Query 038833
Match_columns 120
No_of_seqs 103 out of 219
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 03:47:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/038833.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/038833hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG4315 G-patch nucleic acid b 99.8 6.1E-20 1.3E-24 153.9 1.3 100 16-119 332-445 (455)
2 KOG2837 Protein containing a U 99.2 1.6E-13 3.4E-18 110.6 -6.6 54 23-82 247-309 (309)
3 KOG1999 RNA polymerase II tran 97.9 5.8E-06 1.3E-10 75.9 2.8 96 16-119 916-1021(1024)
4 PF00467 KOW: KOW motif; Inte 97.8 5.2E-05 1.1E-09 42.5 4.1 30 67-96 1-31 (32)
5 smart00739 KOW KOW (Kyprides, 97.4 0.0004 8.6E-09 36.7 3.9 26 65-90 2-28 (28)
6 PRK12281 rplX 50S ribosomal pr 97.2 0.00075 1.6E-08 45.1 4.9 32 66-97 8-40 (76)
7 CHL00141 rpl24 ribosomal prote 97.2 0.00074 1.6E-08 45.8 4.9 31 66-96 10-41 (83)
8 TIGR00405 L26e_arch ribosomal 97.1 0.0018 4E-08 46.9 6.2 50 65-118 87-139 (145)
9 PRK00004 rplX 50S ribosomal pr 96.9 0.0021 4.5E-08 45.2 4.9 32 66-97 6-38 (105)
10 TIGR01079 rplX_bact ribosomal 96.7 0.004 8.6E-08 43.8 4.8 32 66-97 5-37 (104)
11 PRK08559 nusG transcription an 96.6 0.0087 1.9E-07 44.2 6.4 49 65-117 95-146 (153)
12 TIGR00922 nusG transcription t 96.5 0.01 2.2E-07 43.9 6.4 49 66-116 121-170 (172)
13 TIGR01080 rplX_A_E ribosomal p 96.5 0.0056 1.2E-07 43.9 4.7 31 66-96 43-74 (114)
14 PRK01191 rpl24p 50S ribosomal 96.5 0.0064 1.4E-07 44.0 5.1 31 66-96 47-78 (120)
15 PRK05609 nusG transcription an 96.4 0.012 2.5E-07 43.7 6.4 53 65-119 127-180 (181)
16 PTZ00194 60S ribosomal protein 96.4 0.0066 1.4E-07 45.2 4.7 32 66-97 48-80 (143)
17 COG0250 NusG Transcription ant 96.2 0.017 3.6E-07 44.1 6.1 55 63-119 122-177 (178)
18 PRK09014 rfaH transcriptional 95.3 0.055 1.2E-06 39.7 5.8 51 65-118 110-161 (162)
19 TIGR01955 RfaH transcriptional 95.2 0.062 1.4E-06 39.0 5.8 34 66-100 110-144 (159)
20 COG0198 RplX Ribosomal protein 94.9 0.058 1.3E-06 38.2 4.6 29 66-96 6-35 (104)
21 TIGR01956 NusG_myco NusG famil 94.7 0.12 2.6E-06 41.8 6.5 50 65-116 206-256 (258)
22 PF15591 Imm17: Immunity prote 91.8 0.27 5.9E-06 32.8 3.6 28 23-50 10-37 (74)
23 PF11623 DUF3252: Protein of u 90.8 0.74 1.6E-05 28.9 4.6 41 18-61 2-53 (53)
24 COG5164 SPT5 Transcription elo 90.7 0.33 7.2E-06 42.7 4.0 42 58-101 341-387 (607)
25 PRK04313 30S ribosomal protein 86.6 2.9 6.4E-05 33.5 6.6 46 52-97 158-209 (237)
26 PLN00036 40S ribosomal protein 86.3 3.4 7.3E-05 33.6 6.8 37 52-88 161-199 (261)
27 COG1471 RPS4A Ribosomal protei 85.7 3 6.4E-05 33.6 6.1 49 52-100 160-212 (241)
28 KOG1999 RNA polymerase II tran 82.7 4.6 9.9E-05 38.3 6.8 69 18-91 408-487 (1024)
29 PTZ00118 40S ribosomal protein 82.2 6.6 0.00014 31.9 6.9 38 52-89 161-200 (262)
30 PRK04333 50S ribosomal protein 81.7 5.6 0.00012 26.9 5.4 26 66-91 5-31 (84)
31 PTZ00065 60S ribosomal protein 81.4 4.9 0.00011 29.5 5.3 46 67-116 10-57 (130)
32 PTZ00223 40S ribosomal protein 81.1 5.2 0.00011 32.7 5.9 38 52-89 158-197 (273)
33 smart00333 TUDOR Tudor domain. 78.9 11 0.00024 22.3 5.7 51 64-119 2-53 (57)
34 TIGR00739 yajC preprotein tran 75.5 8.7 0.00019 25.8 4.8 30 66-100 39-68 (84)
35 cd01734 YlxS_C YxlS is a Bacil 71.1 16 0.00034 24.0 5.2 49 66-118 23-76 (83)
36 PRK05585 yajC preprotein trans 68.5 15 0.00032 25.8 4.9 30 66-100 54-83 (106)
37 KOG1708 Mitochondrial/chloropl 68.0 9.1 0.0002 30.5 4.0 32 66-97 74-106 (236)
38 PRK04950 ProP expression regul 67.4 15 0.00033 29.1 5.2 43 66-116 168-211 (213)
39 PLN00045 photosystem I reactio 66.8 11 0.00024 26.5 3.8 41 60-100 35-81 (101)
40 PRK06531 yajC preprotein trans 66.0 19 0.00042 25.6 5.1 30 66-98 38-67 (113)
41 PRK05886 yajC preprotein trans 64.7 19 0.00041 25.6 4.8 30 66-100 40-69 (109)
42 PTZ00471 60S ribosomal protein 60.6 11 0.00024 27.8 3.1 25 66-90 6-31 (134)
43 COG1862 YajC Preprotein transl 59.3 27 0.00059 24.3 4.7 30 66-100 45-74 (97)
44 PRK14633 hypothetical protein; 57.8 31 0.00066 25.4 5.1 46 67-119 93-143 (150)
45 PRK08559 nusG transcription an 57.2 31 0.00067 25.2 5.1 28 18-50 95-122 (153)
46 COG1096 Predicted RNA-binding 57.0 92 0.002 24.3 8.9 73 19-91 9-91 (188)
47 COG2163 RPL14A Ribosomal prote 56.4 17 0.00038 26.4 3.5 26 66-91 6-32 (125)
48 PRK14639 hypothetical protein; 55.3 43 0.00093 24.4 5.5 48 65-118 85-133 (140)
49 PF14505 DUF4438: Domain of un 52.6 15 0.00033 29.8 2.9 34 67-100 60-94 (258)
50 PF02576 DUF150: Uncharacteris 51.4 43 0.00092 24.0 4.9 49 67-119 86-139 (141)
51 PRK14637 hypothetical protein; 50.6 56 0.0012 24.2 5.5 44 67-119 97-143 (151)
52 PRK14630 hypothetical protein; 50.5 56 0.0012 23.9 5.5 45 66-119 95-140 (143)
53 TIGR00405 L26e_arch ribosomal 50.3 37 0.00081 24.2 4.5 30 16-50 85-114 (145)
54 PF08863 YolD: YolD-like prote 49.3 32 0.0007 22.2 3.7 40 74-118 52-91 (92)
55 PRK14636 hypothetical protein; 49.1 62 0.0014 24.5 5.7 47 66-119 96-147 (176)
56 PF08141 SspH: Small acid-solu 48.2 52 0.0011 20.8 4.3 37 77-116 20-56 (58)
57 TIGR02861 SASP_H small acid-so 47.5 54 0.0012 20.8 4.3 37 77-116 20-56 (58)
58 PF02427 PSI_PsaE: Photosystem 47.1 76 0.0017 20.4 5.6 52 65-116 1-57 (61)
59 PRK14631 hypothetical protein; 44.7 75 0.0016 24.1 5.5 49 66-119 115-168 (174)
60 PRK14638 hypothetical protein; 44.4 62 0.0014 23.8 4.9 45 66-118 98-143 (150)
61 PF02736 Myosin_N: Myosin N-te 43.9 63 0.0014 18.6 5.9 37 72-115 6-42 (42)
62 TIGR01955 RfaH transcriptional 43.8 42 0.00091 24.0 3.9 31 15-50 106-136 (159)
63 PF03947 Ribosomal_L2_C: Ribos 43.3 50 0.0011 23.9 4.2 34 77-117 34-67 (130)
64 PRK14640 hypothetical protein; 42.0 75 0.0016 23.4 5.1 46 66-119 95-145 (152)
65 PF12701 LSM14: Scd6-like Sm d 41.9 78 0.0017 21.8 4.8 33 64-96 4-37 (96)
66 PF14444 S1-like: S1-like 41.7 65 0.0014 20.5 4.0 32 40-71 5-40 (58)
67 PRK09014 rfaH transcriptional 40.3 53 0.0011 23.8 4.0 29 17-50 109-137 (162)
68 COG5164 SPT5 Transcription elo 37.2 53 0.0011 29.4 4.1 25 67-91 142-167 (607)
69 TIGR00922 nusG transcription t 37.0 60 0.0013 23.6 3.9 30 14-48 116-145 (172)
70 PRK14647 hypothetical protein; 36.8 97 0.0021 22.9 5.0 47 66-119 97-153 (159)
71 PRK14645 hypothetical protein; 36.6 87 0.0019 23.2 4.7 44 66-118 100-144 (154)
72 COG2139 RPL21A Ribosomal prote 36.1 1E+02 0.0022 21.7 4.6 47 66-116 34-91 (98)
73 COG0779 Uncharacterized protei 35.9 1.2E+02 0.0025 22.8 5.3 44 67-118 98-146 (153)
74 TIGR02760 TraI_TIGR conjugativ 35.6 2.6E+02 0.0057 28.8 9.0 79 16-100 680-786 (1960)
75 PTZ00180 60S ribosomal protein 33.8 75 0.0016 25.9 4.2 35 78-117 130-164 (260)
76 PRK03174 sspH acid-soluble spo 33.5 1.1E+02 0.0024 19.5 4.1 37 77-116 20-56 (59)
77 PF15436 PGBA_N: Plasminogen-b 33.4 63 0.0014 25.6 3.7 55 33-89 40-102 (218)
78 TIGR02594 conserved hypothetic 33.2 1.6E+02 0.0035 21.0 5.5 43 64-109 73-115 (129)
79 KOG3421 60S ribosomal protein 33.1 51 0.0011 24.4 2.9 25 67-91 9-34 (136)
80 PRK01625 sspH acid-soluble spo 32.1 1.2E+02 0.0025 19.3 4.1 37 77-116 20-56 (59)
81 cd06553 ASCH_Ef3133_like ASC-1 31.8 87 0.0019 22.5 3.9 34 64-117 42-76 (127)
82 PRK00092 ribosome maturation p 31.4 1.3E+02 0.0028 21.9 4.9 48 65-118 95-147 (154)
83 PF11948 DUF3465: Protein of u 31.2 1.8E+02 0.0038 21.5 5.4 55 20-77 42-98 (131)
84 PRK02749 photosystem I reactio 31.2 1.1E+02 0.0023 20.3 3.8 35 66-100 4-43 (71)
85 PRK02001 hypothetical protein; 31.0 1.9E+02 0.004 21.5 5.7 50 66-118 88-147 (152)
86 PRK00409 recombination and DNA 30.5 1.1E+02 0.0024 28.3 5.2 44 65-118 637-681 (782)
87 PRK04914 ATP-dependent helicas 30.3 3.7E+02 0.0081 25.7 8.7 52 40-95 18-81 (956)
88 CHL00125 psaE photosystem I su 30.1 1.2E+02 0.0025 19.8 3.8 35 66-100 3-42 (64)
89 COG1047 SlpA FKBP-type peptidy 29.7 1.7E+02 0.0037 22.4 5.4 54 52-108 77-131 (174)
90 PRK14632 hypothetical protein; 29.7 1.7E+02 0.0037 22.0 5.4 50 66-118 96-156 (172)
91 PRK14646 hypothetical protein; 29.0 1.5E+02 0.0032 22.0 4.8 46 66-119 98-148 (155)
92 KOG3418 60S ribosomal protein 29.0 62 0.0014 24.0 2.8 22 66-87 6-28 (136)
93 TIGR01171 rplB_bact ribosomal 28.7 87 0.0019 25.6 3.8 33 78-117 156-188 (273)
94 PF13051 DUF3912: Protein of u 28.6 1.2E+02 0.0027 19.5 3.8 23 67-89 5-28 (68)
95 PRK05609 nusG transcription an 28.2 1.2E+02 0.0025 22.1 4.2 29 15-48 124-152 (181)
96 TIGR01069 mutS2 MutS2 family p 27.7 1.4E+02 0.003 27.7 5.3 42 66-117 626-668 (771)
97 PRK14634 hypothetical protein; 27.7 1.4E+02 0.0031 22.0 4.6 45 67-119 99-148 (155)
98 COG0250 NusG Transcription ant 26.7 1.6E+02 0.0034 22.4 4.7 30 16-50 122-151 (178)
99 KOG3401 60S ribosomal protein 26.4 33 0.00072 25.7 1.0 42 55-96 38-82 (145)
100 cd05790 S1_Rrp40 S1_Rrp40: Rrp 25.7 1.2E+02 0.0026 20.4 3.5 9 63-71 2-10 (86)
101 PRK14643 hypothetical protein; 25.6 2.2E+02 0.0048 21.3 5.3 49 67-119 103-158 (164)
102 COG0234 GroS Co-chaperonin Gro 25.6 2.4E+02 0.0052 19.7 5.4 47 39-94 36-84 (96)
103 PF04452 Methyltrans_RNA: RNA 25.6 85 0.0018 24.0 3.2 39 58-96 9-49 (225)
104 PTZ00471 60S ribosomal protein 25.4 98 0.0021 22.9 3.3 28 17-49 4-31 (134)
105 PRK09374 rplB 50S ribosomal pr 24.9 1.1E+02 0.0024 25.0 3.8 33 78-117 158-190 (276)
106 CHL00052 rpl2 ribosomal protei 24.4 1.2E+02 0.0025 24.9 3.9 33 78-117 156-188 (273)
107 PF03646 FlaG: FlaG protein; 24.4 45 0.00098 22.6 1.3 34 85-119 59-92 (107)
108 PRK14635 hypothetical protein; 24.2 1.1E+02 0.0023 22.8 3.4 49 67-118 98-155 (162)
109 COG3109 ProQ Activator of osmo 24.1 1.6E+02 0.0034 23.1 4.3 34 66-102 163-197 (208)
110 PRK09612 rpl2p 50S ribosomal p 23.8 1.3E+02 0.0028 24.2 3.9 32 78-116 123-154 (238)
111 PF02699 YajC: Preprotein tran 21.7 31 0.00066 22.8 0.0 30 66-100 38-67 (82)
112 COG4405 Uncharacterized protei 21.5 1.9E+02 0.0041 21.6 4.1 14 62-75 54-68 (140)
113 TIGR02768 TraA_Ti Ti-type conj 20.8 2.7E+02 0.0058 25.6 5.8 33 66-100 609-647 (744)
114 PHA02104 hypothetical protein 20.4 1.5E+02 0.0033 19.9 3.1 29 14-47 35-64 (89)
No 1
>KOG4315 consensus G-patch nucleic acid binding protein [General function prediction only]
Probab=99.77 E-value=6.1e-20 Score=153.88 Aligned_cols=100 Identities=23% Similarity=0.341 Sum_probs=89.6
Q ss_pred CcccCCcEEEEEeccCCCccceeeeEEEEEecCCc-----------eEE-EeecCceeeecCC-CCCeE-EEecCCCCce
Q 038833 16 YWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY-----------HVL-RADHDELETVIPQ-IEGLV-IVNGAYQGSN 81 (120)
Q Consensus 16 ~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~-----------~~~-~v~q~~LETViP~-~G~~V-Vv~G~~rG~~ 81 (120)
.|++.+|.|||+|+.++.|+||++|++|.||.+.. .+. +++|++|||++|. .|.+| |+.|.|.|..
