Query 030849
Match_columns 170
No_of_seqs 147 out of 1142
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 05:30:33 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/030849.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/030849hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PRK14640 hypothetical protein; 100.0 8.8E-39 1.9E-43 251.1 14.5 125 12-169 13-150 (152)
2 PRK14633 hypothetical protein; 100.0 1.8E-38 3.8E-43 249.0 14.7 126 12-169 11-148 (150)
3 COG0779 Uncharacterized protei 100.0 1.9E-38 4.2E-43 249.3 13.9 125 12-169 15-152 (153)
4 PRK14634 hypothetical protein; 100.0 3.4E-38 7.4E-43 248.6 13.8 125 12-169 14-153 (155)
5 PRK14646 hypothetical protein; 100.0 5.1E-38 1.1E-42 247.6 13.8 123 12-167 14-151 (155)
6 PRK14647 hypothetical protein; 100.0 8.9E-38 1.9E-42 247.0 14.7 131 12-169 15-158 (159)
7 PRK14643 hypothetical protein; 100.0 1.1E-37 2.5E-42 247.6 14.6 131 12-169 16-163 (164)
8 PRK14639 hypothetical protein; 100.0 8.9E-38 1.9E-42 242.6 13.6 127 10-169 2-139 (140)
9 PRK14632 hypothetical protein; 100.0 1.5E-37 3.2E-42 248.7 15.2 136 12-169 15-162 (172)
10 PRK14636 hypothetical protein; 100.0 1.1E-36 2.4E-41 244.4 14.4 127 11-169 11-152 (176)
11 PRK14631 hypothetical protein; 100.0 1.2E-36 2.5E-41 243.9 14.5 126 12-169 15-173 (174)
12 PRK14638 hypothetical protein; 100.0 9.4E-37 2E-41 239.3 13.1 123 12-169 15-149 (150)
13 PRK00092 ribosome maturation p 100.0 2.7E-36 5.8E-41 237.0 14.7 127 12-169 14-153 (154)
14 PRK14630 hypothetical protein; 100.0 7.4E-36 1.6E-40 232.6 12.9 118 12-167 15-143 (143)
15 PF02576 DUF150: Uncharacteris 100.0 6.9E-36 1.5E-40 231.1 11.5 126 12-166 3-141 (141)
16 PRK14641 hypothetical protein; 100.0 2.9E-35 6.4E-40 235.6 15.4 130 16-169 20-172 (173)
17 PRK02001 hypothetical protein; 100.0 9.7E-35 2.1E-39 228.4 13.8 133 12-168 12-152 (152)
18 PRK14637 hypothetical protein; 100.0 2.9E-34 6.2E-39 225.5 13.2 122 12-169 15-148 (151)
19 PRK14642 hypothetical protein; 100.0 4.2E-34 9.2E-39 232.6 14.4 145 12-168 8-180 (197)
20 PRK14635 hypothetical protein; 100.0 2.4E-33 5.3E-38 222.3 15.1 132 13-169 14-161 (162)
21 PRK14644 hypothetical protein; 100.0 5.3E-33 1.2E-37 215.0 13.0 119 12-163 5-136 (136)
22 PRK14645 hypothetical protein; 100.0 9.5E-33 2.1E-37 217.5 11.4 117 12-164 16-145 (154)
23 cd01734 YlxS_C YxlS is a Bacil 99.9 7.5E-23 1.6E-27 145.6 9.3 80 65-169 1-82 (83)
24 PF08496 Peptidase_S49_N: Pept 73.3 11 0.00023 29.9 5.6 47 23-73 96-142 (155)
25 cd02978 KaiB_like KaiB-like fa 70.3 14 0.0003 25.7 5.0 40 23-72 2-41 (72)
26 cd01726 LSm6 The eukaryotic Sm 67.8 6.4 0.00014 26.4 2.8 29 84-121 5-33 (67)
27 KOG1783 Small nuclear ribonucl 65.0 4.9 0.00011 28.2 1.8 29 83-120 10-38 (77)
28 cd01722 Sm_F The eukaryotic Sm 61.4 12 0.00026 25.1 3.2 31 83-122 5-35 (68)
29 PF14438 SM-ATX: Ataxin 2 SM d 53.4 11 0.00025 25.6 2.1 29 84-121 7-35 (77)
30 cd01729 LSm7 The eukaryotic Sm 53.3 17 0.00036 25.5 3.0 33 81-122 4-36 (81)
31 TIGR02654 circ_KaiB circadian 53.1 42 0.00091 24.2 5.0 41 22-72 3-43 (87)
32 PF06257 DUF1021: Protein of u 53.1 64 0.0014 22.7 5.8 55 82-163 10-69 (76)
33 PRK00737 small nuclear ribonuc 51.0 22 0.00047 24.2 3.2 32 82-122 7-38 (72)
34 cd07015 Clp_protease_NfeD Nodu 51.0 20 0.00043 28.7 3.4 61 31-97 5-66 (172)
35 cd01719 Sm_G The eukaryotic Sm 50.7 17 0.00036 24.9 2.6 32 82-122 3-34 (72)
36 PF10842 DUF2642: Protein of u 49.7 61 0.0013 22.1 5.2 32 81-122 13-44 (66)
37 cd01731 archaeal_Sm1 The archa 47.6 22 0.00047 23.7 2.7 30 84-122 5-34 (68)
38 PF01423 LSM: LSM domain ; In 47.1 17 0.00037 23.8 2.1 31 83-122 2-32 (67)
39 PRK09301 circadian clock prote 46.3 60 0.0013 24.2 5.1 41 22-72 6-46 (103)
40 PRK11778 putative inner membra 46.2 19 0.00042 31.8 2.9 67 26-97 91-162 (330)
41 cd01725 LSm2 The eukaryotic Sm 45.3 25 0.00054 24.5 2.8 29 85-122 7-35 (81)
42 cd01721 Sm_D3 The eukaryotic S 45.0 25 0.00055 23.7 2.8 39 84-134 5-43 (70)
43 cd00600 Sm_like The eukaryotic 44.4 24 0.00052 22.5 2.5 29 85-122 2-30 (63)
44 COG1958 LSM1 Small nuclear rib 44.1 24 0.00052 24.2 2.6 31 83-122 11-41 (79)
45 PF07837 FTCD_N: Formiminotran 42.6 19 0.00041 29.3 2.1 22 34-55 95-116 (178)
46 smart00651 Sm snRNP Sm protein 42.5 28 0.00062 22.6 2.7 30 84-122 3-32 (67)
47 cd01723 LSm4 The eukaryotic Sm 40.9 33 0.00071 23.5 2.8 30 84-122 6-35 (76)
48 cd06168 LSm9 The eukaryotic Sm 39.7 38 0.00083 23.4 3.0 32 82-122 3-34 (75)
49 PF00788 RA: Ras association ( 39.5 8.3 0.00018 26.3 -0.4 57 23-81 3-67 (93)
50 cd07021 Clp_protease_NfeD_like 39.3 39 0.00084 27.0 3.4 60 31-96 5-65 (178)
51 PTZ00198 60S ribosomal protein 38.2 66 0.0014 24.7 4.3 32 63-95 19-50 (122)
52 TIGR02024 FtcD glutamate formi 37.5 31 0.00067 30.2 2.8 23 33-55 96-118 (298)
53 cd01733 LSm10 The eukaryotic S 37.5 40 0.00088 23.4 2.9 44 80-135 9-53 (78)
54 COG1481 Uncharacterized protei 36.7 50 0.0011 29.1 3.9 59 38-97 116-174 (308)
55 cd01724 Sm_D1 The eukaryotic S 35.7 43 0.00093 23.9 2.9 30 84-122 6-35 (90)
56 cd01728 LSm1 The eukaryotic Sm 35.3 46 0.001 22.9 2.9 32 82-122 5-36 (74)
57 cd01717 Sm_B The eukaryotic Sm 34.1 44 0.00095 23.0 2.6 31 83-122 4-34 (79)
58 cd01732 LSm5 The eukaryotic Sm 33.6 53 0.0011 22.7 3.0 31 83-122 6-37 (76)
59 PF06649 DUF1161: Protein of u 31.5 55 0.0012 21.5 2.5 28 41-73 1-28 (52)
60 cd04479 RPA3 RPA3: A subfamily 29.3 1.5E+02 0.0032 21.3 4.9 42 76-124 2-43 (101)
61 cd01730 LSm3 The eukaryotic Sm 29.1 67 0.0014 22.3 2.9 31 83-122 4-35 (82)
62 cd01727 LSm8 The eukaryotic Sm 29.1 62 0.0014 21.9 2.7 31 83-122 3-33 (74)
63 TIGR02778 ligD_pol DNA polymer 26.5 87 0.0019 26.7 3.6 27 30-56 121-147 (245)
64 PF11095 Gemin7: Gem-associate 26.1 1.2E+02 0.0027 21.4 3.8 34 82-122 17-50 (80)
65 PF15121 TMEM71: TMEM71 protei 25.6 42 0.00091 26.4 1.4 34 9-42 58-91 (149)
66 cd04866 LigD_Pol_like_3 LigD_P 24.7 1E+02 0.0022 26.0 3.6 64 30-93 100-167 (223)
67 cd04864 LigD_Pol_like_1 LigD_P 24.4 1.2E+02 0.0025 25.7 4.0 26 30-56 107-132 (228)
68 PF09430 DUF2012: Protein of u 23.8 53 0.0012 24.4 1.7 16 60-75 37-52 (123)
69 TIGR02778 ligD_pol DNA polymer 23.5 1E+02 0.0022 26.3 3.4 69 10-98 138-213 (245)
70 cd04865 LigD_Pol_like_2 LigD_P 23.5 1.1E+02 0.0024 25.8 3.6 27 30-56 106-132 (228)
71 cd04863 MtLigD_Pol_like MtLigD 21.7 1.3E+02 0.0027 25.5 3.7 64 30-93 109-175 (231)
72 cd04862 PaeLigD_Pol_like PaeLi 21.2 1.8E+02 0.0039 24.5 4.5 27 30-56 105-131 (227)
73 PF14153 Spore_coat_CotO: Spor 20.8 2.1E+02 0.0046 23.2 4.7 34 114-167 150-183 (185)
74 PF11211 DUF2997: Protein of u 20.6 1.1E+02 0.0024 19.5 2.4 29 26-55 2-37 (48)
75 PF13749 HATPase_c_4: ATP-depe 20.3 47 0.001 23.1 0.8 18 66-83 12-29 (89)
No 1
>PRK14640 hypothetical protein; Provisional
Probab=100.00 E-value=8.8e-39 Score=251.15 Aligned_cols=125 Identities=18% Similarity=0.275 Sum_probs=112.0
Q ss_pred ccccccCCcceeE-----------EEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCC
Q 030849 12 RNRVLNNKMPLWL-----------TQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRI 80 (170)
Q Consensus 12 ~~~~~~~g~~~~~-----------lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~ 80 (170)
.|+++++||++|. |||| ||+++|||+|||+.+||+|+++||++| +|+++|+|||||||++|||++
T Consensus 13 ~p~~~~~G~el~dve~~~~~~~~~lrV~-ID~~~gv~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGl~RpL~~ 88 (152)
T PRK14640 13 EAPVVALGFELWGIEFIRAGKHSTLRVY-IDGENGVSVENCAEVSHQVGAIMDVED---PITEEYYLEVSSPGLDRPLFK 88 (152)
T ss_pred HHHHHhcCCEEEEEEEEecCCCcEEEEE-EECCCCCCHHHHHHHHHHHHHHhcccc---cCCCCeEEEEeCCCCCCcCCC
Confidence 5788999999874 7899 999999999999999999999999999 999999999999999999999
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeec
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTF 158 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~ 158 (170)
++||+||+|+.|+|++.+ +..++++| +|.++++++ ++++ .+..+ +.|||
T Consensus 89 ~~~f~r~~G~~v~V~l~~-------~~~~~k~~~G~L~~v~~~~---------v~l~-----------~~~~~--~~i~~ 139 (152)
T PRK14640 89 VAQFEKYVGQEAAVTLRM-------ATNNRRKFKGVIKAVQGDM---------ITLT-----------VDGKD--EVLAF 139 (152)
T ss_pred HHHHHHhCCCeEEEEEec-------ccCCceEEEEEEEEEeCCE---------EEEE-----------ECCeE--EEEEh
Confidence 999999999999999999 77788888 999999998 4444 11112 68999
Q ss_pred cccceeEEEec
Q 030849 159 DSLRLVRLHSD 169 (170)
Q Consensus 159 ~~I~karL~i~ 169 (170)
++|++|||.++
T Consensus 140 ~~I~ka~l~~~ 150 (152)
T PRK14640 140 TNIQKANIVPN 150 (152)
T ss_pred HHeeeEEEecc
Confidence 99999999875
No 2
>PRK14633 hypothetical protein; Provisional
Probab=100.00 E-value=1.8e-38 Score=249.00 Aligned_cols=126 Identities=21% Similarity=0.301 Sum_probs=112.2
Q ss_pred ccccccCCcceeE----------EEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCCh
Q 030849 12 RNRVLNNKMPLWL----------TQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIP 81 (170)
Q Consensus 12 ~~~~~~~g~~~~~----------lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~ 81 (170)
.|+++++||++|. |||| ||+++|||+|||+.+||+|+++||++| +|+++|+|||||||++|||+++
T Consensus 11 ~p~~~~~G~eL~dve~~~~~~~~lrV~-ID~~~Gv~lddC~~vSr~i~~~LD~~d---~i~~~Y~LEVSSPGldRpL~~~ 86 (150)
T PRK14633 11 EPITADLGYILWGIEVVGSGKLTIRIF-IDHENGVSVDDCQIVSKEISAVFDVED---PVSGKYILEVSSPGMNRQIFNI 86 (150)
T ss_pred HHHHHHCCCEEEEEEEEeCCCcEEEEE-EeCCCCCCHHHHHHHHHHHHHHhccCc---CCCCCeEEEEeCCCCCCCCCCH
Confidence 5788999999884 7899 999999999999999999999999999 9999999999999999999999
Q ss_pred HHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeecc
Q 030849 82 LELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFD 159 (170)
Q Consensus 82 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~~ 159 (170)
+||+||+|+.|+|++++ +.+++++| +|.++++++ ++++- .... .++|||+
T Consensus 87 ~~f~r~~G~~v~V~~~~-------~~~~~~~~~G~L~~v~~~~---------i~l~~----------~~~~--~~~i~~~ 138 (150)
T PRK14633 87 IQAQALVGFNVKAVTLA-------PVGSQTKFKGVLERVEGNN---------VILNL----------EDGK--EISFDFD 138 (150)
T ss_pred HHHHHhCCCeEEEEEec-------ccCCcEEEEEEEEEEeCCE---------EEEEE----------cCCc--EEEEEhH
Confidence 99999999999999999 77788888 999999999 44441 0111 2789999
Q ss_pred ccceeEEEec
Q 030849 160 SLRLVRLHSD 169 (170)
Q Consensus 160 ~I~karL~i~ 169 (170)
+|++|||.++
T Consensus 139 ~I~ka~l~~~ 148 (150)
T PRK14633 139 ELKKLRVSPD 148 (150)
T ss_pred HeeeEEEecc
Confidence 9999999875
No 3
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00 E-value=1.9e-38 Score=249.33 Aligned_cols=125 Identities=26% Similarity=0.382 Sum_probs=112.7
Q ss_pred ccccccCCccee-----------EEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRI 80 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~ 80 (170)
.|.++++|||++ .|||+ ||++||||+|||+.+||+||+.||++| ||++.|+|||||||++|||++
T Consensus 15 ep~~~~lG~ELv~ve~~~~~~~~~lrI~-id~~g~v~lddC~~vSr~is~~LD~ed---pi~~~Y~LEVSSPGldRpL~~ 90 (153)
T COG0779 15 EPVVESLGFELVDVEFVKEGRDSVLRIY-IDKEGGVTLDDCADVSRAISALLDVED---PIEGAYFLEVSSPGLDRPLKT 90 (153)
T ss_pred HHhHhhcCcEEEEEEEEEcCCCcEEEEE-eCCCCCCCHHHHHHHHHHHHHHhccCC---cccccEEEEeeCCCCCCCcCC
Confidence 578999999976 57899 999999999999999999999999999 999999999999999999999
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeec
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTF 158 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~ 158 (170)
++||.||+|+.|+|+++. ++++++.| +|..++++. +++. ..+.+ +.|||
T Consensus 91 ~~~f~r~~G~~Vkv~l~~-------~~~~~k~~~G~i~~~d~~~---------v~~~-----------~~~k~--v~Ip~ 141 (153)
T COG0779 91 AEHFARFIGEKVKVKLRL-------PIEGRKKFEGKIVAVDGET---------VTLE-----------VDGKE--VEIPF 141 (153)
T ss_pred HHHHHHhcCcEEEEEEec-------ccCCceEEEEEEEEEcCCe---------EEEE-----------ECCEE--EEEEc
Confidence 999999999999999999 88889999 999999999 4333 11222 79999
Q ss_pred cccceeEEEec
Q 030849 159 DSLRLVRLHSD 169 (170)
Q Consensus 159 ~~I~karL~i~ 169 (170)
++|+||||.+.
