Query 028179
Match_columns 212
No_of_seqs 136 out of 213
Neff 4.4
Searched_HMMs 46136
Date Fri Mar 29 07:29:02 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/028179.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/028179hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF02536 mTERF: mTERF; InterP 99.7 2.2E-18 4.8E-23 152.6 5.1 123 71-198 167-310 (345)
2 PLN03196 MOC1-like protein; Pr 99.7 3.8E-17 8.2E-22 155.5 9.2 106 77-199 302-408 (487)
3 PLN03196 MOC1-like protein; Pr 99.6 2.1E-15 4.5E-20 143.6 8.9 120 77-197 122-266 (487)
4 PF02536 mTERF: mTERF; InterP 99.5 6E-15 1.3E-19 130.7 3.6 109 77-197 137-277 (345)
5 KOG1267 Mitochondrial transcri 99.1 9.1E-11 2E-15 108.7 6.1 124 71-199 258-398 (413)
6 KOG1267 Mitochondrial transcri 99.1 1.2E-10 2.6E-15 107.9 6.2 76 121-197 261-363 (413)
7 smart00733 Mterf Mitochondrial 97.6 3.2E-05 7E-10 45.1 1.4 29 145-175 2-30 (31)
8 smart00733 Mterf Mitochondrial 91.8 0.17 3.7E-06 28.9 2.4 18 122-139 14-31 (31)
9 PF04695 Pex14_N: Peroxisomal 91.1 0.24 5.1E-06 40.2 3.3 29 126-154 23-51 (136)
10 PF07499 RuvA_C: RuvA, C-termi 88.9 0.3 6.6E-06 32.8 1.9 41 127-167 4-44 (47)
11 PF14490 HHH_4: Helix-hairpin- 88.8 1.5 3.3E-05 33.1 5.9 73 77-185 6-78 (94)
12 cd04790 HTH_Cfa-like_unk Helix 87.6 1.8 3.9E-05 36.3 6.2 21 126-146 147-167 (172)
13 COG1725 Predicted transcriptio 86.7 1.7 3.7E-05 35.5 5.4 88 62-151 20-120 (125)
14 PF07499 RuvA_C: RuvA, C-termi 86.7 0.98 2.1E-05 30.3 3.4 27 78-104 2-28 (47)
15 KOG0550 Molecular chaperone (D 86.3 0.77 1.7E-05 44.7 3.7 93 74-188 332-430 (486)
16 PRK00116 ruvA Holliday junctio 82.0 6.1 0.00013 33.7 7.0 80 83-165 107-187 (192)
17 PRK02249 DNA primase large sub 81.2 1.4 3E-05 41.3 3.0 74 121-208 239-313 (343)
18 PRK14605 ruvA Holliday junctio 79.6 9.8 0.00021 32.7 7.5 86 82-170 106-192 (194)
19 smart00165 UBA Ubiquitin assoc 71.1 7.2 0.00016 24.1 3.4 23 128-150 3-25 (37)
20 PF04695 Pex14_N: Peroxisomal 70.7 5.5 0.00012 32.3 3.5 35 149-188 14-48 (136)
21 PRK14136 recX recombination re 68.7 33 0.00072 32.1 8.5 105 83-190 183-305 (309)
22 PRK14601 ruvA Holliday junctio 68.6 22 0.00047 30.6 6.8 73 84-168 108-181 (183)
23 PF00627 UBA: UBA/TS-N domain; 66.7 12 0.00026 23.5 3.8 24 80-103 3-26 (37)
24 cd00194 UBA Ubiquitin Associat 66.6 10 0.00022 23.5 3.4 23 128-150 3-25 (38)
25 cd01378 MYSc_type_I Myosin mot 66.5 17 0.00038 36.8 6.8 74 73-149 230-307 (674)
26 smart00165 UBA Ubiquitin assoc 66.2 15 0.00033 22.6 4.1 25 80-104 2-26 (37)
27 TIGR00084 ruvA Holliday juncti 65.8 33 0.00072 29.4 7.5 80 85-167 108-188 (191)
28 PRK14606 ruvA Holliday junctio 65.7 26 0.00056 30.1 6.8 74 87-169 112-185 (188)
29 cd01386 MYSc_type_XVIII Myosin 65.7 18 0.00039 37.4 6.7 74 73-149 230-306 (767)
30 PRK00117 recX recombination re 65.1 70 0.0015 25.7 8.9 104 80-185 29-151 (157)
31 cd01380 MYSc_type_V Myosin mot 64.7 22 0.00048 36.2 7.1 73 74-150 234-312 (691)
32 PF03960 ArsC: ArsC family; I 62.8 23 0.0005 26.9 5.5 59 137-199 32-95 (110)
33 KOG0164 Myosin class I heavy c 62.8 18 0.00039 37.9 6.0 84 69-155 236-322 (1001)
34 cd01377 MYSc_type_II Myosin mo 61.7 22 0.00049 36.1 6.5 75 73-150 242-321 (693)
35 PF00627 UBA: UBA/TS-N domain; 61.0 12 0.00026 23.5 3.0 23 128-150 4-26 (37)
36 cd04767 HTH_HspR-like_MBC Heli 59.8 33 0.00072 27.6 6.0 77 84-166 6-87 (120)
37 cd01385 MYSc_type_IX Myosin mo 58.9 28 0.0006 35.5 6.6 79 73-154 238-324 (692)
38 TIGR01448 recD_rel helicase, p 58.5 61 0.0013 33.1 9.0 59 126-184 143-212 (720)
39 PF10440 WIYLD: Ubiquitin-bind 58.2 17 0.00038 26.7 3.8 29 122-150 7-35 (65)
40 cd00124 MYSc Myosin motor doma 57.9 32 0.0007 34.7 6.9 74 73-150 228-309 (679)
41 PF13411 MerR_1: MerR HTH fami 56.5 45 0.00098 22.7 5.6 58 84-149 5-68 (69)
42 cd00194 UBA Ubiquitin Associat 56.4 29 0.00064 21.3 4.2 25 80-104 2-26 (38)
43 smart00422 HTH_MERR helix_turn 55.9 57 0.0012 22.1 6.0 62 84-148 5-68 (70)
44 PF03677 UPF0137: Uncharacteri 54.2 44 0.00096 30.3 6.4 101 67-187 79-184 (243)
45 PF06896 DUF1268: Protein of u 53.4 59 0.0013 26.1 6.4 60 71-149 47-109 (114)
46 COG4103 Uncharacterized protei 52.9 14 0.00031 31.2 2.9 80 77-165 48-144 (148)
47 cd01387 MYSc_type_XV Myosin mo 52.7 41 0.00089 34.2 6.7 76 73-152 228-311 (677)
48 TIGR01558 sm_term_P27 phage te 51.6 17 0.00036 28.3 3.0 33 71-103 6-39 (116)
49 PRK14604 ruvA Holliday junctio 50.5 59 0.0013 28.1 6.5 84 84-169 108-192 (195)
50 KOG0871 Class 2 transcription 50.0 33 0.00071 29.2 4.6 62 71-146 59-122 (156)
51 cd01379 MYSc_type_III Myosin m 49.8 57 0.0012 33.1 7.2 78 74-154 234-319 (653)
52 COG4669 EscJ Type III secretor 49.3 39 0.00085 30.7 5.3 66 76-159 63-130 (246)
53 cd01381 MYSc_type_VII Myosin m 49.3 45 0.00097 33.9 6.3 74 73-150 227-308 (671)
54 COG3747 Phage terminase, small 49.2 29 0.00063 29.6 4.2 94 69-182 42-137 (160)
55 PF02662 FlpD: Methyl-viologen 48.2 30 0.00065 27.6 4.0 23 74-96 74-96 (124)
56 KOG2629 Peroxisomal membrane a 48.1 21 0.00045 33.3 3.4 24 126-149 22-45 (300)
57 PRK00033 clpS ATP-dependent Cl 48.1 27 0.00059 27.4 3.7 61 71-138 32-93 (100)
58 cd01106 HTH_TipAL-Mta Helix-Tu 47.6 78 0.0017 23.8 6.1 81 84-171 5-87 (103)
59 PF13371 TPR_9: Tetratricopept 47.0 21 0.00046 24.0 2.6 38 75-112 7-45 (73)
60 PRK14137 recX recombination re 45.5 2E+02 0.0044 24.8 9.3 67 81-149 59-127 (195)
61 PRK09853 putative selenate red 45.2 7.4 0.00016 41.5 0.1 35 136-194 218-252 (1019)
62 cd02977 ArsC_family Arsenate R 45.1 67 0.0014 24.0 5.4 27 174-200 73-99 (105)
63 PRK14602 ruvA Holliday junctio 45.0 46 0.001 28.8 5.0 27 78-104 154-180 (203)
64 TIGR00014 arsC arsenate reduct 44.6 73 0.0016 24.6 5.7 27 175-201 74-100 (114)
65 cd01384 MYSc_type_XI Myosin mo 43.8 59 0.0013 33.1 6.2 77 73-150 232-314 (674)
66 PRK14603 ruvA Holliday junctio 43.7 38 0.00082 29.3 4.2 26 79-104 152-177 (197)
67 COG0339 Dcp Zn-dependent oligo 43.3 39 0.00084 34.9 4.8 81 72-159 49-132 (683)
68 PF02631 RecX: RecX family; I 43.1 44 0.00095 25.8 4.2 57 128-185 47-117 (121)
69 cd01383 MYSc_type_VIII Myosin 42.8 68 0.0015 32.7 6.5 75 73-151 232-312 (677)
70 PF13348 Y_phosphatase3C: Tyro 42.7 35 0.00076 23.7 3.3 44 87-149 22-66 (68)
71 PRK14603 ruvA Holliday junctio 42.4 35 0.00075 29.5 3.8 85 84-168 107-195 (197)
72 PRK14604 ruvA Holliday junctio 42.0 52 0.0011 28.4 4.8 26 79-104 149-174 (195)
73 PF09286 Pro-kuma_activ: Pro-k 41.4 17 0.00037 28.8 1.7 22 121-142 59-80 (143)
74 PRK14606 ruvA Holliday junctio 40.8 33 0.00071 29.5 3.4 27 78-104 142-168 (188)
75 PF07293 DUF1450: Protein of u 40.1 12 0.00026 28.2 0.6 45 162-211 1-46 (78)
76 TIGR03315 Se_ygfK putative sel 39.9 9.6 0.00021 40.6 0.0 35 136-194 216-250 (1012)
77 smart00242 MYSc Myosin. Large 39.7 70 0.0015 32.5 6.0 74 73-150 236-316 (677)
78 PRK14600 ruvA Holliday junctio 39.7 40 0.00088 28.9 3.8 37 126-164 145-181 (186)
79 PF10440 WIYLD: Ubiquitin-bind 39.4 50 0.0011 24.3 3.7 36 77-113 9-44 (65)
80 PRK14602 ruvA Holliday junctio 39.3 43 0.00092 29.0 3.9 44 126-169 155-199 (203)
81 PF11829 DUF3349: Protein of u 38.9 93 0.002 24.4 5.4 55 70-140 35-92 (96)
82 cd04790 HTH_Cfa-like_unk Helix 38.3 1.1E+02 0.0025 25.5 6.2 82 84-172 6-89 (172)
83 PF13475 DUF4116: Domain of un 37.9 18 0.00039 23.2 1.1 32 140-172 2-33 (49)
84 PF00063 Myosin_head: Myosin h 37.7 54 0.0012 32.8 4.9 78 73-154 231-314 (689)
85 KOG4234 TPR repeat-containing 37.4 65 0.0014 29.4 4.8 108 75-199 146-265 (271)
86 PRK14600 ruvA Holliday junctio 37.3 52 0.0011 28.2 4.1 25 79-103 145-169 (186)
87 cd03035 ArsC_Yffb Arsenate Red 37.3 1.1E+02 0.0024 23.4 5.6 56 137-199 35-96 (105)
88 PRK07562 ribonucleotide-diphos 37.1 72 0.0016 35.1 5.9 58 82-152 715-772 (1220)
89 PF13414 TPR_11: TPR repeat; P 36.9 44 0.00094 22.2 2.9 30 75-104 15-45 (69)
90 KOG4779 Predicted membrane pro 36.2 22 0.00048 27.0 1.4 44 131-191 26-69 (82)
91 PF01988 VIT1: VIT family; In 36.1 46 0.001 28.5 3.6 26 79-104 82-107 (213)
92 TIGR00084 ruvA Holliday juncti 35.6 75 0.0016 27.2 4.8 25 80-104 148-172 (191)
93 PF08784 RPA_C: Replication pr 35.4 31 0.00067 25.9 2.2 39 128-175 51-94 (102)
94 COG0632 RuvA Holliday junction 35.4 1.2E+02 0.0025 26.7 6.0 96 69-164 88-195 (201)
95 PRK14601 ruvA Holliday junctio 35.2 63 0.0014 27.7 4.3 25 79-103 142-166 (183)
96 cd01382 MYSc_type_VI Myosin mo 35.2 1E+02 0.0022 31.6 6.5 74 73-149 258-339 (717)
97 cd04763 HTH_MlrA-like Helix-Tu 35.0 1.5E+02 0.0033 20.3 5.9 57 84-148 5-68 (68)
98 PRK09875 putative hydrolase; P 35.0 41 0.0009 30.7 3.3 29 124-152 260-288 (292)
99 PRK14981 DNA-directed RNA poly 34.3 2.3E+02 0.005 22.3 8.1 34 70-106 29-62 (112)
100 PF03874 RNA_pol_Rpb4: RNA pol 33.5 63 0.0014 24.7 3.7 57 121-184 54-110 (117)
101 PF13543 KSR1-SAM: SAM like do 33.2 1.3E+02 0.0028 24.8 5.5 59 77-148 64-123 (129)
102 PF02631 RecX: RecX family; I 33.2 1.4E+02 0.0031 22.9 5.7 28 122-149 91-118 (121)
103 PF12244 DUF3606: Protein of u 33.1 45 0.00098 23.4 2.6 22 128-149 21-43 (57)
104 KOG0011 Nucleotide excision re 32.6 37 0.00081 32.2 2.6 91 80-192 136-240 (340)
105 PRK13344 spxA transcriptional 32.6 1.3E+02 0.0028 24.1 5.5 58 138-200 37-99 (132)
106 COG5457 Uncharacterized conser 32.3 46 0.00099 24.3 2.5 19 131-149 41-59 (63)
107 PHA02591 hypothetical protein; 31.9 74 0.0016 24.5 3.7 39 102-147 31-69 (83)
108 cd03034 ArsC_ArsC Arsenate Red 31.7 1.6E+02 0.0035 22.6 5.7 60 137-200 35-98 (112)
109 cd04766 HTH_HspR Helix-Turn-He 31.7 2.1E+02 0.0045 21.0 6.5 61 84-148 6-69 (91)
110 cd01104 HTH_MlrA-CarA Helix-Tu 31.2 90 0.0019 21.1 3.8 31 69-100 37-67 (68)
111 PRK13019 clpS ATP-dependent Cl 30.8 95 0.0021 24.0 4.2 62 71-139 26-89 (94)
112 cd08815 Death_TNFRSF25_DR3 Dea 30.6 44 0.00095 25.4 2.3 19 128-146 13-31 (77)
113 PF03394 Pox_E8: Poxvirus E8 p 30.5 21 0.00046 32.0 0.6 27 154-180 213-239 (242)
114 PTZ00014 myosin-A; Provisional 30.2 1.4E+02 0.003 31.4 6.5 78 73-151 325-410 (821)
115 cd08315 Death_TRAILR_DR4_DR5 D 30.2 58 0.0013 25.0 3.0 24 129-152 22-45 (96)
116 PF11626 Rap1_C: TRF2-interact 30.1 1.2E+02 0.0027 22.5 4.7 70 80-171 12-87 (87)
117 PF11372 DUF3173: Domain of un 29.8 76 0.0016 22.9 3.3 38 84-121 7-47 (59)
118 PF01726 LexA_DNA_bind: LexA D 29.5 2.1E+02 0.0046 20.4 6.1 53 70-138 3-55 (65)
119 PHA03004 putative membrane pro 29.1 23 0.0005 32.2 0.6 27 154-180 241-267 (270)
120 TIGR02051 MerR Hg(II)-responsi 28.6 2E+02 0.0043 22.5 5.9 65 84-151 4-70 (124)
121 cd04788 HTH_NolA-AlbR Helix-Tu 28.6 82 0.0018 23.6 3.5 81 84-171 5-87 (96)
122 TIGR02014 BchZ chlorophyllide 28.3 62 0.0014 31.5 3.5 42 135-176 417-461 (468)
123 PF06576 DUF1133: Protein of u 28.0 80 0.0017 27.5 3.7 42 108-149 42-83 (176)
124 PHA02277 hypothetical protein 28.0 3.7E+02 0.0079 22.6 7.6 20 130-149 85-105 (150)
125 PF13926 DUF4211: Domain of un 27.5 83 0.0018 25.5 3.6 83 123-207 37-124 (153)
126 cd08313 Death_TNFR1 Death doma 27.4 68 0.0015 24.1 2.8 24 128-151 13-36 (80)
127 cd04780 HTH_MerR-like_sg5 Heli 27.3 2.7E+02 0.0059 20.9 7.0 71 85-171 6-85 (95)
128 PRK13901 ruvA Holliday junctio 27.2 73 0.0016 27.8 3.4 25 79-103 144-168 (196)
129 cd00592 HTH_MerR-like Helix-Tu 27.2 2.3E+02 0.0049 20.8 5.7 57 84-149 5-68 (100)
130 PRK00118 putative DNA-binding 26.8 1.1E+02 0.0025 24.0 4.1 64 84-169 38-104 (104)
131 PRK13523 NADPH dehydrogenase N 26.7 51 0.0011 30.5 2.4 45 166-210 290-337 (337)
132 PF13432 TPR_16: Tetratricopep 26.7 1.5E+02 0.0033 19.4 4.3 30 75-104 9-39 (65)
133 cd03033 ArsC_15kD Arsenate Red 26.7 2.4E+02 0.0051 22.0 5.9 59 137-201 36-98 (113)
134 KOG2511 Nicotinic acid phospho 26.6 94 0.002 30.1 4.2 56 79-153 53-114 (420)
135 PRK14134 recX recombination re 26.5 2.5E+02 0.0055 25.4 6.8 100 86-186 85-205 (283)
136 PRK05988 formate dehydrogenase 26.4 2.9E+02 0.0062 22.9 6.7 65 75-154 4-69 (156)
137 cd04758 Commd10 COMM_Domain co 26.4 2.6E+02 0.0057 23.4 6.6 53 87-148 45-97 (186)
138 cd04764 HTH_MlrA-like_sg1 Heli 26.3 1.2E+02 0.0027 20.7 3.8 31 69-100 36-66 (67)
139 cd08316 Death_FAS_TNFRSF6 Deat 25.9 1E+02 0.0022 23.9 3.6 27 127-153 21-47 (97)
140 PF03874 RNA_pol_Rpb4: RNA pol 25.7 1.7E+02 0.0037 22.3 4.9 12 137-148 100-111 (117)
141 TIGR01616 nitro_assoc nitrogen 25.6 1.5E+02 0.0033 23.7 4.7 23 175-197 73-95 (126)
142 PF11852 DUF3372: Domain of un 25.3 63 0.0014 27.7 2.6 72 73-160 15-92 (168)
143 cd04752 Commd4 COMM_Domain con 25.1 3.2E+02 0.0069 22.8 6.8 60 80-148 25-84 (174)
144 PF11165 DUF2949: Protein of u 24.9 1.1E+02 0.0023 22.0 3.3 23 128-150 4-27 (58)
145 PRK13901 ruvA Holliday junctio 24.6 2.7E+02 0.0059 24.3 6.4 61 84-150 107-168 (196)
146 cd04775 HTH_Cfa-like Helix-Tur 24.5 3.1E+02 0.0067 20.7 6.1 79 84-172 6-86 (102)
147 cd04765 HTH_MlrA-like_sg2 Heli 24.3 1.4E+02 0.0029 22.8 4.0 34 70-103 38-71 (99)
148 cd01279 HTH_HspR-like Helix-Tu 24.2 2.5E+02 0.0054 21.1 5.5 63 85-156 7-77 (98)
149 PF04539 Sigma70_r3: Sigma-70 24.0 2E+02 0.0043 20.1 4.6 24 136-159 30-53 (78)
150 cd01421 IMPCH Inosine monophos 24.0 24 0.00053 30.7 -0.1 37 128-166 32-68 (187)
151 COG0632 RuvA Holliday junction 24.0 86 0.0019 27.5 3.2 27 78-104 155-181 (201)
152 PRK03902 manganese transport t 24.0 1.9E+02 0.0042 22.8 5.1 82 85-170 28-121 (142)
153 cd08306 Death_FADD Fas-associa 23.8 89 0.0019 23.3 2.9 21 132-152 19-39 (86)
154 smart00657 RPOL4c DNA-directed 23.8 1.3E+02 0.0028 23.7 3.9 57 121-184 52-108 (118)
155 cd04777 HTH_MerR-like_sg1 Heli 23.2 1.4E+02 0.0031 22.5 4.0 31 71-102 37-67 (107)
156 PF09278 MerR-DNA-bind: MerR, 23.0 1E+02 0.0022 20.9 2.9 20 128-147 5-24 (65)
157 PF04752 ChaC: ChaC-like prote 22.6 1.9E+02 0.004 24.7 5.0 46 91-148 126-173 (178)
158 PF06827 zf-FPG_IleRS: Zinc fi 22.6 31 0.00067 20.7 0.2 7 204-210 3-9 (30)
159 PRK13669 hypothetical protein; 22.6 41 0.00088 25.6 0.8 44 162-211 1-46 (78)
160 PF06252 DUF1018: Protein of u 22.6 1.5E+02 0.0033 23.0 4.1 74 92-178 2-75 (119)
161 PF08671 SinI: Anti-repressor 22.3 1.7E+02 0.0036 18.4 3.4 26 77-102 3-28 (30)
162 cd04782 HTH_BltR Helix-Turn-He 22.1 2.4E+02 0.0052 21.1 5.0 32 70-102 38-69 (97)
163 COG1125 OpuBA ABC-type proline 21.8 1.8E+02 0.0039 27.4 4.9 97 90-191 37-136 (309)
164 cd08784 Death_DRs Death Domain 21.7 1E+02 0.0022 22.6 2.8 23 130-152 15-37 (79)
165 smart00342 HTH_ARAC helix_turn 21.4 1.1E+02 0.0024 20.4 2.8 20 87-106 9-28 (84)
166 cd04773 HTH_TioE_rpt2 Second H 21.2 3.7E+02 0.0079 20.5 6.0 64 84-150 5-70 (108)
167 PF14490 HHH_4: Helix-hairpin- 21.1 1.1E+02 0.0024 22.8 3.0 29 124-152 6-34 (94)
168 PF02617 ClpS: ATP-dependent C 20.8 81 0.0018 23.0 2.1 35 71-105 11-46 (82)
169 PF07223 DUF1421: Protein of u 20.7 1E+02 0.0022 29.4 3.3 25 126-150 321-345 (358)
170 COG3077 RelB DNA-damage-induci 20.4 4.2E+02 0.009 20.6 6.2 23 80-102 17-39 (88)
171 COG2355 Zn-dependent dipeptida 20.3 2.4E+02 0.0052 26.4 5.5 43 107-149 258-301 (313)
172 COG1460 Uncharacterized protei 20.3 4.8E+02 0.01 21.2 8.2 84 67-171 27-110 (114)
No 1
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=99.73 E-value=2.2e-18 Score=152.59 Aligned_cols=123 Identities=21% Similarity=0.376 Sum_probs=94.7
Q ss_pred cChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhh--------------------h-hhcCCChhhHHHH
Q 028179 71 LNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEE--------------------R-KRETPELETVSEI 129 (212)
Q Consensus 71 ~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a--------------------~-~~~v~s~e~i~ak 129 (212)
+.-+..++|+..+++|+.+|++.+++.+++.+.+.+.....-+.. . .....+.+++..+
T Consensus 167 l~~~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~ 246 (345)
T PF02536_consen 167 LLSDSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSLSVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPK 246 (345)
T ss_dssp HCGSCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGCGCHC---------------------------THHHHHHHHH
T ss_pred hccccHHHHHHHHHHHHhhcccchhhhHHhhcccceecccccccccccccccccccccccccccccccccccchHhHHHH
Confidence 333444679999999999999999999999998887433321100 0 0011457789999
Q ss_pred HHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeecccccc
Q 028179 130 LGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCK 198 (212)
Q Consensus 130 lefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~R 198 (212)
++||+++|||++||.+++.++|.||++|+| +|+++++||++++|++ .++|+++|++|+||||+|
T Consensus 247 i~~L~~lG~s~~ei~~mv~~~P~iL~~s~e-~l~~k~~fl~~~m~~~----~~~i~~~P~~l~~sLe~r 310 (345)
T PF02536_consen 247 IEFLQSLGFSEEEIAKMVRRFPQILSYSIE-KLKPKFEFLVKEMGLP----LEEIVEFPQYLSYSLEKR 310 (345)
T ss_dssp HHHHHTTT--HHHHHHHHHHSGGGGGS-HH-HHHHHHHHHHHCCT------HHHHHHSCHHHCS-HHHH
T ss_pred HHHHHHhcCcHHHHHHHHHhCcchhhcchh-hhhHHHHHHHHHhCcC----HHHHhhCCceeEechhhh
Confidence 999999999999999999999999999955 5999999999999997 789999999999999986
No 2
>PLN03196 MOC1-like protein; Provisional
Probab=99.70 E-value=3.8e-17 Score=155.48 Aligned_cols=106 Identities=15% Similarity=0.282 Sum_probs=87.5
Q ss_pred HHHHHHHHHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceee
Q 028179 77 KKWEACRQAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLG 155 (212)
Q Consensus 77 ~~we~~v~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg 155 (212)
++++..+++| +.+|++++++..++.+++.+.+ .+++++.+|++||+++||+++||.++|+|+|++|+
T Consensus 302 ~kl~~~~~fL~~~lG~s~e~i~~~v~k~P~il~------------lSe~kl~~kvefL~~~Gls~edI~~mv~k~P~lL~ 369 (487)
T PLN03196 302 AKLAEQQYWLTSKLKIDPEDFGRVIEKLPQIVS------------LNRNVALKHVEFLRGRGFSAQDVAKMVVRCPQILA 369 (487)
T ss_pred HhhhHHHHHHHHhhCCCHHHHHHHHHhcchhhc------------ccHHHHHHHHHHHHHcCCCHHHHHHHHHhCCceee
Confidence 3445555555 4666666666666555543322 47899999999999999999999999999999999
Q ss_pred cCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccccc
Q 028179 156 CDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKG 199 (212)
Q Consensus 156 ~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~Rg 199 (212)
+|+ ++|+++++||++++|++ .++|+++|++|+||||+|=
T Consensus 370 ~S~-~~l~~k~dFlvneMg~~----~~~Iv~fP~~LsySLEkRI 408 (487)
T PLN03196 370 LNL-EIMKPSLEFFKKEMKRP----LKELVEFPAYFTYGLESRI 408 (487)
T ss_pred ccH-HHHHHHHHHHHHHhCCC----HHHHHhChHHhccChhhhh
Confidence 995 89999999999999997 8999999999999999883
No 3
>PLN03196 MOC1-like protein; Provisional
Probab=99.60 E-value=2.1e-15 Score=143.62 Aligned_cols=120 Identities=19% Similarity=0.343 Sum_probs=80.9
Q ss_pred HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccch----------hhhhhh-------------h--cCCChhhHHHHHH
Q 028179 77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAY----------WSEERK-------------R--ETPELETVSEILG 131 (212)
Q Consensus 77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~----------fr~a~~-------------~--~v~s~e~i~akle 131 (212)
+++.-.++||+.+|++..++.+++.+.+.++++.. ++.... . ..--+.++..+++
T Consensus 122 ~~l~Pvl~fL~~lG~s~~~i~~lI~~~P~lL~~sve~~L~P~v~fL~~lGvs~~~i~~~l~r~P~LL~~~~e~~l~p~v~ 201 (487)
T PLN03196 122 KNMIPVLDYLEKLGVTRSSLPELLRRYPQVLHASVVVDLAPVVKYLQGLDVKRQDIPRVLERYPELLGFKLEGTMSTSVA 201 (487)
T ss_pred hhhHHHHHHHHHcCCCHHHHHHHHHhCCceecccHHHHHHHHHHHHHHcCCCHHHHHHHHHhCchhhcCCHHHHHHHHHH
Confidence 45555666666666666666666666655533321 110000 0 0011346778888
Q ss_pred HHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccc
Q 028179 132 YLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDC 197 (212)
Q Consensus 132 fLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~ 197 (212)
||+++|+++++|++++.++|+||+++++++|+|+++||.+ +|++.+++.++|.++|.+|++|+|+
T Consensus 202 fL~~lGvs~~~i~~il~~~P~iL~~sve~~i~P~v~fL~~-lGv~~~~I~~il~~~P~iL~~sle~ 266 (487)
T PLN03196 202 YLVSIGVAPRDIGPMLTRFPEILGMRVGNNIKPKVDYLES-LGLPRLAVARILEKRPYILGFDLEE 266 (487)
T ss_pred HHHHcCCCHHHHHHHHHhCcHHhhcChhhhHHHHHHHHHH-cCCCHHHHHHHHHhCCceeEcCHHH
Confidence 8888888888888888888888888888888888888874 7888888888888888888888875
No 4
>PF02536 mTERF: mTERF; InterPro: IPR003690 This family currently contains one sequence of known function human mitochondrial transcription termination factor (mTERF), a multizipper protein but binds to DNA as a monomer, with evidence pointing to intramolecular leucine zipper interactions []. The precursors contain a mitochondrial targeting sequence, and the mature mTERF exhibits three leucine zippers, of which one is bipartite, and two widely spaced basic domains. Both basic domains and the three leucine zipper motifs are necessary for DNA binding. The leucine zippers are not implicated in a dimerisation role as in other leucine zippers []. The rest of the family consists of hypothetical proteins none of which have any functional information.; PDB: 3M66_A 3OPG_A 3MVA_O 3MVB_O 3N7Q_A 3N6S_A.
