Query 026835
Match_columns 232
No_of_seqs 140 out of 1105
Neff 5.4
Searched_HMMs 46136
Date Fri Mar 29 13:23:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/026835.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/026835hhsearch_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 5.9E-71 1.3E-75 482.7 19.6 213 4-216 4-216 (220)
2 COG0092 RpsC Ribosomal protein 100.0 1.5E-65 3.2E-70 449.4 19.3 202 5-221 5-215 (233)
3 PRK04191 rps3p 30S ribosomal p 100.0 7.2E-64 1.6E-68 435.0 20.5 205 5-220 1-205 (207)
4 TIGR01008 rpsC_E_A ribosomal p 100.0 1.3E-63 2.9E-68 429.7 22.0 194 8-212 2-195 (195)
5 CHL00048 rps3 ribosomal protei 100.0 6E-57 1.3E-61 393.4 22.9 183 6-191 17-212 (214)
6 TIGR01009 rpsC_bact ribosomal 100.0 9.2E-57 2E-61 391.5 21.4 181 6-192 17-206 (211)
7 PRK00310 rpsC 30S ribosomal pr 100.0 2.8E-56 6.1E-61 393.3 22.1 180 6-191 17-205 (232)
8 KOG3181 40S ribosomal protein 100.0 2.7E-53 5.8E-58 362.8 13.2 224 1-224 1-225 (244)
9 PF00189 Ribosomal_S3_C: Ribos 99.9 3.5E-27 7.6E-32 178.6 9.8 82 104-188 1-85 (85)
10 cd02412 30S_S3_KH K homology R 99.8 4.4E-20 9.5E-25 145.8 10.0 87 6-94 16-109 (109)
11 cd02413 40S_S3_KH K homology R 99.8 2.4E-19 5.2E-24 135.2 10.7 80 15-94 1-80 (81)
12 cd02411 archeal_30S_S3_KH K ho 99.7 2.7E-17 5.7E-22 124.4 8.4 84 8-93 2-85 (85)
13 PF07650 KH_2: KH domain syndr 99.5 1.8E-13 3.8E-18 101.1 7.3 77 20-96 1-78 (78)
14 cd02409 KH-II KH-II (K homolo 98.7 7E-08 1.5E-12 67.4 7.7 65 22-88 1-67 (68)
15 smart00322 KH K homology RNA-b 97.3 0.00034 7.3E-09 47.7 3.7 67 44-110 3-69 (69)
16 cd02414 jag_KH jag_K homology 96.8 0.0056 1.2E-07 45.2 7.0 56 23-78 2-58 (77)
17 PF13083 KH_4: KH domain; PDB: 96.2 0.0068 1.5E-07 44.0 4.1 68 20-87 3-72 (73)
18 PRK01064 hypothetical protein; 94.7 0.65 1.4E-05 34.9 10.2 68 22-90 5-76 (78)
19 PRK08406 transcription elongat 93.7 0.22 4.9E-06 41.1 6.4 60 20-79 73-134 (140)
20 cd02134 NusA_KH NusA_K homolog 93.2 0.34 7.5E-06 34.2 5.9 53 22-74 2-55 (61)
21 COG1847 Jag Predicted RNA-bind 92.7 0.31 6.7E-06 43.1 6.0 106 19-124 65-185 (208)
22 cd02410 archeal_CPSF_KH The ar 91.5 0.51 1.1E-05 39.6 5.8 84 21-118 54-138 (145)
23 PRK02821 hypothetical protein; 91.4 3.9 8.5E-05 30.7 9.9 67 21-90 5-74 (77)
24 PRK00468 hypothetical protein; 88.8 7.9 0.00017 28.8 9.6 68 21-88 4-74 (75)
25 TIGR01952 nusA_arch NusA famil 83.9 2.1 4.6E-05 35.5 4.8 60 20-79 74-135 (141)
26 COG1837 Predicted RNA-binding 83.6 13 0.00029 27.8 8.5 45 43-87 27-73 (76)
27 TIGR00436 era GTP-binding prot 83.3 5 0.00011 35.6 7.4 65 21-88 188-267 (270)
28 COG1159 Era GTPase [General fu 81.4 11 0.00025 35.0 9.0 72 21-95 196-283 (298)
29 PRK15494 era GTPase Era; Provi 81.4 5.9 0.00013 36.8 7.3 70 21-93 240-325 (339)
30 COG1782 Predicted metal-depend 80.9 8.2 0.00018 38.8 8.3 50 21-72 77-127 (637)
31 PRK00089 era GTPase Era; Revie 79.2 12 0.00025 33.4 8.2 65 21-88 195-272 (292)
32 TIGR03675 arCOG00543 arCOG0054 72.3 23 0.00049 36.1 9.0 111 21-145 71-186 (630)
33 cd02393 PNPase_KH Polynucleoti 71.7 4.1 8.9E-05 28.6 2.7 28 46-73 4-31 (61)
34 PF13014 KH_3: KH domain 67.1 4.8 0.0001 26.0 2.0 18 55-72 2-19 (43)
35 PF05316 VAR1: Mitochondrial r 64.5 58 0.0013 31.1 9.3 119 65-189 156-348 (350)
36 cd00105 KH-I K homology RNA-bi 63.6 8.7 0.00019 26.0 2.9 27 47-73 3-29 (64)
37 cd02396 PCBP_like_KH K homolog 56.3 10 0.00023 26.5 2.3 26 47-72 3-28 (65)
38 PF00013 KH_1: KH domain syndr 52.4 5 0.00011 27.3 0.1 27 47-73 3-29 (60)
39 cd00554 MECDP_synthase MECDP_s 52.1 76 0.0016 26.8 7.2 50 28-89 82-131 (153)
40 cd02394 vigilin_like_KH K homo 51.1 11 0.00024 25.7 1.8 26 48-73 4-29 (62)
41 PF02542 YgbB: YgbB family; I 47.2 98 0.0021 26.3 7.1 49 28-88 83-131 (157)
42 PF13184 KH_5: NusA-like KH do 45.1 16 0.00034 26.6 1.8 32 43-74 2-38 (69)
43 TIGR00151 ispF 2C-methyl-D-ery 44.8 1.1E+02 0.0024 25.9 7.1 50 28-89 82-131 (155)
44 PRK06418 transcription elongat 44.4 78 0.0017 27.1 6.2 62 21-88 102-165 (166)
45 PRK00084 ispF 2-C-methyl-D-ery 43.7 1.1E+02 0.0025 25.9 7.1 40 44-88 94-133 (159)
46 PRK08406 transcription elongat 40.2 66 0.0014 26.4 5.0 42 30-73 20-61 (140)
47 PRK06418 transcription elongat 38.4 74 0.0016 27.2 5.2 31 43-74 60-90 (166)
48 KOG2192 PolyC-binding hnRNP-K 38.3 50 0.0011 30.9 4.4 81 39-119 43-123 (390)
49 PRK12327 nusA transcription el 38.2 94 0.002 29.7 6.4 56 19-74 202-266 (362)
50 TIGR01953 NusA transcription t 36.7 1.6E+02 0.0036 27.8 7.7 57 18-74 199-264 (341)
51 PRK09202 nusA transcription el 36.6 54 0.0012 32.3 4.6 51 21-71 279-329 (470)
52 cd05213 NAD_bind_Glutamyl_tRNA 35.7 2.7E+02 0.0059 25.3 8.8 53 20-79 25-77 (311)
53 TIGR00013 taut 4-oxalocrotonat 34.5 75 0.0016 21.5 3.9 32 62-93 17-48 (63)
54 COG1942 Uncharacterized protei 33.7 75 0.0016 23.2 3.9 46 48-93 4-49 (69)
55 TIGR03665 arCOG04150 arCOG0415 32.7 30 0.00066 29.2 1.9 58 52-116 6-69 (172)
56 PRK12328 nusA transcription el 31.1 1.1E+02 0.0023 29.6 5.5 63 21-90 285-347 (374)
57 PF12685 SpoIIIAH: SpoIIIAH-li 30.8 2.1E+02 0.0045 24.5 6.8 57 24-86 139-195 (196)
58 PRK12328 nusA transcription el 30.7 2.1E+02 0.0045 27.6 7.4 61 14-74 203-272 (374)
59 PRK05090 hypothetical protein; 30.6 2.6E+02 0.0056 21.7 7.1 24 63-86 45-68 (95)
60 TIGR01952 nusA_arch NusA famil 30.5 97 0.0021 25.7 4.5 43 28-71 18-60 (141)
61 COG0195 NusA Transcription elo 30.2 1.5E+02 0.0033 25.8 5.9 61 21-88 118-179 (190)
62 PLN02862 2-C-methyl-D-erythrit 29.8 2.3E+02 0.005 25.4 7.0 49 28-88 142-190 (216)
63 PF08731 AFT: Transcription fa 29.5 1E+02 0.0022 24.8 4.3 34 17-52 3-36 (111)
64 cd00491 4Oxalocrotonate_Tautom 28.7 1.1E+02 0.0024 20.2 3.9 32 62-93 16-47 (58)
65 PRK12329 nusA transcription el 27.5 1.6E+02 0.0034 29.2 6.0 57 18-74 226-298 (449)
66 PF03780 Asp23: Asp23 family; 26.6 1.3E+02 0.0029 22.5 4.4 57 34-91 47-107 (108)
67 PRK09202 nusA transcription el 26.0 2.6E+02 0.0056 27.7 7.3 59 16-74 199-266 (470)
68 PRK09382 ispDF bifunctional 2- 25.6 2.7E+02 0.0058 26.6 7.1 49 28-88 300-348 (378)
69 PRK12327 nusA transcription el 24.8 1.2E+02 0.0026 29.0 4.6 49 21-69 279-328 (362)
70 PRK13763 putative RNA-processi 24.6 84 0.0018 26.7 3.3 66 47-114 6-73 (180)
71 COG1855 ATPase (PilT family) [ 24.1 98 0.0021 31.2 4.0 51 19-73 464-515 (604)
72 PRK02289 4-oxalocrotonate taut 23.5 1.3E+02 0.0027 20.7 3.5 31 63-93 18-48 (60)
73 KOG2192 PolyC-binding hnRNP-K 23.3 35 0.00075 31.9 0.7 38 41-78 120-157 (390)
74 TIGR01953 NusA transcription t 23.2 1.3E+02 0.0028 28.4 4.5 48 21-68 277-325 (341)
75 COG4604 CeuD ABC-type enteroch 22.9 3.5E+02 0.0075 24.6 6.8 61 45-107 19-79 (252)
76 PRK13764 ATPase; Provisional 22.1 1.5E+02 0.0031 30.4 4.9 51 20-73 460-510 (602)
77 TIGR03675 arCOG00543 arCOG0054 21.8 1.3E+02 0.0028 30.8 4.4 53 20-77 3-56 (630)
78 PRK13763 putative RNA-processi 21.7 2E+02 0.0044 24.4 5.1 65 54-125 105-169 (180)
79 PF13684 Dak1_2: Dihydroxyacet 20.5 1.2E+02 0.0026 28.0 3.7 40 17-61 19-58 (313)
80 KOG2191 RNA-binding protein NO 20.3 1.1E+02 0.0023 29.5 3.2 56 21-76 101-164 (402)
81 COG1534 Predicted RNA-binding 20.1 3E+02 0.0064 21.7 5.2 53 51-110 15-70 (97)
No 1
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=100.00 E-value=5.9e-71 Score=482.65 Aligned_cols=213 Identities=79% Similarity=1.237 Sum_probs=209.5
Q ss_pred ccCceeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCe
Q 026835 4 QISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENS 83 (232)
Q Consensus 4 ~~~~~s~w~a~~~~~~~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~ 83 (232)
|++.+++|++++..+++||+||+++|.++|||+|+|+|+++.++|+||+++||.+||++|+++++|++.|++.|++++++
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 57899999999999999999999999999999999999999999999999999999999999999999999999988899
Q ss_pred eEEEEEEecCCCcChHHHHHHHHHHHhCCccchhhhHHHHHHHHhcCCceeEEEEcccccccceeeeeeecCeeeecccc
Q 026835 84 VELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQP 163 (232)
Q Consensus 84 v~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~~k~~l~~~m~~gakGikI~iSGRL~G~rARte~~~~G~vl~tG~~ 163 (232)
++|++.+|++|++||+++|++||+|||+|++|||+++++++++|++||+||||+|||||+|.|||+|||++|+|||||++
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 cccceeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEccCCcc
Q 026835 164 VNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEE 216 (232)
Q Consensus 164 ~~~~Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~lpd~i~i~~~~~~ 216 (232)
++++|||++.+|+|+||+||||||||+|+||+|++||.++|||+|+|++|++.
