Query 026316
Match_columns 240
No_of_seqs 137 out of 1141
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 06:27:15 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026316.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026316hhsearch_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 4.4E-69 9.4E-74 475.1 19.6 213 4-224 4-216 (220)
2 PRK04191 rps3p 30S ribosomal p 100.0 5.2E-63 1.1E-67 432.6 20.9 205 5-228 1-205 (207)
3 TIGR01008 rpsC_E_A ribosomal p 100.0 2.4E-62 5.2E-67 425.6 22.2 194 8-220 2-195 (195)
4 COG0092 RpsC Ribosomal protein 100.0 1.9E-62 4.2E-67 434.4 19.3 198 6-226 6-212 (233)
5 KOG3181 40S ribosomal protein 100.0 2.3E-62 5.1E-67 424.7 14.0 225 1-233 1-226 (244)
6 CHL00048 rps3 ribosomal protei 100.0 1.2E-54 2.5E-59 381.9 23.3 183 6-199 17-212 (214)
7 TIGR01009 rpsC_bact ribosomal 100.0 9.4E-55 2E-59 381.6 21.1 181 6-200 17-206 (211)
8 PRK00310 rpsC 30S ribosomal pr 100.0 3.7E-54 8E-59 382.6 22.7 180 6-199 17-205 (232)
9 PF00189 Ribosomal_S3_C: Ribos 99.9 3.9E-26 8.4E-31 174.2 10.2 82 104-196 1-85 (85)
10 cd02413 40S_S3_KH K homology R 99.8 2E-19 4.4E-24 137.0 10.9 80 15-94 1-80 (81)
11 cd02412 30S_S3_KH K homology R 99.8 5.1E-19 1.1E-23 140.8 9.8 87 6-94 16-109 (109)
12 cd02411 archeal_30S_S3_KH K ho 99.7 3.8E-17 8.3E-22 124.6 8.7 84 8-93 2-85 (85)
13 PF07650 KH_2: KH domain syndr 99.5 2.1E-13 4.7E-18 101.2 7.2 77 20-96 1-78 (78)
14 cd02409 KH-II KH-II (K homolo 98.7 1.2E-07 2.7E-12 66.4 7.8 65 22-88 1-67 (68)
15 smart00322 KH K homology RNA-b 97.2 0.00039 8.5E-09 47.5 3.7 67 44-110 3-69 (69)
16 cd02414 jag_KH jag_K homology 96.5 0.015 3.3E-07 43.3 7.5 56 23-78 2-58 (77)
17 PF13083 KH_4: KH domain; PDB: 95.9 0.01 2.2E-07 43.5 3.8 67 21-87 4-72 (73)
18 PRK01064 hypothetical protein; 94.2 0.79 1.7E-05 35.0 9.7 69 21-90 4-76 (78)
19 PRK08406 transcription elongat 94.1 0.15 3.2E-06 42.6 6.0 62 18-79 70-134 (140)
20 COG1847 Jag Predicted RNA-bind 93.9 0.54 1.2E-05 42.2 9.5 106 19-124 65-185 (208)
21 cd02134 NusA_KH NusA_K homolog 92.7 0.43 9.3E-06 34.1 5.8 53 22-74 2-55 (61)
22 cd02410 archeal_CPSF_KH The ar 92.5 1.3 2.8E-05 37.7 9.3 85 21-119 54-139 (145)
23 PRK02821 hypothetical protein; 92.1 2.1 4.5E-05 32.6 9.2 68 20-90 4-74 (77)
24 PRK00468 hypothetical protein; 90.1 4.3 9.2E-05 30.7 9.1 69 20-88 3-74 (75)
25 COG1837 Predicted RNA-binding 88.2 5.3 0.00012 30.5 8.5 68 21-88 4-74 (76)
26 TIGR00436 era GTP-binding prot 86.3 3.2 6.9E-05 37.1 7.5 65 21-88 188-267 (270)
27 PRK15494 era GTPase Era; Provi 85.3 3.7 8.1E-05 38.4 7.7 65 21-88 240-319 (339)
28 TIGR01952 nusA_arch NusA famil 84.6 1.6 3.4E-05 36.7 4.4 62 18-79 71-135 (141)
29 PRK00089 era GTPase Era; Revie 84.4 4.7 0.0001 36.1 7.7 65 21-88 195-272 (292)
30 COG1782 Predicted metal-depend 81.5 9.5 0.00021 38.9 9.0 91 22-126 78-170 (637)
31 COG1159 Era GTPase [General fu 76.4 16 0.00036 34.4 8.5 71 21-94 196-282 (298)
32 TIGR03675 arCOG00543 arCOG0054 74.0 24 0.00053 36.2 9.8 84 21-118 71-155 (630)
33 cd02393 PNPase_KH Polynucleoti 70.5 4.5 9.7E-05 28.8 2.6 28 46-73 4-31 (61)
34 PF13014 KH_3: KH domain 65.3 5.3 0.00011 26.1 2.0 17 56-72 3-19 (43)
35 cd00105 KH-I K homology RNA-bi 60.9 10 0.00022 25.8 2.9 27 47-73 3-29 (64)
36 cd02396 PCBP_like_KH K homolog 53.5 12 0.00026 26.5 2.3 26 47-72 3-28 (65)
37 cd05213 NAD_bind_Glutamyl_tRNA 50.6 1.1E+02 0.0023 28.3 8.6 53 20-79 25-77 (311)
38 PF00013 KH_1: KH domain syndr 50.0 5.7 0.00012 27.4 0.1 27 47-73 3-29 (60)
39 cd00554 MECDP_synthase MECDP_s 49.7 62 0.0014 27.7 6.4 71 7-89 55-131 (153)
40 cd02394 vigilin_like_KH K homo 48.3 14 0.0003 25.6 1.9 25 49-73 5-29 (62)
41 TIGR00151 ispF 2C-methyl-D-ery 41.9 94 0.002 26.7 6.3 70 8-89 56-131 (155)
42 PRK06418 transcription elongat 39.3 66 0.0014 27.9 5.0 31 43-74 60-90 (166)
43 PF13184 KH_5: NusA-like KH do 39.2 23 0.00049 26.2 1.9 32 43-74 2-38 (69)
44 PRK09202 nusA transcription el 38.7 42 0.0009 33.5 4.2 57 17-73 274-331 (470)
45 PRK06418 transcription elongat 37.4 94 0.002 27.0 5.7 65 18-88 98-165 (166)
46 PRK12327 nusA transcription el 36.8 1E+02 0.0022 29.8 6.4 54 21-74 204-266 (362)
47 TIGR01953 NusA transcription t 36.4 1.1E+02 0.0023 29.3 6.5 54 21-74 202-264 (341)
48 PF08731 AFT: Transcription fa 33.7 74 0.0016 26.1 4.2 35 17-53 3-37 (111)
49 KOG2192 PolyC-binding hnRNP-K 31.5 59 0.0013 30.9 3.7 80 40-119 44-123 (390)
50 PRK08406 transcription elongat 31.5 1E+02 0.0023 25.6 4.9 41 31-73 21-61 (140)
51 PRK12328 nusA transcription el 30.3 90 0.002 30.5 4.9 53 17-69 280-333 (374)
52 PRK12327 nusA transcription el 29.5 72 0.0016 30.8 4.1 55 17-72 274-331 (362)
53 PLN02862 2-C-methyl-D-erythrit 29.2 1.7E+02 0.0038 26.5 6.2 70 8-89 116-191 (216)
54 PF05316 VAR1: Mitochondrial r 29.0 31 0.00068 33.3 1.5 129 65-196 156-347 (350)
55 COG1855 ATPase (PilT family) [ 29.0 55 0.0012 33.4 3.3 53 17-73 462-515 (604)
56 PRK13764 ATPase; Provisional 28.9 89 0.0019 32.2 4.8 51 20-73 460-510 (602)
57 PRK12328 nusA transcription el 28.6 1.3E+02 0.0029 29.3 5.7 54 21-74 210-272 (374)
58 TIGR01953 NusA transcription t 28.3 76 0.0016 30.3 4.0 53 17-69 272-326 (341)
59 TIGR03665 arCOG04150 arCOG0415 27.0 46 0.001 28.4 2.1 57 53-116 7-69 (172)
60 PF12685 SpoIIIAH: SpoIIIAH-li 25.9 2.8E+02 0.006 24.0 6.8 57 24-86 139-195 (196)
61 TIGR01952 nusA_arch NusA famil 25.5 1.3E+02 0.0028 25.3 4.5 44 28-72 18-61 (141)
62 PF02542 YgbB: YgbB family; I 25.5 1.8E+02 0.0038 25.1 5.3 50 28-89 83-132 (157)
63 PRK00084 ispF 2-C-methyl-D-ery 25.2 1.9E+02 0.004 25.1 5.4 41 44-89 94-134 (159)
64 COG0195 NusA Transcription elo 25.0 1.3E+02 0.0029 26.5 4.6 57 18-74 114-172 (190)
65 PRK12329 nusA transcription el 23.5 2E+02 0.0043 28.9 5.9 54 21-74 229-298 (449)
66 PRK09202 nusA transcription el 22.2 2.1E+02 0.0046 28.5 6.0 54 21-74 204-266 (470)
67 COG4604 CeuD ABC-type enteroch 22.2 3.6E+02 0.0078 24.9 6.9 60 45-106 19-78 (252)
68 TIGR03675 arCOG00543 arCOG0054 22.2 1.1E+02 0.0024 31.5 4.1 53 20-77 3-56 (630)
69 COG1942 Uncharacterized protei 21.6 1.5E+02 0.0032 22.0 3.7 32 62-93 18-49 (69)
70 PRK09382 ispDF bifunctional 2- 20.5 2.8E+02 0.0062 26.6 6.3 49 28-88 300-348 (378)
71 smart00526 H15 Domain in histo 20.3 2.5E+02 0.0055 19.7 4.6 37 95-131 23-60 (66)
72 TIGR00013 taut 4-oxalocrotonat 20.2 1.7E+02 0.0037 19.9 3.6 30 64-93 19-48 (63)
73 PRK05090 hypothetical protein; 20.0 4.4E+02 0.0096 20.7 7.2 38 62-99 44-89 (95)
No 1
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=100.00 E-value=4.4e-69 Score=475.10 Aligned_cols=213 Identities=79% Similarity=1.237 Sum_probs=209.5
Q ss_pred ccCceeeEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCe
Q 026316 4 QISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENS 83 (240)
Q Consensus 4 ~~~~~~kwia~~~~y~~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~ 83 (240)
|++.+++|++|+..+++||+||.++|.++|||+|+|+|+++.++|+||+++|+.+||++|.++++|++.|++.|++++++
T Consensus 4 ~~~~~k~fi~~~~~~~~~re~l~k~~~~agis~ieI~Rt~~~i~V~I~tarPg~vIG~~G~~i~~l~~~L~k~~~~~~~~ 83 (220)
T PTZ00084 4 QISKKRKFVADGVFYAELNEFLSRELAEDGYSGVEVRVTPIRTEIIIRATRTREVLGDKGRRIRELTSLLQKRFGFPEGK 83 (220)
T ss_pred ccchhhHHHHcchhhHHHHHHHHHHHHHCCcceEEEEEcCCcEEEEEEECCCccEEcCCchHHHHHHHHHHHHhCCCCce
Confidence 57889999999999999999999999999999999999999999999999999999999999999999999999988889
Q ss_pred eEEEEEEecCCCcChHHHHHHHHHHHhcCchhHHHHHHHHHHHHHhCCcceeeeeeeceeEEEccccccceeeeEEeeec
Q 026316 84 VELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDG 163 (240)
Q Consensus 84 v~I~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRra~~~~l~~~m~~gakGik~~~~~~~~I~iSGRL~G~rArte~~~~G 163 (240)
++|++.+|++|++||.++|++||+|||+|++||||++++|+++|++||+||| |+|||||+|.|||+|||++|
T Consensus 84 i~i~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGakGik--------I~iSGRL~~EiARtE~~~eG 155 (220)
T PTZ00084 84 VELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCE--------VIVSGKLRAQRAKSMKFRDG 155 (220)
T ss_pred EEEEEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCCceEE--------EEEccchhhHHHHhhHhhcc
Confidence 9999999999999999999999999999999999999999999999999999 99999999779999999999
Q ss_pred eeeecCcccccceeEEEEEEecCCeeeeEEEEEEcCCCcCCCCCCCCCCCCeEEEccCCcc
Q 026316 164 YMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEE 224 (240)
Q Consensus 164 ~vl~tG~~~~~~Idya~~~a~t~~GvlGIKVwI~~~~~p~g~~~p~~~lpd~v~i~~~~~~ 224 (240)
+|||||++++++||||+.+|+|+||+||||||||+++||+|+.||.++|||.|+|++++++
T Consensus 156 rVl~Tg~~~~~~idy~~~~a~t~yGviGVKVwI~~~~~~~~~~~~~~~~pD~~~i~~~~~~ 216 (220)
T PTZ00084 156 YMISTGQPKKDFVDSAVRHVLMRQGVIGVKVKIMLPYDPSGKNGPSAPLPDVITVLEPKEE 216 (220)
T ss_pred EEEecCchHHHheehheEEEcccCceeeEEEEEECCCCcccccCCCCCCCCcEEEeCCccc
Confidence 9999999999999999999999999999999999999999999999999999999999887
