Query 035938
Match_columns 133
No_of_seqs 113 out of 551
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 07:50:27 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/035938.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/035938hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00329 eukaryotic translatio 100.0 1.8E-48 4E-53 299.6 14.5 121 1-125 1-131 (155)
2 PLN00208 translation initiatio 100.0 5.7E-48 1.2E-52 294.3 14.4 129 1-133 1-145 (145)
3 KOG3403 Translation initiation 100.0 6.8E-43 1.5E-47 261.9 5.4 129 1-133 1-145 (145)
4 TIGR00523 eIF-1A eukaryotic/ar 100.0 2.1E-32 4.6E-37 197.2 11.5 88 18-106 2-99 (99)
5 PRK04012 translation initiatio 100.0 4.2E-32 9.2E-37 196.0 11.7 85 22-106 7-100 (100)
6 smart00652 eIF1a eukaryotic tr 100.0 2.8E-31 6.1E-36 185.7 10.4 74 32-105 1-83 (83)
7 cd04456 S1_IF1A_like S1_IF1A_l 100.0 8.5E-29 1.9E-33 171.5 9.6 68 37-104 1-78 (78)
8 cd05793 S1_IF1A S1_IF1A: Trans 100.0 1.9E-28 4E-33 169.3 9.7 68 37-104 1-77 (77)
9 cd05792 S1_eIF1AD_like S1_eIF1 99.9 1.2E-27 2.5E-32 166.3 9.3 68 37-104 1-78 (78)
10 COG0361 InfA Translation initi 99.9 2.4E-25 5.2E-30 153.9 7.2 63 32-94 3-75 (75)
11 PF01176 eIF-1a: Translation i 99.9 1.1E-22 2.3E-27 135.7 6.1 56 34-89 1-65 (65)
12 KOG2925 Predicted translation 99.8 2.2E-22 4.8E-27 155.1 1.7 87 24-110 10-109 (167)
13 TIGR00008 infA translation ini 99.8 1E-20 2.2E-25 128.6 7.6 54 36-89 5-68 (68)
14 PRK12442 translation initiatio 99.8 4.3E-20 9.3E-25 130.8 7.9 57 36-92 7-73 (87)
15 CHL00010 infA translation init 99.6 5.5E-15 1.2E-19 102.0 7.4 57 37-93 8-74 (78)
16 PRK00276 infA translation init 99.6 1.2E-14 2.5E-19 98.7 7.7 55 37-91 8-72 (72)
17 cd04451 S1_IF1 S1_IF1: Transla 99.2 1.4E-10 3.1E-15 76.3 7.3 53 37-89 2-64 (64)
18 cd04466 S1_YloQ_GTPase S1_YloQ 97.0 0.0031 6.7E-08 40.7 5.8 40 50-91 21-61 (68)
19 PRK12289 GTPase RsgA; Reviewed 92.4 0.38 8.2E-06 41.3 6.1 37 51-87 36-73 (352)
20 PRK00098 GTPase RsgA; Reviewed 92.3 0.44 9.5E-06 39.4 6.2 28 50-77 21-49 (298)
21 cd01854 YjeQ_engC YjeQ/EngC. 92.1 0.35 7.6E-06 39.8 5.4 40 49-90 17-57 (287)
22 PRK12288 GTPase RsgA; Reviewed 88.3 1.5 3.3E-05 37.5 6.3 50 38-90 40-99 (347)
23 PRK01889 GTPase RsgA; Reviewed 85.9 1.9 4.2E-05 36.8 5.6 52 36-91 27-90 (356)
24 cd00164 S1_like S1_like: Ribos 81.0 6.2 0.00013 23.5 5.0 25 63-87 39-63 (65)
25 PHA02945 interferon resistance 79.8 13 0.00028 26.7 6.9 57 30-88 6-79 (88)
26 COG0509 GcvH Glycine cleavage 79.4 0.97 2.1E-05 34.4 1.2 40 54-93 3-48 (131)
27 cd04721 BAH_plant_1 BAH, or Br 78.2 5 0.00011 29.8 4.7 48 61-108 3-66 (130)
28 cd05790 S1_Rrp40 S1_Rrp40: Rrp 76.3 6.3 0.00014 27.7 4.5 57 33-89 4-74 (86)
29 cd04454 S1_Rrp4_like S1_Rrp4_l 73.7 10 0.00023 25.0 4.9 56 32-88 3-72 (82)
30 cd05789 S1_Rrp4 S1_Rrp4: Rrp4 73.2 10 0.00022 25.2 4.7 57 33-90 4-78 (86)
31 cd06530 S26_SPase_I The S26 Ty 70.8 5 0.00011 26.4 2.8 28 66-93 14-44 (85)
32 PRK10413 hydrogenase 2 accesso 70.3 13 0.00029 25.9 4.9 53 39-98 6-68 (82)
33 PF00717 Peptidase_S24: Peptid 69.8 1.1 2.4E-05 28.3 -0.6 27 66-93 11-37 (70)
34 PF11302 DUF3104: Protein of u 69.4 6.6 0.00014 27.3 3.2 29 64-92 4-39 (75)
35 cd05791 S1_CSL4 S1_CSL4: CSL4, 68.1 35 0.00076 23.6 6.7 48 32-81 3-76 (92)
36 TIGR02754 sod_Ni_protease nick 64.3 7.7 0.00017 26.0 2.7 27 66-92 12-41 (90)
37 PTZ00248 eukaryotic translatio 63.2 29 0.00063 29.9 6.6 71 31-101 13-102 (319)
38 PF01455 HupF_HypC: HupF/HypC 61.1 16 0.00034 24.5 3.7 54 39-99 6-64 (68)
39 CHL00141 rpl24 ribosomal prote 60.2 13 0.00027 25.9 3.2 33 62-94 5-37 (83)
40 TIGR00074 hypC_hupF hydrogenas 58.7 31 0.00066 23.7 4.9 27 66-99 36-62 (76)
41 PRK10409 hydrogenase assembly 57.5 30 0.00065 24.7 4.8 51 39-98 6-67 (90)
42 COG1093 SUI2 Translation initi 57.1 13 0.00029 31.5 3.4 65 31-95 7-90 (269)
43 cd05685 S1_Tex S1_Tex: The C-t 56.4 43 0.00093 20.2 5.6 50 37-87 3-66 (68)
44 cd06462 Peptidase_S24_S26 The 55.4 13 0.00028 23.7 2.5 28 66-93 14-41 (84)
45 PF13533 Biotin_lipoyl_2: Biot 55.1 15 0.00033 22.6 2.7 32 55-96 8-39 (50)
46 PRK01191 rpl24p 50S ribosomal 52.9 20 0.00043 26.9 3.4 32 63-94 43-74 (120)
47 PRK12281 rplX 50S ribosomal pr 52.8 18 0.00039 24.8 3.0 31 64-94 5-35 (76)
48 PF09902 DUF2129: Uncharacteri 49.9 16 0.00035 24.9 2.4 22 83-104 2-23 (71)
49 PRK04163 exosome complex RNA-b 46.0 53 0.0012 26.5 5.2 50 31-80 59-126 (235)
50 PTZ00194 60S ribosomal protein 44.7 27 0.00059 27.0 3.1 32 63-94 44-75 (143)
51 TIGR00638 Mop molybdenum-pteri 44.7 46 0.00099 20.8 3.8 44 35-78 6-61 (69)
52 COG0298 HypC Hydrogenase matur 44.4 63 0.0014 22.9 4.6 46 39-97 6-63 (82)
53 PRK00004 rplX 50S ribosomal pr 41.0 32 0.0007 24.8 2.9 31 64-94 3-33 (105)
54 cd04719 BAH_Orc1p_animal BAH, 39.5 29 0.00063 26.0 2.6 15 64-78 2-16 (128)
55 PRK02302 hypothetical protein; 39.4 27 0.00059 25.0 2.3 23 82-104 7-29 (89)
56 TIGR03635 S17_bact 30S ribosom 39.2 1.1E+02 0.0023 20.7 5.1 21 52-77 40-60 (71)
57 PRK02886 hypothetical protein; 39.0 31 0.00066 24.6 2.4 22 83-104 6-27 (87)
58 TIGR01439 lp_hng_hel_AbrB loop 38.6 20 0.00044 20.6 1.3 24 54-77 9-32 (43)
59 PF03749 SfsA: Sugar fermentat 38.6 2.1E+02 0.0045 23.1 7.5 66 37-106 6-88 (215)
60 cd06529 S24_LexA-like Peptidas 37.7 19 0.0004 23.0 1.1 26 66-92 14-39 (81)
61 TIGR01080 rplX_A_E ribosomal p 37.2 49 0.0011 24.5 3.4 31 63-93 39-69 (114)
62 TIGR01079 rplX_bact ribosomal 36.9 39 0.00084 24.4 2.8 30 65-94 3-32 (104)
63 PF08206 OB_RNB: Ribonuclease 36.1 67 0.0014 20.3 3.5 22 67-88 33-57 (58)
64 PF03459 TOBE: TOBE domain; I 35.5 41 0.00089 20.8 2.5 33 46-78 27-59 (64)
65 COG1162 Predicted GTPases [Gen 35.3 96 0.0021 26.6 5.3 41 49-92 27-68 (301)
66 PRK05610 rpsQ 30S ribosomal pr 34.8 1.3E+02 0.0029 20.9 5.1 28 52-84 45-73 (84)
67 COG2996 Predicted RNA-bindinin 34.7 1.3E+02 0.0028 25.9 5.9 55 39-95 78-142 (287)
68 smart00316 S1 Ribosomal protei 34.7 1E+02 0.0022 18.3 6.1 53 37-89 5-70 (72)
69 cd05795 Ribosomal_P0_L10e Ribo 34.2 56 0.0012 25.2 3.5 43 52-105 132-175 (175)
70 PF04014 Antitoxin-MazE: Antid 33.9 13 0.00028 22.5 -0.1 26 53-78 8-33 (47)
71 smart00739 KOW KOW (Kyprides, 33.9 73 0.0016 16.4 3.3 24 66-89 2-25 (28)
72 PF10017 Methyltransf_33: Hist 33.2 1.6E+02 0.0035 21.3 5.6 38 61-108 77-115 (127)
73 TIGR02227 sigpep_I_bact signal 33.2 40 0.00087 25.4 2.5 10 68-77 36-45 (163)
74 TIGR03027 pepcterm_export puta 33.2 32 0.0007 25.9 1.9 21 58-78 144-164 (165)
75 cd04452 S1_IF2_alpha S1_IF2_al 33.1 1.3E+02 0.0027 18.9 5.9 52 37-89 6-73 (76)
76 PRK08059 general stress protei 33.1 81 0.0018 22.8 4.0 57 35-91 8-77 (123)
77 COG0198 RplX Ribosomal protein 33.0 62 0.0013 23.7 3.3 31 63-93 2-32 (104)
78 cd05687 S1_RPS1_repeat_ec1_hs1 32.6 1.3E+02 0.0027 18.8 4.7 22 66-87 45-66 (70)
79 PF13986 DUF4224: Domain of un 31.3 28 0.00062 21.7 1.2 16 88-103 14-29 (47)
80 PRK11642 exoribonuclease R; Pr 30.1 5.1E+02 0.011 25.0 10.6 44 67-110 187-239 (813)
81 TIGR00307 S8e ribosomal protei 29.9 1.6E+02 0.0034 22.3 5.2 88 3-110 9-101 (127)
82 COG0093 RplN Ribosomal protein 29.7 2.1E+02 0.0046 21.6 5.8 31 58-89 26-60 (122)
83 smart00357 CSP Cold shock prot 29.5 1.3E+02 0.0027 17.9 3.9 24 66-89 37-63 (64)
84 TIGR02228 sigpep_I_arch signal 28.9 43 0.00093 25.6 2.0 30 57-88 38-68 (158)
85 PTZ00241 40S ribosomal protein 28.6 1.3E+02 0.0029 23.6 4.7 43 38-84 71-136 (158)
86 PRK03598 putative efflux pump 28.2 1.2E+02 0.0025 25.0 4.6 46 37-95 34-79 (331)
87 PLN00207 polyribonucleotide nu 27.9 1.3E+02 0.0027 29.7 5.3 57 32-90 750-822 (891)
88 PF14237 DUF4339: Domain of un 27.7 66 0.0014 19.2 2.3 21 90-110 14-34 (45)
89 PRK01202 glycine cleavage syst 27.6 36 0.00077 25.1 1.3 28 63-90 14-43 (127)
90 PF15057 DUF4537: Domain of un 27.6 1E+02 0.0023 22.6 3.8 39 38-79 15-68 (124)
91 TIGR03077 not_gcvH glycine cle 27.6 38 0.00083 24.6 1.5 30 63-92 6-38 (110)
92 COG2002 AbrB Regulators of sta 27.2 64 0.0014 22.2 2.5 38 54-93 16-53 (89)
93 cd04717 BAH_polybromo BAH, or 26.9 75 0.0016 22.6 2.9 45 64-108 2-63 (121)
94 PRK08577 hypothetical protein; 26.8 58 0.0013 23.7 2.3 24 54-77 15-38 (136)
95 COG1097 RRP4 RNA-binding prote 26.0 2.6E+02 0.0056 23.4 6.2 50 33-82 62-129 (239)
96 cd05707 S1_Rrp5_repeat_sc11 S1 25.7 1.7E+02 0.0037 18.1 5.5 51 37-87 3-66 (68)
97 PRK07252 hypothetical protein; 25.4 2.7E+02 0.0058 20.2 6.3 55 36-90 5-72 (120)
98 PRK10861 signal peptidase I; P 25.2 60 0.0013 28.0 2.4 27 52-80 83-110 (324)
99 cd04714 BAH_BAHCC1 BAH, or Bro 25.0 86 0.0019 22.6 3.0 27 83-109 38-64 (121)
100 PRK12423 LexA repressor; Provi 25.0 48 0.0011 25.8 1.7 38 53-91 116-153 (202)
101 PRK03987 translation initiatio 25.0 2.3E+02 0.0051 23.4 5.8 59 32-90 5-79 (262)
102 cd05702 S1_Rrp5_repeat_hs11_sc 24.9 1.9E+02 0.0041 18.2 5.2 17 66-82 47-63 (70)
103 PRK10276 DNA polymerase V subu 24.8 47 0.001 24.3 1.5 37 52-89 52-88 (139)
104 PF08541 ACP_syn_III_C: 3-Oxoa 24.1 1E+02 0.0022 20.3 3.0 26 65-90 65-90 (90)
105 TIGR02063 RNase_R ribonuclease 23.8 4.5E+02 0.0097 24.6 8.0 44 67-110 173-225 (709)
106 PRK00347 putative DNA-binding 23.7 3.2E+02 0.0069 22.3 6.3 68 35-106 16-100 (234)
107 COG0809 QueA S-adenosylmethion 23.6 5.2E+02 0.011 22.9 8.5 76 34-112 75-157 (348)
108 PF03537 Glyco_hydro_114: Glyc 23.1 88 0.0019 20.8 2.5 16 90-105 37-52 (74)
109 PRK13806 rpsA 30S ribosomal pr 22.5 2.4E+02 0.0052 25.2 5.8 58 34-91 292-363 (491)
110 cd05692 S1_RPS1_repeat_hs4 S1_ 22.2 1.9E+02 0.0041 17.2 5.9 50 37-88 3-66 (69)
111 PF04717 Phage_base_V: Phage-r 21.7 2.4E+02 0.0053 18.4 5.2 43 52-94 30-72 (79)
112 PF01426 BAH: BAH domain; Int 21.6 89 0.0019 21.3 2.4 14 65-78 2-15 (119)
113 PRK00624 glycine cleavage syst 21.4 60 0.0013 23.8 1.5 30 63-92 8-40 (114)
114 CHL00051 rps12 ribosomal prote 20.8 2E+02 0.0043 21.8 4.2 32 39-75 52-83 (123)
115 COG4471 Uncharacterized protei 20.8 95 0.0021 22.4 2.4 22 83-104 7-28 (90)
116 PF13437 HlyD_3: HlyD family s 20.5 2.7E+02 0.0059 18.5 6.9 53 35-91 23-78 (105)
117 PF09866 DUF2093: Uncharacteri 20.2 83 0.0018 19.7 1.7 13 66-78 2-14 (42)
118 PF01938 TRAM: TRAM domain; I 20.0 2.3E+02 0.005 17.5 6.9 29 52-87 29-61 (61)
No 1
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=100.00 E-value=1.8e-48 Score=299.62 Aligned_cols=121 Identities=61% Similarity=0.897 Sum_probs=117.7
Q ss_pred CCCCCCCCCCccccccccCccCCcccceeeeccCCCeEEEEEEEecCCceE---------EEEEeccccceeeEeecCCE
Q 035938 1 MANNKGKGGKKFKNRKRGKNNEGEDQKRELIIKEEGQEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDI 71 (133)
Q Consensus 1 m~~~~~k~gk~~~n~~r~~~~~~~~~~~el~~p~e~e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~ 71 (133)
||+||||||| |+||||+ +++...++|++|++||+||+|+++|||++| +||||||||||+|||++||+
T Consensus 1 mpk~kgkggk---~~~rgk~-~~~~~~rel~~~eegq~~g~V~~~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~ 76 (155)
T PTZ00329 1 MPKNKGKGGK---NRRRGKN-DNEGEKRELVFKEEGQEYAQVLRMLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDI 76 (155)
T ss_pred CCCCCCCCCc---ccccccc-cCccceeeeccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCE
Confidence 9999999999 9999999 999999999999999999999999999998 99999999999999999999
Q ss_pred EEEEeeeCCCCeEEEEEEcCHhHHHHHHHcCCCCccccccccc-ccccCCcceee
Q 035938 72 ILVGFRIYQDDKADVILINTPDEAKRLKNIGELPDGTRLNEGL-LLILMMTPMLF 125 (133)
Q Consensus 72 VlV~~~~~~~~KgdIv~ry~~dqik~L~k~g~~P~~f~~~e~~-~~~~~~~~~~f 125 (133)
|+|+||+|+++||+|||||+++||++|+++|+||+.|.+|++. ||.++++.++|
T Consensus 77 VlVel~~yd~~KgdIi~Ry~~devr~Lk~~g~~P~~~~~~~~~~~~~~~~~~~~f 131 (155)
T PTZ00329 77 ILVSLRDFQDSKADVILKYTPDEARALKQHGELPETAKINETDIFDDEGDDGIEF 131 (155)
T ss_pred EEEeccCCCCCEEEEEEEcCHHHHHHHHHcCCCCcceeeccccccCcCcCCCeEE
Confidence 9999999999999999999999999999999999999999988 88777778999
No 2
>PLN00208 translation initiation factor (eIF); Provisional
Probab=100.00 E-value=5.7e-48 Score=294.29 Aligned_cols=129 Identities=68% Similarity=0.986 Sum_probs=122.6
Q ss_pred CCCCCCCCCCccccccccCccCCcccceeeeccCCCeEEEEEEEecCCceE---------EEEEeccccceeeEeecCCE
Q 035938 1 MANNKGKGGKKFKNRKRGKNNEGEDQKRELIIKEEGQEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDI 71 (133)
Q Consensus 1 m~~~~~k~gk~~~n~~r~~~~~~~~~~~el~~p~e~e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~ 71 (133)
||+||||||| |+||+|+ +++.+.++|++|++||+||+|+++|||++| +||||||||||+|||++||+
T Consensus 1 m~k~k~kggk---~~~~~k~-~~~~~~~el~~p~egq~~g~V~~~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~ 76 (145)
T PLN00208 1 MPKNKGKGGK---NRKRGKN-EADDEKRELIFKEDGQEYAQVLRMLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDI 76 (145)
T ss_pred CCCCCCCCcc---ccccccc-cCccceeecccCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCE
Confidence 9999999999 9999999 999999999999999999999999999998 99999999999999999999
Q ss_pred EEEEeeeCCCCeEEEEEEcCHhHHHHHHHcCCCCcccccccccc-------cccCCcceeeccCCCCCC
Q 035938 72 ILVGFRIYQDDKADVILINTPDEAKRLKNIGELPDGTRLNEGLL-------LILMMTPMLFQDNDIDKI 133 (133)
Q Consensus 72 VlV~~~~~~~~KgdIv~ry~~dqik~L~k~g~~P~~f~~~e~~~-------~~~~~~~~~f~~~did~i 133 (133)
|+|++|+|+++||+|+|||+++||++|+++|+||+.|.+++++. +.++++.++|+++|++.|
T Consensus 77 VlVel~~~d~~KgdIv~ry~~dqvr~Lkk~G~~P~~f~~~~~~~~~~~~~~~~~~~~~~~f~~~~~~~~ 145 (145)
T PLN00208 77 ILVGLRDYQDDKADVILKYMPDEARLLKAYGELPENTRLNEGIAGDLDEEEDGEGDDYIEFEDEDIDKI 145 (145)
T ss_pred EEEEccCCCCCEEEEEEEcCHHHHHHHHHcCCCCcceeeccccccccccccCcccCcceeecccccccC
Confidence 99999999999999999999999999999999999999988772 556666799999999875
No 3
>KOG3403 consensus Translation initiation factor 1A (eIF-1A) [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=6.8e-43 Score=261.89 Aligned_cols=129 Identities=60% Similarity=0.920 Sum_probs=120.7
