Query 026588
Match_columns 236
No_of_seqs 143 out of 1107
Neff 5.3
Searched_HMMs 46136
Date Fri Mar 29 09:58:22 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026588.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026588hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00084 40S ribosomal protein 100.0 1.2E-70 2.5E-75 482.5 20.0 213 4-216 4-216 (220)
2 COG0092 RpsC Ribosomal protein 100.0 3.8E-65 8.3E-70 448.4 19.6 198 5-217 5-211 (233)
3 PRK04191 rps3p 30S ribosomal p 100.0 7.2E-64 1.6E-68 436.4 21.0 203 5-218 1-203 (207)
4 TIGR01008 rpsC_E_A ribosomal p 100.0 1.6E-63 3.5E-68 430.7 22.1 195 7-212 1-195 (195)
5 CHL00048 rps3 ribosomal protei 100.0 5E-57 1.1E-61 395.2 23.1 184 6-192 17-213 (214)
6 TIGR01009 rpsC_bact ribosomal 100.0 5.7E-57 1.2E-61 394.1 21.4 181 6-192 17-206 (211)
7 PRK00310 rpsC 30S ribosomal pr 100.0 2E-56 4.4E-61 395.5 22.3 181 6-192 17-206 (232)
8 KOG3181 40S ribosomal protein 100.0 7.2E-51 1.6E-55 349.4 13.7 226 1-226 1-226 (244)
9 PF00189 Ribosomal_S3_C: Ribos 99.9 3.7E-27 7.9E-32 179.1 9.9 82 104-188 1-85 (85)
10 cd02412 30S_S3_KH K homology R 99.8 3.4E-20 7.3E-25 146.9 9.9 87 6-94 16-109 (109)
11 cd02413 40S_S3_KH K homology R 99.8 1.7E-19 3.7E-24 136.4 10.6 79 15-93 1-79 (81)
12 cd02411 archeal_30S_S3_KH K ho 99.7 1.3E-17 2.8E-22 126.6 8.3 85 7-93 1-85 (85)
13 PF07650 KH_2: KH domain syndr 99.4 2.5E-13 5.5E-18 100.5 7.2 77 20-96 1-78 (78)
14 cd02409 KH-II KH-II (K homolo 98.7 5.7E-08 1.2E-12 68.0 7.7 65 22-88 1-67 (68)
15 smart00322 KH K homology RNA-b 97.2 0.00038 8.3E-09 47.6 3.6 67 44-110 3-69 (69)
16 cd02414 jag_KH jag_K homology 96.9 0.0046 9.9E-08 45.8 7.0 56 23-78 2-58 (77)
17 PF13083 KH_4: KH domain; PDB: 96.4 0.0042 9.2E-08 45.3 4.0 68 20-87 3-72 (73)
18 PRK01064 hypothetical protein; 94.7 0.62 1.4E-05 35.2 10.0 69 22-90 5-76 (78)
19 COG1847 Jag Predicted RNA-bind 94.2 0.38 8.2E-06 42.7 9.2 106 19-124 65-185 (208)
20 PRK08406 transcription elongat 94.2 0.14 3E-06 42.5 6.2 60 20-79 73-134 (140)
21 cd02134 NusA_KH NusA_K homolog 93.8 0.2 4.4E-06 35.5 5.6 53 22-74 2-55 (61)
22 cd02410 archeal_CPSF_KH The ar 93.4 0.73 1.6E-05 38.8 9.0 85 21-119 54-139 (145)
23 PRK02821 hypothetical protein; 91.9 2.6 5.7E-05 31.7 9.4 67 21-90 5-74 (77)
24 PRK00468 hypothetical protein; 90.5 4.7 0.0001 30.1 9.6 68 21-88 4-74 (75)
25 COG1837 Predicted RNA-binding 87.2 6.4 0.00014 29.7 8.4 68 21-88 4-74 (76)
26 TIGR01952 nusA_arch NusA famil 86.6 1.2 2.7E-05 37.1 4.7 60 20-79 74-135 (141)
27 TIGR00436 era GTP-binding prot 84.3 4.2 9E-05 36.3 7.3 65 21-88 188-267 (270)
28 COG1159 Era GTPase [General fu 84.3 7.1 0.00015 36.5 8.9 74 21-97 196-285 (298)
29 PRK15494 era GTPase Era; Provi 82.9 4.6 0.0001 37.6 7.2 70 21-93 240-325 (339)
30 PRK00089 era GTPase Era; Revie 81.9 6.2 0.00014 35.2 7.4 64 21-87 195-271 (292)
31 PF05316 VAR1: Mitochondrial r 81.5 8.6 0.00019 36.7 8.4 122 65-189 156-348 (350)
32 COG1782 Predicted metal-depend 78.7 12 0.00026 37.8 8.7 77 22-112 78-155 (637)
33 cd02393 PNPase_KH Polynucleoti 69.0 4.8 0.0001 28.3 2.5 29 46-74 4-32 (61)
34 PF13014 KH_3: KH domain 66.7 4.6 0.0001 26.2 1.9 18 55-72 2-19 (43)
35 TIGR03675 arCOG00543 arCOG0054 64.8 47 0.001 34.0 9.6 108 21-142 71-183 (630)
36 cd00105 KH-I K homology RNA-bi 62.1 9 0.0002 26.0 2.8 27 47-73 3-29 (64)
37 PF00013 KH_1: KH domain syndr 55.4 4.6 0.0001 27.6 0.4 28 46-73 2-29 (60)
38 cd02396 PCBP_like_KH K homolog 53.5 12 0.00026 26.3 2.3 26 47-72 3-28 (65)
39 cd00554 MECDP_synthase MECDP_s 51.1 55 0.0012 27.8 6.2 50 28-89 82-131 (153)
40 cd02394 vigilin_like_KH K homo 50.9 12 0.00026 25.7 1.9 26 48-73 4-29 (62)
41 TIGR00151 ispF 2C-methyl-D-ery 43.8 80 0.0017 26.9 6.1 50 28-89 82-131 (155)
42 PRK09202 nusA transcription el 43.3 37 0.0008 33.6 4.6 52 21-72 279-330 (470)
43 KOG2192 PolyC-binding hnRNP-K 42.8 22 0.00047 33.3 2.8 76 43-118 47-122 (390)
44 cd05213 NAD_bind_Glutamyl_tRNA 42.6 2E+02 0.0043 26.3 9.1 51 21-78 26-76 (311)
45 PF13184 KH_5: NusA-like KH do 40.9 21 0.00046 26.0 2.0 32 43-74 2-38 (69)
46 PRK06418 transcription elongat 40.1 1E+02 0.0022 26.5 6.3 62 21-88 102-165 (166)
47 PRK12328 nusA transcription el 36.3 73 0.0016 30.8 5.3 63 21-90 285-347 (374)
48 PRK08406 transcription elongat 36.0 1.1E+02 0.0023 25.4 5.6 41 31-73 21-61 (140)
49 PRK06418 transcription elongat 35.6 80 0.0017 27.1 4.9 31 43-74 60-90 (166)
50 PF02542 YgbB: YgbB family; I 35.4 1.8E+02 0.004 24.8 7.1 49 28-88 83-131 (157)
51 TIGR03665 arCOG04150 arCOG0415 33.8 31 0.00066 29.3 2.1 58 52-116 6-69 (172)
52 COG0195 NusA Transcription elo 32.8 78 0.0017 27.7 4.5 62 20-88 117-179 (190)
53 PF08731 AFT: Transcription fa 32.8 82 0.0018 25.5 4.3 34 17-52 3-36 (111)
54 PRK00084 ispF 2-C-methyl-D-ery 32.3 2.1E+02 0.0046 24.5 6.9 40 44-88 94-133 (159)
55 COG1942 Uncharacterized protei 31.4 82 0.0018 23.1 3.8 46 48-93 4-49 (69)
56 PF12685 SpoIIIAH: SpoIIIAH-li 31.3 1.9E+02 0.0041 24.8 6.7 57 24-86 139-195 (196)
57 TIGR00013 taut 4-oxalocrotonat 31.1 87 0.0019 21.3 3.8 32 62-93 17-48 (63)
58 COG1855 ATPase (PilT family) [ 30.6 64 0.0014 32.6 4.0 51 19-73 464-515 (604)
59 PRK12327 nusA transcription el 30.5 78 0.0017 30.3 4.5 50 21-70 279-329 (362)
60 TIGR01953 NusA transcription t 28.4 87 0.0019 29.7 4.4 48 21-68 277-325 (341)
61 PLN02862 2-C-methyl-D-erythrit 28.0 1.8E+02 0.0038 26.2 6.0 49 28-88 142-190 (216)
62 cd00491 4Oxalocrotonate_Tautom 27.8 1.1E+02 0.0024 20.3 3.8 33 61-93 15-47 (58)
63 PF14480 DNA_pol3_a_NI: DNA po 27.5 2.3E+02 0.0049 20.1 7.0 57 26-88 18-74 (76)
64 PRK13764 ATPase; Provisional 26.2 1.1E+02 0.0023 31.4 4.8 51 20-73 460-510 (602)
65 TIGR01952 nusA_arch NusA famil 25.9 1.2E+02 0.0026 25.2 4.3 44 28-72 18-61 (141)
66 PF03780 Asp23: Asp23 family; 25.9 1.3E+02 0.0029 22.6 4.3 58 34-91 47-107 (108)
67 PF05201 GlutR_N: Glutamyl-tRN 25.8 1.4E+02 0.003 24.7 4.7 35 21-55 23-57 (152)
68 TIGR01953 NusA transcription t 25.6 2E+02 0.0043 27.3 6.3 55 20-74 201-264 (341)
69 PRK12327 nusA transcription el 25.6 1.9E+02 0.0042 27.7 6.2 55 20-74 203-266 (362)
70 PRK13763 putative RNA-processi 25.1 87 0.0019 26.7 3.5 61 47-114 6-73 (180)
71 PRK05090 hypothetical protein; 25.0 3.3E+02 0.0072 21.2 7.1 39 62-100 44-90 (95)
72 PF13684 Dak1_2: Dihydroxyacet 23.4 99 0.0021 28.7 3.7 39 17-60 19-57 (313)
73 KOG2192 PolyC-binding hnRNP-K 22.2 33 0.00072 32.1 0.3 38 41-78 120-157 (390)
74 PRK12329 nusA transcription el 20.3 1.5E+02 0.0033 29.4 4.5 50 21-70 311-361 (449)
75 PRK12328 nusA transcription el 20.2 2.5E+02 0.0053 27.3 5.8 55 20-74 209-272 (374)
No 1
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=100.00 E-value=1.2e-70 Score=482.46 Aligned_cols=213 Identities=79% Similarity=1.264 Sum_probs=209.4
Q ss_pred ccCceeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCe
Q 026588 4 QISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENS 83 (236)
Q Consensus 4 ~~~~~s~w~a~~~~~~~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~ 83 (236)
|++.+++|++++..+++||+||.++|.++|||+|+|+|+++.++|+||+++||++||++|.++++|++.|++.|++++++
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 57899999999999999999999999999999999999999999999999999999999999999999999999988889
Q ss_pred eEEEEEEecCCCcChHHHHHHHHHHHhCCchhHhHHHHHHHHHHhcCCceeEEEEccccccceeeeeeeecCeeeecCcc
Q 026588 84 VELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMVSSGQP 163 (236)
Q Consensus 84 i~I~v~~i~~p~~~a~~iA~~Ia~qLekr~~fRr~~k~~i~~~m~~gakGikI~iSGRL~G~rARte~~~~G~vl~tG~~ 163 (236)
++|++.++++|++||+++|++||+|||+|++|||+++++++++|++||+||||+|||||+|.|||+|||++|+|||||++
T Consensus 84 i~i~v~ev~~P~l~A~lvA~~IA~qLe~rv~FRRa~k~ai~~~m~aGakGikI~iSGRL~~EiARtE~~~eGrVl~Tg~~ 163 (220)
T PTZ00084 84 VELFAERVENRGLCAMAQAESLRYKLLEGLPVRRAAYGVLRHVMESGAKGCEVIVSGKLRAQRAKSMKFRDGYMISTGQP 163 (220)
T ss_pred EEEEEEEecCCCcCHHHHHHHHHHHHHhcCcHHHHHHHHHHHHHHcCCceEEEEEccchhhHHHHhhHhhccEEEecCch
Confidence 99999999999999999999999999999999999999999999999999999999999977999999999999999999
Q ss_pred cccceeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEeCCCCc
Q 026588 164 VNEYIDSAVRHVLLRQGVLGIKVKIMLSWDPNGKQGPTTPLPDLVTIHSPKDE 216 (236)
Q Consensus 164 ~~~~Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~~pd~i~i~~~~~~ 216 (236)
++++||||+.+|+|+||++|||||||+++||+|+.||.++|||.|+|++|++.
