Query 032638
Match_columns 136
No_of_seqs 13 out of 15
Neff 2.0
Searched_HMMs 46136
Date Fri Mar 29 04:01:24 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032638.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032638hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN03165 chaperone protein dna 97.1 9.2E-05 2E-09 55.0 -0.3 53 62-114 10-68 (111)
2 PF00684 DnaJ_CXXCXGXG: DnaJ c 96.5 0.0018 4E-08 42.5 2.1 25 87-111 13-54 (66)
3 TIGR02642 phage_xxxx uncharact 96.2 0.0026 5.5E-08 50.8 1.9 26 89-114 99-131 (186)
4 PLN03165 chaperone protein dna 95.4 0.0094 2E-07 44.4 1.7 29 86-114 72-102 (111)
5 PF00684 DnaJ_CXXCXGXG: DnaJ c 95.1 0.015 3.2E-07 38.2 1.9 22 92-113 1-30 (66)
6 PRK14300 chaperone protein Dna 95.1 0.014 2.9E-07 49.1 2.1 23 90-112 146-176 (372)
7 PRK14284 chaperone protein Dna 94.9 0.012 2.6E-07 49.7 1.3 11 90-100 176-186 (391)
8 PRK14285 chaperone protein Dna 94.7 0.015 3.3E-07 48.8 1.5 11 101-111 188-198 (365)
9 PRK10767 chaperone protein Dna 94.6 0.021 4.6E-07 47.6 2.1 11 101-111 184-194 (371)
10 PRK14297 chaperone protein Dna 94.6 0.02 4.3E-07 48.2 1.9 22 90-111 149-178 (380)
11 PRK10767 chaperone protein Dna 94.6 0.017 3.6E-07 48.2 1.4 23 90-112 143-173 (371)
12 PRK14282 chaperone protein Dna 94.6 0.023 5E-07 47.6 2.2 9 91-99 154-162 (369)
13 PRK14295 chaperone protein Dna 94.5 0.018 3.8E-07 48.9 1.4 11 101-111 208-218 (389)
14 PRK14287 chaperone protein Dna 94.5 0.023 4.9E-07 47.9 2.0 23 90-112 139-169 (371)
15 PRK14300 chaperone protein Dna 94.5 0.019 4.2E-07 48.2 1.6 23 89-111 162-197 (372)
16 PRK14278 chaperone protein Dna 94.5 0.02 4.3E-07 48.3 1.6 11 101-111 185-195 (378)
17 TIGR02349 DnaJ_bact chaperone 94.4 0.019 4.2E-07 47.3 1.5 11 101-111 189-199 (354)
18 PRK14288 chaperone protein Dna 94.4 0.023 4.9E-07 47.8 1.9 23 89-111 156-191 (369)
19 PRK14282 chaperone protein Dna 94.4 0.022 4.8E-07 47.7 1.8 11 89-99 169-179 (369)
20 PRK14276 chaperone protein Dna 94.4 0.019 4.2E-07 48.3 1.3 8 92-99 149-156 (380)
21 PRK14280 chaperone protein Dna 94.3 0.027 5.8E-07 47.5 2.0 9 91-99 145-153 (376)
22 PRK14286 chaperone protein Dna 94.2 0.028 6E-07 47.4 2.0 12 101-112 192-203 (372)
23 PRK14293 chaperone protein Dna 94.2 0.026 5.7E-07 47.3 1.8 11 101-111 189-199 (374)
24 PRK14279 chaperone protein Dna 94.2 0.027 5.9E-07 47.8 1.9 22 90-111 174-203 (392)
25 PRK14280 chaperone protein Dna 94.2 0.024 5.2E-07 47.7 1.5 11 89-99 160-170 (376)
26 COG0484 DnaJ DnaJ-class molecu 94.2 0.028 6E-07 49.2 1.9 13 100-112 199-211 (371)
27 PRK14296 chaperone protein Dna 94.1 0.033 7.2E-07 47.0 2.1 10 90-99 150-159 (372)
28 PRK14298 chaperone protein Dna 94.1 0.033 7.1E-07 47.1 2.1 22 90-111 142-171 (377)
29 PRK14296 chaperone protein Dna 94.0 0.03 6.5E-07 47.3 1.8 10 90-99 167-176 (372)
30 PRK14289 chaperone protein Dna 94.0 0.032 6.9E-07 46.9 2.0 25 89-113 154-186 (386)
31 PRK14284 chaperone protein Dna 94.0 0.031 6.8E-07 47.3 1.9 26 89-114 158-191 (391)
32 PRK14276 chaperone protein Dna 94.0 0.033 7.2E-07 46.9 2.0 26 88-113 162-204 (380)
33 PRK14285 chaperone protein Dna 94.0 0.033 7.2E-07 46.8 2.0 24 89-112 146-177 (365)
34 PRK14301 chaperone protein Dna 94.0 0.034 7.3E-07 46.9 2.0 10 90-99 145-154 (373)
35 PRK14288 chaperone protein Dna 93.9 0.038 8.2E-07 46.5 2.2 25 89-113 140-171 (369)
36 PRK14281 chaperone protein Dna 93.9 0.03 6.6E-07 47.5 1.7 11 101-111 208-218 (397)
37 PRK14277 chaperone protein Dna 93.9 0.027 5.9E-07 47.5 1.4 11 101-111 201-211 (386)
38 PRK14290 chaperone protein Dna 93.9 0.033 7.1E-07 46.6 1.8 10 90-99 166-175 (365)
39 PRK14279 chaperone protein Dna 93.8 0.03 6.6E-07 47.6 1.5 25 88-112 189-226 (392)
40 PRK14294 chaperone protein Dna 93.7 0.04 8.7E-07 46.1 2.0 9 91-99 146-154 (366)
41 PRK14286 chaperone protein Dna 93.7 0.034 7.3E-07 46.9 1.5 24 90-113 151-182 (372)
42 PRK14278 chaperone protein Dna 93.6 0.041 8.9E-07 46.5 2.0 25 89-113 139-171 (378)
43 PTZ00037 DnaJ_C chaperone prot 93.6 0.038 8.3E-07 47.9 1.7 24 89-112 166-206 (421)
44 PRK14293 chaperone protein Dna 93.6 0.044 9.6E-07 46.0 2.0 26 89-114 143-176 (374)
45 PRK14291 chaperone protein Dna 93.6 0.045 9.8E-07 46.2 2.1 23 90-112 157-187 (382)
46 TIGR02349 DnaJ_bact chaperone 93.5 0.049 1.1E-06 45.0 2.2 26 89-114 143-176 (354)
47 PRK14298 chaperone protein Dna 93.5 0.045 9.7E-07 46.3 2.0 12 101-112 201-212 (377)
48 PRK14277 chaperone protein Dna 93.5 0.047 1E-06 46.2 2.1 25 89-113 155-187 (386)
49 PRK14297 chaperone protein Dna 93.4 0.04 8.6E-07 46.4 1.5 24 89-112 165-205 (380)
50 PRK14289 chaperone protein Dna 93.3 0.052 1.1E-06 45.7 2.0 24 89-112 197-225 (386)
51 COG1107 Archaea-specific RecJ- 93.3 0.043 9.3E-07 51.8 1.7 27 89-116 2-35 (715)
52 PRK14287 chaperone protein Dna 93.3 0.038 8.3E-07 46.5 1.2 24 89-112 155-195 (371)
53 PRK14283 chaperone protein Dna 93.3 0.053 1.1E-06 45.6 2.0 22 90-111 147-176 (378)
54 PRK14295 chaperone protein Dna 93.1 0.055 1.2E-06 46.0 1.9 26 89-114 166-199 (389)
55 PRK14290 chaperone protein Dna 93.0 0.063 1.4E-06 44.9 2.1 25 89-113 191-220 (365)
56 PRK14291 chaperone protein Dna 92.9 0.064 1.4E-06 45.3 2.1 11 89-99 173-183 (382)
57 PRK14294 chaperone protein Dna 92.9 0.064 1.4E-06 45.0 2.0 11 89-99 161-171 (366)
58 PRK14301 chaperone protein Dna 92.7 0.064 1.4E-06 45.2 1.7 23 90-112 162-197 (373)
59 PRK14281 chaperone protein Dna 92.6 0.062 1.3E-06 45.7 1.5 25 89-113 205-234 (397)
60 PRK14292 chaperone protein Dna 92.2 0.087 1.9E-06 44.0 1.9 13 100-112 199-211 (371)
61 COG0484 DnaJ DnaJ-class molecu 91.9 0.1 2.2E-06 45.7 2.1 24 89-112 142-173 (371)
62 PTZ00037 DnaJ_C chaperone prot 91.6 0.1 2.2E-06 45.3 1.8 26 88-113 191-223 (421)
63 PRK14292 chaperone protein Dna 91.2 0.15 3.3E-06 42.6 2.4 13 101-113 186-198 (371)
64 PRK14283 chaperone protein Dna 89.5 0.21 4.5E-06 42.1 1.7 11 90-100 164-174 (378)
65 PF14369 zf-RING_3: zinc-finge 85.4 0.43 9.3E-06 29.0 1.0 10 100-110 23-32 (35)
66 TIGR00630 uvra excinuclease AB 83.2 0.59 1.3E-05 44.7 1.4 21 89-109 736-770 (924)
67 PF10571 UPF0547: Uncharacteri 81.2 0.84 1.8E-05 26.4 1.0 20 90-112 1-25 (26)
68 KOG0712 Molecular chaperone (D 80.5 0.81 1.8E-05 39.8 1.1 27 84-110 165-198 (337)
69 PRK00488 pheS phenylalanyl-tRN 79.5 0.94 2E-05 39.2 1.2 19 91-110 262-280 (339)
70 PF08271 TF_Zn_Ribbon: TFIIB z 78.0 1.2 2.6E-05 27.1 1.0 20 91-113 2-31 (43)
71 PF12669 P12: Virus attachment 78.0 2.7 5.8E-05 27.9 2.8 36 62-101 3-39 (58)
72 COG2871 NqrF Na+-transporting 76.6 3.7 8.1E-05 36.9 4.1 15 91-105 68-82 (410)
73 PRK14715 DNA polymerase II lar 75.2 2.7 5.8E-05 43.3 3.1 45 88-135 1541-1592(1627)
74 TIGR02538 type_IV_pilB type IV 73.9 1.6 3.5E-05 38.8 1.1 10 100-109 490-499 (564)
75 TIGR02642 phage_xxxx uncharact 73.8 1.8 4E-05 34.7 1.4 15 98-112 99-113 (186)
76 TIGR00354 polC DNA polymerase, 73.3 3.2 6.8E-05 41.4 3.0 46 88-135 1011-1063(1095)
77 COG4260 Membrane protease subu 71.7 1.7 3.6E-05 38.5 0.7 22 88-110 314-345 (345)
78 PRK14714 DNA polymerase II lar 71.5 3.8 8.2E-05 41.6 3.2 46 88-135 1252-1304(1337)
79 TIGR02533 type_II_gspE general 70.6 2 4.3E-05 37.9 1.0 10 100-109 414-423 (486)
80 PRK04023 DNA polymerase II lar 68.3 5 0.00011 40.2 3.2 46 88-135 1036-1088(1121)
81 TIGR00630 uvra excinuclease AB 67.8 3.3 7.1E-05 39.8 1.8 23 89-111 250-287 (924)
82 COG1107 Archaea-specific RecJ- 67.4 2.9 6.2E-05 40.0 1.4 23 90-112 54-82 (715)
83 COG1933 Archaeal DNA polymeras 65.8 4.7 0.0001 34.5 2.2 45 88-134 166-217 (253)
84 PRK00635 excinuclease ABC subu 65.0 3.4 7.3E-05 42.8 1.4 22 88-109 1606-1641(1809)
85 PRK06921 hypothetical protein; 64.7 3.7 8E-05 33.1 1.3 12 90-101 33-44 (266)
86 PRK00349 uvrA excinuclease ABC 64.0 4.3 9.4E-05 39.1 1.9 24 88-111 251-289 (943)
87 PRK00349 uvrA excinuclease ABC 62.9 3.6 7.9E-05 39.6 1.2 22 89-110 738-773 (943)
88 PRK00762 hypA hydrogenase nick 60.9 5.6 0.00012 29.3 1.6 23 85-108 66-102 (124)
89 PF11859 DUF3379: Protein of u 58.9 2.9 6.4E-05 34.8 -0.2 48 17-67 46-94 (232)
90 TIGR00373 conserved hypothetic 57.6 6.9 0.00015 29.8 1.7 24 84-107 104-137 (158)
91 cd03031 GRX_GRX_like Glutaredo 56.8 9.4 0.0002 29.1 2.3 26 87-112 97-124 (147)
92 PF12301 CD99L2: CD99 antigen 56.7 13 0.00028 29.6 3.1 20 61-80 122-141 (169)
93 PF14570 zf-RING_4: RING/Ubox 55.8 3.6 7.9E-05 27.0 -0.1 19 88-106 21-45 (48)
94 PRK00635 excinuclease ABC subu 55.8 6.1 0.00013 41.0 1.4 24 88-111 243-281 (1809)
95 TIGR02007 fdx_isc ferredoxin, 54.2 5.6 0.00012 28.2 0.6 13 94-106 40-52 (110)
96 PF09723 Zn-ribbon_8: Zinc rib 53.6 9 0.00019 23.5 1.4 10 97-106 25-34 (42)
97 KOG2813 Predicted molecular ch 53.2 6.6 0.00014 35.5 1.0 21 90-110 246-268 (406)
98 PRK06266 transcription initiat 53.1 9.7 0.00021 29.7 1.9 24 84-107 112-145 (178)
99 PRK00564 hypA hydrogenase nick 53.0 10 0.00022 27.7 1.8 25 85-109 67-99 (117)
100 COG5349 Uncharacterized protei 52.6 5.5 0.00012 31.1 0.4 16 97-113 20-35 (126)
101 KOG0715 Molecular chaperone (D 51.6 7.9 0.00017 32.2 1.2 36 79-114 171-219 (288)
102 PF01155 HypA: Hydrogenase exp 51.5 9.1 0.0002 27.6 1.4 24 86-109 67-97 (113)
103 PRK00423 tfb transcription ini 51.5 7.5 0.00016 32.1 1.1 25 85-112 7-41 (310)
104 PRK10436 hypothetical protein; 50.8 6.9 0.00015 34.6 0.8 9 100-109 387-395 (462)
105 PTZ00490 Ferredoxin superfamil 50.5 6.9 0.00015 30.1 0.7 14 93-106 72-85 (143)
106 PRK12380 hydrogenase nickel in 50.3 11 0.00024 27.3 1.7 24 86-109 67-97 (113)
107 PLN02593 adrenodoxin-like ferr 49.7 7.1 0.00015 28.3 0.6 24 94-117 37-63 (117)
108 PF07589 VPEP: PEP-CTERM motif 49.2 27 0.00059 19.9 2.9 20 53-72 1-20 (25)
109 TIGR03655 anti_R_Lar restricti 48.7 24 0.00053 22.2 2.9 10 101-110 29-38 (53)
110 TIGR03830 CxxCG_CxxCG_HTH puta 48.1 12 0.00025 25.8 1.4 22 100-122 33-54 (127)
111 COG0178 UvrA Excinuclease ATPa 47.6 9.2 0.0002 37.8 1.1 25 85-109 726-764 (935)
112 TIGR00613 reco DNA repair prot 47.3 19 0.00041 27.5 2.6 38 87-124 145-194 (241)
113 PRK11712 ribonuclease G; Provi 47.2 19 0.0004 32.6 2.9 13 100-112 404-416 (489)
114 KOG2813 Predicted molecular ch 46.4 12 0.00026 33.9 1.6 24 86-109 231-256 (406)
115 PF05957 DUF883: Bacterial pro 45.8 25 0.00054 24.0 2.8 19 59-78 75-93 (94)
116 PF15474 MU117: Meiotically up 45.7 19 0.00041 26.2 2.3 31 94-133 3-33 (97)
117 cd01129 PulE-GspE PulE/GspE Th 45.7 8.9 0.00019 30.8 0.6 12 99-110 251-262 (264)
118 PF10814 DUF2562: Protein of u 45.2 4.4 9.5E-05 32.0 -1.2 26 58-83 94-119 (133)
119 smart00261 FU Furin-like repea 44.7 14 0.00029 21.9 1.2 22 90-112 9-32 (46)
120 PF01412 ArfGap: Putative GTPa 43.4 4.4 9.6E-05 29.0 -1.3 20 87-106 11-41 (116)
121 PRK13130 H/ACA RNA-protein com 42.9 15 0.00031 24.8 1.2 21 89-109 5-28 (56)
122 COG1656 Uncharacterized conser 42.7 14 0.00031 29.7 1.4 18 100-120 99-116 (165)
123 COG2804 PulE Type II secretory 42.6 24 0.00052 32.5 2.9 35 63-109 381-435 (500)
124 PRK11823 DNA repair protein Ra 41.5 14 0.0003 32.1 1.2 25 88-112 6-35 (446)
125 COG2331 Uncharacterized protei 41.4 9.1 0.0002 28.2 0.1 10 88-97 32-41 (82)
126 PRK06835 DNA replication prote 41.1 12 0.00025 31.6 0.7 16 87-102 96-111 (329)
127 TIGR00100 hypA hydrogenase nic 40.9 20 0.00044 26.0 1.8 25 85-109 66-97 (115)
128 COG0375 HybF Zn finger protein 40.9 18 0.00038 27.5 1.5 30 85-114 66-110 (115)
129 TIGR00757 RNaseEG ribonuclease 40.3 13 0.00029 32.5 1.0 13 100-112 392-404 (414)
130 cd01121 Sms Sms (bacterial rad 39.9 14 0.0003 31.7 1.0 22 91-112 2-28 (372)
131 PRK10132 hypothetical protein; 39.9 33 0.00071 25.3 2.8 20 60-80 89-108 (108)
132 COG1530 CafA Ribonucleases G a 39.1 13 0.00027 33.3 0.6 15 98-112 395-409 (487)
133 PRK03824 hypA hydrogenase nick 39.0 35 0.00075 25.5 2.9 12 85-96 66-77 (135)
134 KOG0703 Predicted GTPase-activ 38.8 13 0.00028 32.1 0.6 21 86-106 22-53 (287)
135 TIGR02605 CxxC_CxxC_SSSS putat 38.5 22 0.00048 21.7 1.5 7 100-106 28-34 (52)
136 smart00105 ArfGap Putative GTP 38.3 7.8 0.00017 27.6 -0.7 18 89-106 3-31 (112)
137 cd01675 RNR_III Class III ribo 38.2 18 0.00039 32.5 1.4 17 91-107 520-541 (555)
138 KOG2824 Glutaredoxin-related p 38.2 21 0.00045 31.0 1.7 24 87-110 227-252 (281)
139 PRK06319 DNA topoisomerase I/S 38.1 24 0.00053 33.5 2.3 11 87-97 590-600 (860)
140 KOG0818 GTPase-activating prot 37.9 10 0.00022 36.1 -0.1 18 88-105 7-35 (669)
141 TIGR01941 nqrF NADH:ubiquinone 37.8 14 0.0003 31.0 0.7 13 94-106 66-78 (405)
142 PLN02999 photosystem II oxygen 37.6 27 0.00057 29.0 2.2 24 106-129 76-100 (190)
143 PRK00398 rpoP DNA-directed RNA 37.5 24 0.00052 21.5 1.5 26 90-116 4-38 (46)
144 PLN02248 cellulose synthase-li 37.5 14 0.0003 37.3 0.6 21 86-106 149-174 (1135)
145 COG0675 Transposase and inacti 36.4 19 0.00042 27.1 1.2 38 86-134 306-347 (364)
146 PRK08116 hypothetical protein; 36.0 35 0.00075 27.5 2.6 23 86-108 13-49 (268)
147 PRK14704 anaerobic ribonucleos 35.1 21 0.00046 33.0 1.5 23 85-107 555-581 (618)
148 PF05191 ADK_lid: Adenylate ki 34.9 18 0.00038 22.1 0.6 16 91-106 3-29 (36)
149 PF07092 DUF1356: Protein of u 34.6 26 0.00057 29.5 1.8 33 85-117 23-57 (238)
150 PF03589 Antiterm: Antitermina 34.5 14 0.00031 26.4 0.2 21 101-123 35-55 (95)
151 TIGR02487 NrdD anaerobic ribon 34.2 25 0.00054 31.9 1.7 23 85-107 520-547 (579)
152 PRK05464 Na(+)-translocating N 33.6 18 0.00039 30.4 0.7 13 94-106 70-82 (409)
153 smart00834 CxxC_CXXC_SSSS Puta 33.5 31 0.00067 19.8 1.5 7 100-106 28-34 (41)
154 TIGR00416 sms DNA repair prote 33.4 20 0.00043 31.4 0.9 25 88-112 6-35 (454)
155 COG1885 Uncharacterized protei 33.3 53 0.0011 25.5 3.1 9 97-105 48-56 (115)
156 PF09791 Oxidored-like: Oxidor 33.2 20 0.00044 23.4 0.7 16 93-109 16-31 (48)
157 PF02620 DUF177: Uncharacteriz 32.9 23 0.00051 23.9 1.0 18 89-106 76-94 (119)
158 PRK05978 hypothetical protein; 32.9 20 0.00044 27.9 0.8 14 98-112 33-46 (148)
159 PRK07111 anaerobic ribonucleos 32.7 25 0.00054 33.1 1.5 23 85-107 676-702 (735)
160 KOG2824 Glutaredoxin-related p 32.5 27 0.00059 30.3 1.6 22 89-111 221-242 (281)
161 PF01783 Ribosomal_L32p: Ribos 32.2 44 0.00096 21.7 2.2 19 86-104 23-45 (56)
162 TIGR00595 priA primosomal prot 32.0 22 0.00048 31.4 1.0 18 88-105 212-229 (505)
163 PF08955 BofC_C: BofC C-termin 31.7 19 0.00041 25.6 0.4 12 99-110 2-13 (75)
164 KOG1100 Predicted E3 ubiquitin 31.5 25 0.00055 28.2 1.2 18 89-106 179-197 (207)
165 PRK06418 transcription elongat 31.0 16 0.00034 29.0 -0.1 16 90-105 4-20 (166)
166 PRK15103 paraquat-inducible me 30.8 37 0.00079 29.8 2.1 26 88-113 220-250 (419)
167 KOG3800 Predicted E3 ubiquitin 30.8 18 0.00039 31.7 0.2 18 89-106 25-48 (300)
168 TIGR00757 RNaseEG ribonuclease 30.7 14 0.00031 32.4 -0.4 17 84-100 385-401 (414)
169 PF08792 A2L_zn_ribbon: A2L zi 30.2 32 0.0007 20.7 1.2 11 90-100 4-14 (33)
170 COG3813 Uncharacterized protei 29.6 18 0.00039 26.7 0.0 26 91-117 31-59 (84)
171 PF12732 YtxH: YtxH-like prote 29.5 55 0.0012 21.6 2.3 23 61-83 4-26 (74)
172 TIGR00155 pqiA_fam integral me 29.0 35 0.00075 29.7 1.7 33 85-117 9-52 (403)
173 PRK06835 DNA replication prote 28.4 40 0.00088 28.4 1.9 11 100-110 100-110 (329)
174 KOG0145 RNA-binding protein EL 28.4 31 0.00068 30.8 1.3 31 102-132 317-348 (360)
175 PF01102 Glycophorin_A: Glycop 28.0 69 0.0015 24.3 2.9 15 58-72 68-82 (122)
176 PF02988 PLA2_inh: Phospholipa 28.0 31 0.00067 24.7 1.0 14 91-106 2-15 (83)
177 PRK10220 hypothetical protein; 28.0 35 0.00076 26.2 1.3 19 89-107 3-29 (111)
178 TIGR01167 LPXTG_anchor LPXTG-m 27.9 63 0.0014 18.0 2.1 14 66-79 19-32 (34)
179 PF02420 AFP: Insect antifreez 27.4 26 0.00056 17.4 0.4 11 95-105 2-12 (12)
180 PF06906 DUF1272: Protein of u 26.4 31 0.00067 23.9 0.7 10 98-107 41-50 (57)
181 COG1545 Predicted nucleic-acid 26.4 39 0.00085 25.3 1.4 26 83-108 23-53 (140)
182 cd00296 SIR2 SIR2 superfamily 25.9 46 0.00099 25.0 1.6 21 87-107 111-143 (222)
183 PF02977 CarbpepA_inh: Carboxy 25.9 35 0.00076 22.8 0.9 22 93-114 16-42 (46)
184 PRK09263 anaerobic ribonucleos 25.7 38 0.00083 31.8 1.4 21 85-105 637-666 (711)
185 COG1568 Predicted methyltransf 25.7 49 0.0011 29.7 2.0 30 98-128 91-120 (354)
186 PF07295 DUF1451: Protein of u 25.6 51 0.0011 25.4 1.9 30 82-111 105-143 (146)
187 COG5257 GCD11 Translation init 25.5 46 0.00099 30.4 1.8 31 85-115 53-89 (415)
188 PF14787 zf-CCHC_5: GAG-polypr 25.2 31 0.00068 21.9 0.5 8 98-105 2-9 (36)
189 PF14319 Zn_Tnp_IS91: Transpos 25.2 44 0.00094 24.2 1.4 21 86-106 39-68 (111)
190 smart00291 ZnF_ZZ Zinc-binding 25.0 24 0.00052 21.5 0.0 22 88-109 17-38 (44)
191 PF12172 DUF35_N: Rubredoxin-l 24.6 28 0.00061 20.3 0.3 22 86-107 8-34 (37)
192 PRK11639 zinc uptake transcrip 24.4 23 0.00051 26.8 -0.2 9 99-107 141-149 (169)
193 PRK05580 primosome assembly pr 24.4 35 0.00075 31.3 0.9 19 88-106 380-398 (679)
194 TIGR00686 phnA alkylphosphonat 24.1 38 0.00083 25.9 0.9 18 90-107 3-28 (109)
195 PRK10404 hypothetical protein; 24.1 83 0.0018 22.8 2.6 18 60-78 83-100 (101)
196 PRK14559 putative protein seri 23.7 53 0.0011 30.8 1.9 23 85-107 11-36 (645)
197 PRK12495 hypothetical protein; 23.4 36 0.00078 28.8 0.7 21 87-107 40-67 (226)
198 COG3894 Uncharacterized metal- 23.2 33 0.00072 32.6 0.6 15 91-105 31-45 (614)
199 PRK11032 hypothetical protein; 23.1 55 0.0012 25.9 1.7 31 85-115 120-159 (160)
200 COG2093 DNA-directed RNA polym 23.0 76 0.0016 22.4 2.2 34 89-123 4-49 (64)
201 PRK10811 rne ribonuclease E; R 22.9 35 0.00076 34.4 0.6 15 100-114 403-417 (1068)
202 KOG0712 Molecular chaperone (D 22.9 51 0.0011 29.0 1.6 44 67-110 115-182 (337)
203 PF08273 Prim_Zn_Ribbon: Zinc- 22.7 28 0.0006 21.9 -0.0 13 97-109 25-40 (40)
204 COG2149 Predicted membrane pro 22.6 84 0.0018 24.5 2.5 42 34-79 77-118 (120)
205 PRK11712 ribonuclease G; Provi 22.5 24 0.00053 31.9 -0.5 17 84-100 397-413 (489)
206 TIGR02008 fdx_plant ferredoxin 22.3 46 0.001 22.9 1.0 12 94-106 39-50 (97)
207 PLN03131 hypothetical protein; 21.9 37 0.00081 32.8 0.6 19 88-106 22-51 (705)
208 PRK11788 tetratricopeptide rep 21.6 58 0.0013 25.3 1.5 23 88-110 353-380 (389)
209 PF00111 Fer2: 2Fe-2S iron-sul 21.5 52 0.0011 20.8 1.1 17 93-110 33-52 (78)
210 PRK07609 CDP-6-deoxy-delta-3,4 21.2 41 0.00089 27.0 0.6 12 94-106 36-47 (339)
211 PRK00432 30S ribosomal protein 20.9 47 0.001 21.4 0.7 19 87-105 18-44 (50)
212 PF01927 Mut7-C: Mut7-C RNAse 20.9 43 0.00094 24.7 0.7 18 99-119 92-109 (147)
213 TIGR03826 YvyF flagellar opero 20.9 39 0.00084 26.0 0.4 19 89-107 3-27 (137)
214 PRK08270 anaerobic ribonucleos 20.8 60 0.0013 30.3 1.7 23 85-107 622-648 (656)
215 TIGR02827 RNR_anaer_Bdell anae 20.6 55 0.0012 30.4 1.4 23 85-107 528-555 (586)
216 PLN03136 Ferredoxin; Provision 20.4 45 0.00098 25.7 0.7 12 94-106 90-101 (148)
No 1
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=97.14 E-value=9.2e-05 Score=55.01 Aligned_cols=53 Identities=28% Similarity=0.525 Sum_probs=36.8
Q ss_pred HHHHHHHHHHHHH----HHHhcCCCccccccccccccCCCcc--CCCCccCcceeeecC
Q 032638 62 AIAATVVGAAATL----LVRRTKGSEETEIPLKTCEDCGGSG--ICPECKGEGFVLKKL 114 (136)
Q Consensus 62 aiaa~vVGaAat~----Lvrr~k~~e~~E~~~k~Ce~C~GsG--iCpeCkGEGFVlK~L 114 (136)
+|.+++||-|+.+ |.--+--.++..+....|..|.|+| .|+.|+|.|++..++
T Consensus 10 ~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~v~C~~C~GsG~~~C~~C~G~G~v~~~~ 68 (111)
T PLN03165 10 AISVGVVSIAVGIGIPVFYETQIDNAAKRENTQPCFPCSGTGAQVCRFCVGSGNVTVEL 68 (111)
T ss_pred hhhhhhhhhhhccCCcEEEEEeeehhhhhccCCCCCCCCCCCCcCCCCCcCcCeEEEEe
Confidence 4555666666543 2222222334567788999999999 899999999998765
No 2
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=96.50 E-value=0.0018 Score=42.50 Aligned_cols=25 Identities=48% Similarity=1.141 Sum_probs=13.1
Q ss_pred ccccccccCCCcc-----------------CCCCccCcceee
Q 032638 87 IPLKTCEDCGGSG-----------------ICPECKGEGFVL 111 (136)
Q Consensus 87 ~~~k~Ce~C~GsG-----------------iCpeCkGEGFVl 111 (136)
.....|+.|.|+| .|+.|+|.|+++
T Consensus 13 ~~~~~C~~C~G~G~~~~~~~~~~~~~~~~~~C~~C~G~G~~i 54 (66)
T PF00684_consen 13 KKPKTCPQCNGSGQVTRRQQTPGGVFQMQQTCPKCGGTGKII 54 (66)
T ss_dssp TT-EE-TTSSSSSEEEEEEESSSTTEEEEEE-TTTSSSSEE-
T ss_pred CCCcCCcCCCCeeEEEEEEeCCCeEEEEEEECCCCcceeeEE
Confidence 3445666666666 266666666665
No 3
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=96.23 E-value=0.0026 Score=50.79 Aligned_cols=26 Identities=31% Similarity=0.830 Sum_probs=22.6
Q ss_pred ccccccCCCccC-------CCCccCcceeeecC
Q 032638 89 LKTCEDCGGSGI-------CPECKGEGFVLKKL 114 (136)
Q Consensus 89 ~k~Ce~C~GsGi-------CpeCkGEGFVlK~L 114 (136)
...|+.|+|+|. |++|+|.|++-++.
