Query gi|254780255|ref|YP_003064668.1| 30S ribosomal protein S3 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 227
No_of_seqs 132 out of 1311
Neff 6.6
Searched_HMMs 39220
Date Tue May 24 09:05:30 2011
Command /home/congqian_1/programs/hhpred/hhsearch -i 254780255.hhm -d /home/congqian_1/database/cdd/Cdd.hhm
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 TIGR01009 rpsC_bact ribosomal 100.0 0 0 655.4 19.0 210 1-210 1-216 (217)
2 PRK00310 rpsC 30S ribosomal pr 100.0 0 0 577.5 21.4 213 1-213 1-213 (233)
3 CHL00048 rps3 ribosomal protei 100.0 0 0 540.8 22.3 207 1-207 1-218 (218)
4 COG0092 RpsC Ribosomal protein 100.0 0 0 482.2 18.0 201 12-212 1-202 (233)
5 PRK04191 rps3p 30S ribosomal p 100.0 0 0 411.5 17.7 195 25-220 3-200 (225)
6 PTZ00084 40S ribosomal protein 100.0 0 0 386.8 18.8 200 24-224 6-219 (220)
7 TIGR01008 rpsC_E_A ribosomal p 100.0 0 0 298.3 14.8 179 37-216 13-203 (204)
8 cd02412 30S_S3_KH K homology R 100.0 2.5E-39 6.4E-44 247.1 11.1 108 2-109 1-109 (109)
9 pfam00189 Ribosomal_S3_C Ribos 100.0 6.3E-33 1.6E-37 210.2 8.5 84 119-202 1-85 (85)
10 KOG3181 consensus 99.9 7.1E-27 1.8E-31 175.2 10.6 168 37-205 19-191 (244)
11 pfam00417 Ribosomal_S3_N Ribos 99.9 2.7E-26 7E-31 171.8 5.4 62 1-62 1-62 (62)
12 cd02411 archeal_30S_S3_KH K ho 99.8 6.4E-19 1.6E-23 129.3 9.2 83 26-108 2-85 (85)
13 cd02413 40S_S3_KH K homology R 99.0 1.1E-09 2.9E-14 75.8 7.6 71 38-108 6-79 (81)
14 pfam07650 KH_2 KH domain. 98.8 3.6E-09 9.2E-14 72.9 3.8 54 64-117 2-55 (55)
15 cd02409 KH-II KH-II (K homolo 98.3 1.2E-06 3E-11 58.4 6.1 64 40-103 1-67 (68)
16 COG1847 Jag Predicted RNA-bind 96.0 0.045 1.1E-06 31.9 7.5 103 37-139 65-185 (208)
17 cd02414 jag_KH jag_K homology 95.9 0.012 3.1E-07 35.2 4.3 57 40-96 1-58 (77)
18 cd02410 archeal_CPSF_KH The ar 92.9 0.72 1.8E-05 25.0 8.9 83 41-134 56-139 (145)
19 smart00322 KH K homology RNA-b 92.6 0.095 2.4E-06 30.1 2.6 64 62-125 3-69 (69)
20 PRK00089 era GTP-binding prote 87.1 2.4 6E-05 22.0 8.8 100 19-118 174-293 (296)
21 PRK08406 transcription elongat 86.7 2 5.1E-05 22.4 5.5 48 45-92 17-64 (142)
22 COG1782 Predicted metal-depend 86.5 2.5 6.5E-05 21.8 8.3 112 42-166 80-196 (637)
23 PRK02821 hypothetical protein; 76.6 4 0.0001 20.7 3.9 44 64-107 33-76 (77)
24 TIGR03675 arCOG00543 arCOG0178 70.2 8.7 0.00022 18.7 12.5 105 41-156 73-182 (630)
25 cd02134 NusA_KH NusA_K homolog 66.2 5.3 0.00013 20.0 2.6 53 40-92 2-55 (61)
26 cd02396 PCBP_like_KH K homolog 62.2 6.3 0.00016 19.5 2.4 29 64-92 2-30 (65)
27 COG1159 Era GTPase [General fu 58.9 14 0.00037 17.5 7.8 79 39-117 196-291 (298)
28 PRK01064 hypothetical protein; 54.9 17 0.00043 17.1 4.3 47 59-105 25-76 (78)
29 cd00105 KH-I K homology RNA-bi 52.1 9.8 0.00025 18.4 2.0 28 64-91 2-29 (64)
30 COG4808 Uncharacterized protei 49.6 6.6 0.00017 19.4 0.8 59 151-209 30-102 (152)
31 PRK12328 nusA transcription el 49.4 19 0.00048 16.8 3.1 34 172-206 171-206 (375)
32 PRK00045 hemA glutamyl-tRNA re 47.4 19 0.00048 16.8 2.8 39 36-74 25-63 (429)
33 PRK00468 hypothetical protein; 42.2 27 0.00069 15.9 3.7 62 41-103 6-74 (75)
