Query psy2814
Match_columns 176
No_of_seqs 134 out of 545
Neff 6.8
Searched_HMMs 46136
Date Fri Aug 16 17:38:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2814.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2814hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00062 TATA-box-binding prot 100.0 5.4E-69 1.2E-73 427.2 23.3 176 1-176 2-177 (179)
2 cd04516 TBP_eukaryotes eukaryo 100.0 2.8E-68 6.1E-73 421.7 23.1 173 1-173 2-174 (174)
3 COG2101 SPT15 TATA-box binding 100.0 3.1E-67 6.7E-72 408.9 19.8 174 1-174 8-183 (185)
4 PRK00394 transcription factor; 100.0 4.7E-66 1E-70 410.8 23.4 174 1-174 1-176 (179)
5 KOG3302|consensus 100.0 3.3E-66 7.2E-71 409.0 20.7 176 1-176 23-198 (200)
6 cd04518 TBP_archaea archaeal T 100.0 1.3E-65 2.7E-70 406.6 23.2 172 1-173 2-174 (174)
7 cd00652 TBP_TLF TATA box bindi 100.0 1.3E-65 2.9E-70 406.8 22.8 172 1-172 2-174 (174)
8 cd04517 TLF TBP-like factors ( 100.0 1.2E-64 2.6E-69 401.1 22.9 171 1-172 3-174 (174)
9 PF00352 TBP: Transcription fa 100.0 4.3E-32 9.4E-37 192.2 10.9 86 88-174 1-86 (86)
10 PF00352 TBP: Transcription fa 100.0 1.1E-31 2.4E-36 190.1 10.6 83 1-83 4-86 (86)
11 COG2101 SPT15 TATA-box binding 100.0 1.2E-29 2.6E-34 198.2 10.0 84 1-84 99-184 (185)
12 PRK00394 transcription factor; 100.0 4.3E-29 9.3E-34 198.7 11.3 84 1-84 92-177 (179)
13 cd04518 TBP_archaea archaeal T 100.0 1.2E-28 2.6E-33 195.3 10.8 82 1-82 93-174 (174)
14 cd04516 TBP_eukaryotes eukaryo 99.9 3.3E-27 7.2E-32 187.1 11.1 82 91-173 2-83 (174)
15 PLN00062 TATA-box-binding prot 99.9 6.1E-27 1.3E-31 186.2 11.1 82 91-173 2-83 (179)
16 cd00652 TBP_TLF TATA box bindi 99.9 6.8E-27 1.5E-31 185.4 10.8 81 1-81 93-174 (174)
17 cd04517 TLF TBP-like factors ( 99.9 1.2E-25 2.7E-30 178.1 11.0 82 90-173 2-83 (174)
18 KOG3302|consensus 99.9 2E-21 4.3E-26 154.3 10.2 85 88-173 20-104 (200)
19 PF11858 DUF3378: Domain of un 96.9 0.00092 2E-08 46.8 3.2 35 34-68 27-61 (81)
20 PF11858 DUF3378: Domain of un 96.9 0.0011 2.3E-08 46.5 3.3 35 124-158 26-60 (81)
21 COG4871 Uncharacterized protei 96.9 0.0075 1.6E-07 47.5 8.2 63 17-82 47-109 (193)
22 COG4871 Uncharacterized protei 95.5 0.1 2.3E-06 41.2 8.2 73 96-172 36-108 (193)
23 COG1039 RnhC Ribonuclease HIII 95.0 0.067 1.5E-06 45.7 6.0 42 124-165 27-68 (297)
24 PRK00996 ribonuclease HIII; Pr 94.7 0.069 1.5E-06 46.0 5.6 33 123-155 26-58 (304)
25 COG1039 RnhC Ribonuclease HIII 94.6 0.095 2.1E-06 44.8 5.9 46 34-79 28-73 (297)
26 TIGR00716 rnhC ribonuclease HI 94.4 0.072 1.6E-06 45.5 4.8 35 31-65 22-56 (284)
27 TIGR00716 rnhC ribonuclease HI 93.9 0.11 2.4E-06 44.3 5.1 33 122-154 22-54 (284)
28 PRK00996 ribonuclease HIII; Pr 93.8 0.11 2.4E-06 44.7 5.0 34 32-65 26-59 (304)
29 PRK12475 thiamine/molybdopteri 88.7 1.6 3.6E-05 38.0 6.9 59 14-75 277-336 (338)
30 PRK12475 thiamine/molybdopteri 88.3 1.4 3E-05 38.4 6.2 35 130-166 302-336 (338)
31 PRK11509 hydrogenase-1 operon 84.7 1.6 3.4E-05 33.3 4.0 61 106-167 56-124 (132)
32 TIGR02187 GlrX_arch Glutaredox 84.0 5.1 0.00011 32.2 7.0 116 46-164 78-213 (215)
33 PRK07688 thiamine/molybdopteri 82.7 3.4 7.3E-05 36.0 5.8 59 14-75 277-337 (339)
34 PRK15468 carboxysome structura 70.7 8.2 0.00018 28.5 4.0 34 52-87 72-106 (111)
35 PRK07688 thiamine/molybdopteri 69.6 18 0.00038 31.6 6.7 34 131-166 304-337 (339)
36 cd03065 PDI_b_Calsequestrin_N 69.4 9.6 0.00021 28.2 4.3 30 138-167 89-119 (120)
37 cd02965 HyaE HyaE family; HyaE 68.9 5.2 0.00011 29.5 2.8 52 108-160 51-109 (111)
38 KOG4749|consensus 66.4 2 4.2E-05 37.7 0.1 56 115-170 172-241 (375)
39 PF06277 EutA: Ethanolamine ut 65.5 30 0.00066 31.8 7.5 86 52-154 83-171 (473)
40 PLN00410 U5 snRNP protein, DIM 65.0 14 0.00031 28.3 4.6 64 18-81 45-125 (142)
41 PLN00410 U5 snRNP protein, DIM 64.8 13 0.00029 28.5 4.4 39 131-169 73-122 (142)
42 PRK15468 carboxysome structura 62.5 13 0.00029 27.4 3.8 33 138-172 67-99 (111)
43 cd03065 PDI_b_Calsequestrin_N 59.4 18 0.00038 26.8 4.1 31 46-76 88-119 (120)
44 PTZ00129 40S ribosomal protein 58.7 30 0.00064 27.0 5.3 52 34-85 36-91 (149)
45 PHA02278 thioredoxin-like prot 55.5 18 0.00038 25.9 3.5 24 138-161 74-99 (103)
46 PRK09381 trxA thioredoxin; Pro 54.8 18 0.0004 25.1 3.5 28 139-166 78-107 (109)
47 cd07049 BMC_EutL_repeat1 ethan 52.4 23 0.00051 25.8 3.7 27 145-172 71-99 (103)
48 PRK10996 thioredoxin 2; Provis 51.9 22 0.00048 26.5 3.7 28 139-166 109-138 (139)
49 cd01644 RT_pepA17 RT_pepA17: R 51.7 19 0.00042 29.1 3.5 30 58-87 144-173 (213)
50 TIGR02064 dsrA sulfite reducta 50.1 46 0.001 29.9 5.9 64 31-99 71-160 (402)
51 TIGR00090 iojap_ybeB iojap-lik 48.9 37 0.0008 24.2 4.2 34 52-86 28-61 (99)
52 cd02948 TRX_NDPK TRX domain, T 48.5 27 0.00058 24.3 3.5 26 139-165 74-101 (102)
53 PRK09381 trxA thioredoxin; Pro 48.0 26 0.00056 24.4 3.3 29 47-75 77-107 (109)
54 PF07338 DUF1471: Protein of u 47.8 27 0.00058 22.4 3.0 25 144-168 4-29 (56)
55 cd02963 TRX_DnaJ TRX domain, D 46.5 24 0.00052 25.1 3.0 27 139-165 82-110 (111)
56 KOG0910|consensus 46.4 35 0.00076 26.6 4.0 78 90-168 62-149 (150)
57 PHA02278 thioredoxin-like prot 45.0 30 0.00065 24.7 3.3 25 46-70 73-99 (103)
58 PRK11509 hydrogenase-1 operon 44.9 42 0.00092 25.4 4.2 31 46-76 92-124 (132)
59 cd07047 BMC_PduB_repeat1 1,2-p 44.8 37 0.0008 25.9 3.9 28 145-172 78-105 (134)
60 PF06200 tify: tify domain; I 44.0 63 0.0014 19.0 4.0 27 137-163 5-31 (36)
61 PF13575 DUF4135: Domain of un 43.2 23 0.00049 31.0 2.9 56 57-113 122-177 (370)
62 cd02963 TRX_DnaJ TRX domain, D 42.2 28 0.00061 24.7 2.8 28 47-74 81-110 (111)
63 PF14611 SLS: Mitochondrial in 42.1 1.6E+02 0.0034 23.3 7.5 98 47-170 57-163 (210)
64 cd02393 PNPase_KH Polynucleoti 42.0 56 0.0012 20.9 3.9 29 137-166 32-60 (61)
65 PF05005 Ocnus: Janus/Ocnus fa 41.2 54 0.0012 24.1 4.2 58 25-87 4-62 (108)
66 PF00085 Thioredoxin: Thioredo 41.0 62 0.0013 21.6 4.3 27 139-165 74-102 (103)
67 KOG0910|consensus 40.8 47 0.001 25.9 3.9 32 46-77 116-149 (150)
68 PRK10996 thioredoxin 2; Provis 40.3 40 0.00087 25.1 3.5 29 47-75 108-138 (139)
69 cd07049 BMC_EutL_repeat1 ethan 39.9 49 0.0011 24.2 3.7 28 54-82 71-100 (103)
70 PF13192 Thioredoxin_3: Thiore 38.5 38 0.00083 22.4 2.8 22 143-164 54-76 (76)
71 PF02838 Glyco_hydro_20b: Glyc 37.8 95 0.0021 22.1 5.1 38 45-83 75-112 (124)
72 PF13192 Thioredoxin_3: Thiore 37.6 37 0.0008 22.5 2.6 22 51-72 53-75 (76)
73 PF02410 Oligomerisation: Olig 37.6 65 0.0014 22.8 4.1 29 54-83 30-59 (100)
74 PRK11538 ribosome-associated p 37.0 73 0.0016 23.1 4.3 33 52-85 33-65 (105)
75 TIGR00385 dsbE periplasmic pro 36.2 58 0.0012 25.0 3.9 48 120-167 122-171 (173)
76 cd07996 WGR_MMR_like WGR domai 36.1 91 0.002 20.4 4.4 33 53-85 40-72 (74)
77 PRK10719 eutA reactivating fac 35.9 1.7E+02 0.0037 27.0 7.4 30 124-153 143-173 (475)
78 cd02950 TxlA TRX-like protein 35.7 75 0.0016 23.7 4.4 29 139-167 79-110 (142)
79 cd02985 TRX_CDSP32 TRX family, 34.9 72 0.0016 22.1 4.0 25 139-164 74-100 (103)
80 cd02988 Phd_like_VIAF Phosduci 34.7 28 0.00061 27.8 2.0 37 46-82 153-191 (192)
81 COG2221 DsrA Dissimilatory sul 34.1 31 0.00068 30.1 2.2 61 48-113 61-125 (317)
82 PF03135 CagE_TrbE_VirB: CagE, 34.1 62 0.0013 25.6 3.9 40 49-89 145-184 (205)
83 COG4978 Transcriptional regula 33.9 1.1E+02 0.0024 23.6 5.1 45 44-88 79-124 (153)
84 cd02949 TRX_NTR TRX domain, no 33.6 59 0.0013 22.1 3.3 25 139-163 70-96 (97)
85 CHL00041 rps11 ribosomal prote 33.2 1.5E+02 0.0033 21.8 5.5 52 34-85 21-75 (116)
86 KOG3384|consensus 33.0 29 0.00062 26.8 1.6 27 121-148 100-129 (154)
87 cd02956 ybbN ybbN protein fami 32.7 57 0.0012 21.8 3.0 25 139-163 69-95 (96)
88 TIGR03632 bact_S11 30S ribosom 32.5 1.6E+02 0.0034 21.3 5.5 51 35-85 9-62 (108)
89 PRK13011 formyltetrahydrofolat 32.3 3.1E+02 0.0068 23.2 8.3 95 57-163 10-110 (286)
90 PF12971 NAGLU_N: Alpha-N-acet 32.3 78 0.0017 21.9 3.7 25 144-169 40-64 (86)
91 TIGR03628 arch_S11P archaeal r 31.6 2.1E+02 0.0047 21.1 6.3 52 34-85 10-65 (114)
92 PF10865 DUF2703: Domain of un 31.5 51 0.0011 24.6 2.8 28 64-91 21-48 (120)
93 smart00115 CASc Caspase, inter 31.5 43 0.00094 27.5 2.6 42 43-86 5-46 (241)
94 PRK09607 rps11p 30S ribosomal 31.3 2.2E+02 0.0048 21.6 6.2 53 33-85 16-72 (132)
95 TIGR00411 redox_disulf_1 small 31.2 85 0.0018 20.2 3.6 22 145-166 60-81 (82)
96 PRK06027 purU formyltetrahydro 31.1 3.3E+02 0.0071 23.1 8.1 94 57-164 9-111 (286)
97 PRK10259 hypothetical protein; 31.0 59 0.0013 22.9 2.9 24 144-167 36-59 (86)
98 cd07047 BMC_PduB_repeat1 1,2-p 30.7 79 0.0017 24.1 3.7 28 54-81 78-105 (134)
99 TIGR01068 thioredoxin thioredo 30.4 90 0.0019 20.6 3.7 26 140-165 72-99 (101)
100 PF11399 DUF3192: Protein of u 29.8 86 0.0019 22.9 3.6 20 135-154 78-97 (102)
101 PF10686 DUF2493: Protein of u 29.6 78 0.0017 21.2 3.2 25 147-171 5-29 (71)
102 COG2761 FrnE Predicted dithiol 28.6 81 0.0018 26.2 3.7 78 89-168 135-214 (225)
103 cd03005 PDI_a_ERp46 PDIa famil 28.2 78 0.0017 21.2 3.1 23 139-161 76-100 (102)
104 PTZ00397 macrophage migration 28.1 1.7E+02 0.0037 20.9 5.1 45 44-94 56-101 (116)
105 PF10979 DUF2786: Protein of u 27.8 92 0.002 18.9 3.0 22 64-85 20-41 (43)
106 PF04628 Sedlin_N: Sedlin, N-t 27.2 2.6E+02 0.0056 20.6 6.6 50 122-171 48-103 (132)
107 PF05164 ZapA: Cell division p 27.2 1.3E+02 0.0029 20.1 4.1 38 138-175 2-39 (89)
108 PF11869 DUF3389: Protein of u 27.2 34 0.00073 23.6 1.0 11 142-152 4-14 (75)
109 cd00148 PROF Profilin binds ac 26.7 2.2E+02 0.0047 20.9 5.5 40 45-84 84-127 (127)
110 cd02950 TxlA TRX-like protein 26.5 1.4E+02 0.003 22.3 4.5 30 47-76 78-110 (142)
111 COG0678 AHP1 Peroxiredoxin [Po 26.3 38 0.00082 26.7 1.3 54 31-85 5-74 (165)
112 cd07046 BMC_PduU-EutS 1,2-prop 26.2 1.2E+02 0.0025 22.4 3.8 26 145-172 73-98 (110)
113 PF14359 DUF4406: Domain of un 25.9 59 0.0013 22.9 2.2 33 51-87 1-33 (92)
114 PF02785 Biotin_carb_C: Biotin 25.8 78 0.0017 23.0 2.8 25 146-174 52-76 (107)
115 PHA02956 hypothetical protein; 25.4 65 0.0014 25.0 2.4 23 52-85 113-135 (189)
116 PRK14126 cell division protein 25.4 1.8E+02 0.0039 20.1 4.5 38 137-175 8-45 (85)
117 COG0533 QRI7 Metal-dependent p 25.2 2.5E+02 0.0055 24.8 6.3 46 125-170 125-171 (342)
118 COG4274 Uncharacterized conser 25.2 1.1E+02 0.0023 22.4 3.4 57 58-114 18-76 (104)
119 COG3445 Acid-induced glycyl ra 25.0 27 0.00059 25.5 0.3 34 103-136 70-103 (127)
120 PTZ00051 thioredoxin; Provisio 24.9 87 0.0019 21.0 2.9 21 139-160 74-96 (98)
121 PF14356 DUF4403: Domain of un 24.9 1.2E+02 0.0025 27.2 4.4 53 98-153 5-60 (427)
122 PRK15412 thiol:disulfide inter 24.8 1.5E+02 0.0032 23.0 4.5 52 120-171 127-180 (185)
123 TIGR01175 pilM type IV pilus a 24.8 3.6E+02 0.0078 22.8 7.2 72 69-153 142-215 (348)
124 PF11775 CobT_C: Cobalamin bio 24.6 1.5E+02 0.0032 24.6 4.5 49 43-94 11-59 (219)
125 COG4810 EutS Ethanolamine util 24.5 1.4E+02 0.0029 22.0 3.8 30 141-172 80-109 (121)
126 cd02394 vigilin_like_KH K homo 24.5 1.2E+02 0.0027 18.8 3.4 20 145-166 42-61 (62)
127 PF12864 DUF3822: Protein of u 24.4 3.2E+02 0.0069 22.4 6.6 54 36-89 174-227 (253)
128 PF14657 Integrase_AP2: AP2-li 24.3 1.2E+02 0.0025 18.2 3.0 25 57-81 19-43 (46)
129 cd02975 PfPDO_like_N Pyrococcu 24.2 1.8E+02 0.0038 20.7 4.5 30 139-168 78-111 (113)
130 PF00403 HMA: Heavy-metal-asso 23.8 87 0.0019 19.4 2.5 24 142-165 32-58 (62)
131 PF08002 DUF1697: Protein of u 23.8 1.4E+02 0.0031 22.4 4.1 29 141-169 38-66 (137)
132 PRK05309 30S ribosomal protein 23.6 2E+02 0.0042 21.6 4.7 53 33-85 24-79 (128)
133 PRK09929 hypothetical protein; 23.5 85 0.0018 22.4 2.6 23 145-167 40-62 (91)
134 PF05362 Lon_C: Lon protease ( 22.9 1.6E+02 0.0034 23.9 4.4 36 51-86 50-88 (204)
135 cd00448 YjgF_YER057c_UK114_fam 22.6 99 0.0021 21.1 2.8 36 50-85 10-51 (107)
136 cd03715 RT_ZFREV_like RT_ZFREV 22.5 1.5E+02 0.0032 23.4 4.2 28 61-88 166-193 (210)
137 PF13382 Adenine_deam_C: Adeni 22.4 98 0.0021 24.4 3.0 26 50-76 61-86 (171)
138 PF05132 RNA_pol_Rpc4: RNA pol 22.2 68 0.0015 23.9 2.0 17 135-151 67-83 (131)
139 PRK11023 outer membrane lipopr 22.1 4E+02 0.0087 21.0 7.2 104 46-164 69-172 (191)
140 COG0678 AHP1 Peroxiredoxin [Po 21.9 57 0.0012 25.7 1.5 32 122-153 5-45 (165)
141 PF08002 DUF1697: Protein of u 21.8 1.5E+02 0.0032 22.3 3.8 36 50-87 38-73 (137)
142 cd01645 RT_Rtv RT_Rtv: Reverse 21.6 1.3E+02 0.0029 23.9 3.7 38 49-88 160-197 (213)
143 TIGR01651 CobT cobaltochelatas 21.4 1.5E+02 0.0032 28.3 4.3 46 46-94 394-439 (600)
144 PRK15415 propanediol utilizati 21.3 1.6E+02 0.0034 25.2 4.2 29 145-173 119-147 (266)
145 cd06150 YjgF_YER057c_UK114_lik 21.3 1E+02 0.0022 21.6 2.7 38 50-87 12-50 (105)
146 PF13382 Adenine_deam_C: Adeni 21.2 1.1E+02 0.0025 24.1 3.2 25 143-168 63-87 (171)
147 PRK03988 translation initiatio 21.0 1.5E+02 0.0033 22.6 3.7 31 48-79 72-102 (138)
148 cd02994 PDI_a_TMX PDIa family, 21.0 1.3E+02 0.0029 20.2 3.2 24 141-164 76-100 (101)
149 COG1163 DRG Predicted GTPase [ 20.9 2.2E+02 0.0048 25.3 5.1 76 37-125 168-243 (365)
150 KOG2360|consensus 20.9 1.1E+02 0.0025 27.5 3.4 85 25-113 273-358 (413)
151 PF03481 SUA5: Putative GTP-bi 20.8 2.9E+02 0.0062 20.1 5.1 49 126-174 27-95 (125)
152 PF11525 CopK: Copper resistan 20.8 80 0.0017 21.5 1.9 20 40-60 10-29 (73)
153 COG0799 Uncharacterized homolo 20.7 2E+02 0.0042 21.4 4.1 28 57-85 38-65 (115)
154 PF13098 Thioredoxin_2: Thiore 20.6 1.5E+02 0.0033 20.3 3.5 25 139-163 85-112 (112)
155 smart00878 Biotin_carb_C Bioti 20.5 1.1E+02 0.0024 22.1 2.7 25 146-174 52-76 (107)
156 TIGR01200 Porphyromonas gingiv 20.4 3.2E+02 0.007 23.6 5.9 53 119-171 192-260 (292)
157 PF05406 WGR: WGR domain; Int 20.3 2.6E+02 0.0056 18.7 4.5 34 53-86 43-76 (81)
158 PRK11127 autonomous glycyl rad 20.2 19 0.00042 27.1 -1.3 20 118-137 85-104 (127)
159 COG1364 ArgJ N-acetylglutamate 20.1 96 0.0021 28.0 2.8 22 56-77 284-305 (404)
160 PF03332 PMM: Eukaryotic phosp 20.1 1.2E+02 0.0026 25.1 3.2 90 51-146 49-160 (220)
161 PF11504 Colicin_Ia: Colicin I 20.1 69 0.0015 21.1 1.4 9 30-38 10-18 (72)
162 KOG4180|consensus 20.1 1.6E+02 0.0035 26.1 4.1 73 48-136 254-334 (395)
No 1
>PLN00062 TATA-box-binding protein; Provisional
Probab=100.00 E-value=5.4e-69 Score=427.25 Aligned_cols=176 Identities=57% Similarity=1.019 Sum_probs=173.1
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
++|+|||||++++|++||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|+
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 2 PTLQNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARIIQ 81 (179)
T ss_pred cEEEEEEEEEEcCCcccHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCcccceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHH
Q psy2814 81 QLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELH 160 (176)
Q Consensus 81 ~~g~~~~~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~ 160 (176)
++|+++++.+|+|+|||||+|++++|||+.|+..|+++++||||+||||+||+.+|+++++||+||||+|||||+++|++
T Consensus 82 ~lg~~~~~~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~ 161 (179)
T PLN00062 82 KLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIY 161 (179)
T ss_pred HcCCCcCCCccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHHH
Confidence 99999999999999999999999999999999888899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhcC
Q psy2814 161 EAFDNIYPVLKSFKKQ 176 (176)
Q Consensus 161 ~a~~~i~~~L~~~r~~ 176 (176)
+|++.|+|+|.+||++
T Consensus 162 ~ai~~i~p~L~~~~~~ 177 (179)
T PLN00062 162 TAFENIYPVLTEFRKR 177 (179)
T ss_pred HHHHHHHHHHHHhccC
Confidence 9999999999999975
No 2
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=100.00 E-value=2.8e-68 Score=421.71 Aligned_cols=173 Identities=60% Similarity=1.065 Sum_probs=170.2
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
++|+|||||++++|++||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+|+++.|+++++++|+
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 2 PKIQNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARIIQ 81 (174)
T ss_pred CEEEEEEEEEEcCCeecHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCcccceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHH
Q psy2814 81 QLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELH 160 (176)
Q Consensus 81 ~~g~~~~~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~ 160 (176)
++|+++++.+|+|+|||||+|++++|||++|+..++++++||||+||||+||+.+|+++++||+||||+|||+||++|++
T Consensus 82 ~~g~~~~~~~~~v~Nivat~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~ 161 (174)
T cd04516 82 KLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEIY 161 (174)
T ss_pred HcCCCCCCCceEEEEEEEEEECCCcccHHHHHHhChhccEeCCccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHH
Confidence 99999999999999999999999999999999888899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhh
Q psy2814 161 EAFDNIYPVLKSF 173 (176)
Q Consensus 161 ~a~~~i~~~L~~~ 173 (176)
+|+++|+|+|.+|
T Consensus 162 ~a~~~i~p~L~~~ 174 (174)
T cd04516 162 QAFENIYPILLQF 174 (174)
T ss_pred HHHHHHHHHHhhC
Confidence 9999999999986
No 3
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=100.00 E-value=3.1e-67 Score=408.86 Aligned_cols=174 Identities=39% Similarity=0.665 Sum_probs=169.3
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
|+|+|||||.+|++++||.+++..+++++|||++||||+||+.+|+++++||+|||++||||||+++++.|+++++++|+
T Consensus 8 i~IeNIVAS~~L~~elDL~~~~~~l~~aeYnP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGaKs~ed~~~av~~~~~~L~ 87 (185)
T COG2101 8 ITIENIVASVDLGQELDLEEVALDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGAKSVEDVHRAVKKLAKKLK 87 (185)
T ss_pred cEEEEEEEEechhhhccHHHHHhhCCCCccCHhHCCeeEEEecCCcceEEEEecCcEEEeccCcHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCccc-ceeeeeeEEEEeeeCcccCHHHHHHHcC-CCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHH
Q psy2814 81 QLGHPIKY-QGFKIHNIVCTCDVRFPVKLDALHHVHS-QFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSE 158 (176)
Q Consensus 81 ~~g~~~~~-~~~~i~nIvas~~l~~~i~L~~l~~~~~-~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~ 158 (176)
+.|+++.+ ++++|||||||+|++.++||+.+|..++ ++++|||||||||+||+.+|+++++||.|||+||||||+++|
T Consensus 88 ~~g~~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~ed 167 (185)
T COG2101 88 DGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEED 167 (185)
T ss_pred hcCcCcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCHHH
Confidence 99999987 7999999999999999999999998765 569999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhh
Q psy2814 159 LHEAFDNIYPVLKSFK 174 (176)
Q Consensus 159 ~~~a~~~i~~~L~~~r 174 (176)
+++|+++|++.|.++.
T Consensus 168 ~~~Av~~i~~~L~elg 183 (185)
T COG2101 168 AEQAVEKIQSRLEELG 183 (185)
T ss_pred HHHHHHHHHHHHHHhc
Confidence 9999999999999875
No 4
>PRK00394 transcription factor; Reviewed
Probab=100.00 E-value=4.7e-66 Score=410.78 Aligned_cols=174 Identities=36% Similarity=0.626 Sum_probs=168.9
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
|+|+|||||+++++++||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|+
T Consensus 1 i~i~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~S~~~a~~a~~~~~~~l~ 80 (179)
T PRK00394 1 IKIENIVASTDLGQELDLEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAKSVEDLHEAVKIIIKKLK 80 (179)
T ss_pred CEEEEEEEEEEcCCCcCHHHHHhhCCCceeCcccCceEEEEecCCceEEEEEcCCcEEEEccCCHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCcc-cceeeeeeEEEEeeeCcccCHHHHHHHc-CCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHH
Q psy2814 81 QLGHPIK-YQGFKIHNIVCTCDVRFPVKLDALHHVH-SQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSE 158 (176)
Q Consensus 81 ~~g~~~~-~~~~~i~nIvas~~l~~~i~L~~l~~~~-~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~ 158 (176)
++|+++. ..+|+|+|||||+|++++|||++++..+ .++++||||+||||+||+.+|+++++||+||||+||||||++|
T Consensus 81 ~~g~~~~~~~~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~ 160 (179)
T PRK00394 81 ELGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEED 160 (179)
T ss_pred HcCCCccCCCceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHH
Confidence 9999986 5899999999999999999999999765 3789999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhhh
Q psy2814 159 LHEAFDNIYPVLKSFK 174 (176)
Q Consensus 159 ~~~a~~~i~~~L~~~r 174 (176)
+++|+++|+|.|+++.