T Consensus 99 ~~~C~~C~G~G~~i~~~~~C~~C~G~G~v~~~~ 131 (186)
T TIGR02642 99 SCKCPRCRGTGLIQRRQRECDTCAGTGRFRPTV 131 (186)
T ss_pred CCcCCCCCCeeEEecCCCCCCCCCCccEEeeeE
Confidence 678999999983 99999999987653
No 4
>PLN03165 chaperone protein dnaJ-related; Provisional
Probab=95.35 E-value=0.0094 Score=44.40 Aligned_cols=29 Identities=34% Similarity=0.907 Sum_probs=24.8
Q ss_pred cccccccccCCCcc--CCCCccCcceeeecC
Q 032638 86 EIPLKTCEDCGGSG--ICPECKGEGFVLKKL 114 (136)
Q Consensus 86 E~~~k~Ce~C~GsG--iCpeCkGEGFVlK~L 114 (136)
......|..|.|+| +|+.|+|.|++-+-|
T Consensus 72 ~q~~~~C~~C~G~Gk~~C~~C~G~G~~~~~~ 102 (111)
T PLN03165 72 EKEVSKCINCDGAGSLTCTTCQGSGIQPRYL 102 (111)
T ss_pred EEEEEECCCCCCcceeeCCCCCCCEEEeeee
Confidence 34567999999999 899999999987655
No 5
>PF00684 DnaJ_CXXCXGXG: DnaJ central domain; InterPro: IPR001305 The hsp70 chaperone machine performs many diverse roles in the cell, including folding of nascent proteins, translocation of polypeptides across organelle membranes, coordinating responses to stress, and targeting selected proteins for degradation. DnaJ is a member of the hsp40 family of molecular chaperones, which is also called the J-protein family, the members of which regulate the activity of hsp70s. DnaJ (hsp40) binds to DnaK (hsp70) and stimulates its ATPase activity, generating the ADP-bound state of DnaK, which interacts stably with the polypeptide substrate []. Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation []. DnaJ consists of an N-terminal conserved domain (called 'J' domain) of about 70 amino acid residues, a glycine and phenylalanine-rich domain ('G/F' domain), a central cysteine rich domain (CR-type zinc finger) containing four repeats of a CXXCXGXG motif which can coordinate two zinc atom and a C-terminal domain (CTD) []. This entry represents the central cysteine-rich (CR) domain of DnaJ proteins. This central cysteine rich domain (CR-type zinc finger) has an overall V-shaped extended beta-hairpin topology and contains four repeats of the motif CXXCXGXG where X is any amino acid. The isolated cysteine rich domain folds in zinc dependent fashion. Each set of two repeats binds one unit of zinc. Although this domain has been implicated in substrate binding, no evidence of specific interaction between the isolated DnaJ cysteine rich domain and various hydrophobic peptides has been found [].; GO: 0031072 heat shock protein binding, 0051082 unfolded protein binding; PDB: 1NLT_A 2CTT_A 1EXK_A.
Probab=95.10 E-value=0.015 Score=38.20 Aligned_cols=22 Identities=45% Similarity=1.342 Sum_probs=17.4
Q ss_pred cccCCCccC--------CCCccCcceeeec
Q 032638 92 CEDCGGSGI--------CPECKGEGFVLKK 113 (136)
Q Consensus 92 Ce~C~GsGi--------CpeCkGEGFVlK~ 113 (136)
|+.|.|+|. |+.|+|.|+++..
T Consensus 1 C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~ 30 (66)
T PF00684_consen 1 CPKCNGTGAKPGKKPKTCPQCNGSGQVTRR 30 (66)
T ss_dssp -CCCTTTSB-STTT-EE-TTSSSSSEEEEE
T ss_pred CCcCCCcccCCCCCCcCCcCCCCeeEEEEE
Confidence 788999997 9999999998765
No 6
>PRK14300 chaperone protein DnaJ; Provisional
Probab=95.06 E-value=0.014 Score=49.12 Aligned_cols=23 Identities=39% Similarity=0.928 Sum_probs=14.6
Q ss_pred cccccCCCccC--------CCCccCcceeee
Q 032638 90 KTCEDCGGSGI--------CPECKGEGFVLK 112 (136)
Q Consensus 90 k~Ce~C~GsGi--------CpeCkGEGFVlK 112 (136)
..|+.|.|+|. |+.|+|.|++..
T Consensus 146 ~~C~~C~G~g~~~~~~~~~C~~C~G~G~~~~ 176 (372)
T PRK14300 146 VKCDTCHGSGSEKGETVTTCDACSGVGATRM 176 (372)
T ss_pred cccCCCCCcccCCCCCCccCCCccCeEEEEE
Confidence 56777777763 666666665544
No 7
>PRK14284 chaperone protein DnaJ; Provisional
Probab=94.86 E-value=0.012 Score=49.72 Aligned_cols=11 Identities=55% Similarity=1.241 Sum_probs=5.3
Q ss_pred cccccCCCccC
Q 032638 90 KTCEDCGGSGI 100 (136)
Q Consensus 90 k~Ce~C~GsGi 100 (136)
+.|..|+|+|.
T Consensus 176 ~~C~~C~G~G~ 186 (391)
T PRK14284 176 KVCDRCKGSGQ 186 (391)
T ss_pred eecCccCCeeE
Confidence 34555555543
No 8
>PRK14285 chaperone protein DnaJ; Provisional
Probab=94.74 E-value=0.015 Score=48.84 Aligned_cols=11 Identities=45% Similarity=1.404 Sum_probs=5.8
Q ss_pred CCCccCcceee
Q 032638 101 CPECKGEGFVL 111 (136)
Q Consensus 101 CpeCkGEGFVl 111 (136)
|+.|.|.|++.
T Consensus 188 C~~C~G~G~~~ 198 (365)
T PRK14285 188 CPKCYGNGKII 198 (365)
T ss_pred cCCCCCccccc
Confidence 55555555543
No 9
>PRK10767 chaperone protein DnaJ; Provisional
Probab=94.63 E-value=0.021 Score=47.64 Aligned_cols=11 Identities=45% Similarity=1.431 Sum_probs=5.3
Q ss_pred CCCccCcceee
Q 032638 101 CPECKGEGFVL 111 (136)
Q Consensus 101 CpeCkGEGFVl 111 (136)
|+.|+|.|++.
T Consensus 184 C~~C~G~G~~~ 194 (371)
T PRK10767 184 CPTCHGRGKII 194 (371)
T ss_pred CCCCCCceeEC
Confidence 55555555443
No 10
>PRK14297 chaperone protein DnaJ; Provisional
Probab=94.60 E-value=0.02 Score=48.16 Aligned_cols=22 Identities=41% Similarity=1.156 Sum_probs=13.9
Q ss_pred cccccCCCccC--------CCCccCcceee
Q 032638 90 KTCEDCGGSGI--------CPECKGEGFVL 111 (136)
Q Consensus 90 k~Ce~C~GsGi--------CpeCkGEGFVl 111 (136)
..|+.|.|+|. |+.|+|.|+++
T Consensus 149 ~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~ 178 (380)
T PRK14297 149 ENCETCNGTGAKPGTSPKTCDKCGGTGQIR 178 (380)
T ss_pred ccCCCcccccccCCCcCccCCCccCeEEEE
Confidence 45777777663 66666666654
No 11
>PRK10767 chaperone protein DnaJ; Provisional
Probab=94.58 E-value=0.017 Score=48.21 Aligned_cols=23 Identities=52% Similarity=1.178 Sum_probs=14.9
Q ss_pred cccccCCCcc--------CCCCccCcceeee
Q 032638 90 KTCEDCGGSG--------ICPECKGEGFVLK 112 (136)
Q Consensus 90 k~Ce~C~GsG--------iCpeCkGEGFVlK 112 (136)
..|+.|.|+| .|+.|+|.|.|..
T Consensus 143 ~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~ 173 (371)
T PRK10767 143 VTCDTCHGSGAKPGTSPKTCPTCHGAGQVRM 173 (371)
T ss_pred ccCCCCCCcccCCCCCCccCCCCCCeeEEEE
Confidence 4577777766 4677777766554
No 12
>PRK14282 chaperone protein DnaJ; Provisional
Probab=94.56 E-value=0.023 Score=47.62 Aligned_cols=9 Identities=67% Similarity=1.726 Sum_probs=4.7
Q ss_pred ccccCCCcc
Q 032638 91 TCEDCGGSG 99 (136)
Q Consensus 91 ~Ce~C~GsG 99 (136)
.|..|.|+|
T Consensus 154 ~C~~C~G~G 162 (369)
T PRK14282 154 TCPHCGGTG 162 (369)
T ss_pred cCCCCCccC
Confidence 455555554
No 13
>PRK14295 chaperone protein DnaJ; Provisional
Probab=94.53 E-value=0.018 Score=48.94 Aligned_cols=11 Identities=55% Similarity=1.633 Sum_probs=6.0
Q ss_pred CCCccCcceee
Q 032638 101 CPECKGEGFVL 111 (136)
Q Consensus 101 CpeCkGEGFVl 111 (136)
|+.|+|.|++.
T Consensus 208 C~~C~G~G~~~ 218 (389)
T PRK14295 208 CPDCKGRGLIA 218 (389)
T ss_pred cCCCcceeEEe
Confidence 55555555554
No 14
>PRK14287 chaperone protein DnaJ; Provisional
Probab=94.47 E-value=0.023 Score=47.88 Aligned_cols=23 Identities=43% Similarity=1.012 Sum_probs=13.7
Q ss_pred cccccCCCcc--------CCCCccCcceeee
Q 032638 90 KTCEDCGGSG--------ICPECKGEGFVLK 112 (136)
Q Consensus 90 k~Ce~C~GsG--------iCpeCkGEGFVlK 112 (136)
..|+.|.|+| .|+.|+|.|.+..
T Consensus 139 ~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~ 169 (371)
T PRK14287 139 ETCGTCHGSGAKPGTKPETCSHCGGSGQLNV 169 (371)
T ss_pred ccCCCCCCcccCCCCCCcccCCCCCEEEEEE
Confidence 4566776666 3666666665543
No 15
>PRK14300 chaperone protein DnaJ; Provisional
Probab=94.47 E-value=0.019 Score=48.19 Aligned_cols=23 Identities=39% Similarity=1.210 Sum_probs=15.0
Q ss_pred ccccccCCCccC-------------CCCccCcceee
Q 032638 89 LKTCEDCGGSGI-------------CPECKGEGFVL 111 (136)
Q Consensus 89 ~k~Ce~C~GsGi-------------CpeCkGEGFVl 111 (136)
.+.|..|+|+|. |+.|+|.|++.
T Consensus 162 ~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~ 197 (372)
T PRK14300 162 VTTCDACSGVGATRMQQGFFTIEQACHKCQGNGQII 197 (372)
T ss_pred CccCCCccCeEEEEEeeceEEEEEeCCCCCccceEe
Confidence 456777777763 66666666654
No 16
>PRK14278 chaperone protein DnaJ; Provisional
Probab=94.47 E-value=0.02 Score=48.32 Aligned_cols=11 Identities=55% Similarity=1.416 Sum_probs=5.0
Q ss_pred CCCccCcceee
Q 032638 101 CPECKGEGFVL 111 (136)
Q Consensus 101 CpeCkGEGFVl 111 (136)
|+.|+|.|++.
T Consensus 185 C~~C~G~G~~~ 195 (378)
T PRK14278 185 CPTCRGVGEVI 195 (378)
T ss_pred CCCCCccceee
Confidence 44444444443
No 17
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=94.43 E-value=0.019 Score=47.34 Aligned_cols=11 Identities=55% Similarity=1.476 Sum_probs=5.9
Q ss_pred CCCccCcceee
Q 032638 101 CPECKGEGFVL 111 (136)
Q Consensus 101 CpeCkGEGFVl 111 (136)
|+.|+|.|++.
T Consensus 189 C~~C~G~G~~~ 199 (354)
T TIGR02349 189 CPTCGGEGKII 199 (354)
T ss_pred cCCCCCcceec
Confidence 55555555544
No 18
>PRK14288 chaperone protein DnaJ; Provisional
Probab=94.43 E-value=0.023 Score=47.84 Aligned_cols=23 Identities=43% Similarity=1.224 Sum_probs=12.9
Q ss_pred ccccccCCCccC-------------CCCccCcceee
Q 032638 89 LKTCEDCGGSGI-------------CPECKGEGFVL 111 (136)
Q Consensus 89 ~k~Ce~C~GsGi-------------CpeCkGEGFVl 111 (136)
.+.|..|+|+|. |+.|.|.|++.
T Consensus 156 ~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~~ 191 (369)
T PRK14288 156 LETCKQCNGQGQVFMRQGFMSFAQTCGACQGKGKII 191 (369)
T ss_pred CcCCCCCCCCcEEEEEeceEEEEEecCCCCCCceEc
Confidence 345666666653 66666655554
No 19
>PRK14282 chaperone protein DnaJ; Provisional
Probab=94.43 E-value=0.022 Score=47.73 Aligned_cols=11 Identities=45% Similarity=1.123 Sum_probs=7.0
Q ss_pred ccccccCCCcc
Q 032638 89 LKTCEDCGGSG 99 (136)
Q Consensus 89 ~k~Ce~C~GsG 99 (136)
.+.|..|+|+|
T Consensus 169 ~~~C~~C~G~G 179 (369)
T PRK14282 169 YVTCPKCHGTG 179 (369)
T ss_pred CcCCCCCCCcC
Confidence 45666666666
No 20
>PRK14276 chaperone protein DnaJ; Provisional
Probab=94.36 E-value=0.019 Score=48.35 Aligned_cols=8 Identities=63% Similarity=1.630 Sum_probs=3.3
Q ss_pred cccCCCcc
Q 032638 92 CEDCGGSG 99 (136)
Q Consensus 92 Ce~C~GsG 99 (136)
|+.|.|+|
T Consensus 149 C~~C~G~G 156 (380)
T PRK14276 149 CHTCNGSG 156 (380)
T ss_pred CCCCcCcc
Confidence 44444433
No 21
>PRK14280 chaperone protein DnaJ; Provisional
Probab=94.31 E-value=0.027 Score=47.46 Aligned_cols=9 Identities=67% Similarity=1.560 Sum_probs=4.5
Q ss_pred ccccCCCcc
Q 032638 91 TCEDCGGSG 99 (136)
Q Consensus 91 ~Ce~C~GsG 99 (136)
.|++|.|+|
T Consensus 145 ~C~~C~G~G 153 (376)
T PRK14280 145 TCDTCHGSG 153 (376)
T ss_pred cCCCCCCcc
Confidence 455555544
No 22
>PRK14286 chaperone protein DnaJ; Provisional
Probab=94.23 E-value=0.028 Score=47.38 Aligned_cols=12 Identities=50% Similarity=1.434 Sum_probs=6.6
Q ss_pred CCCccCcceeee
Q 032638 101 CPECKGEGFVLK 112 (136)
Q Consensus 101 CpeCkGEGFVlK 112 (136)
|+.|+|.|++.+
T Consensus 192 C~~C~G~G~~~~ 203 (372)
T PRK14286 192 CPTCRGKGTVIS 203 (372)
T ss_pred CCCCCceeeEec
Confidence 555555555543
No 23
>PRK14293 chaperone protein DnaJ; Provisional
Probab=94.21 E-value=0.026 Score=47.33 Aligned_cols=11 Identities=55% Similarity=1.452 Sum_probs=5.4
Q ss_pred CCCccCcceee
Q 032638 101 CPECKGEGFVL 111 (136)
Q Consensus 101 CpeCkGEGFVl 111 (136)
|+.|+|.|++.
T Consensus 189 C~~C~G~G~~~ 199 (374)
T PRK14293 189 CPTCNGTGQVI 199 (374)
T ss_pred CCCCCcceeEe
Confidence 55555555443
No 24
>PRK14279 chaperone protein DnaJ; Provisional
Probab=94.20 E-value=0.027 Score=47.84 Aligned_cols=22 Identities=45% Similarity=1.235 Sum_probs=11.1
Q ss_pred cccccCCCccC--------CCCccCcceee
Q 032638 90 KTCEDCGGSGI--------CPECKGEGFVL 111 (136)
Q Consensus 90 k~Ce~C~GsGi--------CpeCkGEGFVl 111 (136)
..|..|.|+|. |+.|+|.|++.
T Consensus 174 ~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~ 203 (392)
T PRK14279 174 APCTTCHGSGARPGTSPKVCPTCNGSGVIS 203 (392)
T ss_pred ccCCCCccccccCCCCCCCCCCCcceEEEE
Confidence 34555555553 44455544444
No 25
>PRK14280 chaperone protein DnaJ; Provisional
Probab=94.19 E-value=0.024 Score=47.74 Aligned_cols=11 Identities=64% Similarity=1.428 Sum_probs=7.0
Q ss_pred ccccccCCCcc
Q 032638 89 LKTCEDCGGSG 99 (136)
Q Consensus 89 ~k~Ce~C~GsG 99 (136)
.+.|..|+|+|
T Consensus 160 ~~~C~~C~G~G 170 (376)
T PRK14280 160 KETCSHCGGSG 170 (376)
T ss_pred CccCCCCCCEE
Confidence 45566666665
No 26
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=94.16 E-value=0.028 Score=49.20 Aligned_cols=13 Identities=54% Similarity=0.997 Sum_probs=6.7
Q ss_pred CCCCccCcceeee
Q 032638 100 ICPECKGEGFVLK 112 (136)
Q Consensus 100 iCpeCkGEGFVlK 112 (136)
.|+.|+|.|.|-+
T Consensus 199 pC~~C~G~G~v~~ 211 (371)
T COG0484 199 PCGKCKGKGRVKK 211 (371)
T ss_pred CCCCCCCCCeEee
Confidence 3555555555443
No 27
>PRK14296 chaperone protein DnaJ; Provisional
Probab=94.06 E-value=0.033 Score=47.02 Aligned_cols=10 Identities=50% Similarity=1.149 Sum_probs=5.1
Q ss_pred cccccCCCcc
Q 032638 90 KTCEDCGGSG 99 (136)
Q Consensus 90 k~Ce~C~GsG 99 (136)
..|..|.|+|
T Consensus 150 ~~C~~C~G~G 159 (372)
T PRK14296 150 TNCSKCFGSG 159 (372)
T ss_pred eccCCCCCCc
Confidence 3455555554
No 28
>PRK14298 chaperone protein DnaJ; Provisional
Probab=94.05 E-value=0.033 Score=47.12 Aligned_cols=22 Identities=45% Similarity=1.218 Sum_probs=11.3
Q ss_pred cccccCCCccC--------CCCccCcceee
Q 032638 90 KTCEDCGGSGI--------CPECKGEGFVL 111 (136)
Q Consensus 90 k~Ce~C~GsGi--------CpeCkGEGFVl 111 (136)
..|..|.|+|. |+.|+|.|.|.
T Consensus 142 ~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~ 171 (377)
T PRK14298 142 ERCSTCSGTGAKPGTSPKRCPTCGGTGQVT 171 (377)
T ss_pred ccCCCCCCCcccCCCCCCcCCCCCCccEEE
Confidence 34555555552 55555555443
No 29
>PRK14296 chaperone protein DnaJ; Provisional
Probab=94.04 E-value=0.03 Score=47.28 Aligned_cols=10 Identities=40% Similarity=1.311 Sum_probs=6.0
Q ss_pred cccccCCCcc
Q 032638 90 KTCEDCGGSG 99 (136)
Q Consensus 90 k~Ce~C~GsG 99 (136)
..|..|+|+|
T Consensus 167 ~~C~~C~G~G 176 (372)
T PRK14296 167 HICNNCHGTG 176 (372)
T ss_pred ccCCCCCCCc
Confidence 4566666665
No 30
>PRK14289 chaperone protein DnaJ; Provisional
Probab=94.04 E-value=0.032 Score=46.93 Aligned_cols=25 Identities=44% Similarity=1.091 Sum_probs=17.8
Q ss_pred ccccccCCCccC--------CCCccCcceeeec
Q 032638 89 LKTCEDCGGSGI--------CPECKGEGFVLKK 113 (136)
Q Consensus 89 ~k~Ce~C~GsGi--------CpeCkGEGFVlK~ 113 (136)
.+.|+.|.|+|. |+.|+|.|.++..
T Consensus 154 ~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~ 186 (386)
T PRK14289 154 YVPCSHCHGTGAEGNNGSETCPTCKGSGSVTRV 186 (386)
T ss_pred ecccCCCCCCCCCCCCCCCcCCCCcCeEEEEEE
Confidence 467888888883 7777777766543
No 31
>PRK14284 chaperone protein DnaJ; Provisional
Probab=94.02 E-value=0.031 Score=47.27 Aligned_cols=26 Identities=46% Similarity=1.107 Sum_probs=21.7
Q ss_pred ccccccCCCccC--------CCCccCcceeeecC
Q 032638 89 LKTCEDCGGSGI--------CPECKGEGFVLKKL 114 (136)
Q Consensus 89 ~k~Ce~C~GsGi--------CpeCkGEGFVlK~L 114 (136)
...|+.|.|+|. |+.|+|.|.|....
T Consensus 158 ~~~C~~C~G~G~~~~~~~~~C~~C~G~G~v~~~~ 191 (391)
T PRK14284 158 YKSCDACSGSGANSSQGIKVCDRCKGSGQVVQSR 191 (391)
T ss_pred eccCCCCcccccCCCCCCeecCccCCeeEEEEEe
Confidence 568999999885 99999999887543
No 32
>PRK14276 chaperone protein DnaJ; Provisional
Probab=93.98 E-value=0.033 Score=46.93 Aligned_cols=26 Identities=42% Similarity=0.958 Sum_probs=21.4
Q ss_pred cccccccCCCccC-----------------CCCccCcceeeec
Q 032638 88 PLKTCEDCGGSGI-----------------CPECKGEGFVLKK 113 (136)
Q Consensus 88 ~~k~Ce~C~GsGi-----------------CpeCkGEGFVlK~ 113 (136)
..+.|..|+|+|. |+.|+|.|++.++
T Consensus 162 ~~~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~G~~~~~ 204 (380)
T PRK14276 162 SPVTCGKCHGSGVITVDTQTPLGMMRRQVTCDVCHGTGKEIKE 204 (380)
T ss_pred CCccCCCCCCeeEEEEEEecCCceEEEEEECCCCCCCCccccC
Confidence 4578999999984 8999999888754
No 33
>PRK14285 chaperone protein DnaJ; Provisional
Probab=93.97 E-value=0.033 Score=46.82 Aligned_cols=24 Identities=42% Similarity=0.908 Sum_probs=19.4
Q ss_pred ccccccCCCcc--------CCCCccCcceeee
Q 032638 89 LKTCEDCGGSG--------ICPECKGEGFVLK 112 (136)
Q Consensus 89 ~k~Ce~C~GsG--------iCpeCkGEGFVlK 112 (136)
...|+.|.|+| .|+.|+|.|.|+.
