Query psy17242
Match_columns 172
No_of_seqs 149 out of 507
Neff 6.0
Searched_HMMs 46136
Date Fri Aug 16 16:57:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17242.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17242hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 cd04516 TBP_eukaryotes eukaryo 100.0 6.1E-65 1.3E-69 407.5 21.3 153 19-171 1-153 (174)
2 COG2101 SPT15 TATA-box binding 100.0 3.2E-65 7E-70 405.0 18.2 156 16-171 4-161 (185)
3 PLN00062 TATA-box-binding prot 100.0 1.8E-64 3.9E-69 406.4 21.3 153 19-171 1-153 (179)
4 KOG3302|consensus 100.0 1.3E-63 2.7E-68 401.4 20.1 157 15-171 18-174 (200)
5 cd04518 TBP_archaea archaeal T 100.0 7.9E-62 1.7E-66 389.6 21.1 152 19-171 1-153 (174)
6 cd00652 TBP_TLF TATA box bindi 100.0 1E-61 2.2E-66 388.8 21.2 153 19-171 1-154 (174)
7 PRK00394 transcription factor; 100.0 1E-61 2.2E-66 390.4 21.0 152 20-171 1-154 (179)
8 cd04517 TLF TBP-like factors ( 100.0 3.4E-61 7.4E-66 385.9 21.2 153 18-171 1-154 (174)
9 PF00352 TBP: Transcription fa 100.0 5.6E-32 1.2E-36 193.8 12.0 84 19-102 3-86 (86)
10 COG2101 SPT15 TATA-box binding 100.0 1.5E-29 3.3E-34 201.3 11.5 88 16-103 95-184 (185)
11 PRK00394 transcription factor; 100.0 2.2E-29 4.8E-34 202.8 12.4 87 17-103 89-177 (179)
12 cd04518 TBP_archaea archaeal T 100.0 5.8E-29 1.3E-33 199.5 11.9 86 16-101 89-174 (174)
13 cd00652 TBP_TLF TATA box bindi 99.9 3.8E-27 8.3E-32 188.9 11.7 85 16-100 89-174 (174)
14 PLN00062 TATA-box-binding prot 99.9 1.8E-26 3.8E-31 186.0 11.3 85 18-102 90-175 (179)
15 cd04516 TBP_eukaryotes eukaryo 99.9 4.3E-26 9.3E-31 183.0 11.5 84 17-100 89-173 (174)
16 cd04517 TLF TBP-like factors ( 99.9 1.2E-25 2.7E-30 180.2 11.4 84 17-100 90-174 (174)
17 PF00352 TBP: Transcription fa 99.9 7.9E-26 1.7E-30 161.9 8.2 64 107-171 1-64 (86)
18 KOG3302|consensus 99.9 3.1E-21 6.7E-26 156.0 10.1 86 17-102 110-196 (200)
19 PF11858 DUF3378: Domain of un 97.2 0.00045 9.7E-09 49.2 3.5 35 52-86 26-60 (81)
20 COG4871 Uncharacterized protei 96.9 0.0082 1.8E-07 48.2 8.6 72 27-101 38-109 (193)
21 PF11858 DUF3378: Domain of un 95.8 0.024 5.2E-07 40.3 5.0 30 143-172 26-55 (81)
22 TIGR00716 rnhC ribonuclease HI 95.3 0.038 8.2E-07 47.7 5.5 35 50-84 22-56 (284)
23 PRK00996 ribonuclease HIII; Pr 94.7 0.062 1.4E-06 46.8 5.2 34 51-84 26-59 (304)
24 COG1039 RnhC Ribonuclease HIII 94.5 0.097 2.1E-06 45.5 6.0 44 53-96 28-71 (297)
25 PRK12475 thiamine/molybdopteri 89.8 1.2 2.6E-05 39.2 6.8 60 33-95 277-337 (338)
26 PRK07688 thiamine/molybdopteri 86.3 2.2 4.7E-05 37.6 6.3 60 33-95 277-338 (339)
27 PRK15468 carboxysome structura 77.1 4.6 0.0001 30.4 4.1 35 69-105 70-105 (111)
28 PLN00410 U5 snRNP protein, DIM 68.7 12 0.00027 29.1 5.0 81 20-100 25-125 (142)
29 cd03065 PDI_b_Calsequestrin_N 64.7 11 0.00024 28.3 3.9 30 66-95 89-119 (120)
30 PTZ00129 40S ribosomal protein 64.0 21 0.00046 28.2 5.5 51 54-104 37-91 (149)
31 PF13575 DUF4135: Domain of un 61.6 8.2 0.00018 34.0 3.1 54 78-132 124-177 (370)
32 PRK09381 trxA thioredoxin; Pro 60.4 13 0.00028 26.1 3.5 28 67-94 78-107 (109)
33 cd01644 RT_pepA17 RT_pepA17: R 59.5 12 0.00026 30.7 3.6 29 78-106 145-173 (213)
34 KOG4180|consensus 54.2 23 0.00049 31.9 4.5 73 67-155 254-334 (395)
35 TIGR00090 iojap_ybeB iojap-lik 52.1 31 0.00068 24.9 4.4 34 71-105 28-61 (99)
36 PRK11509 hydrogenase-1 operon 51.0 32 0.00069 26.5 4.4 60 35-95 56-124 (132)
37 PHA02278 thioredoxin-like prot 50.9 23 0.00049 25.6 3.5 24 66-89 74-99 (103)
38 cd02965 HyaE HyaE family; HyaE 49.5 12 0.00026 28.0 1.8 41 126-168 50-96 (111)
39 KOG0910|consensus 49.3 29 0.00062 27.5 4.0 31 66-96 117-149 (150)
40 PRK10996 thioredoxin 2; Provis 48.3 27 0.00058 26.3 3.7 28 67-94 109-138 (139)
41 cd02963 TRX_DnaJ TRX domain, D 47.9 22 0.00047 25.5 3.0 27 67-93 82-110 (111)
42 TIGR02064 dsrA sulfite reducta 45.8 59 0.0013 29.5 6.0 78 51-133 72-179 (402)
43 COG2221 DsrA Dissimilatory sul 44.0 18 0.0004 32.0 2.4 64 67-135 61-128 (317)
44 COG4978 Transcriptional regula 43.6 67 0.0015 25.2 5.3 44 63-106 79-123 (153)
45 PF02410 Oligomerisation: Olig 43.4 49 0.0011 23.8 4.2 29 73-102 30-59 (100)
46 PF03332 PMM: Eukaryotic phosp 43.1 36 0.00078 28.6 3.9 95 69-165 48-160 (220)
47 TIGR03632 bact_S11 30S ribosom 42.8 87 0.0019 23.0 5.6 51 54-104 9-62 (108)
48 PF00085 Thioredoxin: Thioredo 42.4 56 0.0012 21.9 4.3 28 66-93 73-102 (103)
49 CHL00041 rps11 ribosomal prote 42.3 89 0.0019 23.4 5.6 51 54-104 22-75 (116)
50 PRK11538 ribosome-associated p 41.5 62 0.0013 23.8 4.6 33 71-104 33-65 (105)
51 PRK10719 eutA reactivating fac 41.4 1.5E+02 0.0033 27.7 8.0 83 72-171 87-172 (475)
52 cd02988 Phd_like_VIAF Phosduci 39.7 21 0.00045 28.9 2.0 37 66-102 154-192 (192)
53 cd07996 WGR_MMR_like WGR domai 39.7 78 0.0017 21.0 4.6 33 72-104 40-72 (74)
54 cd07049 BMC_EutL_repeat1 ethan 39.6 48 0.001 24.7 3.7 28 73-101 71-100 (103)
55 PTZ00397 macrophage migration 39.3 86 0.0019 22.8 5.1 31 76-106 63-94 (116)
56 PF11775 CobT_C: Cobalamin bio 38.4 52 0.0011 27.6 4.1 48 63-113 12-59 (219)
57 cd02948 TRX_NDPK TRX domain, T 38.0 48 0.001 23.2 3.4 26 67-93 74-101 (102)
58 TIGR03628 arch_S11P archaeal r 37.3 1.7E+02 0.0037 22.0 6.4 51 54-104 11-65 (114)
59 PRK05309 30S ribosomal protein 37.2 1.1E+02 0.0024 23.3 5.5 51 54-104 26-79 (128)
60 cd02393 PNPase_KH Polynucleoti 37.1 74 0.0016 20.7 4.0 28 65-93 32-59 (61)
61 PF13192 Thioredoxin_3: Thiore 36.8 42 0.00091 22.5 2.8 22 70-91 53-75 (76)
62 PRK12475 thiamine/molybdopteri 36.2 70 0.0015 28.1 4.8 44 124-171 278-322 (338)
63 cd02949 TRX_NTR TRX domain, no 35.4 52 0.0011 22.6 3.3 24 67-90 70-95 (97)
64 PRK09607 rps11p 30S ribosomal 34.7 1.8E+02 0.0039 22.5 6.3 51 54-104 18-72 (132)
65 cd02950 TxlA TRX-like protein 34.5 75 0.0016 24.0 4.2 29 67-95 79-110 (142)
66 KOG3946|consensus 34.4 61 0.0013 28.7 4.0 61 86-153 70-139 (338)
67 COG0533 QRI7 Metal-dependent p 34.3 1E+02 0.0022 27.6 5.5 46 53-98 125-171 (342)
68 TIGR01068 thioredoxin thioredo 34.1 62 0.0013 21.5 3.4 28 66-93 70-99 (101)
69 PF12971 NAGLU_N: Alpha-N-acet 33.5 72 0.0016 22.4 3.7 26 71-97 39-64 (86)
70 TIGR00411 redox_disulf_1 small 32.7 78 0.0017 20.5 3.6 22 73-94 60-81 (82)
71 PF06200 tify: tify domain; I 32.5 1.2E+02 0.0025 18.3 4.0 27 65-91 5-31 (36)
72 PF13549 ATP-grasp_5: ATP-gras 31.5 1E+02 0.0022 25.5 4.9 62 53-117 46-107 (222)
73 PF00403 HMA: Heavy-metal-asso 31.5 42 0.0009 21.2 2.0 31 70-104 32-62 (62)
74 PRK13011 formyltetrahydrofolat 31.4 1.8E+02 0.0039 25.0 6.5 82 76-166 10-99 (286)
75 cd04792 LanM-like LanM-like pr 31.4 38 0.00082 32.8 2.6 52 80-132 166-217 (825)
76 PF03135 CagE_TrbE_VirB: CagE, 31.0 66 0.0014 25.6 3.6 38 67-105 144-181 (205)
77 COG4274 Uncharacterized conser 30.7 67 0.0014 23.9 3.2 59 76-134 17-77 (104)
78 PF02838 Glyco_hydro_20b: Glyc 30.6 1.3E+02 0.0028 21.6 4.8 38 64-102 75-112 (124)
79 cd02985 TRX_CDSP32 TRX family, 30.5 94 0.002 21.8 4.0 22 67-89 74-97 (103)
80 cd00148 PROF Profilin binds ac 30.3 1.9E+02 0.0042 21.5 5.8 40 64-103 84-127 (127)
81 PF06277 EutA: Ethanolamine ut 30.2 2.3E+02 0.0051 26.5 7.3 83 71-171 83-169 (473)
82 PF05005 Ocnus: Janus/Ocnus fa 29.9 1E+02 0.0022 23.0 4.2 58 44-106 4-62 (108)
83 cd07046 BMC_PduU-EutS 1,2-prop 29.8 88 0.0019 23.4 3.8 30 73-104 73-103 (110)
84 cd00448 YjgF_YER057c_UK114_fam 29.4 65 0.0014 22.2 2.9 36 69-104 10-51 (107)
85 PF11869 DUF3389: Protein of u 29.4 30 0.00065 24.4 1.1 13 69-81 3-15 (75)
86 COG4547 CobT Cobalamin biosynt 29.2 45 0.00097 31.4 2.5 45 65-112 415-459 (620)
87 cd02956 ybbN ybbN protein fami 29.0 71 0.0015 21.5 3.0 25 66-90 68-94 (96)
88 PF10979 DUF2786: Protein of u 28.9 84 0.0018 19.5 3.0 22 83-104 20-41 (43)
89 cd03005 PDI_a_ERp46 PDIa famil 28.8 75 0.0016 21.5 3.1 22 67-88 76-99 (102)
90 cd07047 BMC_PduB_repeat1 1,2-p 28.5 90 0.002 24.2 3.8 28 73-100 78-105 (134)
91 PF14359 DUF4406: Domain of un 28.4 48 0.001 23.7 2.1 32 70-105 1-32 (92)
92 cd06150 YjgF_YER057c_UK114_lik 28.3 66 0.0014 22.9 2.8 37 69-105 12-49 (105)
93 cd03715 RT_ZFREV_like RT_ZFREV 27.9 1.1E+02 0.0024 24.3 4.4 27 80-106 166-192 (210)
94 PRK03988 translation initiatio 27.7 1.1E+02 0.0024 23.7 4.1 32 66-98 71-102 (138)
95 PF05362 Lon_C: Lon protease ( 27.7 97 0.0021 25.4 4.0 35 70-105 50-88 (204)
96 PF10865 DUF2703: Domain of un 27.6 46 0.001 25.3 2.0 25 83-107 21-45 (120)
97 cd01645 RT_Rtv RT_Rtv: Reverse 27.4 92 0.002 25.0 3.8 38 67-106 159-196 (213)
98 smart00392 PROF Profilin. Bind 27.4 2.6E+02 0.0057 20.8 6.2 40 64-103 86-129 (129)
99 PF14657 Integrase_AP2: AP2-li 26.9 98 0.0021 18.9 3.1 25 76-100 19-43 (46)
100 COG0678 AHP1 Peroxiredoxin [Po 26.9 37 0.0008 27.2 1.4 54 50-104 5-74 (165)
101 PF09967 DUF2201: VWA-like dom 26.1 2.1E+02 0.0045 21.3 5.3 34 67-106 2-35 (126)
102 KOG4749|consensus 26.0 8 0.00017 34.5 -2.8 37 135-171 173-218 (375)
103 TIGR00311 aIF-2beta translatio 25.9 1.2E+02 0.0026 23.3 4.0 26 72-97 71-96 (133)
104 smart00115 CASc Caspase, inter 25.7 54 0.0012 27.1 2.3 41 63-105 6-46 (241)
105 PF01960 ArgJ: ArgJ family; I 25.3 87 0.0019 28.5 3.6 22 75-96 268-289 (388)
106 KOG3384|consensus 25.1 45 0.00098 26.3 1.5 26 141-167 101-129 (154)
107 PF10686 DUF2493: Protein of u 25.0 1.1E+02 0.0024 20.8 3.4 27 75-101 5-31 (71)
108 PF05406 WGR: WGR domain; Int 24.9 2E+02 0.0043 19.6 4.7 34 72-105 43-76 (81)
109 PF12864 DUF3822: Protein of u 24.9 2.7E+02 0.0059 23.0 6.3 55 55-109 174-228 (253)
110 KOG2360|consensus 24.9 1E+02 0.0023 28.2 4.0 81 49-133 277-359 (413)
111 TIGR01651 CobT cobaltochelatas 24.8 1E+02 0.0022 29.7 4.1 45 65-112 394-438 (600)
112 COG4871 Uncharacterized protei 24.6 2.5E+02 0.0054 22.9 5.7 52 115-170 36-87 (193)
113 PF07338 DUF1471: Protein of u 24.6 1.4E+02 0.0031 19.3 3.7 27 74-103 6-33 (56)
114 PF00078 RVT_1: Reverse transc 24.4 1.5E+02 0.0033 22.5 4.5 28 80-107 168-195 (214)
115 PRK15405 ethanolamine utilizat 24.3 1.2E+02 0.0026 25.5 4.0 31 72-103 79-112 (217)
116 PF13382 Adenine_deam_C: Adeni 24.3 88 0.0019 25.0 3.1 27 69-96 61-87 (171)
117 PLN02788 phenylalanine-tRNA sy 24.0 3.8E+02 0.0082 24.5 7.4 58 47-132 216-276 (402)
118 COG0799 Uncharacterized homolo 24.0 1.4E+02 0.0031 22.5 4.0 28 76-104 38-65 (115)
119 COG1654 BirA Biotin operon rep 23.9 66 0.0014 22.6 2.1 22 86-107 31-52 (79)
120 cd03007 PDI_a_ERp29_N PDIa fam 23.9 77 0.0017 23.7 2.5 27 66-92 82-113 (116)
121 smart00653 eIF2B_5 domain pres 23.7 1.6E+02 0.0034 21.9 4.2 33 65-97 47-79 (110)
122 PRK06027 purU formyltetrahydro 23.3 2.9E+02 0.0064 23.6 6.4 82 76-166 9-99 (286)
123 PF11399 DUF3192: Protein of u 23.2 82 0.0018 23.4 2.5 29 54-82 60-97 (102)
124 PTZ00051 thioredoxin; Provisio 23.1 98 0.0021 20.9 2.9 21 67-88 74-96 (98)
125 PF01042 Ribonuc_L-PSP: Endori 22.8 71 0.0015 23.3 2.2 21 84-104 42-62 (121)
126 cd02987 Phd_like_Phd Phosducin 21.9 67 0.0015 25.4 2.0 17 66-82 137-155 (175)
127 PF08002 DUF1697: Protein of u 21.8 1.6E+02 0.0035 22.4 4.1 35 69-105 38-72 (137)
128 COG1364 ArgJ N-acetylglutamate 21.7 83 0.0018 28.8 2.7 22 75-96 284-305 (404)
129 PF03129 HGTP_anticodon: Antic 21.7 1.2E+02 0.0025 20.6 3.0 22 84-105 11-32 (94)
130 PF11111 CENP-M: Centromere pr 21.6 2.9E+02 0.0062 22.5 5.6 37 9-45 52-88 (176)
131 PRK15415 propanediol utilizati 21.5 1.5E+02 0.0032 25.7 4.1 29 73-101 119-147 (266)
132 PRK15124 2'-5' RNA ligase; Pro 21.4 2.1E+02 0.0045 22.3 4.7 57 57-117 72-129 (176)
133 PF06815 RVT_connect: Reverse 21.3 3.5E+02 0.0076 20.1 6.6 32 48-81 2-36 (102)
134 COG0100 RpsK Ribosomal protein 21.2 3E+02 0.0066 21.2 5.4 52 53-104 26-80 (129)
135 PF11525 CopK: Copper resistan 21.1 80 0.0017 22.0 1.9 20 59-79 10-29 (73)
136 cd00032 CASc Caspase, interleu 20.7 60 0.0013 26.8 1.6 41 64-105 8-48 (243)
137 KOG2317|consensus 20.5 2.8E+02 0.0061 21.6 5.1 31 72-104 43-73 (138)
138 PF03799 FtsQ: Cell division p 20.3 2.5E+02 0.0054 19.4 4.6 40 60-102 65-104 (117)
139 PF05132 RNA_pol_Rpc4: RNA pol 20.3 79 0.0017 23.8 2.0 14 66-79 70-83 (131)
140 TIGR00741 yfiA ribosomal subun 20.2 2E+02 0.0043 19.7 4.0 35 65-100 49-83 (95)
No 1
>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=6.1e-65 Score=407.53 Aligned_cols=153 Identities=90% Similarity=1.357 Sum_probs=150.5
Q ss_pred CcEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHH
Q psy17242 19 VPQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARII 98 (172)
Q Consensus 19 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L 98 (172)
+++|+|||||++++|+|||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+|+++.|+++++++|
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 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCccccceEEEEEEEeecCccccHHHHHHHcCCCcccccCCCceeEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 99 QKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 99 ~~~g~~v~~~~f~v~NIvat~~~~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviTg 171 (172)
+++|+++++.+|+|||||||+||+|+||||+||..|.++++||||+||||+||+.+||+++|||+||||||||
T Consensus 81 ~~~g~~~~~~~~~v~Nivat~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitG 153 (174)
T cd04516 81 QKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTG 153 (174)
T ss_pred HHcCCCCCCCceEEEEEEEEEECCCcccHHHHHHhChhccEeCCccCceEEEEecCCcEEEEEeCCCEEEEEe
Confidence 9999999999999999999999999999999999888889999999999999999999999999999999998
No 2
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=100.00 E-value=3.2e-65 Score=405.03 Aligned_cols=156 Identities=46% Similarity=0.790 Sum_probs=151.4
Q ss_pred CCCCcEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHH
Q psy17242 16 GGSVPQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 16 ~~~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~ 95 (172)
.+.+++|+|||||.+|+++|||++++..+++++|||++|||++||+++||+++|||+|||+|||||||.|+++.|+++++
T Consensus 4 ~~~~i~IeNIVAS~~L~~elDL~~~~~~l~~aeYnP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGaKs~ed~~~av~~~~ 83 (185)
T COG2101 4 SEPTITIENIVASVDLGQELDLEEVALDLPGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGAKSVEDVHRAVKKLA 83 (185)
T ss_pred CCCccEEEEEEEEechhhhccHHHHHhhCCCCccCHhHCCeeEEEecCCcceEEEEecCcEEEeccCcHHHHHHHHHHHH
Confidence 46789999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcCCCCcc-ccceEEEEEEEeecCccccHHHHHHHcC-CCcccccCCCceeEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 96 RIIQKLGFPAKF-LDFKIQNMVGSCDVKFPIRLEGLVLTHG-QFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 96 ~~L~~~g~~v~~-~~f~v~NIvat~~~~f~I~Le~la~~~~-~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviTg 171 (172)
++|++.|+++.+ .+++|||||||+|+++++||+++|..++ ++++|||||||||+||+.+|++++|||+|||+||||
T Consensus 84 ~~L~~~g~~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTG 161 (185)
T COG2101 84 KKLKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITG 161 (185)
T ss_pred HHHHhcCcCcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEec
Confidence 999999999886 5899999999999999999999999987 469999999999999999999999999999999999
No 3
>PLN00062 TATA-box-binding protein; Provisional
Probab=100.00 E-value=1.8e-64 Score=406.38 Aligned_cols=153 Identities=88% Similarity=1.334 Sum_probs=150.5
Q ss_pred CcEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHH
Q psy17242 19 VPQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARII 98 (172)
Q Consensus 19 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L 98 (172)
.++|+|||||++++|+|||++||..++|++||||+|||++||+++|+++++||+||||+||||||+|+++.|+++++++|
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 47999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcCCCCccccceEEEEEEEeecCccccHHHHHHHcCCCcccccCCCceeEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 99 QKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 99 ~~~g~~v~~~~f~v~NIvat~~~~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviTg 171 (172)
+++|+++++.+|+|||||||+||+|+|||+.||..|.++++||||+||||+||+.+|++++|||+||||||||
T Consensus 81 ~~lg~~~~~~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitG 153 (179)
T PLN00062 81 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITG 153 (179)
T ss_pred HHcCCCcCCCccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEe
Confidence 9999999999999999999999999999999999888899999999999999999999999999999999998
No 4
>KOG3302|consensus
Probab=100.00 E-value=1.3e-63 Score=401.42 Aligned_cols=157 Identities=82% Similarity=1.248 Sum_probs=155.2
Q ss_pred CCCCCcEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHH
Q psy17242 15 MGGSVPQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKY 94 (172)
Q Consensus 15 ~~~~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~ 94 (172)
++++++.++||||+++++|+|||.+||...+|++|||++|++++||+++|++|++||+||||+||||+|+++++.|++++
T Consensus 18 ~~~i~~~l~nivc~~~~~c~ldLk~ial~~~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~ 97 (200)
T KOG3302|consen 18 DSGLDPTLQNIVCTVNLNCKLDLKEIALHARNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKY 97 (200)
T ss_pred ccccceEEEeEEEEEeccceecHHHHhhhccccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHH
Confidence 36899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCCCCccccceEEEEEEEeecCccccHHHHHHHcCCCcccccCCCceeEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 95 ARIIQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 95 ~~~L~~~g~~v~~~~f~v~NIvat~~~~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviTg 171 (172)
+|+||++||++++.||++||||||||++|+|+||+++..|+.+++||||+||||+|||.+|+++++||+||||++||
T Consensus 98 aRilqkLgf~~~f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~Vvvtg 174 (200)
