Query 040226
Match_columns 137
No_of_seqs 105 out of 1026
Neff 6.1
Searched_HMMs 46136
Date Fri Mar 29 06:20:54 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040226.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040226hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00084 40S ribosomal protein 100.0 1.7E-43 3.7E-48 280.0 14.9 134 3-137 3-137 (220)
2 COG0092 RpsC Ribosomal protein 100.0 1.5E-42 3.3E-47 275.3 14.2 128 7-137 8-142 (233)
3 TIGR01008 rpsC_E_A ribosomal p 100.0 1.9E-41 4.1E-46 264.4 13.9 128 7-137 1-129 (195)
4 PRK04191 rps3p 30S ribosomal p 100.0 9.9E-40 2.2E-44 256.7 15.2 128 6-136 2-130 (207)
5 CHL00048 rps3 ribosomal protei 100.0 1.8E-34 4E-39 227.9 15.8 124 12-136 34-158 (214)
6 TIGR01009 rpsC_bact ribosomal 100.0 6.9E-34 1.5E-38 224.2 14.7 124 9-136 27-151 (211)
7 PRK00310 rpsC 30S ribosomal pr 100.0 3.1E-33 6.7E-38 223.2 14.9 125 8-136 26-151 (232)
8 KOG3181 40S ribosomal protein 99.9 4E-27 8.6E-32 183.2 11.9 135 1-136 1-136 (244)
9 cd02413 40S_S3_KH K homology R 99.9 3.9E-24 8.5E-29 146.1 10.2 80 15-94 1-80 (81)
10 cd02411 archeal_30S_S3_KH K ho 99.9 4.1E-23 8.9E-28 141.7 9.4 85 7-93 1-85 (85)
11 cd02412 30S_S3_KH K homology R 99.9 6.3E-21 1.4E-25 136.4 10.1 84 9-94 26-109 (109)
12 PF07650 KH_2: KH domain syndr 99.7 4.4E-17 9.6E-22 109.2 6.9 77 20-96 1-78 (78)
13 cd02409 KH-II KH-II (K homolo 99.1 7E-10 1.5E-14 70.5 7.8 65 22-88 1-67 (68)
14 smart00322 KH K homology RNA-b 98.1 4.3E-06 9.2E-11 52.1 3.4 67 44-110 3-69 (69)
15 cd02414 jag_KH jag_K homology 97.6 0.00048 1E-08 46.0 7.1 56 23-78 2-58 (77)
16 PF00189 Ribosomal_S3_C: Ribos 97.5 9.9E-05 2.1E-09 50.4 3.3 32 104-136 1-34 (85)
17 PF13083 KH_4: KH domain; PDB: 97.4 0.0002 4.3E-09 47.1 3.9 68 19-86 2-71 (73)
18 cd02410 archeal_CPSF_KH The ar 96.9 0.0096 2.1E-07 44.9 8.9 87 19-119 52-139 (145)
19 PRK01064 hypothetical protein; 96.6 0.038 8.3E-07 37.4 9.2 54 37-90 21-76 (78)
20 COG1847 Jag Predicted RNA-bind 96.6 0.011 2.4E-07 46.9 7.2 110 14-123 60-185 (208)
21 cd02134 NusA_KH NusA_K homolog 95.5 0.052 1.1E-06 34.6 5.4 53 22-74 2-55 (61)
22 PRK02821 hypothetical protein; 95.2 0.38 8.3E-06 32.5 9.1 51 37-90 22-74 (77)
23 COG1159 Era GTPase [General fu 95.2 0.23 4.9E-06 41.5 9.7 83 8-93 187-282 (298)
24 PRK08406 transcription elongat 95.1 0.039 8.4E-07 41.1 4.5 61 19-79 72-134 (140)
25 PRK00468 hypothetical protein; 94.2 0.77 1.7E-05 30.8 8.6 51 37-87 21-73 (75)
26 PRK15494 era GTPase Era; Provi 93.5 1.1 2.3E-05 37.6 10.1 82 9-93 232-326 (339)
27 COG1837 Predicted RNA-binding 93.2 1.2 2.6E-05 30.1 8.2 47 42-88 26-74 (76)
28 TIGR00436 era GTP-binding prot 93.2 0.77 1.7E-05 36.8 8.6 72 10-86 181-265 (270)
29 PRK00089 era GTPase Era; Revie 92.9 1.2 2.7E-05 35.7 9.5 87 11-100 189-286 (292)
30 COG1782 Predicted metal-depend 92.7 1.1 2.3E-05 40.5 9.4 75 22-110 78-153 (637)
31 TIGR03675 arCOG00543 arCOG0054 92.6 1.6 3.6E-05 39.8 10.7 86 20-119 70-156 (630)
32 TIGR01952 nusA_arch NusA famil 90.0 0.58 1.3E-05 35.0 4.3 59 20-78 74-134 (141)
33 cd02393 PNPase_KH Polynucleoti 88.1 0.53 1.2E-05 29.9 2.6 29 45-73 3-31 (61)
34 PRK06418 transcription elongat 85.6 3.6 7.7E-05 31.7 6.4 54 20-74 34-90 (166)
35 PF13014 KH_3: KH domain 85.2 0.7 1.5E-05 27.0 1.8 16 56-71 3-18 (43)
36 cd02396 PCBP_like_KH K homolog 78.6 2 4.2E-05 27.2 2.2 27 46-72 2-28 (65)
37 cd00105 KH-I K homology RNA-bi 77.9 2.7 5.9E-05 25.7 2.8 27 47-73 3-29 (64)
38 TIGR03665 arCOG04150 arCOG0415 76.7 3.8 8.2E-05 31.2 3.7 64 50-120 4-73 (172)
39 PF00013 KH_1: KH domain syndr 75.8 1.1 2.4E-05 27.6 0.5 28 46-73 2-29 (60)
40 PF14698 ASL_C2: Argininosucci 74.7 5.1 0.00011 26.2 3.5 31 96-129 2-36 (70)
41 cd02394 vigilin_like_KH K homo 73.5 2.9 6.2E-05 25.9 2.0 27 47-73 3-29 (62)
42 COG0195 NusA Transcription elo 73.0 16 0.00034 28.7 6.4 28 47-74 78-106 (190)
43 TIGR01953 NusA transcription t 68.4 32 0.00069 29.2 7.8 55 20-74 201-264 (341)
44 COG1534 Predicted RNA-binding 67.3 17 0.00036 25.7 4.9 53 51-110 15-70 (97)
45 PF13184 KH_5: NusA-like KH do 66.8 5.3 0.00011 26.2 2.2 37 44-86 3-44 (69)
46 PRK12327 nusA transcription el 65.4 33 0.00072 29.4 7.3 55 20-74 203-266 (362)
47 PRK08406 transcription elongat 65.2 24 0.00053 26.1 5.8 42 30-73 20-61 (140)
48 PRK09202 nusA transcription el 65.1 10 0.00023 33.5 4.3 59 21-86 279-337 (470)
49 COG0779 Uncharacterized protei 64.1 61 0.0013 24.5 8.6 77 17-99 6-87 (153)
50 TIGR01952 nusA_arch NusA famil 64.0 12 0.00026 27.9 3.9 45 28-73 18-62 (141)
51 PRK12328 nusA transcription el 63.6 37 0.0008 29.4 7.2 55 20-74 209-272 (374)
52 TIGR01953 NusA transcription t 63.1 17 0.00037 30.9 5.1 60 21-87 277-337 (341)
53 PRK12328 nusA transcription el 62.8 20 0.00044 31.0 5.6 62 21-89 285-346 (374)
54 COG4604 CeuD ABC-type enteroch 62.5 44 0.00094 27.3 7.0 61 44-106 18-78 (252)
55 COG1855 ATPase (PilT family) [ 61.1 15 0.00033 33.1 4.6 56 14-73 459-515 (604)
56 COG0195 NusA Transcription elo 59.5 23 0.0005 27.7 4.9 61 21-88 118-179 (190)
57 PRK13763 putative RNA-processi 58.4 15 0.00033 28.1 3.7 71 46-118 5-77 (180)
58 TIGR03112 6_pyr_pter_rel 6-pyr 55.2 70 0.0015 22.7 6.5 63 45-114 28-91 (113)
59 PRK09202 nusA transcription el 55.2 63 0.0014 28.7 7.5 55 20-74 203-266 (470)
60 KOG2191 RNA-binding protein NO 54.7 23 0.0005 30.5 4.5 42 32-73 117-161 (402)
61 PRK13764 ATPase; Provisional 54.1 29 0.00063 31.8 5.3 56 15-73 455-510 (602)
62 PRK13763 putative RNA-processi 54.0 37 0.0008 26.0 5.2 66 54-125 105-170 (180)
63 COG1942 Uncharacterized protei 53.4 26 0.00056 23.0 3.7 46 48-93 4-49 (69)
64 COG1302 Uncharacterized protei 53.0 91 0.002 23.1 7.8 67 24-96 43-119 (131)
65 PRK12327 nusA transcription el 52.9 22 0.00047 30.5 4.1 51 21-71 279-330 (362)
66 PRK12329 nusA transcription el 52.7 69 0.0015 28.4 7.2 55 20-74 228-298 (449)
67 TIGR00253 RNA_bind_YhbY putati 49.6 59 0.0013 22.6 5.2 53 51-110 14-69 (95)
68 KOG2192 PolyC-binding hnRNP-K 47.0 18 0.00039 30.4 2.6 31 44-74 48-78 (390)
69 PRK09509 fieF ferrous iron eff 46.7 88 0.0019 25.4 6.7 74 16-91 213-287 (299)
70 PRK06418 transcription elongat 45.8 75 0.0016 24.4 5.7 61 21-86 102-163 (166)
71 KOG2192 PolyC-binding hnRNP-K 45.7 8 0.00017 32.5 0.4 38 42-79 121-158 (390)
72 PF06069 PerC: PerC transcript 45.2 17 0.00036 25.3 1.9 19 102-120 3-21 (90)
73 PF03780 Asp23: Asp23 family; 44.5 46 0.00099 22.5 4.1 60 32-91 45-107 (108)
74 TIGR00013 taut 4-oxalocrotonat 43.0 49 0.0011 20.1 3.7 29 65-93 20-48 (63)
75 PRK10343 RNA-binding protein Y 42.8 81 0.0017 22.1 5.1 53 51-110 16-71 (97)
76 KOG1676 K-homology type RNA bi 40.2 20 0.00044 32.8 2.1 27 45-71 140-166 (600)
77 COG1094 Predicted RNA-binding 40.1 88 0.0019 24.7 5.4 64 55-124 113-176 (194)
78 PF14552 Tautomerase_2: Tautom 39.7 25 0.00055 23.6 2.1 54 39-93 23-76 (82)
79 PRK12329 nusA transcription el 38.1 50 0.0011 29.3 4.1 51 21-71 311-362 (449)
80 cd02395 SF1_like-KH Splicing f 37.6 25 0.00054 25.4 1.9 22 53-74 15-36 (120)
81 PRK14647 hypothetical protein; 37.1 1.8E+02 0.0039 21.8 8.1 76 18-99 7-87 (159)
82 PRK00092 ribosome maturation p 36.3 1.8E+02 0.0038 21.5 7.8 79 18-99 6-86 (154)
83 TIGR03675 arCOG00543 arCOG0054 35.9 43 0.00093 30.7 3.5 53 20-77 3-56 (630)
84 cd00554 MECDP_synthase MECDP_s 35.5 1.2E+02 0.0026 23.0 5.4 42 44-90 91-132 (153)
85 PF01985 CRS1_YhbY: CRS1 / Yhb 35.0 97 0.0021 20.6 4.4 52 51-109 14-68 (84)
86 PF11324 DUF3126: Protein of u 34.9 60 0.0013 21.2 3.1 20 65-86 1-20 (63)
87 PRK14640 hypothetical protein; 34.8 1.9E+02 0.0041 21.5 7.9 76 18-99 5-85 (152)
88 COG4988 CydD ABC-type transpor 34.5 1E+02 0.0022 28.2 5.5 63 44-106 338-416 (559)
89 KOG2190 PolyC-binding proteins 34.4 32 0.00069 30.7 2.4 27 46-72 45-71 (485)
90 KOG1676 K-homology type RNA bi 34.2 29 0.00063 31.8 2.1 27 45-71 231-257 (600)
91 TIGR00151 ispF 2C-methyl-D-ery 34.1 1.3E+02 0.0027 22.9 5.3 41 44-89 91-131 (155)
92 PF14480 DNA_pol3_a_NI: DNA po 33.9 1.3E+02 0.0027 19.1 6.3 57 26-88 18-74 (76)
93 PRK02289 4-oxalocrotonate taut 33.7 1E+02 0.0022 18.9 4.1 29 65-93 20-48 (60)
94 cd00491 4Oxalocrotonate_Tautom 32.8 92 0.002 18.4 3.7 31 63-93 17-47 (58)
95 PRK00084 ispF 2-C-methyl-D-ery 31.9 1.4E+02 0.003 22.8 5.2 41 44-89 94-134 (159)
96 PF02542 YgbB: YgbB family; I 31.8 1.3E+02 0.0028 23.0 5.0 40 45-89 93-132 (157)
97 PF14955 MRP-S24: Mitochondria 31.6 37 0.0008 25.4 2.0 39 14-52 52-90 (136)
98 COG1782 Predicted metal-depend 31.4 75 0.0016 29.1 4.2 55 19-78 8-63 (637)
99 TIGR03367 queuosine_QueD queuo 31.0 1.1E+02 0.0024 20.6 4.2 43 67-111 50-92 (92)
100 PRK03094 hypothetical protein; 30.6 1.4E+02 0.003 20.3 4.5 37 25-61 13-51 (80)
101 PRK14646 hypothetical protein; 30.1 2.4E+02 0.0051 21.1 8.7 77 18-98 6-87 (155)
102 PRK01271 4-oxalocrotonate taut 29.2 1E+02 0.0023 20.4 3.7 29 65-93 21-49 (76)
103 COG0165 ArgH Argininosuccinate 29.2 66 0.0014 28.6 3.4 35 83-120 349-387 (459)
104 cd05213 NAD_bind_Glutamyl_tRNA 29.0 2.7E+02 0.0058 22.7 6.9 52 20-78 25-76 (311)
105 PRK14633 hypothetical protein; 28.6 2.5E+02 0.0054 20.9 7.6 76 18-99 3-82 (150)
106 PRK14638 hypothetical protein; 28.6 2.5E+02 0.0054 20.9 7.9 79 18-98 7-87 (150)
107 PF01545 Cation_efflux: Cation 27.5 3E+02 0.0065 21.5 7.0 76 14-90 203-280 (284)
108 PRK14636 hypothetical protein; 27.4 2.9E+02 0.0062 21.2 8.4 78 18-99 4-86 (176)
109 PRK00745 4-oxalocrotonate taut 27.3 1.2E+02 0.0026 18.3 3.6 28 66-93 21-48 (62)
110 COG1461 Predicted kinase relat 26.7 67 0.0015 29.2 3.1 56 18-78 251-313 (542)
111 COG0053 MMT1 Predicted Co/Zn/C 26.7 2.8E+02 0.0061 22.9 6.7 61 34-95 233-294 (304)
112 PF02563 Poly_export: Polysacc 26.7 1.3E+02 0.0029 19.6 3.9 28 62-89 52-81 (82)
113 KOG2190 PolyC-binding proteins 24.7 66 0.0014 28.7 2.7 30 43-72 137-166 (485)
114 TIGR03131 malonate_mdcH malona 24.2 2.9E+02 0.0062 21.9 6.1 42 81-122 210-251 (295)
115 PRK14634 hypothetical protein; 24.0 3.1E+02 0.0067 20.5 7.8 78 18-99 6-88 (155)
116 KOG1316 Argininosuccinate lyas 23.6 74 0.0016 27.8 2.7 35 83-120 352-389 (464)
117 PF08731 AFT: Transcription fa 23.5 1.7E+02 0.0038 21.1 4.2 33 18-52 4-36 (111)
118 PRK14632 hypothetical protein; 23.1 3.4E+02 0.0074 20.6 7.6 77 17-99 6-86 (172)
119 PRK04163 exosome complex RNA-b 22.7 1.4E+02 0.0031 23.7 4.0 64 45-115 146-212 (235)
120 PF13684 Dak1_2: Dihydroxyacet 22.7 97 0.0021 25.8 3.2 38 18-60 20-57 (313)
121 PRK13434 F0F1 ATP synthase sub 22.4 2.1E+02 0.0046 21.6 4.8 43 43-95 102-144 (184)
122 KOG2193 IGF-II mRNA-binding pr 22.0 50 0.0011 29.5 1.4 26 46-71 495-520 (584)
123 PF01361 Tautomerase: Tautomer 22.0 1.8E+02 0.0038 17.5 3.6 31 63-93 17-47 (60)
124 KOG2191 RNA-binding protein NO 21.3 86 0.0019 27.1 2.6 29 44-72 39-67 (402)
125 PF00698 Acyl_transf_1: Acyl t 20.6 1.7E+02 0.0038 23.6 4.2 42 81-122 214-255 (318)
126 PRK02220 4-oxalocrotonate taut 20.4 2.1E+02 0.0045 17.1 3.7 30 64-93 19-48 (61)
127 PRK03557 zinc transporter ZitB 20.4 4.8E+02 0.01 21.3 7.3 55 33-91 238-292 (312)
No 1
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=100.00 E-value=1.7e-43 Score=280.03 Aligned_cols=134 Identities=73% Similarity=1.141 Sum_probs=130.0
Q ss_pred cchhhhHhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCC
Q 040226 3 TQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPEN 82 (137)
Q Consensus 3 ~~~~~~~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~ 82 (137)
.|++++++|++|++.+++||+||.++|.++|||+|+|+|+++.++|+|||++||++||++|+++++|++.|++.|+++++
T Consensus 3 ~~~~~~k~fi~~~~~~~~~re~l~k~~~~agis~ieI~Rt~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~~~~~ 82 (220)
T PTZ00084 3 GQISKKRKFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEG 82 (220)
T ss_pred cccchhhHHHHcchhhHHHHHHHHHHHHHCCcceEEEEEcCCcEEEEEEECCCccEEcCCchHHHHHHHHHHHHhCCCCc
Confidence 35789999999999999999999999999999999999999999999999999999999999999999999999998889
Q ss_pred eEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhcccccccccC
Q 040226 83 SVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGLM 137 (137)
Q Consensus 83 ~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~~ 137 (137)
+++|+|.||++|++||.++|++||+|||+|+||||||+ ++++||++|| +||++.
T Consensus 83 ~i~i~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGa-kGikI~ 137 (220)
T PTZ00084 83 KVELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGA-KGCEVI 137 (220)
T ss_pred eEEEEEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCC-ceEEEE
Confidence 99999999999999999999999999999999999999 9999999996 999873
No 2
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-42 Score=275.28 Aligned_cols=128 Identities=31% Similarity=0.404 Sum_probs=122.0
Q ss_pred hhHhHHHhh------HHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC
Q 040226 7 KKRKFVADG------VFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP 80 (137)
Q Consensus 7 ~~~~fi~~~------~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~ 80 (137)
..+.|.+++ .+|.+||+||.++|.+||||+|+|+|+|.+++|+|||+|||+|||++|+++++|++.|+++|+..
T Consensus 8 ~srwfa~~~~~~~~l~ed~kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g~~ 87 (233)
T COG0092 8 KSRWFANKKEYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFGKE 87 (233)
T ss_pred hhhhccccccchHHHHHHHHHHHHHHHHHHhCCcceEEEEecCCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhCCC
Confidence 467777777 99999999999999999999999999999999999999999999999999999999999999963
Q ss_pred CCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhcccccccccC
Q 040226 81 ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGLM 137 (137)
Q Consensus 81 ~~~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~~ 137 (137)
++.|+|.||++|++||+++|++||.|||+|++|||||+ ||+++|++|| +||+++
T Consensus 88 --~v~I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGA-kGiki~ 142 (233)
T COG0092 88 --NVQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGA-KGIKIQ 142 (233)
T ss_pred --CceEEEEEcCCCCcCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcCC-ceeEEE
Confidence 78888999999999999999999999999999999999 9999999997 999874
No 3
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=100.00 E-value=1.9e-41 Score=264.35 Aligned_cols=128 Identities=42% Similarity=0.611 Sum_probs=122.7
Q ss_pred hhHhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q 040226 7 KKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (137)
Q Consensus 7 ~~~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I 86 (137)
++++|++|++++.+||+||.++|.++|||+|+|+|+++.++|+|||++||++||++|+++++|++.|++.++. .+++|
T Consensus 1 ~~kkfi~~~~~~~~ire~l~k~~~~agis~ieI~r~~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~--~~~~I 78 (195)
T TIGR01008 1 IERKFVAEGLKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGL--ENPQI 78 (195)
T ss_pred CcEehHhcchHHHHHHHHHHHHHHhCCeeEEEEEEcCCcEEEEEEECCCceEECCCchHHHHHHHHHHHHhCC--CceEE
Confidence 3689999999999999999999999999999999999999999999999999999999999999999999975 46889
Q ss_pred EEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhcccccccccC
Q 040226 87 YAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGLM 137 (137)
Q Consensus 87 ~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~~ 137 (137)
+|.||++|++||.++|++||+|||+|+||||||+ +++++|++|| +||++.
