Query 031013
Match_columns 167
No_of_seqs 147 out of 514
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 07:56:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/031013.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/031013hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG3302 TATA-box binding prote 100.0 7.1E-59 1.5E-63 372.9 18.1 158 10-167 19-200 (200)
2 PLN00062 TATA-box-binding prot 100.0 4.7E-58 1E-62 367.8 19.9 155 13-167 1-179 (179)
3 cd04516 TBP_eukaryotes eukaryo 100.0 4.9E-57 1.1E-61 360.5 19.8 150 13-162 1-174 (174)
4 COG2101 SPT15 TATA-box binding 100.0 5.4E-56 1.2E-60 351.5 17.6 155 10-164 4-184 (185)
5 cd04518 TBP_archaea archaeal T 100.0 9.4E-55 2E-59 347.4 19.8 149 13-162 1-174 (174)
6 PRK00394 transcription factor; 100.0 1.5E-54 3.3E-59 347.5 20.4 151 15-165 2-178 (179)
7 cd00652 TBP_TLF TATA box bindi 100.0 3.9E-54 8.5E-59 343.6 19.8 149 13-161 1-174 (174)
8 cd04517 TLF TBP-like factors ( 100.0 1.4E-53 2.9E-58 340.6 19.9 149 13-161 2-174 (174)
9 PF00352 TBP: Transcription fa 100.0 3.8E-33 8.1E-38 199.1 11.8 86 77-163 1-86 (86)
10 cd04516 TBP_eukaryotes eukaryo 100.0 7.7E-29 1.7E-33 198.1 11.7 83 80-163 2-84 (174)
11 PLN00062 TATA-box-binding prot 100.0 1.2E-28 2.6E-33 197.8 11.6 83 80-163 2-84 (179)
12 cd04518 TBP_archaea archaeal T 100.0 3.1E-28 6.7E-33 194.7 11.5 84 79-163 1-84 (174)
13 PRK00394 transcription factor; 100.0 3E-28 6.4E-33 195.5 11.4 83 80-163 1-83 (179)
14 COG2101 SPT15 TATA-box binding 100.0 1.5E-28 3.3E-33 195.1 9.5 84 78-162 6-89 (185)
15 cd00652 TBP_TLF TATA box bindi 100.0 4.6E-28 1E-32 193.5 11.6 84 79-163 1-84 (174)
16 cd04517 TLF TBP-like factors ( 99.9 4.7E-27 1E-31 187.8 11.7 83 79-163 2-84 (174)
17 KOG3302 TATA-box binding prote 99.9 2.1E-21 4.6E-26 156.5 10.4 84 78-162 21-104 (200)
18 PF00352 TBP: Transcription fa 99.7 1E-17 2.2E-22 119.4 7.9 60 13-72 3-86 (86)
19 PF11858 DUF3378: Domain of un 96.8 0.0013 2.8E-08 46.7 3.5 36 113-148 26-61 (81)
20 COG4871 Uncharacterized protei 95.5 0.1 2.2E-06 42.0 8.1 73 85-161 36-108 (193)
21 COG1039 RnhC Ribonuclease HIII 94.9 0.078 1.7E-06 45.9 6.3 44 113-156 27-70 (297)
22 PRK00996 ribonuclease HIII; Pr 94.3 0.09 1.9E-06 45.6 5.3 34 112-145 26-59 (304)
23 TIGR00716 rnhC ribonuclease HI 94.0 0.13 2.8E-06 44.2 5.8 34 111-144 22-55 (284)
24 PRK12475 thiamine/molybdopteri 84.5 3.4 7.3E-05 36.2 6.6 36 118-155 301-336 (338)
25 PRK11509 hydrogenase-1 operon 73.3 5.2 0.00011 30.8 3.7 63 93-156 54-124 (132)
26 cd03065 PDI_b_Calsequestrin_N 71.1 8.3 0.00018 28.9 4.4 30 127-156 89-119 (120)
27 PRK07688 thiamine/molybdopteri 68.6 18 0.00038 31.7 6.5 35 121-155 303-337 (339)
28 PF13575 DUF4135: Domain of un 59.2 9.1 0.0002 33.6 3.0 51 51-102 127-177 (370)
29 PRK09381 trxA thioredoxin; Pro 55.7 18 0.00039 25.3 3.5 28 128-155 78-107 (109)
30 cd02965 HyaE HyaE family; HyaE 55.6 15 0.00031 27.4 3.1 69 80-149 29-109 (111)
31 TIGR00411 redox_disulf_1 small 55.5 11 0.00024 24.7 2.3 22 134-155 60-81 (82)
32 PRK10996 thioredoxin 2; Provis 54.6 19 0.00042 27.0 3.7 28 128-155 109-138 (139)
33 PRK13011 formyltetrahydrofolat 54.3 98 0.0021 26.5 8.4 84 61-152 21-110 (286)
34 PHA02278 thioredoxin-like prot 53.4 20 0.00044 25.8 3.5 24 127-150 74-99 (103)
35 cd01644 RT_pepA17 RT_pepA17: R 53.3 22 0.00047 29.0 4.1 36 40-75 137-172 (213)
36 PF13192 Thioredoxin_3: Thiore 52.5 17 0.00037 24.3 2.9 23 131-153 53-76 (76)
37 KOG0910 Thioredoxin-like prote 50.8 27 0.00058 27.6 4.0 78 79-157 62-149 (150)
38 PLN00410 U5 snRNP protein, DIM 48.6 34 0.00075 26.5 4.3 79 80-158 25-122 (142)
39 cd02948 TRX_NDPK TRX domain, T 48.4 27 0.00059 24.4 3.5 26 128-154 74-101 (102)
40 cd02963 TRX_DnaJ TRX domain, D 48.1 22 0.00048 25.4 3.1 27 128-154 82-110 (111)
41 PRK06027 purU formyltetrahydro 47.9 1.4E+02 0.003 25.6 8.3 83 61-153 20-111 (286)
42 KOG4108 Dynein light chain [Ce 46.4 59 0.0013 26.3 5.4 91 26-132 68-169 (174)
43 PF00085 Thioredoxin: Thioredo 45.5 49 0.0011 22.1 4.4 27 128-154 74-102 (103)
44 PF07338 DUF1471: Protein of u 44.4 31 0.00067 22.4 3.0 23 134-156 5-28 (56)
45 KOG4749 Inositol polyphosphate 44.3 6.3 0.00014 35.1 -0.5 54 106-159 174-241 (375)
46 cd07047 BMC_PduB_repeat1 1,2-p 43.7 41 0.00088 26.1 4.0 28 134-161 78-105 (134)
47 TIGR00385 dsbE periplasmic pro 42.2 42 0.00092 25.8 4.0 48 109-156 122-171 (173)
48 PRK15468 carboxysome structura 41.7 32 0.00069 25.9 3.0 31 129-161 69-99 (111)
49 PF04628 Sedlin_N: Sedlin, N-t 41.6 1.2E+02 0.0026 22.6 6.3 50 112-161 49-104 (132)
50 PF06200 tify: tify domain; I 41.2 73 0.0016 19.1 4.0 27 126-152 5-31 (36)
51 COG4871 Uncharacterized protei 41.1 52 0.0011 26.7 4.3 41 31-71 48-109 (193)
52 cd02950 TxlA TRX-like protein 38.4 65 0.0014 24.2 4.4 29 128-156 79-110 (142)
53 TIGR01068 thioredoxin thioredo 37.4 52 0.0011 21.8 3.4 26 129-154 72-99 (101)
54 PF11869 DUF3389: Protein of u 37.3 18 0.0004 25.4 1.1 12 130-141 3-14 (75)
55 cd02949 TRX_NTR TRX domain, no 37.3 48 0.001 22.7 3.3 25 128-152 70-96 (97)
56 PRK10719 eutA reactivating fac 36.9 86 0.0019 29.2 5.6 102 26-142 60-173 (475)
57 PF14657 Integrase_AP2: AP2-li 36.8 57 0.0012 20.0 3.2 24 47-70 20-43 (46)
58 PF06277 EutA: Ethanolamine ut 36.7 77 0.0017 29.5 5.3 101 26-143 57-171 (473)
59 cd02956 ybbN ybbN protein fami 36.2 48 0.001 22.4 3.1 25 128-152 69-95 (96)
60 PRK14126 cell division protein 33.1 1.4E+02 0.003 21.0 5.1 40 125-165 7-46 (85)
61 COG2761 FrnE Predicted dithiol 32.5 64 0.0014 27.1 3.8 94 61-157 119-214 (225)
62 cd03005 PDI_a_ERp46 PDIa famil 32.2 61 0.0013 21.8 3.1 22 129-150 77-100 (102)
63 PRK10259 hypothetical protein; 31.3 59 0.0013 23.2 2.9 23 133-155 36-58 (86)
64 cd02393 PNPase_KH Polynucleoti 31.1 1.1E+02 0.0023 19.9 4.0 30 125-155 31-60 (61)
65 PRK15412 thiol:disulfide inter 30.2 1.1E+02 0.0024 23.9 4.6 52 109-160 127-180 (185)
66 cd04792 LanM-like LanM-like pr 29.7 41 0.00088 32.5 2.5 52 50-102 166-217 (825)
67 PTZ00397 macrophage migration 28.2 1.5E+02 0.0033 21.3 4.8 38 47-84 64-102 (116)
68 PF11399 DUF3192: Protein of u 28.1 1.1E+02 0.0023 22.8 3.9 29 116-144 61-98 (102)
69 KOG0670 U4/U6-associated splic 28.0 3E+02 0.0066 26.7 7.7 132 15-152 504-648 (752)
70 PF05906 DUF865: Herpesvirus-7 27.9 62 0.0013 19.0 2.1 27 109-135 8-34 (35)
71 COG0678 AHP1 Peroxiredoxin [Po 27.9 37 0.00079 27.2 1.5 32 111-142 5-45 (165)
72 TIGR01175 pilM type IV pilus a 27.5 2.2E+02 0.0048 24.1 6.4 67 58-142 142-215 (348)
73 COG4274 Uncharacterized conser 27.5 84 0.0018 23.4 3.2 56 50-105 21-78 (104)
74 TIGR00646 MG010 DNA primase-re 27.3 91 0.002 26.0 3.8 56 16-75 130-185 (218)
75 cd07046 BMC_PduU-EutS 1,2-prop 27.3 1E+02 0.0022 23.0 3.7 26 134-161 73-98 (110)
76 COG1654 BirA Biotin operon rep 27.3 51 0.0011 23.1 2.0 21 56-76 31-51 (79)
77 PF10686 DUF2493: Protein of u 26.9 86 0.0019 21.3 3.1 20 136-155 5-24 (71)
78 PF13098 Thioredoxin_2: Thiore 26.6 1E+02 0.0022 21.2 3.6 24 129-152 86-112 (112)
79 PRK02079 pyrroloquinoline quin 26.5 1.3E+02 0.0028 21.3 4.0 45 112-156 6-62 (88)
80 PF00403 HMA: Heavy-metal-asso 26.4 69 0.0015 20.1 2.4 25 130-154 31-58 (62)
81 KOG3384 Selenoprotein [General 25.2 48 0.001 26.1 1.7 27 111-138 101-130 (154)
82 PF05164 ZapA: Cell division p 25.1 1.6E+02 0.0035 19.8 4.3 39 127-165 2-40 (89)
83 PHA02031 putative DnaG-like pr 24.8 1.4E+02 0.0031 25.7 4.7 73 16-103 182-254 (266)
84 PRK00754 signal recognition pa 24.8 2.3E+02 0.0049 20.5 5.1 51 96-158 39-91 (95)
85 PF12386 Peptidase_C71: Pseudo 24.6 78 0.0017 24.5 2.7 31 58-88 58-88 (142)
86 PF14611 SLS: Mitochondrial in 24.4 92 0.002 24.8 3.3 37 126-164 56-93 (210)
87 PRK15415 propanediol utilizati 24.1 1.2E+02 0.0027 26.1 4.1 29 134-162 119-147 (266)
88 PF13462 Thioredoxin_4: Thiore 24.1 1.1E+02 0.0024 22.4 3.5 23 131-154 140-162 (162)
89 KOG0353 ATP-dependent DNA heli 24.0 5.5E+02 0.012 24.0 8.4 70 61-163 330-416 (695)
90 PF09840 DUF2067: Uncharacteri 23.9 36 0.00078 27.7 0.8 66 36-103 97-162 (190)
91 cd02975 PfPDO_like_N Pyrococcu 23.7 1.7E+02 0.0037 20.9 4.4 31 127-157 77-111 (113)
92 cd07049 BMC_EutL_repeat1 ethan 23.5 1.4E+02 0.0031 22.1 3.9 28 134-161 71-99 (103)
93 cd03024 DsbA_FrnE DsbA family, 23.5 77 0.0017 24.4 2.6 22 131-152 179-200 (201)
94 KOG3946 Glutaminyl cyclase [Po 23.3 1E+02 0.0022 27.3 3.5 65 48-122 65-138 (338)
95 PF12965 DUF3854: Domain of un 23.1 1.1E+02 0.0024 23.2 3.3 26 51-76 81-106 (130)
96 PF03135 CagE_TrbE_VirB: CagE, 22.7 90 0.002 24.7 2.9 33 42-74 148-180 (205)
97 cd02394 vigilin_like_KH K homo 22.7 1E+02 0.0022 19.4 2.7 20 134-155 42-61 (62)
98 PRK09929 hypothetical protein; 22.5 96 0.0021 22.5 2.7 21 135-155 41-61 (91)
99 cd02994 PDI_a_TMX PDIa family, 22.3 1.2E+02 0.0027 20.5 3.2 24 130-153 76-100 (101)
100 cd03007 PDI_a_ERp29_N PDIa fam 22.1 88 0.0019 23.3 2.6 26 128-153 83-113 (116)
101 PTZ00051 thioredoxin; Provisio 21.9 1.1E+02 0.0024 20.5 2.9 21 128-149 74-96 (98)
102 PF11504 Colicin_Ia: Colicin I 21.5 81 0.0018 21.3 2.0 20 110-135 10-29 (72)
103 KOG2648 Diphthamide biosynthes 21.3 1.4E+02 0.0031 27.7 4.1 57 18-74 209-298 (453)
104 cd02996 PDI_a_ERp44 PDIa famil 20.9 99 0.0021 21.4 2.6 23 128-150 81-106 (108)
105 COG0849 ftsA Cell division ATP 20.9 3.2E+02 0.007 24.9 6.4 73 47-143 159-231 (418)
106 COG1490 Dtd D-Tyr-tRNAtyr deac 20.9 2.6E+02 0.0057 22.0 5.0 58 20-77 31-122 (145)
107 cd03364 TOPRIM_DnaG_primases T 20.6 2.4E+02 0.0052 18.7 4.3 55 17-76 21-75 (79)
108 cd03715 RT_ZFREV_like RT_ZFREV 20.5 1.5E+02 0.0033 23.4 3.9 35 43-77 159-193 (210)
109 PF12010 DUF3502: Domain of un 20.4 17 0.00037 27.5 -1.6 54 18-74 58-116 (134)
110 TIGR02653 Lon_rel_chp conserve 20.3 7.2E+02 0.016 24.4 8.8 50 110-160 490-548 (675)
111 cd01645 RT_Rtv RT_Rtv: Reverse 20.2 1.2E+02 0.0027 24.2 3.3 36 42-77 162-197 (213)
112 PF08002 DUF1697: Protein of u 20.1 2.2E+02 0.0048 21.5 4.5 30 130-159 38-67 (137)
113 PF14294 DUF4372: Domain of un 20.1 1.8E+02 0.004 20.0 3.7 28 47-74 48-75 (76)
No 1
>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=100.00 E-value=7.1e-59 Score=372.95 Aligned_cols=158 Identities=75% Similarity=1.204 Sum_probs=154.6
Q ss_pred cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013 10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA 65 (167)
Q Consensus 10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~ 65 (167)
.++.|.++||||+++++|+|||++||+.++|+||||+ +||||+|+++||.|++|++
T Consensus 19 ~~i~~~l~nivc~~~~~c~ldLk~ial~~~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~a 98 (200)
T KOG3302|consen 19 SGLDPTLQNIVCTVNLNCKLDLKEIALHARNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKYA 98 (200)
T ss_pred cccceEEEeEEEEEeccceecHHHHhhhccccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHHH
Confidence 4789999999999999999999999999999999998 8999999999999999999
Q ss_pred HHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCH
Q 031013 66 RIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR 145 (167)
Q Consensus 66 ~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~ 145 (167)
|+||+|||+++|.+|+|||||||||++|+|+|++++..|+.+++||||+||||+|||.+|+++++||+||||++|||++.
T Consensus 99 RilqkLgf~~~f~~fki~nv~asc~vpF~IrLe~~~~~h~~~ssYepel~PgliYrm~~pkv~l~IF~tG~VvvtgA~~~ 178 (200)
T KOG3302|consen 99 RILQKLGFPVKFRDFKINNVVASCDVPFPIRLEGLALRHPVFSSYEPELFPGLIYRMVKPKVVLLIFVTGKVVVTGAKVR 178 (200)
T ss_pred HHHHHcCCCceehheeeEEEEEEEeccceeehhHhhhhCCcccccCcccCceeEEEecCCcEEEEEecCCEEEEEecccH
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHhhhhhcC
Q 031013 146 DETYTAFENIYPVLTEFRKVQQ 167 (167)
Q Consensus 146 e~~~~a~~~i~~~L~~~r~~~~ 167 (167)
+|+.+|+++|||+|.+|||+.+
T Consensus 179 ~~i~~Ai~~IyPil~~frk~~~ 200 (200)
T KOG3302|consen 179 EETYEAIENIYPILLEFRKKLL 200 (200)
T ss_pred HHHHHHHHHHhHHHHHhhhccC
Confidence 9999999999999999999753
No 2
>PLN00062 TATA-box-binding protein; Provisional
Probab=100.00 E-value=4.7e-58 Score=367.83 Aligned_cols=155 Identities=94% Similarity=1.393 Sum_probs=151.2
Q ss_pred eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII 68 (167)
Q Consensus 13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l 68 (167)
.|+|+|||||++++|+|||++||..++|++|||+ +||||+|+++|+.|+++++++|
T Consensus 1 ~~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 1 VPTLQNIVSTVNLDCKLDLKKIALQARNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARII 80 (179)
T ss_pred CcEEEEEEEEEEcCCcccHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 4899999999999999999999999999999998 8999999999999999999999
Q ss_pred HhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013 69 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 148 (167)
Q Consensus 69 ~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~ 148 (167)
+++|+++++.+|+|+|||||+|++++|||+.||..+.++++||||+||||+||+.+|+++++||+||||+|||+||++|+
T Consensus 81 ~~lg~~~~~~~f~v~NIvas~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~ 160 (179)
T PLN00062 81 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYAHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVREEI 160 (179)
T ss_pred HHcCCCcCCCccEEEEEEEEEECCCcccHHHHHHhchhhcccCcccCceEEEEeCCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 99999999999999999999999999999999987778999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhhcC
Q 031013 149 YTAFENIYPVLTEFRKVQQ 167 (167)
Q Consensus 149 ~~a~~~i~~~L~~~r~~~~ 167 (167)
++|++.|+|+|.+||+.+|
T Consensus 161 ~~ai~~i~p~L~~~~~~~~ 179 (179)
T PLN00062 161 YTAFENIYPVLTEFRKRQQ 179 (179)
T ss_pred HHHHHHHHHHHHHhccCCC
Confidence 9999999999999998865
No 3
>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=4.9e-57 Score=360.55 Aligned_cols=150 Identities=84% Similarity=1.302 Sum_probs=146.5
Q ss_pred eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII 68 (167)
Q Consensus 13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l 68 (167)
.|+|+|||||++++|+|||++||..++|++|||+ +||||+|+|+|+.|+++++++|
T Consensus 1 ~~~I~NvVas~~l~~~idL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L 80 (174)
T cd04516 1 VPKIQNIVATVNLGCKLDLKKIALRARNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII 80 (174)
T ss_pred CCEEEEEEEEEEcCCeecHHHHHhhCCCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 4899999999999999999999999999999998 8999999999999999999999
Q ss_pred HhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013 69 QKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 148 (167)
Q Consensus 69 ~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~ 148 (167)
+++|+++++.+|+|+|||||+|++++|||++||..+.++++||||+||||+||+.+|+++++||+||||+|||+||++|+
T Consensus 81 ~~~g~~~~~~~~~v~Nivat~~l~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~pk~~~liF~sGkvvitGaks~~~~ 160 (174)
T cd04516 81 QKLGFPAKFTDFKIQNIVGSCDVKFPIRLEGLAHAHKQFSSYEPELFPGLIYRMVKPKIVLLIFVSGKIVLTGAKSREEI 160 (174)
T ss_pred HHcCCCCCCCceEEEEEEEEEECCCcccHHHHHHhChhccEeCCccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 99999999999999999999999999999999988777999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhh
Q 031013 149 YTAFENIYPVLTEF 162 (167)
Q Consensus 149 ~~a~~~i~~~L~~~ 162 (167)
++|+++|+|+|.+|
T Consensus 161 ~~a~~~i~p~L~~~ 174 (174)
T cd04516 161 YQAFENIYPILLQF 174 (174)
T ss_pred HHHHHHHHHHHhhC
Confidence 99999999999886
No 4
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=100.00 E-value=5.4e-56 Score=351.51 Aligned_cols=155 Identities=43% Similarity=0.705 Sum_probs=148.5
Q ss_pred cCCeeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHH
Q 031013 10 LGAVSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYA 65 (167)
Q Consensus 10 ~~~~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~ 65 (167)
.++.++|+|||||++|+++|||++++..++|+||||+ +||||||+++++.|.++++
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 4678999999999999999999999999999999999 9999999999999999999
Q ss_pred HHHHhcCCCCccc-ceEEEEEEEEEecCCccchHhHHHHcC-CCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccC
Q 031013 66 RIIQKLGFPAKFK-DFKIQNIVGSCDVKFPIRLEGLAYSHG-AFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAK 143 (167)
Q Consensus 66 ~~l~~lg~~~~~~-~~~I~NIvas~~l~~~I~L~~la~~~~-~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGak 143 (167)
++|+++|+++.+. .++|||||||+|+++++||+.+|..++ ++++|||||||||+||+.+|++++|||+|||+||||||
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 9999999998764 899999999999999999999999886 36999999999999999999999999999999999999
Q ss_pred CHHHHHHHHHHHHHHHHhhhh
Q 031013 144 VRDETYTAFENIYPVLTEFRK 164 (167)
Q Consensus 144 s~e~~~~a~~~i~~~L~~~r~ 164 (167)
+++|+++|++++++.|.++..
