homologue 20.5 49 0.0011 28.7 1.1 26 62-87 113-143 (146)
267 TIGR00686 phnA alkylphosphonat 20.4 59 0.0013 27.3 1.4 29 61-96 2-30 (109)
268 smart00685 DM14 Repeats in fly 20.4 3.7E+02 0.0081 20.0 5.7 52 321-372 3-54 (59)
269 PRK12336 translation initiatio 20.2 44 0.00096 30.9 0.8 26 63-88 100-130 (201)
270 KOG3940|consensus 20.2 86 0.0019 31.1 2.7 28 58-85 319-346 (351)
271 PF05443 ROS_MUCR: ROS/MUCR tr 20.1 29 0.00064 30.1 -0.4 16 62-78 73-88 (132)
No 1
>KOG1842|consensus
Probab=100.00 E-value=4.7e-79 Score=596.21 Aligned_cols=363 Identities=31% Similarity=0.539 Sum_probs=322.7
Q ss_pred CcccchHhHHHHHhhhhhHHHHHHHHHHHHHHHHhccCC--CCchhhhhccccCCCcccCCCCCcccccccccccccccc
Q psy4518 1 ASRNHTQRFKTLRDDRYERFSHEINKLIIRLDKLLTNMP--IDPIKKKNHEQAIVPWLDGKDVPRCPNCSRSFNFAKRQH 78 (376)
Q Consensus 1 ~~r~~t~~F~~~R~~~~~~~~le~~~l~~RL~kLl~~~~--~~~~~~~~~Eq~~~~W~~d~~v~~C~~C~~~F~~~~RrH 78 (376)
++||||.+|.++|++++|+|++|+|+|++||.||++++| .++.+++++||++|||.||++|..||.|+.+|++++|||
T Consensus 118 ~vrS~~~eF~~~R~~rid~~~ve~nkLiiRl~rL~~~~~t~~d~~k~k~~EqsvVpW~DDs~V~~CP~Ca~~F~l~rRrH 197 (505)
T KOG1842|consen 118 AVRSHFQEFEKFRNPRIDKYAVETNKLIIRLKRLEEGLPTEKDSVKRKRLEQSVVPWLDDSSVQFCPECANSFGLTRRRH 197 (505)
T ss_pred cHHHhHHHHHHHhcchHHHHHHHHHHHHHHHHHHHccCccccchHHHHHHHhccccccCCCcccccccccchhhhHHHhh
Confidence 579999999999999999999999999999999999999 668899999999999999999999999999999999999
Q ss_pred cccccCccccccccCCcccccccccccCC--CcC----------CCCCCCcccccchHHHHHHHHHHhhhcCCCchhHHH
Q psy4518 79 HCRLCGCIMCHDCSFFLPLNKARQILVEP--ELG----------ESQLSASANSDLNLRLLESREVLKESRNSRPLICDL 146 (376)
Q Consensus 79 HCR~CG~vvC~~CS~~~~l~~~~~~~~~~--~~~----------~~~~~~vRvC~~C~~~l~~r~~~~~~~~~~p~i~~~ 146 (376)
|||+||+|+|.+|+.+++++.+..++..+ +.+ +....++|+|.+|...|+.|....+++.+.|.|++.
T Consensus 198 HCRLCG~VmC~~C~k~iSle~a~~ltsss~~dt~~e~~qq~~~lH~~~~~iRlC~hCl~~L~~R~~~~d~r~~~p~ivq~ 277 (505)
T KOG1842|consen 198 HCRLCGRVMCRDCSKFISLEIAIGLTSSSASDTHFEPNQQKDDLHQHPQPIRLCMHCLDNLFRRKLQQDEREPSPGIVQH 277 (505)
T ss_pred hhhhcchHHHHHHHHhcChHHHHHHhhccCCCCCcCcccCcccccCChhHhHHHHHHHHHHHHHHHhhhhccCCchHHHH
Confidence 99999999999999999988776655211 111 112357999999999999999999998889999999
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHhhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCccCCCCcchhhHH
Q psy4518 147 YDALMGKKQEASKLRAMYLEMIDSLLAGETMYYASDAQALRVKLVRLAENIDTISNKVTTLSSASGAQQASDSPMTMSQR 226 (376)
Q Consensus 147 Ye~L~~~~~~I~~~lP~f~~~l~sL~~g~s~~~l~~a~~lR~kL~~~f~~~d~~skri~~l~~~~~~~~~~~~~~~~q~r 226 (376)
||.|++++++|.+++|.|.+++.||++|+|+|++.+|..||++++++++.||..+|+|+.++.. ||++.+.+
T Consensus 278 Ye~mq~~~k~v~~~~p~Y~~~l~SL~~get~~tlk~~~dLR~k~~el~~s~D~~sKkI~~l~~~--------p~~~~E~q 349 (505)
T KOG1842|consen 278 YEHLQVFRKEVDNLLPLYEDSLNSLKEGETTYTLKHAKDLRKKFLELCESIDGTSKKIANLPSS--------PPSDAEEQ 349 (505)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHhcccccccHhhHHHHHHHHHHHHHHHHHHHHHHHhccCC--------CCChHHHH
Confidence 9999999999999999999999999999999999999999999999999999999999999875 45678999
Q ss_pred HHHHHHHHHHHHHHHcCCCCCCCCChHHHHHHHHHHHHHHHHHHHHH--HHHHHhhccc----ccccccCCCCcc-cccc
Q psy4518 227 LHKSIRQASTNFIRTHLLTLPNVPSDERLAELREERRLAEEARQREE--AIRELRGREE----NFNVETHHGRHS-VSKE 299 (376)
Q Consensus 227 lq~~I~~~a~~FLqe~ml~LksLP~~~~~~~~~~~r~~~~e~r~~~e--~~~e~~~r~~----~~~~~~~~~~~~-~~~~ 299 (376)
||+||+.+|+.|||+.||+|++||+.+++..++.+|+.+.|++++.| ++++..+|.. ..++.+++|+.. +..+
T Consensus 350 Lkk~Irl~a~~~lqEkiL~L~sLPt~e~~~~l~~krk~~te~d~a~e~r~a~~~~~rl~q~q~q~~s~~~~ge~~Si~~g 429 (505)
T KOG1842|consen 350 LKKNIRLEAKQYLQEKILRLQSLPTAEECYHLQVKRKEETESDFAREGREAEKKKERLSQLQKQQSSVSSFGEPLSIKEG 429 (505)
T ss_pred HHHHHHHHHHHHHHHHhccccCCCchHHHHHHHhhHhhhHHHHHHHHHHHHHHHHHhHHHHHHhccccCCCCCCcchhcc
Confidence 99999999999999999999999999999999999999999998887 5556655544 223444555442 2344
Q ss_pred cccccccCCCccccc-cccccchhHHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHhhhhcccc
Q psy4518 300 NNVSLLEAWSPAGTK-SVSSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQEQQTEVN 371 (376)
Q Consensus 300 ~~~~~~~~~s~~~~~-~~e~~~~L~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~~~~~~~~~~~ 371 (376)
++....-+|.|.++. ...+.|||.||+|+|++||+||+++||||||.||+.||+||++||+++|++.+++..
T Consensus 430 s~L~~~~~~l~~s~~~~~s~ddpl~EQi~~I~~~I~qAka~~k~eEv~TLe~NLreL~~Ei~~~q~k~~~~~~ 502 (505)
T KOG1842|consen 430 SELRQTLIVLPSSIEDDTSQDDPLYEQIFLIESFIEQAKAKRKFEEVETLESNLRELHEEIHSIQEKIHDLDL 502 (505)
T ss_pred hHHHHhhccCCccccccccccchHHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHHHHHHhccccc
Confidence 556666789999887 566679999999999999999999999999999999999999999999999887654
No 2
>PF11464 Rbsn: Rabenosyn Rab binding domain; InterPro: IPR021565 Rabenosyn-5 (Rbsn) is a multivalent effector with interacts with the Rab family.Rsbn contains distinct Rab4 and Rab5 binding sites within residues 264-500 and 627-784 respectively []. Rab proteins are GTPases involved in the regulation of all stages of membrane trafficking []. ; PDB: 1Z0K_B 1YZM_A 1Z0J_B.
Probab=99.71 E-value=1.5e-17 Score=114.00 Aligned_cols=42 Identities=48% Similarity=0.746 Sum_probs=39.5
Q ss_pred hHHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHH
Q psy4518 322 LVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQ 363 (376)
Q Consensus 322 L~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~~~ 363 (376)
|.||+++|++||++|+++||||||.+|++||+||+.||+++|
T Consensus 1 LleQi~~I~~~I~qAk~~~r~dEV~~L~~NL~EL~~e~~~qq 42 (42)
T PF11464_consen 1 LLEQINIIESYIKQAKAARRFDEVATLEENLRELQDEIDEQQ 42 (42)
T ss_dssp HHHHHHHHHHHHHHHHHTT-HHHHHHHHHHHHHHHHHHHHHC
T ss_pred CHHHHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHHhcC
Confidence 689999999999999999999999999999999999999874
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=99.70 E-value=2.2e-18 Score=132.35 Aligned_cols=67 Identities=27% Similarity=0.625 Sum_probs=43.2
Q ss_pred CCcccCCCCCcccccccccccccccccccccCccccccccCCc-ccccccccccCCCcCCCCCCCcccccchHHHHH
Q psy4518 53 VPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFL-PLNKARQILVEPELGESQLSASANSDLNLRLLE 128 (376)
Q Consensus 53 ~~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~-~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~ 128 (376)
|.|++|+++..|+.|+++|++++||||||.||.|||+.|+... .++... .....++|||..|+..+.
T Consensus 1 ~~W~~d~~~~~C~~C~~~F~~~~rrhhCr~CG~~vC~~Cs~~~~~~~~~~---------~~~~~~~RvC~~C~~~~~ 68 (69)
T PF01363_consen 1 PHWVPDSEASNCMICGKKFSLFRRRHHCRNCGRVVCSSCSSQRIPLPTPS---------SGSGEPVRVCDSCYSKLQ 68 (69)
T ss_dssp --SSSGGG-SB-TTT--B-BSSS-EEE-TTT--EEECCCS-EEEEET--G---------GTESEEEEE-HHHHHHHH
T ss_pred CCcCCCCCCCcCcCcCCcCCCceeeEccCCCCCEECCchhCCEEcccccc---------cCCCCcCEECHHHHHHhc
Confidence 5899999999999999999999999999999999999999863 333100 012468999999999874
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
Probab=99.48 E-value=1.8e-14 Score=138.83 Aligned_cols=72 Identities=28% Similarity=0.594 Sum_probs=60.9
Q ss_pred hhccccCCCcccCCCCCccccccc-ccccccccccccccCccccccccCC-cccccccccccCCCcCCCCCCCcccccch
Q psy4518 46 KNHEQAIVPWLDGKDVPRCPNCSR-SFNFAKRQHHCRLCGCIMCHDCSFF-LPLNKARQILVEPELGESQLSASANSDLN 123 (376)
Q Consensus 46 ~~~Eq~~~~W~~d~~v~~C~~C~~-~F~~~~RrHHCR~CG~vvC~~CS~~-~~l~~~~~~~~~~~~~~~~~~~vRvC~~C 123 (376)
....-....|+||.++..|+.|++ .|+++.||||||.||.|||..|+.. +.++.. ...++|||+.|
T Consensus 153 ~~~~~~~~~W~PD~ea~~C~~C~~~~Ftl~~RRHHCR~CG~ivC~~Cs~n~~~l~~~------------~~k~~rvC~~C 220 (288)
T KOG1729|consen 153 SPSNNSAAVWLPDSEATECMVCGCTEFTLSERRHHCRNCGDIVCAPCSRNRFLLPNL------------STKPIRVCDIC 220 (288)
T ss_pred CCCCCcCCcccCcccceecccCCCccccHHHHHHHHHhcchHhhhhhhcCccccccc------------CCCCceecHHH
Confidence 344556679999999999999999 9999999999999999999999986 344432 24689999999
Q ss_pred HHHHHH
Q psy4518 124 LRLLES 129 (376)
Q Consensus 124 ~~~l~~ 129 (376)
|..+..
T Consensus 221 F~el~~ 226 (288)
T KOG1729|consen 221 FEELEK 226 (288)
T ss_pred HHHHhc
Confidence 999975
No 6
>PTZ00303 phosphatidylinositol kinase; Provisional
Probab=99.41 E-value=1.6e-13 Score=143.00 Aligned_cols=73 Identities=23% Similarity=0.466 Sum_probs=52.4
Q ss_pred CCCcccCCCC-Ccccccccccccc-----cccccccccCccccccccCC-cccccccccccCCCcCCCCCCCcccccchH
Q psy4518 52 IVPWLDGKDV-PRCPNCSRSFNFA-----KRQHHCRLCGCIMCHDCSFF-LPLNKARQILVEPELGESQLSASANSDLNL 124 (376)
Q Consensus 52 ~~~W~~d~~v-~~C~~C~~~F~~~-----~RrHHCR~CG~vvC~~CS~~-~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~ 124 (376)
.+.|++|.++ ..|+.|++.|+++ .||||||.||+|||+.||.. ..++... +. ...+.....+.|||+.||
T Consensus 450 APvWqpDDEaSdtC~~C~kkFfSlsK~L~~RKHHCRkCGrVFC~~CSSnRs~yp~aK-Lp--KPgsseE~ppRRVCD~CY 526 (1374)
T PTZ00303 450 NPSWQKDDESSDSCPSCGRAFISLSRPLGTRAHHCRSCGIRLCVFCITKRAHYSFAK-LA--KPGSSDEAEERLVCDTCY 526 (1374)
T ss_pred CCCCCCCcccCCcccCcCCcccccccccccccccccCCccccCccccCCcccCcccc-cC--CCCCcccccccchhHHHH
Confidence 5689999975 7899999999743 69999999999999999985 3333321 10 111111235778999999
Q ss_pred HHH
Q psy4518 125 RLL 127 (376)
Q Consensus 125 ~~l 127 (376)
..+
T Consensus 527 dq~ 529 (1374)
T PTZ00303 527 KEY 529 (1374)
T ss_pred HHH
Confidence 555
No 7
>KOG1818|consensus
Probab=99.40 E-value=8.2e-14 Score=144.88 Aligned_cols=67 Identities=31% Similarity=0.646 Sum_probs=58.3
Q ss_pred cCCCcccCCCCCcccccccccccccccccccccCccccccccCC-cccccccccccCCCcCCCCCCCcccccchHHHHHH
Q psy4518 51 AIVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF-LPLNKARQILVEPELGESQLSASANSDLNLRLLES 129 (376)
Q Consensus 51 ~~~~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~-~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~ 129 (376)
..+.|.+.. .|..|.++||+++|+||||.||+|||..||.+ .+++..|. ..+||||+.||..+.+
T Consensus 158 ~~pdW~D~~---~C~rCr~~F~~~~rkHHCr~CG~vFC~qcss~s~~lP~~Gi-----------~~~VRVCd~C~E~l~~ 223 (634)
T KOG1818|consen 158 TAPDWIDSE---ECLRCRVKFGLTNRKHHCRNCGQVFCGQCSSKSLTLPKLGI-----------EKPVRVCDSCYELLTR 223 (634)
T ss_pred CCccccccc---ccceeeeeeeeccccccccccchhhccCccccccCcccccc-----------cccceehhhhHHHhhh
Confidence 467899877 79999999999999999999999999999986 77777654 4699999999999875
Q ss_pred HH
Q psy4518 130 RE 131 (376)
Q Consensus 130 r~ 131 (376)
..
T Consensus 224 ~s 225 (634)
T KOG1818|consen 224 AS 225 (634)
T ss_pred cc
Confidence 43
No 8
>KOG1819|consensus
Probab=99.37 E-value=1.1e-13 Score=138.66 Aligned_cols=64 Identities=31% Similarity=0.623 Sum_probs=55.6
Q ss_pred CCCcccCCCCCcccccccccccccccccccccCccccccccCC-cccccccccccCCCcCCCCCCCccccc-----chHH
Q psy4518 52 IVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF-LPLNKARQILVEPELGESQLSASANSD-----LNLR 125 (376)
Q Consensus 52 ~~~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~-~~l~~~~~~~~~~~~~~~~~~~vRvC~-----~C~~ 125 (376)
.|.|+||.+...|+.|+.+|+.++||||||+||.|||..||.. .++|..+. ++.+|||. +|+.
T Consensus 892 ppawipd~~a~~cmacq~pf~afrrrhhcrncggifcg~cs~asapip~~gl-----------~ka~rvcrpqsnldc~~ 960 (990)
T KOG1819|consen 892 PPAWIPDEDAEQCMACQMPFNAFRRRHHCRNCGGIFCGKCSCASAPIPEHGL-----------DKAPRVCRPQSNLDCLT 960 (990)
T ss_pred CcccCCCCcchhhhhccCcHHHHHHhhhhcccCceeecccccCCCCCccccc-----------ccCceecCCccccccee
Confidence 5679999999999999999999999999999999999999985 67776543 46889999 7765
Q ss_pred H
Q psy4518 126 L 126 (376)
Q Consensus 126 ~ 126 (376)
.
T Consensus 961 r 961 (990)
T KOG1819|consen 961 R 961 (990)
T ss_pred e
Confidence 3
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=99.30 E-value=9.2e-13 Score=97.17 Aligned_cols=54 Identities=31% Similarity=0.685 Sum_probs=44.8
Q ss_pred CCcccccccccccccccccccccCccccccccCCc-ccccccccccCCCcCCCCCCCcccccchHH
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFL-PLNKARQILVEPELGESQLSASANSDLNLR 125 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~-~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~ 125 (376)
+..|+.|++.|+++.|+|||+.||.+||+.|+.+. .++.. ....++|||..|+.
T Consensus 2 ~~~C~~C~~~F~~~~rk~~Cr~Cg~~~C~~C~~~~~~~~~~-----------~~~~~~rvC~~C~~ 56 (57)
T cd00065 2 ASSCMGCGKPFTLTRRRHHCRNCGRIFCSKCSSNRIPLPSM-----------GGGKPVRVCDSCYE 56 (57)
T ss_pred cCcCcccCccccCCccccccCcCcCCcChHHcCCeeecCcc-----------cCCCccEeChHHhC
Confidence 56899999999999999999999999999999974 32221 12469999999985
No 10
>KOG1841|consensus
Probab=98.82 E-value=1e-09 Score=118.99 Aligned_cols=47 Identities=32% Similarity=0.822 Sum_probs=43.6
Q ss_pred ccccCCCcccCCCCCcccccccccccccccccccccCccccccccCC
Q psy4518 48 HEQAIVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 48 ~Eq~~~~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
+-+..|.|++|...+.|+.|.++|++++||||||.||+|+|..|+..
T Consensus 544 lgkkqP~wvpdse~pncm~clqkft~ikrrhhcRacgkVlcgvccne 590 (1287)
T KOG1841|consen 544 LGKKQPSWVPDSEAPNCMDCLQKFTPIKRRHHCRACGKVLCGVCCNE 590 (1287)
T ss_pred cCCCCCccCccccCchHHHHHhhcccccccccchhccceeehhhcch
Confidence 45667899999999999999999999999999999999999998875
No 11
>KOG1843|consensus
Probab=98.42 E-value=6.2e-08 Score=95.98 Aligned_cols=71 Identities=17% Similarity=0.049 Sum_probs=60.3
Q ss_pred hhhccccCCCcccCCCCCcccccccccc-cccccccccccCccccccccCC---cccccccccccCCCcCCCCCCCcccc
Q psy4518 45 KKNHEQAIVPWLDGKDVPRCPNCSRSFN-FAKRQHHCRLCGCIMCHDCSFF---LPLNKARQILVEPELGESQLSASANS 120 (376)
Q Consensus 45 ~~~~Eq~~~~W~~d~~v~~C~~C~~~F~-~~~RrHHCR~CG~vvC~~CS~~---~~l~~~~~~~~~~~~~~~~~~~vRvC 120 (376)
.-.+|-..+.|.+++....|+.|..+|+ ++-||||||.||.++|..|+.. ++.+.. .+.+.|||
T Consensus 144 ~asl~~~ap~f~yskskglfagvSvegsaI~erR~anR~~yg~~cra~~ilsg~vp~p~a------------~d~l~RVl 211 (473)
T KOG1843|consen 144 SASLGGEAPVFLYSKSKGLFAGVSVEGSAIIERREANRKFYGIFCRAKSILSGLVPVPFA------------ADPLQRVL 211 (473)
T ss_pred hhhhcCcCccccccccccceeeeecccceeeecchhhhhhcCccchhhhhhccCCCCCcc------------cCCHHHHH
Confidence 3456777889999999999999999999 8999999999999999999874 333322 25689999
Q ss_pred cchHHHH
Q psy4518 121 DLNLRLL 127 (376)
Q Consensus 121 ~~C~~~l 127 (376)
+.|+..+
T Consensus 212 dS~~~nl 218 (473)
T KOG1843|consen 212 DSCAFNL 218 (473)
T ss_pred hhHhhcc
Confidence 9999888
No 12
>KOG1409|consensus
Probab=98.21 E-value=2.6e-07 Score=90.13 Aligned_cols=65 Identities=28% Similarity=0.549 Sum_probs=52.0
Q ss_pred ccCCCcccCCCCCccccccccccc-----------ccccccccccCccccccccCCc-ccccccccccCCCcCCCCCCCc
Q psy4518 50 QAIVPWLDGKDVPRCPNCSRSFNF-----------AKRQHHCRLCGCIMCHDCSFFL-PLNKARQILVEPELGESQLSAS 117 (376)
Q Consensus 50 q~~~~W~~d~~v~~C~~C~~~F~~-----------~~RrHHCR~CG~vvC~~CS~~~-~l~~~~~~~~~~~~~~~~~~~v 117 (376)
...|.|.++. .|..|+++|.+ -.|.||||.||..||..|++.. .++..+. +-.+
T Consensus 274 ~etpewl~s~---~cQ~c~qpffwn~~~m~~~k~~glr~h~crkcg~avc~~c~s~~~~~p~mg~-----------e~~v 339 (404)
T KOG1409|consen 274 VETPEWLDSD---SCQKCNQPFFWNFRQMWDRKQLGLRQHHCRKCGKAVCGKCSSNRSSYPTMGF-----------EFSV 339 (404)
T ss_pred ecCccccccc---hhhhhCchHHHHHHHHHhhhhhhhhhhhhhhhhhhcCcccccCccccccccc-----------eeEE
Confidence 4578999998 89999999853 3689999999999999998864 3333222 3589
Q ss_pred ccccchHHHHH
Q psy4518 118 ANSDLNLRLLE 128 (376)
Q Consensus 118 RvC~~C~~~l~ 128 (376)
|+|..||..+.
T Consensus 340 R~~~~c~~~i~ 350 (404)
T KOG1409|consen 340 RVCDSCYPTIK 350 (404)
T ss_pred EEecccchhhh
Confidence 99999999985
No 13
>KOG4424|consensus
Probab=98.10 E-value=5.5e-07 Score=92.81 Aligned_cols=62 Identities=23% Similarity=0.450 Sum_probs=51.3
Q ss_pred CcccCCCCCcccccccccc-cccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHH
Q psy4518 54 PWLDGKDVPRCPNCSRSFN-FAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLE 128 (376)
Q Consensus 54 ~W~~d~~v~~C~~C~~~F~-~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~ 128 (376)
.| +..+..|..|..+|+ .+.|||||+.||.|+|+.|+.+....... .+..-|||..|+.+..
T Consensus 410 r~--~~k~~~c~~c~e~~~s~t~~R~~~k~~~~vlc~~cs~~~~~l~~~-----------~s~ssrv~~~~~~~~~ 472 (623)
T KOG4424|consen 410 RR--DNKVTSCDSCEETFNSITFRRHRCKAKGAVLCDKCSDFMAKLSYD-----------NSRSSRVCMDRYLTPS 472 (623)
T ss_pred cc--ccccccchhhcCchhhHHHhhhhhhhccceeeccccchhhhhccc-----------ccchhhhhhhhccCCC
Confidence 56 888999999999999 89999999999999999999976432211 1356799999998875
No 14
>KOG1811|consensus
Probab=97.24 E-value=3.6e-05 Score=80.10 Aligned_cols=67 Identities=21% Similarity=0.422 Sum_probs=50.2
Q ss_pred CCCcccCC----CCCccccccc-ccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHH
Q psy4518 52 IVPWLDGK----DVPRCPNCSR-SFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRL 126 (376)
Q Consensus 52 ~~~W~~d~----~v~~C~~C~~-~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~ 126 (376)
...|++|. +-.-|+.|.. .|..++||||||-||..+|..|+....+...- .++.+.++|+.|+.+
T Consensus 313 l~nfq~darrafs~a~~~a~~R~~~kd~~Rk~~~~g~Ga~e~aa~ea~kgiqEd~----------gse~~Adg~Dq~psv 382 (1141)
T KOG1811|consen 313 LHNFQPDARRAFSEAICMACCREHFKDFNRKHHCRGCGALECAACEAKKGIQEDC----------GSENPADGCDQCPSV 382 (1141)
T ss_pred hhhcChhhhhhhhhhHHHHHHHHHHHHHHHhhhccccchHHHhHHHHhhhhhhcc----------cccCcccccccccch
Confidence 34799998 5567876654 78899999999999999999998864433211 124588999999976
Q ss_pred HH
Q psy4518 127 LE 128 (376)
Q Consensus 127 l~ 128 (376)
-.
T Consensus 383 si 384 (1141)
T KOG1811|consen 383 SI 384 (1141)
T ss_pred hh
Confidence 54
No 15
>KOG0230|consensus
Probab=97.10 E-value=0.00024 Score=80.35 Aligned_cols=49 Identities=24% Similarity=0.557 Sum_probs=39.0
Q ss_pred CCCcccccccccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHHH
Q psy4518 60 DVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLES 129 (376)
Q Consensus 60 ~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~ 129 (376)
..+.|..|+ +.++|+||||.||+|||..|..- ....+|+|..|+.....
T Consensus 4 s~~~~~~~~---t~~~~~~~~~~~g~~~~~~~~~~------------------~~~~i~~~~~~~~~~~~ 52 (1598)
T KOG0230|consen 4 SSNVCYDCD---TSVNRRHHCRVCGRVFCSKCQDS------------------PETSIRVCNECRGQWEQ 52 (1598)
T ss_pred cccchhccc---cccccCCCCcccCceeccccCCC------------------Cccceeehhhhhhhccc
Confidence 345677787 78899999999999999999721 12488999999987743
No 16
>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=97.10 E-value=0.00031 Score=59.59 Aligned_cols=51 Identities=20% Similarity=0.481 Sum_probs=39.6
Q ss_pred CCcccccccccccc-cccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHH
Q psy4518 61 VPRCPNCSRSFNFA-KRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLE 128 (376)
Q Consensus 61 v~~C~~C~~~F~~~-~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~ 128 (376)
...|..|+++|+++ ++.+-|..|+.-||..|+.+.. ..+.-+|..|+..-.
T Consensus 54 ~~~C~~C~~~fg~l~~~~~~C~~C~~~VC~~C~~~~~-----------------~~~~WlC~vC~k~re 105 (118)
T PF02318_consen 54 ERHCARCGKPFGFLFNRGRVCVDCKHRVCKKCGVYSK-----------------KEPIWLCKVCQKQRE 105 (118)
T ss_dssp CSB-TTTS-BCSCTSTTCEEETTTTEEEETTSEEETS-----------------SSCCEEEHHHHHHHH
T ss_pred CcchhhhCCcccccCCCCCcCCcCCccccCccCCcCC-----------------CCCCEEChhhHHHHH
Confidence 34899999999955 6899999999999999987621 246789999987654
No 17
>KOG0230|consensus
Probab=96.12 E-value=0.0021 Score=73.09 Aligned_cols=34 Identities=35% Similarity=1.037 Sum_probs=32.9
Q ss_pred ccCCCCCcccccccccccccccccccccCccccccc
Q psy4518 56 LDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDC 91 (376)
Q Consensus 56 ~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~C 91 (376)
.+|.....|..|.+.|+.++|+||| ||.|+|+.|
T Consensus 92 m~d~s~~ec~~~~~~~~t~Rr~~~~--~gqi~~ss~ 125 (1598)
T KOG0230|consen 92 MPDSSSKECYDCEQKFETFRRKHHC--CGQIFCSSC 125 (1598)
T ss_pred CCccccchhhhhccchhhhhccccc--CccccCCcc
Confidence 7888999999999999999999999 999999999
No 18
>KOG1729|consensus
Probab=94.56 E-value=0.0064 Score=59.25 Aligned_cols=75 Identities=21% Similarity=0.432 Sum_probs=53.7
Q ss_pred cCCCcccCCCCCcccccccccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHH-HHH
Q psy4518 51 AIVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRL-LES 129 (376)
Q Consensus 51 ~~~~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~-l~~ 129 (376)
..|.|+-+..+..|..|...|.|..|.|||+.||+|+|..|+... .. .+. +.+...+..+.....|..|... +..
T Consensus 10 ~~~~~~~~~e~~s~~~~~~e~~~~~r~~~~~~~grv~~~q~~~~k-~~--rk~-~q~r~~~l~~D~~~~~~~~~~~~~~~ 85 (288)
T KOG1729|consen 10 NMVDWQANSEANSCRNCKVEFCFGRRGHPCRECGRVLCRQGTLVK-RC--RKK-LQSRSFFLFNDILVYGNIVSDNKLLN 85 (288)
T ss_pred hhHHHHHhccchhhhhhcccchhhhccCcccccchhhhhhhhhHH-HH--hcc-cccccccccccchhhcccccCHHHHh
Confidence 356899999999999999999999999999999999999997710 00 000 0011112234677888888877 443
No 19
>KOG0993|consensus
Probab=92.34 E-value=0.01 Score=59.56 Aligned_cols=64 Identities=28% Similarity=0.480 Sum_probs=52.5
Q ss_pred CCcccCCCCCcccccccccccccccccccc--cCccccccccCC-cccccccccccCCCcCCCCCCCcccccchHHHHHH
Q psy4518 53 VPWLDGKDVPRCPNCSRSFNFAKRQHHCRL--CGCIMCHDCSFF-LPLNKARQILVEPELGESQLSASANSDLNLRLLES 129 (376)
Q Consensus 53 ~~W~~d~~v~~C~~C~~~F~~~~RrHHCR~--CG~vvC~~CS~~-~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~ 129 (376)
+.|+-|.++..|..|..+|..++-.-||-+ ||+|||-.|+.- +|-.. ...+..||+-|..++.+
T Consensus 460 le~ql~~~ve~c~~~~aS~~slk~e~erl~qq~eqi~~~~~~Katvp~l~-------------~e~~akv~rlq~eL~~s 526 (542)
T KOG0993|consen 460 LEWQLDDDVEQCSNCDASFASLKVEPERLHQQCEQIFCMNCLKATVPSLP-------------NERPAKVCRLQHELLNS 526 (542)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhccHHHHHHHHHHHHHHhHHHhhccccc-------------ccchHHHHHHHHHHhhh
Confidence 469999999999999999999999999988 999999999874 32111 23578899999988764
No 20
>PRK00464 nrdR transcriptional regulator NrdR; Validated
Probab=91.96 E-value=0.071 Score=47.42 Aligned_cols=25 Identities=32% Similarity=0.785 Sum_probs=20.2
Q ss_pred ccccccccc-----------c-cccccccccccCccc
Q psy4518 63 RCPNCSRSF-----------N-FAKRQHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F-----------~-~~~RrHHCR~CG~vv 87 (376)
.||.|+.++ | ..+|+++|..||.-|
T Consensus 2 ~cp~c~~~~~~~~~s~~~~~~~~~~~~~~c~~c~~~f 38 (154)
T PRK00464 2 RCPFCGHPDTRVIDSRPAEDGNAIRRRRECLACGKRF 38 (154)
T ss_pred cCCCCCCCCCEeEeccccCCCCceeeeeeccccCCcc
Confidence 699999888 2 355679999999876
No 21
>TIGR00622 ssl1 transcription factor ssl1. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=89.48 E-value=0.29 Score=41.21 Aligned_cols=43 Identities=23% Similarity=0.640 Sum_probs=33.3
Q ss_pred CCcccCCCCCccccccccccc----------ccccccccccCccccccccCCc
Q psy4518 53 VPWLDGKDVPRCPNCSRSFNF----------AKRQHHCRLCGCIMCHDCSFFL 95 (376)
Q Consensus 53 ~~W~~d~~v~~C~~C~~~F~~----------~~RrHHCR~CG~vvC~~CS~~~ 95 (376)
++|........|..|+++|.- ...+.-|..|+.+||.+|=.++
T Consensus 47 v~~~~~~~~~~C~~C~~~f~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fi 99 (112)
T TIGR00622 47 IPLEEYNGSRFCFGCQGPFPKPPVSPFDELKDSHRYVCAVCKNVFCVDCDVFV 99 (112)
T ss_pred ccccccCCCCcccCcCCCCCCcccccccccccccceeCCCCCCccccccchhh
Confidence 466655555679999999973 2457889999999999996664
No 22
>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=89.04 E-value=0.21 Score=41.82 Aligned_cols=25 Identities=28% Similarity=0.736 Sum_probs=19.1
Q ss_pred cccccccccccccc-cccccccCccc
Q psy4518 63 RCPNCSRSFNFAKR-QHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~~~R-rHHCR~CG~vv 87 (376)
.||.||++|-=++| --+|..||.+|
T Consensus 11 ~Cp~CG~kFYDLnk~PivCP~CG~~~ 36 (108)
T PF09538_consen 11 TCPSCGAKFYDLNKDPIVCPKCGTEF 36 (108)
T ss_pred cCCCCcchhccCCCCCccCCCCCCcc
Confidence 89999999995555 44577777765
No 23
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=88.71 E-value=0.3 Score=48.23 Aligned_cols=63 Identities=21% Similarity=0.354 Sum_probs=38.9
Q ss_pred CCcccccccc--ccc-------ccccccccccC------ccccccccCCcccccccccccCCCcCCCCCCCcccccchHH
Q psy4518 61 VPRCPNCSRS--FNF-------AKRQHHCRLCG------CIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLR 125 (376)
Q Consensus 61 v~~C~~C~~~--F~~-------~~RrHHCR~CG------~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~ 125 (376)
...||.||.. .++ -.|.-||.+|| ++-|..|-..-.+.... +.++ .....+=+|..|..