T KOG3302|consen 98 ARILQKLGFPVKFRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTG 174 (200)
T ss_pred HHHHHHcCCCceehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999998
No 5
>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=7.9e-62 Score=389.56 Aligned_cols=152 Identities=43% Similarity=0.759 Sum_probs=147.7
Q ss_pred CcEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHH
Q psy17242 19 VPQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARII 98 (172)
Q Consensus 19 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L 98 (172)
.++|+|||||++++|+|||++||..++|++|||++|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
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-cccceEEEEEEEeecCccccHHHHHHHcCCCcccccCCCceeEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 99 QKLGFPAK-FLDFKIQNMVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 99 ~~~g~~v~-~~~f~v~NIvat~~~~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviTg 171 (172)
+++|++.. ..+|+|||||||+|++++|||+.||..++ +++||||+||||+||+.+|++++|||+||||||||
T Consensus 81 ~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~la~~~~-~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitG 153 (174)
T cd04518 81 KDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIGLP-NAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITG 153 (174)
T ss_pred HhcCCCccCCCceEEEEEEEEEEcCCccCHHHHHhhCC-CCccCcccCceEEEEecCCcEEEEEeCCCEEEEEe
Confidence 99999865 47899999999999999999999999887 69999999999999999999999999999999999
No 6
>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=1e-61 Score=388.80 Aligned_cols=153 Identities=76% Similarity=1.204 Sum_probs=149.8
Q ss_pred CcEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHH
Q psy17242 19 VPQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARII 98 (172)
Q Consensus 19 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L 98 (172)
.++|+||||+++++|+|||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+|+++.|+++++++|
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-ccccceEEEEEEEeecCccccHHHHHHHcCCCcccccCCCceeEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 99 QKLGFPA-KFLDFKIQNMVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 99 ~~~g~~v-~~~~f~v~NIvat~~~~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviTg 171 (172)
+++|++. ++.+|+|||||||+||+|+|||+.||..++++++||||+||||+||+.+|+++++||+||||+|||
T Consensus 81 ~~~g~~~~~~~~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitG 154 (174)
T cd00652 81 QKLGFPVEKFPEFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITG 154 (174)
T ss_pred HHcCCCccccCceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEe
Confidence 9999987 789999999999999999999999999998789999999999999999999999999999999998
No 7
>PRK00394 transcription factor; Reviewed
Probab=100.00 E-value=1e-61 Score=390.41 Aligned_cols=152 Identities=42% Similarity=0.728 Sum_probs=147.3
Q ss_pred cEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHH
Q psy17242 20 PQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQ 99 (172)
Q Consensus 20 ~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~ 99 (172)
++|+|||||++++++|||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+|+++.|+++++++|+
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 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HcCCCCc-cccceEEEEEEEeecCccccHHHHHHHc-CCCcccccCCCceeEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 100 KLGFPAK-FLDFKIQNMVGSCDVKFPIRLEGLVLTH-GQFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 100 ~~g~~v~-~~~f~v~NIvat~~~~f~I~Le~la~~~-~~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviTg 171 (172)
++|+++. ..+|+|||||||+|++++|||+++|..+ .++++||||+||||+||+.+|++++|||+||||||||
T Consensus 81 ~~g~~~~~~~~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitG 154 (179)
T PRK00394 81 ELGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITG 154 (179)
T ss_pred HcCCCccCCCceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEe
Confidence 9999886 6899999999999999999999999886 3569999999999999999999999999999999999
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=3.4e-61 Score=385.86 Aligned_cols=153 Identities=48% Similarity=0.850 Sum_probs=149.5
Q ss_pred CCcEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHH
Q psy17242 18 SVPQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARI 97 (172)
Q Consensus 18 ~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~ 97 (172)
++++|+||||+++++|+|||+++|..++|++||| +|||++||+++|+++++||+||||+||||||+|+++.|+++++++
T Consensus 1 ~~~~i~Nvvas~~l~~~idL~~la~~l~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~ 79 (174)
T cd04517 1 LDILIVNVVCQFSLRCHIDLRKLALAGRNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARL 79 (174)
T ss_pred CccEEEEEEEEEEcCCcccHHHHHhhCCCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHH
Confidence 4689999999999999999999999999999999 999999999999999999999999999999999999999999999
Q ss_pred HHHcCCCC-ccccceEEEEEEEeecCccccHHHHHHHcCCCcccccCCCceeEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 98 IQKLGFPA-KFLDFKIQNMVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 98 L~~~g~~v-~~~~f~v~NIvat~~~~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviTg 171 (172)
|+++|++. ++.+|+|||||||+|++|+|||++||..+.++++||||+||||+||+.+|+++++||+||||+|||
T Consensus 80 l~~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitG 154 (174)
T cd04517 80 LQKLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTG 154 (174)
T ss_pred HHHcCCCcccCCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEe
Confidence 99999986 789999999999999999999999999888889999999999999999999999999999999999
No 9
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=99.98 E-value=5.6e-32 Score=193.75 Aligned_cols=84 Identities=48% Similarity=0.749 Sum_probs=80.4
Q ss_pred CcEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHH
Q psy17242 19 VPQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARII 98 (172)
Q Consensus 19 ~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L 98 (172)
+++|+||||+++++++|||++||..++|++||||+|||++||+++|+++++||+||||+||||+|+++++.|+++++++|
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 58999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHcC
Q psy17242 99 QKLG 102 (172)
Q Consensus 99 ~~~g 102 (172)
+++|
T Consensus 83 ~~~~ 86 (86)
T PF00352_consen 83 QKLG 86 (86)
T ss_dssp HHTT
T ss_pred HHcC
Confidence 9986
No 10
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=99.96 E-value=1.5e-29 Score=201.31 Aligned_cols=88 Identities=41% Similarity=0.660 Sum_probs=83.5
Q ss_pred CCCCcEEEEEEEEEEcCCccChHHHHhhCCC--cEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHH
Q psy17242 16 GGSVPQLQNIVSTVNLGCKLDLKKIALHARN--AEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARK 93 (172)
Q Consensus 16 ~~~~~~I~NvVas~~l~~~ldL~~la~~~~n--~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k 93 (172)
....++|||||||++|+..+||+.+|..+++ ++|||||||||+||+.+|++.+|||+|||+||||||++||++.|+++
T Consensus 95 ~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK~~ed~~~Av~~ 174 (185)
T COG2101 95 FEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAKSEEDAEQAVEK 174 (185)
T ss_pred CCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCCCHHHHHHHHHH
Confidence 4567999999999999999999999987655 99999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHcCC
Q psy17242 94 YARIIQKLGF 103 (172)
Q Consensus 94 ~~~~L~~~g~ 103 (172)
+.+.|+++|.
T Consensus 175 i~~~L~elgl 184 (185)
T COG2101 175 IQSRLEELGL 184 (185)
T ss_pred HHHHHHHhcc
Confidence 9999999984
No 11
>PRK00394 transcription factor; Reviewed
Probab=99.96 E-value=2.2e-29 Score=202.77 Aligned_cols=87 Identities=40% Similarity=0.710 Sum_probs=84.3
Q ss_pred CCCcEEEEEEEEEEcCCccChHHHHhhC--CCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHH
Q psy17242 17 GSVPQLQNIVSTVNLGCKLDLKKIALHA--RNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKY 94 (172)
Q Consensus 17 ~~~~~I~NvVas~~l~~~ldL~~la~~~--~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~ 94 (172)
..+++|+|||||++++++|||+++|..+ +|++||||+|||++||+++|+++++||+||||+||||||+|+++.|++++
T Consensus 89 ~~~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i 168 (179)
T PRK00394 89 EPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDAEKAVEKI 168 (179)
T ss_pred CCceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHH
Confidence 5689999999999999999999999877 89999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHcCC
Q psy17242 95 ARIIQKLGF 103 (172)
Q Consensus 95 ~~~L~~~g~ 103 (172)
+++|+++|+
T Consensus 169 ~~~l~~~g~ 177 (179)
T PRK00394 169 LEKLEELGL 177 (179)
T ss_pred HHHHHHcCC
Confidence 999999985
No 12
>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=5.8e-29 Score=199.54 Aligned_cols=86 Identities=43% Similarity=0.688 Sum_probs=82.6
Q ss_pred CCCCcEEEEEEEEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHH
Q psy17242 16 GGSVPQLQNIVSTVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 16 ~~~~~~I~NvVas~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~ 95 (172)
....++|+|||||++++++|||+.+|...+|++||||+|||++||+.+|+++++||+||||+||||||+|+++.|+++++
T Consensus 89 ~~~~~~i~NIVas~~l~~~i~L~~la~~~~~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~~~~a~~~i~ 168 (174)
T cd04518 89 EKPEIKVQNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDAKRAVEKLL 168 (174)
T ss_pred CCCceEEEEEEEEEEcCCccCHHHHHhhCCCCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHH
Confidence 35679999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHc
Q psy17242 96 RIIQKL 101 (172)
Q Consensus 96 ~~L~~~ 101 (172)
++|+++
T Consensus 169 ~~l~~~ 174 (174)
T cd04518 169 SRLKEL 174 (174)
T ss_pred HHHhhC
Confidence 999874
No 13
>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=99.95 E-value=3.8e-27 Score=188.89 Aligned_cols=85 Identities=41% Similarity=0.601 Sum_probs=81.1
Q ss_pred CCCCcEEEEEEEEEEcCCccChHHHHhhCC-CcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHH
Q psy17242 16 GGSVPQLQNIVSTVNLGCKLDLKKIALHAR-NAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKY 94 (172)
Q Consensus 16 ~~~~~~I~NvVas~~l~~~ldL~~la~~~~-n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~ 94 (172)
...+++|+||||+++++++|||++||...+ +++||||+|||++||+.+|++|++||+||||+||||||+++++.|++++
T Consensus 89 ~~~~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~~~~a~~~i 168 (174)
T cd00652 89 KFPEFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSREDIYEAVEKI 168 (174)
T ss_pred ccCceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHH
Confidence 456899999999999999999999999875 9999999999999999999999999999999999999999999999999
Q ss_pred HHHHHH
Q psy17242 95 ARIIQK 100 (172)
Q Consensus 95 ~~~L~~ 100 (172)
+++|++
T Consensus 169 ~~~L~~ 174 (174)
T cd00652 169 YPILKE 174 (174)
T ss_pred HHHHhC
Confidence 999864
No 14
>PLN00062 TATA-box-binding protein; Provisional
Probab=99.94 E-value=1.8e-26 Score=185.96 Aligned_cols=85 Identities=31% Similarity=0.517 Sum_probs=81.9
Q ss_pred CCcEEEEEEEEEEcCCccChHHHHh-hCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHH
Q psy17242 18 SVPQLQNIVSTVNLGCKLDLKKIAL-HARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYAR 96 (172)
Q Consensus 18 ~~~~I~NvVas~~l~~~ldL~~la~-~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~ 96 (172)
.+++|+|||||++++.+|||+.||. +.++++||||+|||++||+.+|+++++||+||||+||||||+++++.|++++++
T Consensus 90 ~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~~ai~~i~p 169 (179)
T PLN00062 90 KDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIYTAFENIYP 169 (179)
T ss_pred CccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHHH
Confidence 5899999999999999999999996 468999999999999999999999999999999999999999999999999999
Q ss_pred HHHHcC
Q psy17242 97 IIQKLG 102 (172)
Q Consensus 97 ~L~~~g 102 (172)
+|.+++
T Consensus 170 ~L~~~~ 175 (179)
T PLN00062 170 VLTEFR 175 (179)
T ss_pred HHHHhc
Confidence 999986
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=99.93 E-value=4.3e-26 Score=182.96 Aligned_cols=84 Identities=33% Similarity=0.489 Sum_probs=80.2
Q ss_pred CCCcEEEEEEEEEEcCCccChHHHHh-hCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHH
Q psy17242 17 GSVPQLQNIVSTVNLGCKLDLKKIAL-HARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 17 ~~~~~I~NvVas~~l~~~ldL~~la~-~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~ 95 (172)
..+++|+||||+++++.+|||+.+|. +.++++||||+||||+||+.+|+++++||+||||+|||+||+||++.|++++.
T Consensus 89 ~~~~~v~Nivat~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~~a~~~i~ 168 (174)
T cd04516 89 FTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEIYQAFENIY 168 (174)
T ss_pred CCceEEEEEEEEEECCCcccHHHHHHhChhccEeCCccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHH
Confidence 46899999999999999999999996 46789999999999999999999999999999999999999999999999999
Q ss_pred HHHHH
Q psy17242 96 RIIQK 100 (172)
Q Consensus 96 ~~L~~ 100 (172)
++|.+
T Consensus 169 p~L~~ 173 (174)
T cd04516 169 PILLQ 173 (174)
T ss_pred HHHhh
Confidence 99875
No 16
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=99.93 E-value=1.2e-25 Score=180.23 Aligned_cols=84 Identities=33% Similarity=0.469 Sum_probs=79.8
Q ss_pred CCCcEEEEEEEEEEcCCccChHHHHhh-CCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHH
Q psy17242 17 GSVPQLQNIVSTVNLGCKLDLKKIALH-ARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 17 ~~~~~I~NvVas~~l~~~ldL~~la~~-~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~ 95 (172)
..+++|+||||+++++++|||+++|.. .++++||||+|||++||+.+|+++++||+||||+|||+||+++++.|+++++
T Consensus 90 ~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i~ 169 (174)
T cd04517 90 FSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKIY 169 (174)
T ss_pred CCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHH
Confidence 468999999999999999999999974 5899999999999999999999999999999999999999999999999999
Q ss_pred HHHHH
Q psy17242 96 RIIQK 100 (172)
Q Consensus 96 ~~L~~ 100 (172)
++|.+
T Consensus 170 pil~~ 174 (174)
T cd04517 170 PIVFE 174 (174)
T ss_pred HHHhC
Confidence 99863
No 17
>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=99.93 E-value=7.9e-26 Score=161.87 Aligned_cols=64 Identities=53% Similarity=0.850 Sum_probs=59.2
Q ss_pred cccceEEEEEEEeecCccccHHHHHHHcCCCcccccCCCceeEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 107 FLDFKIQNMVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 107 ~~~f~v~NIvat~~~~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviTg 171 (172)
|.+|+|+|||||++++++|||++||..+ ++++||||+||||+||+.+|+++++||+||||+|||
T Consensus 1 ~~~~~i~NIva~~~l~~~idL~~la~~~-~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itG 64 (86)
T PF00352_consen 1 FPDFKIVNIVASFDLPFEIDLEELAEEL-ENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITG 64 (86)
T ss_dssp -EEEEEEEEEEEEE-SSEB-HHHHHHHS-TTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEE
T ss_pred CCccEEEEEEEEEECCCccCHHHHHhhc-cCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEe
Confidence 5689999999999999999999999998 569999999999999999999999999999999998
No 18
>KOG3302|consensus
Probab=99.85 E-value=3.1e-21 Score=155.97 Aligned_cols=86 Identities=29% Similarity=0.479 Sum_probs=81.6
Q ss_pred CCCcEEEEEEEEEEcCCccChHHHHh-hCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHH
Q psy17242 17 GSVPQLQNIVSTVNLGCKLDLKKIAL-HARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 17 ~~~~~I~NvVas~~l~~~ldL~~la~-~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~ 95 (172)
-.+++|+||+||+|+..+|+|+.++. +...+.||||+||||+||+.+|+++++||.||||++|||++.++.++|+.+|+
T Consensus 110 f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~~~i~~Ai~~Iy 189 (200)
T KOG3302|consen 110 FRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVREETYEAIENIY 189 (200)
T ss_pred ehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccHHHHHHHHHHHh
Confidence 46899999999999999999999997 56789999999999999999999999999999999999999999999999999
Q ss_pred HHHHHcC
Q psy17242 96 RIIQKLG 102 (172)
Q Consensus 96 ~~L~~~g 102 (172)
.+|.++.
T Consensus 190 Pil~~fr 196 (200)
T KOG3302|consen 190 PILLEFR 196 (200)
T ss_pred HHHHHhh
Confidence 9998873
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=97.17 E-value=0.00045 Score=49.21 Aligned_cols=35 Identities=20% Similarity=0.361 Sum_probs=29.1
Q ss_pred cccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHH
Q psy17242 52 KRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEED 86 (172)
Q Consensus 52 e~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~ 86 (172)
..=|+++++.+.+.||+++|.|||++..|...+.+
T Consensus 26 ~~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~~Ae~~ 60 (81)
T PF11858_consen 26 SKPPYAVFQAKYNGVTITAYKSGKVVFQGKNAEQE 60 (81)
T ss_dssp S--TTEEEEEEETTEEEEEETTSEEEEESTTHHHH
T ss_pred CCCCCEEEEEeCCCeEEEEEeCCeEEEECCCHHHH
Confidence 34489999999999999999999999999954443
No 20
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=96.88 E-value=0.0082 Score=48.24 Aligned_cols=72 Identities=21% Similarity=0.232 Sum_probs=57.3
Q ss_pred EEEEcCCccChHHHHhhCCCcEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHc
Q psy17242 27 STVNLGCKLDLKKIALHARNAEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKL 101 (172)
Q Consensus 27 as~~l~~~ldL~~la~~~~n~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~ 101 (172)
+..+-...=-|.-||..++++.|..++ ..++++.- ..-++||.|||+..|-.|++++|++.+..+.+++++.