T Consensus 164 ~~ed~~~Av~~i~~~L~elgl 184 (185)
T COG2101 164 SEEDAEQAVEKIQSRLEELGL 184 (185)
T ss_pred CHHHHHHHHHHHHHHHHHhcc
Confidence 999999999999999998753
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=9.4e-55 Score=347.39 Aligned_cols=149 Identities=42% Similarity=0.697 Sum_probs=143.4
Q ss_pred eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII 68 (167)
Q Consensus 13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l 68 (167)
.|+|+|||||++++|+|||++||..++|+||||+ +||||+|+++|+.|+++++++|
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 4799999999999999999999999999999998 9999999999999999999999
Q ss_pred HhcCCCCc-ccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHH
Q 031013 69 QKLGFPAK-FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDE 147 (167)
Q Consensus 69 ~~lg~~~~-~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~ 147 (167)
+++|++.. ..+|+|+|||||++++++|||+.++..++ +++||||+||||+||+.+|+++++||+||||+||||||++|
T Consensus 81 ~~~g~~~~~~~~~~i~NIVas~~l~~~i~L~~la~~~~-~~~YePe~fpglvyR~~~pk~~~lIF~SGKvvitGaks~~~ 159 (174)
T cd04518 81 KDYGIKVIEKPEIKVQNIVASADLGREVNLDAIAIGLP-NAEYEPEQFPGLVYRLDEPKVVLLLFSSGKMVITGAKSEED 159 (174)
T ss_pred HhcCCCccCCCceEEEEEEEEEEcCCccCHHHHHhhCC-CCccCcccCceEEEEecCCcEEEEEeCCCEEEEEecCCHHH
Confidence 99999864 56899999999999999999999999885 99999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhh
Q 031013 148 TYTAFENIYPVLTEF 162 (167)
Q Consensus 148 ~~~a~~~i~~~L~~~ 162 (167)
+++|++++++.|+++
T Consensus 160 ~~~a~~~i~~~l~~~ 174 (174)
T cd04518 160 AKRAVEKLLSRLKEL 174 (174)
T ss_pred HHHHHHHHHHHHhhC
Confidence 999999999999864
No 6
>PRK00394 transcription factor; Reviewed
Probab=100.00 E-value=1.5e-54 Score=347.52 Aligned_cols=151 Identities=42% Similarity=0.685 Sum_probs=144.9
Q ss_pred eEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHHHh
Q 031013 15 SVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARIIQK 70 (167)
Q Consensus 15 ~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l~~ 70 (167)
+|+|||||++++|+|||++||..++|++|||+ +||||+|+++|+.|+++++++|++
T Consensus 2 ~i~NvVas~~l~~~ldL~~la~~~~n~eYePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~S~~~a~~a~~~~~~~l~~ 81 (179)
T PRK00394 2 KIENIVASTDLGQELDLEKVAEDLPNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAKSVEDLHEAVKIIIKKLKE 81 (179)
T ss_pred EEEEEEEEEEcCCCcCHHHHHhhCCCceeCcccCceEEEEecCCceEEEEEcCCcEEEEccCCHHHHHHHHHHHHHHHHH
Confidence 79999999999999999999999999999998 899999999999999999999999
Q ss_pred cCCCCc-ccceEEEEEEEEEecCCccchHhHHHHcC-CCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013 71 LGFPAK-FKDFKIQNIVGSCDVKFPIRLEGLAYSHG-AFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 148 (167)
Q Consensus 71 lg~~~~-~~~~~I~NIvas~~l~~~I~L~~la~~~~-~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~ 148 (167)
+|+++. ..+|+|+|||||+|++++|||+++|..++ ++++||||+||||+||+.+|+++++||+||||+||||||++|+
T Consensus 82 ~g~~~~~~~~~~i~NiVas~~l~~~i~L~~la~~~~~~~~~YePe~fPglvyR~~~pk~~~lIF~SGKvvitGaks~~~~ 161 (179)
T PRK00394 82 LGIKVIDEPEIKVQNIVASADLGVELNLNAIAIGLGLENIEYEPEQFPGLVYRLDDPKVVVLLFGSGKLVITGAKSEEDA 161 (179)
T ss_pred cCCCccCCCceEEEEEEEEEEcCCeEcHHHHHHhcCcCCcEECcccCceEEEEecCCcEEEEEEcCCEEEEEecCCHHHH
Confidence 999875 67999999999999999999999998863 5899999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhhh
Q 031013 149 YTAFENIYPVLTEFRKV 165 (167)
Q Consensus 149 ~~a~~~i~~~L~~~r~~ 165 (167)
++|+++|+|+|+++...
T Consensus 162 ~~a~~~i~~~l~~~g~~ 178 (179)
T PRK00394 162 EKAVEKILEKLEELGLL 178 (179)
T ss_pred HHHHHHHHHHHHHcCCc
Confidence 99999999999998653
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=3.9e-54 Score=343.63 Aligned_cols=149 Identities=72% Similarity=1.154 Sum_probs=144.5
Q ss_pred eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII 68 (167)
Q Consensus 13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l 68 (167)
.|+|+||||+++++|+|||++||..++|++|||+ +||||+|+++++.|+++++++|
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 3799999999999999999999999999999997 9999999999999999999999
Q ss_pred HhcCCCC-cccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHH
Q 031013 69 QKLGFPA-KFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDE 147 (167)
Q Consensus 69 ~~lg~~~-~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~ 147 (167)
+++|++. ++.+|+|+|||||+++|++|||++||..++++++||||+||||+||+.+|++|++||+||||+||||||++|
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 9999986 889999999999999999999999999986799999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHh
Q 031013 148 TYTAFENIYPVLTE 161 (167)
Q Consensus 148 ~~~a~~~i~~~L~~ 161 (167)
+++|+++|+|+|.+
T Consensus 161 ~~~a~~~i~~~L~~ 174 (174)
T cd00652 161 IYEAVEKIYPILKE 174 (174)
T ss_pred HHHHHHHHHHHHhC
Confidence 99999999999974
No 8
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=100.00 E-value=1.4e-53 Score=340.65 Aligned_cols=149 Identities=44% Similarity=0.841 Sum_probs=144.4
Q ss_pred eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC-----------------------ceeccCCHHHHHHHHHHHHHHHH
Q 031013 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK-----------------------VCTGAKSEQQSKLAARKYARIIQ 69 (167)
Q Consensus 13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~-----------------------v~tGakS~~~a~~a~~k~~~~l~ 69 (167)
.++|+|||||++++|+|||++++..++|+||||+ +|||++|+++|+.|+++++++|+
T Consensus 2 ~~~i~Nvvas~~l~~~idL~~la~~l~n~eYeP~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~l~ 81 (174)
T cd04517 2 DILIVNVVCQFSLRCHIDLRKLALAGRNVEYNPRYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARLLQ 81 (174)
T ss_pred ccEEEEEEEEEEcCCcccHHHHHhhCCCCEEeCCCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHHHH
Confidence 5799999999999999999999999999999998 89999999999999999999999
Q ss_pred hcCCCC-cccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013 70 KLGFPA-KFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 148 (167)
Q Consensus 70 ~lg~~~-~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~ 148 (167)
++|++. ++.+|+|+|||||+|+|++|||++|+..+.++++||||+||||+||+.+|++|++||+||||+|||+||++|+
T Consensus 82 ~~g~~~~~~~~f~v~nIvat~~~~~~i~L~~la~~~~~~~~YePE~fPgliyr~~~p~~t~lIF~sGkivitGaks~~~~ 161 (174)
T cd04517 82 KLGFKVVRFSNFRVVNVLATCSMPFPIRLDELAAKNRSSASYEPELHPGVVYRITGPRATLSIFSTGSVTVTGARSMEDV 161 (174)
T ss_pred HcCCCcccCCceEEEEEEEEEeCCCcccHHHHHHhchhhcEeCCccCCEEEEEECCCcEEEEEeCCCEEEEEecCCHHHH
Confidence 999986 8899999999999999999999999998767999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHh
Q 031013 149 YTAFENIYPVLTE 161 (167)
Q Consensus 149 ~~a~~~i~~~L~~ 161 (167)
++|+++|+|+|.+
T Consensus 162 ~~a~~~i~pil~~ 174 (174)
T cd04517 162 REAVEKIYPIVFE 174 (174)
T ss_pred HHHHHHHHHHHhC
Confidence 9999999999864
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=100.00 E-value=3.8e-33 Score=199.12 Aligned_cols=86 Identities=56% Similarity=0.864 Sum_probs=81.1
Q ss_pred ccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHH
Q 031013 77 FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIY 156 (167)
Q Consensus 77 ~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~ 156 (167)
|++|+|+|||||++++++|||++||..+ ++++||||+|||++||+.+|+++++||+||||+||||||++++++|+++++
T Consensus 1 ~~~~~i~NIva~~~l~~~idL~~la~~~-~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~ 79 (86)
T PF00352_consen 1 FPDFKIVNIVASFDLPFEIDLEELAEEL-ENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKIL 79 (86)
T ss_dssp -EEEEEEEEEEEEE-SSEB-HHHHHHHS-TTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHH
T ss_pred CCccEEEEEEEEEECCCccCHHHHHhhc-cCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHH
Confidence 5789999999999999999999999998 799999999999999999999999999999999999999999999999999
Q ss_pred HHHHhhh
Q 031013 157 PVLTEFR 163 (167)
Q Consensus 157 ~~L~~~r 163 (167)
|+|++++
T Consensus 80 ~~L~~~~ 86 (86)
T PF00352_consen 80 PILQKLG 86 (86)
T ss_dssp HHHHHTT
T ss_pred HHHHHcC
Confidence 9999985
No 10
>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=99.96 E-value=7.7e-29 Score=198.13 Aligned_cols=83 Identities=34% Similarity=0.541 Sum_probs=79.8
Q ss_pred eEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHH
Q 031013 80 FKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL 159 (167)
Q Consensus 80 ~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L 159 (167)
++|+|||||++++++|||++|+..+ ++++||||+||||+||+.+|+++++||+||||+||||||+|+++.|+++++++|
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~i~~~L 80 (174)
T cd04516 2 PKIQNIVATVNLGCKLDLKKIALRA-RNAEYNPKRFAAVIMRIREPKTTALIFSSGKMVCTGAKSEDDSKLAARKYARII 80 (174)
T ss_pred CEEEEEEEEEEcCCeecHHHHHhhC-CCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 6899999999999999999999887 689999999999999999999999999999999999999999999999999999
Q ss_pred Hhhh
Q 031013 160 TEFR 163 (167)
Q Consensus 160 ~~~r 163 (167)
+++-
T Consensus 81 ~~~g 84 (174)
T cd04516 81 QKLG 84 (174)
T ss_pred HHcC
Confidence 8764
No 11
>PLN00062 TATA-box-binding protein; Provisional
Probab=99.96 E-value=1.2e-28 Score=197.81 Aligned_cols=83 Identities=30% Similarity=0.518 Sum_probs=79.7
Q ss_pred eEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHH
Q 031013 80 FKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL 159 (167)
Q Consensus 80 ~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L 159 (167)
++|+|||||++++++|||++|+..+ ++++||||+|||++||+.+|+++++||+||||+||||||+++++.|++++.++|
T Consensus 2 ~~I~NvVas~~l~~~idL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIF~SGKiviTGaks~e~a~~a~~~~~~~L 80 (179)
T PLN00062 2 PTLQNIVSTVNLDCKLDLKKIALQA-RNAEYNPKRFAAVIMRIREPKTTALIFASGKMVCTGAKSEHDSKLAARKYARII 80 (179)
T ss_pred cEEEEEEEEEEcCCcccHHHHHhhC-CCCEECCccCcEEEEEeCCCcEEEEEECCCeEEEEecCCHHHHHHHHHHHHHHH
Confidence 6899999999999999999999877 589999999999999999999999999999999999999999999999999999
Q ss_pred Hhhh
Q 031013 160 TEFR 163 (167)
Q Consensus 160 ~~~r 163 (167)
+++-
T Consensus 81 ~~lg 84 (179)
T PLN00062 81 QKLG 84 (179)
T ss_pred HHcC
Confidence 8764
No 12
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=99.95 E-value=3.1e-28 Score=194.65 Aligned_cols=84 Identities=42% Similarity=0.682 Sum_probs=80.3
Q ss_pred ceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHH
Q 031013 79 DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPV 158 (167)
Q Consensus 79 ~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~ 158 (167)
.++|+|||||++++++|||++|+..+ ++++||||+|||++||+.+|+++++||+||||+||||||+++++.|++++.++
T Consensus 1 ~~~I~NvVas~~l~~~ldL~~la~~~-~n~eY~P~~fpgli~Rl~~Pk~t~lIF~SGKiv~tGaks~~~a~~a~~~~~~~ 79 (174)
T cd04518 1 SLKIENIVASVDLGQELDLEKVAAEL-PNAEYNPDQFPGLVYRLEDPKIAALIFRSGKMVCTGAKSVEDLHRAVKEIIKK 79 (174)
T ss_pred CcEEEEEEEEEEcCCeecHHHHHhhC-CCcEECCCcCcEEEEEccCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHH
Confidence 36899999999999999999999987 68999999999999999999999999999999999999999999999999999
Q ss_pred HHhhh
Q 031013 159 LTEFR 163 (167)
Q Consensus 159 L~~~r 163 (167)
|+++-
T Consensus 80 L~~~g 84 (174)
T cd04518 80 LKDYG 84 (174)
T ss_pred HHhcC
Confidence 98753
No 13
>PRK00394 transcription factor; Reviewed
Probab=99.95 E-value=3e-28 Score=195.49 Aligned_cols=83 Identities=45% Similarity=0.665 Sum_probs=79.5
Q ss_pred eEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHH
Q 031013 80 FKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVL 159 (167)
Q Consensus 80 ~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L 159 (167)
++|+|||||++++++|||++||..+ ++++||||+|||++||+.+|+++++||+||||+||||+|+++++.|++++.++|
T Consensus 1 i~i~NvVas~~l~~~ldL~~la~~~-~n~eYePe~fpgli~Rl~~Pk~t~lIf~sGKiv~tGa~S~~~a~~a~~~~~~~l 79 (179)
T PRK00394 1 IKIENIVASTDLGQELDLEKVAEDL-PNAEYNPEQFPGLVYRLEDPKIAALIFRSGKVVCTGAKSVEDLHEAVKIIIKKL 79 (179)
T ss_pred CEEEEEEEEEEcCCCcCHHHHHhhC-CCceeCcccCceEEEEecCCceEEEEEcCCcEEEEccCCHHHHHHHHHHHHHHH
Confidence 4899999999999999999999887 599999999999999999999999999999999999999999999999999999
Q ss_pred Hhhh
Q 031013 160 TEFR 163 (167)
Q Consensus 160 ~~~r 163 (167)
+++-
T Consensus 80 ~~~g 83 (179)
T PRK00394 80 KELG 83 (179)
T ss_pred HHcC
Confidence 8763
No 14
>COG2101 SPT15 TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=99.95 E-value=1.5e-28 Score=195.11 Aligned_cols=84 Identities=39% Similarity=0.613 Sum_probs=80.4
Q ss_pred cceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHH
Q 031013 78 KDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYP 157 (167)
Q Consensus 78 ~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~ 157 (167)
..++|+|||||.+++.++||++++..+ ++++||||+||||+||+.+||+++|||+|||+|||||||.++++.|++++..
T Consensus 6 ~~i~IeNIVAS~~L~~elDL~~~~~~l-~~aeYnP~qFpGlv~Rl~ePk~a~LIF~SGK~VcTGaKs~ed~~~av~~~~~ 84 (185)
T COG2101 6 PTITIENIVASVDLGQELDLEEVALDL-PGAEYNPEQFPGLVYRLEEPKTAALIFRSGKVVCTGAKSVEDVHRAVKKLAK 84 (185)
T ss_pred CccEEEEEEEEechhhhccHHHHHhhC-CCCccCHhHCCeeEEEecCCcceEEEEecCcEEEeccCcHHHHHHHHHHHHH
Confidence 468999999999999999999999988 6999999999999999999999999999999999999999999999999999
Q ss_pred HHHhh
Q 031013 158 VLTEF 162 (167)
Q Consensus 158 ~L~~~ 162 (167)
.|++.