T Consensus 187 ~~~CPvCGs~P~~s~v~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~---~~~~---~~~~r~e~C~~C~~ 260 (309)
T PRK03564 187 RQFCPVCGSMPVSSVVQIGTTQGLRYLHCNLCESEWHVVRVKCSNCEQSGKLHYWS---LDSE---QAAVKAESCGDCGT 260 (309)
T ss_pred CCCCCCCCCcchhheeeccCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeee---ecCC---CcceEeeecccccc
Confidence 3589999985 332 25788999998 56888897633222210 0010 01234569999988
Q ss_pred HHHH
Q psy4518 126 LLES 129 (376)
Q Consensus 126 ~l~~ 129 (376)
.+..
T Consensus 261 YlK~ 264 (309)
T PRK03564 261 YLKI 264 (309)
T ss_pred ccee
Confidence 7743
No 24
>KOG1841|consensus
Probab=88.31 E-value=0.26 Score=55.36 Aligned_cols=36 Identities=22% Similarity=0.452 Sum_probs=32.1
Q ss_pred ccCCCcccCCCCCcccccccccccccccccccccCccc
Q psy4518 50 QAIVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIM 87 (376)
Q Consensus 50 q~~~~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vv 87 (376)
.....|.+|...++|..|.+.|.++.++|||| |.++
T Consensus 646 e~ksVw~aDg~aPng~la~t~~~~~~e~~hsr--~~ls 681 (1287)
T KOG1841|consen 646 EVKSVWFADGIAPNGELAETRFTFTGERHHSR--GKLS 681 (1287)
T ss_pred eecceeccCCcCCCceecccceeeeccccccc--cccc
Confidence 33456999999999999999999999999999 7776
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=87.19 E-value=0.33 Score=41.62 Aligned_cols=26 Identities=23% Similarity=0.425 Sum_probs=21.0
Q ss_pred Ccccccccccc-cccccccccccCccc
Q psy4518 62 PRCPNCSRSFN-FAKRQHHCRLCGCIM 87 (376)
Q Consensus 62 ~~C~~C~~~F~-~~~RrHHCR~CG~vv 87 (376)
..||.|+++|- +-+.--+|..||.++
T Consensus 10 r~Cp~cg~kFYDLnk~p~vcP~cg~~~ 36 (129)
T TIGR02300 10 RICPNTGSKFYDLNRRPAVSPYTGEQF 36 (129)
T ss_pred ccCCCcCccccccCCCCccCCCcCCcc
Confidence 37999999998 556677888888775
No 26
>KOG2164|consensus
Probab=86.37 E-value=0.19 Score=52.13 Aligned_cols=50 Identities=18% Similarity=0.488 Sum_probs=38.1
Q ss_pred CcccccccccccccccccccccCccccccccC-CcccccccccccCCCcCCCCCCCcccccchHHHHHH
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSF-FLPLNKARQILVEPELGESQLSASANSDLNLRLLES 129 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~-~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~ 129 (376)
..||+|-.++.+-.|- .||.|||..|-- +|..+. ....+-|.-|+.++.-
T Consensus 187 ~~CPICL~~~~~p~~t----~CGHiFC~~CiLqy~~~s~--------------~~~~~~CPiC~s~I~~ 237 (513)
T KOG2164|consen 187 MQCPICLEPPSVPVRT----NCGHIFCGPCILQYWNYSA--------------IKGPCSCPICRSTITL 237 (513)
T ss_pred CcCCcccCCCCccccc----ccCceeeHHHHHHHHhhhc--------------ccCCccCCchhhhccc
Confidence 5899999999876665 399999999965 454331 2466889999998754
No 27
>KOG4275|consensus
Probab=85.85 E-value=0.16 Score=49.25 Aligned_cols=49 Identities=22% Similarity=0.522 Sum_probs=41.3
Q ss_pred CCCCcccccccccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHH
Q psy4518 59 KDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRL 126 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~ 126 (376)
...+.|..|+..|..+.+||-|--|..-||..|| .+. ...|.|..|..+
T Consensus 42 ~~~p~ckacg~~f~~~~~k~~c~dckk~fc~tcs-~v~------------------~~lr~c~~c~r~ 90 (350)
T KOG4275|consen 42 SQAPHCKACGEEFEDAQSKSDCEDCKKEFCATCS-RVS------------------ISLRTCTSCRRV 90 (350)
T ss_pred cccchhhhhchhHhhhhhhhhhhhhhHHHHHHHH-Hhc------------------ccchhhhHHHHH
Confidence 4456899999999999999999999999999999 332 366889888754
No 28
>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=85.29 E-value=0.54 Score=46.39 Aligned_cols=63 Identities=21% Similarity=0.392 Sum_probs=38.2
Q ss_pred CCccccccccc--cc--------ccccccccccC------ccccccccCCcccccccccccCCCcCCCCCCCcc--cccc
Q psy4518 61 VPRCPNCSRSF--NF--------AKRQHHCRLCG------CIMCHDCSFFLPLNKARQILVEPELGESQLSASA--NSDL 122 (376)
Q Consensus 61 v~~C~~C~~~F--~~--------~~RrHHCR~CG------~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vR--vC~~ 122 (376)
...||.||..= ++ -.|..||.+|| ++-|..|-+...+.... +.++ .....+| +|..
T Consensus 184 ~~~CPvCGs~P~~s~~~~~~~~~G~RyL~CslC~teW~~~R~~C~~Cg~~~~l~y~~---~e~~---~~~~~~r~e~C~~ 257 (305)
T TIGR01562 184 RTLCPACGSPPVASMVRQGGKETGLRYLSCSLCATEWHYVRVKCSHCEESKHLAYLS---LEHD---AEKAVLKAETCDS 257 (305)
T ss_pred CCcCCCCCChhhhhhhcccCCCCCceEEEcCCCCCcccccCccCCCCCCCCceeeEe---ecCC---CCCcceEEeeccc
Confidence 34899999843 22 24788999998 56888886642222111 1010 0123455 9999
Q ss_pred hHHHHHH
Q psy4518 123 NLRLLES 129 (376)
Q Consensus 123 C~~~l~~ 129 (376)
|...+..
T Consensus 258 C~~YlK~ 264 (305)
T TIGR01562 258 CQGYLKI 264 (305)
T ss_pred cccchhh
Confidence 9887754
No 29
>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=84.63 E-value=0.26 Score=35.70 Aligned_cols=33 Identities=27% Similarity=0.761 Sum_probs=21.3
Q ss_pred cccccccccccc------cccccccccCccccccccCCc
Q psy4518 63 RCPNCSRSFNFA------KRQHHCRLCGCIMCHDCSFFL 95 (376)
Q Consensus 63 ~C~~C~~~F~~~------~RrHHCR~CG~vvC~~CS~~~ 95 (376)
.|..|.++|... ..++.|..|+.+||-+|=.++
T Consensus 1 ~CfgC~~~~~~~~~~~~~~~~y~C~~C~~~FC~dCD~fi 39 (51)
T PF07975_consen 1 YCFGCQKPFPDGPEKKADSSRYRCPKCKNHFCIDCDVFI 39 (51)
T ss_dssp EETTTTEE-TTS-------EEE--TTTT--B-HHHHHTT
T ss_pred CCccCCCCCCCcccccccCCeEECCCCCCccccCcChhh
Confidence 488999999865 468999999999999996554
No 30
>PF13719 zinc_ribbon_5: zinc-ribbon domain
Probab=84.31 E-value=0.5 Score=31.71 Aligned_cols=25 Identities=36% Similarity=1.004 Sum_probs=18.8
Q ss_pred cccccccccccc-------cccccccccCccc
Q psy4518 63 RCPNCSRSFNFA-------KRQHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~~-------~RrHHCR~CG~vv 87 (376)
.||.|+..|.+- .++.-|..||.+|
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 699999999753 4477777777665
No 31
>PF13717 zinc_ribbon_4: zinc-ribbon domain
Probab=83.88 E-value=0.56 Score=31.34 Aligned_cols=25 Identities=32% Similarity=0.999 Sum_probs=18.4
Q ss_pred cccccccccccc-------cccccccccCccc
Q psy4518 63 RCPNCSRSFNFA-------KRQHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~~-------~RrHHCR~CG~vv 87 (376)
.||.|++.|.+- .++-.|..||.+|
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 699999999753 3567777777764
No 32
>KOG3576|consensus
Probab=80.93 E-value=0.33 Score=44.97 Aligned_cols=33 Identities=27% Similarity=0.667 Sum_probs=25.7
Q ss_pred ccCCCCCccccccccccc---ccc---------cccccccCcccc
Q psy4518 56 LDGKDVPRCPNCSRSFNF---AKR---------QHHCRLCGCIMC 88 (376)
Q Consensus 56 ~~d~~v~~C~~C~~~F~~---~~R---------rHHCR~CG~vvC 88 (376)
-.|.++..|..|++.|++ ++| ||-|+.||.-|=
T Consensus 112 ssd~d~ftCrvCgK~F~lQRmlnrh~kch~~vkr~lct~cgkgfn 156 (267)
T KOG3576|consen 112 SSDQDSFTCRVCGKKFGLQRMLNRHLKCHSDVKRHLCTFCGKGFN 156 (267)
T ss_pred CCCCCeeeeehhhhhhhHHHHHHHHhhhccHHHHHHHhhccCccc
Confidence 456777899999999983 444 788899998764
No 33
>PRK00420 hypothetical protein; Validated
Probab=80.79 E-value=0.95 Score=38.16 Aligned_cols=24 Identities=21% Similarity=0.551 Sum_probs=14.5
Q ss_pred Ccccccccccc-cccccccccccCc
Q psy4518 62 PRCPNCSRSFN-FAKRQHHCRLCGC 85 (376)
Q Consensus 62 ~~C~~C~~~F~-~~~RrHHCR~CG~ 85 (376)
..||.|+.+|. +-..+.-|..||.
T Consensus 24 ~~CP~Cg~pLf~lk~g~~~Cp~Cg~ 48 (112)
T PRK00420 24 KHCPVCGLPLFELKDGEVVCPVHGK 48 (112)
T ss_pred CCCCCCCCcceecCCCceECCCCCC
Confidence 48999998775 3334444444444
No 34
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=79.41 E-value=0.95 Score=31.67 Aligned_cols=24 Identities=25% Similarity=0.793 Sum_probs=18.7
Q ss_pred cccccccccccccc--cccccccCcc
Q psy4518 63 RCPNCSRSFNFAKR--QHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~~~R--rHHCR~CG~v 86 (376)
.|+.|+..|.+... ..+|..||.-
T Consensus 5 ~C~~CG~~~~~~~~~~~~~Cp~CG~~ 30 (46)
T PRK00398 5 KCARCGREVELDEYGTGVRCPYCGYR 30 (46)
T ss_pred ECCCCCCEEEECCCCCceECCCCCCe
Confidence 69999999875544 5888888864
No 35
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=78.85 E-value=0.92 Score=43.91 Aligned_cols=70 Identities=20% Similarity=0.344 Sum_probs=42.9
Q ss_pred CcccCCCCCcccccccc----cc------cccccccccccC------ccccccccCCcccccccccccCCCcCCCCCCCc
Q psy4518 54 PWLDGKDVPRCPNCSRS----FN------FAKRQHHCRLCG------CIMCHDCSFFLPLNKARQILVEPELGESQLSAS 117 (376)
Q Consensus 54 ~W~~d~~v~~C~~C~~~----F~------~~~RrHHCR~CG------~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~v 117 (376)
.|++...++.||.||.. |- --.|=-||.+|- ++-|..|-+...+..-.- .++ .......
T Consensus 178 ~~~e~e~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~CslC~teW~~VR~KC~nC~~t~~l~y~sl---~s~--E~A~vkA 252 (308)
T COG3058 178 ARVENESRQYCPVCGSMPVASMVQIGETEQGLRYLHCSLCETEWHYVRVKCSNCEQSKKLHYWSL---ESS--ELAAVKA 252 (308)
T ss_pred ccccccccccCCCcCCCCcceeeeecCccccchhhhhhhHHHHHHHHHHHhccccccCCccceec---cch--hhhHhhh
Confidence 68888889999999973 21 124778999996 567888855322221100 000 0001345
Q ss_pred ccccchHHHHH
Q psy4518 118 ANSDLNLRLLE 128 (376)
Q Consensus 118 RvC~~C~~~l~ 128 (376)
-+|.+|.+-|.
T Consensus 253 EtC~~C~sYlK 263 (308)
T COG3058 253 ETCGDCNSYLK 263 (308)
T ss_pred hcCCcHHHHHH
Confidence 69999988774
No 36
>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=78.62 E-value=1.5 Score=32.00 Aligned_cols=35 Identities=26% Similarity=0.648 Sum_probs=21.4
Q ss_pred CCCcccc--ccccccccccc----ccccccCccccccccCC
Q psy4518 60 DVPRCPN--CSRSFNFAKRQ----HHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 60 ~v~~C~~--C~~~F~~~~Rr----HHCR~CG~vvC~~CS~~ 94 (376)
....||. |+..|.....- -.|..||..||..|...
T Consensus 17 ~~~~Cp~~~C~~~~~~~~~~~~~~~~C~~C~~~fC~~C~~~ 57 (64)
T PF01485_consen 17 NIRWCPNPDCEYIIEKDDGCNSPIVTCPSCGTEFCFKCGEP 57 (64)
T ss_dssp -CC--TTSST---ECS-SSTTS--CCTTSCCSEECSSSTSE
T ss_pred CccCCCCCCCcccEEecCCCCCCeeECCCCCCcCccccCcc
Confidence 3458977 99988754332 67999999999999753
No 37
>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=77.79 E-value=2 Score=42.44 Aligned_cols=30 Identities=23% Similarity=0.686 Sum_probs=21.3
Q ss_pred cccccccccccccc---cccccccCccccccccCC
Q psy4518 63 RCPNCSRSFNFAKR---QHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 63 ~C~~C~~~F~~~~R---rHHCR~CG~vvC~~CS~~ 94 (376)
.||+|...=.+..+ -.+ .||..||..|...
T Consensus 5 ~CP~Ck~~~y~np~~kl~i~--~CGH~~C~sCv~~ 37 (309)
T TIGR00570 5 GCPRCKTTKYRNPSLKLMVN--VCGHTLCESCVDL 37 (309)
T ss_pred CCCcCCCCCccCcccccccC--CCCCcccHHHHHH
Confidence 79999984322222 233 7999999999875
No 38
>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=77.39 E-value=1 Score=43.98 Aligned_cols=60 Identities=28% Similarity=0.411 Sum_probs=29.3
Q ss_pred Cccccccccc--cc-------ccccccccccC------ccccccccCCc--ccccccccccCCCcCCCCCCCcccccchH
Q psy4518 62 PRCPNCSRSF--NF-------AKRQHHCRLCG------CIMCHDCSFFL--PLNKARQILVEPELGESQLSASANSDLNL 124 (376)
Q Consensus 62 ~~C~~C~~~F--~~-------~~RrHHCR~CG------~vvC~~CS~~~--~l~~~~~~~~~~~~~~~~~~~vRvC~~C~ 124 (376)
..||.||..= ++ -.|..||..|| ++-|..|.+.- .+..... ... ....+=+|..|.
T Consensus 173 g~CPvCGs~P~~s~l~~~~~~G~R~L~Cs~C~t~W~~~R~~Cp~Cg~~~~~~l~~~~~---e~~----~~~rve~C~~C~ 245 (290)
T PF04216_consen 173 GYCPVCGSPPVLSVLRGGEREGKRYLHCSLCGTEWRFVRIKCPYCGNTDHEKLEYFTV---EGE----PAYRVEVCESCG 245 (290)
T ss_dssp SS-TTT---EEEEEEE------EEEEEETTT--EEE--TTS-TTT---SS-EEE---------------SEEEEEETTTT
T ss_pred CcCCCCCCcCceEEEecCCCCccEEEEcCCCCCeeeecCCCCcCCCCCCCcceeeEec---CCC----CcEEEEECCccc
Confidence 5899999842 22 14788999998 56899997632 2221100 000 124556999998
Q ss_pred HHHH
Q psy4518 125 RLLE 128 (376)
Q Consensus 125 ~~l~ 128 (376)
..+.
T Consensus 246 ~YlK 249 (290)
T PF04216_consen 246 SYLK 249 (290)
T ss_dssp EEEE
T ss_pred chHH
Confidence 8763
No 39
>PHA02768 hypothetical protein; Provisional
Probab=76.74 E-value=1 Score=33.19 Aligned_cols=25 Identities=28% Similarity=0.566 Sum_probs=17.0
Q ss_pred cccccccccccc------cccc----cccccCccc
Q psy4518 63 RCPNCSRSFNFA------KRQH----HCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~~------~RrH----HCR~CG~vv 87 (376)
.|+.|++.|+.. .|+| .|-.||++|
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 799999999732 2334 466677655
No 40
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=76.08 E-value=1.5 Score=31.54 Aligned_cols=27 Identities=30% Similarity=0.658 Sum_probs=19.3
Q ss_pred CCcccccccccc-cccccccccccCccc
Q psy4518 61 VPRCPNCSRSFN-FAKRQHHCRLCGCIM 87 (376)
Q Consensus 61 v~~C~~C~~~F~-~~~RrHHCR~CG~vv 87 (376)
...||.|+..|- .-..+++|..||...
T Consensus 20 ~~fCP~Cg~~~m~~~~~r~~C~~Cgyt~ 47 (50)
T PRK00432 20 NKFCPRCGSGFMAEHLDRWHCGKCGYTE 47 (50)
T ss_pred cCcCcCCCcchheccCCcEECCCcCCEE
Confidence 458999998643 334688888888654
No 41
>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=75.87 E-value=1.4 Score=29.32 Aligned_cols=24 Identities=38% Similarity=1.030 Sum_probs=15.0
Q ss_pred cccccccccccccc-------cccccccCcc
Q psy4518 63 RCPNCSRSFNFAKR-------QHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~~~R-------rHHCR~CG~v 86 (376)
.||.|++.|.+-.. +-.|..||..
T Consensus 4 ~CP~C~~~~~v~~~~~~~~~~~v~C~~C~~~ 34 (38)
T TIGR02098 4 QCPNCKTSFRVVDSQLGANGGKVRCGKCGHV 34 (38)
T ss_pred ECCCCCCEEEeCHHHcCCCCCEEECCCCCCE
Confidence 58999988875432 3455555544
No 42
>KOG0320|consensus
Probab=75.39 E-value=0.52 Score=42.70 Aligned_cols=49 Identities=16% Similarity=0.350 Sum_probs=33.0
Q ss_pred CCcccccccccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHHH
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLES 129 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~ 129 (376)
+-.||+|-.+|+- +-----.||.|||..|-.... ..-+.|..|...+..
T Consensus 131 ~~~CPiCl~~~se--k~~vsTkCGHvFC~~Cik~al------------------k~~~~CP~C~kkIt~ 179 (187)
T KOG0320|consen 131 TYKCPICLDSVSE--KVPVSTKCGHVFCSQCIKDAL------------------KNTNKCPTCRKKITH 179 (187)
T ss_pred ccCCCceecchhh--ccccccccchhHHHHHHHHHH------------------HhCCCCCCcccccch
Confidence 3589999988861 111335799999999965321 234788889875543
No 43
>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=74.66 E-value=2 Score=26.68 Aligned_cols=23 Identities=26% Similarity=0.752 Sum_probs=12.6
Q ss_pred cccccccccccccccccccccCccc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vv 87 (376)
.||.|++.-...- .-|.+||..|
T Consensus 2 ~CP~C~~~V~~~~--~~Cp~CG~~F 24 (26)
T PF10571_consen 2 TCPECGAEVPESA--KFCPHCGYDF 24 (26)
T ss_pred cCCCCcCCchhhc--CcCCCCCCCC
Confidence 4677766544332 2466666654
No 44
>smart00154 ZnF_AN1 AN1-like Zinc finger. Zinc finger at the C-terminus of An1, a ubiquitin-like protein in Xenopus laevis.
Probab=74.60 E-value=1.9 Score=29.35 Aligned_cols=25 Identities=28% Similarity=0.957 Sum_probs=19.0
Q ss_pred ccccccccccccccccccccCcccccc
Q psy4518 64 CPNCSRSFNFAKRQHHCRLCGCIMCHD 90 (376)
Q Consensus 64 C~~C~~~F~~~~RrHHCR~CG~vvC~~ 90 (376)
|..|++.-+++ -..|+.||.+||..
T Consensus 1 C~~C~~~~~l~--~f~C~~C~~~FC~~ 25 (39)
T smart00154 1 CHFCRKKVGLT--GFKCRHCGNLFCGE 25 (39)
T ss_pred CcccCCccccc--CeECCccCCccccc
Confidence 56788765554 67899999999964
No 45
>PF15616 TerY-C: TerY-C metal binding domain
Probab=73.37 E-value=1.6 Score=37.84 Aligned_cols=24 Identities=42% Similarity=1.216 Sum_probs=20.0
Q ss_pred CCcccccccccccccccccccccCccccc
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCGCIMCH 89 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG~vvC~ 89 (376)
.+-||.|+..|+|. -| -||+|+|.
T Consensus 77 ~PgCP~CGn~~~fa----~C-~CGkl~Ci 100 (131)
T PF15616_consen 77 APGCPHCGNQYAFA----VC-GCGKLFCI 100 (131)
T ss_pred CCCCCCCcChhcEE----Ee-cCCCEEEe
Confidence 38999999999876 36 79999994
No 46
>KOG3173|consensus
Probab=72.69 E-value=1.8 Score=39.02 Aligned_cols=28 Identities=32% Similarity=0.890 Sum_probs=23.9
Q ss_pred CCCCcccccccccccccccccccccCccccc
Q psy4518 59 KDVPRCPNCSRSFNFAKRQHHCRLCGCIMCH 89 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~ 89 (376)
.....|..|.+.-+++. .||| ||.+||.
T Consensus 103 ~~~~rC~~C~kk~gltg--f~Cr-CG~~fC~ 130 (167)
T KOG3173|consen 103 KKKKRCFKCRKKVGLTG--FKCR-CGNTFCG 130 (167)
T ss_pred ccchhhhhhhhhhcccc--cccc-cCCcccc
Confidence 34567999999999888 9997 9999995
No 47
>PF12773 DZR: Double zinc ribbon
Probab=72.32 E-value=3.2 Score=29.19 Aligned_cols=29 Identities=24% Similarity=0.621 Sum_probs=19.7
Q ss_pred CCCCCcccccccccc-cccccccccccCcc
Q psy4518 58 GKDVPRCPNCSRSFN-FAKRQHHCRLCGCI 86 (376)
Q Consensus 58 d~~v~~C~~C~~~F~-~~~RrHHCR~CG~v 86 (376)
+.++..|+.|+..+. .......|..||..
T Consensus 9 ~~~~~fC~~CG~~l~~~~~~~~~C~~Cg~~ 38 (50)
T PF12773_consen 9 PDDAKFCPHCGTPLPPPDQSKKICPNCGAE 38 (50)
T ss_pred CccccCChhhcCChhhccCCCCCCcCCcCC
Confidence 344678999998876 33445667777764
No 48
>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=71.80 E-value=1.7 Score=33.53 Aligned_cols=56 Identities=23% Similarity=0.511 Sum_probs=31.0
Q ss_pred cccccccccccccccccccccCcc-----ccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHHHH
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCI-----MCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLESR 130 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~v-----vC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~r 130 (376)
.||.|+.+..+.....||-.|+.- +|.+|-..+..-.+-. .---.|.+|..+++++
T Consensus 3 ~CP~C~~~L~~~~~~~~C~~C~~~~~~~a~CPdC~~~Le~LkACG------------AvdYFC~~c~gLiSKk 63 (70)
T PF07191_consen 3 TCPKCQQELEWQGGHYHCEACQKDYKKEAFCPDCGQPLEVLKACG------------AVDYFCNHCHGLISKK 63 (70)
T ss_dssp B-SSS-SBEEEETTEEEETTT--EEEEEEE-TTT-SB-EEEEETT------------EEEEE-TTTT-EE-TT
T ss_pred cCCCCCCccEEeCCEEECccccccceecccCCCcccHHHHHHHhc------------ccceeeccCCceeecc
Confidence 699999999999999999999975 6888866432221110 1224677887776643
No 49
>COG5151 SSL1 RNA polymerase II transcription initiation/nucleotide excision repair factor TFIIH, subunit SSL1 [Transcription / DNA replication, recombination, and repair]
Probab=71.57 E-value=2 Score=42.28 Aligned_cols=43 Identities=26% Similarity=0.649 Sum_probs=35.0
Q ss_pred CCcccCCCCCcccccccccc----------cccccccccccCccccccccCCc
Q psy4518 53 VPWLDGKDVPRCPNCSRSFN----------FAKRQHHCRLCGCIMCHDCSFFL 95 (376)
Q Consensus 53 ~~W~~d~~v~~C~~C~~~F~----------~~~RrHHCR~CG~vvC~~CS~~~ 95 (376)
++|-..-....|..|+-+|- ....|+.|-.|..-||.+|-.++
T Consensus 354 ~p~~~~~ks~~Cf~CQ~~fp~~~~~~~~~~~ss~rY~Ce~CK~~FC~dCdvfi 406 (421)
T COG5151 354 KPEGTNPKSTHCFVCQGPFPKPPVSPFDESTSSGRYQCELCKSTFCSDCDVFI 406 (421)
T ss_pred ccCCCCCCCccceeccCCCCCCCCCcccccccccceechhhhhhhhhhhHHHH
Confidence 47777777789999999773 45789999999999999996543
No 50
>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=69.59 E-value=1.6 Score=36.77 Aligned_cols=33 Identities=21% Similarity=0.304 Sum_probs=23.8
Q ss_pred CcccCCCCCcccccccccccccccccccccCcc
Q psy4518 54 PWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 54 ~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
.+..-...-.|+.|+..|.....-.+|..||..
T Consensus 63 ~I~~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (115)
T TIGR00100 63 NIEDEPVECECEDCSEEVSPEIDLYRCPKCHGI 95 (115)
T ss_pred EEEeeCcEEEcccCCCEEecCCcCccCcCCcCC
Confidence 343444456899999999887666678888763
No 51
>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=68.97 E-value=2.6 Score=29.04 Aligned_cols=25 Identities=28% Similarity=0.805 Sum_probs=13.9
Q ss_pred ccccccccccc---ccccccccccCccc
Q psy4518 63 RCPNCSRSFNF---AKRQHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~---~~RrHHCR~CG~vv 87 (376)
.||.|+...-+ .....-|..||.|+
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~CG~Vl 29 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNCGLVL 29 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT-BBE
T ss_pred CCcCCcCCceEEcCCCCeEECCCCCCEe
Confidence 59999987522 23344555555543
No 52
>KOG0317|consensus
Probab=68.87 E-value=2.1 Score=41.62 Aligned_cols=33 Identities=21% Similarity=0.580 Sum_probs=24.3
Q ss_pred CCCcccccccccccccccccccccCccccccccCCcc
Q psy4518 60 DVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLP 96 (376)
Q Consensus 60 ~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~ 96 (376)
.+..|..|-. ..+---|-.||.|||+.|-..+.
T Consensus 238 a~~kC~LCLe----~~~~pSaTpCGHiFCWsCI~~w~ 270 (293)
T KOG0317|consen 238 ATRKCSLCLE----NRSNPSATPCGHIFCWSCILEWC 270 (293)
T ss_pred CCCceEEEec----CCCCCCcCcCcchHHHHHHHHHH
Confidence 3468999964 23355689999999999976553
No 53
>PF14353 CpXC: CpXC protein
Probab=68.65 E-value=2.2 Score=36.29 Aligned_cols=25 Identities=32% Similarity=0.898 Sum_probs=17.9
Q ss_pred ccccccccccccc---------------------ccccccccCccc
Q psy4518 63 RCPNCSRSFNFAK---------------------RQHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~~~---------------------RrHHCR~CG~vv 87 (376)
.||.|+..|.+.. =.+.|..||..+
T Consensus 3 tCP~C~~~~~~~v~~~I~~~~~p~l~e~il~g~l~~~~CP~Cg~~~ 48 (128)
T PF14353_consen 3 TCPHCGHEFEFEVWTSINADEDPELKEKILDGSLFSFTCPSCGHKF 48 (128)
T ss_pred CCCCCCCeeEEEEEeEEcCcCCHHHHHHHHcCCcCEEECCCCCCce
Confidence 6999999986311 167888888765
No 54
>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=67.58 E-value=3.2 Score=31.24 Aligned_cols=28 Identities=29% Similarity=0.644 Sum_probs=22.4
Q ss_pred CCCcccccccccc--cccccccccccCccc
Q psy4518 60 DVPRCPNCSRSFN--FAKRQHHCRLCGCIM 87 (376)
Q Consensus 60 ~v~~C~~C~~~F~--~~~RrHHCR~CG~vv 87 (376)
....|+.|+..-. ...|.++|..||..+
T Consensus 27 TSq~C~~CG~~~~~~~~~r~~~C~~Cg~~~ 56 (69)
T PF07282_consen 27 TSQTCPRCGHRNKKRRSGRVFTCPNCGFEM 56 (69)
T ss_pred CccCccCcccccccccccceEEcCCCCCEE
Confidence 3458999998665 478899999999874
No 55
>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=65.94 E-value=1.8 Score=36.27 Aligned_cols=28 Identities=25% Similarity=0.643 Sum_probs=19.6
Q ss_pred CCCCcccccccccccccccccccccCcc
Q psy4518 59 KDVPRCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
...-.|..|+..|.+......|..||..
T Consensus 68 p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PF01155_consen 68 PARARCRDCGHEFEPDEFDFSCPRCGSP 95 (113)
T ss_dssp --EEEETTTS-EEECHHCCHH-SSSSSS
T ss_pred CCcEECCCCCCEEecCCCCCCCcCCcCC
Confidence 3456899999999977776788888864
No 56
>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=64.40 E-value=4.1 Score=35.92 Aligned_cols=30 Identities=27% Similarity=0.710 Sum_probs=22.9
Q ss_pred cCCCCCcccccccccccccccccccccCcccc
Q psy4518 57 DGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMC 88 (376)
Q Consensus 57 ~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC 88 (376)
.......|+.|... .-.|-|||+.||+.|=
T Consensus 44 ~~~~~~~C~~C~~~--kp~Rs~HC~~C~~CV~ 73 (174)
T PF01529_consen 44 ENGELKYCSTCKII--KPPRSHHCRVCNRCVL 73 (174)
T ss_pred cCCCCEECcccCCc--CCCcceeccccccccc
Confidence 44445689999863 5679999999998765
No 57
>PF10170 C6_DPF: Cysteine-rich domain; InterPro: IPR018785 This entry represents the N-terminal approximately 100 amino acids of a family of proteins found in a range of organisms, including human, chicken and Drosophila [, , ]. It contains between six and eight highly conserved cysteine residues and a characteristic DPF sequence motif. One member is putatively named as receptor for egg jelly protein but this could not confirmed.