T Consensus 332 ~wlR~dl~VR~is~d~Kgg~ly~~K~~i~dv~gp~scd~r~Dedq~~~qg~irq~~lET~~pr~~Ge~vmvv~gkhkg~~ 411 (455)
T KOG4315|consen 332 SWLRSDLKVRFISKDVKGGRLYEKKVRIVDVVGPTSCDIRMDEDQELVQGNIRQELLETALPRRGGEKVMVVSGKHKGVY 411 (455)
T ss_pred hhhhcceeEEeeccccccchhhhcccceecccCCCccceeccccccccccchHHHHHhhhcccccCceeEEEecccccch
Confidence 89999999999999999999999999999999843 122 4999999999995 67779 9999999999
Q ss_pred EEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 82 ARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 82 g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
|.|+++|.++.++++++... ++.+ .+.||+||+|
T Consensus 412 g~llskd~~Ke~~~v~~~a~---ndvv-~~~~D~v~ey 445 (455)
T KOG4315|consen 412 GSLLSKDLDKETGVVRLVAT---NDVV-TVYLDQVCEY 445 (455)
T ss_pred hhhhhhhhhhhhcceecccc---cchh-hhhHHHHHHh
Confidence 99999999999999999873 5655 4999999987
No 2
>KOG2837 consensus Protein containing a U1-type Zn-finger and implicated in RNA splicing or processing [RNA processing and modification]
Probab=99.20 E-value=1.6e-13 Score=110.58 Aligned_cols=54 Identities=61% Similarity=1.000 Sum_probs=49.6
Q ss_pred EEEEEeccCCCccceeeeEEEEEecCCc---------eEEEeecCceeeecCCCCCeEEEecCCCCceE
Q 038833 23 IVEVMSKAFADKGYCKQKGIVRKVIDKY---------HVLRADHDELETVIPQIEGLVIVNGAYQGSNA 82 (120)
Q Consensus 23 ~Vkii~k~~~~gk~y~~KgvV~~V~~~~---------~~~~v~q~~LETViP~~G~~VVv~G~~rG~~g 82 (120)
+|++++++++. + |++||||.+|++.| .++++||+|||||||+ .||+|.|||..|
T Consensus 247 ~vk~~sk~l~~-k-~K~K~vv~~vid~y~~~~Kld~g~~lk~dq~~lEtvip~----~~vng~yRg~~~ 309 (309)
T KOG2837|consen 247 VVKVISKSLGE-K-YKQKGVVKKVIDDYTGQIKLDSGTVLKVDQEHLETVIPQ----MIVNGAYRGSEA 309 (309)
T ss_pred EEEeehhhhhH-H-hccccHHHHHHHhhhhheeccCCceecccHHHHHHHhHH----HHhhhhhccCCC
Confidence 99999999998 6 99999999999988 6889999999999998 479999999753
No 3
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=97.92 E-value=5.8e-06 Score=75.88 Aligned_cols=96 Identities=20% Similarity=0.189 Sum_probs=80.1
Q ss_pred CcccCCcEEEEEeccCCCccceeeeEEEEEecCCc---------eEEEeecCceeeecCCCCCeE-EEecCCCCceEEEE
Q 038833 16 YWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY---------HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLL 85 (120)
Q Consensus 16 ~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~---------~~~~v~q~~LETViP~~G~~V-Vv~G~~rG~~g~L~ 85 (120)
+| ..++.+.+-+ ++.++...++.++|++|.++. ..+.+..++|+++.|..|+.+ ++.|.++|.+|+++
T Consensus 916 ~~-~~~~~~~~~d-~~~~~~~~G~~~~ir~v~~G~~sv~~~de~~~~~~s~~~~a~~~p~~~d~~k~~~g~~~g~~~~~~ 993 (1024)
T KOG1999|consen 916 NG-GDGNSSWGPD-TSLDTQLVGQTGIIRSVADGGCSVWLGDEGETISNSKPHLAPAPPCKGDDVKSIWGDDRGSTGKLV 993 (1024)
T ss_pred CC-CccceEeccc-ccccceecccccceeeccCCceeeecCCCCcccccccccCccCCCCCCCCcccccccccccccccc
Confidence 56 6677887765 566779999999999999876 377899999999999999999 99999999999999
Q ss_pred EEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 86 GVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 86 ~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
+.|..++.+.+...++ ++.+.+--+||+
T Consensus 994 ~~dg~~g~~~~d~~~~------~k~l~~~~~~k~ 1021 (1024)
T KOG1999|consen 994 GNDGWDGIVRIDETSD------IKILNLGLLCKM 1021 (1024)
T ss_pred CCCcccceeccccccc------chhhhhhhhhhc
Confidence 9999996665544232 456888889987
No 4
>PF00467 KOW: KOW motif; InterPro: IPR005824 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and the bacterial transcription antitermination proteins NusG []. ; PDB: 3BBO_W 2HGJ_X 2HGQ_X 2HGU_X 1NPP_B 1M1G_D 1NPR_A 2XHC_A 2KVQ_G 2JVV_A ....
Probab=97.77 E-value=5.2e-05 Score=42.48 Aligned_cols=30 Identities=17% Similarity=0.511 Sum_probs=27.1
Q ss_pred CCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833 67 IEGLV-IVNGAYQGSNARLLGVDNDKFCAKT 96 (120)
Q Consensus 67 ~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V 96 (120)
+|+.| |+.|+|+|..|++++++.++..+.|
T Consensus 1 ~Gd~V~V~~G~~~G~~G~I~~i~~~~~~V~v 31 (32)
T PF00467_consen 1 VGDTVKVISGPFKGKIGKIVEIDRSKVRVTV 31 (32)
T ss_dssp TTSEEEESSSTTTTEEEEEEEEETTTTEEEE
T ss_pred CCCEEEEeEcCCCCceEEEEEEECCCCEEEE
Confidence 58999 9999999999999999999976654
No 5
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=97.37 E-value=0.0004 Score=36.74 Aligned_cols=26 Identities=23% Similarity=0.586 Sum_probs=23.6
Q ss_pred CCCCCeE-EEecCCCCceEEEEEEeCC
Q 038833 65 PQIEGLV-IVNGAYQGSNARLLGVDND 90 (120)
Q Consensus 65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~ 90 (120)
|.+|+.| |+.|+++|..|++++++.+
T Consensus 2 ~~~G~~V~I~~G~~~g~~g~i~~i~~~ 28 (28)
T smart00739 2 FEVGDTVRVIAGPFKGKVGKVLEVDGE 28 (28)
T ss_pred CCCCCEEEEeECCCCCcEEEEEEEcCC
Confidence 5789999 9999999999999999853
No 6
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=97.22 E-value=0.00075 Score=45.06 Aligned_cols=32 Identities=19% Similarity=0.299 Sum_probs=29.3
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK 97 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~ 97 (120)
+.||+| |+.|.++|..|++++++.++..+.|+
T Consensus 8 ~kGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 40 (76)
T PRK12281 8 KKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVE 40 (76)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 689999 99999999999999999999877763
No 7
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=97.22 E-value=0.00074 Score=45.77 Aligned_cols=31 Identities=19% Similarity=0.256 Sum_probs=29.1
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT 96 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V 96 (120)
+.|++| |+.|+++|..|++++++.++..+.|
T Consensus 10 ~~GD~V~Vi~G~dKGK~G~V~~V~~~~~~V~V 41 (83)
T CHL00141 10 KIGDTVKIISGSDKGKIGEVLKIIKKSNKVIV 41 (83)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEE
Confidence 679999 9999999999999999999988877
No 8
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=97.09 E-value=0.0018 Score=46.88 Aligned_cols=50 Identities=16% Similarity=0.318 Sum_probs=41.6
Q ss_pred CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCce--Eeeeccccccc
Q 038833 65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRV--LNAIDYEDICK 118 (120)
Q Consensus 65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~--v~~~~yddvck 118 (120)
+.+|+.| |+.|+++|..|.+.++|..+..+.|.|.. .+.. ++ ++++++-+
T Consensus 87 ~~~Gd~V~I~~GPf~G~~g~v~~~d~~k~~v~v~l~~---~~~~~~v~-v~~~~l~~ 139 (145)
T TIGR00405 87 IKKGDIVEIISGPFKGERAKVIRVDESKEEVTLELIE---AAVPIPVT-VKGDQVRI 139 (145)
T ss_pred cCCCCEEEEeecCCCCCeEEEEEEcCCCCEEEEEEEE---cCccceEE-EeeeEEEE
Confidence 5799999 99999999999999999888899998886 2343 53 77777754
No 9
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=96.91 E-value=0.0021 Score=45.25 Aligned_cols=32 Identities=19% Similarity=0.231 Sum_probs=29.5
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK 97 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~ 97 (120)
+.|++| |+.|.++|..|++++++.++..+.|+
T Consensus 6 ~kGD~V~Vi~G~dKGk~G~V~~V~~~~~~V~Ve 38 (105)
T PRK00004 6 KKGDTVIVIAGKDKGKRGKVLKVLPKKNKVIVE 38 (105)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEc
Confidence 689999 99999999999999999999888773
No 10
>TIGR01079 rplX_bact ribosomal protein L24, bacterial/organelle. This model recognizes bacterial and organellar forms of ribosomal protein L24. It excludes eukaryotic and archaeal forms, designated L26 in eukaryotes.
Probab=96.66 E-value=0.004 Score=43.85 Aligned_cols=32 Identities=16% Similarity=0.211 Sum_probs=29.3
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK 97 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~ 97 (120)
+.|++| |+.|.++|..|++++++.++..+.|+
T Consensus 5 kkGD~V~Vi~G~dKGK~G~V~~V~~~~~~V~Ve 37 (104)
T TIGR01079 5 KKGDTVKVISGKDKGKRGKVLKVLPKTNKVIVE 37 (104)
T ss_pred cCCCEEEEeEcCCCCcEEEEEEEEcCCCEEEEC
Confidence 579999 99999999999999999999888763
No 11
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=96.58 E-value=0.0087 Score=44.17 Aligned_cols=49 Identities=16% Similarity=0.337 Sum_probs=40.4
Q ss_pred CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCce--Eeeecccccc
Q 038833 65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRV--LNAIDYEDIC 117 (120)
Q Consensus 65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~--v~~~~yddvc 117 (120)
..+|+.| |+.|+++|..|++.++|.++..++|.+..- ... + .++.++++
T Consensus 95 ~~~G~~V~I~~Gpf~g~~g~V~~vd~~k~~v~v~ll~~---~~~~pv-~v~~~~~~ 146 (153)
T PRK08559 95 IKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEA---AVPIPV-TVRGDQVR 146 (153)
T ss_pred CCCCCEEEEeccCCCCceEEEEEEcCCCCEEEEEEECC---cceeeE-EEeccEEE
Confidence 4799999 999999999999999999999999988762 222 4 37777764
No 12
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=96.51 E-value=0.01 Score=43.85 Aligned_cols=49 Identities=12% Similarity=0.218 Sum_probs=37.5
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
..|++| |+.|++.|..|.+..+|.++..|.|.++-=. ....+ .+++++|
T Consensus 121 ~~G~~V~I~~Gpf~G~~g~v~~~~~~~~r~~V~v~~~g-~~~~v-~v~~~~l 170 (172)
T TIGR00922 121 EVGEQVRVNDGPFANFTGTVEEVDYEKSKLKVSVSIFG-RETPV-ELEFSQV 170 (172)
T ss_pred CCCCEEEEeecCCCCcEEEEEEEcCCCCEEEEEEEECC-CceEE-EEcHHHe
Confidence 579999 9999999999999999988878888776511 12234 3776665
No 13
>TIGR01080 rplX_A_E ribosomal protein L24p/L26e, archaeal/eukaryotic. This model represents the archaeal and eukaryotic branch of the ribosomal protein L24p/L26e family. Bacterial and organellar forms are represented by the related TIGR01079.
Probab=96.50 E-value=0.0056 Score=43.91 Aligned_cols=31 Identities=19% Similarity=0.390 Sum_probs=28.6
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT 96 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V 96 (120)
..|+.| |+.|.++|..|++++++..+..+.|
T Consensus 43 kkGD~V~Vi~Gk~KGk~GkV~~V~~~~~~V~V 74 (114)
T TIGR01080 43 RKGDKVRIMRGDFKGHEGKVSKVDLKRYRIYV 74 (114)
T ss_pred ecCCEEEEecCCCCCCEEEEEEEEcCCCEEEE
Confidence 789999 9999999999999999999987766
No 14
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=96.49 E-value=0.0064 Score=44.03 Aligned_cols=31 Identities=16% Similarity=0.328 Sum_probs=29.0
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT 96 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V 96 (120)
..|+.| |+.|.++|..|++++++.++..+.|
T Consensus 47 kkGD~V~VisG~~KGk~GkV~~V~~~~~~V~V 78 (120)
T PRK01191 47 RKGDTVKVMRGDFKGEEGKVVEVDLKRGRIYV 78 (120)
T ss_pred eCCCEEEEeecCCCCceEEEEEEEcCCCEEEE
Confidence 679999 9999999999999999999988876
No 15
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=96.45 E-value=0.012 Score=43.72 Aligned_cols=53 Identities=15% Similarity=0.263 Sum_probs=39.5
Q ss_pred CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
...|++| |+.|+++|..|++.++|.++..|.|.++-=. ....+ .++++++-++
T Consensus 127 ~~~Gd~VrI~~GPf~G~~g~v~~i~~~~~r~~v~l~~~G-~~~~v-~l~~~~l~~~ 180 (181)
T PRK05609 127 FEVGEMVRVIDGPFADFNGTVEEVDYEKSKLKVLVSIFG-RETPV-ELEFSQVEKI 180 (181)
T ss_pred CCCCCEEEEeccCCCCCEEEEEEEeCCCCEEEEEEEECC-CceEE-EEchHHEEEc
Confidence 3689999 9999999999999999987777877766411 12234 4777777553
No 16
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=96.39 E-value=0.0066 Score=45.18 Aligned_cols=32 Identities=19% Similarity=0.364 Sum_probs=29.5
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK 97 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~ 97 (120)
..|+.| |+.|.++|..|++++++..++.+.|.
T Consensus 48 kkGD~V~Vi~Gk~KGk~GkV~~V~~k~~~ViVE 80 (143)
T PTZ00194 48 RKDDEVMVVRGHHKGREGKVTAVYRKKWVIHIE 80 (143)
T ss_pred ecCCEEEEecCCCCCCceEEEEEEcCCCEEEEe
Confidence 679999 99999999999999999999888763
No 17
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=96.19 E-value=0.017 Score=44.13 Aligned_cols=55 Identities=22% Similarity=0.308 Sum_probs=43.2
Q ss_pred ecCCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 63 VIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 63 ViP~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
+-+.+|+.| |+.|+++|..|++.++|.++..++|.+..=. .-..+ .++|+++-++
T Consensus 122 ~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~ifg-r~tPV-el~~~qVek~ 177 (178)
T COG0250 122 VDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSIFG-RPTPV-ELEFDQVEKL 177 (178)
T ss_pred ccCCCCCEEEEeccCCCCccEEEEEEcCcCcEEEEEEEEeC-CceEE-EEehhhEEEe
Confidence 344689999 9999999999999999999888888777511 22344 4888888664
No 18
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=95.32 E-value=0.055 Score=39.66 Aligned_cols=51 Identities=22% Similarity=0.209 Sum_probs=36.7
Q ss_pred CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833 65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118 (120)
Q Consensus 65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck 118 (120)
+..|++| |+.|++.|..|.+..+|. +..+.|.++-= +....+ .++++++-+
T Consensus 110 ~~~G~~V~I~~Gp~~g~eg~v~~~~~-~~r~~v~v~~~-gr~~~v-~v~~~~~~~ 161 (162)
T PRK09014 110 PKPGDKVIITEGAFEGLQAIYTEPDG-EARSILLLNLL-NKQVKH-SVDNTQFRK 161 (162)
T ss_pred CCCCCEEEEecCCCCCcEEEEEEeCC-CeEEEEeehhh-CCcEEE-EECHHHeec
Confidence 4689999 999999999999999984 44566766541 122334 377777654
No 19
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=95.23 E-value=0.062 Score=38.99 Aligned_cols=34 Identities=24% Similarity=0.241 Sum_probs=29.0
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEcc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEK 100 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~ 100 (120)
..|++| |+.|++.|..|.+..+|. +..+.|.|+-
T Consensus 110 ~~G~~V~V~~GPf~g~~g~v~~~~~-~~r~~v~l~~ 144 (159)
T TIGR01955 110 YKGDKVRITDGAFAGFEAIFLEPDG-EKRSMLLLNM 144 (159)
T ss_pred CCCCEEEEeccCCCCcEEEEEEECC-CceEEEEEhh
Confidence 589999 999999999999999984 4467777664
No 20
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=94.87 E-value=0.058 Score=38.17 Aligned_cols=29 Identities=21% Similarity=0.320 Sum_probs=26.2
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT 96 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V 96 (120)
..|+.| |+.|.++|..|.+++++... +.|
T Consensus 6 rkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~V 35 (104)
T COG0198 6 KKGDTVKVIAGKDKGKEGKVLKVLPKK--VVV 35 (104)
T ss_pred ecCCEEEEEecCCCCcceEEEEEecCe--EEE
Confidence 579999 99999999999999999998 544
No 21
>TIGR01956 NusG_myco NusG family protein. This model represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged (long branches in a Neighbor-joining phylogenetic tree) from the bacterial species. And although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system including this family as a member.