T Consensus 85 ~L~~~ 89 (185)
T COG2101 85 KLKDG 89 (185)
T ss_pred HHHhc
Confidence 98863
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=99.95 E-value=4.6e-28 Score=193.46 Aligned_cols=84 Identities=37% Similarity=0.606 Sum_probs=80.4
Q ss_pred ceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHH
Q 031013 79 DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPV 158 (167)
Q Consensus 79 ~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~ 158 (167)
+++|+|||||++++++|||++||..+ ++++||||+|||++||+.+|+++++||+||||+||||+|+++++.|++++.++
T Consensus 1 ~~~i~NvVas~~l~~~idL~~la~~~-~n~~YePe~fpgli~R~~~P~~t~lIf~sGKivitGaks~~~~~~a~~~~~~~ 79 (174)
T cd00652 1 SPKIQNIVATVNLGCELDLRKIALAA-RNAEYNPKRFPGVIMRLREPKTTALIFSSGKMVITGAKSEEDAKLAARKYARI 79 (174)
T ss_pred CcEEEEEEEEEEcCCccCHHHHHhhC-CCcEECCCccceEEEEcCCCcEEEEEECCCEEEEEecCCHHHHHHHHHHHHHH
Confidence 47899999999999999999999987 59999999999999999999999999999999999999999999999999999
Q ss_pred HHhhh
Q 031013 159 LTEFR 163 (167)
Q Consensus 159 L~~~r 163 (167)
|+++-
T Consensus 80 L~~~g 84 (174)
T cd00652 80 LQKLG 84 (174)
T ss_pred HHHcC
Confidence 98764
No 16
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=99.94 E-value=4.7e-27 Score=187.79 Aligned_cols=83 Identities=29% Similarity=0.470 Sum_probs=79.7
Q ss_pred ceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHH
Q 031013 79 DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPV 158 (167)
Q Consensus 79 ~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~ 158 (167)
+++|+|||||++++++|||++++..+ ++++||| +||||+||+.+|+++++||+|||++|||+||++++++|++++.++
T Consensus 2 ~~~i~Nvvas~~l~~~idL~~la~~l-~n~eYeP-~fpgli~R~~~Pk~t~lIF~sGKiviTGaks~~~~~~a~~~~~~~ 79 (174)
T cd04517 2 DILIVNVVCQFSLRCHIDLRKLALAG-RNVEYNP-RYPKVTMRLREPRATASVWSSGKITITGATSEEEAKQAARRAARL 79 (174)
T ss_pred ccEEEEEEEEEEcCCcccHHHHHhhC-CCCEEeC-CCCEEEEEecCCcEEEEEECCCeEEEEccCCHHHHHHHHHHHHHH
Confidence 68999999999999999999999887 6999999 999999999999999999999999999999999999999999999
Q ss_pred HHhhh
Q 031013 159 LTEFR 163 (167)
Q Consensus 159 L~~~r 163 (167)
|+++-
T Consensus 80 l~~~g 84 (174)
T cd04517 80 LQKLG 84 (174)
T ss_pred HHHcC
Confidence 98764
No 17
>KOG3302 consensus TATA-box binding protein (TBP), component of TFIID and TFIIIB [Transcription]
Probab=99.86 E-value=2.1e-21 Score=156.53 Aligned_cols=84 Identities=33% Similarity=0.521 Sum_probs=80.7
Q ss_pred cceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHH
Q 031013 78 KDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYP 157 (167)
Q Consensus 78 ~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~ 157 (167)
.++.++||||++++++++||.+||... .|++|||+.|++++.|+.+|+++++||+||||+||||+|+++++.|..++.+
T Consensus 21 i~~~l~nivc~~~~~c~ldLk~ial~~-~N~ey~Pk~~~aVimrir~P~~ta~I~ssGKi~ctgA~se~~ar~aark~aR 99 (200)
T KOG3302|consen 21 LDPTLQNIVCTVNLNCKLDLKEIALHA-RNAEYNPKRFAAVIMRIRSPRTTALIFSSGKIVCTGAKSEDSARLAARKYAR 99 (200)
T ss_pred cceEEEeEEEEEeccceecHHHHhhhc-cccccCcccccEEEEEEcCCceEEEEecCCcEEEeccCCHHHHHHHHHHHHH
Confidence 368899999999999999999999975 6999999999999999999999999999999999999999999999999999
Q ss_pred HHHhh
Q 031013 158 VLTEF 162 (167)
Q Consensus 158 ~L~~~ 162 (167)
+|+++
T Consensus 100 ilqkL 104 (200)
T KOG3302|consen 100 ILQKL 104 (200)
T ss_pred HHHHc
Confidence 99976
No 18
>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=99.73 E-value=1e-17 Score=119.43 Aligned_cols=60 Identities=43% Similarity=0.622 Sum_probs=56.4
Q ss_pred eeeEEEEEEEEEeCCccchHhHHhhCCCceecCC------------------------ceeccCCHHHHHHHHHHHHHHH
Q 031013 13 VSSVKNIVSTVNLDCKLDLKKIALQARNAEYNPK------------------------VCTGAKSEQQSKLAARKYARII 68 (167)
Q Consensus 13 ~p~I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~------------------------v~tGakS~~~a~~a~~k~~~~l 68 (167)
.++|+||||+++++++|||.+||..++|++|||+ +||||+|+++++.|++++.++|
T Consensus 3 ~~~i~NIva~~~l~~~idL~~la~~~~~~~YePe~fpgl~~r~~~p~~t~~IF~sGki~itGaks~~~~~~a~~~i~~~L 82 (86)
T PF00352_consen 3 DFKIVNIVASFDLPFEIDLEELAEELENVEYEPERFPGLIYRLRNPKATVLIFSSGKIVITGAKSEEEAKKAIEKILPIL 82 (86)
T ss_dssp EEEEEEEEEEEE-SSEB-HHHHHHHSTTEEEETTTESSEEEEETTTTEEEEEETTSEEEEEEESSHHHHHHHHHHHHHHH
T ss_pred ccEEEEEEEEEECCCccCHHHHHhhccCcEEeeccCCeEEEeecCCcEEEEEEcCCEEEEEecCCHHHHHHHHHHHHHHH
Confidence 5899999999999999999999999999999999 8999999999999999999999
Q ss_pred HhcC
Q 031013 69 QKLG 72 (167)
Q Consensus 69 ~~lg 72 (167)
+++|
T Consensus 83 ~~~~ 86 (86)
T PF00352_consen 83 QKLG 86 (86)
T ss_dssp HHTT
T ss_pred HHcC
Confidence 9987
No 19
>PF11858 DUF3378: Domain of unknown function (DUF3378); InterPro: IPR024568 Ribonuclease HIII 3.1.26 from EC cleaves RNA from DNA-RNA hybrids. It catalyses endonucleolytic cleavage to 5'-phospho-monoesters. Two types of ribonuclease H in Bacillus subtilis, RNase HII (rnhB) and RNase HIII (rnhC), are both known experimentally and are quite similar to each other []. The only RNase H homologue in the Mycoplasmas resembles rnhC. Archaeal forms resemble HII more closely than HIII. This entry represents the uncharacterised N-terminal domain of bacterial RNase HIII.; PDB: 3ASM_A 2D0C_A 2D0B_A 2D0A_A.
Probab=96.85 E-value=0.0013 Score=46.68 Aligned_cols=36 Identities=22% Similarity=0.413 Sum_probs=30.5
Q ss_pred CCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHH
Q 031013 113 ELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDET 148 (167)
Q Consensus 113 E~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~ 148 (167)
..=||.+|+...+.+++++|.||||++-|...+.++
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 344999999999999999999999999998766544
No 20
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=95.50 E-value=0.1 Score=42.02 Aligned_cols=73 Identities=22% Similarity=0.252 Sum_probs=58.0
Q ss_pred EEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHHHh
Q 031013 85 IVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTE 161 (167)
Q Consensus 85 Ivas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~ 161 (167)
|.|..|-+++==|.-|+..+ +.+.|.... ..|++..-+ .-+.||.||||.+|--|+++++++.+..+..++.+
T Consensus 36 Vi~~md~~lg~ilplla~l~-P~anY~~kk-~~l~~~kge--rIitiy~sGkVsm~~ikdedEAkeilgel~d~ine 108 (193)
T COG4871 36 VIANMDPPLGGILPLLAPLF-PRANYSDKK-NILILQKGE--RIITIYGSGKVSMTMIKDEDEAKEILGELMDIINE 108 (193)
T ss_pred EEeecCCCcchhHHHhHhhC-CCccccccc-ceEEEeecc--EEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHH
Confidence 45556666666677888887 469998654 778887554 44679999999999999999999999999888765
No 21
>COG1039 RnhC Ribonuclease HIII [DNA replication, recombination, and repair]
Probab=94.90 E-value=0.078 Score=45.94 Aligned_cols=44 Identities=25% Similarity=0.360 Sum_probs=37.8
Q ss_pred CCCCeEEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHHH
Q 031013 113 ELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENIY 156 (167)
Q Consensus 113 E~fPglv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~ 156 (167)
.+.|+.+|+.+.|.+++.+|.|||+++-|-..++.+++-...+.
T Consensus 27 ~~~~~~~f~ak~~gvtv~~Y~Sgk~~~QG~~ae~~~~~~l~~~~ 70 (297)
T COG1039 27 SNPPYTVFAAKSPGVTVTIYKSGKVVIQGKGAEAFAKEFLNPIA 70 (297)
T ss_pred cCCCceEEEeeCCCeEEEEEccceEEEecCCHHHHHHHHhhhhh
Confidence 47799999999999999999999999999988877776665433
No 22
>PRK00996 ribonuclease HIII; Provisional
Probab=94.26 E-value=0.09 Score=45.62 Aligned_cols=34 Identities=32% Similarity=0.700 Sum_probs=29.7
Q ss_pred cCCCCeEEEEEcCCeEEEEEecCceEEEEccCCH
Q 031013 112 PELFPGLIYRMKQPKIVLLIFVSGKIVITGAKVR 145 (167)
Q Consensus 112 PE~fPglv~R~~~pk~t~lIF~SGKvvitGaks~ 145 (167)
+..-|+..|+...+.+++.+|.||||++.|...+
T Consensus 26 ~~~~~~~~f~~k~~~~~it~Y~SGKv~~QG~~ae 59 (304)
T PRK00996 26 PSLPPGAVFAAKKPGVTITAYKSGKVVFQGKGAE 59 (304)
T ss_pred cCCCCceEEEEcCCCeEEEEEeCCEEEEeCCCHH
Confidence 4456899999999999999999999999996544
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=94.03 E-value=0.13 Score=44.23 Aligned_cols=34 Identities=21% Similarity=0.448 Sum_probs=29.8
Q ss_pred ccCCCCeEEEEEcCCeEEEEEecCceEEEEccCC
Q 031013 111 EPELFPGLIYRMKQPKIVLLIFVSGKIVITGAKV 144 (167)
Q Consensus 111 ePE~fPglv~R~~~pk~t~lIF~SGKvvitGaks 144 (167)
.+..=||.+|+...+.+|+.+|.||||++-|...
T Consensus 22 ~~~~~~~~~f~~k~~~~~it~Y~SgKv~fQG~~a 55 (284)
T TIGR00716 22 TKSNPPYTVFQLEGPGVKVTYYQSGKLLIQGKNS 55 (284)
T ss_pred ccCCCCCeEEEEeCCCeEEEEEeCCEEEEeCCCH
Confidence 4555799999999999999999999999999443
No 24
>PRK12475 thiamine/molybdopterin biosynthesis MoeB-like protein; Provisional
Probab=84.52 E-value=3.4 Score=36.22 Aligned_cols=36 Identities=14% Similarity=0.406 Sum_probs=29.1
Q ss_pred EEEEEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHH
Q 031013 118 LIYRMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENI 155 (167)
Q Consensus 118 lv~R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i 155 (167)
+.|+..+ -.+.+|.+|++.|-|.+++.+++.-+.+.
T Consensus 301 ~~~~~~~--~~~~~f~~gr~~~~g~~~~~~a~~~~~~~ 336 (338)
T PRK12475 301 LSFQLDE--YRFVLFTDGRAFIHGTNDIKKAKRLYARY 336 (338)
T ss_pred EEEEECC--EEEEEEcCCcEEEECCCCHHHHHHHHHHh
Confidence 3456555 56789999999999999999998877664
No 25
>PRK11509 hydrogenase-1 operon protein HyaE; Provisional
Probab=73.27 E-value=5.2 Score=30.77 Aligned_cols=63 Identities=13% Similarity=0.142 Sum_probs=43.9
Q ss_pred CccchHhHHHHcC-C---CeeeccCCCCeEE--EEEcCCeEEEEEecCceEE--EEccCCHHHHHHHHHHHH
Q 031013 93 FPIRLEGLAYSHG-A---FSSYEPELFPGLI--YRMKQPKIVLLIFVSGKIV--ITGAKVRDETYTAFENIY 156 (167)
Q Consensus 93 ~~I~L~~la~~~~-~---~~~YePE~fPglv--~R~~~pk~t~lIF~SGKvv--itGaks~e~~~~a~~~i~ 156 (167)
..+=|++|+.+++ . .+.-|-+..|.+- |++.. --|+++|..|+.+ +.|..+.+++.+-++.++
T Consensus 54 ~avvleELa~e~~~~~v~~akVDiD~~~~LA~~fgV~s-iPTLl~FkdGk~v~~i~G~~~k~~l~~~I~~~L 124 (132)
T PRK11509 54 NPVMIGELLREFPDYTWQVAIADLEQSEAIGDRFGVFR-FPATLVFTGGNYRGVLNGIHPWAELINLMRGLV 124 (132)
T ss_pred HHHHHHHHHHHhcCCceEEEEEECCCCHHHHHHcCCcc-CCEEEEEECCEEEEEEeCcCCHHHHHHHHHHHh
Confidence 3455778887764 1 4555666666663 44433 2489999999997 789999988888777655
No 26
>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=71.12 E-value=8.3 Score=28.87 Aligned_cols=30 Identities=13% Similarity=0.176 Sum_probs=24.4
Q ss_pred EEEEEecCce-EEEEccCCHHHHHHHHHHHH
Q 031013 127 IVLLIFVSGK-IVITGAKVRDETYTAFENIY 156 (167)
Q Consensus 127 ~t~lIF~SGK-vvitGaks~e~~~~a~~~i~ 156 (167)
.|+++|.+|+ +-.+|+++.+.+.+.++++.
T Consensus 89 PTl~lfk~G~~v~~~G~~~~~~l~~~l~~~~ 119 (120)
T cd03065 89 DSIYVFKDDEVIEYDGEFAADTLVEFLLDLI 119 (120)
T ss_pred cEEEEEECCEEEEeeCCCCHHHHHHHHHHHh
Confidence 3688999998 55779999999888887764
No 27
>PRK07688 thiamine/molybdopterin biosynthesis ThiF/MoeB-like protein; Validated
Probab=68.57 E-value=18 Score=31.75 Aligned_cols=35 Identities=20% Similarity=0.405 Sum_probs=28.0
Q ss_pred EEcCCeEEEEEecCceEEEEccCCHHHHHHHHHHH
Q 031013 121 RMKQPKIVLLIFVSGKIVITGAKVRDETYTAFENI 155 (167)
Q Consensus 121 R~~~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i 155 (167)
+.+.+.-.+..|++|+++|-|.+++.+++.-+.+.
T Consensus 303 ~vr~~~~~~~~~~~gr~~i~g~~~~~~a~~~~~~~ 337 (339)
T PRK07688 303 SFSLEEKRLVLFKDGRVLVHGTKDISEAKTIYHRY 337 (339)
T ss_pred EEecCCeEEEEEcCCCEEEECCCCHHHHHHHHHHh
Confidence 33344478889999999999999999888777654
No 28
>PF13575 DUF4135: Domain of unknown function (DUF4135)
Probab=59.22 E-value=9.1 Score=33.58 Aligned_cols=51 Identities=22% Similarity=0.251 Sum_probs=37.5
Q ss_pred cCCHHHHHHHHHHHHHHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHH
Q 031013 51 AKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAY 102 (167)
Q Consensus 51 akS~~~a~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~ 102 (167)
+.|.++++.-.+++-..|.=+ +-....|+--+||+|+++.|..||||.|-.
T Consensus 127 c~~~~ev~~yY~r~G~llal~-y~L~~~DlH~ENIIa~g~~PvlIDlETlf~ 177 (370)
T PF13575_consen 127 CNSEEEVERYYYRLGVLLALL-YLLNGTDLHFENIIASGEYPVLIDLETLFH 177 (370)
T ss_pred CCCHHHHHHHHHHHHHHHHHH-HHhCCCcccccceEEeCCCcEEEehhhhCC
Confidence 467788877777766555432 112234788899999999999999998864
No 29
>PRK09381 trxA thioredoxin; Provisional
Probab=55.74 E-value=18 Score=25.29 Aligned_cols=28 Identities=21% Similarity=0.383 Sum_probs=21.3
Q ss_pred EEEEecCceEE--EEccCCHHHHHHHHHHH
Q 031013 128 VLLIFVSGKIV--ITGAKVRDETYTAFENI 155 (167)
Q Consensus 128 t~lIF~SGKvv--itGaks~e~~~~a~~~i 155 (167)
++.+|..|+++ .+|..+.+++...++..
T Consensus 78 t~~~~~~G~~~~~~~G~~~~~~l~~~i~~~ 107 (109)
T PRK09381 78 TLLLFKNGEVAATKVGALSKGQLKEFLDAN 107 (109)
T ss_pred EEEEEeCCeEEEEecCCCCHHHHHHHHHHh
Confidence 46778889877 67888888887776653
No 30
>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=55.63 E-value=15 Score=27.44 Aligned_cols=69 Identities=17% Similarity=0.142 Sum_probs=42.9
Q ss_pred eEEEEEEEEE-ecCCcc----chHhHHHHcCC---CeeeccCCCCeEE--EEEcCCeEEEEEecCceEE--EEccCCHHH
Q 031013 80 FKIQNIVGSC-DVKFPI----RLEGLAYSHGA---FSSYEPELFPGLI--YRMKQPKIVLLIFVSGKIV--ITGAKVRDE 147 (167)
Q Consensus 80 ~~I~NIvas~-~l~~~I----~L~~la~~~~~---~~~YePE~fPglv--~R~~~pk~t~lIF~SGKvv--itGaks~e~ 147 (167)
..|...-|.. ..|... -|++++.+++. .+..+-+..|.+. |++.. -.|+.+|..||++ +.|..+.++
T Consensus 29 ~~v~~f~~~~~~cp~c~~i~P~leela~e~~~~v~f~kVdid~~~~la~~f~V~s-IPTli~fkdGk~v~~~~G~~~~~e 107 (111)
T cd02965 29 DLVLLLAGDPVRFPEVLDVAVVLPELLKAFPGRFRAAVVGRADEQALAARFGVLR-TPALLFFRDGRYVGVLAGIRDWDE 107 (111)
T ss_pred CEEEEecCCcccCcchhhhHhHHHHHHHHCCCcEEEEEEECCCCHHHHHHcCCCc-CCEEEEEECCEEEEEEeCccCHHH
Confidence 4455555553 223322 46677777643 2356777777665 55543 2478999999997 569888876
Q ss_pred HH
Q 031013 148 TY 149 (167)
Q Consensus 148 ~~ 149 (167)
+.
T Consensus 108 ~~ 109 (111)
T cd02965 108 YV 109 (111)
T ss_pred Hh
Confidence 53
No 31
>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=55.55 E-value=11 Score=24.67 Aligned_cols=22 Identities=23% Similarity=0.418 Sum_probs=18.1
Q ss_pred CceEEEEccCCHHHHHHHHHHH
Q 031013 134 SGKIVITGAKVRDETYTAFENI 155 (167)
Q Consensus 134 SGKvvitGaks~e~~~~a~~~i 155 (167)
.|+..+.|..+.+++.+.+++.
T Consensus 60 ~g~~~~~G~~~~~~l~~~l~~~ 81 (82)
T TIGR00411 60 NGDVEFIGAPTKEELVEAIKKR 81 (82)
T ss_pred CCEEEEecCCCHHHHHHHHHhh
Confidence 7788899999999888877653
No 32
>PRK10996 thioredoxin 2; Provisional
Probab=54.57 E-value=19 Score=27.00 Aligned_cols=28 Identities=21% Similarity=0.441 Sum_probs=22.2
Q ss_pred EEEEecCceEE--EEccCCHHHHHHHHHHH
Q 031013 128 VLLIFVSGKIV--ITGAKVRDETYTAFENI 155 (167)
Q Consensus 128 t~lIF~SGKvv--itGaks~e~~~~a~~~i 155 (167)
++++|..|+++ +.|..+.+++++.++++
T Consensus 109 tlii~~~G~~v~~~~G~~~~e~l~~~l~~~ 138 (139)
T PRK10996 109 TIMIFKNGQVVDMLNGAVPKAPFDSWLNEA 138 (139)
T ss_pred EEEEEECCEEEEEEcCCCCHHHHHHHHHHh
Confidence 46778899987 67889988888887764
No 33
>PRK13011 formyltetrahydrofolate deformylase; Reviewed
Probab=54.31 E-value=98 Score=26.54 Aligned_cols=84 Identities=7% Similarity=-0.075 Sum_probs=45.6
Q ss_pred HHHHHHHHHhcCCCCcccceE------EEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCeEEEEEecC
Q 031013 61 ARKYARIIQKLGFPAKFKDFK------IQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPKIVLLIFVS 134 (167)
Q Consensus 61 ~~k~~~~l~~lg~~~~~~~~~------I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk~t~lIF~S 134 (167)
+.++.+.|.+.|+++...+-+ .-.+.+.++++...+++.|...+.. .-.++-=-+..+...++.++.||.|
T Consensus 21 Va~VT~~La~~~vNI~dls~~~~~~~~~F~m~~~~~~p~~~~~~~L~~~L~~---l~~~l~l~i~i~~~~~~~ri~vl~S 97 (286)
T PRK13011 21 VAAVTGFLAEHGCYITELHSFDDRLSGRFFMRVEFHSEEGLDEDALRAGFAP---IAARFGMQWELHDPAARPKVLIMVS 97 (286)
T ss_pred HHHHHHHHHhCCCCEEEeeeeecCCCCeEEEEEEEecCCCCCHHHHHHHHHH---HHHHhCcEEEEeecccCceEEEEEc
Confidence 467888899988874322211 2356777777777777777654321 0011100122233344567888999
Q ss_pred ceEEEEccCCHHHHHHHH
Q 031013 135 GKIVITGAKVRDETYTAF 152 (167)
Q Consensus 135 GKvvitGaks~e~~~~a~ 152 (167)
|. +.+.+.+-.++
T Consensus 98 g~-----g~nl~al~~~~ 110 (286)
T PRK13011 98 KF-----DHCLNDLLYRW 110 (286)
T ss_pred CC-----cccHHHHHHHH
Confidence 83 44555554443
No 34
>PHA02278 thioredoxin-like protein
Probab=53.40 E-value=20 Score=25.83 Aligned_cols=24 Identities=17% Similarity=0.188 Sum_probs=19.9
Q ss_pred EEEEEecCceEE--EEccCCHHHHHH
Q 031013 127 IVLLIFVSGKIV--ITGAKVRDETYT 150 (167)
Q Consensus 127 ~t~lIF~SGKvv--itGaks~e~~~~ 150 (167)
.|+++|..|+.+ +.|..+.+++.+
T Consensus 74 PT~i~fk~G~~v~~~~G~~~~~~l~~ 99 (103)
T PHA02278 74 PVLIGYKDGQLVKKYEDQVTPMQLQE 99 (103)
T ss_pred cEEEEEECCEEEEEEeCCCCHHHHHh
Confidence 478999999999 999888876654
No 35
>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=53.25 E-value=22 Score=29.04 Aligned_cols=36 Identities=14% Similarity=0.242 Sum_probs=31.5
Q ss_pred CceecCCceeccCCHHHHHHHHHHHHHHHHhcCCCC
Q 031013 40 NAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPA 75 (167)
Q Consensus 40 n~eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~~ 75 (167)
+.-|==+++.|+.|++++...++++.++|++.|++.