Probab=64.04 E-value=3.8 Score=33.61 Aligned_cols=36 Identities=25% Similarity=0.462 Sum_probs=26.9
Q ss_pred cccccccccccCccccc--cccCCcccccccccccCCCcCCCCCCCcccccchHHHHH
Q psy4518 73 FAKRQHHCRLCGCIMCH--DCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLE 128 (376)
Q Consensus 73 ~~~RrHHCR~CG~vvC~--~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~ 128 (376)
++.=--||..||+.||. +||-+- .-|.|..|...-.
T Consensus 45 ~LvLGa~CS~C~~~VC~~~~CSlFY--------------------tkrFC~pC~~~~~ 82 (97)
T PF10170_consen 45 FLVLGAPCSICGKPVCVGQDCSLFY--------------------TKRFCLPCVKRNL 82 (97)
T ss_pred EEEECccccccCCceEcCCCccEEe--------------------eCceeHHHHHHHH
Confidence 34445799999999996 598864 3489999976543
No 58
>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=63.79 E-value=3.1 Score=29.53 Aligned_cols=23 Identities=30% Similarity=0.894 Sum_probs=15.7
Q ss_pred cccccccccccccccc-----cccccCc
Q psy4518 63 RCPNCSRSFNFAKRQH-----HCRLCGC 85 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrH-----HCR~CG~ 85 (376)
.|..|+..|.++..-+ .|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (52)
T TIGR02605 7 RCTACGHRFEVLQKMSDDPLATCPECGG 34 (52)
T ss_pred EeCCCCCEeEEEEecCCCCCCCCCCCCC
Confidence 6999999998664433 4555554
No 59
>KOG4739|consensus
Probab=63.65 E-value=13 Score=35.41 Aligned_cols=44 Identities=16% Similarity=0.355 Sum_probs=29.5
Q ss_pred cccccccccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHH
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLE 128 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~ 128 (376)
+|..|+..=+ ....+=-.|+.|||..|.... .-++|..|...+-
T Consensus 5 hCn~C~~~~~--~~~f~LTaC~HvfC~~C~k~~--------------------~~~~C~lCkk~ir 48 (233)
T KOG4739|consen 5 HCNKCFRFPS--QDPFFLTACRHVFCEPCLKAS--------------------SPDVCPLCKKSIR 48 (233)
T ss_pred EeccccccCC--CCceeeeechhhhhhhhcccC--------------------Cccccccccceee
Confidence 6888876322 334444589999999997632 1138999988753
No 60
>PF06750 DiS_P_DiS: Bacterial Peptidase A24 N-terminal domain; InterPro: IPR010627 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Aspartic endopeptidases 3.4.23. from EC of vertebrate, fungal and retroviral origin have been characterised []. More recently, aspartic endopeptidases associated with the processing of bacterial type 4 prepilin [] and archaean preflagellin have been described [, ]. Structurally, aspartic endopeptidases are bilobal enzymes, each lobe contributing a catalytic Asp residue, with an extended active site cleft localised between the two lobes of the molecule. One lobe has probably evolved from the other through a gene duplication event in the distant past. In modern-day enzymes, although the three-dimensional structures are very similar, the amino acid sequences are more divergent, except for the catalytic site motif, which is very conserved. The presence and position of disulphide bridges are other conserved features of aspartic peptidases. All or most aspartate peptidases are endopeptidases. These enzymes have been assigned into clans (proteins which are evolutionary related), and further sub-divided into families, largely on the basis of their tertiary structure. This domain is found at the N terminus of bacterial aspartic peptidases belonging to MEROPS peptidase family A24 (clan AD), subfamily A24A (type IV prepilin peptidase, IPR000045 from INTERPRO). It's function has not been specifically determined; however some of the family have been characterised as bifunctional [], and this domain may contain the N-methylation activity. The domain consists of an intracellular region between a pair of transmembrane domains. This intracellular region contains an invariant proline and four conserved cysteines. These Cys residues are arranged in a two-pair motif, with the Cys residues of a pair separated (usually) by 2 aa and with each pair separated by 21 largely hydrophilic residues (C-X-X-C...X21...C-X-X-C); they have been shown to be essential to the overall function of the enzyme [, ]. The bifunctional enzyme prepilin peptidase (PilD) from Pseudomonas aeruginosa is a key determinant in both type-IV pilus biogenesis and extracellular protein secretion, in its roles as a leader peptidase and methyl transferase (MTase). It is responsible for endopeptidic cleavage of the unique leader peptides that characterise type-IV pilin precursors, as well as proteins with homologous leader sequences that are essential components of the general secretion pathway found in a variety of Gram-negative pathogens. Following removal of the leader peptides, the same enzyme is responsible for the second posttranslational modification that characterises the type-IV pilins and their homologues, namely N-methylation of the newly exposed N-terminal amino acid residue [].
Probab=63.46 E-value=4.5 Score=32.76 Aligned_cols=25 Identities=28% Similarity=0.927 Sum_probs=18.0
Q ss_pred Ccccccccccc---------cccccccccccCcc
Q psy4518 62 PRCPNCSRSFN---------FAKRQHHCRLCGCI 86 (376)
Q Consensus 62 ~~C~~C~~~F~---------~~~RrHHCR~CG~v 86 (376)
+.|+.|+++.. ++.=|.+||.||.-
T Consensus 34 S~C~~C~~~L~~~~lIPi~S~l~lrGrCr~C~~~ 67 (92)
T PF06750_consen 34 SHCPHCGHPLSWWDLIPILSYLLLRGRCRYCGAP 67 (92)
T ss_pred CcCcCCCCcCcccccchHHHHHHhCCCCcccCCC
Confidence 47888888654 35568888888764
No 61
>KOG1814|consensus
Probab=63.34 E-value=5.3 Score=40.76 Aligned_cols=41 Identities=32% Similarity=0.893 Sum_probs=32.4
Q ss_pred CcccCCCCCccccccccccccc--ccccccccCccccccccCCc
Q psy4518 54 PWLDGKDVPRCPNCSRSFNFAK--RQHHCRLCGCIMCHDCSFFL 95 (376)
Q Consensus 54 ~W~~d~~v~~C~~C~~~F~~~~--RrHHCR~CG~vvC~~CS~~~ 95 (376)
.|+... ...||.|...-.-.- -|+||-.||..||.-|+..+
T Consensus 362 kwl~~N-~krCP~C~v~IEr~eGCnKM~C~~c~~~fc~~c~~~l 404 (445)
T KOG1814|consen 362 KWLESN-SKRCPKCKVVIERSEGCNKMHCTKCGTYFCWICAELL 404 (445)
T ss_pred HHHHhc-CCCCCcccceeecCCCccceeeccccccceeehhhhc
Confidence 587655 569999998665443 38999999999999998753
No 62
>smart00647 IBR In Between Ring fingers. the domains occurs between pairs og RING fingers
Probab=63.25 E-value=5.6 Score=28.91 Aligned_cols=34 Identities=26% Similarity=0.737 Sum_probs=26.0
Q ss_pred CCccc--cccccccc----ccccccccccCccccccccCC
Q psy4518 61 VPRCP--NCSRSFNF----AKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 61 v~~C~--~C~~~F~~----~~RrHHCR~CG~vvC~~CS~~ 94 (376)
...|| .|+..... ....-.|..||..||..|...
T Consensus 18 ~~~CP~~~C~~~~~~~~~~~~~~v~C~~C~~~fC~~C~~~ 57 (64)
T smart00647 18 LKWCPAPDCSAAIIVTEEEGCNRVTCPKCGFSFCFRCKVP 57 (64)
T ss_pred ccCCCCCCCcceEEecCCCCCCeeECCCCCCeECCCCCCc
Confidence 44788 88775543 456788999999999999764
No 63
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=62.94 E-value=3.6 Score=34.59 Aligned_cols=25 Identities=20% Similarity=0.538 Sum_probs=19.7
Q ss_pred CcccccccccccccccccccccCcc
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
-.|..|+..|.......-|..||..
T Consensus 71 ~~C~~Cg~~~~~~~~~~~CP~Cgs~ 95 (113)
T PRK12380 71 AWCWDCSQVVEIHQHDAQCPHCHGE 95 (113)
T ss_pred EEcccCCCEEecCCcCccCcCCCCC
Confidence 4899999999876655568888853
No 64
>COG1997 RPL43A Ribosomal protein L37AE/L43A [Translation, ribosomal structure and biogenesis]
Probab=61.03 E-value=5.1 Score=32.21 Aligned_cols=28 Identities=32% Similarity=0.732 Sum_probs=19.3
Q ss_pred CCcccccccccc---cccccccccccCccccc
Q psy4518 61 VPRCPNCSRSFN---FAKRQHHCRLCGCIMCH 89 (376)
Q Consensus 61 v~~C~~C~~~F~---~~~RrHHCR~CG~vvC~ 89 (376)
.+.||.|++. . +-..--.|+.||..|=.
T Consensus 35 ~~~Cp~C~~~-~VkR~a~GIW~C~kCg~~fAG 65 (89)
T COG1997 35 KHVCPFCGRT-TVKRIATGIWKCRKCGAKFAG 65 (89)
T ss_pred CCcCCCCCCc-ceeeeccCeEEcCCCCCeecc
Confidence 4589999987 3 22345678888887743
No 65
>KOG2593|consensus
Probab=60.95 E-value=3.5 Score=42.22 Aligned_cols=32 Identities=28% Similarity=0.681 Sum_probs=25.9
Q ss_pred Cccccccccccc------c---cccccccccCccccccccC
Q psy4518 62 PRCPNCSRSFNF------A---KRQHHCRLCGCIMCHDCSF 93 (376)
Q Consensus 62 ~~C~~C~~~F~~------~---~RrHHCR~CG~vvC~~CS~ 93 (376)
-.||+|+++|+- + ....||-.||.-+=..|+.
T Consensus 129 Y~Cp~C~kkyt~Lea~~L~~~~~~~F~C~~C~gelveDe~~ 169 (436)
T KOG2593|consen 129 YVCPNCQKKYTSLEALQLLDNETGEFHCENCGGELVEDENK 169 (436)
T ss_pred ccCCccccchhhhHHHHhhcccCceEEEecCCCchhccccc
Confidence 379999999972 1 3689999999988877765
No 66
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=60.69 E-value=5 Score=43.69 Aligned_cols=32 Identities=25% Similarity=0.682 Sum_probs=25.3
Q ss_pred CCCCcccccccccccccccccccccCcc------ccccccCC
Q psy4518 59 KDVPRCPNCSRSFNFAKRQHHCRLCGCI------MCHDCSFF 94 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~RrHHCR~CG~v------vC~~CS~~ 94 (376)
.....|+.||.++.. ..|..||.. ||..|-..
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 345589999998853 379999998 99999763
No 67
>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=60.28 E-value=4.1 Score=27.21 Aligned_cols=13 Identities=31% Similarity=1.030 Sum_probs=9.9
Q ss_pred ccccccccccccc
Q psy4518 63 RCPNCSRSFNFAK 75 (376)
Q Consensus 63 ~C~~C~~~F~~~~ 75 (376)
.|+.|+..|.+..
T Consensus 7 ~C~~Cg~~fe~~~ 19 (41)
T smart00834 7 RCEDCGHTFEVLQ 19 (41)
T ss_pred EcCCCCCEEEEEE
Confidence 6888998887543
No 68
>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=59.49 E-value=6.2 Score=27.54 Aligned_cols=29 Identities=28% Similarity=0.881 Sum_probs=20.6
Q ss_pred CcccCCCCCcccccccc--ccccc-ccccccccCc
Q psy4518 54 PWLDGKDVPRCPNCSRS--FNFAK-RQHHCRLCGC 85 (376)
Q Consensus 54 ~W~~d~~v~~C~~C~~~--F~~~~-RrHHCR~CG~ 85 (376)
.|-++ ..||.|+.. +.+.. .++.|+.|+.
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 68877 369999973 22333 6888988874
No 69
>COG2126 RPL37A Ribosomal protein L37E [Translation, ribosomal structure and biogenesis]
Probab=59.26 E-value=4.3 Score=30.15 Aligned_cols=17 Identities=41% Similarity=0.860 Sum_probs=10.0
Q ss_pred cccccccccc--ccccCcc
Q psy4518 70 SFNFAKRQHH--CRLCGCI 86 (376)
Q Consensus 70 ~F~~~~RrHH--CR~CG~v 86 (376)
+|+-.+++.| ||.||+.
T Consensus 7 S~GKrnk~tH~~CRRCGr~ 25 (61)
T COG2126 7 SFGKRNKKTHIRCRRCGRR 25 (61)
T ss_pred cccccCCcceehhhhccch
Confidence 4554444444 7778775
No 70
>KOG0978|consensus
Probab=58.55 E-value=1.6 Score=47.51 Aligned_cols=42 Identities=14% Similarity=0.415 Sum_probs=29.7
Q ss_pred CCcccccccccc--cccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHH
Q psy4518 61 VPRCPNCSRSFN--FAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLR 125 (376)
Q Consensus 61 v~~C~~C~~~F~--~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~ 125 (376)
.-.||.|...|- ++ -.||.+||..|..... +...|-|+.|-.
T Consensus 643 ~LkCs~Cn~R~Kd~vI------~kC~H~FC~~Cvq~r~-----------------etRqRKCP~Cn~ 686 (698)
T KOG0978|consen 643 LLKCSVCNTRWKDAVI------TKCGHVFCEECVQTRY-----------------ETRQRKCPKCNA 686 (698)
T ss_pred ceeCCCccCchhhHHH------HhcchHHHHHHHHHHH-----------------HHhcCCCCCCCC
Confidence 358999997664 22 3699999999976321 236688888854
No 71
>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=58.18 E-value=2.7 Score=28.70 Aligned_cols=32 Identities=22% Similarity=0.545 Sum_probs=23.4
Q ss_pred cccccccccccccccccccccCccccccccCCc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFL 95 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~ 95 (376)
.|++|...|.-...-.-.. ||.+||..|...+
T Consensus 2 ~C~IC~~~~~~~~~~~~l~-C~H~fh~~Ci~~~ 33 (44)
T PF13639_consen 2 ECPICLEEFEDGEKVVKLP-CGHVFHRSCIKEW 33 (44)
T ss_dssp CETTTTCBHHTTSCEEEET-TSEEEEHHHHHHH
T ss_pred CCcCCChhhcCCCeEEEcc-CCCeeCHHHHHHH
Confidence 6999999996533333444 9999999996643
No 72
>KOG1311|consensus
Probab=57.70 E-value=4.5 Score=39.42 Aligned_cols=26 Identities=23% Similarity=0.556 Sum_probs=21.4
Q ss_pred CCcccccccccccccccccccccCcccc
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCGCIMC 88 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG~vvC 88 (376)
...|..|..- .-.|-|||+.|+..|-
T Consensus 113 ~~~C~~C~~~--rPpRs~HCsvC~~CV~ 138 (299)
T KOG1311|consen 113 WKYCDTCQLY--RPPRSSHCSVCNNCVL 138 (299)
T ss_pred eEEcCcCccc--CCCCcccchhhccccc
Confidence 4689999863 5679999999998765
No 73
>COG1327 Predicted transcriptional regulator, consists of a Zn-ribbon and ATP-cone domains [Transcription]
Probab=57.47 E-value=5.4 Score=35.35 Aligned_cols=26 Identities=27% Similarity=0.699 Sum_probs=19.6
Q ss_pred cccccccccc------------cccccccccccCcccc
Q psy4518 63 RCPNCSRSFN------------FAKRQHHCRLCGCIMC 88 (376)
Q Consensus 63 ~C~~C~~~F~------------~~~RrHHCR~CG~vvC 88 (376)
.||.|+..=+ -++||.+|-.||.=|-
T Consensus 2 ~CPfC~~~~tkViDSR~~edg~aIRRRReC~~C~~RFT 39 (156)
T COG1327 2 KCPFCGHEDTKVIDSRPAEEGNAIRRRRECLECGERFT 39 (156)
T ss_pred CCCCCCCCCCeeeecccccccchhhhhhcccccccccc
Confidence 6899987543 3678889999988763
No 74
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=57.39 E-value=5.2 Score=34.72 Aligned_cols=14 Identities=29% Similarity=0.873 Sum_probs=11.2
Q ss_pred CCcccccccccccc
Q psy4518 61 VPRCPNCSRSFNFA 74 (376)
Q Consensus 61 v~~C~~C~~~F~~~ 74 (376)
.-.|+.|+..|.+.
T Consensus 70 ~~~C~~CG~~~~~~ 83 (135)
T PRK03824 70 VLKCRNCGNEWSLK 83 (135)
T ss_pred EEECCCCCCEEecc
Confidence 34799999988875
No 75
>PF09986 DUF2225: Uncharacterized protein conserved in bacteria (DUF2225); InterPro: IPR018708 This conserved bacterial family has no known function.
Probab=57.17 E-value=5.8 Score=37.06 Aligned_cols=14 Identities=0% Similarity=-0.603 Sum_probs=10.7
Q ss_pred CCcccccchHHHHH
Q psy4518 115 SASANSDLNLRLLE 128 (376)
Q Consensus 115 ~~vRvC~~C~~~l~ 128 (376)
-.|.||.+|.-.-.
T Consensus 46 Y~V~vCP~CgyA~~ 59 (214)
T PF09986_consen 46 YEVWVCPHCGYAAF 59 (214)
T ss_pred eeEEECCCCCCccc
Confidence 47899999976544
No 76
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=56.95 E-value=5.2 Score=33.82 Aligned_cols=28 Identities=25% Similarity=0.470 Sum_probs=19.8
Q ss_pred CCCCccccccccccccccc-ccccccCcc
Q psy4518 59 KDVPRCPNCSRSFNFAKRQ-HHCRLCGCI 86 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~Rr-HHCR~CG~v 86 (376)
...-.|..|+..|.+.... -+|..||..
T Consensus 69 p~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 97 (117)
T PRK00564 69 KVELECKDCSHVFKPNALDYGVCEKCHSK 97 (117)
T ss_pred CCEEEhhhCCCccccCCccCCcCcCCCCC
Confidence 3345899999999876443 358888753
No 77
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=56.19 E-value=5 Score=33.89 Aligned_cols=24 Identities=25% Similarity=0.693 Sum_probs=19.0
Q ss_pred ccccccccccccccccccccCccccc
Q psy4518 64 CPNCSRSFNFAKRQHHCRLCGCIMCH 89 (376)
Q Consensus 64 C~~C~~~F~~~~RrHHCR~CG~vvC~ 89 (376)
||.|+.++ ...+.+|..||-.+-.
T Consensus 1 CPvCg~~l--~vt~l~C~~C~t~i~G 24 (113)
T PF09862_consen 1 CPVCGGEL--VVTRLKCPSCGTEIEG 24 (113)
T ss_pred CCCCCCce--EEEEEEcCCCCCEEEe
Confidence 99999865 5567889999887754
No 78
>KOG2807|consensus
Probab=55.51 E-value=5.2 Score=39.65 Aligned_cols=41 Identities=22% Similarity=0.596 Sum_probs=29.8
Q ss_pred CcccCCCCCcccccccccccccccccccccCccccccccCCc
Q psy4518 54 PWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFL 95 (376)
Q Consensus 54 ~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~ 95 (376)
+|........|..|+.. ....-++.|..|-.+||.+|-.++
T Consensus 323 p~~~~~~~~~Cf~C~~~-~~~~~~y~C~~Ck~~FCldCDv~i 363 (378)
T KOG2807|consen 323 PETEYNGSRFCFACQGE-LLSSGRYRCESCKNVFCLDCDVFI 363 (378)
T ss_pred cccccCCCcceeeeccc-cCCCCcEEchhccceeeccchHHH
Confidence 56554445579999321 256678999999999999996654
No 79
>smart00531 TFIIE Transcription initiation factor IIE.
Probab=54.75 E-value=4.9 Score=35.20 Aligned_cols=14 Identities=36% Similarity=1.077 Sum_probs=11.2
Q ss_pred CCCccccccccccc
Q psy4518 60 DVPRCPNCSRSFNF 73 (376)
Q Consensus 60 ~v~~C~~C~~~F~~ 73 (376)
..-.||.|+..|++
T Consensus 98 ~~Y~Cp~C~~~y~~ 111 (147)
T smart00531 98 AYYKCPNCQSKYTF 111 (147)
T ss_pred cEEECcCCCCEeeH
Confidence 34579999999985
No 80
>PF07776 zf-AD: Zinc-finger associated domain (zf-AD) ; InterPro: IPR012934 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 zf-AD domain, also known as ZAD, forms an atypical treble-cleft-like zinc co-ordinating fold. The zf-AD domain is thought to be involved in mediating dimer formation, but does not bind to DNA []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005634 nucleus; PDB: 1PZW_A.
Probab=54.15 E-value=22 Score=26.02 Aligned_cols=21 Identities=5% Similarity=-0.181 Sum_probs=15.0
Q ss_pred CCCcccccchHHHHHHHHHHh
Q psy4518 114 LSASANSDLNLRLLESREVLK 134 (376)
Q Consensus 114 ~~~vRvC~~C~~~l~~r~~~~ 134 (376)
..|..+|..|+..|.....+.
T Consensus 42 ~lp~~IC~~C~~~l~~~~~F~ 62 (75)
T PF07776_consen 42 DLPQQICSSCWEKLQQFYRFR 62 (75)
T ss_dssp SS-SEEEHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHHHH
Confidence 356689999999997654443
No 81
>PTZ00255 60S ribosomal protein L37a; Provisional
Probab=54.05 E-value=6.7 Score=31.78 Aligned_cols=31 Identities=19% Similarity=0.393 Sum_probs=20.5
Q ss_pred CCcccccccc-cc-cccccccccccCccccccc
Q psy4518 61 VPRCPNCSRS-FN-FAKRQHHCRLCGCIMCHDC 91 (376)
Q Consensus 61 v~~C~~C~~~-F~-~~~RrHHCR~CG~vvC~~C 91 (376)
...||+|++. +- ....--+|+.||..|-...
T Consensus 36 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PTZ00255 36 KYFCPFCGKHAVKRQAVGIWRCKGCKKTVAGGA 68 (90)
T ss_pred CccCCCCCCCceeeeeeEEEEcCCCCCEEeCCc
Confidence 3489999852 21 2334578999999885543
No 82
>PF13445 zf-RING_UBOX: RING-type zinc-finger; PDB: 2CT2_A.
Probab=54.00 E-value=4 Score=28.39 Aligned_cols=31 Identities=32% Similarity=0.798 Sum_probs=15.7
Q ss_pred ccccccccccccccccccccCccccccccCCc
Q psy4518 64 CPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFL 95 (376)
Q Consensus 64 C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~ 95 (376)
||+|.. |+-.....-=-.||.+||.+|...+
T Consensus 1 CpIc~e-~~~~~n~P~~L~CGH~~c~~cl~~l 31 (43)
T PF13445_consen 1 CPICKE-FSTEENPPMVLPCGHVFCKDCLQKL 31 (43)
T ss_dssp -TTT-----TTSS-EEE-SSS-EEEHHHHHHH
T ss_pred CCcccc-ccCCCCCCEEEeCccHHHHHHHHHH
Confidence 788888 8654444444569999999886643
No 83
>COG5574 PEX10 RING-finger-containing E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=53.61 E-value=4.3 Score=39.04 Aligned_cols=37 Identities=24% Similarity=0.652 Sum_probs=24.9
Q ss_pred CCCcccCCCCCcccccccccccccccccccccCccccccccC
Q psy4518 52 IVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSF 93 (376)
Q Consensus 52 ~~~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~ 93 (376)
..+..+-++. .|++|...- -.--|..||.|||..|-.
T Consensus 207 ~~pfip~~d~-kC~lC~e~~----~~ps~t~CgHlFC~~Cl~ 243 (271)
T COG5574 207 GLPFIPLADY-KCFLCLEEP----EVPSCTPCGHLFCLSCLL 243 (271)
T ss_pred cCCccccccc-ceeeeeccc----CCcccccccchhhHHHHH
Confidence 3344552222 799997633 234689999999999954
No 84
>PRK03681 hypA hydrogenase nickel incorporation protein; Validated
Probab=52.89 E-value=6.6 Score=33.03 Aligned_cols=25 Identities=16% Similarity=0.496 Sum_probs=18.5
Q ss_pred Cccccccccccccccc-ccccccCcc
Q psy4518 62 PRCPNCSRSFNFAKRQ-HHCRLCGCI 86 (376)
Q Consensus 62 ~~C~~C~~~F~~~~Rr-HHCR~CG~v 86 (376)
-.|..|+..|...... -.|..||..
T Consensus 71 ~~C~~Cg~~~~~~~~~~~~CP~Cgs~ 96 (114)
T PRK03681 71 CWCETCQQYVTLLTQRVRRCPQCHGD 96 (114)
T ss_pred EEcccCCCeeecCCccCCcCcCcCCC
Confidence 4899999998865443 558888864
No 85
>PF10955 DUF2757: Protein of unknown function (DUF2757); InterPro: IPR020115 This entry contains proteins with no known function.
Probab=52.73 E-value=5.7 Score=31.17 Aligned_cols=16 Identities=13% Similarity=-0.180 Sum_probs=12.1
Q ss_pred CCCcc-cccchHHHHHH
Q psy4518 114 LSASA-NSDLNLRLLES 129 (376)
Q Consensus 114 ~~~vR-vC~~C~~~l~~ 129 (376)
+..|+ +|.+|...|..
T Consensus 48 ~i~V~~iCe~C~eaL~~ 64 (76)
T PF10955_consen 48 DIHVKVICEDCQEALER 64 (76)
T ss_pred CEEEEEecHHHHHHHHh
Confidence 34555 89999999864
No 86
>PLN03208 E3 ubiquitin-protein ligase RMA2; Provisional
Probab=52.31 E-value=7.1 Score=36.04 Aligned_cols=68 Identities=12% Similarity=0.151 Sum_probs=37.4
Q ss_pred cccCCCCCcccccccccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHH
Q psy4518 55 WLDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLE 128 (376)
Q Consensus 55 W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~ 128 (376)
-.+......|++|...|.- -.--.||.+||..|-..+......... .............|..|...+.
T Consensus 12 ~~~~~~~~~CpICld~~~d----PVvT~CGH~FC~~CI~~wl~~s~~s~~--~~~~~~~~k~~~~CPvCR~~Is 79 (193)
T PLN03208 12 LVDSGGDFDCNICLDQVRD----PVVTLCGHLFCWPCIHKWTYASNNSRQ--RVDQYDHKREPPKCPVCKSDVS 79 (193)
T ss_pred eccCCCccCCccCCCcCCC----cEEcCCCchhHHHHHHHHHHhcccccc--ccccccccCCCCcCCCCCCcCC
Confidence 3444455689999987752 223579999999997643211000000 0000001234568999987764
No 87
>TIGR00280 L37a ribosomal protein L37a. This model finds eukaryotic ribosomal protein L37a and its archaeal orthologs. The nomeclature is tricky because eukaryotes have proteins called both L37 and L37a.
Probab=52.03 E-value=6.3 Score=31.98 Aligned_cols=31 Identities=23% Similarity=0.524 Sum_probs=20.6
Q ss_pred CCcccccccc-cc-cccccccccccCccccccc
Q psy4518 61 VPRCPNCSRS-FN-FAKRQHHCRLCGCIMCHDC 91 (376)
Q Consensus 61 v~~C~~C~~~-F~-~~~RrHHCR~CG~vvC~~C 91 (376)
...||+|++. +. ....--+|+.||..|-...
T Consensus 35 ~y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGA 67 (91)
T TIGR00280 35 KYVCPFCGKKTVKRGSTGIWTCRKCGAKFAGGA 67 (91)
T ss_pred CccCCCCCCCceEEEeeEEEEcCCCCCEEeCCc
Confidence 3489999852 22 3344578999999885543
No 88
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=51.68 E-value=6.8 Score=35.65 Aligned_cols=26 Identities=35% Similarity=0.825 Sum_probs=17.0
Q ss_pred CCcccccccccccc---cccccccccCcc
Q psy4518 61 VPRCPNCSRSFNFA---KRQHHCRLCGCI 86 (376)
Q Consensus 61 v~~C~~C~~~F~~~---~RrHHCR~CG~v 86 (376)
-=.||.|+..|++. .--.+|..||..
T Consensus 117 ~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 117 FFFCPNCHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred EEECCCCCcEEeHHHHhhcCCcCCCCCCC
Confidence 34699999988753 344566666654
No 89
>PRK03976 rpl37ae 50S ribosomal protein L37Ae; Reviewed
Probab=51.65 E-value=6.4 Score=31.90 Aligned_cols=30 Identities=27% Similarity=0.678 Sum_probs=20.3
Q ss_pred Ccccccccc-cc-cccccccccccCccccccc
Q psy4518 62 PRCPNCSRS-FN-FAKRQHHCRLCGCIMCHDC 91 (376)
Q Consensus 62 ~~C~~C~~~-F~-~~~RrHHCR~CG~vvC~~C 91 (376)
..||+|++. |. ....--+|+.||..|-...
T Consensus 37 y~CpfCgk~~vkR~a~GIW~C~~C~~~~AGGA 68 (90)
T PRK03976 37 HVCPVCGRPKVKRVGTGIWECRKCGAKFAGGA 68 (90)
T ss_pred ccCCCCCCCceEEEEEEEEEcCCCCCEEeCCc
Confidence 479999752 22 3344579999999885543
No 90
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=51.58 E-value=11 Score=41.09 Aligned_cols=47 Identities=21% Similarity=0.463 Sum_probs=32.0
Q ss_pred cccccccccccccccccccccCcc----ccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHHH
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCI----MCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLES 129 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~v----vC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~ 129 (376)
.||.|+..- -..-.-|..||.. +|..|...++ ...+.|..|-..+..
T Consensus 3 ~Cp~Cg~~n--~~~akFC~~CG~~l~~~~Cp~CG~~~~------------------~~~~fC~~CG~~~~~ 53 (645)
T PRK14559 3 ICPQCQFEN--PNNNRFCQKCGTSLTHKPCPQCGTEVP------------------VDEAHCPNCGAETGT 53 (645)
T ss_pred cCCCCCCcC--CCCCccccccCCCCCCCcCCCCCCCCC------------------cccccccccCCcccc
Confidence 699998753 3344469999987 5888866543 355788888665543
No 91
>TIGR00244 transcriptional regulator NrdR. Members of this almost entirely bacterial family contain an ATP cone domain (PFAM:PF03477). There is never more than one member per genome. Common gene symbols given include nrdR, ybaD, ribX and ytcG. The member from Streptomyces coelicolor is found upstream in the operon of the class II oxygen-independent ribonucleotide reductase gene nrdJ and was shown to repress nrdJ expression. Many members of this family are found near genes for riboflavin biosynthesis in Gram-negative bacteria, suggesting a role in that pathway. However, a phylogenetic profiling study associates members of this family with the presence of a palindromic signal with consensus acaCwAtATaTwGtgt, termed the NrdR-box, an upstream element for most operons for ribonucleotide reductase of all three classes in bacterial genomes.
Probab=51.13 E-value=8.6 Score=33.95 Aligned_cols=26 Identities=23% Similarity=0.574 Sum_probs=20.1
Q ss_pred cccccccccc------------cccccccccccCcccc
Q psy4518 63 RCPNCSRSFN------------FAKRQHHCRLCGCIMC 88 (376)
Q Consensus 63 ~C~~C~~~F~------------~~~RrHHCR~CG~vvC 88 (376)
.||.|+..=+ .++||..|-.||.=|-
T Consensus 2 ~CP~C~~~dtkViDSR~~~dg~~IRRRReC~~C~~RFT 39 (147)
T TIGR00244 2 HCPFCQHHNTRVLDSRLVEDGQSIRRRRECLECHERFT 39 (147)
T ss_pred CCCCCCCCCCEeeeccccCCCCeeeecccCCccCCccc
Confidence 6999987332 4678999999998773
No 92
>KOG1314|consensus
Probab=51.09 E-value=5.8 Score=39.77 Aligned_cols=33 Identities=30% Similarity=0.737 Sum_probs=23.5
Q ss_pred CCcccCCCC-----CcccccccccccccccccccccCccc
Q psy4518 53 VPWLDGKDV-----PRCPNCSRSFNFAKRQHHCRLCGCIM 87 (376)
Q Consensus 53 ~~W~~d~~v-----~~C~~C~~~F~~~~RrHHCR~CG~vv 87 (376)
..|.|.... ..|.-|+. | -.-|-||||.|.+.|
T Consensus 78 ~~wkPe~~~D~~~lqfCk~Cqg-Y-KapRSHHCrkCnrCv 115 (414)
T KOG1314|consen 78 LGWKPENPKDEMFLQFCKKCQG-Y-KAPRSHHCRKCNRCV 115 (414)
T ss_pred CCCCCCCChhHHHHHHHhhccC-c-CCCccccchHHHHHH
Confidence 468884433 47888874 1 357999999999875
No 93
>TIGR00373 conserved hypothetical protein TIGR00373. This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain.