T Consensus 164 ~~~~idy~~~~a~t~yGviGVKVwI~~~~~~~~~~~~~~~~pD~~~i~~~~~~ 216 (220)
T PTZ00084 164 KKDFVDSAVRHVLMRQGVIGVKVKIMLPYDPSGKNGPSAPLPDVITVLEPKEE 216 (220)
T ss_pred HHHheehheEEEcccCceeeEEEEEECCCCcccccCCCCCCCCcEEEeCCccc
Confidence 99999999999999999999999999999999999999999999999999986
No 2
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=1.5e-65 Score=449.39 Aligned_cols=202 Identities=32% Similarity=0.437 Sum_probs=190.4
Q ss_pred cCceeeEEecCcChH-------HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHh
Q 026835 5 ISKKRKFVADGVFFA-------ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRF 77 (232)
Q Consensus 5 ~~~~s~w~a~~~~~~-------~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~ 77 (232)
..|.|+||++..+|+ +||+||.++|.+||||+|+|+|+|++++|+||++|||++||++|++|++|+..|+++|
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 469999999877664 4999999999999999999999999999999999999999999999999999999999
Q ss_pred CCCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCccchhhhHHHHHHHHhcCCceeEEEEccccccc-ceeeeeeecCe
Q 026835 78 KFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFKDGY 156 (232)
Q Consensus 78 ~~~~~~v~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~~k~~l~~~m~~gakGikI~iSGRL~G~-rARte~~~~G~ 156 (232)
+. .+++|+|.||++|++||+++|++||+|||+|++|||||+++|+++|++||+||||+|||||+|+ +||+|||.+|+
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 79999999999
Q ss_pred e-eecccccccceeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEccCCcccccCC
Q 026835 157 M-ISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEVYVAP 221 (232)
Q Consensus 157 v-l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~lpd~i~i~~~~~~~~~~~ 221 (232)
| ||| ++++||||+++|+|+||+||||||||+| +.|||++.+.++...+....
T Consensus 163 vplht---lrAdIDyg~a~A~ttyGiiGVKVwI~~g----------e~l~~~~~~~~~~~~~~~~~ 215 (233)
T COG0092 163 VPLHT---LRADIDYGTAEAHTTYGVIGVKVWIYKG----------EVLPDKVEIKEPAEVEEPAE 215 (233)
T ss_pred eEccc---cceeeeeeeEEEEecCceEEEEEEEecC----------CcCCCcccccCccccccccc
Confidence 9 999 9999999999999999999999999998 38899988877666665543
No 3
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=100.00 E-value=7.2e-64 Score=434.96 Aligned_cols=205 Identities=37% Similarity=0.598 Sum_probs=198.0
Q ss_pred cCceeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCee
Q 026835 5 ISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSV 84 (232)
Q Consensus 5 ~~~~s~w~a~~~~~~~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v 84 (232)
|+..++|++++..+.+||+||.+.|.+|||++|+|+|+++.+.|+||+++||.+||++|+++++|+..|++.|+. .++
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 467899999999999999999999999999999999999999999999999999999999999999999999986 468
Q ss_pred EEEEEEecCCCcChHHHHHHHHHHHhCCccchhhhHHHHHHHHhcCCceeEEEEcccccccceeeeeeecCeeeeccccc
Q 026835 85 ELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPV 164 (232)
Q Consensus 85 ~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~~k~~l~~~m~~gakGikI~iSGRL~G~rARte~~~~G~vl~tG~~~ 164 (232)
.|++.+|++|++||.++|++||+|||+|++|||+++++|+++|++||+||||+|||||||.|||+|||++|+|.+||||+
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 ccceeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEccCCcccccC
Q 026835 165 NEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEVYVA 220 (232)
Q Consensus 165 ~~~Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~lpd~i~i~~~~~~~~~~ 220 (232)
...||||+.+|+|+||+||||||||+| +.++||+++|++|++++.++
T Consensus 159 ~tlIdya~~~a~t~~GviGIKVwI~~~---------~~~~pd~~~i~~~~~~~~~~ 205 (207)
T PRK04191 159 EELVDRGFAIAKLKLGIIGVEVRIMPP---------DAKLPDEIEIKEPVEVEEVV 205 (207)
T ss_pred hheeeeEEEEEecCCeeEEEEEEEECC---------CCCCCCEEEEeCCCCccccc
Confidence 999999999999999999999999997 68999999999999888654
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=1.3e-63 Score=429.68 Aligned_cols=194 Identities=49% Similarity=0.734 Sum_probs=188.9
Q ss_pred eeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEE
Q 026835 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (232)
Q Consensus 8 ~s~w~a~~~~~~~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~ 87 (232)
+++|++++..+.+||+||.++|.++|||+|+|+|+++.++|+||+++||.+||++|+++++|++.|+++|+. .+++|+
T Consensus 2 ~kkfi~~~~~~~~ire~l~k~~~~agis~ieI~r~~~~~~I~I~~~rPg~vIG~~g~~i~~l~~~l~k~~~~--~~~~I~ 79 (195)
T TIGR01008 2 ERKFVAEGLKRTLIDEFLKKELREAGYSGVDVRVTPLGTKVIIFAERPGLVIGRGGRRIRELTEKLQKKFGL--ENPQID 79 (195)
T ss_pred cEehHhcchHHHHHHHHHHHHHHhCCeeEEEEEEcCCcEEEEEEECCCceEECCCchHHHHHHHHHHHHhCC--CceEEE
Confidence 578999999999999999999999999999999999999999999999999999999999999999999985 479999
Q ss_pred EEEecCCCcChHHHHHHHHHHHhCCccchhhhHHHHHHHHhcCCceeEEEEcccccccceeeeeeecCeeeecccccccc
Q 026835 88 AEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISSGQPVNEY 167 (232)
Q Consensus 88 v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~~k~~l~~~m~~gakGikI~iSGRL~G~rARte~~~~G~vl~tG~~~~~~ 167 (232)
+.+|++|++||.++|++||+|||+|++|||+++++++++|++||+||||+|||||+|.|||+|||++|+|.|||+|+...
T Consensus 80 v~ev~~p~l~A~lvA~~Ia~qLe~rv~fRra~k~ai~~~m~aGakGikI~iSGRL~GeiARtE~~~eG~v~~sG~Pl~t~ 159 (195)
T TIGR01008 80 VEEVENPELNAQVQAERIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVTISGKLTGERARTEKFAAGYLKHSGEPAEEL 159 (195)
T ss_pred EEEEeCCCcCHHHHHHHHHHHHHccccHHHHHHHHHHHHHHcCCceEEEEEcccccchhhhhhheeccEEecCCCcchhe
Confidence 99999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred eeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEcc
Q 026835 168 IDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHP 212 (232)
Q Consensus 168 Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~lpd~i~i~~ 212 (232)
||||+.+|+|+||+||||||||+| +.+|||+++|++
T Consensus 160 IDya~~~a~t~yGviGIKVwI~~~---------~~~~pD~~~i~~ 195 (195)
T TIGR01008 160 VDKGFAIALLKLGVLGVKVKIMPP---------DVKLPDEVEIKE 195 (195)
T ss_pred eeeEEEEEecCCceEEEEEEEECC---------CCCCCCEEEecC
Confidence 999999999999999999999997 689999999975
No 5
>CHL00048 rps3 ribosomal protein S3
Probab=100.00 E-value=6e-57 Score=393.42 Aligned_cols=183 Identities=20% Similarity=0.270 Sum_probs=175.5
Q ss_pred CceeeEEecCcChHH-------HHHHHHhh----hccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHH
Q 026835 6 SKKRKFVADGVFFAE-------LNEVLTRE----LAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (232)
Q Consensus 6 ~~~s~w~a~~~~~~~-------Ire~i~~~----~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~ 74 (232)
.|+|+||+++++|+. ||+||.+. +.+|||++|+|+|+++.++|+||+++|+.+||++|+++++|++.|+
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 499999999999985 66666665 6899999999999999999999999999999999999999999999
Q ss_pred HHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCccchhhhHHHHHHHHhcCCceeEEEEccccccc-ceeeeeee
Q 026835 75 KRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFK 153 (232)
Q Consensus 75 k~~~~~~~~v~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~~k~~l~~~m~~gakGikI~iSGRL~G~-rARte~~~ 153 (232)
+.|++.++++.|++.++++|++||.++|++||++||+|++|||+++++++++|++||+||||+|||||+|+ |||+|||+
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 99998777899999999999999999999999999999999999999999999999999999999999998 99999999
Q ss_pred cCee-eecccccccceeEEEEEEecCCeeeeEEEEEEcC
Q 026835 154 DGYM-ISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLE 191 (232)
Q Consensus 154 ~G~v-l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~~~ 191 (232)
+|+| ||| ++++||||+.+|+|+||++|||||||++
T Consensus 177 ~G~vpl~t---l~a~Idy~~~~a~t~~G~~GVKVwI~~~ 212 (214)
T CHL00048 177 EGRVPLQT---LRAKIDYCSYPARTIYGVLGIKIWIFKD 212 (214)
T ss_pred cceeECCc---chhheEEEEEEEecCCceEEEEEEEEcC
Confidence 9999 999 9999999999999999999999999987
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=9.2e-57 Score=391.49 Aligned_cols=181 Identities=27% Similarity=0.387 Sum_probs=176.5
Q ss_pred CceeeEEecCcChHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhC
Q 026835 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (232)
Q Consensus 6 ~~~s~w~a~~~~~~~-------Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~ 78 (232)
.|+|+||+++++|+. ||+||+++|.++||++|+|+|+++.++|+||+++|+.+||++|+.+++|++.|++.|+
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 599999999999985 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCccchhhhHHHHHHHHhcCCceeEEEEccccccc-ceeeeeeecCee
Q 026835 79 FPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFKDGYM 157 (232)
Q Consensus 79 ~~~~~v~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~~k~~l~~~m~~gakGikI~iSGRL~G~-rARte~~~~G~v 157 (232)
++++|++.+|++|++||.++|++|+++||+|++|||+++++++++|++||+||||+|||||+|+ |||+|||++|+|
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 6899999999999999999999999999999999999999999999999999999999999998 999999999999
Q ss_pred -eecccccccceeEEEEEEecCCeeeeEEEEEEcCC
Q 026835 158 -ISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEW 192 (232)
Q Consensus 158 -l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~~~~ 192 (232)
||| ++++||||+++|+|+||++|||||||+++
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 99999999999999999999999999983
No 7
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=100.00 E-value=2.8e-56 Score=393.30 Aligned_cols=180 Identities=27% Similarity=0.391 Sum_probs=176.3
Q ss_pred CceeeEEecCcChHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhC
Q 026835 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (232)
Q Consensus 6 ~~~s~w~a~~~~~~~-------Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~ 78 (232)
.|+|.||+++++|+. ||+||+++|.++||++|+|+|+++.++|+||+++|+.+||++|+.+++|++.|++.|+
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 599999999999985 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCccchhhhHHHHHHHHhcCCceeEEEEccccccc-ceeeeeeecCee
Q 026835 79 FPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQ-RAKSMKFKDGYM 157 (232)
Q Consensus 79 ~~~~~v~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~~k~~l~~~m~~gakGikI~iSGRL~G~-rARte~~~~G~v 157 (232)
++++|++.+|++|++||.++|++||++||+|++|||+++++|+++|++||+||||+|||||+|+ |||+|||++|+|
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 -eecccccccceeEEEEEEecCCeeeeEEEEEEcC
Q 026835 158 -ISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIMLE 191 (232)
Q Consensus 158 -l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~~~ 191 (232)
||| ++++||||+.+|+|+||++|||||||++
T Consensus 174 pl~t---~~~~Idy~~~~a~T~~Gv~GVKVwI~~~ 205 (232)
T PRK00310 174 PLHT---LRADIDYGTAEAHTTYGIIGVKVWIYKG 205 (232)
T ss_pred ccce---eeeeeEEEEEEEecCCceEEEEEEEECC
Confidence 999 9999999999999999999999999997
No 8
>KOG3181 consensus 40S ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=2.7e-53 Score=362.80 Aligned_cols=224 Identities=87% Similarity=1.249 Sum_probs=218.0
Q ss_pred CccccCceeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCC
Q 026835 1 MATQISKKRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFP 80 (232)
Q Consensus 1 ~~~~~~~~s~w~a~~~~~~~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~ 80 (232)
|+-+|+...+|++++.+|++++|||.++|.+.|||++|++.||.+++|+|.+.+|..++|.+|.+|++|+...+++|+++
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 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred CCeeEEEEEEecCCCcChHHHHHHHHHHHhCCccchhhhHHHHHHHHhcCCceeEEEEcccccccceeeeeeecCeeeec
Q 026835 81 ENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRFIMESGAKGCEVIVSGKLRAQRAKSMKFKDGYMISS 160 (232)
Q Consensus 81 ~~~v~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~~k~~l~~~m~~gakGikI~iSGRL~G~rARte~~~~G~vl~t 160 (232)
+.++.++.++|.+-.+||..+|+++.++|-.+..+||+++.+|+++|++||+||+|.+||+|+|+||++-+|.+|.++||
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 ccccccceeEEEEEEecCCeeeeEEEEEEcCCCCCCCCCCCCCCCCeEEEccCCccc-ccCCCCc
Q 026835 161 GQPVNEYIDSAVRHVLLRQGVLGIKVKIMLEWDQKGKQGPTTPLPDLVTIHPLKEEV-YVAPATA 224 (232)
Q Consensus 161 G~~~~~~Idya~~~a~Tk~GviGIKVWI~~~~~p~g~~g~~~~lpd~i~i~~~~~~~-~~~~~~~ 224 (232)
|||.+++||-|+.|+.|++|+|||||.||+||||+|.+||..+|||.+.|.+|+|++ .-+|.+.
