Query psy9199
Match_columns 204
No_of_seqs 155 out of 577
Neff 5.6
Searched_HMMs 46136
Date Fri Aug 16 21:24:39 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9199.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9199hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3302|consensus 100.0 1.4E-63 3.1E-68 415.7 18.4 180 22-202 2-183 (200)
2 cd04516 TBP_eukaryotes eukaryo 100.0 8.3E-61 1.8E-65 397.1 19.8 159 44-202 2-162 (174)
3 PLN00062 TATA-box-binding prot 100.0 2.1E-60 4.5E-65 396.3 19.9 159 44-202 2-162 (179)
4 COG2101 SPT15 TATA-box binding 100.0 2.3E-60 4.9E-65 391.0 17.2 162 40-201 4-169 (185)
5 cd04518 TBP_archaea archaeal T 100.0 2.6E-59 5.6E-64 388.1 19.6 160 43-202 1-162 (174)
6 PRK00394 transcription factor; 100.0 3.1E-59 6.6E-64 389.2 19.4 159 44-202 1-163 (179)
7 cd00652 TBP_TLF TATA box bindi 100.0 1.3E-58 2.8E-63 383.7 19.9 160 43-202 1-163 (174)
8 cd04517 TLF TBP-like factors ( 100.0 2.9E-58 6.2E-63 381.8 20.1 161 42-202 1-163 (174)
9 PF00352 TBP: Transcription fa 100.0 4.6E-28 9.9E-33 179.4 11.9 84 42-125 2-86 (86)
10 PF00352 TBP: Transcription fa 99.9 1.7E-27 3.7E-32 176.3 7.1 73 130-202 1-73 (86)
11 COG2101 SPT15 TATA-box binding 99.9 7.1E-26 1.5E-30 186.9 11.1 92 34-126 89-184 (185)
12 PRK00394 transcription factor; 99.9 2.8E-25 6.1E-30 185.2 12.4 86 41-126 89-177 (179)
13 cd04518 TBP_archaea archaeal T 99.9 6E-25 1.3E-29 182.6 12.0 85 40-124 89-174 (174)
14 cd04516 TBP_eukaryotes eukaryo 99.9 3.4E-24 7.4E-29 178.1 7.5 70 133-202 2-71 (174)
15 cd00652 TBP_TLF TATA box bindi 99.9 3.9E-23 8.4E-28 171.5 11.7 84 40-123 89-174 (174)
16 PLN00062 TATA-box-binding prot 99.9 3.1E-22 6.7E-27 167.0 11.4 85 41-125 89-175 (179)
17 cd04517 TLF TBP-like factors ( 99.9 9.3E-22 2E-26 163.4 11.2 83 40-122 89-173 (174)
18 KOG3302|consensus 99.7 7.9E-17 1.7E-21 135.2 9.9 86 40-125 109-196 (200)
19 COG4871 Uncharacterized protei 96.6 0.0099 2.1E-07 49.6 7.6 63 60-124 47-109 (193)
20 PF11858 DUF3378: Domain of un 95.9 0.0093 2E-07 44.0 3.6 31 78-109 30-60 (81)
21 PF11858 DUF3378: Domain of un 95.5 0.012 2.5E-07 43.5 2.7 36 165-200 26-61 (81)
22 PRK12475 thiamine/molybdopteri 91.2 0.55 1.2E-05 42.8 6.1 60 57-118 277-337 (338)
23 TIGR00716 rnhC ribonuclease HI 90.8 0.42 9.2E-06 42.8 5.0 29 78-107 28-56 (284)
24 PRK00996 ribonuclease HIII; Pr 89.8 0.39 8.4E-06 43.4 3.9 35 163-197 25-59 (304)
25 PRK00996 ribonuclease HIII; Pr 89.5 0.53 1.2E-05 42.5 4.5 29 78-107 31-59 (304)
26 TIGR00716 rnhC ribonuclease HI 89.5 0.45 9.7E-06 42.6 4.0 34 163-196 22-55 (284)
27 COG1039 RnhC Ribonuclease HIII 88.1 1.1 2.4E-05 40.5 5.5 42 78-120 31-72 (297)
28 PRK07688 thiamine/molybdopteri 86.2 2.1 4.4E-05 39.1 6.3 60 57-118 277-338 (339)
29 COG1039 RnhC Ribonuclease HIII 85.8 0.69 1.5E-05 41.8 2.9 34 166-199 28-61 (297)
30 COG4871 Uncharacterized protei 82.8 2.8 6E-05 35.3 5.0 61 138-201 36-96 (193)
31 PRK15468 carboxysome structura 74.3 5.5 0.00012 31.2 4.1 33 94-128 72-105 (111)
32 TIGR02187 GlrX_arch Glutaredox 71.5 5.4 0.00012 33.5 3.8 110 89-200 79-208 (215)
33 PLN00410 U5 snRNP protein, DIM 60.5 13 0.00028 30.1 3.8 79 44-123 25-125 (142)
34 PRK12475 thiamine/molybdopteri 54.4 15 0.00033 33.5 3.7 52 146-201 277-330 (338)
35 cd03065 PDI_b_Calsequestrin_N 53.3 19 0.00041 28.1 3.6 30 89-118 89-119 (120)
36 PRK09381 trxA thioredoxin; Pro 50.2 21 0.00046 25.9 3.3 29 89-117 77-107 (109)
37 cd01644 RT_pepA17 RT_pepA17: R 48.5 23 0.00049 30.1 3.6 28 101-128 145-172 (213)
38 KOG0910|consensus 46.8 28 0.00062 28.6 3.8 31 89-119 117-149 (150)
39 PHA02278 thioredoxin-like prot 41.6 32 0.00069 25.8 3.1 24 89-112 74-99 (103)
40 PF14014 DUF4230: Protein of u 41.5 1.2E+02 0.0027 23.6 6.7 73 48-123 41-121 (157)
41 PRK11509 hydrogenase-1 operon 41.3 45 0.00098 26.7 4.1 31 89-119 93-125 (132)
42 cd02963 TRX_DnaJ TRX domain, D 40.9 28 0.00061 25.9 2.7 28 89-116 81-110 (111)
43 PF13575 DUF4135: Domain of un 40.8 26 0.00057 32.0 3.0 54 101-155 124-177 (370)
44 TIGR00090 iojap_ybeB iojap-lik 40.6 57 0.0012 24.5 4.4 44 80-128 18-61 (99)
45 PRK07688 thiamine/molybdopteri 40.2 47 0.001 30.3 4.6 30 172-201 302-331 (339)
46 PF03135 CagE_TrbE_VirB: CagE, 39.7 44 0.00095 27.7 4.0 40 90-130 144-183 (205)
47 PTZ00129 40S ribosomal protein 39.2 77 0.0017 26.1 5.2 47 81-127 41-91 (149)
48 PRK10996 thioredoxin 2; Provis 39.1 39 0.00086 26.3 3.4 29 89-117 108-138 (139)
49 COG4978 Transcriptional regula 37.9 82 0.0018 25.7 5.2 46 86-131 79-125 (153)
50 cd02965 HyaE HyaE family; HyaE 37.0 15 0.00033 28.5 0.7 50 149-200 50-108 (111)
51 KOG3946|consensus 33.0 83 0.0018 28.9 4.8 57 111-175 72-139 (338)
52 COG4274 Uncharacterized conser 32.9 72 0.0016 24.7 3.8 58 100-157 18-77 (104)
53 PF00085 Thioredoxin: Thioredo 32.5 81 0.0018 21.9 3.9 28 89-116 73-102 (103)
54 cd02948 TRX_NDPK TRX domain, T 32.5 56 0.0012 23.7 3.1 27 89-116 73-101 (102)
55 PF11775 CobT_C: Cobalamin bio 32.1 90 0.002 27.2 4.7 48 86-136 12-59 (219)
56 PRK13011 formyltetrahydrofolat 32.0 2.4E+02 0.0052 25.2 7.6 73 114-188 21-99 (286)
57 TIGR01651 CobT cobaltochelatas 31.2 85 0.0018 31.3 4.9 46 89-137 395-440 (600)
58 PRK11538 ribosome-associated p 31.1 99 0.0021 23.6 4.4 32 95-127 34-65 (105)
59 PF02410 Oligomerisation: Olig 31.0 95 0.0021 23.1 4.2 28 98-126 32-60 (100)
60 cd07049 BMC_EutL_repeat1 ethan 30.7 77 0.0017 24.5 3.7 28 96-124 71-100 (103)
61 smart00115 CASc Caspase, inter 30.5 47 0.001 28.6 2.8 42 86-129 6-47 (241)
62 cd02988 Phd_like_VIAF Phosduci 30.1 31 0.00068 28.9 1.6 78 45-124 105-191 (192)
63 TIGR03632 bact_S11 30S ribosom 30.0 1.9E+02 0.0041 22.1 5.8 47 81-127 13-62 (108)
64 cd07996 WGR_MMR_like WGR domai 29.9 1.3E+02 0.0029 20.6 4.6 33 95-127 40-72 (74)
65 CHL00041 rps11 ribosomal prote 29.5 1.6E+02 0.0034 22.9 5.3 46 82-127 27-75 (116)
66 cd02950 TxlA TRX-like protein 28.7 1.1E+02 0.0023 24.0 4.4 31 89-119 78-111 (142)
67 cd00032 CASc Caspase, interleu 28.5 42 0.00091 28.7 2.1 42 87-129 8-49 (243)
68 PF08002 DUF1697: Protein of u 28.0 1.1E+02 0.0023 24.3 4.3 36 92-129 38-73 (137)
69 cd00148 PROF Profilin binds ac 27.9 1.9E+02 0.004 22.4 5.6 36 91-126 88-127 (127)
70 PTZ00397 macrophage migration 27.5 1.7E+02 0.0037 22.0 5.2 40 99-138 63-103 (116)
71 TIGR01068 thioredoxin thioredo 27.3 89 0.0019 21.5 3.4 28 89-116 70-99 (101)
72 PF06200 tify: tify domain; I 27.3 1.3E+02 0.0029 18.8 3.7 28 88-115 5-32 (36)
73 PF11869 DUF3389: Protein of u 27.0 33 0.00071 25.1 1.0 12 182-193 3-14 (75)
74 cd02949 TRX_NTR TRX domain, no 26.6 77 0.0017 22.6 3.0 25 89-113 69-95 (97)
75 PRK05309 30S ribosomal protein 26.3 1.8E+02 0.004 23.0 5.3 46 82-127 31-79 (128)
76 cd02985 TRX_CDSP32 TRX family, 25.6 1.2E+02 0.0025 22.1 3.8 25 89-114 73-99 (103)
77 PF12386 Peptidase_C71: Pseudo 24.8 85 0.0018 25.4 3.0 39 112-150 59-97 (142)
78 smart00392 PROF Profilin. Bind 24.3 2.5E+02 0.0054 21.7 5.7 38 89-126 88-129 (129)
79 COG2221 DsrA Dissimilatory sul 23.9 51 0.0011 30.3 1.9 77 90-174 61-142 (317)
80 PF12971 NAGLU_N: Alpha-N-acet 23.5 1.4E+02 0.0029 21.8 3.8 26 94-120 39-64 (86)
81 PHA02956 hypothetical protein; 23.2 73 0.0016 26.3 2.4 23 94-127 113-135 (189)
82 PF10865 DUF2703: Domain of un 23.1 85 0.0018 24.8 2.8 27 106-132 21-47 (120)
83 PF13549 ATP-grasp_5: ATP-gras 23.1 1.8E+02 0.0039 25.0 5.0 59 80-140 49-107 (222)
84 cd03005 PDI_a_ERp46 PDIa famil 23.1 1.1E+02 0.0023 21.5 3.1 23 89-111 75-99 (102)
85 cd01645 RT_Rtv RT_Rtv: Reverse 22.9 1.3E+02 0.0029 25.0 4.1 41 89-131 158-198 (213)
86 TIGR00411 redox_disulf_1 small 22.8 1.3E+02 0.0029 20.1 3.5 22 96-117 60-81 (82)
87 cd02956 ybbN ybbN protein fami 22.7 97 0.0021 21.7 2.8 25 89-113 68-94 (96)
88 KOG4180|consensus 22.2 1.3E+02 0.0028 28.2 4.1 72 90-177 254-334 (395)
89 cd07046 BMC_PduU-EutS 1,2-prop 22.2 1.4E+02 0.003 23.2 3.7 30 96-127 73-103 (110)
90 PF10979 DUF2786: Protein of u 21.8 1.4E+02 0.003 19.3 3.1 22 106-127 20-41 (43)
91 COG4810 EutS Ethanolamine util 21.7 1.5E+02 0.0032 23.2 3.7 30 93-124 81-110 (121)
92 PF11399 DUF3192: Protein of u 21.5 76 0.0017 24.5 2.2 28 78-105 61-97 (102)
93 cd02393 PNPase_KH Polynucleoti 21.2 1.9E+02 0.0042 19.4 4.0 27 89-116 33-59 (61)
94 PF02838 Glyco_hydro_20b: Glyc 21.1 1.5E+02 0.0033 22.0 3.8 38 87-125 75-112 (124)
95 PF05005 Ocnus: Janus/Ocnus fa 21.1 1.5E+02 0.0032 23.0 3.7 57 68-129 4-62 (108)
96 cd00448 YjgF_YER057c_UK114_fam 20.8 1.2E+02 0.0025 21.7 3.0 36 92-127 10-51 (107)
97 cd03715 RT_ZFREV_like RT_ZFREV 20.5 1.7E+02 0.0036 24.1 4.2 41 89-131 154-194 (210)
98 PRK06027 purU formyltetrahydro 20.5 5E+02 0.011 23.0 7.5 71 114-188 20-99 (286)
99 PF03129 HGTP_anticodon: Antic 20.2 1.8E+02 0.0038 20.5 3.8 29 100-129 5-33 (94)
100 PF00403 HMA: Heavy-metal-asso 20.0 95 0.0021 20.3 2.2 32 92-127 31-62 (62)
No 1
>KOG3302|consensus
Probab=100.00 E-value=1.4e-63 Score=415.65 Aligned_cols=180 Identities=41% Similarity=0.750 Sum_probs=173.9
Q ss_pred CCccccCCCCCCCCCCCCCCCceEEEEEEEEEeeCCccChHHHHhcCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceE
Q psy9199 22 QTVVPIQNHAPPQPPAHDPEVDIIINNVVCSFSVRCHLNLRQIALNGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKIT 100 (204)
Q Consensus 22 ~~~~~i~e~~~~~~~~~~~~~~i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKiv 100 (204)
.|+.+++++..++.+ ++..+++.++||||+++++|+|||.+||..++|+||+|+. |+|+||+++|++|++||+||||+
T Consensus 2 ~~~~~~~~~~~~~~~-~~~~i~~~l~nivc~~~~~c~ldLk~ial~~~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ 80 (200)
T KOG3302|consen 2 ADPESIYENVAKLAD-IDSGLDPTLQNIVCTVNLNCKLDLKEIALHARNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIV 80 (200)
T ss_pred CCcccccccccCccc-cccccceEEEeEEEEEeccceecHHHHhhhccccccCcccccEEEEEEcCCceEEEEecCCcEE
Confidence 467889999999887 7889999999999999999999999999999999999886 99999999999999999999999
Q ss_pred EeecCCHHHHHHHHHHHHHHHHHcCCccccceeeEEEEEEEEeCCCccChHHHHHHcc-ccccCCCCCceeEEEeCCCce
Q psy9199 101 CTGATSEDQSKIAARRYARCLQRLGFKARFTNFRVVNVLGTCSMPFAIRILQFSEKHR-AAEYEPELHPGVTYRITRPKA 179 (204)
Q Consensus 101 itGakS~e~a~~a~~k~~~~L~~lG~~v~~~~f~v~NIvat~~~~~~I~L~~la~~~~-~~~YePe~fPgliyr~~~pk~ 179 (204)
||||+|++++|.|+++++|+||++||+++|.+|++|||||||||||+|+|++++..|+ +++||||+||||+|||.+|++
T Consensus 81 ctgA~se~~ar~aark~aRilqkLgf~~~f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv 160 (200)
T KOG3302|consen 81 CTGAKSEDSARLAARKYARILQKLGFPVKFRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKV 160 (200)
T ss_pred EeccCCHHHHHHHHHHHHHHHHHcCCCceehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcE
Confidence 9999999999999999999999999999999999999999999999999999999998 999999999999999999999
Q ss_pred EEEEeccCcEEEEecCCCCcccc
Q psy9199 180 TLKIFSTGGITVTACNDSNKIPV 202 (204)
Q Consensus 180 t~lIF~sGkivitGak~~~~~~~ 202 (204)
+++||+||||++|||++.++++.