Probab=50.98 E-value=6.6 Score=34.94 Aligned_cols=25 Identities=32% Similarity=0.750 Sum_probs=18.9
Q ss_pred Cccccccccccc---ccccccccccCcc
Q psy4518 62 PRCPNCSRSFNF---AKRQHHCRLCGCI 86 (376)
Q Consensus 62 ~~C~~C~~~F~~---~~RrHHCR~CG~v 86 (376)
=.||.|+..|++ +.--.+|..||..
T Consensus 110 Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 110 FICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred EECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 469999999985 3446778888776
No 94
>PF08274 PhnA_Zn_Ribbon: PhnA Zinc-Ribbon ; InterPro: IPR013987 The PhnA protein family includes the uncharacterised Escherichia coli protein PhnA and its homologues. The E. coli phnA gene is part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage []. The protein is not related to the characterised phosphonoacetate hydrolase designated PhnA []. This entry represents the N-terminal domain of PhnA, which is predicted to form a zinc-ribbon.; PDB: 2AKL_A.
Probab=50.67 E-value=5.9 Score=25.49 Aligned_cols=12 Identities=33% Similarity=1.359 Sum_probs=3.4
Q ss_pred Cccccccccccc
Q psy4518 62 PRCPNCSRSFNF 73 (376)
Q Consensus 62 ~~C~~C~~~F~~ 73 (376)
+.|+.|+..+++
T Consensus 3 p~Cp~C~se~~y 14 (30)
T PF08274_consen 3 PKCPLCGSEYTY 14 (30)
T ss_dssp ---TTT-----E
T ss_pred CCCCCCCCccee
Confidence 578888888876
No 95
>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=50.29 E-value=14 Score=27.64 Aligned_cols=17 Identities=6% Similarity=-0.115 Sum_probs=12.1
Q ss_pred Ccccc-cchHHHHHHHHH
Q psy4518 116 ASANS-DLNLRLLESREV 132 (376)
Q Consensus 116 ~vRvC-~~C~~~l~~r~~ 132 (376)
+.+.| ..|......++.
T Consensus 16 ~~~fCS~~C~~~~~k~qk 33 (59)
T PF09889_consen 16 DESFCSPKCREEYRKRQK 33 (59)
T ss_pred chhhhCHHHHHHHHHHHH
Confidence 45788 589988866544
No 96
>PRK04023 DNA polymerase II large subunit; Validated
Probab=50.13 E-value=12 Score=42.48 Aligned_cols=30 Identities=27% Similarity=0.867 Sum_probs=22.5
Q ss_pred CCCcccccccccccccccccccccCcc-----ccccccC
Q psy4518 60 DVPRCPNCSRSFNFAKRQHHCRLCGCI-----MCHDCSF 93 (376)
Q Consensus 60 ~v~~C~~C~~~F~~~~RrHHCR~CG~v-----vC~~CS~ 93 (376)
....|+.|+... =...|..||.. +|..|-.
T Consensus 625 g~RfCpsCG~~t----~~frCP~CG~~Te~i~fCP~CG~ 659 (1121)
T PRK04023 625 GRRKCPSCGKET----FYRRCPFCGTHTEPVYRCPRCGI 659 (1121)
T ss_pred cCccCCCCCCcC----CcccCCCCCCCCCcceeCccccC
Confidence 345899999974 23689999964 8888843
No 97
>PRK12496 hypothetical protein; Provisional
Probab=50.05 E-value=9 Score=34.33 Aligned_cols=23 Identities=22% Similarity=0.767 Sum_probs=13.2
Q ss_pred cccccccccccccccccccccCc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGC 85 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~ 85 (376)
.|++|++.|..-.-.--|..||.
T Consensus 129 ~C~gC~~~~~~~~~~~~C~~CG~ 151 (164)
T PRK12496 129 VCKGCKKKYPEDYPDDVCEICGS 151 (164)
T ss_pred ECCCCCccccCCCCCCcCCCCCC
Confidence 57777776654333345666664
No 98
>COG5222 Uncharacterized conserved protein, contains RING Zn-finger [General function prediction only]
Probab=49.61 E-value=11 Score=37.08 Aligned_cols=82 Identities=20% Similarity=0.249 Sum_probs=47.4
Q ss_pred CcccccccccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHHHHHHHhhhcCCCc
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLESREVLKESRNSRP 141 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~r~~~~~~~~~~p 141 (376)
-.|+.|+. +++--..-..||..||..|....-++ .--+|..|.. ++...+ ...|
T Consensus 275 LkCplc~~---Llrnp~kT~cC~~~fc~eci~~al~d-----------------sDf~CpnC~r-----kdvlld-~l~p 328 (427)
T COG5222 275 LKCPLCHC---LLRNPMKTPCCGHTFCDECIGTALLD-----------------SDFKCPNCSR-----KDVLLD-GLTP 328 (427)
T ss_pred ccCcchhh---hhhCcccCccccchHHHHHHhhhhhh-----------------ccccCCCccc-----ccchhh-ccCc
Confidence 58999986 33222222579999999997643222 3368999964 111111 2345
Q ss_pred hhHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCCcc
Q psy4518 142 LICDLYDALMGKKQEASKLRAMYLEMIDSLLAGETM 177 (376)
Q Consensus 142 ~i~~~Ye~L~~~~~~I~~~lP~f~~~l~sL~~g~s~ 177 (376)
.+. .+.+|+..|-+-.+.+.+-.+++++
T Consensus 329 D~d--------k~~EvE~~lkkq~~~~gts~d~n~p 356 (427)
T COG5222 329 DID--------KKLEVEKALKKQRKKVGTSDDNNTP 356 (427)
T ss_pred cHH--------HHHHHHHHHHHHHHhcCCCCCCCCc
Confidence 532 2345566666666667666677665
No 99
>PRK11595 DNA utilization protein GntX; Provisional
Probab=49.54 E-value=5.2 Score=37.50 Aligned_cols=21 Identities=33% Similarity=0.812 Sum_probs=13.1
Q ss_pred cccccccccccccccccccccCc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGC 85 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~ 85 (376)
.|..|...|.++ .++|..||.
T Consensus 22 lC~~C~~~l~~~--~~~C~~Cg~ 42 (227)
T PRK11595 22 ICSVCSRALRTL--KTCCPQCGL 42 (227)
T ss_pred ccHHHHhhCCcc--cCcCccCCC
Confidence 566666666553 366777765
No 100
>PF14803 Nudix_N_2: Nudix N-terminal; PDB: 3CNG_C.
Probab=49.52 E-value=6.5 Score=26.01 Aligned_cols=24 Identities=29% Similarity=0.815 Sum_probs=10.7
Q ss_pred ccccccccccc------ccccccccccCcc
Q psy4518 63 RCPNCSRSFNF------AKRQHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~------~~RrHHCR~CG~v 86 (376)
.|+.|+.+..+ -+-|+-|..||.|
T Consensus 2 fC~~CG~~l~~~ip~gd~r~R~vC~~Cg~I 31 (34)
T PF14803_consen 2 FCPQCGGPLERRIPEGDDRERLVCPACGFI 31 (34)
T ss_dssp B-TTT--B-EEE--TT-SS-EEEETTTTEE
T ss_pred ccccccChhhhhcCCCCCccceECCCCCCE
Confidence 57777765442 1336666666655
No 101
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=49.44 E-value=24 Score=26.27 Aligned_cols=25 Identities=28% Similarity=0.446 Sum_probs=20.2
Q ss_pred hhHHHHHHhHHHHHHHHHHHHhhhh
Q psy4518 343 NEVASLENHLKELQEEYFRRQQEQQ 367 (376)
Q Consensus 343 dEV~~L~~NL~EL~~ei~~~~~~~~ 367 (376)
|||..|..-+.||...+.+++.+++
T Consensus 14 EEVevLK~~I~eL~~~n~~Le~EN~ 38 (59)
T PF01166_consen 14 EEVEVLKEQIAELEERNSQLEEENN 38 (59)
T ss_dssp TSHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6888888888888888888887774
No 102
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.25 E-value=9.9 Score=36.62 Aligned_cols=27 Identities=26% Similarity=0.689 Sum_probs=19.8
Q ss_pred CCCCcccccccccccccccccccccCcccc
Q psy4518 59 KDVPRCPNCSRSFNFAKRQHHCRLCGCIMC 88 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC 88 (376)
.....|+.||. +..|.+.|..||.++-
T Consensus 307 ~tS~~C~~cg~---~~~r~~~C~~cg~~~~ 333 (364)
T COG0675 307 YTSKTCPCCGH---LSGRLFKCPRCGFVHD 333 (364)
T ss_pred CCcccccccCC---ccceeEECCCCCCeeh
Confidence 33468999998 4567788888887654
No 103
>KOG3576|consensus
Probab=48.98 E-value=4.2 Score=37.87 Aligned_cols=64 Identities=20% Similarity=0.317 Sum_probs=38.5
Q ss_pred Ccccccccccc--cc----------cccccccccCccccccccCCcccccccccccCCCcCCC-CCCCcccccchHHHH
Q psy4518 62 PRCPNCSRSFN--FA----------KRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGES-QLSASANSDLNLRLL 127 (376)
Q Consensus 62 ~~C~~C~~~F~--~~----------~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~-~~~~vRvC~~C~~~l 127 (376)
..|..|++.|+ |- .|-+.|.+|+..|-..||-..-+....... ...... ....+-||.+|--+-
T Consensus 146 ~lct~cgkgfndtfdlkrh~rthtgvrpykc~~c~kaftqrcsleshl~kvhgv~--~~yaykerr~kl~vcedcg~t~ 222 (267)
T KOG3576|consen 146 HLCTFCGKGFNDTFDLKRHTRTHTGVRPYKCSLCEKAFTQRCSLESHLKKVHGVQ--HQYAYKERRAKLYVCEDCGYTS 222 (267)
T ss_pred HHHhhccCcccchhhhhhhhccccCccccchhhhhHHHHhhccHHHHHHHHcCch--HHHHHHHhhhheeeecccCCCC
Confidence 47999999998 32 345679999999999998742222111000 000000 124678999996543
No 104
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=48.42 E-value=12 Score=41.39 Aligned_cols=36 Identities=31% Similarity=0.806 Sum_probs=23.7
Q ss_pred CCCCccccccccccc--ccccccccccCcc-----ccccccCC
Q psy4518 59 KDVPRCPNCSRSFNF--AKRQHHCRLCGCI-----MCHDCSFF 94 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~--~~RrHHCR~CG~v-----vC~~CS~~ 94 (376)
..+..||.|...+++ ..+.--|..||.- .|..|.+.
T Consensus 442 g~v~~Cp~Cd~~lt~H~~~~~L~CH~Cg~~~~~p~~Cp~Cgs~ 484 (730)
T COG1198 442 GYIAECPNCDSPLTLHKATGQLRCHYCGYQEPIPQSCPECGSE 484 (730)
T ss_pred CCcccCCCCCcceEEecCCCeeEeCCCCCCCCCCCCCCCCCCC
Confidence 345578888887764 4455567777765 66667553
No 105
>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=47.59 E-value=8.2 Score=26.48 Aligned_cols=23 Identities=30% Similarity=0.871 Sum_probs=12.6
Q ss_pred cccccccccccccc-----cccccccCc
Q psy4518 63 RCPNCSRSFNFAKR-----QHHCRLCGC 85 (376)
Q Consensus 63 ~C~~C~~~F~~~~R-----rHHCR~CG~ 85 (376)
.|..|+..|..+.. ..+|..||.
T Consensus 7 ~C~~Cg~~fe~~~~~~~~~~~~CP~Cg~ 34 (42)
T PF09723_consen 7 RCEECGHEFEVLQSISEDDPVPCPECGS 34 (42)
T ss_pred EeCCCCCEEEEEEEcCCCCCCcCCCCCC
Confidence 47777777764432 334555544
No 106
>smart00659 RPOLCX RNA polymerase subunit CX. present in RNA polymerase I, II and III
Probab=47.29 E-value=11 Score=26.40 Aligned_cols=12 Identities=25% Similarity=0.656 Sum_probs=9.9
Q ss_pred cccccccccccc
Q psy4518 63 RCPNCSRSFNFA 74 (376)
Q Consensus 63 ~C~~C~~~F~~~ 74 (376)
.|..|+..|.+.
T Consensus 4 ~C~~Cg~~~~~~ 15 (44)
T smart00659 4 ICGECGRENEIK 15 (44)
T ss_pred ECCCCCCEeecC
Confidence 588999998865
No 107
>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=47.20 E-value=12 Score=32.62 Aligned_cols=18 Identities=22% Similarity=0.503 Sum_probs=12.2
Q ss_pred CcccCCCCCccccccccc
Q psy4518 54 PWLDGKDVPRCPNCSRSF 71 (376)
Q Consensus 54 ~W~~d~~v~~C~~C~~~F 71 (376)
.+..+..-+.|+.|+..+
T Consensus 84 ~~~~~~~~sRC~~CN~~L 101 (147)
T PF01927_consen 84 KLRLDPIFSRCPKCNGPL 101 (147)
T ss_pred ccccCCCCCccCCCCcEe
Confidence 444555566899998755
No 108
>PF01780 Ribosomal_L37ae: Ribosomal L37ae protein family; InterPro: IPR002674 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This ribosomal protein is found in archaebacteria and eukaryotes []. Ribosomal protein L37 has a single zinc finger-like motif of the C2-C2 type [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 4A1E_Y 4A17_Y 4A1C_Y 4A1A_Y 3O58_g 3IZS_m 3O5H_g 1S1I_9 3IZR_m 1YSH_D ....
Probab=46.78 E-value=7.1 Score=31.63 Aligned_cols=29 Identities=24% Similarity=0.603 Sum_probs=18.5
Q ss_pred Cccccccccc-c-cccccccccccCcccccc
Q psy4518 62 PRCPNCSRSF-N-FAKRQHHCRLCGCIMCHD 90 (376)
Q Consensus 62 ~~C~~C~~~F-~-~~~RrHHCR~CG~vvC~~ 90 (376)
..||+|++.= . ....--+|+.||..|-..
T Consensus 36 y~Cp~Cgk~~vkR~a~GIW~C~~C~~~~AGG 66 (90)
T PF01780_consen 36 YTCPFCGKTSVKRVATGIWKCKKCGKKFAGG 66 (90)
T ss_dssp BEESSSSSSEEEEEETTEEEETTTTEEEE-B
T ss_pred CcCCCCCCceeEEeeeEEeecCCCCCEEeCC
Confidence 3799999842 1 223346888888887543
No 109
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=46.63 E-value=12 Score=26.23 Aligned_cols=24 Identities=33% Similarity=0.789 Sum_probs=14.2
Q ss_pred cccccccccccc---c-ccccccccCcc
Q psy4518 63 RCPNCSRSFNFA---K-RQHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~~---~-RrHHCR~CG~v 86 (376)
.||.|+.-.-.- . .++.|+.||.+
T Consensus 2 FCp~Cg~~l~~~~~~~~~~~vC~~Cg~~ 29 (52)
T smart00661 2 FCPKCGNMLIPKEGKEKRRFVCRKCGYE 29 (52)
T ss_pred CCCCCCCccccccCCCCCEEECCcCCCe
Confidence 689998743211 1 25667777754
No 110
>PF11023 DUF2614: Protein of unknown function (DUF2614); InterPro: IPR020912 This entry describes proteins of unknown function, which are thought to be membrane proteins.; GO: 0005887 integral to plasma membrane
Probab=46.54 E-value=8.7 Score=32.34 Aligned_cols=25 Identities=28% Similarity=0.724 Sum_probs=21.1
Q ss_pred cccccccccccccccccccccCccc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vv 87 (376)
.||.|++..-.+.|-.-|-+||...
T Consensus 71 ~CP~C~K~TKmLGr~D~CM~C~~pL 95 (114)
T PF11023_consen 71 ECPNCGKQTKMLGRVDACMHCKEPL 95 (114)
T ss_pred ECCCCCChHhhhchhhccCcCCCcC
Confidence 6999999988888888888887653
No 111
>PRK05978 hypothetical protein; Provisional
Probab=46.51 E-value=10 Score=33.50 Aligned_cols=26 Identities=42% Similarity=0.961 Sum_probs=20.6
Q ss_pred Cccccccc--ccc-cccccccccccCccc
Q psy4518 62 PRCPNCSR--SFN-FAKRQHHCRLCGCIM 87 (376)
Q Consensus 62 ~~C~~C~~--~F~-~~~RrHHCR~CG~vv 87 (376)
-.||.|++ -|. ++.=+.+|..||.-+
T Consensus 34 grCP~CG~G~LF~g~Lkv~~~C~~CG~~~ 62 (148)
T PRK05978 34 GRCPACGEGKLFRAFLKPVDHCAACGEDF 62 (148)
T ss_pred CcCCCCCCCcccccccccCCCccccCCcc
Confidence 58999998 454 667788999999865
No 112
>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=46.50 E-value=13 Score=24.29 Aligned_cols=23 Identities=22% Similarity=0.644 Sum_probs=13.1
Q ss_pred ccccccccccccc-ccccccccCc
Q psy4518 63 RCPNCSRSFNFAK-RQHHCRLCGC 85 (376)
Q Consensus 63 ~C~~C~~~F~~~~-RrHHCR~CG~ 85 (376)
.|..|+..|.+.. -.-.|+.||.
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 3777888777432 2456666664
No 113
>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=46.41 E-value=9.6 Score=25.27 Aligned_cols=19 Identities=21% Similarity=0.761 Sum_probs=8.0
Q ss_pred Ccccccccccc--cccccccc
Q psy4518 62 PRCPNCSRSFN--FAKRQHHC 80 (376)
Q Consensus 62 ~~C~~C~~~F~--~~~RrHHC 80 (376)
+.|..|++.|. ++.....+
T Consensus 4 ~~C~eC~~~f~dSyL~~~F~~ 24 (34)
T PF01286_consen 4 PKCDECGKPFMDSYLLNNFDL 24 (34)
T ss_dssp EE-TTT--EES-SSCCCCTS-
T ss_pred chHhHhCCHHHHHHHHHhCCc
Confidence 46777777774 44443333
No 114
>PF09332 Mcm10: Mcm10 replication factor; InterPro: IPR015411 Mcm10 is a eukaryotic DNA replication factor that regulates the stability and chromatin association of DNA polymerase alpha []. ; PDB: 2KWQ_A.
Probab=46.36 E-value=8.3 Score=38.73 Aligned_cols=37 Identities=27% Similarity=0.640 Sum_probs=13.6
Q ss_pred ccCCCcccC-CCCCcccccccccccccc--cccccccCcc
Q psy4518 50 QAIVPWLDG-KDVPRCPNCSRSFNFAKR--QHHCRLCGCI 86 (376)
Q Consensus 50 q~~~~W~~d-~~v~~C~~C~~~F~~~~R--rHHCR~CG~v 86 (376)
+..+.|++. ..--.|+.|+.....+.| .+||..||..
T Consensus 273 ~H~l~~~~a~KRFFkC~~C~~Rt~sl~r~P~~~C~~Cg~~ 312 (344)
T PF09332_consen 273 GHPLKWHDAVKRFFKCKDCGNRTISLERLPKKHCSNCGSS 312 (344)
T ss_dssp T--EEEEEEE-EEEE-T-TS-EEEESSSS--S--TTT-S-
T ss_pred CCceEEeeeeeeeEECCCCCCeeeecccCCCCCCCcCCcC
Confidence 334445432 222457777775543333 5777777754
No 115
>TIGR00599 rad18 DNA repair protein rad18. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=46.21 E-value=4.1 Score=41.73 Aligned_cols=29 Identities=24% Similarity=0.496 Sum_probs=22.0
Q ss_pred CcccccccccccccccccccccCccccccccCC
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
..|++|...|.- .---.||..||..|-..
T Consensus 27 l~C~IC~d~~~~----PvitpCgH~FCs~CI~~ 55 (397)
T TIGR00599 27 LRCHICKDFFDV----PVLTSCSHTFCSLCIRR 55 (397)
T ss_pred cCCCcCchhhhC----ccCCCCCCchhHHHHHH
Confidence 489999987752 22358999999999653
No 116
>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=46.10 E-value=13 Score=29.95 Aligned_cols=30 Identities=17% Similarity=0.472 Sum_probs=21.7
Q ss_pred CcccccccccccccccccccccCccccccccC
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSF 93 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~ 93 (376)
..|+.|+++|+- ....--.||.+|...|..
T Consensus 79 ~~C~vC~k~l~~--~~f~~~p~~~v~H~~C~~ 108 (109)
T PF10367_consen 79 TKCSVCGKPLGN--SVFVVFPCGHVVHYSCIK 108 (109)
T ss_pred CCccCcCCcCCC--ceEEEeCCCeEEeccccc
Confidence 369999999873 334445778888888853
No 117
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=45.92 E-value=14 Score=42.86 Aligned_cols=49 Identities=24% Similarity=0.632 Sum_probs=32.3
Q ss_pred CcccccccccccccccccccccCcc-----ccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHHH
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCI-----MCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLES 129 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~v-----vC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~ 129 (376)
..||.|+.. ++ ..-|..||.. +|..|-..++.+.. . -..|..|-.-+..
T Consensus 668 rkCPkCG~~-t~---~~fCP~CGs~te~vy~CPsCGaev~~des--------------~-a~~CP~CGtplv~ 721 (1337)
T PRK14714 668 RRCPSCGTE-TY---ENRCPDCGTHTEPVYVCPDCGAEVPPDES--------------G-RVECPRCDVELTP 721 (1337)
T ss_pred EECCCCCCc-cc---cccCcccCCcCCCceeCccCCCccCCCcc--------------c-cccCCCCCCcccc
Confidence 589999984 22 1389999976 49999765442211 1 3579999766543
No 118
>TIGR01384 TFS_arch transcription factor S, archaeal. There has been an apparent duplication event in the Halobacteriaceae lineage (Haloarcula, Haloferax, Haloquadratum, Halobacterium and Natromonas). There appears to be a separate duplication in Methanosphaera stadtmanae.
Probab=45.86 E-value=11 Score=30.65 Aligned_cols=26 Identities=23% Similarity=0.479 Sum_probs=19.7
Q ss_pred cccccccccccccccccccccCcccc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMC 88 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC 88 (376)
.||.|+.-+....-...|+.||...-
T Consensus 2 fC~~Cg~~l~~~~~~~~C~~C~~~~~ 27 (104)
T TIGR01384 2 FCPKCGSLMTPKNGVYVCPSCGYEKE 27 (104)
T ss_pred CCcccCcccccCCCeEECcCCCCccc
Confidence 69999998865555677888887654
No 119
>PF13913 zf-C2HC_2: zinc-finger of a C2HC-type
Probab=45.67 E-value=5 Score=24.46 Aligned_cols=10 Identities=60% Similarity=1.428 Sum_probs=9.2
Q ss_pred cccccccccc
Q psy4518 63 RCPNCSRSFN 72 (376)
Q Consensus 63 ~C~~C~~~F~ 72 (376)
.|+.|+.+|+
T Consensus 4 ~C~~CgR~F~ 13 (25)
T PF13913_consen 4 PCPICGRKFN 13 (25)
T ss_pred cCCCCCCEEC
Confidence 6999999997
No 120
>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=45.57 E-value=7 Score=38.06 Aligned_cols=36 Identities=25% Similarity=0.707 Sum_probs=22.0
Q ss_pred CCCCcccccccccccccccccccccCcc-------------------ccccccCCcc
Q psy4518 59 KDVPRCPNCSRSFNFAKRQHHCRLCGCI-------------------MCHDCSFFLP 96 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~RrHHCR~CG~v-------------------vC~~CS~~~~ 96 (376)
...-.|..|+.. |-..|..|..||.- +|..|-.++.
T Consensus 195 ~R~L~Cs~C~t~--W~~~R~~Cp~Cg~~~~~~l~~~~~e~~~~~rve~C~~C~~YlK 249 (290)
T PF04216_consen 195 KRYLHCSLCGTE--WRFVRIKCPYCGNTDHEKLEYFTVEGEPAYRVEVCESCGSYLK 249 (290)
T ss_dssp EEEEEETTT--E--EE--TTS-TTT---SS-EEE--------SEEEEEETTTTEEEE
T ss_pred cEEEEcCCCCCe--eeecCCCCcCCCCCCCcceeeEecCCCCcEEEEECCcccchHH
Confidence 456689999874 56678899999986 8999988753
No 121
>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=44.99 E-value=5.9 Score=26.38 Aligned_cols=16 Identities=25% Similarity=0.781 Sum_probs=10.4
Q ss_pred ccccccccc-ccccccc
Q psy4518 64 CPNCSRSFN-FAKRQHH 79 (376)
Q Consensus 64 C~~C~~~F~-~~~RrHH 79 (376)
|+.|.+.+. ...||+|
T Consensus 2 C~~C~~Ey~~p~~RR~~ 18 (35)
T PF07503_consen 2 CDDCLKEYFDPSNRRFH 18 (35)
T ss_dssp -HHHHHHHCSTTSTTTT
T ss_pred CHHHHHHHcCCCCCccc
Confidence 677777753 6677776
No 122
>PF14634 zf-RING_5: zinc-RING finger domain
Probab=44.85 E-value=8 Score=26.53 Aligned_cols=32 Identities=28% Similarity=0.711 Sum_probs=22.4
Q ss_pred cccccccccccccccccccccCccccccccCCc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFL 95 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~ 95 (376)
.|++|...|+ -.++-.=-.||-+||..|....
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 4889999882 2223344579999999997643
No 123
>PF09947 DUF2180: Uncharacterized protein conserved in archaea (DUF2180); InterPro: IPR017211 This group represents a predicted zinc finger protein, AF1427 type.
Probab=44.75 E-value=11 Score=29.00 Aligned_cols=45 Identities=16% Similarity=0.069 Sum_probs=27.6
Q ss_pred ccccccCccccccccCCcccccccccccCCCcCCC-----CCCCcccccchHHHH
Q psy4518 78 HHCRLCGCIMCHDCSFFLPLNKARQILVEPELGES-----QLSASANSDLNLRLL 127 (376)
Q Consensus 78 HHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~-----~~~~vRvC~~C~~~l 127 (376)
--|..||.-+|...+....++... +++|++ ...+--+|..|+..+
T Consensus 17 avCivCG~GlC~~H~~~e~~~~~~-----g~yp~~~~~~~~~l~RilC~~C~~a~ 66 (68)
T PF09947_consen 17 AVCIVCGAGLCMDHSKREEIPVWE-----GGYPFPSKKLKKPLPRILCPECHAAL 66 (68)
T ss_pred ehHHhcCchhhHHHHhhhheeeec-----cCCCCccccccCCCCeeecHHHHHHh
Confidence 458889999998887754333221 222222 124555999999865
No 124
>KOG1315|consensus
Probab=44.67 E-value=10 Score=37.49 Aligned_cols=29 Identities=28% Similarity=0.604 Sum_probs=19.3
Q ss_pred ccCCCCCcccccccccccccccccccccCcc
Q psy4518 56 LDGKDVPRCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 56 ~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
..|..+-.|.-|+. =.--|-|||+.|++.
T Consensus 104 ~~~g~~R~C~kC~~--iKPdRaHHCsvC~rC 132 (307)
T KOG1315|consen 104 TSDGAVRYCDKCKC--IKPDRAHHCSVCNRC 132 (307)
T ss_pred cCCCCceeeccccc--ccCCccccchhhhhh
Confidence 44556667777764 134688999999654
No 125
>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=43.94 E-value=8.1 Score=25.23 Aligned_cols=29 Identities=28% Similarity=0.719 Sum_probs=20.3
Q ss_pred cccccccccccccccccccccCccccccccCC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
.|++|...| .....-..||..||..|...
T Consensus 1 ~C~iC~~~~---~~~~~~~~C~H~~c~~C~~~ 29 (45)
T cd00162 1 ECPICLEEF---REPVVLLPCGHVFCRSCIDK 29 (45)
T ss_pred CCCcCchhh---hCceEecCCCChhcHHHHHH
Confidence 388888877 23334455999999999653
No 126
>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=43.71 E-value=7 Score=26.00 Aligned_cols=28 Identities=25% Similarity=0.681 Sum_probs=19.4
Q ss_pred ccccccccccccccccccccCccccccccCC
Q psy4518 64 CPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 64 C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
|++|...+ ......-.||.+||..|...
T Consensus 1 C~iC~~~~---~~~~~~~~CGH~fC~~C~~~ 28 (39)
T PF13923_consen 1 CPICLDEL---RDPVVVTPCGHSFCKECIEK 28 (39)
T ss_dssp ETTTTSB----SSEEEECTTSEEEEHHHHHH
T ss_pred CCCCCCcc---cCcCEECCCCCchhHHHHHH
Confidence 67886644 33446778999999999653
No 127
>KOG3795|consensus
Probab=43.50 E-value=11 Score=34.14 Aligned_cols=24 Identities=29% Similarity=0.693 Sum_probs=18.6
Q ss_pred ccccccccccccccCcc---ccccccC
Q psy4518 70 SFNFAKRQHHCRLCGCI---MCHDCSF 93 (376)
Q Consensus 70 ~F~~~~RrHHCR~CG~v---vC~~CS~ 93 (376)
.|.-...||.|+.||+. ||-+|.-
T Consensus 8 ~~d~ieGRs~C~~C~~SRkFfCY~C~V 34 (230)
T KOG3795|consen 8 SFDPIEGRSTCPGCKSSRKFFCYDCRV 34 (230)
T ss_pred ccCcccccccCCCCCCcceEEEEeecc
Confidence 35556789999999974 8999865
No 128
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=43.17 E-value=16 Score=38.60 Aligned_cols=24 Identities=33% Similarity=0.948 Sum_probs=10.9
Q ss_pred ccccccccccc--ccccccccccCcc
Q psy4518 63 RCPNCSRSFNF--AKRQHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~--~~RrHHCR~CG~v 86 (376)
.||.|+.+.++ -.++-.|..||..
T Consensus 224 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 249 (505)
T TIGR00595 224 CCPNCDVSLTYHKKEGKLRCHYCGYQ 249 (505)
T ss_pred CCCCCCCceEEecCCCeEEcCCCcCc
Confidence 45555544432 2234445555544
No 129
>COG2051 RPS27A Ribosomal protein S27E [Translation, ribosomal structure and biogenesis]
Probab=43.11 E-value=11 Score=28.78 Aligned_cols=27 Identities=30% Similarity=0.917 Sum_probs=21.1
Q ss_pred ccccccc---ccccccccccccccCccccc
Q psy4518 63 RCPNCSR---SFNFAKRQHHCRLCGCIMCH 89 (376)
Q Consensus 63 ~C~~C~~---~F~~~~RrHHCR~CG~vvC~ 89 (376)
.||.|+. -|+--.....|-.||.++|.
T Consensus 21 kCpdC~N~q~vFshast~V~C~~CG~~l~~ 50 (67)
T COG2051 21 KCPDCGNEQVVFSHASTVVTCLICGTTLAE 50 (67)
T ss_pred ECCCCCCEEEEeccCceEEEecccccEEEe
Confidence 6899987 56666677889999988864
No 130
>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=42.76 E-value=11 Score=25.04 Aligned_cols=7 Identities=43% Similarity=1.379 Sum_probs=3.7
Q ss_pred ccccccc
Q psy4518 63 RCPNCSR 69 (376)
Q Consensus 63 ~C~~C~~ 69 (376)
.||.|+.
T Consensus 3 FCp~C~n 9 (35)
T PF02150_consen 3 FCPECGN 9 (35)
T ss_dssp BETTTTS
T ss_pred eCCCCCc
Confidence 4555554
No 131
>KOG1818|consensus
Probab=42.74 E-value=6 Score=42.62 Aligned_cols=31 Identities=16% Similarity=0.316 Sum_probs=27.2
Q ss_pred cccccccccccccccccccccC-ccccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCG-CIMCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG-~vvC~~CS~ 93 (376)
+|..|-+.|+|..+.|||++|| .|+|.-|+.
T Consensus 56 h~np~~~~~~~~~~d~cvkn~G~gv~~ei~tr 87 (634)
T KOG1818|consen 56 HENPNVQLFTLKLTDHCVKNCGHGVHCEIATR 87 (634)
T ss_pred ccCCCcccchhhhHHHHHhcCCcchhHHHHHH
Confidence 7899999999999999999999 888865543
No 132
>KOG0823|consensus
Probab=41.69 E-value=5.9 Score=37.39 Aligned_cols=51 Identities=16% Similarity=0.343 Sum_probs=31.3
Q ss_pred CCCCcccccccccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHH
Q psy4518 59 KDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLE 128 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~ 128 (376)
..--.|.+|-..= +---=-+||..||+.|--.|..-. .....|..|+..+.