34 TIGR01953 NusA transcription t 40.4 29 0.00073 15.7 3.3 29 64-92 253-287 (366)
35 cd02394 vigilin_like_KH K homo 36.2 20 0.00051 16.6 1.5 28 65-92 3-30 (62)
36 pfam00013 KH_1 KH domain. KH m 36.0 25 0.00064 16.1 2.0 28 65-92 3-30 (57)
37 KOG2192 consensus 33.2 15 0.00039 17.3 0.5 35 59-93 120-154 (390)
38 cd02393 PNPase_KH Polynucleoti 31.8 22 0.00056 16.4 1.1 31 62-92 2-32 (61)
39 TIGR03665 arCOG04150 arCOG0415 30.4 42 0.0011 14.8 4.1 64 68-135 4-73 (172)
40 COG0195 NusA Transcription elo 30.2 42 0.0011 14.8 3.2 36 57-92 69-106 (190)
41 TIGR02539 SepCysS Sep-tRNA:Cys 29.8 25 0.00063 16.1 1.1 38 156-200 182-225 (381)
42 TIGR02303 HpaG-C-term 4-hydrox 29.6 11 0.00029 18.0 -0.6 65 30-96 125-208 (249)
43 COG1104 NifS Cysteine sulfinat 29.2 44 0.0011 14.7 2.9 41 169-209 181-221 (386)
44 PRK09202 nusA transcription el 28.2 46 0.0012 14.5 2.8 15 77-91 252-266 (428)
45 KOG1676 consensus 25.2 38 0.00096 15.0 1.4 24 66-89 143-166 (600)
46 TIGR02799 thio_ybgC tol-pal sy 24.2 19 0.00047 16.8 -0.3 26 157-183 24-49 (127)
47 TIGR00284 TIGR00284 dihydropte 23.4 57 0.0014 14.0 2.0 45 42-86 440-489 (529)
48 COG1837 Predicted RNA-binding 23.4 57 0.0014 14.0 6.2 50 54-103 20-74 (76)
49 COG1855 ATPase (PilT family) [ 21.1 63 0.0016 13.7 4.3 14 148-161 344-357 (604)
50 PRK00092 hypothetical protein; 21.0 63 0.0016 13.7 6.5 123 37-172 4-131 (153)
51 KOG2190 consensus 20.4 65 0.0017 13.7 2.1 30 64-93 45-74 (485)
No 1
>TIGR01009 rpsC_bact ribosomal protein S3; InterPro: IPR005704 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 of 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. This family describes the bacterial type of ribosomal protein S3 and also and many chloroplast forms. Chloroplast and mitochondrial forms have large, variable inserts between conserved N-terminal and C-terminal domains. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=655.36 Aligned_cols=210 Identities=55% Similarity=0.933 Sum_probs=206.6
Q ss_pred CCCCCCCCEEEEE-EECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHH--HCCCCCEEEEECCCC-CEEEEEECCCCCC
Q ss_conf 9864578526650-32062156702731257999989999999998774--226422155325885-1899997374100
Q gi|254780255|r 1 MGQKINPILFRLG-VNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLK--QAGVAKILIERTHKN-CRIIVYSARPGLI 76 (227)
Q Consensus 1 MGQKvnP~g~RLg-~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~--~agis~i~I~Rt~~~-i~I~I~~~kP~~i 76 (227)
|||||||+||||| +||+|+|.|||++++|+++|+||++||+||++.|. +|+||+|+|+|+.+. +.|+|||+|||+|
T Consensus 1 MGQKv~P~GfRlGPi~K~W~S~WyA~~k~y~~~L~ED~KIR~~i~k~l~~~~a~iS~veIeR~~~~~v~V~IhtArPg~v 80 (217)
T TIGR01009 1 MGQKVNPIGFRLGPITKDWKSRWYADPKEYAELLHEDLKIRNLIKKELKKKNAGISDVEIERTADKKVRVTIHTARPGIV 80 (217)
T ss_pred CCCEECCCCEECCCCCCCCEEEECCCCCCCHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCEEEEEEEECCCCEE
T ss_conf 99505786401375214510376588753035666438999987321133543313279981699788999982788658
Q ss_pred CCCCCHHHHHHHHHHHCCCC--CEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEE
Q ss_conf 13565348998987640358--7057879981375533778799999998759636899999999853238855999970