T Consensus 142 ~~i~kArl~~~ 152 (153)
T COG0779 142 SDIAKARLVPE 152 (153)
T ss_pred ccchhheeccc
Confidence 99999999875
No 4
>PRK14634 hypothetical protein; Provisional
Probab=100.00 E-value=3.4e-38 Score=248.61 Aligned_cols=125 Identities=22% Similarity=0.281 Sum_probs=111.6
Q ss_pred ccccccCCccee-----------EEEEEEEcCCCC--CCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRSGS--PSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVV 78 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~~g--vtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL 78 (170)
.++++++||++| +|||| ||+++| ||+|||+.+||+||++||++| +|+++|+|||||||++|||
T Consensus 14 ~~~~~~~G~elvdve~~~~~~~~~lrV~-ID~~~g~~v~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL 89 (155)
T PRK14634 14 SATAADKGFELCGIQVLTHLQPMTLQVQ-IRRSSGSDVSLDDCAGFSGPMGEALEASQ---LLTEAYVLEISSPGIGDQL 89 (155)
T ss_pred HHHHHHcCCEEEEEEEEeCCCCcEEEEE-EECCCCCcccHHHHHHHHHHHHHHhcccc---cCCCCeEEEEeCCCCCCcC
Confidence 577889999977 47899 999888 999999999999999999999 9999999999999999999
Q ss_pred CChHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEe
Q 030849 79 RIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNT 156 (170)
Q Consensus 79 ~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~i 156 (170)
++++||+||+|+.|+|++.+ +.+++++| +|.+++++. |+++ .... .++|
T Consensus 90 ~~~~~f~r~~G~~V~V~l~~-------~~~~~k~~~G~L~~~~~~~---------v~l~-----------~~~~--~~~i 140 (155)
T PRK14634 90 SSDRDFQTFRGFPVEVSHRD-------DDGSEQRLEGLLLERNEDH---------LQIN-----------IRGR--IKRI 140 (155)
T ss_pred CCHHHHHHhCCCeEEEEEec-------CCCCeEEEEEEEEEEeCCE---------EEEE-----------ECCE--EEEE
Confidence 99999999999999999999 77788888 999999999 4444 1111 2789
Q ss_pred eccccceeEEEec
Q 030849 157 TFDSLRLVRLHSD 169 (170)
Q Consensus 157 p~~~I~karL~i~ 169 (170)
||++|++|||.++
T Consensus 141 ~~~~I~ka~l~~~ 153 (155)
T PRK14634 141 PRDSVISVRLTNP 153 (155)
T ss_pred EHHHeeeEEeCCC
Confidence 9999999999875
No 5
>PRK14646 hypothetical protein; Provisional
Probab=100.00 E-value=5.1e-38 Score=247.62 Aligned_cols=123 Identities=15% Similarity=0.215 Sum_probs=109.7
Q ss_pred ccccccCCccee-----------EEEEEEEcCCC--CCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRSG--SPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVV 78 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~~--gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL 78 (170)
.|+++++||++| +|||| ||+++ |||+|||+.+||+|+++||++| ||+++|+|||||||++|||
T Consensus 14 ~p~~~~~G~eLvdve~~~~~~~~~LrV~-IDk~~g~gVtldDC~~vSr~is~~LD~~D---~i~~~Y~LEVSSPGldRpL 89 (155)
T PRK14646 14 EKVANEFDLKICSLNIQTNQNPIVIKII-IKKTNGDDISLDDCALFNTPASEEIENSN---LLNCSYVLEISSQGVSDEL 89 (155)
T ss_pred HHHHHHcCCEEEEEEEEeCCCCeEEEEE-EECCCCCCccHHHHHHHHHHHHHHhCcCC---CCCCCeEEEEcCCCCCCcC
Confidence 578899999977 47999 99973 5999999999999999999999 9999999999999999999
Q ss_pred CChHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEe
Q 030849 79 RIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNT 156 (170)
Q Consensus 79 ~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~i 156 (170)
++++||+||+|+.|+|++.+ +.++++.| +|.+++++. ++++ .++. .++|
T Consensus 90 ~~~~df~r~~G~~v~V~l~~-------~~~~~~~~~G~L~~~~~~~---------v~l~-----------~~g~--~~~i 140 (155)
T PRK14646 90 TSERDFKTFKGFPVNVELNQ-------KNSKIKFLNGLLYEKSKDY---------LAIN-----------IKGK--IKKI 140 (155)
T ss_pred CCHHHHHHhCCCEEEEEEec-------CcCCeEEEEEEEEEEeCCE---------EEEE-----------ECCE--EEEE
Confidence 99999999999999999999 77788888 999999999 5554 1122 2789
Q ss_pred eccccceeEEE
Q 030849 157 TFDSLRLVRLH 167 (170)
Q Consensus 157 p~~~I~karL~ 167 (170)
||++|++|||.
T Consensus 141 ~~~~I~ka~L~ 151 (155)
T PRK14646 141 PFNEVLKISLC 151 (155)
T ss_pred EHHHeeeEEeC
Confidence 99999999985
No 6
>PRK14647 hypothetical protein; Provisional
Probab=100.00 E-value=8.9e-38 Score=246.99 Aligned_cols=131 Identities=22% Similarity=0.322 Sum_probs=111.2
Q ss_pred ccccccCCcceeE-----------EEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCC
Q 030849 12 RNRVLNNKMPLWL-----------TQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRI 80 (170)
Q Consensus 12 ~~~~~~~g~~~~~-----------lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~ 80 (170)
.|+++++||++|. |||| ||+++|||+|||+.+||+|+++||++| +|+++|+|||||||++|||++
T Consensus 15 ~~~~~~~G~~L~dv~~~~~~~~~~lrV~-ID~~~gvslddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPG~~RpL~~ 90 (159)
T PRK14647 15 EQVLSSLGLELVELEYKREGREMVLRLF-IDKEGGVNLDDCAEVSRELSEILDVED---FIPERYTLEVSSPGLDRPLKK 90 (159)
T ss_pred HHHHHHCCCEEEEEEEEecCCCeEEEEE-EeCCCCCCHHHHHHHHHHHHHHHcccc---cCCCCeEEEEcCCCCCCcCCC
Confidence 5788999999884 7899 999999999999999999999999998 999999999999999999999
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeec
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTF 158 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~ 158 (170)
++||+||+|+.|+|++.++.++. +-+++++| +|.+++++. ++++. .... .++|||
T Consensus 91 ~~~f~r~~G~~v~V~l~~~~~~~--~~~~~~~~~G~L~~~~~~~---------v~l~~----------~~~~--~~~i~~ 147 (159)
T PRK14647 91 EADYERYAGRLVKVRTFELLADE--AGNKRKTFLGELEGLADGV---------VTIAL----------KEGQ--QARIPL 147 (159)
T ss_pred HHHHHHhCCcEEEEEEecccccc--ccCCceEEEEEEEeecCCE---------EEEEE----------cCCc--EEEEEH
Confidence 99999999999999999833210 01257888 999999998 55541 0011 278999
Q ss_pred cccceeEEEec
Q 030849 159 DSLRLVRLHSD 169 (170)
Q Consensus 159 ~~I~karL~i~ 169 (170)
++|++|+|.++
T Consensus 148 ~~I~ka~l~~e 158 (159)
T PRK14647 148 DKIAKANLEFE 158 (159)
T ss_pred HHCCEEEEeee
Confidence 99999999876
No 7
>PRK14643 hypothetical protein; Provisional
Probab=100.00 E-value=1.1e-37 Score=247.65 Aligned_cols=131 Identities=15% Similarity=0.274 Sum_probs=111.8
Q ss_pred ccccccCCcceeE-----------EEEEEEcC----CCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCC
Q 030849 12 RNRVLNNKMPLWL-----------TQLVACDR----SGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVER 76 (170)
Q Consensus 12 ~~~~~~~g~~~~~-----------lrv~~iD~----~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieR 76 (170)
.|+++++||++|. |||| ||+ +||||+|||+.+||+||++||++| ||+++|+|||||||++|
T Consensus 16 ~p~~~~~G~eL~die~~~~~~~~~lrV~-Id~~~~~~ggvtldDC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGleR 91 (164)
T PRK14643 16 NKELEVLNLKVYEINNLKEFENDMIQIL-VEDILQANKPLDFDILIKANDLVSNKIDQFI---KTSEKYLLEISSSGIEK 91 (164)
T ss_pred HHHHHhcCCEEEEEEEEecCCCcEEEEE-EecCCCcCCCcCHHHHHHHHHHHHHHhCccC---CCCCCeEEEecCCCCCC
Confidence 5789999999874 7999 985 468999999999999999999999 99999999999999999
Q ss_pred CCCChHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeE
Q 030849 77 VVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRL 154 (170)
Q Consensus 77 pL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v 154 (170)
||++++||.||+|+.|+|++++ +.+|+++| +|.+++++.++++... .+ +.....+
T Consensus 92 pL~~~~df~r~~G~~V~V~l~~-------~~~g~k~~~G~L~~~~~~~~~l~l~~---~~-------------~~~~~~~ 148 (164)
T PRK14643 92 QIRSQEELVKALNQWVYVQLNN-------EIKKVKEFEGYVTKYNVNTNTFRFTF---FI-------------KGQKKKL 148 (164)
T ss_pred CCCCHHHHHHhcCCeEEEEEec-------ccCCceEEEEEEEEEeCCcEEEEEEe---ec-------------cCcCcEE
Confidence 9999999999999999999999 77888999 9999999985533211 01 1001127
Q ss_pred EeeccccceeEEEec
Q 030849 155 NTTFDSLRLVRLHSD 169 (170)
Q Consensus 155 ~ip~~~I~karL~i~ 169 (170)
+|||++|++|||+++
T Consensus 149 ~ip~~~I~karl~~~ 163 (164)
T PRK14643 149 DVKYEQIKFIRYAVR 163 (164)
T ss_pred EEeHHHhhheEeccc
Confidence 899999999999876
No 8
>PRK14639 hypothetical protein; Provisional
Probab=100.00 E-value=8.9e-38 Score=242.57 Aligned_cols=127 Identities=14% Similarity=0.260 Sum_probs=108.1
Q ss_pred ccccccccCCccee-----------EEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCC
Q 030849 10 KHRNRVLNNKMPLW-----------LTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVV 78 (170)
Q Consensus 10 ~~~~~~~~~g~~~~-----------~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL 78 (170)
.-.|+++++||++| +|||| ||+++|||+|||+.+||+|+++||++| ||+++|+|||||||++|||
T Consensus 2 ~~ep~~~~~G~eLvdve~~~~~~~~~lrV~-Id~~~gv~iddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGl~RpL 77 (140)
T PRK14639 2 NLEALCKECGVSFYDDELVSENGRKIYRVY-ITKEGGVNLDDCERLSELLSPIFDVEP---PVSGEYFLEVSSPGLERKL 77 (140)
T ss_pred chhHhHHhCCCEEEEEEEEecCCCcEEEEE-EeCCCCCCHHHHHHHHHHHHHHhcccc---ccCCCeEEEEeCCCCCCcC
Confidence 34689999999987 47899 999999999999999999999999999 9999999999999999999
Q ss_pred CChHHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeec
Q 030849 79 RIPLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTF 158 (170)
Q Consensus 79 ~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~ 158 (170)
++++||+||+|+.|+|++.+ .....| +|.++++++ +++... .+. ..++|||
T Consensus 78 ~~~~~f~r~~G~~v~v~l~~-------~~~~~G--~L~~~~~~~---------i~l~~~---------~~~--~~~~i~~ 128 (140)
T PRK14639 78 SKIEHFAKSIGELVKITTNE-------KEKFEG--KIVSVDDEN---------ITLENL---------ENK--EKTTINF 128 (140)
T ss_pred CCHHHHHHhCCCEEEEEECC-------CcEEEE--EEEEEeCCE---------EEEEEc---------cCC--cEEEEEh
Confidence 99999999999999999965 223334 999999998 444210 001 1268999
Q ss_pred cccceeEEEec
Q 030849 159 DSLRLVRLHSD 169 (170)
Q Consensus 159 ~~I~karL~i~ 169 (170)
++|++|||+++
T Consensus 129 ~~I~ka~l~~~ 139 (140)
T PRK14639 129 NDIKKAKTYVE 139 (140)
T ss_pred HHeeeEEEEEe
Confidence 99999999986
No 9
>PRK14632 hypothetical protein; Provisional
Probab=100.00 E-value=1.5e-37 Score=248.67 Aligned_cols=136 Identities=20% Similarity=0.278 Sum_probs=112.2
Q ss_pred ccccccCCccee----------EEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCCh
Q 030849 12 RNRVLNNKMPLW----------LTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIP 81 (170)
Q Consensus 12 ~~~~~~~g~~~~----------~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~ 81 (170)
.|+++++||++| +|||| ||+++|||||||+.+||+|+++||++| +|+++|+|||||||++|||+++
T Consensus 15 ~pv~~~~G~eLvdve~~~~~~~~lrV~-ID~~~GV~ldDC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL~~~ 90 (172)
T PRK14632 15 GPFLASLGLELWGIELSYGGRTVVRLF-VDGPEGVTIDQCAEVSRHVGLALEVED---VISSAYVLEVSSPGLERPFFRA 90 (172)