T Consensus 45 ~~~FdCNICLd~a----kdPVvTlCGHLFCWpClyqWl~~~---------------~~~~~cPVCK~~Vs 95 (230)
T KOG0823|consen 45 GGFFDCNICLDLA----KDPVVTLCGHLFCWPCLYQWLQTR---------------PNSKECPVCKAEVS 95 (230)
T ss_pred CCceeeeeecccc----CCCEEeecccceehHHHHHHHhhc---------------CCCeeCCccccccc
Confidence 3344677776421 111224899999999976654221 24467788877664
No 133
>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=41.19 E-value=14 Score=24.70 Aligned_cols=12 Identities=33% Similarity=1.099 Sum_probs=7.0
Q ss_pred cccccccccccc
Q psy4518 63 RCPNCSRSFNFA 74 (376)
Q Consensus 63 ~C~~C~~~F~~~ 74 (376)
.|+.|+..|++.
T Consensus 3 ~C~~Cg~~Yh~~ 14 (36)
T PF05191_consen 3 ICPKCGRIYHIE 14 (36)
T ss_dssp EETTTTEEEETT
T ss_pred CcCCCCCccccc
Confidence 366666666643
No 134
>KOG4797|consensus
Probab=41.13 E-value=1.1e+02 Score=25.70 Aligned_cols=45 Identities=22% Similarity=0.309 Sum_probs=38.8
Q ss_pred cchhHHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHhhhh
Q psy4518 319 QDPLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQEQQ 367 (376)
Q Consensus 319 ~~~L~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~~~~~~~ 367 (376)
+..+++=|.+|+.-+--|-+ |||..|...++||.....+++.+++
T Consensus 47 DNKIeQAMDLVKtHLmfAVR----EEVe~Lk~qI~eL~er~~~Le~EN~ 91 (123)
T KOG4797|consen 47 DNKIEQAMDLVKTHLMFAVR----EEVEVLKEQIRELEERNSALERENS 91 (123)
T ss_pred chHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34667778999999988876 7999999999999999999988875
No 135
>PF13248 zf-ribbon_3: zinc-ribbon domain
Probab=40.78 E-value=15 Score=22.46 Aligned_cols=21 Identities=33% Similarity=0.912 Sum_probs=10.3
Q ss_pred cccccccccccccccccccccCc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGC 85 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~ 85 (376)
.||.|++. +-..-.-|..||.
T Consensus 4 ~Cp~Cg~~--~~~~~~fC~~CG~ 24 (26)
T PF13248_consen 4 FCPNCGAE--IDPDAKFCPNCGA 24 (26)
T ss_pred CCcccCCc--CCcccccChhhCC
Confidence 56666662 2333344555553
No 136
>PRK14892 putative transcription elongation factor Elf1; Provisional
Probab=40.74 E-value=12 Score=30.79 Aligned_cols=32 Identities=19% Similarity=0.704 Sum_probs=17.8
Q ss_pred CCCcccccccccccccccccccccCccccccccCC
Q psy4518 60 DVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 60 ~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
.+..||.|+. ..+....++ .=|.++|..|..+
T Consensus 20 t~f~CP~Cge-~~v~v~~~k--~~~h~~C~~CG~y 51 (99)
T PRK14892 20 KIFECPRCGK-VSISVKIKK--NIAIITCGNCGLY 51 (99)
T ss_pred cEeECCCCCC-eEeeeecCC--CcceEECCCCCCc
Confidence 4568999994 444333332 3455555555443
No 137
>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=40.71 E-value=11 Score=28.02 Aligned_cols=13 Identities=38% Similarity=1.022 Sum_probs=10.8
Q ss_pred cccccccCccccc
Q psy4518 77 QHHCRLCGCIMCH 89 (376)
Q Consensus 77 rHHCR~CG~vvC~ 89 (376)
--.|-.||+|+|.
T Consensus 18 ~~NCl~CGkIiC~ 30 (57)
T PF06221_consen 18 APNCLNCGKIICE 30 (57)
T ss_pred cccccccChhhcc
Confidence 4578999999986
No 138
>COG5273 Uncharacterized protein containing DHHC-type Zn finger [General function prediction only]
Probab=40.59 E-value=14 Score=36.56 Aligned_cols=29 Identities=24% Similarity=0.539 Sum_probs=20.4
Q ss_pred cCCCCCcccccccccccccccccccccCccc
Q psy4518 57 DGKDVPRCPNCSRSFNFAKRQHHCRLCGCIM 87 (376)
Q Consensus 57 ~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vv 87 (376)
.+.....|..|.. =---|-|||+.||+.|
T Consensus 105 ~~~~~~~C~~C~~--~KP~RS~HC~~Cn~CV 133 (309)
T COG5273 105 KFGTENFCSTCNI--YKPPRSHHCSICNRCV 133 (309)
T ss_pred ccccceecccccc--ccCCCCccchhhcchh
Confidence 3444567888864 1356999999999865
No 139
>KOG2462|consensus
Probab=40.47 E-value=12 Score=36.38 Aligned_cols=31 Identities=26% Similarity=0.626 Sum_probs=20.4
Q ss_pred cCCCCCccccccccccc------ccc----cccccccCccc
Q psy4518 57 DGKDVPRCPNCSRSFNF------AKR----QHHCRLCGCIM 87 (376)
Q Consensus 57 ~d~~v~~C~~C~~~F~~------~~R----rHHCR~CG~vv 87 (376)
++..+..|+.|++.|.- -.| .|-|-.||+-|
T Consensus 157 ~s~ka~~C~~C~K~YvSmpALkMHirTH~l~c~C~iCGKaF 197 (279)
T KOG2462|consen 157 DSKKAFSCKYCGKVYVSMPALKMHIRTHTLPCECGICGKAF 197 (279)
T ss_pred cccccccCCCCCceeeehHHHhhHhhccCCCcccccccccc
Confidence 34667789999997751 122 45577777766
No 140
>smart00778 Prim_Zn_Ribbon Zinc-binding domain of primase-helicase. This region represents the zinc binding domain. It is found in the N-terminal region of the bacteriophage P4 alpha protein, which is a multifunctional protein with origin recognition, helicase and primase activities.
Probab=40.45 E-value=16 Score=24.62 Aligned_cols=22 Identities=41% Similarity=1.158 Sum_probs=14.2
Q ss_pred ccccccc--cccccc----ccccccccC
Q psy4518 63 RCPNCSR--SFNFAK----RQHHCRLCG 84 (376)
Q Consensus 63 ~C~~C~~--~F~~~~----RrHHCR~CG 84 (376)
-||.|+- .|.+.. .-.+|+.||
T Consensus 5 pCP~CGG~DrFr~~d~~g~G~~~C~~Cg 32 (37)
T smart00778 5 PCPNCGGSDRFRFDDKDGRGTWFCSVCG 32 (37)
T ss_pred CCCCCCCccccccccCCCCcCEEeCCCC
Confidence 5999988 666544 234666665
No 141
>PF08996 zf-DNA_Pol: DNA Polymerase alpha zinc finger; InterPro: IPR015088 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 DNA Polymerase alpha zinc finger domain adopts an alpha-helix-like structure, followed by three turns, all of which involve proline. The resulting motif is a helix-turn-helix motif, in contrast to other zinc finger domains, which show anti-parallel sheet and helix conformation. Zinc binding occurs due to the presence of four cysteine residues positioned to bind the metal centre in a tetrahedral coordination geometry. The function of this domain is uncertain: it has been proposed that the zinc finger motif may be an essential part of the DNA binding domain []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0001882 nucleoside binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 3FLO_D 1N5G_A 1K0P_A 1K18_A.
Probab=39.95 E-value=1.1e+02 Score=27.94 Aligned_cols=11 Identities=45% Similarity=1.410 Sum_probs=6.2
Q ss_pred ccccccccccc
Q psy4518 63 RCPNCSRSFNF 73 (376)
Q Consensus 63 ~C~~C~~~F~~ 73 (376)
.||.|+..|.+
T Consensus 20 ~C~~C~~~~~f 30 (188)
T PF08996_consen 20 TCPSCGTEFEF 30 (188)
T ss_dssp E-TTT--EEEE
T ss_pred ECCCCCCCccc
Confidence 69999998864
No 142
>PF13453 zf-TFIIB: Transcription factor zinc-finger
Probab=39.39 E-value=15 Score=24.87 Aligned_cols=9 Identities=33% Similarity=1.331 Sum_probs=5.1
Q ss_pred ccccccccc
Q psy4518 63 RCPNCSRSF 71 (376)
Q Consensus 63 ~C~~C~~~F 71 (376)
.||.|+...
T Consensus 1 ~CP~C~~~l 9 (41)
T PF13453_consen 1 KCPRCGTEL 9 (41)
T ss_pred CcCCCCccc
Confidence 366666543
No 143
>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=39.37 E-value=8.2 Score=23.27 Aligned_cols=10 Identities=30% Similarity=1.202 Sum_probs=8.7
Q ss_pred cccccccccc
Q psy4518 63 RCPNCSRSFN 72 (376)
Q Consensus 63 ~C~~C~~~F~ 72 (376)
.|..|++.|+
T Consensus 3 ~C~~C~~~F~ 12 (27)
T PF13912_consen 3 ECDECGKTFS 12 (27)
T ss_dssp EETTTTEEES
T ss_pred CCCccCCccC
Confidence 6899999997
No 144
>KOG3799|consensus
Probab=38.17 E-value=26 Score=30.58 Aligned_cols=55 Identities=20% Similarity=0.353 Sum_probs=37.7
Q ss_pred CCcccCCCCCccccccc-ccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHH
Q psy4518 53 VPWLDGKDVPRCPNCSR-SFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLR 125 (376)
Q Consensus 53 ~~W~~d~~v~~C~~C~~-~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~ 125 (376)
+.-.+|. .|.+|.+ +|.- -=-|.|-.|.--+|..|...+.+.. ++-.-||..|..
T Consensus 60 aGv~dda---tC~IC~KTKFAD-G~GH~C~YCq~r~CARCGGrv~lrs--------------NKv~wvcnlc~k 115 (169)
T KOG3799|consen 60 AGVGDDA---TCGICHKTKFAD-GCGHNCSYCQTRFCARCGGRVSLRS--------------NKVMWVCNLCRK 115 (169)
T ss_pred cccCcCc---chhhhhhccccc-ccCcccchhhhhHHHhcCCeeeecc--------------CceEEeccCCcH
Confidence 3444554 7999998 4531 1258999999999999977654331 245568888864
No 145
>PF14445 Prok-RING_2: Prokaryotic RING finger family 2
Probab=38.01 E-value=6.4 Score=28.45 Aligned_cols=30 Identities=30% Similarity=0.771 Sum_probs=23.8
Q ss_pred cccccccccccccccccccccCccccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~ 93 (376)
.|-.|+..|.+. .-..|-+||+--|+.|-.
T Consensus 9 ~CDLCn~~~p~~-~LRQCvlCGRWaC~sCW~ 38 (57)
T PF14445_consen 9 SCDLCNSSHPIS-ELRQCVLCGRWACNSCWQ 38 (57)
T ss_pred hHHhhcccCcHH-HHHHHhhhchhhhhhhhh
Confidence 588999988743 234799999999999965
No 146
>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=37.89 E-value=20 Score=26.20 Aligned_cols=27 Identities=33% Similarity=0.784 Sum_probs=17.4
Q ss_pred c-ccCCCCCcccccccccccccccccccccC
Q psy4518 55 W-LDGKDVPRCPNCSRSFNFAKRQHHCRLCG 84 (376)
Q Consensus 55 W-~~d~~v~~C~~C~~~F~~~~RrHHCR~CG 84 (376)
| ........|+.|+. +...-|-|..||
T Consensus 19 ~kl~~p~l~~C~~cG~---~~~~H~vc~~cG 46 (55)
T TIGR01031 19 AKLTAPTLVVCPNCGE---FKLPHRVCPSCG 46 (55)
T ss_pred ccccCCcceECCCCCC---cccCeeECCccC
Confidence 5 44556678999987 344445566666
No 147
>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=37.48 E-value=20 Score=24.67 Aligned_cols=29 Identities=24% Similarity=0.788 Sum_probs=20.8
Q ss_pred CCcccccccccccccccccccccCcc-ccccc
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCGCI-MCHDC 91 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG~v-vC~~C 91 (376)
...|..|++ .+...|+||-.|... +|..|
T Consensus 4 ~~~C~~C~~--~i~g~ry~C~~C~d~dlC~~C 33 (44)
T smart00291 4 SYSCDTCGK--PIVGVRYHCLVCPDYDLCQSC 33 (44)
T ss_pred CcCCCCCCC--CCcCCEEECCCCCCccchHHH
Confidence 347999998 456778899988443 66666
No 148
>PRK14873 primosome assembly protein PriA; Provisional
Probab=37.29 E-value=18 Score=39.56 Aligned_cols=33 Identities=27% Similarity=0.784 Sum_probs=20.8
Q ss_pred CCcccccccccccc--cccccccccCcc----ccccccC
Q psy4518 61 VPRCPNCSRSFNFA--KRQHHCRLCGCI----MCHDCSF 93 (376)
Q Consensus 61 v~~C~~C~~~F~~~--~RrHHCR~CG~v----vC~~CS~ 93 (376)
+..|+.|+.+.++- .+.-.|..||.. .|..|.+
T Consensus 392 ~~~C~~C~~~L~~h~~~~~l~Ch~CG~~~~p~~Cp~Cgs 430 (665)
T PRK14873 392 PARCRHCTGPLGLPSAGGTPRCRWCGRAAPDWRCPRCGS 430 (665)
T ss_pred eeECCCCCCceeEecCCCeeECCCCcCCCcCccCCCCcC
Confidence 34677777766653 235668888764 4666755
No 149
>COG4530 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.85 E-value=18 Score=30.38 Aligned_cols=25 Identities=16% Similarity=0.102 Sum_probs=17.1
Q ss_pred Cccccccccccccccc-ccccccCcc
Q psy4518 62 PRCPNCSRSFNFAKRQ-HHCRLCGCI 86 (376)
Q Consensus 62 ~~C~~C~~~F~~~~Rr-HHCR~CG~v 86 (376)
..||.|+++|--++|+ --|..||.-
T Consensus 10 ridPetg~KFYDLNrdPiVsPytG~s 35 (129)
T COG4530 10 RIDPETGKKFYDLNRDPIVSPYTGKS 35 (129)
T ss_pred ccCccccchhhccCCCccccCccccc
Confidence 4799999999966654 445555543
No 150
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=36.73 E-value=12 Score=41.80 Aligned_cols=28 Identities=36% Similarity=1.057 Sum_probs=0.0
Q ss_pred CcccccccccccccccccccccCcc-----ccccccC
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCI-----MCHDCSF 93 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~v-----vC~~CS~ 93 (376)
-.||.|+.. .=...|..||.. +|..|-.
T Consensus 656 r~Cp~Cg~~----t~~~~Cp~CG~~T~~~~~Cp~C~~ 688 (900)
T PF03833_consen 656 RRCPKCGKE----TFYNRCPECGSHTEPVYVCPDCGI 688 (900)
T ss_dssp -------------------------------------
T ss_pred ccCcccCCc----chhhcCcccCCccccceecccccc
Confidence 368888763 223567777776 6777744
No 151
>PRK05580 primosome assembly protein PriA; Validated
Probab=36.66 E-value=22 Score=38.97 Aligned_cols=24 Identities=33% Similarity=0.955 Sum_probs=11.5
Q ss_pred ccccccccccc--ccccccccccCcc
Q psy4518 63 RCPNCSRSFNF--AKRQHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~--~~RrHHCR~CG~v 86 (376)
.|+.|+.++++ ..+.-.|..||..
T Consensus 392 ~C~~C~~~l~~h~~~~~l~Ch~Cg~~ 417 (679)
T PRK05580 392 ECPHCDASLTLHRFQRRLRCHHCGYQ 417 (679)
T ss_pred CCCCCCCceeEECCCCeEECCCCcCC
Confidence 45555554442 2333445555554
No 152
>KOG2199|consensus
Probab=36.22 E-value=1.3e+02 Score=31.02 Aligned_cols=56 Identities=14% Similarity=0.052 Sum_probs=46.1
Q ss_pred cCCCchhHHHHHHHHHHHHHHHhHHHHHHHHHHhhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHH
Q psy4518 137 RNSRPLICDLYDALMGKKQEASKLRAMYLEMIDSLLAGETMYYASDAQALRVKLVRLAENIDTISNKV 204 (376)
Q Consensus 137 ~~~~p~i~~~Ye~L~~~~~~I~~~lP~f~~~l~sL~~g~s~~~l~~a~~lR~kL~~~f~~~d~~skri 204 (376)
..+.|.+..+|..+..+.-.|...|-.|-+ +-++...|+.+|+++...|+.+-.+=
T Consensus 313 ~~D~~~l~~le~~~~~mgPlid~~Le~idr------------k~~eL~~Ln~~l~~Al~lY~kLm~~~ 368 (462)
T KOG2199|consen 313 VQDDDDLLDLEAAVHQMGPLIDRKLEKIDR------------KHEELSQLNVKLLDALRLYNKLMNEA 368 (462)
T ss_pred cCCCHHHHHHHHHHHHhhhHHHHHHHHHHh------------hHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 345578889999999888888888877765 35788899999999999999998775
No 153
>COG1996 RPC10 DNA-directed RNA polymerase, subunit RPC10 (contains C4-type Zn-finger) [Transcription]
Probab=35.99 E-value=17 Score=26.08 Aligned_cols=23 Identities=30% Similarity=0.946 Sum_probs=14.6
Q ss_pred cccccccccccc--cccccccccCc
Q psy4518 63 RCPNCSRSFNFA--KRQHHCRLCGC 85 (376)
Q Consensus 63 ~C~~C~~~F~~~--~RrHHCR~CG~ 85 (376)
.|..|++.|.+. .+---|..||.
T Consensus 8 ~C~~Cg~~~~~~~~~~~irCp~Cg~ 32 (49)
T COG1996 8 KCARCGREVELDQETRGIRCPYCGS 32 (49)
T ss_pred EhhhcCCeeehhhccCceeCCCCCc
Confidence 688999998733 34445555543
No 154
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=35.68 E-value=20 Score=41.65 Aligned_cols=28 Identities=32% Similarity=0.826 Sum_probs=22.6
Q ss_pred cccccccccccccccccccccCcc---------ccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCI---------MCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~v---------vC~~CS~ 93 (376)
.||.|+..... ..+|..||.- +|..|-.
T Consensus 681 fCP~CGs~te~---vy~CPsCGaev~~des~a~~CP~CGt 717 (1337)
T PRK14714 681 RCPDCGTHTEP---VYVCPDCGAEVPPDESGRVECPRCDV 717 (1337)
T ss_pred cCcccCCcCCC---ceeCccCCCccCCCccccccCCCCCC
Confidence 89999997543 4599999985 7999865
No 155
>PF10263 SprT-like: SprT-like family; InterPro: IPR006640 This is a family of uncharacterised bacterial proteins which includes Escherichia coli SprT (P39902 from SWISSPROT). SprT is described as a regulator of bolA gene in stationary phase []. The majority of members contain the metallopeptidase zinc binding signature which has a HExxH motif, however there is no evidence for them being metallopeptidases.
Probab=35.42 E-value=17 Score=31.59 Aligned_cols=28 Identities=36% Similarity=0.847 Sum_probs=18.5
Q ss_pred CCCCccccccccccccc----ccccccccCcc
Q psy4518 59 KDVPRCPNCSRSFNFAK----RQHHCRLCGCI 86 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~----RrHHCR~CG~v 86 (376)
...-.|+.|+..+.... .++.|+.||..
T Consensus 121 ~~~~~C~~C~~~~~r~~~~~~~~~~C~~C~~~ 152 (157)
T PF10263_consen 121 KYVYRCPSCGREYKRHRRSKRKRYRCGRCGGP 152 (157)
T ss_pred ceEEEcCCCCCEeeeecccchhhEECCCCCCE
Confidence 34457899998775322 25678888764
No 156
>COG1645 Uncharacterized Zn-finger containing protein [General function prediction only]
Probab=35.36 E-value=18 Score=31.39 Aligned_cols=23 Identities=30% Similarity=0.920 Sum_probs=17.1
Q ss_pred cccccccccccccccccccccCccccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~ 93 (376)
+||.|+.+. +| .-|.|||.-|-.
T Consensus 30 hCp~Cg~PL---F~-----KdG~v~CPvC~~ 52 (131)
T COG1645 30 HCPKCGTPL---FR-----KDGEVFCPVCGY 52 (131)
T ss_pred hCcccCCcc---ee-----eCCeEECCCCCc
Confidence 799999863 22 458888888863
No 157
>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=35.22 E-value=21 Score=23.79 Aligned_cols=24 Identities=25% Similarity=0.574 Sum_probs=15.3
Q ss_pred cccccccccc-cccccccccccCcc
Q psy4518 63 RCPNCSRSFN-FAKRQHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~-~~~RrHHCR~CG~v 86 (376)
.|+.|+..|. .-..+.-|..||.+
T Consensus 10 ~C~~C~~~~~~~~dG~~yC~~cG~~ 34 (36)
T PF11781_consen 10 PCPVCGSRWFYSDDGFYYCDRCGHQ 34 (36)
T ss_pred cCCCCCCeEeEccCCEEEhhhCceE
Confidence 4888888654 44556666666654
No 158
>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=35.02 E-value=19 Score=25.16 Aligned_cols=30 Identities=13% Similarity=0.406 Sum_probs=21.3
Q ss_pred cccccccccccccccccccccCcc-ccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCI-MCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~v-vC~~CS~ 93 (376)
.|-.|+. +.+.-.|++|..|... +|..|-.
T Consensus 2 ~CDgCg~-~PI~G~RykC~~C~dyDLC~~C~~ 32 (43)
T cd02342 2 QCDGCGV-LPITGPRYKSKVKEDYDLCTICFS 32 (43)
T ss_pred CCCCCCC-CcccccceEeCCCCCCccHHHHhh
Confidence 4778885 3467788888888665 6666644
No 159
>PRK00415 rps27e 30S ribosomal protein S27e; Reviewed
Probab=34.96 E-value=19 Score=26.84 Aligned_cols=26 Identities=31% Similarity=0.916 Sum_probs=16.3
Q ss_pred ccccccc---ccccccccccccccCcccc
Q psy4518 63 RCPNCSR---SFNFAKRQHHCRLCGCIMC 88 (376)
Q Consensus 63 ~C~~C~~---~F~~~~RrHHCR~CG~vvC 88 (376)
.|+.|+. -|+-.....-|..||.+.|
T Consensus 13 kCp~C~n~q~vFsha~t~V~C~~Cg~~L~ 41 (59)
T PRK00415 13 KCPDCGNEQVVFSHASTVVRCLVCGKTLA 41 (59)
T ss_pred ECCCCCCeEEEEecCCcEEECcccCCCcc
Confidence 5888877 4554455556666666654
No 160
>COG1439 Predicted nucleic acid-binding protein, consists of a PIN domain and a Zn-ribbon module [General function prediction only]
Probab=34.70 E-value=18 Score=33.00 Aligned_cols=22 Identities=36% Similarity=1.017 Sum_probs=14.7
Q ss_pred cccccccccccccccccccccCcc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
.|.+|.+.|. .-.+-|..||.-
T Consensus 141 rC~GC~~~f~--~~~~~Cp~CG~~ 162 (177)
T COG1439 141 RCHGCKRIFP--EPKDFCPICGSP 162 (177)
T ss_pred EEecCceecC--CCCCcCCCCCCc
Confidence 6777777776 556666666653
No 161
>PF10892 DUF2688: Protein of unknown function (DUF2688); InterPro: IPR024392 Members of this protein family are annotated as KleB, and may play a role in the regulation of transcription in plasmids.
Probab=34.59 E-value=13 Score=27.46 Aligned_cols=10 Identities=40% Similarity=0.953 Sum_probs=7.1
Q ss_pred ccccccCccc
Q psy4518 78 HHCRLCGCIM 87 (376)
Q Consensus 78 HHCR~CG~vv 87 (376)
.|||.||..+
T Consensus 11 t~CrRCGk~i 20 (60)
T PF10892_consen 11 TPCRRCGKSI 20 (60)
T ss_pred ehhhhhCccH
Confidence 5788888754
No 162
>PF14835 zf-RING_6: zf-RING of BARD1-type protein; PDB: 1JM7_B.
Probab=34.19 E-value=24 Score=26.84 Aligned_cols=27 Identities=30% Similarity=0.741 Sum_probs=13.3
Q ss_pred cccccccccccccccccc-cccCccccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHC-RLCGCIMCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHC-R~CG~vvC~~CS~ 93 (376)
.|+.|.. +.+.-+| -.|..+||+.|..
T Consensus 9 rCs~C~~----~l~~pv~l~~CeH~fCs~Ci~ 36 (65)
T PF14835_consen 9 RCSICFD----ILKEPVCLGGCEHIFCSSCIR 36 (65)
T ss_dssp S-SSS-S------SS-B---SSS--B-TTTGG
T ss_pred CCcHHHH----HhcCCceeccCccHHHHHHhH
Confidence 6888865 3456666 7899999999964
No 163
>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=33.66 E-value=29 Score=21.93 Aligned_cols=28 Identities=25% Similarity=0.539 Sum_probs=21.6
Q ss_pred cccccccccccccccccccccCccccccc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDC 91 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~C 91 (376)
.|..|++..+-+. -.||..|+-.+...|
T Consensus 2 ~C~~C~~~~~~~~-~Y~C~~c~f~lh~~C 29 (30)
T PF03107_consen 2 WCDVCRRKIDGFY-FYHCSECCFTLHVRC 29 (30)
T ss_pred CCCCCCCCcCCCE-eEEeCCCCCeEcCcc
Confidence 5888988877555 899999987766665
No 164
>PF00096 zf-C2H2: Zinc finger, C2H2 type; InterPro: IPR007087 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. The C2H2 zinc finger is the classical zinc finger domain. The two conserved cysteines and histidines co-ordinate a zinc ion. The following pattern describes the zinc finger: #-X-C-X(1-5)-C-X3-#-X5-#-X2-H-X(3-6)-[H/C], where X can be any amino acid, and numbers in brackets indicate the number of residues. The positions marked # are those that are important for the stable fold of the zinc finger. The final position can be either his or cys. The C2H2 zinc finger is composed of two short beta strands followed by an alpha helix. The amino terminal part of the helix binds the major groove in DNA binding zinc fingers. The accepted consensus binding sequence for Sp1 is usually defined by the asymmetric hexanucleotide core GGGCGG but this sequence does not include, among others, the GAG (=CTC) repeat that constitutes a high-affinity site for Sp1 binding to the wt1 promoter []. This entry represents the classical C2H2 zinc finger domain. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding, 0005622 intracellular; PDB: 2D9H_A 2EPC_A 1SP1_A 1VA3_A 2WBT_B 2ELR_A 2YTP_A 2YTT_A 1VA1_A 2ELO_A ....
Probab=33.62 E-value=15 Score=21.14 Aligned_cols=10 Identities=50% Similarity=1.454 Sum_probs=8.2
Q ss_pred cccccccccc
Q psy4518 63 RCPNCSRSFN 72 (376)
Q Consensus 63 ~C~~C~~~F~ 72 (376)
.|+.|++.|.
T Consensus 2 ~C~~C~~~f~ 11 (23)
T PF00096_consen 2 KCPICGKSFS 11 (23)
T ss_dssp EETTTTEEES
T ss_pred CCCCCCCccC
Confidence 4888988886
No 165
>PF15227 zf-C3HC4_4: zinc finger of C3HC4-type, RING; PDB: 2EGP_A 2ECV_A 2ECJ_A 2YSL_A 2YSJ_A.
Probab=33.52 E-value=13 Score=25.49 Aligned_cols=27 Identities=30% Similarity=0.691 Sum_probs=17.5
Q ss_pred ccccccccccccccccccccCccccccccCC
Q psy4518 64 CPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 64 C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
||+|..-|. .-.=-.||.+||..|...
T Consensus 1 CpiC~~~~~----~Pv~l~CGH~FC~~Cl~~ 27 (42)
T PF15227_consen 1 CPICLDLFK----DPVSLPCGHSFCRSCLER 27 (42)
T ss_dssp ETTTTSB-S----SEEE-SSSSEEEHHHHHH
T ss_pred CCccchhhC----CccccCCcCHHHHHHHHH
Confidence 778887665 111136999999999654
No 166
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=33.45 E-value=25 Score=34.80 Aligned_cols=28 Identities=18% Similarity=0.425 Sum_probs=21.0
Q ss_pred cCCCCCcccccccccccccccccccccCcc
Q psy4518 57 DGKDVPRCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 57 ~d~~v~~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
.+...-.|..|+.. |-.+|..|..||.-
T Consensus 208 ~G~RyL~CslC~te--W~~~R~~C~~Cg~~ 235 (309)
T PRK03564 208 QGLRYLHCNLCESE--WHVVRVKCSNCEQS 235 (309)
T ss_pred CCceEEEcCCCCCc--ccccCccCCCCCCC
Confidence 34556689999864 56669999999974
No 167
>KOG1538|consensus
Probab=33.43 E-value=14 Score=40.18 Aligned_cols=29 Identities=28% Similarity=0.835 Sum_probs=24.8
Q ss_pred ccCCCCCcccccccccc------cccccccccccC
Q psy4518 56 LDGKDVPRCPNCSRSFN------FAKRQHHCRLCG 84 (376)
Q Consensus 56 ~~d~~v~~C~~C~~~F~------~~~RrHHCR~CG 84 (376)
.||..+..||.|.+-|. ...+|.||..|-
T Consensus 1039 lPd~~it~Cp~C~~~F~~eDFEl~vLqKGHCPFCr 1073 (1081)
T KOG1538|consen 1039 LPDASITMCPSCFQMFHSEDFELLVLQKGHCPFCR 1073 (1081)
T ss_pred CCcchhhhCchHHhhhccchhhHHHHhcCCCCccc
Confidence 68999999999999776 357999999884
No 168
>PRK12366 replication factor A; Reviewed
Probab=32.88 E-value=20 Score=39.10 Aligned_cols=26 Identities=27% Similarity=0.760 Sum_probs=21.4
Q ss_pred CCcccccccccccccccccccccCcc
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
.+.||.|+++-.--....+|..||.+
T Consensus 532 y~aCp~CnkKv~~~~g~~~C~~c~~~ 557 (637)
T PRK12366 532 LYLCPNCRKRVEEVDGEYICEFCGEV 557 (637)
T ss_pred EecccccCeEeEcCCCcEECCCCCCC
Confidence 47999999987544577899999988
No 169
>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=32.83 E-value=22 Score=25.33 Aligned_cols=29 Identities=28% Similarity=0.811 Sum_probs=21.1
Q ss_pred cccccccccccccccccccccC---cccccccc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCG---CIMCHDCS 92 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG---~vvC~~CS 92 (376)
.|..|+. ..+...|+||-.|. --+|..|-
T Consensus 2 ~Cd~C~~-~pI~G~R~~C~~C~~~d~DlC~~C~ 33 (48)
T cd02341 2 KCDSCGI-EPIPGTRYHCSECDDGDFDLCQDCV 33 (48)
T ss_pred CCCCCCC-CccccceEECCCCCCCCCccCHHHH
Confidence 4888887 23568899999998 34666663
No 170
>PF01667 Ribosomal_S27e: Ribosomal protein S27; InterPro: IPR000592 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families include mammalian, yeast, Chlamydomonas reinhardtii and Entamoeba histolytica S27, and Methanocaldococcus jannaschii (Methanococcus jannaschii) MJ0250 []. These proteins have from 62 to 87 amino acids. They contain, in their central section, a putative zinc-finger region of the type C-x(2)-C-x(14)-C-x(2)-C.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 1QXF_A 3IZ6_X 2XZN_6 2XZM_6 3U5G_b 3IZB_X 3U5C_b.