Q ss_pred CCCCCCCCCCccccccccCccCCcccceeeeccCCCeEEEEEEEecCCceE---------EEEEeccccceeeEeecCCE
Q 035938 1 MANNKGKGGKKFKNRKRGKNNEGEDQKRELIIKEEGQEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDI 71 (133)
Q Consensus 1 m~~~~~k~gk~~~n~~r~~~~~~~~~~~el~~p~e~e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~ 71 (133)
||+||||||| |+|||++ +++...++|+++++||+||||++||||+++ |||||+||+||+|||.+||+
T Consensus 1 mpknkgkggk---nrRrGkn-end~~kReLvfkEegqeYaQv~kmLGnGr~e~~CfDGvkR~~hiRGklrkkVwi~~GDI 76 (145)
T KOG3403|consen 1 MPKNKGKGGK---NRRRGKN-ENDFEKRELVFKEEGQEYAQVIKMLGNGRLEASCFDGVKRLCHIRGKLRKKVWINQGDI 76 (145)
T ss_pred CCCCCCCCcc---ccccCcc-cccchhhheeehhcchhHHHHHhhhcCCcEEEEEecchhhhhhhhccceeeEeecCCCE
Confidence 9999999999 9999999 999999999999999999999999999997 99999999999999999999
Q ss_pred EEEEeeeCCCCeEEEEEEcCHhHHHHHHHcCCCCccccccccc-ccccC-Ccceee-----ccCCCCCC
Q 035938 72 ILVGFRIYQDDKADVILINTPDEAKRLKNIGELPDGTRLNEGL-LLILM-MTPMLF-----QDNDIDKI 133 (133)
Q Consensus 72 VlV~~~~~~~~KgdIv~ry~~dqik~L~k~g~~P~~f~~~e~~-~~~~~-~~~~~f-----~~~did~i 133 (133)
|||.+++||++||||+.+|+++|++.|+..|+||+.|.+|++. |+.++ ++++.| +++|||+|
T Consensus 77 iLv~lRD~qd~kaDvilKY~~dEar~LK~~Gelpe~~k~Ne~~~~~~e~~d~~~~~~~~~~~~ed~d~~ 145 (145)
T KOG3403|consen 77 ILVGLRDYQDDKADVILKYMPDEARILKAYGELPENAKINETDTFGVEDDDDDIDFDDIEDDDEDIDDI 145 (145)
T ss_pred EEEeeecccccccceehhhChHHHHHHHhcCcCCcccccccccccCccCCccccccccccccccccccC
Confidence 9999999999999999999999999999999999999999998 66653 444555 67888875
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=100.00 E-value=2.1e-32 Score=197.18 Aligned_cols=88 Identities=34% Similarity=0.561 Sum_probs=83.4
Q ss_pred cCccCCcccceeeeccCCCeEEEEEEEecCCceE---------EEEEeccccceeeEeecCCEEEEEeeeCC-CCeEEEE
Q 035938 18 GKNNEGEDQKRELIIKEEGQEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDIILVGFRIYQ-DDKADVI 87 (133)
Q Consensus 18 ~~~~~~~~~~~el~~p~e~e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~VlV~~~~~~-~~KgdIv 87 (133)
+|+ +++....++|.++++|++|+|++++||++| +|||||||||++|||++||+|+|+||+++ +.||+|+
T Consensus 2 ~~~-~~~~~~~~~p~~~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~iwI~~GD~VlVsp~d~~~~~kg~Iv 80 (99)
T TIGR00523 2 GQQ-QEQQIRVRLPRKEEGEILGVIEQMLGAGRVKVRCLDGKTRLGRIPGKLKKRIWIREGDVVIVKPWEFQGDDKCDIV 80 (99)
T ss_pred CcC-ccCcceeeCCCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEEccCCCCccEEEE
Confidence 555 778889999999999999999999999998 99999999999999999999999999998 7899999
Q ss_pred EEcCHhHHHHHHHcCCCCc
Q 035938 88 LINTPDEAKRLKNIGELPD 106 (133)
Q Consensus 88 ~ry~~dqik~L~k~g~~P~ 106 (133)
|||+++||++|+++|+||+
T Consensus 81 ~r~~~~qv~~L~~~g~~p~ 99 (99)
T TIGR00523 81 WRYTKTQVEWLKRKGYLKE 99 (99)
T ss_pred EEcCHHHHHHHHHcCCCCC
Confidence 9999999999999999995
No 5
>PRK04012 translation initiation factor IF-1A; Provisional
Probab=99.98 E-value=4.2e-32 Score=195.97 Aligned_cols=85 Identities=33% Similarity=0.547 Sum_probs=82.1
Q ss_pred CCcccceeeeccCCCeEEEEEEEecCCceE---------EEEEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEEcCH
Q 035938 22 EGEDQKRELIIKEEGQEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILINTP 92 (133)
Q Consensus 22 ~~~~~~~el~~p~e~e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ry~~ 92 (133)
..+....++++|+++|++|+|+++|||++| +|||||||||++|||++||+|+|++|+|+++||+|+|||++
T Consensus 7 ~~~~~~~~~~~p~e~e~~g~V~~~lG~~~~~V~~~dG~~~la~i~GK~Rk~IwI~~GD~VlVe~~~~~~~kg~Iv~r~~~ 86 (100)
T PRK04012 7 DEEVTRVRLPMPEEGEVFGVVEQMLGANRVRVRCMDGVERMGRIPGKMKKRMWIREGDVVIVAPWDFQDEKADIIWRYTK 86 (100)
T ss_pred CCCceeEEccCCCCCEEEEEEEEEcCCCEEEEEeCCCCEEEEEEchhhcccEEecCCCEEEEEecccCCCEEEEEEEcCH
Confidence 567789999999999999999999999998 99999999999999999999999999999999999999999
Q ss_pred hHHHHHHHcCCCCc
Q 035938 93 DEAKRLKNIGELPD 106 (133)
Q Consensus 93 dqik~L~k~g~~P~ 106 (133)
+||++|+++|+||+
T Consensus 87 ~qv~~L~~~g~~~~ 100 (100)
T PRK04012 87 PQVDWLRRKGYISE 100 (100)
T ss_pred HHHHHHHHcCCCCC
Confidence 99999999999985
No 6
>smart00652 eIF1a eukaryotic translation initiation factor 1A.
Probab=99.97 E-value=2.8e-31 Score=185.67 Aligned_cols=74 Identities=55% Similarity=0.811 Sum_probs=72.3
Q ss_pred ccCCCeEEEEEEEecCCceE---------EEEEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEEcCHhHHHHHHHcC
Q 035938 32 IKEEGQEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILINTPDEAKRLKNIG 102 (133)
Q Consensus 32 ~p~e~e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ry~~dqik~L~k~g 102 (133)
.|+++|++|+|++++||++| +||+||||||++|||++||+|+|++|+|+++||+|+|||+++||++|+++|
T Consensus 1 ~p~e~q~~g~V~~~lG~~~~~V~~~dG~~~la~ipgK~Rk~iwI~~GD~VlVe~~~~~~~kg~Iv~r~~~~~vk~L~k~g 80 (83)
T smart00652 1 FKEDGQEIAQVVKMLGNGRLEVMCADGKERLARIPGKMRKKVWIRRGDIVLVDPWDFQDVKADIIYKYTKDEVRWLKKEG 80 (83)
T ss_pred CCCCCcEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEecCCCCCEEEEEEEeCHHHHHHHHHcC
Confidence 37899999999999999998 999999999999999999999999999999999999999999999999999
Q ss_pred CCC
Q 035938 103 ELP 105 (133)
Q Consensus 103 ~~P 105 (133)
+||
T Consensus 81 ~wp 83 (83)
T smart00652 81 ELP 83 (83)
T ss_pred CCC
Confidence 998
No 7
>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=99.96 E-value=8.5e-29 Score=171.50 Aligned_cols=68 Identities=40% Similarity=0.574 Sum_probs=66.1
Q ss_pred eEEEEEEEecCCceE---------EEEEeccccceeeEeecCCEEEEEeeeC-CCCeEEEEEEcCHhHHHHHHHcCCC
Q 035938 37 QEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDIILVGFRIY-QDDKADVILINTPDEAKRLKNIGEL 104 (133)
Q Consensus 37 e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~VlV~~~~~-~~~KgdIv~ry~~dqik~L~k~g~~ 104 (133)
|+||+|++++|||+| +|||||||||++|||++||+|+|+||+| +++||+|+|||+++||++|+++|+|
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 689999999999998 9999999999999999999999999999 6889999999999999999999998
No 8
>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=1.9e-28 Score=169.34 Aligned_cols=68 Identities=57% Similarity=0.866 Sum_probs=66.1
Q ss_pred eEEEEEEEecCCceE---------EEEEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEEcCHhHHHHHHHcCCC
Q 035938 37 QEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILINTPDEAKRLKNIGEL 104 (133)
Q Consensus 37 e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ry~~dqik~L~k~g~~ 104 (133)
|++|+|++++||++| +||+||||||++|||++||+|+|++|||+++||+|+|||+++||++|+++|+|
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 EEYGQVEKMLGNGRLEVRCFDGKKRLCRIRGKMRKRVWINEGDIVLVAPWDFQDDKADIIYKYTPDEVRWLKRKGEL 77 (77)
T ss_pred CEEEEEEEEcCCCEEEEEECCCCEEEEEEchhhcccEEEcCCCEEEEEeccccCCEEEEEEEcCHHHHHHHHHcCcC
Confidence 689999999999998 99999999999999999999999999999999999999999999999999975
No 9
>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=99.95 E-value=1.2e-27 Score=166.32 Aligned_cols=68 Identities=32% Similarity=0.362 Sum_probs=65.9
Q ss_pred eEEEEEEEecCCceE---------EEEEeccccceeeEeecCCEEEEEeeeCCC-CeEEEEEEcCHhHHHHHHHcCCC
Q 035938 37 QEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDIILVGFRIYQD-DKADVILINTPDEAKRLKNIGEL 104 (133)
Q Consensus 37 e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~VlV~~~~~~~-~KgdIv~ry~~dqik~L~k~g~~ 104 (133)
|.+|+|++++|||++ +||+||||||+++||++||||||+||++++ .||+|+|+|+++||++|+++|+|
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 689999999999998 999999999999999999999999999996 59999999999999999999998
No 10
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=99.92 E-value=2.4e-25 Score=153.85 Aligned_cols=63 Identities=33% Similarity=0.472 Sum_probs=60.1
Q ss_pred ccCCCeEEEEEEEecCCceE---------EEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEEcCHhH
Q 035938 32 IKEEGQEYAEVLRMLGNGRL---------RLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILINTPDE 94 (133)
Q Consensus 32 ~p~e~e~~g~V~~~lGn~~~---------~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry~~dq 94 (133)
.|+++|++|+|+++|||++| ++||||||||+ +|||.+||+|+|+|||||++||+|+|||+++|
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 KPDEIEMEGTVIEMLPNGRFRVELENGHERLAHISGKMRKNRIRILPGDVVLVELSPYDLTKGRIVYRYKKDE 75 (75)
T ss_pred cccccEEEEEEEEecCCCEEEEEecCCcEEEEEccCcchheeEEeCCCCEEEEEecccccccccEEEEecCCC
Confidence 35789999999999999998 99999999999 99999999999999999999999999999875
No 11
>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=99.87 E-value=1.1e-22 Score=135.74 Aligned_cols=56 Identities=38% Similarity=0.577 Sum_probs=50.3
Q ss_pred CCCeEEEEEEEecCCceE---------EEEEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEE
Q 035938 34 EEGQEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILI 89 (133)
Q Consensus 34 ~e~e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~r 89 (133)
+|+|++|+|++++||++| ++|+||||||++|||++||+|+|++|+|+++||+|+||
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 EEGEVIGRVTEMLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSPYDKVKGRIIYR 65 (65)
T ss_dssp STTEEEEEEEEEESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEESTTCTTEEEEEEE
T ss_pred CCcEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEecccCCCeEEEEEC
Confidence 579999999999999998 99999999999999999999999999999999999997
No 12
>KOG2925 consensus Predicted translation initiation factor related to eIF-1A [Translation, ribosomal structure and biogenesis]
Probab=99.85 E-value=2.2e-22 Score=155.10 Aligned_cols=87 Identities=22% Similarity=0.262 Sum_probs=80.3
Q ss_pred cccceeeeccCCCeEEEEEEEecCCceE---------EEEEeccccceeeEeecCCEEEEEeeeC---CC-CeEEEEEEc
Q 035938 24 EDQKRELIIKEEGQEYAEVLRMLGNGRL---------RLHWRHQAMHKRVWIAAGDIILVGFRIY---QD-DKADVILIN 90 (133)
Q Consensus 24 ~~~~~el~~p~e~e~~g~V~~~lGn~~~---------~la~IpGKmrkriWI~~GD~VlV~~~~~---~~-~KgdIv~ry 90 (133)
..+..+...+++.|+||+|+++.|||+| .|++||.|||+.|||++|+||+|.|+.+ +. .||.|.|++
T Consensus 10 q~v~de~~~le~~q~IaqVvqlrGsnlheV~danGq~~lvsmP~KfRksiWiRRg~FvvVdpiee~~~g~KVkgeI~yVl 89 (167)
T KOG2925|consen 10 QAVSDEDFTLEECQSIAQVVQLRGSNLHEVMDANGQNSLVSMPAKFRKSIWIRRGSFVVVDPIEEEKSGSKVKGEICYVL 89 (167)
T ss_pred ccccCCCcchhhhhhHHHHHhcCCcchhhhhhcCCceeeeeCCHhhhhceEEeeCCEEEEccccccccCCccceEEEEEE
Confidence 3456678889999999999999999998 9999999999999999999999999998 43 399999999
Q ss_pred CHhHHHHHHHcCCCCccccc
Q 035938 91 TPDEAKRLKNIGELPDGTRL 110 (133)
Q Consensus 91 ~~dqik~L~k~g~~P~~f~~ 110 (133)
..+|++.|++.|+||+.|..
T Consensus 90 ~~d~vr~lqk~g~WPe~F~d 109 (167)
T KOG2925|consen 90 FFDQVRLLQKSGEWPEIFKD 109 (167)
T ss_pred ccHHHHHHHHcCCcchhhhh
Confidence 99999999999999999965
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=99.84 E-value=1e-20 Score=128.63 Aligned_cols=54 Identities=17% Similarity=0.143 Sum_probs=51.6
Q ss_pred CeEEEEEEEecCCceE---------EEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEE
Q 035938 36 GQEYAEVLRMLGNGRL---------RLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILI 89 (133)
Q Consensus 36 ~e~~g~V~~~lGn~~~---------~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~r 89 (133)
-++.|+|+++|||++| ++||||||||+ +|||.+||.|+|++||||++||+|+||
T Consensus 5 ie~~G~V~e~L~~~~f~V~l~ng~~vla~i~GKmr~~rI~I~~GD~V~Ve~spyd~tkgrIi~R 68 (68)
T TIGR00008 5 IEMEGKVTESLPNAMFRVELENGHEVLAHISGKIRMHYIRILPGDKVKVELSPYDLTRGRITYR 68 (68)
T ss_pred EEEEEEEEEECCCCEEEEEECCCCEEEEEecCcchhccEEECCCCEEEEEECcccCCcEeEEeC
Confidence 3789999999999998 99999999997 999999999999999999999999997
No 14
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=99.82 E-value=4.3e-20 Score=130.78 Aligned_cols=57 Identities=21% Similarity=0.212 Sum_probs=54.3
Q ss_pred CeEEEEEEEecCCceE---------EEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEEcCH
Q 035938 36 GQEYAEVLRMLGNGRL---------RLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILINTP 92 (133)
Q Consensus 36 ~e~~g~V~~~lGn~~~---------~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry~~ 92 (133)
-++.|+|+++|||+.| +||||+||||+ +|||.+||.|+|++||||++||+|+|||.+
T Consensus 7 ie~~G~V~e~Lp~~~frV~LenG~~vla~isGKmR~~rIrIl~GD~V~VE~spYDltkGRIiyR~~~ 73 (87)
T PRK12442 7 IELDGIVDEVLPDSRFRVTLENGVEVGAYASGRMRKHRIRILAGDRVTLELSPYDLTKGRINFRHKD 73 (87)
T ss_pred EEEEEEEEEECCCCEEEEEeCCCCEEEEEeccceeeeeEEecCCCEEEEEECcccCCceeEEEEecC
Confidence 4789999999999988 99999999999 999999999999999999999999999973
No 15
>CHL00010 infA translation initiation factor 1
Probab=99.58 E-value=5.5e-15 Score=102.04 Aligned_cols=57 Identities=21% Similarity=0.240 Sum_probs=52.2
Q ss_pred eEEEEEEEecCCceE---------EEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEEcCHh
Q 035938 37 QEYAEVLRMLGNGRL---------RLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILINTPD 93 (133)
Q Consensus 37 e~~g~V~~~lGn~~~---------~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry~~d 93 (133)
++.|+|++.+|++.+ ++|+++||||+ ++|+..||+|.|+||++++++|+|||||...
T Consensus 8 ~~~G~Vik~lg~~~y~V~~~~g~~~~c~~rGklr~~~i~~~vGD~V~ve~~~~~~~~g~Ii~r~~~~ 74 (78)
T CHL00010 8 EMEGLVTESLPNGMFRVRLDNGCQVLGYISGKIRRNSIRILPGDRVKVELSPYDLTKGRIIYRLRNK 74 (78)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEeccceecCCcccCCCCEEEEEEcccCCCeEEEEEEecCC
Confidence 478999999987766 78999999998 7999999999999999999999999999764
No 16
>PRK00276 infA translation initiation factor IF-1; Validated
Probab=99.57 E-value=1.2e-14 Score=98.68 Aligned_cols=55 Identities=22% Similarity=0.238 Sum_probs=50.5
Q ss_pred eEEEEEEEecCCceE---------EEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEEcC
Q 035938 37 QEYAEVLRMLGNGRL---------RLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILINT 91 (133)
Q Consensus 37 e~~g~V~~~lGn~~~---------~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry~ 91 (133)
++.|+|+++++++.+ ++|+++|+||+ ++|+..||+|+|++|++++++|+|||||.