T Consensus 38 ~~md~~lg~ilplla~l~P~anY~~kk-~~l~~~kg--erIitiy~sGkVsm~~ikdedEAkeilgel~d~ineA 109 (193)
T COG4871 38 ANMDPPLGGILPLLAPLFPRANYSDKK-NILILQKG--ERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINEA 109 (193)
T ss_pred eecCCCcchhHHHhHhhCCCccccccc-ceEEEeec--cEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHHH
Confidence 333333333466678888999999776 77777754 4677899999999999999999999999999999874
No 21
>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=95.75 E-value=0.024 Score=40.30 Aligned_cols=30 Identities=23% Similarity=0.311 Sum_probs=26.3
Q ss_pred CCCceeEEEEcCCcEEEEEecCcEEEEEeC
Q psy17242 143 ELFPGLIYRMVKPRIVLLIFVSGKVVLTVK 172 (172)
Q Consensus 143 E~fPGliyR~~~~k~~~lIF~SGkvviTg~ 172 (172)
..=||.+|+...+.+++.++.||||++=||
T Consensus 26 ~~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~ 55 (81)
T PF11858_consen 26 SKPPYAVFQAKYNGVTITAYKSGKVVFQGK 55 (81)
T ss_dssp S--TTEEEEEEETTEEEEEETTSEEEEEST
T ss_pred CCCCCEEEEEeCCCeEEEEEeCCeEEEECC
Confidence 344899999999999999999999999886
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=95.26 E-value=0.038 Score=47.71 Aligned_cols=35 Identities=20% Similarity=0.397 Sum_probs=29.8
Q ss_pred cCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCH
Q psy17242 50 NPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSE 84 (172)
Q Consensus 50 ePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~ 84 (172)
.+..=|+.+++.+.+.+|+++|.|||+++.|...+
T Consensus 22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~ae 56 (284)
T TIGR00716 22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNSE 56 (284)
T ss_pred ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCHH
Confidence 44556899999999999999999999999995433
No 23
>PRK00996 ribonuclease HIII; Provisional
Probab=94.66 E-value=0.062 Score=46.77 Aligned_cols=34 Identities=26% Similarity=0.464 Sum_probs=29.1
Q ss_pred CcccceEEEEEcCCcEEEEEecCCeEEEEeeCCH
Q psy17242 51 PKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSE 84 (172)
Q Consensus 51 Pe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~ 84 (172)
+..-|+.+++.+.+.+++++|.|||+++.|...+
T Consensus 26 ~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae 59 (304)
T PRK00996 26 PSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAE 59 (304)
T ss_pred cCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHH
Confidence 3445789999999999999999999999996443
No 24
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=94.52 E-value=0.097 Score=45.49 Aligned_cols=44 Identities=23% Similarity=0.301 Sum_probs=37.4
Q ss_pred ccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHH
Q psy17242 53 RFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYAR 96 (172)
Q Consensus 53 ~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~ 96 (172)
..|+.+++.+.|.+|+++|.|||+++.|-.+++.+++-...+.+
T Consensus 28 ~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~~~~~ 71 (297)
T COG1039 28 NPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLNPIAQ 71 (297)
T ss_pred CCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhhhhhh
Confidence 67899999999999999999999999999877777766664433
No 25
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=89.77 E-value=1.2 Score=39.19 Aligned_cols=60 Identities=12% Similarity=0.337 Sum_probs=43.6
Q ss_pred CccChHHHHhhCCC-cEEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHH
Q psy17242 33 CKLDLKKIALHARN-AEYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 33 ~~ldL~~la~~~~n-~~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~ 95 (172)
..+|+++++..+.. .+++...| .+.++.. .-.+.+|+.|++++.|.+++.+|+.-..++.
T Consensus 277 ~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~--~~~~~~f~~gr~~~~g~~~~~~a~~~~~~~~ 337 (338)
T PRK12475 277 RRLNLEEIKKRLQKIGKVDANPY-LLSFQLD--EYRFVLFTDGRAFIHGTNDIKKAKRLYARYI 337 (338)
T ss_pred CccCHHHHHHHHhhcCEEEeccc-EEEEEEC--CEEEEEEcCCcEEEECCCCHHHHHHHHHHhc
Confidence 68999999876532 23433333 2344544 4789999999999999999999998777653
No 26
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=86.34 E-value=2.2 Score=37.56 Aligned_cols=60 Identities=17% Similarity=0.362 Sum_probs=45.5
Q ss_pred CccChHHHHhhCCCc--EEcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHH
Q psy17242 33 CKLDLKKIALHARNA--EYNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 33 ~~ldL~~la~~~~n~--~YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~ 95 (172)
..+++++++..++.. ++.. +...++++.+.-.+..|++|++++.|++++.+|+.-..++.
T Consensus 277 ~~i~~~~~~~~l~~~~~~~~~---~~~ll~vr~~~~~~~~~~~gr~~i~g~~~~~~a~~~~~~~~ 338 (339)
T PRK07688 277 EEYDLEELAELLRDRGLDVNV---NPYLLSFSLEEKRLVLFKDGRVLVHGTKDISEAKTIYHRYI 338 (339)
T ss_pred CccCHHHHHHHHHhcccccCC---CcEEEEEecCCeEEEEEcCCCEEEECCCCHHHHHHHHHHhc
Confidence 568999998876433 4443 23455666666899999999999999999999988776653
No 27
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=77.06 E-value=4.6 Score=30.37 Aligned_cols=35 Identities=20% Similarity=0.154 Sum_probs=29.7
Q ss_pred EEecCCeEEEEeeCCHHHHHHHHHHHHHHHHH-cCCCC
Q psy17242 69 LIFSSGKMVCTGAKSEEDSRLAARKYARIIQK-LGFPA 105 (172)
Q Consensus 69 lIf~SGKivitGakS~e~a~~a~~k~~~~L~~-~g~~v 105 (172)
+=-=||.+++||- ..+.+.|++.+.+.|++ +||.+
T Consensus 70 ~DRFsGslvitGd--vs~Ve~Al~~V~~~l~~~L~F~~ 105 (111)
T PRK15468 70 LDRFSGALVIYGS--VGAVEEALSQTVSGLGRLLNYTL 105 (111)
T ss_pred eeccceeEEEEcc--HHHHHHHHHHHHHHHHhhcCccc
Confidence 3345899999997 88999999999999998 88864
No 28
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=68.66 E-value=12 Score=29.07 Aligned_cols=81 Identities=16% Similarity=0.193 Sum_probs=45.4
Q ss_pred cEEEEEEEEEEcCCc-c--ChHHHHhhCCC-cE---EcCcccceE--EEEEcCCcEEEEEecCCeEEE---Ee-------
Q psy17242 20 PQLQNIVSTVNLGCK-L--DLKKIALHARN-AE---YNPKRFAAV--IMRIREPRTTALIFSSGKMVC---TG------- 80 (172)
Q Consensus 20 ~~I~NvVas~~l~~~-l--dL~~la~~~~n-~~---YePe~fpgl--i~R~~~Pk~t~lIf~SGKivi---tG------- 80 (172)
+.|..+-|+-.-.|. + -|+++|....+ +. =|=+..+.+ .|.++.+-.++.+|++|++.+ ||
T Consensus 25 lVVvdF~A~WCgpCk~m~p~l~~la~~~~~~~~~~kVDVDe~~dla~~y~I~~~~t~~~ffk~g~~~vd~~tG~~~k~~~ 104 (142)
T PLN00410 25 LVVIRFGHDWDETCMQMDEVLASVAETIKNFAVIYLVDITEVPDFNTMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINW 104 (142)
T ss_pred EEEEEEECCCChhHHHHHHHHHHHHHHcCCceEEEEEECCCCHHHHHHcCccCCCcEEEEEECCeEEEEEeccccccccc
Confidence 444444444333332 2 25677776655 22 233333433 345565667778999999544 55
Q ss_pred -eCCHHHHHHHHHHHHHHHHH
Q psy17242 81 -AKSEEDSRLAARKYARIIQK 100 (172)
Q Consensus 81 -akS~e~a~~a~~k~~~~L~~ 100 (172)
..+.+++...++.++|--++
T Consensus 105 ~~~~k~~l~~~i~~~~~~a~~ 125 (142)
T PLN00410 105 ALKDKQEFIDIVETVYRGARK 125 (142)
T ss_pred ccCCHHHHHHHHHHHHHHHhc
Confidence 45667777777766665433
No 29
>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=64.74 E-value=11 Score=28.31 Aligned_cols=30 Identities=7% Similarity=0.080 Sum_probs=23.2
Q ss_pred EEEEEecCCe-EEEEeeCCHHHHHHHHHHHH
Q psy17242 66 TTALIFSSGK-MVCTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 66 ~t~lIf~SGK-ivitGakS~e~a~~a~~k~~ 95 (172)
-|+.+|.+|+ +-.+|+++.+++...++++.
T Consensus 89 PTl~lfk~G~~v~~~G~~~~~~l~~~l~~~~ 119 (120)
T cd03065 89 DSIYVFKDDEVIEYDGEFAADTLVEFLLDLI 119 (120)
T ss_pred cEEEEEECCEEEEeeCCCCHHHHHHHHHHHh
Confidence 4999999999 44569988888777766553
No 30
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=63.99 E-value=21 Score=28.22 Aligned_cols=51 Identities=18% Similarity=0.288 Sum_probs=38.0
Q ss_pred cceEEEEEcCCcEEEEEe-cCCeEEEEeeC---CHHHHHHHHHHHHHHHHHcCCC
Q psy17242 54 FAAVIMRIREPRTTALIF-SSGKMVCTGAK---SEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 54 fpgli~R~~~Pk~t~lIf-~SGKivitGak---S~e~a~~a~~k~~~~L~~~g~~ 104 (172)
|+--++-+.+....+++| +||.+-..|.+ |.=.|..|++++++.+.++|+.
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 455566666666555555 56999999987 3447889999999999999876
No 31
>PF13575 DUF4135: Domain of unknown function (DUF4135)
Probab=61.60 E-value=8.2 Score=34.02 Aligned_cols=54 Identities=20% Similarity=0.231 Sum_probs=39.6
Q ss_pred EEeeCCHHHHHHHHHHHHHHHHHcCCCCccccceEEEEEEEeecCccccHHHHHH
Q psy17242 78 CTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVL 132 (172)
Q Consensus 78 itGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~v~NIvat~~~~f~I~Le~la~ 132 (172)
-..+.|.++++.-.+++-..|.=+ +-....|+--+||+|+.+.|..||||.|-.
T Consensus 124 ~~~c~~~~ev~~yY~r~G~llal~-y~L~~~DlH~ENIIa~g~~PvlIDlETlf~ 177 (370)
T PF13575_consen 124 HEPCNSEEEVERYYYRLGVLLALL-YLLNGTDLHFENIIASGEYPVLIDLETLFH 177 (370)
T ss_pred CCCCCCHHHHHHHHHHHHHHHHHH-HHhCCCcccccceEEeCCCcEEEehhhhCC
Confidence 345667888887777766554432 222345888999999999999999999864
No 32
>PRK09381 trxA thioredoxin; Provisional
Probab=60.36 E-value=13 Score=26.14 Aligned_cols=28 Identities=25% Similarity=0.304 Sum_probs=22.0
Q ss_pred EEEEecCCeEE--EEeeCCHHHHHHHHHHH
Q psy17242 67 TALIFSSGKMV--CTGAKSEEDSRLAARKY 94 (172)
Q Consensus 67 t~lIf~SGKiv--itGakS~e~a~~a~~k~ 94 (172)
|+.+|.+|+++ .+|..+.++++..++..
T Consensus 78 t~~~~~~G~~~~~~~G~~~~~~l~~~i~~~ 107 (109)
T PRK09381 78 TLLLFKNGEVAATKVGALSKGQLKEFLDAN 107 (109)
T ss_pred EEEEEeCCeEEEEecCCCCHHHHHHHHHHh
Confidence 78889999988 66888888777666554
No 33
>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=59.53 E-value=12 Score=30.67 Aligned_cols=29 Identities=14% Similarity=0.289 Sum_probs=25.8
Q ss_pred EEeeCCHHHHHHHHHHHHHHHHHcCCCCc
Q psy17242 78 CTGAKSEEDSRLAARKYARIIQKLGFPAK 106 (172)
Q Consensus 78 itGakS~e~a~~a~~k~~~~L~~~g~~v~ 106 (172)
+.|++|++++...++++.++|++.|++.+
T Consensus 145 li~~~s~~e~~~~~~~v~~~L~~~Gf~l~ 173 (213)
T cd01644 145 LVSTDTLNEAVNVAKRLIALLKKGGFNLR 173 (213)
T ss_pred eecCCCHHHHHHHHHHHHHHHHhCCccch
Confidence 45788999999999999999999999754
No 34
>KOG4180|consensus
Probab=54.23 E-value=23 Score=31.86 Aligned_cols=73 Identities=23% Similarity=0.304 Sum_probs=49.5
Q ss_pred EEEEecCCeEEEEeeCCH-------HHHHHHHHHHHHHHHHcCCC-CccccceEEEEEEEeecCccccHHHHHHHcCCCc
Q psy17242 67 TALIFSSGKMVCTGAKSE-------EDSRLAARKYARIIQKLGFP-AKFLDFKIQNMVGSCDVKFPIRLEGLVLTHGQFS 138 (172)
Q Consensus 67 t~lIf~SGKivitGakS~-------e~a~~a~~k~~~~L~~~g~~-v~~~~f~v~NIvat~~~~f~I~Le~la~~~~~~~ 138 (172)
.++-=+||-++|||+-|. .-+..|+..+++++...|-. +-+ - .| ..|.++.++.++.
T Consensus 254 ~~KqKssgl~vctgTGstsw~~~iNria~q~v~d~l~~l~~~~~~~vp~---~-Re-----------~ve~i~~~~nq~l 318 (395)
T KOG4180|consen 254 GVKQKSSGLVVCTGTGSTSWTFNINRIAEQAVGDLLMILLSRDNLQVPF---M-RE-----------LVEEISTAYNQHL 318 (395)
T ss_pred cccccCCCeeEecCCCcceEeecccHHHHHHHHHHHHHHHhcCcccchh---h-hh-----------hhHHHHHHhhhcC
Confidence 445678999999998664 45678888888888887643 211 1 11 2366666666778
Q ss_pred ccccCCCceeEEEEcCC
Q psy17242 139 SYEPELFPGLIYRMVKP 155 (172)
Q Consensus 139 ~YEPE~fPGliyR~~~~ 155 (172)
.|+|+ .|-+-|-+.+|
T Consensus 319 lF~PD-~p~l~fSiRep 334 (395)
T KOG4180|consen 319 LFKPD-RPQLAFSIREP 334 (395)
T ss_pred ccCCC-Ccchhhhhhhh
Confidence 99998 56666666555
No 35
>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=52.10 E-value=31 Score=24.94 Aligned_cols=34 Identities=12% Similarity=0.239 Sum_probs=27.0
Q ss_pred ecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCC
Q psy17242 71 FSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPA 105 (172)
Q Consensus 71 f~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v 105 (172)
+..-=|+|||. |..+++..++.+.+.+++.|...
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 33445777766 99999999999999999988643
No 36
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=50.95 E-value=32 Score=26.52 Aligned_cols=60 Identities=12% Similarity=0.075 Sum_probs=36.5
Q ss_pred cChHHHHhhCC-----CcEEcCcccceEE--EEEcCCcEEEEEecCCeEE--EEeeCCHHHHHHHHHHHH
Q psy17242 35 LDLKKIALHAR-----NAEYNPKRFAAVI--MRIREPRTTALIFSSGKMV--CTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 35 ldL~~la~~~~-----n~~YePe~fpgli--~R~~~Pk~t~lIf~SGKiv--itGakS~e~a~~a~~k~~ 95 (172)
+=|++|+..++ -+.-|-+..+.+- ++++. --|+++|+.||++ +.|..+.++...-+++++
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 34677776543 1233333333332 22221 2399999999997 679988888777666554
No 37
>PHA02278 thioredoxin-like protein
Probab=50.89 E-value=23 Score=25.64 Aligned_cols=24 Identities=8% Similarity=0.159 Sum_probs=19.5
Q ss_pred EEEEEecCCeEE--EEeeCCHHHHHH
Q psy17242 66 TTALIFSSGKMV--CTGAKSEEDSRL 89 (172)
Q Consensus 66 ~t~lIf~SGKiv--itGakS~e~a~~ 89 (172)
-|+++|+.|+.+ +.|..+.+++++
T Consensus 74 PT~i~fk~G~~v~~~~G~~~~~~l~~ 99 (103)
T PHA02278 74 PVLIGYKDGQLVKKYEDQVTPMQLQE 99 (103)
T ss_pred cEEEEEECCEEEEEEeCCCCHHHHHh
Confidence 399999999999 889877766543
No 38
>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=49.50 E-value=12 Score=27.97 Aligned_cols=41 Identities=22% Similarity=0.301 Sum_probs=26.9
Q ss_pred cHHHHHHHcCC---CcccccCCCceeE--EEEcC-CcEEEEEecCcEEE
Q psy17242 126 RLEGLVLTHGQ---FSSYEPELFPGLI--YRMVK-PRIVLLIFVSGKVV 168 (172)
Q Consensus 126 ~Le~la~~~~~---~~~YEPE~fPGli--yR~~~-~k~~~lIF~SGkvv 168 (172)
-|++++..+++ ++..+-+..|.+. |++.. | |+++|..||++
T Consensus 50 ~leela~e~~~~v~f~kVdid~~~~la~~f~V~sIP--Tli~fkdGk~v 96 (111)
T cd02965 50 VLPELLKAFPGRFRAAVVGRADEQALAARFGVLRTP--ALLFFRDGRYV 96 (111)
T ss_pred HHHHHHHHCCCcEEEEEEECCCCHHHHHHcCCCcCC--EEEEEECCEEE
Confidence 45566666653 3355666666654 55543 5 88999999986
No 39
>KOG0910|consensus
Probab=49.30 E-value=29 Score=27.51 Aligned_cols=31 Identities=32% Similarity=0.551 Sum_probs=27.5
Q ss_pred EEEEEecCCeEE--EEeeCCHHHHHHHHHHHHH
Q psy17242 66 TTALIFSSGKMV--CTGAKSEEDSRLAARKYAR 96 (172)
Q Consensus 66 ~t~lIf~SGKiv--itGakS~e~a~~a~~k~~~ 96 (172)
-|+++|.+|+-+ +.|+...+.++..++|+.+
T Consensus 117 PtvlvfknGe~~d~~vG~~~~~~l~~~i~k~l~ 149 (150)
T KOG0910|consen 117 PTVLVFKNGEKVDRFVGAVPKEQLRSLIKKFLK 149 (150)
T ss_pred eEEEEEECCEEeeeecccCCHHHHHHHHHHHhc
Confidence 499999999987 8899999999999998864
No 40
>PRK10996 thioredoxin 2; Provisional
Probab=48.29 E-value=27 Score=26.30 Aligned_cols=28 Identities=25% Similarity=0.312 Sum_probs=22.3
Q ss_pred EEEEecCCeEE--EEeeCCHHHHHHHHHHH
Q psy17242 67 TALIFSSGKMV--CTGAKSEEDSRLAARKY 94 (172)
Q Consensus 67 t~lIf~SGKiv--itGakS~e~a~~a~~k~ 94 (172)
++.+|.+|+++ +.|..+.++.+..++++
T Consensus 109 tlii~~~G~~v~~~~G~~~~e~l~~~l~~~ 138 (139)
T PRK10996 109 TIMIFKNGQVVDMLNGAVPKAPFDSWLNEA 138 (139)
T ss_pred EEEEEECCEEEEEEcCCCCHHHHHHHHHHh
Confidence 67899999988 67888888777776654
No 41
>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=47.94 E-value=22 Score=25.54 Aligned_cols=27 Identities=11% Similarity=0.099 Sum_probs=20.3
Q ss_pred EEEEecCCeEEE--EeeCCHHHHHHHHHH
Q psy17242 67 TALIFSSGKMVC--TGAKSEEDSRLAARK 93 (172)
Q Consensus 67 t~lIf~SGKivi--tGakS~e~a~~a~~k 93 (172)
|+.+|..|+++- .|..+.+++...+++
T Consensus 82 t~~i~~~g~~~~~~~G~~~~~~l~~~i~~ 110 (111)
T cd02963 82 AIVGIINGQVTFYHDSSFTKQHVVDFVRK 110 (111)
T ss_pred EEEEEECCEEEEEecCCCCHHHHHHHHhc
Confidence 788999999984 477777776665554
No 42
>TIGR02064 dsrA sulfite reductase, dissimilatory-type alpha subunit. This model describes the alpha subunit of sulfite reductase.
Probab=45.82 E-value=59 Score=29.55 Aligned_cols=78 Identities=13% Similarity=0.158 Sum_probs=45.7
Q ss_pred CcccceE----EEEEcCCc---------------------EEEEEe-cCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCC
Q psy17242 51 PKRFAAV----IMRIREPR---------------------TTALIF-SSGKMVCTGAKSEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 51 Pe~fpgl----i~R~~~Pk---------------------~t~lIf-~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~ 104 (172)
|++||++ .+|+..|. ..+.+- ++|.|++.|. +.|++....+ .|.+.|++
T Consensus 72 ~~~~p~~~~~~tvRv~~P~G~~~tteqLR~LaDiaekYGsG~~~~tgstqdIiL~gv-~~e~le~i~~----eL~~~G~d 146 (402)
T TIGR02064 72 GEKFPGVAEFHTVRVAQPSGKFYSTDYLRQLCDVWEKYGSGLTNFHGQTGDIVFLGT-QTPQLQEIFE----ELTNLGTD 146 (402)
T ss_pred cccCCCcCeEEEEEEecCCCCCCCHHHHHHHHHHHHHhCCCEEEEeccccCEEEcCC-CHHHHHHHHH----HHhhcccC
Confidence 6778776 35777662 133343 3578888888 5666665554 45567877
Q ss_pred CccccceEEEEEEEe---ecCc-cccHHHHHHH
Q psy17242 105 AKFLDFKIQNMVGSC---DVKF-PIRLEGLVLT 133 (172)
Q Consensus 105 v~~~~f~v~NIvat~---~~~f-~I~Le~la~~ 133 (172)
..-..-.+.|++|.. -+++ .+|=..++..