Q gi|254780255|r 77 IGKKGTDIEKIRKKLSNMTN--SEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIAS 154 (227)
Q Consensus 77 iGkkg~~i~~l~~~L~~~~~--~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~is 154 (227)
||++|.++++|++.|+++++ ++++|+|.||++|++||+|+|++||.|||+|+|||||||++++++|++||+||||+||
T Consensus 81 IGkkG~~iE~l~~~l~k~~~~~k~v~i~I~EVk~p~ldA~LvA~~IA~QlE~RVSFRrAmK~A~~~~~k~GakGiKv~VS 160 (217)
T TIGR01009 81 IGKKGSEIEKLKKALQKLTGSVKEVQINIKEVKRPELDAQLVAQNIARQLENRVSFRRAMKKAIQSAMKAGAKGIKVQVS 160 (217)
T ss_pred ECCCCCHHHHHHHHHHHHHCCEEEEEEEEEECCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf 85788458999999998847835899989874885738788998999998620204689999999986268988899986
Q ss_pred CCCCCCCCCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCCCCC
Q ss_conf 36786422215787525532452000030568999953826679999732885377
Q gi|254780255|r 155 GRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSD 210 (227)
Q Consensus 155 GRl~G~e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~~~~ 210 (227)
|||+||||||+|||+||+|||||||||||||+++|+|+||+||||||||.+|++..
T Consensus 161 GRLgGAEIAR~E~y~EGRvPLHTLRADIDY~~~~A~TTYG~IGVKVWI~kGe~~~~ 216 (217)
T TIGR01009 161 GRLGGAEIARTEWYKEGRVPLHTLRADIDYGFAEAKTTYGIIGVKVWIFKGEVLGG 216 (217)
T ss_pred ECCCCHHHCCCCEEEECCCCCHHHHHHHHHCCCCCEEEEEEEEEEEEEEECCCCCC
T ss_conf 10574211222104327997312220031254412157326779998751502389
No 2
>PRK00310 rpsC 30S ribosomal protein S3; Reviewed
Probab=100.00 E-value=0 Score=577.45 Aligned_cols=213 Identities=57% Similarity=0.952 Sum_probs=207.9
Q ss_pred CCCCCCCCEEEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCC
Q ss_conf 98645785266503206215670273125799998999999999877422642215532588518999973741001356
Q gi|254780255|r 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKK 80 (227)
Q Consensus 1 MGQKvnP~g~RLg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkk 80 (227)
|||||||+|||||+|++|+|.|||++++|+++|+||++||+||+++|.++||++|+|+|+.+.+.|.||+++||++||++
T Consensus 1 MGQKvnP~GfRLGi~k~w~S~Wfa~~k~Y~~~L~eD~kIR~yi~k~~~~agIs~I~IeR~~~~i~V~I~tarPgiiIGkk 80 (233)
T PRK00310 1 MGQKVNPIGFRLGITKDWDSRWYADKKDYADLLHEDLKIRKFLKKKLKKAGVSRIVIERPAKKVRVTIHTARPGIVIGKK 80 (233)
T ss_pred CCCCCCCCCEEECCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHCHHCCEEEEEEEECCCEEEEEEEECCCCCHHCCC
T ss_conf 98988983353145679977187882454799999999999997501015724899997388799999967886312156
Q ss_pred CHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCC
Q ss_conf 53489989876403587057879981375533778799999998759636899999999853238855999970367864
Q gi|254780255|r 81 GTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGA 160 (227)
Q Consensus 81 g~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~ 160 (227)
|+++++|++.|+++++++++|+|.||++|+++|+++|++||+|||+|++|||+|+++++++|++||+||||+||||||||
T Consensus 81 G~~Ie~L~~~L~k~~~~~v~InI~EVk~Pe~~A~lvA~~IA~qLE~Rv~FRra~K~ai~~~~k~gakGIKI~isGRL~Ga 160 (233)
T PRK00310 81 GEDIEKLRKELQKLTGKPVQINIVEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGA 160 (233)
T ss_pred CCHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCEEHHHHHHHHHHHCHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCCC
