Query 047239
Match_columns 180
No_of_seqs 148 out of 548
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 09:06:21 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/047239.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/047239hhsearch_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 1.9E-70 4.2E-75 439.7 23.7 179 2-180 1-179 (179)
2 cd04516 TBP_eukaryotes eukaryo 100.0 1.1E-69 2.5E-74 433.8 23.2 174 2-175 1-174 (174)
3 KOG3302 TATA-box binding prote 100.0 4.7E-68 1E-72 424.0 21.0 180 1-180 21-200 (200)
4 COG2101 SPT15 TATA-box binding 100.0 2.3E-67 5E-72 414.1 20.3 176 1-176 6-183 (185)
5 cd00652 TBP_TLF TATA box bindi 100.0 3E-66 6.6E-71 414.2 22.9 173 2-174 1-174 (174)
6 PRK00394 transcription factor; 100.0 5.4E-66 1.2E-70 414.3 23.3 175 3-177 1-177 (179)
7 cd04518 TBP_archaea archaeal T 100.0 1E-65 2.3E-70 410.9 23.3 173 2-175 1-174 (174)
8 cd04517 TLF TBP-like factors ( 100.0 3E-65 6.4E-70 408.4 23.1 172 2-174 2-174 (174)
9 PF00352 TBP: Transcription fa 100.0 1E-31 2.2E-36 192.0 11.6 84 2-85 3-86 (86)
10 PF00352 TBP: Transcription fa 100.0 7.2E-32 1.6E-36 192.8 10.0 86 90-176 1-86 (86)
11 COG2101 SPT15 TATA-box binding 100.0 1.5E-30 3.2E-35 205.5 10.6 85 2-86 98-184 (185)
12 PRK00394 transcription factor; 100.0 1.9E-29 4.1E-34 202.6 12.0 85 2-86 91-177 (179)
13 cd04518 TBP_archaea archaeal T 100.0 5.1E-29 1.1E-33 199.3 11.4 83 2-84 92-174 (174)
14 cd00652 TBP_TLF TATA box bindi 99.9 3.7E-27 8.1E-32 188.6 11.1 81 2-82 92-173 (174)
15 cd04516 TBP_eukaryotes eukaryo 99.9 4.2E-27 9.1E-32 188.3 10.6 83 93-176 2-84 (174)
16 PLN00062 TATA-box-binding prot 99.9 1E-26 2.2E-31 186.8 11.1 84 2-85 91-175 (179)
17 cd04517 TLF TBP-like factors ( 99.9 1E-25 2.2E-30 180.3 11.2 81 2-82 92-173 (174)
18 KOG3302 TATA-box binding prote 99.9 1.7E-21 3.6E-26 156.4 9.9 85 1-85 111-196 (200)
19 PF11858 DUF3378: Domain of un 97.1 0.00061 1.3E-08 48.2 3.9 36 35-70 26-61 (81)
20 PF11858 DUF3378: Domain of un 96.8 0.0016 3.5E-08 46.1 3.4 36 126-161 26-61 (81)
21 COG4871 Uncharacterized protei 96.6 0.016 3.4E-07 46.2 8.4 62 19-83 47-108 (193)
22 TIGR00716 rnhC ribonuclease HI 95.1 0.047 1E-06 47.0 5.5 36 33-68 22-57 (284)
23 COG1039 RnhC Ribonuclease HIII 94.5 0.1 2.2E-06 45.2 5.9 41 126-166 27-67 (297)
24 COG1039 RnhC Ribonuclease HIII 94.4 0.11 2.3E-06 45.0 5.9 43 36-78 28-70 (297)
25 PRK00996 ribonuclease HIII; Pr 94.4 0.081 1.8E-06 46.0 5.3 35 34-68 26-60 (304)
26 COG4871 Uncharacterized protei 93.8 0.51 1.1E-05 37.8 8.2 73 98-174 36-108 (193)
27 PRK00996 ribonuclease HIII; Pr 93.7 0.13 2.7E-06 44.8 5.2 35 124-158 25-59 (304)
28 TIGR00716 rnhC ribonuclease HI 93.1 0.17 3.8E-06 43.6 5.1 34 124-157 22-55 (284)
29 PRK12475 thiamine/molybdopteri 89.5 1.7 3.7E-05 38.2 7.6 60 16-78 277-337 (338)
30 PRK07688 thiamine/molybdopteri 86.2 2.4 5.1E-05 37.3 6.4 59 16-77 277-337 (339)
31 TIGR02187 GlrX_arch Glutaredox 81.3 14 0.00031 29.9 8.7 115 49-166 79-213 (215)
32 PRK12475 thiamine/molybdopteri 78.4 5.2 0.00011 35.2 5.6 30 139-168 307-336 (338)
33 PRK15468 carboxysome structura 70.8 8.2 0.00018 28.8 4.1 33 54-88 72-105 (111)
34 PLN00410 U5 snRNP protein, DIM 70.3 12 0.00026 29.0 5.2 62 20-81 45-123 (142)
35 cd03065 PDI_b_Calsequestrin_N 66.3 12 0.00025 28.1 4.3 30 140-169 89-119 (120)
36 cd03065 PDI_b_Calsequestrin_N 63.4 12 0.00026 28.0 3.9 30 49-78 89-119 (120)
37 PRK07688 thiamine/molybdopteri 58.4 32 0.00069 30.2 6.2 35 134-168 303-337 (339)
38 KOG4749 Inositol polyphosphate 56.8 3.9 8.4E-05 36.2 0.2 56 118-173 173-242 (375)
39 PRK11509 hydrogenase-1 operon 54.4 26 0.00056 26.9 4.4 30 140-169 93-124 (132)
40 PF13575 DUF4135: Domain of un 53.6 14 0.0003 32.6 3.1 55 60-115 123-177 (370)
41 PRK09381 trxA thioredoxin; Pro 53.1 20 0.00043 25.2 3.4 28 50-77 78-107 (109)
42 PRK10996 thioredoxin 2; Provis 51.4 23 0.00049 26.7 3.7 28 141-168 109-138 (139)
43 PHA02278 thioredoxin-like prot 51.4 22 0.00047 25.6 3.4 24 140-163 74-99 (103)
44 PRK11509 hydrogenase-1 operon 49.4 34 0.00074 26.2 4.4 60 18-78 56-124 (132)
45 PRK09381 trxA thioredoxin; Pro 49.1 31 0.00066 24.2 3.9 28 141-168 78-107 (109)
46 COG1364 ArgJ N-acetylglutamate 48.3 64 0.0014 29.4 6.5 34 50-83 233-270 (404)
47 PTZ00129 40S ribosomal protein 48.3 60 0.0013 25.5 5.6 51 37-87 37-91 (149)
48 KOG0910 Thioredoxin-like prote 46.9 32 0.0007 27.1 3.9 31 49-79 117-149 (150)
49 PHA02278 thioredoxin-like prot 46.7 28 0.00061 25.1 3.4 23 49-71 74-98 (103)
50 cd01644 RT_pepA17 RT_pepA17: R 46.5 27 0.00058 28.6 3.6 28 61-88 145-172 (213)
51 PRK15468 carboxysome structura 46.1 35 0.00076 25.5 3.8 33 140-174 67-99 (111)
52 KOG0910 Thioredoxin-like prote 45.0 37 0.00079 26.8 4.0 76 92-170 62-149 (150)
53 cd02963 TRX_DnaJ TRX domain, D 44.7 26 0.00055 25.1 2.9 27 50-76 82-110 (111)
54 PRK10996 thioredoxin 2; Provis 44.5 39 0.00084 25.4 4.0 28 50-77 109-138 (139)
55 cd02963 TRX_DnaJ TRX domain, D 44.0 27 0.00059 25.0 3.0 27 141-167 82-110 (111)
56 TIGR00090 iojap_ybeB iojap-lik 43.8 51 0.0011 23.7 4.4 34 54-88 28-61 (99)
57 cd02948 TRX_NDPK TRX domain, T 43.4 35 0.00075 23.9 3.4 26 141-167 74-101 (102)
58 PF07338 DUF1471: Protein of u 43.3 33 0.00072 22.2 3.0 25 146-170 4-29 (56)
59 PF06200 tify: tify domain; I 42.9 66 0.0014 19.2 4.0 27 139-165 5-31 (36)
60 cd07049 BMC_EutL_repeat1 ethan 42.6 41 0.00089 24.8 3.7 27 147-174 71-99 (103)
61 COG2221 DsrA Dissimilatory sul 42.6 19 0.00042 31.6 2.3 45 51-100 62-106 (317)
62 cd01554 EPT-like Enol pyruvate 42.3 13 0.00027 32.7 1.1 32 55-90 239-270 (408)
63 cd07047 BMC_PduB_repeat1 1,2-p 42.0 42 0.00091 25.9 3.8 28 147-174 78-105 (134)
64 TIGR02064 dsrA sulfite reducta 41.5 81 0.0018 28.6 6.2 63 33-100 71-159 (402)
65 PF00085 Thioredoxin: Thioredo 38.8 68 0.0015 21.5 4.3 28 49-76 73-102 (103)
66 PF04628 Sedlin_N: Sedlin, N-t 38.3 1.5E+02 0.0032 22.2 6.4 51 124-174 48-104 (132)
67 cd02393 PNPase_KH Polynucleoti 37.4 72 0.0016 20.6 4.0 29 139-168 32-60 (61)
68 COG4978 Transcriptional regula 37.3 87 0.0019 24.5 5.1 45 46-90 79-124 (153)
69 PF09967 DUF2201: VWA-like dom 37.1 1.3E+02 0.0028 22.4 5.8 33 51-89 3-35 (126)
70 cd07049 BMC_EutL_repeat1 ethan 36.9 59 0.0013 24.0 3.8 28 56-84 71-100 (103)
71 PLN00410 U5 snRNP protein, DIM 36.2 70 0.0015 24.7 4.3 78 94-171 26-122 (142)
72 PRK13011 formyltetrahydrofolat 35.6 1.8E+02 0.0038 25.0 7.1 95 59-165 10-110 (286)
73 cd02950 TxlA TRX-like protein 35.3 77 0.0017 23.9 4.4 29 141-169 79-110 (142)
74 cd07996 WGR_MMR_like WGR domai 35.1 99 0.0022 20.4 4.5 33 55-87 40-72 (74)
75 cd02956 ybbN ybbN protein fami 34.9 50 0.0011 22.4 3.0 25 141-165 69-95 (96)
76 PF02410 Oligomerisation: Olig 34.4 80 0.0017 22.5 4.2 29 57-86 31-60 (100)
77 PRK11538 ribosome-associated p 33.7 92 0.002 22.8 4.4 33 54-87 33-65 (105)
78 PF13192 Thioredoxin_3: Thiore 33.2 51 0.0011 22.0 2.8 21 145-165 54-75 (76)
79 TIGR00385 dsbE periplasmic pro 33.0 72 0.0016 24.6 4.0 48 122-169 122-171 (173)
80 cd02988 Phd_like_VIAF Phosduci 32.9 30 0.00065 27.9 1.9 35 50-84 155-191 (192)
81 cd02949 TRX_NTR TRX domain, no 32.2 62 0.0013 22.2 3.2 25 141-165 70-96 (97)
82 COG0533 QRI7 Metal-dependent p 32.1 1.1E+02 0.0024 27.3 5.4 46 36-81 125-171 (342)
83 PF11869 DUF3389: Protein of u 31.7 26 0.00055 24.4 1.1 11 143-153 3-13 (75)
84 TIGR00411 redox_disulf_1 small 31.2 85 0.0018 20.3 3.7 21 147-167 60-80 (82)
85 KOG4180 Predicted kinase [Gene 30.7 93 0.002 27.9 4.6 72 51-138 255-334 (395)
86 PF11399 DUF3192: Protein of u 30.7 42 0.00092 24.7 2.1 19 48-66 80-98 (102)
87 cd02950 TxlA TRX-like protein 30.6 99 0.0022 23.3 4.3 29 50-78 79-110 (142)
88 PF10686 DUF2493: Protein of u 30.5 67 0.0015 21.7 3.0 26 149-174 5-30 (71)
89 TIGR01068 thioredoxin thioredo 30.1 81 0.0018 21.0 3.5 27 50-76 71-99 (101)
90 TIGR03632 bact_S11 30S ribosom 30.0 2E+02 0.0044 21.0 5.7 51 37-87 9-62 (108)
91 PF14611 SLS: Mitochondrial in 29.8 2.6E+02 0.0056 22.3 6.9 34 49-84 57-91 (210)
92 CHL00041 rps11 ribosomal prote 29.1 2.1E+02 0.0046 21.2 5.8 51 37-87 22-75 (116)
93 cd02395 SF1_like-KH Splicing f 28.5 1.8E+02 0.0039 21.7 5.3 29 148-176 68-97 (120)
94 COG0678 AHP1 Peroxiredoxin [Po 28.3 33 0.00072 27.3 1.3 54 33-87 5-74 (165)
95 PF03135 CagE_TrbE_VirB: CagE, 28.3 78 0.0017 25.2 3.6 37 51-88 145-181 (205)
96 PRK06027 purU formyltetrahydro 28.0 2.8E+02 0.0061 23.7 7.1 94 59-166 9-111 (286)
97 PRK10259 hypothetical protein; 27.9 73 0.0016 22.7 2.9 24 146-169 36-59 (86)
98 cd02394 vigilin_like_KH K homo 27.6 87 0.0019 19.8 3.1 20 147-168 42-61 (62)
99 cd07047 BMC_PduB_repeat1 1,2-p 27.5 91 0.002 24.0 3.6 28 56-83 78-105 (134)
100 KOG3384 Selenoprotein [General 27.3 59 0.0013 25.4 2.5 28 33-61 101-131 (154)
101 cd03005 PDI_a_ERp46 PDIa famil 27.0 81 0.0017 21.3 3.0 22 142-163 77-100 (102)
102 cd04792 LanM-like LanM-like pr 26.1 56 0.0012 31.7 2.8 52 63-115 166-217 (825)
103 cd02985 TRX_CDSP32 TRX family, 26.1 1.3E+02 0.0027 21.1 4.0 24 141-165 74-99 (103)
104 KOG2360 Proliferation-associat 26.0 71 0.0015 29.1 3.1 82 28-113 274-356 (413)
105 PRK05309 30S ribosomal protein 25.3 2.5E+02 0.0055 21.2 5.7 51 37-87 26-79 (128)
106 PF11775 CobT_C: Cobalamin bio 25.0 1.3E+02 0.0027 25.2 4.2 48 46-96 12-59 (219)
107 TIGR01651 CobT cobaltochelatas 24.9 1.1E+02 0.0025 29.3 4.4 45 48-95 394-438 (600)
108 PTZ00397 macrophage migration 24.3 2.2E+02 0.0047 20.5 5.1 31 59-89 63-94 (116)
109 cd02965 HyaE HyaE family; HyaE 24.3 1E+02 0.0022 22.9 3.2 52 110-162 51-109 (111)
110 PRK15412 thiol:disulfide inter 24.2 1.6E+02 0.0035 23.0 4.6 52 122-173 127-180 (185)
111 PF13382 Adenine_deam_C: Adeni 24.1 84 0.0018 25.1 3.0 27 52-79 61-87 (171)
112 cd03007 PDI_a_ERp29_N PDIa fam 23.9 80 0.0017 23.5 2.7 26 49-74 82-112 (116)
113 PF14657 Integrase_AP2: AP2-li 23.6 1.2E+02 0.0026 18.4 3.0 25 59-83 19-43 (46)
114 PF00403 HMA: Heavy-metal-asso 23.4 87 0.0019 19.6 2.5 25 143-167 31-58 (62)
115 PF08002 DUF1697: Protein of u 23.3 1.4E+02 0.0031 22.6 4.0 30 143-172 38-67 (137)
116 PF06277 EutA: Ethanolamine ut 23.3 3E+02 0.0066 25.7 6.8 84 54-155 83-170 (473)
117 COG0678 AHP1 Peroxiredoxin [Po 23.3 48 0.001 26.4 1.4 32 124-155 5-45 (165)
118 COG2761 FrnE Predicted dithiol 23.2 1.2E+02 0.0025 25.5 3.7 31 139-170 184-214 (225)
119 TIGR02187 GlrX_arch Glutaredox 22.9 1E+02 0.0022 24.8 3.3 44 31-75 169-213 (215)
120 PF10979 DUF2786: Protein of u 22.9 1.4E+02 0.0029 18.4 3.1 22 66-87 20-41 (43)
121 cd00448 YjgF_YER057c_UK114_fam 22.9 1.1E+02 0.0023 21.1 3.1 36 52-87 10-51 (107)
122 PF14356 DUF4403: Domain of un 22.8 1.4E+02 0.003 27.0 4.4 54 100-156 5-61 (427)
123 cd00148 PROF Profilin binds ac 22.8 2.9E+02 0.0062 20.5 5.6 38 49-86 86-127 (127)
124 PRK15415 propanediol utilizati 22.7 1.3E+02 0.0028 25.9 4.0 29 147-175 119-147 (266)
125 PF13098 Thioredoxin_2: Thiore 22.5 1.4E+02 0.003 20.7 3.6 25 141-165 85-112 (112)
126 COG3445 Acid-induced glycyl ra 22.3 35 0.00077 25.2 0.4 51 105-166 70-120 (127)
127 KOG0670 U4/U6-associated splic 22.2 2.6E+02 0.0056 27.0 6.1 89 77-166 548-649 (752)
128 PRK03988 translation initiatio 22.1 1.4E+02 0.0031 23.0 3.8 30 50-80 72-101 (138)
129 cd06150 YjgF_YER057c_UK114_lik 22.0 1.1E+02 0.0024 21.7 3.0 37 52-88 12-49 (105)
130 PF03799 FtsQ: Cell division p 22.0 2.3E+02 0.0049 19.6 4.7 40 43-85 65-104 (117)
131 TIGR00311 aIF-2beta translatio 21.8 1.4E+02 0.003 22.8 3.7 26 55-80 71-96 (133)
132 PF08002 DUF1697: Protein of u 21.6 1.6E+02 0.0034 22.4 4.0 35 52-88 38-72 (137)
133 PF09345 DUF1987: Domain of un 21.5 1.2E+02 0.0026 22.0 3.1 34 145-178 7-40 (99)
134 PRK02079 pyrroloquinoline quin 21.5 1.9E+02 0.0041 20.4 4.1 45 125-169 6-62 (88)
135 PRK15412 thiol:disulfide inter 21.4 2.1E+02 0.0046 22.3 4.8 52 31-82 127-180 (185)
136 cd07046 BMC_PduU-EutS 1,2-prop 21.3 1.6E+02 0.0034 21.9 3.7 26 147-174 73-98 (110)
137 PF12971 NAGLU_N: Alpha-N-acet 21.2 2.9E+02 0.0063 19.1 6.3 26 54-80 39-64 (86)
138 cd02975 PfPDO_like_N Pyrococcu 21.2 2E+02 0.0044 20.5 4.4 31 140-170 77-111 (113)
139 cd02994 PDI_a_TMX PDIa family, 21.1 1.6E+02 0.0034 20.0 3.6 23 143-165 76-99 (101)
140 PF00013 KH_1: KH domain syndr 21.1 1.4E+02 0.003 18.6 3.1 19 148-168 42-60 (60)
141 PF13541 ChlI: Subunit ChlI of 21.0 2.4E+02 0.0052 21.0 4.8 53 59-113 12-66 (121)
142 PRK09929 hypothetical protein; 20.9 1.1E+02 0.0024 22.1 2.7 23 147-169 40-62 (91)
143 TIGR00385 dsbE periplasmic pro 20.9 1.8E+02 0.0039 22.4 4.3 48 31-78 122-171 (173)
144 PF10865 DUF2703: Domain of un 20.7 94 0.002 23.5 2.5 26 66-91 21-46 (120)
145 PF13549 ATP-grasp_5: ATP-gras 20.5 2E+02 0.0044 23.7 4.6 62 36-100 46-107 (222)
146 TIGR03653 arch_L6P archaeal ri 20.4 4.4E+02 0.0095 20.9 10.3 37 139-178 120-156 (170)
No 1
>PLN00062 TATA-box-binding protein; Provisional
Probab=100.00 E-value=1.9e-70 Score=439.74 Aligned_cols=179 Identities=74% Similarity=1.203 Sum_probs=175.8
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV 81 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L 81 (180)
+|+|+|||||+++++++||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus 1 ~~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 1 VPTLQNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARII 80 (179)
T ss_pred CcEEEEEEEEEEcCCcccHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHH
Q 047239 82 QKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQI 161 (180)
Q Consensus 82 ~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~ 161 (180)
+++|+++++.+|+|+|||||+|++|+|||++||..|.++++||||+||||+||+.+|++|++||+||||+|||+|+++|+
T Consensus 81 ~~lg~~~~~~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~ 160 (179)
T PLN00062 81 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEI 160 (179)
T ss_pred HHcCCCcCCCccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 99999999999999999999999999999999988899999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhccccCC
Q 047239 162 YAAFNNIYPVLNVYVTYDQ 180 (180)
Q Consensus 162 ~~a~~~i~~~L~~~~~~~~ 180 (180)
++|++.|+|+|.+|++.+|
T Consensus 161 ~~ai~~i~p~L~~~~~~~~ 179 (179)
T PLN00062 161 YTAFENIYPVLTEFRKRQQ 179 (179)
T ss_pred HHHHHHHHHHHHHhccCCC
Confidence 9999999999999998865
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=1.1e-69 Score=433.76 Aligned_cols=174 Identities=75% Similarity=1.217 Sum_probs=171.3
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV 81 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L 81 (180)
+|+|+|||||++++|++||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+|+++.|+++++++|
T Consensus 1 ~~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L 80 (174)
T cd04516 1 VPKIQNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII 80 (174)
T ss_pred CCEEEEEEEEEEcCCeecHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHH
Q 047239 82 QKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQI 161 (180)
Q Consensus 82 ~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~ 161 (180)
+++|+++++.+|+|+|||||+|++|+|||++||..|.++++||||+||||+||+.+|+++++||+||||+|||+|+++|+
T Consensus 81 ~~~g~~~~~~~~~v~Nivat~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~ 160 (174)
T cd04516 81 QKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEI 160 (174)
T ss_pred HHcCCCCCCCceEEEEEEEEEECCCcccHHHHHHhChhccEeCCccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 99999999999999999999999999999999988889999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhc
Q 047239 162 YAAFNNIYPVLNVY 175 (180)
Q Consensus 162 ~~a~~~i~~~L~~~ 175 (180)
++|+++|+|+|.+|
T Consensus 161 ~~a~~~i~p~L~~~ 174 (174)
T cd04516 161 YQAFENIYPILLQF 174 (174)
T ss_pred HHHHHHHHHHHhhC
Confidence 99999999999986
No 3
>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=100.00 E-value=4.7e-68 Score=424.04 Aligned_cols=180 Identities=69% Similarity=1.132 Sum_probs=176.5
Q ss_pred CCceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239 1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI 80 (180)
Q Consensus 1 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~ 80 (180)
+.+.++||||+++++|++||.+||...+|++|||++|++++||+++|++|++||+||||+||||+|+++++.|+++++++
T Consensus 21 i~~~l~nivc~~~~~c~ldLk~ial~~~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~aRi 100 (200)
T KOG3302|consen 21 LDPTLQNIVCTVNLNCKLDLKEIALHARNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKYARI 100 (200)
T ss_pred cceEEEeEEEEEeccceecHHHHhhhccccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCCcccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239 81 VQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ 160 (180)
Q Consensus 81 L~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~ 160 (180)
||++|+++++.||++|||+||||++|+|+||+++..|+.+++||||+||||+|||.+|+++++||+||||++|||++.+|
T Consensus 101 lqkLgf~~~f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~~~ 180 (200)
T KOG3302|consen 101 LQKLGFPVKFRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVREE 180 (200)
T ss_pred HHHcCCCceehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccHHH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhccccCC
Q 047239 161 IYAAFNNIYPVLNVYVTYDQ 180 (180)
Q Consensus 161 ~~~a~~~i~~~L~~~~~~~~ 180 (180)
+.+|+++|||+|.+||+.-+
T Consensus 181 i~~Ai~~IyPil~~frk~~~ 200 (200)
T KOG3302|consen 181 TYEAIENIYPILLEFRKKLL 200 (200)
T ss_pred HHHHHHHHhHHHHHhhhccC
Confidence 99999999999999998643
No 4
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=100.00 E-value=2.3e-67 Score=414.07 Aligned_cols=176 Identities=43% Similarity=0.677 Sum_probs=170.2
Q ss_pred CCceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239 1 MAPVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI 80 (180)
Q Consensus 1 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~ 80 (180)
++++|+|||||++|++++||+.++..+++++|||++||||+||+++||+++|||+|||+|||||||.+|++.|+++++++
T Consensus 6 ~~i~IeNIVAS~~L~~elDL~~~~~~l~~aeYnP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGaKs~ed~~~av~~~~~~ 85 (185)
T COG2101 6 PTITIENIVASVDLGQELDLEEVALDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGAKSVEDVHRAVKKLAKK 85 (185)
T ss_pred CccEEEEEEEEechhhhccHHHHHhhCCCCccCHhHCCeeEEEecCCcceEEEEecCcEEEeccCcHHHHHHHHHHHHHH
Confidence 47899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCCccc-ceeeeeeEEEEecCcccchhhHhhh-cCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCH
Q 047239 81 VQKIGFPVQFK-DFKIQNIVGSCDVEFPIKLERLNGF-HAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAR 158 (180)
Q Consensus 81 L~~~g~~~~~~-~~~i~NIva~~~~~~~i~L~~la~~-~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~ 158 (180)
|++.|+++.+. .++|||||||+|++.++||+.+|.. ..++++|||||||||+||+.+|++++|||.|||+||||||++
T Consensus 86 L~~~g~~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~ 165 (185)
T COG2101 86 LKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSE 165 (185)
T ss_pred HHhcCcCcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCH
Confidence 99999999987 7999999999999999999999987 445699999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHhhcc
Q 047239 159 EQIYAAFNNIYPVLNVYV 176 (180)
Q Consensus 159 ~~~~~a~~~i~~~L~~~~ 176 (180)
+|+++|+++|++.|.++.