T Consensus 147 lggsG~~vRti~aC~G~~~C~~a~~DT~~l~~~ 179 (402)
T TIGR02064 147 LGGSGSNLRTPESCVGPARCEFACYDTLKACYE 179 (402)
T ss_pred CCCCCCCccceecCCCcccCCCcccccHHHHHH
Confidence 654455688887542 2233 3454455544
No 43
>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]
Probab=43.99 E-value=18 Score=31.95 Aligned_cols=64 Identities=16% Similarity=0.142 Sum_probs=40.6
Q ss_pred EEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCccccceEEEEEEEe---ecCc-cccHHHHHHHcC
Q psy17242 67 TALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFKIQNMVGSC---DVKF-PIRLEGLVLTHG 135 (172)
Q Consensus 67 t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~v~NIvat~---~~~f-~I~Le~la~~~~ 135 (172)
.+.|-+.+.+-+-|- |.+++. ++.+.|++.|+++-...-.++||+|.- .+.+ -+|-..|+....
T Consensus 61 ~i~iT~rqg~ei~~i-~~e~~~----~v~~~L~~iG~~~G~~G~~vr~i~aC~G~~~C~~a~~Dt~~la~~l~ 128 (317)
T COG2221 61 LIHITSRQGLEIPGI-SPEDAD----DVVEELREIGLPVGSTGPAVRAIVACPGPRTCETALYDTTELARRLE 128 (317)
T ss_pred eEEEEecCceEeccC-CHHHHH----HHHHHHHHcCCCCCCcchhhhhhhcCcCcccccccccChHHHHHHHH
Confidence 444555555555553 566655 455666799999888888899998632 1222 467777777543
No 44
>COG4978 Transcriptional regulator, effector-binding domain/component [Transcription / Signal transduction mechanisms]
Probab=43.62 E-value=67 Score=25.23 Aligned_cols=44 Identities=20% Similarity=0.259 Sum_probs=38.6
Q ss_pred CCcEEEEEecCCeEEEEeeC-CHHHHHHHHHHHHHHHHHcCCCCc
Q psy17242 63 EPRTTALIFSSGKMVCTGAK-SEEDSRLAARKYARIIQKLGFPAK 106 (172)
Q Consensus 63 ~Pk~t~lIf~SGKivitGak-S~e~a~~a~~k~~~~L~~~g~~v~ 106 (172)
++......+.+||+.++=-+ |-++...|++++..-+++.|.++.
T Consensus 79 ~~~~~~~~~P~g~~a~~~~~G~~~~~~~~y~rli~~iee~g~~i~ 123 (153)
T COG4978 79 DIDIKIKTLPKGKYACIIHKGSYEEVEQAYKRLIEYIEENGLEII 123 (153)
T ss_pred CCcceeEEccCceEEEEEEEcCcccHHHHHHHHHHHHHHhCCccc
Confidence 46778889999999888777 899999999999999999998754
No 45
>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=43.35 E-value=49 Score=23.79 Aligned_cols=29 Identities=24% Similarity=0.373 Sum_probs=23.0
Q ss_pred CCeEEEEeeCCHHHHHHHHHHHHHHH-HHcC
Q psy17242 73 SGKMVCTGAKSEEDSRLAARKYARII-QKLG 102 (172)
Q Consensus 73 SGKivitGakS~e~a~~a~~k~~~~L-~~~g 102 (172)
.==|++||. |..+++..++.+.+.+ ++.|
T Consensus 30 dy~II~T~~-S~rh~~aia~~v~~~~~k~~~ 59 (100)
T PF02410_consen 30 DYFIIATGR-SERHVRAIADEVEKALKKEYG 59 (100)
T ss_dssp SEEEEEEES-SHHHHHHHHHHHHHHH-HHTT
T ss_pred CEEEEEEcC-CHHHHHHHHHHHHHHHHHHcC
Confidence 334677765 9999999999999999 5555
No 46
>PF03332 PMM: Eukaryotic phosphomannomutase; InterPro: IPR005002 This enzyme (5.4.2.8 from EC) is involved in the synthesis of the GDP-mannose and dolichol-phosphate-mannose required for a number of critical mannosyl transfer reactions.; GO: 0004615 phosphomannomutase activity, 0019307 mannose biosynthetic process, 0005737 cytoplasm; PDB: 2I55_B 2I54_C 3F9R_A 2FUE_A 2FUC_A 2AMY_A 2Q4R_A.
Probab=43.10 E-value=36 Score=28.57 Aligned_cols=95 Identities=20% Similarity=0.334 Sum_probs=51.5
Q ss_pred EEecCCeEEEE----eeCCHHHHHHHHHHHHHHHHHcCCCCc---cccceEEEEEEEeecCccccHHHHHH------HcC
Q psy17242 69 LIFSSGKMVCT----GAKSEEDSRLAARKYARIIQKLGFPAK---FLDFKIQNMVGSCDVKFPIRLEGLVL------THG 135 (172)
Q Consensus 69 lIf~SGKivit----GakS~e~a~~a~~k~~~~L~~~g~~v~---~~~f~v~NIvat~~~~f~I~Le~la~------~~~ 135 (172)
..|+.|+.... -.-++|..++.++-+.+.+.+++++++ +.+|+ .-++--+-+|..=.+|+=.. .|.
T Consensus 48 ~~y~~~~~~~~~~~~~~lgee~~~~~in~~l~~~~~l~lp~krGtfIE~R-~gmIn~SpiGr~a~~eer~~f~~~D~~~~ 126 (220)
T PF03332_consen 48 VAYKNGELIWSQSIAEFLGEEKLQKLINFCLRYISDLDLPVKRGTFIEFR-GGMINFSPIGRNASQEERDEFDEYDKKHK 126 (220)
T ss_dssp EEEETTEEEEE--HHHHHHHHHHHHHHHHHHHHHHT---S---S-SEEEE-SSEEEE-SS-TTS-HHHHHHHHHHHHHHT
T ss_pred eEEECCCchhhHhHHHHcCHHHHHHHHHHHHHHHHhCCCCccCCCceeec-CCcEEECcccCcCCHHHHHhhhhcChhhh
Confidence 35566655442 333567788888999999999998765 34444 22333344555555443211 111
Q ss_pred ---CCcccccCCCce--eEEEEcCCcEEEEEecCc
Q psy17242 136 ---QFSSYEPELFPG--LIYRMVKPRIVLLIFVSG 165 (172)
Q Consensus 136 ---~~~~YEPE~fPG--liyR~~~~k~~~lIF~SG 165 (172)
..+.-=.+.||. |.|++-+. +.+-||+.|
T Consensus 127 iR~~~v~~L~~~f~d~~L~~siGGq-iSiDvfp~G 160 (220)
T PF03332_consen 127 IREKLVEALKKEFPDFGLTFSIGGQ-ISIDVFPKG 160 (220)
T ss_dssp HHHHHHHHHHHHTCCCSEEEEEETT-TEEEEEETT
T ss_pred HHHHHHHHHHHHCCCCceEEecCCc-eEEccccCC
Confidence 011111357885 99999876 789999887
No 47
>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=42.81 E-value=87 Score=23.04 Aligned_cols=51 Identities=27% Similarity=0.471 Sum_probs=35.3
Q ss_pred cceEEEEEcCCcEEEEEecC-CeEEEEeeCC--HHHHHHHHHHHHHHHHHcCCC
Q psy17242 54 FAAVIMRIREPRTTALIFSS-GKMVCTGAKS--EEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 54 fpgli~R~~~Pk~t~lIf~S-GKivitGakS--~e~a~~a~~k~~~~L~~~g~~ 104 (172)
|+-.++-+.+++-..+.|.| |.+-.-|++. .-.+..+++++.+.++++|++
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 34456666776655556644 7666666642 556888899999999999875
No 48
>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=42.44 E-value=56 Score=21.90 Aligned_cols=28 Identities=29% Similarity=0.389 Sum_probs=22.7
Q ss_pred EEEEEecCCeEE--EEeeCCHHHHHHHHHH
Q psy17242 66 TTALIFSSGKMV--CTGAKSEEDSRLAARK 93 (172)
Q Consensus 66 ~t~lIf~SGKiv--itGakS~e~a~~a~~k 93 (172)
.++.+|.+|+.+ +.|..+.+++...+++
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 7888888888877664
No 49
>CHL00041 rps11 ribosomal protein S11
Probab=42.34 E-value=89 Score=23.35 Aligned_cols=51 Identities=22% Similarity=0.347 Sum_probs=35.3
Q ss_pred cceEEEEEcCCcEEEEEe-cCCeEEEEeeC--CHHHHHHHHHHHHHHHHHcCCC
Q psy17242 54 FAAVIMRIREPRTTALIF-SSGKMVCTGAK--SEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 54 fpgli~R~~~Pk~t~lIf-~SGKivitGak--S~e~a~~a~~k~~~~L~~~g~~ 104 (172)
|+-.++-+.+++..++.| ++|.+-.-|++ +...+..+++++.+.++++|++
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 444555566655555555 44777777775 3667888999999999999875
No 50
>PRK11538 ribosome-associated protein; Provisional
Probab=41.52 E-value=62 Score=23.83 Aligned_cols=33 Identities=18% Similarity=0.293 Sum_probs=26.3
Q ss_pred ecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCC
Q psy17242 71 FSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 71 f~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~ 104 (172)
+...=|++||. |..+++..++.+.+.+++.|..
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 34556777776 8889999999999999988764
No 51
>PRK10719 eutA reactivating factor for ethanolamine ammonia lyase; Provisional
Probab=41.43 E-value=1.5e+02 Score=27.70 Aligned_cols=83 Identities=19% Similarity=0.239 Sum_probs=50.3
Q ss_pred cCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCccccceEEE-EEEEeecCccccHHHHHHHcC-CCcccccCCCcee-
Q psy17242 72 SSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFKIQN-MVGSCDVKFPIRLEGLVLTHG-QFSSYEPELFPGL- 148 (172)
Q Consensus 72 ~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~v~N-Ivat~~~~f~I~Le~la~~~~-~~~~YEPE~fPGl- 148 (172)
.+|=.++||.. ...+.+.+.++++|..+ .+ +||++.+ ++|.+...+. ..+.+..|.-.|+
T Consensus 87 e~~ahIITg~~------~~~~Nl~~~v~~~~~~~-------gdfVVA~AG~----~le~iva~~ASg~avLseEke~gVa 149 (475)
T PRK10719 87 DSGAVIITGET------ARKENAREVVMALSGSA-------GDFVVATAGP----DLESIIAGKGAGAQTLSEERNTRVL 149 (475)
T ss_pred cccEEEEEech------hHHHHHHHHHHHhcccc-------cceeeeccCc----cHHHhhhHHHhhHHHhhhhccCceE
Confidence 45666777763 33456666666666543 33 3476654 4555532221 1122233777785
Q ss_pred EEEEcCCcEEEEEecCcEEEEEe
Q psy17242 149 IYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 149 iyR~~~~k~~~lIF~SGkvviTg 171 (172)
..-+-+-...+.||..|+++-|+
T Consensus 150 ~IDIGgGTT~iaVf~~G~l~~T~ 172 (475)
T PRK10719 150 NIDIGGGTANYALFDAGKVIDTA 172 (475)
T ss_pred EEEeCCCceEEEEEECCEEEEEE
Confidence 55667778899999999999875
No 52
>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=39.73 E-value=21 Score=28.86 Aligned_cols=37 Identities=16% Similarity=0.326 Sum_probs=23.5
Q ss_pred EEEEEecCCeEE--EEeeCCHHHHHHHHHHHHHHHHHcC
Q psy17242 66 TTALIFSSGKMV--CTGAKSEEDSRLAARKYARIIQKLG 102 (172)
Q Consensus 66 ~t~lIf~SGKiv--itGakS~e~a~~a~~k~~~~L~~~g 102 (172)
-|+++|.+|+++ +.|+.+...-+.....+-..|.+.|
T Consensus 154 PTlliyk~G~~v~~ivG~~~~gg~~~~~~~lE~~L~~~g 192 (192)
T cd02988 154 PTILVYRNGDIVKQFIGLLEFGGMNTTMEDLEWLLVQVG 192 (192)
T ss_pred CEEEEEECCEEEEEEeCchhhCCCCCCHHHHHHHHHhcC
Confidence 399999999998 7777544322444445555555443
No 53
>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=39.71 E-value=78 Score=21.03 Aligned_cols=33 Identities=30% Similarity=0.301 Sum_probs=26.8
Q ss_pred cCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCC
Q psy17242 72 SSGKMVCTGAKSEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 72 ~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~ 104 (172)
+.|........|.++|..+++++.+.-.+-||.
T Consensus 40 ~~Gq~~~~~~~s~~~A~~~~~k~~~~K~~~GY~ 72 (74)
T cd07996 40 TKGQSRTKTFDSEEEALKAAEKLIREKLKRGYR 72 (74)
T ss_pred CCCceEEEECCCHHHHHHHHHHHHHHHHhcCCC
Confidence 456677777889999999999998887777874
No 54
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=39.57 E-value=48 Score=24.68 Aligned_cols=28 Identities=18% Similarity=0.313 Sum_probs=23.7
Q ss_pred CCeEE--EEeeCCHHHHHHHHHHHHHHHHHc
Q psy17242 73 SGKMV--CTGAKSEEDSRLAARKYARIIQKL 101 (172)
Q Consensus 73 SGKiv--itGakS~e~a~~a~~k~~~~L~~~ 101 (172)
||.++ ++|. ++.+++.|++...+.|++.
T Consensus 71 sG~vi~ii~G~-dvsdV~sal~~~l~~l~~~ 100 (103)
T cd07049 71 AGEVIGILAGP-SPAEVRSGLNAAIDFIENE 100 (103)
T ss_pred CccEEEEEeCC-CHHHHHHHHHHHHHHHhcc
Confidence 77777 7776 8999999999999988764
No 55
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=39.27 E-value=86 Score=22.77 Aligned_cols=31 Identities=16% Similarity=0.263 Sum_probs=25.2
Q ss_pred EEEEeeCCHHHHHHHHHHHHHHHHH-cCCCCc
Q psy17242 76 MVCTGAKSEEDSRLAARKYARIIQK-LGFPAK 106 (172)
Q Consensus 76 ivitGakS~e~a~~a~~k~~~~L~~-~g~~v~ 106 (172)
|.+.|.++.|+-++-.+.+.+.|++ +|++.+
T Consensus 63 i~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~ 94 (116)
T PTZ00397 63 VTSIGGISRSNNSSIAAAITKILASHLKVKSE 94 (116)
T ss_pred EEEecCCCHHHHHHHHHHHHHHHHHHhCcCcc
Confidence 4455788999999999999999987 788754
No 56
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=38.37 E-value=52 Score=27.64 Aligned_cols=48 Identities=31% Similarity=0.423 Sum_probs=38.7
Q ss_pred CCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCccccceEE
Q psy17242 63 EPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFKIQ 113 (172)
Q Consensus 63 ~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~v~ 113 (172)
+.-+++||-.||.|-- +..+-|..++.-+++.|.++|++++...|+-.
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 5568999999999863 45677778899999999999999876666643
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=37.99 E-value=48 Score=23.23 Aligned_cols=26 Identities=23% Similarity=0.339 Sum_probs=19.6
Q ss_pred EEEEecCCeEE--EEeeCCHHHHHHHHHH
Q psy17242 67 TALIFSSGKMV--CTGAKSEEDSRLAARK 93 (172)
Q Consensus 67 t~lIf~SGKiv--itGakS~e~a~~a~~k 93 (172)
|+.+|++|+.+ +.|+ +.++.+.++++
T Consensus 74 t~~~~~~g~~~~~~~G~-~~~~~~~~i~~ 101 (102)
T cd02948 74 TFLFYKNGELVAVIRGA-NAPLLNKTITE 101 (102)
T ss_pred EEEEEECCEEEEEEecC-ChHHHHHHHhh
Confidence 89999999986 7776 66666665543
No 58
>TIGR03628 arch_S11P archaeal ribosomal protein S11P. This model describes exclusively the archaeal ribosomal protein S11P. It excludes homologous ribosomal proteins S14 from eukaryotes and S11 from bacteria.
Probab=37.27 E-value=1.7e+02 Score=22.01 Aligned_cols=51 Identities=24% Similarity=0.199 Sum_probs=36.9
Q ss_pred cceEEEEEcCCcE--EEEEecCCeEEEEeeC--CHHHHHHHHHHHHHHHHHcCCC
Q psy17242 54 FAAVIMRIREPRT--TALIFSSGKMVCTGAK--SEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 54 fpgli~R~~~Pk~--t~lIf~SGKivitGak--S~e~a~~a~~k~~~~L~~~g~~ 104 (172)
|+--++-+.|.+. ++.-.++|...-.|++ +.=.|..|++++.+...++|++
T Consensus 11 ~NNTiitvTD~~G~~~~~~~S~G~~g~kg~kk~TpyAAq~aa~~~~~~~~~~Gi~ 65 (114)
T TIGR03628 11 FNNTIITITDITGAETIARSSGGMVVKADRDESSPYAAMQAAGRAAEKAKERGIT 65 (114)
T ss_pred CCCeEEEEEcCCCCEEEEEecCcceEeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 4556677777765 4555566666777774 3456889999999999999976
No 59
>PRK05309 30S ribosomal protein S11; Validated
Probab=37.15 E-value=1.1e+02 Score=23.26 Aligned_cols=51 Identities=20% Similarity=0.377 Sum_probs=34.8
Q ss_pred cceEEEEEcCCcEEEEEecC-CeEEEEeeC--CHHHHHHHHHHHHHHHHHcCCC
Q psy17242 54 FAAVIMRIREPRTTALIFSS-GKMVCTGAK--SEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 54 fpgli~R~~~Pk~t~lIf~S-GKivitGak--S~e~a~~a~~k~~~~L~~~g~~ 104 (172)
|+-.++-+.++...++.|.| |.+-.-|++ +...+..+++++.+.+.++|++
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 44455556666555555554 777666665 3556888899999999999875
No 60
>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=37.05 E-value=74 Score=20.67 Aligned_cols=28 Identities=14% Similarity=0.138 Sum_probs=19.8
Q ss_pred cEEEEEecCCeEEEEeeCCHHHHHHHHHH
Q psy17242 65 RTTALIFSSGKMVCTGAKSEEDSRLAARK 93 (172)
Q Consensus 65 k~t~lIf~SGKivitGakS~e~a~~a~~k 93 (172)
.+++.|=.+|.+.++|. +.+..+.|.+.
T Consensus 32 g~~I~i~~~g~v~I~G~-~~~~v~~A~~~ 59 (61)
T cd02393 32 GVKIDIEDDGTVYIAAS-DKEAAEKAKKM 59 (61)
T ss_pred CCEEEeCCCCEEEEEeC-CHHHHHHHHHH
Confidence 45666777899999996 55666666544
No 61
>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=36.78 E-value=42 Score=22.46 Aligned_cols=22 Identities=27% Similarity=0.413 Sum_probs=16.2
Q ss_pred EecCCeEEEEe-eCCHHHHHHHH
Q psy17242 70 IFSSGKMVCTG-AKSEEDSRLAA 91 (172)
Q Consensus 70 If~SGKivitG-akS~e~a~~a~ 91 (172)
++-+|+++.+| ..|.++++..+
T Consensus 53 lvIng~~~~~G~~p~~~el~~~l 75 (76)
T PF13192_consen 53 LVINGKVVFVGRVPSKEELKELL 75 (76)
T ss_dssp EEETTEEEEESS--HHHHHHHHH
T ss_pred EEECCEEEEEecCCCHHHHHHHh
Confidence 35589999999 88888887765
No 62
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=36.17 E-value=70 Score=28.09 Aligned_cols=44 Identities=14% Similarity=0.337 Sum_probs=26.8
Q ss_pred cccHHHHHHHcCCCcccccCCCce-eEEEEcCCcEEEEEecCcEEEEEe
Q psy17242 124 PIRLEGLVLTHGQFSSYEPELFPG-LIYRMVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 124 ~I~Le~la~~~~~~~~YEPE~fPG-liyR~~~~k~~~lIF~SGkvviTg 171 (172)
.+++++++..+.....++-. |. |.++..+ -.+.+|..|+++|-|
T Consensus 278 ~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~~--~~~~~f~~gr~~~~g 322 (338)
T PRK12475 278 RLNLEEIKKRLQKIGKVDAN--PYLLSFQLDE--YRFVLFTDGRAFIHG 322 (338)
T ss_pred ccCHHHHHHHHhhcCEEEec--ccEEEEEECC--EEEEEEcCCcEEEEC
Confidence 45566665554322222221 33 5666655 478899999999977
No 63
>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=35.37 E-value=52 Score=22.63 Aligned_cols=24 Identities=25% Similarity=0.371 Sum_probs=19.5
Q ss_pred EEEEecCCeEE--EEeeCCHHHHHHH
Q psy17242 67 TALIFSSGKMV--CTGAKSEEDSRLA 90 (172)
Q Consensus 67 t~lIf~SGKiv--itGakS~e~a~~a 90 (172)
++.+|..|+++ +.|..+.++....