T Consensus 8 ~~~G~Vi~~~~~~~y~V~~~~g~~~~c~~~Gklr~~~i~i~vGD~V~ve~~~~~~~~g~Iv~r~~ 72 (72)
T PRK00276 8 EMEGTVVEALPNAMFRVELENGHEVLAHISGKMRKNYIRILPGDKVTVELSPYDLTKGRITYRHK 72 (72)
T ss_pred EEEEEEEEEcCCCEEEEEeCCCCEEEEEEccceeeCCcccCCCCEEEEEEcccCCCeEEEEEEeC
Confidence 678999999988655 78999999996 89999999999999999999999999984
No 17
>cd04451 S1_IF1 S1_IF1: Translation Initiation Factor IF1, S1-like RNA-binding domain. IF1 contains an S1-like RNA-binding domain, which is found in a wide variety of RNA-associated proteins. Translation initiation includes a number of interrelated steps preceding the formation of the first peptide bond. In Escherichia coli, the initiation mechanism requires, in addition to mRNA, fMet-tRNA, and ribosomal subunits, the presence of three additional proteins (initiation factors IF1, IF2, and IF3) and at least one GTP molecule. The three initiation factors influence both the kinetics and the stability of ternary complex formation. IF1 is the smallest of the three factors. IF1 enhances the rate of 70S ribosome subunit association and dissociation and the interaction of 30S ribosomal subunit with IF2 and IF3. It stimulates 30S complex formation. In addition, by binding to the A-site of the 30S ribosomal subunit, IF1 may contribute to the fidelity of the selection of the initiation site of th
Probab=99.17 E-value=1.4e-10 Score=76.27 Aligned_cols=53 Identities=21% Similarity=0.195 Sum_probs=46.3
Q ss_pred eEEEEEEEecCCceE---------EEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEE
Q 035938 37 QEYAEVLRMLGNGRL---------RLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILI 89 (133)
Q Consensus 37 e~~g~V~~~lGn~~~---------~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~r 89 (133)
++.|+|++.+||+.+ ++|+++|+||+ ++|+..||+|+++++++++++|.||||
T Consensus 2 ~~~G~Vi~~~~g~~~~V~~~~g~~~~c~~rGklr~~~~~~~vGD~V~~~~~~~~~~~g~I~~~ 64 (64)
T cd04451 2 EMEGVVTEALPNAMFRVELENGHEVLAHISGKMRMNYIRILPGDRVKVELSPYDLTKGRIVYR 64 (64)
T ss_pred eEEEEEEEEeCCCEEEEEeCCCCEEEEEECceeecCCcccCCCCEEEEEEeecCCCEEEEEEC
Confidence 356888888875444 88999999996 899999999999999999889999996
No 18
>cd04466 S1_YloQ_GTPase S1_YloQ_GTPase: YloQ GTase family (also known as YjeQ and CpgA), S1-like RNA-binding domain. Proteins in the YloQ GTase family bind the ribosome and have GTPase activity. The precise role of this family is unknown. The protein structure is composed of three domains: an N-terminal S1 domain, a central GTPase domain, and a C-terminal zinc finger domain. This N-terminal S1 domain binds ssRNA. The central GTPase domain contains nucleotide-binding signature motifs: G1 (walker A), G3 (walker B) and G4 motifs. Experiments show that the bacterial YloQ and YjeQ proteins have low intrinsic GTPase activity. The C-terminal zinc-finger domain has structural similarity to a portion of the DNA-repair protein Rad51. This suggests a possible role for this GTPase as a regulator of translation, perhaps as a translation initiation factor. This family is classified based on the N-terminal S1 domain.
Probab=96.97 E-value=0.0031 Score=40.66 Aligned_cols=40 Identities=15% Similarity=-0.002 Sum_probs=30.8
Q ss_pred eEEEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEEcC
Q 035938 50 RLRLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILINT 91 (133)
Q Consensus 50 ~~~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry~ 91 (133)
..+.|.++|++++ ..++..||+|++++++ ...+-|+.++.
T Consensus 21 ~~~~~~~~~~~~~~~~~~~VGD~V~~~~~~--~~~~~I~~vl~ 61 (68)
T cd04466 21 KIYECRLRGKFRKDKNPPAVGDRVEFEPED--DGEGVIEEILP 61 (68)
T ss_pred eEEEEEEccccccCCCCCCCCcEEEEEECC--CCcEEEEEEec
Confidence 4489999999985 6889999999998754 34566766553
No 19
>PRK12289 GTPase RsgA; Reviewed
Probab=92.36 E-value=0.38 Score=41.33 Aligned_cols=37 Identities=22% Similarity=0.285 Sum_probs=27.1
Q ss_pred EEEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEE
Q 035938 51 LRLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVI 87 (133)
Q Consensus 51 ~~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv 87 (133)
..+|..+|++++ ..-+..||+|++++.++.+..|-|.
T Consensus 36 ~~~~~~r~~lk~~~~~~~vGD~V~~~~~~~~~~~~~I~ 73 (352)
T PRK12289 36 LLLCTRRTRLKKIGQQVMVGDRVIVEEPDWQGQRGAIA 73 (352)
T ss_pred EEEEEcccccccCCCCcccCCEEEEeecCCCCCceEEE
Confidence 467999999986 4458899999999766544555443
No 20
>PRK00098 GTPase RsgA; Reviewed
Probab=92.27 E-value=0.44 Score=39.44 Aligned_cols=28 Identities=14% Similarity=0.036 Sum_probs=22.7
Q ss_pred eEEEEEeccccce-eeEeecCCEEEEEee
Q 035938 50 RLRLHWRHQAMHK-RVWIAAGDIILVGFR 77 (133)
Q Consensus 50 ~~~la~IpGKmrk-riWI~~GD~VlV~~~ 77 (133)
..+.|.++|++++ ..-+..||+|+|++.
T Consensus 21 ~~~~~~~~g~~~~~~~~~~vGD~V~~~~~ 49 (298)
T PRK00098 21 QVYQCRARGKFRKKTNTPAVGDRVEFSAE 49 (298)
T ss_pred CEEEEEeccccccCCCCcCCCCEEEEEEC
Confidence 3488999999985 556788999999863
No 21
>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=92.14 E-value=0.35 Score=39.81 Aligned_cols=40 Identities=15% Similarity=0.078 Sum_probs=28.8
Q ss_pred ceEEEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEEc
Q 035938 49 GRLRLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILIN 90 (133)
Q Consensus 49 ~~~~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry 90 (133)
+..+.|.++|++++ +.-+..||+|++++.+ +..|.|..++
T Consensus 17 ~~~~~~~~~g~~~~~~~~~~vGD~V~~~~~~--~~~~~i~~i~ 57 (287)
T cd01854 17 GGELRCRARGKLRKKGIKPVVGDWVEVEPDD--DGEGVIVRVL 57 (287)
T ss_pred CeEEEEEeccccccCCCCccCCCEEEEEecC--CCcEEEEEEE
Confidence 44589999999986 3558899999998654 3345554444
No 22
>PRK12288 GTPase RsgA; Reviewed
Probab=88.31 E-value=1.5 Score=37.46 Aligned_cols=50 Identities=10% Similarity=0.002 Sum_probs=35.1
Q ss_pred EEEEEEEecCCceE--------EEEEeccccceeeEeecCCEEEEEeeeCCC--CeEEEEEEc
Q 035938 38 EYAEVLRMLGNGRL--------RLHWRHQAMHKRVWIAAGDIILVGFRIYQD--DKADVILIN 90 (133)
Q Consensus 38 ~~g~V~~~lGn~~~--------~la~IpGKmrkriWI~~GD~VlV~~~~~~~--~KgdIv~ry 90 (133)
..|+|+...|+... +.|.++|+++. +..||+|++++.+.+. ..|-|..++
T Consensus 40 ~~g~Vi~~~~~~~~v~~~~g~~~~~~~~g~~~~---~~vGD~V~~~~~~~~~~~~~~~I~~il 99 (347)
T PRK12288 40 QEGIVISRFGQHADVEAADGEVHRCNIRRTIRS---LVTGDRVVWRPGKEALEGVSGVVEAVH 99 (347)
T ss_pred cceEEEEEECCEEEEEeCCCcEEEEEecccCCC---CCCCcEEEEEeCCCcccccceEEEEEe
Confidence 57888888876443 68999999974 7899999998543221 136565554
No 23
>PRK01889 GTPase RsgA; Reviewed
Probab=85.94 E-value=1.9 Score=36.75 Aligned_cols=52 Identities=19% Similarity=0.157 Sum_probs=35.9
Q ss_pred CeEEEEEEEecCCceE-------EEEEeccccce-----eeEeecCCEEEEEeeeCCCCeEEEEEEcC
Q 035938 36 GQEYAEVLRMLGNGRL-------RLHWRHQAMHK-----RVWIAAGDIILVGFRIYQDDKADVILINT 91 (133)
Q Consensus 36 ~e~~g~V~~~lGn~~~-------~la~IpGKmrk-----riWI~~GD~VlV~~~~~~~~KgdIv~ry~ 91 (133)
+-..|+|+...|+... +.|.++|+++. .--...||+|++++ +..|-|..+|.
T Consensus 27 ~~~~g~v~~~~~~~~~v~~~~~~~~~~~~gk~~~~~~~~~~~~~vGD~V~~~~----~~~g~I~~i~p 90 (356)
T PRK01889 27 GLEPGRVVEEHRSGYVVATEEGEVRAEVSGKWRHEAFPPGDRPAVGDWVLLDN----EKKARIVRLLP 90 (356)
T ss_pred CCccEEEEEEECCEEEEEECCcEEEEEecchhhccccccCCCCccCcEEEEec----CCceEEEEEEC
Confidence 3456888888876443 77999999984 13367899999985 23455555443
No 24
>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=81.02 E-value=6.2 Score=23.45 Aligned_cols=25 Identities=16% Similarity=0.121 Sum_probs=19.4
Q ss_pred eeEeecCCEEEEEeeeCCCCeEEEE
Q 035938 63 RVWIAAGDIILVGFRIYQDDKADVI 87 (133)
Q Consensus 63 riWI~~GD~VlV~~~~~~~~KgdIv 87 (133)
+-+++.||.|.|.....+..++.|.
T Consensus 39 ~~~~~~G~~v~~~v~~~d~~~~~i~ 63 (65)
T cd00164 39 SEVFKVGDEVEVKVLEVDPEKGRIS 63 (65)
T ss_pred hhEeCCCCEEEEEEEEEcCCcCEEe
Confidence 4578999999999988776555553
No 25
>PHA02945 interferon resistance protein; Provisional
Probab=79.77 E-value=13 Score=26.66 Aligned_cols=57 Identities=12% Similarity=0.059 Sum_probs=40.2
Q ss_pred eeccCCCe-EEEEEEEecCCceE----------EEEEec------cccceeeEeecCCEEEEEeeeCCCCeEEEEE
Q 035938 30 LIIKEEGQ-EYAEVLRMLGNGRL----------RLHWRH------QAMHKRVWIAAGDIILVGFRIYQDDKADVIL 88 (133)
Q Consensus 30 l~~p~e~e-~~g~V~~~lGn~~~----------~la~Ip------GKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ 88 (133)
+.+|++|| ++|+|.. ...+.+ -+.|++ |-.|-|=.+ +|..|.|.-..-+..||.|=-
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-NGYALYIDLFDYPHSEAILAESVQMHMNRYFKYRDKL-VGKTVKVKVIRVDYTKGYIDV 79 (88)
T ss_pred ecCCCCCcEEEEEEEe-cCceEEEEecccCCcEEEEEeehhhhccceEeeeeEe-cCCEEEEEEEEECCCCCEEEe
Confidence 56899998 6899998 877776 344444 333334444 888888888888888887754
No 26
>COG0509 GcvH Glycine cleavage system H protein (lipoate-binding) [Amino acid transport and metabolism]
Probab=79.45 E-value=0.97 Score=34.44 Aligned_cols=40 Identities=23% Similarity=0.504 Sum_probs=32.8
Q ss_pred EEeccccce---eeEeec-C-CEEEEEeeeC-CCCeEEEEEEcCHh
Q 035938 54 HWRHQAMHK---RVWIAA-G-DIILVGFRIY-QDDKADVILINTPD 93 (133)
Q Consensus 54 a~IpGKmrk---riWI~~-G-D~VlV~~~~~-~~~KgdIv~ry~~d 93 (133)
|.+|..|+. +.||+. | +++.|.+++| |..-|+|+|+-.++
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 567777775 899998 5 7999999998 57789999986554
No 27
>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=78.15 E-value=5 Score=29.84 Aligned_cols=48 Identities=23% Similarity=0.201 Sum_probs=32.6
Q ss_pred ceeeEeecCCEEEEEeee-----------CCC----CeEEEEEEcCHhHHHHHHHcC-CCCccc
Q 035938 61 HKRVWIAAGDIILVGFRI-----------YQD----DKADVILINTPDEAKRLKNIG-ELPDGT 108 (133)
Q Consensus 61 rkriWI~~GD~VlV~~~~-----------~~~----~KgdIv~ry~~dqik~L~k~g-~~P~~f 108 (133)
|.-+.|+.||.|+|.+.+ +.+ ....+.|=|+++|+..+.... ..|.+.
T Consensus 3 r~~~~i~vGD~V~v~~~~~~~~va~Ie~i~ed~~g~~~v~v~WF~~p~E~~~~~~~~~~~~~Ev 66 (130)
T cd04721 3 RNGVTISVHDFVYVLSEEEDRYVAYIEDLYEDKKGSKMVKVRWFHTTDEVGAALSPDSVNPREI 66 (130)
T ss_pred cCCEEEECCCEEEEeCCCCCcEEEEEEEEEEcCCCCEEEEEEEecCHHHhccccCCCCCCCCeE
Confidence 446889999999998643 111 256788888999998854443 444443
No 28
>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=76.32 E-value=6.3 Score=27.66 Aligned_cols=57 Identities=12% Similarity=0.093 Sum_probs=38.6
Q ss_pred cCC-CeEEEEEEEecCCceE------EEEE-----eccccce-eeEeecCCEEEEEeeeCCCC-eEEEEEE
Q 035938 33 KEE-GQEYAEVLRMLGNGRL------RLHW-----RHQAMHK-RVWIAAGDIILVGFRIYQDD-KADVILI 89 (133)
Q Consensus 33 p~e-~e~~g~V~~~lGn~~~------~la~-----IpGKmrk-riWI~~GD~VlV~~~~~~~~-KgdIv~r 89 (133)
|.. +-++|+|+...+.+.. ..|. ++|.-|+ |=.++.||.|.......+.. .-++...
T Consensus 4 P~~gD~VIG~V~~~~~~~~~VdI~s~~~a~L~~~~f~gatk~~rp~L~~GDlV~ArV~~~~~~~~~eLtc~ 74 (86)
T cd05790 4 PAKGDHVIGIVVAKAGDFFKVDIGGSEPASLSYLAFEGATKRNRPNLNVGDLVYARVVKANRDMEPELSCV 74 (86)
T ss_pred CCCCCEEEEEEEEEcCCeEEEEcCCCcceEechHHcccccccccccCCCCCEEEEEEEecCCCCCeEEEEe
Confidence 554 5689999999887665 2333 3455454 67799999999998877643 3444443
No 29
>cd04454 S1_Rrp4_like S1_Rrp4_like: Rrp4-like, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein, and Rrp40 and Csl4 proteins, also represented in this group, are subunits 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=73.71 E-value=10 Score=24.98 Aligned_cols=56 Identities=20% Similarity=0.197 Sum_probs=36.9
Q ss_pred ccCCCe-EEEEEEEecCCceE------EEEEecc-----c-cce-eeEeecCCEEEEEeeeCCCCeEEEEE
Q 035938 32 IKEEGQ-EYAEVLRMLGNGRL------RLHWRHQ-----A-MHK-RVWIAAGDIILVGFRIYQDDKADVIL 88 (133)
Q Consensus 32 ~p~e~e-~~g~V~~~lGn~~~------~la~IpG-----K-mrk-riWI~~GD~VlV~~~~~~~~KgdIv~ 88 (133)
+|..|+ ++|+|++.-.++.+ ..|.+|- . .+. .=+++.||.|.+.....+.. +.|..
T Consensus 3 ~p~~GdiV~G~V~~v~~~~~~V~i~~~~~g~l~~~~~~~~~~~~~~~~~~~GD~i~~~V~~~~~~-~~i~L 72 (82)
T cd04454 3 LPDVGDIVIGIVTEVNSRFWKVDILSRGTARLEDSSATEKDKKEIRKSLQPGDLILAKVISLGDD-MNVLL 72 (82)
T ss_pred CCCCCCEEEEEEEEEcCCEEEEEeCCCceEEeechhccCcchHHHHhcCCCCCEEEEEEEEeCCC-CCEEE
Confidence 466665 69999999887766 2333332 2 111 34579999999999887764 44443
No 30
>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=73.21 E-value=10 Score=25.17 Aligned_cols=57 Identities=16% Similarity=0.135 Sum_probs=35.7
Q ss_pred cCCCe-EEEEEEEecCCceE------EEEEeccc-cc-----ee-----eEeecCCEEEEEeeeCCCCeEEEEEEc
Q 035938 33 KEEGQ-EYAEVLRMLGNGRL------RLHWRHQA-MH-----KR-----VWIAAGDIILVGFRIYQDDKADVILIN 90 (133)
Q Consensus 33 p~e~e-~~g~V~~~lGn~~~------~la~IpGK-mr-----kr-----iWI~~GD~VlV~~~~~~~~KgdIv~ry 90 (133)
|..|+ +.|+|+++...+.+ ..|.+|-. +. .. =.++.||.|.+.....+.+ +.|..-.
T Consensus 4 p~~GdiV~g~V~~i~~~g~~v~i~~~~~G~l~~se~~~~~~~~~~~~~~~~l~vGd~i~~~V~~~~~~-~~i~LS~ 78 (86)
T cd05789 4 PEVGDVVIGRVTEVGFKRWKVDINSPYDAVLPLSEVNLPRTDEDELNMRSYLDEGDLIVAEVQSVDSD-GSVSLHT 78 (86)
T ss_pred CCCCCEEEEEEEEECCCEEEEECCCCeEEEEEHHHccCCCCccchHHHHhhCCCCCEEEEEEEEECCC-CCEEEEe
Confidence 55554 79999998887665 33333311 11 11 1589999999999887654 5554433
No 31
>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=70.84 E-value=5 Score=26.45 Aligned_cols=28 Identities=29% Similarity=0.680 Sum_probs=20.1
Q ss_pred eecCCEEEEEeeeC---CCCeEEEEEEcCHh
Q 035938 66 IAAGDIILVGFRIY---QDDKADVILINTPD 93 (133)
Q Consensus 66 I~~GD~VlV~~~~~---~~~KgdIv~ry~~d 93 (133)
|..||+|+|.++.. ....|||+.-..+.
T Consensus 14 i~~gd~v~v~~~~~~~~~~~~GDiv~~~~~~ 44 (85)
T cd06530 14 LQPGDLVLVNKLSYGFREPKRGDVVVFKSPG 44 (85)
T ss_pred ccCCCEEEEEEeecccCCCCCCCEEEEeCCC
Confidence 67888888888776 35677777666554
No 32
>PRK10413 hydrogenase 2 accessory protein HypG; Provisional
Probab=70.26 E-value=13 Score=25.93 Aligned_cols=53 Identities=21% Similarity=0.061 Sum_probs=33.2
Q ss_pred EEEEEEecCCc-eEEEEEeccccce-ee--------EeecCCEEEEEeeeCCCCeEEEEEEcCHhHHHHH
Q 035938 39 YAEVLRMLGNG-RLRLHWRHQAMHK-RV--------WIAAGDIILVGFRIYQDDKADVILINTPDEAKRL 98 (133)
Q Consensus 39 ~g~V~~~lGn~-~~~la~IpGKmrk-ri--------WI~~GD~VlV~~~~~~~~KgdIv~ry~~dqik~L 98 (133)
-++|+++-|+. ..-+|-+.|--|. ++ .+.+||||||.. |-.+.+.++++++..