T Consensus 164 ~~~~idy~~~~a~t~yGviGVKVwI~~~~~~~~~~~~~~~~pD~~~i~~~~~~ 216 (220)
T PTZ00084 164 KKDFVDSAVRHVLMRQGVIGVKVKIMLPYDPSGKNGPSAPLPDVITVLEPKEE 216 (220)
T ss_pred HHHheehheEEEcccCceeeEEEEEECCCCcccccCCCCCCCCcEEEeCCccc
Confidence 99999999999999999999999999999999999999999999999999987
No 2
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=3.8e-65 Score=448.44 Aligned_cols=198 Identities=33% Similarity=0.469 Sum_probs=187.7
Q ss_pred cCceeeEEecCcChH-------HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHh
Q 026588 5 ISKKRKFVADGVFFA-------ELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRF 77 (236)
Q Consensus 5 ~~~~s~w~a~~~~~~-------~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~ 77 (236)
+.|.|+||++..+|+ +||+||.++|.+||||+|+|+|+|++++|+||+++||++||++|++|++|+..|+++|
T Consensus 5 ~~w~srwfa~~~~~~~~l~ed~kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l~k~~ 84 (233)
T COG0092 5 KDWKSRWFANKKEYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKELEKLF 84 (233)
T ss_pred ccchhhhccccccchHHHHHHHHHHHHHHHHHHhCCcceEEEEecCCceEEEEEeCCCcceEcCCCccHHHHHHHHHHHh
Confidence 479999999888775 4999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCchhHhHHHHHHHHHHhcCCceeEEEEccccccc-eeeeeeeecCe
Q 026588 78 KFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFKDGY 156 (236)
Q Consensus 78 ~~~~~~i~I~v~~i~~p~~~a~~iA~~Ia~qLekr~~fRr~~k~~i~~~m~~gakGikI~iSGRL~G~-rARte~~~~G~ 156 (236)
+. +++.|+|.+|++|++||+++|++||+|||+|++|||+|+++|+++|++||+||||+|||||+|+ +||+|||.+|+
T Consensus 85 g~--~~v~I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGAkGiki~vSGRL~GaeiAR~E~y~eG~ 162 (233)
T COG0092 85 GK--ENVQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGAEIARTEKYREGR 162 (233)
T ss_pred CC--CCceEEEEEcCCCCcCHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHcCCceeEEEEecccchHHHHhHHHHhcce
Confidence 96 3899999999999999999999999999999999999999999999999999999999999999 69999999999
Q ss_pred e-eecCcccccceeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEeCCCCcc
Q 026588 157 M-VSSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLSWDPNGKQGPTTPLPDLVTIHSPKDEE 217 (236)
Q Consensus 157 v-l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~~pd~i~i~~~~~~~ 217 (236)
| ||| ++++||||+++|.|+||+||||||||+|+ .|||.+.+.++...+
T Consensus 163 vplht---lrAdIDyg~a~A~ttyGiiGVKVwI~~ge----------~l~~~~~~~~~~~~~ 211 (233)
T COG0092 163 VPLHT---LRADIDYGTAEAHTTYGVIGVKVWIYKGE----------VLPDKVEIKEPAEVE 211 (233)
T ss_pred eEccc---cceeeeeeeEEEEecCceEEEEEEEecCC----------cCCCcccccCccccc
Confidence 9 999 99999999999999999999999999984 888988887655543
No 3
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=100.00 E-value=7.2e-64 Score=436.37 Aligned_cols=203 Identities=38% Similarity=0.637 Sum_probs=196.5
Q ss_pred cCceeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCee
Q 026588 5 ISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSV 84 (236)
Q Consensus 5 ~~~~s~w~a~~~~~~~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i 84 (236)
|+++++|++++..+.+||+||.+.|.+||||+|+|+|+++.+.|+||+++||++||++|+++++++..|++.|+. .++
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 578899999999999999999999999999999999999999999999999999999999999999999999985 468
Q ss_pred EEEEEEecCCCcChHHHHHHHHHHHhCCchhHhHHHHHHHHHHhcCCceeEEEEccccccceeeeeeeecCeeeecCccc
Q 026588 85 ELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMVSSGQPV 164 (236)
Q Consensus 85 ~I~v~~i~~p~~~a~~iA~~Ia~qLekr~~fRr~~k~~i~~~m~~gakGikI~iSGRL~G~rARte~~~~G~vl~tG~~~ 164 (236)
.|++.++++|++||.++|++||+|||+|++|||+++++|+++|++||+||||+|||||||.|||+|||++|+|.+||||+
T Consensus 79 ~I~v~ev~~p~~~a~~vA~~ia~qLe~r~~fRra~k~~i~~~~~agakGiki~iSGrL~Ge~AR~e~~~eG~v~~~G~pl 158 (207)
T PRK04191 79 QIDVKEVENPELNARVVAFRLANALERGWHFRRAAHSAIRRIMEAGALGVEIIISGKLTGERARTEKFTEGYIKKSGEPA 158 (207)
T ss_pred eEEEEEEeCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCeeEEEEEccccchHHHHhhhhhcceEeccCCcc
Confidence 89999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ccceeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEeCCCCccc
Q 026588 165 NEYIDSAVRHVLLRQGVLGIKVKIMLSWDPNGKQGPTTPLPDLVTIHSPKDEEE 218 (236)
Q Consensus 165 ~~~Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~~pd~i~i~~~~~~~~ 218 (236)
...||||+++|+|+||+||||||||++ +.+|||.++|++|++.++
T Consensus 159 ~tlIdya~~~a~t~~GviGIKVwI~~~---------~~~~pd~~~i~~~~~~~~ 203 (207)
T PRK04191 159 EELVDRGFAIAKLKLGIIGVEVRIMPP---------DAKLPDEIEIKEPVEVEE 203 (207)
T ss_pred hheeeeEEEEEecCCeeEEEEEEEECC---------CCCCCCEEEEeCCCCccc
Confidence 999999999999999999999999996 689999999999988765
No 4
>TIGR01008 rpsC_E_A ribosomal protein S3, eukaryotic/archaeal type. This model describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea. TIGRFAMs model TIGR01009 describes the bacterial/organellar type, although the organellar types have a different architecture with long insertions and may score poorly.
Probab=100.00 E-value=1.6e-63 Score=430.68 Aligned_cols=195 Identities=49% Similarity=0.732 Sum_probs=188.9
Q ss_pred ceeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEE
Q 026588 7 KKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (236)
Q Consensus 7 ~~s~w~a~~~~~~~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I 86 (236)
++++|++++..+.+||+||.++|.++|||+|+|+|+++.++|+||+++||.+||++|+++++|++.|+++|+. .+++|
T Consensus 1 ~~kkfi~~~~~~~~ire~l~k~~~~agis~ieI~r~~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~--~~~~I 78 (195)
T TIGR01008 1 IERKFVAEGLKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGL--ENPQI 78 (195)
T ss_pred CcEehHhcchHHHHHHHHHHHHHHhCCeeEEEEEEcCCcEEEEEEECCCceEECCCchHHHHHHHHHHHHhCC--CceEE
Confidence 3578999999999999999999999999999999999999999999999999999999999999999999985 47899
Q ss_pred EEEEecCCCcChHHHHHHHHHHHhCCchhHhHHHHHHHHHHhcCCceeEEEEccccccceeeeeeeecCeeeecCccccc
Q 026588 87 YAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMVSSGQPVNE 166 (236)
Q Consensus 87 ~v~~i~~p~~~a~~iA~~Ia~qLekr~~fRr~~k~~i~~~m~~gakGikI~iSGRL~G~rARte~~~~G~vl~tG~~~~~ 166 (236)
++.++++|++||.++|++||+|||+|++|||+++++++++|++||+||||+|||||+|+|||+|||++|+|.|||||+..
T Consensus 79 ~v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGakGikI~iSGRL~GeiARtE~~~eG~v~~sG~Pl~t 158 (195)
T TIGR01008 79 DVEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVTISGKLTGERARTEKFAAGYLKHSGEPAEE 158 (195)
T ss_pred EEEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCceEEEEEcccccchhhhhhheeccEEecCCCcchh
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred ceeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEeC
Q 026588 167 YIDSAVRHVLLRQGVLGIKVKIMLSWDPNGKQGPTTPLPDLVTIHS 212 (236)
Q Consensus 167 ~Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~~pd~i~i~~ 212 (236)
.||||+++|+|+||++|||||||++ +.+|||+++|++
T Consensus 159 ~IDya~~~a~t~yGviGIKVwI~~~---------~~~~pD~~~i~~ 195 (195)
T TIGR01008 159 LVDKGFAIALLKLGVLGVKVKIMPP---------DVKLPDEVEIKE 195 (195)
T ss_pred eeeeEEEEEecCCceEEEEEEEECC---------CCCCCCEEEecC
Confidence 9999999999999999999999996 688999999974
No 5
>CHL00048 rps3 ribosomal protein S3
Probab=100.00 E-value=5e-57 Score=395.18 Aligned_cols=184 Identities=20% Similarity=0.254 Sum_probs=176.0
Q ss_pred CceeeEEecCcChHH-------HHHHHHhh----hccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 026588 6 SKKRKFVADGVFFAE-------LNEVLTRE----LAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (236)
Q Consensus 6 ~~~s~w~a~~~~~~~-------Ire~i~k~----~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~ 74 (236)
.++|+||+++++|+. ||+||.++ |.+|||++|+|+|+++.++|+||+++||.+||++|+++++|++.|+
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 489999999999985 67777666 6899999999999999999999999999999999999999999999
Q ss_pred HHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCchhHhHHHHHHHHHHhcCCceeEEEEccccccc-eeeeeeee
Q 026588 75 KRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFK 153 (236)
Q Consensus 75 k~~~~~~~~i~I~v~~i~~p~~~a~~iA~~Ia~qLekr~~fRr~~k~~i~~~m~~gakGikI~iSGRL~G~-rARte~~~ 153 (236)
+.|++.++++.|++.++++|++||.++|++||++||+|++|||+++++++++|++||+||||+|||||+|+ |||+|||+
T Consensus 97 k~~~~~~~~i~I~v~ev~~p~~~A~~iA~~ia~~Le~r~~fRra~~~~i~~~~~~ga~GikI~iSGRL~Gae~AR~e~~~ 176 (214)
T CHL00048 97 KELNSVNRKLNINITEVKKPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGIKIQISGRLNGAEIARVEWIR 176 (214)
T ss_pred HHhCCCCceEEEEEEEecCCCcCHHHHHHHHHHHHhcChhHHHHHHHHHHHHHHhCCcEEEEEEecccCccchheEEEEe
Confidence 99987767899999999999999999999999999999999999999999999999999999999999998 99999999
Q ss_pred cCee-eecCcccccceeEEEEEEecCCeeeeEEEEEEcCC
Q 026588 154 DGYM-VSSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLSW 192 (236)
Q Consensus 154 ~G~v-l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~~~~ 192 (236)
+|+| ||| ++++||||+++|+|+||++|||||||+++
T Consensus 177 ~G~vpl~t---l~a~Idy~~~~a~t~~G~~GVKVwI~~~~ 213 (214)
T CHL00048 177 EGRVPLQT---LRAKIDYCSYPARTIYGVLGIKIWIFKDE 213 (214)
T ss_pred cceeECCc---chhheEEEEEEEecCCceEEEEEEEEcCC
Confidence 9999 999 99999999999999999999999999874
No 6
>TIGR01009 rpsC_bact ribosomal protein S3, bacterial type. TIGRFAMs model TIGR01008 describes S3 of the eukaryotic cytosol and of the archaea.