Probab=94.69 E-value=0.12 Score=41.83 Aligned_cols=50 Identities=18% Similarity=0.379 Sum_probs=37.9
Q ss_pred CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833 65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
+.+|+.| |+.|++.|..|.+.++|.++..+.|.|.-- +....+ .++|++|
T Consensus 206 f~vGd~VrI~dGPF~GfeG~I~eid~~k~Rv~VlV~If-GR~TpV-eL~~~qV 256 (258)
T TIGR01956 206 FRVGNFVKIVDGPFKGIVGKIKKIDQEKKKAIVEVEIL-GKSVDV-DLNFKHL 256 (258)
T ss_pred CCCCCEEEEEecCCCCcEEEEEEEeCCCCEEEEEEEec-CCcEEE-EEchHHE
Confidence 4789999 999999999999999997777777766541 122334 4777766
No 22
>PF15591 Imm17: Immunity protein 17
Probab=91.84 E-value=0.27 Score=32.82 Aligned_cols=28 Identities=21% Similarity=0.281 Sum_probs=23.9
Q ss_pred EEEEEeccCCCccceeeeEEEEEecCCc
Q 038833 23 IVEVMSKAFADKGYCKQKGIVRKVIDKY 50 (120)
Q Consensus 23 ~Vkii~k~~~~gk~y~~KgvV~~V~~~~ 50 (120)
+|+|++....+.++++++|+|...+...
T Consensus 10 ~V~v~~s~p~~~ei~Gk~GVVlG~SeeD 37 (74)
T PF15591_consen 10 EVEVVRSCPCDAEIWGKRGVVLGISEED 37 (74)
T ss_pred EEEEeccCcchhhhcCceeEEEEEecCC
Confidence 6889886677779999999999998755
No 23
>PF11623 DUF3252: Protein of unknown function (DUF3252); InterPro: IPR021659 This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function. ; PDB: 3C4S_B 2JZ2_A.
Probab=90.85 E-value=0.74 Score=28.88 Aligned_cols=41 Identities=29% Similarity=0.404 Sum_probs=28.0
Q ss_pred ccCCcEEEEEeccCCCccceeeeEEEEEecCCc-----------eEEEeecCcee
Q 038833 18 LFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY-----------HVLRADHDELE 61 (120)
Q Consensus 18 l~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~-----------~~~~v~q~~LE 61 (120)
+.|+-.|++++-+ + -||.=.|.|..|.++. +++.++-+.||
T Consensus 2 ilPG~~V~V~n~~--~-~Y~~y~G~VQRvsdgkaaVLFEGGnWdKlvTf~l~eLe 53 (53)
T PF11623_consen 2 ILPGSTVRVKNPN--D-IYYGYEGFVQRVSDGKAAVLFEGGNWDKLVTFRLSELE 53 (53)
T ss_dssp --TT-EEEE--TT--S-TTTT-EEEEEEEETTEEEEEEEETTEEEEEEEEGGGEE
T ss_pred ccCCCEEEEeCCC--C-ccchheEEEEEeeCCeEEEEecCCCceEEEEEEhhhCC
Confidence 4689999997653 4 7999999999999976 56667666665
No 24
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=90.73 E-value=0.33 Score=42.69 Aligned_cols=42 Identities=33% Similarity=0.504 Sum_probs=35.9
Q ss_pred Cceeeec----CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccC
Q 038833 58 DELETVI----PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKG 101 (120)
Q Consensus 58 ~~LETVi----P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g 101 (120)
..||--| |++|..| |=+|+|+|+.|.+.+.|.+. |+|+|.++
T Consensus 341 ~~l~r~i~gRd~aigktVrIr~g~yKG~lGVVKdv~~~~--arVeLhs~ 387 (607)
T COG5164 341 NELERKIVGRDPAIGKTVRIRCGEYKGHLGVVKDVDRNI--ARVELHSN 387 (607)
T ss_pred hhhhccccccccccCceEEEeecccccccceeeeccCce--EEEEEecC
Confidence 4556556 7899999 99999999999999999888 88888884
No 25
>PRK04313 30S ribosomal protein S4e; Validated
Probab=86.63 E-value=2.9 Score=33.48 Aligned_cols=46 Identities=17% Similarity=0.272 Sum_probs=33.3
Q ss_pred EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEeCCc----cEEEEE
Q 038833 52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVDNDK----FCAKTK 97 (120)
Q Consensus 52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~~~----~~~~V~ 97 (120)
+++++...+.-.+| ..|.-+ |..|.+.|.+|++.++.... ..+.++
T Consensus 158 ~i~l~~~kI~~~i~fe~G~l~~itgG~n~GriG~I~~i~~~~~~~~~~V~i~ 209 (237)
T PRK04313 158 LISLPEQEIVDHIPFEEGNLAIITGGKHVGEIGKIKEIEVTKSSKPNIVTLE 209 (237)
T ss_pred EEECCCCceeEEEecCCCCEEEEECCeeeeeEEEEEEEEEccCCCCcEEEEE
Confidence 44554444555666 899999 99999999999999997333 445544
No 26
>PLN00036 40S ribosomal protein S4; Provisional
Probab=86.32 E-value=3.4 Score=33.62 Aligned_cols=37 Identities=14% Similarity=0.316 Sum_probs=30.0
Q ss_pred EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEe
Q 038833 52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVD 88 (120)
Q Consensus 52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d 88 (120)
+++++...+.-.+| ..|.-+ |..|.+.|.+|++.++.
T Consensus 161 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GrvG~I~~i~ 199 (261)
T PLN00036 161 KIDLETNKIVDFIKFDVGNLVMVTGGRNRGRVGVIKNRE 199 (261)
T ss_pred EEeCCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEE
Confidence 44555555666666 899999 99999999999999998
No 27
>COG1471 RPS4A Ribosomal protein S4E [Translation, ribosomal structure and biogenesis]
Probab=85.72 E-value=3 Score=33.58 Aligned_cols=49 Identities=12% Similarity=0.189 Sum_probs=35.8
Q ss_pred EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEeCCc--cEEEEEEcc
Q 038833 52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVDNDK--FCAKTKIEK 100 (120)
Q Consensus 52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~~~--~~~~V~l~~ 100 (120)
+++++...+.-.|| ..|..+ |+.|.|.|.+|++.+|.... ..=+|.+++
T Consensus 160 ~i~lp~~~I~~~i~fe~g~~~~vtgG~h~G~~G~I~~I~~~~~~~~~~v~~e~ 212 (241)
T COG1471 160 KISLPEQKIVEHIKFEEGALVYVTGGRHVGRVGTIVEIEIQESSKPNLVTVED 212 (241)
T ss_pred EEeCCChhheeEeccCCCcEEEEECCccccceEEEEEEEEecCCCccEEEEec
Confidence 55676666666666 889999 99999999999999997553 222345555
No 28
>KOG1999 consensus RNA polymerase II transcription elongation factor DSIF/SUPT5H/SPT5 [Transcription]
Probab=82.67 E-value=4.6 Score=38.31 Aligned_cols=69 Identities=22% Similarity=0.296 Sum_probs=51.0
Q ss_pred ccCCcEEEEEeccCCCccceeeeEEEEEecCCceEEEeecCceeee----------cCCCCCeE-EEecCCCCceEEEEE
Q 038833 18 LFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETV----------IPQIEGLV-IVNGAYQGSNARLLG 86 (120)
Q Consensus 18 l~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~~~~~v~q~~LETV----------iP~~G~~V-Vv~G~~rG~~g~L~~ 86 (120)
++|+=.|.|+ .|.+-|-||+|..|.+...++.-.+++|-.= .-.+|+.| |+.|.|.|.+|-++.
T Consensus 408 F~~GD~VeV~-----~Gel~glkG~ve~vdg~~vti~~~~e~l~~pl~~~~~eLrKyF~~GDhVKVi~G~~eG~tGlVvr 482 (1024)
T KOG1999|consen 408 FSPGDAVEVI-----VGELKGLKGKVESVDGTIVTIMSKHEDLKGPLEVPASELRKYFEPGDHVKVIAGRYEGDTGLVVR 482 (1024)
T ss_pred cCCCCeEEEe-----eeeeccceeEEEeccCceEEEeeccccCCCccccchHhhhhhccCCCeEEEEeccccCCcceEEE
Confidence 5677777776 5678889999999988663333333333221 12489999 999999999999999
Q ss_pred EeCCc
Q 038833 87 VDNDK 91 (120)
Q Consensus 87 ~d~~~ 91 (120)
++...
T Consensus 483 Ve~~~ 487 (1024)
T KOG1999|consen 483 VEQGD 487 (1024)
T ss_pred EeCCe
Confidence 99876
No 29
>PTZ00118 40S ribosomal protein S4; Provisional
Probab=82.20 E-value=6.6 Score=31.94 Aligned_cols=38 Identities=16% Similarity=0.316 Sum_probs=30.1
Q ss_pred EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEeC
Q 038833 52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVDN 89 (120)
Q Consensus 52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~ 89 (120)
+++++...+.-.+| ..|.-+ |..|.+.|.+|++.++..
T Consensus 161 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~~~~ 200 (262)
T PTZ00118 161 RLDLETGKVLEFLKFEVGNLVMITGGHNVGRVGTIVSKEK 200 (262)
T ss_pred EEECCCCceeeEEecCCCCEEEEECCeeceeEEEEEEEEe
Confidence 44555555666666 899999 999999999999998763
No 30
>PRK04333 50S ribosomal protein L14e; Validated
Probab=81.68 E-value=5.6 Score=26.91 Aligned_cols=26 Identities=8% Similarity=0.242 Sum_probs=21.7
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDK 91 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~ 91 (120)
.+|.-| +..|.++|..+.++++-.++
T Consensus 5 ~~GrvV~~~~Grd~gk~~vIv~i~d~~ 31 (84)
T PRK04333 5 EVGRVCVKTAGREAGRKCVIVDIIDKN 31 (84)
T ss_pred cccEEEEEeccCCCCCEEEEEEEecCC
Confidence 357667 88999999999999996665
No 31
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=81.40 E-value=4.9 Score=29.51 Aligned_cols=46 Identities=15% Similarity=0.127 Sum_probs=29.1
Q ss_pred CCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCC-CCCceEeeeccccc
Q 038833 67 IEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGV-NDGRVLNAIDYEDI 116 (120)
Q Consensus 67 ~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~-~~~~~v~~~~yddv 116 (120)
+|.-| |-.|++.|.++.+.+|-..+. |. -+|| .+|-.=..++|.++
T Consensus 10 iGRVvli~~Gp~~GKL~vIVDIID~nR-vL---VDGP~~tgV~Rq~i~~k~l 57 (130)
T PTZ00065 10 PGRLCLIQYGPDAGKLCFIVDIVTPTR-VL---VDGAFITGVKRQSIPLKRL 57 (130)
T ss_pred eceEEEEecCCCCCCEEEEEEEEcCCe-EE---EeCCCcCCcceeEEeccce
Confidence 46555 779999999999999966662 43 3466 43322223555544
No 32
>PTZ00223 40S ribosomal protein S4; Provisional
Probab=81.08 E-value=5.2 Score=32.74 Aligned_cols=38 Identities=16% Similarity=0.367 Sum_probs=29.9
Q ss_pred EEEeecCceeeecC-CCCCeE-EEecCCCCceEEEEEEeC
Q 038833 52 VLRADHDELETVIP-QIEGLV-IVNGAYQGSNARLLGVDN 89 (120)
Q Consensus 52 ~~~v~q~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~ 89 (120)
+++++...+.-.+| ..|.-+ |..|.+.|.+|++.++..
T Consensus 158 ~i~l~~~kI~~~ikfe~G~l~~vtgG~n~GriG~I~~i~~ 197 (273)
T PTZ00223 158 VYNVKEKKVVDLIKNRNGKVVMVTGGANRGRIGEIVSIER 197 (273)
T ss_pred EEECCCCeeeEEEecCCCCEEEEECCeeceeEEEEEEEEe
Confidence 44555555665666 899999 999999999999999953
No 33
>smart00333 TUDOR Tudor domain. Domain of unknown function present in several RNA-binding proteins. 10 copies in the Drosophila Tudor protein. Initial proposal that the survival motor neuron gene product contain a Tudor domain are corroborated by more recent database search techniques such as PSI-BLAST (unpublished).
Probab=78.95 E-value=11 Score=22.28 Aligned_cols=51 Identities=16% Similarity=0.054 Sum_probs=34.7
Q ss_pred cCCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 64 IPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 64 iP~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
.|+.|..| +..-.-+-..|++++++.+ ....|.+.+. |. ...++.++|..+
T Consensus 2 ~~~~G~~~~a~~~d~~wyra~I~~~~~~-~~~~V~f~D~---G~-~~~v~~~~l~~l 53 (57)
T smart00333 2 TFKVGDKVAARWEDGEWYRARIIKVDGE-QLYEVFFIDY---GN-EEVVPPSDLRPL 53 (57)
T ss_pred CCCCCCEEEEEeCCCCEEEEEEEEECCC-CEEEEEEECC---Cc-cEEEeHHHeecC
Confidence 36889888 4443456678999999986 4566777662 22 335888888754
No 34
>TIGR00739 yajC preprotein translocase, YajC subunit. While this protein is part of the preprotein translocase in Escherichia coli, it is not essential for viability or protein secretion. The N-terminus region contains a predicted membrane-spanning region followed by a region consisting almost entirely of residues with charged (acidic, basic, or zwitterionic) side chains. This small protein is about 100 residues in length, and is restricted to bacteria; however, this protein is absent from some lineages, including spirochetes and Mycoplasmas.
Probab=75.48 E-value=8.7 Score=25.78 Aligned_cols=30 Identities=10% Similarity=0.186 Sum_probs=22.5
Q ss_pred CCCCeEEEecCCCCceEEEEEEeCCccEEEEEEcc
Q 038833 66 QIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEK 100 (120)
Q Consensus 66 ~~G~~VVv~G~~rG~~g~L~~~d~~~~~~~V~l~~ 100 (120)
++|++|+..| |-.|++.+++++. +.+++.+
T Consensus 39 ~~Gd~VvT~g---Gi~G~V~~i~d~~--v~vei~~ 68 (84)
T TIGR00739 39 KKGDKVLTIG---GIIGTVTKIAENT--IVIELND 68 (84)
T ss_pred CCCCEEEECC---CeEEEEEEEeCCE--EEEEECC
Confidence 4699995544 5899999999765 6677655
No 35
>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=71.06 E-value=16 Score=24.01 Aligned_cols=49 Identities=22% Similarity=0.411 Sum_probs=31.2
Q ss_pred CCCCeE-EE-e---cCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833 66 QIEGLV-IV-N---GAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118 (120)
Q Consensus 66 ~~G~~V-Vv-~---G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck 118 (120)
..|..| |- . +..+-..|+|.+++.+. +++..... ..+..+ .+||++|.+
T Consensus 23 ~~G~~v~v~~~~~~~~~~~~~G~L~~~~~~~--v~l~~~~~-~~~~~~-~i~~~~I~k 76 (83)
T cd01734 23 AVGKYVHVKLYQPIDGQKEFEGTLLGVDDDT--VTLEVDIK-TRGKTV-EIPLDKIAK 76 (83)
T ss_pred hCCCEEEEEEEcccCCeEEEEEEEEeEeCCE--EEEEEecC-CCCeEE-EEEhHHeeE
Confidence 468888 64 4 33455689999999877 44544421 113345 599999876
No 36
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=68.49 E-value=15 Score=25.79 Aligned_cols=30 Identities=20% Similarity=0.304 Sum_probs=22.3
Q ss_pred CCCCeEEEecCCCCceEEEEEEeCCccEEEEEEcc
Q 038833 66 QIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEK 100 (120)
Q Consensus 66 ~~G~~VVv~G~~rG~~g~L~~~d~~~~~~~V~l~~ 100 (120)
++|++|+..| |-.|++.+++++ .+.+++.+
T Consensus 54 k~Gd~VvT~g---Gi~G~Vv~i~~~--~v~lei~~ 83 (106)
T PRK05585 54 AKGDEVVTNG---GIIGKVTKVSED--FVIIELND 83 (106)
T ss_pred CCCCEEEECC---CeEEEEEEEeCC--EEEEEECC
Confidence 4699994443 589999999874 47777755
No 37
>KOG1708 consensus Mitochondrial/chloroplast ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=67.97 E-value=9.1 Score=30.48 Aligned_cols=32 Identities=16% Similarity=0.169 Sum_probs=27.8
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTK 97 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~ 97 (120)
..|+.| |+-|..+|.-|.+..+...+.-+.|.