T ss_pred HHHHHHCCCEEEEEEEEeCCCcEEEEE-EECCCCCCHHHHHHHHHHHHHHhcccc---cCCCCeEEEEeCCCCCCcCCCH
Confidence 578899999977 47899 999999999999999999999999999 9999999999999999999999
Q ss_pred HHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeecc
Q 030849 82 LELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFD 159 (170)
Q Consensus 82 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~~ 159 (170)
+||+||+|+.|+|++.++.+ ..+++++| +|.+++++. ++++.. .+++++. ....++|||+
T Consensus 91 ~~f~r~iG~~V~V~l~~~~~----~~~g~k~~~G~L~~v~~~~---------i~l~~~-~~~~~~~----~~~~~~i~~~ 152 (172)
T PRK14632 91 EQMSPYVGRQIELTLIDPTP----EWPGRRKFRGELLAVEGDT---------VVLRPE-GAPAPEA----EEAVLRTSWQ 152 (172)
T ss_pred HHHHHhCCCEEEEEEecccc----ccCCceEEEEEEEEEeCCE---------EEEEEc-CcccccC----CceeEEEEhH
Confidence 99999999999999999321 01478888 999999998 444421 1111111 1123799999
Q ss_pred ccceeEEEec
Q 030849 160 SLRLVRLHSD 169 (170)
Q Consensus 160 ~I~karL~i~ 169 (170)
+|++|||.++
T Consensus 153 ~I~ka~l~~~ 162 (172)
T PRK14632 153 GVRKANLIHV 162 (172)
T ss_pred HccEEEEEEE
Confidence 9999999875
No 10
>PRK14636 hypothetical protein; Provisional
Probab=100.00 E-value=1.1e-36 Score=244.40 Aligned_cols=127 Identities=22% Similarity=0.322 Sum_probs=111.0
Q ss_pred cccccccCCccee-----------EEEEEEEcCC--CCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCC
Q 030849 11 HRNRVLNNKMPLW-----------LTQLVACDRS--GSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERV 77 (170)
Q Consensus 11 ~~~~~~~~g~~~~-----------~lrv~~iD~~--~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRp 77 (170)
-.|+++++||++| +|||| ||++ +|||+|||+.+||+||++||++| +|+++|+|||||||++||
T Consensus 11 vep~~~~~GleLvdve~~~~~~~~~lrV~-ID~~~~ggV~lDDC~~vSr~Is~~LD~~d---~i~~~Y~LEVSSPGldRp 86 (176)
T PRK14636 11 IEPEAKALGLDLVRVAMFGGKSDPTLQIM-AERPDTRQLVIEDCAALSRRLSDVFDELD---PIEDAYRLEVSSPGIDRP 86 (176)
T ss_pred HHHHHHHcCCEEEEEEEEcCCCCeEEEEE-EECCCCCCcCHHHHHHHHHHHHHHhccCc---CCCCCeEEEEeCCCCCCC
Confidence 3578999999977 47899 9986 46999999999999999999998 999999999999999999
Q ss_pred CCChHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEE
Q 030849 78 VRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLN 155 (170)
Q Consensus 78 L~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ 155 (170)
|++++||.||+|+.|+|+++. +.+++++| +|.+++++. ++++. .+.. .++
T Consensus 87 L~~~~df~r~~G~~V~V~l~~-------~~~g~k~~~G~L~~v~~~~---------v~l~~----------~~~~--~~~ 138 (176)
T PRK14636 87 LTRPKDFADWAGHEARIALSE-------PLDGRKQFRGELKGIDGDT---------VTIAD----------NKAG--EVI 138 (176)
T ss_pred CCCHHHHHHhCCCeEEEEEec-------ccCCeEEEEEEEEEEeCCE---------EEEEE----------cCCc--EEE
Confidence 999999999999999999999 77788888 999999998 44431 0111 268
Q ss_pred eeccccceeEEEec
Q 030849 156 TTFDSLRLVRLHSD 169 (170)
Q Consensus 156 ip~~~I~karL~i~ 169 (170)
|||++|++|||.++
T Consensus 139 i~~~~I~kA~l~~~ 152 (176)
T PRK14636 139 LPFAAIESAKLILT 152 (176)
T ss_pred EEhHHcceEEEecc
Confidence 99999999999875
No 11
>PRK14631 hypothetical protein; Provisional
Probab=100.00 E-value=1.2e-36 Score=243.87 Aligned_cols=126 Identities=22% Similarity=0.325 Sum_probs=110.4
Q ss_pred ccccccCCccee-----------EEEEEEEcCC------------------CCCCHHHHHHHHHHHHHhhhhhhhcCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRS------------------GSPSMEDIEAFCTTYRARLDEAEIAKSIP 62 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~------------------~gvtlddC~~vSr~is~~LD~~d~~~~i~ 62 (170)
.|+++++||++| +|||| ||++ +|||+|||+.+||+|+++||++| +|+
T Consensus 15 ~p~~~~~G~eLvdve~~~~~~~~~LrV~-ID~~~~~~~~~~~~~~~~~~~~~gvtiddC~~vSr~is~~LD~~d---~i~ 90 (174)
T PRK14631 15 APAVAACGVDLWGIEFLPQGKRSLLRIY-IDRLVEENAEPVINEDGEVEQGRGIGVEDCVRVTQQVGAMLDVHD---PIS 90 (174)
T ss_pred HHHHHHcCCEEEEEEEEeCCCceEEEEE-EecCcccccccccccccccccCCCcCHHHHHHHHHHHHHHhcccc---cCC
Confidence 578999999987 47899 9974 68999999999999999999999 999
Q ss_pred CCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEc--CCcceEeeceeeeEEeecc
Q 030849 63 ENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFD--METECCTWGLADVRINREK 138 (170)
Q Consensus 63 ~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd--~~~~~~~~~~~~v~i~~~k 138 (170)
++|+|||||||++|||++++||+||+|+.|+|++.+ +.+++++| +|.+++ ++. ++++-
T Consensus 91 ~~Y~LEVSSPGldRpL~~~~df~r~~G~~V~V~l~~-------~~~~~k~~~G~L~~v~~~~~~---------v~l~~-- 152 (174)
T PRK14631 91 GEYALEVSSPGWDRPFFQLEQLQGYIGQQVALRLIA-------AVENRRKFQAKLLAVDLENEE---------IQVEV-- 152 (174)
T ss_pred CCeEEEEeCCCCCCcCCCHHHHHHhCCCeEEEEEec-------ccCCceEEEEEEEEeecCCCE---------EEEEE--
Confidence 999999999999999999999999999999999999 77788999 999999 777 44441
Q ss_pred cCCCCCCcccccceeEEeeccccceeEEEec
Q 030849 139 AGKGRPLSKKQREWRLNTTFDSLRLVRLHSD 169 (170)
Q Consensus 139 ~~Kgk~~~~~~~~~~v~ip~~~I~karL~i~ 169 (170)
.... .+.|||++|+||||.++
T Consensus 153 --------~~~~--~~~i~~~~I~ka~L~~~ 173 (174)
T PRK14631 153 --------EGKH--VLDIDSNNIDKANLIYQ 173 (174)
T ss_pred --------cCCc--EEEEEhHHcceEEEeec
Confidence 0011 26899999999999875
No 12
>PRK14638 hypothetical protein; Provisional
Probab=100.00 E-value=9.4e-37 Score=239.27 Aligned_cols=123 Identities=23% Similarity=0.355 Sum_probs=105.9
Q ss_pred ccccccCCccee-----------EEEEEEEcCCCC-CCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRSGS-PSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVR 79 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~~g-vtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~ 79 (170)
.|+++++||++| .|||| ||+++| ||+|||+.+||+|+++||++| +|+++|+|||||||++|||+
T Consensus 15 ~~i~~~~G~elvdve~~~~~~~~~lrV~-ID~~~G~v~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL~ 90 (150)
T PRK14638 15 ERIAEEQGLEIFDVQYRRESRGWVLRII-IDNPVGYVSVRDCELFSREIERFLDRED---LIEHSYTLEVSSPGLDRPLR 90 (150)
T ss_pred HHHHHHcCCEEEEEEEEecCCCcEEEEE-EECCCCCcCHHHHHHHHHHHHHHhcccc---ccCCceEEEEeCCCCCCCCC
Confidence 578899999977 47899 999876 999999999999999999999 99999999999999999999
Q ss_pred ChHHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeecc
Q 030849 80 IPLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFD 159 (170)
Q Consensus 80 ~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~~ 159 (170)
+++||+||+|+.|+|++.+ .....| +|.++++++ ++++. . .. .++|||+
T Consensus 91 ~~~~f~r~~G~~v~V~~~~-------~k~~~G--~L~~~~~~~---------i~l~~----------~-~~--~~~i~~~ 139 (150)
T PRK14638 91 GPKDYVRFTGKLAKIVTKD-------GKTFIG--RIESFVDGT---------ITISD----------E-KE--KYEINID 139 (150)
T ss_pred CHHHHHHhCCCEEEEEECC-------CcEEEE--EEEEEeCCE---------EEEEE----------C-Cc--EEEEEhH
Confidence 9999999999999999964 222333 999999998 55541 1 11 2789999
Q ss_pred ccceeEEEec
Q 030849 160 SLRLVRLHSD 169 (170)
Q Consensus 160 ~I~karL~i~ 169 (170)
+|++|||.++
T Consensus 140 ~I~~a~l~~e 149 (150)
T PRK14638 140 DVKRANLEVE 149 (150)
T ss_pred HcceEEEeee
Confidence 9999999876
No 13
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=100.00 E-value=2.7e-36 Score=237.02 Aligned_cols=127 Identities=28% Similarity=0.403 Sum_probs=111.5
Q ss_pred ccccccCCcceeE-----------EEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCC
Q 030849 12 RNRVLNNKMPLWL-----------TQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRI 80 (170)
Q Consensus 12 ~~~~~~~g~~~~~-----------lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~ 80 (170)
.+.++++||++|. |||+ ||+++|+|+|||+.+||+|+++||+.| +|+++|+|||||||++|||++
T Consensus 14 ~~~~~~~g~~l~dv~~~~~~~~~~l~V~-Id~~~gv~iddc~~~Sr~is~~LD~~d---~i~~~Y~LEVSSPGi~RpL~~ 89 (154)
T PRK00092 14 EPVVEALGYELVDVEYVKEGRDSTLRIY-IDKEGGIDLDDCEEVSRQISAVLDVED---PIPGAYTLEVSSPGLDRPLKK 89 (154)
T ss_pred HHHHHHCCCEEEEEEEEecCCCcEEEEE-EECCCCCCHHHHHHHHHHHHHHhcccc---CCCCCeEEEEeCCCCCCcCCC
Confidence 5788999999874 6888 999999999999999999999999998 999999999999999999999
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeec
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTF 158 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~ 158 (170)
++||+||+|+.|+|++++ +.++.+.| +|.++++++ ++++. ++++ +.++|||
T Consensus 90 ~~~f~r~~G~~v~V~~~~-------~~~~~~~~~G~L~~~~~~~---------i~l~~----~~~~-------~~~~i~~ 142 (154)
T PRK00092 90 ARDFRRFIGREVKVKLYE-------PIDGRKKFQGILLAVDGET---------VTLEV----EGKE-------KEVEIPL 142 (154)
T ss_pred HHHHHHhCCCeEEEEEEc-------ccCCceEEEEEEEEeeCCE---------EEEEE----CCCe-------EEEEEEH
Confidence 999999999999999999 66677777 999999998 44441 1111 1278999
Q ss_pred cccceeEEEec
Q 030849 159 DSLRLVRLHSD 169 (170)
Q Consensus 159 ~~I~karL~i~ 169 (170)
++|++|+|.++
T Consensus 143 ~~I~~a~l~~e 153 (154)
T PRK00092 143 DNIAKARLVVE 153 (154)
T ss_pred HHcceEEEeee
Confidence 99999999886
No 14
>PRK14630 hypothetical protein; Provisional
Probab=100.00 E-value=7.4e-36 Score=232.58 Aligned_cols=118 Identities=15% Similarity=0.264 Sum_probs=103.3
Q ss_pred ccccccCCccee-----------EEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRI 80 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~ 80 (170)
.|.++++||++| +|||| ||+++|||+|||+.+||+|++.|| + +|+++|+|||||||++|||++
T Consensus 15 ~~~~~~~G~eLvdve~~~~~~~~~lrV~-Id~~~gV~idDC~~vSr~i~~~ld--~---~i~~~Y~LEVSSPGldRpL~~ 88 (143)
T PRK14630 15 KNVTDRLGIEIIEINTFRNRNEGKIQIV-LYKKDSFGVDTLCDLHKMILLILE--A---VLKYNFSLEISTPGINRKIKS 88 (143)
T ss_pred HHHHHHcCCEEEEEEEEecCCCcEEEEE-EECCCCCCHHHHHHHHHHHHHHhc--c---cCCCCeEEEEeCCCCCCcCCC
Confidence 578999999987 47899 999999999999999999999996 5 899999999999999999999
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeeccc
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDS 160 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~~~ 160 (170)
++||+||+|+.|+|++.+ +. ..| +|.++++++ ++++ ..+. .+.|||++
T Consensus 89 ~~df~r~~G~~v~V~l~~-------~~-~~G--~L~~~~d~~---------i~l~-----------~~~~--~~~i~~~~ 136 (143)
T PRK14630 89 DREFKIFEGKKIKLMLDN-------DF-EEG--FILEAKADS---------FIFK-----------TDSK--EVNVLYSD 136 (143)
T ss_pred HHHHHHhCCCEEEEEEcC-------cc-eEE--EEEEEeCCE---------EEEE-----------ECCE--EEEEEhHh
Confidence 999999999999999977 44 366 899999999 5554 1111 27899999
Q ss_pred cceeEEE
Q 030849 161 LRLVRLH 167 (170)
Q Consensus 161 I~karL~ 167 (170)
|++|||.