T Consensus 166 ed~~~Av~~i~~~L~elg 183 (185)
T COG2101 166 EDAEQAVEKIQSRLEELG 183 (185)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 999999999999998875
No 5
>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=3e-66 Score=414.22 Aligned_cols=173 Identities=70% Similarity=1.120 Sum_probs=168.7
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV 81 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L 81 (180)
.++|+||||++++++++||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus 1 ~~~i~NvVas~~l~~~idL~~la~~~~n~~YePe~fpgli~R~~~P~~t~lIf~sGKivitGaks~~~~~~a~~~~~~~L 80 (174)
T cd00652 1 SPKIQNIVATVNLGCELDLRKIALAARNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGAKSEEDAKLAARKYARIL 80 (174)
T ss_pred CcEEEEEEEEEEcCCccCHHHHHhhCCCcEECCCccceEEEEcCCCcEEEEEECCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCC-cccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239 82 QKIGFPV-QFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ 160 (180)
Q Consensus 82 ~~~g~~~-~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~ 160 (180)
+++|++. ++.+|+|+|||||++++|+|||++||..+.++++||||+||||+||+.+|++|++||+||||+|||+|+++|
T Consensus 81 ~~~g~~~~~~~~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~ 160 (174)
T cd00652 81 QKLGFPVEKFPEFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSRED 160 (174)
T ss_pred HHcCCCccccCceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHH
Confidence 9999987 888999999999999999999999998877899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhh
Q 047239 161 IYAAFNNIYPVLNV 174 (180)
Q Consensus 161 ~~~a~~~i~~~L~~ 174 (180)
+++|+++|+|+|.+
T Consensus 161 ~~~a~~~i~~~L~~ 174 (174)
T cd00652 161 IYEAVEKIYPILKE 174 (174)
T ss_pred HHHHHHHHHHHHhC
Confidence 99999999999974
No 6
>PRK00394 transcription factor; Reviewed
Probab=100.00 E-value=5.4e-66 Score=414.28 Aligned_cols=175 Identities=42% Similarity=0.626 Sum_probs=169.0
Q ss_pred ceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHH
Q 047239 3 PVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQ 82 (180)
Q Consensus 3 ~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~ 82 (180)
++|+|||||++++++|||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|+++++++|+
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 48999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCCc-ccceeeeeeEEEEecCcccchhhHhhh-cCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239 83 KIGFPVQ-FKDFKIQNIVGSCDVEFPIKLERLNGF-HAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ 160 (180)
Q Consensus 83 ~~g~~~~-~~~~~i~NIva~~~~~~~i~L~~la~~-~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~ 160 (180)
++|+++. ..+|+|+|||||++++++|||++++.. +.++++||||+||||+||+.+|++|++||+||||+||||||++|
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 9999886 679999999999999999999999986 34899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhccc
Q 047239 161 IYAAFNNIYPVLNVYVT 177 (180)
Q Consensus 161 ~~~a~~~i~~~L~~~~~ 177 (180)
+++|+++|+|+|.++..
T Consensus 161 ~~~a~~~i~~~l~~~g~ 177 (179)
T PRK00394 161 AEKAVEKILEKLEELGL 177 (179)
T ss_pred HHHHHHHHHHHHHHcCC
Confidence 99999999999998764
No 7
>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=1e-65 Score=410.91 Aligned_cols=173 Identities=42% Similarity=0.667 Sum_probs=166.9
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV 81 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L 81 (180)
+++|+|||||++++++|||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
T Consensus 1 ~~~I~NvVas~~l~~~ldL~~la~~~~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGaks~~~a~~a~~~~~~~L 80 (174)
T cd04518 1 SLKIENIVASVDLGQELDLEKVAAELPNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGAKSVEDLHRAVKEIIKKL 80 (174)
T ss_pred CcEEEEEEEEEEcCCeecHHHHHhhCCCcEECCCcCcEEEEEccCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCc-ccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239 82 QKIGFPVQ-FKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ 160 (180)
Q Consensus 82 ~~~g~~~~-~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~ 160 (180)
+++|++.. ..+|+|+|||||++++++|||+.|+.. .++++||||+||||+||+.+|++|++||+||||+||||||++|
T Consensus 81 ~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~la~~-~~~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~ 159 (174)
T cd04518 81 KDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIG-LPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEED 159 (174)
T ss_pred HhcCCCccCCCceEEEEEEEEEEcCCccCHHHHHhh-CCCCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHH
Confidence 99999875 458999999999999999999999986 4599999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhc
Q 047239 161 IYAAFNNIYPVLNVY 175 (180)
Q Consensus 161 ~~~a~~~i~~~L~~~ 175 (180)
++.|+++|+|+|.++
T Consensus 160 ~~~a~~~i~~~l~~~ 174 (174)
T cd04518 160 AKRAVEKLLSRLKEL 174 (174)
T ss_pred HHHHHHHHHHHHhhC
Confidence 999999999999864
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=3e-65 Score=408.42 Aligned_cols=172 Identities=46% Similarity=0.855 Sum_probs=168.2
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV 81 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L 81 (180)
.++|+||||++++++++||+++|..++|++||| +|||++||+++|+++++||+|||++|||++|+++++.|++++.++|
T Consensus 2 ~~~i~Nvvas~~l~~~idL~~la~~l~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~l 80 (174)
T cd04517 2 DILIVNVVCQFSLRCHIDLRKLALAGRNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARLL 80 (174)
T ss_pred ccEEEEEEEEEEcCCcccHHHHHhhCCCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHH
Confidence 589999999999999999999999999999999 9999999999999999999999999999999999999999999999
Q ss_pred HHcCCCC-cccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHH
Q 047239 82 QKIGFPV-QFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQ 160 (180)
Q Consensus 82 ~~~g~~~-~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~ 160 (180)
+++|++. ++.+|+|+|||||++++|+|||++|+..|.++++||||+||||+||+.+|++|++||+||||+|||+|+++|
T Consensus 81 ~~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~ 160 (174)
T cd04517 81 QKLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMED 160 (174)
T ss_pred HHcCCCcccCCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHH
Confidence 9999987 889999999999999999999999998888999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhh
Q 047239 161 IYAAFNNIYPVLNV 174 (180)
Q Consensus 161 ~~~a~~~i~~~L~~ 174 (180)
+++|+++|+|+|.+
T Consensus 161 ~~~a~~~i~pil~~ 174 (174)
T cd04517 161 VREAVEKIYPIVFE 174 (174)
T ss_pred HHHHHHHHHHHHhC
Confidence 99999999999974
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=99.97 E-value=1e-31 Score=192.00 Aligned_cols=84 Identities=50% Similarity=0.724 Sum_probs=80.2
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV 81 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L 81 (180)
.++|+||||+++++++|||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|++++.++|
T Consensus 3 ~~~i~NIva~~~l~~~idL~~la~~~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 3 DFKIVNIVASFDLPFEIDLEELAEELENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKILPIL 82 (86)
T ss_dssp EEEEEEEEEEEE-SSEB-HHHHHHHSTTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred ccEEEEEEEEEECCCccCHHHHHhhccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcC
Q 047239 82 QKIG 85 (180)
Q Consensus 82 ~~~g 85 (180)
+++|
T Consensus 83 ~~~~ 86 (86)
T PF00352_consen 83 QKLG 86 (86)
T ss_dssp HHTT
T ss_pred HHcC
Confidence 9986
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=7.2e-32 Score=192.78 Aligned_cols=86 Identities=52% Similarity=0.804 Sum_probs=80.5
Q ss_pred ccceeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHH
Q 047239 90 FKDFKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIY 169 (180)
Q Consensus 90 ~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~ 169 (180)
|.+++|+||||+++++++|||++|+.. .++++||||+|||++||+.+|++|++||+||||+||||+|+++++.|+++++
T Consensus 1 ~~~~~i~NIva~~~l~~~idL~~la~~-~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~ 79 (86)
T PF00352_consen 1 FPDFKIVNIVASFDLPFEIDLEELAEE-LENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKIL 79 (86)
T ss_dssp -EEEEEEEEEEEEE-SSEB-HHHHHHH-STTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHH
T ss_pred CCccEEEEEEEEEECCCccCHHHHHhh-ccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHH
Confidence 568999999999999999999999987 5999999999999999999999999999999999999999999999999999
Q ss_pred HHHhhcc
Q 047239 170 PVLNVYV 176 (180)
Q Consensus 170 ~~L~~~~ 176 (180)
|+|.+|+
T Consensus 80 ~~L~~~~ 86 (86)
T PF00352_consen 80 PILQKLG 86 (86)
T ss_dssp HHHHHTT
T ss_pred HHHHHcC
Confidence 9999985
No 11
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=99.97 E-value=1.5e-30 Score=205.48 Aligned_cols=85 Identities=39% Similarity=0.629 Sum_probs=81.3
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhCCC--cEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHARN--AEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYAR 79 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~~n--~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~ 79 (180)
.++|||||||+|++.++||+.+|..+++ ++|||||||||+||+.+|++.+|||+|||+||||||+++|++.|++++.+
T Consensus 98 ~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~ed~~~Av~~i~~ 177 (185)
T COG2101 98 EIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEKIQS 177 (185)
T ss_pred ceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCHHHHHHHHHHHHH
Confidence 4789999999999999999999987655 99999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCC
Q 047239 80 IVQKIGF 86 (180)
Q Consensus 80 ~L~~~g~ 86 (180)
.|+++|.
T Consensus 178 ~L~elgl 184 (185)
T COG2101 178 RLEELGL 184 (185)
T ss_pred HHHHhcc
Confidence 9999874
No 12
>PRK00394 transcription factor; Reviewed
Probab=99.96 E-value=1.9e-29 Score=202.64 Aligned_cols=85 Identities=40% Similarity=0.662 Sum_probs=82.6
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhC--CCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHA--RNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYAR 79 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~--~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~ 79 (180)
.++|+|||||++++++|||+.+|..+ +|++||||+||||+||+.+|+++++||+||||+||||||++|++.|++++.+
T Consensus 91 ~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~~ 170 (179)
T PRK00394 91 EIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDAEKAVEKILE 170 (179)
T ss_pred ceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHH
Confidence 57999999999999999999999887 9999999999999999999999999999999999999999999999999999
Q ss_pred HHHHcCC
Q 047239 80 IVQKIGF 86 (180)
Q Consensus 80 ~L~~~g~ 86 (180)
+|+++|.
T Consensus 171 ~l~~~g~ 177 (179)
T PRK00394 171 KLEELGL 177 (179)
T ss_pred HHHHcCC
Confidence 9999985
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=5.1e-29 Score=199.34 Aligned_cols=83 Identities=43% Similarity=0.643 Sum_probs=80.5
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIV 81 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L 81 (180)
.++|+|||||++++++|||+.+|..++|++||||+||||+||+.+|+++++||+||||+||||||++|++.|++++.++|
T Consensus 92 ~~~i~NIVas~~l~~~i~L~~la~~~~~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~~~l 171 (174)
T cd04518 92 EIKVQNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDAKRAVEKLLSRL 171 (174)
T ss_pred ceEEEEEEEEEEcCCccCHHHHHhhCCCCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence 57999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHc
Q 047239 82 QKI 84 (180)
Q Consensus 82 ~~~ 84 (180)
+++
T Consensus 172 ~~~ 174 (174)
T cd04518 172 KEL 174 (174)
T ss_pred hhC
Confidence 863
No 14
>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=3.7e-27 Score=188.62 Aligned_cols=81 Identities=42% Similarity=0.578 Sum_probs=78.5
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhhCC-CcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALHAR-NAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI 80 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~~~-n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~ 80 (180)
.++|+||||+++++++|||+.||...+ +++||||+||||+||+.+|++|++||+||||+|||+||++|++.|++++.++
T Consensus 92 ~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i~~~ 171 (174)
T cd00652 92 EFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKIYPI 171 (174)
T ss_pred ceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHH
Confidence 579999999999999999999999885 9999999999999999999999999999999999999999999999999999
Q ss_pred HH
Q 047239 81 VQ 82 (180)
Q Consensus 81 L~ 82 (180)
|.
T Consensus 172 L~ 173 (174)
T cd00652 172 LK 173 (174)
T ss_pred Hh
Confidence 86
No 15
>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=99.94 E-value=4.2e-27 Score=188.30 Aligned_cols=83 Identities=33% Similarity=0.476 Sum_probs=79.4
Q ss_pred eeeeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHHHH
Q 047239 93 FKIQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVL 172 (180)
Q Consensus 93 ~~i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L 172 (180)
++|+|||||++++++|||++|+.. .++++||||+||||+||+.+|++|++||+||||+||||+|.++++.|+++++++|
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 PKIQNIVATVNLGCKLDLKKIALR-ARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII 80 (174)
T ss_pred CEEEEEEEEEEcCCeecHHHHHhh-CCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 589999999999999999999975 7889999999999999999999999999999999999999999999999999999
Q ss_pred hhcc
Q 047239 173 NVYV 176 (180)
Q Consensus 173 ~~~~ 176 (180)
.++-
T Consensus 81 ~~~g 84 (174)
T cd04516 81 QKLG 84 (174)
T ss_pred HHcC
Confidence 8764
No 16
>PLN00062 TATA-box-binding protein; Provisional
Probab=99.94 E-value=1e-26 Score=186.75 Aligned_cols=84 Identities=33% Similarity=0.496 Sum_probs=80.7
Q ss_pred CceEEEEEEEEEcCCccCHHHHHh-hCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIAL-HARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI 80 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~-~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~ 80 (180)
.++|+|||||+|++++|||+.||. +.++++||||+||||+||+.+|+++++||+||||++||+||++|++.|++++.++
T Consensus 91 ~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~~ai~~i~p~ 170 (179)
T PLN00062 91 DFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIYTAFENIYPV 170 (179)
T ss_pred ccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHH
Confidence 579999999999999999999996 4689999999999999999999999999999999999999999999999999999
Q ss_pred HHHcC
Q 047239 81 VQKIG 85 (180)
Q Consensus 81 L~~~g 85 (180)
|.+++
T Consensus 171 L~~~~ 175 (179)
T PLN00062 171 LTEFR 175 (179)
T ss_pred HHHhc
Confidence 99876
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=1e-25 Score=180.31 Aligned_cols=81 Identities=31% Similarity=0.449 Sum_probs=77.8
Q ss_pred CceEEEEEEEEEcCCccCHHHHHhh-CCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239 2 APVIQNIVATINLECKLDLKKIALH-ARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARI 80 (180)
Q Consensus 2 ~~~I~NvVas~~l~~~ldL~~la~~-~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~ 80 (180)
.++|+||||+++++++|||+.+|.. .++++||||+|||++||+.+|+++++||+||||+|||+||++|++.|++++.++
T Consensus 92 ~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~pi 171 (174)
T cd04517 92 NFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIYPI 171 (174)
T ss_pred ceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHHH
Confidence 5799999999999999999999975 589999999999999999999999999999999999999999999999999998
Q ss_pred HH
Q 047239 81 VQ 82 (180)
Q Consensus 81 L~ 82 (180)
|.
