Query 030718
Match_columns 172
No_of_seqs 145 out of 330
Neff 5.0
Searched_HMMs 46136
Date Fri Mar 29 03:33:04 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030718.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030718hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2925 Predicted translation 100.0 5.3E-46 1.1E-50 295.2 6.1 165 1-171 1-167 (167)
2 cd05792 S1_eIF1AD_like S1_eIF1 100.0 4.2E-38 9.1E-43 226.6 11.3 78 23-106 1-78 (78)
3 smart00652 eIF1a eukaryotic tr 100.0 4.8E-35 1E-39 212.6 11.7 83 18-107 1-83 (83)
4 PLN00208 translation initiatio 100.0 3E-34 6.5E-39 227.2 11.1 92 14-112 24-115 (145)
5 TIGR00523 eIF-1A eukaryotic/ar 100.0 3.6E-33 7.8E-38 208.9 10.9 87 16-108 13-99 (99)
6 cd04456 S1_IF1A_like S1_IF1A_l 100.0 6.6E-33 1.4E-37 199.4 11.1 78 23-106 1-78 (78)
7 PTZ00329 eukaryotic translatio 100.0 4.8E-33 1E-37 222.3 11.0 91 15-112 25-115 (155)
8 PRK04012 translation initiatio 100.0 7.2E-32 1.6E-36 202.2 11.7 87 15-108 14-100 (100)
9 cd05793 S1_IF1A S1_IF1A: Trans 100.0 4.7E-30 1E-34 184.1 10.9 77 23-106 1-77 (77)
10 PF01176 eIF-1a: Translation i 99.9 8.1E-26 1.8E-30 156.7 6.6 65 20-91 1-65 (65)
11 KOG3403 Translation initiation 99.9 1.8E-24 4E-29 167.8 4.2 91 15-112 25-115 (145)
12 COG0361 InfA Translation initi 99.8 6.6E-21 1.4E-25 136.4 8.6 72 18-96 3-75 (75)
13 TIGR00008 infA translation ini 99.7 2.1E-16 4.5E-21 111.4 8.7 62 23-91 6-68 (68)
14 PRK12442 translation initiatio 99.5 3E-14 6.5E-19 104.6 9.0 64 23-93 8-72 (87)
15 CHL00010 infA translation init 99.5 3.1E-13 6.6E-18 97.0 8.2 66 23-95 8-74 (78)
16 PRK00276 infA translation init 99.4 1.2E-12 2.5E-17 92.4 8.6 64 23-93 8-72 (72)
17 cd04451 S1_IF1 S1_IF1: Transla 99.0 1.6E-09 3.4E-14 74.2 7.5 61 24-91 3-64 (64)
18 cd04466 S1_YloQ_GTPase S1_YloQ 97.8 0.00015 3.2E-09 49.0 7.0 60 26-95 3-63 (68)
19 PRK12288 GTPase RsgA; Reviewed 95.0 0.095 2.1E-06 46.8 7.5 68 24-102 40-107 (347)
20 PRK00098 GTPase RsgA; Reviewed 94.7 0.13 2.9E-06 44.5 7.4 61 25-95 2-63 (298)
21 PRK12289 GTPase RsgA; Reviewed 93.6 0.34 7.4E-06 43.5 7.8 69 19-95 4-79 (352)
22 cd01854 YjeQ_engC YjeQ/EngC. 93.1 0.28 6.1E-06 42.2 6.4 65 26-103 1-66 (287)
23 PRK01889 GTPase RsgA; Reviewed 87.3 2.1 4.5E-05 38.2 6.7 67 21-102 26-97 (356)
24 PF01455 HupF_HypC: HupF/HypC 87.2 3.4 7.3E-05 28.9 6.4 54 25-100 6-63 (68)
25 cd04721 BAH_plant_1 BAH, or Br 86.1 1.4 3E-05 34.2 4.4 50 55-104 2-59 (130)
26 PRK10413 hydrogenase 2 accesso 84.6 4.5 9.7E-05 29.5 6.2 43 26-71 7-53 (82)
27 TIGR00074 hypC_hupF hydrogenas 81.7 5.2 0.00011 28.7 5.5 52 26-100 7-61 (76)
28 COG0298 HypC Hydrogenase matur 78.6 13 0.00028 27.3 6.7 65 26-112 7-74 (82)
29 PHA02945 interferon resistance 76.6 29 0.00062 25.8 8.3 63 16-91 6-70 (88)
30 PRK10409 hydrogenase assembly 72.0 12 0.00025 27.8 5.2 39 26-71 7-52 (90)
31 PF02736 Myosin_N: Myosin N-te 67.9 12 0.00026 23.5 3.9 32 17-49 7-38 (42)
32 KOG2107 Uncharacterized conser 66.6 9 0.00019 31.8 3.9 39 21-71 92-130 (179)
33 cd00164 S1_like S1_like: Ribos 62.5 26 0.00056 21.6 4.9 47 25-72 2-53 (65)
34 PF15057 DUF4537: Domain of un 61.7 25 0.00054 27.0 5.4 48 25-73 16-67 (124)
35 PF07039 DUF1325: SGF29 tudor- 57.5 18 0.0004 28.1 4.1 48 23-70 19-81 (130)
36 cd05795 Ribosomal_P0_L10e Ribo 56.4 18 0.00039 29.2 4.0 40 50-107 135-175 (175)
37 cd04479 RPA3 RPA3: A subfamily 55.5 31 0.00066 25.4 4.8 29 24-53 20-48 (101)
38 PF11302 DUF3104: Protein of u 52.8 23 0.0005 25.6 3.6 47 60-112 5-51 (75)
39 PTZ00454 26S protease regulato 51.4 43 0.00094 30.5 6.1 52 20-72 64-115 (398)
40 PF09038 53-BP1_Tudor: Tumour 51.0 49 0.0011 26.0 5.5 36 26-73 22-57 (122)
41 TIGR01439 lp_hng_hel_AbrB loop 50.4 6.4 0.00014 23.8 0.4 25 47-71 7-31 (43)
42 PF12859 Apc1: Anaphase-promot 49.7 21 0.00046 26.4 3.2 36 34-70 8-43 (105)
43 PF04014 Antitoxin-MazE: Antid 47.7 3.1 6.8E-05 26.4 -1.4 28 44-71 4-31 (47)
44 PF03803 Scramblase: Scramblas 45.7 1.4E+02 0.0029 24.2 7.7 65 18-92 111-177 (221)
45 PRK11642 exoribonuclease R; Pr 45.4 1.2E+02 0.0026 30.5 8.5 48 62-112 187-239 (813)
46 PTZ00361 26 proteosome regulat 44.6 61 0.0013 30.1 6.0 51 20-71 102-152 (438)
47 TIGR00638 Mop molybdenum-pteri 44.4 55 0.0012 21.3 4.3 50 21-70 6-58 (69)
48 cd04717 BAH_polybromo BAH, or 43.9 33 0.00072 25.6 3.5 52 59-110 2-63 (121)
49 PF08661 Rep_fac-A_3: Replicat 43.8 64 0.0014 23.8 5.0 33 24-56 23-56 (109)
50 PF04076 BOF: Bacterial OB fol 43.6 59 0.0013 24.4 4.8 46 24-70 39-84 (103)
51 COG1162 Predicted GTPases [Gen 43.2 49 0.0011 29.5 4.9 66 26-104 7-76 (301)
52 PF09902 DUF2129: Uncharacteri 42.8 28 0.0006 24.7 2.7 22 85-106 2-23 (71)
53 TIGR03689 pup_AAA proteasome A 42.7 41 0.00088 32.0 4.6 48 24-72 108-155 (512)
54 PF10017 Methyltransf_33: Hist 42.5 36 0.00078 25.9 3.6 27 78-104 82-108 (127)
55 cd04713 BAH_plant_3 BAH, or Br 39.3 87 0.0019 24.5 5.4 49 57-106 17-74 (146)
56 KOG2406 MADS box transcription 37.8 25 0.00054 34.0 2.4 46 27-72 104-158 (635)
57 cd06555 ASCH_PF0470_like ASC-1 37.4 1.2E+02 0.0026 23.1 5.7 54 32-103 15-68 (109)
58 PTZ00240 60S ribosomal protein 37.0 42 0.00091 30.2 3.6 44 50-111 149-193 (323)
59 PRK02302 hypothetical protein; 34.6 42 0.0009 24.9 2.7 22 85-106 8-29 (89)
60 cd05790 S1_Rrp40 S1_Rrp40: Rrp 34.6 1.2E+02 0.0026 22.0 5.1 52 18-72 3-61 (86)
61 PRK02886 hypothetical protein; 34.2 44 0.00095 24.7 2.7 22 85-106 6-27 (87)
62 KOG0650 WD40 repeat nucleolar 34.0 70 0.0015 31.6 4.7 43 45-95 514-556 (733)
63 PRK01191 rpl24p 50S ribosomal 33.5 63 0.0014 25.2 3.6 33 57-96 42-74 (120)
64 cd04714 BAH_BAHCC1 BAH, or Bro 33.1 72 0.0016 24.1 3.9 50 61-110 4-63 (121)
65 PRK03598 putative efflux pump 32.4 1.4E+02 0.003 25.8 6.0 56 32-94 227-282 (331)
66 PRK12281 rplX 50S ribosomal pr 31.7 62 0.0013 23.0 3.1 30 60-96 6-35 (76)
67 PF01287 eIF-5a: Eukaryotic el 31.5 71 0.0015 22.3 3.3 45 26-72 7-57 (69)
68 cd06253 M14_ASTE_ASPA_like_3 A 30.9 1.3E+02 0.0028 26.2 5.6 44 20-68 251-295 (298)
69 cd04719 BAH_Orc1p_animal BAH, 30.5 48 0.001 25.8 2.6 48 60-107 3-64 (128)
70 PF03459 TOBE: TOBE domain; I 30.3 70 0.0015 20.6 3.0 51 20-70 3-56 (64)
71 PF07093 SGT1: SGT1 protein; 29.9 27 0.00058 33.4 1.2 35 36-70 91-134 (589)
72 TIGR01080 rplX_A_E ribosomal p 29.9 85 0.0018 24.2 3.8 32 57-95 38-69 (114)
73 PTZ00194 60S ribosomal protein 28.9 81 0.0017 25.4 3.6 32 57-95 43-74 (143)
74 PF01426 BAH: BAH domain; Int 28.7 1.1E+02 0.0023 21.9 4.0 13 61-73 3-15 (119)
75 PF11776 DUF3315: Domain of un 28.7 68 0.0015 21.1 2.7 21 51-71 23-44 (52)
76 TIGR00358 3_prime_RNase VacB a 28.3 3.2E+02 0.0068 26.6 8.2 48 62-112 121-173 (654)
77 PF09378 HAS-barrel: HAS barre 27.6 67 0.0015 22.1 2.7 27 61-94 23-49 (91)
78 COG0198 RplX Ribosomal protein 26.9 88 0.0019 23.8 3.4 30 59-95 3-32 (104)
79 TIGR00230 sfsA sugar fermentat 26.6 4.1E+02 0.0088 22.7 7.8 74 26-108 12-100 (232)
80 PF08605 Rad9_Rad53_bind: Fung 26.5 2.8E+02 0.0062 21.7 6.3 42 26-71 27-70 (131)
81 PF12961 DUF3850: Domain of Un 26.3 1.1E+02 0.0024 21.8 3.6 30 62-93 30-59 (72)
82 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 25.5 2.2E+02 0.0048 19.3 5.6 53 18-71 3-65 (86)
83 PRK08577 hypothetical protein; 25.3 36 0.00079 25.9 1.1 23 49-71 15-37 (136)
84 PRK09521 exosome complex RNA-b 25.3 2.7E+02 0.0059 22.4 6.2 60 22-93 11-77 (189)
85 cd06251 M14_ASTE_ASPA_like_1 A 24.8 1.7E+02 0.0038 25.1 5.3 45 19-68 240-284 (287)
86 KOG4679 Uncharacterized protei 24.3 84 0.0018 30.2 3.4 50 19-70 329-389 (572)
87 cd04508 TUDOR Tudor domains ar 24.3 1.3E+02 0.0029 18.1 3.4 26 25-50 16-42 (48)
88 PTZ00007 (NAP-L) nucleosome as 24.1 93 0.002 28.2 3.5 16 96-111 258-273 (337)
89 PF08206 OB_RNB: Ribonuclease 24.0 61 0.0013 21.3 1.8 35 51-91 24-58 (58)
90 cd06529 S24_LexA-like Peptidas 23.8 49 0.0011 22.0 1.4 12 61-72 14-25 (81)
91 PRK05054 exoribonuclease II; P 23.3 5.1E+02 0.011 25.2 8.6 50 61-112 122-176 (644)
92 PRK00004 rplX 50S ribosomal pr 23.3 1E+02 0.0022 23.1 3.1 30 60-96 4-33 (105)
93 PF05610 DUF779: Protein of un 23.3 1.5E+02 0.0033 22.3 4.0 32 18-50 61-92 (95)
94 cd06254 M14_ASTE_ASPA_like_4 A 23.2 1.3E+02 0.0028 25.8 4.2 28 20-47 245-272 (288)
95 PRK04163 exosome complex RNA-b 23.2 2.3E+02 0.005 23.9 5.6 53 17-70 59-121 (235)
96 KOG2199 Signal transducing ada 23.0 33 0.00072 32.2 0.5 30 84-113 235-269 (462)
97 TIGR03673 rpl14p_arch 50S ribo 22.8 3E+02 0.0065 21.7 5.8 54 53-112 38-91 (131)
98 TIGR00156 conserved hypothetic 22.6 1.8E+02 0.0039 22.7 4.5 46 24-70 62-107 (126)
99 PF13030 DUF3891: Protein of u 22.6 69 0.0015 27.0 2.3 50 39-93 165-218 (221)
100 CHL00141 rpl24 ribosomal prote 22.0 1.2E+02 0.0026 21.9 3.1 33 57-96 5-37 (83)
101 PF12616 DUF3775: Protein of u 21.9 19 0.0004 25.8 -1.1 10 58-67 24-33 (75)
102 COG1222 RPT1 ATP-dependent 26S 21.5 3E+02 0.0064 25.8 6.3 91 18-112 68-179 (406)
103 PF03079 ARD: ARD/ARD' family; 20.9 1.3E+02 0.0029 24.1 3.5 31 31-71 99-129 (157)
104 smart00739 KOW KOW (Kyprides, 20.8 1.5E+02 0.0033 15.7 3.2 25 61-92 2-26 (28)
105 TIGR02063 RNase_R ribonuclease 20.8 5.9E+02 0.013 24.9 8.5 48 62-112 173-225 (709)
106 PRK10053 hypothetical protein; 20.8 2E+02 0.0042 22.7 4.4 45 25-70 67-111 (130)
107 smart00743 Agenet Tudor-like d 20.6 2.1E+02 0.0046 18.4 3.9 19 25-43 21-39 (61)
108 TIGR00061 L21 ribosomal protei 20.6 3E+02 0.0065 20.6 5.2 57 32-95 6-69 (101)
No 1
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=5.3e-46 Score=295.17 Aligned_cols=165 Identities=48% Similarity=0.756 Sum_probs=129.7
Q ss_pred CCCcchhHHHHHhhccCCCCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcC
Q 030718 1 MKGGRKNLKRAAEEQSLTLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKD 80 (172)
Q Consensus 1 M~~~Rk~~~~~~~e~~~~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~ 80 (172)
|..+||++.+++.++..+|.+.|+||||++++|||||+|++++|+.+||+||+||||+||||||+||||+|..+ .+.
T Consensus 1 ~atkkry~~q~v~de~~~le~~q~IaqVvqlrGsnlheV~danGq~~lvsmP~KfRksiWiRRg~FvvVdpiee---~~~ 77 (167)
T KOG2925|consen 1 MATKKRYLKQAVSDEDFTLEECQSIAQVVQLRGSNLHEVMDANGQNSLVSMPAKFRKSIWIRRGSFVVVDPIEE---EKS 77 (167)
T ss_pred CccchhhhcccccCCCcchhhhhhHHHHHhcCCcchhhhhhcCCceeeeeCCHhhhhceEEeeCCEEEEccccc---ccc
Confidence 67889999999998899999999999999999999999999999999999999999999999999999999654 345
Q ss_pred CCeeeEEEEEEeCHHHHHHHHhCCCCchhhhccCCCCCCchhh-hhhccCcccCC-CCCCCCCCCCCcccCcCCCCCccc
Q 030718 81 GSKVACIVTKVLFYEQVRALQKSTEWPEIFKSTNSDDANGSLE-RQACNHEENDQ-SESDDDDGLPPLEANINRMKPMEL 158 (172)
Q Consensus 81 ~~KvkgeIv~vl~~~qvk~Lrk~g~WP~~F~~~~~~~~~~~~~-~~~~~~~~~~~-~~~~ddD~l~~L~~N~NR~~~~~~ 158 (172)
|+||+|+|+|||..+||+.|+|.|+||+.|... +.+.... .+-+-+...+. ++++++|+.||||+||||.++...
T Consensus 78 g~KVkgeI~yVl~~d~vr~lqk~g~WPe~F~d~---alk~n~~~~t~e~~~dd~ls~sese~ddds~l~~ntnr~~~~~~ 154 (167)
T KOG2925|consen 78 GSKVKGEICYVLFFDQVRLLQKSGEWPEIFKDT---ALKPNEKSSTIEQHEDDGLSDSESEDDDDSPLQANTNRLRPFGV 154 (167)
T ss_pred CCccceEEEEEEccHHHHHHHHcCCcchhhhhc---ccccccccCCcccccccCCCCcccccccCCchhccccccCcccc
Confidence 999999999999999999999999999999874 1110000 00011111111 222344556999999999997655
Q ss_pred cccCccCccCCCC
Q 030718 159 QTESESDSESDTD 171 (172)
Q Consensus 159 ~~~s~~~~~~~~~ 171 (172)
-++++.++.+|+|
T Consensus 155 eee~e~~~~a~s~ 167 (167)
T KOG2925|consen 155 EEEAETDSGADSD 167 (167)
T ss_pred cccCcccccCCCC
Confidence 5555555444543
No 2
>cd05792 S1_eIF1AD_like S1_eIF1AD_like: eukaryotic translation initiation factor 1A domain containing protein (eIF1AD)-like, S1-like RNA-binding domain. eIF1AD is also known as MGC11102 protein. Little is known about the function of eIF1AD. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins, including translation initiation factor IF1A (also referred to as eIF1A in eukaryotes). eIF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors.