T Consensus 161 G~pv~dyi~ta~rhVllrQGVlGIkVkIMlpydp~g~~GP~~pLPD~v~i~ePkee~~~~~p~~~ 225 (244)
T KOG3181|consen 161 GQPVKDYIDTAVRHVLLRQGVLGIKVKIMLPYDPKGKLGPKKPLPDRVTILEPKEEEPITAPAQV 225 (244)
T ss_pred CCcHHHHHHHHHHhhhhhcceeeeEEEEeccCCcccCcCCCCCCCCeeEEeCccccccccCchhh
Confidence 999999999999999999999999999999999999999999999999999999998 4445443
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=3.5e-27 Score=178.59 Aligned_cols=82 Identities=37% Similarity=0.560 Sum_probs=79.1
Q ss_pred HHHHHHhCCccchhhhHHHHHHH-HhcCCceeEEEEccccccc-ceeeeeeecCee-eecccccccceeEEEEEEecCCe
Q 026835 104 SLRYKLLGGLAVRRACYGVLRFI-MESGAKGCEVIVSGKLRAQ-RAKSMKFKDGYM-ISSGQPVNEYIDSAVRHVLLRQG 180 (232)
Q Consensus 104 ~Ia~~Lekr~~fRr~~k~~l~~~-m~~gakGikI~iSGRL~G~-rARte~~~~G~v-l~tG~~~~~~Idya~~~a~Tk~G 180 (232)
+|+++||++.+||++++++++.+ |+++++||||+|||||+|. |||+++|++|.+ +|+ ++++|||++.+++|++|
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 026835 181 VLGIKVKI 188 (232)
Q Consensus 181 viGIKVWI 188 (232)
++||||||
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=99.82 E-value=4.4e-20 Score=145.77 Aligned_cols=87 Identities=24% Similarity=0.388 Sum_probs=82.5
Q ss_pred CceeeEEecCcChHH-------HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhC
Q 026835 6 SKKRKFVADGVFFAE-------LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (232)
Q Consensus 6 ~~~s~w~a~~~~~~~-------Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~ 78 (232)
.|+|.||+++.+|+. ||+||.+.|..|||++|+|+|+++.++|+||+++||++||++|+.|++|+..|++.++
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 599999999888885 9999999999999999999999999999999999999999999999999999999997
Q ss_pred CCCCeeEEEEEEecCC
Q 026835 79 FPENSVELYAEKVNNR 94 (232)
Q Consensus 79 ~~~~~v~I~v~ev~~p 94 (232)
+ .++.|+|.||.+|
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=2.4e-19 Score=135.18 Aligned_cols=80 Identities=91% Similarity=1.285 Sum_probs=75.2
Q ss_pred CcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEEecCC
Q 026835 15 GVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNR 94 (232)
Q Consensus 15 ~~~~~~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~p 94 (232)
+..+++||+||.+.|.+||||+|+|+|+++.++|+|||++||.+||++|+++++|++.|++.|+++|+++++.+++|.+.
T Consensus 1 ~~~~~~Ire~l~k~~~~agis~IeI~Rt~~~i~I~I~tarPg~vIG~~G~~i~~L~~~L~k~~~~~~~~i~v~~~~v~~~ 80 (81)
T cd02413 1 GVFYAELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEGSVELYAEKVANR 80 (81)
T ss_pred CchhHHHHHHHHHHHHhCCeeeEEEEEcCCeEEEEEEeCCCceEECCCchhHHHHHHHHHHHhCCCCCeEEEEEEEcccC
Confidence 35788999999999999999999999999999999999999999999999999999999999999889998888888763
No 12
>cd02411 archeal_30S_S3_KH K homology RNA-binding domain (KH) of the archaeal 30S small ribosomal subunit S3 protein. S3 is part of the head region of the 30S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=99.71 E-value=2.7e-17 Score=124.45 Aligned_cols=84 Identities=38% Similarity=0.662 Sum_probs=78.9
Q ss_pred eeeEEecCcChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEE
Q 026835 8 KRKFVADGVFFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (232)
Q Consensus 8 ~s~w~a~~~~~~~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~ 87 (232)
.++|++++..+.+||+||.+.|..||+|+|+|+|+++.+.|+||+++||.+||++|+++++|+..|++.|+. .++.|+
T Consensus 2 ~~~~~~~~~~~~~Ir~fl~~~~~~agIs~IeI~r~~~~i~V~I~t~~pg~iIGk~G~~I~~l~~~l~k~~~~--~~v~I~ 79 (85)
T cd02411 2 ERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGL--ENPQID 79 (85)
T ss_pred eEeHHhcchHHHHHHHHHHhhhhhCcccEEEEEEcCCcEEEEEEECCCCceECCCchhHHHHHHHHHHHhCC--CCceEE
Confidence 577889999999999999999999999999999999999999999999999999999999999999999984 478899
Q ss_pred EEEecC
Q 026835 88 AEKVNN 93 (232)
Q Consensus 88 v~ev~~ 93 (232)
|.+|++
T Consensus 80 v~ev~~ 85 (85)
T cd02411 80 VQEVEN 85 (85)
T ss_pred EEEecC
Confidence 998864
No 13
>PF07650 KH_2: KH domain syndrome, contains KH motifs.; InterPro: IPR004044 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-2 KH domain include eukaryotic and prokaryotic S3 family of ribosomal proteins, and the prokaryotic GTP-binding protein, era.; GO: 0003723 RNA binding; PDB: 2XR1_B 3OAR_C 3OFX_C 1VS7_C 3I1O_C 2WWL_C 3R8O_C 2QAL_C 3J00_C 3J0V_F ....
Probab=99.46 E-value=1.8e-13 Score=101.06 Aligned_cols=77 Identities=27% Similarity=0.427 Sum_probs=71.8
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhC-CCCCeeEEEEEEecCCCc
Q 026835 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK-FPENSVELYAEKVNNRGL 96 (232)
Q Consensus 20 ~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~-~~~~~v~I~v~ev~~p~~ 96 (232)
+||+||.+++..+++++++|+|+++.+.|++|+++|+++||++|+.|+++...+++.+. +.+.+|.+++.+|++|++
T Consensus 1 eI~~~l~~~~~~~~~~~i~I~r~~~~~~i~i~~~~~~ivIGk~G~~ik~i~~~~~k~l~~~~~~~V~l~v~~V~~~~~ 78 (78)
T PF07650_consen 1 EIRYFLFKEIKKAGISDIEIERTPDQIIIVIKASQPGIVIGKKGSNIKKIREELRKELEKLLNKKVFLNVVKVKKPWR 78 (78)
T ss_dssp HHHHHHHHHTTTTTEEEEEEEESSSEEEEEEEESSHHHHHTGGGHHHHHHHHHHHHHHHHHCSSSEEEEEEEESSCGG
T ss_pred ChhhhHHhhhhhccCceEEEEEcCCeEEEEEeCCCccHhHHhhhHHHHHHHHHHHHHHhhcCCCcEEEEEEEecCCCC
Confidence 58999999999999999999999999999999999999999999999999999999884 445899999999999974
No 14
>cd02409 KH-II KH-II (K homology RNA-binding domain, type II). KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins (e.g. ribosomal protein S3), transcription factors (e.g. NusA_K), and post-transcriptional modifiers of mRNA (e.g. hnRNP K). There are two different KH domains that belong to different protein folds, but they share a single KH motif. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In addition to their KH core domain, KH-II proteins have an N-terminal alpha helical extension while KH-I proteins have a C-terminal alpha helical extension.
Probab=98.72 E-value=7e-08 Score=67.42 Aligned_cols=65 Identities=42% Similarity=0.616 Sum_probs=58.0
Q ss_pred HHHHHhhhccCCeeeeEEEEcCCeEEEEEEecC--CceeecCCcchHHHHHHHHHHHhCCCCCeeEEEE
Q 026835 22 NEVLTRELAEDGYSGVEVRVTPVRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (232)
Q Consensus 22 re~i~~~~~~agis~ieI~rt~~~i~I~I~~~r--Pg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (232)
|+||.+.+..+++++|+|++.++...+.+++.. |+.+||++|+.++.++..+++.++ +.++.|++
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 36666654
No 15
>smart00322 KH K homology RNA-binding domain.
Probab=97.27 E-value=0.00034 Score=47.75 Aligned_cols=67 Identities=19% Similarity=0.262 Sum_probs=51.3
Q ss_pred CeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHh
Q 026835 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLL 110 (232)
Q Consensus 44 ~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~p~~~a~~iA~~Ia~~Le 110 (232)
..++|.|+...|+.+||++|+.+++|++.+...+..++.........+..+..++...++.|..+++
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 4577889999999999999999999998887655543332234556777888888888888887763
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=96.84 E-value=0.0056 Score=45.18 Aligned_cols=56 Identities=20% Similarity=0.287 Sum_probs=47.4
Q ss_pred HHHHhhhccCCe-eeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhC
Q 026835 23 EVLTRELAEDGY-SGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (232)
Q Consensus 23 e~i~~~~~~agi-s~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~ 78 (232)
+||++.+...|+ +.+++......+.+.|....+|.+||++|+.++.|+..+...++
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 577777777775 35666677788999999999999999999999999999998776
No 17
>PF13083 KH_4: KH domain; PDB: 3GKU_B.
Probab=96.23 E-value=0.0068 Score=44.03 Aligned_cols=68 Identities=13% Similarity=0.149 Sum_probs=45.5
Q ss_pred HHHHHHHhhhccCCeeeeEEE--EcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEE
Q 026835 20 ELNEVLTRELAEDGYSGVEVR--VTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (232)
Q Consensus 20 ~Ire~i~~~~~~agis~ieI~--rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~ 87 (232)
.+++|+...+...+=-.+++. .....+.+.+.....|.+||++|+.++.|+..+....+-...++.|.
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 367777777643332224444 34567888888889999999999999999999998775433455443
No 18
>PRK01064 hypothetical protein; Provisional
Probab=94.72 E-value=0.65 Score=34.92 Aligned_cols=68 Identities=10% Similarity=0.185 Sum_probs=46.9
Q ss_pred HHHHHhhhcc--CCeeeeEEEEcCCeEEEEEEecCC--ceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEE
Q 026835 22 NEVLTRELAE--DGYSGVEVRVTPVRTEIIIRATRT--QNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (232)
Q Consensus 22 re~i~~~~~~--agis~ieI~rt~~~i~I~I~~~rP--g~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~e 90 (232)
=+||-+.|-. ..+. ++-......+.+.+++... |.+||++|+.++.++..+.....-.+.++.+.+.+
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 LAYIVKNLVDRPEEVH-IKEVQGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIME 76 (78)
T ss_pred HHHHHHHhcCCCCeEE-EEEEeCCCEEEEEEEECcccceEEECCCCccHHHHHHHHHHHHhhCCCEEEEEEec
Confidence 3455554432 2222 4444445677788888765 78999999999999999998776555778777654
No 19
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=93.67 E-value=0.22 Score=41.09 Aligned_cols=60 Identities=12% Similarity=0.266 Sum_probs=48.2
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCC--eEEEEEEecCCceeecCCcchHHHHHHHHHHHhCC
Q 026835 20 ELNEVLTRELAEDGYSGVEVRVTPV--RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (232)
Q Consensus 20 ~Ire~i~~~~~~agis~ieI~rt~~--~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~ 79 (232)
...+|+.+.|..+.+.++.|..... .+.+.+.-..-+..||++|+.++.++..+...|+.