T ss_conf 63689999999997489538999996054403050399999858603289999999999999759984699982475773
Q ss_pred CCCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCCCCCCCC
Q ss_conf 22215787525532452000030568999953826679999732885377211
Q gi|254780255|r 161 ELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSDS 213 (227)
Q Consensus 161 e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~~~~~~~ 213 (227)
||||+||+++|+||||||+|||||++++|+|+||+||||||||.+|+++..+.
T Consensus 161 EiAR~E~~~eGrvPL~Tlra~IDY~~~~A~T~yGiiGVKVWi~~ge~~~~~~~ 213 (233)
T PRK00310 161 EIARTEWYREGRVPLHTLRADIDYATAEAHTTYGVIGVKVWIFKGEVLGGPRA 213 (233)
T ss_pred CHHHEEEEEECEEECHHEEECCCEEEEEEECCCCCEEEEEEEECCCCCCCCCC
T ss_conf 01005658723463230143363899899868621799999987750698641
No 3
>CHL00048 rps3 ribosomal protein S3
Probab=100.00 E-value=0 Score=540.79 Aligned_cols=207 Identities=43% Similarity=0.702 Sum_probs=200.3
Q ss_pred CCCCCCCCEEEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHH--------CCCCCEEEEECCCCCEEEEEECC
Q ss_conf 9864578526650320621567027312579999899999999987742--------26422155325885189999737
Q gi|254780255|r 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQ--------AGVAKILIERTHKNCRIIVYSAR 72 (227)
Q Consensus 1 MGQKvnP~g~RLg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~--------agis~i~I~Rt~~~i~I~I~~~k 72 (227)
|||||||+|||||++++|+|.|||++++|+++|+||++||+||++++.. +||++|+|+|+.+.+.|.||+++
T Consensus 1 MGQKvnP~gfRLgi~k~w~S~Wfa~~k~Y~~~l~eD~~IR~~i~~~l~~~~~~~~~~a~Is~I~I~R~~~~i~v~I~tar 80 (218)
T CHL00048 1 MGQKINPLGFRLGITQKHHSLWFAQPKNYSEGLQEDKKIRDCIKNYVQKNIRISSGVEGIARIEIQKKIDLIQVIIYTGF 80 (218)
T ss_pred CCCCCCCEEEEECCCCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEEECCEEEEEEEECC
T ss_conf 97988976043113679800778874465899999999999999998764311124465669999982577999999657
Q ss_pred CCCCCCCCCHHHHHHHHHHHCCC---CCEEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEE
Q ss_conf 41001356534899898764035---870578799813755337787999999987596368999999998532388559
Q gi|254780255|r 73 PGLIIGKKGTDIEKIRKKLSNMT---NSEIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGV 149 (227)
Q Consensus 73 P~~iiGkkg~~i~~l~~~L~~~~---~~~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGi 149 (227)
||+++|++|+++++|++.|++++ ++++.+++.|+++|+++|+++|++||+|||+|++|||+|+++++++|++||+|+
T Consensus 81 pg~iigk~g~~i~~L~~~L~k~~~~~~~~v~inv~evk~P~~~A~liA~~Ia~qLEkR~sfRra~k~~i~~~~k~g~kGi 160 (218)
T CHL00048 81 PKLLIENKGRGIEELQINLQKELNSVNRKLNINITKVKNPYGEPNILAEYIAGQLENRVSFRKAMKKAIELAEKADIKGI 160 (218)
T ss_pred CCCEECCCHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEE
T ss_conf 51141565245999999999972877717999999953855021668999999987332299999999999997499629
Q ss_pred EEEEECCCCCCCCCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCC
Q ss_conf 9997036786422215787525532452000030568999953826679999732885
Q gi|254780255|r 150 KVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDE 207 (227)
Q Consensus 150 kI~isGRl~G~e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~ 207 (227)
||+||||||||||||+||+++|+||||||+|||||++++|+|+||+||||||||.+|.