T Consensus 172 l~ 173 (174)
T cd04517 172 VF 173 (174)
T ss_pred Hh
Confidence 85
No 18
>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=99.86 E-value=1.7e-21 Score=156.44 Aligned_cols=85 Identities=29% Similarity=0.443 Sum_probs=80.4
Q ss_pred CCceEEEEEEEEEcCCccCHHHHHhh-CCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHH
Q 047239 1 MAPVIQNIVATINLECKLDLKKIALH-ARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYAR 79 (180)
Q Consensus 1 ~~~~I~NvVas~~l~~~ldL~~la~~-~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~ 79 (180)
+.++|+||+||+|+.++|+|+.++.. ...+.||||.||||+||+.+|+++++||.||||++|||++.++.++|+++|.+
T Consensus 111 ~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~~~i~~Ai~~IyP 190 (200)
T KOG3302|consen 111 RDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVREETYEAIENIYP 190 (200)
T ss_pred hheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccHHHHHHHHHHHhH
Confidence 36899999999999999999999975 57899999999999999999999999999999999999999999999999999
Q ss_pred HHHHcC
Q 047239 80 IVQKIG 85 (180)
Q Consensus 80 ~L~~~g 85 (180)
+|.++.
T Consensus 191 il~~fr 196 (200)
T KOG3302|consen 191 ILLEFR 196 (200)
T ss_pred HHHHhh
Confidence 998763
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=97.13 E-value=0.00061 Score=48.22 Aligned_cols=36 Identities=28% Similarity=0.360 Sum_probs=30.2
Q ss_pred CccceEEEEecCCcEEEEEecCCcEEEEccCCHHHH
Q 047239 35 SRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQA 70 (180)
Q Consensus 35 e~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~ 70 (180)
..=|+.+++.+.+.+++++|.|||++..|...+..|
T Consensus 26 ~~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~~Ae~~A 61 (81)
T PF11858_consen 26 SKPPYAVFQAKYNGVTITAYKSGKVVFQGKNAEQEA 61 (81)
T ss_dssp S--TTEEEEEEETTEEEEEETTSEEEEESTTHHHHH
T ss_pred CCCCCEEEEEeCCCeEEEEEeCCeEEEECCCHHHHH
Confidence 344899999999999999999999999999655555
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=96.76 E-value=0.0016 Score=46.08 Aligned_cols=36 Identities=31% Similarity=0.444 Sum_probs=29.6
Q ss_pred cCCceeEEEecCCeEEEEEecCceEEEEcccCHHHH
Q 047239 126 ELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQI 161 (180)
Q Consensus 126 e~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~ 161 (180)
..=||..|+...+.+|+.+|.||||++.|...+.++
T Consensus 26 ~~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~~Ae~~A 61 (81)
T PF11858_consen 26 SKPPYAVFQAKYNGVTITAYKSGKVVFQGKNAEQEA 61 (81)
T ss_dssp S--TTEEEEEEETTEEEEEETTSEEEEESTTHHHHH
T ss_pred CCCCCEEEEEeCCCeEEEEEeCCeEEEECCCHHHHH
Confidence 334899999999999999999999999999654433
No 21
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=96.63 E-value=0.016 Score=46.25 Aligned_cols=62 Identities=23% Similarity=0.269 Sum_probs=52.5
Q ss_pred CHHHHHhhCCCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHHH
Q 047239 19 DLKKIALHARNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQK 83 (180)
Q Consensus 19 dL~~la~~~~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~ 83 (180)
-|.-||..++++.|..++ ..++++.- ..-+.||.|||+..|-.|++++|++++..+.+++++
T Consensus 47 ilplla~l~P~anY~~kk-~~l~~~kg--erIitiy~sGkVsm~~ikdedEAkeilgel~d~ine 108 (193)
T COG4871 47 ILPLLAPLFPRANYSDKK-NILILQKG--ERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINE 108 (193)
T ss_pred hHHHhHhhCCCccccccc-ceEEEeec--cEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHH
Confidence 356678888999999765 67777754 456789999999999999999999999999998886
No 22
>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=95.06 E-value=0.047 Score=47.03 Aligned_cols=36 Identities=22% Similarity=0.385 Sum_probs=30.3
Q ss_pred cCCccceEEEEecCCcEEEEEecCCcEEEEccCCHH
Q 047239 33 NPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSES 68 (180)
Q Consensus 33 ePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~ 68 (180)
.+..=|+.+|+.+.|.+|+.+|.|||++..|...++
T Consensus 22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~ae~ 57 (284)
T TIGR00716 22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNSEK 57 (284)
T ss_pred ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCHHH
Confidence 445568999999999999999999999999954433
No 23
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=94.46 E-value=0.1 Score=45.16 Aligned_cols=41 Identities=37% Similarity=0.455 Sum_probs=35.7
Q ss_pred cCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHH
Q 047239 126 ELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFN 166 (180)
Q Consensus 126 e~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~ 166 (180)
..-|+.+|+...|.+|+.+|.|||+++.|-..++.+++-..
T Consensus 27 ~~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~ 67 (297)
T COG1039 27 SNPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLN 67 (297)
T ss_pred cCCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhh
Confidence 37789999999999999999999999999987776666554
No 24
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=94.41 E-value=0.11 Score=45.01 Aligned_cols=43 Identities=30% Similarity=0.325 Sum_probs=37.1
Q ss_pred ccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHH
Q 047239 36 RFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYA 78 (180)
Q Consensus 36 ~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~ 78 (180)
..|+.+|+.+.|.+|+.+|.|||+++.|-.+++-+++-...+.
T Consensus 28 ~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~~~~ 70 (297)
T COG1039 28 NPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLNPIA 70 (297)
T ss_pred CCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhhhhh
Confidence 6789999999999999999999999999988777776666443
No 25
>PRK00996 ribonuclease HIII; Provisional
Probab=94.37 E-value=0.081 Score=45.99 Aligned_cols=35 Identities=31% Similarity=0.470 Sum_probs=29.6
Q ss_pred CCccceEEEEecCCcEEEEEecCCcEEEEccCCHH
Q 047239 34 PSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSES 68 (180)
Q Consensus 34 Pe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~ 68 (180)
+..-|+..|+.+.+.+++.+|.|||+++.|...++
T Consensus 26 ~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae~ 60 (304)
T PRK00996 26 PSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAEA 60 (304)
T ss_pred cCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHHH
Confidence 34567999999999999999999999999964433
No 26
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=93.77 E-value=0.51 Score=37.75 Aligned_cols=73 Identities=19% Similarity=0.193 Sum_probs=55.3
Q ss_pred eEEEEecCcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHHHHHHHHhh
Q 047239 98 IVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNV 174 (180)
Q Consensus 98 Iva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L~~ 174 (180)
+.+..+-+++=-|..|+.- .+++.|.- .-.-|+++.- ..-+.|+.||||.+|--++++++++++..+..++.+
T Consensus 36 Vi~~md~~lg~ilplla~l-~P~anY~~-kk~~l~~~kg--erIitiy~sGkVsm~~ikdedEAkeilgel~d~ine 108 (193)
T COG4871 36 VIANMDPPLGGILPLLAPL-FPRANYSD-KKNILILQKG--ERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINE 108 (193)
T ss_pred EEeecCCCcchhHHHhHhh-CCCccccc-ccceEEEeec--cEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHH
Confidence 3555565665556667654 55688884 4566777644 456789999999999999999999999999988875
No 27
>PRK00996 ribonuclease HIII; Provisional
Probab=93.72 E-value=0.13 Score=44.80 Aligned_cols=35 Identities=46% Similarity=0.754 Sum_probs=30.2
Q ss_pred CCcCCceeEEEecCCeEEEEEecCceEEEEcccCH
Q 047239 124 EPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAR 158 (180)
Q Consensus 124 ePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~ 158 (180)
.+..-|+..|+...+.+|+.+|.||||++.|...+
T Consensus 25 ~~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae 59 (304)
T PRK00996 25 TPSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAE 59 (304)
T ss_pred ccCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHH
Confidence 34556899999999999999999999999996543
No 28
>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=93.12 E-value=0.17 Score=43.55 Aligned_cols=34 Identities=24% Similarity=0.490 Sum_probs=29.9
Q ss_pred CCcCCceeEEEecCCeEEEEEecCceEEEEcccC
Q 047239 124 EPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKA 157 (180)
Q Consensus 124 ePe~fpgli~r~~~p~~t~lIF~sGkivitGaks 157 (180)
++..=||..|+...+.+|+.+|.||||++.|...
T Consensus 22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~a 55 (284)
T TIGR00716 22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNS 55 (284)
T ss_pred ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCH
Confidence 4556799999999999999999999999999543
No 29
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=89.49 E-value=1.7 Score=38.17 Aligned_cols=60 Identities=15% Similarity=0.354 Sum_probs=43.2
Q ss_pred CccCHHHHHhhCC-CcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHH
Q 047239 16 CKLDLKKIALHAR-NAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYA 78 (180)
Q Consensus 16 ~~ldL~~la~~~~-n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~ 78 (180)
..+|+++++..+. -..++...| .+.++.. .-.+.+|+.|++.+.|++++.+|+.-..++.
T Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~~f~~gr~~~~g~~~~~~a~~~~~~~~ 337 (338)
T PRK12475 277 RRLNLEEIKKRLQKIGKVDANPY-LLSFQLD--EYRFVLFTDGRAFIHGTNDIKKAKRLYARYI 337 (338)
T ss_pred CccCHHHHHHHHhhcCEEEeccc-EEEEEEC--CEEEEEEcCCcEEEECCCCHHHHHHHHHHhc
Confidence 5899999987653 123332222 3456554 4688899999999999999999988777653
No 30
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=86.17 E-value=2.4 Score=37.33 Aligned_cols=59 Identities=22% Similarity=0.387 Sum_probs=44.4
Q ss_pred CccCHHHHHhhCCCc--EEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHH
Q 047239 16 CKLDLKKIALHARNA--EYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKY 77 (180)
Q Consensus 16 ~~ldL~~la~~~~n~--~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i 77 (180)
..+++++++..+... ++.. +.+.++++.+.-.+..|++|++++.|++++..|+.-..++
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 468888888776432 3433 3345566666689999999999999999999998877665
No 31
>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=81.34 E-value=14 Score=29.85 Aligned_cols=115 Identities=17% Similarity=0.114 Sum_probs=65.3
Q ss_pred EEEEEecCCcEE---EEccCCHHHHHHHHHHHHHHHHHcCCCCcc---------c-ceeeeeeEEEEecCccc---chhh
Q 047239 49 TTALIFSSGKIV---CTGAKSESQAKLAARKYARIVQKIGFPVQF---------K-DFKIQNIVGSCDVEFPI---KLER 112 (180)
Q Consensus 49 ~t~lIf~SGKiv---itGaks~~~~~~a~~~i~~~L~~~g~~~~~---------~-~~~i~NIva~~~~~~~i---~L~~ 112 (180)
-|+.+|.+|+.+ ..|..+.+++..-++.+... ..-+..... . ...|.-..+..+-+|+. -+++
T Consensus 79 Pt~~~f~~g~~~~~~~~G~~~~~~l~~~i~~~~~~-~~~~~~L~~~~~~~l~~~~~pv~I~~F~a~~C~~C~~~~~~l~~ 157 (215)
T TIGR02187 79 PTTIILEEGKDGGIRYTGIPAGYEFAALIEDIVRV-SQGEPGLSEKTVELLQSLDEPVRIEVFVTPTCPYCPYAVLMAHK 157 (215)
T ss_pred CEEEEEeCCeeeEEEEeecCCHHHHHHHHHHHHHh-cCCCCCCCHHHHHHHHhcCCCcEEEEEECCCCCCcHHHHHHHHH
Confidence 388999999886 47998888876666655422 211111111 1 12333334554444441 2444
Q ss_pred HhhhcC--CCCccCCcCCceeE--EEecCCeEEEEEecCceEEEEcccCHHHHHHHHH
Q 047239 113 LNGFHA--MFSTYEPELFPGLI--YRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFN 166 (180)
Q Consensus 113 la~~~~--~~~~YePe~fpgli--~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~ 166 (180)
++..+. ....+|++.+|.+. |.+.. --|+.+|..|+. +.|..+.+++.+.+.
T Consensus 158 l~~~~~~i~~~~vD~~~~~~~~~~~~V~~-vPtl~i~~~~~~-~~G~~~~~~l~~~l~ 213 (215)
T TIGR02187 158 FALANDKILGEMIEANENPDLAEKYGVMS-VPKIVINKGVEE-FVGAYPEEQFLEYIL 213 (215)
T ss_pred HHHhcCceEEEEEeCCCCHHHHHHhCCcc-CCEEEEecCCEE-EECCCCHHHHHHHHH
Confidence 443321 12346777777764 33322 236778888875 889999888777664
No 32
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=78.36 E-value=5.2 Score=35.16 Aligned_cols=30 Identities=13% Similarity=0.367 Sum_probs=26.2
Q ss_pred eEEEEEecCceEEEEcccCHHHHHHHHHHH
Q 047239 139 NVTMLIFLSGKVVITGAKAREQIYAAFNNI 168 (180)
Q Consensus 139 ~~t~lIF~sGkivitGaks~~~~~~a~~~i 168 (180)
.-.+.+|++|+++|-|.+++.+++.-+++.
T Consensus 307 ~~~~~~f~~gr~~~~g~~~~~~a~~~~~~~ 336 (338)
T PRK12475 307 EYRFVLFTDGRAFIHGTNDIKKAKRLYARY 336 (338)
T ss_pred CEEEEEEcCCcEEEECCCCHHHHHHHHHHh
Confidence 478999999999999999999988877654
No 33
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=70.82 E-value=8.2 Score=28.80 Aligned_cols=33 Identities=15% Similarity=0.202 Sum_probs=28.1
Q ss_pred ecCCcEEEEccCCHHHHHHHHHHHHHHHHH-cCCCC
Q 047239 54 FSSGKIVCTGAKSESQAKLAARKYARIVQK-IGFPV 88 (180)
Q Consensus 54 f~SGKivitGaks~~~~~~a~~~i~~~L~~-~g~~~ 88 (180)
-=||.+++||. ..+.+.|++.+.+.|++ +||.+
T Consensus 72 RFsGslvitGd--vs~Ve~Al~~V~~~l~~~L~F~~ 105 (111)
T PRK15468 72 RFSGALVIYGS--VGAVEEALSQTVSGLGRLLNYTL 105 (111)
T ss_pred ccceeEEEEcc--HHHHHHHHHHHHHHHHhhcCccc
Confidence 45899999995 78888999999999997 78754
No 34
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=70.26 E-value=12 Score=29.03 Aligned_cols=62 Identities=19% Similarity=0.216 Sum_probs=38.5
Q ss_pred HHHHHhhCCC-cE---EcCCccceE--EEEecCCcEEEEEecCCcE-EE--Ec--------cCCHHHHHHHHHHHHHHH
Q 047239 20 LKKIALHARN-AE---YNPSRFSAV--TMRIKEPKTTALIFSSGKI-VC--TG--------AKSESQAKLAARKYARIV 81 (180)
Q Consensus 20 L~~la~~~~n-~~---YePe~fpgl--i~r~~~P~~t~lIf~SGKi-vi--tG--------aks~~~~~~a~~~i~~~L 81 (180)
|+++|..+++ +. -|=++.|.+ .|.++.|-.++.+|++|++ +- || ..+.+++...++.+.+--
T Consensus 45 l~~la~~~~~~~~~~kVDVDe~~dla~~y~I~~~~t~~~ffk~g~~~vd~~tG~~~k~~~~~~~k~~l~~~i~~~~~~a 123 (142)
T PLN00410 45 LASVAETIKNFAVIYLVDITEVPDFNTMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWALKDKQEFIDIVETVYRGA 123 (142)
T ss_pred HHHHHHHcCCceEEEEEECCCCHHHHHHcCccCCCcEEEEEECCeEEEEEecccccccccccCCHHHHHHHHHHHHHHH
Confidence 5777777655 22 244444444 4566666678889999994 43 55 456666666666666543
No 35
>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=66.25 E-value=12 Score=28.06 Aligned_cols=30 Identities=10% Similarity=0.245 Sum_probs=24.3
Q ss_pred EEEEEecCce-EEEEcccCHHHHHHHHHHHH
Q 047239 140 VTMLIFLSGK-VVITGAKAREQIYAAFNNIY 169 (180)
Q Consensus 140 ~t~lIF~sGk-ivitGaks~~~~~~a~~~i~ 169 (180)
-|+.+|.+|+ +-..|+++.+.+...++.+.
T Consensus 89 PTl~lfk~G~~v~~~G~~~~~~l~~~l~~~~ 119 (120)
T cd03065 89 DSIYVFKDDEVIEYDGEFAADTLVEFLLDLI 119 (120)
T ss_pred cEEEEEECCEEEEeeCCCCHHHHHHHHHHHh
Confidence 4889999998 55779999988888777653
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=63.42 E-value=12 Score=28.02 Aligned_cols=30 Identities=10% Similarity=0.086 Sum_probs=23.5
Q ss_pred EEEEEecCCc-EEEEccCCHHHHHHHHHHHH
Q 047239 49 TTALIFSSGK-IVCTGAKSESQAKLAARKYA 78 (180)
Q Consensus 49 ~t~lIf~SGK-ivitGaks~~~~~~a~~~i~ 78 (180)
-|+.+|.+|+ +-.+|+.+.+++...++++.
T Consensus 89 PTl~lfk~G~~v~~~G~~~~~~l~~~l~~~~ 119 (120)
T cd03065 89 DSIYVFKDDEVIEYDGEFAADTLVEFLLDLI 119 (120)
T ss_pred cEEEEEECCEEEEeeCCCCHHHHHHHHHHHh
Confidence 3899999999 44569999988877776653
No 37
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=58.45 E-value=32 Score=30.23 Aligned_cols=35 Identities=14% Similarity=0.386 Sum_probs=28.5
Q ss_pred EecCCeEEEEEecCceEEEEcccCHHHHHHHHHHH
Q 047239 134 RMKKPNVTMLIFLSGKVVITGAKAREQIYAAFNNI 168 (180)
Q Consensus 134 r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i 168 (180)
+.+.+.-.+..|++|+++|-|.+++.+++.-+.+.
T Consensus 303 ~vr~~~~~~~~~~~gr~~i~g~~~~~~a~~~~~~~ 337 (339)
T PRK07688 303 SFSLEEKRLVLFKDGRVLVHGTKDISEAKTIYHRY 337 (339)
T ss_pred EEecCCeEEEEEcCCCEEEECCCCHHHHHHHHHHh
Confidence 44444589999999999999999999888777653
No 38
>KOG4749 consensus Inositol polyphosphate kinase [Signal transduction mechanisms]
Probab=56.79 E-value=3.9 Score=36.24 Aligned_cols=56 Identities=32% Similarity=0.578 Sum_probs=44.6
Q ss_pred CCCCccCC-cCCceeEEEec--------CCeEEEEEecCceEEEEcc-----cCHHHHHHHHHHHHHHHh
Q 047239 118 AMFSTYEP-ELFPGLIYRMK--------KPNVTMLIFLSGKVVITGA-----KAREQIYAAFNNIYPVLN 173 (180)
Q Consensus 118 ~~~~~YeP-e~fpgli~r~~--------~p~~t~lIF~sGkivitGa-----ks~~~~~~a~~~i~~~L~ 173 (180)
.+-++|+| ++|.|=.=||. .|.=.+.||.+|..+.-|. |+..++..|++.+...+.
