Query psy10593
Match_columns 275
No_of_seqs 185 out of 482
Neff 3.7
Searched_HMMs 46136
Date Fri Aug 16 22:20:18 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10593.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10593hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2925|consensus 100.0 2.1E-34 4.5E-39 247.3 4.6 162 3-210 1-165 (167)
2 cd05792 S1_eIF1AD_like S1_eIF1 100.0 7.9E-33 1.7E-37 214.5 11.2 78 26-103 1-78 (78)
3 smart00652 eIF1a eukaryotic tr 100.0 2.4E-32 5.2E-37 213.0 11.9 83 21-104 1-83 (83)
4 TIGR00523 eIF-1A eukaryotic/ar 100.0 2.5E-32 5.4E-37 219.5 11.8 95 11-105 5-99 (99)
5 PLN00208 translation initiatio 100.0 8.8E-32 1.9E-36 229.4 12.1 94 15-109 22-115 (145)
6 PRK04012 translation initiatio 100.0 4.1E-31 8.9E-36 212.9 11.7 89 16-105 12-100 (100)
7 PTZ00329 eukaryotic translatio 100.0 3.8E-31 8.2E-36 227.5 11.7 94 16-110 23-116 (155)
8 cd04456 S1_IF1A_like S1_IF1A_l 100.0 1.8E-30 3.9E-35 200.6 11.3 78 26-103 1-78 (78)
9 cd05793 S1_IF1A S1_IF1A: Trans 100.0 2.8E-28 6.1E-33 187.8 11.0 77 26-103 1-77 (77)
10 PF01176 eIF-1a: Translation i 99.9 6.5E-24 1.4E-28 157.7 7.7 65 23-88 1-65 (65)
11 COG0361 InfA Translation initi 99.9 6.9E-23 1.5E-27 158.3 8.9 72 21-93 3-75 (75)
12 KOG3403|consensus 99.8 2.2E-22 4.7E-27 169.2 2.6 93 16-109 23-115 (145)
13 TIGR00008 infA translation ini 99.8 1.8E-18 3.8E-23 131.6 8.7 62 26-88 6-68 (68)
14 PRK12442 translation initiatio 99.7 4E-17 8.6E-22 129.5 9.1 65 26-91 8-73 (87)
15 CHL00010 infA translation init 99.5 3.7E-14 7.9E-19 109.4 8.9 66 26-92 8-74 (78)
16 PRK00276 infA translation init 99.5 1.3E-13 2.9E-18 104.3 9.0 64 26-90 8-72 (72)
17 KOG2925|consensus 99.5 4.4E-14 9.6E-19 122.3 4.4 46 127-172 63-111 (167)
18 cd05792 S1_eIF1AD_like S1_eIF1 99.2 2.3E-11 4.9E-16 94.9 4.9 38 127-164 41-78 (78)
19 cd04451 S1_IF1 S1_IF1: Transla 99.2 2E-10 4.3E-15 84.3 8.4 62 26-88 2-64 (64)
20 PLN00208 translation initiatio 98.6 4.3E-08 9.3E-13 84.5 5.9 47 127-174 73-119 (145)
21 cd04456 S1_IF1A_like S1_IF1A_l 98.6 3.5E-08 7.6E-13 76.6 4.8 38 127-164 41-78 (78)
22 smart00652 eIF1a eukaryotic tr 98.6 4E-08 8.7E-13 77.0 4.9 39 126-165 45-83 (83)
23 TIGR00523 eIF-1A eukaryotic/ar 98.5 1.6E-07 3.5E-12 76.1 5.1 40 127-166 60-99 (99)
24 PTZ00329 eukaryotic translatio 98.3 9.5E-07 2.1E-11 77.0 6.0 44 127-171 73-116 (155)
25 cd05793 S1_IF1A S1_IF1A: Trans 97.8 2.4E-05 5.2E-10 60.7 4.6 37 126-163 40-76 (77)
26 cd04466 S1_YloQ_GTPase S1_YloQ 97.8 0.00014 3.1E-09 52.5 7.5 60 28-91 2-62 (68)
27 PRK04012 translation initiatio 97.6 0.00012 2.5E-09 59.7 5.0 38 127-165 62-99 (100)
28 PRK00098 GTPase RsgA; Reviewed 95.6 0.053 1.2E-06 50.4 7.9 61 28-92 2-63 (298)
29 PRK12289 GTPase RsgA; Reviewed 94.8 0.12 2.7E-06 49.8 8.0 69 22-92 4-79 (352)
30 PRK12288 GTPase RsgA; Reviewed 94.6 0.13 2.9E-06 49.4 7.7 62 27-92 40-102 (347)
31 cd01854 YjeQ_engC YjeQ/EngC. 93.9 0.2 4.3E-06 46.4 7.1 65 29-100 1-66 (287)
32 PRK01889 GTPase RsgA; Reviewed 89.3 1.2 2.7E-05 42.7 7.1 62 24-92 26-92 (356)
33 PF01176 eIF-1a: Translation i 83.2 1.4 3E-05 32.7 3.1 22 127-149 44-65 (65)
34 cd00164 S1_like S1_like: Ribos 80.6 7.5 0.00016 26.0 5.8 49 28-77 2-55 (65)
35 PF02736 Myosin_N: Myosin N-te 72.8 6.5 0.00014 27.0 3.8 32 20-52 7-38 (42)
36 cd04721 BAH_plant_1 BAH, or Br 71.9 7.1 0.00015 32.9 4.5 31 59-90 3-33 (130)
37 COG4048 Uncharacterized protei 69.9 4.8 0.0001 34.3 3.1 23 124-146 72-94 (123)
38 PF15057 DUF4537: Domain of un 69.5 14 0.00031 30.8 5.8 50 27-77 15-68 (124)
39 PF11948 DUF3465: Protein of u 68.4 23 0.00051 30.6 7.0 74 28-109 42-124 (131)
40 PF01455 HupF_HypC: HupF/HypC 66.4 18 0.00039 27.5 5.3 57 28-98 6-64 (68)
41 TIGR00638 Mop molybdenum-pteri 65.3 30 0.00065 24.6 6.1 52 23-74 5-59 (69)
42 KOG2107|consensus 64.0 8.8 0.00019 34.7 3.7 38 25-74 93-130 (179)
43 PF03459 TOBE: TOBE domain; I 63.9 15 0.00033 25.9 4.3 53 22-74 2-57 (64)
44 PF09038 53-BP1_Tudor: Tumour 61.0 23 0.00051 30.3 5.5 95 29-161 22-117 (122)
45 CHL00075 rpl21 ribosomal prote 60.4 57 0.0012 27.1 7.6 26 129-154 48-73 (108)
46 cd05685 S1_Tex S1_Tex: The C-t 57.9 52 0.0011 22.5 6.1 48 26-75 3-56 (68)
47 PRK10413 hydrogenase 2 accesso 56.6 38 0.00082 26.9 5.7 57 29-96 7-67 (82)
48 TIGR00074 hypC_hupF hydrogenas 55.7 38 0.00082 26.5 5.5 52 29-97 7-61 (76)
49 PHA02945 interferon resistance 55.5 86 0.0019 25.6 7.6 67 19-87 6-79 (88)
50 COG1162 Predicted GTPases [Gen 54.1 33 0.00071 33.3 5.9 69 28-103 6-78 (301)
51 PF04076 BOF: Bacterial OB fol 53.6 42 0.0009 27.5 5.7 46 27-73 39-84 (103)
52 PRK05573 rplU 50S ribosomal pr 53.4 85 0.0018 25.7 7.5 28 128-155 45-72 (103)
53 PRK10409 hydrogenase assembly 52.5 44 0.00096 27.0 5.6 53 29-96 7-66 (90)
54 TIGR00061 L21 ribosomal protei 46.2 1.1E+02 0.0025 25.0 7.1 25 129-153 45-69 (101)
55 cd06555 ASCH_PF0470_like ASC-1 46.1 68 0.0015 26.7 5.9 54 35-100 15-68 (109)
56 cd04479 RPA3 RPA3: A subfamily 44.5 52 0.0011 26.3 4.9 29 27-56 20-48 (101)
57 TIGR00230 sfsA sugar fermentat 44.0 1.5E+02 0.0032 27.7 8.4 123 28-168 11-151 (232)
58 PF03749 SfsA: Sugar fermentat 42.8 1.6E+02 0.0034 27.0 8.3 116 41-170 10-140 (215)
59 KOG3403|consensus 42.1 43 0.00093 29.3 4.2 42 128-170 74-115 (145)
60 COG0298 HypC Hydrogenase matur 41.9 1.6E+02 0.0034 23.9 7.1 54 29-96 7-63 (82)
61 PRK11642 exoribonuclease R; Pr 40.0 97 0.0021 33.7 7.4 48 64-111 186-241 (813)
62 cd05791 S1_CSL4 S1_CSL4: CSL4, 39.7 63 0.0014 25.4 4.6 56 21-77 3-74 (92)
63 PTZ00454 26S protease regulato 39.5 76 0.0016 31.3 6.1 50 24-74 65-114 (398)
64 PF00717 Peptidase_S24: Peptid 38.4 9.6 0.00021 27.0 -0.2 27 64-92 11-37 (70)
65 TIGR03689 pup_AAA proteasome A 37.8 53 0.0012 33.8 4.9 49 25-75 107-155 (512)
66 PF08661 Rep_fac-A_3: Replicat 36.9 85 0.0018 25.1 5.0 43 27-73 23-66 (109)
67 PF09884 DUF2111: Uncharacteri 36.2 36 0.00079 27.5 2.7 24 123-146 53-77 (84)
68 COG1096 Predicted RNA-binding 36.1 3.1E+02 0.0067 25.2 9.0 107 24-149 10-132 (188)
69 PRK12278 50S ribosomal protein 35.0 1.9E+02 0.0041 26.9 7.6 30 129-158 46-75 (221)
70 cd04482 RPA2_OBF_like RPA2_OBF 34.0 66 0.0014 25.2 3.9 38 36-73 17-57 (91)
71 PF04014 Antitoxin-MazE: Antid 34.0 16 0.00035 25.1 0.4 30 47-76 4-33 (47)
72 TIGR00156 conserved hypothetic 33.6 1.1E+02 0.0025 26.1 5.5 46 27-73 62-107 (126)
73 PF07039 DUF1325: SGF29 tudor- 33.4 72 0.0016 26.9 4.3 62 26-88 19-96 (130)
74 TIGR02754 sod_Ni_protease nick 32.7 47 0.001 25.1 2.8 28 64-91 12-41 (90)
75 TIGR01439 lp_hng_hel_AbrB loop 32.2 35 0.00075 22.3 1.8 26 51-76 8-33 (43)
76 PRK10053 hypothetical protein; 32.1 1.2E+02 0.0026 26.0 5.4 46 27-73 66-111 (130)
77 cd04719 BAH_Orc1p_animal BAH, 31.9 44 0.00095 28.4 2.7 30 62-91 2-31 (128)
78 cd04453 S1_RNase_E S1_RNase_E: 31.1 2.5E+02 0.0055 21.7 6.9 52 25-76 9-69 (88)
79 TIGR02063 RNase_R ribonuclease 30.2 2.7E+02 0.0058 29.4 8.6 48 64-111 172-227 (709)
80 COG0509 GcvH Glycine cleavage 30.2 24 0.00051 30.6 0.8 41 52-92 3-48 (131)
81 KOG4225|consensus 29.4 21 0.00046 36.6 0.5 90 81-170 250-359 (489)
82 PRK05054 exoribonuclease II; P 28.6 5E+02 0.011 27.4 10.3 48 64-111 122-178 (644)
83 PRK00347 putative DNA-binding 28.5 4.4E+02 0.0095 24.4 8.8 75 27-105 8-100 (234)
84 cd06530 S26_SPase_I The S26 Ty 28.4 59 0.0013 24.0 2.7 28 64-91 14-43 (85)
85 PF01426 BAH: BAH domain; Int 27.8 58 0.0013 25.2 2.6 29 64-92 3-32 (119)
86 PRK12281 rplX 50S ribosomal pr 27.7 89 0.0019 24.3 3.6 31 62-93 5-35 (76)
87 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 27.3 2.6E+02 0.0057 20.7 6.9 57 21-78 3-69 (86)
88 PRK06299 rpsA 30S ribosomal pr 26.6 6.9E+02 0.015 25.3 10.6 64 24-89 374-443 (565)
89 PF11302 DUF3104: Protein of u 26.1 39 0.00085 26.8 1.4 28 63-90 5-38 (75)
90 TIGR00358 3_prime_RNase VacB a 25.9 4.5E+02 0.0098 27.6 9.4 48 64-111 120-175 (654)
91 PRK13806 rpsA 30S ribosomal pr 25.9 5.8E+02 0.013 25.8 9.9 64 24-89 293-362 (491)
92 PF03079 ARD: ARD/ARD' family; 25.4 98 0.0021 27.1 3.8 30 35-74 100-129 (157)
93 PF11782 DUF3319: Protein of u 24.3 62 0.0014 26.4 2.2 41 91-133 38-80 (88)
94 cd05790 S1_Rrp40 S1_Rrp40: Rrp 23.9 3.4E+02 0.0073 21.6 6.3 54 21-77 3-63 (86)
95 COG3269 Predicted RNA-binding 23.5 91 0.002 24.6 2.9 27 126-152 36-62 (73)
96 PF10115 HlyU: Transcriptional 23.4 94 0.002 25.4 3.1 46 101-149 2-49 (91)
97 COG1222 RPT1 ATP-dependent 26S 22.6 3.4E+02 0.0074 27.7 7.4 81 23-104 70-170 (406)
98 COG0048 RpsL Ribosomal protein 22.2 1.4E+02 0.0031 25.9 4.1 50 39-91 58-109 (129)
99 PTZ00361 26 proteosome regulat 22.1 2E+02 0.0042 29.1 5.7 50 24-74 103-152 (438)
100 smart00318 SNc Staphylococcal 22.0 2.1E+02 0.0047 22.9 5.0 28 27-54 3-30 (138)
101 PF09902 DUF2129: Uncharacteri 22.0 92 0.002 24.2 2.7 22 82-103 2-23 (71)
102 cd04508 TUDOR Tudor domains ar 21.9 1.5E+02 0.0032 19.6 3.4 27 27-53 15-42 (48)
103 KOG3841|consensus 21.8 46 0.001 33.8 1.2 13 217-229 116-128 (455)
104 TIGR02228 sigpep_I_arch signal 21.4 63 0.0014 28.0 1.9 21 124-144 123-143 (158)
105 PRK01191 rpl24p 50S ribosomal 21.4 1.4E+02 0.0031 25.4 3.9 31 62-93 44-74 (120)
106 PRK00286 xseA exodeoxyribonucl 21.3 5.5E+02 0.012 25.2 8.5 85 35-119 40-139 (438)
107 PF00166 Cpn10: Chaperonin 10 21.2 1.1E+02 0.0024 24.0 3.1 46 17-76 22-70 (93)
108 PF03803 Scramblase: Scramblas 21.1 4.5E+02 0.0097 23.0 7.2 62 23-88 113-176 (221)
109 PF01336 tRNA_anti-codon: OB-f 21.1 1.7E+02 0.0038 20.3 3.8 47 27-73 3-54 (75)
110 PRK08577 hypothetical protein; 20.7 73 0.0016 26.3 2.1 25 52-76 15-39 (136)
111 TIGR00237 xseA exodeoxyribonuc 20.6 4.9E+02 0.011 25.9 8.1 95 25-119 24-133 (432)
112 PF10447 EXOSC1: Exosome compo 20.5 3.1E+02 0.0067 21.7 5.4 12 62-73 67-78 (82)
113 PRK10676 DNA-binding transcrip 20.4 2.2E+02 0.0047 26.5 5.3 50 24-73 199-251 (263)
114 PTZ00194 60S ribosomal protein 20.1 1E+02 0.0023 27.0 2.9 30 62-92 45-74 (143)
No 1
>KOG2925|consensus
Probab=100.00 E-value=2.1e-34 Score=247.35 Aligned_cols=162 Identities=33% Similarity=0.479 Sum_probs=136.6
Q ss_pred ccccchhhhhhhhhccCCCCCCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecC---CC
Q psy10593 3 KATKRKHVQKELLSQEYRVPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEE---GN 79 (275)
Q Consensus 3 ~~tKRKhv~~E~l~~e~~lP~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~---~~ 79 (275)
.+|||||+.+.++ .+...|.+.|+||+|++.+|||+|+|+.++|...|++||.|||+.|||+||+||+|+|.++ ++
T Consensus 1 ~atkkry~~q~v~-de~~~le~~q~IaqVvqlrGsnlheV~danGq~~lvsmP~KfRksiWiRRg~FvvVdpiee~~~g~ 79 (167)
T KOG2925|consen 1 MATKKRYLKQAVS-DEDFTLEECQSIAQVVQLRGSNLHEVMDANGQNSLVSMPAKFRKSIWIRRGSFVVVDPIEEEKSGS 79 (167)
T ss_pred Cccchhhhccccc-CCCcchhhhhhHHHHHhcCCcchhhhhhcCCceeeeeCCHhhhhceEEeeCCEEEEccccccccCC
Confidence 3689999999998 8888999999999999999999999999999999999999999999999999999999998 88
Q ss_pred CeEEEEEEEeChhhHHHHHHCCCCCcccccCcccccccccccccCCCCCceEEEeecCCCCeeeEEEEEecChhhHHHHH
Q psy10593 80 KVKAEIEQILDKKYISFLKQQLKLPPIENGDIVHHFQEIGEQQAKPYRDLTLHLLNKEEGNKVKAEIEQILDKKYISFLK 159 (275)
Q Consensus 80 kvKGeIV~ry~kdqVK~Lrk~G~WPkeF~~~~~~~~~e~~~~~~~~~r~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lk 159 (275)
||+|+|.|+|..+||+.|+|.|+||+.|.+.++++..... | +=.|.+
T Consensus 80 KVkgeI~yVl~~d~vr~lqk~g~WPe~F~d~alk~n~~~~-----t------~e~~~d---------------------- 126 (167)
T KOG2925|consen 80 KVKGEICYVLFFDQVRLLQKSGEWPEIFKDTALKPNEKSS-----T------IEQHED---------------------- 126 (167)
T ss_pred ccceEEEEEEccHHHHHHHHcCCcchhhhhcccccccccC-----C------cccccc----------------------
Confidence 9999999999999999999999999999999888733221 0 000000
Q ss_pred HhCCCCcccccchhccccCCCCCCCCcccCCCCCCceeeceeccccccccc
Q psy10593 160 QQNSWPFTEDSAEDKAKSNCEDSDDEMLNGNLNRRNNVMTEFSNRTKSGQF 210 (275)
Q Consensus 160 k~~~WP~~F~~~~~~~~~~~~~~dDdDLfvNtNR~~~~~~~~~~~~~~~~~ 210 (275)
.++ ..++++++||++||+||||.+++=.|--+-|.+|.=
T Consensus 127 -d~l-----------s~sese~ddds~l~~ntnr~~~~~~eee~e~~~~a~ 165 (167)
T KOG2925|consen 127 -DGL-----------SDSESEDDDDSPLQANTNRLRPFGVEEEAETDSGAD 165 (167)
T ss_pred -cCC-----------CCcccccccCCchhccccccCcccccccCcccccCC
Confidence 011 122355568899999999999998887777777643
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=7.9e-33 Score=214.50 Aligned_cols=78 Identities=53% Similarity=0.946 Sum_probs=76.9
Q ss_pred cEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHHHHCCCC
Q psy10593 26 NNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQLKL 103 (275)
Q Consensus 26 Q~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~Lrk~G~W 103 (275)
|.||+|++++|||+|+|+|+||+++||+||||||+++|||+||||||+||++++|+||+|+|+|+++||++|+++|+|
T Consensus 1 q~i~rV~~~~G~n~~~V~~~dG~~~l~~iP~KfRk~iWIkrGd~VlV~p~~~~~kvkgeIv~i~~~~qvk~L~k~g~W 78 (78)
T cd05792 1 QQIVRVLGSKGNNLHEVETPNGSRYLVSMPTKFRKNIWIKRGDFVLVEPIEEGDKVKAEIVKILTRDHVKYIKEEGLW 78 (78)
T ss_pred CeEEEEEEcCCCcEEEEEcCCCCEEEEEechhhcccEEEEeCCEEEEEecccCCceEEEEEEEECHHHHHHHHHcCCC
Confidence 689999999999999999999999999999999999999999999999999998999999999999999999999999
No 3
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=99.98 E-value=2.4e-32 Score=212.98 Aligned_cols=83 Identities=31% Similarity=0.564 Sum_probs=81.2
Q ss_pred CCCCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHHHHC
Q psy10593 21 VPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQ 100 (275)
Q Consensus 21 lP~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~Lrk~ 100 (275)
.|++||++|+|++++|||+|+|+|+||+++||+||||||++|||++||+|+|+||+++ ++||+|+|+|+++||++|+++
T Consensus 1 ~p~e~q~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~~~~-~~kg~Iv~r~~~~~vk~L~k~ 79 (83)
T smart00652 1 FKEDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWDFQ-DVKADIIYKYTKDEVRWLKKE 79 (83)
T ss_pred CCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEecCCC-CCEEEEEEEeCHHHHHHHHHc
Confidence 4789999999999999999999999999999999999999999999999999999987 999999999999999999999
Q ss_pred CCCC
Q psy10593 101 LKLP 104 (275)
Q Consensus 101 G~WP 104 (275)
|+||
T Consensus 80 g~wp 83 (83)
T smart00652 80 GELP 83 (83)
T ss_pred CCCC
Confidence 9999
No 4
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=99.98 E-value=2.5e-32 Score=219.53 Aligned_cols=95 Identities=27% Similarity=0.378 Sum_probs=87.5
Q ss_pred hhhhhhccCCCCCCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeC
Q psy10593 11 QKELLSQEYRVPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILD 90 (275)
Q Consensus 11 ~~E~l~~e~~lP~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~ 90 (275)
+.+....++|.+++||++|+|++++|+|+|+|+|+||.++||+||||||++|||++||+|+|+|||+++++||+|+|+|+
T Consensus 5 ~~~~~~~~~p~~~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp~d~~~~~kg~Iv~r~~ 84 (99)
T TIGR00523 5 QEQQIRVRLPRKEEGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPWEFQGDDKCDIVWRYT 84 (99)
T ss_pred ccCcceeeCCCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEEccCCCCccEEEEEEcC
Confidence 33433356666679999999999999999999999999999999999999999999999999999998899999999999
Q ss_pred hhhHHHHHHCCCCCc
Q psy10593 91 KKYISFLKQQLKLPP 105 (275)
Q Consensus 91 kdqVK~Lrk~G~WPk 105 (275)
++||++|+++|+||+
T Consensus 85 ~~qv~~L~~~g~~p~ 99 (99)
T TIGR00523 85 KTQVEWLKRKGYLKE 99 (99)
T ss_pred HHHHHHHHHcCCCCC
Confidence 999999999999994
No 5
>PLN00208 translation initiation factor (eIF); Provisional
Probab=99.97 E-value=8.8e-32 Score=229.37 Aligned_cols=94 Identities=22% Similarity=0.270 Sum_probs=90.7
Q ss_pred hhccCCCCCCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhH
Q psy10593 15 LSQEYRVPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYI 94 (275)
Q Consensus 15 l~~e~~lP~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqV 94 (275)
...+++.|++||+||+|++++|+|+|+|+|+||.++||+|||||||+|||++||+|||++|+++ ++||+|+|+|+++||
T Consensus 22 ~~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~VlVel~~~d-~~KgdIv~ry~~dqv 100 (145)
T PLN00208 22 EKRELIFKEDGQEYAQVLRMLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLRDYQ-DDKADVILKYMPDEA 100 (145)
T ss_pred ceeecccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCEEEEEccCCC-CCEEEEEEEcCHHHH
Confidence 3479999999999999999999999999999999999999999999999999999999999986 999999999999999
Q ss_pred HHHHHCCCCCccccc
Q psy10593 95 SFLKQQLKLPPIENG 109 (275)
Q Consensus 95 K~Lrk~G~WPkeF~~ 109 (275)
++|+++|+||+.|..