T Consensus 79 ~v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGa-kGikI~ 129 (195)
T TIGR01008 79 DVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGA-KGVEVT 129 (195)
T ss_pred EEEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCC-ceEEEE
Confidence 9999999999999999999999999999999999 9999999996 999873
No 4
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=100.00 E-value=9.9e-40 Score=256.71 Aligned_cols=128 Identities=33% Similarity=0.492 Sum_probs=123.3
Q ss_pred hhhHhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEE
Q 040226 6 SKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVE 85 (137)
Q Consensus 6 ~~~~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~ 85 (137)
+++++|++|++++.+||+||.+.|.+||||+|+|+|+++.+.|+||+++||++||++|+++++|++.|++.++. .++.
T Consensus 2 ~~~~~fi~~~~~~~~irefi~~~~~~AgIs~IeI~Rt~~~i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~~~--~~v~ 79 (207)
T PRK04191 2 AIEKKFVEEGLKKVMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGL--ENPQ 79 (207)
T ss_pred chhhHHHHcchHHHHHHHHHHhhhhhcceeEEEEEEcCCcEEEEEEECCCCeEECCCchhHHHHHHHHHHHhCC--Ccee
Confidence 57899999999999999999999999999999999999999999999999999999999999999999999975 4588
Q ss_pred EEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhccccccccc
Q 040226 86 LYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGL 136 (137)
Q Consensus 86 I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~ 136 (137)
|+|.||++|++||.++|++||+|||+|+||||||+ +++++|++|| +||++
T Consensus 80 I~v~ev~~p~~~a~~vA~~ia~qLe~r~~fRra~k~~i~~~~~aga-kGiki 130 (207)
T PRK04191 80 IDVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGA-LGVEI 130 (207)
T ss_pred EEEEEEeCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCC-eeEEE
Confidence 88999999999999999999999999999999999 9999999996 99987
No 5
>CHL00048 rps3 ribosomal protein S3
Probab=100.00 E-value=1.8e-34 Score=227.90 Aligned_cols=124 Identities=15% Similarity=0.161 Sum_probs=114.3
Q ss_pred HHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEe
Q 040226 12 VADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKV 91 (137)
Q Consensus 12 i~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev 91 (137)
.+|.+++..|.+||.+++.+||||+|+|+|+++.++|+||+++||++||++|+++++|++.|++.++..++++.|+|.||
T Consensus 34 ~eD~~ir~~i~~~l~~~~~~agis~i~I~r~~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~k~~~~~~~~i~I~v~ev 113 (214)
T CHL00048 34 QEDKKIRDCIKNYVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLLIERKGRGIEELQINLQKELNSVNRKLNINITEV 113 (214)
T ss_pred HHHHHHHHHHHHHHHhhhhhCCeeEEEEEEcCCeEEEEEEECCCceEECCCcHhHHHHHHHHHHHhCCCCceEEEEEEEe
Confidence 45666666666666666899999999999999999999999999999999999999999999999987777899999999
Q ss_pred cCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhccccccccc
Q 040226 92 NNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGL 136 (137)
Q Consensus 92 ~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~ 136 (137)
++|++||.++|++||.|||+|++||||++ +++++|++|| +||++
T Consensus 114 ~~p~~~A~~iA~~ia~~Le~r~~fRra~~~~i~~~~~~ga-~GikI 158 (214)
T CHL00048 114 KKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADI-KGIKI 158 (214)
T ss_pred cCCCcCHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHhCC-cEEEE
Confidence 99999999999999999999999999999 9999999995 99987
No 6
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=100.00 E-value=6.9e-34 Score=224.19 Aligned_cols=124 Identities=21% Similarity=0.282 Sum_probs=119.6
Q ss_pred HhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q 040226 9 RKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (137)
Q Consensus 9 ~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i 88 (137)
+.|.+...+|.+||+||.++|.++|||+|+|+||++.++|+||+++||++||++|+++++|++.|++.++ .++.|++
T Consensus 27 k~Y~~~l~eD~~IR~~i~k~~~~agis~IeI~rt~~~i~I~I~~~~pg~vIG~~g~~i~~l~~~l~~~~~---~~~~i~v 103 (211)
T TIGR01009 27 KEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKKGSEIEKLRKDLQKLTG---KEVQINI 103 (211)
T ss_pred chhHHHHHHHHHHHHHHHHHhhhCCcceEEEEEcCCceEEEEEeCCCcceeCCCchHHHHHHHHHHHHhC---CceEEEE
Confidence 6788899999999999999999999999999999999999999999999999999999999999999997 5789999
Q ss_pred EEecCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhccccccccc
Q 040226 89 EKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGL 136 (137)
Q Consensus 89 ~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~ 136 (137)
.+|++|+++|.++|++||+|||+|+|||||++ +++++|++|| +||++
T Consensus 104 ~~v~~p~~~a~~iA~~ia~~Le~~~~fRr~~~~~i~~~~~~g~-~GikI 151 (211)
T TIGR01009 104 AEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGA-KGIKV 151 (211)
T ss_pred EEecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCC-cEEEE
Confidence 99999999999999999999999999999999 9999999995 99986
No 7
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=100.00 E-value=3.1e-33 Score=223.18 Aligned_cols=125 Identities=22% Similarity=0.290 Sum_probs=120.0
Q ss_pred hHhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEE
Q 040226 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (137)
Q Consensus 8 ~~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~ 87 (137)
.+.|.+...+|.+||+||.++|.++|||+|+|+|+++.++|+||+++||+++|++|.++++|++.|++.|+ .++.|+
T Consensus 26 ~k~Y~~~L~eD~~IRe~i~k~~~~agis~IeI~R~~~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~~~~~---~~~~i~ 102 (232)
T PRK00310 26 KKDYADLLHEDLKIRKFLKKKLKKAGVSRIEIERPAKRVRVTIHTARPGIVIGKKGAEIEKLRKELEKLTG---KPVQIN 102 (232)
T ss_pred cchhHHHHHHHHHHHHHHHHhHhhCceeEEEEEEcCCeEEEEEEECCCccccCCCcHHHHHHHHHHHHHhC---CceEEE
Confidence 46788899999999999999999999999999999999999999999999999999999999999999996 578899
Q ss_pred EEEecCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhccccccccc
Q 040226 88 AEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGL 136 (137)
Q Consensus 88 i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~ 136 (137)
|.||++|+++|.++|++||+|||+|+|||||++ +++++|++|| +||+|
T Consensus 103 v~ev~~p~~~a~~iA~~ia~~Le~r~~fRr~~~~~i~~~~~~g~-~GikI 151 (232)
T PRK00310 103 IVEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGA-KGIKV 151 (232)
T ss_pred EEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCC-cEEEE
Confidence 999999999999999999999999999999999 9999999995 99986
No 8
>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=99.95 E-value=4e-27 Score=183.19 Aligned_cols=135 Identities=83% Similarity=1.191 Sum_probs=130.8
Q ss_pred CccchhhhHhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC
Q 040226 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP 80 (137)
Q Consensus 1 m~~~~~~~~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~ 80 (137)
|+-+++-.++|+.||+++++++|||.++|.+.|||++|+.-||.+++|+|.+++|.-++|.+|.+|.+|+...+++|++.
T Consensus 1 ~a~~iSkkrkfv~dGvf~AELnef~treLaedGySgvEvRvtptr~eiIi~atrtq~vlGEkgrRirelt~lvqkRf~f~ 80 (244)
T KOG3181|consen 1 MALQISKKRKFVADGVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKFP 80 (244)
T ss_pred CccccchhhhhhhcchhHHHHHHHHHHHHHhcCcCceEEEeeccceeEEEEecchhhhhhhcchhHHHHHHHHHHhcCCC
Confidence 55567778999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHH-HHHHHHhccccccccc
Q 040226 81 ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYIL-IISQILSNKALRSCGL 136 (137)
Q Consensus 81 ~~~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~k-ai~~a~~~ga~kG~~~ 136 (137)
+.+|+++.++|.+.++||...|+++.++|-.+.++|||.. +++.+|++|| |||++
T Consensus 81 ~~svelyaEkV~~rGLcAiaQaeslryKllgGlavRRA~ygvlr~vmesgA-kGcev 136 (244)
T KOG3181|consen 81 EGSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGA-KGCEV 136 (244)
T ss_pred CCcEEEehhhhhccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHccC-CccEE
Confidence 9999999999999999999999999999999999999999 9999999997 99986
No 9
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.91 E-value=3.9e-24 Score=146.13 Aligned_cols=80 Identities=91% Similarity=1.285 Sum_probs=77.2
Q ss_pred hHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCC
Q 040226 15 GVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNR 94 (137)
Q Consensus 15 ~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P 94 (137)
|+++++||+||.+++.+||||+|+|+||++.++|+|||++||++||++|+++++|++.|++.|++.++++++++++|.+.
T Consensus 1 ~~~~~~Ire~l~k~~~~agis~IeI~Rt~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~~i~v~~~~v~~~ 80 (81)
T cd02413 1 GVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEGSVELYAEKVANR 80 (81)
T ss_pred CchhHHHHHHHHHHHHhCCeeeEEEEEcCCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCCeEEEEEEEcccC
Confidence 46889999999999999999999999999999999999999999999999999999999999999999999999999875
No 10
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.89 E-value=4.1e-23 Score=141.67 Aligned_cols=85 Identities=38% Similarity=0.647 Sum_probs=80.0
Q ss_pred hhHhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q 040226 7 KKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (137)
Q Consensus 7 ~~~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I 86 (137)
++++|++||+++.+||+||.+.|..||||+|+|+|+++.+.|+|||++||+++|++|+++++|+..|++.++. +++.|
T Consensus 1 ~~~~~~~~~~~~~~Ir~fl~~~~~~agIs~IeI~r~~~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l~k~~~~--~~v~I 78 (85)
T cd02411 1 VERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGL--ENPQI 78 (85)
T ss_pred CeEeHHhcchHHHHHHHHHHhhhhhCcccEEEEEEcCCcEEEEEEECCCCceECCCchhHHHHHHHHHHHhCC--CCceE
Confidence 3689999999999999999999999999999999999999999999999999999999999999999999974 47888
Q ss_pred EEEEecC
Q 040226 87 YAEKVNN 93 (137)
Q Consensus 87 ~i~ev~~ 93 (137)
+|.||++
T Consensus 79 ~v~ev~~ 85 (85)
T cd02411 79 DVQEVEN 85 (85)
T ss_pred EEEEecC
Confidence 8999875
No 11
>cd02412 30S_S3_KH K homology RNA-binding (KH) domain of the prokaryotic 30S small ribosomal subunit protein S3. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.85 E-value=6.3e-21 Score=136.40 Aligned_cols=84 Identities=20% Similarity=0.308 Sum_probs=79.8
Q ss_pred HhHHHhhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q 040226 9 RKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (137)
Q Consensus 9 ~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i 88 (137)
++|.+...+|.+||+||.+.+..||||+|+|+|+++.++|+|||++||++||++|+++++|++.|++.++. +++.|+|
T Consensus 26 ~~y~~~l~ed~~IR~yL~k~~~~agis~I~I~R~~~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~~~~--~~~~I~V 103 (109)
T cd02412 26 KDYAELLHEDLKIRKFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIEKLRKELQKLLGN--KKVRINI 103 (109)
T ss_pred hhhHHHHHhHHHHHHHHHHHHhhCCccEEEEEEcCCCEEEEEEeCCCCcccCCchHHHHHHHHHHHHHhCC--CceEEEE
Confidence 57888999999999999999999999999999999999999999999999999999999999999999864 5789999
Q ss_pred EEecCC
Q 040226 89 EKVNNR 94 (137)
Q Consensus 89 ~ev~~P 94 (137)
.||.+|
T Consensus 104 ~ev~~P 109 (109)
T cd02412 104 VEVKKP 109 (109)
T ss_pred EEecCC
Confidence 999998
No 12
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=99.70 E-value=4.4e-17 Score=109.20 Aligned_cols=77 Identities=27% Similarity=0.427 Sum_probs=72.3
Q ss_pred HHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC-CCCCeEEEEEEEecCCCc
Q 040226 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK-FPENSVELYAEKVNNRGL 96 (137)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~-~~~~~i~I~i~ev~~P~l 96 (137)
+||+||.+++..+|+++++|+|+++.+.|++|+++||++||++|+.+++|+..+++.+. +.+++|.+++.+|++|++
T Consensus 1 eI~~~l~~~~~~~~~~~i~I~r~~~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~~~~~~~V~l~v~~V~~~~~ 78 (78)
T PF07650_consen 1 EIRYFLFKEIKKAGISDIEIERTPDQIIIVIKASQPGIVIGKKGSNIKKIREELRKELEKLLNKKVFLNVVKVKKPWR 78 (78)
T ss_dssp HHHHHHHHHTTTTTEEEEEEEESSSEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHHHHCSSSEEEEEEEESSCGG
T ss_pred ChhhhHHhhhhhccCceEEEEEcCCeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHhhcCCCcEEEEEEEecCCCC
Confidence 58999999999999999999999999999999999999999999999999999999994 446889999999999975
No 13
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=99.09 E-value=7e-10 Score=70.55 Aligned_cols=65 Identities=42% Similarity=0.616 Sum_probs=57.9
Q ss_pred HHHHHhhhccCCccceEEEEcCCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q 040226 22 NEVLTRELAEDGYSGVEVRVTPVRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (137)
Q Consensus 22 re~l~k~~~~agis~IeI~R~~~~i~I~I~~ar--Pg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i 88 (137)
|+|+.+.+..+|+++|+|.++++...+.+++.. ||.+||++|+.++.++..+.+.+. ++++.|++
T Consensus 1 r~~l~~~~~~~~i~~i~i~~~~~~~~~~i~~~~~~~g~lIGk~G~~l~~l~~l~~~~~~--~~~~~i~v 67 (68)
T cd02409 1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLR--KKRVKIDV 67 (68)
T ss_pred ChHHHHHHHHCCCCeEEEEEcCCcEEEEEEECCCCCceEECCCCccHHHHHHHHHHHcC--CCceEEEE
Confidence 578999999999999999999888999999999 999999999999999999999883 46666654
No 14
>smart00322 KH K homology RNA-binding domain.
Probab=98.07 E-value=4.3e-06 Score=52.07 Aligned_cols=67 Identities=19% Similarity=0.262 Sum_probs=53.2
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHH
Q 040226 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLL 110 (137)
Q Consensus 44 ~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~liA~~ia~qLe 110 (137)
..++|.|+...||.+||++|..+++|++.....+...+..-...+..|..|..++...++.|..+++
T Consensus 3 ~~~~i~i~~~~~~~liG~~G~~i~~i~~~~~~~i~~~~~~~~~~~v~i~g~~~~v~~a~~~i~~~~~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred eEEEEEEcchhcceeECCCchHHHHHHHHHCCEEEECCCCCCccEEEEEcCHHHHHHHHHHHHHHhC
Confidence 4678899999999999999999999998886655433322134567899999999999999988864
No 15
>cd02414 jag_KH jag_K homology RNA-binding domain. The KH domain is found in proteins homologous to the Bacillus subtilis protein Jag, which is associated with SpoIIIJ and is necessary for the third stage of sporulation. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=97.56 E-value=0.00048 Score=45.96 Aligned_cols=56 Identities=20% Similarity=0.287 Sum_probs=47.7
Q ss_pred HHHHhhhccCCc-cceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 040226 23 EVLTRELAEDGY-SGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (137)
Q Consensus 23 e~l~k~~~~agi-s~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~ 78 (137)
+|+.+-+...|+ ..+++....+.+.+.+....||.+||++|+.++.|+..+...++
T Consensus 2 ~~L~~il~~mg~~~~v~~~~~~~~i~i~i~~~~~g~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 2 EFLEEVLELMGIEADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred hHHHHHHHHcCCCcEEEEEecCCEEEEEEecCCCCeEECCCCccHHHHHHHHHHHHh
Confidence 577777777776 34777777889999999999999999999999999998888776
No 16
>PF00189 Ribosomal_S3_C: Ribosomal protein S3, C-terminal domain; InterPro: IPR001351 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 S3 is one of the proteins from the small ribosomal subunit. In Escherichia coli, S3 is known to be involved in the binding of initiator Met-tRNA. This family of ribosomal proteins includes S3 from bacteria, algae and plant chloroplast, cyanelle, archaebacteria, plant mitochondria, vertebrates, insects, Caenorhabditis elegans and yeast []. This entry is the C-terminal domain.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2XZN_C 2XZM_C 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C ....
Probab=97.51 E-value=9.9e-05 Score=50.38 Aligned_cols=32 Identities=25% Similarity=0.358 Sum_probs=28.9
Q ss_pred HHHHHHHcChHHHHHHH-HHHHH-Hhccccccccc
Q 040226 104 SLRYKLLGGLAVRRYIL-IISQI-LSNKALRSCGL 136 (137)
Q Consensus 104 ~ia~qLe~Rv~fRRa~k-ai~~a-~~~ga~kG~~~ 136 (137)
+|+++||++.+|||+++ +++.+ +++|+ +||++
T Consensus 1 ~i~~~l~k~~~~r~~i~~~~~~i~~~~~~-~GikI 34 (85)
T PF00189_consen 1 FIAQKLEKRISFRRIIKKIIRRIMMNKGI-KGIKI 34 (85)
T ss_dssp HHHHHHHTTSTHHHHHHHHHHHHHHCTTS-SEEEE
T ss_pred ChHHHHhcCcHHHHHHHHHHHHHHhhccc-ceEEE
Confidence 58999999999999999 99999 77785 99986
No 17
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=97.43 E-value=0.0002 Score=47.13 Aligned_cols=68 Identities=13% Similarity=0.162 Sum_probs=46.2
Q ss_pred HHHHHHHHhhhccCCccceEEE--EcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q 040226 19 AELNEVLTRELAEDGYSGVEVR--VTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (137)
Q Consensus 19 ~~Ire~l~k~~~~agis~IeI~--R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I 86 (137)
..+++|+..-+...+=-.+++. .....+.+.+...-+|.+||++|+.++.|+..+....+-...++.|
T Consensus 2 e~l~~~l~~l~~~~~~v~v~~~~~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~~v 71 (73)
T PF13083_consen 2 EFLEDFLKNLVDKPMDVEVTIEIEEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAANKHGKRVRV 71 (73)
T ss_dssp ---HHHHHHHHHHTT--EEEEEEETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHHHT-SS-EE
T ss_pred chHHHHHHHHhCCcCeEEEEEEEcCCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHHHhCCCEEEE
Confidence 3566777776643332224443 4577999999999999999999999999999988877544455554
No 18
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=96.92 E-value=0.0096 Score=44.88 Aligned_cols=87 Identities=22% Similarity=0.281 Sum_probs=60.2
Q ss_pred HHHHHHHHhhhc-cCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcC
Q 040226 19 AELNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLC 97 (137)
Q Consensus 19 ~~Ire~l~k~~~-~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~ 97 (137)
..-++.+.+-.+ +||+.++.. .++.=+|+|++.+||+++|++|..+.++.. .+|+ .-. -+..|-+.
T Consensus 52 e~A~~~I~~ivP~ea~i~di~F--d~~tGEV~IeaeKPG~ViGk~g~~~reI~~----~tgW---~p~----vvRtpPi~ 118 (145)
T cd02410 52 EEAIKIILEIVPEEAGITDIYF--DDDTGEVIIEAEKPGLVIGKGGSTLREITR----ETGW---APK----VVRTPPIQ 118 (145)
T ss_pred HHHHHHHHHhCCCccCceeeEe--cCCCcEEEEEEcCCeEEEecCchhHHHHHH----HhCC---eeE----EEecCCCC
Confidence 344566666555 678876655 677788999999999999999988877665 5554 223 36777777
Q ss_pred HHHHHHHHHHHHHcChHHHHHH
Q 040226 98 AIAQAESLRYKLLGGLAVRRYI 119 (137)
Q Consensus 98 A~liA~~ia~qLe~Rv~fRRa~ 119 (137)
+..+ +.+.+-|-+-..+|+-+
T Consensus 119 S~ti-~~ir~~l~~~~~eR~~~ 139 (145)
T cd02410 119 SRTV-KSIRRFLRREREERKEI 139 (145)
T ss_pred cHHH-HHHHHHHHHhHHHHHHH
Confidence 7766 44666666656666543
No 19
>PRK01064 hypothetical protein; Provisional
Probab=96.61 E-value=0.038 Score=37.44 Aligned_cols=54 Identities=11% Similarity=0.173 Sum_probs=41.4
Q ss_pred eEEEEcCCeEEEEEEeccc--ceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q 040226 37 VEVRVTPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (137)
Q Consensus 37 IeI~R~~~~i~I~I~~arP--g~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~e 90 (137)
|+-......+.+.+++... |.+||++|..++.++..+.......+.++.+.|.+
T Consensus 21 V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~~~~~~~~rv~leI~~ 76 (78)
T PRK01064 21 IKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIME 76 (78)
T ss_pred EEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhhCCCEEEEEEec
Confidence 4433445677788888776 88999999999999999998776556777766554
No 20
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=96.56 E-value=0.011 Score=46.95 Aligned_cols=110 Identities=16% Similarity=0.173 Sum_probs=76.8
Q ss_pred hhHHHHHHHHHHHhhhccCCcc-ceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCC---CeEEEEEE
Q 040226 14 DGVFFAELNEVLTRELAEDGYS-GVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPE---NSVELYAE 89 (137)
Q Consensus 14 ~~~~~~~Ire~l~k~~~~agis-~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~---~~i~I~i~ 89 (137)
...+...+.+||..-+..-|++ .|.+......+.+.|....|+.+||++|+.++.|+...+-.++... .+|.+++.