Probab=100.00 E-value=5.7e-57 Score=394.10 Aligned_cols=181 Identities=27% Similarity=0.387 Sum_probs=176.6
Q ss_pred CceeeEEecCcChHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 026588 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (236)
Q Consensus 6 ~~~s~w~a~~~~~~~-------Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~ 78 (236)
+++|+||+++++|+. ||+||.++|.++|||+|+|+||++.++|+||+++|+.+||++|+.+++|++.|++.|+
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 489999999999985 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCchhHhHHHHHHHHHHhcCCceeEEEEccccccc-eeeeeeeecCee
Q 026588 79 FPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFKDGYM 157 (236)
Q Consensus 79 ~~~~~i~I~v~~i~~p~~~a~~iA~~Ia~qLekr~~fRr~~k~~i~~~m~~gakGikI~iSGRL~G~-rARte~~~~G~v 157 (236)
++++|++.++++|++||.++|++||++||+|++|||+++++++++|++||+||||+|||||+|+ |||+|||++|+|
T Consensus 97 ---~~~~i~v~~v~~p~~~a~~iA~~ia~~Le~~~~fRr~~~~~i~~~~~~g~~GikI~isGRl~g~e~Ar~e~~~~G~v 173 (211)
T TIGR01009 97 ---KEVQINIAEVKRPELDAQLVADNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVSGRLGGAEIARTEWYKEGRV 173 (211)
T ss_pred ---CceEEEEEEecCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHhcCCcEEEEEEecccCchhhhheeeeeeCcc
Confidence 5799999999999999999999999999999999999999999999999999999999999998 999999999999
Q ss_pred -eecCcccccceeEEEEEEecCCeeeeEEEEEEcCC
Q 026588 158 -VSSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLSW 192 (236)
Q Consensus 158 -l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~~~~ 192 (236)
||| ++++||||+++|+|+||++|||||||+++
T Consensus 174 pl~t---~~~~Idy~~~~a~T~~G~~GvKVwI~~~~ 206 (211)
T TIGR01009 174 PLHT---LRADIDYATAEAHTTYGIIGVKVWIFKGE 206 (211)
T ss_pred Cccc---chhhcEEEEEEEEcCCceEEEEEEEEcCC
Confidence 999 99999999999999999999999999985
No 7
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=100.00 E-value=2e-56 Score=395.51 Aligned_cols=181 Identities=27% Similarity=0.381 Sum_probs=176.7
Q ss_pred CceeeEEecCcChHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 026588 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (236)
Q Consensus 6 ~~~s~w~a~~~~~~~-------Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~ 78 (236)
+++|.||+++++|+. ||+||.++|.++||++|+|+|+++.+.|+||+++|+.+||++|+.+++|++.|++.|+
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 489999999999985 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCchhHhHHHHHHHHHHhcCCceeEEEEccccccc-eeeeeeeecCee
Q 026588 79 FPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFKDGYM 157 (236)
Q Consensus 79 ~~~~~i~I~v~~i~~p~~~a~~iA~~Ia~qLekr~~fRr~~k~~i~~~m~~gakGikI~iSGRL~G~-rARte~~~~G~v 157 (236)
++++|++.++++|++||.++|++||++||+|++|||+++++|+++|++||+||||+|||||+|+ |||+|||++|+|
T Consensus 97 ---~~~~i~v~ev~~p~~~a~~iA~~ia~~Le~r~~fRr~~~~~i~~~~~~g~~GikI~isGRl~g~e~Ar~e~~~~G~v 173 (232)
T PRK00310 97 ---KPVQINIVEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKVQVSGRLGGAEIARTEWYREGRV 173 (232)
T ss_pred ---CceEEEEEEecCCCcCHHHHHHHHHHHHHccchHHHHHHHHHHHHHHcCCcEEEEEEcCCCCcceeeeEEEeeeccc
Confidence 6899999999999999999999999999999999999999999999999999999999999998 999999999999
Q ss_pred -eecCcccccceeEEEEEEecCCeeeeEEEEEEcCC
Q 026588 158 -VSSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLSW 192 (236)
Q Consensus 158 -l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~~~~ 192 (236)
||| ++++||||+++|+|+||++|||||||+++
T Consensus 174 pl~t---~~~~Idy~~~~a~T~~Gv~GVKVwI~~~~ 206 (232)
T PRK00310 174 PLHT---LRADIDYGTAEAHTTYGIIGVKVWIYKGE 206 (232)
T ss_pred ccce---eeeeeEEEEEEEecCCceEEEEEEEECCC
Confidence 999 99999999999999999999999999985
No 8
>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=7.2e-51 Score=349.38 Aligned_cols=226 Identities=86% Similarity=1.265 Sum_probs=220.8
Q ss_pred CccccCceeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC
Q 026588 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP 80 (236)
Q Consensus 1 ~~~~~~~~s~w~a~~~~~~~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~ 80 (236)
|.-+|+.+++|.+++.+|++++|||.++|.+.|||++|++-||.+++|+|.+.+|..++|.+|.+|++|+...+++|+++
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 66788899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeEEEEEEecCCCcChHHHHHHHHHHHhCCchhHhHHHHHHHHHHhcCCceeEEEEccccccceeeeeeeecCeeeec
Q 026588 81 ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMVSS 160 (236)
Q Consensus 81 ~~~i~I~v~~i~~p~~~a~~iA~~Ia~qLekr~~fRr~~k~~i~~~m~~gakGikI~iSGRL~G~rARte~~~~G~vl~t 160 (236)
+.++.++.+++.+-.+||..+|+++.++|-.+..+||+++-+++++|++||+||+|.+||+|+|+||++-+|..|.|.||
T Consensus 81 ~~svelyaEkV~~rGLcAiaQaeslryKllgGlavRRA~ygvlr~vmesgAkGceviVSGKLrgqRAKsmKF~DG~mIhS 160 (244)
T KOG3181|consen 81 EGSVELYAEKVANRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVIVSGKLRGQRAKSMKFVDGLMIHS 160 (244)
T ss_pred CCcEEEehhhhhccchhHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHccCCccEEEEeccchhhhhhccccccceEEec
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CcccccceeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEeCCCCccccccCccee
Q 026588 161 GQPVNEYIDSAVRHVLLRQGVLGIKVKIMLSWDPNGKQGPTTPLPDLVTIHSPKDEEEYVKPTLVA 226 (236)
Q Consensus 161 G~~~~~~Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~~pd~i~i~~~~~~~~~~~~~~~~ 226 (236)
|||.+.+||-|+.|+.|++|+|||||.||+++||+|.+||...|||.+.|.+|++.+++.+|..+.
T Consensus 161 G~pv~dyi~ta~rhVllrQGVlGIkVkIMlpydp~g~~GP~~pLPD~v~i~ePkee~~~~~p~~~~ 226 (244)
T KOG3181|consen 161 GQPVKDYIDTAVRHVLLRQGVLGIKVKIMLPYDPKGKLGPKKPLPDRVTILEPKEEEPITAPAQVA 226 (244)
T ss_pred CCcHHHHHHHHHHhhhhhcceeeeEEEEeccCCcccCcCCCCCCCCeeEEeCccccccccCchhhh
Confidence 999999999999999999999999999999999999999999999999999999999998886543
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=99.94 E-value=3.7e-27 Score=179.08 Aligned_cols=82 Identities=37% Similarity=0.556 Sum_probs=78.9
Q ss_pred HHHHHHhCCchhHhHHHHHHHHH-HhcCCceeEEEEccccccc-eeeeeeeecCee-eecCcccccceeEEEEEEecCCe
Q 026588 104 SLRYKLLGGLAVRRACYGVLRFI-MESGAKGCEVIVSGKLRAQ-RAKSMKFKDGYM-VSSGQPVNEYIDSAVRHVLLRQG 180 (236)
Q Consensus 104 ~Ia~qLekr~~fRr~~k~~i~~~-m~~gakGikI~iSGRL~G~-rARte~~~~G~v-l~tG~~~~~~Idya~~~a~Tk~G 180 (236)
+|+++||++.+||++++++++.+ |+.|++||||+|||||+|. |||+++|.+|.+ +|+ ++++|||++.++.|++|
T Consensus 1 ~i~~~l~k~~~~r~~i~~~~~~i~~~~~~~GikI~isGRl~g~~rar~~~~~~G~i~~~~---~~~~Idy~~~~~~tk~G 77 (85)
T PF00189_consen 1 FIAQKLEKRISFRRIIKKIIRRIMMNKGIKGIKIQISGRLNGAERARTEKFKKGKISLQT---FKSNIDYASSHAKTKYG 77 (85)
T ss_dssp HHHHHHHTTSTHHHHHHHHHHHHHHCTTSSEEEEEEESSGGGTSSSEEEEEEEESSSSSS---STTEEEEEEEEEEESSS
T ss_pred ChHHHHhcCcHHHHHHHHHHHHHHhhcccceEEEEEeecCCCCccceEEEEECCCCcccc---ceeeeeEEEEEEEcCCe
Confidence 58999999999999999999999 7789999999999999996 999999999999 777 99999999999999999
Q ss_pred eeeEEEEE
Q 026588 181 VLGIKVKI 188 (236)
Q Consensus 181 viGIKVWI 188 (236)
++||||||
T Consensus 78 ~~GIKVwI 85 (85)
T PF00189_consen 78 VIGIKVWI 85 (85)
T ss_dssp EEEEEEEE
T ss_pred eEEEEEEC
Confidence 99999998
No 10
>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=99.83 E-value=3.4e-20 Score=146.91 Aligned_cols=87 Identities=24% Similarity=0.388 Sum_probs=82.4
Q ss_pred CceeeEEecCcChHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 026588 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (236)
Q Consensus 6 ~~~s~w~a~~~~~~~-------Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~ 78 (236)
+++|.||+++++|+. ||+||.+.|..||||+|+|+|+++.++|+||+++||++||++|+.+++|++.|++.++
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 589999999988885 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCC
Q 026588 79 FPENSVELYAEKVNNR 94 (236)
Q Consensus 79 ~~~~~i~I~v~~i~~p 94 (236)
+ .++.|+|.++.+|
T Consensus 96 ~--~~~~I~V~ev~~P 109 (109)
T cd02412 96 N--KKVRINIVEVKKP 109 (109)
T ss_pred C--CceEEEEEEecCC
Confidence 5 5799999999987
No 11
>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=1.7e-19 Score=136.44 Aligned_cols=79 Identities=91% Similarity=1.279 Sum_probs=74.7
Q ss_pred CcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026588 15 GVFFAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (236)
Q Consensus 15 ~~~~~~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i~~ 93 (236)
+..+++||+||.++|.+||||+|+|+||++.++|+||+++||++||++|+.+++|++.|++.|+++|+++.+.+++|.+
T Consensus 1 ~~~~~~Ire~l~k~~~~agis~IeI~Rt~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~~i~v~~~~v~~ 79 (81)
T cd02413 1 GVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEGSVELYAEKVAN 79 (81)
T ss_pred CchhHHHHHHHHHHHHhCCeeeEEEEEcCCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCCeEEEEEEEccc
Confidence 3568899999999999999999999999999999999999999999999999999999999999988888888888875
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=99.73 E-value=1.3e-17 Score=126.57 Aligned_cols=85 Identities=38% Similarity=0.651 Sum_probs=79.2
Q ss_pred ceeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEE
Q 026588 7 KKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (236)
Q Consensus 7 ~~s~w~a~~~~~~~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I 86 (236)
++++|++++..+.+||+||.+.|..||+|+|+|+|+++.+.|+||+++||.+||++|+++++|+..|++.|+. .++.|
T Consensus 1 ~~~~~~~~~~~~~~Ir~fl~~~~~~agIs~IeI~r~~~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l~k~~~~--~~v~I 78 (85)
T cd02411 1 VERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGL--ENPQI 78 (85)
T ss_pred CeEeHHhcchHHHHHHHHHHhhhhhCcccEEEEEEcCCcEEEEEEECCCCceECCCchhHHHHHHHHHHHhCC--CCceE
Confidence 3578889999999999999999999999999999999999999999999999999999999999999999974 47889
Q ss_pred EEEEecC
Q 026588 87 YAEKVNN 93 (236)
Q Consensus 87 ~v~~i~~ 93 (236)
++.++++
T Consensus 79 ~v~ev~~ 85 (85)
T cd02411 79 DVQEVEN 85 (85)
T ss_pred EEEEecC
Confidence 9988864
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=99.44 E-value=2.5e-13 Score=100.53 Aligned_cols=77 Identities=27% Similarity=0.427 Sum_probs=71.4
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC-CCCCeeEEEEEEecCCCc
Q 026588 20 ELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK-FPENSVELYAEKVNNRGL 96 (236)
Q Consensus 20 ~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~-~~~~~i~I~v~~i~~p~~ 96 (236)
+||+||.+++..+|+++++|+|+++.+.|++|+++|+++||++|+.++++...+++.+. +.+++|.+++.+|++|++
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 345889999999999974
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=98.74 E-value=5.7e-08 Score=68.05 Aligned_cols=65 Identities=42% Similarity=0.616 Sum_probs=58.0
Q ss_pred HHHHHhhhccCCeeeeEEEEcCCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026588 22 NEVLTRELAEDGYSGVEVRVTPMRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (236)
Q Consensus 22 re~i~k~~~~agis~IeI~rt~~~i~I~I~~~r--Pg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v 88 (236)
|+||.+.|..+++++|+|+++++...+.+++.. ||.+||++|+.++.++..+++.++ ++++.|++
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 589999999999999999999888999999998 999999999999999999999883 35666654
No 15
>smart00322 KH K homology RNA-binding domain.