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 4899999999999999998854443 34444555677789999999999999999988875
No 20
>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=93.19 E-value=0.34 Score=34.19 Aligned_cols=53 Identities=15% Similarity=0.289 Sum_probs=42.9
Q ss_pred HHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecCCceeecCCcchHHHHHHHHH
Q 026835 22 NEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (232)
Q Consensus 22 re~i~~~~~~agis~ieI~rt-~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~ 74 (232)
.+|+.+.+.-+.+.++.+... .+...+.+....-+..||++|+.++.+++.+.
T Consensus 2 ~~~i~n~~~p~~i~~V~~~~~~~~~~~v~V~~~~~~~aIGk~G~nI~~~~~l~~ 55 (61)
T cd02134 2 AEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLG 55 (61)
T ss_pred HHHHHHhcCcccceEEEEecCCCcEEEEEECcccceeeECCCCHHHHHHHHHHC
Confidence 478888888888888877654 46777777778888999999999988887775
No 21
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=92.66 E-value=0.31 Score=43.07 Aligned_cols=106 Identities=17% Similarity=0.168 Sum_probs=75.4
Q ss_pred HHHHHHHHhhhccCCe-eeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCC---CeeEEEEEEecC-
Q 026835 19 AELNEVLTRELAEDGY-SGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPE---NSVELYAEKVNN- 93 (232)
Q Consensus 19 ~~Ire~i~~~~~~agi-s~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~---~~v~I~v~ev~~- 93 (232)
.++.+||...+..-|+ +.|.+...+..+.+.|....++.+||++|+.++.|+...+..++... .++.+++..-..
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 5699999998887664 56778888899999999999999999999999999998887776321 345555433221
Q ss_pred CCcChHHHHHHHHHHHhCC-c---------cchhhhHHHHH
Q 026835 94 RGLCAIAQAESLRYKLLGG-L---------AVRRACYGVLR 124 (232)
Q Consensus 94 p~~~a~~iA~~Ia~~Lekr-~---------~fRr~~k~~l~ 124 (232)
-.-.=..+|+.+|.+..+. . +=||+++.++.
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 1122345677777776432 2 23677777775
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=91.55 E-value=0.51 Score=39.57 Aligned_cols=84 Identities=20% Similarity=0.255 Sum_probs=53.1
Q ss_pred HHHHHHhhhc-cCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChH
Q 026835 21 LNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI 99 (232)
Q Consensus 21 Ire~i~~~~~-~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~p~~~a~ 99 (232)
-++.|.+... .||+.++ .-.++.=+|+|++.+||+++|++|..++++.. .+| .. ..-+..|-+.+.
T Consensus 54 A~~~I~~ivP~ea~i~di--~Fd~~tGEV~IeaeKPG~ViGk~g~~~reI~~----~tg---W~----p~vvRtpPi~S~ 120 (145)
T cd02410 54 AIKIILEIVPEEAGITDI--YFDDDTGEVIIEAEKPGLVIGKGGSTLREITR----ETG---WA----PKVVRTPPIQSR 120 (145)
T ss_pred HHHHHHHhCCCccCceee--EecCCCcEEEEEEcCCeEEEecCchhHHHHHH----HhC---Ce----eEEEecCCCCcH
Confidence 5566666443 5788755 44566678899999999999999987766554 344 22 333456666666
Q ss_pred HHHHHHHHHHhCCccchhh
Q 026835 100 AQAESLRYKLLGGLAVRRA 118 (232)
Q Consensus 100 ~iA~~Ia~~Lekr~~fRr~ 118 (232)
.+ +.|.+.|.....+|+-
T Consensus 121 ti-~~ir~~l~~~~~eR~~ 138 (145)
T cd02410 121 TV-KSIRRFLRREREERKE 138 (145)
T ss_pred HH-HHHHHHHHHhHHHHHH
Confidence 54 3455555444444443
No 23
>PRK02821 hypothetical protein; Provisional
Probab=91.43 E-value=3.9 Score=30.67 Aligned_cols=67 Identities=19% Similarity=0.224 Sum_probs=46.3
Q ss_pred HHHHHHhhhcc-CCeeeeEEEEcCCeEEEEEEecC--CceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEE
Q 026835 21 LNEVLTRELAE-DGYSGVEVRVTPVRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (232)
Q Consensus 21 Ire~i~~~~~~-agis~ieI~rt~~~i~I~I~~~r--Pg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~e 90 (232)
+=+||-+.|-. -.=-.++.+.....+.+.|+++. -|.+||++|+.++.++..+.-. .++++.+++.+
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 AVEHLVRGIVDNPDDVRVDSHTNRRGRTLEVRVHPDDLGKVIGRGGRTATALRTVVAAI---GGRGVRVDVVD 74 (77)
T ss_pred HHHHHHHHhCCCCCeEEEEEEECCCcEEEEEEEChhhCcceeCCCCchHHHHHHHHHHh---cCCeEEEEEEe
Confidence 44555555532 22223555555667778888854 4679999999999999999987 34888888765
No 24
>PRK00468 hypothetical protein; Provisional
Probab=88.82 E-value=7.9 Score=28.80 Aligned_cols=68 Identities=16% Similarity=0.217 Sum_probs=43.0
Q ss_pred HHHHHHhhhccC-CeeeeEEEEcCCeEEEEEEecC--CceeecCCcchHHHHHHHHHHHhCCCCCeeEEEE
Q 026835 21 LNEVLTRELAED-GYSGVEVRVTPVRTEIIIRATR--TQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (232)
Q Consensus 21 Ire~i~~~~~~a-gis~ieI~rt~~~i~I~I~~~r--Pg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (232)
+=+||-+.|-.. .=-.++.......+.+.|+++. -|.+||++|+.++.|+..+.-.-...+.++.+++
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 334555555321 1122444445566777777763 4689999999999999999865433346666554
No 25
>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=83.86 E-value=2.1 Score=35.52 Aligned_cols=60 Identities=15% Similarity=0.267 Sum_probs=44.7
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCe--EEEEEEecCCceeecCCcchHHHHHHHHHHHhCC
Q 026835 20 ELNEVLTRELAEDGYSGVEVRVTPVR--TEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (232)
Q Consensus 20 ~Ire~i~~~~~~agis~ieI~rt~~~--i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~ 79 (232)
.+.+|+.+.|.-|.+.+|.+...+.. ..|.+--..-+..||++|++++.....+...++.
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 38999999999999999988653223 3333434456789999999998888877776664
No 26
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=83.62 E-value=13 Score=27.84 Aligned_cols=45 Identities=18% Similarity=0.267 Sum_probs=31.7
Q ss_pred CCeEEEEEEec--CCceeecCCcchHHHHHHHHHHHhCCCCCeeEEE
Q 026835 43 PVRTEIIIRAT--RTQNVLGEKGRRIRELTSVVQKRFKFPENSVELY 87 (232)
Q Consensus 43 ~~~i~I~I~~~--rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~ 87 (232)
...+.+.|+++ =-|.+||++|+.++.|+..|.-.=.-.+.++.++
T Consensus 27 ~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~~~~~~v~i~ 73 (76)
T COG1837 27 EKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGSKDSKRVVVE 73 (76)
T ss_pred CCeEEEEEEECcccccceecCCChhHHHHHHHHHHhcccCceEEEEE
Confidence 55666666665 5568999999999999999986554333445444
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=83.34 E-value=5 Score=35.60 Aligned_cols=65 Identities=22% Similarity=0.339 Sum_probs=42.6
Q ss_pred HHHHHHhhhccC-Cee-eeEEE---EcC---CeEEEEEEecCCc---eeecCCcchHHHH----HHHHHHHhCCCCCeeE
Q 026835 21 LNEVLTRELAED-GYS-GVEVR---VTP---VRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (232)
Q Consensus 21 Ire~i~~~~~~a-gis-~ieI~---rt~---~~i~I~I~~~rPg---~iIG~~g~~i~~l----~~~L~k~~~~~~~~v~ 85 (232)
|||-+...+... -|+ .++|+ ..+ ..+...|++.|++ ++||++|+.|+++ ++.|++.|+ .+|+
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 777776665542 111 12222 222 2477889998875 6999999999766 566788888 6777
Q ss_pred EEE
Q 026835 86 LYA 88 (232)
Q Consensus 86 I~v 88 (232)
+.+
T Consensus 265 l~l 267 (270)
T TIGR00436 265 LEL 267 (270)
T ss_pred EEE
Confidence 654
No 28
>COG1159 Era GTPase [General function prediction only]
Probab=81.44 E-value=11 Score=35.04 Aligned_cols=72 Identities=22% Similarity=0.258 Sum_probs=45.7
Q ss_pred HHHHHHhhhccC--CeeeeEEEEcC------CeEEEEEEecCC---ceeecCCcchHHHH----HHHHHHHhCCCCCeeE
Q 026835 21 LNEVLTRELAED--GYSGVEVRVTP------VRTEIIIRATRT---QNVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (232)
Q Consensus 21 Ire~i~~~~~~a--gis~ieI~rt~------~~i~I~I~~~rP---g~iIG~~g~~i~~l----~~~L~k~~~~~~~~v~ 85 (232)
|||=+...+.+. -...++|++.. ..+.-+|+++|- +++||++|+.|+++ +..|++.|+ .+|.
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 565554444331 12346665432 256677888765 47999999999765 677888888 5677
Q ss_pred EEE-EEecCCC
Q 026835 86 LYA-EKVNNRG 95 (232)
Q Consensus 86 I~v-~ev~~p~ 95 (232)
+++ ++|++..
T Consensus 273 L~L~VKVk~~W 283 (298)
T COG1159 273 LELWVKVKKNW 283 (298)
T ss_pred EEEEEEEcccc
Confidence 664 4566543
No 29
>PRK15494 era GTPase Era; Provisional
Probab=81.44 E-value=5.9 Score=36.78 Aligned_cols=70 Identities=26% Similarity=0.399 Sum_probs=45.4
Q ss_pred HHHHHHhhhccC-Ce-eeeEEEEc---C---CeEEEEEEecCCc---eeecCCcchHHHH----HHHHHHHhCCCCCeeE
Q 026835 21 LNEVLTRELAED-GY-SGVEVRVT---P---VRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVE 85 (232)
Q Consensus 21 Ire~i~~~~~~a-gi-s~ieI~rt---~---~~i~I~I~~~rPg---~iIG~~g~~i~~l----~~~L~k~~~~~~~~v~ 85 (232)
|||-+...+... -| ..++|+.- . ..|...||+.|++ +|||++|+.|+++ +..|++.|+ .+|.
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 787777766542 11 11333321 2 2477889999887 5999999999766 566788888 5666
Q ss_pred EEE-EEecC
Q 026835 86 LYA-EKVNN 93 (232)
Q Consensus 86 I~v-~ev~~ 93 (232)
+.+ ++|++
T Consensus 317 l~l~Vkv~~ 325 (339)
T PRK15494 317 LFLFVKVRE 325 (339)
T ss_pred EEEEEEECC
Confidence 664 34443
No 30
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=80.90 E-value=8.2 Score=38.80 Aligned_cols=50 Identities=24% Similarity=0.420 Sum_probs=36.7
Q ss_pred HHHHHHhhh-ccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHH
Q 026835 21 LNEVLTREL-AEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSV 72 (232)
Q Consensus 21 Ire~i~~~~-~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~ 72 (232)
-++.|.+.. ..||++. |.-..+.=+|+|++.+||++||+.|+.++++...
T Consensus 77 A~~~I~eivP~ea~i~~--i~Fd~~tGEViIea~KPGlvigk~g~~~reI~~~ 127 (637)
T COG1782 77 ARKIILEIVPEEAGITD--IYFDDDTGEVIIEAKKPGLVIGKGGSTLREITAE 127 (637)
T ss_pred HHHHHHHhCccccCcee--EEecCCCceEEEEecCCceEEecCchHHHHHHHH
Confidence 344444444 3588886 5556777889999999999999999877665544
No 31
>PRK00089 era GTPase Era; Reviewed
Probab=79.22 E-value=12 Score=33.39 Aligned_cols=65 Identities=28% Similarity=0.402 Sum_probs=41.9
Q ss_pred HHHHHHhhhccC-Cee-eeEEE---E-cCCeEEEEEEecCCc---eeecCCcchHHHH----HHHHHHHhCCCCCeeEEE
Q 026835 21 LNEVLTRELAED-GYS-GVEVR---V-TPVRTEIIIRATRTQ---NVLGEKGRRIREL----TSVVQKRFKFPENSVELY 87 (232)
Q Consensus 21 Ire~i~~~~~~a-gis-~ieI~---r-t~~~i~I~I~~~rPg---~iIG~~g~~i~~l----~~~L~k~~~~~~~~v~I~ 87 (232)
|||-+...|... -|+ .++|+ . ....+.-.|++.+++ ++||++|+.|+++ ++.|++.|+ .+|.++
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 677776666542 111 12222 1 223477788998875 6999999999766 566888888 566655
Q ss_pred E
Q 026835 88 A 88 (232)
Q Consensus 88 v 88 (232)
+
T Consensus 272 l 272 (292)
T PRK00089 272 L 272 (292)
T ss_pred E
Confidence 4
No 32
>TIGR03675 arCOG00543 arCOG00543 universal archaeal KH-domain/beta-lactamase-domain protein. This family of proteins is universal in the archaea and consistsof an N-terminal type-1 KH-domain (pfam00013) a central beta-lactamase-domain (pfam00753) with a C-terminal motif associated with RNA metabolism (pfam07521). KH-domains are associated with RNA-binding, so taken together, this protein is a likely metal-dependent RNAase. This family was defined in as arCOG01782.
