Query 029796
Match_columns 187
No_of_seqs 106 out of 331
Neff 4.8
Searched_HMMs 46136
Date Fri Mar 29 03:47:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/029796.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/029796hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PLN00036 40S ribosomal protein 100.0 2.4E-77 5.3E-82 517.9 23.3 182 5-187 80-261 (261)
2 PTZ00118 40S ribosomal protein 100.0 6.8E-77 1.5E-81 515.3 23.5 181 5-186 80-260 (262)
3 PTZ00223 40S ribosomal protein 100.0 1.3E-76 2.7E-81 515.9 23.6 181 5-186 77-258 (273)
4 PRK04313 30S ribosomal protein 100.0 1.9E-69 4.1E-74 463.6 21.8 160 5-165 76-237 (237)
5 COG1471 RPS4A Ribosomal protei 100.0 1.9E-67 4E-72 448.8 20.4 162 5-167 79-241 (241)
6 KOG0378 40S ribosomal protein 100.0 9.5E-66 2.1E-70 440.4 14.5 181 5-186 80-260 (263)
7 PF00900 Ribosomal_S4e: Riboso 100.0 1E-36 2.3E-41 222.0 10.3 77 19-95 1-77 (77)
8 PF00467 KOW: KOW motif; Inte 97.1 0.00053 1.2E-08 41.8 3.2 31 102-135 1-31 (32)
9 smart00739 KOW KOW (Kyprides, 97.0 0.00064 1.4E-08 39.1 2.7 27 99-125 1-27 (28)
10 TIGR01080 rplX_A_E ribosomal p 95.0 0.06 1.3E-06 42.2 5.4 40 96-138 38-77 (114)
11 PRK01191 rpl24p 50S ribosomal 93.2 0.25 5.4E-06 39.2 5.6 38 97-137 43-80 (120)
12 PRK12281 rplX 50S ribosomal pr 91.9 0.26 5.7E-06 35.9 3.9 38 98-138 5-42 (76)
13 CHL00141 rpl24 ribosomal prote 91.1 0.35 7.6E-06 35.7 4.0 39 97-138 6-44 (83)
14 PRK00004 rplX 50S ribosomal pr 90.4 0.39 8.4E-06 36.9 3.7 37 98-137 3-39 (105)
15 PTZ00194 60S ribosomal protein 89.4 0.82 1.8E-05 37.3 5.1 57 98-154 45-105 (143)
16 TIGR01079 rplX_bact ribosomal 86.6 1.2 2.5E-05 34.3 4.1 28 99-126 3-30 (104)
17 PF13051 DUF3912: Protein of u 81.2 4.5 9.8E-05 28.7 4.9 49 102-154 5-54 (68)
18 COG2163 RPL14A Ribosomal prote 69.5 5.1 0.00011 32.0 3.0 26 100-125 5-30 (125)
19 COG0198 RplX Ribosomal protein 69.4 7.8 0.00017 30.0 3.9 29 98-126 3-31 (104)
20 PRK02290 3-dehydroquinate synt 66.0 30 0.00065 32.0 7.6 63 26-91 256-328 (344)
21 PF14001 YdfZ: YdfZ protein 65.4 12 0.00026 26.8 3.9 42 99-144 9-56 (64)
22 PTZ00065 60S ribosomal protein 64.6 8.1 0.00018 31.1 3.3 32 100-135 8-39 (130)
23 PF01959 DHQS: 3-dehydroquinat 61.2 21 0.00045 33.2 5.7 75 26-116 266-345 (354)
24 PRK04333 50S ribosomal protein 60.1 11 0.00023 28.0 3.0 33 99-135 3-35 (84)
25 KOG1784 Small Nuclear ribonucl 55.8 25 0.00054 26.9 4.4 60 59-122 10-75 (96)
26 PRK14898 DNA-directed RNA poly 52.9 76 0.0017 32.5 8.6 78 8-87 111-195 (858)
27 cd03706 mtEFTU_III Domain III 52.7 83 0.0018 22.5 6.7 40 79-122 52-92 (93)
28 PTZ00471 60S ribosomal protein 50.1 17 0.00038 29.4 2.9 24 100-123 5-28 (134)
29 PF07076 DUF1344: Protein of u 47.9 43 0.00093 23.7 4.3 35 56-90 11-49 (61)
30 cd03704 eRF3c_III This family 47.7 58 0.0013 23.9 5.3 48 75-123 56-108 (108)
31 TIGR00405 L26e_arch ribosomal 47.4 36 0.00079 26.6 4.4 26 100-125 87-112 (145)
32 cd02899 PLAT_SR Scavenger rece 47.2 84 0.0018 24.2 6.2 61 100-173 41-108 (109)
33 PF04773 FecR: FecR protein; 46.8 97 0.0021 21.6 9.7 67 54-120 3-76 (98)
34 PRK08559 nusG transcription an 45.4 37 0.0008 27.2 4.2 29 98-126 93-121 (153)
35 PF01588 tRNA_bind: Putative t 44.4 60 0.0013 23.7 4.9 21 116-136 2-24 (95)
36 PRK05609 nusG transcription an 44.2 27 0.00058 28.0 3.3 29 97-125 124-152 (181)
37 cd05741 Ig_CEACAM_D1_like Firs 40.6 47 0.001 22.8 3.7 31 25-55 50-80 (92)
38 TIGR00922 nusG transcription t 40.5 31 0.00067 27.5 3.1 28 98-125 118-145 (172)
39 PF12961 DUF3850: Domain of Un 39.4 30 0.00065 25.2 2.5 18 71-88 21-38 (72)
40 TIGR01955 RfaH transcriptional 38.6 51 0.0011 25.8 4.0 83 34-124 51-133 (159)
41 cd05892 Ig_Myotilin_C C-termin 36.3 76 0.0016 22.0 4.2 35 20-54 27-63 (75)
42 KOG3401 60S ribosomal protein 34.8 31 0.00068 28.3 2.2 52 91-142 40-94 (145)
43 cd03705 EF1_alpha_III Domain I 34.7 86 0.0019 22.7 4.4 35 78-115 59-100 (104)
44 cd01234 PH_CADPS CADPS (Ca2+-d 34.6 28 0.00061 27.5 1.8 42 31-77 21-62 (117)
45 PF00924 MS_channel: Mechanose 33.8 49 0.0011 26.6 3.2 38 99-146 60-97 (206)
46 PF01176 eIF-1a: Translation i 33.8 1.4E+02 0.003 20.5 5.1 43 47-91 5-54 (65)
47 TIGR00739 yajC preprotein tran 33.4 1E+02 0.0022 22.6 4.6 32 100-140 38-69 (84)
48 KOG1999 RNA polymerase II tran 33.3 69 0.0015 33.6 4.8 37 87-125 449-485 (1024)
49 COG1792 MreC Cell shape-determ 31.1 3.8E+02 0.0082 23.8 11.9 36 117-155 234-270 (284)
50 smart00536 AXH domain in Ataxi 30.9 1.6E+02 0.0035 23.3 5.6 77 63-156 7-84 (116)
51 TIGR01956 NusG_myco NusG famil 30.8 57 0.0012 29.1 3.3 30 96-125 202-231 (258)
52 PRK09014 rfaH transcriptional 30.7 81 0.0018 24.9 4.0 26 99-124 109-134 (162)
53 KOG1708 Mitochondrial/chloropl 30.6 83 0.0018 27.6 4.2 29 98-126 71-99 (236)
54 COG1917 Uncharacterized conser 30.4 80 0.0017 23.8 3.8 56 47-112 41-98 (131)
55 COG1188 Ribosome-associated he 30.1 65 0.0014 24.9 3.2 35 55-93 29-63 (100)
56 KOG1999 RNA polymerase II tran 29.7 1E+02 0.0022 32.5 5.3 54 100-155 582-636 (1024)
57 cd04478 RPA2_DBD_D RPA2_DBD_D: 29.2 2.1E+02 0.0045 20.2 6.6 54 14-67 8-72 (95)
58 PF09285 Elong-fact-P_C: Elong 28.8 1.4E+02 0.003 20.6 4.3 36 59-95 19-54 (56)
59 cd05792 S1_eIF1AD_like S1_eIF1 28.8 1.3E+02 0.0028 22.1 4.4 38 48-88 3-48 (78)
60 KOG2333 Uncharacterized conser 28.6 9.8 0.00021 37.2 -1.9 16 1-16 544-560 (614)
61 PF02239 Cytochrom_D1: Cytochr 28.3 4E+02 0.0087 24.2 8.5 46 54-101 74-119 (369)
62 cd01723 LSm4 The eukaryotic Sm 28.2 1.3E+02 0.0028 21.3 4.3 49 116-166 24-73 (76)
63 PF05709 Sipho_tail: Phage tai 27.6 2.7E+02 0.0059 22.5 6.7 54 57-111 159-233 (249)
64 PRK09612 rpl2p 50S ribosomal p 27.0 4.4E+02 0.0095 23.2 9.3 71 76-154 86-158 (238)
65 COG0250 NusG Transcription ant 26.8 68 0.0015 26.7 3.0 30 96-125 120-149 (178)
66 PF10781 DSRB: Dextransucrase 26.8 1.5E+02 0.0032 21.0 4.2 29 80-108 2-35 (62)
67 PTZ00141 elongation factor 1- 26.7 3.7E+02 0.0081 25.1 8.2 52 78-130 381-436 (446)
68 PF00717 Peptidase_S24: Peptid 26.6 1.4E+02 0.0029 19.6 4.0 28 76-110 8-35 (70)
69 PF11717 Tudor-knot: RNA bindi 26.1 2E+02 0.0043 19.0 4.9 37 100-136 1-38 (55)
70 PF12791 RsgI_N: Anti-sigma fa 26.0 1.4E+02 0.003 19.6 3.9 35 57-91 3-38 (56)
71 PF07569 Hira: TUP1-like enhan 25.2 2.2E+02 0.0047 24.1 5.9 56 20-75 20-93 (219)
72 KOG3418 60S ribosomal protein 24.9 70 0.0015 26.0 2.6 24 100-123 5-28 (136)
73 cd03707 EFTU_III Domain III of 24.4 2.6E+02 0.0056 19.6 6.2 27 79-108 52-78 (90)
74 PRK05585 yajC preprotein trans 24.0 2.6E+02 0.0056 21.4 5.5 40 100-149 53-92 (106)
75 cd04708 BAH_plantDCM_II BAH, o 23.8 87 0.0019 26.9 3.2 44 78-127 7-54 (202)
76 KOG3586 TBX1 and related T-box 23.5 1.2E+02 0.0026 29.0 4.2 99 10-114 128-251 (437)
77 PRK10708 hypothetical protein; 23.4 1.7E+02 0.0036 20.7 3.9 29 80-108 2-35 (62)
78 TIGR03318 YdfZ_fam putative se 23.4 56 0.0012 23.4 1.6 41 100-144 11-57 (65)
79 PLN00208 translation initiatio 23.1 4.1E+02 0.0088 21.8 6.8 69 19-91 7-83 (145)
80 COG5164 SPT5 Transcription elo 22.8 1.1E+02 0.0025 29.9 4.0 43 81-125 123-165 (607)
81 PF06487 SAP18: Sin3 associate 22.1 89 0.0019 24.6 2.7 50 21-89 69-120 (120)
82 PF11476 TgMIC1: Toxoplasma go 22.0 2.8E+02 0.006 22.2 5.4 72 56-127 3-91 (137)
83 smart00306 HintN Hint (Hedgeho 22.0 2.7E+02 0.0059 19.1 8.3 55 101-155 23-78 (100)
84 PF04246 RseC_MucC: Positive r 21.8 75 0.0016 24.5 2.2 61 32-94 6-67 (135)
85 PF08529 NusA_N: NusA N-termin 21.8 1.7E+02 0.0037 22.4 4.2 48 39-91 46-96 (122)
86 cd04456 S1_IF1A_like S1_IF1A_l 21.7 2.4E+02 0.0052 20.4 4.7 32 59-90 12-50 (78)
87 KOG4547 WD40 repeat-containing 21.4 2.6E+02 0.0056 27.6 6.2 94 20-123 110-221 (541)
88 PF14505 DUF4438: Domain of un 21.0 69 0.0015 28.6 2.0 59 102-172 60-118 (258)
89 PF03321 GH3: GH3 auxin-respon 21.0 92 0.002 29.8 3.1 68 14-88 307-380 (528)
90 PF00659 POLO_box: POLO box du 20.6 2.8E+02 0.0061 18.7 5.0 19 56-74 10-28 (68)
91 PF06068 TIP49: TIP49 C-termin 20.5 77 0.0017 30.0 2.4 40 56-95 139-187 (398)
92 PTZ00329 eukaryotic translatio 20.3 4.6E+02 0.01 21.7 6.6 70 19-91 7-83 (155)
93 cd05774 Ig_CEACAM_D1 First imm 20.1 1.5E+02 0.0033 22.1 3.6 32 24-55 62-93 (105)
94 PF11396 DUF2874: Protein of u 20.0 1.1E+02 0.0025 19.9 2.5 22 13-34 39-60 (61)
No 1
>PLN00036 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=2.4e-77 Score=517.86 Aligned_cols=182 Identities=80% Similarity=1.285 Sum_probs=178.9
Q ss_pred eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796 5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT 84 (187)
Q Consensus 5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT 84 (187)
++||||||||||||++||||||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+|||
T Consensus 80 ~~fPvG~mDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrni~~~d~~~k~~Dt 159 (261)
T PLN00036 80 KTYPAGFMDVISIPKTNENFRLLYDTKGRFRLHRINDEEAKFKLCKVRKIQFGQKGIPYLNTHDGRTIRYPDPLIKANDT 159 (261)
T ss_pred CCCCCceeEEEEEcCCCCeEEEEECCCceEEEEEcChHHccceEEEEEEEEEecCCeEEEEecCCceeccCCCccccCCE
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEcc
Q 029796 85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP 164 (187)
Q Consensus 85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp 164 (187)
|+|+||+++|++|+||++||+||||||+|+|++|+|.+|+++++++++||++|++|++|+|+++||||||++++|||+||
T Consensus 160 v~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~~~~~~~~iV~i~d~~g~~F~T~~~~vfvIG~~~kp~isLp 239 (261)
T PLN00036 160 IKIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNREKHKGSFEIIHVKDATGHEFATRLGNVFVIGKGTKPWISLP 239 (261)
T ss_pred EEEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998899999999
Q ss_pred CCceeeeehhHHHHHHHHHHHhC
Q 029796 165 KGKGIKLSIIEEARKRQAAQAAA 187 (187)
Q Consensus 165 ~~~Gi~~~~~e~~~~~~~~~~~~ 187 (187)
+++|||++++|| |++++++.++
T Consensus 240 ~~~gi~~~~~e~-r~~~~~~~~~ 261 (261)
T PLN00036 240 KGKGIKLSIIEE-ARKRLAAGQA 261 (261)
T ss_pred CCCCcccchHHH-HHHhhhhhcC
Confidence 999999999999 9999988764
No 2
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=6.8e-77 Score=515.33 Aligned_cols=181 Identities=55% Similarity=0.929 Sum_probs=178.0
Q ss_pred eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796 5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT 84 (187)
Q Consensus 5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT 84 (187)
++||||||||||||+||||||||||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+|||
T Consensus 80 ~~fPvG~mDVIsI~kt~e~yRvl~D~kGr~~l~~I~~eeA~~KLcKV~~k~~~~gg~~~l~~hDGrni~~~d~~ik~~Dt 159 (262)
T PTZ00118 80 CTYPVGFMDVVSLTKTNEYFRLLYDTKGRFVPHKITNEEAKYKLCRVKKTFLGPKEVSIAVTHDGRTIRYVHPDVKVGDS 159 (262)
T ss_pred CCCCCceeEEEEEcCCCCeEEEEECCCccEEEEEcCHHHhcceEEEEeEEEECCCCeEEEEecCcceeccCCCcccCCCE
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEcc
Q 029796 85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP 164 (187)
Q Consensus 85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp 164 (187)
|+|+||+++|++|+||++||+||||||+|+|++|+|.+++++++++++|||+|++|++|+|+++||||||++++|||+||
T Consensus 160 v~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~~~~~~~~V~i~d~~g~~F~T~~~~vfvIG~~~kp~islp 239 (262)
T PTZ00118 160 LRLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEKHPGSFDLIHVKDSRGKTFATRLSNVFVIGVGTKPYVSLP 239 (262)
T ss_pred EEEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCcEEEEEeCCCCeEEEEeeeEEEEccCCCeeEeCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999998899999999
Q ss_pred CCceeeeehhHHHHHHHHHHHh
Q 029796 165 KGKGIKLSIIEEARKRQAAQAA 186 (187)
Q Consensus 165 ~~~Gi~~~~~e~~~~~~~~~~~ 186 (187)
++||||+|++|| |++++++++
T Consensus 240 ~~kgi~~~~~e~-~~~~~~~~~ 260 (262)
T PTZ00118 240 RERGIKKDIIEE-RRNRLAKAL 260 (262)
T ss_pred CCCCccccHHHH-HHHHHHHHh
Confidence 999999999999 999998865
No 3
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=100.00 E-value=1.3e-76 Score=515.89 Aligned_cols=181 Identities=45% Similarity=0.742 Sum_probs=177.4
Q ss_pred eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796 5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT 84 (187)
Q Consensus 5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT 84 (187)
++||||||||||||++|||||||||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+|||
T Consensus 77 ~~~PvGlMDVIsI~kt~e~yRvl~D~kGrf~l~~I~~eeA~~KLcKV~~k~~~~gG~~ql~~hDGrnI~~~d~~~k~~Dt 156 (273)
T PTZ00223 77 GKYPAGFMDVVEIPKTGDRFRILYDVKGRFALVKVSEAEAQIKLMKVVNVYTATGRIPVAVTHDGHRIRYPDPRTSRGDT 156 (273)
T ss_pred CCCCCceeEEEEEcCCCCeEEEEECCCCcEEEEEcChHHccceEEEEEEEEEecCCeeEEEecCCceeccCCccccCCCE
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccC-CCceEEc
Q 029796 85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKG-SKPWVSL 163 (187)
Q Consensus 85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~-~~p~IsL 163 (187)
|+|+||+++|++|+||++||+||||||+|+|++|+|.+|+.+++++++||++|++|++|+|+++||||||++ ++|||+|
T Consensus 157 v~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~~~~~~~iv~i~d~~g~~F~T~~~~VfvIG~~~~kp~IsL 236 (273)
T PTZ00223 157 LVYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIERHPGAFDIARLKDASGHEFATRAANIFVIGKDMNSVPVTL 236 (273)
T ss_pred EEEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEecCCCCCEEEEEeCCCCeEEEEeeeEEEEeCCCCCcceEC
Confidence 999999999999999999999999999999999999999999999999999999999999999999999985 6999999
Q ss_pred cCCceeeeehhHHHHHHHHHHHh
Q 029796 164 PKGKGIKLSIIEEARKRQAAQAA 186 (187)
Q Consensus 164 p~~~Gi~~~~~e~~~~~~~~~~~ 186 (187)
|++||||||++|| |++++++++
T Consensus 237 p~~kgi~~~~~e~-~~~~~~~~~ 258 (273)
T PTZ00223 237 PKQQGLRINVIQE-REEKLIAAE 258 (273)
T ss_pred cCCCCccccHHHH-HHHHHHHHH
Confidence 9999999999999 999997765
No 4
>PRK04313 30S ribosomal protein S4e; Validated
Probab=100.00 E-value=1.9e-69 Score=463.62 Aligned_cols=160 Identities=39% Similarity=0.629 Sum_probs=157.1
Q ss_pred eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCC-CCcccCC
Q 029796 5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPD-PLIKAND 83 (187)
Q Consensus 5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d-~~ik~~D 83 (187)
++||||||||||||++||+|||+||++|||.+|+|++|||+||||||++|++++||+|||+|||||||+++| |.||+||
T Consensus 76 ~~~PvGlmDVIsI~~~~e~yRvl~d~kgr~~l~~I~~eea~~KL~KV~~k~~~~gG~~ql~~hDGrni~~~~~~~~k~~D 155 (237)
T PRK04313 76 YKFPVGLMDVISIPETGEYYRVLPDEKGRLVLIPISEEEAKLKLCKIENKTTVKGGKIQLNLHDGRNILVDVEDDYKTGD 155 (237)
T ss_pred cccCcCceeEEEEccCCCeEEEEECCCCcEEEEECChHHccceEEEEEeEEEecCCEEEEEecCCceEEccCccccccCC
Confidence 789999999999999999999999999999999999999999999999999999999999999999999988 9999999
Q ss_pred eEEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEEEeeceEEEEccCCCceEE
Q 029796 84 TIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVS 162 (187)
Q Consensus 84 Tv~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~Is 162 (187)
||+|+||+|+|++|+||++||+||||||+|+|++|+|.+|++++ +++++||++|++|++|+|+++||||||+ ++|+|+
T Consensus 156 tv~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~d~~G~~F~T~~~~vfvIG~-~kp~is 234 (237)
T PRK04313 156 SLLISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLEDKDGEKFETILDYVFVIGK-EKPVIK 234 (237)
T ss_pred EEEEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEEcCCCCEEEEEeeeEEEEcC-CCccee
Confidence 99999999999999999999999999999999999999999999 6779999999999999999999999997 999999
Q ss_pred ccC
Q 029796 163 LPK 165 (187)
Q Consensus 163 Lp~ 165 (187)
||.