Probab=100.00 E-value=4.2e-38 Score=226.62 Aligned_cols=78 Identities=36% Similarity=0.683 Sum_probs=75.7
Q ss_pred cEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHh
Q 030718 23 QSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQK 102 (172)
Q Consensus 23 q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk 102 (172)
|+||+|++++|||+|+|+|+||+++||+||+||||+|||||||||||+||++ ++|++|+|+|||+++||++|++
T Consensus 1 q~i~rV~~~~G~n~~~V~~~dG~~~l~~iP~KfRk~iWIkrGd~VlV~p~~~------~~kvkgeIv~i~~~~qvk~L~k 74 (78)
T cd05792 1 QQIVRVLGSKGNNLHEVETPNGSRYLVSMPTKFRKNIWIKRGDFVLVEPIEE------GDKVKAEIVKILTRDHVKYIKE 74 (78)
T ss_pred CeEEEEEEcCCCcEEEEEcCCCCEEEEEechhhcccEEEEeCCEEEEEeccc------CCceEEEEEEEECHHHHHHHHH
Confidence 7899999999999999999999999999999999999999999999999975 5789999999999999999999
Q ss_pred CCCC
Q 030718 103 STEW 106 (172)
Q Consensus 103 ~g~W 106 (172)
+|+|
T Consensus 75 ~g~W 78 (78)
T cd05792 75 EGLW 78 (78)
T ss_pred cCCC
Confidence 9999
No 3
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=100.00 E-value=4.8e-35 Score=212.61 Aligned_cols=83 Identities=36% Similarity=0.530 Sum_probs=79.7
Q ss_pred CCCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHH
Q 030718 18 TLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQV 97 (172)
Q Consensus 18 ~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qv 97 (172)
.|++||+||+|++++|||+|+|+|+||.++||+|||||||+|||++||||||++|++ ++++|+|+|+|+++||
T Consensus 1 ~p~e~q~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~~~-------~~~kg~Iv~r~~~~~v 73 (83)
T smart00652 1 FKEDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWDF-------QDVKADIIYKYTKDEV 73 (83)
T ss_pred CCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEecCC-------CCCEEEEEEEeCHHHH
Confidence 478999999999999999999999999999999999999999999999999999975 2589999999999999
Q ss_pred HHHHhCCCCc
Q 030718 98 RALQKSTEWP 107 (172)
Q Consensus 98 k~Lrk~g~WP 107 (172)
|+|+++|+||
T Consensus 74 k~L~k~g~wp 83 (83)
T smart00652 74 RWLKKEGELP 83 (83)
T ss_pred HHHHHcCCCC
Confidence 9999999999
No 4
>PLN00208 translation initiation factor (eIF); Provisional
Probab=100.00 E-value=3e-34 Score=227.16 Aligned_cols=92 Identities=24% Similarity=0.319 Sum_probs=87.7
Q ss_pred hccCCCCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeC
Q 030718 14 EQSLTLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLF 93 (172)
Q Consensus 14 e~~~~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~ 93 (172)
-+++.|++||+||+|++++|||+|+|+|+||.++||+|||||||+|||++||+|||++|++ .++||+|+|+|+
T Consensus 24 ~el~~p~egq~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~VlVel~~~-------d~~KgdIv~ry~ 96 (145)
T PLN00208 24 RELIFKEDGQEYAQVLRMLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLRDY-------QDDKADVILKYM 96 (145)
T ss_pred eecccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCEEEEEccCC-------CCCEEEEEEEcC
Confidence 3489999999999999999999999999999999999999999999999999999999986 357899999999
Q ss_pred HHHHHHHHhCCCCchhhhc
Q 030718 94 YEQVRALQKSTEWPEIFKS 112 (172)
Q Consensus 94 ~~qvk~Lrk~g~WP~~F~~ 112 (172)
++||++|++.|+||+.|..
T Consensus 97 ~dqvr~Lkk~G~~P~~f~~ 115 (145)
T PLN00208 97 PDEARLLKAYGELPENTRL 115 (145)
T ss_pred HHHHHHHHHcCCCCcceee
Confidence 9999999999999999977
No 5
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=100.00 E-value=3.6e-33 Score=208.88 Aligned_cols=87 Identities=20% Similarity=0.287 Sum_probs=81.4
Q ss_pred cCCCCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 16 SLTLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 16 ~~~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
+|.++++|+||+|++++|||+|+|+|+||.++||+|||||||+|||++||||||+||++ ..++||+|+|+|+++
T Consensus 13 ~p~~~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp~d~------~~~~kg~Iv~r~~~~ 86 (99)
T TIGR00523 13 LPRKEEGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPWEF------QGDDKCDIVWRYTKT 86 (99)
T ss_pred CCCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEEccC------CCCccEEEEEEcCHH
Confidence 55667999999999999999999999999999999999999999999999999999985 235789999999999
Q ss_pred HHHHHHhCCCCch
Q 030718 96 QVRALQKSTEWPE 108 (172)
Q Consensus 96 qvk~Lrk~g~WP~ 108 (172)
||++|+++|+||+
T Consensus 87 qv~~L~~~g~~p~ 99 (99)
T TIGR00523 87 QVEWLKRKGYLKE 99 (99)
T ss_pred HHHHHHHcCCCCC
Confidence 9999999999994
No 6
>cd04456 S1_IF1A_like S1_IF1A_like: Translation initiation factor IF1A-like, S1-like RNA-binding domain. IF1A is also referred to as eIF1A in eukaryotes and aIF1A in archaea. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=100.00 E-value=6.6e-33 Score=199.39 Aligned_cols=78 Identities=35% Similarity=0.554 Sum_probs=75.0
Q ss_pred cEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHh
Q 030718 23 QSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQK 102 (172)
Q Consensus 23 q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk 102 (172)
|+||+|++++|||+|+|+|+||.++||+|||||||+|||++||||||+||++ ++++||+|+|+|+++||++|++
T Consensus 1 q~i~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~~------~~~~kg~Iv~r~~~~~vk~L~k 74 (78)
T cd04456 1 QQIVRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIEE------GEDVKADIIFVYCKDHVRSLKK 74 (78)
T ss_pred CeEEEEEEECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEEEeccc------CCCceEEEEEEeCHHHHHHHHH
Confidence 7899999999999999999999999999999999999999999999999974 4578999999999999999999
Q ss_pred CCCC
Q 030718 103 STEW 106 (172)
Q Consensus 103 ~g~W 106 (172)
+|+|
T Consensus 75 ~g~w 78 (78)
T cd04456 75 EGFL 78 (78)
T ss_pred cCcC
Confidence 9998
No 7
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=100.00 E-value=4.8e-33 Score=222.30 Aligned_cols=91 Identities=24% Similarity=0.321 Sum_probs=87.1
Q ss_pred ccCCCCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCH
Q 030718 15 QSLTLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFY 94 (172)
Q Consensus 15 ~~~~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~ 94 (172)
+++.|++||+||+|++++||++|+|+|+||.++||+|||||||+|||++||+|||++|++ .++||+|+|+|++
T Consensus 25 el~~~eegq~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~VlVel~~y-------d~~KgdIi~Ry~~ 97 (155)
T PTZ00329 25 ELVFKEEGQEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDF-------QDSKADVILKYTP 97 (155)
T ss_pred eeccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCEEEEeccCC-------CCCEEEEEEEcCH
Confidence 388999999999999999999999999999999999999999999999999999999986 2478999999999
Q ss_pred HHHHHHHhCCCCchhhhc
Q 030718 95 EQVRALQKSTEWPEIFKS 112 (172)
Q Consensus 95 ~qvk~Lrk~g~WP~~F~~ 112 (172)
+||++|++.|+||+.|..
T Consensus 98 devr~Lk~~g~~P~~~~~ 115 (155)
T PTZ00329 98 DEARALKQHGELPETAKI 115 (155)
T ss_pred HHHHHHHHcCCCCcceee
Confidence 999999999999999977
No 8
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=99.97 E-value=7.2e-32 Score=202.23 Aligned_cols=87 Identities=21% Similarity=0.254 Sum_probs=82.5
Q ss_pred ccCCCCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCH
Q 030718 15 QSLTLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFY 94 (172)
Q Consensus 15 ~~~~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~ 94 (172)
.+++|++||++|+|++++|||+|+|+|+||.++||+|||||||+|||++||||+|++|++ + +.||+|+|+|++
T Consensus 14 ~~~~p~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~-----~--~~kg~Iv~r~~~ 86 (100)
T PRK04012 14 RLPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDF-----Q--DEKADIIWRYTK 86 (100)
T ss_pred EccCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEeccc-----C--CCEEEEEEEcCH
Confidence 488999999999999999999999999999999999999999999999999999999985 2 468999999999
Q ss_pred HHHHHHHhCCCCch
Q 030718 95 EQVRALQKSTEWPE 108 (172)
Q Consensus 95 ~qvk~Lrk~g~WP~ 108 (172)
+||++|+++|++|+
T Consensus 87 ~qv~~L~~~g~~~~ 100 (100)
T PRK04012 87 PQVDWLRRKGYISE 100 (100)
T ss_pred HHHHHHHHcCCCCC
Confidence 99999999999984
No 9
>cd05793 S1_IF1A S1_IF1A: Translation initiation factor IF1A, also referred to as eIF1A in eukaryotes and aIF1A in archaea, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. IF1A is essential for translation initiation. eIF1A acts synergistically with eIF1 to mediate assembly of ribosomal initiation complexes at the initiation codon and maintain the accuracy of this process by recognizing and destabilizing aberrant preinitiation complexes from the mRNA. Without eIF1A and eIF1, 43S ribosomal preinitiation complexes can bind to the cap-proximal region, but are unable to reach the initiation codon. eIF1a also enhances the formation of 5'-terminal complexes in the presence of other translation initiation factors. This protein family is only found in eukaryotes and archaea.
Probab=99.97 E-value=4.7e-30 Score=184.13 Aligned_cols=77 Identities=23% Similarity=0.280 Sum_probs=73.1
Q ss_pred cEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHh
Q 030718 23 QSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQK 102 (172)
Q Consensus 23 q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk 102 (172)
|++|+|++++|||+|+|+|+||.++||+|||||||+|||++||||+|++|++ +++||+|+|+|+++||++|++
T Consensus 1 e~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~-------d~~kg~Iv~r~~~~~v~~L~~ 73 (77)
T cd05793 1 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDF-------QDDKADIIYKYTPDEVRWLKR 73 (77)
T ss_pred CEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEeccc-------cCCEEEEEEEcCHHHHHHHHH
Confidence 6899999999999999999999999999999999999999999999999975 357899999999999999999
Q ss_pred CCCC
Q 030718 103 STEW 106 (172)
Q Consensus 103 ~g~W 106 (172)
+|++
T Consensus 74 ~g~i 77 (77)
T cd05793 74 KGEL 77 (77)
T ss_pred cCcC
Confidence 9874
No 10
>PF01176 eIF-1a: Translation initiation factor 1A / IF-1; InterPro: IPR006196 The S1 domain of around 70 amino acids, originally identified in ribosomal protein S1, is found in a large number of RNA-associated proteins. It has been shown that S1 proteins bind RNA through their S1 domains with some degree of sequence specificity. This type of S1 domain is found in translation initiation factor 1. The solution structure of one S1 RNA-binding domain from Escherichia coli polynucleotide phosphorylase has been determined []. It displays some similarity with the cold shock domain (CSD) (IPR002059 from INTERPRO). Both the S1 and the CSD domain consist of an antiparallel beta barrel of the same topology with 5 beta strands. This fold is also shared by many other proteins of unrelated function and is known as the OB fold. However, the S1 and CSD fold can be distinguished from the other OB folds by the presence of a short 3(10) helix at the end of strand 3. This unique feature is likely to form a part of the DNA/RNA-binding site. This entry is specific for bacterial, chloroplastic and eukaryotic IF-1 type S1 domains.; GO: 0003723 RNA binding, 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1JT8_A 3I4O_A 1AH9_A 1ZO1_W 1D7Q_A 2OQK_A 2DGY_A 1HR0_W.
Probab=99.92 E-value=8.1e-26 Score=156.73 Aligned_cols=65 Identities=40% Similarity=0.621 Sum_probs=57.4
Q ss_pred CCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEE
Q 030718 20 QDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKV 91 (172)
Q Consensus 20 ~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~v 91 (172)
+++|+||+|++++|||+|+|+|+||.++||+||||||++|||++||||||++|++ ++++|+|+|+
T Consensus 1 ee~e~~~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~~-------d~~kG~Ii~r 65 (65)
T PF01176_consen 1 EEGEVIGRVTEMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPY-------DKVKGRIIYR 65 (65)
T ss_dssp STTEEEEEEEEEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTT-------CTTEEEEEEE
T ss_pred CCcEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEeccc-------CCCeEEEEEC
Confidence 5799999999999999999999999999999999999999999999999999975 2578999986
No 11
>KOG3403 consensus Translation initiation factor 1A (eIF-1A) [Translation, ribosomal structure and biogenesis]
Probab=99.90 E-value=1.8e-24 Score=167.81 Aligned_cols=91 Identities=23% Similarity=0.314 Sum_probs=85.5
Q ss_pred ccCCCCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCH
Q 030718 15 QSLTLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFY 94 (172)
Q Consensus 15 ~~~~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~ 94 (172)
++...++||+|+||++|+||.+++|.|.||..|||+|.||+||+|||..||+|||...++ ++ -+|+|+..|++
T Consensus 25 eLvfkEegqeYaQv~kmLGnGr~e~~CfDGvkR~~hiRGklrkkVwi~~GDIiLv~lRD~-----qd--~kaDvilKY~~ 97 (145)
T KOG3403|consen 25 ELVFKEEGQEYAQVIKMLGNGRLEASCFDGVKRLCHIRGKLRKKVWINQGDIILVGLRDY-----QD--DKADVILKYMP 97 (145)
T ss_pred heeehhcchhHHHHHhhhcCCcEEEEEecchhhhhhhhccceeeEeecCCCEEEEeeecc-----cc--cccceehhhCh
Confidence 377888999999999999999999999999999999999999999999999999999986 34 36999999999
Q ss_pred HHHHHHHhCCCCchhhhc
Q 030718 95 EQVRALQKSTEWPEIFKS 112 (172)
Q Consensus 95 ~qvk~Lrk~g~WP~~F~~ 112 (172)
++++.|+..|.+|+.|..
T Consensus 98 dEar~LK~~Gelpe~~k~ 115 (145)
T KOG3403|consen 98 DEARILKAYGELPENAKI 115 (145)
T ss_pred HHHHHHHhcCcCCccccc
Confidence 999999999999998876
No 12
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=99.84 E-value=6.6e-21 Score=136.39 Aligned_cols=72 Identities=15% Similarity=0.092 Sum_probs=66.4
Q ss_pred CCCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHH
Q 030718 18 TLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQ 96 (172)
Q Consensus 18 ~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~q 96 (172)
.|+++++.++|++++||++|.|+|.||..++|+||||+|+ +|||..||.|+|++|++| . -+|.|+|+|+++|
T Consensus 3 ~~d~~e~~g~V~e~L~~~~f~v~~edg~~~~ahI~GKmr~~~i~I~~GD~V~Ve~~~~d-----~--~kg~I~~Ry~~~~ 75 (75)
T COG0361 3 KPDEIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYD-----L--TKGRIVYRYKKDE 75 (75)
T ss_pred cccccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEecccc-----c--ccccEEEEecCCC
Confidence 4578999999999999999999999999999999999999 999999999999999872 4 3699999999864
No 13
>TIGR00008 infA translation initiation factor IF-1. This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (pfam00575).
Probab=99.68 E-value=2.1e-16 Score=111.37 Aligned_cols=62 Identities=18% Similarity=0.051 Sum_probs=57.0
Q ss_pred cEEEEEEeecCCceEEEEeCCCCEEEEEeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEE
Q 030718 23 QSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKV 91 (172)
Q Consensus 23 q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~v 91 (172)
++.++|++++||..|.|+|.||.++||+||||||+ +|||..||.|+|++|+++ . -||.|+|+
T Consensus 6 e~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd-----~--tkgrIi~R 68 (68)
T TIGR00008 6 EMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYD-----L--TRGRITYR 68 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECccc-----C--CcEeEEeC
Confidence 57899999999999999999999999999999995 999999999999999873 3 36999985
No 14
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=99.55 E-value=3e-14 Score=104.57 Aligned_cols=64 Identities=13% Similarity=-0.056 Sum_probs=59.6
Q ss_pred cEEEEEEeecCCceEEEEeCCCCEEEEEeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeC
Q 030718 23 QSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLF 93 (172)
Q Consensus 23 q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~ 93 (172)
++.+.|+++++|..|.|.|.+|.++||+|+||||+ +|||..||.|+|++|+++ . -+|.|+|+|.
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYD-----l--tkGRIiyR~~ 72 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYD-----L--TKGRINFRHK 72 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECccc-----C--CceeEEEEec
Confidence 57899999999999999999999999999999999 999999999999999873 3 3699999997
No 15
>CHL00010 infA translation initiation factor 1
Probab=99.46 E-value=3.1e-13 Score=97.01 Aligned_cols=66 Identities=18% Similarity=0.062 Sum_probs=58.9
Q ss_pred cEEEEEEeecCCceEEEEeCCCCEEEEEeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 23 QSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 23 q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
++.++|++.+|++.|.|.|.+|..++|+++||||+ ++|+..||+|.|++|.+ ++ -+|.|+|+|...