T Consensus 74 f~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV~ 106 (236)
T KOG1708|consen 74 FFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVVK 106 (236)
T ss_pred ecCCEEEEEecccCCccceEEEEeecCceEEEc
Confidence 479999 99999999999999998887667663
No 38
>PRK04950 ProP expression regulator; Provisional
Probab=67.44 E-value=15 Score=29.08 Aligned_cols=43 Identities=16% Similarity=0.417 Sum_probs=33.0
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
+.|..| |-.| ..-.-|++++|+.++ +.|||++|. .+ .+.-|+|
T Consensus 168 ~~gq~v~vk~g-~~~~~a~i~ei~kd~--v~vql~~Gl----~~-~v~ae~l 211 (213)
T PRK04950 168 TVGQAVKVKAG-KSAMDATVLEITKDD--VRVQLDSGL----SM-IVRAEHL 211 (213)
T ss_pred ccCCEEEEecc-CCCCceEEEEEecCc--EEEEcCCCc----EE-EEeHhhh
Confidence 469999 8888 455789999999999 999999964 23 3555554
No 39
>PLN00045 photosystem I reaction center subunit IV; Provisional
Probab=66.75 E-value=11 Score=26.47 Aligned_cols=41 Identities=20% Similarity=0.348 Sum_probs=32.7
Q ss_pred eeeecCCCCCeE-EEecC--CCCceEEEEEEeCC---ccEEEEEEcc
Q 038833 60 LETVIPQIEGLV-IVNGA--YQGSNARLLGVDND---KFCAKTKIEK 100 (120)
Q Consensus 60 LETViP~~G~~V-Vv~G~--~rG~~g~L~~~d~~---~~~~~V~l~~ 100 (120)
=.++-|+.|.+| |++-+ +-..+|++.++|.+ +|-++|+++.
T Consensus 35 pp~ig~~RGskVrIlR~ESYWyn~vGtVvsVDq~~girYPVvVRF~k 81 (101)
T PLN00045 35 PPPIGPKRGSKVKILRPESYWFNDVGKVVAVDQDPGVRYPVVVRFEK 81 (101)
T ss_pred CCCcccCCCCEEEEccccceeecCcceEEEEeCCCCcccceEEEeee
Confidence 345677889999 99644 36789999999988 7889998875
No 40
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=66.04 E-value=19 Score=25.64 Aligned_cols=30 Identities=20% Similarity=0.165 Sum_probs=22.9
Q ss_pred CCCCeEEEecCCCCceEEEEEEeCCccEEEEEE
Q 038833 66 QIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKI 98 (120)
Q Consensus 66 ~~G~~VVv~G~~rG~~g~L~~~d~~~~~~~V~l 98 (120)
++|++||-.| |..|++.+++.+...+.+++
T Consensus 38 k~GD~VvT~G---Gi~G~V~~I~~~~~~v~le~ 67 (113)
T PRK06531 38 QKGDEVVTIG---GLYGTVDEVDTEAKTIVLDV 67 (113)
T ss_pred CCCCEEEECC---CcEEEEEEEecCCCEEEEEE
Confidence 4699995554 58999999998776676665
No 41
>PRK05886 yajC preprotein translocase subunit YajC; Validated
Probab=64.72 E-value=19 Score=25.57 Aligned_cols=30 Identities=23% Similarity=0.349 Sum_probs=22.1
Q ss_pred CCCCeEEEecCCCCceEEEEEEeCCccEEEEEEcc
Q 038833 66 QIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEK 100 (120)
Q Consensus 66 ~~G~~VVv~G~~rG~~g~L~~~d~~~~~~~V~l~~ 100 (120)
++|++|+..| |..|++.+++.+ .+.+++.+
T Consensus 40 k~GD~VvT~g---Gi~G~V~~I~d~--~v~leia~ 69 (109)
T PRK05886 40 QPGDRVHTTS---GLQATIVGITDD--TVDLEIAP 69 (109)
T ss_pred CCCCEEEECC---CeEEEEEEEeCC--EEEEEECC
Confidence 4699995544 589999999865 47777754
No 42
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=60.59 E-value=11 Score=27.84 Aligned_cols=25 Identities=20% Similarity=0.355 Sum_probs=19.8
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCC
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDND 90 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~ 90 (120)
++|.-| ||+|.|+|..|.++.-..+
T Consensus 6 kpgkVVivL~GR~AGkKaVivk~~dd 31 (134)
T PTZ00471 6 KPGKVVIVTSGRYAGRKAVIVQNFDT 31 (134)
T ss_pred cCCEEEEEEccccCCcEEEEEeecCC
Confidence 457667 8899999999988876444
No 43
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=59.33 E-value=27 Score=24.28 Aligned_cols=30 Identities=17% Similarity=0.262 Sum_probs=23.5
Q ss_pred CCCCeEEEecCCCCceEEEEEEeCCccEEEEEEcc
Q 038833 66 QIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEK 100 (120)
Q Consensus 66 ~~G~~VVv~G~~rG~~g~L~~~d~~~~~~~V~l~~ 100 (120)
+.|++|+..| |..|++.+++.+. +.|.+..
T Consensus 45 ~kGD~VvT~g---Gi~G~V~~v~d~~--v~I~l~~ 74 (97)
T COG1862 45 KKGDEVVTIG---GIVGTVTKVGDDT--VEIELGD 74 (97)
T ss_pred cCCCEEEEcC---CeEEEEEEEecCc--EEEEECC
Confidence 4699995554 6999999999887 7777764
No 44
>PRK14633 hypothetical protein; Provisional
Probab=57.81 E-value=31 Score=25.43 Aligned_cols=46 Identities=22% Similarity=0.369 Sum_probs=31.0
Q ss_pred CCCeE-EEe----cCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 67 IEGLV-IVN----GAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 67 ~G~~V-Vv~----G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
.|..| |.. +..+-..|+|.+.+.+. +++.+.. +..+ .+||++|.+.
T Consensus 93 ~G~~v~V~~~~~~~~~~~~~G~L~~v~~~~--i~l~~~~----~~~~-~i~~~~I~ka 143 (150)
T PRK14633 93 VGFNVKAVTLAPVGSQTKFKGVLERVEGNN--VILNLED----GKEI-SFDFDELKKL 143 (150)
T ss_pred CCCeEEEEEecccCCcEEEEEEEEEEeCCE--EEEEEcC----CcEE-EEEhHHeeeE
Confidence 68888 643 34566779999998876 4444433 2335 4999999863
No 45
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=57.23 E-value=31 Score=25.22 Aligned_cols=28 Identities=25% Similarity=0.292 Sum_probs=23.9
Q ss_pred ccCCcEEEEEeccCCCccceeeeEEEEEecCCc
Q 038833 18 LFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY 50 (120)
Q Consensus 18 l~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~ 50 (120)
+.+|=.|+|+ +|.|-+..|.|.++....
T Consensus 95 ~~~G~~V~I~-----~Gpf~g~~g~V~~vd~~k 122 (153)
T PRK08559 95 IKEGDIVELI-----AGPFKGEKARVVRVDESK 122 (153)
T ss_pred CCCCCEEEEe-----ccCCCCceEEEEEEcCCC
Confidence 6799999998 678889999999998644
No 46
>COG1096 Predicted RNA-binding protein (consists of S1 domain and a Zn-ribbon domain) [Translation, ribosomal structure and biogenesis]
Probab=56.98 E-value=92 Score=24.27 Aligned_cols=73 Identities=16% Similarity=0.327 Sum_probs=47.2
Q ss_pred cCCcEEEEEeccCCCccceeeeEEEEEecCCc-------eEEEeecCceeeecCCCCCeE---EEecCCCCceEEEEEEe
Q 038833 19 FKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY-------HVLRADHDELETVIPQIEGLV---IVNGAYQGSNARLLGVD 88 (120)
Q Consensus 19 ~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~-------~~~~v~q~~LETViP~~G~~V---Vv~G~~rG~~g~L~~~d 88 (120)
.|+=.+-....-+.+..-|.+.|.|.+..-+. +.+.+...--++.+|+.|+-| |.....+...-++..++
T Consensus 9 ~PGd~~a~~EE~~~G~gt~~~~g~i~Aa~~G~~~~d~~n~~~~V~p~~~~~~~~K~GdiV~grV~~v~~~~a~V~i~~ve 88 (188)
T COG1096 9 LPGDVLAVIEEFLPGEGTYEEGGEIRAAATGVVRRDDKNRVISVKPGKKTPPLPKGGDIVYGRVTDVREQRALVRIVGVE 88 (188)
T ss_pred cCcceeeeeeeeecCCCeEeECCEEEEeecccEEEcccceEEEeccCCCCCCCCCCCCEEEEEEeeccceEEEEEEEEEe
Confidence 34444444433333444566677776665433 567777777789999999998 55666666777888887
Q ss_pred CCc
Q 038833 89 NDK 91 (120)
Q Consensus 89 ~~~ 91 (120)
...
T Consensus 89 ~~~ 91 (188)
T COG1096 89 GKE 91 (188)
T ss_pred ccc
Confidence 754
No 47
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=56.36 E-value=17 Score=26.39 Aligned_cols=26 Identities=15% Similarity=0.488 Sum_probs=22.2
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDK 91 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~ 91 (120)
.+|.=| ++.|.++|..+.++++-.++
T Consensus 6 ~~GrVvvv~~GR~aGkk~VIv~~iDd~ 32 (125)
T COG2163 6 EVGRVVVVTAGRFAGKKVVIVKIIDDN 32 (125)
T ss_pred cCCeEEEEecceeCCceEEEEEEccCC
Confidence 467666 88999999999999998777
No 48
>PRK14639 hypothetical protein; Provisional
Probab=55.33 E-value=43 Score=24.41 Aligned_cols=48 Identities=21% Similarity=0.323 Sum_probs=32.7
Q ss_pred CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833 65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118 (120)
Q Consensus 65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck 118 (120)
...|..| |-....+-..|+|.+.+.+. +++....+ +..+ .+||++|.+
T Consensus 85 r~~G~~v~v~l~~~~~~~G~L~~~~~~~--i~l~~~~~---~~~~-~i~~~~I~k 133 (140)
T PRK14639 85 KSIGELVKITTNEKEKFEGKIVSVDDEN--ITLENLEN---KEKT-TINFNDIKK 133 (140)
T ss_pred HhCCCEEEEEECCCcEEEEEEEEEeCCE--EEEEEccC---CcEE-EEEhHHeee
Confidence 3478889 75444677889999999876 54433221 2335 499999876
No 49
>PF14505 DUF4438: Domain of unknown function (DUF4438); PDB: 3N99_N 3DCL_A.
Probab=52.60 E-value=15 Score=29.82 Aligned_cols=34 Identities=15% Similarity=0.192 Sum_probs=26.2
Q ss_pred CCCeE-EEecCCCCceEEEEEEeCCccEEEEEEcc
Q 038833 67 IEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEK 100 (120)
Q Consensus 67 ~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~ 100 (120)
+|... |+.|+-+|+.|.++-....-.-+.|.++.
T Consensus 60 iGN~A~VvSG~AKG~~G~VtGkHGGieHVlV~F~~ 94 (258)
T PF14505_consen 60 IGNEAKVVSGDAKGAKGVVTGKHGGIEHVLVDFPD 94 (258)
T ss_dssp BT-EEEE-SSTTTT-EEEEEEEETTTTEEEEE--H
T ss_pred cCceeEEeecccCCCcCeEecccCCeeeEEEECCH
Confidence 68999 99999999999999999888788888765
No 50
>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=51.43 E-value=43 Score=23.96 Aligned_cols=49 Identities=27% Similarity=0.340 Sum_probs=26.8
Q ss_pred CCCeE-EEe-cCCCC---ceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 67 IEGLV-IVN-GAYQG---SNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 67 ~G~~V-Vv~-G~~rG---~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
.|..| |-. .+..| ..|+|.+.+.+. +++++..+. ....+ .++|++|.+.
T Consensus 86 iG~~v~v~~~~~~~~~~~~~G~L~~~~~~~--i~l~~~~~~-~~~~~-~I~~~~I~ka 139 (141)
T PF02576_consen 86 IGRKVKVKLKQPVNGRKEFEGKLLEVDEDE--ITLEVEGKG-KKKEV-EIPFSDIKKA 139 (141)
T ss_dssp -SEEEEEE-SS-SSS-SEEEEEEEEEETTE--EEEEEE-SS--EEEE-EE-SS--SS-
T ss_pred cCCeEEEEEeccCCCcEEEEEEEEEEeCCE--EEEEECCcc-ceEEE-EEEHHHCceE
Confidence 58888 553 33333 489999999876 666666532 11335 5999998763
No 51
>PRK14637 hypothetical protein; Provisional
Probab=50.58 E-value=56 Score=24.16 Aligned_cols=44 Identities=16% Similarity=0.087 Sum_probs=29.4
Q ss_pred CCCeE-EEe-cCCCCc-eEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 67 IEGLV-IVN-GAYQGS-NARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 67 ~G~~V-Vv~-G~~rG~-~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
.|..| |-. | .+.. .|+|.+.+.+. +++... +..+ .+||++|.+.
T Consensus 97 ~G~~V~V~l~~-~~~~~~G~L~~~~d~~--v~l~~~-----~~~~-~i~~~~I~ka 143 (151)
T PRK14637 97 VGETVKVWFEC-TGQWQVGTIAEADETC--LVLTSD-----GVPV-TIPYVQITKA 143 (151)
T ss_pred CCCEEEEEECC-CCcEEEEEEEEEeCCE--EEEEEC-----CEEE-EEEHHHeeeE
Confidence 68889 754 4 3345 59999999876 444332 3435 5999998763
No 52
>PRK14630 hypothetical protein; Provisional
Probab=50.54 E-value=56 Score=23.90 Aligned_cols=45 Identities=13% Similarity=0.110 Sum_probs=29.5
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
..|..| |-...-. ..|+|.+.+.+. +++... +..+ .+||++|.+.
T Consensus 95 ~~G~~v~V~l~~~~-~~G~L~~~~d~~--i~l~~~-----~~~~-~i~~~~I~ka 140 (143)
T PRK14630 95 FEGKKIKLMLDNDF-EEGFILEAKADS--FIFKTD-----SKEV-NVLYSDVKKA 140 (143)
T ss_pred hCCCEEEEEEcCcc-eEEEEEEEeCCE--EEEEEC-----CEEE-EEEhHhcceE
Confidence 368888 6543222 389999998776 544433 2335 5999999863
No 53
>TIGR00405 L26e_arch ribosomal protein L24p/L26e, archaeal. This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons.
Probab=50.29 E-value=37 Score=24.19 Aligned_cols=30 Identities=23% Similarity=0.245 Sum_probs=25.4
Q ss_pred CcccCCcEEEEEeccCCCccceeeeEEEEEecCCc
Q 038833 16 YWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY 50 (120)
Q Consensus 16 ~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~ 50 (120)
..+.+|=.|+|+ +|-|-+-.|.|.++.+..
T Consensus 85 ~~~~~Gd~V~I~-----~GPf~G~~g~v~~~d~~k 114 (145)
T TIGR00405 85 ESIKKGDIVEII-----SGPFKGERAKVIRVDESK 114 (145)
T ss_pred cccCCCCEEEEe-----ecCCCCCeEEEEEEcCCC
Confidence 458999999998 678999999999997643
No 54
>PF08863 YolD: YolD-like protein; InterPro: IPR014962 These proteins are functionally uncharacterised. However it has been predicted that these proteins are functionally equivalent to the UmuD subunit of polymerase V from Gram-negative bacteria [].
Probab=49.32 E-value=32 Score=22.20 Aligned_cols=40 Identities=23% Similarity=0.361 Sum_probs=29.6
Q ss_pred ecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833 74 NGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118 (120)
Q Consensus 74 ~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck 118 (120)
.|.+.-..|++..+|...-...+ .+.+ +. ...++|++|+.
T Consensus 52 ~g~~~~~~G~I~~id~~~~~l~~--~~~~--~~-~~~I~~~~I~~ 91 (92)
T PF08863_consen 52 DGYYQSVTGTIHKIDEINRTLKL--KDED--GE-TEKIPFDDIID 91 (92)
T ss_pred CCeeEEEEEEEEEEcCCCCEEEE--EeCC--CC-EEEEEhhhEEE
Confidence 58888899999999999866654 4322 33 33699999985
No 55
>PRK14636 hypothetical protein; Provisional
Probab=49.12 E-value=62 Score=24.54 Aligned_cols=47 Identities=15% Similarity=0.166 Sum_probs=30.9
Q ss_pred CCCCeE-E-EecCC---CCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 66 QIEGLV-I-VNGAY---QGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 66 ~~G~~V-V-v~G~~---rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
..|..| | ++.+. +-..|+|.+.+.+. +++.+.. +..+ .+||++|.+.