T Consensus 161 ~l~IF~tG~VvvtgA~~~~~i~~ 183 (200)
T KOG3302|consen 161 VLLIFVTGKVVVTGAKVREETYE 183 (200)
T ss_pred EEEEecCCEEEEEecccHHHHHH
Confidence 99999999999999999988753
No 2
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=100.00 E-value=8.3e-61 Score=397.07 Aligned_cols=159 Identities=45% Similarity=0.833 Sum_probs=153.7
Q ss_pred eEEEEEEEEEeeCCccChHHHHhcCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHH
Q psy9199 44 IIINNVVCSFSVRCHLNLRQIALNGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQ 122 (204)
Q Consensus 44 i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~ 122 (204)
++|+|||||++++|+|||++|+..++|++|||++ +.++||+++|+++++||+||||+||||+|+|+++.|+++++++|+
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L~ 81 (174)
T cd04516 2 PKIQNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARIIQ 81 (174)
T ss_pred CEEEEEEEEEEcCCeecHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHHH
Confidence 6899999999999999999999999999999998 666899999999999999999999999999999999999999999
Q ss_pred HcCCccccceeeEEEEEEEEeCCCccChHHHHHHcc-ccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecCCCCccc
Q psy9199 123 RLGFKARFTNFRVVNVLGTCSMPFAIRILQFSEKHR-AAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACNDSNKIP 201 (204)
Q Consensus 123 ~lG~~v~~~~f~v~NIvat~~~~~~I~L~~la~~~~-~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~~~ 201 (204)
++|+++++.+|+||||||||||+|+|||++||..|+ +++||||+||||+||+.+||++++||+||||+|||||+++|++
T Consensus 82 ~~g~~~~~~~~~v~Nivat~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~ 161 (174)
T cd04516 82 KLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEIY 161 (174)
T ss_pred HcCCCCCCCceEEEEEEEEEECCCcccHHHHHHhChhccEeCCccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHHH
Confidence 999999999999999999999999999999998776 9999999999999999999999999999999999999999876
Q ss_pred c
Q psy9199 202 V 202 (204)
Q Consensus 202 ~ 202 (204)
.
T Consensus 162 ~ 162 (174)
T cd04516 162 Q 162 (174)
T ss_pred H
Confidence 4
No 3
>PLN00062 TATA-box-binding protein; Provisional
Probab=100.00 E-value=2.1e-60 Score=396.28 Aligned_cols=159 Identities=43% Similarity=0.801 Sum_probs=153.7
Q ss_pred eEEEEEEEEEeeCCccChHHHHhcCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHH
Q psy9199 44 IIINNVVCSFSVRCHLNLRQIALNGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQ 122 (204)
Q Consensus 44 i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~ 122 (204)
++|+|||||++++|+|||++|+..++|++|||++ +.++||+++|+++++||+||||+||||||+++++.|+++++++|+
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L~ 81 (179)
T PLN00062 2 PTLQNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARIIQ 81 (179)
T ss_pred cEEEEEEEEEEcCCcccHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHHH
Confidence 6899999999999999999999999999999997 666899999999999999999999999999999999999999999
Q ss_pred HcCCccccceeeEEEEEEEEeCCCccChHHHHHHcc-ccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecCCCCccc
Q psy9199 123 RLGFKARFTNFRVVNVLGTCSMPFAIRILQFSEKHR-AAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACNDSNKIP 201 (204)
Q Consensus 123 ~lG~~v~~~~f~v~NIvat~~~~~~I~L~~la~~~~-~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~~~ 201 (204)
++|+++++.+|+|||||||+||+|+|||+.||..|+ +++||||+||||+||+.+|+++++||+||||+|||||+++|++
T Consensus 82 ~lg~~~~~~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~ 161 (179)
T PLN00062 82 KLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIY 161 (179)
T ss_pred HcCCCcCCCccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHHH
Confidence 999999999999999999999999999999998776 9999999999999999999999999999999999999999876
Q ss_pred c
Q psy9199 202 V 202 (204)
Q Consensus 202 ~ 202 (204)
.
T Consensus 162 ~ 162 (179)
T PLN00062 162 T 162 (179)
T ss_pred H
Confidence 4
No 4
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=100.00 E-value=2.3e-60 Score=391.03 Aligned_cols=162 Identities=29% Similarity=0.525 Sum_probs=155.4
Q ss_pred CCCceEEEEEEEEEeeCCccChHHHHhcCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHH
Q psy9199 40 PEVDIIINNVVCSFSVRCHLNLRQIALNGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYA 118 (204)
Q Consensus 40 ~~~~i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~ 118 (204)
....++|+|||||.+|+++|||+.++..++++||||++ +.++||+++|++++|||+|||||||||||.++++.|+++++
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 46778999999999999999999999999999999997 44479999999999999999999999999999999999999
Q ss_pred HHHHHcCCccccc-eeeEEEEEEEEeCCCccChHHHHHHcc--ccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecC
Q psy9199 119 RCLQRLGFKARFT-NFRVVNVLGTCSMPFAIRILQFSEKHR--AAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACN 195 (204)
Q Consensus 119 ~~L~~lG~~v~~~-~f~v~NIvat~~~~~~I~L~~la~~~~--~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak 195 (204)
++|+++|+++.+. .++|||||||+|+++++||+.+|..+. +++|||||||||+||+.+|++++|||+|||+||||||
T Consensus 84 ~~L~~~g~~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGLVYRl~~P~VV~LiF~SGK~ViTGaK 163 (185)
T COG2101 84 KKLKDGGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDEPRVVLLLFGSGKLVITGAK 163 (185)
T ss_pred HHHHhcCcCcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCeeEEEcCCCCEEEEEecCCcEEEecCC
Confidence 9999999999988 899999999999999999999999887 6999999999999999999999999999999999999
Q ss_pred CCCccc
Q psy9199 196 DSNKIP 201 (204)
Q Consensus 196 ~~~~~~ 201 (204)
+++|++
T Consensus 164 ~~ed~~ 169 (185)
T COG2101 164 SEEDAE 169 (185)
T ss_pred CHHHHH
Confidence 999875
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=2.6e-59 Score=388.13 Aligned_cols=160 Identities=28% Similarity=0.478 Sum_probs=153.3
Q ss_pred ceEEEEEEEEEeeCCccChHHHHhcCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHH
Q psy9199 43 DIIINNVVCSFSVRCHLNLRQIALNGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCL 121 (204)
Q Consensus 43 ~i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L 121 (204)
.++|+|||||++++|+|||++|+..++|++|||++ +.++||+++|+++++||+||||+||||+|+++++.|+++++++|
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 36899999999999999999999999999999987 66689999999999999999999999999999999999999999
Q ss_pred HHcCCcccc-ceeeEEEEEEEEeCCCccChHHHHHHccccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecCCCCcc
Q psy9199 122 QRLGFKARF-TNFRVVNVLGTCSMPFAIRILQFSEKHRAAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACNDSNKI 200 (204)
Q Consensus 122 ~~lG~~v~~-~~f~v~NIvat~~~~~~I~L~~la~~~~~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~~ 200 (204)
+++|+++.. .+|+|+|||||++++++|||+.||..+++++||||+||||+||+.+|+++++||+||||+|||||+++++
T Consensus 81 ~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~la~~~~~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~~ 160 (174)
T cd04518 81 KDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIGLPNAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEEDA 160 (174)
T ss_pred HhcCCCccCCCceEEEEEEEEEEcCCccCHHHHHhhCCCCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 999998754 5899999999999999999999999999999999999999999999999999999999999999999987
Q ss_pred cc
Q psy9199 201 PV 202 (204)
Q Consensus 201 ~~ 202 (204)
+.
T Consensus 161 ~~ 162 (174)
T cd04518 161 KR 162 (174)
T ss_pred HH
Confidence 64
No 6
>PRK00394 transcription factor; Reviewed
Probab=100.00 E-value=3.1e-59 Score=389.20 Aligned_cols=159 Identities=28% Similarity=0.479 Sum_probs=152.6
Q ss_pred eEEEEEEEEEeeCCccChHHHHhcCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHH
Q psy9199 44 IIINNVVCSFSVRCHLNLRQIALNGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQ 122 (204)
Q Consensus 44 i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~ 122 (204)
++|+|||||++++|+|||++||..++|++|||++ +.++||+++|+++++||+||||+||||+|+++++.|+++++++|+
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 5799999999999999999999999999999997 666899999999999999999999999999999999999999999
Q ss_pred HcCCccc-cceeeEEEEEEEEeCCCccChHHHHHHc--cccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecCCCCc
Q psy9199 123 RLGFKAR-FTNFRVVNVLGTCSMPFAIRILQFSEKH--RAAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACNDSNK 199 (204)
Q Consensus 123 ~lG~~v~-~~~f~v~NIvat~~~~~~I~L~~la~~~--~~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~ 199 (204)
++|+++. ..+|+|+|||||++++++|||++||..+ ++++||||+||||+||+.+|+++++||+||||+|||||++++
T Consensus 81 ~~g~~~~~~~~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~ 160 (179)
T PRK00394 81 ELGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEED 160 (179)
T ss_pred HcCCCccCCCceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHH
Confidence 9999986 5699999999999999999999999987 799999999999999999999999999999999999999998
Q ss_pred ccc
Q psy9199 200 IPV 202 (204)
Q Consensus 200 ~~~ 202 (204)
++.
T Consensus 161 ~~~ 163 (179)
T PRK00394 161 AEK 163 (179)
T ss_pred HHH
Confidence 764
No 7
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=100.00 E-value=1.3e-58 Score=383.68 Aligned_cols=160 Identities=45% Similarity=0.773 Sum_probs=153.9
Q ss_pred ceEEEEEEEEEeeCCccChHHHHhcCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHH
Q psy9199 43 DIIINNVVCSFSVRCHLNLRQIALNGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCL 121 (204)
Q Consensus 43 ~i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L 121 (204)
.++|+||||+++++|+|||++||..++|++|||++ +.++||+++|+++++||+||||+||||+|+++++.|+++++++|
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 36899999999999999999999999999999987 66689999999999999999999999999999999999999999
Q ss_pred HHcCCcc-ccceeeEEEEEEEEeCCCccChHHHHHHcc-ccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecCCCCc
Q psy9199 122 QRLGFKA-RFTNFRVVNVLGTCSMPFAIRILQFSEKHR-AAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACNDSNK 199 (204)
Q Consensus 122 ~~lG~~v-~~~~f~v~NIvat~~~~~~I~L~~la~~~~-~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~ 199 (204)
+++|+++ ++.+|+|+|||||++|+|+|||++||..++ +++||||+||||+||+.+|++|++||+||||+|||||++++
T Consensus 81 ~~~g~~~~~~~~~~v~NIvas~~l~~~i~L~~la~~~~~~~~YePe~fpgli~r~~~pk~t~lIF~sGkvvitGaks~~~ 160 (174)
T cd00652 81 QKLGFPVEKFPEFKVQNIVASCDLGFPIRLEELALKHPENASYEPELFPGLIYRMDEPKVVLLIFVSGKIVITGAKSRED 160 (174)
T ss_pred HHcCCCccccCceEEEEEEEEEECCCcccHHHHHhhhhcccEECCccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHH
Confidence 9999987 888999999999999999999999999997 99999999999999999999999999999999999999998
Q ss_pred ccc
Q psy9199 200 IPV 202 (204)
Q Consensus 200 ~~~ 202 (204)
++.
T Consensus 161 ~~~ 163 (174)
T cd00652 161 IYE 163 (174)
T ss_pred HHH
Confidence 763
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=2.9e-58 Score=381.82 Aligned_cols=161 Identities=63% Similarity=1.019 Sum_probs=153.7
Q ss_pred CceEEEEEEEEEeeCCccChHHHHhcCCCceeeCCCceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHH
Q psy9199 42 VDIIINNVVCSFSVRCHLNLRQIALNGVNVEYRRENGMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCL 121 (204)
Q Consensus 42 ~~i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L 121 (204)
++++|+||||+++++|+|||++|+..++|++|||.++.++||+++|+++++||+||||+|||+||+++++.|+++++++|
T Consensus 1 ~~~~i~Nvvas~~l~~~idL~~la~~l~n~eYeP~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~l 80 (174)
T cd04517 1 LDILIVNVVCQFSLRCHIDLRKLALAGRNVEYNPRYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARLL 80 (174)
T ss_pred CccEEEEEEEEEEcCCcccHHHHHhhCCCCEEeCCCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHH
Confidence 46899999999999999999999999999999994366689999999999999999999999999999999999999999
Q ss_pred HHcCCcc-ccceeeEEEEEEEEeCCCccChHHHHHHcc-ccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecCCCCc
Q psy9199 122 QRLGFKA-RFTNFRVVNVLGTCSMPFAIRILQFSEKHR-AAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACNDSNK 199 (204)
Q Consensus 122 ~~lG~~v-~~~~f~v~NIvat~~~~~~I~L~~la~~~~-~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~ 199 (204)
+++|++. ++.+|+|+|||||+++||+|||++||..+. +++||||+||||+||+.+|++|++||+||||+|||+|++++
T Consensus 81 ~~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~ 160 (174)
T cd04517 81 QKLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMED 160 (174)
T ss_pred HHcCCCcccCCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHH
Confidence 9999986 888999999999999999999999998875 99999999999999999999999999999999999999998
Q ss_pred ccc
Q psy9199 200 IPV 202 (204)
Q Consensus 200 ~~~ 202 (204)
++.
T Consensus 161 ~~~ 163 (174)
T cd04517 161 VRE 163 (174)
T ss_pred HHH
Confidence 764
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=99.95 E-value=4.6e-28 Score=179.39 Aligned_cols=84 Identities=40% Similarity=0.552 Sum_probs=78.3
Q ss_pred CceEEEEEEEEEeeCCccChHHHHhcCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHH
Q psy9199 42 VDIIINNVVCSFSVRCHLNLRQIALNGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARC 120 (204)
Q Consensus 42 ~~i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~ 120 (204)
.+++|+||||+++++++|||++||..++|++|||++ +.++||+++|+++++||+||||+||||+|+++++.|+++++++
T Consensus 2 ~~~~i~NIva~~~l~~~idL~~la~~~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~~~ 81 (86)
T PF00352_consen 2 PDFKIVNIVASFDLPFEIDLEELAEELENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKILPI 81 (86)
T ss_dssp EEEEEEEEEEEEE-SSEB-HHHHHHHSTTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHHH
T ss_pred CccEEEEEEEEEECCCccCHHHHHhhccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHH
Confidence 468999999999999999999999999999999997 5558999999999999999999999999999999999999999
Q ss_pred HHHcC
Q psy9199 121 LQRLG 125 (204)
Q Consensus 121 L~~lG 125 (204)
|+++|
T Consensus 82 L~~~~ 86 (86)
T PF00352_consen 82 LQKLG 86 (86)
T ss_dssp HHHTT
T ss_pred HHHcC
Confidence 99986
No 10
>PF00352 TBP: Transcription factor TFIID (or TATA-binding protein, TBP); InterPro: IPR000814 The TATA-box binding protein (TBP) is required for the initiation of transcription by RNA polymerases I, II and III, from promoters with or without a TATA box [, ]. TBP associates with a host of factors, including the general transcription factors TFIIA, -B, -D, -E, and -H, to form huge multi-subunit pre-initiation complexes on the core promoter. Through its association with different transcription factors, TBP can initiate transcription from different RNA polymerases. There are several related TBPs, including TBP-like (TBPL) proteins []. The C-terminal core of TBP (~180 residues) is highly conserved and contains two 77-amino acid repeats that produce a saddle-shaped structure that straddles the DNA; this region binds to the TATA box and interacts with transcription factors and regulatory proteins []. By contrast, the N-terminal region varies in both length and sequence.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0006367 transcription initiation from RNA polymerase II promoter; PDB: 1D3U_A 1PCZ_B 1AIS_A 1NGM_A 1TBP_A 1TBA_B 1YTB_A 1RM1_A 1YTF_A 1NH2_A ....