T Consensus 173 sqisey~PLDLfSG~k~rm~~AikaL~~~pqnnlrvF~nG~lv~gg~~~g~~kt~s~i~~~~~~~~k~~l 242 (375)
T KOG4749|consen 173 SQISEYDPLDLFSGSKERMHKAIKALYSTPQNNLRVFLNGSLVFGGLGGGICKTTSEIELAFEDALKDFL 242 (375)
T ss_pred hhhhccCchhhccccHHHHHHHHHHHhhccccceeEEeccceeecccCCCcccchhhhhHHHHHHHHHHh
Confidence 46699999 99999877764 4777899999999999885 456778888887766543
No 39
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=54.35 E-value=26 Score=26.88 Aligned_cols=30 Identities=13% Similarity=0.339 Sum_probs=24.5
Q ss_pred EEEEEecCceEE--EEcccCHHHHHHHHHHHH
Q 047239 140 VTMLIFLSGKVV--ITGAKAREQIYAAFNNIY 169 (180)
Q Consensus 140 ~t~lIF~sGkiv--itGaks~~~~~~a~~~i~ 169 (180)
-|+++|..|+.+ +.|..+.+++.+-++.++
T Consensus 93 PTLl~FkdGk~v~~i~G~~~k~~l~~~I~~~L 124 (132)
T PRK11509 93 PATLVFTGGNYRGVLNGIHPWAELINLMRGLV 124 (132)
T ss_pred CEEEEEECCEEEEEEeCcCCHHHHHHHHHHHh
Confidence 389999999996 789999888877776554
No 40
>PF13575 DUF4135: Domain of unknown function (DUF4135)
Probab=53.59 E-value=14 Score=32.65 Aligned_cols=55 Identities=18% Similarity=0.216 Sum_probs=41.4
Q ss_pred EEEccCCHHHHHHHHHHHHHHHHHcCCCCcccceeeeeeEEEEecCcccchhhHhh
Q 047239 60 VCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNG 115 (180)
Q Consensus 60 vitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~ 115 (180)
--..+.|.++++.-..++-..|.=+ +-....|+--.||+|+.+.|+.||||-|-.
T Consensus 123 ~~~~c~~~~ev~~yY~r~G~llal~-y~L~~~DlH~ENIIa~g~~PvlIDlETlf~ 177 (370)
T PF13575_consen 123 EHEPCNSEEEVERYYYRLGVLLALL-YLLNGTDLHFENIIASGEYPVLIDLETLFH 177 (370)
T ss_pred cCCCCCCHHHHHHHHHHHHHHHHHH-HHhCCCcccccceEEeCCCcEEEehhhhCC
Confidence 3345668888888777776665422 234556888999999999999999999864
No 41
>PRK09381 trxA thioredoxin; Provisional
Probab=53.11 E-value=20 Score=25.17 Aligned_cols=28 Identities=32% Similarity=0.374 Sum_probs=21.7
Q ss_pred EEEEecCCcEE--EEccCCHHHHHHHHHHH
Q 047239 50 TALIFSSGKIV--CTGAKSESQAKLAARKY 77 (180)
Q Consensus 50 t~lIf~SGKiv--itGaks~~~~~~a~~~i 77 (180)
++.+|.+|+++ .+|..+.++++..++..
T Consensus 78 t~~~~~~G~~~~~~~G~~~~~~l~~~i~~~ 107 (109)
T PRK09381 78 TLLLFKNGEVAATKVGALSKGQLKEFLDAN 107 (109)
T ss_pred EEEEEeCCeEEEEecCCCCHHHHHHHHHHh
Confidence 68889999988 66888888776666544
No 42
>PRK10996 thioredoxin 2; Provisional
Probab=51.41 E-value=23 Score=26.70 Aligned_cols=28 Identities=32% Similarity=0.566 Sum_probs=21.8
Q ss_pred EEEEecCceEE--EEcccCHHHHHHHHHHH
Q 047239 141 TMLIFLSGKVV--ITGAKAREQIYAAFNNI 168 (180)
Q Consensus 141 t~lIF~sGkiv--itGaks~~~~~~a~~~i 168 (180)
|+.+|..|+++ +.|..+.+++...++.+
T Consensus 109 tlii~~~G~~v~~~~G~~~~e~l~~~l~~~ 138 (139)
T PRK10996 109 TIMIFKNGQVVDMLNGAVPKAPFDSWLNEA 138 (139)
T ss_pred EEEEEECCEEEEEEcCCCCHHHHHHHHHHh
Confidence 46778899987 67888888888877654
No 43
>PHA02278 thioredoxin-like protein
Probab=51.37 E-value=22 Score=25.65 Aligned_cols=24 Identities=13% Similarity=0.210 Sum_probs=20.0
Q ss_pred EEEEEecCceEE--EEcccCHHHHHH
Q 047239 140 VTMLIFLSGKVV--ITGAKAREQIYA 163 (180)
Q Consensus 140 ~t~lIF~sGkiv--itGaks~~~~~~ 163 (180)
-|+++|..|+.+ +.|..+.+++.+
T Consensus 74 PT~i~fk~G~~v~~~~G~~~~~~l~~ 99 (103)
T PHA02278 74 PVLIGYKDGQLVKKYEDQVTPMQLQE 99 (103)
T ss_pred cEEEEEECCEEEEEEeCCCCHHHHHh
Confidence 478999999999 999888777654
No 44
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=49.37 E-value=34 Score=26.21 Aligned_cols=60 Identities=12% Similarity=0.093 Sum_probs=37.7
Q ss_pred cCHHHHHhhCC-----CcEEcCCccceEE--EEecCCcEEEEEecCCcEE--EEccCCHHHHHHHHHHHH
Q 047239 18 LDLKKIALHAR-----NAEYNPSRFSAVT--MRIKEPKTTALIFSSGKIV--CTGAKSESQAKLAARKYA 78 (180)
Q Consensus 18 ldL~~la~~~~-----n~~YePe~fpgli--~r~~~P~~t~lIf~SGKiv--itGaks~~~~~~a~~~i~ 78 (180)
+=|++|+..++ -+.-+-+..+.+- |.++. --|+++|++|+.+ +.|..+.++...-+++++
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 34677777543 2233444444442 33221 1389999999997 679999988877776654
No 45
>PRK09381 trxA thioredoxin; Provisional
Probab=49.09 E-value=31 Score=24.18 Aligned_cols=28 Identities=29% Similarity=0.468 Sum_probs=20.7
Q ss_pred EEEEecCceEE--EEcccCHHHHHHHHHHH
Q 047239 141 TMLIFLSGKVV--ITGAKAREQIYAAFNNI 168 (180)
Q Consensus 141 t~lIF~sGkiv--itGaks~~~~~~a~~~i 168 (180)
|+.+|..|+++ ..|..+.+++...++..
T Consensus 78 t~~~~~~G~~~~~~~G~~~~~~l~~~i~~~ 107 (109)
T PRK09381 78 TLLLFKNGEVAATKVGALSKGQLKEFLDAN 107 (109)
T ss_pred EEEEEeCCeEEEEecCCCCHHHHHHHHHHh
Confidence 46777889877 66888888877776543
No 46
>COG1364 ArgJ N-acetylglutamate synthase (N-acetylornithine aminotransferase) [Amino acid transport and metabolism]
Probab=48.31 E-value=64 Score=29.36 Aligned_cols=34 Identities=18% Similarity=0.216 Sum_probs=18.8
Q ss_pred EEEEecCCc----EEEEccCCHHHHHHHHHHHHHHHHH
Q 047239 50 TALIFSSGK----IVCTGAKSESQAKLAARKYARIVQK 83 (180)
Q Consensus 50 t~lIf~SGK----ivitGaks~~~~~~a~~~i~~~L~~ 83 (180)
++++++||. -+.......++.+.|+..+.+.|.+
T Consensus 233 tv~llAnG~~g~~~i~~~~~~~~~f~~al~~v~~~LAk 270 (404)
T COG1364 233 TVLLLANGASGNPEITEESPDLAEFKEALTEVCQDLAK 270 (404)
T ss_pred hHhhhhcCccCCccccccCccHHHHHHHHHHHHHHHHH
Confidence 456666652 3334445566666666666655544
No 47
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=48.30 E-value=60 Score=25.54 Aligned_cols=51 Identities=18% Similarity=0.298 Sum_probs=35.8
Q ss_pred cceEEEEecCCcEEE-EEecCCcEEEEccC---CHHHHHHHHHHHHHHHHHcCCC
Q 047239 37 FSAVTMRIKEPKTTA-LIFSSGKIVCTGAK---SESQAKLAARKYARIVQKIGFP 87 (180)
Q Consensus 37 fpgli~r~~~P~~t~-lIf~SGKivitGak---s~~~~~~a~~~i~~~L~~~g~~ 87 (180)
|+.-++-+.+..-.. ...++|.+-..|++ +.=.|..|++++++...++|+.
T Consensus 37 ~NNTiItiTD~~G~~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~ 91 (149)
T PTZ00129 37 FNDTFIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGIN 91 (149)
T ss_pred cCCeEEEEEcccCCEEEEEecCcceecccccCCCHHHHHHHHHHHHHHHHHcCCe
Confidence 344455555554443 44566999999988 3457888999999999888874
No 48
>KOG0910 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=46.86 E-value=32 Score=27.06 Aligned_cols=31 Identities=29% Similarity=0.515 Sum_probs=27.3
Q ss_pred EEEEEecCCcEE--EEccCCHHHHHHHHHHHHH
Q 047239 49 TTALIFSSGKIV--CTGAKSESQAKLAARKYAR 79 (180)
Q Consensus 49 ~t~lIf~SGKiv--itGaks~~~~~~a~~~i~~ 79 (180)
-|+++|.+|.-+ +.|+...+.++..++|+.+
T Consensus 117 PtvlvfknGe~~d~~vG~~~~~~l~~~i~k~l~ 149 (150)
T KOG0910|consen 117 PTVLVFKNGEKVDRFVGAVPKEQLRSLIKKFLK 149 (150)
T ss_pred eEEEEEECCEEeeeecccCCHHHHHHHHHHHhc
Confidence 389999999987 8899999999999988764
No 49
>PHA02278 thioredoxin-like protein
Probab=46.75 E-value=28 Score=25.05 Aligned_cols=23 Identities=13% Similarity=0.254 Sum_probs=19.1
Q ss_pred EEEEEecCCcEE--EEccCCHHHHH
Q 047239 49 TTALIFSSGKIV--CTGAKSESQAK 71 (180)
Q Consensus 49 ~t~lIf~SGKiv--itGaks~~~~~ 71 (180)
-|+++|++|+.+ +.|..+.++++
T Consensus 74 PT~i~fk~G~~v~~~~G~~~~~~l~ 98 (103)
T PHA02278 74 PVLIGYKDGQLVKKYEDQVTPMQLQ 98 (103)
T ss_pred cEEEEEECCEEEEEEeCCCCHHHHH
Confidence 389999999999 88887777654
No 50
>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=46.47 E-value=27 Score=28.57 Aligned_cols=28 Identities=18% Similarity=0.297 Sum_probs=25.1
Q ss_pred EEccCCHHHHHHHHHHHHHHHHHcCCCC
Q 047239 61 CTGAKSESQAKLAARKYARIVQKIGFPV 88 (180)
Q Consensus 61 itGaks~~~~~~a~~~i~~~L~~~g~~~ 88 (180)
+.|+++++++...++++.++|++.|+++
T Consensus 145 li~~~s~~e~~~~~~~v~~~L~~~Gf~l 172 (213)
T cd01644 145 LVSTDTLNEAVNVAKRLIALLKKGGFNL 172 (213)
T ss_pred eecCCCHHHHHHHHHHHHHHHHhCCccc
Confidence 4578899999999999999999999865
No 51
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=46.12 E-value=35 Score=25.49 Aligned_cols=33 Identities=24% Similarity=0.276 Sum_probs=26.2
Q ss_pred EEEEEecCceEEEEcccCHHHHHHHHHHHHHHHhh
Q 047239 140 VTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNV 174 (180)
Q Consensus 140 ~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L~~ 174 (180)
+-++=--||.+++||. .++++.|++.+...|.+
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 4444456899999997 57899999988888776
No 52
>KOG0910 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=44.98 E-value=37 Score=26.75 Aligned_cols=76 Identities=21% Similarity=0.220 Sum_probs=53.4
Q ss_pred ceeeeeeEEEEecCcccc---hhhHhhhc-------CCCCccCCcCCceeEEEecCCeEEEEEecCceEE--EEcccCHH
Q 047239 92 DFKIQNIVGSCDVEFPIK---LERLNGFH-------AMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVV--ITGAKARE 159 (180)
Q Consensus 92 ~~~i~NIva~~~~~~~i~---L~~la~~~-------~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkiv--itGaks~~ 159 (180)
..-+.+.-|..+-||.+= |++++.++ .-+++=+||+ ...|.+.-- -|+++|.+|..+ +.|+-..+
T Consensus 62 ~PVlVdF~A~WCgPCk~l~P~l~~~~~~~~g~~k~~kvdtD~~~el--a~~Y~I~av-PtvlvfknGe~~d~~vG~~~~~ 138 (150)
T KOG0910|consen 62 VPVLVDFHAEWCGPCKMLGPILEELVSEYAGKFKLYKVDTDEHPEL--AEDYEISAV-PTVLVFKNGEKVDRFVGAVPKE 138 (150)
T ss_pred CCEEEEEecCcCccHhHhhHHHHHHHHhhcCeEEEEEEccccccch--Hhhcceeee-eEEEEEECCEEeeeecccCCHH
Confidence 455778889999888764 55555441 1234444554 446666532 589999999987 89999999
Q ss_pred HHHHHHHHHHH
Q 047239 160 QIYAAFNNIYP 170 (180)
Q Consensus 160 ~~~~a~~~i~~ 170 (180)
.+...+++..+
T Consensus 139 ~l~~~i~k~l~ 149 (150)
T KOG0910|consen 139 QLRSLIKKFLK 149 (150)
T ss_pred HHHHHHHHHhc
Confidence 99998887764
No 53
>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=44.69 E-value=26 Score=25.14 Aligned_cols=27 Identities=11% Similarity=0.126 Sum_probs=20.6
Q ss_pred EEEEecCCcEEE--EccCCHHHHHHHHHH
Q 047239 50 TALIFSSGKIVC--TGAKSESQAKLAARK 76 (180)
Q Consensus 50 t~lIf~SGKivi--tGaks~~~~~~a~~~ 76 (180)
|+.+|..|+++- .|..+.+++...+++
T Consensus 82 t~~i~~~g~~~~~~~G~~~~~~l~~~i~~ 110 (111)
T cd02963 82 AIVGIINGQVTFYHDSSFTKQHVVDFVRK 110 (111)
T ss_pred EEEEEECCEEEEEecCCCCHHHHHHHHhc
Confidence 688899999984 477788877666554
No 54
>PRK10996 thioredoxin 2; Provisional
Probab=44.46 E-value=39 Score=25.39 Aligned_cols=28 Identities=25% Similarity=0.364 Sum_probs=22.4
Q ss_pred EEEEecCCcEE--EEccCCHHHHHHHHHHH
Q 047239 50 TALIFSSGKIV--CTGAKSESQAKLAARKY 77 (180)
Q Consensus 50 t~lIf~SGKiv--itGaks~~~~~~a~~~i 77 (180)
++.+|.+|+++ +.|..+.++++..++++
T Consensus 109 tlii~~~G~~v~~~~G~~~~e~l~~~l~~~ 138 (139)
T PRK10996 109 TIMIFKNGQVVDMLNGAVPKAPFDSWLNEA 138 (139)
T ss_pred EEEEEECCEEEEEEcCCCCHHHHHHHHHHh
Confidence 67889999988 67888888887776654
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=43.95 E-value=27 Score=24.98 Aligned_cols=27 Identities=7% Similarity=0.241 Sum_probs=19.1
Q ss_pred EEEEecCceEE--EEcccCHHHHHHHHHH
Q 047239 141 TMLIFLSGKVV--ITGAKAREQIYAAFNN 167 (180)
Q Consensus 141 t~lIF~sGkiv--itGaks~~~~~~a~~~ 167 (180)
|+.+|..|+++ ..|..+.+++...+++
T Consensus 82 t~~i~~~g~~~~~~~G~~~~~~l~~~i~~ 110 (111)
T cd02963 82 AIVGIINGQVTFYHDSSFTKQHVVDFVRK 110 (111)
T ss_pred EEEEEECCEEEEEecCCCCHHHHHHHHhc
Confidence 36677888877 4587888877776654
No 56
>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=43.78 E-value=51 Score=23.70 Aligned_cols=34 Identities=15% Similarity=0.245 Sum_probs=26.7
Q ss_pred ecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCC
Q 047239 54 FSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPV 88 (180)
Q Consensus 54 f~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~ 88 (180)
+..-=|+|||. |..+++..++.+.+.+++.|..+
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 33445777855 99999999999999999887643
No 57
>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=43.41 E-value=35 Score=23.93 Aligned_cols=26 Identities=27% Similarity=0.511 Sum_probs=20.1
Q ss_pred EEEEecCceEE--EEcccCHHHHHHHHHH
Q 047239 141 TMLIFLSGKVV--ITGAKAREQIYAAFNN 167 (180)
Q Consensus 141 t~lIF~sGkiv--itGaks~~~~~~a~~~ 167 (180)
|+++|..|+.+ +.|+ +.+++.++++.
T Consensus 74 t~~~~~~g~~~~~~~G~-~~~~~~~~i~~ 101 (102)
T cd02948 74 TFLFYKNGELVAVIRGA-NAPLLNKTITE 101 (102)
T ss_pred EEEEEECCEEEEEEecC-ChHHHHHHHhh
Confidence 57888999876 7787 67788877764
No 58
>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=43.34 E-value=33 Score=22.19 Aligned_cols=25 Identities=12% Similarity=0.201 Sum_probs=20.6
Q ss_pred cCceEEEEcc-cCHHHHHHHHHHHHH
Q 047239 146 LSGKVVITGA-KAREQIYAAFNNIYP 170 (180)
Q Consensus 146 ~sGkivitGa-ks~~~~~~a~~~i~~ 170 (180)
+-|.|.++|. .+++|+.+++..-..
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 59
>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=42.86 E-value=66 Score=19.15 Aligned_cols=27 Identities=15% Similarity=0.321 Sum_probs=21.3
Q ss_pred eEEEEEecCceEEEEcccCHHHHHHHH
Q 047239 139 NVTMLIFLSGKVVITGAKAREQIYAAF 165 (180)
Q Consensus 139 ~~t~lIF~sGkivitGaks~~~~~~a~ 165 (180)
...+.||-.|+|.+.-.=.++.+++.+
T Consensus 5 ~~qLTIfY~G~V~Vfd~v~~~Ka~~im 31 (36)
T PF06200_consen 5 TAQLTIFYGGQVCVFDDVPPDKAQEIM 31 (36)
T ss_pred CCcEEEEECCEEEEeCCCCHHHHHHHH
Confidence 466899999999999876777666544
No 60
>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=42.60 E-value=41 Score=24.84 Aligned_cols=27 Identities=15% Similarity=0.438 Sum_probs=22.1
Q ss_pred CceEE--EEcccCHHHHHHHHHHHHHHHhh
Q 047239 147 SGKVV--ITGAKAREQIYAAFNNIYPVLNV 174 (180)
Q Consensus 147 sGkiv--itGaks~~~~~~a~~~i~~~L~~ 174 (180)
||.++ ++|. ++.+++.|++.....|.+
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 77777 6665 699999999999888764
No 61
>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]
Probab=42.59 E-value=19 Score=31.63 Aligned_cols=45 Identities=24% Similarity=0.299 Sum_probs=29.4
Q ss_pred EEEecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCCcccceeeeeeEE
Q 047239 51 ALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVG 100 (180)
Q Consensus 51 ~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~NIva 100 (180)
+.|-+.+.+-+.|- |.+++. ++.+.|++.|+++-.....++||+|
T Consensus 62 i~iT~rqg~ei~~i-~~e~~~----~v~~~L~~iG~~~G~~G~~vr~i~a 106 (317)
T COG2221 62 IHITSRQGLEIPGI-SPEDAD----DVVEELREIGLPVGSTGPAVRAIVA 106 (317)
T ss_pred EEEEecCceEeccC-CHHHHH----HHHHHHHHcCCCCCCcchhhhhhhc
Confidence 34444444444442 566654 5556667999998888888889984
No 62
>cd01554 EPT-like Enol pyruvate transferases family includes EPSP synthases and UDP-N-acetylglucosamine enolpyruvyl transferase. Both enzymes catalyze the reaction of enolpyruvyl transfer.
Probab=42.34 E-value=13 Score=32.74 Aligned_cols=32 Identities=9% Similarity=0.305 Sum_probs=24.9
Q ss_pred cCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCCcc
Q 047239 55 SSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQF 90 (180)
Q Consensus 55 ~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~ 90 (180)
..|++.++|....+ ....+.+.|+++|.++..