T Consensus 161 KI~vsGRLnGaeiAR~e~~~~G~vpL~Tlra~IdY~~~~a~T~yG~~GvKVWi~~ge~ 218 (218)
T CHL00048 161 KIQISGRLNGAEIARVEWIREGRVPLQTLRAKIDYCSYTARTIYGVLGIKVWIFKDEE 218 (218)
T ss_pred EEEEEECCCCHHHHHEEEEEECCEECCEEEECCEEEEEEEECCCCEEEEEEEEECCCC
T ss_conf 9999605672323120204506235420132560788899868850899999976999
No 4
>COG0092 RpsC Ribosomal protein S3 [Translation, ribosomal structure and biogenesis]
Probab=100.00 E-value=0 Score=482.24 Aligned_cols=201 Identities=57% Similarity=0.921 Sum_probs=195.4
Q ss_pred EEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHH
Q ss_conf 50320621567027312579999899999999987742264221553258851899997374100135653489989876
Q gi|254780255|r 12 LGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKL 91 (227)
Q Consensus 12 Lg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L 91 (227)
||++++|.|.||+++++|+.+|++|++||+||.+.|.+||||+|+|+|+++.+.|+||+++||++||++|.+|++|++.|
T Consensus 1 ~gi~~~w~srwfa~~~~~~~~l~ed~kIre~l~k~l~~Ag~s~veIeR~~~~~~V~I~aarPg~VIGk~G~~I~~L~~~l 80 (233)
T COG0092 1 LGITKDWKSRWFANKKEYAKLLVEDLKIREFLEKELSNAGISGVEIERTPKGTRVTIHAARPGLVIGKKGSNIEKLRKEL 80 (233)
T ss_pred CCCCCCCHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCCEECCCCCCHHHHHHHH
T ss_conf 97654301232015341057778899999999999875784548999669843999995798315757971099999999
Q ss_pred HCCCCC-EEEEEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEE
Q ss_conf 403587-0578799813755337787999999987596368999999998532388559999703678642221578752
Q gi|254780255|r 92 SNMTNS-EIHLSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLE 170 (227)
Q Consensus 92 ~~~~~~-~v~i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~ 170 (227)
+++++. +++|+|.||++|++||+++|++||.|||+|++|||||+++++++|++||+||||+|||||+|+||||+|||.+
T Consensus 81 ~k~~g~~~v~I~i~EV~~peL~A~lvA~~IA~qLErrv~FRRA~k~ai~~~M~aGAkGiki~vSGRL~GaeiAR~E~y~e 160 (233)
T COG0092 81 EKLFGKENVQINIEEVKKPELDAQLVAESIAQQLERRVSFRRAMKRAIQRAMRAGAKGIKIQVSGRLGGAEIARTEKYRE 160 (233)
T ss_pred HHHHCCCCCEEEEEECCCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCHHHHHHHHHHHC
T ss_conf 99849997449999767878498999999999997440899999999999997368655999932220488876778746
Q ss_pred CCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCCCCCCC
Q ss_conf 553245200003056899995382667999973288537721
Q gi|254780255|r 171 GRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVSDSD 212 (227)
Q Consensus 171 G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~~~~~~ 212 (227)
|+|||||++|||||++++|+|+||+||||||||.+++++++.