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~-----~~--~~g~Ii~r~~~~ 74 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPY-----DL--TKGRIIYRLRNK 74 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEccc-----CC--CeEEEEEEecCC
Confidence 46799999999999999999999999999999997 69999999999999864 23 369999999753
No 16
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=99.42 E-value=1.2e-12 Score=92.42 Aligned_cols=64 Identities=22% Similarity=0.092 Sum_probs=57.1
Q ss_pred cEEEEEEeecCCceEEEEeCCCCEEEEEeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeC
Q 030718 23 QSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLF 93 (172)
Q Consensus 23 q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~ 93 (172)
+..++|++.+|++.|.|.|.+|..++|+++||||+ ++|+..||+|+|++|.+ +++ +|.|+|+|.
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~-----~~~--~g~Iv~r~~ 72 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPY-----DLT--KGRITYRHK 72 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEEEccc-----CCC--eEEEEEEeC
Confidence 56799999999999999999999999999999994 89999999999999864 233 599999983
No 17
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=99.01 E-value=1.6e-09 Score=74.24 Aligned_cols=61 Identities=18% Similarity=0.053 Sum_probs=52.6
Q ss_pred EEEEEEeecCCceEEEEeCCCCEEEEEeecccc-ceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEE
Q 030718 24 SIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQ-KSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKV 91 (172)
Q Consensus 24 ~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfR-K~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~v 91 (172)
+-++|++..|++.|.|.|.+|..++|++++||| +++|+..||+|+++++.+ ++. +|.|+|+
T Consensus 3 ~~G~Vi~~~~g~~~~V~~~~g~~~~c~~rGklr~~~~~~~vGD~V~~~~~~~-----~~~--~g~I~~~ 64 (64)
T cd04451 3 MEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPY-----DLT--KGRIVYR 64 (64)
T ss_pred EEEEEEEEeCCCEEEEEeCCCCEEEEEECceeecCCcccCCCCEEEEEEeec-----CCC--EEEEEEC
Confidence 458999999989999999999999999999999 489999999999998743 232 5899884
No 18
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=97.75 E-value=0.00015 Score=48.98 Aligned_cols=60 Identities=17% Similarity=0.162 Sum_probs=47.7
Q ss_pred EEEEeecCCceEEEEeCCCCEEEEEeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 26 MQVVSLRGSNLIEVLDAKDEKSLALFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 26 ~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
++|++..| +.|.|.+.+|..++|.++++|++ ..++-.||+|++++++ .+ .+-|+.+|-..
T Consensus 3 grVv~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VGD~V~~~~~~------~~---~~~I~~vl~R~ 63 (68)
T cd04466 3 GLIIKAIG-GFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEPED------DG---EGVIEEILPRK 63 (68)
T ss_pred EEEEEEEC-CEEEEEeCCCeEEEEEEccccccCCCCCCCCcEEEEEECC------CC---cEEEEEEeccc
Confidence 68888887 67889998788999999999984 5789999999998742 12 47788887543
No 19
>PRK12288 GTPase RsgA; Reviewed
Probab=95.05 E-value=0.095 Score=46.83 Aligned_cols=68 Identities=19% Similarity=0.094 Sum_probs=51.6
Q ss_pred EEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHh
Q 030718 24 SIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQK 102 (172)
Q Consensus 24 ~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk 102 (172)
..++|++..|+ .|.|.+.+|+.+.|.++++|++ +-.||+|++++.+. ......|.|..||.+. ..|.+
T Consensus 40 ~~g~Vi~~~~~-~~~v~~~~g~~~~~~~~g~~~~---~~vGD~V~~~~~~~-----~~~~~~~~I~~il~R~--n~L~R 107 (347)
T PRK12288 40 QEGIVISRFGQ-HADVEAADGEVHRCNIRRTIRS---LVTGDRVVWRPGKE-----ALEGVSGVVEAVHPRT--SVLTR 107 (347)
T ss_pred cceEEEEEECC-EEEEEeCCCcEEEEEecccCCC---CCCCcEEEEEeCCC-----cccccceEEEEEeccc--ceEEC
Confidence 57999999885 6789999999999999999975 77899999985321 0011248899998877 45543
No 20
>PRK00098 GTPase RsgA; Reviewed
Probab=94.73 E-value=0.13 Score=44.49 Aligned_cols=61 Identities=11% Similarity=0.049 Sum_probs=45.3
Q ss_pred EEEEEeecCCceEEEEeCCCCEEEEEeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 25 IMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 25 I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
-++|++..| +.|.|.+.+|..+.|.++++|++ +.-+-.||+|+|++.+ ++ .|-|..|+.+.
T Consensus 2 ~g~v~~~~~-~~~~v~~~~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~-------~~--~g~i~~i~~R~ 63 (298)
T PRK00098 2 EGLIIKALG-GFYYVESEDGQVYQCRARGKFRKKTNTPAVGDRVEFSAEN-------ND--EGVILEIHERK 63 (298)
T ss_pred eEEEEEEEC-CEEEEEECCCCEEEEEeccccccCCCCcCCCCEEEEEECC-------CC--cEEEEEEeCCC
Confidence 378888886 57788888899999999999984 3345579999998631 11 36677676655
No 21
>PRK12289 GTPase RsgA; Reviewed
Probab=93.58 E-value=0.34 Score=43.46 Aligned_cols=69 Identities=19% Similarity=0.197 Sum_probs=49.1
Q ss_pred CCCCcEEEEEEeecCCceEEEEeCCC------CEEEEEeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEE
Q 030718 19 LQDGQSIMQVVSLRGSNLIEVLDAKD------EKSLALFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKV 91 (172)
Q Consensus 19 p~e~q~I~rV~~~~G~nl~eV~~~dG------~~~L~~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~v 91 (172)
+...+..++|++..|+ .|.|.+.+| ...+|...++||+ ..-+-.||.|++++.++ .+ ..|-|..|
T Consensus 4 ~~~~~~~g~V~~~~~~-~y~V~~~~~~~~~~~~~~~~~~r~~lk~~~~~~~vGD~V~~~~~~~-----~~--~~~~I~~v 75 (352)
T PRK12289 4 TTTSQLLGTVVAVQAN-FYRVQLDEPQNLNPPSLLLCTRRTRLKKIGQQVMVGDRVIVEEPDW-----QG--QRGAIAEV 75 (352)
T ss_pred cccCcccEEEEEEECC-EEEEEECCCcccCcceEEEEEcccccccCCCCcccCCEEEEeecCC-----CC--CceEEEEE
Confidence 4556788999999885 567877654 4789999999985 23378899999985331 12 24777777
Q ss_pred eCHH
Q 030718 92 LFYE 95 (172)
Q Consensus 92 l~~~ 95 (172)
|-+.
T Consensus 76 lpR~ 79 (352)
T PRK12289 76 LPRK 79 (352)
T ss_pred eccc
Confidence 7655
No 22
>cd01854 YjeQ_engC YjeQ/EngC. YjeQ (YloQ in Bacillus subtilis) represents a protein family whose members are broadly conserved in bacteria and have been shown to be essential to the growth of E. coli and B. subtilis. Proteins of the YjeQ family contain all sequence motifs typical of the vast class of P-loop-containing GTPases, but show a circular permutation, with a G4-G1-G3 pattern of motifs as opposed to the regular G1-G3-G4 pattern seen in most GTPases. All YjeQ family proteins display a unique domain architecture, which includes an N-terminal OB-fold RNA-binding domain, the central permuted GTPase domain, and a zinc knuckle-like C-terminal cysteine domain. This domain architecture suggests a role for YjeQ as a regulator of translation.
Probab=93.14 E-value=0.28 Score=42.25 Aligned_cols=65 Identities=17% Similarity=0.236 Sum_probs=47.8
Q ss_pred EEEEeecCCceEEEEeCCCCEEEEEeeccccce-EEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHhC
Q 030718 26 MQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKS-MWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQKS 103 (172)
Q Consensus 26 ~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~-vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk~ 103 (172)
++|++..| +.|.|.+. |..+.|.++++|++. .-+-.||+|++++.+ + -.|.|..||.+. ..|.+.
T Consensus 1 g~v~~~~~-~~~~v~~~-~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~-------~--~~~~i~~i~~R~--~~l~R~ 66 (287)
T cd01854 1 GRVIAVHG-GFYDVETE-GGELRCRARGKLRKKGIKPVVGDWVEVEPDD-------D--GEGVIVRVLPRK--NLLSRP 66 (287)
T ss_pred CEEEEEEC-CEEEEEEC-CeEEEEEeccccccCCCCccCCCEEEEEecC-------C--CcEEEEEEECCC--ceEEcc
Confidence 46777777 57788875 788999999999853 337789999998632 2 248888888776 345443
No 23
>PRK01889 GTPase RsgA; Reviewed
Probab=87.28 E-value=2.1 Score=38.23 Aligned_cols=67 Identities=16% Similarity=0.169 Sum_probs=47.9
Q ss_pred CCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccc-----eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 21 DGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQK-----SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 21 e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK-----~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
++-..++|++..|+ .|.|.+.+| .+.|.+.+|||. +--+-.||.|++++ + + .|.|..||.+.
T Consensus 26 ~~~~~g~v~~~~~~-~~~v~~~~~-~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~~-~-------~---~g~I~~i~pR~ 92 (356)
T PRK01889 26 EGLEPGRVVEEHRS-GYVVATEEG-EVRAEVSGKWRHEAFPPGDRPAVGDWVLLDN-E-------K---KARIVRLLPRR 92 (356)
T ss_pred cCCccEEEEEEECC-EEEEEECCc-EEEEEecchhhccccccCCCCccCcEEEEec-C-------C---ceEEEEEECCC
Confidence 44567999999874 667877665 567999999984 22356899999984 1 1 37888888777
Q ss_pred HHHHHHh
Q 030718 96 QVRALQK 102 (172)
Q Consensus 96 qvk~Lrk 102 (172)
. .|.+
T Consensus 93 ~--~L~R 97 (356)
T PRK01889 93 S--LFSR 97 (356)
T ss_pred c--eEEc
Confidence 3 5544
No 24
>PF01455 HupF_HypC: HupF/HypC family; InterPro: IPR001109 The large subunit of [NiFe]-hydrogenase, as well as other nickel metalloenzymes, is synthesised as a precursor devoid of the metalloenzyme active site. This precursor then undergoes a complex post-translational maturation process that requires a number of accessory proteins. The hydrogenase expression/formation proteins (HupF/HypC) form a family of small proteins that are hydrogenase precursor-specific chaperones required for this maturation process []. They are believed to keep the hydrogenase precursor in a conformation accessible for metal incorporation [, ].; PDB: 3D3R_A 2Z1C_C 2OT2_A.
Probab=87.17 E-value=3.4 Score=28.85 Aligned_cols=54 Identities=17% Similarity=0.178 Sum_probs=34.8
Q ss_pred EEEEEee-cCCceEEEEeCCCCEEEEE---eeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHH
Q 030718 25 IMQVVSL-RGSNLIEVLDAKDEKSLAL---FPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRAL 100 (172)
Q Consensus 25 I~rV~~~-~G~nl~eV~~~dG~~~L~~---iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~L 100 (172)
=+||++. .+.+.-.|. ..|.++-+. +|. ++.||||||.. |-.+.++++++.+..
T Consensus 6 P~~Vv~v~~~~~~A~v~-~~G~~~~V~~~lv~~-------v~~Gd~VLVHa--------------G~Ai~~ideeeA~e~ 63 (68)
T PF01455_consen 6 PGRVVEVDEDGGMAVVD-FGGVRREVSLALVPD-------VKVGDYVLVHA--------------GFAIEKIDEEEAEET 63 (68)
T ss_dssp EEEEEEEETTTTEEEEE-ETTEEEEEEGTTCTS-------B-TT-EEEEET--------------TEEEEEE-HHHHHHH
T ss_pred cEEEEEEeCCCCEEEEE-cCCcEEEEEEEEeCC-------CCCCCEEEEec--------------ChhheeCCHHHHHHH
Confidence 3678888 345555554 457777664 444 89999999994 456778888877664
No 25
>cd04721 BAH_plant_1 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=86.13 E-value=1.4 Score=34.25 Aligned_cols=50 Identities=14% Similarity=0.086 Sum_probs=33.4
Q ss_pred ccceEEEeeCCEEEEecCCcch------hhc--CCCeeeEEEEEEeCHHHHHHHHhCC
Q 030718 55 FQKSMWIKRGSFVVVDESGKEK------AIK--DGSKVACIVTKVLFYEQVRALQKST 104 (172)
Q Consensus 55 fRK~vWIkrGD~VlV~p~~~~~------~~e--~~~KvkgeIv~vl~~~qvk~Lrk~g 104 (172)
.|+-++||.||+|+|.+.+... .+. .++.....+.|-++++++..+++..
T Consensus 2 ~r~~~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~ 59 (130)
T cd04721 2 CRNGVTISVHDFVYVLSEEEDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPD 59 (130)
T ss_pred ccCCEEEECCCEEEEeCCCCCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCC
Confidence 3788999999999998643000 001 1233477888889999998865544
No 26
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=84.56 E-value=4.5 Score=29.45 Aligned_cols=43 Identities=14% Similarity=-0.003 Sum_probs=27.7
Q ss_pred EEEEeecCCc-eEEEEeCCCCEEEEE---eeccccceEEEeeCCEEEEec
Q 030718 26 MQVVSLRGSN-LIEVLDAKDEKSLAL---FPAKFQKSMWIKRGSFVVVDE 71 (172)
Q Consensus 26 ~rV~~~~G~n-l~eV~~~dG~~~L~~---iP~KfRK~vWIkrGD~VlV~p 71 (172)
+||++..|.. .+-.....|.++-++ +|.- ...++.||||||..
T Consensus 7 ~kVi~i~~~~~~~A~vd~~Gv~r~V~l~Lv~~~---~~~~~vGDyVLVHa 53 (82)
T PRK10413 7 GQVLAVGEDIHQLAQVEVCGIKRDVNIALICEG---NPADLLGQWVLVHV 53 (82)
T ss_pred eEEEEECCCCCcEEEEEcCCeEEEEEeeeeccC---CcccccCCEEEEec
Confidence 6788887764 333344567777775 4321 02478999999995
No 27
>TIGR00074 hypC_hupF hydrogenase assembly chaperone HypC/HupF. An additional proposed function is to shuttle the iron atom that has been liganded at the HypC/HypD complex to the precursor of the large hydrogenase (HycE) subunit. PubMed:12441107.
Probab=81.75 E-value=5.2 Score=28.68 Aligned_cols=52 Identities=25% Similarity=0.187 Sum_probs=32.9
Q ss_pred EEEEeecCCceEEEEeCCCCEEEEE---eeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHH
Q 030718 26 MQVVSLRGSNLIEVLDAKDEKSLAL---FPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRAL 100 (172)
Q Consensus 26 ~rV~~~~G~nl~eV~~~dG~~~L~~---iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~L 100 (172)
+||++..|+ .-.| ...|.++-++ +| -++.||||||.. |-.+.++..++.+..
T Consensus 7 ~~V~~i~~~-~A~v-~~~G~~~~v~l~lv~-------~~~vGD~VLVH~--------------G~Ai~~ide~eA~e~ 61 (76)
T TIGR00074 7 GQVVEIDEN-IALV-EFCGIKRDVSLDLVG-------EVKVGDYVLVHV--------------GFAISVLDEEEARET 61 (76)
T ss_pred eEEEEEcCC-EEEE-EcCCeEEEEEEEeeC-------CCCCCCEEEEec--------------ChhhhhCCHHHHHHH
Confidence 678888774 3333 3456665544 44 278999999995 334556677765544
No 28
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=78.60 E-value=13 Score=27.32 Aligned_cols=65 Identities=18% Similarity=0.242 Sum_probs=43.2
Q ss_pred EEEEeecCCceEEEEeCCCCEEEEE---eeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHh
Q 030718 26 MQVVSLRGSNLIEVLDAKDEKSLAL---FPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQK 102 (172)
Q Consensus 26 ~rV~~~~G~nl~eV~~~dG~~~L~~---iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk 102 (172)
+||++.-++|.+-+...-|.+|-+. ++. =+|.||||||.. |--+.++..++.|.-
T Consensus 7 gqI~~I~~~~~~A~Vd~gGvkreV~l~Lv~~------~v~~GdyVLVHv--------------GfAi~~idEeeAket-- 64 (82)
T COG0298 7 GQIVEIDDNNHLAIVDVGGVKREVNLDLVGE------EVKVGDYVLVHV--------------GFAMSKIDEEEAKET-- 64 (82)
T ss_pred cEEEEEeCCCceEEEEeccEeEEEEeeeecC------ccccCCEEEEEe--------------eEEEeecCHHHHHHH--
Confidence 5788888888777777788666554 554 478999999984 444566677765543
Q ss_pred CCCCchhhhc
Q 030718 103 STEWPEIFKS 112 (172)
Q Consensus 103 ~g~WP~~F~~ 112 (172)
...|-+-|..
T Consensus 65 le~l~e~~~~ 74 (82)
T COG0298 65 LEALQEMFDA 74 (82)
T ss_pred HHHHHHHHHh
Confidence 2334444433
No 29
>PHA02945 interferon resistance protein; Provisional
Probab=76.57 E-value=29 Score=25.81 Aligned_cols=63 Identities=17% Similarity=0.122 Sum_probs=41.7
Q ss_pred cCCCCCCcE-EEEEEeecCCceEEEEeC-CCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEE
Q 030718 16 SLTLQDGQS-IMQVVSLRGSNLIEVLDA-KDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKV 91 (172)
Q Consensus 16 ~~~p~e~q~-I~rV~~~~G~nl~eV~~~-dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~v 91 (172)
+..|++|+. ||+|.. .+...|--... .|.+-++.+---..-.=|||--|+| + |.|+.+-|+++
T Consensus 6 y~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l-~-----------GqkvV~KVirV 70 (88)
T PHA02945 6 YSLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKL-V-----------GKTVKVKVIRV 70 (88)
T ss_pred ecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEe-c-----------CCEEEEEEEEE
Confidence 467999985 677777 66555543333 3666665554335577899987777 2 46677777776
No 30
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=71.96 E-value=12 Score=27.79 Aligned_cols=39 Identities=15% Similarity=0.150 Sum_probs=26.0
Q ss_pred EEEEeecCCceEEEEeCCCCEEEEEeeccccceE-------EEeeCCEEEEec
Q 030718 26 MQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSM-------WIKRGSFVVVDE 71 (172)
Q Consensus 26 ~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~v-------WIkrGD~VlV~p 71 (172)
+||++..|+ .-+....|.++-++|- .+ .++.||||||..