Probab=32.57 E-value=20 Score=26.34 Aligned_cols=26 Identities=31% Similarity=0.961 Sum_probs=13.2
Q ss_pred ccccccc---ccccccccccccccCcccc
Q psy4518 63 RCPNCSR---SFNFAKRQHHCRLCGCIMC 88 (376)
Q Consensus 63 ~C~~C~~---~F~~~~RrHHCR~CG~vvC 88 (376)
.|+.|.. -|+-...-.-|..||.++|
T Consensus 9 kCp~C~~~q~vFSha~t~V~C~~Cg~~L~ 37 (55)
T PF01667_consen 9 KCPGCYNIQTVFSHAQTVVKCVVCGTVLA 37 (55)
T ss_dssp E-TTT-SEEEEETT-SS-EE-SSSTSEEE
T ss_pred ECCCCCCeeEEEecCCeEEEcccCCCEec
Confidence 5888887 4554455556666666665
No 171
>PF14369 zf-RING_3: zinc-finger
Probab=32.36 E-value=26 Score=23.19 Aligned_cols=9 Identities=44% Similarity=1.350 Sum_probs=7.0
Q ss_pred ccccccccc
Q psy4518 63 RCPNCSRSF 71 (376)
Q Consensus 63 ~C~~C~~~F 71 (376)
.||.|+..|
T Consensus 23 ~CP~C~~gF 31 (35)
T PF14369_consen 23 ACPRCHGGF 31 (35)
T ss_pred CCcCCCCcE
Confidence 688888766
No 172
>PF05605 zf-Di19: Drought induced 19 protein (Di19), zinc-binding; InterPro: IPR008598 This entry consists of several drought induced 19 (Di19) like and RING finger 114 proteins. Di19 has been found to be strongly expressed in both the roots and leaves of Arabidopsis thaliana during progressive drought [], whilst RING finger proteins are thought to play a role in spermatogenesis. The precise function is unknown.
Probab=31.79 E-value=21 Score=25.59 Aligned_cols=31 Identities=26% Similarity=0.641 Sum_probs=18.9
Q ss_pred ccccccccccccc-----ccccccccCccccccccC
Q psy4518 63 RCPNCSRSFNFAK-----RQHHCRLCGCIMCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~-----RrHHCR~CG~vvC~~CS~ 93 (376)
.||.|++.|+... ...|..--..++|.-|+.
T Consensus 4 ~CP~C~~~~~~~~L~~H~~~~H~~~~~~v~CPiC~~ 39 (54)
T PF05605_consen 4 TCPYCGKGFSESSLVEHCEDEHRSESKNVVCPICSS 39 (54)
T ss_pred CCCCCCCccCHHHHHHHHHhHCcCCCCCccCCCchh
Confidence 6999999776321 234444444567766665
No 173
>KOG1313|consensus
Probab=31.79 E-value=16 Score=35.60 Aligned_cols=27 Identities=26% Similarity=0.679 Sum_probs=18.8
Q ss_pred CCCcccccccccccccccccccccCcccc
Q psy4518 60 DVPRCPNCSRSFNFAKRQHHCRLCGCIMC 88 (376)
Q Consensus 60 ~v~~C~~C~~~F~~~~RrHHCR~CG~vvC 88 (376)
.++.|.-|..+ ---|-|||+.|++.|=
T Consensus 101 ~~SfC~KC~~p--K~prTHHCsiC~kCVL 127 (309)
T KOG1313|consen 101 NDSFCNKCNYP--KSPRTHHCSICNKCVL 127 (309)
T ss_pred cccHHhhcCCC--CCCCcchhhHHhhHhh
Confidence 34577777764 2467899999988653
No 174
>PF12172 DUF35_N: Rubredoxin-like zinc ribbon domain (DUF35_N); InterPro: IPR022002 This domain has no known function and is found in conserved hypothetical archaeal and bacterial proteins. The domain is duplicated in O53566 from SWISSPROT. The structure of a DUF35 representative reveals two long N-terminal helices followed by a rubredoxin-like zinc ribbon domain represented in this family and a C-terminal OB fold domain. Zinc is chelated by the four conserved cysteines in the alignment. ; PDB: 3IRB_A.
Probab=31.62 E-value=14 Score=24.33 Aligned_cols=20 Identities=35% Similarity=0.865 Sum_probs=7.3
Q ss_pred cccccccccccccccccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCG 84 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG 84 (376)
.|..|+.-+ +--+..|..||
T Consensus 13 rC~~Cg~~~--~pPr~~Cp~C~ 32 (37)
T PF12172_consen 13 RCRDCGRVQ--FPPRPVCPHCG 32 (37)
T ss_dssp E-TTT--EE--ES--SEETTTT
T ss_pred EcCCCCCEe--cCCCcCCCCcC
Confidence 455555432 33345555554
No 175
>PF15135 UPF0515: Uncharacterised protein UPF0515
Probab=31.07 E-value=29 Score=33.31 Aligned_cols=35 Identities=23% Similarity=0.613 Sum_probs=27.7
Q ss_pred CcccCCCCCcccccccccc-------cccccccccccCcccc
Q psy4518 54 PWLDGKDVPRCPNCSRSFN-------FAKRQHHCRLCGCIMC 88 (376)
Q Consensus 54 ~W~~d~~v~~C~~C~~~F~-------~~~RrHHCR~CG~vvC 88 (376)
.|-.-+.|+.|..|.+.|. +-.-..||..||..|=
T Consensus 125 rvp~rKeVSRCr~C~~rYDPVP~dkmwG~aef~C~~C~h~F~ 166 (278)
T PF15135_consen 125 RVPQRKEVSRCRKCRKRYDPVPCDKMWGIAEFHCPKCRHNFR 166 (278)
T ss_pred ccCcccccccccccccccCCCccccccceeeeecccccccch
Confidence 3466788999999999885 3345789999999864
No 176
>cd07178 terB_like_YebE tellurium resistance terB-like protein, subgroup 3. This family includes several uncharacterized bacterial proteins including an Escherichia coli protein called YebE. Protein sequence homology analysis shows they are similar to tellurium resistance protein terB, but the function of this family is unknown.
Probab=30.51 E-value=38 Score=27.43 Aligned_cols=28 Identities=21% Similarity=0.266 Sum_probs=21.5
Q ss_pred HHHHHHHHHHHhcCchh--HHHHHHhHHHH
Q psy4518 328 NIKQFIKEARMAHRYNE--VASLENHLKEL 355 (376)
Q Consensus 328 ~v~~~I~~A~~~rrfdE--V~~L~~NL~EL 355 (376)
+|+.||.-|+.+|++|| ...+..-+.++
T Consensus 2 ~lrami~aAkADG~id~~E~~~I~~~~~~~ 31 (95)
T cd07178 2 LLRAMIAAAKADGHIDEAERARILGELGEA 31 (95)
T ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHHHHh
Confidence 68999999999999986 44555555554
No 177
>COG1405 SUA7 Transcription initiation factor TFIIIB, Brf1 subunit/Transcription initiation factor TFIIB [Transcription]
Probab=30.44 E-value=27 Score=34.26 Aligned_cols=27 Identities=22% Similarity=0.757 Sum_probs=18.7
Q ss_pred Ccccccccc---cccccccccccccCcccc
Q psy4518 62 PRCPNCSRS---FNFAKRQHHCRLCGCIMC 88 (376)
Q Consensus 62 ~~C~~C~~~---F~~~~RrHHCR~CG~vvC 88 (376)
..||.|+.. ..+-+..+-|..||-|+=
T Consensus 2 ~~CpeCg~~~~~~d~~~ge~VC~~CG~Vi~ 31 (285)
T COG1405 2 MSCPECGSTNIITDYERGEIVCADCGLVLE 31 (285)
T ss_pred CCCCCCCCccceeeccCCeEEeccCCEEec
Confidence 479999986 223456777777777653
No 178
>PRK02935 hypothetical protein; Provisional
Probab=30.33 E-value=26 Score=29.26 Aligned_cols=25 Identities=24% Similarity=0.676 Sum_probs=21.1
Q ss_pred cccccccccccccccccccccCccc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vv 87 (376)
.||.|++.=..+-|-.-|-+||...
T Consensus 72 ~CP~C~K~TKmLGrvD~CM~C~~PL 96 (110)
T PRK02935 72 ICPSCEKPTKMLGRVDACMHCNQPL 96 (110)
T ss_pred ECCCCCchhhhccceeecCcCCCcC
Confidence 7999999888888888888887654
No 179
>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=30.31 E-value=20 Score=25.86 Aligned_cols=28 Identities=11% Similarity=-0.081 Sum_probs=18.8
Q ss_pred cccccccccccccccccccccCccccccccCC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
.|++|+..|.- --...||.+||..|-..
T Consensus 3 ~Cpi~~~~~~~----Pv~~~~G~v~~~~~i~~ 30 (63)
T smart00504 3 LCPISLEVMKD----PVILPSGQTYERRAIEK 30 (63)
T ss_pred CCcCCCCcCCC----CEECCCCCEEeHHHHHH
Confidence 58888876652 23457888888877553
No 180
>PF02151 UVR: UvrB/uvrC motif; InterPro: IPR001943 During the process of Escherichia coli nucleotide excision repair, DNA damage recognition and processing are achieved by the action of the uvrA, uvrB, and uvrC gene products []. UvrB and UvrC share a common domain of around 35 amino acids, the so called UVR domain. This domain in UvrB can interact with the homologous domain in UvrC throughout a putative coiled coil structure. This interaction is important for the incision of the damaged strand [].; GO: 0003677 DNA binding, 0004518 nuclease activity, 0006289 nucleotide-excision repair; PDB: 3PXG_D 3PXI_C 1E52_B 1QOJ_B 2D7D_B 2NMV_B.
Probab=30.18 E-value=1.6e+02 Score=19.26 Aligned_cols=35 Identities=20% Similarity=0.425 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHH
Q psy4518 324 QQITNIKQFIKEARMAHRYNEVASLENHLKELQEE 358 (376)
Q Consensus 324 EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~e 358 (376)
+.+.-++.-..+|-..-.||+.+.|-.-+..|+.+
T Consensus 2 ~~i~~l~~~m~~a~~~~dfE~Aa~~Rd~i~~l~~q 36 (36)
T PF02151_consen 2 KLIKELEEKMEEAVENEDFEKAARLRDQIKALKKQ 36 (36)
T ss_dssp HHHHHHHHHHHHHHHTT-CHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHcCHHHHHHHHHHHHHHHcC
Confidence 44566778889999999999999998888887653
No 181
>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=30.11 E-value=27 Score=24.12 Aligned_cols=29 Identities=21% Similarity=0.684 Sum_probs=22.2
Q ss_pred ccccccccccccccccccccc-CccccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLC-GCIMCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~C-G~vvC~~CS~ 93 (376)
.|.+|+. .++..|++|..| .--+|..|-.
T Consensus 2 ~Cd~C~~--~i~G~ry~C~~C~d~dLC~~C~~ 31 (43)
T cd02340 2 ICDGCQG--PIVGVRYKCLVCPDYDLCESCEA 31 (43)
T ss_pred CCCCCCC--cCcCCeEECCCCCCccchHHhhC
Confidence 5889998 467789999999 4557777743
No 182
>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=29.94 E-value=16 Score=24.24 Aligned_cols=28 Identities=32% Similarity=0.674 Sum_probs=19.3
Q ss_pred ccccccccccccccccccccCccccccccCC
Q psy4518 64 CPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 64 C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
|++|...|.... .=..||..||..|...
T Consensus 1 C~iC~~~~~~~~---~~~~C~H~fC~~C~~~ 28 (41)
T PF00097_consen 1 CPICLEPFEDPV---ILLPCGHSFCRDCLRK 28 (41)
T ss_dssp ETTTSSBCSSEE---EETTTSEEEEHHHHHH
T ss_pred CCcCCccccCCC---EEecCCCcchHHHHHH
Confidence 677877665333 3457888899888664
No 183
>PHA00732 hypothetical protein
Probab=29.78 E-value=34 Score=26.92 Aligned_cols=10 Identities=30% Similarity=0.826 Sum_probs=8.7
Q ss_pred cccccccccc
Q psy4518 63 RCPNCSRSFN 72 (376)
Q Consensus 63 ~C~~C~~~F~ 72 (376)
.|..|++.|+
T Consensus 3 ~C~~Cgk~F~ 12 (79)
T PHA00732 3 KCPICGFTTV 12 (79)
T ss_pred cCCCCCCccC
Confidence 5999999997
No 184
>PHA02942 putative transposase; Provisional
Probab=29.55 E-value=34 Score=34.87 Aligned_cols=28 Identities=32% Similarity=0.793 Sum_probs=19.7
Q ss_pred CCCccccccccc-ccccccccccccCccc
Q psy4518 60 DVPRCPNCSRSF-NFAKRQHHCRLCGCIM 87 (376)
Q Consensus 60 ~v~~C~~C~~~F-~~~~RrHHCR~CG~vv 87 (376)
....|+.|+..= .+-.|.|.|..||...
T Consensus 324 TSq~Cs~CG~~~~~l~~r~f~C~~CG~~~ 352 (383)
T PHA02942 324 SSVSCPKCGHKMVEIAHRYFHCPSCGYEN 352 (383)
T ss_pred CCccCCCCCCccCcCCCCEEECCCCCCEe
Confidence 345799999632 2445788999998864
No 185
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=29.44 E-value=1e+02 Score=25.11 Aligned_cols=44 Identities=20% Similarity=0.281 Sum_probs=32.7
Q ss_pred cchhHHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHh
Q psy4518 319 QDPLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQ 364 (376)
Q Consensus 319 ~~~L~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~~~~ 364 (376)
.+-|..+++-|..-|.++++++ +++..|..-..+|..+|..++.
T Consensus 45 ~e~lr~~rN~~sk~I~~~~~~~--~~~~~l~~e~~~lk~~i~~le~ 88 (108)
T PF02403_consen 45 LEELRAERNELSKEIGKLKKAG--EDAEELKAEVKELKEEIKELEE 88 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHCHTT--CCTHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHHHHHHHhhCc--ccHHHHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999998 6666666666666555555443
No 186
>PF14447 Prok-RING_4: Prokaryotic RING finger family 4
Probab=29.43 E-value=26 Score=25.82 Aligned_cols=17 Identities=35% Similarity=0.917 Sum_probs=12.6
Q ss_pred cCCCCCccccccccccc
Q psy4518 57 DGKDVPRCPNCSRSFNF 73 (376)
Q Consensus 57 ~d~~v~~C~~C~~~F~~ 73 (376)
|.+..+.||+|+++|..
T Consensus 35 ~~~rYngCPfC~~~~~~ 51 (55)
T PF14447_consen 35 PGERYNGCPFCGTPFEF 51 (55)
T ss_pred ChhhccCCCCCCCcccC
Confidence 34456789999998863
No 187
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=29.42 E-value=24 Score=30.60 Aligned_cols=24 Identities=25% Similarity=0.606 Sum_probs=17.2
Q ss_pred cccccccccccccc---c--ccccccCcc
Q psy4518 63 RCPNCSRSFNFAKR---Q--HHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~~~R---r--HHCR~CG~v 86 (376)
.|+.|+.+-+.+.+ . .+|..||..
T Consensus 99 lC~~C~sPdT~l~k~~r~~~l~C~ACGa~ 127 (133)
T TIGR00311 99 ICRECNRPDTRIIKEGRVSLLKCEACGAK 127 (133)
T ss_pred ECCCCCCCCcEEEEeCCeEEEecccCCCC
Confidence 79999999884433 2 477777764
No 188
>PRK09678 DNA-binding transcriptional regulator; Provisional
Probab=29.16 E-value=29 Score=26.96 Aligned_cols=26 Identities=27% Similarity=0.727 Sum_probs=18.5
Q ss_pred Cccccccccc----------cccccccccc--ccCccc
Q psy4518 62 PRCPNCSRSF----------NFAKRQHHCR--LCGCIM 87 (376)
Q Consensus 62 ~~C~~C~~~F----------~~~~RrHHCR--~CG~vv 87 (376)
..||.|+..- ++..|.+-|. .||..|
T Consensus 2 m~CP~Cg~~a~irtSr~~s~~~~~~Y~qC~N~eCg~tF 39 (72)
T PRK09678 2 FHCPLCQHAAHARTSRYITDTTKERYHQCQNVNCSATF 39 (72)
T ss_pred ccCCCCCCccEEEEChhcChhhheeeeecCCCCCCCEE
Confidence 3699999765 2456677887 787765
No 189
>PF00569 ZZ: Zinc finger, ZZ type; InterPro: IPR000433 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents ZZ-type zinc finger domains, named because of their ability to bind two zinc ions []. These domains contain 4-6 Cys residues that participate in zinc binding (plus additional Ser/His residues), including a Cys-X2-Cys motif found in other zinc finger domains. These zinc fingers are thought to be involved in protein-protein interactions. The structure of the ZZ domain shows that it belongs to the family of cross-brace zinc finger motifs that include the PHD, RING, and FYVE domains []. ZZ-type zinc finger domains are found in: Transcription factors P300 and CBP. Plant proteins involved in light responses, such as Hrb1. E3 ubiquitin ligases MEX and MIB2 (6.3.2 from EC). Dystrophin and its homologues. Single copies of the ZZ zinc finger occur in the transcriptional adaptor/coactivator proteins P300, in cAMP response element-binding protein (CREB)-binding protein (CBP) and ADA2. CBP provides several binding sites for transcriptional coactivators. The site of interaction with the tumour suppressor protein p53 and the oncoprotein E1A with CBP/P300 is a Cys-rich region that incorporates two zinc-binding motifs: ZZ-type and TAZ2-type. The ZZ-type zinc finger of CBP contains two twisted anti-parallel beta-sheets and a short alpha-helix, and binds two zinc ions []. One zinc ion is coordinated by four cysteine residues via 2 Cys-X2-Cys motifs, and the third zinc ion via a third Cys-X-Cys motif and a His-X-His motif. The first zinc cluster is strictly conserved, whereas the second zinc cluster displays variability in the position of the two His residues. In Arabidopsis thaliana (Mouse-ear cress), the hypersensitive to red and blue 1 (Hrb1) protein, which regulating both red and blue light responses, contains a ZZ-type zinc finger domain []. ZZ-type zinc finger domains have also been identified in the testis-specific E3 ubiquitin ligase MEX that promotes death receptor-induced apoptosis []. MEX has four putative zinc finger domains: one ZZ-type, one SWIM-type and two RING-type. The region containing the ZZ-type and RING-type zinc fingers is required for interaction with UbcH5a and MEX self-association, whereas the SWIM domain was critical for MEX ubiquitination. In addition, the Cys-rich domains of dystrophin, utrophin and an 87kDa post-synaptic protein contain a ZZ-type zinc finger with high sequence identity to P300/CBP ZZ-type zinc fingers. In dystrophin and utrophin, the ZZ-type zinc finger lies between a WW domain (flanked by and EF hand) and the C-terminal coiled-coil domain. Dystrophin is thought to act as a link between the actin cytoskeleton and the extracellular matrix, and perturbations of the dystrophin-associated complex, for example, between dystrophin and the transmembrane glycoprotein beta-dystroglycan, may lead to muscular dystrophy. Dystrophin and its autosomal homologue utrophin interact with beta-dystroglycan via their C-terminal regions, which are comprised of a WW domain, an EF hand domain and a ZZ-type zinc finger domain []. The WW domain is the primary site of interaction between dystrophin or utrophin and dystroglycan, while the EF hand and ZZ-type zinc finger domains stabilise and strengthen this interaction. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0008270 zinc ion binding; PDB: 1TOT_A 2DIP_A 2FC7_A 2E5R_A.
Probab=28.88 E-value=18 Score=25.24 Aligned_cols=22 Identities=23% Similarity=0.646 Sum_probs=13.8
Q ss_pred CcccccccccccccccccccccC
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCG 84 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG 84 (376)
..|..|+.. .+...|+||..|.
T Consensus 5 ~~C~~C~~~-~i~g~Ry~C~~C~ 26 (46)
T PF00569_consen 5 YTCDGCGTD-PIIGVRYHCLVCP 26 (46)
T ss_dssp CE-SSS-SS-SEESSEEEESSSS
T ss_pred eECcCCCCC-cCcCCeEECCCCC
Confidence 468888873 3456778888874
No 190
>KOG0810|consensus
Probab=28.79 E-value=5.8e+02 Score=25.19 Aligned_cols=27 Identities=22% Similarity=0.477 Sum_probs=22.4
Q ss_pred HhcCchhHHHHHHhHHHHHHHHHHHHh
Q psy4518 338 MAHRYNEVASLENHLKELQEEYFRRQQ 364 (376)
Q Consensus 338 ~~rrfdEV~~L~~NL~EL~~ei~~~~~ 364 (376)
-+-|++||.-||.++.||.+=|..|..
T Consensus 201 iq~Rh~~ik~LEksi~ELhqlFlDMa~ 227 (297)
T KOG0810|consen 201 IQERHDEIKKLEKSIRELHQLFLDMAV 227 (297)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999887766654
No 191
>PF04423 Rad50_zn_hook: Rad50 zinc hook motif; InterPro: IPR007517 The Mre11 complex (Mre11 Rad50 Nbs1) is central to chromosomal maintenance and functions in homologous recombination, telomere maintenance and sister chromatid association. The Rad50 coiled-coil region contains a dimer interface at the apex of the coiled coils in which pairs of conserved Cys-X-X-Cys motifs form interlocking hooks that bind one Zn ion. This alignment includes the zinc hook motif and a short stretch of coiled-coil on either side.; GO: 0004518 nuclease activity, 0005524 ATP binding, 0008270 zinc ion binding, 0006281 DNA repair; PDB: 1L8D_B.
Probab=28.72 E-value=20 Score=25.74 Aligned_cols=10 Identities=40% Similarity=1.168 Sum_probs=5.6
Q ss_pred cccccccccc
Q psy4518 63 RCPNCSRSFN 72 (376)
Q Consensus 63 ~C~~C~~~F~ 72 (376)
.||.|+.+|+
T Consensus 22 ~CPlC~r~l~ 31 (54)
T PF04423_consen 22 CCPLCGRPLD 31 (54)
T ss_dssp E-TTT--EE-
T ss_pred cCCCCCCCCC
Confidence 7999999996
No 192
>PF13005 zf-IS66: zinc-finger binding domain of transposase IS66 ; InterPro: IPR024474 This entry represents a predicted helix-turn-helix domain from insertion element IS66 transposases [].
Probab=28.71 E-value=35 Score=23.47 Aligned_cols=10 Identities=30% Similarity=1.152 Sum_probs=6.9
Q ss_pred cccccccccc
Q psy4518 63 RCPNCSRSFN 72 (376)
Q Consensus 63 ~C~~C~~~F~ 72 (376)
.|+.|+..|.
T Consensus 4 ~C~~Cg~~l~ 13 (47)
T PF13005_consen 4 ACPDCGGELK 13 (47)
T ss_pred cCCCCCceee
Confidence 5777777664
No 193
>cd02249 ZZ Zinc finger, ZZ type. Zinc finger present in dystrophin, CBP/p300 and many other proteins. The ZZ motif coordinates one or two zinc ions and most likely participates in ligand binding or molecular scaffolding. Many proteins containing ZZ motifs have other zinc-binding motifs as well, and the majority serve as scaffolds in pathways involving acetyltransferase, protein kinase, or ubiqitin-related activity. ZZ proteins can be grouped into the following functional classes: chromatin modifying, cytoskeletal scaffolding, ubiquitin binding or conjugating, and membrane receptor or ion-channel modifying proteins.
Probab=28.59 E-value=27 Score=24.24 Aligned_cols=29 Identities=24% Similarity=0.742 Sum_probs=21.5
Q ss_pred cccccccccccccccccccccC-ccccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCG-CIMCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG-~vvC~~CS~ 93 (376)
.|..|++ .+...+.||-.|. --+|..|-.
T Consensus 2 ~C~~C~~--~i~g~r~~C~~C~d~dLC~~Cf~ 31 (46)
T cd02249 2 SCDGCLK--PIVGVRYHCLVCEDFDLCSSCYA 31 (46)
T ss_pred CCcCCCC--CCcCCEEECCCCCCCcCHHHHHC
Confidence 4889998 3556899999997 447777744
No 194
>TIGR00595 priA primosomal protein N'. All proteins in this family for which functions are known are components of the primosome which is involved in replication, repair, and recombination.This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=28.40 E-value=33 Score=36.24 Aligned_cols=22 Identities=41% Similarity=1.002 Sum_probs=15.0
Q ss_pred cccccc-----cccccCcc-ccccccCC
Q psy4518 73 FAKRQH-----HCRLCGCI-MCHDCSFF 94 (376)
Q Consensus 73 ~~~RrH-----HCR~CG~v-vC~~CS~~ 94 (376)
|++||- .|+.||.+ .|..|+..
T Consensus 204 flnrrGya~~~~C~~Cg~~~~C~~C~~~ 231 (505)
T TIGR00595 204 FLNRRGYSKNLLCRSCGYILCCPNCDVS 231 (505)
T ss_pred EEeCCcCCCeeEhhhCcCccCCCCCCCc
Confidence 556654 58888877 57888653
No 195
>PLN00209 ribosomal protein S27; Provisional
Probab=28.32 E-value=28 Score=27.98 Aligned_cols=27 Identities=22% Similarity=0.791 Sum_probs=18.4
Q ss_pred ccccccc---ccccccccccccccCccccc
Q psy4518 63 RCPNCSR---SFNFAKRQHHCRLCGCIMCH 89 (376)
Q Consensus 63 ~C~~C~~---~F~~~~RrHHCR~CG~vvC~ 89 (376)
.|+.|.. -|+-...-.-|-.||.++|.
T Consensus 38 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 67 (86)
T PLN00209 38 KCQGCFNITTVFSHSQTVVVCGSCQTVLCQ 67 (86)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 6999987 45555556667777777663
No 196
>COG1773 Rubredoxin [Energy production and conversion]
Probab=28.30 E-value=23 Score=26.10 Aligned_cols=12 Identities=25% Similarity=1.043 Sum_probs=10.5
Q ss_pred ccccccccCccc
Q psy4518 76 RQHHCRLCGCIM 87 (376)
Q Consensus 76 RrHHCR~CG~vv 87 (376)
+++.|+.||-|+
T Consensus 2 ~~~~C~~CG~vY 13 (55)
T COG1773 2 KRWRCSVCGYVY 13 (55)
T ss_pred CceEecCCceEe
Confidence 478999999987
No 197
>cd04476 RPA1_DBD_C RPA1_DBD_C: A subfamily of OB folds corresponding to the C-terminal OB fold, the ssDNA-binding domain (DBD)-C, of human RPA1 (also called RPA70). RPA1 is the large subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). In addition to DBD-C, RPA1 contains three other OB folds: DBD-A, DBD-B, and RPA1N. The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B. RPA1 DBD-C is involved in DNA binding and trimerization. It contains two structural insertions not found to date in other OB-folds: a zinc ribbon and a three-helix bundle. RPA1 DBD-C also contains a Cys4-type zinc-binding motif, which plays a role in the ssDNA binding fun
Probab=28.04 E-value=29 Score=30.57 Aligned_cols=28 Identities=21% Similarity=0.529 Sum_probs=21.5
Q ss_pred CCCccccccccccccc-ccccccccCccc
Q psy4518 60 DVPRCPNCSRSFNFAK-RQHHCRLCGCIM 87 (376)
Q Consensus 60 ~v~~C~~C~~~F~~~~-RrHHCR~CG~vv 87 (376)
-...||.|.++..... ...+|..||..+
T Consensus 33 ~Y~aC~~C~kkv~~~~~~~~~C~~C~~~~ 61 (166)
T cd04476 33 WYPACPGCNKKVVEEGNGTYRCEKCNKSV 61 (166)
T ss_pred EEccccccCcccEeCCCCcEECCCCCCcC
Confidence 3567999999876444 778888888765
No 198
>PRK09720 cybC cytochrome b562; Provisional
Probab=28.03 E-value=98 Score=25.63 Aligned_cols=43 Identities=21% Similarity=0.258 Sum_probs=34.0
Q ss_pred cccccchhHHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHH
Q psy4518 315 SVSSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFR 361 (376)
Q Consensus 315 ~~e~~~~L~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~ 361 (376)
-..-+|.|+.||.-...+. .+|++||..+....|.++..+|..
T Consensus 55 y~~Gld~lI~qID~A~~La----~~GkL~eAK~~a~~l~~~Rn~yHk 97 (100)
T PRK09720 55 FRHGFDILVGQIDDALKLA----NEGKVKEAQAAAEQLKTTRNSYHK 97 (100)
T ss_pred HHHHHHHHHHHHHHHHHHH----HcCCHHHHHHHHHHHHHHHHHHHH
Confidence 3445778888876655544 479999999999999999999864
No 199
>PRK12495 hypothetical protein; Provisional
Probab=27.77 E-value=68 Score=30.27 Aligned_cols=25 Identities=24% Similarity=0.546 Sum_probs=16.1
Q ss_pred CcccccccccccccccccccccCccccccccCC
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
.+|+.|+.+.- ++=|.++|..|-..
T Consensus 43 ~hC~~CG~PIp--------a~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 43 AHCDECGDPIF--------RHDGQEFCPTCQQP 67 (226)
T ss_pred hhcccccCccc--------CCCCeeECCCCCCc
Confidence 37999998642 34566666666554
No 200
>KOG3896|consensus
Probab=27.62 E-value=27 Score=34.99 Aligned_cols=29 Identities=28% Similarity=0.654 Sum_probs=23.9
Q ss_pred cccccccccccccccccccCccccccccCC
Q psy4518 65 PNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 65 ~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
..|+ .|.-+.--.-||.|..+-|..|+.+
T Consensus 13 c~cg-~~~pl~~L~FCRyC~klrc~~Cv~h 41 (449)
T KOG3896|consen 13 CTCG-KFRPLPDLVFCRYCFKLRCDDCVLH 41 (449)
T ss_pred eecc-ccccccceeeeeccccccccccccc
Confidence 4566 5777778889999999999999875
No 201
>PTZ00083 40S ribosomal protein S27; Provisional
Probab=27.52 E-value=29 Score=27.78 Aligned_cols=27 Identities=33% Similarity=0.915 Sum_probs=18.2
Q ss_pred ccccccc---ccccccccccccccCccccc
Q psy4518 63 RCPNCSR---SFNFAKRQHHCRLCGCIMCH 89 (376)
Q Consensus 63 ~C~~C~~---~F~~~~RrHHCR~CG~vvC~ 89 (376)
.|+.|.. -|+-...-.-|-.||.++|.
T Consensus 37 kCp~C~n~q~VFShA~t~V~C~~Cg~~L~~ 66 (85)
T PTZ00083 37 KCPGCSQITTVFSHAQTVVLCGGCSSQLCQ 66 (85)
T ss_pred ECCCCCCeeEEEecCceEEEccccCCEeec
Confidence 6999987 45555556667777777663
No 202
>PF13465 zf-H2C2_2: Zinc-finger double domain; PDB: 2EN7_A 1TF6_A 1TF3_A 2ELT_A 2EOS_A 2EN2_A 2DMD_A 2WBS_A 2WBU_A 2EM5_A ....
Probab=27.43 E-value=22 Score=21.58 Aligned_cols=11 Identities=45% Similarity=1.271 Sum_probs=9.3
Q ss_pred Ccccccccccc
Q psy4518 62 PRCPNCSRSFN 72 (376)
Q Consensus 62 ~~C~~C~~~F~ 72 (376)
-.|+.|++.|.
T Consensus 15 ~~C~~C~k~F~ 25 (26)
T PF13465_consen 15 YKCPYCGKSFS 25 (26)
T ss_dssp EEESSSSEEES
T ss_pred CCCCCCcCeeC
Confidence 47999999985
No 203
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=27.35 E-value=75 Score=28.94 Aligned_cols=25 Identities=32% Similarity=0.837 Sum_probs=16.5
Q ss_pred ccccccccccc---ccccccccccCccc
Q psy4518 63 RCPNCSRSFNF---AKRQHHCRLCGCIM 87 (376)
Q Consensus 63 ~C~~C~~~F~~---~~RrHHCR~CG~vv 87 (376)
.||.|+.+|+| +.--..|..||..+
T Consensus 115 ~C~~~~~r~sfdeA~~~~F~Cp~Cg~~L 142 (176)
T COG1675 115 VCPNCHVKYSFDEAMELGFTCPKCGEDL 142 (176)
T ss_pred eCCCCCCcccHHHHHHhCCCCCCCCchh
Confidence 69999998875 22335666666654
No 204
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=27.31 E-value=39 Score=37.39 Aligned_cols=35 Identities=17% Similarity=0.447 Sum_probs=27.2
Q ss_pred cCCCcccCCCCCccccccc--ccccccccccccccCc
Q psy4518 51 AIVPWLDGKDVPRCPNCSR--SFNFAKRQHHCRLCGC 85 (376)
Q Consensus 51 ~~~~W~~d~~v~~C~~C~~--~F~~~~RrHHCR~CG~ 85 (376)
.++.|--...++.|+.|+- .|..+.+.+.|..||.