Probab=99.52 E-value=6e-15 Score=130.73 Aligned_cols=109 Identities=24% Similarity=0.455 Sum_probs=95.1
Q ss_pred HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeec
Q 028179 77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGC 156 (212)
Q Consensus 77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~ 156 (212)
..|++.+++|..+|++++....++.+.+.+... .+++++.++++||+++||+++++.+++.++|.+|++
T Consensus 137 ~~~~~~v~~l~~lG~~~~~~~~vi~~~P~~l~~-----------~~~~~~~~~v~~L~~~G~~~~~i~~~l~~~P~~l~~ 205 (345)
T PF02536_consen 137 EKIKERVEFLKELGFDPEKIGRVIAKNPRLLLS-----------DSESELKPKVEFLRSLGFSKEDIGKLLRKCPRLLSL 205 (345)
T ss_dssp HHHHCHHHHHCCCTSSHHHHCCCHHHHHHHHCG-----------SCCCCCHHHHHHHHHCTT-GHHHHHHHHHTTTGGGC
T ss_pred hHHHHHHHHHHHhCCCchhhcccccccchhhcc-----------ccHHHHHHHHHHHHhhcccchhhhHHhhcccceecc
Confidence 789999999999999999999999998644322 356889999999999999999999999999999999
Q ss_pred Cccc--------------------------------hhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccc
Q 028179 157 DIEH--------------------------------ELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDC 197 (212)
Q Consensus 157 SVEe--------------------------------~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~ 197 (212)
|+++ +++++++||.+ .|++.+++.+++.++|+||+||+|+
T Consensus 206 s~~~~l~~~~~l~~~~~~~~~~~i~~~p~il~~~~~~l~~~i~~L~~-lG~s~~ei~~mv~~~P~iL~~s~e~ 277 (345)
T PF02536_consen 206 SVEKILEPVLYLLSSGGVEEERVIKKFPQILSLSEEKLKPKIEFLQS-LGFSEEEIAKMVRRFPQILSYSIEK 277 (345)
T ss_dssp GCHC---------------------------THHHHHHHHHHHHHHT-TT--HHHHHHHHHHSGGGGGS-HHH
T ss_pred cccccccccccccccccccccccccccccccccchHhHHHHHHHHHH-hcCcHHHHHHHHHhCcchhhcchhh
Confidence 9876 69999999996 8999999999999999999999986
No 5
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.11 E-value=9.1e-11 Score=108.71 Aligned_cols=124 Identities=22% Similarity=0.274 Sum_probs=102.3
Q ss_pred cChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccch-----------------hhhhhhhcCCChhhHHHHHHHH
Q 028179 71 LNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAY-----------------WSEERKRETPELETVSEILGYL 133 (212)
Q Consensus 71 ~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~-----------------fr~a~~~~v~s~e~i~aklefL 133 (212)
+.-.--++.++.+++|+.+||+.+++..|+.|.+.+++-.- .++.. ....++.++..++|||
T Consensus 258 ~~~~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~~~~~~k~p~-~l~~s~~~l~~~ie~l 336 (413)
T KOG1267|consen 258 LSYSSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKNPKHILKFPQ-LLRSSEDKLKPRIEFL 336 (413)
T ss_pred hcccccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhcchhhhhhhh-hhhccchhhhhhHHHH
Confidence 44445578999999999999999999999999997632210 01111 0124556799999999
Q ss_pred HhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeeccccccc
Q 028179 134 RNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKG 199 (212)
Q Consensus 134 ksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~Rg 199 (212)
..+|+++.++.++++++|+++++|+|..++++.+|+.+.++.. -+.+...|.+++|++|+|-
T Consensus 337 ~~~g~~~~q~~~~~~~~Pq~l~~s~~~~~~~~~~~~~~~~~~p----~~~~~~~p~~~~y~le~ri 398 (413)
T KOG1267|consen 337 LSLGFSDVQILEMVKRFPQYLSFSLEKILKRKYEYLLKGLLRP----LSALVSFPAFFGYSLEKRI 398 (413)
T ss_pred HHcCCcHHHHHHHHhhccHHhhhhHHhhhhhhHHHHHHHcCch----HHHHhccchhhccchhhcc
Confidence 9999999999999999999999998889999999999988763 5899999999999999984
No 6
>KOG1267 consensus Mitochondrial transcription termination factor, mTERF [Transcription; General function prediction only]
Probab=99.09 E-value=1.2e-10 Score=107.89 Aligned_cols=76 Identities=22% Similarity=0.475 Sum_probs=70.3
Q ss_pred CChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccc---------------------------hhhhhhhhhhhcc
Q 028179 121 PELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEH---------------------------ELRNNVQILGKDW 173 (212)
Q Consensus 121 ~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe---------------------------~LkpkveFL~~~v 173 (212)
.+++++..|+++|+++||+.+||..+++|+|++|++|++. +|.+++|||.. .
T Consensus 261 ~~~~~i~~kv~~l~~~Gf~~~di~~~~~k~P~~l~~s~~~~~~~~~~~~~~~~~~~k~p~~l~~s~~~l~~~ie~l~~-~ 339 (413)
T KOG1267|consen 261 SSEKTLEPKVEVLKSLGFSREEIWKMVKKCPQILGYSVKKNLKTTEYLLKNPKHILKFPQLLRSSEDKLKPRIEFLLS-L 339 (413)
T ss_pred cccccHHHHHHHHHHcCCCHHHHHHHHHhCchheEeehhhhhHHHHHHHhcchhhhhhhhhhhccchhhhhhHHHHHH-c
Confidence 4789999999999999999999999999999999999665 39999999996 6
Q ss_pred CcCchhHHHHHHhCCceeeccccc
Q 028179 174 GIEGKYLRNLLLRNPKVLGYNVDC 197 (212)
Q Consensus 174 GL~g~~l~~~I~r~P~ILgYSLE~ 197 (212)
|++...+..++.++|++++||+|+
T Consensus 340 g~~~~q~~~~~~~~Pq~l~~s~~~ 363 (413)
T KOG1267|consen 340 GFSDVQILEMVKRFPQYLSFSLEK 363 (413)
T ss_pred CCcHHHHHHHHhhccHHhhhhHHh
Confidence 999999999999999999999994
No 7
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=97.58 E-value=3.2e-05 Score=45.15 Aligned_cols=29 Identities=45% Similarity=0.885 Sum_probs=26.9
Q ss_pred HHHhhcCceeecCccchhhhhhhhhhhccCc
Q 028179 145 KLLKKFPEVLGCDIEHELRNNVQILGKDWGI 175 (212)
Q Consensus 145 k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL 175 (212)
+++.++|.||++| +++|+++++||. ++|+
T Consensus 2 ~~~~~~P~il~~~-~~~l~~~~~~l~-~~g~ 30 (31)
T smart00733 2 KILKKFPQILGYS-EKKLKPKVEFLK-ELGF 30 (31)
T ss_pred chhhhCcCccccc-HHHhhHHHHHHH-HcCC
Confidence 5789999999999 999999999999 6887
No 8
>smart00733 Mterf Mitochondrial termination factor repeats. Human mitochondrial termination factor is a DNA-binding protein that acts as a transcription termination factor. Six repeats occur in human mTERF, that also are present in numerous plant proteins.
Probab=91.80 E-value=0.17 Score=28.95 Aligned_cols=18 Identities=17% Similarity=0.377 Sum_probs=16.4
Q ss_pred ChhhHHHHHHHHHhCCCC
Q 028179 122 ELETVSEILGYLRNLSLS 139 (212)
Q Consensus 122 s~e~i~aklefLksLG~S 139 (212)
+++++..+++||+++|++
T Consensus 14 ~~~~l~~~~~~l~~~g~~ 31 (31)
T smart00733 14 SEKKLKPKVEFLKELGFS 31 (31)
T ss_pred cHHHhhHHHHHHHHcCCC
Confidence 579999999999999985
No 9
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=91.05 E-value=0.24 Score=40.23 Aligned_cols=29 Identities=14% Similarity=0.326 Sum_probs=23.1
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhhcCcee
Q 028179 126 VSEILGYLRNLSLSDDDIRKLLKKFPEVL 154 (212)
Q Consensus 126 i~aklefLksLG~Sd~eI~k~vkK~P~IL 154 (212)
+.+|++||++=|++++||..++++.+.-=
T Consensus 23 ~~~k~~FL~sKGLt~~EI~~al~~a~~~~ 51 (136)
T PF04695_consen 23 LEKKIAFLESKGLTEEEIDEALGRAGSPP 51 (136)
T ss_dssp HHHHHHHHHHCT--HHHHHHHHHHHT--S
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHhcCCcc
Confidence 66999999999999999999999977655
No 10
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=88.87 E-value=0.3 Score=32.78 Aligned_cols=41 Identities=24% Similarity=0.376 Sum_probs=28.7
Q ss_pred HHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhh
Q 028179 127 SEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQ 167 (212)
Q Consensus 127 ~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~Lkpkve 167 (212)
...++-|.+|||++.|+.+++++-..-=+.++|+-||..+.
T Consensus 4 ~d~~~AL~~LGy~~~e~~~av~~~~~~~~~~~e~~ik~aLk 44 (47)
T PF07499_consen 4 EDALEALISLGYSKAEAQKAVSKLLEKPGMDVEELIKQALK 44 (47)
T ss_dssp HHHHHHHHHTTS-HHHHHHHHHHHHHSTTS-HHHHHHHHHC
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHh
Confidence 46778899999999999999998754334456666655443
No 11
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=88.77 E-value=1.5 Score=33.09 Aligned_cols=73 Identities=22% Similarity=0.182 Sum_probs=47.0
Q ss_pred HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeec
Q 028179 77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGC 156 (212)
Q Consensus 77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~ 156 (212)
..-++.+.+|..+|+++..+.++..+- | ++...+|+..|+.|..
T Consensus 6 ~~~~~~~~~L~~~gl~~~~a~kl~~~y---------------------------------g---~~ai~~l~~nPY~L~~ 49 (94)
T PF14490_consen 6 RGLRELMAFLQEYGLSPKLAMKLYKKY---------------------------------G---DDAIEILKENPYRLIE 49 (94)
T ss_dssp ---HHHHHHHHHTT--HHHHHHHHHHH-------------------------------------TTHHHHHHH-STCCCB
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHH---------------------------------h---HHHHHHHHHChHHHHH
Confidence 334667788888888888887776653 1 2445778899999999
Q ss_pred CccchhhhhhhhhhhccCcCchhHHHHHH
Q 028179 157 DIEHELRNNVQILGKDWGIEGKYLRNLLL 185 (212)
Q Consensus 157 SVEe~LkpkveFL~~~vGL~g~~l~~~I~ 185 (212)
++..-==.++|.+-..+|++.++..++.+
T Consensus 50 ~i~gi~F~~aD~iA~~~g~~~~d~~Ri~A 78 (94)
T PF14490_consen 50 DIDGIGFKTADKIALKLGIEPDDPRRIRA 78 (94)
T ss_dssp -SSSSBHHHHHHHHHTTT--TT-HHHHHH
T ss_pred HccCCCHHHHHHHHHHcCCCCCCHHHHHH
Confidence 87777778888888889998777666544
No 12
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=87.62 E-value=1.8 Score=36.29 Aligned_cols=21 Identities=19% Similarity=0.523 Sum_probs=18.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHH
Q 028179 126 VSEILGYLRNLSLSDDDIRKL 146 (212)
Q Consensus 126 i~aklefLksLG~Sd~eI~k~ 146 (212)
..+=.+||.++|+|++|+..+
T Consensus 147 p~~h~~~l~~~g~~~~~~~~i 167 (172)
T cd04790 147 PEAHQEFLQSLGIPEDEIERI 167 (172)
T ss_pred cHHHHHHHHHcCCCHHHHHHH
Confidence 348899999999999999875
No 13
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=86.75 E-value=1.7 Score=35.47 Aligned_cols=88 Identities=17% Similarity=0.194 Sum_probs=59.4
Q ss_pred hhhhhhhcccChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc------cccchhhhhhhhcC-------CChhhHHH
Q 028179 62 STAQVQSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGH------IHSAYWSEERKRET-------PELETVSE 128 (212)
Q Consensus 62 ~~~~~~~~~~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl------~~S~~fr~a~~~~v-------~s~e~i~a 128 (212)
--.+...-++.++|+ -=..++.-..+|.+|-++.++..-..+- ++.++|-.+..... ...+.+..
T Consensus 20 Ik~~I~~g~l~pGdk--LPSvRelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~~~~~~~~~l~~ 97 (125)
T COG1725 20 IKEQIASGELKPGDK--LPSVRELAKDLGVNPNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQLKRELAEEELEE 97 (125)
T ss_pred HHHHHHhCCcCCCCC--CCcHHHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHHHHHHHHHHHHH
Confidence 333444444555432 1234555589999999998888776543 78888876542222 33444667
Q ss_pred HHHHHHhCCCCHHHHHHHHhhcC
Q 028179 129 ILGYLRNLSLSDDDIRKLLKKFP 151 (212)
Q Consensus 129 klefLksLG~Sd~eI~k~vkK~P 151 (212)
.|+-++.+|+|.++|..++++..
T Consensus 98 ~I~~~~~~G~s~eei~~~~~~~~ 120 (125)
T COG1725 98 FIEEAKALGLSLEEILELLKEIY 120 (125)
T ss_pred HHHHHHHcCCCHHHHHHHHHHHH
Confidence 77778899999999999998764
No 14
>PF07499 RuvA_C: RuvA, C-terminal domain; InterPro: IPR011114 In prokaryotes, RuvA, RuvB, and RuvC process the universal DNA intermediate of homologous recombination, termed Holliday junction. The tetrameric DNA helicase RuvA specifically binds to the Holliday junction and facilitates the isomerization of the junction from the stacked folded configuration to the square-planar structure []. In the RuvA tetramer, each subunit consists of three domains, I, II and III, where I and II form the major core that is responsible for Holliday junction binding and base pair rearrangements of Holliday junction executed at the crossover point, whereas domain III regulates branch migration through direct contact with RuvB. The domain represents the C-terminal domain III of RuvA. This domain plays a significant role in the ATP-dependent branch migration of the hetero-duplex through direct contact with RuvB []. Within the Holliday junction, this domain makes no interaction with the DNA.; GO: 0005524 ATP binding, 0009378 four-way junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination, 0009379 Holliday junction helicase complex; PDB: 1HJP_A 1CUK_A 1C7Y_A 1IXS_A 1IXR_B 1BVS_E 2ZTC_A 2ZTD_B 2H5X_A.
Probab=86.67 E-value=0.98 Score=30.29 Aligned_cols=27 Identities=26% Similarity=0.386 Sum_probs=23.8
Q ss_pred HHHHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 78 KWEACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 78 ~we~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
.+++++++|.+|||++.++..++.++.
T Consensus 2 ~~~d~~~AL~~LGy~~~e~~~av~~~~ 28 (47)
T PF07499_consen 2 ALEDALEALISLGYSKAEAQKAVSKLL 28 (47)
T ss_dssp HHHHHHHHHHHTTS-HHHHHHHHHHHH
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHHHhh
Confidence 468999999999999999999999985
No 15
>KOG0550 consensus Molecular chaperone (DnaJ superfamily) [Posttranslational modification, protein turnover, chaperones]
Probab=86.26 E-value=0.77 Score=44.73 Aligned_cols=93 Identities=20% Similarity=0.214 Sum_probs=63.1
Q ss_pred HHHHHHHHHHHHhhhCCCChHH--HHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCC----HHHHHHHH
Q 028179 74 EERKKWEACRQALSTFNFSTEE--EDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLS----DDDIRKLL 147 (212)
Q Consensus 74 ~~~~~we~~v~~L~~LGfspe~--v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~S----d~eI~k~v 147 (212)
.+.++||++|+.++.+.=...+ .++.+.+|. -.-+-.++.++++.||++ ++||.++-
T Consensus 332 l~le~~e~AV~d~~~a~q~~~s~e~r~~l~~A~-----------------~aLkkSkRkd~ykilGi~~~as~~eikkay 394 (486)
T KOG0550|consen 332 LALEKWEEAVEDYEKAMQLEKDCEIRRTLREAQ-----------------LALKKSKRKDWYKILGISRNASDDEIKKAY 394 (486)
T ss_pred HHHHHHHHHHHHHHHHHhhccccchHHHHHHHH-----------------HHHHHhhhhhHHHHhhhhhhcccchhhhHH
Confidence 4678999999999654443333 666777764 123455789999999996 56699888
Q ss_pred hhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCC
Q 028179 148 KKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNP 188 (212)
Q Consensus 148 kK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P 188 (212)
+|-|-+..-+....=+..-|..-+++|- .-.|++.|
T Consensus 395 rk~AL~~Hpd~~agsq~eaE~kFkevge-----Ay~il~d~ 430 (486)
T KOG0550|consen 395 RKLALVHHPDKNAGSQKEAEAKFKEVGE-----AYTILSDP 430 (486)
T ss_pred HHHHHHhCCCcCcchhHHHHHHHHHHHH-----HHHHhcCH
Confidence 7777776655433335566777677775 45666665
No 16
>PRK00116 ruvA Holliday junction DNA helicase RuvA; Reviewed
Probab=81.97 E-value=6.1 Score=33.66 Aligned_cols=80 Identities=13% Similarity=0.171 Sum_probs=48.2
Q ss_pred HHHhh-hCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccch
Q 028179 83 RQALS-TFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHE 161 (212)
Q Consensus 83 v~~L~-~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~ 161 (212)
.+.|. .=|+.++.+.+++....+.... +.............+...+++|.+||+++.++.++++++-.- ..++++-
T Consensus 107 ~~~L~~v~Gig~k~A~~I~~~l~~~~~~--~~~~~~~~~~~~~~~~ev~~aL~~LG~~~~~a~~~~~~~~~~-~~~~~~~ 183 (192)
T PRK00116 107 VKALTKVPGIGKKTAERIVLELKDKLAA--AASAAAAAAAASSALEEAVSALVALGYKPKEASKAVAKILKE-AASVEEL 183 (192)
T ss_pred HHHHHhCCCCCHHHHHHHHHHHHHHhhc--ccccccccccccchHHHHHHHHHHcCCCHHHHHHHHHHHhcc-CCCHHHH
Confidence 34564 4499999999998775443321 000000000112236789999999999999999999988321 2344444
Q ss_pred hhhh
Q 028179 162 LRNN 165 (212)
Q Consensus 162 Lkpk 165 (212)
||..
T Consensus 184 i~~a 187 (192)
T PRK00116 184 IREA 187 (192)
T ss_pred HHHH
Confidence 4433
No 17
>PRK02249 DNA primase large subunit; Validated
Probab=81.16 E-value=1.4 Score=41.33 Aligned_cols=74 Identities=24% Similarity=0.395 Sum_probs=47.1
Q ss_pred CChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHH-HhCCceeeccccccc
Q 028179 121 PELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLL-LRNPKVLGYNVDCKG 199 (212)
Q Consensus 121 ~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I-~r~P~ILgYSLE~Rg 199 (212)
++-..--+-.-||+++|++-+|+..+++..| .++ |+.-+=++++.. |.+|. .+|. -..-+|++| |
T Consensus 239 L~h~~R~~l~~FL~~iG~~~deil~~~~~~~---~f~-e~~~~Y~irH~~---G~~G~--~~Y~p~sC~~m~s~-----g 304 (343)
T PRK02249 239 LPHTARFAITSFLLNIGMSVDEIVELFRNAP---DFD-EEKTRYQVEHIA---GETGG--TEYTPPSCETMRTY-----G 304 (343)
T ss_pred CChHHHHHHHHHHHhcCCCHHHHHHHHhhCC---Ccc-HHHHHHHHHHHh---cccCC--CCCCCccHHHHHHc-----C
Confidence 3444445667799999999999999999887 344 444455666654 55443 1111 111144444 8
Q ss_pred ccccccchh
Q 028179 200 DCMAQCTRC 208 (212)
Q Consensus 200 ~c~~~c~rc 208 (212)
+|.+-|..|
T Consensus 305 ~C~~~d~lC 313 (343)
T PRK02249 305 LCVGKDDLC 313 (343)
T ss_pred CCCCchhhh
Confidence 898888766
No 18
>PRK14605 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=79.56 E-value=9.8 Score=32.70 Aligned_cols=86 Identities=15% Similarity=0.207 Sum_probs=51.2
Q ss_pred HHHHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccc
Q 028179 82 CRQAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEH 160 (212)
Q Consensus 82 ~v~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe 160 (212)
-.+.| +.=|+.++.+.+++....+-.... |.... .....+.....+..|.+||+++.++.+++++.-.--..++++
T Consensus 106 D~~~L~~vpGIGkKtAerIilELk~Ki~~~-~~~~~--~~~~~~~~~e~~~aL~~LGy~~~~a~~ai~~~~~~~~~~~~~ 182 (194)
T PRK14605 106 NAELLSTIPGIGKKTASRIVLELKDKIAKN-WEAGV--LSQVTEANSDILATLTALGYSSSEAAKAISSLGDNGDLPLEE 182 (194)
T ss_pred CHHHHHhCCCCCHHHHHHHHHHHHHHHHhh-hhccc--cccccchHHHHHHHHHHcCCCHHHHHHHHHHhhccCCCCHHH
Confidence 34566 566888888888765433221110 10000 001123356788999999999999999999872112446666
Q ss_pred hhhhhhhhhh
Q 028179 161 ELRNNVQILG 170 (212)
Q Consensus 161 ~LkpkveFL~ 170 (212)
-+|..+.+|.
T Consensus 183 ~ir~aLk~l~ 192 (194)
T PRK14605 183 RIKLALNYFN 192 (194)
T ss_pred HHHHHHHHhh
Confidence 6666665553
No 19
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=71.06 E-value=7.2 Score=24.12 Aligned_cols=23 Identities=22% Similarity=0.304 Sum_probs=20.7
Q ss_pred HHHHHHHhCCCCHHHHHHHHhhc
Q 028179 128 EILGYLRNLSLSDDDIRKLLKKF 150 (212)
Q Consensus 128 aklefLksLG~Sd~eI~k~vkK~ 150 (212)
.+++-|.++|++++++..++++.
T Consensus 3 ~~v~~L~~mGf~~~~a~~aL~~~ 25 (37)
T smart00165 3 EKIDQLLEMGFSREEALKALRAA 25 (37)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 67889999999999999999875
No 20
>PF04695 Pex14_N: Peroxisomal membrane anchor protein (Pex14p) conserved region; InterPro: IPR006785 This conserved region defines a group of peroxisomal membrane anchor proteins which bind the PTS1 (peroxisomal targeting signal) receptor and are required for the import of PTS1-containing proteins into peroxisomes. Loss of functional Pex14p results in defects in both the PTS1 and PTS2-dependent import pathways. Deletion analysis of this conserved region implicates it in selective peroxisome degradation. In the majority of members this region is situated at the N terminus of the protein [, ].; GO: 0005777 peroxisome, 0016020 membrane; PDB: 2W85_A 2W84_A 3FF5_B.
Probab=70.68 E-value=5.5 Score=32.27 Aligned_cols=35 Identities=20% Similarity=0.307 Sum_probs=26.1
Q ss_pred hcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCC
Q 028179 149 KFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNP 188 (212)
Q Consensus 149 K~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P 188 (212)
+.|.|-..+ +-.|++||+++ ||++++|...+.+-+
T Consensus 14 ~~p~V~~sp----~~~k~~FL~sK-GLt~~EI~~al~~a~ 48 (136)
T PF04695_consen 14 QDPKVRNSP----LEKKIAFLESK-GLTEEEIDEALGRAG 48 (136)
T ss_dssp CTTTCCCS-----HHHHHHHHHHC-T--HHHHHHHHHHHT
T ss_pred CCcccccCC----HHHHHHHHHcC-CCCHHHHHHHHHhcC
Confidence 478888777 56899999998 999999988887644
No 21
>PRK14136 recX recombination regulator RecX; Provisional
Probab=68.73 E-value=33 Score=32.10 Aligned_cols=105 Identities=13% Similarity=0.172 Sum_probs=56.0
Q ss_pred HHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHh------------
Q 028179 83 RQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLK------------ 148 (212)
Q Consensus 83 v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vk------------ 148 (212)
.+.|..-|++++.+..++.++.+. +.-..|-+.-+..-.+..-......-|+.-|++++.|..++.
T Consensus 183 r~KL~kkG~~ee~IE~VIerLke~gYLDDeRFAesyVr~R~~kkGp~rIrqELrQKGId~eLIEqALeeieEDE~E~A~~ 262 (309)
T PRK14136 183 ARKLAPYADESDSVEPLLDALEREGWLSDARFAESLVHRRASRVGSARIVSELKRHAVGDALVESVGAQLRETEFERAQA 262 (309)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHcCCcCHHHHHHHHHHHHhhchhHHHHHHHHHHcCCCHHHHHHHHHhccHhHHHHHHH
Confidence 344455699999999999997664 222222222111111111122334556677777776666554
Q ss_pred ----hcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCce
Q 028179 149 ----KFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKV 190 (212)
Q Consensus 149 ----K~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~I 190 (212)
|+..+-. . .......+.||... |++.+.+.+.|...=..
T Consensus 263 L~eKK~~~~~~-d-~kek~K~iRfL~rR-GFS~D~I~~vLk~~~de 305 (309)
T PRK14136 263 VWRKKFGALPQ-T-PAERAKQARFLAAR-GFSSATIVKLLKVGDDE 305 (309)
T ss_pred HHHHHhcccCc-C-HHHHHHHHHHHHHC-CCCHHHHHHHHHhchhc
Confidence 3332211 1 12233447888875 88877777776654333
No 22
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=68.59 E-value=22 Score=30.58 Aligned_cols=73 Identities=15% Similarity=0.185 Sum_probs=45.1
Q ss_pred HHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchh
Q 028179 84 QAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHEL 162 (212)
Q Consensus 84 ~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~L 162 (212)
+.| +.=|+.++.+++++....+-... .. .........++-|.+||+++.|+.+++++-. ..++|+-+
T Consensus 108 ~~L~~vpGIGkKtAeRIilELkdK~~~--------~~-~~~~~~~ea~~AL~~LGy~~~ea~~a~~~~~---~~~~eeli 175 (183)
T PRK14601 108 SVLKKVPGIGPKSAKRIIAELSDAKTK--------LE-NVSDDKSEALAALLTLGFKQEKIIKVLASCQ---STGTSELI 175 (183)
T ss_pred HHHhhCCCCCHHHHHHHHHHHHHHhhc--------cC-CCCccHHHHHHHHHHcCCCHHHHHHHHHhcc---cCCHHHHH
Confidence 344 45677777777766554321110 00 1112346788999999999999999999874 44666666
Q ss_pred hhhhhh
Q 028179 163 RNNVQI 168 (212)
Q Consensus 163 kpkveF 168 (212)
|..+..
T Consensus 176 r~aLk~ 181 (183)
T PRK14601 176 KEALKK 181 (183)
T ss_pred HHHHHh
Confidence 655443
No 23
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=66.74 E-value=12 Score=23.47 Aligned_cols=24 Identities=29% Similarity=0.325 Sum_probs=18.5
Q ss_pred HHHHHHhhhCCCChHHHHHHHHhh
Q 028179 80 EACRQALSTFNFSTEEEDKILGKA 103 (212)
Q Consensus 80 e~~v~~L~~LGfspe~v~~il~rA 103 (212)
++.++-|...||+.+.+.+.+.+.
T Consensus 3 ~~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 3 EEKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHc
Confidence 456777876799999998888876
No 24
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=66.58 E-value=10 Score=23.54 Aligned_cols=23 Identities=30% Similarity=0.410 Sum_probs=20.5
Q ss_pred HHHHHHHhCCCCHHHHHHHHhhc
Q 028179 128 EILGYLRNLSLSDDDIRKLLKKF 150 (212)
Q Consensus 128 aklefLksLG~Sd~eI~k~vkK~ 150 (212)
.+++-|.++|++++++..++++.
T Consensus 3 ~~v~~L~~mGf~~~~~~~AL~~~ 25 (38)
T cd00194 3 EKLEQLLEMGFSREEARKALRAT 25 (38)
T ss_pred HHHHHHHHcCCCHHHHHHHHHHh
Confidence 57889999999999999998865
No 25
>cd01378 MYSc_type_I Myosin motor domain, type I myosins. Myosin I generates movement at the leading edge in cell motility, and class I myosins have been implicated in phagocytosis and vesicle transport. Myosin I, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 picon
Probab=66.53 E-value=17 Score=36.79 Aligned_cols=74 Identities=18% Similarity=0.364 Sum_probs=49.1
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhhh--cCCChhhHHHHHHHHHhCCCCHHHHHHHHh
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERKR--ETPELETVSEILGYLRNLSLSDDDIRKLLK 148 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~~--~v~s~e~i~aklefLksLG~Sd~eI~k~vk 148 (212)
.+|...|++.+++|+.+||++++...|+.-.-++ +|.-.|...... .+.+.+ .-.++.- =||++.+++..++.
T Consensus 230 ~~d~~~f~~~~~al~~lG~s~~e~~~i~~ilaaILhLGni~f~~~~~~~~~~~~~~-~l~~~a~--LLgv~~~~L~~~l~ 306 (674)
T cd01378 230 IDDKKDFKETQNAMKVIGFSEDEQDEIFRIVAAILHLGNVQFAENGDGAAVISDKD-VLDFAAY--LLGVDPSELEKALT 306 (674)
T ss_pred ccHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEeccCCCccccCChH-HHHHHHH--HcCCCHHHHHHHhc
Confidence 3678999999999999999999977776665443 444445433212 222233 2223332 37999999999987
Q ss_pred h
Q 028179 149 K 149 (212)
Q Consensus 149 K 149 (212)
+
T Consensus 307 ~ 307 (674)
T cd01378 307 S 307 (674)
T ss_pred c
Confidence 4
No 26
>smart00165 UBA Ubiquitin associated domain. Present in Rad23, SNF1-like kinases. The newly-found UBA in p62 is known to bind ubiquitin.
Probab=66.21 E-value=15 Score=22.62 Aligned_cols=25 Identities=36% Similarity=0.260 Sum_probs=21.0
Q ss_pred HHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 80 EACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 80 e~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
++.++-|..+||+.+.+...+.+..
T Consensus 2 ~~~v~~L~~mGf~~~~a~~aL~~~~ 26 (37)
T smart00165 2 EEKIDQLLEMGFSREEALKALRAAN 26 (37)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhC
Confidence 4677888999999999988888863
No 27
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=65.82 E-value=33 Score=29.38 Aligned_cols=80 Identities=19% Similarity=0.265 Sum_probs=46.0
Q ss_pred Hh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhh
Q 028179 85 AL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELR 163 (212)
Q Consensus 85 ~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~Lk 163 (212)
.| +.=|+.++.+.+|+....+-..... ... ............++.|.+||+++.++.+++.+-..-=..++++-+|
T Consensus 108 ~L~~ipGiGkKtAerIileLk~k~~~~~--~~~-~~~~~~~~~~e~~~aL~~LGy~~~e~~~ai~~~~~~~~~~~~~li~ 184 (191)
T TIGR00084 108 ALVKIPGVGKKTAERLLLELKGKLKGNK--NLE-MFTPTEAARDELFEALVSLGYKPQEIQQALKKIKNKPDFAIEQDIE 184 (191)
T ss_pred HHHhCCCCCHHHHHHHHHHHHhhhcccc--ccc-ccccccchHHHHHHHHHHcCCCHHHHHHHHHHHhhcCCCCHHHHHH
Confidence 45 6779999999998744322111100 000 0001123356788999999999999999998752100234444444
Q ss_pred hhhh
Q 028179 164 NNVQ 167 (212)
Q Consensus 164 pkve 167 (212)
..+.
