Query 032340
Match_columns 142
No_of_seqs 136 out of 1198
Neff 6.2
Searched_HMMs 46136
Date Fri Mar 29 12:48:59 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/032340.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/032340hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14633 hypothetical protein; 100.0 3.6E-36 7.9E-41 227.1 13.2 110 1-141 37-148 (150)
2 PRK14640 hypothetical protein; 100.0 3.9E-36 8.4E-41 227.4 13.0 109 1-141 40-150 (152)
3 PRK14634 hypothetical protein; 100.0 1.2E-35 2.5E-40 225.4 12.3 109 1-141 41-153 (155)
4 COG0779 Uncharacterized protei 100.0 1.4E-35 3.1E-40 224.4 12.6 109 1-141 42-152 (153)
5 PRK14647 hypothetical protein; 100.0 2.2E-35 4.8E-40 224.6 13.0 110 1-141 42-158 (159)
6 PRK14632 hypothetical protein; 100.0 3.8E-35 8.2E-40 226.0 13.6 117 1-141 41-162 (172)
7 PRK14646 hypothetical protein; 100.0 4.2E-35 9.1E-40 222.4 12.2 107 1-139 41-151 (155)
8 PRK14639 hypothetical protein; 100.0 1.3E-34 2.7E-39 216.6 12.9 107 1-141 31-139 (140)
9 PRK14643 hypothetical protein; 100.0 1.6E-34 3.4E-39 221.0 12.7 111 5-141 51-163 (164)
10 PRK14636 hypothetical protein; 100.0 2.8E-34 6.2E-39 221.8 13.0 110 1-141 39-152 (176)
11 PRK00092 ribosome maturation p 100.0 3.3E-34 7.2E-39 216.8 13.0 111 1-141 41-153 (154)
12 PRK14638 hypothetical protein; 100.0 6.3E-34 1.4E-38 215.0 12.2 105 1-141 42-149 (150)
13 PRK14631 hypothetical protein; 100.0 1.2E-33 2.5E-38 218.1 13.1 106 5-141 64-173 (174)
14 PRK14641 hypothetical protein; 100.0 1.6E-33 3.5E-38 217.1 13.0 120 1-142 43-173 (173)
15 PF02576 DUF150: Uncharacteris 100.0 5.8E-34 1.3E-38 212.2 9.6 110 1-138 30-141 (141)
16 PRK02001 hypothetical protein; 100.0 7.5E-33 1.6E-37 209.5 12.5 115 1-140 36-152 (152)
17 PRK14635 hypothetical protein; 100.0 1.1E-31 2.3E-36 205.0 13.3 110 5-141 47-161 (162)
18 PRK14642 hypothetical protein; 100.0 1.2E-31 2.7E-36 209.9 13.1 121 5-140 49-180 (197)
19 PRK14630 hypothetical protein; 100.0 7.5E-32 1.6E-36 202.3 11.1 102 1-139 42-143 (143)
20 PRK14637 hypothetical protein; 100.0 2.3E-31 4.9E-36 201.2 11.8 104 1-141 42-148 (151)
21 PRK14644 hypothetical protein; 100.0 3.5E-30 7.6E-35 191.8 11.3 102 2-135 33-136 (136)
22 PRK14645 hypothetical protein; 100.0 2.7E-30 5.8E-35 196.0 10.8 99 1-136 43-145 (154)
23 cd01734 YlxS_C YxlS is a Bacil 99.9 2E-24 4.3E-29 148.2 10.3 80 37-141 1-82 (83)
24 cd04479 RPA3 RPA3: A subfamily 62.4 27 0.00058 24.3 5.3 45 48-99 2-46 (101)
25 cd01726 LSm6 The eukaryotic Sm 58.0 20 0.00043 23.0 3.7 27 56-93 5-33 (67)
26 cd01729 LSm7 The eukaryotic Sm 56.8 23 0.0005 23.8 4.0 31 53-94 4-36 (81)
27 cd00600 Sm_like The eukaryotic 54.7 29 0.00063 21.3 4.0 26 57-93 2-29 (63)
28 PF14472 DUF4429: Domain of un 52.3 24 0.00052 24.2 3.6 39 89-139 2-40 (94)
29 PF01423 LSM: LSM domain ; In 51.7 30 0.00065 21.6 3.8 29 55-94 2-32 (67)
30 PRK00737 small nuclear ribonuc 51.1 37 0.00079 22.1 4.2 29 54-93 7-37 (72)
31 cd01722 Sm_F The eukaryotic Sm 50.9 31 0.00067 22.2 3.8 28 55-93 5-34 (68)
32 cd01731 archaeal_Sm1 The archa 49.9 32 0.0007 22.0 3.7 28 56-94 5-34 (68)
33 COG1481 Uncharacterized protei 48.2 14 0.00029 31.3 2.1 59 10-69 116-174 (308)
34 cd06168 LSm9 The eukaryotic Sm 47.5 41 0.00089 22.3 4.0 30 54-94 3-34 (75)
35 smart00651 Sm snRNP Sm protein 43.5 46 0.00099 20.7 3.7 27 56-93 3-31 (67)
36 PF06649 DUF1161: Protein of u 42.7 28 0.00061 21.9 2.4 28 13-45 1-28 (52)
37 cd07015 Clp_protease_NfeD Nodu 42.3 33 0.00072 26.3 3.4 59 5-69 7-66 (172)
38 cd01719 Sm_G The eukaryotic Sm 41.9 50 0.0011 21.6 3.7 29 54-93 3-33 (72)
39 COG1958 LSM1 Small nuclear rib 40.9 50 0.0011 21.7 3.7 30 54-94 10-41 (79)
40 PF07837 FTCD_N: Formiminotran 40.9 22 0.00047 27.8 2.1 22 6-27 95-116 (178)
41 PF06257 DUF1021: Protein of u 40.1 1.1E+02 0.0023 20.6 5.2 36 54-99 10-50 (76)
42 cd01728 LSm1 The eukaryotic Sm 40.1 61 0.0013 21.4 4.0 30 53-93 4-35 (74)
43 PF14438 SM-ATX: Ataxin 2 SM d 38.6 46 0.001 21.6 3.2 34 56-100 7-44 (77)
44 cd01721 Sm_D3 The eukaryotic S 37.8 65 0.0014 20.8 3.8 27 56-93 5-33 (70)
45 cd01717 Sm_B The eukaryotic Sm 36.8 64 0.0014 21.3 3.7 30 55-94 4-34 (79)
46 TIGR02024 FtcD glutamate formi 36.6 35 0.00075 28.8 2.8 22 6-27 97-118 (298)
47 cd01732 LSm5 The eukaryotic Sm 36.6 78 0.0017 21.0 4.1 28 55-93 6-36 (76)
48 PF08496 Peptidase_S49_N: Pept 36.4 65 0.0014 24.5 4.1 40 2-45 103-142 (155)
49 PF10842 DUF2642: Protein of u 35.6 1.3E+02 0.0028 19.7 5.1 36 53-98 13-48 (66)
50 PF10882 bPH_5: Bacterial PH d 35.0 59 0.0013 21.8 3.4 29 89-139 4-32 (100)
51 PF09493 DUF2389: Tryptophan-r 33.8 97 0.0021 19.7 4.0 44 77-137 8-53 (60)
52 TIGR02450 tryptophan-rich cons 32.4 1.1E+02 0.0024 19.5 4.1 45 77-136 9-53 (61)
53 cd01727 LSm8 The eukaryotic Sm 32.3 90 0.002 20.3 3.8 29 55-94 3-33 (74)
54 cd07021 Clp_protease_NfeD_like 31.0 65 0.0014 24.6 3.4 37 5-47 7-43 (178)
55 cd01723 LSm4 The eukaryotic Sm 31.0 1E+02 0.0022 20.2 3.9 28 56-93 6-34 (76)
56 cd01725 LSm2 The eukaryotic Sm 29.6 1.1E+02 0.0023 20.5 3.9 26 57-93 7-34 (81)
57 TIGR02778 ligD_pol DNA polymer 29.3 72 0.0016 26.1 3.5 62 3-64 122-186 (245)
58 PF11095 Gemin7: Gem-associate 28.7 1.4E+02 0.0029 20.4 4.2 17 54-70 17-33 (80)
59 cd01733 LSm10 The eukaryotic S 28.2 1.2E+02 0.0025 20.2 3.8 30 53-93 10-42 (78)
60 cd04862 PaeLigD_Pol_like PaeLi 27.6 81 0.0018 25.5 3.5 62 3-64 106-170 (227)
61 cd01730 LSm3 The eukaryotic Sm 27.0 1.3E+02 0.0029 19.9 4.0 29 55-93 4-34 (82)
62 cd04861 LigD_Pol_like LigD_Pol 26.8 85 0.0019 25.4 3.5 62 3-64 106-170 (227)
63 cd04866 LigD_Pol_like_3 LigD_P 26.7 86 0.0019 25.3 3.5 63 3-65 101-167 (223)
64 PF08661 Rep_fac-A_3: Replicat 26.7 80 0.0017 22.0 3.0 48 47-99 4-51 (109)
65 PF09430 DUF2012: Protein of u 26.3 46 0.00099 23.8 1.7 14 34-47 39-52 (123)
66 cd04865 LigD_Pol_like_2 LigD_P 26.2 89 0.0019 25.3 3.5 62 3-64 107-171 (228)
67 PF13749 HATPase_c_4: ATP-depe 26.0 32 0.0007 23.0 0.8 19 37-55 11-29 (89)
68 KOG1783 Small nuclear ribonucl 25.8 47 0.001 22.4 1.5 16 55-70 10-25 (77)
69 cd04863 MtLigD_Pol_like MtLigD 25.6 92 0.002 25.3 3.5 63 3-65 110-175 (231)
70 cd01213 tensin Tensin Phosphot 24.9 1E+02 0.0022 23.0 3.4 33 13-47 24-56 (138)
71 cd07020 Clp_protease_NfeD_1 No 22.9 1.1E+02 0.0024 23.2 3.3 35 6-46 8-42 (187)
72 PF00404 Dockerin_1: Dockerin 22.1 1.3E+02 0.0028 15.3 2.7 19 2-20 2-20 (21)
73 cd01724 Sm_D1 The eukaryotic S 21.9 1.8E+02 0.0039 19.9 3.9 27 56-93 6-34 (90)
74 PF14485 DUF4431: Domain of un 21.7 88 0.0019 19.0 2.1 15 53-67 11-25 (48)
75 PF13620 CarboxypepD_reg: Carb 20.9 59 0.0013 20.5 1.3 14 34-47 47-60 (82)
76 PF14153 Spore_coat_CotO: Spor 20.5 2.5E+02 0.0054 21.9 4.9 38 82-139 144-183 (185)
No 1
>PRK14633 hypothetical protein; Provisional
Probab=100.00 E-value=3.6e-36 Score=227.11 Aligned_cols=110 Identities=20% Similarity=0.300 Sum_probs=100.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||+++|||+|||+.+||+|+.+||++| ||+++|+|||||||++|||++++||+||+|+.|+|+++. +.+
T Consensus 37 ~ID~~~Gv~lddC~~vSr~i~~~LD~~d---~i~~~Y~LEVSSPGldRpL~~~~~f~r~~G~~v~V~~~~-------~~~ 106 (150)
T PRK14633 37 FIDHENGVSVDDCQIVSKEISAVFDVED---PVSGKYILEVSSPGMNRQIFNIIQAQALVGFNVKAVTLA-------PVG 106 (150)
T ss_pred EEeCCCCCCHHHHHHHHHHHHHHhccCc---CCCCCeEEEEeCCCCCCCCCCHHHHHHhCCCeEEEEEec-------ccC
Confidence 4799999999999999999999999998 899999999999999999999999999999999999999 888
Q ss_pred CCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 81 SDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 81 g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
|+++| +|.+++++++++.+. .|+ .++|||++|++|||.++
T Consensus 107 ~~~~~~G~L~~v~~~~i~l~~~------------~~~---------~~~i~~~~I~ka~l~~~ 148 (150)
T PRK14633 107 SQTKFKGVLERVEGNNVILNLE------------DGK---------EISFDFDELKKLRVSPD 148 (150)
T ss_pred CcEEEEEEEEEEeCCEEEEEEc------------CCc---------EEEEEhHHeeeEEEecc
Confidence 99999 999999999988642 111 46899999999999875
No 2
>PRK14640 hypothetical protein; Provisional
Probab=100.00 E-value=3.9e-36 Score=227.36 Aligned_cols=109 Identities=18% Similarity=0.241 Sum_probs=100.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||+++|||+|||+.+||+|+.+||++| ||+++|+|||||||++|||++++||+||+|+.|+|+++. +++
T Consensus 40 ~ID~~~gv~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGl~RpL~~~~~f~r~~G~~v~V~l~~-------~~~ 109 (152)
T PRK14640 40 YIDGENGVSVENCAEVSHQVGAIMDVED---PITEEYYLEVSSPGLDRPLFKVAQFEKYVGQEAAVTLRM-------ATN 109 (152)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHhcccc---cCCCCeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEEEec-------ccC
Confidence 4799999999999999999999999998 899999999999999999999999999999999999999 888
Q ss_pred CCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 81 SDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 81 g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
|+++| +|.+++++++++.+. |+ .+.|||++|++|||.++
T Consensus 110 ~~k~~~G~L~~v~~~~v~l~~~-------------~~---------~~~i~~~~I~ka~l~~~ 150 (152)
T PRK14640 110 NRRKFKGVIKAVQGDMITLTVD-------------GK---------DEVLAFTNIQKANIVPN 150 (152)
T ss_pred CceEEEEEEEEEeCCEEEEEEC-------------Ce---------EEEEEhHHeeeEEEecc
Confidence 99999 999999999888742 22 35799999999999865
No 3
>PRK14634 hypothetical protein; Provisional
Probab=100.00 E-value=1.2e-35 Score=225.43 Aligned_cols=109 Identities=21% Similarity=0.260 Sum_probs=99.7
Q ss_pred CCCCCCC--CCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCC
Q 032340 1 MSNKSGS--PSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSP 78 (142)
Q Consensus 1 liD~~~g--vslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~ 78 (142)
+||+++| ||+|||+.+||+|++.||++| ||+++|+|||||||++|||++++||+||+|+.|+|++++ +
T Consensus 41 ~ID~~~g~~v~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL~~~~~f~r~~G~~V~V~l~~-------~ 110 (155)
T PRK14634 41 QIRRSSGSDVSLDDCAGFSGPMGEALEASQ---LLTEAYVLEISSPGIGDQLSSDRDFQTFRGFPVEVSHRD-------D 110 (155)
T ss_pred EEECCCCCcccHHHHHHHHHHHHHHhcccc---cCCCCeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEEEec-------C
Confidence 4788888 999999999999999999998 899999999999999999999999999999999999999 8
Q ss_pred CCCCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 79 SESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 79 ~~g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
.+|+++| +|.+++++.+++.+. |+ .++|||++|++|||..+
T Consensus 111 ~~~~k~~~G~L~~~~~~~v~l~~~-------------~~---------~~~i~~~~I~ka~l~~~ 153 (155)
T PRK14634 111 DGSEQRLEGLLLERNEDHLQINIR-------------GR---------IKRIPRDSVISVRLTNP 153 (155)
T ss_pred CCCeEEEEEEEEEEeCCEEEEEEC-------------CE---------EEEEEHHHeeeEEeCCC
Confidence 8899999 999999999988641 11 46899999999999875
No 4
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=1.4e-35 Score=224.36 Aligned_cols=109 Identities=27% Similarity=0.402 Sum_probs=100.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||++||||+|||+++||+||+.||++| ||++.|+|||||||++|||++.+||.||+|+.|+|+++. |++
T Consensus 42 ~id~~g~v~lddC~~vSr~is~~LD~ed---pi~~~Y~LEVSSPGldRpL~~~~~f~r~~G~~Vkv~l~~-------~~~ 111 (153)
T COG0779 42 YIDKEGGVTLDDCADVSRAISALLDVED---PIEGAYFLEVSSPGLDRPLKTAEHFARFIGEKVKVKLRL-------PIE 111 (153)
T ss_pred EeCCCCCCCHHHHHHHHHHHHHHhccCC---cccccEEEEeeCCCCCCCcCCHHHHHHhcCcEEEEEEec-------ccC
Confidence 4789999999999999999999999998 999999999999999999999999999999999999999 999
Q ss_pred CCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 81 SDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 81 g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
|+++| .|..++++.+++.+. ++ .++|||++|++|||++.