T Consensus 7 ~kVv~i~~~--~A~vd~~Gv~reV~l~-----Lv~~~~~~~~~~vGDyVLVHa 52 (90)
T PRK10409 7 GQIRTIDGN--QAKVDVCGIQRDVDLT-----LVGSCDENGQPRVGQWVLVHV 52 (90)
T ss_pred eEEEEEcCC--eEEEEcCCeEEEEEEe-----eecccCCCCccCCCCEEEEec
Confidence 678887775 3444456777766542 11 468999999995
No 31
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=67.90 E-value=12 Score=23.45 Aligned_cols=32 Identities=6% Similarity=0.110 Sum_probs=25.0
Q ss_pred CCCCCCcEEEEEEeecCCceEEEEeCCCCEEEE
Q 030718 17 LTLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLA 49 (172)
Q Consensus 17 ~~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~ 49 (172)
+-|.++=+.|.|+. ..++.+.|.+.+|+++.+
T Consensus 7 pD~~egfv~g~I~~-~~g~~vtV~~~~G~~~tv 38 (42)
T PF02736_consen 7 PDPKEGFVKGEIIE-EEGDKVTVKTEDGKEVTV 38 (42)
T ss_dssp EESSSSEEEEEEEE-EESSEEEEEETTTEEEEE
T ss_pred eCCcccEEEEEEEE-EcCCEEEEEECCCCEEEe
Confidence 45677778999994 455669999999998765
No 32
>KOG2107 consensus Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=66.55 E-value=9 Score=31.77 Aligned_cols=39 Identities=18% Similarity=0.509 Sum_probs=29.8
Q ss_pred CCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEec
Q 030718 21 DGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDE 71 (172)
Q Consensus 21 e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p 71 (172)
+.+.|--|+ -|+.-|.|.+.|+.-. +||+.+||+|++-+
T Consensus 92 ~deeiR~il--~GtgYfDVrd~dd~WI----------Ri~vekGDlivlPa 130 (179)
T KOG2107|consen 92 EDEEIRYIL--EGTGYFDVRDKDDQWI----------RIFVEKGDLIVLPA 130 (179)
T ss_pred chhheEEEe--ecceEEeeccCCCCEE----------EEEEecCCEEEecC
Confidence 344554443 5889999999997655 49999999999764
No 33
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=62.53 E-value=26 Score=21.60 Aligned_cols=47 Identities=23% Similarity=0.065 Sum_probs=30.3
Q ss_pred EEEEEeecCCceEEEEeCCCCEEEEEeeccccc-----eEEEeeCCEEEEecC
Q 030718 25 IMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQK-----SMWIKRGSFVVVDES 72 (172)
Q Consensus 25 I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK-----~vWIkrGD~VlV~p~ 72 (172)
.|+|++...+. +.|....|.+-++.++.-... .-+++.||.|.|...
T Consensus 2 ~g~V~~v~~~g-~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~ 53 (65)
T cd00164 2 TGKVVSITKFG-VFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVL 53 (65)
T ss_pred EEEEEEEEeee-EEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEE
Confidence 46777777544 447777777777765543322 356788888877754
No 34
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=61.71 E-value=25 Score=27.00 Aligned_cols=48 Identities=10% Similarity=-0.121 Sum_probs=36.1
Q ss_pred EEEEEeecCCceEEEEeCCCCEEEEE----eeccccceEEEeeCCEEEEecCC
Q 030718 25 IMQVVSLRGSNLIEVLDAKDEKSLAL----FPAKFQKSMWIKRGSFVVVDESG 73 (172)
Q Consensus 25 I~rV~~~~G~nl~eV~~~dG~~~L~~----iP~KfRK~vWIkrGD~VlV~p~~ 73 (172)
.++|.+...+..|.|+..+|.+..+. |+...-..-=++.||+||+- |+
T Consensus 16 ~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~-~~ 67 (124)
T PF15057_consen 16 PGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALSDAMRHSLQVGDKVLAP-WE 67 (124)
T ss_pred eEEEEEccCCCEEEEEECCCCEEEeChHHeEEccCcccCcCCCCCEEEEe-cC
Confidence 56788888999999999888776663 34444445668999999998 54
No 35
>PF07039 DUF1325: SGF29 tudor-like domain; InterPro: IPR010750 SAGA-associated factor 29 is involved in transcriptional regulation, probably through association with histone acetyltransferase (HAT) complexes like the TFTC-HAT or STAGA complexes. It also may be involved in MYC-mediated oncogenic transformation. It is a component of the ATAC complex, which is a complex with histone acetyltransferase activity on histones H3 and H4 []. This entry represents a domain found in yeast and human SAGA-associated factor 29 proteins that is related to the tudor domain. ; PDB: 3MP6_A 3MP1_A 3MP8_A 3MET_B 3ME9_A 3MEU_B 3MEA_A 3MEV_B 3LX7_A 3MEW_A.
Probab=57.55 E-value=18 Score=28.10 Aligned_cols=48 Identities=23% Similarity=0.224 Sum_probs=28.8
Q ss_pred cEEEEEEeecCCc-eEEEEeCCCC----------EEEEEeecccc----ceEEEeeCCEEEEe
Q 030718 23 QSIMQVVSLRGSN-LIEVLDAKDE----------KSLALFPAKFQ----KSMWIKRGSFVVVD 70 (172)
Q Consensus 23 q~I~rV~~~~G~n-l~eV~~~dG~----------~~L~~iP~KfR----K~vWIkrGD~VlV~ 70 (172)
=++|+|++--|.+ .|+|+++|-. ..+.-||.+.+ ...=...|..||.-
T Consensus 19 WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~~~~~~~~~~~~f~~g~~VLAl 81 (130)
T PF07039_consen 19 WILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPKKAPPDTDPLAEFPKGTKVLAL 81 (130)
T ss_dssp EEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-SB--TTT-GGGS--TT-EEEEE
T ss_pred EEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCCccCCCCCchhhCCCCCEEEEE
Confidence 3789999987776 9999999865 34445666221 23334666666665
No 36
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=56.40 E-value=18 Score=29.16 Aligned_cols=40 Identities=30% Similarity=0.330 Sum_probs=31.1
Q ss_pred Eeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHhCCCCc
Q 030718 50 LFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQKSTEWP 107 (172)
Q Consensus 50 ~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk~g~WP 107 (172)
-||+|..+ +||| ..||++|.+ |++ ++++|++-|++.|.=|
T Consensus 135 giptki~~G~i~i-~~d~~v~k~---------G~~--------v~~~~A~lL~~l~i~P 175 (175)
T cd05795 135 GIPTKIEKGKIEI-ISDVVVVKK---------GEK--------VGASEATLLNKLNIKP 175 (175)
T ss_pred CCceEEecCEEEE-ecCeEEecC---------CCC--------cCHHHHHHHHHcCCCC
Confidence 47888775 6888 469999884 543 6999999999988755
No 37
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=55.47 E-value=31 Score=25.39 Aligned_cols=29 Identities=7% Similarity=0.132 Sum_probs=24.6
Q ss_pred EEEEEEeecCCceEEEEeCCCCEEEEEeec
Q 030718 24 SIMQVVSLRGSNLIEVLDAKDEKSLALFPA 53 (172)
Q Consensus 24 ~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~ 53 (172)
.+++|++..|+ .+.+.|+||...-+.++.
T Consensus 20 ivGkV~~~~~~-~~~~~~~Dg~~v~v~l~~ 48 (101)
T cd04479 20 IVGKVEKVDGD-SLTLISSDGVNVTVELNR 48 (101)
T ss_pred EEEEEEEecCC-eEEEEcCCCCEEEEEeCC
Confidence 68999999997 899999999777777654
No 38
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=52.85 E-value=23 Score=25.58 Aligned_cols=47 Identities=17% Similarity=0.155 Sum_probs=25.4
Q ss_pred EEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHhCCCCchhhhc
Q 030718 60 WIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQKSTEWPEIFKS 112 (172)
Q Consensus 60 WIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk~g~WP~~F~~ 112 (172)
-+|.||||||............+==-|+|++.-.-. +.+.-|.-|.-
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gga------R~P~~~tlFQV 51 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGGA------RDPKVPTLFQV 51 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEeccc------cCCCCCceEEE
Confidence 479999999996431000011122368888875532 34444555544
No 39
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=51.40 E-value=43 Score=30.51 Aligned_cols=52 Identities=13% Similarity=0.100 Sum_probs=44.7
Q ss_pred CCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecC
Q 030718 20 QDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDES 72 (172)
Q Consensus 20 ~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~ 72 (172)
.....|+.|++..+.+++.|....|.++++.+.+...+.. ++.|+-|.+...
T Consensus 64 ~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~~v~~~~~ 115 (398)
T PTZ00454 64 SVPLVIGQFLEMIDSNYGIVSSTSGSNYYVRILSTLNREL-LKPNASVALHRH 115 (398)
T ss_pred CCCceEEEEEEEEcCCEEEEEcCCCCEEEEecccccCHhh-CCCCCEEEeecc
Confidence 4578999999999999999999999999999988776554 688999988753
No 40
>PF09038 53-BP1_Tudor: Tumour suppressor p53-binding protein-1 Tudor; InterPro: IPR015125 This domain consist of ten beta-strands and a carboxy-terminal alpha-helix. The amino-terminal five beta-strands and the C-terminal five beta-strands adopt folds that are identical to each other. The domain is essential for the recruitment of proteins to double stranded breaks in DNA, which is mediated by interaction with methylated Lys 79 of histone H3 []. ; PDB: 3LGL_A 1XNI_B 3LGF_A 2G3R_A 2IG0_A 3LH0_A 1SSF_A.
Probab=51.03 E-value=49 Score=25.97 Aligned_cols=36 Identities=22% Similarity=0.170 Sum_probs=28.1
Q ss_pred EEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCC
Q 030718 26 MQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESG 73 (172)
Q Consensus 26 ~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~ 73 (172)
++|+...|+++|.|...||...- |+--|+|+++|-+
T Consensus 22 G~I~~~~~~~kykv~FdDG~~~~------------v~~~div~~dplp 57 (122)
T PF09038_consen 22 GKITSDKGKNKYKVLFDDGYECR------------VLGKDIVVCDPLP 57 (122)
T ss_dssp EEEEEEETTTEEEEEETTS-EEE------------EECCCEEEESSS-
T ss_pred ceEeecCCCCeEEEEecCCccce------------eccCcEEEEccee
Confidence 78999999999999999997653 3345899998754
No 41
>TIGR01439 lp_hng_hel_AbrB looped-hinge helix DNA binding domain, AbrB family. This DNA-binding domain family includes AbrB, a transition state regulator in Bacillus subtilis, whose DNA-binding domain structure in solution was determined by NMR. The domain binds DNA as a dimer in what is termed a looped-hinge helix fold. Some members of the family have two copies of the domain in tandem. The domain is found usually at the N-terminus of a small protein. This model excludes members of family TIGR02609.
Probab=50.44 E-value=6.4 Score=23.75 Aligned_cols=25 Identities=16% Similarity=0.295 Sum_probs=22.0
Q ss_pred EEEEeeccccceEEEeeCCEEEEec
Q 030718 47 SLALFPAKFQKSMWIKRGSFVVVDE 71 (172)
Q Consensus 47 ~L~~iP~KfRK~vWIkrGD~VlV~p 71 (172)
.-+.||.+||+.+=++.||.|.+.+
T Consensus 7 gri~iP~~~r~~l~~~~gd~~~i~~ 31 (43)
T TIGR01439 7 GQIVIPKEIREKLGLKEGDRLEVIR 31 (43)
T ss_pred CeEEecHHHHHHcCcCCCCEEEEEE
Confidence 3467999999999999999999885
No 42
>PF12859 Apc1: Anaphase-promoting complex subunit 1
Probab=49.65 E-value=21 Score=26.36 Aligned_cols=36 Identities=11% Similarity=0.123 Sum_probs=29.3
Q ss_pred CceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEe
Q 030718 34 SNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVD 70 (172)
Q Consensus 34 ~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~ 70 (172)
.....|...+|+.+.+.||-..++..|+.. .++|-.
T Consensus 8 ~~~~~vy~~~G~~~~v~LPF~V~~~~~~~~-GlLLqR 43 (105)
T PF12859_consen 8 KDQAHVYFPSGESYTVPLPFEVSSAWPLPR-GLLLQR 43 (105)
T ss_pred CCEEEEEeCCCCEEEEEeceEeeEEeccCC-EEEEEE
Confidence 577889999999999999999988777776 455543
No 43
>PF04014 Antitoxin-MazE: Antidote-toxin recognition MazE; InterPro: IPR007159 This domain is found in AbrB from Bacillus subtilis. The product of the abrB gene is an ambiactive repressor and activator of the transcription of genes expressed during the transition state between vegetative growth and the onset of stationary phase and sporulation []. AbrB is thought to interact directly with the transcription initiation regions of genes under its control []. AbrB contains a helix-turn-helix structure, but this domain ends before the helix-turn-helix begins []. The product of the B. subtilis gene spoVT is another member of this family and is also a transcriptional regulator []. DNA-binding activity in this AbrB homologue requires hexamerisation []. Another family member has been isolated from the Sulfolobus solfataricus and has been identified as a homologue of bacterial repressor-like proteins. The Escherichia coli family member SohA or Prl1F appears to be bifunctional and is able to regulate its own expression as well as relieve the export block imposed by high-level synthesis of beta-galactosidase hybrid proteins [].; PDB: 2L66_A 2GLW_A 3TND_D 2W1T_B 2RO5_B 2FY9_A 2RO3_B 1UB4_C 3ZVK_G 1YFB_B ....
Probab=47.71 E-value=3.1 Score=26.39 Aligned_cols=28 Identities=14% Similarity=0.292 Sum_probs=23.6
Q ss_pred CCEEEEEeeccccceEEEeeCCEEEEec
Q 030718 44 DEKSLALFPAKFQKSMWIKRGSFVVVDE 71 (172)
Q Consensus 44 G~~~L~~iP~KfRK~vWIkrGD~VlV~p 71 (172)
|...-+.||..|++.+=|+.||.|.+..
T Consensus 4 g~s~~v~iPk~~~~~l~l~~Gd~v~i~~ 31 (47)
T PF04014_consen 4 GNSGQVTIPKEIREKLGLKPGDEVEIEV 31 (47)
T ss_dssp TTCSEEEE-HHHHHHTTSSTTTEEEEEE
T ss_pred CCCceEECCHHHHHHcCCCCCCEEEEEE
Confidence 4556788999999999999999999986
No 44
>PF03803 Scramblase: Scramblase ; InterPro: IPR005552 Scramblase is palmitoylated and contains a potential protein kinase C phosphorylation site. Scramblase exhibits Ca2+-activated phospholipid scrambling activity in vitro. There are also possible SH3 and WW binding motifs. Scramblase is involved in the redistribution of phospholipids after cell activation or injury [].
Probab=45.68 E-value=1.4e+02 Score=24.24 Aligned_cols=65 Identities=12% Similarity=0.036 Sum_probs=39.7
Q ss_pred CCCCCcEEEEEEeec--CCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEe
Q 030718 18 TLQDGQSIMQVVSLR--GSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVL 92 (172)
Q Consensus 18 ~p~e~q~I~rV~~~~--G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl 92 (172)
.-..|+.|+.|.+.- ....|.|.+++|+. +..|.|.+-.----+.=.|-|.++ ++..-|.|.+..
T Consensus 111 ~~p~g~~iG~I~q~~~~~~~~f~I~d~~~~~-~~~I~gp~~~~~~~~~~~F~I~~~---------~~~~vg~I~k~w 177 (221)
T PF03803_consen 111 ESPPGNLIGSIRQPFSCCRPNFDIFDANGNP-IFTIKGPCCCCSCCCDWEFEIKDP---------NGQEVGSITKKW 177 (221)
T ss_pred ecCCCcEEEEEEEcCcccceEEEEEECCCce-EEEEeCCcceeccccceeeeeecc---------cCcEEEEEEEec
Confidence 345699999999954 48889999999965 456665532100012223444443 234568888654
No 45
>PRK11642 exoribonuclease R; Provisional
Probab=45.44 E-value=1.2e+02 Score=30.53 Aligned_cols=48 Identities=23% Similarity=0.274 Sum_probs=32.2
Q ss_pred eeCCEEEEecCCcchhhcCCCeeeEEEEEEeCH-----HHHHHHHhCCCCchhhhc
Q 030718 62 KRGSFVVVDESGKEKAIKDGSKVACIVTKVLFY-----EQVRALQKSTEWPEIFKS 112 (172)
Q Consensus 62 krGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~-----~qvk~Lrk~g~WP~~F~~ 112 (172)
+.||.|+|..-.+ +.. ..+..|.|+.+|.. -++..+...--+|.+|..
T Consensus 187 ~~gd~V~v~I~~~--p~~-~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~~Fp~ 239 (813)
T PRK11642 187 RMGFVVVVELTQR--PTR-RTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQ 239 (813)
T ss_pred CCCCEEEEEEecC--CCc-CCCCCEEEEEEecCCCCcchHHHHHHHHcCCCCCCCH
Confidence 5689999985332 122 33467999999986 255666666667888865
No 46
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=44.65 E-value=61 Score=30.10 Aligned_cols=51 Identities=12% Similarity=0.066 Sum_probs=41.8
Q ss_pred CCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEec
Q 030718 20 QDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDE 71 (172)
Q Consensus 20 ~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p 71 (172)
.....|++|++..+.|++.|....|..+++.|-+...+.. ++.|+-|.+..