T Consensus 137 ~~~YvDDili~~~s~~e~~~~~~~v~~~L~~~Gf~l 172 (213)
T cd01644 137 RNFYVDDILVSTDTLNEAVNVAKRLIALLKKGGFNL 172 (213)
T ss_pred HeeecccceecCCCHHHHHHHHHHHHHHHHhCCccc
Confidence 345655699999999999999999999999999974
No 36
>PF13192 Thioredoxin_3: Thioredoxin domain; PDB: 1ZYP_B 1ZYN_A 1HYU_A 1ILO_A 1J08_F 2YWM_B 2AYT_B 2HLS_B 1A8L_A 2K8S_B ....
Probab=52.52 E-value=17 Score=24.34 Aligned_cols=23 Identities=26% Similarity=0.569 Sum_probs=17.0
Q ss_pred EecCceEEEEc-cCCHHHHHHHHH
Q 031013 131 IFVSGKIVITG-AKVRDETYTAFE 153 (167)
Q Consensus 131 IF~SGKvvitG-aks~e~~~~a~~ 153 (167)
++-+|+++.+| ..+.+++.+.++
T Consensus 53 lvIng~~~~~G~~p~~~el~~~l~ 76 (76)
T PF13192_consen 53 LVINGKVVFVGRVPSKEELKELLE 76 (76)
T ss_dssp EEETTEEEEESS--HHHHHHHHHH
T ss_pred EEECCEEEEEecCCCHHHHHHHhC
Confidence 35589999999 899988887764
No 37
>KOG0910 consensus Thioredoxin-like protein [Posttranslational modification, protein turnover, chaperones]
Probab=50.79 E-value=27 Score=27.60 Aligned_cols=78 Identities=15% Similarity=0.199 Sum_probs=51.6
Q ss_pred ceEEEEEEEEEecCCccc---hHhHHHHcC---CCeeeccCCCCeE--EEEEcCCeEEEEEecCceEE--EEccCCHHHH
Q 031013 79 DFKIQNIVGSCDVKFPIR---LEGLAYSHG---AFSSYEPELFPGL--IYRMKQPKIVLLIFVSGKIV--ITGAKVRDET 148 (167)
Q Consensus 79 ~~~I~NIvas~~l~~~I~---L~~la~~~~---~~~~YePE~fPgl--v~R~~~pk~t~lIF~SGKvv--itGaks~e~~ 148 (167)
..-+++.-|+.+=|+++= |++++.++. ..+.=|-+.+|-+ .|.+.- --|+++|.+|..+ +.|+-..+.+
T Consensus 62 ~PVlVdF~A~WCgPCk~l~P~l~~~~~~~~g~~k~~kvdtD~~~ela~~Y~I~a-vPtvlvfknGe~~d~~vG~~~~~~l 140 (150)
T KOG0910|consen 62 VPVLVDFHAEWCGPCKMLGPILEELVSEYAGKFKLYKVDTDEHPELAEDYEISA-VPTVLVFKNGEKVDRFVGAVPKEQL 140 (150)
T ss_pred CCEEEEEecCcCccHhHhhHHHHHHHHhhcCeEEEEEEccccccchHhhcceee-eeEEEEEECCEEeeeecccCCHHHH
Confidence 456788888888787653 444544421 1223333444443 344432 2478999999987 9999999999
Q ss_pred HHHHHHHHH
Q 031013 149 YTAFENIYP 157 (167)
Q Consensus 149 ~~a~~~i~~ 157 (167)
.+.++++++
T Consensus 141 ~~~i~k~l~ 149 (150)
T KOG0910|consen 141 RSLIKKFLK 149 (150)
T ss_pred HHHHHHHhc
Confidence 999988765
No 38
>PLN00410 U5 snRNP protein, DIM1 family; Provisional
Probab=48.62 E-value=34 Score=26.49 Aligned_cols=79 Identities=22% Similarity=0.307 Sum_probs=45.8
Q ss_pred eEEEEEEEEEecCCcc---chHhHHHHcCCCe---eeccCCCCeE--EEEEcCCeEEEEEecCceEEE---Ec-------
Q 031013 80 FKIQNIVGSCDVKFPI---RLEGLAYSHGAFS---SYEPELFPGL--IYRMKQPKIVLLIFVSGKIVI---TG------- 141 (167)
Q Consensus 80 ~~I~NIvas~~l~~~I---~L~~la~~~~~~~---~YePE~fPgl--v~R~~~pk~t~lIF~SGKvvi---tG------- 141 (167)
+-|...-|+.+-++.. -|+++|.+++..+ .=|=+..|.+ .|.+..+-.++.+|..|++.+ ||
T Consensus 25 lVVvdF~A~WCgpCk~m~p~l~~la~~~~~~~~~~kVDVDe~~dla~~y~I~~~~t~~~ffk~g~~~vd~~tG~~~k~~~ 104 (142)
T PLN00410 25 LVVIRFGHDWDETCMQMDEVLASVAETIKNFAVIYLVDITEVPDFNTMYELYDPCTVMFFFRNKHIMIDLGTGNNNKINW 104 (142)
T ss_pred EEEEEEECCCChhHHHHHHHHHHHHHHcCCceEEEEEECCCCHHHHHHcCccCCCcEEEEEECCeEEEEEeccccccccc
Confidence 4455555655544422 3455665553212 1233333433 245555556677999999655 77
Q ss_pred -cCCHHHHHHHHHHHHHH
Q 031013 142 -AKVRDETYTAFENIYPV 158 (167)
Q Consensus 142 -aks~e~~~~a~~~i~~~ 158 (167)
..+.+++.+.++.+++-
T Consensus 105 ~~~~k~~l~~~i~~~~~~ 122 (142)
T PLN00410 105 ALKDKQEFIDIVETVYRG 122 (142)
T ss_pred ccCCHHHHHHHHHHHHHH
Confidence 57778888888877764
No 39
>cd02948 TRX_NDPK TRX domain, TRX and NDP-kinase (NDPK) fusion protein family; most members of this group are fusion proteins which contain one redox active TRX domain containing a CXXC motif and three NDPK domains, and are characterized as intermediate chains (ICs) of axonemal outer arm dynein. Dyneins are molecular motors that generate force against microtubules to produce cellular movement, and are divided into two classes: axonemal and cytoplasmic. They are supramolecular complexes consisting of three protein groups classified according to size: dynein heavy, intermediate and light chains. Axonemal dyneins form two structures, the inner and outer arms, which are attached to doublet microtubules throughout the cilia and flagella. The human homolog is the sperm-specific Sptrx-2, presumed to be a component of the human sperm axoneme architecture. Included in this group is another human protein, TRX-like protein 2, a smaller fusion protein containing one TRX and one NDPK domain, which
Probab=48.35 E-value=27 Score=24.42 Aligned_cols=26 Identities=23% Similarity=0.406 Sum_probs=19.7
Q ss_pred EEEEecCceEE--EEccCCHHHHHHHHHH
Q 031013 128 VLLIFVSGKIV--ITGAKVRDETYTAFEN 154 (167)
Q Consensus 128 t~lIF~SGKvv--itGaks~e~~~~a~~~ 154 (167)
|+++|..|+.+ +.|+ +.+.+.++++.
T Consensus 74 t~~~~~~g~~~~~~~G~-~~~~~~~~i~~ 101 (102)
T cd02948 74 TFLFYKNGELVAVIRGA-NAPLLNKTITE 101 (102)
T ss_pred EEEEEECCEEEEEEecC-ChHHHHHHHhh
Confidence 57889999976 7776 66777777764
No 40
>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=48.10 E-value=22 Score=25.37 Aligned_cols=27 Identities=4% Similarity=0.178 Sum_probs=19.6
Q ss_pred EEEEecCceEE--EEccCCHHHHHHHHHH
Q 031013 128 VLLIFVSGKIV--ITGAKVRDETYTAFEN 154 (167)
Q Consensus 128 t~lIF~SGKvv--itGaks~e~~~~a~~~ 154 (167)
|+.+|..|+++ ..|..+.+++.+.+++
T Consensus 82 t~~i~~~g~~~~~~~G~~~~~~l~~~i~~ 110 (111)
T cd02963 82 AIVGIINGQVTFYHDSSFTKQHVVDFVRK 110 (111)
T ss_pred EEEEEECCEEEEEecCCCCHHHHHHHHhc
Confidence 46677888887 4577888877776654
No 41
>PRK06027 purU formyltetrahydrofolate deformylase; Reviewed
Probab=47.87 E-value=1.4e+02 Score=25.59 Aligned_cols=83 Identities=13% Similarity=0.069 Sum_probs=47.6
Q ss_pred HHHHHHHHHhcCCCCcccceE------EEEEEEEEec-CCccchHhHHHHcCCCeeeccCCCCeEEEEEc--CCeEEEEE
Q 031013 61 ARKYARIIQKLGFPAKFKDFK------IQNIVGSCDV-KFPIRLEGLAYSHGAFSSYEPELFPGLIYRMK--QPKIVLLI 131 (167)
Q Consensus 61 ~~k~~~~l~~lg~~~~~~~~~------I~NIvas~~l-~~~I~L~~la~~~~~~~~YePE~fPglv~R~~--~pk~t~lI 131 (167)
+.++.+.|.+.|.++...+.. .-.+...+++ +.+.+++.|...+.. ...|+ ++...+. .++.++.|
T Consensus 20 Va~Vt~~La~~g~NI~d~s~~~~~~~g~F~m~i~v~~~~~~~~~~~L~~~L~~---l~~~l--~l~i~l~~~~~~~ri~v 94 (286)
T PRK06027 20 VAAVSNFLYEHGGNIVDADQFVDPETGRFFMRVEFEGDGLIFNLETLRADFAA---LAEEF--EMDWRLLDSAERKRVVI 94 (286)
T ss_pred HHHHHHHHHHCCCCEEEceeEEcCCCCeEEEEEEEEeCCCCCCHHHHHHHHHH---HHHHh--CCEEEEcccccCcEEEE
Confidence 457888999999874333222 3456666777 556677766654421 11111 2333332 34567889
Q ss_pred ecCceEEEEccCCHHHHHHHHH
Q 031013 132 FVSGKIVITGAKVRDETYTAFE 153 (167)
Q Consensus 132 F~SGKvvitGaks~e~~~~a~~ 153 (167)
|.||. +.+.+.+-++++
T Consensus 95 l~Sg~-----gsnl~al~~~~~ 111 (286)
T PRK06027 95 LVSKE-----DHCLGDLLWRWR 111 (286)
T ss_pred EEcCC-----CCCHHHHHHHHH
Confidence 99997 555556655543
No 42
>KOG4108 consensus Dynein light chain [Cell motility]
Probab=46.35 E-value=59 Score=26.33 Aligned_cols=91 Identities=19% Similarity=0.279 Sum_probs=49.5
Q ss_pred CCccchHhH--------HhhCCCceecCCceeccCCHHHHHHHHHHHHHHHHhcCCCCcccceEEEEEEEEE-ecCCccc
Q 031013 26 DCKLDLKKI--------ALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSC-DVKFPIR 96 (167)
Q Consensus 26 ~~~ldL~~i--------a~~~~n~eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~-~l~~~I~ 96 (167)
+.+|++..+ .+.+.+.+|||+.+ ..-++.-++.+-..|+++|++ .++..-.|--+ ..+..
T Consensus 68 ~~~F~~~~v~~iI~~vl~e~L~~~~Y~~~~a-----~~lt~elae~I~~rvK~l~~~----RYK~Vv~V~ige~~gqG-- 136 (174)
T KOG4108|consen 68 GKKFPAERVEKIIEAVLTEKLADAEYDPDEA-----LQLTKELAEEIKDRVKELGYP----RYKYVVQVMIGEQLGQG-- 136 (174)
T ss_pred CccCCHHHHHHHHHHHHHHHhhhhccCHHHH-----HHHHHHHHHHHHHHHHhcCCC----ceEEEEEEEEhhhhcch--
Confidence 455665543 46678889988643 344555566666677788865 44433222221 12221
Q ss_pred hHhHHHHcCCCeeeccCCCCeEEEEEcCCe--EEEEEe
Q 031013 97 LEGLAYSHGAFSSYEPELFPGLIYRMKQPK--IVLLIF 132 (167)
Q Consensus 97 L~~la~~~~~~~~YePE~fPglv~R~~~pk--~t~lIF 132 (167)
+.. ...+-+|++.=..+.|.+.+|. +.+++|
T Consensus 137 ---v~~--~sr~lWD~~~D~~~t~~f~~~S~favv~vf 169 (174)
T KOG4108|consen 137 ---VYI--ASRCLWDEDRDGFVTYVFENPSLFAVVTVF 169 (174)
T ss_pred ---HHH--HHHhhhccccCCceEEEEecCceeeeehhh
Confidence 111 1357778776555666665554 334444
No 43
>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=45.46 E-value=49 Score=22.08 Aligned_cols=27 Identities=22% Similarity=0.418 Sum_probs=20.1
Q ss_pred EEEEecCceEE--EEccCCHHHHHHHHHH
Q 031013 128 VLLIFVSGKIV--ITGAKVRDETYTAFEN 154 (167)
Q Consensus 128 t~lIF~SGKvv--itGaks~e~~~~a~~~ 154 (167)
++.+|.+|+.+ +.|..+.+++.+.+++
T Consensus 74 t~~~~~~g~~~~~~~g~~~~~~l~~~i~~ 102 (103)
T PF00085_consen 74 TIIFFKNGKEVKRYNGPRNAESLIEFIEK 102 (103)
T ss_dssp EEEEEETTEEEEEEESSSSHHHHHHHHHH
T ss_pred EEEEEECCcEEEEEECCCCHHHHHHHHHc
Confidence 35566777665 7899999998887764
No 44
>PF07338 DUF1471: Protein of unknown function (DUF1471); InterPro: IPR010854 This entry consists of several hypothetical Enterobacterial proteins of around 90 residues in length. Some of the proteins are annotated as ydgH precursors and contain two copies of this region, one at the N terminus and the other at the C terminus. The function of this family is unknown.; PDB: 2NOC_A 2JNA_B 4EVU_B.
Probab=44.44 E-value=31 Score=22.45 Aligned_cols=23 Identities=22% Similarity=0.319 Sum_probs=19.8
Q ss_pred CceEEEEcc-CCHHHHHHHHHHHH
Q 031013 134 SGKIVITGA-KVRDETYTAFENIY 156 (167)
Q Consensus 134 SGKvvitGa-ks~e~~~~a~~~i~ 156 (167)
-|.|.++|. .|++|+.+++.+-.
T Consensus 5 iG~Isvs~~~~s~~d~~~~la~kA 28 (56)
T PF07338_consen 5 IGTISVSGNFGSPDDAEEALAKKA 28 (56)
T ss_dssp EEEEEEEEECSSHHHHHHHHHHHH
T ss_pred EEEEEEccccCCHHHHHHHHHHHH
Confidence 488999999 99999999987644
No 45
>KOG4749 consensus Inositol polyphosphate kinase [Signal transduction mechanisms]
Probab=44.31 E-value=6.3 Score=35.09 Aligned_cols=54 Identities=33% Similarity=0.573 Sum_probs=42.1
Q ss_pred CCeeecc-CCCCeEEEEEc--------CCeEEEEEecCceEEEEccC-----CHHHHHHHHHHHHHHH
Q 031013 106 AFSSYEP-ELFPGLIYRMK--------QPKIVLLIFVSGKIVITGAK-----VRDETYTAFENIYPVL 159 (167)
Q Consensus 106 ~~~~YeP-E~fPglv~R~~--------~pk~t~lIF~SGKvvitGak-----s~e~~~~a~~~i~~~L 159 (167)
.-++|+| ++|.|=.=||. .|.--+-||.+|..|.-|.+ ...++..|++.+...+
T Consensus 174 qisey~PLDLfSG~k~rm~~AikaL~~~pqnnlrvF~nG~lv~gg~~~g~~kt~s~i~~~~~~~~k~~ 241 (375)
T KOG4749|consen 174 QISEYDPLDLFSGSKERMHKAIKALYSTPQNNLRVFLNGSLVFGGLGGGICKTTSEIELAFEDALKDF 241 (375)
T ss_pred hhhccCchhhccccHHHHHHHHHHHhhccccceeEEeccceeecccCCCcccchhhhhHHHHHHHHHH
Confidence 4689999 89999887765 47777899999999998864 4566777777665543
No 46
>cd07047 BMC_PduB_repeat1 1,2-propanediol utilization protein B (PduB), Bacterial Micro-Compartment (BMC) domain repeat 1. PduB proteins are homologs of the carboxysome shell protein. They are encoded within the pdu operon and might be required for the formation of the outer shell of the bacterial pdu polyhedral organelles involved in coenzyme B12-dependent degradation of 1,2-propanediol. Although it has been suggested that PduB might form hexamers and further assemble into the flat facets of the polyhedral outer shell of pdu organelles at present no experimental evidence directly supports this view. PduB proteins contain two tandem BMC domains repeats. This CD contains repeat 1 (the first BMC domain of PduB).
Probab=43.69 E-value=41 Score=26.06 Aligned_cols=28 Identities=18% Similarity=0.251 Sum_probs=22.7
Q ss_pred CceEEEEccCCHHHHHHHHHHHHHHHHh
Q 031013 134 SGKIVITGAKVRDETYTAFENIYPVLTE 161 (167)
Q Consensus 134 SGKvvitGaks~e~~~~a~~~i~~~L~~ 161 (167)
.|.+++||+.++.+++.|++.....+.+
T Consensus 78 kg~vvitGg~dVs~V~~aVeaa~~~v~~ 105 (134)
T cd07047 78 HGSLILFGAEDVSDVRRAVEVALSETEK 105 (134)
T ss_pred eEEEEEEcCCCHHHHHHHHHHHHHHHHH
Confidence 6779999999999987777776666554
No 47
>TIGR00385 dsbE periplasmic protein thiol:disulfide oxidoreductases, DsbE subfamily. Involved in the biogenesis of c-type cytochromes as well as in disulfide bond formation in some periplasmic proteins.
Probab=42.16 E-value=42 Score=25.83 Aligned_cols=48 Identities=17% Similarity=0.086 Sum_probs=33.4
Q ss_pred eeccCCCCeEEEEEcCCeEEEEEecCceEE--EEccCCHHHHHHHHHHHH
Q 031013 109 SYEPELFPGLIYRMKQPKIVLLIFVSGKIV--ITGAKVRDETYTAFENIY 156 (167)
Q Consensus 109 ~YePE~fPglv~R~~~pk~t~lIF~SGKvv--itGaks~e~~~~a~~~i~ 156 (167)
.+||..--+-.|.......+++|..+|+|+ .+|.-+.+++.+.++.++
T Consensus 122 ~~D~~~~~~~~~~v~~~P~~~~id~~G~i~~~~~G~~~~~~l~~~l~~~~ 171 (173)
T TIGR00385 122 LIDPNGKLGLDLGVYGAPETFLVDGNGVILYRHAGPLNNEVWTEGFLPAM 171 (173)
T ss_pred EECCCCchHHhcCCeeCCeEEEEcCCceEEEEEeccCCHHHHHHHHHHHh
Confidence 456665444455555544689999999987 458888888887776654
No 48
>PRK15468 carboxysome structural protein EutS; Provisional
Probab=41.65 E-value=32 Score=25.87 Aligned_cols=31 Identities=26% Similarity=0.214 Sum_probs=24.3
Q ss_pred EEEecCceEEEEccCCHHHHHHHHHHHHHHHHh
Q 031013 129 LLIFVSGKIVITGAKVRDETYTAFENIYPVLTE 161 (167)
Q Consensus 129 ~lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~ 161 (167)
++=--||.+++||.-| +++.|++.+...|.+
T Consensus 69 F~DRFsGslvitGdvs--~Ve~Al~~V~~~l~~ 99 (111)
T PRK15468 69 FLDRFSGALVIYGSVG--AVEEALSQTVSGLGR 99 (111)
T ss_pred eeeccceeEEEEccHH--HHHHHHHHHHHHHHh
Confidence 4445689999999654 688888888888776
No 49
>PF04628 Sedlin_N: Sedlin, N-terminal conserved region; InterPro: IPR006722 Sedlin is a 140 amino-acid protein with a putative role in endoplasmic reticulum-to-Golgi transport. Several missense mutations and deletion mutations in the SEDL gene, which result in protein truncation by frame shift, are responsible for spondyloepiphyseal dysplasia tarda, a progressive skeletal disorder (OMIM:313400). [].; GO: 0006888 ER to Golgi vesicle-mediated transport, 0005622 intracellular; PDB: 3PR6_A 2J3W_A 1H3Q_A.