T Consensus 70 t~~i~~~g~~v~~~~g~~~~~~~~~~ 95 (97)
T cd02949 70 TVQFFKDKELVKEISGVKMKSEYREF 95 (97)
T ss_pred EEEEEECCeEEEEEeCCccHHHHHHh
Confidence 78899999999 7888888776554
No 64
>PRK09607 rps11p 30S ribosomal protein S11P; Reviewed
Probab=34.73 E-value=1.8e+02 Score=22.48 Aligned_cols=51 Identities=24% Similarity=0.228 Sum_probs=35.7
Q ss_pred cceEEEEEcCCcE-EEEEe-cCCeEEEEeeC--CHHHHHHHHHHHHHHHHHcCCC
Q psy17242 54 FAAVIMRIREPRT-TALIF-SSGKMVCTGAK--SEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 54 fpgli~R~~~Pk~-t~lIf-~SGKivitGak--S~e~a~~a~~k~~~~L~~~g~~ 104 (172)
|+--++-+.|.+. .++.| ++|...-.|++ +.=.|..|++++.+.+.++|++
T Consensus 18 ~NNTivtvTD~~G~~~~~~~S~G~~g~kg~kK~TpyAAq~aae~~~~~~~~~Gi~ 72 (132)
T PRK09607 18 FNNTIITITDLTGAETIAKSSGGMVVKADRDESSPYAAMQAAEKAAEDAKEKGIT 72 (132)
T ss_pred cCCeEEEEEcCCCCEEEEEecCcceeeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 4555667777766 24444 45666666663 3457899999999999999976
No 65
>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=34.54 E-value=75 Score=24.00 Aligned_cols=29 Identities=7% Similarity=0.072 Sum_probs=21.7
Q ss_pred EEEEe-cCCeEE--EEeeCCHHHHHHHHHHHH
Q psy17242 67 TALIF-SSGKMV--CTGAKSEEDSRLAARKYA 95 (172)
Q Consensus 67 t~lIf-~SGKiv--itGakS~e~a~~a~~k~~ 95 (172)
|+.+| .+|+++ +.|....++++..+++++
T Consensus 79 t~v~~~~~G~~v~~~~G~~~~~~l~~~l~~l~ 110 (142)
T cd02950 79 HFVFLDREGNEEGQSIGLQPKQVLAQNLDALV 110 (142)
T ss_pred EEEEECCCCCEEEEEeCCCCHHHHHHHHHHHH
Confidence 67777 589998 789888777766666555
No 66
>KOG3946|consensus
Probab=34.41 E-value=61 Score=28.68 Aligned_cols=61 Identities=20% Similarity=0.304 Sum_probs=42.2
Q ss_pred HHHHHHHHHHHHHHHcCCCCccc---c------ceEEEEEEEeecCccccHHHHHHHcCCCcccccCCCceeEEEEc
Q psy17242 86 DSRLAARKYARIIQKLGFPAKFL---D------FKIQNMVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLIYRMV 153 (172)
Q Consensus 86 ~a~~a~~k~~~~L~~~g~~v~~~---~------f~v~NIvat~~~~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~ 153 (172)
..+++-+-+...|+++|..++.. + ..+.||+||.|-.-+ ..+---|-||--.|||..+++.
T Consensus 70 g~~~vr~~i~~~l~~l~w~ve~~~f~~~tp~g~~~f~nii~tl~~~A~-------r~lVlachydsk~~p~~~~vga 139 (338)
T KOG3946|consen 70 GSRQVRRFIIQHLRNLGWAVETDAFTDNTPLGTRNFNNLIATLDPNAS-------RYLVLACHYDSKIFPGGMFVGA 139 (338)
T ss_pred ccHHHHHHHHHHHHhcCceeeeccccccCcceeeeeeeEEEecCCCcc-------hheeeecccccccCCCcceEee
Confidence 34666677888899999765422 1 238999999984432 2222348899999999998763
No 67
>COG0533 QRI7 Metal-dependent proteases with possible chaperone activity [Posttranslational modification, protein turnover, chaperones]
Probab=34.32 E-value=1e+02 Score=27.65 Aligned_cols=46 Identities=20% Similarity=0.309 Sum_probs=41.3
Q ss_pred ccceEEEEEcCCcEEEEEecC-CeEEEEeeCCHHHHHHHHHHHHHHH
Q psy17242 53 RFAAVIMRIREPRTTALIFSS-GKMVCTGAKSEEDSRLAARKYARII 98 (172)
Q Consensus 53 ~fpgli~R~~~Pk~t~lIf~S-GKivitGakS~e~a~~a~~k~~~~L 98 (172)
.||.+.+-..--.+.+.-+++ |++-+-|...-+.+=+|++|++|.|
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 899999999988899999999 9999999977777789999999764
No 68
>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=34.06 E-value=62 Score=21.53 Aligned_cols=28 Identities=32% Similarity=0.432 Sum_probs=19.6
Q ss_pred EEEEEecCCeEE--EEeeCCHHHHHHHHHH
Q psy17242 66 TTALIFSSGKMV--CTGAKSEEDSRLAARK 93 (172)
Q Consensus 66 ~t~lIf~SGKiv--itGakS~e~a~~a~~k 93 (172)
.++.+|.+|+.+ +.|..+.+++...+++
T Consensus 70 P~~~~~~~g~~~~~~~g~~~~~~l~~~l~~ 99 (101)
T TIGR01068 70 PTLLLFKNGKEVDRSVGALPKAALKQLINK 99 (101)
T ss_pred CEEEEEeCCcEeeeecCCCCHHHHHHHHHh
Confidence 367888999875 5678777766665543
No 69
>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=33.55 E-value=72 Score=22.35 Aligned_cols=26 Identities=23% Similarity=0.244 Sum_probs=18.6
Q ss_pred ecCCeEEEEeeCCHHHHHHHHHHHHHH
Q psy17242 71 FSSGKMVCTGAKSEEDSRLAARKYARI 97 (172)
Q Consensus 71 f~SGKivitGakS~e~a~~a~~k~~~~ 97 (172)
-.+|||+|+|. |.-.+..|++..++.
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 37899999999 666777777776654
No 70
>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=32.72 E-value=78 Score=20.54 Aligned_cols=22 Identities=27% Similarity=0.342 Sum_probs=18.0
Q ss_pred CCeEEEEeeCCHHHHHHHHHHH
Q psy17242 73 SGKMVCTGAKSEEDSRLAARKY 94 (172)
Q Consensus 73 SGKivitGakS~e~a~~a~~k~ 94 (172)
.|+..+.|..+.++.+..+++.
T Consensus 60 ~g~~~~~G~~~~~~l~~~l~~~ 81 (82)
T TIGR00411 60 NGDVEFIGAPTKEELVEAIKKR 81 (82)
T ss_pred CCEEEEecCCCHHHHHHHHHhh
Confidence 8888999998998887776653
No 71
>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=32.53 E-value=1.2e+02 Score=18.30 Aligned_cols=27 Identities=11% Similarity=0.180 Sum_probs=20.7
Q ss_pred cEEEEEecCCeEEEEeeCCHHHHHHHH
Q psy17242 65 RTTALIFSSGKMVCTGAKSEEDSRLAA 91 (172)
Q Consensus 65 k~t~lIf~SGKivitGakS~e~a~~a~ 91 (172)
...++||-.|++.+.=.=+.|.++..+
T Consensus 5 ~~qLTIfY~G~V~Vfd~v~~~Ka~~im 31 (36)
T PF06200_consen 5 TAQLTIFYGGQVCVFDDVPPDKAQEIM 31 (36)
T ss_pred CCcEEEEECCEEEEeCCCCHHHHHHHH
Confidence 457889999999998766777666544
No 72
>PF13549 ATP-grasp_5: ATP-grasp domain; PDB: 1WR2_A.
Probab=31.47 E-value=1e+02 Score=25.53 Aligned_cols=62 Identities=21% Similarity=0.204 Sum_probs=36.8
Q ss_pred ccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCccccceEEEEEE
Q psy17242 53 RFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFKIQNMVG 117 (172)
Q Consensus 53 ~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~v~NIva 117 (172)
-|| +++|+..|+..=+ -.-| -|..|-+|.++++.|++++...+++..-......+-||-++.
T Consensus 46 g~P-vvlKi~sp~i~HK-sd~G-gV~L~l~~~~~v~~a~~~l~~~~~~~~p~~~~~gvlVq~m~~ 107 (222)
T PF13549_consen 46 GFP-VVLKIVSPDIAHK-SDVG-GVRLNLNSPEEVREAFERLRERVAAHHPGARIDGVLVQEMAP 107 (222)
T ss_dssp -SS-EEEEEE-TT---H-HHHT--EEEEE-SHHHHHHHHHHHHHHHHHH-TT----EEEEEE---
T ss_pred CCC-EEEEEecCCCCcC-CCCC-cEEECCCCHHHHHHHHHHHHHHHHHhCCCCccceEEEEEccc
Confidence 366 7888887764311 1113 457788999999999999999999876555666777888765
No 73
>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=31.46 E-value=42 Score=21.22 Aligned_cols=31 Identities=16% Similarity=0.210 Sum_probs=20.4
Q ss_pred EecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCC
Q psy17242 70 IFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 70 If~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~ 104 (172)
=+.+|++.+++..+. .-.+++.+.|+++||+
T Consensus 32 d~~~~~v~v~~~~~~----~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 32 DLETKTVTVTYDPDK----TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp ETTTTEEEEEESTTT----SCHHHHHHHHHHTTSE
T ss_pred ECCCCEEEEEEecCC----CCHHHHHHHHHHhCcC
Confidence 466788889887544 1225577777778763
No 74
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=31.45 E-value=1.8e+02 Score=25.01 Aligned_cols=82 Identities=12% Similarity=0.058 Sum_probs=47.0
Q ss_pred EEEEeeCCHHHHHHHHHHHHHHHHHcCCCCccccce------EEEEEEEeecCccccHHHHHHHcCCCcccccCCCceeE
Q psy17242 76 MVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFK------IQNMVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLI 149 (172)
Q Consensus 76 ivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~------v~NIvat~~~~f~I~Le~la~~~~~~~~YEPE~fPGli 149 (172)
+.+.|..+.- -+.++.+.|.+.|..+...+-. .-.+.+.++++-..+++.|...+.. .-.|+ ++.
T Consensus 10 itv~G~DrpG----IVa~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~p~~~~~~~L~~~L~~---l~~~l--~l~ 80 (286)
T PRK13011 10 LTLSCPSAAG----IVAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSEEGLDEDALRAGFAP---IAARF--GMQ 80 (286)
T ss_pred EEEEeCCCCC----HHHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecCCCCCHHHHHHHHHH---HHHHh--CcE
Confidence 4555664443 3556777788888765432221 2246677777777778777654432 11122 333
Q ss_pred EEE--cCCcEEEEEecCcE
Q psy17242 150 YRM--VKPRIVLLIFVSGK 166 (172)
Q Consensus 150 yR~--~~~k~~~lIF~SGk 166 (172)
.++ ..++.++.||.||.
T Consensus 81 i~i~~~~~~~ri~vl~Sg~ 99 (286)
T PRK13011 81 WELHDPAARPKVLIMVSKF 99 (286)
T ss_pred EEEeecccCceEEEEEcCC
Confidence 333 34567889999984
No 75
>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=31.38 E-value=38 Score=32.82 Aligned_cols=52 Identities=19% Similarity=0.263 Sum_probs=38.7
Q ss_pred eeCCHHHHHHHHHHHHHHHHHcCCCCccccceEEEEEEEeecCccccHHHHHH
Q psy17242 80 GAKSEEDSRLAARKYARIIQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVL 132 (172)
Q Consensus 80 GakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~v~NIvat~~~~f~I~Le~la~ 132 (172)
-+.|.+++++-.+++-..|.=+ +-....|+--+||+|..+.|.-||||.|..
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 3567888887777766554432 223356888999999999999999999853
No 76
>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=31.03 E-value=66 Score=25.62 Aligned_cols=38 Identities=18% Similarity=0.219 Sum_probs=29.6
Q ss_pred EEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCC
Q psy17242 67 TALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPA 105 (172)
Q Consensus 67 t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v 105 (172)
...=+.+..|++. ++|.++++..++++...|+..|+.+
T Consensus 144 ~~~G~~~~~i~v~-~~~~~~l~~~~~~v~~~l~~~G~~~ 181 (205)
T PF03135_consen 144 VSFGYYHFTIVVF-ADDPEELDDKVAEVSSALNNLGFVA 181 (205)
T ss_pred eeeeeeEEEEEEE-cCCHHHHHHHHHHHHHHHHHCCCEE
Confidence 3344555556666 5599999999999999999999864
No 77
>COG4274 Uncharacterized conserved protein [Function unknown]
Probab=30.73 E-value=67 Score=23.94 Aligned_cols=59 Identities=14% Similarity=0.103 Sum_probs=44.7
Q ss_pred EEEEeeCCHHHHHHHHHHHHHHHHHcCCCCcc--ccceEEEEEEEeecCccccHHHHHHHc
Q psy17242 76 MVCTGAKSEEDSRLAARKYARIIQKLGFPAKF--LDFKIQNMVGSCDVKFPIRLEGLVLTH 134 (172)
Q Consensus 76 ivitGakS~e~a~~a~~k~~~~L~~~g~~v~~--~~f~v~NIvat~~~~f~I~Le~la~~~ 134 (172)
..=.|+|+..+.-+=.+.+.+.|++.|.+++. --+-.-.+|+.+..+-+..+-.++..+
T Consensus 17 ~Td~Gaktlke~p~R~~av~~~les~G~k~~~~y~T~GeYD~V~i~EapDda~~~~~~l~l 77 (104)
T COG4274 17 FTDQGAKTLKETPKRAAAVRALLESMGGKVKEQYWTLGEYDVVAIVEAPDDAVATRFSLAL 77 (104)
T ss_pred ccHhHHHHHhhCHHHHHHHHHHHHHcCcEEEEEEEeeccccEEEEEecCCHHHHHHHHHHH
Confidence 34468888888877788888899999988663 235566777888888888888877654
No 78
>PF02838 Glyco_hydro_20b: Glycosyl hydrolase family 20, domain 2; InterPro: IPR015882 Glycoside hydrolase family 20 GH20 from CAZY comprises enzymes with several known activities; beta-hexosaminidase (3.2.1.52 from EC); lacto-N-biosidase (3.2.1.140 from EC). Carbonyl oxygen of the C-2 acetamido group of the substrate acts as the catalytic nucleophile/base in this family of enzymes. In the brain and other tissues, beta-hexosaminidase A degrades GM2 gangliosides; specifically, the enzyme hydrolyses terminal non-reducing N-acetyl-D-hexosamine residues in N-acetyl-beta-D-hexosaminides. There are 3 forms of beta-hexosaminidase: hexosaminidase A is a trimer, with one alpha, one beta-A and one beta-B chain; hexosaminidase B is a tetramer of two beta-A and two beta-B chains; and hexosaminidase S is a homodimer of alpha chains. The two beta chains are derived from the cleavage of a precursor. Mutations in the beta-chain lead to Sandhoff disease, a lysosomal storage disorder characterised by accumulation of GM2 ganglioside []. This entry represents the alpha and beta subunit of beta-N-acetylhexosaminidase. It contains a similar fold but lacks the catalytic centre.; GO: 0004563 beta-N-acetylhexosaminidase activity, 0005975 carbohydrate metabolic process; PDB: 3SUT_A 3SUS_A 3GH7_A 3SUR_A 3SUW_A 3SUV_A 3SUU_A 3GH5_A 3GH4_A 2J4G_B ....
Probab=30.61 E-value=1.3e+02 Score=21.62 Aligned_cols=38 Identities=8% Similarity=0.112 Sum_probs=32.1
Q ss_pred CcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcC
Q psy17242 64 PRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLG 102 (172)
Q Consensus 64 Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g 102 (172)
+...-+-.++++|.|.|+ +...+..|++-+.++|+..+
T Consensus 75 ~E~Y~L~i~~~~I~I~a~-~~~G~~yg~qTL~Qll~~~~ 112 (124)
T PF02838_consen 75 EEGYRLSISPKGITIEAS-DPAGLFYGLQTLRQLLRQSG 112 (124)
T ss_dssp TT-EEEEEESSEEEEEES-SHHHHHHHHHHHHHHSBTCS
T ss_pred CcceEEEEECCEEEEEEc-CchHHHHHHHHHHHHhhccC
Confidence 467778888899999988 89999999999999987763
No 79
>cd02985 TRX_CDSP32 TRX family, chloroplastic drought-induced stress protein of 32 kD (CDSP32); CDSP32 is composed of two TRX domains, a C-terminal TRX domain which contains a redox active CXXC motif and an N-terminal TRX-like domain which contains an SXXS sequence instead of the redox active motif. CDSP32 is a stress-inducible TRX, i.e., it acts as a TRX by reducing protein disulfides and is induced by environmental and oxidative stress conditions. It plays a critical role in plastid defense against oxidative damage, a role related to its function as a physiological electron donor to BAS1, a plastidic 2-cys peroxiredoxin. Plants lacking CDSP32 exhibit decreased photosystem II photochemical efficiencies and chlorophyll retention compared to WT controls, as well as an increased proportion of BAS1 in its overoxidized monomeric form.
Probab=30.51 E-value=94 Score=21.76 Aligned_cols=22 Identities=14% Similarity=0.255 Sum_probs=15.8
Q ss_pred EEEEecCCeEE--EEeeCCHHHHHH
Q psy17242 67 TALIFSSGKMV--CTGAKSEEDSRL 89 (172)
Q Consensus 67 t~lIf~SGKiv--itGakS~e~a~~ 89 (172)
|+.+|++|+++ ..|+ +.++++.
T Consensus 74 t~~~~~~G~~v~~~~G~-~~~~l~~ 97 (103)
T cd02985 74 HFLFYKDGEKIHEEEGI-GPDELIG 97 (103)
T ss_pred EEEEEeCCeEEEEEeCC-CHHHHHH
Confidence 78999999987 6776 3444443
No 80
>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=30.32 E-value=1.9e+02 Score=21.51 Aligned_cols=40 Identities=13% Similarity=0.224 Sum_probs=31.3
Q ss_pred CcEEEEEecCCeEEEEeeCC----HHHHHHHHHHHHHHHHHcCC
Q psy17242 64 PRTTALIFSSGKMVCTGAKS----EEDSRLAARKYARIIQKLGF 103 (172)
Q Consensus 64 Pk~t~lIf~SGKivitGakS----~e~a~~a~~k~~~~L~~~g~ 103 (172)
.+.-+.+..++..++.|.-. ...+..++.++++.|++.|+
T Consensus 84 ~~~Gi~i~kT~~~ivi~~y~e~~~~g~~~~~v~~ladYL~~~gy 127 (127)
T cd00148 84 GAGGVVIVKTKQALVIGMYEEGVQPGQANKVVEKLADYLRSQGY 127 (127)
T ss_pred CCCeEEEEECCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 34557778888888877643 45899999999999999885
No 81
>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=30.21 E-value=2.3e+02 Score=26.50 Aligned_cols=83 Identities=20% Similarity=0.370 Sum_probs=50.9
Q ss_pred ecCCeEEEEeeCC-HHHHHHHHHHHHHHHHHcCCCCccccceEEEEEEEeecCccccHHHHHHHcCC-CcccccCCCcee
Q psy17242 71 FSSGKMVCTGAKS-EEDSRLAARKYARIIQKLGFPAKFLDFKIQNMVGSCDVKFPIRLEGLVLTHGQ-FSSYEPELFPGL 148 (172)
Q Consensus 71 f~SGKivitGakS-~e~a~~a~~k~~~~L~~~g~~v~~~~f~v~NIvat~~~~f~I~Le~la~~~~~-~~~YEPE~fPGl 148 (172)
-.||=++|||-.. .|.|+..++.+. ...| +| +|||+. | |||.+-..... -..|--| .-..
T Consensus 83 I~TGAVIITGETArKeNA~~v~~~Ls---~~aG------DF----VVATAG-P---dLEsiiAgkGsGA~~~S~~-~~~~ 144 (473)
T PF06277_consen 83 IDTGAVIITGETARKENAREVLHALS---GFAG------DF----VVATAG-P---DLESIIAGKGSGAAALSKE-HHTV 144 (473)
T ss_pred CccccEEEecchhhhhhHHHHHHHHH---HhcC------CE----EEEccC-C---CHHHHHhccCccHHHHhhh-hCCe
Confidence 3689999999532 344444444333 1233 23 688887 2 99998665542 2334333 2234
Q ss_pred EEE--EcCCcEEEEEecCcEEEEEe
Q psy17242 149 IYR--MVKPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 149 iyR--~~~~k~~~lIF~SGkvviTg 171 (172)
+.- +-+-..-+.+|-.|++.=|+
T Consensus 145 V~NiDIGGGTtN~avf~~G~v~~T~ 169 (473)
T PF06277_consen 145 VANIDIGGGTTNIAVFDNGEVIDTA 169 (473)
T ss_pred EEEEEeCCCceeEEEEECCEEEEEE
Confidence 444 44666789999999998875
No 82
>PF05005 Ocnus: Janus/Ocnus family (Ocnus); InterPro: IPR007702 This family is comprised of the Ocnus, Janus-A and Janus-B proteins. These proteins have been found to be testes specific in Drosophila melanogaster [].; PDB: 2OZX_A 2OZW_A 2NMM_C 2AI6_A 2HW4_A.