T Consensus 185 ~aLk 188 (191)
T TIGR00084 185 EALK 188 (191)
T ss_pred HHHH
Confidence 4433
No 28
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=65.71 E-value=26 Score=30.11 Aligned_cols=74 Identities=15% Similarity=0.210 Sum_probs=44.0
Q ss_pred hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhh
Q 028179 87 STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNV 166 (212)
Q Consensus 87 ~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~Lkpkv 166 (212)
+.=|+.++.+.+++-...+=... ....+.......++-|.+||+++.|+.+++++--. =..++|+-||..+
T Consensus 112 ~vpGIGkKtAerIilELkdK~~~--------~~~~~~~~~~e~~~AL~~LGy~~~ea~~av~~~~~-~~~~~e~lik~AL 182 (188)
T PRK14606 112 KLPGISKKTAERIVMELKDEFES--------AGIKDMRIYHESLEALVSLGYPEKQAREAVKHVYR-EGMKTSELIKEAL 182 (188)
T ss_pred hCCCCCHHHHHHHHHHHHHhhcc--------ccCCCcccHHHHHHHHHHcCCCHHHHHHHHHHHhh-CCCCHHHHHHHHH
Confidence 45566666666666443221110 00111123567789999999999999999998621 0456666666655
Q ss_pred hhh
Q 028179 167 QIL 169 (212)
Q Consensus 167 eFL 169 (212)
..|
T Consensus 183 k~l 185 (188)
T PRK14606 183 KFL 185 (188)
T ss_pred HHH
Confidence 554
No 29
>cd01386 MYSc_type_XVIII Myosin motor domain, type XVIII myosins. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the
Probab=65.66 E-value=18 Score=37.40 Aligned_cols=74 Identities=12% Similarity=0.068 Sum_probs=48.2
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhh-hhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhh
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEE-RKRETPELETVSEILGYLRNLSLSDDDIRKLLKK 149 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a-~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK 149 (212)
.+|.+.|++..++|+.+||++++...|+.-.-++ +|.-.|... ....+.+.+.+ .++.- =||++.+++.+++-+
T Consensus 230 ~~D~~~f~~~~~Al~~lGfs~~e~~~If~iLaaILhLGNi~f~~~~~~~~~~~~~~~-~~vA~--LLgv~~~~L~~al~~ 306 (767)
T cd01386 230 QKAAIDFSRLQQAMEVLGISEGEQRAIWRVLAAIYHLGAAGATKVAGRKQFARPEWA-QKAAE--LLGCPLEELSSATFK 306 (767)
T ss_pred ccHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccCceeeecCCccccCCHHHH-HHHHH--HhCCCHHHHHHHhcc
Confidence 3567899999999999999999987776665444 444334331 11222333322 23333 379999999998744
No 30
>PRK00117 recX recombination regulator RecX; Reviewed
Probab=65.14 E-value=70 Score=25.72 Aligned_cols=104 Identities=19% Similarity=0.216 Sum_probs=55.5
Q ss_pred HHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhhhcC-CChhhHHHHHHHHHhCCCCHHHHHHHHhhcC-----
Q 028179 80 EACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERKRET-PELETVSEILGYLRNLSLSDDDIRKLLKKFP----- 151 (212)
Q Consensus 80 e~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~~~v-~s~e~i~aklefLksLG~Sd~eI~k~vkK~P----- 151 (212)
.+.++.|..-|++++.+..++.+.... ..-.-|-+...... ...........-|+.-|++.+.|..++...+
T Consensus 29 ~el~~kL~~kg~~~~~i~~vl~~l~~~~~ldD~~~a~~~~~~~~~~~~g~~~I~~~L~~kGi~~~~I~~~l~~~~~d~~e 108 (157)
T PRK00117 29 AELRRKLAAKGFSEEVIEAVLDRLKEEGLLDDERFAESFVRSRARKGYGPRRIRQELRQKGVDREIIEEALAELDIDWEE 108 (157)
T ss_pred HHHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHHHHHhCCchHHHHHHHHHHcCCCHHHHHHHHHHcCccHHH
Confidence 345666767788888888888876542 22212211111111 1111233445667788998888888887654
Q ss_pred -----------ceeecCccchhhhhhhhhhhccCcCchhHHHHHH
Q 028179 152 -----------EVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLL 185 (212)
Q Consensus 152 -----------~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~ 185 (212)
..-+.+ .......+.||... |++.+.+.+.|.
T Consensus 109 ~a~~~~~k~~~~~~~~~-~~~k~Ki~~~L~rk-GF~~~~I~~~l~ 151 (157)
T PRK00117 109 LARELARKKFRRPLPDD-AKEKAKLVRFLARR-GFSMDVIQRVLR 151 (157)
T ss_pred HHHHHHHHHcCCCCCCC-HHHHHHHHHHHHHC-CCCHHHHHHHHH
Confidence 111111 11223455677654 777665555544
No 31
>cd01380 MYSc_type_V Myosin motor domain, type V myosins. Myosins V transport a variety of intracellular cargo processively along actin filaments, such as membraneous organelles and mRNA. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an act
Probab=64.66 E-value=22 Score=36.18 Aligned_cols=73 Identities=23% Similarity=0.255 Sum_probs=49.2
Q ss_pred HHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhhhc--C-CChhhHHHHHHHHH-hCCCCHHHHHHHH
Q 028179 74 EERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERKRE--T-PELETVSEILGYLR-NLSLSDDDIRKLL 147 (212)
Q Consensus 74 ~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~~~--v-~s~e~i~aklefLk-sLG~Sd~eI~k~v 147 (212)
+|.+.|++.+++|+.+||++++...|+.-.-++ +|.-.|....... + .+.+ .++... =||++.+++.+++
T Consensus 234 ~d~~~f~~~~~al~~lg~s~~e~~~I~~iLaaILhLGni~F~~~~~~~~~~~~~~~----~l~~~a~LLgv~~~~L~~~l 309 (691)
T cd01380 234 DDAEDFNATVQALTLLGISEEQQMDIFKLLAALLHLGNIEIEATRNDSSSISPKDE----NLQIACELLGVDASDLRKWL 309 (691)
T ss_pred ChHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccceeeeccCCccceecCChH----HHHHHHHHhCCCHHHHHHHH
Confidence 678999999999999999999988776664443 4544454432111 1 1122 233333 4799999999988
Q ss_pred hhc
Q 028179 148 KKF 150 (212)
Q Consensus 148 kK~ 150 (212)
.+.
T Consensus 310 ~~~ 312 (691)
T cd01380 310 VKR 312 (691)
T ss_pred HhC
Confidence 763
No 32
>PF03960 ArsC: ArsC family; InterPro: IPR006660 Several bacterial taxon have a chromosomal resistance system, encoded by the ars operon, for the detoxification of arsenate, arsenite, and antimonite []. This system transports arsenite and antimonite out of the cell. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. Arsenate, however, must first be reduced to arsenite before it is extruded. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance. ArsC is an approximately 150-residue arsenate reductase that uses reduced glutathione (GSH) to convert arsenate to arsenite with a redox active cysteine residue in the active site. ArsC forms an active quaternary complex with GSH, arsenate, and glutaredoxin 1 (Grx1). The three ligands must be present simultaneously for reduction to occur []. The arsC family also comprises the Spx proteins which are GRAM-positive bacterial transcription factors that regulate the transcription of multiple genes in response to disulphide stress []. The arsC protein structure has been solved []. It belongs to the thioredoxin superfamily fold which is defined by a beta-sheet core surrounded by alpha-helices. The active cysteine residue of ArsC is located in the loop between the first beta-strand and the first helix, which is also conserved in the Spx protein and its homologues.; PDB: 2KOK_A 1SK1_A 1SK2_A 1JZW_A 1J9B_A 1S3C_A 1SD8_A 1SD9_A 1I9D_A 1SK0_A ....
Probab=62.83 E-value=23 Score=26.93 Aligned_cols=59 Identities=24% Similarity=0.373 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHhhcCceeecCccchhhhhhhhhhh-----ccCcCchhHHHHHHhCCceeeccccccc
Q 028179 137 SLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGK-----DWGIEGKYLRNLLLRNPKVLGYNVDCKG 199 (212)
Q Consensus 137 G~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~-----~vGL~g~~l~~~I~r~P~ILgYSLE~Rg 199 (212)
++|.+++..++++.. .++++-+.++-....+ .-.++.+++-++|+.+|.+|-..|=-.|
T Consensus 32 p~s~~el~~~l~~~~----~~~~~lin~~~~~~k~l~~~~~~~~s~~e~i~~l~~~p~LikRPIi~~~ 95 (110)
T PF03960_consen 32 PLSREELRELLSKLG----NGPDDLINTRSKTYKELGKLKKDDLSDEELIELLLENPKLIKRPIIVDG 95 (110)
T ss_dssp ---HHHHHHHHHHHT----SSGGGGB-TTSHHHHHTTHHHCTTSBHHHHHHHHHHSGGGB-SSEEEET
T ss_pred CCCHHHHHHHHHHhc----ccHHHHhcCccchHhhhhhhhhhhhhhHHHHHHHHhChhheeCCEEEEC
Confidence 368899999988765 2334444444333332 1246778888999999999887765544
No 33
>KOG0164 consensus Myosin class I heavy chain [Cytoskeleton]
Probab=62.81 E-value=18 Score=37.91 Aligned_cols=84 Identities=18% Similarity=0.284 Sum_probs=55.3
Q ss_pred cccChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccch--hhhhhhhcCCChhhHHHHHHHHH-hCCCCHHHHHH
Q 028179 69 ITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAY--WSEERKRETPELETVSEILGYLR-NLSLSDDDIRK 145 (212)
Q Consensus 69 ~~~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~--fr~a~~~~v~s~e~i~aklefLk-sLG~Sd~eI~k 145 (212)
...+..|...|.++.++++.+||++|++..++.-.-.+++-+. |-..-........ +-|.++. -++...+++.+
T Consensus 236 ~v~sinD~~dfk~V~~Am~vIgFs~eEVe~v~~iiAavLhLGNv~f~~~ed~~~~~~~---~~l~~~aell~v~~del~~ 312 (1001)
T KOG0164|consen 236 KVSSINDASDFKAVQKAMRVIGFSEEEVESVLSIIAAVLHLGNVEFADNEDSSGIVNG---AQLKYIAELLSVTGDELER 312 (1001)
T ss_pred hhcccccHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccceEEeecCcccccchh---HHHHHHHHHHcCCHHHHHH
Confidence 3456668899999999999999999999888766444432221 1111101111111 6677777 67999999999
Q ss_pred HHhhcCceee
Q 028179 146 LLKKFPEVLG 155 (212)
Q Consensus 146 ~vkK~P~ILg 155 (212)
++..+-..=+
T Consensus 313 aL~~Rtvaa~ 322 (1001)
T KOG0164|consen 313 ALTSRTVAAG 322 (1001)
T ss_pred HHHHHHHHhc
Confidence 9887644433
No 34
>cd01377 MYSc_type_II Myosin motor domain, type II myosins. Myosin II mediates cortical contraction in cell motility, and is the motor in smooth and skeletal muscle. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydro
Probab=61.67 E-value=22 Score=36.14 Aligned_cols=75 Identities=16% Similarity=0.229 Sum_probs=48.6
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhh---hhhcCCChhhHHHHHHHHHhCCCCHHHHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEE---RKRETPELETVSEILGYLRNLSLSDDDIRKLL 147 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a---~~~~v~s~e~i~aklefLksLG~Sd~eI~k~v 147 (212)
.+|.+.|++.+++|+.+||++++...|+.=.-++ +|.--|... ....+.+.+ .-.++.. =||++.+++.+++
T Consensus 242 ~~d~~~f~~~~~al~~lG~~~~e~~~i~~iLaaILhLGni~F~~~~~~~~~~~~~~~-~l~~~a~--LLgv~~~~L~~~l 318 (693)
T cd01377 242 VDDAEEFKLTDEAFDILGFSDEEKNSIFKIVAAILHLGNIKFKQRQREEQAELDGTE-EADKAAH--LLGVNSADLLKAL 318 (693)
T ss_pred CcHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEEecCCCCccccCChH-HHHHHHH--HhCCCHHHHHHHh
Confidence 3678999999999999999999877777665454 343334332 111222222 2222222 3799999999988
Q ss_pred hhc
Q 028179 148 KKF 150 (212)
Q Consensus 148 kK~ 150 (212)
...
T Consensus 319 ~~~ 321 (693)
T cd01377 319 LHP 321 (693)
T ss_pred cce
Confidence 753
No 35
>PF00627 UBA: UBA/TS-N domain; InterPro: IPR000449 UBA domains are a commonly occurring sequence motif of approximately 45 amino acid residues that are found in diverse proteins involved in the ubiquitin/proteasome pathway, DNA excision-repair, and cell signalling via protein kinases []. The human homologue of yeast Rad23A is one example of a nucleotide excision-repair protein that contains both an internal and a C-terminal UBA domain. The solution structure of human Rad23A UBA(2) showed that the domain forms a compact three-helix bundle []. Comparison of the structures of UBA(1) and UBA(2) reveals that both form very similar folds and have a conserved large hydrophobic surface patch which may be a common protein-interacting surface present in diverse UBA domains. Evidence that ubiquitin binds to UBA domains leads to the prediction that the hydrophobic surface patch of UBA domains interacts with the hydrophobic surface on the five-stranded beta-sheet of ubiquitin []. This domain is similar in sequence to the N-terminal domain of translation elongation factor EF1B (or EF-Ts) from bacteria, mitochondria and chloroplasts. More information about EF1B (EF-Ts) proteins can be found at Protein of the Month: Elongation Factors [].; GO: 0005515 protein binding; PDB: 2DAI_A 2OO9_C 2JUJ_A 1WHC_A 1YLA_A 2O25_B 3K9O_A 3K9P_A 3F92_A 3E46_A ....
Probab=61.02 E-value=12 Score=23.50 Aligned_cols=23 Identities=22% Similarity=0.348 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCCHHHHHHHHhhc
Q 028179 128 EILGYLRNLSLSDDDIRKLLKKF 150 (212)
Q Consensus 128 aklefLksLG~Sd~eI~k~vkK~ 150 (212)
.+|+-|..+||++++..+++++.
T Consensus 4 ~~v~~L~~mGf~~~~~~~AL~~~ 26 (37)
T PF00627_consen 4 EKVQQLMEMGFSREQAREALRAC 26 (37)
T ss_dssp HHHHHHHHHTS-HHHHHHHHHHT
T ss_pred HHHHHHHHcCCCHHHHHHHHHHc
Confidence 67888998899999999998864
No 36
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=59.83 E-value=33 Score=27.64 Aligned_cols=77 Identities=17% Similarity=0.167 Sum_probs=45.9
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhh--HHHHHHHHHh-CCCCHHHHHHHHhhcCceee--cCc
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELET--VSEILGYLRN-LSLSDDDIRKLLKKFPEVLG--CDI 158 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~--i~aklefLks-LG~Sd~eI~k~vkK~P~ILg--~SV 158 (212)
++.+.+|+++.+++.--.+ |++... +. ...-.-+++. .-..|..|+. +|++-++|..+++.+|.-+. ++
T Consensus 6 eVA~~~GVs~~TLR~wE~~--GLl~p~--r~-~G~R~Ys~~dv~rL~~I~~L~~e~G~~l~eI~~~L~l~~~~~~~~~~- 79 (120)
T cd04767 6 VVAELLNIHPETLRIWERH--GLIKPA--RR-NGQRLYSNNDLKRLRFIKKLINEKGLNIAGVKQILSMYPCWSIRDCD- 79 (120)
T ss_pred HHHHHHCcCHHHHHHHHHC--CCCCCc--CC-CCcEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHHhCccccccccc-
Confidence 3456788888877644332 442110 00 0011122333 2345666765 99999999999999999887 66
Q ss_pred cchhhhhh
Q 028179 159 EHELRNNV 166 (212)
Q Consensus 159 Ee~Lkpkv 166 (212)
++..+.+-
T Consensus 80 ~~~~~~~~ 87 (120)
T cd04767 80 EGGRKSKT 87 (120)
T ss_pred CCCccCCC
Confidence 55555444
No 37
>cd01385 MYSc_type_IX Myosin motor domain, type IX myosins. Myosin IX is a processive single-headed motor, which might play a role in signalling. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the hea
Probab=58.93 E-value=28 Score=35.54 Aligned_cols=79 Identities=18% Similarity=0.291 Sum_probs=51.8
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhh------hhcCCChhhHHHHHHHHHhCCCCHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEER------KRETPELETVSEILGYLRNLSLSDDDIR 144 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~------~~~v~s~e~i~aklefLksLG~Sd~eI~ 144 (212)
.+|.+.|++.+++|+.+||++++...|+.-.-++ +|---|.... ...+.+++.+ .++.. =||++.+++.
T Consensus 238 ~dd~~~f~~~~~al~~lG~~~~~~~~i~~iLaaILhLGni~F~~~~~~~~~~~~~~~~~~~l-~~~a~--LLgv~~~~L~ 314 (692)
T cd01385 238 EDEKHEFERLKQAMEMVGFLAATQKQIFAVLSAVLLLGNVTYKKRATYHRDESLEVGNPEVV-DLLSQ--LLKVKRETLM 314 (692)
T ss_pred CCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccCceeeecccCCCCCceecCCHHHH-HHHHH--HhCCCHHHHH
Confidence 4678999999999999999999888777665444 3433343321 1122333322 23333 3899999999
Q ss_pred HHHhhcCcee
Q 028179 145 KLLKKFPEVL 154 (212)
Q Consensus 145 k~vkK~P~IL 154 (212)
+++.....+.
T Consensus 315 ~~l~~~~~~~ 324 (692)
T cd01385 315 EALTKKRTVT 324 (692)
T ss_pred HHhccCeEEe
Confidence 9998755443
No 38
>TIGR01448 recD_rel helicase, putative, RecD/TraA family. This model describes a family similar to RecD, the exodeoxyribonuclease V alpha chain of TIGR01447. Members of this family, however, are not found in a context of RecB and RecC and are longer by about 200 amino acids at the amino end. Chlamydia muridarum has both a member of this family and a RecD.
Probab=58.46 E-value=61 Score=33.11 Aligned_cols=59 Identities=19% Similarity=0.117 Sum_probs=40.1
Q ss_pred HHHHHHHHHhCCCCHHHH-----------HHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHH
Q 028179 126 VSEILGYLRNLSLSDDDI-----------RKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLL 184 (212)
Q Consensus 126 i~aklefLksLG~Sd~eI-----------~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I 184 (212)
....+.||..+|++...+ ..+|+.+|+.|..++..-==.++|.+-..+|+..++..++-
T Consensus 143 ~~~~~~~L~~~gi~~~~a~ki~~~yg~~~~~~i~~nPY~L~~~i~gigF~~aD~iA~~~g~~~~d~~Ri~ 212 (720)
T TIGR01448 143 ERRLLAGLQGLGIGIKLAQRIYKFYQADTLDRVEKDPYLLAEDVKGIGFLTADQLAQALGIALNDPRRIT 212 (720)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhHHHHHHHHhCchhhhhhcCCCCHHHHHHHHHHcCCCCCCHHHHH
Confidence 556778999999997544 44577888888776665445566666666777655555543
No 39
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=58.18 E-value=17 Score=26.67 Aligned_cols=29 Identities=28% Similarity=0.484 Sum_probs=25.2
Q ss_pred ChhhHHHHHHHHHhCCCCHHHHHHHHhhc
Q 028179 122 ELETVSEILGYLRNLSLSDDDIRKLLKKF 150 (212)
Q Consensus 122 s~e~i~aklefLksLG~Sd~eI~k~vkK~ 150 (212)
+.+.+.+-++.++.|||++.+|..+|++-
T Consensus 7 ~~~R~daA~dam~~lG~~~~~v~~vl~~L 35 (65)
T PF10440_consen 7 GNERIDAALDAMRQLGFSKKQVRPVLKNL 35 (65)
T ss_pred CcHHHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 34778899999999999999999988864
No 40
>cd00124 MYSc Myosin motor domain. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new actin subunit. The release of Pi causes the head to pivot and move the fila
Probab=57.88 E-value=32 Score=34.75 Aligned_cols=74 Identities=18% Similarity=0.249 Sum_probs=49.5
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhhhc-----CCChhhHHHHHHHHH-hCCCCHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERKRE-----TPELETVSEILGYLR-NLSLSDDDIR 144 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~~~-----v~s~e~i~aklefLk-sLG~Sd~eI~ 144 (212)
.+|.+.|++.+++|+.+||++++...++.-.-++ +|.--|....... +.+.+ .++... =||++.+++.
T Consensus 228 ~~d~~~f~~~~~al~~lg~~~~e~~~i~~iLaaILhLGni~f~~~~~~~~~~~~~~~~~----~l~~~a~LLgv~~~~L~ 303 (679)
T cd00124 228 IDDAEEFEELKEALKSLGFSEEEIESIFRILAAILHLGNIEFKSVGGEGQEAAEVKNTE----VLSKAAELLGLDPEELE 303 (679)
T ss_pred CCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCeeEEecCCCCcceeecCCHH----HHHHHHHHhCCCHHHHH
Confidence 4678999999999999999999988887765444 4444443321111 12222 233333 4799999999
Q ss_pred HHHhhc
Q 028179 145 KLLKKF 150 (212)
Q Consensus 145 k~vkK~ 150 (212)
+++...
T Consensus 304 ~~l~~~ 309 (679)
T cd00124 304 EALTYK 309 (679)
T ss_pred HHhhcc
Confidence 998754
No 41
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=56.55 E-value=45 Score=22.70 Aligned_cols=58 Identities=22% Similarity=0.224 Sum_probs=35.8
Q ss_pred HHhhhCCCChHHHHHHHHhhhhc------cccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhh
Q 028179 84 QALSTFNFSTEEEDKILGKAFGH------IHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKK 149 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl------~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK 149 (212)
++-+.+|+++..++.-..+-. + .+..+|.... -..-..+..|+..|+|-++|.++++.
T Consensus 5 eva~~~gvs~~tlr~y~~~gl-l~~~~~~~g~r~y~~~d-------v~~l~~i~~l~~~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 5 EVAKLLGVSPSTLRYYEREGL-LPPPRDENGYRYYSEED-------VERLREIKELRKQGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHTTTTHHHHHHHHHTTS-STTBESTTSSEEE-HHH-------HHHHHHHHHHHHTTTHHHHHHHHH--
T ss_pred HHHHHHCcCHHHHHHHHHhcC-cccccccCceeeccHHH-------HHHHHHHHHHHHCcCCHHHHHHHHcc
Confidence 445788999988877755522 2 1223443333 22335666777899999999998863
No 42
>cd00194 UBA Ubiquitin Associated domain. The UBA domain is a commonly occurring sequence motif in some members of the ubiquitination pathway, UV excision repair proteins, and certain protein kinases. Although its specific role is so far unknown, it has been suggested that UBA domains are involved in conferring protein target specificity. The domain, a compact three helix bundle, has a conserved GFP-loop and the proline is thought to be critical for binding. The UBA domain is distinct from the conserved three helical domain seen in the N-terminus of EF-TS and eukaryotic NAC proteins.
Probab=56.38 E-value=29 Score=21.35 Aligned_cols=25 Identities=32% Similarity=0.299 Sum_probs=20.6
Q ss_pred HHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 80 EACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 80 e~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
++.++-|..+||+.+.+..++.++.
T Consensus 2 ~~~v~~L~~mGf~~~~~~~AL~~~~ 26 (38)
T cd00194 2 EEKLEQLLEMGFSREEARKALRATN 26 (38)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHhC
Confidence 4567888899999999988888863
No 43
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=55.91 E-value=57 Score=22.12 Aligned_cols=62 Identities=16% Similarity=0.134 Sum_probs=34.7
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhH--HHHHHHHHhCCCCHHHHHHHHh
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETV--SEILGYLRNLSLSDDDIRKLLK 148 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i--~aklefLksLG~Sd~eI~k~vk 148 (212)
++-+.+|+++..++..... |+.... .+...-.-..+.+.+ -..+..|++.|++-++|..++.
T Consensus 5 eva~~~gvs~~tlr~~~~~--gli~~~-~~~~~g~r~y~~~dl~~l~~i~~lr~~g~~~~~i~~~l~ 68 (70)
T smart00422 5 EVAKLAGVSVRTLRYYERI--GLLPPP-IRTEGGYRLYSDEDLERLRFIKRLKELGFSLEEIKELLE 68 (70)
T ss_pred HHHHHHCcCHHHHHHHHHC--CCCCCC-ccCCCCCEecCHHHHHHHHHHHHHHHcCCCHHHHHHHHh
Confidence 3446788999888776543 432110 000000011233333 3456666789999999998874
No 44
>PF03677 UPF0137: Uncharacterised protein family (UPF0137); InterPro: IPR005350 This family of bacterial proteins includes a number of plasmid-encoded virulence proteins.
Probab=54.19 E-value=44 Score=30.33 Aligned_cols=101 Identities=20% Similarity=0.376 Sum_probs=72.4
Q ss_pred hhcccChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHH-hCCCCHHHHHH
Q 028179 67 QSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLR-NLSLSDDDIRK 145 (212)
Q Consensus 67 ~~~~~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLk-sLG~Sd~eI~k 145 (212)
|+.-|-+| ++..+++.|+...+..-...+-+.-++|=+.||| .-+.|.+ =..+++..+..
T Consensus 79 Q~vlL~GE---rI~kvreiLk~~~y~egtFSaWl~l~ygnrqt~Y----------------N~L~YYElf~~LP~~~lk~ 139 (243)
T PF03677_consen 79 QAVLLHGE---RIKKVREILKSMNYREGTFSAWLILTYGNRQTPY----------------NFLQYYELFISLPDKNLKS 139 (243)
T ss_pred hHHHHhHH---HHHHHHHHHhhccCccchHHHHHHHHHccccCch----------------HHHHHHHHHHhCCCcchHH
Confidence 33444444 5677888888888888777777777776666664 4455555 44677766666
Q ss_pred HHhhcC----ceeecCccchhhhhhhhhhhccCcCchhHHHHHHhC
Q 028179 146 LLKKFP----EVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRN 187 (212)
Q Consensus 146 ~vkK~P----~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~ 187 (212)
.+.+.| ++|+.+ +..++.|++++.+--|++..++-..|.+.
T Consensus 140 ~~~~mP~qa~Y~LASR-kG~~ekK~~ii~~~~G~tkse~i~ii~~~ 184 (243)
T PF03677_consen 140 EFQSMPRQAAYTLASR-KGSQEKKVEIIGNYNGETKSEAIDIIRKE 184 (243)
T ss_pred HHHhhhHHHHHHHHhc-cCcHHHHHHHHHHhcCCChHHHHHHHHHh
Confidence 666666 588888 99999999999999999876666666553
No 45
>PF06896 DUF1268: Protein of unknown function (DUF1268); InterPro: IPR009681 This entry is represented by Bacteriophage bIL286, Orf51. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. This family consists of several bacterial and phage proteins of around 115 residues in length. The function of this family is unknown.
Probab=53.35 E-value=59 Score=26.10 Aligned_cols=60 Identities=18% Similarity=0.371 Sum_probs=44.3
Q ss_pred cChHHHHHHHHHHHHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHH--hCCCCHHHHHHHH
Q 028179 71 LNDEERKKWEACRQAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLR--NLSLSDDDIRKLL 147 (212)
Q Consensus 71 ~~~~~~~~we~~v~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLk--sLG~Sd~eI~k~v 147 (212)
....+....++...|| +.||++.+.+.++ ... ..+....-+.|+. -.|.+++++..+.
T Consensus 47 ~~~~~~~~~~~~~~Fi~~iL~L~dkq~ekl-~~i------------------D~~~~~e~~~yl~~rl~G~sD~~i~~~~ 107 (114)
T PF06896_consen 47 IDEASRNILKEMLKFIQDILKLNDKQVEKL-EDI------------------DFEDLQEIVSYLVMRLQGMSDEQIELAE 107 (114)
T ss_pred HHHhHHHHHHHHHHHHHHHHCCCHHHHHHH-hcC------------------CHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 3444566678889999 7999999999777 443 2355556666666 4599999999886
Q ss_pred hh
Q 028179 148 KK 149 (212)
Q Consensus 148 kK 149 (212)
++
T Consensus 108 ~~ 109 (114)
T PF06896_consen 108 KE 109 (114)
T ss_pred hc
Confidence 65
No 46
>COG4103 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=52.86 E-value=14 Score=31.15 Aligned_cols=80 Identities=21% Similarity=0.320 Sum_probs=49.6
Q ss_pred HHHHHHHHHh-hhCCCChHHHHHHHHhhhhc---------cccchhhhhhhhcCCChhhHHHHHHHHH---hCCCCHHHH
Q 028179 77 KKWEACRQAL-STFNFSTEEEDKILGKAFGH---------IHSAYWSEERKRETPELETVSEILGYLR---NLSLSDDDI 143 (212)
Q Consensus 77 ~~we~~v~~L-~~LGfspe~v~~il~rA~gl---------~~S~~fr~a~~~~v~s~e~i~aklefLk---sLG~Sd~eI 143 (212)
..|++-++.| +.+|++++.+..++..+.+. +.|.++||.. ++ .++++++ .+=..|.++
T Consensus 48 ~E~~a~r~il~~~f~i~~~~l~ali~~~e~~~~Ea~d~y~fts~l~r~Ld------~e---~R~eli~~mweIa~ADg~l 118 (148)
T COG4103 48 SEREAFRAILKENFGIDGEELDALIEAGEEAGYEAIDLYSFTSVLKRHLD------EE---QRLELIGLMWEIAYADGEL 118 (148)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHhcC------HH---HHHHHHHHHHHHHHccccc
Confidence 4577788888 79999999999999987654 2333333333 44 6666665 333333333
Q ss_pred H----HHHhhcCceeecCccchhhhh
Q 028179 144 R----KLLKKFPEVLGCDIEHELRNN 165 (212)
Q Consensus 144 ~----k~vkK~P~ILg~SVEe~Lkpk 165 (212)
. .++.|--.+||.|.++.++++
T Consensus 119 ~e~Ed~vi~RvAeLLgV~~~d~V~~r 144 (148)
T COG4103 119 DESEDHVIWRVAELLGVSPEDRVRAR 144 (148)
T ss_pred cHHHHHHHHHHHHHhCCCHHHHHHHH
Confidence 2 345555566666666555554
No 47
>cd01387 MYSc_type_XV Myosin motor domain, type XV myosins. In vertebrates, myosin XV appears to be expressed in sensory tissue and play a role in hearing. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis caus
Probab=52.67 E-value=41 Score=34.24 Aligned_cols=76 Identities=13% Similarity=0.236 Sum_probs=50.1
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhh-----hhcCCChhhHHHHHHHHH-hCCCCHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEER-----KRETPELETVSEILGYLR-NLSLSDDDIR 144 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~-----~~~v~s~e~i~aklefLk-sLG~Sd~eI~ 144 (212)
.+|.+.|++..++|+.+||+.++...++.-.-++ +|--.|...- ...+.+.+. ++... =||++.+++.
T Consensus 228 ~~d~~~f~~~~~al~~lg~~~~e~~~i~~iLaaILhLGni~F~~~~~~~~~~~~~~~~~~----l~~~a~LLgv~~~~L~ 303 (677)
T cd01387 228 KSDADDFRRLLAAMEVLGFSSEDQDSIFRILASILHLGNVYFEKRETDAQEVASVVSARE----IQAVAELLQISPEGLQ 303 (677)
T ss_pred cCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcCeEEeeccCCCCcccccCCHHH----HHHHHHHhCCCHHHHH
Confidence 3677899999999999999999877777665454 4444453211 012233332 22233 4799999999
Q ss_pred HHHhhcCc
Q 028179 145 KLLKKFPE 152 (212)
Q Consensus 145 k~vkK~P~ 152 (212)
+++...-.
T Consensus 304 ~~lt~~~~ 311 (677)
T cd01387 304 KAITFKVT 311 (677)
T ss_pred HHhccCeE
Confidence 99976543
No 48
>TIGR01558 sm_term_P27 phage terminase, small subunit, putative, P27 family. Members tend to be adjacent to the phage terminase large subunit gene.