T Consensus 96 ~~G~~V~V~l~~~~~g~k~~~G~L~~v~~~~--v~l~~~~----~~~~-~i~~~~I~kA 147 (176)
T PRK14636 96 WAGHEARIALSEPLDGRKQFRGELKGIDGDT--VTIADNK----AGEV-ILPFAAIESA 147 (176)
T ss_pred hCCCeEEEEEecccCCeEEEEEEEEEEeCCE--EEEEEcC----CcEE-EEEhHHcceE
Confidence 368888 5 45443 44589999998876 5554433 2335 5999998763
No 56
>PF08141 SspH: Small acid-soluble spore protein H family; InterPro: IPR012610 This family consists of the small acid-soluble spore proteins (SASP) of the H type (sspH). SspH are unique to spores of Bacillus subtilis and are expressed only in the forespore compartment during sporulation of this organism. The sspH genes are monocistronic and are recognised by the forespore-specific sigma factor for RNA polymerase - sigma-G. The specific role of this protein is unclear but is thought to play a role in sporulation under conditions different from that of the common laboratory tests of spore properties [].; GO: 0030436 asexual sporulation, 0042601 endospore-forming forespore
Probab=48.25 E-value=52 Score=20.82 Aligned_cols=37 Identities=16% Similarity=0.203 Sum_probs=28.7
Q ss_pred CCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833 77 YQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 77 ~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
|.|.---+.++|.++..|+|...+.+ +... .+|..+|
T Consensus 20 y~G~pV~Ie~vde~~~tA~V~~l~~p--~~~~-~Vpv~~L 56 (58)
T PF08141_consen 20 YNGVPVWIEHVDEENGTARVHPLDNP--EEEQ-EVPVNDL 56 (58)
T ss_pred ECCEEEEEEEEcCCCCeEEEEECCCC--CcEE-EEEHHHc
Confidence 67788899999999999999998655 3333 4777665
No 57
>TIGR02861 SASP_H small acid-soluble spore protein, H-type. This model is derived from pfam08141 but has been expanded to include in the seed corresponding proteins from three species of Clostridium. Members of this family should occur only in endospore-forming bacteria, typically with two members per genome, but may be absent from the genomes of some endospore-forming bacteria. SspH (previously designated YfjU) was shown to be expressed specifically in spores of Bacillus subtilis.
Probab=47.47 E-value=54 Score=20.75 Aligned_cols=37 Identities=19% Similarity=0.253 Sum_probs=28.6
Q ss_pred CCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833 77 YQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 77 ~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
|.|.---+.++|.++.+|+|...+.| ++.. .+|..+|
T Consensus 20 Y~G~pV~Ie~vde~~~tA~V~~l~~p--~~~~-~Vpv~~L 56 (58)
T TIGR02861 20 YKGVPVYIEHVDEQSGTARVYSLDNP--GKEQ-DVPVNDL 56 (58)
T ss_pred ECCEEEEEEEEcCCCCeEEEEECCCC--CcEE-EEEHHHc
Confidence 67888899999999999999988755 3333 3776665
No 58
>PF02427 PSI_PsaE: Photosystem I reaction centre subunit IV / PsaE; InterPro: IPR003375 PsaE is a 69 amino acid polypeptide from photosystem I present on the stromal side of the thylakoid membrane. The structure is comprised of a well-defined five-stranded beta-sheet similar to SH3 domains []. This subunit may form complexes with ferredoxin and ferredoxin-oxidoreductase in the photosystem I reaction centre.; GO: 0015979 photosynthesis, 0009522 photosystem I, 0009538 photosystem I reaction center; PDB: 1PSF_A 1PSE_A 2WSF_E 2WSC_E 2O01_E 2WSE_E 1GXI_E 1JB0_E 3PCQ_E 1QP2_A ....
Probab=47.12 E-value=76 Score=20.43 Aligned_cols=52 Identities=13% Similarity=0.212 Sum_probs=31.7
Q ss_pred CCCCCeE-EEecC--CCCceEEEEEEeCC--ccEEEEEEccCCCCCceEeeeccccc
Q 038833 65 PQIEGLV-IVNGA--YQGSNARLLGVDND--KFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 65 P~~G~~V-Vv~G~--~rG~~g~L~~~d~~--~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
|+.|.+| |++-+ +-..+|++.++|.+ ++-++|+++.-.-.|-.-.++..+.+
T Consensus 1 i~rgskVrIlR~ESYWyn~vGtV~svdqs~i~YPV~VRF~kvNY~g~nTnnfa~~El 57 (61)
T PF02427_consen 1 IKRGSKVRILRKESYWYNEVGTVASVDQSGIRYPVVVRFDKVNYAGVNTNNFALDEL 57 (61)
T ss_dssp S-TTSEEEE-SSSSTTTTSEEEEEEETTSSSSSSEEEE-SSS-SSSSSEEEE-GGGE
T ss_pred CCCCCEEEEccccceeecccceEEEEccCCccccEEEEEEEecccCccccccchhhh
Confidence 4679999 99644 37789999999977 68888888753222222234555444
No 59
>PRK14631 hypothetical protein; Provisional
Probab=44.73 E-value=75 Score=24.08 Aligned_cols=49 Identities=29% Similarity=0.259 Sum_probs=31.2
Q ss_pred CCCCeE-EE-e---cCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 66 QIEGLV-IV-N---GAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 66 ~~G~~V-Vv-~---G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
..|..| |- . +..+-..|+|.+++-++..+++.+.. +..+ .++|++|.+.
T Consensus 115 ~~G~~V~V~l~~~~~~~k~~~G~L~~v~~~~~~v~l~~~~----~~~~-~i~~~~I~ka 168 (174)
T PRK14631 115 YIGQQVALRLIAAVENRRKFQAKLLAVDLENEEIQVEVEG----KHVL-DIDSNNIDKA 168 (174)
T ss_pred hCCCeEEEEEecccCCceEEEEEEEEeecCCCEEEEEEcC----CcEE-EEEhHHcceE
Confidence 468888 54 3 33566789999999333335555443 2335 5999998763
No 60
>PRK14638 hypothetical protein; Provisional
Probab=44.35 E-value=62 Score=23.81 Aligned_cols=45 Identities=16% Similarity=0.103 Sum_probs=30.6
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck 118 (120)
..|..| |-....+-.+|+|.+.+.+. +++... +..+ .+||++|.+
T Consensus 98 ~~G~~v~V~~~~~k~~~G~L~~~~~~~--i~l~~~-----~~~~-~i~~~~I~~ 143 (150)
T PRK14638 98 FTGKLAKIVTKDGKTFIGRIESFVDGT--ITISDE-----KEKY-EINIDDVKR 143 (150)
T ss_pred hCCCEEEEEECCCcEEEEEEEEEeCCE--EEEEEC-----CcEE-EEEhHHcce
Confidence 368888 65433577899999999766 444322 3435 499999876
No 61
>PF02736 Myosin_N: Myosin N-terminal SH3-like domain; InterPro: IPR004009 This domain has an SH3-like fold. It is found at the N terminus of many but not all myosins. The function of this domain is unknown.; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 2EC6_A 2W4H_M 1O1E_P 1O1D_D 1O18_A 1O1C_P 1O1B_D 1O1F_A 2W4A_M 2W4G_M ....
Probab=43.91 E-value=63 Score=18.58 Aligned_cols=37 Identities=16% Similarity=0.297 Sum_probs=24.9
Q ss_pred EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccc
Q 038833 72 IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYED 115 (120)
Q Consensus 72 Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~ydd 115 (120)
|=.-+..-..|.+++++.++ ++|++.+| +.+ .++.||
T Consensus 6 vpD~~egfv~g~I~~~~g~~--vtV~~~~G----~~~-tv~~dd 42 (42)
T PF02736_consen 6 VPDPKEGFVKGEIIEEEGDK--VTVKTEDG----KEV-TVKKDD 42 (42)
T ss_dssp EEESSSSEEEEEEEEEESSE--EEEEETTT----EEE-EEEGGG
T ss_pred EeCCcccEEEEEEEEEcCCE--EEEEECCC----CEE-EeCCCC
Confidence 33334445678999998888 78888874 434 377665
No 62
>TIGR01955 RfaH transcriptional activator RfaH. This model represents the transcriptional activator protein, RfaH. This protein is most closely related to the transcriptional termination/antitermination protein NusG (TIGR00922) and contains the KOW motif (pfam00467). This protein appears to be limited to the gamma proteobacteria. In E. coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.
Probab=43.81 E-value=42 Score=24.00 Aligned_cols=31 Identities=16% Similarity=0.161 Sum_probs=25.4
Q ss_pred CCcccCCcEEEEEeccCCCccceeeeEEEEEecCCc
Q 038833 15 DYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY 50 (120)
Q Consensus 15 ~~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~ 50 (120)
...+.+|=.|+|+ +|-|-+-.|.|.++.+..
T Consensus 106 ~~~~~~G~~V~V~-----~GPf~g~~g~v~~~~~~~ 136 (159)
T TIGR01955 106 TTLPYKGDKVRIT-----DGAFAGFEAIFLEPDGEK 136 (159)
T ss_pred ccCCCCCCEEEEe-----ccCCCCcEEEEEEECCCc
Confidence 4578899999998 678888999999987543
No 63
>PF03947 Ribosomal_L2_C: Ribosomal Proteins L2, C-terminal domain; InterPro: IPR022669 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. Ribosomal protein L2 is one of the proteins from the large ribosomal subunit. This entry represents the best conserved region located in the C-terminal section of these proteins.In Escherichia coli, L2 is known to bind to the 23S rRNA and to have peptidyltransferase activity. It belongs to a family of ribosomal proteins which, on the basis of sequence similarities [, ], groups: Eubacterial L2. Algal and plant chloroplast L2. Cyanelle L2. Archaebacterial L2. Plant L2. Slime mold L2. Marchantia polymorpha mitochondrial L2. Paramecium tetraurelia mitochondrial L2. Fission yeast K5, K37 and KD4. Yeast YL6. Vertebrate L8. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 3MRZ_C 3F1H_D 3PYO_C 3F1F_D 3PYV_C 3PYR_C 1VSA_B 3D5B_D 3PYT_C 3MS1_C ....
Probab=43.25 E-value=50 Score=23.89 Aligned_cols=34 Identities=12% Similarity=0.257 Sum_probs=25.2
Q ss_pred CCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccc
Q 038833 77 YQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC 117 (120)
Q Consensus 77 ~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvc 117 (120)
-.|..|+|++.+.+. ++|+|.+| + +..++.+..|
T Consensus 34 aAGt~a~ii~k~~~~--~~ikLPSG----~-~k~v~~~c~A 67 (130)
T PF03947_consen 34 AAGTYAQIISKEGNY--VVIKLPSG----E-IKLVSSNCRA 67 (130)
T ss_dssp STTBBEEEEEEESSE--EEEEETTS----E-EEEEETTSEE
T ss_pred eCCCEEEEEEeccce--eEEEecCC----C-eEeecccceE
Confidence 478999999999844 88999985 3 4456666544
No 64
>PRK14640 hypothetical protein; Provisional
Probab=42.02 E-value=75 Score=23.37 Aligned_cols=46 Identities=11% Similarity=0.164 Sum_probs=30.7
Q ss_pred CCCCeE-EEe----cCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 66 QIEGLV-IVN----GAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 66 ~~G~~V-Vv~----G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
..|..| |-. +..+-..|+|.+.+.+. +++... ++.+ .+||++|.+.
T Consensus 95 ~~G~~v~V~l~~~~~~~k~~~G~L~~v~~~~--v~l~~~-----~~~~-~i~~~~I~ka 145 (152)
T PRK14640 95 YVGQEAAVTLRMATNNRRKFKGVIKAVQGDM--ITLTVD-----GKDE-VLAFTNIQKA 145 (152)
T ss_pred hCCCeEEEEEecccCCceEEEEEEEEEeCCE--EEEEEC-----CeEE-EEEhHHeeeE
Confidence 368888 642 33566789999998766 444433 2334 4999998763
No 65
>PF12701 LSM14: Scd6-like Sm domain; PDB: 2RM4_A 2FB7_A 2VC8_A 2VXF_A 2VXE_A.
Probab=41.91 E-value=78 Score=21.83 Aligned_cols=33 Identities=12% Similarity=0.159 Sum_probs=27.2
Q ss_pred cCCCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833 64 IPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT 96 (120)
Q Consensus 64 iP~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V 96 (120)
.|-+|.++ ++....-.-.|.|.++|..+..+++
T Consensus 4 ~~~IGs~ISlisk~~iRYeG~L~~Id~~~sTItL 37 (96)
T PF12701_consen 4 DPYIGSKISLISKSDIRYEGILYSIDTEDSTITL 37 (96)
T ss_dssp CCCTTCEEEEEETTTEEEEEEEEEEETTTTEEEE
T ss_pred ccccCCEEEEEECCCcEEEEEEEEEcCCCCEEEe
Confidence 35679999 9988888888999999998866654
No 66
>PF14444 S1-like: S1-like
Probab=41.71 E-value=65 Score=20.53 Aligned_cols=32 Identities=25% Similarity=0.445 Sum_probs=22.0
Q ss_pred eEEEEEecCCc----eEEEeecCceeeecCCCCCeE
Q 038833 40 KGIVRKVIDKY----HVLRADHDELETVIPQIEGLV 71 (120)
Q Consensus 40 KgvV~~V~~~~----~~~~v~q~~LETViP~~G~~V 71 (120)
.|+|..+.+.| ..+=..-+-+.--+|+.|++|
T Consensus 5 ~GvVTkl~~~yG~IDe~vFF~~~vv~G~~P~vGdrV 40 (58)
T PF14444_consen 5 TGVVTKLCDDYGFIDEDVFFQTDVVKGNVPKVGDRV 40 (58)
T ss_pred EEEEEEEeCCcceEcccEEEEcccEecCCCccCCEE
Confidence 57788877766 223333444667899999999
No 67
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=40.25 E-value=53 Score=23.75 Aligned_cols=29 Identities=10% Similarity=-0.054 Sum_probs=24.4
Q ss_pred cccCCcEEEEEeccCCCccceeeeEEEEEecCCc
Q 038833 17 WLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY 50 (120)
Q Consensus 17 Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~ 50 (120)
.+.+|=.|+|+ +|.|-+..|+|..+.+..
T Consensus 109 ~~~~G~~V~I~-----~Gp~~g~eg~v~~~~~~~ 137 (162)
T PRK09014 109 TPKPGDKVIIT-----EGAFEGLQAIYTEPDGEA 137 (162)
T ss_pred CCCCCCEEEEe-----cCCCCCcEEEEEEeCCCe
Confidence 47889999998 678999999999987654
No 68
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=37.23 E-value=53 Score=29.36 Aligned_cols=25 Identities=20% Similarity=0.300 Sum_probs=23.8
Q ss_pred CCCeE-EEecCCCCceEEEEEEeCCc
Q 038833 67 IEGLV-IVNGAYQGSNARLLGVDNDK 91 (120)
Q Consensus 67 ~G~~V-Vv~G~~rG~~g~L~~~d~~~ 91 (120)
.|+.| ||.|.|.+-.|.+.-||.++
T Consensus 142 ~gD~vkVI~g~~~~d~g~V~rI~~~~ 167 (607)
T COG5164 142 KGDLVKVIEGGEMVDIGTVPRIDGEK 167 (607)
T ss_pred cCCeEEEeccccccccceEEEecCce
Confidence 79999 99999999999999999888
No 69
>TIGR00922 nusG transcription termination/antitermination factor NusG. Archaeal proteins once termed NusG share the KOW domain but are actually a ribosomal protein corresponding to L24p in bacterial and L26e in eukaryotes (TIGR00405).
Probab=37.03 E-value=60 Score=23.60 Aligned_cols=30 Identities=23% Similarity=0.130 Sum_probs=25.3
Q ss_pred CCCcccCCcEEEEEeccCCCccceeeeEEEEEecC
Q 038833 14 QDYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVID 48 (120)
Q Consensus 14 ~~~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~ 48 (120)
....+.+|=.|+|+ +|.|-+..|+|..+..
T Consensus 116 ~~~~~~~G~~V~I~-----~Gpf~G~~g~v~~~~~ 145 (172)
T TIGR00922 116 PKIDFEVGEQVRVN-----DGPFANFTGTVEEVDY 145 (172)
T ss_pred cccCCCCCCEEEEe-----ecCCCCcEEEEEEEcC
Confidence 34668899999998 6789999999999974
No 70
>PRK14647 hypothetical protein; Provisional
Probab=36.80 E-value=97 Score=22.89 Aligned_cols=47 Identities=17% Similarity=0.184 Sum_probs=30.8
Q ss_pred CCCCeE-EE-ec--------CCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 66 QIEGLV-IV-NG--------AYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 66 ~~G~~V-Vv-~G--------~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
..|..| |- .. ..+-..|+|.+.+.+. +++.+.. ++.+ .+||++|.+.