No 2
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=100.00 E-value=5.2e-63 Score=432.60 Aligned_cols=205 Identities=37% Similarity=0.598 Sum_probs=198.3
Q ss_pred cCceeeEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCee
Q 026316 5 ISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSV 84 (240)
Q Consensus 5 ~~~~~kwia~~~~y~~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v 84 (240)
|+++++|++|+..+.+||+||.+.|.++||++|+|+|+++.+.|+||+++|+.+||++|+++++|+..|++.|+. .++
T Consensus 1 ~~~~~~fi~~~~~~~~irefi~~~~~~AgIs~IeI~Rt~~~i~I~I~ta~PGivIGk~G~~I~klk~~Lkk~~~~--~~v 78 (207)
T PRK04191 1 MAIEKKFVEEGLKKVMIDEYLAKELYRAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKNIRELTEILEKKFGL--ENP 78 (207)
T ss_pred CchhhHHHHcchHHHHHHHHHHhhhhhcceeEEEEEEcCCcEEEEEEECCCCeEECCCchhHHHHHHHHHHHhCC--Cce
Confidence 567899999999999999999999999999999999999999999999999999999999999999999999975 468
Q ss_pred EEEEEEecCCCcChHHHHHHHHHHHhcCchhHHHHHHHHHHHHHhCCcceeeeeeeceeEEEccccccceeeeEEeeece
Q 026316 85 ELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGY 164 (240)
Q Consensus 85 ~I~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRra~~~~l~~~m~~gakGik~~~~~~~~I~iSGRL~G~rArte~~~~G~ 164 (240)
.|++.+|.+|++||.++|++||+|||+|++|||+++++|+++|++||+||| |+|||||+|+|||+|||++|+
T Consensus 79 ~I~v~ev~~p~~~a~~vA~~ia~qLe~r~~fRra~k~~i~~~~~agakGik--------i~iSGrL~Ge~AR~e~~~eG~ 150 (207)
T PRK04191 79 QIDVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVE--------IIISGKLTGERARTEKFTEGY 150 (207)
T ss_pred eEEEEEEeCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCeeEE--------EEEccccchHHHHhhhhhcce
Confidence 999999999999999999999999999999999999999999999999999 999999999999999999999
Q ss_pred eeecCcccccceeEEEEEEecCCeeeeEEEEEEcCCCcCCCCCCCCCCCCeEEEccCCcccccC
Q 026316 165 MISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEVYVA 228 (240)
Q Consensus 165 vl~tG~~~~~~Idya~~~a~t~~GvlGIKVwI~~~~~p~g~~~p~~~lpd~v~i~~~~~~~~~~ 228 (240)
|.+||||+...||||+++|+|+||+||||||||++ +.++||.++|++|+++++++
T Consensus 151 v~~~G~pl~tlIdya~~~a~t~~GviGIKVwI~~~---------~~~~pd~~~i~~~~~~~~~~ 205 (207)
T PRK04191 151 IKKSGEPAEELVDRGFAIAKLKLGIIGVEVRIMPP---------DAKLPDEIEIKEPVEVEEVV 205 (207)
T ss_pred EeccCCcchheeeeEEEEEecCCeeEEEEEEEECC---------CCCCCCEEEEeCCCCccccc
Confidence 99999999999999999999999999999999997 68999999999998887665
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=2.4e-62 Score=425.63 Aligned_cols=194 Identities=49% Similarity=0.734 Sum_probs=188.9
Q ss_pred eeeEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEE
Q 026316 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (240)
Q Consensus 8 ~~kwia~~~~y~~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~ 87 (240)
+++|++|+..+.+||+||.++|.++||++|+|+|+++.++|+||+++|+.+||++|+++++|++.|+++|+. .+++|+
T Consensus 2 ~kkfi~~~~~~~~ire~l~k~~~~agis~ieI~r~~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~--~~~~I~ 79 (195)
T TIGR01008 2 ERKFVAEGLKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGL--ENPQID 79 (195)
T ss_pred cEehHhcchHHHHHHHHHHHHHHhCCeeEEEEEEcCCcEEEEEEECCCceEECCCchHHHHHHHHHHHHhCC--CceEEE
Confidence 578999999999999999999999999999999999999999999999999999999999999999999985 479999
Q ss_pred EEEecCCCcChHHHHHHHHHHHhcCchhHHHHHHHHHHHHHhCCcceeeeeeeceeEEEccccccceeeeEEeeeceeee
Q 026316 88 AEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKFKDGYMIS 167 (240)
Q Consensus 88 v~~v~~p~~~a~~iA~~ia~~Le~~~~fRra~~~~l~~~m~~gakGik~~~~~~~~I~iSGRL~G~rArte~~~~G~vl~ 167 (240)
+.+|.+|++||.++|++||+|||+|++||||++++|+++|++||+||| |+|||||+|+|||+|||++|+|.|
T Consensus 80 v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGakGik--------I~iSGRL~GeiARtE~~~eG~v~~ 151 (195)
T TIGR01008 80 VEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAKGVE--------VTISGKLTGERARTEKFAAGYLKH 151 (195)
T ss_pred EEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCceEE--------EEEcccccchhhhhhheeccEEec
Confidence 999999999999999999999999999999999999999999999999 999999999999999999999999
Q ss_pred cCcccccceeEEEEEEecCCeeeeEEEEEEcCCCcCCCCCCCCCCCCeEEEcc
Q 026316 168 SGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHP 220 (240)
Q Consensus 168 tG~~~~~~Idya~~~a~t~~GvlGIKVwI~~~~~p~g~~~p~~~lpd~v~i~~ 220 (240)
||+|+...||||+++|+|+||+||||||||++ +.++||.++|++
T Consensus 152 sG~Pl~t~IDya~~~a~t~yGviGIKVwI~~~---------~~~~pD~~~i~~ 195 (195)
T TIGR01008 152 SGEPAEELVDKGFAIALLKLGVLGVKVKIMPP---------DVKLPDEVEIKE 195 (195)
T ss_pred CCCcchheeeeEEEEEecCCceEEEEEEEECC---------CCCCCCEEEecC
Confidence 99999999999999999999999999999997 689999999964
No 4
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.9e-62 Score=434.40 Aligned_cols=198 Identities=32% Similarity=0.446 Sum_probs=187.1
Q ss_pred CceeeEeecCcchHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhC
Q 026316 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (240)
Q Consensus 6 ~~~~kwia~~~~y~~-------Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~ 78 (240)
...|+||++...|++ ||+||+++|.+||||+|+|+|+|++++|+||++|||+|||++|++|++|+..|+++|+
T Consensus 6 ~w~srwfa~~~~~~~~l~ed~kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~g 85 (233)
T COG0092 6 DWKSRWFANKKEYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLFG 85 (233)
T ss_pred cchhhhccccccchHHHHHHHHHHHHHHHHHHhCCcceEEEEecCCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHhC
Confidence 578999999887764 9999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCeeEEEEEEecCCCcChHHHHHHHHHHHhcCchhHHHHHHHHHHHHHhCCcceeeeeeeceeEEEccccccc-eeee
Q 026316 79 FPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQ-RAKS 157 (240)
Q Consensus 79 ~~~~~v~I~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRra~~~~l~~~m~~gakGik~~~~~~~~I~iSGRL~G~-rArt 157 (240)
.. +++|++.+|++|++||+++|++||+|||+|++||||++++|+++|++||+||| |+|||||+|+ +||+
T Consensus 86 ~~--~v~I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGAkGik--------i~vSGRL~GaeiAR~ 155 (233)
T COG0092 86 KE--NVQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIK--------IQVSGRLGGAEIART 155 (233)
T ss_pred CC--CceEEEEEcCCCCcCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcCCceeE--------EEEecccchHHHHhH
Confidence 63 89999999999999999999999999999999999999999999999999999 9999999999 6999
Q ss_pred EEeeecee-eecCcccccceeEEEEEEecCCeeeeEEEEEEcCCCcCCCCCCCCCCCCeEEEccCCcccc
Q 026316 158 MKFKDGYM-ISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEVY 226 (240)
Q Consensus 158 e~~~~G~v-l~tG~~~~~~Idya~~~a~t~~GvlGIKVwI~~~~~p~g~~~p~~~lpd~v~i~~~~~~~~ 226 (240)
|||.+|+| ||| ++++||||+++|+|+||+||||||||+| ..|||.+.+.++..++.
T Consensus 156 E~y~eG~vplht---lrAdIDyg~a~A~ttyGiiGVKVwI~~g----------e~l~~~~~~~~~~~~~~ 212 (233)
T COG0092 156 EKYREGRVPLHT---LRADIDYGTAEAHTTYGVIGVKVWIYKG----------EVLPDKVEIKEPAEVEE 212 (233)
T ss_pred HHHhcceeEccc---cceeeeeeeEEEEecCceEEEEEEEecC----------CcCCCcccccCcccccc
Confidence 99999999 999 9999999999999999999999999997 38889888766555543
No 5
>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.3e-62 Score=424.67 Aligned_cols=225 Identities=86% Similarity=1.244 Sum_probs=218.7
Q ss_pred CccccCceeeEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCC
Q 026316 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP 80 (240)
Q Consensus 1 ~~~~~~~~~kwia~~~~y~~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~ 80 (240)
|+.+|+.+++|++|+.+|+|++|||+++|.+.|||++|++.||.+++|+|.+++|+.++|.+|++|++|+..++++|+++
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 77889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeEEEEEEecCCCcChHHHHHHHHHHHhcCchhHHHHHHHHHHHHHhCCcceeeeeeeceeEEEccccccceeeeEEe
Q 026316 81 ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQRAKSMKF 160 (240)
Q Consensus 81 ~~~v~I~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRra~~~~l~~~m~~gakGik~~~~~~~~I~iSGRL~G~rArte~~ 160 (240)
+.+|+|++++|.+.+|||..+|++|+++|..++++||||+.+|+++|++||+||+ |++||+|+|+||++++|
T Consensus 81 ~~svelyaEkV~~rGLcAiaQaeslryKllgGlavRRA~ygvlr~vmesgAkGce--------viVSGKLrgqRAKsmKF 152 (244)
T KOG3181|consen 81 EGSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCE--------VIVSGKLRGQRAKSMKF 152 (244)
T ss_pred CCcEEEehhhhhccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHccCCccE--------EEEeccchhhhhhcccc
Confidence 9999999999999999999999999999999999999999999999999999999 99999999999999999
Q ss_pred eeceeeecCcccccceeEEEEEEecCCeeeeEEEEEEcCCCcCCCCCCCCCCCCeEEEccCCccc-ccCCcccc
Q 026316 161 KDGYMISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEV-YVAPATAT 233 (240)
Q Consensus 161 ~~G~vl~tG~~~~~~Idya~~~a~t~~GvlGIKVwI~~~~~p~g~~~p~~~lpd~v~i~~~~~~~-~~~~~~~~ 233 (240)
.+|.|+|||||.+++||.|++|++|++|||||||+||+||||+|++||..+|||.|+|.+|++++ +.+|.+..