T Consensus 102 ~~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-l~~~~~v~l~~ 152 (438)
T PTZ00361 102 GSPLSVGTLEEIIDENHAIVSSSVGPEYYVNILSFVDKEQ-LEPGCSVLLHN 152 (438)
T ss_pred CCCcEEEEEEEEeCCCeEEEEeCCCCEEEEeccCcCCHhh-CCCCCEEEEcC
Confidence 3467999999999999999999999999999887765433 56777777664
No 47
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=44.44 E-value=55 Score=21.30 Aligned_cols=50 Identities=22% Similarity=0.091 Sum_probs=34.4
Q ss_pred CCcEEEEEEee-cCCceEEEE--eCCCCEEEEEeeccccceEEEeeCCEEEEe
Q 030718 21 DGQSIMQVVSL-RGSNLIEVL--DAKDEKSLALFPAKFQKSMWIKRGSFVVVD 70 (172)
Q Consensus 21 e~q~I~rV~~~-~G~nl~eV~--~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~ 70 (172)
.++.-|+|.+. .|+.+.+|. +.+|.+..+.||.+--..+=++.|+-|.+.
T Consensus 6 ~N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~ 58 (69)
T TIGR00638 6 RNQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAV 58 (69)
T ss_pred ccEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEE
Confidence 46777777777 344555555 556668889999876555666788876665
No 48
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=43.92 E-value=33 Score=25.58 Aligned_cols=52 Identities=12% Similarity=0.040 Sum_probs=33.0
Q ss_pred EEEeeCCEEEEecCCc-chh-------h-c-CCCeeeEEEEEEeCHHHHHHHHhCCCCchhh
Q 030718 59 MWIKRGSFVVVDESGK-EKA-------I-K-DGSKVACIVTKVLFYEQVRALQKSTEWPEIF 110 (172)
Q Consensus 59 vWIkrGD~VlV~p~~~-~~~-------~-e-~~~KvkgeIv~vl~~~qvk~Lrk~g~WP~~F 110 (172)
++++-||+|+|.+.+. ..+ | + .++.....+.|-|.++++......-++|.+.
T Consensus 2 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~~~Ev 63 (121)
T cd04717 2 LQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEV 63 (121)
T ss_pred CEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccccCce
Confidence 4688999999975431 000 0 1 1133567888899999987766666666554
No 49
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=43.76 E-value=64 Score=23.76 Aligned_cols=33 Identities=6% Similarity=-0.006 Sum_probs=23.8
Q ss_pred EEEEEEeec-CCceEEEEeCCCCEEEEEeecccc
Q 030718 24 SIMQVVSLR-GSNLIEVLDAKDEKSLALFPAKFQ 56 (172)
Q Consensus 24 ~I~rV~~~~-G~nl~eV~~~dG~~~L~~iP~KfR 56 (172)
.|++|.+.. +++.+.+.|.||.+..+.++.-..
T Consensus 23 ivGkv~~~~~~g~~~~l~~~d~~~V~v~l~~~~~ 56 (109)
T PF08661_consen 23 IVGKVESVDPDGGSATLSTSDGGQVTVSLNPPSD 56 (109)
T ss_dssp EEEEEEEE-TTSSEEEEE-TTS-EEEEEESS--S
T ss_pred EEEEEeeEcCCCCEEEEEcCCCCEEEEEeCCCCC
Confidence 578888775 678999999999999999886554
No 50
>PF04076 BOF: Bacterial OB fold (BOF) protein; InterPro: IPR005220 Proteins in this entry have an OB-fold fold (oligonucleotide/oligosaccharide binding motif). Analysis of the predicted nucleotide-binding site of the OB-fold suggests that they lack nucleic acid-binding properties. They contain an predicted N-terminal signal peptide which indicates that they localise to the periplasm where they may function to bind proteins, small molecules, or other typical OB-fold ligands. As hypothesised for the distantly related OB-fold containing bacterial enterotoxins, the loss of nucleotide-binding function and the rapid evolution of the OB-fold ligand-binding site may be associated with the presence of members in mobile genetic elements and their potential role in bacterial pathogenicity [].; PDB: 1NNX_A.
Probab=43.59 E-value=59 Score=24.40 Aligned_cols=46 Identities=11% Similarity=-0.004 Sum_probs=33.2
Q ss_pred EEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEe
Q 030718 24 SIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVD 70 (172)
Q Consensus 24 ~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~ 70 (172)
.-++|++.+|.+.|...+..| +..+.|+.+.-.-.=|..++-|-+.
T Consensus 39 L~G~Iv~~l~~d~Y~F~D~TG-~I~VeId~~~w~g~~vt~~~~Vri~ 84 (103)
T PF04076_consen 39 LEGNIVKQLGDDKYLFRDATG-EIEVEIDDDVWRGQTVTPDDKVRIS 84 (103)
T ss_dssp EEEEEEEEEETTEEEEEETTE-EEEEE--GGGSTT----TTSEEEEE
T ss_pred EEEEEEEEecCCEEEEECCCC-cEEEEEChhhcCCcccCCCCEEEEE
Confidence 357899999999999999999 7889999986655557777777654
No 51
>COG1162 Predicted GTPases [General function prediction only]
Probab=43.15 E-value=49 Score=29.55 Aligned_cols=66 Identities=17% Similarity=0.155 Sum_probs=46.0
Q ss_pred EEEEeecCCceEEEEeC---CCCEEEEEeeccccce-EEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHH
Q 030718 26 MQVVSLRGSNLIEVLDA---KDEKSLALFPAKFQKS-MWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQ 101 (172)
Q Consensus 26 ~rV~~~~G~nl~eV~~~---dG~~~L~~iP~KfRK~-vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lr 101 (172)
++|++.. +++|.|.+. +++...|...++||++ .=.=.||+|++++.. ..|-|..|+.+. -.|.
T Consensus 7 g~v~~~~-~g~y~v~~~~~~~~~~~~~~~r~~lr~~~~~~vVGD~V~~~~~~----------~~g~I~~i~~Rk--n~L~ 73 (301)
T COG1162 7 GRVVKVD-AGFYGVRLEEEVDGEVYRCRARGNLRKKDLKPVVGDRVVFEDEN----------NNGVIEKILPRK--NVLI 73 (301)
T ss_pred cEEEEee-CCEEEEEEccccccceeeeeeecceeccCccccccCeEEEecCC----------CcceEEEEeccc--Ccee
Confidence 4444443 367777666 4788999999999987 445579999998632 128999999877 4444
Q ss_pred hCC
Q 030718 102 KST 104 (172)
Q Consensus 102 k~g 104 (172)
+-.
T Consensus 74 Rp~ 76 (301)
T COG1162 74 RPP 76 (301)
T ss_pred CCc
Confidence 433
No 52
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=42.82 E-value=28 Score=24.72 Aligned_cols=22 Identities=14% Similarity=0.199 Sum_probs=19.8
Q ss_pred eEEEEEEeCHHHHHHHHhCCCC
Q 030718 85 ACIVTKVLFYEQVRALQKSTEW 106 (172)
Q Consensus 85 kgeIv~vl~~~qvk~Lrk~g~W 106 (172)
.|-|||.++-.+++.|++-|..
T Consensus 2 ~gliVyl~~~k~~r~L~kfG~i 23 (71)
T PF09902_consen 2 QGLIVYLYSLKDARQLRKFGDI 23 (71)
T ss_pred eEEEEEEechHhHHhHhhcccE
Confidence 4889999999999999999953
No 53
>TIGR03689 pup_AAA proteasome ATPase. In the Actinobacteria, as shown for Mycobacterium tuberculosis, some proteins are modified by ligation between an epsilon-amino group of a lysine side chain and the C-terminal carboxylate of the ubiquitin-like protein Pup. This modification leads to protein degradation by the archaeal-like proteasome found in the Actinobacteria. Members of this protein family belong to the AAA family of ATPases and tend to be clustered with the genes for Pup, the Pup ligase PafA, and structural components of the proteasome. This protein forms hexameric rings with ATPase activity.
Probab=42.69 E-value=41 Score=32.01 Aligned_cols=48 Identities=19% Similarity=0.336 Sum_probs=41.2
Q ss_pred EEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecC
Q 030718 24 SIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDES 72 (172)
Q Consensus 24 ~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~ 72 (172)
.+++|.+.+|.+++.|....|..+++.+.+.+...- ++.|+-|+|++.
T Consensus 108 ~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~g~~~~~~~~ 155 (512)
T TIGR03689 108 EIATLKEVLGDGRALVVDHSGEERVVKLAGALADEL-IRAGDSLLVDPK 155 (512)
T ss_pred ceEEEEEEeCCCeEEEEeCCCCeEEeehhhhhCHhh-CCCCCEEEEccc
Confidence 455999999999999999999999999888887543 689999999863
No 54
>PF10017 Methyltransf_33: Histidine-specific methyltransferase, SAM-dependent; InterPro: IPR019257 This domain is found in methyltransferases and various hypothetical proteins.
Probab=42.53 E-value=36 Score=25.92 Aligned_cols=27 Identities=19% Similarity=0.238 Sum_probs=23.5
Q ss_pred hcCCCeeeEEEEEEeCHHHHHHHHhCC
Q 030718 78 IKDGSKVACIVTKVLFYEQVRALQKST 104 (172)
Q Consensus 78 ~e~~~KvkgeIv~vl~~~qvk~Lrk~g 104 (172)
+.+|+++.-++.++|+.++++.|-.+.
T Consensus 82 ~~~GE~I~~e~S~Ky~~~~~~~l~~~a 108 (127)
T PF10017_consen 82 FKEGERIHTENSYKYSPEEFEALAEQA 108 (127)
T ss_pred ECCCCEEEEEEeeCcCHHHHHHHHHHC
Confidence 457899999999999999999987663
No 55
>cd04713 BAH_plant_3 BAH, or Bromo Adjacent Homology domain, plant-specific sub-family with unknown function. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=39.31 E-value=87 Score=24.53 Aligned_cols=49 Identities=12% Similarity=0.146 Sum_probs=30.8
Q ss_pred ceEEEeeCCEEEEecCCcchh-------hc--CCCeeeEEEEEEeCHHHHHHHHhCCCC
Q 030718 57 KSMWIKRGSFVVVDESGKEKA-------IK--DGSKVACIVTKVLFYEQVRALQKSTEW 106 (172)
Q Consensus 57 K~vWIkrGD~VlV~p~~~~~~-------~e--~~~KvkgeIv~vl~~~qvk~Lrk~g~W 106 (172)
..+=++-||+|+|.+.+..++ |. .++.....|.|-|+++++...+. +.|
T Consensus 17 dg~~y~vgD~Vlv~~~~~~~pyI~~I~~i~~~~~~~~~v~V~WFyRpeEi~~~~~-~~~ 74 (146)
T cd04713 17 DGNKYRLEDCVLLVPEDDQKPYIAIIKDIYKQEEGSLKLEVQWLYRPEEIEKKKG-GNW 74 (146)
T ss_pred CCEEEECCCEEEEeCCCCCCCEEEEEEEEEEcCCCCEEEEEEeeECHHHhccccc-ccc
Confidence 334478899999986431111 11 12446888999999999976443 445
No 56
>KOG2406 consensus MADS box transcription factor [Transcription]
Probab=37.75 E-value=25 Score=33.96 Aligned_cols=46 Identities=15% Similarity=0.328 Sum_probs=37.3
Q ss_pred EEEeecCCceEEEEeCCCCEEEEE----eecccc-----ceEEEeeCCEEEEecC
Q 030718 27 QVVSLRGSNLIEVLDAKDEKSLAL----FPAKFQ-----KSMWIKRGSFVVVDES 72 (172)
Q Consensus 27 rV~~~~G~nl~eV~~~dG~~~L~~----iP~KfR-----K~vWIkrGD~VlV~p~ 72 (172)
+|.++.|++...|.+.||+-.|.. ||.=+- .+|||.-|+.+|+-|.
T Consensus 104 eiska~~s~~aRi~D~DGEFLLIEAA~~LPkWldpens~nRVfi~gGel~Ilp~~ 158 (635)
T KOG2406|consen 104 EISKAFPSAFARIIDEDGEFLLIEAADSLPKWLDPENSDNRVFIHGGELIILPPE 158 (635)
T ss_pred HHHHhcCcceEEEEcCCCCEEeehhhhhcccccCcccccceEEEECCEEEEeccc
Confidence 466789999999999999998875 664333 6899999999999643
No 57
>cd06555 ASCH_PF0470_like ASC-1 homology domain, subfamily similar to Pyrococcus furiosus Pf0470. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=37.41 E-value=1.2e+02 Score=23.07 Aligned_cols=54 Identities=20% Similarity=0.360 Sum_probs=41.6
Q ss_pred cCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHhC
Q 030718 32 RGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQKS 103 (172)
Q Consensus 32 ~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk~ 103 (172)
.|--.+|+.+.|.+. -=|+.||.++...|+ .+.++...|+.|..-+.-++|-+.
T Consensus 15 ~G~KtiEiRlnD~kr------------~~ikvGD~I~f~~~~------~~~~l~v~V~~i~~Y~sF~~ll~~ 68 (109)
T cd06555 15 SGKKTIEIRLNDEKR------------QQIKVGDKILFNDLD------TGQQLLVKVVDIRKYDSFRELLEE 68 (109)
T ss_pred cCCCEEEEEecccch------------hcCCCCCEEEEEEcC------CCcEEEEEEEEEEecCCHHHHHHh
Confidence 466778888887543 237899999998875 367799999999888888887655
No 58
>PTZ00240 60S ribosomal protein P0; Provisional
Probab=37.01 E-value=42 Score=30.16 Aligned_cols=44 Identities=23% Similarity=0.145 Sum_probs=33.3
Q ss_pred Eeeccccc-eEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHhCCCCchhhh
Q 030718 50 LFPAKFQK-SMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQKSTEWPEIFK 111 (172)
Q Consensus 50 ~iP~KfRK-~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk~g~WP~~F~ 111 (172)
-||+|+.| +||| ..|++||.. |++ ++.+|..-|++.|.=|-.|.
T Consensus 149 GIpTkI~kGkIeI-~~d~~v~k~---------Ge~--------V~~~~A~LL~~L~IkP~~~g 193 (323)
T PTZ00240 149 NIATKIAKGMVEI-VTEKKVLSV---------GDK--------VDNSTATLLQKLNISPFYYQ 193 (323)
T ss_pred CCCeEecCcEEEE-ecCeEEecC---------CCC--------cCHHHHHHHHHcCCCeEEEE
Confidence 47777765 5888 468888874 544 58899999999998888773
No 59
>PRK02302 hypothetical protein; Provisional
Probab=34.64 E-value=42 Score=24.94 Aligned_cols=22 Identities=14% Similarity=0.267 Sum_probs=20.3
Q ss_pred eEEEEEEeCHHHHHHHHhCCCC
Q 030718 85 ACIVTKVLFYEQVRALQKSTEW 106 (172)
Q Consensus 85 kgeIv~vl~~~qvk~Lrk~g~W 106 (172)
.|-|||.++-.+++.|+|-|.+
T Consensus 8 ~glIVyl~~~k~~r~LrkfG~I 29 (89)
T PRK02302 8 IGLIVYLYYNRDARKLSKYGDI 29 (89)
T ss_pred eEEEEEEeecHhHHHHhhcCcE
Confidence 6999999999999999999954
No 60
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=34.59 E-value=1.2e+02 Score=21.99 Aligned_cols=52 Identities=15% Similarity=0.096 Sum_probs=33.2
Q ss_pred CCCCCc-EEEEEEeecCCceEEEEeCCCCEEEEEee-----cccc-ceEEEeeCCEEEEecC
Q 030718 18 TLQDGQ-SIMQVVSLRGSNLIEVLDAKDEKSLALFP-----AKFQ-KSMWIKRGSFVVVDES 72 (172)
Q Consensus 18 ~p~e~q-~I~rV~~~~G~nl~eV~~~dG~~~L~~iP-----~KfR-K~vWIkrGD~VlV~p~ 72 (172)
.|..|. +|++|+... ++.|.|.... ...+.|| +.-| .+--++.||+|++.-.
T Consensus 3 ~P~~gD~VIG~V~~~~-~~~~~VdI~s--~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~ 61 (86)
T cd05790 3 VPAKGDHVIGIVVAKA-GDFFKVDIGG--SEPASLSYLAFEGATKRNRPNLNVGDLVYARVV 61 (86)
T ss_pred cCCCCCEEEEEEEEEc-CCeEEEEcCC--CcceEechHHcccccccccccCCCCCEEEEEEE
Confidence 466665 677777765 5778887654 2344444 3322 3467999999998853
No 61
>PRK02886 hypothetical protein; Provisional
Probab=34.20 E-value=44 Score=24.74 Aligned_cols=22 Identities=18% Similarity=0.125 Sum_probs=20.2
Q ss_pred eEEEEEEeCHHHHHHHHhCCCC
Q 030718 85 ACIVTKVLFYEQVRALQKSTEW 106 (172)
Q Consensus 85 kgeIv~vl~~~qvk~Lrk~g~W 106 (172)
.|-|||.++-.+++.|++-|.+
T Consensus 6 ~glIVyl~~~k~~r~LrkyG~I 27 (87)
T PRK02886 6 QGIIVWLHSLKQAKQLRKFGNV 27 (87)
T ss_pred eEEEEEEeecHhHHHHhhcCcE
Confidence 6999999999999999999964
No 62
>KOG0650 consensus WD40 repeat nucleolar protein Bop1, involved in ribosome biogenesis [Translation, ribosomal structure and biogenesis]
Probab=34.04 E-value=70 Score=31.63 Aligned_cols=43 Identities=12% Similarity=0.288 Sum_probs=33.5
Q ss_pred CEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 45 EKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 45 ~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
.......|.++|..-|=++|||+-+..- ..+ .++.+||=|.+.