T Consensus 631 ~i~Y~~in~~~~~C~~CG~~Ge~~~~~~~~~CP~CG~ 667 (711)
T PRK09263 631 RVGYLGTNTPIDECYECGFTGEFECTEKGFTCPKCGN 667 (711)
T ss_pred CCCeEEeCCCCcccCCCCCCccccCCCCCCcCcCCCC
Confidence 5888888888999999996 2223556689999996
No 205
>PRK04351 hypothetical protein; Provisional
Probab=27.08 E-value=31 Score=30.48 Aligned_cols=26 Identities=15% Similarity=0.538 Sum_probs=14.3
Q ss_pred Ccccccccccccc----cccccccccCccc
Q psy4518 62 PRCPNCSRSFNFA----KRQHHCRLCGCIM 87 (376)
Q Consensus 62 ~~C~~C~~~F~~~----~RrHHCR~CG~vv 87 (376)
=.|..|+..+.-. .+++.|+.||..+
T Consensus 113 Y~C~~Cg~~~~r~Rr~n~~~yrCg~C~g~L 142 (149)
T PRK04351 113 YECQSCGQQYLRKRRINTKRYRCGKCRGKL 142 (149)
T ss_pred EECCCCCCEeeeeeecCCCcEEeCCCCcEe
Confidence 3677788755322 1345566666543
No 206
>PF11593 Med3: Mediator complex subunit 3 fungal; InterPro: IPR020998 The Mediator complex is a coactivator involved in the regulated transcription of nearly all RNA polymerase II-dependent genes. Mediator functions as a bridge to convey information from gene-specific regulatory proteins to the basal RNA polymerase II transcription machinery. The Mediator complex, having a compact conformation in its free form, is recruited to promoters by direct interactions with regulatory proteins and serves for the assembly of a functional preinitiation complex with RNA polymerase II and the general transcription factors. On recruitment the Mediator complex unfolds to an extended conformation and partially surrounds RNA polymerase II, specifically interacting with the unphosphorylated form of the C-terminal domain (CTD) of RNA polymerase II. The Mediator complex dissociates from the RNA polymerase II holoenzyme and stays at the promoter when transcriptional elongation begins. The Mediator complex is composed of at least 31 subunits: MED1, MED4, MED6, MED7, MED8, MED9, MED10, MED11, MED12, MED13, MED13L, MED14, MED15, MED16, MED17, MED18, MED19, MED20, MED21, MED22, MED23, MED24, MED25, MED26, MED27, MED29, MED30, MED31, CCNC, CDK8 and CDC2L6/CDK11. The subunits form at least three structurally distinct submodules. The head and the middle modules interact directly with RNA polymerase II, whereas the elongated tail module interacts with gene-specific regulatory proteins. Mediator containing the CDK8 module is less active than Mediator lacking this module in supporting transcriptional activation. The head module contains: MED6, MED8, MED11, SRB4/MED17, SRB5/MED18, ROX3/MED19, SRB2/MED20 and SRB6/MED22. The middle module contains: MED1, MED4, NUT1/MED5, MED7, CSE2/MED9, NUT2/MED10, SRB7/MED21 and SOH1/MED31. CSE2/MED9 interacts directly with MED4. The tail module contains: MED2, PGD1/MED3, RGR1/MED14, GAL11/MED15 and SIN4/MED16. The CDK8 module contains: MED12, MED13, CCNC and CDK8. Individual preparations of the Mediator complex lacking one or more distinct subunits have been variously termed ARC, CRSP, DRIP, PC2, SMCC and TRAP. This entry represents the subunit Med3, which is a physical target for Cyc8-Tup1, a yeast transcriptional co-repressor []. ; GO: 0001104 RNA polymerase II transcription cofactor activity, 0006357 regulation of transcription from RNA polymerase II promoter, 0016592 mediator complex
Probab=27.03 E-value=1.8e+02 Score=29.58 Aligned_cols=47 Identities=13% Similarity=0.229 Sum_probs=32.3
Q ss_pred HHHHHHhhcCCCccccHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q psy4518 164 YLEMIDSLLAGETMYYASDAQALRVKLVRLAENIDTISNKVTTLSSA 210 (376)
Q Consensus 164 f~~~l~sL~~g~s~~~l~~a~~lR~kL~~~f~~~d~~skri~~l~~~ 210 (376)
|-.++..|.........+.=.-+|.||++++..+..+|+-+..|.+-
T Consensus 48 Fi~tma~Ie~~~~~s~qeKFl~IR~KlleL~~~lQ~lS~df~~LqPL 94 (379)
T PF11593_consen 48 FIQTMANIEEMNNKSPQEKFLLIRSKLLELYNKLQELSSDFQKLQPL 94 (379)
T ss_pred HHHHHHHhhcccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhchH
Confidence 33444455332222234445569999999999999999999998763
No 207
>KOG1829|consensus
Probab=26.90 E-value=22 Score=38.24 Aligned_cols=32 Identities=28% Similarity=0.757 Sum_probs=28.2
Q ss_pred cccccccccc--cccccccccccCccccccccCC
Q psy4518 63 RCPNCSRSFN--FAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 63 ~C~~C~~~F~--~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
.|-.|+..++ +..+-.-|+.+|.-||+.|-..
T Consensus 342 ~CAgC~~~i~~~~~~~~R~C~y~G~y~C~~Ch~~ 375 (580)
T KOG1829|consen 342 RCAGCGHTIGPDLEQRPRLCRYLGKYFCDCCHQN 375 (580)
T ss_pred eecccCCCcccccccchhHhhhhhhhhCchhccc
Confidence 7999999998 5667778999999999999764
No 208
>PHA00733 hypothetical protein
Probab=26.86 E-value=35 Score=29.22 Aligned_cols=27 Identities=26% Similarity=0.621 Sum_probs=17.0
Q ss_pred Ccccccccccccc----------cccccccccCcccc
Q psy4518 62 PRCPNCSRSFNFA----------KRQHHCRLCGCIMC 88 (376)
Q Consensus 62 ~~C~~C~~~F~~~----------~RrHHCR~CG~vvC 88 (376)
-.|+.|++.|.-. ...+.|..||+.|.
T Consensus 74 y~C~~Cgk~Fss~s~L~~H~r~h~~~~~C~~CgK~F~ 110 (128)
T PHA00733 74 YVCPLCLMPFSSSVSLKQHIRYTEHSKVCPVCGKEFR 110 (128)
T ss_pred ccCCCCCCcCCCHHHHHHHHhcCCcCccCCCCCCccC
Confidence 3799999998721 12346666666554
No 209
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=26.61 E-value=28 Score=29.54 Aligned_cols=27 Identities=22% Similarity=0.619 Sum_probs=19.6
Q ss_pred CCCcccccccccccccccccccccCcc
Q psy4518 60 DVPRCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 60 ~v~~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
.+-.|..|+..|..-.-.+-|..||..
T Consensus 69 ~~~~C~~C~~~~~~e~~~~~CP~C~s~ 95 (115)
T COG0375 69 AECWCLDCGQEVELEELDYRCPKCGSI 95 (115)
T ss_pred cEEEeccCCCeecchhheeECCCCCCC
Confidence 345799999999855444458888865
No 210
>PRK08271 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=26.54 E-value=41 Score=36.59 Aligned_cols=36 Identities=14% Similarity=0.415 Sum_probs=27.4
Q ss_pred ccccCCCcccCCCCCcccccccccccccccccccccCc
Q psy4518 48 HEQAIVPWLDGKDVPRCPNCSRSFNFAKRQHHCRLCGC 85 (376)
Q Consensus 48 ~Eq~~~~W~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~ 85 (376)
.+..++.|--...++.|+.|+.. ...-.++|..||.
T Consensus 553 ~~~~i~Yf~in~~~~iC~~CG~~--~~g~~~~CP~CGs 588 (623)
T PRK08271 553 AKTGCNYFAFNVKITICNDCHHI--DKRTGKRCPICGS 588 (623)
T ss_pred HHcCCceEEeCCCCccCCCCCCc--CCCCCcCCcCCCC
Confidence 44457889888889999999953 2334688999997
No 211
>KOG2932|consensus
Probab=26.52 E-value=38 Score=33.54 Aligned_cols=35 Identities=23% Similarity=0.513 Sum_probs=25.7
Q ss_pred ccCCCCCcccccccccccccccccccccCccccccccC
Q psy4518 56 LDGKDVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSF 93 (376)
Q Consensus 56 ~~d~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~ 93 (376)
+....|+.|-.|+.+.-+.-|.-- |..|||-+|-.
T Consensus 85 ~l~p~VHfCd~Cd~PI~IYGRmIP---CkHvFCl~CAr 119 (389)
T KOG2932|consen 85 QLGPRVHFCDRCDFPIAIYGRMIP---CKHVFCLECAR 119 (389)
T ss_pred ccCcceEeecccCCcceeeecccc---cchhhhhhhhh
Confidence 344458899999988877777655 45689988843
No 212
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=26.49 E-value=31 Score=29.41 Aligned_cols=23 Identities=22% Similarity=0.587 Sum_probs=14.9
Q ss_pred Ccccccccccccc-cc----c--ccccccCc
Q psy4518 62 PRCPNCSRSFNFA-KR----Q--HHCRLCGC 85 (376)
Q Consensus 62 ~~C~~C~~~F~~~-~R----r--HHCR~CG~ 85 (376)
-.| .|+..|++. .. . ..|..||.
T Consensus 71 ~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs 100 (124)
T PRK00762 71 IEC-ECGYEGVVDEDEIDHYAAVIECPVCGN 100 (124)
T ss_pred EEe-eCcCcccccccchhccccCCcCcCCCC
Confidence 489 999998753 11 1 24777774
No 213
>PF10013 DUF2256: Uncharacterized protein conserved in bacteria (DUF2256); InterPro: IPR017136 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function.
Probab=26.20 E-value=21 Score=24.83 Aligned_cols=15 Identities=40% Similarity=1.050 Sum_probs=12.1
Q ss_pred Ccccccccccccccc
Q psy4518 62 PRCPNCSRSFNFAKR 76 (376)
Q Consensus 62 ~~C~~C~~~F~~~~R 76 (376)
..|+.|+.+|++..+
T Consensus 9 K~C~~C~rpf~WRKK 23 (42)
T PF10013_consen 9 KICPVCGRPFTWRKK 23 (42)
T ss_pred CcCcccCCcchHHHH
Confidence 479999999987543
No 214
>COG0498 ThrC Threonine synthase [Amino acid transport and metabolism]
Probab=26.17 E-value=27 Score=36.03 Aligned_cols=26 Identities=38% Similarity=0.756 Sum_probs=22.7
Q ss_pred CcccccccccccccccccccccCccc
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCIM 87 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~vv 87 (376)
..|..|+..|.-....++|+.||..+
T Consensus 6 ~rc~~cg~~f~~a~~~~~c~~cGl~l 31 (411)
T COG0498 6 LRCLKCGREFSQALLQGLCPDCGLFL 31 (411)
T ss_pred eecCCCCcchhhHHhhCcCCcCCccc
Confidence 57999999999777799999999865
No 215
>KOG2177|consensus
Probab=25.82 E-value=19 Score=33.26 Aligned_cols=29 Identities=28% Similarity=0.576 Sum_probs=23.0
Q ss_pred CCcccccccccccccccccccccCccccccccC
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSF 93 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~ 93 (376)
.-.|++|...|.-- ..-.||..||..|..
T Consensus 13 ~~~C~iC~~~~~~p----~~l~C~H~~c~~C~~ 41 (386)
T KOG2177|consen 13 ELTCPICLEYFREP----VLLPCGHNFCRACLT 41 (386)
T ss_pred cccChhhHHHhhcC----ccccccchHhHHHHH
Confidence 34899999988755 666799999988864
No 216
>PRK01343 zinc-binding protein; Provisional
Probab=25.80 E-value=36 Score=25.24 Aligned_cols=13 Identities=23% Similarity=0.710 Sum_probs=10.4
Q ss_pred CCccccccccccc
Q psy4518 61 VPRCPNCSRSFNF 73 (376)
Q Consensus 61 v~~C~~C~~~F~~ 73 (376)
...||+|+++|..
T Consensus 9 ~~~CP~C~k~~~~ 21 (57)
T PRK01343 9 TRPCPECGKPSTR 21 (57)
T ss_pred CCcCCCCCCcCcC
Confidence 3589999999864
No 217
>PF13894 zf-C2H2_4: C2H2-type zinc finger; PDB: 2ELX_A 2EPP_A 2DLK_A 1X6H_A 2EOU_A 2EMB_A 2GQJ_A 2CSH_A 2WBT_B 2ELM_A ....
Probab=25.39 E-value=28 Score=19.54 Aligned_cols=10 Identities=50% Similarity=1.394 Sum_probs=6.1
Q ss_pred cccccccccc
Q psy4518 63 RCPNCSRSFN 72 (376)
Q Consensus 63 ~C~~C~~~F~ 72 (376)
.|+.|+..|.
T Consensus 2 ~C~~C~~~~~ 11 (24)
T PF13894_consen 2 QCPICGKSFR 11 (24)
T ss_dssp E-SSTS-EES
T ss_pred CCcCCCCcCC
Confidence 4888888876
No 218
>COG1779 C4-type Zn-finger protein [General function prediction only]
Probab=25.29 E-value=32 Score=31.86 Aligned_cols=31 Identities=19% Similarity=0.605 Sum_probs=22.1
Q ss_pred cccccccccccccccccccccCcc-----ccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCI-----MCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~v-----vC~~CS~ 93 (376)
.||.|+..|-...+.+.=.+-|.| +|..|.-
T Consensus 16 ~CPvCg~~l~~~~~~~~IPyFG~V~i~t~~C~~CgY 51 (201)
T COG1779 16 DCPVCGGTLKAHMYLYDIPYFGEVLISTGVCERCGY 51 (201)
T ss_pred cCCcccceeeEEEeeecCCccceEEEEEEEccccCC
Confidence 699999877766666666666766 5666643
No 219
>PLN02195 cellulose synthase A
Probab=25.20 E-value=32 Score=39.07 Aligned_cols=22 Identities=32% Similarity=0.868 Sum_probs=0.0
Q ss_pred ccccCc-----------cccccccCCcccccccccccCCCcCCCCCCCcccccchHH
Q psy4518 80 CRLCGC-----------IMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLR 125 (376)
Q Consensus 80 CR~CG~-----------vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~ 125 (376)
|..||. |-|+.| ..-||+.||.
T Consensus 9 c~~cgd~~~~~~~g~~fvaC~eC------------------------~~pvCrpCye 41 (977)
T PLN02195 9 CATCGEEVGVDSNGEAFVACHEC------------------------SYPLCKACLE 41 (977)
T ss_pred ceecccccCcCCCCCeEEEeccC------------------------CCccccchhh
No 220
>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=24.88 E-value=32 Score=21.98 Aligned_cols=22 Identities=27% Similarity=0.819 Sum_probs=15.0
Q ss_pred cccccccccccccccccccccCccccc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCH 89 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~ 89 (376)
.|.+|+. ..++-|..||..+|+
T Consensus 4 ~C~vC~~-----~~kY~Cp~C~~~~CS 25 (30)
T PF04438_consen 4 LCSVCGN-----PAKYRCPRCGARYCS 25 (30)
T ss_dssp EETSSSS-----EESEE-TTT--EESS
T ss_pred CCccCcC-----CCEEECCCcCCceeC
Confidence 5788876 467889999999886
No 221
>COG1998 RPS31 Ribosomal protein S27AE [Translation, ribosomal structure and biogenesis]
Probab=24.83 E-value=38 Score=24.40 Aligned_cols=24 Identities=33% Similarity=0.744 Sum_probs=14.8
Q ss_pred Cccccccc-ccc-cccccccccccCc
Q psy4518 62 PRCPNCSR-SFN-FAKRQHHCRLCGC 85 (376)
Q Consensus 62 ~~C~~C~~-~F~-~~~RrHHCR~CG~ 85 (376)
..||.|+. .|= .-.-|.||-.||.
T Consensus 20 ~~CPrCG~gvfmA~H~dR~~CGkCgy 45 (51)
T COG1998 20 RFCPRCGPGVFMADHKDRWACGKCGY 45 (51)
T ss_pred ccCCCCCCcchhhhcCceeEeccccc
Confidence 46888885 342 2334677777775
No 222
>PF05615 THOC7: Tho complex subunit 7; InterPro: IPR008501 The Tho complex (THOC) is involved in transcription elongation and mRNA export from the nucleus []. This entry represents the subunit THOC7, which is found in higher eukaryotes, and the non-homologous subunit Mft1p found in yeast. The funtions of these subunits are unknown, and it is not known if these subunits are functionally equivalent.
Probab=24.82 E-value=2.5e+02 Score=23.92 Aligned_cols=19 Identities=16% Similarity=0.326 Sum_probs=15.0
Q ss_pred HHHHHHHHHHHHHHhcCCC
Q psy4518 191 VRLAENIDTISNKVTTLSS 209 (376)
Q Consensus 191 ~~~f~~~d~~skri~~l~~ 209 (376)
...=.+||.+++.|...|+
T Consensus 111 r~~k~eyd~La~~I~~~p~ 129 (139)
T PF05615_consen 111 RQNKEEYDALAKKINSQPT 129 (139)
T ss_pred HHHHHHHHHHHHHHhcCCC
Confidence 3344599999999999884
No 223
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=24.67 E-value=33 Score=29.99 Aligned_cols=24 Identities=25% Similarity=0.634 Sum_probs=16.9
Q ss_pred cccccccccccccc-----cccccccCcc
Q psy4518 63 RCPNCSRSFNFAKR-----QHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~~~R-----rHHCR~CG~v 86 (376)
.|+.|+.+-+.+.+ -.+|..||..
T Consensus 104 lC~~C~spdT~l~k~~r~~~l~C~ACGa~ 132 (138)
T PRK03988 104 ICPECGSPDTKLIKEGRIWVLKCEACGAE 132 (138)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCC
Confidence 79999999884443 3466666654
No 224
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=24.61 E-value=36 Score=31.50 Aligned_cols=18 Identities=39% Similarity=0.964 Sum_probs=11.0
Q ss_pred ccccccccCcc----ccccccC
Q psy4518 76 RQHHCRLCGCI----MCHDCSF 93 (376)
Q Consensus 76 RrHHCR~CG~v----vC~~CS~ 93 (376)
.-+||..||.+ +|.-|+.
T Consensus 53 ~i~~C~~C~~~te~d~C~ICsd 74 (198)
T COG0353 53 NIKHCSVCGNLTESDPCDICSD 74 (198)
T ss_pred cCccccccCCcCCCCcCcCcCC
Confidence 34566666655 6777765
No 225
>COG4338 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=24.50 E-value=12 Score=26.73 Aligned_cols=14 Identities=43% Similarity=1.144 Sum_probs=12.0
Q ss_pred cccccccccccccc
Q psy4518 63 RCPNCSRSFNFAKR 76 (376)
Q Consensus 63 ~C~~C~~~F~~~~R 76 (376)
.||.|+.+|++..+
T Consensus 14 ICpvCqRPFsWRkK 27 (54)
T COG4338 14 ICPVCQRPFSWRKK 27 (54)
T ss_pred hhhhhcCchHHHHH
Confidence 79999999987654
No 226
>KOG2824|consensus
Probab=24.50 E-value=51 Score=32.11 Aligned_cols=9 Identities=56% Similarity=0.958 Sum_probs=4.9
Q ss_pred HHHHhccCC
Q psy4518 31 LDKLLTNMP 39 (376)
Q Consensus 31 L~kLl~~~~ 39 (376)
|.+||..+|
T Consensus 217 L~~lL~~~p 225 (281)
T KOG2824|consen 217 LGKLLKGIP 225 (281)
T ss_pred HHHHHhcCC
Confidence 555555554
No 227
>PF02945 Endonuclease_7: Recombination endonuclease VII; InterPro: IPR004211 This family of proteins which includes Bacteriophage T4 endonuclease VII, Mycobacteriophage D29 gene 59, and other as yet uncharacterised proteins. The T4 endonuclease VII (Endo VII) recognises a broad spectrum of DNA substrates ranging from branched DNAs to single base mismatches. The structure of this enzyme has been resolved and it was found that the monomers form an elongated, intertwined molecular dimer that exibits extreme domain swapping. Two pairs of antiparallel helices which form a novel 'four-helix cross' motif are the major dimerisation elements [].; PDB: 3GOX_A 3FC3_A 1EN7_B 1E7L_B 2QNF_A 2QNC_A 1E7D_A.
Probab=24.43 E-value=25 Score=27.89 Aligned_cols=24 Identities=25% Similarity=0.509 Sum_probs=11.8
Q ss_pred cccccccccccccc---cccccccCcc
Q psy4518 63 RCPNCSRSFNFAKR---QHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~~~R---rHHCR~CG~v 86 (376)
.|++|+.++....+ --||-.||.|
T Consensus 24 ~C~iC~~~~~~~~~~~~vDHdH~tG~v 50 (81)
T PF02945_consen 24 RCAICGKPLPGESRKLVVDHDHKTGRV 50 (81)
T ss_dssp E-TTT-SEEETTCGGCEEEE-TTTTBE
T ss_pred cCcCCCCCcccCCCcceecCCCCCCCc
Confidence 79999985543333 2355555553
No 228
>COG1592 Rubrerythrin [Energy production and conversion]
Probab=24.27 E-value=1.1e+02 Score=27.59 Aligned_cols=21 Identities=29% Similarity=0.831 Sum_probs=10.0
Q ss_pred cccccccccccccccccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCG 84 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG 84 (376)
.|+.||-.+-- -=--.|..||
T Consensus 136 vC~vCGy~~~g-e~P~~CPiCg 156 (166)
T COG1592 136 VCPVCGYTHEG-EAPEVCPICG 156 (166)
T ss_pred EcCCCCCcccC-CCCCcCCCCC
Confidence 47777643322 2333455554
No 229
>PF03833 PolC_DP2: DNA polymerase II large subunit DP2; InterPro: IPR016033 DP2 is the large subunit of a two-subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit. This entry represents the N-terminal ~950 residue component of DP2.; GO: 0003887 DNA-directed DNA polymerase activity; PDB: 3O59_X.
Probab=24.17 E-value=26 Score=39.21 Aligned_cols=57 Identities=12% Similarity=0.117 Sum_probs=0.0
Q ss_pred HHHHHHHHHhcCCCCCC--CccCCCCcchhhHHHHHHHH--------HHHHHHHHHcCCCCCCCCCh
Q psy4518 196 NIDTISNKVTTLSSASG--AQQASDSPMTMSQRLHKSIR--------QASTNFIRTHLLTLPNVPSD 252 (376)
Q Consensus 196 ~~d~~skri~~l~~~~~--~~~~~~~~~~~q~rlq~~I~--------~~a~~FLqe~ml~LksLP~~ 252 (376)
.++...-+++.|+...+ +.+...+..-=+++.|-=|- ...+.|+-+-|-.+=.||.-
T Consensus 783 EIgvsvEkLrELGY~~Di~G~pL~~~dQivELk~QDIils~~aaeyllkva~FIDdLLek~Ygle~f 849 (900)
T PF03833_consen 783 EIGVSVEKLRELGYTHDIYGKPLESDDQIVELKVQDIILSEDAAEYLLKVAKFIDDLLEKYYGLEPF 849 (900)
T ss_dssp -------------------------------------------------------------------
T ss_pred hcCCCHHHHHHhCccccccCCccCCccceeEeehhcEecchhHHHHHHHHHHHHHHHHHHHhCCCcc
Confidence 45666677777765321 00000000001456664442 23456676666666666654
No 230
>COG0333 RpmF Ribosomal protein L32 [Translation, ribosomal structure and biogenesis]
Probab=23.85 E-value=41 Score=24.94 Aligned_cols=21 Identities=33% Similarity=0.986 Sum_probs=14.3
Q ss_pred CCcccccccccccccccccccccC
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCG 84 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG 84 (376)
+..|+.|+. +..+-|-|..||
T Consensus 27 ~~~c~~cG~---~~l~Hrvc~~cg 47 (57)
T COG0333 27 LSVCPNCGE---YKLPHRVCLKCG 47 (57)
T ss_pred ceeccCCCC---cccCceEcCCCC
Confidence 568999986 345555677776
No 231
>KOG4317|consensus
Probab=23.84 E-value=43 Score=33.22 Aligned_cols=27 Identities=22% Similarity=0.597 Sum_probs=22.4
Q ss_pred CCCCcccccccccccccccccccccCccccc
Q psy4518 59 KDVPRCPNCSRSFNFAKRQHHCRLCGCIMCH 89 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~ 89 (376)
+..-.|++|++.| |++.|..|.-.+|+
T Consensus 5 s~~~~C~ic~vq~----~~YtCPRCn~~YCs 31 (383)
T KOG4317|consen 5 SSFLACGICGVQK----REYTCPRCNLLYCS 31 (383)
T ss_pred Cceeecccccccc----ccccCCCCCcccee
Confidence 4455799999876 56999999999996
No 232
>PF14471 DUF4428: Domain of unknown function (DUF4428)
Probab=23.77 E-value=28 Score=25.04 Aligned_cols=10 Identities=20% Similarity=-0.051 Sum_probs=7.7
Q ss_pred ccccchHHHH
Q psy4518 118 ANSDLNLRLL 127 (376)
Q Consensus 118 RvC~~C~~~l 127 (376)
-||.+|+..+
T Consensus 21 ~iC~~C~~Kl 30 (51)
T PF14471_consen 21 YICKDCLKKL 30 (51)
T ss_pred cchHHHHHHh
Confidence 4888888776
No 233
>PRK08402 replication factor A; Reviewed
Probab=23.56 E-value=41 Score=34.00 Aligned_cols=30 Identities=23% Similarity=0.382 Sum_probs=22.5
Q ss_pred CCCCCcccccccccc--cccccccccccCccc
Q psy4518 58 GKDVPRCPNCSRSFN--FAKRQHHCRLCGCIM 87 (376)
Q Consensus 58 d~~v~~C~~C~~~F~--~~~RrHHCR~CG~vv 87 (376)
....+.||.|++++. -......|..||.+-
T Consensus 209 ~~~y~aCp~CnKkv~~~~~~~~~~Ce~~~~v~ 240 (355)
T PRK08402 209 VLVYDACPECRRKVDYDPATDTWICPEHGEVE 240 (355)
T ss_pred CeeEecCCCCCeEEEEecCCCCEeCCCCCCcC
Confidence 345689999999885 245678899998753
No 234
>PRK06260 threonine synthase; Validated
Probab=23.34 E-value=41 Score=34.18 Aligned_cols=24 Identities=21% Similarity=0.717 Sum_probs=19.3
Q ss_pred cccccccccccccccccccccCcc
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
.|..|+..|......+.|..||..
T Consensus 5 ~C~~cg~~~~~~~~~~~Cp~cg~~ 28 (397)
T PRK06260 5 KCIECGKEYDPDEIIYTCPECGGL 28 (397)
T ss_pred EECCCCCCCCCCCccccCCCCCCe
Confidence 699999999866666779888865
No 235
>KOG0153|consensus
Probab=23.22 E-value=18 Score=36.18 Aligned_cols=20 Identities=20% Similarity=0.391 Sum_probs=14.6
Q ss_pred CCCCCccccccccccccccc
Q psy4518 58 GKDVPRCPNCSRSFNFAKRQ 77 (376)
Q Consensus 58 d~~v~~C~~C~~~F~~~~Rr 77 (376)
+..-..|-+|..+|++++.+
T Consensus 38 ~~~gkECKICtrPfT~Frw~ 57 (377)
T KOG0153|consen 38 EPYGKECKICTRPFTIFRWC 57 (377)
T ss_pred cccCCccceecCcceEEEec
Confidence 44456899999999977543
No 236
>TIGR03655 anti_R_Lar restriction alleviation protein, Lar family. Restriction alleviation proteins provide a countermeasure to host cell restriction enzyme defense against foreign DNA such as phage or plasmids. This family consists of homologs to the phage antirestriction protein Lar, and most members belong to phage genomes or prophage regions of bacterial genomes.
Probab=23.21 E-value=54 Score=23.48 Aligned_cols=8 Identities=38% Similarity=1.128 Sum_probs=6.1
Q ss_pred cccccccc
Q psy4518 63 RCPNCSRS 70 (376)
Q Consensus 63 ~C~~C~~~ 70 (376)
-||+|+..
T Consensus 3 PCPfCGg~ 10 (53)
T TIGR03655 3 PCPFCGGA 10 (53)
T ss_pred CCCCCCCc
Confidence 58999873
No 237
>PHA02926 zinc finger-like protein; Provisional
Probab=22.85 E-value=27 Score=33.03 Aligned_cols=53 Identities=21% Similarity=0.356 Sum_probs=30.2
Q ss_pred Ccccccccccccccccccc------cccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHH
Q psy4518 62 PRCPNCSRSFNFAKRQHHC------RLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLL 127 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHC------R~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l 127 (376)
..|++|-...- -.+.-.+ ..||.+||-.|-..+.-... .....+.|+.|....
T Consensus 171 ~eCgICmE~I~-eK~~~~eRrFGIL~~CnHsFCl~CIr~Wr~~r~------------~~~~~rsCPiCR~~f 229 (242)
T PHA02926 171 KECGICYEVVY-SKRLENDRYFGLLDSCNHIFCITCINIWHRTRR------------ETGASDNCPICRTRF 229 (242)
T ss_pred CCCccCccccc-cccccccccccccCCCCchHHHHHHHHHHHhcc------------ccCcCCcCCCCccee
Confidence 37999975321 0011222 48999999999776532110 013557788886543
No 238
>PF09845 DUF2072: Zn-ribbon containing protein (DUF2072); InterPro: IPR018645 This archaeal Zinc-ribbon containing proteins have no known function.
Probab=22.55 E-value=37 Score=29.43 Aligned_cols=24 Identities=29% Similarity=0.707 Sum_probs=12.4
Q ss_pred Cccccccccccc--ccccccccccCc
Q psy4518 62 PRCPNCSRSFNF--AKRQHHCRLCGC 85 (376)
Q Consensus 62 ~~C~~C~~~F~~--~~RrHHCR~CG~ 85 (376)
+.|..|++.|-- ..=.-.|..||.
T Consensus 2 H~Ct~Cg~~f~dgs~eil~GCP~CGg 27 (131)
T PF09845_consen 2 HQCTKCGRVFEDGSKEILSGCPECGG 27 (131)
T ss_pred cccCcCCCCcCCCcHHHHccCcccCC
Confidence 456667766641 112345666653
No 239
>PF05458 Siva: Cd27 binding protein (Siva); InterPro: IPR022773 Siva binds to the CD27 cytoplasmic tail. It has a DD homology region, a box-B-like ring finger, and a zinc finger-like domain. Overexpression of Siva in various cell lines induces apoptosis, suggesting an important role for Siva in the CD27-transduced apoptotic pathway []. Siva-1 binds to and inhibits BCL-X(L)-mediated protection against UV radiation-induced apoptosis. Indeed, the unique amphipathic helical region (SAH) present in Siva-1 is required for its binding to BCL-X(L) and sensitising cells to UV radiation. Natural complexes of Siva-1/BCL-X(L) are detected in HUT78 and murine thymocyte, suggesting a potential role for Siva-1 in regulating T cell homeostasis []. This family contains both Siva-1 and the shorter Siva-2 lacking the sequence coded by exon 2. It has been suggested that Siva-2 could regulate the function of Siva-1 [].
Probab=22.48 E-value=30 Score=31.47 Aligned_cols=13 Identities=38% Similarity=1.122 Sum_probs=6.3
Q ss_pred ccccCcccccccc
Q psy4518 80 CRLCGCIMCHDCS 92 (376)
Q Consensus 80 CR~CG~vvC~~CS 92 (376)
|-.||.++|..|+
T Consensus 142 C~~C~~~~Cs~Cs 154 (175)
T PF05458_consen 142 CSSCSEVFCSLCS 154 (175)
T ss_pred hhchhhhhhcCcc
Confidence 4444444555554
No 240
>COG4855 Uncharacterized protein conserved in archaea [Function unknown]
Probab=22.44 E-value=32 Score=26.41 Aligned_cols=61 Identities=10% Similarity=0.091 Sum_probs=33.4
Q ss_pred cccccccccccccccccccccCccccccccCCcccccccccccCCCcCCC-----CCCCcccccchHHHHH
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGES-----QLSASANSDLNLRLLE 128 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~-----~~~~vRvC~~C~~~l~ 128 (376)
.|..|...=.-+.----|-.||.-+|.........+.- .++.|++ ...+--+|..|++.+.