T Consensus 153 ~DG~mIhSG~pv~dyi~ta~rhVllrQGVlGIkVkIMlpydp~g~~GP~~pLPD~v~i~ePkee~~~~~p~~~~ 226 (244)
T KOG3181|consen 153 VDGLMIHSGQPVKDYIDTAVRHVLLRQGVLGIKVKIMLPYDPKGKLGPKKPLPDRVTILEPKEEEPITAPAQVA 226 (244)
T ss_pred ccceEEecCCcHHHHHHHHHHhhhhhcceeeeEEEEeccCCcccCcCCCCCCCCeeEEeCccccccccCchhhh
Confidence 99999999999999999999999999999999999999999999999999999999999999986 45555443
No 6
>CHL00048 rps3 ribosomal protein S3
Probab=100.00 E-value=1.2e-54 Score=381.86 Aligned_cols=183 Identities=20% Similarity=0.270 Sum_probs=175.3
Q ss_pred CceeeEeecCcchHH-------HHHHHHhh----hccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHH
Q 026316 6 SKKRKFVADGVFFAE-------LNEVLTRE----LAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 6 ~~~~kwia~~~~y~~-------Ire~l~k~----~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~ 74 (240)
.+.|+||+++++|++ ||+||.+. +.++||++|+|+|+++.++|+||+++|+.+||++|+++++|++.|+
T Consensus 17 ~~~S~W~a~~~~y~~~l~eD~~ir~~i~~~l~~~~~~agis~i~I~r~~~~~~I~I~~~~Pg~vIG~~g~~i~~l~~~L~ 96 (214)
T CHL00048 17 KHHSLWFAQPKNYSEGLQEDKKIRDCIKNYVQKNIKYEGIARIEIQRKIDLIQVIIYTGFPKLLIERKGRGIEELQINLQ 96 (214)
T ss_pred CCceEEecChhhhHHHHHHHHHHHHHHHHHHHhhhhhCCeeEEEEEEcCCeEEEEEEECCCceEECCCcHhHHHHHHHHH
Confidence 378999999999996 66666655 7899999999999999999999999999999999999999999999
Q ss_pred HHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHhcCchhHHHHHHHHHHHHHhCCcceeeeeeeceeEEEccccccc-
Q 026316 75 KRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQ- 153 (240)
Q Consensus 75 k~~~~~~~~v~I~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRra~~~~l~~~m~~gakGik~~~~~~~~I~iSGRL~G~- 153 (240)
+.|++++++++|++.++++|++||.++|++||++||+|++|||+++++++++|++||+||| |+|||||+|+
T Consensus 97 k~~~~~~~~i~I~v~ev~~p~~~A~~iA~~ia~~Le~r~~fRra~~~~i~~~~~~ga~Gik--------I~iSGRL~Gae 168 (214)
T CHL00048 97 KELNSVNRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIK--------IQISGRLNGAE 168 (214)
T ss_pred HHhCCCCceEEEEEEEecCCCcCHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHhCCcEEE--------EEEecccCccc
Confidence 9998877789999999999999999999999999999999999999999999999999999 9999999998
Q ss_pred eeeeEEeeecee-eecCcccccceeEEEEEEecCCeeeeEEEEEEcC
Q 026316 154 RAKSMKFKDGYM-ISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLE 199 (240)
Q Consensus 154 rArte~~~~G~v-l~tG~~~~~~Idya~~~a~t~~GvlGIKVwI~~~ 199 (240)
|||+|||++|+| ||| ++++||||+.+|+|+||++|||||||++
T Consensus 169 ~AR~e~~~~G~vpl~t---l~a~Idy~~~~a~t~~G~~GVKVwI~~~ 212 (214)
T CHL00048 169 IARVEWIREGRVPLQT---LRAKIDYCSYPARTIYGVLGIKIWIFKD 212 (214)
T ss_pred hheEEEEecceeECCc---chhheEEEEEEEecCCceEEEEEEEEcC
Confidence 999999999999 999 9999999999999999999999999987
No 7
>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=9.4e-55 Score=381.63 Aligned_cols=181 Identities=27% Similarity=0.387 Sum_probs=176.4
Q ss_pred CceeeEeecCcchHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhC
Q 026316 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (240)
Q Consensus 6 ~~~~kwia~~~~y~~-------Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~ 78 (240)
.+.|.||+++++|++ ||+||.++|.++||++|+|+||++.++|+||+++|+.+||++|+++++|++.|++.|+
T Consensus 17 ~w~S~Wfa~~k~Y~~~l~eD~~IR~~i~k~~~~agis~IeI~rt~~~i~I~I~~~~pg~vIG~~g~~i~~l~~~l~~~~~ 96 (211)
T TIGR01009 17 DWKSRWYANPKEYAKLLHEDLKIRNYIKKELSNAGISDVEIERPADKIRVTIHTARPGIVIGKKGSEIEKLRKDLQKLTG 96 (211)
T ss_pred CCceEEccCcchhHHHHHHHHHHHHHHHHHhhhCCcceEEEEEcCCceEEEEEeCCCcceeCCCchHHHHHHHHHHHHhC
Confidence 488999999999996 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCCCcChHHHHHHHHHHHhcCchhHHHHHHHHHHHHHhCCcceeeeeeeceeEEEccccccc-eeee
Q 026316 79 FPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQ-RAKS 157 (240)
Q Consensus 79 ~~~~~v~I~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRra~~~~l~~~m~~gakGik~~~~~~~~I~iSGRL~G~-rArt 157 (240)
++++|++.++++|++||.++|++|+++||+|++|||+++++|+.+|++||+||| |+|||||+|+ |||+
T Consensus 97 ---~~~~i~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRr~~~~~i~~~~~~g~~Gik--------I~isGRl~g~e~Ar~ 165 (211)
T TIGR01009 97 ---KEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIK--------VQVSGRLGGAEIART 165 (211)
T ss_pred ---CceEEEEEEecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCCcEEE--------EEEecccCchhhhhe
Confidence 579999999999999999999999999999999999999999999999999999 9999999998 9999
Q ss_pred EEeeecee-eecCcccccceeEEEEEEecCCeeeeEEEEEEcCC
Q 026316 158 MKFKDGYM-ISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEW 200 (240)
Q Consensus 158 e~~~~G~v-l~tG~~~~~~Idya~~~a~t~~GvlGIKVwI~~~~ 200 (240)
|||++|+| ||| ++++||||+++|+|+||++|||||||+++
T Consensus 166 e~~~~G~vpl~t---~~~~Idy~~~~a~T~~G~~GvKVwI~~~~ 206 (211)
T TIGR01009 166 EWYKEGRVPLHT---LRADIDYATAEAHTTYGIIGVKVWIFKGE 206 (211)
T ss_pred eeeeeCccCccc---chhhcEEEEEEEEcCCceEEEEEEEEcCC
Confidence 99999999 999 99999999999999999999999999983
No 8
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=100.00 E-value=3.7e-54 Score=382.62 Aligned_cols=180 Identities=27% Similarity=0.391 Sum_probs=176.2
Q ss_pred CceeeEeecCcchHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhC
Q 026316 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (240)
Q Consensus 6 ~~~~kwia~~~~y~~-------Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~ 78 (240)
.+.|.||++..+|++ ||+||+++|.++||++|+|+|+++.++|+||+++|+.+||++|.++++|++.|++.|+
T Consensus 17 ~w~S~Wya~~k~Y~~~L~eD~~IRe~i~k~~~~agis~IeI~R~~~~i~I~I~~~rP~~iiG~~g~~i~~l~~~L~~~~~ 96 (232)
T PRK00310 17 DWDSRWYADKKDYADLLHEDLKIRKFLKKKLKKAGVSRIEIERPAKRVRVTIHTARPGIVIGKKGAEIEKLRKELEKLTG 96 (232)
T ss_pred CCCCeEeCCcchhHHHHHHHHHHHHHHHHhHhhCceeEEEEEEcCCeEEEEEEECCCccccCCCcHHHHHHHHHHHHHhC
Confidence 488999999999996 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCCCcChHHHHHHHHHHHhcCchhHHHHHHHHHHHHHhCCcceeeeeeeceeEEEccccccc-eeee
Q 026316 79 FPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEFNFLVSSKVIVSGKLRAQ-RAKS 157 (240)
Q Consensus 79 ~~~~~v~I~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRra~~~~l~~~m~~gakGik~~~~~~~~I~iSGRL~G~-rArt 157 (240)
++++|++.++++|++||.++|++|+++||+|++|||+++++|+++|++||+||| |+|||||+|+ |||+
T Consensus 97 ---~~~~i~v~ev~~p~~~a~~iA~~ia~~Le~r~~fRr~~~~~i~~~~~~g~~Gik--------I~isGRl~g~e~Ar~ 165 (232)
T PRK00310 97 ---KPVQINIVEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIK--------VQVSGRLGGAEIART 165 (232)
T ss_pred ---CceEEEEEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCcEEE--------EEEcCCCCcceeeeE
Confidence 589999999999999999999999999999999999999999999999999999 9999999998 9999
Q ss_pred EEeeecee-eecCcccccceeEEEEEEecCCeeeeEEEEEEcC
Q 026316 158 MKFKDGYM-ISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLE 199 (240)
Q Consensus 158 e~~~~G~v-l~tG~~~~~~Idya~~~a~t~~GvlGIKVwI~~~ 199 (240)
|||++|+| ||| ++++||||+.+|+|+||+||||||||++
T Consensus 166 e~~~~G~vpl~t---~~~~Idy~~~~a~T~~Gv~GVKVwI~~~ 205 (232)
T PRK00310 166 EWYREGRVPLHT---LRADIDYGTAEAHTTYGIIGVKVWIYKG 205 (232)
T ss_pred EEeeecccccce---eeeeeEEEEEEEecCCceEEEEEEEECC
Confidence 99999999 999 9999999999999999999999999997
No 9
>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=99.93 E-value=3.9e-26 Score=174.25 Aligned_cols=82 Identities=37% Similarity=0.560 Sum_probs=78.8
Q ss_pred HHHHHHhcCchhHHHHHHHHHHH-HHhCCcceeeeeeeceeEEEccccccc-eeeeEEeeecee-eecCcccccceeEEE
Q 026316 104 SLRYKLLGGLAVRRACYGVLRFI-MESGAKGCEFNFLVSSKVIVSGKLRAQ-RAKSMKFKDGYM-ISSGQPVNEYIDSAV 180 (240)
Q Consensus 104 ~ia~~Le~~~~fRra~~~~l~~~-m~~gakGik~~~~~~~~I~iSGRL~G~-rArte~~~~G~v-l~tG~~~~~~Idya~ 180 (240)
+|+++||++.+||++++++++.+ |+.|++||| |+|||||+|. |||+++|++|+| +|+ ++++|||++
T Consensus 1 ~i~~~l~k~~~~r~~i~~~~~~i~~~~~~~Gik--------I~isGRl~g~~rar~~~~~~G~i~~~~---~~~~Idy~~ 69 (85)
T PF00189_consen 1 FIAQKLEKRISFRRIIKKIIRRIMMNKGIKGIK--------IQISGRLNGAERARTEKFKKGKISLQT---FKSNIDYAS 69 (85)
T ss_dssp HHHHHHHTTSTHHHHHHHHHHHHHHCTTSSEEE--------EEEESSGGGTSSSEEEEEEEESSSSSS---STTEEEEEE
T ss_pred ChHHHHhcCcHHHHHHHHHHHHHHhhcccceEE--------EEEeecCCCCccceEEEEECCCCcccc---ceeeeeEEE
Confidence 58999999999999999999999 778999999 9999999996 999999999999 777 999999999
Q ss_pred EEEecCCeeeeEEEEE
Q 026316 181 RHVLLRQGVLGIKVKI 196 (240)
Q Consensus 181 ~~a~t~~GvlGIKVwI 196 (240)
.++.|++|++||||||
T Consensus 70 ~~~~tk~G~~GIKVwI 85 (85)
T PF00189_consen 70 SHAKTKYGVIGIKVWI 85 (85)
T ss_dssp EEEEESSSEEEEEEEE
T ss_pred EEEEcCCeeEEEEEEC
Confidence 9999999999999998
No 10
>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=99.81 E-value=2e-19 Score=136.95 Aligned_cols=80 Identities=91% Similarity=1.285 Sum_probs=76.1
Q ss_pred CcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCC
Q 026316 15 GVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNR 94 (240)
Q Consensus 15 ~~~y~~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~~v~~p 94 (240)
+..+++||+||.+.|.+||||+|+|+||+++++|+|||++||.+||++|+++++|++.|++.|+++|+++++++++|.+.
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 46789999999999999999999999999999999999999999999999999999999999999999999888998764
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=99.79 E-value=5.1e-19 Score=140.76 Aligned_cols=87 Identities=24% Similarity=0.388 Sum_probs=82.4
Q ss_pred CceeeEeecCcchHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhC
Q 026316 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (240)
Q Consensus 6 ~~~~kwia~~~~y~~-------Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~ 78 (240)
...|.||+++.+|+. ||+||.+.|..+||++|+|+|+++.++|+||+++||.+||++|+.+++|++.|++.++
T Consensus 16 ~~~s~W~~~~~~y~~~l~ed~~IR~yL~k~~~~agis~I~I~R~~~~i~I~I~t~rPg~vIG~~G~~i~~L~~~l~~~~~ 95 (109)
T cd02412 16 DWDSRWYADKKDYAELLHEDLKIRKFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKGAGIEKLRKELQKLLG 95 (109)
T ss_pred CCcceEcCCchhhHHHHHhHHHHHHHHHHHHhhCCccEEEEEEcCCCEEEEEEeCCCCcccCCchHHHHHHHHHHHHHhC
Confidence 478999999999996 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCC
Q 026316 79 FPENSVELYAEKVNNR 94 (240)
Q Consensus 79 ~~~~~v~I~v~~v~~p 94 (240)
+ .++.|++.+|.+|
T Consensus 96 ~--~~~~I~V~ev~~P 109 (109)
T cd02412 96 N--KKVRINIVEVKKP 109 (109)
T ss_pred C--CceEEEEEEecCC
Confidence 4 4799999999987
No 12
>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=99.71 E-value=3.8e-17 Score=124.56 Aligned_cols=84 Identities=38% Similarity=0.662 Sum_probs=79.2
Q ss_pred eeeEeecCcchHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEE
Q 026316 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (240)
Q Consensus 8 ~~kwia~~~~y~~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~ 87 (240)
+++|++|+..+..||+||.+.|..+||++|+|+|+++.+.|+||+++||.+||++|+++++|+..|++.|+. .++.|+
T Consensus 2 ~~~~~~~~~~~~~Ir~fl~~~~~~agIs~IeI~r~~~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l~k~~~~--~~v~I~ 79 (85)
T cd02411 2 ERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGL--ENPQID 79 (85)
T ss_pred eEeHHhcchHHHHHHHHHHhhhhhCcccEEEEEEcCCcEEEEEEECCCCceECCCchhHHHHHHHHHHHhCC--CCceEE
Confidence 578999999999999999999999999999999999999999999999999999999999999999999974 478999
Q ss_pred EEEecC
Q 026316 88 AEKVNN 93 (240)
Q Consensus 88 v~~v~~ 93 (240)
+.++.+
T Consensus 80 v~ev~~ 85 (85)
T cd02411 80 VQEVEN 85 (85)
T ss_pred EEEecC
Confidence 998864
No 13
>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=99.45 E-value=2.1e-13 Score=101.21 Aligned_cols=77 Identities=27% Similarity=0.427 Sum_probs=71.9
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhC-CCCCeeEEEEEEecCCCc
Q 026316 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK-FPENSVELYAEKVNNRGL 96 (240)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~-~~~~~v~I~v~~v~~p~~ 96 (240)
+|++||.+++..+|+++++|+|+++.+.|++|+++|+.+||++|+.|++|+..+++.+. +.+.+|.|++.+|++|++
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 58999999999999999999999999999999999999999999999999999999884 445899999999999974
No 14
>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=98.67 E-value=1.2e-07 Score=66.36 Aligned_cols=65 Identities=42% Similarity=0.616 Sum_probs=57.7
Q ss_pred HHHHHhhhccCCeeeeEEEEcCCeEEEEEEecc--cceeecCCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026316 22 NEVLTRELAEDGYSGVEVRVTPVRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (240)
Q Consensus 22 re~l~k~~~~agis~IeI~rt~~~i~I~I~~~r--P~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (240)
|+||.+.|..+++++|+|+++++...+.+++.. |+.+||++|+.++.++..+++.++ +.++.|++
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 579999999999999999999888999999998 999999999999999999999883 45666654
No 15
>smart00322 KH K homology RNA-binding domain.