Probab=99.94 E-value=1.7e-27 Score=176.35 Aligned_cols=73 Identities=37% Similarity=0.759 Sum_probs=67.6
Q ss_pred cceeeEEEEEEEEeCCCccChHHHHHHccccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecCCCCcccc
Q psy9199 130 FTNFRVVNVLGTCSMPFAIRILQFSEKHRAAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACNDSNKIPV 202 (204)
Q Consensus 130 ~~~f~v~NIvat~~~~~~I~L~~la~~~~~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~~~~ 202 (204)
|.+|+|+||||+++++++|||++||..+++++||||+||||+||+.+|+++++||+||||+|||||++++++.
T Consensus 1 ~~~~~i~NIva~~~l~~~idL~~la~~~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~ 73 (86)
T PF00352_consen 1 FPDFKIVNIVASFDLPFEIDLEELAEELENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKK 73 (86)
T ss_dssp -EEEEEEEEEEEEE-SSEB-HHHHHHHSTTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHH
T ss_pred CCccEEEEEEEEEECCCccCHHHHHhhccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHH
Confidence 5689999999999999999999999999999999999999999999999999999999999999999998753
No 11
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=99.93 E-value=7.1e-26 Score=186.94 Aligned_cols=92 Identities=32% Similarity=0.461 Sum_probs=84.3
Q ss_pred CCCCCCCCCceEEEEEEEEEeeCCccChHHHHhcCCC--ceeeCCC--ceEEEEecCCcEEEEEeCCCceEEeecCCHHH
Q psy9199 34 QPPAHDPEVDIIINNVVCSFSVRCHLNLRQIALNGVN--VEYRREN--GMVTMKLRKPYTTASIWSSGKITCTGATSEDQ 109 (204)
Q Consensus 34 ~~~~~~~~~~i~I~NVVas~~l~~~ldL~~la~~~~n--~eYePe~--g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~ 109 (204)
+..++...+.++|||||||++|+..+||+.+|..+++ +|||||| |+ +||+.+|++.+|||+||||||||||+++|
T Consensus 89 ~g~~~~~~p~i~iQNIVaSadL~~~lnL~~iA~~lg~e~~eYEPEqFPGL-VYRl~~P~VV~LiF~SGK~ViTGaK~~ed 167 (185)
T COG2101 89 GGIDIDFEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGL-VYRLDEPRVVLLLFGSGKLVITGAKSEED 167 (185)
T ss_pred cCcCcCCCCceEEEEEEEEeccCccccHHHHHHhccccccccccccCCee-EEEcCCCCEEEEEecCCcEEEecCCCHHH
Confidence 3444666889999999999999999999999987655 9999998 66 79999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHcCC
Q psy9199 110 SKIAARRYARCLQRLGF 126 (204)
Q Consensus 110 a~~a~~k~~~~L~~lG~ 126 (204)
++.|++++.+.|+++|.
T Consensus 168 ~~~Av~~i~~~L~elgl 184 (185)
T COG2101 168 AEQAVEKIQSRLEELGL 184 (185)
T ss_pred HHHHHHHHHHHHHHhcc
Confidence 99999999999999874
No 12
>PRK00394 transcription factor; Reviewed
Probab=99.93 E-value=2.8e-25 Score=185.23 Aligned_cols=86 Identities=33% Similarity=0.499 Sum_probs=81.8
Q ss_pred CCceEEEEEEEEEeeCCccChHHHHhcC--CCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHH
Q psy9199 41 EVDIIINNVVCSFSVRCHLNLRQIALNG--VNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRY 117 (204)
Q Consensus 41 ~~~i~I~NVVas~~l~~~ldL~~la~~~--~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~ 117 (204)
..+++|+|||||++++++|||+.|+..+ +|++||||+ +.++||+++|+++++||+||||+||||||+++++.|++++
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 6789999999999999999999999887 999999997 5558999999999999999999999999999999999999
Q ss_pred HHHHHHcCC
Q psy9199 118 ARCLQRLGF 126 (204)
Q Consensus 118 ~~~L~~lG~ 126 (204)
+++|+++|.
T Consensus 169 ~~~l~~~g~ 177 (179)
T PRK00394 169 LEKLEELGL 177 (179)
T ss_pred HHHHHHcCC
Confidence 999999986
No 13
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=99.92 E-value=6e-25 Score=182.58 Aligned_cols=85 Identities=32% Similarity=0.441 Sum_probs=80.1
Q ss_pred CCCceEEEEEEEEEeeCCccChHHHHhcCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHH
Q psy9199 40 PEVDIIINNVVCSFSVRCHLNLRQIALNGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYA 118 (204)
Q Consensus 40 ~~~~i~I~NVVas~~l~~~ldL~~la~~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~ 118 (204)
...+++|+|||||++++++|||+.|+...+|++||||+ +.++||+.+|+++++||+||||+||||||+++++.|+++++
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 36789999999999999999999999999999999997 55589999999999999999999999999999999999999
Q ss_pred HHHHHc
Q psy9199 119 RCLQRL 124 (204)
Q Consensus 119 ~~L~~l 124 (204)
++|+++
T Consensus 169 ~~l~~~ 174 (174)
T cd04518 169 SRLKEL 174 (174)
T ss_pred HHHhhC
Confidence 999874
No 14
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=99.90 E-value=3.4e-24 Score=178.05 Aligned_cols=70 Identities=26% Similarity=0.464 Sum_probs=67.4
Q ss_pred eeEEEEEEEEeCCCccChHHHHHHccccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecCCCCcccc
Q psy9199 133 FRVVNVLGTCSMPFAIRILQFSEKHRAAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACNDSNKIPV 202 (204)
Q Consensus 133 f~v~NIvat~~~~~~I~L~~la~~~~~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~~~~ 202 (204)
++|+|||||++++++|||++||..+++++||||+||||+||+.+|+++++||+||||+||||||+++++.
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~ 71 (174)
T cd04516 2 PKIQNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKL 71 (174)
T ss_pred CEEEEEEEEEEcCCeecHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHH
Confidence 6899999999999999999999988999999999999999999999999999999999999999998763
No 15
>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=99.89 E-value=3.9e-23 Score=171.54 Aligned_cols=84 Identities=25% Similarity=0.329 Sum_probs=78.8
Q ss_pred CCCceEEEEEEEEEeeCCccChHHHHhcCC-CceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHH
Q psy9199 40 PEVDIIINNVVCSFSVRCHLNLRQIALNGV-NVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRY 117 (204)
Q Consensus 40 ~~~~i~I~NVVas~~l~~~ldL~~la~~~~-n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~ 117 (204)
...+++|+|||||++++++|||+.||...+ +++||||+ +.++||+.+|+++++||+||||+||||||+++++.|++++
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 467899999999999999999999999885 99999998 5558999999999999999999999999999999999999
Q ss_pred HHHHHH
Q psy9199 118 ARCLQR 123 (204)
Q Consensus 118 ~~~L~~ 123 (204)
+++|.+
T Consensus 169 ~~~L~~ 174 (174)
T cd00652 169 YPILKE 174 (174)
T ss_pred HHHHhC
Confidence 999863
No 16
>PLN00062 TATA-box-binding protein; Provisional
Probab=99.88 E-value=3.1e-22 Score=167.03 Aligned_cols=85 Identities=26% Similarity=0.326 Sum_probs=79.7
Q ss_pred CCceEEEEEEEEEeeCCccChHHHHh-cCCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHH
Q psy9199 41 EVDIIINNVVCSFSVRCHLNLRQIAL-NGVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYA 118 (204)
Q Consensus 41 ~~~i~I~NVVas~~l~~~ldL~~la~-~~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~ 118 (204)
..+++|+|||||++++.+|||+.||. ..++++||||+ +.++||+.+|+++++||+||||++||+||+++++.|+++++
T Consensus 89 ~~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~~~ai~~i~ 168 (179)
T PLN00062 89 FKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEIYTAFENIY 168 (179)
T ss_pred CCccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHHH
Confidence 47899999999999999999999996 46899999998 55589999999999999999999999999999999999999
Q ss_pred HHHHHcC
Q psy9199 119 RCLQRLG 125 (204)
Q Consensus 119 ~~L~~lG 125 (204)
.+|.+++
T Consensus 169 p~L~~~~ 175 (179)
T PLN00062 169 PVLTEFR 175 (179)
T ss_pred HHHHHhc
Confidence 9999876
No 17
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=99.87 E-value=9.3e-22 Score=163.40 Aligned_cols=83 Identities=24% Similarity=0.312 Sum_probs=77.7
Q ss_pred CCCceEEEEEEEEEeeCCccChHHHHhc-CCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHH
Q psy9199 40 PEVDIIINNVVCSFSVRCHLNLRQIALN-GVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRY 117 (204)
Q Consensus 40 ~~~~i~I~NVVas~~l~~~ldL~~la~~-~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~ 117 (204)
...+++|+||||+++++++|||+.|+.. .++++||||+ +.++||+.+|+++++||+||||+|||+||+++++.|++++
T Consensus 89 ~~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~~~a~~~i 168 (174)
T cd04517 89 RFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDVREAVEKI 168 (174)
T ss_pred cCCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHHHHHHHHH
Confidence 3678999999999999999999999975 5899999998 5568999999999999999999999999999999999999
Q ss_pred HHHHH
Q psy9199 118 ARCLQ 122 (204)
Q Consensus 118 ~~~L~ 122 (204)
+.+|.
T Consensus 169 ~pil~ 173 (174)
T cd04517 169 YPIVF 173 (174)
T ss_pred HHHHh
Confidence 99885
No 18
>KOG3302|consensus
Probab=99.70 E-value=7.9e-17 Score=135.21 Aligned_cols=86 Identities=28% Similarity=0.309 Sum_probs=79.4
Q ss_pred CCCceEEEEEEEEEeeCCccChHHHHhc-CCCceeeCCC-ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHH
Q psy9199 40 PEVDIIINNVVCSFSVRCHLNLRQIALN-GVNVEYRREN-GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRY 117 (204)
Q Consensus 40 ~~~~i~I~NVVas~~l~~~ldL~~la~~-~~n~eYePe~-g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~ 117 (204)
+..+++|+|||||+++..+|+|+.++.. ...+.||||. +.++||+.+|+++++||.||||++|||++.++.++|+.++
T Consensus 109 ~f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~~~i~~Ai~~I 188 (200)
T KOG3302|consen 109 KFRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVREETYEAIENI 188 (200)
T ss_pred eehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccHHHHHHHHHHH
Confidence 4778999999999999999999999975 6778999997 5558999999999999999999999999999999999999
Q ss_pred HHHHHHcC
Q psy9199 118 ARCLQRLG 125 (204)
Q Consensus 118 ~~~L~~lG 125 (204)
+.+|.++.
T Consensus 189 yPil~~fr 196 (200)
T KOG3302|consen 189 YPILLEFR 196 (200)
T ss_pred hHHHHHhh
Confidence 99998873
No 19
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=96.62 E-value=0.0099 Score=49.60 Aligned_cols=63 Identities=17% Similarity=0.199 Sum_probs=54.2
Q ss_pred ChHHHHhcCCCceeeCCCceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHc
Q psy9199 60 NLRQIALNGVNVEYRRENGMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQRL 124 (204)
Q Consensus 60 dL~~la~~~~n~eYePe~g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~l 124 (204)
=|.-|+..++++.|..+.++++++.- ..-+.||.|||+..|-.|++++|++++..+.+++++.
T Consensus 47 ilplla~l~P~anY~~kk~~l~~~kg--erIitiy~sGkVsm~~ikdedEAkeilgel~d~ineA 109 (193)
T COG4871 47 ILPLLAPLFPRANYSDKKNILILQKG--ERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINEA 109 (193)
T ss_pred hHHHhHhhCCCcccccccceEEEeec--cEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHHH
Confidence 35667888899999998888766654 4577899999999999999999999999999999875
No 20
>PF11858 DUF3378: Domain of unknown function (DUF3378); InterPro: IPR024568 Ribonuclease HIII 3.1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other []. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This entry represents the uncharacterised N-terminal domain of bacterial RNase HIII.; PDB: 3ASM_A 2D0C_A 2D0B_A 2D0A_A.
Probab=95.94 E-value=0.0093 Score=44.01 Aligned_cols=31 Identities=19% Similarity=0.300 Sum_probs=26.4
Q ss_pred ceEEEEecCCcEEEEEeCCCceEEeecCCHHH
Q psy9199 78 GMVTMKLRKPYTTASIWSSGKITCTGATSEDQ 109 (204)
Q Consensus 78 g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~ 109 (204)
|. +++.+-+.|++.+|.|||++..|...+.+
T Consensus 30 ~~-~f~aK~~~~tIt~Y~SGKV~FQG~~Ae~~ 60 (81)
T PF11858_consen 30 YA-VFQAKYNGVTITAYKSGKVVFQGKNAEQE 60 (81)
T ss_dssp TE-EEEEEETTEEEEEETTSEEEEESTTHHHH
T ss_pred CE-EEEEeCCCeEEEEEeCCeEEEECCCHHHH
Confidence 66 69999999999999999999999844433
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=95.51 E-value=0.012 Score=43.50 Aligned_cols=36 Identities=11% Similarity=0.237 Sum_probs=29.9
Q ss_pred CCCceeEEEeCCCceEEEEeccCcEEEEecCCCCcc
Q psy9199 165 ELHPGVTYRITRPKATLKIFSTGGITVTACNDSNKI 200 (204)
Q Consensus 165 e~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~~ 200 (204)
..=||.+|+.+.+++|+.+|.||||++=|...+.++
T Consensus 26 ~~~p~~~f~aK~~~~tIt~Y~SGKV~FQG~~Ae~~A 61 (81)
T PF11858_consen 26 SKPPYAVFQAKYNGVTITAYKSGKVVFQGKNAEQEA 61 (81)
T ss_dssp S--TTEEEEEEETTEEEEEETTSEEEEESTTHHHHH
T ss_pred CCCCCEEEEEeCCCeEEEEEeCCeEEEECCCHHHHH
Confidence 344999999999999999999999999998655443
No 22
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=91.18 E-value=0.55 Score=42.84 Aligned_cols=60 Identities=15% Similarity=0.196 Sum_probs=43.9
Q ss_pred CccChHHHHhcCCCc-eeeCCCceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHH
Q psy9199 57 CHLNLRQIALNGVNV-EYRRENGMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYA 118 (204)
Q Consensus 57 ~~ldL~~la~~~~n~-eYePe~g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~ 118 (204)
..+|+++++..+... .++.. +. .++++-..-.+.+|+.|++++.|.+++.+|+.-..++.