T Consensus 97 ~~G~~v~V~l~~~~~~~~~~~~~~~~G~L~~~~~~~--v~l~~~~----~~~~-~i~~~~I~ka 153 (159)
T PRK14647 97 YAGRLVKVRTFELLADEAGNKRKTFLGELEGLADGV--VTIALKE----GQQA-RIPLDKIAKA 153 (159)
T ss_pred hCCcEEEEEEeccccccccCCceEEEEEEEeecCCE--EEEEEcC----CcEE-EEEHHHCCEE
Confidence 368888 54 32 2466789999998765 5554432 3335 4999999763
No 71
>PRK14645 hypothetical protein; Provisional
Probab=36.62 E-value=87 Score=23.24 Aligned_cols=44 Identities=9% Similarity=0.051 Sum_probs=29.8
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck 118 (120)
..|..| |-. ..+-..|+|.+.+.+. +++... +..+ .+||++|.+
T Consensus 100 ~~G~~v~v~~-~~k~~~G~L~~~~d~~--i~l~~~-----~~~~-~i~~~~I~~ 144 (154)
T PRK14645 100 FAGLKAKVRG-PGENFTGRIKAVSGDQ--VTFDVG-----GEDR-TLRIGTFQA 144 (154)
T ss_pred hCCCEEEEEc-CCeEEEEEEEEEeCCE--EEEEEC-----CeEE-EEEHHHhhh
Confidence 368888 754 3466789999998776 444433 3435 499999853
No 72
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=36.10 E-value=1e+02 Score=21.65 Aligned_cols=47 Identities=19% Similarity=0.378 Sum_probs=30.6
Q ss_pred CCCCeE-EE-ec---------CCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833 66 QIEGLV-IV-NG---------AYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 66 ~~G~~V-Vv-~G---------~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
.+|+.| |. ++ .|-|.+|++...-.+.+.+.|. .|. +...+ .+.-++|
T Consensus 34 ~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~V~v~--~G~-k~K~l-iv~peHL 91 (98)
T COG2139 34 KVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRGRAYKVEVY--DGN-KEKTL-IVRPEHL 91 (98)
T ss_pred cCCCEEEEEeCcccccCCCCccccCcceEEEeccCCEEEEEEe--cCC-ceEEE-EeCHHHc
Confidence 467777 43 43 3679999999999999877765 333 23333 3555554
No 73
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=35.86 E-value=1.2e+02 Score=22.75 Aligned_cols=44 Identities=18% Similarity=0.354 Sum_probs=30.4
Q ss_pred CCCeE-EEe----cCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833 67 IEGLV-IVN----GAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118 (120)
Q Consensus 67 ~G~~V-Vv~----G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck 118 (120)
.|..| |-. ...+-..|+|.++|++. +++.++. ..+ .+||+++.|
T Consensus 98 ~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~--v~~~~~~-----k~v-~Ip~~~i~k 146 (153)
T COG0779 98 IGEKVKVKLRLPIEGRKKFEGKIVAVDGET--VTLEVDG-----KEV-EIPFSDIAK 146 (153)
T ss_pred cCcEEEEEEecccCCceEEEEEEEEEcCCe--EEEEECC-----EEE-EEEcccchh
Confidence 57777 554 33555789999999888 5544333 446 499999876
No 74
>TIGR02760 TraI_TIGR conjugative transfer relaxase protein TraI. This protein is a component of the relaxosome complex. In the process of conjugative plasmid transfer the realaxosome binds to the plasmid at the oriT (origin of transfer) site. The relaxase protein TraI mediates the single-strand nicking and ATP-dependent unwinding (relaxation, helicase activity) of the plasmid molecule. These two activities reside in separate domains of the protein.
Probab=35.60 E-value=2.6e+02 Score=28.83 Aligned_cols=79 Identities=9% Similarity=0.125 Sum_probs=52.2
Q ss_pred CcccCCcEEEEEeccCCCccceeeeEEEEEecCCc----------eEEEeecCce-----------eeecC-CCCCeE-E
Q 038833 16 YWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY----------HVLRADHDEL-----------ETVIP-QIEGLV-I 72 (120)
Q Consensus 16 ~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~----------~~~~v~q~~L-----------ETViP-~~G~~V-V 72 (120)
...++|-+|+. +.++.+.+.-++|.+|.... ..+.++.+.| ...+| +.|+++ .
T Consensus 680 ~~Yr~Gdvv~~----y~~~~~~~~~y~V~~V~~~~n~L~l~~~dG~~~~~~p~~l~~~~~~~svy~~~~l~ia~Gdrl~~ 755 (1960)
T TIGR02760 680 AHYKQGMVIRF----WQKGKIPHDDYVVTNVNKHNNTLTLKDAQGKTQKFKPSSLKDLERPFSVYRPEQLEVAAGERLQV 755 (1960)
T ss_pred hhcCCCCEEEe----ecccCccCCcEEEEEEeCCCCEEEEEcCCCCEEEECHHHhcccccceeeeccccccccCCCEEEE
Confidence 45588999987 44455666667888887532 3334555544 33467 789999 5
Q ss_pred Ee-----cCCCCceEEEEEEeCCccEEEEEEcc
Q 038833 73 VN-----GAYQGSNARLLGVDNDKFCAKTKIEK 100 (120)
Q Consensus 73 v~-----G~~rG~~g~L~~~d~~~~~~~V~l~~ 100 (120)
-+ |--+|..+++.+++... ++|+..+
T Consensus 756 trn~~~~gl~ng~~~tV~~i~~~~--i~l~~~~ 786 (1960)
T TIGR02760 756 TGNHFHSRVRNGELLTVSSINNEG--ITLITED 786 (1960)
T ss_pred ccCCcccCccCCCEEEEEEEcCCe--EEEEeCC
Confidence 52 44578899999999876 5555544
No 75
>PTZ00180 60S ribosomal protein L8; Provisional
Probab=33.84 E-value=75 Score=25.87 Aligned_cols=35 Identities=14% Similarity=0.248 Sum_probs=25.3
Q ss_pred CCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccc
Q 038833 78 QGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC 117 (120)
Q Consensus 78 rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvc 117 (120)
.|..|+|++.+.+...++|+|.||. +..++.+..|
T Consensus 130 AGt~A~ii~k~k~~~~~~vkLPSGe-----~r~v~~~c~A 164 (260)
T PTZ00180 130 SGCYATIIGHSDDGGKTRIRLPSGQ-----KKTVSSLSRA 164 (260)
T ss_pred cCCeEEEEEEcccCCEEEEECCCCC-----eEeECCCCeE
Confidence 6889999998766667889999864 4446655443
No 76
>PRK03174 sspH acid-soluble spore protein H; Provisional
Probab=33.54 E-value=1.1e+02 Score=19.47 Aligned_cols=37 Identities=16% Similarity=0.207 Sum_probs=28.0
Q ss_pred CCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833 77 YQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 77 ~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
|.|.---+.++|.++.+|+|...+.|. +.. .+|..+|
T Consensus 20 Y~G~pV~Ie~vde~~~tA~I~~l~~p~--~~~-~Vpv~~L 56 (59)
T PRK03174 20 YNGVPIYIQHVDEQNGTARIHPLDNPN--QEQ-SVPLASL 56 (59)
T ss_pred ECCEEEEEEEEcCCCCeEEEEECCCCC--cEE-EEEHHHh
Confidence 778888999999999999999887653 323 3665554
No 77
>PF15436 PGBA_N: Plasminogen-binding protein pgbA N-terminal
Probab=33.40 E-value=63 Score=25.64 Aligned_cols=55 Identities=22% Similarity=0.257 Sum_probs=34.2
Q ss_pred CccceeeeEEEEEecCCceE------EEeecCceee--ecCCCCCeEEEecCCCCceEEEEEEeC
Q 038833 33 DKGYCKQKGIVRKVIDKYHV------LRADHDELET--VIPQIEGLVIVNGAYQGSNARLLGVDN 89 (120)
Q Consensus 33 ~gk~y~~KgvV~~V~~~~~~------~~v~q~~LET--ViP~~G~~VVv~G~~rG~~g~L~~~d~ 89 (120)
+..---..++|.++.++... ..+.|++|=| +.|+.|+.||++--| ..|-|+.=|.
T Consensus 40 ~~~~IiA~a~V~~~~~g~A~~kf~~fd~L~Q~aLP~p~~~pk~GD~vil~~~Y--~rallIAPn~ 102 (218)
T PF15436_consen 40 DHSSIIARAVVISKKNGVAKAKFSVFDSLKQDALPTPKMVPKKGDEVILNYLY--NRALLIAPNQ 102 (218)
T ss_pred CcceeeeEEEEEEecCCeeEEEEeehhhhhhhcCCCCccccCCCCEEEEeecc--cceEEEcCCH
Confidence 33445556666666665522 2577888865 788999999886333 3455554443
No 78
>TIGR02594 conserved hypothetical protein TIGR02594. Members of this protein family known so far are restricted to the bacteria, and for the most to the proteobacteria. The function is unknown.
Probab=33.22 E-value=1.6e+02 Score=20.97 Aligned_cols=43 Identities=14% Similarity=0.164 Sum_probs=28.7
Q ss_pred cCCCCCeEEEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEe
Q 038833 64 IPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLN 109 (120)
Q Consensus 64 iP~~G~~VVv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~ 109 (120)
-|++|+-|+......|.+|-.+..+.++. ++.+..|...+. |.
T Consensus 73 ~p~~GDiv~f~~~~~~HVGi~~g~~~~~g--~i~~lgGNq~~~-V~ 115 (129)
T TIGR02594 73 KPAYGCIAVKRRGGGGHVGFVVGKDKQTG--TIIVLGGNQGDR-VR 115 (129)
T ss_pred CCCccEEEEEECCCCCEEEEEEeEcCCCC--EEEEeeCCCCCe-EE
Confidence 37889887554333789999999887753 455676655444 54
No 79
>KOG3421 consensus 60S ribosomal protein L14 [Translation, ribosomal structure and biogenesis]
Probab=33.10 E-value=51 Score=24.44 Aligned_cols=25 Identities=12% Similarity=0.235 Sum_probs=20.3
Q ss_pred CCCeE-EEecCCCCceEEEEEEeCCc
Q 038833 67 IEGLV-IVNGAYQGSNARLLGVDNDK 91 (120)
Q Consensus 67 ~G~~V-Vv~G~~rG~~g~L~~~d~~~ 91 (120)
+|.-+ |..|+|.|.+.-+.+++.++
T Consensus 9 VGrva~v~~G~~~GkL~AIVdviDqn 34 (136)
T KOG3421|consen 9 VGRVALVSFGPDAGKLVAIVDVIDQN 34 (136)
T ss_pred cceEEEEEecCCCceEEEEEEeecch
Confidence 35444 77899999999999998777
No 80
>PRK01625 sspH acid-soluble spore protein H; Provisional
Probab=32.15 E-value=1.2e+02 Score=19.33 Aligned_cols=37 Identities=14% Similarity=0.175 Sum_probs=27.7
Q ss_pred CCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833 77 YQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 77 ~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
|.|.---+.++|.++..|+|...+.|. +.. .+|..+|
T Consensus 20 Y~G~pV~Iq~vde~~~tA~V~~~~~p~--~e~-~Vpv~~L 56 (59)
T PRK01625 20 YEGVPVWIESCDEQSGVAQVYDVSNPG--ESV-HVDVTAL 56 (59)
T ss_pred ECCEEEEEEEEcCCCCeEEEEecCCCC--cEE-EEEHHHc
Confidence 678888999999999999999887653 323 3665544
No 81
>cd06553 ASCH_Ef3133_like ASC-1 homology domain, subfamily similar to Enterococcus faecalis Ef3133. The ASCH domain, a small beta-barrel domain found in all three kingdoms of life, resembles the RNA-binding PUA domain and may also interact with RNA. ASCH has been proposed to function as an RNA-binding domain during coactivation, RNA-processing and the regulation of prokaryotic translation.
Probab=31.83 E-value=87 Score=22.55 Aligned_cols=34 Identities=15% Similarity=0.444 Sum_probs=21.7
Q ss_pred cCCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccc
Q 038833 64 IPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC 117 (120)
Q Consensus 64 iP~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvc 117 (120)
+|++|+.- |++|. .+..+.+++.+ |..++|++|.
T Consensus 42 ~p~vG~~~Ivld~~-------------g~p~cvi~~~~-------V~~~~f~~vt 76 (127)
T cd06553 42 LPKVGDYSIILDGQ-------------GKPVCIIETTE-------VEVVPFNDVT 76 (127)
T ss_pred CCCCCcEEEEECCC-------------CCEEEEEEEEE-------EEEEEcccCC
Confidence 89999955 66662 23345556554 6667777765
No 82
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=31.39 E-value=1.3e+02 Score=21.90 Aligned_cols=48 Identities=21% Similarity=0.256 Sum_probs=30.8
Q ss_pred CCCCCeE-EE-e---cCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833 65 PQIEGLV-IV-N---GAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118 (120)
Q Consensus 65 P~~G~~V-Vv-~---G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck 118 (120)
...|..| |- + +..+-..|+|.+.+.+. +++..... ...+ .++|++|.+
T Consensus 95 r~~G~~v~V~~~~~~~~~~~~~G~L~~~~~~~--i~l~~~~~---~~~~-~i~~~~I~~ 147 (154)
T PRK00092 95 RFIGREVKVKLYEPIDGRKKFQGILLAVDGET--VTLEVEGK---EKEV-EIPLDNIAK 147 (154)
T ss_pred HhCCCeEEEEEEcccCCceEEEEEEEEeeCCE--EEEEECCC---eEEE-EEEHHHcce
Confidence 4478888 64 2 33445589999999876 44443321 1245 499999876
No 83
>PF11948 DUF3465: Protein of unknown function (DUF3465); InterPro: IPR021856 This family of proteins are functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 131 to 151 amino acids in length. This protein has a conserved HWTH sequence motif.
Probab=31.24 E-value=1.8e+02 Score=21.45 Aligned_cols=55 Identities=25% Similarity=0.295 Sum_probs=36.5
Q ss_pred CCcEEEEEeccCCCccceeeeEEEEEecCCceEEEeecCceeeecC--CCCCeEEEecCC
Q 038833 20 KGIIVEVMSKAFADKGYCKQKGIVRKVIDKYHVLRADHDELETVIP--QIEGLVIVNGAY 77 (120)
Q Consensus 20 ~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~~~~~v~q~~LETViP--~~G~~VVv~G~~ 77 (120)
.+-++|+........+ .|+.+ .++.++-+++=++.-.|-+=|| +.|+.|-+.|+|
T Consensus 42 ~G~V~~vLpdd~~Gsr--HQ~Fi-v~l~~g~tllIahNIDlaprip~l~~GD~V~f~GeY 98 (131)
T PF11948_consen 42 CGTVVKVLPDDNKGSR--HQRFI-VRLSSGQTLLIAHNIDLAPRIPWLQKGDQVEFYGEY 98 (131)
T ss_pred cEEEEEECcccCCCCc--ceEEE-EEeCCCCEEEEEeccCccccCcCcCCCCEEEEEEEE
Confidence 4567777655444333 55544 4455555666666667778888 689999888988
No 84
>PRK02749 photosystem I reaction center subunit IV; Provisional
Probab=31.17 E-value=1.1e+02 Score=20.32 Aligned_cols=35 Identities=17% Similarity=0.261 Sum_probs=26.8
Q ss_pred CCCCeE-EEecC--CCCceEEEEEEeCC--ccEEEEEEcc
Q 038833 66 QIEGLV-IVNGA--YQGSNARLLGVDND--KFCAKTKIEK 100 (120)
Q Consensus 66 ~~G~~V-Vv~G~--~rG~~g~L~~~d~~--~~~~~V~l~~ 100 (120)
+.|++| |++-+ +-..+|++.++|.+ ++-++|+++.