Probab=97.23 E-value=0.00039 Score=47.52 Aligned_cols=67 Identities=19% Similarity=0.262 Sum_probs=51.1
Q ss_pred CeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHh
Q 026316 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLL 110 (240)
Q Consensus 44 ~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~~v~~p~~~a~~iA~~ia~~Le 110 (240)
..+.|.|+...++.+||++|..+++|++.....+.............+..+..++...++.|..+++
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 4678889999999999999999999998887655443322234566777888888888888877653
No 16
>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=96.52 E-value=0.015 Score=43.26 Aligned_cols=56 Identities=20% Similarity=0.287 Sum_probs=47.7
Q ss_pred HHHHhhhccCCe-eeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhC
Q 026316 23 EVLTRELAEDGY-SGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (240)
Q Consensus 23 e~l~k~~~~agi-s~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~ 78 (240)
+||++.+...|+ ..+++......+.+.|....++.+||++|+.++.|+..+...++
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 678888877776 45667777888999999999999999999999999999988776
No 17
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=95.95 E-value=0.01 Score=43.53 Aligned_cols=67 Identities=13% Similarity=0.171 Sum_probs=45.2
Q ss_pred HHHHHHhhhccCCeeeeEEE--EcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEE
Q 026316 21 LNEVLTRELAEDGYSGVEVR--VTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (240)
Q Consensus 21 Ire~l~k~~~~agis~IeI~--rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~ 87 (240)
+++|+...+...+=-.+++. .....+.+.+.....|.+||++|+.++.|+..++...+....++.|.
T Consensus 4 l~~~l~~l~~~~~~v~v~~~~~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~~v~ 72 (73)
T PF13083_consen 4 LEDFLKNLVDKPMDVEVTIEIEEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAANKHGKRVRVE 72 (73)
T ss_dssp -HHHHHHHHHHTT--EEEEEEETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHHHT-SS-EEE
T ss_pred HHHHHHHHhCCcCeEEEEEEEcCCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHHHhCCCEEEEe
Confidence 67777777753332224444 34678888888888999999999999999999988775444455443
No 18
>PRK01064 hypothetical protein; Provisional
Probab=94.18 E-value=0.79 Score=34.98 Aligned_cols=69 Identities=10% Similarity=0.192 Sum_probs=48.5
Q ss_pred HHHHHHhhhcc--CCeeeeEEEEcCCeEEEEEEeccc--ceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEEE
Q 026316 21 LNEVLTRELAE--DGYSGVEVRVTPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (240)
Q Consensus 21 Ire~l~k~~~~--agis~IeI~rt~~~i~I~I~~~rP--~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~~ 90 (240)
+=+||-+.|-. ..+. |+-......+.+.+++... |.+||++|+.++.++..+...-...+.++.+.+.+
T Consensus 4 Lv~~iv~~LVd~Pe~V~-V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~~~~~~~~rv~leI~~ 76 (78)
T PRK01064 4 FLAYIVKNLVDRPEEVH-IKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIME 76 (78)
T ss_pred HHHHHHHHhcCCCCeEE-EEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhhCCCEEEEEEec
Confidence 44566665543 2222 4444446778888888766 68999999999999999998776556778877654
No 19
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=94.05 E-value=0.15 Score=42.62 Aligned_cols=62 Identities=11% Similarity=0.299 Sum_probs=48.3
Q ss_pred hH-HHHHHHHhhhccCCeeeeEEEEcCCe--EEEEEEecccceeecCCcccHHHHHHHHHHHhCC
Q 026316 18 FA-ELNEVLTRELAEDGYSGVEVRVTPVR--TEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (240)
Q Consensus 18 y~-~Ire~l~k~~~~agis~IeI~rt~~~--i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~ 79 (240)
|+ ...+|+.+.|..+...++.|...... +.+.+.-..-+..||++|+.++.++..+...|+.
T Consensus 70 ~s~d~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 70 YSDDPEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred cCCCHHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 54 38999999999999999988544433 3444444556679999999999999999988875
No 20
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=93.85 E-value=0.54 Score=42.16 Aligned_cols=106 Identities=17% Similarity=0.158 Sum_probs=76.9
Q ss_pred HHHHHHHHhhhccCCe-eeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCC---CCeeEEEEEEecC-
Q 026316 19 AELNEVLTRELAEDGY-SGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP---ENSVELYAEKVNN- 93 (240)
Q Consensus 19 ~~Ire~l~k~~~~agi-s~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~---~~~v~I~v~~v~~- 93 (240)
.++.+||...+..-|+ +.|.+....+.+.+.|....++.+||++|+.++.|+...+-.++.. ..+|.+++.....
T Consensus 65 ~~~~~~L~ell~~m~~~~~i~v~~~~~~v~~~i~~~~~~~LIG~~Gk~LdALQ~L~n~~l~~~~g~~~~v~ldv~~yRer 144 (208)
T COG1847 65 QEAKDYLEELLELMDFEVTITVSEEGRRVVVSIEGEDAGRLIGKHGKTLDALQYLANLYLNKIGGKFKRVTLDVGDYRER 144 (208)
T ss_pred HHHHHHHHHHHHHhCCceEEEEeecCcEEEEEecCCchhhhhccCCcchHHHHHHHHHHhhhhcCcceEEEEEhhhHHHH
Confidence 5699999999988776 5677888899999999999999999999999999998888777532 1355555543322
Q ss_pred CCcChHHHHHHHHHHHhcC-c---------hhHHHHHHHHH
Q 026316 94 RGLCAIAQAESLRYKLLGG-L---------AVRRACYGVLR 124 (240)
Q Consensus 94 p~~~a~~iA~~ia~~Le~~-~---------~fRra~~~~l~ 124 (240)
..-.=..+|+.+|.+..+. - +=||+++.+|.
T Consensus 145 R~e~L~~LA~~~A~rV~~tg~~v~L~pM~~~ERkIVH~~l~ 185 (208)
T COG1847 145 RKETLIKLAERAAERVLETGRSVELEPMPPFERKIVHTALS 185 (208)
T ss_pred HHHHHHHHHHHHHHHHHhhCCeeecCCCCHHHHHHHHHHHH
Confidence 1223345677777776432 1 24778888774
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=92.70 E-value=0.43 Score=34.14 Aligned_cols=53 Identities=15% Similarity=0.289 Sum_probs=42.4
Q ss_pred HHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeecCCcccHHHHHHHHH
Q 026316 22 NEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 22 re~l~k~~~~agis~IeI~rt-~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~ 74 (240)
.+|+.+.+.-+.+.++++... .+...|.+....-+..||++|++++.+++.+.
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 478888888888888877654 46777777777778899999999998888776
No 22
>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=92.48 E-value=1.3 Score=37.71 Aligned_cols=85 Identities=20% Similarity=0.246 Sum_probs=55.7
Q ss_pred HHHHHHhhhc-cCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChH
Q 026316 21 LNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI 99 (240)
Q Consensus 21 Ire~l~k~~~-~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~~v~~p~~~a~ 99 (240)
-++.|.+... +||+.+ |...++.=+|+|++.+||+++|++|..++++.... | +...-+..|-+.+.
T Consensus 54 A~~~I~~ivP~ea~i~d--i~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~~t----g-------W~p~vvRtpPi~S~ 120 (145)
T cd02410 54 AIKIILEIVPEEAGITD--IYFDDDTGEVIIEAEKPGLVIGKGGSTLREITRET----G-------WAPKVVRTPPIQSR 120 (145)
T ss_pred HHHHHHHhCCCccCcee--eEecCCCcEEEEEEcCCeEEEecCchhHHHHHHHh----C-------CeeEEEecCCCCcH
Confidence 4555555443 478764 55567778999999999999999998777765433 3 23444566666666
Q ss_pred HHHHHHHHHHhcCchhHHHH
Q 026316 100 AQAESLRYKLLGGLAVRRAC 119 (240)
Q Consensus 100 ~iA~~ia~~Le~~~~fRra~ 119 (240)
.+ +.+++.|......|+-+
T Consensus 121 ti-~~ir~~l~~~~~eR~~~ 139 (145)
T cd02410 121 TV-KSIRRFLRREREERKEI 139 (145)
T ss_pred HH-HHHHHHHHHhHHHHHHH
Confidence 54 45555555555555543
No 23
>PRK02821 hypothetical protein; Provisional
Probab=92.14 E-value=2.1 Score=32.65 Aligned_cols=68 Identities=19% Similarity=0.241 Sum_probs=47.8
Q ss_pred HHHHHHHhhhcc-CCeeeeEEEEcCCeEEEEEEeccc--ceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEEE
Q 026316 20 ELNEVLTRELAE-DGYSGVEVRVTPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (240)
Q Consensus 20 ~Ire~l~k~~~~-agis~IeI~rt~~~i~I~I~~~rP--~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~~ 90 (240)
++=+||.+.|-. -.=-.|+.+.....+.+.|+++.- |.+||++|+.++.++..+.-. .++++.+.+.+
T Consensus 4 ~lv~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~---~~~~v~leI~~ 74 (77)
T PRK02821 4 DAVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI---GGRGVRVDVVD 74 (77)
T ss_pred HHHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh---cCCeEEEEEEe
Confidence 455666666543 222235555556778888888643 469999999999999999977 34788888765
No 24
>PRK00468 hypothetical protein; Provisional
Probab=90.11 E-value=4.3 Score=30.69 Aligned_cols=69 Identities=17% Similarity=0.234 Sum_probs=44.9
Q ss_pred HHHHHHHhhhccC-CeeeeEEEEcCCeEEEEEEeccc--ceeecCCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026316 20 ELNEVLTRELAED-GYSGVEVRVTPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (240)
Q Consensus 20 ~Ire~l~k~~~~a-gis~IeI~rt~~~i~I~I~~~rP--~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (240)
++=+||-+.|-.. .=-.|+.......+.+.|+++.- |.+||++|+.++.|+..+.-.-...+.++.+.+
T Consensus 3 ~Lv~~iv~~LVd~Pe~v~V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~leI 74 (75)
T PRK00468 3 ELVETIAKALVDNPDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVEI 74 (75)
T ss_pred HHHHHHHHHhcCCCCeEEEEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHHHHHhcCCCEEEEEE
Confidence 3445666665432 22224444556778788888643 469999999999999999865443345666554
No 25
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=88.22 E-value=5.3 Score=30.50 Aligned_cols=68 Identities=18% Similarity=0.253 Sum_probs=42.1
Q ss_pred HHHHHHhhhccC-CeeeeEEEEcCCeEEEEEEeccc--ceeecCCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026316 21 LNEVLTRELAED-GYSGVEVRVTPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (240)
Q Consensus 21 Ire~l~k~~~~a-gis~IeI~rt~~~i~I~I~~~rP--~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (240)
+=+|+-+.|-.. .=-+++..-......+.|+++.. |-+||++|+.++.|+..|.-.=...+.++.+++
T Consensus 4 lv~~ivk~lVd~Pd~v~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~~~~~~v~i~i 74 (76)
T COG1837 4 LVEFIVKPLVDNPDDVRVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGSKDSKRVVVEI 74 (76)
T ss_pred HHHHHHHHhcCCccceEEEEEecCCeEEEEEEECcccccceecCCChhHHHHHHHHHHhcccCceEEEEEe
Confidence 445555555432 22223333346677777777654 569999999999999999865443344555443
No 26
>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=86.35 E-value=3.2 Score=37.10 Aligned_cols=65 Identities=22% Similarity=0.329 Sum_probs=43.1
Q ss_pred HHHHHHhhhccC-Cee-eeEEEE---cC---CeEEEEEEecccc---eeecCCcccHHHH----HHHHHHHhCCCCCeeE
Q 026316 21 LNEVLTRELAED-GYS-GVEVRV---TP---VRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (240)
Q Consensus 21 Ire~l~k~~~~a-gis-~IeI~r---t~---~~i~I~I~~~rP~---~iIG~~g~~i~~l----~~~L~k~~~~~~~~v~ 85 (240)
|||.+...+.+. -|+ .++|+. .+ ..|...|++.|+. +|||++|+.|+++ ++.|++.|+ .+|.