T Consensus 112 ~~k~~~G~i~~~d~~~v~~~~~-------------~k---------~v~Ip~~~i~kArl~~~ 152 (153)
T COG0779 112 GRKKFEGKIVAVDGETVTLEVD-------------GK---------EVEIPFSDIAKARLVPE 152 (153)
T ss_pred CceEEEEEEEEEcCCeEEEEEC-------------CE---------EEEEEcccchhheeccc
Confidence 99999 999999999887642 22 47999999999999874
No 5
>PRK14647 hypothetical protein; Provisional
Probab=100.00 E-value=2.2e-35 Score=224.60 Aligned_cols=110 Identities=23% Similarity=0.357 Sum_probs=98.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||+++|||+|||+.+||+|+++||++| ||+++|+|||||||++|||++++||+||+|+.|+|+++. +++
T Consensus 42 ~ID~~~gvslddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPG~~RpL~~~~~f~r~~G~~v~V~l~~-------~~~ 111 (159)
T PRK14647 42 FIDKEGGVNLDDCAEVSRELSEILDVED---FIPERYTLEVSSPGLDRPLKKEADYERYAGRLVKVRTFE-------LLA 111 (159)
T ss_pred EEeCCCCCCHHHHHHHHHHHHHHHcccc---cCCCCeEEEEcCCCCCCcCCCHHHHHHhCCcEEEEEEec-------ccc
Confidence 4799999999999999999999999988 899999999999999999999999999999999999998 653
Q ss_pred -----CCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 81 -----SDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 81 -----g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
|+++| +|.+++++.+++++. .++ .++|||++|++|+|.++
T Consensus 112 ~~~~~~~~~~~G~L~~~~~~~v~l~~~------------~~~---------~~~i~~~~I~ka~l~~e 158 (159)
T PRK14647 112 DEAGNKRKTFLGELEGLADGVVTIALK------------EGQ---------QARIPLDKIAKANLEFE 158 (159)
T ss_pred ccccCCceEEEEEEEeecCCEEEEEEc------------CCc---------EEEEEHHHCCEEEEeee
Confidence 67888 999999999887641 111 46899999999999876
No 6
>PRK14632 hypothetical protein; Provisional
Probab=100.00 E-value=3.8e-35 Score=225.96 Aligned_cols=117 Identities=18% Similarity=0.248 Sum_probs=100.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCC-
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPS- 79 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~- 79 (142)
+||+++|||+|||+.+||+|+++||+++ +|+++|+|||||||++|||++++||+||+|+.|+|++++ +.
T Consensus 41 ~ID~~~GV~ldDC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL~~~~~f~r~iG~~V~V~l~~-------~~~ 110 (172)
T PRK14632 41 FVDGPEGVTIDQCAEVSRHVGLALEVED---VISSAYVLEVSSPGLERPFFRAEQMSPYVGRQIELTLID-------PTP 110 (172)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHhcccc---cCCCCeEEEEeCCCCCCcCCCHHHHHHhCCCEEEEEEec-------ccc
Confidence 4799999999999999999999999988 899999999999999999999999999999999999998 66
Q ss_pred --CCCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 80 --ESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 80 --~g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
+|+++| +|.+++++.+++++. .+++++. ....++|||++|++|||.++
T Consensus 111 ~~~g~k~~~G~L~~v~~~~i~l~~~----------~~~~~~~----~~~~~~i~~~~I~ka~l~~~ 162 (172)
T PRK14632 111 EWPGRRKFRGELLAVEGDTVVLRPE----------GAPAPEA----EEAVLRTSWQGVRKANLIHV 162 (172)
T ss_pred ccCCceEEEEEEEEEeCCEEEEEEc----------CcccccC----CceeEEEEhHHccEEEEEEE
Confidence 478899 999999999988742 1111111 11247899999999999865
No 7
>PRK14646 hypothetical protein; Provisional
Probab=100.00 E-value=4.2e-35 Score=222.41 Aligned_cols=107 Identities=18% Similarity=0.219 Sum_probs=97.1
Q ss_pred CCCCC--CCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCC
Q 032340 1 MSNKS--GSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSP 78 (142)
Q Consensus 1 liD~~--~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~ 78 (142)
+||++ +|||+|||+.+||+|+++||++| ||++.|+|||||||++|||++++||+||+|+.|+|++++ +
T Consensus 41 ~IDk~~g~gVtldDC~~vSr~is~~LD~~D---~i~~~Y~LEVSSPGldRpL~~~~df~r~~G~~v~V~l~~-------~ 110 (155)
T PRK14646 41 IIKKTNGDDISLDDCALFNTPASEEIENSN---LLNCSYVLEISSQGVSDELTSERDFKTFKGFPVNVELNQ-------K 110 (155)
T ss_pred EEECCCCCCccHHHHHHHHHHHHHHhCcCC---CCCCCeEEEEcCCCCCCcCCCHHHHHHhCCCEEEEEEec-------C
Confidence 36886 36999999999999999999998 899999999999999999999999999999999999999 8
Q ss_pred CCCCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEe
Q 032340 79 SESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLH 139 (142)
Q Consensus 79 ~~g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~ 139 (142)
.+|++.| .|.+++++.+++.. .|+ .+.|||++|++|||+
T Consensus 111 ~~~~~~~~G~L~~~~~~~v~l~~-------------~g~---------~~~i~~~~I~ka~L~ 151 (155)
T PRK14646 111 NSKIKFLNGLLYEKSKDYLAINI-------------KGK---------IKKIPFNEVLKISLC 151 (155)
T ss_pred cCCeEEEEEEEEEEeCCEEEEEE-------------CCE---------EEEEEHHHeeeEEeC
Confidence 8899999 99999999988863 122 468999999999996
No 8
>PRK14639 hypothetical protein; Provisional
Probab=100.00 E-value=1.3e-34 Score=216.57 Aligned_cols=107 Identities=18% Similarity=0.237 Sum_probs=94.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||+++|||+|||+.+||+|+++||++| ||+++|+|||||||++|||++++||+||+|+.|+|++.+
T Consensus 31 ~Id~~~gv~iddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGl~RpL~~~~~f~r~~G~~v~v~l~~---------- 97 (140)
T PRK14639 31 YITKEGGVNLDDCERLSELLSPIFDVEP---PVSGEYFLEVSSPGLERKLSKIEHFAKSIGELVKITTNE---------- 97 (140)
T ss_pred EEeCCCCCCHHHHHHHHHHHHHHhcccc---ccCCCeEEEEeCCCCCCcCCCHHHHHHhCCCEEEEEECC----------
Confidence 4799999999999999999999999998 899999999999999999999999999999999999864
Q ss_pred CCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 81 SDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 81 g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
.++| +|.++++++++++.. ..++ .++|||++|++|||+++
T Consensus 98 -~~~~~G~L~~~~~~~i~l~~~-----------~~~~---------~~~i~~~~I~ka~l~~~ 139 (140)
T PRK14639 98 -KEKFEGKIVSVDDENITLENL-----------ENKE---------KTTINFNDIKKAKTYVE 139 (140)
T ss_pred -CcEEEEEEEEEeCCEEEEEEc-----------cCCc---------EEEEEhHHeeeEEEEEe
Confidence 4666 999999999888531 0111 36899999999999986
No 9
>PRK14643 hypothetical protein; Provisional
Probab=100.00 E-value=1.6e-34 Score=221.05 Aligned_cols=111 Identities=16% Similarity=0.325 Sum_probs=97.3
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCCCCce
Q 032340 5 SGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGV 84 (142)
Q Consensus 5 ~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~ 84 (142)
+||||+|||+.+||+||++||++| ||++.|+|||||||++|||++++||+||+|+.|+|+++. +.+|+++
T Consensus 51 ~ggvtldDC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGleRpL~~~~df~r~~G~~V~V~l~~-------~~~g~k~ 120 (164)
T PRK14643 51 NKPLDFDILIKANDLVSNKIDQFI---KTSEKYLLEISSSGIEKQIRSQEELVKALNQWVYVQLNN-------EIKKVKE 120 (164)
T ss_pred CCCcCHHHHHHHHHHHHHHhCccC---CCCCCeEEEecCCCCCCCCCCHHHHHHhcCCeEEEEEec-------ccCCceE
Confidence 468999999999999999999998 899999999999999999999999999999999999999 8899999
Q ss_pred E--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 85 F--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 85 ~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
| .|.+++++.+++...+. ++ ..++ .++|||++|++|||+++
T Consensus 121 ~~G~L~~~~~~~~~l~l~~~-~~------~~~~---------~~~ip~~~I~karl~~~ 163 (164)
T PRK14643 121 FEGYVTKYNVNTNTFRFTFF-IK------GQKK---------KLDVKYEQIKFIRYAVR 163 (164)
T ss_pred EEEEEEEEeCCcEEEEEEee-cc------CcCc---------EEEEeHHHhhheEeccc
Confidence 9 99999999887764321 00 0111 46899999999999876
No 10
>PRK14636 hypothetical protein; Provisional
Probab=100.00 E-value=2.8e-34 Score=221.82 Aligned_cols=110 Identities=22% Similarity=0.334 Sum_probs=98.2
Q ss_pred CCCCC--CCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCC
Q 032340 1 MSNKS--GSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSP 78 (142)
Q Consensus 1 liD~~--~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~ 78 (142)
+||++ ||||+|||+.+||+||..||+.+ ||++.|+|||||||++|||++++||+||+|+.|+|+++. +
T Consensus 39 ~ID~~~~ggV~lDDC~~vSr~Is~~LD~~d---~i~~~Y~LEVSSPGldRpL~~~~df~r~~G~~V~V~l~~-------~ 108 (176)
T PRK14636 39 MAERPDTRQLVIEDCAALSRRLSDVFDELD---PIEDAYRLEVSSPGIDRPLTRPKDFADWAGHEARIALSE-------P 108 (176)
T ss_pred EEECCCCCCcCHHHHHHHHHHHHHHhccCc---CCCCCeEEEEeCCCCCCCCCCHHHHHHhCCCeEEEEEec-------c
Confidence 36775 46999999999999999999988 899999999999999999999999999999999999999 8
Q ss_pred CCCCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 79 SESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 79 ~~g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
++|+++| +|.+++++.+++.+. +++ .++|||++|++|||.++
T Consensus 109 ~~g~k~~~G~L~~v~~~~v~l~~~------------~~~---------~~~i~~~~I~kA~l~~~ 152 (176)
T PRK14636 109 LDGRKQFRGELKGIDGDTVTIADN------------KAG---------EVILPFAAIESAKLILT 152 (176)
T ss_pred cCCeEEEEEEEEEEeCCEEEEEEc------------CCc---------EEEEEhHHcceEEEecc
Confidence 8899999 999999999887642 111 36899999999999864
No 11
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=100.00 E-value=3.3e-34 Score=216.78 Aligned_cols=111 Identities=30% Similarity=0.454 Sum_probs=99.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||+++|+|+|||+.+||+|+.+||+.+ +|+++|+|||||||++|||++++||+||+|+.|+|++++ +.+
T Consensus 41 ~Id~~~gv~iddc~~~Sr~is~~LD~~d---~i~~~Y~LEVSSPGi~RpL~~~~~f~r~~G~~v~V~~~~-------~~~ 110 (154)
T PRK00092 41 YIDKEGGIDLDDCEEVSRQISAVLDVED---PIPGAYTLEVSSPGLDRPLKKARDFRRFIGREVKVKLYE-------PID 110 (154)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHhcccc---CCCCCeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEEEEc-------ccC
Confidence 4788999999999999999999999988 899999999999999999999999999999999999998 777
Q ss_pred CCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 81 SDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 81 g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
|.+.| +|.+++++.+++.+. |++ + .++|||++|++|+|.++
T Consensus 111 ~~~~~~G~L~~~~~~~i~l~~~-------------~~~---~----~~~i~~~~I~~a~l~~e 153 (154)
T PRK00092 111 GRKKFQGILLAVDGETVTLEVE-------------GKE---K----EVEIPLDNIAKARLVVE 153 (154)
T ss_pred CceEEEEEEEEeeCCEEEEEEC-------------CCe---E----EEEEEHHHcceEEEeee
Confidence 88888 999999999887642 111 1 46899999999999876
No 12
>PRK14638 hypothetical protein; Provisional
Probab=100.00 E-value=6.3e-34 Score=214.95 Aligned_cols=105 Identities=25% Similarity=0.341 Sum_probs=93.3
Q ss_pred CCCCCCC-CCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCC
Q 032340 1 MSNKSGS-PSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPS 79 (142)
Q Consensus 1 liD~~~g-vslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~ 79 (142)