T Consensus 161 ~~~a~~~i~~~l~~~g 176 (179)
T PRK00394 161 AEKAVEKILEKLEELG 176 (179)
T ss_pred HHHHHHHHHHHHHHcC
Confidence 9999999999999875
No 5
>KOG3302|consensus
Probab=100.00 E-value=3.3e-66 Score=409.02 Aligned_cols=176 Identities=56% Similarity=0.992 Sum_probs=173.6
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
+.++||||+++++|++||.+||...+|++|||++|++++||++.|++|++||+||||+||||+|+++++.|+++++++||
T Consensus 23 ~~l~nivc~~~~~c~ldLk~ial~~~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~aRilq 102 (200)
T KOG3302|consen 23 PTLQNIVCTVNLNCKLDLKEIALHARNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKYARILQ 102 (200)
T ss_pred eEEEeEEEEEeccceecHHHHhhhccccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHHHHHHH
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCcccceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHH
Q psy2814 81 QLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELH 160 (176)
Q Consensus 81 ~~g~~~~~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~ 160 (176)
++||++++.||++|||+||||++|+|+||.|+..|+.+++||||+||||+|||.+|+++++||+||||++|||++.+|+.
T Consensus 103 kLgf~~~f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~~~i~ 182 (200)
T KOG3302|consen 103 KLGFPVKFRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVREETY 182 (200)
T ss_pred HcCCCceehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccHHHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhcC
Q psy2814 161 EAFDNIYPVLKSFKKQ 176 (176)
Q Consensus 161 ~a~~~i~~~L~~~r~~ 176 (176)
+|+++|+|+|.+|||+
T Consensus 183 ~Ai~~IyPil~~frk~ 198 (200)
T KOG3302|consen 183 EAIENIYPILLEFRKK 198 (200)
T ss_pred HHHHHHhHHHHHhhhc
Confidence 9999999999999985
No 6
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=100.00 E-value=1.3e-65 Score=406.58 Aligned_cols=172 Identities=37% Similarity=0.669 Sum_probs=166.9
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
++|+|||||++++++|||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|+
T Consensus 2 ~~I~NvVas~~l~~~ldL~~la~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGaks~~~a~~a~~~~~~~L~ 81 (174)
T cd04518 2 LKIENIVASVDLGQELDLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGAKSVEDLHRAVKEIIKKLK 81 (174)
T ss_pred cEEEEEEEEEEcCCeecHHHHHhhCCCcEECCCcCcEEEEEccCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHH
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCcc-cceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHH
Q psy2814 81 QLGHPIK-YQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSEL 159 (176)
Q Consensus 81 ~~g~~~~-~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~ 159 (176)
++|++.. ..+|+|+|||||++++++|||++++..++ +++||||+||||+||+.+|+++++||+||||+||||||++|+
T Consensus 82 ~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~la~~~~-~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~~ 160 (174)
T cd04518 82 DYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIGLP-NAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDA 160 (174)
T ss_pred hcCCCccCCCceEEEEEEEEEEcCCccCHHHHHhhCC-CCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 9999876 47999999999999999999999998775 899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhh
Q psy2814 160 HEAFDNIYPVLKSF 173 (176)
Q Consensus 160 ~~a~~~i~~~L~~~ 173 (176)
++|+++|+|.|+++
T Consensus 161 ~~a~~~i~~~l~~~ 174 (174)
T cd04518 161 KRAVEKLLSRLKEL 174 (174)
T ss_pred HHHHHHHHHHHhhC
Confidence 99999999999874
No 7
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=100.00 E-value=1.3e-65 Score=406.76 Aligned_cols=172 Identities=56% Similarity=1.004 Sum_probs=168.3
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
++|+||||+++++|++||.+||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|+
T Consensus 2 ~~i~NvVas~~l~~~idL~~la~~~~n~~YePe~fpgli~R~~~P~~t~lIf~sGKivitGaks~~~~~~a~~~~~~~L~ 81 (174)
T cd00652 2 PKIQNIVATVNLGCELDLRKIALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGAKSEEDAKLAARKYARILQ 81 (174)
T ss_pred cEEEEEEEEEEcCCccCHHHHHhhCCCcEECCCccceEEEEcCCCcEEEEEECCCEEEEEecCCHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcCCCc-ccceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHH
Q psy2814 81 QLGHPI-KYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSEL 159 (176)
Q Consensus 81 ~~g~~~-~~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~ 159 (176)
++|+++ ++.+|+|+|||||++++++|||++|+..++++++||||+||||+||+.+|++|++||+||||+||||||++|+
T Consensus 82 ~~g~~~~~~~~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~ 161 (174)
T cd00652 82 KLGFPVEKFPEFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDI 161 (174)
T ss_pred HcCCCccccCceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHH
Confidence 999987 7899999999999999999999999998878999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHh
Q psy2814 160 HEAFDNIYPVLKS 172 (176)
Q Consensus 160 ~~a~~~i~~~L~~ 172 (176)
++|+++|+|+|.+
T Consensus 162 ~~a~~~i~~~L~~ 174 (174)
T cd00652 162 YEAVEKIYPILKE 174 (174)
T ss_pred HHHHHHHHHHHhC
Confidence 9999999999974
No 8
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=100.00 E-value=1.2e-64 Score=401.12 Aligned_cols=171 Identities=37% Similarity=0.742 Sum_probs=167.2
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
++|+|||||+++++++||+++|..++|++||| +|||++||+++|+++++||+|||++|||++|+++++.|+++++++|+
T Consensus 3 ~~i~Nvvas~~l~~~idL~~la~~l~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 3 ILIVNVVCQFSLRCHIDLRKLALAGRNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred cEEEEEEEEEEcCCcccHHHHHhhCCCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999 99999999999999999999999999999999999999999999999
Q ss_pred hcCCCc-ccceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHH
Q psy2814 81 QLGHPI-KYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSEL 159 (176)
Q Consensus 81 ~~g~~~-~~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~ 159 (176)
++|++. ++.+|+|+||||++|++++|||++|+..+.++++||||+||||+||+.+|++|++||+||||+|||+|+++|+
T Consensus 82 ~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~ 161 (174)
T cd04517 82 KLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDV 161 (174)
T ss_pred HcCCCcccCCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 999987 7899999999999999999999999988888999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHh
Q psy2814 160 HEAFDNIYPVLKS 172 (176)
Q Consensus 160 ~~a~~~i~~~L~~ 172 (176)
++|+++|+|+|.+
T Consensus 162 ~~a~~~i~pil~~ 174 (174)
T cd04517 162 REAVEKIYPIVFE 174 (174)
T ss_pred HHHHHHHHHHHhC
Confidence 9999999999974
No 9
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=99.98 E-value=4.3e-32 Score=192.19 Aligned_cols=86 Identities=45% Similarity=0.817 Sum_probs=80.8
Q ss_pred cceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHHHH
Q psy2814 88 YQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIY 167 (176)
Q Consensus 88 ~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~i~ 167 (176)
|++++|+||||+++++++|||++|+..+ ++++||||+|||++||+.+|+++++||+||||+||||+|++++++|+++++
T Consensus 1 ~~~~~i~NIva~~~l~~~idL~~la~~~-~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~ 79 (86)
T PF00352_consen 1 FPDFKIVNIVASFDLPFEIDLEELAEEL-ENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKIL 79 (86)
T ss_dssp -EEEEEEEEEEEEE-SSEB-HHHHHHHS-TTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHH
T ss_pred CCccEEEEEEEEEECCCccCHHHHHhhc-cCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHH
Confidence 4789999999999999999999999877 899999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhh
Q psy2814 168 PVLKSFK 174 (176)
Q Consensus 168 ~~L~~~r 174 (176)
|+|++++
T Consensus 80 ~~L~~~~ 86 (86)
T PF00352_consen 80 PILQKLG 86 (86)
T ss_dssp HHHHHTT
T ss_pred HHHHHcC
Confidence 9999985
No 10
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=99.97 E-value=1.1e-31 Score=190.10 Aligned_cols=83 Identities=37% Similarity=0.670 Sum_probs=79.2
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
++|+||||+++++++|||.+||..++|++|||++|||++||+++|+++++||+||||+|||++|+++++.|+++++++|+
T Consensus 4 ~~i~NIva~~~l~~~idL~~la~~~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~~~L~ 83 (86)
T PF00352_consen 4 FKIVNIVASFDLPFEIDLEELAEELENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKILPILQ 83 (86)
T ss_dssp EEEEEEEEEEE-SSEB-HHHHHHHSTTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHHHHH
T ss_pred cEEEEEEEEEECCCccCHHHHHhhccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hcC
Q psy2814 81 QLG 83 (176)
Q Consensus 81 ~~g 83 (176)
++|
T Consensus 84 ~~~ 86 (86)
T PF00352_consen 84 KLG 86 (86)
T ss_dssp HTT
T ss_pred HcC
Confidence 986
No 11
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=99.96 E-value=1.2e-29 Score=198.18 Aligned_cols=84 Identities=39% Similarity=0.636 Sum_probs=80.5
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCC--cEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRY--SEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKI 78 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n--~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~ 78 (176)
|+|||||||++|+.++||+.+|..+.+ ++||||+||||+||+.+|++.++||+|||+||||+|+++|++.|++++.+.
T Consensus 99 i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~ed~~~Av~~i~~~ 178 (185)
T COG2101 99 IKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKIQSR 178 (185)
T ss_pred eEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCHHHHHHHHHHHHHH
Confidence 689999999999999999999987654 999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCC
Q psy2814 79 LKQLGH 84 (176)
Q Consensus 79 L~~~g~ 84 (176)
|+++|.
T Consensus 179 L~elgl 184 (185)
T COG2101 179 LEELGL 184 (185)
T ss_pred HHHhcc
Confidence 999874
No 12
>PRK00394 transcription factor; Reviewed
Probab=99.96 E-value=4.3e-29 Score=198.71 Aligned_cols=84 Identities=38% Similarity=0.638 Sum_probs=81.5
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcC--CCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRV--RYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKI 78 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~--~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~ 78 (176)
++|+|||||++++++|||+.+|... +|++||||+||||+||+.+|+++++||+||||+||||||+++++.|+++++++
T Consensus 92 ~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~~~ 171 (179)
T PRK00394 92 IKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDAEKAVEKILEK 171 (179)
T ss_pred eEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHH
Confidence 4799999999999999999999876 89999999999999999999999999999999999999999999999999999
Q ss_pred HHhcCC
Q psy2814 79 LKQLGH 84 (176)
Q Consensus 79 L~~~g~ 84 (176)
|+++|+
T Consensus 172 l~~~g~ 177 (179)
T PRK00394 172 LEELGL 177 (179)
T ss_pred HHHcCC
Confidence 999985
No 13
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=99.96 E-value=1.2e-28 Score=195.31 Aligned_cols=82 Identities=37% Similarity=0.620 Sum_probs=79.5
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~ 80 (176)
++|+|||||++++++|||+.+|...+|++||||+||||+||+.+|+++++||+||||+|||+||+++++.|+++++++|+
T Consensus 93 ~~i~NIVas~~l~~~i~L~~la~~~~~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~~~l~ 172 (174)
T cd04518 93 IKVQNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDAKRAVEKLLSRLK 172 (174)
T ss_pred eEEEEEEEEEEcCCccCHHHHHhhCCCCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHHh
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred hc
Q psy2814 81 QL 82 (176)
Q Consensus 81 ~~ 82 (176)
++
T Consensus 173 ~~ 174 (174)
T cd04518 173 EL 174 (174)
T ss_pred hC
Confidence 64
No 14
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=99.95 E-value=3.3e-27 Score=187.08 Aligned_cols=82 Identities=29% Similarity=0.487 Sum_probs=78.5
Q ss_pred eeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHHHHHHH
Q psy2814 91 FKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVL 170 (176)
Q Consensus 91 ~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~i~~~L 170 (176)
++|+|||||++++++|||++|+..+ ++++||||+||||+||+.+|+++++||+||||+||||+|+++++.|+++++++|
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L 80 (174)
T cd04516 2 PKIQNIVATVNLGCKLDLKKIALRA-RNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII 80 (174)
T ss_pred CEEEEEEEEEEcCCeecHHHHHhhC-CCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 6899999999999999999999654 779999999999999999999999999999999999999999999999999999
Q ss_pred Hhh
Q psy2814 171 KSF 173 (176)
Q Consensus 171 ~~~ 173 (176)
+++
T Consensus 81 ~~~ 83 (174)
T cd04516 81 QKL 83 (174)
T ss_pred HHc
Confidence 875
No 15
>PLN00062 TATA-box-binding protein; Provisional
Probab=99.94 E-value=6.1e-27 Score=186.23 Aligned_cols=82 Identities=27% Similarity=0.474 Sum_probs=78.3
Q ss_pred eeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHHHHHHH
Q psy2814 91 FKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVL 170 (176)
Q Consensus 91 ~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~i~~~L 170 (176)
++|+|||||++++++|||++|+... ++++||||+||||+||+.+|+++++||+||||+||||||+++++.|++++.++|
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 2 PTLQNIVSTVNLDCKLDLKKIALQA-RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARII 80 (179)
T ss_pred cEEEEEEEEEEcCCcccHHHHHhhC-CCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 5899999999999999999999654 789999999999999999999999999999999999999999999999999999
Q ss_pred Hhh
Q psy2814 171 KSF 173 (176)
Q Consensus 171 ~~~ 173 (176)
++.
T Consensus 81 ~~l 83 (179)
T PLN00062 81 QKL 83 (179)
T ss_pred HHc
Confidence 874
No 16
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=99.94 E-value=6.8e-27 Score=185.39 Aligned_cols=81 Identities=35% Similarity=0.575 Sum_probs=77.9
Q ss_pred CeEEEEEEEEEeCCccChhhHhhcCC-CcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHH
Q psy2814 1 MHYQNMVGTISVGCPLDLNQINSRVR-YSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKIL 79 (176)
Q Consensus 1 ~~I~Nvvas~~l~~~idL~~la~~~~-n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L 79 (176)
.+|+|||||++++++|||++||...+ +++||||+|||++||+.+|++|++||+||||+|||+||+++++.|++++.++|
T Consensus 93 ~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i~~~L 172 (174)
T cd00652 93 FKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPIL 172 (174)
T ss_pred eEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence 37999999999999999999999875 99999999999999999999999999999999999999999999999999998
Q ss_pred Hh
Q psy2814 80 KQ 81 (176)
Q Consensus 80 ~~ 81 (176)
++
T Consensus 173 ~~ 174 (174)
T cd00652 173 KE 174 (174)
T ss_pred hC
Confidence 64
No 17
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=99.93 E-value=1.2e-25 Score=178.13 Aligned_cols=82 Identities=28% Similarity=0.500 Sum_probs=78.3
Q ss_pred eeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHHHHHH
Q psy2814 90 GFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPV 169 (176)
Q Consensus 90 ~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~i~~~ 169 (176)
+++|+||||+++++++|||++++..+ ++++||| +||||+||+.+|+++++||+|||++|||+||+++++.|++++.++
T Consensus 2 ~~~i~Nvvas~~l~~~idL~~la~~l-~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~ 79 (174)
T cd04517 2 DILIVNVVCQFSLRCHIDLRKLALAG-RNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARL 79 (174)
T ss_pred ccEEEEEEEEEEcCCcccHHHHHhhC-CCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHH
Confidence 68999999999999999999999654 7899999 999999999999999999999999999999999999999999999
Q ss_pred HHhh
Q psy2814 170 LKSF 173 (176)
Q Consensus 170 L~~~ 173 (176)
|++.
T Consensus 80 l~~~ 83 (174)
T cd04517 80 LQKL 83 (174)
T ss_pred HHHc
Confidence 9874
No 18
>KOG3302|consensus
Probab=99.86 E-value=2e-21 Score=154.29 Aligned_cols=85 Identities=32% Similarity=0.527 Sum_probs=80.7
Q ss_pred cceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHHHH
Q psy2814 88 YQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIY 167 (176)
Q Consensus 88 ~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~i~ 167 (176)
..++.++||||++++++++||.+|+. +..|++|||+.|+++++|++.|++|++||+||||+||||+|+++.+.|.+++.
T Consensus 20 ~i~~~l~nivc~~~~~c~ldLk~ial-~~~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~a 98 (200)
T KOG3302|consen 20 GLDPTLQNIVCTVNLNCKLDLKEIAL-HARNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKYA 98 (200)
T ss_pred ccceEEEeEEEEEeccceecHHHHhh-hccccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHHH
Confidence 36788999999999999999999994 56899999999999999999999999999999999999999999999999999
Q ss_pred HHHHhh
Q psy2814 168 PVLKSF 173 (176)
Q Consensus 168 ~~L~~~ 173 (176)
++|++.
T Consensus 99 RilqkL 104 (200)
T KOG3302|consen 99 RILQKL 104 (200)
T ss_pred HHHHHc
Confidence 999874
No 19
>PF11858 DUF3378: Domain of unknown function (DUF3378); InterPro: IPR024568 Ribonuclease HIII 3.1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other []. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This entry represents the uncharacterised N-terminal domain of bacterial RNase HIII.; PDB: 3ASM_A 2D0C_A 2D0B_A 2D0A_A.
Probab=96.93 E-value=0.00092 Score=46.82 Aligned_cols=35 Identities=23% Similarity=0.301 Sum_probs=28.9
Q ss_pred CCceEEEEEcCCeEEEEEecCccEEEEcccCHHHH
Q psy2814 34 KFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDC 68 (176)
Q Consensus 34 ~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~ 68 (176)
.=|+.+++.+.+.|++++|.|||++.-|...+..|
T Consensus 27 ~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~~Ae~~A 61 (81)
T PF11858_consen 27 KPPYAVFQAKYNGVTITAYKSGKVVFQGKNAEQEA 61 (81)
T ss_dssp --TTEEEEEEETTEEEEEETTSEEEEESTTHHHHH
T ss_pred CCCCEEEEEeCCCeEEEEEeCCeEEEECCCHHHHH
Confidence 33899999999999999999999999999444433
No 20
>PF11858 DUF3378: Domain of unknown function (DUF3378); InterPro: IPR024568 Ribonuclease HIII 3.1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other []. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This entry represents the uncharacterised N-terminal domain of bacterial RNase HIII.; PDB: 3ASM_A 2D0C_A 2D0B_A 2D0A_A.
Probab=96.89 E-value=0.0011 Score=46.49 Aligned_cols=35 Identities=17% Similarity=0.358 Sum_probs=28.9
Q ss_pred CCCceeEEEEcCCeEEEEEeccceEEEEecCCHHH
Q psy2814 124 ELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSE 158 (176)
Q Consensus 124 e~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~ 158 (176)
..-|+..|+...+.+|+++|.||||++-|...+.+
T Consensus 26 ~~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~~Ae~~ 60 (81)
T PF11858_consen 26 SKPPYAVFQAKYNGVTITAYKSGKVVFQGKNAEQE 60 (81)
T ss_dssp S--TTEEEEEEETTEEEEEETTSEEEEESTTHHHH
T ss_pred CCCCCEEEEEeCCCeEEEEEeCCeEEEECCCHHHH
Confidence 33489999999999999999999999999954433
No 21
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=96.88 E-value=0.0075 Score=47.49 Aligned_cols=63 Identities=19% Similarity=0.205 Sum_probs=53.8
Q ss_pred ChhhHhhcCCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhc
Q psy2814 17 DLNQINSRVRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQL 82 (176)
Q Consensus 17 dL~~la~~~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~ 82 (176)
=|..||..++++.|..++ .+++++.-+ .-++||.|||+.+|-.+++++|+..+..+..++++.
T Consensus 47 ilplla~l~P~anY~~kk-~~l~~~kge--rIitiy~sGkVsm~~ikdedEAkeilgel~d~ineA 109 (193)
T COG4871 47 ILPLLAPLFPRANYSDKK-NILILQKGE--RIITIYGSGKVSMTMIKDEDEAKEILGELMDIINEA 109 (193)
T ss_pred hHHHhHhhCCCccccccc-ceEEEeecc--EEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHHH
Confidence 356677788999999887 788888665 556799999999999999999999999999998874
No 22
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=95.54 E-value=0.1 Score=41.16 Aligned_cols=73 Identities=16% Similarity=0.268 Sum_probs=55.0
Q ss_pred EEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHHHHHHHHh
Q psy2814 96 IVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLKS 172 (176)
Q Consensus 96 Ivas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~i~~~L~~ 172 (176)
|.+..|=+++=-|..|+..+ +++.|... -..|+++.-+. -++||.||||.+|--|+++++++++..+..++.+
T Consensus 36 Vi~~md~~lg~ilplla~l~-P~anY~~k-k~~l~~~kger--Iitiy~sGkVsm~~ikdedEAkeilgel~d~ine 108 (193)
T COG4871 36 VIANMDPPLGGILPLLAPLF-PRANYSDK-KNILILQKGER--IITIYGSGKVSMTMIKDEDEAKEILGELMDIINE 108 (193)
T ss_pred EEeecCCCcchhHHHhHhhC-CCcccccc-cceEEEeeccE--EEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHH
Confidence 34444545555566677666 45889854 46777775554 4669999999999999999999999999888765
No 23
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=94.98 E-value=0.067 Score=45.73 Aligned_cols=42 Identities=21% Similarity=0.377 Sum_probs=35.4
Q ss_pred CCCceeEEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHH
Q psy2814 124 ELFPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDN 165 (176)
Q Consensus 124 e~fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~ 165 (176)
.+.|+..|....|.+|+.+|.|||+++-|--.++.+++-...
T Consensus 27 ~~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~~ 68 (297)
T COG1039 27 SNPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLNP 68 (297)
T ss_pred cCCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhhh
Confidence 367899999999999999999999999999766666655443
No 24
>PRK00996 ribonuclease HIII; Provisional
Probab=94.71 E-value=0.069 Score=46.01 Aligned_cols=33 Identities=30% Similarity=0.681 Sum_probs=28.9
Q ss_pred CCCCceeEEEEcCCeEEEEEeccceEEEEecCC
Q psy2814 123 PELFPGLIYRMVKPRVVLLIFVNGRIVITGAKS 155 (176)
Q Consensus 123 Pe~fpgl~~r~~~~~~t~~IF~sGkivitGaks 155 (176)
+..-|+..|+...+.+|+.+|.||||++.|...
T Consensus 26 ~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~a 58 (304)
T PRK00996 26 PSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGA 58 (304)
T ss_pred cCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCH
Confidence 345689999999999999999999999999643
No 25
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=94.56 E-value=0.095 Score=44.83 Aligned_cols=46 Identities=22% Similarity=0.215 Sum_probs=38.8
Q ss_pred CCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHH
Q psy2814 34 KFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKIL 79 (176)
Q Consensus 34 ~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L 79 (176)
..|+.+++.+.|.+|+++|.|||+++-|--+++-++.-...++..+
T Consensus 28 ~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~~~~~~~ 73 (297)
T COG1039 28 NPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLNPIAQTV 73 (297)
T ss_pred CCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhhhhhhhh
Confidence 5689999999999999999999999999988887777666544443
No 26
>TIGR00716 rnhC ribonuclease HIII. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III.
Probab=94.35 E-value=0.072 Score=45.49 Aligned_cols=35 Identities=29% Similarity=0.395 Sum_probs=29.8
Q ss_pred ccCCCceEEEEEcCCeEEEEEecCccEEEEcccCH
Q psy2814 31 NPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHE 65 (176)
Q Consensus 31 ~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~ 65 (176)
.+..=|+.+++.+.|.+|+++|.|||++..|...+
T Consensus 22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~ae 56 (284)
T TIGR00716 22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNSE 56 (284)
T ss_pred ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCHH
Confidence 44555899999999999999999999999995443
No 27
>TIGR00716 rnhC ribonuclease HIII. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III.
Probab=93.92 E-value=0.11 Score=44.34 Aligned_cols=33 Identities=18% Similarity=0.425 Sum_probs=29.3
Q ss_pred CCCCCceeEEEEcCCeEEEEEeccceEEEEecC
Q psy2814 122 EPELFPGLIYRMVKPRVVLLIFVNGRIVITGAK 154 (176)
Q Consensus 122 ePe~fpgl~~r~~~~~~t~~IF~sGkivitGak 154 (176)
++..=|+..|+...+.+|+++|.||||++.|..
T Consensus 22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~ 54 (284)
T TIGR00716 22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKN 54 (284)
T ss_pred ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCC
Confidence 455568999999999999999999999999953
No 28
>PRK00996 ribonuclease HIII; Provisional
Probab=93.83 E-value=0.11 Score=44.72 Aligned_cols=34 Identities=29% Similarity=0.464 Sum_probs=29.1
Q ss_pred cCCCceEEEEEcCCeEEEEEecCccEEEEcccCH
Q psy2814 32 PGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHE 65 (176)
Q Consensus 32 P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~ 65 (176)
+..-|+..++.+.+.+++++|.|||+++.|...+
T Consensus 26 ~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae 59 (304)
T PRK00996 26 PSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAE 59 (304)
T ss_pred cCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHH
Confidence 3445799999999999999999999999996433
No 29
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=88.74 E-value=1.6 Score=37.96 Aligned_cols=59 Identities=17% Similarity=0.341 Sum_probs=42.0
Q ss_pred CccChhhHhhcCC-CcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHH
Q psy2814 14 CPLDLNQINSRVR-YSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKF 75 (176)
Q Consensus 14 ~~idL~~la~~~~-n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i 75 (176)
..+|+++++..+. -.+++...| .+.++..+ -.+.+|.+|++.+.|++++++|+.-..++
T Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~--~~~~~f~~gr~~~~g~~~~~~a~~~~~~~ 336 (338)
T PRK12475 277 RRLNLEEIKKRLQKIGKVDANPY-LLSFQLDE--YRFVLFTDGRAFIHGTNDIKKAKRLYARY 336 (338)
T ss_pred CccCHHHHHHHHhhcCEEEeccc-EEEEEECC--EEEEEEcCCcEEEECCCCHHHHHHHHHHh
Confidence 5788888876543 123433322 34455544 78889999999999999999999876665
No 30
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=88.35 E-value=1.4 Score=38.42 Aligned_cols=35 Identities=14% Similarity=0.413 Sum_probs=28.7
Q ss_pred EEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHHH
Q psy2814 130 IYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNI 166 (176)
Q Consensus 130 ~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~i 166 (176)
.++..+ -.+.+|+.|++.|-|.+++++++.-+.++
T Consensus 302 ~~~~~~--~~~~~f~~gr~~~~g~~~~~~a~~~~~~~ 336 (338)
T PRK12475 302 SFQLDE--YRFVLFTDGRAFIHGTNDIKKAKRLYARY 336 (338)
T ss_pred EEEECC--EEEEEEcCCcEEEECCCCHHHHHHHHHHh
Confidence 366555 46789999999999999999998877664
No 31
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=84.68 E-value=1.6 Score=33.28 Aligned_cols=61 Identities=15% Similarity=0.212 Sum_probs=39.9
Q ss_pred cCHHHHHHHcC-C---CcccCCCCCceeE--EEEcCCeEEEEEeccceEE--EEecCCHHHHHHHHHHHH
Q psy2814 106 VKLDALHHVHS-Q---FSSYEPELFPGLI--YRMVKPRVVLLIFVNGRIV--ITGAKSRSELHEAFDNIY 167 (176)
Q Consensus 106 i~L~~l~~~~~-~---~~~YePe~fpgl~--~r~~~~~~t~~IF~sGkiv--itGaks~~~~~~a~~~i~ 167 (176)
+=|++|+..++ . .+.-|-+..|.+- |++.. --|+++|+.|+.+ +.|..+.+++.+-++.++
T Consensus 56 vvleELa~e~~~~~v~~akVDiD~~~~LA~~fgV~s-iPTLl~FkdGk~v~~i~G~~~k~~l~~~I~~~L 124 (132)
T PRK11509 56 VMIGELLREFPDYTWQVAIADLEQSEAIGDRFGVFR-FPATLVFTGGNYRGVLNGIHPWAELINLMRGLV 124 (132)
T ss_pred HHHHHHHHHhcCCceEEEEEECCCCHHHHHHcCCcc-CCEEEEEECCEEEEEEeCcCCHHHHHHHHHHHh
Confidence 33666666543 1 3344444445443 44433 2389999999996 889999999888877664
No 32
>TIGR02187 GlrX_arch Glutaredoxin-like domain protein. This family of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different.