T Consensus 6 P~kVi~i~~~~~~~A~vd~~Gv~r~V~l~Lv~~~~~~~~vGDyVLVHa-------GfAi~~ideeeA~et 68 (82)
T PRK10413 6 PGQVLAVGEDIHQLAQVEVCGIKRDVNIALICEGNPADLLGQWVLVHV-------GFAMSIIDEDEAKAT 68 (82)
T ss_pred ceEEEEECCCCCcEEEEEcCCeEEEEEeeeeccCCcccccCCEEEEec-------chhhhhCCHHHHHHH
Confidence 46777777764 3355555554444 22 235799999975 555666777776653
No 33
>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=69.78 E-value=1.1 Score=28.33 Aligned_cols=27 Identities=26% Similarity=0.511 Sum_probs=14.8
Q ss_pred eecCCEEEEEeeeCCCCeEEEEEEcCHh
Q 035938 66 IAAGDIILVGFRIYQDDKADVILINTPD 93 (133)
Q Consensus 66 I~~GD~VlV~~~~~~~~KgdIv~ry~~d 93 (133)
|..||+|+|++.. ....|+|+.....+
T Consensus 11 i~~Gd~v~v~~~~-~~~~gdivv~~~~~ 37 (70)
T PF00717_consen 11 IKDGDIVLVDPSS-EPKDGDIVVVKIDG 37 (70)
T ss_dssp SSTTEEEEEEETS----TTSEEEEEETT
T ss_pred eeCCCEEEEEEcC-CCccCeEEEEEECC
Confidence 4577888877654 33455555554443
No 34
>PF11302 DUF3104: Protein of unknown function (DUF3104); InterPro: IPR021453 This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=69.43 E-value=6.6 Score=27.34 Aligned_cols=29 Identities=24% Similarity=0.258 Sum_probs=21.5
Q ss_pred eEeecCCEEEEEeeeCC----C-C--eEEEEEEcCH
Q 035938 64 VWIAAGDIILVGFRIYQ----D-D--KADVILINTP 92 (133)
Q Consensus 64 iWI~~GD~VlV~~~~~~----~-~--KgdIv~ry~~ 92 (133)
+-+++||+|+|...... + + -|+|++.-.-
T Consensus 4 L~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~gg 39 (75)
T PF11302_consen 4 LSVKPGDTVIVQDEQEVGQKQDKDWWMGQVIHCEGG 39 (75)
T ss_pred cccCCCCEEEEecCccccccCCCCcEEEEEEEEecc
Confidence 45899999999988732 1 1 6999987543
No 35
>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=68.12 E-value=35 Score=23.64 Aligned_cols=48 Identities=17% Similarity=0.046 Sum_probs=29.9
Q ss_pred ccCCC-eEEEEEEEecCCceEEEEEe------------ccccc-------------eeeEeecCCEEEEEeeeCCC
Q 035938 32 IKEEG-QEYAEVLRMLGNGRLRLHWR------------HQAMH-------------KRVWIAAGDIILVGFRIYQD 81 (133)
Q Consensus 32 ~p~e~-e~~g~V~~~lGn~~~~la~I------------pGKmr-------------kriWI~~GD~VlV~~~~~~~ 81 (133)
.|..| -++|+|+.+...... |.| .|-+| .+=.+++||+|......+++
T Consensus 3 ~P~~GDiVig~V~~v~~~~~~--v~I~~v~~~~l~~~~~g~l~~~dv~~~~~d~~~~~~~f~~GDiV~AkVis~~~ 76 (92)
T cd05791 3 LPKVGSIVIARVTRINPRFAK--VDILCVGGRPLKESFRGVIRKEDIRATEKDKVEMYKCFRPGDIVRAKVISLGD 76 (92)
T ss_pred CCCCCCEEEEEEEEEcCCEEE--EEEEEecCeecCCCcccEEEHHHccccccchHHHHhhcCCCCEEEEEEEEcCC
Confidence 46655 489999998754433 222 12222 12345999999999887764
No 36
>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=64.30 E-value=7.7 Score=26.01 Aligned_cols=27 Identities=22% Similarity=0.373 Sum_probs=18.1
Q ss_pred eecCCEEEEEeeeC-C--CCeEEEEEEcCH
Q 035938 66 IAAGDIILVGFRIY-Q--DDKADVILINTP 92 (133)
Q Consensus 66 I~~GD~VlV~~~~~-~--~~KgdIv~ry~~ 92 (133)
++.||+|+|.+... . ...|+|+..+.+
T Consensus 12 l~~GD~vlv~~~~~~~~~~~~Gdivv~~~~ 41 (90)
T TIGR02754 12 LPPGDRIIVVPWLKIFRVPPIGNVVVVRHP 41 (90)
T ss_pred cCCCCEEEEEEccccCCCCCCCeEEEEecC
Confidence 56899999997432 2 234888866654
No 37
>PTZ00248 eukaryotic translation initiation factor 2 subunit 1; Provisional
Probab=63.24 E-value=29 Score=29.92 Aligned_cols=71 Identities=15% Similarity=0.173 Sum_probs=48.8
Q ss_pred eccCCCe-EEEEEEEecCCceE----------EEEEec----cccce-eeEeecCCEEEEEeeeCCCCeEEEEE---EcC
Q 035938 31 IIKEEGQ-EYAEVLRMLGNGRL----------RLHWRH----QAMHK-RVWIAAGDIILVGFRIYQDDKADVIL---INT 91 (133)
Q Consensus 31 ~~p~e~e-~~g~V~~~lGn~~~----------~la~Ip----GKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~---ry~ 91 (133)
.+|+.|+ +.|+|+++...+.| -|.|++ ++.+. +=-++.||.|.|.....+..||.|.. +.+
T Consensus 13 ~~P~~GdvV~g~V~~I~d~GafV~L~EY~gvEGlIhiSElS~~ri~~i~d~vkvGd~v~vkVl~VD~ekg~IdLS~K~v~ 92 (319)
T PTZ00248 13 KFPEEDDLVMVKVVRITEMGAYVSLLEYDDIEGMILMSELSKRRIRSINKLIRVGRHEVVVVLRVDKEKGYIDLSKKRVS 92 (319)
T ss_pred hCCCCCCEEEEEEEEEeCCeEEEEecCCCCcEEEEEHHHhcccccCCHHHhcCCCCEEEEEEEEEeCCCCEEEEEeeecc
Confidence 3576665 78889988887776 233333 33333 34489999999999988888888876 567
Q ss_pred HhHHHHHHHc
Q 035938 92 PDEAKRLKNI 101 (133)
Q Consensus 92 ~dqik~L~k~ 101 (133)
+++.+.+.+.
T Consensus 93 ~~pw~~~~e~ 102 (319)
T PTZ00248 93 PEDIEACEEK 102 (319)
T ss_pred cchHHHHHHh
Confidence 7766666543
No 38
>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=61.06 E-value=16 Score=24.50 Aligned_cols=54 Identities=19% Similarity=0.105 Sum_probs=33.2
Q ss_pred EEEEEEecCCceEEEEEeccccce-e---eE-eecCCEEEEEeeeCCCCeEEEEEEcCHhHHHHHH
Q 035938 39 YAEVLRMLGNGRLRLHWRHQAMHK-R---VW-IAAGDIILVGFRIYQDDKADVILINTPDEAKRLK 99 (133)
Q Consensus 39 ~g~V~~~lGn~~~~la~IpGKmrk-r---iW-I~~GD~VlV~~~~~~~~KgdIv~ry~~dqik~L~ 99 (133)
-++|+++-+++..-+|.+.|--|. . +. +.+||+|||.. |-.+-+.++++++...
T Consensus 6 P~~Vv~v~~~~~~A~v~~~G~~~~V~~~lv~~v~~Gd~VLVHa-------G~Ai~~ideeeA~e~l 64 (68)
T PF01455_consen 6 PGRVVEVDEDGGMAVVDFGGVRREVSLALVPDVKVGDYVLVHA-------GFAIEKIDEEEAEETL 64 (68)
T ss_dssp EEEEEEEETTTTEEEEEETTEEEEEEGTTCTSB-TT-EEEEET-------TEEEEEE-HHHHHHHH
T ss_pred cEEEEEEeCCCCEEEEEcCCcEEEEEEEEeCCCCCCCEEEEec-------ChhheeCCHHHHHHHH
Confidence 467777754455555666664443 1 23 78999999973 5677788888877653
No 39
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=60.21 E-value=13 Score=25.94 Aligned_cols=33 Identities=15% Similarity=0.203 Sum_probs=27.0
Q ss_pred eeeEeecCCEEEEEeeeCCCCeEEEEEEcCHhH
Q 035938 62 KRVWIAAGDIILVGFRIYQDDKADVILINTPDE 94 (133)
Q Consensus 62 kriWI~~GD~VlV~~~~~~~~KgdIv~ry~~dq 94 (133)
.++-|++||.|.|--=++-...|.|..++...+
T Consensus 5 ~~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~~ 37 (83)
T CHL00141 5 KKMHVKIGDTVKIISGSDKGKIGEVLKIIKKSN 37 (83)
T ss_pred eeCcccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 367899999999987766677899999987765
No 40
>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=58.70 E-value=31 Score=23.75 Aligned_cols=27 Identities=26% Similarity=0.354 Sum_probs=20.2
Q ss_pred eecCCEEEEEeeeCCCCeEEEEEEcCHhHHHHHH
Q 035938 66 IAAGDIILVGFRIYQDDKADVILINTPDEAKRLK 99 (133)
Q Consensus 66 I~~GD~VlV~~~~~~~~KgdIv~ry~~dqik~L~ 99 (133)
+.+||||||.. |-.+.+.++++++...
T Consensus 36 ~~vGD~VLVH~-------G~Ai~~ide~eA~e~l 62 (76)
T TIGR00074 36 VKVGDYVLVHV-------GFAISVLDEEEARETL 62 (76)
T ss_pred CCCCCEEEEec-------ChhhhhCCHHHHHHHH
Confidence 68999999975 5566777777776543
No 41
>PRK10409 hydrogenase assembly chaperone; Provisional
Probab=57.53 E-value=30 Score=24.65 Aligned_cols=51 Identities=14% Similarity=0.044 Sum_probs=32.4
Q ss_pred EEEEEEecCCceEEEEEeccccce-ee----------EeecCCEEEEEeeeCCCCeEEEEEEcCHhHHHHH
Q 035938 39 YAEVLRMLGNGRLRLHWRHQAMHK-RV----------WIAAGDIILVGFRIYQDDKADVILINTPDEAKRL 98 (133)
Q Consensus 39 ~g~V~~~lGn~~~~la~IpGKmrk-ri----------WI~~GD~VlV~~~~~~~~KgdIv~ry~~dqik~L 98 (133)
-++|+++-|+ .-+|.+.|--|. .+ .++.||||||.. |--+.+.++++++..
T Consensus 6 P~kVv~i~~~--~A~vd~~Gv~reV~l~Lv~~~~~~~~~~vGDyVLVHa-------GfAi~~ideeeA~et 67 (90)
T PRK10409 6 PGQIRTIDGN--QAKVDVCGIQRDVDLTLVGSCDENGQPRVGQWVLVHV-------GFAMSVINEAEARDT 67 (90)
T ss_pred ceEEEEEcCC--eEEEEcCCeEEEEEEeeecccCCCCccCCCCEEEEec-------ChHHhhCCHHHHHHH
Confidence 3677777664 355555665554 22 257999999985 455666777776543
No 42
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=57.08 E-value=13 Score=31.46 Aligned_cols=65 Identities=14% Similarity=0.152 Sum_probs=49.5
Q ss_pred eccCCCe-EEEEEEEecCCceE----------EEEEec----cccce-eeEeecCCEEEEEeeeCCCCeEEEEEEc---C
Q 035938 31 IIKEEGQ-EYAEVLRMLGNGRL----------RLHWRH----QAMHK-RVWIAAGDIILVGFRIYQDDKADVILIN---T 91 (133)
Q Consensus 31 ~~p~e~e-~~g~V~~~lGn~~~----------~la~Ip----GKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry---~ 91 (133)
.+|++|+ ++|.|.++..-|-+ -+.||+ |..|. |=.+++|-.|++--..-+..+|-|-.-+ +
T Consensus 7 ~~PeeGEiVv~tV~~V~~~GAyv~L~EY~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~rg~IDLSlkrV~ 86 (269)
T COG1093 7 EYPEEGEIVVGTVKQVADYGAYVELDEYPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPKRGHIDLSLKRVT 86 (269)
T ss_pred CCCCCCcEEEEEEEEeeccccEEEeeccCCeeeeEEHHHHHHHHHHHHHHHhhcCCeEEEEEEEEcCCCCeEeeehhhCC
Confidence 3699998 79999999887766 445554 56665 6789999999999999999998776544 4
Q ss_pred HhHH
Q 035938 92 PDEA 95 (133)
Q Consensus 92 ~dqi 95 (133)
.+|.
T Consensus 87 ~~q~ 90 (269)
T COG1093 87 EHQR 90 (269)
T ss_pred HHHH
Confidence 4444
No 43
>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=56.36 E-value=43 Score=20.25 Aligned_cols=50 Identities=16% Similarity=0.152 Sum_probs=31.7
Q ss_pred eEEEEEEEecCCceE--------EEEEeccccce------eeEeecCCEEEEEeeeCCCCeEEEE
Q 035938 37 QEYAEVLRMLGNGRL--------RLHWRHQAMHK------RVWIAAGDIILVGFRIYQDDKADVI 87 (133)
Q Consensus 37 e~~g~V~~~lGn~~~--------~la~IpGKmrk------riWI~~GD~VlV~~~~~~~~KgdIv 87 (133)
.+.|+|+.+...+.| -+++++ .+.- .-+++.||.|.|.....+..++.|.
T Consensus 3 ~~~g~V~~i~~~G~fv~l~~~~~g~~~~~-~l~~~~~~~~~~~~~~Gd~v~v~i~~vd~~~~~i~ 66 (68)
T cd05685 3 VLEGVVTNVTDFGAFVDIGVKQDGLIHIS-KMADRFVSHPSDVVSVGDIVEVKVISIDEERGRIS 66 (68)
T ss_pred EEEEEEEEEecccEEEEcCCCCEEEEEHH-HCCCccccCHHHhcCCCCEEEEEEEEEECCCCEEe
Confidence 467888888777776 233332 2221 1246899999999887776666654
No 44
>cd06462 Peptidase_S24_S26 The S24, S26 LexA/signal peptidase superfamily contains LexA-related and type I signal peptidase families. The S24 LexA protein domains include: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The S26 type I signal peptidase (SPase) family also includes mitochondrial inner membrane protease (IMP)-like members. SPases are essential membrane-bound proteases which function to cleave away the amino-terminal signal peptide from the translocated pre-protein, thus playing a crucial role in the tr
Probab=55.41 E-value=13 Score=23.69 Aligned_cols=28 Identities=29% Similarity=0.671 Sum_probs=20.4
Q ss_pred eecCCEEEEEeeeCCCCeEEEEEEcCHh
Q 035938 66 IAAGDIILVGFRIYQDDKADVILINTPD 93 (133)
Q Consensus 66 I~~GD~VlV~~~~~~~~KgdIv~ry~~d 93 (133)
|..||+|+|.+.......|+|+......
T Consensus 14 i~~gd~v~i~~~~~~~~~G~iv~~~~~~ 41 (84)
T cd06462 14 IPDGDLVLVDKSSYEPKRGDIVVFRLPG 41 (84)
T ss_pred ccCCCEEEEEecCCCCcCCEEEEEEcCC
Confidence 7889999999877656677776555444
No 45
>PF13533 Biotin_lipoyl_2: Biotin-lipoyl like
Probab=55.06 E-value=15 Score=22.59 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=23.0
Q ss_pred EeccccceeeEeecCCEEEEEeeeCCCCeEEEEEEcCHhHHH
Q 035938 55 WRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILINTPDEAK 96 (133)
Q Consensus 55 ~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ry~~dqik 96 (133)
.++|+.. .+.+++||.| ++|++++++..++..
T Consensus 8 ~~~G~V~-~v~V~~G~~V---------kkGd~L~~ld~~~~~ 39 (50)
T PF13533_consen 8 PVSGRVE-SVYVKEGQQV---------KKGDVLLVLDSPDLQ 39 (50)
T ss_pred CCCEEEE-EEEecCCCEE---------cCCCEEEEECcHHHH
Confidence 3445332 5678888887 589999999887665
No 46
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=52.93 E-value=20 Score=26.92 Aligned_cols=32 Identities=13% Similarity=0.209 Sum_probs=27.0
Q ss_pred eeEeecCCEEEEEeeeCCCCeEEEEEEcCHhH
Q 035938 63 RVWIAAGDIILVGFRIYQDDKADVILINTPDE 94 (133)
Q Consensus 63 riWI~~GD~VlV~~~~~~~~KgdIv~ry~~dq 94 (133)
.+-|+.||.|.|--=.+-...|.|+-++...+
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~~ 74 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRG 74 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCCC
Confidence 57899999999987777778899999886655
No 47
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=52.84 E-value=18 Score=24.78 Aligned_cols=31 Identities=13% Similarity=0.148 Sum_probs=25.0
Q ss_pred eEeecCCEEEEEeeeCCCCeEEEEEEcCHhH
Q 035938 64 VWIAAGDIILVGFRIYQDDKADVILINTPDE 94 (133)
Q Consensus 64 iWI~~GD~VlV~~~~~~~~KgdIv~ry~~dq 94 (133)
+-|++||.|.|--=.+-...|.|+..+...+
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~~ 35 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKKN 35 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 5699999999887666667899999987665
No 48
>PF09902 DUF2129: Uncharacterized protein conserved in bacteria (DUF2129); InterPro: IPR016979 This is a group of uncharacterised conserved proteins.
Probab=49.90 E-value=16 Score=24.93 Aligned_cols=22 Identities=14% Similarity=0.534 Sum_probs=19.6
Q ss_pred eEEEEEEcCHhHHHHHHHcCCC
Q 035938 83 KADVILINTPDEAKRLKNIGEL 104 (133)
Q Consensus 83 KgdIv~ry~~dqik~L~k~g~~ 104 (133)
.|=|||-|+--+++.|++.|.+
T Consensus 2 ~gliVyl~~~k~~r~L~kfG~i 23 (71)
T PF09902_consen 2 QGLIVYLYSLKDARQLRKFGDI 23 (71)
T ss_pred eEEEEEEechHhHHhHhhcccE
Confidence 3779999999999999999965
No 49
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=46.02 E-value=53 Score=26.51 Aligned_cols=50 Identities=16% Similarity=0.178 Sum_probs=32.8
Q ss_pred eccCCC-eEEEEEEEecCCceE------EEEEec-----cc-c----ce-eeEeecCCEEEEEeeeCC
Q 035938 31 IIKEEG-QEYAEVLRMLGNGRL------RLHWRH-----QA-M----HK-RVWIAAGDIILVGFRIYQ 80 (133)
Q Consensus 31 ~~p~e~-e~~g~V~~~lGn~~~------~la~Ip-----GK-m----rk-riWI~~GD~VlV~~~~~~ 80 (133)
..|..| -++|+|+...+.+.+ ..|.+| +. . +. +=++++||+|.+.-...+
T Consensus 59 y~P~vGDiViG~V~~i~~~~~~vdI~~~~~g~L~~s~i~~~~~~~d~~~~~~~~~~GDlV~akV~~i~ 126 (235)
T PRK04163 59 YIPKVGDLVIGKVTDVTFSGWEVDINSPYKAYLPVSEVLGRPVNVEGTDLRKYLDIGDYIIAKVKDVD 126 (235)
T ss_pred ccCCCCCEEEEEEEEEeCceEEEEeCCCceeEEEHHHcCCCccccchhhhHhhCCCCCEEEEEEEEEC
Confidence 456664 589999999887665 233333 21 1 11 446799999998876654
No 50
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=44.69 E-value=27 Score=26.99 Aligned_cols=32 Identities=9% Similarity=0.005 Sum_probs=24.0
Q ss_pred eeEeecCCEEEEEeeeCCCCeEEEEEEcCHhH
Q 035938 63 RVWIAAGDIILVGFRIYQDDKADVILINTPDE 94 (133)
Q Consensus 63 riWI~~GD~VlV~~~~~~~~KgdIv~ry~~dq 94 (133)
.+-|+.||.|.|-.=.+-...|.|+.++....
T Consensus 44 s~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~ 75 (143)
T PTZ00194 44 SMPVRKDDEVMVVRGHHKGREGKVTAVYRKKW 75 (143)
T ss_pred cceeecCCEEEEecCCCCCCceEEEEEEcCCC
Confidence 57788899888887766667788888765543
No 51
>TIGR00638 Mop molybdenum-pterin binding domain. This model describes a multigene family of molybdenum-pterin binding proteins of about 70 amino acids in Clostridium pasteurianum, as a tandemly-repeated domain C-terminal to an unrelated domain in ModE, a molybdate transport gene repressor of E. coli, and in single or tandemly paired domains in several related proteins.