T Consensus 146 ~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~ 177 (365)
T PRK14285 146 NMLCESCLGKKSEKGTSPSICNMCNGSGRVMQ 177 (365)
T ss_pred cccCCCCCCcccCCCCCCccCCCccCceeEEe
Confidence 45799999988 4899999988764
No 34
>PRK14301 chaperone protein DnaJ; Provisional
Probab=93.95 E-value=0.034 Score=46.91 Aligned_cols=10 Identities=80% Similarity=1.770 Sum_probs=5.5
Q ss_pred cccccCCCcc
Q 032638 90 KTCEDCGGSG 99 (136)
Q Consensus 90 k~Ce~C~GsG 99 (136)
..|+.|.|+|
T Consensus 145 ~~C~~C~G~G 154 (373)
T PRK14301 145 VTCDDCGGSG 154 (373)
T ss_pred ccCCCCCCcc
Confidence 3455555555
No 35
>PRK14288 chaperone protein DnaJ; Provisional
Probab=93.93 E-value=0.038 Score=46.55 Aligned_cols=25 Identities=40% Similarity=1.115 Sum_probs=20.7
Q ss_pred ccccccCCCcc-------CCCCccCcceeeec
Q 032638 89 LKTCEDCGGSG-------ICPECKGEGFVLKK 113 (136)
Q Consensus 89 ~k~Ce~C~GsG-------iCpeCkGEGFVlK~ 113 (136)
.+.|+.|.|+| .|+.|+|.|.|...
T Consensus 140 ~~~C~~C~G~G~~~~~~~~C~~C~G~G~~~~~ 171 (369)
T PRK14288 140 QSVCESCDGTGAKDKALETCKQCNGQGQVFMR 171 (369)
T ss_pred eccCCCCCCcccCCCCCcCCCCCCCCcEEEEE
Confidence 34899999988 59999999988643
No 36
>PRK14281 chaperone protein DnaJ; Provisional
Probab=93.91 E-value=0.03 Score=47.53 Aligned_cols=11 Identities=64% Similarity=1.458 Sum_probs=5.3
Q ss_pred CCCccCcceee
Q 032638 101 CPECKGEGFVL 111 (136)
Q Consensus 101 CpeCkGEGFVl 111 (136)
|+.|+|.|++.
T Consensus 208 C~~C~G~G~~~ 218 (397)
T PRK14281 208 CPTCGGEGRVV 218 (397)
T ss_pred cCCCcceeeee
Confidence 55555555443
No 37
>PRK14277 chaperone protein DnaJ; Provisional
Probab=93.90 E-value=0.027 Score=47.53 Aligned_cols=11 Identities=45% Similarity=1.292 Sum_probs=5.3
Q ss_pred CCCccCcceee
Q 032638 101 CPECKGEGFVL 111 (136)
Q Consensus 101 CpeCkGEGFVl 111 (136)
|+.|+|.|++.
T Consensus 201 C~~C~G~G~~~ 211 (386)
T PRK14277 201 CDRCHGEGKII 211 (386)
T ss_pred CCCCCcceeec
Confidence 45555555443
No 38
>PRK14290 chaperone protein DnaJ; Provisional
Probab=93.88 E-value=0.033 Score=46.64 Aligned_cols=10 Identities=50% Similarity=1.205 Sum_probs=5.3
Q ss_pred cccccCCCcc
Q 032638 90 KTCEDCGGSG 99 (136)
Q Consensus 90 k~Ce~C~GsG 99 (136)
..|..|+|+|
T Consensus 166 ~~C~~C~G~G 175 (365)
T PRK14290 166 ITCPTCHGTG 175 (365)
T ss_pred ccCCCCCCcC
Confidence 4455555555
No 39
>PRK14279 chaperone protein DnaJ; Provisional
Probab=93.85 E-value=0.03 Score=47.57 Aligned_cols=25 Identities=40% Similarity=1.180 Sum_probs=17.9
Q ss_pred cccccccCCCccC-------------CCCccCcceeee
Q 032638 88 PLKTCEDCGGSGI-------------CPECKGEGFVLK 112 (136)
Q Consensus 88 ~~k~Ce~C~GsGi-------------CpeCkGEGFVlK 112 (136)
..+.|..|.|+|. |+.|+|.|++.+
T Consensus 189 ~~~~C~~C~G~G~~~~~~g~~~~~~~C~~C~G~G~~i~ 226 (392)
T PRK14279 189 SPKVCPTCNGSGVISRNQGAFGFSEPCTDCRGTGSIIE 226 (392)
T ss_pred CCCCCCCCcceEEEEEEecceEEEEecCCCCceeEEeC
Confidence 3467888888873 777777777654
No 40
>PRK14294 chaperone protein DnaJ; Provisional
Probab=93.72 E-value=0.04 Score=46.14 Aligned_cols=9 Identities=78% Similarity=1.693 Sum_probs=4.8
Q ss_pred ccccCCCcc
Q 032638 91 TCEDCGGSG 99 (136)
Q Consensus 91 ~Ce~C~GsG 99 (136)
.|..|.|+|
T Consensus 146 ~C~~C~G~G 154 (366)
T PRK14294 146 TCEECHGSG 154 (366)
T ss_pred cCCCCCCcc
Confidence 455555555
No 41
>PRK14286 chaperone protein DnaJ; Provisional
Probab=93.66 E-value=0.034 Score=46.88 Aligned_cols=24 Identities=46% Similarity=1.254 Sum_probs=14.5
Q ss_pred cccccCCCcc--------CCCCccCcceeeec
Q 032638 90 KTCEDCGGSG--------ICPECKGEGFVLKK 113 (136)
Q Consensus 90 k~Ce~C~GsG--------iCpeCkGEGFVlK~ 113 (136)
..|+.|.|+| .|+.|+|.|.|+..
T Consensus 151 ~~C~~C~G~G~~~~~~~~~C~~C~G~G~v~~~ 182 (372)
T PRK14286 151 ESCVDCNGSGASKGSSPTTCPDCGGSGQIRRT 182 (372)
T ss_pred ccCCCCcCCCcCCCCCCccCCCCcCeEEEEEE
Confidence 4566666665 36666666665543
No 42
>PRK14278 chaperone protein DnaJ; Provisional
Probab=93.65 E-value=0.041 Score=46.45 Aligned_cols=25 Identities=36% Similarity=0.846 Sum_probs=21.4
Q ss_pred ccccccCCCcc--------CCCCccCcceeeec
Q 032638 89 LKTCEDCGGSG--------ICPECKGEGFVLKK 113 (136)
Q Consensus 89 ~k~Ce~C~GsG--------iCpeCkGEGFVlK~ 113 (136)
...|+.|.|+| .|+.|+|.|.+...
T Consensus 139 ~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~ 171 (378)
T PRK14278 139 AVLCDRCHGKGTAGDSKPVTCDTCGGRGEVQTV 171 (378)
T ss_pred eccCCCCcCccCCCCCCceecCCccCceEEEEE
Confidence 46799999998 59999999988754
No 43
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=93.59 E-value=0.038 Score=47.92 Aligned_cols=24 Identities=33% Similarity=1.023 Sum_probs=16.0
Q ss_pred ccccccCCCcc-----------------CCCCccCcceeee
Q 032638 89 LKTCEDCGGSG-----------------ICPECKGEGFVLK 112 (136)
Q Consensus 89 ~k~Ce~C~GsG-----------------iCpeCkGEGFVlK 112 (136)
...|..|+|+| .|+.|+|.|++++
T Consensus 166 ~~~C~~C~G~G~~~~~~~~g~~~~q~~~~C~~C~G~G~~i~ 206 (421)
T PTZ00037 166 FVDCKLCNGQGIRVQIRQMGSMIHQTQSTCNSCNGQGKIIP 206 (421)
T ss_pred CccCCCCCCCCeEEEEEeecceeeEEEEeCCCCCCcceecc
Confidence 45677777777 3777777776664
No 44
>PRK14293 chaperone protein DnaJ; Provisional
Probab=93.58 E-value=0.044 Score=45.99 Aligned_cols=26 Identities=50% Similarity=1.062 Sum_probs=22.2
Q ss_pred ccccccCCCccC--------CCCccCcceeeecC
Q 032638 89 LKTCEDCGGSGI--------CPECKGEGFVLKKL 114 (136)
Q Consensus 89 ~k~Ce~C~GsGi--------CpeCkGEGFVlK~L 114 (136)
...|+.|.|+|. |+.|+|.|.+.+..
T Consensus 143 ~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~ 176 (374)
T PRK14293 143 LETCETCRGSGAKPGTGPTTCSTCGGAGQVRRAT 176 (374)
T ss_pred cccCCCCCCcCCCCCCCCeeCCCCCCcceEEEEE
Confidence 468999999885 99999999987654
No 45
>PRK14291 chaperone protein DnaJ; Provisional
Probab=93.56 E-value=0.045 Score=46.17 Aligned_cols=23 Identities=48% Similarity=1.285 Sum_probs=13.2
Q ss_pred cccccCCCccC--------CCCccCcceeee
Q 032638 90 KTCEDCGGSGI--------CPECKGEGFVLK 112 (136)
Q Consensus 90 k~Ce~C~GsGi--------CpeCkGEGFVlK 112 (136)
..|..|.|+|. |+.|+|.|.++.
T Consensus 157 ~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~ 187 (382)
T PRK14291 157 VPCEACGGTGYDPGSGEKVCPTCGGSGEIYQ 187 (382)
T ss_pred ccCCCCccccCCCCCCCccCCCCCCceEEEE
Confidence 45666666662 555555555543
No 46
>TIGR02349 DnaJ_bact chaperone protein DnaJ. This model represents bacterial forms of DnaJ, part of the DnaK-DnaJ-GrpE chaperone system. The three components typically are encoded by consecutive genes. DnaJ homologs occur in many genomes, typically not near DnaK and GrpE-like genes; most such genes are not included by this family. Eukaryotic (mitochondrial and chloroplast) forms are not included in the scope of this family.
Probab=93.54 E-value=0.049 Score=44.99 Aligned_cols=26 Identities=42% Similarity=1.071 Sum_probs=22.3
Q ss_pred ccccccCCCcc--------CCCCccCcceeeecC
Q 032638 89 LKTCEDCGGSG--------ICPECKGEGFVLKKL 114 (136)
Q Consensus 89 ~k~Ce~C~GsG--------iCpeCkGEGFVlK~L 114 (136)
...|..|.|+| .|+.|+|.|+|+...
T Consensus 143 ~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~ 176 (354)
T TIGR02349 143 KESCETCHGTGAKPGTDPKTCPTCGGTGQVRRQQ 176 (354)
T ss_pred CCcCCCCCCCCCCCCCCCccCCCCCCeeEEEEEE
Confidence 46799999998 499999999988654
No 47
>PRK14298 chaperone protein DnaJ; Provisional
Probab=93.52 E-value=0.045 Score=46.32 Aligned_cols=12 Identities=58% Similarity=1.193 Sum_probs=6.3
Q ss_pred CCCccCcceeee
Q 032638 101 CPECKGEGFVLK 112 (136)
Q Consensus 101 CpeCkGEGFVlK 112 (136)
|+.|+|.|.|.+
T Consensus 201 C~~C~G~g~v~~ 212 (377)
T PRK14298 201 CPVCSGTGKVRK 212 (377)
T ss_pred CCCCCCccEEEE
Confidence 555555555543
No 48
>PRK14277 chaperone protein DnaJ; Provisional
Probab=93.52 E-value=0.047 Score=46.16 Aligned_cols=25 Identities=44% Similarity=1.111 Sum_probs=21.3
Q ss_pred ccccccCCCccC--------CCCccCcceeeec
Q 032638 89 LKTCEDCGGSGI--------CPECKGEGFVLKK 113 (136)
Q Consensus 89 ~k~Ce~C~GsGi--------CpeCkGEGFVlK~ 113 (136)
...|..|.|+|. |+.|+|.|.+...
T Consensus 155 ~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~ 187 (386)
T PRK14277 155 FEKCDVCKGSGAKPGSKPVTCPVCHGTGQVRTR 187 (386)
T ss_pred eccCCCCCCCCcCCCCCCccCCCCCCEEEEEEE
Confidence 467999999885 9999999988754
No 49
>PRK14297 chaperone protein DnaJ; Provisional
Probab=93.39 E-value=0.04 Score=46.37 Aligned_cols=24 Identities=50% Similarity=1.251 Sum_probs=15.3
Q ss_pred ccccccCCCcc-----------------CCCCccCcceeee
Q 032638 89 LKTCEDCGGSG-----------------ICPECKGEGFVLK 112 (136)
Q Consensus 89 ~k~Ce~C~GsG-----------------iCpeCkGEGFVlK 112 (136)
...|..|.|+| .|+.|+|.|++.+
T Consensus 165 ~~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~G~~~~ 205 (380)
T PRK14297 165 PKTCDKCGGTGQIRVQRNTPLGSFVSTTTCDKCGGSGKVIE 205 (380)
T ss_pred CccCCCccCeEEEEEEEEcCCceeEEEEeCCCCCCCceEcC
Confidence 45677777776 3666666666544
No 50
>PRK14289 chaperone protein DnaJ; Provisional
Probab=93.32 E-value=0.052 Score=45.69 Aligned_cols=24 Identities=46% Similarity=1.079 Sum_probs=14.4
Q ss_pred ccccccCCCcc-----CCCCccCcceeee
Q 032638 89 LKTCEDCGGSG-----ICPECKGEGFVLK 112 (136)
Q Consensus 89 ~k~Ce~C~GsG-----iCpeCkGEGFVlK 112 (136)
...|..|+|.| .|+.|+|.|+|.+
T Consensus 197 ~~~C~~C~G~G~~~~~~C~~C~G~g~v~~ 225 (386)
T PRK14289 197 QSTCPTCNGEGKIIKKKCKKCGGEGIVYG 225 (386)
T ss_pred EEecCCCCccccccCcCCCCCCCCcEEee
Confidence 34566666666 4666666666654
No 51
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=93.30 E-value=0.043 Score=51.83 Aligned_cols=27 Identities=44% Similarity=1.232 Sum_probs=24.8
Q ss_pred ccccccCCCcc-------CCCCccCcceeeecCCH
Q 032638 89 LKTCEDCGGSG-------ICPECKGEGFVLKKLSE 116 (136)
Q Consensus 89 ~k~Ce~C~GsG-------iCpeCkGEGFVlK~Lse 116 (136)
.++|++|+|.| .||-|.|-||+ +++++
T Consensus 2 ~~~C~~C~g~G~i~v~~e~c~vc~gtG~~-~~~d~ 35 (715)
T COG1107 2 IKKCPECGGKGKIVVGEEECPVCHGTGFS-DDFDP 35 (715)
T ss_pred CccccccCCCceEeeeeeecccccccccc-cccCh
Confidence 57899999999 49999999999 99987
No 52
>PRK14287 chaperone protein DnaJ; Provisional
Probab=93.29 E-value=0.038 Score=46.54 Aligned_cols=24 Identities=50% Similarity=1.283 Sum_probs=16.2
Q ss_pred ccccccCCCcc-----------------CCCCccCcceeee
Q 032638 89 LKTCEDCGGSG-----------------ICPECKGEGFVLK 112 (136)
Q Consensus 89 ~k~Ce~C~GsG-----------------iCpeCkGEGFVlK 112 (136)
.+.|..|.|+| .|+.|.|.|++.+
T Consensus 155 ~~~C~~C~G~G~~~~~~~~~~G~~~~~~~C~~C~G~G~~~~ 195 (371)
T PRK14287 155 PETCSHCGGSGQLNVEQNTPFGRVVNRRVCHHCEGTGKIIK 195 (371)
T ss_pred CcccCCCCCEEEEEEEEecCCceEEEEEeCCCCCCCCcccc
Confidence 45677777776 3777777776643
No 53
>PRK14283 chaperone protein DnaJ; Provisional
Probab=93.29 E-value=0.053 Score=45.62 Aligned_cols=22 Identities=50% Similarity=1.082 Sum_probs=12.6
Q ss_pred cccccCCCccC--------CCCccCcceee
Q 032638 90 KTCEDCGGSGI--------CPECKGEGFVL 111 (136)
Q Consensus 90 k~Ce~C~GsGi--------CpeCkGEGFVl 111 (136)
..|+.|.|+|. |+.|+|.|.++
T Consensus 147 ~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~ 176 (378)
T PRK14283 147 KKCPVCNGSRAEPGSEVKTCPTCGGTGQVK 176 (378)
T ss_pred ccCCCCCccccCCCCCCccCCCcCCccEEE
Confidence 45666666553 55555555554
No 54
>PRK14295 chaperone protein DnaJ; Provisional
Probab=93.14 E-value=0.055 Score=45.98 Aligned_cols=26 Identities=38% Similarity=1.054 Sum_probs=21.2
Q ss_pred ccccccCCCcc--------CCCCccCcceeeecC
Q 032638 89 LKTCEDCGGSG--------ICPECKGEGFVLKKL 114 (136)
Q Consensus 89 ~k~Ce~C~GsG--------iCpeCkGEGFVlK~L 114 (136)
...|+.|.|+| .|+.|+|.|.|+...
T Consensus 166 ~~~C~~C~G~G~~~~~~~~~C~~C~G~G~~~~~~ 199 (389)
T PRK14295 166 QAPCPACSGTGAKNGTTPRVCPTCSGTGQVSRNS 199 (389)
T ss_pred cccCCCCcccccCCCCCCcCCCCCCCEeEEEEEe
Confidence 45799999987 499999999888754
No 55
>PRK14290 chaperone protein DnaJ; Provisional
Probab=92.98 E-value=0.063 Score=44.95 Aligned_cols=25 Identities=48% Similarity=1.229 Sum_probs=22.2
Q ss_pred ccccccCCCcc-----CCCCccCcceeeec
Q 032638 89 LKTCEDCGGSG-----ICPECKGEGFVLKK 113 (136)
Q Consensus 89 ~k~Ce~C~GsG-----iCpeCkGEGFVlK~ 113 (136)
...|..|+|.| .|+.|+|.|+|.+.
T Consensus 191 ~~~C~~C~G~G~~~~~~C~~C~G~g~v~~~ 220 (365)
T PRK14290 191 VTTCRTCGGRGRIPEEKCPRCNGTGTVVVN 220 (365)
T ss_pred EEeCCCCCCceeEccCCCCCCCCceeEEEe
Confidence 46899999999 89999999998764
No 56
>PRK14291 chaperone protein DnaJ; Provisional
Probab=92.93 E-value=0.064 Score=45.26 Aligned_cols=11 Identities=64% Similarity=1.359 Sum_probs=6.7
Q ss_pred ccccccCCCcc
Q 032638 89 LKTCEDCGGSG 99 (136)
Q Consensus 89 ~k~Ce~C~GsG 99 (136)
...|..|.|+|
T Consensus 173 ~~~C~~C~G~G 183 (382)
T PRK14291 173 EKVCPTCGGSG 183 (382)
T ss_pred CccCCCCCCce
Confidence 44566666665
No 57
>PRK14294 chaperone protein DnaJ; Provisional
Probab=92.91 E-value=0.064 Score=44.95 Aligned_cols=11 Identities=64% Similarity=1.383 Sum_probs=6.4
Q ss_pred ccccccCCCcc
Q 032638 89 LKTCEDCGGSG 99 (136)
Q Consensus 89 ~k~Ce~C~GsG 99 (136)
...|..|.|+|
T Consensus 161 ~~~C~~C~G~G 171 (366)
T PRK14294 161 PTTCPQCGGSG 171 (366)
T ss_pred cccCCCcCCeE
Confidence 34566666665
No 58
>PRK14301 chaperone protein DnaJ; Provisional
Probab=92.68 E-value=0.064 Score=45.24 Aligned_cols=23 Identities=61% Similarity=1.421 Sum_probs=13.8
Q ss_pred cccccCCCcc-------------CCCCccCcceeee
Q 032638 90 KTCEDCGGSG-------------ICPECKGEGFVLK 112 (136)
Q Consensus 90 k~Ce~C~GsG-------------iCpeCkGEGFVlK 112 (136)
..|..|.|+| .|+.|+|.|++.+
T Consensus 162 ~~C~~C~G~G~v~~~~G~~~~~~~C~~C~G~G~~~~ 197 (373)
T PRK14301 162 ETCRHCGGSGQVRQSQGFFQIAVPCPVCRGEGRVIT 197 (373)
T ss_pred cccCCccCeeEEEEEeeeEEEEEeCCCCCceeeecC
Confidence 4677777766 3666666665543
No 59
>PRK14281 chaperone protein DnaJ; Provisional
Probab=92.59 E-value=0.062 Score=45.68 Aligned_cols=25 Identities=44% Similarity=1.155 Sum_probs=21.5
Q ss_pred ccccccCCCccC-----CCCccCcceeeec
Q 032638 89 LKTCEDCGGSGI-----CPECKGEGFVLKK 113 (136)
Q Consensus 89 ~k~Ce~C~GsGi-----CpeCkGEGFVlK~ 113 (136)
...|..|+|+|. |+.|+|.|+|.++
T Consensus 205 ~~~C~~C~G~G~~~~~~C~~C~G~g~v~~~ 234 (397)
T PRK14281 205 ITACPTCGGEGRVVKDRCPACYGEGIKQGE 234 (397)
T ss_pred EEecCCCcceeeeeCCCCCCCCCCccEecc
Confidence 448999999995 9999999998753
No 60
>PRK14292 chaperone protein DnaJ; Provisional
Probab=92.17 E-value=0.087 Score=44.03 Aligned_cols=13 Identities=46% Similarity=0.997 Sum_probs=7.1
Q ss_pred CCCCccCcceeee
Q 032638 100 ICPECKGEGFVLK 112 (136)
Q Consensus 100 iCpeCkGEGFVlK 112 (136)
.|+.|+|.|.|.+
T Consensus 199 ~C~~C~G~g~v~~ 211 (371)
T PRK14292 199 PCTVCRGRGRTLK 211 (371)
T ss_pred CCCCCCCceEEee
Confidence 4555555555543
No 61
>COG0484 DnaJ DnaJ-class molecular chaperone with C-terminal Zn finger domain [Posttranslational modification, protein turnover, chaperones]
Probab=91.90 E-value=0.1 Score=45.72 Aligned_cols=24 Identities=50% Similarity=1.092 Sum_probs=14.6
Q ss_pred ccccccCCCcc--------CCCCccCcceeee
Q 032638 89 LKTCEDCGGSG--------ICPECKGEGFVLK 112 (136)
Q Consensus 89 ~k~Ce~C~GsG--------iCpeCkGEGFVlK 112 (136)
...|+.|.||| .|+.|+|.|+|..
T Consensus 142 ~~~C~~C~GsGak~gt~~~tC~tC~G~G~v~~ 173 (371)
T COG0484 142 SVTCSTCHGSGAKPGTDPKTCPTCNGSGQVRT 173 (371)
T ss_pred eeECCcCCCCCCCCCCCCCcCCCCCCcCeEEE
Confidence 35566666664 5666666666543
No 62
>PTZ00037 DnaJ_C chaperone protein; Provisional
Probab=91.61 E-value=0.1 Score=45.32 Aligned_cols=26 Identities=35% Similarity=0.949 Sum_probs=22.3
Q ss_pred cccccccCCCcc-------CCCCccCcceeeec
Q 032638 88 PLKTCEDCGGSG-------ICPECKGEGFVLKK 113 (136)
Q Consensus 88 ~~k~Ce~C~GsG-------iCpeCkGEGFVlK~ 113 (136)
....|..|+|+| .|+.|+|.|.|.+.
T Consensus 191 ~~~~C~~C~G~G~~i~~~~~C~~C~G~g~v~~~ 223 (421)
T PTZ00037 191 TQSTCNSCNGQGKIIPESKKCKNCSGKGVKKTR 223 (421)
T ss_pred EEEeCCCCCCcceeccccccCCcCCCcceeeee
Confidence 456899999999 39999999999754
No 63
>PRK14292 chaperone protein DnaJ; Provisional
Probab=91.25 E-value=0.15 Score=42.55 Aligned_cols=13 Identities=46% Similarity=1.380 Sum_probs=8.2
Q ss_pred CCCccCcceeeec
Q 032638 101 CPECKGEGFVLKK 113 (136)
Q Consensus 101 CpeCkGEGFVlK~ 113 (136)
|+.|+|.|+..++
T Consensus 186 C~~C~G~G~~~~~ 198 (371)
T PRK14292 186 CPTCRGEGQIITD 198 (371)
T ss_pred cCCCcccceecCC
Confidence 6666666666543
No 64
>PRK14283 chaperone protein DnaJ; Provisional
Probab=89.48 E-value=0.21 Score=42.12 Aligned_cols=11 Identities=64% Similarity=1.440 Sum_probs=5.7
Q ss_pred cccccCCCccC
Q 032638 90 KTCEDCGGSGI 100 (136)
Q Consensus 90 k~Ce~C~GsGi 100 (136)
..|..|.|+|.
T Consensus 164 ~~C~~C~G~G~ 174 (378)
T PRK14283 164 KTCPTCGGTGQ 174 (378)
T ss_pred ccCCCcCCccE
Confidence 44555555544
No 65
>PF14369 zf-RING_3: zinc-finger
Probab=85.39 E-value=0.43 Score=29.00 Aligned_cols=10 Identities=70% Similarity=1.810 Sum_probs=8.0
Q ss_pred CCCCccCccee
Q 032638 100 ICPECKGEGFV 110 (136)
Q Consensus 100 iCpeCkGEGFV 110 (136)
.||+|.| |||
T Consensus 23 ~CP~C~~-gFv 32 (35)
T PF14369_consen 23 ACPRCHG-GFV 32 (35)
T ss_pred CCcCCCC-cEe
Confidence 4888885 887
No 66
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=83.24 E-value=0.59 Score=44.72 Aligned_cols=21 Identities=43% Similarity=1.053 Sum_probs=17.9
Q ss_pred ccccccCCCcc--------------CCCCccCcce
Q 032638 89 LKTCEDCGGSG--------------ICPECKGEGF 109 (136)
Q Consensus 89 ~k~Ce~C~GsG--------------iCpeCkGEGF 109 (136)
.--|+.|.|.| .||.|.|..|
T Consensus 736 ~G~C~~C~G~G~~~~~~~f~~~~~~~C~~C~G~R~ 770 (924)
T TIGR00630 736 GGRCEACQGDGVIKIEMHFLPDVYVPCEVCKGKRY 770 (924)
T ss_pred CCCCCCCccceEEEEEccCCCCcccCCCCcCCcee
Confidence 45699999988 6999999887
No 67
>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=81.20 E-value=0.84 Score=26.43 Aligned_cols=20 Identities=45% Similarity=1.364 Sum_probs=12.8
Q ss_pred cccccCCC-----ccCCCCccCcceeee
Q 032638 90 KTCEDCGG-----SGICPECKGEGFVLK 112 (136)
Q Consensus 90 k~Ce~C~G-----sGiCpeCkGEGFVlK 112 (136)
|.|++|+. .-+||.| ||.|+
T Consensus 1 K~CP~C~~~V~~~~~~Cp~C---G~~F~ 25 (26)
T PF10571_consen 1 KTCPECGAEVPESAKFCPHC---GYDFE 25 (26)
T ss_pred CcCCCCcCCchhhcCcCCCC---CCCCc
Confidence 46777764 4567777 55554
No 68
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=80.46 E-value=0.81 Score=39.84 Aligned_cols=27 Identities=37% Similarity=0.898 Sum_probs=22.3
Q ss_pred cccccccccccCCCcc-------CCCCccCccee
Q 032638 84 ETEIPLKTCEDCGGSG-------ICPECKGEGFV 110 (136)
Q Consensus 84 ~~E~~~k~Ce~C~GsG-------iCpeCkGEGFV 110 (136)
..+..+-.|.+|+|+| .|+.|+|.+++
T Consensus 165 ~~qs~q~~C~~C~G~G~~~~~kd~C~~C~G~~~v 198 (337)
T KOG0712|consen 165 MVQSPQLVCDSCNGSGETISLKDRCKTCSGAKVV 198 (337)
T ss_pred ccccceeEeccCCCccccccccccCcccccchhh
Confidence 3467788899999988 59999999986
No 69
>PRK00488 pheS phenylalanyl-tRNA synthetase subunit alpha; Validated
Probab=79.47 E-value=0.94 Score=39.20 Aligned_cols=19 Identities=53% Similarity=1.452 Sum_probs=16.6
Q ss_pred ccccCCCccCCCCccCccee
Q 032638 91 TCEDCGGSGICPECKGEGFV 110 (136)
Q Consensus 91 ~Ce~C~GsGiCpeCkGEGFV 110 (136)
.|..|+|.| |+-||+.|++
T Consensus 262 ~~~~~~g~g-c~~ck~~~Wi 280 (339)
T PRK00488 262 SCFKCGGKG-CRVCKGTGWL 280 (339)
T ss_pred EEeccCCCc-ccccCCCCce
Confidence 588999877 9999999975
No 70
>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=78.01 E-value=1.2 Score=27.10 Aligned_cols=20 Identities=45% Similarity=1.399 Sum_probs=12.4
Q ss_pred ccccCCCcc----------CCCCccCcceeeec
Q 032638 91 TCEDCGGSG----------ICPECKGEGFVLKK 113 (136)
Q Consensus 91 ~Ce~C~GsG----------iCpeCkGEGFVlK~ 113 (136)
.|+.||.+. +|++| |.|+..