Probab=84.05 E-value=5.1 Score=32.19 Aligned_cols=116 Identities=15% Similarity=0.085 Sum_probs=66.4
Q ss_pred eEEEEEecCccEE---EEcccCHHHHHHHHHHHHHHHHhcCC--Ccc--------cceeeeeeEEEEeeeCcc---cCHH
Q psy2814 46 RTTCLAFQSGKLL---ILGAKHEHDCKLASRKFAKILKQLGH--PIK--------YQGFKIHNIVCTCDVRFP---VKLD 109 (176)
Q Consensus 46 ~~t~~If~sGKiv---itGaks~~~~~~a~~~i~~~L~~~g~--~~~--------~~~~~i~nIvas~~l~~~---i~L~ 109 (176)
-.|+.+|.+|+.+ ..|..+.++...-++.+... ..-+. +.. .....|.-..+..+-+|+ --++
T Consensus 78 ~Pt~~~f~~g~~~~~~~~G~~~~~~l~~~i~~~~~~-~~~~~~L~~~~~~~l~~~~~pv~I~~F~a~~C~~C~~~~~~l~ 156 (215)
T TIGR02187 78 VPTTIILEEGKDGGIRYTGIPAGYEFAALIEDIVRV-SQGEPGLSEKTVELLQSLDEPVRIEVFVTPTCPYCPYAVLMAH 156 (215)
T ss_pred cCEEEEEeCCeeeEEEEeecCCHHHHHHHHHHHHHh-cCCCCCCCHHHHHHHHhcCCCcEEEEEECCCCCCcHHHHHHHH
Confidence 3588999999885 47998888877766665422 21111 110 012233334444333333 1234
Q ss_pred HHHHHcC--CCcccCCCCCceeE--EEEcCCeEEEEEeccceEEEEecCCHHHHHHHHH
Q psy2814 110 ALHHVHS--QFSSYEPELFPGLI--YRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFD 164 (176)
Q Consensus 110 ~l~~~~~--~~~~YePe~fpgl~--~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~ 164 (176)
+++...+ ....+|++.+|.+. |.+.. --|+.+|..|+. +.|..+.+++.+.+.
T Consensus 157 ~l~~~~~~i~~~~vD~~~~~~~~~~~~V~~-vPtl~i~~~~~~-~~G~~~~~~l~~~l~ 213 (215)
T TIGR02187 157 KFALANDKILGEMIEANENPDLAEKYGVMS-VPKIVINKGVEE-FVGAYPEEQFLEYIL 213 (215)
T ss_pred HHHHhcCceEEEEEeCCCCHHHHHHhCCcc-CCEEEEecCCEE-EECCCCHHHHHHHHH
Confidence 4443322 12346777777665 44322 236778988875 889999888877664
No 33
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=82.68 E-value=3.4 Score=36.03 Aligned_cols=59 Identities=17% Similarity=0.337 Sum_probs=42.6
Q ss_pred CccChhhHhhcCCCc--EEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHH
Q psy2814 14 CPLDLNQINSRVRYS--EYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKF 75 (176)
Q Consensus 14 ~~idL~~la~~~~n~--~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i 75 (176)
..+++.+++..+... ++.. +...++.+.+.-.+..|.+|+++|.|++++.+|+.-..++
T Consensus 277 ~~i~~~~~~~~l~~~~~~~~~---~~~ll~vr~~~~~~~~~~~gr~~i~g~~~~~~a~~~~~~~ 337 (339)
T PRK07688 277 EEYDLEELAELLRDRGLDVNV---NPYLLSFSLEEKRLVLFKDGRVLVHGTKDISEAKTIYHRY 337 (339)
T ss_pred CccCHHHHHHHHHhcccccCC---CcEEEEEecCCeEEEEEcCCCEEEECCCCHHHHHHHHHHh
Confidence 356777777655322 3333 3445566666689999999999999999999998876654
No 34
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=70.68 E-value=8.2 Score=28.46 Aligned_cols=34 Identities=24% Similarity=0.166 Sum_probs=29.0
Q ss_pred ecCccEEEEcccCHHHHHHHHHHHHHHHHh-cCCCcc
Q psy2814 52 FQSGKLLILGAKHEHDCKLASRKFAKILKQ-LGHPIK 87 (176)
Q Consensus 52 f~sGKivitGaks~~~~~~a~~~i~~~L~~-~g~~~~ 87 (176)
--||.+++||. +++.+.|++.+.+.|++ +||.+.
T Consensus 72 RFsGslvitGd--vs~Ve~Al~~V~~~l~~~L~F~~~ 106 (111)
T PRK15468 72 RFSGALVIYGS--VGAVEEALSQTVSGLGRLLNYTLC 106 (111)
T ss_pred ccceeEEEEcc--HHHHHHHHHHHHHHHHhhcCcccc
Confidence 46899999995 88899999999999998 787643
No 35
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=69.59 E-value=18 Score=31.56 Aligned_cols=34 Identities=24% Similarity=0.553 Sum_probs=28.1
Q ss_pred EEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHHH
Q psy2814 131 YRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNI 166 (176)
Q Consensus 131 ~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~i 166 (176)
+|..+ -.+..|++|+++|-|.+++.+++.-+.++
T Consensus 304 vr~~~--~~~~~~~~gr~~i~g~~~~~~a~~~~~~~ 337 (339)
T PRK07688 304 FSLEE--KRLVLFKDGRVLVHGTKDISEAKTIYHRY 337 (339)
T ss_pred EecCC--eEEEEEcCCCEEEECCCCHHHHHHHHHHh
Confidence 55434 78899999999999999999988877654
No 36
>cd03065 PDI_b_Calsequestrin_N PDIb family, Calsequestrin subfamily, N-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2
Probab=69.40 E-value=9.6 Score=28.25 Aligned_cols=30 Identities=17% Similarity=0.237 Sum_probs=24.5
Q ss_pred EEEEEeccce-EEEEecCCHHHHHHHHHHHH
Q psy2814 138 VVLLIFVNGR-IVITGAKSRSELHEAFDNIY 167 (176)
Q Consensus 138 ~t~~IF~sGk-ivitGaks~~~~~~a~~~i~ 167 (176)
-|+.+|.+|+ +-..|+++.+.+.+.+++|.
T Consensus 89 PTl~lfk~G~~v~~~G~~~~~~l~~~l~~~~ 119 (120)
T cd03065 89 DSIYVFKDDEVIEYDGEFAADTLVEFLLDLI 119 (120)
T ss_pred cEEEEEECCEEEEeeCCCCHHHHHHHHHHHh
Confidence 3788999998 55779999999888887764
No 37
>cd02965 HyaE HyaE family; HyaE is also called HupG and HoxO. They are proteins serving a critical role in the assembly of multimeric [NiFe] hydrogenases, the enzymes that catalyze the oxidation of molecular hydrogen to enable microorganisms to utilize hydrogen as the sole energy source. The E. coli HyaE protein is a chaperone that specifically interacts with the twin-arginine translocation (Tat) signal peptide of the [NiFe] hydrogenase-1 beta subunit precursor. Tat signal peptides target precursor proteins to the Tat protein export system, which facilitates the transport of fully folded proteins across the inner membrane. HyaE may be involved in regulating the traffic of [NiFe] hydrogenase-1 on the Tat transport pathway.
Probab=68.85 E-value=5.2 Score=29.46 Aligned_cols=52 Identities=21% Similarity=0.300 Sum_probs=32.8
Q ss_pred HHHHHHHcCCC---cccCCCCCceeE--EEEcCCeEEEEEeccceEE--EEecCCHHHHH
Q psy2814 108 LDALHHVHSQF---SSYEPELFPGLI--YRMVKPRVVLLIFVNGRIV--ITGAKSRSELH 160 (176)
Q Consensus 108 L~~l~~~~~~~---~~YePe~fpgl~--~r~~~~~~t~~IF~sGkiv--itGaks~~~~~ 160 (176)
|++++..++.. +..+-+..|.+. |++.. --|+.+|+.|+++ +.|..+.+++.
T Consensus 51 leela~e~~~~v~f~kVdid~~~~la~~f~V~s-IPTli~fkdGk~v~~~~G~~~~~e~~ 109 (111)
T cd02965 51 LPELLKAFPGRFRAAVVGRADEQALAARFGVLR-TPALLFFRDGRYVGVLAGIRDWDEYV 109 (111)
T ss_pred HHHHHHHCCCcEEEEEEECCCCHHHHHHcCCCc-CCEEEEEECCEEEEEEeCccCHHHHh
Confidence 55566554432 244555556554 55543 2388999999997 56888877764
No 38
>KOG4749|consensus
Probab=66.36 E-value=2 Score=37.65 Aligned_cols=56 Identities=39% Similarity=0.648 Sum_probs=43.5
Q ss_pred cCCCcccCC-CCCceeEEEE--------cCCeEEEEEeccceEEEEec-----CCHHHHHHHHHHHHHHH
Q psy2814 115 HSQFSSYEP-ELFPGLIYRM--------VKPRVVLLIFVNGRIVITGA-----KSRSELHEAFDNIYPVL 170 (176)
Q Consensus 115 ~~~~~~YeP-e~fpgl~~r~--------~~~~~t~~IF~sGkivitGa-----ks~~~~~~a~~~i~~~L 170 (176)
..+-.+|+| ++|.|=.-|| ..|.-.+.||.+|..+.-|. |+..++..|+..+...+
T Consensus 172 ~sqisey~PLDLfSG~k~rm~~AikaL~~~pqnnlrvF~nG~lv~gg~~~g~~kt~s~i~~~~~~~~k~~ 241 (375)
T KOG4749|consen 172 ISQISEYDPLDLFSGSKERMHKAIKALYSTPQNNLRVFLNGSLVFGGLGGGICKTTSEIELAFEDALKDF 241 (375)
T ss_pred hhhhhccCchhhccccHHHHHHHHHHHhhccccceeEEeccceeecccCCCcccchhhhhHHHHHHHHHH
Confidence 456799999 9999987665 35677899999999999885 45667777777766544
No 39
>PF06277 EutA: Ethanolamine utilisation protein EutA; InterPro: IPR009377 Proteins in this entry are EutA ethanolamine utilization proteins, reactivating factors for ethanolamine ammonia lyase, encoded by the ethanolamine utilization eut operon. The holoenzyme of adenosylcobalamin-dependent ethanolamine ammonia-lyase (EutBC, IPR0092462 from INTERPRO, IPR010628 from INTERPRO), which is part of the ethanolamine utilization pathway [, , ], undergoes suicidal inactivation during catalysis as well as inactivation in the absence of substrate. The inactivation involves the irreversible cleavage of the Co-C bond of the coenzyme. The inactivated holoenzyme undergoes rapid and continuous reactivation in the presence of ATP, Mg2+, and free adenosylcobalamin in permeabilised cells (in situ), homogenate, and cell extracts of Escherichia coli. The EutA protein is essential for reactivation. It was demonstrated with purified recombinant EutA that both the suicidally inactivated and O2-inactivated holoethanolamine ammonia lyase underwent rapid reactivation in vitro by EutA in the presence of adenosylcobalamin, ATP, and Mg2+ []. The inactive enzyme-cyanocobalamin complex was also activated in situ and in vitro by EutA under the same conditions. Thus EutA is believed to be the only component of the reactivating factor for ethanolamine ammonia lyase. Reactivation and activation occur through the exchange of modified coenzyme for free intact adenosylcobalamin []. Bacteria that harbor the ethanolamine utilization pathway can use ethanolamine as a source of carbon and nitrogen. For more information on the ethanolamine utilization pathway, please see IPR009194 from INTERPRO, IPR012408 from INTERPRO.
Probab=65.54 E-value=30 Score=31.78 Aligned_cols=86 Identities=16% Similarity=0.299 Sum_probs=53.1
Q ss_pred ecCccEEEEccc-CHHHHHHHHHHHHHHHHhcCCCcccceeeeeeEEEEeeeCcccCHHHHHHHcC-CCcccCCCCCcee
Q psy2814 52 FQSGKLLILGAK-HEHDCKLASRKFAKILKQLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHS-QFSSYEPELFPGL 129 (176)
Q Consensus 52 f~sGKivitGak-s~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~nIvas~~l~~~i~L~~l~~~~~-~~~~YePe~fpgl 129 (176)
-.+|-++|||-. ..|.|+.. ...|...= -|| ||||+- | |||.+-...+ .-..|.-+.+-.+
T Consensus 83 I~TGAVIITGETArKeNA~~v----~~~Ls~~a-----GDF----VVATAG---P-dLEsiiAgkGsGA~~~S~~~~~~V 145 (473)
T PF06277_consen 83 IDTGAVIITGETARKENAREV----LHALSGFA-----GDF----VVATAG---P-DLESIIAGKGSGAAALSKEHHTVV 145 (473)
T ss_pred CccccEEEecchhhhhhHHHH----HHHHHHhc-----CCE----EEEccC---C-CHHHHHhccCccHHHHhhhhCCeE
Confidence 368999999953 23334443 43443320 122 577765 3 8998876554 3355655543333
Q ss_pred E-EEEcCCeEEEEEeccceEEEEecC
Q psy2814 130 I-YRMVKPRVVLLIFVNGRIVITGAK 154 (176)
Q Consensus 130 ~-~r~~~~~~t~~IF~sGkivitGak 154 (176)
. +-+-+.-..+.+|..|+++=|+|=
T Consensus 146 ~NiDIGGGTtN~avf~~G~v~~T~cl 171 (473)
T PF06277_consen 146 ANIDIGGGTTNIAVFDNGEVIDTACL 171 (473)
T ss_pred EEEEeCCCceeEEEEECCEEEEEEEE
Confidence 2 555667788999999999999873
No 40
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=64.97 E-value=14 Score=28.34 Aligned_cols=64 Identities=11% Similarity=0.244 Sum_probs=37.3
Q ss_pred hhhHhhcCCC-c---EEccCCCceE--EEEEcCCeEEEEEecCccEEE---Ec--------ccCHHHHHHHHHHHHHHHH
Q psy2814 18 LNQINSRVRY-S---EYNPGKFHGL--IMKILNPRTTCLAFQSGKLLI---LG--------AKHEHDCKLASRKFAKILK 80 (176)
Q Consensus 18 L~~la~~~~n-~---~Y~P~~fpgl--~~R~~~p~~t~~If~sGKivi---tG--------aks~~~~~~a~~~i~~~L~ 80 (176)
|+++|....+ + .-|=+..|.+ .+.++.|-+++.+|.+|++.+ || ..+.+++...++.+.+--.
T Consensus 45 l~~la~~~~~~~~~~kVDVDe~~dla~~y~I~~~~t~~~ffk~g~~~vd~~tG~~~k~~~~~~~k~~l~~~i~~~~~~a~ 124 (142)
T PLN00410 45 LASVAETIKNFAVIYLVDITEVPDFNTMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWALKDKQEFIDIVETVYRGAR 124 (142)
T ss_pred HHHHHHHcCCceEEEEEECCCCHHHHHHcCccCCCcEEEEEECCeEEEEEecccccccccccCCHHHHHHHHHHHHHHHh
Confidence 4666666554 2 2233333333 355566667888999999544 55 4566666666666665544
Q ss_pred h
Q psy2814 81 Q 81 (176)
Q Consensus 81 ~ 81 (176)
+
T Consensus 125 ~ 125 (142)
T PLN00410 125 K 125 (142)
T ss_pred c
Confidence 3
No 41
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=64.81 E-value=13 Score=28.46 Aligned_cols=39 Identities=31% Similarity=0.622 Sum_probs=27.9
Q ss_pred EEEcCCeEEEEEeccceEEE---Ee--------cCCHHHHHHHHHHHHHH
Q psy2814 131 YRMVKPRVVLLIFVNGRIVI---TG--------AKSRSELHEAFDNIYPV 169 (176)
Q Consensus 131 ~r~~~~~~t~~IF~sGkivi---tG--------aks~~~~~~a~~~i~~~ 169 (176)
|.+.++-.++.+|++|++.+ || ..+.+++.+.++.+++-
T Consensus 73 y~I~~~~t~~~ffk~g~~~vd~~tG~~~k~~~~~~~k~~l~~~i~~~~~~ 122 (142)
T PLN00410 73 YELYDPCTVMFFFRNKHIMIDLGTGNNNKINWALKDKQEFIDIVETVYRG 122 (142)
T ss_pred cCccCCCcEEEEEECCeEEEEEecccccccccccCCHHHHHHHHHHHHHH
Confidence 55555556777999999655 66 56777888888877764
No 42
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=62.47 E-value=13 Score=27.37 Aligned_cols=33 Identities=24% Similarity=0.302 Sum_probs=26.7
Q ss_pred EEEEEeccceEEEEecCCHHHHHHHHHHHHHHHHh
Q psy2814 138 VVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLKS 172 (176)
Q Consensus 138 ~t~~IF~sGkivitGaks~~~~~~a~~~i~~~L~~ 172 (176)
+-++=--||.+++||. .++++.|++.+...|++
T Consensus 67 igF~DRFsGslvitGd--vs~Ve~Al~~V~~~l~~ 99 (111)
T PRK15468 67 IGFLDRFSGALVIYGS--VGAVEEALSQTVSGLGR 99 (111)
T ss_pred EeeeeccceeEEEEcc--HHHHHHHHHHHHHHHHh
Confidence 3344456899999997 88999999999988876
No 43
>cd03065 PDI_b_Calsequestrin_N PDIb family, Calsequestrin subfamily, N-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2
Probab=59.37 E-value=18 Score=26.82 Aligned_cols=31 Identities=6% Similarity=-0.014 Sum_probs=24.1
Q ss_pred eEEEEEecCcc-EEEEcccCHHHHHHHHHHHH
Q psy2814 46 RTTCLAFQSGK-LLILGAKHEHDCKLASRKFA 76 (176)
Q Consensus 46 ~~t~~If~sGK-ivitGaks~~~~~~a~~~i~ 76 (176)
-.|+.+|.+|+ +-.+|+++.+.+...++++.
T Consensus 88 iPTl~lfk~G~~v~~~G~~~~~~l~~~l~~~~ 119 (120)
T cd03065 88 EDSIYVFKDDEVIEYDGEFAADTLVEFLLDLI 119 (120)
T ss_pred ccEEEEEECCEEEEeeCCCCHHHHHHHHHHHh
Confidence 35999999999 45669999888887766553
No 44
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=58.69 E-value=30 Score=26.95 Aligned_cols=52 Identities=13% Similarity=0.200 Sum_probs=37.6
Q ss_pred CCceEEEEEcCCeEEEEEe-cCccEEEEccc---CHHHHHHHHHHHHHHHHhcCCC
Q psy2814 34 KFHGLIMKILNPRTTCLAF-QSGKLLILGAK---HEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 34 ~fpgl~~R~~~p~~t~~If-~sGKivitGak---s~~~~~~a~~~i~~~L~~~g~~ 85 (176)
.|+.-++-+.+..-..++| ++|.+-..|.+ |.=.+..|++.+++...++|+.
T Consensus 36 s~NNTiItiTD~~G~~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~ 91 (149)
T PTZ00129 36 SFNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGIN 91 (149)
T ss_pred ccCCeEEEEEcccCCEEEEEecCcceecccccCCCHHHHHHHHHHHHHHHHHcCCe
Confidence 3445555666665554444 56999999987 3447889999999999998875
No 45
>PHA02278 thioredoxin-like protein
Probab=55.53 E-value=18 Score=25.87 Aligned_cols=24 Identities=25% Similarity=0.430 Sum_probs=19.9
Q ss_pred EEEEEeccceEE--EEecCCHHHHHH
Q psy2814 138 VVLLIFVNGRIV--ITGAKSRSELHE 161 (176)
Q Consensus 138 ~t~~IF~sGkiv--itGaks~~~~~~ 161 (176)
.|+.+|+.|+.+ +.|..+.+++.+
T Consensus 74 PT~i~fk~G~~v~~~~G~~~~~~l~~ 99 (103)
T PHA02278 74 PVLIGYKDGQLVKKYEDQVTPMQLQE 99 (103)
T ss_pred cEEEEEECCEEEEEEeCCCCHHHHHh
Confidence 378999999999 999888877654
No 46
>PRK09381 trxA thioredoxin; Provisional
Probab=54.82 E-value=18 Score=25.13 Aligned_cols=28 Identities=39% Similarity=0.612 Sum_probs=21.0
Q ss_pred EEEEeccceEE--EEecCCHHHHHHHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELHEAFDNI 166 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~~a~~~i 166 (176)
++.+|..|+++ ..|..+.++++..++..
T Consensus 78 t~~~~~~G~~~~~~~G~~~~~~l~~~i~~~ 107 (109)
T PRK09381 78 TLLLFKNGEVAATKVGALSKGQLKEFLDAN 107 (109)
T ss_pred EEEEEeCCeEEEEecCCCCHHHHHHHHHHh
Confidence 46677888877 66888888888777654
No 47
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=52.42 E-value=23 Score=25.83 Aligned_cols=27 Identities=15% Similarity=0.482 Sum_probs=22.6
Q ss_pred cceEE--EEecCCHHHHHHHHHHHHHHHHh
Q psy2814 145 NGRIV--ITGAKSRSELHEAFDNIYPVLKS 172 (176)
Q Consensus 145 sGkiv--itGaks~~~~~~a~~~i~~~L~~ 172 (176)
||.++ ++|. ++++++.|++.....|.+
T Consensus 71 sG~vi~ii~G~-dvsdV~sal~~~l~~l~~ 99 (103)
T cd07049 71 AGEVIGILAGP-SPAEVRSGLNAAIDFIEN 99 (103)
T ss_pred CccEEEEEeCC-CHHHHHHHHHHHHHHHhc
Confidence 78877 7765 899999999999888765
No 48
>PRK10996 thioredoxin 2; Provisional
Probab=51.92 E-value=22 Score=26.49 Aligned_cols=28 Identities=25% Similarity=0.606 Sum_probs=21.7
Q ss_pred EEEEeccceEE--EEecCCHHHHHHHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELHEAFDNI 166 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~~a~~~i 166 (176)
++.+|.+|+++ +.|..+.+++++.++++
T Consensus 109 tlii~~~G~~v~~~~G~~~~e~l~~~l~~~ 138 (139)
T PRK10996 109 TIMIFKNGQVVDMLNGAVPKAPFDSWLNEA 138 (139)
T ss_pred EEEEEECCEEEEEEcCCCCHHHHHHHHHHh
Confidence 46678888877 67888888888887764
No 49
>cd01644 RT_pepA17 RT_pepA17: Reverse transcriptase (RTs) in retrotransposons. This subfamily represents the RT domain of a multifunctional enzyme. C-terminal to the RT domain is a domain homologous to aspartic proteinases (corresponding to Merops family A17) encoded by retrotransposons and retroviruses. RT catalyzes DNA replication from an RNA template and is responsible for the replication of retroelements.
Probab=51.71 E-value=19 Score=29.13 Aligned_cols=30 Identities=10% Similarity=0.347 Sum_probs=26.4
Q ss_pred EEEcccCHHHHHHHHHHHHHHHHhcCCCcc
Q psy2814 58 LILGAKHEHDCKLASRKFAKILKQLGHPIK 87 (176)
Q Consensus 58 vitGaks~~~~~~a~~~i~~~L~~~g~~~~ 87 (176)
++.|++|++++...++++..+|++.|++.+
T Consensus 144 ili~~~s~~e~~~~~~~v~~~L~~~Gf~l~ 173 (213)
T cd01644 144 ILVSTDTLNEAVNVAKRLIALLKKGGFNLR 173 (213)
T ss_pred ceecCCCHHHHHHHHHHHHHHHHhCCccch
Confidence 355888999999999999999999998764
No 50
>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit. This model describes the alpha subunit of sulfite reductase.
Probab=50.11 E-value=46 Score=29.88 Aligned_cols=64 Identities=19% Similarity=0.300 Sum_probs=40.5
Q ss_pred ccCCCceE----EEEEcCCe---------------------EEEEEe-cCccEEEEcccCHHHHHHHHHHHHHHHHhcCC
Q psy2814 31 NPGKFHGL----IMKILNPR---------------------TTCLAF-QSGKLLILGAKHEHDCKLASRKFAKILKQLGH 84 (176)
Q Consensus 31 ~P~~fpgl----~~R~~~p~---------------------~t~~If-~sGKivitGaks~~~~~~a~~~i~~~L~~~g~ 84 (176)
.|+.||++ .+|+.-|. ..+.+- ++|.|++.|. +.+++....+ .|.+.|+
T Consensus 71 ~~~~~p~~~~~~tvRv~~P~G~~~tteqLR~LaDiaekYGsG~~~~tgstqdIiL~gv-~~e~le~i~~----eL~~~G~ 145 (402)
T TIGR02064 71 QGEKFPGVAEFHTVRVAQPSGKFYSTDYLRQLCDVWEKYGSGLTNFHGQTGDIVFLGT-QTPQLQEIFE----ELTNLGT 145 (402)
T ss_pred CcccCCCcCeEEEEEEecCCCCCCCHHHHHHHHHHHHHhCCCEEEEeccccCEEEcCC-CHHHHHHHHH----HHhhccc
Confidence 36888887 37777661 133343 3578888888 6666666544 4556787
Q ss_pred CcccceeeeeeEEEE
Q psy2814 85 PIKYQGFKIHNIVCT 99 (176)
Q Consensus 85 ~~~~~~~~i~nIvas 99 (176)
+.....-.+.|++|.
T Consensus 146 dlggsG~~vRti~aC 160 (402)
T TIGR02064 146 DLGGSGSNLRTPESC 160 (402)
T ss_pred CCCCCCCCccceecC
Confidence 765555567777643
No 51
>TIGR00090 iojap_ybeB iojap-like ribosome-associated protein. This model describes a widely distributed family of bacterial proteins related to iojap from plants. It includes YbeB from E. coli. The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. More recent work in bacteria suggests that the bacterial iojap-related protein physically associates with ribosomes. The function remains unknown.