T Consensus 137 I~ka~lv 143 (143)
T PRK14630 137 VKKAKLS 143 (143)
T ss_pred cceEEEC
Confidence 9999984
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=6.9e-36 Score=231.09 Aligned_cols=126 Identities=29% Similarity=0.491 Sum_probs=87.1
Q ss_pred ccccccCCccee-----------EEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRI 80 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~ 80 (170)
.|+++++||++| .|||+ ||+++|||+|||+++||+|++.||+++ +|+++|+|||||||++|||++
T Consensus 3 ~~~~~~~g~~l~~v~~~~~~~~~~l~V~-id~~~gv~lddc~~~sr~i~~~LD~~d---~i~~~y~LEVSSPG~~r~L~~ 78 (141)
T PF02576_consen 3 EPLLEELGLELVDVEVVKEGGNRILRVF-IDKDGGVSLDDCEKVSRAISALLDAED---PIPEDYTLEVSSPGIDRPLKS 78 (141)
T ss_dssp HHHH-S-SSEEEEEEEEEETTEEEEEEE-EE-SS---HHHHHHHHHHHGGGTTTS-------S-EEEEEE--SSSS--SS
T ss_pred ccchhhcCCEEEEEEEEECCCCEEEEEE-EEeCCCCCHHHHHHHHHHHHHHHcccc---ccCcceEEEEeCCCCCCcCCC
Confidence 478899999977 47899 999999999999999999999999998 999999999999999999999
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeec
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTF 158 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~ 158 (170)
++||.+|+|+.|+|++.+ +.++++.| +|.+++++++++++. .|+++ ..++|||
T Consensus 79 ~~~~~~~iG~~v~v~~~~-------~~~~~~~~~G~L~~~~~~~i~l~~~-----------~~~~~-------~~~~I~~ 133 (141)
T PF02576_consen 79 PRDFERFIGRKVKVKLKQ-------PVNGRKEFEGKLLEVDEDEITLEVE-----------GKGKK-------KEVEIPF 133 (141)
T ss_dssp HHHHHHH-SEEEEEE-SS--------SSS-SEEEEEEEEEETTEEEEEEE------------SS-E-------EEEEE-S
T ss_pred HHHHHHhcCCeEEEEEec-------cCCCcEEEEEEEEEEeCCEEEEEEC-----------Cccce-------EEEEEEH
Confidence 999999999999999998 66777787 999999999443221 11111 2379999
Q ss_pred cccceeEE
Q 030849 159 DSLRLVRL 166 (170)
Q Consensus 159 ~~I~karL 166 (170)
++|++|||
T Consensus 134 ~~I~ka~L 141 (141)
T PF02576_consen 134 SDIKKARL 141 (141)
T ss_dssp S--SS-EE
T ss_pred HHCceEeC
Confidence 99999997
No 16
>PRK14641 hypothetical protein; Provisional
Probab=100.00 E-value=2.9e-35 Score=235.55 Aligned_cols=130 Identities=20% Similarity=0.294 Sum_probs=107.1
Q ss_pred ccCCccee-----------EEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCC----CCeEEEEecCCCCCCCCC
Q 030849 16 LNNKMPLW-----------LTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIP----ENTSLEVSSPGVERVVRI 80 (170)
Q Consensus 16 ~~~g~~~~-----------~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~----~~Y~LEVSSPGieRpL~~ 80 (170)
+++||++| +|||+ ||+++|||||||+.+||+||++||++| +++ ++|+|||||||++|||++
T Consensus 20 ~~~G~eLvdve~~~~~~~~~lrV~-ID~~~gv~lDdC~~vSr~Is~~LD~~d---~i~~~~~~~Y~LEVSSPGldRpL~~ 95 (173)
T PRK14641 20 KGEGVYLVSMTVKGSGKGRKIEVL-LDADTGIRIDQCAFFSRRIRERLEEDE---ELLGLVGEDFDLMVSSPGLGEPIIL 95 (173)
T ss_pred ccCCeEEEEEEEEeCCCCcEEEEE-EeCCCCCCHHHHHHHHHHHHHHhCccc---ccccCCCCCeEEEEeCCCCCCcCCC
Confidence 79999977 47899 999999999999999999999999988 554 799999999999999999
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEc-----CCcceEeeceeeeEEeecccC-CCCCCcccccce
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFD-----METECCTWGLADVRINREKAG-KGRPLSKKQREW 152 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd-----~~~~~~~~~~~~v~i~~~k~~-Kgk~~~~~~~~~ 152 (170)
++||+||+|+.|+|++.+ +.++++.| +|.+++ ++. +++...+.+ |+++ .. ..
T Consensus 96 ~~~f~r~~G~~V~V~l~~-------~~~~~~~~~G~L~~~~~~~~~~~~---------v~~~~~~~~~~~~~--~~--~~ 155 (173)
T PRK14641 96 PRQYGRHVGRLLRVTYRD-------EEGSEHEVTGHLQEVSLTEGEGAS---------IVLKPEQKKKKGKQ--EE--TE 155 (173)
T ss_pred HHHHHHhCCCEEEEEEec-------ccCCeEEEEEEEEeeecccCCCCc---------EEEEeccccccccC--CC--Cc
Confidence 999999999999999999 66777788 999986 333 444432222 2221 11 22
Q ss_pred eEEeeccccceeEEEec
Q 030849 153 RLNTTFDSLRLVRLHSD 169 (170)
Q Consensus 153 ~v~ip~~~I~karL~i~ 169 (170)
.+++||++|++|++.+|
T Consensus 156 ~~~v~~~~v~~A~vevE 172 (173)
T PRK14641 156 NITLELDAVIRAVPEAE 172 (173)
T ss_pred eEEEEhHHccceeeeee
Confidence 47999999999999887
No 17
>PRK02001 hypothetical protein; Validated
Probab=100.00 E-value=9.7e-35 Score=228.35 Aligned_cols=133 Identities=20% Similarity=0.219 Sum_probs=104.1
Q ss_pred ccccccCCcceeE--------EEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHH
Q 030849 12 RNRVLNNKMPLWL--------TQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLE 83 (170)
Q Consensus 12 ~~~~~~~g~~~~~--------lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~ 83 (170)
.++++++||++|. |||+ ||+++|||+|||+.+||+|+++||+.+ ++|+|||||||++|||++++|
T Consensus 12 e~~~~~~g~eLvdv~~~~~~~lrV~-ID~~~Gv~lddC~~vSr~is~~LD~~d------~~Y~LEVSSPGldRpL~~~~~ 84 (152)
T PRK02001 12 EELLEGPELFLVDLTISPDNKIVVE-IDGDEGVWIEDCVELSRAIEHNLDREE------EDFELEVGSAGLTSPLKVPRQ 84 (152)
T ss_pred HhhhhhcCcEEEEEEEEcCCEEEEE-EECCCCCCHHHHHHHHHHHHHHhcCCC------CCeEEEEeCCCCCCcCCCHHH
Confidence 5788999999884 7899 999999999999999999999999775 899999999999999999999
Q ss_pred HHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeeccccce
Q 030849 84 LERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRL 163 (170)
Q Consensus 84 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~~~I~k 163 (170)
|+||+|+.|+|++.+ .....| +|.+++++++++...-. ...+.+||++. + ...++|||++|++
T Consensus 85 f~r~~G~~v~V~l~~-------~~~~~G--~L~~~~~~~i~l~~~~~----~~~~~~k~~~~--~--~~~~~i~~~~I~k 147 (152)
T PRK02001 85 YKKNIGRELEVLTKN-------GKKIEG--ELKSADENDITLEVKAR----EPKEGGKGKVT--V--EKEETITYDDIKE 147 (152)
T ss_pred HHHhCCCEEEEEECC-------CCEEEE--EEEEEeCCEEEEEEccc----ccccccccccc--c--ceeEEEEhHheee
Confidence 999999999999954 222333 99999999844321100 00011233322 1 1237999999999
Q ss_pred eEEEe
Q 030849 164 VRLHS 168 (170)
Q Consensus 164 arL~i 168 (170)
|+|.+
T Consensus 148 a~l~~ 152 (152)
T PRK02001 148 AKVII 152 (152)
T ss_pred EEEeC
Confidence 99975
No 18
>PRK14637 hypothetical protein; Provisional
Probab=100.00 E-value=2.9e-34 Score=225.48 Aligned_cols=122 Identities=20% Similarity=0.243 Sum_probs=101.9
Q ss_pred ccccccCCccee-----------EEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRI 80 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~ 80 (170)
.|+++++||++| +|||+ ||+++|||+|||+++||+|+++||+.+ + +++|+|||||||++|||++
T Consensus 15 ~p~~~~~g~eLvdve~~~~~~~~~lrV~-ID~~~gV~iddC~~vSr~Is~~LD~~~---~-~~~y~LEVSSPGldRpL~~ 89 (151)
T PRK14637 15 EPVVEGLGCKLVDLSRRVQQAQGRVRAV-IYSAGGVGLDDCARVHRILVPRLEALG---G-VRDVFLEVSSPGIERVIKN 89 (151)
T ss_pred HHHHHhcCCEEEEEEEEecCCCcEEEEE-EECCCCCCHHHHHHHHHHHHHHhcccc---c-ccCcEEEEeCCCCCCCCCC
Confidence 578899999977 47899 999999999999999999999999754 3 5789999999999999999
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCC-CceEEEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeecc
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSES-DGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFD 159 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~-~~~f~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~~ 159 (170)
++||+||+|+.|+|++.. .... .| +|.+++++. ++++. ... .+.|||+
T Consensus 90 ~~~f~r~~G~~V~V~l~~-------~~~~~~G--~L~~~~d~~---------v~l~~-----------~~~--~~~i~~~ 138 (151)
T PRK14637 90 AAEFSIFVGETVKVWFEC-------TGQWQVG--TIAEADETC---------LVLTS-----------DGV--PVTIPYV 138 (151)
T ss_pred HHHHHHhCCCEEEEEECC-------CCcEEEE--EEEEEeCCE---------EEEEE-----------CCE--EEEEEHH
Confidence 999999999999999822 1122 34 899999998 55541 111 2789999
Q ss_pred ccceeEEEec
Q 030849 160 SLRLVRLHSD 169 (170)
Q Consensus 160 ~I~karL~i~ 169 (170)
+|++|||.+.