T Consensus 2 ~Cp~Cg~~~~~~D~~~g~~vC~~C---G~Vl~e 31 (43)
T PF08271_consen 2 KCPNCGSKEIVFDPERGELVCPNC---GLVLEE 31 (43)
T ss_dssp SBTTTSSSEEEEETTTTEEEETTT----BBEE-
T ss_pred CCcCCcCCceEEcCCCCeEECCCC---CCEeec
Confidence 467776543 78888 777764
No 71
>PF12669 P12: Virus attachment protein p12 family
Probab=77.97 E-value=2.7 Score=27.90 Aligned_cols=36 Identities=25% Similarity=0.501 Sum_probs=16.5
Q ss_pred HHHHHHHHHHHHHHHHhc-CCCccccccccccccCCCccCC
Q 032638 62 AIAATVVGAAATLLVRRT-KGSEETEIPLKTCEDCGGSGIC 101 (136)
Q Consensus 62 aiaa~vVGaAat~Lvrr~-k~~e~~E~~~k~Ce~C~GsGiC 101 (136)
+|++.|+++++.+++|+. |.... ..-|..|+|.+-|
T Consensus 3 II~~Ii~~~~~~v~~r~~~k~~K~----G~~c~gCs~~sgC 39 (58)
T PF12669_consen 3 IIGIIILAAVAYVAIRKFIKDKKK----GGCCCGCSGCSGC 39 (58)
T ss_pred eHHHHHHHHHHHHHHHHHHHHhhc----CCCCCCCCCCCCc
Confidence 344555555554443433 22211 1456677554445
No 72
>COG2871 NqrF Na+-transporting NADH:ubiquinone oxidoreductase, subunit NqrF [Energy production and conversion]
Probab=76.64 E-value=3.7 Score=36.94 Aligned_cols=15 Identities=47% Similarity=1.234 Sum_probs=13.0
Q ss_pred ccccCCCccCCCCcc
Q 032638 91 TCEDCGGSGICPECK 105 (136)
Q Consensus 91 ~Ce~C~GsGiCpeCk 105 (136)
.=+.|||-|-|.+|+
T Consensus 68 i~SaCGGggsC~QCk 82 (410)
T COG2871 68 ISSACGGGGSCGQCK 82 (410)
T ss_pred cccCCCCCccccccE
Confidence 346899999999997
No 73
>PRK14715 DNA polymerase II large subunit; Provisional
Probab=75.18 E-value=2.7 Score=43.32 Aligned_cols=45 Identities=31% Similarity=0.633 Sum_probs=38.3
Q ss_pred cccccccCCC-------ccCCCCccCcceeeecCCHHHHHHHHHHHhhhhhhhcc
Q 032638 88 PLKTCEDCGG-------SGICPECKGEGFVLKKLSEETAERARLTAKNMATRYTA 135 (136)
Q Consensus 88 ~~k~Ce~C~G-------sGiCpeCkGEGFVlK~Lsee~A~kAR~~AKNmATRyTA 135 (136)
|.--| .||- +|-||+|-| =|.=-.|+-+.+|=-..||.||++|..
T Consensus 1541 Q~~RC-kC~~kyRR~PL~G~C~kCGg--~~ilTV~kGsv~KYl~~a~~~~~~y~v 1592 (1627)
T PRK14715 1541 QEFRC-KCGAKYRRVPLKGKCPKCGS--KLILTVSKGAVEKYMPVAKMMAEKYNV 1592 (1627)
T ss_pred cceee-cCCCccccCCCCCcCcccCC--eEEEEEecchHHHHHHHHHHHHHHcCc
Confidence 45679 9996 799999988 455578999999999999999999963
No 74
>TIGR02538 type_IV_pilB type IV-A pilus assembly ATPase PilB. This model describes a protein of type IV pilus biogenesis designated PilB in Pseudomonas aeruginosa but PilF in Neisseria gonorrhoeae; the more common usage, reflected here, is PilB. This protein is an ATPase involved in protein export for pilin assembly and is closely related to GspE (TIGR02533) of type II secretion, also called the main terminal branch of the general secretion pathway. Note that type IV pilus systems are often divided into type IV-A and IV-B, with the latter group including bundle-forming pilus, mannose-sensitive hemagglutinin, etc. Members of this family are found in type IV-A systems.
Probab=73.85 E-value=1.6 Score=38.81 Aligned_cols=10 Identities=40% Similarity=1.115 Sum_probs=8.9
Q ss_pred CCCCccCcce
Q 032638 100 ICPECKGEGF 109 (136)
Q Consensus 100 iCpeCkGEGF 109 (136)
-|++|+|.||
T Consensus 490 gC~~C~~~Gy 499 (564)
T TIGR02538 490 GCDECSNTGY 499 (564)
T ss_pred CCcccCCCCC
Confidence 4999999997
No 75
>TIGR02642 phage_xxxx uncharacterized phage protein. This uncharacterized protein is found in prophage regions of Shewanella oneidensis MR-1, Vibrio vulnificus YJ016, Yersinia pseudotuberculosis IP 32953, and Aeromonas hydrophila ATCC7966. It appears to have regions of sequence similarity to phage lambda antitermination protein Q.
Probab=73.83 E-value=1.8 Score=34.69 Aligned_cols=15 Identities=40% Similarity=1.134 Sum_probs=14.2
Q ss_pred ccCCCCccCcceeee
Q 032638 98 SGICPECKGEGFVLK 112 (136)
Q Consensus 98 sGiCpeCkGEGFVlK 112 (136)
+-.||.|.|.|++.+
T Consensus 99 ~~~C~~C~G~G~~i~ 113 (186)
T TIGR02642 99 SCKCPRCRGTGLIQR 113 (186)
T ss_pred CCcCCCCCCeeEEec
Confidence 789999999999997
No 76
>TIGR00354 polC DNA polymerase, archaeal type II, large subunit. This model represents the large subunit, DP2, of a two subunit novel Archaeal replicative DNA polymerase first characterized for Pyrococcus furiosus. Structure of DP2 appears to be organized 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.
Probab=73.32 E-value=3.2 Score=41.44 Aligned_cols=46 Identities=20% Similarity=0.372 Sum_probs=39.1
Q ss_pred cccccccCCC-------ccCCCCccCcceeeecCCHHHHHHHHHHHhhhhhhhcc
Q 032638 88 PLKTCEDCGG-------SGICPECKGEGFVLKKLSEETAERARLTAKNMATRYTA 135 (136)
Q Consensus 88 ~~k~Ce~C~G-------sGiCpeCkGEGFVlK~Lsee~A~kAR~~AKNmATRyTA 135 (136)
|..-|..|+- +|-||+|-| =|.=-.++-+.+|=-..||+||+||..
T Consensus 1011 Q~fRC~kC~~kYRR~PL~G~C~kCGg--~lilTV~~GsV~KYl~~s~~la~~Y~v 1063 (1095)
T TIGR00354 1011 QEVRCTKCNTKYRRIPLVGKCLKCGN--NLTLTVSKGSVMKYLELSKFLAENYNV 1063 (1095)
T ss_pred cceeecccCCccccCCCCCcccccCC--eEEEEEecchhHhhHHHHHHHHHHcCc
Confidence 4568999996 799999988 455568899999999999999999963
No 77
>COG4260 Membrane protease subunit, stomatin/prohibitin family [Amino acid transport and metabolism]
Probab=71.74 E-value=1.7 Score=38.54 Aligned_cols=22 Identities=59% Similarity=1.490 Sum_probs=13.4
Q ss_pred cccccccCC-Ccc---------CCCCccCccee
Q 032638 88 PLKTCEDCG-GSG---------ICPECKGEGFV 110 (136)
Q Consensus 88 ~~k~Ce~C~-GsG---------iCpeCkGEGFV 110 (136)
..+.|.+|| |+- .||+| |.|||
T Consensus 314 k~nfc~ncG~~~t~~~~ng~a~fcp~c-gq~~~ 345 (345)
T COG4260 314 KLNFCLNCGCGTTADFDNGKAKFCPEC-GQGFV 345 (345)
T ss_pred ccccccccCcccccCCccchhhhChhh-cCCCC
Confidence 456778887 332 58888 44553
No 78
>PRK14714 DNA polymerase II large subunit; Provisional
Probab=71.46 E-value=3.8 Score=41.63 Aligned_cols=46 Identities=33% Similarity=0.580 Sum_probs=39.4
Q ss_pred cccccccCCC-------ccCCCCccCcceeeecCCHHHHHHHHHHHhhhhhhhcc
Q 032638 88 PLKTCEDCGG-------SGICPECKGEGFVLKKLSEETAERARLTAKNMATRYTA 135 (136)
Q Consensus 88 ~~k~Ce~C~G-------sGiCpeCkGEGFVlK~Lsee~A~kAR~~AKNmATRyTA 135 (136)
|.--|..||- +|-||+|-| =|.=-.++-+.+|=-..||+||++|..
T Consensus 1252 Q~~RC~kC~~kyRR~PL~G~C~kCGg--~iilTv~~Gsv~KYl~~a~~~~~~y~~ 1304 (1337)
T PRK14714 1252 QEFRCLKCGTKYRRMPLAGKCRKCGG--RIILTVHEGSVEKYLDTAKMVATEYNV 1304 (1337)
T ss_pred cceeecccCcccccCCCCCcccccCC--eEEEEEecchHHHHHHHHHHHHHHcCc
Confidence 4568999996 799999988 455678999999999999999999963
No 79
>TIGR02533 type_II_gspE general secretory pathway protein E. This family describes GspE, the E protein of the type II secretion system, also called the main terminal branch of the general secretion pathway. This model separates GspE from the PilB protein of type IV pilin biosynthesis.
Probab=70.56 E-value=2 Score=37.86 Aligned_cols=10 Identities=40% Similarity=1.248 Sum_probs=8.9
Q ss_pred CCCCccCcce
Q 032638 100 ICPECKGEGF 109 (136)
Q Consensus 100 iCpeCkGEGF 109 (136)
-|++|+|.||
T Consensus 414 GC~~C~~tGy 423 (486)
T TIGR02533 414 GCPHCNHTGY 423 (486)
T ss_pred CchhccCCCC
Confidence 4999999997
No 80
>PRK04023 DNA polymerase II large subunit; Validated
Probab=68.27 E-value=5 Score=40.19 Aligned_cols=46 Identities=28% Similarity=0.635 Sum_probs=38.6
Q ss_pred cccccccCCC-------ccCCCCccCcceeeecCCHHHHHHHHHHHhhhhhhhcc
Q 032638 88 PLKTCEDCGG-------SGICPECKGEGFVLKKLSEETAERARLTAKNMATRYTA 135 (136)
Q Consensus 88 ~~k~Ce~C~G-------sGiCpeCkGEGFVlK~Lsee~A~kAR~~AKNmATRyTA 135 (136)
|.--|..||. +|-||+|. |=|.=-.++-+.+|=-..||+||.+|..
T Consensus 1036 Q~fRC~kC~~kYRR~PL~G~C~kCG--g~lilTVh~GsV~KYl~~s~~la~~Y~v 1088 (1121)
T PRK04023 1036 QEFRCTKCGAKYRRPPLSGKCPKCG--GNLILTVHKGSVEKYLEVSKKLAEEYGV 1088 (1121)
T ss_pred cceeecccCcccccCCCCCcCccCC--CeEEEEEecchHHHHHHHHHHHHHHcCC
Confidence 4568999997 79999993 4466678999999999999999999963
No 81
>TIGR00630 uvra excinuclease ABC, A subunit. This family is based on the phylogenomic analysis of JA Eisen (1999, Ph.D. Thesis, Stanford University).
Probab=67.82 E-value=3.3 Score=39.81 Aligned_cols=23 Identities=48% Similarity=1.090 Sum_probs=19.5
Q ss_pred ccccccCCCc---------------cCCCCccCcceee
Q 032638 89 LKTCEDCGGS---------------GICPECKGEGFVL 111 (136)
Q Consensus 89 ~k~Ce~C~Gs---------------GiCpeCkGEGFVl 111 (136)
.-.|++|+-+ |-||.|.|-|++.
T Consensus 250 ~~~c~~~g~~~~~~~~~~FSfNsp~G~Cp~C~G~G~~~ 287 (924)
T TIGR00630 250 HAACPECGFSLPELEPRLFSFNSPYGACPECSGLGIKQ 287 (924)
T ss_pred cccCcccCcccCcCChhhcCCCCCcCCCCCCccceeee
Confidence 3579999876 7799999999975
No 82
>COG1107 Archaea-specific RecJ-like exonuclease, contains DnaJ-type Zn finger domain [DNA replication, recombination, and repair]
Probab=67.39 E-value=2.9 Score=40.03 Aligned_cols=23 Identities=52% Similarity=1.203 Sum_probs=18.5
Q ss_pred cccccCCCcc------CCCCccCcceeee
Q 032638 90 KTCEDCGGSG------ICPECKGEGFVLK 112 (136)
Q Consensus 90 k~Ce~C~GsG------iCpeCkGEGFVlK 112 (136)
.-|+.|.|.| -||+|.|-|.+++
T Consensus 54 ~pc~~c~gkG~V~v~~~c~~c~G~gkv~~ 82 (715)
T COG1107 54 IPCPKCRGKGTVTVYDTCPECGGTGKVLT 82 (715)
T ss_pred CCCCeeccceeEEEEeecccCCCceeEEe
Confidence 3688888888 4888888888875
No 83
>COG1933 Archaeal DNA polymerase II, large subunit [DNA replication, recombination, and repair]
Probab=65.77 E-value=4.7 Score=34.49 Aligned_cols=45 Identities=31% Similarity=0.547 Sum_probs=38.1
Q ss_pred cccccccCCC-------ccCCCCccCcceeeecCCHHHHHHHHHHHhhhhhhhc
Q 032638 88 PLKTCEDCGG-------SGICPECKGEGFVLKKLSEETAERARLTAKNMATRYT 134 (136)
Q Consensus 88 ~~k~Ce~C~G-------sGiCpeCkGEGFVlK~Lsee~A~kAR~~AKNmATRyT 134 (136)
+..-|..|+- +|-|+.|+| =+.--.++++..|---.+|-++|+|+
T Consensus 166 q~~rc~~c~~k~rr~pl~g~c~kcg~--~~~ltv~~g~v~kyL~~t~~~~~~y~ 217 (253)
T COG1933 166 QEFRCVKCNTKFRRPPLDGKCPICGG--KIVLTVSKGAIEKYLGTAKMLVTEYK 217 (253)
T ss_pred heeehHhhhhhhcCCCccccccccCC--eEEEEEeccHHHHHHHHHHHHHHHcC
Confidence 4567888874 899999999 56667788899999999999999997
No 84
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=64.97 E-value=3.4 Score=42.77 Aligned_cols=22 Identities=41% Similarity=0.945 Sum_probs=18.7
Q ss_pred cccccccCCCcc--------------CCCCccCcce
Q 032638 88 PLKTCEDCGGSG--------------ICPECKGEGF 109 (136)
Q Consensus 88 ~~k~Ce~C~GsG--------------iCpeCkGEGF 109 (136)
+.--||.|.|.| .|+.|+|..|
T Consensus 1606 ~~GrC~~C~G~G~i~i~m~fl~dv~~~C~~C~G~R~ 1641 (1809)
T PRK00635 1606 KQGQCSDCWGLGYQWIDRAFYALEKRPCPTCSGFRI 1641 (1809)
T ss_pred CCCCCCCCccCceEEEecccCCCcccCCCCCCCcCC
Confidence 345699999999 4999999887
No 85
>PRK06921 hypothetical protein; Provisional
Probab=64.70 E-value=3.7 Score=33.09 Aligned_cols=12 Identities=33% Similarity=0.811 Sum_probs=6.9
Q ss_pred cccccCCCccCC
Q 032638 90 KTCEDCGGSGIC 101 (136)
Q Consensus 90 k~Ce~C~GsGiC 101 (136)
.+|+.|+++|.-
T Consensus 33 ~~Cp~C~dtG~i 44 (266)
T PRK06921 33 YDCPKCKDRGII 44 (266)
T ss_pred CCCCCCCCCEEE
Confidence 456666655554
No 86
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=64.03 E-value=4.3 Score=39.10 Aligned_cols=24 Identities=42% Similarity=0.880 Sum_probs=19.9
Q ss_pred cccccccCCC---------------ccCCCCccCcceee
Q 032638 88 PLKTCEDCGG---------------SGICPECKGEGFVL 111 (136)
Q Consensus 88 ~~k~Ce~C~G---------------sGiCpeCkGEGFVl 111 (136)
..-.|++|+- .|-||.|.|-|++.
T Consensus 251 ~~~~c~~~g~~~~~~~p~~FSfN~p~G~Cp~C~G~G~~~ 289 (943)
T PRK00349 251 EKFACPVCGFSIPELEPRLFSFNSPYGACPTCDGLGVKL 289 (943)
T ss_pred ccccCcccCCCcCcCChhhcCCCCccCCCCcCCCceeEe
Confidence 4557999994 48899999999985
No 87
>PRK00349 uvrA excinuclease ABC subunit A; Reviewed
Probab=62.95 E-value=3.6 Score=39.61 Aligned_cols=22 Identities=41% Similarity=0.969 Sum_probs=17.1
Q ss_pred ccccccCCCcc--------------CCCCccCccee
Q 032638 89 LKTCEDCGGSG--------------ICPECKGEGFV 110 (136)
Q Consensus 89 ~k~Ce~C~GsG--------------iCpeCkGEGFV 110 (136)
.--|+.|.|.| .||.|.|..|=
T Consensus 738 ~G~C~~C~G~G~~~~~~~f~~~~~~~C~~C~G~R~~ 773 (943)
T PRK00349 738 GGRCEACQGDGVIKIEMHFLPDVYVPCDVCKGKRYN 773 (943)
T ss_pred CCCCCcccccceEEEEeccCCCccccCccccCcccc
Confidence 34599998885 79999998873
No 88
>PRK00762 hypA hydrogenase nickel incorporation protein; Provisional
Probab=60.85 E-value=5.6 Score=29.31 Aligned_cols=23 Identities=26% Similarity=0.534 Sum_probs=16.5
Q ss_pred ccccccccccCCCc--------------cCCCCccCcc
Q 032638 85 TEIPLKTCEDCGGS--------------GICPECKGEG 108 (136)
Q Consensus 85 ~E~~~k~Ce~C~Gs--------------GiCpeCkGEG 108 (136)
.....-.| +||-. -.||+|.+..
T Consensus 66 ~vp~~~~C-~Cg~~~~~~~~~~~~~~~~~~CP~Cgs~~ 102 (124)
T PRK00762 66 MIPVEIEC-ECGYEGVVDEDEIDHYAAVIECPVCGNKR 102 (124)
T ss_pred ecCeeEEe-eCcCcccccccchhccccCCcCcCCCCCC
Confidence 34556789 99966 3599998544
No 89
>PF11859 DUF3379: Protein of unknown function (DUF3379); InterPro: IPR021806 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 234 to 251 amino acids in length.
Probab=58.93 E-value=2.9 Score=34.82 Aligned_cols=48 Identities=29% Similarity=0.296 Sum_probs=28.4
Q ss_pred eeccccceeccccCceeeeeecch-hhhhhccccccccchhhHHHHHHHHHH
Q 032638 17 TRDLKLRVCTGLHGKAFSSIDIKS-QEQERKLPTVSSALPETAASVAIAATV 67 (136)
Q Consensus 17 ~~~~~~~v~~~~~~~~~~s~~vk~-q~~~r~~~~v~~Alpetaas~aiaa~v 67 (136)
.+-+++.||.++.|++.+++-.+- +.++|+..+...|+ |||+|.++|+
T Consensus 46 ~~Al~VdVPddLAdkiLl~Qs~~~~~~~r~~f~r~~lAl---AASVAFv~Gl 94 (232)
T PF11859_consen 46 EQALKVDVPDDLADKILLRQSLEEHQVQRPRFARWHLAL---AASVAFVVGL 94 (232)
T ss_pred HHHcCCCCCccHHHHHHhhchhhhhhhhccchHHHHHHH---HHHHHHHHHH
Confidence 345778899999999654443322 23333435665554 7776655443
No 90
>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=57.58 E-value=6.9 Score=29.76 Aligned_cols=24 Identities=25% Similarity=0.408 Sum_probs=19.8
Q ss_pred cccccccccccCC----------CccCCCCccCc
Q 032638 84 ETEIPLKTCEDCG----------GSGICPECKGE 107 (136)
Q Consensus 84 ~~E~~~k~Ce~C~----------GsGiCpeCkGE 107 (136)
+.+...-.|+.|+ ....||+|.|+
T Consensus 104 e~~~~~Y~Cp~c~~r~tf~eA~~~~F~Cp~Cg~~ 137 (158)
T TIGR00373 104 ETNNMFFICPNMCVRFTFNEAMELNFTCPRCGAM 137 (158)
T ss_pred ccCCCeEECCCCCcEeeHHHHHHcCCcCCCCCCE
Confidence 4567888999998 46899999886
No 91
>cd03031 GRX_GRX_like Glutaredoxin (GRX) family, GRX-like domain containing protein subfamily; composed of uncharacterized eukaryotic proteins containing a GRX-like domain having only one conserved cysteine, aligning to the C-terminal cysteine of the CXXC motif of GRXs. This subfamily is predominantly composed of plant proteins. GRX is a glutathione (GSH) dependent reductase, catalyzing the disulfide reduction of target proteins via a redox active CXXC motif using a similar dithiol mechanism employed by TRXs. GRX has preference for mixed GSH disulfide substrates, in which it uses a monothiol mechanism where only the N-terminal cysteine is required. Proteins containing only the C-terminal cysteine are generally redox inactive.
Probab=56.85 E-value=9.4 Score=29.09 Aligned_cols=26 Identities=38% Similarity=0.818 Sum_probs=21.0
Q ss_pred ccccccccCCCcc--CCCCccCcceeee
Q 032638 87 IPLKTCEDCGGSG--ICPECKGEGFVLK 112 (136)
Q Consensus 87 ~~~k~Ce~C~GsG--iCpeCkGEGFVlK 112 (136)
.....|+.|||.+ .|+.|+|-=.|+.
T Consensus 97 ~~~~~C~~Cgg~rfv~C~~C~Gs~k~~~ 124 (147)
T cd03031 97 AGGGVCEGCGGARFVPCSECNGSCKVFA 124 (147)
T ss_pred cCCCCCCCCCCcCeEECCCCCCcceEEe
Confidence 3456799999988 5999999877764
No 92
>PF12301 CD99L2: CD99 antigen like protein 2; InterPro: IPR022078 This family of proteins is found in eukaryotes. Proteins in this family are typically between 165 and 237 amino acids in length. CD99L2 and CD99 are involved in trans-endothelial migration of neutrophils in vitro and in the recruitment of neutrophils into inflamed peritoneum.
Probab=56.68 E-value=13 Score=29.55 Aligned_cols=20 Identities=25% Similarity=0.469 Sum_probs=16.3
Q ss_pred HHHHHHHHHHHHHHHHHhcC
Q 032638 61 VAIAATVVGAAATLLVRRTK 80 (136)
Q Consensus 61 ~aiaa~vVGaAat~Lvrr~k 80 (136)
.||++++|||++.++...+|
T Consensus 122 sav~valvGAvsSyiaYqkK 141 (169)
T PF12301_consen 122 SAVVVALVGAVSSYIAYQKK 141 (169)
T ss_pred HHHHHHHHHHHHHHHHHHhh
Confidence 46777899999999987765
No 93
>PF14570 zf-RING_4: RING/Ubox like zinc-binding domain; PDB: 1E4U_A 1UR6_B.
Probab=55.82 E-value=3.6 Score=27.04 Aligned_cols=19 Identities=32% Similarity=0.983 Sum_probs=8.9
Q ss_pred cccccccC------CCccCCCCccC
Q 032638 88 PLKTCEDC------GGSGICPECKG 106 (136)
Q Consensus 88 ~~k~Ce~C------~GsGiCpeCkG 106 (136)
..++|-+| .+.|.||.|+-
T Consensus 21 gf~IC~~C~~~i~~~~~g~CPgCr~ 45 (48)
T PF14570_consen 21 GFQICRFCYHDILENEGGRCPGCRE 45 (48)
T ss_dssp S----HHHHHHHTTSS-SB-TTT--
T ss_pred CCcHHHHHHHHHHhccCCCCCCCCC
Confidence 34677777 58999999974
No 94
>PRK00635 excinuclease ABC subunit A; Provisional
Probab=55.80 E-value=6.1 Score=40.98 Aligned_cols=24 Identities=25% Similarity=0.688 Sum_probs=19.6
Q ss_pred cccccccCCCc---------------cCCCCccCcceee
Q 032638 88 PLKTCEDCGGS---------------GICPECKGEGFVL 111 (136)
Q Consensus 88 ~~k~Ce~C~Gs---------------GiCpeCkGEGFVl 111 (136)
..-.|++|+-+ |-||+|+|-|+++
T Consensus 243 ~~~~cp~~~~~~~~~~p~~FSfNsp~GaCp~C~GlG~~~ 281 (1809)
T PRK00635 243 TQATIPETQQTYTPLTPQLFSPHSLEDRCPQCQGSGIFI 281 (1809)
T ss_pred ccccCCccCcccCcCChhhcCCCCccccCCCCCCccccc
Confidence 45679999654 7799999999986
No 95
>TIGR02007 fdx_isc ferredoxin, 2Fe-2S type, ISC system. This family consists of proteobacterial ferredoxins associated with and essential to the ISC system of 2Fe-2S cluster assembly. This family is closely related to (but excludes) eukaryotic (mitochondrial) adrenodoxins, which are ferredoxins involved in electron transfer to P450 cytochromes.
Probab=54.21 E-value=5.6 Score=28.21 Aligned_cols=13 Identities=31% Similarity=0.777 Sum_probs=11.3
Q ss_pred cCCCccCCCCccC
Q 032638 94 DCGGSGICPECKG 106 (136)
Q Consensus 94 ~C~GsGiCpeCkG 106 (136)
.|+|.|.|..|..