Probab=41.59 E-value=1.2e+02 Score=22.63 Aligned_cols=50 Identities=14% Similarity=0.293 Sum_probs=36.3
Q ss_pred cCCCCeEEEEEcCCeEEEEEecCc-eEEEEcc-----CCHHHHHHHHHHHHHHHHh
Q 031013 112 PELFPGLIYRMKQPKIVLLIFVSG-KIVITGA-----KVRDETYTAFENIYPVLTE 161 (167)
Q Consensus 112 PE~fPglv~R~~~pk~t~lIF~SG-KvvitGa-----ks~e~~~~a~~~i~~~L~~ 161 (167)
.+.|=|+++++.+-++...+=.|| |+++.-. ...++++.-+++++..-.+
T Consensus 49 ~~~yLg~l~~~~~~~vygyvT~t~~Kfvl~~~~~~~~~~d~~ik~fF~~vh~~Y~~ 104 (132)
T PF04628_consen 49 SDMYLGLLDPFEDYKVYGYVTNTGIKFVLVHDMSDNSIRDEDIKQFFKEVHELYVK 104 (132)
T ss_dssp SCSEEEEEEEETTEEEEEEETTT--EEEEEECGGG-S--HHHHHHHHHHHHHHHHH
T ss_pred cccccCceehhhhHHHHhhhccCceeEEEEEecccCCcchHHHHHHHHHHHHHHHH
Confidence 478899999999988888888888 6665543 5677888888888776443
No 50
>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=41.23 E-value=73 Score=19.13 Aligned_cols=27 Identities=19% Similarity=0.295 Sum_probs=20.7
Q ss_pred eEEEEEecCceEEEEccCCHHHHHHHH
Q 031013 126 KIVLLIFVSGKIVITGAKVRDETYTAF 152 (167)
Q Consensus 126 k~t~lIF~SGKvvitGaks~e~~~~a~ 152 (167)
...+.||-.|+|.+.-.=+++.+++.+
T Consensus 5 ~~qLTIfY~G~V~Vfd~v~~~Ka~~im 31 (36)
T PF06200_consen 5 TAQLTIFYGGQVCVFDDVPPDKAQEIM 31 (36)
T ss_pred CCcEEEEECCEEEEeCCCCHHHHHHHH
Confidence 456889999999999877776655543
No 51
>COG4871 Uncharacterized protein conserved in archaea [Function unknown]
Probab=41.09 E-value=52 Score=26.70 Aligned_cols=41 Identities=27% Similarity=0.228 Sum_probs=34.4
Q ss_pred hHhHHhhCCCceecCC---------------------ceeccCCHHHHHHHHHHHHHHHHhc
Q 031013 31 LKKIALQARNAEYNPK---------------------VCTGAKSEQQSKLAARKYARIIQKL 71 (167)
Q Consensus 31 L~~ia~~~~n~eY~P~---------------------v~tGakS~~~a~~a~~k~~~~l~~l 71 (167)
|..||...+++.|+.+ ..|-.+.+++|+..+..+.+++++.
T Consensus 48 lplla~l~P~anY~~kk~~l~~~kgerIitiy~sGkVsm~~ikdedEAkeilgel~d~ineA 109 (193)
T COG4871 48 LPLLAPLFPRANYSDKKNILILQKGERIITIYGSGKVSMTMIKDEDEAKEILGELMDIINEA 109 (193)
T ss_pred HHHhHhhCCCcccccccceEEEeeccEEEEEccCCeEEeeeecCHHHHHHHHHHHHHHHHHH
Confidence 6678889999999987 2344699999999999999999873
No 52
>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=38.42 E-value=65 Score=24.25 Aligned_cols=29 Identities=7% Similarity=0.146 Sum_probs=22.0
Q ss_pred EEEEe-cCceEE--EEccCCHHHHHHHHHHHH
Q 031013 128 VLLIF-VSGKIV--ITGAKVRDETYTAFENIY 156 (167)
Q Consensus 128 t~lIF-~SGKvv--itGaks~e~~~~a~~~i~ 156 (167)
++.+| ..|+++ ++|....+++.+.++.++
T Consensus 79 t~v~~~~~G~~v~~~~G~~~~~~l~~~l~~l~ 110 (142)
T cd02950 79 HFVFLDREGNEEGQSIGLQPKQVLAQNLDALV 110 (142)
T ss_pred EEEEECCCCCEEEEEeCCCCHHHHHHHHHHHH
Confidence 45566 478887 789998888888877665
No 53
>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=37.45 E-value=52 Score=21.83 Aligned_cols=26 Identities=31% Similarity=0.402 Sum_probs=17.4
Q ss_pred EEEecCceEE--EEccCCHHHHHHHHHH
Q 031013 129 LLIFVSGKIV--ITGAKVRDETYTAFEN 154 (167)
Q Consensus 129 ~lIF~SGKvv--itGaks~e~~~~a~~~ 154 (167)
+.+|..|+.+ +.|..+.+++.+.+++
T Consensus 72 ~~~~~~g~~~~~~~g~~~~~~l~~~l~~ 99 (101)
T TIGR01068 72 LLLFKNGKEVDRSVGALPKAALKQLINK 99 (101)
T ss_pred EEEEeCCcEeeeecCCCCHHHHHHHHHh
Confidence 4455666653 5688888877777654
No 54
>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=37.25 E-value=18 Score=25.37 Aligned_cols=12 Identities=42% Similarity=0.647 Sum_probs=9.7
Q ss_pred EEecCceEEEEc
Q 031013 130 LIFVSGKIVITG 141 (167)
Q Consensus 130 lIF~SGKvvitG 141 (167)
.=|+.||++.|-
T Consensus 3 I~Fs~GKiI~t~ 14 (75)
T PF11869_consen 3 IEFSQGKIIATP 14 (75)
T ss_pred EEecCCeEEEcc
Confidence 359999999873
No 55
>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=37.25 E-value=48 Score=22.73 Aligned_cols=25 Identities=24% Similarity=0.428 Sum_probs=19.8
Q ss_pred EEEEecCceEE--EEccCCHHHHHHHH
Q 031013 128 VLLIFVSGKIV--ITGAKVRDETYTAF 152 (167)
Q Consensus 128 t~lIF~SGKvv--itGaks~e~~~~a~ 152 (167)
++.+|..|+++ +.|..+.+++.+.+
T Consensus 70 t~~i~~~g~~v~~~~g~~~~~~~~~~l 96 (97)
T cd02949 70 TVQFFKDKELVKEISGVKMKSEYREFI 96 (97)
T ss_pred EEEEEECCeEEEEEeCCccHHHHHHhh
Confidence 57788999998 88888888776654
No 56
>PRK10719 eutA reactivating factor for ethanolamine ammonia lyase; Provisional
Probab=36.88 E-value=86 Score=29.19 Aligned_cols=102 Identities=17% Similarity=0.221 Sum_probs=61.2
Q ss_pred CCccchHhHHhhC----CCceecCC-------ceeccCCHHHHHHHHHHHHHHHHhcCCCCcccceEEEEEEEEEecCCc
Q 031013 26 DCKLDLKKIALQA----RNAEYNPK-------VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFP 94 (167)
Q Consensus 26 ~~~ldL~~ia~~~----~n~eY~P~-------v~tGakS~~~a~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~ 94 (167)
...+|-+.|..-. +.+-..|+ ++||..+ ..+.+.+.++++|..+. +| |||++.+..+
T Consensus 60 ~~~ID~~~i~~~V~~ey~~Agi~~~die~~ahIITg~~~------~~~Nl~~~v~~~~~~~g--df----VVA~AG~~le 127 (475)
T PRK10719 60 QGEIDEAAIKELIEEEYQKAGIAPESIDSGAVIITGETA------RKENAREVVMALSGSAG--DF----VVATAGPDLE 127 (475)
T ss_pred CccccHHHHHHHHHHHHHHcCCCHHHccccEEEEEechh------HHHHHHHHHHHhccccc--ce----eeeccCccHH
Confidence 3567777665433 44445555 7787653 45667777888776521 11 4576654332
Q ss_pred cchHhHHHHcCCCeeeccCCCCeE-EEEEcCCeEEEEEecCceEEEEcc
Q 031013 95 IRLEGLAYSHGAFSSYEPELFPGL-IYRMKQPKIVLLIFVSGKIVITGA 142 (167)
Q Consensus 95 I~L~~la~~~~~~~~YePE~fPgl-v~R~~~pk~t~lIF~SGKvvitGa 142 (167)
=-+..+|... +.+..|.-.|+ ..-+-.....+.||..|+++-|+.
T Consensus 128 ~iva~~ASg~---avLseEke~gVa~IDIGgGTT~iaVf~~G~l~~T~~ 173 (475)
T PRK10719 128 SIIAGKGAGA---QTLSEERNTRVLNIDIGGGTANYALFDAGKVIDTAC 173 (475)
T ss_pred HhhhHHHhhH---HHhhhhccCceEEEEeCCCceEEEEEECCEEEEEEE
Confidence 2233333322 22223555555 567777888899999999998875
No 57
>PF14657 Integrase_AP2: AP2-like DNA-binding integrase domain
Probab=36.79 E-value=57 Score=19.96 Aligned_cols=24 Identities=17% Similarity=0.220 Sum_probs=20.3
Q ss_pred ceeccCCHHHHHHHHHHHHHHHHh
Q 031013 47 VCTGAKSEQQSKLAARKYARIIQK 70 (167)
Q Consensus 47 v~tGakS~~~a~~a~~k~~~~l~~ 70 (167)
.-.|-++..||+.++.++...+++
T Consensus 20 ~k~GF~TkkeA~~~~~~~~~~~~~ 43 (46)
T PF14657_consen 20 TKRGFKTKKEAEKALAKIEAELEN 43 (46)
T ss_pred EcCCCCcHHHHHHHHHHHHHHHHc
Confidence 456899999999999998887764
No 58
>PF06277 EutA: Ethanolamine utilisation protein EutA; InterPro: IPR009377 Proteins in this entry are EutA ethanolamine utilization proteins, reactivating factors for ethanolamine ammonia lyase, encoded by the ethanolamine utilization eut operon. The holoenzyme of adenosylcobalamin-dependent ethanolamine ammonia-lyase (EutBC, IPR0092462 from INTERPRO, IPR010628 from INTERPRO), which is part of the ethanolamine utilization pathway [, , ], undergoes suicidal inactivation during catalysis as well as inactivation in the absence of substrate. The inactivation involves the irreversible cleavage of the Co-C bond of the coenzyme. The inactivated holoenzyme undergoes rapid and continuous reactivation in the presence of ATP, Mg2+, and free adenosylcobalamin in permeabilised cells (in situ), homogenate, and cell extracts of Escherichia coli. The EutA protein is essential for reactivation. It was demonstrated with purified recombinant EutA that both the suicidally inactivated and O2-inactivated holoethanolamine ammonia lyase underwent rapid reactivation in vitro by EutA in the presence of adenosylcobalamin, ATP, and Mg2+ []. The inactive enzyme-cyanocobalamin complex was also activated in situ and in vitro by EutA under the same conditions. Thus EutA is believed to be the only component of the reactivating factor for ethanolamine ammonia lyase. Reactivation and activation occur through the exchange of modified coenzyme for free intact adenosylcobalamin []. Bacteria that harbor the ethanolamine utilization pathway can use ethanolamine as a source of carbon and nitrogen. For more information on the ethanolamine utilization pathway, please see IPR009194 from INTERPRO, IPR012408 from INTERPRO.
Probab=36.74 E-value=77 Score=29.51 Aligned_cols=101 Identities=18% Similarity=0.329 Sum_probs=59.9
Q ss_pred CCccchHhHHhhCCC----ceecCC-------ceeccCCHHHHHHHHHHHHHHHHhcCCCCcccceEEEEEEEEEecCCc
Q 031013 26 DCKLDLKKIALQARN----AEYNPK-------VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFP 94 (167)
Q Consensus 26 ~~~ldL~~ia~~~~n----~eY~P~-------v~tGakS~~~a~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~ 94 (167)
...+|-+.|..-.++ +-..|+ ++||-.. -|+=++.++..|... --+| ||||+- |
T Consensus 57 ~~~ID~~al~~iv~~eY~~Agi~p~~I~TGAVIITGETA---rKeNA~~v~~~Ls~~--aGDF-------VVATAG---P 121 (473)
T PF06277_consen 57 QTEIDAEALKEIVEEEYRKAGITPEDIDTGAVIITGETA---RKENAREVLHALSGF--AGDF-------VVATAG---P 121 (473)
T ss_pred CCccCHHHHHHHHHHHHHHcCCCHHHCccccEEEecchh---hhhhHHHHHHHHHHh--cCCE-------EEEccC---C
Confidence 467888877654433 333444 7787432 223334444444442 1112 688886 2
Q ss_pred cchHhHHHHcCCC-eeeccCCCCeEEEEE--cCCeEEEEEecCceEEEEccC
Q 031013 95 IRLEGLAYSHGAF-SSYEPELFPGLIYRM--KQPKIVLLIFVSGKIVITGAK 143 (167)
Q Consensus 95 I~L~~la~~~~~~-~~YePE~fPglv~R~--~~pk~t~lIF~SGKvvitGak 143 (167)
|||.+-...+.. ..|--+ ....+.-+ -.--.-+.+|..|+++-|++=
T Consensus 122 -dLEsiiAgkGsGA~~~S~~-~~~~V~NiDIGGGTtN~avf~~G~v~~T~cl 171 (473)
T PF06277_consen 122 -DLESIIAGKGSGAAALSKE-HHTVVANIDIGGGTTNIAVFDNGEVIDTACL 171 (473)
T ss_pred -CHHHHHhccCccHHHHhhh-hCCeEEEEEeCCCceeEEEEECCEEEEEEEE
Confidence 999887766643 355544 34455444 455566889999999999873
No 59
>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=36.17 E-value=48 Score=22.36 Aligned_cols=25 Identities=20% Similarity=0.460 Sum_probs=18.3
Q ss_pred EEEEecCceEE--EEccCCHHHHHHHH
Q 031013 128 VLLIFVSGKIV--ITGAKVRDETYTAF 152 (167)
Q Consensus 128 t~lIF~SGKvv--itGaks~e~~~~a~ 152 (167)
++.+|..|+.+ ..|..+.+++..-+
T Consensus 69 t~~~~~~g~~~~~~~g~~~~~~l~~~l 95 (96)
T cd02956 69 TVYLFAAGQPVDGFQGAQPEEQLRQML 95 (96)
T ss_pred EEEEEeCCEEeeeecCCCCHHHHHHHh
Confidence 46677888875 78888888776643
No 60
>PRK14126 cell division protein ZapA; Provisional
Probab=33.06 E-value=1.4e+02 Score=20.98 Aligned_cols=40 Identities=10% Similarity=0.145 Sum_probs=30.8
Q ss_pred CeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHHHhhhhh
Q 031013 125 PKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165 (167)
Q Consensus 125 pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~~r~~ 165 (167)
.++.+.|+..-.-+. |..+++.+.++.+.+=..+.++++.
T Consensus 7 ~~v~V~I~G~~Y~i~-~~e~ee~l~~vA~~vd~km~ei~~~ 46 (85)
T PRK14126 7 TRINVEIYGQQYTIV-GDESTSHIRMVAAIVDDKMRELNEK 46 (85)
T ss_pred ceEEEEECCEEEEec-CCCcHHHHHHHHHHHHHHHHHHHHh
Confidence 346666665554444 7889999999999999999998864
No 61
>COG2761 FrnE Predicted dithiol-disulfide isomerase involved in polyketide biosynthesis [Secondary metabolites biosynthesis, transport, and catabolism]
Probab=32.53 E-value=64 Score=27.10 Aligned_cols=94 Identities=11% Similarity=0.171 Sum_probs=53.7
Q ss_pred HHHHHHHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeE--EEEEcCCeEEEEEecCceEE
Q 031013 61 ARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGL--IYRMKQPKIVLLIFVSGKIV 138 (167)
Q Consensus 61 ~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPgl--v~R~~~pk~t~lIF~SGKvv 138 (167)
...|.+.|++.-|. .-+|+.=.+|++..--...+|.+.+...+.. -.|--+..--. --+|.=..+=.+|| .||+.
T Consensus 119 ~~~~~~~lf~AyF~-eg~nI~D~dVL~diA~~~GLD~~~~~~~L~s-~~~~~avr~d~~~A~e~gI~gVP~fv~-d~~~~ 195 (225)
T COG2761 119 QDRFLEALFEAYFE-EGRNIGDEDVLADIAEEVGLDREEFKADLAS-DAAKDAVRQDEAAAQEMGIRGVPTFVF-DGKYA 195 (225)
T ss_pred HHHHHHHHHHHHhc-cCCCCCcHHHHHHHHHHhCCCHHHHHHHHhC-hHHHHHHHHHHHHHHHCCCccCceEEE-cCcEe
Confidence 34556666654342 2234455566666666777788777765421 22211111000 00111233445666 99999
Q ss_pred EEccCCHHHHHHHHHHHHH
Q 031013 139 ITGAKVRDETYTAFENIYP 157 (167)
Q Consensus 139 itGaks~e~~~~a~~~i~~ 157 (167)
|.|+-+++-+..|++.+..
T Consensus 196 V~Gaq~~~v~~~al~~~~~ 214 (225)
T COG2761 196 VSGAQPYDVLEDALRQLLA 214 (225)
T ss_pred ecCCCCHHHHHHHHHHHHh
Confidence 9999999999999887754
No 62
>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=32.16 E-value=61 Score=21.83 Aligned_cols=22 Identities=32% Similarity=0.475 Sum_probs=15.2
Q ss_pred EEEecCceEE--EEccCCHHHHHH
Q 031013 129 LLIFVSGKIV--ITGAKVRDETYT 150 (167)
Q Consensus 129 ~lIF~SGKvv--itGaks~e~~~~ 150 (167)
+.+|..|+.+ ..|.++.+++.+
T Consensus 77 ~~~~~~g~~~~~~~G~~~~~~l~~ 100 (102)
T cd03005 77 LLLFKDGEKVDKYKGTRDLDSLKE 100 (102)
T ss_pred EEEEeCCCeeeEeeCCCCHHHHHh
Confidence 5566777654 789998876643
No 63
>PRK10259 hypothetical protein; Provisional
Probab=31.25 E-value=59 Score=23.24 Aligned_cols=23 Identities=17% Similarity=0.166 Sum_probs=19.4
Q ss_pred cCceEEEEccCCHHHHHHHHHHH
Q 031013 133 VSGKIVITGAKVRDETYTAFENI 155 (167)
Q Consensus 133 ~SGKvvitGaks~e~~~~a~~~i 155 (167)
.-|-|.++|..+++|+++.+.+-
T Consensus 36 kiG~VSvsg~~s~~d~~~~La~K 58 (86)
T PRK10259 36 KIGVVSADGASTLDALEAKLAEK 58 (86)
T ss_pred cceEEEEecCCCHHHHHHHHHHH
Confidence 45889999999999999987654
No 64
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=31.09 E-value=1.1e+02 Score=19.85 Aligned_cols=30 Identities=17% Similarity=0.162 Sum_probs=20.0
Q ss_pred CeEEEEEecCceEEEEccCCHHHHHHHHHHH
Q 031013 125 PKIVLLIFVSGKIVITGAKVRDETYTAFENI 155 (167)
Q Consensus 125 pk~t~lIF~SGKvvitGaks~e~~~~a~~~i 155 (167)
..+++.|=.+|.|.|+|. +.+.++.|.+.|
T Consensus 31 tg~~I~i~~~g~v~I~G~-~~~~v~~A~~~I 60 (61)
T cd02393 31 TGVKIDIEDDGTVYIAAS-DKEAAEKAKKMI 60 (61)
T ss_pred HCCEEEeCCCCEEEEEeC-CHHHHHHHHHHh
Confidence 345555666899999994 345677776544
No 65
>PRK15412 thiol:disulfide interchange protein DsbE; Provisional
Probab=30.24 E-value=1.1e+02 Score=23.88 Aligned_cols=52 Identities=13% Similarity=0.093 Sum_probs=37.3
Q ss_pred eeccCCCCeEEEEEcCCeEEEEEecCceEEE--EccCCHHHHHHHHHHHHHHHH
Q 031013 109 SYEPELFPGLIYRMKQPKIVLLIFVSGKIVI--TGAKVRDETYTAFENIYPVLT 160 (167)
Q Consensus 109 ~YePE~fPglv~R~~~pk~t~lIF~SGKvvi--tGaks~e~~~~a~~~i~~~L~ 160 (167)
-+||+..-+..|.....-.+++|..+|+|+- .|.-+.+++++.++.+++...