Probab=51.59 E-value=17 Score=28.32 Aligned_cols=33 Identities=18% Similarity=0.400 Sum_probs=24.0
Q ss_pred cChHHHHHHHHHHHHhhhCC-CChHHHHHHHHhh
Q 028179 71 LNDEERKKWEACRQALSTFN-FSTEEEDKILGKA 103 (212)
Q Consensus 71 ~~~~~~~~we~~v~~L~~LG-fspe~v~~il~rA 103 (212)
|+++-++.|...+..|+..| ++.-+...+-..+
T Consensus 6 L~~~ak~~w~ri~~~L~~~~~l~~~D~~~l~~yc 39 (116)
T TIGR01558 6 LGKEGKDEWKRVAPELKGSGILTNLDRDALLRYC 39 (116)
T ss_pred HhHHHHHHHHHHHHHHHHcCCchHHHHHHHHHHH
Confidence 77888899999999998777 5666654444433
No 49
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=50.52 E-value=59 Score=28.06 Aligned_cols=84 Identities=17% Similarity=0.169 Sum_probs=49.2
Q ss_pred HHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchh
Q 028179 84 QAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHEL 162 (212)
Q Consensus 84 ~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~L 162 (212)
..| +.=|+.++.+++++....+-.......... .... .......++-|.+||+++.|+.+++.+--.-=..++++-+
T Consensus 108 ~~L~kvpGIGkKtAerIilELk~K~~~~~~~~~~-~~~~-~~~~~e~~~aL~~LGy~~~ea~~ai~~i~~~~~~~~~~~i 185 (195)
T PRK14604 108 ARLARVPGIGKKTAERIVLELKGKIDVRQLSGST-SPAV-SALDRELSEILISLGYSAAEAAAAIAALPSDAPPDLEERL 185 (195)
T ss_pred HHHhhCCCCCHHHHHHHHHHHHHHhccccccccc-cccc-cccHHHHHHHHHHcCCCHHHHHHHHHHHhhcCCCCHHHHH
Confidence 455 567888888888876654322100000000 0011 1224678899999999999999999875210034666666
Q ss_pred hhhhhhh
Q 028179 163 RNNVQIL 169 (212)
Q Consensus 163 kpkveFL 169 (212)
|..+.+|
T Consensus 186 r~aLk~l 192 (195)
T PRK14604 186 RLALRYF 192 (195)
T ss_pred HHHHHHh
Confidence 6665554
No 50
>KOG0871 consensus Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=50.00 E-value=33 Score=29.24 Aligned_cols=62 Identities=13% Similarity=0.135 Sum_probs=38.4
Q ss_pred cChHHHHHH--HHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHH
Q 028179 71 LNDEERKKW--EACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKL 146 (212)
Q Consensus 71 ~~~~~~~~w--e~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~ 146 (212)
-+.|+.|++ |-+.++|+.|||. +-+..+..-...+... ..+-..|-.-|+..|++++|+.+-
T Consensus 59 c~~e~KKTIa~EHV~KALe~LgF~-eYiee~~~vl~~~K~~-------------~~~~~~kssk~e~~Gi~eEEL~~q 122 (156)
T KOG0871|consen 59 CNKEAKKTIAPEHVIKALENLGFG-EYIEEAEEVLENCKEE-------------AKKRRRKSSKFEKSGIPEEELLRQ 122 (156)
T ss_pred HhHHhcccCCHHHHHHHHHHcchH-HHHHHHHHHHHHHHHH-------------HHHhhhhhhhHHhcCCCHHHHHHH
Confidence 455666655 5678888899988 5554443333211111 123456777788899999998753
No 51
>cd01379 MYSc_type_III Myosin motor domain, type III myosins. Myosin III has been shown to play a role in the vision process in insects and in hearing in mammals. Myosin III, an unconventional myosin, does not form dimers. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the
Probab=49.81 E-value=57 Score=33.11 Aligned_cols=78 Identities=14% Similarity=0.189 Sum_probs=50.9
Q ss_pred HHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhh------hhcCCChhhHHHHHHHHHhCCCCHHHHHH
Q 028179 74 EERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEER------KRETPELETVSEILGYLRNLSLSDDDIRK 145 (212)
Q Consensus 74 ~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~------~~~v~s~e~i~aklefLksLG~Sd~eI~k 145 (212)
+|...|++.+++|+.+||++++...|+.-.-++ +|.-.|.... ...+.+.+.+ .++.- =||++.+++.+
T Consensus 234 ~~~~~f~~~~~al~~lg~~~~e~~~I~~iLaaILhLGNi~F~~~~~~~~~~~~~i~~~~~l-~~~A~--LLgv~~~~L~~ 310 (653)
T cd01379 234 FYKDQFEQIEQCFRVIGFTDEEVGSVYRILAAILNLGDIEFGSVASEHQTDKSRVSNVAAL-ENAAS--LLCIRSDELQE 310 (653)
T ss_pred hHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEEeccccCCCcccccCCHHHH-HHHHH--HhCCCHHHHHH
Confidence 467899999999999999999987777665444 4444454321 1122333322 22332 37999999999
Q ss_pred HHhhcCcee
Q 028179 146 LLKKFPEVL 154 (212)
Q Consensus 146 ~vkK~P~IL 154 (212)
++...-.+.
T Consensus 311 ~L~~~~~~~ 319 (653)
T cd01379 311 ALTSHCVVT 319 (653)
T ss_pred HhcccEEEe
Confidence 998654433
No 52
>COG4669 EscJ Type III secretory pathway, lipoprotein EscJ [Intracellular trafficking and secretion]
Probab=49.31 E-value=39 Score=30.74 Aligned_cols=66 Identities=14% Similarity=0.221 Sum_probs=49.5
Q ss_pred HHHHHHHHHHhhhCCCChHHHHHHHHhhh--hccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCce
Q 028179 76 RKKWEACRQALSTFNFSTEEEDKILGKAF--GHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEV 153 (212)
Q Consensus 76 ~~~we~~v~~L~~LGfspe~v~~il~rA~--gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~I 153 (212)
..++.++++.|+.=|++.+.-..+..-++ |+..|| .+| ++|+.|.++ .++...+++.+.|
T Consensus 63 ~~~fa~Av~iL~~~GlPr~~f~~l~d~Fp~dgLVsSP-----------~eE--kaR~~~~~e-----Q~le~tLs~mDGV 124 (246)
T COG4669 63 ESDFAEAVEILNQNGLPRKKFTTLGDIFPKDGLVSSP-----------TEE--KARLNYAKE-----QQLEQTLSKMDGV 124 (246)
T ss_pred HHHHHHHHHHHHhcCCCCCCCCcHHHhCCcccccCCc-----------HHH--HHHHHHHHH-----HHHHHHHHhcCce
Confidence 35789999999999999987654433322 344443 334 588888874 8999999999999
Q ss_pred eecCcc
Q 028179 154 LGCDIE 159 (212)
Q Consensus 154 Lg~SVE 159 (212)
+..+|.
T Consensus 125 i~ArV~ 130 (246)
T COG4669 125 ISARVH 130 (246)
T ss_pred EEEEEE
Confidence 998865
No 53
>cd01381 MYSc_type_VII Myosin motor domain, type VII myosins. Myosins in this group have been associated with functions in sensory systems such as vision and hearing. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydr
Probab=49.30 E-value=45 Score=33.93 Aligned_cols=74 Identities=16% Similarity=0.170 Sum_probs=48.6
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhh-----hhcCCChhhHHHHHHHHH-hCCCCHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEER-----KRETPELETVSEILGYLR-NLSLSDDDIR 144 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~-----~~~v~s~e~i~aklefLk-sLG~Sd~eI~ 144 (212)
.+|.+.|++.+++|+.+||++++...|+.=.-++ +|.-.|.... ...+.+.+ .++... =||++.+++.
T Consensus 227 ~dD~~~f~~~~~al~~lG~~~~e~~~i~~ilaaILhLGni~F~~~~~~~~~~~~i~~~~----~l~~~a~LLgv~~~~L~ 302 (671)
T cd01381 227 RDDAKDFADIRSAMKVLMFTDQEIWEIFKLLAAILHIGNLRFEATEVDNLAACEVDDTP----NLQRVAQLLGVPIQDLM 302 (671)
T ss_pred ccHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEeeccCCCCCceeeCChH----HHHHHHHHhCCCHHHHh
Confidence 3578999999999999999999987776664443 4444454321 11122222 223333 4799999999
Q ss_pred HHHhhc
Q 028179 145 KLLKKF 150 (212)
Q Consensus 145 k~vkK~ 150 (212)
+++...
T Consensus 303 ~~lt~~ 308 (671)
T cd01381 303 DALTSR 308 (671)
T ss_pred hhhceE
Confidence 998743
No 54
>COG3747 Phage terminase, small subunit [DNA replication, recombination, and repair]
Probab=49.23 E-value=29 Score=29.64 Aligned_cols=94 Identities=12% Similarity=0.151 Sum_probs=63.4
Q ss_pred cccChHHHHHHHHHHHHhhhCCC-ChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHH-HHHHH
Q 028179 69 ITLNDEERKKWEACRQALSTFNF-STEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDD-DIRKL 146 (212)
Q Consensus 69 ~~~~~~~~~~we~~v~~L~~LGf-spe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~-eI~k~ 146 (212)
.-|++.-.+.|-+.+-+|..+++ .+.+..-+-..+. .-+....-++-|+.+|++-+ .....
T Consensus 42 dwLd~~A~~~Wrrvvp~L~e~~ll~~~D~~~Le~YC~-----------------~ysiY~~av~~lkk~G~ii~~~~~g~ 104 (160)
T COG3747 42 DWLDPTAKKEWRRVVPFLEELKLLKPADLTLLELYCV-----------------AYSIYRNAVAHLKKHGFIITNQFSGR 104 (160)
T ss_pred cccCHHHHHHHHHHHHHHHHhccCCHHHHHHHHHHHH-----------------HHHHHHHHHHHHHHcceeeeccccce
Confidence 45999999999999999966654 3333211111121 12555577888888999844 44555
Q ss_pred HhhcCceeecCccchhhhhhhhhhhccCcCchhHHH
Q 028179 147 LKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRN 182 (212)
Q Consensus 147 vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~ 182 (212)
++++|.+=.+| ....++--|-+++|++...-.+
T Consensus 105 ~krNPav~~~s---dA~~~l~klaSeLGltP~arak 137 (160)
T COG3747 105 VKRNPAVQAAS---DAIRNLLKLASELGLTPSARAK 137 (160)
T ss_pred ecCChHHHHHH---HHHHHHHHHHHHhCCChHHHHh
Confidence 99999998888 3566677778889998444333
No 55
>PF02662 FlpD: Methyl-viologen-reducing hydrogenase, delta subunit; InterPro: IPR003813 Methyl-viologen-reducing hydrogenase (MVH) is one of the enzymes involved in methanogenesis and coded in the mth-flp-mvh-mrt cluster of methane genes in Methanothermobacter thermautotrophicus (Methanobacterium thermoformicicum) []. No specific functions have been assigned to the delta subunit.; GO: 0015948 methanogenesis, 0055114 oxidation-reduction process
Probab=48.18 E-value=30 Score=27.61 Aligned_cols=23 Identities=17% Similarity=0.270 Sum_probs=20.2
Q ss_pred HHHHHHHHHHHHhhhCCCChHHH
Q 028179 74 EERKKWEACRQALSTFNFSTEEE 96 (212)
Q Consensus 74 ~~~~~we~~v~~L~~LGfspe~v 96 (212)
--.++.+...+.|+.+|++||++
T Consensus 74 ~a~~Rv~~~k~~L~~~Gi~~eRv 96 (124)
T PF02662_consen 74 RAEKRVERLKKLLEELGIEPERV 96 (124)
T ss_pred HHHHHHHHHHHHHHHcCCChhHe
Confidence 34678889999999999999998
No 56
>KOG2629 consensus Peroxisomal membrane anchor protein (peroxin) [Cell wall/membrane/envelope biogenesis; Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=48.11 E-value=21 Score=33.35 Aligned_cols=24 Identities=17% Similarity=0.475 Sum_probs=22.4
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhh
Q 028179 126 VSEILGYLRNLSLSDDDIRKLLKK 149 (212)
Q Consensus 126 i~aklefLksLG~Sd~eI~k~vkK 149 (212)
+-.|.+||++-|++++||..++++
T Consensus 22 li~kr~FLksKGLT~eEI~eAfk~ 45 (300)
T KOG2629|consen 22 LIKKREFLKSKGLTEEEIQEAFKR 45 (300)
T ss_pred HHHHHHHHHhcCCCHHHHHHHHHh
Confidence 558999999999999999999997
No 57
>PRK00033 clpS ATP-dependent Clp protease adaptor protein ClpS; Reviewed
Probab=48.10 E-value=27 Score=27.36 Aligned_cols=61 Identities=15% Similarity=0.162 Sum_probs=44.2
Q ss_pred cChHHHHHHHHHHHHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCC
Q 028179 71 LNDEERKKWEACRQAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSL 138 (212)
Q Consensus 71 ~~~~~~~~we~~v~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~ 138 (212)
|=++|-.+.++++.+| +.+|++.+.+.++...+..- |.+ . .-+-..|....+.+-+..+|+
T Consensus 32 L~NDd~ntmd~Vv~vL~~vf~~s~~~A~~iml~vH~~-G~a-----v-v~~~~~e~AE~~~~~l~~~~L 93 (100)
T PRK00033 32 LHNDDYTPMEFVVYVLQKFFGYDRERATQIMLEVHNE-GKA-----V-VGVCTREVAETKVEQVHQHGL 93 (100)
T ss_pred EEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhcC-CcE-----E-EEEEcHHHHHHHHHHHHcCCC
Confidence 5667788899999999 89999999999999888632 111 1 111245667778877776666
No 58
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=47.59 E-value=78 Score=23.82 Aligned_cols=81 Identities=19% Similarity=0.198 Sum_probs=45.1
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhH--HHHHHHHHhCCCCHHHHHHHHhhcCceeecCccch
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETV--SEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHE 161 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i--~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~ 161 (212)
++-+.+|+++.+++..... |++... -+...-.-..+++.+ -..+.+|+.+|+|-++|..++.... ....+.
T Consensus 5 eva~~~gvs~~tlR~ye~~--Gll~~~-~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~----~~~~~~ 77 (103)
T cd01106 5 EVAKLTGVSVRTLHYYDEI--GLLKPS-RRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPS----EDLLEA 77 (103)
T ss_pred HHHHHHCcCHHHHHHHHHC--CCCCCC-ccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcCc----HHHHHH
Confidence 3446789999998765443 442110 000000011233333 3457789999999999999998664 222334
Q ss_pred hhhhhhhhhh
Q 028179 162 LRNNVQILGK 171 (212)
Q Consensus 162 LkpkveFL~~ 171 (212)
|......|..
T Consensus 78 l~~~~~~l~~ 87 (103)
T cd01106 78 LREQKELLEE 87 (103)
T ss_pred HHHHHHHHHH
Confidence 4445555443
No 59
>PF13371 TPR_9: Tetratricopeptide repeat
Probab=46.99 E-value=21 Score=24.00 Aligned_cols=38 Identities=11% Similarity=0.267 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHh-hhCCCChHHHHHHHHhhhhccccchh
Q 028179 75 ERKKWEACRQAL-STFNFSTEEEDKILGKAFGHIHSAYW 112 (212)
Q Consensus 75 ~~~~we~~v~~L-~~LGfspe~v~~il~rA~gl~~S~~f 112 (212)
.+++|+++.+++ ..+-++|+++.-...++.-+...+-|
T Consensus 7 ~~~~~~~A~~~~~~~l~~~p~~~~~~~~~a~~~~~~g~~ 45 (73)
T PF13371_consen 7 QQEDYEEALEVLERALELDPDDPELWLQRARCLFQLGRY 45 (73)
T ss_pred hCCCHHHHHHHHHHHHHhCcccchhhHHHHHHHHHhccH
Confidence 356788999999 68888999887777776433444333
No 60
>PRK14137 recX recombination regulator RecX; Provisional
Probab=45.53 E-value=2e+02 Score=24.83 Aligned_cols=67 Identities=12% Similarity=0.025 Sum_probs=38.5
Q ss_pred HHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhh
Q 028179 81 ACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKK 149 (212)
Q Consensus 81 ~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK 149 (212)
|..+.|..-|++++.+..++.++.+. +.-.-|-+.... .+-......-.-|+.-|++++.|..++..
T Consensus 59 ELr~KL~~kg~~~e~Ie~vI~rL~e~gyLDD~rfAe~~~~--~k~~Gp~rI~~eL~qKGI~~~lI~~al~~ 127 (195)
T PRK14137 59 ELRAKLERRSEDEALVTEVLERVQELGYQDDAQVARAENS--RRGVGALRVRQTLRRRGVEETLIEETLAA 127 (195)
T ss_pred HHHHHHHhcCCCHHHHHHHHHHHHHcCCCCHHHHHHHHHH--hcCchHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 44455666799999999999997664 322222222100 01111223445566788888777776654
No 61
>PRK09853 putative selenate reductase subunit YgfK; Provisional
Probab=45.18 E-value=7.4 Score=41.49 Aligned_cols=35 Identities=23% Similarity=0.463 Sum_probs=23.3
Q ss_pred CCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeecc
Q 028179 136 LSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYN 194 (212)
Q Consensus 136 LG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYS 194 (212)
|||+.+||.++. .||..+=|| .-+|.=||++|||.
T Consensus 218 hgcp~~eie~i~-------------------~~~~~~k~~-----~~~~k~nptllg~~ 252 (1019)
T PRK09853 218 HGCPPHEIEAIA-------------------RYLLEEKGL-----NTFVKLNPTLLGYE 252 (1019)
T ss_pred cCCCHHHHHHHH-------------------HHHHhccCC-----ceEEeeCcccccHH
Confidence 688888887763 355544455 45777777777775
No 62
>cd02977 ArsC_family Arsenate Reductase (ArsC) family; composed of TRX-fold arsenic reductases and similar proteins including the transcriptional regulator, Spx. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX), through a single catalytic cysteine. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases. Spx is a general regulator that exerts negative and positive control over transcription initiation by binding to the C-terminal domain of the alpha subunit of RNA polymerase.
Probab=45.15 E-value=67 Score=23.99 Aligned_cols=27 Identities=19% Similarity=0.361 Sum_probs=20.8
Q ss_pred CcCchhHHHHHHhCCceeecccccccc
Q 028179 174 GIEGKYLRNLLLRNPKVLGYNVDCKGD 200 (212)
Q Consensus 174 GL~g~~l~~~I~r~P~ILgYSLE~Rg~ 200 (212)
+++.++.-++|+++|.+|-..|=-.|+
T Consensus 73 ~ls~~e~~~~l~~~p~LikRPii~~~~ 99 (105)
T cd02977 73 ELSDEEALELMAEHPKLIKRPIVVDGD 99 (105)
T ss_pred CCCHHHHHHHHHhCcCeeeCCEEEECC
Confidence 456678889999999999887755444
No 63
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=45.03 E-value=46 Score=28.80 Aligned_cols=27 Identities=15% Similarity=0.367 Sum_probs=24.2
Q ss_pred HHHHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 78 KWEACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 78 ~we~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
..++++++|..||+++.++.+++.++.
T Consensus 154 ~~~ea~~AL~~LGy~~~ea~~av~~~~ 180 (203)
T PRK14602 154 VFRDALAGLANLGYGEEEARPVLKEVL 180 (203)
T ss_pred hHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 358999999999999999999998873
No 64
>TIGR00014 arsC arsenate reductase (glutaredoxin). composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate.
Probab=44.64 E-value=73 Score=24.64 Aligned_cols=27 Identities=19% Similarity=0.332 Sum_probs=21.0
Q ss_pred cCchhHHHHHHhCCceeeccccccccc
Q 028179 175 IEGKYLRNLLLRNPKVLGYNVDCKGDC 201 (212)
Q Consensus 175 L~g~~l~~~I~r~P~ILgYSLE~Rg~c 201 (212)
++.++.-++|+++|.+|-..|=-.|+-
T Consensus 74 ls~~e~i~~l~~~P~LikRPIi~~~~~ 100 (114)
T TIGR00014 74 LSDQELLDAMVAHPILLERPIVVAGDG 100 (114)
T ss_pred CCHHHHHHHHHHCcCcccCCeEEECCE
Confidence 445667789999999998888776764
No 65
>cd01384 MYSc_type_XI Myosin motor domain, plant-specific type XI myosin, involved in organelle transport. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates from an actin filament. ATP hydrolysis causes the head to pivot and associate with a new act
Probab=43.77 E-value=59 Score=33.14 Aligned_cols=77 Identities=16% Similarity=0.163 Sum_probs=48.8
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhh---hhcCCChhhHHHHHHHHH-hCCCCHHHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEER---KRETPELETVSEILGYLR-NLSLSDDDIRKL 146 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~---~~~v~s~e~i~aklefLk-sLG~Sd~eI~k~ 146 (212)
.+|.+.|++..++|+.+||++++...|+.-.-++ +|.-.|.... ...+...+. ...++... =||++.+++.++
T Consensus 232 ~~D~~~f~~~~~al~~lG~~~~e~~~I~~iLaaILhLGni~F~~~~~~~~~~~~~~~~-~~~l~~~a~LLgv~~~~L~~~ 310 (674)
T cd01384 232 VDDAEEYLATRRAMDVVGISEEEQDAIFRVVAAILHLGNIEFAKGEEIDSSVLKDEKS-EFHLKTAAELLMCDEKALEDA 310 (674)
T ss_pred cchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhccceeeeccCCCCcccccCccc-HHHHHHHHHHhCCCHHHHHHH
Confidence 3578999999999999999999877777665454 4444443321 011111100 12233333 479999999998
Q ss_pred Hhhc
Q 028179 147 LKKF 150 (212)
Q Consensus 147 vkK~ 150 (212)
+...
T Consensus 311 L~~~ 314 (674)
T cd01384 311 LCKR 314 (674)
T ss_pred hccc
Confidence 8754
No 66
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=43.70 E-value=38 Score=29.26 Aligned_cols=26 Identities=15% Similarity=0.227 Sum_probs=23.4
Q ss_pred HHHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 79 WEACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 79 we~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
-++++.+|..||++++++.+++.+..
T Consensus 152 ~~ea~~AL~~LGy~~~ea~~al~~i~ 177 (197)
T PRK14603 152 AEDAVLALLALGFREAQVRSVVAELL 177 (197)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 47899999999999999999998873
No 67
>COG0339 Dcp Zn-dependent oligopeptidases [Amino acid transport and metabolism]
Probab=43.28 E-value=39 Score=34.87 Aligned_cols=81 Identities=19% Similarity=0.151 Sum_probs=64.3
Q ss_pred ChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHH-HhCCCCHH--HHHHHHh
Q 028179 72 NDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYL-RNLSLSDD--DIRKLLK 148 (212)
Q Consensus 72 ~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefL-ksLG~Sd~--eI~k~vk 148 (212)
.+.+..+||-.+..|..+|=...++..++-...+.-.++.++.+- +.+.+||.-+ -.||...+ +..+.|.
T Consensus 49 ~~~~~pt~~n~v~~Le~~~~~L~rv~~~~~~l~~v~~~~elr~a~-------e~~~pklse~~~~l~~~~~Lf~~~~al~ 121 (683)
T COG0339 49 ANPDAPTWENTVEPLERAGDRLGRVWSVVSHLNSVHNSPELREAY-------EEILPKLSEFSNDLGQNPGLFARYKALW 121 (683)
T ss_pred cCCCCCcHHHHHHHHHHHhhHHHHHHHHHHHHHhcCCCHHHHHHH-------HHhhHHHHHHHHHhhcCHHHHHHHHHHh
Confidence 333899999999999999999999999998887778888888877 5555666544 49999875 4456788
Q ss_pred hcCceeecCcc
Q 028179 149 KFPEVLGCDIE 159 (212)
Q Consensus 149 K~P~ILg~SVE 159 (212)
..|+-++.+.|
T Consensus 122 ~~~e~~~ld~e 132 (683)
T COG0339 122 QSPESAGLDPE 132 (683)
T ss_pred cCcccccCCHH
Confidence 89998888844
No 68
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=43.08 E-value=44 Score=25.78 Aligned_cols=57 Identities=12% Similarity=0.188 Sum_probs=27.2
Q ss_pred HHHHHHHhCCCCHHHHHHHHhh--------------cCceeecCccchhhhhhhhhhhccCcCchhHHHHHH
Q 028179 128 EILGYLRNLSLSDDDIRKLLKK--------------FPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLL 185 (212)
Q Consensus 128 aklefLksLG~Sd~eI~k~vkK--------------~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~ 185 (212)
....-|+.-|++.+.|..++.. ++.....+-.......+.||... |++...+...|.
T Consensus 47 ~I~~~L~~kGi~~~~i~~~l~~~~~~e~a~~~~~kk~~~~~~~~~~~~~~K~~~~L~rr-GF~~~~i~~vi~ 117 (121)
T PF02631_consen 47 RIRQKLKQKGIDREIIEEALEEYDEEEEALELAEKKYRRYRKPSDRKRKQKLIRFLMRR-GFSYDVIRRVIS 117 (121)
T ss_dssp HHHHHHHHTT--HHHHHHHHTCS-HHHHHHHHHHHHHHHTTTS-CHHHHHHHHHHHHHT-T--HHHHHHHCH
T ss_pred HHHHHHHHHCCChHHHHHHHHHhhHHHHHHHHHHHHHhcccCCCCHHHHHHHHHHHHHC-CCCHHHHHHHHh
Confidence 4445566677777766666652 22222222133444456777764 787555555443
No 69
>cd01383 MYSc_type_VIII Myosin motor domain, plant-specific type VIII myosins, a subgroup which has been associated with endocytosis, cytokinesis, cell-to-cell coupling and gating at plasmodesmata. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the plus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of force. Upon ATP binding, the myosin head dissociates f
Probab=42.77 E-value=68 Score=32.73 Aligned_cols=75 Identities=12% Similarity=0.148 Sum_probs=48.3
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhh---hcCCChhhHHHHHHHHH-hCCCCHHHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERK---RETPELETVSEILGYLR-NLSLSDDDIRKL 146 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~---~~v~s~e~i~aklefLk-sLG~Sd~eI~k~ 146 (212)
.+|.+.|++.+++|+.+||++++...|+.=.-++ +|---|..... ..+.+.+ .++... =||++.+++.++
T Consensus 232 ~dd~~~f~~~~~al~~lG~~~~e~~~I~~iLaaILhLGNi~F~~~~~~~~~~~~~~~----~l~~~a~LLgv~~~~L~~~ 307 (677)
T cd01383 232 VDDAQRFHTLVEALDIVHISKEDQENVFAMLAAVLWLGNVSFTVIDNENHVEPVADE----ALSTAAKLIGCNIEDLMLA 307 (677)
T ss_pred ccHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceEEEecCCCcccccCChH----HHHHHHHHhCCCHHHHHHH
Confidence 4678899999999999999999977776654444 34333432211 1112222 233333 379999999998
Q ss_pred HhhcC
Q 028179 147 LKKFP 151 (212)
Q Consensus 147 vkK~P 151 (212)
+.+.=
T Consensus 308 l~~~~ 312 (677)
T cd01383 308 LSTRK 312 (677)
T ss_pred hhhcE
Confidence 87543
No 70
>PF13348 Y_phosphatase3C: Tyrosine phosphatase family C-terminal region; PDB: 1YWF_A 2OZ5_B.
Probab=42.67 E-value=35 Score=23.72 Aligned_cols=44 Identities=27% Similarity=0.387 Sum_probs=26.0
Q ss_pred hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHH-hCCCCHHHHHHHHhh
Q 028179 87 STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLR-NLSLSDDDIRKLLKK 149 (212)
Q Consensus 87 ~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLk-sLG~Sd~eI~k~vkK 149 (212)
..++..++....++.......| ..-.||+ .+|++++++.++=.+
T Consensus 22 ~~~~~~~e~l~~~l~~i~~~yG-------------------s~e~Yl~~~lgl~~~~i~~Lr~~ 66 (68)
T PF13348_consen 22 SLMSVRPEYLEAALDAIDERYG-------------------SVENYLREELGLSEEDIERLRER 66 (68)
T ss_dssp HHHS--HHHHHHHHHHHHHHHS-------------------SHHHHHHHT-T--HHHHHHHHHH
T ss_pred hhcCccHHHHHHHHHHHHHHcC-------------------CHHHHHHHcCCCCHHHHHHHHHH
Confidence 3667778877777666542222 3457996 889999999987543
No 71
>PRK14603 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=42.38 E-value=35 Score=29.48 Aligned_cols=85 Identities=9% Similarity=0.114 Sum_probs=47.7
Q ss_pred HHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcC--CChhhHHHHHHHHHhCCCCHHHHHHHHhhcC-ceeecCcc
Q 028179 84 QAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRET--PELETVSEILGYLRNLSLSDDDIRKLLKKFP-EVLGCDIE 159 (212)
Q Consensus 84 ~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v--~s~e~i~aklefLksLG~Sd~eI~k~vkK~P-~ILg~SVE 159 (212)
+.| +.=|+.++.+.+++....+-.....-........ .+.......++-|.+||+++.|+.+++++-. .--..++|
T Consensus 107 ~~L~kvpGIGkKtAerIilELkdK~~~~~~~~~~~~~~~~~~~~~~~ea~~AL~~LGy~~~ea~~al~~i~~~~~~~~~e 186 (197)
T PRK14603 107 RLLTSASGVGKKLAERIALELKGKVPEHLLAGPAGGGGTKVSSTAAEDAVLALLALGFREAQVRSVVAELLAQNPEASAQ 186 (197)
T ss_pred HHHhhCCCCCHHHHHHHHHHHHHHhhhhcccccccccccccCCccHHHHHHHHHHcCCCHHHHHHHHHHHHhcCCCCCHH
Confidence 455 5678888888888765433221100000000001 1112356788999999999999999998742 11134555
Q ss_pred chhhhhhhh
Q 028179 160 HELRNNVQI 168 (212)
Q Consensus 160 e~LkpkveF 168 (212)
+-+|..+..
T Consensus 187 ~lir~aLk~ 195 (197)
T PRK14603 187 TLIRKALKR 195 (197)
T ss_pred HHHHHHHHh
Confidence 555554443
No 72
>PRK14604 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=41.95 E-value=52 Score=28.39 Aligned_cols=26 Identities=12% Similarity=0.110 Sum_probs=23.4
Q ss_pred HHHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 79 WEACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 79 we~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
-++++.+|..|||+++++.+++.++.
T Consensus 149 ~~e~~~aL~~LGy~~~ea~~ai~~i~ 174 (195)
T PRK14604 149 DRELSEILISLGYSAAEAAAAIAALP 174 (195)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 37899999999999999999998873
No 73
>PF09286 Pro-kuma_activ: Pro-kumamolisin, activation domain ; InterPro: IPR015366 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This domain is found at the N terminus of peptidases belonging to MEROPS peptidase family S53 (sedolisin, clan SB). The domain adopts a ferredoxin-like fold, with an alpha+beta sandwich. Cleavage of the domain results in activation of the peptidase []. ; GO: 0008236 serine-type peptidase activity; PDB: 1T1E_A 3EDY_A 3EE6_A.