T Consensus 40 ~CgG~G~CgtC~v 52 (110)
T TIGR02007 40 ACEKSCACTTCHC 52 (110)
T ss_pred cCCCCceeCCCEE
Confidence 5999999999943
No 96
>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=53.60 E-value=9 Score=23.46 Aligned_cols=10 Identities=40% Similarity=0.936 Sum_probs=6.6
Q ss_pred CccCCCCccC
Q 032638 97 GSGICPECKG 106 (136)
Q Consensus 97 GsGiCpeCkG 106 (136)
..-.||+|.+
T Consensus 25 ~~~~CP~Cg~ 34 (42)
T PF09723_consen 25 DPVPCPECGS 34 (42)
T ss_pred CCCcCCCCCC
Confidence 4556777766
No 97
>KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=53.17 E-value=6.6 Score=35.49 Aligned_cols=21 Identities=43% Similarity=1.134 Sum_probs=10.8
Q ss_pred cccccCCCccC--CCCccCccee
Q 032638 90 KTCEDCGGSGI--CPECKGEGFV 110 (136)
Q Consensus 90 k~Ce~C~GsGi--CpeCkGEGFV 110 (136)
++|.-|.|-|. |--|+|+|=|
T Consensus 246 ~~C~tC~grG~k~C~TC~gtgsl 268 (406)
T KOG2813|consen 246 KECHTCKGRGKKPCTTCSGTGSL 268 (406)
T ss_pred ccCCcccCCCCcccccccCccce
Confidence 34444444443 5566666644
No 98
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=53.09 E-value=9.7 Score=29.70 Aligned_cols=24 Identities=25% Similarity=0.503 Sum_probs=19.1
Q ss_pred cccccccccccCC----------CccCCCCccCc
Q 032638 84 ETEIPLKTCEDCG----------GSGICPECKGE 107 (136)
Q Consensus 84 ~~E~~~k~Ce~C~----------GsGiCpeCkGE 107 (136)
+.+.+.-.|+.|+ ..-.||.|.|+
T Consensus 112 e~~~~~Y~Cp~C~~rytf~eA~~~~F~Cp~Cg~~ 145 (178)
T PRK06266 112 EENNMFFFCPNCHIRFTFDEAMEYGFRCPQCGEM 145 (178)
T ss_pred ccCCCEEECCCCCcEEeHHHHhhcCCcCCCCCCC
Confidence 4466788999996 46899999876
No 99
>PRK00564 hypA hydrogenase nickel incorporation protein; Provisional
Probab=53.04 E-value=10 Score=27.69 Aligned_cols=25 Identities=24% Similarity=0.683 Sum_probs=16.9
Q ss_pred ccccccccccCCCc------c--CCCCccCcce
Q 032638 85 TEIPLKTCEDCGGS------G--ICPECKGEGF 109 (136)
Q Consensus 85 ~E~~~k~Ce~C~Gs------G--iCpeCkGEGF 109 (136)
...-+-.|.+||-. . .||.|.+..+
T Consensus 67 ~vp~~~~C~~Cg~~~~~~~~~~~~CP~Cgs~~~ 99 (117)
T PRK00564 67 DEKVELECKDCSHVFKPNALDYGVCEKCHSKNV 99 (117)
T ss_pred ecCCEEEhhhCCCccccCCccCCcCcCCCCCce
Confidence 34456789999832 2 3999986543
No 100
>COG5349 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.60 E-value=5.5 Score=31.11 Aligned_cols=16 Identities=44% Similarity=1.032 Sum_probs=12.1
Q ss_pred CccCCCCccCcceeeec
Q 032638 97 GSGICPECKGEGFVLKK 113 (136)
Q Consensus 97 GsGiCpeCkGEGFVlK~ 113 (136)
=-|.||+| |||-+|.-
T Consensus 20 l~grCP~C-GeGrLF~g 35 (126)
T COG5349 20 LRGRCPRC-GEGRLFRG 35 (126)
T ss_pred hcCCCCCC-CCchhhhh
Confidence 35789999 78877754
No 101
>KOG0715 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=51.62 E-value=7.9 Score=32.24 Aligned_cols=36 Identities=31% Similarity=0.723 Sum_probs=28.8
Q ss_pred cCCCccccccccccccCCCcc-------------CCCCccCcceeeecC
Q 032638 79 TKGSEETEIPLKTCEDCGGSG-------------ICPECKGEGFVLKKL 114 (136)
Q Consensus 79 ~k~~e~~E~~~k~Ce~C~GsG-------------iCpeCkGEGFVlK~L 114 (136)
....+++....+.|.-|.|.| -|+.|+|.|.|++.=
T Consensus 171 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~c~~~~~~~~~~ 219 (288)
T KOG0715|consen 171 FGSGAEEGAKRESCKTCSGRGLVSNPKEDPFILYTCSYCLGRGLVLRDN 219 (288)
T ss_pred cCcCcccccccccchhhhCcccccccccCCcceeecccccccceeccch
Confidence 334467788889999999999 399999999998763
No 102
>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=51.54 E-value=9.1 Score=27.56 Aligned_cols=24 Identities=29% Similarity=0.688 Sum_probs=15.1
Q ss_pred cccccccccCCCcc-------CCCCccCcce
Q 032638 86 EIPLKTCEDCGGSG-------ICPECKGEGF 109 (136)
Q Consensus 86 E~~~k~Ce~C~GsG-------iCpeCkGEGF 109 (136)
..-.-.|.+||-.. .||.|.+..+
T Consensus 67 ~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (113)
T PF01155_consen 67 VPARARCRDCGHEFEPDEFDFSCPRCGSPDV 97 (113)
T ss_dssp E--EEEETTTS-EEECHHCCHH-SSSSSS-E
T ss_pred cCCcEECCCCCCEEecCCCCCCCcCCcCCCc
Confidence 34566899999765 5999998765
No 103
>PRK00423 tfb transcription initiation factor IIB; Reviewed
Probab=51.50 E-value=7.5 Score=32.09 Aligned_cols=25 Identities=32% Similarity=0.925 Sum_probs=17.1
Q ss_pred ccccccccccCCCc----------cCCCCccCcceeee
Q 032638 85 TEIPLKTCEDCGGS----------GICPECKGEGFVLK 112 (136)
Q Consensus 85 ~E~~~k~Ce~C~Gs----------GiCpeCkGEGFVlK 112 (136)
++.....|++||++ -+|.+| |+|+.
T Consensus 7 ~~~~~~~Cp~Cg~~~iv~d~~~Ge~vC~~C---G~Vl~ 41 (310)
T PRK00423 7 EEEEKLVCPECGSDKLIYDYERGEIVCADC---GLVIE 41 (310)
T ss_pred hcccCCcCcCCCCCCeeEECCCCeEeeccc---CCccc
Confidence 34555679999863 358888 66664
No 104
>PRK10436 hypothetical protein; Provisional
Probab=50.84 E-value=6.9 Score=34.64 Aligned_cols=9 Identities=33% Similarity=0.984 Sum_probs=7.4
Q ss_pred CCCCccCcce
Q 032638 100 ICPECKGEGF 109 (136)
Q Consensus 100 iCpeCkGEGF 109 (136)
-|+.|++ ||
T Consensus 387 GC~~C~~-Gy 395 (462)
T PRK10436 387 GCEHCYH-GY 395 (462)
T ss_pred CchhhcC-CC
Confidence 4999986 87
No 105
>PTZ00490 Ferredoxin superfamily; Provisional
Probab=50.47 E-value=6.9 Score=30.07 Aligned_cols=14 Identities=29% Similarity=0.783 Sum_probs=12.0
Q ss_pred ccCCCccCCCCccC
Q 032638 93 EDCGGSGICPECKG 106 (136)
Q Consensus 93 e~C~GsGiCpeCkG 106 (136)
..|||.|.|..|.-
T Consensus 72 ~~CGG~g~CgtC~V 85 (143)
T PTZ00490 72 GTCNGCMQCATCHV 85 (143)
T ss_pred ccCCCCCEeCCCEE
Confidence 36999999999974
No 106
>PRK12380 hydrogenase nickel incorporation protein HybF; Provisional
Probab=50.29 E-value=11 Score=27.30 Aligned_cols=24 Identities=33% Similarity=0.807 Sum_probs=17.0
Q ss_pred cccccccccCCC-------ccCCCCccCcce
Q 032638 86 EIPLKTCEDCGG-------SGICPECKGEGF 109 (136)
Q Consensus 86 E~~~k~Ce~C~G-------sGiCpeCkGEGF 109 (136)
...+-.|.+||. ...||.|.+.++
T Consensus 67 vp~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (113)
T PRK12380 67 KPAQAWCWDCSQVVEIHQHDAQCPHCHGERL 97 (113)
T ss_pred eCcEEEcccCCCEEecCCcCccCcCCCCCCc
Confidence 445668999984 245999987654
No 107
>PLN02593 adrenodoxin-like ferredoxin protein
Probab=49.67 E-value=7.1 Score=28.34 Aligned_cols=24 Identities=38% Similarity=0.594 Sum_probs=16.4
Q ss_pred cCCCccCCCCccCc---ceeeecCCHH
Q 032638 94 DCGGSGICPECKGE---GFVLKKLSEE 117 (136)
Q Consensus 94 ~C~GsGiCpeCkGE---GFVlK~Lsee 117 (136)
.|+|.|.|+.|.-. +=.+.+|++.
T Consensus 37 ~CgG~g~C~tC~V~V~~~~~~~~l~~~ 63 (117)
T PLN02593 37 ACEGSLACSTCHVIVMDEKVYNKLPEP 63 (117)
T ss_pred cCCCcceeCCCEEEEecCccccCCCCC
Confidence 59999999999642 1225566554
No 108
>PF07589 VPEP: PEP-CTERM motif; InterPro: IPR013424 This entry describes a 25-residue region including an invariant Pro-Glu-Pro (PEP) motif, a thirteen residue strongly hydrophobic sequence likely to span the membrane, and a five-residue strongly basic motif that often contains four Arg residues. In most cases, this motif is found within nine residues of the C-terminal end of the protein. Proteins containing this motif typically have signal sequences at the N terminus [].
Probab=49.21 E-value=27 Score=19.87 Aligned_cols=20 Identities=20% Similarity=0.368 Sum_probs=10.7
Q ss_pred cchhhHHHHHHHHHHHHHHH
Q 032638 53 ALPETAASVAIAATVVGAAA 72 (136)
Q Consensus 53 Alpetaas~aiaa~vVGaAa 72 (136)
++||-+......++++|.+.
T Consensus 1 ~VPEPst~~l~~~gl~~l~~ 20 (25)
T PF07589_consen 1 PVPEPSTLALLGLGLLGLAF 20 (25)
T ss_pred CCCCcHHHHHHHHHHHHHHH
Confidence 36775554445555555444
No 109
>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=48.70 E-value=24 Score=22.23 Aligned_cols=10 Identities=40% Similarity=0.969 Sum_probs=6.1
Q ss_pred CCCccCccee
Q 032638 101 CPECKGEGFV 110 (136)
Q Consensus 101 CpeCkGEGFV 110 (136)
|+.|..+|=+
T Consensus 29 C~~Cga~~~~ 38 (53)
T TIGR03655 29 CSTCGASGPV 38 (53)
T ss_pred CCCCCCCccc
Confidence 6666666544
No 110
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=48.10 E-value=12 Score=25.77 Aligned_cols=22 Identities=27% Similarity=0.614 Sum_probs=14.3
Q ss_pred CCCCccCcceeeecCCHHHHHHH
Q 032638 100 ICPECKGEGFVLKKLSEETAERA 122 (136)
Q Consensus 100 iCpeCkGEGFVlK~Lsee~A~kA 122 (136)
.|++| ||.|+-..+.++.....
T Consensus 33 ~C~~C-Ge~~~~~e~~~~~~~~i 54 (127)
T TIGR03830 33 YCPAC-GEELLDPEESKRNSAAL 54 (127)
T ss_pred ECCCC-CCEEEcHHHHHHHHHHH
Confidence 68888 67777666665554443
No 111
>COG0178 UvrA Excinuclease ATPase subunit [DNA replication, recombination, and repair]
Probab=47.61 E-value=9.2 Score=37.79 Aligned_cols=25 Identities=32% Similarity=0.942 Sum_probs=20.2
Q ss_pred ccccccccccCCCccC--------------CCCccCcce
Q 032638 85 TEIPLKTCEDCGGSGI--------------CPECKGEGF 109 (136)
Q Consensus 85 ~E~~~k~Ce~C~GsGi--------------CpeCkGEGF 109 (136)
-....--||.|.|.|. |+.|+|.=|
T Consensus 726 FNvkGGRCe~C~GdG~ikIeM~FLpdVyv~CevC~GkRY 764 (935)
T COG0178 726 FNVKGGRCEACQGDGVIKIEMHFLPDVYVPCEVCHGKRY 764 (935)
T ss_pred ccCCCcCCccccCCceEEEEeccCCCceeeCCCcCCccc
Confidence 3456678999999995 999999766
No 112
>TIGR00613 reco DNA repair protein RecO. All proteins in this family for which functions are known are DNA binding proteins that are involved in the initiation of recombination or recombinational repair.
Probab=47.34 E-value=19 Score=27.51 Aligned_cols=38 Identities=21% Similarity=0.531 Sum_probs=26.5
Q ss_pred ccccccccCC------------CccCCCCccCcceeeecCCHHHHHHHHH
Q 032638 87 IPLKTCEDCG------------GSGICPECKGEGFVLKKLSEETAERARL 124 (136)
Q Consensus 87 ~~~k~Ce~C~------------GsGiCpeCkGEGFVlK~Lsee~A~kAR~ 124 (136)
.....|..|| |.-+|++|.+.++--..++++...-.+.
T Consensus 145 p~l~~C~~cg~~~~~~~fs~~~gg~~C~~c~~~~~~~~~~~~~~l~~~~~ 194 (241)
T TIGR00613 145 LDLDKCAVCGSKEDLIYFSMTYGGALCRQCGEKDPHAIPIDPKLLRLLRY 194 (241)
T ss_pred cccCccCCCCCcCCCceEchhcCeEEChhhCccCCCceecCHHHHHHHHH
Confidence 3456888887 4558999999887555677776654443
No 113
>PRK11712 ribonuclease G; Provisional
Probab=47.19 E-value=19 Score=32.57 Aligned_cols=13 Identities=46% Similarity=1.055 Sum_probs=9.3
Q ss_pred CCCCccCcceeee
Q 032638 100 ICPECKGEGFVLK 112 (136)
Q Consensus 100 iCpeCkGEGFVlK 112 (136)
.||-|+|.|+|..
T Consensus 404 ~Cp~C~G~G~v~s 416 (489)
T PRK11712 404 ECPTCHGRGTVKT 416 (489)
T ss_pred CCCCCCCCCCcCC
Confidence 4677888887754
No 114
>KOG2813 consensus Predicted molecular chaperone, contains DnaJ domain [Posttranslational modification, protein turnover, chaperones]
Probab=46.36 E-value=12 Score=33.90 Aligned_cols=24 Identities=42% Similarity=0.811 Sum_probs=19.0
Q ss_pred cccccccccCCCccC--CCCccCcce
Q 032638 86 EIPLKTCEDCGGSGI--CPECKGEGF 109 (136)
Q Consensus 86 E~~~k~Ce~C~GsGi--CpeCkGEGF 109 (136)
.-+...|--|.|.|+ |+-|+|.|-
T Consensus 231 ~gt~~~C~~C~G~G~~~C~tC~grG~ 256 (406)
T KOG2813|consen 231 IGTHDLCYMCHGRGIKECHTCKGRGK 256 (406)
T ss_pred CCccchhhhccCCCcccCCcccCCCC
Confidence 344567888999997 999999884
No 115
>PF05957 DUF883: Bacterial protein of unknown function (DUF883); InterPro: IPR010279 This family consists of several bacterial proteins of unknown function that include the Escherichia coli genes for ElaB, YgaM and YqjD.
Probab=45.83 E-value=25 Score=24.03 Aligned_cols=19 Identities=58% Similarity=0.649 Sum_probs=12.7
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 032638 59 ASVAIAATVVGAAATLLVRR 78 (136)
Q Consensus 59 as~aiaa~vVGaAat~Lvrr 78 (136)
.|++||++ ||..+.+|++|
T Consensus 75 ~svgiAag-vG~llG~Ll~R 93 (94)
T PF05957_consen 75 QSVGIAAG-VGFLLGLLLRR 93 (94)
T ss_pred HHHHHHHH-HHHHHHHHHhC
Confidence 44555555 77778788776
No 116
>PF15474 MU117: Meiotically up-regulated gene family
Probab=45.70 E-value=19 Score=26.16 Aligned_cols=31 Identities=32% Similarity=0.539 Sum_probs=19.2
Q ss_pred cCCCccCCCCccCcceeeecCCHHHHHHHHHHHhhhhhhh
Q 032638 94 DCGGSGICPECKGEGFVLKKLSEETAERARLTAKNMATRY 133 (136)
Q Consensus 94 ~C~GsGiCpeCkGEGFVlK~Lsee~A~kAR~~AKNmATRy 133 (136)
+|.||++|+. +.+..++=.+|.-.= +--++|
T Consensus 3 dCkGS~~C~~--------~~~~~~~C~~A~~~~-~~~~~Y 33 (97)
T PF15474_consen 3 DCKGSSLCGT--------KRGNVDACDRAINQF-DDDTIY 33 (97)
T ss_pred CCCcCccCCC--------CCccHHHHHHHHHhc-CCCceE
Confidence 7999999998 455555555554332 333444
No 117
>cd01129 PulE-GspE PulE/GspE The type II secretory pathway is the main terminal branch of the general secretory pathway (GSP). It is responsible for the export the majority of Gram-negative bacterial exoenzymes and toxins. PulE is a cytoplasmic protein of the GSP, which contains an ATP binding site and a tetracysteine motif. This subgroup also includes PillB and HofB.
Probab=45.66 E-value=8.9 Score=30.80 Aligned_cols=12 Identities=33% Similarity=0.847 Sum_probs=9.3
Q ss_pred cCCCCccCccee
Q 032638 99 GICPECKGEGFV 110 (136)
Q Consensus 99 GiCpeCkGEGFV 110 (136)
..|++|+|.||.
T Consensus 251 ~gC~~C~~~G~~ 262 (264)
T cd01129 251 KGCEHCFGTGYK 262 (264)
T ss_pred CCchhhCCCCCC
Confidence 468888888873
No 118
>PF10814 DUF2562: Protein of unknown function (DUF2562); InterPro: IPR024245 This protein of unknown function appears to be found predominantly in Mycobacterium spp.
Probab=45.22 E-value=4.4 Score=31.97 Aligned_cols=26 Identities=42% Similarity=0.466 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHhcCCCc
Q 032638 58 AASVAIAATVVGAAATLLVRRTKGSE 83 (136)
Q Consensus 58 aas~aiaa~vVGaAat~Lvrr~k~~e 83 (136)
.+.++++...+|+.++.|+||++..|
T Consensus 94 iagv~~~vLagGavAfsivRRs~~~e 119 (133)
T PF10814_consen 94 IAGVAVAVLAGGAVAFSIVRRSSRPE 119 (133)
T ss_pred HHHHHHHHHhccceEEEEeecCCCCC
Confidence 34466677778999999999987643
No 119
>smart00261 FU Furin-like repeats.
Probab=44.70 E-value=14 Score=21.86 Aligned_cols=22 Identities=41% Similarity=1.026 Sum_probs=17.2
Q ss_pred cccccCCC--ccCCCCccCcceeee
Q 032638 90 KTCEDCGG--SGICPECKGEGFVLK 112 (136)
Q Consensus 90 k~Ce~C~G--sGiCpeCkGEGFVlK 112 (136)
..|..|.| ...|-.|+. ||.|.
T Consensus 9 ~~C~~C~~~~~~~C~~C~~-~~~l~ 32 (46)
T smart00261 9 PECATCTGPGPDDCTSCKH-GFFLD 32 (46)
T ss_pred ccccccCCcCcCcCccCCc-ccCCC
Confidence 56888998 668999976 77664
No 120
>PF01412 ArfGap: Putative GTPase activating protein for Arf; InterPro: IPR001164 This entry describes a family of small GTPase activating proteins, for example ARF1-directed GTPase-activating protein, the cycle control GTPase activating protein (GAP) GCS1 which is important for the regulation of the ADP ribosylation factor ARF, a member of the Ras superfamily of GTP-binding proteins []. The GTP-bound form of ARF is essential for the maintenance of normal Golgi morphology, it participates in recruitment of coat proteins which are required for budding and fission of membranes. Before the fusion with an acceptor compartment the membrane must be uncoated. This step required the hydrolysis of GTP associated to ARF. These proteins contain a characteristic zinc finger motif (Cys-x2-Cys-x(16,17)-x2-Cys) which displays some similarity to the C4-type GATA zinc finger. The ARFGAP domain display no obvious similarity to other GAP proteins. The 3D structure of the ARFGAP domain of the PYK2-associated protein beta has been solved []. It consists of a three-stranded beta-sheet surrounded by 5 alpha helices. The domain is organised around a central zinc atom which is coordinated by 4 cysteines. The ARFGAP domain is clearly unrelated to the other GAP proteins structures which are exclusively helical. Classical GAP proteins accelerate GTPase activity by supplying an arginine finger to the active site. The crystal structure of ARFGAP bound to ARF revealed that the ARFGAP domain does not supply an arginine to the active site which suggests a more indirect role of the ARFGAP domain in the GTPase hydrolysis []. The Rev protein of human immunodeficiency virus type 1 (HIV-1) facilitates nuclear export of unspliced and partly-spliced viral RNAs []. Rev contains an RNA-binding domain and an effector domain; the latter is believed to interact with a cellular cofactor required for the Rev response and hence HIV-1 replication. Human Rev interacting protein (hRIP) specifically interacts with the Rev effector. The amino acid sequence of hRIP is characterised by an N-terminal, C-4 class zinc finger motif.; GO: 0008060 ARF GTPase activator activity, 0008270 zinc ion binding, 0032312 regulation of ARF GTPase activity; PDB: 2P57_A 2CRR_A 2OWA_B 3O47_B 3DWD_A 1DCQ_A 2CRW_A 3MDB_D 3FEH_A 3LJU_X ....
Probab=43.40 E-value=4.4 Score=28.97 Aligned_cols=20 Identities=50% Similarity=1.052 Sum_probs=13.1
Q ss_pred ccccccccCC-----------CccCCCCccC
Q 032638 87 IPLKTCEDCG-----------GSGICPECKG 106 (136)
Q Consensus 87 ~~~k~Ce~C~-----------GsGiCpeCkG 106 (136)
..-+.|-||| |.-+|.+|.|
T Consensus 11 ~~N~~CaDCg~~~p~w~s~~~GiflC~~Cag 41 (116)
T PF01412_consen 11 PGNKVCADCGAPNPTWASLNYGIFLCLECAG 41 (116)
T ss_dssp TTCTB-TTT-SBS--EEETTTTEEE-HHHHH
T ss_pred cCcCcCCCCCCCCCCEEEeecChhhhHHHHH
Confidence 4568899997 5668999986
No 121
>PRK13130 H/ACA RNA-protein complex component Nop10p; Reviewed
Probab=42.91 E-value=15 Score=24.81 Aligned_cols=21 Identities=38% Similarity=1.013 Sum_probs=16.1
Q ss_pred ccccccCCCcc---CCCCccCcce
Q 032638 89 LKTCEDCGGSG---ICPECKGEGF 109 (136)
Q Consensus 89 ~k~Ce~C~GsG---iCpeCkGEGF 109 (136)
...|++||-.. .||.|.++=+
T Consensus 5 mr~C~~CgvYTLk~~CP~CG~~t~ 28 (56)
T PRK13130 5 IRKCPKCGVYTLKEICPVCGGKTK 28 (56)
T ss_pred ceECCCCCCEEccccCcCCCCCCC
Confidence 56899999865 5999987643
No 122
>COG1656 Uncharacterized conserved protein [Function unknown]
Probab=42.71 E-value=14 Score=29.66 Aligned_cols=18 Identities=56% Similarity=1.117 Sum_probs=10.6
Q ss_pred CCCCccCcceeeecCCHHHHH
Q 032638 100 ICPECKGEGFVLKKLSEETAE 120 (136)
Q Consensus 100 iCpeCkGEGFVlK~Lsee~A~ 120 (136)
.||+|||+ |-++|.|.+.
T Consensus 99 RCp~CN~~---L~~vs~eev~ 116 (165)
T COG1656 99 RCPECNGE---LEKVSREEVK 116 (165)
T ss_pred cCcccCCE---eccCcHHHHh
Confidence 36666664 6666666543
No 123
>COG2804 PulE Type II secretory pathway, ATPase PulE/Tfp pilus assembly pathway, ATPase PilB [Cell motility and secretion / Intracellular trafficking and secretion]
Probab=42.60 E-value=24 Score=32.54 Aligned_cols=35 Identities=37% Similarity=0.852 Sum_probs=23.4
Q ss_pred HHHHHHHHHHHHHHHhcCCCccccccccccccCCCcc--------------------CCCCccCcce
Q 032638 63 IAATVVGAAATLLVRRTKGSEETEIPLKTCEDCGGSG--------------------ICPECKGEGF 109 (136)
Q Consensus 63 iaa~vVGaAat~Lvrr~k~~e~~E~~~k~Ce~C~GsG--------------------iCpeCkGEGF 109 (136)
++..+.|..+==|||| .|+.|.... -|+.|+|.||
T Consensus 381 l~s~l~gViaQRLvr~------------lC~~C~~~~~~~~~~~~~~~~~~~~~~~~GC~~C~~~Gy 435 (500)
T COG2804 381 LASSLLGVIAQRLVRR------------LCPHCKEECEPEELARLGLSESLPLYRAVGCEACNGSGY 435 (500)
T ss_pred HHHHHHHHHHHHHHhh------------hCchhcccccchhhhhhcccccccccccCCchhhccCCc
Confidence 4445566666666654 566666666 4889988887
No 124
>PRK11823 DNA repair protein RadA; Provisional
Probab=41.53 E-value=14 Score=32.10 Aligned_cols=25 Identities=32% Similarity=0.906 Sum_probs=19.7
Q ss_pred cccccccCCCc-----cCCCCccCcceeee
Q 032638 88 PLKTCEDCGGS-----GICPECKGEGFVLK 112 (136)
Q Consensus 88 ~~k~Ce~C~Gs-----GiCpeCkGEGFVlK 112 (136)
..-.|..||-+ |.||.|+.-|=+-.
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp~C~~w~t~~e 35 (446)
T PRK11823 6 TAYVCQECGAESPKWLGRCPECGAWNTLVE 35 (446)
T ss_pred CeEECCcCCCCCcccCeeCcCCCCccceee
Confidence 45789999975 89999988775544
No 125
>COG2331 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=41.35 E-value=9.1 Score=28.16 Aligned_cols=10 Identities=70% Similarity=1.683 Sum_probs=4.3
Q ss_pred cccccccCCC
Q 032638 88 PLKTCEDCGG 97 (136)
Q Consensus 88 ~~k~Ce~C~G 97 (136)
+.-+||+|++
T Consensus 32 plt~ce~c~a 41 (82)
T COG2331 32 PLTTCEECGA 41 (82)
T ss_pred ccccChhhCh
Confidence 3344444443
No 126
>PRK06835 DNA replication protein DnaC; Validated
Probab=41.10 E-value=12 Score=31.59 Aligned_cols=16 Identities=25% Similarity=0.465 Sum_probs=11.2
Q ss_pred ccccccccCCCccCCC
Q 032638 87 IPLKTCEDCGGSGICP 102 (136)
Q Consensus 87 ~~~k~Ce~C~GsGiCp 102 (136)
.+...|+.|+++|.-.