+||+++| ||+|||+.+||+|+++||++| +|+++|+|||||||++|||++++||+||+|+.|+|++.+
T Consensus 42 ~ID~~~G~v~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL~~~~~f~r~~G~~v~V~~~~--------- 109 (150)
T PRK14638 42 IIDNPVGYVSVRDCELFSREIERFLDRED---LIEHSYTLEVSSPGLDRPLRGPKDYVRFTGKLAKIVTKD--------- 109 (150)
T ss_pred EEECCCCCcCHHHHHHHHHHHHHHhcccc---ccCCceEEEEeCCCCCCCCCCHHHHHHhCCCEEEEEECC---------
Confidence 4788866 999999999999999999998 899999999999999999999999999999999999964
Q ss_pred CCCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 80 ESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 80 ~g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
.++| +|.+++++.+++.. +++ .++|||++|++|||.++
T Consensus 110 --~k~~~G~L~~~~~~~i~l~~-------------~~~---------~~~i~~~~I~~a~l~~e 149 (150)
T PRK14638 110 --GKTFIGRIESFVDGTITISD-------------EKE---------KYEINIDDVKRANLEVE 149 (150)
T ss_pred --CcEEEEEEEEEeCCEEEEEE-------------CCc---------EEEEEhHHcceEEEeee
Confidence 5667 99999999888751 111 36899999999999875
No 13
>PRK14631 hypothetical protein; Provisional
Probab=100.00 E-value=1.2e-33 Score=218.06 Aligned_cols=106 Identities=21% Similarity=0.239 Sum_probs=95.3
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCCCCce
Q 032340 5 SGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGV 84 (142)
Q Consensus 5 ~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~ 84 (142)
++|||+|||+.+||+|+++||++| ||++.|+|||||||++|||++++||+||+|+.|+|+++. +.+|+++
T Consensus 64 ~~gvtiddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL~~~~df~r~~G~~V~V~l~~-------~~~~~k~ 133 (174)
T PRK14631 64 GRGIGVEDCVRVTQQVGAMLDVHD---PISGEYALEVSSPGWDRPFFQLEQLQGYIGQQVALRLIA-------AVENRRK 133 (174)
T ss_pred CCCcCHHHHHHHHHHHHHHhcccc---cCCCCeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEEEec-------ccCCceE
Confidence 468999999999999999999998 899999999999999999999999999999999999999 8889999
Q ss_pred E--EEEeEe--CCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 85 F--RLISFD--METECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 85 ~--~L~~~~--~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
| +|.+++ ++.+++.+. .++ .+.|||++|++|||.+.
T Consensus 134 ~~G~L~~v~~~~~~v~l~~~------------~~~---------~~~i~~~~I~ka~L~~~ 173 (174)
T PRK14631 134 FQAKLLAVDLENEEIQVEVE------------GKH---------VLDIDSNNIDKANLIYQ 173 (174)
T ss_pred EEEEEEEeecCCCEEEEEEc------------CCc---------EEEEEhHHcceEEEeec
Confidence 9 999999 888877642 011 36899999999999864
No 14
>PRK14641 hypothetical protein; Provisional
Probab=100.00 E-value=1.6e-33 Score=217.06 Aligned_cols=120 Identities=20% Similarity=0.277 Sum_probs=98.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCC----CCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIP----ENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTG 76 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~----~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~ 76 (142)
+||+++|||||||+++||+|++.||+++ +++ ++|+|||||||++|||++++||+||+|+.|+|++++
T Consensus 43 ~ID~~~gv~lDdC~~vSr~Is~~LD~~d---~i~~~~~~~Y~LEVSSPGldRpL~~~~~f~r~~G~~V~V~l~~------ 113 (173)
T PRK14641 43 LLDADTGIRIDQCAFFSRRIRERLEEDE---ELLGLVGEDFDLMVSSPGLGEPIILPRQYGRHVGRLLRVTYRD------ 113 (173)
T ss_pred EEeCCCCCCHHHHHHHHHHHHHHhCccc---ccccCCCCCeEEEEeCCCCCCcCCCHHHHHHhCCCEEEEEEec------
Confidence 4799999999999999999999999988 554 799999999999999999999999999999999998
Q ss_pred CCCCCCceE--EEEeEe-----CCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeecC
Q 032340 77 SPSESDGVF--RLISFD-----METECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSDC 142 (142)
Q Consensus 77 ~~~~g~k~~--~L~~~~-----~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~~ 142 (142)
+.+|+++| +|.+++ ++.+++... .+.+|++ +.+...+++||++|++|++++|.
T Consensus 114 -~~~~~~~~~G~L~~~~~~~~~~~~v~~~~~--------~~~~~~~----~~~~~~~~v~~~~v~~A~vevE~ 173 (173)
T PRK14641 114 -EEGSEHEVTGHLQEVSLTEGEGASIVLKPE--------QKKKKGK----QEETENITLELDAVIRAVPEAEL 173 (173)
T ss_pred -ccCCeEEEEEEEEeeecccCCCCcEEEEec--------ccccccc----CCCCceEEEEhHHccceeeeeeC
Confidence 88888889 999997 555555421 1112222 11123579999999999999873
No 15
>PF02576 DUF150: Uncharacterised BCR, YhbC family COG0779; InterPro: IPR003728 The RimP protein facilitates maturation of the 30S ribsomal subunit, and is required for the efficient production of translationally competent ribosmomes [].; PDB: 1IB8_A.
Probab=100.00 E-value=5.8e-34 Score=212.22 Aligned_cols=110 Identities=34% Similarity=0.574 Sum_probs=78.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||+++|||+|||+.+||+|++.||.++ +|+++|+|||||||++|||++++||++|+|+.|+|++++ +.+
T Consensus 30 ~id~~~gv~lddc~~~sr~i~~~LD~~d---~i~~~y~LEVSSPG~~r~L~~~~~~~~~iG~~v~v~~~~-------~~~ 99 (141)
T PF02576_consen 30 FIDKDGGVSLDDCEKVSRAISALLDAED---PIPEDYTLEVSSPGIDRPLKSPRDFERFIGRKVKVKLKQ-------PVN 99 (141)
T ss_dssp EEE-SS---HHHHHHHHHHHGGGTTTS-------S-EEEEEE--SSSS--SSHHHHHHH-SEEEEEE-SS--------SS
T ss_pred EEEeCCCCCHHHHHHHHHHHHHHHcccc---ccCcceEEEEeCCCCCCcCCCHHHHHHhcCCeEEEEEec-------cCC
Confidence 3688889999999999999999999988 899999999999999999999999999999999999998 778
Q ss_pred CCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEE
Q 032340 81 SDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRL 138 (142)
Q Consensus 81 g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl 138 (142)
|.+.| .|.+++++++++.+. .++++ + .++|||++|++|||
T Consensus 100 ~~~~~~G~L~~~~~~~i~l~~~-----------~~~~~---~----~~~I~~~~I~ka~L 141 (141)
T PF02576_consen 100 GRKEFEGKLLEVDEDEITLEVE-----------GKGKK---K----EVEIPFSDIKKARL 141 (141)
T ss_dssp S-SEEEEEEEEEETTEEEEEEE------------SS-E---E----EEEE-SS--SS-EE
T ss_pred CcEEEEEEEEEEeCCEEEEEEC-----------Cccce---E----EEEEEHHHCceEeC
Confidence 88888 999999999998764 12221 1 57999999999997
No 16
>PRK02001 hypothetical protein; Validated
Probab=100.00 E-value=7.5e-33 Score=209.53 Aligned_cols=115 Identities=20% Similarity=0.240 Sum_probs=93.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||+++|||+|||+.+||+|+++||+.+ ++|+|||||||++|||++++||+||+|+.|+|++.+
T Consensus 36 ~ID~~~Gv~lddC~~vSr~is~~LD~~d------~~Y~LEVSSPGldRpL~~~~~f~r~~G~~v~V~l~~---------- 99 (152)
T PRK02001 36 EIDGDEGVWIEDCVELSRAIEHNLDREE------EDFELEVGSAGLTSPLKVPRQYKKNIGRELEVLTKN---------- 99 (152)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHhcCCC------CCeEEEEeCCCCCCcCCCHHHHHHhCCCEEEEEECC----------
Confidence 4799999999999999999999999765 899999999999999999999999999999999964
Q ss_pred CCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEee
Q 032340 81 SDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHS 140 (142)
Q Consensus 81 g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~ 140 (142)
.+.| +|.+++++++++.+.-.. ..+.+||+... ...++|||++|++|+|.+
T Consensus 100 -~~~~~G~L~~~~~~~i~l~~~~~~----~~~~~k~~~~~----~~~~~i~~~~I~ka~l~~ 152 (152)
T PRK02001 100 -GKKIEGELKSADENDITLEVKARE----PKEGGKGKVTV----EKEETITYDDIKEAKVII 152 (152)
T ss_pred -CCEEEEEEEEEeCCEEEEEEcccc----ccccccccccc----ceeEEEEhHheeeEEEeC
Confidence 5667 999999999988753110 01122333221 225789999999999974
No 17
>PRK14635 hypothetical protein; Provisional
Probab=99.98 E-value=1.1e-31 Score=205.01 Aligned_cols=110 Identities=22% Similarity=0.283 Sum_probs=89.5
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCCCCce
Q 032340 5 SGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGV 84 (142)
Q Consensus 5 ~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~ 84 (142)
+||||||||+++||+|+++||+.+ |+ ++|+|||||||++|||++++||+||+|+.|+|++..+ |.++
T Consensus 47 ~~gv~lddC~~vSr~is~~LD~~d---~~-~~Y~LEVSSPGldRpL~~~~~~~r~~G~~v~v~~~~~---------~~~~ 113 (162)
T PRK14635 47 YGSVSLLECEQVSRKLKEELERIS---PD-LDFTLKVSSAGAERKLRLPEDLDRFRGIPVRLVFRSE---------ESEK 113 (162)
T ss_pred CCCcCHHHHHHHHHHHHHHhCCCC---CC-CCeEEEEcCCCCCCcCCCHHHHHHhCCCEEEEEEecC---------CCcE
Confidence 689999999999999999999887 65 8999999999999999999999999999999998652 1223
Q ss_pred E-----EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 85 F-----RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 85 ~-----~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
| +|.+++++++++.+.. |++++.. ...++|||++|++|||.++
T Consensus 114 ~~g~~g~L~~~~~~~v~l~~~~-----------k~~~~~~---~~~~~ip~~~I~ka~l~~e 161 (162)
T PRK14635 114 WQEGIFRLVNRDGDQVELEKFQ-----------KGKKSKV---KKQTTLNLKDILKGNLYVE 161 (162)
T ss_pred EEecceEEEEEcCCEEEEEEec-----------ccccccC---CeEEEEEhHHeeeeEEEEe
Confidence 2 6999999998887531 1111111 1247899999999999986
No 18
>PRK14642 hypothetical protein; Provisional
Probab=99.97 E-value=1.2e-31 Score=209.92 Aligned_cols=121 Identities=24% Similarity=0.291 Sum_probs=96.2
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC----
Q 032340 5 SGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE---- 80 (142)
Q Consensus 5 ~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~---- 80 (142)
++|||+|||+.+||+|+.+||+++ . +.|+||||||||+|||++++||+||+|+.|+|+++. +++
T Consensus 49 ~~gVtidDC~~vSR~Is~~LDve~----~-~y~~LEVSSPGldRPLk~~~df~rfiG~~V~V~l~~-------pi~~~~~ 116 (197)
T PRK14642 49 EQFVTVEDCEKVTRQLQFALEVDG----V-DYKRLEVSSPGIDRPLRHEQDFERFAGEVIDITLKA-------PIGAAAG 116 (197)
T ss_pred CCCccHHHHHHHHHHHHHHhcccC----c-cccEEEEeCCCCCCCCCCHHHHHHhCCCeEEEEEec-------ccccccc
Confidence 468999999999999999999876 2 445899999999999999999999999999999998 555
Q ss_pred -----CCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEee
Q 032340 81 -----SDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHS 140 (142)
Q Consensus 81 -----g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~ 140 (142)
++++| +|.++++++++|+|..++.+..-+...|||.+ .+...+.|+|++|++|||.+
T Consensus 117 ~~~~~~rk~f~G~L~~~~~~~i~l~~~~~~~~k~g~~~~k~~~~---~~~~~~~~~~~eik~a~l~p 180 (197)
T PRK14642 117 GQVSANRKKFRGTLERAESGGWQIVWSDEPPVKPGQRVSKKRVP---APLQALGFTLDELREARLAP 180 (197)
T ss_pred ccccCCceEEEEEEEEEcCCEEEEEEeecccCCCcccccccccc---ccceeEEeehhheeeEEEEE
Confidence 78899 99999999999999743211110011233321 12235899999999999975
No 19
>PRK14630 hypothetical protein; Provisional
Probab=99.97 E-value=7.5e-32 Score=202.26 Aligned_cols=102 Identities=17% Similarity=0.278 Sum_probs=88.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||+++|||+|||+.+||+|+..|| + ||+++|+|||||||++|||++++||+||+|+.|+|++.. +..