T Consensus 188 ire~~~~~~~~e~p~~~~~~~~~~~~~~~~~~~i~~~i~v~~~s~k~iiig~~g~~ik~i~~~ar~~l~~~~~---~~v~ 264 (270)
T TIGR00436 188 IREKIIRYTKEEIPHSVRVEIERKSFNEKGLLKIHALISVERESQKKIIIGKNGSMIKAIGIAARKDILELFD---CDVF 264 (270)
T ss_pred HHHHHHHhcccccCceEEEEEEEEEECCCCeEEEEEEEEECcCCceeEEEcCCcHHHHHHHHHHHHHHHHHhC---CCEE
Confidence 777776655532 121 233322 22 3578889999886 7999999999765 567888887 5677
Q ss_pred EEE
Q 026316 86 LYA 88 (240)
Q Consensus 86 I~v 88 (240)
+.+
T Consensus 265 l~l 267 (270)
T TIGR00436 265 LEL 267 (270)
T ss_pred EEE
Confidence 654
No 27
>PRK15494 era GTPase Era; Provisional
Probab=85.28 E-value=3.7 Score=38.37 Aligned_cols=65 Identities=25% Similarity=0.405 Sum_probs=43.5
Q ss_pred HHHHHHhhhccC-Ce-eeeEEEEc------CCeEEEEEEecccc---eeecCCcccHHHH----HHHHHHHhCCCCCeeE
Q 026316 21 LNEVLTRELAED-GY-SGVEVRVT------PVRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (240)
Q Consensus 21 Ire~l~k~~~~a-gi-s~IeI~rt------~~~i~I~I~~~rP~---~iIG~~g~~i~~l----~~~L~k~~~~~~~~v~ 85 (240)
|||-+...+.+. -| ..|+|..- ...|...||+.|++ +|||++|+.|+++ +..|++.|+ .+|.
T Consensus 240 iRe~~~~~~~~EiP~~~~v~i~~~~~~~~~~~~i~~~i~v~~~sqk~iiiG~~g~~ik~i~~~ar~~le~~~~---~~v~ 316 (339)
T PRK15494 240 TREQLFLNLQKELPYKLTVQTEKWEDLKDKSVKINQVIVVSRESYKTIILGKNGSKIKEIGAKSRMQMERFFG---FPVH 316 (339)
T ss_pred HHHHHHhhCCcccCceEEEEEEEEEEcCCCeEEEEEEEEECCCCceeEEEcCCcHHHHHHHHHHHHHHHHHhC---CCeE
Confidence 777777666542 11 12333321 22577899999987 6999999999765 667888888 4666
Q ss_pred EEE
Q 026316 86 LYA 88 (240)
Q Consensus 86 I~v 88 (240)
+.+
T Consensus 317 l~l 319 (339)
T PRK15494 317 LFL 319 (339)
T ss_pred EEE
Confidence 553
No 28
>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=84.61 E-value=1.6 Score=36.74 Aligned_cols=62 Identities=16% Similarity=0.296 Sum_probs=45.6
Q ss_pred hHH-HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEe--cccceeecCCcccHHHHHHHHHHHhCC
Q 026316 18 FAE-LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRA--TRTQNVLGEKGRRIRELTSVVQKRFKF 79 (240)
Q Consensus 18 y~~-Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~--~rP~~iIG~~g~~i~~l~~~L~k~~~~ 79 (240)
|++ +.+|+.+.|.-|.+.+|.+.-.+.....++.+ ..-+..||++|++++.....+...++.
T Consensus 71 ys~D~~~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 71 YSENLEEFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred cCCCHHHHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 543 89999999999999999875532333333444 345579999999999888888777764
No 29
>PRK00089 era GTPase Era; Reviewed
Probab=84.43 E-value=4.7 Score=36.10 Aligned_cols=65 Identities=28% Similarity=0.402 Sum_probs=42.2
Q ss_pred HHHHHHhhhccC-Cee-eeEEE---E-cCCeEEEEEEecccc---eeecCCcccHHHH----HHHHHHHhCCCCCeeEEE
Q 026316 21 LNEVLTRELAED-GYS-GVEVR---V-TPVRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVELY 87 (240)
Q Consensus 21 Ire~l~k~~~~a-gis-~IeI~---r-t~~~i~I~I~~~rP~---~iIG~~g~~i~~l----~~~L~k~~~~~~~~v~I~ 87 (240)
|||-+...|.+. -|+ .++|+ . ....|.-.|++.++. +|||++|+.|+++ +..|++.|+ .+|.+.
T Consensus 195 iRe~~~~~l~~e~p~~~~v~~~~~~~~~~~~i~~~i~v~~~~~k~i~ig~~g~~i~~i~~~ar~~l~~~~~---~~v~l~ 271 (292)
T PRK00089 195 IREKLLRLLGDELPYSVAVEIEKFEERGLVRIEATIYVERDSQKGIIIGKGGAMLKKIGTEARKDIEKLLG---KKVFLE 271 (292)
T ss_pred HHHHHHhhCCccCCceEEEEEEEEEECCeEEEEEEEEEccCCceeEEEeCCcHHHHHHHHHHHHHHHHHhC---CCEEEE
Confidence 577766666432 221 12222 1 234577889999886 7999999999765 567888887 466655
Q ss_pred E
Q 026316 88 A 88 (240)
Q Consensus 88 v 88 (240)
+
T Consensus 272 l 272 (292)
T PRK00089 272 L 272 (292)
T ss_pred E
Confidence 3
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=81.49 E-value=9.5 Score=38.92 Aligned_cols=91 Identities=22% Similarity=0.252 Sum_probs=54.7
Q ss_pred HHHHHhhh-ccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHH
Q 026316 22 NEVLTREL-AEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIA 100 (240)
Q Consensus 22 re~l~k~~-~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~~v~~p~~~a~~ 100 (240)
++.+.+.. .+||++. |....+.-+|+|++.+||++||++|+.++++..... +...-+..|-+....
T Consensus 78 ~~~I~eivP~ea~i~~--i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~tg-----------W~p~ivR~PPi~S~t 144 (637)
T COG1782 78 RKIILEIVPEEAGITD--IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAETG-----------WAPKIVRTPPIQSRT 144 (637)
T ss_pred HHHHHHhCccccCcee--EEecCCCceEEEEecCCceEEecCchHHHHHHHHhC-----------CcceeeecCCCchhh
Confidence 33344333 2478876 666788889999999999999999987776654432 223335566565555
Q ss_pred HHHHHHHHHhcCc-hhHHHHHHHHHHH
Q 026316 101 QAESLRYKLLGGL-AVRRACYGVLRFI 126 (240)
Q Consensus 101 iA~~ia~~Le~~~-~fRra~~~~l~~~ 126 (240)
+ ++|+.-|.+-. .-|+++++.=+++
T Consensus 145 i-~~ir~~l~~~~~eR~~iL~~vg~rI 170 (637)
T COG1782 145 I-KSIREILRSERKERREILRNVGRRI 170 (637)
T ss_pred H-HHHHHHHHHhHHHHHHHHHHHHHHh
Confidence 4 34444444332 2233444433444
No 31
>COG1159 Era GTPase [General function prediction only]
Probab=76.39 E-value=16 Score=34.45 Aligned_cols=71 Identities=23% Similarity=0.277 Sum_probs=45.3
Q ss_pred HHHHHHhhhccC--CeeeeEEEEc------CCeEEEEEEecccc---eeecCCcccHHHH----HHHHHHHhCCCCCeeE
Q 026316 21 LNEVLTRELAED--GYSGVEVRVT------PVRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (240)
Q Consensus 21 Ire~l~k~~~~a--gis~IeI~rt------~~~i~I~I~~~rP~---~iIG~~g~~i~~l----~~~L~k~~~~~~~~v~ 85 (240)
|||=+-..+.+. -...|+|.+. ...+.-.||++|-+ ++||++|+.|+++ +..|++.|+ .+|.
T Consensus 196 iREk~~~~l~eElPhsv~VeIe~~~~~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~---~kV~ 272 (298)
T COG1159 196 IREKLLLLLREELPHSVAVEIEEFEEREKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLG---CKVY 272 (298)
T ss_pred HHHHHHHhcccccCceEEEEEEEEEecCCCeEEEEEEEEEecCCccceEECCCcHHHHHHHHHHHHHHHHHhC---CceE
Confidence 566554444331 1234666543 24677788988765 7999999999765 678888998 4666
Q ss_pred EEE-EEecCC
Q 026316 86 LYA-EKVNNR 94 (240)
Q Consensus 86 I~v-~~v~~p 94 (240)
+.+ ++|++.
T Consensus 273 L~L~VKVk~~ 282 (298)
T COG1159 273 LELWVKVKKN 282 (298)
T ss_pred EEEEEEEccc
Confidence 553 345544
No 32
>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=74.04 E-value=24 Score=36.20 Aligned_cols=84 Identities=21% Similarity=0.279 Sum_probs=54.1
Q ss_pred HHHHHHhhhc-cCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChH
Q 026316 21 LNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI 99 (240)
Q Consensus 21 Ire~l~k~~~-~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~~v~~p~~~a~ 99 (240)
-++.|.+... +||+.+ |...++.=+|+|.+.+||.+||++|..++++.... | +...-+..|-+...
T Consensus 71 ~~~~i~~~~~~~~~~~~--~~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~~----~-------w~~~~~~~~~~~~~ 137 (630)
T TIGR03675 71 AIEKIKEIVPEEAGITD--IYFDDVTGEVIIEAEKPGLVIGKGGSTLREITAET----G-------WTPKVVRTPPIESK 137 (630)
T ss_pred HHHHHHHhCCCcCCcee--EEecCCCceEEEEEcCCeEEEecCcchHHHHHHHh----C-------CeeeEEecCCCCcH
Confidence 4455555443 478764 55667778999999999999999998877765443 2 23344566767666
Q ss_pred HHHHHHHHHHhcCchhHHH
Q 026316 100 AQAESLRYKLLGGLAVRRA 118 (240)
Q Consensus 100 ~iA~~ia~~Le~~~~fRra 118 (240)
.+ +.|++.|.+....|+-
T Consensus 138 ~~-~~~~~~~~~~~~~r~~ 155 (630)
T TIGR03675 138 TI-KNIREYLRSESEERKE 155 (630)
T ss_pred HH-HHHHHHHHHhHHHHHH
Confidence 55 4455555544444443
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=70.45 E-value=4.5 Score=28.76 Aligned_cols=28 Identities=18% Similarity=0.455 Sum_probs=21.0
Q ss_pred EEEEEEecccceeecCCcccHHHHHHHH
Q 026316 46 TEIIIRATRTQNVLGEKGRRIRELTSVV 73 (240)
Q Consensus 46 i~I~I~~~rP~~iIG~~g~~i~~l~~~L 73 (240)
..+.|-..+-+.+||++|+.+++|++.-
T Consensus 4 ~~i~Ip~~~ig~iIGkgG~~ik~I~~~t 31 (61)
T cd02393 4 ETMKIPPDKIRDVIGPGGKTIKKIIEET 31 (61)
T ss_pred EEEEeChhheeeeECCCchHHHHHHHHH
Confidence 4455666677889999999988876644
No 34
>PF13014 KH_3: KH domain
Probab=65.32 E-value=5.3 Score=26.12 Aligned_cols=17 Identities=24% Similarity=0.575 Sum_probs=14.1
Q ss_pred ceeecCCcccHHHHHHH
Q 026316 56 QNVLGEKGRRIRELTSV 72 (240)
Q Consensus 56 ~~iIG~~g~~i~~l~~~ 72 (240)
+.|||++|..|++|++.
T Consensus 3 g~iIG~~G~~I~~I~~~ 19 (43)
T PF13014_consen 3 GRIIGKGGSTIKEIREE 19 (43)
T ss_pred CeEECCCChHHHHHHHH
Confidence 57999999999887754
No 35
>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=60.87 E-value=10 Score=25.84 Aligned_cols=27 Identities=15% Similarity=0.473 Sum_probs=20.4
Q ss_pred EEEEEecccceeecCCcccHHHHHHHH
Q 026316 47 EIIIRATRTQNVLGEKGRRIRELTSVV 73 (240)
Q Consensus 47 ~I~I~~~rP~~iIG~~g~~i~~l~~~L 73 (240)
++.|-...-+.+||++|+.+++|++.-
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s 29 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREET 29 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHH
Confidence 344555666789999999998887764
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=53.47 E-value=12 Score=26.45 Aligned_cols=26 Identities=15% Similarity=0.549 Sum_probs=19.4
Q ss_pred EEEEEecccceeecCCcccHHHHHHH
Q 026316 47 EIIIRATRTQNVLGEKGRRIRELTSV 72 (240)
Q Consensus 47 ~I~I~~~rP~~iIG~~g~~i~~l~~~ 72 (240)
++.|-...-+.+||++|..+++|++.