T Consensus 235 l~~ 237 (237)
T PRK04313 235 LPE 237 (237)
T ss_pred CCC
Confidence 984
No 5
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-67 Score=448.77 Aligned_cols=162 Identities=45% Similarity=0.698 Sum_probs=158.9
Q ss_pred eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796 5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT 84 (187)
Q Consensus 5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT 84 (187)
|+||||||||||||+|||+||||||.+|+|.||+|++|||.||||||++|++++||++|||||||||++++|+.|++|||
T Consensus 79 ~kfPVGlmDVisip~tgE~yRvl~d~~grl~l~~is~EeA~~Kl~kV~nKt~vkgG~~QLn~hDGrni~~~d~~~k~~Dt 158 (241)
T COG1471 79 YKFPVGLMDVISIPKTGEHYRVLPDEKGRLVLHPISAEEASYKLCKVKNKTTVKGGRIQLNLHDGRNIRLEDDNYKTGDT 158 (241)
T ss_pred ccCCcceEEEEEECCCCceEEEEecCCccEEEEecChhhccceEEEEEeEEEecCCEEEEEecCCceeeccCCccccccE
Confidence 79999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEc
Q 029796 85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSL 163 (187)
Q Consensus 85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsL 163 (187)
|++++|+++|++||||++|++||||||+|+|++|+|.+|+.++ +++|+|+++|.+|+.|+|+++||||||+ ++|||+|
T Consensus 159 v~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~~~g~~F~T~~~yVfvIG~-~k~~i~l 237 (241)
T COG1471 159 VKISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVEDEEGNTFQTIKDYVFVIGE-DKPVISL 237 (241)
T ss_pred EEEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEecCCCCceEEeeeEEEEEcC-CCceEeC
Confidence 9999999999999999999999999999999999999999998 6669999999999999999999999997 9999999
Q ss_pred cCCc
Q 029796 164 PKGK 167 (187)
Q Consensus 164 p~~~ 167 (187)
|+++
T Consensus 238 ~~e~ 241 (241)
T COG1471 238 PKEK 241 (241)
T ss_pred CCCC
Confidence 9874
No 6
>KOG0378 consensus 40S ribosomal protein S4 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=9.5e-66 Score=440.43 Aligned_cols=181 Identities=63% Similarity=1.076 Sum_probs=178.5
Q ss_pred eecccceeEEEEecCCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCe
Q 029796 5 FSFGTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDT 84 (187)
Q Consensus 5 ~kfPvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DT 84 (187)
.+||+|||||++|++|||+||++||++|+|.+|+|++|||+||||||++++.+.+|+|+|++||||+||||||.+|++||
T Consensus 80 ~~yp~g~mDvisiekTge~fr~iyd~k~~F~~hrI~~eeakyKLcKVrk~f~~tkGiP~lvthDg~tIrypDplIk~~dt 159 (263)
T KOG0378|consen 80 STYPAGFMDVISIEKTGEHFRLIYDQKGRFAVHRITSEEAKYKLCKVRKIFLGTKGIPHLVTHDGRTIRYPDPLIKVNDT 159 (263)
T ss_pred cccccceeEEEEecccchhhhhhhhcccceEEEEeccccccceeeeeEEEEeeccCcceEEccCCceEecCCcccCccce
Confidence 36999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred EEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEcc
Q 029796 85 IKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLP 164 (187)
Q Consensus 85 v~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp 164 (187)
+++++++++|.++++|+.|++||++||+|+||+|+|.+.++|+|++++||++|++|++|+|+++|+|+||++++||||||
T Consensus 160 I~~~~~t~kit~~ikf~~~~~~~vtgg~n~gRig~i~~rerh~G~f~vvhvkdt~gnsFatrLsNifvIgkgnKpwisLP 239 (263)
T KOG0378|consen 160 IKIDLETSKITDFIKFDTGNLCMVTGGANLGRIGVIKNRERHPGSFDVVHVKDTNGNSFATRLSNIFVIGEGNKPWISLP 239 (263)
T ss_pred eeccCCCceeeeeeccCccceeeeeccccccccccccccccCCCceEEEEEEecCCcEeeeeeccEEEEecCCCccccCc
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCceeeeehhHHHHHHHHHHHh
Q 029796 165 KGKGIKLSIIEEARKRQAAQAA 186 (187)
Q Consensus 165 ~~~Gi~~~~~e~~~~~~~~~~~ 186 (187)
+++||+++++|| ||+|++++.
T Consensus 240 kgkgi~~siaEe-~dkrl~~k~ 260 (263)
T KOG0378|consen 240 KGKGIALSIAEE-RDKRLAAKI 260 (263)
T ss_pred cccCccchhhHH-HHHHHhhhc
Confidence 999999999999 999999875
No 7
>PF00900 Ribosomal_S4e: Ribosomal family S4e; InterPro: IPR013845 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. A number of eukaryotic and archaeal ribosomal proteins can be grouped on the basis of sequence similarities. One of these families includes yeast S7 (YS6); archaeal S4e; and mammalian and plant cytoplasmic S4 []. Two highly similar isoforms of mammalian S4 exist, one coded by a gene on chromosome Y, and the other on chromosome X. These proteins have 233 to 264 amino acids. This entry represents the central region of these proteins.; PDB: 2XZM_W 2XZN_W 3IZ6_D 3KBG_A 3U5G_E 3U5C_E 3IZB_D.
Probab=100.00 E-value=1e-36 Score=222.05 Aligned_cols=77 Identities=61% Similarity=1.011 Sum_probs=69.8
Q ss_pred CCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCeEEEecCCCeee
Q 029796 19 KTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 95 (187)
Q Consensus 19 kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~ 95 (187)
+|||+|||+||++|+|.+|+|++|||+||||||++|++++||+|||+|||||||+|+||.||+||||+++||++||+
T Consensus 1 kt~e~yRvl~d~kgr~~l~~I~~eea~~KLckV~~k~~~~gG~~ql~~hDGrni~~~~~~~k~~Dtv~i~l~~~kI~ 77 (77)
T PF00900_consen 1 KTGEHYRVLYDTKGRFVLHPISEEEAKYKLCKVRNKTTGKGGKPQLNTHDGRNIRYPDPDIKTNDTVVIDLPTQKIV 77 (77)
T ss_dssp CTTEEEEEEE-TTS-EEEEEE-TTGGGEEEEEEEEEEEEGGGEEEEEETTTEEEES-SST--TTEEEEEETTTTEEE
T ss_pred CCCcEEEEEECCCCcEEEEECCHHHccCeEEEEeEEEEecCCcEEEEecCceEEEcCcCCccCCCEEEEECCCCcCC
Confidence 68999999999999999999999999999999999999999999999999999999999999999999999999985
No 8
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=97.14 E-value=0.00053 Score=41.81 Aligned_cols=31 Identities=29% Similarity=0.560 Sum_probs=26.2
Q ss_pred CCcEEEEECCCcceeEEEEEEEEEecCCccEEEE
Q 029796 102 VGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 135 (187)
Q Consensus 102 ~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i 135 (187)
+|+.|+|+.|++.|+.|+|.++..+. +.|++
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~---~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSK---VRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTT---TEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCC---CEEEE
Confidence 59999999999999999999997643 55655
No 9
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.04 E-value=0.00064 Score=39.14 Aligned_cols=27 Identities=37% Similarity=0.661 Sum_probs=24.6
Q ss_pred EecCCcEEEEECCCcceeEEEEEEEEE
Q 029796 99 KFDVGNIVMVTGGRNRGRVGIIKNREK 125 (187)
Q Consensus 99 ~fe~G~~~~vtgG~n~G~vG~I~~i~~ 125 (187)
+|++|+.++|++|.+.|.+|+|.++..
T Consensus 1 ~~~~G~~V~I~~G~~~g~~g~i~~i~~ 27 (28)
T smart00739 1 KFEVGDTVRVIAGPFKGKVGKVLEVDG 27 (28)
T ss_pred CCCCCCEEEEeECCCCCcEEEEEEEcC
Confidence 478999999999999999999999853
No 10
>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=94.99 E-value=0.06 Score=42.23 Aligned_cols=40 Identities=15% Similarity=0.228 Sum_probs=32.5
Q ss_pred eEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029796 96 DFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 138 (187)
Q Consensus 96 ~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~ 138 (187)
+.+++..|+.+.|++|++-|..|+|.++... .+.|.|+.-
T Consensus 38 r~~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~~---~~~V~Vegv 77 (114)
T TIGR01080 38 RALPVRKGDKVRIMRGDFKGHEGKVSKVDLK---RYRIYVEGV 77 (114)
T ss_pred ccceeecCCEEEEecCCCCCCEEEEEEEEcC---CCEEEEcCe
Confidence 5568899999999999999999999999743 245667653
No 11
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=93.21 E-value=0.25 Score=39.19 Aligned_cols=38 Identities=18% Similarity=0.308 Sum_probs=30.8
Q ss_pred EEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029796 97 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 137 (187)
Q Consensus 97 ~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d 137 (187)
.+++..|+.+.|+.|+.-|..|+|.++.... +.|+|+.
T Consensus 43 ~~~IkkGD~V~VisG~~KGk~GkV~~V~~~~---~~V~VeG 80 (120)
T PRK01191 43 SLPVRKGDTVKVMRGDFKGEEGKVVEVDLKR---GRIYVEG 80 (120)
T ss_pred cceEeCCCEEEEeecCCCCceEEEEEEEcCC---CEEEEeC
Confidence 4578899999999999999999999996543 3466654
No 12
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=91.88 E-value=0.26 Score=35.88 Aligned_cols=38 Identities=21% Similarity=0.459 Sum_probs=31.8
Q ss_pred EEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029796 98 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 138 (187)
Q Consensus 98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~ 138 (187)
+++..|+.+.|+.|+.-|++|+|.++.+.. +.|.+++-
T Consensus 5 ~~I~kGD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegv 42 (76)
T PRK12281 5 LKVKKGDMVKVIAGDDKGKTGKVLAVLPKK---NRVIVEGV 42 (76)
T ss_pred ccccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCc
Confidence 478899999999999999999999997643 45777654
No 13
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=91.11 E-value=0.35 Score=35.74 Aligned_cols=39 Identities=15% Similarity=0.434 Sum_probs=32.0
Q ss_pred EEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcC
Q 029796 97 FIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDA 138 (187)
Q Consensus 97 ~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~ 138 (187)
.+++..|+.+.|+.|+.-|+.|+|.++.+.. +.|++++-
T Consensus 6 ~~~I~~GD~V~Vi~G~dKGK~G~V~~V~~~~---~~V~Vegv 44 (83)
T CHL00141 6 KMHVKIGDTVKIISGSDKGKIGEVLKIIKKS---NKVIVKGI 44 (83)
T ss_pred eCcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcCc
Confidence 3478899999999999999999999997543 46777643
No 14
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=90.37 E-value=0.39 Score=36.89 Aligned_cols=37 Identities=22% Similarity=0.504 Sum_probs=30.0
Q ss_pred EEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEc
Q 029796 98 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQD 137 (187)
Q Consensus 98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d 137 (187)
.++..|+.+.|+.|++-|.+|+|.++.... +.|+|++
T Consensus 3 ~~i~kGD~V~Vi~G~dKGk~G~V~~V~~~~---~~V~Veg 39 (105)
T PRK00004 3 MKIKKGDTVIVIAGKDKGKRGKVLKVLPKK---NKVIVEG 39 (105)
T ss_pred CcccCCCEEEEeEcCCCCcEEEEEEEEcCC---CEEEEcC
Confidence 378899999999999999999999996543 3455554
No 15
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=89.42 E-value=0.82 Score=37.30 Aligned_cols=57 Identities=25% Similarity=0.308 Sum_probs=38.2
Q ss_pred EEecCCcEEEEECCCcceeEEEEEEEEEecCCc--cEEEEEcCCCCeEE--EeeceEEEEc
Q 029796 98 IKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSF--ETIHIQDALGHEFA--TRLGNVFTIG 154 (187)
Q Consensus 98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~--~~V~i~d~~g~~F~--T~~~~vfvIG 154 (187)
+++..|+.+.|+.|++-|..|+|.++....+.. +=|.+.-..|..++ --.+||+++-
T Consensus 45 ~~IkkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVEgvn~~Kk~gk~~e~PIh~SNV~iv~ 105 (143)
T PTZ00194 45 MPVRKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIEKITREKANGEPVQIGIHPSNVIITK 105 (143)
T ss_pred ceeecCCEEEEecCCCCCCceEEEEEEcCCCEEEEeCeEEEecCCCEeecCcCchheEEEc
Confidence 478889999999999999999999997644321 22233335554433 2346666654
No 16
>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=86.61 E-value=1.2 Score=34.32 Aligned_cols=28 Identities=25% Similarity=0.470 Sum_probs=25.4
Q ss_pred EecCCcEEEEECCCcceeEEEEEEEEEe
Q 029796 99 KFDVGNIVMVTGGRNRGRVGIIKNREKH 126 (187)
Q Consensus 99 ~fe~G~~~~vtgG~n~G~vG~I~~i~~~ 126 (187)
++..|+.+.|+.|+.-|.+|+|.++.+.