T Consensus 60 ~~~~~~~~~~~L~ell~~m~~~~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~ 139 (208)
T COG1847 60 IEKIAQEAKDYLEELLELMDFEVTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVG 139 (208)
T ss_pred hhHHHHHHHHHHHHHHHHhCCceEEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhh
Confidence 3456688999999999988874 5888888999999999999999999999999999988887665321 24554443
Q ss_pred EecCC-CcCHHHHHHHHHHHH-HcC--------hHH-HHHHH-HHH
Q 040226 90 KVNNR-GLCAIAQAESLRYKL-LGG--------LAV-RRYIL-IIS 123 (137)
Q Consensus 90 ev~~P-~l~A~liA~~ia~qL-e~R--------v~f-RRa~k-ai~ 123 (137)
.-... .-.=..+|+.+|.|. +.+ .|| ||.++ +++
T Consensus 140 ~yRerR~e~L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~ 185 (208)
T COG1847 140 DYRERRKETLIKLAERAAERVLETGRSVELEPMPPFERKIVHTALS 185 (208)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHH
Confidence 32211 111234666666664 222 344 77777 665
No 21
>cd02134 NusA_KH NusA_K homology RNA-binding domain (KH). NusA is an essential multifunctional transcription elongation factor that is universally conserved among prokaryotes and archaea. NusA anti-termination function plays an important role in the expression of ribosomal rrn operons. During transcription of many other genes, NusA-induced RNAP pausing provides a mechanism for synchronizing transcription and translation . The N-terminal RNAP-binding domain (NTD) is connected through a flexible hinge helix to three globular domains, S1, KH1 and KH2. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices.
Probab=95.49 E-value=0.052 Score=34.65 Aligned_cols=53 Identities=15% Similarity=0.289 Sum_probs=43.7
Q ss_pred HHHHHhhhccCCccceEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 040226 22 NEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 22 re~l~k~~~~agis~IeI~R~-~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~ 74 (137)
.+|+.+-+..+.+.+|.+... .+...|.+....-|..||++|..++.+++.+.
T Consensus 2 ~~~i~n~~~p~~i~~V~~~~~~~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~ 55 (61)
T cd02134 2 AEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLG 55 (61)
T ss_pred HHHHHHhcCcccceEEEEecCCCcEEEEEECcccceeeECCCCHHHHHHHHHHC
Confidence 467777888888999888654 47888888888889999999999998887665
No 22
>PRK02821 hypothetical protein; Provisional
Probab=95.21 E-value=0.38 Score=32.50 Aligned_cols=51 Identities=20% Similarity=0.253 Sum_probs=38.6
Q ss_pred eEEEEcCCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q 040226 37 VEVRVTPVRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (137)
Q Consensus 37 IeI~R~~~~i~I~I~~ar--Pg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~e 90 (137)
|+.+.....+.+.|+++. -|-+||++|..++.++..+.-. .++++.+.|.+
T Consensus 22 V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~leI~~ 74 (77)
T PRK02821 22 VDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI---GGRGVRVDVVD 74 (77)
T ss_pred EEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh---cCCeEEEEEEe
Confidence 444455666777777765 3579999999999999999977 35788876665
No 23
>COG1159 Era GTPase [General function prediction only]
Probab=95.20 E-value=0.23 Score=41.54 Aligned_cols=83 Identities=20% Similarity=0.345 Sum_probs=57.7
Q ss_pred hHhHHHhhHHHHHHHHHHHhhhccCCccceEEEEc----C--CeEEEEEEecccc---eeeccCcccHHHH----HHHHH
Q 040226 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVT----P--VRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQ 74 (137)
Q Consensus 8 ~~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~----~--~~i~I~I~~arPg---~viG~~g~~i~~L----~~~L~ 74 (137)
-.+|+.-.++++++=.|+..+++.+ +.|+|++. . ..+.-+|++.|.+ ++||++|+.|+++ +..++
T Consensus 187 ~~rf~~aEiiREk~~~~l~eElPhs--v~VeIe~~~~~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie 264 (298)
T COG1159 187 PERFLAAEIIREKLLLLLREELPHS--VAVEIEEFEEREKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIE 264 (298)
T ss_pred hHHHHHHHHHHHHHHHhcccccCce--EEEEEEEEEecCCCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHH
Confidence 3467777777777777777777764 44777653 2 2566688888875 7999999999775 67788
Q ss_pred HHhCCCCCeEEEEEEEecC
Q 040226 75 KRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 75 k~~~~~~~~i~I~i~ev~~ 93 (137)
+.|+. +-.+.++|.--++
T Consensus 265 ~l~~~-kV~L~L~VKVk~~ 282 (298)
T COG1159 265 KLLGC-KVYLELWVKVKKN 282 (298)
T ss_pred HHhCC-ceEEEEEEEEccc
Confidence 88874 3456665554333
No 24
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=95.14 E-value=0.039 Score=41.10 Aligned_cols=61 Identities=11% Similarity=0.268 Sum_probs=48.3
Q ss_pred HHHHHHHHhhhccCCccceEEEEcC--CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q 040226 19 AELNEVLTRELAEDGYSGVEVRVTP--VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (137)
Q Consensus 19 ~~Ire~l~k~~~~agis~IeI~R~~--~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~ 79 (137)
....+|+.+-+..+++.++.|.... ..+.|.+....-|..||++|+.++.++..+.+.++.
T Consensus 72 ~d~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 72 DDPEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred CCHHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 3467899999999999999985443 345566666777889999999999999988877764
No 25
>PRK00468 hypothetical protein; Provisional
Probab=94.19 E-value=0.77 Score=30.78 Aligned_cols=51 Identities=16% Similarity=0.187 Sum_probs=36.2
Q ss_pred eEEEEcCCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeEEEE
Q 040226 37 VEVRVTPVRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (137)
Q Consensus 37 IeI~R~~~~i~I~I~~ar--Pg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~ 87 (137)
|+.....+.+.+.++++. -|.+||++|..++.++..+.-.-...+.++.+.
T Consensus 21 V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~le 73 (75)
T PRK00468 21 VNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVE 73 (75)
T ss_pred EEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHHHHHhcCCCEEEEE
Confidence 444445566777777764 367999999999999999986654445666653
No 26
>PRK15494 era GTPase Era; Provisional
Probab=93.45 E-value=1.1 Score=37.56 Aligned_cols=82 Identities=22% Similarity=0.326 Sum_probs=51.6
Q ss_pred HhHHHhhHHHHHHHHHHHhhhccCCccceEEEEc---C---CeEEEEEEecccc---eeeccCcccHHHH----HHHHHH
Q 040226 9 RKFVADGVFFAELNEVLTRELAEDGYSGVEVRVT---P---VRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQK 75 (137)
Q Consensus 9 ~~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R~---~---~~i~I~I~~arPg---~viG~~g~~i~~L----~~~L~k 75 (137)
.+|+--.++++++=+++..+++.+ ..|+|+.- . ..|...||+.|++ ++||++|+.|+++ +..|++
T Consensus 232 ~~~~~~eiiRe~~~~~~~~EiP~~--~~v~i~~~~~~~~~~~~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~ 309 (339)
T PRK15494 232 MRFIAAEITREQLFLNLQKELPYK--LTVQTEKWEDLKDKSVKINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMER 309 (339)
T ss_pred HHHHHHHHHHHHHHhhCCcccCce--EEEEEEEEEEcCCCeEEEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHH
Confidence 355555566666666666665543 22444431 2 2477899999997 6999999999775 667888
Q ss_pred HhCCCCCeEEEEEEEecC
Q 040226 76 RFKFPENSVELYAEKVNN 93 (137)
Q Consensus 76 ~~~~~~~~i~I~i~ev~~ 93 (137)
.|+. +-.+.++|.--++
T Consensus 310 ~~~~-~v~l~l~Vkv~~~ 326 (339)
T PRK15494 310 FFGF-PVHLFLFVKVREL 326 (339)
T ss_pred HhCC-CeEEEEEEEECCC
Confidence 8873 2345555543333
No 27
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=93.22 E-value=1.2 Score=30.14 Aligned_cols=47 Identities=17% Similarity=0.241 Sum_probs=33.5
Q ss_pred cCCeEEEEEEeccc--ceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q 040226 42 TPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (137)
Q Consensus 42 ~~~~i~I~I~~arP--g~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i 88 (137)
....+.+.++++.. |-+||++|..++.|+..|...-.-.++++.+.+
T Consensus 26 ~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~~~~~~v~i~i 74 (76)
T COG1837 26 GEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGSKDSKRVVVEI 74 (76)
T ss_pred cCCeEEEEEEECcccccceecCCChhHHHHHHHHHHhcccCceEEEEEe
Confidence 35576666666654 569999999999999999865543345566543
No 28
>TIGR00436 era GTP-binding protein Era. Era is an essential GTPase in Escherichia coli and many other bacteria. It plays a role in ribosome biogenesis. Few bacteria lack this protein.
Probab=93.17 E-value=0.77 Score=36.76 Aligned_cols=72 Identities=17% Similarity=0.324 Sum_probs=44.4
Q ss_pred hHHHhhHHHHHHHHHHHhhhccCCccceEEEE---cC---CeEEEEEEecccc---eeeccCcccHHHH----HHHHHHH
Q 040226 10 KFVADGVFFAELNEVLTRELAEDGYSGVEVRV---TP---VRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKR 76 (137)
Q Consensus 10 ~fi~~~~~~~~Ire~l~k~~~~agis~IeI~R---~~---~~i~I~I~~arPg---~viG~~g~~i~~L----~~~L~k~ 76 (137)
+|.-..++++++=+++..+++.+ ..++|+. .+ ..|...|++.|++ ++||++|+.|+++ +..|++.
T Consensus 181 ~~~~~e~ire~~~~~~~~e~p~~--~~~~~~~~~~~~~~~~~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~~~ 258 (270)
T TIGR00436 181 RFKISEIIREKIIRYTKEEIPHS--VRVEIERKSFNEKGLLKIHALISVERESQKKIIIGKNGSMIKAIGIAARKDILEL 258 (270)
T ss_pred HHHHHHHHHHHHHHhcccccCce--EEEEEEEEEECCCCeEEEEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHHHH
Confidence 34444444444444444454433 2244432 22 2578899999985 7999999999775 5677878
Q ss_pred hCCCCCeEEE
Q 040226 77 FKFPENSVEL 86 (137)
Q Consensus 77 ~~~~~~~i~I 86 (137)
|+ .+|.+
T Consensus 259 ~~---~~v~l 265 (270)
T TIGR00436 259 FD---CDVFL 265 (270)
T ss_pred hC---CCEEE
Confidence 86 45544
No 29
>PRK00089 era GTPase Era; Reviewed
Probab=92.95 E-value=1.2 Score=35.66 Aligned_cols=87 Identities=22% Similarity=0.265 Sum_probs=49.9
Q ss_pred HHHhhHHHHHHHHHHHhhhccCCccceEEEE----cCCeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCC
Q 040226 11 FVADGVFFAELNEVLTRELAEDGYSGVEVRV----TPVRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKF 79 (137)
Q Consensus 11 fi~~~~~~~~Ire~l~k~~~~agis~IeI~R----~~~~i~I~I~~arPg---~viG~~g~~i~~L----~~~L~k~~~~ 79 (137)
|.-..++++++=+++..+++.+ ..++|+. ....|.-.|++.+++ ++||++|+.|+++ +..|++.|+.
T Consensus 189 ~~~~EiiRe~~~~~l~~e~p~~--~~v~~~~~~~~~~~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~~ 266 (292)
T PRK00089 189 FLAAEIIREKLLRLLGDELPYS--VAVEIEKFEERGLVRIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLGK 266 (292)
T ss_pred HHHHHHHHHHHHhhCCccCCce--EEEEEEEEEECCeEEEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhCC
Confidence 3334444444444444444433 1233322 223577799999985 7999999999775 5677778873
Q ss_pred CCCeEEEEEEEecCCCcCHHH
Q 040226 80 PENSVELYAEKVNNRGLCAIA 100 (137)
Q Consensus 80 ~~~~i~I~i~ev~~P~l~A~l 100 (137)
+-.+.++|.--++=--++..
T Consensus 267 -~v~l~l~vkv~~~w~~~~~~ 286 (292)
T PRK00089 267 -KVFLELWVKVKKGWRDDEKA 286 (292)
T ss_pred -CEEEEEEEEECCCccCCHHH
Confidence 33455555544443444433
No 30
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=92.70 E-value=1.1 Score=40.50 Aligned_cols=75 Identities=21% Similarity=0.318 Sum_probs=50.9
Q ss_pred HHHHHhhhc-cCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHH
Q 040226 22 NEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIA 100 (137)
Q Consensus 22 re~l~k~~~-~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~l 100 (137)
++.+.+-.+ +||+++ |.-..+.-+|.|.+.+||.+||+.|+...++.. ..++. + . -+..|-+.+..
T Consensus 78 ~~~I~eivP~ea~i~~--i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~----~tgW~-p--~----ivR~PPi~S~t 144 (637)
T COG1782 78 RKIILEIVPEEAGITD--IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITA----ETGWA-P--K----IVRTPPIQSRT 144 (637)
T ss_pred HHHHHHhCccccCcee--EEecCCCceEEEEecCCceEEecCchHHHHHHH----HhCCc-c--e----eeecCCCchhh
Confidence 344444443 688887 445778889999999999999999988877655 44442 2 2 26677777776
Q ss_pred HHHHHHHHHH
Q 040226 101 QAESLRYKLL 110 (137)
Q Consensus 101 iA~~ia~qLe 110 (137)
+- +|.+-|-
T Consensus 145 i~-~ir~~l~ 153 (637)
T COG1782 145 IK-SIREILR 153 (637)
T ss_pred HH-HHHHHHH
Confidence 63 3444333
No 31
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=92.57 E-value=1.6 Score=39.76 Aligned_cols=86 Identities=22% Similarity=0.293 Sum_probs=58.4
Q ss_pred HHHHHHHhhhc-cCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCH
Q 040226 20 ELNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCA 98 (137)
Q Consensus 20 ~Ire~l~k~~~-~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A 98 (137)
+-++.+.+-.+ +||++++.. .++.=+|.|.+.+||.+||+.|..+.++.. .+++ .-. -++.|-+.+
T Consensus 70 ~~~~~i~~~~~~~~~~~~~~f--~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~----~~~w---~~~----~~~~~~~~~ 136 (630)
T TIGR03675 70 EAIEKIKEIVPEEAGITDIYF--DDVTGEVIIEAEKPGLVIGKGGSTLREITA----ETGW---TPK----VVRTPPIES 136 (630)
T ss_pred HHHHHHHHhCCCcCCceeEEe--cCCCceEEEEEcCCeEEEecCcchHHHHHH----HhCC---eee----EEecCCCCc
Confidence 34456666554 688876555 677788999999999999999988877665 4554 222 367787877
Q ss_pred HHHHHHHHHHHHcChHHHHHH
Q 040226 99 IAQAESLRYKLLGGLAVRRYI 119 (137)
Q Consensus 99 ~liA~~ia~qLe~Rv~fRRa~ 119 (137)
..+- .+..-|-+-...|+-+
T Consensus 137 ~~~~-~~~~~~~~~~~~r~~~ 156 (630)
T TIGR03675 137 KTIK-NIREYLRSESEERKEF 156 (630)
T ss_pred HHHH-HHHHHHHHhHHHHHHH
Confidence 7663 4555555555555444
No 32
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=90.04 E-value=0.58 Score=35.00 Aligned_cols=59 Identities=15% Similarity=0.249 Sum_probs=43.9
Q ss_pred HHHHHHHhhhccCCccceEEEEcC--CeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 040226 20 ELNEVLTRELAEDGYSGVEVRVTP--VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (137)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~R~~--~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~ 78 (137)
-+.+|+.+-|..|.+.+|.+.-.+ ....|.+.-.--+..||++|++++.....+...++
T Consensus 74 D~~~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~d 134 (141)
T TIGR01952 74 NLEEFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHD 134 (141)
T ss_pred CHHHHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccC
Confidence 357899999999999999886532 23445555555678999999999888777765554
No 33
>cd02393 PNPase_KH Polynucleotide phosphorylase (PNPase) K homology RNA-binding domain (KH). PNPase is a polyribonucleotide nucleotidyl transferase that degrades mRNA in prokaryotes and plant chloroplasts. The C-terminal region of PNPase contains domains homologous to those in other RNA binding proteins: a KH domain and an S1 domain. KH domains bind single-stranded RNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=88.14 E-value=0.53 Score=29.85 Aligned_cols=29 Identities=17% Similarity=0.412 Sum_probs=23.3
Q ss_pred eEEEEEEecccceeeccCcccHHHHHHHH
Q 040226 45 RTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (137)
Q Consensus 45 ~i~I~I~~arPg~viG~~g~~i~~L~~~L 73 (137)
...+.|-..+-|.+||++|+.+++|++.-
T Consensus 3 ~~~i~Ip~~~ig~iIGkgG~~ik~I~~~t 31 (61)
T cd02393 3 IETMKIPPDKIRDVIGPGGKTIKKIIEET 31 (61)
T ss_pred EEEEEeChhheeeeECCCchHHHHHHHHH
Confidence 35567777788999999999999887744
No 34
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=85.64 E-value=3.6 Score=31.68 Aligned_cols=54 Identities=15% Similarity=0.246 Sum_probs=36.7
Q ss_pred HHHHHHHhhhccCCccceEEEEc---CCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 040226 20 ELNEVLTRELAEDGYSGVEVRVT---PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~R~---~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~ 74 (137)
.+-+-|-+...+..+++.+..+. .+++-+.+..+. |..||++|+.++.|++.|-
T Consensus 34 ~i~~~l~~l~~~~~l~~~~~~k~~~~ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lg 90 (166)
T PRK06418 34 EVSKVLLKLEEDKELKDVEYKKAYEVDDLVILLVTSGP-RIPIGKGGKIAKALSRKLG 90 (166)
T ss_pred HHHHHHHHhhccccccCceEEEEEEeCCEEEEEEeCCC-cccccccchHHHHHHHHhC
Confidence 33344443333334556666654 678887787788 9999999999998877664
No 35
>PF13014 KH_3: KH domain
Probab=85.16 E-value=0.7 Score=26.98 Aligned_cols=16 Identities=25% Similarity=0.650 Sum_probs=14.2
Q ss_pred ceeeccCcccHHHHHH
Q 040226 56 QNVLGEKGRRIRELTS 71 (137)
Q Consensus 56 g~viG~~g~~i~~L~~ 71 (137)
|.+||++|..|++|++
T Consensus 3 g~iIG~~G~~I~~I~~ 18 (43)
T PF13014_consen 3 GRIIGKGGSTIKEIRE 18 (43)
T ss_pred CeEECCCChHHHHHHH
Confidence 6799999999998876
No 36
>cd02396 PCBP_like_KH K homology RNA-binding domain, PCBP_like. Members of this group possess KH domains in a tandem arrangement. Most members, similar to the poly(C) binding proteins (PCBPs) and Nova, containing three KH domains, with the first and second domains, which are represented here, in tandem arrangement, followed by a large spacer region, with the third domain near the C-terminal end of the protein. The poly(C) binding proteins (PCBPs) can be divided into two groups, hnRNPs K/J and the alphaCPs, which share a triple KH domain configuration and poly(C) binding specificity. They play roles in mRNA stabilization, translational activation, and translational silencing. Nova-1 and Nova-2 are nuclear RNA-binding proteins that regulate splicing. This group also contains plant proteins that seem to have two tandem repeat arrrangements, like Hen4, a protein that plays a role in AGAMOUS (AG) pre-mRNA processing and important step in plant development. In general, KH binds single-stran
Probab=78.57 E-value=2 Score=27.23 Aligned_cols=27 Identities=15% Similarity=0.513 Sum_probs=21.6
Q ss_pred EEEEEEecccceeeccCcccHHHHHHH
Q 040226 46 TEIIIRATRTQNVLGEKGRRIRELTSV 72 (137)
Q Consensus 46 i~I~I~~arPg~viG~~g~~i~~L~~~ 72 (137)
+++.+-...-|.+||++|..+++|++.
T Consensus 2 ~r~~ip~~~vg~iIG~~G~~i~~i~~~ 28 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREE 28 (65)
T ss_pred EEEEECHHHcCeeECCCcHHHHHHHHH
Confidence 455666677788999999999988874
No 37
>cd00105 KH-I K homology RNA-binding domain, type I. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA. There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is folded into a beta alpha alpha beta unit. In addition to the core, type II KH domains (e.g. ribosomal protein S3) include N-terminal extension and type I KH domains (e.g. hnRNP K) contain C-terminal extension.
Probab=77.95 E-value=2.7 Score=25.67 Aligned_cols=27 Identities=15% Similarity=0.473 Sum_probs=21.1
Q ss_pred EEEEEecccceeeccCcccHHHHHHHH
Q 040226 47 EIIIRATRTQNVLGEKGRRIRELTSVV 73 (137)
Q Consensus 47 ~I~I~~arPg~viG~~g~~i~~L~~~L 73 (137)
++.|-...-+.+||++|..+++|++.-
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s 29 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREET 29 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHH
Confidence 455555667889999999999988754
No 38
>TIGR03665 arCOG04150 arCOG04150 universal archaeal KH domain protein. This family of proteins is universal among the 41 archaeal genomes analyzed in and is not observed outside of the archaea. The proteins contain a single KH domain (pfam00013) which is likely to confer the ability to bind RNA.