T Consensus 239 ~~~~v~i~~~~~~~----~~~~~~~~L~~~G~~v~~ 270 (408)
T cd01554 239 APGRLVLQNVGINE----TRTGIIDVLRAMGAKIEI 270 (408)
T ss_pred cCCeEEEecCCCCc----hhhHHHHHHHHcCCEEEE
Confidence 45889999986433 678899999999987654
No 63
>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=41.98 E-value=42 Score=25.89 Aligned_cols=28 Identities=14% Similarity=0.222 Sum_probs=21.5
Q ss_pred CceEEEEcccCHHHHHHHHHHHHHHHhh
Q 047239 147 SGKVVITGAKAREQIYAAFNNIYPVLNV 174 (180)
Q Consensus 147 sGkivitGaks~~~~~~a~~~i~~~L~~ 174 (180)
.|.+++||+.+..+++.|++.-...+.+
T Consensus 78 kg~vvitGg~dVs~V~~aVeaa~~~v~~ 105 (134)
T cd07047 78 HGSLILFGAEDVSDVRRAVEVALSETEK 105 (134)
T ss_pred eEEEEEEcCCCHHHHHHHHHHHHHHHHH
Confidence 7889999999999977766665555544
No 64
>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit. This model describes the alpha subunit of sulfite reductase.
Probab=41.49 E-value=81 Score=28.58 Aligned_cols=63 Identities=17% Similarity=0.269 Sum_probs=38.8
Q ss_pred cCCccceE----EEEecCCc---------------------EEEEEe-cCCcEEEEccCCHHHHHHHHHHHHHHHHHcCC
Q 047239 33 NPSRFSAV----TMRIKEPK---------------------TTALIF-SSGKIVCTGAKSESQAKLAARKYARIVQKIGF 86 (180)
Q Consensus 33 ePe~fpgl----i~r~~~P~---------------------~t~lIf-~SGKivitGaks~~~~~~a~~~i~~~L~~~g~ 86 (180)
.|++||++ .+|+..|. -.+.+- ++|.|++.|. +.+++....+ .|...|+
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 47888886 47777772 123333 3578888877 5666655544 4556677
Q ss_pred CCcccceeeeeeEE
Q 047239 87 PVQFKDFKIQNIVG 100 (180)
Q Consensus 87 ~~~~~~~~i~NIva 100 (180)
+.....-.+.|++|
T Consensus 146 dlggsG~~vRti~a 159 (402)
T TIGR02064 146 DLGGSGSNLRTPES 159 (402)
T ss_pred CCCCCCCCccceec
Confidence 66544455777774
No 65
>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=38.77 E-value=68 Score=21.52 Aligned_cols=28 Identities=25% Similarity=0.351 Sum_probs=22.8
Q ss_pred EEEEEecCCcEE--EEccCCHHHHHHHHHH
Q 047239 49 TTALIFSSGKIV--CTGAKSESQAKLAARK 76 (180)
Q Consensus 49 ~t~lIf~SGKiv--itGaks~~~~~~a~~~ 76 (180)
-++.+|.+|+.+ ..|..+.+++...+++
T Consensus 73 Pt~~~~~~g~~~~~~~g~~~~~~l~~~i~~ 102 (103)
T PF00085_consen 73 PTIIFFKNGKEVKRYNGPRNAESLIEFIEK 102 (103)
T ss_dssp SEEEEEETTEEEEEEESSSSHHHHHHHHHH
T ss_pred CEEEEEECCcEEEEEECCCCHHHHHHHHHc
Confidence 378899999987 7888899988877764
No 66
>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=38.29 E-value=1.5e+02 Score=22.17 Aligned_cols=51 Identities=18% Similarity=0.258 Sum_probs=37.5
Q ss_pred CCcCCceeEEEecCCeEEEEEecCc-eEEEEcc-----cCHHHHHHHHHHHHHHHhh
Q 047239 124 EPELFPGLIYRMKKPNVTMLIFLSG-KVVITGA-----KAREQIYAAFNNIYPVLNV 174 (180)
Q Consensus 124 ePe~fpgli~r~~~p~~t~lIF~sG-kivitGa-----ks~~~~~~a~~~i~~~L~~ 174 (180)
..++|=|+++++.+-++-.-+=+|| |+++.-. ...++++..++.++..-.+
T Consensus 48 ~~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~~~~~~~~d~~ik~fF~~vh~~Y~~ 104 (132)
T PF04628_consen 48 SSDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHDMSDNSIRDEDIKQFFKEVHELYVK 104 (132)
T ss_dssp SSCSEEEEEEEETTEEEEEEETTT--EEEEEECGGG-S--HHHHHHHHHHHHHHHHH
T ss_pred ccccccCceehhhhHHHHhhhccCceeEEEEEecccCCcchHHHHHHHHHHHHHHHH
Confidence 3478889999999988888888888 6655543 5788899888888876544
No 67
>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=37.36 E-value=72 Score=20.62 Aligned_cols=29 Identities=28% Similarity=0.206 Sum_probs=21.5
Q ss_pred eEEEEEecCceEEEEcccCHHHHHHHHHHH
Q 047239 139 NVTMLIFLSGKVVITGAKAREQIYAAFNNI 168 (180)
Q Consensus 139 ~~t~lIF~sGkivitGaks~~~~~~a~~~i 168 (180)
.+++.|=.+|.|.|+|. +.+.++.|.+.|
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 45566666899999995 467788887654
No 68
>COG4978 Transcriptional regulator, effector-binding domain/component [Transcription / Signal transduction mechanisms]
Probab=37.34 E-value=87 Score=24.50 Aligned_cols=45 Identities=16% Similarity=0.224 Sum_probs=38.7
Q ss_pred CCcEEEEEecCCcEEEEccC-CHHHHHHHHHHHHHHHHHcCCCCcc
Q 047239 46 EPKTTALIFSSGKIVCTGAK-SESQAKLAARKYARIVQKIGFPVQF 90 (180)
Q Consensus 46 ~P~~t~lIf~SGKivitGak-s~~~~~~a~~~i~~~L~~~g~~~~~ 90 (180)
++......+.+||+.++=-+ +.++...|.+++...+++.|+.+..
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 46778889999998888777 8999999999999999999986643
No 69
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=37.12 E-value=1.3e+02 Score=22.39 Aligned_cols=33 Identities=24% Similarity=0.283 Sum_probs=25.9
Q ss_pred EEEecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCCc
Q 047239 51 ALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQ 89 (180)
Q Consensus 51 ~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~ 89 (180)
+.|=.||+| |.++++..+..+..++++.+.++.
T Consensus 3 vaiDtSGSi------s~~~l~~fl~ev~~i~~~~~~~v~ 35 (126)
T PF09967_consen 3 VAIDTSGSI------SDEELRRFLSEVAGILRRFPAEVH 35 (126)
T ss_pred EEEECCCCC------CHHHHHHHHHHHHHHHHhCCCCEE
Confidence 456677777 788999999999999998865543
No 70
>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=36.87 E-value=59 Score=24.01 Aligned_cols=28 Identities=11% Similarity=0.312 Sum_probs=23.1
Q ss_pred CCcEE--EEccCCHHHHHHHHHHHHHHHHHc
Q 047239 56 SGKIV--CTGAKSESQAKLAARKYARIVQKI 84 (180)
Q Consensus 56 SGKiv--itGaks~~~~~~a~~~i~~~L~~~ 84 (180)
||.++ ++|. ++.|++.|++...+.|++.
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 67777 6655 9999999999999988754
No 71
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=36.23 E-value=70 Score=24.74 Aligned_cols=78 Identities=17% Similarity=0.279 Sum_probs=42.7
Q ss_pred eeeeeEEEEecCccc---chhhHhhhcCCCC---ccCCcCCcee--EEEecCCeEEEEEecCceEEE---Ec--------
Q 047239 94 KIQNIVGSCDVEFPI---KLERLNGFHAMFS---TYEPELFPGL--IYRMKKPNVTMLIFLSGKVVI---TG-------- 154 (180)
Q Consensus 94 ~i~NIva~~~~~~~i---~L~~la~~~~~~~---~YePe~fpgl--i~r~~~p~~t~lIF~sGkivi---tG-------- 154 (180)
-+...-|+.+-||.. -|+++|.++...+ .=|=+..|.+ .|.+..+-.++.+|..|++.+ ||
T Consensus 26 VVvdF~A~WCgpCk~m~p~l~~la~~~~~~~~~~kVDVDe~~dla~~y~I~~~~t~~~ffk~g~~~vd~~tG~~~k~~~~ 105 (142)
T PLN00410 26 VVIRFGHDWDETCMQMDEVLASVAETIKNFAVIYLVDITEVPDFNTMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINWA 105 (142)
T ss_pred EEEEEECCCChhHHHHHHHHHHHHHHcCCceEEEEEECCCCHHHHHHcCccCCCcEEEEEECCeEEEEEecccccccccc
Confidence 344445555554422 2556665422211 1122223332 455555556777999999655 67
Q ss_pred ccCHHHHHHHHHHHHHH
Q 047239 155 AKAREQIYAAFNNIYPV 171 (180)
Q Consensus 155 aks~~~~~~a~~~i~~~ 171 (180)
..+.+++.+.++.++.-
T Consensus 106 ~~~k~~l~~~i~~~~~~ 122 (142)
T PLN00410 106 LKDKQEFIDIVETVYRG 122 (142)
T ss_pred cCCHHHHHHHHHHHHHH
Confidence 56777787777777654
No 72
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=35.59 E-value=1.8e+02 Score=25.01 Aligned_cols=95 Identities=6% Similarity=-0.082 Sum_probs=49.8
Q ss_pred EEEEccCCHHHHHHHHHHHHHHHHHcCCCCccccee------eeeeEEEEecCcccchhhHhhhcCCCCccCCcCCceeE
Q 047239 59 IVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFK------IQNIVGSCDVEFPIKLERLNGFHAMFSTYEPELFPGLI 132 (180)
Q Consensus 59 ivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~------i~NIva~~~~~~~i~L~~la~~~~~~~~YePe~fpgli 132 (180)
+.+.|..+.-- +.++.+.|.+.|.++...+-. .=.+.+.++++...++++|... ... .-.++---+.
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----VAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSEEGLDEDALRAG-FAP--IAARFGMQWE 82 (286)
T ss_pred EEEEeCCCCCH----HHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecCCCCCHHHHHHH-HHH--HHHHhCcEEE
Confidence 44556644443 456777778888765432221 1135566666766667666532 111 1112211122
Q ss_pred EEecCCeEEEEEecCceEEEEcccCHHHHHHHH
Q 047239 133 YRMKKPNVTMLIFLSGKVVITGAKAREQIYAAF 165 (180)
Q Consensus 133 ~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~ 165 (180)
.+...++.++.||.||. ..+.+.+-+++
T Consensus 83 i~~~~~~~ri~vl~Sg~-----g~nl~al~~~~ 110 (286)
T PRK13011 83 LHDPAARPKVLIMVSKF-----DHCLNDLLYRW 110 (286)
T ss_pred EeecccCceEEEEEcCC-----cccHHHHHHHH
Confidence 33344567899999993 33566665554
No 73
>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=35.30 E-value=77 Score=23.90 Aligned_cols=29 Identities=7% Similarity=0.244 Sum_probs=21.6
Q ss_pred EEEEe-cCceEE--EEcccCHHHHHHHHHHHH
Q 047239 141 TMLIF-LSGKVV--ITGAKAREQIYAAFNNIY 169 (180)
Q Consensus 141 t~lIF-~sGkiv--itGaks~~~~~~a~~~i~ 169 (180)
|+.+| ..|+++ +.|....+++...++.++
T Consensus 79 t~v~~~~~G~~v~~~~G~~~~~~l~~~l~~l~ 110 (142)
T cd02950 79 HFVFLDREGNEEGQSIGLQPKQVLAQNLDALV 110 (142)
T ss_pred EEEEECCCCCEEEEEeCCCCHHHHHHHHHHHH
Confidence 44566 578887 789988888888777655
No 74
>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=35.06 E-value=99 Score=20.43 Aligned_cols=33 Identities=30% Similarity=0.268 Sum_probs=26.3
Q ss_pred cCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCC
Q 047239 55 SSGKIVCTGAKSESQAKLAARKYARIVQKIGFP 87 (180)
Q Consensus 55 ~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~ 87 (180)
+.|........|.++|..+++++.+.-.+.||.
T Consensus 40 ~~Gq~~~~~~~s~~~A~~~~~k~~~~K~~~GY~ 72 (74)
T cd07996 40 TKGQSRTKTFDSEEEALKAAEKLIREKLKRGYR 72 (74)
T ss_pred CCCceEEEECCCHHHHHHHHHHHHHHHHhcCCC
Confidence 456666777889999999999999887777874
No 75
>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=34.87 E-value=50 Score=22.36 Aligned_cols=25 Identities=32% Similarity=0.588 Sum_probs=17.9
Q ss_pred EEEEecCceEE--EEcccCHHHHHHHH
Q 047239 141 TMLIFLSGKVV--ITGAKAREQIYAAF 165 (180)
Q Consensus 141 t~lIF~sGkiv--itGaks~~~~~~a~ 165 (180)
|+.+|..|+.+ ..|..+.+++...+
T Consensus 69 t~~~~~~g~~~~~~~g~~~~~~l~~~l 95 (96)
T cd02956 69 TVYLFAAGQPVDGFQGAQPEEQLRQML 95 (96)
T ss_pred EEEEEeCCEEeeeecCCCCHHHHHHHh
Confidence 46667788875 77888888776643
No 76
>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=34.44 E-value=80 Score=22.54 Aligned_cols=29 Identities=24% Similarity=0.350 Sum_probs=22.7
Q ss_pred CcEEEEccCCHHHHHHHHHHHHHHH-HHcCC
Q 047239 57 GKIVCTGAKSESQAKLAARKYARIV-QKIGF 86 (180)
Q Consensus 57 GKivitGaks~~~~~~a~~~i~~~L-~~~g~ 86 (180)
-=|++|| +|..+++..++.+.+.+ ++.|.
T Consensus 31 y~II~T~-~S~rh~~aia~~v~~~~~k~~~~ 60 (100)
T PF02410_consen 31 YFIIATG-RSERHVRAIADEVEKALKKEYGE 60 (100)
T ss_dssp EEEEEEE-SSHHHHHHHHHHHHHHH-HHTT-
T ss_pred EEEEEEc-CCHHHHHHHHHHHHHHHHHHcCC
Confidence 3467776 59999999999999999 55553
No 77
>PRK11538 ribosome-associated protein; Provisional
Probab=33.66 E-value=92 Score=22.78 Aligned_cols=33 Identities=21% Similarity=0.337 Sum_probs=26.0
Q ss_pred ecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCC
Q 047239 54 FSSGKIVCTGAKSESQAKLAARKYARIVQKIGFP 87 (180)
Q Consensus 54 f~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~ 87 (180)
+...=|++||. |..+++..++.+.+.+++.|..
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 34555777765 9999999999999999987764
No 78
>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=33.20 E-value=51 Score=21.98 Aligned_cols=21 Identities=29% Similarity=0.605 Sum_probs=15.3
Q ss_pred ecCceEEEEc-ccCHHHHHHHH
Q 047239 145 FLSGKVVITG-AKAREQIYAAF 165 (180)
Q Consensus 145 F~sGkivitG-aks~~~~~~a~ 165 (180)
+-+|++...| ..+.+++...+
T Consensus 54 vIng~~~~~G~~p~~~el~~~l 75 (76)
T PF13192_consen 54 VINGKVVFVGRVPSKEELKELL 75 (76)
T ss_dssp EETTEEEEESS--HHHHHHHHH
T ss_pred EECCEEEEEecCCCHHHHHHHh
Confidence 4479999999 88888887765
No 79
>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=33.02 E-value=72 Score=24.64 Aligned_cols=48 Identities=19% Similarity=0.128 Sum_probs=32.4
Q ss_pred ccCCcCCceeEEEecCCeEEEEEecCceEE--EEcccCHHHHHHHHHHHH
Q 047239 122 TYEPELFPGLIYRMKKPNVTMLIFLSGKVV--ITGAKAREQIYAAFNNIY 169 (180)
Q Consensus 122 ~YePe~fpgli~r~~~p~~t~lIF~sGkiv--itGaks~~~~~~a~~~i~ 169 (180)
.+||..--+-.|.....-.+++|..+|+|+ .+|.-+.+++.+.++.++
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 356655444455554434799999999987 457778888777665543
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=32.85 E-value=30 Score=27.87 Aligned_cols=35 Identities=17% Similarity=0.310 Sum_probs=21.6
Q ss_pred EEEEecCCcEE--EEccCCHHHHHHHHHHHHHHHHHc
Q 047239 50 TALIFSSGKIV--CTGAKSESQAKLAARKYARIVQKI 84 (180)
Q Consensus 50 t~lIf~SGKiv--itGaks~~~~~~a~~~i~~~L~~~ 84 (180)
|+++|.+|+++ +.|..+...-+.....+-..|.+.
T Consensus 155 Tlliyk~G~~v~~ivG~~~~gg~~~~~~~lE~~L~~~ 191 (192)
T cd02988 155 TILVYRNGDIVKQFIGLLEFGGMNTTMEDLEWLLVQV 191 (192)
T ss_pred EEEEEECCEEEEEEeCchhhCCCCCCHHHHHHHHHhc
Confidence 89999999998 677654432233344444444433
No 81
>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=32.22 E-value=62 Score=22.21 Aligned_cols=25 Identities=24% Similarity=0.397 Sum_probs=19.4
Q ss_pred EEEEecCceEE--EEcccCHHHHHHHH
Q 047239 141 TMLIFLSGKVV--ITGAKAREQIYAAF 165 (180)
Q Consensus 141 t~lIF~sGkiv--itGaks~~~~~~a~ 165 (180)
++.+|..|+++ +.|..+.+++.+.+
T Consensus 70 t~~i~~~g~~v~~~~g~~~~~~~~~~l 96 (97)
T cd02949 70 TVQFFKDKELVKEISGVKMKSEYREFI 96 (97)
T ss_pred EEEEEECCeEEEEEeCCccHHHHHHhh
Confidence 57788999998 78888887766543
No 82
>COG0533 QRI7 Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=32.11 E-value=1.1e+02 Score=27.27 Aligned_cols=46 Identities=22% Similarity=0.304 Sum_probs=41.6
Q ss_pred ccceEEEEecCCcEEEEEecC-CcEEEEccCCHHHHHHHHHHHHHHH
Q 047239 36 RFSAVTMRIKEPKTTALIFSS-GKIVCTGAKSESQAKLAARKYARIV 81 (180)
Q Consensus 36 ~fpgli~r~~~P~~t~lIf~S-GKivitGaks~~~~~~a~~~i~~~L 81 (180)
.||.+..-...-.+.+.-+++ |++-+-|...-+.+=+|++|++|.|
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 899999999998999999999 9999999977777889999999764
No 83
>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=31.70 E-value=26 Score=24.45 Aligned_cols=11 Identities=36% Similarity=0.694 Sum_probs=9.2
Q ss_pred EEecCceEEEE
Q 047239 143 LIFLSGKVVIT 153 (180)
Q Consensus 143 lIF~sGkivit 153 (180)
.=|+.|||++|
T Consensus 3 I~Fs~GKiI~t 13 (75)
T PF11869_consen 3 IEFSQGKIIAT 13 (75)
T ss_pred EEecCCeEEEc
Confidence 34999999987
No 84
>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=31.25 E-value=85 Score=20.33 Aligned_cols=21 Identities=29% Similarity=0.534 Sum_probs=17.5
Q ss_pred CceEEEEcccCHHHHHHHHHH
Q 047239 147 SGKVVITGAKAREQIYAAFNN 167 (180)
Q Consensus 147 sGkivitGaks~~~~~~a~~~ 167 (180)
.|+..+.|..+.+++...++.
T Consensus 60 ~g~~~~~G~~~~~~l~~~l~~ 80 (82)
T TIGR00411 60 NGDVEFIGAPTKEELVEAIKK 80 (82)
T ss_pred CCEEEEecCCCHHHHHHHHHh
Confidence 777889999899988887765
No 85
>KOG4180 consensus Predicted kinase [General function prediction only]
Probab=30.73 E-value=93 Score=27.87 Aligned_cols=72 Identities=25% Similarity=0.355 Sum_probs=43.0
Q ss_pred EEEecCCcEEEEccCCH-------HHHHHHHHHHHHHHHHcCCC-CcccceeeeeeEEEEecCcccchhhHhhhcCCCCc
Q 047239 51 ALIFSSGKIVCTGAKSE-------SQAKLAARKYARIVQKIGFP-VQFKDFKIQNIVGSCDVEFPIKLERLNGFHAMFST 122 (180)
Q Consensus 51 ~lIf~SGKivitGaks~-------~~~~~a~~~i~~~L~~~g~~-~~~~~~~i~NIva~~~~~~~i~L~~la~~~~~~~~ 122 (180)
+.-=+||=++|||+-|. .-+..++.-++.++...|-. +.+- .| ..++++.++.+...