T Consensus 4 ~rGskVrIlR~ESYWyn~vGtV~svD~sgi~YPV~VRF~k 43 (71)
T PRK02749 4 SRGDKVRILRPESYWYNEVGTVASVDKSGIKYPVIVRFDK 43 (71)
T ss_pred ccCCEEEEccccceeecCcceEEEEccCCCeeeEEEEeee
Confidence 468899 99644 36789999999977 5778887764
No 85
>PRK02001 hypothetical protein; Validated
Probab=31.01 E-value=1.9e+02 Score=21.47 Aligned_cols=50 Identities=14% Similarity=0.203 Sum_probs=32.1
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCC---------CCCceEeeeccccccc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGV---------NDGRVLNAIDYEDICK 118 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~---------~~~~~v~~~~yddvck 118 (120)
..|..| |-....+-..|+|.+.+.+. +++...... ..+..+ .++|++|.+
T Consensus 88 ~~G~~v~V~l~~~~~~~G~L~~~~~~~--i~l~~~~~~~~~~~k~~~~~~~~~-~i~~~~I~k 147 (152)
T PRK02001 88 NIGRELEVLTKNGKKIEGELKSADEND--ITLEVKAREPKEGGKGKVTVEKEE-TITYDDIKE 147 (152)
T ss_pred hCCCEEEEEECCCCEEEEEEEEEeCCE--EEEEEcccccccccccccccceeE-EEEhHheee
Confidence 478888 65433577889999999776 555444210 012234 499999876
No 86
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=30.53 E-value=1.1e+02 Score=28.34 Aligned_cols=44 Identities=18% Similarity=0.261 Sum_probs=29.7
Q ss_pred CCCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccccc
Q 038833 65 PQIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICK 118 (120)
Q Consensus 65 P~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck 118 (120)
+++|++| |.. -|+.|++++++.++ .+.|++.. ..+ .++.+++.+
T Consensus 637 ~~~Gd~V~v~~---~~~~g~v~~i~~~~-~~~V~~g~-----~k~-~v~~~~l~~ 681 (782)
T PRK00409 637 LKVGDEVKYLS---LGQKGEVLSIPDDK-EAIVQAGI-----MKM-KVPLSDLEK 681 (782)
T ss_pred CCCCCEEEEcc---CCceEEEEEEcCCC-eEEEEECC-----EEE-EEeHHHcee
Confidence 5789999 754 45789999997533 57777632 234 377776643
No 87
>PRK04914 ATP-dependent helicase HepA; Validated
Probab=30.26 E-value=3.7e+02 Score=25.75 Aligned_cols=52 Identities=13% Similarity=0.092 Sum_probs=38.6
Q ss_pred eEEEEEecCCc-----------eEEEeecCceeeecCCCCCeE-EEecCCCCceEEEEEEeCCccEEE
Q 038833 40 KGIVRKVIDKY-----------HVLRADHDELETVIPQIEGLV-IVNGAYQGSNARLLGVDNDKFCAK 95 (120)
Q Consensus 40 KgvV~~V~~~~-----------~~~~v~q~~LETViP~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~ 95 (120)
=|+|.+|.++. +++.++..-|--|++.+|+.| .-.| ...++.++.+.+....
T Consensus 18 lG~v~~~d~r~vtv~fpas~e~R~ya~~~apl~Rv~~~~g~~v~~~~~----~~~~v~~v~~~~gl~~ 81 (956)
T PRK04914 18 LGTVVAVDGRTVTLLFPATGENRLYARNDAPLTRVMFNPGDTITSHEG----WQLTVEEVEEENGLLT 81 (956)
T ss_pred cEEEEEEeCCEEEEEecCCCCceeeecCCCCceeeecCCCCEEEecCC----CEEEEEEEeccCCcEE
Confidence 47888887766 677889999999999999999 6565 4455555655554443
No 88
>CHL00125 psaE photosystem I subunit IV; Reviewed
Probab=30.05 E-value=1.2e+02 Score=19.76 Aligned_cols=35 Identities=17% Similarity=0.264 Sum_probs=26.8
Q ss_pred CCCCeE-EEecC--CCCceEEEEEEeCC--ccEEEEEEcc
Q 038833 66 QIEGLV-IVNGA--YQGSNARLLGVDND--KFCAKTKIEK 100 (120)
Q Consensus 66 ~~G~~V-Vv~G~--~rG~~g~L~~~d~~--~~~~~V~l~~ 100 (120)
+.|.+| |++-+ +-..+|++.++|.+ ++-++|+++.
T Consensus 3 ~rGskVrIlR~ESYWyn~vGtV~svd~~gi~YPV~VRF~k 42 (64)
T CHL00125 3 KRGSKVRILRKESYWYNEIGTVATVDQSGIRYPVLVRFEK 42 (64)
T ss_pred ccCCEEEEccccceeecCcceEEEEcCCCCCccEEEEEee
Confidence 468899 99644 36788999999876 5778888765
No 89
>COG1047 SlpA FKBP-type peptidyl-prolyl cis-trans isomerases 2 [Posttranslational modification, protein turnover, chaperones]
Probab=29.66 E-value=1.7e+02 Score=22.42 Aligned_cols=54 Identities=20% Similarity=0.226 Sum_probs=37.6
Q ss_pred EEEeecCceeee-cCCCCCeEEEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceE
Q 038833 52 VLRADHDELETV-IPQIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVL 108 (120)
Q Consensus 52 ~~~v~q~~LETV-iP~~G~~VVv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v 108 (120)
+..++-+.+.-. -|.+|..|.+.+...-..|++.+++.++ |+|.++. |.-|+.+
T Consensus 77 vq~vp~~~F~~~~~~~vGm~~~~~~~~~~~~~~V~~V~~~~--V~VDfNH-pLAGktL 131 (174)
T COG1047 77 VQRVPRDEFQGVGELEVGMEVEAEGGDGEIPGVVTEVSGDR--VTVDFNH-PLAGKTL 131 (174)
T ss_pred eEEecHHHhCcCCCCCCCcEEEEcCCCceeeEEEEEEcCCE--EEEeCCC-cCCCCeE
Confidence 334555555555 5688888877666677789999999888 7776654 5567755
No 90
>PRK14632 hypothetical protein; Provisional
Probab=29.66 E-value=1.7e+02 Score=22.01 Aligned_cols=50 Identities=16% Similarity=0.231 Sum_probs=30.8
Q ss_pred CCCCeE-EE-ecC------CCCceEEEEEEeCCccEEEEEEccCCC---CCceEeeeccccccc
Q 038833 66 QIEGLV-IV-NGA------YQGSNARLLGVDNDKFCAKTKIEKGVN---DGRVLNAIDYEDICK 118 (120)
Q Consensus 66 ~~G~~V-Vv-~G~------~rG~~g~L~~~d~~~~~~~V~l~~g~~---~~~~v~~~~yddvck 118 (120)
..|..| |- ..+ .+-..|+|.+.+.+. +++.....+. .+..+ .++|++|.+
T Consensus 96 ~iG~~V~V~l~~~~~~~~g~k~~~G~L~~v~~~~--i~l~~~~~~~~~~~~~~~-~i~~~~I~k 156 (172)
T PRK14632 96 YVGRQIELTLIDPTPEWPGRRKFRGELLAVEGDT--VVLRPEGAPAPEAEEAVL-RTSWQGVRK 156 (172)
T ss_pred hCCCEEEEEEeccccccCCceEEEEEEEEEeCCE--EEEEEcCcccccCCceeE-EEEhHHccE
Confidence 368888 64 442 356679999998776 5555432110 11234 599999876
No 91
>PRK14646 hypothetical protein; Provisional
Probab=29.04 E-value=1.5e+02 Score=21.95 Aligned_cols=46 Identities=20% Similarity=0.207 Sum_probs=29.8
Q ss_pred CCCCeE-EE-ecC---CCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 66 QIEGLV-IV-NGA---YQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 66 ~~G~~V-Vv-~G~---~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
..|..| |- ..+ .+-..|+|.+.+.+. +++.+. ++.+ .+||++|.+.
T Consensus 98 ~~G~~v~V~l~~~~~~~~~~~G~L~~~~~~~--v~l~~~-----g~~~-~i~~~~I~ka 148 (155)
T PRK14646 98 FKGFPVNVELNQKNSKIKFLNGLLYEKSKDY--LAINIK-----GKIK-KIPFNEVLKI 148 (155)
T ss_pred hCCCEEEEEEecCcCCeEEEEEEEEEEeCCE--EEEEEC-----CEEE-EEEHHHeeeE
Confidence 368888 54 332 233469999999876 555432 3445 4999999763
No 92
>KOG3418 consensus 60S ribosomal protein L27 [Translation, ribosomal structure and biogenesis]
Probab=29.04 E-value=62 Score=23.97 Aligned_cols=22 Identities=23% Similarity=0.468 Sum_probs=17.9
Q ss_pred CCCCeE-EEecCCCCceEEEEEE
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGV 87 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~ 87 (120)
++|.-| |+.|.|.|..+.+++-
T Consensus 6 kPgkvv~v~sG~yAg~KaVivk~ 28 (136)
T KOG3418|consen 6 KPGKVVLVLSGRYAGKKAVIVKN 28 (136)
T ss_pred cCCcEEEeecccccCccEEEEee
Confidence 568888 9999999998876654
No 93
>TIGR01171 rplB_bact ribosomal protein L2, bacterial/organellar. This model distinguishes bacterial and organellar ribosomal protein L2 from its counterparts in the archaea nad in the eukaryotic cytosol. Plant mitochondrial examples tend to have long, variable inserts.
Probab=28.69 E-value=87 Score=25.60 Aligned_cols=33 Identities=15% Similarity=0.280 Sum_probs=23.5
Q ss_pred CCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccc
Q 038833 78 QGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC 117 (120)
Q Consensus 78 rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvc 117 (120)
.|..|+|++.+.+ .++|+|.||. +..++.+..|
T Consensus 156 AGt~A~ii~k~~~--~~~vkLPSGe-----~r~i~~~c~A 188 (273)
T TIGR01171 156 AGTSAQILAKEGG--YVTLRLPSGE-----MRMVLKECRA 188 (273)
T ss_pred cCCeEEEEEecCC--EEEEECCCCC-----eEEECCcCeE
Confidence 6888999987754 4889999853 4456666544
No 94
>PF13051 DUF3912: Protein of unknown function (DUF3912)
Probab=28.64 E-value=1.2e+02 Score=19.49 Aligned_cols=23 Identities=13% Similarity=0.225 Sum_probs=17.9
Q ss_pred CCCeE-EEecCCCCceEEEEEEeC
Q 038833 67 IEGLV-IVNGAYQGSNARLLGVDN 89 (120)
Q Consensus 67 ~G~~V-Vv~G~~rG~~g~L~~~d~ 89 (120)
.|.+. |=.|+||-..|.+.....
T Consensus 5 ~gqkayikdgp~rnrigivk~~e~ 28 (68)
T PF13051_consen 5 VGQKAYIKDGPYRNRIGIVKKNEK 28 (68)
T ss_pred cccEeeeccCCccceeEEEecchh
Confidence 46677 778999999998877654
No 95
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=28.17 E-value=1.2e+02 Score=22.14 Aligned_cols=29 Identities=24% Similarity=0.241 Sum_probs=25.2
Q ss_pred CCcccCCcEEEEEeccCCCccceeeeEEEEEecC
Q 038833 15 DYWLFKGIIVEVMSKAFADKGYCKQKGIVRKVID 48 (120)
Q Consensus 15 ~~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~ 48 (120)
...+.+|=.|+|+ +|.|-+..|.|..+..
T Consensus 124 ~~~~~~Gd~VrI~-----~GPf~G~~g~v~~i~~ 152 (181)
T PRK05609 124 KVDFEVGEMVRVI-----DGPFADFNGTVEEVDY 152 (181)
T ss_pred ccCCCCCCEEEEe-----ccCCCCCEEEEEEEeC
Confidence 4678899999998 6789999999999973
No 96
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=27.73 E-value=1.4e+02 Score=27.69 Aligned_cols=42 Identities=12% Similarity=0.158 Sum_probs=29.3
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccc
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC 117 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvc 117 (120)
++|+.| |. .-|+.|++++++. +..+.|++.. ..+ .++.+++.
T Consensus 626 ~~Gd~V~v~---~~~~~g~v~~i~~-~~~~~V~~g~-----~k~-~v~~~~l~ 668 (771)
T TIGR01069 626 KIGDKVRIR---YFGQKGKIVQILG-GNKWNVTVGG-----MRM-KVHGSELE 668 (771)
T ss_pred CCCCEEEEc---cCCceEEEEEEcC-CCeEEEEECC-----EEE-EEeHHHce
Confidence 889999 64 4678999999974 4457777643 224 37777764
No 97
>PRK14634 hypothetical protein; Provisional
Probab=27.70 E-value=1.4e+02 Score=21.97 Aligned_cols=45 Identities=20% Similarity=0.215 Sum_probs=30.3
Q ss_pred CCCeE-E-EecC---CCCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 67 IEGLV-I-VNGA---YQGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 67 ~G~~V-V-v~G~---~rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
.|..| | +..+ .+-..|+|.+.+.+. +++.+. +..+ .+||++|.+.
T Consensus 99 ~G~~V~V~l~~~~~~~k~~~G~L~~~~~~~--v~l~~~-----~~~~-~i~~~~I~ka 148 (155)
T PRK14634 99 RGFPVEVSHRDDDGSEQRLEGLLLERNEDH--LQINIR-----GRIK-RIPRDSVISV 148 (155)
T ss_pred CCCeEEEEEecCCCCeEEEEEEEEEEeCCE--EEEEEC-----CEEE-EEEHHHeeeE
Confidence 68888 6 4432 356789999998776 444432 3435 4999999864
No 98
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=26.67 E-value=1.6e+02 Score=22.36 Aligned_cols=30 Identities=20% Similarity=0.206 Sum_probs=25.2
Q ss_pred CcccCCcEEEEEeccCCCccceeeeEEEEEecCCc
Q 038833 16 YWLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDKY 50 (120)
Q Consensus 16 ~Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~~ 50 (120)
.=+.+|=.|||+ +|-|.+.+|.|..|....
T Consensus 122 ~~~e~Gd~VrI~-----~GpFa~f~g~V~evd~ek 151 (178)
T COG0250 122 VDFEPGDVVRII-----DGPFAGFKAKVEEVDEEK 151 (178)
T ss_pred ccCCCCCEEEEe-----ccCCCCccEEEEEEcCcC
Confidence 346788899998 678999999999998764
No 99
>KOG3401 consensus 60S ribosomal protein L26 [Translation, ribosomal structure and biogenesis]
Probab=26.39 E-value=33 Score=25.65 Aligned_cols=42 Identities=17% Similarity=0.284 Sum_probs=31.8
Q ss_pred eecCceeeecC-CCCCeE-EEecCCCC-ceEEEEEEeCCccEEEE
Q 038833 55 ADHDELETVIP-QIEGLV-IVNGAYQG-SNARLLGVDNDKFCAKT 96 (120)
Q Consensus 55 v~q~~LETViP-~~G~~V-Vv~G~~rG-~~g~L~~~d~~~~~~~V 96 (120)
+.|.+-=+-+| ..++.| |.+|.++| +.|...++-..++...+
T Consensus 38 LR~~y~vrs~pir~ddev~v~rg~~kG~q~G~v~~vyrKk~~iyi 82 (145)
T KOG3401|consen 38 LRQKYNVRSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRKKYVIYI 82 (145)
T ss_pred HHHHhCccccceeeccEEEEEeccccccccceehhhhhhhheeee
Confidence 44444445566 567889 99999999 99999999888876554
No 100
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=25.74 E-value=1.2e+02 Score=20.42 Aligned_cols=9 Identities=22% Similarity=0.301 Sum_probs=7.5
Q ss_pred ecCCCCCeE
Q 038833 63 VIPQIEGLV 71 (120)
Q Consensus 63 ViP~~G~~V 71 (120)
-+|++|+.|
T Consensus 2 Y~P~~gD~V 10 (86)
T cd05790 2 YVPAKGDHV 10 (86)
T ss_pred CcCCCCCEE
Confidence 479999987
No 101
>PRK14643 hypothetical protein; Provisional
Probab=25.62 E-value=2.2e+02 Score=21.28 Aligned_cols=49 Identities=12% Similarity=0.140 Sum_probs=30.7
Q ss_pred CCCeE-EE-ecC---CCCceEEEEEEeCCccEEEEEE--ccCCCCCceEeeecccccccc
Q 038833 67 IEGLV-IV-NGA---YQGSNARLLGVDNDKFCAKTKI--EKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 67 ~G~~V-Vv-~G~---~rG~~g~L~~~d~~~~~~~V~l--~~g~~~~~~v~~~~yddvck~ 119 (120)
.|..| |- ..+ .+-..|+|.+.+.+. +++.+ ..+. .+..+ .+||++|.+.