T Consensus 3 r~~ip~~~vg~iIG~~G~~i~~i~~~ 28 (65)
T cd02396 3 RLLVPSSQAGSIIGKGGSTIKEIREE 28 (65)
T ss_pred EEEECHHHcCeeECCCcHHHHHHHHH
Confidence 34444555678999999999888766
No 37
>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=50.62 E-value=1.1e+02 Score=28.26 Aligned_cols=53 Identities=25% Similarity=0.272 Sum_probs=37.3
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCC
Q 026316 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (240)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~ 79 (240)
++.+++.......++..+-|-.|.|+++|++++..+. ...+.+.+.|...++.
T Consensus 25 ~~~~~l~~l~~~~~~~e~viLsTCNR~EiY~~~~~~~-------~~~~~~~~~l~~~~~~ 77 (311)
T cd05213 25 ELKEALRRLLEKPGISEAVLLSTCNRVELYLVGDNFH-------KLADELEELLAELLNE 77 (311)
T ss_pred HHHHHHHHHhcCCCCceEEEEecCCeEEEEEEeCCcc-------hhHHHHHHHHHHhcCc
Confidence 3566776666667889999999999999998875543 2234556666666553
No 38
>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=49.99 E-value=5.7 Score=27.35 Aligned_cols=27 Identities=22% Similarity=0.476 Sum_probs=20.0
Q ss_pred EEEEEecccceeecCCcccHHHHHHHH
Q 026316 47 EIIIRATRTQNVLGEKGRRIRELTSVV 73 (240)
Q Consensus 47 ~I~I~~~rP~~iIG~~g~~i~~l~~~L 73 (240)
.+.|-...-+.|||++|+.+++|++.-
T Consensus 3 ~i~vp~~~~~~iIG~~G~~i~~I~~~t 29 (60)
T PF00013_consen 3 RIEVPSSLVGRIIGKKGSNIKEIEEET 29 (60)
T ss_dssp EEEEEHHHHHHHHTGGGHHHHHHHHHH
T ss_pred EEEECHHHcCEEECCCCCcHHHhhhhc
Confidence 445555666789999999998876654
No 39
>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=49.70 E-value=62 Score=27.74 Aligned_cols=71 Identities=18% Similarity=0.194 Sum_probs=47.8
Q ss_pred ceeeEeecCcchHH---HHHHHH---hhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCC
Q 026316 7 KKRKFVADGVFFAE---LNEVLT---RELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP 80 (240)
Q Consensus 7 ~~~kwia~~~~y~~---Ire~l~---k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~ 80 (240)
..-.||-+.....+ =+.||+ +.+.+.||. ..++.++|-+.+|.+ +..+.++++.|.+.++.+
T Consensus 55 DIG~~Fp~~d~~~k~~~S~~lL~~~~~~~~~~g~~-------i~niD~tii~e~PKi-----~p~~~~m~~~ls~~L~~~ 122 (153)
T cd00554 55 DIGEHFPDTDPKWKGADSRILLEEALKLIREKGYE-------IVNIDITIIAERPKI-----SPYREAMRANLAELLGIP 122 (153)
T ss_pred cccccCCCCChhhCCCCHHHHHHHHHHHHHHcCCE-------EEEEEEEEEecCCcc-----hHHHHHHHHHHHHHhCCC
Confidence 34457766543222 233333 244566664 346778899999977 678899999999999987
Q ss_pred CCeeEEEEE
Q 026316 81 ENSVELYAE 89 (240)
Q Consensus 81 ~~~v~I~v~ 89 (240)
..+|.|...
T Consensus 123 ~~~V~iKat 131 (153)
T cd00554 123 PSRVNIKAT 131 (153)
T ss_pred CceEEEEEe
Confidence 677776654
No 40
>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=48.34 E-value=14 Score=25.58 Aligned_cols=25 Identities=24% Similarity=0.401 Sum_probs=18.6
Q ss_pred EEEecccceeecCCcccHHHHHHHH
Q 026316 49 IIRATRTQNVLGEKGRRIRELTSVV 73 (240)
Q Consensus 49 ~I~~~rP~~iIG~~g~~i~~l~~~L 73 (240)
.|=...-+.+||++|+.+++|++.-
T Consensus 5 ~Vp~~~~~~iIG~~G~~i~~i~~~~ 29 (62)
T cd02394 5 EIPKKLHRFIIGKKGSNIRKIMEET 29 (62)
T ss_pred EeCHHHhhhccCCCCCcHHHHHHHh
Confidence 3334455689999999999887754
No 41
>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=41.95 E-value=94 Score=26.74 Aligned_cols=70 Identities=21% Similarity=0.184 Sum_probs=46.6
Q ss_pred eeeEeecCcchHH---HHHHHHh---hhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCC
Q 026316 8 KRKFVADGVFFAE---LNEVLTR---ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPE 81 (240)
Q Consensus 8 ~~kwia~~~~y~~---Ire~l~k---~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~ 81 (240)
.-.||-+.....+ =+.||++ .+.+.||. ..++.++|-+.+|.+ +....++++.|.+.++.+.
T Consensus 56 IG~~Fpdtd~~~k~~~S~~lL~~~~~~~~~~g~~-------i~niD~tii~e~PKi-----~p~~~~m~~~la~~L~~~~ 123 (155)
T TIGR00151 56 IGKHFPDTDPRWKGADSRVLLRHAVALIKEKGYR-------IGNVDITIIAQRPKL-----LPHIPAMRENIAELLGIPL 123 (155)
T ss_pred CcccCCCCChhhCCCCHHHHHHHHHHHHHHcCCE-------EEEEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCc
Confidence 4456766533322 2333333 44556664 246777888999977 6788999999999999876
Q ss_pred CeeEEEEE
Q 026316 82 NSVELYAE 89 (240)
Q Consensus 82 ~~v~I~v~ 89 (240)
.+|.|.+.
T Consensus 124 ~~V~iKat 131 (155)
T TIGR00151 124 DSVNVKAT 131 (155)
T ss_pred ceEEEEEe
Confidence 67776654
No 42
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=39.25 E-value=66 Score=27.91 Aligned_cols=31 Identities=10% Similarity=0.203 Sum_probs=24.7
Q ss_pred CCeEEEEEEecccceeecCCcccHHHHHHHHH
Q 026316 43 PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 43 ~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~ 74 (240)
.+++-+.+.... |.-||++|+.++.|++.|.
T Consensus 60 ddrvIfvV~~gd-g~aIGk~G~~ik~l~~~lg 90 (166)
T PRK06418 60 DDLVILLVTSGP-RIPIGKGGKIAKALSRKLG 90 (166)
T ss_pred CCEEEEEEeCCC-cccccccchHHHHHHHHhC
Confidence 577777777777 8899999999888777665
No 43
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=39.24 E-value=23 Score=26.18 Aligned_cols=32 Identities=22% Similarity=0.499 Sum_probs=25.2
Q ss_pred CCeEEEEEEecc-----cceeecCCcccHHHHHHHHH
Q 026316 43 PVRTEIIIRATR-----TQNVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 43 ~~~i~I~I~~~r-----P~~iIG~~g~~i~~l~~~L~ 74 (240)
.+++.|.++... -|..+|.+|.+++.+.+.|.
T Consensus 2 G~r~kvaV~~~~~~~d~vG~~iG~~G~rik~i~~~L~ 38 (69)
T PF13184_consen 2 GNRTKVAVKSGDPNIDPVGACIGKKGSRIKAISEELN 38 (69)
T ss_dssp TTEEEEEEEESSTTS-HHHHHH-CCCCCHHHHHHHTT
T ss_pred CceEEEEEEcCCCCcCcceecCccccHHHHHHHHHhC
Confidence 357788888877 45799999999999888874
No 44
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=38.66 E-value=42 Score=33.48 Aligned_cols=57 Identities=12% Similarity=0.306 Sum_probs=43.5
Q ss_pred chHH-HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHH
Q 026316 17 FFAE-LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (240)
Q Consensus 17 ~y~~-Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L 73 (240)
.|+. ..+|+.+.|.-+.+.+|.+........|++--..-+..||++|++++......
T Consensus 274 ~~s~d~~~fi~nal~pa~v~~v~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l~ 331 (470)
T PRK09202 274 LWSDDPAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKLT 331 (470)
T ss_pred EcCCCHHHHHHHhCCCCEEEEEEEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHHH
Confidence 3443 78999999999999999776655666666666677789999999997655443
No 45
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=37.35 E-value=94 Score=26.96 Aligned_cols=65 Identities=20% Similarity=0.195 Sum_probs=46.8
Q ss_pred hHH-HHHHHHhhhccCCeeeeEEEEcCCeEEEE-EEecccc-eeecCCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026316 18 FAE-LNEVLTRELAEDGYSGVEVRVTPVRTEII-IRATRTQ-NVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (240)
Q Consensus 18 y~~-Ire~l~k~~~~agis~IeI~rt~~~i~I~-I~~~rP~-~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (240)
|++ +.+|+.+.|.-|.+.++.+.-.+++...+ +++.+-. .-+ ...++.+...+++++| +.+.+.+
T Consensus 98 ~s~d~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~~Dk~~l---~~k~e~~~~v~~kltg---k~v~~~f 165 (166)
T PRK06418 98 KTNDIKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSRRDRRRL---PAKPELLESILSKITG---TEVKIRV 165 (166)
T ss_pred cCCCHHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECHHHhhcc---cccHHHHHHHHHHHHC---CcEEEEe
Confidence 555 99999999999999999888777765444 6664321 122 4567899999999998 4565543
No 46
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=36.81 E-value=1e+02 Score=29.76 Aligned_cols=54 Identities=24% Similarity=0.402 Sum_probs=41.4
Q ss_pred HHHHHHhhhccCCeeeeE---EEEcC-CeEEEEEEecccc-----eeecCCcccHHHHHHHHH
Q 026316 21 LNEVLTRELAEDGYSGVE---VRVTP-VRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 21 Ire~l~k~~~~agis~Ie---I~rt~-~~i~I~I~~~rP~-----~iIG~~g~~i~~l~~~L~ 74 (240)
+++.|+.+...-.=+-|+ |-|.| .+++|-+++..|+ ..+|.+|.+++.+.+.|.
T Consensus 204 v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~ 266 (362)
T PRK12327 204 VKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELK 266 (362)
T ss_pred HHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhC
Confidence 777777777764333344 45554 8999999999887 589999999999988884
No 47
>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=36.44 E-value=1.1e+02 Score=29.30 Aligned_cols=54 Identities=26% Similarity=0.446 Sum_probs=41.3
Q ss_pred HHHHHHhhhccCCeeeeE---EEEcC-CeEEEEEEecccc-----eeecCCcccHHHHHHHHH
Q 026316 21 LNEVLTRELAEDGYSGVE---VRVTP-VRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 21 Ire~l~k~~~~agis~Ie---I~rt~-~~i~I~I~~~rP~-----~iIG~~g~~i~~l~~~L~ 74 (240)
+++.|+.+..+-.=+-|+ |-|-| .+++|-+++..|+ ..+|.+|.+++.+.+.|.
T Consensus 202 v~~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ 264 (341)
T TIGR01953 202 VKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELN 264 (341)
T ss_pred HHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhC
Confidence 777777777764323344 45654 8999999999887 589999999999988884
No 48
>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=33.69 E-value=74 Score=26.05 Aligned_cols=35 Identities=11% Similarity=0.212 Sum_probs=27.7
Q ss_pred chHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEec
Q 026316 17 FFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRAT 53 (240)
Q Consensus 17 ~y~~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~ 53 (240)
+..+|..||.+.+...||. |-|+| ++...|+..+.