Probab=76.69 E-value=3.8 Score=31.19 Aligned_cols=64 Identities=14% Similarity=0.258 Sum_probs=43.5
Q ss_pred EEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE----EEe--cCCCcCHHHHHHHHHHHHHcChHHHHHHH
Q 040226 50 IRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA----EKV--NNRGLCAIAQAESLRYKLLGGLAVRRYIL 120 (137)
Q Consensus 50 I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i----~ev--~~P~l~A~liA~~ia~qLe~Rv~fRRa~k 120 (137)
|-..+-|.+||++|+.+++|.+.. +. +|+|+- ..| ..++.++..-|..+...|-...++..|++
T Consensus 4 Ip~~kig~vIG~gG~~Ik~I~~~t----gv---~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e~A~~ 73 (172)
T TIGR03665 4 IPKDRIGVLIGKGGETKKEIEERT----GV---KLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALK 73 (172)
T ss_pred CCHHHhhhHhCCchhHHHHHHHHh----Cc---EEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHHHHHH
Confidence 344566789999999998877744 32 233322 234 56777888889998888877766555543
No 39
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=75.77 E-value=1.1 Score=27.59 Aligned_cols=28 Identities=21% Similarity=0.458 Sum_probs=21.9
Q ss_pred EEEEEEecccceeeccCcccHHHHHHHH
Q 040226 46 TEIIIRATRTQNVLGEKGRRIRELTSVV 73 (137)
Q Consensus 46 i~I~I~~arPg~viG~~g~~i~~L~~~L 73 (137)
.++.+....-|.+||++|..+++|++.-
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t 29 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEET 29 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHH
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhc
Confidence 3566667777889999999998877744
No 40
>PF14698 ASL_C2: Argininosuccinate lyase C-terminal; PDB: 1XWO_A 2E9F_A 1TJW_C 1TJU_A 1DCN_B 1K7W_B 1HY1_C 1TJV_B 1AUW_A 1U15_B ....
Probab=74.72 E-value=5.1 Score=26.18 Aligned_cols=31 Identities=19% Similarity=0.145 Sum_probs=21.9
Q ss_pred cCHHHHHHHHHHHHHcChHHHHHHH-H---HHHHHhcc
Q 040226 96 LCAIAQAESLRYKLLGGLAVRRYIL-I---ISQILSNK 129 (137)
Q Consensus 96 l~A~liA~~ia~qLe~Rv~fRRa~k-a---i~~a~~~g 129 (137)
+.|.=+|++++.+ ++|||.|=+ . .+.+.+.|
T Consensus 2 ~~ATdlAD~LVr~---GipFR~AH~iVg~~V~~a~~~~ 36 (70)
T PF14698_consen 2 STATDLADYLVRK---GIPFREAHHIVGRLVRLAEEEG 36 (70)
T ss_dssp GGHHHHHHHHHHT---TS-HHHHHHHHHHHHHHHHHTT
T ss_pred ccHHHHHHHHHHc---CCCHHHHHHHHHHHHHHHHHcC
Confidence 4677789999987 999999987 3 34444444
No 41
>cd02394 vigilin_like_KH K homology RNA-binding domain_vigilin_like. The vigilin family is a large and extended family of multiple KH-domain proteins, including vigilin, also called high density lipoprotein binding protien (HBP), fungal Scp160 and bicaudal-C. Yeast Scp160p has been shown to bind RNA and to associate with both soluble and membrane-bound polyribosomes as a mRNP component. Bicaudal-C is a RNA-binding molecule believed to function in embryonic development at the post-transcriptional level. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=73.46 E-value=2.9 Score=25.86 Aligned_cols=27 Identities=26% Similarity=0.454 Sum_probs=20.1
Q ss_pred EEEEEecccceeeccCcccHHHHHHHH
Q 040226 47 EIIIRATRTQNVLGEKGRRIRELTSVV 73 (137)
Q Consensus 47 ~I~I~~arPg~viG~~g~~i~~L~~~L 73 (137)
++.|-...=+.+||++|+.+++|++.-
T Consensus 3 ~i~Vp~~~~~~iIG~~G~~i~~i~~~~ 29 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGSNIRKIMEET 29 (62)
T ss_pred EEEeCHHHhhhccCCCCCcHHHHHHHh
Confidence 344444556789999999999988744
No 42
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=72.96 E-value=16 Score=28.68 Aligned_cols=28 Identities=11% Similarity=0.296 Sum_probs=20.7
Q ss_pred EEEEEeccc-ceeeccCcccHHHHHHHHH
Q 040226 47 EIIIRATRT-QNVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 47 ~I~I~~arP-g~viG~~g~~i~~L~~~L~ 74 (137)
.+.+-..-| |..+|++|..++.+.+.|-
T Consensus 78 ~~~~~~~d~vG~~iG~~G~rvk~i~~eLg 106 (190)
T COG0195 78 VSNVVKIDPVGACIGKRGSRVKAVSEELG 106 (190)
T ss_pred EEeecCcCchhhhccCCChHHHHHHHHhC
Confidence 333333445 8899999999999888765
No 43
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=68.44 E-value=32 Score=29.22 Aligned_cols=55 Identities=24% Similarity=0.358 Sum_probs=40.4
Q ss_pred HHHHHHHhhhccCCccceEE---EEc-CCeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q 040226 20 ELNEVLTRELAEDGYSGVEV---RVT-PVRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI---~R~-~~~i~I~I~~arPg-----~viG~~g~~i~~L~~~L~ 74 (137)
++++.|..+.++-.=+-|+| -|- ..+++|-+++..|+ .++|.+|.+++.+.+.|.
T Consensus 201 ~v~~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ 264 (341)
T TIGR01953 201 FVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELN 264 (341)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhC
Confidence 45666777776532223555 455 47999999999885 599999999999888774
No 44
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=67.26 E-value=17 Score=25.69 Aligned_cols=53 Identities=17% Similarity=0.149 Sum_probs=38.2
Q ss_pred EecccceeeccCccc---HHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHH
Q 040226 51 RATRTQNVLGEKGRR---IRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLL 110 (137)
Q Consensus 51 ~~arPg~viG~~g~~---i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~liA~~ia~qLe 110 (137)
|..+|-+.||++|-+ ++++...|..+= -|.|.-..+-.-+...+|+.|+++..
T Consensus 15 h~l~piv~IGk~Glte~vi~Ei~~aL~~re-------LIKVkvl~~~~edr~eia~~l~~~~~ 70 (97)
T COG1534 15 HHLKPIVQIGKNGLTEGVIKEIDRALEARE-------LIKVKVLQNAREDKKEIAEALAEETG 70 (97)
T ss_pred ccCCceEEecCCccCHHHHHHHHHHHHhCC-------cEEEEeeccchhhHHHHHHHHHHHhC
Confidence 677899999999843 677777777431 23345566666788999999988754
No 45
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=66.81 E-value=5.3 Score=26.18 Aligned_cols=37 Identities=19% Similarity=0.516 Sum_probs=27.6
Q ss_pred CeEEEEEEecc-----cceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q 040226 44 VRTEIIIRATR-----TQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (137)
Q Consensus 44 ~~i~I~I~~ar-----Pg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I 86 (137)
+++.|.++... -|..+|.+|..++.|.+.|. +.+|.|
T Consensus 3 ~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~------gekIdv 44 (69)
T PF13184_consen 3 NRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELN------GEKIDV 44 (69)
T ss_dssp TEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTT------T-EEEE
T ss_pred ceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhC------CCeEEE
Confidence 56778888877 57899999999999888764 256665
No 46
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=65.43 E-value=33 Score=29.38 Aligned_cols=55 Identities=24% Similarity=0.386 Sum_probs=40.3
Q ss_pred HHHHHHHhhhccCCccceEEE---Ec-CCeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q 040226 20 ELNEVLTRELAEDGYSGVEVR---VT-PVRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~---R~-~~~i~I~I~~arPg-----~viG~~g~~i~~L~~~L~ 74 (137)
++++.|..+.++-.=+-|+|. |- ..+++|-+++..|+ ..+|.+|.+++.+.+.|.
T Consensus 203 ~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~ 266 (362)
T PRK12327 203 LVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELK 266 (362)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhC
Confidence 455666667665322335554 55 47999999999885 599999999999988873
No 47
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=65.19 E-value=24 Score=26.06 Aligned_cols=42 Identities=10% Similarity=0.215 Sum_probs=31.3
Q ss_pred ccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHH
Q 040226 30 AEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (137)
Q Consensus 30 ~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L 73 (137)
.++..-++-+ ..+.+-+.+.....|..+|++|+.++.+++.+
T Consensus 20 t~~~~~dc~~--d~~~vi~vV~~~~vG~~IG~~G~rI~~i~e~l 61 (140)
T PRK08406 20 TGATVKDCII--DDDRIIFVVKEGDMGLAIGKGGENVKRLEEKL 61 (140)
T ss_pred hCCCceEEEE--eCCEEEEEEeCCCccccCCcCchHHHHHHHHh
Confidence 3444444433 34888888888899999999999999986544
No 48
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=65.07 E-value=10 Score=33.53 Aligned_cols=59 Identities=12% Similarity=0.230 Sum_probs=46.7
Q ss_pred HHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q 040226 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (137)
Q Consensus 21 Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I 86 (137)
..+|+.+.|..|.+.+|.+......+.|.+....-+..||++|++++.... +++ ++|+|
T Consensus 279 ~~~fi~nal~pa~v~~v~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~----l~g---~~idi 337 (470)
T PRK09202 279 PAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASK----LTG---WKIDI 337 (470)
T ss_pred HHHHHHHhCCCCEEEEEEEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHH----HHC---CeEEE
Confidence 468999999999999998766667888888888888999999999976554 333 56665
No 49
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=64.05 E-value=61 Score=24.53 Aligned_cols=77 Identities=13% Similarity=0.182 Sum_probs=53.3
Q ss_pred HHHHHHHHHHhhhccCCccceEE--EEcCCeEEEEEEecccceeeccCcccH---HHHHHHHHHHhCCCCCeEEEEEEEe
Q 040226 17 FFAELNEVLTRELAEDGYSGVEV--RVTPVRTEIIIRATRTQNVLGEKGRRI---RELTSVVQKRFKFPENSVELYAEKV 91 (137)
Q Consensus 17 ~~~~Ire~l~k~~~~agis~IeI--~R~~~~i~I~I~~arPg~viG~~g~~i---~~L~~~L~k~~~~~~~~i~I~i~ev 91 (137)
+...+.+.+..-+...|+.=+++ .+....-.+-|+.-+| +|-.+ .++...+.-.|..+++-..=+..||
T Consensus 6 ~~~~v~~liep~~~~lG~ELv~ve~~~~~~~~~lrI~id~~------g~v~lddC~~vSr~is~~LD~edpi~~~Y~LEV 79 (153)
T COG0779 6 ITEKVTELIEPVVESLGFELVDVEFVKEGRDSVLRIYIDKE------GGVTLDDCADVSRAISALLDVEDPIEGAYFLEV 79 (153)
T ss_pred hHHHHHHHHHHhHhhcCcEEEEEEEEEcCCCcEEEEEeCCC------CCCCHHHHHHHHHHHHHHhccCCcccccEEEEe
Confidence 34567778888888888765554 4544456666777777 34444 6677788888875555556788999
Q ss_pred cCCCcCHH
Q 040226 92 NNRGLCAI 99 (137)
Q Consensus 92 ~~P~l~A~ 99 (137)
+.|+++-.
T Consensus 80 SSPGldRp 87 (153)
T COG0779 80 SSPGLDRP 87 (153)
T ss_pred eCCCCCCC
Confidence 99998743
No 50
>TIGR01952 nusA_arch NusA family KH domain protein, archaeal. This model represents a family of archaeal proteins found in a single copy per genome. It contains two KH domains (pfam00013) and is most closely related to the central region bacterial NusA, a transcription termination factor named for its iteraction with phage lambda protein N in E. coli. The proteins required for antitermination by N include NusA, NusB, nusE (ribosomal protein S10), and nusG. This system, on the whole, appears not to be present in the Archaea.
Probab=63.97 E-value=12 Score=27.91 Aligned_cols=45 Identities=9% Similarity=0.299 Sum_probs=31.6
Q ss_pred hhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHH
Q 040226 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (137)
Q Consensus 28 ~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L 73 (137)
.+.++..-++.+.-.. ++-+.+..+..|..+|++|+.++.+++.+
T Consensus 18 ~~t~~~~~dc~~d~~~-riifvV~~g~vG~~IG~~G~rIk~i~el~ 62 (141)
T TIGR01952 18 DMTGATVVDCLIDDRN-RVVFVVKEGEMGAAIGKGGENVKRLEELI 62 (141)
T ss_pred HHhCCceEEEEecCCc-EEEEEEcCCCccccCCCCchHHHHHHHhc
Confidence 4455555556553222 77777788888999999999999985433
No 51
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=63.58 E-value=37 Score=29.41 Aligned_cols=55 Identities=20% Similarity=0.239 Sum_probs=40.4
Q ss_pred HHHHHHHhhhccCCccceEEE---Ec-CCeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q 040226 20 ELNEVLTRELAEDGYSGVEVR---VT-PVRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~---R~-~~~i~I~I~~arPg-----~viG~~g~~i~~L~~~L~ 74 (137)
++++.|..+.++-.=+-|+|. |- ..++.|-+++.-|+ .++|.+|.+++.+.+.|.
T Consensus 209 ~v~~Lfe~EVPEI~dG~VeIk~IARepG~RtKVAV~S~d~~iDPvGacIG~~G~rI~~I~~eL~ 272 (374)
T PRK12328 209 FLEALLELEVPEIKDGEVIIIHSARIPGERAKVALFSNNPNIDPIGATVGVKGVRINAVSKELN 272 (374)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeccCcceeEEEEEcCCCCCChHHhhcCCCcchHHHHHHHhC
Confidence 455666777765322335554 55 47999999999986 589999999999888773
No 52
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=63.12 E-value=17 Score=30.89 Aligned_cols=60 Identities=15% Similarity=0.215 Sum_probs=43.1
Q ss_pred HHHHHHhhhccCCccceEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEE
Q 040226 21 LNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (137)
Q Consensus 21 Ire~l~k~~~~agis~IeI~R~-~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~ 87 (137)
..+|+.+-|..|.+.+|.|... .....|.+--..-+..||++|++++--.. ++| .+|+|.
T Consensus 277 ~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la~~----l~g---~~IdI~ 337 (341)
T TIGR01953 277 PAEFIANALSPAKVISVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLASK----LTG---WNIDVK 337 (341)
T ss_pred HHHHHHHhcCCceEEEEEEEcCCCcEEEEEEChHHcchhhcCCChhHHHHHH----HhC---CEEEEE
Confidence 4689999999999999987443 34566666666677899999999865433 444 566653
No 53
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=62.83 E-value=20 Score=30.98 Aligned_cols=62 Identities=18% Similarity=0.212 Sum_probs=44.4
Q ss_pred HHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEE
Q 040226 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (137)
Q Consensus 21 Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ 89 (137)
..+|+.+-|..|.+.+|.+.-......|++.-..-+..||++|++++-... ++| .+|+|.-.
T Consensus 285 ~~~fI~Nal~Pa~V~~V~i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA~~----LtG---wkIDI~s~ 346 (374)
T PRK12328 285 PEIFIARALAPAIISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRLASM----LTG---YEIELNEI 346 (374)
T ss_pred HHHHHHHhCCCceeeEEEEcCCCcEEEEEEChHHhhhhhcCCChhHHHHHH----HhC---CEEEEEEC
Confidence 468899999999999998764445666666666667899999999865433 444 56665433
No 54
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=62.49 E-value=44 Score=27.26 Aligned_cols=61 Identities=13% Similarity=0.159 Sum_probs=48.7
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHH
Q 040226 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR 106 (137)
Q Consensus 44 ~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~liA~~ia 106 (137)
+.+.+.|..+.--.+||.+|++...|-......++..+.+|.|.=.++.+ .+..-+|+.+.
T Consensus 18 ~~isl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~~d~G~i~i~g~~~~~--~~s~~LAk~lS 78 (252)
T COG4604 18 DDVSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKKDSGEITIDGLELTS--TPSKELAKKLS 78 (252)
T ss_pred ccceeeecCCceeEEECCCCccHHHHHHHHHHhccccCceEEEeeeeccc--CChHHHHHHHH
Confidence 46777788888888999999999999999999998777788876666665 45666777654
No 55
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=61.06 E-value=15 Score=33.11 Aligned_cols=56 Identities=25% Similarity=0.359 Sum_probs=39.2
Q ss_pred hhHHHHHHHHHHHhhhccCCccceEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHH
Q 040226 14 DGVFFAELNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (137)
Q Consensus 14 ~~~~~~~Ire~l~k~~~~agis~IeI~R~-~~~i~I~I~~arPg~viG~~g~~i~~L~~~L 73 (137)
.+....+|.+++++.++. +++++-. +...-|.+.-..-+.+||++|.++++|.+.|
T Consensus 459 ~~~a~~~i~~~i~r~~p~----~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~kl 515 (604)
T COG1855 459 LKLAEEEIEREIKRYLPG----DVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKL 515 (604)
T ss_pred hHHHHHHHHHHHHHhCCC----CceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHh
Confidence 456677888888888775 4555545 3455555554556779999999998876643
No 56
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=59.46 E-value=23 Score=27.71 Aligned_cols=61 Identities=11% Similarity=0.188 Sum_probs=44.1
Q ss_pred HHHHHHhhhccCCccceEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q 040226 21 LNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (137)
Q Consensus 21 Ire~l~k~~~~agis~IeI~R~-~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i 88 (137)
..+|+.+-|..|.+.+|.+.-. .....+.+.-..-+..||++|+.++-..+ .++ ++++|..
T Consensus 118 ~~~fI~nal~Pa~v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~----Ltg---~~i~I~~ 179 (190)
T COG0195 118 PAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQ----LTG---WEIDIET 179 (190)
T ss_pred HHHHHHHhcCcceEeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHH----HhC---CEEEEEe
Confidence 5688888888999999999874 23566666667778899999988865554 333 5566533
No 57
>PRK13763 putative RNA-processing protein; Provisional
Probab=58.41 E-value=15 Score=28.10 Aligned_cols=71 Identities=14% Similarity=0.225 Sum_probs=43.8
Q ss_pred EEEEEEecccceeeccCcccHHHHHHHHHHHhCCCC--CeEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHH
Q 040226 46 TEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPE--NSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRY 118 (137)
Q Consensus 46 i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~--~~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa 118 (137)
..+.|-..+-|.+||++|+.++.|.+...-.....+ ..|.|... ..++.++..-|..+...|-...++-.|
T Consensus 5 ~~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~~--~~~d~~~i~kA~~~I~ai~~gf~~e~A 77 (180)
T PRK13763 5 EYVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEPT--DGEDPLAVLKARDIVKAIGRGFSPEKA 77 (180)
T ss_pred EEEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEeC--CCCCHHHHHHHHHHHHHHhcCCCHHHH
Confidence 345566677889999999999887774422111111 22222111 167778888888888887776544443
No 58
>TIGR03112 6_pyr_pter_rel 6-pyruvoyl tetrahydropterin synthase-related domain. Members of this family are small proteins, or small domains of larger proteins, that occur in certain Firmicutes in the same regions as members of families TIGR03110 and TIGR03111. Members of TIGR03110 resemble exosortase, a proposed protein sorting transpeptidase (see TIGR02602). TIGR03111 represents a small clade among the group 2 glycosyltransferases. Members of the current protein family resemble eukaryotic known and prokaryotic predicted 6-pyruvoyl tetrahydropterin synthases.
Probab=55.23 E-value=70 Score=22.71 Aligned_cols=63 Identities=10% Similarity=0.030 Sum_probs=35.8
Q ss_pred eEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCC-CeEEEEEEEecCCCcCHHHHHHHHHHHHHcChH
Q 040226 45 RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPE-NSVELYAEKVNNRGLCAIAQAESLRYKLLGGLA 114 (137)
Q Consensus 45 ~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~-~~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~ 114 (137)
.++|++.....|+ + ....|++.|.+.+.--+ +.++ .+.+...-+-.|..+|.+|.++|....+
T Consensus 28 ~vev~v~g~~~g~-v-----Df~~lk~~l~~v~~~~DH~~LN-dv~~f~~~~PTaEniA~~i~~~l~~~l~ 91 (113)
T TIGR03112 28 EITIFVIKKEDKF-I-----LFNDVEKKVEKYLKPYQNKYLN-DLEPFDKINPTLENIGDYFFDEIKKLLK 91 (113)
T ss_pred EEEEEEEecCCeE-E-----EHHHHHHHHHHHHHcCCCceec-cCCccCCCCCCHHHHHHHHHHHHHHhhc
Confidence 5666665544333 2 35666666655443222 3333 4444432223899999999999987654
No 59
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=55.21 E-value=63 Score=28.69 Aligned_cols=55 Identities=20% Similarity=0.434 Sum_probs=40.6
Q ss_pred HHHHHHHhhhccCCccceEEE---EcC-CeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q 040226 20 ELNEVLTRELAEDGYSGVEVR---VTP-VRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~---R~~-~~i~I~I~~arPg-----~viG~~g~~i~~L~~~L~ 74 (137)
++++.|..+.+.-.=+-|+|. |.| .+.+|-+++.-|. .++|.+|.+++.+.+.|.