Probab=48.94 E-value=37 Score=24.21 Aligned_cols=34 Identities=15% Similarity=0.144 Sum_probs=27.8
Q ss_pred ecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCc
Q psy2814 52 FQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPI 86 (176)
Q Consensus 52 f~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~ 86 (176)
+..--|++||. |..+.+..++.+.+.+++.|.++
T Consensus 28 ~~dy~VI~Tg~-S~rh~~aia~~v~~~~k~~~~~~ 61 (99)
T TIGR00090 28 IADYFVIASGT-SSRHVKAIADNVEEELKEAGLKP 61 (99)
T ss_pred ccCEEEEEEeC-CHHHHHHHHHHHHHHHHHcCCCc
Confidence 44556778877 99999999999999999988643
No 52
>cd02948 TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which
Probab=48.46 E-value=27 Score=24.31 Aligned_cols=26 Identities=31% Similarity=0.603 Sum_probs=20.3
Q ss_pred EEEEeccceEE--EEecCCHHHHHHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELHEAFDN 165 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~~a~~~ 165 (176)
|+.+|+.|+.+ +.|+ +++++.++++.
T Consensus 74 t~~~~~~g~~~~~~~G~-~~~~~~~~i~~ 101 (102)
T cd02948 74 TFLFYKNGELVAVIRGA-NAPLLNKTITE 101 (102)
T ss_pred EEEEEECCEEEEEEecC-ChHHHHHHHhh
Confidence 57788999875 7787 78888887764
No 53
>PRK09381 trxA thioredoxin; Provisional
Probab=47.96 E-value=26 Score=24.37 Aligned_cols=29 Identities=24% Similarity=0.226 Sum_probs=21.9
Q ss_pred EEEEEecCccEE--EEcccCHHHHHHHHHHH
Q psy2814 47 TTCLAFQSGKLL--ILGAKHEHDCKLASRKF 75 (176)
Q Consensus 47 ~t~~If~sGKiv--itGaks~~~~~~a~~~i 75 (176)
.++.+|.+|+++ .+|..+.++++..++..
T Consensus 77 Pt~~~~~~G~~~~~~~G~~~~~~l~~~i~~~ 107 (109)
T PRK09381 77 PTLLLFKNGEVAATKVGALSKGQLKEFLDAN 107 (109)
T ss_pred CEEEEEeCCeEEEEecCCCCHHHHHHHHHHh
Confidence 378889999988 66888888777665543
No 54
>PF07338 DUF1471: Protein of unknown function (DUF1471); InterPro: IPR010854 This entry consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some of the proteins are annotated as ydgH precursors and contain two copies of this region, one at the N terminus and the other at the C terminus. The function of this family is unknown.; PDB: 2NOC_A 2JNA_B 4EVU_B.
Probab=47.78 E-value=27 Score=22.39 Aligned_cols=25 Identities=24% Similarity=0.294 Sum_probs=20.6
Q ss_pred ccceEEEEec-CCHHHHHHHHHHHHH
Q psy2814 144 VNGRIVITGA-KSRSELHEAFDNIYP 168 (176)
Q Consensus 144 ~sGkivitGa-ks~~~~~~a~~~i~~ 168 (176)
+-|.|.++|. .+++|+++++.+-..
T Consensus 4 ~iG~Isvs~~~~s~~d~~~~la~kAd 29 (56)
T PF07338_consen 4 KIGTISVSGNFGSPDDAEEALAKKAD 29 (56)
T ss_dssp EEEEEEEEEECSSHHHHHHHHHHHHH
T ss_pred EEEEEEEccccCCHHHHHHHHHHHHH
Confidence 3489999998 899999999876543
No 55
>cd02963 TRX_DnaJ TRX domain, DnaJ domain containing protein family; composed of uncharacterized proteins of about 500-800 amino acids, containing an N-terminal DnaJ domain followed by one redox active TRX domain. DnaJ is a member of the 40 kDa heat-shock protein (Hsp40) family of molecular chaperones, which regulate the activity of Hsp70s. TRX is involved in the redox regulation of many protein substrates through the reduction of disulfide bonds. TRX has been implicated to catalyse the reduction of Hsp33, a chaperone holdase that binds to unfolded protein intermediates. The presence of DnaJ and TRX domains in members of this family suggests that they could be involved in a redox-regulated chaperone network.
Probab=46.52 E-value=24 Score=25.06 Aligned_cols=27 Identities=7% Similarity=0.260 Sum_probs=19.3
Q ss_pred EEEEeccceEE--EEecCCHHHHHHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELHEAFDN 165 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~~a~~~ 165 (176)
|+.+|..|+++ ..|..+.+++.+.+++
T Consensus 82 t~~i~~~g~~~~~~~G~~~~~~l~~~i~~ 110 (111)
T cd02963 82 AIVGIINGQVTFYHDSSFTKQHVVDFVRK 110 (111)
T ss_pred EEEEEECCEEEEEecCCCCHHHHHHHHhc
Confidence 45677888877 4577788887776654
No 56
>KOG0910|consensus
Probab=46.35 E-value=35 Score=26.57 Aligned_cols=78 Identities=15% Similarity=0.185 Sum_probs=48.8
Q ss_pred eeeeeeEEEEeeeCcccC---HHHHHHHc-C--CCcccCCCCCce--eEEEEcCCeEEEEEeccceEE--EEecCCHHHH
Q psy2814 90 GFKIHNIVCTCDVRFPVK---LDALHHVH-S--QFSSYEPELFPG--LIYRMVKPRVVLLIFVNGRIV--ITGAKSRSEL 159 (176)
Q Consensus 90 ~~~i~nIvas~~l~~~i~---L~~l~~~~-~--~~~~YePe~fpg--l~~r~~~~~~t~~IF~sGkiv--itGaks~~~~ 159 (176)
..-+.+..|.-+=||.+= |++++.++ + ..+.=|-+.+|- ..|.+.- --|+++|.+|..+ +.|+...+.+
T Consensus 62 ~PVlVdF~A~WCgPCk~l~P~l~~~~~~~~g~~k~~kvdtD~~~ela~~Y~I~a-vPtvlvfknGe~~d~~vG~~~~~~l 140 (150)
T KOG0910|consen 62 VPVLVDFHAEWCGPCKMLGPILEELVSEYAGKFKLYKVDTDEHPELAEDYEISA-VPTVLVFKNGEKVDRFVGAVPKEQL 140 (150)
T ss_pred CCEEEEEecCcCccHhHhhHHHHHHHHhhcCeEEEEEEccccccchHhhcceee-eeEEEEEECCEEeeeecccCCHHHH
Confidence 455777778777777664 44444332 1 012222222332 2355543 2488999999987 8999999999
Q ss_pred HHHHHHHHH
Q psy2814 160 HEAFDNIYP 168 (176)
Q Consensus 160 ~~a~~~i~~ 168 (176)
...+++..+
T Consensus 141 ~~~i~k~l~ 149 (150)
T KOG0910|consen 141 RSLIKKFLK 149 (150)
T ss_pred HHHHHHHhc
Confidence 999888764
No 57
>PHA02278 thioredoxin-like protein
Probab=44.96 E-value=30 Score=24.68 Aligned_cols=25 Identities=8% Similarity=0.180 Sum_probs=20.3
Q ss_pred eEEEEEecCccEE--EEcccCHHHHHH
Q psy2814 46 RTTCLAFQSGKLL--ILGAKHEHDCKL 70 (176)
Q Consensus 46 ~~t~~If~sGKiv--itGaks~~~~~~ 70 (176)
-.|+.+|.+|+.+ +.|..+.+++++
T Consensus 73 iPT~i~fk~G~~v~~~~G~~~~~~l~~ 99 (103)
T PHA02278 73 TPVLIGYKDGQLVKKYEDQVTPMQLQE 99 (103)
T ss_pred ccEEEEEECCEEEEEEeCCCCHHHHHh
Confidence 4589999999999 889877776653
No 58
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=44.91 E-value=42 Score=25.43 Aligned_cols=31 Identities=16% Similarity=0.141 Sum_probs=25.6
Q ss_pred eEEEEEecCccEE--EEcccCHHHHHHHHHHHH
Q psy2814 46 RTTCLAFQSGKLL--ILGAKHEHDCKLASRKFA 76 (176)
Q Consensus 46 ~~t~~If~sGKiv--itGaks~~~~~~a~~~i~ 76 (176)
-.|+.+|++|+.+ +.|..+.++...-+++++
T Consensus 92 iPTLl~FkdGk~v~~i~G~~~k~~l~~~I~~~L 124 (132)
T PRK11509 92 FPATLVFTGGNYRGVLNGIHPWAELINLMRGLV 124 (132)
T ss_pred CCEEEEEECCEEEEEEeCcCCHHHHHHHHHHHh
Confidence 4599999999997 779999988888776654
No 59
>cd07047 BMC_PduB_repeat1 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 1. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduB).
Probab=44.82 E-value=37 Score=25.94 Aligned_cols=28 Identities=18% Similarity=0.373 Sum_probs=21.8
Q ss_pred cceEEEEecCCHHHHHHHHHHHHHHHHh
Q psy2814 145 NGRIVITGAKSRSELHEAFDNIYPVLKS 172 (176)
Q Consensus 145 sGkivitGaks~~~~~~a~~~i~~~L~~ 172 (176)
.|.+++||+.++++++.|++.-...+.+
T Consensus 78 kg~vvitGg~dVs~V~~aVeaa~~~v~~ 105 (134)
T cd07047 78 HGSLILFGAEDVSDVRRAVEVALSETEK 105 (134)
T ss_pred eEEEEEEcCCCHHHHHHHHHHHHHHHHH
Confidence 7889999999999977777666555544
No 60
>PF06200 tify: tify domain; InterPro: IPR010399 The tify domain is a 36-amino acid domain only found among Embryophyta (land plants). It has been named after the most conserved amino acid pattern (TIF[F/Y]XG) it contains, but was previously known as the Zim domain. As the use of uppercase characters (TIFY) might imply that the domain is fully conserved across proteins, a lowercase lettering has been chosen in an attempt to highlight the reality of its natural variability. Based on the domain architecture, tify domain containing proteins can be classified into two groups. Group I is formed by proteins possessing a CCT (CONSTANS, CO-like, and TOC1) domain and a GATA-type zinc finger in addition to the tify domain. Group II contains proteins characterised by the tify domain but lacking a GATA-type zinc finger. Tify domain containing proteins might be involved in developmental processes and some of them have features that are characteristic for transcription factors: a nuclear localisation and the presence of a putative DNA-binding domain []. Some proteins known to contain a tify domain include: Arabidopsis thaliana Zinc-finger protein expressed in Inflorescence Meristem (ZIM), a putative transcription factor involved in inflorescence and flower development [, ]. A. thaliana ZIM-like proteins (ZML) []. A. thaliana PEAPOD1 and PEAPOD2 (PPD1 and PPD2) [].
Probab=44.02 E-value=63 Score=19.01 Aligned_cols=27 Identities=19% Similarity=0.337 Sum_probs=21.2
Q ss_pred eEEEEEeccceEEEEecCCHHHHHHHH
Q psy2814 137 RVVLLIFVNGRIVITGAKSRSELHEAF 163 (176)
Q Consensus 137 ~~t~~IF~sGkivitGaks~~~~~~a~ 163 (176)
...++||-.|+|.+.-.=.++.+++.+
T Consensus 5 ~~qLTIfY~G~V~Vfd~v~~~Ka~~im 31 (36)
T PF06200_consen 5 TAQLTIFYGGQVCVFDDVPPDKAQEIM 31 (36)
T ss_pred CCcEEEEECCEEEEeCCCCHHHHHHHH
Confidence 456889999999999877777666543
No 61
>PF13575 DUF4135: Domain of unknown function (DUF4135)
Probab=43.21 E-value=23 Score=30.98 Aligned_cols=56 Identities=14% Similarity=0.216 Sum_probs=40.8
Q ss_pred EEEEcccCHHHHHHHHHHHHHHHHhcCCCcccceeeeeeEEEEeeeCcccCHHHHHH
Q psy2814 57 LLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHH 113 (176)
Q Consensus 57 ivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~nIvas~~l~~~i~L~~l~~ 113 (176)
|--..+.+.++++.-..++-..|.=+ +-....|+--.||+|+++.|+.||||-|..
T Consensus 122 I~~~~c~~~~ev~~yY~r~G~llal~-y~L~~~DlH~ENIIa~g~~PvlIDlETlf~ 177 (370)
T PF13575_consen 122 IEHEPCNSEEEVERYYYRLGVLLALL-YLLNGTDLHFENIIASGEYPVLIDLETLFH 177 (370)
T ss_pred ecCCCCCCHHHHHHHHHHHHHHHHHH-HHhCCCcccccceEEeCCCcEEEehhhhCC
Confidence 33456667788777777766555432 223446888999999999999999998874
No 62
>cd02963 TRX_DnaJ TRX domain, DnaJ domain containing protein family; composed of uncharacterized proteins of about 500-800 amino acids, containing an N-terminal DnaJ domain followed by one redox active TRX domain. DnaJ is a member of the 40 kDa heat-shock protein (Hsp40) family of molecular chaperones, which regulate the activity of Hsp70s. TRX is involved in the redox regulation of many protein substrates through the reduction of disulfide bonds. TRX has been implicated to catalyse the reduction of Hsp33, a chaperone holdase that binds to unfolded protein intermediates. The presence of DnaJ and TRX domains in members of this family suggests that they could be involved in a redox-regulated chaperone network.
Probab=42.25 E-value=28 Score=24.69 Aligned_cols=28 Identities=11% Similarity=0.087 Sum_probs=20.9
Q ss_pred EEEEEecCccEEE--EcccCHHHHHHHHHH
Q psy2814 47 TTCLAFQSGKLLI--LGAKHEHDCKLASRK 74 (176)
Q Consensus 47 ~t~~If~sGKivi--tGaks~~~~~~a~~~ 74 (176)
.|+.+|..|+++- .|..+.+++...+++
T Consensus 81 Pt~~i~~~g~~~~~~~G~~~~~~l~~~i~~ 110 (111)
T cd02963 81 PAIVGIINGQVTFYHDSSFTKQHVVDFVRK 110 (111)
T ss_pred CEEEEEECCEEEEEecCCCCHHHHHHHHhc
Confidence 4788999999984 577788777666554
No 63
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=42.12 E-value=1.6e+02 Score=23.33 Aligned_cols=98 Identities=11% Similarity=0.186 Sum_probs=54.0
Q ss_pred EEEE-EecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcccceeeeeeEEEEe-----eeCcccCHHHHHHHcCCCcc
Q psy2814 47 TTCL-AFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGFKIHNIVCTC-----DVRFPVKLDALHHVHSQFSS 120 (176)
Q Consensus 47 ~t~~-If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~nIvas~-----~l~~~i~L~~l~~~~~~~~~ 120 (176)
+++. ..+.++|.|||. ...++.+...+.++|++. .-..+.+.-+...+ ..-.+-.|+.+.....-..+
T Consensus 57 ~~I~~~~~~~~i~I~g~--k~~~~~i~~~i~~~l~~i----~~~~i~l~~~~~~~~~~~~~~~~~~~l~~i~~~t~~~ie 130 (210)
T PF14611_consen 57 AKIEVSRSENRIRITGT--KSTAEYIEASINEILSNI----RTEEIDLSPIISKHSEKKNSQFTPDLLEEIQKLTNVYIE 130 (210)
T ss_pred ceEEEecCCcEEEEEcc--HHHHHHHHHHHHHHHhhc----EEEEEecchhhhhhcccccccccHHHHHHHHHHHcEEEE
Confidence 4443 357799999996 556666777777777765 22223232222111 12235556666665555556
Q ss_pred cCCCCCceeEEEEcCCeEEEEEeccceEEEEe---cCCHHHHHHHHHHHHHHH
Q psy2814 121 YEPELFPGLIYRMVKPRVVLLIFVNGRIVITG---AKSRSELHEAFDNIYPVL 170 (176)
Q Consensus 121 YePe~fpgl~~r~~~~~~t~~IF~sGkivitG---aks~~~~~~a~~~i~~~L 170 (176)
+.|+.. ++.|++ +.+++.+..|-+-++-.+
T Consensus 131 ~~~~~~--------------------~~~i~~~~~~~~~~~~~~a~RlL~~a~ 163 (210)
T PF14611_consen 131 KNPDGN--------------------KLKISWLASPENEKRADRAKRLLLWAL 163 (210)
T ss_pred ECCCCC--------------------eEEEEEEeeccccchHHHHHHHHHHhc
Confidence 665521 122222 156777777777666554
No 64
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=42.00 E-value=56 Score=20.94 Aligned_cols=29 Identities=21% Similarity=0.217 Sum_probs=21.5
Q ss_pred eEEEEEeccceEEEEecCCHHHHHHHHHHH
Q psy2814 137 RVVLLIFVNGRIVITGAKSRSELHEAFDNI 166 (176)
Q Consensus 137 ~~t~~IF~sGkivitGaks~~~~~~a~~~i 166 (176)
.+++.|=.+|.|.|+|. +.+.++.|.+.|
T Consensus 32 g~~I~i~~~g~v~I~G~-~~~~v~~A~~~I 60 (61)
T cd02393 32 GVKIDIEDDGTVYIAAS-DKEAAEKAKKMI 60 (61)
T ss_pred CCEEEeCCCCEEEEEeC-CHHHHHHHHHHh
Confidence 45555666899999996 677888887654
No 65
>PF05005 Ocnus: Janus/Ocnus family (Ocnus); InterPro: IPR007702 This family is comprised of the Ocnus, Janus-A and Janus-B proteins. These proteins have been found to be testes specific in Drosophila melanogaster [].; PDB: 2OZX_A 2OZW_A 2NMM_C 2AI6_A 2HW4_A.
Probab=41.21 E-value=54 Score=24.06 Aligned_cols=58 Identities=16% Similarity=0.208 Sum_probs=42.4
Q ss_pred CCCcEEc-cCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcc
Q psy2814 25 VRYSEYN-PGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIK 87 (176)
Q Consensus 25 ~~n~~Y~-P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~ 87 (176)
.+.++=+ +-+|.-+.+|+..+. -...|.++.|.+..+-=...++++.+.|+++|+.++
T Consensus 4 vP~V~id~~G~fKYvLi~v~~~~-----~~~~k~iVRG~~~~~yH~di~d~~~~el~~~gl~~~ 62 (108)
T PF05005_consen 4 VPDVDIDPEGVFKYVLIRVTDHG-----SGESKYIVRGYKRAEYHADIYDEVQEELEKLGLCTE 62 (108)
T ss_dssp S-SEEEESSSEEEEEEEEEES-G--------EEEEEEEETT-SSHHHHHHHHHHHHHHCTEEEE
T ss_pred CCeEEecCCceEEEEEEEEEeCC-----CCEEEEEEECCcchhhHHHHHHHHHHHHHHcCCeEE
Confidence 4667777 557778888888776 567899999999888777889999999999987544
No 66
>PF00085 Thioredoxin: Thioredoxin; InterPro: IPR013766 Thioredoxins [, , , ] are small disulphide-containing redox proteins that have been found in all the kingdoms of living organisms. Thioredoxin serves as a general protein disulphide oxidoreductase. It interacts with a broad range of proteins by a redox mechanism based on reversible oxidation of two cysteine thiol groups to a disulphide, accompanied by the transfer of two electrons and two protons. The net result is the covalent interconversion of a disulphide and a dithiol. In the NADPH-dependent protein disulphide reduction, thioredoxin reductase (TR) catalyses the reduction of oxidised thioredoxin (trx) by NADPH using FAD and its redox-active disulphide; reduced thioredoxin then directly reduces the disulphide in the substrate protein []. Thioredoxin is present in prokaryotes and eukaryotes and the sequence around the redox-active disulphide bond is well conserved. All thioredoxins contain a cis-proline located in a loop preceding beta-strand 4, which makes contact with the active site cysteines, and is important for stability and function []. Thioredoxin belongs to a structural family that includes glutaredoxin, glutathione peroxidase, bacterial protein disulphide isomerase DsbA, and the N-terminal domain of glutathione transferase []. Thioredoxins have a beta-alpha unit preceding the motif common to all these proteins. A number of eukaryotic proteins contain domains evolutionary related to thioredoxin, most of them are protein disulphide isomerases (PDI). PDI (5.3.4.1 from EC) [, , ] is an endoplasmic reticulum multi-functional enzyme that catalyses the formation and rearrangement of disulphide bonds during protein folding []. All PDI contains two or three (ERp72) copies of the thioredoxin domain, each of which contributes to disulphide isomerase activity, but which are functionally non-equivalent []. Moreover, PDI exhibits chaperone-like activity towards proteins that contain no disulphide bonds, i.e. behaving independently of its disulphide isomerase activity []. The various forms of PDI which are currently known are: PDI major isozyme; a multifunctional protein that also function as the beta subunit of prolyl 4-hydroxylase (1.14.11.2 from EC), as a component of oligosaccharyl transferase (2.4.1.119 from EC), as thyroxine deiodinase (3.8.1.4 from EC), as glutathione-insulin transhydrogenase (1.8.4.2 from EC) and as a thyroid hormone-binding protein ERp60 (ER-60; 58 Kd microsomal protein). ERp60 was originally thought to be a phosphoinositide-specific phospholipase C isozyme and later to be a protease. ERp72. ERp5. Bacterial proteins that act as thiol:disulphide interchange proteins that allows disulphide bond formation in some periplasmic proteins also contain a thioredoxin domain. These proteins include: Escherichia coli DsbA (or PrfA) and its orthologs in Vibrio cholerae (TtcpG) and Haemophilus influenzae (Por). E. coli DsbC (or XpRA) and its orthologues in Erwinia chrysanthemi and H. influenzae. E. coli DsbD (or DipZ) and its H. influenzae orthologue. E. coli DsbE (or CcmG) and orthologues in H. influenzae. Rhodobacter capsulatus (Rhodopseudomonas capsulata) (HelX), Rhiziobiacae (CycY and TlpA). This entry represents the thioredoxin domain.; GO: 0045454 cell redox homeostasis; PDB: 3ED3_B 1EP7_A 1EP8_B 1TOF_A 2OE3_B 2OE1_B 2OE0_B 1V98_A 3H79_A 3CXG_A ....
Probab=41.02 E-value=62 Score=21.55 Aligned_cols=27 Identities=26% Similarity=0.537 Sum_probs=20.0
Q ss_pred EEEEeccceEE--EEecCCHHHHHHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELHEAFDN 165 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~~a~~~ 165 (176)
++.+|.+|+.+ +.|..+.+++.+.+++
T Consensus 74 t~~~~~~g~~~~~~~g~~~~~~l~~~i~~ 102 (103)
T PF00085_consen 74 TIIFFKNGKEVKRYNGPRNAESLIEFIEK 102 (103)
T ss_dssp EEEEEETTEEEEEEESSSSHHHHHHHHHH
T ss_pred EEEEEECCcEEEEEECCCCHHHHHHHHHc
Confidence 35567777665 7888899999887764
No 67
>KOG0910|consensus
Probab=40.79 E-value=47 Score=25.87 Aligned_cols=32 Identities=28% Similarity=0.460 Sum_probs=27.8
Q ss_pred eEEEEEecCccEE--EEcccCHHHHHHHHHHHHH
Q psy2814 46 RTTCLAFQSGKLL--ILGAKHEHDCKLASRKFAK 77 (176)
Q Consensus 46 ~~t~~If~sGKiv--itGaks~~~~~~a~~~i~~ 77 (176)
-.|+++|.+|.-+ +.|+...+.+...++++.+
T Consensus 116 vPtvlvfknGe~~d~~vG~~~~~~l~~~i~k~l~ 149 (150)
T KOG0910|consen 116 VPTVLVFKNGEKVDRFVGAVPKEQLRSLIKKFLK 149 (150)
T ss_pred eeEEEEEECCEEeeeecccCCHHHHHHHHHHHhc
Confidence 4589999999987 8999999999999888764
No 68
>PRK10996 thioredoxin 2; Provisional
Probab=40.26 E-value=40 Score=25.08 Aligned_cols=29 Identities=17% Similarity=0.248 Sum_probs=22.7
Q ss_pred EEEEEecCccEE--EEcccCHHHHHHHHHHH
Q psy2814 47 TTCLAFQSGKLL--ILGAKHEHDCKLASRKF 75 (176)
Q Consensus 47 ~t~~If~sGKiv--itGaks~~~~~~a~~~i 75 (176)
.++.+|.+|+++ +.|..+.++++..++++
T Consensus 108 Ptlii~~~G~~v~~~~G~~~~e~l~~~l~~~ 138 (139)
T PRK10996 108 PTIMIFKNGQVVDMLNGAVPKAPFDSWLNEA 138 (139)
T ss_pred CEEEEEECCEEEEEEcCCCCHHHHHHHHHHh
Confidence 467889999988 67888888777776653
No 69
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=39.88 E-value=49 Score=24.17 Aligned_cols=28 Identities=7% Similarity=0.268 Sum_probs=23.6
Q ss_pred CccEE--EEcccCHHHHHHHHHHHHHHHHhc
Q psy2814 54 SGKLL--ILGAKHEHDCKLASRKFAKILKQL 82 (176)
Q Consensus 54 sGKiv--itGaks~~~~~~a~~~i~~~L~~~ 82 (176)
||.++ ++|. ++++.+.|++...+.|++.
T Consensus 71 sG~vi~ii~G~-dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 71 AGEVIGILAGP-SPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred CccEEEEEeCC-CHHHHHHHHHHHHHHHhcc
Confidence 77777 6666 9999999999999988764
No 70
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=38.50 E-value=38 Score=22.38 Aligned_cols=22 Identities=36% Similarity=0.762 Sum_probs=16.0
Q ss_pred eccceEEEEe-cCCHHHHHHHHH
Q psy2814 143 FVNGRIVITG-AKSRSELHEAFD 164 (176)
Q Consensus 143 F~sGkivitG-aks~~~~~~a~~ 164 (176)
+-+|++...| ..+.++++..++
T Consensus 54 vIng~~~~~G~~p~~~el~~~l~ 76 (76)
T PF13192_consen 54 VINGKVVFVGRVPSKEELKELLE 76 (76)
T ss_dssp EETTEEEEESS--HHHHHHHHHH
T ss_pred EECCEEEEEecCCCHHHHHHHhC
Confidence 4479999999 888888887653
No 71
>PF02838 Glyco_hydro_20b: Glycosyl hydrolase family 20, domain 2; InterPro: IPR015882 Glycoside hydrolase family 20 GH20 from CAZY comprises enzymes with several known activities; beta-hexosaminidase (3.2.1.52 from EC); lacto-N-biosidase (3.2.1.140 from EC). Carbonyl oxygen of the C-2 acetamido group of the substrate acts as the catalytic nucleophile/base in this family of enzymes. In the brain and other tissues, beta-hexosaminidase A degrades GM2 gangliosides; specifically, the enzyme hydrolyses terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. There are 3 forms of beta-hexosaminidase: hexosaminidase A is a trimer, with one alpha, one beta-A and one beta-B chain; hexosaminidase B is a tetramer of two beta-A and two beta-B chains; and hexosaminidase S is a homodimer of alpha chains. The two beta chains are derived from the cleavage of a precursor. Mutations in the beta-chain lead to Sandhoff disease, a lysosomal storage disorder characterised by accumulation of GM2 ganglioside []. This entry represents the alpha and beta subunit of beta-N-acetylhexosaminidase. It contains a similar fold but lacks the catalytic centre.; GO: 0004563 beta-N-acetylhexosaminidase activity, 0005975 carbohydrate metabolic process; PDB: 3SUT_A 3SUS_A 3GH7_A 3SUR_A 3SUW_A 3SUV_A 3SUU_A 3GH5_A 3GH4_A 2J4G_B ....