T Consensus 101 r~Lkk~G~~P~~f~~ 115 (145)
T PLN00208 101 RLLKAYGELPENTRL 115 (145)
T ss_pred HHHHHcCCCCcceee
Confidence 999999999999964
No 6
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=99.97 E-value=4.1e-31 Score=212.92 Aligned_cols=89 Identities=25% Similarity=0.399 Sum_probs=86.6
Q ss_pred hccCCCCCCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHH
Q psy10593 16 SQEYRVPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYIS 95 (275)
Q Consensus 16 ~~e~~lP~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK 95 (275)
..++++|++||++|+|++++|||+|+|+|+||.++||+||||||++|||++||+|+|+||+++ +.||+|+|+|+++||+
T Consensus 12 ~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~~-~~kg~Iv~r~~~~qv~ 90 (100)
T PRK04012 12 RVRLPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDFQ-DEKADIIWRYTKPQVD 90 (100)
T ss_pred eEEccCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEecccC-CCEEEEEEEcCHHHHH
Confidence 479999999999999999999999999999999999999999999999999999999999997 9999999999999999
Q ss_pred HHHHCCCCCc
Q psy10593 96 FLKQQLKLPP 105 (275)
Q Consensus 96 ~Lrk~G~WPk 105 (275)
+|+++|++|+
T Consensus 91 ~L~~~g~~~~ 100 (100)
T PRK04012 91 WLRRKGYISE 100 (100)
T ss_pred HHHHcCCCCC
Confidence 9999999984
No 7
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=99.97 E-value=3.8e-31 Score=227.52 Aligned_cols=94 Identities=22% Similarity=0.306 Sum_probs=90.6
Q ss_pred hccCCCCCCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHH
Q psy10593 16 SQEYRVPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYIS 95 (275)
Q Consensus 16 ~~e~~lP~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK 95 (275)
..+++.|++||+||+|++++|+++|+|+|+||.++||+|||||||+|||++||+|+|+||+++ ++||+|+|+|+++||+
T Consensus 23 ~rel~~~eegq~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~VlVel~~yd-~~KgdIi~Ry~~devr 101 (155)
T PTZ00329 23 KRELVFKEEGQEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRDFQ-DSKADVILKYTPDEAR 101 (155)
T ss_pred eeeeccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCEEEEeccCCC-CCEEEEEEEcCHHHHH
Confidence 479999999999999999999999999999999999999999999999999999999999986 9999999999999999
Q ss_pred HHHHCCCCCcccccC
Q psy10593 96 FLKQQLKLPPIENGD 110 (275)
Q Consensus 96 ~Lrk~G~WPkeF~~~ 110 (275)
+|+++|+||+.|.-.
T Consensus 102 ~Lk~~g~~P~~~~~~ 116 (155)
T PTZ00329 102 ALKQHGELPETAKIN 116 (155)
T ss_pred HHHHcCCCCcceeec
Confidence 999999999999654
No 8
>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=99.97 E-value=1.8e-30 Score=200.58 Aligned_cols=78 Identities=47% Similarity=0.772 Sum_probs=76.5
Q ss_pred cEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHHHHCCCC
Q psy10593 26 NNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQLKL 103 (275)
Q Consensus 26 Q~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~Lrk~G~W 103 (275)
|+||+|++++|||+|+|+|+||+++||+||||||++|||++||+|+|+||++++++||+|+|+|+++||++|+++|+|
T Consensus 1 q~i~~V~~~lG~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~~~~~~~~kg~Iv~r~~~~~vk~L~k~g~w 78 (78)
T cd04456 1 QQIVRVLRMLGNNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPIEEGEDVKADIIFVYCKDHVRSLKKEGFL 78 (78)
T ss_pred CeEEEEEEECCCCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEEEecccCCCceEEEEEEeCHHHHHHHHHcCcC
Confidence 689999999999999999999999999999999999999999999999999977999999999999999999999998
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=99.95 E-value=2.8e-28 Score=187.82 Aligned_cols=77 Identities=26% Similarity=0.454 Sum_probs=74.6
Q ss_pred cEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHHHHCCCC
Q psy10593 26 NNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQLKL 103 (275)
Q Consensus 26 Q~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~Lrk~G~W 103 (275)
|++|+|++++|||+|+|+|+||+++||+||||||++|||++||+|+|+||+++ ++||+|+|+|+++||++|+++|++
T Consensus 1 e~~g~V~~~~g~~~~~V~~~~g~~~la~i~gK~rk~iwI~~GD~V~Ve~~~~d-~~kg~Iv~r~~~~~v~~L~~~g~i 77 (77)
T cd05793 1 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQ-DDKADIIYKYTPDEVRWLKRKGEL 77 (77)
T ss_pred CEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEecccc-CCEEEEEEEcCHHHHHHHHHcCcC
Confidence 68999999999999999999999999999999999999999999999999985 999999999999999999999974
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=99.90 E-value=6.5e-24 Score=157.73 Aligned_cols=65 Identities=45% Similarity=0.723 Sum_probs=59.1
Q ss_pred CCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEE
Q psy10593 23 EDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQI 88 (275)
Q Consensus 23 ~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~r 88 (275)
+++|++|+|++++|||+|+|+|+||.+++|+||||||++|||++||+|+|+||+++ ++||+|+||
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 EEGEVIGRVTEMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPYD-KVKGRIIYR 65 (65)
T ss_dssp STTEEEEEEEEEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTTC-TTEEEEEEE
T ss_pred CCcEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEecccC-CCeEEEEEC
Confidence 58999999999999999999999999999999999999999999999999999987 999999997
No 11
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=99.88 E-value=6.9e-23 Score=158.31 Aligned_cols=72 Identities=24% Similarity=0.327 Sum_probs=68.8
Q ss_pred CCCCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccc-eeeeeCCCEEEEeeecCCCCeEEEEEEEeChhh
Q psy10593 21 VPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-NIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKY 93 (275)
Q Consensus 21 lP~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRK-rIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdq 93 (275)
.|+++++.|+|++++||++|+|+|.||..++||||||||+ +|||.+||.|+|+||+++ ..+|+|+|||+++|
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-LTKGRIVYRYKKDE 75 (75)
T ss_pred cccccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEecccc-cccccEEEEecCCC
Confidence 4588999999999999999999999999999999999999 899999999999999987 88999999999875
No 12
>KOG3403|consensus
Probab=99.85 E-value=2.2e-22 Score=169.20 Aligned_cols=93 Identities=22% Similarity=0.292 Sum_probs=88.4
Q ss_pred hccCCCCCCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHH
Q psy10593 16 SQEYRVPEDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYIS 95 (275)
Q Consensus 16 ~~e~~lP~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK 95 (275)
+.++...++||++|+|++|||+++++|.|.||..|||+|+||+||+|||..||+|||...|++ +.+|+|+.+|++++++
T Consensus 23 kReLvfkEegqeYaQv~kmLGnGr~e~~CfDGvkR~~hiRGklrkkVwi~~GDIiLv~lRD~q-d~kaDvilKY~~dEar 101 (145)
T KOG3403|consen 23 KRELVFKEEGQEYAQVIKMLGNGRLEASCFDGVKRLCHIRGKLRKKVWINQGDIILVGLRDYQ-DDKADVILKYMPDEAR 101 (145)
T ss_pred hhheeehhcchhHHHHHhhhcCCcEEEEEecchhhhhhhhccceeeEeecCCCEEEEeeeccc-ccccceehhhChHHHH
Confidence 467778889999999999999999999999999999999999999999999999999999987 8899999999999999
Q ss_pred HHHHCCCCCccccc
Q psy10593 96 FLKQQLKLPPIENG 109 (275)
Q Consensus 96 ~Lrk~G~WPkeF~~ 109 (275)
.|+..|.+|+.|.-
T Consensus 102 ~LK~~Gelpe~~k~ 115 (145)
T KOG3403|consen 102 ILKAYGELPENAKI 115 (145)
T ss_pred HHHhcCcCCccccc
Confidence 99999999987754
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=99.77 E-value=1.8e-18 Score=131.59 Aligned_cols=62 Identities=26% Similarity=0.307 Sum_probs=59.0
Q ss_pred cEEEEEEEecCCceEEEEeCCCcEEEEEecccccc-eeeeeCCCEEEEeeecCCCCeEEEEEEE
Q psy10593 26 NNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-NIWIKPGDFVIVKPIEEGNKVKAEIEQI 88 (275)
Q Consensus 26 Q~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRK-rIWIKrGD~VLVeP~D~~~kvKGeIV~r 88 (275)
++.|+|++++|++.|.|+|+||.+++|+||||||+ +|||.+||.|+|++|+++ ..||+|+||
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-LTRGRITYR 68 (68)
T ss_pred EEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECccc-CCcEeEEeC
Confidence 68899999999999999999999999999999996 799999999999999886 889999996
No 14
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=99.71 E-value=4e-17 Score=129.47 Aligned_cols=65 Identities=15% Similarity=0.093 Sum_probs=60.9
Q ss_pred cEEEEEEEecCCceEEEEeCCCcEEEEEecccccc-eeeeeCCCEEEEeeecCCCCeEEEEEEEeCh
Q psy10593 26 NNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-NIWIKPGDFVIVKPIEEGNKVKAEIEQILDK 91 (275)
Q Consensus 26 Q~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRK-rIWIKrGD~VLVeP~D~~~kvKGeIV~ry~k 91 (275)
++.|+|+++++++.|.|+|+||.++||+|+||||+ +|||.+||.|+|++|+++ ..||+|+|+|.+
T Consensus 8 e~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYD-ltkGRIiyR~~~ 73 (87)
T PRK12442 8 ELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYD-LTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECccc-CCceeEEEEecC
Confidence 68999999999999999999999999999999999 699999999999987765 679999999973
No 15
>CHL00010 infA translation initiation factor 1
Probab=99.53 E-value=3.7e-14 Score=109.37 Aligned_cols=66 Identities=27% Similarity=0.275 Sum_probs=61.0
Q ss_pred cEEEEEEEecCCceEEEEeCCCcEEEEEecccccce-eeeeCCCEEEEeeecCCCCeEEEEEEEeChh
Q psy10593 26 NNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNN-IWIKPGDFVIVKPIEEGNKVKAEIEQILDKK 92 (275)
Q Consensus 26 Q~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKr-IWIKrGD~VLVeP~D~~~kvKGeIV~ry~kd 92 (275)
++.|+|++.+|++.|.|.|+||+.++|+++||||++ +|+..||+|.|+||+.+ +.+|.|+|+|.+.
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~-~~~g~Ii~r~~~~ 74 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYD-LTKGRIIYRLRNK 74 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEcccC-CCeEEEEEEecCC
Confidence 478999999999999999999999999999999984 99999999999988765 7799999999865
No 16
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=99.49 E-value=1.3e-13 Score=104.32 Aligned_cols=64 Identities=23% Similarity=0.284 Sum_probs=59.1
Q ss_pred cEEEEEEEecCCceEEEEeCCCcEEEEEecccccc-eeeeeCCCEEEEeeecCCCCeEEEEEEEeC
Q psy10593 26 NNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-NIWIKPGDFVIVKPIEEGNKVKAEIEQILD 90 (275)
Q Consensus 26 Q~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRK-rIWIKrGD~VLVeP~D~~~kvKGeIV~ry~ 90 (275)
++.|+|++++|++.|.|.|.||..++|+++||||+ ++|+..||+|+|++|+.+ +.+|.|||+|.
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~-~~~g~Iv~r~~ 72 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYD-LTKGRITYRHK 72 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEEEcccC-CCeEEEEEEeC
Confidence 67899999999999999999999999999999996 699999999999988765 66899999984
No 17
>KOG2925|consensus
Probab=99.46 E-value=4.4e-14 Score=122.26 Aligned_cols=46 Identities=28% Similarity=0.355 Sum_probs=44.3
Q ss_pred CCceEEEeecCC---CCeeeEEEEEecChhhHHHHHHhCCCCcccccch
Q psy10593 127 RDLTLHLLNKEE---GNKVKAEIEQILDKKYISFLKQQNSWPFTEDSAE 172 (275)
Q Consensus 127 r~~~~~v~pi~E---g~KVkaEI~~IL~kd~IK~lkk~~~WP~~F~~~~ 172 (275)
||+||||+||+| |+||||||+.||..||+++|+|+|.||+.|.+..