Probab=44.66 E-value=46 Score=20.77 Aligned_cols=44 Identities=7% Similarity=-0.041 Sum_probs=24.9
Q ss_pred CCeEEEEEEEecCCce------------EEEEEeccccceeeEeecCCEEEEEeee
Q 035938 35 EGQEYAEVLRMLGNGR------------LRLHWRHQAMHKRVWIAAGDIILVGFRI 78 (133)
Q Consensus 35 e~e~~g~V~~~lGn~~------------~~la~IpGKmrkriWI~~GD~VlV~~~~ 78 (133)
.+++-|+|.++...+. ...|.++.+--..+-+.+||.|.+...+
T Consensus 6 ~N~l~g~I~~i~~~g~~~~v~l~~~~~~~l~a~i~~~~~~~l~l~~G~~v~~~ik~ 61 (69)
T TIGR00638 6 RNQLKGKVVAIEDGDVNAEVDLLLGGGTKLTAVITLESVAELGLKPGKEVYAVIKA 61 (69)
T ss_pred ccEEEEEEEEEEECCCeEEEEEEECCCCEEEEEecHHHHhhCCCCCCCEEEEEEEC
Confidence 4566666666633332 2444555433345567788888776554
No 52
>COG0298 HypC Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=44.38 E-value=63 Score=22.92 Aligned_cols=46 Identities=22% Similarity=0.261 Sum_probs=29.9
Q ss_pred EEEEEEecCCceE------------EEEEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEEcCHhHHHH
Q 035938 39 YAEVLRMLGNGRL------------RLHWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILINTPDEAKR 97 (133)
Q Consensus 39 ~g~V~~~lGn~~~------------~la~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ry~~dqik~ 97 (133)
-|+|+++-+++.. .|..++. =++.||||||.- |--+-+...++++.
T Consensus 6 PgqI~~I~~~~~~A~Vd~gGvkreV~l~Lv~~------~v~~GdyVLVHv-------GfAi~~idEeeAke 63 (82)
T COG0298 6 PGQIVEIDDNNHLAIVDVGGVKREVNLDLVGE------EVKVGDYVLVHV-------GFAMSKIDEEEAKE 63 (82)
T ss_pred ccEEEEEeCCCceEEEEeccEeEEEEeeeecC------ccccCCEEEEEe-------eEEEeecCHHHHHH
Confidence 3677777776642 4444444 467899999873 45566667777654
No 53
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=40.99 E-value=32 Score=24.78 Aligned_cols=31 Identities=16% Similarity=0.212 Sum_probs=24.2
Q ss_pred eEeecCCEEEEEeeeCCCCeEEEEEEcCHhH
Q 035938 64 VWIAAGDIILVGFRIYQDDKADVILINTPDE 94 (133)
Q Consensus 64 iWI~~GD~VlV~~~~~~~~KgdIv~ry~~dq 94 (133)
+-|++||.|.|--=.+-...|.|..++...+
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~~ 33 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKKN 33 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 3589999999887666667899998886655
No 54
>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=39.45 E-value=29 Score=25.97 Aligned_cols=15 Identities=27% Similarity=0.346 Sum_probs=12.8
Q ss_pred eEeecCCEEEEEeee
Q 035938 64 VWIAAGDIILVGFRI 78 (133)
Q Consensus 64 iWI~~GD~VlV~~~~ 78 (133)
+-|+.||+|+|.+.+
T Consensus 2 ~~i~vGd~VlI~~~d 16 (128)
T cd04719 2 LTIEVGDFVLIEGED 16 (128)
T ss_pred eEEecCCEEEEECCC
Confidence 458899999999876
No 55
>PRK02302 hypothetical protein; Provisional
Probab=39.39 E-value=27 Score=24.96 Aligned_cols=23 Identities=13% Similarity=0.369 Sum_probs=20.7
Q ss_pred CeEEEEEEcCHhHHHHHHHcCCC
Q 035938 82 DKADVILINTPDEAKRLKNIGEL 104 (133)
Q Consensus 82 ~KgdIv~ry~~dqik~L~k~g~~ 104 (133)
-.|=|||-|+--+++.|++.|.+
T Consensus 7 R~glIVyl~~~k~~r~LrkfG~I 29 (89)
T PRK02302 7 RIGLIVYLYYNRDARKLSKYGDI 29 (89)
T ss_pred eeEEEEEEeecHhHHHHhhcCcE
Confidence 36899999999999999999965
No 56
>TIGR03635 S17_bact 30S ribosomal protein S17. This model describes the bacterial ribosomal small subunit protein S17, while excluding cytosolic eukaryotic homologs and archaeal homologs. The model finds many, but not, chloroplast and mitochondrial counterparts to bacterial S17.
Probab=39.17 E-value=1.1e+02 Score=20.71 Aligned_cols=21 Identities=10% Similarity=-0.008 Sum_probs=15.2
Q ss_pred EEEEeccccceeeEeecCCEEEEEee
Q 035938 52 RLHWRHQAMHKRVWIAAGDIILVGFR 77 (133)
Q Consensus 52 ~la~IpGKmrkriWI~~GD~VlV~~~ 77 (133)
++||-|.- -.+.||.|.+...
T Consensus 40 ~~aHD~~~-----~~k~GD~V~I~ec 60 (71)
T TIGR03635 40 YHAHDENN-----ECKVGDVVRIIET 60 (71)
T ss_pred EEEECCCC-----CCCCCCEEEEEEc
Confidence 67777743 2789999998763
No 57
>PRK02886 hypothetical protein; Provisional
Probab=38.96 E-value=31 Score=24.63 Aligned_cols=22 Identities=18% Similarity=0.516 Sum_probs=20.1
Q ss_pred eEEEEEEcCHhHHHHHHHcCCC
Q 035938 83 KADVILINTPDEAKRLKNIGEL 104 (133)
Q Consensus 83 KgdIv~ry~~dqik~L~k~g~~ 104 (133)
.|-|||-|+--+++.|++.|.+
T Consensus 6 ~glIVyl~~~k~~r~LrkyG~I 27 (87)
T PRK02886 6 QGIIVWLHSLKQAKQLRKFGNV 27 (87)
T ss_pred eEEEEEEeecHhHHHHhhcCcE
Confidence 6889999999999999999965
No 58
>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=38.61 E-value=20 Score=20.58 Aligned_cols=24 Identities=13% Similarity=0.044 Sum_probs=21.1
Q ss_pred EEeccccceeeEeecCCEEEEEee
Q 035938 54 HWRHQAMHKRVWIAAGDIILVGFR 77 (133)
Q Consensus 54 a~IpGKmrkriWI~~GD~VlV~~~ 77 (133)
..||..+|+.+-+..||.|.+...
T Consensus 9 i~iP~~~r~~l~~~~gd~~~i~~~ 32 (43)
T TIGR01439 9 IVIPKEIREKLGLKEGDRLEVIRV 32 (43)
T ss_pred EEecHHHHHHcCcCCCCEEEEEEe
Confidence 568999999999999999998864
No 59
>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=38.56 E-value=2.1e+02 Score=23.09 Aligned_cols=66 Identities=14% Similarity=0.133 Sum_probs=43.3
Q ss_pred eEEEEEEEecCCceEEEEEec--cccceeeEeecCCEEEEEeeeCC--CCeEEEEEEcCH-------------hHHHHHH
Q 035938 37 QEYAEVLRMLGNGRLRLHWRH--QAMHKRVWIAAGDIILVGFRIYQ--DDKADVILINTP-------------DEAKRLK 99 (133)
Q Consensus 37 e~~g~V~~~lGn~~~~la~Ip--GKmrkriWI~~GD~VlV~~~~~~--~~KgdIv~ry~~-------------dqik~L~ 99 (133)
.+.+.|. +.++....||+| |+|+--+ .+|-.|++++++-. ..+-+++-.+.. .=+.++.
T Consensus 6 RF~~~v~--l~~g~~~~~H~pntGRl~ell--~pG~~v~l~~~~~~~RKt~y~l~av~~~~~~~V~int~~~N~lv~~~l 81 (215)
T PF03749_consen 6 RFLADVE--LDDGEEVTAHCPNTGRLKELL--VPGARVLLSKSDNPKRKTKYTLEAVEKDNGVWVGINTQLPNRLVEEAL 81 (215)
T ss_pred cEEEEEE--ECCCCEEEEEcCCCCcchhhc--cCCCEEEEEECCCCCCCCcEEEEEEEcCCCeEEEEccchHHHHHHHHH
Confidence 3444443 455778889998 6666543 39999999998754 234455444433 3467778
Q ss_pred HcCCCCc
Q 035938 100 NIGELPD 106 (133)
Q Consensus 100 k~g~~P~ 106 (133)
..|.+|.
T Consensus 82 ~~~~i~~ 88 (215)
T PF03749_consen 82 ENGLIPE 88 (215)
T ss_pred HcCCCcc
Confidence 8888885
No 60
>cd06529 S24_LexA-like Peptidase S24 LexA-like proteins are involved in the SOS response leading to the repair of single-stranded DNA within the bacterial cell. This family includes: the lambda repressor CI/C2 family and related bacterial prophage repressor proteins; LexA (EC 3.4.21.88), the repressor of genes in the cellular SOS response to DNA damage; MucA and the related UmuD proteins, which are lesion-bypass DNA polymerases, induced in response to mitogenic DNA damage; RulA, a component of the rulAB locus that confers resistance to UV, and RuvA, which is a component of the RuvABC resolvasome that catalyzes the resolution of Holliday junctions that arise during genetic recombination and DNA repair. The LexA-like proteins contain two-domains: an N-terminal DNA binding domain and a C-terminal domain (CTD) that provides LexA dimerization as well as cleavage activity. They undergo autolysis, cleaving at an Ala-Gly or a Cys-Gly bond, separating the DNA-binding domain from the rest of the
Probab=37.68 E-value=19 Score=23.03 Aligned_cols=26 Identities=23% Similarity=0.376 Sum_probs=14.7
Q ss_pred eecCCEEEEEeeeCCCCeEEEEEEcCH
Q 035938 66 IAAGDIILVGFRIYQDDKADVILINTP 92 (133)
Q Consensus 66 I~~GD~VlV~~~~~~~~KgdIv~ry~~ 92 (133)
|..||+|+|++... ...|+|+-....
T Consensus 14 i~~gd~lii~~~~~-~~~g~i~~~~~~ 39 (81)
T cd06529 14 IPDGDLVLVDPSDT-PRDGDIVVARLD 39 (81)
T ss_pred cCCCCEEEEcCCCC-CCCCCEEEEEEC
Confidence 66777777776543 334554444433
No 61
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=37.19 E-value=49 Score=24.50 Aligned_cols=31 Identities=10% Similarity=0.130 Sum_probs=25.3
Q ss_pred eeEeecCCEEEEEeeeCCCCeEEEEEEcCHh
Q 035938 63 RVWIAAGDIILVGFRIYQDDKADVILINTPD 93 (133)
Q Consensus 63 riWI~~GD~VlV~~~~~~~~KgdIv~ry~~d 93 (133)
.+-|+.||.|.|--=.+....|.|+.++...
T Consensus 39 ~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~~ 69 (114)
T TIGR01080 39 ALPVRKGDKVRIMRGDFKGHEGKVSKVDLKR 69 (114)
T ss_pred cceeecCCEEEEecCCCCCCEEEEEEEEcCC
Confidence 5789999999998777777789999987443
No 62
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=36.91 E-value=39 Score=24.44 Aligned_cols=30 Identities=17% Similarity=0.135 Sum_probs=23.7
Q ss_pred EeecCCEEEEEeeeCCCCeEEEEEEcCHhH
Q 035938 65 WIAAGDIILVGFRIYQDDKADVILINTPDE 94 (133)
Q Consensus 65 WI~~GD~VlV~~~~~~~~KgdIv~ry~~dq 94 (133)
.|+.||.|.|--=.+-...|.|+..+...+
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~~~ 32 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPKTN 32 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcCCC
Confidence 589999999877665566899999887655
No 63
>PF08206 OB_RNB: Ribonuclease B OB domain; InterPro: IPR013223 This domain includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.; PDB: 2ID0_D 2IX1_A 2IX0_A.
Probab=36.12 E-value=67 Score=20.29 Aligned_cols=22 Identities=23% Similarity=0.318 Sum_probs=14.2
Q ss_pred ecCCEEEEEeeeCCCC---eEEEEE
Q 035938 67 AAGDIILVGFRIYQDD---KADVIL 88 (133)
Q Consensus 67 ~~GD~VlV~~~~~~~~---KgdIv~ 88 (133)
..||.|+|.....+.. .|+|+.
T Consensus 33 ~~gD~V~v~i~~~~~~~~~eg~vv~ 57 (58)
T PF08206_consen 33 MDGDKVLVRITPPSRGKRPEGEVVE 57 (58)
T ss_dssp -TT-EEEEEEEESSSEEEEEEEEEE
T ss_pred CCCCEEEEEEecCCCCCCCCEEEEe
Confidence 3699999999983322 477764
No 64
>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=35.55 E-value=41 Score=20.85 Aligned_cols=33 Identities=15% Similarity=0.233 Sum_probs=21.0
Q ss_pred cCCceEEEEEeccccceeeEeecCCEEEEEeee
Q 035938 46 LGNGRLRLHWRHQAMHKRVWIAAGDIILVGFRI 78 (133)
Q Consensus 46 lGn~~~~la~IpGKmrkriWI~~GD~VlV~~~~ 78 (133)
+|++....|+++..-...+-+.+||-|.+..-+
T Consensus 27 ~~~~~~l~a~it~~~~~~L~L~~G~~V~~~ik~ 59 (64)
T PF03459_consen 27 LGGGETLTARITPESAEELGLKPGDEVYASIKA 59 (64)
T ss_dssp ETTSEEEEEEEEHHHHHHCT-STT-EEEEEE-G
T ss_pred ECCCCEEEEEEcHHHHHHcCCCCCCEEEEEEeh
Confidence 344444777887776677888899988877644
No 65
>COG1162 Predicted GTPases [General function prediction only]
Probab=35.35 E-value=96 Score=26.63 Aligned_cols=41 Identities=12% Similarity=0.038 Sum_probs=30.8
Q ss_pred ceEEEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEEcCH
Q 035938 49 GRLRLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILINTP 92 (133)
Q Consensus 49 ~~~~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry~~ 92 (133)
+....|..+|+||+ ..-...||+|.+++..-. |-|..++.+
T Consensus 27 ~~~~~~~~r~~lr~~~~~~vVGD~V~~~~~~~~---g~I~~i~~R 68 (301)
T COG1162 27 GEVYRCRARGNLRKKDLKPVVGDRVVFEDENNN---GVIEKILPR 68 (301)
T ss_pred cceeeeeeecceeccCccccccCeEEEecCCCc---ceEEEEecc
Confidence 33688999999998 488889999999877532 666665543
No 66
>PRK05610 rpsQ 30S ribosomal protein S17; Reviewed
Probab=34.79 E-value=1.3e+02 Score=20.94 Aligned_cols=28 Identities=14% Similarity=0.066 Sum_probs=18.6
Q ss_pred EEEEeccccceeeEeecCCEEEEEe-eeCCCCeE
Q 035938 52 RLHWRHQAMHKRVWIAAGDIILVGF-RIYQDDKA 84 (133)
Q Consensus 52 ~la~IpGKmrkriWI~~GD~VlV~~-~~~~~~Kg 84 (133)
++||-|.- -.+.||+|++.. +|....|.
T Consensus 45 ~~aHD~~n-----~~k~GD~V~I~e~rPlSK~K~ 73 (84)
T PRK05610 45 YHAHDENN-----EAKIGDVVRIMETRPLSKTKR 73 (84)
T ss_pred EEEECCCC-----CCCCCCEEEEEEcccCCCCEE
Confidence 67777753 278999998875 34454443
No 67
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=34.74 E-value=1.3e+02 Score=25.85 Aligned_cols=55 Identities=20% Similarity=0.254 Sum_probs=37.3
Q ss_pred EEEEEEec-CCceE--------EEEEeccccc-eeeEeecCCEEEEEeeeCCCCeEEEEEEcCHhHH
Q 035938 39 YAEVLRML-GNGRL--------RLHWRHQAMH-KRVWIAAGDIILVGFRIYQDDKADVILINTPDEA 95 (133)
Q Consensus 39 ~g~V~~~l-Gn~~~--------~la~IpGKmr-kriWI~~GD~VlV~~~~~~~~KgdIv~ry~~dqi 95 (133)
.+.|++.. .-|.| .+..+.-.=. +.+|..+||.++|.+.- +.+++|.=....+++
T Consensus 78 ~~~Vv~v~~~lGaFlD~Gl~KDl~vp~~elp~~~~~wpq~Gd~l~v~l~~--Dkk~Ri~g~~a~~~~ 142 (287)
T COG2996 78 WLKVVEVNKDLGAFLDWGLPKDLLVPLDELPTLKSLWPQKGDKLLVYLYV--DKKGRIWGTLAIEKI 142 (287)
T ss_pred EEEEEEEcCCcceEEecCCCcceeeehhhcccccccCCCCCCEEEEEEEE--ccCCcEEEEecchhH
Confidence 56677666 44555 4444443323 48999999999998863 678888877766554
No 68
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=34.66 E-value=1e+02 Score=18.26 Aligned_cols=53 Identities=15% Similarity=0.112 Sum_probs=33.2
Q ss_pred eEEEEEEEecCCceE------EEEEeccc-cce------eeEeecCCEEEEEeeeCCCCeEEEEEE
Q 035938 37 QEYAEVLRMLGNGRL------RLHWRHQA-MHK------RVWIAAGDIILVGFRIYQDDKADVILI 89 (133)
Q Consensus 37 e~~g~V~~~lGn~~~------~la~IpGK-mrk------riWI~~GD~VlV~~~~~~~~KgdIv~r 89 (133)
.+.|+|+....++.+ ..|.+|-. +.. .-+++.||.|.|.....+..++.|...
T Consensus 5 ~v~g~V~~v~~~g~~v~i~~~~~g~l~~~~~~~~~~~~~~~~~~~G~~v~~~V~~~~~~~~~i~ls 70 (72)
T smart00316 5 VVEGTVTEITPFGAFVDLGNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEEKGRIILS 70 (72)
T ss_pred EEEEEEEEEEccEEEEEeCCCCEEEEEHHHCCccccCCHHHeecCCCEEEEEEEEEeCCCCEEEEE
Confidence 467888887776665 22333211 111 245899999999988887666666543
No 69
>cd05795 Ribosomal_P0_L10e Ribosomal protein L10 family, P0 and L10e subfamily; composed of eukaryotic 60S ribosomal protein P0 and the archaeal P0 homolog, L10e. P0 or L10e forms a tight complex with multiple copies of the small acidic protein L12(e). This complex forms a stalk structure on the large subunit of the ribosome. The stalk is known to contain the binding site for elongation factors G and Tu (EF-G and EF-Tu, respectively); however, there is disagreement as to whether or not L10 is involved in forming the binding site. The stalk is believed to be associated with GTPase activities in protein synthesis. In a neuroblastoma cell line, L10 has been shown to interact with the SH3 domain of Src and to activate the binding of the Nck1 adaptor protein with skeletal proteins such as the Wiskott-Aldrich Syndrome Protein (WASP) and the WASP-interacting protein (WIP). These eukaryotic and archaeal P0 sequences have an additional C-terminal domain homologous with acidic proteins P1 and P2.