T Consensus 514 v~~~I~~~k~i~~vtWHrkGDYlatV~~------~~~--~~~VliHQLSK~ 556 (733)
T KOG0650|consen 514 VCIVIKHPKSIRQVTWHRKGDYLATVMP------DSG--NKSVLIHQLSKR 556 (733)
T ss_pred eEEEEecCCccceeeeecCCceEEEecc------CCC--cceEEEEecccc
Confidence 4566778999999999999999887742 234 358888888865
No 63
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=33.54 E-value=63 Score=25.20 Aligned_cols=33 Identities=21% Similarity=0.206 Sum_probs=24.5
Q ss_pred ceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHH
Q 030718 57 KSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQ 96 (172)
Q Consensus 57 K~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~q 96 (172)
+++=|++||.|.|-...+ .| ..|.|+.|+.+.+
T Consensus 42 r~~~IkkGD~V~VisG~~-----KG--k~GkV~~V~~~~~ 74 (120)
T PRK01191 42 RSLPVRKGDTVKVMRGDF-----KG--EEGKVVEVDLKRG 74 (120)
T ss_pred ccceEeCCCEEEEeecCC-----CC--ceEEEEEEEcCCC
Confidence 345699999999986432 34 4699999988764
No 64
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=33.13 E-value=72 Score=24.06 Aligned_cols=50 Identities=14% Similarity=0.150 Sum_probs=29.6
Q ss_pred EeeCCEEEEecCCc-chh--------hc-CCCeeeEEEEEEeCHHHHHHHHhCCCCchhh
Q 030718 61 IKRGSFVVVDESGK-EKA--------IK-DGSKVACIVTKVLFYEQVRALQKSTEWPEIF 110 (172)
Q Consensus 61 IkrGD~VlV~p~~~-~~~--------~e-~~~KvkgeIv~vl~~~qvk~Lrk~g~WP~~F 110 (172)
++-||+|+|.+.+. ..+ .+ .++.....+.|-|.++++...++....|.+.
T Consensus 4 ~~vGD~V~v~~~~~~~~pyIgrI~~i~e~~~g~~~~~v~WfyrPeEt~~~~~~~~~~~Ev 63 (121)
T cd04714 4 IRVGDCVLFKSPGRPSLPYVARIESLWEDPEGNMVVRVKWYYRPEETKGGRKPNHGEKEL 63 (121)
T ss_pred EEcCCEEEEeCCCCCCCCEEEEEEEEEEcCCCCEEEEEEEEEcHHHccCcccccCCCCce
Confidence 56677777764321 000 01 1234578889999999887766655555443
No 65
>PRK03598 putative efflux pump membrane fusion protein; Provisional
Probab=32.38 E-value=1.4e+02 Score=25.76 Aligned_cols=56 Identities=13% Similarity=0.016 Sum_probs=42.6
Q ss_pred cCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCH
Q 030718 32 RGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFY 94 (172)
Q Consensus 32 ~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~ 94 (172)
.|..++.+...+.-...+.+|.+ ..-+|+.|+-|.|....+ .+....|.|.+|...
T Consensus 227 ~G~~l~~I~~~~~~~v~~~V~e~--~~~~i~~Gq~v~v~~~~~-----~~~~~~g~V~~Is~~ 282 (331)
T PRK03598 227 AGSTVFTLSLTRPVWVRAYVDER--NLGQAQPGRKVLLYTDGR-----PDKPYHGQIGFVSPT 282 (331)
T ss_pred CCCeEEEEecCCceEEEEEECHH--HHhhCCCCCEEEEEEcCC-----CCcEEEEEEEEEcCc
Confidence 47788888877777777888886 445899999999986432 234689999999764
No 66
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=31.66 E-value=62 Score=23.01 Aligned_cols=30 Identities=30% Similarity=0.317 Sum_probs=22.0
Q ss_pred EEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHH
Q 030718 60 WIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQ 96 (172)
Q Consensus 60 WIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~q 96 (172)
=|++||-|.|-... ..| | .|.|..|+.+.+
T Consensus 6 ~I~kGD~V~Vi~G~-----dKG-K-~G~V~~V~~~~~ 35 (76)
T PRK12281 6 KVKKGDMVKVIAGD-----DKG-K-TGKVLAVLPKKN 35 (76)
T ss_pred cccCCCEEEEeEcC-----CCC-c-EEEEEEEEcCCC
Confidence 48999999987532 133 3 599999988763
No 67
>PF01287 eIF-5a: Eukaryotic elongation factor 5A hypusine, DNA-binding OB fold; InterPro: IPR020189 A five-stranded beta-barrel was first noted as a common structure among four proteins binding single-stranded nucleic acids (staphylococcal nuclease and aspartyl-tRNA synthetase) or oligosaccharides (B subunits of enterotoxin and verotoxin-1), and has been termed the oligonucleotide/oligosaccharide binding motif, or OB fold, a five-stranded beta-sheet coiled to form a closed beta-barrel capped by an alpha helix located between the third and fourth strands []. Two ribosomal proteins, S17 and S1, are members of this class, and have different variations of the OB fold theme. Comparisons with other OB fold nucleic acid binding proteins suggest somewhat different mechanisms of nucleic acid recognition in each case []. There are many nucleic acid-binding proteins that contain domains with this OB-fold structure, including anticodon-binding tRNA synthetases, ssDNA-binding proteins (CDC13, telomere-end binding proteins), phage ssDNA-binding proteins (gp32, gp2.5, gpV), cold shock proteins, DNA ligases, RNA-capping enzymes, DNA replication initiators and RNA polymerase subunit RBP8 []. This entry represents the RNA-binding domain of translation elongation factor IF5A [].; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0043022 ribosome binding, 0006452 translational frameshifting, 0045901 positive regulation of translational elongation, 0045905 positive regulation of translational termination; PDB: 1IZ6_B 3CPF_A 1KHI_A 1BKB_A 1XTD_A 3ER0_A 3HKS_B 1X6O_A 2EIF_A 1EIF_A.
Probab=31.47 E-value=71 Score=22.32 Aligned_cols=45 Identities=18% Similarity=0.400 Sum_probs=35.0
Q ss_pred EEEEeecCCceEEEEeCCCCEEE-EEee-----ccccceEEEeeCCEEEEecC
Q 030718 26 MQVVSLRGSNLIEVLDAKDEKSL-ALFP-----AKFQKSMWIKRGSFVVVDES 72 (172)
Q Consensus 26 ~rV~~~~G~nl~eV~~~dG~~~L-~~iP-----~KfRK~vWIkrGD~VlV~p~ 72 (172)
.+|+...|.+...+++.+|.++= +.|| .++|.++ ..|.=|+|.-+
T Consensus 7 yqli~I~~Dg~lsLMde~get~eDl~lP~~el~~ei~~~~--~~g~~~~Vtv~ 57 (69)
T PF01287_consen 7 YQLIDIDGDGFLSLMDEDGETREDLKLPDGELGEEIKAKF--EEGKEVLVTVL 57 (69)
T ss_dssp EEEEEEETTTEEEEEETTS-EEEEEECCSHHHHHHHHHHH--HTTCEEEEEEE
T ss_pred EEEEEEccCcEEEEEcCCCCeeccEEecccchhHHHHhhc--cCCCeEEEEEE
Confidence 57778889999999999999999 9999 5555544 78887777654
No 68
>cd06253 M14_ASTE_ASPA_like_3 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=30.86 E-value=1.3e+02 Score=26.18 Aligned_cols=44 Identities=20% Similarity=0.287 Sum_probs=27.2
Q ss_pred CCCcEEEEEEeecCCc-eEEEEeCCCCEEEEEeeccccceEEEeeCCEEE
Q 030718 20 QDGQSIMQVVSLRGSN-LIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVV 68 (172)
Q Consensus 20 ~e~q~I~rV~~~~G~n-l~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~Vl 68 (172)
+.||.|++|+.+.+++ ..+|.-+-.-..++ .|..-+|.+||.|.
T Consensus 251 ~~Gq~lg~i~dp~~g~~~~~v~Ap~dGiv~~-----~~~~p~v~~G~~l~ 295 (298)
T cd06253 251 KRGDVIGEIVDPLEGEVIEEVIAPCDGILFT-----LREYPLVYEGSLVA 295 (298)
T ss_pred CCCCEEEEEeCCCCCCeeEEEEcCCCeEEEE-----eecCCeecCCceEE
Confidence 4688888888887665 55555553333333 34556677777664
No 69
>cd04719 BAH_Orc1p_animal BAH, or Bromo Adjacent Homology domain, as present in animal homologs of Saccharomyces cerevisiae Orc1p. Orc1 is part of the Yeast Sir1-origin recognition complex. The Orc1p BAH doman functions in epigenetic silencing. In vertebrates, a similar ORC protein complex exists, which has been shown essential for DNA replication in Xenopus laevis. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=30.49 E-value=48 Score=25.84 Aligned_cols=48 Identities=17% Similarity=0.160 Sum_probs=28.3
Q ss_pred EEeeCCEEEEecCCcch-------hhcCC-----CeeeEEEEEEeCHHHHHHHH--hCCCCc
Q 030718 60 WIKRGSFVVVDESGKEK-------AIKDG-----SKVACIVTKVLFYEQVRALQ--KSTEWP 107 (172)
Q Consensus 60 WIkrGD~VlV~p~~~~~-------~~e~~-----~KvkgeIv~vl~~~qvk~Lr--k~g~WP 107 (172)
=|+.||+|||.+.+... .+.++ ...++.|-|-|.+.++...+ ..|.||
T Consensus 3 ~i~vGd~VlI~~~d~~~~yVAkI~~i~e~~~~~~~~~~~~VqWy~R~~Ev~~~~~~~~~~~~ 64 (128)
T cd04719 3 TIEVGDFVLIEGEDADGPDVARILHLYEDGNEDDDPKRAIVQWFSRPSEVPKNKRKLLGREP 64 (128)
T ss_pred EEecCCEEEEECCCCCCCcEeeehhhhccccCCcccceEEEEcccChHHccccchhhccCCC
Confidence 37899999999765210 11221 13467777777777774333 234566
No 70
>PF03459 TOBE: TOBE domain; InterPro: IPR005116 The TOBE domain [] (Transport-associated OB) always occurs as a dimer as the C-terminal strand of each domain is supplied by the partner. It is probably involved in the recognition of small ligands such as molybdenum (P46930 from SWISSPROT) and sulphate (P16676 from SWISSPROT), and is found in ABC transporters immediately after the ATPase domain.; GO: 0005215 transporter activity, 0005524 ATP binding, 0016820 hydrolase activity, acting on acid anhydrides, catalyzing transmembrane movement of substances, 0006810 transport, 0043190 ATP-binding cassette (ABC) transporter complex; PDB: 1G29_2 1H9M_B 1H9J_A 1H9K_A 1H9R_B 1O7L_C 1H9S_A 1B9N_A 1B9M_A 1GUS_C ....
Probab=30.30 E-value=70 Score=20.64 Aligned_cols=51 Identities=20% Similarity=0.070 Sum_probs=33.6
Q ss_pred CCCcEEEEEEee--cCC-ceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEe
Q 030718 20 QDGQSIMQVVSL--RGS-NLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVD 70 (172)
Q Consensus 20 ~e~q~I~rV~~~--~G~-nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~ 70 (172)
..++.=|+|... .|. -.+.+.+.++....++|+.+....+=++.|+-|.+.
T Consensus 3 ~~N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ 56 (64)
T PF03459_consen 3 ARNQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYAS 56 (64)
T ss_dssp TSEEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEE
T ss_pred CCcEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEE
Confidence 445555555544 442 345566677777999999988888888899977665
No 71
>PF07093 SGT1: SGT1 protein; InterPro: IPR010770 This family consists of several eukaryotic SGT1 proteins. Human SGT1 or hSGT1 is known to suppress GCR2 and is highly expressed in the muscle and heart. The function of this family is unknown although it has been speculated that SGT1 may be functionally analogous to the Gcr2p protein of Saccharomyces cerevisiae which is known to be a regulatory factor of glycolytic gene expression [].
Probab=29.90 E-value=27 Score=33.42 Aligned_cols=35 Identities=26% Similarity=0.543 Sum_probs=25.7
Q ss_pred eEEEEeCCCCEEEEE----e-----eccccceEEEeeCCEEEEe
Q 030718 36 LIEVLDAKDEKSLAL----F-----PAKFQKSMWIKRGSFVVVD 70 (172)
Q Consensus 36 l~eV~~~dG~~~L~~----i-----P~KfRK~vWIkrGD~VlV~ 70 (172)
.+.|.+.||+-.|+. | |....+||||..|-+.||-
T Consensus 91 ~i~V~D~DGEfLLIEaa~~LP~Wl~p~~~~NRvwi~~G~l~iIp 134 (589)
T PF07093_consen 91 FIRVWDSDGEFLLIEAADVLPKWLTPENSENRVWIHNGKLHIIP 134 (589)
T ss_pred EEEEECCCCchHHHHHHHhCccccCCCCcCCCEEEECCEEEEeC
Confidence 344666777665553 3 4556799999999999998
No 72
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=29.86 E-value=85 Score=24.15 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=23.7
Q ss_pred ceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 57 KSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 57 K~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
+.+=|++||-|.|--..+ .| ..|.|+.|+.+.
T Consensus 38 r~~~IkkGD~V~Vi~Gk~-----KG--k~GkV~~V~~~~ 69 (114)
T TIGR01080 38 RALPVRKGDKVRIMRGDF-----KG--HEGKVSKVDLKR 69 (114)
T ss_pred ccceeecCCEEEEecCCC-----CC--CEEEEEEEEcCC
Confidence 455699999999986432 34 579999998554
No 73
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=28.90 E-value=81 Score=25.35 Aligned_cols=32 Identities=25% Similarity=0.217 Sum_probs=23.2
Q ss_pred ceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 57 KSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 57 K~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
+++=|+.||-|+|-...+ .| ..|.|+.|+...
T Consensus 43 Rs~~IkkGD~V~Vi~Gk~-----KG--k~GkV~~V~~k~ 74 (143)
T PTZ00194 43 RSMPVRKDDEVMVVRGHH-----KG--REGKVTAVYRKK 74 (143)
T ss_pred ccceeecCCEEEEecCCC-----CC--CceEEEEEEcCC
Confidence 345599999999986543 34 359999998766
No 74
>PF01426 BAH: BAH domain; InterPro: IPR001025 The BAH (bromo-adjacent homology) family contains proteins such as eukaryotic DNA (cytosine-5) methyltransferases IPR001525 from INTERPRO, the origin recognition complex 1 (Orc1) proteins, as well as several proteins involved in transcriptional regulation. The BAH domain appears to act as a protein-protein interaction module specialised in gene silencing, as suggested for example by its interaction within yeast Orc1p with the silent information regulator Sir1p. The BAH module might therefore play an important role by linking DNA methylation, replication and transcriptional regulation [].; GO: 0003677 DNA binding; PDB: 4DA4_A 3PT6_B 3AV6_A 3AV5_A 3AV4_A 3PT9_A 3SWR_A 3PTA_A 1M4Z_A 1ZBX_A ....
Probab=28.72 E-value=1.1e+02 Score=21.91 Aligned_cols=13 Identities=38% Similarity=0.537 Sum_probs=10.6
Q ss_pred EeeCCEEEEecCC
Q 030718 61 IKRGSFVVVDESG 73 (172)
Q Consensus 61 IkrGD~VlV~p~~ 73 (172)
++.||+|+|.+.+
T Consensus 3 ~~vGD~V~v~~~~ 15 (119)
T PF01426_consen 3 YKVGDFVYVKPDD 15 (119)
T ss_dssp EETTSEEEEECTS
T ss_pred EeCCCEEEEeCCC
Confidence 6789999998765
No 75
>PF11776 DUF3315: Domain of unknown function (DUF3315); InterPro: IPR024572 This is a bacterial family of uncharacterised proteins, which include YohN from Escherichia coli K12.; PDB: 2L1S_A.
Probab=28.68 E-value=68 Score=21.08 Aligned_cols=21 Identities=29% Similarity=0.645 Sum_probs=11.6
Q ss_pred eeccccceEEEeeC-CEEEEec
Q 030718 51 FPAKFQKSMWIKRG-SFVVVDE 71 (172)
Q Consensus 51 iP~KfRK~vWIkrG-D~VlV~p 71 (172)
||.-=|-.=|++-| |||||+.
T Consensus 23 L~~Pp~G~~Wvrv~~dyvLv~~ 44 (52)
T PF11776_consen 23 LPAPPRGYHWVRVGGDYVLVAI 44 (52)
T ss_dssp -----TTEEEEE-SSEEEEEET
T ss_pred CCcCCCCCEeEEECCeEEEEEc
Confidence 34444556799875 5999995
No 76
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases. This model is defined to identify a pair of paralogous 3-prime exoribonucleases in E. coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterized originally as required for the expression of virulence genes, but is now recognized as the exoribonuclease RNase R (Rnr). Its paralog in E. coli and H. influenzae is designated exoribonuclease II (Rnb). Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cutoff to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3-prime exoribonucleases.
Probab=28.28 E-value=3.2e+02 Score=26.60 Aligned_cols=48 Identities=19% Similarity=0.142 Sum_probs=31.9
Q ss_pred eeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH-----HHHHHHhCCCCchhhhc
Q 030718 62 KRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE-----QVRALQKSTEWPEIFKS 112 (172)
Q Consensus 62 krGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~-----qvk~Lrk~g~WP~~F~~ 112 (172)
+.||.|+|..-.+ ++.+ ....|.|+.+|... ++..+...--+|.+|..
T Consensus 121 ~~g~~V~v~i~~~--p~~~-~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~~f~~ 173 (654)
T TIGR00358 121 AEGDKVVVELTEY--PLRR-NLFYGEITQILGNNDDPLIPWWVTLARHEIPFEFPD 173 (654)
T ss_pred CCCCEEEEEEccC--CCCC-CCceEEEEEEEcCCCCcccHHHHHHHHcCcCCCCCH
Confidence 4699999883222 2333 34689999999754 36666666556888865
No 77
>PF09378 HAS-barrel: HAS barrel domain; InterPro: IPR018538 The HAS barrel is named after HerA-ATP Synthase. In ATP synthases, this domain is implicated in the assembly of the catalytic toroid and docking of accessory subunits, such as the subunit of the ATP synthase complex. Similar roles in docking of the functional partner, the NurA nuclease, and assembly of the HerA toroid complex appear likely for the HAS-barrel of the HerA family []. ; PDB: 3OAA_I.
Probab=27.64 E-value=67 Score=22.09 Aligned_cols=27 Identities=33% Similarity=0.535 Sum_probs=19.6
Q ss_pred EeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCH
Q 030718 61 IKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFY 94 (172)
Q Consensus 61 IkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~ 94 (172)
++.|+||.+..- .+.++-|-|..+.+.