Probab=72.27 E-value=23 Score=36.12 Aligned_cols=111 Identities=21% Similarity=0.220 Sum_probs=63.2
Q ss_pred HHHHHHhhh-ccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChH
Q 026835 21 LNEVLTREL-AEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAI 99 (232)
Q Consensus 21 Ire~i~~~~-~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~p~~~a~ 99 (232)
-++.|.+.. .+||+.++ .-.+..=+|+|.+.+||.+||+.|..++++.+. +| .. ..-+..|-+...
T Consensus 71 ~~~~i~~~~~~~~~~~~~--~f~~~~~~v~i~~~~p~~~~~~~~~~~~~i~~~----~~---w~----~~~~~~~~~~~~ 137 (630)
T TIGR03675 71 AIEKIKEIVPEEAGITDI--YFDDVTGEVIIEAEKPGLVIGKGGSTLREITAE----TG---WT----PKVVRTPPIESK 137 (630)
T ss_pred HHHHHHHhCCCcCCceeE--EecCCCceEEEEEcCCeEEEecCcchHHHHHHH----hC---Ce----eeEEecCCCCcH
Confidence 455555544 35788654 455677788999999999999999887765543 33 22 333556666666
Q ss_pred HHHHHHHHHHhCCccchhhh-HHHHHHHHh---cCCceeEEEEccccccc
Q 026835 100 AQAESLRYKLLGGLAVRRAC-YGVLRFIME---SGAKGCEVIVSGKLRAQ 145 (232)
Q Consensus 100 ~iA~~Ia~~Lekr~~fRr~~-k~~l~~~m~---~gakGikI~iSGRL~G~ 145 (232)
.+ +.|.+-|.+....|+-+ ++.=+++-+ ..-.=++|..=|=.+..
T Consensus 138 ~~-~~~~~~~~~~~~~r~~~l~~~~~~i~~~~~~~~~~m~i~~LGg~~eV 186 (630)
T TIGR03675 138 TI-KNIREYLRSESEERKEFLRKLGRRIHRDPIFKDRWVRVTALGGFREV 186 (630)
T ss_pred HH-HHHHHHHHHhHHHHHHHHHHHHHhhcCCCCCCCCeEEEEEEecCCcc
Confidence 55 34444444433333333 222223322 13334666665544433
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=71.67 E-value=4.1 Score=28.57 Aligned_cols=28 Identities=18% Similarity=0.455 Sum_probs=21.3
Q ss_pred EEEEEEecCCceeecCCcchHHHHHHHH
Q 026835 46 TEIIIRATRTQNVLGEKGRRIRELTSVV 73 (232)
Q Consensus 46 i~I~I~~~rPg~iIG~~g~~i~~l~~~L 73 (232)
..+.|-..+-+.+||++|+.+++|++.-
T Consensus 4 ~~i~Ip~~~ig~iIGkgG~~ik~I~~~t 31 (61)
T cd02393 4 ETMKIPPDKIRDVIGPGGKTIKKIIEET 31 (61)
T ss_pred EEEEeChhheeeeECCCchHHHHHHHHH
Confidence 4455666778899999999988766643
No 34
>PF13014 KH_3: KH domain
Probab=67.08 E-value=4.8 Score=25.97 Aligned_cols=18 Identities=22% Similarity=0.543 Sum_probs=14.5
Q ss_pred CceeecCCcchHHHHHHH
Q 026835 55 TQNVLGEKGRRIRELTSV 72 (232)
Q Consensus 55 Pg~iIG~~g~~i~~l~~~ 72 (232)
-+.|||++|..|++|++.
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
>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=64.49 E-value=58 Score=31.08 Aligned_cols=119 Identities=12% Similarity=0.148 Sum_probs=79.7
Q ss_pred hHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHH-HHHHhCC---c--cchhhhHHHHH--------------
Q 026835 65 RIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESL-RYKLLGG---L--AVRRACYGVLR-------------- 124 (232)
Q Consensus 65 ~i~~l~~~L~k~~~~~~~~v~I~v~ev~~p~~~a~~iA~~I-a~~Lekr---~--~fRr~~k~~l~-------------- 124 (232)
....|...|...+. ++|.|....++=|+++..++.++| ...+.+. . .|+|.+...+-
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 45577778888886 899999999999999999999999 4444432 1 23333221110
Q ss_pred -------------------------------------HHHhcCCceeEEEEcccccccceeee--eeecCee--------
Q 026835 125 -------------------------------------FIMESGAKGCEVIVSGKLRAQRAKSM--KFKDGYM-------- 157 (232)
Q Consensus 125 -------------------------------------~~m~~gakGikI~iSGRL~G~rARte--~~~~G~v-------- 157 (232)
-.|.--.-|..++.+||+.-...|+- .+..|..
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 01123467999999999998754544 4444542
Q ss_pred -------eecccccccceeEEEEEEecCCeeeeEEEEEE
Q 026835 158 -------ISSGQPVNEYIDSAVRHVLLRQGVLGIKVKIM 189 (232)
Q Consensus 158 -------l~tG~~~~~~Idya~~~a~Tk~GviGIKVWI~ 189 (232)
|.- +..+.+...-.-.++.|.+||||..-
T Consensus 313 n~~n~ykLNy---i~~n~~i~~~s~inknGKynIkvkLN 348 (350)
T PF05316_consen 313 NINNNYKLNY---IPSNHNIYNNSNINKNGKYNIKVKLN 348 (350)
T ss_pred hcccceeecc---cCCcceeccccccccCceeeeEEEEe
Confidence 222 45556666666688999999999763
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=63.61 E-value=8.7 Score=25.95 Aligned_cols=27 Identities=15% Similarity=0.473 Sum_probs=20.9
Q ss_pred EEEEEecCCceeecCCcchHHHHHHHH
Q 026835 47 EIIIRATRTQNVLGEKGRRIRELTSVV 73 (232)
Q Consensus 47 ~I~I~~~rPg~iIG~~g~~i~~l~~~L 73 (232)
++.|-...-+.+||++|+.++++++.-
T Consensus 3 ~i~ip~~~~~~vIG~~G~~i~~I~~~s 29 (64)
T cd00105 3 RVLVPSSLVGRIIGKGGSTIKEIREET 29 (64)
T ss_pred EEEEchhhcceeECCCCHHHHHHHHHH
Confidence 445555677899999999998877664
No 37
>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=56.34 E-value=10 Score=26.49 Aligned_cols=26 Identities=15% Similarity=0.549 Sum_probs=20.0
Q ss_pred EEEEEecCCceeecCCcchHHHHHHH
Q 026835 47 EIIIRATRTQNVLGEKGRRIRELTSV 72 (232)
Q Consensus 47 ~I~I~~~rPg~iIG~~g~~i~~l~~~ 72 (232)
++.|-...-+.+||++|..+++|++.
T Consensus 3 r~~ip~~~vg~iIG~~G~~i~~i~~~ 28 (65)
T cd02396 3 RLLVPSSQAGSIIGKGGSTIKEIREE 28 (65)
T ss_pred EEEECHHHcCeeECCCcHHHHHHHHH
Confidence 44555566778999999999887765
No 38
>PF00013 KH_1: KH domain syndrome, contains KH motifs.; InterPro: IPR018111 The K homology (KH) domain was first identified in the human heterogeneous nuclear ribonucleoprotein (hnRNP) K. It is a domain of around 70 amino acids that is present in a wide variety of quite diverse nucleic acid-binding proteins []. It has been shown to bind RNA [, ]. Like many other RNA-binding motifs, KH motifs are found in one or multiple copies (14 copies in chicken vigilin) and, at least for hnRNP K (three copies) and FMR-1 (two copies), each motif is necessary for in vitro RNA binding activity, suggesting that they may function cooperatively or, in the case of single KH motif proteins (for example, Mer1p), independently []. According to structural [, , ] analysis the KH domain can be separated in two groups. The first group or type-1 contain a beta-alpha-alpha-beta-beta-alpha structure, whereas in the type-2 the two last beta-sheet are located in the N-terminal part of the domain (alpha-beta-beta-alpha-alpha-beta). Sequence similarity between these two folds are limited to a short region (VIGXXGXXI) in the RNA binding motif. This motif is located between helice 1 and 2 in type-1 and between helice 2 and 3 in type-2. Proteins known to contain a type-1 KH domain include bacterial polyribonucleotide nucleotidyltransferases (2.7.7.8 from EC); vertebrate fragile X mental retardation protein 1 (FMR1); eukaryotic heterogeneous nuclear ribonucleoprotein K (hnRNP K), one of at least 20 major proteins that are part of hnRNP particles in mammalian cells; mammalian poly(rC) binding proteins; Artemia salina glycine-rich protein GRP33; yeast PAB1-binding protein 2 (PBP2); vertebrate vigilin; and human high-density lipoprotein binding protein (HDL-binding protein). More information about these proteins can be found at Protein of the Month: RNA Exosomes [].; GO: 0003723 RNA binding; PDB: 1TUA_A 2Z0S_A 1WE8_A 4AM3_B 4AIM_A 4AID_A 2HH3_A 2JVZ_A 1J4W_A 2HH2_A ....
Probab=52.42 E-value=5 Score=27.35 Aligned_cols=27 Identities=22% Similarity=0.476 Sum_probs=20.5
Q ss_pred EEEEEecCCceeecCCcchHHHHHHHH
Q 026835 47 EIIIRATRTQNVLGEKGRRIRELTSVV 73 (232)
Q Consensus 47 ~I~I~~~rPg~iIG~~g~~i~~l~~~L 73 (232)
++.|....-+.+||++|..+++|++.-
T Consensus 3 ~i~vp~~~~~~iIG~~G~~i~~I~~~t 29 (60)
T PF00013_consen 3 RIEVPSSLVGRIIGKKGSNIKEIEEET 29 (60)
T ss_dssp EEEEEHHHHHHHHTGGGHHHHHHHHHH
T ss_pred EEEECHHHcCEEECCCCCcHHHhhhhc
Confidence 455666677889999999988776654
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=52.09 E-value=76 Score=26.83 Aligned_cols=50 Identities=22% Similarity=0.314 Sum_probs=38.3
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEE
Q 026835 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (232)
Q Consensus 28 ~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ 89 (232)
.+...||. ..++.++|-+.+|.+ +..+.++++.|.+.++++..+|+|...
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 246778999999976 678899999999999987677776653
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=51.12 E-value=11 Score=25.72 Aligned_cols=26 Identities=23% Similarity=0.425 Sum_probs=19.5
Q ss_pred EEEEecCCceeecCCcchHHHHHHHH
Q 026835 48 IIIRATRTQNVLGEKGRRIRELTSVV 73 (232)
Q Consensus 48 I~I~~~rPg~iIG~~g~~i~~l~~~L 73 (232)
+.|-...-+.+||++|+.+++|++.-
T Consensus 4 i~Vp~~~~~~iIG~~G~~i~~i~~~~ 29 (62)
T cd02394 4 VEIPKKLHRFIIGKKGSNIRKIMEET 29 (62)
T ss_pred EEeCHHHhhhccCCCCCcHHHHHHHh
Confidence 34444566789999999999887754
No 41
>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=47.17 E-value=98 Score=26.30 Aligned_cols=49 Identities=27% Similarity=0.334 Sum_probs=37.6
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEE
Q 026835 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (232)
Q Consensus 28 ~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (232)
.+...||. ..++.++|-+.+|.+ +..+.++++.|.+.++++..+|+|..
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 55667764 236778999999976 67889999999999998767777664
No 42
>PF13184 KH_5: NusA-like KH domain; PDB: 1HH2_P 1L2F_A 2ATW_A 1K0R_B 2ASB_A.