T Consensus 139 ~I~ka~L~~~ 148 (151)
T PRK14637 139 QITKAQLHPA 148 (151)
T ss_pred HeeeEEEEEE
Confidence 9999999875
No 19
>PRK14642 hypothetical protein; Provisional
Probab=100.00 E-value=4.2e-34 Score=232.57 Aligned_cols=145 Identities=23% Similarity=0.235 Sum_probs=111.8
Q ss_pred ccccccCCcceeE--------EEEEEEcC-------------CCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEe
Q 030849 12 RNRVLNNKMPLWL--------TQLVACDR-------------SGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVS 70 (170)
Q Consensus 12 ~~~~~~~g~~~~~--------lrv~~iD~-------------~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVS 70 (170)
.++++++||++|. |||| ||+ ++|||+|||+.+||+|+++||+++ . +.|+||||
T Consensus 8 epvv~~lG~eLvdve~~~~~~LrV~-ID~~~~~~~~~~~~~~~~gVtidDC~~vSR~Is~~LDve~---~--~y~~LEVS 81 (197)
T PRK14642 8 EQTVTGLGYDLVEIERSAGGLLRVT-IDLPWVPPTEGAPVGPEQFVTVEDCEKVTRQLQFALEVDG---V--DYKRLEVS 81 (197)
T ss_pred HHHHHHcCCEEEEEEEecCCEEEEE-EecCccccccccccccCCCccHHHHHHHHHHHHHHhcccC---c--cccEEEEe
Confidence 4788999999884 7899 997 467999999999999999999886 2 33479999
Q ss_pred cCCCCCCCCChHHHHhcCCCeEEEEEEecccc--CCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeeccc---CCCC
Q 030849 71 SPGVERVVRIPLELERFKDRAMYVKYVGETVT--TGSPSESDGVF--RLISFDMETECCTWGLADVRINREKA---GKGR 143 (170)
Q Consensus 71 SPGieRpL~~~~~f~r~~G~~v~V~l~~~~~~--~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~---~Kgk 143 (170)
|||++|||++++||.||+|+.|+|+++.+.++ .++...++++| +|.++++++++++|.-++. .++. +|||
T Consensus 82 SPGldRPLk~~~df~rfiG~~V~V~l~~pi~~~~~~~~~~~rk~f~G~L~~~~~~~i~l~~~~~~~---~k~g~~~~k~~ 158 (197)
T PRK14642 82 SPGIDRPLRHEQDFERFAGEVIDITLKAPIGAAAGGQVSANRKKFRGTLERAESGGWQIVWSDEPP---VKPGQRVSKKR 158 (197)
T ss_pred CCCCCCCCCCHHHHHHhCCCeEEEEEeccccccccccccCCceEEEEEEEEEcCCEEEEEEeeccc---CCCcccccccc
Confidence 99999999999999999999999999983321 00011268888 9999999998877764321 0111 2444
Q ss_pred CCcccccceeEEeeccccceeEEEe
Q 030849 144 PLSKKQREWRLNTTFDSLRLVRLHS 168 (170)
Q Consensus 144 ~~~~~~~~~~v~ip~~~I~karL~i 168 (170)
.+... ..+.|+|++|++|||.+
T Consensus 159 ~~~~~---~~~~~~~~eik~a~l~p 180 (197)
T PRK14642 159 VPAPL---QALGFTLDELREARLAP 180 (197)
T ss_pred ccccc---eeEEeehhheeeEEEEE
Confidence 32222 23799999999999986
No 20
>PRK14635 hypothetical protein; Provisional
Probab=100.00 E-value=2.4e-33 Score=222.32 Aligned_cols=132 Identities=22% Similarity=0.318 Sum_probs=100.6
Q ss_pred cccccCCccee-----------EEEEEEEcC----CCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCC
Q 030849 13 NRVLNNKMPLW-----------LTQLVACDR----SGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERV 77 (170)
Q Consensus 13 ~~~~~~g~~~~-----------~lrv~~iD~----~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRp 77 (170)
+.+ ++||++| +|||+ ||+ +||||||||+++||+|+++||+.| ++ ++|+|||||||++||
T Consensus 14 ~~~-~~g~el~dve~~~~~~~~~lrV~-ID~~~~~~~gv~lddC~~vSr~is~~LD~~d---~~-~~Y~LEVSSPGldRp 87 (162)
T PRK14635 14 RVL-ALPVKLYSLKVNQRPNHSLIEVV-LDNLEHPYGSVSLLECEQVSRKLKEELERIS---PD-LDFTLKVSSAGAERK 87 (162)
T ss_pred HHH-CCCCEEEEEEEEecCCCcEEEEE-EecCCCCCCCcCHHHHHHHHHHHHHHhCCCC---CC-CCeEEEEcCCCCCCc
Confidence 445 4699976 47899 997 588999999999999999999988 75 899999999999999
Q ss_pred CCChHHHHhcCCCeEEEEEEeccccCCCCCC-CCceEEEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEe
Q 030849 78 VRIPLELERFKDRAMYVKYVGETVTTGSPSE-SDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNT 156 (170)
Q Consensus 78 L~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~-~~~~f~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~i 156 (170)
|++++||.||+|+.|+|++..+... ... +.+ +|.+++++++ +++.. . |+++. .... .++|
T Consensus 88 L~~~~~~~r~~G~~v~v~~~~~~~~---~~~g~~g--~L~~~~~~~v---------~l~~~-~-k~~~~-~~~~--~~~i 148 (162)
T PRK14635 88 LRLPEDLDRFRGIPVRLVFRSEESE---KWQEGIF--RLVNRDGDQV---------ELEKF-Q-KGKKS-KVKK--QTTL 148 (162)
T ss_pred CCCHHHHHHhCCCEEEEEEecCCCc---EEEecce--EEEEEcCCEE---------EEEEe-c-ccccc-cCCe--EEEE
Confidence 9999999999999999998652100 111 112 6999999984 33311 1 11111 1122 2799
Q ss_pred eccccceeEEEec
Q 030849 157 TFDSLRLVRLHSD 169 (170)
Q Consensus 157 p~~~I~karL~i~ 169 (170)
||++|++|||.++
T Consensus 149 p~~~I~ka~l~~e 161 (162)
T PRK14635 149 NLKDILKGNLYVE 161 (162)
T ss_pred EhHHeeeeEEEEe
Confidence 9999999999986
No 21
>PRK14644 hypothetical protein; Provisional
Probab=100.00 E-value=5.3e-33 Score=214.96 Aligned_cols=119 Identities=17% Similarity=0.222 Sum_probs=102.1
Q ss_pred ccccccCCccee-----------EEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRI 80 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~ 80 (170)
.|+++++||++| +|||| ||++ ++|||+.+||+|+++||+.| +++++|.|||||||++|||++
T Consensus 5 e~~~~~~g~el~dve~~~~~~~~~LrV~-Idk~---~iddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL~~ 77 (136)
T PRK14644 5 EKLLEKFGNKINEIKIVKEDGDLFLEVI-LNSR---DLKDIEELTKEISDFIDNLS---VEFDFDSLDISSPGFDMDYET 77 (136)
T ss_pred hhhHHhcCCEEEEEEEEeCCCCEEEEEE-ECCC---CHHHHHHHHHHHHHHhcccc---CCCCCeEEEEECCCCCCCCCH
Confidence 588999999977 47899 9985 79999999999999999999 999999999999999999998
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeec
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTF 158 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~ 158 (170)
+||.||+|+.|+|++++ ++++++.| +|.++++++++++|.. || ....++|++
T Consensus 78 -~~f~r~~G~~v~V~l~~-------~~~~~~~~~G~L~~v~~~~i~l~~~~-----------k~-------~~~~i~~~~ 131 (136)
T PRK14644 78 -DELENHIGEIIDVSLNK-------EVNKTDFITGELLENNPETITLKWNC-----------KG-------QFRKVEINK 131 (136)
T ss_pred -HHHHHhCCCeEEEEEcc-------CcCCeEEEEEEEEEEeCCEEEEEEec-----------CC-------cEEEEEECH
Confidence 69999999999999999 77788888 9999999995544321 11 122378999
Q ss_pred cccce
Q 030849 159 DSLRL 163 (170)
Q Consensus 159 ~~I~k 163 (170)
++|++
T Consensus 132 ~~i~~ 136 (136)
T PRK14644 132 ENIKK 136 (136)
T ss_pred HHhcC
Confidence 99874
No 22
>PRK14645 hypothetical protein; Provisional
Probab=100.00 E-value=9.5e-33 Score=217.48 Aligned_cols=117 Identities=20% Similarity=0.238 Sum_probs=97.6
Q ss_pred ccccccCCccee-----------EEEEEEEcCC--CCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCC
Q 030849 12 RNRVLNNKMPLW-----------LTQLVACDRS--GSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVV 78 (170)
Q Consensus 12 ~~~~~~~g~~~~-----------~lrv~~iD~~--~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL 78 (170)
.++++++||++| +|||| ||++ +|||+|||+.+||+|+++||++| +|+++|+|||||||++|||
T Consensus 16 ~~~~~~~G~elvdve~~~~~~~~ilrV~-ID~~~~~~v~lddC~~vSr~is~~LD~~d---~i~~~Y~LEVSSPGldRpL 91 (154)
T PRK14645 16 EGALEPLGYEVLEVQVQRSGGKRIVLVR-IDRKDEQPVTVEDLERASRALEAELDRLD---PIEGEYRLEVESPGPKRPL 91 (154)
T ss_pred HHHHHHcCCEEEEEEEEeCCCCeEEEEE-EECCCCCCcCHHHHHHHHHHHHHHhcccc---cCCCceEEEEeCCCCCCCC
Confidence 578899999977 47899 9974 45999999999999999999999 9999999999999999999
Q ss_pred CChHHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeec
Q 030849 79 RIPLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTF 158 (170)
Q Consensus 79 ~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~ 158 (170)
++++||.||+|+.|+|++ . .....| +|.+++++. |+++ .++. .++|||
T Consensus 92 ~~~~df~r~~G~~v~v~~-~-------~k~~~G--~L~~~~d~~---------i~l~-----------~~~~--~~~i~~ 139 (154)
T PRK14645 92 FTARHFERFAGLKAKVRG-P-------GENFTG--RIKAVSGDQ---------VTFD-----------VGGE--DRTLRI 139 (154)
T ss_pred CCHHHHHHhCCCEEEEEc-C-------CeEEEE--EEEEEeCCE---------EEEE-----------ECCe--EEEEEH
Confidence 999999999999999975 2 112233 999999998 5444 1122 278999
Q ss_pred ccccee
Q 030849 159 DSLRLV 164 (170)
Q Consensus 159 ~~I~ka 164 (170)
++|+++
T Consensus 140 ~~I~~~ 145 (154)
T PRK14645 140 GTFQAN 145 (154)
T ss_pred HHhhhh
Confidence 999755
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=99.89 E-value=7.5e-23 Score=145.65 Aligned_cols=80 Identities=30% Similarity=0.414 Sum_probs=66.5
Q ss_pred eEEEEecCCCCCCCCChHHHHhcCCCeEEEEEEeccccCCCCCCCCceE--EEEEEcCCcceEeeceeeeEEeecccCCC
Q 030849 65 TSLEVSSPGVERVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVF--RLISFDMETECCTWGLADVRINREKAGKG 142 (170)
Q Consensus 65 Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f--~L~~vd~~~~~~~~~~~~v~i~~~k~~Kg 142 (170)
|+|||||||++|||++++||+||+|+.|+|++.. +++++++| .|.++++++ ++++.. .|+
T Consensus 1 Y~LEVSSPGl~RpL~~~~~~~r~~G~~v~v~~~~-------~~~~~~~~~G~L~~~~~~~---------v~l~~~--~~~ 62 (83)
T cd01734 1 YFLEVSSPGAERPLKKEADFERAVGKYVHVKLYQ-------PIDGQKEFEGTLLGVDDDT---------VTLEVD--IKT 62 (83)
T ss_pred CEEEEcCCCCCCcCCCHHHHHHhCCCEEEEEEEc-------ccCCeEEEEEEEEeEeCCE---------EEEEEe--cCC
Confidence 8999999999999999999999999999999998 66778888 999999998 444321 111
Q ss_pred CCCcccccceeEEeeccccceeEEEec
Q 030849 143 RPLSKKQREWRLNTTFDSLRLVRLHSD 169 (170)
Q Consensus 143 k~~~~~~~~~~v~ip~~~I~karL~i~ 169 (170)
+ ...++|||++|++|+|.++
T Consensus 63 ~-------~~~~~i~~~~I~ka~l~~~ 82 (83)
T cd01734 63 R-------GKTVEIPLDKIAKARLAPE 82 (83)
T ss_pred C-------CeEEEEEhHHeeEEEEEEE
Confidence 1 1237999999999999886
No 24
>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=73.28 E-value=11 Score=29.89 Aligned_cols=47 Identities=21% Similarity=0.263 Sum_probs=40.2
Q ss_pred eEEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCC
Q 030849 23 WLTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPG 73 (170)
Q Consensus 23 ~~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPG 73 (170)
..-|+|.+|=+|.|.-.+++.+-+.|+++|.... |= +.-.|=+.|||
T Consensus 96 ~~~r~~VldF~Gdi~A~~v~~LReeisail~~a~---~~-DeV~~rLES~G 142 (155)
T PF08496_consen 96 PKPRLFVLDFKGDIKASEVESLREEISAILSVAT---PE-DEVLVRLESPG 142 (155)
T ss_pred CCCeEEEEecCCCccHHHHHHHHHHHHHHHHhCC---CC-CeEEEEEecCC
Confidence 3457787798999999999999999999999887 43 77788888998
No 25
>cd02978 KaiB_like KaiB-like family; composed of the circadian clock proteins, KaiB and the N-terminal KaiB-like sensory domain of SasA. KaiB is an essential protein in maintaining circadian rhythm. It was originally discovered from the cyanobacterium Synechococcus as part of the circadian clock gene cluster, kaiABC. KaiB attenuates KaiA-enhanced KaiC autokinase activity by interacting with KaiA-KaiC complexes in a circadian fashion. KaiB is membrane-associated as well as cytosolic. The amount of membrane-associated protein peaks in the evening (at circadian time (CT) 12-16) while the cytosolic form peaks later (at CT 20). The rhythmic localization of KaiB may function in regulating the formation of Kai complexes. SasA is a sensory histidine kinase which associates with KaiC. Although it is not an essential oscillator component, it is important in enhancing kaiABC expression and is important in metabolic growth control under day/night cycle conditions. SasA contains an N-terminal sensor
Probab=70.30 E-value=14 Score=25.74 Aligned_cols=40 Identities=15% Similarity=0.120 Sum_probs=28.3
Q ss_pred eEEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecC
Q 030849 23 WLTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSP 72 (170)
Q Consensus 23 ~~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSP 72 (170)
|.|++| ++....-|..+.+.+.+.+...+ ++.|.|||.=.
T Consensus 2 ~~L~Ly-v~g~tp~S~~ai~nl~~i~e~~l---------~~~~~LeVIDv 41 (72)
T cd02978 2 YVLRLY-VAGRTPKSERALQNLKRILEELL---------GGPYELEVIDV 41 (72)
T ss_pred eEEEEE-ECCCCchHHHHHHHHHHHHHHhc---------CCcEEEEEEEc
Confidence 678999 99877777777666655544332 58999999643
No 26
>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=67.84 E-value=6.4 Score=26.39 Aligned_cols=29 Identities=24% Similarity=0.229 Sum_probs=23.5
Q ss_pred HHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCC
Q 030849 84 LERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDME 121 (170)
Q Consensus 84 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~ 121 (170)
+..++|+.|.|.++. ....+| +|.++|+.
T Consensus 5 L~~~~~~~V~V~Lk~-------g~~~~G--~L~~~D~~ 33 (67)
T cd01726 5 LKAIIGRPVVVKLNS-------GVDYRG--ILACLDGY 33 (67)
T ss_pred HHhhCCCeEEEEECC-------CCEEEE--EEEEEccc
Confidence 478899999999988 445566 99999865
No 27
>KOG1783 consensus Small nuclear ribonucleoprotein F [RNA processing and modification]
Probab=65.03 E-value=4.9 Score=28.22 Aligned_cols=29 Identities=24% Similarity=0.289 Sum_probs=22.9
Q ss_pred HHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcC
Q 030849 83 ELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDM 120 (170)
Q Consensus 83 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~ 120 (170)
=+..++|++|.|++.+ ..+.+| +|...|.
T Consensus 10 fl~~iiGr~V~VKl~s-------gvdyrG--~l~~lDg 38 (77)
T KOG1783|consen 10 FLKAIIGRTVVVKLNS-------GVDYRG--TLVCLDG 38 (77)
T ss_pred HHHHHhCCeEEEEecC-------Cccccc--eehhhhh
Confidence 3568999999999999 677888 6666653
No 28
>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=61.40 E-value=12 Score=25.14 Aligned_cols=31 Identities=26% Similarity=0.246 Sum_probs=24.3
Q ss_pred HHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 83 ELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 83 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
.+..++|+.|.|.+++ ....+| +|.++|+.-
T Consensus 5 ~L~~~~g~~V~V~Lk~-------g~~~~G--~L~~~D~~m 35 (68)
T cd01722 5 FLNDLTGKPVIVKLKW-------GMEYKG--TLVSVDSYM 35 (68)
T ss_pred HHHHcCCCEEEEEECC-------CcEEEE--EEEEECCCE
Confidence 3467899999999998 445566 899998653
No 29
>PF14438 SM-ATX: Ataxin 2 SM domain; PDB: 1M5Q_1.