T Consensus 277 ~~~~~~~~~~~~~~~~~~~~~-~~-~~~~~~~~~~~~~f~~gr~~~~g~~~~~~a~~~~~~~~ 337 (338)
T PRK12475 277 RRLNLEEIKKRLQKIGKVDAN-PY-LLSFQLDEYRFVLFTDGRAFIHGTNDIKKAKRLYARYI 337 (338)
T ss_pred CccCHHHHHHHHhhcCEEEec-cc-EEEEEECCEEEEEEcCCcEEEECCCCHHHHHHHHHHhc
Confidence 689999998776432 23322 33 24444445789999999999999999999998877653
No 23
>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=90.82 E-value=0.42 Score=42.77 Aligned_cols=29 Identities=28% Similarity=0.410 Sum_probs=25.3
Q ss_pred ceEEEEecCCcEEEEEeCCCceEEeecCCH
Q psy9199 78 GMVTMKLRKPYTTASIWSSGKITCTGATSE 107 (204)
Q Consensus 78 g~vi~Rl~~P~~tvlIF~SGKivitGakS~ 107 (204)
+. +++.+.|.+|+.+|.|||++..|...+
T Consensus 28 ~~-~f~~k~~~~~it~Y~SgKv~fQG~~ae 56 (284)
T TIGR00716 28 YT-VFQLEGPGVKVTYYQSGKLLIQGKNSE 56 (284)
T ss_pred Ce-EEEEeCCCeEEEEEeCCEEEEeCCCHH
Confidence 66 699999999999999999999995433
No 24
>PRK00996 ribonuclease HIII; Provisional
Probab=89.75 E-value=0.39 Score=43.38 Aligned_cols=35 Identities=20% Similarity=0.534 Sum_probs=30.1
Q ss_pred CCCCCceeEEEeCCCceEEEEeccCcEEEEecCCC
Q psy9199 163 EPELHPGVTYRITRPKATLKIFSTGGITVTACNDS 197 (204)
Q Consensus 163 ePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~ 197 (204)
.+..-|+..|+.+.+++++.++.||||++-|...+
T Consensus 25 ~~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae 59 (304)
T PRK00996 25 TPSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAE 59 (304)
T ss_pred ccCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHH
Confidence 34567899999999999999999999999996543
No 25
>PRK00996 ribonuclease HIII; Provisional
Probab=89.51 E-value=0.53 Score=42.51 Aligned_cols=29 Identities=31% Similarity=0.531 Sum_probs=25.4
Q ss_pred ceEEEEecCCcEEEEEeCCCceEEeecCCH
Q psy9199 78 GMVTMKLRKPYTTASIWSSGKITCTGATSE 107 (204)
Q Consensus 78 g~vi~Rl~~P~~tvlIF~SGKivitGakS~ 107 (204)
+. +++.+.+.+++.+|.|||++..|...+
T Consensus 31 ~~-~f~~k~~~~~it~Y~SGKv~~QG~~ae 59 (304)
T PRK00996 31 GA-VFAAKKPGVTITAYKSGKVVFQGKGAE 59 (304)
T ss_pred ce-EEEEcCCCeEEEEEeCCEEEEeCCCHH
Confidence 66 699999999999999999999996433
No 26
>TIGR00716 rnhC ribonuclease HIII. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other. The only RNase H homolog in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This model describes bacterial RNase III.
Probab=89.47 E-value=0.45 Score=42.62 Aligned_cols=34 Identities=12% Similarity=0.336 Sum_probs=30.0
Q ss_pred CCCCCceeEEEeCCCceEEEEeccCcEEEEecCC
Q psy9199 163 EPELHPGVTYRITRPKATLKIFSTGGITVTACND 196 (204)
Q Consensus 163 ePe~fPgliyr~~~pk~t~lIF~sGkivitGak~ 196 (204)
++..=|+..|+.+.+++|+.+|.||||++=|...
T Consensus 22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~a 55 (284)
T TIGR00716 22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNS 55 (284)
T ss_pred ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCH
Confidence 5566799999999999999999999999999443
No 27
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=88.12 E-value=1.1 Score=40.52 Aligned_cols=42 Identities=24% Similarity=0.281 Sum_probs=35.0
Q ss_pred ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHH
Q psy9199 78 GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARC 120 (204)
Q Consensus 78 g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~ 120 (204)
+. +++.+.|.+++.+|.|||+++.|--+++.++.-...+.+.
T Consensus 31 ~~-~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~~~~~~ 72 (297)
T COG1039 31 YT-VFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLNPIAQT 72 (297)
T ss_pred ce-EEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhhhhhhh
Confidence 56 5999999999999999999999987777777766654444
No 28
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=86.20 E-value=2.1 Score=39.12 Aligned_cols=60 Identities=13% Similarity=0.195 Sum_probs=46.1
Q ss_pred CccChHHHHhcCCCc--eeeCCCceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHH
Q psy9199 57 CHLNLRQIALNGVNV--EYRRENGMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYA 118 (204)
Q Consensus 57 ~~ldL~~la~~~~n~--eYePe~g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~ 118 (204)
..+++++++..+... +++. ... .++.+.+.-.+..|++|++++.|.+++.+|+.-..++.
T Consensus 277 ~~i~~~~~~~~l~~~~~~~~~-~~~-ll~vr~~~~~~~~~~~gr~~i~g~~~~~~a~~~~~~~~ 338 (339)
T PRK07688 277 EEYDLEELAELLRDRGLDVNV-NPY-LLSFSLEEKRLVLFKDGRVLVHGTKDISEAKTIYHRYI 338 (339)
T ss_pred CccCHHHHHHHHHhcccccCC-CcE-EEEEecCCeEEEEEcCCCEEEECCCCHHHHHHHHHHhc
Confidence 568999998876433 3332 234 47777777899999999999999999999998877653
No 29
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=85.78 E-value=0.69 Score=41.82 Aligned_cols=34 Identities=15% Similarity=0.304 Sum_probs=30.4
Q ss_pred CCceeEEEeCCCceEEEEeccCcEEEEecCCCCc
Q psy9199 166 LHPGVTYRITRPKATLKIFSTGGITVTACNDSNK 199 (204)
Q Consensus 166 ~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~ 199 (204)
.-|+.+|+.+.|++++.++.|||+++=|--.++.
T Consensus 28 ~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~ 61 (297)
T COG1039 28 NPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAF 61 (297)
T ss_pred CCCceEEEeeCCCeEEEEEccceEEEecCCHHHH
Confidence 7799999999999999999999999998765544
No 30
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=82.79 E-value=2.8 Score=35.27 Aligned_cols=61 Identities=13% Similarity=0.235 Sum_probs=49.6
Q ss_pred EEEEEeCCCccChHHHHHHccccccCCCCCceeEEEeCCCceEEEEeccCcEEEEecCCCCccc
Q psy9199 138 VLGTCSMPFAIRILQFSEKHRAAEYEPELHPGVTYRITRPKATLKIFSTGGITVTACNDSNKIP 201 (204)
Q Consensus 138 Ivat~~~~~~I~L~~la~~~~~~~YePe~fPgliyr~~~pk~t~lIF~sGkivitGak~~~~~~ 201 (204)
|.|..+-+++==|..|+..+|++.|.-.. .-|++.. -..-+.|+.||||.+|--|++++++
T Consensus 36 Vi~~md~~lg~ilplla~l~P~anY~~kk-~~l~~~k--gerIitiy~sGkVsm~~ikdedEAk 96 (193)
T COG4871 36 VIANMDPPLGGILPLLAPLFPRANYSDKK-NILILQK--GERIITIYGSGKVSMTMIKDEDEAK 96 (193)
T ss_pred EEeecCCCcchhHHHhHhhCCCccccccc-ceEEEee--ccEEEEEccCCeEEeeeecCHHHHH
Confidence 56777777777788889889999998775 6677764 3467789999999999999998875
No 31
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=74.28 E-value=5.5 Score=31.16 Aligned_cols=33 Identities=24% Similarity=0.231 Sum_probs=29.2
Q ss_pred eCCCceEEeecCCHHHHHHHHHHHHHHHHH-cCCcc
Q psy9199 94 WSSGKITCTGATSEDQSKIAARRYARCLQR-LGFKA 128 (204)
Q Consensus 94 F~SGKivitGakS~e~a~~a~~k~~~~L~~-lG~~v 128 (204)
.=||.+++|| +..+.+.|++.+.+.|++ +||.+
T Consensus 72 RFsGslvitG--dvs~Ve~Al~~V~~~l~~~L~F~~ 105 (111)
T PRK15468 72 RFSGALVIYG--SVGAVEEALSQTVSGLGRLLNYTL 105 (111)
T ss_pred ccceeEEEEc--cHHHHHHHHHHHHHHHHhhcCccc
Confidence 4589999999 699999999999999998 88864
No 32
>TIGR02187 GlrX_arch Glutaredoxin-like domain protein. This family of archaeal proteins contains a C-terminal domain with homology to bacterial and eukaryotic glutaredoxins, including a CPYC motif. There is an N-terminal domain which has even more distant homology to glutaredoxins. The name "glutaredoxin" may be inappropriate in the sense of working in tandem with glutathione and glutathione reductase which may not be present in the archaea. The overall domain structure appears to be related to bacterial alkylhydroperoxide reductases, but the homology may be distant enough that the function of this family is wholly different.
Probab=71.46 E-value=5.4 Score=33.48 Aligned_cols=110 Identities=11% Similarity=0.052 Sum_probs=61.3
Q ss_pred EEEEEeCCCceE---EeecCCHHHHHHHHHHHHHHHHHcCC--ccc-------cc-eeeEEEEEEEEeCCCc---cChHH
Q psy9199 89 TTASIWSSGKIT---CTGATSEDQSKIAARRYARCLQRLGF--KAR-------FT-NFRVVNVLGTCSMPFA---IRILQ 152 (204)
Q Consensus 89 ~tvlIF~SGKiv---itGakS~e~a~~a~~k~~~~L~~lG~--~v~-------~~-~f~v~NIvat~~~~~~---I~L~~ 152 (204)
.|+++|..|+.+ ..|..+.++...-++.++.+ ...+. +.. .. ...|.-..++.+-+++ --++.
T Consensus 79 Pt~~~f~~g~~~~~~~~G~~~~~~l~~~i~~~~~~-~~~~~~L~~~~~~~l~~~~~pv~I~~F~a~~C~~C~~~~~~l~~ 157 (215)
T TIGR02187 79 PTTIILEEGKDGGIRYTGIPAGYEFAALIEDIVRV-SQGEPGLSEKTVELLQSLDEPVRIEVFVTPTCPYCPYAVLMAHK 157 (215)
T ss_pred CEEEEEeCCeeeEEEEeecCCHHHHHHHHHHHHHh-cCCCCCCCHHHHHHHHhcCCCcEEEEEECCCCCCcHHHHHHHHH
Confidence 588999999986 47998888877777666432 21111 111 01 1223333455444443 12344
Q ss_pred HHHHcc---ccccCCCCCceeEEEeCCC-ceEEEEeccCcEEEEecCCCCcc
Q psy9199 153 FSEKHR---AAEYEPELHPGVTYRITRP-KATLKIFSTGGITVTACNDSNKI 200 (204)
Q Consensus 153 la~~~~---~~~YePe~fPgliyr~~~p-k~t~lIF~sGkivitGak~~~~~ 200 (204)
++..++ ...++++.+|.+.-+..-. -=|+++|..|+. +.|....+++
T Consensus 158 l~~~~~~i~~~~vD~~~~~~~~~~~~V~~vPtl~i~~~~~~-~~G~~~~~~l 208 (215)
T TIGR02187 158 FALANDKILGEMIEANENPDLAEKYGVMSVPKIVINKGVEE-FVGAYPEEQF 208 (215)
T ss_pred HHHhcCceEEEEEeCCCCHHHHHHhCCccCCEEEEecCCEE-EECCCCHHHH
Confidence 444443 3446777777764332111 126777887875 8898887765
No 33
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=60.51 E-value=13 Score=30.09 Aligned_cols=79 Identities=15% Similarity=0.187 Sum_probs=50.0
Q ss_pred eEEEEEEEEEeeCCc-c--ChHHHHhcCCC-ce-ee------CCCceEEEEecCCcEEEEEeCCCceEE---ee------
Q psy9199 44 IIINNVVCSFSVRCH-L--NLRQIALNGVN-VE-YR------RENGMVTMKLRKPYTTASIWSSGKITC---TG------ 103 (204)
Q Consensus 44 i~I~NVVas~~l~~~-l--dL~~la~~~~n-~e-Ye------Pe~g~vi~Rl~~P~~tvlIF~SGKivi---tG------ 103 (204)
+.+..+-|+-.-.|. + =|+++|...++ +. |. |+... .|++++|-+++.+|++|++.+ +|
T Consensus 25 lVVvdF~A~WCgpCk~m~p~l~~la~~~~~~~~~~kVDVDe~~dla~-~y~I~~~~t~~~ffk~g~~~vd~~tG~~~k~~ 103 (142)
T PLN00410 25 LVVIRFGHDWDETCMQMDEVLASVAETIKNFAVIYLVDITEVPDFNT-MYELYDPCTVMFFFRNKHIMIDLGTGNNNKIN 103 (142)
T ss_pred EEEEEEECCCChhHHHHHHHHHHHHHHcCCceEEEEEECCCCHHHHH-HcCccCCCcEEEEEECCeEEEEEecccccccc
Confidence 445556555444553 3 36888887766 44 43 22233 477776767888999999544 55
Q ss_pred --cCCHHHHHHHHHHHHHHHHH
Q psy9199 104 --ATSEDQSKIAARRYARCLQR 123 (204)
Q Consensus 104 --akS~e~a~~a~~k~~~~L~~ 123 (204)
..+.++....++.+++--++
T Consensus 104 ~~~~~k~~l~~~i~~~~~~a~~ 125 (142)
T PLN00410 104 WALKDKQEFIDIVETVYRGARK 125 (142)
T ss_pred cccCCHHHHHHHHHHHHHHHhc
Confidence 56777777777777665444
No 34
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=54.41 E-value=15 Score=33.47 Aligned_cols=52 Identities=12% Similarity=0.326 Sum_probs=33.5
Q ss_pred CccChHHHHHHcc-ccccCCCCCce-eEEEeCCCceEEEEeccCcEEEEecCCCCccc
Q psy9199 146 FAIRILQFSEKHR-AAEYEPELHPG-VTYRITRPKATLKIFSTGGITVTACNDSNKIP 201 (204)
Q Consensus 146 ~~I~L~~la~~~~-~~~YePe~fPg-liyr~~~pk~t~lIF~sGkivitGak~~~~~~ 201 (204)
..++++.++..+. ...++.. |. |.|+.. .-.+.+|..|+++|-|.++..+++
T Consensus 277 ~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~~--~~~~~~f~~gr~~~~g~~~~~~a~ 330 (338)
T PRK12475 277 RRLNLEEIKKRLQKIGKVDAN--PYLLSFQLD--EYRFVLFTDGRAFIHGTNDIKKAK 330 (338)
T ss_pred CccCHHHHHHHHhhcCEEEec--ccEEEEEEC--CEEEEEEcCCcEEEECCCCHHHHH
Confidence 3466666665543 2222222 33 345543 478999999999999999988764
No 35
>cd03065 PDI_b_Calsequestrin_N PDIb family, Calsequestrin subfamily, N-terminal TRX-fold domain; Calsequestrin is the major calcium storage protein in the sarcoplasmic reticulum (SR) of skeletal and cardiac muscle. It stores calcium ions in sufficient quantities (up to 20 mM) to allow repetitive contractions and is essential to maintain movement, respiration and heart beat. A missense mutation in human cardiac calsequestrin is associated with catecholamine-induced polymorphic ventricular tachycardia (CPVT), a rare disease characterized by seizures or sudden death in response to physiologic or emotional stress. Calsequestrin is a highly acidic protein with up to 50 calcium binding sites formed simply by the clustering of two or more acidic residues. The monomer contains three redox inactive TRX-fold domains. Calsequestrin is condensed as a linear polymer in the SR lumen and is membrane-anchored through binding with intra-membrane proteins triadin, junctin and ryanodine receptor (RyR) Ca2
Probab=53.33 E-value=19 Score=28.07 Aligned_cols=30 Identities=7% Similarity=0.078 Sum_probs=23.7
Q ss_pred EEEEEeCCCce-EEeecCCHHHHHHHHHHHH
Q psy9199 89 TTASIWSSGKI-TCTGATSEDQSKIAARRYA 118 (204)
Q Consensus 89 ~tvlIF~SGKi-vitGakS~e~a~~a~~k~~ 118 (204)
.|+++|.+|++ -..|+.+.+.+...++++.