Probab=29.89 E-value=1e+02 Score=22.96 Aligned_cols=58 Identities=17% Similarity=0.256 Sum_probs=40.7
Q ss_pred CCCcEEc-CcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCc
Q psy17242 44 ARNAEYN-PKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAK 106 (172)
Q Consensus 44 ~~n~~Ye-Pe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~ 106 (172)
.+.++=+ +..|-=+.+|+..+. -...|.++-|.+..+-=...++++.+.|+++|+.++
T Consensus 4 vP~V~id~~G~fKYvLi~v~~~~-----~~~~k~iVRG~~~~~yH~di~d~~~~el~~~gl~~~ 62 (108)
T PF05005_consen 4 VPDVDIDPEGVFKYVLIRVTDHG-----SGESKYIVRGYKRAEYHADIYDEVQEELEKLGLCTE 62 (108)
T ss_dssp S-SEEEESSSEEEEEEEEEES-G--------EEEEEEEETT-SSHHHHHHHHHHHHHHCTEEEE
T ss_pred CCeEEecCCceEEEEEEEEEeCC-----CCEEEEEEECCcchhhHHHHHHHHHHHHHHcCCeEE
Confidence 3455556 446766777877766 567899999999877777889999999999987554
No 83
>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=29.78 E-value=88 Score=23.39 Aligned_cols=30 Identities=30% Similarity=0.488 Sum_probs=25.7
Q ss_pred CCeEEEEeeCCHHHHHHHHHHHHHHHHH-cCCC
Q psy17242 73 SGKMVCTGAKSEEDSRLAARKYARIIQK-LGFP 104 (172)
Q Consensus 73 SGKivitGakS~e~a~~a~~k~~~~L~~-~g~~ 104 (172)
+|-++++| ++.+.+.|++.....+++ ++|.
T Consensus 73 ~g~vii~G--dvsaV~aAl~a~~~~~~~~~~f~ 103 (110)
T cd07046 73 SGALVITG--DVSEVESALEAVVDYLRETLGFT 103 (110)
T ss_pred eEEEEEEE--CHHHHHHHHHHHHHHHhhccCce
Confidence 67788999 899999999999999887 5664
No 84
>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=29.38 E-value=65 Score=22.23 Aligned_cols=36 Identities=22% Similarity=0.361 Sum_probs=27.5
Q ss_pred EEecCCeEEEEe------eCCHHHHHHHHHHHHHHHHHcCCC
Q psy17242 69 LIFSSGKMVCTG------AKSEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 69 lIf~SGKivitG------akS~e~a~~a~~k~~~~L~~~g~~ 104 (172)
.+|.||-+-... ..-.++++.+++++.++|+..|..
T Consensus 10 ~~~~sGq~~~~~~~~~~~~~~~~Q~~~~~~ni~~~L~~~g~~ 51 (107)
T cd00448 10 LVFVSGQIPLDPDGELVPGDIEAQTRQALENLEAVLEAAGGS 51 (107)
T ss_pred EEEEeccCCcCCCCcccCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence 567777665532 334789999999999999999976
No 85
>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=29.36 E-value=30 Score=24.36 Aligned_cols=13 Identities=38% Similarity=0.654 Sum_probs=10.1
Q ss_pred EEecCCeEEEEee
Q psy17242 69 LIFSSGKMVCTGA 81 (172)
Q Consensus 69 lIf~SGKivitGa 81 (172)
.=|++|||+.|--
T Consensus 3 I~Fs~GKiI~t~~ 15 (75)
T PF11869_consen 3 IEFSQGKIIATPH 15 (75)
T ss_pred EEecCCeEEEcce
Confidence 4599999998843
No 86
>COG4547 CobT Cobalamin biosynthesis protein CobT (nicotinate-mononucleotide:5, 6-dimethylbenzimidazole phosphoribosyltransferase) [Coenzyme metabolism]
Probab=29.17 E-value=45 Score=31.43 Aligned_cols=45 Identities=24% Similarity=0.316 Sum_probs=37.8
Q ss_pred cEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCccccceE
Q psy17242 65 RTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFKI 112 (172)
Q Consensus 65 k~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~v 112 (172)
-+|..|-.||.| +.+-..-|...+..+++.|.++|.++....|+-
T Consensus 415 vVtlviDnSGSM---rGRpItvAatcAdilArtLeRcgVk~eIlGFTT 459 (620)
T COG4547 415 VVTLVIDNSGSM---RGRPITVAATCADILARTLERCGVKVEILGFTT 459 (620)
T ss_pred hheeeeccCCCc---CCcceehhHHHHHHHHHHHHHcCCceEEeeeee
Confidence 468899999987 566777888999999999999999887766664
No 87
>cd02956 ybbN ybbN protein family; ybbN is a hypothetical protein containing a redox-inactive TRX-like domain. Its gene has been sequenced from several gammaproteobacteria and actinobacteria.
Probab=29.03 E-value=71 Score=21.55 Aligned_cols=25 Identities=36% Similarity=0.565 Sum_probs=19.0
Q ss_pred EEEEEecCCeEE--EEeeCCHHHHHHH
Q psy17242 66 TTALIFSSGKMV--CTGAKSEEDSRLA 90 (172)
Q Consensus 66 ~t~lIf~SGKiv--itGakS~e~a~~a 90 (172)
.++.+|..|+.+ ..|..+.++++.-
T Consensus 68 Pt~~~~~~g~~~~~~~g~~~~~~l~~~ 94 (96)
T cd02956 68 PTVYLFAAGQPVDGFQGAQPEEQLRQM 94 (96)
T ss_pred CEEEEEeCCEEeeeecCCCCHHHHHHH
Confidence 378888999986 7788877776543
No 88
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=28.94 E-value=84 Score=19.47 Aligned_cols=22 Identities=27% Similarity=0.443 Sum_probs=19.4
Q ss_pred CHHHHHHHHHHHHHHHHHcCCC
Q psy17242 83 SEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 83 S~e~a~~a~~k~~~~L~~~g~~ 104 (172)
++.++..|+.+..+.+.+.|++
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 89
>cd03005 PDI_a_ERp46 PDIa family, endoplasmic reticulum protein 46 (ERp46) subfamily; ERp46 is an ER-resident protein containing three redox active TRX domains. Yeast complementation studies show that ERp46 can substitute for protein disulfide isomerase (PDI) function in vivo. It has been detected in many tissues, however, transcript and protein levels do not correlate in all tissues, suggesting regulation at a posttranscriptional level. An identical protein, named endoPDI, has been identified as an endothelial PDI that is highly expressed in the endothelium of tumors and hypoxic lesions. It has a protective effect on cells exposed to hypoxia.
Probab=28.78 E-value=75 Score=21.47 Aligned_cols=22 Identities=27% Similarity=0.554 Sum_probs=17.3
Q ss_pred EEEEecCCeEE--EEeeCCHHHHH
Q psy17242 67 TALIFSSGKMV--CTGAKSEEDSR 88 (172)
Q Consensus 67 t~lIf~SGKiv--itGakS~e~a~ 88 (172)
|+.+|..|+.+ ..|.++.+++.
T Consensus 76 t~~~~~~g~~~~~~~G~~~~~~l~ 99 (102)
T cd03005 76 TLLLFKDGEKVDKYKGTRDLDSLK 99 (102)
T ss_pred EEEEEeCCCeeeEeeCCCCHHHHH
Confidence 78888999865 78998877654
No 90
>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=28.51 E-value=90 Score=24.21 Aligned_cols=28 Identities=25% Similarity=0.277 Sum_probs=23.7
Q ss_pred CCeEEEEeeCCHHHHHHHHHHHHHHHHH
Q psy17242 73 SGKMVCTGAKSEEDSRLAARKYARIIQK 100 (172)
Q Consensus 73 SGKivitGakS~e~a~~a~~k~~~~L~~ 100 (172)
+|-+++||+.++.+.+.|++.-.+.+.+
T Consensus 78 kg~vvitGg~dVs~V~~aVeaa~~~v~~ 105 (134)
T cd07047 78 HGSLILFGAEDVSDVRRAVEVALSETEK 105 (134)
T ss_pred eEEEEEEcCCCHHHHHHHHHHHHHHHHH
Confidence 6779999999999988888887777665
No 91
>PF14359 DUF4406: Domain of unknown function (DUF4406)
Probab=28.45 E-value=48 Score=23.75 Aligned_cols=32 Identities=25% Similarity=0.421 Sum_probs=24.9
Q ss_pred EecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCC
Q psy17242 70 IFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPA 105 (172)
Q Consensus 70 If~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v 105 (172)
||-||.|. |-. +.-+.++.+.++.|++.|+.+
T Consensus 1 iYIaGPmt--G~~--~~N~~~f~~~a~~L~~~G~~v 32 (92)
T PF14359_consen 1 IYIAGPMT--GLP--DYNRPAFNAAAKRLRAKGYEV 32 (92)
T ss_pred CeEeCCcC--CCc--chHHHHHHHHHHHHHHCCCEE
Confidence 46778876 664 555899999999999999754
No 92
>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=28.33 E-value=66 Score=22.91 Aligned_cols=37 Identities=14% Similarity=0.228 Sum_probs=27.4
Q ss_pred EEecCCeEEEEe-eCCHHHHHHHHHHHHHHHHHcCCCC
Q psy17242 69 LIFSSGKMVCTG-AKSEEDSRLAARKYARIIQKLGFPA 105 (172)
Q Consensus 69 lIf~SGKivitG-akS~e~a~~a~~k~~~~L~~~g~~v 105 (172)
.+|-||-+-.-. ..-.++++.+++++..+|+..|...
T Consensus 12 ~v~iSGq~~~~~~~~~~~Q~~~~~~nl~~~L~~~G~~~ 49 (105)
T cd06150 12 TVYLAGQVADDTSADITGQTRQVLAKIDALLAEAGSDK 49 (105)
T ss_pred EEEEeCcCCcCCCCCHHHHHHHHHHHHHHHHHHcCCCH
Confidence 577777654421 2247899999999999999999763
No 93
>cd03715 RT_ZFREV_like RT_ZFREV_like: A subfamily of reverse transcriptases (RTs) found in sequences similar to the intact endogenous retrovirus ZFERV from zebrafish and to Moloney murine leukemia virus RT. An RT gene is usually indicative of a mobile element such as a retrotransposon or retrovirus. RTs occur in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. These elements can be divided into two major groups. One group contains retroviruses and DNA viruses whose propagation involves an RNA intermediate. They are grouped together with transposable elements containing long terminal repeats (LTRs). The other group, also called poly(A)-type retrotransposons, contain fungal mitochondrial introns and transposable elements that lack LTRs. Phylogenetic analysis suggests that ZFERV belongs to a distinct group of retroviruses.
Probab=27.93 E-value=1.1e+02 Score=24.35 Aligned_cols=27 Identities=26% Similarity=0.352 Sum_probs=23.5
Q ss_pred eeCCHHHHHHHHHHHHHHHHHcCCCCc
Q psy17242 80 GAKSEEDSRLAARKYARIIQKLGFPAK 106 (172)
Q Consensus 80 GakS~e~a~~a~~k~~~~L~~~g~~v~ 106 (172)
++++.|+..+.++.+.+.|++.|+.+.
T Consensus 166 ~s~~~~e~~~~l~~v~~~l~~~gl~l~ 192 (210)
T cd03715 166 AADSEEDCLKGTDALLTHLGELGYKVS 192 (210)
T ss_pred ecCCHHHHHHHHHHHHHHHHHCCCCcC
Confidence 345899999999999999999998764
No 94
>PRK03988 translation initiation factor IF-2 subunit beta; Validated
Probab=27.68 E-value=1.1e+02 Score=23.71 Aligned_cols=32 Identities=19% Similarity=0.263 Sum_probs=27.1
Q ss_pred EEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHH
Q psy17242 66 TTALIFSSGKMVCTGAKSEEDSRLAARKYARII 98 (172)
Q Consensus 66 ~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L 98 (172)
+...+ .+|+.++.|.-+.++++..++++++..
T Consensus 71 t~g~i-~~~~lii~G~~~~~~i~~~L~~yI~~y 102 (138)
T PRK03988 71 TAGNI-EGGRLILQGKFSPRVINEKIDRYVKEY 102 (138)
T ss_pred Cceee-cCCEEEEEEeeCHHHHHHHHHHHHHhc
Confidence 34455 899999999999999999999998763
No 95
>PF05362 Lon_C: Lon protease (S16) C-terminal proteolytic domain; InterPro: IPR008269 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ]. This signature defines the C-terminal proteolytic domain of the archael, bacterial and eukaryotic Lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (Lon protease family, clan SF). In the eukaryotes the majority of the proteins are located in the mitochondrial matrix [, ]. In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response [].; GO: 0004176 ATP-dependent peptidase activity, 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1Z0E_E 1Z0G_E 1Z0T_F 1Z0C_A 1Z0V_A 1Z0B_A 1Z0W_A 2KJP_A 2X36_F 3K1J_B ....
Probab=27.67 E-value=97 Score=25.39 Aligned_cols=35 Identities=17% Similarity=0.280 Sum_probs=20.7
Q ss_pred EecCCeEEEEeeCCHHHHHHH----HHHHHHHHHHcCCCC
Q psy17242 70 IFSSGKMVCTGAKSEEDSRLA----ARKYARIIQKLGFPA 105 (172)
Q Consensus 70 If~SGKivitGakS~e~a~~a----~~k~~~~L~~~g~~v 105 (172)
+-.+|++..||-- .+.++++ ..-+...++++|.+.
T Consensus 50 ~~G~G~l~~tG~l-g~v~kES~~~A~~~~k~~~~~~~~~~ 88 (204)
T PF05362_consen 50 IPGKGKLIITGNL-GDVMKESAKIAFSYLKANLKRIGIDP 88 (204)
T ss_dssp EESSSEEEEESSB-HHHHHHHHHHHHHHHHHHHHCCSSTC
T ss_pred ccCcceeEeeccc-chhHHHHHHHHHHHHHhhhccccccc
Confidence 4489999999963 2344444 444444445566553
No 96
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=27.62 E-value=46 Score=25.28 Aligned_cols=25 Identities=24% Similarity=0.441 Sum_probs=21.9
Q ss_pred CHHHHHHHHHHHHHHHHHcCCCCcc
Q psy17242 83 SEEDSRLAARKYARIIQKLGFPAKF 107 (172)
Q Consensus 83 S~e~a~~a~~k~~~~L~~~g~~v~~ 107 (172)
+.+.+++|++++.+.|+.+|+.+++
T Consensus 21 Tg~~L~~av~~l~~~L~~~Giev~l 45 (120)
T PF10865_consen 21 TGETLREAVKELAPVLAPLGIEVRL 45 (120)
T ss_pred HHHHHHHHHHHHHHHHHhCCcEEEE
Confidence 4678999999999999999998765
No 97
>cd01645 RT_Rtv RT_Rtv: Reverse transcriptases (RTs) from retroviruses (Rtvs). RTs catalyze the conversion of single-stranded RNA into double-stranded viral DNA for integration into host chromosomes. Proteins in this subfamily contain long terminal repeats (LTRs) and are multifunctional enzymes with RNA-directed DNA polymerase, DNA directed DNA polymerase, and ribonuclease hybrid (RNase H) activities. The viral RNA genome enters the cytoplasm as part of a nucleoprotein complex, and the process of reverse transcription generates in the cytoplasm forming a linear DNA duplex via an intricate series of steps. This duplex DNA is colinear with its RNA template, but contains terminal duplications known as LTRs that are not present in viral RNA. It has been proposed that two specialized template switches, known as strand-transfer reactions or "jumps", are required to generate the LTRs.
Probab=27.44 E-value=92 Score=25.05 Aligned_cols=38 Identities=8% Similarity=0.128 Sum_probs=28.6
Q ss_pred EEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCc
Q psy17242 67 TALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAK 106 (172)
Q Consensus 67 t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~ 106 (172)
.+..|-..=+ -++++.++..++.+.+.+.|++.|+.+.
T Consensus 159 ~~~~Y~DDil--i~s~~~~~~~~~l~~v~~~l~~~gl~ln 196 (213)
T cd01645 159 VIYHYMDDIL--IASDLEGQLREIYEELRQTLLRWGLTIP 196 (213)
T ss_pred EEEEEcCCEE--EEcCCHHHHHHHHHHHHHHHHHCCCEeC
Confidence 3455555433 2456899999999999999999998754
No 98
>smart00392 PROF Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline.
Probab=27.37 E-value=2.6e+02 Score=20.75 Aligned_cols=40 Identities=13% Similarity=0.214 Sum_probs=31.8
Q ss_pred CcEEEEEecCCeEEEEeeCC----HHHHHHHHHHHHHHHHHcCC
Q psy17242 64 PRTTALIFSSGKMVCTGAKS----EEDSRLAARKYARIIQKLGF 103 (172)
Q Consensus 64 Pk~t~lIf~SGKivitGakS----~e~a~~a~~k~~~~L~~~g~ 103 (172)
.+.-+.+..+...++.|.-. ..++..++.++++.|++.|+
T Consensus 86 ~~~Gv~i~kT~~aivI~~y~e~~~~g~~~~~v~~ladYL~~~Gy 129 (129)
T smart00392 86 GAGGVVIVKTKQALIIGMYKEGVQPGQANKTVEKLADYLRSSGY 129 (129)
T ss_pred CCceEEEEECCCEEEEEECCCCCChHHHHHHHHHHHHHHHHcCC
Confidence 45567788888887776643 35899999999999999885
No 99
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=26.91 E-value=98 Score=18.91 Aligned_cols=25 Identities=16% Similarity=0.191 Sum_probs=20.4
Q ss_pred EEEEeeCCHHHHHHHHHHHHHHHHH
Q psy17242 76 MVCTGAKSEEDSRLAARKYARIIQK 100 (172)
Q Consensus 76 ivitGakS~e~a~~a~~k~~~~L~~ 100 (172)
+.-.|.++..+|+.++.++...+++
T Consensus 19 ~~k~GF~TkkeA~~~~~~~~~~~~~ 43 (46)
T PF14657_consen 19 KTKRGFKTKKEAEKALAKIEAELEN 43 (46)
T ss_pred EEcCCCCcHHHHHHHHHHHHHHHHc
Confidence 4457899999999999998877654
No 100
>COG0678 AHP1 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=26.89 E-value=37 Score=27.25 Aligned_cols=54 Identities=22% Similarity=0.172 Sum_probs=38.8
Q ss_pred cCcccceEEEEEc---------CCcEEEEEecCCeEEEEeeC-------CHHHHHHHHHHHHHHHHHcCCC
Q psy17242 50 NPKRFAAVIMRIR---------EPRTTALIFSSGKMVCTGAK-------SEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 50 ePe~fpgli~R~~---------~Pk~t~lIf~SGKivitGak-------S~e~a~~a~~k~~~~L~~~g~~ 104 (172)
..+++|.+.+|.+ .+..+..+|+..|+++.|.- |..+ --+..+.++.++..|.+
T Consensus 5 vg~klP~vtf~tr~~~~~~~~~~~~ts~~lf~gKkVvlf~lPGAFTPTCS~~h-lPgY~~~~d~f~~kGVD 74 (165)
T COG0678 5 VGKKLPAVTFKTRVGDETADGWVDVTTDDLFKGKKVVLFSLPGAFTPTCSSSH-LPGYLELADEFKAKGVD 74 (165)
T ss_pred cCCcCCceEeEEeeccccCCCcccccHHHhcCCCEEEEEeCCCccCCCccccc-CccHHHHHHHHHHcCCc
Confidence 3467899998887 45678899999999998752 2222 13556677778888875
No 101
>PF09967 DUF2201: VWA-like domain (DUF2201); InterPro: IPR018698 This family of various hypothetical bacterial proteins has no known function.
Probab=26.14 E-value=2.1e+02 Score=21.32 Aligned_cols=34 Identities=24% Similarity=0.296 Sum_probs=27.0
Q ss_pred EEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCc
Q psy17242 67 TALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAK 106 (172)
Q Consensus 67 t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~ 106 (172)
.+.|=.||.| |.++++..+..+..++++.+.++.
T Consensus 2 ~vaiDtSGSi------s~~~l~~fl~ev~~i~~~~~~~v~ 35 (126)
T PF09967_consen 2 VVAIDTSGSI------SDEELRRFLSEVAGILRRFPAEVH 35 (126)
T ss_pred EEEEECCCCC------CHHHHHHHHHHHHHHHHhCCCCEE
Confidence 3456677777 789999999999999998866554
No 102
>KOG4749|consensus
Probab=25.96 E-value=8 Score=34.54 Aligned_cols=37 Identities=38% Similarity=0.664 Sum_probs=29.6
Q ss_pred CCCccccc-CCCceeEEEEc--------CCcEEEEEecCcEEEEEe
Q psy17242 135 GQFSSYEP-ELFPGLIYRMV--------KPRIVLLIFVSGKVVLTV 171 (172)
Q Consensus 135 ~~~~~YEP-E~fPGliyR~~--------~~k~~~lIF~SGkvviTg 171 (172)
.+..+|+| ++|.|=.=||. .|.=-+.||.+|..|.-|
T Consensus 173 sqisey~PLDLfSG~k~rm~~AikaL~~~pqnnlrvF~nG~lv~gg 218 (375)
T KOG4749|consen 173 SQISEYDPLDLFSGSKERMHKAIKALYSTPQNNLRVFLNGSLVFGG 218 (375)
T ss_pred hhhhccCchhhccccHHHHHHHHHHHhhccccceeEEeccceeecc
Confidence 35689999 99999777764 366688999999998765
No 103
>TIGR00311 aIF-2beta translation initiation factor aIF-2, beta subunit, putative.