T Consensus 96 ~~~y~Cp~C~dtG~i~ 111 (329)
T PRK06835 96 EMKYTCPKCKDTGFIN 111 (329)
T ss_pred CCCCCCCCCCCCCCcC
Confidence 3445788888888773
No 127
>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=40.92 E-value=20 Score=25.97 Aligned_cols=25 Identities=36% Similarity=0.676 Sum_probs=17.6
Q ss_pred ccccccccccCCC-------ccCCCCccCcce
Q 032638 85 TEIPLKTCEDCGG-------SGICPECKGEGF 109 (136)
Q Consensus 85 ~E~~~k~Ce~C~G-------sGiCpeCkGEGF 109 (136)
...-.-.|.+|+- ...||.|.+.++
T Consensus 66 ~~p~~~~C~~Cg~~~~~~~~~~~CP~Cgs~~~ 97 (115)
T TIGR00100 66 DEPVECECEDCSEEVSPEIDLYRCPKCHGIML 97 (115)
T ss_pred eeCcEEEcccCCCEEecCCcCccCcCCcCCCc
Confidence 3445678999963 456999987654
No 128
>COG0375 HybF Zn finger protein HypA/HybF (possibly regulating hydrogenase expression) [General function prediction only]
Probab=40.90 E-value=18 Score=27.50 Aligned_cols=30 Identities=33% Similarity=0.777 Sum_probs=20.7
Q ss_pred ccccccccccCCC-------ccCCCCcc--------CcceeeecC
Q 032638 85 TEIPLKTCEDCGG-------SGICPECK--------GEGFVLKKL 114 (136)
Q Consensus 85 ~E~~~k~Ce~C~G-------sGiCpeCk--------GEGFVlK~L 114 (136)
.+...-.|.+|+. ..+||.|. |+++-+|.+
T Consensus 66 ~~p~~~~C~~C~~~~~~e~~~~~CP~C~s~~~~i~~G~el~i~~i 110 (115)
T COG0375 66 EEPAECWCLDCGQEVELEELDYRCPKCGSINLRIIGGDELIIKSI 110 (115)
T ss_pred EeccEEEeccCCCeecchhheeECCCCCCCceEEecCCeeEEEEE
Confidence 3444557999965 46799998 566666654
No 129
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=40.32 E-value=13 Score=32.53 Aligned_cols=13 Identities=46% Similarity=1.273 Sum_probs=9.5
Q ss_pred CCCCccCcceeee
Q 032638 100 ICPECKGEGFVLK 112 (136)
Q Consensus 100 iCpeCkGEGFVlK 112 (136)
.||-|+|.|+|..
T Consensus 392 ~Cp~C~G~G~v~s 404 (414)
T TIGR00757 392 VCPHCSGTGIVKT 404 (414)
T ss_pred CCCCCcCeeEEcc
Confidence 4677888888764
No 130
>cd01121 Sms Sms (bacterial radA) DNA repair protein. This protein is not related to archael radA any more than is to other RecA-like NTPases. Sms has a role in recombination and recombinational repair and is responsible for the stabilization or processing of branched DNA molecules.
Probab=39.93 E-value=14 Score=31.68 Aligned_cols=22 Identities=36% Similarity=0.954 Sum_probs=17.8
Q ss_pred ccccCCCc-----cCCCCccCcceeee
Q 032638 91 TCEDCGGS-----GICPECKGEGFVLK 112 (136)
Q Consensus 91 ~Ce~C~Gs-----GiCpeCkGEGFVlK 112 (136)
.|.+||-. |.||.|+--|=+-.
T Consensus 2 ~c~~cg~~~~~~~g~cp~c~~w~~~~e 28 (372)
T cd01121 2 VCSECGYVSPKWLGKCPECGEWNTLVE 28 (372)
T ss_pred CCCCCCCCCCCccEECcCCCCceeeee
Confidence 59999974 89999988776554
No 131
>PRK10132 hypothetical protein; Provisional
Probab=39.93 E-value=33 Score=25.33 Aligned_cols=20 Identities=40% Similarity=0.353 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHHhcC
Q 032638 60 SVAIAATVVGAAATLLVRRTK 80 (136)
Q Consensus 60 s~aiaa~vVGaAat~Lvrr~k 80 (136)
++.||++ ||..+.+|+.|.|
T Consensus 89 svgiaag-vG~llG~Ll~RR~ 108 (108)
T PRK10132 89 SVGTAAA-VGIFIGALLSLRK 108 (108)
T ss_pred HHHHHHH-HHHHHHHHHhccC
Confidence 4555554 7888878877643
No 132
>COG1530 CafA Ribonucleases G and E [Translation, ribosomal structure and biogenesis]
Probab=39.10 E-value=13 Score=33.25 Aligned_cols=15 Identities=53% Similarity=1.028 Sum_probs=11.4
Q ss_pred ccCCCCccCcceeee
Q 032638 98 SGICPECKGEGFVLK 112 (136)
Q Consensus 98 sGiCpeCkGEGFVlK 112 (136)
+..||.|+|.|.+.-
T Consensus 395 ~~~cp~c~G~g~v~~ 409 (487)
T COG1530 395 SERCPGCKGTGHVRS 409 (487)
T ss_pred eeECCCceeeEEEec
Confidence 457888888888764
No 133
>PRK03824 hypA hydrogenase nickel incorporation protein; Provisional
Probab=38.97 E-value=35 Score=25.47 Aligned_cols=12 Identities=33% Similarity=0.919 Sum_probs=9.0
Q ss_pred ccccccccccCC
Q 032638 85 TEIPLKTCEDCG 96 (136)
Q Consensus 85 ~E~~~k~Ce~C~ 96 (136)
.....-.|.+||
T Consensus 66 ~~p~~~~C~~CG 77 (135)
T PRK03824 66 EEEAVLKCRNCG 77 (135)
T ss_pred ecceEEECCCCC
Confidence 344667899998
No 134
>KOG0703 consensus Predicted GTPase-activating protein [Signal transduction mechanisms]
Probab=38.85 E-value=13 Score=32.08 Aligned_cols=21 Identities=52% Similarity=1.162 Sum_probs=17.0
Q ss_pred cccccccccCCCcc-----------CCCCccC
Q 032638 86 EIPLKTCEDCGGSG-----------ICPECKG 106 (136)
Q Consensus 86 E~~~k~Ce~C~GsG-----------iCpeCkG 106 (136)
+..-+.|-|||..| ||-+|.|
T Consensus 22 ~~~N~~CADC~a~~P~WaSwnlGvFiC~~C~g 53 (287)
T KOG0703|consen 22 EPDNKVCADCGAKGPRWASWNLGVFICLRCAG 53 (287)
T ss_pred CcccCcccccCCCCCCeEEeecCeEEEeeccc
Confidence 34488999998654 8999998
No 135
>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=38.47 E-value=22 Score=21.68 Aligned_cols=7 Identities=71% Similarity=1.858 Sum_probs=4.4
Q ss_pred CCCCccC
Q 032638 100 ICPECKG 106 (136)
Q Consensus 100 iCpeCkG 106 (136)
.||+|.+
T Consensus 28 ~CP~Cg~ 34 (52)
T TIGR02605 28 TCPECGG 34 (52)
T ss_pred CCCCCCC
Confidence 4666665
No 136
>smart00105 ArfGap Putative GTP-ase activating proteins for the small GTPase, ARF. Putative zinc fingers with GTPase activating proteins (GAPs) towards the small GTPase, Arf. The GAP of ARD1 stimulates GTPase hydrolysis for ARD1 but not ARFs.
Probab=38.34 E-value=7.8 Score=27.64 Aligned_cols=18 Identities=50% Similarity=1.211 Sum_probs=13.6
Q ss_pred ccccccCCCcc-----------CCCCccC
Q 032638 89 LKTCEDCGGSG-----------ICPECKG 106 (136)
Q Consensus 89 ~k~Ce~C~GsG-----------iCpeCkG 106 (136)
-+.|-||+..+ ||.+|.|
T Consensus 3 N~~CaDC~~~~p~w~s~~~GifvC~~Csg 31 (112)
T smart00105 3 NKKCFDCGAPNPTWASVNLGVFLCIECSG 31 (112)
T ss_pred CCcccCCCCCCCCcEEeccceeEhHHhHH
Confidence 46799998544 6888876
No 137
>cd01675 RNR_III Class III ribonucleotide reductase. Ribonucleotide reductase (RNR) catalyzes the reductive synthesis of deoxyribonucleotides from their corresponding ribonucleotides. It provides the precursors necessary for DNA synthesis. RNRs are separated into three classes based on their metallocofactor usage. Class I RNRs, found in eukaryotes, bacteria, and bacteriophage, use a diiron-tyrosyl radical. Class II RNRs, found in bacteria, bacteriophage, algae and archaea, use coenzyme B12 (adenosylcobalamin, AdoCbl). Class III RNRs, found in strict or facultative anaerobic bacteria, bacteriophage, and archaea, use an FeS cluster and S-adenosylmethionine to generate a glycyl radical. Many organisms have more than one class of RNR present in their genomes. All three RNRs have a ten-stranded alpha-beta barrel domain that is structurally similar to the domain of PFL (pyruvate formate lyase). The class III enzyme from phage T4 consists of two subunits, this model covers the larger subunit w
Probab=38.25 E-value=18 Score=32.54 Aligned_cols=17 Identities=53% Similarity=1.331 Sum_probs=14.9
Q ss_pred ccccCCCcc-----CCCCccCc
Q 032638 91 TCEDCGGSG-----ICPECKGE 107 (136)
Q Consensus 91 ~Ce~C~GsG-----iCpeCkGE 107 (136)
.|++||-.+ .||.|..+
T Consensus 520 ~C~~CG~~~~~~~~~CP~CGs~ 541 (555)
T cd01675 520 ICNDCGYIGEGEGFKCPKCGSE 541 (555)
T ss_pred cCCCCCCCCcCCCCCCcCCCCc
Confidence 999999988 89999644
No 138
>KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=38.23 E-value=21 Score=31.00 Aligned_cols=24 Identities=38% Similarity=0.803 Sum_probs=12.6
Q ss_pred ccccccccCCCcc--CCCCccCccee
Q 032638 87 IPLKTCEDCGGSG--ICPECKGEGFV 110 (136)
Q Consensus 87 ~~~k~Ce~C~GsG--iCpeCkGEGFV 110 (136)
+....|+.|||-+ .|..|+|-==|
T Consensus 227 ~~~~~C~~CGg~rFlpC~~C~GS~kv 252 (281)
T KOG2824|consen 227 EGGGVCESCGGARFLPCSNCHGSCKV 252 (281)
T ss_pred CCCCcCCCcCCcceEecCCCCCceee
Confidence 3345566666655 36666554333
No 139
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=38.13 E-value=24 Score=33.48 Aligned_cols=11 Identities=18% Similarity=0.570 Sum_probs=7.5
Q ss_pred ccccccccCCC
Q 032638 87 IPLKTCEDCGG 97 (136)
Q Consensus 87 ~~~k~Ce~C~G 97 (136)
.....|+.||+
T Consensus 590 ~~~~~CP~Cg~ 600 (860)
T PRK06319 590 VTEIDCPKCHK 600 (860)
T ss_pred ccCcccCCCCC
Confidence 34567999964
No 140
>KOG0818 consensus GTPase-activating proteins of the GIT family [Signal transduction mechanisms]
Probab=37.88 E-value=10 Score=36.08 Aligned_cols=18 Identities=39% Similarity=1.043 Sum_probs=14.5
Q ss_pred cccccccCCC-----------ccCCCCcc
Q 032638 88 PLKTCEDCGG-----------SGICPECK 105 (136)
Q Consensus 88 ~~k~Ce~C~G-----------sGiCpeCk 105 (136)
+.|+|.|||| +=||.||-
T Consensus 7 ~~evC~DC~~~dp~WASvnrGt~lC~eCc 35 (669)
T KOG0818|consen 7 SSEVCADCSGPDPSWASVNRGTFLCDECC 35 (669)
T ss_pred hhhhhcccCCCCCcceeecCceEehHhhh
Confidence 5689999984 56899984
No 141
>TIGR01941 nqrF NADH:ubiquinone oxidoreductase, Na(+)-translocating, F subunit. This model represents the NqrF subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria. This oxidoreductase complex functions primarily as a sodium ion pump.
Probab=37.80 E-value=14 Score=31.00 Aligned_cols=13 Identities=46% Similarity=1.365 Sum_probs=11.8
Q ss_pred cCCCccCCCCccC
Q 032638 94 DCGGSGICPECKG 106 (136)
Q Consensus 94 ~C~GsGiCpeCkG 106 (136)
.|+|.|.|..|+.
T Consensus 66 ~C~g~G~Cg~C~v 78 (405)
T TIGR01941 66 ACGGGGTCGQCRV 78 (405)
T ss_pred cCCCccEeCCCEE
Confidence 4999999999986
No 142
>PLN02999 photosystem II oxygen-evolving enhancer 3 protein (PsbQ)
Probab=37.60 E-value=27 Score=29.01 Aligned_cols=24 Identities=29% Similarity=0.465 Sum_probs=19.8
Q ss_pred CcceeeecCCH-HHHHHHHHHHhhh
Q 032638 106 GEGFVLKKLSE-ETAERARLTAKNM 129 (136)
Q Consensus 106 GEGFVlK~Lse-e~A~kAR~~AKNm 129 (136)
-|+|++-.||+ |+|.++|.+|+++
T Consensus 76 Kerfy~p~lspeeAaaRiK~sA~dL 100 (190)
T PLN02999 76 KEKYFMPGLSPEDAAARIKQTAEGL 100 (190)
T ss_pred HHhccCCCCCHHHHHHHHHHHHHHH
Confidence 37899999975 5778999999975
No 143
>PRK00398 rpoP DNA-directed RNA polymerase subunit P; Provisional
Probab=37.49 E-value=24 Score=21.51 Aligned_cols=26 Identities=27% Similarity=0.655 Sum_probs=16.4
Q ss_pred cccccCCC---------ccCCCCccCcceeeecCCH
Q 032638 90 KTCEDCGG---------SGICPECKGEGFVLKKLSE 116 (136)
Q Consensus 90 k~Ce~C~G---------sGiCpeCkGEGFVlK~Lse 116 (136)
-.|++||. .-.||.|.++ +++|.-++
T Consensus 4 y~C~~CG~~~~~~~~~~~~~Cp~CG~~-~~~~~~~~ 38 (46)
T PRK00398 4 YKCARCGREVELDEYGTGVRCPYCGYR-ILFKERPP 38 (46)
T ss_pred EECCCCCCEEEECCCCCceECCCCCCe-EEEccCCC
Confidence 35777775 3569999654 55555443
No 144
>PLN02248 cellulose synthase-like protein
Probab=37.47 E-value=14 Score=37.27 Aligned_cols=21 Identities=52% Similarity=1.206 Sum_probs=16.9
Q ss_pred cccccccccC-----CCccCCCCccC
Q 032638 86 EIPLKTCEDC-----GGSGICPECKG 106 (136)
Q Consensus 86 E~~~k~Ce~C-----~GsGiCpeCkG 106 (136)
|-..++|-|| ...|+||.||-
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~ 174 (1135)
T PLN02248 149 ECGFKICRDCYIDAVKSGGICPGCKE 174 (1135)
T ss_pred cccchhHHhHhhhhhhcCCCCCCCcc
Confidence 4567889998 46899999984
No 145
>COG0675 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=36.44 E-value=19 Score=27.06 Aligned_cols=38 Identities=42% Similarity=0.635 Sum_probs=24.4
Q ss_pred cccccccccCC----CccCCCCccCcceeeecCCHHHHHHHHHHHhhhhhhhc
Q 032638 86 EIPLKTCEDCG----GSGICPECKGEGFVLKKLSEETAERARLTAKNMATRYT 134 (136)
Q Consensus 86 E~~~k~Ce~C~----GsGiCpeCkGEGFVlK~Lsee~A~kAR~~AKNmATRyT 134 (136)
.-+-++|+.|| +...||.| ||++- +=.-+|.|.+.|+.
T Consensus 306 ~~tS~~C~~cg~~~~r~~~C~~c---g~~~~--------rD~naa~Ni~~~~~ 347 (364)
T COG0675 306 YYTSKTCPCCGHLSGRLFKCPRC---GFVHD--------RDVNAALNIARRAL 347 (364)
T ss_pred CCCcccccccCCccceeEECCCC---CCeeh--------hhHHHHHHHHHHhc
Confidence 45669999999 34568877 44432 22345667777764
No 146
>PRK08116 hypothetical protein; Validated
Probab=36.04 E-value=35 Score=27.52 Aligned_cols=23 Identities=39% Similarity=0.537 Sum_probs=16.0
Q ss_pred cccccccccCCCcc--------------CCCCccCcc
Q 032638 86 EIPLKTCEDCGGSG--------------ICPECKGEG 108 (136)
Q Consensus 86 E~~~k~Ce~C~GsG--------------iCpeCkGEG 108 (136)
+.....|+.||+.+ .|++|..+.
T Consensus 13 ~~~~~~C~~Cg~~~~~~~~~~~~~~~~~~~c~C~~~~ 49 (268)
T PRK08116 13 EDGGEYCEVCGKRIEKVVELLGKNRIVPIMCECEREA 49 (268)
T ss_pred cccCccCcCCCCcceeeecccCcceecCCCCCChHHH
Confidence 45667899998763 477776653
No 147
>PRK14704 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=35.13 E-value=21 Score=32.99 Aligned_cols=23 Identities=35% Similarity=0.990 Sum_probs=17.5
Q ss_pred ccccccccccCCCccC----CCCccCc
Q 032638 85 TEIPLKTCEDCGGSGI----CPECKGE 107 (136)
Q Consensus 85 ~E~~~k~Ce~C~GsGi----CpeCkGE 107 (136)
.-.+.-.|.+||-+|. ||.|-.+
T Consensus 555 in~~~~~C~~CGy~g~~~~~CP~CG~~ 581 (618)
T PRK14704 555 INHPVDRCKCCSYHGVIGNECPSCGNE 581 (618)
T ss_pred eCCCCeecCCCCCCCCcCccCcCCCCC
Confidence 3566789999997654 9999643
No 148
>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=34.85 E-value=18 Score=22.09 Aligned_cols=16 Identities=44% Similarity=1.344 Sum_probs=10.9
Q ss_pred ccccCCCc-----------cCCCCccC
Q 032638 91 TCEDCGGS-----------GICPECKG 106 (136)
Q Consensus 91 ~Ce~C~Gs-----------GiCpeCkG 106 (136)
.|+.||-+ |+|..|.|
T Consensus 3 ~C~~Cg~~Yh~~~~pP~~~~~Cd~cg~ 29 (36)
T PF05191_consen 3 ICPKCGRIYHIEFNPPKVEGVCDNCGG 29 (36)
T ss_dssp EETTTTEEEETTTB--SSTTBCTTTTE
T ss_pred CcCCCCCccccccCCCCCCCccCCCCC
Confidence 56666643 77888876
No 149
>PF07092 DUF1356: Protein of unknown function (DUF1356); InterPro: IPR009790 This family consists of several hypothetical mammalian proteins of around 250 residues in length. The function of this family is unknown.
Probab=34.64 E-value=26 Score=29.48 Aligned_cols=33 Identities=24% Similarity=0.534 Sum_probs=23.7
Q ss_pred ccccccccccCCC--ccCCCCccCcceeeecCCHH
Q 032638 85 TEIPLKTCEDCGG--SGICPECKGEGFVLKKLSEE 117 (136)
Q Consensus 85 ~E~~~k~Ce~C~G--sGiCpeCkGEGFVlK~Lsee 117 (136)
+.+..--|++..| +=.||-|+|-|-+=|...++
T Consensus 23 ~~~~~~py~e~~g~~~vtCPTCqGtGrIP~eqe~q 57 (238)
T PF07092_consen 23 EDISSFPYVEFTGRDSVTCPTCQGTGRIPREQENQ 57 (238)
T ss_pred cccccCccccccCCCCCcCCCCcCCccCCccchhc
Confidence 3555566677665 44799999999988876543
No 150
>PF03589 Antiterm: Antitermination protein; InterPro: IPR003222 This entry consists of antitermination proteins found in bacteriophages, such as protein Q from phage lambda, and some bacterial homologues. Protein Q positively regulates expression of the phage late gene operon by binding to the bacterial host RNA polymerase (RNAP) and modifying it. The modified RNAP transcribes through termination sites that otherwise prevent expression of the regulated genes [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=34.51 E-value=14 Score=26.45 Aligned_cols=21 Identities=33% Similarity=0.765 Sum_probs=10.7
Q ss_pred CCCccCcceeeecCCHHHHHHHH
Q 032638 101 CPECKGEGFVLKKLSEETAERAR 123 (136)
Q Consensus 101 CpeCkGEGFVlK~Lsee~A~kAR 123 (136)
|++|.|-|| ..++.+.|-+|-
T Consensus 35 c~rcgg~G~--sr~~~~~a~~al 55 (95)
T PF03589_consen 35 CERCGGRGY--SRLPSSRAIEAL 55 (95)
T ss_pred hhhhcCCCC--CCCChHHHHHHH
Confidence 444444444 455666555543
No 151
>TIGR02487 NrdD anaerobic ribonucleoside-triphosphate reductase. This model represents the oxygen-sensitive (anaerobic, class III) ribonucleotide reductase. The mechanism of the enzyme involves a glycine-centered radical, a C-terminal zinc binding site, and a set of conserved active site cysteines and asparagines. This enzyme requires an activating component, NrdG, a radical-SAM domain containing enzyme (TIGR02491). Together the two form an alpha-2/beta-2 heterodimer.
Probab=34.21 E-value=25 Score=31.90 Aligned_cols=23 Identities=43% Similarity=1.144 Sum_probs=17.7
Q ss_pred ccccccccccCCCcc-----CCCCccCc
Q 032638 85 TEIPLKTCEDCGGSG-----ICPECKGE 107 (136)
Q Consensus 85 ~E~~~k~Ce~C~GsG-----iCpeCkGE 107 (136)
.-.+.-.|.+||-.| -||.|..+
T Consensus 520 ~n~~~~~C~~CG~~g~~~~~~CP~Cgs~ 547 (579)
T TIGR02487 520 INPPVDVCEDCGYTGEGLNDKCPKCGSH 547 (579)
T ss_pred eccCCccCCCCCCCCCCCCCcCcCCCCc
Confidence 456778999999665 59999654
No 152
>PRK05464 Na(+)-translocating NADH-quinone reductase subunit F; Provisional
Probab=33.59 E-value=18 Score=30.40 Aligned_cols=13 Identities=46% Similarity=1.334 Sum_probs=11.9
Q ss_pred cCCCccCCCCccC
Q 032638 94 DCGGSGICPECKG 106 (136)
Q Consensus 94 ~C~GsGiCpeCkG 106 (136)
.|+|.|.|..|+.
T Consensus 70 ~C~g~G~CgtC~v 82 (409)
T PRK05464 70 ACGGGGSCGQCRV 82 (409)
T ss_pred CCCCccEeCCCEE
Confidence 5999999999986
No 153
>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=33.48 E-value=31 Score=19.75 Aligned_cols=7 Identities=71% Similarity=1.858 Sum_probs=4.4
Q ss_pred CCCCccC
Q 032638 100 ICPECKG 106 (136)
Q Consensus 100 iCpeCkG 106 (136)
.||+|.+
T Consensus 28 ~CP~Cg~ 34 (41)
T smart00834 28 TCPECGG 34 (41)
T ss_pred CCCCCCC
Confidence 4666665
No 154
>TIGR00416 sms DNA repair protein RadA. The gene protuct codes for a probable ATP-dependent protease involved in both DNA repair and degradation of proteins, peptides, glycopeptides. Also known as sms. Residues 11-28 of the SEED alignment contain a putative Zn binding domain. Residues 110-117 of the seed contain a putative ATP binding site both documented in Haemophilus and in Listeria monocytogenes. for E.coli see ( J. BACTERIOL. 178:5045-5048(1996)).
Probab=33.38 E-value=20 Score=31.40 Aligned_cols=25 Identities=28% Similarity=0.811 Sum_probs=19.5
Q ss_pred cccccccCCCc-----cCCCCccCcceeee
Q 032638 88 PLKTCEDCGGS-----GICPECKGEGFVLK 112 (136)
Q Consensus 88 ~~k~Ce~C~Gs-----GiCpeCkGEGFVlK 112 (136)
+.-.|..||-. |-||.|+--|=+-.
T Consensus 6 ~~y~C~~Cg~~~~~~~g~Cp~C~~w~t~~~ 35 (454)
T TIGR00416 6 SKFVCQHCGADSPKWQGKCPACHAWNTITE 35 (454)
T ss_pred CeEECCcCCCCCccccEECcCCCCccccch
Confidence 45789999975 88999988775543
No 155
>COG1885 Uncharacterized protein conserved in archaea [Function unknown]
Probab=33.26 E-value=53 Score=25.48 Aligned_cols=9 Identities=56% Similarity=1.353 Sum_probs=5.9
Q ss_pred CccCCCCcc
Q 032638 97 GSGICPECK 105 (136)
Q Consensus 97 GsGiCpeCk 105 (136)
|+-.||.|.
T Consensus 48 G~t~CP~Cg 56 (115)
T COG1885 48 GSTSCPKCG 56 (115)
T ss_pred ccccCCCCC
Confidence 666677774
No 156
>PF09791 Oxidored-like: Oxidoreductase-like protein, N-terminal; InterPro: IPR019180 This entry represents the N-terminal domain of various oxidoreductase-like proteins whose exact function is, as yet, unknown.
Probab=33.16 E-value=20 Score=23.42 Aligned_cols=16 Identities=38% Similarity=1.080 Sum_probs=13.3
Q ss_pred ccCCCccCCCCccCcce
Q 032638 93 EDCGGSGICPECKGEGF 109 (136)
Q Consensus 93 e~C~GsGiCpeCkGEGF 109 (136)
++|=||| |..|-=+.|
T Consensus 16 ~~CCgSG-C~~CVwd~Y 31 (48)
T PF09791_consen 16 DECCGSG-CAPCVWDVY 31 (48)
T ss_pred ccccccC-CccchhHHH
Confidence 6899999 999976665
No 157
>PF02620 DUF177: Uncharacterized ACR, COG1399; InterPro: IPR003772 This entry describes proteins of unknown function.
Probab=32.92 E-value=23 Score=23.91 Aligned_cols=18 Identities=44% Similarity=1.117 Sum_probs=14.2
Q ss_pred cccc-ccCCCccCCCCccC
Q 032638 89 LKTC-EDCGGSGICPECKG 106 (136)
Q Consensus 89 ~k~C-e~C~GsGiCpeCkG 106 (136)
...| ++|.|..+|+.|-.