T Consensus 89 PTl~lfk~G~~v~~~G~~~~~~l~~~l~~~~ 119 (120)
T cd03065 89 DSIYVFKDDEVIEYDGEFAADTLVEFLLDLI 119 (120)
T ss_pred cEEEEEECCEEEEeeCCCCHHHHHHHHHHHh
Confidence 59999999994 4559989888888777653
No 36
>PRK09381 trxA thioredoxin; Provisional
Probab=50.25 E-value=21 Score=25.93 Aligned_cols=29 Identities=24% Similarity=0.253 Sum_probs=22.5
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIAARRY 117 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a~~k~ 117 (204)
.++.+|.+|+++ ..|..+.++++..++..
T Consensus 77 Pt~~~~~~G~~~~~~~G~~~~~~l~~~i~~~ 107 (109)
T PRK09381 77 PTLLLFKNGEVAATKVGALSKGQLKEFLDAN 107 (109)
T ss_pred CEEEEEeCCeEEEEecCCCCHHHHHHHHHHh
Confidence 478899999988 66888888777766654
No 37
>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=48.48 E-value=23 Score=30.15 Aligned_cols=28 Identities=18% Similarity=0.272 Sum_probs=25.1
Q ss_pred EeecCCHHHHHHHHHHHHHHHHHcCCcc
Q psy9199 101 CTGATSEDQSKIAARRYARCLQRLGFKA 128 (204)
Q Consensus 101 itGakS~e~a~~a~~k~~~~L~~lG~~v 128 (204)
+.|+++++++...++++..+|++.|+++
T Consensus 145 li~~~s~~e~~~~~~~v~~~L~~~Gf~l 172 (213)
T cd01644 145 LVSTDTLNEAVNVAKRLIALLKKGGFNL 172 (213)
T ss_pred eecCCCHHHHHHHHHHHHHHHHhCCccc
Confidence 4577899999999999999999999975
No 38
>KOG0910|consensus
Probab=46.81 E-value=28 Score=28.61 Aligned_cols=31 Identities=16% Similarity=0.410 Sum_probs=27.9
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIAARRYAR 119 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a~~k~~~ 119 (204)
.|+++|.+|+-+ +.|+...+.++..++|+++
T Consensus 117 PtvlvfknGe~~d~~vG~~~~~~l~~~i~k~l~ 149 (150)
T KOG0910|consen 117 PTVLVFKNGEKVDRFVGAVPKEQLRSLIKKFLK 149 (150)
T ss_pred eEEEEEECCEEeeeecccCCHHHHHHHHHHHhc
Confidence 599999999988 8899999999999998864
No 39
>PHA02278 thioredoxin-like protein
Probab=41.56 E-value=32 Score=25.81 Aligned_cols=24 Identities=8% Similarity=0.070 Sum_probs=19.6
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKI 112 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~ 112 (204)
.|+++|+.|+.+ +.|..+.+++++
T Consensus 74 PT~i~fk~G~~v~~~~G~~~~~~l~~ 99 (103)
T PHA02278 74 PVLIGYKDGQLVKKYEDQVTPMQLQE 99 (103)
T ss_pred cEEEEEECCEEEEEEeCCCCHHHHHh
Confidence 589999999999 888877776553
No 40
>PF14014 DUF4230: Protein of unknown function (DUF4230)
Probab=41.55 E-value=1.2e+02 Score=23.63 Aligned_cols=73 Identities=12% Similarity=0.199 Sum_probs=43.5
Q ss_pred EEEEEEeeCCccChHHHHhcCCCceeeCCCceEEEEecCCcEE--------EEEeCCCceEEeecCCHHHHHHHHHHHHH
Q psy9199 48 NVVCSFSVRCHLNLRQIALNGVNVEYRRENGMVTMKLRKPYTT--------ASIWSSGKITCTGATSEDQSKIAARRYAR 119 (204)
Q Consensus 48 NVVas~~l~~~ldL~~la~~~~n~eYePe~g~vi~Rl~~P~~t--------vlIF~SGKivitGakS~e~a~~a~~k~~~ 119 (204)
=++..+.+...+||.++-. ++.+.+++.+.+.+.+..|+.. ..+|.+-.-.... -+.++...+.++..+
T Consensus 41 ~~~~~g~v~~GiDLs~i~~--~~i~~d~~~~~i~I~LP~~~i~~~~id~~~~~~~~~~~~~~~~-~~~~~~~~~~~~a~~ 117 (157)
T PF14014_consen 41 LVIYPGTVKAGIDLSKIKE--EDIEVDEDGKTITITLPPPEILSVEIDEDSIKVYDEKGGWFNP-ITPEDQNEAQKEAKK 117 (157)
T ss_pred EEEEEEEEEEEEEhHHCCc--ceEEEcCCCCEEEEECCCcEEeeeecCccceEEEEccCCccCC-CCHHHHHHHHHHHHH
Confidence 3556667777789988764 4566666666667778777643 4454332223332 355566666666555
Q ss_pred HHHH
Q psy9199 120 CLQR 123 (204)
Q Consensus 120 ~L~~ 123 (204)
.+++
T Consensus 118 ~~~~ 121 (157)
T PF14014_consen 118 KIEQ 121 (157)
T ss_pred HHHH
Confidence 5443
No 41
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=41.32 E-value=45 Score=26.68 Aligned_cols=31 Identities=10% Similarity=0.127 Sum_probs=25.4
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIAARRYAR 119 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a~~k~~~ 119 (204)
.|+++|++||.+ +.|..+.++...-+++++.
T Consensus 93 PTLl~FkdGk~v~~i~G~~~k~~l~~~I~~~L~ 125 (132)
T PRK11509 93 PATLVFTGGNYRGVLNGIHPWAELINLMRGLVE 125 (132)
T ss_pred CEEEEEECCEEEEEEeCcCCHHHHHHHHHHHhc
Confidence 499999999997 6799899888887776543
No 42
>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=40.87 E-value=28 Score=25.87 Aligned_cols=28 Identities=11% Similarity=0.090 Sum_probs=21.4
Q ss_pred EEEEEeCCCceEE--eecCCHHHHHHHHHH
Q psy9199 89 TTASIWSSGKITC--TGATSEDQSKIAARR 116 (204)
Q Consensus 89 ~tvlIF~SGKivi--tGakS~e~a~~a~~k 116 (204)
.|+.+|..|+++- .|..+.++++..+++
T Consensus 81 Pt~~i~~~g~~~~~~~G~~~~~~l~~~i~~ 110 (111)
T cd02963 81 PAIVGIINGQVTFYHDSSFTKQHVVDFVRK 110 (111)
T ss_pred CEEEEEECCEEEEEecCCCCHHHHHHHHhc
Confidence 4788999999984 477788877666654
No 43
>PF13575 DUF4135: Domain of unknown function (DUF4135)
Probab=40.77 E-value=26 Score=31.96 Aligned_cols=54 Identities=17% Similarity=0.181 Sum_probs=40.0
Q ss_pred EeecCCHHHHHHHHHHHHHHHHHcCCccccceeeEEEEEEEEeCCCccChHHHHH
Q psy9199 101 CTGATSEDQSKIAARRYARCLQRLGFKARFTNFRVVNVLGTCSMPFAIRILQFSE 155 (204)
Q Consensus 101 itGakS~e~a~~a~~k~~~~L~~lG~~v~~~~f~v~NIvat~~~~~~I~L~~la~ 155 (204)
-..|.+.+++++-.+++-..|.=+ +-....++--.||+|+.+.|+.||||-|-.
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 345667888887777766654432 334445788899999999999999998864
No 44
>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=40.62 E-value=57 Score=24.48 Aligned_cols=44 Identities=23% Similarity=0.280 Sum_probs=31.7
Q ss_pred EEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCcc
Q psy9199 80 VTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKA 128 (204)
Q Consensus 80 vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v 128 (204)
+++.+++- + -+..-=|+||| +|.-+++..++.+.+.+++.|..+
T Consensus 18 ~vldv~~~-~---~~~dy~VI~Tg-~S~rh~~aia~~v~~~~k~~~~~~ 61 (99)
T TIGR00090 18 VVLDVRGK-S---SIADYFVIASG-TSSRHVKAIADNVEEELKEAGLKP 61 (99)
T ss_pred EEEECCCC-C---cccCEEEEEEe-CCHHHHHHHHHHHHHHHHHcCCCc
Confidence 34666542 2 13344577887 599999999999999999988753
No 45
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=40.24 E-value=47 Score=30.27 Aligned_cols=30 Identities=17% Similarity=0.305 Sum_probs=24.2
Q ss_pred EEeCCCceEEEEeccCcEEEEecCCCCccc
Q psy9199 172 YRITRPKATLKIFSTGGITVTACNDSNKIP 201 (204)
Q Consensus 172 yr~~~pk~t~lIF~sGkivitGak~~~~~~ 201 (204)
.+.+.+.-.+..|.+|+++|-|.+++.+++
T Consensus 302 l~vr~~~~~~~~~~~gr~~i~g~~~~~~a~ 331 (339)
T PRK07688 302 LSFSLEEKRLVLFKDGRVLVHGTKDISEAK 331 (339)
T ss_pred EEEecCCeEEEEEcCCCEEEECCCCHHHHH
Confidence 344455589999999999999999987764
No 46
>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=39.74 E-value=44 Score=27.66 Aligned_cols=40 Identities=15% Similarity=0.085 Sum_probs=31.6
Q ss_pred EEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCcccc
Q psy9199 90 TASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKARF 130 (204)
Q Consensus 90 tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~~ 130 (204)
...=+.+..|++.| +|+++++..++++...|...|+.+..
T Consensus 144 ~~~G~~~~~i~v~~-~~~~~l~~~~~~v~~~l~~~G~~~~~ 183 (205)
T PF03135_consen 144 VSFGYYHFTIVVFA-DDPEELDDKVAEVSSALNNLGFVAVR 183 (205)
T ss_pred eeeeeeEEEEEEEc-CCHHHHHHHHHHHHHHHHHCCCEEEE
Confidence 34455566667775 69999999999999999999986443
No 47
>PTZ00129 40S ribosomal protein S14; Provisional
Probab=39.20 E-value=77 Score=26.07 Aligned_cols=47 Identities=15% Similarity=0.196 Sum_probs=35.6
Q ss_pred EEEecCCcEEEE-EeCCCceEEeecC---CHHHHHHHHHHHHHHHHHcCCc
Q psy9199 81 TMKLRKPYTTAS-IWSSGKITCTGAT---SEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 81 i~Rl~~P~~tvl-IF~SGKivitGak---S~e~a~~a~~k~~~~L~~lG~~ 127 (204)
++-+.|..-.++ ..++|.+-..|.+ +.-.|..|++++++...++|++
T Consensus 41 iItiTD~~G~~~~w~SsG~~gfKg~r~KsTpyAAq~aa~~~a~k~~~~Gi~ 91 (149)
T PTZ00129 41 FIHVTDLSGRETLVRVTGGMKVKADRDESSPYAAMMAAQDVAARCKELGIN 91 (149)
T ss_pred EEEEEcccCCEEEEEecCcceecccccCCCHHHHHHHHHHHHHHHHHcCCe
Confidence 456666654444 4466999999887 4557899999999999999885
No 48
>PRK10996 thioredoxin 2; Provisional
Probab=39.06 E-value=39 Score=26.34 Aligned_cols=29 Identities=17% Similarity=0.219 Sum_probs=23.1
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIAARRY 117 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a~~k~ 117 (204)
.++++|.+|+++ +.|..+.++.+..++++
T Consensus 108 Ptlii~~~G~~v~~~~G~~~~e~l~~~l~~~ 138 (139)
T PRK10996 108 PTIMIFKNGQVVDMLNGAVPKAPFDSWLNEA 138 (139)
T ss_pred CEEEEEECCEEEEEEcCCCCHHHHHHHHHHh
Confidence 468899999988 67888888877777654
No 49
>COG4978 Transcriptional regulator, effector-binding domain/component [Transcription / Signal transduction mechanisms]
Probab=37.93 E-value=82 Score=25.70 Aligned_cols=46 Identities=15% Similarity=0.153 Sum_probs=39.8
Q ss_pred CCcEEEEEeCCCceEEeecC-CHHHHHHHHHHHHHHHHHcCCccccc
Q psy9199 86 KPYTTASIWSSGKITCTGAT-SEDQSKIAARRYARCLQRLGFKARFT 131 (204)
Q Consensus 86 ~P~~tvlIF~SGKivitGak-S~e~a~~a~~k~~~~L~~lG~~v~~~ 131 (204)
++......+.+||+.|+=-+ +-++...+.+++..-+++.|.++...
T Consensus 79 ~~~~~~~~~P~g~~a~~~~~G~~~~~~~~y~rli~~iee~g~~i~g~ 125 (153)
T COG4978 79 DIDIKIKTLPKGKYACIIHKGSYEEVEQAYKRLIEYIEENGLEIIGP 125 (153)
T ss_pred CCcceeEEccCceEEEEEEEcCcccHHHHHHHHHHHHHHhCCcccCc
Confidence 46788889999999888777 99999999999999999999875553
No 50
>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=37.00 E-value=15 Score=28.50 Aligned_cols=50 Identities=16% Similarity=0.260 Sum_probs=32.4
Q ss_pred ChHHHHHHcc----ccccCCCCCceeE--EEeCC-CceEEEEeccCcEE--EEecCCCCcc
Q psy9199 149 RILQFSEKHR----AAEYEPELHPGVT--YRITR-PKATLKIFSTGGIT--VTACNDSNKI 200 (204)
Q Consensus 149 ~L~~la~~~~----~~~YePe~fPgli--yr~~~-pk~t~lIF~sGkiv--itGak~~~~~ 200 (204)
-|++|+.+++ .+..+-+..|.+. |++.. | |+++|..|+++ +.|..+.+++
T Consensus 50 ~leela~e~~~~v~f~kVdid~~~~la~~f~V~sIP--Tli~fkdGk~v~~~~G~~~~~e~ 108 (111)
T cd02965 50 VLPELLKAFPGRFRAAVVGRADEQALAARFGVLRTP--ALLFFRDGRYVGVLAGIRDWDEY 108 (111)
T ss_pred HHHHHHHHCCCcEEEEEEECCCCHHHHHHcCCCcCC--EEEEEECCEEEEEEeCccCHHHH
Confidence 3556666654 3355666666664 55543 4 88999999997 5687776665
No 51
>KOG3946|consensus
Probab=33.04 E-value=83 Score=28.92 Aligned_cols=57 Identities=19% Similarity=0.338 Sum_probs=40.6
Q ss_pred HHHHHHHHHHHHHcCCcccccee---------eEEEEEEEEeCCCccChHHHHHHc--cccccCCCCCceeEEEeC
Q psy9199 111 KIAARRYARCLQRLGFKARFTNF---------RVVNVLGTCSMPFAIRILQFSEKH--RAAEYEPELHPGVTYRIT 175 (204)
Q Consensus 111 ~~a~~k~~~~L~~lG~~v~~~~f---------~v~NIvat~~~~~~I~L~~la~~~--~~~~YePe~fPgliyr~~ 175 (204)
+.+-+-+...|+++|..+....| .++||+||.+-. |..| -.|-|+...||+..|++.