Probab=25.88 E-value=1.2e+02 Score=23.34 Aligned_cols=26 Identities=15% Similarity=0.215 Sum_probs=23.8
Q ss_pred cCCeEEEEeeCCHHHHHHHHHHHHHH
Q psy17242 72 SSGKMVCTGAKSEEDSRLAARKYARI 97 (172)
Q Consensus 72 ~SGKivitGakS~e~a~~a~~k~~~~ 97 (172)
.+|+.++.|.-+.++++..++++++.
T Consensus 71 ~~~rlii~G~~~~~~i~~~L~~yI~~ 96 (133)
T TIGR00311 71 EGGRLILQGKFTHFLLNERIEDYVRK 96 (133)
T ss_pred cCCEEEEEeecCHHHHHHHHHHHHhh
Confidence 68999999999999999999998865
No 104
>smart00115 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues. Cysteine aspartases that mediate programmed cell death (apoptosis). Caspases are synthesised as zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologues.
Probab=25.71 E-value=54 Score=27.13 Aligned_cols=41 Identities=22% Similarity=0.431 Sum_probs=25.1
Q ss_pred CCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCC
Q psy17242 63 EPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPA 105 (172)
Q Consensus 63 ~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v 105 (172)
+|+-.++|+.+.+.- +......+..=++.+.+.|+++||++
T Consensus 6 ~p~g~alII~n~~f~--~~~~r~g~~~D~~~l~~~f~~lgF~V 46 (241)
T smart00115 6 KPRGLALIINNENFH--SLPRRNGTDVDAENLTELFQSLGYEV 46 (241)
T ss_pred CCCcEEEEEECccCC--CCcCCCCcHHHHHHHHHHHHHCCCEE
Confidence 567778888877763 22233334444566777777777765
No 105
>PF01960 ArgJ: ArgJ family; InterPro: IPR002813 ArgJ is a bifunctional protein that catalyses the first 2.3.1.35 from EC and fifth steps 2.3.1.1 from EC in arginine biosynthesis []. The structure has been determined for glutamate N-acetyltransferase 2 (ornithine acetyltransferase; 2.3.1.35 from EC), an ArgJ-like protein from Streptomyces clavuligerus [].; GO: 0004358 glutamate N-acetyltransferase activity, 0006526 arginine biosynthetic process; PDB: 1VRA_A 1VZ7_A 1VZ8_D 2VZK_H 2V4I_A 2YEP_E 1VZ6_A 3IT4_A 3IT6_D.
Probab=25.31 E-value=87 Score=28.49 Aligned_cols=22 Identities=50% Similarity=0.647 Sum_probs=19.5
Q ss_pred eEEEEeeCCHHHHHHHHHHHHH
Q psy17242 75 KMVCTGAKSEEDSRLAARKYAR 96 (172)
Q Consensus 75 KivitGakS~e~a~~a~~k~~~ 96 (172)
.|.++||+|+++|+.+++.++.
T Consensus 268 ~v~V~GA~s~~~A~~iAraIa~ 289 (388)
T PF01960_consen 268 EVTVTGARSEEDARKIARAIAN 289 (388)
T ss_dssp EEEEEEESSHHHHHHHHHHHHT
T ss_pred EEEEecCCCHHHHHHHHHHHhc
Confidence 4789999999999999998874
No 106
>KOG3384|consensus
Probab=25.06 E-value=45 Score=26.29 Aligned_cols=26 Identities=38% Similarity=0.606 Sum_probs=18.0
Q ss_pred ccCCCceeEEE---EcCCcEEEEEecCcEE
Q psy17242 141 EPELFPGLIYR---MVKPRIVLLIFVSGKV 167 (172)
Q Consensus 141 EPE~fPGliyR---~~~~k~~~lIF~SGkv 167 (172)
+|++|||+.-+ -.+|. +.|.=.+||+
T Consensus 101 ~~~kFp~vkvkyVrg~~P~-l~llDadgk~ 129 (154)
T KOG3384|consen 101 EPEKFPGVKVKYVRGSDPV-LKLLDADGKH 129 (154)
T ss_pred chhhCCCceEEEecCCCCe-eEeecCCCCc
Confidence 89999998553 45674 4466677765
No 107
>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=24.98 E-value=1.1e+02 Score=20.78 Aligned_cols=27 Identities=15% Similarity=0.259 Sum_probs=20.6
Q ss_pred eEEEEeeCCHHHHHHHHHHHHHHHHHc
Q psy17242 75 KMVCTGAKSEEDSRLAARKYARIIQKL 101 (172)
Q Consensus 75 KivitGakS~e~a~~a~~k~~~~L~~~ 101 (172)
||++||.++-.|.....+.+-+.+++.
T Consensus 5 rVli~GgR~~~D~~~i~~~Ld~~~~~~ 31 (71)
T PF10686_consen 5 RVLITGGRDWTDHELIWAALDKVHARH 31 (71)
T ss_pred EEEEEECCccccHHHHHHHHHHHHHhC
Confidence 789999999888777666666665555
No 108
>PF05406 WGR: WGR domain; InterPro: IPR008893 This domain is named after the most conserved central motif of the domain. It is found in a variety of polyA polymerases as well as the Escherichia coli molybdate metabolism regulator P33345 from SWISSPROT and other proteins of unknown function.The domain is found in isolation in proteins such as Q9JN21 from SWISSPROT and is between 70 and 80 residues in length. ; PDB: 2EOC_A 2RA8_A 4DQY_C 2CR9_A.
Probab=24.93 E-value=2e+02 Score=19.55 Aligned_cols=34 Identities=21% Similarity=0.169 Sum_probs=26.9
Q ss_pred cCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCC
Q psy17242 72 SSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPA 105 (172)
Q Consensus 72 ~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v 105 (172)
+.|+..+....|.++|..+++++.+.-.+.|+..
T Consensus 43 ~~gq~~~~~f~s~~eA~~~f~~~~~~K~~~gy~~ 76 (81)
T PF05406_consen 43 SKGQTRIKPFDSEEEAIKEFEKLFKEKTGKGYEE 76 (81)
T ss_dssp SSEEEEEEEESSHHHHHHHHHHHHHHHHSSTSCC
T ss_pred CcCcEEEEeCCCHHHHHHHHHHHHHHHHcCCCcc
Confidence 4567777788899999999999888777778753
No 109
>PF12864 DUF3822: Protein of unknown function (DUF3822); InterPro: IPR024213 This is a family of uncharacterised bacterial proteins. However, structural-similarity searches indicate the family takes on an actin-like ATPase fold.; PDB: 3HRG_A.
Probab=24.88 E-value=2.7e+02 Score=23.00 Aligned_cols=55 Identities=9% Similarity=0.154 Sum_probs=40.4
Q ss_pred ceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCcccc
Q psy17242 55 AAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLD 109 (172)
Q Consensus 55 pgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~ 109 (172)
.-+.+-+.+-...+.+|..||+...=.=+.+.+...+=-++-.++++|++.+...
T Consensus 174 ~~ly~~~~~~~~~i~~~~~~kL~~~N~F~~~~~eD~lYYlL~v~~Ql~ld~e~~~ 228 (253)
T PF12864_consen 174 RKLYVHFHDNQFDIFVFKNGKLLFFNSFEYQTAEDFLYYLLFVWEQLGLDPEKDE 228 (253)
T ss_dssp -EEEEEE-SSEEEEEEEETTEEEEEEEEE--SHHHHHHHHHHHHHHTT--TTT-E
T ss_pred cEEEEEEECCEEEEEEEECCEEEEEEEEecCChHHHHHHHHHHHHHcCCCccccE
Confidence 3455667778899999999999998877788888899999999999999765433
No 110
>KOG2360|consensus
Probab=24.86 E-value=1e+02 Score=28.22 Aligned_cols=81 Identities=17% Similarity=0.255 Sum_probs=60.1
Q ss_pred EcCcccceEEEEEcCCcEEEEEecCCeEEEEeeCCHHHHH-HHHHHHHHHHHHcCCCCccccceEEEEE-EEeecCcccc
Q psy17242 49 YNPKRFAAVIMRIREPRTTALIFSSGKMVCTGAKSEEDSR-LAARKYARIIQKLGFPAKFLDFKIQNMV-GSCDVKFPIR 126 (172)
Q Consensus 49 YePe~fpgli~R~~~Pk~t~lIf~SGKivitGakS~e~a~-~a~~k~~~~L~~~g~~v~~~~f~v~NIv-at~~~~f~I~ 126 (172)
=.|+.|+.+.+=+-+|.|+-..-.+++-.++|+..+++-+ ++++.+..+++++-.. |.+ ++-++ +||+++..++
T Consensus 277 ~~~~~~~~v~~iL~DpscSgSgm~~r~~~~~~~e~~~~~rL~~L~~fq~~~~~hal~--fp~--~k~vvystcs~~reen 352 (413)
T KOG2360|consen 277 ATPEKFRDVTYILVDPSCSGSGMVSRQDEDPGAETESPERLENLQSFQIRILKHALT--FPN--LKRLVYSTCSLHREEN 352 (413)
T ss_pred CCcccccceeEEEeCCCCCCCccccceeeccCCCcccHHHHHHHHHHHHHHHHHHhc--CCc--hhheeeecchhhhhhh
Confidence 4678899999999999999999999999999988777665 4555666666654222 333 33444 9999999988
Q ss_pred HHHHHHH
Q psy17242 127 LEGLVLT 133 (172)
Q Consensus 127 Le~la~~ 133 (172)
=+..+..
T Consensus 353 e~vv~d~ 359 (413)
T KOG2360|consen 353 EQVVQEV 359 (413)
T ss_pred hHHHHHH
Confidence 7666643
No 111
>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=24.81 E-value=1e+02 Score=29.66 Aligned_cols=45 Identities=27% Similarity=0.325 Sum_probs=36.4
Q ss_pred cEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCCccccceE
Q psy17242 65 RTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFKI 112 (172)
Q Consensus 65 k~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~v 112 (172)
.+++||=.||.|. .+..+-|..++.-+.+.|+++|+++....|.-
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 4689999999995 44455677789999999999999987766664
No 112
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.60 E-value=2.5e+02 Score=22.91 Aligned_cols=52 Identities=23% Similarity=0.216 Sum_probs=37.0
Q ss_pred EEEEeecCccccHHHHHHHcCCCcccccCCCceeEEEEcCCcEEEEEecCcEEEEE
Q psy17242 115 MVGSCDVKFPIRLEGLVLTHGQFSSYEPELFPGLIYRMVKPRIVLLIFVSGKVVLT 170 (172)
Q Consensus 115 Ivat~~~~f~I~Le~la~~~~~~~~YEPE~fPGliyR~~~~k~~~lIF~SGkvviT 170 (172)
+.|..|=+++=-|.-|+--++. +.|.- .---|++.. -..-..|+.||||.+|
T Consensus 36 Vi~~md~~lg~ilplla~l~P~-anY~~-kk~~l~~~k--gerIitiy~sGkVsm~ 87 (193)
T COG4871 36 VIANMDPPLGGILPLLAPLFPR-ANYSD-KKNILILQK--GERIITIYGSGKVSMT 87 (193)
T ss_pred EEeecCCCcchhHHHhHhhCCC-ccccc-ccceEEEee--ccEEEEEccCCeEEee
Confidence 4566676777777778777776 88873 445566663 3446789999999887
No 113
>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=24.57 E-value=1.4e+02 Score=19.27 Aligned_cols=27 Identities=30% Similarity=0.385 Sum_probs=21.2
Q ss_pred CeEEEEee-CCHHHHHHHHHHHHHHHHHcCC
Q psy17242 74 GKMVCTGA-KSEEDSRLAARKYARIIQKLGF 103 (172)
Q Consensus 74 GKivitGa-kS~e~a~~a~~k~~~~L~~~g~ 103 (172)
|.|.++|. .|+++++.++.+-+ .+.|-
T Consensus 6 G~Isvs~~~~s~~d~~~~la~kA---d~~GA 33 (56)
T PF07338_consen 6 GTISVSGNFGSPDDAEEALAKKA---DEKGA 33 (56)
T ss_dssp EEEEEEEECSSHHHHHHHHHHHH---HHTT-
T ss_pred EEEEEccccCCHHHHHHHHHHHH---HHcCC
Confidence 78899998 89999998877766 55664
No 114
>PF00078 RVT_1: Reverse transcriptase (RNA-dependent DNA polymerase); InterPro: IPR000477 The use of an RNA template to produce DNA, for integration into the host genome and exploitation of a host cell, is a strategy employed in the replication of retroid elements, such as the retroviruses and bacterial retrons. The enzyme catalysing polymerisation is an RNA-directed DNA-polymerase, or reverse trancriptase (RT) (2.7.7.49 from EC). Reverse transcriptase occurs in a variety of mobile elements, including retrotransposons, retroviruses, group II introns, bacterial msDNAs, hepadnaviruses, and caulimoviruses. Retroviral reverse transcriptase is synthesised as part of the POL polyprotein that contains; an aspartyl protease, a reverse transcriptase, RNase H and integrase. POL polyprotein undergoes specific enzymatic cleavage to yield the mature proteins. The discovery of retroelements in the prokaryotes raises intriguing questions concerning their roles in bacteria and the origin and evolution of reverse transcriptases and whether the bacterial reverse transcriptases are older than eukaryotic reverse transcriptases [].; GO: 0003723 RNA binding, 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 3RWE_C 3DU6_B 3DU5_A 3KYL_A 2WOM_B 1DTQ_A 2OPS_A 3FFI_A 1VRU_B ....
Probab=24.35 E-value=1.5e+02 Score=22.52 Aligned_cols=28 Identities=21% Similarity=0.264 Sum_probs=23.6
Q ss_pred eeCCHHHHHHHHHHHHHHHHHcCCCCcc
Q psy17242 80 GAKSEEDSRLAARKYARIIQKLGFPAKF 107 (172)
Q Consensus 80 GakS~e~a~~a~~k~~~~L~~~g~~v~~ 107 (172)
++++.+++....+.+...++++|+.+..
T Consensus 168 ~~~~~~~~~~~~~~i~~~~~~~gl~ln~ 195 (214)
T PF00078_consen 168 ISKSKEELQKILEKISQWLEELGLKLNP 195 (214)
T ss_dssp EESSHHHHHHHHHHHHHHHHHTTSBCSS
T ss_pred EECCHHHHHHHHHHHHHHHHHCCCEECh
Confidence 4557999999999999999999976543
No 115
>PRK15405 ethanolamine utilization protein EutL; Provisional
Probab=24.34 E-value=1.2e+02 Score=25.50 Aligned_cols=31 Identities=16% Similarity=0.375 Sum_probs=25.1
Q ss_pred cCCeE--EEEeeCCHHHHHHHHHHHHHHHHH-cCC
Q psy17242 72 SSGKM--VCTGAKSEEDSRLAARKYARIIQK-LGF 103 (172)
Q Consensus 72 ~SGKi--vitGakS~e~a~~a~~k~~~~L~~-~g~ 103 (172)
-+||+ +++|. ++.+++.|++...+.|++ +||
T Consensus 79 ~~G~viiIi~G~-dvsdVrsAveaa~~~i~~~~~f 112 (217)
T PRK15405 79 LAGEVIGILAGP-NPAEVRAGLDAMVAFIENGAAF 112 (217)
T ss_pred CCccEEEEEeCC-CHHHHHHHHHHHHHHHHhhhce
Confidence 47787 55554 899999999999999988 564
No 116
>PF13382 Adenine_deam_C: Adenine deaminase C-terminal domain; PDB: 3T8L_B 3T81_A 3NQB_A.
Probab=24.29 E-value=88 Score=25.04 Aligned_cols=27 Identities=26% Similarity=0.452 Sum_probs=19.2
Q ss_pred EEecCCeEEEEeeCCHHHHHHHHHHHHH
Q psy17242 69 LIFSSGKMVCTGAKSEEDSRLAARKYAR 96 (172)
Q Consensus 69 lIf~SGKivitGakS~e~a~~a~~k~~~ 96 (172)
.-+.|+.|++.|. +.++...|++++.+
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 3445899999999 89999999887763
No 117
>PLN02788 phenylalanine-tRNA synthetase
Probab=24.05 E-value=3.8e+02 Score=24.50 Aligned_cols=58 Identities=21% Similarity=0.352 Sum_probs=37.1
Q ss_pred cEEcCcccceEEEEEcCCcEEEEEecCCe---EEEEeeCCHHHHHHHHHHHHHHHHHcCCCCccccceEEEEEEEeecCc
Q psy17242 47 AEYNPKRFAAVIMRIREPRTTALIFSSGK---MVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFKIQNMVGSCDVKF 123 (172)
Q Consensus 47 ~~YePe~fpgli~R~~~Pk~t~lIf~SGK---ivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~v~NIvat~~~~f 123 (172)
..|.|..||. .+|...+-|+-.|| +.--|-=.. ++|+++|++.+ . -+-|
T Consensus 216 ~r~~~s~fPf-----t~Ps~e~dI~~~g~WlEvlG~G~vhP-----------~Vl~~~gi~~~--------~----g~Af 267 (402)
T PLN02788 216 MRWVDAYFPF-----TNPSFELEIFFKGEWLEVLGCGVTEQ-----------EILKNNGRSDN--------V----AWAF 267 (402)
T ss_pred eEEecCCCCC-----CCCCeEEEEEECCEEEEEeeEEEEcH-----------HHHHHcCCCCC--------c----EEEE
Confidence 4677776664 38999999998898 444444333 35567776521 1 2346
Q ss_pred cccHHHHHH
Q psy17242 124 PIRLEGLVL 132 (172)
Q Consensus 124 ~I~Le~la~ 132 (172)
.|+||.|+.
T Consensus 268 glgLeRLam 276 (402)
T PLN02788 268 GLGLERLAM 276 (402)
T ss_pred EEeHHHHHH
Confidence 788888874
No 118
>COG0799 Uncharacterized homolog of plant Iojap protein [Function unknown]
Probab=24.03 E-value=1.4e+02 Score=22.53 Aligned_cols=28 Identities=18% Similarity=0.254 Sum_probs=23.3
Q ss_pred EEEEeeCCHHHHHHHHHHHHHHHHHcCCC
Q psy17242 76 MVCTGAKSEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 76 ivitGakS~e~a~~a~~k~~~~L~~~g~~ 104 (172)
|+|||. |..+++.-++.+...+++.|+.
T Consensus 38 VIatg~-s~rhv~Aiad~i~~~~k~~g~~ 65 (115)
T COG0799 38 VIATGN-SSRHVKAIADNVKEELKEAGEV 65 (115)
T ss_pred EEEEeC-chHHHHHHHHHHHHHHHHcCCC
Confidence 667776 7888999999999999888864
No 119
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=23.88 E-value=66 Score=22.62 Aligned_cols=22 Identities=23% Similarity=0.136 Sum_probs=18.7
Q ss_pred HHHHHHHHHHHHHHHcCCCCcc
Q psy17242 86 DSRLAARKYARIIQKLGFPAKF 107 (172)
Q Consensus 86 ~a~~a~~k~~~~L~~~g~~v~~ 107 (172)
-.|.|+.|-++.|++.|+++..
T Consensus 31 iSRtaVwK~Iq~Lr~~G~~I~s 52 (79)
T COG1654 31 ISRTAVWKHIQQLREEGVDIES 52 (79)
T ss_pred ccHHHHHHHHHHHHHhCCceEe
Confidence 3578999999999999998753
No 120
>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=23.85 E-value=77 Score=23.75 Aligned_cols=27 Identities=15% Similarity=0.284 Sum_probs=19.6
Q ss_pred EEEEEecCCe----EEEEee-CCHHHHHHHHH
Q psy17242 66 TTALIFSSGK----MVCTGA-KSEEDSRLAAR 92 (172)
Q Consensus 66 ~t~lIf~SGK----ivitGa-kS~e~a~~a~~ 92 (172)
.|+++|.+|. +...|. ++.+++..-++
T Consensus 82 PTl~lF~~g~~~~~~~Y~G~~r~~~~lv~~v~ 113 (116)
T cd03007 82 PVIYLFHGGDFENPVPYSGADVTVDALQRFLK 113 (116)
T ss_pred CEEEEEeCCCcCCCccCCCCcccHHHHHHHHH
Confidence 3888888885 678887 88877665443
No 121
>smart00653 eIF2B_5 domain present in translation initiation factor eIF2B and eIF5.
Probab=23.71 E-value=1.6e+02 Score=21.93 Aligned_cols=33 Identities=18% Similarity=0.288 Sum_probs=27.5
Q ss_pred cEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHH
Q psy17242 65 RTTALIFSSGKMVCTGAKSEEDSRLAARKYARI 97 (172)
Q Consensus 65 k~t~lIf~SGKivitGakS~e~a~~a~~k~~~~ 97 (172)
.+...+=.+|+.+++|.-+.++++..++++++.