T Consensus 23 v~~GeyV~i~~~-------~~~~vlG~V~~i~~~ 49 (91)
T PF09378_consen 23 VRVGEYVVIEYD-------DGEKVLGMVTSISRG 49 (91)
T ss_dssp -BTTEEEEES-----------TTEEEEEEEEES-
T ss_pred CCcCeEEEEEEe-------chhhhhhhhheeEEc
Confidence 679999999852 367899999999886
No 78
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=26.92 E-value=88 Score=23.81 Aligned_cols=30 Identities=33% Similarity=0.281 Sum_probs=22.6
Q ss_pred EEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 59 MWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 59 vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
+=|+.||.|+|-.-.+ .| -.|.|+.+|.+.
T Consensus 3 ~~IrkGD~V~Vi~Gkd-----KG--k~GkVl~v~~k~ 32 (104)
T COG0198 3 MKVKKGDTVKVIAGKD-----KG--KEGKVLKVLPKK 32 (104)
T ss_pred cceecCCEEEEEecCC-----CC--cceEEEEEecCe
Confidence 4589999999986432 34 369999998875
No 79
>TIGR00230 sfsA sugar fermentation stimulation protein. probable regulatory factor involved in maltose metabolism contains a putative DNA binding domain. Isolated as a gene which enabled E.coli strain MK2001 to use maltose.
Probab=26.56 E-value=4.1e+02 Score=22.71 Aligned_cols=74 Identities=16% Similarity=0.135 Sum_probs=43.7
Q ss_pred EEEEeecCCceEEEEeC-CCCEEEEEee--ccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCH--------
Q 030718 26 MQVVSLRGSNLIEVLDA-KDEKSLALFP--AKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFY-------- 94 (172)
Q Consensus 26 ~rV~~~~G~nl~eV~~~-dG~~~L~~iP--~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~-------- 94 (172)
|+.++-. |+|.|.+. +|+..+|++| |+|.-.+ ..|--|++.+.+- .+-|-+..++-+.+.
T Consensus 12 ~~fi~R~--nRF~~~V~~~G~~~~aH~pNtGrl~ell--~pG~~vll~~~~~-----p~rK~~y~l~~v~~~g~~V~int 82 (232)
T TIGR00230 12 GRLIGRY--NRFLVDVEVDGRRETAHCPNTGRLTELI--FPGNDVGLSKSDN-----GGRKLSYTWEAVQCDGGWVLVNT 82 (232)
T ss_pred EEEEeec--CCEEEEEEECCeEEEEEcCCCCCChhhc--CCCCEEEEEECCC-----CCCCCCEEEEEEEECCeEEEEcC
Confidence 4444433 67777654 8999999987 5566544 3888888876541 123434444444332
Q ss_pred ----HHHHHHHhCCCCch
Q 030718 95 ----EQVRALQKSTEWPE 108 (172)
Q Consensus 95 ----~qvk~Lrk~g~WP~ 108 (172)
.=+.++.++|.+|.
T Consensus 83 ~~~N~l~~~~l~~~~i~~ 100 (232)
T TIGR00230 83 QLQNRLFKVAIPSSKISE 100 (232)
T ss_pred ccHHHHHHHHHHcCCCcc
Confidence 22556666777764
No 80
>PF08605 Rad9_Rad53_bind: Fungal Rad9-like Rad53-binding; InterPro: IPR013914 In Saccharomyces cerevisiae (Baker s yeast), the Rad9 is a key adaptor protein in DNA damage checkpoint pathways. DNA damage induces Rad9 phosphorylation, and Rad53 specifically associates with this region of Rad9, when phosphorylated, via the Rad53 IPR000253 from INTERPRO domain []. There is no clear higher eukaryotic ortholog to Rad9.
Probab=26.45 E-value=2.8e+02 Score=21.68 Aligned_cols=42 Identities=19% Similarity=0.045 Sum_probs=31.0
Q ss_pred EEEEeecCCc--eEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEec
Q 030718 26 MQVVSLRGSN--LIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDE 71 (172)
Q Consensus 26 ~rV~~~~G~n--l~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p 71 (172)
|+++.. |.+ ++.|...||. ..|+..==+.+=||-||.|.|.-
T Consensus 27 a~~~~~-~~~~~~~~V~Fedg~---~~i~~~dv~~LDlRIGD~Vkv~~ 70 (131)
T PF08605_consen 27 ATCVGS-GVDRDRSLVRFEDGT---YEIKNEDVKYLDLRIGDTVKVDG 70 (131)
T ss_pred EEEEee-cCCCCeEEEEEecCc---eEeCcccEeeeeeecCCEEEECC
Confidence 555655 443 5999999998 45555445778899999999983
No 81
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=26.31 E-value=1.1e+02 Score=21.80 Aligned_cols=30 Identities=17% Similarity=0.229 Sum_probs=22.1
Q ss_pred eeCCEEEEecCCcchhhcCCCeeeEEEEEEeC
Q 030718 62 KRGSFVVVDESGKEKAIKDGSKVACIVTKVLF 93 (172)
Q Consensus 62 krGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~ 93 (172)
+.||+++...|+- .--.|..+.++|+||+.
T Consensus 30 ~VGD~L~L~E~~~--~~YTGr~~~~~Ityi~~ 59 (72)
T PF12961_consen 30 QVGDILVLREWDN--GEYTGREIEAEITYITD 59 (72)
T ss_pred CCCCEEEEEEecC--CCccccEEEEEEEEEee
Confidence 4577888888762 12347789999999986
No 82
>cd05789 S1_Rrp4 S1_Rrp4: Rrp4 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=25.51 E-value=2.2e+02 Score=19.33 Aligned_cols=53 Identities=11% Similarity=0.080 Sum_probs=29.6
Q ss_pred CCCCCcE-EEEEEeecCCceEEEEeCCCCEEEEEeeccccceE---------EEeeCCEEEEec
Q 030718 18 TLQDGQS-IMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSM---------WIKRGSFVVVDE 71 (172)
Q Consensus 18 ~p~e~q~-I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~v---------WIkrGD~VlV~p 71 (172)
.|..|+. .|+|++... .-+.|....+.+-++.+-.=+..++ +++.||.|.+.-
T Consensus 3 ~p~~GdiV~g~V~~i~~-~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V 65 (86)
T cd05789 3 IPEVGDVVIGRVTEVGF-KRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEV 65 (86)
T ss_pred cCCCCCEEEEEEEEECC-CEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEE
Confidence 4677775 788888654 4466666655444444321111111 467777777664
No 83
>PRK08577 hypothetical protein; Provisional
Probab=25.29 E-value=36 Score=25.94 Aligned_cols=23 Identities=17% Similarity=0.446 Sum_probs=20.4
Q ss_pred EEeeccccceEEEeeCCEEEEec
Q 030718 49 ALFPAKFQKSMWIKRGSFVVVDE 71 (172)
Q Consensus 49 ~~iP~KfRK~vWIkrGD~VlV~p 71 (172)
+-||..+|+++=|+.||+|.+..
T Consensus 15 i~ip~~~r~~l~~~~g~~~~~~~ 37 (136)
T PRK08577 15 ITIPLEIREALGIREGMYVLLIA 37 (136)
T ss_pred EEecHHHHHHcCcCCCCEEEEEE
Confidence 45999999999999999998863
No 84
>PRK09521 exosome complex RNA-binding protein Csl4; Provisional
Probab=25.29 E-value=2.7e+02 Score=22.40 Aligned_cols=60 Identities=20% Similarity=0.162 Sum_probs=32.1
Q ss_pred CcEEEEEEe-ecCCceEEEEeCCCCEEEEEeecccc-----ceEEEeeCCEEEEecCCc-chhhcCCCeeeEEEEEEeC
Q 030718 22 GQSIMQVVS-LRGSNLIEVLDAKDEKSLALFPAKFQ-----KSMWIKRGSFVVVDESGK-EKAIKDGSKVACIVTKVLF 93 (172)
Q Consensus 22 ~q~I~rV~~-~~G~nl~eV~~~dG~~~L~~iP~KfR-----K~vWIkrGD~VlV~p~~~-~~~~e~~~KvkgeIv~vl~ 93 (172)
||.|+.+.. ..|.|.|. ++....+.+.|.++ ++||+ .||.. ......|+-|.|.|+.|..
T Consensus 11 Ge~l~~~~e~~~G~Gty~----~~~~i~as~~G~~~id~~~~~Isv--------~P~~~~~~~~~~GdiV~GkV~~i~~ 77 (189)
T PRK09521 11 GDYLAVIEEYLPGEGTYE----DNGEVYASVVGKVFIDDINRKISV--------IPFKKTPPLLKKGDIVYGRVVDVKE 77 (189)
T ss_pred CCccccccceEcCCCEEe----eCCEEEEEeeEEEEEcCCCCEEEE--------ecCcCCCCCCCCCCEEEEEEEEEcC
Confidence 555554322 35778776 24456676777664 24444 45532 1122346667777777633
No 85
>cd06251 M14_ASTE_ASPA_like_1 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=24.84 E-value=1.7e+02 Score=25.06 Aligned_cols=45 Identities=16% Similarity=0.188 Sum_probs=28.1
Q ss_pred CCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEE
Q 030718 19 LQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVV 68 (172)
Q Consensus 19 p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~Vl 68 (172)
...||.|++|..+.|....+|..+-.-..++ .+..-.|++||.|+
T Consensus 240 V~~G~~ig~i~d~~~~~~~~v~ap~~G~v~~-----~~~~~~v~~G~~l~ 284 (287)
T cd06251 240 VKKGQLLATITDPFGEEEAEVKAPFDGIVIG-----RNNLPLVNEGDALF 284 (287)
T ss_pred ECCCCEEEEEECCCCCceEEEECCCCeEEEE-----ecCCCccCCCCEEE
Confidence 3468888888888887776666653322222 23445577777765
No 86
>KOG4679 consensus Uncharacterized protein PSP1 (suppressor of DNA polymerase alpha mutations in yeast) [General function prediction only]
Probab=24.33 E-value=84 Score=30.19 Aligned_cols=50 Identities=18% Similarity=0.442 Sum_probs=29.5
Q ss_pred CCCCcEEEEEEeecCC-----------ceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEe
Q 030718 19 LQDGQSIMQVVSLRGS-----------NLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVD 70 (172)
Q Consensus 19 p~e~q~I~rV~~~~G~-----------nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~ 70 (172)
+.+++...+.+...-+ -+..|-.-.|..-|..+|.+|- .-.+||+|+||+
T Consensus 329 ~~enr~~~ss~g~~psr~s~s~~~~~~p~~~i~s~~~~~el~~~P~~~~--~i~~r~~y~IVe 389 (572)
T KOG4679|consen 329 WNENRTLWSSVGSKPSRNSSSVSLAYAPLVDIPSKRGKLELLSLPQNFS--SILPRGDYYIVE 389 (572)
T ss_pred cccccccceeeccccCccccchhhccccceecccCccchhhhcCchhhh--hhcccCcEEEEe
Confidence 4456666665555443 1222333356666777777765 446788888887
No 87
>cd04508 TUDOR Tudor domains are found in many eukaryotic organisms and have been implicated in protein-protein interactions in which methylated protein substrates bind to these domains. For example, the Tudor domain of Survival of Motor Neuron (SMN) binds to symmetrically dimethylated arginines of arginine-glycine (RG) rich sequences found in the C-terminal tails of Sm proteins. The SMN protein is linked to spinal muscular atrophy. Another example is the tandem tudor domains of 53BP1, which bind to histone H4 specifically dimethylated at Lys20 (H4-K20me2). 53BP1 is a key transducer of the DNA damage checkpoint signal.
Probab=24.33 E-value=1.3e+02 Score=18.14 Aligned_cols=26 Identities=12% Similarity=0.164 Sum_probs=19.7
Q ss_pred EEEEEeecCCceEEEEeCC-CCEEEEE
Q 030718 25 IMQVVSLRGSNLIEVLDAK-DEKSLAL 50 (172)
Q Consensus 25 I~rV~~~~G~nl~eV~~~d-G~~~L~~ 50 (172)
=|+|++..+++.+.|..-| |....+.
T Consensus 16 ra~V~~~~~~~~~~V~f~DyG~~~~v~ 42 (48)
T cd04508 16 RAKITSILSDGKVEVFFVDYGNTEVVP 42 (48)
T ss_pred EEEEEEECCCCcEEEEEEcCCCcEEEe
Confidence 4677888878889998888 7766543
No 88
>PTZ00007 (NAP-L) nucleosome assembly protein -L; Provisional
Probab=24.06 E-value=93 Score=28.19 Aligned_cols=16 Identities=6% Similarity=0.015 Sum_probs=13.0
Q ss_pred HHHHHHhCCCCchhhh
Q 030718 96 QVRALQKSTEWPEIFK 111 (172)
Q Consensus 96 qvk~Lrk~g~WP~~F~ 111 (172)
+|-...+..+||....
T Consensus 258 eiG~~ikd~IIP~AV~ 273 (337)
T PTZ00007 258 EIGITIRDKLIPYAVY 273 (337)
T ss_pred HHHHHHHHhcccccHH
Confidence 6788899999997653
No 89
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=24.05 E-value=61 Score=21.33 Aligned_cols=35 Identities=20% Similarity=0.245 Sum_probs=19.4
Q ss_pred eeccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEE
Q 030718 51 FPAKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKV 91 (172)
Q Consensus 51 iP~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~v 91 (172)
||.+--+..| -||.|+|..... ..+.+-.|+|+.|
T Consensus 24 Ip~~~l~~A~--~gD~V~v~i~~~----~~~~~~eg~vv~V 58 (58)
T PF08206_consen 24 IPPRNLNGAM--DGDKVLVRITPP----SRGKRPEGEVVEV 58 (58)
T ss_dssp E-HHHHTTS---TT-EEEEEEEES----SSEEEEEEEEEE-
T ss_pred ECHHHHCCCC--CCCEEEEEEecC----CCCCCCCEEEEeC
Confidence 4444444433 699999986431 2345678998875
No 90
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=23.82 E-value=49 Score=21.97 Aligned_cols=12 Identities=50% Similarity=0.755 Sum_probs=9.0
Q ss_pred EeeCCEEEEecC
Q 030718 61 IKRGSFVVVDES 72 (172)
Q Consensus 61 IkrGD~VlV~p~ 72 (172)
|+.||+|+|++.
T Consensus 14 i~~gd~lii~~~ 25 (81)
T cd06529 14 IPDGDLVLVDPS 25 (81)
T ss_pred cCCCCEEEEcCC
Confidence 677888888864
No 91
>PRK05054 exoribonuclease II; Provisional
Probab=23.30 E-value=5.1e+02 Score=25.23 Aligned_cols=50 Identities=12% Similarity=0.102 Sum_probs=32.9
Q ss_pred EeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH-----HHHHHHhCCCCchhhhc
Q 030718 61 IKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE-----QVRALQKSTEWPEIFKS 112 (172)
Q Consensus 61 IkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~-----qvk~Lrk~g~WP~~F~~ 112 (172)
.+.||+|+|..-.+ +...+....|.|+.+|... ++..+..+--+|.+|..
T Consensus 122 ~~~gd~V~v~i~~~--p~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l~~~f~~ 176 (644)
T PRK05054 122 FKEGDWVVAELRRH--PLKGDRGFYAEITQFITDADDHFAPWWVTLARHNLEREAPA 176 (644)
T ss_pred CCCCCEEEEEEecC--CCCCCCCceEEEEEEECCCCCCccHHHHHHHHcCCCCCCCc
Confidence 45699999985322 1221222589999999753 45666666667988876
No 92
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=23.29 E-value=1e+02 Score=23.13 Aligned_cols=30 Identities=33% Similarity=0.297 Sum_probs=21.9
Q ss_pred EEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHH
Q 030718 60 WIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQ 96 (172)
Q Consensus 60 WIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~q 96 (172)
=|++||.|.|-... ..| -.|.|..|+...+
T Consensus 4 ~i~kGD~V~Vi~G~-----dKG--k~G~V~~V~~~~~ 33 (105)
T PRK00004 4 KIKKGDTVIVIAGK-----DKG--KRGKVLKVLPKKN 33 (105)
T ss_pred cccCCCEEEEeEcC-----CCC--cEEEEEEEEcCCC
Confidence 38999999987533 134 3699999987764
No 93
>PF05610 DUF779: Protein of unknown function (DUF779); InterPro: IPR008497 This family consists of several bacterial proteins of unknown function.
Probab=23.26 E-value=1.5e+02 Score=22.31 Aligned_cols=32 Identities=19% Similarity=0.176 Sum_probs=27.7
Q ss_pred CCCCCcEEEEEEeecCCceEEEEeCCCCEEEEE
Q 030718 18 TLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLAL 50 (172)
Q Consensus 18 ~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~ 50 (172)
.-...|.|.-|+..+| .-|.++.+.|+.++.+
T Consensus 61 ywkht~L~iDVv~GrG-~~FSLE~~~G~rF~~r 92 (95)
T PF05610_consen 61 YWKHTQLTIDVVPGRG-GGFSLEAPEGKRFLTR 92 (95)
T ss_pred HhhCcEEEEEEEecCC-CeeeccCCCCcEEEEe
Confidence 3456789999999999 7799999999999876
No 94
>cd06254 M14_ASTE_ASPA_like_4 A functionally uncharacterized subgroup of the Succinylglutamate desuccinylase (ASTE)/aspartoacylase (ASPA) subfamily which is part of the M14 family of metallocarboxypeptidases. ASTE catalyzes the fifth and last step in arginine catabolism by the arginine succinyltransferase pathway, and aspartoacylase (ASPA, also known as aminoacylase 2, and ACY-2; EC:3.5.1.15) cleaves N-acetyl L-aspartic acid (NAA) into aspartate and acetate. NAA is abundant in the brain, and hydrolysis of NAA by ASPA may help maintain white matter. ASPA is an NAA scavenger in other tissues. Mutations in the gene encoding ASPA cause Canavan disease (CD), a fatal progressive neurodegenerative disorder involving dysmyelination and spongiform degeneration of white matter in children. This enzyme binds zinc which is necessary for activity. Measurement of elevated NAA levels in urine is used in the diagnosis of CD.