T Consensus 203 ~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ 266 (470)
T PRK09202 203 FLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELG 266 (470)
T ss_pred HHHHHHHHhCcccccCeEEEEEEeecCcceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhC
Confidence 456667777765432335554 554 7999999998885 699999999999988874
No 60
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=54.71 E-value=23 Score=30.53 Aligned_cols=42 Identities=17% Similarity=0.294 Sum_probs=28.9
Q ss_pred CCccceEEEEcCCe---EEEEEEecccceeeccCcccHHHHHHHH
Q 040226 32 DGYSGVEVRVTPVR---TEIIIRATRTQNVLGEKGRRIRELTSVV 73 (137)
Q Consensus 32 agis~IeI~R~~~~---i~I~I~~arPg~viG~~g~~i~~L~~~L 73 (137)
+++.++.=.++|++ ++|.+-.+--|.+||++|..++.+++.-
T Consensus 117 ~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqs 161 (402)
T KOG2191|consen 117 AKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQS 161 (402)
T ss_pred cCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhh
Confidence 34455544566664 5555555667899999999999887743
No 61
>PRK13764 ATPase; Provisional
Probab=54.14 E-value=29 Score=31.79 Aligned_cols=56 Identities=21% Similarity=0.361 Sum_probs=37.0
Q ss_pred hHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHH
Q 040226 15 GVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (137)
Q Consensus 15 ~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L 73 (137)
...+.+|.+.+.+.+ .|...+++. ..+...|.+--.--+.+||++|..|+++.+.|
T Consensus 455 ~~~~~~~~~~~~~~~--~~~~~~~~~-~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~ 510 (602)
T PRK13764 455 RLAEKEIEREIKRYL--PGPVEVEVV-SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKL 510 (602)
T ss_pred HHHHHHHHHHHHHhc--CCceEEEEe-cCCeEEEEEChhhhhHHhccCcchHHHHHHHh
Confidence 344556666666666 556667776 45556555544445679999999998876643
No 62
>PRK13763 putative RNA-processing protein; Provisional
Probab=54.04 E-value=37 Score=25.95 Aligned_cols=66 Identities=12% Similarity=0.110 Sum_probs=39.3
Q ss_pred ccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHHHHHHH
Q 040226 54 RTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQI 125 (137)
Q Consensus 54 rPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~kai~~a 125 (137)
.-|.+||++|+.++.|++.-.-.+...+..+. +. - +.+..-.|......|-+..+.-.+.+-++..
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~--i~--G--~~~~~~~A~~~I~~li~g~~~~~~~~~l~~~ 170 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVA--II--G--DPEQVEIAREAIEMLIEGAPHGTVYKFLERK 170 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCCEEE--EE--e--CHHHHHHHHHHHHHHHcCCCcHHHHHHHHHH
Confidence 46789999999888776644333333233333 22 2 3355566666666666666666666544443
No 63
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=53.40 E-value=26 Score=23.02 Aligned_cols=46 Identities=15% Similarity=0.123 Sum_probs=31.8
Q ss_pred EEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 48 IIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 48 I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
|+|+..+++.-=..+-+-++++.+.+.+.+|..+..+.|-|.|+..
T Consensus 4 v~Ik~~~g~~~~~~K~~la~~vT~~~~~~lg~~~~~i~Viieev~~ 49 (69)
T COG1942 4 VNIKLFEGRLDEEQKAELAAEVTEVTVETLGKDPSAIHVIIEEVPP 49 (69)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHHhCCCcccEEEEEEecCh
Confidence 4556555333222233446889999999999877788998888864
No 64
>COG1302 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.04 E-value=91 Score=23.06 Aligned_cols=67 Identities=16% Similarity=0.147 Sum_probs=44.4
Q ss_pred HHHhhhccCCccc-eEEEEcCCe-EEEEEEecccceeeccCcccH--------HHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 24 VLTRELAEDGYSG-VEVRVTPVR-TEIIIRATRTQNVLGEKGRRI--------RELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 24 ~l~k~~~~agis~-IeI~R~~~~-i~I~I~~arPg~viG~~g~~i--------~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
=+.+.|.+.++++ +.++...+. +.|.+|+--+ =|..+ +.+++.++..+++.-..|+|+|.-|.-
T Consensus 43 ~~~e~l~~~n~~kGV~Ve~~~~~~v~VDvyi~v~------YGv~IpeVa~~Iq~~V~~~v~~mtgl~v~~VNV~V~gV~~ 116 (131)
T COG1302 43 GLTEKLGKENVTKGVKVEVGEDQSVAVDVYIIVE------YGVKIPEVAENIQERVKEEVENMTGLKVVEVNVHVVGVKV 116 (131)
T ss_pred hHHHHhCccccCCCeEEEecCCCcEEEEEEEEEe------cCCchHHHHHHHHHHHHHHHHHhhCCceEEEEEEEEEeEe
Confidence 3444556666654 888886554 7777776432 24443 556777777888876788988888876
Q ss_pred CCc
Q 040226 94 RGL 96 (137)
Q Consensus 94 P~l 96 (137)
|..
T Consensus 117 ~k~ 119 (131)
T COG1302 117 KKE 119 (131)
T ss_pred cCC
Confidence 654
No 65
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=52.88 E-value=22 Score=30.50 Aligned_cols=51 Identities=16% Similarity=0.229 Sum_probs=37.7
Q ss_pred HHHHHHhhhccCCccceEEEEc-CCeEEEEEEecccceeeccCcccHHHHHH
Q 040226 21 LNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTS 71 (137)
Q Consensus 21 Ire~l~k~~~~agis~IeI~R~-~~~i~I~I~~arPg~viG~~g~~i~~L~~ 71 (137)
..+|+.+-|..|.+.+|.+... .....|.+.-..-+..||++|++++--..
T Consensus 279 ~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~ 330 (362)
T PRK12327 279 PAEFVANALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAAR 330 (362)
T ss_pred HHHHHHHhCCCceEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHHH
Confidence 4689999999999999987432 23556666656667899999999865443
No 66
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=52.74 E-value=69 Score=28.45 Aligned_cols=55 Identities=18% Similarity=0.276 Sum_probs=39.2
Q ss_pred HHHHHHHhhhccCCccceEE---EEc--------CCeEEEEEEecccc-----eeeccCcccHHHHHHHHH
Q 040226 20 ELNEVLTRELAEDGYSGVEV---RVT--------PVRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI---~R~--------~~~i~I~I~~arPg-----~viG~~g~~i~~L~~~L~ 74 (137)
+++..|..+.+.-.=+-|+| -|. ..+++|-+++.-|+ .+||.+|.+++.+.+.|.
T Consensus 228 lv~~Lfe~EVPEI~dG~VeIk~IAREa~~~~ripG~RtKVAV~S~d~~VDPvGacVG~kG~RI~~I~~eL~ 298 (449)
T PRK12329 228 LVVYLFENEVPEIEEGVVRIVAVAREANPPSRYVGPRTKIAVDTLERDVDPVGACIGARGSRIQAVVNELR 298 (449)
T ss_pred HHHHHHHhhCcccccCeEEEEEEEecCCCCCCCCcceeEEEEEcCCCCCChhhccCCCCcchHHHHHHHhC
Confidence 34566666666432222554 464 46999999999885 599999999999888873
No 67
>TIGR00253 RNA_bind_YhbY putative RNA-binding protein, YhbY family. A combination of crystal structure, molecular modeling, and bioinformatic data together suggest that members of this family, including YhbY of E. coli, are RNA binding proteins.
Probab=49.65 E-value=59 Score=22.63 Aligned_cols=53 Identities=15% Similarity=0.189 Sum_probs=35.0
Q ss_pred EecccceeeccCccc---HHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHH
Q 040226 51 RATRTQNVLGEKGRR---IRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLL 110 (137)
Q Consensus 51 ~~arPg~viG~~g~~---i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~liA~~ia~qLe 110 (137)
|.-.|-+.||++|-. ++++...|... .=|.|. -..+-..+..-+|+.|+++..
T Consensus 14 h~l~p~v~IGK~Glt~~vi~ei~~aL~~h-----ELIKVk--vl~~~~~~~~e~a~~i~~~~~ 69 (95)
T TIGR00253 14 HHLKPVVLVGKNGLTEGVIKEIEQALEHR-----ELIKVK--VATEDREDKTLIAEALVKETG 69 (95)
T ss_pred CCCCCeEEECCCCCCHHHHHHHHHHHHhC-----CcEEEE--ecCCChhHHHHHHHHHHHHHC
Confidence 556799999999854 57777777642 223333 245555677778888877753
No 68
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=46.95 E-value=18 Score=30.42 Aligned_cols=31 Identities=23% Similarity=0.495 Sum_probs=25.5
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHH
Q 040226 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 44 ~~i~I~I~~arPg~viG~~g~~i~~L~~~L~ 74 (137)
-.+.|-+.+-..|.|+|++|++|+.|+....
T Consensus 48 ~e~ril~~sk~agavigkgg~nik~lr~d~n 78 (390)
T KOG2192|consen 48 VELRILLQSKNAGAVIGKGGKNIKALRTDYN 78 (390)
T ss_pred eeEEEEEecccccceeccccccHHHHhhhcc
Confidence 3466778888899999999999999887544
No 69
>PRK09509 fieF ferrous iron efflux protein F; Reviewed
Probab=46.67 E-value=88 Score=25.38 Aligned_cols=74 Identities=14% Similarity=0.120 Sum_probs=44.7
Q ss_pred HHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEeccccee-eccCcccHHHHHHHHHHHhCCCCCeEEEEEEEe
Q 040226 16 VFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNV-LGEKGRRIRELTSVVQKRFKFPENSVELYAEKV 91 (137)
Q Consensus 16 ~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~v-iG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev 91 (137)
-...+|++-+.+.-.-.++.++.+.+......+.+|..-|+-. +..-..-.+++++.|++.++ .-.+.|.+++.
T Consensus 213 ~~~~~I~~~i~~~~~v~~v~~l~~~~~G~~~~v~v~i~v~~~~~~~e~h~i~~~ie~~l~~~~~--~~~v~ihveP~ 287 (299)
T PRK09509 213 EERQEIIDIVTSWPGVSGAHDLRTRQSGPTRFIQLHLEMEDNLPLVQAHMIADQVEQALLRRFP--GSDVIIHQDPC 287 (299)
T ss_pred HHHHHHHHHHHhCCCCcCceeeeeEeeCCeEEEEEEEEECCCCCHHHHHHHHHHHHHHHHHhCC--CCEEEEEeCCC
Confidence 3455677776553333456778887777777888888766442 22222234667777777665 24567666654
No 70
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=45.83 E-value=75 Score=24.41 Aligned_cols=61 Identities=20% Similarity=0.188 Sum_probs=42.1
Q ss_pred HHHHHHhhhccCCccceEEEEcCCeEEEE-EEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEE
Q 040226 21 LNEVLTRELAEDGYSGVEVRVTPVRTEII-IRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (137)
Q Consensus 21 Ire~l~k~~~~agis~IeI~R~~~~i~I~-I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I 86 (137)
+.+|+.+-|..|.+.++.+.-.+++...+ ++..+-- -++-...++.+...+.+.+| +.+.+
T Consensus 102 ~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~~D--k~~l~~k~e~~~~v~~kltg---k~v~~ 163 (166)
T PRK06418 102 IKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSRRD--RRRLPAKPELLESILSKITG---TEVKI 163 (166)
T ss_pred HHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECHHH--hhcccccHHHHHHHHHHHHC---CcEEE
Confidence 67899999999999999997777764443 5554211 11124567889999999887 55554
No 71
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=45.67 E-value=8 Score=32.50 Aligned_cols=38 Identities=24% Similarity=0.562 Sum_probs=31.9
Q ss_pred cCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q 040226 42 TPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (137)
Q Consensus 42 ~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~ 79 (137)
.|-.++.-||-+-.|.+||++|..|++|++.-.-+++.
T Consensus 121 ~pce~rllihqs~ag~iigrngskikelrekcsarlki 158 (390)
T KOG2192|consen 121 SPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLKI 158 (390)
T ss_pred CchhhhhhhhhhhccceecccchhHHHHHHhhhhhhhh
Confidence 34456677899999999999999999999988887753
No 72
>PF06069 PerC: PerC transcriptional activator; InterPro: IPR024684 This family includes PerC, which is a transcriptional activator of EaeA/BfpA expression in enteropathogenic bacteria []. It also includes a number of uncharacterised proteins, such as Orf40 from bacteriophage SfV.
Probab=45.24 E-value=17 Score=25.31 Aligned_cols=19 Identities=16% Similarity=-0.080 Sum_probs=17.1
Q ss_pred HHHHHHHHHcChHHHHHHH
Q 040226 102 AESLRYKLLGGLAVRRYIL 120 (137)
Q Consensus 102 A~~ia~qLe~Rv~fRRa~k 120 (137)
-|.+|++||.+--||||..
T Consensus 3 ~d~~Ae~LE~kGl~RRAA~ 21 (90)
T PF06069_consen 3 HDKKAEELEAKGLWRRAAT 21 (90)
T ss_pred chHHHHHHHHcccHHHHHH
Confidence 3679999999999999985
No 73
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=44.50 E-value=46 Score=22.53 Aligned_cols=60 Identities=15% Similarity=0.130 Sum_probs=35.1
Q ss_pred CCccceEEEEc-CCeEEEEEEeccc-ceeeccCccc-HHHHHHHHHHHhCCCCCeEEEEEEEe
Q 040226 32 DGYSGVEVRVT-PVRTEIIIRATRT-QNVLGEKGRR-IRELTSVVQKRFKFPENSVELYAEKV 91 (137)
Q Consensus 32 agis~IeI~R~-~~~i~I~I~~arP-g~viG~~g~~-i~~L~~~L~k~~~~~~~~i~I~i~ev 91 (137)
..-.++.+... .+.+.|.++..-. |.=+-.-... -+++++.|++.+++....|+|.|..|
T Consensus 45 ~~~~~v~v~~~~~~~i~v~l~v~v~~g~~i~~v~~~iq~~V~~~v~~~tg~~v~~V~V~V~~v 107 (108)
T PF03780_consen 45 RPSKGVKVEVDEDGGITVDLHVVVEYGVNIPEVAEEIQEKVKEAVEEMTGIEVSEVNVHVEDV 107 (108)
T ss_pred CCCCCeEEEEccCcceEEEEEEEEECCccHHHHHHHHHHHHHHHHHHHHCCeeEEEEEEEEec
Confidence 33456778766 6777777665421 1111111112 25677777778887667888887765
No 74
>TIGR00013 taut 4-oxalocrotonate tautomerase family enzyme. 4-oxalocrotonate tautomerase is a homohexamer in which each monomer is very small, at about 62 amino acids. Pro-1 of the mature protein serves as a general base. The enzyme functions in meta-cleavage pathways of aromatic hydrocarbon catabolism. Because several Arg residues located near the active site in the crystal structure of Pseudomonas putida are not conserved among all members of this family, because the literature describes a general role in the isomerization of beta,gamma-unsaturated enones to their alpha,beta-isomers, and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.
Probab=42.97 E-value=49 Score=20.14 Aligned_cols=29 Identities=10% Similarity=0.155 Sum_probs=23.3
Q ss_pred cHHHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 65 RIRELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 65 ~i~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
-++.+.+.|...++.....+.|.+.++..
T Consensus 20 l~~~it~~l~~~lg~~~~~v~V~i~e~~~ 48 (63)
T TIGR00013 20 LIEGVTEAMAETLGANLESIVVIIDEMPK 48 (63)
T ss_pred HHHHHHHHHHHHhCCCcccEEEEEEEcCH
Confidence 45778888888998877888888888763
No 75
>PRK10343 RNA-binding protein YhbY; Provisional
Probab=42.83 E-value=81 Score=22.08 Aligned_cols=53 Identities=9% Similarity=0.152 Sum_probs=35.1
Q ss_pred EecccceeeccCccc---HHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHH
Q 040226 51 RATRTQNVLGEKGRR---IRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLL 110 (137)
Q Consensus 51 ~~arPg~viG~~g~~---i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~liA~~ia~qLe 110 (137)
|.-.|-+.||++|-+ ++++.+.|... .=|.|.| ..+-..+..-+|+.|+++..
T Consensus 16 h~l~Pvv~IGk~Glt~~vi~ei~~aL~~h-----ELIKvkv--~~~~~~~~~e~~~~i~~~~~ 71 (97)
T PRK10343 16 HPLKPVVLLGSNGLTEGVLAEIEQALEHH-----ELIKVKI--ATEDRETKTLIVEAIVRETG 71 (97)
T ss_pred CCCCCeEEECCCCCCHHHHHHHHHHHHHC-----CcEEEEe--cCCChhHHHHHHHHHHHHHC
Confidence 667899999999864 56666666642 2234333 35555667778888887763
No 76
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=40.25 E-value=20 Score=32.77 Aligned_cols=27 Identities=30% Similarity=0.573 Sum_probs=23.9
Q ss_pred eEEEEEEecccceeeccCcccHHHHHH
Q 040226 45 RTEIIIRATRTQNVLGEKGRRIRELTS 71 (137)
Q Consensus 45 ~i~I~I~~arPg~viG~~g~~i~~L~~ 71 (137)
..+|.|=+.|-|.|||++|+.++.|++
T Consensus 140 tqeI~IPa~k~GlIIGKgGETikqlqe 166 (600)
T KOG1676|consen 140 TQEILIPANKCGLIIGKGGETIKQLQE 166 (600)
T ss_pred eeeeccCccceeeEeccCccHHHHHHh
Confidence 567778889999999999999999877
No 77
>COG1094 Predicted RNA-binding protein (contains KH domains) [General function prediction only]
Probab=40.13 E-value=88 Score=24.73 Aligned_cols=64 Identities=11% Similarity=0.208 Sum_probs=41.7
Q ss_pred cceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHHHHHH
Q 040226 55 TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILIISQ 124 (137)
Q Consensus 55 Pg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~kai~~ 124 (137)
-|.+||++|...+-+.+.-.-........|.| +-.| +..-+|....+-|-++.+...+-+-+++
T Consensus 113 kgRIIG~~GkTr~~IE~lt~~~I~V~g~tVai----iG~~--~~v~iAr~AVemli~G~~h~~Vy~fLer 176 (194)
T COG1094 113 KGRIIGREGKTRRAIEELTGVYISVYGKTVAI----IGGF--EQVEIAREAVEMLINGAPHGKVYKFLER 176 (194)
T ss_pred hceeeCCCchHHHHHHHHhCCeEEEeCcEEEE----ecCh--hhhHHHHHHHHHHHcCCCchhHHHHHHH
Confidence 46799999987766555433322222344443 4443 5667899999999999998777664443
No 78
>PF14552 Tautomerase_2: Tautomerase enzyme; PDB: 2AAG_C 2AAL_A 2AAJ_A 1MWW_C.
Probab=39.67 E-value=25 Score=23.64 Aligned_cols=54 Identities=11% Similarity=0.070 Sum_probs=30.8
Q ss_pred EEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 39 VRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 39 I~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
+.|+.+.+-|.|.+..|.- ...|-+=.+.|.+.|+..+|..+..|.|.+.|...
T Consensus 23 ~~Rs~~~v~I~It~~~gRs-~e~K~~ly~~l~~~L~~~~gi~p~Dv~I~l~e~~~ 76 (82)
T PF14552_consen 23 IDRSDDFVIIQITSGAGRS-TEQKKALYRALAERLAEKLGIRPEDVMIVLVENPR 76 (82)
T ss_dssp -TS-TT-EEEEEEECS----HHHHHHHHHHHHHHHHHHH---GGGEEEEEEEE-G
T ss_pred CCCCCCEEEEEEEECCCCC-HHHHHHHHHHHHHHHHHHcCCCHHHEEEEEEECCc
Confidence 6788888888776654321 22222234678888888899888889988888764
No 79
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=38.06 E-value=50 Score=29.33 Aligned_cols=51 Identities=10% Similarity=0.204 Sum_probs=37.9
Q ss_pred HHHHHHhhhccCCccceEEEEc-CCeEEEEEEecccceeeccCcccHHHHHH
Q 040226 21 LNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTS 71 (137)
Q Consensus 21 Ire~l~k~~~~agis~IeI~R~-~~~i~I~I~~arPg~viG~~g~~i~~L~~ 71 (137)
..+|+.+-|..|.+.+|.+... .....|++.-..-+..||++|++++--..
T Consensus 311 p~~fI~NaLsPA~V~~V~i~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs~ 362 (449)
T PRK12329 311 PATYIANALSPARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAAR 362 (449)
T ss_pred HHHHHHHhcCCceeeEEEEEcCCCcEEEEEEChHhcchhhcCCChhHHHHHH
Confidence 4688999999999999987432 23556666666677899999999865443
No 80
>cd02395 SF1_like-KH Splicing factor 1 (SF1) K homology RNA-binding domain (KH). Splicing factor 1 (SF1) specifically recognizes the intron branch point sequence (BPS) UACUAAC in the pre-mRNA transcripts during spliceosome assembly. We show that the KH-QUA2 region of SF1 defines an enlarged KH (hnRNP K) fold which is necessary and sufficient for BPS binding. KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=37.56 E-value=25 Score=25.38 Aligned_cols=22 Identities=18% Similarity=0.368 Sum_probs=17.5
Q ss_pred cccceeeccCcccHHHHHHHHH
Q 040226 53 TRTQNVLGEKGRRIRELTSVVQ 74 (137)
Q Consensus 53 arPg~viG~~g~~i~~L~~~L~ 74 (137)
-+-|.+||.+|..+++|.+.-.