T Consensus 76 ~~~c~~~C~~~~~~~~~~~ 94 (119)
T PF02620_consen 76 KPLCSEDCKGEMLCPVCGA 94 (119)
T ss_pred cccCcccCcccccCCcccc
Confidence 4567 79999999998854
No 158
>PRK05978 hypothetical protein; Provisional
Probab=32.88 E-value=20 Score=27.94 Aligned_cols=14 Identities=50% Similarity=1.298 Sum_probs=6.4
Q ss_pred ccCCCCccCcceeee
Q 032638 98 SGICPECKGEGFVLK 112 (136)
Q Consensus 98 sGiCpeCkGEGFVlK 112 (136)
.|.||+| |||=+|+
T Consensus 33 ~grCP~C-G~G~LF~ 46 (148)
T PRK05978 33 RGRCPAC-GEGKLFR 46 (148)
T ss_pred cCcCCCC-CCCcccc
Confidence 3445555 4444443
No 159
>PRK07111 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=32.66 E-value=25 Score=33.13 Aligned_cols=23 Identities=35% Similarity=0.918 Sum_probs=17.7
Q ss_pred ccccccccccCCCcc----CCCCccCc
Q 032638 85 TEIPLKTCEDCGGSG----ICPECKGE 107 (136)
Q Consensus 85 ~E~~~k~Ce~C~GsG----iCpeCkGE 107 (136)
.-.+.-.|.+||-.| .||.|..+
T Consensus 676 in~~~~~C~~CG~~~~~~~~CP~CG~~ 702 (735)
T PRK07111 676 INHPVDRCPVCGYLGVIEDKCPKCGST 702 (735)
T ss_pred eCCCCeecCCCCCCCCcCccCcCCCCc
Confidence 456778999999766 49999643
No 160
>KOG2824 consensus Glutaredoxin-related protein [Posttranslational modification, protein turnover, chaperones]
Probab=32.53 E-value=27 Score=30.30 Aligned_cols=22 Identities=41% Similarity=0.993 Sum_probs=18.8
Q ss_pred ccccccCCCccCCCCccCcceee
Q 032638 89 LKTCEDCGGSGICPECKGEGFVL 111 (136)
Q Consensus 89 ~k~Ce~C~GsGiCpeCkGEGFVl 111 (136)
++.++ |.+.|-|..|-|.+||+
T Consensus 221 L~~~p-~~~~~~C~~CGg~rFlp 242 (281)
T KOG2824|consen 221 LKGIP-CEGGGVCESCGGARFLP 242 (281)
T ss_pred HhcCC-CCCCCcCCCcCCcceEe
Confidence 34566 99999999999999996
No 161
>PF01783 Ribosomal_L32p: Ribosomal L32p protein family; InterPro: IPR002677 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 [, ]. Ribosomal protein L32p is part of the 50S ribosomal subunit. This family is found in both prokaryotes and eukaryotes. Ribosomal protein L32 of yeast binds to and regulates the splicing and the translation of the transcript of its own gene [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit; PDB: 3PYT_2 3F1F_5 3PYV_2 3D5B_5 3MRZ_2 3D5D_5 3F1H_5 1VSP_Y 3PYR_2 3MS1_2 ....
Probab=32.23 E-value=44 Score=21.65 Aligned_cols=19 Identities=37% Similarity=1.088 Sum_probs=14.8
Q ss_pred cccccccccCCC----ccCCCCc
Q 032638 86 EIPLKTCEDCGG----SGICPEC 104 (136)
Q Consensus 86 E~~~k~Ce~C~G----sGiCpeC 104 (136)
-.....|+.||- --+|+.|
T Consensus 23 ~~~l~~c~~cg~~~~~H~vc~~c 45 (56)
T PF01783_consen 23 APNLVKCPNCGEPKLPHRVCPSC 45 (56)
T ss_dssp TTSEEESSSSSSEESTTSBCTTT
T ss_pred ccceeeeccCCCEecccEeeCCC
Confidence 336789999985 3579999
No 162
>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=32.02 E-value=22 Score=31.40 Aligned_cols=18 Identities=33% Similarity=0.818 Sum_probs=11.7
Q ss_pred cccccccCCCccCCCCcc
Q 032638 88 PLKTCEDCGGSGICPECK 105 (136)
Q Consensus 88 ~~k~Ce~C~GsGiCpeCk 105 (136)
+.-.|.+||-.--||.|.
T Consensus 212 ~~~~C~~Cg~~~~C~~C~ 229 (505)
T TIGR00595 212 KNLLCRSCGYILCCPNCD 229 (505)
T ss_pred CeeEhhhCcCccCCCCCC
Confidence 445677777766666665
No 163
>PF08955 BofC_C: BofC C-terminal domain; InterPro: IPR015050 The C-terminal domain of the bacterial protein, bypass of forespore C (BofC), contains a three-stranded beta-sheet and three alpha-helices. The exact function is unknown []. ; PDB: 2BW2_A.
Probab=31.67 E-value=19 Score=25.60 Aligned_cols=12 Identities=42% Similarity=0.988 Sum_probs=5.9
Q ss_pred cCCCCccCccee
Q 032638 99 GICPECKGEGFV 110 (136)
Q Consensus 99 GiCpeCkGEGFV 110 (136)
-|+|.||..||+
T Consensus 2 DiSP~~K~ngYf 13 (75)
T PF08955_consen 2 DISPLCKENGYF 13 (75)
T ss_dssp S--TGGGT---E
T ss_pred CCChhHhcCeeE
Confidence 379999999986
No 164
>KOG1100 consensus Predicted E3 ubiquitin ligase [Posttranslational modification, protein turnover, chaperones]
Probab=31.49 E-value=25 Score=28.22 Aligned_cols=18 Identities=39% Similarity=0.916 Sum_probs=15.1
Q ss_pred ccccccCCC-ccCCCCccC
Q 032638 89 LKTCEDCGG-SGICPECKG 106 (136)
Q Consensus 89 ~k~Ce~C~G-sGiCpeCkG 106 (136)
.--|+.|+. -.+||-|+.
T Consensus 179 l~lC~~C~~~~~~CPiC~~ 197 (207)
T KOG1100|consen 179 LCLCGICDESLRICPICRS 197 (207)
T ss_pred eEecccccccCccCCCCcC
Confidence 456899998 899999986
No 165
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=30.98 E-value=16 Score=29.03 Aligned_cols=16 Identities=44% Similarity=1.279 Sum_probs=13.7
Q ss_pred cccccCCCccC-CCCcc
Q 032638 90 KTCEDCGGSGI-CPECK 105 (136)
Q Consensus 90 k~Ce~C~GsGi-CpeCk 105 (136)
-.|+-|--||| ||+|.
T Consensus 4 p~~~~c~kt~ilC~~c~ 20 (166)
T PRK06418 4 PICEVCVKTGLLCPRCQ 20 (166)
T ss_pred ceeeEEeccCccChhHH
Confidence 36999999995 99996
No 166
>PRK15103 paraquat-inducible membrane protein A; Provisional
Probab=30.83 E-value=37 Score=29.81 Aligned_cols=26 Identities=31% Similarity=0.990 Sum_probs=17.6
Q ss_pred cccccccCC-----CccCCCCccCcceeeec
Q 032638 88 PLKTCEDCG-----GSGICPECKGEGFVLKK 113 (136)
Q Consensus 88 ~~k~Ce~C~-----GsGiCpeCkGEGFVlK~ 113 (136)
....|++|+ +...||+|...=+-=+.
T Consensus 220 ~l~~C~~Cd~l~~~~~a~CpRC~~~L~~~~~ 250 (419)
T PRK15103 220 GLRSCSCCTAILPADQPVCPRCHTKGYVRRR 250 (419)
T ss_pred CCCcCCCCCCCCCCCCCCCCCCCCcCcCCCC
Confidence 355699998 55579999766433333
No 167
>KOG3800 consensus Predicted E3 ubiquitin ligase containing RING finger, subunit of transcription/repair factor TFIIH and CDK-activating kinase assembly factor [Posttranslational modification, protein turnover, chaperones]
Probab=30.80 E-value=18 Score=31.69 Aligned_cols=18 Identities=44% Similarity=1.060 Sum_probs=14.4
Q ss_pred ccccccC------CCccCCCCccC
Q 032638 89 LKTCEDC------GGSGICPECKG 106 (136)
Q Consensus 89 ~k~Ce~C------~GsGiCpeCkG 106 (136)
...||.| -|+|.||+|.-
T Consensus 25 H~lCEsCvd~iF~~g~~~CpeC~~ 48 (300)
T KOG3800|consen 25 HRLCESCVDRIFSLGPAQCPECMV 48 (300)
T ss_pred chHHHHHHHHHHhcCCCCCCcccc
Confidence 3468888 69999999964
No 168
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family. The C-terminal half of RNase E (excluded from the seed alignment for this model) lacks ribonuclease activity but participates in mRNA degradation by organizing the degradosome.
Probab=30.69 E-value=14 Score=32.38 Aligned_cols=17 Identities=35% Similarity=0.759 Sum_probs=13.8
Q ss_pred cccccccccccCCCccC
Q 032638 84 ETEIPLKTCEDCGGSGI 100 (136)
Q Consensus 84 ~~E~~~k~Ce~C~GsGi 100 (136)
..|.-.+.|+.|+|+|.
T Consensus 385 L~e~~~~~Cp~C~G~G~ 401 (414)
T TIGR00757 385 LMEVLGTVCPHCSGTGI 401 (414)
T ss_pred hHHHhcCCCCCCcCeeE
Confidence 45666789999999994
No 169
>PF08792 A2L_zn_ribbon: A2L zinc ribbon domain; InterPro: IPR014900 This zinc ribbon protein is found associated with some viral A2L transcription factors [].
Probab=30.17 E-value=32 Score=20.67 Aligned_cols=11 Identities=64% Similarity=1.564 Sum_probs=5.6
Q ss_pred cccccCCCccC
Q 032638 90 KTCEDCGGSGI 100 (136)
Q Consensus 90 k~Ce~C~GsGi 100 (136)
+.|+.|++.||
T Consensus 4 ~~C~~C~~~~i 14 (33)
T PF08792_consen 4 KKCSKCGGNGI 14 (33)
T ss_pred eEcCCCCCCeE
Confidence 44555555544
No 170
>COG3813 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.58 E-value=18 Score=26.67 Aligned_cols=26 Identities=38% Similarity=1.068 Sum_probs=17.4
Q ss_pred ccccCCC---ccCCCCccCcceeeecCCHH
Q 032638 91 TCEDCGG---SGICPECKGEGFVLKKLSEE 117 (136)
Q Consensus 91 ~Ce~C~G---sGiCpeCkGEGFVlK~Lsee 117 (136)
.|-||-- .|+||.|-|| ||-+-.-++
T Consensus 31 FCadCae~~l~g~CPnCGGe-lv~RP~RPa 59 (84)
T COG3813 31 FCADCAENRLHGLCPNCGGE-LVARPIRPA 59 (84)
T ss_pred hhHhHHHHhhcCcCCCCCch-hhcCcCChH
Confidence 3556644 6999999875 666655554
No 171
>PF12732 YtxH: YtxH-like protein; InterPro: IPR024623 This family of uncharacterised proteins is found in bacteria. Proteins in this family are typically between 100 and 143 amino acids in length. The N-terminal region is the most conserved.
Probab=29.47 E-value=55 Score=21.60 Aligned_cols=23 Identities=39% Similarity=0.446 Sum_probs=17.5
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCc
Q 032638 61 VAIAATVVGAAATLLVRRTKGSE 83 (136)
Q Consensus 61 ~aiaa~vVGaAat~Lvrr~k~~e 83 (136)
..++-+++|+++.+|.--.++.+
T Consensus 4 g~l~Ga~~Ga~~glL~aP~sG~e 26 (74)
T PF12732_consen 4 GFLAGAAAGAAAGLLFAPKSGKE 26 (74)
T ss_pred HHHHHHHHHHHHHHHhCCCCcHH
Confidence 45677889999999987666544
No 172
>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=28.98 E-value=35 Score=29.74 Aligned_cols=33 Identities=21% Similarity=0.354 Sum_probs=21.9
Q ss_pred ccccccccccCC-----------CccCCCCccCcceeeecCCHH
Q 032638 85 TEIPLKTCEDCG-----------GSGICPECKGEGFVLKKLSEE 117 (136)
Q Consensus 85 ~E~~~k~Ce~C~-----------GsGiCpeCkGEGFVlK~Lsee 117 (136)
++.+.-.|++|+ ..-.||+|..+=+--+..|-+
T Consensus 9 ~~~~~~~C~~Cd~l~~~~~l~~g~~a~CpRCg~~L~~~~~~~~~ 52 (403)
T TIGR00155 9 PAAKHILCSQCDMLVALPRIESGQKAACPRCGTTLTVGWDWSLQ 52 (403)
T ss_pred CCCCeeeCCCCCCcccccCCCCCCeeECCCCCCCCcCCCCCCHH
Confidence 345566799998 334699998776554544443
No 173
>PRK06835 DNA replication protein DnaC; Validated
Probab=28.44 E-value=40 Score=28.42 Aligned_cols=11 Identities=55% Similarity=1.546 Sum_probs=10.3
Q ss_pred CCCCccCccee
Q 032638 100 ICPECKGEGFV 110 (136)
Q Consensus 100 iCpeCkGEGFV 110 (136)
-||.|++.|||
T Consensus 100 ~Cp~C~dtG~i 110 (329)
T PRK06835 100 TCPKCKDTGFI 110 (329)
T ss_pred CCCCCCCCCCc
Confidence 59999999998
No 174
>KOG0145 consensus RNA-binding protein ELAV/HU (RRM superfamily) [RNA processing and modification]
Probab=28.36 E-value=31 Score=30.78 Aligned_cols=31 Identities=32% Similarity=0.575 Sum_probs=20.2
Q ss_pred CCccCccee-eecCCHHHHHHHHHHHhhhhhh
Q 032638 102 PECKGEGFV-LKKLSEETAERARLTAKNMATR 132 (136)
Q Consensus 102 peCkGEGFV-lK~Lsee~A~kAR~~AKNmATR 132 (136)
-.|||-||| |-+-.|++-+-+-++.-+|+.|
T Consensus 317 nkCKGfgFVtMtNYdEAamAi~sLNGy~lg~r 348 (360)
T KOG0145|consen 317 NKCKGFGFVTMTNYDEAAMAIASLNGYRLGDR 348 (360)
T ss_pred ccccceeEEEecchHHHHHHHHHhcCccccce
Confidence 479999999 5566555555555555555444
No 175
>PF01102 Glycophorin_A: Glycophorin A; InterPro: IPR001195 Proteins in this group are responsible for the molecular basis of the blood group antigens, surface markers on the outside of the red blood cell membrane. Most of these markers are proteins, but some are carbohydrates attached to lipids or proteins [Reid M.E., Lomas-Francis C. The Blood Group Antigen FactsBook Academic Press, London / San Diego, (1997)]. Glycophorin A (PAS-2) and glycophorin B (PAS-3) belong to the MNS blood group system and are associated with antigens that include M/N, S/s, U, He, Mi(a), M(c), Vw, Mur, M(g), Vr, M(e), Mt(a), St(a), Ri(a), Cl(a), Ny(a), Hut, Hil, M(v), Far, Mit, Dantu, Hop, Nob, En(a), ENKT, amongst others. Glycophorin A is the major sialoglycoprotein of the erythrocyte membrane []. Structurally, glycophorin A consists of an N-terminal extracellular domain, heavily glycosylated on serine and threonine residues, followed by a transmembrane region and a C-terminal cytoplasmic domain. Other glycophorins in this entry such as Glycophorin B and Glycophorin E represent minor sialoglycoproteins in the erythrocyte membrane.; GO: 0016021 integral to membrane; PDB: 2KPF_B 1AFO_B 2KPE_A.
Probab=28.03 E-value=69 Score=24.29 Aligned_cols=15 Identities=20% Similarity=0.279 Sum_probs=9.0
Q ss_pred HHHHHHHHHHHHHHH
Q 032638 58 AASVAIAATVVGAAA 72 (136)
Q Consensus 58 aas~aiaa~vVGaAa 72 (136)
.--+.+.|||+|..+
T Consensus 68 ~Ii~gv~aGvIg~Il 82 (122)
T PF01102_consen 68 GIIFGVMAGVIGIIL 82 (122)
T ss_dssp HHHHHHHHHHHHHHH
T ss_pred ehhHHHHHHHHHHHH
Confidence 334456677777665
No 176
>PF02988 PLA2_inh: Phospholipase A2 inhibitor; InterPro: IPR004126 Proteins in this entry inhibit basic phospholipase A2 isozymes in snake's venom [, ].; GO: 0004859 phospholipase inhibitor activity, 0005576 extracellular region
Probab=27.99 E-value=31 Score=24.74 Aligned_cols=14 Identities=57% Similarity=1.414 Sum_probs=13.0
Q ss_pred ccccCCCccCCCCccC
Q 032638 91 TCEDCGGSGICPECKG 106 (136)
Q Consensus 91 ~Ce~C~GsGiCpeCkG 106 (136)
+||.|.+.| +.|.|
T Consensus 2 ~CEvC~~~G--~~C~G 15 (83)
T PF02988_consen 2 SCEVCHGSG--KDCSG 15 (83)
T ss_pred CcceecCcC--CCCCC
Confidence 699999999 89998
No 177
>PRK10220 hypothetical protein; Provisional
Probab=27.99 E-value=35 Score=26.20 Aligned_cols=19 Identities=47% Similarity=1.078 Sum_probs=13.8
Q ss_pred ccccccCCC--------ccCCCCccCc
Q 032638 89 LKTCEDCGG--------SGICPECKGE 107 (136)
Q Consensus 89 ~k~Ce~C~G--------sGiCpeCkGE 107 (136)
..-|+.|+. -=+||||..|
T Consensus 3 lP~CP~C~seytY~d~~~~vCpeC~hE 29 (111)
T PRK10220 3 LPHCPKCNSEYTYEDNGMYICPECAHE 29 (111)
T ss_pred CCcCCCCCCcceEcCCCeEECCcccCc
Confidence 346888864 3589999876
No 178
>TIGR01167 LPXTG_anchor LPXTG-motif cell wall anchor domain. A common feature of this proteins containing this domain appears to be a high proportion of charged and zwitterionic residues immediatedly upstream of the LPXTG motif. This model differs from other descriptions of the LPXTG region by including a portion of that upstream charged region.
Probab=27.93 E-value=63 Score=18.03 Aligned_cols=14 Identities=29% Similarity=0.498 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHhc
Q 032638 66 TVVGAAATLLVRRT 79 (136)
Q Consensus 66 ~vVGaAat~Lvrr~ 79 (136)
.+++.+..++.||.
T Consensus 19 ~l~~~~~~~~~~rk 32 (34)
T TIGR01167 19 LLLGLGGLLLRKRK 32 (34)
T ss_pred HHHHHHHHHheecc
Confidence 44444444444443
No 179
>PF02420 AFP: Insect antifreeze protein repeat; InterPro: IPR003460 Antifreeze proteins (AFPs) are a class of proteins that are able to bind to and inhibit the growth of macromolecular ice, thereby permitting an organism to survive subzero temperatures by decreasing the probability of ice nucleation in their bodies []. These proteins have been characterised from a variety of organisms, including fish, plants, bacteria, fungi and arthropods. This entry represents insect AFPs of the type found in Tenebrio molitor (Yellow mealworm) and in Dendroides canadensis (Pyrochroid beetle). The structure of these AFPs consists of a right-handed beta-helix with 12 residues per coil. Each 12 residue-repeat contains two cys residues that form a disulphide bridge. The beta-helices of insect AFPs present a highly rigid array of threonine residues and bound water molecules that can effectively mimic the ice lattice. As such, beta-helical AFPs provide a more effective coverage of the ice surface compared to the alpha-helical fish AFPs []. A second insect antifreeze from Choristoneura fumiferana (Spruce budworm) (IPR007928 from INTERPRO) also consists of beta-helices, however in these proteins the helices form a left-handed twist; these proteins show no sequence homology to the current entry, but may act by a similar mechanism. The beta-helix motif may be used as an AFP structural motif in non-homologous proteins from other (non-fish) organisms as well.; PDB: 1EZG_B 1L1I_A.
Probab=27.44 E-value=26 Score=17.40 Aligned_cols=11 Identities=36% Similarity=0.830 Sum_probs=8.9
Q ss_pred CCCccCCCCcc
Q 032638 95 CGGSGICPECK 105 (136)
Q Consensus 95 C~GsGiCpeCk 105 (136)
|-||..|++|.
T Consensus 2 CT~s~~C~~a~ 12 (12)
T PF02420_consen 2 CTGSTNCNNAT 12 (12)
T ss_dssp EESSSTBTTSS
T ss_pred cccCCCCcCCC
Confidence 77888998873
No 180
>PF06906 DUF1272: Protein of unknown function (DUF1272); InterPro: IPR010696 This family consists of several hypothetical bacterial proteins of around 80 residues in length. This family contains a number of conserved cysteine residues and its function is unknown.
Probab=26.38 E-value=31 Score=23.85 Aligned_cols=10 Identities=60% Similarity=1.703 Sum_probs=8.6
Q ss_pred ccCCCCccCc
Q 032638 98 SGICPECKGE 107 (136)
Q Consensus 98 sGiCpeCkGE 107 (136)
.|+||.|.||
T Consensus 41 ~~~CPNCgGe 50 (57)
T PF06906_consen 41 NGVCPNCGGE 50 (57)
T ss_pred cCcCcCCCCc
Confidence 5899999886
No 181
>COG1545 Predicted nucleic-acid-binding protein containing a Zn-ribbon [General function prediction only]
Probab=26.37 E-value=39 Score=25.33 Aligned_cols=26 Identities=31% Similarity=0.829 Sum_probs=19.8
Q ss_pred ccccccccccccCCC-----ccCCCCccCcc
Q 032638 83 EETEIPLKTCEDCGG-----SGICPECKGEG 108 (136)
Q Consensus 83 e~~E~~~k~Ce~C~G-----sGiCpeCkGEG 108 (136)
.+..+-.--|..||- .-.||.|..++
T Consensus 23 ~~~kl~g~kC~~CG~v~~PPr~~Cp~C~~~~ 53 (140)
T COG1545 23 KEGKLLGTKCKKCGRVYFPPRAYCPKCGSET 53 (140)
T ss_pred hhCcEEEEEcCCCCeEEcCCcccCCCCCCCC
Confidence 334566778999985 57899999885
No 182
>cd00296 SIR2 SIR2 superfamily of proteins includes silent information regulator 2 (Sir2) enzymes which catalyze NAD+-dependent protein/histone deacetylation, where the acetyl group from the lysine epsilon-amino group is transferred to the ADP-ribose moiety of NAD+, producing nicotinamide and the novel metabolite O-acetyl-ADP-ribose. Sir2 proteins, also known as sirtuins, are found in all eukaryotes and many archaea and prokaryotes and have been shown to regulate gene silencing, DNA repair, metabolic enzymes, and life span. The most-studied function, gene silencing, involves the inactivation of chromosome domains containing key regulatory genes by packaging them into a specialized chromatin structure that is inaccessible to DNA-binding proteins. The oligomerization state of Sir2 appears to be organism-dependent, sometimes occurring as a monomer and sometimes as a multimer. Also included in this superfamily is a group of uncharacterized Sir2-like proteins which lack certain key catalytic
Probab=25.89 E-value=46 Score=25.00 Aligned_cols=21 Identities=33% Similarity=0.917 Sum_probs=16.2
Q ss_pred ccccccccCC------------CccCCCCccCc
Q 032638 87 IPLKTCEDCG------------GSGICPECKGE 107 (136)
Q Consensus 87 ~~~k~Ce~C~------------GsGiCpeCkGE 107 (136)
+....|..|+ .-..||.|.|.
T Consensus 111 ~~~~~C~~C~~~~~~~~~~~~~~~p~C~~C~~~ 143 (222)
T cd00296 111 LDRVRCTSCGKEYPRDEVLEREKPPRCPKCGGL 143 (222)
T ss_pred CCccEECCCCCCcchhhhhhccCCCCCCCCCCc
Confidence 4556799997 45789999875
No 183
>PF02977 CarbpepA_inh: Carboxypeptidase A inhibitor; InterPro: IPR004231 Peptide proteinase inhibitors can be found as single domain proteins or as single or multiple domains within proteins; these are referred to as either simple or compound inhibitors, respectively. In many cases they are synthesised as part of a larger precursor protein, either as a prepropeptide or as an N-terminal domain associated with an inactive peptidase or zymogen. This domain prevents access of the substrate to the active site. Removal of the N-terminal inhibitor domain either by interaction with a second peptidase or by autocatalytic cleavage activates the zymogen. Other inhibitors interact direct with proteinases using a simple noncovalent lock and key mechanism; while yet others use a conformational change-based trapping mechanism that depends on their structural and thermodynamic properties. This family is represented by the well-characterised metallocarboxypeptidase A inhibitor (MCPI) from potatoes, which belongs to the MEROPS inhibitor family I37, clan IE. It inhibits metallopeptidases belonging to MEROPS peptidase family M14, carboxypeptidase A. In Russet Burbank potatoes, it is a mixture of approximately equal amounts of two polypeptide chains containing 38 or 39 amino acid residues. The chains differ in their amino terminal sequence only [] and are resistant to fragmentation by proteases []. The structure of the complex between bovine carboxypeptidase A and the 39-amino-acid carboxypeptidase A inhibitor from potatoes has been determined at 2.5-A resolution []. The potato inhibitor is synthesised as a precursor, having a 29 residue N-terminal signal peptide, a 27 residue pro-peptide, the 39 residue mature inhibitor region and a 7 residue C-terminal extension. The 7 residue C-terminal extension is involved in inhibitor inactivation and may be required for targeting to the vacuole where the mature active inhibitor accumulates []. The N-terminal region and the mature inhibitor are weakly related to other solananaceous proteins found in this entry, from potato, tomato and henbane, which have been incorrectly described as metallocarboxipeptidase inhibitors [].; GO: 0008191 metalloendopeptidase inhibitor activity; PDB: 4CPA_I 1H20_A 2HLG_A.
Probab=25.87 E-value=35 Score=22.75 Aligned_cols=22 Identities=32% Similarity=0.728 Sum_probs=14.5
Q ss_pred ccCCCccCCCCc-----cCcceeeecC
Q 032638 93 EDCGGSGICPEC-----KGEGFVLKKL 114 (136)
Q Consensus 93 e~C~GsGiCpeC-----kGEGFVlK~L 114 (136)
.||.|--+|+.| ..+||+-..+
T Consensus 16 sDC~g~tlC~~C~k~~~t~~g~~~~~~ 42 (46)
T PF02977_consen 16 SDCSGITLCQWCWKLKKTCGGYVGSAC 42 (46)
T ss_dssp CCCTTSSSS-EE-CCCEBCC--EEEEE
T ss_pred ccccceeehHHHHhcccCCCCccccee
Confidence 589999999999 3677775443
No 184
>PRK09263 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=25.75 E-value=38 Score=31.80 Aligned_cols=21 Identities=43% Similarity=1.208 Sum_probs=16.6
Q ss_pred ccccccccccCCCcc---------CCCCcc
Q 032638 85 TEIPLKTCEDCGGSG---------ICPECK 105 (136)
Q Consensus 85 ~E~~~k~Ce~C~GsG---------iCpeCk 105 (136)
.-.+.-.|.+||-.| .||.|.
T Consensus 637 in~~~~~C~~CG~~Ge~~~~~~~~~CP~CG 666 (711)
T PRK09263 637 TNTPIDECYECGFTGEFECTEKGFTCPKCG 666 (711)
T ss_pred eCCCCcccCCCCCCccccCCCCCCcCcCCC
Confidence 446678999999764 699995
No 185
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=25.70 E-value=49 Score=29.68 Aligned_cols=30 Identities=30% Similarity=0.523 Sum_probs=25.7
Q ss_pred ccCCCCccCcceeeecCCHHHHHHHHHHHhh
Q 032638 98 SGICPECKGEGFVLKKLSEETAERARLTAKN 128 (136)
Q Consensus 98 sGiCpeCkGEGFVlK~Lsee~A~kAR~~AKN 128 (136)
+--|+-|.|.|..|+. -+|--+|-|.-||+
T Consensus 91 ~~~C~~CeGrgi~l~~-f~dll~kf~eiaK~ 120 (354)
T COG1568 91 DYTCECCEGRGISLQA-FKDLLEKFREIAKD 120 (354)
T ss_pred cccccCcCCccccchh-HHHHHHHHHHHHhc
Confidence 4568889999999999 78888999999887
No 186
>PF07295 DUF1451: Protein of unknown function (DUF1451); InterPro: IPR009912 This family consists of several hypothetical bacterial proteins of around 160 residues in length. Members of this family contain four highly conserved cysteine resides toward the C-terminal region of the protein. The function of this family is unknown.