T Consensus 127 ~~D~~~~~~~~~gv~~~P~t~vid~~G~i~~~~~G~~~~~~l~~~i~~~~~~~~ 180 (185)
T PRK15412 127 LFDGDGMLGLDLGVYGAPETFLIDGNGIIRYRHAGDLNPRVWESEIKPLWEKYS 180 (185)
T ss_pred EEcCCccHHHhcCCCcCCeEEEECCCceEEEEEecCCCHHHHHHHHHHHHHHHH
Confidence 4566655555566655557899999999764 466788888888887776543
No 66
>cd04792 LanM-like LanM-like proteins. LanM is a bifunctional enzyme, involved in the synthesis of class II lantibiotics. It is responsible for both the dehydration and the cyclization of the precursor-peptide during lantibiotic synthesis. The C-terminal domain shows similarity to LanC, the cyclase component of the lan operon, but the N terminus seems to be unrelated to the dehydratase, LanB.
Probab=29.74 E-value=41 Score=32.48 Aligned_cols=52 Identities=19% Similarity=0.250 Sum_probs=39.4
Q ss_pred ccCCHHHHHHHHHHHHHHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHH
Q 031013 50 GAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAY 102 (167)
Q Consensus 50 GakS~~~a~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~ 102 (167)
-+.|.++++.--+++-..|.=+ +-....|+--+||+|+++.|.-||||.|-.
T Consensus 166 ~c~~~~e~~~fY~r~G~llal~-y~L~~tD~H~ENiIA~g~~PvlIDlETlf~ 217 (825)
T cd04792 166 PCQSKEEVERYYYRLGGLLALL-YLLNATDLHFENIIASGEYPVLIDLETLFH 217 (825)
T ss_pred CCCCHHHHHHHHHHHHHHHHHH-HHcCCcccchhhheeeCCCceEEeeHHhcC
Confidence 3678888888888876665532 223345888999999999999999999743
No 67
>PTZ00397 macrophage migration inhibition factor-like protein; Provisional
Probab=28.15 E-value=1.5e+02 Score=21.33 Aligned_cols=38 Identities=13% Similarity=0.183 Sum_probs=28.6
Q ss_pred ceeccCCHHHHHHHHHHHHHHHHh-cCCCCcccceEEEE
Q 031013 47 VCTGAKSEQQSKLAARKYARIIQK-LGFPAKFKDFKIQN 84 (167)
Q Consensus 47 v~tGakS~~~a~~a~~k~~~~l~~-lg~~~~~~~~~I~N 84 (167)
.+.|..+.++-+.-.+.+.+.|++ +|++..---+.+++
T Consensus 64 ~~~g~~~~e~k~~l~~~i~~~l~~~lgi~~~rv~I~f~~ 102 (116)
T PTZ00397 64 TSIGGISRSNNSSIAAAITKILASHLKVKSERVYIEFKD 102 (116)
T ss_pred EEecCCCHHHHHHHHHHHHHHHHHHhCcCcccEEEEEEE
Confidence 445889999999999999999987 89975433333333
No 68
>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=28.08 E-value=1.1e+02 Score=22.76 Aligned_cols=29 Identities=31% Similarity=0.480 Sum_probs=22.0
Q ss_pred CeEEEEEc---------CCeEEEEEecCceEEEEccCC
Q 031013 116 PGLIYRMK---------QPKIVLLIFVSGKIVITGAKV 144 (167)
Q Consensus 116 Pglv~R~~---------~pk~t~lIF~SGKvvitGaks 144 (167)
-=|.||.. +-.||-++|.+||++--|-+.
T Consensus 61 qVLfYrT~~~~sDG~TTkDECTplvF~n~~LvgWG~~a 98 (102)
T PF11399_consen 61 QVLFYRTQHKKSDGITTKDECTPLVFKNGKLVGWGDDA 98 (102)
T ss_pred EEEEEEEeeEcCCCCccCCceEEEEEECCEEEEEcHHh
Confidence 44567764 246999999999999988654
No 69
>KOG0670 consensus U4/U6-associated splicing factor PRP4 [RNA processing and modification]
Probab=28.01 E-value=3e+02 Score=26.68 Aligned_cols=132 Identities=19% Similarity=0.160 Sum_probs=80.1
Q ss_pred eEEEEEEEEEeCCccchHhHHhhC-CCceecCCceeccCCHHHHHHHHHHHHHHHHhcCC---CCcccceEEE---EEEE
Q 031013 15 SVKNIVSTVNLDCKLDLKKIALQA-RNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGF---PAKFKDFKIQ---NIVG 87 (167)
Q Consensus 15 ~I~NVV~s~~l~~~ldL~~ia~~~-~n~eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~---~~~~~~~~I~---NIva 87 (167)
+=.|=.|.+--.-++||+++..+. +|+ .---+-+-.-..-+--.++.|+++|+ +++..++-|+ ||+-
T Consensus 504 ~hknHLClVFE~LslNLRevLKKyG~nv------GL~ikaVRsYaqQLflALklLK~c~vlHaDIKPDNiLVNE~k~iLK 577 (752)
T KOG0670|consen 504 KHKNHLCLVFEPLSLNLREVLKKYGRNV------GLHIKAVRSYAQQLFLALKLLKKCGVLHADIKPDNILVNESKNILK 577 (752)
T ss_pred hhcceeEEEehhhhchHHHHHHHhCccc------ceeehHHHHHHHHHHHHHHHHHhcCeeecccCccceEeccCcceee
Confidence 345778888888899999998865 342 11112222222233334577889997 4666666664 8999
Q ss_pred EEecCCccchH--hHHHHcCCCeeeccCCCCeEEEE----EcCCeEEEEEecCceEEEEccCCHHHHHHHH
Q 031013 88 SCDVKFPIRLE--GLAYSHGAFSSYEPELFPGLIYR----MKQPKIVLLIFVSGKIVITGAKVRDETYTAF 152 (167)
Q Consensus 88 s~~l~~~I~L~--~la~~~~~~~~YePE~fPglv~R----~~~pk~t~lIF~SGKvvitGaks~e~~~~a~ 152 (167)
-||+|..-... +++--+-.--.--||+-=|+-|- +..-.|++-=.-||||...|..+-+-++-.+
T Consensus 578 LCDfGSA~~~~eneitPYLVSRFYRaPEIiLG~~yd~~iD~WSvgctLYElYtGkIlFpG~TNN~MLrl~m 648 (752)
T KOG0670|consen 578 LCDFGSASFASENEITPYLVSRFYRAPEIILGLPYDYPIDTWSVGCTLYELYTGKILFPGRTNNQMLRLFM 648 (752)
T ss_pred eccCccccccccccccHHHHHHhccCcceeecCcccCCccceeeceeeEEeeccceecCCCCcHHHHHHHH
Confidence 99998743322 11111100112246766666654 2234567666789999999999986555444
No 70
>PF05906 DUF865: Herpesvirus-7 repeat of unknown function (DUF865)
Probab=27.94 E-value=62 Score=18.99 Aligned_cols=27 Identities=15% Similarity=0.298 Sum_probs=20.9
Q ss_pred eeccCCCCeEEEEEcCCeEEEEEecCc
Q 031013 109 SYEPELFPGLIYRMKQPKIVLLIFVSG 135 (167)
Q Consensus 109 ~YePE~fPglv~R~~~pk~t~lIF~SG 135 (167)
.-.|.-+.-|.|+.-+..-+..+|+-|
T Consensus 8 qerpqphnpltfkpvkttgtavvfsag 34 (35)
T PF05906_consen 8 QERPQPHNPLTFKPVKTTGTAVVFSAG 34 (35)
T ss_pred ccCCCCCCccceeeeeccceEEEeecc
Confidence 335666778899888777788899887
No 71
>COG0678 AHP1 Peroxiredoxin [Posttranslational modification, protein turnover, chaperones]
Probab=27.85 E-value=37 Score=27.20 Aligned_cols=32 Identities=13% Similarity=0.223 Sum_probs=25.6
Q ss_pred ccCCCCeEEEEEc---------CCeEEEEEecCceEEEEcc
Q 031013 111 EPELFPGLIYRMK---------QPKIVLLIFVSGKIVITGA 142 (167)
Q Consensus 111 ePE~fPglv~R~~---------~pk~t~lIF~SGKvvitGa 142 (167)
..+.+|.++||.+ .+..+-.+|...||+++|.
T Consensus 5 vg~klP~vtf~tr~~~~~~~~~~~~ts~~lf~gKkVvlf~l 45 (165)
T COG0678 5 VGKKLPAVTFKTRVGDETADGWVDVTTDDLFKGKKVVLFSL 45 (165)
T ss_pred cCCcCCceEeEEeeccccCCCcccccHHHhcCCCEEEEEeC
Confidence 3467899999887 3456678999999999975
No 72
>TIGR01175 pilM type IV pilus assembly protein PilM. This protein is required for the assembly of the type IV fimbria in Pseudomonas aeruginosa responsible for twitching motility, and for a similar pilus-like structure in Synechocystis. It is also found in species such as Deinococcus described as having natural transformation (for which a type IV pilus-like structure is proposed) but not fimbria.
Probab=27.55 E-value=2.2e+02 Score=24.11 Aligned_cols=67 Identities=15% Similarity=0.223 Sum_probs=43.8
Q ss_pred HHHHHHHHHHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHH-----cCC-CeeeccCCCC-eEEEEEcCCeEEEE
Q 031013 58 KLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYS-----HGA-FSSYEPELFP-GLIYRMKQPKIVLL 130 (167)
Q Consensus 58 ~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~-----~~~-~~~YePE~fP-glv~R~~~pk~t~l 130 (167)
+..++.+.+.+++.|+++. .||++.+|.. ++. ....++ .-+ .++.-+-...+++.
T Consensus 142 ~~~v~~~~~~~~~aGl~~~-----------------~id~~~~Al~~~~~~~~~~~~~~~~-~~~~~~lvdiG~~~t~l~ 203 (348)
T TIGR01175 142 KEVVDSRLHALKLAGLEPK-----------------VVDVESFALLRAWRLLGEQLASRTY-RLTDAALVDIGATSSTLN 203 (348)
T ss_pred HHHHHHHHHHHHHcCCceE-----------------EEecHHHHHHHHHHHHHhhCccccc-cCceEEEEEECCCcEEEE
Confidence 4567788888999998732 2333444321 111 122333 334 78889998999999
Q ss_pred EecCceEEEEcc
Q 031013 131 IFVSGKIVITGA 142 (167)
Q Consensus 131 IF~SGKvvitGa 142 (167)
||..|++..+..
T Consensus 204 i~~~g~~~~~r~ 215 (348)
T TIGR01175 204 LLHPGRMLFTRE 215 (348)
T ss_pred EEECCeEEEEEE
Confidence 999999988654
No 73
>COG4274 Uncharacterized conserved protein [Function unknown]
Probab=27.48 E-value=84 Score=23.37 Aligned_cols=56 Identities=13% Similarity=0.132 Sum_probs=44.2
Q ss_pred ccCCHHHHHHHHHHHHHHHHhcCCCCccc--ceEEEEEEEEEecCCccchHhHHHHcC
Q 031013 50 GAKSEQQSKLAARKYARIIQKLGFPAKFK--DFKIQNIVGSCDVKFPIRLEGLAYSHG 105 (167)
Q Consensus 50 GakS~~~a~~a~~k~~~~l~~lg~~~~~~--~~~I~NIvas~~l~~~I~L~~la~~~~ 105 (167)
|+|+..|.-+=++.+-+.+++.|.+++.. .+-..-+|+-+..|.+..+-.++..++
T Consensus 21 Gaktlke~p~R~~av~~~les~G~k~~~~y~T~GeYD~V~i~EapDda~~~~~~l~l~ 78 (104)
T COG4274 21 GAKTLKETPKRAAAVRALLESMGGKVKEQYWTLGEYDVVAIVEAPDDAVATRFSLALA 78 (104)
T ss_pred HHHHHhhCHHHHHHHHHHHHHcCcEEEEEEEeeccccEEEEEecCCHHHHHHHHHHHH
Confidence 88888888777788888999999986543 466677888888899988888877653
No 74
>TIGR00646 MG010 DNA primase-related protein. The DNA primase DnaG of E. coli and its apparent orthologs in other eubacterial species are approximately 600 residues in length. Within this set, a conspicuous outlier in percent identity, as seen in a UPGMA difference tree, is the branch containing the Mycoplasmas. This lineage is also unique in containing the small, DNA primase-related protein modelled by this alignment, which is homologous to the central third of DNA primase. Several small regions of sequence similarity specifically to Mycoplasma sequences rather than to all DnaG homologs suggests that the divergence of this protein from DnaG post-dated the separation of bacterial lineages. The function of this DNA primase-related protein is unknown.
Probab=27.32 E-value=91 Score=26.05 Aligned_cols=56 Identities=18% Similarity=0.192 Sum_probs=39.8
Q ss_pred EEEEEEEEEeCCccchHhHHhhCCCceecCCceeccCCHHHHHHHHHHHHHHHHhcCCCC
Q 031013 16 VKNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPA 75 (167)
Q Consensus 16 I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~~ 75 (167)
|.|+|| .+|..+-.+++...-+. +-++++-.-.+-+..+.|+.|..++|++.|+.+
T Consensus 130 i~naVA--slGTALT~~q~~lLkr~--~~~~Iil~~D~D~AG~~Aa~r~~~~L~~~G~~v 185 (218)
T TIGR00646 130 ILNCLP--LCGLTISDKQMKFFKQK--KIEKIFICFDNDFAGKNAAANLEEILKKAGFIT 185 (218)
T ss_pred CCeEEE--cCchHhHHHHHHHHhcc--CCCEEEEEeCCCHHHHHHHHHHHHHHHHCCCeE
Confidence 568885 45666666666543221 234577777778889999999999999999863
No 75
>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=27.30 E-value=1e+02 Score=22.97 Aligned_cols=26 Identities=42% Similarity=0.526 Sum_probs=22.0
Q ss_pred CceEEEEccCCHHHHHHHHHHHHHHHHh
Q 031013 134 SGKIVITGAKVRDETYTAFENIYPVLTE 161 (167)
Q Consensus 134 SGKvvitGaks~e~~~~a~~~i~~~L~~ 161 (167)
+|-+++|| +..+++.|++.....+.+
T Consensus 73 ~g~vii~G--dvsaV~aAl~a~~~~~~~ 98 (110)
T cd07046 73 SGALVITG--DVSEVESALEAVVDYLRE 98 (110)
T ss_pred eEEEEEEE--CHHHHHHHHHHHHHHHhh
Confidence 67888999 889999999988877654
No 76
>COG1654 BirA Biotin operon repressor [Transcription]
Probab=27.26 E-value=51 Score=23.12 Aligned_cols=21 Identities=19% Similarity=0.185 Sum_probs=18.0
Q ss_pred HHHHHHHHHHHHHHhcCCCCc
Q 031013 56 QSKLAARKYARIIQKLGFPAK 76 (167)
Q Consensus 56 ~a~~a~~k~~~~l~~lg~~~~ 76 (167)
=+|.|++|.++.|++.|+++.
T Consensus 31 iSRtaVwK~Iq~Lr~~G~~I~ 51 (79)
T COG1654 31 ISRTAVWKHIQQLREEGVDIE 51 (79)
T ss_pred ccHHHHHHHHHHHHHhCCceE
Confidence 358899999999999999843
No 77
>PF10686 DUF2493: Protein of unknown function (DUF2493); InterPro: IPR019627 This entry is represented by Mycobacteriophage D29, Gp61. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Members of this family are mainly Proteobacteria. The function is not known.
Probab=26.85 E-value=86 Score=21.28 Aligned_cols=20 Identities=15% Similarity=0.386 Sum_probs=14.3
Q ss_pred eEEEEccCCHHHHHHHHHHH
Q 031013 136 KIVITGAKVRDETYTAFENI 155 (167)
Q Consensus 136 KvvitGaks~e~~~~a~~~i 155 (167)
+|+|||+++-.|.....+.+
T Consensus 5 rVli~GgR~~~D~~~i~~~L 24 (71)
T PF10686_consen 5 RVLITGGRDWTDHELIWAAL 24 (71)
T ss_pred EEEEEECCccccHHHHHHHH
Confidence 68999999887666544443
No 78
>PF13098 Thioredoxin_2: Thioredoxin-like domain; PDB: 1T3B_A 2L57_A 1EEJ_B 1TJD_A 1JZD_B 1JZO_A 1G0T_B 3GV1_A 1V58_A 2H0H_A ....
Probab=26.57 E-value=1e+02 Score=21.22 Aligned_cols=24 Identities=29% Similarity=0.463 Sum_probs=14.7
Q ss_pred EEEec-CceEE--EEccCCHHHHHHHH
Q 031013 129 LLIFV-SGKIV--ITGAKVRDETYTAF 152 (167)
Q Consensus 129 ~lIF~-SGKvv--itGaks~e~~~~a~ 152 (167)
+.++. .||++ ++|..+.+++...+
T Consensus 86 ~~~~d~~G~~v~~~~G~~~~~~l~~~L 112 (112)
T PF13098_consen 86 IVFLDKDGKIVYRIPGYLSPEELLKML 112 (112)
T ss_dssp EEECTTTSCEEEEEESS--HHHHHHHH
T ss_pred EEEEcCCCCEEEEecCCCCHHHHHhhC
Confidence 34443 57744 79999999887653
No 79
>PRK02079 pyrroloquinoline quinone biosynthesis protein PqqD; Provisional
Probab=26.49 E-value=1.3e+02 Score=21.35 Aligned_cols=45 Identities=18% Similarity=0.446 Sum_probs=35.3
Q ss_pred cCCCCeEEEEEcC-CeEEEEEecCceEEE-----------EccCCHHHHHHHHHHHH
Q 031013 112 PELFPGLIYRMKQ-PKIVLLIFVSGKIVI-----------TGAKVRDETYTAFENIY 156 (167)
Q Consensus 112 PE~fPglv~R~~~-pk~t~lIF~SGKvvi-----------tGaks~e~~~~a~~~i~ 156 (167)
|.+-||..+|... ..+-+++|+-|-|.+ -|.+|.+++-+.+..-|
T Consensus 6 p~l~~~~rl~~d~~~~~~vlL~PEgmi~Lnetg~~Iw~~~DG~~tv~eIi~~L~~~y 62 (88)
T PRK02079 6 PTLRPGYRFQWEPAQNCHVLLYPEGMIKLNESAGEILGLIDGKRTVAAIIAELQQQF 62 (88)
T ss_pred cccCCCcccccccccCceEEEcCCeeeeechHHHHHHHHccCCCCHHHHHHHHHHHc
Confidence 6777888888765 457799999999987 67788888877776555
No 80
>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=26.43 E-value=69 Score=20.07 Aligned_cols=25 Identities=12% Similarity=0.169 Sum_probs=18.6
Q ss_pred EEecCceEEEEccCCH---HHHHHHHHH
Q 031013 130 LIFVSGKIVITGAKVR---DETYTAFEN 154 (167)
Q Consensus 130 lIF~SGKvvitGaks~---e~~~~a~~~ 154 (167)
.=|.+|+++|++.... +++.+++++
T Consensus 31 vd~~~~~v~v~~~~~~~~~~~i~~~i~~ 58 (62)
T PF00403_consen 31 VDLETKTVTVTYDPDKTSIEKIIEAIEK 58 (62)
T ss_dssp EETTTTEEEEEESTTTSCHHHHHHHHHH
T ss_pred EECCCCEEEEEEecCCCCHHHHHHHHHH
Confidence 4578899999998665 677766654
No 81
>KOG3384 consensus Selenoprotein [General function prediction only]
Probab=25.19 E-value=48 Score=26.10 Aligned_cols=27 Identities=37% Similarity=0.594 Sum_probs=19.4
Q ss_pred ccCCCCeEEEE---EcCCeEEEEEecCceEE
Q 031013 111 EPELFPGLIYR---MKQPKIVLLIFVSGKIV 138 (167)
Q Consensus 111 ePE~fPglv~R---~~~pk~t~lIF~SGKvv 138 (167)
+|++|||+..+ -.+|.+ .+.=.+||+-
T Consensus 101 ~~~kFp~vkvkyVrg~~P~l-~llDadgk~k 130 (154)
T KOG3384|consen 101 EPEKFPGVKVKYVRGSDPVL-KLLDADGKHK 130 (154)
T ss_pred chhhCCCceEEEecCCCCee-EeecCCCCcc
Confidence 79999999654 345654 5677888863
No 82
>PF05164 ZapA: Cell division protein ZapA; InterPro: IPR007838 This entry a structural domain found in the cell division protein ZapA, as well as in related proteins. This domain has a core structure consisting of two layers alpha/beta, and has a long C-terminal helix that forms dimeric parallel and tetrameric antiparallel coiled coils []. ZapA interacts with FtsZ, where FtsZ is part of a mid-cell cytokinetic structure termed the Z-ring that recruits a hierarchy of fission related proteins early in the bacterial cell cycle. ZapA drives the polymerisation and filament bundling of FtsZ, thereby contributing to the spatio-temporal tuning of the Z-ring.; PDB: 1T3U_B 1W2E_B 3HNW_A.