T Consensus 42 ~Id~~~gV~idDC~~vSr~i~~~ld--~---~i~~~Y~LEVSSPGldRpL~~~~df~r~~G~~v~V~l~~-------~~~ 109 (143)
T PRK14630 42 VLYKKDSFGVDTLCDLHKMILLILE--A---VLKYNFSLEISTPGINRKIKSDREFKIFEGKKIKLMLDN-------DFE 109 (143)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHhc--c---cCCCCeEEEEeCCCCCCcCCCHHHHHHhCCCEEEEEEcC-------cce
Confidence 4789999999999999999999996 4 789999999999999999999999999999999999977 432
Q ss_pred CCceEEEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEe
Q 032340 81 SDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLH 139 (142)
Q Consensus 81 g~k~~~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~ 139 (142)
.+ .|.+++++++++.. .++ .+.|||++|++|||.
T Consensus 110 -~G--~L~~~~d~~i~l~~-------------~~~---------~~~i~~~~I~ka~lv 143 (143)
T PRK14630 110 -EG--FILEAKADSFIFKT-------------DSK---------EVNVLYSDVKKAKLS 143 (143)
T ss_pred -EE--EEEEEeCCEEEEEE-------------CCE---------EEEEEhHhcceEEEC
Confidence 11 79999999988752 111 478999999999984
No 20
>PRK14637 hypothetical protein; Provisional
Probab=99.97 E-value=2.3e-31 Score=201.24 Aligned_cols=104 Identities=22% Similarity=0.324 Sum_probs=88.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCC
Q 032340 1 MSNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSE 80 (142)
Q Consensus 1 liD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~ 80 (142)
+||+++|||+|||+.+||+|++.||..+ + .++|+|||||||++|||++++||+||+|+.|+|++..
T Consensus 42 ~ID~~~gV~iddC~~vSr~Is~~LD~~~---~-~~~y~LEVSSPGldRpL~~~~~f~r~~G~~V~V~l~~---------- 107 (151)
T PRK14637 42 VIYSAGGVGLDDCARVHRILVPRLEALG---G-VRDVFLEVSSPGIERVIKNAAEFSIFVGETVKVWFEC---------- 107 (151)
T ss_pred EEECCCCCCHHHHHHHHHHHHHHhcccc---c-ccCcEEEEeCCCCCCCCCCHHHHHHhCCCEEEEEECC----------
Confidence 4799999999999999999999999754 2 4789999999999999999999999999999999822
Q ss_pred CCceE---EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEeec
Q 032340 81 SDGVF---RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 81 g~k~~---~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
.+.| +|.+++++.+++.. +|+ .+.|||++|++|||++.
T Consensus 108 -~~~~~~G~L~~~~d~~v~l~~-------------~~~---------~~~i~~~~I~ka~L~~~ 148 (151)
T PRK14637 108 -TGQWQVGTIAEADETCLVLTS-------------DGV---------PVTIPYVQITKAQLHPA 148 (151)
T ss_pred -CCcEEEEEEEEEeCCEEEEEE-------------CCE---------EEEEEHHHeeeEEEEEE
Confidence 2222 89999999988762 111 46899999999999874
No 21
>PRK14644 hypothetical protein; Provisional
Probab=99.97 E-value=3.5e-30 Score=191.81 Aligned_cols=102 Identities=21% Similarity=0.269 Sum_probs=89.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCCC
Q 032340 2 SNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSES 81 (142)
Q Consensus 2 iD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~g 81 (142)
||++ ++|||+.+||+|+++||+.+ |++++|+|||||||++|||++ +||+||+|+.|+|++++ +++|
T Consensus 33 Idk~---~iddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL~~-~~f~r~~G~~v~V~l~~-------~~~~ 98 (136)
T PRK14644 33 LNSR---DLKDIEELTKEISDFIDNLS---VEFDFDSLDISSPGFDMDYET-DELENHIGEIIDVSLNK-------EVNK 98 (136)
T ss_pred ECCC---CHHHHHHHHHHHHHHhcccc---CCCCCeEEEEECCCCCCCCCH-HHHHHhCCCeEEEEEcc-------CcCC
Confidence 5653 79999999999999999998 899999999999999999998 69999999999999999 8889
Q ss_pred CceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccce
Q 032340 82 DGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRL 135 (142)
Q Consensus 82 ~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~k 135 (142)
++.| .|.+++++++++.+.. ||+. ..++|++++|++
T Consensus 99 ~~~~~G~L~~v~~~~i~l~~~~-----------k~~~-------~~i~~~~~~i~~ 136 (136)
T PRK14644 99 TDFITGELLENNPETITLKWNC-----------KGQF-------RKVEINKENIKK 136 (136)
T ss_pred eEEEEEEEEEEeCCEEEEEEec-----------CCcE-------EEEEECHHHhcC
Confidence 9999 9999999999988642 3331 147899999874
No 22
>PRK14645 hypothetical protein; Provisional
Probab=99.97 E-value=2.7e-30 Score=195.97 Aligned_cols=99 Identities=21% Similarity=0.272 Sum_probs=85.6
Q ss_pred CCCCC--CCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCC
Q 032340 1 MSNKS--GSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSP 78 (142)
Q Consensus 1 liD~~--~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~ 78 (142)
+||++ ++|++|||+++||+|+.+||+.| +|+++|+|||||||++|||++++||+||+|+.|+|+.
T Consensus 43 ~ID~~~~~~v~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL~~~~df~r~~G~~v~v~~---------- 109 (154)
T PRK14645 43 RIDRKDEQPVTVEDLERASRALEAELDRLD---PIEGEYRLEVESPGPKRPLFTARHFERFAGLKAKVRG---------- 109 (154)
T ss_pred EEECCCCCCcCHHHHHHHHHHHHHHhcccc---cCCCceEEEEeCCCCCCCCCCHHHHHHhCCCEEEEEc----------
Confidence 36763 46999999999999999999998 8999999999999999999999999999999999974
Q ss_pred CCCCceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeeccccccee
Q 032340 79 SESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLV 136 (142)
Q Consensus 79 ~~g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~ka 136 (142)
++++| +|.+++++.+++.+ +|+ .++|||++|+++
T Consensus 110 --~~k~~~G~L~~~~d~~i~l~~-------------~~~---------~~~i~~~~I~~~ 145 (154)
T PRK14645 110 --PGENFTGRIKAVSGDQVTFDV-------------GGE---------DRTLRIGTFQAN 145 (154)
T ss_pred --CCeEEEEEEEEEeCCEEEEEE-------------CCe---------EEEEEHHHhhhh
Confidence 24566 99999999988763 122 468999999755
No 23
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold. The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet. This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=99.92 E-value=2e-24 Score=148.17 Aligned_cols=80 Identities=29% Similarity=0.356 Sum_probs=69.6
Q ss_pred eEEEEecCCCCCCCCChHHHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCCeeEEEEeecceehhhcccCCC
Q 032340 37 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKG 114 (142)
Q Consensus 37 Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kg 114 (142)
|+|||||||++|||++++||+||+|+.|+|++.. +++|+++| +|.+++++++++.+. .|+
T Consensus 1 Y~LEVSSPGl~RpL~~~~~~~r~~G~~v~v~~~~-------~~~~~~~~~G~L~~~~~~~v~l~~~-----------~~~ 62 (83)
T cd01734 1 YFLEVSSPGAERPLKKEADFERAVGKYVHVKLYQ-------PIDGQKEFEGTLLGVDDDTVTLEVD-----------IKT 62 (83)
T ss_pred CEEEEcCCCCCCcCCCHHHHHHhCCCEEEEEEEc-------ccCCeEEEEEEEEeEeCCEEEEEEe-----------cCC
Confidence 8999999999999999999999999999999998 78888888 999999999888742 111
Q ss_pred CCccccccceeeeecccccceeEEeec
Q 032340 115 RPLSKKQREWRLNTTFDSLRLVRLHSD 141 (142)
Q Consensus 115 k~~~~k~~~~~~~ip~~~I~karl~~~ 141 (142)
+ ...+.|||++|++|||.++
T Consensus 63 ~-------~~~~~i~~~~I~ka~l~~~ 82 (83)
T cd01734 63 R-------GKTVEIPLDKIAKARLAPE 82 (83)
T ss_pred C-------CeEEEEEhHHeeEEEEEEE
Confidence 1 1157999999999999876
No 24
>cd04479 RPA3 RPA3: A subfamily of OB folds similar to human RPA3 (also called RPA14). RPA3 is the smallest subunit of Replication protein A (RPA). RPA is a nuclear ssDNA binding protein (SSB) which appears to be involved in all aspects of DNA metabolism including replication, recombination, and repair. RPA also mediates specific interactions of various nuclear proteins. In animals, plants, and fungi, RPA is a heterotrimer with subunits of 70KDa (RPA1), 32kDa (RPA2), and 14 KDa (RPA3). RPA3 is believed to have a structural role in assembly of the RPA heterotrimer.
Probab=62.43 E-value=27 Score=24.29 Aligned_cols=45 Identities=18% Similarity=0.056 Sum_probs=31.5
Q ss_pred CCCCChHHHHhcCCCeEEEEEeeccccCCCCCCCCceEEEEeEeCCeeEEEE
Q 032340 48 RVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTW 99 (142)
Q Consensus 48 RpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~~L~~~~~~~~~~~~ 99 (142)
+|.-+.+++.+|+|+.|++.-+-. ..+|. .+.+.+.|+..+++.+
T Consensus 2 ~prVn~~~L~~f~gk~V~ivGkV~------~~~~~-~~~~~~~Dg~~v~v~l 46 (101)
T cd04479 2 TPRINGAMLSQFVGKTVRIVGKVE------KVDGD-SLTLISSDGVNVTVEL 46 (101)
T ss_pred CceeCHHHHHhhCCCEEEEEEEEE------EecCC-eEEEEcCCCCEEEEEe
Confidence 567788999999999999876542 22333 4567676766666654
No 25
>cd01726 LSm6 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. LSm6 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=58.02 E-value=20 Score=22.97 Aligned_cols=27 Identities=22% Similarity=0.182 Sum_probs=21.7
Q ss_pred HHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 56 LERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 56 f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
++.++|+.|.|.+++ | +.| +|.++|.-
T Consensus 5 L~~~~~~~V~V~Lk~----------g-~~~~G~L~~~D~~ 33 (67)
T cd01726 5 LKAIIGRPVVVKLNS----------G-VDYRGILACLDGY 33 (67)
T ss_pred HHhhCCCeEEEEECC----------C-CEEEEEEEEEccc
Confidence 478899999999987 3 344 89999864
No 26
>cd01729 LSm7 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. LSm7 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=56.79 E-value=23 Score=23.76 Aligned_cols=31 Identities=26% Similarity=0.443 Sum_probs=24.9
Q ss_pred hHHHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCCe
Q 032340 53 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMET 94 (142)
Q Consensus 53 ~~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~~ 94 (142)
..++.+++|+.|.|.+++ | +.| .|.++|.--
T Consensus 4 ~~~L~~~i~k~V~V~l~~----------g-r~~~G~L~~~D~~m 36 (81)
T cd01729 4 ILDLSKYVDKKIRVKFQG----------G-REVTGILKGYDQLL 36 (81)
T ss_pred hhhHHHhcCCeEEEEECC----------C-cEEEEEEEEEcCcc
Confidence 457889999999999987 3 455 899998763
No 27
>cd00600 Sm_like 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. Sm-like proteins exist in archaea as well as prokaryotes that form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=54.70 E-value=29 Score=21.29 Aligned_cols=26 Identities=19% Similarity=0.331 Sum_probs=21.2
Q ss_pred HhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 57 ERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 57 ~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
+.++|+.|.|.+.+ .+.| .|.++|..
T Consensus 2 ~~~~g~~V~V~l~~-----------g~~~~G~L~~~D~~ 29 (63)
T cd00600 2 KDLVGKTVRVELKD-----------GRVLEGVLVAFDKY 29 (63)
T ss_pred hHHCCCEEEEEECC-----------CcEEEEEEEEECCC
Confidence 46789999999988 3455 99999987
No 28
>PF14472 DUF4429: Domain of unknown function (DUF4429)
Probab=52.31 E-value=24 Score=24.22 Aligned_cols=39 Identities=28% Similarity=0.361 Sum_probs=24.6
Q ss_pred eEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEe
Q 032340 89 SFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLH 139 (142)
Q Consensus 89 ~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~ 139 (142)
++|++.++|+|.-. ....-+.++| +.+||+++|.-+.+.