Probab=53.44 E-value=11 Score=25.60 Aligned_cols=29 Identities=21% Similarity=0.128 Sum_probs=20.0
Q ss_pred HHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCC
Q 030849 84 LERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDME 121 (170)
Q Consensus 84 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~ 121 (170)
+...+|+.|.|++++ ....+| .+.+++.+
T Consensus 7 ~~~lvG~~V~V~~~~-------G~~yeG--if~s~s~~ 35 (77)
T PF14438_consen 7 LTNLVGQTVEVTTKN-------GSVYEG--IFHSASPE 35 (77)
T ss_dssp HHTTTTSEEEEEETT-------S-EEEE--EEEEE-T-
T ss_pred HHhCcCCEEEEEECC-------CCEEEE--EEEeCCCc
Confidence 457899999999988 333555 77777765
No 30
>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=53.29 E-value=17 Score=25.48 Aligned_cols=33 Identities=30% Similarity=0.515 Sum_probs=25.9
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
..++.+++|+.|.|.+++ ..+..| +|.++|.-.
T Consensus 4 ~~~L~~~i~k~V~V~l~~-------gr~~~G--~L~~~D~~m 36 (81)
T cd01729 4 ILDLSKYVDKKIRVKFQG-------GREVTG--ILKGYDQLL 36 (81)
T ss_pred hhhHHHhcCCeEEEEECC-------CcEEEE--EEEEEcCcc
Confidence 457889999999999988 334455 899998764
No 31
>TIGR02654 circ_KaiB circadian clock protein KaiB. Members of this protein family are the circadian clock protein KaiB of Cyanobacteria, encoded in the circadian clock gene cluster kaiABC. KaiB has homologs of unknown function in some Archaea and Proteobacteria, and has paralogs of unknown function in some Cyanobacteria. KaiB forms homodimers, homotetramers, and multimeric complexes with KaiA and/or KaiC.
Probab=53.13 E-value=42 Score=24.19 Aligned_cols=41 Identities=10% Similarity=0.133 Sum_probs=28.2
Q ss_pred eeEEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecC
Q 030849 22 LWLTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSP 72 (170)
Q Consensus 22 ~~~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSP 72 (170)
.|.||+| +-....-|..+.+.+.+.+. +. .++.|.|||-=+
T Consensus 3 ~~~LrLy-vag~~p~S~~ai~nl~~i~e----~~-----l~g~y~LeVIDv 43 (87)
T TIGR02654 3 TYVLKLY-VAGNTPNSVRALKTLKNILE----TE-----FQGVYALKVIDV 43 (87)
T ss_pred eEEEEEE-EeCCCchHHHHHHHHHHHHH----Hh-----cCCceEEEEEEc
Confidence 5889999 87766677776666655544 33 235699999754
No 32
>PF06257 DUF1021: Protein of unknown function (DUF1021); InterPro: IPR009366 This entry consists of several hypothetical bacterial proteins of unknown function.; PDB: 3FB9_A.
Probab=53.08 E-value=64 Score=22.66 Aligned_cols=55 Identities=13% Similarity=0.082 Sum_probs=30.9
Q ss_pred HHHHhcCCCeEEEEEEeccccCCCCCCCCceE-----EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEe
Q 030849 82 LELERFKDRAMYVKYVGETVTTGSPSESDGVF-----RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNT 156 (170)
Q Consensus 82 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f-----~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~i 156 (170)
++...++|+.|.++... |+++. .|.++=..-.+ |.++. ......++.+
T Consensus 10 ~~l~~~vG~~V~l~a~~----------GRkK~~~r~GvL~~tYPsvFv-------V~l~~----------~~~~~~rvSy 62 (76)
T PF06257_consen 10 KELESHVGKRVKLKANK----------GRKKIIEREGVLEETYPSVFV-------VELDQ----------EENQFERVSY 62 (76)
T ss_dssp HHHHHTTTSEEEEEE------------SSS--S-EEEEEEEE-SSEEE-------EEES-----------S-SS-EEEEE
T ss_pred HHHHHcCCCEEEEEEcC----------CceEEEEEEEEEEeecCcEEE-------EEEcc----------CCCceEEEEE
Confidence 46778999999998876 44444 66666555533 33331 1222345888
Q ss_pred eccccce
Q 030849 157 TFDSLRL 163 (170)
Q Consensus 157 p~~~I~k 163 (170)
.|+||--
T Consensus 63 SYsDvLT 69 (76)
T PF06257_consen 63 SYSDVLT 69 (76)
T ss_dssp EHHHHHT
T ss_pred Eeehhcc
Confidence 8888753
No 33
>PRK00737 small nuclear ribonucleoprotein; Provisional
Probab=51.02 E-value=22 Score=24.17 Aligned_cols=32 Identities=22% Similarity=0.315 Sum_probs=24.4
Q ss_pred HHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 82 LELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 82 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
.-+.+++|+.|.|.+++ .....| +|.++|+.-
T Consensus 7 ~~L~~~~~k~V~V~lk~-------g~~~~G--~L~~~D~~m 38 (72)
T PRK00737 7 DVLNNALNSPVLVRLKG-------GREFRG--ELQGYDIHM 38 (72)
T ss_pred HHHHHhCCCEEEEEECC-------CCEEEE--EEEEEcccc
Confidence 34567899999999988 344556 899998863
No 34
>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=51.00 E-value=20 Score=28.69 Aligned_cols=61 Identities=10% Similarity=0.084 Sum_probs=38.6
Q ss_pred cCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCC-CCCCChHHHHhcCCCeEEEEEE
Q 030849 31 DRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVE-RVVRIPLELERFKDRAMYVKYV 97 (170)
Q Consensus 31 D~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGie-RpL~~~~~f~r~~G~~v~V~l~ 97 (170)
.-+|.|+-.....+.|.+..+-+ + . .....|++.|||=. ..-....+..++...+|.+...
T Consensus 5 ~i~G~I~~~~~~~l~~~l~~A~~--~---~-~~~i~l~inSPGG~v~~~~~I~~~i~~~~~pvv~~v~ 66 (172)
T cd07015 5 QIKGQITSYTYDQFDRYITIAEQ--D---N-AEAIIIELDTPGGRADAAGNIVQRIQQSKIPVIIYVY 66 (172)
T ss_pred EEeeEECHhHHHHHHHHHHHHhc--C---C-CCeEEEEEECCCCCHHHHHHHHHHHHhcCcCEEEEEe
Confidence 34466776666677777776644 2 2 26789999999965 4444455555666566655443
No 35
>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=50.71 E-value=17 Score=24.91 Aligned_cols=32 Identities=28% Similarity=0.426 Sum_probs=25.1
Q ss_pred HHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 82 LELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 82 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
.++..+++++|.|.+++ .....| +|.++|+--
T Consensus 3 ~~L~~~i~k~V~V~L~~-------g~~~~G--~L~~~D~~m 34 (72)
T cd01719 3 PELKKYMDKKLSLKLNG-------NRKVSG--ILRGFDPFM 34 (72)
T ss_pred hhhHHhCCCeEEEEECC-------CeEEEE--EEEEEcccc
Confidence 46788999999999988 444555 899998654
No 36
>PF10842 DUF2642: Protein of unknown function (DUF2642); InterPro: IPR020139 This entry contains proteins with no known function.
Probab=49.70 E-value=61 Score=22.14 Aligned_cols=32 Identities=13% Similarity=0.146 Sum_probs=26.0
Q ss_pred hHHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 81 PLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 81 ~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
.++++..+|+.+.|.+.. . ..+| +|.++..|.
T Consensus 13 yq~lq~liG~~vvV~T~~-------g-~v~G--~L~~V~pDh 44 (66)
T PF10842_consen 13 YQTLQSLIGQRVVVQTTR-------G-SVRG--ILVDVKPDH 44 (66)
T ss_pred HHHHHHhcCCEEEEEEcC-------C-cEEE--EEEeecCCE
Confidence 467889999999998855 1 2366 899999999
No 37
>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=47.59 E-value=22 Score=23.72 Aligned_cols=30 Identities=33% Similarity=0.480 Sum_probs=23.3
Q ss_pred HHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 84 LERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 84 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
++.++|+.|.|.+++ .....| +|.++|+--
T Consensus 5 L~~~~~~~V~V~l~~-------g~~~~G--~L~~~D~~m 34 (68)
T cd01731 5 LKDSLNKPVLVKLKG-------GKEVRG--RLKSYDQHM 34 (68)
T ss_pred HHHhcCCEEEEEECC-------CCEEEE--EEEEECCcc
Confidence 567799999999987 334455 899998864
No 38
>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=47.13 E-value=17 Score=23.77 Aligned_cols=31 Identities=23% Similarity=0.297 Sum_probs=24.3
Q ss_pred HHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 83 ELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 83 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
.++.++|++|.|.+.+ ....+| +|.++|+.-
T Consensus 2 ~L~~~~g~~V~V~l~~-------g~~~~G--~L~~~D~~~ 32 (67)
T PF01423_consen 2 FLQKLIGKRVRVELKN-------GRTYRG--TLVSFDQFM 32 (67)
T ss_dssp HHHHTTTSEEEEEETT-------SEEEEE--EEEEEETTE
T ss_pred hhHHhCCcEEEEEEeC-------CEEEEE--EEEEeechh
Confidence 3578899999999988 334455 999999864
No 39
>PRK09301 circadian clock protein KaiB; Provisional
Probab=46.30 E-value=60 Score=24.16 Aligned_cols=41 Identities=10% Similarity=0.156 Sum_probs=28.0
Q ss_pred eeEEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecC
Q 030849 22 LWLTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSP 72 (170)
Q Consensus 22 ~~~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSP 72 (170)
.|.||+| +-....-|..+.+.+.+.+ +.. .++.|.|||-=.
T Consensus 6 ~~~LrLy-Vag~tp~S~~ai~nL~~ic----E~~-----l~g~y~LeVIDv 46 (103)
T PRK09301 6 TYILKLY-VAGNTPNSVRALKTLKNIL----ETE-----FKGVYALKVIDV 46 (103)
T ss_pred eEEEEEE-EeCCCchHHHHHHHHHHHH----HHh-----cCCceEEEEEEc
Confidence 5789999 8776667776666655544 433 235699999754
No 40
>PRK11778 putative inner membrane peptidase; Provisional
Probab=46.18 E-value=19 Score=31.84 Aligned_cols=67 Identities=21% Similarity=0.172 Sum_probs=41.0
Q ss_pred EEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCC-----CCCChHHHHhcCCCeEEEEEE
Q 030849 26 QLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVER-----VVRIPLELERFKDRAMYVKYV 97 (170)
Q Consensus 26 rv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieR-----pL~~~~~f~r~~G~~v~V~l~ 97 (170)
+|+.|+-+|.|+-.....+.+.|.+.|.... +- ..-.|.+.|||-.= -......| |..|.+|.+...
T Consensus 91 ~v~VI~~~G~I~~~~~~~l~e~i~a~l~~A~---~~-~aVvLridSpGG~v~~s~~a~~~l~~l-r~~~kpVva~v~ 162 (330)
T PRK11778 91 RLFVLDFKGDIDASEVESLREEITAILAVAK---PG-DEVLLRLESPGGVVHGYGLAASQLQRL-RDAGIPLTVAVD 162 (330)
T ss_pred eEEEEEEEEEECCCcchhhHHHHHHHHHhcc---CC-CeEEEEEeCCCCchhHHHHHHHHHHHH-HhcCCCEEEEEC
Confidence 3443455555655555567788888887655 22 67899999999751 11112223 335778877653
No 41
>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=45.29 E-value=25 Score=24.55 Aligned_cols=29 Identities=17% Similarity=0.147 Sum_probs=23.7
Q ss_pred HhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 85 ERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 85 ~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
+...|+.|.|.++. ....+| +|.++|+--
T Consensus 7 ~~l~g~~V~VeLKn-------g~~~~G--~L~~vD~~M 35 (81)
T cd01725 7 KTLVGKEVTVELKN-------DLSIRG--TLHSVDQYL 35 (81)
T ss_pred HhCCCCEEEEEECC-------CcEEEE--EEEEECCCc
Confidence 78899999999998 445567 899998774
No 42
>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=45.03 E-value=25 Score=23.74 Aligned_cols=39 Identities=21% Similarity=0.240 Sum_probs=28.1
Q ss_pred HHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCcceEeeceeeeEE
Q 030849 84 LERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTWGLADVRI 134 (170)
Q Consensus 84 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~~~~~~~~~~v~i 134 (170)
+....|+.|.|.++. ....+| +|.++|+.- -..+.++..
T Consensus 5 L~~~~g~~V~VeLk~-------g~~~~G--~L~~~D~~M---Nl~L~~~~~ 43 (70)
T cd01721 5 LHEAEGHIVTVELKT-------GEVYRG--KLIEAEDNM---NCQLKDVTV 43 (70)
T ss_pred HhhCCCCEEEEEECC-------CcEEEE--EEEEEcCCc---eeEEEEEEE
Confidence 467899999999998 445667 899998853 334445543
No 43
>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=44.42 E-value=24 Score=22.55 Aligned_cols=29 Identities=17% Similarity=0.279 Sum_probs=22.7
Q ss_pred HhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 85 ERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 85 ~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
..++|+.|.|.+.+ .....| +|.++|+..
T Consensus 2 ~~~~g~~V~V~l~~-------g~~~~G--~L~~~D~~~ 30 (63)
T cd00600 2 KDLVGKTVRVELKD-------GRVLEG--VLVAFDKYM 30 (63)
T ss_pred hHHCCCEEEEEECC-------CcEEEE--EEEEECCCC
Confidence 35789999999988 334455 999999883
No 44
>COG1958 LSM1 Small nuclear ribonucleoprotein (snRNP) homolog [Transcription]
Probab=44.13 E-value=24 Score=24.22 Aligned_cols=31 Identities=26% Similarity=0.388 Sum_probs=23.6
Q ss_pred HHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 83 ELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 83 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
-+.+++|+.|.|.+++ .....| +|.++|..-
T Consensus 11 ~l~~~~~~~V~V~lk~-------g~~~~G--~L~~~D~~m 41 (79)
T COG1958 11 FLKKLLNKRVLVKLKN-------GREYRG--TLVGFDQYM 41 (79)
T ss_pred HHHHhhCCEEEEEECC-------CCEEEE--EEEEEccce
Confidence 3567788999999988 334455 999998874
No 45
>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=42.63 E-value=19 Score=29.29 Aligned_cols=22 Identities=18% Similarity=0.341 Sum_probs=17.7
Q ss_pred CCCCHHHHHHHHHHHHHhhhhh
Q 030849 34 GSPSMEDIEAFCTTYRARLDEA 55 (170)
Q Consensus 34 ~gvtlddC~~vSr~is~~LD~~ 55 (170)
+++||++|.++++.+...|-.+
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 5799999999999999988754
No 46
>smart00651 Sm snRNP Sm proteins. small nuclear ribonucleoprotein particles (snRNPs) involved in pre-mRNA splicing
Probab=42.51 E-value=28 Score=22.60 Aligned_cols=30 Identities=23% Similarity=0.328 Sum_probs=23.4
Q ss_pred HHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 84 LERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 84 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
+..++|+.|.|.+++ .....| +|.++|+..