Probab=34.18 E-value=56 Score=25.16 Aligned_cols=43 Identities=19% Similarity=0.215 Sum_probs=32.5
Q ss_pred EEEEeccccce-eeEeecCCEEEEEeeeCCCCeEEEEEEcCHhHHHHHHHcCCCC
Q 035938 52 RLHWRHQAMHK-RVWIAAGDIILVGFRIYQDDKADVILINTPDEAKRLKNIGELP 105 (133)
Q Consensus 52 ~la~IpGKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry~~dqik~L~k~g~~P 105 (133)
+-.-||.++.+ .|+| ..|+++|.. |+ ..+++|++-|+..|.=|
T Consensus 132 ~~lgiptki~~G~i~i-~~d~~v~k~-------G~---~v~~~~A~lL~~l~i~P 175 (175)
T cd05795 132 QALGIPTKIEKGKIEI-ISDVVVVKK-------GE---KVGASEATLLNKLNIKP 175 (175)
T ss_pred HHcCCceEEecCEEEE-ecCeEEecC-------CC---CcCHHHHHHHHHcCCCC
Confidence 55678888888 7888 458888753 43 36899999999988755
No 70
>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=33.91 E-value=13 Score=22.55 Aligned_cols=26 Identities=8% Similarity=0.074 Sum_probs=21.1
Q ss_pred EEEeccccceeeEeecCCEEEEEeee
Q 035938 53 LHWRHQAMHKRVWIAAGDIILVGFRI 78 (133)
Q Consensus 53 la~IpGKmrkriWI~~GD~VlV~~~~ 78 (133)
..+||-.+++.+-|.+||.|.+...+
T Consensus 8 ~v~iPk~~~~~l~l~~Gd~v~i~~~~ 33 (47)
T PF04014_consen 8 QVTIPKEIREKLGLKPGDEVEIEVEG 33 (47)
T ss_dssp EEEE-HHHHHHTTSSTTTEEEEEEET
T ss_pred eEECCHHHHHHcCCCCCCEEEEEEeC
Confidence 35789899998899999999998763
No 71
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=33.89 E-value=73 Score=16.41 Aligned_cols=24 Identities=17% Similarity=0.261 Sum_probs=19.0
Q ss_pred eecCCEEEEEeeeCCCCeEEEEEE
Q 035938 66 IAAGDIILVGFRIYQDDKADVILI 89 (133)
Q Consensus 66 I~~GD~VlV~~~~~~~~KgdIv~r 89 (133)
+.+||.|.|--=++....|.|+..
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i 25 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEV 25 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEE
Confidence 468999999887777778887754
No 72
>PF10017 Methyltransf_33: Histidine-specific methyltransferase, SAM-dependent; InterPro: IPR019257 This domain is found in methyltransferases and various hypothetical proteins.
Probab=33.24 E-value=1.6e+02 Score=21.33 Aligned_cols=38 Identities=16% Similarity=0.196 Sum_probs=26.7
Q ss_pred ceeeEeecCCEEEEEeeeCCCCeEEEEEEcCHhHHHHHHHc-CCCCccc
Q 035938 61 HKRVWIAAGDIILVGFRIYQDDKADVILINTPDEAKRLKNI-GELPDGT 108 (133)
Q Consensus 61 rkriWI~~GD~VlV~~~~~~~~KgdIv~ry~~dqik~L~k~-g~~P~~f 108 (133)
...|-+++|..|.+ +..|+|+++++..|... |+-|...
T Consensus 77 ~~~i~~~~GE~I~~----------e~S~Ky~~~~~~~l~~~aGl~~~~~ 115 (127)
T PF10017_consen 77 DLTIHFKEGERIHT----------ENSYKYSPEEFEALAEQAGLEVEKR 115 (127)
T ss_pred CceeEECCCCEEEE----------EEeeCcCHHHHHHHHHHCCCeeEEE
Confidence 34456666666664 46799999999999877 6655443
No 73
>TIGR02227 sigpep_I_bact signal peptidase I, bacterial type. A related model finds a simlar protein in many archaea and a few bacteria, as well as a microsomal (endoplasmic reticulum) protein in eukaryotes.
Probab=33.22 E-value=40 Score=25.36 Aligned_cols=10 Identities=50% Similarity=0.474 Sum_probs=4.6
Q ss_pred cCCEEEEEee
Q 035938 68 AGDIILVGFR 77 (133)
Q Consensus 68 ~GD~VlV~~~ 77 (133)
.||+|+|...
T Consensus 36 ~Gd~vlv~k~ 45 (163)
T TIGR02227 36 EGDRILVNKF 45 (163)
T ss_pred CCCEEEEEEe
Confidence 4444444443
No 74
>TIGR03027 pepcterm_export putative polysaccharide export protein, PEP-CTERM sytem-associated. This protein family belongs to the larger set of polysaccharide biosynthesis/export proteins described by Pfam model pfam02563. Members of this family are variable in either containing of lacking a 78-residue insert, but appear to fall within a single clade, nevertheless, where the regions in which the gene is found encode components of the PEP-CTERM/EpsH proposed exosortase protein sorting system.
Probab=33.15 E-value=32 Score=25.89 Aligned_cols=21 Identities=14% Similarity=0.276 Sum_probs=16.2
Q ss_pred cccceeeEeecCCEEEEEeee
Q 035938 58 QAMHKRVWIAAGDIILVGFRI 78 (133)
Q Consensus 58 GKmrkriWI~~GD~VlV~~~~ 78 (133)
|.+...+++++||+|.|..+.
T Consensus 144 g~~~~n~~L~~gD~I~Vp~~~ 164 (165)
T TIGR03027 144 GDVTANVELKPGDVLIIPESW 164 (165)
T ss_pred CCccCCceeCCCCEEEEeccc
Confidence 556677889999999887654
No 75
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=33.15 E-value=1.3e+02 Score=18.93 Aligned_cols=52 Identities=15% Similarity=0.111 Sum_probs=31.8
Q ss_pred eEEEEEEEecCCceE-EE---------EEeccccce-e-----eEeecCCEEEEEeeeCCCCeEEEEEE
Q 035938 37 QEYAEVLRMLGNGRL-RL---------HWRHQAMHK-R-----VWIAAGDIILVGFRIYQDDKADVILI 89 (133)
Q Consensus 37 e~~g~V~~~lGn~~~-~l---------a~IpGKmrk-r-----iWI~~GD~VlV~~~~~~~~KgdIv~r 89 (133)
.+.|+|+.+...+.+ .+ +|++ .+.. + =-++.||.|.|.....+..++.|...
T Consensus 6 ~~~g~V~~v~~~g~~v~l~~~~~~~gll~~s-~l~~~~~~~~~~~~~~Gd~v~vkv~~~d~~~~~i~ls 73 (76)
T cd04452 6 LVVVTVKSIADMGAYVSLLEYGNIEGMILLS-ELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGYIDLS 73 (76)
T ss_pred EEEEEEEEEEccEEEEEEcCCCCeEEEEEhH-HcCCcccCCHHHeeCCCCEEEEEEEEEECCCCEEEEE
Confidence 477888888776665 22 2222 1211 1 12589999999888776656665543
No 76
>PRK08059 general stress protein 13; Validated
Probab=33.08 E-value=81 Score=22.75 Aligned_cols=57 Identities=16% Similarity=0.168 Sum_probs=36.5
Q ss_pred CCeEEEEEEEecCCceE--------EEEEec---cccce--eeEeecCCEEEEEeeeCCCCeEEEEEEcC
Q 035938 35 EGQEYAEVLRMLGNGRL--------RLHWRH---QAMHK--RVWIAAGDIILVGFRIYQDDKADVILINT 91 (133)
Q Consensus 35 e~e~~g~V~~~lGn~~~--------~la~Ip---GKmrk--riWI~~GD~VlV~~~~~~~~KgdIv~ry~ 91 (133)
...+.|+|+.+...+.+ -++|++ ...-. .-.++.||.|.|.....+..++.|.....
T Consensus 8 G~iv~G~V~~i~~~G~fV~i~~~~~Gli~~sel~~~~~~~~~~~~~vGD~I~vkI~~id~~~~~i~lslk 77 (123)
T PRK08059 8 GSVVTGKVTGIQPYGAFVALDEETQGLVHISEITHGFVKDIHDFLSVGDEVKVKVLSVDEEKGKISLSIR 77 (123)
T ss_pred CCEEEEEEEEEecceEEEEECCCCEEEEEHHHCCcccccCHHHcCCCCCEEEEEEEEEECCCCeEEEEEE
Confidence 34678899998887776 122222 11111 12468899999998887766777776653
No 77
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=33.02 E-value=62 Score=23.71 Aligned_cols=31 Identities=13% Similarity=0.153 Sum_probs=23.9
Q ss_pred eeEeecCCEEEEEeeeCCCCeEEEEEEcCHh
Q 035938 63 RVWIAAGDIILVGFRIYQDDKADVILINTPD 93 (133)
Q Consensus 63 riWI~~GD~VlV~~~~~~~~KgdIv~ry~~d 93 (133)
.+.|+.||.|+|--=.+-...|.|+-.|...
T Consensus 2 ~~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~ 32 (104)
T COG0198 2 KMKVKKGDTVKVIAGKDKGKEGKVLKVLPKK 32 (104)
T ss_pred CcceecCCEEEEEecCCCCcceEEEEEecCe
Confidence 3568999999997666666678888888764
No 78
>cd05687 S1_RPS1_repeat_ec1_hs1 S1_RPS1_repeat_ec1_hs1: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 1 of the Escherichia coli and Homo sapiens RPS1 (ec1 and hs1, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=32.59 E-value=1.3e+02 Score=18.77 Aligned_cols=22 Identities=23% Similarity=0.380 Sum_probs=16.8
Q ss_pred eecCCEEEEEeeeCCCCeEEEE
Q 035938 66 IAAGDIILVGFRIYQDDKADVI 87 (133)
Q Consensus 66 I~~GD~VlV~~~~~~~~KgdIv 87 (133)
+++||.|.+....++...+.|.
T Consensus 45 ~~~Gd~i~~~i~~~~~~~~~i~ 66 (70)
T cd05687 45 VKVGDEVEVYVLRVEDEEGNVV 66 (70)
T ss_pred CCCCCEEEEEEEEEECCCCeEE
Confidence 6899999998888775555554
No 79
>PF13986 DUF4224: Domain of unknown function (DUF4224)
Probab=31.28 E-value=28 Score=21.66 Aligned_cols=16 Identities=13% Similarity=0.196 Sum_probs=13.7
Q ss_pred EEcCHhHHHHHHHcCC
Q 035938 88 LINTPDEAKRLKNIGE 103 (133)
Q Consensus 88 ~ry~~dqik~L~k~g~ 103 (133)
|+....|++||+++|.
T Consensus 14 ~k~~~~Q~~~L~~~Gi 29 (47)
T PF13986_consen 14 YKRPSKQIRWLRRNGI 29 (47)
T ss_pred CCCHHHHHHHHHHCCC
Confidence 5678899999999983
No 80
>PRK11642 exoribonuclease R; Provisional
Probab=30.10 E-value=5.1e+02 Score=25.02 Aligned_cols=44 Identities=9% Similarity=0.009 Sum_probs=32.1
Q ss_pred ecCCEEEEEeeeCCC----CeEEEEEEcCH-----hHHHHHHHcCCCCccccc
Q 035938 67 AAGDIILVGFRIYQD----DKADVILINTP-----DEAKRLKNIGELPDGTRL 110 (133)
Q Consensus 67 ~~GD~VlV~~~~~~~----~KgdIv~ry~~-----dqik~L~k~g~~P~~f~~ 110 (133)
+.||+|+|+...|.. -.|.|+.++.. -++..+...-.+|.+|..
T Consensus 187 ~~gd~V~v~I~~~p~~~~~~~g~iv~vLG~~~d~~~d~~~il~~~~ip~~Fp~ 239 (813)
T PRK11642 187 RMGFVVVVELTQRPTRRTKAVGKIVEVLGDNMGTGMAVDIALRTHEIPYIWPQ 239 (813)
T ss_pred CCCCEEEEEEecCCCcCCCCCEEEEEEecCCCCcchHHHHHHHHcCCCCCCCH
Confidence 468999999977642 26999999954 356666666667877754
No 81
>TIGR00307 S8e ribosomal protein S8.e. Archaeal and eukaryotic ribosomal protein S8. This model could easily have been split into two models, one for eukaryotic S8 and one for archaeal S8; eukaryotic forms invariably have in insert of about 80 residues that archaeal forms of S8 do not.
Probab=29.93 E-value=1.6e+02 Score=22.34 Aligned_cols=88 Identities=18% Similarity=0.174 Sum_probs=50.5
Q ss_pred CCCCCCCCccccccccCccCCcccceeeeccCC---CeEEEEEEEecCCceEEEEEeccccceeeEeecCCEEEEEeeeC
Q 035938 3 NNKGKGGKKFKNRKRGKNNEGEDQKRELIIKEE---GQEYAEVLRMLGNGRLRLHWRHQAMHKRVWIAAGDIILVGFRIY 79 (133)
Q Consensus 3 ~~~~k~gk~~~n~~r~~~~~~~~~~~el~~p~e---~e~~g~V~~~lGn~~~~la~IpGKmrkriWI~~GD~VlV~~~~~ 79 (133)
+.|-.|||+...+++.|. |-. ..|.+ |+...+.+..+|+|.- +...+=|++=|. |+.
T Consensus 9 ~rk~TGGr~~~~rkKRk~-ElG------r~pa~T~ig~~r~~~vR~rGGn~K------------~Ralr~~~~Nv~-~~~ 68 (127)
T TIGR00307 9 RRKPTGGKYRQARKKRKY-ELG------REPAETKIGERRIKKVRTRGGNKK------------VRLLRDETANVS-DPE 68 (127)
T ss_pred cccCCCCccccccccchh-hcC------CCccccccCccEEEEEEcCCCceE------------EEEEEeeeeEEe-ccc
Confidence 456678875444444443 221 11222 4446666778887763 224444555553 222
Q ss_pred C--CCeEEEEEEcCHhHHHHHHHcCCCCccccc
Q 035938 80 Q--DDKADVILINTPDEAKRLKNIGELPDGTRL 110 (133)
Q Consensus 80 ~--~~KgdIv~ry~~dqik~L~k~g~~P~~f~~ 110 (133)
+ ..|..|+.+...+.=..|.+.+.|-+..-+
T Consensus 69 ~~~t~k~kIl~Vv~NpaN~~yvR~niitKGaII 101 (127)
T TIGR00307 69 TGKVKKVEIAGVVENPANNHYVRRNVITKGAIV 101 (127)
T ss_pred CCeEEEEEEEEEEECCCCHHHhhcCcEecceEE
Confidence 2 338888888877777888888887665533
No 82
>COG0093 RplN Ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=29.70 E-value=2.1e+02 Score=21.63 Aligned_cols=31 Identities=29% Similarity=0.467 Sum_probs=20.8
Q ss_pred cccceeeEeecCCEEEEEeeeCCC----CeEEEEEE
Q 035938 58 QAMHKRVWIAAGDIILVGFRIYQD----DKADVILI 89 (133)
Q Consensus 58 GKmrkriWI~~GD~VlV~~~~~~~----~KgdIv~r 89 (133)
|..+++ +-..||.|.|+.-+--+ +||||++-
T Consensus 26 gg~~r~-~A~vGD~ivvsVKka~P~~~vKkg~V~~A 60 (122)
T COG0093 26 GGSRRR-YAGVGDIIVVSVKKAIPRGMVKKGDVVKA 60 (122)
T ss_pred cccccc-ccCCCCEEEEEEeeccCCcceeccceEEE
Confidence 555555 77889999988876543 36776553
No 83
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=29.50 E-value=1.3e+02 Score=17.95 Aligned_cols=24 Identities=13% Similarity=0.156 Sum_probs=16.5
Q ss_pred eecCCEEEEEeeeCCC---CeEEEEEE
Q 035938 66 IAAGDIILVGFRIYQD---DKADVILI 89 (133)
Q Consensus 66 I~~GD~VlV~~~~~~~---~KgdIv~r 89 (133)
+..||.|++....++. ..|.|+.+
T Consensus 37 ~~~Gd~V~~~i~~~~~~~~~~a~~v~~ 63 (64)
T smart00357 37 LREGDEVEFKVVSPRGGGKPEAENVVK 63 (64)
T ss_pred CCCCCEEEEEEEEccCCCCcEEEEEEe
Confidence 6689999999876422 25676654
No 84
>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=28.86 E-value=43 Score=25.64 Aligned_cols=30 Identities=30% Similarity=0.271 Sum_probs=15.7
Q ss_pred ccccceeeEeecCCEEEEEeeeCC-CCeEEEEE
Q 035938 57 HQAMHKRVWIAAGDIILVGFRIYQ-DDKADVIL 88 (133)
Q Consensus 57 pGKmrkriWI~~GD~VlV~~~~~~-~~KgdIv~ 88 (133)
.+.|.-. +.+||+|++.+..+. ...||||-
T Consensus 38 g~SM~Pt--l~~GD~vlv~~~~~~~~~~GDIVv 68 (158)
T TIGR02228 38 SGSMEPT--FNTGDLILVTGADPNDIQVGDVIT 68 (158)
T ss_pred CCCCcCC--ccCCCEEEEEecccCCCCCCCEEE
Confidence 3444433 356777777764332 34566553
No 85
>PTZ00241 40S ribosomal protein S11; Provisional
Probab=28.59 E-value=1.3e+02 Score=23.63 Aligned_cols=43 Identities=16% Similarity=0.152 Sum_probs=27.2
Q ss_pred EEEEEEEecCCceE----------------------EEEEeccccceeeEeecCCEEEEEe-eeCCCCeE
Q 035938 38 EYAEVLRMLGNGRL----------------------RLHWRHQAMHKRVWIAAGDIILVGF-RIYQDDKA 84 (133)
Q Consensus 38 ~~g~V~~~lGn~~~----------------------~la~IpGKmrkriWI~~GD~VlV~~-~~~~~~Kg 84 (133)
+.|+|+..-.+..+ +.||.|..+. ++.||+|.|.. +|...+|.
T Consensus 71 l~G~VvS~KM~KTIVV~ve~~~~h~kY~K~~kr~kk~~aHd~~~~~----~kvGD~V~I~EcRPLSKTKr 136 (158)
T PTZ00241 71 LRGVVISTKMKRTIIIRRDYLHYVKKYNRYEKRHKNIPVHCSPCFD----VKEGDIVVVGQCRPLSKTVR 136 (158)
T ss_pred EEEEEEEccCCccEEEEEEEEEecCccceEEEeeecEEEeCCccCC----CCCCCEEEEEEcCCCCCcee
Confidence 56777776665443 4555544444 78999998876 45555543
No 86
>PRK03598 putative efflux pump membrane fusion protein; Provisional
Probab=28.19 E-value=1.2e+02 Score=25.03 Aligned_cols=46 Identities=11% Similarity=-0.041 Sum_probs=33.2
Q ss_pred eEEEEEEEecCCceEEEEEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEEcCHhHH
Q 035938 37 QEYAEVLRMLGNGRLRLHWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILINTPDEA 95 (133)
Q Consensus 37 e~~g~V~~~lGn~~~~la~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ry~~dqi 95 (133)
.+.|+|. .....+-+.++|.. ..+++.+||.| .+|++++++...+.