T Consensus 63 Rg~FvvVdpiee~~~g~KVkgeI~yVl~~d~vr~lqk~g~WPe~F~d~a 111 (167)
T KOG2925|consen 63 RGSFVVVDPIEEEKSGSKVKGEICYVLFFDQVRLLQKSGEWPEIFKDTA 111 (167)
T ss_pred eCCEEEEccccccccCCccceEEEEEEccHHHHHHHHcCCcchhhhhcc
Confidence 899999999999 9999999999999999999999999999998754
No 18
>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=99.18 E-value=2.3e-11 Score=94.85 Aligned_cols=38 Identities=37% Similarity=0.607 Sum_probs=37.4
Q ss_pred CCceEEEeecCCCCeeeEEEEEecChhhHHHHHHhCCC
Q psy10593 127 RDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNSW 164 (275)
Q Consensus 127 r~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lkk~~~W 164 (275)
||+||+|+|+++|+||||||++||+++|||+|+++|.|
T Consensus 41 rGd~VlV~p~~~~~kvkgeIv~i~~~~qvk~L~k~g~W 78 (78)
T cd05792 41 RGDFVLVEPIEEGDKVKAEIVKILTRDHVKYIKEEGLW 78 (78)
T ss_pred eCCEEEEEecccCCceEEEEEEEECHHHHHHHHHcCCC
Confidence 69999999999999999999999999999999999999
No 19
>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=99.15 E-value=2e-10 Score=84.34 Aligned_cols=62 Identities=26% Similarity=0.271 Sum_probs=55.1
Q ss_pred cEEEEEEEecCCceEEEEeCCCcEEEEEecccccc-eeeeeCCCEEEEeeecCCCCeEEEEEEE
Q psy10593 26 NNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-NIWIKPGDFVIVKPIEEGNKVKAEIEQI 88 (275)
Q Consensus 26 Q~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRK-rIWIKrGD~VLVeP~D~~~kvKGeIV~r 88 (275)
++.|+|++.+|++.|.|++.||..++|+++||||+ ++|+..||+|+++++.++ +.+|.|+|+
T Consensus 2 ~~~G~Vi~~~~g~~~~V~~~~g~~~~c~~rGklr~~~~~~~vGD~V~~~~~~~~-~~~g~I~~~ 64 (64)
T cd04451 2 EMEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYD-LTKGRIVYR 64 (64)
T ss_pred eEEEEEEEEeCCCEEEEEeCCCCEEEEEECceeecCCcccCCCCEEEEEEeecC-CCEEEEEEC
Confidence 35689999999999999999999999999999995 699999999999988654 447999986
No 20
>PLN00208 translation initiation factor (eIF); Provisional
Probab=98.65 E-value=4.3e-08 Score=84.47 Aligned_cols=47 Identities=13% Similarity=-0.019 Sum_probs=42.4
Q ss_pred CCceEEEeecCCCCeeeEEEEEecChhhHHHHHHhCCCCcccccchhc
Q psy10593 127 RDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNSWPFTEDSAEDK 174 (275)
Q Consensus 127 r~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lkk~~~WP~~F~~~~~~ 174 (275)
+|++|+|. +.+.+++||+|++.|+++||++|++.|.||+.|...+.+
T Consensus 73 ~GD~VlVe-l~~~d~~KgdIv~ry~~dqvr~Lkk~G~~P~~f~~~~~~ 119 (145)
T PLN00208 73 AGDIILVG-LRDYQDDKADVILKYMPDEARLLKAYGELPENTRLNEGI 119 (145)
T ss_pred CCCEEEEE-ccCCCCCEEEEEEEcCHHHHHHHHHcCCCCcceeecccc
Confidence 49999998 678899999999999999999999999999999875544
No 21
>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=98.65 E-value=3.5e-08 Score=76.64 Aligned_cols=38 Identities=32% Similarity=0.261 Sum_probs=37.0
Q ss_pred CCceEEEeecCCCCeeeEEEEEecChhhHHHHHHhCCC
Q psy10593 127 RDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNSW 164 (275)
Q Consensus 127 r~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lkk~~~W 164 (275)
||+||+|+|.+.|+++||+|+++|++||||+|+++|.|
T Consensus 41 ~GD~VlV~~~~~~~~~kg~Iv~r~~~~~vk~L~k~g~w 78 (78)
T cd04456 41 RGDFLIVDPIEEGEDVKADIIFVYCKDHVRSLKKEGFL 78 (78)
T ss_pred CCCEEEEEecccCCCceEEEEEEeCHHHHHHHHHcCcC
Confidence 59999999999999999999999999999999999998
No 22
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=98.64 E-value=4e-08 Score=77.04 Aligned_cols=39 Identities=23% Similarity=0.212 Sum_probs=36.8
Q ss_pred CCCceEEEeecCCCCeeeEEEEEecChhhHHHHHHhCCCC
Q psy10593 126 YRDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNSWP 165 (275)
Q Consensus 126 ~r~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lkk~~~WP 165 (275)
-||++|+|+|.+.+ ++||+|+++++++|||+|+++|.||
T Consensus 45 ~~GD~VlVe~~~~~-~~kg~Iv~r~~~~~vk~L~k~g~wp 83 (83)
T smart00652 45 RRGDIVLVDPWDFQ-DVKADIIYKYTKDEVRWLKKEGELP 83 (83)
T ss_pred cCCCEEEEEecCCC-CCEEEEEEEeCHHHHHHHHHcCCCC
Confidence 36999999999876 9999999999999999999999999
No 23
>TIGR00523 eIF-1A eukaryotic/archaeal initiation factor 1A. Recommended nomenclature: eIF-1A for eukaryotes, aIF-1A for Archaea. Also called eIF-4C
Probab=98.50 E-value=1.6e-07 Score=76.08 Aligned_cols=40 Identities=15% Similarity=0.032 Sum_probs=38.4
Q ss_pred CCceEEEeecCCCCeeeEEEEEecChhhHHHHHHhCCCCc
Q psy10593 127 RDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNSWPF 166 (275)
Q Consensus 127 r~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lkk~~~WP~ 166 (275)
+|++|+|+|.+.++++||+|+++|++|||++|+++|.||.
T Consensus 60 ~GD~VlVsp~d~~~~~kg~Iv~r~~~~qv~~L~~~g~~p~ 99 (99)
T TIGR00523 60 EGDVVIVKPWEFQGDDKCDIVWRYTKTQVEWLKRKGYLKE 99 (99)
T ss_pred CCCEEEEEEccCCCCccEEEEEEcCHHHHHHHHHcCCCCC
Confidence 5999999999999899999999999999999999999993
No 24
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=98.33 E-value=9.5e-07 Score=76.98 Aligned_cols=44 Identities=16% Similarity=0.027 Sum_probs=40.7
Q ss_pred CCceEEEeecCCCCeeeEEEEEecChhhHHHHHHhCCCCcccccc
Q psy10593 127 RDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNSWPFTEDSA 171 (275)
Q Consensus 127 r~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lkk~~~WP~~F~~~ 171 (275)
+|++|+|.| .+.+++||.|++.|+++||++|++.|.||+.|...
T Consensus 73 ~GD~VlVel-~~yd~~KgdIi~Ry~~devr~Lk~~g~~P~~~~~~ 116 (155)
T PTZ00329 73 IGDIILVSL-RDFQDSKADVILKYTPDEARALKQHGELPETAKIN 116 (155)
T ss_pred CCCEEEEec-cCCCCCEEEEEEEcCHHHHHHHHHcCCCCcceeec
Confidence 399999998 88999999999999999999999999999999643
No 25
>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=97.84 E-value=2.4e-05 Score=60.66 Aligned_cols=37 Identities=14% Similarity=0.074 Sum_probs=34.1
Q ss_pred CCCceEEEeecCCCCeeeEEEEEecChhhHHHHHHhCC
Q psy10593 126 YRDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNS 163 (275)
Q Consensus 126 ~r~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lkk~~~ 163 (275)
-||++|+|+|.+. +++||+|++.|++|||++|++.|.
T Consensus 40 ~~GD~V~Ve~~~~-d~~kg~Iv~r~~~~~v~~L~~~g~ 76 (77)
T cd05793 40 NEGDIVLVAPWDF-QDDKADIIYKYTPDEVRWLKRKGE 76 (77)
T ss_pred cCCCEEEEEeccc-cCCEEEEEEEcCHHHHHHHHHcCc
Confidence 3699999999987 899999999999999999999874
No 26
>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=97.77 E-value=0.00014 Score=52.54 Aligned_cols=60 Identities=30% Similarity=0.422 Sum_probs=48.6
Q ss_pred EEEEEEecCCceEEEEeCCCcEEEEEecccccc-eeeeeCCCEEEEeeecCCCCeEEEEEEEeCh
Q psy10593 28 IVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-NIWIKPGDFVIVKPIEEGNKVKAEIEQILDK 91 (275)
Q Consensus 28 IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRK-rIWIKrGD~VLVeP~D~~~kvKGeIV~ry~k 91 (275)
.|+|++..| +.|.|.+++|....|.++|++++ ..++-.||.|++++.+.+ .|-|+.++..
T Consensus 2 ~grVv~~~~-~~~~v~~~~~~~~~~~~~~~~~~~~~~~~VGD~V~~~~~~~~---~~~I~~vl~R 62 (68)
T cd04466 2 EGLIIKAIG-GFYYVETEDGKIYECRLRGKFRKDKNPPAVGDRVEFEPEDDG---EGVIEEILPR 62 (68)
T ss_pred CEEEEEEEC-CEEEEEeCCCeEEEEEEccccccCCCCCCCCcEEEEEECCCC---cEEEEEEecc
Confidence 378888887 67899998788999999999985 488999999999976533 5777777754
No 27
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=97.57 E-value=0.00012 Score=59.70 Aligned_cols=38 Identities=13% Similarity=0.073 Sum_probs=35.7
Q ss_pred CCceEEEeecCCCCeeeEEEEEecChhhHHHHHHhCCCC
Q psy10593 127 RDLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNSWP 165 (275)
Q Consensus 127 r~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lkk~~~WP 165 (275)
+|++|+|+|.+.+ +.||+|++.|+++||++|++.|.=|
T Consensus 62 ~GD~VlVe~~~~~-~~kg~Iv~r~~~~qv~~L~~~g~~~ 99 (100)
T PRK04012 62 EGDVVIVAPWDFQ-DEKADIIWRYTKPQVDWLRRKGYIS 99 (100)
T ss_pred CCCEEEEEecccC-CCEEEEEEEcCHHHHHHHHHcCCCC
Confidence 6999999999887 8999999999999999999999866
No 28
>PRK00098 GTPase RsgA; Reviewed
Probab=95.56 E-value=0.053 Score=50.38 Aligned_cols=61 Identities=25% Similarity=0.284 Sum_probs=47.9
Q ss_pred EEEEEEecCCceEEEEeCCCcEEEEEecccccc-eeeeeCCCEEEEeeecCCCCeEEEEEEEeChh
Q psy10593 28 IVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-NIWIKPGDFVIVKPIEEGNKVKAEIEQILDKK 92 (275)
Q Consensus 28 IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRK-rIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kd 92 (275)
.|+|++..| +.|.|.+.+|....|.++|+|++ ..-+-.||+|++++.+.+ .|-|..++...
T Consensus 2 ~g~v~~~~~-~~~~v~~~~~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~~~---~g~i~~i~~R~ 63 (298)
T PRK00098 2 EGLIIKALG-GFYYVESEDGQVYQCRARGKFRKKTNTPAVGDRVEFSAENND---EGVILEIHERK 63 (298)
T ss_pred eEEEEEEEC-CEEEEEECCCCEEEEEeccccccCCCCcCCCCEEEEEECCCC---cEEEEEEeCCC
Confidence 488999886 57789888899999999999985 356778999999975322 57777777655
No 29
>PRK12289 GTPase RsgA; Reviewed
Probab=94.78 E-value=0.12 Score=49.85 Aligned_cols=69 Identities=13% Similarity=0.167 Sum_probs=53.0
Q ss_pred CCCCcEEEEEEEecCCceEEEEeCCC------cEEEEEecccccce-eeeeCCCEEEEeeecCCCCeEEEEEEEeChh
Q psy10593 22 PEDLNNIVKITQNSGNNLHQIENHSG------EKYFVSMPGKFRNN-IWIKPGDFVIVKPIEEGNKVKAEIEQILDKK 92 (275)
Q Consensus 22 P~egQ~IgrVv~~lG~nlfeVec~DG------~~rLa~IPGKfRKr-IWIKrGD~VLVeP~D~~~kvKGeIV~ry~kd 92 (275)
+...++.|+|++..|+ .|.|.+.+| ...+|...+++|+. .-+..||.|++++.+.. +..|-|..++...
T Consensus 4 ~~~~~~~g~V~~~~~~-~y~V~~~~~~~~~~~~~~~~~~r~~lk~~~~~~~vGD~V~~~~~~~~-~~~~~I~~vlpR~ 79 (352)
T PRK12289 4 TTTSQLLGTVVAVQAN-FYRVQLDEPQNLNPPSLLLCTRRTRLKKIGQQVMVGDRVIVEEPDWQ-GQRGAIAEVLPRK 79 (352)
T ss_pred cccCcccEEEEEEECC-EEEEEECCCcccCcceEEEEEcccccccCCCCcccCCEEEEeecCCC-CCceEEEEEeccc
Confidence 4556788999998874 678887664 46889999999863 45899999999975543 3578888888766
No 30
>PRK12288 GTPase RsgA; Reviewed
Probab=94.57 E-value=0.13 Score=49.39 Aligned_cols=62 Identities=19% Similarity=0.259 Sum_probs=50.5
Q ss_pred EEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCC-CeEEEEEEEeChh
Q psy10593 27 NIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGN-KVKAEIEQILDKK 92 (275)
Q Consensus 27 ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~-kvKGeIV~ry~kd 92 (275)
+.|+|++..|+ .|.|.+.+|..+.|.++|+++. +-.||.|++++.+... ...|.|..++...
T Consensus 40 ~~g~Vi~~~~~-~~~v~~~~g~~~~~~~~g~~~~---~~vGD~V~~~~~~~~~~~~~~~I~~il~R~ 102 (347)
T PRK12288 40 QEGIVISRFGQ-HADVEAADGEVHRCNIRRTIRS---LVTGDRVVWRPGKEALEGVSGVVEAVHPRT 102 (347)
T ss_pred cceEEEEEECC-EEEEEeCCCcEEEEEecccCCC---CCCCcEEEEEeCCCcccccceEEEEEeccc
Confidence 67999998885 6789999999999999999975 8899999999654321 1358899888776
No 31
>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=93.88 E-value=0.2 Score=46.35 Aligned_cols=65 Identities=25% Similarity=0.407 Sum_probs=50.2
Q ss_pred EEEEEecCCceEEEEeCCCcEEEEEecccccce-eeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHHHHC
Q psy10593 29 VKITQNSGNNLHQIENHSGEKYFVSMPGKFRNN-IWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQ 100 (275)
Q Consensus 29 grVv~~lG~nlfeVec~DG~~rLa~IPGKfRKr-IWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~Lrk~ 100 (275)
|+|++..| +.|.|..+ |....|.++|+|++. .-+-.||.|++++.+. ..|.|..++.+. ..|.+.
T Consensus 1 g~v~~~~~-~~~~v~~~-~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~~---~~~~i~~i~~R~--~~l~R~ 66 (287)
T cd01854 1 GRVIAVHG-GFYDVETE-GGELRCRARGKLRKKGIKPVVGDWVEVEPDDD---GEGVIVRVLPRK--NLLSRP 66 (287)
T ss_pred CEEEEEEC-CEEEEEEC-CeEEEEEeccccccCCCCccCCCEEEEEecCC---CcEEEEEEECCC--ceEEcc
Confidence 57888777 67888774 778999999999864 5589999999997653 378999999866 344443
No 32
>PRK01889 GTPase RsgA; Reviewed
Probab=89.31 E-value=1.2 Score=42.67 Aligned_cols=62 Identities=19% Similarity=0.299 Sum_probs=47.2
Q ss_pred CCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccc-----eeeeeCCCEEEEeeecCCCCeEEEEEEEeChh
Q psy10593 24 DLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-----NIWIKPGDFVIVKPIEEGNKVKAEIEQILDKK 92 (275)
Q Consensus 24 egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRK-----rIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kd 92 (275)
++-..|+|++..| +.|.|...+| ...|.++||++. .--.-.||.|++++ + ..|-|..+|.+.
T Consensus 26 ~~~~~g~v~~~~~-~~~~v~~~~~-~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~~-~----~~g~I~~i~pR~ 92 (356)
T PRK01889 26 EGLEPGRVVEEHR-SGYVVATEEG-EVRAEVSGKWRHEAFPPGDRPAVGDWVLLDN-E----KKARIVRLLPRR 92 (356)
T ss_pred cCCccEEEEEEEC-CEEEEEECCc-EEEEEecchhhccccccCCCCccCcEEEEec-C----CceEEEEEECCC
Confidence 4456799999887 5667887666 467999999984 23478899999986 2 258888888776
No 33
>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=83.20 E-value=1.4 Score=32.74 Aligned_cols=22 Identities=23% Similarity=0.037 Sum_probs=18.4
Q ss_pred CCceEEEeecCCCCeeeEEEEEe
Q psy10593 127 RDLTLHLLNKEEGNKVKAEIEQI 149 (275)
Q Consensus 127 r~~~~~v~pi~Eg~KVkaEI~~I 149 (275)
||++++|+|- +.+++||+|++.
T Consensus 44 ~GD~V~V~~~-~~d~~kG~Ii~r 65 (65)
T PF01176_consen 44 RGDFVLVEPS-PYDKVKGRIIYR 65 (65)
T ss_dssp TTEEEEEEES-TTCTTEEEEEEE
T ss_pred CCCEEEEEec-ccCCCeEEEEEC
Confidence 5999999994 555999999874
No 34
>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=80.55 E-value=7.5 Score=26.04 Aligned_cols=49 Identities=22% Similarity=0.123 Sum_probs=35.0
Q ss_pred EEEEEEecCCceEEEEeCCCcEEEEEecccccc-----eeeeeCCCEEEEeeecC
Q psy10593 28 IVKITQNSGNNLHQIENHSGEKYFVSMPGKFRN-----NIWIKPGDFVIVKPIEE 77 (275)
Q Consensus 28 IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRK-----rIWIKrGD~VLVeP~D~ 77 (275)
.|+|++...++ +.|++.+|.+-+++++.--.. +-+++.||.|.+.....
T Consensus 2 ~g~V~~v~~~g-~~v~l~~~~~g~~~~~~~~~~~~~~~~~~~~~G~~v~~~v~~~ 55 (65)
T cd00164 2 TGKVVSITKFG-VFVELEDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEV 55 (65)
T ss_pred EEEEEEEEeee-EEEEecCCCEEEEEHHHCCCccccCHhhEeCCCCEEEEEEEEE
Confidence 57888877554 458888888777776654322 35789999999996653
No 35
>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=72.84 E-value=6.5 Score=26.97 Aligned_cols=32 Identities=13% Similarity=0.123 Sum_probs=26.3
Q ss_pred CCCCCCcEEEEEEEecCCceEEEEeCCCcEEEE
Q psy10593 20 RVPEDLNNIVKITQNSGNNLHQIENHSGEKYFV 52 (275)
Q Consensus 20 ~lP~egQ~IgrVv~~lG~nlfeVec~DG~~rLa 52 (275)
|-|.++=+.|.|+. ..++.+.|++.||+++.+
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 45677889999995 666779999999998865
No 36
>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=71.94 E-value=7.1 Score=32.86 Aligned_cols=31 Identities=35% Similarity=0.446 Sum_probs=20.7
Q ss_pred cceeeeeCCCEEEEeeecCCCCeEEEEEEEeC
Q psy10593 59 RNNIWIKPGDFVIVKPIEEGNKVKAEIEQILD 90 (275)
Q Consensus 59 RKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~ 90 (275)
|+.+.|+.||+|+|.+.+ +..--|.|...+.
T Consensus 3 r~~~~i~vGD~V~v~~~~-~~~~va~Ie~i~e 33 (130)
T cd04721 3 RNGVTISVHDFVYVLSEE-EDRYVAYIEDLYE 33 (130)
T ss_pred cCCEEEECCCEEEEeCCC-CCcEEEEEEEEEE
Confidence 566899999999999754 2234444444444
No 37
>COG4048 Uncharacterized protein conserved in archaea [Function unknown]
Probab=69.87 E-value=4.8 Score=34.25 Aligned_cols=23 Identities=30% Similarity=0.479 Sum_probs=21.1
Q ss_pred CCCCCceEEEeecCCCCeeeEEE
Q psy10593 124 KPYRDLTLHLLNKEEGNKVKAEI 146 (275)
Q Consensus 124 ~~~r~~~~~v~pi~Eg~KVkaEI 146 (275)
-||||.-++|.||.++.+|-|-|
T Consensus 72 GpY~G~pVVV~Pik~~g~viaAi 94 (123)
T COG4048 72 GPYRGLPVVVAPIKDEGEVIAAI 94 (123)
T ss_pred CccCCceEEEEEeccCCeEEEEE
Confidence 49999999999999999998875
No 38
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=69.52 E-value=14 Score=30.75 Aligned_cols=50 Identities=14% Similarity=0.060 Sum_probs=37.4
Q ss_pred EEEEEEEecCCceEEEEeCCCcEEEEE----ecccccceeeeeCCCEEEEeeecC
Q psy10593 27 NIVKITQNSGNNLHQIENHSGEKYFVS----MPGKFRNNIWIKPGDFVIVKPIEE 77 (275)
Q Consensus 27 ~IgrVv~~lG~nlfeVec~DG~~rLa~----IPGKfRKrIWIKrGD~VLVeP~D~ 77 (275)
-.|+|.+.+.++.|.|+..+|....+. |+...-.+-=++.||+||+- |+.