T Consensus 3 L~~~~~~~V~V~l~~-------g~~~~G--~L~~~D~~~ 32 (67)
T smart00651 3 LKKLIGKRVLVELKN-------GREYRG--TLKGFDQFM 32 (67)
T ss_pred hHHhCCcEEEEEECC-------CcEEEE--EEEEECccc
Confidence 567899999999988 333455 899999763
No 47
>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=40.92 E-value=33 Score=23.53 Aligned_cols=30 Identities=20% Similarity=0.287 Sum_probs=24.0
Q ss_pred HHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 84 LERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 84 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
++...|+.|.|.++. ....+| +|.++|+.-
T Consensus 6 L~~~~g~~V~VeLkn-------g~~~~G--~L~~~D~~m 35 (76)
T cd01723 6 LKTAQNHPMLVELKN-------GETYNG--HLVNCDNWM 35 (76)
T ss_pred HHhcCCCEEEEEECC-------CCEEEE--EEEEEcCCC
Confidence 367899999999998 445566 899998863
No 48
>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=39.68 E-value=38 Score=23.40 Aligned_cols=32 Identities=16% Similarity=0.218 Sum_probs=24.5
Q ss_pred HHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 82 LELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 82 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
..+..++|+.|+|++.+ .....| +|..+|...
T Consensus 3 ~~L~~~l~~~v~V~l~d-------gR~~~G--~l~~~D~~~ 34 (75)
T cd06168 3 QKLRSLLGRTMRIHMTD-------GRTLVG--VFLCTDRDC 34 (75)
T ss_pred hHHHHhcCCeEEEEEcC-------CeEEEE--EEEEEcCCC
Confidence 35678899999999988 333444 888888775
No 49
>PF00788 RA: Ras association (RalGDS/AF-6) domain; InterPro: IPR000159 Proteins with this domain are mostly RasGTP effectors and include guanine-nucleotide releasing factor in mammals []. This factor stimulates the dissociation of GDP from the Ras-related RALA and RALB GTPases, which allows GTP binding and activation of the GTPases. It interacts and acts as an effector molecule for R-ras, K-Ras and Rap []. The domain is also present in a number of other proteins among them the sexual differentiation protein in yeast that is essential for mating and meiosis and yeast adenylate cyclase. These proteins contain repeated leucine-rich (LRR) segments.; GO: 0007165 signal transduction; PDB: 3EC8_A 2C5L_D 2BYF_A 2CS4_A 3KH0_A 2B3A_A 1RAX_A 2RGF_A 1WGR_A 1WXA_A ....
Probab=39.47 E-value=8.3 Score=26.32 Aligned_cols=57 Identities=12% Similarity=0.066 Sum_probs=34.1
Q ss_pred eEEEEEEEcCCC------CCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEE--EEecCCCCCCCCCh
Q 030849 23 WLTQLVACDRSG------SPSMEDIEAFCTTYRARLDEAEIAKSIPENTSL--EVSSPGVERVVRIP 81 (170)
Q Consensus 23 ~~lrv~~iD~~~------gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~L--EVSSPGieRpL~~~ 81 (170)
..|||| ..... .|.+.-...+...|..+|+.-.. ..-+..|.| ...++|.+|+|...
T Consensus 3 ~~lrVy-~~~~~~~~~~k~i~v~~~tTa~evi~~~l~k~~l-~~~~~~y~L~~~~~~~~~er~L~~~ 67 (93)
T PF00788_consen 3 GVLRVY-DGDGSPGSTYKTIKVSSSTTAREVIEMALEKFGL-AEDPSDYCLVEVEESGGEERPLDDD 67 (93)
T ss_dssp EEEEEE-ETTSSSCCSEEEEEEETTSBHHHHHHHHHHHTTT-SSSGGGEEEEEEECTTTEEEEETTT
T ss_pred eEEEEE-cCCCCCCccEEEEEECCCCCHHHHHHHHHHHhCC-CCCCCCEEEEEEEcCCCEEEEcCCC
Confidence 357787 43321 14444444555555555554431 023578999 89999999988754
No 50
>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=39.27 E-value=39 Score=26.98 Aligned_cols=60 Identities=10% Similarity=0.031 Sum_probs=35.0
Q ss_pred cCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCC-CCCCChHHHHhcCCCeEEEEE
Q 030849 31 DRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVE-RVVRIPLELERFKDRAMYVKY 96 (170)
Q Consensus 31 D~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGie-RpL~~~~~f~r~~G~~v~V~l 96 (170)
+-+|.|+-.....+.|.|..+.+. + .....|++.|||=. ......-+..+....++.+..
T Consensus 5 ~i~g~I~~~~~~~l~~~l~~a~~~-----~-~~~ivl~inspGG~v~~~~~I~~~l~~~~~pvva~V 65 (178)
T cd07021 5 PIEGEIDPGLAAFVERALKEAKEE-----G-ADAVVLDIDTPGGRVDSALEIVDLILNSPIPTIAYV 65 (178)
T ss_pred EEeeEECHHHHHHHHHHHHHHHhC-----C-CCeEEEEEECcCCCHHHHHHHHHHHHhCCCCEEEEE
Confidence 334667776666677766666442 2 36789999999955 233333333334445554444
No 51
>PTZ00198 60S ribosomal protein L22; Provisional
Probab=38.20 E-value=66 Score=24.69 Aligned_cols=32 Identities=16% Similarity=0.218 Sum_probs=28.9
Q ss_pred CCeEEEEecCCCCCCCCChHHHHhcCCCeEEEE
Q 030849 63 ENTSLEVSSPGVERVVRIPLELERFKDRAMYVK 95 (170)
Q Consensus 63 ~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~ 95 (170)
-.|++..|.| ++--+..+.+|++|+-..++|.
T Consensus 19 ~kF~IDCt~P-veD~I~d~a~fekfL~erIKV~ 50 (122)
T PTZ00198 19 KKFKIDCTIP-AEDGIIDLSGFEQFLQDRIKVD 50 (122)
T ss_pred eEEEEEcCCc-ccCCcccHHHHHHHHHHhEEEC
Confidence 5799999999 8888899999999999999994
No 52
>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=37.54 E-value=31 Score=30.24 Aligned_cols=23 Identities=22% Similarity=0.361 Sum_probs=20.1
Q ss_pred CCCCCHHHHHHHHHHHHHhhhhh
Q 030849 33 SGSPSMEDIEAFCTTYRARLDEA 55 (170)
Q Consensus 33 ~~gvtlddC~~vSr~is~~LD~~ 55 (170)
=+++|+|+|.++++.+...+-.+
T Consensus 96 l~~~t~eec~~lA~~vg~~i~~~ 118 (298)
T TIGR02024 96 VRNVTMEECVELAKEFGKRLGEE 118 (298)
T ss_pred CCCCCHHHHHHHHHHHHHHHHHh
Confidence 36899999999999999888754
No 53
>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=37.51 E-value=40 Score=23.39 Aligned_cols=44 Identities=23% Similarity=0.267 Sum_probs=30.5
Q ss_pred ChHHH-HhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCcceEeeceeeeEEe
Q 030849 80 IPLEL-ERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETECCTWGLADVRIN 135 (170)
Q Consensus 80 ~~~~f-~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~~~~~~~~~~v~i~ 135 (170)
++-.| +...|+.|.|.++. ....+| +|.++|+.- -..+.++++.
T Consensus 9 tl~~~L~~l~g~~V~VeLKn-------g~~~~G--~L~~vD~~M---Nl~L~~~~~~ 53 (78)
T cd01733 9 TLIILLQGLQGKVVTVELRN-------ETTVTG--RIASVDAFM---NIRLAKVTII 53 (78)
T ss_pred hHHHHHHHCCCCEEEEEECC-------CCEEEE--EEEEEcCCc---eeEEEEEEEE
Confidence 34445 77899999999998 445666 899998774 3345555543
No 54
>COG1481 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.66 E-value=50 Score=29.13 Aligned_cols=59 Identities=19% Similarity=0.032 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChHHHHhcCCCeEEEEEE
Q 030849 38 MEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPLELERFKDRAMYVKYV 97 (170)
Q Consensus 38 lddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~~f~r~~G~~v~V~l~ 97 (170)
-|+|..-+-..++.|-.=...+|....|.||+|||+-+--+. .....+..|..+++.-+
T Consensus 116 ~~~~~~~~ylrGAFLagGSis~Pe~~~YhLEi~s~~ee~a~~-L~~l~~~f~l~ak~~er 174 (308)
T COG1481 116 SDDEDFRAYLRGAFLAGGSISDPETSSYHLEISSNYEEHALA-LVKLLRRFGLNAKIIER 174 (308)
T ss_pred ccHHHHHHHHHHHHHcCCccCCCCCCceeEEEecCcHHHHHH-HHHHHHHhccchheeee
Confidence 478888888888988733222377789999999999984433 33444455666555443
No 55
>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=35.74 E-value=43 Score=23.95 Aligned_cols=30 Identities=10% Similarity=0.227 Sum_probs=24.1
Q ss_pred HHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 84 LERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 84 f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
++...|+.|.|.++. ....+| +|.++|+.-
T Consensus 6 L~~l~g~~V~VeLKn-------g~~~~G--~L~~vD~~M 35 (90)
T cd01724 6 LMKLTNETVTIELKN-------GTIVHG--TITGVDPSM 35 (90)
T ss_pred HHhCCCCEEEEEECC-------CCEEEE--EEEEEcCce
Confidence 478899999999998 445566 899998774
No 56
>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=35.30 E-value=46 Score=22.92 Aligned_cols=32 Identities=25% Similarity=0.106 Sum_probs=25.1
Q ss_pred HHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 82 LELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 82 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
..+..++++.|.|.+++ .....| +|.++|...
T Consensus 5 ~~L~~~l~k~v~V~l~~-------gr~~~G--~L~~fD~~~ 36 (74)
T cd01728 5 ASLVDDLDKKVVVLLRD-------GRKLIG--ILRSFDQFA 36 (74)
T ss_pred HHHHHhcCCEEEEEEcC-------CeEEEE--EEEEECCcc
Confidence 46788999999999988 333444 999999774
No 57
>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=34.09 E-value=44 Score=22.98 Aligned_cols=31 Identities=13% Similarity=0.257 Sum_probs=23.9
Q ss_pred HHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 83 ELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 83 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
.+..++|+.|.|++++ .....| +|.++|...
T Consensus 4 ~l~~~l~~~V~V~l~d-------gR~~~G--~L~~~D~~~ 34 (79)
T cd01717 4 KMLQLINYRLRVTLQD-------GRQFVG--QFLAFDKHM 34 (79)
T ss_pred hhHHHcCCEEEEEECC-------CcEEEE--EEEEEcCcc
Confidence 4678899999999988 333344 899998775
No 58
>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=33.59 E-value=53 Score=22.72 Aligned_cols=31 Identities=23% Similarity=0.354 Sum_probs=23.4
Q ss_pred HH-HhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 83 EL-ERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 83 ~f-~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
+| .+++++.|.|++++ .....| +|.++|.--
T Consensus 6 ~~L~~~~~~~V~V~l~~-------gr~~~G--~L~g~D~~m 37 (76)
T cd01732 6 ELIDKCIGSRIWIVMKS-------DKEFVG--TLLGFDDYV 37 (76)
T ss_pred HHHHHhCCCEEEEEECC-------CeEEEE--EEEEeccce
Confidence 44 67899999999988 333444 899998764
No 59
>PF06649 DUF1161: Protein of unknown function (DUF1161); InterPro: IPR010595 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=31.47 E-value=55 Score=21.49 Aligned_cols=28 Identities=11% Similarity=0.182 Sum_probs=22.0
Q ss_pred HHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCC
Q 030849 41 IEAFCTTYRARLDEAEIAKSIPENTSLEVSSPG 73 (170)
Q Consensus 41 C~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPG 73 (170)
|+.+-..|.+.+.... . ..|+|||=.-+
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 7888888888888775 3 88999986544
No 60
>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=29.29 E-value=1.5e+02 Score=21.30 Aligned_cols=42 Identities=19% Similarity=0.066 Sum_probs=28.5
Q ss_pred CCCCChHHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCcce
Q 030849 76 RVVRIPLELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMETEC 124 (170)
Q Consensus 76 RpL~~~~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~~~ 124 (170)
+|.-..+++.+|+|+.|++--+-. ..++. .+.+.+.|+..++
T Consensus 2 ~prVn~~~L~~f~gk~V~ivGkV~------~~~~~-~~~~~~~Dg~~v~ 43 (101)
T cd04479 2 TPRINGAMLSQFVGKTVRIVGKVE------KVDGD-SLTLISSDGVNVT 43 (101)
T ss_pred CceeCHHHHHhhCCCEEEEEEEEE------EecCC-eEEEEcCCCCEEE
Confidence 566778899999999999976552 22233 3467776665544
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=29.06 E-value=67 Score=22.29 Aligned_cols=31 Identities=35% Similarity=0.512 Sum_probs=22.9
Q ss_pred HH-HhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 83 EL-ERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 83 ~f-~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
+| +.++++.|.|.+++ ..+..| +|.++|.--
T Consensus 4 ~~l~~~~~k~V~V~l~~-------gr~~~G--~L~~fD~~m 35 (82)
T cd01730 4 DLIRLSLDERVYVKLRG-------DRELRG--RLHAYDQHL 35 (82)
T ss_pred HHHHHhCCCEEEEEECC-------CCEEEE--EEEEEccce
Confidence 44 66799999999988 333444 899998764
No 62
>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=29.05 E-value=62 Score=21.94 Aligned_cols=31 Identities=29% Similarity=0.343 Sum_probs=23.6
Q ss_pred HHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 83 ELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 83 ~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
.+..++++.|.|++.+ .....| +|..+|...