T Consensus 72 ~~vr~~i~~~l~~l~w~ve~~~f~~~tp~g~~~f~nii~tl~~~--------A~r~lVlachydsk~~p~~~~vga 139 (338)
T KOG3946|consen 72 RQVRRFIIQHLRNLGWAVETDAFTDNTPLGTRNFNNLIATLDPN--------ASRYLVLACHYDSKIFPGGMFVGA 139 (338)
T ss_pred HHHHHHHHHHHHhcCceeeeccccccCcceeeeeeeEEEecCCC--------cchheeeecccccccCCCcceEee
Confidence 44555667788888976555422 289999998855 3333 278999999999997763
No 52
>COG4274 Uncharacterized conserved protein [Function unknown]
Probab=32.90 E-value=72 Score=24.73 Aligned_cols=58 Identities=19% Similarity=0.149 Sum_probs=46.3
Q ss_pred EEeecCCHHHHHHHHHHHHHHHHHcCCccccc--eeeEEEEEEEEeCCCccChHHHHHHc
Q psy9199 100 TCTGATSEDQSKIAARRYARCLQRLGFKARFT--NFRVVNVLGTCSMPFAIRILQFSEKH 157 (204)
Q Consensus 100 vitGakS~e~a~~a~~k~~~~L~~lG~~v~~~--~f~v~NIvat~~~~~~I~L~~la~~~ 157 (204)
.=.|+|+..+--+=++.+.+.|++.|.+++.. .+-.--+|+.+..|-+..+-.++...
T Consensus 18 Td~Gaktlke~p~R~~av~~~les~G~k~~~~y~T~GeYD~V~i~EapDda~~~~~~l~l 77 (104)
T COG4274 18 TDQGAKTLKETPKRAAAVRALLESMGGKVKEQYWTLGEYDVVAIVEAPDDAVATRFSLAL 77 (104)
T ss_pred cHhHHHHHhhCHHHHHHHHHHHHHcCcEEEEEEEeeccccEEEEEecCCHHHHHHHHHHH
Confidence 34588888888887888889999999987765 45667788888999988888887654
No 53
>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=32.50 E-value=81 Score=21.87 Aligned_cols=28 Identities=14% Similarity=0.196 Sum_probs=23.3
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIAARR 116 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a~~k 116 (204)
.++++|.+|+.+ ..|..+.+++...+++
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 588899999987 7888899988887764
No 54
>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=32.46 E-value=56 Score=23.73 Aligned_cols=27 Identities=15% Similarity=0.222 Sum_probs=20.4
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIAARR 116 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a~~k 116 (204)
.|+++|++|+.+ +.|+ +.++.+.++++
T Consensus 73 Pt~~~~~~g~~~~~~~G~-~~~~~~~~i~~ 101 (102)
T cd02948 73 PTFLFYKNGELVAVIRGA-NAPLLNKTITE 101 (102)
T ss_pred cEEEEEECCEEEEEEecC-ChHHHHHHHhh
Confidence 388999999976 7786 77776666654
No 55
>PF11775 CobT_C: Cobalamin biosynthesis protein CobT VWA domain
Probab=32.09 E-value=90 Score=27.23 Aligned_cols=48 Identities=23% Similarity=0.254 Sum_probs=39.6
Q ss_pred CCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccccceeeEE
Q psy9199 86 KPYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKARFTNFRVV 136 (204)
Q Consensus 86 ~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~~~~f~v~ 136 (204)
+.-+++||-.||.|-- +..+-|..++.-+.+.|.++|+++....|+-.
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 4457999999999963 45677777889999999999999888877765
No 56
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=32.00 E-value=2.4e+02 Score=25.16 Aligned_cols=73 Identities=4% Similarity=-0.164 Sum_probs=43.4
Q ss_pred HHHHHHHHHHcCCccccceee------EEEEEEEEeCCCccChHHHHHHccccccCCCCCceeEEEeCCCceEEEEeccC
Q psy9199 114 ARRYARCLQRLGFKARFTNFR------VVNVLGTCSMPFAIRILQFSEKHRAAEYEPELHPGVTYRITRPKATLKIFSTG 187 (204)
Q Consensus 114 ~~k~~~~L~~lG~~v~~~~f~------v~NIvat~~~~~~I~L~~la~~~~~~~YePe~fPgliyr~~~pk~t~lIF~sG 187 (204)
+.++.+.|.+.|+++...+-+ .=.+.+.++++...+++.|...+....-+=.+ -+..+...++.++.||.||
T Consensus 21 Va~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~p~~~~~~~L~~~L~~l~~~l~l--~i~i~~~~~~~ri~vl~Sg 98 (286)
T PRK13011 21 VAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSEEGLDEDALRAGFAPIAARFGM--QWELHDPAARPKVLIMVSK 98 (286)
T ss_pred HHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecCCCCCHHHHHHHHHHHHHHhCc--EEEEeecccCceEEEEEcC
Confidence 456667788888775544322 22466777778778888887654322111111 1233334556789999999
Q ss_pred c
Q psy9199 188 G 188 (204)
Q Consensus 188 k 188 (204)
.
T Consensus 99 ~ 99 (286)
T PRK13011 99 F 99 (286)
T ss_pred C
Confidence 4
No 57
>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=31.22 E-value=85 Score=31.31 Aligned_cols=46 Identities=28% Similarity=0.317 Sum_probs=38.0
Q ss_pred EEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccccceeeEEE
Q psy9199 89 TTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKARFTNFRVVN 137 (204)
Q Consensus 89 ~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~~~~f~v~N 137 (204)
+++||=.||.|. | +..+-|..++.-|.+.|+.+|+++....|+-..
T Consensus 395 V~LLID~SGSM~--~-r~~~vA~~~a~iLa~aL~~~gIp~eVlGFtt~a 440 (600)
T TIGR01651 395 VTLLIDNSGSMR--G-RPITVAATCADILARTLERCGVKVEILGFTTRA 440 (600)
T ss_pred EEEEEECCccCC--C-CHHHHHHHHHHHHHHHHHHCCCCeEEEeecccc
Confidence 688999999995 3 456667778999999999999998888777643
No 58
>PRK11538 ribosome-associated protein; Provisional
Probab=31.13 E-value=99 Score=23.62 Aligned_cols=32 Identities=22% Similarity=0.270 Sum_probs=26.2
Q ss_pred CCCceEEeecCCHHHHHHHHHHHHHHHHHcCCc
Q psy9199 95 SSGKITCTGATSEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 95 ~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~ 127 (204)
...=|+|||. |.-+++..++.+.+.+++.|..
T Consensus 34 ~Dy~VIatg~-S~rh~~aia~~v~~~~k~~~~~ 65 (105)
T PRK11538 34 TDCMIICTGT-SSRHVMSIADHVVQESRAAGLL 65 (105)
T ss_pred cCEEEEEEeC-CHHHHHHHHHHHHHHHHHcCCC
Confidence 3555777775 9999999999999999988764
No 59
>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=31.03 E-value=95 Score=23.10 Aligned_cols=28 Identities=29% Similarity=0.352 Sum_probs=22.7
Q ss_pred ceEEeecCCHHHHHHHHHHHHHHH-HHcCC
Q psy9199 98 KITCTGATSEDQSKIAARRYARCL-QRLGF 126 (204)
Q Consensus 98 KivitGakS~e~a~~a~~k~~~~L-~~lG~ 126 (204)
=|+||| +|.-+++..++.+.+.+ ++.|.
T Consensus 32 ~II~T~-~S~rh~~aia~~v~~~~~k~~~~ 60 (100)
T PF02410_consen 32 FIIATG-RSERHVRAIADEVEKALKKEYGE 60 (100)
T ss_dssp EEEEEE-SSHHHHHHHHHHHHHHH-HHTT-
T ss_pred EEEEEc-CCHHHHHHHHHHHHHHHHHHcCC
Confidence 467787 59999999999999999 55553
No 60
>cd07049 BMC_EutL_repeat1 ethanolamine utilization protein S (EutS), Bacterial Micro-Compartment (BMC) domain repeat 1. EutL proteins are homologs of the carboxysome shell protein. They are encoded within the eut operon and might be required for the formation of the outer shell of the bacterial eut polyhedral organelles which are involved in the cobalamin-dependent degradation of ethanolamine. Although it has been suggested that EutL might form hexamers and further assemble into the flat facets of the polyhedral outer shell of the eut organelles at present no experimental evidence directly supports this view. EutL proteins contain two tandem BMC domains. This CD includes domain 1 (the first BMC domain of EutL).
Probab=30.75 E-value=77 Score=24.53 Aligned_cols=28 Identities=11% Similarity=0.208 Sum_probs=23.7
Q ss_pred CCceE--EeecCCHHHHHHHHHHHHHHHHHc
Q psy9199 96 SGKIT--CTGATSEDQSKIAARRYARCLQRL 124 (204)
Q Consensus 96 SGKiv--itGakS~e~a~~a~~k~~~~L~~l 124 (204)
||.++ ++|. ++.+++.|++...+.|++.
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 7775 9999999999999988764
No 61
>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=30.54 E-value=47 Score=28.57 Aligned_cols=42 Identities=19% Similarity=0.333 Sum_probs=27.4
Q ss_pred CCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccc
Q psy9199 86 KPYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKAR 129 (204)
Q Consensus 86 ~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~ 129 (204)
+|+-.++|+.+.+.- +......+..=++.+.+.|+++||+|.
T Consensus 6 ~p~g~alII~n~~f~--~~~~r~g~~~D~~~l~~~f~~lgF~V~ 47 (241)
T smart00115 6 KPRGLALIINNENFH--SLPRRNGTDVDAENLTELFQSLGYEVH 47 (241)
T ss_pred CCCcEEEEEECccCC--CCcCCCCcHHHHHHHHHHHHHCCCEEE
Confidence 677888888888763 233344444455677777778877654
No 62
>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=30.08 E-value=31 Score=28.87 Aligned_cols=78 Identities=13% Similarity=0.153 Sum_probs=39.1
Q ss_pred EEEEEEEEEeeCCcc---ChHHHHhcCCCcee---eCCCceEEEEec-CCcEEEEEeCCCceE--EeecCCHHHHHHHHH
Q psy9199 45 IINNVVCSFSVRCHL---NLRQIALNGVNVEY---RRENGMVTMKLR-KPYTTASIWSSGKIT--CTGATSEDQSKIAAR 115 (204)
Q Consensus 45 ~I~NVVas~~l~~~l---dL~~la~~~~n~eY---ePe~g~vi~Rl~-~P~~tvlIF~SGKiv--itGakS~e~a~~a~~ 115 (204)
.|..+.+..--.|.+ -|++||...+.+.+ +-+. . +-++. .--.|+++|++|+++ +.|....-.-+-...
T Consensus 105 VVV~Fya~wc~~C~~m~~~l~~LA~k~~~vkFvkI~ad~-~-~~~~~i~~lPTlliyk~G~~v~~ivG~~~~gg~~~~~~ 182 (192)
T cd02988 105 VVVHLYKDGIPLCRLLNQHLSELARKFPDTKFVKIISTQ-C-IPNYPDKNLPTILVYRNGDIVKQFIGLLEFGGMNTTME 182 (192)
T ss_pred EEEEEECCCCchHHHHHHHHHHHHHHCCCCEEEEEEhHH-h-HhhCCCCCCCEEEEEECCEEEEEEeCchhhCCCCCCHH
Confidence 344444444445543 47777776544332 1111 1 01111 112599999999998 677644322233344
Q ss_pred HHHHHHHHc
Q psy9199 116 RYARCLQRL 124 (204)
Q Consensus 116 k~~~~L~~l 124 (204)
.+-..|.+.
T Consensus 183 ~lE~~L~~~ 191 (192)
T cd02988 183 DLEWLLVQV 191 (192)
T ss_pred HHHHHHHhc
Confidence 444444443
No 63
>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=30.03 E-value=1.9e+02 Score=22.09 Aligned_cols=47 Identities=21% Similarity=0.434 Sum_probs=33.1
Q ss_pred EEEecCCcEEEEEe-CCCceEEeecC--CHHHHHHHHHHHHHHHHHcCCc
Q psy9199 81 TMKLRKPYTTASIW-SSGKITCTGAT--SEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 81 i~Rl~~P~~tvlIF-~SGKivitGak--S~e~a~~a~~k~~~~L~~lG~~ 127 (204)
++=+.+++-.++.| |+|.+-.-|++ +.-.+..+++++.+.++++|++
T Consensus 13 ~itlTd~~g~~~~~~S~G~~gfkg~rk~t~~Aa~~~a~~~~~~~~~~gi~ 62 (108)
T TIGR03632 13 IVTITDPQGNVLSWASAGAVGFKGSKKSTPYAAQLAAEDAAKKAKEFGMK 62 (108)
T ss_pred EEEEEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 35556665445555 44766666665 5677889999999999999874
No 64
>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=29.94 E-value=1.3e+02 Score=20.64 Aligned_cols=33 Identities=21% Similarity=0.315 Sum_probs=26.6
Q ss_pred CCCceEEeecCCHHHHHHHHHHHHHHHHHcCCc
Q psy9199 95 SSGKITCTGATSEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 95 ~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~ 127 (204)
+.|......+.|.++|..+++++.+.-.+-||.
T Consensus 40 ~~Gq~~~~~~~s~~~A~~~~~k~~~~K~~~GY~ 72 (74)
T cd07996 40 TKGQSRTKTFDSEEEALKAAEKLIREKLKRGYR 72 (74)
T ss_pred CCCceEEEECCCHHHHHHHHHHHHHHHHhcCCC
Confidence 456677777889999999999998887777874
No 65
>CHL00041 rps11 ribosomal protein S11
Probab=29.55 E-value=1.6e+02 Score=22.91 Aligned_cols=46 Identities=22% Similarity=0.287 Sum_probs=32.4
Q ss_pred EEecCCcEEEEEe-CCCceEEeecC--CHHHHHHHHHHHHHHHHHcCCc
Q psy9199 82 MKLRKPYTTASIW-SSGKITCTGAT--SEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 82 ~Rl~~P~~tvlIF-~SGKivitGak--S~e~a~~a~~k~~~~L~~lG~~ 127 (204)
+=+.+++-.++.| |+|.+-.-|++ +...+..+++++.+.++++|++
T Consensus 27 iTlTd~~G~~l~~~S~G~~gfKg~rK~T~~Aa~~~a~~~~~~~~~~gi~ 75 (116)
T CHL00041 27 VTVTDVRGRVISWSSAGACGFKGARKGTPFAAQTAAENAIRTVIDQGMK 75 (116)
T ss_pred EEEEcCCCCEEEEEecCceeeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 4444554334444 55777777776 6778899999999999999875
No 66
>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=28.72 E-value=1.1e+02 Score=24.04 Aligned_cols=31 Identities=6% Similarity=0.003 Sum_probs=22.9
Q ss_pred EEEEEe-CCCceE--EeecCCHHHHHHHHHHHHH
Q psy9199 89 TTASIW-SSGKIT--CTGATSEDQSKIAARRYAR 119 (204)
Q Consensus 89 ~tvlIF-~SGKiv--itGakS~e~a~~a~~k~~~ 119 (204)
-++.+| .+|+++ +.|....++.+..+++++.