Probab=41.40 E-value=17 Score=28.82 Aligned_cols=22 Identities=23% Similarity=0.419 Sum_probs=16.7
Q ss_pred CChhhHHHHHHHHHhCCCCHHH
Q 028179 121 PELETVSEILGYLRNLSLSDDD 142 (212)
Q Consensus 121 ~s~e~i~aklefLksLG~Sd~e 142 (212)
++++.++++.+||++.|++..+
T Consensus 59 p~~~~v~~V~~wL~~~G~~~~~ 80 (143)
T PF09286_consen 59 PSPEDVAAVKSWLKSHGLTVVE 80 (143)
T ss_dssp --HHHHHHHHHHHHHCT-EEEE
T ss_pred CCHHHHHHHHHHHHHcCCceeE
Confidence 7889999999999999997544
No 74
>PRK14606 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=40.83 E-value=33 Score=29.47 Aligned_cols=27 Identities=7% Similarity=0.325 Sum_probs=24.2
Q ss_pred HHHHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 78 KWEACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 78 ~we~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
.+++++.+|..||++++++.+++.++.
T Consensus 142 ~~~e~~~AL~~LGy~~~ea~~av~~~~ 168 (188)
T PRK14606 142 IYHESLEALVSLGYPEKQAREAVKHVY 168 (188)
T ss_pred cHHHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 468899999999999999999998873
No 75
>PF07293 DUF1450: Protein of unknown function (DUF1450); InterPro: IPR009910 This entry consists of several hypothetical bacterial proteins of around 80 residues in length representing two families. Members contain four highly conserved cysteine residues and their function is unknown.
Probab=40.14 E-value=12 Score=28.23 Aligned_cols=45 Identities=16% Similarity=0.350 Sum_probs=31.2
Q ss_pred hhhhhhhhhhccCcCchhHHHHHHhCCceeecccc-cccccccccchhhcc
Q 028179 162 LRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVD-CKGDCMAQCTRCWVR 211 (212)
Q Consensus 162 LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE-~Rg~c~~~c~rcw~r 211 (212)
|+|.|||=.+++....+.+.+.+.++|.+ | ..-+|.+.|+.|-.+
T Consensus 1 m~piVefC~~Nl~~g~~~~~~~Le~~p~~-----~Vie~gCl~~Cg~C~~~ 46 (78)
T PF07293_consen 1 MNPIVEFCVSNLASGTDQVYEKLEKDPDI-----DVIEYGCLSYCGPCAKK 46 (78)
T ss_pred CCceEEEcccCchhhhHHHHHHHhcCCCc-----cEEEcChhhhCcCCCCC
Confidence 57888898887644335566777778764 3 234799999999643
No 76
>TIGR03315 Se_ygfK putative selenate reductase, YgfK subunit. Members of this protein family are YgfK, predicted to be one subunit of a three-subunit, molybdopterin-containing selenate reductase. This enzyme is found, typically, in genomic regions associated with xanthine dehydrogenase homologs predicted to belong to the selenium-dependent molybdenum hydroxylases (SDMH). Therefore, the selenate reductase is suggested to play a role in furnishing selenide for SelD, the selenophosphate synthase.
Probab=39.88 E-value=9.6 Score=40.59 Aligned_cols=35 Identities=26% Similarity=0.503 Sum_probs=22.8
Q ss_pred CCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCceeecc
Q 028179 136 LSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYN 194 (212)
Q Consensus 136 LG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYS 194 (212)
|||+.+||.++. .||..+=|| .-+|.=||++|||.
T Consensus 216 hgcp~~eie~i~-------------------~~~~~~k~~-----~~~~k~nptllg~~ 250 (1012)
T TIGR03315 216 HGCPPDEIEAIC-------------------RYLLEEKGL-----HTFVKLNPTLLGYK 250 (1012)
T ss_pred cCCCHHHHHHHH-------------------HHHHhccCC-----ceEEeeCcccccHH
Confidence 688888877763 355544455 35677777777775
No 77
>smart00242 MYSc Myosin. Large ATPases. ATPase; molecular motor. Muscle contraction consists of a cyclical interaction between myosin and actin. The core of the myosin structure is similar in fold to that of kinesin.
Probab=39.71 E-value=70 Score=32.45 Aligned_cols=74 Identities=19% Similarity=0.281 Sum_probs=48.8
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhhhc----CCChhhHHHHHHHHH-hCCCCHHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERKRE----TPELETVSEILGYLR-NLSLSDDDIRK 145 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~~~----v~s~e~i~aklefLk-sLG~Sd~eI~k 145 (212)
.+|...|++.+++|+.+||+.++...|+.-.-++ +|.--|....... +.+.+ .++... =||++.+++.+
T Consensus 236 ~~d~~~f~~~~~al~~lG~~~~e~~~I~~iLaaILhLGni~F~~~~~~~~~~~~~~~~----~l~~~a~LLgv~~~~L~~ 311 (677)
T smart00242 236 IDDAEEFKETLNAMRVLGFSEEEQESIFKILAAILHLGNIEFEEGRNDNAASTVKDKE----ELENAAELLGVDPEELEK 311 (677)
T ss_pred CCHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceeEEecCCCCcccccCCHH----HHHHHHHHhCCCHHHHHH
Confidence 4578999999999999999999887777665454 4444453322111 22222 223333 47999999999
Q ss_pred HHhhc
Q 028179 146 LLKKF 150 (212)
Q Consensus 146 ~vkK~ 150 (212)
++...
T Consensus 312 ~l~~~ 316 (677)
T smart00242 312 ALTKR 316 (677)
T ss_pred Hhccc
Confidence 88753
No 78
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.68 E-value=40 Score=28.90 Aligned_cols=37 Identities=14% Similarity=0.183 Sum_probs=26.7
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhh
Q 028179 126 VSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRN 164 (212)
Q Consensus 126 i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~Lkp 164 (212)
....++-|.+||+++.|+.+++++-=. ..++|+-+|.
T Consensus 145 ~~e~~~aL~~LGy~~~ea~~al~~v~~--~~~~eelir~ 181 (186)
T PRK14600 145 NDDALAALISLGYEKTKAFNAIQKIKP--NLSTQDIIRK 181 (186)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHhhc--CCCHHHHHHH
Confidence 456789999999999999999987611 3344444443
No 79
>PF10440 WIYLD: Ubiquitin-binding WIYLD domain; InterPro: IPR018848 This entry represents a presumed domain which has been predicted to contain three alpha helices. It was named the WIYLD domain based on the pattern of the ost conserved residues []. This domain appears to be specific to plant SET-domain proteins. ; GO: 0018024 histone-lysine N-methyltransferase activity
Probab=39.37 E-value=50 Score=24.27 Aligned_cols=36 Identities=17% Similarity=0.390 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhh
Q 028179 77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWS 113 (212)
Q Consensus 77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr 113 (212)
.+..++....+.|||+.+.+..++.+...+.+.. |.
T Consensus 9 ~R~daA~dam~~lG~~~~~v~~vl~~LL~lY~~n-W~ 44 (65)
T PF10440_consen 9 ERIDAALDAMRQLGFSKKQVRPVLKNLLKLYDGN-WE 44 (65)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHcCC-ch
Confidence 4667888999999999999999999988776655 53
No 80
>PRK14602 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=39.32 E-value=43 Score=29.03 Aligned_cols=44 Identities=27% Similarity=0.394 Sum_probs=31.3
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhhcCce-eecCccchhhhhhhhh
Q 028179 126 VSEILGYLRNLSLSDDDIRKLLKKFPEV-LGCDIEHELRNNVQIL 169 (212)
Q Consensus 126 i~aklefLksLG~Sd~eI~k~vkK~P~I-Lg~SVEe~LkpkveFL 169 (212)
....++-|.+||+++.|+.+++++-..- -..++|+-+|..+..|
T Consensus 155 ~~ea~~AL~~LGy~~~ea~~av~~~~~~~~~~~~e~lir~ALk~l 199 (203)
T PRK14602 155 FRDALAGLANLGYGEEEARPVLKEVLEEEPDLDVGGALRAALKAL 199 (203)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHHhhcCCCCCHHHHHHHHHHHh
Confidence 5677899999999999999999875210 1345566666655554
No 81
>PF11829 DUF3349: Protein of unknown function (DUF3349); InterPro: IPR021784 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 99 to 124 amino acids in length. ; PDB: 2KVC_A 3OL3_B 3OL4_A 2LKY_A.
Probab=38.89 E-value=93 Score=24.41 Aligned_cols=55 Identities=15% Similarity=0.146 Sum_probs=33.4
Q ss_pred ccChHHHHHHHHHHHHh---hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCH
Q 028179 70 TLNDEERKKWEACRQAL---STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSD 140 (212)
Q Consensus 70 ~~~~~~~~~we~~v~~L---~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd 140 (212)
.|++||-. +.+.-| .....+..++..+..+. ....|+++.|.++.+-|...||+-
T Consensus 35 ~Ltd~ev~---~Va~~L~~~~~~~~~~~dI~~~I~~v-------------t~~~P~~~di~RV~~~Laa~GWPl 92 (96)
T PF11829_consen 35 RLTDDEVA---EVAAELAARGDPPVDRIDIGVAITRV-------------TDELPTPEDIERVRARLAAAGWPL 92 (96)
T ss_dssp TS-HHHHH---HHHHHHHHHTSS-BSCCHHHHHHHHH-------------CSS-S-HHHHHHHHHHHHTTT-GC
T ss_pred cCCHHHHH---HHHHHHHhcCCCCCCHHHHHHHHHHH-------------HcCCcCHHHHHHHHHHHHhCCCCC
Confidence 35666443 333444 23334667776666664 256699999999999999999963
No 82
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=38.31 E-value=1.1e+02 Score=25.47 Aligned_cols=82 Identities=21% Similarity=0.180 Sum_probs=46.8
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhh--HHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccch
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELET--VSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHE 161 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~--i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~ 161 (212)
++-+.+|+++.+++-.-.. |++.... +..--.-..+++. --..+.+|+++|+|=++|..++..... ++...
T Consensus 6 evA~~~gvs~~tLRyYe~~--GLl~p~~-r~~~gyR~Y~~~dl~rL~~I~~lr~~G~sL~eI~~ll~~~~~----~~~~~ 78 (172)
T cd04790 6 QLARQFGLSRSTLLYYERI--GLLSPSA-RSESNYRLYGERDLERLEQICAYRSAGVSLEDIRSLLQQPGD----DATDV 78 (172)
T ss_pred HHHHHHCcCHHHHHHHHHC--CCCCCCc-cCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCCh----hHHHH
Confidence 3447889999888665443 5521100 0000000122232 226777889999999999999986543 33345
Q ss_pred hhhhhhhhhhc
Q 028179 162 LRNNVQILGKD 172 (212)
Q Consensus 162 LkpkveFL~~~ 172 (212)
|..+.+.|.++
T Consensus 79 L~~~~~~l~~e 89 (172)
T cd04790 79 LRRRLAELNRE 89 (172)
T ss_pred HHHHHHHHHHH
Confidence 66666666554
No 83
>PF13475 DUF4116: Domain of unknown function (DUF4116)
Probab=37.91 E-value=18 Score=23.18 Aligned_cols=32 Identities=22% Similarity=0.211 Sum_probs=24.6
Q ss_pred HHHHHHHHhhcCceeecCccchhhhhhhhhhhc
Q 028179 140 DDDIRKLLKKFPEVLGCDIEHELRNNVQILGKD 172 (212)
Q Consensus 140 d~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~ 172 (212)
++-+..++++.|.+|.+= .+.||..-||..+-
T Consensus 2 ~e~v~~~v~~~~~~l~~~-~~~lk~D~e~vl~a 33 (49)
T PF13475_consen 2 REFVLEAVKKNGYALQYA-SEELKNDKEFVLKA 33 (49)
T ss_pred HHHHHHHHHhCCHHHHHh-CHHHhCCHHHHHHH
Confidence 455778899999998874 77888888777653
No 84
>PF00063 Myosin_head: Myosin head (motor domain); InterPro: IPR001609 Muscle contraction is caused by sliding between the thick and thin filaments of the myofibril. Myosin is a major component of thick filaments and exists as a hexamer of 2 heavy chains [], 2 alkali light chains, and 2 regulatory light chains. The heavy chain can be subdivided into the N-terminal globular head and the C-terminal coiled-coil rod-like tail, although some forms have a globular region in their C-terminal. There are many cell-specific isoforms of myosin heavy chains, coded for by a multi-gene family []. Myosin interacts with actin to convert chemical energy, in the form of ATP, to mechanical energy []. The 3-D structure of the head portion of myosin has been determined [] and a model for actin-myosin complex has been constructed []. The globular head is well conserved, some highly-conserved regions possibly relating to functional and structural domains []. The rod-like tail starts with an invariant proline residue, and contains many repeats of a 28 residue region, interrupted at 4 regularly-spaced points known as skip residues. Although the sequence of the tail is not well conserved, the chemical character is, hydrophobic, charged and skip residues occuring in a highly ordered and repeated fashion [].; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 1LKX_A 2V26_A 2BKI_A 3L9I_A 2BKH_A 2X51_A 2VB6_A 2VAS_A 1OE9_A 1W8J_A ....
Probab=37.68 E-value=54 Score=32.82 Aligned_cols=78 Identities=21% Similarity=0.276 Sum_probs=48.9
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhh---hcCCChhhHHHHHHHHH-hCCCCHHHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERK---RETPELETVSEILGYLR-NLSLSDDDIRKL 146 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~---~~v~s~e~i~aklefLk-sLG~Sd~eI~k~ 146 (212)
.+|.+.|++-+++|+.|||++++...++.=.-++ +|.--|..... ..+.+.+. ++... =||++.+++.++
T Consensus 231 ~~d~~~f~~l~~al~~lg~~~~e~~~I~~iLaaILhLGni~F~~~~~~~~~~~~~~~~----l~~~a~LLgv~~~~L~~~ 306 (689)
T PF00063_consen 231 IDDAEEFQELKDALKTLGFSDEEIDDIFRILAAILHLGNIEFVEDESDESAEVENSEE----LQKAAELLGVDSEELEKA 306 (689)
T ss_dssp CTHHHHHHHHHHHHHHTT--HHHHHHHHHHHHHHHHHTTSSEEEETTSSSEEESTSHH----HHHHHHHTTS-HHHHHHH
T ss_pred ccCHHHhhhhhhhhccccCchhHHHHHHHHHHHHhhhccccccccccccceeechHHH----HHHhhhhcCCCHHHHHHH
Confidence 4678899999999999999999888777665443 44433444331 12233343 33333 479999999999
Q ss_pred HhhcCcee
Q 028179 147 LKKFPEVL 154 (212)
Q Consensus 147 vkK~P~IL 154 (212)
+.......
T Consensus 307 l~~~~~~~ 314 (689)
T PF00063_consen 307 LTTRTIKV 314 (689)
T ss_dssp HHSEEEES
T ss_pred Hhhccccc
Confidence 97554433
No 85
>KOG4234 consensus TPR repeat-containing protein [General function prediction only]
Probab=37.42 E-value=65 Score=29.39 Aligned_cols=108 Identities=16% Similarity=0.358 Sum_probs=74.5
Q ss_pred HHHHHHHHHHHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHH---hCCCCHHHHHHHHhhc
Q 028179 75 ERKKWEACRQAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLR---NLSLSDDDIRKLLKKF 150 (212)
Q Consensus 75 ~~~~we~~v~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLk---sLG~Sd~eI~k~vkK~ 150 (212)
.+.+||++++.- +.+-+.|-..+.+.+||+-+ .. .++...-|+-+| .+.=+..+.++.+.+-
T Consensus 146 Kl~k~e~aI~dcsKaiel~pty~kAl~RRAeay--------ek------~ek~eealeDyKki~E~dPs~~ear~~i~rl 211 (271)
T KOG4234|consen 146 KLRKWESAIEDCSKAIELNPTYEKALERRAEAY--------EK------MEKYEEALEDYKKILESDPSRREAREAIARL 211 (271)
T ss_pred HhhhHHHHHHHHHhhHhcCchhHHHHHHHHHHH--------Hh------hhhHHHHHHHHHHHHHhCcchHHHHHHHHhc
Confidence 457899999988 89999998888899888622 11 244555555555 3455678999999999
Q ss_pred CceeecCccchhhhh--------hhhhhhccCcCchhHHHHHHhCCceeeccccccc
Q 028179 151 PEVLGCDIEHELRNN--------VQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKG 199 (212)
Q Consensus 151 P~ILg~SVEe~Lkpk--------veFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~Rg 199 (212)
|.++.=. .++||-- =.|..+-+||+.+.+ -++++|.-=+|||.=.|
T Consensus 212 ~~~i~er-nEkmKee~m~kLKdlGN~iL~pFGlStdnF--qmvqd~nTGsySi~fk~ 265 (271)
T KOG4234|consen 212 PPKINER-NEKMKEEMMEKLKDLGNFILSPFGLSTDNF--QMVQDPNTGSYSINFKG 265 (271)
T ss_pred CHHHHHH-HHHHHHHHHHHHHHhhhhhcccccccccce--eeeeCCCCCceeEEecC
Confidence 9998766 4455542 234445567766655 36677877778876554
No 86
>PRK14600 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=37.35 E-value=52 Score=28.23 Aligned_cols=25 Identities=12% Similarity=0.157 Sum_probs=22.7
Q ss_pred HHHHHHHhhhCCCChHHHHHHHHhh
Q 028179 79 WEACRQALSTFNFSTEEEDKILGKA 103 (212)
Q Consensus 79 we~~v~~L~~LGfspe~v~~il~rA 103 (212)
-++++.+|.+||++++++..++.++
T Consensus 145 ~~e~~~aL~~LGy~~~ea~~al~~v 169 (186)
T PRK14600 145 NDDALAALISLGYEKTKAFNAIQKI 169 (186)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 3789999999999999999998876
No 87
>cd03035 ArsC_Yffb Arsenate Reductase (ArsC) family, Yffb subfamily; Yffb is an uncharacterized bacterial protein encoded by the yffb gene, related to the thioredoxin-fold arsenic reductases, ArsC. The structure of Yffb and the conservation of the catalytic cysteine suggest that it is likely to function as a glutathione (GSH)-dependent thiol reductase. ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from GSH via glutaredoxin, through a single catalytic cysteine.
Probab=37.28 E-value=1.1e+02 Score=23.42 Aligned_cols=56 Identities=18% Similarity=0.221 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccC------cCchhHHHHHHhCCceeeccccccc
Q 028179 137 SLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWG------IEGKYLRNLLLRNPKVLGYNVDCKG 199 (212)
Q Consensus 137 G~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vG------L~g~~l~~~I~r~P~ILgYSLE~Rg 199 (212)
++|.+|+..++++.. +++-+..+-.... +.| ++.+++-++|+.+|.+|-..|=..|
T Consensus 35 p~s~~eL~~~l~~~g------~~~li~~~~~~yk-~l~l~~~~~~s~~e~~~~l~~~p~LikRPIi~~~ 96 (105)
T cd03035 35 GLDAATLERWLAKVG------WETLLNKRGTTWR-KLDDAQKAALDAAKAIALMLEHPSLIKRPVLETG 96 (105)
T ss_pred CCCHHHHHHHHHHhC------hHHHHccCchHHH-hCChhhhccCCHHHHHHHHHhCcCeeecceEEeC
Confidence 456777777777654 2444444433333 233 3446677899999999887765444
No 88
>PRK07562 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=37.11 E-value=72 Score=35.07 Aligned_cols=58 Identities=22% Similarity=0.313 Sum_probs=34.5
Q ss_pred HHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCc
Q 028179 82 CRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPE 152 (212)
Q Consensus 82 ~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ 152 (212)
..+.|+.+|++.+.+.++...+.+.. | . ...+. --.+-|+..||++++|.++=.-.|.
T Consensus 715 l~~~L~~lG~~~~~i~~i~~~~~~~G-s--l-----~~~~~-----i~~~~l~~~Gf~~~~~~~~~~~l~~ 772 (1220)
T PRK07562 715 VPEALRTLGYSESQIAEIEAYAVGHG-T--L-----NQAPG-----INHSTLKAKGFTDEKIEKVEAALKS 772 (1220)
T ss_pred HHHHHHHcCCCHHHHHHHHHHhhcCC-C--c-----cCCCC-----CCHHHHhhcCCcHHHHHHHHHHhhh
Confidence 34567888888888888887764431 1 0 11110 0123567789999998875444443
No 89
>PF13414 TPR_11: TPR repeat; PDB: 2HO1_B 2FI7_B 2DBA_A 3Q4A_B 2C2L_D 3Q47_B 3Q49_B 2PL2_B 3IEG_B 2FBN_A ....
Probab=36.87 E-value=44 Score=22.23 Aligned_cols=30 Identities=3% Similarity=0.216 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHh-hhCCCChHHHHHHHHhhh
Q 028179 75 ERKKWEACRQAL-STFNFSTEEEDKILGKAF 104 (212)
Q Consensus 75 ~~~~we~~v~~L-~~LGfspe~v~~il~rA~ 104 (212)
+.++|+++...+ +.+-++|+.+.....++.
T Consensus 15 ~~~~~~~A~~~~~~ai~~~p~~~~~~~~~g~ 45 (69)
T PF13414_consen 15 QQGDYEEAIEYFEKAIELDPNNAEAYYNLGL 45 (69)
T ss_dssp HTTHHHHHHHHHHHHHHHSTTHHHHHHHHHH
T ss_pred HcCCHHHHHHHHHHHHHcCCCCHHHHHHHHH
Confidence 467889999988 688889999887777765
No 90
>KOG4779 consensus Predicted membrane protein [Function unknown]
Probab=36.18 E-value=22 Score=27.04 Aligned_cols=44 Identities=18% Similarity=0.351 Sum_probs=32.3
Q ss_pred HHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHHHhCCcee
Q 028179 131 GYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVL 191 (212)
Q Consensus 131 efLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~IL 191 (212)
.||+.+|||.++- |. .|-+ ++++|+++--|+..+ +.+.+.|-|.
T Consensus 26 RFL~riGws~d~~-------~g-FG~~-q~tiKS~~~~LIrav--------rTvmrvPLI~ 69 (82)
T KOG4779|consen 26 RFLKRIGWSTDQG-------IG-FGED-QPTIKSQLMNLIRAV--------RTVMRVPLII 69 (82)
T ss_pred HHHHHhCcCcccC-------cc-cCCC-CccHHHHHHHHHHHH--------HHHHhcchhh
Confidence 6999999998752 22 5556 788999998888642 6777777654
No 91
>PF01988 VIT1: VIT family; InterPro: IPR008217 Proteins containing this entry have no known function and are predicted to be integral membrane proteins. They include the Ccc1 protein from Saccharomyces cerevisiae (Baker's yeast) (P47818 from SWISSPROT) that may have a role in regulating calcium levels [].
Probab=36.07 E-value=46 Score=28.50 Aligned_cols=26 Identities=15% Similarity=0.111 Sum_probs=22.1
Q ss_pred HHHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 79 WEACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 79 we~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
-+|-++.++..|++++++.++.....
T Consensus 82 ~~el~~iy~~~Gl~~~~a~~i~~~l~ 107 (213)
T PF01988_consen 82 KEELVEIYRAKGLSEEDAEEIAEELS 107 (213)
T ss_pred HHHHHHHHHHCCCCHHHHHHHHHHHH
Confidence 35888999888999999999988864
No 92
>TIGR00084 ruvA Holliday junction DNA helicase, RuvA subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=35.57 E-value=75 Score=27.22 Aligned_cols=25 Identities=20% Similarity=0.275 Sum_probs=22.9
Q ss_pred HHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 80 EACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 80 e~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
++++++|..||++++++.+++.++.
T Consensus 148 ~e~~~aL~~LGy~~~e~~~ai~~~~ 172 (191)
T TIGR00084 148 DELFEALVSLGYKPQEIQQALKKIK 172 (191)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHHHh
Confidence 7899999999999999999998874
No 93
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=35.41 E-value=31 Score=25.86 Aligned_cols=39 Identities=26% Similarity=0.587 Sum_probs=26.4
Q ss_pred HHHHHHHh-----CCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCc
Q 028179 128 EILGYLRN-----LSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGI 175 (212)
Q Consensus 128 aklefLks-----LG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL 175 (212)
.+++||+. -|++-++|.+-+ +++ ++.++..++||.++ |.
T Consensus 51 ~Vl~~i~~~~~~~~Gv~v~~I~~~l-------~~~-~~~v~~al~~L~~e-G~ 94 (102)
T PF08784_consen 51 KVLNFIKQQPNSEEGVHVDEIAQQL-------GMS-ENEVRKALDFLSNE-GH 94 (102)
T ss_dssp HHHHHHHC----TTTEEHHHHHHHS-------TS--HHHHHHHHHHHHHT-TS
T ss_pred HHHHHHHhcCCCCCcccHHHHHHHh-------CcC-HHHHHHHHHHHHhC-Ce
Confidence 44555553 477777777655 556 77899999999976 44
No 94
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=35.38 E-value=1.2e+02 Score=26.66 Aligned_cols=96 Identities=17% Similarity=0.214 Sum_probs=52.2
Q ss_pred cccChHHHHHHHHH-----HHHh-hhCCCChHHHHHHHHhhhhc----cccchhhhhhhhcCCC-hhhHHHHHHHHHhCC
Q 028179 69 ITLNDEERKKWEAC-----RQAL-STFNFSTEEEDKILGKAFGH----IHSAYWSEERKRETPE-LETVSEILGYLRNLS 137 (212)
Q Consensus 69 ~~~~~~~~~~we~~-----v~~L-~~LGfspe~v~~il~rA~gl----~~S~~fr~a~~~~v~s-~e~i~aklefLksLG 137 (212)
+.++.-+.++...+ +++| +.=|...+.+.+|+...-+= .....+.......... ......-++-|.+||
T Consensus 88 aiLs~~~~~~l~~aI~~~d~~~L~k~PGIGkKtAerivleLk~K~~~~~~~~~~~~~~~~~~~~~~~~~~~~v~AL~~LG 167 (201)
T COG0632 88 AILSNLDPEELAQAIANEDVKALSKIPGIGKKTAERIVLELKGKLAAFLKGDGGSPAEDLSLDESSPALEEAVEALVALG 167 (201)
T ss_pred HHHcCCCHHHHHHHHHhcChHhhhcCCCCCHHHHHHHHHHHhhhhhhhcccccccccccccccccchhhhHHHHHHHHcC
Confidence 34444444444444 3466 56789999999988764331 1111110111011111 011222289999999
Q ss_pred CCHHHHHHHHhhcCce-eecCccchhhh
Q 028179 138 LSDDDIRKLLKKFPEV-LGCDIEHELRN 164 (212)
Q Consensus 138 ~Sd~eI~k~vkK~P~I-Lg~SVEe~Lkp 164 (212)
+++.|+.+++++.+.= -+.++++-+|.
T Consensus 168 y~~~e~~~av~~v~~~~~~~~~~~~Ik~ 195 (201)
T COG0632 168 YKEKEIKKAVKKVLKENPDADVEELIKE 195 (201)
T ss_pred CCHHHHHHHHHHHHhcCCCCCHHHHHHH
Confidence 9999999999987754 33444444443
No 95
>PRK14601 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=35.17 E-value=63 Score=27.72 Aligned_cols=25 Identities=28% Similarity=0.279 Sum_probs=22.9
Q ss_pred HHHHHHHhhhCCCChHHHHHHHHhh
Q 028179 79 WEACRQALSTFNFSTEEEDKILGKA 103 (212)
Q Consensus 79 we~~v~~L~~LGfspe~v~~il~rA 103 (212)
.++++++|..||+++.++.+++.++
T Consensus 142 ~~ea~~AL~~LGy~~~ea~~a~~~~ 166 (183)
T PRK14601 142 KSEALAALLTLGFKQEKIIKVLASC 166 (183)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHhc
Confidence 4789999999999999999998876
No 96
>cd01382 MYSc_type_VI Myosin motor domain, type VI myosins. Myosin VI is a monomeric myosin, which moves towards the minus-end of actin filaments, in contrast to most other myosins. It has been implicated in endocytosis, secretion, and cell migration. This catalytic (head) domain has ATPase activity and belongs to the larger group of P-loop NTPases. Myosins are actin-dependent molecular motors that play important roles in muscle contraction, cell motility, and organelle transport. The head domain is a molecular motor, which utilizes ATP hydrolysis to generate directed movement toward the minus end along actin filaments. A cyclical interaction between myosin and actin provides the driving force. Rates of ATP hydrolysis and consequently the speed of movement along actin filaments vary widely, from about 0.04 micrometer per second for myosin I to 4.5 micrometer per second for myosin II in skeletal muscle. Myosin II moves in discrete steps about 5-10 nm long and generates 1-5 piconewtons of
Probab=35.15 E-value=1e+02 Score=31.63 Aligned_cols=74 Identities=16% Similarity=0.212 Sum_probs=48.0
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhhh----cC--CChhhHHHHHHHHHhCCCCHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERKR----ET--PELETVSEILGYLRNLSLSDDDIR 144 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~~----~v--~s~e~i~aklefLksLG~Sd~eI~ 144 (212)
.+|.+.|++.+++|+.+||++++...++.-.-++ +|--.|...... .+ .+.+.+ .++.- =||++.+++.
T Consensus 258 ~dD~~~f~~~~~Al~~lg~s~~e~~~i~~iLaaILhLGni~F~~~~~~~~~~~~~~~~~~~l-~~~a~--LLgv~~~~L~ 334 (717)
T cd01382 258 LDDYGDFQRMCVALKKIGLDDTEKLDLFRVVAGVLHLGNIDFEEAGSTSGGCNVKNQSEQSL-EYCAE--LLGLDQDDLR 334 (717)
T ss_pred CcHHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhcCceeEeccCCCCCcceecCCCHHHH-HHHHH--HcCCCHHHHH
Confidence 3678999999999999999999988877665554 343334331100 11 122222 22222 4899999999
Q ss_pred HHHhh
Q 028179 145 KLLKK 149 (212)
Q Consensus 145 k~vkK 149 (212)
+++..
T Consensus 335 ~~l~~ 339 (717)
T cd01382 335 VSLTT 339 (717)
T ss_pred HHHhh
Confidence 98875
No 97
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=35.03 E-value=1.5e+02 Score=20.34 Aligned_cols=57 Identities=9% Similarity=0.097 Sum_probs=34.2
Q ss_pred HHhhhCCCChHHHHHHHHhhhhcc-------ccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHh
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHI-------HSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLK 148 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~-------~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vk 148 (212)
++-+.+|+++..++.--.+ .|+. +..+|.... .. .-..+..|+..|+|-++|.++++
T Consensus 5 e~A~~~gVs~~tlr~ye~~-~gl~~~~r~~~g~R~yt~~d------i~-~l~~i~~l~~~g~~l~~i~~~l~ 68 (68)
T cd04763 5 EVALLTGIKPHVLRAWERE-FGLLKPQRSDGGHRLFNDAD------ID-RILEIKRWIDNGVQVSKVKKLLS 68 (68)
T ss_pred HHHHHHCcCHHHHHHHHHh-cCCCCCCcCCCCCcccCHHH------HH-HHHHHHHHHHcCCCHHHHHHHhC
Confidence 4457888888888765333 2332 222333332 11 22446666779999999998864
No 98
>PRK09875 putative hydrolase; Provisional
Probab=35.01 E-value=41 Score=30.66 Aligned_cols=29 Identities=21% Similarity=0.385 Sum_probs=23.8
Q ss_pred hhHHHHHHHHHhCCCCHHHHHHHHhhcCc
Q 028179 124 ETVSEILGYLRNLSLSDDDIRKLLKKFPE 152 (212)
Q Consensus 124 e~i~aklefLksLG~Sd~eI~k~vkK~P~ 152 (212)
..+...+..|+..|+|+++|.+++..+|.