T Consensus 47 gt~g~id~~~rlii~G~~~~~~i~~~l~~yI~~ 79 (110)
T smart00653 47 GTQGSIDGKGRLIVNGRFTPKKLQDLLRRYIKE 79 (110)
T ss_pred CCceeECCCCeEEEEEeeCHHHHHHHHHHHHHh
Confidence 345556566999999999999999999998865
No 122
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=23.26 E-value=2.9e+02 Score=23.62 Aligned_cols=82 Identities=15% Similarity=0.082 Sum_probs=47.4
Q ss_pred EEEEeeCCHHHHHHHHHHHHHHHHHcCCCCccccce------EEEEEEEeec-CccccHHHHHHHcCCCcccccCCCcee
Q psy17242 76 MVCTGAKSEEDSRLAARKYARIIQKLGFPAKFLDFK------IQNMVGSCDV-KFPIRLEGLVLTHGQFSSYEPELFPGL 148 (172)
Q Consensus 76 ivitGakS~e~a~~a~~k~~~~L~~~g~~v~~~~f~------v~NIvat~~~-~f~I~Le~la~~~~~~~~YEPE~fPGl 148 (172)
+.+.|..+.. -+.++.+.|.+.|..+...+.. .-.+...++. +.+.+++.|...+.. ..-|+ ++
T Consensus 9 itv~G~DrpG----IVa~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~~~~~~~~~L~~~L~~---l~~~l--~l 79 (286)
T PRK06027 9 LTLSCPDRPG----IVAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDGLIFNLETLRADFAA---LAEEF--EM 79 (286)
T ss_pred EEEECCCCCc----HHHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCCCCCCHHHHHHHHHH---HHHHh--CC
Confidence 4555664443 3456777888888765433322 2345566666 557777777655432 11133 34
Q ss_pred EEEEc--CCcEEEEEecCcE
Q psy17242 149 IYRMV--KPRIVLLIFVSGK 166 (172)
Q Consensus 149 iyR~~--~~k~~~lIF~SGk 166 (172)
..++. .++.++.||.||.
T Consensus 80 ~i~l~~~~~~~ri~vl~Sg~ 99 (286)
T PRK06027 80 DWRLLDSAERKRVVILVSKE 99 (286)
T ss_pred EEEEcccccCcEEEEEEcCC
Confidence 44443 3567889999986
No 123
>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=23.20 E-value=82 Score=23.38 Aligned_cols=29 Identities=28% Similarity=0.495 Sum_probs=21.9
Q ss_pred cceEEEEEcC---------CcEEEEEecCCeEEEEeeC
Q psy17242 54 FAAVIMRIRE---------PRTTALIFSSGKMVCTGAK 82 (172)
Q Consensus 54 fpgli~R~~~---------Pk~t~lIf~SGKivitGak 82 (172)
+.=|.||... -.||-++|.+||++--|-+
T Consensus 60 ~qVLfYrT~~~~sDG~TTkDECTplvF~n~~LvgWG~~ 97 (102)
T PF11399_consen 60 VQVLFYRTQHKKSDGITTKDECTPLVFKNGKLVGWGDD 97 (102)
T ss_pred EEEEEEEEeeEcCCCCccCCceEEEEEECCEEEEEcHH
Confidence 3445677642 3699999999999988864
No 124
>PTZ00051 thioredoxin; Provisional
Probab=23.10 E-value=98 Score=20.85 Aligned_cols=21 Identities=33% Similarity=0.550 Sum_probs=15.8
Q ss_pred EEEEecCCeEE--EEeeCCHHHHH
Q psy17242 67 TALIFSSGKMV--CTGAKSEEDSR 88 (172)
Q Consensus 67 t~lIf~SGKiv--itGakS~e~a~ 88 (172)
|+++|+.||++ +.|+ +.++++
T Consensus 74 t~~~~~~g~~~~~~~G~-~~~~~~ 96 (98)
T PTZ00051 74 TFKVFKNGSVVDTLLGA-NDEALK 96 (98)
T ss_pred EEEEEeCCeEEEEEeCC-CHHHhh
Confidence 68899999998 7787 445443
No 125
>PF01042 Ribonuc_L-PSP: Endoribonuclease L-PSP; InterPro: IPR006175 This domain is found in endoribonuclease, that is active on single-stranded mRNA and inhibits protein synthesis by cleavage of mRNA []. Previously it was thought to inhibit protein synthesis initiation []. This endoribonuclease may also be involved in the regulation of purine biosynthesis []. ; PDB: 3GTZ_B 3V4D_E 1J7H_A 3R0P_D 2IG8_A 1QD9_B 3L7Q_E 3VCZ_A 3QUW_A 2EWC_K ....
Probab=22.78 E-value=71 Score=23.28 Aligned_cols=21 Identities=33% Similarity=0.447 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHcCCC
Q psy17242 84 EEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 84 ~e~a~~a~~k~~~~L~~~g~~ 104 (172)
+++++.+++++.+.|++.|..
T Consensus 42 ~~Q~~~~l~ni~~~L~~~G~~ 62 (121)
T PF01042_consen 42 EEQTRQALDNIERILAAAGAS 62 (121)
T ss_dssp HHHHHHHHHHHHHHHHHTTS-
T ss_pred HHHHHHHHHhhhhhhhcCCCc
Confidence 789999999999999999976
No 126
>cd02987 Phd_like_Phd Phosducin (Phd)-like family, Phd subfamily; Phd is a cytosolic regulator of G protein functions. It specifically binds G protein betagamma (Gbg)-subunits with high affinity, resulting in the solubilization of Gbg from the plasma membrane. This impedes the formation of a functional G protein trimer (G protein alphabetagamma), thereby inhibiting G protein-mediated signal transduction. Phd also inhibits the GTPase activity of G protein alpha. Phd can be phosphorylated by protein kinase A and G protein-coupled receptor kinase 2, leading to its inactivation. Phd was originally isolated from the retina, where it is highly expressed and has been implicated to play an important role in light adaptation. It is also found in the pineal gland, liver, spleen, striated muscle and the brain. 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=21.85 E-value=67 Score=25.39 Aligned_cols=17 Identities=12% Similarity=0.477 Sum_probs=14.0
Q ss_pred EEEEEecCCeEE--EEeeC
Q psy17242 66 TTALIFSSGKMV--CTGAK 82 (172)
Q Consensus 66 ~t~lIf~SGKiv--itGak 82 (172)
.|+++|..|+++ +.|+.
T Consensus 137 PTlllyk~G~~v~~~vG~~ 155 (175)
T cd02987 137 PALLVYKGGELIGNFVRVT 155 (175)
T ss_pred CEEEEEECCEEEEEEechH
Confidence 399999999999 56663
No 127
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=21.81 E-value=1.6e+02 Score=22.35 Aligned_cols=35 Identities=17% Similarity=0.319 Sum_probs=20.7
Q ss_pred EEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCC
Q psy17242 69 LIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPA 105 (172)
Q Consensus 69 lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v 105 (172)
+...||.++++...+.+++...+++.+. +++|+++
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 5789999999966666665555444332 3477764
No 128
>COG1364 ArgJ N-acetylglutamate synthase (N-acetylornithine aminotransferase) [Amino acid transport and metabolism]
Probab=21.69 E-value=83 Score=28.77 Aligned_cols=22 Identities=50% Similarity=0.659 Sum_probs=19.6
Q ss_pred eEEEEeeCCHHHHHHHHHHHHH
Q psy17242 75 KMVCTGAKSEEDSRLAARKYAR 96 (172)
Q Consensus 75 KivitGakS~e~a~~a~~k~~~ 96 (172)
.+.++||+|.++|+.+++.++.
T Consensus 284 eV~V~GA~~~~~A~~iA~~Ia~ 305 (404)
T COG1364 284 EVTVTGAASEEDARVIARAIAN 305 (404)
T ss_pred EEEEeCCCCHHHHHHHHHHHhc
Confidence 3789999999999999999874
No 129
>PF03129 HGTP_anticodon: Anticodon binding domain; InterPro: IPR004154 tRNA synthetases, or tRNA ligases are involved in protein synthesis. This domain is found in histidyl, glycyl, threonyl and prolyl tRNA synthetases [] it is probably the anticodon binding domain [].; GO: 0004812 aminoacyl-tRNA ligase activity, 0005524 ATP binding; PDB: 1KOG_B 1EVL_D 1EVK_B 1QF6_A 1FYF_B 2I4O_A 2I4M_A 2I4N_A 2I4L_A 1HC7_D ....
Probab=21.67 E-value=1.2e+02 Score=20.65 Aligned_cols=22 Identities=23% Similarity=0.283 Sum_probs=18.8
Q ss_pred HHHHHHHHHHHHHHHHHcCCCC
Q psy17242 84 EEDSRLAARKYARIIQKLGFPA 105 (172)
Q Consensus 84 ~e~a~~a~~k~~~~L~~~g~~v 105 (172)
.+++..-+.++++.|++.|+.+
T Consensus 11 ~~~~~~~a~~l~~~L~~~gi~v 32 (94)
T PF03129_consen 11 DEEIIEYAQELANKLRKAGIRV 32 (94)
T ss_dssp HHHHHHHHHHHHHHHHHTTSEE
T ss_pred cHHHHHHHHHHHHHHHHCCCEE
Confidence 6788889999999999999643
No 130
>PF11111 CENP-M: Centromere protein M (CENP-M); InterPro: IPR020987 The prime candidate for specifying centromere identity is the array of nucleosomes assembles associated with CENP-A []. CENP-A recruits a nucleosome associated complex (CENP-A-NAC complex) comprised of CENP-M which this entry represents, along with two other proteins []. Assembly of the CENP-A NAC at centromeres is partly dependent on CENP-M. The CENP-A NAC is essential, as disruption of the complex causes errors of chromosome alignment and segregation that preclude cell survival [].
Probab=21.64 E-value=2.9e+02 Score=22.48 Aligned_cols=37 Identities=22% Similarity=0.284 Sum_probs=30.7
Q ss_pred CCCCCCCCCCCcEEEEEEEEEEcCCccChHHHHhhCC
Q psy17242 9 PMTPVDMGGSVPQLQNIVSTVNLGCKLDLKKIALHAR 45 (172)
Q Consensus 9 ~~~~~~~~~~~~~I~NvVas~~l~~~ldL~~la~~~~ 45 (172)
...|.+....+|+|-=||-..|+.+...|+.....+.
T Consensus 52 LPLp~e~~~lRprIDlIVFvinl~sk~SL~~ve~SL~ 88 (176)
T PF11111_consen 52 LPLPSENNNLRPRIDLIVFVINLHSKYSLQSVEASLS 88 (176)
T ss_pred CCCcccccCCCceeEEEEEEEecCCcccHHHHHHHHh
Confidence 3456666788999999999999999999998876554
No 131
>PRK15415 propanediol utilization protein PduB; Provisional
Probab=21.47 E-value=1.5e+02 Score=25.69 Aligned_cols=29 Identities=21% Similarity=0.314 Sum_probs=25.2
Q ss_pred CCeEEEEeeCCHHHHHHHHHHHHHHHHHc
Q psy17242 73 SGKMVCTGAKSEEDSRLAARKYARIIQKL 101 (172)
Q Consensus 73 SGKivitGakS~e~a~~a~~k~~~~L~~~ 101 (172)
+|+++++|+-++.+++.|++.-.+.+.+.
T Consensus 119 ~G~~ii~g~gDVs~Vr~AVeaa~~~~~~~ 147 (266)
T PRK15415 119 HGSLIIFGAEDVSDVRRAVEVALKELDRT 147 (266)
T ss_pred ceEEEEEeCCCHHHHHHHHHHHHHHHHhh
Confidence 49999999999999999998888777663
No 132
>PRK15124 2'-5' RNA ligase; Provisional
Probab=21.38 E-value=2.1e+02 Score=22.28 Aligned_cols=57 Identities=11% Similarity=0.058 Sum_probs=37.3
Q ss_pred EEEEEcCCcEEEEEecCCeEEEEeeCC-HHHHHHHHHHHHHHHHHcCCCCccccceEEEEEE
Q psy17242 57 VIMRIREPRTTALIFSSGKMVCTGAKS-EEDSRLAARKYARIIQKLGFPAKFLDFKIQNMVG 117 (172)
Q Consensus 57 li~R~~~Pk~t~lIf~SGKivitGakS-~e~a~~a~~k~~~~L~~~g~~v~~~~f~v~NIva 117 (172)
..+++.. +-.|.+.++++.|.+. .+++..=.+.+.+.++++|+..+.+.|+=+--+|
T Consensus 72 F~l~l~~----~g~Fp~prvlwlg~~~~~~~L~~L~~~l~~~l~~~G~~~e~r~f~PHiTLa 129 (176)
T PRK15124 72 FTLTLDD----AGQWPRSRVVWLGMRQPPRGLLQLANMLRSQAARSGCYQSPQPFHPHITLL 129 (176)
T ss_pred eEEEECc----ccCcCCCCEEEEEcCCCCHHHHHHHHHHHHHHHHcCCCCCCCCCCCCEeec
Confidence 3455543 3355667899999964 4566666677778888999976666665444443
No 133
>PF06815 RVT_connect: Reverse transcriptase connection domain; InterPro: IPR010659 This domain is known as the connection domain. This domain lies between the thumb and palm domains [].; GO: 0003964 RNA-directed DNA polymerase activity, 0006278 RNA-dependent DNA replication; PDB: 1MU2_B 1S9E_B 3QO9_A 1IKY_A 2ZE2_B 3KLF_J 3V6D_B 2YKN_A 1TV6_A 1S9G_B ....
Probab=21.29 E-value=3.5e+02 Score=20.06 Aligned_cols=32 Identities=28% Similarity=0.390 Sum_probs=23.6
Q ss_pred EEcCcccceEEEEE---cCCcEEEEEecCCeEEEEee
Q psy17242 48 EYNPKRFAAVIMRI---REPRTTALIFSSGKMVCTGA 81 (172)
Q Consensus 48 ~YePe~fpgli~R~---~~Pk~t~lIf~SGKivitGa 81 (172)
-|||+. -|+..+ .+-..+-.||..+|..-||-
T Consensus 2 YYdp~k--~Liaeiqk~g~~qwtYqi~Q~~k~LktGk 36 (102)
T PF06815_consen 2 YYDPEK--ELIAEIQKQGQGQWTYQIYQPFKNLKTGK 36 (102)
T ss_dssp -BBTTS--SEEEEEEEEETTEEEEEEEETTEEEEEEE
T ss_pred CCCCCC--cEEEEEEEecCCeEEEEEEcCCccccccc
Confidence 488886 355444 45678999999999999883
No 134
>COG0100 RpsK Ribosomal protein S11 [Translation, ribosomal structure and biogenesis]
Probab=21.18 E-value=3e+02 Score=21.24 Aligned_cols=52 Identities=25% Similarity=0.406 Sum_probs=40.0
Q ss_pred ccceEEEEEcCCcEEEEEec-CCeEEEEeeC--CHHHHHHHHHHHHHHHHHcCCC
Q psy17242 53 RFAAVIMRIREPRTTALIFS-SGKMVCTGAK--SEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 53 ~fpgli~R~~~Pk~t~lIf~-SGKivitGak--S~e~a~~a~~k~~~~L~~~g~~ 104 (172)
-|+-=++-+.|+.-.+++|+ ||.+..-|.+ +.-.|..|++.+.+..++.|++
T Consensus 26 sfNNTivtitD~~Gn~i~wassG~~gfk~~rk~tpyAA~~aa~~aa~~a~e~Gi~ 80 (129)
T COG0100 26 SFNNTIVTITDLTGNVIIWASSGGMGFKGSRKSTPYAAQLAAEDAAKKAKEHGIK 80 (129)
T ss_pred ccCCcEEEecCCCCCEEEEEecCCceEcCCCCCCHHHHHHHHHHHHHHHHHhCcc
Confidence 45666777888877777774 6899998887 3556778888999998888875
No 135
>PF11525 CopK: Copper resistance protein K; InterPro: IPR021604 CopK is a periplasmic dimeric protein which is strongly up-regulated in the presence of copper, leading to a high periplasmic accumulation []. CopK has two different binding sites for Cu(I), each with a different affinity for the metal. Binding of the first Cu(I) ion induces a conformational change of CopK which involves dissociation of the dimeric apo-protein. Binding of a second Cu(I) further increases the plasticity of the protein. CopK has features that are common with functionally related proteins such as a structure consisting of an all-beta fold and a methionine-rich Cu(I) binding site []. ; PDB: 3N7E_B 3N7D_B 3DSP_A 3DSO_A 2K0Q_A 2KM0_A 2LEL_A.
Probab=21.06 E-value=80 Score=22.05 Aligned_cols=20 Identities=30% Similarity=0.629 Sum_probs=14.2
Q ss_pred EEEcCCcEEEEEecCCeEEEE
Q psy17242 59 MRIREPRTTALIFSSGKMVCT 79 (172)
Q Consensus 59 ~R~~~Pk~t~lIf~SGKivit 79 (172)
+.+.+ -.|+.||..|||-.-
T Consensus 10 i~LkD-GstvyiFKDGKMamE 29 (73)
T PF11525_consen 10 IPLKD-GSTVYIFKDGKMAME 29 (73)
T ss_dssp EEBTT-SEEEEEETTS-EEEE
T ss_pred EecCC-CCEEEEEcCCceehh
Confidence 45555 479999999999653
No 136
>cd00032 CASc Caspase, interleukin-1 beta converting enzyme (ICE) homologues; Cysteine-dependent aspartate-directed proteases that mediate programmed cell death (apoptosis). Caspases are synthesized as inactive zymogens and activated by proteolysis of the peptide backbone adjacent to an aspartate. The resulting two subunits associate to form an (alpha)2(beta)2-tetramer which is the active enzyme. Activation of caspases can be mediated by other caspase homologs.
Probab=20.68 E-value=60 Score=26.79 Aligned_cols=41 Identities=22% Similarity=0.434 Sum_probs=24.9
Q ss_pred CcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCCC
Q psy17242 64 PRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLGFPA 105 (172)
Q Consensus 64 Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~v 105 (172)
|+..++|+.+++.-- .....+.+..=++.+.+.|+++||++
T Consensus 8 ~~g~aLII~n~~f~~-~~~~r~g~~~D~~~l~~~f~~lgF~V 48 (243)
T cd00032 8 RRGLALIINNENFDK-GLKDRDGTDVDAENLTKLFESLGYEV 48 (243)
T ss_pred CCCEEEEEechhcCC-CCCCCCChHHHHHHHHHHHHHCCCEE
Confidence 677788888876632 12223334444566777777777765
No 137
>KOG2317|consensus
Probab=20.54 E-value=2.8e+02 Score=21.62 Aligned_cols=31 Identities=23% Similarity=0.258 Sum_probs=25.6
Q ss_pred cCCeEEEEeeCCHHHHHHHHHHHHHHHHHcCCC
Q psy17242 72 SSGKMVCTGAKSEEDSRLAARKYARIIQKLGFP 104 (172)
Q Consensus 72 ~SGKivitGakS~e~a~~a~~k~~~~L~~~g~~ 104 (172)
.|||++-.|. .++++.+++++..+|+..|-.
T Consensus 43 ~s~~~~~gg~--~~q~~q~l~n~~~il~~a~a~ 73 (138)
T KOG2317|consen 43 PSMKLVEGGI--VDQTEQALLNLEEILKAAGAS 73 (138)
T ss_pred CCCCEeccch--HHHHHHHHHHHHHHHHHhccC
Confidence 4667777666 789999999999999998854
No 138
>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=20.28 E-value=2.5e+02 Score=19.40 Aligned_cols=40 Identities=15% Similarity=0.179 Sum_probs=26.4
Q ss_pred EEcCCcEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHHcC
Q psy17242 60 RIREPRTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQKLG 102 (172)
Q Consensus 60 R~~~Pk~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~~g 102 (172)
....+..-.+.+.+|..|..|... ....++++..+++++.
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 334444455566789999999964 6667777777777764
No 139
>PF05132 RNA_pol_Rpc4: RNA polymerase III RPC4; InterPro: IPR007811 This family comprises a specific subunit for Pol III, the tRNA specific polymerase.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006383 transcription from RNA polymerase III promoter, 0005666 DNA-directed RNA polymerase III complex
Probab=20.25 E-value=79 Score=23.81 Aligned_cols=14 Identities=21% Similarity=0.261 Sum_probs=12.1
Q ss_pred EEEEEecCCeEEEE
Q psy17242 66 TTALIFSSGKMVCT 79 (172)
Q Consensus 66 ~t~lIf~SGKivit 79 (172)
.++.|++|||+.+-
T Consensus 70 GkL~V~kSGkv~l~ 83 (131)
T PF05132_consen 70 GKLRVHKSGKVTLK 83 (131)
T ss_pred EEEEEEeCCcEEEE
Confidence 58899999999875
No 140
>TIGR00741 yfiA ribosomal subunit interface protein. The member of this family from E. coli is now recognized as a protein at the interace between ribosomal large and small subunits, with about 1/3 as many copies per cell as the number of ribosomes.
Probab=20.17 E-value=2e+02 Score=19.74 Aligned_cols=35 Identities=17% Similarity=0.261 Sum_probs=22.9
Q ss_pred cEEEEEecCCeEEEEeeCCHHHHHHHHHHHHHHHHH
Q psy17242 65 RTTALIFSSGKMVCTGAKSEEDSRLAARKYARIIQK 100 (172)
Q Consensus 65 k~t~lIf~SGKivitGakS~e~a~~a~~k~~~~L~~ 100 (172)
.|.+.+--.|.. +.+..+.+++..|++...+.|++
T Consensus 49 ~~~i~v~~~g~~-l~a~~~~~d~~~Aid~a~~kler 83 (95)
T TIGR00741 49 KVEATIYTPGGV-IRASAEHEDMYAAIDLAIDKLER 83 (95)
T ss_pred EEEEEEEcCCCE-EEEEEecCcHHHHHHHHHHHHHH
Confidence 466777666664 34444566788888877777664
Done!