T Consensus 78 Pt~v~~~~~G~~v~~~~G~~~~~~l~~~l~~l~~ 111 (142)
T cd02950 78 PHFVFLDREGNEEGQSIGLQPKQVLAQNLDALVA 111 (142)
T ss_pred CEEEEECCCCCEEEEEeCCCCHHHHHHHHHHHHc
Confidence 467788 589998 6798888887776665543
No 67
>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=28.55 E-value=42 Score=28.75 Aligned_cols=42 Identities=17% Similarity=0.304 Sum_probs=26.9
Q ss_pred CcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccc
Q psy9199 87 PYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKAR 129 (204)
Q Consensus 87 P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~ 129 (204)
|+..+||+.+++.-- .......+..=++.+.+.|+++||+|.
T Consensus 8 ~~g~aLII~n~~f~~-~~~~r~g~~~D~~~l~~~f~~lgF~V~ 49 (243)
T cd00032 8 RRGLALIINNENFDK-GLKDRDGTDVDAENLTKLFESLGYEVE 49 (243)
T ss_pred CCCEEEEEechhcCC-CCCCCCChHHHHHHHHHHHHHCCCEEE
Confidence 777888888887642 122344444555677777888887643
No 68
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=28.02 E-value=1.1e+02 Score=24.27 Aligned_cols=36 Identities=14% Similarity=0.276 Sum_probs=23.9
Q ss_pred EEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccc
Q psy9199 92 SIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKAR 129 (204)
Q Consensus 92 lIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~ 129 (204)
....||.++.+...+.+++...+++.+. +++|+++.
T Consensus 38 Tyi~SGNvvf~~~~~~~~l~~~ie~~l~--~~fG~~v~ 73 (137)
T PF08002_consen 38 TYIQSGNVVFESDRDPAELAAKIEKALE--ERFGFDVP 73 (137)
T ss_dssp EETTTTEEEEEESS-HHHHHHHHHHHHH--HH-TT---
T ss_pred EEEeeCCEEEecCCChHHHHHHHHHHHH--HhcCCCeE
Confidence 5679999999977788887777776555 46788643
No 69
>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=27.93 E-value=1.9e+02 Score=22.44 Aligned_cols=36 Identities=17% Similarity=0.246 Sum_probs=25.0
Q ss_pred EEEeCCCceEEeecC----CHHHHHHHHHHHHHHHHHcCC
Q psy9199 91 ASIWSSGKITCTGAT----SEDQSKIAARRYARCLQRLGF 126 (204)
Q Consensus 91 vlIF~SGKivitGak----S~e~a~~a~~k~~~~L~~lG~ 126 (204)
+.+..++..++.|.- ....+..++.++++.|++.|+
T Consensus 88 i~i~kT~~~ivi~~y~e~~~~g~~~~~v~~ladYL~~~gy 127 (127)
T cd00148 88 VVIVKTKQALVIGMYEEGVQPGQANKVVEKLADYLRSQGY 127 (127)
T ss_pred EEEEECCCEEEEEEcCCCCCHHHHHHHHHHHHHHHHHcCC
Confidence 334444444444433 466899999999999999886
No 70
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=27.54 E-value=1.7e+02 Score=22.00 Aligned_cols=40 Identities=18% Similarity=0.212 Sum_probs=29.5
Q ss_pred eEEeecCCHHHHHHHHHHHHHHHHH-cCCccccceeeEEEE
Q psy9199 99 ITCTGATSEDQSKIAARRYARCLQR-LGFKARFTNFRVVNV 138 (204)
Q Consensus 99 ivitGakS~e~a~~a~~k~~~~L~~-lG~~v~~~~f~v~NI 138 (204)
|.+.|..+.++-++-.+.+.+.|++ +|++..-.-+.++++
T Consensus 63 i~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~rv~I~f~~~ 103 (116)
T PTZ00397 63 VTSIGGISRSNNSSIAAAITKILASHLKVKSERVYIEFKDC 103 (116)
T ss_pred EEEecCCCHHHHHHHHHHHHHHHHHHhCcCcccEEEEEEEC
Confidence 3445778999999999999999987 788755544444443
No 71
>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=27.35 E-value=89 Score=21.51 Aligned_cols=28 Identities=21% Similarity=0.274 Sum_probs=20.1
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIAARR 116 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a~~k 116 (204)
.++.+|.+|+.+ +.|..+.+++...+++
T Consensus 70 P~~~~~~~g~~~~~~~g~~~~~~l~~~l~~ 99 (101)
T TIGR01068 70 PTLLLFKNGKEVDRSVGALPKAALKQLINK 99 (101)
T ss_pred CEEEEEeCCcEeeeecCCCCHHHHHHHHHh
Confidence 478888999875 5577777776666553
No 72
>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=27.27 E-value=1.3e+02 Score=18.83 Aligned_cols=28 Identities=11% Similarity=0.189 Sum_probs=21.2
Q ss_pred cEEEEEeCCCceEEeecCCHHHHHHHHH
Q psy9199 88 YTTASIWSSGKITCTGATSEDQSKIAAR 115 (204)
Q Consensus 88 ~~tvlIF~SGKivitGakS~e~a~~a~~ 115 (204)
...+.||..|++.+.-.=+.+.++..+.
T Consensus 5 ~~qLTIfY~G~V~Vfd~v~~~Ka~~im~ 32 (36)
T PF06200_consen 5 TAQLTIFYGGQVCVFDDVPPDKAQEIML 32 (36)
T ss_pred CCcEEEEECCEEEEeCCCCHHHHHHHHH
Confidence 4678899999999987667776665543
No 73
>PF11869 DUF3389: Protein of unknown function (DUF3389); InterPro: IPR021811 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are about 80 amino acids in length.
Probab=27.02 E-value=33 Score=25.13 Aligned_cols=12 Identities=42% Similarity=0.451 Sum_probs=9.9
Q ss_pred EEeccCcEEEEe
Q psy9199 182 KIFSTGGITVTA 193 (204)
Q Consensus 182 lIF~sGkivitG 193 (204)
.=|+.|||++|-
T Consensus 3 I~Fs~GKiI~t~ 14 (75)
T PF11869_consen 3 IEFSQGKIIATP 14 (75)
T ss_pred EEecCCeEEEcc
Confidence 459999999874
No 74
>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=26.59 E-value=77 Score=22.57 Aligned_cols=25 Identities=8% Similarity=0.215 Sum_probs=19.9
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIA 113 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a 113 (204)
.++.+|..|+++ +.|..+.++....
T Consensus 69 Pt~~i~~~g~~v~~~~g~~~~~~~~~~ 95 (97)
T cd02949 69 PTVQFFKDKELVKEISGVKMKSEYREF 95 (97)
T ss_pred cEEEEEECCeEEEEEeCCccHHHHHHh
Confidence 478899999999 7888888776554
No 75
>PRK05309 30S ribosomal protein S11; Validated
Probab=26.29 E-value=1.8e+02 Score=22.98 Aligned_cols=46 Identities=20% Similarity=0.353 Sum_probs=32.3
Q ss_pred EEecCCcEEEEEe-CCCceEEeecC--CHHHHHHHHHHHHHHHHHcCCc
Q psy9199 82 MKLRKPYTTASIW-SSGKITCTGAT--SEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 82 ~Rl~~P~~tvlIF-~SGKivitGak--S~e~a~~a~~k~~~~L~~lG~~ 127 (204)
+=+.++.-.++.| |+|.+-.-|++ +...+..+++++.+.+.++|++
T Consensus 31 itlTd~~G~~~~~~S~G~~gfKg~rK~T~~Aa~~aa~~~~~~~~~~gi~ 79 (128)
T PRK05309 31 VTITDRQGNVISWASAGGLGFKGSRKSTPYAAQVAAEDAAKKAKEHGMK 79 (128)
T ss_pred EEEEcCCCCEEEEEecCccEeCCCccCCHHHHHHHHHHHHHHHHHcCCc
Confidence 4455555444444 44777666665 6677888999999999999885
No 76
>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=25.62 E-value=1.2e+02 Score=22.10 Aligned_cols=25 Identities=12% Similarity=0.086 Sum_probs=17.4
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIAA 114 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a~ 114 (204)
.|+++|++|+++ ..|+ +.++++..+
T Consensus 73 Pt~~~~~~G~~v~~~~G~-~~~~l~~~~ 99 (103)
T cd02985 73 PHFLFYKDGEKIHEEEGI-GPDELIGDV 99 (103)
T ss_pred CEEEEEeCCeEEEEEeCC-CHHHHHHHH
Confidence 378999999987 6776 555444433
No 77
>PF12386 Peptidase_C71: Pseudomurein endo-isopeptidase Pei; InterPro: IPR022119 This peptidase has the catalytic triad C-H-D at the C-terminal end, a triad similar to that in thiol proteases and animal transglutaminases. It catalyses the in vitro lysis of M. marburgensis cells under reducing conditions and exhibits characteristics of metal-activated peptidases.
Probab=24.81 E-value=85 Score=25.37 Aligned_cols=39 Identities=18% Similarity=0.387 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHHcCCccccceeeEEEEEEEEeCCCccCh
Q psy9199 112 IAARRYARCLQRLGFKARFTNFRVVNVLGTCSMPFAIRI 150 (204)
Q Consensus 112 ~a~~k~~~~L~~lG~~v~~~~f~v~NIvat~~~~~~I~L 150 (204)
.|.+-|.++++.+|++|+|...++.-.-++.--+..++|
T Consensus 59 D~~Qlf~~v~~~lGY~Vq~~HVk~rc~~g~wygH~~LRv 97 (142)
T PF12386_consen 59 DACQLFYRVIESLGYDVQFEHVKCRCNSGKWYGHYRLRV 97 (142)
T ss_pred hHHHHHHHHHHhcCceEEEEEEEEEecCCceeeEEEEEe
Confidence 567888999999999999998888755555333333443
No 78
>smart00392 PROF Profilin. Binds actin monomers, membrane polyphosphoinositides and poly-L-proline.
Probab=24.33 E-value=2.5e+02 Score=21.70 Aligned_cols=38 Identities=16% Similarity=0.205 Sum_probs=25.9
Q ss_pred EEEEEeCCCceEEeecC----CHHHHHHHHHHHHHHHHHcCC
Q psy9199 89 TTASIWSSGKITCTGAT----SEDQSKIAARRYARCLQRLGF 126 (204)
Q Consensus 89 ~tvlIF~SGKivitGak----S~e~a~~a~~k~~~~L~~lG~ 126 (204)
.-+.|..+.+.++.|-- ....+..++.++++.|+..|+
T Consensus 88 ~Gv~i~kT~~aivI~~y~e~~~~g~~~~~v~~ladYL~~~Gy 129 (129)
T smart00392 88 GGVVIVKTKQALIIGMYKEGVQPGQANKTVEKLADYLRSSGY 129 (129)
T ss_pred ceEEEEECCCEEEEEECCCCCChHHHHHHHHHHHHHHHHcCC
Confidence 33444444444444433 456999999999999999885
No 79
>COG2221 DsrA Dissimilatory sulfite reductase (desulfoviridin), alpha and beta subunits [Energy production and conversion]
Probab=23.89 E-value=51 Score=30.32 Aligned_cols=77 Identities=16% Similarity=0.203 Sum_probs=49.4
Q ss_pred EEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccccceeeEEEEEEE-----EeCCCccChHHHHHHccccccCC
Q psy9199 90 TASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKARFTNFRVVNVLGT-----CSMPFAIRILQFSEKHRAAEYEP 164 (204)
Q Consensus 90 tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~~~~f~v~NIvat-----~~~~~~I~L~~la~~~~~~~YeP 164 (204)
.+.|-+.+.+-+-|- |.+++..+ ...|++.|+++-.....|+||+|. |. .--+|-..|+.+...-.+|+
T Consensus 61 ~i~iT~rqg~ei~~i-~~e~~~~v----~~~L~~iG~~~G~~G~~vr~i~aC~G~~~C~-~a~~Dt~~la~~l~e~f~~~ 134 (317)
T COG2221 61 LIHITSRQGLEIPGI-SPEDADDV----VEELREIGLPVGSTGPAVRAIVACPGPRTCE-TALYDTTELARRLEEEFLEV 134 (317)
T ss_pred eEEEEecCceEeccC-CHHHHHHH----HHHHHHcCCCCCCcchhhhhhhcCcCccccc-ccccChHHHHHHHHHHhhcC
Confidence 445556666666664 77776655 456679999999998899999973 22 23478888887554333333
Q ss_pred CCCceeEEEe
Q psy9199 165 ELHPGVTYRI 174 (204)
Q Consensus 165 e~fPgliyr~ 174 (204)
- +|. .||+
T Consensus 135 ~-~P~-KfKI 142 (317)
T COG2221 135 P-VPY-KFKI 142 (317)
T ss_pred C-CCc-eEEE
Confidence 3 455 4544
No 80
>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=23.48 E-value=1.4e+02 Score=21.77 Aligned_cols=26 Identities=23% Similarity=0.225 Sum_probs=19.4
Q ss_pred eCCCceEEeecCCHHHHHHHHHHHHHH
Q psy9199 94 WSSGKITCTGATSEDQSKIAARRYARC 120 (204)
Q Consensus 94 F~SGKivitGakS~e~a~~a~~k~~~~ 120 (204)
-.+|||++.|. |.-.+-.|+...++.
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 47999999997 888888888766653
No 81
>PHA02956 hypothetical protein; Provisional
Probab=23.20 E-value=73 Score=26.34 Aligned_cols=23 Identities=39% Similarity=0.514 Sum_probs=17.9
Q ss_pred eCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCc
Q psy9199 94 WSSGKITCTGATSEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 94 F~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~ 127 (204)
-+||||+|-|- -+.+.|+-.|++
T Consensus 113 sssgkiicegi-----------giid~lr~~gid 135 (189)
T PHA02956 113 SSSGKIICEGI-----------GIIDKLRLHGID 135 (189)
T ss_pred cCCCcEEeecc-----------hHHHHHHHcCch
Confidence 46899999998 566677777765
No 82
>PF10865 DUF2703: Domain of unknown function (DUF2703); InterPro: IPR021219 This family of protein has no known function.
Probab=23.11 E-value=85 Score=24.78 Aligned_cols=27 Identities=22% Similarity=0.393 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHHHHHHHcCCccccce
Q psy9199 106 SEDQSKIAARRYARCLQRLGFKARFTN 132 (204)
Q Consensus 106 S~e~a~~a~~k~~~~L~~lG~~v~~~~ 132 (204)
+-+.+++|++++...|+.+|+.+++..
T Consensus 21 Tg~~L~~av~~l~~~L~~~Giev~l~~ 47 (120)
T PF10865_consen 21 TGETLREAVKELAPVLAPLGIEVRLEE 47 (120)
T ss_pred HHHHHHHHHHHHHHHHHhCCcEEEEEE
Confidence 567899999999999999999887764
No 83
>PF13549 ATP-grasp_5: ATP-grasp domain; PDB: 1WR2_A.
Probab=23.09 E-value=1.8e+02 Score=25.03 Aligned_cols=59 Identities=15% Similarity=0.054 Sum_probs=34.4
Q ss_pred EEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccccceeeEEEEEE
Q psy9199 80 VTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKARFTNFRVVNVLG 140 (204)
Q Consensus 80 vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~~~~f~v~NIva 140 (204)
|++|+..|...=+- .---|..|-+|.++++.|++++...+++..-......+-||-++.
T Consensus 49 vvlKi~sp~i~HKs--d~GgV~L~l~~~~~v~~a~~~l~~~~~~~~p~~~~~gvlVq~m~~ 107 (222)
T PF13549_consen 49 VVLKIVSPDIAHKS--DVGGVRLNLNSPEEVREAFERLRERVAAHHPGARIDGVLVQEMAP 107 (222)
T ss_dssp EEEEEE-TT---HH--HHT-EEEEE-SHHHHHHHHHHHHHHHHHH-TT----EEEEEE---
T ss_pred EEEEEecCCCCcCC--CCCcEEECCCCHHHHHHHHHHHHHHHHHhCCCCccceEEEEEccc
Confidence 35888777643111 112467788999999999999999999876666667777777754
No 84
>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=23.06 E-value=1.1e+02 Score=21.48 Aligned_cols=23 Identities=22% Similarity=0.325 Sum_probs=17.9
Q ss_pred EEEEEeCCCceE--EeecCCHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSK 111 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~ 111 (204)
.++.+|..|+.+ ..|.++.+++.