Probab=25.12 E-value=1.6e+02 Score=19.76 Aligned_cols=39 Identities=15% Similarity=0.059 Sum_probs=28.9
Q ss_pred EEEEEecCceEEEEccCCHHHHHHHHHHHHHHHHhhhhh
Q 031013 127 IVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRKV 165 (167)
Q Consensus 127 ~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~~r~~ 165 (167)
+.+.|+..-.-+-.+..+++.++++.+.+-..+.++++.
T Consensus 2 V~v~I~G~~y~i~~~~~~ee~l~~~a~~i~~~i~~~~~~ 40 (89)
T PF05164_consen 2 VKVTILGREYRIKCPDEDEEYLRKAAELINEKINEIKKK 40 (89)
T ss_dssp EEEEETTEEEEECETGCGHHHHHHHHHHHHHHHHHHCTT
T ss_pred eEEEECCEEEEeecCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 445555444333337889999999999999999998865
No 83
>PHA02031 putative DnaG-like primase
Probab=24.83 E-value=1.4e+02 Score=25.67 Aligned_cols=73 Identities=12% Similarity=0.003 Sum_probs=50.1
Q ss_pred EEEEEEEEEeCCccchHhHHhhCCCceecCCceeccCCHHHHHHHHHHHHHHHHhcCCCCcccceEEEEEEEEEecCCcc
Q 031013 16 VKNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPI 95 (167)
Q Consensus 16 I~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~I 95 (167)
|.|+||+ ||..|--+++....+. |.++++.=-.+-+.-+.|+.+.+++|...|++++ ...+|..-
T Consensus 182 ~~naVA~--LGTALT~~q~~~L~r~--~~~~Vil~fDgD~AG~~Aa~ra~~~l~~~~~~v~-----------vv~lP~g~ 246 (266)
T PHA02031 182 EVFAVAL--LGTRLRDRLAAILLQQ--TCPRVLIFLDGDPAGVDGSAGAMRRLRPLLIEGQ-----------VIITPDGF 246 (266)
T ss_pred cceEEEC--CcccCCHHHHHHHHhc--CCCCEEEEeCCCHHHHHHHHHHHHHHHHcCCceE-----------EEECCCCC
Confidence 4577775 6777776666654443 4567776666778888999999999998887532 23456666
Q ss_pred chHhHHHH
Q 031013 96 RLEGLAYS 103 (167)
Q Consensus 96 ~L~~la~~ 103 (167)
|-+.+..+
T Consensus 247 DPDd~ir~ 254 (266)
T PHA02031 247 DPKDLERE 254 (266)
T ss_pred ChHHHHHH
Confidence 76666543
No 84
>PRK00754 signal recognition particle protein Srp19; Provisional
Probab=24.76 E-value=2.3e+02 Score=20.53 Aligned_cols=51 Identities=18% Similarity=0.285 Sum_probs=31.8
Q ss_pred chHhHHHHcCCCeeeccC-CCCeEEEEEcCCeEEEEEe-cCceEEEEccCCHHHHHHHHHHHHHH
Q 031013 96 RLEGLAYSHGAFSSYEPE-LFPGLIYRMKQPKIVLLIF-VSGKIVITGAKVRDETYTAFENIYPV 158 (167)
Q Consensus 96 ~L~~la~~~~~~~~YePE-~fPglv~R~~~pk~t~lIF-~SGKvvitGaks~e~~~~a~~~i~~~ 158 (167)
++...+..++-.+..||+ .||.-- | .+|.|.|--..+..++-..+..-++.
T Consensus 39 EI~~a~~~lgl~~~~e~~K~yPr~~------------~e~~GRv~V~~~~~K~~ll~~Ia~~I~~ 91 (95)
T PRK00754 39 EIIEAAEKLGLNPEVEPDKAYPRSW------------WEVSGRVLVDKVGSKTNTLRMIAKEIKK 91 (95)
T ss_pred HHHHHHHHcCCCeEEeeCCCCCchH------------hcCCCEEEECCCCCHHHHHHHHHHHHHH
Confidence 344445566666778876 677641 4 57888887666766666555444443
No 85
>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=24.56 E-value=78 Score=24.55 Aligned_cols=31 Identities=26% Similarity=0.484 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHHhcCCCCcccceEEEEEEEE
Q 031013 58 KLAARKYARIIQKLGFPAKFKDFKIQNIVGS 88 (167)
Q Consensus 58 ~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas 88 (167)
-.|.+-|-++++.||++++|.-+++.-.-++
T Consensus 58 tD~~Qlf~~v~~~lGY~Vq~~HVk~rc~~g~ 88 (142)
T PF12386_consen 58 TDACQLFYRVIESLGYDVQFEHVKCRCNSGK 88 (142)
T ss_pred hhHHHHHHHHHHhcCceEEEEEEEEEecCCc
Confidence 3567889999999999998888777744444
No 86
>PF14611 SLS: Mitochondrial inner-membrane-bound regulator
Probab=24.36 E-value=92 Score=24.83 Aligned_cols=37 Identities=22% Similarity=0.233 Sum_probs=27.2
Q ss_pred eEEE-EEecCceEEEEccCCHHHHHHHHHHHHHHHHhhhh
Q 031013 126 KIVL-LIFVSGKIVITGAKVRDETYTAFENIYPVLTEFRK 164 (167)
Q Consensus 126 k~t~-lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~~r~ 164 (167)
++++ +.+..++|.|||.++ .++.+...|..+|.+.+.
T Consensus 56 ~~~I~~~~~~~~i~I~g~k~--~~~~i~~~i~~~l~~i~~ 93 (210)
T PF14611_consen 56 GAKIEVSRSENRIRITGTKS--TAEYIEASINEILSNIRT 93 (210)
T ss_pred CceEEEecCCcEEEEEccHH--HHHHHHHHHHHHHhhcEE
Confidence 3444 356789999999776 477777788888877664
No 87
>PRK15415 propanediol utilization protein PduB; Provisional
Probab=24.09 E-value=1.2e+02 Score=26.06 Aligned_cols=29 Identities=24% Similarity=0.272 Sum_probs=24.5
Q ss_pred CceEEEEccCCHHHHHHHHHHHHHHHHhh
Q 031013 134 SGKIVITGAKVRDETYTAFENIYPVLTEF 162 (167)
Q Consensus 134 SGKvvitGaks~e~~~~a~~~i~~~L~~~ 162 (167)
.|+++++|+-+..+++.|++.-...+.++
T Consensus 119 ~G~~ii~g~gDVs~Vr~AVeaa~~~~~~~ 147 (266)
T PRK15415 119 HGSLIIFGAEDVSDVRRAVEVALKELDRT 147 (266)
T ss_pred ceEEEEEeCCCHHHHHHHHHHHHHHHHhh
Confidence 39999999999999999998877766554
No 88
>PF13462 Thioredoxin_4: Thioredoxin; PDB: 3FEU_A 3HZ8_A 3DVW_A 3A3T_E 3GMF_A 1Z6M_A 3GYK_C 3BCK_A 3BD2_A 3BCI_A ....
Probab=24.07 E-value=1.1e+02 Score=22.41 Aligned_cols=23 Identities=22% Similarity=0.475 Sum_probs=19.3
Q ss_pred EecCceEEEEccCCHHHHHHHHHH
Q 031013 131 IFVSGKIVITGAKVRDETYTAFEN 154 (167)
Q Consensus 131 IF~SGKvvitGaks~e~~~~a~~~ 154 (167)
+|.+||. +.|..+.+++.+++++
T Consensus 140 ~~inG~~-~~~~~~~~~l~~~Id~ 162 (162)
T PF13462_consen 140 FFINGKY-VVGPYTIEELKELIDK 162 (162)
T ss_dssp EEETTCE-EETTTSHHHHHHHHHH
T ss_pred EEECCEE-eCCCCCHHHHHHHHcC
Confidence 5569999 5889999999998874
No 89
>KOG0353 consensus ATP-dependent DNA helicase [General function prediction only]
Probab=23.98 E-value=5.5e+02 Score=23.99 Aligned_cols=70 Identities=24% Similarity=0.296 Sum_probs=44.7
Q ss_pred HHHHHHHHHhcCCCCc-----------------ccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEc
Q 031013 61 ARKYARIIQKLGFPAK-----------------FKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMK 123 (167)
Q Consensus 61 ~~k~~~~l~~lg~~~~-----------------~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~ 123 (167)
.+++++.|+.+|+... -..=+||-||||.-.|..||
T Consensus 330 ~ekva~alkn~gi~a~~yha~lep~dks~~hq~w~a~eiqvivatvafgmgid--------------------------- 382 (695)
T KOG0353|consen 330 CEKVAKALKNHGIHAGAYHANLEPEDKSGAHQGWIAGEIQVIVATVAFGMGID--------------------------- 382 (695)
T ss_pred HHHHHHHHHhcCccccccccccCccccccccccccccceEEEEEEeeecccCC---------------------------
Confidence 3577888998886421 01246888899888877665
Q ss_pred CCeEEEEEecCceEEEEccCCHHHHHHHHHHHHHHHHhhh
Q 031013 124 QPKIVLLIFVSGKIVITGAKVRDETYTAFENIYPVLTEFR 163 (167)
Q Consensus 124 ~pk~t~lIF~SGKvvitGaks~e~~~~a~~~i~~~L~~~r 163 (167)
+|.+++.|..| -.||.|.-.+|-.+|+-.+-+-+
T Consensus 383 kpdvrfvihhs------l~ksienyyqasarillrmtkqk 416 (695)
T KOG0353|consen 383 KPDVRFVIHHS------LPKSIENYYQASARILLRMTKQK 416 (695)
T ss_pred CCCeeEEEecc------cchhHHHHHHHHHHHHHHHhhhc
Confidence 34455555444 25788888887777665544433
No 90
>PF09840 DUF2067: Uncharacterized protein conserved in archaea (DUF2067); InterPro: IPR019202 This family of archaeal proteins, have no known function.
Probab=23.92 E-value=36 Score=27.70 Aligned_cols=66 Identities=17% Similarity=0.181 Sum_probs=53.5
Q ss_pred hhCCCceecCCceeccCCHHHHHHHHHHHHHHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHH
Q 031013 36 LQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYS 103 (167)
Q Consensus 36 ~~~~n~eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~ 103 (167)
...-+++|+..++...-+.++....++++.++++.+-+.+... ++.++++....-...|.+.+...
T Consensus 97 ~~G~~ae~~~~~i~T~a~~eev~~l~~~Lse~~~e~~~~~~~~--~aK~vi~~~s~~~g~~p~evie~ 162 (190)
T PF09840_consen 97 LLGYKAEYREDVIKTDAPLEEVVELAERLSEIYKELRFQPLGT--KAKRVIAAVSYATGLDPEEVIEE 162 (190)
T ss_pred hCCCeeEEeCCeEEecCCHHHHHHHHHHHHHHHHHHhcCccCH--HHHHHHHHHHHHhCCCHHHHHHH
Confidence 3446789999888888899999999999999999975543222 38899999999899999888753
No 91
>cd02975 PfPDO_like_N Pyrococcus furiosus protein disulfide oxidoreductase (PfPDO)-like family, N-terminal TRX-fold subdomain; composed of proteins with similarity to PfPDO, a redox active thermostable protein believed to be the archaeal counterpart of bacterial DsbA and eukaryotic protein disulfide isomerase (PDI), which are both involved in oxidative protein folding. PfPDO contains two redox active CXXC motifs in two contiguous TRX-fold subdomains. The active site in the N-terminal TRX-fold subdomain is required for isomerase but not for reductase activity of PfPDO. The exclusive presence of PfPDO-like proteins in extremophiles may suggest that they have a special role in adaptation to extreme conditions.
Probab=23.75 E-value=1.7e+02 Score=20.89 Aligned_cols=31 Identities=19% Similarity=0.165 Sum_probs=24.3
Q ss_pred EEEEEecC----ceEEEEccCCHHHHHHHHHHHHH
Q 031013 127 IVLLIFVS----GKIVITGAKVRDETYTAFENIYP 157 (167)
Q Consensus 127 ~t~lIF~S----GKvvitGaks~e~~~~a~~~i~~ 157 (167)
.++++|.. |++...|..+.+++.+-++.|+.
T Consensus 77 Pt~~i~~~g~~~~~~~~~G~~~~~el~~~i~~i~~ 111 (113)
T cd02975 77 PTTIFLQDGGKDGGIRYYGLPAGYEFASLIEDIVR 111 (113)
T ss_pred CEEEEEeCCeecceEEEEecCchHHHHHHHHHHHh
Confidence 36777865 66778999999999888887764
No 92
>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=23.50 E-value=1.4e+02 Score=22.08 Aligned_cols=28 Identities=11% Similarity=0.286 Sum_probs=21.4
Q ss_pred CceEE-EEccCCHHHHHHHHHHHHHHHHh
Q 031013 134 SGKIV-ITGAKVRDETYTAFENIYPVLTE 161 (167)
Q Consensus 134 SGKvv-itGaks~e~~~~a~~~i~~~L~~ 161 (167)
||.++ |.|+.++.|++.|++.+...|.+
T Consensus 71 sG~vi~ii~G~dvsdV~sal~~~l~~l~~ 99 (103)
T cd07049 71 AGEVIGILAGPSPAEVRSGLNAAIDFIEN 99 (103)
T ss_pred CccEEEEEeCCCHHHHHHHHHHHHHHHhc
Confidence 67766 34456778999999999888765
No 93
>cd03024 DsbA_FrnE DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=23.45 E-value=77 Score=24.43 Aligned_cols=22 Identities=23% Similarity=0.406 Sum_probs=18.3
Q ss_pred EecCceEEEEccCCHHHHHHHH
Q 031013 131 IFVSGKIVITGAKVRDETYTAF 152 (167)
Q Consensus 131 IF~SGKvvitGaks~e~~~~a~ 152 (167)
++.+|+..+.|+.+.+.+.+++
T Consensus 179 ~vv~g~~~~~G~~~~~~~~~~i 200 (201)
T cd03024 179 FVFNGKYAVSGAQPPEVFLQAL 200 (201)
T ss_pred EEECCeEeecCCCCHHHHHHHh
Confidence 3448899999999999888776
No 94
>KOG3946 consensus Glutaminyl cyclase [Posttranslational modification, protein turnover, chaperones]
Probab=23.32 E-value=1e+02 Score=27.25 Aligned_cols=65 Identities=17% Similarity=0.316 Sum_probs=40.7
Q ss_pred eeccCCHHHHHHHHHHHHHHHHhcCCCCccc---------ceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeE
Q 031013 48 CTGAKSEQQSKLAARKYARIIQKLGFPAKFK---------DFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGL 118 (167)
Q Consensus 48 ~tGakS~~~a~~a~~k~~~~l~~lg~~~~~~---------~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPgl 118 (167)
+.|.+. .+.+-+-+...|+++|..+... ...++||++|.+-.-+ ..+---|-|+-..||+.
T Consensus 65 vpgs~g---~~~vr~~i~~~l~~l~w~ve~~~f~~~tp~g~~~f~nii~tl~~~A~-------r~lVlachydsk~~p~~ 134 (338)
T KOG3946|consen 65 VPGSPG---SRQVRRFIIQHLRNLGWAVETDAFTDNTPLGTRNFNNLIATLDPNAS-------RYLVLACHYDSKIFPGG 134 (338)
T ss_pred cCCCCc---cHHHHHHHHHHHHhcCceeeeccccccCcceeeeeeeEEEecCCCcc-------hheeeecccccccCCCc
Confidence 345544 3444455667788889754322 2348999999885432 22222478999999998
Q ss_pred EEEE
Q 031013 119 IYRM 122 (167)
Q Consensus 119 v~R~ 122 (167)
.|+.
T Consensus 135 ~~vg 138 (338)
T KOG3946|consen 135 MFVG 138 (338)
T ss_pred ceEe
Confidence 8664
No 95
>PF12965 DUF3854: Domain of unknown function (DUF3854); InterPro: IPR024385 This is a family of uncharacterised proteins, found by clustering human gut metagenomic sequences [].
Probab=23.11 E-value=1.1e+02 Score=23.17 Aligned_cols=26 Identities=15% Similarity=0.429 Sum_probs=22.3
Q ss_pred cCCHHHHHHHHHHHHHHHHhcCCCCc
Q 031013 51 AKSEQQSKLAARKYARIIQKLGFPAK 76 (167)
Q Consensus 51 akS~~~a~~a~~k~~~~l~~lg~~~~ 76 (167)
.++......|++++.+.|++.|..++
T Consensus 81 ~~Tn~~V~~a~~~l~~~L~~~G~~v~ 106 (130)
T PF12965_consen 81 PKTNKNVRRAIKRLGKLLKEAGCKVK 106 (130)
T ss_pred cchhHHHHHHHHHHHHHHHHCCCEEE
Confidence 45679999999999999999998643
No 96
>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=22.69 E-value=90 Score=24.72 Aligned_cols=33 Identities=15% Similarity=0.210 Sum_probs=27.4
Q ss_pred eecCCceeccCCHHHHHHHHHHHHHHHHhcCCC
Q 031013 42 EYNPKVCTGAKSEQQSKLAARKYARIIQKLGFP 74 (167)
Q Consensus 42 eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~ 74 (167)
+|.-.++.=++|.++++..++++.+.|+..|+.
T Consensus 148 ~~~~~i~v~~~~~~~l~~~~~~v~~~l~~~G~~ 180 (205)
T PF03135_consen 148 YYHFTIVVFADDPEELDDKVAEVSSALNNLGFV 180 (205)
T ss_pred eeEEEEEEEcCCHHHHHHHHHHHHHHHHHCCCE
Confidence 333336666899999999999999999999996
No 97
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=22.66 E-value=1e+02 Score=19.42 Aligned_cols=20 Identities=40% Similarity=0.519 Sum_probs=16.0
Q ss_pred CceEEEEccCCHHHHHHHHHHH
Q 031013 134 SGKIVITGAKVRDETYTAFENI 155 (167)
Q Consensus 134 SGKvvitGaks~e~~~~a~~~i 155 (167)
++.|+|+|. .+.+..|.+.|
T Consensus 42 ~~~v~I~G~--~~~v~~A~~~i 61 (62)
T cd02394 42 SDTITITGP--KENVEKAKEEI 61 (62)
T ss_pred CCEEEEEcC--HHHHHHHHHHh
Confidence 689999999 56788887655
No 98
>PRK09929 hypothetical protein; Provisional
Probab=22.49 E-value=96 Score=22.47 Aligned_cols=21 Identities=10% Similarity=0.112 Sum_probs=17.9
Q ss_pred ceEEEEccCCHHHHHHHHHHH
Q 031013 135 GKIVITGAKVRDETYTAFENI 155 (167)
Q Consensus 135 GKvvitGaks~e~~~~a~~~i 155 (167)
|-|.++|..+++|+++++.+-
T Consensus 41 GtVSvs~~~s~~d~~~~La~K 61 (91)
T PRK09929 41 GTISTSNEMSTADAKEDLIKK 61 (91)
T ss_pred EEEEEcCCCCHHHHHHHHHHH
Confidence 788889999999999988654
No 99
>cd02994 PDI_a_TMX PDIa family, TMX subfamily; composed of proteins similar to the TRX-related human transmembrane protein, TMX. TMX is a type I integral membrane protein; the N-terminal redox active TRX domain is present in the endoplasmic reticulum (ER) lumen while the C-terminus is oriented towards the cytoplasm. It is expressed in many cell types and its active site motif (CPAC) is unique. In vitro, TMX reduces interchain disulfides of insulin and renatures inactive RNase containing incorrect disulfide bonds. The C. elegans homolog, DPY-11, is expressed only in the hypodermis and resides in the cytoplasm. It is required for body and sensory organ morphogeneis. Another uncharacterized TRX-related transmembrane protein, human TMX4, is included in the alignment. The active site sequence of TMX4 is CPSC.