T Consensus 255 ~KqKssgl~vctgTGstsw~~~iNria~q~v~d~l~~l~~~~~~~vp~~----Re-----------~ve~i~~~~nq~ll 319 (395)
T KOG4180|consen 255 VKQKSSGLVVCTGTGSTSWTFNINRIAEQAVGDLLMILLSRDNLQVPFM----RE-----------LVEEISTAYNQHLL 319 (395)
T ss_pred ccccCCCeeEecCCCcceEeecccHHHHHHHHHHHHHHHhcCcccchhh----hh-----------hhHHHHHHhhhcCc
Confidence 35578999999998664 34556777777777766532 2111 01 12444445667788
Q ss_pred cCCcCCceeEEEecCC
Q 047239 123 YEPELFPGLIYRMKKP 138 (180)
Q Consensus 123 YePe~fpgli~r~~~p 138 (180)
|+|+ .|-+-|-+++|
T Consensus 320 F~PD-~p~l~fSiRep 334 (395)
T KOG4180|consen 320 FKPD-RPQLAFSIREP 334 (395)
T ss_pred cCCC-Ccchhhhhhhh
Confidence 8888 35555544443
No 86
>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=30.69 E-value=42 Score=24.73 Aligned_cols=19 Identities=37% Similarity=0.650 Sum_probs=16.8
Q ss_pred cEEEEEecCCcEEEEccCC
Q 047239 48 KTTALIFSSGKIVCTGAKS 66 (180)
Q Consensus 48 ~~t~lIf~SGKivitGaks 66 (180)
.||-++|.+||++--|-+.
T Consensus 80 ECTplvF~n~~LvgWG~~a 98 (102)
T PF11399_consen 80 ECTPLVFKNGKLVGWGDDA 98 (102)
T ss_pred ceEEEEEECCEEEEEcHHh
Confidence 6999999999999998743
No 87
>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=30.55 E-value=99 Score=23.28 Aligned_cols=29 Identities=7% Similarity=0.076 Sum_probs=21.7
Q ss_pred EEEEe-cCCcEE--EEccCCHHHHHHHHHHHH
Q 047239 50 TALIF-SSGKIV--CTGAKSESQAKLAARKYA 78 (180)
Q Consensus 50 t~lIf-~SGKiv--itGaks~~~~~~a~~~i~ 78 (180)
++.+| .+|+++ +.|....++++..+++++
T Consensus 79 t~v~~~~~G~~v~~~~G~~~~~~l~~~l~~l~ 110 (142)
T cd02950 79 HFVFLDREGNEEGQSIGLQPKQVLAQNLDALV 110 (142)
T ss_pred EEEEECCCCCEEEEEeCCCCHHHHHHHHHHHH
Confidence 56777 589998 679888887776666555
No 88
>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=30.53 E-value=67 Score=21.74 Aligned_cols=26 Identities=19% Similarity=0.230 Sum_probs=17.5
Q ss_pred eEEEEcccCHHHHHHHHHHHHHHHhh
Q 047239 149 KVVITGAKAREQIYAAFNNIYPVLNV 174 (180)
Q Consensus 149 kivitGaks~~~~~~a~~~i~~~L~~ 174 (180)
+|+|||+++-.|.+...+.+-.++.+
T Consensus 5 rVli~GgR~~~D~~~i~~~Ld~~~~~ 30 (71)
T PF10686_consen 5 RVLITGGRDWTDHELIWAALDKVHAR 30 (71)
T ss_pred EEEEEECCccccHHHHHHHHHHHHHh
Confidence 68999999987766655554444433
No 89
>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=30.09 E-value=81 Score=20.96 Aligned_cols=27 Identities=37% Similarity=0.470 Sum_probs=19.5
Q ss_pred EEEEecCCcEE--EEccCCHHHHHHHHHH
Q 047239 50 TALIFSSGKIV--CTGAKSESQAKLAARK 76 (180)
Q Consensus 50 t~lIf~SGKiv--itGaks~~~~~~a~~~ 76 (180)
++.+|.+|+.+ ..|..+.+++...+++
T Consensus 71 ~~~~~~~g~~~~~~~g~~~~~~l~~~l~~ 99 (101)
T TIGR01068 71 TLLLFKNGKEVDRSVGALPKAALKQLINK 99 (101)
T ss_pred EEEEEeCCcEeeeecCCCCHHHHHHHHHh
Confidence 67788999875 5678877776666554
No 90
>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=29.99 E-value=2e+02 Score=20.98 Aligned_cols=51 Identities=27% Similarity=0.474 Sum_probs=34.2
Q ss_pred cceEEEEecCCcEEEEEe-cCCcEEEEccCC--HHHHHHHHHHHHHHHHHcCCC
Q 047239 37 FSAVTMRIKEPKTTALIF-SSGKIVCTGAKS--ESQAKLAARKYARIVQKIGFP 87 (180)
Q Consensus 37 fpgli~r~~~P~~t~lIf-~SGKivitGaks--~~~~~~a~~~i~~~L~~~g~~ 87 (180)
|+-.++-+.+++-..+.| |+|.+-..|++. .-.+..+++++.+.++++|+.
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 345566666765545555 447776666653 556788888999888888863
No 91
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=29.79 E-value=2.6e+02 Score=22.27 Aligned_cols=34 Identities=24% Similarity=0.283 Sum_probs=23.4
Q ss_pred EEE-EEecCCcEEEEccCCHHHHHHHHHHHHHHHHHc
Q 047239 49 TTA-LIFSSGKIVCTGAKSESQAKLAARKYARIVQKI 84 (180)
Q Consensus 49 ~t~-lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~ 84 (180)
+++ ...+.++|.+||. ...++.+...+.+++++.
T Consensus 57 ~~I~~~~~~~~i~I~g~--k~~~~~i~~~i~~~l~~i 91 (210)
T PF14611_consen 57 AKIEVSRSENRIRITGT--KSTAEYIEASINEILSNI 91 (210)
T ss_pred ceEEEecCCcEEEEEcc--HHHHHHHHHHHHHHHhhc
Confidence 444 4467799999995 455666666777777654
No 92
>CHL00041 rps11 ribosomal protein S11
Probab=29.12 E-value=2.1e+02 Score=21.19 Aligned_cols=51 Identities=22% Similarity=0.320 Sum_probs=34.3
Q ss_pred cceEEEEecCCcEEEEEe-cCCcEEEEccCC--HHHHHHHHHHHHHHHHHcCCC
Q 047239 37 FSAVTMRIKEPKTTALIF-SSGKIVCTGAKS--ESQAKLAARKYARIVQKIGFP 87 (180)
Q Consensus 37 fpgli~r~~~P~~t~lIf-~SGKivitGaks--~~~~~~a~~~i~~~L~~~g~~ 87 (180)
|+--++-+.+++-..+.| |+|.+-..|++. ...+..+++++.+.+.++|+.
T Consensus 22 ~NNTiiTlTd~~G~~l~~~S~G~~gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~ 75 (116)
T CHL00041 22 FNNTIVTVTDVRGRVISWSSAGACGFKGARKGTPFAAQTAAENAIRTVIDQGMK 75 (116)
T ss_pred cCCEEEEEEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 444555565555444444 558777777753 567888888999888888764
No 93
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. 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=28.49 E-value=1.8e+02 Score=21.72 Aligned_cols=29 Identities=24% Similarity=0.259 Sum_probs=22.3
Q ss_pred ceEEEEcccC-HHHHHHHHHHHHHHHhhcc
Q 047239 148 GKVVITGAKA-REQIYAAFNNIYPVLNVYV 176 (180)
Q Consensus 148 GkivitGaks-~~~~~~a~~~i~~~L~~~~ 176 (180)
|.|.|++... .+.+..|.+.|..+|....
T Consensus 68 lhV~I~a~~~~~e~~~~A~~~I~~ll~~~~ 97 (120)
T cd02395 68 LHVLITAETPPEEALAKAVEAIEELLKPAI 97 (120)
T ss_pred cEEEEEeCCcHHHHHHHHHHHHHHHhccCC
Confidence 7788887642 6889999999888887543
No 94
>COG0678 AHP1 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=28.34 E-value=33 Score=27.29 Aligned_cols=54 Identities=22% Similarity=0.190 Sum_probs=39.0
Q ss_pred cCCccceEEEEec---------CCcEEEEEecCCcEEEEccC-------CHHHHHHHHHHHHHHHHHcCCC
Q 047239 33 NPSRFSAVTMRIK---------EPKTTALIFSSGKIVCTGAK-------SESQAKLAARKYARIVQKIGFP 87 (180)
Q Consensus 33 ePe~fpgli~r~~---------~P~~t~lIf~SGKivitGak-------s~~~~~~a~~~i~~~L~~~g~~ 87 (180)
..+++|.+.+|.+ .+..+..+|++.|+++.|.- |..++ -+.....+.++..|.+
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 3567899998887 45678899999999998742 33333 4566677777777764
No 95
>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=28.32 E-value=78 Score=25.22 Aligned_cols=37 Identities=14% Similarity=0.174 Sum_probs=28.9
Q ss_pred EEEecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCC
Q 047239 51 ALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPV 88 (180)
Q Consensus 51 ~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~ 88 (180)
..=+.+..|++. ++|.++++..++++...|+..|+.+
T Consensus 145 ~~G~~~~~i~v~-~~~~~~l~~~~~~v~~~l~~~G~~~ 181 (205)
T PF03135_consen 145 SFGYYHFTIVVF-ADDPEELDDKVAEVSSALNNLGFVA 181 (205)
T ss_pred eeeeeEEEEEEE-cCCHHHHHHHHHHHHHHHHHCCCEE
Confidence 344445556666 6699999999999999999998854
No 96
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=27.97 E-value=2.8e+02 Score=23.72 Aligned_cols=94 Identities=10% Similarity=0.074 Sum_probs=51.0
Q ss_pred EEEEccCCHHHHHHHHHHHHHHHHHcCCCCcccceee------eeeEEEEec-CcccchhhHhhhcCCCCccCCcCCcee
Q 047239 59 IVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKI------QNIVGSCDV-EFPIKLERLNGFHAMFSTYEPELFPGL 131 (180)
Q Consensus 59 ivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i------~NIva~~~~-~~~i~L~~la~~~~~~~~YePe~fpgl 131 (180)
+.+.|..+..- +.++.+.|.+.|.++......+ =.+...+++ +.+.+++.|... .+ ....|+ ++
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----VAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDGLIFNLETLRAD-FA--ALAEEF--EM 79 (286)
T ss_pred EEEECCCCCcH----HHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCCCCCCHHHHHHH-HH--HHHHHh--CC
Confidence 44555544433 4567777888887664333222 234455555 556666666432 11 111122 23
Q ss_pred EEEe--cCCeEEEEEecCceEEEEcccCHHHHHHHHH
Q 047239 132 IYRM--KKPNVTMLIFLSGKVVITGAKAREQIYAAFN 166 (180)
Q Consensus 132 i~r~--~~p~~t~lIF~sGkivitGaks~~~~~~a~~ 166 (180)
...+ ..++.++.||.||. |. +.+.+-++++
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 33567899999998 44 6777766653
No 97
>PRK10259 hypothetical protein; Provisional
Probab=27.95 E-value=73 Score=22.66 Aligned_cols=24 Identities=21% Similarity=0.183 Sum_probs=20.1
Q ss_pred cCceEEEEcccCHHHHHHHHHHHH
Q 047239 146 LSGKVVITGAKAREQIYAAFNNIY 169 (180)
Q Consensus 146 ~sGkivitGaks~~~~~~a~~~i~ 169 (180)
+-|-|.++|..+++|+++.+..-.
T Consensus 36 kiG~VSvsg~~s~~d~~~~La~KA 59 (86)
T PRK10259 36 KIGVVSADGASTLDALEAKLAEKA 59 (86)
T ss_pred cceEEEEecCCCHHHHHHHHHHHH
Confidence 568999999999999999886543
No 98
>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=27.64 E-value=87 Score=19.77 Aligned_cols=20 Identities=35% Similarity=0.514 Sum_probs=16.9
Q ss_pred CceEEEEcccCHHHHHHHHHHH
Q 047239 147 SGKVVITGAKAREQIYAAFNNI 168 (180)
Q Consensus 147 sGkivitGaks~~~~~~a~~~i 168 (180)
++.|+|+|. .+.+..|.+.|
T Consensus 42 ~~~v~I~G~--~~~v~~A~~~i 61 (62)
T cd02394 42 SDTITITGP--KENVEKAKEEI 61 (62)
T ss_pred CCEEEEEcC--HHHHHHHHHHh
Confidence 799999999 57888888765
No 99
>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=27.45 E-value=91 Score=24.04 Aligned_cols=28 Identities=21% Similarity=0.252 Sum_probs=23.8
Q ss_pred CCcEEEEccCCHHHHHHHHHHHHHHHHH
Q 047239 56 SGKIVCTGAKSESQAKLAARKYARIVQK 83 (180)
Q Consensus 56 SGKivitGaks~~~~~~a~~~i~~~L~~ 83 (180)
+|-+++||+.++.+++.|++--...+.+
T Consensus 78 kg~vvitGg~dVs~V~~aVeaa~~~v~~ 105 (134)
T cd07047 78 HGSLILFGAEDVSDVRRAVEVALSETEK 105 (134)
T ss_pred eEEEEEEcCCCHHHHHHHHHHHHHHHHH
Confidence 7889999999999988888877777664
No 100
>KOG3384 consensus Selenoprotein [General function prediction only]
Probab=27.28 E-value=59 Score=25.43 Aligned_cols=28 Identities=25% Similarity=0.500 Sum_probs=20.8
Q ss_pred cCCccceEEEEe---cCCcEEEEEecCCcEEE
Q 047239 33 NPSRFSAVTMRI---KEPKTTALIFSSGKIVC 61 (180)
Q Consensus 33 ePe~fpgli~r~---~~P~~t~lIf~SGKivi 61 (180)
+|++|||+.++- .+| ...++-.+||+--
T Consensus 101 ~~~kFp~vkvkyVrg~~P-~l~llDadgk~kE 131 (154)
T KOG3384|consen 101 EPEKFPGVKVKYVRGSDP-VLKLLDADGKHKE 131 (154)
T ss_pred chhhCCCceEEEecCCCC-eeEeecCCCCccc
Confidence 899999986553 345 5678889998743
No 101
>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=26.97 E-value=81 Score=21.31 Aligned_cols=22 Identities=23% Similarity=0.529 Sum_probs=14.7
Q ss_pred EEEecCceEE--EEcccCHHHHHH
Q 047239 142 MLIFLSGKVV--ITGAKAREQIYA 163 (180)
Q Consensus 142 ~lIF~sGkiv--itGaks~~~~~~ 163 (180)
+.+|..|+.+ ..|.++.+++.+
T Consensus 77 ~~~~~~g~~~~~~~G~~~~~~l~~ 100 (102)
T cd03005 77 LLLFKDGEKVDKYKGTRDLDSLKE 100 (102)
T ss_pred EEEEeCCCeeeEeeCCCCHHHHHh
Confidence 5556667654 788988776543
No 102
>cd04792 LanM-like LanM-like proteins. LanM is a bifunctional enzyme, involved in the synthesis of class II lantibiotics. It is responsible for both the dehydration and the cyclization of the precursor-peptide during lantibiotic synthesis. The C-terminal domain shows similarity to LanC, the cyclase component of the lan operon, but the N terminus seems to be unrelated to the dehydratase, LanB.
Probab=26.14 E-value=56 Score=31.74 Aligned_cols=52 Identities=17% Similarity=0.264 Sum_probs=39.7
Q ss_pred ccCCHHHHHHHHHHHHHHHHHcCCCCcccceeeeeeEEEEecCcccchhhHhh
Q 047239 63 GAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNG 115 (180)
Q Consensus 63 Gaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~ 115 (180)
-+.|.++++.-.+++-..|.=+ +-....|+--+||+|+.+.|.-||||-|..
T Consensus 166 ~c~~~~e~~~fY~r~G~llal~-y~L~~tD~H~ENiIA~g~~PvlIDlETlf~ 217 (825)
T cd04792 166 PCQSKEEVERYYYRLGGLLALL-YLLNATDLHFENIIASGEYPVLIDLETLFH 217 (825)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH-HHcCCcccchhhheeeCCCceEEeeHHhcC
Confidence 3567888887777776665422 334567888999999999999999999864
No 103
>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=26.11 E-value=1.3e+02 Score=21.06 Aligned_cols=24 Identities=13% Similarity=0.374 Sum_probs=17.3
Q ss_pred EEEEecCceEE--EEcccCHHHHHHHH
Q 047239 141 TMLIFLSGKVV--ITGAKAREQIYAAF 165 (180)
Q Consensus 141 t~lIF~sGkiv--itGaks~~~~~~a~ 165 (180)
|+++|..|+++ ..|+. ++++...+
T Consensus 74 t~~~~~~G~~v~~~~G~~-~~~l~~~~ 99 (103)
T cd02985 74 HFLFYKDGEKIHEEEGIG-PDELIGDV 99 (103)
T ss_pred EEEEEeCCeEEEEEeCCC-HHHHHHHH
Confidence 68888999977 77874 55655544
No 104
>KOG2360 consensus Proliferation-associated nucleolar protein (NOL1) [Cell cycle control, cell division, chromosome partitioning]
Probab=26.02 E-value=71 Score=29.12 Aligned_cols=82 Identities=18% Similarity=0.277 Sum_probs=57.8
Q ss_pred CCcEEcCCccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHH-HHHHHHHHHHHHcCCCCcccceeeeeeEEEEecCc
Q 047239 28 RNAEYNPSRFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAK-LAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEF 106 (180)
Q Consensus 28 ~n~~YePe~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~-~a~~~i~~~L~~~g~~~~~~~~~i~NIva~~~~~~ 106 (180)
-++ -.|+.|+.+.+=+-+|.|+-..-.+++-.++|+..+++-+ +++..+.-++.++-.. |.+.+ .-+.++|+++-
T Consensus 274 ~~t-~~~~~~~~v~~iL~DpscSgSgm~~r~~~~~~~e~~~~~rL~~L~~fq~~~~~hal~--fp~~k-~vvystcs~~r 349 (413)
T KOG2360|consen 274 LNT-ATPEKFRDVTYILVDPSCSGSGMVSRQDEDPGAETESPERLENLQSFQIRILKHALT--FPNLK-RLVYSTCSLHR 349 (413)
T ss_pred cCC-CCcccccceeEEEeCCCCCCCccccceeeccCCCcccHHHHHHHHHHHHHHHHHHhc--CCchh-heeeecchhhh
Confidence 344 5688899999999999999999999999999988877766 4455555444443221 33333 23449999888
Q ss_pred ccchhhH
Q 047239 107 PIKLERL 113 (180)
Q Consensus 107 ~i~L~~l 113 (180)
..|=+-.
T Consensus 350 eene~vv 356 (413)
T KOG2360|consen 350 EENEQVV 356 (413)
T ss_pred hhhhHHH
Confidence 8774433
No 105
>PRK05309 30S ribosomal protein S11; Validated
Probab=25.32 E-value=2.5e+02 Score=21.20 Aligned_cols=51 Identities=18% Similarity=0.359 Sum_probs=33.8
Q ss_pred cceEEEEecCCcEEEEEec-CCcEEEEccCC--HHHHHHHHHHHHHHHHHcCCC
Q 047239 37 FSAVTMRIKEPKTTALIFS-SGKIVCTGAKS--ESQAKLAARKYARIVQKIGFP 87 (180)
Q Consensus 37 fpgli~r~~~P~~t~lIf~-SGKivitGaks--~~~~~~a~~~i~~~L~~~g~~ 87 (180)
|+-.++-+.++.-..+.|+ +|.+-..|++. ...+..+++++.+.+.++|+.