Probab=97.22 E-value=0.00038 Score=47.59 Aligned_cols=67 Identities=18% Similarity=0.253 Sum_probs=50.8
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHh
Q 026588 44 MRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLL 110 (236)
Q Consensus 44 ~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i~~p~~~a~~iA~~Ia~qLe 110 (236)
..+.|.|+...|+.+||++|..+++|++.....+...+.........+..+..++...++.|..+++
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 4578889999999999999999999998887655433222133456677788888888888887763
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=96.91 E-value=0.0046 Score=45.82 Aligned_cols=56 Identities=20% Similarity=0.287 Sum_probs=47.8
Q ss_pred HHHHhhhccCCe-eeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 026588 23 EVLTRELAEDGY-SGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (236)
Q Consensus 23 e~i~k~~~~agi-s~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~ 78 (236)
+||.+-+...|+ +.+++......+.+.|....+|.+||++|+.++.|+..+...++
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 578877777775 35667777888999999999999999999999999999998776
No 17
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=96.44 E-value=0.0042 Score=45.28 Aligned_cols=68 Identities=13% Similarity=0.149 Sum_probs=46.0
Q ss_pred HHHHHHHhhhccCCeeeeEEE--EcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEE
Q 026588 20 ELNEVLTRELAEDGYSGVEVR--VTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (236)
Q Consensus 20 ~Ire~i~k~~~~agis~IeI~--rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~ 87 (236)
.+++|+..-+...+=-.+++. .....+.+.+.....|.+||++|+.++.|+..+....+-...++.|.
T Consensus 3 ~l~~~l~~l~~~~~~v~v~~~~~~~~~~i~v~i~~ed~g~lIGk~G~tl~ALq~l~~~~~~~~~~~~~v~ 72 (73)
T PF13083_consen 3 FLEDFLKNLVDKPMDVEVTIEIEEDGDTIVVNIDGEDAGRLIGKHGKTLNALQYLVNAAANKHGKRVRVE 72 (73)
T ss_dssp --HHHHHHHHHHTT--EEEEEEETTTTEEEEEEESCCCHHHCTTHHHHHHHHHHHHHHHHHHT-SS-EEE
T ss_pred hHHHHHHHHhCCcCeEEEEEEEcCCceEEEEEECCCccceEECCCCeeHHHHHHHHHHHHHhCCCEEEEe
Confidence 367777777654332234444 44678888888899999999999999999999988765333455443
No 18
>PRK01064 hypothetical protein; Provisional
Probab=94.68 E-value=0.62 Score=35.17 Aligned_cols=69 Identities=10% Similarity=0.151 Sum_probs=46.8
Q ss_pred HHHHHhhhcc-CCeeeeEEEEcCCeEEEEEEeccc--ceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEE
Q 026588 22 NEVLTRELAE-DGYSGVEVRVTPMRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (236)
Q Consensus 22 re~i~k~~~~-agis~IeI~rt~~~i~I~I~~~rP--g~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~ 90 (236)
=+||-+.|-. -.=-.|+-......+.+.+++... |.+||++|+.++.++..+.....-.+.++.+.+.+
T Consensus 5 v~~iv~~LVd~Pe~V~V~~~~~~~~~~~~l~v~~~D~g~vIGk~G~~i~air~l~~~~~~~~~~rv~leI~~ 76 (78)
T PRK01064 5 LAYIVKNLVDRPEEVHIKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIME 76 (78)
T ss_pred HHHHHHHhcCCCCeEEEEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhhCCCEEEEEEec
Confidence 3455555542 212224444446677888888766 78999999999999999987766445777777654
No 19
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=94.24 E-value=0.38 Score=42.70 Aligned_cols=106 Identities=17% Similarity=0.159 Sum_probs=75.0
Q ss_pred HHHHHHHHhhhccCCe-eeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCC---CCeeEEEEEEecC-
Q 026588 19 AELNEVLTRELAEDGY-SGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP---ENSVELYAEKVNN- 93 (236)
Q Consensus 19 ~~Ire~i~k~~~~agi-s~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~---~~~i~I~v~~i~~- 93 (236)
.++.+||...+..-|+ +.|.+...++.+.+.|....++.+||++|+.++.|+......++.. ..++.+++..-..
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 5699999998888664 5688888899999999999999999999999999999888777532 1345444432211
Q ss_pred CCcChHHHHHHHHHHHhCC-c---------hhHhHHHHHHH
Q 026588 94 RGLCAIAQAESLRYKLLGG-L---------AVRRACYGVLR 124 (236)
Q Consensus 94 p~~~a~~iA~~Ia~qLekr-~---------~fRr~~k~~i~ 124 (236)
-.-.=..+|+.+|.+..+. . +=||+++.+++
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 1222345677777776432 2 23667777664
No 20
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=94.21 E-value=0.14 Score=42.46 Aligned_cols=60 Identities=12% Similarity=0.264 Sum_probs=49.0
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCC--eEEEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q 026588 20 ELNEVLTRELAEDGYSGVEVRVTPM--RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (236)
Q Consensus 20 ~Ire~i~k~~~~agis~IeI~rt~~--~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~ 79 (236)
...+|+.+.|..+.+.++.|..... .+.|.+.-..-+..||++|+.++.++..+...|+.
T Consensus 73 d~~~fI~n~l~Pa~V~~v~I~~~~~~~~~~V~V~~~d~g~aIGK~G~ni~la~~L~~~~~di 134 (140)
T PRK08406 73 DPEEFIKNIFAPAAVRSVTIKKKNGDKVAYVEVAPEDKGIAIGKNGKNIERAKDLAKRHFDI 134 (140)
T ss_pred CHHHHHHHHcCCCEEEEEEEEecCCcEEEEEEECccccchhhCCCCHHHHHHHHHhCCccCC
Confidence 4899999999999999999854433 34555666777889999999999999999888875
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=93.84 E-value=0.2 Score=35.50 Aligned_cols=53 Identities=15% Similarity=0.291 Sum_probs=43.9
Q ss_pred HHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 026588 22 NEVLTRELAEDGYSGVEVRVT-PMRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (236)
Q Consensus 22 re~i~k~~~~agis~IeI~rt-~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~ 74 (236)
.+|+.+.+.-+.+.++.+... .+...|.+....-+..||++|+.++.+++.+.
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 478888888888898887654 46788888888889999999999998877765
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=93.39 E-value=0.73 Score=38.81 Aligned_cols=85 Identities=20% Similarity=0.235 Sum_probs=55.6
Q ss_pred HHHHHHhhhc-cCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChH
Q 026588 21 LNEVLTRELA-EDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI 99 (236)
Q Consensus 21 Ire~i~k~~~-~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i~~p~~~a~ 99 (236)
-++.|.+... +||+.++.. .++.=+|+|++.+||++||++|..++++... +| .. ..-+..|-+.+.
T Consensus 54 A~~~I~~ivP~ea~i~di~F--d~~tGEV~IeaeKPG~ViGk~g~~~reI~~~----tg---W~----p~vvRtpPi~S~ 120 (145)
T cd02410 54 AIKIILEIVPEEAGITDIYF--DDDTGEVIIEAEKPGLVIGKGGSTLREITRE----TG---WA----PKVVRTPPIQSR 120 (145)
T ss_pred HHHHHHHhCCCccCceeeEe--cCCCcEEEEEEcCCeEEEecCchhHHHHHHH----hC---Ce----eEEEecCCCCcH
Confidence 4556665443 578876555 5566688999999999999999887765543 44 22 223456666666
Q ss_pred HHHHHHHHHHhCCchhHhHH
Q 026588 100 AQAESLRYKLLGGLAVRRAC 119 (236)
Q Consensus 100 ~iA~~Ia~qLekr~~fRr~~ 119 (236)
.+ +.|.+.|.....+|+-+
T Consensus 121 ti-~~ir~~l~~~~~eR~~~ 139 (145)
T cd02410 121 TV-KSIRRFLRREREERKEI 139 (145)
T ss_pred HH-HHHHHHHHHhHHHHHHH
Confidence 55 45666666666666544
No 23
>PRK02821 hypothetical protein; Provisional
Probab=91.87 E-value=2.6 Score=31.73 Aligned_cols=67 Identities=19% Similarity=0.208 Sum_probs=46.2
Q ss_pred HHHHHHhhhcc-CCeeeeEEEEcCCeEEEEEEecc--cceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEE
Q 026588 21 LNEVLTRELAE-DGYSGVEVRVTPMRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (236)
Q Consensus 21 Ire~i~k~~~~-agis~IeI~rt~~~i~I~I~~~r--Pg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~ 90 (236)
+=+||-+.|-+ -.=-.++.+.....+.+.|+++. -|.+|||+|+.++.++..+.-.. ++++.+++.+
T Consensus 5 lv~~ivk~LVd~Pe~V~V~~~~~~~~~~i~l~v~~~D~GrVIGk~Gr~i~AIRtlv~a~~---~~~v~leI~~ 74 (77)
T PRK02821 5 AVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAIG---GRGVRVDVVD 74 (77)
T ss_pred HHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHHhc---CCeEEEEEEe
Confidence 44555555542 22233555555666777777744 56799999999999999999873 3788888765
No 24
>PRK00468 hypothetical protein; Provisional
Probab=90.45 E-value=4.7 Score=30.13 Aligned_cols=68 Identities=16% Similarity=0.208 Sum_probs=42.8
Q ss_pred HHHHHHhhhcc-CCeeeeEEEEcCCeEEEEEEec--ccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026588 21 LNEVLTRELAE-DGYSGVEVRVTPMRTEIIIRAT--RTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (236)
Q Consensus 21 Ire~i~k~~~~-agis~IeI~rt~~~i~I~I~~~--rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v 88 (236)
+=+||-+.|-. -.=-.++.+.....+.+.++++ --|.+|||+|+.++.|+..+.-.-...+.++.+++
T Consensus 4 Lv~~iv~~LVd~Pe~v~V~~~~~~~~~~~~l~v~~~D~GrVIGk~Gr~i~AIRtvv~aaa~k~~~rv~leI 74 (75)
T PRK00468 4 LVETIAKALVDNPDAVQVNEIEGEQSVILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVEI 74 (75)
T ss_pred HHHHHHHHhcCCCCeEEEEEEeCCCeEEEEEEEChhhCcceecCCChhHHHHHHHHHHHHhcCCCEEEEEE
Confidence 33455555543 2222344444556677777775 45689999999999999999865433345666554
No 25
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=87.23 E-value=6.4 Score=29.69 Aligned_cols=68 Identities=18% Similarity=0.238 Sum_probs=40.7
Q ss_pred HHHHHHhhhcc-CCeeeeEEEEcCCeEEEEEEe--cccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026588 21 LNEVLTRELAE-DGYSGVEVRVTPMRTEIIIRA--TRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (236)
Q Consensus 21 Ire~i~k~~~~-agis~IeI~rt~~~i~I~I~~--~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v 88 (236)
+=+|+-+.|-+ -.=-+++.+-....+.+.|++ .--|.+|||+|+.++.|+..|.-.-.-.++++.+++
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 33455554433 222223333335565555555 556789999999999999999865543334555443
No 26
>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=86.63 E-value=1.2 Score=37.06 Aligned_cols=60 Identities=15% Similarity=0.240 Sum_probs=45.8
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCC--eEEEEEEecccceeeccCcccHHHHHHHHHHHhCC
Q 026588 20 ELNEVLTRELAEDGYSGVEVRVTPM--RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (236)
Q Consensus 20 ~Ire~i~k~~~~agis~IeI~rt~~--~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~ 79 (236)
.+.+|+.+.|.-|.+.+|.+...+. ...|.+--..-+..||++|+.++.....+...++.