T Consensus 15 Y~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~~~~~~~L~~GD~VLA~-~~~ 68 (124)
T PF15057_consen 15 YPGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALSDAMRHSLQVGDKVLAP-WEP 68 (124)
T ss_pred EeEEEEEccCCCEEEEEECCCCEEEeChHHeEEccCcccCcCCCCCEEEEe-cCc
Confidence 468999999999999999888765542 33333335578999999998 543
No 39
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=68.43 E-value=23 Score=30.63 Aligned_cols=74 Identities=12% Similarity=0.027 Sum_probs=48.8
Q ss_pred EEEEEEecCC-------ceEEEEeCCCcEEEEE-ecccccceeeeeCCCEEEEe-eecCCCCeEEEEEEEeChhhHHHHH
Q psy10593 28 IVKITQNSGN-------NLHQIENHSGEKYFVS-MPGKFRNNIWIKPGDFVIVK-PIEEGNKVKAEIEQILDKKYISFLK 98 (275)
Q Consensus 28 IgrVv~~lG~-------nlfeVec~DG~~rLa~-IPGKfRKrIWIKrGD~VLVe-P~D~~~kvKGeIV~ry~kdqVK~Lr 98 (275)
.|+|++.+.. .+|-|.+++|.+.++- ==.-+-+-=|++.||.|.+- -|+.+ +..|-|-|--.++
T Consensus 42 ~G~V~~vLpdd~~GsrHQ~Fiv~l~~g~tllIahNIDlaprip~l~~GD~V~f~GeYe~n-~kggvIHWTH~dp------ 114 (131)
T PF11948_consen 42 CGTVVKVLPDDNKGSRHQRFIVRLSSGQTLLIAHNIDLAPRIPWLQKGDQVEFYGEYEWN-PKGGVIHWTHHDP------ 114 (131)
T ss_pred cEEEEEECcccCCCCcceEEEEEeCCCCEEEEEeccCccccCcCcCCCCEEEEEEEEEEC-CCCCEEEeeccCC------
Confidence 6777776654 5799999999998852 11111222589999999998 45544 4455665555544
Q ss_pred HCCCCCccccc
Q psy10593 99 QQLKLPPIENG 109 (275)
Q Consensus 99 k~G~WPkeF~~ 109 (275)
.|-||..|..
T Consensus 115 -~~~h~~Gwl~ 124 (131)
T PF11948_consen 115 -RGRHPDGWLK 124 (131)
T ss_pred -CCCCCCeeEE
Confidence 3777777654
No 40
>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=66.40 E-value=18 Score=27.48 Aligned_cols=57 Identities=16% Similarity=0.191 Sum_probs=34.6
Q ss_pred EEEEEEe-cCCceEEEEeCCCcEEEEEecccccceee-eeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHHH
Q psy10593 28 IVKITQN-SGNNLHQIENHSGEKYFVSMPGKFRNNIW-IKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLK 98 (275)
Q Consensus 28 IgrVv~~-lG~nlfeVec~DG~~rLa~IPGKfRKrIW-IKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~Lr 98 (275)
=++|++. .+++.-.|.. +|..+-+.+. .+- +++||+|||- -|-.+.++++++.++..
T Consensus 6 P~~Vv~v~~~~~~A~v~~-~G~~~~V~~~-----lv~~v~~Gd~VLVH--------aG~Ai~~ideeeA~e~l 64 (68)
T PF01455_consen 6 PGRVVEVDEDGGMAVVDF-GGVRREVSLA-----LVPDVKVGDYVLVH--------AGFAIEKIDEEEAEETL 64 (68)
T ss_dssp EEEEEEEETTTTEEEEEE-TTEEEEEEGT-----TCTSB-TT-EEEEE--------TTEEEEEE-HHHHHHHH
T ss_pred cEEEEEEeCCCCEEEEEc-CCcEEEEEEE-----EeCCCCCCCEEEEe--------cChhheeCCHHHHHHHH
Confidence 3678887 3455555554 4666655432 122 8999999998 34677888888776643
No 41
>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=65.34 E-value=30 Score=24.55 Aligned_cols=52 Identities=15% Similarity=0.098 Sum_probs=38.1
Q ss_pred CCCcEEEEEEEe-cCCceEEEE--eCCCcEEEEEecccccceeeeeCCCEEEEee
Q psy10593 23 EDLNNIVKITQN-SGNNLHQIE--NHSGEKYFVSMPGKFRNNIWIKPGDFVIVKP 74 (275)
Q Consensus 23 ~egQ~IgrVv~~-lG~nlfeVe--c~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP 74 (275)
..++.-|+|.+. .|+...+|. +.+|....|.||.+--..+=+++||-|.+..
T Consensus 5 ~~N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~i 59 (69)
T TIGR00638 5 ARNQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAVI 59 (69)
T ss_pred cccEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEEE
Confidence 357788888887 244445555 5566688899998776777789999888773
No 42
>KOG2107|consensus
Probab=63.96 E-value=8.8 Score=34.73 Aligned_cols=38 Identities=16% Similarity=0.404 Sum_probs=29.9
Q ss_pred CcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEee
Q psy10593 25 LNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKP 74 (275)
Q Consensus 25 gQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP 74 (275)
.+.|--|+ -|++.|.|+..|+.-. |||+.+||+|++-+
T Consensus 93 deeiR~il--~GtgYfDVrd~dd~WI----------Ri~vekGDlivlPa 130 (179)
T KOG2107|consen 93 DEEIRYIL--EGTGYFDVRDKDDQWI----------RIFVEKGDLIVLPA 130 (179)
T ss_pred hhheEEEe--ecceEEeeccCCCCEE----------EEEEecCCEEEecC
Confidence 34444443 5999999999998766 78999999999874
No 43
>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=63.88 E-value=15 Score=25.92 Aligned_cols=53 Identities=15% Similarity=0.130 Sum_probs=37.0
Q ss_pred CCCCcEEEEEEEec--C-CceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEee
Q psy10593 22 PEDLNNIVKITQNS--G-NNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKP 74 (275)
Q Consensus 22 P~egQ~IgrVv~~l--G-~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP 74 (275)
+..++.-|+|.... | .....+.+.+|....|.|+.+-...+=+++||-|.+..
T Consensus 2 s~~N~l~g~V~~ie~~g~~~~v~~~~~~~~~l~a~it~~~~~~L~L~~G~~V~~~i 57 (64)
T PF03459_consen 2 SARNQLPGTVESIENLGSEVEVTLDLGGGETLTARITPESAEELGLKPGDEVYASI 57 (64)
T ss_dssp STSEEEEEEEEEEEESSSEEEEEEEETTSEEEEEEEEHHHHHHCT-STT-EEEEEE
T ss_pred CCCcEEEEEEEEEEECCCeEEEEEEECCCCEEEEEEcHHHHHHcCCCCCCEEEEEE
Confidence 34566666665443 3 23456677777779999999888888899999998874
No 44
>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=61.01 E-value=23 Score=30.34 Aligned_cols=95 Identities=19% Similarity=0.239 Sum_probs=61.7
Q ss_pred EEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHHHHCCCCCcccc
Q psy10593 29 VKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQLKLPPIEN 108 (275)
Q Consensus 29 grVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~Lrk~G~WPkeF~ 108 (275)
|+|+...|+++|.|...||.+.- ++.-|+|+++|...+. + |+-+..+ .||-....
T Consensus 22 G~I~~~~~~~kykv~FdDG~~~~------------v~~~div~~dplpl~~----e-V~A~~ed--------dY~~~GvV 76 (122)
T PF09038_consen 22 GKITSDKGKNKYKVLFDDGYECR------------VLGKDIVVCDPLPLGT----E-VTALSED--------DYFSPGVV 76 (122)
T ss_dssp EEEEEEETTTEEEEEETTS-EEE------------EECCCEEEESSS-TTE----E-EEECCTT--------CTSEEEEE
T ss_pred ceEeecCCCCeEEEEecCCccce------------eccCcEEEEcceeccc----e-eEEeecC--------CcccccEE
Confidence 89999999999999999998753 5667999999887652 2 2333333 67777665
Q ss_pred cCcccccccccccccCCCCCceEEEeecCCCCeee-EEEEEecChhhHHHHHHh
Q psy10593 109 GDIVHHFQEIGEQQAKPYRDLTLHLLNKEEGNKVK-AEIEQILDKKYISFLKQQ 161 (275)
Q Consensus 109 ~~~~~~~~e~~~~~~~~~r~~~~~v~pi~Eg~KVk-aEI~~IL~kd~IK~lkk~ 161 (275)
.+.. ++. .+.+.+|. .+ |++.. .--.=||..||..-||++
T Consensus 77 ~~h~---~~~--------~e~yY~Ve-~d-G~~~~~~r~~viLs~~Q~~~Lre~ 117 (122)
T PF09038_consen 77 KGHK---TDS--------GEVYYCVE-TD-GQRKRYQRKDVILSADQANRLREQ 117 (122)
T ss_dssp EEEE---EET--------TEEEEEEE-ET-TEEEEEEGGGEEEEHHHHHCCCCC
T ss_pred EEEE---ccC--------CcEEEEEE-EC-CCEEEEEeeeEEEcHHHHHHHHHh
Confidence 4322 221 24566666 44 65432 222337889999888876
No 45
>CHL00075 rpl21 ribosomal protein L21
Probab=60.43 E-value=57 Score=27.10 Aligned_cols=26 Identities=23% Similarity=-0.024 Sum_probs=17.6
Q ss_pred ceEEEeecCCCCeeeEEEEEecChhh
Q psy10593 129 LTLHLLNKEEGNKVKAEIEQILDKKY 154 (275)
Q Consensus 129 ~~~~v~pi~Eg~KVkaEI~~IL~kd~ 154 (275)
.+++=.|.-+|.+|.|+|+.-.--+-
T Consensus 48 ~~~iG~P~v~~a~V~a~V~~h~r~~K 73 (108)
T CHL00075 48 EILIGKPWLENATVKGRILHHFRGKK 73 (108)
T ss_pred CeEECCcEecCcEEEEEEEeecCCCC
Confidence 34455677788999999886544333
No 46
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=57.91 E-value=52 Score=22.54 Aligned_cols=48 Identities=17% Similarity=0.126 Sum_probs=33.3
Q ss_pred cEEEEEEEecCCceEEEEeCCCcEEEEEecccccce------eeeeCCCEEEEeee
Q psy10593 26 NNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNN------IWIKPGDFVIVKPI 75 (275)
Q Consensus 26 Q~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKr------IWIKrGD~VLVeP~ 75 (275)
...|+|+.....+.| |++.++..-+++++ .+... -+++.||.|.|...
T Consensus 3 ~~~g~V~~i~~~G~f-v~l~~~~~g~~~~~-~l~~~~~~~~~~~~~~Gd~v~v~i~ 56 (68)
T cd05685 3 VLEGVVTNVTDFGAF-VDIGVKQDGLIHIS-KMADRFVSHPSDVVSVGDIVEVKVI 56 (68)
T ss_pred EEEEEEEEEecccEE-EEcCCCCEEEEEHH-HCCCccccCHHHhcCCCCEEEEEEE
Confidence 567899998877766 78888866666654 22221 14699999998854
No 47
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=56.57 E-value=38 Score=26.90 Aligned_cols=57 Identities=16% Similarity=0.045 Sum_probs=33.7
Q ss_pred EEEEEecCCceEEEE-eCCCcEEEEE---ecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHH
Q psy10593 29 VKITQNSGNNLHQIE-NHSGEKYFVS---MPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISF 96 (275)
Q Consensus 29 grVv~~lG~nlfeVe-c~DG~~rLa~---IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~ 96 (275)
++|++.-|+...... ..+|.+|-++ +|.- ...++.||||||-. |-.+.++.+++.++
T Consensus 7 ~kVi~i~~~~~~~A~vd~~Gv~r~V~l~Lv~~~---~~~~~vGDyVLVHa--------GfAi~~ideeeA~e 67 (82)
T PRK10413 7 GQVLAVGEDIHQLAQVEVCGIKRDVNIALICEG---NPADLLGQWVLVHV--------GFAMSIIDEDEAKA 67 (82)
T ss_pred eEEEEECCCCCcEEEEEcCCeEEEEEeeeeccC---CcccccCCEEEEec--------chhhhhCCHHHHHH
Confidence 688888887422232 2356666655 3210 01478999999983 44455666666544
No 48
>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=55.70 E-value=38 Score=26.51 Aligned_cols=52 Identities=25% Similarity=0.263 Sum_probs=32.5
Q ss_pred EEEEEecCCceEEEEeCCCcEEEEE---ecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHH
Q psy10593 29 VKITQNSGNNLHQIENHSGEKYFVS---MPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFL 97 (275)
Q Consensus 29 grVv~~lG~nlfeVec~DG~~rLa~---IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~L 97 (275)
++|++..|+ .-.|. ..|.++-++ +| -+++||||||-. |-.+.++++++.++.
T Consensus 7 ~~V~~i~~~-~A~v~-~~G~~~~v~l~lv~-------~~~vGD~VLVH~--------G~Ai~~ide~eA~e~ 61 (76)
T TIGR00074 7 GQVVEIDEN-IALVE-FCGIKRDVSLDLVG-------EVKVGDYVLVHV--------GFAISVLDEEEARET 61 (76)
T ss_pred eEEEEEcCC-EEEEE-cCCeEEEEEEEeeC-------CCCCCCEEEEec--------ChhhhhCCHHHHHHH
Confidence 678887764 33333 346555443 33 388999999983 445666777766543
No 49
>PHA02945 interferon resistance protein; Provisional
Probab=55.53 E-value=86 Score=25.58 Aligned_cols=67 Identities=21% Similarity=0.146 Sum_probs=38.2
Q ss_pred CCCCCCCc-EEEEEEEecCCceEEEEeCC-CcEEEEEecccccceeeee-----CCCEEEEeeecCCCCeEEEEEE
Q psy10593 19 YRVPEDLN-NIVKITQNSGNNLHQIENHS-GEKYFVSMPGKFRNNIWIK-----PGDFVIVKPIEEGNKVKAEIEQ 87 (275)
Q Consensus 19 ~~lP~egQ-~IgrVv~~lG~nlfeVec~D-G~~rLa~IPGKfRKrIWIK-----rGD~VLVeP~D~~~kvKGeIV~ 87 (275)
+..|++|+ ++|+|.. .+.+.|-=..+- |.+=+.++.--....-||| .|..|.|.-..-+ +.||-|--
T Consensus 6 y~~P~~GelvigtV~~-~d~ga~v~L~EY~g~eg~i~~seveva~~wvK~rd~l~GqkvV~KVirVd-~~kg~IDl 79 (88)
T PHA02945 6 YSLPNVGDVLKGKVYE-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKLVGKTVKVKVIRVD-YTKGYIDV 79 (88)
T ss_pred ecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEecCCEEEEEEEEEC-CCCCEEEe
Confidence 46899998 5888888 666655444433 7777776663333334555 4444444443322 44555543
No 50
>COG1162 Predicted GTPases [General function prediction only]
Probab=54.09 E-value=33 Score=33.29 Aligned_cols=69 Identities=20% Similarity=0.268 Sum_probs=51.5
Q ss_pred EEEEEEecCCceEEEEeCC---CcEEEEEecccccce-eeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHHHHCCCC
Q psy10593 28 IVKITQNSGNNLHQIENHS---GEKYFVSMPGKFRNN-IWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQLKL 103 (275)
Q Consensus 28 IgrVv~~lG~nlfeVec~D---G~~rLa~IPGKfRKr-IWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~Lrk~G~W 103 (275)
.|+|++.. +|.|.|.+.+ ++...|...|+||++ .-.-.||.|.+++... .|-|..++.+. ..|.+-..+
T Consensus 6 ~g~v~~~~-~g~y~v~~~~~~~~~~~~~~~r~~lr~~~~~~vVGD~V~~~~~~~----~g~I~~i~~Rk--n~L~Rp~v~ 78 (301)
T COG1162 6 RGRVVKVD-AGFYGVRLEEEVDGEVYRCRARGNLRKKDLKPVVGDRVVFEDENN----NGVIEKILPRK--NVLIRPPVA 78 (301)
T ss_pred CcEEEEee-CCEEEEEEccccccceeeeeeecceeccCccccccCeEEEecCCC----cceEEEEeccc--CceeCCccc
Confidence 45555544 4788888774 778889999999998 7888999999996642 28899998877 455554443
No 51
>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=53.56 E-value=42 Score=27.53 Aligned_cols=46 Identities=15% Similarity=0.182 Sum_probs=36.5
Q ss_pred EEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEe
Q psy10593 27 NIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVK 73 (275)
Q Consensus 27 ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVe 73 (275)
+-|.|++.+|++.|......| +..+.|+.+.-.-.=|.++|.|-+.
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 679999999999999999999 8889999997777789999999887
No 52
>PRK05573 rplU 50S ribosomal protein L21; Validated
Probab=53.41 E-value=85 Score=25.68 Aligned_cols=28 Identities=25% Similarity=0.083 Sum_probs=19.8
Q ss_pred CceEEEeecCCCCeeeEEEEEecChhhH
Q psy10593 128 DLTLHLLNKEEGNKVKAEIEQILDKKYI 155 (275)
Q Consensus 128 ~~~~~v~pi~Eg~KVkaEI~~IL~kd~I 155 (275)
+.+++=.|.-+|.+|+|+|..-.--+-|
T Consensus 45 ~~~~iG~P~l~~a~V~A~V~~~~k~~Ki 72 (103)
T PRK05573 45 EEVKIGAPYVEGAKVTAEVVEHGRGKKV 72 (103)
T ss_pred CCEEECCeEcCCCEEEEEEEeccCCCcE
Confidence 4455667888899999999876544433
No 53
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=52.47 E-value=44 Score=27.05 Aligned_cols=53 Identities=15% Similarity=0.130 Sum_probs=31.8
Q ss_pred EEEEEecCCceEEEEeCCCcEEEEEeccccccee-------eeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHH
Q psy10593 29 VKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNI-------WIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISF 96 (275)
Q Consensus 29 grVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrI-------WIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~ 96 (275)
++|++.-|+ . -+....|.++-++|- .+ .++.||||||-- |--+.++.+++.+.
T Consensus 7 ~kVv~i~~~-~-A~vd~~Gv~reV~l~-----Lv~~~~~~~~~~vGDyVLVHa--------GfAi~~ideeeA~e 66 (90)
T PRK10409 7 GQIRTIDGN-Q-AKVDVCGIQRDVDLT-----LVGSCDENGQPRVGQWVLVHV--------GFAMSVINEAEARD 66 (90)
T ss_pred eEEEEEcCC-e-EEEEcCCeEEEEEEe-----eecccCCCCccCCCCEEEEec--------ChHHhhCCHHHHHH
Confidence 678887664 3 333345666655542 12 478999999983 33355666665543
No 54
>TIGR00061 L21 ribosomal protein L21. Eubacterial and chloroplast.
Probab=46.17 E-value=1.1e+02 Score=25.00 Aligned_cols=25 Identities=32% Similarity=0.062 Sum_probs=17.6
Q ss_pred ceEEEeecCCCCeeeEEEEEecChh
Q psy10593 129 LTLHLLNKEEGNKVKAEIEQILDKK 153 (275)
Q Consensus 129 ~~~~v~pi~Eg~KVkaEI~~IL~kd 153 (275)
..++=.|.-+|.+|+|+|+.-.--+
T Consensus 45 ~~~iG~P~l~~a~V~a~V~~~~r~~ 69 (101)
T TIGR00061 45 DVKIGKPYVEGAKVVAEVEKHGRGK 69 (101)
T ss_pred CeEECCeEcCCCEEEEEEEeecCCC
Confidence 4445568888999999998654333
No 55
>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=46.10 E-value=68 Score=26.68 Aligned_cols=54 Identities=19% Similarity=0.298 Sum_probs=41.8
Q ss_pred cCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHHHHHC
Q psy10593 35 SGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISFLKQQ 100 (275)
Q Consensus 35 lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~Lrk~ 100 (275)
.|.-.+++.+.|... --|+.||.++..-|+.+..+..+|+++..=+.-++|-+.