T Consensus 26 ~NNTiitlTd~~G~~~~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~ 79 (128)
T PRK05309 26 FNNTIVTITDRQGNVISWASAGGLGFKGSRKSTPYAAQVAAEDAAKKAKEHGMK 79 (128)
T ss_pred CCCEEEEEEcCCCCEEEEEecCccEeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 4455555666554444554 47776666653 556788888898888888874
No 106
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=24.96 E-value=1.3e+02 Score=25.21 Aligned_cols=48 Identities=29% Similarity=0.389 Sum_probs=37.9
Q ss_pred CCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCCcccceeee
Q 047239 46 EPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQ 96 (180)
Q Consensus 46 ~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~ 96 (180)
+.-+++||=.||+|-- +..+-+..++.-+++.|.++|+++....|+-.
T Consensus 12 d~~VtlLID~SGSMrg---r~~~vA~~~adila~aL~~~gvp~EVlGFtT~ 59 (219)
T PF11775_consen 12 DTVVTLLIDCSGSMRG---RPIEVAALCADILARALERCGVPVEVLGFTTR 59 (219)
T ss_pred CeEEEEEEeCCcCCCC---ChHHHHHHHHHHHHHHHHhCCCCeEEEeeecC
Confidence 4457899999999863 45667777889999999999998876666643
No 107
>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=24.87 E-value=1.1e+02 Score=29.26 Aligned_cols=45 Identities=27% Similarity=0.326 Sum_probs=36.0
Q ss_pred cEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCCcccceee
Q 047239 48 KTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKI 95 (180)
Q Consensus 48 ~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i 95 (180)
.+++||=.||+|. .+..+-|..++.-+.+.|+.+|+++....|.-
T Consensus 394 ~V~LLID~SGSM~---~r~~~vA~~~a~iLa~aL~~~gIp~eVlGFtt 438 (600)
T TIGR01651 394 VVTLLIDNSGSMR---GRPITVAATCADILARTLERCGVKVEILGFTT 438 (600)
T ss_pred EEEEEEECCccCC---CCHHHHHHHHHHHHHHHHHHCCCCeEEEeecc
Confidence 3688999999995 44555677789999999999999887766664
No 108
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=24.30 E-value=2.2e+02 Score=20.55 Aligned_cols=31 Identities=16% Similarity=0.234 Sum_probs=24.6
Q ss_pred EEEEccCCHHHHHHHHHHHHHHHHH-cCCCCc
Q 047239 59 IVCTGAKSESQAKLAARKYARIVQK-IGFPVQ 89 (180)
Q Consensus 59 ivitGaks~~~~~~a~~~i~~~L~~-~g~~~~ 89 (180)
|.+.|..+.++-+.-.+.+.+.|++ +|++..
T Consensus 63 i~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~ 94 (116)
T PTZ00397 63 VTSIGGISRSNNSSIAAAITKILASHLKVKSE 94 (116)
T ss_pred EEEecCCCHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 4445788999999999999999985 787653
No 109
>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=24.26 E-value=1e+02 Score=22.88 Aligned_cols=52 Identities=15% Similarity=0.211 Sum_probs=31.6
Q ss_pred hhhHhhhcCC---CCccCCcCCceeE--EEecCCeEEEEEecCceEE--EEcccCHHHHH
Q 047239 110 LERLNGFHAM---FSTYEPELFPGLI--YRMKKPNVTMLIFLSGKVV--ITGAKAREQIY 162 (180)
Q Consensus 110 L~~la~~~~~---~~~YePe~fpgli--~r~~~p~~t~lIF~sGkiv--itGaks~~~~~ 162 (180)
|++++.++.. .+..+-+..|.+. |++.. --|+.+|..|+++ +.|..+.+++.
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 5556655332 2344555555543 55443 1388999999997 56888776653
No 110
>PRK15412 thiol:disulfide interchange protein DsbE; Provisional
Probab=24.18 E-value=1.6e+02 Score=22.98 Aligned_cols=52 Identities=13% Similarity=0.123 Sum_probs=37.2
Q ss_pred ccCCcCCceeEEEecCCeEEEEEecCceEEE--EcccCHHHHHHHHHHHHHHHh
Q 047239 122 TYEPELFPGLIYRMKKPNVTMLIFLSGKVVI--TGAKAREQIYAAFNNIYPVLN 173 (180)
Q Consensus 122 ~YePe~fpgli~r~~~p~~t~lIF~sGkivi--tGaks~~~~~~a~~~i~~~L~ 173 (180)
-+||+..-+..|.....-.+++|.++|+|+- .|.-+.++++..++.+++.+.
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 4566655555566555558999999999864 466778888888887776654
No 111
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=24.14 E-value=84 Score=25.06 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=19.2
Q ss_pred EEecCCcEEEEccCCHHHHHHHHHHHHH
Q 047239 52 LIFSSGKIVCTGAKSESQAKLAARKYAR 79 (180)
Q Consensus 52 lIf~SGKivitGaks~~~~~~a~~~i~~ 79 (180)
.=+.|+.|++.|. |.+|...|++++.+
T Consensus 61 ~ahDshniiviG~-~~~dm~~A~n~l~~ 87 (171)
T PF13382_consen 61 VAHDSHNIIVIGT-NDEDMALAANRLIE 87 (171)
T ss_dssp --TTT--EEEEES-SHHHHHHHHHHHHH
T ss_pred cccCCCCEEEEEC-CHHHHHHHHHHHHH
Confidence 4455899999998 89999899887763
No 112
>cd03007 PDI_a_ERp29_N PDIa family, endoplasmic reticulum protein 29 (ERp29) subfamily; ERp29 is a ubiquitous ER-resident protein expressed in high levels in secretory cells. It forms homodimers and higher oligomers in vitro and in vivo. It contains a redox inactive TRX-like domain at the N-terminus, which is homologous to the redox active TRX (a) domains of PDI, and a C-terminal helical domain similar to the C-terminal domain of P5. The expression profile of ERp29 suggests a role in secretory protein production distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase.
Probab=23.92 E-value=80 Score=23.51 Aligned_cols=26 Identities=15% Similarity=0.264 Sum_probs=19.4
Q ss_pred EEEEEecCCc----EEEEcc-CCHHHHHHHH
Q 047239 49 TTALIFSSGK----IVCTGA-KSESQAKLAA 74 (180)
Q Consensus 49 ~t~lIf~SGK----ivitGa-ks~~~~~~a~ 74 (180)
-|+++|.+|. +...|. ++.+++..-+
T Consensus 82 PTl~lF~~g~~~~~~~Y~G~~r~~~~lv~~v 112 (116)
T cd03007 82 PVIYLFHGGDFENPVPYSGADVTVDALQRFL 112 (116)
T ss_pred CEEEEEeCCCcCCCccCCCCcccHHHHHHHH
Confidence 3788899885 678887 8888775544
No 113
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=23.60 E-value=1.2e+02 Score=18.40 Aligned_cols=25 Identities=20% Similarity=0.169 Sum_probs=20.4
Q ss_pred EEEEccCCHHHHHHHHHHHHHHHHH
Q 047239 59 IVCTGAKSESQAKLAARKYARIVQK 83 (180)
Q Consensus 59 ivitGaks~~~~~~a~~~i~~~L~~ 83 (180)
+.-.|.++..+|+.++.++...+++
T Consensus 19 ~~k~GF~TkkeA~~~~~~~~~~~~~ 43 (46)
T PF14657_consen 19 KTKRGFKTKKEAEKALAKIEAELEN 43 (46)
T ss_pred EEcCCCCcHHHHHHHHHHHHHHHHc
Confidence 4557899999999999998877653
No 114
>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=23.44 E-value=87 Score=19.62 Aligned_cols=25 Identities=20% Similarity=0.238 Sum_probs=18.1
Q ss_pred EEecCceEEEEcccCH---HHHHHHHHH
Q 047239 143 LIFLSGKVVITGAKAR---EQIYAAFNN 167 (180)
Q Consensus 143 lIF~sGkivitGaks~---~~~~~a~~~ 167 (180)
.=|.+|+++|++.... +++.++++.
T Consensus 31 vd~~~~~v~v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 31 VDLETKTVTVTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp EETTTTEEEEEESTTTSCHHHHHHHHHH
T ss_pred EECCCCEEEEEEecCCCCHHHHHHHHHH
Confidence 3477899999998665 666666654
No 115
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=23.35 E-value=1.4e+02 Score=22.61 Aligned_cols=30 Identities=17% Similarity=0.201 Sum_probs=23.9
Q ss_pred EEecCceEEEEcccCHHHHHHHHHHHHHHH
Q 047239 143 LIFLSGKVVITGAKAREQIYAAFNNIYPVL 172 (180)
Q Consensus 143 lIF~sGkivitGaks~~~~~~a~~~i~~~L 172 (180)
....||.|+++...+.+++...++..+.--
T Consensus 38 Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~ 67 (137)
T PF08002_consen 38 TYIQSGNVVFESDRDPAELAAKIEKALEER 67 (137)
T ss_dssp EETTTTEEEEEESS-HHHHHHHHHHHHHHH
T ss_pred EEEeeCCEEEecCCChHHHHHHHHHHHHHh
Confidence 667999999998888888888888776543
No 116
>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=23.35 E-value=3e+02 Score=25.65 Aligned_cols=84 Identities=19% Similarity=0.351 Sum_probs=51.6
Q ss_pred ecCCcEEEEccCC-HHHHHHHHHHHHHHHHHcCCCCcccceeeeeeEEEEecCcccchhhHhhh-cCCCCccCCcCCcee
Q 047239 54 FSSGKIVCTGAKS-ESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVGSCDVEFPIKLERLNGF-HAMFSTYEPELFPGL 131 (180)
Q Consensus 54 f~SGKivitGaks-~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~NIva~~~~~~~i~L~~la~~-~~~~~~YePe~fpgl 131 (180)
-.+|=+++||-.. .|.|+..++.+... .| || +|||+- | |||.+-.. ...-..|.-+.. ..
T Consensus 83 I~TGAVIITGETArKeNA~~v~~~Ls~~---aG------DF----VVATAG---P-dLEsiiAgkGsGA~~~S~~~~-~~ 144 (473)
T PF06277_consen 83 IDTGAVIITGETARKENAREVLHALSGF---AG------DF----VVATAG---P-DLESIIAGKGSGAAALSKEHH-TV 144 (473)
T ss_pred CccccEEEecchhhhhhHHHHHHHHHHh---cC------CE----EEEccC---C-CHHHHHhccCccHHHHhhhhC-Ce
Confidence 3689999999633 44454444444322 11 23 457765 3 89988543 334455554433 33
Q ss_pred E--EEecCCeEEEEEecCceEEEEcc
Q 047239 132 I--YRMKKPNVTMLIFLSGKVVITGA 155 (180)
Q Consensus 132 i--~r~~~p~~t~lIF~sGkivitGa 155 (180)
+ ..+-+-...+.+|..|+++=|++
T Consensus 145 V~NiDIGGGTtN~avf~~G~v~~T~c 170 (473)
T PF06277_consen 145 VANIDIGGGTTNIAVFDNGEVIDTAC 170 (473)
T ss_pred EEEEEeCCCceeEEEEECCEEEEEEE
Confidence 3 34556668899999999998876
No 117
>COG0678 AHP1 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=23.28 E-value=48 Score=26.41 Aligned_cols=32 Identities=19% Similarity=0.257 Sum_probs=26.1
Q ss_pred CCcCCceeEEEec---------CCeEEEEEecCceEEEEcc
Q 047239 124 EPELFPGLIYRMK---------KPNVTMLIFLSGKVVITGA 155 (180)
Q Consensus 124 ePe~fpgli~r~~---------~p~~t~lIF~sGkivitGa 155 (180)
..+.+|.++||.+ .+..+-.+|...||++.|.
T Consensus 5 vg~klP~vtf~tr~~~~~~~~~~~~ts~~lf~gKkVvlf~l 45 (165)
T COG0678 5 VGKKLPAVTFKTRVGDETADGWVDVTTDDLFKGKKVVLFSL 45 (165)
T ss_pred cCCcCCceEeEEeeccccCCCcccccHHHhcCCCEEEEEeC
Confidence 4577899999877 4567889999999999874
No 118
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=23.21 E-value=1.2e+02 Score=25.52 Aligned_cols=31 Identities=23% Similarity=0.515 Sum_probs=25.4
Q ss_pred eEEEEEecCceEEEEcccCHHHHHHHHHHHHH
Q 047239 139 NVTMLIFLSGKVVITGAKAREQIYAAFNNIYP 170 (180)
Q Consensus 139 ~~t~lIF~sGkivitGaks~~~~~~a~~~i~~ 170 (180)
.+=.+|| .||+.|.|+-+++....|++.+..
T Consensus 184 gVP~fv~-d~~~~V~Gaq~~~v~~~al~~~~~ 214 (225)
T COG2761 184 GVPTFVF-DGKYAVSGAQPYDVLEDALRQLLA 214 (225)
T ss_pred cCceEEE-cCcEeecCCCCHHHHHHHHHHHHh
Confidence 3446677 999999999999999999877653
No 119
>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=22.91 E-value=1e+02 Score=24.77 Aligned_cols=44 Identities=11% Similarity=-0.069 Sum_probs=28.8
Q ss_pred EEcCCccceEEEEecCC-cEEEEEecCCcEEEEccCCHHHHHHHHH
Q 047239 31 EYNPSRFSAVTMRIKEP-KTTALIFSSGKIVCTGAKSESQAKLAAR 75 (180)
Q Consensus 31 ~YePe~fpgli~r~~~P-~~t~lIf~SGKivitGaks~~~~~~a~~ 75 (180)
.++++.++.+.-+..-. --|+.++..|+. ..|..+.++....+.
T Consensus 169 ~vD~~~~~~~~~~~~V~~vPtl~i~~~~~~-~~G~~~~~~l~~~l~ 213 (215)
T TIGR02187 169 MIEANENPDLAEKYGVMSVPKIVINKGVEE-FVGAYPEEQFLEYIL 213 (215)
T ss_pred EEeCCCCHHHHHHhCCccCCEEEEecCCEE-EECCCCHHHHHHHHH
Confidence 36777777654332111 126778988875 889999888776654
No 120
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=22.90 E-value=1.4e+02 Score=18.35 Aligned_cols=22 Identities=32% Similarity=0.427 Sum_probs=19.2
Q ss_pred CHHHHHHHHHHHHHHHHHcCCC
Q 047239 66 SESQAKLAARKYARIVQKIGFP 87 (180)
Q Consensus 66 s~~~~~~a~~~i~~~L~~~g~~ 87 (180)
+++++..|+.+..+.+.+.|++
T Consensus 20 ~~~EA~~A~~kAq~Lm~ky~i~ 41 (43)
T PF10979_consen 20 NEHEAEAALAKAQRLMAKYGID 41 (43)
T ss_pred CHHHHHHHHHHHHHHHHHhCCc
Confidence 6779999999999999998864
No 121
>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=22.85 E-value=1.1e+02 Score=21.08 Aligned_cols=36 Identities=25% Similarity=0.370 Sum_probs=27.8
Q ss_pred EEecCCcEEEEc------cCCHHHHHHHHHHHHHHHHHcCCC
Q 047239 52 LIFSSGKIVCTG------AKSESQAKLAARKYARIVQKIGFP 87 (180)
Q Consensus 52 lIf~SGKivitG------aks~~~~~~a~~~i~~~L~~~g~~ 87 (180)
.+|.||-+-... ..-.++++.+++++.+.|+..|..
T Consensus 10 ~~~~sGq~~~~~~~~~~~~~~~~Q~~~~~~ni~~~L~~~g~~ 51 (107)
T cd00448 10 LVFVSGQIPLDPDGELVPGDIEAQTRQALENLEAVLEAAGGS 51 (107)
T ss_pred EEEEeccCCcCCCCcccCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence 577777765542 335788999999999999999875
No 122
>PF14356 DUF4403: Domain of unknown function (DUF4403)
Probab=22.84 E-value=1.4e+02 Score=27.03 Aligned_cols=54 Identities=22% Similarity=0.340 Sum_probs=38.3
Q ss_pred EEEecCcccchhhHhhh---cCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEccc
Q 047239 100 GSCDVEFPIKLERLNGF---HAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAK 156 (180)
Q Consensus 100 a~~~~~~~i~L~~la~~---~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGak 156 (180)
++.++|..|.|..|... ..+..-|+.+.++.- ..+-.+.+.+..+|.|.++|..
T Consensus 5 S~i~vPv~i~l~~l~~~~n~~lp~~~~~~~~~~~~---~~~~~i~~~v~R~g~i~i~~~~ 61 (427)
T PF14356_consen 5 SSINVPVEIPLADLEDALNRKLPGEFYGDDDFPDD---LNNDDIRYKVWRTGPITITGNG 61 (427)
T ss_pred cEEEEEEEEEHHHHHHHHhhhCchhhcCCCCCCCc---cccceEEEEEEecCceEEEecC
Confidence 56778888998888643 456677777777665 3334567777888888888763
No 123
>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=22.82 E-value=2.9e+02 Score=20.49 Aligned_cols=38 Identities=18% Similarity=0.285 Sum_probs=29.6
Q ss_pred EEEEEecCCcEEEEccCC----HHHHHHHHHHHHHHHHHcCC
Q 047239 49 TTALIFSSGKIVCTGAKS----ESQAKLAARKYARIVQKIGF 86 (180)
Q Consensus 49 ~t~lIf~SGKivitGaks----~~~~~~a~~~i~~~L~~~g~ 86 (180)
.-+.+..++..++.|.-. ...+..++.++++.|+..|+
T Consensus 86 ~Gi~i~kT~~~ivi~~y~e~~~~g~~~~~v~~ladYL~~~gy 127 (127)
T cd00148 86 GGVVIVKTKQALVIGMYEEGVQPGQANKVVEKLADYLRSQGY 127 (127)
T ss_pred CeEEEEECCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 446677778877776643 55899999999999998875
No 124
>PRK15415 propanediol utilization protein PduB; Provisional
Probab=22.66 E-value=1.3e+02 Score=25.88 Aligned_cols=29 Identities=21% Similarity=0.267 Sum_probs=24.3
Q ss_pred CceEEEEcccCHHHHHHHHHHHHHHHhhc
Q 047239 147 SGKVVITGAKAREQIYAAFNNIYPVLNVY 175 (180)
Q Consensus 147 sGkivitGaks~~~~~~a~~~i~~~L~~~ 175 (180)
.|+++++|+-+..+++.|++.-...+.++
T Consensus 119 ~G~~ii~g~gDVs~Vr~AVeaa~~~~~~~ 147 (266)
T PRK15415 119 HGSLIIFGAEDVSDVRRAVEVALKELDRT 147 (266)
T ss_pred ceEEEEEeCCCHHHHHHHHHHHHHHHHhh
Confidence 39999999999999999998777666554
No 125
>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=22.47 E-value=1.4e+02 Score=20.69 Aligned_cols=25 Identities=28% Similarity=0.510 Sum_probs=15.2
Q ss_pred EEEEec-CceEE--EEcccCHHHHHHHH
Q 047239 141 TMLIFL-SGKVV--ITGAKAREQIYAAF 165 (180)
Q Consensus 141 t~lIF~-sGkiv--itGaks~~~~~~a~ 165 (180)
|+.++. .|+++ ++|..+.+++...+
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 344453 68854 79999998887653
No 126
>COG3445 Acid-induced glycyl radical enzyme [General function prediction only]
Probab=22.28 E-value=35 Score=25.23 Aligned_cols=51 Identities=22% Similarity=0.186 Sum_probs=34.0
Q ss_pred CcccchhhHhhhcCCCCccCCcCCceeEEEecCCeEEEEEecCceEEEEcccCHHHHHHHHH
Q 047239 105 EFPIKLERLNGFHAMFSTYEPELFPGLIYRMKKPNVTMLIFLSGKVVITGAKAREQIYAAFN 166 (180)
Q Consensus 105 ~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~p~~t~lIF~sGkivitGaks~~~~~~a~~ 166 (180)
+..+|..-|..+..+.+--+||.||-|+.|. ||+-+=..+-++|+-++.+.