T Consensus 74 D~~~fI~N~l~PA~V~~V~i~~~~~~~~a~V~V~~~d~~~AIGk~G~Ni~la~~l~~~~~dI 135 (141)
T TIGR01952 74 NLEEFVANKLAPAEVKNVTVSEFNGKKVAYVEVHPRDKGIAIGKGGKNIERAKELAKRHHDI 135 (141)
T ss_pred CHHHHHHHcCCCceEEEEEEEcCCCCEEEEEEEChhhhhhhhCCCchhHHHHHHHhcCccCC
Confidence 3899999999999999998865322 23344444566789999999998888887777764
No 27
>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=84.34 E-value=4.2 Score=36.25 Aligned_cols=65 Identities=22% Similarity=0.344 Sum_probs=42.5
Q ss_pred HHHHHHhhhccC-Cee-eeEEE---EcC---CeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeeE
Q 026588 21 LNEVLTRELAED-GYS-GVEVR---VTP---MRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (236)
Q Consensus 21 Ire~i~k~~~~a-gis-~IeI~---rt~---~~i~I~I~~~rPg---~iIG~kg~~i~~l----~~~L~k~~~~~~~~i~ 85 (236)
|||.+...+... -|+ .++|+ ..+ ..+...|++.|++ +|||++|+.|+++ ++.|++.|+ .+|.
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 677776655542 111 12332 222 2478889998885 7999999999765 567888888 5676
Q ss_pred EEE
Q 026588 86 LYA 88 (236)
Q Consensus 86 I~v 88 (236)
+.+
T Consensus 265 l~l 267 (270)
T TIGR00436 265 LEL 267 (270)
T ss_pred EEE
Confidence 553
No 28
>COG1159 Era GTPase [General function prediction only]
Probab=84.31 E-value=7.1 Score=36.51 Aligned_cols=74 Identities=22% Similarity=0.215 Sum_probs=46.8
Q ss_pred HHHHHHhhhccCC--eeeeEEEEc------CCeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeeE
Q 026588 21 LNEVLTRELAEDG--YSGVEVRVT------PMRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (236)
Q Consensus 21 Ire~i~k~~~~ag--is~IeI~rt------~~~i~I~I~~~rPg---~iIG~kg~~i~~l----~~~L~k~~~~~~~~i~ 85 (236)
|||=+-..+.+.= ...++|++. ...+.-+||++|-+ ++||++|+.|+++ +..|++.|+ .+|.
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 5554444443321 344666543 23567778887664 7999999999765 677888998 5666
Q ss_pred EEE-EEecCCCcC
Q 026588 86 LYA-EKVNNRGLC 97 (236)
Q Consensus 86 I~v-~~i~~p~~~ 97 (236)
+++ +++++...+
T Consensus 273 L~L~VKVk~~W~~ 285 (298)
T COG1159 273 LELWVKVKKNWRD 285 (298)
T ss_pred EEEEEEEcccccc
Confidence 653 566655443
No 29
>PRK15494 era GTPase Era; Provisional
Probab=82.93 E-value=4.6 Score=37.62 Aligned_cols=70 Identities=24% Similarity=0.391 Sum_probs=45.3
Q ss_pred HHHHHHhhhccC-Ce-eeeEEEEc---C---CeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeeE
Q 026588 21 LNEVLTRELAED-GY-SGVEVRVT---P---MRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (236)
Q Consensus 21 Ire~i~k~~~~a-gi-s~IeI~rt---~---~~i~I~I~~~rPg---~iIG~kg~~i~~l----~~~L~k~~~~~~~~i~ 85 (236)
|||-+...|... -| ..++|+.- . ..|...||+.+++ +|||++|+.|+++ +..|++.|+ .+|.
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 777776666542 11 12333321 2 2477899999887 6999999999765 567888888 5666
Q ss_pred EEE-EEecC
Q 026588 86 LYA-EKVNN 93 (236)
Q Consensus 86 I~v-~~i~~ 93 (236)
+.+ ++|++
T Consensus 317 l~l~Vkv~~ 325 (339)
T PRK15494 317 LFLFVKVRE 325 (339)
T ss_pred EEEEEEECC
Confidence 553 44444
No 30
>PRK00089 era GTPase Era; Reviewed
Probab=81.88 E-value=6.2 Score=35.22 Aligned_cols=64 Identities=27% Similarity=0.405 Sum_probs=41.6
Q ss_pred HHHHHHhhhccC-Cee-eeEEE---E-cCCeEEEEEEecccc---eeeccCcccHHHH----HHHHHHHhCCCCCeeEEE
Q 026588 21 LNEVLTRELAED-GYS-GVEVR---V-TPMRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVELY 87 (236)
Q Consensus 21 Ire~i~k~~~~a-gis-~IeI~---r-t~~~i~I~I~~~rPg---~iIG~kg~~i~~l----~~~L~k~~~~~~~~i~I~ 87 (236)
|||-+...|... -|+ .++|+ . ....+.-.||+.+++ +|||++|+.|+++ +..|++.|+ .+|.+.
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 677766666542 111 12222 1 233477889998886 6999999999765 566888888 566655
No 31
>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=81.45 E-value=8.6 Score=36.66 Aligned_cols=122 Identities=12% Similarity=0.145 Sum_probs=80.3
Q ss_pred cHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHH-HHHHhC---Cc--hhHhHHHHHHH--------------
Q 026588 65 RIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESL-RYKLLG---GL--AVRRACYGVLR-------------- 124 (236)
Q Consensus 65 ~i~~l~~~L~k~~~~~~~~i~I~v~~i~~p~~~a~~iA~~I-a~qLek---r~--~fRr~~k~~i~-------------- 124 (236)
....|...|...+. ++|.|+..+++=|+++..+++++| ...+.+ +. .|+|.+...+.
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 44577777888886 899999999999999999999999 333332 21 23333221110
Q ss_pred -------------------------------------HHHhcCCceeEEEEccccccceeee--eeeecCee--------
Q 026588 125 -------------------------------------FIMESGAKGCEVIVSGKLRAQRAKS--MKFKDGYM-------- 157 (236)
Q Consensus 125 -------------------------------------~~m~~gakGikI~iSGRL~G~rARt--e~~~~G~v-------- 157 (236)
..|..-.-|..++.+||+.-...|+ ..+..|..
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 0112356799999999999764444 44444543
Q ss_pred ----eecCcccccceeEEEEEEecCCeeeeEEEEEE
Q 026588 158 ----VSSGQPVNEYIDSAVRHVLLRQGVLGIKVKIM 189 (236)
Q Consensus 158 ----l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~ 189 (236)
.....-...+.+...-.-.++.|.+||||..-
T Consensus 313 n~~n~ykLNyi~~n~~i~~~s~inknGKynIkvkLN 348 (350)
T PF05316_consen 313 NINNNYKLNYIPSNHNIYNNSNINKNGKYNIKVKLN 348 (350)
T ss_pred hcccceeecccCCcceeccccccccCceeeeEEEEe
Confidence 01111245666666666788999999999763
No 32
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=78.71 E-value=12 Score=37.77 Aligned_cols=77 Identities=21% Similarity=0.281 Sum_probs=48.4
Q ss_pred HHHHHhhh-ccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHH
Q 026588 22 NEVLTREL-AEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIA 100 (236)
Q Consensus 22 re~i~k~~-~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i~~p~~~a~~ 100 (236)
++.|.+.. ..||++. |.-..+.=.|.|++.+||++||+.|+.++++... .+ .. ..-+..|-+....
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--IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAE----TG---WA----PKIVRTPPIQSRT 144 (637)
T ss_pred HHHHHHhCccccCcee--EEecCCCceEEEEecCCceEEecCchHHHHHHHH----hC---Cc----ceeeecCCCchhh
Confidence 44444444 3588887 4456777889999999999999999887665543 33 11 2224456565555
Q ss_pred HHHHHHHHHhCC
Q 026588 101 QAESLRYKLLGG 112 (236)
Q Consensus 101 iA~~Ia~qLekr 112 (236)
+ +.|.+-|.+.
T Consensus 145 i-~~ir~~l~~~ 155 (637)
T COG1782 145 I-KSIREILRSE 155 (637)
T ss_pred H-HHHHHHHHHh
Confidence 5 3455555443
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=68.99 E-value=4.8 Score=28.34 Aligned_cols=29 Identities=17% Similarity=0.428 Sum_probs=22.0
Q ss_pred EEEEEEecccceeeccCcccHHHHHHHHH
Q 026588 46 TEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (236)
Q Consensus 46 i~I~I~~~rPg~iIG~kg~~i~~l~~~L~ 74 (236)
..+.|-..+-+.+||++|+.+++|++.-.
T Consensus 4 ~~i~Ip~~~ig~iIGkgG~~ik~I~~~tg 32 (61)
T cd02393 4 ETMKIPPDKIRDVIGPGGKTIKKIIEETG 32 (61)
T ss_pred EEEEeChhheeeeECCCchHHHHHHHHHC
Confidence 44566667788999999999988766543
No 34
>PF13014 KH_3: KH domain
Probab=66.68 E-value=4.6 Score=26.17 Aligned_cols=18 Identities=22% Similarity=0.543 Sum_probs=14.5
Q ss_pred cceeeccCcccHHHHHHH
Q 026588 55 TQNVLGEKGRRIRELTSV 72 (236)
Q Consensus 55 Pg~iIG~kg~~i~~l~~~ 72 (236)
-+.|||++|..|++|++.
T Consensus 2 vg~iIG~~G~~I~~I~~~ 19 (43)
T PF13014_consen 2 VGRIIGKGGSTIKEIREE 19 (43)
T ss_pred cCeEECCCChHHHHHHHH
Confidence 367999999999887654
No 35
>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=64.80 E-value=47 Score=33.96 Aligned_cols=108 Identities=20% Similarity=0.229 Sum_probs=63.2
Q ss_pred HHHHHHhhh-ccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChH
Q 026588 21 LNEVLTREL-AEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI 99 (236)
Q Consensus 21 Ire~i~k~~-~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i~~p~~~a~ 99 (236)
-++.|.+.. .+||+.++.. .+..=+|.|.+.+||++||+.|..++++... +| .. ..-+..|-+.+.
T Consensus 71 ~~~~i~~~~~~~~~~~~~~f--~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~----~~---w~----~~~~~~~~~~~~ 137 (630)
T TIGR03675 71 AIEKIKEIVPEEAGITDIYF--DDVTGEVIIEAEKPGLVIGKGGSTLREITAE----TG---WT----PKVVRTPPIESK 137 (630)
T ss_pred HHHHHHHhCCCcCCceeEEe--cCCCceEEEEEcCCeEEEecCcchHHHHHHH----hC---Ce----eeEEecCCCCcH
Confidence 455555544 3578875554 5566788999999999999999887765543 33 12 223456666666
Q ss_pred HHHHHHHHHHhCCchhHhHHHHHH-HHHHh---cCCceeEEEEcccc
Q 026588 100 AQAESLRYKLLGGLAVRRACYGVL-RFIME---SGAKGCEVIVSGKL 142 (236)
Q Consensus 100 ~iA~~Ia~qLekr~~fRr~~k~~i-~~~m~---~gakGikI~iSGRL 142 (236)
.+ +.|.+.|.+....|+-+-+.+ +++-+ ..-.=+++..=|=.