T Consensus 15 ~G~KtiEiRlnD~kr------------~~ikvGD~I~f~~~~~~~~l~v~V~~i~~Y~sF~~ll~~ 68 (109)
T cd06555 15 SGKKTIEIRLNDEKR------------QQIKVGDKILFNDLDTGQQLLVKVVDIRKYDSFRELLEE 68 (109)
T ss_pred cCCCEEEEEecccch------------hcCCCCCEEEEEEcCCCcEEEEEEEEEEecCCHHHHHHh
Confidence 355667777776543 248999999999887666799999999887877877765
No 56
>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=44.55 E-value=52 Score=26.31 Aligned_cols=29 Identities=14% Similarity=0.184 Sum_probs=25.0
Q ss_pred EEEEEEEecCCceEEEEeCCCcEEEEEecc
Q psy10593 27 NIVKITQNSGNNLHQIENHSGEKYFVSMPG 56 (275)
Q Consensus 27 ~IgrVv~~lG~nlfeVec~DG~~rLa~IPG 56 (275)
++|+|++..|+ .+.+.|+||....+.++.
T Consensus 20 ivGkV~~~~~~-~~~~~~~Dg~~v~v~l~~ 48 (101)
T cd04479 20 IVGKVEKVDGD-SLTLISSDGVNVTVELNR 48 (101)
T ss_pred EEEEEEEecCC-eEEEEcCCCCEEEEEeCC
Confidence 68999999887 899999999888777664
No 57
>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=44.01 E-value=1.5e+02 Score=27.65 Aligned_cols=123 Identities=18% Similarity=0.208 Sum_probs=71.2
Q ss_pred EEEEEEecCCceEEEEeC-CCcEEEEEec--ccccceeeeeCCCEEEEeeecCC-CCeEEEEEEEeCh------------
Q psy10593 28 IVKITQNSGNNLHQIENH-SGEKYFVSMP--GKFRNNIWIKPGDFVIVKPIEEG-NKVKAEIEQILDK------------ 91 (275)
Q Consensus 28 IgrVv~~lG~nlfeVec~-DG~~rLa~IP--GKfRKrIWIKrGD~VLVeP~D~~-~kvKGeIV~ry~k------------ 91 (275)
.|+.++-. |+|.|.+. ||++.+||+| |||... +.+|--|++.+.+.. .|.+-+++-+...
T Consensus 11 ~~~fi~R~--nRF~~~V~~~G~~~~aH~pNtGrl~el--l~pG~~vll~~~~~p~rK~~y~l~~v~~~g~~V~int~~~N 86 (232)
T TIGR00230 11 RGRLIGRY--NRFLVDVEVDGRRETAHCPNTGRLTEL--IFPGNDVGLSKSDNGGRKLSYTWEAVQCDGGWVLVNTQLQN 86 (232)
T ss_pred EEEEEeec--CCEEEEEEECCeEEEEEcCCCCCChhh--cCCCCEEEEEECCCCCCCCCEEEEEEEECCeEEEEcCccHH
Confidence 46666655 67777755 8999999997 566654 459999999987642 2444444444432
Q ss_pred hhHHHHHHCCCCCcccccCcccc-cccccccccCCCCCceEEEeecCCCCeeeEEEEEe-cChhhHHHHHHhCCCCccc
Q psy10593 92 KYISFLKQQLKLPPIENGDIVHH-FQEIGEQQAKPYRDLTLHLLNKEEGNKVKAEIEQI-LDKKYISFLKQQNSWPFTE 168 (275)
Q Consensus 92 dqVK~Lrk~G~WPkeF~~~~~~~-~~e~~~~~~~~~r~~~~~v~pi~Eg~KVkaEI~~I-L~kd~IK~lkk~~~WP~~F 168 (275)
.=+.++.++|.+|. |......+ .--.|. + .|=||++= ..+.++=-|+-.+ |-. ..-+.+|-+=
T Consensus 87 ~l~~~~l~~~~i~~-l~~~~~ikrEv~~g~---~-SRiDfll~---~~~~~~~vEVKsvtL~~------~~~A~FPDAp 151 (232)
T TIGR00230 87 RLFKVAIPSSKISE-LDGYEVRKREVKYGN---R-SRIDFLLG---ESNERMYVEVKSATLKK------EILALFPDAP 151 (232)
T ss_pred HHHHHHHHcCCCcc-ccCcceEeeccccCC---C-CcEEEEEe---cCCCcEEEEEccEEeCC------CCEEECCCCc
Confidence 23567777888885 43221111 012222 1 67788663 2222566666554 432 2346777443
No 58
>PF03749 SfsA: Sugar fermentation stimulation protein; InterPro: IPR005224 The sugar fermentation stimulation protein is a probable regulatory factor involved in maltose metabolism. It contains a putative DNA-binding domain, and was isolated as a gene which enabled Escherichia coli W3110 (strain MK2001) to use maltose [].
Probab=42.75 E-value=1.6e+02 Score=27.03 Aligned_cols=116 Identities=18% Similarity=0.150 Sum_probs=67.6
Q ss_pred EEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCC-CCeEEEEEEEeCh-------------hhHHHHHHCCCCCcc
Q psy10593 41 QIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEG-NKVKAEIEQILDK-------------KYISFLKQQLKLPPI 106 (275)
Q Consensus 41 eVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~-~kvKGeIV~ry~k-------------dqVK~Lrk~G~WPke 106 (275)
+|+..||+...||+|.-=|..=-+.+|--|++.+.+.. .|.+.+++-+... .=+.++.+.|.+| .
T Consensus 10 ~v~l~~g~~~~~H~pntGRl~ell~pG~~v~l~~~~~~~RKt~y~l~av~~~~~~~V~int~~~N~lv~~~l~~~~i~-~ 88 (215)
T PF03749_consen 10 DVELDDGEEVTAHCPNTGRLKELLVPGARVLLSKSDNPKRKTKYTLEAVEKDNGVWVGINTQLPNRLVEEALENGLIP-E 88 (215)
T ss_pred EEEECCCCEEEEEcCCCCcchhhccCCCEEEEEECCCCCCCCcEEEEEEEcCCCeEEEEccchHHHHHHHHHHcCCCc-c
Confidence 45556799999999744443323349999999987642 2566666666655 3467778888887 3
Q ss_pred cccCcccccccccccccCCCCCceEEEeecCCCCeeeEEEEEe-cChhhHHHHHHhCCCCccccc
Q psy10593 107 ENGDIVHHFQEIGEQQAKPYRDLTLHLLNKEEGNKVKAEIEQI-LDKKYISFLKQQNSWPFTEDS 170 (275)
Q Consensus 107 F~~~~~~~~~e~~~~~~~~~r~~~~~v~pi~Eg~KVkaEI~~I-L~kd~IK~lkk~~~WP~~F~~ 170 (275)
|..-...+ -|..---.|=||++-.+- .+.=-|+-.+ |-.+ ....+|.+-++
T Consensus 89 l~~~~~i~----rEv~~g~sR~Dfll~~~~---~~~~vEVKsvtL~~~------~~a~FPDApT~ 140 (215)
T PF03749_consen 89 LSGYSEIR----REVKYGNSRFDFLLEDNG---GKCYVEVKSVTLVED------GIAMFPDAPTE 140 (215)
T ss_pred ccCcceEe----eceeeCCccEEEEEEcCC---CCEEEEEeeeEeccC------CcccCCCccch
Confidence 44221111 122222355678765443 2555566555 3332 34578844443
No 59
>KOG3403|consensus
Probab=42.11 E-value=43 Score=29.27 Aligned_cols=42 Identities=14% Similarity=0.019 Sum_probs=35.3
Q ss_pred CceEEEeecCCCCeeeEEEEEecChhhHHHHHHhCCCCccccc
Q psy10593 128 DLTLHLLNKEEGNKVKAEIEQILDKKYISFLKQQNSWPFTEDS 170 (275)
Q Consensus 128 ~~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~lkk~~~WP~~F~~ 170 (275)
|+. |+.-+..++-=||-|.+--.+|..+.||..|.-|+.|..
T Consensus 74 GDI-iLv~lRD~qd~kaDvilKY~~dEar~LK~~Gelpe~~k~ 115 (145)
T KOG3403|consen 74 GDI-ILVGLRDYQDDKADVILKYMPDEARILKAYGELPENAKI 115 (145)
T ss_pred CCE-EEEeeecccccccceehhhChHHHHHHHhcCcCCccccc
Confidence 454 556677788889999999999999999999999977754
No 60
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=41.90 E-value=1.6e+02 Score=23.85 Aligned_cols=54 Identities=24% Similarity=0.207 Sum_probs=36.0
Q ss_pred EEEEEecCCceEEEEeCCCcEEEEE---ecccccceeeeeCCCEEEEeeecCCCCeEEEEEEEeChhhHHH
Q psy10593 29 VKITQNSGNNLHQIENHSGEKYFVS---MPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQILDKKYISF 96 (275)
Q Consensus 29 grVv~~lG~nlfeVec~DG~~rLa~---IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdqVK~ 96 (275)
|+|++.-+++.+-+..--|.+|-+. ++. =++.||||||- .|--+.++..++.+.
T Consensus 7 gqI~~I~~~~~~A~Vd~gGvkreV~l~Lv~~------~v~~GdyVLVH--------vGfAi~~idEeeAke 63 (82)
T COG0298 7 GQIVEIDDNNHLAIVDVGGVKREVNLDLVGE------EVKVGDYVLVH--------VGFAMSKIDEEEAKE 63 (82)
T ss_pred cEEEEEeCCCceEEEEeccEeEEEEeeeecC------ccccCCEEEEE--------eeEEEeecCHHHHHH
Confidence 6788888877555555567666544 443 47899999998 344455677776554
No 61
>PRK11642 exoribonuclease R; Provisional
Probab=40.04 E-value=97 Score=33.66 Aligned_cols=48 Identities=17% Similarity=0.198 Sum_probs=34.2
Q ss_pred eeCCCEEEEee--ecC-CCCeEEEEEEEeCh-----hhHHHHHHCCCCCcccccCc
Q psy10593 64 IKPGDFVIVKP--IEE-GNKVKAEIEQILDK-----KYISFLKQQLKLPPIENGDI 111 (275)
Q Consensus 64 IKrGD~VLVeP--~D~-~~kvKGeIV~ry~k-----dqVK~Lrk~G~WPkeF~~~~ 111 (275)
.+.||.|+|+. |.. +..-.|.|+.++.. -++..+...--+|.+|..++
T Consensus 186 ~~~gd~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~~Fp~~v 241 (813)
T PRK11642 186 ARMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQAV 241 (813)
T ss_pred CCCCCEEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCCCCCHHH
Confidence 46789999995 332 34578999999965 35666666666788887654
No 62
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 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 S. 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=39.68 E-value=63 Score=25.39 Aligned_cols=56 Identities=18% Similarity=0.228 Sum_probs=32.2
Q ss_pred CCCCC-cEEEEEEEecCCceEEEEe--------CC---CcEEEEEecccccc----eeeeeCCCEEEEeeecC
Q psy10593 21 VPEDL-NNIVKITQNSGNNLHQIEN--------HS---GEKYFVSMPGKFRN----NIWIKPGDFVIVKPIEE 77 (275)
Q Consensus 21 lP~eg-Q~IgrVv~~lG~nlfeVec--------~D---G~~rLa~IPGKfRK----rIWIKrGD~VLVeP~D~ 77 (275)
.|..| -++|+|+.. +.+...|.. +. |..+.-.++..... +-.+++||+|.+.....
T Consensus 3 ~P~~GDiVig~V~~v-~~~~~~v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~ 74 (92)
T cd05791 3 LPKVGSIVIARVTRI-NPRFAKVDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISL 74 (92)
T ss_pred CCCCCCEEEEEEEEE-cCCEEEEEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEc
Confidence 56655 589999986 466666655 21 22222222221111 23569999999986654
No 63
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=39.50 E-value=76 Score=31.33 Aligned_cols=50 Identities=18% Similarity=0.285 Sum_probs=44.3
Q ss_pred CCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEee
Q psy10593 24 DLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKP 74 (275)
Q Consensus 24 egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP 74 (275)
....+|.|++.++.++.-|...+|.++++.+.+...+.. +++|+-|.+..
T Consensus 65 ~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~~~~v~~~~ 114 (398)
T PTZ00454 65 VPLVIGQFLEMIDSNYGIVSSTSGSNYYVRILSTLNREL-LKPNASVALHR 114 (398)
T ss_pred CCceEEEEEEEEcCCEEEEEcCCCCEEEEecccccCHhh-CCCCCEEEeec
Confidence 467899999999999999999999999999998886544 79999999884
No 64
>PF00717 Peptidase_S24: Peptidase S24-like peptidase classification. ; InterPro: IPR019759 In the MEROPS database peptidases and peptidase homologues are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry based on a common structural fold: Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, N-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins. Peptidase families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; N, asparagine; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule. In the case of the asparagine endopeptidases, the nucleophile is asparagine and all are self-processing endopeptidases. In many instances the structural protein fold that characterises the clan or family may have lost its catalytic activity, yet retain its function in protein recognition and binding. Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes []. They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence []. Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases []. Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base []. The geometric orientations of the catalytic residues are similar between families, despite different protein folds []. The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) [, ].; PDB: 1KCA_H 3BDN_A 1F39_A 1JHH_A 1JHE_B 3JSP_A 1JHF_B 1JHC_A 3JSO_B 1B12_D ....
Probab=38.43 E-value=9.6 Score=27.05 Aligned_cols=27 Identities=33% Similarity=0.459 Sum_probs=12.1
Q ss_pred eeCCCEEEEeeecCCCCeEEEEEEEeChh
Q psy10593 64 IKPGDFVIVKPIEEGNKVKAEIEQILDKK 92 (275)
Q Consensus 64 IKrGD~VLVeP~D~~~kvKGeIV~ry~kd 92 (275)
|+.||+|+|++... -..|+|+....+.
T Consensus 11 i~~Gd~v~v~~~~~--~~~gdivv~~~~~ 37 (70)
T PF00717_consen 11 IKDGDIVLVDPSSE--PKDGDIVVVKIDG 37 (70)
T ss_dssp SSTTEEEEEEETS-----TTSEEEEEETT
T ss_pred eeCCCEEEEEEcCC--CccCeEEEEEECC
Confidence 34566666665431 2344444444433
No 65
>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=37.83 E-value=53 Score=33.81 Aligned_cols=49 Identities=27% Similarity=0.521 Sum_probs=42.1
Q ss_pred CcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeee
Q psy10593 25 LNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPI 75 (275)
Q Consensus 25 gQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~ 75 (275)
|+ +++|.+.+|.+++.|...+|..+++++.+.+...- +++||-|+|++.
T Consensus 107 g~-~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~~-~~~g~~~~~~~~ 155 (512)
T TIGR03689 107 GE-IATLKEVLGDGRALVVDHSGEERVVKLAGALADEL-IRAGDSLLVDPK 155 (512)
T ss_pred Cc-eEEEEEEeCCCeEEEEeCCCCeEEeehhhhhCHhh-CCCCCEEEEccc
Confidence 44 45899999999999999999999999999887642 689999999853
No 66
>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=36.88 E-value=85 Score=25.13 Aligned_cols=43 Identities=14% Similarity=0.138 Sum_probs=27.5
Q ss_pred EEEEEEEec-CCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEe
Q psy10593 27 NIVKITQNS-GNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVK 73 (275)
Q Consensus 27 ~IgrVv~~l-G~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVe 73 (275)
++|+|.+.- +++.+.+.|.||....+.++.-..- ..+.+|-|-
T Consensus 23 ivGkv~~~~~~g~~~~l~~~d~~~V~v~l~~~~~~----~~~~~vEvi 66 (109)
T PF08661_consen 23 IVGKVESVDPDGGSATLSTSDGGQVTVSLNPPSDE----ELSKYVEVI 66 (109)
T ss_dssp EEEEEEEE-TTSSEEEEE-TTS-EEEEEESS--SS-------SEEEEE
T ss_pred EEEEEeeEcCCCCEEEEEcCCCCEEEEEeCCCCCC----CCCCEEEEE
Confidence 688888866 5789999999999999998865432 235566554
No 67
>PF09884 DUF2111: Uncharacterized protein conserved in archaea (DUF2111); InterPro: IPR012029 There are currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, members of PIRSF036667 from PIRSF possess a domain homologous to these proteins fused within a signal transduction sensor protein containing PAS/PAC and GAF domains. Therefore, it is possible that members of this family are involved in signal transduction (possibly as a sensor).
Probab=36.20 E-value=36 Score=27.54 Aligned_cols=24 Identities=21% Similarity=0.398 Sum_probs=20.9
Q ss_pred cCCCCCceEEEeecCCC-CeeeEEE
Q psy10593 123 AKPYRDLTLHLLNKEEG-NKVKAEI 146 (275)
Q Consensus 123 ~~~~r~~~~~v~pi~Eg-~KVkaEI 146 (275)
.-||.|--++|.||.++ ++|-|-|
T Consensus 53 ~G~Y~G~PViV~PI~~~~g~viaAi 77 (84)
T PF09884_consen 53 EGPYKGVPVIVAPIKDEDGEVIAAI 77 (84)
T ss_pred CcccCCeeEEEEEEEcCCCCEEEEE
Confidence 35999999999999999 6888765
No 68
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=36.08 E-value=3.1e+02 Score=25.20 Aligned_cols=107 Identities=16% Similarity=0.180 Sum_probs=60.3
Q ss_pred CCcEEEEEEE-ecCCceEEEEeCCCcEEEEEecccccc---------------eeeeeCCCEEEEeeecCCCCeEEEEEE
Q psy10593 24 DLNNIVKITQ-NSGNNLHQIENHSGEKYFVSMPGKFRN---------------NIWIKPGDFVIVKPIEEGNKVKAEIEQ 87 (275)
Q Consensus 24 egQ~IgrVv~-~lG~nlfeVec~DG~~rLa~IPGKfRK---------------rIWIKrGD~VLVeP~D~~~kvKGeIV~ 87 (275)
+|+.+|...+ ..|.+.++. || ...|...|.+.. -.-.|+||+|+-.-.+. +...-++.
T Consensus 10 PGd~~a~~EE~~~G~gt~~~---~g-~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v--~~~~a~V~ 83 (188)
T COG1096 10 PGDVLAVIEEFLPGEGTYEE---GG-EIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDV--REQRALVR 83 (188)
T ss_pred CcceeeeeeeeecCCCeEeE---CC-EEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeec--cceEEEEE
Confidence 4777777777 345555554 33 333444444432 24567899999987654 22344444
Q ss_pred EeChhhHHHHHHCCCCCcccccCcccccccccccccCCCCCceEEEeecCCCCeeeEEEEEe
Q psy10593 88 ILDKKYISFLKQQLKLPPIENGDIVHHFQEIGEQQAKPYRDLTLHLLNKEEGNKVKAEIEQI 149 (275)
Q Consensus 88 ry~kdqVK~Lrk~G~WPkeF~~~~~~~~~e~~~~~~~~~r~~~~~v~pi~Eg~KVkaEI~~I 149 (275)
++.-++.. -..|..|... -|.+.+..---++.+|.| ..||=|+|-++..