T Consensus 103 ~G~~V~V~l~~~~~g~k~~~G~L~~~~~~~--~~l~l~~~~~~-~~~~~-~ip~~~I~ka 158 (164)
T PRK14643 103 LNQWVYVQLNNEIKKVKEFEGYVTKYNVNT--NTFRFTFFIKG-QKKKL-DVKYEQIKFI 158 (164)
T ss_pred cCCeEEEEEecccCCceEEEEEEEEEeCCc--EEEEEEeeccC-cCcEE-EEeHHHhhhe
Confidence 68888 64 333 345689999999887 44432 2211 23445 4999998763
No 102
>COG0234 GroS Co-chaperonin GroES (HSP10) [Posttranslational modification, protein turnover, chaperones]
Probab=25.60 E-value=2.4e+02 Score=19.69 Aligned_cols=47 Identities=26% Similarity=0.339 Sum_probs=28.7
Q ss_pred eeEEEEEecCCceEEEeecCceeeecC--CCCCeEEEecCCCCceEEEEEEeCCccEE
Q 038833 39 QKGIVRKVIDKYHVLRADHDELETVIP--QIEGLVIVNGAYQGSNARLLGVDNDKFCA 94 (120)
Q Consensus 39 ~KgvV~~V~~~~~~~~v~q~~LETViP--~~G~~VVv~G~~rG~~g~L~~~d~~~~~~ 94 (120)
++|.|..|-.+. .+.+- +-+.| +.|++| +.++|.| +-+.+|.+++..
T Consensus 36 ~~g~VvAVG~G~----~~~~g-~~~~~~VkvGD~V-lf~ky~G---~evk~dgeeyli 84 (96)
T COG0234 36 QEGEVVAVGPGR----RDENG-ELVPLDVKVGDRV-LFGKYAG---TEVKIDGEEYLI 84 (96)
T ss_pred cceEEEEEccce----ecCCC-CEeccccccCCEE-EECccCC---cEEEECCEEEEE
Confidence 777888776542 22222 22333 578887 7788988 556667777543
No 103
>PF04452 Methyltrans_RNA: RNA methyltransferase; InterPro: IPR006700 Methyltransferases (Mtases) are responsible for the transfer of methyl groups between two molecules. The transfer of the methyl group from the ubiquitous S-adenosyl-L-methionine (AdoMet) to either nitrogen, oxygen or carbon atoms is frequently employed in diverse organisms. The reaction is catalyzed by Mtases and modifies DNA, RNA, proteins or small molecules, such as catechol, for regulatory purposes. Proteins in this entry belong to the RsmE family of Mtases, this is supported by crystal structural studying, which show a close structural homology to other known methyltransferases []. This entry contains RsmE of Escherichia coli, which specifically methylates the uridine in position 1498 of 16S rRNA in the fully assembled 30S ribosomal subunit [, ].; GO: 0008168 methyltransferase activity, 0006364 rRNA processing; PDB: 1NXZ_B 1VHY_B 2EGW_A 2EGV_A 2Z0Y_A 2CX8_A 3KW2_A 1VHK_D 1Z85_B 1V6Z_A ....
Probab=25.60 E-value=85 Score=24.01 Aligned_cols=39 Identities=10% Similarity=0.158 Sum_probs=29.2
Q ss_pred CceeeecC-CCCCeE-EEecCCCCceEEEEEEeCCccEEEE
Q 038833 58 DELETVIP-QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKT 96 (120)
Q Consensus 58 ~~LETViP-~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V 96 (120)
.||-.|+= ++|+.| +..|.-.--.|++.+++.+...+.+
T Consensus 9 ~Hl~~VlR~k~Gd~i~v~dg~g~~~~a~i~~i~~~~~~~~i 49 (225)
T PF04452_consen 9 HHLVKVLRLKEGDSIEVFDGDGGEYRAEITEISKKSATLRI 49 (225)
T ss_dssp HHHHTTST--TT-EEEEEESSSEEEEEEEEEEESSEEEEEE
T ss_pred HHHHHhcCCCCCCEEEEEECCCCEEEEEEEECcCcEEEEEE
Confidence 35656666 789999 9999889999999999988854433
No 104
>PTZ00471 60S ribosomal protein L27; Provisional
Probab=25.40 E-value=98 Score=22.87 Aligned_cols=28 Identities=25% Similarity=0.417 Sum_probs=22.2
Q ss_pred cccCCcEEEEEeccCCCccceeeeEEEEEecCC
Q 038833 17 WLFKGIIVEVMSKAFADKGYCKQKGIVRKVIDK 49 (120)
Q Consensus 17 Wl~~~I~Vkii~k~~~~gk~y~~KgvV~~V~~~ 49 (120)
.+.||-+|=+. .|+|.++|++|....|.
T Consensus 4 ~~kpgkVVivL-----~GR~AGkKaVivk~~dd 31 (134)
T PTZ00471 4 FLKPGKVVIVT-----SGRYAGRKAVIVQNFDT 31 (134)
T ss_pred cccCCEEEEEE-----ccccCCcEEEEEeecCC
Confidence 46788887554 67999999999998774
No 105
>PRK09374 rplB 50S ribosomal protein L2; Validated
Probab=24.93 E-value=1.1e+02 Score=25.04 Aligned_cols=33 Identities=18% Similarity=0.289 Sum_probs=23.2
Q ss_pred CCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccc
Q 038833 78 QGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC 117 (120)
Q Consensus 78 rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvc 117 (120)
.|..|+|++.+.+ .++|+|.||. +..++.+..|
T Consensus 158 AGt~A~ii~k~~~--~~~vkLPSGe-----~r~i~~~c~A 190 (276)
T PRK09374 158 AGTSAQLVAKEGK--YATLRLPSGE-----VRKVLAECRA 190 (276)
T ss_pred cCCeEEEEEecCC--EEEEECCCCC-----eEEEcccccE
Confidence 6788999987644 4889999853 4456665543
No 106
>CHL00052 rpl2 ribosomal protein L2
Probab=24.44 E-value=1.2e+02 Score=24.88 Aligned_cols=33 Identities=21% Similarity=0.314 Sum_probs=22.9
Q ss_pred CCceEEEEEEeCCccEEEEEEccCCCCCceEeeecccccc
Q 038833 78 QGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDIC 117 (120)
Q Consensus 78 rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvc 117 (120)
.|..|+|++.+.+ .+.|+|.||. +..++.+..|
T Consensus 156 AGt~A~ii~k~~~--~~~vkLPSGe-----~r~v~~~c~A 188 (273)
T CHL00052 156 AGAVAKLIAKEGK--SATLKLPSGE-----VRLISKNCSA 188 (273)
T ss_pred cCCeEEEEEecCC--EEEEECCCCC-----eEEECCcCeE
Confidence 6888999998644 4889999853 3346655443
No 107
>PF03646 FlaG: FlaG protein; InterPro: IPR005186 Although these proteins are known to be important for flagellar their exact function is unknown.; PDB: 2HC5_A.
Probab=24.40 E-value=45 Score=22.59 Aligned_cols=34 Identities=24% Similarity=0.314 Sum_probs=21.9
Q ss_pred EEEeCCccEEEEEEccCCCCCceEeeecccccccc
Q 038833 85 LGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDICKL 119 (120)
Q Consensus 85 ~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddvck~ 119 (120)
-++|++-....|++.+.. +|++|+.+|-+.+-++
T Consensus 59 F~vde~~~~~vVkViD~~-T~eVIRqIP~Ee~l~l 92 (107)
T PF03646_consen 59 FSVDEESGRVVVKVIDKE-TGEVIRQIPPEELLDL 92 (107)
T ss_dssp EEEEEETTEEEEEEEETT-T-SEEEEE-HHHHHHH
T ss_pred EEEecCCCcEEEEEEECC-CCcEEEeCCcHHHHHH
Confidence 355666566777777633 6899999998877654
No 108
>PRK14635 hypothetical protein; Provisional
Probab=24.23 E-value=1.1e+02 Score=22.75 Aligned_cols=49 Identities=20% Similarity=0.196 Sum_probs=28.6
Q ss_pred CCCeE-EE--e-c--CCCCceEEEEEEeCCccEEEEEEccC--C-CCCceEeeeccccccc
Q 038833 67 IEGLV-IV--N-G--AYQGSNARLLGVDNDKFCAKTKIEKG--V-NDGRVLNAIDYEDICK 118 (120)
Q Consensus 67 ~G~~V-Vv--~-G--~~rG~~g~L~~~d~~~~~~~V~l~~g--~-~~~~~v~~~~yddvck 118 (120)
.|..| |- . | .+.|-.|+|.+.+.+. +++.+... . ..+..+ .+||++|.+
T Consensus 98 ~G~~v~v~~~~~~~~~~~g~~g~L~~~~~~~--v~l~~~~k~~~~~~~~~~-~ip~~~I~k 155 (162)
T PRK14635 98 RGIPVRLVFRSEESEKWQEGIFRLVNRDGDQ--VELEKFQKGKKSKVKKQT-TLNLKDILK 155 (162)
T ss_pred CCCEEEEEEecCCCcEEEecceEEEEEcCCE--EEEEEecccccccCCeEE-EEEhHHeee
Confidence 57776 43 1 2 3446666999998876 44444211 0 013334 599999876
No 109
>COG3109 ProQ Activator of osmoprotectant transporter ProP [Signal transduction mechanisms]
Probab=24.13 E-value=1.6e+02 Score=23.12 Aligned_cols=34 Identities=15% Similarity=0.419 Sum_probs=26.8
Q ss_pred CCCCeE-EEecCCCCceEEEEEEeCCccEEEEEEccCC
Q 038833 66 QIEGLV-IVNGAYQGSNARLLGVDNDKFCAKTKIEKGV 102 (120)
Q Consensus 66 ~~G~~V-Vv~G~~rG~~g~L~~~d~~~~~~~V~l~~g~ 102 (120)
..|+.+ |=-|. --.-++++++..+. +.|||.+|.
T Consensus 163 ~~g~~~kVk~G~-~a~~AtvlEv~Kd~--vRVqL~~Gl 197 (208)
T COG3109 163 TVGQALKVKAGQ-NAMDATVLEITKDG--VRVQLNSGL 197 (208)
T ss_pred hccceeeecccc-ccccceEEEEeccc--eEEeecCCc
Confidence 368888 66664 45678999999887 899999975
No 110
>PRK09612 rpl2p 50S ribosomal protein L2P; Validated
Probab=23.76 E-value=1.3e+02 Score=24.19 Aligned_cols=32 Identities=16% Similarity=0.287 Sum_probs=22.4
Q ss_pred CCceEEEEEEeCCccEEEEEEccCCCCCceEeeeccccc
Q 038833 78 QGSNARLLGVDNDKFCAKTKIEKGVNDGRVLNAIDYEDI 116 (120)
Q Consensus 78 rG~~g~L~~~d~~~~~~~V~l~~g~~~~~~v~~~~yddv 116 (120)
.|..|+|++.+.+ .++|+|.||. +..++.+..
T Consensus 123 AGt~A~Ii~k~~~--~~~vkLPSGe-----~r~i~~~c~ 154 (238)
T PRK09612 123 SGTYALVVGHEGD--KVIVQLPSGK-----IKELNPRCR 154 (238)
T ss_pred CCCeEEEEEecCC--EEEEECCCCC-----eEEECCcCe
Confidence 6888999998744 4889999863 334555543
No 111
>PF02699 YajC: Preprotein translocase subunit; InterPro: IPR003849 Secretion across the inner membrane in some Gram-negative bacteria occurs via the preprotein translocase pathway. Proteins are produced in the cytoplasm as precursors, and require a chaperone subunit to direct them to the translocase component []. From there, the mature proteins are either targeted to the outer membrane, or remain as periplasmic proteins []. The translocase protein subunits are encoded on the bacterial chromosome. The translocase itself comprises 7 proteins, including a chaperone (SecB), ATPase (SecA), an integral membrane complex (SecY, SecE and SecG), and two additional membrane proteins that promote the release of the mature peptide into the periplasm (SecD and SecF) []. Other cytoplasmic/periplasmic proteins play a part in preprotein translocase activity, namely YidC and YajC []. The latter is bound in a complex to SecD and SecF, and plays a part in stabilising and regulating secretion through the SecYEG integral membrane component via SecA []. Homologues of the YajC gene have been found in a range of pathogenic and commensal microbes. Brucella abortis YajC- and SecD-like proteins were shown to stimulate a Th1 cell-mediated immune response in mice, and conferred protection when challenged with B.abortis []. Therefore, these proteins may have an antigenic role as well as a secretory one in virulent bacteria []. A number of previously uncharacterised "hypothetical" proteins also show similarity to E.coli YajC, suggesting that this family is wider than first thought []. More recently, the precise interactions between the E.coli SecYEG complex, SecD, SecF, YajC and YidC have been studied []. Rather than acting individually, the four proteins form a heterotetrameric complex and associate with the SecYEG heterotrimeric complex []. The SecF and YajC subunits link the complex to the integral membrane translocase. ; PDB: 2RDD_B.
Probab=21.69 E-value=31 Score=22.85 Aligned_cols=30 Identities=20% Similarity=0.320 Sum_probs=0.0
Q ss_pred CCCCeEEEecCCCCceEEEEEEeCCccEEEEEEcc
Q 038833 66 QIEGLVIVNGAYQGSNARLLGVDNDKFCAKTKIEK 100 (120)
Q Consensus 66 ~~G~~VVv~G~~rG~~g~L~~~d~~~~~~~V~l~~ 100 (120)
++|++|+..| |-.|++.+++++. +.+++.+
T Consensus 38 k~Gd~VvT~g---Gi~G~V~~i~~~~--v~lei~~ 67 (82)
T PF02699_consen 38 KPGDEVVTIG---GIYGTVVEIDDDT--VVLEIAP 67 (82)
T ss_dssp -----------------------------------
T ss_pred CCCCEEEECC---cEEEEEEEEeCCE--EEEEECC
Confidence 4688994433 4889999996555 6676665
No 112
>COG4405 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.47 E-value=1.9e+02 Score=21.58 Aligned_cols=14 Identities=21% Similarity=0.610 Sum_probs=10.6
Q ss_pred eecCCCCCeE-EEec
Q 038833 62 TVIPQIEGLV-IVNG 75 (120)
Q Consensus 62 TViP~~G~~V-Vv~G 75 (120)
-..|++|.-+ |++|
T Consensus 54 ep~p~vG~~~iv~d~ 68 (140)
T COG4405 54 EPYPTVGEFVIVLDG 68 (140)
T ss_pred cCCCCCCceEEEEcC
Confidence 4567779988 8876
No 113
>TIGR02768 TraA_Ti Ti-type conjugative transfer relaxase TraA. This protein contains domains distinctive of a single strand exonuclease (N-terminus, MobA/MobL, pfam03389) as well as a helicase domain (central region, homologous to the corresponding region of the F-type relaxase TraI, TIGR02760). This protein likely fills the same role as TraI(F), nicking (at the oriT site) and unwinding the coiled plasmid prior to conjugative transfer.
Probab=20.77 E-value=2.7e+02 Score=25.60 Aligned_cols=33 Identities=9% Similarity=0.272 Sum_probs=25.6
Q ss_pred CCCCeE-EE-e----cCCCCceEEEEEEeCCccEEEEEEcc
Q 038833 66 QIEGLV-IV-N----GAYQGSNARLLGVDNDKFCAKTKIEK 100 (120)
Q Consensus 66 ~~G~~V-Vv-~----G~~rG~~g~L~~~d~~~~~~~V~l~~ 100 (120)
+.|++| .. | |-+-|.+|++.+++.+. ++|.+++
T Consensus 609 ~~GDrV~~~~N~~~~gv~NGd~g~V~~i~~~~--i~v~~~~ 647 (744)
T TIGR02768 609 AAGDRIVFLENNRDLGVKNGMLGTVEEIEDGR--LVVQLDS 647 (744)
T ss_pred cCCCEEEEEecccccCCcCCCEEEEEEecCCe--EEEEECC
Confidence 689999 55 2 66789999999998654 6677765
No 114
>PHA02104 hypothetical protein
Probab=20.41 E-value=1.5e+02 Score=19.93 Aligned_cols=29 Identities=28% Similarity=0.548 Sum_probs=21.2
Q ss_pred CCCcccCCc-EEEEEeccCCCccceeeeEEEEEec
Q 038833 14 QDYWLFKGI-IVEVMSKAFADKGYCKQKGIVRKVI 47 (120)
Q Consensus 14 ~~~Wl~~~I-~Vkii~k~~~~gk~y~~KgvV~~V~ 47 (120)
.-+|--|+| +|+|= +.+|+-+.|.|-...
T Consensus 35 ti~w~fp~i~ev~ig-----~s~yfa~~gkiynat 64 (89)
T PHA02104 35 TIFWTFPGITEVRIG-----SSTYFAQNGKIYNAT 64 (89)
T ss_pred EEEEecCCcEEEEec-----ceeeehhCCeEEeeE
Confidence 358999999 57764 447888888776654
Done!