Probab=25.63 E-value=51 Score=25.44 Aligned_cols=30 Identities=30% Similarity=0.633 Sum_probs=23.2
Q ss_pred CccccccccccccCCCc---------cCCCCccCcceee
Q 032638 82 SEETEIPLKTCEDCGGS---------GICPECKGEGFVL 111 (136)
Q Consensus 82 ~e~~E~~~k~Ce~C~Gs---------GiCpeCkGEGFVl 111 (136)
-|-.-.-.-.|..||-. -.||+|.+..|.=
T Consensus 105 GE~~g~G~l~C~~Cg~~~~~~~~~~l~~Cp~C~~~~F~R 143 (146)
T PF07295_consen 105 GEVVGPGTLVCENCGHEVELTHPERLPPCPKCGHTEFTR 143 (146)
T ss_pred CcEecCceEecccCCCEEEecCCCcCCCCCCCCCCeeee
Confidence 44455667899999864 5799999999964
No 187
>COG5257 GCD11 Translation initiation factor 2, gamma subunit (eIF-2gamma; GTPase) [Translation, ribosomal structure and biogenesis]
Probab=25.47 E-value=46 Score=30.45 Aligned_cols=31 Identities=23% Similarity=0.666 Sum_probs=23.8
Q ss_pred ccccccccccCCC------ccCCCCccCcceeeecCC
Q 032638 85 TEIPLKTCEDCGG------SGICPECKGEGFVLKKLS 115 (136)
Q Consensus 85 ~E~~~k~Ce~C~G------sGiCpeCkGEGFVlK~Ls 115 (136)
.+...-.|++|.. ...||+|..|.=+++..|
T Consensus 53 Ad~~i~kC~~c~~~~~y~~~~~C~~cg~~~~l~R~VS 89 (415)
T COG5257 53 ADAKIYKCPECYRPECYTTEPKCPNCGAETELVRRVS 89 (415)
T ss_pred ccCceEeCCCCCCCcccccCCCCCCCCCCccEEEEEE
Confidence 3667788999996 578999999886665544
No 188
>PF14787 zf-CCHC_5: GAG-polyprotein viral zinc-finger; PDB: 1CL4_A 1DSV_A.
Probab=25.24 E-value=31 Score=21.93 Aligned_cols=8 Identities=50% Similarity=1.651 Sum_probs=4.4
Q ss_pred ccCCCCcc
Q 032638 98 SGICPECK 105 (136)
Q Consensus 98 sGiCpeCk 105 (136)
.|+||+|+
T Consensus 2 ~~~CprC~ 9 (36)
T PF14787_consen 2 PGLCPRCG 9 (36)
T ss_dssp --C-TTTS
T ss_pred CccCcccC
Confidence 47999996
No 189
>PF14319 Zn_Tnp_IS91: Transposase zinc-binding domain
Probab=25.17 E-value=44 Score=24.24 Aligned_cols=21 Identities=38% Similarity=0.977 Sum_probs=15.2
Q ss_pred cccccccccCCC---------ccCCCCccC
Q 032638 86 EIPLKTCEDCGG---------SGICPECKG 106 (136)
Q Consensus 86 E~~~k~Ce~C~G---------sGiCpeCkG 106 (136)
--....|++||- +-.||.|.+
T Consensus 39 G~~~~~C~~Cg~~~~~~~SCk~R~CP~C~~ 68 (111)
T PF14319_consen 39 GFHRYRCEDCGHEKIVYNSCKNRHCPSCQA 68 (111)
T ss_pred CcceeecCCCCceEEecCcccCcCCCCCCC
Confidence 345678998884 457999975
No 190
>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=25.03 E-value=24 Score=21.54 Aligned_cols=22 Identities=23% Similarity=0.540 Sum_probs=18.3
Q ss_pred cccccccCCCccCCCCccCcce
Q 032638 88 PLKTCEDCGGSGICPECKGEGF 109 (136)
Q Consensus 88 ~~k~Ce~C~GsGiCpeCkGEGF 109 (136)
.+-.|..|...-||++|-.+|-
T Consensus 17 ~ry~C~~C~d~dlC~~Cf~~~~ 38 (44)
T smart00291 17 VRYHCLVCPDYDLCQSCFAKGS 38 (44)
T ss_pred CEEECCCCCCccchHHHHhCcC
Confidence 3557999999999999987764
No 191
>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=24.63 E-value=28 Score=20.29 Aligned_cols=22 Identities=32% Similarity=0.984 Sum_probs=11.1
Q ss_pred cccccccccCCCc-----cCCCCccCc
Q 032638 86 EIPLKTCEDCGGS-----GICPECKGE 107 (136)
Q Consensus 86 E~~~k~Ce~C~Gs-----GiCpeCkGE 107 (136)
+.....|.+||.. ..||.|-++
T Consensus 8 ~l~~~rC~~Cg~~~~pPr~~Cp~C~s~ 34 (37)
T PF12172_consen 8 RLLGQRCRDCGRVQFPPRPVCPHCGSD 34 (37)
T ss_dssp -EEEEE-TTT--EEES--SEETTTT--
T ss_pred EEEEEEcCCCCCEecCCCcCCCCcCcc
Confidence 3445568888865 678888654
No 192
>PRK11639 zinc uptake transcriptional repressor; Provisional
Probab=24.42 E-value=23 Score=26.82 Aligned_cols=9 Identities=33% Similarity=1.047 Sum_probs=4.9
Q ss_pred cCCCCccCc
Q 032638 99 GICPECKGE 107 (136)
Q Consensus 99 GiCpeCkGE 107 (136)
|+||+|...
T Consensus 141 GiC~~C~~~ 149 (169)
T PRK11639 141 GLCAACVEV 149 (169)
T ss_pred EEChhhcCc
Confidence 566666443
No 193
>PRK05580 primosome assembly protein PriA; Validated
Probab=24.42 E-value=35 Score=31.29 Aligned_cols=19 Identities=42% Similarity=1.151 Sum_probs=10.8
Q ss_pred cccccccCCCccCCCCccC
Q 032638 88 PLKTCEDCGGSGICPECKG 106 (136)
Q Consensus 88 ~~k~Ce~C~GsGiCpeCkG 106 (136)
+.-.|.+||-.-.||.|.+
T Consensus 380 ~~~~C~~Cg~~~~C~~C~~ 398 (679)
T PRK05580 380 PFLLCRDCGWVAECPHCDA 398 (679)
T ss_pred CceEhhhCcCccCCCCCCC
Confidence 4456777775555555543
No 194
>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=24.08 E-value=38 Score=25.86 Aligned_cols=18 Identities=39% Similarity=0.951 Sum_probs=12.7
Q ss_pred cccccCCC--------ccCCCCccCc
Q 032638 90 KTCEDCGG--------SGICPECKGE 107 (136)
Q Consensus 90 k~Ce~C~G--------sGiCpeCkGE 107 (136)
--|+.|+. -=+||||-.|
T Consensus 3 p~CP~C~seytY~dg~~~iCpeC~~E 28 (109)
T TIGR00686 3 PPCPKCNSEYTYHDGTQLICPSCLYE 28 (109)
T ss_pred CcCCcCCCcceEecCCeeECcccccc
Confidence 35788864 3589999765
No 195
>PRK10404 hypothetical protein; Provisional
Probab=24.08 E-value=83 Score=22.85 Aligned_cols=18 Identities=33% Similarity=0.577 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHh
Q 032638 60 SVAIAATVVGAAATLLVRR 78 (136)
Q Consensus 60 s~aiaa~vVGaAat~Lvrr 78 (136)
++.|+++ ||..+.+|++|
T Consensus 83 avGiaag-vGlllG~Ll~R 100 (101)
T PRK10404 83 GIGVGAA-VGLVLGLLLAR 100 (101)
T ss_pred HHHHHHH-HHHHHHHHHhc
Confidence 4445544 78777777665
No 196
>PRK14559 putative protein serine/threonine phosphatase; Provisional
Probab=23.74 E-value=53 Score=30.78 Aligned_cols=23 Identities=35% Similarity=0.821 Sum_probs=16.6
Q ss_pred ccccccccccCCCc---cCCCCccCc
Q 032638 85 TEIPLKTCEDCGGS---GICPECKGE 107 (136)
Q Consensus 85 ~E~~~k~Ce~C~Gs---GiCpeCkGE 107 (136)
....-+.|..||.+ ..||+|.-+
T Consensus 11 n~~~akFC~~CG~~l~~~~Cp~CG~~ 36 (645)
T PRK14559 11 NPNNNRFCQKCGTSLTHKPCPQCGTE 36 (645)
T ss_pred CCCCCccccccCCCCCCCcCCCCCCC
Confidence 34456789999887 458888755
No 197
>PRK12495 hypothetical protein; Provisional
Probab=23.40 E-value=36 Score=28.79 Aligned_cols=21 Identities=33% Similarity=1.132 Sum_probs=16.4
Q ss_pred ccccccccCC-------CccCCCCccCc
Q 032638 87 IPLKTCEDCG-------GSGICPECKGE 107 (136)
Q Consensus 87 ~~~k~Ce~C~-------GsGiCpeCkGE 107 (136)
...+.|++|| |--+||.|...
T Consensus 40 msa~hC~~CG~PIpa~pG~~~Cp~CQ~~ 67 (226)
T PRK12495 40 MTNAHCDECGDPIFRHDGQEFCPTCQQP 67 (226)
T ss_pred cchhhcccccCcccCCCCeeECCCCCCc
Confidence 3458999998 66789999843
No 198
>COG3894 Uncharacterized metal-binding protein [General function prediction only]
Probab=23.25 E-value=33 Score=32.64 Aligned_cols=15 Identities=40% Similarity=1.097 Sum_probs=13.1
Q ss_pred ccccCCCccCCCCcc
Q 032638 91 TCEDCGGSGICPECK 105 (136)
Q Consensus 91 ~Ce~C~GsGiCpeCk 105 (136)
.=++|||-|-|+.|+
T Consensus 31 i~s~cggk~~cgkc~ 45 (614)
T COG3894 31 IRSVCGGKGTCGKCQ 45 (614)
T ss_pred EeeecCCCccccceE
Confidence 447899999999996
No 199
>PRK11032 hypothetical protein; Provisional
Probab=23.13 E-value=55 Score=25.86 Aligned_cols=31 Identities=23% Similarity=0.637 Sum_probs=23.0
Q ss_pred ccccccccccCCCc---------cCCCCccCcceeeecCC
Q 032638 85 TEIPLKTCEDCGGS---------GICPECKGEGFVLKKLS 115 (136)
Q Consensus 85 ~E~~~k~Ce~C~Gs---------GiCpeCkGEGFVlK~Ls 115 (136)
.-.-.-.|+.||-. --||+|.+..|.=+-|+
T Consensus 120 vg~G~LvC~~Cg~~~~~~~p~~i~pCp~C~~~~F~R~~~~ 159 (160)
T PRK11032 120 VGLGNLVCEKCHHHLAFYTPEVLPLCPKCGHDQFQRRPFE 159 (160)
T ss_pred eecceEEecCCCCEEEecCCCcCCCCCCCCCCeeeeCCCC
Confidence 34456789999853 46999999999755554
No 200
>COG2093 DNA-directed RNA polymerase, subunit E'' [Transcription]
Probab=22.98 E-value=76 Score=22.43 Aligned_cols=34 Identities=32% Similarity=0.826 Sum_probs=19.7
Q ss_pred ccccccC-----CCccCCCCccCc-------ceeeecCCHHHHHHHH
Q 032638 89 LKTCEDC-----GGSGICPECKGE-------GFVLKKLSEETAERAR 123 (136)
Q Consensus 89 ~k~Ce~C-----~GsGiCpeCkGE-------GFVlK~Lsee~A~kAR 123 (136)
++-|-.| ..+-+||.|.++ |||+= +.+|.-+-|+
T Consensus 4 ~kAC~~Ck~l~~~d~e~CP~Cgs~~~te~W~G~~iI-idpe~SeIAk 49 (64)
T COG2093 4 EKACKNCKRLTPEDTEICPVCGSTDLTEEWFGLLII-IDPEKSEIAK 49 (64)
T ss_pred hHHHhhccccCCCCCccCCCCCCcccchhhccEEEE-EcCcHHHHHH
Confidence 4556666 355668888777 66654 3444444443
No 201
>PRK10811 rne ribonuclease E; Reviewed
Probab=22.90 E-value=35 Score=34.39 Aligned_cols=15 Identities=40% Similarity=0.995 Sum_probs=12.0
Q ss_pred CCCCccCcceeeecC
Q 032638 100 ICPECKGEGFVLKKL 114 (136)
Q Consensus 100 iCpeCkGEGFVlK~L 114 (136)
.||.|.|.|+|++.-
T Consensus 403 ~Cp~C~GtG~v~s~e 417 (1068)
T PRK10811 403 VCPRCSGTGTVRDNE 417 (1068)
T ss_pred cCcccCCCcccccHH
Confidence 688999999987654
No 202
>KOG0712 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=22.89 E-value=51 Score=28.99 Aligned_cols=44 Identities=30% Similarity=0.613 Sum_probs=27.8
Q ss_pred HHHHHHHHHHHhcCC------CccccccccccccCCCccC------------------CCCccCccee
Q 032638 67 VVGAAATLLVRRTKG------SEETEIPLKTCEDCGGSGI------------------CPECKGEGFV 110 (136)
Q Consensus 67 vVGaAat~Lvrr~k~------~e~~E~~~k~Ce~C~GsGi------------------CpeCkGEGFV 110 (136)
.+|...-+.+.++.- +--....-..|..|.|+|+ |..|+|.|..
T Consensus 115 y~G~s~kl~l~~~~iCs~C~GsGgksg~~~~C~~C~GsGv~~~~~~~gPg~~qs~q~~C~~C~G~G~~ 182 (337)
T KOG0712|consen 115 YMGKSKKLFLSRNFICSKCSGSGGKSGSAPKCTTCRGSGVQTRTRQMGPGMVQSPQLVCDSCNGSGET 182 (337)
T ss_pred hcCCccceecccCccCCcCCCCCCCCCCCCCCCCCCCCCceeEEEeccccccccceeEeccCCCcccc
Confidence 455555555555532 1123444557888888875 8888888887
No 203
>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=22.70 E-value=28 Score=21.94 Aligned_cols=13 Identities=54% Similarity=1.393 Sum_probs=5.2
Q ss_pred CccCCCCc---cCcce
Q 032638 97 GSGICPEC---KGEGF 109 (136)
Q Consensus 97 GsGiCpeC---kGEGF 109 (136)
|+.+|-.| .|.||
T Consensus 25 G~~~C~~C~~~~GDG~ 40 (40)
T PF08273_consen 25 GTWICRQCGGDAGDGF 40 (40)
T ss_dssp S-EEETTTTBE-----
T ss_pred CCEECCCCCCcCCCCC
Confidence 44588888 45554
No 204
>COG2149 Predicted membrane protein [Function unknown]
Probab=22.62 E-value=84 Score=24.45 Aligned_cols=42 Identities=17% Similarity=0.062 Sum_probs=26.4
Q ss_pred eeeecchhhhhhccccccccchhhHHHHHHHHHHHHHHHHHHHHhc
Q 032638 34 SSIDIKSQEQERKLPTVSSALPETAASVAIAATVVGAAATLLVRRT 79 (136)
Q Consensus 34 ~s~~vk~q~~~r~~~~v~~Alpetaas~aiaa~vVGaAat~Lvrr~ 79 (136)
.-++++.|.+++...... ..--=.++++.|||+.+++|+-.+
T Consensus 77 r~~~~~~amrr~~~~p~~----~i~~~~av~lvVv~~~~~llv~~~ 118 (120)
T COG2149 77 RWQRVERAMRRGFYLPYL----NIWLYLAVGLVVVGVIVLLLVLYQ 118 (120)
T ss_pred HHHHHHHHHHcCCCCCcc----chHHHHHHHHHHHHHHHHHHHHHh
Confidence 335666666666444332 223346788889999998887543
No 205
>PRK11712 ribonuclease G; Provisional
Probab=22.48 E-value=24 Score=31.85 Aligned_cols=17 Identities=24% Similarity=0.571 Sum_probs=13.7
Q ss_pred cccccccccccCCCccC
Q 032638 84 ETEIPLKTCEDCGGSGI 100 (136)
Q Consensus 84 ~~E~~~k~Ce~C~GsGi 100 (136)
..|.-.+.|+-|+|+|.
T Consensus 397 l~~~l~~~Cp~C~G~G~ 413 (489)
T PRK11712 397 LEHVLCGECPTCHGRGT 413 (489)
T ss_pred hHHHhcCCCCCCCCCCC
Confidence 45666789999999994
No 206
>TIGR02008 fdx_plant ferredoxin [2Fe-2S]. This model represents single domain 2Fe-2S (also called plant type) ferredoxins. In general, these occur as a single domain proteins or with a chloroplast transit peptide. Species tend to be photosynthetic, but several forms may occur in one species and individually may not be associated with photocynthesis. Halobacterial forms differ somewhat in architecture; they score between trusted and noise cutoffs. Sequences scoring below the noise cutoff tend to be ferredoxin-related domains of larger proteins.
Probab=22.35 E-value=46 Score=22.88 Aligned_cols=12 Identities=42% Similarity=1.315 Sum_probs=9.9
Q ss_pred cCCCccCCCCccC
Q 032638 94 DCGGSGICPECKG 106 (136)
Q Consensus 94 ~C~GsGiCpeCkG 106 (136)
.|+ .|.|..|+.
T Consensus 39 ~C~-~G~Cg~C~v 50 (97)
T TIGR02008 39 SCR-AGACSTCAG 50 (97)
T ss_pred CCC-CccCCCCce
Confidence 477 799999984
No 207
>PLN03131 hypothetical protein; Provisional
Probab=21.86 E-value=37 Score=32.82 Aligned_cols=19 Identities=42% Similarity=1.158 Sum_probs=15.4
Q ss_pred cccccccCCCcc-----------CCCCccC
Q 032638 88 PLKTCEDCGGSG-----------ICPECKG 106 (136)
Q Consensus 88 ~~k~Ce~C~GsG-----------iCpeCkG 106 (136)
.-+.|-||+..+ ||.+|.|
T Consensus 22 gNk~CADCga~~P~WASiNlGIFICi~CSG 51 (705)
T PLN03131 22 PNRRCINCNSLGPQFVCTNFWTFICMTCSG 51 (705)
T ss_pred CCCccccCCCCCCCeeEeccceEEchhchh
Confidence 457899998654 7999987
No 208
>PRK11788 tetratricopeptide repeat protein; Provisional
Probab=21.64 E-value=58 Score=25.30 Aligned_cols=23 Identities=35% Similarity=0.807 Sum_probs=17.6
Q ss_pred cccccccCCCc-----cCCCCccCccee
Q 032638 88 PLKTCEDCGGS-----GICPECKGEGFV 110 (136)
Q Consensus 88 ~~k~Ce~C~Gs-----GiCpeCkGEGFV 110 (136)
+.-.|..||-+ -+||.|.+-|-+
T Consensus 353 p~~~c~~cg~~~~~~~~~c~~c~~~~~~ 380 (389)
T PRK11788 353 PRYRCRNCGFTARTLYWHCPSCKAWETI 380 (389)
T ss_pred CCEECCCCCCCCccceeECcCCCCccCc
Confidence 34679999875 489999987643
No 209
>PF00111 Fer2: 2Fe-2S iron-sulfur cluster binding domain; InterPro: IPR001041 The ferredoxin protein family are electron carrier proteins with an iron-sulphur cofactor that act in a wide variety of metabolic reactions. Ferredoxins can be divided into several subgroups depending upon the physiological nature of the iron-sulphur cluster(s) and according to sequence similarities. This entry represents members of the 2Fe-2S ferredoxin family that have a general core structure consisting of beta(2)-alpha-beta(2), which includes putidaredoxin and terpredoxin, and adrenodoxin [, , , ]. They are proteins of around one hundred amino acids with four conserved cysteine residues to which the 2Fe-2S cluster is ligated. This conserved region is also found as a domain in various metabolic enzymes and in multidomain proteins, such as aldehyde oxidoreductase (N-terminal), xanthine oxidase (N-terminal), phthalate dioxygenase reductase (C-terminal), succinate dehydrogenase iron-sulphur protein (N-terminal), and methane monooxygenase reductase (N-terminal).; GO: 0009055 electron carrier activity, 0051536 iron-sulfur cluster binding; PDB: 3M9S_C 2FUG_L 3IAS_L 2YBB_3 3IAM_3 3I9V_3 1JQ4_A 1DOX_A 1DOY_A 2KAJ_A ....
Probab=21.53 E-value=52 Score=20.76 Aligned_cols=17 Identities=53% Similarity=1.173 Sum_probs=13.2
Q ss_pred ccCCCccCCCCccC---ccee
Q 032638 93 EDCGGSGICPECKG---EGFV 110 (136)
Q Consensus 93 e~C~GsGiCpeCkG---EGFV 110 (136)
..|+|.+ |.-|.. +|-+
T Consensus 33 ~~C~~g~-Cg~C~v~v~~G~~ 52 (78)
T PF00111_consen 33 YSCGGGG-CGTCRVRVLEGEV 52 (78)
T ss_dssp TSSSSSS-SSTTEEEEEESEE
T ss_pred cCCCCCc-cCCcEEEEeeCcc
Confidence 5798877 999985 3666
No 210
>PRK07609 CDP-6-deoxy-delta-3,4-glucoseen reductase; Validated
Probab=21.21 E-value=41 Score=27.00 Aligned_cols=12 Identities=50% Similarity=1.348 Sum_probs=10.2
Q ss_pred cCCCccCCCCccC
Q 032638 94 DCGGSGICPECKG 106 (136)
Q Consensus 94 ~C~GsGiCpeCkG 106 (136)
.|+ .|.|..|+.
T Consensus 36 ~C~-~G~Cg~C~~ 47 (339)
T PRK07609 36 GCK-NGACGSCKG 47 (339)
T ss_pred CCC-CeECCCCEE
Confidence 386 899999986
No 211
>PRK00432 30S ribosomal protein S27ae; Validated
Probab=20.92 E-value=47 Score=21.44 Aligned_cols=19 Identities=32% Similarity=0.690 Sum_probs=12.4
Q ss_pred ccccccccCCC--------ccCCCCcc
Q 032638 87 IPLKTCEDCGG--------SGICPECK 105 (136)
Q Consensus 87 ~~~k~Ce~C~G--------sGiCpeCk 105 (136)
...+.|+.||. .-.|+.|.
T Consensus 18 ~~~~fCP~Cg~~~m~~~~~r~~C~~Cg 44 (50)
T PRK00432 18 RKNKFCPRCGSGFMAEHLDRWHCGKCG 44 (50)
T ss_pred EccCcCcCCCcchheccCCcEECCCcC
Confidence 45678888876 44566664
No 212
>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=20.92 E-value=43 Score=24.75 Aligned_cols=18 Identities=39% Similarity=0.931 Sum_probs=11.6
Q ss_pred cCCCCccCcceeeecCCHHHH
Q 032638 99 GICPECKGEGFVLKKLSEETA 119 (136)
Q Consensus 99 GiCpeCkGEGFVlK~Lsee~A 119 (136)
..|+.||| .|.+.+++.+
T Consensus 92 sRC~~CN~---~L~~v~~~~v 109 (147)
T PF01927_consen 92 SRCPKCNG---PLRPVSKEEV 109 (147)
T ss_pred CccCCCCc---Eeeechhhcc
Confidence 45777777 6666666544
No 213
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=20.90 E-value=39 Score=26.01 Aligned_cols=19 Identities=47% Similarity=1.310 Sum_probs=14.9
Q ss_pred ccccccCC------CccCCCCccCc
Q 032638 89 LKTCEDCG------GSGICPECKGE 107 (136)
Q Consensus 89 ~k~Ce~C~------GsGiCpeCkGE 107 (136)
...|..|| |.-+||.|.-+
T Consensus 3 l~nC~~CgklF~~~~~~iCp~C~~~ 27 (137)
T TIGR03826 3 LANCPKCGRLFVKTGRDVCPSCYEE 27 (137)
T ss_pred CccccccchhhhhcCCccCHHHhHH
Confidence 56799996 67799999753
No 214
>PRK08270 anaerobic ribonucleoside triphosphate reductase; Provisional
Probab=20.76 E-value=60 Score=30.26 Aligned_cols=23 Identities=26% Similarity=0.637 Sum_probs=17.4
Q ss_pred ccccccccccCCCcc----CCCCccCc
Q 032638 85 TEIPLKTCEDCGGSG----ICPECKGE 107 (136)
Q Consensus 85 ~E~~~k~Ce~C~GsG----iCpeCkGE 107 (136)
.-.+.-.|.+||-.+ -||.|..+
T Consensus 622 in~~~~~C~~CG~~~g~~~~CP~CG~~ 648 (656)
T PRK08270 622 ITPTFSICPKHGYLSGEHEFCPKCGEE 648 (656)
T ss_pred eCCCCcccCCCCCcCCCCCCCcCCcCc
Confidence 455677899999744 69999654
No 215
>TIGR02827 RNR_anaer_Bdell anaerobic ribonucleoside-triphosphate reductase. Members of this family belong to the class III anaerobic ribonucleoside-triphosphate reductases (RNR). These glycine-radical-containing enzymes are oxygen-sensitive and operate under anaerobic conditions. The genes for this family are pair with genes for an acitivating protein that creates a glycine radical. Members of this family, though related, fall outside the scope of TIGR02487, a functionally equivalent protein set; no genome has members in both familes. Identification as RNR is supported by gene pairing with the activating protein, lack of other anaerobic RNR, and presence of an upstream regulatory element strongly conserved upstream of most RNR operons.
Probab=20.62 E-value=55 Score=30.38 Aligned_cols=23 Identities=30% Similarity=0.800 Sum_probs=17.7
Q ss_pred ccccccccccCCC-cc----CCCCccCc
Q 032638 85 TEIPLKTCEDCGG-SG----ICPECKGE 107 (136)
Q Consensus 85 ~E~~~k~Ce~C~G-sG----iCpeCkGE 107 (136)
.-.+.-.|.+||- .| .||.|-.+
T Consensus 528 in~~~siC~~CGy~~g~~~~~CP~CGs~ 555 (586)
T TIGR02827 528 FNIKITICNDCHHIDKRTLHRCPVCGSA 555 (586)
T ss_pred eCCCCeecCCCCCcCCCcCCcCcCCCCc
Confidence 3457789999998 56 79999643
No 216
>PLN03136 Ferredoxin; Provisional
Probab=20.36 E-value=45 Score=25.71 Aligned_cols=12 Identities=42% Similarity=1.295 Sum_probs=10.4
Q ss_pred cCCCccCCCCccC
Q 032638 94 DCGGSGICPECKG 106 (136)
Q Consensus 94 ~C~GsGiCpeCkG 106 (136)
.|+ .|.|..|++
T Consensus 90 sCr-~G~CGtC~~ 101 (148)
T PLN03136 90 SCR-AGSCSSCAG 101 (148)
T ss_pred CCC-CccCCCCEE
Confidence 387 999999987
Done!