T Consensus 84 i~~ve~~~-----r~~~~~~~~~--ihvs~~~~~~~~~~~d~f------~~GDivrA~Vis~ 132 (188)
T COG1096 84 IVGVEGKE-----RELATSGAAD--IHVSQVRDGYVEKLSDAF------RIGDIVRARVIST 132 (188)
T ss_pred EEEEeccc-----ccCCCCceee--EEEEeccccccccccccc------ccccEEEEEEEec
Confidence 44444322 1133334332 333455555666777666 6699999998875
No 69
>PRK12278 50S ribosomal protein L21/unknown domain fusion protein; Provisional
Probab=34.99 E-value=1.9e+02 Score=26.90 Aligned_cols=30 Identities=13% Similarity=0.063 Sum_probs=20.6
Q ss_pred ceEEEeecCCCCeeeEEEEEecChhhHHHH
Q psy10593 129 LTLHLLNKEEGNKVKAEIEQILDKKYISFL 158 (275)
Q Consensus 129 ~~~~v~pi~Eg~KVkaEI~~IL~kd~IK~l 158 (275)
.++|=.|.-+|.+|+|+|+.-+--+-|..+
T Consensus 46 ~~~iG~P~v~~a~V~A~V~~~~kg~Ki~vf 75 (221)
T PRK12278 46 NVTVGAPFVDGAAVQAEVIEQIKGDKVIHF 75 (221)
T ss_pred CeEECCeEecCCEEEEEEEeecCCCCEEEE
Confidence 344556778889999999876655555433
No 70
>cd04482 RPA2_OBF_like RPA2_OBF_like: A subgroup of uncharacterized archaeal OB folds with similarity to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a 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). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle depende
Probab=34.01 E-value=66 Score=25.24 Aligned_cols=38 Identities=29% Similarity=0.417 Sum_probs=27.0
Q ss_pred CCceEEEEeCCCcEEEEEeccc--ccce-eeeeCCCEEEEe
Q psy10593 36 GNNLHQIENHSGEKYFVSMPGK--FRNN-IWIKPGDFVIVK 73 (275)
Q Consensus 36 G~nlfeVec~DG~~rLa~IPGK--fRKr-IWIKrGD~VLVe 73 (275)
|.-.|++.+.++....+...+. +++. ..++.||.|+|.
T Consensus 17 GH~yFtlkD~~~~i~cv~f~~~g~~~~~~~~l~~Gd~V~v~ 57 (91)
T cd04482 17 GHVFFKISDGTGEIDCAAYEPTKEFRDVVRLLIPGDEVTVY 57 (91)
T ss_pred CCEEEEEECCCcEEEEEEECcccccccccCCCCCCCEEEEE
Confidence 3455666666666666666655 6654 789999999987
No 71
>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=34.01 E-value=16 Score=25.14 Aligned_cols=30 Identities=30% Similarity=0.479 Sum_probs=24.7
Q ss_pred CcEEEEEecccccceeeeeCCCEEEEeeec
Q psy10593 47 GEKYFVSMPGKFRNNIWIKPGDFVIVKPIE 76 (275)
Q Consensus 47 G~~rLa~IPGKfRKrIWIKrGD~VLVeP~D 76 (275)
|...-+.||..+++..=|+.||.|.+...+
T Consensus 4 g~s~~v~iPk~~~~~l~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 4 GNSGQVTIPKEIREKLGLKPGDEVEIEVEG 33 (47)
T ss_dssp TTCSEEEE-HHHHHHTTSSTTTEEEEEEET
T ss_pred CCCceEECCHHHHHHcCCCCCCEEEEEEeC
Confidence 344567899999999999999999999775
No 72
>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=33.63 E-value=1.1e+02 Score=26.09 Aligned_cols=46 Identities=24% Similarity=0.312 Sum_probs=40.2
Q ss_pred EEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEe
Q psy10593 27 NIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVK 73 (275)
Q Consensus 27 ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVe 73 (275)
+-|.|++.+|++.|......|. ..+.|+.+.=+-.=|.++|.|-+.
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 6799999999999999999995 778998877666778899999887
No 73
>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=33.37 E-value=72 Score=26.95 Aligned_cols=62 Identities=13% Similarity=0.113 Sum_probs=36.4
Q ss_pred cEEEEEEEecCCc-eEEEEeCCCc----------EEEEEeccccc----ceeeeeCCCEEEEeeecC-CCCeEEEEEEE
Q psy10593 26 NNIVKITQNSGNN-LHQIENHSGE----------KYFVSMPGKFR----NNIWIKPGDFVIVKPIEE-GNKVKAEIEQI 88 (275)
Q Consensus 26 Q~IgrVv~~lG~n-lfeVec~DG~----------~rLa~IPGKfR----KrIWIKrGD~VLVeP~D~-~~kvKGeIV~r 88 (275)
=++|+|++..|++ .|+|+.+|-. ..+.-||.+.. ...=...|+.||.- |.. ..==+|.|+-.
T Consensus 19 WIla~Vv~~~~~~~rYeV~D~d~~~~~~~~~~~~~~iIPLP~~~~~~~~~~~~f~~g~~VLAl-YP~TT~FY~A~V~~~ 96 (130)
T PF07039_consen 19 WILAEVVKYNSDGNRYEVEDPDPEEEKKRYKLSRKQIIPLPKKAPPDTDPLAEFPKGTKVLAL-YPDTTCFYPATVVSP 96 (130)
T ss_dssp EEEEEEEEEETTTTEEEEEETTTCTTTEEEEEEGGGEEEE-SB--TTT-GGGS--TT-EEEEE--TTSSEEEEEEEEEE
T ss_pred EEEEEEEEEeCCCCEEEEecCCCCCCCceEEeCHHHEEECCCccCCCCCchhhCCCCCEEEEE-CCCCceEEEEEEEeC
Confidence 3899999999888 9999999865 34456676222 23446778888876 221 11135555554
No 74
>TIGR02754 sod_Ni_protease nickel-type superoxide dismutase maturation protease. Members of this protein family are apparent proteases encoded adjacent to the genes for a nickel-type superoxide dismutase. This family belongs to the same larger family (see Pfam model pfam00717) as signal peptidase I, an unusual serine protease suggested to have a Ser/Lys catalytic dyad.
Probab=32.67 E-value=47 Score=25.06 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=16.5
Q ss_pred eeCCCEEEEeeecC--CCCeEEEEEEEeCh
Q psy10593 64 IKPGDFVIVKPIEE--GNKVKAEIEQILDK 91 (275)
Q Consensus 64 IKrGD~VLVeP~D~--~~kvKGeIV~ry~k 91 (275)
++.||+|+|.+... .....|+|+-...+
T Consensus 12 l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~ 41 (90)
T TIGR02754 12 LPPGDRIIVVPWLKIFRVPPIGNVVVVRHP 41 (90)
T ss_pred cCCCCEEEEEEccccCCCCCCCeEEEEecC
Confidence 46788888886422 11224777766654
No 75
>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=32.21 E-value=35 Score=22.26 Aligned_cols=26 Identities=27% Similarity=0.459 Sum_probs=22.8
Q ss_pred EEEecccccceeeeeCCCEEEEeeec
Q psy10593 51 FVSMPGKFRNNIWIKPGDFVIVKPIE 76 (275)
Q Consensus 51 La~IPGKfRKrIWIKrGD~VLVeP~D 76 (275)
-+.||.++|+.+=+..||.+.+.+..
T Consensus 8 ri~iP~~~r~~l~~~~gd~~~i~~~~ 33 (43)
T TIGR01439 8 QIVIPKEIREKLGLKEGDRLEVIRVE 33 (43)
T ss_pred eEEecHHHHHHcCcCCCCEEEEEEeC
Confidence 35799999999999999999999653
No 76
>PRK10053 hypothetical protein; Provisional
Probab=32.07 E-value=1.2e+02 Score=26.03 Aligned_cols=46 Identities=15% Similarity=0.277 Sum_probs=41.4
Q ss_pred EEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEe
Q psy10593 27 NIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVK 73 (275)
Q Consensus 27 ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVe 73 (275)
.-|.|++.+|+..|.-....|+ ..+.|+.+.-.-.=|.+.|.|-+.
T Consensus 66 L~G~Iv~~lg~d~Y~F~D~tG~-I~VeID~~~w~G~~v~p~~kV~I~ 111 (130)
T PRK10053 66 LRGNLIDHKGDDRYVFRDKSGE-INVIIPAAVFDGREVQPDQMININ 111 (130)
T ss_pred EEEEEEEEeCCceEEEECCCCc-EEEEeCHHHcCCCcCCCCCEEEEE
Confidence 6799999999999999999994 778999988777889999999887
No 77
>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=31.86 E-value=44 Score=28.42 Aligned_cols=30 Identities=23% Similarity=0.406 Sum_probs=20.7
Q ss_pred eeeeCCCEEEEeeecCCCCeEEEEEEEeCh
Q psy10593 62 IWIKPGDFVIVKPIEEGNKVKAEIEQILDK 91 (275)
Q Consensus 62 IWIKrGD~VLVeP~D~~~kvKGeIV~ry~k 91 (275)
+=|+.||+|+|.+-|.+..--|.|...|..
T Consensus 2 ~~i~vGd~VlI~~~d~~~~yVAkI~~i~e~ 31 (128)
T cd04719 2 LTIEVGDFVLIEGEDADGPDVARILHLYED 31 (128)
T ss_pred eEEecCCEEEEECCCCCCCcEeeehhhhcc
Confidence 348899999999876433456666665553
No 78
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme) to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=31.13 E-value=2.5e+02 Score=21.75 Aligned_cols=52 Identities=10% Similarity=0.178 Sum_probs=36.4
Q ss_pred CcEEEEEEEecCC-ceEEEEeCCCcEEEEEeccc-------ccc-eeeeeCCCEEEEeeec
Q psy10593 25 LNNIVKITQNSGN-NLHQIENHSGEKYFVSMPGK-------FRN-NIWIKPGDFVIVKPIE 76 (275)
Q Consensus 25 gQ~IgrVv~~lG~-nlfeVec~DG~~rLa~IPGK-------fRK-rIWIKrGD~VLVeP~D 76 (275)
+-..|+|+..... +-.-|.+.+|..-++++..= .++ .--++.||.|+|.-..
T Consensus 9 ~iy~g~V~~i~~~~~GaFV~l~~g~~Gllh~seis~~~~~~v~~~~~~~~~Gd~v~VqV~~ 69 (88)
T cd04453 9 NIYLGRVKKIVPGLQAAFVDIGLGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVK 69 (88)
T ss_pred CEEEEEEEEeccCCcEEEEEeCCCCEEEEEhHHcCchhccccCCHHHcCCCCCEEEEEEEE
Confidence 3468999999875 45667888888888887531 111 1248899999999433
No 79
>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=30.20 E-value=2.7e+02 Score=29.44 Aligned_cols=48 Identities=17% Similarity=0.227 Sum_probs=33.7
Q ss_pred eeCCCEEEEee--ecC-CCCeEEEEEEEeCh-----hhHHHHHHCCCCCcccccCc
Q psy10593 64 IKPGDFVIVKP--IEE-GNKVKAEIEQILDK-----KYISFLKQQLKLPPIENGDI 111 (275)
Q Consensus 64 IKrGD~VLVeP--~D~-~~kvKGeIV~ry~k-----dqVK~Lrk~G~WPkeF~~~~ 111 (275)
.+.||.|+|+. |+. +..-.|.|+.++.. -+++.+....-+|.+|.++.
T Consensus 172 ~~~g~~v~v~i~~~p~~~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i~~~f~~~v 227 (709)
T TIGR02063 172 AEEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPEEV 227 (709)
T ss_pred CCCCCEEEEEEccCCCCCCCceEEEEEEeCCCCcccchHHHHHHHcCcCCCCCHHH
Confidence 35689999995 432 34678999999954 35666666666788887654
No 80
>COG0509 GcvH Glycine cleavage system H protein (lipoate-binding) [Amino acid transport and metabolism]
Probab=30.20 E-value=24 Score=30.56 Aligned_cols=41 Identities=12% Similarity=0.259 Sum_probs=29.1
Q ss_pred EEecccccce---eeeeC-C-CEEEEeeecCCCCeEEEEEEEeChh
Q psy10593 52 VSMPGKFRNN---IWIKP-G-DFVIVKPIEEGNKVKAEIEQILDKK 92 (275)
Q Consensus 52 a~IPGKfRKr---IWIKr-G-D~VLVeP~D~~~kvKGeIV~ry~kd 92 (275)
+.+|..++.. .||+. | +.+.|.--++..+.-|+|+|+=-++
T Consensus 3 ~~~p~~l~Y~~~heWvr~e~d~~~tvGiT~~aq~~lGdiv~Velpe 48 (131)
T COG0509 3 CNIPDDLKYTAEHEWVRVEGDGTATVGITDYAQDQLGDIVFVELPE 48 (131)
T ss_pred ccccccceeccceEEEEecCCCEEEEeCCHHHHHhcCCEEEEEcCC
Confidence 4567777654 99998 4 7778876665446788888886655
No 81
>KOG4225|consensus
Probab=29.35 E-value=21 Score=36.59 Aligned_cols=90 Identities=18% Similarity=0.058 Sum_probs=51.2
Q ss_pred eEEEEEEEeChhhHHHHHH-----CCCCCcccccCccc----cccc--------ccccccCCCC-CceEEEeecCCCCee
Q psy10593 81 VKAEIEQILDKKYISFLKQ-----QLKLPPIENGDIVH----HFQE--------IGEQQAKPYR-DLTLHLLNKEEGNKV 142 (275)
Q Consensus 81 vKGeIV~ry~kdqVK~Lrk-----~G~WPkeF~~~~~~----~~~e--------~~~~~~~~~r-~~~~~v~pi~Eg~KV 142 (275)
.||+|||++.+=+-.|+-- .|+.|..+.+-.+. ++++ .||--|++-+ ++.=+=.-..+|++|
T Consensus 250 ~kGDIVyI~rkvD~nWyeGEhhGr~GifP~sYvE~~~~~e~~qP~~~~P~q~~~~g~a~A~y~F~~~s~~Els~~kge~v 329 (489)
T KOG4225|consen 250 NKGDIVYILRKVDQNWYEGEHHGRVGIFPASYVEILTPREKAQPARPPPQQVLEQGEAIAKYNFNADSPVELSLRKGERV 329 (489)
T ss_pred CCCCEEEEEeeccCceeeeeecceecceechheeecCcccccCcCCCCcccccccccccccCCCCCCCchhcccccCceE
Confidence 5899999998877777764 48999888765544 3343 6666676544 322122233445544
Q ss_pred eEEE--EEecChhhHHHHHHhCCCCccccc
Q psy10593 143 KAEI--EQILDKKYISFLKQQNSWPFTEDS 170 (275)
Q Consensus 143 kaEI--~~IL~kd~IK~lkk~~~WP~~F~~ 170 (275)
+-.- -.=-|.--|--+..+|..|-.|-+
T Consensus 330 ~L~r~vd~nw~eG~i~g~~rqgifP~SyVe 359 (489)
T KOG4225|consen 330 TLTRQVDENWYEGKIPGTNRQGIFPASYVE 359 (489)
T ss_pred EEEEeccCceeeccccccccccccchhHhh
Confidence 3221 000244445555666777755543
No 82
>PRK05054 exoribonuclease II; Provisional
Probab=28.57 E-value=5e+02 Score=27.39 Aligned_cols=48 Identities=19% Similarity=0.113 Sum_probs=34.4
Q ss_pred eeCCCEEEEeee--cC--CCCeEEEEEEEeCh-----hhHHHHHHCCCCCcccccCc
Q psy10593 64 IKPGDFVIVKPI--EE--GNKVKAEIEQILDK-----KYISFLKQQLKLPPIENGDI 111 (275)
Q Consensus 64 IKrGD~VLVeP~--D~--~~kvKGeIV~ry~k-----dqVK~Lrk~G~WPkeF~~~~ 111 (275)
.+.||.|.|+.. .. +....|.|+.++.. -++..+..+--+|.+|..+.
T Consensus 122 ~~~gd~V~v~i~~~p~~~~~~~~g~i~~~lG~~~d~~~d~~~il~~~~l~~~f~~~~ 178 (644)
T PRK05054 122 FKEGDWVVAELRRHPLKGDRGFYAEITQFITDADDHFAPWWVTLARHNLEREAPAGG 178 (644)
T ss_pred CCCCCEEEEEEecCCCCCCCCceEEEEEEECCCCCCccHHHHHHHHcCCCCCCCchh
Confidence 567999999943 22 22368999999954 35666666666899998765
No 83
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=28.45 E-value=4.4e+02 Score=24.45 Aligned_cols=75 Identities=16% Similarity=0.236 Sum_probs=48.1
Q ss_pred EEEEEEEecCCceEEEEeC--CCcEEEEEec--ccccceeeeeCCCEEEEeeecCC-CCeE--EEEEE------Ee----
Q psy10593 27 NIVKITQNSGNNLHQIENH--SGEKYFVSMP--GKFRNNIWIKPGDFVIVKPIEEG-NKVK--AEIEQ------IL---- 89 (275)
Q Consensus 27 ~IgrVv~~lG~nlfeVec~--DG~~rLa~IP--GKfRKrIWIKrGD~VLVeP~D~~-~kvK--GeIV~------ry---- 89 (275)
+.|+.++-. |+|.|.+. ||+..+||+| |||+-. +.+|--|++.+.+.. .|-+ -+.+. +.
T Consensus 8 ~~g~fi~R~--nRF~~~V~~~~g~~~~aH~pntGRl~el--l~pG~~v~l~~~~~pkrK~~~~~~l~~~~~~~~V~int~ 83 (234)
T PRK00347 8 QEATLIKRY--KRFLADVELDDGEELTAHCPNTGRMTGL--LTPGNTVWLSTSDNPKRKYPHTWELTETPNGRLIGINTA 83 (234)
T ss_pred eEEEEEEec--CCEEEEEEECCCCEEEEEcCCCCCChhh--ccCCCEEEEEECCCCCCccceEEEEEEeCCCeEEEECcc
Confidence 466776655 78888765 6999999997 566664 449999999976532 1222 22222 21
Q ss_pred -ChhhHHHHHHCCCCCc
Q psy10593 90 -DKKYISFLKQQLKLPP 105 (275)
Q Consensus 90 -~kdqVK~Lrk~G~WPk 105 (275)
...=+.++.++|.+|.
T Consensus 84 ~~N~l~~~~l~~~~i~~ 100 (234)
T PRK00347 84 LPNKLVEEALEAGLIPE 100 (234)
T ss_pred cHHHHHHHHHHcCCCcc
Confidence 2233677777888883
No 84
>cd06530 S26_SPase_I The S26 Type I signal peptidase (SPase; LepB; leader peptidase B; leader peptidase I; EC 3.4.21.89) family members are essential membrane-bound serine proteases that function to cleave the amino-terminal signal peptide extension from proteins that are translocated across biological membranes. The bacterial signal peptidase I, which is the most intensively studied, has two N-terminal transmembrane segments inserted in the plasma membrane and a hydrophilic, C-terminal catalytic region that is located in the periplasmic space. Although the bacterial signal peptidase I is monomeric, signal peptidases of eukaryotic cells commonly function as oligomeric complexes containing two divergent copies of the catalytic monomer. These are the IMP1 and IMP2 signal peptidases of the mitochondrial inner membrane that remove leader peptides from nuclear- and mitochondrial-encoded proteins. Also, two components of the endoplasmic reticulum signal peptidase in mammals (18-kDa and 21-kDa
Probab=28.40 E-value=59 Score=24.02 Aligned_cols=28 Identities=21% Similarity=0.535 Sum_probs=12.4
Q ss_pred eeCCCEEEEeeecCC--CCeEEEEEEEeCh
Q psy10593 64 IKPGDFVIVKPIEEG--NKVKAEIEQILDK 91 (275)
Q Consensus 64 IKrGD~VLVeP~D~~--~kvKGeIV~ry~k 91 (275)
++.||+|+|.+.... .-..|+|+....+
T Consensus 14 i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~ 43 (85)
T cd06530 14 LQPGDLVLVNKLSYGFREPKRGDVVVFKSP 43 (85)
T ss_pred ccCCCEEEEEEeecccCCCCCCCEEEEeCC
Confidence 455555555543321 1234554444433
No 85
>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=27.79 E-value=58 Score=25.19 Aligned_cols=29 Identities=45% Similarity=0.587 Sum_probs=20.9
Q ss_pred eeCCCEEEEeeec-CCCCeEEEEEEEeChh
Q psy10593 64 IKPGDFVIVKPIE-EGNKVKAEIEQILDKK 92 (275)
Q Consensus 64 IKrGD~VLVeP~D-~~~kvKGeIV~ry~kd 92 (275)
++.||+|+|.+.+ .+...-|.|..++...