Probab=22.35 E-value=1.2e+02 Score=20.51 Aligned_cols=24 Identities=13% Similarity=0.198 Sum_probs=15.1
Q ss_pred EEecCceE-EEEccCCHHHHHHHHH
Q 031013 130 LIFVSGKI-VITGAKVRDETYTAFE 153 (167)
Q Consensus 130 lIF~SGKv-vitGaks~e~~~~a~~ 153 (167)
.+|..|++ ...|..+.+++.+.++
T Consensus 76 ~~~~~g~~~~~~G~~~~~~l~~~i~ 100 (101)
T cd02994 76 YHAKDGVFRRYQGPRDKEDLISFIE 100 (101)
T ss_pred EEeCCCCEEEecCCCCHHHHHHHHh
Confidence 34566654 3568888877766543
No 100
>cd03007 PDI_a_ERp29_N PDIa family, endoplasmic reticulum protein 29 (ERp29) subfamily; ERp29 is a ubiquitous ER-resident protein expressed in high levels in secretory cells. It forms homodimers and higher oligomers in vitro and in vivo. It contains a redox inactive TRX-like domain at the N-terminus, which is homologous to the redox active TRX (a) domains of PDI, and a C-terminal helical domain similar to the C-terminal domain of P5. The expression profile of ERp29 suggests a role in secretory protein production distinct from that of PDI. It has also been identified as a member of the thyroglobulin folding complex. The Drosophila homolog, Wind, is the product of windbeutel, an essential gene in the development of dorsal-ventral patterning. Wind is required for correct targeting of Pipe, a Golgi-resident type II transmembrane protein with homology to 2-O-sulfotransferase.
Probab=22.12 E-value=88 Score=23.33 Aligned_cols=26 Identities=23% Similarity=0.402 Sum_probs=18.7
Q ss_pred EEEEecCce----EEEEcc-CCHHHHHHHHH
Q 031013 128 VLLIFVSGK----IVITGA-KVRDETYTAFE 153 (167)
Q Consensus 128 t~lIF~SGK----vvitGa-ks~e~~~~a~~ 153 (167)
|+++|.+|. +.-.|. ++.+++..-+.
T Consensus 83 Tl~lF~~g~~~~~~~Y~G~~r~~~~lv~~v~ 113 (116)
T cd03007 83 VIYLFHGGDFENPVPYSGADVTVDALQRFLK 113 (116)
T ss_pred EEEEEeCCCcCCCccCCCCcccHHHHHHHHH
Confidence 567788885 667897 88887765543
No 101
>PTZ00051 thioredoxin; Provisional
Probab=21.94 E-value=1.1e+02 Score=20.52 Aligned_cols=21 Identities=24% Similarity=0.520 Sum_probs=14.6
Q ss_pred EEEEecCceEE--EEccCCHHHHH
Q 031013 128 VLLIFVSGKIV--ITGAKVRDETY 149 (167)
Q Consensus 128 t~lIF~SGKvv--itGaks~e~~~ 149 (167)
++++|..|+++ +.|+. .++++
T Consensus 74 t~~~~~~g~~~~~~~G~~-~~~~~ 96 (98)
T PTZ00051 74 TFKVFKNGSVVDTLLGAN-DEALK 96 (98)
T ss_pred EEEEEeCCeEEEEEeCCC-HHHhh
Confidence 47788999988 77764 34443
No 102
>PF11504 Colicin_Ia: Colicin Ia; InterPro: IPR014740 Colicins are plasmid-encoded polypeptide toxins produced by and active against Escherichia coli and closely related bacteria. Colicins are released into the environment to reduce competition from other bacterial strains. Colicins bind to outer membrane receptors, using them to translocate to the cytoplasm or cytoplasmic membrane, where they exert their cytotoxic effect, including depolarisation of the cytoplasmic membrane, DNase activity, RNase activity, or inhibition of murein synthesis. Channel-forming colicins (colicins A, B, E1, Ia, Ib, and N) are transmembrane proteins that depolarize the cytoplasmic membrane, leading to dissipation of cellular energy []. These colicins contain at least three domains: an N-terminal translocation domain responsible for movement across the outer membrane and periplasmic space; a central domain responsible for receptor recognition; and a C-terminal cytotoxic domain responsible for channel formation in the cytoplasmic membrane []. This entry represents the central receptor recognition domain, which has an alpha/beta two-layer sandwich structure.; GO: 0019835 cytolysis, 0050829 defense response to Gram-negative bacterium, 0016021 integral to membrane; PDB: 2HDI_B 1CII_A.
Probab=21.45 E-value=81 Score=21.31 Aligned_cols=20 Identities=50% Similarity=0.665 Sum_probs=10.2
Q ss_pred eccCCCCeEEEEEcCCeEEEEEecCc
Q 031013 110 YEPELFPGLIYRMKQPKIVLLIFVSG 135 (167)
Q Consensus 110 YePE~fPglv~R~~~pk~t~lIF~SG 135 (167)
-.||.|||--- .--.||.||
T Consensus 10 vspekfpgrss------tn~~i~vsg 29 (72)
T PF11504_consen 10 VSPEKFPGRSS------TNHSIFVSG 29 (72)
T ss_dssp H-TTTS-EEEE------EEEEEEE-S
T ss_pred eCcccCCCCCC------CCceEEEcC
Confidence 46999999632 223466664
No 103
>KOG2648 consensus Diphthamide biosynthesis protein [Translation, ribosomal structure and biogenesis]
Probab=21.26 E-value=1.4e+02 Score=27.66 Aligned_cols=57 Identities=14% Similarity=0.192 Sum_probs=46.6
Q ss_pred EEEEEEEeCCccchHhHHh-hCCCceecCC--------------------------------ceeccCCHHHHHHHHHHH
Q 031013 18 NIVSTVNLDCKLDLKKIAL-QARNAEYNPK--------------------------------VCTGAKSEQQSKLAARKY 64 (167)
Q Consensus 18 NVV~s~~l~~~ldL~~ia~-~~~n~eY~P~--------------------------------v~tGakS~~~a~~a~~k~ 64 (167)
++|--++=+.++|+..++. ..+-..|+|. ++.|+-+.+.-+.+++++
T Consensus 209 ~li~iGD~~~~le~~mi~np~~~~~~ydp~s~kl~~E~y~~~~m~~rR~~~vekardA~~iGlivGTLG~qg~~~vl~~L 288 (453)
T KOG2648|consen 209 ALIFIGDGRFHLESSMIANPGLPAYRYDPYSKKLTRESYDHSRMLRRRYYLVEKARDARTIGLIVGTLGRQGNREVLEHL 288 (453)
T ss_pred eEEEecCCCcchhHHHHhCCCCCeEEeCCccCceeecccchHHHHHHHHHHHHHHhcCCeEEEEEecccccCCHHHHHHH
Confidence 4555555567888888887 4556799997 889999999999999999
Q ss_pred HHHHHhcCCC
Q 031013 65 ARIIQKLGFP 74 (167)
Q Consensus 65 ~~~l~~lg~~ 74 (167)
.+++++.|.+
T Consensus 289 ~~~~~~~Gkk 298 (453)
T KOG2648|consen 289 RKLLKAAGKK 298 (453)
T ss_pred HHHHHHcCCc
Confidence 9999999964
No 104
>cd02996 PDI_a_ERp44 PDIa family, endoplasmic reticulum protein 44 (ERp44) subfamily; ERp44 is an ER-resident protein, induced during stress, involved in thiol-mediated ER retention. It contains an N-terminal TRX domain, similar to that of PDIa, with a CXFS motif followed by two redox inactive TRX-like domains, homologous to the b and b' domains of PDI. The CXFS motif in the N-terminal domain allows ERp44 to form stable reversible mixed disulfides with its substrates. Through this activity, ERp44 mediates the ER localization of Ero1alpha, a protein that oxidizes protein disulfide isomerases into their active form. ERp44 also prevents the secretion of unassembled cargo protein with unpaired cysteines. It also modulates the activity of inositol 1,4,5-triphosphate type I receptor (IP3R1), an intracellular channel protein that mediates calcium release from the ER to the cytosol.
Probab=20.92 E-value=99 Score=21.44 Aligned_cols=23 Identities=17% Similarity=0.231 Sum_probs=15.3
Q ss_pred EEEEecCce---EEEEccCCHHHHHH
Q 031013 128 VLLIFVSGK---IVITGAKVRDETYT 150 (167)
Q Consensus 128 t~lIF~SGK---vvitGaks~e~~~~ 150 (167)
|+.+|..|+ ...+|.++.+++.+
T Consensus 81 tl~~~~~g~~~~~~~~g~~~~~~l~~ 106 (108)
T cd02996 81 TLKLFRNGMMMKREYRGQRSVEALAE 106 (108)
T ss_pred EEEEEeCCcCcceecCCCCCHHHHHh
Confidence 355677777 44568888876643
No 105
>COG0849 ftsA Cell division ATPase FtsA [Cell division and chromosome partitioning]
Probab=20.91 E-value=3.2e+02 Score=24.90 Aligned_cols=73 Identities=23% Similarity=0.312 Sum_probs=51.8
Q ss_pred ceeccCCHHHHHHHHHHHHHHHHhcCCCCcccceEEEEEEEEEecCCccchHhHHHHcCCCeeeccCCCCeEEEEEcCCe
Q 031013 47 VCTGAKSEQQSKLAARKYARIIQKLGFPAKFKDFKIQNIVGSCDVKFPIRLEGLAYSHGAFSSYEPELFPGLIYRMKQPK 126 (167)
Q Consensus 47 v~tGakS~~~a~~a~~k~~~~l~~lg~~~~~~~~~I~NIvas~~l~~~I~L~~la~~~~~~~~YePE~fPglv~R~~~pk 126 (167)
++||.+ ..++.+.+.++++|.+ |.||+. +.+|....--++=|.| +..+..-|-.-.
T Consensus 159 vit~~~------~~~~Nl~k~v~r~gl~-------v~~i~l----------~plAsa~a~L~~dEke-lGv~lIDiG~GT 214 (418)
T COG0849 159 VITGPK------NILENLEKCVERAGLK-------VDNIVL----------EPLASALAVLTEDEKE-LGVALIDIGGGT 214 (418)
T ss_pred EEEcch------HHHHHHHHHHHHhCCC-------eeeEEE----------ehhhhhhhccCcccHh-cCeEEEEeCCCc
Confidence 677765 4678899999999886 555553 4456543222333334 466677888888
Q ss_pred EEEEEecCceEEEEccC
Q 031013 127 IVLLIFVSGKIVITGAK 143 (167)
Q Consensus 127 ~t~lIF~SGKvvitGak 143 (167)
+.+.||..|+++-||.-
T Consensus 215 TdIai~~~G~l~~~~~i 231 (418)
T COG0849 215 TDIAIYKNGALRYTGVI 231 (418)
T ss_pred EEEEEEECCEEEEEeeE
Confidence 99999999999999874
No 106
>COG1490 Dtd D-Tyr-tRNAtyr deacylase [Translation, ribosomal structure and biogenesis]
Probab=20.89 E-value=2.6e+02 Score=21.98 Aligned_cols=58 Identities=16% Similarity=0.221 Sum_probs=43.1
Q ss_pred EEEEEeCCccchHhHHhhCCCce-ecCC---------------------------------ceeccCCHHHHHHHHHHHH
Q 031013 20 VSTVNLDCKLDLKKIALQARNAE-YNPK---------------------------------VCTGAKSEQQSKLAARKYA 65 (167)
Q Consensus 20 V~s~~l~~~ldL~~ia~~~~n~e-Y~P~---------------------------------v~tGakS~~~a~~a~~k~~ 65 (167)
|+...-+.+-|.+.++.++.|-+ |+-+ --++|.+.+.|+.-.++|.
T Consensus 31 vGV~~~Dt~~~a~~l~~Ki~~lRiF~D~~gKmN~sv~di~G~iL~VSQFTL~adt~kG~RPsFs~aa~p~~A~~lYe~f~ 110 (145)
T COG1490 31 VGVTHDDTEEDADYLAEKILNLRIFEDEEGKMNLSVQDVGGEILVVSQFTLYADTKKGRRPSFSKAAKPDQAEELYEYFV 110 (145)
T ss_pred EeecCCCCHHHHHHHHHHHhceEeecCcccccccCHHHcCCcEEEEEEEEEeecccCCCCCCccccCChHHHHHHHHHHH
Confidence 44444456778888888887742 2222 4567889999999999999
Q ss_pred HHHHhcCCCCcc
Q 031013 66 RIIQKLGFPAKF 77 (167)
Q Consensus 66 ~~l~~lg~~~~~ 77 (167)
+.|++.|.+++.
T Consensus 111 ~~lr~~~~~V~t 122 (145)
T COG1490 111 ELLRELGIKVET 122 (145)
T ss_pred HHHHhcCCccee
Confidence 999999987543
No 107
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. E. coli DnaG is a single subunit enzyme.
Probab=20.56 E-value=2.4e+02 Score=18.67 Aligned_cols=55 Identities=20% Similarity=0.331 Sum_probs=36.0
Q ss_pred EEEEEEEEeCCccchHhHHhhCCCceecCCceeccCCHHHHHHHHHHHHHHHHhcCCCCc
Q 031013 17 KNIVSTVNLDCKLDLKKIALQARNAEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAK 76 (167)
Q Consensus 17 ~NVV~s~~l~~~ldL~~ia~~~~n~eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~~~ 76 (167)
.|+|++. |+.+.-..+.. +.. |..+++.-..+-+..+.|++++.+.|++.|+.+.
T Consensus 21 ~~~va~~--G~~~~~~~~~~-L~~--~~~~vii~~D~D~aG~~a~~~~~~~l~~~g~~~~ 75 (79)
T cd03364 21 KNVVASL--GTALTEEQAEL-LKR--LAKEVILAFDGDEAGQKAALRALELLLKLGLNVR 75 (79)
T ss_pred CCEEECC--CccCcHHHHHH-HHh--cCCeEEEEECCCHHHHHHHHHHHHHHHHCCCeEE
Confidence 4666553 44443333332 222 2455777777778889999999999999998744
No 108
>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=20.49 E-value=1.5e+02 Score=23.36 Aligned_cols=35 Identities=17% Similarity=0.225 Sum_probs=29.0
Q ss_pred ecCCceeccCCHHHHHHHHHHHHHHHHhcCCCCcc
Q 031013 43 YNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKF 77 (167)
Q Consensus 43 Y~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~~~~ 77 (167)
|-=+++.++.+.++.....+.+.+.|++.|+.+..
T Consensus 159 Y~DDili~s~~~~e~~~~l~~v~~~l~~~gl~l~~ 193 (210)
T cd03715 159 YVDDLLLAADSEEDCLKGTDALLTHLGELGYKVSP 193 (210)
T ss_pred ECCcEEEecCCHHHHHHHHHHHHHHHHHCCCCcCH
Confidence 33347778889999999999999999999997543
No 109
>PF12010 DUF3502: Domain of unknown function (DUF3502); InterPro: IPR022627 This domain is about 140 amino acids in length and is functionally uncharacterised. It is found in bacteria C-terminal to PF01547 from PFAM.
Probab=20.44 E-value=17 Score=27.52 Aligned_cols=54 Identities=19% Similarity=0.258 Sum_probs=39.9
Q ss_pred EEEEEEEeCCccchHhHHhhCCC-----ceecCCceeccCCHHHHHHHHHHHHHHHHhcCCC
Q 031013 18 NIVSTVNLDCKLDLKKIALQARN-----AEYNPKVCTGAKSEQQSKLAARKYARIIQKLGFP 74 (167)
Q Consensus 18 NVV~s~~l~~~ldL~~ia~~~~n-----~eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~ 74 (167)
+.+.|--+|..+|-..+...+.+ .+|.|..++|.-.++ .++.++...|+..|++
T Consensus 58 ~~~~s~~~GF~fD~s~Vk~Eiaa~~~v~~~Y~~~L~~G~vd~e---~~~~~~~~kLk~AGid 116 (134)
T PF12010_consen 58 NAKPSPLLGFTFDPSPVKNEIAACSNVWSEYYPPLETGLVDPE---EALPEFNEKLKAAGID 116 (134)
T ss_pred hCccCcccCeeECCchhHHHHHHHHHHHHHHHHHHHccCCCHH---HHHHHHHHHHHHhChH
Confidence 34556667888888877655543 378888999998754 4578889999999985
No 110
>TIGR02653 Lon_rel_chp conserved hypothetical protein. This model describes a protein family of unknown function, about 690 residues in length, in which some members show C-terminal sequence similarity to Pfam model pfam05362, which is the Lon protease C-terminal proteolytic domain, from MEROPS family S16. However, the annotated catalytic sites of E. coli Lon protease are not conserved in members of this family. Members have a motif GP[RK][GS]TGKS, similar to the ATP-binding P-loop motif GxxGxGK[ST].
Probab=20.25 E-value=7.2e+02 Score=24.35 Aligned_cols=50 Identities=20% Similarity=0.330 Sum_probs=29.3
Q ss_pred eccCCCCeEEEEEcCC---e-----EEE-EEecCceEEEEccCCHHHHHHHHHHHHHHHH
Q 031013 110 YEPELFPGLIYRMKQP---K-----IVL-LIFVSGKIVITGAKVRDETYTAFENIYPVLT 160 (167)
Q Consensus 110 YePE~fPglv~R~~~p---k-----~t~-lIF~SGKvvitGaks~e~~~~a~~~i~~~L~ 160 (167)
-+|. -||++|-+.-. . +-+ .+=.+||+.+||-..-+.++++++..+..++
T Consensus 490 ~~p~-~pGvv~GLA~t~~Gg~~Ly~IE~~~~~G~Gkl~lTG~~lg~vmKESa~~A~sy~k 548 (675)
T TIGR02653 490 AGPP-KPGVVYAVTQNESGKVGLYRFEVQVSAGSGKHSVSGLGSNTTAKESIRVAFDYFK 548 (675)
T ss_pred CCCC-CCeEEEEEEEcCCCCeEEEEEEEEEeCCCCceeeccCCchHHHHHHHHHHHHHHH
Confidence 3444 38988876421 1 111 2346899999995555556666555555544
No 111
>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=20.19 E-value=1.2e+02 Score=24.16 Aligned_cols=36 Identities=11% Similarity=0.146 Sum_probs=29.9
Q ss_pred eecCCceeccCCHHHHHHHHHHHHHHHHhcCCCCcc
Q 031013 42 EYNPKVCTGAKSEQQSKLAARKYARIIQKLGFPAKF 77 (167)
Q Consensus 42 eY~P~v~tGakS~~~a~~a~~k~~~~l~~lg~~~~~ 77 (167)
.|==+++.+++|.++...+.+.+.+.|++.|+.+..
T Consensus 162 ~Y~DDili~s~~~~~~~~~l~~v~~~l~~~gl~ln~ 197 (213)
T cd01645 162 HYMDDILIASDLEGQLREIYEELRQTLLRWGLTIPP 197 (213)
T ss_pred EEcCCEEEEcCCHHHHHHHHHHHHHHHHHCCCEeCH
Confidence 344447788999999999999999999999987544
No 112
>PF08002 DUF1697: Protein of unknown function (DUF1697); InterPro: IPR012545 This family contains many hypothetical bacterial proteins.; PDB: 2HIY_B.
Probab=20.09 E-value=2.2e+02 Score=21.54 Aligned_cols=30 Identities=17% Similarity=0.152 Sum_probs=24.8
Q ss_pred EEecCceEEEEccCCHHHHHHHHHHHHHHH
Q 031013 130 LIFVSGKIVITGAKVRDETYTAFENIYPVL 159 (167)
Q Consensus 130 lIF~SGKvvitGaks~e~~~~a~~~i~~~L 159 (167)
+...||.|+++...+.+++...+++.+..-
T Consensus 38 Tyi~SGNvvf~~~~~~~~l~~~ie~~l~~~ 67 (137)
T PF08002_consen 38 TYIQSGNVVFESDRDPAELAAKIEKALEER 67 (137)
T ss_dssp EETTTTEEEEEESS-HHHHHHHHHHHHHHH
T ss_pred EEEeeCCEEEecCCChHHHHHHHHHHHHHh
Confidence 678999999998899999999888877643
No 113
>PF14294 DUF4372: Domain of unknown function (DUF4372)
Probab=20.06 E-value=1.8e+02 Score=19.98 Aligned_cols=28 Identities=18% Similarity=0.150 Sum_probs=25.7
Q ss_pred ceeccCCHHHHHHHHHHHHHHHHhcCCC
Q 031013 47 VCTGAKSEQQSKLAARKYARIIQKLGFP 74 (167)
Q Consensus 47 v~tGakS~~~a~~a~~k~~~~l~~lg~~ 74 (167)
+.+|.+|..|...++.--...|-.+|+.
T Consensus 48 QL~~~~SLRdI~~~l~a~~~klyHlG~~ 75 (76)
T PF14294_consen 48 QLTGRESLRDIEDCLNAHSSKLYHLGIK 75 (76)
T ss_pred HHcccCcHHHHHHHHHHhHHHHhhcCCC
Confidence 8899999999999999999999999874
Done!