Probab=45.15 E-value=16 Score=26.61 Aligned_cols=32 Identities=22% Similarity=0.499 Sum_probs=25.6
Q ss_pred CCeEEEEEEecC-----CceeecCCcchHHHHHHHHH
Q 026835 43 PVRTEIIIRATR-----TQNVLGEKGRRIRELTSVVQ 74 (232)
Q Consensus 43 ~~~i~I~I~~~r-----Pg~iIG~~g~~i~~l~~~L~ 74 (232)
.+++.|.++... -|..+|.+|.+++.+.+.|.
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 357788888887 56799999999999888874
No 43
>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=44.75 E-value=1.1e+02 Score=25.88 Aligned_cols=50 Identities=24% Similarity=0.295 Sum_probs=37.9
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEE
Q 026835 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAE 89 (232)
Q Consensus 28 ~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ 89 (232)
.+...||. ..++.++|-+.+|.+ +....++++.|.+.++++..+|+|...
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 44556664 246778888999976 678899999999999987677776653
No 44
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=44.44 E-value=78 Score=27.08 Aligned_cols=62 Identities=21% Similarity=0.214 Sum_probs=45.7
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEE-EEecCCc-eeecCCcchHHHHHHHHHHHhCCCCCeeEEEE
Q 026835 21 LNEVLTRELAEDGYSGVEVRVTPVRTEII-IRATRTQ-NVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (232)
Q Consensus 21 Ire~i~~~~~~agis~ieI~rt~~~i~I~-I~~~rPg-~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (232)
+.+|+.+.|.-|.+.++.+...+++...+ +++..-. ..+ ...++.+.+.+++++| +.+.+.+
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 89999999999999999998888865444 6664321 122 4567889999999998 6666554
No 45
>PRK00084 ispF 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase; Reviewed
Probab=43.75 E-value=1.1e+02 Score=25.93 Aligned_cols=40 Identities=23% Similarity=0.339 Sum_probs=32.6
Q ss_pred CeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEE
Q 026835 44 VRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (232)
Q Consensus 44 ~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (232)
.++.++|-+.+|.+ +....++++.|.+.++++..+|+|..
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 35777889999976 67889999999999998766777665
No 46
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=40.21 E-value=66 Score=26.44 Aligned_cols=42 Identities=10% Similarity=0.213 Sum_probs=30.7
Q ss_pred ccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHH
Q 026835 30 AEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (232)
Q Consensus 30 ~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L 73 (232)
-++..-.|-+. .+.+.+.+.....|..+|++|++++.+++.+
T Consensus 20 t~~~~~dc~~d--~~~vi~vV~~~~vG~~IG~~G~rI~~i~e~l 61 (140)
T PRK08406 20 TGATVKDCIID--DDRIIFVVKEGDMGLAIGKGGENVKRLEEKL 61 (140)
T ss_pred hCCCceEEEEe--CCEEEEEEeCCCccccCCcCchHHHHHHHHh
Confidence 34444444333 3888888888899999999999999985544
No 47
>PRK06418 transcription elongation factor NusA-like protein; Validated
Probab=38.40 E-value=74 Score=27.21 Aligned_cols=31 Identities=10% Similarity=0.203 Sum_probs=24.4
Q ss_pred CCeEEEEEEecCCceeecCCcchHHHHHHHHH
Q 026835 43 PVRTEIIIRATRTQNVLGEKGRRIRELTSVVQ 74 (232)
Q Consensus 43 ~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~ 74 (232)
.+++-+.+.... |.-||++|+.+++|++.|.
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 567766666677 8899999999888777665
No 48
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=38.29 E-value=50 Score=30.85 Aligned_cols=81 Identities=15% Similarity=0.231 Sum_probs=46.8
Q ss_pred EEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCccchhh
Q 026835 39 VRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRA 118 (232)
Q Consensus 39 I~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~ 118 (232)
++|..-.++|.+....-|.|||++|++|+.|+....-....++.+--=.|..|..-...---+-..|--.||.+...+.-
T Consensus 43 ~k~~r~e~ril~~sk~agavigkgg~nik~lr~d~na~v~vpds~~peri~tisad~~ti~~ilk~iip~lee~f~~~~p 122 (390)
T KOG2192|consen 43 FKRSRVELRILLQSKNAGAVIGKGGKNIKALRTDYNASVSVPDSSGPERILTISADIETIGEILKKIIPTLEEGFQLPSP 122 (390)
T ss_pred hhhcceeEEEEEecccccceeccccccHHHHhhhccceeeccCCCCCceeEEEeccHHHHHHHHHHHhhhhhhCCCCCCc
Confidence 33444556778888899999999999999988765543333221111111122222222233446666778877765554
Q ss_pred h
Q 026835 119 C 119 (232)
Q Consensus 119 ~ 119 (232)
+
T Consensus 123 c 123 (390)
T KOG2192|consen 123 C 123 (390)
T ss_pred h
Confidence 4
No 49
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=38.23 E-value=94 Score=29.67 Aligned_cols=56 Identities=23% Similarity=0.363 Sum_probs=42.6
Q ss_pred HHHHHHHHhhhccCCeeeeE---EEEcC-CeEEEEEEecCCce-----eecCCcchHHHHHHHHH
Q 026835 19 AELNEVLTRELAEDGYSGVE---VRVTP-VRTEIIIRATRTQN-----VLGEKGRRIRELTSVVQ 74 (232)
Q Consensus 19 ~~Ire~i~~~~~~agis~ie---I~rt~-~~i~I~I~~~rPg~-----iIG~~g~~i~~l~~~L~ 74 (232)
..+++.|+.+...-.=+-|+ |.|.| .+++|-+++..|+. .||.+|.+++.+.+.|.
T Consensus 202 ~~v~~Lfe~EVPEI~~G~VeIk~iaR~pG~RtKVAV~s~~~~iDpvGa~iG~~G~rI~~i~~el~ 266 (362)
T PRK12327 202 GLVKRLFELEVPEIYDGTVEIKSIAREAGDRTKIAVRSNNPNVDAKGACVGPKGQRVQNIVSELK 266 (362)
T ss_pred HHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCchheeECCCChhHHHHHHHhC
Confidence 34888888877764333344 55654 79999999998865 99999999999988885
No 50
>TIGR01953 NusA transcription termination factor NusA. This model describes NusA, or N utilization substance protein A, a bacterial transcription termination factor. It binds to RNA polymerase alpha subunit and promotes termination at certain RNA hairpin structures. It is named for the interaction in E. coli of phage lambda antitermination protein N with the N-utilization substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and nusG. This model represents a region of NusA shared in all bacterial forms, and including an S1 (pfam00575) and a KH (pfam00013) RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this model, with two repeats of 50-residue domain rich in acidic amino acids.
Probab=36.70 E-value=1.6e+02 Score=27.76 Aligned_cols=57 Identities=25% Similarity=0.363 Sum_probs=42.9
Q ss_pred hHHHHHHHHhhhccCCeeeeE---EEEcC-CeEEEEEEecCCce-----eecCCcchHHHHHHHHH
Q 026835 18 FAELNEVLTRELAEDGYSGVE---VRVTP-VRTEIIIRATRTQN-----VLGEKGRRIRELTSVVQ 74 (232)
Q Consensus 18 ~~~Ire~i~~~~~~agis~ie---I~rt~-~~i~I~I~~~rPg~-----iIG~~g~~i~~l~~~L~ 74 (232)
-..+++.|+.+...-.=+-|+ |-|.| .+++|-+++..|+. .+|.+|.+++.+.+.|.
T Consensus 199 ~~~v~~Lfe~EVPEI~dG~VeI~~iaR~pG~RtKvAV~s~~~~iDpvga~vG~~G~ri~~i~~el~ 264 (341)
T TIGR01953 199 PEFVKELLKLEVPEIADGIIEIKKIAREPGYRTKIAVESNDENIDPVGACVGPKGSRIQAISKELN 264 (341)
T ss_pred HHHHHHHHHHhCccccCCeEEEEEEeeCCcceeEEEEEcCCCCCCcceeeECCCCchHHHHHHHhC
Confidence 335888888877754323334 56665 79999999998864 99999999999988884
No 51
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=36.63 E-value=54 Score=32.33 Aligned_cols=51 Identities=14% Similarity=0.268 Sum_probs=41.6
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHH
Q 026835 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTS 71 (232)
Q Consensus 21 Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~ 71 (232)
..+|+.+.|.-|.+.+|.+......+.|++--..-+..||++|++++...+
T Consensus 279 ~~~fi~nal~pa~v~~v~~~~~~~~~~v~V~~~~~~~AIGk~G~Nvrla~~ 329 (470)
T PRK09202 279 PAQFIINALSPAEVSSVVVDEDEHSADVVVPDDQLSLAIGKNGQNVRLASK 329 (470)
T ss_pred HHHHHHHhCCCCEEEEEEEeCCCCEEEEEECcchHHHhhCCCCeeHHHHHH
Confidence 788999999999999997766666777777777888999999999865443
No 52
>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=35.68 E-value=2.7e+02 Score=25.34 Aligned_cols=53 Identities=25% Similarity=0.272 Sum_probs=37.2
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCC
Q 026835 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKF 79 (232)
Q Consensus 20 ~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~ 79 (232)
++.+++.......++..+-|-.|.|+++|++++..+. ...+.+.+.|...+++
T Consensus 25 ~~~~~l~~l~~~~~~~e~viLsTCNR~EiY~~~~~~~-------~~~~~~~~~l~~~~~~ 77 (311)
T cd05213 25 ELKEALRRLLEKPGISEAVLLSTCNRVELYLVGDNFH-------KLADELEELLAELLNE 77 (311)
T ss_pred HHHHHHHHHhcCCCCceEEEEecCCeEEEEEEeCCcc-------hhHHHHHHHHHHhcCc
Confidence 3566776666667889999999999999998875542 2234556666665553
No 53
>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=34.52 E-value=75 Score=21.53 Aligned_cols=32 Identities=13% Similarity=0.179 Sum_probs=25.2
Q ss_pred CcchHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026835 62 KGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (232)
Q Consensus 62 ~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~ 93 (232)
+.+-++.+.+.|...++.+...+.+.+.++..
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 34456788888899999888889888887654
No 54
>COG1942 Uncharacterized protein, 4-oxalocrotonate tautomerase homolog [General function prediction only]
Probab=33.68 E-value=75 Score=23.21 Aligned_cols=46 Identities=15% Similarity=0.123 Sum_probs=31.5
Q ss_pred EEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026835 48 IIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (232)
Q Consensus 48 I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~ 93 (232)
|+|...+.+.--..|.+-++.+++.+.+.+|.++..+.|-+.++..
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 3445544222222244557899999999999888888888888765
No 55
>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=32.68 E-value=30 Score=29.17 Aligned_cols=58 Identities=14% Similarity=0.250 Sum_probs=38.5
Q ss_pred ecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEE----EEe--cCCCcChHHHHHHHHHHHhCCccch
Q 026835 52 ATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA----EKV--NNRGLCAIAQAESLRYKLLGGLAVR 116 (232)
Q Consensus 52 ~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v----~ev--~~p~~~a~~iA~~Ia~~Lekr~~fR 116 (232)
..+-+.+||++|+.+++|++...- +++++- ..| ..++.++..-|..+...|-++.++.
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 345678999999988887665542 233322 233 4566778888888888887765533
No 56
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=31.13 E-value=1.1e+02 Score=29.62 Aligned_cols=63 Identities=17% Similarity=0.203 Sum_probs=43.5
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEE
Q 026835 21 LNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEK 90 (232)
Q Consensus 21 Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~e 90 (232)
..+|+.+.|.-|.+.+|.+........+++--..-++.||++|++++- -++++| .++.|.-.+
T Consensus 285 ~~~fI~Nal~Pa~V~~V~i~~~~~~~~V~V~~~qlslAIGk~GqNvrL----A~~LtG---wkIDI~s~~ 347 (374)
T PRK12328 285 PEIFIARALAPAIISSVKIEEEEKKAIVTLLSDQKSKAIGKNGINIRL----ASMLTG---YEIELNEIG 347 (374)
T ss_pred HHHHHHHhCCCceeeEEEEcCCCcEEEEEEChHHhhhhhcCCChhHHH----HHHHhC---CEEEEEECC
Confidence 788999999999998887763334455555555667899999999853 234455 566655433
No 57
>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=30.76 E-value=2.1e+02 Score=24.47 Aligned_cols=57 Identities=12% Similarity=0.345 Sum_probs=40.5
Q ss_pred HHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEE
Q 026835 24 VLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVEL 86 (232)
Q Consensus 24 ~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I 86 (232)
.|+..+...||..+-..-..+.+.|++.+.. + ......++...+.+.++++..+|.|
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 4455667789999999888999999888865 1 3557789999999999987677765
No 58
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=30.70 E-value=2.1e+02 Score=27.63 Aligned_cols=61 Identities=20% Similarity=0.199 Sum_probs=45.3
Q ss_pred cCcChHHHHHHHHhhhccCCeeeeE---EEEcC-CeEEEEEEecCCce-----eecCCcchHHHHHHHHH
Q 026835 14 DGVFFAELNEVLTRELAEDGYSGVE---VRVTP-VRTEIIIRATRTQN-----VLGEKGRRIRELTSVVQ 74 (232)
Q Consensus 14 ~~~~~~~Ire~i~~~~~~agis~ie---I~rt~-~~i~I~I~~~rPg~-----iIG~~g~~i~~l~~~L~ 74 (232)
....-..+++.|+.+...-.=+-|+ |.|.| .+++|-+++..|+. .||.+|.+|+.+.+.|.