T Consensus 3 ~~vGD~V~v~~~~~~~~~~v~~I~~i~~~~ 32 (119)
T PF01426_consen 3 YKVGDFVYVKPDDPPEPPYVARIEEIWEDK 32 (119)
T ss_dssp EETTSEEEEECTSTTSEEEEEEEEEEEEET
T ss_pred EeCCCEEEEeCCCCCCCCEEEEEEEEEcCC
Confidence 6889999999776 2335677777775443
No 86
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=27.67 E-value=89 Score=24.31 Aligned_cols=31 Identities=26% Similarity=0.336 Sum_probs=23.4
Q ss_pred eeeeCCCEEEEeeecCCCCeEEEEEEEeChhh
Q psy10593 62 IWIKPGDFVIVKPIEEGNKVKAEIEQILDKKY 93 (275)
Q Consensus 62 IWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdq 93 (275)
+-|++||.|.|---.+. ...|.|+.++.+.+
T Consensus 5 ~~I~kGD~V~Vi~G~dK-GK~G~V~~V~~~~~ 35 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDK-GKTGKVLAVLPKKN 35 (76)
T ss_pred ccccCCCEEEEeEcCCC-CcEEEEEEEEcCCC
Confidence 46999999999854433 34699999988763
No 87
>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=27.29 E-value=2.6e+02 Score=20.70 Aligned_cols=57 Identities=12% Similarity=0.188 Sum_probs=37.2
Q ss_pred CCCCCc-EEEEEEEecCCceEEEEeCCCcEEEEEeccccc----ce-----eeeeCCCEEEEeeecCC
Q psy10593 21 VPEDLN-NIVKITQNSGNNLHQIENHSGEKYFVSMPGKFR----NN-----IWIKPGDFVIVKPIEEG 78 (275)
Q Consensus 21 lP~egQ-~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfR----Kr-----IWIKrGD~VLVeP~D~~ 78 (275)
.|..|+ +.|+|++... .-+.|...++.+=++++..=.. +. =.++.||.|.+.....+
T Consensus 3 ~p~~GdiV~g~V~~i~~-~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~ 69 (86)
T cd05789 3 IPEVGDVVIGRVTEVGF-KRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVD 69 (86)
T ss_pred cCCCCCEEEEEEEEECC-CEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEEC
Confidence 355565 6899999654 5577888777666655543221 11 16899999999865543
No 88
>PRK06299 rpsA 30S ribosomal protein S1; Reviewed
Probab=26.63 E-value=6.9e+02 Score=25.34 Aligned_cols=64 Identities=14% Similarity=-0.023 Sum_probs=39.3
Q ss_pred CCcEEEEEEEecCCceEEEEeCCCcEEEEEecccc-----cc-eeeeeCCCEEEEeeecCCCCeEEEEEEEe
Q psy10593 24 DLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKF-----RN-NIWIKPGDFVIVKPIEEGNKVKAEIEQIL 89 (275)
Q Consensus 24 egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKf-----RK-rIWIKrGD~VLVeP~D~~~kvKGeIV~ry 89 (275)
...+.|+|......+ +-|.+.+|..-++++..=. +. .-+++.||.|.|.....+ ..++.|..-+
T Consensus 374 G~~v~g~V~~v~~~G-~fV~l~~~v~g~i~~s~l~~~~~~~~~~~~~~~Gd~v~v~Il~vd-~~~~~i~ls~ 443 (565)
T PRK06299 374 GDVVEGKVKNITDFG-AFVGLEGGIDGLVHLSDISWDKKGEEAVELYKKGDEVEAVVLKVD-VEKERISLGI 443 (565)
T ss_pred CCEEEEEEEEEecce-EEEECCCCCEEEEEHHHcCccccccChHhhCCCCCEEEEEEEEEe-CCCCEEEEEE
Confidence 345778888876554 4477777777777664321 11 257899999998754332 2344554443
No 89
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=26.12 E-value=39 Score=26.77 Aligned_cols=28 Identities=29% Similarity=0.303 Sum_probs=18.3
Q ss_pred eeeCCCEEEEeeecCC------CCeEEEEEEEeC
Q psy10593 63 WIKPGDFVIVKPIEEG------NKVKAEIEQILD 90 (275)
Q Consensus 63 WIKrGD~VLVeP~D~~------~kvKGeIV~ry~ 90 (275)
-+|+||+|||+.-... +==-|+|++.-.
T Consensus 5 ~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~g 38 (75)
T PF11302_consen 5 SVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEG 38 (75)
T ss_pred ccCCCCEEEEecCccccccCCCCcEEEEEEEEec
Confidence 4899999999965421 112567776654
No 90
>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=25.89 E-value=4.5e+02 Score=27.65 Aligned_cols=48 Identities=23% Similarity=0.178 Sum_probs=33.6
Q ss_pred eeCCCEEEEee--ecC-CCCeEEEEEEEeChh-----hHHHHHHCCCCCcccccCc
Q psy10593 64 IKPGDFVIVKP--IEE-GNKVKAEIEQILDKK-----YISFLKQQLKLPPIENGDI 111 (275)
Q Consensus 64 IKrGD~VLVeP--~D~-~~kvKGeIV~ry~kd-----qVK~Lrk~G~WPkeF~~~~ 111 (275)
.+.||.|.|+. |+. +..-.|.|+.++... ++..+...--+|.+|..++
T Consensus 120 ~~~g~~V~v~i~~~p~~~~~~~g~i~~~lG~~~d~~~~~~~il~~~~i~~~f~~~v 175 (654)
T TIGR00358 120 LAEGDKVVVELTEYPLRRNLFYGEITQILGNNDDPLIPWWVTLARHEIPFEFPDGV 175 (654)
T ss_pred CCCCCEEEEEEccCCCCCCCceEEEEEEEcCCCCcccHHHHHHHHcCcCCCCCHHH
Confidence 46799999993 332 346789999999643 4666666656788886643
No 91
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=25.86 E-value=5.8e+02 Score=25.81 Aligned_cols=64 Identities=20% Similarity=0.161 Sum_probs=41.3
Q ss_pred CCcEEEEEEEecCCceEEEEeCCCcEEEEEecc-----cccc-eeeeeCCCEEEEeeecCCCCeEEEEEEEe
Q psy10593 24 DLNNIVKITQNSGNNLHQIENHSGEKYFVSMPG-----KFRN-NIWIKPGDFVIVKPIEEGNKVKAEIEQIL 89 (275)
Q Consensus 24 egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPG-----KfRK-rIWIKrGD~VLVeP~D~~~kvKGeIV~ry 89 (275)
...+-|+|+.....+.| |.+..|..-+++++. +..+ .-+++.||.|-|.-...+ ..++.|.--+
T Consensus 293 G~~v~G~V~~v~~~G~f-V~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD-~e~~ri~Ls~ 362 (491)
T PRK13806 293 GDKVTGKVVRLAPFGAF-VEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDID-PAKRRISLSL 362 (491)
T ss_pred CCEEEEEEEEEeCceEE-EEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEE-ccCCEEEEEE
Confidence 45678999988765555 577778888887653 1111 247999999998854432 3345555444
No 92
>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=25.35 E-value=98 Score=27.06 Aligned_cols=30 Identities=17% Similarity=0.376 Sum_probs=23.2
Q ss_pred cCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEee
Q psy10593 35 SGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKP 74 (275)
Q Consensus 35 lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP 74 (275)
-|++.|.|...|+.-. +|.+.+||++.|-+
T Consensus 100 ~G~g~Fdvr~~~~~wi----------ri~~e~GDli~vP~ 129 (157)
T PF03079_consen 100 DGSGYFDVRDGDDVWI----------RILCEKGDLIVVPA 129 (157)
T ss_dssp ECEEEEEEE-TTCEEE----------EEEEETTCEEEE-T
T ss_pred CcEEEEEEEcCCCEEE----------EEEEcCCCEEecCC
Confidence 6999999998887654 46789999999874
No 93
>PF11782 DUF3319: Protein of unknown function (DUF3319); InterPro: IPR021753 This is a family of short bacterial proteins, a few of which are annotated as being minor tail protein. Otherwise the function is unknown.
Probab=24.28 E-value=62 Score=26.40 Aligned_cols=41 Identities=20% Similarity=0.206 Sum_probs=32.8
Q ss_pred hhhHHHHHHCC--CCCcccccCcccccccccccccCCCCCceEEE
Q psy10593 91 KKYISFLKQQL--KLPPIENGDIVHHFQEIGEQQAKPYRDLTLHL 133 (275)
Q Consensus 91 kdqVK~Lrk~G--~WPkeF~~~~~~~~~e~~~~~~~~~r~~~~~v 133 (275)
+.+|.||-+.| .-|++|....... +-+..|..-|+|..+-=
T Consensus 38 KksIdww~dt~siI~P~efssl~~~~--~~~~~~~En~~G~~ikN 80 (88)
T PF11782_consen 38 KKSIDWWCDTGSIIDPKEFSSLASKR--EVGQGQSENFNGFTIKN 80 (88)
T ss_pred HHHHHHHHhcccccCchhhcchhhcc--ccCccceecccceEeec
Confidence 57899999999 7889999877666 66677777899987643
No 94
>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=23.94 E-value=3.4e+02 Score=21.59 Aligned_cols=54 Identities=15% Similarity=0.241 Sum_probs=36.3
Q ss_pred CCCC-CcEEEEEEEecCCceEEEEeCCCcEEEEE-----ecccccc-eeeeeCCCEEEEeeecC
Q psy10593 21 VPED-LNNIVKITQNSGNNLHQIENHSGEKYFVS-----MPGKFRN-NIWIKPGDFVIVKPIEE 77 (275)
Q Consensus 21 lP~e-gQ~IgrVv~~lG~nlfeVec~DG~~rLa~-----IPGKfRK-rIWIKrGD~VLVeP~D~ 77 (275)
.|.. +-+||+|+.. .++.|.|....- ..|. ++|.-|+ +=-++.||+|.+.-...
T Consensus 3 ~P~~gD~VIG~V~~~-~~~~~~VdI~s~--~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~ 63 (86)
T cd05790 3 VPAKGDHVIGIVVAK-AGDFFKVDIGGS--EPASLSYLAFEGATKRNRPNLNVGDLVYARVVKA 63 (86)
T ss_pred cCCCCCEEEEEEEEE-cCCeEEEEcCCC--cceEechHHcccccccccccCCCCCEEEEEEEec
Confidence 3554 4689999996 568899987543 2233 4444333 36799999999986443
No 95
>COG3269 Predicted RNA-binding protein, contains TRAM domain [General function prediction only]
Probab=23.47 E-value=91 Score=24.62 Aligned_cols=27 Identities=19% Similarity=0.356 Sum_probs=23.4
Q ss_pred CCCceEEEeecCCCCeeeEEEEEecCh
Q psy10593 126 YRDLTLHLLNKEEGNKVKAEIEQILDK 152 (275)
Q Consensus 126 ~r~~~~~v~pi~Eg~KVkaEI~~IL~k 152 (275)
..|+++||.--+.|++|+-.|..++..
T Consensus 36 veGfvVFVp~a~~Gd~V~vkI~~v~~~ 62 (73)
T COG3269 36 VEGFVVFVPGAEVGDEVKVKITKVKPN 62 (73)
T ss_pred EEEEEEEeCCCCCCCeeeEEEEEeecc
Confidence 348999999999999999999998754
No 96
>PF10115 HlyU: Transcriptional activator HlyU; InterPro: IPR018772 This is a family of hypothetical prokaryotic proteins, with no known function. One of the proteins in this entry corresponds to the transcriptional activator HlyU, indicating a possible similar role in other members.
Probab=23.43 E-value=94 Score=25.42 Aligned_cols=46 Identities=17% Similarity=0.203 Sum_probs=30.6
Q ss_pred CCCCcccccCcccccccccccccCCCCCceEEEeecCCCC--eeeEEEEEe
Q psy10593 101 LKLPPIENGDIVHHFQEIGEQQAKPYRDLTLHLLNKEEGN--KVKAEIEQI 149 (275)
Q Consensus 101 G~WPkeF~~~~~~~~~e~~~~~~~~~r~~~~~v~pi~Eg~--KVkaEI~~I 149 (275)
++|.+-|.......+. +-.+--|.|..+...|+.||. .|-|-|+.=
T Consensus 2 ~~~s~LFGg~~~~~~~---~~ep~eYkgf~I~~~P~~egGQfRvag~I~K~ 49 (91)
T PF10115_consen 2 SFFSRLFGGGKKSEPK---EAEPVEYKGFLIYPEPMSEGGQFRVAGRIEKE 49 (91)
T ss_pred cHHHHhhCCCCCCCCC---ccCCeEeCCEEEEeCccccCCceeEEEEEEec
Confidence 4455556433333322 334445999999999999998 788888763
No 97
>COG1222 RPT1 ATP-dependent 26S proteasome regulatory subunit [Posttranslational modification, protein turnover, chaperones]
Probab=22.55 E-value=3.4e+02 Score=27.67 Aligned_cols=81 Identities=16% Similarity=0.201 Sum_probs=54.6
Q ss_pred CCCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEe----------eecCC-------CCeEEEE
Q psy10593 23 EDLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVK----------PIEEG-------NKVKAEI 85 (275)
Q Consensus 23 ~egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVe----------P~D~~-------~kvKGeI 85 (275)
+...++|+|++.++.+.+-|....|-..++.+.+..-+ =-+++|+.|-+. |.+.+ ...+.++
T Consensus 70 ~~pl~vg~v~e~id~~~~iVks~~g~~~vV~i~~~vd~-~~L~pG~rVal~~~s~~Iv~vLp~~~Dp~V~~M~v~e~Pdv 148 (406)
T COG1222 70 EPPLIVGTVLEVLDDGRAIVKSSTGPKFVVNILSFVDR-DLLEPGMRVALNRDSYSIVRVLPPEVDPRVSVMEVEEKPDV 148 (406)
T ss_pred CCCceEEEEEEEcCCceEEEEeCCCCeEEEeccCCcCH-HHcCCCCEEEEcCCcceeeeeCCCccCchhheeeeccCCCC
Confidence 35679999999999999999999999999988755433 235555555544 22211 1223333
Q ss_pred EEEe---ChhhHHHHHHCCCCC
Q psy10593 86 EQIL---DKKYISFLKQQLKLP 104 (275)
Q Consensus 86 V~ry---~kdqVK~Lrk~G~WP 104 (275)
.|-= .++||++|++.=.+|
T Consensus 149 tY~dIGGL~~Qi~EirE~VELP 170 (406)
T COG1222 149 TYEDIGGLDEQIQEIREVVELP 170 (406)
T ss_pred ChhhccCHHHHHHHHHHHhccc
Confidence 3321 468999999887777
No 98
>COG0048 RpsL Ribosomal protein S12 [Translation, ribosomal structure and biogenesis]
Probab=22.19 E-value=1.4e+02 Score=25.94 Aligned_cols=50 Identities=12% Similarity=0.167 Sum_probs=36.8
Q ss_pred eEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCC--CeEEEEEEEeCh
Q psy10593 39 LHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGN--KVKAEIEQILDK 91 (275)
Q Consensus 39 lfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~--kvKGeIV~ry~k 91 (275)
-..|.+.||.++.|-|||==.. |.+-|.|||+-.-.++ -|+--||..-..
T Consensus 58 ~~RVrL~NG~~VtAyiPg~Gh~---lqEH~~Vli~G~~v~DlPGVRy~vvrg~~d 109 (129)
T COG0048 58 VARVRLINGKEVTAYIPGEGHN---LQEHSEVLIRGGRVKDLPGVRYKVVRGALD 109 (129)
T ss_pred eEEEEeeCCcEEEEEcCCCCcc---ccccCEEEEecCccCCCCCceEEEEEEcch
Confidence 4678999999999999997666 9999999999433211 355556555443
No 99
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=22.11 E-value=2e+02 Score=29.08 Aligned_cols=50 Identities=14% Similarity=0.265 Sum_probs=42.9
Q ss_pred CCcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEee
Q psy10593 24 DLNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKP 74 (275)
Q Consensus 24 egQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP 74 (275)
....+|.|+++.+.+.+.|....|..+++.+.+..-+. -+++|+-|.+..
T Consensus 103 ~~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~~~~~~~-~l~~~~~v~l~~ 152 (438)
T PTZ00361 103 SPLSVGTLEEIIDENHAIVSSSVGPEYYVNILSFVDKE-QLEPGCSVLLHN 152 (438)
T ss_pred CCcEEEEEEEEeCCCeEEEEeCCCCEEEEeccCcCCHh-hCCCCCEEEEcC
Confidence 46789999999999999999999999999998877543 368999998873
No 100
>smart00318 SNc Staphylococcal nuclease homologues.
Probab=22.00 E-value=2.1e+02 Score=22.86 Aligned_cols=28 Identities=0% Similarity=-0.086 Sum_probs=21.8
Q ss_pred EEEEEEEecCCceEEEEeCCCcEEEEEe
Q psy10593 27 NIVKITQNSGNNLHQIENHSGEKYFVSM 54 (275)
Q Consensus 27 ~IgrVv~~lG~nlfeVec~DG~~rLa~I 54 (275)
+-|+|+....++.|.|.+++|....++|
T Consensus 3 ~~~~V~~V~DGDT~~v~~~~~~~~~vrL 30 (138)
T smart00318 3 IRGVVERVLDGDTIRVRLPKNKLITIRL 30 (138)
T ss_pred eeEEEEEEecCCEEEEEeCCCCEEEEEE
Confidence 5688999999999999998875444443
No 101
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=21.98 E-value=92 Score=24.22 Aligned_cols=22 Identities=14% Similarity=0.034 Sum_probs=19.7
Q ss_pred EEEEEEEeChhhHHHHHHCCCC
Q psy10593 82 KAEIEQILDKKYISFLKQQLKL 103 (275)
Q Consensus 82 KGeIV~ry~kdqVK~Lrk~G~W 103 (275)
.|-|||.++..+++.|++-|.+
T Consensus 2 ~gliVyl~~~k~~r~L~kfG~i 23 (71)
T PF09902_consen 2 QGLIVYLYSLKDARQLRKFGDI 23 (71)
T ss_pred eEEEEEEechHhHHhHhhcccE
Confidence 4889999999999999999864
No 102
>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=21.88 E-value=1.5e+02 Score=19.61 Aligned_cols=27 Identities=19% Similarity=0.068 Sum_probs=21.2
Q ss_pred EEEEEEEecCCceEEEEeCC-CcEEEEE
Q psy10593 27 NIVKITQNSGNNLHQIENHS-GEKYFVS 53 (275)
Q Consensus 27 ~IgrVv~~lG~nlfeVec~D-G~~rLa~ 53 (275)
--|+|++..+++.+.|..-| |..-.+.