T Consensus 3 ~ikkGD~V~Vi~G~dKGK~G~V~~V~~~ 30 (104)
T TIGR01079 3 KIKKGDTVKVISGKDKGKRGKVLKVLPK 30 (104)
T ss_pred cccCCCEEEEeEcCCCCcEEEEEEEEcC
Confidence 6788999999999999999999999654
No 17
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=81.18 E-value=4.5 Score=28.70 Aligned_cols=49 Identities=27% Similarity=0.507 Sum_probs=37.0
Q ss_pred CCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEEEeeceEEEEc
Q 029796 102 VGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIG 154 (187)
Q Consensus 102 ~G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIG 154 (187)
+|..|+|-.|.+.-|+|.++.-+... ++|.+|. ++...+--+..+..+|
T Consensus 5 ~gqkayikdgp~rnrigivk~~e~q~~~~f~ivi----~~q~i~velkdivlvg 54 (68)
T PF13051_consen 5 VGQKAYIKDGPYRNRIGIVKKNEKQLESHFAIVI----GEQSIDVELKDIVLVG 54 (68)
T ss_pred cccEeeeccCCccceeEEEecchhhcCCcEEEEE----CCeEEEEEeeeEEEEE
Confidence 48899999999999999999888766 4445542 3345666677777777
No 18
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=69.53 E-value=5.1 Score=31.97 Aligned_cols=26 Identities=35% Similarity=0.552 Sum_probs=24.0
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEE
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNREK 125 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i~~ 125 (187)
+++|-.|+++.|+.+|+-.+|..+..
T Consensus 5 l~~GrVvvv~~GR~aGkk~VIv~~iD 30 (125)
T COG2163 5 LEVGRVVVVTAGRFAGKKVVIVKIID 30 (125)
T ss_pred ccCCeEEEEecceeCCceEEEEEEcc
Confidence 78999999999999999999998854
No 19
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=69.39 E-value=7.8 Score=30.03 Aligned_cols=29 Identities=24% Similarity=0.475 Sum_probs=24.5
Q ss_pred EEecCCcEEEEECCCcceeEEEEEEEEEe
Q 029796 98 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 126 (187)
Q Consensus 98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~ 126 (187)
.+...|+.++|+.|++-|..|+|.++...
T Consensus 3 ~~IrkGD~V~Vi~GkdKGk~GkVl~v~~k 31 (104)
T COG0198 3 MKVKKGDTVKVIAGKDKGKEGKVLKVLPK 31 (104)
T ss_pred cceecCCEEEEEecCCCCcceEEEEEecC
Confidence 45677999999999999999999988553
No 20
>PRK02290 3-dehydroquinate synthase; Provisional
Probab=65.98 E-value=30 Score=32.04 Aligned_cols=63 Identities=24% Similarity=0.160 Sum_probs=38.1
Q ss_pred EEEcCCCceEEEEcC--chhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCC--------CcccCCeEEEecCC
Q 029796 26 LLYDTKGRFRLHSLR--DEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP--------LIKANDTIKLDLEE 91 (187)
Q Consensus 26 vl~d~kg~f~l~~I~--~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~--------~ik~~DTv~i~l~~ 91 (187)
++.|.+|+-+...+- +=|. .=|..|+-+. .|....+.+.|..|||+-.| +.|+||.|+..+++
T Consensus 256 lvVd~~G~tR~~~VGRvKIE~-RPL~lIeAe~--~g~~~~viLQnaetIrlv~~dG~~vsVt~Lk~GD~VL~~~~~ 328 (344)
T PRK02290 256 LVVDADGNTREAIVGRVKIEK-RPLLLIEAEY--GGKRIRTILQNAETIRLVTPDGKPVSVVDLKPGDEVLGYLEE 328 (344)
T ss_pred EEEeCCCCEEEEEeeEEEEee-ccEEEEEEEe--CCeEEEEEEecCcEEEEECCCCCEeeeeecCCCCEEEEEecC
Confidence 456777776655432 1121 2456666655 56777788888888876433 45666666666554
No 21
>PF14001 YdfZ: YdfZ protein
Probab=65.38 E-value=12 Score=26.76 Aligned_cols=42 Identities=26% Similarity=0.496 Sum_probs=30.0
Q ss_pred EecCCcEEEEECCCcceeEEEEEEEEEec------CCccEEEEEcCCCCeEE
Q 029796 99 KFDVGNIVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 144 (187)
Q Consensus 99 ~fe~G~~~~vtgG~n~G~vG~I~~i~~~~------~s~~~V~i~d~~g~~F~ 144 (187)
++.+|+.+|+-| +|.+|+|+.|.... .....|.+++.+| .|+
T Consensus 9 ~i~~G~rVMiag---tG~~gvikAih~~gl~~eq~rR~kcVel~g~~g-~f~ 56 (64)
T PF14001_consen 9 AITTGSRVMIAG---TGATGVIKAIHADGLTAEQIRRAKCVELEGCEG-RFA 56 (64)
T ss_pred cCCCCCEEEEcC---CCcccEEeeeecCCCCHHHhhhccEEEEeCCCc-eEc
Confidence 456799999977 67888899886632 2337888987776 454
No 22
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=64.56 E-value=8.1 Score=31.10 Aligned_cols=32 Identities=13% Similarity=0.347 Sum_probs=27.2
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEE
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 135 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i 135 (187)
.|+|-+|+|.-|.+.|+.++|++|..+ |.|.|
T Consensus 8 VEiGRVvli~~Gp~~GKL~vIVDIID~----nRvLV 39 (130)
T PTZ00065 8 VEPGRLCLIQYGPDAGKLCFIVDIVTP----TRVLV 39 (130)
T ss_pred eeeceEEEEecCCCCCCEEEEEEEEcC----CeEEE
Confidence 378999999999999999999999764 45555
No 23
>PF01959 DHQS: 3-dehydroquinate synthase (EC 4.6.1.3); InterPro: IPR002812 3-Dehydroquinate synthase (4.2.3.4 from EC) is an enzyme in the common pathway of aromatic amino acid biosynthesis that catalyses the conversion of 3-deoxy-D-arabino-heptulosonic acid 7-phosphate (DAHP) into 3-dehydroquinic acid []. This synthesis of aromatic amino acids is an essential metabolic function for most prokaryotic as well as lower eukaryotic cells, including plants. The pathway is absent in humans; therefore, DHQS represents a potential target for the development of novel and selective antimicrobial agents. Owing to the threat posed by the spread of pathogenic bacteria resistant to many currently used antimicrobial drugs, there is clearly a need to develop new anti-infective drugs acting at novel targets. A further potential use for DHQS inhibitors is as herbicides [].; GO: 0016491 oxidoreductase activity, 0055114 oxidation-reduction process
Probab=61.24 E-value=21 Score=33.21 Aligned_cols=75 Identities=23% Similarity=0.302 Sum_probs=44.5
Q ss_pred EEEcCCCceEEEEcC--chhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCeEEEecCCCeeeeEEEecCC
Q 029796 26 LLYDTKGRFRLHSLR--DEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVG 103 (187)
Q Consensus 26 vl~d~kg~f~l~~I~--~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G 103 (187)
++.|.+|+-+...+- +=| +.=|..|+-.. .|....+.+.|..|||+-.| +++.+....+++|
T Consensus 266 lvVd~~G~tR~~~VGRvKIE-~RPLllIeA~~--~g~~~svilQnaetIRlv~p-------------~G~~vsVt~Lk~G 329 (354)
T PF01959_consen 266 LVVDADGRTRTAIVGRVKIE-RRPLLLIEAEA--DGKRISVILQNAETIRLVGP-------------DGEPVSVTELKPG 329 (354)
T ss_pred EEEeCCCCEEEEEeeEEEEe-ecceEEEEEEe--CCeEEEEEEecCcEEEEECC-------------CCCEeeeeecCCC
Confidence 456777766554432 122 23466666655 56777788888888876433 3444445555555
Q ss_pred cEEEE---ECCCccee
Q 029796 104 NIVMV---TGGRNRGR 116 (187)
Q Consensus 104 ~~~~v---tgG~n~G~ 116 (187)
+.+++ .+|||.|.
T Consensus 330 D~vL~~~~~~~RHfG~ 345 (354)
T PF01959_consen 330 DEVLVYLEEAGRHFGM 345 (354)
T ss_pred CEEEEEecCCCcccce
Confidence 54443 37899884
No 24
>PRK04333 50S ribosomal protein L14e; Validated
Probab=60.09 E-value=11 Score=28.05 Aligned_cols=33 Identities=24% Similarity=0.460 Sum_probs=27.2
Q ss_pred EecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEE
Q 029796 99 KFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHI 135 (187)
Q Consensus 99 ~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i 135 (187)
.+++|-+|++.-|+..|+..+|.++... +.|.|
T Consensus 3 ~v~~GrvV~~~~Grd~gk~~vIv~i~d~----~~vlV 35 (84)
T PRK04333 3 AIEVGRVCVKTAGREAGRKCVIVDIIDK----NFVLV 35 (84)
T ss_pred cccccEEEEEeccCCCCCEEEEEEEecC----CEEEE
Confidence 4688999999999999999999998432 45655
No 25
>KOG1784 consensus Small Nuclear ribonucleoprotein splicing factor [RNA processing and modification]
Probab=55.78 E-value=25 Score=26.94 Aligned_cols=60 Identities=20% Similarity=0.205 Sum_probs=36.5
Q ss_pred CCeeEEEccCceEEeeCCCCcccCCeEEEecC------CCeeeeEEEecCCcEEEEECCCcceeEEEEEE
Q 029796 59 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLE------ENKITDFIKFDVGNIVMVTGGRNRGRVGIIKN 122 (187)
Q Consensus 59 gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l~------~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~ 122 (187)
+...++.|.|||++.-.=.-+.-.--+.|+-. +.+=++.+++- .+++.|-|.+-+|-|-|
T Consensus 10 n~~V~vIt~DGr~ivgsLkGFDq~tNlii~~~heRi~s~~~gv~q~~lG----lyiirgeNva~ig~iDE 75 (96)
T KOG1784|consen 10 NQRVSVITNDGRVIVGSLKGFDQTTNLIIDESHERIFSETEGVEQIVLG----LYIIRGENVAVIGEIDE 75 (96)
T ss_pred hceEEEEecCCeEEEEEeccccccceeeehhhHhhhhhhhcchhheeeE----EEEEecCccceeeecch
Confidence 45678999999999643112222222444432 11112334443 78999999999998876
No 26
>PRK14898 DNA-directed RNA polymerase subunit A''; Provisional
Probab=52.93 E-value=76 Score=32.55 Aligned_cols=78 Identities=17% Similarity=0.192 Sum_probs=55.2
Q ss_pred ccceeEEEEecCCCceEEEEEcCCCceEEEEcCc---hhhceeEEEEe----eeEEeeCCeeEEEccCceEEeeCCCCcc
Q 029796 8 GTLLTDVVSIPKTNENFRLLYDTKGRFRLHSLRD---EEAKFKLCKVR----SVQFGQKGIPYINTYDGRTIRYPDPLIK 80 (187)
Q Consensus 8 PvGlMDVIsI~kt~e~yRvl~d~kg~f~l~~I~~---eEa~~KLcKV~----~k~~~~gg~~ql~~hDGrni~~~d~~ik 80 (187)
++|-++++..+ .+.+=+-+|++++....+++. -++.-||.||+ +.-.++.++|.++..||+-.......++
T Consensus 111 ~~~~~e~~~~~--~~~~V~s~d~~~k~~~~~v~~v~r~~~~~~l~~I~t~~Grei~vT~~H~~~v~~~g~~~~~~a~~l~ 188 (858)
T PRK14898 111 KIGGHEVCDLP--IEIYALSLDQDEKVHWKRIISVIRHKANGKLIKIKTESGRTIRATPYHSFVTRKDNEVIPVEGSELK 188 (858)
T ss_pred ccCCceEEecC--CCcEEEEECCCCcEEEEEeeeEEeccCCCcEEEEEeCCCcEEEECCCCeEEEeeCCeEEEeeHHhCC
Confidence 34555666554 233334478888888888875 23445889888 4557789999999999987765666899
Q ss_pred cCCeEEE
Q 029796 81 ANDTIKL 87 (187)
Q Consensus 81 ~~DTv~i 87 (187)
+||-|.+
T Consensus 189 ~GD~i~~ 195 (858)
T PRK14898 189 IGDWLPV 195 (858)
T ss_pred CCCEEee
Confidence 9998755
No 27
>cd03706 mtEFTU_III Domain III of mitochondrial EF-TU (mtEF-TU). mtEF-TU is highly conserved and is 55-60% identical to bacterial EF-TU. The overall structure is similar to that observed in the Escherichia coli and Thermus aquaticus EF-TU. However, compared with that observed in prokaryotic EF-TU the nucleotide-binding domain (domain I) of EF-TUmt is in a different orientation relative to the rest of the structure. Furthermore, domain III is followed by a short 11-amino acid extension that forms one helical turn. This extension seems to be specific to the mitochondrial factors and has not been observed in any of the prokaryotic factors.
Probab=52.70 E-value=83 Score=22.49 Aligned_cols=40 Identities=18% Similarity=0.404 Sum_probs=24.7
Q ss_pred cccCCeEEEecCCCeeeeEEEecCCcEEEE-ECCCcceeEEEEEE
Q 029796 79 IKANDTIKLDLEENKITDFIKFDVGNIVMV-TGGRNRGRVGIIKN 122 (187)
Q Consensus 79 ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v-tgG~n~G~vG~I~~ 122 (187)
+++||+..+.+.-.+ -+..+.|.-.++ .+|+.+| .|+|.+
T Consensus 52 l~~g~~~~v~i~l~~---p~~~~~g~rf~lR~~~~tvg-~G~V~~ 92 (93)
T cd03706 52 VMPGEDTKVTLILRR---PMVLEKGQRFTLRDGNRTIG-TGLVTD 92 (93)
T ss_pred eCCCCEEEEEEEECC---cEEEeeCCEEEEEECCEEEE-EEEEEe
Confidence 788888877776432 224555666555 5665555 677654
No 28
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=50.09 E-value=17 Score=29.41 Aligned_cols=24 Identities=38% Similarity=0.684 Sum_probs=21.3
Q ss_pred ecCCcEEEEECCCcceeEEEEEEE
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNR 123 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i 123 (187)
+.+|..|+|..|+++|+-++|...
T Consensus 5 ~kpgkVVivL~GR~AGkKaVivk~ 28 (134)
T PTZ00471 5 LKPGKVVIVTSGRYAGRKAVIVQN 28 (134)
T ss_pred ccCCEEEEEEccccCCcEEEEEee
Confidence 468999999999999999988764
No 29
>PF07076 DUF1344: Protein of unknown function (DUF1344); InterPro: IPR009780 This family consists of several short, hypothetical bacterial proteins of around 80 residues in length. Members of this family are found in Rhizobium, Agrobacterium and Brucella species. The function of this family is unknown.
Probab=47.90 E-value=43 Score=23.71 Aligned_cols=35 Identities=14% Similarity=0.151 Sum_probs=27.2
Q ss_pred EeeCCeeEEEccCceEEeeCC----CCcccCCeEEEecC
Q 029796 56 FGQKGIPYINTYDGRTIRYPD----PLIKANDTIKLDLE 90 (187)
Q Consensus 56 ~~~gg~~ql~~hDGrni~~~d----~~ik~~DTv~i~l~ 90 (187)
.+......|.|.||.++..|. +.+++|..|++-..
T Consensus 11 ~id~~~~titLdDGksy~lp~ef~~~~L~~G~kV~V~yd 49 (61)
T PF07076_consen 11 SIDPETMTITLDDGKSYKLPEEFDFDGLKPGMKVVVFYD 49 (61)
T ss_pred EEcCCceEEEecCCCEEECCCcccccccCCCCEEEEEEE
Confidence 355677899999999998774 46888888877654
No 30
>cd03704 eRF3c_III This family represents eEF1alpha-like C-terminal region of eRF3 homologous to the domain III of EF-Tu. eRF3 is a GTPase, which enhances the termination efficiency by stimulating the eRF1 activity in a GTP-dependent manner. The C-terminal region is responsible for translation termination activity and is essential for viability. Saccharomyces cerevisiae eRF3 (Sup35p) is a translation termination factor which is divided into three regions N, M and a C-terminal eEF1a-like region essential for translation termination. Sup35NM is a non-pathogenic prion-like protein with the property of aggregating into polymer-like fibrils.
Probab=47.74 E-value=58 Score=23.92 Aligned_cols=48 Identities=19% Similarity=0.320 Sum_probs=30.0
Q ss_pred CCC-CcccCCeEEEecCCCeeeeEEEecC----CcEEEEECCCcceeEEEEEEE
Q 029796 75 PDP-LIKANDTIKLDLEENKITDFIKFDV----GNIVMVTGGRNRGRVGIIKNR 123 (187)
Q Consensus 75 ~d~-~ik~~DTv~i~l~~~kI~~~i~fe~----G~~~~vtgG~n~G~vG~I~~i 123 (187)
.+| .++.||...+.+...+=+-.=+|+. |..++--+|+.+| .|.|.+|
T Consensus 56 ~~p~~l~~g~~a~v~i~~~~pi~~e~~~~~~~lGRf~lR~~g~Tva-~G~V~~~ 108 (108)
T cd03704 56 KRPRFVKSGMKVIARLETTGPICLEKFEDFPQLGRFTLRDEGKTIA-IGKVLKL 108 (108)
T ss_pred cCCcEeCCCCEEEEEEEeCCcEEEEEcccCCCcccEEEEeCCCEEE-EEEEEEC
Confidence 344 6899999999986554221122322 6666667777766 7877653
No 31
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=47.41 E-value=36 Score=26.58 Aligned_cols=26 Identities=19% Similarity=0.371 Sum_probs=24.7
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEE
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNREK 125 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i~~ 125 (187)
|.+|+.+.|+.|.=.|..|.|.++..
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~ 112 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDE 112 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcC
Confidence 89999999999999999999999865
No 32
>cd02899 PLAT_SR Scavenger receptor protein. A subfamily of PLAT (Polycystin-1, Lipoxygenase, Alpha-Toxin) domain or LH2 (Lipoxygenase homology 2) domain. It consists of an eight stranded beta-barrel. The domain can be found in various domain architectures, in case of lipoxygenases, alpha toxin, lipases and polycystin, but also as a single domain or as repeats.The putative function of this domain is to facilitate access to sequestered membrane or micelle bound substrates. This subfamily contains Toxoplasma gondii Scavenger protein TgSR1.