T Consensus 138 ~~-~~~~~~~~~~~~~r~~~l~~~~~~i~~~~~~~~~~m~i~~LGg~ 183 (630)
T TIGR03675 138 TI-KNIREYLRSESEERKEFLRKLGRRIHRDPIFKDRWVRVTALGGF 183 (630)
T ss_pred HH-HHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCCCCeEEEEEEecC
Confidence 55 455666655555554333333 33322 12234566654433
No 36
>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=62.06 E-value=9 Score=25.98 Aligned_cols=27 Identities=15% Similarity=0.473 Sum_probs=21.2
Q ss_pred EEEEEecccceeeccCcccHHHHHHHH
Q 026588 47 EIIIRATRTQNVLGEKGRRIRELTSVV 73 (236)
Q Consensus 47 ~I~I~~~rPg~iIG~kg~~i~~l~~~L 73 (236)
++.|-...-+.+||++|..++++++.-
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s 29 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREET 29 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHH
Confidence 455566677899999999998887764
No 37
>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=55.41 E-value=4.6 Score=27.62 Aligned_cols=28 Identities=21% Similarity=0.458 Sum_probs=21.4
Q ss_pred EEEEEEecccceeeccCcccHHHHHHHH
Q 026588 46 TEIIIRATRTQNVLGEKGRRIRELTSVV 73 (236)
Q Consensus 46 i~I~I~~~rPg~iIG~kg~~i~~l~~~L 73 (236)
.++.+-...-+.+||++|..+++|++.-
T Consensus 2 ~~i~vp~~~~~~iIG~~G~~i~~I~~~t 29 (60)
T PF00013_consen 2 ERIEVPSSLVGRIIGKKGSNIKEIEEET 29 (60)
T ss_dssp EEEEEEHHHHHHHHTGGGHHHHHHHHHH
T ss_pred EEEEECHHHcCEEECCCCCcHHHhhhhc
Confidence 3456666777889999999988876654
No 38
>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=53.48 E-value=12 Score=26.31 Aligned_cols=26 Identities=15% Similarity=0.549 Sum_probs=20.0
Q ss_pred EEEEEecccceeeccCcccHHHHHHH
Q 026588 47 EIIIRATRTQNVLGEKGRRIRELTSV 72 (236)
Q Consensus 47 ~I~I~~~rPg~iIG~kg~~i~~l~~~ 72 (236)
++.|-...-+.+||++|..+++|++.
T Consensus 3 r~~ip~~~vg~iIG~~G~~i~~i~~~ 28 (65)
T cd02396 3 RLLVPSSQAGSIIGKGGSTIKEIREE 28 (65)
T ss_pred EEEECHHHcCeeECCCcHHHHHHHHH
Confidence 44555566678999999999887765
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=51.06 E-value=55 Score=27.80 Aligned_cols=50 Identities=20% Similarity=0.302 Sum_probs=37.7
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEE
Q 026588 28 ELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (236)
Q Consensus 28 ~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~ 89 (236)
.+...||. ..++.++|-+.+|.+ +....++++.|++.++.+..+|+|...
T Consensus 82 ~~~~~g~~-------i~niD~tii~e~PKi-----~p~~~~m~~~ls~~L~~~~~~V~iKat 131 (153)
T cd00554 82 LIREKGYE-------IVNIDITIIAERPKI-----SPYREAMRANLAELLGIPPSRVNIKAT 131 (153)
T ss_pred HHHHcCCE-------EEEEEEEEEecCCcc-----hHHHHHHHHHHHHHhCCCCceEEEEEe
Confidence 44556654 346778999999977 667899999999999986667776653
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=50.94 E-value=12 Score=25.71 Aligned_cols=26 Identities=23% Similarity=0.425 Sum_probs=19.8
Q ss_pred EEEEecccceeeccCcccHHHHHHHH
Q 026588 48 IIIRATRTQNVLGEKGRRIRELTSVV 73 (236)
Q Consensus 48 I~I~~~rPg~iIG~kg~~i~~l~~~L 73 (236)
+.|=...-+.+||++|+.+++|++.-
T Consensus 4 i~Vp~~~~~~iIG~~G~~i~~i~~~~ 29 (62)
T cd02394 4 VEIPKKLHRFIIGKKGSNIRKIMEET 29 (62)
T ss_pred EEeCHHHhhhccCCCCCcHHHHHHHh
Confidence 44444566789999999999887754
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=43.77 E-value=80 Score=26.90 Aligned_cols=50 Identities=24% Similarity=0.294 Sum_probs=37.2
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEE
Q 026588 28 ELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (236)
Q Consensus 28 ~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~ 89 (236)
.+...|+. ..++.++|-+.+|.+ +....++++.|.+.++++..+|+|...
T Consensus 82 ~~~~~g~~-------i~niD~tii~e~PKi-----~p~~~~m~~~la~~L~~~~~~V~iKat 131 (155)
T TIGR00151 82 LIKEKGYR-------IGNVDITIIAQRPKL-----LPHIPAMRENIAELLGIPLDSVNVKAT 131 (155)
T ss_pred HHHHcCCE-------EEEEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEEe
Confidence 44556653 345777888999976 667899999999999986667776653
No 42
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=43.33 E-value=37 Score=33.62 Aligned_cols=52 Identities=13% Similarity=0.279 Sum_probs=42.8
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHH
Q 026588 21 LNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSV 72 (236)
Q Consensus 21 Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~ 72 (236)
..+|+.+.|.-|.+.+|.+......+.|.+--..-+..||++|+.++.....
T Consensus 279 ~~~fi~nal~pa~v~~v~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~l 330 (470)
T PRK09202 279 PAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASKL 330 (470)
T ss_pred HHHHHHHhCCCCEEEEEEEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHHH
Confidence 7899999999999999987666667777777788889999999998654433
No 43
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=42.84 E-value=22 Score=33.34 Aligned_cols=76 Identities=13% Similarity=0.178 Sum_probs=42.2
Q ss_pred CCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCchhHhH
Q 026588 43 PMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRA 118 (236)
Q Consensus 43 ~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i~~p~~~a~~iA~~Ia~qLekr~~fRr~ 118 (236)
.-.++|-+.+..-|.|||+.|+.|+.|+.+..-...+++.+--=.+.-|..-.-.---+-..|--.||.+.+.+.-
T Consensus 47 r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f~~~~p 122 (390)
T KOG2192|consen 47 RVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGFQLPSP 122 (390)
T ss_pred ceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCCCCCCc
Confidence 3456777888899999999999999987765433322211110011111111112223445666677777655543
No 44
>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=42.57 E-value=2e+02 Score=26.31 Aligned_cols=51 Identities=24% Similarity=0.285 Sum_probs=36.2
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 026588 21 LNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (236)
Q Consensus 21 Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~ 78 (236)
+.+++.......++..+-|-.|.|+++|++++..+. ...+.+.+.|...++
T Consensus 26 ~~~~l~~l~~~~~~~e~viLsTCNR~EiY~~~~~~~-------~~~~~~~~~l~~~~~ 76 (311)
T cd05213 26 LKEALRRLLEKPGISEAVLLSTCNRVELYLVGDNFH-------KLADELEELLAELLN 76 (311)
T ss_pred HHHHHHHHhcCCCCceEEEEecCCeEEEEEEeCCcc-------hhHHHHHHHHHHhcC
Confidence 566666655667899999999999999999876543 223455566666555
No 45
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=40.93 E-value=21 Score=26.04 Aligned_cols=32 Identities=22% Similarity=0.499 Sum_probs=25.4
Q ss_pred CCeEEEEEEecc-----cceeeccCcccHHHHHHHHH
Q 026588 43 PMRTEIIIRATR-----TQNVLGEKGRRIRELTSVVQ 74 (236)
Q Consensus 43 ~~~i~I~I~~~r-----Pg~iIG~kg~~i~~l~~~L~ 74 (236)
.++++|.++... -|..+|.+|.+++.+.+.|.
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 357788888888 56799999999999888774
No 46
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=40.15 E-value=1e+02 Score=26.48 Aligned_cols=62 Identities=21% Similarity=0.214 Sum_probs=45.1
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEE-EEecccc-eeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026588 21 LNEVLTRELAEDGYSGVEVRVTPMRTEII-IRATRTQ-NVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (236)
Q Consensus 21 Ire~i~k~~~~agis~IeI~rt~~~i~I~-I~~~rPg-~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v 88 (236)
+.+|+++-|.-|.+.++.+...+++...+ +++..-. .-+ ...++.+.+.+++++| +.+.+.+
T Consensus 102 ~~~fl~Nl~~PA~V~gV~i~~~~dG~~~~kV~Vd~~Dk~~l---~~k~e~~~~v~~kltg---k~v~~~f 165 (166)
T PRK06418 102 IKKLAVQLLSPARVLGVNTVWLPDGTVQYVIRVSRRDRRRL---PAKPELLESILSKITG---TEVKIRV 165 (166)
T ss_pred HHHHHHhcCCCcEEEEEEEEEeCCCcEEEEEEECHHHhhcc---cccHHHHHHHHHHHHC---CcEEEEe
Confidence 89999999999999999998777764444 6664321 122 3457889999999998 6666554
No 47
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=36.32 E-value=73 Score=30.80 Aligned_cols=63 Identities=17% Similarity=0.198 Sum_probs=44.9
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEE
Q 026588 21 LNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (236)
Q Consensus 21 Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~ 90 (236)
..+|+.+.|.-|.+.+|.+........|++--..-++.||++|+.++.- ++++| .++.|.-.+
T Consensus 285 ~~~fI~Nal~Pa~V~~V~i~~~~~~~~V~V~~~qlslAIGk~GqNvrLA----~~LtG---wkIDI~s~~ 347 (374)
T PRK12328 285 PEIFIARALAPAIISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRLA----SMLTG---YEIELNEIG 347 (374)
T ss_pred HHHHHHHhCCCceeeEEEEcCCCcEEEEEEChHHhhhhhcCCChhHHHH----HHHhC---CEEEEEECC
Confidence 7899999999999999987643455566655566778999999998543 34455 466655443
No 48
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=36.01 E-value=1.1e+02 Score=25.35 Aligned_cols=41 Identities=10% Similarity=0.215 Sum_probs=30.1
Q ss_pred cCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHH
Q 026588 31 EDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (236)
Q Consensus 31 ~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L 73 (236)
++..-+|-+ ..+.+.+.+.....|..+|++|++++.+++.+
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 34888888888899999999999999985544
No 49
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=35.64 E-value=80 Score=27.13 Aligned_cols=31 Identities=10% Similarity=0.202 Sum_probs=24.7
Q ss_pred CCeEEEEEEecccceeeccCcccHHHHHHHHH
Q 026588 43 PMRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (236)
Q Consensus 43 ~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~ 74 (236)
.+.+-+.+..+. |.-||++|+.++.|++.|.
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 8999999999888777664
No 50
>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=35.38 E-value=1.8e+02 Score=24.76 Aligned_cols=49 Identities=24% Similarity=0.322 Sum_probs=36.9
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026588 28 ELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (236)
Q Consensus 28 ~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v 88 (236)
.+...||. ..++.++|-+.+|.+ +..+.++++.|.+.++++..+|+|..
T Consensus 83 ~~~~~g~~-------i~niD~tii~e~PKi-----~p~~~~m~~~la~~L~~~~~~V~iKa 131 (157)
T PF02542_consen 83 LLREKGYR-------IVNIDITIIAERPKI-----SPYRPAMRENLAKLLGIPPDRVNIKA 131 (157)
T ss_dssp HHHHTTEE-------EEEEEEEEESSSSTT-----GGGHHHHHHHHHHHHTS-GGGEEEEE
T ss_pred HHHHcCcE-------EEEEEEEEEcCCCcc-----HHHHHHHHHHHHHHhCCCcceEEEEE
Confidence 45566754 345677899999977 67789999999999998766777654
No 51
>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=33.78 E-value=31 Score=29.27 Aligned_cols=58 Identities=14% Similarity=0.250 Sum_probs=38.9
Q ss_pred ecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE----EEe--cCCCcChHHHHHHHHHHHhCCchhH
Q 026588 52 ATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA----EKV--NNRGLCAIAQAESLRYKLLGGLAVR 116 (236)
Q Consensus 52 ~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v----~~i--~~p~~~a~~iA~~Ia~qLekr~~fR 116 (236)
..+-+.+||++|+.+++|++...- +++|+- +.| ..++.++..-|..+-..|-++.++.
T Consensus 6 ~~kig~vIG~gG~~Ik~I~~~tgv-------~I~Id~~~g~V~I~~~t~d~~~i~kA~~~I~~i~~gf~~e 69 (172)
T TIGR03665 6 KDRIGVLIGKGGETKKEIEERTGV-------KLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPE 69 (172)
T ss_pred HHHhhhHhCCchhHHHHHHHHhCc-------EEEEEcCCceEEEecCCCCHHHHHHHHHHHHHHHcCCCHH
Confidence 355678999999998887665542 333332 234 4577778888888888887765543
No 52
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=32.82 E-value=78 Score=27.68 Aligned_cols=62 Identities=11% Similarity=0.203 Sum_probs=45.1
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCC-eEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026588 20 ELNEVLTRELAEDGYSGVEVRVTPM-RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (236)
Q Consensus 20 ~Ire~i~k~~~~agis~IeI~rt~~-~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v 88 (236)
...+|+.+.|.-+...+|.+....+ ...+.+.-..-+..||+.|+.++... ++++ .++.|..