T Consensus 34 ~v~G~v~---~~~i~v~a~~~G~V-~~i~v~~Gd~V---------~kG~~L~~ld~~~~ 79 (331)
T PRK03598 34 TLYGNVD---IRTVNLGFRVGGRL-ASLAVDEGDAV---------KAGQVLGELDAAPY 79 (331)
T ss_pred EEEEEEe---eEEEEeecccCcEE-EEEEcCCCCEE---------cCCCEEEEEChHHH
Confidence 4566665 12223777888877 47889999997 58999999987754
No 87
>PLN00207 polyribonucleotide nucleotidyltransferase; Provisional
Probab=27.92 E-value=1.3e+02 Score=29.66 Aligned_cols=57 Identities=21% Similarity=0.217 Sum_probs=42.4
Q ss_pred ccCCCeEE--EEEEEecCCceE--------EEEEeccccce-e-----eEeecCCEEEEEeeeCCCCeEEEEEEc
Q 035938 32 IKEEGQEY--AEVLRMLGNGRL--------RLHWRHQAMHK-R-----VWIAAGDIILVGFRIYQDDKADVILIN 90 (133)
Q Consensus 32 ~p~e~e~~--g~V~~~lGn~~~--------~la~IpGKmrk-r-----iWI~~GD~VlV~~~~~~~~KgdIv~ry 90 (133)
.|+.|++| |+|+.+...|.| -|+||+ .+.. + =-++.||.|.|.....+. ++.|.+.+
T Consensus 750 ~~~vG~iy~~g~V~~I~~FGaFVeL~~g~EGLVHIS-eLs~~rv~~~~dv~kvGD~V~VkVi~ID~-~grI~LSl 822 (891)
T PLN00207 750 VPTVGDIYRNCEIKSIAPYGAFVEIAPGREGLCHIS-ELSSNWLAKPEDAFKVGDRIDVKLIEVND-KGQLRLSR 822 (891)
T ss_pred CcCCCcEEECcEEEEEeccEEEEEeCCCCEEEEEhh-hcCCccccCHHHhcCCCCEEEEEEEEECC-CCcEEEEE
Confidence 36789999 599999988887 677776 3321 1 237889999999998876 67777665
No 88
>PF14237 DUF4339: Domain of unknown function (DUF4339)
Probab=27.69 E-value=66 Score=19.19 Aligned_cols=21 Identities=24% Similarity=0.322 Sum_probs=18.0
Q ss_pred cCHhHHHHHHHcCCCCccccc
Q 035938 90 NTPDEAKRLKNIGELPDGTRL 110 (133)
Q Consensus 90 y~~dqik~L~k~g~~P~~f~~ 110 (133)
|+.+|++.|.+.|.+..+..+
T Consensus 14 ~s~~el~~l~~~g~i~~~tlv 34 (45)
T PF14237_consen 14 FSLEELRQLISSGEIDPDTLV 34 (45)
T ss_pred cCHHHHHHHHHcCCCCCCCeE
Confidence 688999999999999887654
No 89
>PRK01202 glycine cleavage system protein H; Provisional
Probab=27.64 E-value=36 Score=25.13 Aligned_cols=28 Identities=21% Similarity=0.566 Sum_probs=16.7
Q ss_pred eeEee-cCCEEEEEeeeCC-CCeEEEEEEc
Q 035938 63 RVWIA-AGDIILVGFRIYQ-DDKADVILIN 90 (133)
Q Consensus 63 riWI~-~GD~VlV~~~~~~-~~KgdIv~ry 90 (133)
++||+ .|+.+.|.+++|- ..=|+|+|.=
T Consensus 14 H~Wv~~~~~~~~vGit~~a~~~lG~i~~v~ 43 (127)
T PRK01202 14 HEWVRVEGDTATVGITDHAQEQLGDIVFVE 43 (127)
T ss_pred cEEEEEcCCEEEEeeCHHHHhhcCCeeEEE
Confidence 57776 3566777776663 3345666554
No 90
>PF15057 DUF4537: Domain of unknown function (DUF4537)
Probab=27.62 E-value=1e+02 Score=22.56 Aligned_cols=39 Identities=21% Similarity=0.192 Sum_probs=24.2
Q ss_pred EEEEEEEecCCceE---------------EEEEeccccceeeEeecCCEEEEEeeeC
Q 035938 38 EYAEVLRMLGNGRL---------------RLHWRHQAMHKRVWIAAGDIILVGFRIY 79 (133)
Q Consensus 38 ~~g~V~~~lGn~~~---------------~la~IpGKmrkriWI~~GD~VlV~~~~~ 79 (133)
--|+|.+.+..+++ -+..+.+.| +--++.||+||+- |+-
T Consensus 15 Y~GtV~~~~~~~~~lV~f~~~~~~~v~~~~iI~~~~~~--~~~L~~GD~VLA~-~~~ 68 (124)
T PF15057_consen 15 YPGTVKKCVSSGQFLVEFDDGDTQEVPISDIIALSDAM--RHSLQVGDKVLAP-WEP 68 (124)
T ss_pred EeEEEEEccCCCEEEEEECCCCEEEeChHHeEEccCcc--cCcCCCCCEEEEe-cCc
Confidence 35777777755554 122223333 5668899999998 553
No 91
>TIGR03077 not_gcvH glycine cleavage protein H-like protein, Chlamydial. The H protein (GcvH) of the glycine cleavage system shuttles the methylamine group of glycine from the P protein to the T protein. Most Chlamydia but lack the P and T proteins, and have a single homolog of GcvH that appears deeply split from canonical GcvH in molecular phylogenetic trees. The protein family modeled here is observed the Chlamydial GcvH homolog, so far always seen as part of a two-gene operon, downstream of a member of the uncharacterized protein family TIGR03076. The function of this protein is unknown.
Probab=27.61 E-value=38 Score=24.63 Aligned_cols=30 Identities=23% Similarity=0.632 Sum_probs=23.6
Q ss_pred eeEee--cCCEEEEEeeeC-CCCeEEEEEEcCH
Q 035938 63 RVWIA--AGDIILVGFRIY-QDDKADVILINTP 92 (133)
Q Consensus 63 riWI~--~GD~VlV~~~~~-~~~KgdIv~ry~~ 92 (133)
++|++ .++.+.|.+++| +..-|+|+|.=.+
T Consensus 6 H~Wv~~~~~~~~~vGiT~~aq~~lG~i~~v~lp 38 (110)
T TIGR03077 6 HVWILPIHSQVVRLGLTSRMQENLGNILHIDLP 38 (110)
T ss_pred cEEEEEcCCCEEEEeeCHHHHHhcCCEEEEECC
Confidence 79998 367999999998 4567899988443
No 92
>COG2002 AbrB Regulators of stationary/sporulation gene expression [Transcription]
Probab=27.23 E-value=64 Score=22.16 Aligned_cols=38 Identities=13% Similarity=0.062 Sum_probs=28.1
Q ss_pred EEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEEcCHh
Q 035938 54 HWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILINTPD 93 (133)
Q Consensus 54 a~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ry~~d 93 (133)
.-||-..|+++=|++||.|.+.-...+.. -|+-+|.+.
T Consensus 16 IvIPkeiR~~lgi~~Gd~lei~~~~~~~~--ivl~k~~~~ 53 (89)
T COG2002 16 IVIPKEIREALGIKEGDVLEIIVDGDGGR--IVLKKYKPA 53 (89)
T ss_pred EEecHHHHHHhCCCCCCEEEEEEeCCCCE--EEEEECCcc
Confidence 34899999999999999999887653322 555666654
No 93
>cd04717 BAH_polybromo BAH, or Bromo Adjacent Homology domain, as present in polybromo and yeast RSC1/2. The human polybromo protein (BAF180) is a component of the SWI/SNF chromatin-remodeling complex PBAF. It is thought that polybromo participates in transcriptional regulation. Saccharomyces cerevisiae RSC1 and RSC2 are part of the 15-subunit nucleosome remodeling RSC complex. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=26.87 E-value=75 Score=22.63 Aligned_cols=45 Identities=13% Similarity=-0.006 Sum_probs=28.4
Q ss_pred eEeecCCEEEEEeeeC-------------CC----CeEEEEEEcCHhHHHHHHHcCCCCccc
Q 035938 64 VWIAAGDIILVGFRIY-------------QD----DKADVILINTPDEAKRLKNIGELPDGT 108 (133)
Q Consensus 64 iWI~~GD~VlV~~~~~-------------~~----~KgdIv~ry~~dqik~L~k~g~~P~~f 108 (133)
+.++.||.|+|...+- .+ ....+.|=|.++|+......-..|.+.
T Consensus 2 ~~~~vGD~V~v~~~~~~~~~~i~~I~~i~~~~~g~~~~~~~Wf~rP~et~~~~~~~~~~~Ev 63 (121)
T cd04717 2 LQYRVGDCVYVANPEDPSKPIIFRIERLWKDEDGEKFFFGCWFYRPEETFHEPTRKFYKNEV 63 (121)
T ss_pred CEEECCCEEEEeCCCCCCCCEEEEEeEEEECCCCCEEEEEEEEeChHHccCCCccccccCce
Confidence 3578899999875431 11 135677778888887655544455554
No 94
>PRK08577 hypothetical protein; Provisional
Probab=26.77 E-value=58 Score=23.74 Aligned_cols=24 Identities=13% Similarity=-0.014 Sum_probs=19.9
Q ss_pred EEeccccceeeEeecCCEEEEEee
Q 035938 54 HWRHQAMHKRVWIAAGDIILVGFR 77 (133)
Q Consensus 54 a~IpGKmrkriWI~~GD~VlV~~~ 77 (133)
..||-.+|+.+-|++||.|.+...
T Consensus 15 i~ip~~~r~~l~~~~g~~~~~~~~ 38 (136)
T PRK08577 15 ITIPLEIREALGIREGMYVLLIAD 38 (136)
T ss_pred EEecHHHHHHcCcCCCCEEEEEEE
Confidence 358999999999999999987643
No 95
>COG1097 RRP4 RNA-binding protein Rrp4 and related proteins (contain S1 domain and KH domain) [Translation, ribosomal structure and biogenesis]
Probab=25.97 E-value=2.6e+02 Score=23.37 Aligned_cols=50 Identities=12% Similarity=0.114 Sum_probs=33.2
Q ss_pred cC-CCeEEEEEEEecCCceE------EEEE-----ecccc-----c-eeeEeecCCEEEEEeeeCCCC
Q 035938 33 KE-EGQEYAEVLRMLGNGRL------RLHW-----RHQAM-----H-KRVWIAAGDIILVGFRIYQDD 82 (133)
Q Consensus 33 p~-e~e~~g~V~~~lGn~~~------~la~-----IpGKm-----r-kriWI~~GD~VlV~~~~~~~~ 82 (133)
|+ .+.++|+|+.....+.. .-|. ++++. + .+=.+..||+|+..-..++.+
T Consensus 62 P~~gD~VIG~I~~v~~~~W~VDI~sp~~A~L~ls~~~~r~~~~~~~~~r~~l~vGD~v~AkV~~vd~~ 129 (239)
T COG1097 62 PEVGDVVIGKIIEVGPSGWKVDIGSPYPALLSLSDFLRRKFENAEKDLRPFLNVGDLVYAKVVDVDRD 129 (239)
T ss_pred CCCCCEEEEEEEEEcccceEEEcCCccceEeehhhhhcccccccccccccccccCCEEEEEEEEccCC
Confidence 44 56799999999887665 2222 22222 1 145678999999998887643
No 96
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=25.75 E-value=1.7e+02 Score=18.13 Aligned_cols=51 Identities=10% Similarity=0.061 Sum_probs=32.1
Q ss_pred eEEEEEEEecCCceE--------EEEEec---c-ccce-eeEeecCCEEEEEeeeCCCCeEEEE
Q 035938 37 QEYAEVLRMLGNGRL--------RLHWRH---Q-AMHK-RVWIAAGDIILVGFRIYQDDKADVI 87 (133)
Q Consensus 37 e~~g~V~~~lGn~~~--------~la~Ip---G-Kmrk-riWI~~GD~VlV~~~~~~~~KgdIv 87 (133)
.+.|.|+++...+.+ -++|++ . ...+ .=-++.||.|.+.....+..++.|.
T Consensus 3 ~v~g~V~~v~~~Gv~V~l~~~~~G~v~~s~l~~~~~~~~~~~~~~Gd~v~~~v~~~d~~~~~i~ 66 (68)
T cd05707 3 VVRGFVKNIANNGVFVTLGRGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGRIE 66 (68)
T ss_pred EEEEEEEEEECccEEEEeCCCCEEEEEHHHCCchhhcCHhhccCCCCEEEEEEEEEeCCCCEEe
Confidence 467888888777765 122221 1 1111 1226889999999888887777764
No 97
>PRK07252 hypothetical protein; Provisional
Probab=25.44 E-value=2.7e+02 Score=20.24 Aligned_cols=55 Identities=11% Similarity=0.111 Sum_probs=36.3
Q ss_pred CeEEEEEEEecCCceE--------EEEEec---c-ccce-eeEeecCCEEEEEeeeCCCCeEEEEEEc
Q 035938 36 GQEYAEVLRMLGNGRL--------RLHWRH---Q-AMHK-RVWIAAGDIILVGFRIYQDDKADVILIN 90 (133)
Q Consensus 36 ~e~~g~V~~~lGn~~~--------~la~Ip---G-Kmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry 90 (133)
..+.|+|+.+...+.| -++|++ . .+.. .=-++.||.|.|.....+..+++|...+
T Consensus 5 ~iv~G~V~~V~~~G~fVei~~~~~GllhiseLs~~~~~~~~~~~~vGD~V~VkI~~iD~~~~ri~lSl 72 (120)
T PRK07252 5 DKLKGTITGIKPYGAFVALENGTTGLIHISEIKTGFIDNIHQLLKVGEEVLVQVVDFDEYTGKASLSL 72 (120)
T ss_pred CEEEEEEEEEeCcEEEEEECCCCEEEEEHHHcCCccccChhhccCCCCEEEEEEEEEeCCCCEEEEEE
Confidence 4578889888887776 222222 1 1111 1136889999999998887788887664
No 98
>PRK10861 signal peptidase I; Provisional
Probab=25.23 E-value=60 Score=27.96 Aligned_cols=27 Identities=26% Similarity=0.230 Sum_probs=16.5
Q ss_pred EEEEecc-ccceeeEeecCCEEEEEeeeCC
Q 035938 52 RLHWRHQ-AMHKRVWIAAGDIILVGFRIYQ 80 (133)
Q Consensus 52 ~la~IpG-KmrkriWI~~GD~VlV~~~~~~ 80 (133)
...+||| .|.-. +..||+|+|....|.
T Consensus 83 ~~~~Ips~SM~PT--L~~GD~IlVnK~~yg 110 (324)
T PRK10861 83 EPFQIPSGSMMPT--LLIGDFILVEKFAYG 110 (324)
T ss_pred EEEEECCCcCcCc--ccCCCEEEEEEeecC
Confidence 5566664 44433 357788888777663
No 99
>cd04714 BAH_BAHCC1 BAH, or Bromo Adjacent Homology domain, as present in mammalian BAHCC1 and similar proteins. BAHCC1 stands for BAH domain and coiled-coil containing 1. BAH domains are found in a variety of proteins playing roles in transcriptional silencing and the remodeling of chromatin. It is assumed that in most or all of these instances the BAH domain mediates protein-protein interactions.
Probab=25.04 E-value=86 Score=22.64 Aligned_cols=27 Identities=15% Similarity=0.011 Sum_probs=17.8
Q ss_pred eEEEEEEcCHhHHHHHHHcCCCCcccc
Q 035938 83 KADVILINTPDEAKRLKNIGELPDGTR 109 (133)
Q Consensus 83 KgdIv~ry~~dqik~L~k~g~~P~~f~ 109 (133)
...+.|=|.++|+...++....|.+..
T Consensus 38 ~~~v~WfyrPeEt~~~~~~~~~~~EvF 64 (121)
T cd04714 38 VVRVKWYYRPEETKGGRKPNHGEKELF 64 (121)
T ss_pred EEEEEEEEcHHHccCcccccCCCCceE
Confidence 467788888998876555545555443
No 100
>PRK12423 LexA repressor; Provisional
Probab=25.00 E-value=48 Score=25.80 Aligned_cols=38 Identities=13% Similarity=0.049 Sum_probs=22.4
Q ss_pred EEEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEEcC
Q 035938 53 LHWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILINT 91 (133)
Q Consensus 53 la~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ry~ 91 (133)
...+.|-=.----|..||+|+|++. .+...|+|+-...
T Consensus 116 ~l~V~GdSM~~~~i~~Gd~viv~~~-~~~~~Gdivv~~~ 153 (202)
T PRK12423 116 LLQVQGDSMIDDGILDGDLVGVHRS-PEARDGQIVVARL 153 (202)
T ss_pred EEEEecCcCCCCCcCCCCEEEEeCC-CcCCCCCEEEEEE
Confidence 3444443221235789999999976 3444677665443
No 101
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=25.00 E-value=2.3e+02 Score=23.45 Aligned_cols=59 Identities=15% Similarity=0.102 Sum_probs=37.8
Q ss_pred ccCCC-eEEEEEEEecCCceE-E---------EEEec----cccce-eeEeecCCEEEEEeeeCCCCeEEEEEEc
Q 035938 32 IKEEG-QEYAEVLRMLGNGRL-R---------LHWRH----QAMHK-RVWIAAGDIILVGFRIYQDDKADVILIN 90 (133)
Q Consensus 32 ~p~e~-e~~g~V~~~lGn~~~-~---------la~Ip----GKmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry 90 (133)
+|..| .+.|+|+.+...+.| . ++|++ ++++. +=.++.||.|.|.....+..++.|...+
T Consensus 5 ~P~~GdiV~G~V~~I~~~G~fV~L~e~~gieGlI~iSEls~~~i~~i~~~~kvGd~V~vkVi~VD~~k~~I~LSl 79 (262)
T PRK03987 5 WPEEGELVVGTVKEVKDFGAFVTLDEYPGKEGFIHISEVASGWVKNIRDHVKEGQKVVCKVIRVDPRKGHIDLSL 79 (262)
T ss_pred CCCCCCEEEEEEEEEECCEEEEEECCCCCcEEEEEHHHcCcccccCHHHhCCCCCEEEEEEEEEecccCeEEEEE
Confidence 45555 478999998887776 2 22222 11111 1246899999999988887777665443
No 102
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=24.89 E-value=1.9e+02 Score=18.23 Aligned_cols=17 Identities=18% Similarity=0.022 Sum_probs=13.0
Q ss_pred eecCCEEEEEeeeCCCC
Q 035938 66 IAAGDIILVGFRIYQDD 82 (133)
Q Consensus 66 I~~GD~VlV~~~~~~~~ 82 (133)
+++||.|.+-....+..
T Consensus 47 ~~~Gd~i~~kVl~~d~~ 63 (70)
T cd05702 47 FKIGQKIKARVIGGHDA 63 (70)
T ss_pred CCCCCEEEEEEEEEeCc
Confidence 57899998888776644
No 103
>PRK10276 DNA polymerase V subunit UmuD; Provisional
Probab=24.76 E-value=47 Score=24.31 Aligned_cols=37 Identities=16% Similarity=0.240 Sum_probs=21.1
Q ss_pred EEEEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEE
Q 035938 52 RLHWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILI 89 (133)
Q Consensus 52 ~la~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~r 89 (133)
+..+++|-=.----|..||+|+|++.. ....|+|+-.
T Consensus 52 f~l~V~GdSM~~~~I~~GD~liVd~~~-~~~~Gdivv~ 88 (139)
T PRK10276 52 YFVKASGDSMIDAGISDGDLLIVDSAI-TASHGDIVIA 88 (139)
T ss_pred EEEEEecCCCCCCCCCCCCEEEEECCC-CCCCCCEEEE
Confidence 444555442221237899999999764 2334665543
No 104
>PF08541 ACP_syn_III_C: 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III C terminal ; InterPro: IPR013747 This domain is found on 3-Oxoacyl-[acyl-carrier-protein (ACP)] synthase III 2.3.1.41 from EC, the enzyme responsible for initiating the chain of reactions of the fatty acid synthase in plants and bacteria. ; GO: 0016747 transferase activity, transferring acyl groups other than amino-acyl groups, 0008610 lipid biosynthetic process; PDB: 3IL3_A 1ZOW_C 3GWE_B 3GWA_B 1UB7_B 3LED_B 2EBD_A 1HNJ_A 2EFT_B 1HN9_B ....
Probab=24.07 E-value=1e+02 Score=20.31 Aligned_cols=26 Identities=19% Similarity=-0.066 Sum_probs=18.4
Q ss_pred EeecCCEEEEEeeeCCCCeEEEEEEc
Q 035938 65 WIAAGDIILVGFRIYQDDKADVILIN 90 (133)
Q Consensus 65 WI~~GD~VlV~~~~~~~~KgdIv~ry 90 (133)
-+++||.|++--......-|-++++|
T Consensus 65 ~~~~Gd~vl~~~~G~G~~~~~~~~~~ 90 (90)
T PF08541_consen 65 RIKPGDRVLLVGFGAGFSWGAAVLRW 90 (90)
T ss_dssp SSCTTEEEEEEEEETTTEEEEEEEE-
T ss_pred CCCCCCEEEEEEEEhhheeEEEEEEC
Confidence 36689988887776666667777765
No 105
>TIGR02063 RNase_R ribonuclease R. This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in E. coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Scoring between trusted and noise cutoffs to the model are shorter, divergent forms from the Chlamydiae, and divergent forms from the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans.