Probab=47.24 E-value=84 Score=24.18 Aligned_cols=61 Identities=18% Similarity=0.393 Sum_probs=39.4
Q ss_pred ecCCcEEEE-ECCCcceeEEEEEEEEEe-----cCCc-cEEEEEcCCCCeEEEeeceEEEEccCCCceEEccCCceeeee
Q 029796 100 FDVGNIVMV-TGGRNRGRVGIIKNREKH-----KGSF-ETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLS 172 (187)
Q Consensus 100 fe~G~~~~v-tgG~n~G~vG~I~~i~~~-----~~s~-~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp~~~Gi~~~ 172 (187)
|+.|+.--. +.... +|.|..|+.. ++.+ +-|.|+|.+|+. +.|...+ |+.-|-++=|+++
T Consensus 41 F~~G~~d~F~v~~~d---LG~l~~i~l~n~g~~~~Wf~~~V~V~~~~g~~------~~Fpc~r----Wla~~~~~~v~~~ 107 (109)
T cd02899 41 FYPGSLKRIRFRAAD---VGDINAIILSNTALNDPWYCDYVRIKSEDGKV------FAFNVKR----WIGYPYEQSVEVS 107 (109)
T ss_pred cCCCceEEEEECccc---cCceEEEEEECCCCCCCceeeEEEEECCCCCE------EEEEcce----eeCCchhceEEEe
Confidence 666655432 22344 4445555442 2444 889999866644 5599988 9999999988876
Q ss_pred h
Q 029796 173 I 173 (187)
Q Consensus 173 ~ 173 (187)
+
T Consensus 108 ~ 108 (109)
T cd02899 108 L 108 (109)
T ss_pred c
Confidence 4
No 33
>PF04773 FecR: FecR protein; InterPro: IPR006860 FecR is involved in regulation of iron dicitrate transport. In the absence of citrate FecR inactivates FecI. FecR is probably a sensor that recognises iron dicitrate in the periplasm.
Probab=46.84 E-value=97 Score=21.58 Aligned_cols=67 Identities=16% Similarity=0.153 Sum_probs=39.9
Q ss_pred eEEeeCCeeEEEccCceEEeeC-CCCc-----ccCCeEEEecCCCeeeeEEEecCCc-EEEEECCCcceeEEEE
Q 029796 54 VQFGQKGIPYINTYDGRTIRYP-DPLI-----KANDTIKLDLEENKITDFIKFDVGN-IVMVTGGRNRGRVGII 120 (187)
Q Consensus 54 k~~~~gg~~ql~~hDGrni~~~-d~~i-----k~~DTv~i~l~~~kI~~~i~fe~G~-~~~vtgG~n~G~vG~I 120 (187)
..+..++..+|.+.||..++.. +..+ ...+...+.|..|++.-.++=.... +.+-|....++-.|+-
T Consensus 3 i~T~~~~~~~i~l~dgs~v~l~~~s~~~~~~~~~~~~~~~~L~~G~~~~~~~~~~~~~~~V~T~~~~i~v~GT~ 76 (98)
T PF04773_consen 3 IRTGAGSRAEIALSDGSRVRLGPNSRVSVDRDSGSEPTRLRLLSGEILFDVSPGKKRPFEVRTPTATIGVRGTR 76 (98)
T ss_pred EEcCCCCEEEEEECCCCEEEECCCcEEEEEcccCCCceEEEEcCCCEEEEEcccCCCCEEEEeCCEEEEEecCE
Confidence 4577899999999999999763 3334 3445556666666654333222222 5555555555554443
No 34
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=45.43 E-value=37 Score=27.20 Aligned_cols=29 Identities=17% Similarity=0.275 Sum_probs=26.6
Q ss_pred EEecCCcEEEEECCCcceeEEEEEEEEEe
Q 029796 98 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 126 (187)
Q Consensus 98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~ 126 (187)
..|.+|..+-|+.|.-.|..|.|.++..+
T Consensus 93 ~~~~~G~~V~I~~Gpf~g~~g~V~~vd~~ 121 (153)
T PRK08559 93 EGIKEGDIVELIAGPFKGEKARVVRVDES 121 (153)
T ss_pred cCCCCCCEEEEeccCCCCceEEEEEEcCC
Confidence 56999999999999999999999999764
No 35
>PF01588 tRNA_bind: Putative tRNA binding domain; InterPro: IPR002547 This domain is found in prokaryotic methionyl-tRNA synthetases, prokaryotic phenylalanyl tRNA synthetases the yeast GU4 nucleic-binding protein (G4p1 or p42, ARC1) [], human tyrosyl-tRNA synthetase [], and endothelial-monocyte activating polypeptide II. G4p1 binds specifically to tRNA form a complex with methionyl-tRNA synthetases []. In human tyrosyl-tRNA synthetase this domain may direct tRNA to the active site of the enzyme []. This domain may perform a common function in tRNA aminoacylation [].; GO: 0000049 tRNA binding; PDB: 3BU2_C 1PYB_A 2Q2I_A 2Q2H_A 1JJC_B 1EIY_B 1PYS_B 3HFZ_B 3TEH_B 2CWP_A ....
Probab=44.37 E-value=60 Score=23.72 Aligned_cols=21 Identities=33% Similarity=0.392 Sum_probs=16.2
Q ss_pred eEEEEEEEEEecCCc--cEEEEE
Q 029796 116 RVGIIKNREKHKGSF--ETIHIQ 136 (187)
Q Consensus 116 ~vG~I~~i~~~~~s~--~~V~i~ 136 (187)
++|+|.+.+.||.+. .+..+.
T Consensus 2 ~vg~I~~~~~hp~sdkL~~~~Vd 24 (95)
T PF01588_consen 2 RVGKILEVEPHPNSDKLYVLKVD 24 (95)
T ss_dssp EEEEEEEEEEETTSSSEEEEEEE
T ss_pred EEEEEEEEEECCCCCEEEEEEEE
Confidence 689999999999876 444443
No 36
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=44.19 E-value=27 Score=27.99 Aligned_cols=29 Identities=24% Similarity=0.398 Sum_probs=26.3
Q ss_pred EEEecCCcEEEEECCCcceeEEEEEEEEE
Q 029796 97 FIKFDVGNIVMVTGGRNRGRVGIIKNREK 125 (187)
Q Consensus 97 ~i~fe~G~~~~vtgG~n~G~vG~I~~i~~ 125 (187)
...|++|+.+-|++|.=.|..|.|.++..
T Consensus 124 ~~~~~~Gd~VrI~~GPf~G~~g~v~~i~~ 152 (181)
T PRK05609 124 KVDFEVGEMVRVIDGPFADFNGTVEEVDY 152 (181)
T ss_pred ccCCCCCCEEEEeccCCCCCEEEEEEEeC
Confidence 46799999999999999999999999854
No 37
>cd05741 Ig_CEACAM_D1_like First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) and similar proteins. Ig_CEACAM_D1_like : immunoglobulin (IG)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily-like. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions, it is a cell adhesion molecule, and a signaling molecule that regulates the growth of tumor cells, it is an angiogenic factor, and is a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two [D1, D4] or four [D1-D4] Ig-like domains on the cell surf
Probab=40.61 E-value=47 Score=22.83 Aligned_cols=31 Identities=16% Similarity=0.192 Sum_probs=26.2
Q ss_pred EEEEcCCCceEEEEcCchhhceeEEEEeeeE
Q 029796 25 RLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQ 55 (187)
Q Consensus 25 Rvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~ 55 (187)
|+-.+.++.|.+..+.++++..-.|+|....
T Consensus 50 R~~~~~~~sL~I~~l~~~DsG~Y~c~v~~~~ 80 (92)
T cd05741 50 RETIYPNGSLLIQNLTKEDSGTYTLQIISTN 80 (92)
T ss_pred eEEEcCCceEEEccCCchhcEEEEEEEEcCC
Confidence 4556666999999999999999999998864
No 38
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=40.52 E-value=31 Score=27.53 Aligned_cols=28 Identities=29% Similarity=0.452 Sum_probs=25.4
Q ss_pred EEecCCcEEEEECCCcceeEEEEEEEEE
Q 029796 98 IKFDVGNIVMVTGGRNRGRVGIIKNREK 125 (187)
Q Consensus 98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~ 125 (187)
..|.+|+.+.|++|.=.|..|+|.++..
T Consensus 118 ~~~~~G~~V~I~~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 118 IDFEVGEQVRVNDGPFANFTGTVEEVDY 145 (172)
T ss_pred cCCCCCCEEEEeecCCCCcEEEEEEEcC
Confidence 5589999999999999999999999854
No 39
>PF12961 DUF3850: Domain of Unknown Function with PDB structure (DUF3850)
Probab=39.41 E-value=30 Score=25.18 Aligned_cols=18 Identities=28% Similarity=0.322 Sum_probs=15.3
Q ss_pred EEeeCCCCcccCCeEEEe
Q 029796 71 TIRYPDPLIKANDTIKLD 88 (187)
Q Consensus 71 ni~~~d~~ik~~DTv~i~ 88 (187)
-||..|.+|++||.|.+.
T Consensus 21 EiRkNDRdf~VGD~L~L~ 38 (72)
T PF12961_consen 21 EIRKNDRDFQVGDILVLR 38 (72)
T ss_pred EEEecCCCCCCCCEEEEE
Confidence 357789999999999985
No 40
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=38.60 E-value=51 Score=25.79 Aligned_cols=83 Identities=18% Similarity=0.267 Sum_probs=46.4
Q ss_pred eEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCeEEEecCCCeeeeEEEecCCcEEEEECCCc
Q 029796 34 FRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRN 113 (187)
Q Consensus 34 f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~vtgG~n 113 (187)
+.+.+.+.++..+. .|.+ ..|...+.-.+|+....++..+..--.. .-..........|++|+.+.|++|.-
T Consensus 51 YvFv~~~~~~~~~~--~i~~----~~gv~~~v~~~~~p~~I~~~~i~~l~~~--~~~~~~~~~~~~~~~G~~V~V~~GPf 122 (159)
T TIGR01955 51 YLFIEFDPEVDSWT--TIRS----TRGVSRFVRFGGHPAPVPDDLIHQLRQY--EPKDSVPPATTLPYKGDKVRITDGAF 122 (159)
T ss_pred eEEEEEccCCCceE--EEec----CCCcCEEECCCCCcccCCHHHHHHHHhc--cccccCCccccCCCCCCEEEEeccCC
Confidence 44666665543332 2211 1456666555665555555322211000 00010112335699999999999999
Q ss_pred ceeEEEEEEEE
Q 029796 114 RGRVGIIKNRE 124 (187)
Q Consensus 114 ~G~vG~I~~i~ 124 (187)
.|..|.|.++.
T Consensus 123 ~g~~g~v~~~~ 133 (159)
T TIGR01955 123 AGFEAIFLEPD 133 (159)
T ss_pred CCcEEEEEEEC
Confidence 99999999985
No 41
>cd05892 Ig_Myotilin_C C-terminal immunoglobulin (Ig)-like domain of myotilin. Ig_Myotilin_C: C-terminal immunoglobulin (Ig)-like domain of myotilin. Mytolin belongs to the palladin-myotilin-myopalladin family. Proteins belonging to the latter family contain multiple Ig-like domains and function as scaffolds, modulating actin cytoskeleton. Myotilin is most abundant in skeletal and cardiac muscle, and is involved in maintaining sarcomere integrity. It binds to alpha-actinin, filamin and actin. Mutations in myotilin lead to muscle disorders.
Probab=36.31 E-value=76 Score=21.99 Aligned_cols=35 Identities=11% Similarity=0.269 Sum_probs=28.7
Q ss_pred CCceEEEEEcCCC--ceEEEEcCchhhceeEEEEeee
Q 029796 20 TNENFRLLYDTKG--RFRLHSLRDEEAKFKLCKVRSV 54 (187)
Q Consensus 20 t~e~yRvl~d~kg--~f~l~~I~~eEa~~KLcKV~~k 54 (187)
.+.+|++..+..| .|.+..+..+++..-.|...|.
T Consensus 27 ~~~r~~~~~~~~g~~~L~I~~~~~~D~G~Y~C~A~N~ 63 (75)
T cd05892 27 NTDRISLYQDNSGRVTLLIKNVNKKDAGWYTVSAVNE 63 (75)
T ss_pred CCCeEEEEEcCCCcEEEEECCCChhhCEEEEEEEEcC
Confidence 3468899888877 5778899999999889998874
No 42
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=34.83 E-value=31 Score=28.29 Aligned_cols=52 Identities=17% Similarity=0.240 Sum_probs=37.9
Q ss_pred CCeeeeEEEecCCcEEEEECCCcce-eEEEEEEEEEecCC--ccEEEEEcCCCCe
Q 029796 91 ENKITDFIKFDVGNIVMVTGGRNRG-RVGIIKNREKHKGS--FETIHIQDALGHE 142 (187)
Q Consensus 91 ~~kI~~~i~fe~G~~~~vtgG~n~G-~vG~I~~i~~~~~s--~~~V~i~d~~g~~ 142 (187)
..=.+..+|+..++.+-|.+|+..| .+|.|.++-+..-. .+.|.-+-++|..
T Consensus 40 ~~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyie~v~~eK~nGt~ 94 (145)
T KOG3401|consen 40 QKYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYIERVQREKANGTT 94 (145)
T ss_pred HHhCccccceeeccEEEEEeccccccccceehhhhhhhheeeeEeEEEeeccCcc
Confidence 3345788999999999999999999 99999988664321 2445555455544
No 43
>cd03705 EF1_alpha_III Domain III of EF-1. Eukaryotic elongation factor 1 (EF-1) is responsible for the GTP-dependent binding of aminoacyl-tRNAs to ribosomes. EF-1 is composed of four subunits: the alpha chain, which binds GTP and aminoacyl-tRNAs, the gamma chain that probably plays a role in anchoring the complex to other cellular components and the beta and delta (or beta') chains. This family is the alpha subunit, and represents the counterpart of bacterial EF-Tu for the archaea (aEF-1 alpha) and eukaryotes (eEF-1 alpha).
Probab=34.70 E-value=86 Score=22.67 Aligned_cols=35 Identities=14% Similarity=0.285 Sum_probs=24.4
Q ss_pred CcccCCeEEEecCCCeeeeEEEecC-------CcEEEEECCCcce
Q 029796 78 LIKANDTIKLDLEENKITDFIKFDV-------GNIVMVTGGRNRG 115 (187)
Q Consensus 78 ~ik~~DTv~i~l~~~kI~~~i~fe~-------G~~~~vtgG~n~G 115 (187)
.++.||...+.|..++ -+.+|+ |..+++-+|+.+|
T Consensus 59 ~l~~n~~a~v~l~~~~---pi~~e~~~~~~~lgrf~lrd~~~Tva 100 (104)
T cd03705 59 FLKSGDAAIVKIVPQK---PLVVETFSEYPPLGRFAVRDMGQTVA 100 (104)
T ss_pred ccCCCCEEEEEEEECC---eeEEEEcccCCCccCEEEEeCCCEEE
Confidence 5899999999886554 345555 7777776666554
No 44
>cd01234 PH_CADPS CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS (Ca2+-dependent activator protein) Pleckstrin homology (PH) domain. CADPS is a calcium-dependent activator involved in secretion. It contains a central PH domain that binds to phosphoinositide 4,5 bisphosphate containing liposomes. However, membrane association may also be mediated by binding to phosphatidlyserine via general electrostatic interactions. PH domains share little sequence conservation, but all have a common fold, which is electrostatically polarized. PH domains also have diverse functions. They are often involved in targeting proteins to the plasma membrane, but few display strong specificity in lipid binding. Any specificity is usually determined by loop regions or insertions in the N-terminus of the domain, which are not conserved across all PH domains.
Probab=34.60 E-value=28 Score=27.51 Aligned_cols=42 Identities=24% Similarity=0.360 Sum_probs=33.2
Q ss_pred CCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCC
Q 029796 31 KGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP 77 (187)
Q Consensus 31 kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~ 77 (187)
++.|+|+.+|+= .+-+|--+-|..-+...+|| ||-|+-|.+|
T Consensus 21 KRwFvL~qvsQY--tfamcsy~ekks~P~e~~ql---dGyTvDy~~~ 62 (117)
T cd01234 21 KRFFVLVQVSQY--TFAMCSYREKKAEPTEFIQL---DGYTVDYMPE 62 (117)
T ss_pred eeEEEEEchhHH--HHHHHhhhhhcCCchhheee---cceEEeccCC
Confidence 345788877753 34678888888899999998 9999988764
No 45
>PF00924 MS_channel: Mechanosensitive ion channel; InterPro: IPR006685 Mechanosensitive (MS) channels provide protection against hypo-osmotic shock, responding both to stretching of the cell membrane and to membrane depolarisation. They are present in the membranes of organisms from the three domains of life: bacteria, archaea, and eukarya []. There are two families of MS channels: large-conductance MS channels (MscL) and small-conductance MS channels (MscS or YGGB). The pressure threshold for MscS opening is 50% that of MscL []. The MscS family is much larger and more variable in size and sequence than the MscL family. Much of the diversity in MscS proteins occurs in the size of the transmembrane regions, which ranges from three to eleven transmembrane helices, although the three C-terminal helices are conserved. This family contains sequences form the MscS family of proteins. MscS folds as a homo-heptamer with a cylindrical shape, and can be divided into transmembrane and extramembrane regions: an N-terminal periplasmic region, a transmembrane region, and a C-terminal cytoplasmic region (middle and C-terminal domains). The transmembrane region forms a channel through the membrane that opens into a chamber enclosed by the extramembrane portion, the latter connecting to the cytoplasm through distinct portals [].; GO: 0055085 transmembrane transport, 0016020 membrane; PDB: 2OAU_E 2VV5_F.