T Consensus 260 ~i~~~~ip~L~~~Gvse~~I~~m~~~NP~ 288 (292)
T PRK09875 260 YLLTTFIPQLRQSGFSQADVDVMLRENPS 288 (292)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHCHH
Confidence 44677788888889999999999988884
No 99
>PRK14981 DNA-directed RNA polymerase subunit F; Provisional
Probab=34.30 E-value=2.3e+02 Score=22.27 Aligned_cols=34 Identities=12% Similarity=0.185 Sum_probs=23.2
Q ss_pred ccChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc
Q 028179 70 TLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGH 106 (212)
Q Consensus 70 ~~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl 106 (212)
.++.+.+++++++-.|-+. +|+++.+++....+.
T Consensus 29 els~~~~ktl~y~~kFsk~---~~e~a~elve~L~~~ 62 (112)
T PRK14981 29 ELSYELRRTLDYLNRFSKL---DPEDAEELVEELLEL 62 (112)
T ss_pred chhHHHHHHHHHHHHHhCC---CHHHHHHHHHHHHHc
Confidence 5677777777777766543 677777777776443
No 100
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=33.47 E-value=63 Score=24.74 Aligned_cols=57 Identities=21% Similarity=0.346 Sum_probs=38.2
Q ss_pred CChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHH
Q 028179 121 PELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLL 184 (212)
Q Consensus 121 ~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I 184 (212)
.+.+.+..-++.|+.+|+++.|+..++.-.|. + .+.++.-++-+.+ .++.+++.++|
T Consensus 54 ~~~e~~~~l~~~L~~~~L~~~E~~qi~Nl~P~----~-~~El~~ii~~~~~--r~~ee~l~~iL 110 (117)
T PF03874_consen 54 QNPESIKELREELKKFGLTEFEILQIINLRPT----T-AVELRAIIESLES--RFSEEDLEEIL 110 (117)
T ss_dssp SSHHHHHHHHHHHTTSTS-HHHHHHHHHH--S----S-HHHHHHHSTTGTT--TSTHHHHHHHH
T ss_pred CCHHHHHHHHHHHhcccCCHHHHHHHhcCCCC----C-HHHHHHHHHHhcc--CCCHHHHHHHH
Confidence 45677888889999999999999999999995 3 3356666666654 35555554444
No 101
>PF13543 KSR1-SAM: SAM like domain present in kinase suppressor RAS 1
Probab=33.20 E-value=1.3e+02 Score=24.84 Aligned_cols=59 Identities=20% Similarity=0.255 Sum_probs=37.5
Q ss_pred HHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcC-CChhhHHHHHHHHHhCCCCHHHHHHHHh
Q 028179 77 KKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRET-PELETVSEILGYLRNLSLSDDDIRKLLK 148 (212)
Q Consensus 77 ~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v-~s~e~i~aklefLksLG~Sd~eI~k~vk 148 (212)
...-+-...|...|++|+.+..++.+...+ .... ++++ ..-+.|...|.+++|..++.+
T Consensus 64 ~~yP~l~~WL~vVgl~~~~i~~i~~~~~tL----------e~Llemsd~---el~~~l~~~g~~~EE~rRL~~ 123 (129)
T PF13543_consen 64 NSYPSLRQWLRVVGLRPESIQAILSKVLTL----------EALLEMSDE---ELKEILNRCGAREEECRRLCR 123 (129)
T ss_pred ccCCcHHHHhhhcCCCHHHHHHHHHhhcCH----------HHHHhCCHH---HHHHHHHHhCCCHHHHHHHHH
Confidence 344555666788899999998887764211 0111 4555 334455568888888888765
No 102
>PF02631 RecX: RecX family; InterPro: IPR003783 RecX is a putative bacterial regulatory protein []. The gene encoding RecX is found downstream of recA, and it is suggested that the RecX protein might be regulator of RecA activity by interaction with the RecA protein or filament [].; GO: 0006282 regulation of DNA repair; PDB: 3DFG_A 3D5L_B 3C1D_B 3E3V_A.
Probab=33.18 E-value=1.4e+02 Score=22.86 Aligned_cols=28 Identities=18% Similarity=0.385 Sum_probs=22.1
Q ss_pred ChhhHHHHHHHHHhCCCCHHHHHHHHhh
Q 028179 122 ELETVSEILGYLRNLSLSDDDIRKLLKK 149 (212)
Q Consensus 122 s~e~i~aklefLksLG~Sd~eI~k~vkK 149 (212)
......+.+.||..-|||.+.|..++.+
T Consensus 91 ~~~~~~K~~~~L~rrGF~~~~i~~vi~~ 118 (121)
T PF02631_consen 91 DRKRKQKLIRFLMRRGFSYDVIRRVISE 118 (121)
T ss_dssp CHHHHHHHHHHHHHTT--HHHHHHHCHH
T ss_pred CHHHHHHHHHHHHHCCCCHHHHHHHHhh
Confidence 4566778889999999999999999875
No 103
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=33.15 E-value=45 Score=23.35 Aligned_cols=22 Identities=9% Similarity=0.392 Sum_probs=18.4
Q ss_pred HHHHHHH-hCCCCHHHHHHHHhh
Q 028179 128 EILGYLR-NLSLSDDDIRKLLKK 149 (212)
Q Consensus 128 aklefLk-sLG~Sd~eI~k~vkK 149 (212)
.-+.|+. .||+|++++..+|++
T Consensus 21 ~ev~ywa~~~gvt~~~L~~AV~~ 43 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLREAVRA 43 (57)
T ss_pred HHHHHHHHHHCcCHHHHHHHHHH
Confidence 4566776 999999999999986
No 104
>KOG0011 consensus Nucleotide excision repair factor NEF2, RAD23 component [Replication, recombination and repair]
Probab=32.63 E-value=37 Score=32.21 Aligned_cols=91 Identities=21% Similarity=0.294 Sum_probs=59.9
Q ss_pred HHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeec---
Q 028179 80 EACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGC--- 156 (212)
Q Consensus 80 e~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~--- 156 (212)
|..|.-+-..|...|++.+.++-+| -+++ +-||||- -|++++.-.....+.|...+-
T Consensus 136 e~~V~~Im~MGy~re~V~~AlRAaf----------------NNPe---RAVEYLl-~GIP~~~~~~~~~~~~~~~~~~p~ 195 (340)
T KOG0011|consen 136 EQTVQQIMEMGYDREEVERALRAAF----------------NNPE---RAVEYLL-NGIPEDAEVPEPEKSTAAAAELPA 195 (340)
T ss_pred HHHHHHHHHhCccHHHHHHHHHHhh----------------CChh---hhHHHHh-cCCcccccCCcccCCcccCCCCCC
Confidence 6667778889999999988887775 1334 8889986 377765333333333333332
Q ss_pred ---------C--ccchhhhhhhhhhhccCcCchhHHHHHHhCCceee
Q 028179 157 ---------D--IEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLG 192 (212)
Q Consensus 157 ---------S--VEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILg 192 (212)
. +++.-....+||.+.--| ..++++|-+||.+|-
T Consensus 196 ~~~p~~~~~~~~~~~~~~~~l~fLr~~~qf--~~lR~~iqqNP~ll~ 240 (340)
T KOG0011|consen 196 NAQPLDLFPQGAVEASGGDPLEFLRNQPQF--QQLRQMIQQNPELLH 240 (340)
T ss_pred CCChhhcCCccchhhhcCCchhhhhccHHH--HHHHHHHhhCHHHHH
Confidence 1 344444668899875443 578899999998874
No 105
>PRK13344 spxA transcriptional regulator Spx; Reviewed
Probab=32.60 E-value=1.3e+02 Score=24.07 Aligned_cols=58 Identities=17% Similarity=0.245 Sum_probs=32.3
Q ss_pred CCHHHHHHHHhhcCceeecCccchhhhhhhhhhhcc-----CcCchhHHHHHHhCCceeecccccccc
Q 028179 138 LSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDW-----GIEGKYLRNLLLRNPKVLGYNVDCKGD 200 (212)
Q Consensus 138 ~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~v-----GL~g~~l~~~I~r~P~ILgYSLE~Rg~ 200 (212)
.+.+++..++++.. .++++-+..+-.+..+ . .++.+++-++|+.+|.+|-..|=..|+
T Consensus 37 ~s~~eL~~~l~~~~----~~~~~lin~~~~~~k~-L~~~~~~ls~~e~i~ll~~~P~LikRPIv~~~~ 99 (132)
T PRK13344 37 LTKEEILAILTKTE----NGIESIVSSKNRYAKA-LDCDIEELSVNEVIDLIQENPRILKSPILIDDK 99 (132)
T ss_pred CCHHHHHHHHHHhC----CCHHHhhccCcHHHHh-CCcchhcCCHHHHHHHHHhCccceeCcEEEeCC
Confidence 46677777777642 2223333333333321 2 244466678888888888776654443
No 106
>COG5457 Uncharacterized conserved small protein [Function unknown]
Probab=32.31 E-value=46 Score=24.31 Aligned_cols=19 Identities=26% Similarity=0.347 Sum_probs=17.0
Q ss_pred HHHHhCCCCHHHHHHHHhh
Q 028179 131 GYLRNLSLSDDDIRKLLKK 149 (212)
Q Consensus 131 efLksLG~Sd~eI~k~vkK 149 (212)
+.|+.+|+|+.|+...+.|
T Consensus 41 ~~L~DiGisR~d~~~e~~k 59 (63)
T COG5457 41 HLLSDIGISRADIEAEAAK 59 (63)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 5678999999999999887
No 107
>PHA02591 hypothetical protein; Provisional
Probab=31.90 E-value=74 Score=24.54 Aligned_cols=39 Identities=18% Similarity=0.235 Sum_probs=30.8
Q ss_pred hhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHH
Q 028179 102 KAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLL 147 (212)
Q Consensus 102 rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~v 147 (212)
+..+..++.||-| |++.+.....-|..+|+|..+|+..+
T Consensus 31 k~vqv~~~ryfi~-------~~dd~~~vA~eL~eqGlSqeqIA~~L 69 (83)
T PHA02591 31 KVVQVGQTRYFVE-------SEDDLISVTHELARKGFTVEKIASLL 69 (83)
T ss_pred HhheeCCEEEEEe-------ccchHHHHHHHHHHcCCCHHHHHHHh
Confidence 3335678888844 55888899999999999999999873
No 108
>cd03034 ArsC_ArsC Arsenate Reductase (ArsC) family, ArsC subfamily; arsenic reductases similar to that encoded by arsC on the R733 plasmid of Escherichia coli. E. coli ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], the first step in the detoxification of arsenic, using reducing equivalents derived from glutathione (GSH) via glutaredoxin (GRX). ArsC contains a single catalytic cysteine, within a thioredoxin fold, that forms a covalent thiolate-As(V) intermediate, which is reduced by GRX through a mixed GSH-arsenate intermediate. This family of predominantly bacterial enzymes is unrelated to two other families of arsenate reductases which show similarity to low-molecular-weight acid phosphatases and phosphotyrosyl phosphatases.
Probab=31.73 E-value=1.6e+02 Score=22.56 Aligned_cols=60 Identities=18% Similarity=0.253 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHhhcCceeecCccchhhhhhhhhhh----ccCcCchhHHHHHHhCCceeecccccccc
Q 028179 137 SLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGK----DWGIEGKYLRNLLLRNPKVLGYNVDCKGD 200 (212)
Q Consensus 137 G~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~----~vGL~g~~l~~~I~r~P~ILgYSLE~Rg~ 200 (212)
+++.+|+..++++.+ .++++-+..+-.-..+ .-+++.++.-++|+.+|.+|-..|=-.|+
T Consensus 35 ~~t~~el~~~l~~~~----~~~~~lin~~~~~y~~l~~~~~~ls~~e~i~ll~~~P~LikRPIi~~~~ 98 (112)
T cd03034 35 PPTAAELRELLAKLG----ISPRDLLRTKEAPYKELGLADPELSDEELIDAMAAHPILIERPIVVTGD 98 (112)
T ss_pred CcCHHHHHHHHHHcC----CCHHHHHhcCCchHHHcCCCccCCCHHHHHHHHHhCcCcccCCEEEECC
Confidence 456777777777654 2333333333222221 12455566778999999998888755444
No 109
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=31.72 E-value=2.1e+02 Score=21.01 Aligned_cols=61 Identities=8% Similarity=0.028 Sum_probs=35.4
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhh--HHHHHHHHHh-CCCCHHHHHHHHh
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELET--VSEILGYLRN-LSLSDDDIRKLLK 148 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~--i~aklefLks-LG~Sd~eI~k~vk 148 (212)
++-+.+|+++..++.-... |++.. .+.....-..+.+. .-..+..|+. +|++-++|..++.
T Consensus 6 e~A~~~gvs~~tLr~ye~~--Gli~p--~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 6 VAAELSGMHPQTLRLYERL--GLLSP--SRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred HHHHHHCcCHHHHHHHHHC--CCcCC--CcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3447888999888777553 55321 01100000122232 3345666665 9999999999987
No 110
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=31.22 E-value=90 Score=21.13 Aligned_cols=31 Identities=6% Similarity=0.054 Sum_probs=24.8
Q ss_pred cccChHHHHHHHHHHHHhhhCCCChHHHHHHH
Q 028179 69 ITLNDEERKKWEACRQALSTFNFSTEEEDKIL 100 (212)
Q Consensus 69 ~~~~~~~~~~we~~v~~L~~LGfspe~v~~il 100 (212)
...+++|-..+.......+ .||+++++.+++
T Consensus 37 r~yt~~~v~~l~~i~~l~~-~g~~l~~i~~~~ 67 (68)
T cd01104 37 RLYSEADVARLRLIRRLTS-EGVRISQAAALA 67 (68)
T ss_pred eecCHHHHHHHHHHHHHHH-CCCCHHHHHHHh
Confidence 4678888888877776666 999999998775
No 111
>PRK13019 clpS ATP-dependent Clp protease adaptor; Reviewed
Probab=30.81 E-value=95 Score=24.01 Aligned_cols=62 Identities=16% Similarity=0.085 Sum_probs=45.4
Q ss_pred cChHHHHHHHHHH-HHhh-hCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCC
Q 028179 71 LNDEERKKWEACR-QALS-TFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLS 139 (212)
Q Consensus 71 ~~~~~~~~we~~v-~~L~-~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~S 139 (212)
|=++|--++++++ .+|+ .+|.+.+.+..+...+..- |.+ . .-+-..|....+.+-|...|++
T Consensus 26 L~NDd~~t~dfVi~~vl~~vf~~s~~~A~~iml~vH~~-G~a-----v-v~~~~~E~AE~~~~~l~~~glt 89 (94)
T PRK13019 26 VLNDDFNTFEHVVNCLLKAIPGMSEDRAWRLMITAHKE-GSA-----V-VWVGPLEQAELYHQQLTDAGLT 89 (94)
T ss_pred EEcCCCCCHHHHHHHHHHHhcCCCHHHHHHHHHHHhcC-CcE-----E-EEEecHHHHHHHHHHHHHcccc
Confidence 5667788899999 5666 6899999999999988632 211 1 1113457788899999999875
No 112
>cd08815 Death_TNFRSF25_DR3 Death domain of Tumor Necrosis Factor Receptor superfamily 25. Death Domain (DD) found in Tumor Necrosis Factor (TNF) receptor superfamily 25 (TNFRSF25), also known as TRAMP (TNF receptor-related apoptosis-mediating protein), LARD, APO-3, WSL-1, or DR3 (Death Receptor-3). TNFRSF25 is primarily expressed in T cells, is activated by binding to its ligand TL1A, and plays an important role in T-cell function. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=30.60 E-value=44 Score=25.35 Aligned_cols=19 Identities=21% Similarity=0.473 Sum_probs=14.6
Q ss_pred HHHHHHHhCCCCHHHHHHH
Q 028179 128 EILGYLRNLSLSDDDIRKL 146 (212)
Q Consensus 128 aklefLksLG~Sd~eI~k~ 146 (212)
.-=+|++.||+|+-+|..+
T Consensus 13 ~wk~F~R~LGLsdn~Ie~~ 31 (77)
T cd08815 13 RWKEFVRTLGLREAEIEAV 31 (77)
T ss_pred HHHHHHHHcCCcHhHHHHH
Confidence 3347899999999987654
No 113
>PF03394 Pox_E8: Poxvirus E8 protein; InterPro: IPR005057 This family of poxvirus E8 proteins have no known function.
Probab=30.45 E-value=21 Score=32.03 Aligned_cols=27 Identities=11% Similarity=0.212 Sum_probs=23.6
Q ss_pred eecCccchhhhhhhhhhhccCcCchhH
Q 028179 154 LGCDIEHELRNNVQILGKDWGIEGKYL 180 (212)
Q Consensus 154 Lg~SVEe~LkpkveFL~~~vGL~g~~l 180 (212)
=|+||-.++.|-||||+++.|++.+++
T Consensus 213 Pg~SvTTKiTP~VEyLM~KL~l~k~dv 239 (242)
T PF03394_consen 213 PGLSVTTKITPGVEYLMNKLNLTKEDV 239 (242)
T ss_pred CCceeeeccCHHHHHHHHHhCCCccce
Confidence 388999999999999999999986554
No 114
>PTZ00014 myosin-A; Provisional
Probab=30.24 E-value=1.4e+02 Score=31.36 Aligned_cols=78 Identities=14% Similarity=0.168 Sum_probs=49.1
Q ss_pred hHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhc--cccchhhhhhh-----hcCCChhhHHHHHHHHH-hCCCCHHHHH
Q 028179 73 DEERKKWEACRQALSTFNFSTEEEDKILGKAFGH--IHSAYWSEERK-----RETPELETVSEILGYLR-NLSLSDDDIR 144 (212)
Q Consensus 73 ~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~-----~~v~s~e~i~aklefLk-sLG~Sd~eI~ 144 (212)
-+|.+.|++..++++.+||++++...++.-.-++ +|--.|..... ......+.. ..++... =||++.+++.
T Consensus 325 ~dD~~~f~~~~~A~~~lg~s~~e~~~If~ilaaILhLGNi~F~~~~~~~~~~~~~i~~~~~-~~l~~~a~LLgv~~~~L~ 403 (821)
T PTZ00014 325 IDDVKDFEEVMESFDSMGLSESQIEDIFSILSGVLLLGNVEIEGKEEGGLTDAAAISDESL-EVFNEACELLFLDYESLK 403 (821)
T ss_pred CchHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHhhcceeEeccccCCCCCceeccCCCH-HHHHHHHHHhCCCHHHHH
Confidence 3678999999999999999999988887665454 44444443211 111111110 1222222 4799999999
Q ss_pred HHHhhcC
Q 028179 145 KLLKKFP 151 (212)
Q Consensus 145 k~vkK~P 151 (212)
+++...-
T Consensus 404 ~~L~~~~ 410 (821)
T PTZ00014 404 KELTVKV 410 (821)
T ss_pred HHhhceE
Confidence 9887543
No 115
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=30.15 E-value=58 Score=24.97 Aligned_cols=24 Identities=21% Similarity=0.183 Sum_probs=20.8
Q ss_pred HHHHHHhCCCCHHHHHHHHhhcCc
Q 028179 129 ILGYLRNLSLSDDDIRKLLKKFPE 152 (212)
Q Consensus 129 klefLksLG~Sd~eI~k~vkK~P~ 152 (212)
--+|.+.||+|+.+|..+-..+|.
T Consensus 22 Wk~laR~LGLse~~I~~i~~~~~~ 45 (96)
T cd08315 22 WNRLMRQLGLSENEIDVAKANERV 45 (96)
T ss_pred HHHHHHHcCCCHHHHHHHHHHCCC
Confidence 345778999999999999999997
No 116
>PF11626 Rap1_C: TRF2-interacting telomeric protein/Rap1 - C terminal domain; InterPro: IPR021661 This family of proteins represents the C-terminal domain of the protein Rap-1, which plays a distinct role in silencing at the silent mating-type loci and telomeres []. The Rap-1 C terminus adopts an all-helical fold. Rap1 carries out its function by recruiting the Sir3 and Sir4 proteins to chromatin via its C-terminal domain []. ; PDB: 3K6G_C 3CZ6_A 3OWT_A.
Probab=30.08 E-value=1.2e+02 Score=22.46 Aligned_cols=70 Identities=23% Similarity=0.267 Sum_probs=38.1
Q ss_pred HHHHHHhhhCCCChHHHHHHHHhhhh----c--cccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCce
Q 028179 80 EACRQALSTFNFSTEEEDKILGKAFG----H--IHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEV 153 (212)
Q Consensus 80 e~~v~~L~~LGfspe~v~~il~rA~g----l--~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~I 153 (212)
+.+..+|..++.++..+...+...+. + -..++|..+....+. +-..+++.++++|+
T Consensus 12 ~~v~~aL~~tSgd~~~a~~~vl~~l~~g~~~P~n~~GiWT~eDD~~L~---------------~~~~~~~~~L~~kh--- 73 (87)
T PF11626_consen 12 EFVTHALYATSGDPELARRFVLNFLQAGKGIPDNMPGIWTPEDDEMLR---------------SGDKDDIERLIKKH--- 73 (87)
T ss_dssp HHHHHHHHHTTTBHHHHHHHHHHCHCHTTSS-TT-TT---HHHHHHHT---------------S--HHHHHHHHHHH---
T ss_pred HHHHHHHHHhCCCHHHHHHHHHHHHHcCCCCCCCCCCCcCHHHHHHHH---------------cCCHHHHHHHHHHh---
Confidence 35566777777777777663333211 1 123455555422221 12678888888887
Q ss_pred eecCccchhhhhhhhhhh
Q 028179 154 LGCDIEHELRNNVQILGK 171 (212)
Q Consensus 154 Lg~SVEe~LkpkveFL~~ 171 (212)
+ .+++..+.+||.+
T Consensus 74 ---G-~~~i~~R~~FL~k 87 (87)
T PF11626_consen 74 ---G-EERIERRKEFLEK 87 (87)
T ss_dssp -----HHHHHHHHHHHT-
T ss_pred ---C-HHHHHHHHHHHhC
Confidence 4 5688888888864
No 117
>PF11372 DUF3173: Domain of unknown function (DUF3173); InterPro: IPR021512 This family of proteins with unknown function appears to be restricted to Firmicutes.
Probab=29.78 E-value=76 Score=22.92 Aligned_cols=38 Identities=18% Similarity=0.323 Sum_probs=30.0
Q ss_pred HHhhhCCCChHHHHHHHHhhhhc---cccchhhhhhhhcCC
Q 028179 84 QALSTFNFSTEEEDKILGKAFGH---IHSAYWSEERKRETP 121 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl---~~S~~fr~a~~~~v~ 121 (212)
+-|-.|||++-.++.+++.|-.+ .|-++|.+-+...+|
T Consensus 7 ~dLi~lGf~~~tA~~IIrqAK~~lV~~G~~~Y~nkRlg~VP 47 (59)
T PF11372_consen 7 KDLIELGFSESTARDIIRQAKALLVQKGFSFYNNKRLGRVP 47 (59)
T ss_pred HHHHHcCCCHHHHHHHHHHHHHHHHHcCCCcccCCccCccc
Confidence 45667899999999999999776 577778777755555
No 118
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=29.50 E-value=2.1e+02 Score=20.35 Aligned_cols=53 Identities=19% Similarity=0.251 Sum_probs=36.7
Q ss_pred ccChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCC
Q 028179 70 TLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSL 138 (212)
Q Consensus 70 ~~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~ 138 (212)
.|.+-|++-.+...++...=|.+| ++++| ++++|+. |..++..-|+-|+.-|+
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~P-t~rEI-a~~~g~~--------------S~~tv~~~L~~Le~kG~ 55 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPP-TVREI-AEALGLK--------------STSTVQRHLKALERKGY 55 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS----HHHH-HHHHTSS--------------SHHHHHHHHHHHHHTTS
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCC-CHHHH-HHHhCCC--------------ChHHHHHHHHHHHHCcC
Confidence 467788889999999999999999 66666 4444443 45778888888888886
No 119
>PHA03004 putative membrane protein; Provisional
Probab=29.08 E-value=23 Score=32.24 Aligned_cols=27 Identities=11% Similarity=0.199 Sum_probs=23.6
Q ss_pred eecCccchhhhhhhhhhhccCcCchhH
Q 028179 154 LGCDIEHELRNNVQILGKDWGIEGKYL 180 (212)
Q Consensus 154 Lg~SVEe~LkpkveFL~~~vGL~g~~l 180 (212)
=|.||-.++.|.||||+++.|++.+++
T Consensus 241 Pg~SvTTKITPaVEyLM~KL~l~k~dv 267 (270)
T PHA03004 241 PGLSVTTKITPAVEYLMDKLNLTKEDV 267 (270)
T ss_pred CCceeeeccCHHHHHHHHHhCCCccce
Confidence 378999999999999999999986554
No 120
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=28.63 E-value=2e+02 Score=22.51 Aligned_cols=65 Identities=15% Similarity=0.094 Sum_probs=36.8
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhh--HHHHHHHHHhCCCCHHHHHHHHhhcC
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELET--VSEILGYLRNLSLSDDDIRKLLKKFP 151 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~--i~aklefLksLG~Sd~eI~k~vkK~P 151 (212)
++-+.+|+++.+++ ...+- |++..+. +..--.-.-+++. .-..|..|+.+|||-+||..++...-
T Consensus 4 e~a~~~gvs~~tlR-~Ye~~-GLl~~~~-r~~~g~R~Y~~~~l~~l~~I~~l~~~G~sl~eI~~~l~~~~ 70 (124)
T TIGR02051 4 ELAKAAGVNVETIR-YYERK-GLLPEPD-RPEGGYRRYPEETVKRLRFIKRAQELGFSLEEIGGLLGLVD 70 (124)
T ss_pred HHHHHHCcCHHHHH-HHHHC-CCCCCCc-cCCCCCEeECHHHHHHHHHHHHHHHCCCCHHHHHHHHhccc
Confidence 44578899999884 33443 5532110 0000000011222 22567778899999999999997543
No 121
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=28.57 E-value=82 Score=23.62 Aligned_cols=81 Identities=16% Similarity=0.099 Sum_probs=45.5
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhH--HHHHHHHHhCCCCHHHHHHHHhhcCceeecCccch
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETV--SEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHE 161 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i--~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~ 161 (212)
++-+.+|+++.+++--- + .|++..+. +..--.-.-+++.+ -..+..|+.+|+|-+||..++..... ++.+.
T Consensus 5 eva~~~gvs~~tlR~ye-~-~Gll~p~~-r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~~~----~~~~~ 77 (96)
T cd04788 5 ELARRTGLSVRTLHHYD-H-IGLLSPSQ-RTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGPDF----DPLEL 77 (96)
T ss_pred HHHHHHCcCHHHHHHHH-H-CCCCCCCc-cCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCCCh----hHHHH
Confidence 34467888888885543 3 24432210 00000011233433 35677888999999999999986542 33445
Q ss_pred hhhhhhhhhh
Q 028179 162 LRNNVQILGK 171 (212)
Q Consensus 162 LkpkveFL~~ 171 (212)
|..+.+-|..
T Consensus 78 l~~~~~~l~~ 87 (96)
T cd04788 78 LRRQLARLEE 87 (96)
T ss_pred HHHHHHHHHH
Confidence 5555555544
No 122
>TIGR02014 BchZ chlorophyllide reductase subunit Z. This model represents the Z subunit of the three-subunit enzyme, (bacterio)chlorophyllide reductase. This enzyme is responsible for the reduction of the chlorin B-ring and is closely related to the protochlorophyllide reductase complex which reduces the D-ring. Both of these complexes in turn are homologous to nitrogenase.
Probab=28.26 E-value=62 Score=31.50 Aligned_cols=42 Identities=19% Similarity=0.326 Sum_probs=36.4
Q ss_pred hCCCC---HHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcC
Q 028179 135 NLSLS---DDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIE 176 (212)
Q Consensus 135 sLG~S---d~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~ 176 (212)
++-|+ +.++.++|++.|.+.+.|.-.+||.+.|-+-.+-|.+
T Consensus 417 ~~~w~~~a~~~l~~~~~~~p~~~r~~~~~~~~~~~e~~a~~~~~~ 461 (468)
T TIGR02014 417 PLPWDPEANAILDRIVEKAPVISRISAARELRDAAENLAASAGAD 461 (468)
T ss_pred CCCCCHHHHHHHHhhhhhCCeEEEecccchHHHHHHHHHHHcCCC
Confidence 45777 4678899999999999999999999999998888874
No 123
>PF06576 DUF1133: Protein of unknown function (DUF1133); InterPro: IPR010557 This family consists of a number of hypothetical proteins from Escherichia coli O157:H7 and Salmonella typhi. The function of this family is unknown.
Probab=28.04 E-value=80 Score=27.45 Aligned_cols=42 Identities=10% Similarity=0.231 Sum_probs=34.6
Q ss_pred ccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhh
Q 028179 108 HSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKK 149 (212)
Q Consensus 108 ~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK 149 (212)
+.+||.+.....-.++..|...+.-|+.-|++.+|+...++.
T Consensus 42 ~g~mfnqLl~s~kitKtaI~~aLr~mkKsGi~k~EL~~~~~e 83 (176)
T PF06576_consen 42 GGNMFNQLLASKKITKTAINEALRRMKKSGISKPELEAFLRE 83 (176)
T ss_pred hhhHHHHHHhcccccHHHHHHHHHHHHHhcCCcHHHHHHHHH
Confidence 456777777666677888999999999999999999998764
No 124
>PHA02277 hypothetical protein
Probab=27.96 E-value=3.7e+02 Score=22.62 Aligned_cols=20 Identities=15% Similarity=0.321 Sum_probs=16.1
Q ss_pred HHHHH-hCCCCHHHHHHHHhh
Q 028179 130 LGYLR-NLSLSDDDIRKLLKK 149 (212)
Q Consensus 130 lefLk-sLG~Sd~eI~k~vkK 149 (212)
...++ .||++++.+.+++.|
T Consensus 85 ~~iMeDELgi~eek~~KA~~k 105 (150)
T PHA02277 85 MIIMEDELGVTQEKVGKAKDK 105 (150)
T ss_pred HHHHHHHhCCCHHHHHHHHHH
Confidence 34455 899999999999876
No 125
>PF13926 DUF4211: Domain of unknown function (DUF4211)
Probab=27.51 E-value=83 Score=25.55 Aligned_cols=83 Identities=19% Similarity=0.208 Sum_probs=53.0
Q ss_pred hhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecC---ccchhhhhhhhhhhccCcCchhHHHHHHhCCceeecccc--c
Q 028179 123 LETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCD---IEHELRNNVQILGKDWGIEGKYLRNLLLRNPKVLGYNVD--C 197 (212)
Q Consensus 123 ~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~S---VEe~LkpkveFL~~~vGL~g~~l~~~I~r~P~ILgYSLE--~ 197 (212)
.+..+..|++|.+.-+.++-+..+..+.=+....+ ||+.+...-+=|.....+ ...+...|..+|.+--..++ .