Probab=37.84 E-value=95 Score=22.13 Aligned_cols=38 Identities=13% Similarity=0.155 Sum_probs=32.7
Q ss_pred CeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcC
Q psy2814 45 PRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLG 83 (176)
Q Consensus 45 p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g 83 (176)
+...-+-.++++|.|.|. +...+..|++-+..+|+..+
T Consensus 75 ~E~Y~L~i~~~~I~I~a~-~~~G~~yg~qTL~Qll~~~~ 112 (124)
T PF02838_consen 75 EEGYRLSISPKGITIEAS-DPAGLFYGLQTLRQLLRQSG 112 (124)
T ss_dssp TT-EEEEEESSEEEEEES-SHHHHHHHHHHHHHHSBTCS
T ss_pred CcceEEEEECCEEEEEEc-CchHHHHHHHHHHHHhhccC
Confidence 567778888899999999 99999999999999998764
No 72
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=37.59 E-value=37 Score=22.46 Aligned_cols=22 Identities=18% Similarity=0.303 Sum_probs=16.5
Q ss_pred EecCccEEEEc-ccCHHHHHHHH
Q psy2814 51 AFQSGKLLILG-AKHEHDCKLAS 72 (176)
Q Consensus 51 If~sGKivitG-aks~~~~~~a~ 72 (176)
++-+|++...| ..|.++++..+
T Consensus 53 lvIng~~~~~G~~p~~~el~~~l 75 (76)
T PF13192_consen 53 LVINGKVVFVGRVPSKEELKELL 75 (76)
T ss_dssp EEETTEEEEESS--HHHHHHHHH
T ss_pred EEECCEEEEEecCCCHHHHHHHh
Confidence 35589999999 98999888765
No 73
>PF02410 Oligomerisation: Oligomerisation domain; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear [, ]. This entry contains the bacterial protein YbeB (P0AAT6 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2O5A_A 2ID1_B 3UPS_A.
Probab=37.55 E-value=65 Score=22.79 Aligned_cols=29 Identities=21% Similarity=0.321 Sum_probs=23.4
Q ss_pred CccEEEEcccCHHHHHHHHHHHHHHH-HhcC
Q psy2814 54 SGKLLILGAKHEHDCKLASRKFAKIL-KQLG 83 (176)
Q Consensus 54 sGKivitGaks~~~~~~a~~~i~~~L-~~~g 83 (176)
.--|++||. |..+++..++.+.+.+ ++.|
T Consensus 30 dy~II~T~~-S~rh~~aia~~v~~~~~k~~~ 59 (100)
T PF02410_consen 30 DYFIIATGR-SERHVRAIADEVEKALKKEYG 59 (100)
T ss_dssp SEEEEEEES-SHHHHHHHHHHHHHHH-HHTT
T ss_pred CEEEEEEcC-CHHHHHHHHHHHHHHHHHHcC
Confidence 445677775 9999999999999999 5555
No 74
>PRK11538 ribosome-associated protein; Provisional
Probab=36.96 E-value=73 Score=23.06 Aligned_cols=33 Identities=6% Similarity=0.075 Sum_probs=27.0
Q ss_pred ecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCC
Q psy2814 52 FQSGKLLILGAKHEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 52 f~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~ 85 (176)
+...-|++||. |.-+++..++.+.+.+++.|..
T Consensus 33 ~~Dy~VIatg~-S~rh~~aia~~v~~~~k~~~~~ 65 (105)
T PRK11538 33 ITDCMIICTGT-SSRHVMSIADHVVQESRAAGLL 65 (105)
T ss_pred ccCEEEEEEeC-CHHHHHHHHHHHHHHHHHcCCC
Confidence 44666788887 9999999999999999988754
No 75
>TIGR00385 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily. Involved in the biogenesis of c-type cytochromes as well as in disulfide bond formation in some periplasmic proteins.
Probab=36.19 E-value=58 Score=24.97 Aligned_cols=48 Identities=21% Similarity=0.165 Sum_probs=32.7
Q ss_pred ccCCCCCceeEEEEcCCeEEEEEeccceEE--EEecCCHHHHHHHHHHHH
Q psy2814 120 SYEPELFPGLIYRMVKPRVVLLIFVNGRIV--ITGAKSRSELHEAFDNIY 167 (176)
Q Consensus 120 ~YePe~fpgl~~r~~~~~~t~~IF~sGkiv--itGaks~~~~~~a~~~i~ 167 (176)
.+||+.--+-.|...+.-.++.|.++|+|+ .+|.-+.+++++.++.++
T Consensus 122 ~~D~~~~~~~~~~v~~~P~~~~id~~G~i~~~~~G~~~~~~l~~~l~~~~ 171 (173)
T TIGR00385 122 LIDPNGKLGLDLGVYGAPETFLVDGNGVILYRHAGPLNNEVWTEGFLPAM 171 (173)
T ss_pred EECCCCchHHhcCCeeCCeEEEEcCCceEEEEEeccCCHHHHHHHHHHHh
Confidence 356654444445555544689999999987 457778888887766654
No 76
>cd07996 WGR_MMR_like WGR domain of molybdate metabolism regulator and related proteins. The WGR domain is found in the putative Escherichia coli molybdate metabolism regulator and related bacterial proteins, as well as in various other bacterial proteins of unknown function. It has been called WGR after the most conserved central motif of the domain. The domain appears to occur in single-domain proteins and in a variety of domain architectures, together with ATP-dependent DNA ligase domains, WD40 repeats, leucine-rich repeats, and other domains. It has been proposed to function as a nucleic acid binding domain.
Probab=36.10 E-value=91 Score=20.41 Aligned_cols=33 Identities=15% Similarity=0.083 Sum_probs=27.5
Q ss_pred cCccEEEEcccCHHHHHHHHHHHHHHHHhcCCC
Q psy2814 53 QSGKLLILGAKHEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 53 ~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~ 85 (176)
+.|......+.|.++|..+++++.+.-.+.||.
T Consensus 40 ~~Gq~~~~~~~s~~~A~~~~~k~~~~K~~~GY~ 72 (74)
T cd07996 40 TKGQSRTKTFDSEEEALKAAEKLIREKLKRGYR 72 (74)
T ss_pred CCCceEEEECCCHHHHHHHHHHHHHHHHhcCCC
Confidence 467777888889999999999998887777874
No 77
>PRK10719 eutA reactivating factor for ethanolamine ammonia lyase; Provisional
Probab=35.94 E-value=1.7e+02 Score=26.99 Aligned_cols=30 Identities=13% Similarity=0.177 Sum_probs=25.0
Q ss_pred CCCceeE-EEEcCCeEEEEEeccceEEEEec
Q psy2814 124 ELFPGLI-YRMVKPRVVLLIFVNGRIVITGA 153 (176)
Q Consensus 124 e~fpgl~-~r~~~~~~t~~IF~sGkivitGa 153 (176)
|...|+. +-+-.....+.||..|++.-|++
T Consensus 143 Eke~gVa~IDIGgGTT~iaVf~~G~l~~T~~ 173 (475)
T PRK10719 143 ERNTRVLNIDIGGGTANYALFDAGKVIDTAC 173 (475)
T ss_pred hccCceEEEEeCCCceEEEEEECCEEEEEEE
Confidence 6666765 77888889999999999998876
No 78
>cd02950 TxlA TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport.
Probab=35.73 E-value=75 Score=23.73 Aligned_cols=29 Identities=14% Similarity=0.284 Sum_probs=22.2
Q ss_pred EEEEe-ccceEE--EEecCCHHHHHHHHHHHH
Q psy2814 139 VLLIF-VNGRIV--ITGAKSRSELHEAFDNIY 167 (176)
Q Consensus 139 t~~IF-~sGkiv--itGaks~~~~~~a~~~i~ 167 (176)
++.+| ..|+++ +.|....+++++.++.++
T Consensus 79 t~v~~~~~G~~v~~~~G~~~~~~l~~~l~~l~ 110 (142)
T cd02950 79 HFVFLDREGNEEGQSIGLQPKQVLAQNLDALV 110 (142)
T ss_pred EEEEECCCCCEEEEEeCCCCHHHHHHHHHHHH
Confidence 45566 578887 789988888888877765
No 79
>cd02985 TRX_CDSP32 TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif. CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form.
Probab=34.89 E-value=72 Score=22.12 Aligned_cols=25 Identities=20% Similarity=0.295 Sum_probs=18.1
Q ss_pred EEEEeccceEE--EEecCCHHHHHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELHEAFD 164 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~~a~~ 164 (176)
|+.+|+.|+++ ..|+ +++++.+.+.
T Consensus 74 t~~~~~~G~~v~~~~G~-~~~~l~~~~~ 100 (103)
T cd02985 74 HFLFYKDGEKIHEEEGI-GPDELIGDVL 100 (103)
T ss_pred EEEEEeCCeEEEEEeCC-CHHHHHHHHH
Confidence 68888999976 7787 5666665543
No 80
>cd02988 Phd_like_VIAF Phosducin (Phd)-like family, Viral inhibitor of apoptosis (IAP)-associated factor (VIAF) subfamily; VIAF is a Phd-like protein that functions in caspase activation during apoptosis. It was identified as an IAP binding protein through a screen of a human B-cell library using a prototype IAP. VIAF lacks a consensus IAP binding motif and while it does not function as an IAP antagonist, it still plays a regulatory role in the complete activation of caspases. VIAF itself is a substrate for IAP-mediated ubiquitination, suggesting that it may be a target of IAPs in the prevention of cell death. The similarity of VIAF to Phd points to a potential role distinct from apoptosis regulation. Phd functions as a cytosolic regulator of G protein by specifically binding to G protein betagamma (Gbg)-subunits. The C-terminal domain of Phd adopts a thioredoxin fold, but it does not contain a CXXC motif. Phd interacts with G protein beta mostly through the N-terminal helical domain.
Probab=34.74 E-value=28 Score=27.78 Aligned_cols=37 Identities=16% Similarity=0.287 Sum_probs=23.5
Q ss_pred eEEEEEecCccEE--EEcccCHHHHHHHHHHHHHHHHhc
Q psy2814 46 RTTCLAFQSGKLL--ILGAKHEHDCKLASRKFAKILKQL 82 (176)
Q Consensus 46 ~~t~~If~sGKiv--itGaks~~~~~~a~~~i~~~L~~~ 82 (176)
-.|+++|.+|+++ +.|..+...-+-....+-..|.+.
T Consensus 153 lPTlliyk~G~~v~~ivG~~~~gg~~~~~~~lE~~L~~~ 191 (192)
T cd02988 153 LPTILVYRNGDIVKQFIGLLEFGGMNTTMEDLEWLLVQV 191 (192)
T ss_pred CCEEEEEECCEEEEEEeCchhhCCCCCCHHHHHHHHHhc
Confidence 3599999999998 778755433233444454445444
No 81
>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]
Probab=34.11 E-value=31 Score=30.06 Aligned_cols=61 Identities=18% Similarity=0.152 Sum_probs=37.6
Q ss_pred EEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcccceeeeeeEEEEe-eeC---cccCHHHHHH
Q psy2814 48 TCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGFKIHNIVCTC-DVR---FPVKLDALHH 113 (176)
Q Consensus 48 t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~nIvas~-~l~---~~i~L~~l~~ 113 (176)
.+.|-+.+.+-+-|- |.+++.. +...|++.|+++-...-.++||+|-- ... --+|-..|+.
T Consensus 61 ~i~iT~rqg~ei~~i-~~e~~~~----v~~~L~~iG~~~G~~G~~vr~i~aC~G~~~C~~a~~Dt~~la~ 125 (317)
T COG2221 61 LIHITSRQGLEIPGI-SPEDADD----VVEELREIGLPVGSTGPAVRAIVACPGPRTCETALYDTTELAR 125 (317)
T ss_pred eEEEEecCceEeccC-CHHHHHH----HHHHHHHcCCCCCCcchhhhhhhcCcCcccccccccChHHHHH
Confidence 445555555555554 6666655 45666799999888777888988532 211 1345555554
No 82
>PF03135 CagE_TrbE_VirB: CagE, TrbE, VirB family, component of type IV transporter system; InterPro: IPR018145 This domain is found in (amongst others): the Helicobacter pylori protein CagE (see examples), which together with other proteins from the cag pathogenicity island (PAI), encodes a type IV transporter secretion system. The precise role of CagE is not known, but studies in animal models have shown that it is essential for pathogenesis in Helicobacter pylori induced gastritis and peptic ulceration []. Indeed, the expression of the cag PAI has been shown to be essential for stimulating human gastric epithelial cell apoptosis in vitro []. Similar type IV transport systems are also found in other bacteria. This domain is also found in proteins from the trb and Vir conjugal transfer systems in Agrobacterium tumefaciens and homologues of VirB proteins from other species.; GO: 0005524 ATP binding
Probab=34.09 E-value=62 Score=25.56 Aligned_cols=40 Identities=8% Similarity=0.168 Sum_probs=30.8
Q ss_pred EEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcccc
Q psy2814 49 CLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKYQ 89 (176)
Q Consensus 49 ~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~ 89 (176)
..=+.+..|++.|- |.++++..++++...|...|+.+..+
T Consensus 145 ~~G~~~~~i~v~~~-~~~~l~~~~~~v~~~l~~~G~~~~~e 184 (205)
T PF03135_consen 145 SFGYYHFTIVVFAD-DPEELDDKVAEVSSALNNLGFVAVRE 184 (205)
T ss_pred eeeeeEEEEEEEcC-CHHHHHHHHHHHHHHHHHCCCEEEEe
Confidence 34455556666655 99999999999999999999875543
No 83
>COG4978 Transcriptional regulator, effector-binding domain/component [Transcription / Signal transduction mechanisms]
Probab=33.88 E-value=1.1e+02 Score=23.62 Aligned_cols=45 Identities=13% Similarity=0.139 Sum_probs=39.4
Q ss_pred CCeEEEEEecCccEEEEccc-CHHHHHHHHHHHHHHHHhcCCCccc
Q psy2814 44 NPRTTCLAFQSGKLLILGAK-HEHDCKLASRKFAKILKQLGHPIKY 88 (176)
Q Consensus 44 ~p~~t~~If~sGKivitGak-s~~~~~~a~~~i~~~L~~~g~~~~~ 88 (176)
++......+.+||+.++=-+ |-++...+.+++...+++.|..+..
T Consensus 79 ~~~~~~~~~P~g~~a~~~~~G~~~~~~~~y~rli~~iee~g~~i~g 124 (153)
T COG4978 79 DIDIKIKTLPKGKYACIIHKGSYEEVEQAYKRLIEYIEENGLEIIG 124 (153)
T ss_pred CCcceeEEccCceEEEEEEEcCcccHHHHHHHHHHHHHHhCCcccC
Confidence 56788889999998888777 8999999999999999999987654
No 84
>cd02949 TRX_NTR TRX domain, novel NADPH thioredoxin reductase (NTR) family; composed of fusion proteins found only in oxygenic photosynthetic organisms containing both TRX and NTR domains. The TRX domain functions as a protein disulfide reductase via the reversible oxidation of an active center dithiol present in a CXXC motif, while the NTR domain functions as a reductant to oxidized TRX. The fusion protein is bifunctional, showing both TRX and NTR activities, but it is not an independent NTR/TRX system. In plants, the protein is found exclusively in shoots and mature leaves and is localized in the chloroplast. It is involved in plant protection against oxidative stress.
Probab=33.64 E-value=59 Score=22.14 Aligned_cols=25 Identities=32% Similarity=0.529 Sum_probs=19.4
Q ss_pred EEEEeccceEE--EEecCCHHHHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELHEAF 163 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~~a~ 163 (176)
++.+|..|+++ +.|..+.+++.+.+
T Consensus 70 t~~i~~~g~~v~~~~g~~~~~~~~~~l 96 (97)
T cd02949 70 TVQFFKDKELVKEISGVKMKSEYREFI 96 (97)
T ss_pred EEEEEECCeEEEEEeCCccHHHHHHhh
Confidence 57788999988 78888887776543
No 85
>CHL00041 rps11 ribosomal protein S11
Probab=33.18 E-value=1.5e+02 Score=21.76 Aligned_cols=52 Identities=15% Similarity=0.292 Sum_probs=35.4
Q ss_pred CCceEEEEEcCCeEEEEEec-CccEEEEccc--CHHHHHHHHHHHHHHHHhcCCC
Q psy2814 34 KFHGLIMKILNPRTTCLAFQ-SGKLLILGAK--HEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 34 ~fpgl~~R~~~p~~t~~If~-sGKivitGak--s~~~~~~a~~~i~~~L~~~g~~ 85 (176)
.|+--++-+.++.-..+.|+ +|.+-..|++ +...++.+++++.+.+.++|+.
T Consensus 21 t~NNTiiTlTd~~G~~l~~~S~G~~gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~ 75 (116)
T CHL00041 21 SFNNTIVTVTDVRGRVISWSSAGACGFKGARKGTPFAAQTAAENAIRTVIDQGMK 75 (116)
T ss_pred ccCCEEEEEEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 34555566666655555554 4777777764 4567888899999999988764
No 86
>KOG3384|consensus
Probab=33.03 E-value=29 Score=26.82 Aligned_cols=27 Identities=33% Similarity=0.561 Sum_probs=19.2
Q ss_pred cCCCCCceeEEE---EcCCeEEEEEeccceE
Q psy2814 121 YEPELFPGLIYR---MVKPRVVLLIFVNGRI 148 (176)
Q Consensus 121 YePe~fpgl~~r---~~~~~~t~~IF~sGki 148 (176)
=+|++|||+..+ -.+|. ..+.=.+||+
T Consensus 100 d~~~kFp~vkvkyVrg~~P~-l~llDadgk~ 129 (154)
T KOG3384|consen 100 DEPEKFPGVKVKYVRGSDPV-LKLLDADGKH 129 (154)
T ss_pred CchhhCCCceEEEecCCCCe-eEeecCCCCc
Confidence 389999998744 45664 4456788875
No 87
>cd02956 ybbN ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.
Probab=32.66 E-value=57 Score=21.85 Aligned_cols=25 Identities=24% Similarity=0.562 Sum_probs=17.9
Q ss_pred EEEEeccceEE--EEecCCHHHHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELHEAF 163 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~~a~ 163 (176)
++.+|..|+.+ ..|..+.+++..-+
T Consensus 69 t~~~~~~g~~~~~~~g~~~~~~l~~~l 95 (96)
T cd02956 69 TVYLFAAGQPVDGFQGAQPEEQLRQML 95 (96)
T ss_pred EEEEEeCCEEeeeecCCCCHHHHHHHh
Confidence 46677788775 77888888777643
No 88
>TIGR03632 bact_S11 30S ribosomal protein S11. This model describes the bacterial 30S ribosomal protein S11. Cutoffs are set such that the model excludes archaeal and eukaryotic ribosomal proteins, but many chloroplast and mitochondrial equivalents of S11 are detected.
Probab=32.52 E-value=1.6e+02 Score=21.31 Aligned_cols=51 Identities=29% Similarity=0.453 Sum_probs=34.7
Q ss_pred CceEEEEEcCCeEEEEEecC-ccEEEEccc--CHHHHHHHHHHHHHHHHhcCCC
Q psy2814 35 FHGLIMKILNPRTTCLAFQS-GKLLILGAK--HEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 35 fpgl~~R~~~p~~t~~If~s-GKivitGak--s~~~~~~a~~~i~~~L~~~g~~ 85 (176)
|+--++-+.++.-..+.|.| |.+-..|.+ +.-.++.+++++.+.++++|+.
T Consensus 9 ~NNT~itlTd~~g~~~~~~S~G~~gfkg~rk~t~~Aa~~~a~~~~~~~~~~gi~ 62 (108)
T TIGR03632 9 FNNTIVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFGMK 62 (108)
T ss_pred CCCEEEEEEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 44556667776655556644 666666654 3456888889999999998864
No 89
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=32.33 E-value=3.1e+02 Score=23.24 Aligned_cols=95 Identities=13% Similarity=-0.032 Sum_probs=50.1
Q ss_pred EEEEcccCHHHHHHHHHHHHHHHHhcCCCcccceee------eeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCceeE
Q psy2814 57 LLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGFK------IHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPGLI 130 (176)
Q Consensus 57 ivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~------i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpgl~ 130 (176)
+.+.|..++-- +.++.+.|.+.|..+...+-. .=.+...++++...+++.|...+.. .-.++-=-+.
T Consensus 10 itv~G~DrpGI----Va~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~p~~~~~~~L~~~L~~---l~~~l~l~i~ 82 (286)
T PRK13011 10 LTLSCPSAAGI----VAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSEEGLDEDALRAGFAP---IAARFGMQWE 82 (286)
T ss_pred EEEEeCCCCCH----HHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecCCCCCHHHHHHHHHH---HHHHhCcEEE
Confidence 45566644443 445677788888765542222 1134555666666777777643211 1112211122
Q ss_pred EEEcCCeEEEEEeccceEEEEecCCHHHHHHHH
Q psy2814 131 YRMVKPRVVLLIFVNGRIVITGAKSRSELHEAF 163 (176)
Q Consensus 131 ~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~ 163 (176)
.+...++.++.||.||. |. +.+.+-+++
T Consensus 83 i~~~~~~~ri~vl~Sg~----g~-nl~al~~~~ 110 (286)
T PRK13011 83 LHDPAARPKVLIMVSKF----DH-CLNDLLYRW 110 (286)
T ss_pred EeecccCceEEEEEcCC----cc-cHHHHHHHH
Confidence 33334556788999993 44 566665554
No 90
>PF12971 NAGLU_N: Alpha-N-acetylglucosaminidase (NAGLU) N-terminal domain; InterPro: IPR024240 Alpha-N-acetylglucosaminidase, is a lysosomal enzyme required for the stepwise degradation of heparan sulphate []. Mutations on the alpha-N-acetylglucosaminidase (NAGLU) gene can lead to Mucopolysaccharidosis type IIIB (MPS IIIB; or Sanfilippo syndrome type B) characterised by neurological dysfunction but relatively mild somatic manifestations []. The structure shows that the enzyme is composed of three domains. This entry represents the N-terminal domain of Alpha-N-acetylglucosaminidase which has an alpha-beta fold [].; PDB: 4A4A_A 2VC9_A 2VCC_A 2VCB_A 2VCA_A.
Probab=32.29 E-value=78 Score=21.85 Aligned_cols=25 Identities=32% Similarity=0.401 Sum_probs=19.3
Q ss_pred ccceEEEEecCCHHHHHHHHHHHHHH
Q psy2814 144 VNGRIVITGAKSRSELHEAFDNIYPV 169 (176)
Q Consensus 144 ~sGkivitGaks~~~~~~a~~~i~~~ 169 (176)
.+|||+|.|. |...+..|+..-++.
T Consensus 40 ~~gki~I~G~-s~vala~Gl~~YLk~ 64 (86)
T PF12971_consen 40 DNGKIVIRGN-SGVALASGLNWYLKY 64 (86)
T ss_dssp SSS-EEEEES-SHHHHHHHHHHHHHH
T ss_pred CCCeEEEEeC-CHHHHHHHHHHHHHH
Confidence 6899999999 788888888776554
No 91
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=31.58 E-value=2.1e+02 Score=21.10 Aligned_cols=52 Identities=15% Similarity=0.130 Sum_probs=36.9
Q ss_pred CCceEEEEEcCCeE-E-EEEecCccEEEEccc--CHHHHHHHHHHHHHHHHhcCCC
Q psy2814 34 KFHGLIMKILNPRT-T-CLAFQSGKLLILGAK--HEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 34 ~fpgl~~R~~~p~~-t-~~If~sGKivitGak--s~~~~~~a~~~i~~~L~~~g~~ 85 (176)
.|+.-++-+.+.+- . +.-.++|...-.|++ +.=.++.|++++.+...++|+.
T Consensus 10 s~NNTiitvTD~~G~~~~~~~S~G~~g~kg~kk~TpyAAq~aa~~~~~~~~~~Gi~ 65 (114)
T TIGR03628 10 SFNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGIT 65 (114)
T ss_pred cCCCeEEEEEcCCCCEEEEEecCcceEeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 35566677777766 3 455555666666763 4556889999999999999875
No 92
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=31.50 E-value=51 Score=24.62 Aligned_cols=28 Identities=18% Similarity=0.345 Sum_probs=23.4
Q ss_pred CHHHHHHHHHHHHHHHHhcCCCccccee
Q psy2814 64 HEHDCKLASRKFAKILKQLGHPIKYQGF 91 (176)
Q Consensus 64 s~~~~~~a~~~i~~~L~~~g~~~~~~~~ 91 (176)
+-+.+.+|++.+.+.|+.+|+.+.+...
T Consensus 21 Tg~~L~~av~~l~~~L~~~Giev~l~~~ 48 (120)
T PF10865_consen 21 TGETLREAVKELAPVLAPLGIEVRLEEI 48 (120)
T ss_pred HHHHHHHHHHHHHHHHHhCCcEEEEEEE
Confidence 4678899999999999999998776433
No 93
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=31.46 E-value=43 Score=27.47 Aligned_cols=42 Identities=12% Similarity=0.327 Sum_probs=28.2
Q ss_pred cCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCc
Q psy2814 43 LNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPI 86 (176)
Q Consensus 43 ~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~ 86 (176)
++|+-.++|+.+.+.- +......+..=++.+.+.|+++||++
T Consensus 5 ~~p~g~alII~n~~f~--~~~~r~g~~~D~~~l~~~f~~lgF~V 46 (241)
T smart00115 5 SKPRGLALIINNENFH--SLPRRNGTDVDAENLTELFQSLGYEV 46 (241)
T ss_pred CCCCcEEEEEECccCC--CCcCCCCcHHHHHHHHHHHHHCCCEE
Confidence 3678888888888763 33344445555667777888887743
No 94
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=31.27 E-value=2.2e+02 Score=21.61 Aligned_cols=53 Identities=19% Similarity=0.179 Sum_probs=36.6
Q ss_pred CCCceEEEEEcCCeE-EEEEec-CccEEEEccc--CHHHHHHHHHHHHHHHHhcCCC
Q psy2814 33 GKFHGLIMKILNPRT-TCLAFQ-SGKLLILGAK--HEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 33 ~~fpgl~~R~~~p~~-t~~If~-sGKivitGak--s~~~~~~a~~~i~~~L~~~g~~ 85 (176)
..|+.-++-+.|.+- .++.|+ .|...-.|++ +.=.++.|++++.+...++|+.
T Consensus 16 as~NNTivtvTD~~G~~~~~~~S~G~~g~kg~kK~TpyAAq~aae~~~~~~~~~Gi~ 72 (132)
T PRK09607 16 ASFNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKGIT 72 (132)
T ss_pred cccCCeEEEEEcCCCCEEEEEecCcceeeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 345666677777766 244554 5555556663 4457899999999999999875
No 95
>TIGR00411 redox_disulf_1 small redox-active disulfide protein 1. This protein is homologous to a family of proteins that includes thioredoxins, glutaredoxins, protein-disulfide isomerases, and others, some of which have several such domains. The sequence of this protein at the redox-active disufide site, CPYC, matches glutaredoxins rather than thioredoxins, although its overall sequence seems closer to thioredoxins. It is suggested to be a ribonucleotide-reducing system component distinct from thioredoxin or glutaredoxin.