Probab=33.83 E-value=49 Score=26.57 Aligned_cols=38 Identities=16% Similarity=0.210 Sum_probs=19.1
Q ss_pred EecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEe
Q 029796 99 KFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATR 146 (187)
Q Consensus 99 ~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~ 146 (187)
||++|+.+-+- |..|+|.+|.. . ...+++.+|+...-+
T Consensus 60 pf~vGD~I~i~-----~~~G~V~~I~l----~-~t~l~~~~g~~v~IP 97 (206)
T PF00924_consen 60 PFKVGDRIEIG-----GVEGRVEEIGL----R-STRLRTWDGEIVIIP 97 (206)
T ss_dssp SS-TT-EEESS-----S-EEEEEEE-S----S-EEEEEETTS-EEEEE
T ss_pred CccCCCEEEEE-----EeehHHHhcCc----c-eeeeecCCCCEEEEE
Confidence 45555553332 77888888843 2 255667777654433
No 46
>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=33.75 E-value=1.4e+02 Score=20.54 Aligned_cols=43 Identities=16% Similarity=0.150 Sum_probs=27.6
Q ss_pred eEEEEeeeEEeeCCeeEEEccCceEEeeCCC-------CcccCCeEEEecCC
Q 029796 47 KLCKVRSVQFGQKGIPYINTYDGRTIRYPDP-------LIKANDTIKLDLEE 91 (187)
Q Consensus 47 KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~-------~ik~~DTv~i~l~~ 91 (187)
-+|+|.. ...++...+.+.||.+++..=| -++.||.|++++..
T Consensus 5 ~~~~V~~--~lG~~~~~V~~~dg~~~l~~i~gK~r~~iwI~~GD~V~V~~~~ 54 (65)
T PF01176_consen 5 VIGRVTE--MLGNNLFEVECEDGEERLARIPGKFRKRIWIKRGDFVLVEPSP 54 (65)
T ss_dssp EEEEEEE--EESSSEEEEEETTSEEEEEEE-HHHHTCC---TTEEEEEEEST
T ss_pred EEEEEEE--ECCCCEEEEEeCCCCEEEEEeccceeeeEecCCCCEEEEEecc
Confidence 3566765 3347777888888888854312 57889999998764
No 47
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=33.45 E-value=1e+02 Score=22.61 Aligned_cols=32 Identities=25% Similarity=0.407 Sum_probs=24.2
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCC
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALG 140 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g 140 (187)
+.+|+.++.+|| -+|+|.++.. +.+.++.+.|
T Consensus 38 L~~Gd~VvT~gG----i~G~V~~i~d-----~~v~vei~~g 69 (84)
T TIGR00739 38 LKKGDKVLTIGG----IIGTVTKIAE-----NTIVIELNDN 69 (84)
T ss_pred CCCCCEEEECCC----eEEEEEEEeC-----CEEEEEECCC
Confidence 567888888775 6899999863 5677877666
No 48
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=33.28 E-value=69 Score=33.64 Aligned_cols=37 Identities=27% Similarity=0.557 Sum_probs=29.2
Q ss_pred EecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEE
Q 029796 87 LDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125 (187)
Q Consensus 87 i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~ 125 (187)
|+++..+... -|++|+.|=|+.|+|-|..|.|+.++.
T Consensus 449 l~~~~~eLrK--yF~~GDhVKVi~G~~eG~tGlVvrVe~ 485 (1024)
T KOG1999|consen 449 LEVPASELRK--YFEPGDHVKVIAGRYEGDTGLVVRVEQ 485 (1024)
T ss_pred cccchHhhhh--hccCCCeEEEEeccccCCcceEEEEeC
Confidence 3444444433 378999999999999999999999976
No 49
>COG1792 MreC Cell shape-determining protein [Cell envelope biogenesis, outer membrane]
Probab=31.06 E-value=3.8e+02 Score=23.77 Aligned_cols=36 Identities=22% Similarity=0.364 Sum_probs=28.4
Q ss_pred EEEEEEEEEec-CCccEEEEEcCCCCeEEEeeceEEEEcc
Q 029796 117 VGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGK 155 (187)
Q Consensus 117 vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIG~ 155 (187)
||+|..++.+. +.+..|.++-.. -.+++.||+++..
T Consensus 234 Vg~V~~v~~~~~~~~~~v~~~P~a---~~~~l~~v~l~~~ 270 (284)
T COG1792 234 VGEVSSVKLDDYGLFKVVIVKPAA---SLDRLRYVLLVKR 270 (284)
T ss_pred EEEEEEEEeCCCceeEEEEEeccc---ccccceEEEEEec
Confidence 78888888766 566888887654 3789999999985
No 50
>smart00536 AXH domain in Ataxins and HMG containing proteins. unknown function
Probab=30.91 E-value=1.6e+02 Score=23.29 Aligned_cols=77 Identities=16% Similarity=0.201 Sum_probs=44.7
Q ss_pred EEEccCceEEeeCCCCcccCCeEEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCc-cEEEEEcCCCC
Q 029796 63 YINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQDALGH 141 (187)
Q Consensus 63 ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~-~~V~i~d~~g~ 141 (187)
+|.+|+|++-++.| +++.|.+.-...+ +-++++..-...|......|. ..|.=.++.. ..|+++=.-++
T Consensus 7 ~I~l~~G~~krvED--l~teDfi~sa~~s----~~~~l~~stv~~i~~~~~~~~----v~itF~~g~~~~~v~~ev~~eH 76 (116)
T smart00536 7 RLCLANGSNKKVED--LKTEDFIRSAECS----NDEEIQMSTVKRIGSSGLPSV----VTLTFDPGVEDALLTVECQVEH 76 (116)
T ss_pred EEEecCCCeeeeec--cchhhhHhhhccC----CcccccceeEEEeCCCCCcce----EEEEEEecCccceEEEEEecCC
Confidence 46669999888755 7888888776665 344555555555554333222 1233333322 66666644445
Q ss_pred eEEEeeceEEEEccC
Q 029796 142 EFATRLGNVFTIGKG 156 (187)
Q Consensus 142 ~F~T~~~~vfvIG~~ 156 (187)
.| ||-|+|
T Consensus 77 Pf-------FV~gqG 84 (116)
T smart00536 77 PF-------FVKGKG 84 (116)
T ss_pred Ce-------EEcCcc
Confidence 44 777765
No 51
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=30.76 E-value=57 Score=29.10 Aligned_cols=30 Identities=40% Similarity=0.661 Sum_probs=27.2
Q ss_pred eEEEecCCcEEEEECCCcceeEEEEEEEEE
Q 029796 96 DFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125 (187)
Q Consensus 96 ~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~ 125 (187)
..+.|++|+.+-|+.|.=.|..|+|.++..
T Consensus 202 ~~~~f~vGd~VrI~dGPF~GfeG~I~eid~ 231 (258)
T TIGR01956 202 NLSKFRVGNFVKIVDGPFKGIVGKIKKIDQ 231 (258)
T ss_pred cccCCCCCCEEEEEecCCCCcEEEEEEEeC
Confidence 457799999999999999999999999864
No 52
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=30.66 E-value=81 Score=24.94 Aligned_cols=26 Identities=23% Similarity=0.325 Sum_probs=24.2
Q ss_pred EecCCcEEEEECCCcceeEEEEEEEE
Q 029796 99 KFDVGNIVMVTGGRNRGRVGIIKNRE 124 (187)
Q Consensus 99 ~fe~G~~~~vtgG~n~G~vG~I~~i~ 124 (187)
.|++|+.+.|++|.=.|..|.|.++.
T Consensus 109 ~~~~G~~V~I~~Gp~~g~eg~v~~~~ 134 (162)
T PRK09014 109 TPKPGDKVIITEGAFEGLQAIYTEPD 134 (162)
T ss_pred CCCCCCEEEEecCCCCCcEEEEEEeC
Confidence 58999999999999999999999874
No 53
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=30.56 E-value=83 Score=27.56 Aligned_cols=29 Identities=28% Similarity=0.502 Sum_probs=17.1
Q ss_pred EEecCCcEEEEECCCcceeEEEEEEEEEe
Q 029796 98 IKFDVGNIVMVTGGRNRGRVGIIKNREKH 126 (187)
Q Consensus 98 i~fe~G~~~~vtgG~n~G~vG~I~~i~~~ 126 (187)
-.|--|+++=|.-|+..|+.|.+..+.++
T Consensus 71 w~ff~GDtVeVlvGkDkGkqG~Vtqv~r~ 99 (236)
T KOG1708|consen 71 WHFFFGDTVEVLVGKDKGKQGEVTQVIRH 99 (236)
T ss_pred eeEecCCEEEEEecccCCccceEEEEeec
Confidence 34445666666666666666666665544
No 54
>COG1917 Uncharacterized conserved protein, contains double-stranded beta-helix domain [Function unknown]
Probab=30.41 E-value=80 Score=23.80 Aligned_cols=56 Identities=20% Similarity=0.249 Sum_probs=37.1
Q ss_pred eEEEEeeeEEeeCCeeEEEccC-c-eEEeeCCCCcccCCeEEEecCCCeeeeEEEecCCcEEEEECCC
Q 029796 47 KLCKVRSVQFGQKGIPYINTYD-G-RTIRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGR 112 (187)
Q Consensus 47 KLcKV~~k~~~~gg~~ql~~hD-G-rni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~vtgG~ 112 (187)
.-|++...+.-+|+.+..++|+ + .++.+-+. .+.+.+.. +.+.+.+|+...+=-|.
T Consensus 41 ~~~~~~~v~~~~G~~~~~H~hp~~~~~~~Vl~G------~~~~~~~g----~~~~l~~Gd~i~ip~g~ 98 (131)
T COG1917 41 ENLSVVLVTFEPGAVIPWHTHPLGEQTIYVLEG------EGTVQLEG----EKKELKAGDVIIIPPGV 98 (131)
T ss_pred ceEEEEEEEECCCcccccccCCCcceEEEEEec------EEEEEecC----CceEecCCCEEEECCCC
Confidence 4588999999999999999998 6 44443222 23344442 45566677766665543
No 55
>COG1188 Ribosome-associated heat shock protein implicated in the recycling of the 50S subunit (S4 paralog) [Translation, ribosomal structure and biogenesis]
Probab=30.07 E-value=65 Score=24.88 Aligned_cols=35 Identities=14% Similarity=0.381 Sum_probs=27.7
Q ss_pred EEeeCCeeEEEccCceEEeeCCCCcccCCeEEEecCCCe
Q 029796 55 QFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENK 93 (187)
Q Consensus 55 ~~~~gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~k 93 (187)
.++.+|++++ +|.... |...+|+||.|.|.+....
T Consensus 29 ~~~~~GrV~v---NG~~aK-pS~~VK~GD~l~i~~~~~~ 63 (100)
T COG1188 29 EMIEGGRVKV---NGQRAK-PSKEVKVGDILTIRFGNKE 63 (100)
T ss_pred HHHHCCeEEE---CCEEcc-cccccCCCCEEEEEeCCcE
Confidence 3466888888 577775 7778999999999998643
No 56
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=29.73 E-value=1e+02 Score=32.47 Aligned_cols=54 Identities=22% Similarity=0.285 Sum_probs=42.0
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEec-CCccEEEEEcCCCCeEEEeeceEEEEcc
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNREKHK-GSFETIHIQDALGHEFATRLGNVFTIGK 155 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i~~~~-~s~~~V~i~d~~g~~F~T~~~~vfvIG~ 155 (187)
..+++++-+++|.|.|+-|.|.+|.+.. =..+.-++| ++-.|-++..|+..+|.
T Consensus 582 I~~kD~Vkvi~Gp~~g~~G~v~~i~r~~~F~h~r~~~E--n~Gv~vck~k~~~~~g~ 636 (1024)
T KOG1999|consen 582 IRVKDTVKVIGGPSKGREGEVLHIYRPFVFLHSRKNLE--NGGVFVCKEKNLILAGG 636 (1024)
T ss_pred ecccceEEEecCCCCCccCccceeecceeeeeehhhcc--cCCeEEEecCCceeccc
Confidence 4679999999999999999999997632 111334454 55589999999999995
No 57
>cd04478 RPA2_DBD_D RPA2_DBD_D: A subfamily of OB folds corresponding to the OB fold of the central ssDNA-binding domain (DBD)-D of human RPA2 (also called RPA32). RPA2 is a subunit of Replication protein A (RPA). RPA is a nuclear ssDNA-binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). The major DNA binding activity of RPA is associated with RPA1 DBD-A and DBD-B; RPA2 DBD-D is a weak ssDNA-binding domain. RPA2 DBD-D is also involved in trimerization. The ssDNA binding mechanism is believed to be multistep and to involve conformational change. N-terminal to human RPA2 DBD-D is a domain containing all the known phosphorylation sites of RPA. Human RPA2 is phosphorylated in a cell cycle dependent manner in response to DNA dam
Probab=29.19 E-value=2.1e+02 Score=20.18 Aligned_cols=54 Identities=15% Similarity=0.184 Sum_probs=39.9
Q ss_pred EEEecCCCceEEEE-EcCCCceEEEEcCchhh----c------eeEEEEeeeEEeeCCeeEEEcc
Q 029796 14 VVSIPKTNENFRLL-YDTKGRFRLHSLRDEEA----K------FKLCKVRSVQFGQKGIPYINTY 67 (187)
Q Consensus 14 VIsI~kt~e~yRvl-~d~kg~f~l~~I~~eEa----~------~KLcKV~~k~~~~gg~~ql~~h 67 (187)
|.++...+.++++- -|..|.+....-...+. . =.+.||.++...-+|.+||..+
T Consensus 8 V~~~~~~~~~~~~tL~D~TG~I~~~~W~~~~~~~~~~~~~~~~g~~v~v~G~v~~~~g~~ql~i~ 72 (95)
T cd04478 8 VRNVEEQSTNITYTIDDGTGTIEVRQWLDDDNDDSSEVEPIEEGTYVRVFGNLKSFQGKKSIMAF 72 (95)
T ss_pred EEeeeEcccEEEEEEECCCCcEEEEEeCCCCCcccccccccccCCEEEEEEEEcccCCeeEEEEE
Confidence 67777777777776 56788887666544432 1 2589999999888999999876
No 58
>PF09285 Elong-fact-P_C: Elongation factor P, C-terminal; InterPro: IPR015365 These nucleic acid binding domains are predominantly found in elongation factor P, where they adopt an OB-fold, with five beta-strands forming a beta-barrel in a Greek-key topology []. ; GO: 0043043 peptide biosynthetic process, 0005737 cytoplasm; PDB: 1YBY_A 3OYY_B 1UEB_B 3HUW_V 3HUY_V 3A5Z_H.
Probab=28.82 E-value=1.4e+02 Score=20.58 Aligned_cols=36 Identities=22% Similarity=0.326 Sum_probs=23.6
Q ss_pred CCeeEEEccCceEEeeCCCCcccCCeEEEecCCCeee
Q 029796 59 KGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKIT 95 (187)
Q Consensus 59 gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~ 95 (187)
+..-...|..|-.+.+| +-++.||.|++|-.+++=+
T Consensus 19 ~~~K~A~letG~~i~VP-~FI~~Gd~I~VdT~~g~Yv 54 (56)
T PF09285_consen 19 SSYKPATLETGAEIQVP-LFIEEGDKIKVDTRDGSYV 54 (56)
T ss_dssp TTEEEEEETTS-EEEEE-TT--TT-EEEEETTTTEEE
T ss_pred CCccEEEEcCCCEEEcc-ceecCCCEEEEECCCCeEe
Confidence 34455667788888864 4799999999999987643
No 59
>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=28.76 E-value=1.3e+02 Score=22.06 Aligned_cols=38 Identities=18% Similarity=0.315 Sum_probs=21.9
Q ss_pred EEEEeeeEEee-CCeeEEEccCceEEeeCCCC-------cccCCeEEEe
Q 029796 48 LCKVRSVQFGQ-KGIPYINTYDGRTIRYPDPL-------IKANDTIKLD 88 (187)
Q Consensus 48 LcKV~~k~~~~-gg~~ql~~hDGrni~~~d~~-------ik~~DTv~i~ 88 (187)
+|||.+ .. ++...+.+.||.+.+..=|. +|-||-|+++
T Consensus 3 i~rV~~---~~G~n~~~V~~~dG~~~l~~iP~KfRk~iWIkrGd~VlV~ 48 (78)
T cd05792 3 IVRVLG---SKGNNLHEVETPNGSRYLVSMPTKFRKNIWIKRGDFVLVE 48 (78)
T ss_pred EEEEEE---cCCCcEEEEEcCCCCEEEEEechhhcccEEEEeCCEEEEE
Confidence 466655 23 44455666777777554332 6666666665
No 60
>KOG2333 consensus Uncharacterized conserved protein [General function prediction only]
Probab=28.62 E-value=9.8 Score=37.16 Aligned_cols=16 Identities=31% Similarity=0.600 Sum_probs=13.5
Q ss_pred Cccceec-ccceeEEEE
Q 029796 1 MSFFFSF-GTLLTDVVS 16 (187)
Q Consensus 1 ~~~~~kf-PvGlMDVIs 16 (187)
||||++| ||||.|++-
T Consensus 544 lSF~~RYiPv~l~e~lp 560 (614)
T KOG2333|consen 544 LSFFHRYIPVGLLEVLP 560 (614)
T ss_pred HHHHHhhchHHHhhcCc
Confidence 6899998 999998863
No 61
>PF02239 Cytochrom_D1: Cytochrome D1 heme domain; PDB: 1NNO_B 1HZU_A 1N15_B 1N50_A 1GJQ_A 1BL9_B 1NIR_B 1N90_B 1HZV_A 1AOQ_A ....