T Consensus 203 SRt~p~~v~~Lfe~EVPEI~dG~VeIk~IARepG~RtKVAV~S~d~~iDPvGacIG~~G~rI~~I~~eL~ 272 (374)
T PRK12328 203 SRTSPKFLEALLELEVPEIKDGEVIIIHSARIPGERAKVALFSNNPNIDPIGATVGVKGVRINAVSKELN 272 (374)
T ss_pred EcCCHHHHHHHHHHhCccccCCeEEEEEEeccCcceeEEEEEcCCCCCChHHhhcCCCcchHHHHHHHhC
Confidence 3334445888888888764333344 55654 79999999998875 89999999999988884
No 59
>PRK05090 hypothetical protein; Validated
Probab=30.59 E-value=2.6e+02 Score=21.70 Aligned_cols=24 Identities=21% Similarity=0.423 Sum_probs=19.4
Q ss_pred cchHHHHHHHHHHHhCCCCCeeEE
Q 026835 63 GRRIRELTSVVQKRFKFPENSVEL 86 (232)
Q Consensus 63 g~~i~~l~~~L~k~~~~~~~~v~I 86 (232)
|+-=+.|...|.+.|+++..+|.|
T Consensus 45 GkAN~ali~~LAk~l~v~ks~I~i 68 (95)
T PRK05090 45 GQANAHLLKFLAKQFRVAKSQVVI 68 (95)
T ss_pred ChHHHHHHHHHHHHhCCChhhEEE
Confidence 555589999999999998766665
No 60
>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=30.50 E-value=97 Score=25.67 Aligned_cols=43 Identities=9% Similarity=0.275 Sum_probs=28.7
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHH
Q 026835 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTS 71 (232)
Q Consensus 28 ~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~ 71 (232)
.+.++..-.|.+.-.. ++-.++.....|..+|.+|++++.+++
T Consensus 18 ~~t~~~~~dc~~d~~~-riifvV~~g~vG~~IG~~G~rIk~i~e 60 (141)
T TIGR01952 18 DMTGATVVDCLIDDRN-RVVFVVKEGEMGAAIGKGGENVKRLEE 60 (141)
T ss_pred HHhCCceEEEEecCCc-EEEEEEcCCCccccCCCCchHHHHHHH
Confidence 4445666666554422 555555556778999999999999843
No 61
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=30.16 E-value=1.5e+02 Score=25.76 Aligned_cols=61 Identities=11% Similarity=0.186 Sum_probs=43.4
Q ss_pred HHHHHHhhhccCCeeeeEEEEcCC-eEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEE
Q 026835 21 LNEVLTRELAEDGYSGVEVRVTPV-RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (232)
Q Consensus 21 Ire~i~~~~~~agis~ieI~rt~~-~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (232)
..+|+.+.|.-|.+.+|.+.-... ...+.+.-..-+..||++|+.++-. +++++ .++.|..
T Consensus 118 ~~~fI~nal~Pa~v~~V~~~~~d~~~~~v~V~~~~~~~aIGk~G~Nvrla----~~Ltg---~~i~I~~ 179 (190)
T COG0195 118 PAEFIKNALAPAEVLSVNIKEDDGHVAIVVVPPDQLSLAIGKGGQNVRLA----SQLTG---WEIDIET 179 (190)
T ss_pred HHHHHHHhcCcceEeEEEEEeCCCcEEEEEECHHHHhhccCcccHHHHHH----HHHhC---CEEEEEe
Confidence 788999999999999998887433 4555566667778999999777544 34444 4555443
No 62
>PLN02862 2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase
Probab=29.82 E-value=2.3e+02 Score=25.36 Aligned_cols=49 Identities=18% Similarity=0.165 Sum_probs=37.0
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEE
Q 026835 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (232)
Q Consensus 28 ~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (232)
.+..+||. ..++.++|-+.+|.+ +..+.++++.|.+.++++..+|+|..
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 44556654 235777889999976 67889999999999998766676654
No 63
>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=29.45 E-value=1e+02 Score=24.81 Aligned_cols=34 Identities=12% Similarity=0.217 Sum_probs=26.8
Q ss_pred ChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEe
Q 026835 17 FFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRA 52 (232)
Q Consensus 17 ~~~~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~ 52 (232)
+..+|..||.+.+...||. |-|+| ++...|+..+
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 4578999999999999988 77999 5666766444
No 64
>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=28.69 E-value=1.1e+02 Score=20.20 Aligned_cols=32 Identities=19% Similarity=0.315 Sum_probs=25.2
Q ss_pred CcchHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026835 62 KGRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (232)
Q Consensus 62 ~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~ 93 (232)
+.+-.+.+.+.+.+.++.+...+.+.+.++..
T Consensus 16 k~~l~~~i~~~l~~~~g~~~~~v~V~i~e~~~ 47 (58)
T cd00491 16 KRELIERVTEAVSEILGAPEATIVVIIDEMPK 47 (58)
T ss_pred HHHHHHHHHHHHHHHhCcCcccEEEEEEEeCc
Confidence 44556788888889999888889988888654
No 65
>PRK12329 nusA transcription elongation factor NusA; Provisional
Probab=27.53 E-value=1.6e+02 Score=29.21 Aligned_cols=57 Identities=19% Similarity=0.289 Sum_probs=42.5
Q ss_pred hHHHHHHHHhhhccC--CeeeeE-EEEc--------CCeEEEEEEecCCce-----eecCCcchHHHHHHHHH
Q 026835 18 FAELNEVLTRELAED--GYSGVE-VRVT--------PVRTEIIIRATRTQN-----VLGEKGRRIRELTSVVQ 74 (232)
Q Consensus 18 ~~~Ire~i~~~~~~a--gis~ie-I~rt--------~~~i~I~I~~~rPg~-----iIG~~g~~i~~l~~~L~ 74 (232)
-..+++.|+.+.... |+-.|. |-|. ..+++|-+++..|+. .||.+|.+|+.+.+.|.
T Consensus 226 p~lv~~Lfe~EVPEI~dG~VeIk~IAREa~~~~ripG~RtKVAV~S~d~~VDPvGacVG~kG~RI~~I~~eL~ 298 (449)
T PRK12329 226 AGLVVYLFENEVPEIEEGVVRIVAVAREANPPSRYVGPRTKIAVDTLERDVDPVGACIGARGSRIQAVVNELR 298 (449)
T ss_pred HHHHHHHHHhhCcccccCeEEEEEEEecCCCCCCCCcceeEEEEEcCCCCCChhhccCCCCcchHHHHHHHhC
Confidence 334788888877653 433332 5665 468999999998865 89999999999988884
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=26.60 E-value=1.3e+02 Score=22.51 Aligned_cols=57 Identities=18% Similarity=0.190 Sum_probs=33.8
Q ss_pred eeeeEEEEc-CCeEEEEEEec--CCceeecCCcch-HHHHHHHHHHHhCCCCCeeEEEEEEe
Q 026835 34 YSGVEVRVT-PVRTEIIIRAT--RTQNVLGEKGRR-IRELTSVVQKRFKFPENSVELYAEKV 91 (232)
Q Consensus 34 is~ieI~rt-~~~i~I~I~~~--rPg~iIG~~g~~-i~~l~~~L~k~~~~~~~~v~I~v~ev 91 (232)
..++.++.. ...+.|.+++. .+..+ -.-.+. -+++++.|++.+++.-..++|.+..+
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 SKGVKVEVDEDGGITVDLHVVVEYGVNI-PEVAEEIQEKVKEAVEEMTGIEVSEVNVHVEDV 107 (108)
T ss_pred CCCeEEEEccCcceEEEEEEEEECCccH-HHHHHHHHHHHHHHHHHHHCCeeEEEEEEEEec
Confidence 445667666 66677766663 22111 111222 25777778888898767788777654
No 67
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=26.02 E-value=2.6e+02 Score=27.66 Aligned_cols=59 Identities=19% Similarity=0.351 Sum_probs=44.2
Q ss_pred cChHHHHHHHHhhhccCCeeeeE---EEEcC-CeEEEEEEecCCce-----eecCCcchHHHHHHHHH
Q 026835 16 VFFAELNEVLTRELAEDGYSGVE---VRVTP-VRTEIIIRATRTQN-----VLGEKGRRIRELTSVVQ 74 (232)
Q Consensus 16 ~~~~~Ire~i~~~~~~agis~ie---I~rt~-~~i~I~I~~~rPg~-----iIG~~g~~i~~l~~~L~ 74 (232)
..-..+++.|+.+...-.=+-|+ |-|.| .+++|-+++..|.+ .+|.+|.+|+.+.+.|.
T Consensus 199 t~p~~l~~Lf~~EVPEI~~G~ieIk~iaR~pG~RaKvAV~s~d~~iDpvga~vG~~G~ri~~i~~el~ 266 (470)
T PRK09202 199 THPEFLKKLFEQEVPEIADGLIEIKAIARDPGSRAKIAVKSNDPRIDPVGACVGMRGSRIQAISNELG 266 (470)
T ss_pred CcHHHHHHHHHHhCcccccCeEEEEEEeecCcceeEEEEEcCCCCCChhHccCCCCCchHHHHHHHhC
Confidence 33445888888887764333344 55665 79999999988864 89999999999998884
No 68
>PRK09382 ispDF bifunctional 2-C-methyl-D-erythritol 4-phosphate cytidylyltransferase/2-C-methyl-D-erythritol 2,4-cyclodiphosphate synthase protein; Provisional
Probab=25.55 E-value=2.7e+02 Score=26.55 Aligned_cols=49 Identities=16% Similarity=0.255 Sum_probs=37.3
Q ss_pred hhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEE
Q 026835 28 ELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYA 88 (232)
Q Consensus 28 ~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v 88 (232)
.+...|+. ..++.++|-+.+|.+ +....++++.|.+.++++..+|+|..
T Consensus 300 ~~~~~~~~-------~~n~d~~i~~~~pk~-----~~~~~~~~~~~~~~l~~~~~~v~~ka 348 (378)
T PRK09382 300 FVREAGGE-------IINADVTIIAEAPKI-----GPHKQAMRENLAEILGIPKDRVSVKA 348 (378)
T ss_pred HHHHcCCE-------EEEEEEEEEecCCcc-----hHHHHHHHHHHHHHhCCCcceEEEEE
Confidence 44556654 236778999999976 67889999999999998766676654
No 69
>PRK12327 nusA transcription elongation factor NusA; Provisional
Probab=24.80 E-value=1.2e+02 Score=28.97 Aligned_cols=49 Identities=16% Similarity=0.236 Sum_probs=35.9
Q ss_pred HHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecCCceeecCCcchHHHH
Q 026835 21 LNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIREL 69 (232)
Q Consensus 21 Ire~i~~~~~~agis~ieI~rt-~~~i~I~I~~~rPg~iIG~~g~~i~~l 69 (232)
..+|+.+.|.-|.+.++.+... .....|++--..-+..||++|++++--
T Consensus 279 ~~~fi~nal~Pa~v~~v~i~~~~~~~~~v~V~~~~~~~AIGk~G~Nv~la 328 (362)
T PRK12327 279 PAEFVANALSPAKVVSVEVDDEEEKAARVVVPDYQLSLAIGKEGQNARLA 328 (362)
T ss_pred HHHHHHHhCCCceEEEEEEEcCCCcEEEEEEChhhcchhhcCCChhHHHH
Confidence 7889999999999999987432 233444444456678999999998543
No 70
>PRK13763 putative RNA-processing protein; Provisional
Probab=24.61 E-value=84 Score=26.72 Aligned_cols=66 Identities=15% Similarity=0.247 Sum_probs=39.7
Q ss_pred EEEEEecCCceeecCCcchHHHHHHHHHHHhCCCC--CeeEEEEEEecCCCcChHHHHHHHHHHHhCCcc
Q 026835 47 EIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPE--NSVELYAEKVNNRGLCAIAQAESLRYKLLGGLA 114 (232)
Q Consensus 47 ~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~--~~v~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~ 114 (232)
.+.|-..+.+.+||++|+.++.|++...-...+.. ..|.|.. ...++..+..-|..+...|-++..