T Consensus 15 N~IG~IIGPgG~tiK~i~~eTg 36 (120)
T cd02395 15 NFVGLILGPRGNTLKQLEKETG 36 (120)
T ss_pred CeeEEEECCCChHHHHHHHHHC
Confidence 3457899999999999877554
No 81
>PRK14647 hypothetical protein; Provisional
Probab=37.05 E-value=1.8e+02 Score=21.80 Aligned_cols=76 Identities=16% Similarity=0.180 Sum_probs=44.7
Q ss_pred HHHHHHHHHhhhccCCccceEEEEc--CCeEEEEEEecccceeeccCcccH---HHHHHHHHHHhCCCCCeEEEEEEEec
Q 040226 18 FAELNEVLTRELAEDGYSGVEVRVT--PVRTEIIIRATRTQNVLGEKGRRI---RELTSVVQKRFKFPENSVELYAEKVN 92 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI~R~--~~~i~I~I~~arPg~viG~~g~~i---~~L~~~L~k~~~~~~~~i~I~i~ev~ 92 (137)
...|.+.+..-+...||.=++++-. .....+.|+.-+|+ |-.+ ..+...|...|...++--.=|..||+
T Consensus 7 ~~~i~~~i~~~~~~~G~~L~dv~~~~~~~~~~lrV~ID~~~------gvslddC~~vSr~is~~LD~~d~i~~~Y~LEVS 80 (159)
T PRK14647 7 VDRVTELAEQVLSSLGLELVELEYKREGREMVLRLFIDKEG------GVNLDDCAEVSRELSEILDVEDFIPERYTLEVS 80 (159)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEEEecCCCeEEEEEEeCCC------CCCHHHHHHHHHHHHHHHcccccCCCCeEEEEc
Confidence 3456777777777888876666543 33333444444553 4444 56666777766532221123568999
Q ss_pred CCCcCHH
Q 040226 93 NRGLCAI 99 (137)
Q Consensus 93 ~P~l~A~ 99 (137)
.|+++=.
T Consensus 81 SPG~~Rp 87 (159)
T PRK14647 81 SPGLDRP 87 (159)
T ss_pred CCCCCCc
Confidence 9998743
No 82
>PRK00092 ribosome maturation protein RimP; Reviewed
Probab=36.34 E-value=1.8e+02 Score=21.53 Aligned_cols=79 Identities=15% Similarity=0.132 Sum_probs=43.4
Q ss_pred HHHHHHHHHhhhccCCccc--eEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCC
Q 040226 18 FAELNEVLTRELAEDGYSG--VEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRG 95 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~--IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~ 95 (137)
...|.+.+..-+...|+.= |++.+....-.+.|+.-.|+- -.=....++...+...|...+.--.=+..||+.|+
T Consensus 6 ~~~i~~~~~~~~~~~g~~l~dv~~~~~~~~~~l~V~Id~~~g---v~iddc~~~Sr~is~~LD~~d~i~~~Y~LEVSSPG 82 (154)
T PRK00092 6 EEQLTELIEPVVEALGYELVDVEYVKEGRDSTLRIYIDKEGG---IDLDDCEEVSRQISAVLDVEDPIPGAYTLEVSSPG 82 (154)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEEEecCCCcEEEEEEECCCC---CCHHHHHHHHHHHHHHhccccCCCCCeEEEEeCCC
Confidence 4467788887788778654 555554333334444444431 12223456666676666422210012468999999
Q ss_pred cCHH
Q 040226 96 LCAI 99 (137)
Q Consensus 96 l~A~ 99 (137)
++=.
T Consensus 83 i~Rp 86 (154)
T PRK00092 83 LDRP 86 (154)
T ss_pred CCCc
Confidence 8753
No 83
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=35.85 E-value=43 Score=30.69 Aligned_cols=53 Identities=21% Similarity=0.370 Sum_probs=38.5
Q ss_pred HHHHHHHhhhc-cCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHh
Q 040226 20 ELNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRF 77 (137)
Q Consensus 20 ~Ire~l~k~~~-~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~ 77 (137)
.|++-+.+.++ ++.+++||.+ +-+|.|||-.|..+... |.-+++|-+.|+|+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~e----gp~~~~~~~~~~~~~~~-~~~~~~~~~~~~~r~ 56 (630)
T TIGR03675 3 EIKEIINELLPKDIKITDVEFE----GPELVIYTKNPELFAKD-DDLVKELAKKLRKRI 56 (630)
T ss_pred HHHHHHHHhCCCCCeEEEEEEe----CCeEEEEeCCHHHhccc-hHHHHHHHHHhhceE
Confidence 45555666665 6789998885 57899999999988764 456677777776644
No 84
>cd00554 MECDP_synthase MECDP_synthase (2-C-methyl-D-erythritol-2,4-cyclodiphosphate synthase), encoded by the ispF gene, catalyzes the formation of 2-C-methyl-D-erythritol 2,4-cyclodiphosphate (MEC) in the non-mevalonate deoxyxylulose (DOXP) pathway for isoprenoid biosynthesis. This pathway is present in bacteria, plants and some protozoa but is distinct from that used by mammals and Archaea. MECDP_synthase forms a homotrimer, carrying three active sites, each of which is formed in a cleft between pairs of subunits.
Probab=35.54 E-value=1.2e+02 Score=23.01 Aligned_cols=42 Identities=19% Similarity=0.252 Sum_probs=33.0
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q 040226 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (137)
Q Consensus 44 ~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~e 90 (137)
..+.++|-+.+|.+ +.-..++++.|.+.++....+|+|+.+-
T Consensus 91 ~niD~tii~e~PKi-----~p~~~~m~~~ls~~L~~~~~~V~iKatT 132 (153)
T cd00554 91 VNIDITIIAERPKI-----SPYREAMRANLAELLGIPPSRVNIKATT 132 (153)
T ss_pred EEEEEEEEecCCcc-----hHHHHHHHHHHHHHhCCCCceEEEEEec
Confidence 35677888999966 5678999999999999866677776553
No 85
>PF01985 CRS1_YhbY: CRS1 / YhbY (CRM) domain; InterPro: IPR001890 The CRM domain is an ~100-amino acid RNA-binding domain. The name chloroplast RNA splicing and ribosome maturation (CRM) has been suggested to reflect the functions established for the four characterised members of the family: Zea mays (Maize) CRS1 (Q9FYT6 from SWISSPROT), CAF1 (Q84N49 from SWISSPROT) and CAF2 (Q84N48 from SWISSPROT) proteins and the Escherichia coli protein YhbY (P0AGK4 from SWISSPROT). The CRM domain is found in eubacteria, archaea, and plants. The CRM domain is represented as a stand-alone protein in archaea and bacteria, and in single- and multi-domain proteins in plants. It has been suggested that prokaryotic CRM proteins existed as ribosome-associated proteins prior to the divergence of archaea and bacteria, and that they were co-opted in the plant lineage as RNA binding modules by incorporation into diverse protein contexts. Plant CRM domains are predicted to reside not only in the chloroplast, but also in the mitochondrion and the nucleo/cytoplasmic compartment. The diversity of the CRM domain family in plants suggests a diverse set of RNA targets [, ]. The CRM domain is a compact alpha/beta domain consisting of a four-stranded beta sheet and three alpha helices with an alpha-beta-alpha-beta-alpha-beta-beta topology. The beta sheet face is basic, consistent with a role in RNA binding. Proximal to the basic beta sheet face is another moiety that could contribute to nucleic acid recognition. Connecting strand beta1 and helix alpha2 is a loop with a six amino acid motif, GxxG flanked by large aliphatic residues, within which one 'x' is typically a basic residue []. Escherichia coli YhbY is associated with pre-50S ribosomal subunits, which implies a function in ribosome assembly. GFP fused to a single-domain CRM protein from maize localises to the nucleolus, suggesting that an analogous activity may have been retained in plants []. A CRM domain containing protein in plant chloroplasts has been shown to function in group I and II intron splicing []. In vitro experiments with an isolated maize CRM domain have shown it to have RNA binding activity. These and other results suggest that the CRM domain evolved in the context of ribosome function prior to the divergence of Archaea and Bacteria, that this function has been maintained in extant prokaryotes, and that the domain was recruited to serve as an RNA binding module during the evolution of plant genomes []. YhbY has a fold similar to that of the C-terminal domain of translation initiation factor 3 (IF3C), which binds to 16S rRNA in the 30S ribosome [].; GO: 0003723 RNA binding; PDB: 1RQ8_A 1JO0_B 1LN4_A.
Probab=35.01 E-value=97 Score=20.61 Aligned_cols=52 Identities=21% Similarity=0.224 Sum_probs=27.5
Q ss_pred EecccceeeccCccc---HHHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHH
Q 040226 51 RATRTQNVLGEKGRR---IRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKL 109 (137)
Q Consensus 51 ~~arPg~viG~~g~~---i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~liA~~ia~qL 109 (137)
|.-.|-+-||++|-. ++++...|.+. .=|.|.+ ..++..+..-+|+.|+++.
T Consensus 14 ~~l~p~v~IGk~Glt~~vi~~i~~~l~~~-----eLvKVk~--~~~~~~~~~~~~~~l~~~t 68 (84)
T PF01985_consen 14 HHLKPVVQIGKNGLTDGVIEEIDDALEKH-----ELVKVKV--LGNCREDRKEIAEQLAEKT 68 (84)
T ss_dssp TTC--SEEE-TTSS-HHHHHHHHHHHHHH-----SEEEEEE--TT--HHHHHHHHHHHHHHH
T ss_pred cCCCCeEEECCCCCCHHHHHHHHHHHHhC-----CeeEEEE--ccCCHHHHHHHHHHHHHHh
Confidence 345788899999864 56666666653 2233333 3456666666666666654
No 86
>PF11324 DUF3126: Protein of unknown function (DUF3126); InterPro: IPR021473 This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=34.88 E-value=60 Score=21.15 Aligned_cols=20 Identities=15% Similarity=0.488 Sum_probs=16.0
Q ss_pred cHHHHHHHHHHHhCCCCCeEEE
Q 040226 65 RIRELTSVVQKRFKFPENSVEL 86 (137)
Q Consensus 65 ~i~~L~~~L~k~~~~~~~~i~I 86 (137)
++++|+..|++.|+ ++.+.|
T Consensus 1 Ei~klq~yLr~~f~--n~~i~v 20 (63)
T PF11324_consen 1 EIKKLQAYLRRTFG--NPGITV 20 (63)
T ss_pred ChHHHHHHHHHHhC--CCceEE
Confidence 47899999999997 466664
No 87
>PRK14640 hypothetical protein; Provisional
Probab=34.80 E-value=1.9e+02 Score=21.49 Aligned_cols=76 Identities=14% Similarity=0.169 Sum_probs=44.8
Q ss_pred HHHHHHHHHhhhccCCccceEEE--EcCCeEEEEEEecccceeeccCcccH---HHHHHHHHHHhCCCCCeEEEEEEEec
Q 040226 18 FAELNEVLTRELAEDGYSGVEVR--VTPVRTEIIIRATRTQNVLGEKGRRI---RELTSVVQKRFKFPENSVELYAEKVN 92 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI~--R~~~~i~I~I~~arPg~viG~~g~~i---~~L~~~L~k~~~~~~~~i~I~i~ev~ 92 (137)
...+.+.+..-+...|+.=++++ +....-.+.|+.-+|+ |-.+ ..+...|...+...++--.=+..||+
T Consensus 5 ~~~i~~li~p~~~~~G~el~dve~~~~~~~~~lrV~ID~~~------gv~lddC~~vSr~is~~LD~~d~i~~~Y~LEVS 78 (152)
T PRK14640 5 EQRLTDLLEAPVVALGFELWGIEFIRAGKHSTLRVYIDGEN------GVSVENCAEVSHQVGAIMDVEDPITEEYYLEVS 78 (152)
T ss_pred HHHHHHHHHHHHHhcCCEEEEEEEEecCCCcEEEEEEECCC------CCCHHHHHHHHHHHHHHhcccccCCCCeEEEEe
Confidence 44677777777777887665554 4333334444545553 3344 55666777666533221123568999
Q ss_pred CCCcCHH
Q 040226 93 NRGLCAI 99 (137)
Q Consensus 93 ~P~l~A~ 99 (137)
.|+++=.
T Consensus 79 SPGl~Rp 85 (152)
T PRK14640 79 SPGLDRP 85 (152)
T ss_pred CCCCCCc
Confidence 9998743
No 88
>COG4988 CydD ABC-type transport system involved in cytochrome bd biosynthesis, ATPase and permease components [Energy production and conversion / Posttranslational modification, protein turnover, chaperones]
Probab=34.51 E-value=1e+02 Score=28.22 Aligned_cols=63 Identities=14% Similarity=0.172 Sum_probs=45.7
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEE---EEEe-------------cCCCcCHHHHHHHHH
Q 040226 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY---AEKV-------------NNRGLCAIAQAESLR 106 (137)
Q Consensus 44 ~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~---i~ev-------------~~P~l~A~liA~~ia 106 (137)
..++.++...+--.++|++|++...|-+.|...+.-....|.+| ..++ .+|++-|.-+.++|.
T Consensus 338 ~~l~~t~~~g~~talvG~SGaGKSTLl~lL~G~~~~~~G~I~vng~~l~~l~~~~~~k~i~~v~Q~p~lf~gTireNi~ 416 (559)
T COG4988 338 SDLNLTIKAGQLTALVGASGAGKSTLLNLLLGFLAPTQGEIRVNGIDLRDLSPEAWRKQISWVSQNPYLFAGTIRENIL 416 (559)
T ss_pred CCceeEecCCcEEEEECCCCCCHHHHHHHHhCcCCCCCceEEECCccccccCHHHHHhHeeeeCCCCccccccHHHHhh
Confidence 45666666666668999999999999999988775334456555 3333 378888888888874
No 89
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=34.41 E-value=32 Score=30.68 Aligned_cols=27 Identities=11% Similarity=0.405 Sum_probs=24.5
Q ss_pred EEEEEEecccceeeccCcccHHHHHHH
Q 040226 46 TEIIIRATRTQNVLGEKGRRIRELTSV 72 (137)
Q Consensus 46 i~I~I~~arPg~viG~~g~~i~~L~~~ 72 (137)
+++-.++..+|-+||++|..+++++..
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~ 71 (485)
T KOG2190|consen 45 YRLLCHVKEVGSIIGKKGDIVKKIRKE 71 (485)
T ss_pred EEEEeccccceeEEccCcHHHHHHhhc
Confidence 688999999999999999999998853
No 90
>KOG1676 consensus K-homology type RNA binding proteins [RNA processing and modification]
Probab=34.18 E-value=29 Score=31.77 Aligned_cols=27 Identities=19% Similarity=0.457 Sum_probs=21.9
Q ss_pred eEEEEEEecccceeeccCcccHHHHHH
Q 040226 45 RTEIIIRATRTQNVLGEKGRRIRELTS 71 (137)
Q Consensus 45 ~i~I~I~~arPg~viG~~g~~i~~L~~ 71 (137)
..+|.|=-..-|+|||++|+.|++|..
T Consensus 231 ~~~V~VPr~~VG~IIGkgGE~IKklq~ 257 (600)
T KOG1676|consen 231 TREVKVPRSKVGIIIGKGGEMIKKLQN 257 (600)
T ss_pred eeEEeccccceeeEEecCchHHHHHhh
Confidence 566666666778999999999998766
No 91
>TIGR00151 ispF 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase. Members of this protein family are 2C-methyl-D-erythritol 2,4-cyclodiphosphate synthase, the IspF protein of the deoxyxylulose (non-mevalonate) pathway of IPP biosynthesis. This protein occurs as an IspDF bifunctional fusion protein in about 20 percent of bacterial genomes.
Probab=34.14 E-value=1.3e+02 Score=22.94 Aligned_cols=41 Identities=22% Similarity=0.235 Sum_probs=32.4
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEE
Q 040226 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (137)
Q Consensus 44 ~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ 89 (137)
..+.++|-+.+|.+ +.-..++++.|.+.++....+|+|+.+
T Consensus 91 ~niD~tii~e~PKi-----~p~~~~m~~~la~~L~~~~~~V~iKat 131 (155)
T TIGR00151 91 GNVDITIIAQRPKL-----LPHIPAMRENIAELLGIPLDSVNVKAT 131 (155)
T ss_pred EEEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEEe
Confidence 35677888999966 567899999999999986667777655
No 92
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=33.91 E-value=1.3e+02 Score=19.11 Aligned_cols=57 Identities=12% Similarity=0.127 Sum_probs=41.6
Q ss_pred HhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE
Q 040226 26 TRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (137)
Q Consensus 26 ~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i 88 (137)
...+.++-|.+|.+.+.....++.+.... .+ .-+.+..+.+.|++.|+.. .+|.+.+
T Consensus 18 ~~~f~~~~I~kv~v~k~~~~w~f~l~~~~--~l---~~~~~~~~~~~l~~~F~~i-a~v~~~i 74 (76)
T PF14480_consen 18 NPLFEDAEIEKVTVHKKSRKWRFHLSSPH--IL---PFEVYQKFEEKLKKQFSHI-AKVELII 74 (76)
T ss_pred hhhhcccEEEEEEEEccCCEEEEEEEeCC--cC---CHHHHHHHHHHHHHHhCCc-CeEEEEE
Confidence 45667888999999999998888776644 33 2356789999999998642 3666543
No 93
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=33.74 E-value=1e+02 Score=18.90 Aligned_cols=29 Identities=24% Similarity=0.450 Sum_probs=23.8
Q ss_pred cHHHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 65 RIRELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 65 ~i~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
-.+.+.+.+.+.|+.+...|.|.+.|+..
T Consensus 20 L~~~it~a~~~~~~~p~~~v~V~i~ev~~ 48 (60)
T PRK02289 20 LAREVTEVVSRIAKAPKEAIHVFINDMPE 48 (60)
T ss_pred HHHHHHHHHHHHhCcCcceEEEEEEEeCh
Confidence 35778888888999878899999999864
No 94
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=32.82 E-value=92 Score=18.40 Aligned_cols=31 Identities=16% Similarity=0.291 Sum_probs=23.8
Q ss_pred cccHHHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 63 GRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 63 g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
.+-.+.|.+.+.+.++.....+.|.+.|+..
T Consensus 17 ~~l~~~i~~~l~~~~g~~~~~v~V~i~e~~~ 47 (58)
T cd00491 17 RELIERVTEAVSEILGAPEATIVVIIDEMPK 47 (58)
T ss_pred HHHHHHHHHHHHHHhCcCcccEEEEEEEeCc
Confidence 3345778888888898877889998888753
No 95
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=31.91 E-value=1.4e+02 Score=22.81 Aligned_cols=41 Identities=22% Similarity=0.330 Sum_probs=31.9
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEE
Q 040226 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (137)
Q Consensus 44 ~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ 89 (137)
..+.++|-+.+|.+ +.-.+++++.|.+.++....+|+|+.+
T Consensus 94 ~niD~tii~e~PKi-----~p~~~~m~~~la~~L~i~~~~V~iKat 134 (159)
T PRK00084 94 GNVDITIIAQRPKM-----APHIEEMRANIAEDLGIPLDDVNVKAT 134 (159)
T ss_pred EEEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEEe
Confidence 35667888999966 567899999999999986666776554
No 96
>PF02542 YgbB: YgbB family; InterPro: IPR003526 MECDP (2-C-methyl-D-erythritol 2,4-cyclodiphosphate) synthetase, an enzyme in the non-mevalonate pathway of isoprenoid synthesis, isoprenoids being essential in all organisms. Isoprenoids can also be synthesized through the mevalonate pathway. The non-mevolante route is used by many bacteria and human pathogens, including Mycobacterium tuberculosis and Plasmodium falciparum. This route appears to involve seven enzymes. MECDP synthetase catalyses the intramolecular attack by a phosphate group on a diphosphate, with cytidine monophosphate (CMP) acting as the leaving group to give the cyclic diphosphate product MEDCP. The enzyme is a trimer with three active sites shared between adjacent copies of the protein. The enzyme also has two metal binding sites, the metals playing key roles in catalysis[]. A number of proteins from eukaryotes and prokaryotes share this common N-terminal signature and appear to be involved in terpenoid biosynthesis. The YgbB protein is a putative enzyme of this type [].; GO: 0008685 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase activity, 0016114 terpenoid biosynthetic process; PDB: 3T80_B 3GHZ_A 2PMP_A 3F6M_A 3FPI_A 3RE3_A 1T0A_C 1W57_A 1W55_A 3B6N_A ....