Probab=23.22 E-value=1.3e+02 Score=25.84 Aligned_cols=28 Identities=21% Similarity=0.137 Sum_probs=16.9
Q ss_pred CCCcEEEEEEeecCCceEEEEeCCCCEE
Q 030718 20 QDGQSIMQVVSLRGSNLIEVLDAKDEKS 47 (172)
Q Consensus 20 ~e~q~I~rV~~~~G~nl~eV~~~dG~~~ 47 (172)
..||.|+.|+.+.|.-..+|.-|-.-..
T Consensus 245 ~~G~~lg~i~dp~g~~~~~i~Ap~dG~v 272 (288)
T cd06254 245 QKGALLGYVTDYFGNVIAEYRAPFDGVV 272 (288)
T ss_pred cCCCEEEEEECCCCCceEEEEcCCCcEE
Confidence 3577777777777666666655543333
No 95
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=23.17 E-value=2.3e+02 Score=23.86 Aligned_cols=53 Identities=13% Similarity=0.105 Sum_probs=32.4
Q ss_pred CCCCCCc-EEEEEEeecCCceEEEEeCCCCEEEEEe---eccc------cceEEEeeCCEEEEe
Q 030718 17 LTLQDGQ-SIMQVVSLRGSNLIEVLDAKDEKSLALF---PAKF------QKSMWIKRGSFVVVD 70 (172)
Q Consensus 17 ~~p~e~q-~I~rV~~~~G~nl~eV~~~dG~~~L~~i---P~Kf------RK~vWIkrGD~VlV~ 70 (172)
..|..|+ +|++|+... ++.+.|....+..-+.++ ..+. +-+-+++.||+|.+.
T Consensus 59 y~P~vGDiViG~V~~i~-~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~ak 121 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVT-FSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAK 121 (235)
T ss_pred ccCCCCCEEEEEEEEEe-CceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEE
Confidence 5677776 677777765 456777776554433332 2221 113467999999876
No 96
>KOG2199 consensus Signal transducing adaptor protein STAM/STAM2 [Signal transduction mechanisms]
Probab=23.05 E-value=33 Score=32.18 Aligned_cols=30 Identities=17% Similarity=0.065 Sum_probs=26.3
Q ss_pred eeEEEEEEeCHHHHHHHHhC-----CCCchhhhcc
Q 030718 84 VACIVTKVLFYEQVRALQKS-----TEWPEIFKST 113 (172)
Q Consensus 84 vkgeIv~vl~~~qvk~Lrk~-----g~WP~~F~~~ 113 (172)
.+|+||.||..-.-.||+-. |+.|..|...
T Consensus 235 kaGdIItVLd~s~~~WWKG~~~~~~GlFPsnfVT~ 269 (462)
T KOG2199|consen 235 KAGDIITVLDDSDPNWWKGENHRGIGLFPSNFVTA 269 (462)
T ss_pred ecCcEEEEcccCCcchhccccCCcccccchhhhhh
Confidence 68999999999999999854 8999999773
No 97
>TIGR03673 rpl14p_arch 50S ribosomal protein L14P. Part of the 50S ribosomal subunit. Forms a cluster with proteins L3 and L24e, part of which may contact the 16S rRNA in 2 intersubunit bridges.
Probab=22.78 E-value=3e+02 Score=21.70 Aligned_cols=54 Identities=11% Similarity=0.037 Sum_probs=30.8
Q ss_pred ccccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHHHHHHHhCCCCchhhhc
Q 030718 53 AKFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQVRALQKSTEWPEIFKS 112 (172)
Q Consensus 53 ~KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~qvk~Lrk~g~WP~~F~~ 112 (172)
++.++.=+-.-||+|+|.--..- +...+..++|-|+.- +. ..-|+.|.|. .|.+
T Consensus 38 g~~~r~~~a~iGD~IvvsVK~~~-p~~kg~v~kAVIVRt--kk--~~~R~dGs~i-~Fdd 91 (131)
T TIGR03673 38 GVKRRLPCAGVGDMVVVSVKKGT-PEMRKQVFKAVVVRQ--RK--EYRRPDGTRV-KFED 91 (131)
T ss_pred CCcccCCccccCCEEEEEEEECC-ccccCCEeEEEEEEe--Cc--ceecCCCcEE-EeCC
Confidence 44444457889999999843221 233456677777764 22 1234567666 3544
No 98
>TIGR00156 conserved hypothetical protein TIGR00156. As of the last revision, this family consists only of two proteins from Escherichia coli and one from the related species Haemophilus influenzae.
Probab=22.63 E-value=1.8e+02 Score=22.75 Aligned_cols=46 Identities=15% Similarity=0.126 Sum_probs=32.9
Q ss_pred EEEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEe
Q 030718 24 SIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVD 70 (172)
Q Consensus 24 ~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~ 70 (172)
.=+.|++.+|...|...+..|. ..+.|+.+.=+-+=|..+|-|-+.
T Consensus 62 L~G~Iv~~l~~d~Y~F~D~TG~-I~VeId~~~w~G~~v~p~d~V~I~ 107 (126)
T TIGR00156 62 LRGNIISHIGDDRYVFRDKSGE-INVVIPAAVWNGREVQPKDMVNIS 107 (126)
T ss_pred EEEEEEEEeCCceEEEECCCCC-EEEEECHHHcCCCcCCCCCEEEEE
Confidence 3478999999999999999995 677887654333344555555543
No 99
>PF13030 DUF3891: Protein of unknown function (DUF3891)
Probab=22.59 E-value=69 Score=26.98 Aligned_cols=50 Identities=16% Similarity=0.034 Sum_probs=29.5
Q ss_pred EEeCCCCEEEEEeeccc--cceEEEeeC--CEEEEecCCcchhhcCCCeeeEEEEEEeC
Q 030718 39 VLDAKDEKSLALFPAKF--QKSMWIKRG--SFVVVDESGKEKAIKDGSKVACIVTKVLF 93 (172)
Q Consensus 39 V~~~dG~~~L~~iP~Kf--RK~vWIkrG--D~VlV~p~~~~~~~e~~~KvkgeIv~vl~ 93 (172)
|+..-|.++...+|.-. +.+++|... +.|.|+||+|+ .+++.-.|.+++-
T Consensus 165 C~~~p~~~~~~eip~~~~g~~~~~~~~~~~~~i~v~PwPF~-----~~~f~v~v~~r~v 218 (221)
T PF13030_consen 165 CMNEPGETRELEIPWFKGGDERLQITWIDDGTIRVDPWPFE-----KDEFTVSVEYRLV 218 (221)
T ss_pred hCCCCCCCccccCCCCCCCceeEEEEecCCCeEEecccccc-----CCceEEEEEEEEC
Confidence 33334555555555322 356677654 58899999983 4456666665543
No 100
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=21.99 E-value=1.2e+02 Score=21.89 Aligned_cols=33 Identities=27% Similarity=0.301 Sum_probs=24.0
Q ss_pred ceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHHH
Q 030718 57 KSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYEQ 96 (172)
Q Consensus 57 K~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~q 96 (172)
.++=|++||-|.|--..+ .| | .|.|..|+...+
T Consensus 5 ~~~~I~~GD~V~Vi~G~d-----KG-K-~G~V~~V~~~~~ 37 (83)
T CHL00141 5 KKMHVKIGDTVKIISGSD-----KG-K-IGEVLKIIKKSN 37 (83)
T ss_pred eeCcccCCCEEEEeEcCC-----CC-c-EEEEEEEEcCCC
Confidence 345699999998875432 34 3 699999998764
No 101
>PF12616 DUF3775: Protein of unknown function (DUF3775); InterPro: IPR022254 This domain family is found in bacteria, and is approximately 80 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=21.93 E-value=19 Score=25.81 Aligned_cols=10 Identities=60% Similarity=1.205 Sum_probs=8.1
Q ss_pred eEEEeeCCEE
Q 030718 58 SMWIKRGSFV 67 (172)
Q Consensus 58 ~vWIkrGD~V 67 (172)
.+||-||||=
T Consensus 24 LmwiGRGd~~ 33 (75)
T PF12616_consen 24 LMWIGRGDFE 33 (75)
T ss_pred HHHhcCCCCC
Confidence 4799999884
No 102
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=21.51 E-value=3e+02 Score=25.78 Aligned_cols=91 Identities=16% Similarity=0.147 Sum_probs=59.8
Q ss_pred CCCCCcEEEEEEeecCCceEEEEeCCCCEEEEEeecccc-------ceEEEeeCCEEEEecCCcchhhcCCCeee-----
Q 030718 18 TLQDGQSIMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQ-------KSMWIKRGSFVVVDESGKEKAIKDGSKVA----- 85 (172)
Q Consensus 18 ~p~e~q~I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfR-------K~vWIkrGD~VlV~p~~~~~~~e~~~Kvk----- 85 (172)
.-+...+|++|+...+.+++-|....|-++++.+-+-.- -+|=+.+..|-||..-+- +.+-.|.
T Consensus 68 l~~~pl~vg~v~e~id~~~~iVks~~g~~~vV~i~~~vd~~~L~pG~rVal~~~s~~Iv~vLp~----~~Dp~V~~M~v~ 143 (406)
T COG1222 68 LKEPPLIVGTVLEVLDDGRAIVKSSTGPKFVVNILSFVDRDLLEPGMRVALNRDSYSIVRVLPP----EVDPRVSVMEVE 143 (406)
T ss_pred hcCCCceEEEEEEEcCCceEEEEeCCCCeEEEeccCCcCHHHcCCCCEEEEcCCcceeeeeCCC----ccCchhheeeec
Confidence 345578999999999999999999999999998754333 256677777777764331 1121111
Q ss_pred --EEEEEE---eCHHHHHHHHhCCCC----chhhhc
Q 030718 86 --CIVTKV---LFYEQVRALQKSTEW----PEIFKS 112 (172)
Q Consensus 86 --geIv~v---l~~~qvk~Lrk~g~W----P~~F~~ 112 (172)
.++.|= =.++||++||..=.. |+-|..
T Consensus 144 e~PdvtY~dIGGL~~Qi~EirE~VELPL~~PElF~~ 179 (406)
T COG1222 144 EKPDVTYEDIGGLDEQIQEIREVVELPLKNPELFEE 179 (406)
T ss_pred cCCCCChhhccCHHHHHHHHHHHhcccccCHHHHHH
Confidence 111110 036899999987555 466755
No 103
>PF03079 ARD: ARD/ARD' family; InterPro: IPR004313 The two acireductone dioxygenase enzymes (ARD and ARD', previously known as E-2 and E-2') from Klebsiella pneumoniae share the same amino acid sequence Q9ZFE7 from SWISSPROT, but bind different metal ions: ARD binds Ni2+, ARD' binds Fe2+ []. ARD and ARD' can be experimentally interconverted by removal of the bound metal ion and reconstitution with the appropriate metal ion. The two enzymes share the same substrate, 1,2-dihydroxy-3-keto-5-(methylthio)pentene, but yield different products. ARD' yields the alpha-keto precursor of methionine (and formate), thus forming part of the ubiquitous methionine salvage pathway that converts 5'-methylthioadenosine (MTA) to methionine. This pathway is responsible for the tight control of the concentration of MTA, which is a powerful inhibitor of polyamine biosynthesis and transmethylation reactions []. ARD yields methylthiopropanoate, carbon monoxide and formate, and thus prevents the conversion of MTA to methionine. The role of the ARD catalysed reaction is unclear: methylthiopropanoate is cytotoxic, and carbon monoxide can activate guanylyl cyclase, leading to increased intracellular cGMP levels [, ]. This family also contains other proteins, whose functions are not well characterised.; GO: 0010309 acireductone dioxygenase [iron(II)-requiring] activity, 0055114 oxidation-reduction process; PDB: 1VR3_A 1ZRR_A 2HJI_A.
Probab=20.88 E-value=1.3e+02 Score=24.09 Aligned_cols=31 Identities=26% Similarity=0.447 Sum_probs=22.5
Q ss_pred ecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEec
Q 030718 31 LRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVDE 71 (172)
Q Consensus 31 ~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~p 71 (172)
..|+..|.|...++.-. +|.+..||+++|-+
T Consensus 99 ~~G~g~Fdvr~~~~~wi----------ri~~e~GDli~vP~ 129 (157)
T PF03079_consen 99 VDGSGYFDVRDGDDVWI----------RILCEKGDLIVVPA 129 (157)
T ss_dssp EECEEEEEEE-TTCEEE----------EEEEETTCEEEE-T
T ss_pred eCcEEEEEEEcCCCEEE----------EEEEcCCCEEecCC
Confidence 37889999998876543 36788999999864
No 104
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=20.84 E-value=1.5e+02 Score=15.75 Aligned_cols=25 Identities=24% Similarity=0.078 Sum_probs=16.8
Q ss_pred EeeCCEEEEecCCcchhhcCCCeeeEEEEEEe
Q 030718 61 IKRGSFVVVDESGKEKAIKDGSKVACIVTKVL 92 (172)
Q Consensus 61 IkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl 92 (172)
++.|+.|.|---.+ .+ ..|.|+.+-
T Consensus 2 ~~~G~~V~I~~G~~-----~g--~~g~i~~i~ 26 (28)
T smart00739 2 FEVGDTVRVIAGPF-----KG--KVGKVLEVD 26 (28)
T ss_pred CCCCCEEEEeECCC-----CC--cEEEEEEEc
Confidence 46899999885433 24 468888763
No 105
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=20.81 E-value=5.9e+02 Score=24.89 Aligned_cols=48 Identities=15% Similarity=0.131 Sum_probs=31.6
Q ss_pred eeCCEEEEecCCcchhhcCCCeeeEEEEEEeCH-----HHHHHHHhCCCCchhhhc
Q 030718 62 KRGSFVVVDESGKEKAIKDGSKVACIVTKVLFY-----EQVRALQKSTEWPEIFKS 112 (172)
Q Consensus 62 krGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~-----~qvk~Lrk~g~WP~~F~~ 112 (172)
+.||.|+|..-.+ ++. ...-.|.|+.+|.. -++..+...--+|.+|..
T Consensus 173 ~~g~~v~v~i~~~--p~~-~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i~~~f~~ 225 (709)
T TIGR02063 173 EEGDKVLVEITKY--PDR-NRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPE 225 (709)
T ss_pred CCCCEEEEEEccC--CCC-CCCceEEEEEEeCCCCcccchHHHHHHHcCcCCCCCH
Confidence 4689999985222 122 34468999999975 356666666567888865
No 106
>PRK10053 hypothetical protein; Provisional
Probab=20.78 E-value=2e+02 Score=22.66 Aligned_cols=45 Identities=11% Similarity=0.183 Sum_probs=35.3
Q ss_pred EEEEEeecCCceEEEEeCCCCEEEEEeeccccceEEEeeCCEEEEe
Q 030718 25 IMQVVSLRGSNLIEVLDAKDEKSLALFPAKFQKSMWIKRGSFVVVD 70 (172)
Q Consensus 25 I~rV~~~~G~nl~eV~~~dG~~~L~~iP~KfRK~vWIkrGD~VlV~ 70 (172)
=+.|++.+|+..|...+..|+ .-+.|+.+.-.-.=|...|-|-+.
T Consensus 67 ~G~Iv~~lg~d~Y~F~D~tG~-I~VeID~~~w~G~~v~p~~kV~I~ 111 (130)
T PRK10053 67 RGNLIDHKGDDRYVFRDKSGE-INVIIPAAVFDGREVQPDQMININ 111 (130)
T ss_pred EEEEEEEeCCceEEEECCCCc-EEEEeCHHHcCCCcCCCCCEEEEE
Confidence 478899999999999999995 778898775555556677766654
No 107
>smart00743 Agenet Tudor-like domain present in plant sequences. Domain in plant sequences with possible chromatin-associated functions.
Probab=20.59 E-value=2.1e+02 Score=18.36 Aligned_cols=19 Identities=16% Similarity=-0.043 Sum_probs=16.3
Q ss_pred EEEEEeecCCceEEEEeCC
Q 030718 25 IMQVVSLRGSNLIEVLDAK 43 (172)
Q Consensus 25 I~rV~~~~G~nl~eV~~~d 43 (172)
-|+|++..|++.|.|...+
T Consensus 21 ~a~V~~~~~~~~~~V~~~~ 39 (61)
T smart00743 21 EAVVTKVLGDGKYLVRYLT 39 (61)
T ss_pred EEEEEEECCCCEEEEEECC
Confidence 3889999998889998887
No 108
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=20.59 E-value=3e+02 Score=20.58 Aligned_cols=57 Identities=21% Similarity=0.250 Sum_probs=30.3
Q ss_pred cCCceEEEEeCCCCEEEE-Eeec------cccceEEEeeCCEEEEecCCcchhhcCCCeeeEEEEEEeCHH
Q 030718 32 RGSNLIEVLDAKDEKSLA-LFPA------KFQKSMWIKRGSFVVVDESGKEKAIKDGSKVACIVTKVLFYE 95 (172)
Q Consensus 32 ~G~nl~eV~~~dG~~~L~-~iP~------KfRK~vWIkrGD~VlV~p~~~~~~~e~~~KvkgeIv~vl~~~ 95 (172)
.|+.+|.|..-| ...+ .|++ -|.+-+-+.-|+.+++.. |.-++.+|.|+|+.-...+
T Consensus 6 ~gGkQykV~~Gd--~i~Ve~l~~~~G~~i~l~~VLlv~~~~~~~iG~-----P~l~~a~V~a~V~~~~r~~ 69 (101)
T TIGR00061 6 IGGKQYKVEEGQ--TVRIEKLDAAPGDTVEFDKVLMVNKGGDVKIGK-----PYVEGAKVVAEVEKHGRGK 69 (101)
T ss_pred ECCEEEEEeCCC--EEEEcccCCCCCCEEEEEEEEEEecCCCeEECC-----eEcCCCEEEEEEEeecCCC
Confidence 356666666543 2222 2322 344555555666666653 1234667888887654433
Done!