Probab=28.34 E-value=4e+02 Score=24.20 Aligned_cols=46 Identities=13% Similarity=0.093 Sum_probs=28.2
Q ss_pred eEEeeCCeeEEEccCceEEeeCCCCcccCCeEEEecCCCeeeeEEEec
Q 029796 54 VQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDLEENKITDFIKFD 101 (187)
Q Consensus 54 k~~~~gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~~~i~fe 101 (187)
..++.+-.-.-...|||-+... .+..++..++|..+.+++..||-.
T Consensus 74 i~~G~~~~~i~~s~DG~~~~v~--n~~~~~v~v~D~~tle~v~~I~~~ 119 (369)
T PF02239_consen 74 IKVGGNPRGIAVSPDGKYVYVA--NYEPGTVSVIDAETLEPVKTIPTG 119 (369)
T ss_dssp EE-SSEEEEEEE--TTTEEEEE--EEETTEEEEEETTT--EEEEEE--
T ss_pred EecCCCcceEEEcCCCCEEEEE--ecCCCceeEeccccccceeecccc
Confidence 3444444444556799988643 367888889999999999988764
No 62
>cd01723 LSm4 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet. LSm4 is one of at least seven subunits that assemble onto U6 snRNA to form a seven-membered ring structure. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=28.17 E-value=1.3e+02 Score=21.28 Aligned_cols=49 Identities=12% Similarity=0.265 Sum_probs=32.1
Q ss_pred eEEEEEEEEEecCCc-cEEEEEcCCCCeEEEeeceEEEEccCCCceEEccCC
Q 029796 116 RVGIIKNREKHKGSF-ETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKG 166 (187)
Q Consensus 116 ~vG~I~~i~~~~~s~-~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp~~ 166 (187)
-.|++.+...++.=. +-+...+.+|+.+ +..+.+|+=|. .=-+|++|..
T Consensus 24 ~~G~L~~~D~~mNi~L~~~~~~~~~g~~~-~~~~~v~IRG~-~I~~i~~p~~ 73 (76)
T cd01723 24 YNGHLVNCDNWMNIHLREVICTSKDGDKF-WKMPECYIRGN-TIKYLRVPDE 73 (76)
T ss_pred EEEEEEEEcCCCceEEEeEEEECCCCcEe-eeCCcEEEeCC-EEEEEEcCHH
Confidence 478999887766322 3344555677654 35688999996 5556777753
No 63
>PF05709 Sipho_tail: Phage tail protein; InterPro: IPR008841 This family consists of several Siphovirus and other phage tail component proteins as well as some bacterial proteins of unknown function. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.; PDB: 4DIV_X 2X8K_C.
Probab=27.61 E-value=2.7e+02 Score=22.55 Aligned_cols=54 Identities=28% Similarity=0.444 Sum_probs=26.3
Q ss_pred eeCCeeEEEccCceEEeeCCC---CcccCCeEEEecCCCee------------------eeEEEecCCcEEEEECC
Q 029796 57 GQKGIPYINTYDGRTIRYPDP---LIKANDTIKLDLEENKI------------------TDFIKFDVGNIVMVTGG 111 (187)
Q Consensus 57 ~~gg~~ql~~hDGrni~~~d~---~ik~~DTv~i~l~~~kI------------------~~~i~fe~G~~~~vtgG 111 (187)
.....++++..++ .+.+.++ ++..||+|+||-+.+.+ .++++|.+|..-+-+.|
T Consensus 159 ~~~~~~~i~~~~~-~~~~~~~~~~~~~~gd~i~Id~~~~~v~~ng~~~~~~~~~~~~~~~~f~~L~~G~N~i~~~~ 233 (249)
T PF05709_consen 159 GDSSNITINNGQT-VFQFGNPKEIDLTAGDTIVIDSEKDTVYLNGQNSINNNAIGRLTNSDFPKLPPGENTISITG 233 (249)
T ss_dssp CESSSEEEEECCT-EEEEE-EE----STSCEEEECCTTCEEECTTEE-CCCSSST----T----B-BTSEEEEES-
T ss_pred ccccEEEEecCce-eEEecCccccccCCCcEEEEECCCCEEEEeCceeeccccccccccCCCCEECCCCCEEEEEE
Confidence 3344466666666 4433332 37889999998654332 25666666665555544
No 64
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=26.97 E-value=4.4e+02 Score=23.21 Aligned_cols=71 Identities=23% Similarity=0.256 Sum_probs=45.7
Q ss_pred CCCcccCCeEEE-ecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeece-EEEE
Q 029796 76 DPLIKANDTIKL-DLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGN-VFTI 153 (187)
Q Consensus 76 d~~ik~~DTv~i-~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~-vfvI 153 (187)
+..+++|+++-| ++|.+.++--|.+.+|+=+-+. +.+|.-++|..-+ . +.+.|+=.+|+. .....+ --.|
T Consensus 86 ~~~i~~Gn~lpL~~IP~Gt~I~NIE~~pG~Ggkl~--RSAGt~A~Ii~k~---~--~~~~vkLPSGe~-r~i~~~c~Ati 157 (238)
T PRK09612 86 SAEIKPGNTLPLGEIPEGTPVCNIESRPGDGGKFA--RSSGTYALVVGHE---G--DKVIVQLPSGKI-KELNPRCRATI 157 (238)
T ss_pred CCCCCCccccCHhhCCCCCEEEEEEecCCCCcceE--EcCCCeEEEEEec---C--CEEEEECCCCCe-EEECCcCeEEE
Confidence 446788888877 7899999999988888722211 4677788877642 2 345555567764 444444 3345
Q ss_pred c
Q 029796 154 G 154 (187)
Q Consensus 154 G 154 (187)
|
T Consensus 158 G 158 (238)
T PRK09612 158 G 158 (238)
T ss_pred E
Confidence 6
No 65
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=26.84 E-value=68 Score=26.71 Aligned_cols=30 Identities=17% Similarity=0.367 Sum_probs=26.7
Q ss_pred eEEEecCCcEEEEECCCcceeEEEEEEEEE
Q 029796 96 DFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125 (187)
Q Consensus 96 ~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~ 125 (187)
....|++|+.+-|+.|.=+|..|+|.++..
T Consensus 120 ~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ 149 (178)
T COG0250 120 PKVDFEPGDVVRIIDGPFAGFKAKVEEVDE 149 (178)
T ss_pred ccccCCCCCEEEEeccCCCCccEEEEEEcC
Confidence 446789999999999999999999999854
No 66
>PF10781 DSRB: Dextransucrase DSRB; InterPro: IPR019717 DSRB is a novel dextransucrase which produces a dextran different from the typical dextran, as it contains (1-6) and (1-2) linkages, when this strain is grown in the presence of sucrose [].
Probab=26.79 E-value=1.5e+02 Score=20.99 Aligned_cols=29 Identities=28% Similarity=0.484 Sum_probs=16.0
Q ss_pred ccCCeEEEecC-----CCeeeeEEEecCCcEEEE
Q 029796 80 KANDTIKLDLE-----ENKITDFIKFDVGNIVMV 108 (187)
Q Consensus 80 k~~DTv~i~l~-----~~kI~~~i~fe~G~~~~v 108 (187)
|+||.|.+.-. ++.|+..=+|.+|-+.+|
T Consensus 2 kvnD~VtVKTDG~~rR~G~ilavE~F~EG~MYLv 35 (62)
T PF10781_consen 2 KVNDRVTVKTDGGPRREGVILAVEPFNEGTMYLV 35 (62)
T ss_pred ccccEEEEecCCcccccceEEEEeeccCcEEEEE
Confidence 45666655544 345566666666654443
No 67
>PTZ00141 elongation factor 1- alpha; Provisional
Probab=26.71 E-value=3.7e+02 Score=25.15 Aligned_cols=52 Identities=27% Similarity=0.313 Sum_probs=34.1
Q ss_pred CcccCCeEEEecCCCeeeeEEEe----cCCcEEEEECCCcceeEEEEEEEEEecCCc
Q 029796 78 LIKANDTIKLDLEENKITDFIKF----DVGNIVMVTGGRNRGRVGIIKNREKHKGSF 130 (187)
Q Consensus 78 ~ik~~DTv~i~l~~~kI~~~i~f----e~G~~~~vtgG~n~G~vG~I~~i~~~~~s~ 130 (187)
.++.||...+.|...+=+-.-+| .-|..++.-+|.-+| .|.|.++....||-
T Consensus 381 ~l~~g~~a~v~l~~~~pi~~e~~~~~~~lgrfilrd~g~tva-~G~I~~v~~~~~~~ 436 (446)
T PTZ00141 381 AIKSGDAAIVKMVPTKPMCVEVFNEYPPLGRFAVRDMKQTVA-VGVIKSVEKKEGSG 436 (446)
T ss_pred EECCCCEEEEEEEECCceEEeecccCCCCccEEEEECCCEEE-EEEEEEEecCCCcc
Confidence 57889998888864443222333 246677777776555 79998887665554
No 68
>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=26.59 E-value=1.4e+02 Score=19.64 Aligned_cols=28 Identities=32% Similarity=0.451 Sum_probs=17.8
Q ss_pred CCCcccCCeEEEecCCCeeeeEEEecCCcEEEEEC
Q 029796 76 DPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTG 110 (187)
Q Consensus 76 d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~vtg 110 (187)
.|.|+.||.|.++-.. +...|+.+++.-
T Consensus 8 ~P~i~~Gd~v~v~~~~-------~~~~gdivv~~~ 35 (70)
T PF00717_consen 8 EPTIKDGDIVLVDPSS-------EPKDGDIVVVKI 35 (70)
T ss_dssp GGTSSTTEEEEEEETS----------TTSEEEEEE
T ss_pred ccCeeCCCEEEEEEcC-------CCccCeEEEEEE
Confidence 4778888888888333 667788777743
No 69
>PF11717 Tudor-knot: RNA binding activity-knot of a chromodomain ; PDB: 2EKO_A 2RO0_A 2RNZ_A 1WGS_A 3E9G_A 3E9F_A 2K3X_A 2K3Y_A 2EFI_A 2F5K_F ....
Probab=26.09 E-value=2e+02 Score=18.98 Aligned_cols=37 Identities=22% Similarity=0.238 Sum_probs=28.2
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEecCCc-cEEEEE
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSF-ETIHIQ 136 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~-~~V~i~ 136 (187)
|++|..|++.-+...-.-++|.+++..++.. =.||-.
T Consensus 1 ~~vG~~v~~~~~~~~~y~A~I~~~r~~~~~~~YyVHY~ 38 (55)
T PF11717_consen 1 FEVGEKVLCKYKDGQWYEAKILDIREKNGEPEYYVHYQ 38 (55)
T ss_dssp --TTEEEEEEETTTEEEEEEEEEEEECTTCEEEEEEET
T ss_pred CCcCCEEEEEECCCcEEEEEEEEEEecCCCEEEEEEcC
Confidence 6889999999999999999999998865543 455553
No 70
>PF12791 RsgI_N: Anti-sigma factor N-terminus; InterPro: IPR024449 The heat shock genes in Bacillus subtilis can be classified into several groups according to their regulation [], and the sigma gene, sigI, of Bacillus subtilis belongs to the group IV heat-shock response genes and has many orthologues in the bacterial phylum Firmicutes []. Regulation of sigma factor I is carried out by RsgI from the same operon. This entry represents the N-terminal cytoplasmic portion of RsgI ('upstream' of the single transmembrane helix) which has been shown to interact directly with Sigma-I [].
Probab=25.98 E-value=1.4e+02 Score=19.57 Aligned_cols=35 Identities=23% Similarity=0.326 Sum_probs=26.0
Q ss_pred eeCCeeEEEccCceEEeeC-CCCcccCCeEEEecCC
Q 029796 57 GQKGIPYINTYDGRTIRYP-DPLIKANDTIKLDLEE 91 (187)
Q Consensus 57 ~~gg~~ql~~hDGrni~~~-d~~ik~~DTv~i~l~~ 91 (187)
.+++...+-|.||.=++.+ .+..++|+-+.++..+
T Consensus 3 i~~~~aiVlT~dGeF~~ik~~~~~~vG~eI~~~~~~ 38 (56)
T PF12791_consen 3 IKKKYAIVLTPDGEFIKIKRKPGMEVGQEIEFDEKD 38 (56)
T ss_pred CcCCEEEEEcCCCcEEEEeCCCCCcccCEEEEechh
Confidence 3567778899999988664 3458999988887543
No 71
>PF07569 Hira: TUP1-like enhancer of split; InterPro: IPR011494 The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain IPR001680 from INTERPRO.; GO: 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=25.18 E-value=2.2e+02 Score=24.06 Aligned_cols=56 Identities=18% Similarity=0.377 Sum_probs=42.2
Q ss_pred CCceEEEEEcCCCceEEEEcCchhhceeE------------------EEEeeeEEeeCCeeEEEccCceEEeeC
Q 029796 20 TNENFRLLYDTKGRFRLHSLRDEEAKFKL------------------CKVRSVQFGQKGIPYINTYDGRTIRYP 75 (187)
Q Consensus 20 t~e~yRvl~d~kg~f~l~~I~~eEa~~KL------------------cKV~~k~~~~gg~~ql~~hDGrni~~~ 75 (187)
...+|-+.....|.|..=.+....+-++- ..|+...+-+.|.|.+.+.+|..+.|+
T Consensus 20 ~~~~~Ll~iT~~G~l~vWnl~~~k~~~~~~Si~pll~~~~~~~~~~~~~i~~~~lt~~G~PiV~lsng~~y~y~ 93 (219)
T PF07569_consen 20 CNGSYLLAITSSGLLYVWNLKKGKAVLPPVSIAPLLNSSPVSDKSSSPNITSCSLTSNGVPIVTLSNGDSYSYS 93 (219)
T ss_pred eCCCEEEEEeCCCeEEEEECCCCeeccCCccHHHHhcccccccCCCCCcEEEEEEcCCCCEEEEEeCCCEEEec
Confidence 46777777888888877666655544443 566777777899999999999999884
No 72
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=24.93 E-value=70 Score=26.02 Aligned_cols=24 Identities=29% Similarity=0.609 Sum_probs=20.6
Q ss_pred ecCCcEEEEECCCcceeEEEEEEE
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNR 123 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i 123 (187)
|.+|..++++.|+++|+-.+|..-
T Consensus 5 lkPgkvv~v~sG~yAg~KaVivk~ 28 (136)
T KOG3418|consen 5 LKPGKVVLVLSGRYAGKKAVIVKN 28 (136)
T ss_pred ccCCcEEEeecccccCccEEEEee
Confidence 578999999999999988877653
No 73
>cd03707 EFTU_III Domain III of elongation factor (EF) Tu. Ef-Tu consists of three structural domains, designated I, II and III. Domain III adopts a beta barrel structure. Domain III is involved in binding to both charged tRNA and binding to elongation factor Ts (EF-Ts). EF-Ts is the guanine-nucleotide-exchange factor for EF-Tu. EF-Tu and EF-G participate in the elongation phase during protein biosynthesis on the ribosome. Their functional cycles depend on GTP binding and its hydrolysis. The EF-Tu complexed with GTP and aminoacyl-tRNA delivers tRNA to the ribosome, whereas EF-G stimulates translocation, a process in which tRNA and mRNA movements occur in the ribosome. Crystallographic studies revealed structural similarities ("molecular mimicry") between tertiary structures of EF-G and the EF-Tu-aminoacyl-tRNA ternary complex. Domains III, IV, and V of EF-G mimic the tRNA structure in the EF-Tu ternary complex; domains III, IV and V can be related to the acceptor stem, anticodon helix
Probab=24.36 E-value=2.6e+02 Score=19.64 Aligned_cols=27 Identities=19% Similarity=0.293 Sum_probs=16.0
Q ss_pred cccCCeEEEecCCCeeeeEEEecCCcEEEE
Q 029796 79 IKANDTIKLDLEENKITDFIKFDVGNIVMV 108 (187)
Q Consensus 79 ik~~DTv~i~l~~~kI~~~i~fe~G~~~~v 108 (187)
+++||+..+.|.-.+ -+.++.|.-.++
T Consensus 52 i~~g~~~~v~l~l~~---pv~~~~~~rf~l 78 (90)
T cd03707 52 VMPGDNVKMTVELIH---PIALEKGLRFAI 78 (90)
T ss_pred cCCCCEEEEEEEECC---cEEEecCCEEEE
Confidence 888888777776432 234555544444
No 74
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=23.98 E-value=2.6e+02 Score=21.37 Aligned_cols=40 Identities=15% Similarity=0.197 Sum_probs=28.3
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeece
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGN 149 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~ 149 (187)
+++|+.++.+|| -+|+|.++.. +.|.++-++| ..-|+..+
T Consensus 53 Lk~Gd~VvT~gG----i~G~Vv~i~~-----~~v~lei~~g-~~i~~~r~ 92 (106)
T PRK05585 53 LAKGDEVVTNGG----IIGKVTKVSE-----DFVIIELNDD-TEIKIQKS 92 (106)
T ss_pred cCCCCEEEECCC----eEEEEEEEeC-----CEEEEEECCC-eEEEEEhH
Confidence 567888888775 6899999853 6788886666 44555544
No 75
>cd04708 BAH_plantDCM_II BAH, or Bromo Adjacent Homology domain, second copy present in DNA (Cytosine-5)-methyltransferases (DCM) from plants. DNA methylation, or the covalent addition of a methyl group to cytosine within the context of the CpG dinucleotide, has profound effects on the genome. These effects include transcriptional repression via inhibition of transcription factor binding, the recruitment of methyl-binding proteins and their associated chromatin remodeling factors, X chromosome inactivation, imprinting, and the suppression of parasitic DNA sequences. DNA methylation is also essential for proper embryonic development and is an important player in both DNA repair and genome stability. 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=23.83 E-value=87 Score=26.91 Aligned_cols=44 Identities=18% Similarity=0.138 Sum_probs=31.4
Q ss_pred CcccCCeEEEecCCCeeeeEEEecCCcEEEEECCCcce----eEEEEEEEEEec
Q 029796 78 LIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRG----RVGIIKNREKHK 127 (187)
Q Consensus 78 ~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G----~vG~I~~i~~~~ 127 (187)
.|++||.|-+. | +++.|+.....--.+|+|+| +||.|.+|....