Probab=31.21 E-value=85 Score=20.16 Aligned_cols=22 Identities=36% Similarity=0.546 Sum_probs=17.8
Q ss_pred cceEEEEecCCHHHHHHHHHHH
Q psy2814 145 NGRIVITGAKSRSELHEAFDNI 166 (176)
Q Consensus 145 sGkivitGaks~~~~~~a~~~i 166 (176)
.|+..+.|..+.+++.+.++..
T Consensus 60 ~g~~~~~G~~~~~~l~~~l~~~ 81 (82)
T TIGR00411 60 NGDVEFIGAPTKEELVEAIKKR 81 (82)
T ss_pred CCEEEEecCCCHHHHHHHHHhh
Confidence 6777899998999988877653
No 96
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=31.13 E-value=3.3e+02 Score=23.08 Aligned_cols=94 Identities=13% Similarity=0.123 Sum_probs=52.1
Q ss_pred EEEEcccCHHHHHHHHHHHHHHHHhcCCCcccceeee------eeEEEEeee-CcccCHHHHHHHcCCCcccCCCCCcee
Q psy2814 57 LLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGFKI------HNIVCTCDV-RFPVKLDALHHVHSQFSSYEPELFPGL 129 (176)
Q Consensus 57 ivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i------~nIvas~~l-~~~i~L~~l~~~~~~~~~YePe~fpgl 129 (176)
+.+.|...+.- +..+.+.|.+.|..+......+ =.+...+++ +.+.+++.|...+. ....|+ ++
T Consensus 9 itv~G~DrpGI----Va~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~~~~~~~~~L~~~L~---~l~~~l--~l 79 (286)
T PRK06027 9 LTLSCPDRPGI----VAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDGLIFNLETLRADFA---ALAEEF--EM 79 (286)
T ss_pred EEEECCCCCcH----HHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCCCCCCHHHHHHHHH---HHHHHh--CC
Confidence 45566644443 3457778888887765533333 233444555 44666666664321 111122 23
Q ss_pred EEEE--cCCeEEEEEeccceEEEEecCCHHHHHHHHH
Q psy2814 130 IYRM--VKPRVVLLIFVNGRIVITGAKSRSELHEAFD 164 (176)
Q Consensus 130 ~~r~--~~~~~t~~IF~sGkivitGaks~~~~~~a~~ 164 (176)
...+ ..++.++.||.||. |. +.+.+-++++
T Consensus 80 ~i~l~~~~~~~ri~vl~Sg~----gs-nl~al~~~~~ 111 (286)
T PRK06027 80 DWRLLDSAERKRVVILVSKE----DH-CLGDLLWRWR 111 (286)
T ss_pred EEEEcccccCcEEEEEEcCC----CC-CHHHHHHHHH
Confidence 3333 33456788999998 55 6777776654
No 97
>PRK10259 hypothetical protein; Provisional
Probab=31.05 E-value=59 Score=22.88 Aligned_cols=24 Identities=17% Similarity=0.177 Sum_probs=20.0
Q ss_pred ccceEEEEecCCHHHHHHHHHHHH
Q psy2814 144 VNGRIVITGAKSRSELHEAFDNIY 167 (176)
Q Consensus 144 ~sGkivitGaks~~~~~~a~~~i~ 167 (176)
+-|-|.++|..+++|+++.+.+-.
T Consensus 36 kiG~VSvsg~~s~~d~~~~La~KA 59 (86)
T PRK10259 36 KIGVVSADGASTLDALEAKLAEKA 59 (86)
T ss_pred cceEEEEecCCCHHHHHHHHHHHH
Confidence 568899999999999999877643
No 98
>cd07047 BMC_PduB_repeat1 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 1. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduB).
Probab=30.67 E-value=79 Score=24.13 Aligned_cols=28 Identities=21% Similarity=0.325 Sum_probs=23.7
Q ss_pred CccEEEEcccCHHHHHHHHHHHHHHHHh
Q psy2814 54 SGKLLILGAKHEHDCKLASRKFAKILKQ 81 (176)
Q Consensus 54 sGKivitGaks~~~~~~a~~~i~~~L~~ 81 (176)
+|-+++||+.++.+.+.|++--...+.+
T Consensus 78 kg~vvitGg~dVs~V~~aVeaa~~~v~~ 105 (134)
T cd07047 78 HGSLILFGAEDVSDVRRAVEVALSETEK 105 (134)
T ss_pred eEEEEEEcCCCHHHHHHHHHHHHHHHHH
Confidence 7889999999999988887777777665
No 99
>TIGR01068 thioredoxin thioredoxin. Several proteins, such as protein disulfide isomerase, have two or more copies of a domain closely related to thioredoxin. This model is designed to recognize authentic thioredoxin, a small protein that should be hit exactly once by this model.
Probab=30.39 E-value=90 Score=20.56 Aligned_cols=26 Identities=35% Similarity=0.620 Sum_probs=16.8
Q ss_pred EEEeccceEE--EEecCCHHHHHHHHHH
Q psy2814 140 LLIFVNGRIV--ITGAKSRSELHEAFDN 165 (176)
Q Consensus 140 ~~IF~sGkiv--itGaks~~~~~~a~~~ 165 (176)
+.+|..|+.+ +.|..+.+++.+.++.
T Consensus 72 ~~~~~~g~~~~~~~g~~~~~~l~~~l~~ 99 (101)
T TIGR01068 72 LLLFKNGKEVDRSVGALPKAALKQLINK 99 (101)
T ss_pred EEEEeCCcEeeeecCCCCHHHHHHHHHh
Confidence 4455666653 5578887777776654
No 100
>PF11399 DUF3192: Protein of unknown function (DUF3192); InterPro: IPR021534 Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed.
Probab=29.82 E-value=86 Score=22.86 Aligned_cols=20 Identities=35% Similarity=0.519 Sum_probs=17.1
Q ss_pred CCeEEEEEeccceEEEEecC
Q psy2814 135 KPRVVLLIFVNGRIVITGAK 154 (176)
Q Consensus 135 ~~~~t~~IF~sGkivitGak 154 (176)
...||-++|.+|+++=-|-+
T Consensus 78 kDECTplvF~n~~LvgWG~~ 97 (102)
T PF11399_consen 78 KDECTPLVFKNGKLVGWGDD 97 (102)
T ss_pred CCceEEEEEECCEEEEEcHH
Confidence 34799999999999988864
No 101
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=29.57 E-value=78 Score=21.20 Aligned_cols=25 Identities=20% Similarity=0.367 Sum_probs=17.4
Q ss_pred eEEEEecCCHHHHHHHHHHHHHHHH
Q psy2814 147 RIVITGAKSRSELHEAFDNIYPVLK 171 (176)
Q Consensus 147 kivitGaks~~~~~~a~~~i~~~L~ 171 (176)
+|+|||+++-.|.+...+.+-.++.
T Consensus 5 rVli~GgR~~~D~~~i~~~Ld~~~~ 29 (71)
T PF10686_consen 5 RVLITGGRDWTDHELIWAALDKVHA 29 (71)
T ss_pred EEEEEECCccccHHHHHHHHHHHHH
Confidence 6899999998776665555544443
No 102
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=28.55 E-value=81 Score=26.16 Aligned_cols=78 Identities=10% Similarity=0.196 Sum_probs=42.5
Q ss_pred ceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCCCce--eEEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHHHH
Q psy2814 89 QGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPELFPG--LIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFDNI 166 (176)
Q Consensus 89 ~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~fpg--l~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~~i 166 (176)
+|+.=.+|++..--...+|++.+...+.. -.|--+..-- .--+|.-..+=.+|| .||+.|.|+.+++-+..|++.+
T Consensus 135 ~nI~D~dVL~diA~~~GLD~~~~~~~L~s-~~~~~avr~d~~~A~e~gI~gVP~fv~-d~~~~V~Gaq~~~v~~~al~~~ 212 (225)
T COG2761 135 RNIGDEDVLADIAEEVGLDREEFKADLAS-DAAKDAVRQDEAAAQEMGIRGVPTFVF-DGKYAVSGAQPYDVLEDALRQL 212 (225)
T ss_pred CCCCcHHHHHHHHHHhCCCHHHHHHHHhC-hHHHHHHHHHHHHHHHCCCccCceEEE-cCcEeecCCCCHHHHHHHHHHH
Confidence 34444455555555666777766653311 1111110000 000111122334555 9999999999999999999887
Q ss_pred HH
Q psy2814 167 YP 168 (176)
Q Consensus 167 ~~ 168 (176)
..
T Consensus 213 ~~ 214 (225)
T COG2761 213 LA 214 (225)
T ss_pred Hh
Confidence 64
No 103
>cd03005 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.
Probab=28.19 E-value=78 Score=21.21 Aligned_cols=23 Identities=35% Similarity=0.625 Sum_probs=15.3
Q ss_pred EEEEeccceEE--EEecCCHHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELHE 161 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~~ 161 (176)
|+.+|..|+.+ ..|.++.+++.+
T Consensus 76 t~~~~~~g~~~~~~~G~~~~~~l~~ 100 (102)
T cd03005 76 TLLLFKDGEKVDKYKGTRDLDSLKE 100 (102)
T ss_pred EEEEEeCCCeeeEeeCCCCHHHHHh
Confidence 35566677654 788888777654
No 104
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=28.07 E-value=1.7e+02 Score=20.87 Aligned_cols=45 Identities=11% Similarity=0.038 Sum_probs=31.3
Q ss_pred CCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHh-cCCCcccceeeee
Q psy2814 44 NPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQ-LGHPIKYQGFKIH 94 (176)
Q Consensus 44 ~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~-~g~~~~~~~~~i~ 94 (176)
+|-+.+.| .+.|.++.|+-++-.+.+.+.|++ +|++..---+.++
T Consensus 56 ~p~a~v~i------~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~rv~I~f~ 101 (116)
T PTZ00397 56 DGCCFVRV------TSIGGISRSNNSSIAAAITKILASHLKVKSERVYIEFK 101 (116)
T ss_pred CceEEEEE------EEecCCCHHHHHHHHHHHHHHHHHHhCcCcccEEEEEE
Confidence 45555544 445888999999999999999976 6887554333333
No 105
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=27.79 E-value=92 Score=18.88 Aligned_cols=22 Identities=23% Similarity=0.418 Sum_probs=19.5
Q ss_pred CHHHHHHHHHHHHHHHHhcCCC
Q psy2814 64 HEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 64 s~~~~~~a~~~i~~~L~~~g~~ 85 (176)
+++++..|+.+..+.+.+.|++
T Consensus 20 ~~~EA~~A~~kAq~Lm~ky~i~ 41 (43)
T PF10979_consen 20 NEHEAEAALAKAQRLMAKYGID 41 (43)
T ss_pred CHHHHHHHHHHHHHHHHHhCCc
Confidence 6779999999999999998875
No 106
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=27.19 E-value=2.6e+02 Score=20.62 Aligned_cols=50 Identities=12% Similarity=0.283 Sum_probs=35.7
Q ss_pred CCCCCceeEEEEcCCeEEEEEeccc-eEEEEec-----CCHHHHHHHHHHHHHHHH
Q psy2814 122 EPELFPGLIYRMVKPRVVLLIFVNG-RIVITGA-----KSRSELHEAFDNIYPVLK 171 (176)
Q Consensus 122 ePe~fpgl~~r~~~~~~t~~IF~sG-kivitGa-----ks~~~~~~a~~~i~~~L~ 171 (176)
..+.|-|+++++.+-++..-+=.|| |+++.=. ...++++.-++++...-.
T Consensus 48 ~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~~~~~~~~d~~ik~fF~~vh~~Y~ 103 (132)
T PF04628_consen 48 SSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHDMSDNSIRDEDIKQFFKEVHELYV 103 (132)
T ss_dssp SSCSEEEEEEEETTEEEEEEETTT--EEEEEECGGG-S--HHHHHHHHHHHHHHHH
T ss_pred ccccccCceehhhhHHHHhhhccCceeEEEEEecccCCcchHHHHHHHHHHHHHHH
Confidence 4577889999998888888888888 6655433 577888888888876644
No 107
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=27.17 E-value=1.3e+02 Score=20.07 Aligned_cols=38 Identities=18% Similarity=0.139 Sum_probs=27.3
Q ss_pred EEEEEeccceEEEEecCCHHHHHHHHHHHHHHHHhhhc
Q psy2814 138 VVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLKSFKK 175 (176)
Q Consensus 138 ~t~~IF~sGkivitGaks~~~~~~a~~~i~~~L~~~r~ 175 (176)
+++.|+..-.-+-.+..+++.++++.+.|-..+.++++
T Consensus 2 V~v~I~G~~y~i~~~~~~ee~l~~~a~~i~~~i~~~~~ 39 (89)
T PF05164_consen 2 VKVTILGREYRIKCPDEDEEYLRKAAELINEKINEIKK 39 (89)
T ss_dssp EEEEETTEEEEECETGCGHHHHHHHHHHHHHHHHHHCT
T ss_pred eEEEECCEEEEeecCCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34445444333333677999999999999999998876
No 108
>PF11869 DUF3389: Protein of unknown function (DUF3389); InterPro: IPR021811 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=27.16 E-value=34 Score=23.57 Aligned_cols=11 Identities=36% Similarity=0.622 Sum_probs=9.0
Q ss_pred EeccceEEEEe
Q psy2814 142 IFVNGRIVITG 152 (176)
Q Consensus 142 IF~sGkivitG 152 (176)
=|+.|||+.|-
T Consensus 4 ~Fs~GKiI~t~ 14 (75)
T PF11869_consen 4 EFSQGKIIATP 14 (75)
T ss_pred EecCCeEEEcc
Confidence 49999999873
No 109
>cd00148 PROF Profilin binds actin monomers, membrane polyphosphoinositides such as PI(4,5)P2, and poly-L-proline. Profilin can inhibit actin polymerization into F-actin by binding to monomeric actin (G-actin) and terminal F-actin subunits, but - as a regulator of the cytoskeleton - it may also promote actin polymerization. It plays a role in the assembly of branched actin filament networks, by activating WASP via binding to WASP's proline rich domain. Profilin may link the cytoskeleton with major signalling pathways by interacting with components of the phosphatidylinositol cycle and Ras pathway.
Probab=26.71 E-value=2.2e+02 Score=20.94 Aligned_cols=40 Identities=15% Similarity=0.233 Sum_probs=30.8
Q ss_pred CeEEEEEecCccEEEEcccC----HHHHHHHHHHHHHHHHhcCC
Q psy2814 45 PRTTCLAFQSGKLLILGAKH----EHDCKLASRKFAKILKQLGH 84 (176)
Q Consensus 45 p~~t~~If~sGKivitGaks----~~~~~~a~~~i~~~L~~~g~ 84 (176)
.+.-+.+..++..++.|.-. ...+..++.++++.|.+.|+
T Consensus 84 ~~~Gi~i~kT~~~ivi~~y~e~~~~g~~~~~v~~ladYL~~~gy 127 (127)
T cd00148 84 GAGGVVIVKTKQALVIGMYEEGVQPGQANKVVEKLADYLRSQGY 127 (127)
T ss_pred CCCeEEEEECCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 33456777788877777643 45899999999999999885
No 110
>cd02950 TxlA TRX-like protein A (TxlA) family; TxlA was originally isolated from the cyanobacterium Synechococcus. It is found only in oxygenic photosynthetic organisms. TRX is a small enzyme that participate in redox reactions, via the reversible oxidation of an active site dithiol present in a CXXC motif. Disruption of the txlA gene suggests that the protein is involved in the redox regulation of the structure and function of photosynthetic apparatus. The plant homolog (designated as HCF164) is localized in the chloroplast and is involved in the assembly of the cytochrome b6f complex, which takes a central position in photosynthetic electron transport.
Probab=26.54 E-value=1.4e+02 Score=22.29 Aligned_cols=30 Identities=7% Similarity=0.067 Sum_probs=21.8
Q ss_pred EEEEEe-cCccEE--EEcccCHHHHHHHHHHHH
Q psy2814 47 TTCLAF-QSGKLL--ILGAKHEHDCKLASRKFA 76 (176)
Q Consensus 47 ~t~~If-~sGKiv--itGaks~~~~~~a~~~i~ 76 (176)
.++.+| .+|+++ +.|....++++..++.++
T Consensus 78 Pt~v~~~~~G~~v~~~~G~~~~~~l~~~l~~l~ 110 (142)
T cd02950 78 PHFVFLDREGNEEGQSIGLQPKQVLAQNLDALV 110 (142)
T ss_pred CEEEEECCCCCEEEEEeCCCCHHHHHHHHHHHH
Confidence 466778 589998 789888877766655544
No 111
>COG0678 AHP1 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=26.33 E-value=38 Score=26.67 Aligned_cols=54 Identities=17% Similarity=0.098 Sum_probs=37.1
Q ss_pred ccCCCceEEEEEc---------CCeEEEEEecCccEEEEccc-------CHHHHHHHHHHHHHHHHhcCCC
Q psy2814 31 NPGKFHGLIMKIL---------NPRTTCLAFQSGKLLILGAK-------HEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 31 ~P~~fpgl~~R~~---------~p~~t~~If~sGKivitGak-------s~~~~~~a~~~i~~~L~~~g~~ 85 (176)
..+++|.+.+|.+ .+..+-.+|.+.|+++.|.. |..++ -+.....+.++..|.+
T Consensus 5 vg~klP~vtf~tr~~~~~~~~~~~~ts~~lf~gKkVvlf~lPGAFTPTCS~~hl-PgY~~~~d~f~~kGVD 74 (165)
T COG0678 5 VGKKLPAVTFKTRVGDETADGWVDVTTDDLFKGKKVVLFSLPGAFTPTCSSSHL-PGYLELADEFKAKGVD 74 (165)
T ss_pred cCCcCCceEeEEeeccccCCCcccccHHHhcCCCEEEEEeCCCccCCCcccccC-ccHHHHHHHHHHcCCc
Confidence 3467788888877 45678899999999999853 22222 2345566667777765
No 112
>cd07046 BMC_PduU-EutS 1,2-propanediol utilization protein U (PduU)/ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain. PduU encapsulates several related enzymes within a shell composed of a few thousand protein subunits. PduU exists as a hexamer which might further assemble into the flat facets of the polyhedral outer shell of the pdu organelle. This proteinaceous noncarboxysome microcompartment is involved in coenzyme B12-dependent degradation of 1,2-propanediol. The core of PduU is related to the typical BMC domain and its natural oligomeric state is a cyclic hexamer. Unlike other typical BMC domain proteins, the 3D topology of PduU reveals a circular permuted variation on the typical BMC fold which leads to several unique features. The exact functions related to those unique features are still not clear. Another difference is the presence of a deep cavity on one side of the hexamer as well as an intermolecular six-stranded beta barrel that seems to
Probab=26.15 E-value=1.2e+02 Score=22.37 Aligned_cols=26 Identities=35% Similarity=0.600 Sum_probs=22.0
Q ss_pred cceEEEEecCCHHHHHHHHHHHHHHHHh
Q psy2814 145 NGRIVITGAKSRSELHEAFDNIYPVLKS 172 (176)
Q Consensus 145 sGkivitGaks~~~~~~a~~~i~~~L~~ 172 (176)
+|.++++| +.++++.|++.....+.+
T Consensus 73 ~g~vii~G--dvsaV~aAl~a~~~~~~~ 98 (110)
T cd07046 73 SGALVITG--DVSEVESALEAVVDYLRE 98 (110)
T ss_pred eEEEEEEE--CHHHHHHHHHHHHHHHhh
Confidence 67888999 799999999988877654
No 113
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=25.92 E-value=59 Score=22.89 Aligned_cols=33 Identities=21% Similarity=0.225 Sum_probs=25.0
Q ss_pred EecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcc
Q psy2814 51 AFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIK 87 (176)
Q Consensus 51 If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~ 87 (176)
||-||.|. |-. +.-+.++.+.++.|+..|+.+-
T Consensus 1 iYIaGPmt--G~~--~~N~~~f~~~a~~L~~~G~~vv 33 (92)
T PF14359_consen 1 IYIAGPMT--GLP--DYNRPAFNAAAKRLRAKGYEVV 33 (92)
T ss_pred CeEeCCcC--CCc--chHHHHHHHHHHHHHHCCCEEe
Confidence 46677775 654 5557899999999999997644
No 114
>PF02785 Biotin_carb_C: Biotin carboxylase C-terminal domain; InterPro: IPR005482 Acetyl-CoA carboxylase is found in all animals, plants, and bacteria and catalyzes the first committed step in fatty acid synthesis. It is a multicomponent enzyme containing a biotin carboxylase activity, a biotin carboxyl carrier protein, and a carboxyltransferase functionality. The "B-domain" extends from the main body of the subunit where it folds into two alpha-helical regions and three strands of beta-sheet. Following the excursion into the B-domain, the polypeptide chain folds back into the body of the protein where it forms an eight-stranded antiparallel beta-sheet. In addition to this major secondary structural element, the C-terminal domain also contains a smaller three-stranded antiparallel beta-sheet and seven alpha-helices []. ; GO: 0016874 ligase activity; PDB: 1W96_B 1W93_A 3VA7_A 2GPW_A 2W70_A 3G8D_A 1DV2_A 2VR1_B 2J9G_B 1DV1_A ....
Probab=25.77 E-value=78 Score=22.99 Aligned_cols=25 Identities=16% Similarity=0.329 Sum_probs=19.4
Q ss_pred ceEEEEecCCHHHHHHHHHHHHHHHHhhh
Q psy2814 146 GRIVITGAKSRSELHEAFDNIYPVLKSFK 174 (176)
Q Consensus 146 GkivitGaks~~~~~~a~~~i~~~L~~~r 174 (176)
+|+++.|. + -.+|++++...|.+++
T Consensus 52 aKliv~g~-~---R~~Ai~~l~~AL~e~~ 76 (107)
T PF02785_consen 52 AKLIVHGP-D---REEAIARLRRALAETV 76 (107)
T ss_dssp EEEEEEES-S---HHHHHHHHHHHHHHHE
T ss_pred hhheeecc-c---hHHHHHHHHhhcceEE
Confidence 78999988 3 4568888888888774
No 115
>PHA02956 hypothetical protein; Provisional
Probab=25.44 E-value=65 Score=25.05 Aligned_cols=23 Identities=26% Similarity=0.310 Sum_probs=18.1
Q ss_pred ecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCC
Q psy2814 52 FQSGKLLILGAKHEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 52 f~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~ 85 (176)
-+||||+|-|- -+.++|+-.|++
T Consensus 113 sssgkiicegi-----------giid~lr~~gid 135 (189)
T PHA02956 113 SSSGKIICEGI-----------GIIDKLRLHGID 135 (189)
T ss_pred cCCCcEEeecc-----------hHHHHHHHcCch
Confidence 36899999998 367777777765
No 116
>PRK14126 cell division protein ZapA; Provisional
Probab=25.41 E-value=1.8e+02 Score=20.10 Aligned_cols=38 Identities=16% Similarity=0.243 Sum_probs=28.1
Q ss_pred eEEEEEeccceEEEEecCCHHHHHHHHHHHHHHHHhhhc
Q psy2814 137 RVVLLIFVNGRIVITGAKSRSELHEAFDNIYPVLKSFKK 175 (176)
Q Consensus 137 ~~t~~IF~sGkivitGaks~~~~~~a~~~i~~~L~~~r~ 175 (176)
++.+.|+-.-.- |.|..+++.+..+.+.+-..+++.++
T Consensus 8 ~v~V~I~G~~Y~-i~~~e~ee~l~~vA~~vd~km~ei~~ 45 (85)
T PRK14126 8 RINVEIYGQQYT-IVGDESTSHIRMVAAIVDDKMRELNE 45 (85)
T ss_pred eEEEEECCEEEE-ecCCCcHHHHHHHHHHHHHHHHHHHH
Confidence 455566544433 44788999999999999998888765
No 117
>COG0533 QRI7 Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=25.20 E-value=2.5e+02 Score=24.80 Aligned_cols=46 Identities=24% Similarity=0.357 Sum_probs=40.8
Q ss_pred CCceeEEEEcCCeEEEEEecc-ceEEEEecCCHHHHHHHHHHHHHHH
Q psy2814 125 LFPGLIYRMVKPRVVLLIFVN-GRIVITGAKSRSELHEAFDNIYPVL 170 (176)
Q Consensus 125 ~fpgl~~r~~~~~~t~~IF~s-GkivitGaks~~~~~~a~~~i~~~L 170 (176)
.||.+..-.++.-+.+.-+++ |++-+.|.+.=+-+-+|++++.+.|
T Consensus 125 ~~p~v~LlVSGGHTqli~~~~~g~y~ilGeTlDdA~Gea~DKvAR~l 171 (342)
T COG0533 125 AFPPVALLVSGGHTQLIAVRGIGRYEVLGETLDDAAGEAFDKVARLL 171 (342)
T ss_pred CCCcEEEEEecCceEEEEEcCCCcEEEEeeechhhhhHHHHHHHHHh
Confidence 899999888888888888888 9999999987777889999998865
No 118
>COG4274 Uncharacterized conserved protein [Function unknown]
Probab=25.19 E-value=1.1e+02 Score=22.40 Aligned_cols=57 Identities=12% Similarity=0.086 Sum_probs=45.8
Q ss_pred EEEcccCHHHHHHHHHHHHHHHHhcCCCccc--ceeeeeeEEEEeeeCcccCHHHHHHH
Q psy2814 58 LILGAKHEHDCKLASRKFAKILKQLGHPIKY--QGFKIHNIVCTCDVRFPVKLDALHHV 114 (176)
Q Consensus 58 vitGaks~~~~~~a~~~i~~~L~~~g~~~~~--~~~~i~nIvas~~l~~~i~L~~l~~~ 114 (176)
.=.|+|+..+.-+-+..+.+.|++.|.+++. ..+-.-.+|+.+..|-+..+-.++..