T Consensus 2 sfDg~~V~i~~~g~--~a~~~~~~~G----------~~~ipl~~i~gV~~~ 40 (94)
T PF14472_consen 2 SFDGDTVRIRWGGW--RAPRAKRALG----------EKTIPLSAISGVEWK 40 (94)
T ss_pred EEcCCEEEEEECCc--cchhhhccCC----------CEEEEHHHcceEEEE
Confidence 68899999998611 1111111222 358999999988775
No 29
>PF01423 LSM: LSM domain ; InterPro: IPR001163 This family is found in Lsm (like-Sm) proteins and in bacterial Lsm-related Hfq proteins. In each case, the domain adopts a core structure consisting of an open beta-barrel with an SH3-like topology. Lsm (like-Sm) proteins have diverse functions, and are thought to be important modulators of RNA biogenesis and function [, ]. The Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6) []. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker []. In other snRNPs, certain Sm proteins are replaced with different Lsm proteins, such as with U7 snRNPs, in which the D1 and D2 Sm proteins are replaced with U7-specific Lsm10 and Lsm11 proteins, where Lsm11 plays a role in histone U7-specific RNA processing []. Lsm proteins are also found in archaebacteria, which do not have any splicing apparatus suggesting a more general role for Lsm proteins. The pleiotropic translational regulator Hfq (host factor Q) is a bacterial Lsm-like protein, which modulates the structure of numerous RNA molecules by binding preferentially to A/U-rich sequences in RNA []. Hfq forms an Lsm-like fold, however, unlike the heptameric Sm proteins, Hfq forms a homo-hexameric ring.; PDB: 1D3B_K 2Y9D_D 2Y9A_D 2Y9C_R 3VRI_C 2Y9B_K 3QUI_D 3M4G_H 3INZ_E 1U1S_C ....
Probab=51.73 E-value=30 Score=21.64 Aligned_cols=29 Identities=21% Similarity=0.340 Sum_probs=23.5
Q ss_pred HHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCCe
Q 032340 55 ELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMET 94 (142)
Q Consensus 55 ~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~~ 94 (142)
.++.++|..|.|.+.+ | +.+ .|.++|..-
T Consensus 2 ~L~~~~g~~V~V~l~~----------g-~~~~G~L~~~D~~~ 32 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKN----------G-RTYRGTLVSFDQFM 32 (67)
T ss_dssp HHHHTTTSEEEEEETT----------S-EEEEEEEEEEETTE
T ss_pred hhHHhCCcEEEEEEeC----------C-EEEEEEEEEeechh
Confidence 3678999999999988 3 445 999999875
No 30
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=51.10 E-value=37 Score=22.11 Aligned_cols=29 Identities=21% Similarity=0.345 Sum_probs=22.8
Q ss_pred HHHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 54 LELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 54 ~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
.-+.+++|+.|.|.+++ | +.| .|.++|..
T Consensus 7 ~~L~~~~~k~V~V~lk~----------g-~~~~G~L~~~D~~ 37 (72)
T PRK00737 7 DVLNNALNSPVLVRLKG----------G-REFRGELQGYDIH 37 (72)
T ss_pred HHHHHhCCCEEEEEECC----------C-CEEEEEEEEEccc
Confidence 34578899999999987 3 444 89999975
No 31
>cd01722 Sm_F The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form 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. Sm subunit F is capable of forming both homo- and hetero-heptamer ring structures. To form the hetero-heptamer, Sm subunit F initially binds subunits E and G to form a trimer which then assembles onto snRNA along with the D3/B and D1/D2 heterodimers.
Probab=50.89 E-value=31 Score=22.16 Aligned_cols=28 Identities=21% Similarity=0.211 Sum_probs=22.1
Q ss_pred HHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 55 ELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 55 ~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
.++.++|+.|.|.+++ | +.| +|.++|..
T Consensus 5 ~L~~~~g~~V~V~Lk~----------g-~~~~G~L~~~D~~ 34 (68)
T cd01722 5 FLNDLTGKPVIVKLKW----------G-MEYKGTLVSVDSY 34 (68)
T ss_pred HHHHcCCCEEEEEECC----------C-cEEEEEEEEECCC
Confidence 3477899999999998 2 444 89999865
No 32
>cd01731 archaeal_Sm1 The archaeal sm1 proteins: The Sm proteins are conserved in all three domains of life and are always associated with U-rich RNA sequences. They function to mediate RNA-RNA interactions and RNA biogenesis. All Sm proteins contain a common sequence motif in two segments, Sm1 and Sm2, separated by a short variable linker. Eukaryotic Sm proteins form part of specific small nuclear ribonucleoproteins (snRNPs) that are involved in the processing of pre-mRNAs to mature mRNAs, and are a major component of the eukaryotic spliceosome. Most snRNPs consist of seven Sm proteins (B/B', D1, D2, D3, E, F and G) arranged in a ring on a uridine-rich sequence (Sm site), plus a small nuclear RNA (snRNA) (either U1, U2, U5 or U4/6). Since archaebacteria do not have any splicing apparatus, Sm proteins of archaebacteria may play a more general role. Archaeal Lsm proteins are likely to represent the ancestral Sm domain.
Probab=49.88 E-value=32 Score=21.96 Aligned_cols=28 Identities=29% Similarity=0.396 Sum_probs=22.1
Q ss_pred HHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCCe
Q 032340 56 LERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMET 94 (142)
Q Consensus 56 f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~~ 94 (142)
++.++|+.|.|.+++ | +.| +|.++|.--
T Consensus 5 L~~~~~~~V~V~l~~----------g-~~~~G~L~~~D~~m 34 (68)
T cd01731 5 LKDSLNKPVLVKLKG----------G-KEVRGRLKSYDQHM 34 (68)
T ss_pred HHHhcCCEEEEEECC----------C-CEEEEEEEEECCcc
Confidence 567899999999987 3 344 899998863
No 33
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=48.17 E-value=14 Score=31.35 Aligned_cols=59 Identities=19% Similarity=0.022 Sum_probs=40.5
Q ss_pred HHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEe
Q 032340 10 MEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYV 69 (142)
Q Consensus 10 lddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~~~ 69 (142)
-|+|..-+-..++.|-.-.+.+|....|.||+|||+-+--+.-..=+ +..|..+++.-.
T Consensus 116 ~~~~~~~~ylrGAFLagGSis~Pe~~~YhLEi~s~~ee~a~~L~~l~-~~f~l~ak~~er 174 (308)
T COG1481 116 SDDEDFRAYLRGAFLAGGSISDPETSSYHLEISSNYEEHALALVKLL-RRFGLNAKIIER 174 (308)
T ss_pred ccHHHHHHHHHHHHHcCCccCCCCCCceeEEEecCcHHHHHHHHHHH-HHhccchheeee
Confidence 46777777778888864444457778999999999999554444444 455666666543
No 34
>cd06168 LSm9 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. LSm9 proteins have a single Sm-like domain 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=47.54 E-value=41 Score=22.31 Aligned_cols=30 Identities=13% Similarity=0.248 Sum_probs=24.1
Q ss_pred HHHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCCe
Q 032340 54 LELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMET 94 (142)
Q Consensus 54 ~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~~ 94 (142)
..+..++|+.|+|++.+ .+.| .|..+|...
T Consensus 3 ~~L~~~l~~~v~V~l~d-----------gR~~~G~l~~~D~~~ 34 (75)
T cd06168 3 QKLRSLLGRTMRIHMTD-----------GRTLVGVFLCTDRDC 34 (75)
T ss_pred hHHHHhcCCeEEEEEcC-----------CeEEEEEEEEEcCCC
Confidence 45678899999999998 3555 899998775
No 35
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=43.46 E-value=46 Score=20.71 Aligned_cols=27 Identities=19% Similarity=0.327 Sum_probs=22.0
Q ss_pred HHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 56 LERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 56 f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
++.++|+.|.|.+.+ | +.+ .|.++|..
T Consensus 3 L~~~~~~~V~V~l~~----------g-~~~~G~L~~~D~~ 31 (67)
T smart00651 3 LKKLIGKRVLVELKN----------G-REYRGTLKGFDQF 31 (67)
T ss_pred hHHhCCcEEEEEECC----------C-cEEEEEEEEECcc
Confidence 568899999999988 3 344 89999976
No 36
>PF06649 DUF1161: Protein of unknown function (DUF1161); InterPro: IPR010595 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=42.70 E-value=28 Score=21.92 Aligned_cols=28 Identities=11% Similarity=0.182 Sum_probs=22.3
Q ss_pred HHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCC
Q 032340 13 IEAFCTTYRARLDEAEIAKSIPENTSLEVSSPG 45 (142)
Q Consensus 13 c~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPG 45 (142)
|+.+-..|...+.... . ..|+|||=.-+
T Consensus 1 CE~lk~eI~~KI~anG----V-~~ftLeiV~nd 28 (52)
T PF06649_consen 1 CEELKAEIEQKIIANG----V-SSFTLEIVPND 28 (52)
T ss_pred ChHHHHHHHHHHHHcC----C-CceEEEEeeCc
Confidence 7888888999888776 3 88999986544
No 37
>cd07015 Clp_protease_NfeD Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially cle
Probab=42.33 E-value=33 Score=26.31 Aligned_cols=59 Identities=10% Similarity=0.095 Sum_probs=34.0
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCC-CCCCChHHHHhcCCCeEEEEEe
Q 032340 5 SGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVE-RVVRIPLELERFKDRAMYVKYV 69 (142)
Q Consensus 5 ~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGie-RpL~~~~~f~r~~G~~v~V~~~ 69 (142)
+|.|+-.....+.|.+..+-+ + + .....|++.|||=. .+-...-+.-++...+|.+...
T Consensus 7 ~G~I~~~~~~~l~~~l~~A~~--~---~-~~~i~l~inSPGG~v~~~~~I~~~i~~~~~pvv~~v~ 66 (172)
T cd07015 7 KGQITSYTYDQFDRYITIAEQ--D---N-AEAIIIELDTPGGRADAAGNIVQRIQQSKIPVIIYVY 66 (172)
T ss_pred eeEECHhHHHHHHHHHHHHhc--C---C-CCeEEEEEECCCCCHHHHHHHHHHHHhcCcCEEEEEe
Confidence 355665555566676666543 2 1 26789999999843 2223334444555566655444
No 38
>cd01719 Sm_G 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. Sm subunit G binds subunits E and F to form a trimer which then assembles onto snRNA along with the D1/D2 and D3/B heterodimers forming 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=41.90 E-value=50 Score=21.58 Aligned_cols=29 Identities=28% Similarity=0.386 Sum_probs=23.3
Q ss_pred HHHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 54 LELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 54 ~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
.++..++|+.|.|.+++ | +.+ +|.++|.-
T Consensus 3 ~~L~~~i~k~V~V~L~~----------g-~~~~G~L~~~D~~ 33 (72)
T cd01719 3 PELKKYMDKKLSLKLNG----------N-RKVSGILRGFDPF 33 (72)
T ss_pred hhhHHhCCCeEEEEECC----------C-eEEEEEEEEEccc
Confidence 46788999999999987 3 344 99999955
No 39
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=40.95 E-value=50 Score=21.70 Aligned_cols=30 Identities=20% Similarity=0.338 Sum_probs=23.3
Q ss_pred HHHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCCe
Q 032340 54 LELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMET 94 (142)
Q Consensus 54 ~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~~ 94 (142)
.-+.+++|+.|.|.+++ | +.| +|.++|..-
T Consensus 10 ~~l~~~~~~~V~V~lk~----------g-~~~~G~L~~~D~~m 41 (79)
T COG1958 10 SFLKKLLNKRVLVKLKN----------G-REYRGTLVGFDQYM 41 (79)
T ss_pred HHHHHhhCCEEEEEECC----------C-CEEEEEEEEEccce
Confidence 34567888999999998 4 445 999999864
No 40
>PF07837 FTCD_N: Formiminotransferase domain, N-terminal subdomain; InterPro: IPR012886 The formiminotransferase (FT) domain of formiminotransferase-cyclodeaminase (FTCD) forms a homodimer, with each protomer being comprised of two subdomains. The formiminotransferase domain has an N-terminal subdomain that is made up of a six-stranded mixed beta-pleated sheet and five alpha helices, which are arranged on the external surface of the beta sheet. This, in turn, faces the beta-sheet of the C-terminal subdomain to form a double beta-sheet layer. The two subdomains are separated by a short linker sequence, which is not thought to be any more flexible than the remainder of the molecule. The substrate is predicted to form a number of contacts with residues found in both the N-terminal and C-terminal subdomains []. This entry represents the N-terminal subdomain of the formiminotransferase domain.; GO: 0005542 folic acid binding, 0016740 transferase activity, 0008152 metabolic process; PDB: 2PFD_C 1QD1_B.