T Consensus 117 d~~~fI~nal~Pa~v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla~----~Ltg---~~i~I~~ 179 (190)
T COG0195 117 DPAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLAS----QLTG---WEIDIET 179 (190)
T ss_pred CHHHHHHHhcCcceEeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHHH----HHhC---CEEEEEe
Confidence 3889999999999999999887433 56666666777899999998775544 4444 4555543
No 53
>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=32.82 E-value=82 Score=25.48 Aligned_cols=34 Identities=12% Similarity=0.216 Sum_probs=26.7
Q ss_pred ChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEe
Q 026588 17 FFAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRA 52 (236)
Q Consensus 17 ~~~~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~ 52 (236)
...+|..||.+.|...||. |.|+| ++...|+..+
T Consensus 3 ~k~~ikpwlq~~~~~~Gi~-iVIer-Sd~~ki~FkC 36 (111)
T PF08731_consen 3 DKDEIKPWLQKIFYPQGIG-IVIER-SDKKKIVFKC 36 (111)
T ss_pred chHHHHHHHHHHhhhcCce-EEEEe-cCCceEEEEE
Confidence 4568999999988889987 88999 6666766444
No 54
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=32.30 E-value=2.1e+02 Score=24.46 Aligned_cols=40 Identities=23% Similarity=0.337 Sum_probs=32.0
Q ss_pred CeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026588 44 MRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (236)
Q Consensus 44 ~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v 88 (236)
.++.++|-+.+|.+ +.-..++++.|.+.++++..+|+|..
T Consensus 94 ~niD~tii~e~PKi-----~p~~~~m~~~la~~L~i~~~~V~iKa 133 (159)
T PRK00084 94 GNVDITIIAQRPKM-----APHIEEMRANIAEDLGIPLDDVNVKA 133 (159)
T ss_pred EEEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEE
Confidence 45677888999976 56789999999999998666677664
No 55
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=31.35 E-value=82 Score=23.12 Aligned_cols=46 Identities=15% Similarity=0.123 Sum_probs=31.8
Q ss_pred EEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026588 48 IIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (236)
Q Consensus 48 I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i~~ 93 (236)
|+|.+.+...--..|.+-++++++.+.+.+|.++..+.|-+.++..
T Consensus 4 v~Ik~~~g~~~~~~K~~la~~vT~~~~~~lg~~~~~i~Viieev~~ 49 (69)
T COG1942 4 VNIKLFEGRLDEEQKAELAAEVTEVTVETLGKDPSAIHVIIEEVPP 49 (69)
T ss_pred EEEEecCCCCCHHHHHHHHHHHHHHHHHHhCCCcccEEEEEEecCh
Confidence 4555555333222345567899999999999887888888888754
No 56
>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=31.29 E-value=1.9e+02 Score=24.83 Aligned_cols=57 Identities=12% Similarity=0.344 Sum_probs=40.3
Q ss_pred HHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEE
Q 026588 24 VLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (236)
Q Consensus 24 ~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I 86 (236)
.|++.++..||..+-..-..+.+.|++.+.. + ......++...+.+.+|++..+|.|
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 3455666789999999999999999888765 1 3557789999999999986666664
No 57
>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=31.13 E-value=87 Score=21.28 Aligned_cols=32 Identities=13% Similarity=0.179 Sum_probs=24.9
Q ss_pred CcccHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026588 62 KGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (236)
Q Consensus 62 kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i~~ 93 (236)
+.+-++.+.+.|...+|.+...+.+.+.++..
T Consensus 17 K~~l~~~it~~l~~~lg~~~~~v~V~i~e~~~ 48 (63)
T TIGR00013 17 KRQLIEGVTEAMAETLGANLESIVVIIDEMPK 48 (63)
T ss_pred HHHHHHHHHHHHHHHhCCCcccEEEEEEEcCH
Confidence 44556888888999999888888888877643
No 58
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=30.62 E-value=64 Score=32.61 Aligned_cols=51 Identities=27% Similarity=0.454 Sum_probs=34.8
Q ss_pred HHHHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHHHHH
Q 026588 19 AELNEVLTRELAEDGYSGVEVRVT-PMRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (236)
Q Consensus 19 ~~Ire~i~k~~~~agis~IeI~rt-~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L 73 (236)
.+|.++|++.+.. +++++-. ++...|.+.-...+.+||++|+++++|.+.|
T Consensus 464 ~~i~~~i~r~~p~----~~eVe~~gd~~avv~vpe~~i~~vigk~g~~i~~ie~kl 515 (604)
T COG1855 464 EEIEREIKRYLPG----DVEVEVVGDGRAVVKVPEKYIPKVIGKGGKRIKEIEKKL 515 (604)
T ss_pred HHHHHHHHHhCCC----CceEEEecCCeEEEEeCHHHhhHHhhcccchHHHHHHHh
Confidence 3477777777664 4455444 4556666665677789999999998765543
No 59
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=30.46 E-value=78 Score=30.33 Aligned_cols=50 Identities=16% Similarity=0.237 Sum_probs=37.4
Q ss_pred HHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHH
Q 026588 21 LNEVLTRELAEDGYSGVEVRVT-PMRTEIIIRATRTQNVLGEKGRRIRELT 70 (236)
Q Consensus 21 Ire~i~k~~~~agis~IeI~rt-~~~i~I~I~~~rPg~iIG~kg~~i~~l~ 70 (236)
..+|+.+.|.-|.+.++.+... .....|++--..-+..||++|++++.-.
T Consensus 279 ~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la~ 329 (362)
T PRK12327 279 PAEFVANALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLAA 329 (362)
T ss_pred HHHHHHHhCCCceEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHHH
Confidence 8899999999999999987432 2345555555667789999999986433
No 60
>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=28.40 E-value=87 Score=29.72 Aligned_cols=48 Identities=19% Similarity=0.288 Sum_probs=36.9
Q ss_pred HHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHH
Q 026588 21 LNEVLTRELAEDGYSGVEVRVT-PMRTEIIIRATRTQNVLGEKGRRIRE 68 (236)
Q Consensus 21 Ire~i~k~~~~agis~IeI~rt-~~~i~I~I~~~rPg~iIG~kg~~i~~ 68 (236)
..+|+.+.|.-|.+.+|++... .....|.+--..-++.||++|++++.
T Consensus 277 ~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~aIGk~G~Nv~l 325 (341)
T TIGR01953 277 PAEFIANALSPAKVISVEVLDEDKHSAEVVVPDDQLSLAIGKGGQNVRL 325 (341)
T ss_pred HHHHHHHhcCCceEEEEEEEcCCCcEEEEEEChHHcchhhcCCChhHHH
Confidence 7899999999999999987443 34455555556677899999999854
No 61
>PLN02862 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Probab=27.97 E-value=1.8e+02 Score=26.21 Aligned_cols=49 Identities=18% Similarity=0.163 Sum_probs=36.2
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026588 28 ELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (236)
Q Consensus 28 ~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v 88 (236)
.+..+|+. ..++.++|-+.+|.+ +....++++.|.+.++.+..+|+|..
T Consensus 142 ll~~~G~~-------I~NvD~tII~q~PKi-----~p~~~~m~~~La~lL~i~~~~VnIKA 190 (216)
T PLN02862 142 LMHEAGYE-------IGNLDATLILQRPKL-----SPHKEAIRSNLSKLLGADPSVVNLKA 190 (216)
T ss_pred HHHHcCCE-------EEEEEEEEEcCCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEE
Confidence 34556654 345677888999976 56789999999999998666666554
No 62
>cd00491 4Oxalocrotonate_Tautomerase 4-Oxalocrotonate Tautomerase: Catalyzes the isomerization of unsaturated ketones. The structure is a homohexamer that is arranged as a trimer of dimers. The hexamer contains six active sites, each formed by residues from three monomers, two from one dimer and the third from a neighboring monomer. Each monomer is a beta-alpha-beta fold with two small beta strands at the C-terminus that fold back on themselves. A pair of monomers form a dimer with two-fold symmetry, consisting of a 4-stranded beta sheet with two helices on one side and two additional small beta strands at each end. The dimers are assembled around a 3-fold axis of rotation to form a hexamer, with the short beta strands from each dimer contacting the neighboring dimers.
Probab=27.80 E-value=1.1e+02 Score=20.27 Aligned_cols=33 Identities=18% Similarity=0.323 Sum_probs=25.4
Q ss_pred cCcccHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026588 61 EKGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (236)
Q Consensus 61 ~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i~~ 93 (236)
.+.+-.+.+.+.+.+.++.+...+.+.+.++..
T Consensus 15 qk~~l~~~i~~~l~~~~g~~~~~v~V~i~e~~~ 47 (58)
T cd00491 15 QKRELIERVTEAVSEILGAPEATIVVIIDEMPK 47 (58)
T ss_pred HHHHHHHHHHHHHHHHhCcCcccEEEEEEEeCc
Confidence 345556888888899999888888888877643
No 63
>PF14480 DNA_pol3_a_NI: DNA polymerase III polC-type N-terminus I
Probab=27.46 E-value=2.3e+02 Score=20.07 Aligned_cols=57 Identities=12% Similarity=0.133 Sum_probs=41.7
Q ss_pred HhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEE
Q 026588 26 TRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (236)
Q Consensus 26 ~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v 88 (236)
...|.++-+.++.+.+..+..++++.. |..+ .-+.+..+.+.|++.|+.. .++.+.+
T Consensus 18 ~~~f~~~~I~kv~v~k~~~~w~f~l~~--~~~l---~~~~~~~~~~~l~~~F~~i-a~v~~~i 74 (76)
T PF14480_consen 18 NPLFEDAEIEKVTVHKKSRKWRFHLSS--PHIL---PFEVYQKFEEKLKKQFSHI-AKVELII 74 (76)
T ss_pred hhhhcccEEEEEEEEccCCEEEEEEEe--CCcC---CHHHHHHHHHHHHHHhCCc-CeEEEEE
Confidence 456778889999999999988876666 4443 3567889999999988732 3555443
No 64
>PRK13764 ATPase; Provisional
Probab=26.16 E-value=1.1e+02 Score=31.43 Aligned_cols=51 Identities=24% Similarity=0.434 Sum_probs=34.3
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHHH
Q 026588 20 ELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (236)
Q Consensus 20 ~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L 73 (236)
+|.+-|.+.+ .|...+++. ..+...|++--..-+.+||++|..|+++.+.|
T Consensus 460 ~~~~~~~~~~--~~~~~~~~~-~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~ 510 (602)
T PRK13764 460 EIEREIKRYL--PGPVEVEVV-SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKL 510 (602)
T ss_pred HHHHHHHHhc--CCceEEEEe-cCCeEEEEEChhhhhHHhccCcchHHHHHHHh
Confidence 3666666666 556667766 45566555544555679999999998765544
No 65
>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=25.93 E-value=1.2e+02 Score=25.23 Aligned_cols=44 Identities=9% Similarity=0.282 Sum_probs=28.9
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecccceeeccCcccHHHHHHH
Q 026588 28 ELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLGEKGRRIRELTSV 72 (236)
Q Consensus 28 ~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~ 72 (236)
.+..+..-+|.+.-.. ++-..+.....|..+|++|+.++.+++.
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 3445555566554322 5555555567789999999999988533
No 66
>PF03780 Asp23: Asp23 family; InterPro: IPR005531 This entry represents the alkaline shock protein 23 family. These small proteins are involved in alkaline pH tolerance of Staphylococcus aureus [,].