T Consensus 18 Td~Gaktlke~p~R~~av~~~les~G~k~~~~y~T~GeYD~V~i~EapDda~~~~~~l~ 76 (104)
T COG4274 18 TDQGAKTLKETPKRAAAVRALLESMGGKVKEQYWTLGEYDVVAIVEAPDDAVATRFSLA 76 (104)
T ss_pred cHhHHHHHhhCHHHHHHHHHHHHHcCcEEEEEEEeeccccEEEEEecCCHHHHHHHHHH
Confidence 3458999988888888899999999988765 55677888888888888887777654
No 119
>COG3445 Acid-induced glycyl radical enzyme [General function prediction only]
Probab=24.96 E-value=27 Score=25.52 Aligned_cols=34 Identities=18% Similarity=0.228 Sum_probs=24.1
Q ss_pred CcccCHHHHHHHcCCCcccCCCCCceeEEEEcCC
Q psy2814 103 RFPVKLDALHHVHSQFSSYEPELFPGLIYRMVKP 136 (176)
Q Consensus 103 ~~~i~L~~l~~~~~~~~~YePe~fpgl~~r~~~~ 136 (176)
+..+|.+-|..+..+.+--.||.||-|..|.++-
T Consensus 70 gqhlnvnvl~retledav~~pekypqltirvsgy 103 (127)
T COG3445 70 GQHLNVNVLRRETLEDAVKHPEKYPQLTIRVSGY 103 (127)
T ss_pred CceeeeeeeehhhHHHHhhCcccCCceEEEEeeE
Confidence 4566666565554466778899999998886553
No 120
>PTZ00051 thioredoxin; Provisional
Probab=24.95 E-value=87 Score=20.96 Aligned_cols=21 Identities=33% Similarity=0.650 Sum_probs=15.5
Q ss_pred EEEEeccceEE--EEecCCHHHHH
Q psy2814 139 VLLIFVNGRIV--ITGAKSRSELH 160 (176)
Q Consensus 139 t~~IF~sGkiv--itGaks~~~~~ 160 (176)
|+.+|..|+++ +.|+ ..++++
T Consensus 74 t~~~~~~g~~~~~~~G~-~~~~~~ 96 (98)
T PTZ00051 74 TFKVFKNGSVVDTLLGA-NDEALK 96 (98)
T ss_pred EEEEEeCCeEEEEEeCC-CHHHhh
Confidence 57788999987 7776 566654
No 121
>PF14356 DUF4403: Domain of unknown function (DUF4403)
Probab=24.93 E-value=1.2e+02 Score=27.22 Aligned_cols=53 Identities=21% Similarity=0.293 Sum_probs=37.3
Q ss_pred EEeeeCcccCHHHHHHHc---CCCcccCCCCCceeEEEEcCCeEEEEEeccceEEEEec
Q psy2814 98 CTCDVRFPVKLDALHHVH---SQFSSYEPELFPGLIYRMVKPRVVLLIFVNGRIVITGA 153 (176)
Q Consensus 98 as~~l~~~i~L~~l~~~~---~~~~~YePe~fpgl~~r~~~~~~t~~IF~sGkivitGa 153 (176)
.+.++|..|.|..|.... -....|+.+.++.- ..+-.+...+.++|.|.++|.
T Consensus 5 S~i~vPv~i~l~~l~~~~n~~lp~~~~~~~~~~~~---~~~~~i~~~v~R~g~i~i~~~ 60 (427)
T PF14356_consen 5 SSINVPVEIPLADLEDALNRKLPGEFYGDDDFPDD---LNNDDIRYKVWRTGPITITGN 60 (427)
T ss_pred cEEEEEEEEEHHHHHHHHhhhCchhhcCCCCCCCc---cccceEEEEEEecCceEEEec
Confidence 467788999999887632 24466777766554 334467778888888888876
No 122
>PRK15412 thiol:disulfide interchange protein DsbE; Provisional
Probab=24.83 E-value=1.5e+02 Score=23.00 Aligned_cols=52 Identities=15% Similarity=0.155 Sum_probs=36.9
Q ss_pred ccCCCCCceeEEEEcCCeEEEEEeccceEEE--EecCCHHHHHHHHHHHHHHHH
Q psy2814 120 SYEPELFPGLIYRMVKPRVVLLIFVNGRIVI--TGAKSRSELHEAFDNIYPVLK 171 (176)
Q Consensus 120 ~YePe~fpgl~~r~~~~~~t~~IF~sGkivi--tGaks~~~~~~a~~~i~~~L~ 171 (176)
-+||+..-+..|.....-.++.|.++|+|+- .|.-+++++++.++.+++...
T Consensus 127 ~~D~~~~~~~~~gv~~~P~t~vid~~G~i~~~~~G~~~~~~l~~~i~~~~~~~~ 180 (185)
T PRK15412 127 LFDGDGMLGLDLGVYGAPETFLIDGNGIIRYRHAGDLNPRVWESEIKPLWEKYS 180 (185)
T ss_pred EEcCCccHHHhcCCCcCCeEEEECCCceEEEEEecCCCHHHHHHHHHHHHHHHH
Confidence 4466654444566666557899999998764 567788888888888876654
No 123
>TIGR01175 pilM type IV pilus assembly protein PilM. This protein is required for the assembly of the type IV fimbria in Pseudomonas aeruginosa responsible for twitching motility, and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria.
Probab=24.81 E-value=3.6e+02 Score=22.76 Aligned_cols=72 Identities=15% Similarity=0.051 Sum_probs=44.1
Q ss_pred HHHHHHHHHHHHhcCCCcccceeeeeeEEEEeeeCcccCHHHHHHHcCCC-cccCCCCCc-eeEEEEcCCeEEEEEeccc
Q psy2814 69 KLASRKFAKILKQLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQF-SSYEPELFP-GLIYRMVKPRVVLLIFVNG 146 (176)
Q Consensus 69 ~~a~~~i~~~L~~~g~~~~~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~-~~YePe~fp-gl~~r~~~~~~t~~IF~sG 146 (176)
+..++.+.+.+++.|+++..-+ .-++-|..+...++++ .+.++ ..+ .++.-+-...+++.||..|
T Consensus 142 ~~~v~~~~~~~~~aGl~~~~id------------~~~~Al~~~~~~~~~~~~~~~~-~~~~~~lvdiG~~~t~l~i~~~g 208 (348)
T TIGR01175 142 KEVVDSRLHALKLAGLEPKVVD------------VESFALLRAWRLLGEQLASRTY-RLTDAALVDIGATSSTLNLLHPG 208 (348)
T ss_pred HHHHHHHHHHHHHcCCceEEEe------------cHHHHHHHHHHHHHhhCccccc-cCceEEEEEECCCcEEEEEEECC
Confidence 4556778888899988764221 1122222222212121 22333 344 7789998999999999999
Q ss_pred eEEEEec
Q psy2814 147 RIVITGA 153 (176)
Q Consensus 147 kivitGa 153 (176)
++..+..
T Consensus 209 ~~~~~r~ 215 (348)
T TIGR01175 209 RMLFTRE 215 (348)
T ss_pred eEEEEEE
Confidence 9988653
No 124
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=24.62 E-value=1.5e+02 Score=24.56 Aligned_cols=49 Identities=22% Similarity=0.268 Sum_probs=39.4
Q ss_pred cCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcccceeeee
Q psy2814 43 LNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGFKIH 94 (176)
Q Consensus 43 ~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~ 94 (176)
.+..++++|=.||.|-- +..+-+..++.-+++.|.++|+++....|+-.
T Consensus 11 ~d~~VtlLID~SGSMrg---r~~~vA~~~adila~aL~~~gvp~EVlGFtT~ 59 (219)
T PF11775_consen 11 RDTVVTLLIDCSGSMRG---RPIEVAALCADILARALERCGVPVEVLGFTTR 59 (219)
T ss_pred CCeEEEEEEeCCcCCCC---ChHHHHHHHHHHHHHHHHhCCCCeEEEeeecC
Confidence 46678999999999853 56677777889999999999999887666654
No 125
>COG4810 EutS Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=24.51 E-value=1.4e+02 Score=21.98 Aligned_cols=30 Identities=27% Similarity=0.377 Sum_probs=22.4
Q ss_pred EEeccceEEEEecCCHHHHHHHHHHHHHHHHh
Q psy2814 141 LIFVNGRIVITGAKSRSELHEAFDNIYPVLKS 172 (176)
Q Consensus 141 ~IF~sGkivitGaks~~~~~~a~~~i~~~L~~ 172 (176)
+==-||.+++||. ...+++|+++...-|-+
T Consensus 80 lDRFsGalvltGd--v~aVE~aLkqv~~~L~e 109 (121)
T COG4810 80 LDRFSGALVLTGD--VGAVEEALKQVVSGLGE 109 (121)
T ss_pred eecccceEEEEcc--hHHHHHHHHHHHHHHHH
Confidence 3345899999996 67788888877776654
No 126
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=24.48 E-value=1.2e+02 Score=18.81 Aligned_cols=20 Identities=30% Similarity=0.536 Sum_probs=16.6
Q ss_pred cceEEEEecCCHHHHHHHHHHH
Q psy2814 145 NGRIVITGAKSRSELHEAFDNI 166 (176)
Q Consensus 145 sGkivitGaks~~~~~~a~~~i 166 (176)
++.|+|+|. .+.+..|.+.|
T Consensus 42 ~~~v~I~G~--~~~v~~A~~~i 61 (62)
T cd02394 42 SDTITITGP--KENVEKAKEEI 61 (62)
T ss_pred CCEEEEEcC--HHHHHHHHHHh
Confidence 789999998 67888887765
No 127
>PF12864 DUF3822: Protein of unknown function (DUF3822); InterPro: IPR024213 This is a family of uncharacterised bacterial proteins. However, structural-similarity searches indicate the family takes on an actin-like ATPase fold.; PDB: 3HRG_A.
Probab=24.41 E-value=3.2e+02 Score=22.37 Aligned_cols=54 Identities=17% Similarity=0.197 Sum_probs=40.6
Q ss_pred ceEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcccc
Q psy2814 36 HGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKYQ 89 (176)
Q Consensus 36 pgl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~ 89 (176)
+-+.+-+.+-...+.+|.+||+...=.=+.+.+...+=-++-.++++|++...-
T Consensus 174 ~~ly~~~~~~~~~i~~~~~~kL~~~N~F~~~~~eD~lYYlL~v~~Ql~ld~e~~ 227 (253)
T PF12864_consen 174 RKLYVHFHDNQFDIFVFKNGKLLFFNSFEYQTAEDFLYYLLFVWEQLGLDPEKD 227 (253)
T ss_dssp -EEEEEE-SSEEEEEEEETTEEEEEEEEE--SHHHHHHHHHHHHHHTT--TTT-
T ss_pred cEEEEEEECCEEEEEEEECCEEEEEEEEecCChHHHHHHHHHHHHHcCCCcccc
Confidence 455677778899999999999999888788888888888999999999986643
No 128
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=24.35 E-value=1.2e+02 Score=18.25 Aligned_cols=25 Identities=20% Similarity=0.139 Sum_probs=20.7
Q ss_pred EEEEcccCHHHHHHHHHHHHHHHHh
Q psy2814 57 LLILGAKHEHDCKLASRKFAKILKQ 81 (176)
Q Consensus 57 ivitGaks~~~~~~a~~~i~~~L~~ 81 (176)
+.-.|.++..+|+.++.++...+.+
T Consensus 19 ~~k~GF~TkkeA~~~~~~~~~~~~~ 43 (46)
T PF14657_consen 19 KTKRGFKTKKEAEKALAKIEAELEN 43 (46)
T ss_pred EEcCCCCcHHHHHHHHHHHHHHHHc
Confidence 4557899999999999998877654
No 129
>cd02975 PfPDO_like_N Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI), which are both involved in oxidative protein folding. PfPDO contains two redox active CXXC motifs in two contiguous TRX-fold subdomains. The active site in the N-terminal TRX-fold subdomain is required for isomerase but not for reductase activity of PfPDO. The exclusive presence of PfPDO-like proteins in extremophiles may suggest that they have a special role in adaptation to extreme conditions.
Probab=24.19 E-value=1.8e+02 Score=20.67 Aligned_cols=30 Identities=17% Similarity=0.278 Sum_probs=23.4
Q ss_pred EEEEecc----ceEEEEecCCHHHHHHHHHHHHH
Q psy2814 139 VLLIFVN----GRIVITGAKSRSELHEAFDNIYP 168 (176)
Q Consensus 139 t~~IF~s----GkivitGaks~~~~~~a~~~i~~ 168 (176)
|+.+|.. |++...|..+.+++.+-++.|+.
T Consensus 78 t~~i~~~g~~~~~~~~~G~~~~~el~~~i~~i~~ 111 (113)
T cd02975 78 TTIFLQDGGKDGGIRYYGLPAGYEFASLIEDIVR 111 (113)
T ss_pred EEEEEeCCeecceEEEEecCchHHHHHHHHHHHh
Confidence 5667765 66678999999999888887764
No 130
>PF00403 HMA: Heavy-metal-associated domain; InterPro: IPR006121 Proteins that transport heavy metals in micro-organisms and mammals share similarities in their sequences and structures. These proteins provide an important focus for research, some being involved in bacterial resistance to toxic metals, such as lead and cadmium, while others are involved in inherited human syndromes, such as Wilson's and Menke's diseases []. A conserved domain has been found in a number of these heavy metal transport or detoxification proteins []. The domain, which has been termed Heavy-Metal-Associated (HMA), contains two conserved cysteines that are probably involved in metal binding. Structure solution of the fourth HMA domain of the Menke's copper transporting ATPase shows a well-defined structure comprising a four-stranded antiparallel beta-sheet and two alpha helices packed in an alpha-beta sandwich fold []. This fold is common to other domains and is classified as "ferredoxin-like".; GO: 0046872 metal ion binding, 0030001 metal ion transport; PDB: 2VOY_A 1P6T_A 1KQK_A 2RML_A 1JWW_A 3K7R_F 1FES_A 1CC8_A 1FD8_A 2GGP_A ....
Probab=23.80 E-value=87 Score=19.41 Aligned_cols=24 Identities=13% Similarity=0.210 Sum_probs=17.7
Q ss_pred EeccceEEEEecCCH---HHHHHHHHH
Q psy2814 142 IFVNGRIVITGAKSR---SELHEAFDN 165 (176)
Q Consensus 142 IF~sGkivitGaks~---~~~~~a~~~ 165 (176)
=|.+|+++|++.... +++.+++++
T Consensus 32 d~~~~~v~v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 32 DLETKTVTVTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp ETTTTEEEEEESTTTSCHHHHHHHHHH
T ss_pred ECCCCEEEEEEecCCCCHHHHHHHHHH
Confidence 467899999988665 777776654
No 131
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=23.77 E-value=1.4e+02 Score=22.38 Aligned_cols=29 Identities=14% Similarity=0.276 Sum_probs=24.0
Q ss_pred EEeccceEEEEecCCHHHHHHHHHHHHHH
Q psy2814 141 LIFVNGRIVITGAKSRSELHEAFDNIYPV 169 (176)
Q Consensus 141 ~IF~sGkivitGaks~~~~~~a~~~i~~~ 169 (176)
+...||.|+++...++++++..++..+..
T Consensus 38 Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~ 66 (137)
T PF08002_consen 38 TYIQSGNVVFESDRDPAELAAKIEKALEE 66 (137)
T ss_dssp EETTTTEEEEEESS-HHHHHHHHHHHHHH
T ss_pred EEEeeCCEEEecCCChHHHHHHHHHHHHH
Confidence 57899999999888999999888877654
No 132
>PRK05309 30S ribosomal protein S11; Validated
Probab=23.59 E-value=2e+02 Score=21.61 Aligned_cols=53 Identities=23% Similarity=0.347 Sum_probs=35.3
Q ss_pred CCCceEEEEEcCCeEEEEEecC-ccEEEEccc--CHHHHHHHHHHHHHHHHhcCCC
Q psy2814 33 GKFHGLIMKILNPRTTCLAFQS-GKLLILGAK--HEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 33 ~~fpgl~~R~~~p~~t~~If~s-GKivitGak--s~~~~~~a~~~i~~~L~~~g~~ 85 (176)
..|+-.++-+.++.-..+.|+| |.+-..|++ +...+..+++++.+.+.++|+.
T Consensus 24 ~t~NNTiitlTd~~G~~~~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~ 79 (128)
T PRK05309 24 ATFNNTIVTITDRQGNVISWASAGGLGFKGSRKSTPYAAQVAAEDAAKKAKEHGMK 79 (128)
T ss_pred ccCCCEEEEEEcCCCCEEEEEecCccEeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 3445555666666555555555 666666654 4556888889999999988874
No 133
>PRK09929 hypothetical protein; Provisional
Probab=23.51 E-value=85 Score=22.38 Aligned_cols=23 Identities=17% Similarity=0.143 Sum_probs=18.6
Q ss_pred cceEEEEecCCHHHHHHHHHHHH
Q psy2814 145 NGRIVITGAKSRSELHEAFDNIY 167 (176)
Q Consensus 145 sGkivitGaks~~~~~~a~~~i~ 167 (176)
-|-|.++|..+++|+++.+.+-.
T Consensus 40 iGtVSvs~~~s~~d~~~~La~KA 62 (91)
T PRK09929 40 IGTISTSNEMSTADAKEDLIKKA 62 (91)
T ss_pred eEEEEEcCCCCHHHHHHHHHHHH
Confidence 37888888889999999887643
No 134
>PF05362 Lon_C: Lon protease (S16) C-terminal proteolytic domain; InterPro: IPR008269 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 signature defines the C-terminal proteolytic domain of the archael, bacterial and eukaryotic Lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (Lon protease family, clan SF). In the eukaryotes the majority of the proteins are located in the mitochondrial matrix [, ]. In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response [].; GO: 0004176 ATP-dependent peptidase activity, 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1Z0E_E 1Z0G_E 1Z0T_F 1Z0C_A 1Z0V_A 1Z0B_A 1Z0W_A 2KJP_A 2X36_F 3K1J_B ....
Probab=22.88 E-value=1.6e+02 Score=23.85 Aligned_cols=36 Identities=28% Similarity=0.312 Sum_probs=21.1
Q ss_pred EecCccEEEEcccC---HHHHHHHHHHHHHHHHhcCCCc
Q psy2814 51 AFQSGKLLILGAKH---EHDCKLASRKFAKILKQLGHPI 86 (176)
Q Consensus 51 If~sGKivitGaks---~~~~~~a~~~i~~~L~~~g~~~ 86 (176)
+-.+|++..||.-+ .|.++.|..-+...++++|.+.
T Consensus 50 ~~G~G~l~~tG~lg~v~kES~~~A~~~~k~~~~~~~~~~ 88 (204)
T PF05362_consen 50 IPGKGKLIITGNLGDVMKESAKIAFSYLKANLKRIGIDP 88 (204)
T ss_dssp EESSSEEEEESSBHHHHHHHHHHHHHHHHHHHHCCSSTC
T ss_pred ccCcceeEeecccchhHHHHHHHHHHHHHhhhccccccc
Confidence 44899999999632 2333444444444455566554
No 135
>cd00448 YjgF_YER057c_UK114_family YjgF, YER057c, and UK114 belong to a large family of proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=22.58 E-value=99 Score=21.10 Aligned_cols=36 Identities=22% Similarity=0.338 Sum_probs=27.5
Q ss_pred EEecCccEEEE------cccCHHHHHHHHHHHHHHHHhcCCC
Q psy2814 50 LAFQSGKLLIL------GAKHEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 50 ~If~sGKivit------Gaks~~~~~~a~~~i~~~L~~~g~~ 85 (176)
.+|.||-+-.. ...-.++++.+++++.+.|+..|.+
T Consensus 10 ~~~~sGq~~~~~~~~~~~~~~~~Q~~~~~~ni~~~L~~~g~~ 51 (107)
T cd00448 10 LVFVSGQIPLDPDGELVPGDIEAQTRQALENLEAVLEAAGGS 51 (107)
T ss_pred EEEEeccCCcCCCCcccCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence 56777766553 2345788999999999999999986
No 136
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=22.51 E-value=1.5e+02 Score=23.38 Aligned_cols=28 Identities=25% Similarity=0.379 Sum_probs=24.1
Q ss_pred cccCHHHHHHHHHHHHHHHHhcCCCccc
Q psy2814 61 GAKHEHDCKLASRKFAKILKQLGHPIKY 88 (176)
Q Consensus 61 Gaks~~~~~~a~~~i~~~L~~~g~~~~~ 88 (176)
++++.++....++.+.+.|++.|+.+..
T Consensus 166 ~s~~~~e~~~~l~~v~~~l~~~gl~l~~ 193 (210)
T cd03715 166 AADSEEDCLKGTDALLTHLGELGYKVSP 193 (210)
T ss_pred ecCCHHHHHHHHHHHHHHHHHCCCCcCH
Confidence 4458999999999999999999987665
No 137
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=22.38 E-value=98 Score=24.44 Aligned_cols=26 Identities=23% Similarity=0.574 Sum_probs=18.5
Q ss_pred EEecCccEEEEcccCHHHHHHHHHHHH
Q psy2814 50 LAFQSGKLLILGAKHEHDCKLASRKFA 76 (176)
Q Consensus 50 ~If~sGKivitGaks~~~~~~a~~~i~ 76 (176)
.-+.|+.+++.|. +.++...|++++.
T Consensus 61 ~ahDshniiviG~-~~~dm~~A~n~l~ 86 (171)
T PF13382_consen 61 VAHDSHNIIVIGT-NDEDMALAANRLI 86 (171)
T ss_dssp --TTT--EEEEES-SHHHHHHHHHHHH
T ss_pred cccCCCCEEEEEC-CHHHHHHHHHHHH
Confidence 3455899999999 9999999977665
No 138
>PF05132 RNA_pol_Rpc4: RNA polymerase III RPC4; InterPro: IPR007811 This family comprises a specific subunit for Pol III, the tRNA specific polymerase.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006383 transcription from RNA polymerase III promoter, 0005666 DNA-directed RNA polymerase III complex
Probab=22.20 E-value=68 Score=23.87 Aligned_cols=17 Identities=12% Similarity=0.210 Sum_probs=13.4
Q ss_pred CCeEEEEEeccceEEEE
Q psy2814 135 KPRVVLLIFVNGRIVIT 151 (176)
Q Consensus 135 ~~~~t~~IF~sGkivit 151 (176)
+.--++.|++|||+.+-
T Consensus 67 G~iGkL~V~kSGkv~l~ 83 (131)
T PF05132_consen 67 GQIGKLRVHKSGKVTLK 83 (131)
T ss_pred CeeEEEEEEeCCcEEEE
Confidence 34567899999999874
No 139
>PRK11023 outer membrane lipoprotein; Provisional
Probab=22.06 E-value=4e+02 Score=21.03 Aligned_cols=104 Identities=15% Similarity=0.126 Sum_probs=56.4
Q ss_pred eEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcccceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCCCC
Q psy2814 46 RTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEPEL 125 (176)
Q Consensus 46 ~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YePe~ 125 (176)
+..+.+ .+|++.++|.=.-++.+..+.++++.++- ..--.-+++|.. .-+++...+=..+......-...++.
T Consensus 69 ~I~V~v-~~G~V~L~G~V~~~~~k~~A~~ia~~v~G--V~~V~N~l~V~~---~~~~~~~~~D~~It~kik~~L~~~~~- 141 (191)
T PRK11023 69 RINVTA-YQGKVLLTGQSPNAELSERAKQIAMGVEG--VNEVYNEIRQGQ---PIGLGTASKDTWITTKVRSQLLTSDS- 141 (191)
T ss_pred eEEEEE-ECCEEEEEEEeCCHHHHHHHHHHHhcCCC--ceeecceeeecc---ccccccccCcHHHHHHHHHHHhcCCC-
Confidence 344444 57999999998888888887777755442 211112233321 11222222212233221111223444
Q ss_pred CceeEEEEcCCeEEEEEeccceEEEEecCCHHHHHHHHH
Q psy2814 126 FPGLIYRMVKPRVVLLIFVNGRIVITGAKSRSELHEAFD 164 (176)
Q Consensus 126 fpgl~~r~~~~~~t~~IF~sGkivitGaks~~~~~~a~~ 164 (176)
+++. .+.+..+ +|.++++|.-+.++.+.|.+
T Consensus 142 v~~~-------~I~V~t~-~G~V~L~G~v~~~e~~~a~~ 172 (191)
T PRK11023 142 VKSS-------NVKVTTE-NGEVFLLGLVTQREAKAAAD 172 (191)
T ss_pred CCcc-------eEEEEEE-CcEEEEEEEeCHHHHHHHHH
Confidence 2332 4556665 89999999988877766654
No 140
>COG0678 AHP1 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=21.91 E-value=57 Score=25.70 Aligned_cols=32 Identities=9% Similarity=0.170 Sum_probs=25.7
Q ss_pred CCCCCceeEEEEc---------CCeEEEEEeccceEEEEec
Q psy2814 122 EPELFPGLIYRMV---------KPRVVLLIFVNGRIVITGA 153 (176)
Q Consensus 122 ePe~fpgl~~r~~---------~~~~t~~IF~sGkivitGa 153 (176)
..+.+|.+.||.+ .+..+-.+|...||++.|.
T Consensus 5 vg~klP~vtf~tr~~~~~~~~~~~~ts~~lf~gKkVvlf~l 45 (165)
T COG0678 5 VGKKLPAVTFKTRVGDETADGWVDVTTDDLFKGKKVVLFSL 45 (165)
T ss_pred cCCcCCceEeEEeeccccCCCcccccHHHhcCCCEEEEEeC
Confidence 3467899998876 4567788999999999985
No 141
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=21.84 E-value=1.5e+02 Score=22.31 Aligned_cols=36 Identities=14% Similarity=0.235 Sum_probs=21.1
Q ss_pred EEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcc
Q psy2814 50 LAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIK 87 (176)
Q Consensus 50 ~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~ 87 (176)
+...||+++.+...+.+++...+++.+. +.+|+++.
T Consensus 38 Tyi~SGNvvf~~~~~~~~l~~~ie~~l~--~~fG~~v~ 73 (137)
T PF08002_consen 38 TYIQSGNVVFESDRDPAELAAKIEKALE--ERFGFDVP 73 (137)
T ss_dssp EETTTTEEEEEESS-HHHHHHHHHHHHH--HH-TT---
T ss_pred EEEeeCCEEEecCCChHHHHHHHHHHHH--HhcCCCeE
Confidence 5789999999966666666665444332 45676543
No 142
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=21.63 E-value=1.3e+02 Score=23.86 Aligned_cols=38 Identities=13% Similarity=0.162 Sum_probs=28.5
Q ss_pred EEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCccc
Q psy2814 49 CLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKY 88 (176)
Q Consensus 49 ~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~ 88 (176)
+..|-..= + .++++.++..++++.+...|++.|+.+..
T Consensus 160 ~~~Y~DDi-l-i~s~~~~~~~~~l~~v~~~l~~~gl~ln~ 197 (213)
T cd01645 160 IYHYMDDI-L-IASDLEGQLREIYEELRQTLLRWGLTIPP 197 (213)
T ss_pred EEEEcCCE-E-EEcCCHHHHHHHHHHHHHHHHHCCCEeCH
Confidence 34444433 2 34668999999999999999999987765
No 143
>TIGR01651 CobT cobaltochelatase, CobT subunit. This model describes the aerobic cobalamin pathway Pseudomonas denitrificans CobT gene product, which is a cobalt chelatase subunit, with a MW ~70 kDa. The aerobic pathway cobalt chelatase is a heterotrimeric, ATP-dependent enzyme that catalyzes cobalt insertion during cobalamin biosynthesis. The other two subunits are the P. denitrificans CobS (TIGR01650) and CobN (pfam02514 CobN/Magnesium Chelatase) proteins. To avoid potential confusion with the nonhomologous Salmonella typhimurium/E.coli cobT gene product, the P. denitrificans gene symbol is not used in the name of this model.
Probab=21.39 E-value=1.5e+02 Score=28.27 Aligned_cols=46 Identities=20% Similarity=0.244 Sum_probs=37.2
Q ss_pred eEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcccceeeee
Q psy2814 46 RTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGFKIH 94 (176)
Q Consensus 46 ~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~ 94 (176)
.++++|=.||.|. .+.++-+..++.-+.+-|..+|+++....|+-.