T Consensus 3 ~k~~ikpwlq~~~~~~Gi~-iVIer-Sd~~ki~FkCk 37 (111)
T PF08731_consen 3 DKDEIKPWLQKIFYPQGIG-IVIER-SDKKKIVFKCK 37 (111)
T ss_pred chHHHHHHHHHHhhhcCce-EEEEe-cCCceEEEEEe
Confidence 4578999999999999988 77999 66677765553
No 49
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=31.51 E-value=59 Score=30.94 Aligned_cols=80 Identities=15% Similarity=0.234 Sum_probs=44.0
Q ss_pred EEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHhcCchhHHHH
Q 026316 40 RVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRAC 119 (240)
Q Consensus 40 ~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRra~ 119 (240)
+|....+.|-+....-|.|||++|++|+.|+....-....++.+--=.+.-|..-.-..--+-..|--.||.+...+.-|
T Consensus 44 k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f~~~~pc 123 (390)
T KOG2192|consen 44 KRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGFQLPSPC 123 (390)
T ss_pred hhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCCCCCCch
Confidence 34344566677778889999999999999887654332222110000111121111122234456666778777655555
No 50
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=31.46 E-value=1e+02 Score=25.59 Aligned_cols=41 Identities=10% Similarity=0.216 Sum_probs=29.6
Q ss_pred cCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHH
Q 026316 31 EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (240)
Q Consensus 31 ~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L 73 (240)
++..-+|-+ ..+++.+.+.....|..+|++|++++.+++.+
T Consensus 21 ~~~~~dc~~--d~~~vi~vV~~~~vG~~IG~~G~rI~~i~e~l 61 (140)
T PRK08406 21 GATVKDCII--DDDRIIFVVKEGDMGLAIGKGGENVKRLEEKL 61 (140)
T ss_pred CCCceEEEE--eCCEEEEEEeCCCccccCCcCchHHHHHHHHh
Confidence 344444433 23788888888888999999999999985544
No 51
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=30.33 E-value=90 Score=30.45 Aligned_cols=53 Identities=17% Similarity=0.268 Sum_probs=37.4
Q ss_pred chHH-HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHH
Q 026316 17 FFAE-LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIREL 69 (240)
Q Consensus 17 ~y~~-Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l 69 (240)
.|+. ..+|+.+.|.-|.+.+|.+........+++--..-+..||++|++++.-
T Consensus 280 ~~s~D~~~fI~Nal~Pa~V~~V~i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA 333 (374)
T PRK12328 280 EYSNVPEIFIARALAPAIISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRLA 333 (374)
T ss_pred EcCCCHHHHHHHhCCCceeeEEEEcCCCcEEEEEEChHHhhhhhcCCChhHHHH
Confidence 3443 8899999999998888877633344444444445567999999998643
No 52
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=29.47 E-value=72 Score=30.78 Aligned_cols=55 Identities=16% Similarity=0.186 Sum_probs=38.0
Q ss_pred chHH-HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEe--cccceeecCCcccHHHHHHH
Q 026316 17 FFAE-LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRA--TRTQNVLGEKGRRIRELTSV 72 (240)
Q Consensus 17 ~y~~-Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~--~rP~~iIG~~g~~i~~l~~~ 72 (240)
.|++ ..+|+.+.|.-|.+.+|.+.. +..-.+++++ ..-+..||++|++++.-...
T Consensus 274 ~~s~d~~~fi~nal~Pa~v~~v~i~~-~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~~L 331 (362)
T PRK12327 274 DWSEDPAEFVANALSPAKVVSVEVDD-EEEKAARVVVPDYQLSLAIGKEGQNARLAARL 331 (362)
T ss_pred EcCCCHHHHHHHhCCCceEEEEEEEc-CCCcEEEEEEChhhcchhhcCCChhHHHHHHH
Confidence 4554 889999999999999997743 3323344444 44557999999998654433
No 53
>PLN02862 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Probab=29.16 E-value=1.7e+02 Score=26.55 Aligned_cols=70 Identities=14% Similarity=0.080 Sum_probs=46.0
Q ss_pred eeeEeecCcchHH---HHHHHHh---hhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCC
Q 026316 8 KRKFVADGVFFAE---LNEVLTR---ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPE 81 (240)
Q Consensus 8 ~~kwia~~~~y~~---Ire~l~k---~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~ 81 (240)
.-.||-+.....+ =+.||++ .+.+.||. ..++.++|-+.+|.+ +..+.++++.|.+.++.+.
T Consensus 116 IG~~FPdtd~~~Kg~~S~~lL~~a~~ll~~~G~~-------I~NvD~tII~q~PKi-----~p~~~~m~~~La~lL~i~~ 183 (216)
T PLN02862 116 IGQIFPDTDPKWKGADSSVFIKEAVRLMHEAGYE-------IGNLDATLILQRPKL-----SPHKEAIRSNLSKLLGADP 183 (216)
T ss_pred ccccCCCCChhhCCCCHHHHHHHHHHHHHHcCCE-------EEEEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCc
Confidence 4456765543322 2333332 44566764 236777888999977 6788999999999999876
Q ss_pred CeeEEEEE
Q 026316 82 NSVELYAE 89 (240)
Q Consensus 82 ~~v~I~v~ 89 (240)
.+|.|...
T Consensus 184 ~~VnIKAt 191 (216)
T PLN02862 184 SVVNLKAK 191 (216)
T ss_pred ceEEEEEe
Confidence 66666543
No 54
>PF05316 VAR1: Mitochondrial ribosomal protein (VAR1); InterPro: IPR007980 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 [, ]. This family consists of the VAR1 mitochondrial ribosomal proteins found in yeast. Mitochondria possess their own ribosomes responsible for the synthesis of a small number of proteins encoded by the mitochondrial genome. VAR1 is the only protein in the yeast mitochondrial ribosome to be encoded in the mitochondria - the remaining approximately 80 ribosomal proteins are encoded in the nucleus []. VAR1 along with 15S rRNA are necessary for the formation of mature 37S subunits [].; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005761 mitochondrial ribosome
Probab=29.02 E-value=31 Score=33.29 Aligned_cols=129 Identities=13% Similarity=0.206 Sum_probs=78.1
Q ss_pred cHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHH-HHHHh---cCc--hhHHHHHHHHH----------HH--
Q 026316 65 RIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESL-RYKLL---GGL--AVRRACYGVLR----------FI-- 126 (240)
Q Consensus 65 ~i~~l~~~L~k~~~~~~~~v~I~v~~v~~p~~~a~~iA~~i-a~~Le---~~~--~fRra~~~~l~----------~~-- 126 (240)
....|...|...++ ++|.|.+.+++=++++..++.++| ...+. ++. .|+|.+...+. .+
T Consensus 156 n~n~LsniLS~yyN---KkV~I~PIkLkY~Y~NsdIlsk~I~~~d~~k~n~~i~~~y~k~L~n~mp~lN~~~I~~nyI~n 232 (350)
T PF05316_consen 156 NYNNLSNILSYYYN---KKVTIEPIKLKYPYNNSDILSKYISINDMNKYNNGISMNYQKNLNNNMPKLNDKNISMNYINN 232 (350)
T ss_pred hHHHHHHHHHHHhc---CceEEEEeEEeeeeccHHHHHHHHHHhhhHhhcchhhHHHHHHHHhhccccchhhHHHHHHHH
Confidence 45677888888885 799999999999999999999999 33333 222 23333322111 00
Q ss_pred ----HH---hCC-------------------c-----ceeeeeeeceeEEEccccccceeee--EEeeecee----eecC
Q 026316 127 ----ME---SGA-------------------K-----GCEFNFLVSSKVIVSGKLRAQRAKS--MKFKDGYM----ISSG 169 (240)
Q Consensus 127 ----m~---~ga-------------------k-----Gik~~~~~~~~I~iSGRL~G~rArt--e~~~~G~v----l~tG 169 (240)
.. ... . =..|--||+..++.+||+.-...|| ..+..|.. ..-|
T Consensus 233 inn~n~~kyNnii~nnnN~~ni~niyn~~nin~i~~n~L~~KyLvG~si~~kGrl~~~~~Rs~~~~l~~Gtf~N~~y~~~ 312 (350)
T PF05316_consen 233 INNINNIKYNNIILNNNNNKNINNIYNSLNINNIPMNLLMYKYLVGWSILFKGRLLNNISRSNKYNLLKGTFNNKLYNWG 312 (350)
T ss_pred HhhhhhhhhhhhhccccchhHHHHHHhhcccccchHHHHHHhhhheeEEEEeeeeccccchhhhhhhhhcchhhHHHHhh
Confidence 00 000 0 0112345555599999999874444 44445654 1111
Q ss_pred c--------ccccceeEEEEEEecCCeeeeEEEEE
Q 026316 170 Q--------PVNEYIDSAVRHVLLRQGVLGIKVKI 196 (240)
Q Consensus 170 ~--------~~~~~Idya~~~a~t~~GvlGIKVwI 196 (240)
. -...+.+...-.-.++.|.+||||..
T Consensus 313 n~~n~ykLNyi~~n~~i~~~s~inknGKynIkvkL 347 (350)
T PF05316_consen 313 NINNNYKLNYIPSNHNIYNNSNINKNGKYNIKVKL 347 (350)
T ss_pred hcccceeecccCCcceeccccccccCceeeeEEEE
Confidence 1 03445555555567899999999986
No 55
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=29.00 E-value=55 Score=33.40 Aligned_cols=53 Identities=26% Similarity=0.399 Sum_probs=34.5
Q ss_pred chHHHHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeecCCcccHHHHHHHH
Q 026316 17 FFAELNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (240)
Q Consensus 17 ~y~~Ire~l~k~~~~agis~IeI~rt-~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L 73 (240)
-+.+|.+++.+.+.. .++++.. +....|.+.-..-+.+||++|++|++|.+.|
T Consensus 462 a~~~i~~~i~r~~p~----~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~kl 515 (604)
T COG1855 462 AEEEIEREIKRYLPG----DVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKL 515 (604)
T ss_pred HHHHHHHHHHHhCCC----CceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHh
Confidence 344577777777765 4555555 3455555444455679999999998876544
No 56
>PRK13764 ATPase; Provisional
Probab=28.95 E-value=89 Score=32.24 Aligned_cols=51 Identities=24% Similarity=0.434 Sum_probs=32.5
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHH
Q 026316 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (240)
Q Consensus 20 ~Ire~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L 73 (240)
+|.+.+.+.+ .|...+++. ..+...|++--.--..+||++|.+|+++.+.|
T Consensus 460 ~~~~~~~~~~--~~~~~~~~~-~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~ 510 (602)
T PRK13764 460 EIEREIKRYL--PGPVEVEVV-SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKL 510 (602)
T ss_pred HHHHHHHHhc--CCceEEEEe-cCCeEEEEEChhhhhHHhccCcchHHHHHHHh
Confidence 4666666666 556666666 34455444433344569999999998866554
No 57
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=28.56 E-value=1.3e+02 Score=29.33 Aligned_cols=54 Identities=22% Similarity=0.310 Sum_probs=41.6
Q ss_pred HHHHHHhhhccCCeeeeE---EEEcC-CeEEEEEEecccc-----eeecCCcccHHHHHHHHH
Q 026316 21 LNEVLTRELAEDGYSGVE---VRVTP-VRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 21 Ire~l~k~~~~agis~Ie---I~rt~-~~i~I~I~~~rP~-----~iIG~~g~~i~~l~~~L~ 74 (240)
+++.|+.+..+-.=+-|+ |-|.| .+++|-+++..|+ ..+|.+|.+|+.+.+.|.
T Consensus 210 v~~Lfe~EVPEI~dG~VeIk~IARepG~RtKVAV~S~d~~iDPvGacIG~~G~rI~~I~~eL~ 272 (374)
T PRK12328 210 LEALLELEVPEIKDGEVIIIHSARIPGERAKVALFSNNPNIDPIGATVGVKGVRINAVSKELN 272 (374)
T ss_pred HHHHHHHhCccccCCeEEEEEEeccCcceeEEEEEcCCCCCChHHhhcCCCcchHHHHHHHhC
Confidence 788888877764333344 45554 7999999999887 589999999999888884
No 58
>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=28.26 E-value=76 Score=30.33 Aligned_cols=53 Identities=17% Similarity=0.281 Sum_probs=37.2
Q ss_pred chHH-HHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeecCCcccHHHH
Q 026316 17 FFAE-LNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIREL 69 (240)
Q Consensus 17 ~y~~-Ire~l~k~~~~agis~IeI~rt-~~~i~I~I~~~rP~~iIG~~g~~i~~l 69 (240)
.|++ ..+|+.+.|.-|.+.+|+|... .....|++--..-+..||++|++++.-
T Consensus 272 ~~s~d~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~la 326 (341)
T TIGR01953 272 EYSDDPAEFIANALSPAKVISVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRLA 326 (341)
T ss_pred EcCCCHHHHHHHhcCCceEEEEEEEcCCCcEEEEEEChHHcchhhcCCChhHHHH
Confidence 4554 8899999999999999977443 234444443345557999999998643
No 59
>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=26.98 E-value=46 Score=28.36 Aligned_cols=57 Identities=14% Similarity=0.257 Sum_probs=37.2
Q ss_pred cccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEE----EEe--cCCCcChHHHHHHHHHHHhcCchhH
Q 026316 53 TRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA----EKV--NNRGLCAIAQAESLRYKLLGGLAVR 116 (240)
Q Consensus 53 ~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v----~~v--~~p~~~a~~iA~~ia~~Le~~~~fR 116 (240)
.+-+.+||++|+.+++|++...- +++++- ..| ..++..+..-|..+-..|-++..+.
T Consensus 7 ~kig~vIG~gG~~Ik~I~~~tgv-------~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e 69 (172)
T TIGR03665 7 DRIGVLIGKGGETKKEIEERTGV-------KLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE 69 (172)
T ss_pred HHhhhHhCCchhHHHHHHHHhCc-------EEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH
Confidence 45567999999888887665442 333331 233 4566677788888888887765533
No 60
>PF12685 SpoIIIAH: SpoIIIAH-like protein; InterPro: IPR024232 Stage III sporulation protein AH (SpoIIIAH) is a protein that is involved in forespore engulfment. It forms a channel with SpoIIIAH that is open on the forespore end and closed (or gated) on the mother cell end. This allows sigma-E-directed gene expression in the mother-cell compartment of the sporangium to trigger the activation of sigma-G forespore-specific gene expression by a pathway of intercellular signaling. This family of proteins is found in bacteria, archaea and eukaryotes and so must have a wider function than in sporulation. Proteins in this family are typically between 174 and 223 amino acids in length.; PDB: 3UZ0_A 3TUF_A.