T Consensus 37 k~~F~~~ve~lv~~aldp~f~~~l~~~~de~fl~a~~~id~~~~~~~~~l~~ss~W-~~~f~~aL~~~P~l~v~~~~~~~ 115 (153)
T PF13926_consen 37 KEHFKIYVEWLVSNALDPDFLQELEDERDEYFLPALKKIDDELQGRKDSLLSSSAW-KPDFKKALETYPELSVTEISYHT 115 (153)
T ss_pred HHHHHHHHHHHHHHHcCHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhceeeeccC-CHHHHHHHHHCCCeEEEecCCCC
Confidence 35667788888877777777777764433333333 344566555555554445 36688999999998666665 4
Q ss_pred ccccccccch
Q 028179 198 KGDCMAQCTR 207 (212)
Q Consensus 198 Rg~c~~~c~r 207 (212)
...|.| |+|
T Consensus 116 ~~~C~A-C~~ 124 (153)
T PF13926_consen 116 GPSCDA-CNR 124 (153)
T ss_pred CCcCcc-cCC
Confidence 556655 554
No 126
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation a
Probab=27.42 E-value=68 Score=24.10 Aligned_cols=24 Identities=25% Similarity=0.436 Sum_probs=20.7
Q ss_pred HHHHHHHhCCCCHHHHHHHHhhcC
Q 028179 128 EILGYLRNLSLSDDDIRKLLKKFP 151 (212)
Q Consensus 128 aklefLksLG~Sd~eI~k~vkK~P 151 (212)
.--+|.+.||+|+.+|..+-..+|
T Consensus 13 ~wk~~~R~LGlse~~Id~ie~~~~ 36 (80)
T cd08313 13 RWKEFVRRLGLSDNEIERVELDHR 36 (80)
T ss_pred HHHHHHHHcCCCHHHHHHHHHhCC
Confidence 444688899999999999999888
No 127
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.32 E-value=2.7e+02 Score=20.94 Aligned_cols=71 Identities=17% Similarity=0.165 Sum_probs=44.7
Q ss_pred HhhhCCCChHHHHHHHHhhhhccc--------cchhhhhhhhcCCChhhHHHHHHHHH-hCCCCHHHHHHHHhhcCceee
Q 028179 85 ALSTFNFSTEEEDKILGKAFGHIH--------SAYWSEERKRETPELETVSEILGYLR-NLSLSDDDIRKLLKKFPEVLG 155 (212)
Q Consensus 85 ~L~~LGfspe~v~~il~rA~gl~~--------S~~fr~a~~~~v~s~e~i~aklefLk-sLG~Sd~eI~k~vkK~P~ILg 155 (212)
+-+.+|+++..++-.... |++. ..+|.... -..-..+..|+ .+|++=++|..++..
T Consensus 6 va~~~gvs~~tlR~Ye~~--GLl~p~~r~~~g~r~Y~~~d-------v~~l~~I~~L~~~~G~~l~~I~~~l~~------ 70 (95)
T cd04780 6 LSKRSGVSVATIKYYLRE--GLLPEGRRLAPNQAEYSEAH-------VERLRLIRALQQEGGLPISQIKEVLDA------ 70 (95)
T ss_pred HHHHHCcCHHHHHHHHHC--CCCCCCcCCCCCCeecCHHH-------HHHHHHHHHHHHHcCCCHHHHHHHHHh------
Confidence 446788888887655443 4421 12222222 22335566777 499999999999986
Q ss_pred cCccchhhhhhhhhhh
Q 028179 156 CDIEHELRNNVQILGK 171 (212)
Q Consensus 156 ~SVEe~LkpkveFL~~ 171 (212)
.. ++.+-...++|.+
T Consensus 71 ~~-~~~~~~~~~~~~~ 85 (95)
T cd04780 71 IA-DASLPSTLLALAV 85 (95)
T ss_pred cC-cccHHHHHHHHHH
Confidence 33 5577777777765
No 128
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=27.24 E-value=73 Score=27.80 Aligned_cols=25 Identities=8% Similarity=0.258 Sum_probs=23.3
Q ss_pred HHHHHHHhhhCCCChHHHHHHHHhh
Q 028179 79 WEACRQALSTFNFSTEEEDKILGKA 103 (212)
Q Consensus 79 we~~v~~L~~LGfspe~v~~il~rA 103 (212)
.++++.+|.+||+++.++.+++..+
T Consensus 144 ~~ea~~AL~~LGy~~~ea~~al~~v 168 (196)
T PRK13901 144 FKELEQSIVNMGFDRKLVNSAIKEI 168 (196)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 6899999999999999999999886
No 129
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.17 E-value=2.3e+02 Score=20.79 Aligned_cols=57 Identities=25% Similarity=0.297 Sum_probs=36.0
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccc-----cchhhhhhhhcCCChhhHH--HHHHHHHhCCCCHHHHHHHHhh
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIH-----SAYWSEERKRETPELETVS--EILGYLRNLSLSDDDIRKLLKK 149 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~-----S~~fr~a~~~~v~s~e~i~--aklefLksLG~Sd~eI~k~vkK 149 (212)
++-+.+|+++..++..... |++. .+++. .+.+.+. ..+..|+..|++-++|..++..
T Consensus 5 eva~~~gi~~~tlr~~~~~--Gll~~~~~~~g~r~-------y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~ 68 (100)
T cd00592 5 EVAKLLGVSVRTLRYYEEK--GLLPPERSENGYRL-------YSEEDLERLRLIRRLRELGLSLKEIRELLDA 68 (100)
T ss_pred HHHHHHCcCHHHHHHHHHC--CCcCCCcCCCCCcc-------cCHHHHHHHHHHHHHHHcCCCHHHHHHHHhc
Confidence 4557889999998877553 4421 12221 2233332 4455666899999999999863
No 130
>PRK00118 putative DNA-binding protein; Validated
Probab=26.77 E-value=1.1e+02 Score=24.00 Aligned_cols=64 Identities=25% Similarity=0.367 Sum_probs=40.2
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHH-hCCCCH--HHHHHHHhhcCceeecCccc
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLR-NLSLSD--DDIRKLLKKFPEVLGCDIEH 160 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLk-sLG~Sd--~eI~k~vkK~P~ILg~SVEe 160 (212)
++-+.+|+++.++.+.+.|+-.. -.+.-.++.|++ ...+.+ +.+..+..++|. |+
T Consensus 38 EIAe~lGIS~~TV~r~L~RArkk----------------Lr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~------~~ 95 (104)
T PRK00118 38 EIAEEFNVSRQAVYDNIKRTEKL----------------LEDYEEKLHLYEKFIERNELFDKIAYLKEKYPD------DE 95 (104)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHH----------------HHHHHHHHChHHHHHHHHHHHHHHHHHHHcccc------cH
Confidence 34477899999998888887421 122335566665 334432 566777777774 66
Q ss_pred hhhhhhhhh
Q 028179 161 ELRNNVQIL 169 (212)
Q Consensus 161 ~LkpkveFL 169 (212)
+|+.-++.|
T Consensus 96 ~~~~~~~~~ 104 (104)
T PRK00118 96 ELKKLIEIL 104 (104)
T ss_pred HHHHHHhhC
Confidence 777766543
No 131
>PRK13523 NADPH dehydrogenase NamA; Provisional
Probab=26.73 E-value=51 Score=30.49 Aligned_cols=45 Identities=20% Similarity=0.217 Sum_probs=33.0
Q ss_pred hhhhhhccCcCchhHHHHHHhCCceeecccccccccc---cccchhhc
Q 028179 166 VQILGKDWGIEGKYLRNLLLRNPKVLGYNVDCKGDCM---AQCTRCWV 210 (212)
Q Consensus 166 veFL~~~vGL~g~~l~~~I~r~P~ILgYSLE~Rg~c~---~~c~rcw~ 210 (212)
++-++++.+.+.-.+.+-+..+|.+..--.+.+++++ .+|-|||-
T Consensus 290 a~~~l~~g~~D~V~~gR~~iadP~~~~k~~~~~~~~~~~~~~~~~~~~ 337 (337)
T PRK13523 290 AEEILQNNRADLIFIGRELLRNPYFPRIAAKELGFEIEAPKQYERAWG 337 (337)
T ss_pred HHHHHHcCCCChHHhhHHHHhCccHHHHHHHHcCCCCCCcchhhhccC
Confidence 3333434445556677888889999999999999765 67999993
No 132
>PF13432 TPR_16: Tetratricopeptide repeat; PDB: 3CVP_A 3CVL_A 3CVQ_A 3CV0_A 2GW1_B 3CVN_A 3QKY_A 2PL2_B.
Probab=26.71 E-value=1.5e+02 Score=19.39 Aligned_cols=30 Identities=3% Similarity=0.088 Sum_probs=23.5
Q ss_pred HHHHHHHHHHHh-hhCCCChHHHHHHHHhhh
Q 028179 75 ERKKWEACRQAL-STFNFSTEEEDKILGKAF 104 (212)
Q Consensus 75 ~~~~we~~v~~L-~~LGfspe~v~~il~rA~ 104 (212)
++++|+++.+.+ ..+...|+.....+..+.
T Consensus 9 ~~g~~~~A~~~~~~~l~~~P~~~~a~~~lg~ 39 (65)
T PF13432_consen 9 QQGDYDEAIAAFEQALKQDPDNPEAWYLLGR 39 (65)
T ss_dssp HCTHHHHHHHHHHHHHCCSTTHHHHHHHHHH
T ss_pred HcCCHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 567889999999 688888888877666653
No 133
>cd03033 ArsC_15kD Arsenate Reductase (ArsC) family, 15kD protein subfamily; composed of proteins of unknown function with similarity to thioredoxin-fold arsenic reductases, ArsC. It is encoded by an ORF present in a gene cluster associated with nitrogen fixation that also encodes dinitrogenase reductase ADP-ribosyltransferase (DRAT) and dinitrogenase reductase activating glycohydrolase (DRAG). ArsC catalyzes the reduction of arsenate [As(V)] to arsenite [As(III)], using reducing equivalents derived from glutathione via glutaredoxin, through a single catalytic cysteine.
Probab=26.71 E-value=2.4e+02 Score=22.01 Aligned_cols=59 Identities=10% Similarity=0.224 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhc----cCcCchhHHHHHHhCCceeeccccccccc
Q 028179 137 SLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKD----WGIEGKYLRNLLLRNPKVLGYNVDCKGDC 201 (212)
Q Consensus 137 G~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~----vGL~g~~l~~~I~r~P~ILgYSLE~Rg~c 201 (212)
++|.+|+..++++.+ +++-+..+-....+. -.++.+++-++|+.+|.++-..|=..++.
T Consensus 36 p~s~~eL~~~l~~~g------~~~l~n~~~~~~r~~~~~~~~ls~~e~~~ll~~~P~LikRPIv~~~~~ 98 (113)
T cd03033 36 PWTAETLRPFFGDLP------VAEWFNPAAPRVKSGEVVPEALDEEEALALMIADPLLIRRPLMQVGDR 98 (113)
T ss_pred CCCHHHHHHHHHHcC------HHHHHhcccHHHHhcCCCccCCCHHHHHHHHHhCcceeeCCeEEECCE
Confidence 456777777777553 122222222222210 13455667789999999998887665554
No 134
>KOG2511 consensus Nicotinic acid phosphoribosyltransferase [Coenzyme transport and metabolism]
Probab=26.63 E-value=94 Score=30.11 Aligned_cols=56 Identities=25% Similarity=0.265 Sum_probs=40.4
Q ss_pred HHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHH------HhhcCc
Q 028179 79 WEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKL------LKKFPE 152 (212)
Q Consensus 79 we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~------vkK~P~ 152 (212)
-|||..+|..|-|.+|+.+-+=+..++ .++ +-.+||+++.+|+..+..+ +.+-|.
T Consensus 53 Lee~irfl~N~~lt~eei~~lkk~lP~----------------~ee---af~eyl~~l~~s~~~~~aIsegSvvf~k~pl 113 (420)
T KOG2511|consen 53 LEEQIRFLANLKLTDEEIDYLKKELPY----------------LEE---AFYEYLRGLNCSDHPEEAISEGSVVFEKKPL 113 (420)
T ss_pred HHHHHHHHhhcCCCHHHHHHHHHhCCC----------------ChH---HHHHHHhhcCCCcCchhhcccCceeccCCce
Confidence 389999999999999999655333331 134 8899999999997666543 455663
Q ss_pred e
Q 028179 153 V 153 (212)
Q Consensus 153 I 153 (212)
|
T Consensus 114 i 114 (420)
T KOG2511|consen 114 I 114 (420)
T ss_pred E
Confidence 3
No 135
>PRK14134 recX recombination regulator RecX; Provisional
Probab=26.54 E-value=2.5e+02 Score=25.40 Aligned_cols=100 Identities=12% Similarity=0.048 Sum_probs=55.4
Q ss_pred hhhCCCChHHHHHHHHhhhhc--cccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCce----------
Q 028179 86 LSTFNFSTEEEDKILGKAFGH--IHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEV---------- 153 (212)
Q Consensus 86 L~~LGfspe~v~~il~rA~gl--~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~I---------- 153 (212)
|..-|++++.+..++.+..+. +.-..|-+.-+..-.+.-.-...-.-|+.-|++++.|..++...+.-
T Consensus 85 L~~k~~~~~~Ie~vI~~L~e~~yldD~ryA~~yv~~~~~~~G~~~I~~eL~qKGI~~~iIe~al~~~~~e~e~e~a~~l~ 164 (283)
T PRK14134 85 LYLKEYDEDAVNRVIRFLKEYNFIDDDKYCDMYIREKINSYGRNKIKYTLLNKGIKENIIIEKINNIDEEKEKKVAYKLA 164 (283)
T ss_pred HHhCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHhhhHHHHHHHHHHCCCCHHHHHHHHHhCChhhHHHHHHHHH
Confidence 335799999999999997664 33222222211111111112233456778899998888887765421
Q ss_pred -------eec--CccchhhhhhhhhhhccCcCchhHHHHHHh
Q 028179 154 -------LGC--DIEHELRNNVQILGKDWGIEGKYLRNLLLR 186 (212)
Q Consensus 154 -------Lg~--SVEe~LkpkveFL~~~vGL~g~~l~~~I~r 186 (212)
-.. +....-+..+.||... |++.+.+...|..
T Consensus 165 ~Kk~~~~~~~~~~~~k~k~Kl~~~L~rr-GFs~~~I~~vl~~ 205 (283)
T PRK14134 165 EKKYKILILSEKNKFKIYKKLGPYLISR-GYSSNIAEWILNE 205 (283)
T ss_pred HHhhcccccccccHHHHHHHHHHHHHHC-CCCHHHHHHHHHH
Confidence 111 1011223456788865 8887666655543
No 136
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=26.36 E-value=2.9e+02 Score=22.95 Aligned_cols=65 Identities=9% Similarity=0.040 Sum_probs=42.7
Q ss_pred HHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHH-hCCCCHHHHHHHHhhcCce
Q 028179 75 ERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLR-NLSLSDDDIRKLLKKFPEV 153 (212)
Q Consensus 75 ~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLk-sLG~Sd~eI~k~vkK~P~I 153 (212)
+..++++..+.+..-+-....+-.++..+++..| ..+. ..++++. .+|++..+|..+++-||.+
T Consensus 4 ~~~~~~~i~~ii~~y~~~~~~li~~L~~vQ~~~G-----------~Ip~----e~~~~iA~~l~v~~~~V~~vatFY~~f 68 (156)
T PRK05988 4 EPWDAARIAAIIAEHKHLEGALLPILHAIQDEFG-----------YVPE----DAVPVIAEALNLSRAEVHGVITFYHDF 68 (156)
T ss_pred chhHHHHHHHHHHHcCCCHHHHHHHHHHHHHHcC-----------CCCH----HHHHHHHHHhCCCHHHHHHHHHHhhcc
Confidence 3444555566666666667777777766653322 1122 3455555 7899999999999999987
Q ss_pred e
Q 028179 154 L 154 (212)
Q Consensus 154 L 154 (212)
=
T Consensus 69 ~ 69 (156)
T PRK05988 69 R 69 (156)
T ss_pred C
Confidence 3
No 137
>cd04758 Commd10 COMM_Domain containing protein 10. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=26.36 E-value=2.6e+02 Score=23.44 Aligned_cols=53 Identities=13% Similarity=0.200 Sum_probs=34.6
Q ss_pred hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHh
Q 028179 87 STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLK 148 (212)
Q Consensus 87 ~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vk 148 (212)
+..+++++++..+++-.. -.|+++... ..+++ ...+-|+.+|++++++.-+.+
T Consensus 45 ~~~~~~~~~l~~vi~~l~-----~il~~A~k~-nl~~~---~L~~~L~~l~l~~e~~~~~~~ 97 (186)
T cd04758 45 EAFKLLSQDLKLLLETIS-----FILEQAAYH-NLKPS---NLQQQLRNILLLEDKASAFVN 97 (186)
T ss_pred HHhCCChHHHHHHHHHHH-----HHHHHHHHh-cCCHH---HHHHHHHHcCCCHHHHHHHHH
Confidence 688888888877776652 234445423 34456 344577899999887775543
No 138
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=26.26 E-value=1.2e+02 Score=20.67 Aligned_cols=31 Identities=23% Similarity=0.229 Sum_probs=25.2
Q ss_pred cccChHHHHHHHHHHHHhhhCCCChHHHHHHH
Q 028179 69 ITLNDEERKKWEACRQALSTFNFSTEEEDKIL 100 (212)
Q Consensus 69 ~~~~~~~~~~we~~v~~L~~LGfspe~v~~il 100 (212)
...+.+|-..+.......+ .|++.+++..++
T Consensus 36 R~y~~~~l~~l~~i~~l~~-~g~~l~~i~~~l 66 (67)
T cd04764 36 RYYTDEDIELLKKIKTLLE-KGLSIKEIKEIL 66 (67)
T ss_pred eeeCHHHHHHHHHHHHHHH-CCCCHHHHHHHh
Confidence 3578888888888777666 999999998765
No 139
>cd08316 Death_FAS_TNFRSF6 Death domain of FAS or TNF receptor superfamily member 6. Death Domain (DD) found in the FS7-associated cell surface antigen (FAS). FAS, also known as TNFRSF6 (TNF receptor superfamily member 6), APT1, CD95, FAS1, or APO-1, together with FADD (Fas-associating via Death Domain) and caspase 8, is an integral part of the death inducing signalling complex (DISC), which plays an important role in the induction of apoptosis and is activated by binding of the ligand FasL to FAS. FAS also plays a critical role in self-tolerance by eliminating cell types (autoreactive T and B cells) that contribute to autoimmunity. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in sign
Probab=25.86 E-value=1e+02 Score=23.93 Aligned_cols=27 Identities=19% Similarity=0.364 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCCCHHHHHHHHhhcCce
Q 028179 127 SEILGYLRNLSLSDDDIRKLLKKFPEV 153 (212)
Q Consensus 127 ~aklefLksLG~Sd~eI~k~vkK~P~I 153 (212)
+.--+|-+.||+|+.+|..+-..+|.=
T Consensus 21 ~~wK~faR~lglse~~Id~I~~~~~~d 47 (97)
T cd08316 21 KDVKKFVRKSGLSEPKIDEIKLDNPQD 47 (97)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHcCCCC
Confidence 345568889999999999999999974
No 140
>PF03874 RNA_pol_Rpb4: RNA polymerase Rpb4; InterPro: IPR005574 The eukaryotic RNA polymerase subunits RPB4 and RPB7 form a heterodimer that reversibly associates with the RNA polymerase II core. Archaeal cells contain a single RNAP made up of about 12 subunits, displaying considerable homology to the eukaryotic RNAPII subunits. The RPB4 and RPB7 homologs are called subunits F and E, respectively, and have been shown to form a stable heterodimer. While the RPB7 homologue is reasonably well conserved, the similarity between the eukaryotic RPB4 and the archaeal F subunit is barely detectable [].; GO: 0003899 DNA-directed RNA polymerase activity, 0006351 transcription, DNA-dependent; PDB: 3AYH_A 3H3V_E 4A3C_D 3PO3_D 3HOX_D 2R92_D 3HOU_D 1Y77_D 2R7Z_D 3QT1_D ....
Probab=25.65 E-value=1.7e+02 Score=22.27 Aligned_cols=12 Identities=25% Similarity=0.717 Sum_probs=7.7
Q ss_pred CCCHHHHHHHHh
Q 028179 137 SLSDDDIRKLLK 148 (212)
Q Consensus 137 G~Sd~eI~k~vk 148 (212)
.++++++.+++.
T Consensus 100 r~~ee~l~~iL~ 111 (117)
T PF03874_consen 100 RFSEEDLEEILD 111 (117)
T ss_dssp TSTHHHHHHHHH
T ss_pred CCCHHHHHHHHH
Confidence 367777776654
No 141
>TIGR01616 nitro_assoc nitrogenase-associated protein. This model describes a small family of uncharacterized proteins found so far in alpha and gamma proteobacteria and in Nostoc sp. PCC 7120, a cyanobacterium. The gene for this protein is associated with nitrogenase genes. This family shows sequence similarity to TIGR00014, a glutaredoxin-dependent arsenate reductase that converts arsentate to arsenite for disposal. This family is one of several included in Pfam model pfam03960.
Probab=25.60 E-value=1.5e+02 Score=23.72 Aligned_cols=23 Identities=13% Similarity=0.183 Sum_probs=14.6
Q ss_pred cCchhHHHHHHhCCceeeccccc
Q 028179 175 IEGKYLRNLLLRNPKVLGYNVDC 197 (212)
Q Consensus 175 L~g~~l~~~I~r~P~ILgYSLE~ 197 (212)
++.+++-++++.+|.++-..|=-
T Consensus 73 ls~~e~i~lm~~~P~LIKRPIi~ 95 (126)
T TIGR01616 73 IDEASALALMVSDPLLIRRPLMD 95 (126)
T ss_pred CCHHHHHHHHHhCcCeEeCCEEE
Confidence 44455667777777777665533
No 142
>PF11852 DUF3372: Domain of unknown function (DUF3372); InterPro: IPR024561 This entry represents the uncharacterised C-terminal domain of secreted (or membrane-anchored) pullulanases of Gram-negative bacteria and pullulanase-type starch debranching enzymes of plants. Both enzymes hydrolyse alpha-1,6 glycosidic linkages. Pullulan is an unusual, industrially important polysaccharide in which short alpha-1,4 chains (maltotriose) are connected in alpha-1,6 linkages. Enzymes that cleave alpha-1,6 linkages in pullulan and release maltotriose are called pullulanases although pullulan itself may not be the natural substrate. ; PDB: 2Y4S_A 2FH8_A 2FH6_A 2Y5E_A 2FHC_A 2FHB_A 2FHF_A 2FGZ_A.
Probab=25.33 E-value=63 Score=27.68 Aligned_cols=72 Identities=14% Similarity=0.186 Sum_probs=47.3
Q ss_pred hHHHHHHHHHHHHhh--hCCCChHHHHHHHHhhhhc----cccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHH
Q 028179 73 DEERKKWEACRQALS--TFNFSTEEEDKILGKAFGH----IHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKL 146 (212)
Q Consensus 73 ~~~~~~we~~v~~L~--~LGfspe~v~~il~rA~gl----~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~ 146 (212)
+++...|......|. .+-=+++++..+.+.+.++ ..|+.||-. +.+.|.++|.|..+ |
T Consensus 15 ~kn~~~W~~i~~ll~d~~~kP~~~~I~~a~~~f~elL~iR~SspLFrL~------ta~~I~~rv~F~n~-G--------- 78 (168)
T PF11852_consen 15 DKNGDNWPLIRPLLADPALKPSPADIAAASAYFQELLRIRKSSPLFRLG------TAEEIQQRVTFHNT-G--------- 78 (168)
T ss_dssp HHHGGGHHHHHHHHCTCCGS--HHHHHHHHHHHHHHHHHHCT-GGGG--------SHHHHHHHEEEES--S---------
T ss_pred cccccchhhhhhhccCCccCCCHHHHHHHHHHHHHHHHHhccCccccCC------CHHHHHHhccccCC-C---------
Confidence 456789999999993 6666777887777777776 477777544 46778888887642 2
Q ss_pred HhhcCceeecCccc
Q 028179 147 LKKFPEVLGCDIEH 160 (212)
Q Consensus 147 vkK~P~ILg~SVEe 160 (212)
=...|.++.++|++
T Consensus 79 ~~q~pGvIvM~idD 92 (168)
T PF11852_consen 79 PDQTPGVIVMSIDD 92 (168)
T ss_dssp TT--TTEEEEEEE-
T ss_pred CCCCCcEEEEEecC
Confidence 12468999999887
No 143
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=25.12 E-value=3.2e+02 Score=22.85 Aligned_cols=60 Identities=15% Similarity=0.148 Sum_probs=39.0
Q ss_pred HHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHh
Q 028179 80 EACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLK 148 (212)
Q Consensus 80 e~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vk 148 (212)
|+........||+..+++.+++-.. -.+.++.... .+++ .-.+-|..+|++++.+.-+.+
T Consensus 25 ~~~~kl~~~~~~~~~~lk~~va~l~-----fiL~~A~k~n-~~~~---~l~~eL~~lglp~e~~~~l~~ 84 (174)
T cd04752 25 EKVLKLTADAKFESGDVKASIAVLS-----FILSSAAKYN-VDGE---SLSSELQQLGLPKEHATSLCR 84 (174)
T ss_pred HHHHHHHHHhCCCHhhHHHHHHHHH-----HHHHHHHHcC-CCHH---HHHHHHHHcCCCHHHHHHHHH
Confidence 4445555799999999988887753 1233344233 3455 344567888999988776655
No 144
>PF11165 DUF2949: Protein of unknown function (DUF2949); InterPro: IPR021336 This family of proteins with unknown function appear to be restricted to Cyanobacteria.
Probab=24.86 E-value=1.1e+02 Score=22.01 Aligned_cols=23 Identities=26% Similarity=0.537 Sum_probs=19.7
Q ss_pred HHHHHHH-hCCCCHHHHHHHHhhc
Q 028179 128 EILGYLR-NLSLSDDDIRKLLKKF 150 (212)
Q Consensus 128 aklefLk-sLG~Sd~eI~k~vkK~ 150 (212)
+-+.||. .+|+|++.|..+++..
T Consensus 4 ~l~~fL~~el~ls~~~i~lalr~~ 27 (58)
T PF11165_consen 4 QLIRFLQEELGLSEASIALALRQQ 27 (58)
T ss_pred HHHHHHHHHcCCCHHHHHHHHHhH
Confidence 5678999 9999999999998853
No 145
>PRK13901 ruvA Holliday junction DNA helicase RuvA; Provisional
Probab=24.57 E-value=2.7e+02 Score=24.27 Aligned_cols=61 Identities=15% Similarity=0.182 Sum_probs=37.3
Q ss_pred HHh-hhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhc
Q 028179 84 QAL-STFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKF 150 (212)
Q Consensus 84 ~~L-~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~ 150 (212)
+.| +.=|+.++.|.+|+....+-.... . . ...........++-|.+||+++.|+.+++++.
T Consensus 107 ~~L~~vpGIGkKtAeRIIlELkdKl~~~--~-~---~~~~~~~~~ea~~AL~~LGy~~~ea~~al~~v 168 (196)
T PRK13901 107 ELISKVKGIGNKMAGKIFLKLRGKLVKN--D-E---LESSLFKFKELEQSIVNMGFDRKLVNSAIKEI 168 (196)
T ss_pred HHHhhCCCCCHHHHHHHHHHHHHhhccc--c-c---cccCcccHHHHHHHHHHcCCCHHHHHHHHHHH
Confidence 344 455777777777765543322110 0 0 00111235678899999999999999999864
No 146
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=24.53 E-value=3.1e+02 Score=20.66 Aligned_cols=79 Identities=19% Similarity=0.113 Sum_probs=44.3
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhh--HHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccch
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELET--VSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHE 161 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~--i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~ 161 (212)
++-+.+|+++.+++---.. |++.+ .+...-.-..+++. .-..+..|+.+|+|-++|..++.... ..+.
T Consensus 6 eva~~~gvs~~tLR~ye~~--Gll~~--~r~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~~~~------~~~~ 75 (102)
T cd04775 6 QMSRKFGVSRSTLLYYESI--GLIPS--ARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQPH------VQAI 75 (102)
T ss_pred HHHHHHCcCHHHHHHHHHC--CCCCC--CCCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHcCCc------HHHH
Confidence 3446788888888544332 55311 11100001122333 33556677899999999999887532 2455
Q ss_pred hhhhhhhhhhc
Q 028179 162 LRNNVQILGKD 172 (212)
Q Consensus 162 LkpkveFL~~~ 172 (212)
+..+.+.|...
T Consensus 76 l~~~~~~l~~~ 86 (102)
T cd04775 76 LEERLQSLNRE 86 (102)
T ss_pred HHHHHHHHHHH
Confidence 66666666543
No 147
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.27 E-value=1.4e+02 Score=22.80 Aligned_cols=34 Identities=9% Similarity=0.086 Sum_probs=30.2
Q ss_pred ccChHHHHHHHHHHHHhhhCCCChHHHHHHHHhh
Q 028179 70 TLNDEERKKWEACRQALSTFNFSTEEEDKILGKA 103 (212)
Q Consensus 70 ~~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA 103 (212)
..+++|-..+...+..|+..||+.+++.+++...
T Consensus 38 ~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~ 71 (99)
T cd04765 38 YYRPKDVELLLLIKHLLYEKGYTIEGAKQALKED 71 (99)
T ss_pred eeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhc
Confidence 5788899999999888999999999999998764
No 148
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.18 E-value=2.5e+02 Score=21.13 Aligned_cols=63 Identities=13% Similarity=0.181 Sum_probs=38.1
Q ss_pred HhhhCCCChHHHHHHHHhhhhcc-------ccchhhhhhhhcCCChhhHHHHHHHHHh-CCCCHHHHHHHHhhcCceeec
Q 028179 85 ALSTFNFSTEEEDKILGKAFGHI-------HSAYWSEERKRETPELETVSEILGYLRN-LSLSDDDIRKLLKKFPEVLGC 156 (212)
Q Consensus 85 ~L~~LGfspe~v~~il~rA~gl~-------~S~~fr~a~~~~v~s~e~i~aklefLks-LG~Sd~eI~k~vkK~P~ILg~ 156 (212)
+-+.+|+++..++.... .|++ +..+|.... -..-..+..|+. +|+|-++|..++.-..++-.+
T Consensus 7 va~~~gVs~~tLR~ye~--~Gli~p~r~~~g~R~Ys~~d-------v~~l~~I~~L~~~~G~~l~~i~~~l~l~~~~~~l 77 (98)
T cd01279 7 AAELLGIHPQTLRVYDR--LGLVSPARTNGGGRRYSNND-------LELLRQVQRLSQDEGFNLAGIKRIIELYPQVLLL 77 (98)
T ss_pred HHHHHCcCHHHHHHHHH--CCCCCCCcCCCCCeeECHHH-------HHHHHHHHHHHHHCCCCHHHHHHHHHhhhHHHHH
Confidence 44678888888876644 2442 222222221 112344556665 999999999999876655433
No 149
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=24.05 E-value=2e+02 Score=20.07 Aligned_cols=24 Identities=25% Similarity=0.454 Sum_probs=16.8
Q ss_pred CCCCHHHHHHHHhhcCceeecCcc
Q 028179 136 LSLSDDDIRKLLKKFPEVLGCDIE 159 (212)
Q Consensus 136 LG~Sd~eI~k~vkK~P~ILg~SVE 159 (212)
+|+|.+++..++...-..+..+.+
T Consensus 30 lgis~~~v~~~l~~~~~~~Sl~~~ 53 (78)
T PF04539_consen 30 LGISVEEVRELLQASRRPVSLDLP 53 (78)
T ss_dssp HTS-HHHHHHHHHHHSCCEESSHC
T ss_pred HcccHHHHHHHHHhCCCCeEEeee
Confidence 689999988888776666666643
No 150
>cd01421 IMPCH Inosine monophosphate cyclohydrolase domain. This is the N-terminal domain in the purine biosynthesis pathway protein ATIC (purH). The bifunctional ATIC protein contains a C-terminal ATIC formylase domain that formylates 5-aminoimidazole-4-carboxamide-ribonucleotide. The IMPCH domain then converts the formyl-5-aminoimidazole-4-carboxamide-ribonucleotide to inosine monophosphate. This is the final step in de novo purine production.