T Consensus 3 ~L~~~l~~~V~V~l~d-------gr~~~G--~L~~~D~~~ 33 (74)
T cd01727 3 TLEDYLNKTVSVITVD-------GRVIVG--TLKGFDQAT 33 (74)
T ss_pred hHHHhcCCEEEEEECC-------CcEEEE--EEEEEcccc
Confidence 4678899999999987 333445 899998764
No 63
>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=26.51 E-value=87 Score=26.70 Aligned_cols=27 Identities=19% Similarity=0.091 Sum_probs=23.7
Q ss_pred EcCCCCCCHHHHHHHHHHHHHhhhhhh
Q 030849 30 CDRSGSPSMEDIEAFCTTYRARLDEAE 56 (170)
Q Consensus 30 iD~~~gvtlddC~~vSr~is~~LD~~d 56 (170)
.|...+++.++|.++++.+.++||+..
T Consensus 121 LDP~~~~~f~~v~~~A~~~r~~L~~lg 147 (245)
T TIGR02778 121 LDPGPGVAWKLVVEAAQLIRELLDELG 147 (245)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 456667999999999999999999876
No 64
>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=26.11 E-value=1.2e+02 Score=21.43 Aligned_cols=34 Identities=9% Similarity=0.087 Sum_probs=21.7
Q ss_pred HHHHhcCCCeEEEEEEeccccCCCCCCCCceEEEEEEcCCc
Q 030849 82 LELERFKDRAMYVKYVGETVTTGSPSESDGVFRLISFDMET 122 (170)
Q Consensus 82 ~~f~r~~G~~v~V~l~~~~~~~~~~~~~~~~f~L~~vd~~~ 122 (170)
+-+....|++|.+++++ .....+.|.-.+.+...
T Consensus 17 r~l~~~~gk~v~f~l~e-------~t~V~a~F~a~d~~~~~ 50 (80)
T PF11095_consen 17 RSLLAMVGKPVEFTLHE-------NTTVSARFGACDIDVSN 50 (80)
T ss_dssp HHHHHCTTSEEEEEEGG-------G-EEEEEEEEE-TTS-E
T ss_pred HHHHHhcCCceEEEEeC-------CeEEEEEEEEecCchhe
Confidence 45667889999999999 44567755444444444
No 65
>PF15121 TMEM71: TMEM71 protein family
Probab=25.60 E-value=42 Score=26.35 Aligned_cols=34 Identities=21% Similarity=0.492 Sum_probs=27.6
Q ss_pred cccccccccCCcceeEEEEEEEcCCCCCCHHHHH
Q 030849 9 LKHRNRVLNNKMPLWLTQLVACDRSGSPSMEDIE 42 (170)
Q Consensus 9 ~~~~~~~~~~g~~~~~lrv~~iD~~~gvtlddC~ 42 (170)
-..+|+...+||-.|.=-=|..|+||-|||.=|.
T Consensus 58 CRRSPRLLtNGYYi~TEDSFl~D~dGNITLsPsq 91 (149)
T PF15121_consen 58 CRRSPRLLTNGYYIWTEDSFLCDEDGNITLSPSQ 91 (149)
T ss_pred cccCchhhcCccEEEeccceeecCCCCEeecCcc
Confidence 4568999999999998765548999989987663
No 66
>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=24.67 E-value=1e+02 Score=25.97 Aligned_cols=64 Identities=13% Similarity=0.048 Sum_probs=39.9
Q ss_pred EcCCCCCCHHHHHHHHHHHHHhhhhhhhcCC--CCCCeEEEEecCCC--CCCCCChHHHHhcCCCeEE
Q 030849 30 CDRSGSPSMEDIEAFCTTYRARLDEAEIAKS--IPENTSLEVSSPGV--ERVVRIPLELERFKDRAMY 93 (170)
Q Consensus 30 iD~~~gvtlddC~~vSr~is~~LD~~d~~~~--i~~~Y~LEVSSPGi--eRpL~~~~~f~r~~G~~v~ 93 (170)
.|...+++.++|.++.+.+.++|++...... -++.=-|=|=-|=- .......+.|.+++.+.+.
T Consensus 100 LDP~~~~~f~~v~~~A~~vr~~L~~lgL~~f~KTSG~kGlHV~vPl~~~~~~~~~~r~fa~~iA~~l~ 167 (223)
T cd04866 100 LDPPSRDHFSLAVEAANLLKEILDALGLTSFVKTSGNKGLQVYIPLPDNKFTYDETRLFTEFIAEYLC 167 (223)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHcCCccceEccCCCeEEEEEEcCCCCCCHHHHHHHHHHHHHHHH
Confidence 4666689999999999999999998762100 11333344444422 2334456667766666554
No 67
>cd04864 LigD_Pol_like_1 LigD_Pol_like_1: Polymerase (Pol) domain of mostly bacterial LigD proteins similar to Pseudomonas aeruginosa (Pae) LigD, subgroup 1. 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=24.40 E-value=1.2e+02 Score=25.68 Aligned_cols=26 Identities=27% Similarity=0.316 Sum_probs=22.3
Q ss_pred EcCCCCCCHHHHHHHHHHHHHhhhhhh
Q 030849 30 CDRSGSPSMEDIEAFCTTYRARLDEAE 56 (170)
Q Consensus 30 iD~~~gvtlddC~~vSr~is~~LD~~d 56 (170)
.|.. +.+..+|.++.+.+..+|++..
T Consensus 107 LDP~-~~~f~~v~~~A~~~r~~L~~~g 132 (228)
T cd04864 107 LDPS-ADDIEAVRTAALAVRELLDELG 132 (228)
T ss_pred cCCC-CCCHHHHHHHHHHHHHHHHHcC
Confidence 3444 7799999999999999999876
No 68
>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=23.78 E-value=53 Score=24.44 Aligned_cols=16 Identities=38% Similarity=0.372 Sum_probs=13.0
Q ss_pred CCCCCeEEEEecCCCC
Q 030849 60 SIPENTSLEVSSPGVE 75 (170)
Q Consensus 60 ~i~~~Y~LEVSSPGie 75 (170)
.-++.|.|||.||...
T Consensus 37 Vp~GsY~L~V~s~~~~ 52 (123)
T PF09430_consen 37 VPPGSYLLEVHSPDYV 52 (123)
T ss_pred CCCceEEEEEECCCcc
Confidence 3458999999999864
No 69
>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=23.46 E-value=1e+02 Score=26.32 Aligned_cols=69 Identities=10% Similarity=0.147 Sum_probs=53.8
Q ss_pred ccccccccCCccee-------EEEEEEEcCCCCCCHHHHHHHHHHHHHhhhhhhhcCCCCCCeEEEEecCCCCCCCCChH
Q 030849 10 KHRNRVLNNKMPLW-------LTQLVACDRSGSPSMEDIEAFCTTYRARLDEAEIAKSIPENTSLEVSSPGVERVVRIPL 82 (170)
Q Consensus 10 ~~~~~~~~~g~~~~-------~lrv~~iD~~~gvtlddC~~vSr~is~~LD~~d~~~~i~~~Y~LEVSSPGieRpL~~~~ 82 (170)
--|.+.+++|++.+ .|.|| +--....+-+++-.+++.|...|.... |+-|+. +
T Consensus 138 ~~r~~L~~lgL~~f~KTSG~kGlHV~-vPl~~~~~~~~~r~fa~~iA~~l~~~~-----Pd~~t~--------------~ 197 (245)
T TIGR02778 138 LIRELLDELGLESFVKTSGGKGLHVY-VPLRPTLSWDEVKDFAKALAQALAQQM-----PDRFTA--------------E 197 (245)
T ss_pred HHHHHHHHcCCccceEccCCCeEEEE-EECCCCCCHHHHHHHHHHHHHHHHHHC-----chhhhh--------------H
Confidence 34677888999866 58999 877778999999999999999999775 355444 4
Q ss_pred HHHhcCCCeEEEEEEe
Q 030849 83 ELERFKDRAMYVKYVG 98 (170)
Q Consensus 83 ~f~r~~G~~v~V~l~~ 98 (170)
-.+...|.+|.|-+.+
T Consensus 198 ~~k~~R~gkvfiDylq 213 (245)
T TIGR02778 198 MSKKNRVGKIFVDYLR 213 (245)
T ss_pred hhHHhCCCCEEEECcc
Confidence 4567777888887766
No 70
>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=23.46 E-value=1.1e+02 Score=25.83 Aligned_cols=27 Identities=30% Similarity=0.305 Sum_probs=23.6
Q ss_pred EcCCCCCCHHHHHHHHHHHHHhhhhhh
Q 030849 30 CDRSGSPSMEDIEAFCTTYRARLDEAE 56 (170)
Q Consensus 30 iD~~~gvtlddC~~vSr~is~~LD~~d 56 (170)
.|...+++.++|.++.+.+...||+..
T Consensus 106 LDP~~~~~f~~v~~~A~~vr~~L~~lg 132 (228)
T cd04865 106 LDPQPGTSFEDVVEVALLVREVLDELG 132 (228)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 455568999999999999999999876
No 71
>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=21.66 E-value=1.3e+02 Score=25.51 Aligned_cols=64 Identities=14% Similarity=0.094 Sum_probs=37.8
Q ss_pred EcCCCCCCHHHHHHHHHHHHHhhhhhhhcCC--CCCCeEEEEecCCC-CCCCCChHHHHhcCCCeEE
Q 030849 30 CDRSGSPSMEDIEAFCTTYRARLDEAEIAKS--IPENTSLEVSSPGV-ERVVRIPLELERFKDRAMY 93 (170)
Q Consensus 30 iD~~~gvtlddC~~vSr~is~~LD~~d~~~~--i~~~Y~LEVSSPGi-eRpL~~~~~f~r~~G~~v~ 93 (170)
.|...+++.++|.++++.+.++||+...... -++.=-|=|=-|=- .......+.|.+++.+.+.
T Consensus 109 LDP~~~~~f~~v~~~A~~~r~~L~~lgL~s~~KTSG~kGlHV~vPl~~~~~~~~vr~fa~~~A~~l~ 175 (231)
T cd04863 109 LDPGEPAGLVECARVALWLRDRLAALGLASFPKTSGSKGLHLYVPLDGPVSSDQTKEFAKALARELE 175 (231)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHcCCccceECCCCCeEEEEEEcCCCCCHHHHHHHHHHHHHHHH
Confidence 4666789999999999999999998762100 11222333333311 1223344666666665543
No 72
>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=21.17 E-value=1.8e+02 Score=24.52 Aligned_cols=27 Identities=19% Similarity=0.107 Sum_probs=23.7
Q ss_pred EcCCCCCCHHHHHHHHHHHHHhhhhhh
Q 030849 30 CDRSGSPSMEDIEAFCTTYRARLDEAE 56 (170)
Q Consensus 30 iD~~~gvtlddC~~vSr~is~~LD~~d 56 (170)
.|...+++.++|.++.+.+.++|++..
T Consensus 105 LDP~~~~~f~~v~~~A~~~r~~L~~lg 131 (227)
T cd04862 105 LDPGPGVPWKAVVEAALLVRELLDELG 131 (227)
T ss_pred CCCCCCCCHHHHHHHHHHHHHHHHHcC
Confidence 456667999999999999999999776
No 73
>PF14153 Spore_coat_CotO: Spore coat protein CotO
Probab=20.76 E-value=2.1e+02 Score=23.24 Aligned_cols=34 Identities=15% Similarity=0.304 Sum_probs=23.7
Q ss_pred EEEEEcCCcceEeeceeeeEEeecccCCCCCCcccccceeEEeeccccceeEEE
Q 030849 114 RLISFDMETECCTWGLADVRINREKAGKGRPLSKKQREWRLNTTFDSLRLVRLH 167 (170)
Q Consensus 114 ~L~~vd~~~~~~~~~~~~v~i~~~k~~Kgk~~~~~~~~~~v~ip~~~I~karL~ 167 (170)
.|.+.+++. |.+... .... .+.|+|++|...++.
T Consensus 150 ~I~~~~~~~---------v~i~~~---------~~~~--~~~i~~~~I~sI~~i 183 (185)
T PF14153_consen 150 IILSYDEGE---------VSIMPF---------NQGE--EIEIPIDDITSIKMI 183 (185)
T ss_pred EEEeccCCE---------EEEecc---------CCCc--ceEeehhheeeeeec
Confidence 899999888 666521 0111 278999999988763
No 74
>PF11211 DUF2997: Protein of unknown function (DUF2997); InterPro: IPR021375 This family of proteins has no known function.
Probab=20.57 E-value=1.1e+02 Score=19.46 Aligned_cols=29 Identities=7% Similarity=-0.017 Sum_probs=21.6
Q ss_pred EEEEEcCCC-------CCCHHHHHHHHHHHHHhhhhh
Q 030849 26 QLVACDRSG-------SPSMEDIEAFCTTYRARLDEA 55 (170)
Q Consensus 26 rv~~iD~~~-------gvtlddC~~vSr~is~~LD~~ 55 (170)
++. |++|| |+.=..|..+++.|.++|...
T Consensus 2 ~~~-I~~dG~V~~~v~G~~G~~C~~~t~~lE~~LG~v 37 (48)
T PF11211_consen 2 EFT-IYPDGRVEEEVEGFKGSSCLEATAALEEALGTV 37 (48)
T ss_pred EEE-ECCCcEEEEEEEeccChhHHHHHHHHHHHhCce
Confidence 344 56664 455679999999999999754
No 75
>PF13749 HATPase_c_4: ATP-dependent DNA helicase recG C-terminal; PDB: 3LMM_D.
Probab=20.34 E-value=47 Score=23.09 Aligned_cols=18 Identities=22% Similarity=0.112 Sum_probs=10.1
Q ss_pred EEEEecCCCCCCCCChHH
Q 030849 66 SLEVSSPGVERVVRIPLE 83 (170)
Q Consensus 66 ~LEVSSPGieRpL~~~~~ 83 (170)
.+|++|||-=.+=.++++
T Consensus 12 riei~nPG~l~~~~t~~~ 29 (89)
T PF13749_consen 12 RIEISNPGGLPGGVTIEN 29 (89)
T ss_dssp EEEEEEES---TT--TTT
T ss_pred EEEEEcCCcCCCCCCHHH
Confidence 699999997765555554
Done!