Probab=25.91 E-value=2.8e+02 Score=23.99 Aligned_cols=57 Identities=12% Similarity=0.345 Sum_probs=40.4
Q ss_pred HHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEE
Q 026316 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (240)
Q Consensus 24 ~l~k~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I 86 (240)
.++..+...||..+-+.-..+.+.|++.+.. + ......++...+.+.+|.+..+|.|
T Consensus 139 ~iE~llkakGf~davv~~~~~~v~VvV~~~~----L--~~~~~~~I~diV~~~~~v~~~~I~V 195 (196)
T PF12685_consen 139 EIENLLKAKGFEDAVVFIEDDSVDVVVKADK----L--SDAEAAQIIDIVMRETGVPAENISV 195 (196)
T ss_dssp HHHHHHHTTS-SEEEEE-SSSEEEEEEE-S---------HHHHHHHHHHHHHHHC-STSEEEE
T ss_pred HHHHHHHhCCCCceEEEeeCCEEEEEEeCCC----C--CHHHHHHHHHHHHHHhCCCcCeEEe
Confidence 3455667789999999999999999888765 2 2457789999999999987666665
No 61
>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=25.48 E-value=1.3e+02 Score=25.29 Aligned_cols=44 Identities=9% Similarity=0.282 Sum_probs=28.1
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHH
Q 026316 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSV 72 (240)
Q Consensus 28 ~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~ 72 (240)
.+..+..-.|.+.-.. ++-..+.....|..+|++|++++.+++.
T Consensus 18 ~~t~~~~~dc~~d~~~-riifvV~~g~vG~~IG~~G~rIk~i~el 61 (141)
T TIGR01952 18 DMTGATVVDCLIDDRN-RVVFVVKEGEMGAAIGKGGENVKRLEEL 61 (141)
T ss_pred HHhCCceEEEEecCCc-EEEEEEcCCCccccCCCCchHHHHHHHh
Confidence 3344555555543322 5555555566778999999999998533
No 62
>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=25.45 E-value=1.8e+02 Score=25.13 Aligned_cols=50 Identities=26% Similarity=0.327 Sum_probs=38.0
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEE
Q 026316 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (240)
Q Consensus 28 ~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ 89 (240)
.+.+.||. ..++.++|-+.+|.+ +..+.++++.|.+.++.+..+|.|...
T Consensus 83 ~~~~~g~~-------i~niD~tii~e~PKi-----~p~~~~m~~~la~~L~~~~~~V~iKat 132 (157)
T PF02542_consen 83 LLREKGYR-------IVNIDITIIAERPKI-----SPYRPAMRENLAKLLGIPPDRVNIKAT 132 (157)
T ss_dssp HHHHTTEE-------EEEEEEEEESSSSTT-----GGGHHHHHHHHHHHHTS-GGGEEEEEE
T ss_pred HHHHcCcE-------EEEEEEEEEcCCCcc-----HHHHHHHHHHHHHHhCCCcceEEEEEe
Confidence 55667764 236778899999977 678999999999999987667776653
No 63
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=25.18 E-value=1.9e+02 Score=25.05 Aligned_cols=41 Identities=22% Similarity=0.330 Sum_probs=33.2
Q ss_pred CeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEE
Q 026316 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (240)
Q Consensus 44 ~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ 89 (240)
.++.++|-+.+|.+ +....++++.|.+.++.+..+|.|...
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 36777888999977 678899999999999987666776653
No 64
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=25.01 E-value=1.3e+02 Score=26.50 Aligned_cols=57 Identities=12% Similarity=0.260 Sum_probs=40.4
Q ss_pred hH-HHHHHHHhhhccCCeeeeEEEEcCC-eEEEEEEecccceeecCCcccHHHHHHHHH
Q 026316 18 FA-ELNEVLTRELAEDGYSGVEVRVTPV-RTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 18 y~-~Ire~l~k~~~~agis~IeI~rt~~-~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~ 74 (240)
|+ ...+|+.+.|.-+...+|.+.-... ...+.+.-..-+..||++|+.++..++...
T Consensus 114 ~s~d~~~fI~nal~Pa~v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~~Ltg 172 (190)
T COG0195 114 WSEDPAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLASQLTG 172 (190)
T ss_pred eCCCHHHHHHHhcCcceEeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHHHHhC
Confidence 44 3889999999999999888876423 444445555566899999988765554433
No 65
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=23.46 E-value=2e+02 Score=28.87 Aligned_cols=54 Identities=20% Similarity=0.345 Sum_probs=40.8
Q ss_pred HHHHHHhhhccC--CeeeeE-EEEc--------CCeEEEEEEecccc-----eeecCCcccHHHHHHHHH
Q 026316 21 LNEVLTRELAED--GYSGVE-VRVT--------PVRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 21 Ire~l~k~~~~a--gis~Ie-I~rt--------~~~i~I~I~~~rP~-----~iIG~~g~~i~~l~~~L~ 74 (240)
+.+.|+.+.... |+-.|. |-|. ..+++|-+++..|+ ..||.+|.+|+.+.+.|.
T Consensus 229 v~~Lfe~EVPEI~dG~VeIk~IAREa~~~~ripG~RtKVAV~S~d~~VDPvGacVG~kG~RI~~I~~eL~ 298 (449)
T PRK12329 229 VVYLFENEVPEIEEGVVRIVAVAREANPPSRYVGPRTKIAVDTLERDVDPVGACIGARGSRIQAVVNELR 298 (449)
T ss_pred HHHHHHhhCcccccCeEEEEEEEecCCCCCCCCcceeEEEEEcCCCCCChhhccCCCCcchHHHHHHHhC
Confidence 677777777654 433333 5564 47999999999887 589999999999988884
No 66
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=22.18 E-value=2.1e+02 Score=28.55 Aligned_cols=54 Identities=20% Similarity=0.446 Sum_probs=41.4
Q ss_pred HHHHHHhhhccCCeeeeE---EEEcC-CeEEEEEEecccc-----eeecCCcccHHHHHHHHH
Q 026316 21 LNEVLTRELAEDGYSGVE---VRVTP-VRTEIIIRATRTQ-----NVLGEKGRRIRELTSVVQ 74 (240)
Q Consensus 21 Ire~l~k~~~~agis~Ie---I~rt~-~~i~I~I~~~rP~-----~iIG~~g~~i~~l~~~L~ 74 (240)
+++.|+.+...-.=+-|+ |-|.| .+++|-+++..|. ..+|.+|.+|+.+.+.|.
T Consensus 204 l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ 266 (470)
T PRK09202 204 LKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELG 266 (470)
T ss_pred HHHHHHHhCcccccCeEEEEEEeecCcceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhC
Confidence 777777777764333344 45654 7999999998887 589999999999988884
No 67
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=22.17 E-value=3.6e+02 Score=24.95 Aligned_cols=60 Identities=13% Similarity=0.178 Sum_probs=45.3
Q ss_pred eEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHH
Q 026316 45 RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLR 106 (240)
Q Consensus 45 ~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~~v~~p~~~a~~iA~~ia 106 (240)
.+.+.|....--.+||.+|.+-..|-+.+..+++....++.|.=.++.. -+..-+|+.|.
T Consensus 19 ~isl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~~d~G~i~i~g~~~~~--~~s~~LAk~lS 78 (252)
T COG4604 19 DVSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKKDSGEITIDGLELTS--TPSKELAKKLS 78 (252)
T ss_pred cceeeecCCceeEEECCCCccHHHHHHHHHHhccccCceEEEeeeeccc--CChHHHHHHHH
Confidence 4555566666667999999999999999999999888888877666655 45556666554
No 68
>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=22.15 E-value=1.1e+02 Score=31.49 Aligned_cols=53 Identities=21% Similarity=0.342 Sum_probs=39.5
Q ss_pred HHHHHHHhhhc-cCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHh
Q 026316 20 ELNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRF 77 (240)
Q Consensus 20 ~Ire~l~k~~~-~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~ 77 (240)
+|++-+.+.+. ++.+++||.+- -+|.||+..|..+.. ++.-+++|.+.|+|+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~eg----p~~~~~~~~~~~~~~-~~~~~~~~~~~~~~r~ 56 (630)
T TIGR03675 3 EIKEIINELLPKDIKITDVEFEG----PELVIYTKNPELFAK-DDDLVKELAKKLRKRI 56 (630)
T ss_pred HHHHHHHHhCCCCCeEEEEEEeC----CeEEEEeCCHHHhcc-chHHHHHHHHHhhceE
Confidence 46666666775 67899998875 678999999998765 4466777777777754
No 69
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=21.61 E-value=1.5e+02 Score=22.03 Aligned_cols=32 Identities=19% Similarity=0.211 Sum_probs=26.2
Q ss_pred CcccHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026316 62 KGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (240)
Q Consensus 62 ~g~~i~~l~~~L~k~~~~~~~~v~I~v~~v~~ 93 (240)
|-+-++++++.+.+.+|.+...+.+-+.+++.
T Consensus 18 K~~la~~vT~~~~~~lg~~~~~i~Viieev~~ 49 (69)
T COG1942 18 KAELAAEVTEVTVETLGKDPSAIHVIIEEVPP 49 (69)
T ss_pred HHHHHHHHHHHHHHHhCCCcccEEEEEEecCh
Confidence 33456899999999999988888888888865
No 70
>PRK09382 ispDF bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional
Probab=20.54 E-value=2.8e+02 Score=26.63 Aligned_cols=49 Identities=16% Similarity=0.255 Sum_probs=37.5
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeecCCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026316 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (240)
Q Consensus 28 ~~~~agis~IeI~rt~~~i~I~I~~~rP~~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (240)
.+.+.||. ..++.++|-+.+|.+ +....++++.|.+.++++..+|+|..
T Consensus 300 ~~~~~~~~-------~~n~d~~i~~~~pk~-----~~~~~~~~~~~~~~l~~~~~~v~~ka 348 (378)
T PRK09382 300 FVREAGGE-------IINADVTIIAEAPKI-----GPHKQAMRENLAEILGIPKDRVSVKA 348 (378)
T ss_pred HHHHcCCE-------EEEEEEEEEecCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEE
Confidence 44556654 246778899999977 67889999999999998766676654
No 71
>smart00526 H15 Domain in histone families 1 and 5.
Probab=20.32 E-value=2.5e+02 Score=19.73 Aligned_cols=37 Identities=16% Similarity=0.029 Sum_probs=25.3
Q ss_pred CcChHHHHHHHHHHHh-cCchhHHHHHHHHHHHHHhCC
Q 026316 95 GLCAIAQAESLRYKLL-GGLAVRRACYGVLRFIMESGA 131 (240)
Q Consensus 95 ~~~a~~iA~~ia~~Le-~~~~fRra~~~~l~~~m~~ga 131 (240)
+.|...|..+|...-. ....|+..++.+|+...+.|.
T Consensus 23 GsS~~aI~kyi~~~~~~~~~~~~~~l~~~Lk~~v~~G~ 60 (66)
T smart00526 23 GSSLQAIKKYIEANYKVLPNNFRSLLKLALKKLVASGK 60 (66)
T ss_pred CCCHHHHHHHHHHhCCCChHHHHHHHHHHHHHHHhcCc
Confidence 5677788888877722 123577778888877777664
No 72
>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=20.25 E-value=1.7e+02 Score=19.91 Aligned_cols=30 Identities=10% Similarity=0.166 Sum_probs=24.3
Q ss_pred ccHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026316 64 RRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (240)
Q Consensus 64 ~~i~~l~~~L~k~~~~~~~~v~I~v~~v~~ 93 (240)
+-++.+.+.|...+|.+...+.+.+.++..
T Consensus 19 ~l~~~it~~l~~~lg~~~~~v~V~i~e~~~ 48 (63)
T TIGR00013 19 QLIEGVTEAMAETLGANLESIVVIIDEMPK 48 (63)
T ss_pred HHHHHHHHHHHHHhCCCcccEEEEEEEcCH
Confidence 446788888999999888888888887754
No 73
>PRK05090 hypothetical protein; Validated
Probab=20.01 E-value=4.4e+02 Score=20.73 Aligned_cols=38 Identities=16% Similarity=0.230 Sum_probs=26.9
Q ss_pred CcccHHHHHHHHHHHhCCCCCeeEEE--------EEEecCCCcChH
Q 026316 62 KGRRIRELTSVVQKRFKFPENSVELY--------AEKVNNRGLCAI 99 (240)
Q Consensus 62 ~g~~i~~l~~~L~k~~~~~~~~v~I~--------v~~v~~p~~~a~ 99 (240)
+|+-=++|...|.+.|+.+..+|+|. ...|..|.--+.
T Consensus 44 eGkAN~ali~~LAk~l~v~ks~I~i~~G~tsr~K~v~I~~~~~~~~ 89 (95)
T PRK05090 44 DGQANAHLLKFLAKQFRVAKSQVVIEKGELGRHKQVRIINPQQIPP 89 (95)
T ss_pred CChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEEEEcCcccChH
Confidence 35555899999999999887777764 555666654333
Done!