Probab=23.76 E-value=4.5e+02 Score=24.56 Aligned_cols=44 Identities=18% Similarity=0.126 Sum_probs=30.0
Q ss_pred ecCCEEEEEeeeCC----CCeEEEEEEcC-----HhHHHHHHHcCCCCccccc
Q 035938 67 AAGDIILVGFRIYQ----DDKADVILINT-----PDEAKRLKNIGELPDGTRL 110 (133)
Q Consensus 67 ~~GD~VlV~~~~~~----~~KgdIv~ry~-----~dqik~L~k~g~~P~~f~~ 110 (133)
..||+|+|+...|. .-.|.|+.++. .-++..+...--+|.+|..
T Consensus 173 ~~g~~v~v~i~~~p~~~~~~~g~i~~~lg~~~d~~~~~~~il~~~~i~~~f~~ 225 (709)
T TIGR02063 173 EEGDKVLVEITKYPDRNRPAIGKVVEILGHADDPGIDILIIIRKHGIPYEFPE 225 (709)
T ss_pred CCCCEEEEEEccCCCCCCCceEEEEEEeCCCCcccchHHHHHHHcCcCCCCCH
Confidence 46899999996553 23799999994 3455655555556776654
No 106
>PRK00347 putative DNA-binding transcriptional regulator; Reviewed
Probab=23.74 E-value=3.2e+02 Score=22.31 Aligned_cols=68 Identities=13% Similarity=0.106 Sum_probs=41.4
Q ss_pred CCeEEEEEEEecCCceEEEEEec--cccceeeEeecCCEEEEEeeeCCCCe----EEEEEEc-----------CHhHHHH
Q 035938 35 EGQEYAEVLRMLGNGRLRLHWRH--QAMHKRVWIAAGDIILVGFRIYQDDK----ADVILIN-----------TPDEAKR 97 (133)
Q Consensus 35 e~e~~g~V~~~lGn~~~~la~Ip--GKmrkriWI~~GD~VlV~~~~~~~~K----gdIv~ry-----------~~dqik~ 97 (133)
.+...|.|. ++++...+||+| |+|+-- +.+|-.|++.+.+-..-| -+.+... ...=+.+
T Consensus 16 ~nRF~~~V~--~~~g~~~~aH~pntGRl~el--l~pG~~v~l~~~~~pkrK~~~~~~l~~~~~~~~V~int~~~N~l~~~ 91 (234)
T PRK00347 16 YKRFLADVE--LDDGEELTAHCPNTGRMTGL--LTPGNTVWLSTSDNPKRKYPHTWELTETPNGRLIGINTALPNKLVEE 91 (234)
T ss_pred cCCEEEEEE--ECCCCEEEEEcCCCCCChhh--ccCCCEEEEEECCCCCCccceEEEEEEeCCCeEEEECcccHHHHHHH
Confidence 355666663 345667889997 777763 339999999987643222 2232221 1233567
Q ss_pred HHHcCCCCc
Q 035938 98 LKNIGELPD 106 (133)
Q Consensus 98 L~k~g~~P~ 106 (133)
+.+.|.+|.
T Consensus 92 ~l~~~~i~~ 100 (234)
T PRK00347 92 ALEAGLIPE 100 (234)
T ss_pred HHHcCCCcc
Confidence 777888885
No 107
>COG0809 QueA S-adenosylmethionine:tRNA-ribosyltransferase-isomerase (queuine synthetase) [Translation, ribosomal structure and biogenesis]
Probab=23.57 E-value=5.2e+02 Score=22.86 Aligned_cols=76 Identities=14% Similarity=0.135 Sum_probs=45.9
Q ss_pred CCCeEEEEEEEecCCceE-EEEEeccccce--eeEeecCCEEEEEeeeCCCCeEEEEEEcC--HhH--HHHHHHcCCCCc
Q 035938 34 EEGQEYAEVLRMLGNGRL-RLHWRHQAMHK--RVWIAAGDIILVGFRIYQDDKADVILINT--PDE--AKRLKNIGELPD 106 (133)
Q Consensus 34 ~e~e~~g~V~~~lGn~~~-~la~IpGKmrk--riWI~~GD~VlV~~~~~~~~KgdIv~ry~--~dq--ik~L~k~g~~P~ 106 (133)
..+.+...+.+.+++++. .+++...+++. ++|+-.| +.+...+-. +-|..+-++. ... ...|-+.|++|-
T Consensus 75 ~g~~vEvll~~~~~~~~w~al~~~~kr~k~G~~i~f~~~--l~a~v~e~~-~~g~~~l~F~~~~~~~l~e~L~~~G~~PL 151 (348)
T COG0809 75 SGGKVEVLLERRLDDNRWLALIKPSKRLKAGDEIYFGDG--LKATVLERL-EHGLRLLEFDYEGIFSLLELLEKYGEMPL 151 (348)
T ss_pred CCceEEEEEEeecCCCcEEEEeccccCCCCCCEEEeCCC--ceEEEEEec-CCceEEEEEecCCchhHHHHHHHcCCCCC
Confidence 357788888998888776 77777778776 6777665 222222222 2223333333 222 468888999765
Q ss_pred cccccc
Q 035938 107 GTRLNE 112 (133)
Q Consensus 107 ~f~~~e 112 (133)
--.+..
T Consensus 152 PPYI~~ 157 (348)
T COG0809 152 PPYIKR 157 (348)
T ss_pred CcccCC
Confidence 444444
No 108
>PF03537 Glyco_hydro_114: Glycoside-hydrolase family GH114; InterPro: IPR004352 Eighty-one archaeal-like genes, ranging in size from 4-20kb, are clustered in 15 regions of the Thermotoga maritima genome []. Conservation of gene order between T. maritima and Archaea in many of these regions suggests that lateral gene transfer may have occurred between thermophilic Eubacteria and Archaea []. One of the T. maritima sequences (hypothetical protein TM1410) shares similarity with Methanocaldococcus jannaschii (Methanococcus jannaschii) hypothetical protein MJ1477 and with hypothetical protein DR0705 from Deinococcus radiodurans. The sequences are characterised by relatively variable N- and C-terminal domains, and a more conserved central domain. They share no similarity with any other known, functionally or structurally characterised proteins. ; PDB: 2AAM_F.
Probab=23.10 E-value=88 Score=20.84 Aligned_cols=16 Identities=31% Similarity=0.345 Sum_probs=11.2
Q ss_pred cCHhHHHHHHHcCCCC
Q 035938 90 NTPDEAKRLKNIGELP 105 (133)
Q Consensus 90 y~~dqik~L~k~g~~P 105 (133)
+++++|..|++.|...
T Consensus 37 ~~~~~I~~L~~~G~~v 52 (74)
T PF03537_consen 37 FSKEEIARLKAQGKKV 52 (74)
T ss_dssp --HHHHHHHHHTT-EE
T ss_pred CCHHHHHHHHHCCCEE
Confidence 7799999999999443
No 109
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=22.53 E-value=2.4e+02 Score=25.21 Aligned_cols=58 Identities=19% Similarity=0.207 Sum_probs=40.9
Q ss_pred CCCeEEEEEEEecCCceE--------EEEEecc-----ccce-eeEeecCCEEEEEeeeCCCCeEEEEEEcC
Q 035938 34 EEGQEYAEVLRMLGNGRL--------RLHWRHQ-----AMHK-RVWIAAGDIILVGFRIYQDDKADVILINT 91 (133)
Q Consensus 34 ~e~e~~g~V~~~lGn~~~--------~la~IpG-----Kmrk-riWI~~GD~VlV~~~~~~~~KgdIv~ry~ 91 (133)
....+.|+|+.+...+.| -++|++- +..+ .-+++.||.|.|.....+..++.|..-+.
T Consensus 292 ~G~~v~G~V~~v~~~G~fV~l~~gv~Glvh~sels~~~~~~~~~~~~~~Gd~v~vkVl~iD~e~~ri~Ls~K 363 (491)
T PRK13806 292 AGDKVTGKVVRLAPFGAFVEILPGIEGLVHVSEMSWTRRVNKPEDVVAPGDAVAVKIKDIDPAKRRISLSLR 363 (491)
T ss_pred CCCEEEEEEEEEeCceEEEEeCCCcEEEEEHHHcCcccccCCHHHcCCCCCEEEEEEEEEEccCCEEEEEEe
Confidence 345689999999988887 3555542 1122 34789999999999888777777766553
No 110
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=22.17 E-value=1.9e+02 Score=17.25 Aligned_cols=50 Identities=16% Similarity=0.143 Sum_probs=29.7
Q ss_pred eEEEEEEEecCCceE--------EEEEeccccce------eeEeecCCEEEEEeeeCCCCeEEEEE
Q 035938 37 QEYAEVLRMLGNGRL--------RLHWRHQAMHK------RVWIAAGDIILVGFRIYQDDKADVIL 88 (133)
Q Consensus 37 e~~g~V~~~lGn~~~--------~la~IpGKmrk------riWI~~GD~VlV~~~~~~~~KgdIv~ 88 (133)
.+.|+|+.+...+.+ -+.|++ .+.. .=+++.||.|.|.....+. .+.|..
T Consensus 3 ~~~g~V~~i~~~g~~v~i~~~~~g~l~~~-~l~~~~~~~~~~~~~~Gd~v~v~v~~~~~-~~~i~l 66 (69)
T cd05692 3 VVEGTVTRLKPFGAFVELGGGISGLVHIS-QIAHKRVKDVKDVLKEGDKVKVKVLSIDA-RGRISL 66 (69)
T ss_pred EEEEEEEEEEeeeEEEEECCCCEEEEEhH-HcCCcccCCHHHccCCCCEEEEEEEEECC-CCcEEE
Confidence 467788887776665 222222 1111 1247889999998876665 555543
No 111
>PF04717 Phage_base_V: Phage-related baseplate assembly protein; InterPro: IPR006531 This domain occurs in a family of phage (and bacteriocin) proteins related to the phage P2 V gene product, which forms the small spike at the tip of the tail []. Homologs in general are annotated as baseplate assembly protein V. At least one member is encoded within a region of Pectobacterium carotovorum (Erwinia carotovora) described as a bacteriocin, a phage tail-derived module able to kill bacteria closely related to the host strain. It is also found in Vgr-related proteins. Genes encoding type VI secretion systems (T6SS) are widely distributed in pathogenic Gram-negative bacterial species. In Vibrio cholerae, T6SS have been found to secrete three related proteins extracellularly, VgrG-1, VgrG-2, and VgrG-3. VgrG-1 can covalently cross-link actin in vitro, and this activity was used to demonstrate that V. cholerae can translocate VgrG-1 into macrophages by a T6SS-dependent mechanism. VgrG-related proteins likely assemble into a trimeric complex that is analogous to that formed by the two trimeric proteins gp27 and gp5 that make up the baseplate "tail spike" of Escherichia coli bacteriophage T4. The VgrG components of the T6SS apparatus might assemble a "cell-puncturing device" analogous to phage tail spikes to deliver effector protein domains through membranes of target host cells []. Gp5 is an integral component of the virion baseplate of bacteriophage T4. T4 Gp5 consists of 3 domains connected via long linkers: the N-terminal oligosaccharide/oligonucleotide-binding (OB)-fold domain, the middle lysozyme domain, and the C-terminal triplestranded-helix. The equivalent of the Gp5 OB-fold domain in the structure of VgrG is the domain of unknown function comprising residues 380-470 and conserved in all known VgrGs. This entry represents the OB-fold domain which consists of a 5-stranded antiparallel-barrel with a Greek-key topology [].; PDB: 3AQJ_C 3QR8_A 2P5Z_X.
Probab=21.66 E-value=2.4e+02 Score=18.35 Aligned_cols=43 Identities=19% Similarity=0.005 Sum_probs=23.9
Q ss_pred EEEEeccccceeeEeecCCEEEEEeeeCCCCeEEEEEEcCHhH
Q 035938 52 RLHWRHQAMHKRVWIAAGDIILVGFRIYQDDKADVILINTPDE 94 (133)
Q Consensus 52 ~la~IpGKmrkriWI~~GD~VlV~~~~~~~~KgdIv~ry~~dq 94 (133)
.++.-.|..+-...-..||-|+|.....+...+-|+-.+..++
T Consensus 30 ~~~~~ag~~g~~~~P~iGeqV~v~~~~Gd~~~~~vlg~l~~~~ 72 (79)
T PF04717_consen 30 VLQPRAGGWGFWFPPEIGEQVLVLFPGGDPERPVVLGSLYSDA 72 (79)
T ss_dssp E--S-BSSSB------TT-EEEEEEGGCTTTSEEEEEEE--SS
T ss_pred eeehhccCCeeEccCCCCcEEEEEccCCcCCCCEEEEEECCCC
Confidence 3444556455567778999999999777788999998876553
No 112
>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=21.58 E-value=89 Score=21.29 Aligned_cols=14 Identities=21% Similarity=0.128 Sum_probs=11.5
Q ss_pred EeecCCEEEEEeee
Q 035938 65 WIAAGDIILVGFRI 78 (133)
Q Consensus 65 WI~~GD~VlV~~~~ 78 (133)
-++.||+|+|.+.+
T Consensus 2 ~~~vGD~V~v~~~~ 15 (119)
T PF01426_consen 2 TYKVGDFVYVKPDD 15 (119)
T ss_dssp EEETTSEEEEECTS
T ss_pred EEeCCCEEEEeCCC
Confidence 46789999998876
No 113
>PRK00624 glycine cleavage system protein H; Provisional
Probab=21.36 E-value=60 Score=23.78 Aligned_cols=30 Identities=23% Similarity=0.609 Sum_probs=23.2
Q ss_pred eeEeec--CCEEEEEeeeCC-CCeEEEEEEcCH
Q 035938 63 RVWIAA--GDIILVGFRIYQ-DDKADVILINTP 92 (133)
Q Consensus 63 riWI~~--GD~VlV~~~~~~-~~KgdIv~ry~~ 92 (133)
+.|++. ++.+.|.+++|- ..-|+|+|.=.+
T Consensus 8 H~Wv~~~~~~~~~vGiT~~a~~~lG~i~~v~lp 40 (114)
T PRK00624 8 HVWIEPIHSRIVRLGLTSKMQENLGNILHIDLP 40 (114)
T ss_pred cEEEEEcCCCEEEEeeCHHHHHhcCCEEEEECC
Confidence 799983 579999999984 557888887433
No 114
>CHL00051 rps12 ribosomal protein S12
Probab=20.84 E-value=2e+02 Score=21.84 Aligned_cols=32 Identities=22% Similarity=0.156 Sum_probs=24.2
Q ss_pred EEEEEEecCCceEEEEEeccccceeeEeecCCEEEEE
Q 035938 39 YAEVLRMLGNGRLRLHWRHQAMHKRVWIAAGDIILVG 75 (133)
Q Consensus 39 ~g~V~~~lGn~~~~la~IpGKmrkriWI~~GD~VlV~ 75 (133)
+|+|. |-|+..++|+|||-=. -+.+-|.|||.
T Consensus 52 varVr--Lsngk~v~AyIPGeGh---nlqehs~VLvr 83 (123)
T CHL00051 52 VARVR--LTSGFEITAYIPGIGH---NLQEHSVVLVR 83 (123)
T ss_pred EEEEE--ccCCCEEEEEcCCCCc---cccccCEEEEe
Confidence 44443 4677789999998764 68888888887
No 115
>COG4471 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=20.78 E-value=95 Score=22.35 Aligned_cols=22 Identities=18% Similarity=0.527 Sum_probs=20.0
Q ss_pred eEEEEEEcCHhHHHHHHHcCCC
Q 035938 83 KADVILINTPDEAKRLKNIGEL 104 (133)
Q Consensus 83 KgdIv~ry~~dqik~L~k~g~~ 104 (133)
.|-|||-|+--+++.|++-|.+
T Consensus 7 ~givVYl~~~K~aRqLrkfG~v 28 (90)
T COG4471 7 QGIVVYLYSLKDARQLRKFGDV 28 (90)
T ss_pred eEEEEEEehhhhhHHHHhcCCE
Confidence 6889999999999999999865
No 116
>PF13437 HlyD_3: HlyD family secretion protein
Probab=20.46 E-value=2.7e+02 Score=18.50 Aligned_cols=53 Identities=17% Similarity=0.139 Sum_probs=39.7
Q ss_pred CCeEEEEEEEecCCceEEEEEeccccceeeEee-cCCEEEEEeeeCCC--CeEEEEEEcC
Q 035938 35 EGQEYAEVLRMLGNGRLRLHWRHQAMHKRVWIA-AGDIILVGFRIYQD--DKADVILINT 91 (133)
Q Consensus 35 e~e~~g~V~~~lGn~~~~la~IpGKmrkriWI~-~GD~VlV~~~~~~~--~KgdIv~ry~ 91 (133)
.|+.++.|... +....-+.+|.+... +|+ .|+-|.+...++.. -.|.|.+...
T Consensus 23 ~g~~l~~i~~~--~~~~v~~~v~~~~~~--~i~~~g~~v~v~~~~~~~~~~~g~V~~I~~ 78 (105)
T PF13437_consen 23 AGQPLAEIVDT--DDLWVEAYVPEKDIA--RIKDPGQKVTVRLDPGPEKTIEGKVSSISP 78 (105)
T ss_pred CCCEEEEEEcc--ceEEEEEEEChHhhc--ceEeCCCEEEEEECCCCCcEEEEEEEEEeC
Confidence 57778887775 556688888877664 454 99999999875543 3899998887
No 117
>PF09866 DUF2093: Uncharacterized protein conserved in bacteria (DUF2093); InterPro: IPR018661 This family of various hypothetical prokaryotic proteins has no known function.
Probab=20.23 E-value=83 Score=19.68 Aligned_cols=13 Identities=8% Similarity=0.235 Sum_probs=11.0
Q ss_pred eecCCEEEEEeee
Q 035938 66 IAAGDIILVGFRI 78 (133)
Q Consensus 66 I~~GD~VlV~~~~ 78 (133)
+++|++|++..+.
T Consensus 2 l~pG~~V~CAVTg 14 (42)
T PF09866_consen 2 LSPGSFVRCAVTG 14 (42)
T ss_pred ccCCCEEEEEeeC
Confidence 5799999999875
No 118
>PF01938 TRAM: TRAM domain; InterPro: IPR002792 The TRAM (after TRM2 and miaB) domain is a 60-70-residue-long module that is found in: Two distinct classes of tRNA-modifying enzymes, namely uridine methylases of the TRM2 family and enzymes of the miaB family that are involved in 2- methylthioadenine formation In several other proteins associated with the translation machinery In a family of small uncharacterised archaeal proteins that are predicted to have a role in the regulation of tRNA modification and/or translation The TRAM domain can be found alone or in association with other domains, such as the catalytic biotin/lipoate synthetase-like domain, the RNA methylase domain, the ribosomal S2 domain and the eIF2-beta domain. The TRAM domain is predicted to bind tRNA and deliver the RNA-modifying enzymatic domain to their targets []. Secondary structure prediction indicates that the TRAM domain adopts a simple beta-barrel fold. The conservation pattern of the TRAM domain consists primarily of small and hydrophobic residues that correspond to five beta-strands in the predicted secondary structure [].; PDB: 1YEZ_A 2BH2_A 1UWV_A 1YVC_A.
Probab=20.03 E-value=2.3e+02 Score=17.49 Aligned_cols=29 Identities=7% Similarity=0.241 Sum_probs=18.0
Q ss_pred EEEEeccccceeeEeec--CCEEEEEeeeCCCC--eEEEE
Q 035938 52 RLHWRHQAMHKRVWIAA--GDIILVGFRIYQDD--KADVI 87 (133)
Q Consensus 52 ~la~IpGKmrkriWI~~--GD~VlV~~~~~~~~--KgdIv 87 (133)
+.+.++|. .+ ||+|.|........ .|+++
T Consensus 29 ~~V~v~~~-------~~~iG~~v~v~I~~~~~~~l~G~~v 61 (61)
T PF01938_consen 29 KVVFVPGG-------LPLIGEFVKVRITKAKKNYLFGELV 61 (61)
T ss_dssp EEEEETT---------T--TEEEEEEEEEE-SSEEEEEEE
T ss_pred eEEEECCC-------CCCCCCEEEEEEEEeeCCcEEEEEC
Confidence 55666665 45 99999998775533 66664
Done!