T Consensus 70 gqhlnvnvl~retledav~~pekypqltirv-----------sgyavrfnsltpeqqrdvi~ 120 (127)
T COG3445 70 GQHLNVNVLRRETLEDAVKHPEKYPQLTIRV-----------SGYAVRFNSLTPEQQRDVIA 120 (127)
T ss_pred CceeeeeeeehhhHHHHhhCcccCCceEEEE-----------eeEEEEeccCCHHHhhhHHH
Confidence 4556666666556677888999999998875 45555455556666665554
No 127
>KOG0670 consensus U4/U6-associated splicing factor PRP4 [RNA processing and modification]
Probab=22.22 E-value=2.6e+02 Score=27.04 Aligned_cols=89 Identities=18% Similarity=0.343 Sum_probs=54.6
Q ss_pred HHHHHHHcCC---CCcccceee---eeeEEEEecCcccchh--hHhhhcCCCCcc-CCcCCceeEEE--e--cCCeEEEE
Q 047239 77 YARIVQKIGF---PVQFKDFKI---QNIVGSCDVEFPIKLE--RLNGFHAMFSTY-EPELFPGLIYR--M--KKPNVTML 143 (180)
Q Consensus 77 i~~~L~~~g~---~~~~~~~~i---~NIva~~~~~~~i~L~--~la~~~~~~~~Y-ePe~fpgli~r--~--~~p~~t~l 143 (180)
.++.|+++|+ +++..|+-| .||+--||+|..-... ++.- ++..--| -||+.=|+-|- + ..-.||+-
T Consensus 548 ALklLK~c~vlHaDIKPDNiLVNE~k~iLKLCDfGSA~~~~eneitP-YLVSRFYRaPEIiLG~~yd~~iD~WSvgctLY 626 (752)
T KOG0670|consen 548 ALKLLKKCGVLHADIKPDNILVNESKNILKLCDFGSASFASENEITP-YLVSRFYRAPEIILGLPYDYPIDTWSVGCTLY 626 (752)
T ss_pred HHHHHHhcCeeecccCccceEeccCcceeeeccCccccccccccccH-HHHHHhccCcceeecCcccCCccceeeceeeE
Confidence 3467788885 666666555 4888888888633221 1110 1111122 46777777664 2 22356666
Q ss_pred EecCceEEEEcccCHHHHHHHHH
Q 047239 144 IFLSGKVVITGAKAREQIYAAFN 166 (180)
Q Consensus 144 IF~sGkivitGaks~~~~~~a~~ 166 (180)
=.-||||..-|.++...++..++
T Consensus 627 ElYtGkIlFpG~TNN~MLrl~me 649 (752)
T KOG0670|consen 627 ELYTGKILFPGRTNNQMLRLFME 649 (752)
T ss_pred EeeccceecCCCCcHHHHHHHHH
Confidence 66899999999998777666553
No 128
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=22.14 E-value=1.4e+02 Score=22.95 Aligned_cols=30 Identities=17% Similarity=0.286 Sum_probs=26.0
Q ss_pred EEEEecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239 50 TALIFSSGKIVCTGAKSESQAKLAARKYARI 80 (180)
Q Consensus 50 t~lIf~SGKivitGaks~~~~~~a~~~i~~~ 80 (180)
...+ .+|+.+++|.-+..++...++++++.
T Consensus 72 ~g~i-~~~~lii~G~~~~~~i~~~L~~yI~~ 101 (138)
T PRK03988 72 AGNI-EGGRLILQGKFSPRVINEKIDRYVKE 101 (138)
T ss_pred ceee-cCCEEEEEEeeCHHHHHHHHHHHHHh
Confidence 3455 89999999999999999999998865
No 129
>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=22.00 E-value=1.1e+02 Score=21.67 Aligned_cols=37 Identities=14% Similarity=0.225 Sum_probs=27.6
Q ss_pred EEecCCcEEEEc-cCCHHHHHHHHHHHHHHHHHcCCCC
Q 047239 52 LIFSSGKIVCTG-AKSESQAKLAARKYARIVQKIGFPV 88 (180)
Q Consensus 52 lIf~SGKivitG-aks~~~~~~a~~~i~~~L~~~g~~~ 88 (180)
.+|-||-+-... ..-+++++.+++++..+|+..|...
T Consensus 12 ~v~iSGq~~~~~~~~~~~Q~~~~~~nl~~~L~~~G~~~ 49 (105)
T cd06150 12 TVYLAGQVADDTSADITGQTRQVLAKIDALLAEAGSDK 49 (105)
T ss_pred EEEEeCcCCcCCCCCHHHHHHHHHHHHHHHHHHcCCCH
Confidence 577777654421 2358899999999999999998754
No 130
>PF03799 FtsQ: Cell division protein FtsQ; InterPro: IPR005548 FtsQ is one of several cell division proteins. FtsQ interacts with other Fts proteins, reviewed in []. The precise function of FtsQ is unknown.; PDB: 2VH1_B 2VH2_B 2ALJ_A 1YR1_A.
Probab=22.00 E-value=2.3e+02 Score=19.64 Aligned_cols=40 Identities=13% Similarity=0.170 Sum_probs=25.4
Q ss_pred EecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHHHcC
Q 047239 43 RIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIG 85 (180)
Q Consensus 43 r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~g 85 (180)
....+..-.+.+.+|..|..|..+ ....++++..+++++.
T Consensus 65 ~~~~~~~~~l~l~dg~~V~lg~~~---~~~kl~~~~~i~~~~~ 104 (117)
T PF03799_consen 65 SYDPRGSWTLYLDDGVEVKLGRSD---LAEKLQRLVKILPQLE 104 (117)
T ss_dssp EEETTSCEEEE-SSS-EEEEESST---HHHHHHHHHHHHHCCC
T ss_pred EECCCCeEEEEECCCcEEEEcCcC---HHHHHHHHHHHHHHHH
Confidence 333444455666789999999874 5566777777776653
No 131
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=21.83 E-value=1.4e+02 Score=22.84 Aligned_cols=26 Identities=15% Similarity=0.277 Sum_probs=23.6
Q ss_pred cCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239 55 SSGKIVCTGAKSESQAKLAARKYARI 80 (180)
Q Consensus 55 ~SGKivitGaks~~~~~~a~~~i~~~ 80 (180)
.+|+.+++|.-+..++...++++++.
T Consensus 71 ~~~rlii~G~~~~~~i~~~L~~yI~~ 96 (133)
T TIGR00311 71 EGGRLILQGKFTHFLLNERIEDYVRK 96 (133)
T ss_pred cCCEEEEEeecCHHHHHHHHHHHHhh
Confidence 68999999999999999999988855
No 132
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=21.61 E-value=1.6e+02 Score=22.38 Aligned_cols=35 Identities=20% Similarity=0.366 Sum_probs=21.5
Q ss_pred EEecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCC
Q 047239 52 LIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPV 88 (180)
Q Consensus 52 lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~ 88 (180)
+...||+++.+...+.+++...+++.+. +++|+++
T Consensus 38 Tyi~SGNvvf~~~~~~~~l~~~ie~~l~--~~fG~~v 72 (137)
T PF08002_consen 38 TYIQSGNVVFESDRDPAELAAKIEKALE--ERFGFDV 72 (137)
T ss_dssp EETTTTEEEEEESS-HHHHHHHHHHHHH--HH-TT--
T ss_pred EEEeeCCEEEecCCChHHHHHHHHHHHH--HhcCCCe
Confidence 5789999999966666666655554442 3577754
No 133
>PF09345 DUF1987: Domain of unknown function (DUF1987); InterPro: IPR018530 This family of proteins are functionally uncharacterised.
Probab=21.53 E-value=1.2e+02 Score=22.00 Aligned_cols=34 Identities=26% Similarity=0.487 Sum_probs=30.2
Q ss_pred ecCceEEEEcccCHHHHHHHHHHHHHHHhhcccc
Q 047239 145 FLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTY 178 (180)
Q Consensus 145 F~sGkivitGaks~~~~~~a~~~i~~~L~~~~~~ 178 (180)
+.+|..-|.|-.=+|+...-++-|+..|.+|-+.
T Consensus 7 ~~~g~l~i~GeSypEn~~~Fy~Pi~~wl~~Yl~~ 40 (99)
T PF09345_consen 7 FDTGRLEISGESYPENAFAFYQPILDWLEAYLAE 40 (99)
T ss_pred ccCCEEEEecccCccCHHHHHHHHHHHHHHHHhC
Confidence 6799999999998999999999999988888654
No 134
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=21.47 E-value=1.9e+02 Score=20.42 Aligned_cols=45 Identities=22% Similarity=0.519 Sum_probs=34.3
Q ss_pred CcCCceeEEEecC-CeEEEEEecCceEEE-----------EcccCHHHHHHHHHHHH
Q 047239 125 PELFPGLIYRMKK-PNVTMLIFLSGKVVI-----------TGAKAREQIYAAFNNIY 169 (180)
Q Consensus 125 Pe~fpgli~r~~~-p~~t~lIF~sGkivi-----------tGaks~~~~~~a~~~i~ 169 (180)
|.+-||..+|... ..+-+++|+-|-|.+ -|.+|.+++-..+..-|
T Consensus 6 p~l~~~~rl~~d~~~~~~vlL~PEgmi~Lnetg~~Iw~~~DG~~tv~eIi~~L~~~y 62 (88)
T PRK02079 6 PTLRPGYRFQWEPAQNCHVLLYPEGMIKLNESAGEILGLIDGKRTVAAIIAELQQQF 62 (88)
T ss_pred cccCCCcccccccccCceEEEcCCeeeeechHHHHHHHHccCCCCHHHHHHHHHHHc
Confidence 6777787777543 578899999999987 67788888776665544
No 135
>PRK15412 thiol:disulfide interchange protein DsbE; Provisional
Probab=21.45 E-value=2.1e+02 Score=22.30 Aligned_cols=52 Identities=12% Similarity=0.067 Sum_probs=33.8
Q ss_pred EEcCCccceEEEEecCCcEEEEEecCCcEEEE--ccCCHHHHHHHHHHHHHHHH
Q 047239 31 EYNPSRFSAVTMRIKEPKTTALIFSSGKIVCT--GAKSESQAKLAARKYARIVQ 82 (180)
Q Consensus 31 ~YePe~fpgli~r~~~P~~t~lIf~SGKivit--Gaks~~~~~~a~~~i~~~L~ 82 (180)
-++|+..-+..|.....-.+++|..+|+|+-+ |.-+.++.+..++.+.+...
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 34554333333444444478999999998754 66778888887777776554
No 136
>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=21.31 E-value=1.6e+02 Score=21.91 Aligned_cols=26 Identities=31% Similarity=0.455 Sum_probs=21.7
Q ss_pred CceEEEEcccCHHHHHHHHHHHHHHHhh
Q 047239 147 SGKVVITGAKAREQIYAAFNNIYPVLNV 174 (180)
Q Consensus 147 sGkivitGaks~~~~~~a~~~i~~~L~~ 174 (180)
+|.++++| +..+++.|++.....+.+
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 789999999988777654
No 137
>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=21.20 E-value=2.9e+02 Score=19.11 Aligned_cols=26 Identities=27% Similarity=0.290 Sum_probs=18.6
Q ss_pred ecCCcEEEEccCCHHHHHHHHHHHHHH
Q 047239 54 FSSGKIVCTGAKSESQAKLAARKYARI 80 (180)
Q Consensus 54 f~SGKivitGaks~~~~~~a~~~i~~~ 80 (180)
-.+|||+++|. |.-.+-.|++..++.
T Consensus 39 ~~~gki~I~G~-s~vala~Gl~~YLk~ 64 (86)
T PF12971_consen 39 ADNGKIVIRGN-SGVALASGLNWYLKY 64 (86)
T ss_dssp -SSS-EEEEES-SHHHHHHHHHHHHHH
T ss_pred CCCCeEEEEeC-CHHHHHHHHHHHHHH
Confidence 37899999998 666777777776654
No 138
>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=21.19 E-value=2e+02 Score=20.54 Aligned_cols=31 Identities=16% Similarity=0.204 Sum_probs=23.7
Q ss_pred EEEEEecC----ceEEEEcccCHHHHHHHHHHHHH
Q 047239 140 VTMLIFLS----GKVVITGAKAREQIYAAFNNIYP 170 (180)
Q Consensus 140 ~t~lIF~s----GkivitGaks~~~~~~a~~~i~~ 170 (180)
-|+++|.. |++...|..+.+++..-++.|+.
T Consensus 77 Pt~~i~~~g~~~~~~~~~G~~~~~el~~~i~~i~~ 111 (113)
T cd02975 77 PTTIFLQDGGKDGGIRYYGLPAGYEFASLIEDIVR 111 (113)
T ss_pred CEEEEEeCCeecceEEEEecCchHHHHHHHHHHHh
Confidence 36677765 66678899999898888887764
No 139
>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=21.09 E-value=1.6e+02 Score=20.02 Aligned_cols=23 Identities=13% Similarity=0.213 Sum_probs=14.5
Q ss_pred EEecCceE-EEEcccCHHHHHHHH
Q 047239 143 LIFLSGKV-VITGAKAREQIYAAF 165 (180)
Q Consensus 143 lIF~sGki-vitGaks~~~~~~a~ 165 (180)
.+|..|++ ...|..+.+++...+
T Consensus 76 ~~~~~g~~~~~~G~~~~~~l~~~i 99 (101)
T cd02994 76 YHAKDGVFRRYQGPRDKEDLISFI 99 (101)
T ss_pred EEeCCCCEEEecCCCCHHHHHHHH
Confidence 34566664 456888877776554
No 140
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=21.08 E-value=1.4e+02 Score=18.63 Aligned_cols=19 Identities=37% Similarity=0.382 Sum_probs=15.5
Q ss_pred ceEEEEcccCHHHHHHHHHHH
Q 047239 148 GKVVITGAKAREQIYAAFNNI 168 (180)
Q Consensus 148 GkivitGaks~~~~~~a~~~i 168 (180)
..|.|+| +.+.++.|.+.|
T Consensus 42 ~~v~I~G--~~~~v~~A~~~I 60 (60)
T PF00013_consen 42 DIVTISG--SPEQVEKAKKMI 60 (60)
T ss_dssp EEEEEEE--SHHHHHHHHHHH
T ss_pred EEEEEEe--CHHHHHHHHhhC
Confidence 5788998 689999998765
No 141
>PF13541 ChlI: Subunit ChlI of Mg-chelatase
Probab=20.97 E-value=2.4e+02 Score=21.03 Aligned_cols=53 Identities=15% Similarity=0.221 Sum_probs=36.3
Q ss_pred EEEEccCCHHHHHHHHHHHHHHHHHcCCCCcccceeeeeeE-E-EEecCcccchhhH
Q 047239 59 IVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIV-G-SCDVEFPIKLERL 113 (180)
Q Consensus 59 ivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~NIv-a-~~~~~~~i~L~~l 113 (180)
+.+.|--+ ..++++.+++...|++.|++....++.| |+. + .-.-+-.+||.-.
T Consensus 12 ~~ivGl~~-~av~esr~Rv~~al~~~g~~~p~~~i~V-Nlap~~l~k~g~~~DLaIA 66 (121)
T PF13541_consen 12 FNIVGLPD-TAVKESRERVRSALKNSGFPFPNQDITV-NLAPADLKKEGPAFDLAIA 66 (121)
T ss_pred eEEecCch-HHHHHHHHHHHHHHHhcCCCCCcceeee-EEEeCCEEEeeeeehHHHH
Confidence 56777633 5667888999999999999988888776 654 3 1222345565543
No 142
>PRK09929 hypothetical protein; Provisional
Probab=20.92 E-value=1.1e+02 Score=22.06 Aligned_cols=23 Identities=4% Similarity=0.020 Sum_probs=18.8
Q ss_pred CceEEEEcccCHHHHHHHHHHHH
Q 047239 147 SGKVVITGAKAREQIYAAFNNIY 169 (180)
Q Consensus 147 sGkivitGaks~~~~~~a~~~i~ 169 (180)
-|-|.++|..++.|+++++..-.
T Consensus 40 iGtVSvs~~~s~~d~~~~La~KA 62 (91)
T PRK09929 40 IGTISTSNEMSTADAKEDLIKKA 62 (91)
T ss_pred eEEEEEcCCCCHHHHHHHHHHHH
Confidence 38888999999999999886543
No 143
>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=20.90 E-value=1.8e+02 Score=22.36 Aligned_cols=48 Identities=13% Similarity=0.079 Sum_probs=30.1
Q ss_pred EEcCCccceEEEEecCCcEEEEEecCCcEEE--EccCCHHHHHHHHHHHH
Q 047239 31 EYNPSRFSAVTMRIKEPKTTALIFSSGKIVC--TGAKSESQAKLAARKYA 78 (180)
Q Consensus 31 ~YePe~fpgli~r~~~P~~t~lIf~SGKivi--tGaks~~~~~~a~~~i~ 78 (180)
.++|..--+-.|....--.+++|..+|+++- +|.-+.++....++.+.
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 3455432222334333336899999999985 47778888777665543
No 144
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=20.73 E-value=94 Score=23.45 Aligned_cols=26 Identities=15% Similarity=0.381 Sum_probs=22.1
Q ss_pred CHHHHHHHHHHHHHHHHHcCCCCccc
Q 047239 66 SESQAKLAARKYARIVQKIGFPVQFK 91 (180)
Q Consensus 66 s~~~~~~a~~~i~~~L~~~g~~~~~~ 91 (180)
+-+.+.+|++++.+.|+.+|+.+.+.
T Consensus 21 Tg~~L~~av~~l~~~L~~~Giev~l~ 46 (120)
T PF10865_consen 21 TGETLREAVKELAPVLAPLGIEVRLE 46 (120)
T ss_pred HHHHHHHHHHHHHHHHHhCCcEEEEE
Confidence 46788899999999999999977654
No 145
>PF13549 ATP-grasp_5: ATP-grasp domain; PDB: 1WR2_A.
Probab=20.47 E-value=2e+02 Score=23.71 Aligned_cols=62 Identities=16% Similarity=0.156 Sum_probs=36.8
Q ss_pred ccceEEEEecCCcEEEEEecCCcEEEEccCCHHHHHHHHHHHHHHHHHcCCCCcccceeeeeeEE
Q 047239 36 RFSAVTMRIKEPKTTALIFSSGKIVCTGAKSESQAKLAARKYARIVQKIGFPVQFKDFKIQNIVG 100 (180)
Q Consensus 36 ~fpgli~r~~~P~~t~lIf~SGKivitGaks~~~~~~a~~~i~~~L~~~g~~~~~~~~~i~NIva 100 (180)
-|| +.+|+..|+..= --.-| -|..|-+|.++++.|++++...+++..-......+-||-|+.
T Consensus 46 g~P-vvlKi~sp~i~H-Ksd~G-gV~L~l~~~~~v~~a~~~l~~~~~~~~p~~~~~gvlVq~m~~ 107 (222)
T PF13549_consen 46 GFP-VVLKIVSPDIAH-KSDVG-GVRLNLNSPEEVREAFERLRERVAAHHPGARIDGVLVQEMAP 107 (222)
T ss_dssp -SS-EEEEEE-TT----HHHHT--EEEEE-SHHHHHHHHHHHHHHHHHH-TT----EEEEEE---
T ss_pred CCC-EEEEEecCCCCc-CCCCC-cEEECCCCHHHHHHHHHHHHHHHHHhCCCCccceEEEEEccc
Confidence 356 788888886431 11123 456778899999999999999999876666667777887765
No 146
>TIGR03653 arch_L6P archaeal ribosomal protein L6P. Members of this protein family are the archaeal ribosomal protein L6P. The top-scoring proteins not selected by this model are eukaryotic cytosolic ribosomal protein L9. Bacterial ribosomal protein L6 scores lower and is described by a distinct model.
Probab=20.42 E-value=4.4e+02 Score=20.86 Aligned_cols=37 Identities=19% Similarity=0.171 Sum_probs=24.2
Q ss_pred eEEEEEecCceEEEEcccCHHHHHHHHHHHHHHHhhcccc
Q 047239 139 NVTMLIFLSGKVVITGAKAREQIYAAFNNIYPVLNVYVTY 178 (180)
Q Consensus 139 ~~t~lIF~sGkivitGaks~~~~~~a~~~i~~~L~~~~~~ 178 (180)
.+++.+=.+ .|++.|. +.+.+-+....|.- +.+.|..
T Consensus 120 gI~v~~~~~-~I~i~G~-DKq~Vgq~AA~Ir~-~~~~~~~ 156 (170)
T TIGR03653 120 GVKVKVKGE-EVIVTGI-DKEDVGQTAANIEQ-ATRIKGR 156 (170)
T ss_pred CeEEEecCC-EEEEEeC-CHHHHHHHHHHHHH-hhcccCC
Confidence 455555445 7999999 56788877777766 3444443
Done!