T Consensus 75 Pt~~~~~~g~~~~~~~G~~~~~~l~ 99 (102)
T cd03005 75 PTLLLFKDGEKVDKYKGTRDLDSLK 99 (102)
T ss_pred CEEEEEeCCCeeeEeeCCCCHHHHH
Confidence 378888999865 78988877654
No 85
>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=22.92 E-value=1.3e+02 Score=25.02 Aligned_cols=41 Identities=12% Similarity=0.075 Sum_probs=30.4
Q ss_pred EEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccccc
Q psy9199 89 TTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKARFT 131 (204)
Q Consensus 89 ~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~~~ 131 (204)
+.+..|-..=+ + ++++.+++.++.+.+...|++.|+.+...
T Consensus 158 ~~~~~Y~DDil-i-~s~~~~~~~~~l~~v~~~l~~~gl~ln~~ 198 (213)
T cd01645 158 IVIYHYMDDIL-I-ASDLEGQLREIYEELRQTLLRWGLTIPPE 198 (213)
T ss_pred eEEEEEcCCEE-E-EcCCHHHHHHHHHHHHHHHHHCCCEeCHH
Confidence 34555555433 3 35699999999999999999999876554
No 86
>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=22.78 E-value=1.3e+02 Score=20.13 Aligned_cols=22 Identities=18% Similarity=0.373 Sum_probs=18.1
Q ss_pred CCceEEeecCCHHHHHHHHHHH
Q psy9199 96 SGKITCTGATSEDQSKIAARRY 117 (204)
Q Consensus 96 SGKivitGakS~e~a~~a~~k~ 117 (204)
.|+..+.|..+.++.+..+++.
T Consensus 60 ~g~~~~~G~~~~~~l~~~l~~~ 81 (82)
T TIGR00411 60 NGDVEFIGAPTKEELVEAIKKR 81 (82)
T ss_pred CCEEEEecCCCHHHHHHHHHhh
Confidence 8888999998999888777653
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=22.73 E-value=97 Score=21.66 Aligned_cols=25 Identities=24% Similarity=0.408 Sum_probs=19.2
Q ss_pred EEEEEeCCCceE--EeecCCHHHHHHH
Q psy9199 89 TTASIWSSGKIT--CTGATSEDQSKIA 113 (204)
Q Consensus 89 ~tvlIF~SGKiv--itGakS~e~a~~a 113 (204)
.++.+|..|+.+ ..|..+.++++.-
T Consensus 68 Pt~~~~~~g~~~~~~~g~~~~~~l~~~ 94 (96)
T cd02956 68 PTVYLFAAGQPVDGFQGAQPEEQLRQM 94 (96)
T ss_pred CEEEEEeCCEEeeeecCCCCHHHHHHH
Confidence 578888999986 7788788776653
No 88
>KOG4180|consensus
Probab=22.17 E-value=1.3e+02 Score=28.18 Aligned_cols=72 Identities=21% Similarity=0.276 Sum_probs=47.6
Q ss_pred EEEEeCCCceEEeecCCH-------HHHHHHHHHHHHHHHHcCCc-cccceeeEEEEEEEEeCCCccChHHHHHHcc-cc
Q psy9199 90 TASIWSSGKITCTGATSE-------DQSKIAARRYARCLQRLGFK-ARFTNFRVVNVLGTCSMPFAIRILQFSEKHR-AA 160 (204)
Q Consensus 90 tvlIF~SGKivitGakS~-------e~a~~a~~k~~~~L~~lG~~-v~~~~f~v~NIvat~~~~~~I~L~~la~~~~-~~ 160 (204)
.++-=+||-++|||.-|. .-+..++..++.++...|-. +.+. .=..+.++..+- ..
T Consensus 254 ~~KqKssgl~vctgTGstsw~~~iNria~q~v~d~l~~l~~~~~~~vp~~---------------Re~ve~i~~~~nq~l 318 (395)
T KOG4180|consen 254 GVKQKSSGLVVCTGTGSTSWTFNINRIAEQAVGDLLMILLSRDNLQVPFM---------------RELVEEISTAYNQHL 318 (395)
T ss_pred cccccCCCeeEecCCCcceEeecccHHHHHHHHHHHHHHHhcCcccchhh---------------hhhhHHHHHHhhhcC
Confidence 446678999999997653 45677788888888877643 2221 112255555553 88
Q ss_pred ccCCCCCceeEEEeCCC
Q psy9199 161 EYEPELHPGVTYRITRP 177 (204)
Q Consensus 161 ~YePe~fPgliyr~~~p 177 (204)
.|+|+ .|-+-|-+++|
T Consensus 319 lF~PD-~p~l~fSiRep 334 (395)
T KOG4180|consen 319 LFKPD-RPQLAFSIREP 334 (395)
T ss_pred ccCCC-Ccchhhhhhhh
Confidence 89998 37777766665
No 89
>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=22.15 E-value=1.4e+02 Score=23.23 Aligned_cols=30 Identities=30% Similarity=0.459 Sum_probs=25.8
Q ss_pred CCceEEeecCCHHHHHHHHHHHHHHHHH-cCCc
Q psy9199 96 SGKITCTGATSEDQSKIAARRYARCLQR-LGFK 127 (204)
Q Consensus 96 SGKivitGakS~e~a~~a~~k~~~~L~~-lG~~ 127 (204)
+|-++++| +..+++.|++.....+++ ++|.
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 999999999999999887 5664
No 90
>PF10979 DUF2786: Protein of unknown function (DUF2786); InterPro: IPR024498 This domain is found in proteins that have no known function.
Probab=21.80 E-value=1.4e+02 Score=19.26 Aligned_cols=22 Identities=18% Similarity=0.389 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHHHHHHHHcCCc
Q psy9199 106 SEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 106 S~e~a~~a~~k~~~~L~~lG~~ 127 (204)
++.++..|+.+..+.+.+.|++
T Consensus 20 ~~~EA~~A~~kAq~Lm~ky~i~ 41 (43)
T PF10979_consen 20 NEHEAEAALAKAQRLMAKYGID 41 (43)
T ss_pred CHHHHHHHHHHHHHHHHHhCCc
Confidence 7779999999999999998874
No 91
>COG4810 EutS Ethanolamine utilization protein [Amino acid transport and metabolism]
Probab=21.73 E-value=1.5e+02 Score=23.24 Aligned_cols=30 Identities=23% Similarity=0.182 Sum_probs=24.7
Q ss_pred EeCCCceEEeecCCHHHHHHHHHHHHHHHHHc
Q psy9199 93 IWSSGKITCTGATSEDQSKIAARRYARCLQRL 124 (204)
Q Consensus 93 IF~SGKivitGakS~e~a~~a~~k~~~~L~~l 124 (204)
=--||-+++|| +....+.|++++..-|.++
T Consensus 81 DRFsGalvltG--dv~aVE~aLkqv~~~L~e~ 110 (121)
T COG4810 81 DRFSGALVLTG--DVGAVEEALKQVVSGLGEL 110 (121)
T ss_pred ecccceEEEEc--chHHHHHHHHHHHHHHHHH
Confidence 34589999999 6888889999988888774
No 92
>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=21.52 E-value=76 Score=24.50 Aligned_cols=28 Identities=18% Similarity=0.287 Sum_probs=21.5
Q ss_pred ceEEEEec---------CCcEEEEEeCCCceEEeecC
Q psy9199 78 GMVTMKLR---------KPYTTASIWSSGKITCTGAT 105 (204)
Q Consensus 78 g~vi~Rl~---------~P~~tvlIF~SGKivitGak 105 (204)
-.+.||.. .-.||-|+|.+||++--|-+
T Consensus 61 qVLfYrT~~~~sDG~TTkDECTplvF~n~~LvgWG~~ 97 (102)
T PF11399_consen 61 QVLFYRTQHKKSDGITTKDECTPLVFKNGKLVGWGDD 97 (102)
T ss_pred EEEEEEEeeEcCCCCccCCceEEEEEECCEEEEEcHH
Confidence 34567764 33599999999999999863
No 93
>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=21.24 E-value=1.9e+02 Score=19.41 Aligned_cols=27 Identities=11% Similarity=0.211 Sum_probs=19.2
Q ss_pred EEEEEeCCCceEEeecCCHHHHHHHHHH
Q psy9199 89 TTASIWSSGKITCTGATSEDQSKIAARR 116 (204)
Q Consensus 89 ~tvlIF~SGKivitGakS~e~a~~a~~k 116 (204)
+.+-|=.+|.+.++|. +.+.+..|.+.
T Consensus 33 ~~I~i~~~g~v~I~G~-~~~~v~~A~~~ 59 (61)
T cd02393 33 VKIDIEDDGTVYIAAS-DKEAAEKAKKM 59 (61)
T ss_pred CEEEeCCCCEEEEEeC-CHHHHHHHHHH
Confidence 4555666899999995 66666666554
No 94
>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=21.11 E-value=1.5e+02 Score=22.02 Aligned_cols=38 Identities=13% Similarity=-0.007 Sum_probs=32.1
Q ss_pred CcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcC
Q psy9199 87 PYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLG 125 (204)
Q Consensus 87 P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG 125 (204)
+....|-.++++|.|.|. +...+..|+.-+.++|+..+
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 357888888899999997 99999999999999987763
No 95
>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=21.08 E-value=1.5e+02 Score=23.02 Aligned_cols=57 Identities=14% Similarity=0.125 Sum_probs=37.5
Q ss_pred CCCceeeCCC--ceEEEEecCCcEEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccc
Q psy9199 68 GVNVEYRREN--GMVTMKLRKPYTTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKAR 129 (204)
Q Consensus 68 ~~n~eYePe~--g~vi~Rl~~P~~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~ 129 (204)
++.++=+|+- --|.+|+..+. -...|.++-|.+..+-=....+++.+.|+++|+.++
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 3445555442 22456776665 567899999999888777889999999999988544
No 96
>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=20.76 E-value=1.2e+02 Score=21.69 Aligned_cols=36 Identities=22% Similarity=0.266 Sum_probs=27.8
Q ss_pred EEeCCCceEEe------ecCCHHHHHHHHHHHHHHHHHcCCc
Q psy9199 92 SIWSSGKITCT------GATSEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 92 lIF~SGKivit------GakS~e~a~~a~~k~~~~L~~lG~~ 127 (204)
++|-||-+-.. ...-.++++.+++++.++|+..|..
T Consensus 10 ~~~~sGq~~~~~~~~~~~~~~~~Q~~~~~~ni~~~L~~~g~~ 51 (107)
T cd00448 10 LVFVSGQIPLDPDGELVPGDIEAQTRQALENLEAVLEAAGGS 51 (107)
T ss_pred EEEEeccCCcCCCCcccCCCHHHHHHHHHHHHHHHHHHcCCC
Confidence 56777766553 2346789999999999999999986
No 97
>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=20.50 E-value=1.7e+02 Score=24.15 Aligned_cols=41 Identities=17% Similarity=0.187 Sum_probs=29.5
Q ss_pred EEEEEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCccccc
Q psy9199 89 TTASIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFKARFT 131 (204)
Q Consensus 89 ~tvlIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~v~~~ 131 (204)
+.+.+|-.- |.+.| ++.++....++.+.+.|++.|+.+...
T Consensus 154 ~~~~~Y~DD-ili~s-~~~~e~~~~l~~v~~~l~~~gl~l~~~ 194 (210)
T cd03715 154 TILLQYVDD-LLLAA-DSEEDCLKGTDALLTHLGELGYKVSPK 194 (210)
T ss_pred eEEEEECCc-EEEec-CCHHHHHHHHHHHHHHHHHCCCCcCHH
Confidence 334444433 34444 699999999999999999999876543
No 98
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=20.48 E-value=5e+02 Score=23.04 Aligned_cols=71 Identities=10% Similarity=0.020 Sum_probs=42.1
Q ss_pred HHHHHHHHHHcCCccccceeeE------EEEEEEEeC-CCccChHHHHHHccccccCCCCCceeEEEe--CCCceEEEEe
Q psy9199 114 ARRYARCLQRLGFKARFTNFRV------VNVLGTCSM-PFAIRILQFSEKHRAAEYEPELHPGVTYRI--TRPKATLKIF 184 (204)
Q Consensus 114 ~~k~~~~L~~lG~~v~~~~f~v------~NIvat~~~-~~~I~L~~la~~~~~~~YePe~fPgliyr~--~~pk~t~lIF 184 (204)
+.++.+.|.+.|+++......+ -.+...+++ +.+.+++.|...+....-+= ++..++ ..++.++.||
T Consensus 20 Va~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~~~~~~~~~L~~~L~~l~~~l----~l~i~l~~~~~~~ri~vl 95 (286)
T PRK06027 20 VAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDGLIFNLETLRADFAALAEEF----EMDWRLLDSAERKRVVIL 95 (286)
T ss_pred HHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCCCCCCHHHHHHHHHHHHHHh----CCEEEEcccccCcEEEEE
Confidence 4566778888988765543333 345556666 66777777765554221111 122333 3456789999
Q ss_pred ccCc
Q psy9199 185 STGG 188 (204)
Q Consensus 185 ~sGk 188 (204)
.||.
T Consensus 96 ~Sg~ 99 (286)
T PRK06027 96 VSKE 99 (286)
T ss_pred EcCC
Confidence 9997
No 99
>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=20.16 E-value=1.8e+02 Score=20.47 Aligned_cols=29 Identities=17% Similarity=0.265 Sum_probs=21.6
Q ss_pred EEeecCCHHHHHHHHHHHHHHHHHcCCccc
Q psy9199 100 TCTGATSEDQSKIAARRYARCLQRLGFKAR 129 (204)
Q Consensus 100 vitGakS~e~a~~a~~k~~~~L~~lG~~v~ 129 (204)
++.|.+ .+++..-+.++...|++.|+.+.
T Consensus 5 i~~~~~-~~~~~~~a~~l~~~L~~~gi~v~ 33 (94)
T PF03129_consen 5 IPVGKK-DEEIIEYAQELANKLRKAGIRVE 33 (94)
T ss_dssp EESSCS-HHHHHHHHHHHHHHHHHTTSEEE
T ss_pred EEeCCC-cHHHHHHHHHHHHHHHHCCCEEE
Confidence 334433 77888899999999999996543
No 100
>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=20.03 E-value=95 Score=20.26 Aligned_cols=32 Identities=9% Similarity=0.230 Sum_probs=19.6
Q ss_pred EEeCCCceEEeecCCHHHHHHHHHHHHHHHHHcCCc
Q psy9199 92 SIWSSGKITCTGATSEDQSKIAARRYARCLQRLGFK 127 (204)
Q Consensus 92 lIF~SGKivitGakS~e~a~~a~~k~~~~L~~lG~~ 127 (204)
.=+.+|++.+++..+. ...+++.+.|+++||+
T Consensus 31 vd~~~~~v~v~~~~~~----~~~~~i~~~i~~~Gy~ 62 (62)
T PF00403_consen 31 VDLETKTVTVTYDPDK----TSIEKIIEAIEKAGYE 62 (62)
T ss_dssp EETTTTEEEEEESTTT----SCHHHHHHHHHHTTSE
T ss_pred EECCCCEEEEEEecCC----CCHHHHHHHHHHhCcC
Confidence 3466788888886443 1124566667777774
Done!