T Consensus 15 yra~V~~~~~~~~~~V~f~DyG~~~~v~ 42 (48)
T cd04508 15 YRAKITSILSDGKVEVFFVDYGNTEVVP 42 (48)
T ss_pred EEEEEEEECCCCcEEEEEEcCCCcEEEe
Confidence 45888888888899999988 8766543
No 103
>KOG3841|consensus
Probab=21.81 E-value=46 Score=33.80 Aligned_cols=13 Identities=46% Similarity=0.593 Sum_probs=10.8
Q ss_pred HHHHHHhhhcccc
Q psy10593 217 WYLRYIKHRCNKK 229 (275)
Q Consensus 217 ~~~~~~~~~~~~~ 229 (275)
...|||||||||-
T Consensus 116 LIarYIKlrtgkt 128 (455)
T KOG3841|consen 116 LIARYIKLRTGKT 128 (455)
T ss_pred HHHHHHHHhcCCc
Confidence 4579999999973
No 104
>TIGR02228 sigpep_I_arch signal peptidase I, archaeal type. This model represents signal peptidase I from most archaea, a subunit of the eukaryotic endoplasmic reticulum signal peptidase I complex, and an apparent signal peptidase I from a small number of bacteria. It is related to but does not overlap in hits with TIGR02227, the bacterial and mitochondrial signal peptidase I.
Probab=21.44 E-value=63 Score=28.03 Aligned_cols=21 Identities=14% Similarity=0.216 Sum_probs=13.7
Q ss_pred CCCCCceEEEeecCCCCeeeE
Q psy10593 124 KPYRDLTLHLLNKEEGNKVKA 144 (275)
Q Consensus 124 ~~~r~~~~~v~pi~Eg~KVka 144 (275)
-||=|..+.+.+-.+|..+-+
T Consensus 123 iP~~G~~~~~~~~~~~~~~~~ 143 (158)
T TIGR02228 123 IPFAGYVLVFAPQAIGAAALL 143 (158)
T ss_pred cCcccEEEEEeecCchhhhhH
Confidence 577777777777666655433
No 105
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=21.43 E-value=1.4e+02 Score=25.44 Aligned_cols=31 Identities=16% Similarity=0.083 Sum_probs=24.8
Q ss_pred eeeeCCCEEEEeeecCCCCeEEEEEEEeChhh
Q psy10593 62 IWIKPGDFVIVKPIEEGNKVKAEIEQILDKKY 93 (275)
Q Consensus 62 IWIKrGD~VLVeP~D~~~kvKGeIV~ry~kdq 93 (275)
+-|+.||.|.|---.+. ...|.|+.++.+.+
T Consensus 44 ~~IkkGD~V~VisG~~K-Gk~GkV~~V~~~~~ 74 (120)
T PRK01191 44 LPVRKGDTVKVMRGDFK-GEEGKVVEVDLKRG 74 (120)
T ss_pred ceEeCCCEEEEeecCCC-CceEEEEEEEcCCC
Confidence 78999999999865543 35799999988764
No 106
>PRK00286 xseA exodeoxyribonuclease VII large subunit; Reviewed
Probab=21.32 E-value=5.5e+02 Score=25.22 Aligned_cols=85 Identities=19% Similarity=0.151 Sum_probs=51.3
Q ss_pred cCCceEEEEeCCCcEEEEEecccccce-eeeeCCCEEEEe----eecCCCCeEE---EEEEEe-------ChhhHHHHHH
Q psy10593 35 SGNNLHQIENHSGEKYFVSMPGKFRNN-IWIKPGDFVIVK----PIEEGNKVKA---EIEQIL-------DKKYISFLKQ 99 (275)
Q Consensus 35 lG~nlfeVec~DG~~rLa~IPGKfRKr-IWIKrGD~VLVe----P~D~~~kvKG---eIV~ry-------~kdqVK~Lrk 99 (275)
-|.-.|+....+....-+...+..++. .+++.|+-|+|. .|+-.+...= +|.... ..+=.+.|.+
T Consensus 40 sGH~Yf~Lkd~~a~i~~~~~~~~~~~~~~~~~~G~~v~v~g~~~~y~~~g~~ql~v~~i~~~g~G~l~~~~~~lk~~L~~ 119 (438)
T PRK00286 40 SGHWYFTLKDEIAQIRCVMFKGSARRLKFKPEEGMKVLVRGKVSLYEPRGDYQLIVEEIEPAGIGALAAAFEQLKEKLAA 119 (438)
T ss_pred CCeEEEEEEcCCcEEEEEEEcChhhcCCCCCCCCCEEEEEEEEEEECCCCCEEEEEEEeeeCCccHHHHHHHHHHHHHHH
Confidence 455566666666655555555655443 789999999998 2432211111 111111 1223456888
Q ss_pred CCCCCcccccCccccccccc
Q psy10593 100 QLKLPPIENGDIVHHFQEIG 119 (275)
Q Consensus 100 ~G~WPkeF~~~~~~~~~e~~ 119 (275)
+|++..+-....|.-|+-||
T Consensus 120 eGlfd~~~k~~lP~~p~~I~ 139 (438)
T PRK00286 120 EGLFDPERKKPLPFFPKRIG 139 (438)
T ss_pred CCCCChhhcCCCCCCCCEEE
Confidence 89998887777777777776
No 107
>PF00166 Cpn10: Chaperonin 10 Kd subunit; InterPro: IPR020818 The chaperonins are `helper' molecules required for correct folding and subsequent assembly of some proteins []. These are required for normal cell growth [], and are stress-induced, acting to stabilise or protect disassembled polypeptides under heat-shock conditions. Type I chaperonins present in eubacteria, mitochondria and chloroplasts require the concerted action of 2 proteins, chaperonin 60 (cpn60) and chaperonin 10 (cpn10) []. The 10 kDa chaperonin (cpn10 - or groES in bacteria) exists as a ring-shaped oligomer of between six to eight identical subunits, while the 60 kDa chaperonin (cpn60 - or groEL in bacteria) forms a structure comprising 2 stacked rings, each ring containing 7 identical subunits []. These ring structures assemble by self-stimulation in the presence of Mg2+-ATP. The central cavity of the cylindrical cpn60 tetradecamer provides as isolated environment for protein folding whilst cpn-10 binds to cpn-60 and synchronizes the release of the folded protein in an Mg2+-ATP dependent manner []. The binding of cpn10 to cpn60 inhibits the weak ATPase activity of cpn60. Escherichia coli GroES has also been shown to bind ATP cooperatively, and with an affinity comparable to that of GroEL []. Each GroEL subunit contains three structurally distinct domains: an apical, an intermediate and an equatorial domain. The apical domain contains the binding sites for both GroES and the unfolded protein substrate. The equatorial domain contains the ATP-binding site and most of the oligomeric contacts. The intermediate domain links the apical and equatorial domains and transfers allosteric information between them. The GroEL oligomer is a tetradecamer, cylindrically shaped, that is organised in two heptameric rings stacked back to back. Each GroEL ring contains a central cavity, known as the `Anfinsen cage', that provides an isolated environment for protein folding. The identical 10 kDa subunits of GroES form a dome-like heptameric oligomer in solution. ATP binding to GroES may be important in charging the seven subunits of the interacting GroEL ring with ATP, to facilitate cooperative ATP binding and hydrolysis for substrate protein release.; GO: 0006457 protein folding, 0005737 cytoplasm; PDB: 1PF9_Q 1AON_P 1SX4_T 1SVT_R 2C7D_P 1PCQ_O 2C7C_Q 1GRU_Q 1WNR_F 1P3H_I ....
Probab=21.25 E-value=1.1e+02 Score=24.01 Aligned_cols=46 Identities=24% Similarity=0.276 Sum_probs=29.9
Q ss_pred ccCCCCCC---CcEEEEEEEecCCceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeec
Q psy10593 17 QEYRVPED---LNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIE 76 (275)
Q Consensus 17 ~e~~lP~e---gQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D 76 (275)
.-+.+|+. ....|+|++ .|.+... .+|+.. -..++.||.|+..++.
T Consensus 22 ~GiiLp~~~~~~~~~G~Vva-VG~G~~~---~~g~~~----------~~~vk~GD~Vl~~~~~ 70 (93)
T PF00166_consen 22 SGIILPESAKEKPNQGKVVA-VGPGRYN---ENGEEV----------PMDVKVGDKVLFPKYA 70 (93)
T ss_dssp TSCCE-CCSSSSEEEEEEEE-E-SEEET---TTSSEE----------ETSS-TTSEEEEETTT
T ss_pred ceEEeccccccccceeEEEE-cCCcccc---CCCcEe----------eeeeeeccEEeccccC
Confidence 45566643 347888887 7777665 677633 2358899999999775
No 108
>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=21.12 E-value=4.5e+02 Score=22.96 Aligned_cols=62 Identities=18% Similarity=0.096 Sum_probs=37.6
Q ss_pred CCCcEEEEEEEecC--CceEEEEeCCCcEEEEEecccccceeeeeCCCEEEEeeecCCCCeEEEEEEE
Q psy10593 23 EDLNNIVKITQNSG--NNLHQIENHSGEKYFVSMPGKFRNNIWIKPGDFVIVKPIEEGNKVKAEIEQI 88 (275)
Q Consensus 23 ~egQ~IgrVv~~lG--~nlfeVec~DG~~rLa~IPGKfRKrIWIKrGD~VLVeP~D~~~kvKGeIV~r 88 (275)
.+|+.+|.|.+..+ ...|.|..++|+.. ..|.|..-..---..=+|-+.++ ++..-|.|...
T Consensus 113 p~g~~iG~I~q~~~~~~~~f~I~d~~~~~~-~~I~gp~~~~~~~~~~~F~I~~~---~~~~vg~I~k~ 176 (221)
T PF03803_consen 113 PPGNLIGSIRQPFSCCRPNFDIFDANGNPI-FTIKGPCCCCSCCCDWEFEIKDP---NGQEVGSITKK 176 (221)
T ss_pred CCCcEEEEEEEcCcccceEEEEEECCCceE-EEEeCCcceeccccceeeeeecc---cCcEEEEEEEe
Confidence 37999999999554 88999999999654 56666532110011122333332 22556888754
No 109
>PF01336 tRNA_anti-codon: OB-fold nucleic acid binding domain; InterPro: IPR004365 The OB-fold (oligonucleotide/oligosaccharide-binding fold) is found in all three kingdoms and its common architecture presents a binding face that has adapted to bind different ligands. The OB-fold is a five/six-stranded closed beta-barrel formed by 70-80 amino acid residues. The strands are connected by loops of varying length which form the functional appendages of the protein. The majority of OB-fold proteins use the same face for ligand binding or as an active site. Different OB-fold proteins use this 'fold-related binding face' to, variously, bind oligosaccharides, oligonucleotides, proteins, metal ions and catalytic substrates. This entry contains OB-fold domains that bind to nucleic acids []. It includes the anti-codon binding domain of lysyl, aspartyl, and asparaginyl-tRNA synthetases (See IPR004364 from INTERPRO). Aminoacyl-tRNA synthetases catalyse the addition of an amino acid to the appropriate tRNA molecule 6.1.1 from EC. This domain is found in RecG helicase involved in DNA repair. Replication factor A is a heterotrimeric complex, that contains a subunit in this family [, ]. This domain is also found at the C terminus of bacterial DNA polymerase III alpha chain.; GO: 0003676 nucleic acid binding; PDB: 1BBU_A 1KRS_A 1BBW_A 1KRT_A 1EQR_B 1IL2_B 1C0A_A 3KFU_A 1EOV_A 1ASY_A ....
Probab=21.09 E-value=1.7e+02 Score=20.32 Aligned_cols=47 Identities=23% Similarity=0.197 Sum_probs=28.2
Q ss_pred EEEEEEEe--cCCceEEEEeCCCcEEE-EEecc-c-ccceeeeeCCCEEEEe
Q psy10593 27 NIVKITQN--SGNNLHQIENHSGEKYF-VSMPG-K-FRNNIWIKPGDFVIVK 73 (275)
Q Consensus 27 ~IgrVv~~--lG~nlfeVec~DG~~rL-a~IPG-K-fRKrIWIKrGD~VLVe 73 (275)
+.|+|... .|+....+.+.||.-.+ |.+.+ . .+..=-+++||.|.|.
T Consensus 3 v~G~V~~~~~~~~~~~~~~l~D~tg~i~~~~~~~~~~~~~~~l~~g~~v~v~ 54 (75)
T PF01336_consen 3 VEGRVTSIRRSGGKIVFFTLEDGTGSIQVVFFNEEYERFREKLKEGDIVRVR 54 (75)
T ss_dssp EEEEEEEEEEEETTEEEEEEEETTEEEEEEEETHHHHHHHHTS-TTSEEEEE
T ss_pred EEEEEEEEEcCCCCEEEEEEEECCccEEEEEccHHhhHHhhcCCCCeEEEEE
Confidence 34555554 56667777777776444 44444 1 2222458899999998
No 110
>PRK08577 hypothetical protein; Provisional
Probab=20.67 E-value=73 Score=26.32 Aligned_cols=25 Identities=20% Similarity=0.452 Sum_probs=21.4
Q ss_pred EEecccccceeeeeCCCEEEEeeec
Q psy10593 52 VSMPGKFRNNIWIKPGDFVIVKPIE 76 (275)
Q Consensus 52 a~IPGKfRKrIWIKrGD~VLVeP~D 76 (275)
.-||..+|+.+=|++||.|.+..-+
T Consensus 15 i~ip~~~r~~l~~~~g~~~~~~~~~ 39 (136)
T PRK08577 15 ITIPLEIREALGIREGMYVLLIADT 39 (136)
T ss_pred EEecHHHHHHcCcCCCCEEEEEEEC
Confidence 4589999999999999999987443
No 111
>TIGR00237 xseA exodeoxyribonuclease VII, large subunit. This family consist of exodeoxyribonuclease VII, large subunit XseA which catalyses exonucleolytic cleavage in either the 5'-3' or 3'-5' direction to yield 5'-phosphomononucleotides. Exonuclease VII consists of one large subunit and four small subunits.
Probab=20.58 E-value=4.9e+02 Score=25.95 Aligned_cols=95 Identities=12% Similarity=0.045 Sum_probs=58.8
Q ss_pred CcEEEEEEEecCCceEEEEeCCCcEEEEEecccccce-eeeeCCCEEEEe----eecCCCCeEEEEEEEe----------
Q psy10593 25 LNNIVKITQNSGNNLHQIENHSGEKYFVSMPGKFRNN-IWIKPGDFVIVK----PIEEGNKVKAEIEQIL---------- 89 (275)
Q Consensus 25 gQ~IgrVv~~lG~nlfeVec~DG~~rLa~IPGKfRKr-IWIKrGD~VLVe----P~D~~~kvKGeIV~ry---------- 89 (275)
||+-.--...-|.-.|+....+...+-+...+..++. ...+.|+-|+|. .|+-.+...=.|..+-
T Consensus 24 GEisn~~~~~sGH~YFtLkD~~a~i~~vmf~~~~~~l~f~~~~G~~V~v~g~v~~y~~~G~~ql~v~~i~~~G~G~l~~~ 103 (432)
T TIGR00237 24 GEISNFTQPVSGHWYFTLKDENAQVRCVMFRGNNNRLKFRPQNGQQVLVRGGISVYEPRGDYQIICFEMQPAGEGLLQLA 103 (432)
T ss_pred EEecCCeeCCCceEEEEEEcCCcEEEEEEEcChhhCCCCCCCCCCEEEEEEEEEEECCCCcEEEEEEEeccCChHHHHHH
Confidence 4433332334466677777776666667777776553 889999999998 3443211111111111
Q ss_pred ChhhHHHHHHCCCCCcccccCccccccccc
Q psy10593 90 DKKYISFLKQQLKLPPIENGDIVHHFQEIG 119 (275)
Q Consensus 90 ~kdqVK~Lrk~G~WPkeF~~~~~~~~~e~~ 119 (275)
..+=.+.|.++|++..+-....|.-|+-||
T Consensus 104 ~~~lk~~L~~eGlfd~~~k~~lP~~p~~i~ 133 (432)
T TIGR00237 104 YEQLKEKLAAEGLFDQEYKKPLPHFPKRVG 133 (432)
T ss_pred HHHHHHHHHHCCCCCchhcCCCCCCCCEEE
Confidence 223346788889998888888888887776
No 112
>PF10447 EXOSC1: Exosome component EXOSC1/CSL4; InterPro: IPR019495 The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions []. The proteins in this entry are components of the exosome 3'->5' exoribonuclease complex. They do not have exonuclease activity, but are required for the 3'-processing of the 7S pre-RNA to the mature 5.8S rRNA and for mRNA decay [, ].; PDB: 2NN6_I.
Probab=20.50 E-value=3.1e+02 Score=21.66 Aligned_cols=12 Identities=33% Similarity=0.628 Sum_probs=7.5
Q ss_pred eeeeCCCEEEEe
Q psy10593 62 IWIKPGDFVIVK 73 (275)
Q Consensus 62 IWIKrGD~VLVe 73 (275)
-.+++||+|...
T Consensus 67 ~~FrpGDIVrA~ 78 (82)
T PF10447_consen 67 DCFRPGDIVRAR 78 (82)
T ss_dssp GT--SSSEEEEE
T ss_pred hccCCCCEEEEE
Confidence 467888888765
No 113
>PRK10676 DNA-binding transcriptional regulator ModE; Provisional
Probab=20.41 E-value=2.2e+02 Score=26.49 Aligned_cols=50 Identities=16% Similarity=0.202 Sum_probs=38.3
Q ss_pred CCcEEEEEEEec-CCceEEEE--eCCCcEEEEEecccccceeeeeCCCEEEEe
Q psy10593 24 DLNNIVKITQNS-GNNLHQIE--NHSGEKYFVSMPGKFRNNIWIKPGDFVIVK 73 (275)
Q Consensus 24 egQ~IgrVv~~l-G~nlfeVe--c~DG~~rLa~IPGKfRKrIWIKrGD~VLVe 73 (275)
.|.+-|+|.+.. |+...+|. +++|....|.|+.+=-..+=+++|+-|.+.
T Consensus 199 rN~l~g~V~~i~~~~~~~~V~l~l~~g~~l~A~IT~~s~~~L~L~~G~~V~a~ 251 (263)
T PRK10676 199 DNQLPGTISHIERGAEQSEVLMALPDGQTLCATVPNNEAARLSLQQGDAVTAY 251 (263)
T ss_pred hheEEEEEEEEEeCCCcEEEEEEeCCCCEEEEEecHHHHHhcCCCCCCEEEEE
Confidence 478889999886 45544444 668888889999876666778899988876
No 114
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=20.10 E-value=1e+02 Score=27.02 Aligned_cols=30 Identities=17% Similarity=0.194 Sum_probs=24.2
Q ss_pred eeeeCCCEEEEeeecCCCCeEEEEEEEeChh
Q psy10593 62 IWIKPGDFVIVKPIEEGNKVKAEIEQILDKK 92 (275)
Q Consensus 62 IWIKrGD~VLVeP~D~~~kvKGeIV~ry~kd 92 (275)
+-|+.||.|.|-.-++. ...|.|+.++.+.
T Consensus 45 ~~IkkGD~V~Vi~Gk~K-Gk~GkV~~V~~k~ 74 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHHK-GREGKVTAVYRKK 74 (143)
T ss_pred ceeecCCEEEEecCCCC-CCceEEEEEEcCC
Confidence 78999999999976654 3569999998766
Done!