T Consensus 7 ~Y~vgD~VYv~-p-----~~f~~~~~~~~~~~~G~N~~~~p~~I~qI~ei~~~k 54 (202)
T cd04708 7 TYSVGDFLYVS-P-----DAFAEEERERATFKAGRNVGLKAFVVCQVLEIVVEK 54 (202)
T ss_pred EEecCCeEEEC-c-----ccccccccccccccccccCCCCCcEEEEEEEEEecc
Confidence 46777777776 3 34555556777778899976 799999996533
No 76
>KOG3586 consensus TBX1 and related T-box transcription factors [Transcription]
Probab=23.53 E-value=1.2e+02 Score=28.99 Aligned_cols=99 Identities=22% Similarity=0.298 Sum_probs=62.6
Q ss_pred ceeEEEEecCCCceEEEEEcC-------------CCceEEEEcCchh--------hceeEEEEeeeEEeeCCeeEEEccC
Q 029796 10 LLTDVVSIPKTNENFRLLYDT-------------KGRFRLHSLRDEE--------AKFKLCKVRSVQFGQKGIPYINTYD 68 (187)
Q Consensus 10 GlMDVIsI~kt~e~yRvl~d~-------------kg~f~l~~I~~eE--------a~~KLcKV~~k~~~~gg~~ql~~hD 68 (187)
=+||||-++ ++.||-.|.. .+|+.+|+=++-- ..|-=+|.+|..+-++|++.||--.
T Consensus 128 vlmDvVPvD--~KRYRYayH~S~WlvAGkADp~~p~R~yvHPDSP~sGe~wmkqiVSFdK~KLTNNelD~nGHIILNSMH 205 (437)
T KOG3586|consen 128 VLMDVVPVD--SKRYRYAYHSSSWLVAGKADPAPPPRVYVHPDSPASGEQWMKQIVSFDKLKLTNNELDDNGHIILNSMH 205 (437)
T ss_pred EEEeEEecc--cceeeeeecccceeeecCCCCCCCCceeeCCCCCCCHHHHHHhhhchheeeccccccccCCcEeeeccc
Confidence 379999996 7999999964 5688888755321 1233468899999999999997533
Q ss_pred ceE----EeeCCCCcccCCeEEEecCCCeeeeEEEecCCcEEEEECCCcc
Q 029796 69 GRT----IRYPDPLIKANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNR 114 (187)
Q Consensus 69 Grn----i~~~d~~ik~~DTv~i~l~~~kI~~~i~fe~G~~~~vtgG~n~ 114 (187)
--- |.+-|+. +|+.+....+ +=...+-|++=.---||.=.|.
T Consensus 206 kYQPRvHvV~~~~~---~~s~~~~~~~-e~~kTF~FpET~FtAVTAYQNq 251 (437)
T KOG3586|consen 206 KYQPRVHVVYLDPG---NDSNKYVEKN-EGFKTFVFPETVFTAVTAYQNQ 251 (437)
T ss_pred ccCCceEEEEecCC---CCcccccccc-ccceeEeccceeEEEEeecccc
Confidence 211 1111221 1555555443 2235667777776666666664
No 77
>PRK10708 hypothetical protein; Provisional
Probab=23.40 E-value=1.7e+02 Score=20.73 Aligned_cols=29 Identities=21% Similarity=0.428 Sum_probs=15.5
Q ss_pred ccCCeEEEecC-----CCeeeeEEEecCCcEEEE
Q 029796 80 KANDTIKLDLE-----ENKITDFIKFDVGNIVMV 108 (187)
Q Consensus 80 k~~DTv~i~l~-----~~kI~~~i~fe~G~~~~v 108 (187)
|+||.|.+.-. ++.|+..=+|.+|-+.+|
T Consensus 2 kvnD~VtVKTDG~~rR~G~iLavE~F~EG~MyLv 35 (62)
T PRK10708 2 KVNDRVTVKTDGGPRRPGVVLAVEEFSEGTMYLV 35 (62)
T ss_pred ccccEEEEecCCCccccceEEEEeeccCcEEEEE
Confidence 45666655544 344555555555554443
No 78
>TIGR03318 YdfZ_fam putative selenium-binding protein YdfZ. This small protein has a very limited distribution, being found so far only among some gamma-Proteobacteria. The member from Escherichia coli was shown to bind selenium in the absence of a working SelD-dependent selenium incorporation system. Note that while the E. coli member contains a single Cys residue, a likely selenium binding site, some other members of this protein family contain two Cys residues or none.
Probab=23.35 E-value=56 Score=23.42 Aligned_cols=41 Identities=24% Similarity=0.452 Sum_probs=27.6
Q ss_pred ecCCcEEEEECCCcceeEEEEEEEEEec------CCccEEEEEcCCCCeEE
Q 029796 100 FDVGNIVMVTGGRNRGRVGIIKNREKHK------GSFETIHIQDALGHEFA 144 (187)
Q Consensus 100 fe~G~~~~vtgG~n~G~vG~I~~i~~~~------~s~~~V~i~d~~g~~F~ 144 (187)
+..|+.+||.| +|++|+|+.|.--. .....|.|+..+| .|.
T Consensus 11 it~G~rVMia~---tG~tgvikaIh~dglt~~Q~rR~k~Vel~g~e~-~f~ 57 (65)
T TIGR03318 11 ITTGSRVMIAG---TGHTGVIKAIHTEGLTAEQARREKCVELEGCEE-RFA 57 (65)
T ss_pred cCCCcEEEEec---CCccceeehhhhCCCCHHHhhhccEEEEecccc-eec
Confidence 45699999987 67788888886521 2336788875554 454
No 79
>PLN00208 translation initiation factor (eIF); Provisional
Probab=23.09 E-value=4.1e+02 Score=21.77 Aligned_cols=69 Identities=19% Similarity=0.074 Sum_probs=38.1
Q ss_pred CCCceEEEEEcCCCce-EEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCC-------CcccCCeEEEecC
Q 029796 19 KTNENFRLLYDTKGRF-RLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP-------LIKANDTIKLDLE 90 (187)
Q Consensus 19 kt~e~yRvl~d~kg~f-~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~-------~ik~~DTv~i~l~ 90 (187)
+-++++|=.-...+-- .-.+. ++| .-=+|+|+. ...++...+.+.||.+.+..=| -++.||-|++.+.
T Consensus 7 kggk~~~~~k~~~~~~~~el~~-p~e-gq~~g~V~~--~lGn~~~~V~c~dG~~rLa~IpGKmRKrIWI~~GD~VlVel~ 82 (145)
T PLN00208 7 KGGKNRKRGKNEADDEKRELIF-KED-GQEYAQVLR--MLGNGRCEALCIDGTKRLCHIRGKMRKKVWIAAGDIILVGLR 82 (145)
T ss_pred CCccccccccccCccceeeccc-CCC-CcEEEEEEE--EcCCCEEEEEECCCCEEEEEEeccceeeEEecCCCEEEEEcc
Confidence 3456666544443332 22222 233 336788876 3457788888888887753211 2556666666655
Q ss_pred C
Q 029796 91 E 91 (187)
Q Consensus 91 ~ 91 (187)
+
T Consensus 83 ~ 83 (145)
T PLN00208 83 D 83 (145)
T ss_pred C
Confidence 4
No 80
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=22.83 E-value=1.1e+02 Score=29.88 Aligned_cols=43 Identities=16% Similarity=0.175 Sum_probs=33.5
Q ss_pred cCCeEEEecCCCeeeeEEEecCCcEEEEECCCcceeEEEEEEEEE
Q 029796 81 ANDTIKLDLEENKITDFIKFDVGNIVMVTGGRNRGRVGIIKNREK 125 (187)
Q Consensus 81 ~~DTv~i~l~~~kI~~~i~fe~G~~~~vtgG~n~G~vG~I~~i~~ 125 (187)
-+|+.-|+.|.+.+-. -|..|++|-|+-|.+.+.+|.|..|+.
T Consensus 123 ~~~~~rl~~p~~~lRk--~f~~gD~vkVI~g~~~~d~g~V~rI~~ 165 (607)
T COG5164 123 YHFEQRLCGPWGRLRK--GFYKGDLVKVIEGGEMVDIGTVPRIDG 165 (607)
T ss_pred eccCceeecchhhhhc--ccccCCeEEEeccccccccceEEEecC
Confidence 3455666666555433 378899999999999999999999976
No 81
>PF06487 SAP18: Sin3 associated polypeptide p18 (SAP18); InterPro: IPR010516 This family consists of several eukaryotic Sin3 associated polypeptide p18 (SAP18) sequences. SAP18 is known to be a component of the Sin3-containing complex, which is responsible for the repression of transcription via the modification of histone polypeptides []. SAP18 is also present in the ASAP complex which is thought to be involved in the regulation of splicing during the execution of programmed cell death [].; PDB: 2HDE_A 4A90_A 4A6Q_A 4A8X_C.
Probab=22.06 E-value=89 Score=24.60 Aligned_cols=50 Identities=36% Similarity=0.569 Sum_probs=24.9
Q ss_pred CceEEEEE-cCC-CceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCeEEEec
Q 029796 21 NENFRLLY-DTK-GRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKLDL 89 (187)
Q Consensus 21 ~e~yRvl~-d~k-g~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l 89 (187)
--.||++| |.+ |+|...++-. | ..+.+|. .|.+|+. |-.+.+||-+-+.|
T Consensus 69 r~~F~~VypD~~~~r~~~kdlGs---------v---~~g~~~~-----d~~kTL~--~~~F~iGDyidvaI 120 (120)
T PF06487_consen 69 RLSFRLVYPDTRSGRYVSKDLGS---------V---VSGRKGP-----DDNKTLA--DLRFVIGDYIDVAI 120 (120)
T ss_dssp EEEEEEEEECTTTTCEEEEEEEE---------E---ETTB--T-----TTTSBCG--GGT--TT-EEEEEE
T ss_pred EEEEEEEeecCCCCceeeecCCe---------E---ECCCCCC-----CcccCHh--hCCcccCCEEEEeC
Confidence 34789987 745 7776555432 1 1122222 4555554 45677777776543
No 82
>PF11476 TgMIC1: Toxoplasma gondii micronemal protein 1 TgMIC1; InterPro: IPR024691 MIC1 is released as part of a complex by Toxoplasma gondii prior to invasion. The complex, which consists of MIC4-MIC1-MIC6, participates in host cell attachment and penetration, and is critical in invasion. This entry represents the C-terminal domain of MIC1, which has a galectin-like fold that interacts with and stabilises MIC6, providing a mechanism for an exit from the early secretory compartments and trafficking of the complex to micronemes [].; PDB: 2BVB_A 2K2S_A.
Probab=22.02 E-value=2.8e+02 Score=22.24 Aligned_cols=72 Identities=14% Similarity=0.251 Sum_probs=37.4
Q ss_pred EeeCCeeEEEccCceEE--eeCCCC--cccCC--eEEEecC---------CCeeeeEEEec--CCcEEEEECCCcceeEE
Q 029796 56 FGQKGIPYINTYDGRTI--RYPDPL--IKAND--TIKLDLE---------ENKITDFIKFD--VGNIVMVTGGRNRGRVG 118 (187)
Q Consensus 56 ~~~gg~~ql~~hDGrni--~~~d~~--ik~~D--Tv~i~l~---------~~kI~~~i~fe--~G~~~~vtgG~n~G~vG 118 (187)
-+-|...|..+|.|..+ -|..|. +.+|. ++..+.. ++.=-|.+.++ .|.-.+-+|=-|.||+.
T Consensus 3 ~i~gds~~a~l~~gqql~~t~~s~~l~v~vgsch~l~~nf~d~~l~f~t~s~s~~d~ve~~~~ag~~~ltiglg~~gr~~ 82 (137)
T PF11476_consen 3 RIHGDSTQAMLHEGQQLMVTFSSPQLHVSVGSCHSLTVNFSDYFLSFQTTSNSGFDEVEVDDPAGPGELTIGLGHSGRVT 82 (137)
T ss_dssp E-SSSEEEEEE-CTEEEEEEEE-SCEEEEECTTEEEEEETTTTEEEEESSSSSS-EEEE---EEEEEEEEEEESSSS-EE
T ss_pred EEEcchHHHHHhcCceEEEEEecceeeEEecchhheeehhccceEEeecCCCCccceEEeccCCCceeEEEecCCCceEE
Confidence 34577888888888876 445553 23333 2333333 23333333333 24556667777888888
Q ss_pred EEEEEEEec
Q 029796 119 IIKNREKHK 127 (187)
Q Consensus 119 ~I~~i~~~~ 127 (187)
++-..-+..
T Consensus 83 vv~~y~~~~ 91 (137)
T PF11476_consen 83 VVFQYTRNN 91 (137)
T ss_dssp EEEEEEETT
T ss_pred EEEEeeccC
Confidence 877776644
No 83
>smart00306 HintN Hint (Hedgehog/Intein) domain N-terminal region. Hedgehog/Intein domain, N-terminal region. Domain has been split to accommodate large insertions of endonucleases.
Probab=22.00 E-value=2.7e+02 Score=19.10 Aligned_cols=55 Identities=13% Similarity=0.154 Sum_probs=30.5
Q ss_pred cCCcEEEEECCCcceeEEE-EEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEcc
Q 029796 101 DVGNIVMVTGGRNRGRVGI-IKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGK 155 (187)
Q Consensus 101 e~G~~~~vtgG~n~G~vG~-I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~ 155 (187)
.+|+.++...+.+...... +.......+...++.|+..+|.++..-.+.-|.+.+
T Consensus 23 ~~g~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~i~~~~g~~i~~T~~H~~~~~~ 78 (100)
T smart00306 23 EEGDKVLALDEGTLKYSPVKVFLVREPKGEKKFYRIKTENGREITLTPDHLLLVRD 78 (100)
T ss_pred CCCCEEEEecCCCcEEEEEEEEEEEcCCcceeEEEEEECCCCEEEECCCCEEEEec
Confidence 4677777776633222211 122222334558888888888777755555555543
No 84
>PF04246 RseC_MucC: Positive regulator of sigma(E), RseC/MucC; InterPro: IPR007359 This bacterial family of integral membrane proteins represents a positive regulator of the sigma(E) transcription factor, namely RseC/MucC. The sigma(E) transcription factor is up-regulated by cell envelope protein misfolding, and regulates the expression of genes that are collectively termed ECF (devoted to Extra-Cellular Functions) []. In Pseudomonas aeruginosa, derepression of sigma(E) is associated with the alginate-overproducing phenotype characteristic of chronic respiratory tract colonization in cystic fibrosis patients. The mechanism by which RseC/MucC positively regulates the sigma(E) transcription factor is unknown. RseC is also thought to have a role in thiamine biosynthesis in Salmonella typhimurium []. In addition, this family also includes an N-terminal part of RnfF, a Rhodobacter capsulatus protein, of unknown function, that is essential for nitrogen fixation. This protein also contains a domain found in ApbE protein IPR003374 from INTERPRO, which is itself involved in thiamine biosynthesis.
Probab=21.84 E-value=75 Score=24.53 Aligned_cols=61 Identities=18% Similarity=0.215 Sum_probs=33.2
Q ss_pred CceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeC-CCCcccCCeEEEecCCCee
Q 029796 32 GRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYP-DPLIKANDTIKLDLEENKI 94 (187)
Q Consensus 32 g~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~-d~~ik~~DTv~i~l~~~kI 94 (187)
|....+++....|- .-|. .+...+.+..-+...+....++.+ +...++||.|.+.++++..
T Consensus 6 ~~~~~V~~~r~saC-~~C~-~~~~Cg~~~~~~~~~~~~~~~~~~~~~~~~~GD~V~v~i~~~~~ 67 (135)
T PF04246_consen 6 GGIAWVEVQRSSAC-GSCS-ASGGCGTGLLAKLFSGKPITFRAPNPIGAKVGDRVEVEIPESSL 67 (135)
T ss_pred CCEEEEEEccCCcC-cccC-CCCCCCcchhhhhcCCCcEEEEecCCCCCCCCCEEEEEeccchH
Confidence 44555555555553 3444 111222222222333334455543 4579999999999998764
No 85
>PF08529 NusA_N: NusA N-terminal domain; InterPro: IPR013735 This entry represents the N-terminal RNA polymerase-binding domain of bacterial transcription factors such as NusA (N-utilising substance A). NusA is involved in transcriptional pausing, termination and anti-termination. NusA from Thermotoga maritima contains an N-terminal domain and three RNA-binding domains (one S1 domain and two KH domains). The N-terminal domain consists of a bifurcated coiled beta-sheet within an alpha/beta(3)/alpha/beta/alpha fold, which can be divided into two subdomains: a globular head and a helical body. The globular head subdomain may interact with RNA polymerase, while the helical body displays a similar structure to that of the helical domain in sigma70 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0031554 regulation of transcription termination, DNA-dependent; PDB: 1K0R_B 1HH2_P 1L2F_A 2KWP_A.