Probab=40.91 E-value=22 Score=27.79 Aligned_cols=22 Identities=18% Similarity=0.341 Sum_probs=17.2
Q ss_pred CCCCHHHHHHHHHHHHHhhhhh
Q 032340 6 GSPSMEDIEAFCTTYRARLDEA 27 (142)
Q Consensus 6 ~gvslddc~~vSr~i~~~LD~~ 27 (142)
+++||++|.++++.+...+-.+
T Consensus 95 ~~~t~eec~~~A~~~g~~i~~~ 116 (178)
T PF07837_consen 95 SGVTMEECAELARELGERIGEE 116 (178)
T ss_dssp ES--HHHHHHHHHHHHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHHHHHHh
Confidence 4689999999999999988654
No 41
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=40.15 E-value=1.1e+02 Score=20.64 Aligned_cols=36 Identities=14% Similarity=-0.051 Sum_probs=22.6
Q ss_pred HHHHhcCCCeEEEEEeeccccCCCCCCCCceE-----EEEeEeCCeeEEEE
Q 032340 54 LELERFKDRAMYVKYVGETVTTGSPSESDGVF-----RLISFDMETECCTW 99 (142)
Q Consensus 54 ~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~-----~L~~~~~~~~~~~~ 99 (142)
++...++|+.|.++.+. |+++. .|.++=..-+++.+
T Consensus 10 ~~l~~~vG~~V~l~a~~----------GRkK~~~r~GvL~~tYPsvFvV~l 50 (76)
T PF06257_consen 10 KELESHVGKRVKLKANK----------GRKKIIEREGVLEETYPSVFVVEL 50 (76)
T ss_dssp HHHHHTTTSEEEEEE------------SSS--S-EEEEEEEE-SSEEEEEE
T ss_pred HHHHHcCCCEEEEEEcC----------CceEEEEEEEEEEeecCcEEEEEE
Confidence 56788999999999776 56655 66666666555554
No 42
>cd01728 LSm1 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. LSm1 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=40.12 E-value=61 Score=21.40 Aligned_cols=30 Identities=23% Similarity=0.103 Sum_probs=24.4
Q ss_pred hHHHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 53 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 53 ~~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
...++.++++.|.|.+++ | +.| .|.++|.-
T Consensus 4 ~~~L~~~l~k~v~V~l~~----------g-r~~~G~L~~fD~~ 35 (74)
T cd01728 4 TASLVDDLDKKVVVLLRD----------G-RKLIGILRSFDQF 35 (74)
T ss_pred hHHHHHhcCCEEEEEEcC----------C-eEEEEEEEEECCc
Confidence 356788999999999988 3 455 99999976
No 43
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=38.63 E-value=46 Score=21.64 Aligned_cols=34 Identities=15% Similarity=0.054 Sum_probs=21.2
Q ss_pred HHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC--eeEEEEe
Q 032340 56 LERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME--TECCTWG 100 (142)
Q Consensus 56 f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~--~~~~~~~ 100 (142)
+..++|..|.|++++ |. .| .+.+++.+ ...+.++
T Consensus 7 ~~~lvG~~V~V~~~~----------G~-~yeGif~s~s~~~~~~~vvLk 44 (77)
T PF14438_consen 7 LTNLVGQTVEVTTKN----------GS-VYEGIFHSASPESNEFDVVLK 44 (77)
T ss_dssp HHTTTTSEEEEEETT----------S--EEEEEEEEE-T---T--EEEE
T ss_pred HHhCcCCEEEEEECC----------CC-EEEEEEEeCCCcccceeEEEE
Confidence 457899999999988 33 35 88888775 3444443
No 44
>cd01721 Sm_D3 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form 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. Sm subunit D3 heterodimerizes with subunit B and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=37.77 E-value=65 Score=20.81 Aligned_cols=27 Identities=19% Similarity=0.278 Sum_probs=21.4
Q ss_pred HHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 56 LERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 56 f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
++...|+.|.|.+++ | ..+ +|.++|+-
T Consensus 5 L~~~~g~~V~VeLk~----------g-~~~~G~L~~~D~~ 33 (70)
T cd01721 5 LHEAEGHIVTVELKT----------G-EVYRGKLIEAEDN 33 (70)
T ss_pred HhhCCCCEEEEEECC----------C-cEEEEEEEEEcCC
Confidence 467899999999998 3 333 89999885
No 45
>cd01717 Sm_B The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form 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. Sm subunit B heterodimerizes with subunit D3 and three such heterodimers form a hexameric ring structure with alternating B and D3 subunits. The D3 - B heterodimer also assembles into a heptameric ring containing D1, D2, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=36.78 E-value=64 Score=21.25 Aligned_cols=30 Identities=10% Similarity=0.249 Sum_probs=23.4
Q ss_pred HHHhcCCCeEEEEEeeccccCCCCCCCCceE-EEEeEeCCe
Q 032340 55 ELERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDMET 94 (142)
Q Consensus 55 ~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~-~L~~~~~~~ 94 (142)
.+..++|+.|.|++.+ |+... .|..+|...
T Consensus 4 ~l~~~l~~~V~V~l~d----------gR~~~G~L~~~D~~~ 34 (79)
T cd01717 4 KMLQLINYRLRVTLQD----------GRQFVGQFLAFDKHM 34 (79)
T ss_pred hhHHHcCCEEEEEECC----------CcEEEEEEEEEcCcc
Confidence 4678899999999988 43333 999998764
No 46
>TIGR02024 FtcD glutamate formiminotransferase. This model covers enzymes from metazoa as well as gram-positive bacteria and archaea. In humans, deficiency of this enzyme results in a disease phenotype. The crystal structure of the enzyme has been studied in the context of the catalytic mechanism.
Probab=36.65 E-value=35 Score=28.80 Aligned_cols=22 Identities=23% Similarity=0.392 Sum_probs=19.2
Q ss_pred CCCCHHHHHHHHHHHHHhhhhh
Q 032340 6 GSPSMEDIEAFCTTYRARLDEA 27 (142)
Q Consensus 6 ~gvslddc~~vSr~i~~~LD~~ 27 (142)
+++|+++|.++++.+...+-.+
T Consensus 97 ~~~t~eec~~lA~~vg~~i~~~ 118 (298)
T TIGR02024 97 RNVTMEECVELAKEFGKRLGEE 118 (298)
T ss_pred CCCCHHHHHHHHHHHHHHHHHh
Confidence 5799999999999999888643
No 47
>cd01732 LSm5 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=36.57 E-value=78 Score=20.98 Aligned_cols=28 Identities=21% Similarity=0.399 Sum_probs=22.1
Q ss_pred HH-HhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 55 EL-ERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 55 ~f-~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
+| .+++++.|.|.+++ | +.+ .|.++|.-
T Consensus 6 ~~L~~~~~~~V~V~l~~----------g-r~~~G~L~g~D~~ 36 (76)
T cd01732 6 ELIDKCIGSRIWIVMKS----------D-KEFVGTLLGFDDY 36 (76)
T ss_pred HHHHHhCCCEEEEEECC----------C-eEEEEEEEEeccc
Confidence 44 78899999999988 3 445 89998875
No 48
>PF08496 Peptidase_S49_N: Peptidase family S49 N-terminal; InterPro: IPR013703 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) [, ]. This domain is found to the N terminus of bacterial signal peptidases that belong to the MEROPS peptidase family S49 (protease IV family, clan SK) (see also IPR002142 from INTERPRO) [, ]. ; GO: 0004252 serine-type endopeptidase activity, 0005886 plasma membrane
Probab=36.35 E-value=65 Score=24.45 Aligned_cols=40 Identities=20% Similarity=0.311 Sum_probs=34.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCC
Q 032340 2 SNKSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPG 45 (142)
Q Consensus 2 iD~~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPG 45 (142)
+|=+|+|.-...+.+-++|+++|..+. | .+...|=+.|||
T Consensus 103 ldF~Gdi~A~~v~~LReeisail~~a~---~-~DeV~~rLES~G 142 (155)
T PF08496_consen 103 LDFKGDIKASEVESLREEISAILSVAT---P-EDEVLVRLESPG 142 (155)
T ss_pred EecCCCccHHHHHHHHHHHHHHHHhCC---C-CCeEEEEEecCC
Confidence 455788999999999999999999887 3 377888888998
No 49
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=35.62 E-value=1.3e+02 Score=19.72 Aligned_cols=36 Identities=8% Similarity=0.049 Sum_probs=28.0
Q ss_pred hHHHHhcCCCeEEEEEeeccccCCCCCCCCceEEEEeEeCCeeEEE
Q 032340 53 PLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCT 98 (142)
Q Consensus 53 ~~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~~L~~~~~~~~~~~ 98 (142)
..+++..+|..+.|..... .+.| +|.++..|.++++
T Consensus 13 yq~lq~liG~~vvV~T~~g------~v~G----~L~~V~pDhIvl~ 48 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTRG------SVRG----ILVDVKPDHIVLE 48 (66)
T ss_pred HHHHHHhcCCEEEEEEcCC------cEEE----EEEeecCCEEEEE
Confidence 3678899999999987551 2223 8999999999876
No 50
>PF10882 bPH_5: Bacterial PH domain; InterPro: IPR020482 This entry contains membrane proteins with no known function.
Probab=35.03 E-value=59 Score=21.84 Aligned_cols=29 Identities=17% Similarity=0.391 Sum_probs=20.9
Q ss_pred eEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEe
Q 032340 89 SFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLH 139 (142)
Q Consensus 89 ~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~ 139 (142)
.++++.++|.+.. + ..+||+++|..+.+.
T Consensus 4 ~v~~~~l~I~~~~------------~----------~~~Ip~~~I~~v~~~ 32 (100)
T PF10882_consen 4 EVDDDGLIIRWPF------------G----------KITIPLAEIESVELV 32 (100)
T ss_pred EEECCEEEEEEcc------------c----------cEEEEHHHcEEEEec
Confidence 5678888877542 1 257999999988765
No 51
>PF09493 DUF2389: Tryptophan-rich protein (DUF2389); InterPro: IPR012663 Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesize tryptophan de novo.
Probab=33.79 E-value=97 Score=19.69 Aligned_cols=44 Identities=14% Similarity=0.178 Sum_probs=25.8
Q ss_pred CCCCCCceEEEEeE--eCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeE
Q 032340 77 SPSESDGVFRLISF--DMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVR 137 (142)
Q Consensus 77 ~~~~g~k~~~L~~~--~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~kar 137 (142)
.|++|.+.|.+..+ ++++..++ .++.|.-. .++.|++.+++...
T Consensus 8 ~p~~g~rHF~V~~~~~~~~~~~v~-~~~av~~~----------------~~~~i~w~~Lkd~~ 53 (60)
T PF09493_consen 8 QPINGERHFLVTNVEGDEDGRVVE-LVEAVDSK----------------RRFWINWRELKDRS 53 (60)
T ss_pred CccCCcEEEEEEEEeecCCCeEEE-eEeeeccC----------------cEEEEeHHHhCCcc
Confidence 37889999955444 45555555 22222110 15789998887543
No 52
>TIGR02450 tryptophan-rich conserved hypothetical protein. Members of this family are small hypothetical proteins of 60 to 100 residues from Cyanobacteria and some Proteobacteria. Prochlorococcus marinus strains have two members, other species one only. Interestingly, of the eight most conserved residues, four are aromatic and three are invariant tryptophans. It appears all species that encode this protein can synthesize tryptophan de novo.
Probab=32.39 E-value=1.1e+02 Score=19.50 Aligned_cols=45 Identities=11% Similarity=0.157 Sum_probs=25.2
Q ss_pred CCCCCCceEEEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeeccccccee
Q 032340 77 SPSESDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLV 136 (142)
Q Consensus 77 ~~~~g~k~~~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~ka 136 (142)
.|++|.+.|.+..+.+++-.+...+..+-. . ..++.|++.+++.-
T Consensus 9 ~~~~g~rHF~v~~~~~e~~~v~~~l~~a~~------~---------~~~~~i~w~~Lkd~ 53 (61)
T TIGR02450 9 TPINGERHFVVVNYGDEGGQVWVEMVSVVD------V---------KISFRVNWQDLKDP 53 (61)
T ss_pred CccCCceEEEEEEEecCCCeEEEEEhhhcc------c---------CcEEEEeHHHhCCh
Confidence 378899999666665554333222211111 0 11578899888753
No 53
>cd01727 LSm8 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. LSm8 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=32.34 E-value=90 Score=20.28 Aligned_cols=29 Identities=31% Similarity=0.427 Sum_probs=22.7
Q ss_pred HHHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCCe
Q 032340 55 ELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMET 94 (142)
Q Consensus 55 ~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~~ 94 (142)
.+..++++.|.|++.+ .+.| .|.++|...
T Consensus 3 ~L~~~l~~~V~V~l~d-----------gr~~~G~L~~~D~~~ 33 (74)
T cd01727 3 TLEDYLNKTVSVITVD-----------GRVIVGTLKGFDQAT 33 (74)
T ss_pred hHHHhcCCEEEEEECC-----------CcEEEEEEEEEcccc
Confidence 4678899999999987 3445 899998753
No 54
>cd07021 Clp_protease_NfeD_like Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentiall
Probab=31.01 E-value=65 Score=24.64 Aligned_cols=37 Identities=14% Similarity=0.214 Sum_probs=24.4
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCC
Q 032340 5 SGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVE 47 (142)
Q Consensus 5 ~~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGie 47 (142)
+|.|+-.....+.|.|..+.+. + -....|++.|||=.
T Consensus 7 ~g~I~~~~~~~l~~~l~~a~~~-----~-~~~ivl~inspGG~ 43 (178)
T cd07021 7 EGEIDPGLAAFVERALKEAKEE-----G-ADAVVLDIDTPGGR 43 (178)
T ss_pred eeEECHHHHHHHHHHHHHHHhC-----C-CCeEEEEEECcCCC
Confidence 4556665556666666665542 2 26789999999943
No 55
>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=30.98 E-value=1e+02 Score=20.18 Aligned_cols=28 Identities=18% Similarity=0.225 Sum_probs=21.5
Q ss_pred HHhcCCCeEEEEEeeccccCCCCCCCCceE-EEEeEeCC
Q 032340 56 LERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 93 (142)
Q Consensus 56 f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~-~L~~~~~~ 93 (142)
++...|+.|.|.+++ |.... .|.++|+.