T Consensus 394 ~V~LLID~SGSM~---~r~~~vA~~~a~iLa~aL~~~gIp~eVlGFtt~ 439 (600)
T TIGR01651 394 VVTLLIDNSGSMR---GRPITVAATCADILARTLERCGVKVEILGFTTR 439 (600)
T ss_pred EEEEEEECCccCC---CCHHHHHHHHHHHHHHHHHHCCCCeEEEeeccc
Confidence 5788999999995 445666777889999999999999887666654
No 144
>PRK15415 propanediol utilization protein PduB; Provisional
Probab=21.34 E-value=1.6e+02 Score=25.16 Aligned_cols=29 Identities=24% Similarity=0.386 Sum_probs=23.6
Q ss_pred cceEEEEecCCHHHHHHHHHHHHHHHHhh
Q psy2814 145 NGRIVITGAKSRSELHEAFDNIYPVLKSF 173 (176)
Q Consensus 145 sGkivitGaks~~~~~~a~~~i~~~L~~~ 173 (176)
.|+++++|+-+.++++.|++.-...+.++
T Consensus 119 ~G~~ii~g~gDVs~Vr~AVeaa~~~~~~~ 147 (266)
T PRK15415 119 HGSLIIFGAEDVSDVRRAVEVALKELDRT 147 (266)
T ss_pred ceEEEEEeCCCHHHHHHHHHHHHHHHHhh
Confidence 39999999999999999987766655543
No 145
>cd06150 YjgF_YER057c_UK114_like_2 This group of proteins belong to a large family of YjgF/YER057c/UK114-like proteins present in bacteria, archaea, and eukaryotes with no definitive function. The conserved domain is similar in structure to chorismate mutase but there is no sequence similarity and no functional connection. Members of this family have been implicated in isoleucine (Yeo7, Ibm1, aldR) and purine (YjgF) biosynthesis, as well as threonine anaerobic degradation (tdcF) and mitochondrial DNA maintenance (Ibm1). This domain homotrimerizes forming a distinct intersubunit cavity that may serve as a small molecule binding site.
Probab=21.32 E-value=1e+02 Score=21.60 Aligned_cols=38 Identities=13% Similarity=0.150 Sum_probs=27.7
Q ss_pred EEecCccEEEE-cccCHHHHHHHHHHHHHHHHhcCCCcc
Q psy2814 50 LAFQSGKLLIL-GAKHEHDCKLASRKFAKILKQLGHPIK 87 (176)
Q Consensus 50 ~If~sGKivit-Gaks~~~~~~a~~~i~~~L~~~g~~~~ 87 (176)
.+|-||-+-.- +..-.++++.+++++..+|+..|....
T Consensus 12 ~v~iSGq~~~~~~~~~~~Q~~~~~~nl~~~L~~~G~~~~ 50 (105)
T cd06150 12 TVYLAGQVADDTSADITGQTRQVLAKIDALLAEAGSDKS 50 (105)
T ss_pred EEEEeCcCCcCCCCCHHHHHHHHHHHHHHHHHHcCCCHH
Confidence 46666654332 123578999999999999999997654
No 146
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=21.25 E-value=1.1e+02 Score=24.08 Aligned_cols=25 Identities=12% Similarity=0.275 Sum_probs=20.2
Q ss_pred eccceEEEEecCCHHHHHHHHHHHHH
Q psy2814 143 FVNGRIVITGAKSRSELHEAFDNIYP 168 (176)
Q Consensus 143 F~sGkivitGaks~~~~~~a~~~i~~ 168 (176)
+.|+.+++.|. +.+++..|++++.+
T Consensus 63 hDshniiviG~-~~~dm~~A~n~l~~ 87 (171)
T PF13382_consen 63 HDSHNIIVIGT-NDEDMALAANRLIE 87 (171)
T ss_dssp TTT--EEEEES-SHHHHHHHHHHHHH
T ss_pred cCCCCEEEEEC-CHHHHHHHHHHHHH
Confidence 44899999999 89999999999875
No 147
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=21.02 E-value=1.5e+02 Score=22.59 Aligned_cols=31 Identities=13% Similarity=0.184 Sum_probs=26.3
Q ss_pred EEEEecCccEEEEcccCHHHHHHHHHHHHHHH
Q psy2814 48 TCLAFQSGKLLILGAKHEHDCKLASRKFAKIL 79 (176)
Q Consensus 48 t~~If~sGKivitGaks~~~~~~a~~~i~~~L 79 (176)
...+ .+|+.++.|.-+..+++..++++++..
T Consensus 72 ~g~i-~~~~lii~G~~~~~~i~~~L~~yI~~y 102 (138)
T PRK03988 72 AGNI-EGGRLILQGKFSPRVINEKIDRYVKEY 102 (138)
T ss_pred ceee-cCCEEEEEEeeCHHHHHHHHHHHHHhc
Confidence 3445 899999999999999999988888663
No 148
>cd02994 PDI_a_TMX PDIa family, TMX subfamily; composed of proteins similar to the TRX-related human transmembrane protein, TMX. TMX is a type I integral membrane protein; the N-terminal redox active TRX domain is present in the endoplasmic reticulum (ER) lumen while the C-terminus is oriented towards the cytoplasm. It is expressed in many cell types and its active site motif (CPAC) is unique. In vitro, TMX reduces interchain disulfides of insulin and renatures inactive RNase containing incorrect disulfide bonds. The C. elegans homolog, DPY-11, is expressed only in the hypodermis and resides in the cytoplasm. It is required for body and sensory organ morphogeneis. Another uncharacterized TRX-related transmembrane protein, human TMX4, is included in the alignment. The active site sequence of TMX4 is CPSC.
Probab=20.99 E-value=1.3e+02 Score=20.25 Aligned_cols=24 Identities=13% Similarity=0.252 Sum_probs=14.9
Q ss_pred EEeccceE-EEEecCCHHHHHHHHH
Q psy2814 141 LIFVNGRI-VITGAKSRSELHEAFD 164 (176)
Q Consensus 141 ~IF~sGki-vitGaks~~~~~~a~~ 164 (176)
.+|..|++ ...|.++.+++...++
T Consensus 76 ~~~~~g~~~~~~G~~~~~~l~~~i~ 100 (101)
T cd02994 76 YHAKDGVFRRYQGPRDKEDLISFIE 100 (101)
T ss_pred EEeCCCCEEEecCCCCHHHHHHHHh
Confidence 34566654 3568888877766543
No 149
>COG1163 DRG Predicted GTPase [General function prediction only]
Probab=20.95 E-value=2.2e+02 Score=25.32 Aligned_cols=76 Identities=26% Similarity=0.288 Sum_probs=50.0
Q ss_pred eEEEEEcCCeEEEEEecCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCcccceeeeeeEEEEeeeCcccCHHHHHHHcC
Q psy2814 37 GLIMKILNPRTTCLAFQSGKLLILGAKHEHDCKLASRKFAKILKQLGHPIKYQGFKIHNIVCTCDVRFPVKLDALHHVHS 116 (176)
Q Consensus 37 gl~~R~~~p~~t~~If~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~nIvas~~l~~~i~L~~l~~~~~ 116 (176)
|..+.-+.|.+++.-..+|=|.++|+....++... .+..+|++.| |+|-.. -....+.++.+.....
T Consensus 168 GIrlnk~~p~V~I~kk~~gGI~i~~t~~l~~~d~~--~ir~iL~Ey~---------I~nA~V--~Ir~dvTlDd~id~l~ 234 (365)
T COG1163 168 GIRLNKRPPDVTIKKKESGGIRINGTGPLTHLDED--TVRAILREYR---------IHNADV--LIREDVTLDDLIDALE 234 (365)
T ss_pred CeEecCCCCceEEEEeccCCEEEecccccccCCHH--HHHHHHHHhC---------cccceE--EEecCCcHHHHHHHHh
Confidence 55566667888988999999999998766544433 4555666654 444322 3345577787776555
Q ss_pred CCcccCCCC
Q psy2814 117 QFSSYEPEL 125 (176)
Q Consensus 117 ~~~~YePe~ 125 (176)
.|-.|-|.+
T Consensus 235 ~nrvY~p~l 243 (365)
T COG1163 235 GNRVYKPAL 243 (365)
T ss_pred hcceeeeeE
Confidence 666777664
No 150
>KOG2360|consensus
Probab=20.93 E-value=1.1e+02 Score=27.53 Aligned_cols=85 Identities=14% Similarity=0.191 Sum_probs=60.5
Q ss_pred CCCcEEccCCCceEEEEEcCCeEEEEEecCccEEEEcccCHHHHH-HHHHHHHHHHHhcCCCcccceeeeeeEEEEeeeC
Q psy2814 25 VRYSEYNPGKFHGLIMKILNPRTTCLAFQSGKLLILGAKHEHDCK-LASRKFAKILKQLGHPIKYQGFKIHNIVCTCDVR 103 (176)
Q Consensus 25 ~~n~~Y~P~~fpgl~~R~~~p~~t~~If~sGKivitGaks~~~~~-~a~~~i~~~L~~~g~~~~~~~~~i~nIvas~~l~ 103 (176)
+.++ -.|+.|+.+.+=+-+|.|+-+.--++.-.++|+..+++-+ ++++.+.-+..++-.. |++.+ .-+.++|+++
T Consensus 273 f~~t-~~~~~~~~v~~iL~DpscSgSgm~~r~~~~~~~e~~~~~rL~~L~~fq~~~~~hal~--fp~~k-~vvystcs~~ 348 (413)
T KOG2360|consen 273 FLNT-ATPEKFRDVTYILVDPSCSGSGMVSRQDEDPGAETESPERLENLQSFQIRILKHALT--FPNLK-RLVYSTCSLH 348 (413)
T ss_pred ccCC-CCcccccceeEEEeCCCCCCCccccceeeccCCCcccHHHHHHHHHHHHHHHHHHhc--CCchh-heeeecchhh
Confidence 3455 6688899999999999999999999999999988777766 4455555555554211 22211 2345899999
Q ss_pred cccCHHHHHH
Q psy2814 104 FPVKLDALHH 113 (176)
Q Consensus 104 ~~i~L~~l~~ 113 (176)
...|=+..+.
T Consensus 349 reene~vv~d 358 (413)
T KOG2360|consen 349 REENEQVVQE 358 (413)
T ss_pred hhhhhHHHHH
Confidence 8888665554
No 151
>PF03481 SUA5: Putative GTP-binding controlling metal-binding; InterPro: IPR005145 The function of this domain is unknown, it is found in P32579 from SWISSPROT and its relatives. It is found C-terminal to the IPR006070 from INTERPRO.; PDB: 2EQA_A 3AJE_A 4E1B_A 2YV4_A.
Probab=20.84 E-value=2.9e+02 Score=20.09 Aligned_cols=49 Identities=20% Similarity=0.413 Sum_probs=24.8
Q ss_pred CceeEEEEcCCeEEEEEecc-------ceEEEEecC-------------CHHHHHHHHHHHHHHHHhhh
Q psy2814 126 FPGLIYRMVKPRVVLLIFVN-------GRIVITGAK-------------SRSELHEAFDNIYPVLKSFK 174 (176)
Q Consensus 126 fpgl~~r~~~~~~t~~IF~s-------GkivitGak-------------s~~~~~~a~~~i~~~L~~~r 174 (176)
-||..||=.-|++.+.++.+ +++.+.+.. ..++.+++.+.++..|+++-
T Consensus 27 sPG~~~~HYaP~~~~~l~~~~~~~~~~~~v~~l~~~~~~~~~~~~~~l~~~~d~~~~A~~Lf~~LR~~D 95 (125)
T PF03481_consen 27 SPGMKYRHYAPRAPVYLVEAIEELIKGKKVGVLAFEETKSSFDIVYSLSLPGDPEEAARNLFAALRELD 95 (125)
T ss_dssp ---------S-SSEEEEEEHHHHHHHTS-EEEEECCGCTGCGSEEEEEESTTSHHHHHHHHHHHHHHHH
T ss_pred CCCccccccCCCCcEEEEeehhhhccCCcEEEEEeCCcccccceEEEecCCCCHHHHHHHHHHHHHHHh
Confidence 68888887777777777753 233232222 34688889999999988764
No 152
>PF11525 CopK: Copper resistance protein K; InterPro: IPR021604 CopK is a periplasmic dimeric protein which is strongly up-regulated in the presence of copper, leading to a high periplasmic accumulation []. CopK has two different binding sites for Cu(I), each with a different affinity for the metal. Binding of the first Cu(I) ion induces a conformational change of CopK which involves dissociation of the dimeric apo-protein. Binding of a second Cu(I) further increases the plasticity of the protein. CopK has features that are common with functionally related proteins such as a structure consisting of an all-beta fold and a methionine-rich Cu(I) binding site []. ; PDB: 3N7E_B 3N7D_B 3DSP_A 3DSO_A 2K0Q_A 2KM0_A 2LEL_A.
Probab=20.82 E-value=80 Score=21.53 Aligned_cols=20 Identities=20% Similarity=0.453 Sum_probs=13.8
Q ss_pred EEEcCCeEEEEEecCccEEEE
Q psy2814 40 MKILNPRTTCLAFQSGKLLIL 60 (176)
Q Consensus 40 ~R~~~p~~t~~If~sGKivit 60 (176)
+.+.+ -.|+.||..||+-.-
T Consensus 10 i~LkD-GstvyiFKDGKMamE 29 (73)
T PF11525_consen 10 IPLKD-GSTVYIFKDGKMAME 29 (73)
T ss_dssp EEBTT-SEEEEEETTS-EEEE
T ss_pred EecCC-CCEEEEEcCCceehh
Confidence 33444 579999999999764
No 153
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=20.66 E-value=2e+02 Score=21.40 Aligned_cols=28 Identities=18% Similarity=0.284 Sum_probs=23.8
Q ss_pred EEEEcccCHHHHHHHHHHHHHHHHhcCCC
Q psy2814 57 LLILGAKHEHDCKLASRKFAKILKQLGHP 85 (176)
Q Consensus 57 ivitGaks~~~~~~a~~~i~~~L~~~g~~ 85 (176)
|++||. |..+.+.-++.+...+++.|+.
T Consensus 38 VIatg~-s~rhv~Aiad~i~~~~k~~g~~ 65 (115)
T COG0799 38 VIATGN-SSRHVKAIADNVKEELKEAGEV 65 (115)
T ss_pred EEEEeC-chHHHHHHHHHHHHHHHHcCCC
Confidence 677777 8899999999999999988864
No 154
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=20.62 E-value=1.5e+02 Score=20.25 Aligned_cols=25 Identities=32% Similarity=0.530 Sum_probs=15.4
Q ss_pred EEEEec-cceEE--EEecCCHHHHHHHH
Q psy2814 139 VLLIFV-NGRIV--ITGAKSRSELHEAF 163 (176)
Q Consensus 139 t~~IF~-sGkiv--itGaks~~~~~~a~ 163 (176)
|+.++. .|+++ ++|..+.+++.+.+
T Consensus 85 t~~~~d~~G~~v~~~~G~~~~~~l~~~L 112 (112)
T PF13098_consen 85 TIVFLDKDGKIVYRIPGYLSPEELLKML 112 (112)
T ss_dssp EEEECTTTSCEEEEEESS--HHHHHHHH
T ss_pred EEEEEcCCCCEEEEecCCCCHHHHHhhC
Confidence 444553 68844 79999999887653
No 155
>smart00878 Biotin_carb_C Biotin carboxylase C-terminal domain. Biotin carboxylase is a component of the acetyl-CoA carboxylase multi-component enzyme which catalyses the first committed step in fatty acid synthesis in animals, plants and bacteria. Most of the active site residues reported in reference are in this C-terminal domain.
Probab=20.50 E-value=1.1e+02 Score=22.15 Aligned_cols=25 Identities=20% Similarity=0.531 Sum_probs=19.2
Q ss_pred ceEEEEecCCHHHHHHHHHHHHHHHHhhh
Q psy2814 146 GRIVITGAKSRSELHEAFDNIYPVLKSFK 174 (176)
Q Consensus 146 GkivitGaks~~~~~~a~~~i~~~L~~~r 174 (176)
+|+++.|. + -++|++++...|.+++
T Consensus 52 AKliv~g~-~---R~~A~~rl~~aL~e~~ 76 (107)
T smart00878 52 AKLIVHGE-T---REEAIARLRRALDEFR 76 (107)
T ss_pred eEEEEEcC-C---HHHHHHHHHHHHHhCE
Confidence 78999987 3 4557888888888765
No 156
>TIGR01200 Porphyromonas gingivalis paralogous family TIGR01200. No identifiable homologs outside Porphyromonas gingivalis.
Probab=20.41 E-value=3.2e+02 Score=23.62 Aligned_cols=53 Identities=32% Similarity=0.335 Sum_probs=31.1
Q ss_pred cccCCCCC---ceeEEEEcCCeEEEEEeccceEEEEec-------------CCHHHHHHHHHHHHHHHH
Q psy2814 119 SSYEPELF---PGLIYRMVKPRVVLLIFVNGRIVITGA-------------KSRSELHEAFDNIYPVLK 171 (176)
Q Consensus 119 ~~YePe~f---pgl~~r~~~~~~t~~IF~sGkivitGa-------------ks~~~~~~a~~~i~~~L~ 171 (176)
..+-|..| |||+..+.+.+-....-.+|---+.+. .+.++.+.+++++.+...
T Consensus 192 v~~GP~kf~GLPGLILei~d~~~~y~f~~~gi~~~~~~~PI~~~~~~ye~~~~ree~rk~~r~~~e~~~ 260 (292)
T TIGR01200 192 LSDGPYIFRGLPGLIVAIRSDDGEYVFELNGMQEITFPSPIYLVNTPYEKLYSREESRKEIRNIYENYY 260 (292)
T ss_pred CCCCCcccCCCCeEEEEEEecCceEEEEEeeeEeccCCCceEEcCCCccccccHHHHHHHHHHHHHHHH
Confidence 56667666 899988876543333333333222222 355677777777776544
No 157
>PF05406 WGR: WGR domain; InterPro: IPR008893 This domain is named after the most conserved central motif of the domain. It is found in a variety of polyA polymerases as well as the Escherichia coli molybdate metabolism regulator P33345 from SWISSPROT and other proteins of unknown function.The domain is found in isolation in proteins such as Q9JN21 from SWISSPROT and is between 70 and 80 residues in length. ; PDB: 2EOC_A 2RA8_A 4DQY_C 2CR9_A.
Probab=20.28 E-value=2.6e+02 Score=18.67 Aligned_cols=34 Identities=18% Similarity=0.035 Sum_probs=27.1
Q ss_pred cCccEEEEcccCHHHHHHHHHHHHHHHHhcCCCc
Q psy2814 53 QSGKLLILGAKHEHDCKLASRKFAKILKQLGHPI 86 (176)
Q Consensus 53 ~sGKivitGaks~~~~~~a~~~i~~~L~~~g~~~ 86 (176)
+.|...+....|+++|..+++++...-.+.|+..
T Consensus 43 ~~gq~~~~~f~s~~eA~~~f~~~~~~K~~~gy~~ 76 (81)
T PF05406_consen 43 SKGQTRIKPFDSEEEAIKEFEKLFKEKTGKGYEE 76 (81)
T ss_dssp SSEEEEEEEESSHHHHHHHHHHHHHHHHSSTSCC
T ss_pred CcCcEEEEeCCCHHHHHHHHHHHHHHHHcCCCcc
Confidence 4577788888899999999888887776777754
No 158
>PRK11127 autonomous glycyl radical cofactor GrcA; Provisional
Probab=20.18 E-value=19 Score=27.14 Aligned_cols=20 Identities=25% Similarity=0.300 Sum_probs=16.0
Q ss_pred CcccCCCCCceeEEEEcCCe
Q psy2814 118 FSSYEPELFPGLIYRMVKPR 137 (176)
Q Consensus 118 ~~~YePe~fpgl~~r~~~~~ 137 (176)
.+.=+||.||.|+.|..+=.
T Consensus 85 dAqk~PEkYpdLiVRVsGYS 104 (127)
T PRK11127 85 DAVKHPEKYPQLTIRVSGYA 104 (127)
T ss_pred HHHhChhcCCCeEEEEeeEE
Confidence 35568999999999987743
No 159
>COG1364 ArgJ N-acetylglutamate synthase (N-acetylornithine aminotransferase) [Amino acid transport and metabolism]
Probab=20.12 E-value=96 Score=27.97 Aligned_cols=22 Identities=27% Similarity=0.522 Sum_probs=19.6
Q ss_pred cEEEEcccCHHHHHHHHHHHHH
Q psy2814 56 KLLILGAKHEHDCKLASRKFAK 77 (176)
Q Consensus 56 KivitGaks~~~~~~a~~~i~~ 77 (176)
.+.++||+|.++++.+++.++.
T Consensus 284 eV~V~GA~~~~~A~~iA~~Ia~ 305 (404)
T COG1364 284 EVTVTGAASEEDARVIARAIAN 305 (404)
T ss_pred EEEEeCCCCHHHHHHHHHHHhc
Confidence 3789999999999999998874
No 160
>PF03332 PMM: Eukaryotic phosphomannomutase; InterPro: IPR005002 This enzyme (5.4.2.8 from EC) is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions.; GO: 0004615 phosphomannomutase activity, 0019307 mannose biosynthetic process, 0005737 cytoplasm; PDB: 2I55_B 2I54_C 3F9R_A 2FUE_A 2FUC_A 2AMY_A 2Q4R_A.
Probab=20.12 E-value=1.2e+02 Score=25.11 Aligned_cols=90 Identities=19% Similarity=0.332 Sum_probs=47.2
Q ss_pred EecCccEEE----EcccCHHHHHHHHHHHHHHHHhcCCCccc---ceeeeeeEEEEeeeCcccCHHHHHHHcCCCcccCC
Q psy2814 51 AFQSGKLLI----LGAKHEHDCKLASRKFAKILKQLGHPIKY---QGFKIHNIVCTCDVRFPVKLDALHHVHSQFSSYEP 123 (176)
Q Consensus 51 If~sGKivi----tGaks~~~~~~a~~~i~~~L~~~g~~~~~---~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~~YeP 123 (176)
.|+.|+... .-.-+++..++.++-+.+.+.+++++++- -+++=-.|+-| -+|..=.+++=. ...+|||
T Consensus 49 ~y~~~~~~~~~~~~~~lgee~~~~~in~~l~~~~~l~lp~krGtfIE~R~gmIn~S-piGr~a~~eer~----~f~~~D~ 123 (220)
T PF03332_consen 49 AYKNGELIWSQSIAEFLGEEKLQKLINFCLRYISDLDLPVKRGTFIEFRGGMINFS-PIGRNASQEERD----EFDEYDK 123 (220)
T ss_dssp EEETTEEEEE--HHHHHHHHHHHHHHHHHHHHHHT---S---S-SEEEESSEEEE--SS-TTS-HHHHH----HHHHHHH
T ss_pred EEECCCchhhHhHHHHcCHHHHHHHHHHHHHHHHhCCCCccCCCceeecCCcEEEC-cccCcCCHHHHH----hhhhcCh
Confidence 445554433 34456788899999999999999987663 33333333333 234433333211 1122333
Q ss_pred -------------CCCc--eeEEEEcCCeEEEEEeccc
Q psy2814 124 -------------ELFP--GLIYRMVKPRVVLLIFVNG 146 (176)
Q Consensus 124 -------------e~fp--gl~~r~~~~~~t~~IF~sG 146 (176)
+.|| +|.|++-+. +++-||+.|
T Consensus 124 ~~~iR~~~v~~L~~~f~d~~L~~siGGq-iSiDvfp~G 160 (220)
T PF03332_consen 124 KHKIREKLVEALKKEFPDFGLTFSIGGQ-ISIDVFPKG 160 (220)
T ss_dssp HHTHHHHHHHHHHHHTCCCSEEEEEETT-TEEEEEETT
T ss_pred hhhHHHHHHHHHHHHCCCCceEEecCCc-eEEccccCC
Confidence 4577 488998765 677777766
No 161
>PF11504 Colicin_Ia: Colicin Ia; InterPro: IPR014740 Colicins are plasmid-encoded polypeptide toxins produced by and active against Escherichia coli and closely related bacteria. Colicins are released into the environment to reduce competition from other bacterial strains. Colicins bind to outer membrane receptors, using them to translocate to the cytoplasm or cytoplasmic membrane, where they exert their cytotoxic effect, including depolarisation of the cytoplasmic membrane, DNase activity, RNase activity, or inhibition of murein synthesis. Channel-forming colicins (colicins A, B, E1, Ia, Ib, and N) are transmembrane proteins that depolarize the cytoplasmic membrane, leading to dissipation of cellular energy []. These colicins contain at least three domains: an N-terminal translocation domain responsible for movement across the outer membrane and periplasmic space; a central domain responsible for receptor recognition; and a C-terminal cytotoxic domain responsible for channel formation in the cytoplasmic membrane []. This entry represents the central receptor recognition domain, which has an alpha/beta two-layer sandwich structure.; GO: 0019835 cytolysis, 0050829 defense response to Gram-negative bacterium, 0016021 integral to membrane; PDB: 2HDI_B 1CII_A.
Probab=20.07 E-value=69 Score=21.10 Aligned_cols=9 Identities=44% Similarity=0.744 Sum_probs=5.5
Q ss_pred EccCCCceE
Q psy2814 30 YNPGKFHGL 38 (176)
Q Consensus 30 Y~P~~fpgl 38 (176)
-.||+|||-
T Consensus 10 vspekfpgr 18 (72)
T PF11504_consen 10 VSPEKFPGR 18 (72)
T ss_dssp H-TTTS-EE
T ss_pred eCcccCCCC
Confidence 368999994
No 162
>KOG4180|consensus
Probab=20.07 E-value=1.6e+02 Score=26.14 Aligned_cols=73 Identities=15% Similarity=0.232 Sum_probs=47.5
Q ss_pred EEEEecCccEEEEcccCH-------HHHHHHHHHHHHHHHhcCCC-cccceeeeeeEEEEeeeCcccCHHHHHHHcCCCc
Q psy2814 48 TCLAFQSGKLLILGAKHE-------HDCKLASRKFAKILKQLGHP-IKYQGFKIHNIVCTCDVRFPVKLDALHHVHSQFS 119 (176)
Q Consensus 48 t~~If~sGKivitGaks~-------~~~~~a~~~i~~~L~~~g~~-~~~~~~~i~nIvas~~l~~~i~L~~l~~~~~~~~ 119 (176)
.+.-=+||=++|||+-|. .-+.+++..++.++...|-. +-+. .=..++++..+.+..
T Consensus 254 ~~KqKssgl~vctgTGstsw~~~iNria~q~v~d~l~~l~~~~~~~vp~~---------------Re~ve~i~~~~nq~l 318 (395)
T KOG4180|consen 254 GVKQKSSGLVVCTGTGSTSWTFNINRIAEQAVGDLLMILLSRDNLQVPFM---------------RELVEEISTAYNQHL 318 (395)
T ss_pred cccccCCCeeEecCCCcceEeecccHHHHHHHHHHHHHHHhcCcccchhh---------------hhhhHHHHHHhhhcC
Confidence 335678999999998664 35677888888888877543 1110 111245555666888
Q ss_pred ccCCCCCceeEEEEcCC
Q psy2814 120 SYEPELFPGLIYRMVKP 136 (176)
Q Consensus 120 ~YePe~fpgl~~r~~~~ 136 (176)
.|+|+ .|-+-|-+++|
T Consensus 319 lF~PD-~p~l~fSiRep 334 (395)
T KOG4180|consen 319 LFKPD-RPQLAFSIREP 334 (395)
T ss_pred ccCCC-Ccchhhhhhhh
Confidence 99998 46666655554
Done!