Probab=21.76 E-value=1.7e+02 Score=22.41 Aligned_cols=48 Identities=13% Similarity=0.259 Sum_probs=23.4
Q ss_pred cCchhhceeEEEEeeeEEee---CCeeEEEccCceEEeeCCCCcccCCeEEEecCC
Q 029796 39 LRDEEAKFKLCKVRSVQFGQ---KGIPYINTYDGRTIRYPDPLIKANDTIKLDLEE 91 (187)
Q Consensus 39 I~~eEa~~KLcKV~~k~~~~---gg~~ql~~hDGrni~~~d~~ik~~DTv~i~l~~ 91 (187)
|+.+...+++++. +.++. ....++.+.|.+. .+|++++||++.+.++.
T Consensus 46 id~~~g~i~v~~~--~~VV~d~~d~~~eI~l~eAk~---~~~~~~vGD~i~~~i~~ 96 (122)
T PF08529_consen 46 IDEDTGEIKVYRK--KEVVEDVEDPDTEISLSEAKK---IDPNAEVGDEIEEEIDP 96 (122)
T ss_dssp EETTTTEEEEEEE--EEEETT-S-TTTEEEHHHHHC---CCTT--TTCEEEEE---
T ss_pred EECCCCeEEEEEE--eeecCCccCccceeeHHHHHh---hCCCCccCCEEEecCCh
Confidence 3344444555553 23333 3344455555432 26889999999998864
No 86
>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=21.69 E-value=2.4e+02 Score=20.35 Aligned_cols=32 Identities=22% Similarity=0.194 Sum_probs=17.7
Q ss_pred CCeeEEEccCceEEeeCCC-------CcccCCeEEEecC
Q 029796 59 KGIPYINTYDGRTIRYPDP-------LIKANDTIKLDLE 90 (187)
Q Consensus 59 gg~~ql~~hDGrni~~~d~-------~ik~~DTv~i~l~ 90 (187)
++...+.+.||.+++..=| -++.||-|++++.
T Consensus 12 ~~~~~V~~~dg~~~l~~i~gK~Rk~iwI~~GD~VlV~~~ 50 (78)
T cd04456 12 NNRHEVECADGQRRLVSIPGKLRKNIWIKRGDFLIVDPI 50 (78)
T ss_pred CCEEEEEECCCCEEEEEEchhhccCEEEcCCCEEEEEec
Confidence 4455555566666643211 2677777777643
No 87
>KOG4547 consensus WD40 repeat-containing protein [General function prediction only]
Probab=21.38 E-value=2.6e+02 Score=27.60 Aligned_cols=94 Identities=16% Similarity=0.217 Sum_probs=59.2
Q ss_pred CCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeE--EEccCceEEeeCCCCcccCCeEEEecCCCeeeeE
Q 029796 20 TNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPY--INTYDGRTIRYPDPLIKANDTIKLDLEENKITDF 97 (187)
Q Consensus 20 t~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~q--l~~hDGrni~~~d~~ik~~DTv~i~l~~~kI~~~ 97 (187)
.+.+-+++|...+.+.+..|.. |.|++..+..+..-.++ ..+.||.......-.+| +++++++|++.+
T Consensus 110 ~~~~~~ciyS~~ad~~v~~~~~-----~~~~~~~~~~~~~~~~~sl~is~D~~~l~~as~~ik-----~~~~~~kevv~~ 179 (541)
T KOG4547|consen 110 DAQRLGCIYSVGADLKVVYILE-----KEKVIIRIWKEQKPLVSSLCISPDGKILLTASRQIK-----VLDIETKEVVIT 179 (541)
T ss_pred cccccCceEecCCceeEEEEec-----ccceeeeeeccCCCccceEEEcCCCCEEEeccceEE-----EEEccCceEEEE
Confidence 3677889999999999988877 55777766655333221 23446666654444454 678899998887
Q ss_pred EEec----------------CCcEEEEECCCcceeEEEEEEE
Q 029796 98 IKFD----------------VGNIVMVTGGRNRGRVGIIKNR 123 (187)
Q Consensus 98 i~fe----------------~G~~~~vtgG~n~G~vG~I~~i 123 (187)
++=- .|.+++-..+.+.|-.+...+=
T Consensus 180 ftgh~s~v~t~~f~~~~~g~~G~~vLssa~~~r~i~~w~v~~ 221 (541)
T KOG4547|consen 180 FTGHGSPVRTLSFTTLIDGIIGKYVLSSAAAERGITVWVVEK 221 (541)
T ss_pred ecCCCcceEEEEEEEeccccccceeeeccccccceeEEEEEc
Confidence 7522 2455555555555655555443
No 88
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=21.04 E-value=69 Score=28.60 Aligned_cols=59 Identities=31% Similarity=0.584 Sum_probs=30.2
Q ss_pred CCcEEEEECCCcceeEEEEEEEEEecCCccEEEEEcCCCCeEEEeeceEEEEccCCCceEEccCCceeeee
Q 029796 102 VGNIVMVTGGRNRGRVGIIKNREKHKGSFETIHIQDALGHEFATRLGNVFTIGKGSKPWVSLPKGKGIKLS 172 (187)
Q Consensus 102 ~G~~~~vtgG~n~G~vG~I~~i~~~~~s~~~V~i~d~~g~~F~T~~~~vfvIG~~~~p~IsLp~~~Gi~~~ 172 (187)
.||.|.|+.|...|+.|.++. +|-+. +-|.+. |..-.-.-+.|| ++-.|. -.++|++|.
T Consensus 60 iGN~A~VvSG~AKG~~G~VtG--kHGGi-eHVlV~------F~~e~~ekl~i~--DkI~Ik-a~GqGL~L~ 118 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAKGVVTG--KHGGI-EHVLVD------FPDEVLEKLAIG--DKIQIK-AFGQGLKLT 118 (258)
T ss_dssp BT-EEEE-SSTTTT-EEEEEE--EETTT-TEEEEE--------HHHHTT--TT---EEEEE-E--TT-BBT
T ss_pred cCceeEEeecccCCCcCeEec--ccCCe-eeEEEE------CCHHHHhhccCC--CEEEEE-EEcCCcccC
Confidence 599999999999999999986 45555 444442 333322334555 343332 236666664
No 89
>PF03321 GH3: GH3 auxin-responsive promoter; InterPro: IPR004993 Transcription of the gene family, GH3, has been shown to be specifically induced by the plant hormone auxin. The auxin-responsive GH3 gene promoter is composed of multiple auxin response elements (AuxREs), and each AuxRE contributes incrementally to the strong auxin inducibility to the promoter.; PDB: 4EPL_A 4EQ4_B 4EWV_B 4EQL_B 4EPM_A.
Probab=20.97 E-value=92 Score=29.80 Aligned_cols=68 Identities=19% Similarity=0.342 Sum_probs=37.9
Q ss_pred EEEecC--CCceEEEEEcCCCceEEEEcCchh----hceeEEEEeeeEEeeCCeeEEEccCceEEeeCCCCcccCCeEEE
Q 029796 14 VVSIPK--TNENFRLLYDTKGRFRLHSLRDEE----AKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDPLIKANDTIKL 87 (187)
Q Consensus 14 VIsI~k--t~e~yRvl~d~kg~f~l~~I~~eE----a~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~~ik~~DTv~i 87 (187)
+|+||- .+..|.+.++.. .|.+.+.++.+ .+-+.+-......++.=.+.|+|..| +| .|..||.|.+
T Consensus 307 ~i~i~~~~~~~~~~l~~~~~-ffEFip~~~~~~~~~~~~~~l~~~ele~G~~YelviTt~~G---Ly---RY~iGDvVrv 379 (528)
T PF03321_consen 307 FIGIPLDPEDPGYVLAPDSG-FFEFIPVDEDEQNPSEQPKTLLLHELEVGEEYELVITTNSG---LY---RYRIGDVVRV 379 (528)
T ss_dssp EEEEES-CCC--EEE-TTSS-EEEEEE-STT-------SSSEEGGG--TT-EEEEEEESTTS----S---SEEECEEEEE
T ss_pred EEEEecCCCCCceEeecCCe-EEEEEeccCCcccccCCCceecHHHhcCCCeEEEEEecccc---ee---eeecCCEEEE
Confidence 345554 478899999998 99999998754 22345555555555555556666666 22 4677777765
Q ss_pred e
Q 029796 88 D 88 (187)
Q Consensus 88 ~ 88 (187)
.
T Consensus 380 ~ 380 (528)
T PF03321_consen 380 T 380 (528)
T ss_dssp E
T ss_pred e
Confidence 4
No 90
>PF00659 POLO_box: POLO box duplicated region; InterPro: IPR000959 A subgroup of serine/threonine protein kinases, Polo or Polo-like kinases play multiple roles during the cell cycle. Polo kinases are required at several key points through mitosis, starting from control of the G2/M transition through phosphorylation of Cdc25C and mitotic cyclins. Polo kinases are characterised by an amino terminal catalytic domain, and a carboxy terminal non-catalytic domain consisting of three blocks of conserved sequences known as polo boxes which form one single functional domain []. The domain is named after its founding member encoded by the polo gene of Drosophila melanogaster []. This domain of around 70 amino acids has been found in species ranging from yeast to mammals. Polo boxes appear to mediate interaction with multiple proteins through protein:protein interactions; some but not all of these proteins are substrates for the kinase domain of the molecule []. The crystal structure of the polo domain of the murine protein, Sak, is dimeric, consisting of two alpha-helices and two six-stranded beta-sheets []. The topology of one polypeptide subunit of the dimer consists of, from its N- to C terminus, an extended strand segment, five beta-strands, one alpha-helix (A) and a C-terminal beta-strand. Beta-strands from one subunit form a contiguous antiparallel beta-sheet with beta-strands from the second subunit. The two beta-sheets pack with a crossing angle of 110 degrees, orienting the hydrophobic surfaces inward and the hydrophilic surfaces outward. Helix A, which is colinear with beta-strand 6 of the same polypeptide, buries a large portion of the non-overlapping hydrophobic beta-sheet surfaces. Interactions involving helices A comprise a majority of the hydrophobic core structure and also the dimer interface. Point mutations in the Polo box of the budding yeast Cdc5 protein abolish the ability of overexpressed Cdc5 to interact with the spindle poles and to organise cytokinetic structures [].; GO: 0005515 protein binding; PDB: 1MBY_B 3P37_A 3MHN_A 1Q4K_A 3HIK_A 3Q1I_A 3P35_A 3MHQ_A 1UMW_B 3MQ8_B ....
Probab=20.57 E-value=2.8e+02 Score=18.69 Aligned_cols=19 Identities=21% Similarity=0.090 Sum_probs=15.4
Q ss_pred EeeCCeeEEEccCceEEee
Q 029796 56 FGQKGIPYINTYDGRTIRY 74 (187)
Q Consensus 56 ~~~gg~~ql~~hDGrni~~ 74 (187)
..+.|.+|++++|+..+..
T Consensus 10 ~LSng~vqv~FnD~tkivl 28 (68)
T PF00659_consen 10 QLSNGTVQVNFNDHTKIVL 28 (68)
T ss_dssp EETTSEEEEEETTS-EEEE
T ss_pred EEeCCCEEEEEeCCCEEEE
Confidence 3568999999999999975
No 91
>PF06068 TIP49: TIP49 C-terminus; InterPro: IPR010339 This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway []. TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases [].; GO: 0003678 DNA helicase activity, 0005524 ATP binding; PDB: 2XSZ_E 2CQA_A 2C9O_C.
Probab=20.49 E-value=77 Score=29.98 Aligned_cols=40 Identities=18% Similarity=0.211 Sum_probs=27.6
Q ss_pred EeeCCeeEEEccCceEEeeCCC---------CcccCCeEEEecCCCeee
Q 029796 56 FGQKGIPYINTYDGRTIRYPDP---------LIKANDTIKLDLEENKIT 95 (187)
Q Consensus 56 ~~~gg~~ql~~hDGrni~~~d~---------~ik~~DTv~i~l~~~kI~ 95 (187)
..+.+++.|-|.|+....--+| .+++||.+.|+-.+|+|.
T Consensus 139 ~~~~~~i~LkT~~~~~~l~l~~~i~~~l~kekV~~GDVI~Id~~tG~V~ 187 (398)
T PF06068_consen 139 TIKHGKITLKTTDMEKTLKLGPKIYEQLQKEKVRVGDVIYIDKNTGRVK 187 (398)
T ss_dssp SS-EEEEEEEETTCEEEEEE-CHHHHHHHHTT--TTCEEEEETTTTEEE
T ss_pred cceEEEEEEEEcCCceEecCCHHHHHHHHHhCCccCcEEEEECCCCeEE
Confidence 3456788888888887732233 789999999999998764
No 92
>PTZ00329 eukaryotic translation initiation factor 1A; Provisional
Probab=20.25 E-value=4.6e+02 Score=21.71 Aligned_cols=70 Identities=19% Similarity=0.095 Sum_probs=39.1
Q ss_pred CCCceEEEEEcCCCceEEEEcCchhhceeEEEEeeeEEeeCCeeEEEccCceEEeeCCC-------CcccCCeEEEecCC
Q 029796 19 KTNENFRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQFGQKGIPYINTYDGRTIRYPDP-------LIKANDTIKLDLEE 91 (187)
Q Consensus 19 kt~e~yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~~~~gg~~ql~~hDGrni~~~d~-------~ik~~DTv~i~l~~ 91 (187)
|-|+++|=--+..+--.---+-++| .-=+|+|.. +..++...+.+.||.+++..=| -|+.||.|++++..
T Consensus 7 kggk~~~rgk~~~~~~~rel~~~ee-gq~~g~V~~--~LGn~~f~V~c~dG~~rLa~I~GKmRK~IWI~~GD~VlVel~~ 83 (155)
T PTZ00329 7 KGGKNRRRGKNDNEGEKRELVFKEE-GQEYAQVLR--MLGNGRLEAYCFDGVKRLCHIRGKMRKRVWINIGDIILVSLRD 83 (155)
T ss_pred CCCcccccccccCccceeeeccCCC-CcEEEEEEE--EcCCCEEEEEECCCCEEEEEeeccceeeEEecCCCEEEEeccC
Confidence 4466666654444322111112333 336788876 3457788888888888753211 25667777766544
No 93
>cd05774 Ig_CEACAM_D1 First immunoglobulin (Ig)-like domain of carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM). IG_CEACAM_D1: immunoglobulin (Ig)-like domain 1 in carcinoembryonic antigen (CEA) related cell adhesion molecule (CEACAM) protein subfamily. The CEA family is a group of anchored or secreted glycoproteins, expressed by epithelial cells, leukocytes, endothelial cells and placenta. The CEA family is divided into the CEACAM and pregnancy-specific glycoprotein (PSG) subfamilies. This group represents the CEACAM subfamily. CEACAM1 has many important cellular functions, it is a cell adhesion molecule, and a signaling molecule that regulates the growth of tumor cells, it is an angiogenic factor, and is a receptor for bacterial and viral pathogens, including mouse hepatitis virus (MHV). In mice, four isoforms of CEACAM1 generated by alternative splicing have either two [D1, D4] or four [D1-D4] Ig-like domains on the cell surface. This family corresponds to the D
Probab=20.14 E-value=1.5e+02 Score=22.13 Aligned_cols=32 Identities=9% Similarity=0.139 Sum_probs=27.4
Q ss_pred EEEEEcCCCceEEEEcCchhhceeEEEEeeeE
Q 029796 24 FRLLYDTKGRFRLHSLRDEEAKFKLCKVRSVQ 55 (187)
Q Consensus 24 yRvl~d~kg~f~l~~I~~eEa~~KLcKV~~k~ 55 (187)
-|.....+|.|.++.++.+++.+-.|.+.+..
T Consensus 62 gR~~~~~ngSL~I~~v~~~D~G~Y~~~v~~~~ 93 (105)
T cd05774 62 GRETIYPNGSLLIQNVTQKDTGFYTLQTITTN 93 (105)
T ss_pred CcEEEeCCCcEEEecCCcccCEEEEEEEEeCC
Confidence 46667778999999999999999999998754
No 94
>PF11396 DUF2874: Protein of unknown function (DUF2874); InterPro: IPR021533 This bacterial family of proteins are probable periplasmic proteins with unknown function. There are between one and four copies of this domain per sequence. ; PDB: 3DUE_A 3U1W_B 3DB7_A 4DSD_A 3ELG_A.
Probab=20.03 E-value=1.1e+02 Score=19.86 Aligned_cols=22 Identities=18% Similarity=0.522 Sum_probs=17.5
Q ss_pred EEEEecCCCceEEEEEcCCCce
Q 029796 13 DVVSIPKTNENFRLLYDTKGRF 34 (187)
Q Consensus 13 DVIsI~kt~e~yRvl~d~kg~f 34 (187)
=.+++.+.+..+.|.+|.+|.+
T Consensus 39 Y~v~l~~~~~~~~v~fd~~G~~ 60 (61)
T PF11396_consen 39 YEVELKKGGNEYEVYFDANGNW 60 (61)
T ss_dssp EEEEETETTTSEEEEEETTS-E
T ss_pred EEEEEEEeCCeEEEEEcCCCCC
Confidence 3577778889999999999987
Done!