Probab=25.90 E-value=1.3e+02 Score=22.60 Aligned_cols=58 Identities=16% Similarity=0.130 Sum_probs=34.3
Q ss_pred eeeeEEEEc-CCeEEEEEEec--ccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEEEe
Q 026588 34 YSGVEVRVT-PMRTEIIIRAT--RTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKV 91 (236)
Q Consensus 34 is~IeI~rt-~~~i~I~I~~~--rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~~i 91 (236)
-.++.++.. ...+.|.+++. .+..+-.--.+--+++++.|++.+++.-..++|.+..+
T Consensus 47 ~~~v~v~~~~~~~i~v~l~v~v~~g~~i~~v~~~iq~~V~~~v~~~tg~~v~~V~V~V~~v 107 (108)
T PF03780_consen 47 SKGVKVEVDEDGGITVDLHVVVEYGVNIPEVAEEIQEKVKEAVEEMTGIEVSEVNVHVEDV 107 (108)
T ss_pred CCCeEEEEccCcceEEEEEEEEECCccHHHHHHHHHHHHHHHHHHHHCCeeEEEEEEEEec
Confidence 455677766 66777766663 22222111111225677778888898767788777654
No 67
>PF05201 GlutR_N: Glutamyl-tRNAGlu reductase, N-terminal domain; InterPro: IPR015895 Tetrapyrroles are large macrocyclic compounds derived from a common biosynthetic pathway []. The end-product, uroporphyrinogen III, is used to synthesise a number of important molecules, including vitamin B12, haem, sirohaem, chlorophyll, coenzyme F430 and phytochromobilin []. The first stage in tetrapyrrole synthesis is the synthesis of 5-aminoaevulinic acid ALA via two possible routes: (1) condensation of succinyl CoA and glycine (C4 pathway) using ALA synthase (2.3.1.37 from EC), or (2) decarboxylation of glutamate (C5 pathway) via three different enzymes, glutamyl-tRNA synthetase (6.1.1.17 from EC) to charge a tRNA with glutamate, glutamyl-tRNA reductase (1.2.1.70 from EC) to reduce glutamyl-tRNA to glutamate-1-semialdehyde (GSA), and GSA aminotransferase (5.4.3.8 from EC) to catalyse a transamination reaction to produce ALA. The second stage is to convert ALA to uroporphyrinogen III, the first macrocyclic tetrapyrrolic structure in the pathway. This is achieved by the action of three enzymes in one common pathway: porphobilinogen (PBG) synthase (or ALA dehydratase, 4.2.1.24 from EC) to condense two ALA molecules to generate porphobilinogen; hydroxymethylbilane synthase (or PBG deaminase, 2.5.1.61 from EC) to polymerise four PBG molecules into preuroporphyrinogen (tetrapyrrole structure); and uroporphyrinogen III synthase (4.2.1.75 from EC) to link two pyrrole units together (rings A and D) to yield uroporphyrinogen III. Uroporphyrinogen III is the first branch point of the pathway. To synthesise cobalamin (vitamin B12), sirohaem, and coenzyme F430, uroporphyrinogen III needs to be converted into precorrin-2 by the action of uroporphyrinogen III methyltransferase (2.1.1.107 from EC). To synthesise haem and chlorophyll, uroporphyrinogen III needs to be decarboxylated into coproporphyrinogen III by the action of uroporphyrinogen III decarboxylase (4.1.1.37 from EC) []. This entry represents the N-terminal domain of glutamyl-tRNA reductase (1.2.1.70 from EC), which reduces glutamyl-tRNA to glutamate-1-semialdehyde during the first stage of tetrapyrrole biosynthesis by the C5 pathway [, ]. The enzyme requires NADPH as a cofactor.; GO: 0008883 glutamyl-tRNA reductase activity, 0050661 NADP binding, 0033014 tetrapyrrole biosynthetic process, 0055114 oxidation-reduction process; PDB: 1GPJ_A.
Probab=25.83 E-value=1.4e+02 Score=24.71 Aligned_cols=35 Identities=23% Similarity=0.170 Sum_probs=24.0
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEeccc
Q 026588 21 LNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRT 55 (236)
Q Consensus 21 Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rP 55 (236)
+.+.+.......|+..+-|-.|.|+++|++++..+
T Consensus 23 ~~~~l~~l~~~~~i~e~viLsTCNR~Eiy~~~~~~ 57 (152)
T PF05201_consen 23 LPEALAELKSFPGIEEAVILSTCNRVEIYVVSDDP 57 (152)
T ss_dssp HHH---HHHHHTT-SEEEEEEETTEEEEEEES-TT
T ss_pred HHHHHHHHhccCCCceEEEeecCCeEEEEEEeCcc
Confidence 44444434445789999999999999999988766
No 68
>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=25.63 E-value=2e+02 Score=27.31 Aligned_cols=55 Identities=24% Similarity=0.393 Sum_probs=40.9
Q ss_pred HHHHHHHhhhccC--CeeeeE-EEEc-CCeEEEEEEecccce-----eeccCcccHHHHHHHHH
Q 026588 20 ELNEVLTRELAED--GYSGVE-VRVT-PMRTEIIIRATRTQN-----VLGEKGRRIRELTSVVQ 74 (236)
Q Consensus 20 ~Ire~i~k~~~~a--gis~Ie-I~rt-~~~i~I~I~~~rPg~-----iIG~kg~~i~~l~~~L~ 74 (236)
.+++.|+.+...- |.-.|. |.|- ..+++|-+++..|++ .+|.+|.+++.+.+.|.
T Consensus 201 ~v~~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ 264 (341)
T TIGR01953 201 FVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELN 264 (341)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhC
Confidence 3777777766653 433333 5565 478999999999875 89999999999888874
No 69
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=25.59 E-value=1.9e+02 Score=27.66 Aligned_cols=55 Identities=22% Similarity=0.401 Sum_probs=40.7
Q ss_pred HHHHHHHhhhccC--CeeeeE-EEEc-CCeEEEEEEecccce-----eeccCcccHHHHHHHHH
Q 026588 20 ELNEVLTRELAED--GYSGVE-VRVT-PMRTEIIIRATRTQN-----VLGEKGRRIRELTSVVQ 74 (236)
Q Consensus 20 ~Ire~i~k~~~~a--gis~Ie-I~rt-~~~i~I~I~~~rPg~-----iIG~kg~~i~~l~~~L~ 74 (236)
.+++.|..+...- |+-.|. |.|- ..+++|-+++..|++ .||.+|.+++.+.+.|.
T Consensus 203 ~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~ 266 (362)
T PRK12327 203 LVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELK 266 (362)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhC
Confidence 3677777766653 433333 4565 478999999998875 89999999999888874
No 70
>PRK13763 putative RNA-processing protein; Provisional
Probab=25.12 E-value=87 Score=26.72 Aligned_cols=61 Identities=18% Similarity=0.286 Sum_probs=39.8
Q ss_pred EEEEEecccceeeccCcccHHHHHHHHHHHhCCCCCeeEEEEE----Eec---CCCcChHHHHHHHHHHHhCCch
Q 026588 47 EIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE----KVN---NRGLCAIAQAESLRYKLLGGLA 114 (236)
Q Consensus 47 ~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~~~~~~i~I~v~----~i~---~p~~~a~~iA~~Ia~qLekr~~ 114 (236)
.+.|-..+.+.+||++|+.++.|++.. +. +++++-. .|. .++..+..-|..+-..|-++..
T Consensus 6 ~i~IP~~kig~iIG~gGk~Ik~I~e~t----g~---~I~i~~~~g~V~I~~~~~~d~~~i~kA~~~I~ai~~gf~ 73 (180)
T PRK13763 6 YVKIPKDRIGVLIGKKGETKKEIEERT----GV---KLEIDSETGEVIIEPTDGEDPLAVLKARDIVKAIGRGFS 73 (180)
T ss_pred EEEcCHHHhhhHhccchhHHHHHHHHH----Cc---EEEEECCCCeEEEEeCCCCCHHHHHHHHHHHHHHhcCCC
Confidence 344555677889999998888876654 32 2332221 233 5677778888888888877644
No 71
>PRK05090 hypothetical protein; Validated
Probab=25.03 E-value=3.3e+02 Score=21.17 Aligned_cols=39 Identities=15% Similarity=0.229 Sum_probs=26.1
Q ss_pred CcccHHHHHHHHHHHhCCCCCeeEE--------EEEEecCCCcChHH
Q 026588 62 KGRRIRELTSVVQKRFKFPENSVEL--------YAEKVNNRGLCAIA 100 (236)
Q Consensus 62 kg~~i~~l~~~L~k~~~~~~~~i~I--------~v~~i~~p~~~a~~ 100 (236)
+|+-=++|...|.+.|+++..+|.| ....|..|.--+..
T Consensus 44 eGkAN~ali~~LAk~l~v~ks~I~i~~G~tsr~K~v~I~~~~~~~~~ 90 (95)
T PRK05090 44 DGQANAHLLKFLAKQFRVAKSQVVIEKGELGRHKQVRIINPQQIPPE 90 (95)
T ss_pred CChHHHHHHHHHHHHhCCChhhEEEEecCCCCceEEEEcCcccChHh
Confidence 3555589999999999987666765 23455555544433
No 72
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=23.42 E-value=99 Score=28.75 Aligned_cols=39 Identities=21% Similarity=0.094 Sum_probs=29.3
Q ss_pred ChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecccceeec
Q 026588 17 FFAELNEVLTRELAEDGYSGVEVRVTPMRTEIIIRATRTQNVLG 60 (236)
Q Consensus 17 ~~~~Ire~i~k~~~~agis~IeI~rt~~~i~I~I~~~rPg~iIG 60 (236)
...++|++|... |=| +-+--+...++|+|||..||.++.
T Consensus 19 ~~~~lr~~L~~~----GdS-lvVv~~~~~~kVHvHT~~Pg~vle 57 (313)
T PF13684_consen 19 DAEELRARLEEL----GDS-LVVVGDDDLVKVHVHTNDPGAVLE 57 (313)
T ss_pred CHHHHHHHHHhc----CCE-EEEEecCCeEEEEEeeCCHHHHHH
Confidence 556688877643 322 555577889999999999999886
No 73
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=22.19 E-value=33 Score=32.14 Aligned_cols=38 Identities=24% Similarity=0.530 Sum_probs=31.7
Q ss_pred EcCCeEEEEEEecccceeeccCcccHHHHHHHHHHHhC
Q 026588 41 VTPMRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (236)
Q Consensus 41 rt~~~i~I~I~~~rPg~iIG~kg~~i~~l~~~L~k~~~ 78 (236)
+.|-.++.-||-.--|-+|||+|..|++|++.-+-+++
T Consensus 120 ~~pce~rllihqs~ag~iigrngskikelrekcsarlk 157 (390)
T KOG2192|consen 120 PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLK 157 (390)
T ss_pred CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhh
Confidence 34556777889999999999999999999998876664
No 74
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=20.34 E-value=1.5e+02 Score=29.37 Aligned_cols=50 Identities=10% Similarity=0.211 Sum_probs=37.7
Q ss_pred HHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecccceeeccCcccHHHHH
Q 026588 21 LNEVLTRELAEDGYSGVEVRVT-PMRTEIIIRATRTQNVLGEKGRRIRELT 70 (236)
Q Consensus 21 Ire~i~k~~~~agis~IeI~rt-~~~i~I~I~~~rPg~iIG~kg~~i~~l~ 70 (236)
..+|+.+.|.-|.+.+|.+... .....|++--..-++.||++|++++--.
T Consensus 311 p~~fI~NaLsPA~V~~V~i~~~~~k~a~V~V~~~qlslAIGK~GqNvrLAs 361 (449)
T PRK12329 311 PATYIANALSPARVDEVRLVDPEGRHAHVLVPPDQLSLAIGKEGQNVRLAA 361 (449)
T ss_pred HHHHHHHhcCCceeeEEEEEcCCCcEEEEEEChHhcchhhcCCChhHHHHH
Confidence 7899999999999999987442 2345555555677789999999986433
No 75
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=20.25 E-value=2.5e+02 Score=27.27 Aligned_cols=55 Identities=20% Similarity=0.209 Sum_probs=41.3
Q ss_pred HHHHHHHhhhccCCeeeeE---EEEc-CCeEEEEEEecccce-----eeccCcccHHHHHHHHH
Q 026588 20 ELNEVLTRELAEDGYSGVE---VRVT-PMRTEIIIRATRTQN-----VLGEKGRRIRELTSVVQ 74 (236)
Q Consensus 20 ~Ire~i~k~~~~agis~Ie---I~rt-~~~i~I~I~~~rPg~-----iIG~kg~~i~~l~~~L~ 74 (236)
.+++.|+.+...-.=+-|+ |.|- ..+++|-+++..|++ .||.+|.+++.+.+.|.
T Consensus 209 ~v~~Lfe~EVPEI~dG~VeIk~IARepG~RtKVAV~S~d~~iDPvGacIG~~G~rI~~I~~eL~ 272 (374)
T PRK12328 209 FLEALLELEVPEIKDGEVIIIHSARIPGERAKVALFSNNPNIDPIGATVGVKGVRINAVSKELN 272 (374)
T ss_pred HHHHHHHHhCccccCCeEEEEEEeccCcceeEEEEEcCCCCCChHHhhcCCCcchHHHHHHHhC
Confidence 4777777777653323344 4565 478999999999975 89999999999888874
Done!