Probab=31.85 E-value=1.3e+02 Score=22.95 Aligned_cols=40 Identities=20% Similarity=0.244 Sum_probs=31.5
Q ss_pred eEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEE
Q 040226 45 RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (137)
Q Consensus 45 ~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ 89 (137)
.+.++|-+.+|.+ +.-..++++.|.+.++....+|+|..+
T Consensus 93 niD~tii~e~PKi-----~p~~~~m~~~la~~L~~~~~~V~iKat 132 (157)
T PF02542_consen 93 NIDITIIAERPKI-----SPYRPAMRENLAKLLGIPPDRVNIKAT 132 (157)
T ss_dssp EEEEEEESSSSTT-----GGGHHHHHHHHHHHHTS-GGGEEEEEE
T ss_pred EEEEEEEcCCCcc-----HHHHHHHHHHHHHHhCCCcceEEEEEe
Confidence 5677889999966 567899999999999986667776554
No 97
>PF14955 MRP-S24: Mitochondrial ribosome subunit S24
Probab=31.62 E-value=37 Score=25.41 Aligned_cols=39 Identities=8% Similarity=-0.143 Sum_probs=30.8
Q ss_pred hhHHHHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEe
Q 040226 14 DGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRA 52 (137)
Q Consensus 14 ~~~~~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~ 52 (137)
.-..|.+||.|+.--|...--+.|-|+|..+.|.|.--.
T Consensus 52 ~~~eD~fIRkFi~GTf~~~l~sEiiIKRr~N~I~Ia~~~ 90 (136)
T PF14955_consen 52 RTVEDVFIRKFIRGTFPGLLASEIIIKRRHNVIRIAGIV 90 (136)
T ss_pred hhhHHHHHHHhccCCCchhcchhhhhhhcccEEEEeEee
Confidence 456788999998877777666899999999988875433
No 98
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=31.42 E-value=75 Score=29.13 Aligned_cols=55 Identities=18% Similarity=0.301 Sum_probs=41.1
Q ss_pred HHHHHHHHhhhc-cCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 040226 19 AELNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (137)
Q Consensus 19 ~~Ire~l~k~~~-~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~ 78 (137)
.++++-+...++ ++.|.+|+. .+-++.+|+-.|..+.- +|.-+++|-+.|+|+.-
T Consensus 8 ~ei~~~i~~~~p~~~~It~vef----EGPelvvY~k~P~~~~~-~~dlik~lAk~lrKRI~ 63 (637)
T COG1782 8 EEIRNKINEILPSDVKITDVEF----EGPELVVYTKNPELFAK-DGDLIKDLAKDLRKRII 63 (637)
T ss_pred HHHHHHHHHhCCCcCceEEEEe----cCCeEEEEecCHHHhcc-chhHHHHHHHHHhhceE
Confidence 356677777777 577777776 46788999999988765 45778888888888654
No 99
>TIGR03367 queuosine_QueD queuosine biosynthesis protein QueD. Members of this protein family, closely related to eukaryotic 6-pyruvoyl tetrahydrobiopterin synthase enzymes, are the QueD protein of queuosine biosynthesis. Queuosine is a hypermodified base in the wobble position of tRNAs for Tyr, His, Asp, and Asn in many species. This modification, although widespread, appears not to be important for viability. The queuosine precursor made by this enzyme may be converted instead to archeaosine as in some Archaea.
Probab=31.02 E-value=1.1e+02 Score=20.61 Aligned_cols=43 Identities=14% Similarity=0.098 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhCCCCCeEEEEEEEecCCCcCHHHHHHHHHHHHHc
Q 040226 67 RELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLG 111 (137)
Q Consensus 67 ~~L~~~L~k~~~~~~~~i~I~i~ev~~P~l~A~liA~~ia~qLe~ 111 (137)
..|+..++.....-+.+.-..+.+..+| .+..+|.+|..+|..
T Consensus 50 ~~lk~~~~~i~~~lDh~~Lne~~~~~~p--T~E~ia~~i~~~l~~ 92 (92)
T TIGR03367 50 SDLKAIVKEVVDRLDHALLNDVPGLENP--TAENLARWIYDRLKA 92 (92)
T ss_pred HHHHHHHHHHHHhCCCcEeeCCCCCCCC--CHHHHHHHHHHHHhC
Confidence 4444444443321133443233344455 889999999998863
No 100
>PRK03094 hypothetical protein; Provisional
Probab=30.63 E-value=1.4e+02 Score=20.30 Aligned_cols=37 Identities=22% Similarity=0.406 Sum_probs=25.8
Q ss_pred HHhhhccCCccceEEEEc--CCeEEEEEEecccceeecc
Q 040226 25 LTRELAEDGYSGVEVRVT--PVRTEIIIRATRTQNVLGE 61 (137)
Q Consensus 25 l~k~~~~agis~IeI~R~--~~~i~I~I~~arPg~viG~ 61 (137)
+...|...||.=+.+.-. ...+.-.++++.+.-+.|-
T Consensus 13 i~~~L~~~GYeVv~l~~~~~~~~~Da~VitG~d~n~mgi 51 (80)
T PRK03094 13 VQQALKQKGYEVVQLRSEQDAQGCDCCVVTGQDSNVMGI 51 (80)
T ss_pred HHHHHHHCCCEEEecCcccccCCcCEEEEeCCCcceecc
Confidence 345566778988878432 3567778888888877774
No 101
>PRK14646 hypothetical protein; Provisional
Probab=30.08 E-value=2.4e+02 Score=21.12 Aligned_cols=77 Identities=12% Similarity=0.105 Sum_probs=46.4
Q ss_pred HHHHHHHHHhhhccCCccceEEE--EcCCeEEEEEEecccceeeccCcccH---HHHHHHHHHHhCCCCCeEEEEEEEec
Q 040226 18 FAELNEVLTRELAEDGYSGVEVR--VTPVRTEIIIRATRTQNVLGEKGRRI---RELTSVVQKRFKFPENSVELYAEKVN 92 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI~--R~~~~i~I~I~~arPg~viG~~g~~i---~~L~~~L~k~~~~~~~~i~I~i~ev~ 92 (137)
..+|.+.+...+.+.|+.=++++ +....-.+.||.-+|+ | +|-++ ..+...|...|...++==.=|..||+
T Consensus 6 ~~~i~~li~p~~~~~G~eLvdve~~~~~~~~~LrV~IDk~~---g-~gVtldDC~~vSr~is~~LD~~D~i~~~Y~LEVS 81 (155)
T PRK14646 6 KSKLEILLEKVANEFDLKICSLNIQTNQNPIVIKIIIKKTN---G-DDISLDDCALFNTPASEEIENSNLLNCSYVLEIS 81 (155)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEEEEeCCCCeEEEEEEECCC---C-CCccHHHHHHHHHHHHHHhCcCCCCCCCeEEEEc
Confidence 45778888888888898766665 4444444555555662 0 13334 45566666666432221133568999
Q ss_pred CCCcCH
Q 040226 93 NRGLCA 98 (137)
Q Consensus 93 ~P~l~A 98 (137)
.|+++=
T Consensus 82 SPGldR 87 (155)
T PRK14646 82 SQGVSD 87 (155)
T ss_pred CCCCCC
Confidence 999873
No 102
>PRK01271 4-oxalocrotonate tautomerase; Provisional
Probab=29.20 E-value=1e+02 Score=20.41 Aligned_cols=29 Identities=10% Similarity=0.310 Sum_probs=24.9
Q ss_pred cHHHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 65 RIRELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 65 ~i~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
-.+++.+.+.+.+|.....+.|.|.|+..
T Consensus 21 La~~iT~a~~~~lg~~~e~v~V~I~ev~~ 49 (76)
T PRK01271 21 LAADITDVIIRHLNSKDSSISIALQQIQP 49 (76)
T ss_pred HHHHHHHHHHHHhCcCcceEEEEEEEcCH
Confidence 35888999999999988899999999874
No 103
>COG0165 ArgH Argininosuccinate lyase [Amino acid transport and metabolism]
Probab=29.19 E-value=66 Score=28.64 Aligned_cols=35 Identities=17% Similarity=0.104 Sum_probs=25.9
Q ss_pred eEEEEEEEe----cCCCcCHHHHHHHHHHHHHcChHHHHHHH
Q 040226 83 SVELYAEKV----NNRGLCAIAQAESLRYKLLGGLAVRRYIL 120 (137)
Q Consensus 83 ~i~I~i~ev----~~P~l~A~liA~~ia~qLe~Rv~fRRa~k 120 (137)
.+.++.+.. ..=+..|.-+|++++. +++|||-|=.
T Consensus 349 ~l~vn~e~~~~a~~~gfs~aTdlAd~lv~---kGvPFReAh~ 387 (459)
T COG0165 349 GLTVNKERMREAAEAGFSTATDLADYLVR---KGVPFREAHE 387 (459)
T ss_pred cCeeCHHHHHHHhhcccchHHHHHHHHHH---cCCCHHHHHH
Confidence 455544433 2335778999999998 8999999987
No 104
>cd05213 NAD_bind_Glutamyl_tRNA_reduct NADP-binding domain of glutamyl-tRNA reductase. Glutamyl-tRNA reductase catalyzes the conversion of glutamyl-tRNA to glutamate-1-semialdehyde, initiating the synthesis of tetrapyrrole. Whereas tRNAs are generally associated with peptide bond formation in protein translation, here the tRNA activates glutamate in the initiation of tetrapyrrole biosynthesis in archaea, plants and many bacteria. In the first step, activated glutamate is reduced to glutamate-1-semi-aldehyde via the NADPH dependent glutamyl-tRNA reductase. Glutamyl-tRNA reductase forms a V-shaped dimer. Each monomer has 3 domains: an N-terminal catalytic domain, a classic nucleotide binding domain, and a C-terminal dimerization domain. Although the representative structure 1GPJ lacks a bound NADPH, a theoretical binding pocket has been described. (PMID 11172694). Amino acid dehydrogenase (DH)-like NAD(P)-binding domains are members of the Rossmann fold superfamily and include glutamate,
Probab=29.05 E-value=2.7e+02 Score=22.75 Aligned_cols=52 Identities=25% Similarity=0.302 Sum_probs=36.6
Q ss_pred HHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 040226 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (137)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~ 78 (137)
.+.+++.......++..+-|--|.++++|+.++..|. ...+.+.+.|...++
T Consensus 25 ~~~~~l~~l~~~~~~~e~viLsTCNR~EiY~~~~~~~-------~~~~~~~~~l~~~~~ 76 (311)
T cd05213 25 ELKEALRRLLEKPGISEAVLLSTCNRVELYLVGDNFH-------KLADELEELLAELLN 76 (311)
T ss_pred HHHHHHHHHhcCCCCceEEEEecCCeEEEEEEeCCcc-------hhHHHHHHHHHHhcC
Confidence 4556666666667899999999999999998875542 223556666665554
No 105
>PRK14633 hypothetical protein; Provisional
Probab=28.63 E-value=2.5e+02 Score=20.87 Aligned_cols=76 Identities=17% Similarity=0.221 Sum_probs=45.6
Q ss_pred HHHHHHHHHhhhccCCccceEEEEcC-CeEEEEEEecccceeeccCcccH---HHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 18 FAELNEVLTRELAEDGYSGVEVRVTP-VRTEIIIRATRTQNVLGEKGRRI---RELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI~R~~-~~i~I~I~~arPg~viG~~g~~i---~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
...+.+.+..-+.+.|+.=++++-.. ....+.|+.-+|+ |-.+ ..+...|...+...++--.=+..||+.
T Consensus 3 ~~~i~~lv~p~~~~~G~eL~dve~~~~~~~~lrV~ID~~~------Gv~lddC~~vSr~i~~~LD~~d~i~~~Y~LEVSS 76 (150)
T PRK14633 3 LDDLYEIVEPITADLGYILWGIEVVGSGKLTIRIFIDHEN------GVSVDDCQIVSKEISAVFDVEDPVSGKYILEVSS 76 (150)
T ss_pred HHHHHHHHHHHHHHCCCEEEEEEEEeCCCcEEEEEEeCCC------CCCHHHHHHHHHHHHHHhccCcCCCCCeEEEEeC
Confidence 34677888888888898666665432 1224444545553 4444 556666766665332212335689999
Q ss_pred CCcCHH
Q 040226 94 RGLCAI 99 (137)
Q Consensus 94 P~l~A~ 99 (137)
|+++=.
T Consensus 77 PGldRp 82 (150)
T PRK14633 77 PGMNRQ 82 (150)
T ss_pred CCCCCC
Confidence 998843
No 106
>PRK14638 hypothetical protein; Provisional
Probab=28.62 E-value=2.5e+02 Score=20.89 Aligned_cols=79 Identities=13% Similarity=0.104 Sum_probs=45.6
Q ss_pred HHHHHHHHHhhhccCCccceEEE--EcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCC
Q 040226 18 FAELNEVLTRELAEDGYSGVEVR--VTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRG 95 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI~--R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~ 95 (137)
...+.+.+..-+...|+.=++|+ +....-.+.|+.-+|+--+ .=.....+...|...|...++--.=+..||+.|+
T Consensus 7 ~~~i~~~~~~i~~~~G~elvdve~~~~~~~~~lrV~ID~~~G~v--~lddC~~vSr~is~~LD~~d~i~~~Y~LEVSSPG 84 (150)
T PRK14638 7 LEKVRKEAERIAEEQGLEIFDVQYRRESRGWVLRIIIDNPVGYV--SVRDCELFSREIERFLDREDLIEHSYTLEVSSPG 84 (150)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEEEEecCCCcEEEEEEECCCCCc--CHHHHHHHHHHHHHHhccccccCCceEEEEeCCC
Confidence 34677777778888888666665 4444444455555552100 1123356667777766532221123568999999
Q ss_pred cCH
Q 040226 96 LCA 98 (137)
Q Consensus 96 l~A 98 (137)
++=
T Consensus 85 ldR 87 (150)
T PRK14638 85 LDR 87 (150)
T ss_pred CCC
Confidence 884
No 107
>PF01545 Cation_efflux: Cation efflux family; InterPro: IPR002524 Members of this family are integral membrane proteins, that are found to increase tolerance to divalent metal ions such as cadmium, zinc, and cobalt. These proteins are considered to be efflux pumps that remove these ions from cells [, ], however others are implicated in ion uptake []. The family has six predicted transmembrane domains. Members of the family are variable in length because of variably sized inserts, often containing low-complexity sequence.; GO: 0008324 cation transmembrane transporter activity, 0006812 cation transport, 0055085 transmembrane transport, 0016021 integral to membrane; PDB: 3BYP_B 3BYR_A 3H90_B 2QFI_B 2ZZT_A.
Probab=27.49 E-value=3e+02 Score=21.49 Aligned_cols=76 Identities=9% Similarity=0.079 Sum_probs=43.8
Q ss_pred hhHHHHHHHHHHHhhhccCCccceEEEEcCC-eEEEEEEeccccee-eccCcccHHHHHHHHHHHhCCCCCeEEEEEEE
Q 040226 14 DGVFFAELNEVLTRELAEDGYSGVEVRVTPV-RTEIIIRATRTQNV-LGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (137)
Q Consensus 14 ~~~~~~~Ire~l~k~~~~agis~IeI~R~~~-~i~I~I~~arPg~v-iG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~e 90 (137)
+.....++++.+.+.-.-..+.++.+.+... ...+.+|...|+-. ++..-+..+++++.+++.++. -..+.|.+++
T Consensus 203 ~~~~~~~i~~~i~~~~~v~~v~~~~~~~~g~~~~~v~i~v~v~~~~~v~~~~~i~~~i~~~l~~~~~~-i~~v~I~~~p 280 (284)
T PF01545_consen 203 DPELVEKIRRIIESVPGVIEVHDLRVWQVGRNKYVVEIHVQVDPDMSVEEAHEIRERIEKRLREKFPG-IYDVTIHIEP 280 (284)
T ss_dssp HHHHHHHHHHHHHHTSS-SEEEEEEEEEETT-EEEEEEEEEETTTSBHHHHHHHHHHHHHHHHHHSTT-CEEEEEEEEE
T ss_pred cccchhHHHHhhccCCceEeccceEEEEecCCcEEEEEEEEeCCCCCHHHHHHHHHHHHHHHHHhCCC-cEEEEEEEEe
Confidence 3344567777776632334466677777766 88888888766554 222222346777777777742 1234454443
No 108
>PRK14636 hypothetical protein; Provisional
Probab=27.35 E-value=2.9e+02 Score=21.20 Aligned_cols=78 Identities=18% Similarity=0.176 Sum_probs=46.7
Q ss_pred HHHHHHHHHhhhccCCccceEEEEc--CCeEEEEEEecccceeeccCccc---HHHHHHHHHHHhCCCCCeEEEEEEEec
Q 040226 18 FAELNEVLTRELAEDGYSGVEVRVT--PVRTEIIIRATRTQNVLGEKGRR---IRELTSVVQKRFKFPENSVELYAEKVN 92 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI~R~--~~~i~I~I~~arPg~viG~~g~~---i~~L~~~L~k~~~~~~~~i~I~i~ev~ 92 (137)
...|.+.+...+...|+.=++++-. ...-.+.|+.-+|+ .+|-. ...+...|...|...++-=.=|..||+
T Consensus 4 ~~~i~~lvep~~~~~GleLvdve~~~~~~~~~lrV~ID~~~----~ggV~lDDC~~vSr~Is~~LD~~d~i~~~Y~LEVS 79 (176)
T PRK14636 4 IAALTALIEPEAKALGLDLVRVAMFGGKSDPTLQIMAERPD----TRQLVIEDCAALSRRLSDVFDELDPIEDAYRLEVS 79 (176)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEEEEcCCCCeEEEEEEECCC----CCCcCHHHHHHHHHHHHHHhccCcCCCCCeEEEEe
Confidence 3567788888888888766555543 33444455555662 12233 466777777777533221123568999
Q ss_pred CCCcCHH
Q 040226 93 NRGLCAI 99 (137)
Q Consensus 93 ~P~l~A~ 99 (137)
.|+++=.
T Consensus 80 SPGldRp 86 (176)
T PRK14636 80 SPGIDRP 86 (176)
T ss_pred CCCCCCC
Confidence 9998843
No 109
>PRK00745 4-oxalocrotonate tautomerase; Provisional
Probab=27.34 E-value=1.2e+02 Score=18.30 Aligned_cols=28 Identities=25% Similarity=0.450 Sum_probs=22.8
Q ss_pred HHHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 66 IRELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 66 i~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
.+.+.+.+.+.|+.....+.|.+.|+..
T Consensus 21 ~~~it~~l~~~~~~p~~~v~V~i~e~~~ 48 (62)
T PRK00745 21 VEEITRVTVETLGCPPESVDIIITDVKR 48 (62)
T ss_pred HHHHHHHHHHHcCCChhHEEEEEEEcCh
Confidence 4778888999999877888888888753
No 110
>COG1461 Predicted kinase related to dihydroxyacetone kinase [General function prediction only]
Probab=26.74 E-value=67 Score=29.20 Aligned_cols=56 Identities=20% Similarity=0.211 Sum_probs=35.8
Q ss_pred HHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeeccC---cc----cHHHHHHHHHHHhC
Q 040226 18 FAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEK---GR----RIRELTSVVQKRFK 78 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG~~---g~----~i~~L~~~L~k~~~ 78 (137)
.-++|++|.+. |=| +-|-.+.+.++|.|||..||.++-.. |. .++..+..-....+
T Consensus 251 ~~~fr~~L~~~----GDS-lvva~d~~~vKVHiHT~~Pg~vL~~~~~yG~l~kiKIenM~~Q~~~~~~ 313 (542)
T COG1461 251 EDEFREKLSKL----GDS-LVVANDEDIVKVHIHTNDPGLVLELAQKYGELSKIKIENMREQHEEVLE 313 (542)
T ss_pred HHHHHHHHHhc----CCe-EEEEecCCceEEEEecCCHHHHHHHHHHhCceEEEehhhhhHHHhhhcc
Confidence 44566665532 222 77777888899999999999987543 22 34555555554443
No 111
>COG0053 MMT1 Predicted Co/Zn/Cd cation transporters [Inorganic ion transport and metabolism]
Probab=26.73 E-value=2.8e+02 Score=22.86 Aligned_cols=61 Identities=16% Similarity=0.201 Sum_probs=40.8
Q ss_pred ccceEEEEcCCeEEEEEEecccceeeccCcccH-HHHHHHHHHHhCCCCCeEEEEEEEecCCC
Q 040226 34 YSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRI-RELTSVVQKRFKFPENSVELYAEKVNNRG 95 (137)
Q Consensus 34 is~IeI~R~~~~i~I~I~~arPg~viG~~g~~i-~~L~~~L~k~~~~~~~~i~I~i~ev~~P~ 95 (137)
+-++..++.+..+.+.+|..-|+-+--.+...+ +++.+.|++.++. ...+.|.+++...++
T Consensus 233 v~~lr~R~~G~~~~id~~i~v~~~ls~~eah~I~~~ie~~i~~~~~~-~~~v~IhveP~~~~~ 294 (304)
T COG0053 233 VHDLRTRKSGSRIFIDVHIEVDPDLSLEEAHEIADEVEKRIKKEFPK-VADVTIHVEPLGEKE 294 (304)
T ss_pred eecceeeeeCCeEEEEEEEEECCCCChHHHHHHHHHHHHHHHHhcCC-CceEEEEecCCcccc
Confidence 444556666899999999988866544444443 7788888877762 256777777665544
No 112
>PF02563 Poly_export: Polysaccharide biosynthesis/export protein; InterPro: IPR003715 The extracellular polysaccharide colanic acid (CA) is produced by species of the family Enterobacteriaceae. In Escherichia coli (strain K12) the CA cluster comprises 19 genes. The wzx gene encodes a protein with multiple transmembrane segments that may function in export of the CA repeat unit from the cytoplasm into the periplasm in a process analogous to O-unit export. The CA gene clusters may be involved in the export of polysaccharide from the cell [].; GO: 0015159 polysaccharide transmembrane transporter activity, 0015774 polysaccharide transport, 0016020 membrane; PDB: 2W8I_E 2W8H_E 2J58_D.