T Consensus 6 ~i~IP~~kig~iIG~gGk~Ik~I~e~tg~~I~i~~~~g~V~I~~--~~~~d~~~i~kA~~~I~ai~~gf~ 73 (180)
T PRK13763 6 YVKIPKDRIGVLIGKKGETKKEIEERTGVKLEIDSETGEVIIEP--TDGEDPLAVLKARDIVKAIGRGFS 73 (180)
T ss_pred EEEcCHHHhhhHhccchhHHHHHHHHHCcEEEEECCCCeEEEEe--CCCCCHHHHHHHHHHHHHHhcCCC
Confidence 34445567788999999888877665432222111 2222111 115677778888888888877644
No 71
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=24.10 E-value=98 Score=31.19 Aligned_cols=51 Identities=27% Similarity=0.455 Sum_probs=33.2
Q ss_pred HHHHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecCCceeecCCcchHHHHHHHH
Q 026835 19 AELNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (232)
Q Consensus 19 ~~Ire~i~~~~~~agis~ieI~rt-~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L 73 (232)
.+|.++|.+.+.. .++++-. +...-|.+.-..-+.+||++|++|++|.+.|
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 3455444 3445555544566789999999998765543
No 72
>PRK02289 4-oxalocrotonate tautomerase; Provisional
Probab=23.52 E-value=1.3e+02 Score=20.66 Aligned_cols=31 Identities=23% Similarity=0.419 Sum_probs=25.0
Q ss_pred cchHHHHHHHHHHHhCCCCCeeEEEEEEecC
Q 026835 63 GRRIRELTSVVQKRFKFPENSVELYAEKVNN 93 (232)
Q Consensus 63 g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~ 93 (232)
.+-++.+.+.+.+.|+.+...+.+.+.++..
T Consensus 18 ~~L~~~it~a~~~~~~~p~~~v~V~i~ev~~ 48 (60)
T PRK02289 18 NALAREVTEVVSRIAKAPKEAIHVFINDMPE 48 (60)
T ss_pred HHHHHHHHHHHHHHhCcCcceEEEEEEEeCh
Confidence 3445777888888999988999999998864
No 73
>KOG2192 consensus PolyC-binding hnRNP-K protein HRB57A/hnRNP, contains KH domain [RNA processing and modification; General function prediction only]
Probab=23.34 E-value=35 Score=31.88 Aligned_cols=38 Identities=24% Similarity=0.538 Sum_probs=31.7
Q ss_pred EcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHhC
Q 026835 41 VTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFK 78 (232)
Q Consensus 41 rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~ 78 (232)
+.|-.++..||-.--|.+|||+|..|++|++.-.-+++
T Consensus 120 ~~pce~rllihqs~ag~iigrngskikelrekcsarlk 157 (390)
T KOG2192|consen 120 PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSARLK 157 (390)
T ss_pred CCchhhhhhhhhhhccceecccchhHHHHHHhhhhhhh
Confidence 44556777889899999999999999999998776654
No 74
>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=23.16 E-value=1.3e+02 Score=28.45 Aligned_cols=48 Identities=19% Similarity=0.284 Sum_probs=35.8
Q ss_pred HHHHHHhhhccCCeeeeEEEEc-CCeEEEEEEecCCceeecCCcchHHH
Q 026835 21 LNEVLTRELAEDGYSGVEVRVT-PVRTEIIIRATRTQNVLGEKGRRIRE 68 (232)
Q Consensus 21 Ire~i~~~~~~agis~ieI~rt-~~~i~I~I~~~rPg~iIG~~g~~i~~ 68 (232)
..+|+.+.|.-|.+.+|.|... .....|++--..-++.||++|++++-
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 7889999999999999987443 23444444445677899999999853
No 75
>COG4604 CeuD ABC-type enterochelin transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=22.86 E-value=3.5e+02 Score=24.62 Aligned_cols=61 Identities=13% Similarity=0.171 Sum_probs=46.2
Q ss_pred eEEEEEEecCCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHHH
Q 026835 45 RTEIIIRATRTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRY 107 (232)
Q Consensus 45 ~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~p~~~a~~iA~~Ia~ 107 (232)
.+.+.|.....-.+||.+|++-.-|-+.+..+++....++.|+=.++.+ -+..-+|+.++-
T Consensus 19 ~isl~i~~g~iTs~IGPNGAGKSTLLS~~sRL~~~d~G~i~i~g~~~~~--~~s~~LAk~lSI 79 (252)
T COG4604 19 DVSLDIPKGGITSIIGPNGAGKSTLLSMMSRLLKKDSGEITIDGLELTS--TPSKELAKKLSI 79 (252)
T ss_pred cceeeecCCceeEEECCCCccHHHHHHHHHHhccccCceEEEeeeeccc--CChHHHHHHHHH
Confidence 4455566666667999999999999999999999877888877666665 455666666543
No 76
>PRK13764 ATPase; Provisional
Probab=22.10 E-value=1.5e+02 Score=30.38 Aligned_cols=51 Identities=24% Similarity=0.434 Sum_probs=32.7
Q ss_pred HHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHH
Q 026835 20 ELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVV 73 (232)
Q Consensus 20 ~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L 73 (232)
+|.+-+.+.+ .|...+++. ..+...|++--.--+.+||++|.+|+++.+.|
T Consensus 460 ~~~~~~~~~~--~~~~~~~~~-~~~~~~v~~~~~~~~~~~~k~~~~~~~~~~~~ 510 (602)
T PRK13764 460 EIEREIKRYL--PGPVEVEVV-SDNKAVVYVPEKDIPKVIGKGGKRIKKIEKKL 510 (602)
T ss_pred HHHHHHHHhc--CCceEEEEe-cCCeEEEEEChhhhhHHhccCcchHHHHHHHh
Confidence 3666666666 456667666 34555444433444579999999998765544
No 77
>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=21.81 E-value=1.3e+02 Score=30.78 Aligned_cols=53 Identities=21% Similarity=0.342 Sum_probs=39.4
Q ss_pred HHHHHHHhhhc-cCCeeeeEEEEcCCeEEEEEEecCCceeecCCcchHHHHHHHHHHHh
Q 026835 20 ELNEVLTRELA-EDGYSGVEVRVTPVRTEIIIRATRTQNVLGEKGRRIRELTSVVQKRF 77 (232)
Q Consensus 20 ~Ire~i~~~~~-~agis~ieI~rt~~~i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~~ 77 (232)
+|++-+.+.+. ++.+++|+.+- -+|.||+..|..+.. ++.-+++|-+.|+|+.
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~~eg----p~~~~~~~~~~~~~~-~~~~~~~~~~~~~~r~ 56 (630)
T TIGR03675 3 EIKEIINELLPKDIKITDVEFEG----PELVIYTKNPELFAK-DDDLVKELAKKLRKRI 56 (630)
T ss_pred HHHHHHHHhCCCCCeEEEEEEeC----CeEEEEeCCHHHhcc-chHHHHHHHHHhhceE
Confidence 46666666774 67899998864 678999999988765 3466777777777754
No 78
>PRK13763 putative RNA-processing protein; Provisional
Probab=21.74 E-value=2e+02 Score=24.37 Aligned_cols=65 Identities=14% Similarity=0.113 Sum_probs=33.3
Q ss_pred CCceeecCCcchHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHhCCccchhhhHHHHHH
Q 026835 54 RTQNVLGEKGRRIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLLGGLAVRRACYGVLRF 125 (232)
Q Consensus 54 rPg~iIG~~g~~i~~l~~~L~k~~~~~~~~v~I~v~ev~~p~~~a~~iA~~Ia~~Lekr~~fRr~~k~~l~~ 125 (232)
..|.+||++|+.++.|++.-.-.+.+.++.+. +. - .....-.|......|-.+...-++. ..|+.
T Consensus 105 ~~griIG~~G~~~k~ie~~t~~~i~i~~~~v~--i~---G-~~~~~~~A~~~I~~li~g~~~~~~~-~~l~~ 169 (180)
T PRK13763 105 IKGRIIGEGGKTRRIIEELTGVDISVYGKTVA--II---G-DPEQVEIAREAIEMLIEGAPHGTVY-KFLER 169 (180)
T ss_pred HhhheeCCCcHHHHHHHHHHCcEEEEcCCEEE--EE---e-CHHHHHHHHHHHHHHHcCCCcHHHH-HHHHH
Confidence 46789999998877655543322222222222 21 1 3344455555555565555444333 33443
No 79
>PF13684 Dak1_2: Dihydroxyacetone kinase family
Probab=20.51 E-value=1.2e+02 Score=28.03 Aligned_cols=40 Identities=20% Similarity=0.070 Sum_probs=30.0
Q ss_pred ChHHHHHHHHhhhccCCeeeeEEEEcCCeEEEEEEecCCceeecC
Q 026835 17 FFAELNEVLTRELAEDGYSGVEVRVTPVRTEIIIRATRTQNVLGE 61 (232)
Q Consensus 17 ~~~~Ire~i~~~~~~agis~ieI~rt~~~i~I~I~~~rPg~iIG~ 61 (232)
+..++|++|... |=| +-+--+...++|.|||..||.++..
T Consensus 19 ~~~~lr~~L~~~----GdS-lvVv~~~~~~kVHvHT~~Pg~vle~ 58 (313)
T PF13684_consen 19 DAEELRARLEEL----GDS-LVVVGDDDLVKVHVHTNDPGAVLEY 58 (313)
T ss_pred CHHHHHHHHHhc----CCE-EEEEecCCeEEEEEeeCCHHHHHHH
Confidence 566788877654 323 4466778899999999999998764
No 80
>KOG2191 consensus RNA-binding protein NOVA1/PASILLA and related KH domain proteins [RNA processing and modification; General function prediction only]
Probab=20.32 E-value=1.1e+02 Score=29.50 Aligned_cols=56 Identities=16% Similarity=0.303 Sum_probs=36.6
Q ss_pred HHHHHHhhhcc-----CCeeeeEEEEcCCe---EEEEEEecCCceeecCCcchHHHHHHHHHHH
Q 026835 21 LNEVLTRELAE-----DGYSGVEVRVTPVR---TEIIIRATRTQNVLGEKGRRIRELTSVVQKR 76 (232)
Q Consensus 21 Ire~i~~~~~~-----agis~ieI~rt~~~---i~I~I~~~rPg~iIG~~g~~i~~l~~~L~k~ 76 (232)
+.+||..+++. +++..+.=.+++++ ++|.+=..--|++||+.|..|+.+++.-.-+
T Consensus 101 v~efI~dKire~p~~~~k~v~~~~pqt~~r~kqikivvPNstag~iigkggAtiK~~~Eqsga~ 164 (402)
T KOG2191|consen 101 VHEFIADKIREKPQAVAKPVDILQPQTPDRIKQIKIVVPNSTAGMIIGKGGATIKAIQEQSGAW 164 (402)
T ss_pred HHHHHHHHHHHhHHhhcCCccccCCCCccccceeEEeccCCcccceecCCcchHHHHHHhhCcc
Confidence 67777666653 34444433455655 4455545566899999999999888775543
No 81
>COG1534 Predicted RNA-binding protein containing KH domain, possibly ribosomal protein [Translation, ribosomal structure and biogenesis]
Probab=20.09 E-value=3e+02 Score=21.65 Aligned_cols=53 Identities=17% Similarity=0.150 Sum_probs=33.2
Q ss_pred EecCCceeecCCcc---hHHHHHHHHHHHhCCCCCeeEEEEEEecCCCcChHHHHHHHHHHHh
Q 026835 51 RATRTQNVLGEKGR---RIRELTSVVQKRFKFPENSVELYAEKVNNRGLCAIAQAESLRYKLL 110 (232)
Q Consensus 51 ~~~rPg~iIG~~g~---~i~~l~~~L~k~~~~~~~~v~I~v~ev~~p~~~a~~iA~~Ia~~Le 110 (232)
|..+|-..||++|- -|+++...|... =-|.|.-..+..-+-..+|+.|+.+..
T Consensus 15 h~l~piv~IGk~Glte~vi~Ei~~aL~~r-------eLIKVkvl~~~~edr~eia~~l~~~~~ 70 (97)
T COG1534 15 HHLKPIVQIGKNGLTEGVIKEIDRALEAR-------ELIKVKVLQNAREDKKEIAEALAEETG 70 (97)
T ss_pred ccCCceEEecCCccCHHHHHHHHHHHHhC-------CcEEEEeeccchhhHHHHHHHHHHHhC
Confidence 56678888998873 356666666531 123444456666677777777776643
Done!