T Consensus 6 L~~~~g~~V~VeLkn----------g~~~~G~L~~~D~~ 34 (76)
T cd01723 6 LKTAQNHPMLVELKN----------GETYNGHLVNCDNW 34 (76)
T ss_pred HHhcCCCEEEEEECC----------CCEEEEEEEEEcCC
Confidence 467899999999987 32222 89999886
No 56
>cd01725 LSm2 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. LSm2 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=29.63 E-value=1.1e+02 Score=20.45 Aligned_cols=26 Identities=15% Similarity=0.106 Sum_probs=20.8
Q ss_pred HhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 57 ERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 57 ~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
+...|+.|.|.+++ | ..+ +|.++|+-
T Consensus 7 ~~l~g~~V~VeLKn----------g-~~~~G~L~~vD~~ 34 (81)
T cd01725 7 KTLVGKEVTVELKN----------D-LSIRGTLHSVDQY 34 (81)
T ss_pred HhCCCCEEEEEECC----------C-cEEEEEEEEECCC
Confidence 78899999999987 2 233 89998876
No 57
>TIGR02778 ligD_pol DNA polymerase LigD, polymerase domain. DNA repair of double-stranded breaks by non-homologous end joining (NHEJ) is accomplished by a two-protein system that is present in a minority of prokaryotes. One component is the Ku protein (see TIGR02772), which binds DNA ends. The other is a DNA ligase, a protein that is a multidomain polypeptide in most of those bacteria that have NHEJ, a permuted polypeptide in Mycobacterium tuberculosis and a few other species, and the product of tandem genes in some other bacteria. This model represents the polymerase domain.
Probab=29.35 E-value=72 Score=26.14 Aligned_cols=62 Identities=13% Similarity=0.070 Sum_probs=38.3
Q ss_pred CCCCCCCHHHHHHHHHHHHHhhhhhhhcCCC--CCCeEEEEecCCCC-CCCCChHHHHhcCCCeE
Q 032340 3 NKSGSPSMEDIEAFCTTYRARLDEAEIAKSI--PENTSLEVSSPGVE-RVVRIPLELERFKDRAM 64 (142)
Q Consensus 3 D~~~gvslddc~~vSr~i~~~LD~~d~~~~i--~~~Y~LEVSSPGie-RpL~~~~~f~r~~G~~v 64 (142)
|...+++.++|.++.+.+.+.|++.++.... ++.=-|-|=-|=-. ......+.|.+++.+.+
T Consensus 122 DP~~~~~f~~v~~~A~~~r~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l 186 (245)
T TIGR02778 122 DPGPGVAWKLVVEAAQLIRELLDELGLESFVKTSGGKGLHVYVPLRPTLSWDEVKDFAKALAQAL 186 (245)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEECCCCCCHHHHHHHHHHHHHHH
Confidence 5666799999999999999999987742221 23334444444211 12234456666665554
No 58
>PF11095 Gemin7: Gem-associated protein 7 (Gemin7); InterPro: IPR020338 Gem-associated protein 7 (Gemin7) is a component of the survival of motor neuron complex, which functions in the assembly of spliceosomal small nuclear ribonucleoproteins. Gemin7 interacts with several Sm proteins of spliceosomal small nuclear ribonucleoproteins, especially SmE []. Gem-associated protein 7 is found in the nucleoplasm, in nuclear "gems" (Gemini of Cajal bodies), and in the cytoplasm. Three transcript variants encoding the same protein have been found for this gene [].; GO: 0032797 SMN complex; PDB: 1Y96_D.
Probab=28.73 E-value=1.4e+02 Score=20.39 Aligned_cols=17 Identities=6% Similarity=-0.038 Sum_probs=14.1
Q ss_pred HHHHhcCCCeEEEEEee
Q 032340 54 LELERFKDRAMYVKYVG 70 (142)
Q Consensus 54 ~~f~r~~G~~v~V~~~~ 70 (142)
+-+....|+.|.+++++
T Consensus 17 r~l~~~~gk~v~f~l~e 33 (80)
T PF11095_consen 17 RSLLAMVGKPVEFTLHE 33 (80)
T ss_dssp HHHHHCTTSEEEEEEGG
T ss_pred HHHHHhcCCceEEEEeC
Confidence 44667889999999998
No 59
>cd01733 LSm10 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. LSm10 is an SmD1-like protein which is thought to bind U7 snRNA along with LSm11 and five other Sm subunits to form a 7-member ring structure. LSm10 and the U7 snRNP of which it is a part are thought to play an important role in histone mRNA 3' processing.
Probab=28.22 E-value=1.2e+02 Score=20.19 Aligned_cols=30 Identities=17% Similarity=0.235 Sum_probs=22.7
Q ss_pred hHHH-HhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 53 PLEL-ERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 53 ~~~f-~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
.-.| +...|+.|.|.+++ |. .+ .|.++|+.
T Consensus 10 l~~~L~~l~g~~V~VeLKn----------g~-~~~G~L~~vD~~ 42 (78)
T cd01733 10 LIILLQGLQGKVVTVELRN----------ET-TVTGRIASVDAF 42 (78)
T ss_pred HHHHHHHCCCCEEEEEECC----------CC-EEEEEEEEEcCC
Confidence 3444 78899999999998 32 33 89898876
No 60
>cd04862 PaeLigD_Pol_like PaeLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The PaeLigD Pol domain in vitro, in a manganese-dependent fashion, catalyzes templated extensions of 5'-overhang duplex DNA, and nontemplated single-nu
Probab=27.59 E-value=81 Score=25.53 Aligned_cols=62 Identities=11% Similarity=0.062 Sum_probs=37.9
Q ss_pred CCCCCCCHHHHHHHHHHHHHhhhhhhhcCCC--CCCeEEEEecCCC-CCCCCChHHHHhcCCCeE
Q 032340 3 NKSGSPSMEDIEAFCTTYRARLDEAEIAKSI--PENTSLEVSSPGV-ERVVRIPLELERFKDRAM 64 (142)
Q Consensus 3 D~~~gvslddc~~vSr~i~~~LD~~d~~~~i--~~~Y~LEVSSPGi-eRpL~~~~~f~r~~G~~v 64 (142)
|...+++..+|.++.+.+.+.|++.++.... ++.=-|-|=-|=- .......+.|.+++.+.+
T Consensus 106 DP~~~~~f~~v~~~A~~~r~~L~~lgL~~~~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~lA~~l 170 (227)
T cd04862 106 DPGPGVPWKAVVEAALLVRELLDELGLESFVKTSGGKGLHVVVPLAPRAGWDEVKAFAKALAQHL 170 (227)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHH
Confidence 5566799999999999999999987742211 2333344444411 122234455666665554
No 61
>cd01730 LSm3 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. LSm3 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=27.00 E-value=1.3e+02 Score=19.93 Aligned_cols=29 Identities=31% Similarity=0.460 Sum_probs=21.8
Q ss_pred HH-HhcCCCeEEEEEeeccccCCCCCCCCceE-EEEeEeCC
Q 032340 55 EL-ERFKDRAMYVKYVGETVTTGSPSESDGVF-RLISFDME 93 (142)
Q Consensus 55 ~f-~r~~G~~v~V~~~~~~~~~~~~~~g~k~~-~L~~~~~~ 93 (142)
+| +.+.++.|.|.+++ |+... .|.++|.-
T Consensus 4 ~~l~~~~~k~V~V~l~~----------gr~~~G~L~~fD~~ 34 (82)
T cd01730 4 DLIRLSLDERVYVKLRG----------DRELRGRLHAYDQH 34 (82)
T ss_pred HHHHHhCCCEEEEEECC----------CCEEEEEEEEEccc
Confidence 44 66799999999988 43333 89999875
No 62
>cd04861 LigD_Pol_like LigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. PaeLigD is monomeric, containing an N-terminal phosphoesterase module, a central polymerase (Pol) domain, and a C-terminal ATP-dependent ligase domain. Mycobacterium tuberculosis (Mt)LigD, also found in this group, is monomeric and contains the same modules but these are arranged differently: an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase do
Probab=26.80 E-value=85 Score=25.40 Aligned_cols=62 Identities=16% Similarity=0.118 Sum_probs=39.0
Q ss_pred CCCCCCCHHHHHHHHHHHHHhhhhhhhcCCC--CCCeEEEEecCCC-CCCCCChHHHHhcCCCeE
Q 032340 3 NKSGSPSMEDIEAFCTTYRARLDEAEIAKSI--PENTSLEVSSPGV-ERVVRIPLELERFKDRAM 64 (142)
Q Consensus 3 D~~~gvslddc~~vSr~i~~~LD~~d~~~~i--~~~Y~LEVSSPGi-eRpL~~~~~f~r~~G~~v 64 (142)
|...+++..+|.++...+.+.||+.++.... ++.=-|-|=.|=- .......+.|.+++.+.+
T Consensus 106 DP~~~~~f~~v~~~A~~vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~r~fa~~iA~~l 170 (227)
T cd04861 106 DPGPGVPFEDVVEAALLLRELLDELGLESFPKTSGGKGLHVYVPLAPRYTWDEVRAFAKALAREL 170 (227)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHH
Confidence 5556899999999999999999987742222 2343444444422 122345566666665544
No 63
>cd04866 LigD_Pol_like_3 LigD_Pol_like_3: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 3. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated repair DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=26.73 E-value=86 Score=25.34 Aligned_cols=63 Identities=11% Similarity=0.064 Sum_probs=41.6
Q ss_pred CCCCCCCHHHHHHHHHHHHHhhhhhhhcCCC--CCCeEEEEecCCC--CCCCCChHHHHhcCCCeEE
Q 032340 3 NKSGSPSMEDIEAFCTTYRARLDEAEIAKSI--PENTSLEVSSPGV--ERVVRIPLELERFKDRAMY 65 (142)
Q Consensus 3 D~~~gvslddc~~vSr~i~~~LD~~d~~~~i--~~~Y~LEVSSPGi--eRpL~~~~~f~r~~G~~v~ 65 (142)
|...+++.++|.++.+.+.+.|++.++.+.. ++.=-|-|=-|=- .......+.|.+++.+.+.
T Consensus 101 DP~~~~~f~~v~~~A~~vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~~r~fa~~iA~~l~ 167 (223)
T cd04866 101 DPPSRDHFSLAVEAANLLKEILDALGLTSFVKTSGNKGLQVYIPLPDNKFTYDETRLFTEFIAEYLC 167 (223)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHH
Confidence 5556899999999999999999987743222 2444444544432 2344566677777666553
No 64
>PF08661 Rep_fac-A_3: Replication factor A protein 3; InterPro: IPR013970 Replication factor A is involved in eukaryotic DNA replication, recombination and repair. ; PDB: 2PI2_H 1L1O_D 3KDF_A 2Z6K_D 1QUQ_D 2PQA_D.
Probab=26.70 E-value=80 Score=21.97 Aligned_cols=48 Identities=15% Similarity=0.027 Sum_probs=26.1
Q ss_pred CCCCCChHHHHhcCCCeEEEEEeeccccCCCCCCCCceEEEEeEeCCeeEEEE
Q 032340 47 ERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTW 99 (142)
Q Consensus 47 eRpL~~~~~f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~~L~~~~~~~~~~~~ 99 (142)
.+|.-+..++.+|.|+.|++.-+-..- ..+.+.+.|...++..+++..
T Consensus 4 ~~pRVn~~~L~~~~gk~VrivGkv~~~-----~~~g~~~~l~~~d~~~V~v~l 51 (109)
T PF08661_consen 4 PTPRVNGSMLSQFVGKTVRIVGKVESV-----DPDGGSATLSTSDGGQVTVSL 51 (109)
T ss_dssp --EEE-GGGGGGGTTSEEEEEEEEEEE------TTSSEEEEE-TTS-EEEEEE
T ss_pred CcceECHHHHHhhCCCeEEEEEEEeeE-----cCCCCEEEEEcCCCCEEEEEe
Confidence 467778899999999999986554111 111234455554555555543
No 65
>PF09430 DUF2012: Protein of unknown function (DUF2012); InterPro: IPR019008 This domain is found in different proteins, including uncharacterised protein family UPF0480 and nodal modulators. A nodal modulator has been identified as part of a protein complex that participates in the nodal signaling pathway during vertebrate development [].
Probab=26.29 E-value=46 Score=23.81 Aligned_cols=14 Identities=43% Similarity=0.510 Sum_probs=12.0
Q ss_pred CCCeEEEEecCCCC
Q 032340 34 PENTSLEVSSPGVE 47 (142)
Q Consensus 34 ~~~Y~LEVSSPGie 47 (142)
++.|.|||.||...
T Consensus 39 ~GsY~L~V~s~~~~ 52 (123)
T PF09430_consen 39 PGSYLLEVHSPDYV 52 (123)
T ss_pred CceEEEEEECCCcc
Confidence 58999999999863
No 66
>cd04865 LigD_Pol_like_2 LigD_Pol_like_2: Polymerase (Pol) domain of bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 2. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The Pol domains of PaeLigD and Mycobacterium tuberculosis (Mt)LigD are stimulated by manganese, are error-prone, and prefer adding rNTPs to dNTPs in vitro; however PaeLigD and MtLigD belong to other subgroups, proteins in this subgroup await functional characterization.
Probab=26.22 E-value=89 Score=25.32 Aligned_cols=62 Identities=16% Similarity=0.153 Sum_probs=37.8
Q ss_pred CCCCCCCHHHHHHHHHHHHHhhhhhhhcCCC--CCCeEEEEecCCCC-CCCCChHHHHhcCCCeE
Q 032340 3 NKSGSPSMEDIEAFCTTYRARLDEAEIAKSI--PENTSLEVSSPGVE-RVVRIPLELERFKDRAM 64 (142)
Q Consensus 3 D~~~gvslddc~~vSr~i~~~LD~~d~~~~i--~~~Y~LEVSSPGie-RpL~~~~~f~r~~G~~v 64 (142)
|...+++.++|.++.+.+...||+.++.... ++.=-|-|=.|=-. ......+.|.+++.+.+
T Consensus 107 DP~~~~~f~~v~~~A~~vr~~L~~lgL~sf~KTSG~kGlHv~vPl~~~~~~~~~r~fa~~iA~~l 171 (228)
T cd04865 107 DPQPGTSFEDVVEVALLVREVLDELGLRGYPKTSGARGLHIYVPIAPRYTFEEVRRFAELLAREV 171 (228)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHH
Confidence 5556899999999999999999988742211 23333444444211 12234455666665554
No 67
>PF13749 HATPase_c_4: ATP-dependent DNA helicase recG C-terminal; PDB: 3LMM_D.