Probab=24.05 E-value=24 Score=30.67 Aligned_cols=37 Identities=22% Similarity=0.539 Sum_probs=29.7
Q ss_pred HHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhh
Q 028179 128 EILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNV 166 (212)
Q Consensus 128 aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~Lkpkv 166 (212)
..-+||++.|++-..|.+ +..+|++|+-+|. +|.|++
T Consensus 32 GTAk~L~e~GI~v~~V~k-~TgfpE~l~GRVK-TLHP~i 68 (187)
T cd01421 32 GTAKFLKEAGIPVTDVSD-ITGFPEILGGRVK-TLHPKI 68 (187)
T ss_pred HHHHHHHHcCCeEEEhhh-ccCCcHhhCCccc-cCChhh
Confidence 455788889997777765 4679999999976 999987
No 151
>COG0632 RuvA Holliday junction resolvasome, DNA-binding subunit [DNA replication, recombination, and repair]
Probab=24.02 E-value=86 Score=27.46 Aligned_cols=27 Identities=22% Similarity=0.337 Sum_probs=23.1
Q ss_pred HHHHHHHHhhhCCCChHHHHHHHHhhh
Q 028179 78 KWEACRQALSTFNFSTEEEDKILGKAF 104 (212)
Q Consensus 78 ~we~~v~~L~~LGfspe~v~~il~rA~ 104 (212)
.-++.+++|..||++++++.+++..+.
T Consensus 155 ~~~~~v~AL~~LGy~~~e~~~av~~v~ 181 (201)
T COG0632 155 ALEEAVEALVALGYKEKEIKKAVKKVL 181 (201)
T ss_pred hhhHHHHHHHHcCCCHHHHHHHHHHHH
Confidence 335559999999999999999999985
No 152
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=24.00 E-value=1.9e+02 Score=22.78 Aligned_cols=82 Identities=11% Similarity=0.093 Sum_probs=52.3
Q ss_pred HhhhCCCChHHHHHHHHhhhh--ccccchhhhhhhhcCCChhh--HHHH--------HHHHHhCCCCHHHHHHHHhhcCc
Q 028179 85 ALSTFNFSTEEEDKILGKAFG--HIHSAYWSEERKRETPELET--VSEI--------LGYLRNLSLSDDDIRKLLKKFPE 152 (212)
Q Consensus 85 ~L~~LGfspe~v~~il~rA~g--l~~S~~fr~a~~~~v~s~e~--i~ak--------lefLksLG~Sd~eI~k~vkK~P~ 152 (212)
..+.+|+++.++..++.+..+ +.... ++ . ...+++.- +... -.||..+|.+++++..-..+.++
T Consensus 28 la~~l~vs~~svs~~l~~L~~~Gli~~~--~~-~-~i~LT~~G~~~a~~~~~~h~~~e~~l~~l~~~~~~~~~~a~~iEH 103 (142)
T PRK03902 28 IAEALSVHPSSVTKMVQKLDKDEYLIYE--KY-R-GLVLTPKGKKIGKRLVYRHELLEQFLRIIGVDESKIYNDVEGIEH 103 (142)
T ss_pred HHHHhCCChhHHHHHHHHHHHCCCEEEe--cC-c-eEEECHHHHHHHHHHHHHHHHHHHHHHHhCcCHHHHHHHHHHHhh
Confidence 347899999999999977543 22100 00 0 01112221 2222 36777899999999999999999
Q ss_pred eeecCccchhhhhhhhhh
Q 028179 153 VLGCDIEHELRNNVQILG 170 (212)
Q Consensus 153 ILg~SVEe~LkpkveFL~ 170 (212)
++.-...++|..-++|+.
T Consensus 104 ~ls~e~~~rl~~~~~~~~ 121 (142)
T PRK03902 104 HLSWNAIDRIGDLVQYFE 121 (142)
T ss_pred cCCHHHHHHHHHHHcchh
Confidence 987666666666666664
No 153
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain),
Probab=23.83 E-value=89 Score=23.29 Aligned_cols=21 Identities=29% Similarity=0.498 Sum_probs=18.3
Q ss_pred HHHhCCCCHHHHHHHHhhcCc
Q 028179 132 YLRNLSLSDDDIRKLLKKFPE 152 (212)
Q Consensus 132 fLksLG~Sd~eI~k~vkK~P~ 152 (212)
+-+.||+|+.+|..+-..+|.
T Consensus 19 laR~LGlse~~Id~i~~~~~~ 39 (86)
T cd08306 19 LARKLGLSETKIESIEEAHPR 39 (86)
T ss_pred HHHHcCCCHHHHHHHHHHCCC
Confidence 445899999999999999994
No 154
>smart00657 RPOL4c DNA-directed RNA-polymerase II subunit.
Probab=23.79 E-value=1.3e+02 Score=23.66 Aligned_cols=57 Identities=25% Similarity=0.262 Sum_probs=42.3
Q ss_pred CChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhhccCcCchhHHHHH
Q 028179 121 PELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGKDWGIEGKYLRNLL 184 (212)
Q Consensus 121 ~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~~vGL~g~~l~~~I 184 (212)
.+++.+.+.++.|+..|+.+.|+..++.-.|. + .+.++.-++-+.+. ++++.+.++|
T Consensus 52 ~~~e~i~~~~~~L~~~~L~k~E~~~i~Nl~P~----s-~~E~~~lI~sl~~r--~~ee~l~~iL 108 (118)
T smart00657 52 KNREIVRAVRTLLKSKKLHKFEIAQLGNLRPE----T-AEEAQLLIPSLEER--IDEEELEELL 108 (118)
T ss_pred CCHHHHHHHHHHHHhcCCCHHHHHHHhCCCCC----C-HHHHHHHhhhhhcc--CCHHHHHHHH
Confidence 57899999999999999999999999998886 3 33566666666643 5554444444
No 155
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.19 E-value=1.4e+02 Score=22.51 Aligned_cols=31 Identities=19% Similarity=0.155 Sum_probs=25.0
Q ss_pred cChHHHHHHHHHHHHhhhCCCChHHHHHHHHh
Q 028179 71 LNDEERKKWEACRQALSTFNFSTEEEDKILGK 102 (212)
Q Consensus 71 ~~~~~~~~we~~v~~L~~LGfspe~v~~il~r 102 (212)
.+++|. .|=..+..|+.+||+.+++..++..
T Consensus 37 Y~~~~~-~~l~~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 37 FDEKCQ-DDLEFILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred cCHHHH-HHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 455555 5777889999999999999998864
No 156
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=22.96 E-value=1e+02 Score=20.88 Aligned_cols=20 Identities=40% Similarity=0.670 Sum_probs=15.0
Q ss_pred HHHHHHHhCCCCHHHHHHHH
Q 028179 128 EILGYLRNLSLSDDDIRKLL 147 (212)
Q Consensus 128 aklefLksLG~Sd~eI~k~v 147 (212)
..|..++.+|||=+||..++
T Consensus 5 ~~I~~~r~lGfsL~eI~~~l 24 (65)
T PF09278_consen 5 QFIRRLRELGFSLEEIRELL 24 (65)
T ss_dssp HHHHHHHHTT--HHHHHHHH
T ss_pred HHHHHHHHcCCCHHHHHHHH
Confidence 34666779999999999999
No 157
>PF04752 ChaC: ChaC-like protein; InterPro: IPR006840 The ChaC protein is thought to be associated with the putative ChaA Ca2+/H+ cation transport protein in Escherichia coli. Its function is not known. This family also includes homologues regions from several other bacterial and eukaryotic proteins.
Probab=22.64 E-value=1.9e+02 Score=24.68 Aligned_cols=46 Identities=26% Similarity=0.309 Sum_probs=35.6
Q ss_pred CChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCC--CCHHHHHHHHh
Q 028179 91 FSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLS--LSDDDIRKLLK 148 (212)
Q Consensus 91 fspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG--~Sd~eI~k~vk 148 (212)
.+.+++-++++.|.|..|+ |.|=+-.-.+.|+.+| +.|+++..+.+
T Consensus 126 ~~~~~~A~~Ia~a~G~~G~------------N~eYL~~l~~~L~~~gp~i~D~~l~~L~~ 173 (178)
T PF04752_consen 126 LPLEEIARIIATASGPSGS------------NREYLFNLAEALRELGPGIRDPHLFALER 173 (178)
T ss_pred CCHHHHHHHHhheECcCcC------------CHHHHHHHHHHHHHhCCCCCChHHHHHHH
Confidence 3667777777777766665 5688889999999999 99988877654
No 158
>PF06827 zf-FPG_IleRS: Zinc finger found in FPG and IleRS; InterPro: IPR010663 Zinc finger (Znf) domains are relatively small protein motifs which contain multiple finger-like protrusions that make tandem contacts with their target molecule. Some of these domains bind zinc, but many do not; instead binding other metals such as iron, or no metal at all. For example, some family members form salt bridges to stabilise the finger-like folds. They were first identified as a DNA-binding motif in transcription factor TFIIIA from Xenopus laevis (African clawed frog), however they are now recognised to bind DNA, RNA, protein and/or lipid substrates [, , , , ]. Their binding properties depend on the amino acid sequence of the finger domains and of the linker between fingers, as well as on the higher-order structures and the number of fingers. Znf domains are often found in clusters, where fingers can have different binding specificities. There are many superfamilies of Znf motifs, varying in both sequence and structure. They display considerable versatility in binding modes, even between members of the same class (e.g. some bind DNA, others protein), suggesting that Znf motifs are stable scaffolds that have evolved specialised functions. For example, Znf-containing proteins function in gene transcription, translation, mRNA trafficking, cytoskeleton organisation, epithelial development, cell adhesion, protein folding, chromatin remodelling and zinc sensing, to name but a few []. Zinc-binding motifs are stable structures, and they rarely undergo conformational changes upon binding their target. This entry represents a zinc finger domain found at the C-terminal in both DNA glycosylase/AP lyase enzymes and in isoleucyl tRNA synthetase. In these two types of enzymes, the C-terminal domain forms a zinc finger. Some related proteins may not bind zinc. DNA glycosylase/AP lyase enzymes are involved in base excision repair of DNA damaged by oxidation or by mutagenic agents. These enzymes have both DNA glycosylase activity (3.2.2 from EC) and AP lyase activity (4.2.99.18 from EC) []. Examples include formamidopyrimidine-DNA glycosylases (Fpg; MutM) and endonuclease VIII (Nei). Formamidopyrimidine-DNA glycosylases (Fpg, MutM) is a trifunctional DNA base excision repair enzyme that removes a wide range of oxidation-damaged bases (N-glycosylase activity; 3.2.2.23 from EC) and cleaves both the 3'- and 5'-phosphodiester bonds of the resulting apurinic/apyrimidinic site (AP lyase activity; 4.2.99.18 from EC). Fpg has a preference for oxidised purines, excising oxidized purine bases such as 7,8-dihydro-8-oxoguanine (8-oxoG). ITs AP (apurinic/apyrimidinic) lyase activity introduces nicks in the DNA strand, cleaving the DNA backbone by beta-delta elimination to generate a single-strand break at the site of the removed base with both 3'- and 5'-phosphates. Fpg is a monomer composed of 2 domains connected by a flexible hinge []. The two DNA-binding motifs (a zinc finger and the helix-two-turns-helix motifs) suggest that the oxidized base is flipped out from double-stranded DNA in the binding mode and excised by a catalytic mechanism similar to that of bifunctional base excision repair enzymes []. Fpg binds one ion of zinc at the C terminus, which contains four conserved and essential cysteines []. Endonuclease VIII (Nei) has the same enzyme activities as Fpg above, but with a preference for oxidized pyrimidines, such as thymine glycol, 5,6-dihydrouracil and 5,6-dihydrothymine [, ]. An Fpg-type zinc finger is also found at the C terminus of isoleucyl tRNA synthetase (6.1.1.5 from EC) [, ]. This enzyme catalyses the attachment of isoleucine to tRNA(Ile). As IleRS can inadvertently accommodate and process structurally similar amino acids such as valine, to avoid such errors it has two additional distinct tRNA(Ile)-dependent editing activities. One activity is designated as 'pre-transfer' editing and involves the hydrolysis of activated Val-AMP. The other activity is designated 'post-transfer' editing and involves deacylation of mischarged Val-tRNA(Ile) []. More information about these proteins can be found at Protein of the Month: Zinc Fingers [].; GO: 0003824 catalytic activity; PDB: 1K82_C 1Q39_A 2OQ4_B 2OPF_A 1K3X_A 1K3W_A 1Q3B_A 2EA0_A 1Q3C_A 2XZF_A ....
Probab=22.62 E-value=31 Score=20.72 Aligned_cols=7 Identities=57% Similarity=1.962 Sum_probs=3.4
Q ss_pred ccchhhc
Q 028179 204 QCTRCWV 210 (212)
Q Consensus 204 ~c~rcw~ 210 (212)
.|.|||-
T Consensus 3 ~C~rC~~ 9 (30)
T PF06827_consen 3 KCPRCWN 9 (30)
T ss_dssp B-TTT--
T ss_pred cCccCCC
Confidence 5899995
No 159
>PRK13669 hypothetical protein; Provisional
Probab=22.56 E-value=41 Score=25.56 Aligned_cols=44 Identities=18% Similarity=0.344 Sum_probs=29.4
Q ss_pred hhhhhhhhhhccCcCc-hhHHHHHHhCCceeecccc-cccccccccchhhcc
Q 028179 162 LRNNVQILGKDWGIEG-KYLRNLLLRNPKVLGYNVD-CKGDCMAQCTRCWVR 211 (212)
Q Consensus 162 LkpkveFL~~~vGL~g-~~l~~~I~r~P~ILgYSLE-~Rg~c~~~c~rcw~r 211 (212)
++|-|||=+++. ..| +..-+.+.++|.+ | ..-+|.+.|+-|-.+
T Consensus 1 m~piVEfC~sNl-~~G~~~~~~~Le~dP~~-----dVie~gCls~CG~C~~~ 46 (78)
T PRK13669 1 MNPIVEFCVSNL-ASGSQAAFEKLEKDPNL-----DVLEYGCLGYCGICSEG 46 (78)
T ss_pred CCceeeehhcch-hhhHHHHHHHHHhCCCc-----eEEEcchhhhCcCcccC
Confidence 568889988876 223 2324456788853 3 455799999999654
No 160
>PF06252 DUF1018: Protein of unknown function (DUF1018); InterPro: IPR009363 This family consists of several bacterial and phage proteins, related to Gp16 of phage Mu, of unknown function.
Probab=22.56 E-value=1.5e+02 Score=23.00 Aligned_cols=74 Identities=15% Similarity=0.203 Sum_probs=40.1
Q ss_pred ChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhhcCceeecCccchhhhhhhhhhh
Q 028179 92 STEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKLLKKFPEVLGCDIEHELRNNVQILGK 171 (212)
Q Consensus 92 spe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK~P~ILg~SVEe~LkpkveFL~~ 171 (212)
+.|.=+.++....|-..+ .-++...+..+|+.|+.+||....=.+--...|..- ......++.-|-.
T Consensus 2 ddd~YR~~L~~~~Gk~S~---------k~lt~~el~~vl~~l~~~G~k~~~~~~~~~~~~~~~----~~~q~~KI~aLw~ 68 (119)
T PF06252_consen 2 DDDTYRALLQRVTGKSSS---------KDLTEAELEKVLDELKRLGFKPPKPARRPGRRPGMA----TSAQLRKIRALWK 68 (119)
T ss_pred CHHHHHHHHHHHhChhhH---------HHCCHHHHHHHHHHHHHccCcCccccccCCCCCCCc----chHHHHHHHHHHH
Confidence 445556666665543221 126778889999999999993111111111122222 2345566776666
Q ss_pred ccCcCch
Q 028179 172 DWGIEGK 178 (212)
Q Consensus 172 ~vGL~g~ 178 (212)
++|..+.
T Consensus 69 ~~~~~~~ 75 (119)
T PF06252_consen 69 QLGKPGA 75 (119)
T ss_pred HhhccCC
Confidence 6665544
No 161
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=22.26 E-value=1.7e+02 Score=18.38 Aligned_cols=26 Identities=19% Similarity=0.249 Sum_probs=18.5
Q ss_pred HHHHHHHHHhhhCCCChHHHHHHHHh
Q 028179 77 KKWEACRQALSTFNFSTEEEDKILGK 102 (212)
Q Consensus 77 ~~we~~v~~L~~LGfspe~v~~il~r 102 (212)
+.|-+-+.-....|++.++++..+..
T Consensus 3 ~EW~~Li~eA~~~Gls~eeir~FL~~ 28 (30)
T PF08671_consen 3 EEWVELIKEAKESGLSKEEIREFLEF 28 (30)
T ss_dssp HHHHHHHHHHHHTT--HHHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 35777777778899999999887654
No 162
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.08 E-value=2.4e+02 Score=21.10 Aligned_cols=32 Identities=16% Similarity=0.117 Sum_probs=23.8
Q ss_pred ccChHHHHHHHHHHHHhhhCCCChHHHHHHHHh
Q 028179 70 TLNDEERKKWEACRQALSTFNFSTEEEDKILGK 102 (212)
Q Consensus 70 ~~~~~~~~~we~~v~~L~~LGfspe~v~~il~r 102 (212)
..+++|...+.. +..|+.+||+.+++..++..
T Consensus 38 ~Y~~~~~~~l~~-I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 38 YYTLEQFEQLDI-ILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred cCCHHHHHHHHH-HHHHHHcCCCHHHHHHHHhc
Confidence 355666666655 55689999999999988764
No 163
>COG1125 OpuBA ABC-type proline/glycine betaine transport systems, ATPase components [Amino acid transport and metabolism]
Probab=21.83 E-value=1.8e+02 Score=27.37 Aligned_cols=97 Identities=14% Similarity=0.208 Sum_probs=63.2
Q ss_pred CCChHHHHHHHHhhhhc-cccchhhhhhhhcCCChhhHHHHHHHHH-hCCCC-HHHHHHHHhhcCceeecCccchhhhhh
Q 028179 90 NFSTEEEDKILGKAFGH-IHSAYWSEERKRETPELETVSEILGYLR-NLSLS-DDDIRKLLKKFPEVLGCDIEHELRNNV 166 (212)
Q Consensus 90 Gfspe~v~~il~rA~gl-~~S~~fr~a~~~~v~s~e~i~aklefLk-sLG~S-d~eI~k~vkK~P~ILg~SVEe~Lkpkv 166 (212)
|--.-+..+|.-|..+. -|.=++.... ..-...-+++.++-|-- .+|+= ---|..=+.--|.+++.+ +++++.++
T Consensus 37 GsGKTTtLkMINrLiept~G~I~i~g~~-i~~~d~~~LRr~IGYviQqigLFPh~Tv~eNIa~VP~L~~w~-k~~i~~r~ 114 (309)
T COG1125 37 GSGKTTTLKMINRLIEPTSGEILIDGED-ISDLDPVELRRKIGYVIQQIGLFPHLTVAENIATVPKLLGWD-KERIKKRA 114 (309)
T ss_pred CCcHHHHHHHHhcccCCCCceEEECCee-cccCCHHHHHHhhhhhhhhcccCCCccHHHHHHhhhhhcCCC-HHHHHHHH
Confidence 34455667777776543 1221121112 11234667889999877 88863 445566666779999999 89999999
Q ss_pred hhhhhccCcCchhHHHHHHhCCcee
Q 028179 167 QILGKDWGIEGKYLRNLLLRNPKVL 191 (212)
Q Consensus 167 eFL~~~vGL~g~~l~~~I~r~P~IL 191 (212)
+-|.+-+||+ ..+|.-|+|.=|
T Consensus 115 ~ELl~lvgL~---p~~~~~RyP~eL 136 (309)
T COG1125 115 DELLDLVGLD---PSEYADRYPHEL 136 (309)
T ss_pred HHHHHHhCCC---HHHHhhcCchhc
Confidence 9999999997 224666666433
No 164
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=21.68 E-value=1e+02 Score=22.55 Aligned_cols=23 Identities=30% Similarity=0.512 Sum_probs=20.4
Q ss_pred HHHHHhCCCCHHHHHHHHhhcCc
Q 028179 130 LGYLRNLSLSDDDIRKLLKKFPE 152 (212)
Q Consensus 130 lefLksLG~Sd~eI~k~vkK~P~ 152 (212)
-++.+.||+|+.+|..+-..+|.
T Consensus 15 k~laR~LGls~~~I~~ie~~~~~ 37 (79)
T cd08784 15 KRFFRKLGLSDNEIKVAELDNPQ 37 (79)
T ss_pred HHHHHHcCCCHHHHHHHHHcCCc
Confidence 35777999999999999999997
No 165
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=21.36 E-value=1.1e+02 Score=20.42 Aligned_cols=20 Identities=15% Similarity=0.330 Sum_probs=14.6
Q ss_pred hhCCCChHHHHHHHHhhhhc
Q 028179 87 STFNFSTEEEDKILGKAFGH 106 (212)
Q Consensus 87 ~~LGfspe~v~~il~rA~gl 106 (212)
+.+|+++....+++.+..+.
T Consensus 9 ~~~~~s~~~l~~~f~~~~~~ 28 (84)
T smart00342 9 EALGMSPRHLQRLFKKETGT 28 (84)
T ss_pred HHhCCCHHHHHHHHHHHhCc
Confidence 67888888887777776543
No 166
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=21.16 E-value=3.7e+02 Score=20.53 Aligned_cols=64 Identities=8% Similarity=0.080 Sum_probs=37.5
Q ss_pred HHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhh--HHHHHHHHHhCCCCHHHHHHHHhhc
Q 028179 84 QALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELET--VSEILGYLRNLSLSDDDIRKLLKKF 150 (212)
Q Consensus 84 ~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~--i~aklefLksLG~Sd~eI~k~vkK~ 150 (212)
++-+.+|+++..++---.. |++... .+...-.-.-+++. .-..+..|+.+|+|-++|..++...
T Consensus 5 eva~~~gvs~~tlR~ye~~--Gll~p~-~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~~ 70 (108)
T cd04773 5 ELAHLLGVPPSTLRHWEKE--GLLSPD-REPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQL 70 (108)
T ss_pred HHHHHHCcCHHHHHHHHHC--CCCCCC-cCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHh
Confidence 4457889999988665433 552110 00000000122333 3356778889999999999999864
No 167
>PF14490 HHH_4: Helix-hairpin-helix containing domain; PDB: 3GPL_A 3E1S_A 3GP8_A.
Probab=21.09 E-value=1.1e+02 Score=22.84 Aligned_cols=29 Identities=28% Similarity=0.481 Sum_probs=20.3
Q ss_pred hhHHHHHHHHHhCCCCHHHHHHHHhhcCc
Q 028179 124 ETVSEILGYLRNLSLSDDDIRKLLKKFPE 152 (212)
Q Consensus 124 e~i~aklefLksLG~Sd~eI~k~vkK~P~ 152 (212)
..+...+.||..+|+|...+.++.++|-.
T Consensus 6 ~~~~~~~~~L~~~gl~~~~a~kl~~~yg~ 34 (94)
T PF14490_consen 6 RGLRELMAFLQEYGLSPKLAMKLYKKYGD 34 (94)
T ss_dssp ---HHHHHHHHHTT--HHHHHHHHHHH-T
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHHHHHhH
Confidence 34567899999999999999999988643
No 168
>PF02617 ClpS: ATP-dependent Clp protease adaptor protein ClpS; InterPro: IPR003769 In the bacterial cytosol, ATP-dependent protein degradation is performed by several different chaperone-protease pairs, including ClpAP. ClpS directly influences the ClpAP machine by binding to the N-terminal domain of the chaperone ClpA. The degradation of ClpAP substrates, both SsrA-tagged proteins and ClpA itself, is specifically inhibited by ClpS. ClpS modifies ClpA substrate specificity, potentially redirecting degradation by ClpAP toward aggregated proteins []. ClpS is a small alpha/beta protein that consists of three alpha-helices connected to three antiparallel beta-strands []. The protein has a globular shape, with a curved layer of three antiparallel alpha-helices over a twisted antiparallel beta-sheet. Dimerization of ClpS may occur through its N-terminal domain. This short extended N-terminal region in ClpS is followed by the central seven-residue beta-strand, which is flanked by two other beta-strands in a small beta-sheet. ; GO: 0030163 protein catabolic process; PDB: 3O2O_B 1MBU_D 3O2B_C 2WA9_D 3O1F_A 2W9R_A 1MG9_A 1MBX_C 2WA8_C 1R6O_D ....
Probab=20.77 E-value=81 Score=23.00 Aligned_cols=35 Identities=23% Similarity=0.303 Sum_probs=25.8
Q ss_pred cChHHHHHHHHHHHHh-hhCCCChHHHHHHHHhhhh
Q 028179 71 LNDEERKKWEACRQAL-STFNFSTEEEDKILGKAFG 105 (212)
Q Consensus 71 ~~~~~~~~we~~v~~L-~~LGfspe~v~~il~rA~g 105 (212)
|=++|--.+++++..| +.+|.+.+.+..+...+..
T Consensus 11 L~NDe~ht~~~Vi~~L~~~~~~s~~~A~~~a~~v~~ 46 (82)
T PF02617_consen 11 LWNDEVHTFEQVIDVLRRVFGCSEEQARQIAMEVHR 46 (82)
T ss_dssp EE--SSSBHHHHHHHHHHHC---HHHHHHHHHHHHH
T ss_pred EEcCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHhH
Confidence 4467778889999999 7999999999999988863
No 169
>PF07223 DUF1421: Protein of unknown function (DUF1421); InterPro: IPR010820 This family represents a conserved region approximately 350 residues long within a number of plant proteins of unknown function.
Probab=20.74 E-value=1e+02 Score=29.39 Aligned_cols=25 Identities=8% Similarity=0.450 Sum_probs=21.9
Q ss_pred HHHHHHHHHhCCCCHHHHHHHHhhc
Q 028179 126 VSEILGYLRNLSLSDDDIRKLLKKF 150 (212)
Q Consensus 126 i~aklefLksLG~Sd~eI~k~vkK~ 150 (212)
+...||-+.++||++|+|+.+|.|.
T Consensus 321 ~ddvidKv~~MGf~rDqV~a~v~rl 345 (358)
T PF07223_consen 321 YDDVIDKVASMGFRRDQVRATVRRL 345 (358)
T ss_pred HHHHHHHHHHcCCcHHHHHHHHHHH
Confidence 5578888999999999999999874
No 170
>COG3077 RelB DNA-damage-inducible protein J [DNA replication, recombination, and repair]
Probab=20.36 E-value=4.2e+02 Score=20.56 Aligned_cols=23 Identities=9% Similarity=0.216 Sum_probs=20.8
Q ss_pred HHHHHHhhhCCCChHHHHHHHHh
Q 028179 80 EACRQALSTFNFSTEEEDKILGK 102 (212)
Q Consensus 80 e~~v~~L~~LGfspe~v~~il~r 102 (212)
+++..+|+.+|+++.++-+|+..
T Consensus 17 ~eA~~Vl~~mGlt~S~airm~L~ 39 (88)
T COG3077 17 EEATAVLEEMGLTISDAIRMFLT 39 (88)
T ss_pred HHHHHHHHHhCCCHHHHHHHHHH
Confidence 78899999999999999888766
No 171
>COG2355 Zn-dependent dipeptidase, microsomal dipeptidase homolog [Amino acid transport and metabolism]
Probab=20.31 E-value=2.4e+02 Score=26.44 Aligned_cols=43 Identities=12% Similarity=0.197 Sum_probs=34.4
Q ss_pred cccchhhhhh-hhcCCChhhHHHHHHHHHhCCCCHHHHHHHHhh
Q 028179 107 IHSAYWSEER-KRETPELETVSEILGYLRNLSLSDDDIRKLLKK 149 (212)
Q Consensus 107 ~~S~~fr~a~-~~~v~s~e~i~aklefLksLG~Sd~eI~k~vkK 149 (212)
++|.|+.-.. ....-...++..-++-|...|+++++|.++..+
T Consensus 258 lGsDf~g~~~~p~gled~~~l~~l~~~L~~~G~~e~~i~~i~~~ 301 (313)
T COG2355 258 LGSDFDGGTGPPDGLEDVGKLPNLTAALIERGYSEEEIEKIAGE 301 (313)
T ss_pred ecccccCCCCCchhhcChhHHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 6787776655 245566788999999999999999999998764
No 172
>COG1460 Uncharacterized protein conserved in archaea [Function unknown]
Probab=20.25 E-value=4.8e+02 Score=21.21 Aligned_cols=84 Identities=18% Similarity=0.302 Sum_probs=56.8
Q ss_pred hhcccChHHHHHHHHHHHHhhhCCCChHHHHHHHHhhhhccccchhhhhhhhcCCChhhHHHHHHHHHhCCCCHHHHHHH
Q 028179 67 QSITLNDEERKKWEACRQALSTFNFSTEEEDKILGKAFGHIHSAYWSEERKRETPELETVSEILGYLRNLSLSDDDIRKL 146 (212)
Q Consensus 67 ~~~~~~~~~~~~we~~v~~L~~LGfspe~v~~il~rA~gl~~S~~fr~a~~~~v~s~e~i~aklefLksLG~Sd~eI~k~ 146 (212)
+-..+..+++..|+++..|-+ ++|+.+++++...-.+.. + .+.++.|+.=+ +==+.+|+..+
T Consensus 27 ~~~eL~y~~~~al~y~~kFak---ldpe~a~e~veEL~~i~~------------~-~e~~avkIadI--~P~t~~ElRsI 88 (114)
T COG1460 27 REEELTYEQREALEYAEKFAK---LDPEKARELVEELLSIVK------------M-SEKIAVKIADI--MPRTPDELRSI 88 (114)
T ss_pred ccccchHHHHHHHHHHHHHhc---CCHHHHHHHHHHHHhhcc------------c-cHHHHHHHHHh--CCCCHHHHHHH
Confidence 345688888888888887765 468888888877643321 1 35555555433 23467888888
Q ss_pred HhhcCceeecCccchhhhhhhhhhh
Q 028179 147 LKKFPEVLGCDIEHELRNNVQILGK 171 (212)
Q Consensus 147 vkK~P~ILg~SVEe~LkpkveFL~~ 171 (212)
+.+.=..+ + ++.|+.-.|++.+
T Consensus 89 la~e~~~~--s-~E~l~~Ildiv~K 110 (114)
T COG1460 89 LAKERVML--S-DEELDKILDIVDK 110 (114)
T ss_pred HHHccCCC--C-HHHHHHHHHHHHH
Confidence 88887777 4 6677777777654
Done!