T Consensus 9 KCY~C~eeGKDtdAV~iCIVCG~GlC~EHli~eE~p~w-----~G~YP~p~k~~K~~lpRilC~~C~~a~~ 74 (76)
T COG4855 9 KCYDCAEEGKDTDAVGICIVCGMGLCMEHLIREETPMW-----GGGYPFPAKKLKKTLPRILCVECHEAIK 74 (76)
T ss_pred HHHHHHHhCCCcccEEEEEEeCchHHHHHHHhhhcccc-----cCCCCCcchhhhccCCceeeHHHHHHhh
Confidence 45555543223333456778888888765443222211 0233332 2357779999998764
No 241
>KOG1356|consensus
Probab=22.39 E-value=47 Score=37.07 Aligned_cols=107 Identities=16% Similarity=0.176 Sum_probs=53.8
Q ss_pred CCCcccCC--CCCcccccccccccccccccccccCccccccccCCcccccccccccCCCcCCCCCCCcccccchHHHHHH
Q psy4518 52 IVPWLDGK--DVPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLPLNKARQILVEPELGESQLSASANSDLNLRLLES 129 (376)
Q Consensus 52 ~~~W~~d~--~v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~l~~~~~~~~~~~~~~~~~~~vRvC~~C~~~l~~ 129 (376)
.+.|.... ...-|..|.+. +++=.--|+.||..||-.|...+.+.....-. .+. -...-.-.+|..|+..-.-
T Consensus 218 ~~a~k~a~~g~~~mC~~C~~t--lfn~hw~C~~C~~~~Cl~C~r~~~p~~~~~e~--a~k-~~~~~~~C~~~q~h~~~~L 292 (889)
T KOG1356|consen 218 KVAWKRAVKGIREMCDRCETT--LFNIHWRCPRCGFGVCLDCYRKWYPRLSKEEV--AEK-CEFSWLKCNKGQCHALSEL 292 (889)
T ss_pred ccchhhcccCcchhhhhhccc--ccceeEEccccCCeeeecchhhccccchHhHh--hhh-hhHHHHhcCCccccchhhc
Confidence 34564332 23568889873 33334569999999999998876421111000 000 0000122344444332110
Q ss_pred HHHHhhhcCCCchhHHHHHHHHHHH--HHHHhHHHHHHH
Q psy4518 130 REVLKESRNSRPLICDLYDALMGKK--QEASKLRAMYLE 166 (376)
Q Consensus 130 r~~~~~~~~~~p~i~~~Ye~L~~~~--~~I~~~lP~f~~ 166 (376)
+.-....-..+..+++.+..+. -.|..++|--.+
T Consensus 293 ---m~Tq~i~~~al~~~~~~~h~~r~k~~I~~~cpcl~~ 328 (889)
T KOG1356|consen 293 ---MPTQIIPGSALLDLSDRVHAVREKFGIKAHCPCLKK 328 (889)
T ss_pred ---ccccccchhhhhhHHHHHHHHHHHhhHHhhChhHHh
Confidence 0000011125667888888877 677777775543
No 242
>PF07361 Cytochrom_B562: Cytochrome b562; InterPro: IPR009155 Cytochrome b562 is a haem-containing protein that is expressed in the periplasm of Escherichia coli. In b-type cytochromes, the haem atom is not covalently attached to the polypeptide. Cytochrome b562 has a four-helical bundle structure that is structurally similar to that found in members of the cytochrome c family (IPR002321 from INTERPRO). Cytochrome b562 has a reduction potential of 167 mV, which sets the energy yield possible in metabolism and is also a key determinant of the rate at which redox reactions proceed [].; GO: 0005506 iron ion binding, 0009055 electron carrier activity, 0020037 heme binding, 0042597 periplasmic space; PDB: 4ER9_A 3IQ6_G 2QLA_B 3FOO_A 3M79_C 256B_A 3NMI_F 3HNK_A 3NMK_D 2BC5_A ....
Probab=22.34 E-value=1.5e+02 Score=24.41 Aligned_cols=44 Identities=23% Similarity=0.379 Sum_probs=35.7
Q ss_pred cccccchhHHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHH
Q psy4518 315 SVSSQDPLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRR 362 (376)
Q Consensus 315 ~~e~~~~L~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~~ 362 (376)
-.+.++.|+.|+..++. +-.+|.++|+...-..|.+|..||..-
T Consensus 58 Y~~Gl~~li~~id~a~~----~~~~G~l~~AK~~l~~l~~lR~eyHkk 101 (103)
T PF07361_consen 58 YQEGLDKLIDQIDKAEA----LAEAGKLDEAKAALKKLDDLRKEYHKK 101 (103)
T ss_dssp HHHHHHHHHHHHHHHHH----HHHTTHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHH----HHHCCCHHHHHHHHHHHHHHHHHHhHh
Confidence 45557788888877765 446899999999999999999999753
No 243
>PRK12286 rpmF 50S ribosomal protein L32; Reviewed
Probab=22.13 E-value=49 Score=24.43 Aligned_cols=23 Identities=30% Similarity=0.787 Sum_probs=13.5
Q ss_pred CCCCcccccccccccccccccccccC
Q psy4518 59 KDVPRCPNCSRSFNFAKRQHHCRLCG 84 (376)
Q Consensus 59 ~~v~~C~~C~~~F~~~~RrHHCR~CG 84 (376)
.....|+.|+. +...-|-|..||
T Consensus 25 ~~l~~C~~CG~---~~~~H~vC~~CG 47 (57)
T PRK12286 25 PGLVECPNCGE---PKLPHRVCPSCG 47 (57)
T ss_pred CcceECCCCCC---ccCCeEECCCCC
Confidence 34557999986 233344455555
No 244
>PF08273 Prim_Zn_Ribbon: Zinc-binding domain of primase-helicase; InterPro: IPR013237 This entry is represented by bacteriophage T7 Gp4. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This entry represents a zinc binding domain found in the N-terminal region of the bacteriophage T7 Gp4 and P4 alpha protein. P4 is a multifunctional protein with origin recognition, helicase and primase activities [, , ].; GO: 0003896 DNA primase activity, 0004386 helicase activity, 0008270 zinc ion binding; PDB: 1NUI_B.
Probab=22.12 E-value=42 Score=23.02 Aligned_cols=21 Identities=38% Similarity=0.994 Sum_probs=10.0
Q ss_pred ccccccc--ccc-ccc----cccccccc
Q psy4518 63 RCPNCSR--SFN-FAK----RQHHCRLC 83 (376)
Q Consensus 63 ~C~~C~~--~F~-~~~----RrHHCR~C 83 (376)
-||.|+- .|. +.. ..-+|+.|
T Consensus 5 pCP~CGG~DrFri~~d~~~~G~~~C~~C 32 (40)
T PF08273_consen 5 PCPICGGKDRFRIFDDKDGRGTWICRQC 32 (40)
T ss_dssp --TTTT-TTTEEEETT----S-EEETTT
T ss_pred CCCCCcCccccccCcCcccCCCEECCCC
Confidence 4899987 455 444 33455555
No 245
>KOG2462|consensus
Probab=22.01 E-value=90 Score=30.44 Aligned_cols=27 Identities=30% Similarity=0.944 Sum_probs=20.8
Q ss_pred CCcccccccccc-cc--------------cccccccccCccc
Q psy4518 61 VPRCPNCSRSFN-FA--------------KRQHHCRLCGCIM 87 (376)
Q Consensus 61 v~~C~~C~~~F~-~~--------------~RrHHCR~CG~vv 87 (376)
...|+.|++.++ .. .+-++|..||+++
T Consensus 130 r~~c~eCgk~ysT~snLsrHkQ~H~~~~s~ka~~C~~C~K~Y 171 (279)
T KOG2462|consen 130 RYKCPECGKSYSTSSNLSRHKQTHRSLDSKKAFSCKYCGKVY 171 (279)
T ss_pred ceeccccccccccccccchhhcccccccccccccCCCCCcee
Confidence 457999999887 33 4567889999884
No 246
>PF14584 DUF4446: Protein of unknown function (DUF4446)
Probab=21.96 E-value=67 Score=28.47 Aligned_cols=37 Identities=19% Similarity=0.396 Sum_probs=30.4
Q ss_pred cCchhHHHHHHhHHHHHHHHHHHHhhhhcccccCCCC
Q psy4518 340 HRYNEVASLENHLKELQEEYFRRQQEQQTEVNDSGLV 376 (376)
Q Consensus 340 rrfdEV~~L~~NL~EL~~ei~~~~~~~~~~~~~~~~~ 376 (376)
..++++..+...++++++++..++.....-++.-|+|
T Consensus 50 ~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~kvgvv 86 (151)
T PF14584_consen 50 ELFDQIDELKEELEELEKRIEELEEKLRNCVQKVGVV 86 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhccceEEEE
Confidence 3578889999999999999999998887777766654
No 247
>smart00184 RING Ring finger. E3 ubiquitin-protein ligase activity is intrinsic to the RING domain of c-Cbl and is likely to be a general function of this domain; Various RING fingers exhibit binding activity towards E2 ubiquitin-conjugating enzymes (Ubc' s)
Probab=21.83 E-value=30 Score=21.41 Aligned_cols=26 Identities=27% Similarity=0.784 Sum_probs=15.5
Q ss_pred ccccccccccccccccccccCccccccccC
Q psy4518 64 CPNCSRSFNFAKRQHHCRLCGCIMCHDCSF 93 (376)
Q Consensus 64 C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~ 93 (376)
|++|.... +...-..||.+||..|..
T Consensus 1 C~iC~~~~----~~~~~~~C~H~~c~~C~~ 26 (39)
T smart00184 1 CPICLEEL----KDPVVLPCGHTFCRSCIR 26 (39)
T ss_pred CCcCccCC----CCcEEecCCChHHHHHHH
Confidence 55666552 222234588888888855
No 248
>PF13901 DUF4206: Domain of unknown function (DUF4206)
Probab=21.76 E-value=52 Score=30.37 Aligned_cols=35 Identities=29% Similarity=0.639 Sum_probs=20.6
Q ss_pred cCCCcccCCCCCccccccccccc-ccccccccccCcc
Q psy4518 51 AIVPWLDGKDVPRCPNCSRSFNF-AKRQHHCRLCGCI 86 (376)
Q Consensus 51 ~~~~W~~d~~v~~C~~C~~~F~~-~~RrHHCR~CG~v 86 (376)
.+-||+.+. +..|+.|+.-|.- =.++.+|..|.++
T Consensus 163 ~IfPF~~~~-~~~C~~C~~v~H~~C~~~~~CpkC~R~ 198 (202)
T PF13901_consen 163 IIFPFQIDT-TVRCPKCKSVFHKSCFRKKSCPKCARR 198 (202)
T ss_pred CCCCCCCCC-eeeCCcCccccchhhcCCCCCCCcHhH
Confidence 355777744 5578888877761 1123666666553
No 249
>PF06397 Desulfoferrod_N: Desulfoferrodoxin, N-terminal domain; InterPro: IPR004462 This domain is found as essentially the full length of desulforedoxin, a 37-residue homodimeric non-haem iron protein. It is also found as the N-terminal domain of desulfoferrodoxin (rbo), a homodimeric non-haem iron protein with 2 Fe atoms per monomer in different oxidation states. This domain binds the ferric rather than the ferrous Fe of desulfoferrodoxin. Neelaredoxin, a monomeric blue non-haem iron protein, lacks this domain.; GO: 0005506 iron ion binding; PDB: 1DFX_A 1VZI_B 2JI2_D 1VZH_B 2JI3_C 2JI1_C 1VZG_A 1CFW_A 2LK5_B 1DHG_B ....
Probab=21.72 E-value=33 Score=23.04 Aligned_cols=11 Identities=36% Similarity=0.839 Sum_probs=6.2
Q ss_pred cccccccCccc
Q psy4518 77 QHHCRLCGCIM 87 (376)
Q Consensus 77 rHHCR~CG~vv 87 (376)
-+.|..||.||
T Consensus 6 ~YkC~~CGniV 16 (36)
T PF06397_consen 6 FYKCEHCGNIV 16 (36)
T ss_dssp EEE-TTT--EE
T ss_pred EEEccCCCCEE
Confidence 36799999886
No 250
>PF06476 DUF1090: Protein of unknown function (DUF1090); InterPro: IPR009468 This family consists of several bacterial proteins of unknown function and is known as YqjC in Escherichia coli.
Probab=21.67 E-value=1.9e+02 Score=24.39 Aligned_cols=35 Identities=26% Similarity=0.300 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHH
Q psy4518 323 VQQITNIKQFIKEARMAHRYNEVASLENHLKELQE 357 (376)
Q Consensus 323 ~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ 357 (376)
...+.-|+.-|..|++.|.-.-|.-|+.-|.+++.
T Consensus 23 ~~K~~~Ie~qI~~Ak~~gN~~rv~GLe~AL~~v~~ 57 (115)
T PF06476_consen 23 EAKEQAIEKQIEYAKAHGNQHRVAGLEKALEEVKA 57 (115)
T ss_pred HHHHHHHHHHHHHHHHcCCHHHHHHHHHHHHHHHh
Confidence 56777899999999999999999999999988843
No 251
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=21.66 E-value=42 Score=29.23 Aligned_cols=23 Identities=26% Similarity=0.781 Sum_probs=15.1
Q ss_pred CcccccccccccccccccccccCcc
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCI 86 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~v 86 (376)
..|..|+.-| +--+..|-.||.-
T Consensus 30 ~kC~~CG~v~--~PPr~~Cp~C~~~ 52 (140)
T COG1545 30 TKCKKCGRVY--FPPRAYCPKCGSE 52 (140)
T ss_pred EEcCCCCeEE--cCCcccCCCCCCC
Confidence 4677777654 5566667777664
No 252
>PF14257 DUF4349: Domain of unknown function (DUF4349)
Probab=21.64 E-value=2.4e+02 Score=26.80 Aligned_cols=43 Identities=12% Similarity=0.215 Sum_probs=33.8
Q ss_pred hhHHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHhhh
Q psy4518 321 PLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQEQ 366 (376)
Q Consensus 321 ~L~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~~~~~~ 366 (376)
-|+++..-+.++++ ++...+|+-.++.-|.+++.||+.++...
T Consensus 143 ~l~~~~~rl~~ll~---ka~~~~d~l~ie~~L~~v~~eIe~~~~~~ 185 (262)
T PF14257_consen 143 NLEAEEERLLELLE---KAKTVEDLLEIERELSRVRSEIEQLEGQL 185 (262)
T ss_pred HHHHHHHHHHHHHH---hcCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45555555555555 55599999999999999999999988754
No 253
>KOG4343|consensus
Probab=21.64 E-value=1.6e+02 Score=31.48 Aligned_cols=48 Identities=21% Similarity=0.084 Sum_probs=40.6
Q ss_pred hh-HHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHhhhhc
Q psy4518 321 PL-VQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQEQQT 368 (376)
Q Consensus 321 ~L-~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~~~~~~~~ 368 (376)
+| .+|+.|=-.+-+.+-+-+|=|=+..|++||++|-.|=+.++++++.
T Consensus 279 v~krqQRmIKNResA~~SRkKKKEy~~~Le~rLq~ll~Ene~Lk~ENat 327 (655)
T KOG4343|consen 279 VLKRQQRMIKNRESACQSRKKKKEYMLGLEARLQALLSENEQLKKENAT 327 (655)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHH
Confidence 56 5776666667788888888899999999999999999999999863
No 254
>TIGR00155 pqiA_fam integral membrane protein, PqiA family. This family consists of uncharacterized predicted integral membrane proteins found, so far, only in the Proteobacteria. Of two members in E. coli, one is induced by paraquat and is designated PqiA, paraquat-inducible protein A.
Probab=21.50 E-value=64 Score=33.16 Aligned_cols=28 Identities=14% Similarity=0.512 Sum_probs=19.3
Q ss_pred CCCcccccccccccccccccccccCcccc
Q psy4518 60 DVPRCPNCSRSFNFAKRQHHCRLCGCIMC 88 (376)
Q Consensus 60 ~v~~C~~C~~~F~~~~RrHHCR~CG~vvC 88 (376)
....|+.|+..+. -..+.+|..||...-
T Consensus 214 ~~~~C~~Cd~~~~-~~~~a~CpRC~~~L~ 241 (403)
T TIGR00155 214 KLRSCSACHTTIL-PAQEPVCPRCSTPLY 241 (403)
T ss_pred CCCcCCCCCCccC-CCCCcCCcCCCCccc
Confidence 4556999998553 245677888888764
No 255
>PRK07591 threonine synthase; Validated
Probab=21.45 E-value=47 Score=34.18 Aligned_cols=25 Identities=20% Similarity=0.596 Sum_probs=19.6
Q ss_pred CcccccccccccccccccccccCccc
Q psy4518 62 PRCPNCSRSFNFAKRQHHCRLCGCIM 87 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrHHCR~CG~vv 87 (376)
-.|..|+..|..-.. .-|..||..+
T Consensus 19 l~C~~Cg~~~~~~~~-~~C~~cg~~l 43 (421)
T PRK07591 19 LKCRECGAEYPLGPI-HVCEECFGPL 43 (421)
T ss_pred EEeCCCCCcCCCCCC-ccCCCCCCeE
Confidence 479999999986555 8898888654
No 256
>TIGR03278 methan_mark_10 putative methanogenesis marker protein 10. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The presence of motifs with seven invariant Cys residues in the N-terminal 50 residues, including three instances of CXXC, would be consistent with function as an oxidoreductase with FeS clusters. The exact function is unknown, but likely is linked to methanogenesis. In most genomes, the member of this family is encoded by a gene next to, and divergently transcribed from, the methyl coenzyme M reductase operon.
Probab=21.35 E-value=65 Score=33.16 Aligned_cols=31 Identities=23% Similarity=0.488 Sum_probs=25.2
Q ss_pred ccccccccccccccccccccc--CccccccccC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLC--GCIMCHDCSF 93 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~C--G~vvC~~CS~ 93 (376)
.|+-|..+=+.....-+|+.| +.+.|..|..
T Consensus 12 ~C~wC~~p~~~~~~~~~c~~C~~~~~~C~yC~~ 44 (404)
T TIGR03278 12 FCRYCYFKKVDDEQPFGCKNCPPGTKGCDYCTR 44 (404)
T ss_pred cCCCCCCCCCCCCCCCCCCcCCCCCCCCCCCCc
Confidence 688898877766677899999 6788988865
No 257
>PHA02565 49 recombination endonuclease VII; Provisional
Probab=21.33 E-value=56 Score=29.15 Aligned_cols=19 Identities=26% Similarity=0.513 Sum_probs=12.6
Q ss_pred cccccccccccccc---ccccc
Q psy4518 63 RCPNCSRSFNFAKR---QHHCR 81 (376)
Q Consensus 63 ~C~~C~~~F~~~~R---rHHCR 81 (376)
.|++|+.+|.-..+ --||-
T Consensus 22 ~CaiC~~~l~~~~~~~~vDHDH 43 (157)
T PHA02565 22 ICPLCKRELDGDVSKNHLDHDH 43 (157)
T ss_pred cCCCCCCccCCCccccccCCCC
Confidence 69999999863322 34555
No 258
>PRK05580 primosome assembly protein PriA; Validated
Probab=21.32 E-value=46 Score=36.51 Aligned_cols=17 Identities=41% Similarity=0.983 Sum_probs=12.9
Q ss_pred cccccCcc-ccccccCCc
Q psy4518 79 HCRLCGCI-MCHDCSFFL 95 (376)
Q Consensus 79 HCR~CG~v-vC~~CS~~~ 95 (376)
.|+.||.+ .|..|+..+
T Consensus 383 ~C~~Cg~~~~C~~C~~~l 400 (679)
T PRK05580 383 LCRDCGWVAECPHCDASL 400 (679)
T ss_pred EhhhCcCccCCCCCCCce
Confidence 58999977 488887643
No 259
>PF03966 Trm112p: Trm112p-like protein; InterPro: IPR005651 This family of short proteins have no known function. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The function of this family is uncertain. The bacterial members are about 60-70 amino acids in length and the eukaryotic examples are about 120 amino acids in length. The C terminus contains the strongest conservation. The entry contains 2 families: Trm112, which is required for tRNA methylation in Saccharomyces cerevisiae (Baker's yeast) and is found in complexes with 2 tRNA methylases (TRM9 and TRM11) also with putative methyltransferase YDR140W []. The zinc-finger protein Ynr046w is plurifunctional and a component of the eRF1 methyltransferase in yeast []. The crystal structure of Ynr046w has been determined to 1.7 A resolution. It comprises a zinc-binding domain built from both the N- and C-terminal sequences and an inserted domain, absent from bacterial and archaeal orthologs of the protein, composed of three alpha-helices []. UPF0434, which are proteins that are functionally uncharacterised. ; PDB: 3Q87_A 2KPI_A 2K5R_A 2HF1_A 2JS4_A 2J6A_A 2JR6_A 2PK7_A 2JNY_A.
Probab=21.23 E-value=45 Score=25.10 Aligned_cols=9 Identities=33% Similarity=1.084 Sum_probs=4.1
Q ss_pred ccccccccc
Q psy4518 63 RCPNCSRSF 71 (376)
Q Consensus 63 ~C~~C~~~F 71 (376)
.||.|..+.
T Consensus 9 ~Cp~ck~pL 17 (68)
T PF03966_consen 9 ACPVCKGPL 17 (68)
T ss_dssp B-TTTSSBE
T ss_pred cCCCCCCcc
Confidence 455555544
No 260
>KOG1812|consensus
Probab=21.21 E-value=49 Score=33.77 Aligned_cols=51 Identities=29% Similarity=0.671 Sum_probs=0.0
Q ss_pred HHHHhccCCCCchhhhhccccCCCcccCCCCCcccccccccccccc--cccccccCccccccc
Q psy4518 31 LDKLLTNMPIDPIKKKNHEQAIVPWLDGKDVPRCPNCSRSFNFAKR--QHHCRLCGCIMCHDC 91 (376)
Q Consensus 31 L~kLl~~~~~~~~~~~~~Eq~~~~W~~d~~v~~C~~C~~~F~~~~R--rHHCR~CG~vvC~~C 91 (376)
+.|+.+....+....+.+. -.|. .||.|+..--+... .-+|| ||.-||..|
T Consensus 285 ykk~~~~~~~d~~~~~~la---~~wr------~CpkC~~~ie~~~GCnhm~Cr-C~~~fcy~C 337 (384)
T KOG1812|consen 285 YKKLNPEEYVDDITLKYLA---KRWR------QCPKCKFMIELSEGCNHMTCR-CGHQFCYMC 337 (384)
T ss_pred HHHhCCcccccHHHHHHHH---HhcC------cCcccceeeeecCCcceEEee-ccccchhhc
No 261
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=21.06 E-value=42 Score=28.16 Aligned_cols=23 Identities=26% Similarity=0.678 Sum_probs=17.3
Q ss_pred cccccccccccccc-----cccccccCc
Q psy4518 63 RCPNCSRSFNFAKR-----QHHCRLCGC 85 (376)
Q Consensus 63 ~C~~C~~~F~~~~R-----rHHCR~CG~ 85 (376)
.|+.|+.+-+.+.+ -.+|..||.
T Consensus 82 lC~~C~spdT~l~k~~r~~~l~C~aCGa 109 (110)
T smart00653 82 LCPECGSPDTELIKENRLFFLKCEACGA 109 (110)
T ss_pred ECCCCCCCCcEEEEeCCeEEEEccccCC
Confidence 79999999885443 456888874
No 262
>smart00109 C1 Protein kinase C conserved region 1 (C1) domains (Cysteine-rich domains). Some bind phorbol esters and diacylglycerol. Some bind RasGTP. Zinc-binding domains.
Probab=21.01 E-value=46 Score=22.38 Aligned_cols=35 Identities=17% Similarity=0.359 Sum_probs=23.8
Q ss_pred CCcccccccccccccccccccccCccccccccCCc
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFL 95 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~ 95 (376)
...|..|++.+....--..|+.||.++=..|...+
T Consensus 11 ~~~C~~C~~~i~~~~~~~~C~~C~~~~H~~C~~~v 45 (49)
T smart00109 11 PTKCCVCRKSIWGSFQGLRCSWCKVKCHKKCAEKV 45 (49)
T ss_pred CCCccccccccCcCCCCcCCCCCCchHHHHHHhhc
Confidence 45799999987643335678888766545666544
No 263
>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=20.98 E-value=44 Score=24.30 Aligned_cols=30 Identities=23% Similarity=0.645 Sum_probs=17.7
Q ss_pred cccccccccccccccccccccCccccccccCC
Q psy4518 63 RCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFF 94 (376)
Q Consensus 63 ~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~ 94 (376)
.|..|+..++-.=|+.- .=|..+|+.|..+
T Consensus 1 ~C~~C~~~~Tp~WR~g~--~~~~~LCNaCgl~ 30 (54)
T cd00202 1 ACSNCGTTTTPLWRRGP--SGGSTLCNACGLY 30 (54)
T ss_pred CCCCCCCCCCcccccCC--CCcchHHHHHHHH
Confidence 37777777764333332 3456677777654
No 264
>COG1198 PriA Primosomal protein N' (replication factor Y) - superfamily II helicase [DNA replication, recombination, and repair]
Probab=20.77 E-value=62 Score=35.91 Aligned_cols=17 Identities=12% Similarity=0.128 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHH
Q psy4518 225 QRLHKSIRQASTNFIRT 241 (376)
Q Consensus 225 ~rlq~~I~~~a~~FLqe 241 (376)
--||..++.-+..|...
T Consensus 606 p~i~~~~~~dy~~F~~~ 622 (730)
T COG1198 606 PAIQALKRGDYEAFYEQ 622 (730)
T ss_pred HHHHHHHhcCHHHHHHH
Confidence 34777777777777765
No 265
>PHA03158 hypothetical protein; Provisional
Probab=20.71 E-value=2e+02 Score=26.71 Aligned_cols=38 Identities=29% Similarity=0.371 Sum_probs=28.5
Q ss_pred HHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHhhh
Q psy4518 323 VQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQEQ 366 (376)
Q Consensus 323 ~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~~~~~~ 366 (376)
+|-..|++..++.|++-++--| ..+||++||+.+++..
T Consensus 233 ~EK~~~~kQllka~kkc~~~s~------~~~~leeei~eleks~ 270 (273)
T PHA03158 233 KEKAAILKQLLKAAKKCCKNSE------HEKELEEEIEELEKSL 270 (273)
T ss_pred HHhHHHHHHHHHHHHHHhcchH------HHHHHHHHHHHHHHhh
Confidence 6777888999999999988765 3456666776666654
No 266
>smart00731 SprT SprT homologues. Predicted to have roles in transcription elongation. Contains a conserved HExxH motif, indicating a metalloprotease function.
Probab=20.54 E-value=49 Score=28.70 Aligned_cols=26 Identities=23% Similarity=0.685 Sum_probs=16.0
Q ss_pred Cccccccccccccc-----ccccccccCccc
Q psy4518 62 PRCPNCSRSFNFAK-----RQHHCRLCGCIM 87 (376)
Q Consensus 62 ~~C~~C~~~F~~~~-----RrHHCR~CG~vv 87 (376)
=.|..|+..+...+ .+..|+.||..+
T Consensus 113 y~C~~C~~~~~~~rr~~~~~~y~C~~C~g~l 143 (146)
T smart00731 113 YRCTGCGQRYLRVRRSNNVSRYRCGKCGGKL 143 (146)
T ss_pred EECCCCCCCCceEccccCcceEEcCCCCCEE
Confidence 36888888765221 346677777654
No 267
>TIGR00686 phnA alkylphosphonate utilization operon protein PhnA. The protein family includes an uncharacterized member designated phnA in Escherichia coli, part of a large operon associated with alkylphosphonate uptake and carbon-phosphorus bond cleavage. This protein is not related to the characterized phosphonoacetate hydrolase designated PhnA by Kulakova, et al. (2001, 1997).
Probab=20.42 E-value=59 Score=27.27 Aligned_cols=29 Identities=21% Similarity=0.826 Sum_probs=20.2
Q ss_pred CCcccccccccccccccccccccCccccccccCCcc
Q psy4518 61 VPRCPNCSRSFNFAKRQHHCRLCGCIMCHDCSFFLP 96 (376)
Q Consensus 61 v~~C~~C~~~F~~~~RrHHCR~CG~vvC~~CS~~~~ 96 (376)
.+.||.|+..|++-.. ...+|..|...|+
T Consensus 2 lp~CP~C~seytY~dg-------~~~iCpeC~~EW~ 30 (109)
T TIGR00686 2 LPPCPKCNSEYTYHDG-------TQLICPSCLYEWN 30 (109)
T ss_pred CCcCCcCCCcceEecC-------CeeECcccccccc
Confidence 4689999999986544 2347777766554
No 268
>smart00685 DM14 Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241.
Probab=20.36 E-value=3.7e+02 Score=20.01 Aligned_cols=52 Identities=13% Similarity=0.098 Sum_probs=43.6
Q ss_pred hhHHHHHHHHHHHHHHHHhcCchhHHHHHHhHHHHHHHHHHHHhhhhccccc
Q psy4518 321 PLVQQITNIKQFIKEARMAHRYNEVASLENHLKELQEEYFRRQQEQQTEVND 372 (376)
Q Consensus 321 ~L~EQ~~~v~~~I~~A~~~rrfdEV~~L~~NL~EL~~ei~~~~~~~~~~~~~ 372 (376)
-|++=...-+..-.+||..|.-+......+=.+-++.-|...+....+.+|+
T Consensus 3 ~L~~R~~~yk~Aa~~AK~~gd~~kAr~~~R~~K~~~~~I~~~~aG~pVd~~~ 54 (59)
T smart00685 3 LLQQRQEQYKQAALQAKRAGDEEKARRHLRIAKQFDDAIKAARAGRPVDLSE 54 (59)
T ss_pred HHHHHHHHHHHHHHHHHHcCCHHHHHHHHHHHhhHHHHHHHHHCCCCCChhc
Confidence 3555556678888999999999999999999999999999988887776654
No 269
>PRK12336 translation initiation factor IF-2 subunit beta; Provisional
Probab=20.24 E-value=44 Score=30.91 Aligned_cols=26 Identities=19% Similarity=0.416 Sum_probs=18.6
Q ss_pred cccccccccccccc-----cccccccCcccc
Q psy4518 63 RCPNCSRSFNFAKR-----QHHCRLCGCIMC 88 (376)
Q Consensus 63 ~C~~C~~~F~~~~R-----rHHCR~CG~vvC 88 (376)
.|+.|+.+-+.+.+ -.+|..||..-.
T Consensus 100 ~C~~C~~pdT~l~k~~~~~~l~C~aCGa~~~ 130 (201)
T PRK12336 100 ICSECGLPDTRLVKEDRVLMLRCDACGAHRP 130 (201)
T ss_pred ECCCCCCCCcEEEEcCCeEEEEcccCCCCcc
Confidence 89999999885444 246777777644
No 270
>KOG3940|consensus
Probab=20.22 E-value=86 Score=31.07 Aligned_cols=28 Identities=29% Similarity=0.596 Sum_probs=19.8
Q ss_pred CCCCCcccccccccccccccccccccCc
Q psy4518 58 GKDVPRCPNCSRSFNFAKRQHHCRLCGC 85 (376)
Q Consensus 58 d~~v~~C~~C~~~F~~~~RrHHCR~CG~ 85 (376)
..+...|+.|+..|+-.-.-.||-.||.
T Consensus 319 ~~s~~~Cp~cg~r~~~~~~ak~~~~c~~ 346 (351)
T KOG3940|consen 319 NPSYVQCPHCGRRFNEQAAAKHIPKCVN 346 (351)
T ss_pred CCCcccCccccccchHHHHHhhcccccc
Confidence 3345589999999995555556666654
No 271
>PF05443 ROS_MUCR: ROS/MUCR transcriptional regulator protein; InterPro: IPR008807 This family consists of several ROS/MUCR transcriptional regulator proteins. The ros chromosomal gene is present in octopine and nopaline strains of Agrobacterium tumefaciens as well as in Rhizobium meliloti (Sinorhizobium meliloti). This gene encodes a 15.5 kDa protein that specifically represses the virC and virD operons in the virulence region of the Ti plasmid [] and is necessary for succinoglycan production []. S. meliloti can produce two types of acidic exopolysaccharides, succinoglycan and galactoglucan, that are interchangeable for infection of Medicago sativa (Alfalfa) nodules. MucR from S. meliloti acts as a transcriptional repressor that blocks the expression of the exp genes responsible for galactoglucan production therefore allowing the exclusive production of succinoglycan [].; GO: 0003677 DNA binding, 0008270 zinc ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2JSP_A.
Probab=20.09 E-value=29 Score=30.09 Aligned_cols=16 Identities=25% Similarity=0.717 Sum_probs=10.1
Q ss_pred Ccccccccccccccccc
Q psy4518 62 PRCPNCSRSFNFAKRQH 78 (376)
Q Consensus 62 ~~C~~C~~~F~~~~RrH 78 (376)
-.|..||++|..+ +||
T Consensus 73 i~clecGk~~k~L-krH 88 (132)
T PF05443_consen 73 IICLECGKKFKTL-KRH 88 (132)
T ss_dssp EE-TBT--EESBH-HHH
T ss_pred eEEccCCcccchH-HHH
Confidence 4799999999987 444
Done!