Probab=26.02 E-value=32 Score=23.01 Aligned_cols=19 Identities=21% Similarity=0.106 Sum_probs=10.3
Q ss_pred eEEEEecCCCCCCCCChHH
Q 032340 37 TSLEVSSPGVERVVRIPLE 55 (142)
Q Consensus 37 Y~LEVSSPGieRpL~~~~~ 55 (142)
=++|++|||-=.+=.++++
T Consensus 11 driei~nPG~l~~~~t~~~ 29 (89)
T PF13749_consen 11 DRIEISNPGGLPGGVTIEN 29 (89)
T ss_dssp TEEEEEEES---TT--TTT
T ss_pred CEEEEEcCCcCCCCCCHHH
Confidence 3699999997765555554
No 68
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=25.75 E-value=47 Score=22.42 Aligned_cols=16 Identities=25% Similarity=0.216 Sum_probs=13.9
Q ss_pred HHHhcCCCeEEEEEee
Q 032340 55 ELERFKDRAMYVKYVG 70 (142)
Q Consensus 55 ~f~r~~G~~v~V~~~~ 70 (142)
=+..++|++|.|++.+
T Consensus 10 fl~~iiGr~V~VKl~s 25 (77)
T KOG1783|consen 10 FLKAIIGRTVVVKLNS 25 (77)
T ss_pred HHHHHhCCeEEEEecC
Confidence 3568999999999988
No 69
>cd04863 MtLigD_Pol_like MtLigD_Pol_like: Polymerase (Pol) domain of bacterial LigD proteins similar to Mycobacterium tuberculosis (Mt)LigD. The LigD Pol domain belongs to the archaeal/eukaryal primase (AEP) superfamily. In prokaryotes, LigD along with Ku is required for non-homologous end joining (NHEJ)-mediated repair of DNA double-strand breaks (DSB). NHEJ-mediated DNA DSB repair is error-prone. MtLigD is monomeric and contains an N-terminal Pol domain, a central phosphoesterase module, and a C-terminal ligase domain. It has been suggested that LigD Pol contributes to NHEJ-mediated DNA DSB repair in vivo, by filling in short 5'-overhangs with ribonucleotides; the filled in termini would then be sealed by the associated LigD ligase domain, resulting in short stretches of RNA incorporated into the genomic DNA. The MtLigD Pol domain is stimulated by manganese, is error-prone, and prefers adding rNTPs to dNTPs in vitro. The MtLigD Pol domain has been shown to prefer DNA gapped substrates
Probab=25.56 E-value=92 Score=25.27 Aligned_cols=63 Identities=13% Similarity=0.082 Sum_probs=39.2
Q ss_pred CCCCCCCHHHHHHHHHHHHHhhhhhhhcCCC--CCCeEEEEecCCC-CCCCCChHHHHhcCCCeEE
Q 032340 3 NKSGSPSMEDIEAFCTTYRARLDEAEIAKSI--PENTSLEVSSPGV-ERVVRIPLELERFKDRAMY 65 (142)
Q Consensus 3 D~~~gvslddc~~vSr~i~~~LD~~d~~~~i--~~~Y~LEVSSPGi-eRpL~~~~~f~r~~G~~v~ 65 (142)
|...+++.++|.++.+.+.++|++.++.+.. ++.=-|-|=-|=- .......+.|.+++.+.+.
T Consensus 110 DP~~~~~f~~v~~~A~~~r~~L~~lgL~s~~KTSG~kGlHV~vPl~~~~~~~~vr~fa~~~A~~l~ 175 (231)
T cd04863 110 DPGEPAGLVECARVALWLRDRLAALGLASFPKTSGSKGLHLYVPLDGPVSSDQTKEFAKALARELE 175 (231)
T ss_pred CCCCCCCHHHHHHHHHHHHHHHHHcCCccceECCCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHH
Confidence 5667899999999999999999988742221 2333344433311 1223445667766666553
No 70
>cd01213 tensin Tensin Phosphotyrosine-binding (PTB) domain. Tensin Phosphotyrosine-binding (PTB) domain. Tensin is a a focal adhesion protein, which contains a C-terminal SH2 domain followed by a PTB domain. PTB domains have a PH-like fold and are found in various eukaryotic signaling molecules. They were initially identified based upon their ability to recognize phosphorylated tyrosine residues. In contrast to SH2 domains, which recognize phosphotyrosine and adjacent carboxy-terminal residues, PTB-domain binding specificity is conferred by residues amino-terminal to the phosphotyrosine. More recent studies have found that some types of PTB domains can bind to peptides which are not tyrosine phosphorylated or lack tyrosine residues altogether.
Probab=24.86 E-value=1e+02 Score=23.00 Aligned_cols=33 Identities=21% Similarity=0.164 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCC
Q 032340 13 IEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVE 47 (142)
Q Consensus 13 c~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGie 47 (142)
-..+.+++...+..+.. |-+-...|.||+.||-
T Consensus 24 ~~av~kAv~~~l~~~~~--~~~t~vh~kVS~qGIt 56 (138)
T cd01213 24 NEAIKKAIAQCSGQAPD--PQATEVHFKVSSQGIT 56 (138)
T ss_pred cHHHHHHHHHHHhcCCC--CCceEEEEEEEcCCee
Confidence 35788888888853321 2234789999999984
No 71
>cd07020 Clp_protease_NfeD_1 Nodulation formation efficiency D (NfeD) is a membrane-bound ClpP-class protease. Nodulation formation efficiency D (NfeD; stomatin operon partner protein, STOPP; DUF107) is a member of membrane-anchored ClpP-class proteases. Currently, more than 300 NfeD homologs have been identified - all of which are bacterial or archaeal in origin. Majority of these genomes have been shown to possess operons containing a homologous NfeD/stomatin gene pair, causing NfeD to be previously named STOPP (stomatin operon partner protein). NfeD homologs can be divided into two groups: long and short forms. Long-form homologs have a putative ClpP-class serine protease domain while the short form homologs do not. Downstream from the ClpP-class domain is the so-called NfeD or DUF107 domain. N-terminal region of the NfeD homolog PH1510 (1510-N or PH1510-N) from Pyrococcus horikoshii has been shown to possess serine protease activity and has a Ser-Lys catalytic dyad, preferentially c
Probab=22.87 E-value=1.1e+02 Score=23.22 Aligned_cols=35 Identities=11% Similarity=0.209 Sum_probs=22.5
Q ss_pred CCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCC
Q 032340 6 GSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGV 46 (142)
Q Consensus 6 ~gvslddc~~vSr~i~~~LD~~d~~~~i~~~Y~LEVSSPGi 46 (142)
|.|+-.+-..+.+.|..+-+ + + ...-.|.|.|||=
T Consensus 8 g~I~~~~~~~l~~~l~~a~~--~---~-~~~vvl~InSpGG 42 (187)
T cd07020 8 GAITPATADYLERAIDQAEE--G---G-ADALIIELDTPGG 42 (187)
T ss_pred eEEChHHHHHHHHHHHHHHh--C---C-CCEEEEEEECCCC
Confidence 44555555666666665543 2 2 2668899999994
No 72
>PF00404 Dockerin_1: Dockerin type I repeat; InterPro: IPR018242 Gram-positive, thermophilic anaerobes such as Clostridium thermocellum or Clostridium cellulolyticum secretes a highly active and thermostable cellulase complex (cellulosome) responsible for the degradation of crystalline cellulose [, ]. The cellulosome contains at least 30 polypeptides, the majority of the enzymes are endoglucanases (3.2.1.4 from EC), but there are also some xylanases (3.2.1.8 from EC), beta-glucosidases (3.2.1.21 from EC) and endo-beta-1,3-1,4-glucanases (3.2.1.73 from EC). Complete sequence data for many of these enzymes has been obtained. A majority of these proteins contain a highly conserved type I dockerin domain of about 65 to 70 residues, which is generally (but not always) located in the C terminus. The dockerin domain is the binding partner of the cohesin domain (see IPR002102 from INTERPRO). The cohesin-dockerin interaction is the crucial interaction for complex formation in the cellulosome []. The dockerin domain contains a tandem repeat of two calcium-binding loop-helix motifs (distinct from EF-hand Ca-binding motifs). These motifs are about 24 amino acids in length. This entry represents these repeated Ca-binding motifs.; GO: 0004553 hydrolase activity, hydrolyzing O-glycosyl compounds, 0005975 carbohydrate metabolic process; PDB: 3P0D_J 1OHZ_B 2CCL_B 1DAV_A 1DAQ_A 2VN5_B 2VN6_B.
Probab=22.07 E-value=1.3e+02 Score=15.29 Aligned_cols=19 Identities=16% Similarity=0.148 Sum_probs=15.4
Q ss_pred CCCCCCCCHHHHHHHHHHH
Q 032340 2 SNKSGSPSMEDIEAFCTTY 20 (142)
Q Consensus 2 iD~~~gvslddc~~vSr~i 20 (142)
++.+|.|+.-|++.+-+.|
T Consensus 2 vN~DG~vna~D~~~lk~yl 20 (21)
T PF00404_consen 2 VNGDGKVNAIDLALLKKYL 20 (21)
T ss_dssp TTSSSSSSHHHHHHHHHHH
T ss_pred CCCCCcCCHHHHHHHHHHh
Confidence 4678889999999887765
No 73
>cd01724 Sm_D1 The eukaryotic Sm and Sm-like (LSm) proteins associate with RNA to form 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. Sm subunit D1 heterodimerizes with subunit D2 and three such heterodimers form a hexameric ring structure with alternating D1 and D2 subunits. The D1 - D2 heterodimer also assembles into a heptameric ring containing DB, D3, E, F, and G subunits. Sm-like proteins exist in archaea as well as prokaryotes which form heptameric and hexameric ring structures similar to those found in eukaryotes.
Probab=21.92 E-value=1.8e+02 Score=19.87 Aligned_cols=27 Identities=7% Similarity=0.251 Sum_probs=21.4
Q ss_pred HHhcCCCeEEEEEeeccccCCCCCCCCceE--EEEeEeCC
Q 032340 56 LERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDME 93 (142)
Q Consensus 56 f~r~~G~~v~V~~~~~~~~~~~~~~g~k~~--~L~~~~~~ 93 (142)
++...|+.|.|.+++ | ..+ .|.++|+.
T Consensus 6 L~~l~g~~V~VeLKn----------g-~~~~G~L~~vD~~ 34 (90)
T cd01724 6 LMKLTNETVTIELKN----------G-TIVHGTITGVDPS 34 (90)
T ss_pred HHhCCCCEEEEEECC----------C-CEEEEEEEEEcCc
Confidence 478899999999998 3 233 89888876
No 74
>PF14485 DUF4431: Domain of unknown function (DUF4431)
Probab=21.71 E-value=88 Score=19.05 Aligned_cols=15 Identities=13% Similarity=0.056 Sum_probs=13.0
Q ss_pred hHHHHhcCCCeEEEE
Q 032340 53 PLELERFKDRAMYVK 67 (142)
Q Consensus 53 ~~~f~r~~G~~v~V~ 67 (142)
.+.|++++|+.|+|+
T Consensus 11 ~~~~~~~~Gk~V~V~ 25 (48)
T PF14485_consen 11 YSYLKSLLGKRVSVT 25 (48)
T ss_pred hHHHHHhcCCeEEEE
Confidence 567888999999996
No 75
>PF13620 CarboxypepD_reg: Carboxypeptidase regulatory-like domain; PDB: 3MN8_D 3P0D_I 3KCP_A 2B59_B 1UWY_A 1H8L_A 1QMU_A 2NSM_A.
Probab=20.93 E-value=59 Score=20.55 Aligned_cols=14 Identities=43% Similarity=0.781 Sum_probs=10.9
Q ss_pred CCCeEEEEecCCCC
Q 032340 34 PENTSLEVSSPGVE 47 (142)
Q Consensus 34 ~~~Y~LEVSSPGie 47 (142)
++.|.|.|+.||-.
T Consensus 47 ~g~Y~l~v~~~g~~ 60 (82)
T PF13620_consen 47 PGTYTLRVSAPGYQ 60 (82)
T ss_dssp SEEEEEEEEBTTEE
T ss_pred CEeEEEEEEECCcc
Confidence 37899999888854
No 76
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=20.54 E-value=2.5e+02 Score=21.93 Aligned_cols=38 Identities=13% Similarity=0.281 Sum_probs=26.6
Q ss_pred CceE--EEEeEeCCeeEEEEeecceehhhcccCCCCCccccccceeeeecccccceeEEe
Q 032340 82 DGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLH 139 (142)
Q Consensus 82 ~k~~--~L~~~~~~~~~~~~~~~~v~~~~~~~~kgk~~~~k~~~~~~~ip~~~I~karl~ 139 (142)
.+.| .|.+++++.+.|... ..|. .+.|++++|..+++.
T Consensus 144 ~~~Y~G~I~~~~~~~v~i~~~-----------~~~~---------~~~i~~~~I~sI~~i 183 (185)
T PF14153_consen 144 DKSYRGIILSYDEGEVSIMPF-----------NQGE---------EIEIPIDDITSIKMI 183 (185)
T ss_pred CceEEEEEEeccCCEEEEecc-----------CCCc---------ceEeehhheeeeeec
Confidence 4556 899999998766421 1111 468999999999873
Done!