Probab=26.67 E-value=1.3e+02 Score=19.56 Aligned_cols=28 Identities=14% Similarity=0.253 Sum_probs=17.0
Q ss_pred CcccHHHHHHHHHHHhCCC--CCeEEEEEE
Q 040226 62 KGRRIRELTSVVQKRFKFP--ENSVELYAE 89 (137)
Q Consensus 62 ~g~~i~~L~~~L~k~~~~~--~~~i~I~i~ 89 (137)
.|..+.++++.|++.+... ++.+.+.+.
T Consensus 52 ~G~T~~e~~~~I~~~l~~~~~~p~V~V~v~ 81 (82)
T PF02563_consen 52 AGLTLEEAEEEIKQRLQKYYRDPQVSVTVA 81 (82)
T ss_dssp TT--HHHHHHHHHHHHTTTSSS--EEEEEE
T ss_pred CCCCHHHHHHHHHHHHHHHhcCCeEEEEEe
Confidence 4778899999888887532 566666554
No 113
>KOG2190 consensus PolyC-binding proteins alphaCP-1 and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=24.69 E-value=66 Score=28.72 Aligned_cols=30 Identities=17% Similarity=0.458 Sum_probs=24.6
Q ss_pred CCeEEEEEEecccceeeccCcccHHHHHHH
Q 040226 43 PVRTEIIIRATRTQNVLGEKGRRIRELTSV 72 (137)
Q Consensus 43 ~~~i~I~I~~arPg~viG~~g~~i~~L~~~ 72 (137)
+..+++.+-...-|-+||++|..|+++++.
T Consensus 137 ~v~~RLlVp~sq~GslIGK~G~~Ik~Ire~ 166 (485)
T KOG2190|consen 137 EVTCRLLVPSSQVGSLIGKGGSLIKEIREE 166 (485)
T ss_pred ceEEEEEechhheeeeeccCcHHHHHHHHh
Confidence 345777777777788999999999999886
No 114
>TIGR03131 malonate_mdcH malonate decarboxylase, epsilon subunit. Members of this protein family are the epsilon subunit of malonate decarboxylase. This subunit has malonyl-CoA/dephospho-CoA acyltransferase activity. Malonate decarboxylase may be a soluble enzyme, or linked to membrane subunits and active as a sodium pump. The epsilon subunit is closely related to the malonyl CoA-acyl carrier protein (ACP) transacylase family described by TIGR00128, but acts on an ACP subunit of malonate decarboxylase that has an unusual coenzyme A derivative as its prothetic group.
Probab=24.17 E-value=2.9e+02 Score=21.92 Aligned_cols=42 Identities=5% Similarity=-0.103 Sum_probs=30.4
Q ss_pred CCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHHHH
Q 040226 81 ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILII 122 (137)
Q Consensus 81 ~~~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~kai 122 (137)
.+++-+.-.--..+..++..+++++..||-+-+.|.++++.+
T Consensus 210 ~~~ip~~S~~~g~~~~~~~~~~~~~~~~l~~pV~~~~~i~~l 251 (295)
T TIGR03131 210 APRLPYLSGIDARLVRDAAQIRDDLARQIATPVDWHDCMQAA 251 (295)
T ss_pred CCCceEEECCCCeecCCHHHHHHHHHHHhcCCCcHHHHHHHH
Confidence 345554333334455678888999999999999999998843
No 115
>PRK14634 hypothetical protein; Provisional
Probab=24.04 E-value=3.1e+02 Score=20.47 Aligned_cols=78 Identities=9% Similarity=0.204 Sum_probs=45.4
Q ss_pred HHHHHHHHHhhhccCCccceEE--EEcCCeEEEEEEecccceeeccCcccH---HHHHHHHHHHhCCCCCeEEEEEEEec
Q 040226 18 FAELNEVLTRELAEDGYSGVEV--RVTPVRTEIIIRATRTQNVLGEKGRRI---RELTSVVQKRFKFPENSVELYAEKVN 92 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI--~R~~~~i~I~I~~arPg~viG~~g~~i---~~L~~~L~k~~~~~~~~i~I~i~ev~ 92 (137)
...+.+.+..-+...|+.=+++ .+....-.+.|+.-+|+- .+-.+ ..+...|...|...++--.=+..||+
T Consensus 6 ~~~i~~l~~~~~~~~G~elvdve~~~~~~~~~lrV~ID~~~g----~~v~lddC~~vSr~is~~LD~~d~i~~~Y~LEVS 81 (155)
T PRK14634 6 LPDLETLASATAADKGFELCGIQVLTHLQPMTLQVQIRRSSG----SDVSLDDCAGFSGPMGEALEASQLLTEAYVLEIS 81 (155)
T ss_pred HHHHHHHHHHHHHHcCCEEEEEEEEeCCCCcEEEEEEECCCC----CcccHHHHHHHHHHHHHHhcccccCCCCeEEEEe
Confidence 3467788887778888765444 454444444555555521 01333 55667777766532221123568999
Q ss_pred CCCcCHH
Q 040226 93 NRGLCAI 99 (137)
Q Consensus 93 ~P~l~A~ 99 (137)
.|+++-.
T Consensus 82 SPGldRp 88 (155)
T PRK14634 82 SPGIGDQ 88 (155)
T ss_pred CCCCCCc
Confidence 9998853
No 116
>KOG1316 consensus Argininosuccinate lyase [Amino acid transport and metabolism]
Probab=23.56 E-value=74 Score=27.83 Aligned_cols=35 Identities=17% Similarity=0.124 Sum_probs=22.5
Q ss_pred eEEEEEEEe---cCCCcCHHHHHHHHHHHHHcChHHHHHHH
Q 040226 83 SVELYAEKV---NNRGLCAIAQAESLRYKLLGGLAVRRYIL 120 (137)
Q Consensus 83 ~i~I~i~ev---~~P~l~A~liA~~ia~qLe~Rv~fRRa~k 120 (137)
.+.||-+.+ -.|+..|.-+|++++ .+++|||.+-.
T Consensus 352 tltvn~e~m~~aLt~dmlATdlA~YLV---rKGvPFRqtHh 389 (464)
T KOG1316|consen 352 TLTVNQENMEKALTPDMLATDLAYYLV---RKGVPFRQTHH 389 (464)
T ss_pred heeECHHHHhhccCchhhHhHHHHHHH---HcCCCchhhhh
Confidence 345543333 346666666666665 47999999877
No 117
>PF08731 AFT: Transcription factor AFT; InterPro: IPR014842 AFT (activator of iron transcription) is an iron regulated transcriptional activator that regulates the expression of genes involved in iron homeostasis. This entry includes the paralogous pair of transcription factors AFT1 and AFT2.
Probab=23.48 E-value=1.7e+02 Score=21.09 Aligned_cols=33 Identities=12% Similarity=0.280 Sum_probs=24.2
Q ss_pred HHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEe
Q 040226 18 FAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRA 52 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~ 52 (137)
+..|..||.+.+...||. |-|+|. |...|+-.+
T Consensus 4 k~~ikpwlq~~~~~~Gi~-iVIerS-d~~ki~FkC 36 (111)
T PF08731_consen 4 KDEIKPWLQKIFYPQGIG-IVIERS-DKKKIVFKC 36 (111)
T ss_pred hHHHHHHHHHHhhhcCce-EEEEec-CCceEEEEE
Confidence 457889999988899987 899994 444554343
No 118
>PRK14632 hypothetical protein; Provisional
Probab=23.14 E-value=3.4e+02 Score=20.64 Aligned_cols=77 Identities=18% Similarity=0.152 Sum_probs=46.1
Q ss_pred HHHHHHHHHHhhhccCCccceEEEEcC-CeEEEEEEecccceeeccCcccH---HHHHHHHHHHhCCCCCeEEEEEEEec
Q 040226 17 FFAELNEVLTRELAEDGYSGVEVRVTP-VRTEIIIRATRTQNVLGEKGRRI---RELTSVVQKRFKFPENSVELYAEKVN 92 (137)
Q Consensus 17 ~~~~Ire~l~k~~~~agis~IeI~R~~-~~i~I~I~~arPg~viG~~g~~i---~~L~~~L~k~~~~~~~~i~I~i~ev~ 92 (137)
....|.+.+..-+...|+.=++|+... ....+.|+.-+|+ |-.+ ..+...|...|...+.-=.=|..||+
T Consensus 6 ~~~~i~~li~pv~~~~G~eLvdve~~~~~~~~lrV~ID~~~------GV~ldDC~~vSr~is~~LD~~d~i~~~Y~LEVS 79 (172)
T PRK14632 6 LDATIADMAGPFLASLGLELWGIELSYGGRTVVRLFVDGPE------GVTIDQCAEVSRHVGLALEVEDVISSAYVLEVS 79 (172)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEEEEeCCCcEEEEEEECCC------CCCHHHHHHHHHHHHHHhcccccCCCCeEEEEe
Confidence 345788888888888898776665542 2233444444443 3444 55666676666432211123568999
Q ss_pred CCCcCHH
Q 040226 93 NRGLCAI 99 (137)
Q Consensus 93 ~P~l~A~ 99 (137)
.|+++=.
T Consensus 80 SPGldRp 86 (172)
T PRK14632 80 SPGLERP 86 (172)
T ss_pred CCCCCCc
Confidence 9998843
No 119
>PRK04163 exosome complex RNA-binding protein Rrp4; Provisional
Probab=22.72 E-value=1.4e+02 Score=23.68 Aligned_cols=64 Identities=16% Similarity=0.068 Sum_probs=43.9
Q ss_pred eEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEE---EEecCCCcCHHHHHHHHHHHHHcChHH
Q 040226 45 RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA---EKVNNRGLCAIAQAESLRYKLLGGLAV 115 (137)
Q Consensus 45 ~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i---~ev~~P~l~A~liA~~ia~qLe~Rv~f 115 (137)
++.+.|-...-+.+||++|..++.|.+ .++. +|.|-. .-|..|+..+...|...-+.+|+..+-
T Consensus 146 G~~~~V~~~~i~~lig~~g~~i~~l~~----~~~~---~I~ig~NG~VwI~~~~~~~~~~a~~~I~~~e~~~~~ 212 (235)
T PRK04163 146 GTIVEIKPVKVPRVIGKKGSMINMLKE----ETGC---DIIVGQNGRIWIKGPDEEDEEIAIEAIKKIEREAHT 212 (235)
T ss_pred CEEEEECHHHHHhhcCCCChhHhhhhh----hhCc---EEEEcCCcEEEEeeCCHHHHHHHHHHHHHHHhhhhc
Confidence 455555555555677888877777665 3442 333322 457889999999999999999988774
No 120
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=22.68 E-value=97 Score=25.77 Aligned_cols=38 Identities=21% Similarity=0.136 Sum_probs=27.3
Q ss_pred HHHHHHHHHhhhccCCccceEEEEcCCeEEEEEEecccceeec
Q 040226 18 FAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLG 60 (137)
Q Consensus 18 ~~~Ire~l~k~~~~agis~IeI~R~~~~i~I~I~~arPg~viG 60 (137)
...+|++|... |=| +-+--+.+.++|.|||..||.++.
T Consensus 20 ~~~lr~~L~~~----GdS-lvVv~~~~~~kVHvHT~~Pg~vle 57 (313)
T PF13684_consen 20 AEELRARLEEL----GDS-LVVVGDDDLVKVHVHTNDPGAVLE 57 (313)
T ss_pred HHHHHHHHHhc----CCE-EEEEecCCeEEEEEeeCCHHHHHH
Confidence 44566666533 322 555577889999999999999885
No 121
>PRK13434 F0F1 ATP synthase subunit delta; Provisional
Probab=22.41 E-value=2.1e+02 Score=21.56 Aligned_cols=43 Identities=16% Similarity=0.249 Sum_probs=30.1
Q ss_pred CCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEecCCC
Q 040226 43 PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRG 95 (137)
Q Consensus 43 ~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~P~ 95 (137)
...+.++++++.|= ..+.+++|++.|++.+| ++|. +....+|+
T Consensus 102 ~~~~~~~V~sA~~L-----s~~q~~~l~~~L~k~~g---~~v~--l~~~vDps 144 (184)
T PRK13434 102 KGRVRAQIVSYPSL-----EPAQVDKLGSILSEKFK---SEFI--LEVSEDKN 144 (184)
T ss_pred cCeEEEEEEEcCCC-----CHHHHHHHHHHHHHHHC---CEeE--EEeeeChH
Confidence 44677788998882 35678999999999997 4444 34444553
No 122
>KOG2193 consensus IGF-II mRNA-binding protein IMP, contains RRM and KH domains [RNA processing and modification; General function prediction only]
Probab=22.03 E-value=50 Score=29.54 Aligned_cols=26 Identities=27% Similarity=0.546 Sum_probs=18.7
Q ss_pred EEEEEEecccceeeccCcccHHHHHH
Q 040226 46 TEIIIRATRTQNVLGEKGRRIRELTS 71 (137)
Q Consensus 46 i~I~I~~arPg~viG~~g~~i~~L~~ 71 (137)
+.|.+-+.--|.|||++|+...+|+.
T Consensus 495 thirVPs~~aGRvIGKGGktVnELQn 520 (584)
T KOG2193|consen 495 THIRVPSSAAGRVIGKGGKTVNELQN 520 (584)
T ss_pred eeeeccchhhhhhhccccccHHHHhc
Confidence 44444455567899999999988765
No 123
>PF01361 Tautomerase: Tautomerase enzyme; InterPro: IPR004370 4-Oxalocrotonate tautomerase (4-OT) catalyzes the isomerisation of beta,gamma-unsaturated enones to their alpha,beta-isomers. The enzyme is part of a plasmid-encoded pathway, which enables bacteria harbouring the plasmid to use various aromatic hydrocarbons as their sole sources of carbon and energy. The enzyme is a barrel-shaped hexamer, which can be viewed as a trimer of dimers. The hexamer contains a hydrophobic core formed by three beta-sheets and surrounded by three pairs of alpha-helices. Each 4-OT monomer of 62 amino acids has a relatively simple beta-alpha-beta fold as described by the structure of the enzyme from Pseudomonas putida []. The monomer begins with a conserved proline at the start of a beta-strand, followed by an alpha-helix and a 310 helix preceding a second parallel beta-strand, and ends with a beta-hairpin near the C terminus. The dimer results from antiparallel interactions between the beta-sheets and alpha-helices of the two monomers, forming a four-stranded beta-sheet with antiparallel alpha-helices on one side, creating two active sites, one at each end of the beta-sheet. Three dimers further associate to form a hexamer by the interactions of the strands of the C-terminal beta-hairpin loops with the edges of the four-stranded beta-sheets of neighbouring dimers, creating a series of cross-links that stabilise the hexamer Pro-1 of the mature protein functions as the general base while Arg-39 and an ordered water molecule each provide a hydrogen bond to the C-2 oxygen of substrate. Arg-39 plays an additional role in the binding of the C-1 carboxylate group. Arg-11 participates both in substrate binding and in catalysis. It interacts with the C-6 carboxylate group, thereby holding the substrate in place and drawing electron density to the C-5 position. The hydrophobic nature of the active site, which lowers the pKa of Pro-1 and provides a favourable environment for catalysis, is largely maintained by Phe-50. Because several Arg residues located near the active site are not conserved among all members of this family and because of the presence of fairly distantly related paralogs in Campylobacter jejuni, the family is regarded as not necessarily uniform in function.; GO: 0016853 isomerase activity, 0006725 cellular aromatic compound metabolic process; PDB: 4OTA_H 4OTC_G 4OTB_J 2FM7_A 1BJP_B 1S0Y_K 3EJ9_E 3EJ7_K 3EJ3_I 3MB2_A ....
Probab=21.97 E-value=1.8e+02 Score=17.46 Aligned_cols=31 Identities=16% Similarity=0.250 Sum_probs=23.4
Q ss_pred cccHHHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 63 GRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 63 g~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
.+-++++.+.+.+.++.....+.|.+.|+..
T Consensus 17 ~~l~~~it~~~~~~lg~~~~~i~V~i~E~~~ 47 (60)
T PF01361_consen 17 RELAEAITDAVVEVLGIPPERISVVIEEVPP 47 (60)
T ss_dssp HHHHHHHHHHHHHHHTS-GGGEEEEEEEE-C
T ss_pred HHHHHHHHHHHHHHhCcCCCeEEEEEEEECh
Confidence 3346888888999999877789999999864
No 124
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=21.33 E-value=86 Score=27.15 Aligned_cols=29 Identities=17% Similarity=0.347 Sum_probs=23.6
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHH
Q 040226 44 VRTEIIIRATRTQNVLGEKGRRIRELTSV 72 (137)
Q Consensus 44 ~~i~I~I~~arPg~viG~~g~~i~~L~~~ 72 (137)
..++|-|-..--|.|||++|+.|.+|+++
T Consensus 39 y~ikvLips~AaGsIIGKGG~ti~~lqk~ 67 (402)
T KOG2191|consen 39 YFLKVLIPSYAAGSIIGKGGQTIVQLQKE 67 (402)
T ss_pred eEEEEEeecccccceeccchHHHHHHHhc
Confidence 36777777778899999999999887664
No 125
>PF00698 Acyl_transf_1: Acyl transferase domain; InterPro: IPR014043 Enzymes like bacterial malonyl CoA-acly carrier protein transacylase (2.3.1.39 from EC) and eukaryotic fatty acid synthase (2.3.1.85 from EC) that are involved in fatty acid biosynthesis belong to this group. Also included are the polyketide synthases 6-methylsalicylic acid synthase (2.3.1 from EC), a multifunctional enzyme that involved in the biosynthesis of patulin and conidial green pigment synthase (2.3.1 from EC).; PDB: 3HHD_C 2JFD_D 2JFK_A 3G87_A 3IM9_A 2QO3_B 3IM8_A 3EZO_A 2QJ3_A 2QC3_A ....
Probab=20.56 E-value=1.7e+02 Score=23.61 Aligned_cols=42 Identities=12% Similarity=0.033 Sum_probs=33.4
Q ss_pred CCeEEEEEEEecCCCcCHHHHHHHHHHHHHcChHHHHHHHHH
Q 040226 81 ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRYILII 122 (137)
Q Consensus 81 ~~~i~I~i~ev~~P~l~A~liA~~ia~qLe~Rv~fRRa~kai 122 (137)
++++.+.-.---.|..++.+.+++.+.||-+-+.|..+++++
T Consensus 214 ~p~ip~~S~~~g~~~~~~~~~~~~~~~~l~~pV~f~~~v~~l 255 (318)
T PF00698_consen 214 PPKIPVYSNVTGRPYDDPELIAEYWARQLRSPVRFREAVEAL 255 (318)
T ss_dssp CCSSEEEETTTSSBEHSHHHHHHHHHHHHHSHEEHHHHHHHH
T ss_pred cccccceeecccccccccccchhHHHhccCCcCChHHHHHHH
Confidence 566776555455566778899999999999999999999855
No 126
>PRK02220 4-oxalocrotonate tautomerase; Provisional
Probab=20.43 E-value=2.1e+02 Score=17.12 Aligned_cols=30 Identities=13% Similarity=0.337 Sum_probs=23.4
Q ss_pred ccHHHHHHHHHHHhCCCCCeEEEEEEEecC
Q 040226 64 RRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (137)
Q Consensus 64 ~~i~~L~~~L~k~~~~~~~~i~I~i~ev~~ 93 (137)
+-++.|.+.+...++.+...+.+.+.|+..
T Consensus 19 ~l~~~it~~l~~~~~~p~~~v~V~i~e~~~ 48 (61)
T PRK02220 19 ALVKDVTAAVSKNTGAPAEHIHVIINEMSK 48 (61)
T ss_pred HHHHHHHHHHHHHhCcChhhEEEEEEEeCh
Confidence 345778888888999877788888888653
No 127
>PRK03557 zinc transporter ZitB; Provisional
Probab=20.39 E-value=4.8e+02 Score=21.32 Aligned_cols=55 Identities=5% Similarity=0.114 Sum_probs=31.6
Q ss_pred CccceEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeEEEEEEEe
Q 040226 33 GYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKV 91 (137)
Q Consensus 33 gis~IeI~R~~~~i~I~I~~arPg~viG~~g~~i~~L~~~L~k~~~~~~~~i~I~i~ev 91 (137)
++.++.+.+..+..-+.+|..-|+-. ..-+-.+++++.|++.++. ..+.|.++.-
T Consensus 238 ~vh~l~~~~~G~~~~v~~hv~v~~~~--~~~~i~~~i~~~l~~~~~i--~~vtIh~e~~ 292 (312)
T PRK03557 238 NVHHVHVWMVGEKPVMTLHVQVIPPH--DHDALLDRIQDYLMHHYQI--EHATIQMEYQ 292 (312)
T ss_pred eEEEEEEEEeCCeEEEEEEEEECCCC--CHHHHHHHHHHHHHHhCCC--CEEEEEeccC
Confidence 35567777777788888888765321 1111234555555555553 4577666643
Done!