T Consensus 161 G~vplhtlrAdIDyg~a~A~ttyGiiGVKVwI~~ge~l~~~~ 202 (233)
T COG0092 161 GRVPLHTLRADIDYGTAEAHTTYGVIGVKVWIYKGEVLPDKV 202 (233)
T ss_pred CEEECCCCCCEEEEEEEEEEECCCEEEEEEEEECCCCCCCCC
T ss_conf 634745661000343688860374688999995687178755
No 5
>PRK04191 rps3p 30S ribosomal protein S3P; Reviewed
Probab=100.00 E-value=0 Score=411.51 Aligned_cols=195 Identities=32% Similarity=0.498 Sum_probs=187.1
Q ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCC-CEEEEEE
Q ss_conf 731257999989999999998774226422155325885189999737410013565348998987640358-7057879
Q gi|254780255|r 25 RGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN-SEIHLSV 103 (227)
Q Consensus 25 ~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~-~~v~i~v 103 (227)
-.+.|.....+|.+||+||.++|.+|||++|+|+||++.+.|+||+++||++||++|.++++|++.|++.|+ .+++|+|
T Consensus 3 i~k~fi~~~~~~~~Ireyl~k~l~~Agis~IeIeRt~~~~~I~I~tarPG~vIGr~G~~i~~L~~~L~k~~~~~~~~I~V 82 (225)
T PRK04191 3 IEKKFVQEGVKKTLIDEYLAKELERAGYGGMEIKKTPLGTRITIYAERPGMVIGRGGKTIRELTETLEKKFGLENPQIDV 82 (225)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCHHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 56899983028999999999877767854599998689469999948985155578377999999999983999744999
Q ss_pred EEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEECCCCC--CCEEEE
Q ss_conf 981375533778799999998759636899999999853238855999970367864222157875255324--520000
Q gi|254780255|r 104 NEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPL--QTLRAH 181 (227)
Q Consensus 104 ~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~vpl--~t~~a~ 181 (227)
.||.+|++||.++|++||+|||+|++|||+|+++++++|++||+||||+||||||| ||||+|||++|+||| ||++++
T Consensus 83 ~EV~~P~l~A~lvAe~IA~qLErr~~fRRa~k~ai~~~m~aGAkGikI~iSGRL~G-E~ARtE~~~eG~vplsG~~~~~~ 161 (225)
T PRK04191 83 KEVENPELNARVVAFRIANALERGWHFRRAAHSAIRRIMEAGAKGVEIIISGKLTG-ERARFEKFMEGYIKKSGEPAEEL 161 (225)
T ss_pred EEEECCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCH-HHHHHHHHHCCEEECCCCCCHHH
T ss_conf 99518774889999999999862428999999999999974897689998056348-88776687377646689830652
Q ss_pred CEEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCHH
Q ss_conf 305689999538266799997328853772113433202
Q gi|254780255|r 182 IDYGTAVAETAYGSCGIKVYVSLRDEVSDSDSTIPAAEH 220 (227)
Q Consensus 182 idy~~~~a~T~~G~~GvKVwi~~~~~~~~~~~~~~~~~~ 220 (227)
|||++++|+|+||++||||||+.+|+.+||...+..+++
T Consensus 162 IDya~~~A~tk~GviGVKVwI~k~~~~~pd~~~i~~~~~ 200 (225)
T PRK04191 162 VDRGFAIAKLKLGIIGVTVRIMPPDVKLPDEIEIKEPEE 200 (225)
T ss_pred EEEEEEEEECCCEEEEEEEEEECCCCCCCCEEEEECCCC
T ss_conf 135899995587048899999899977998799848775
No 6
>PTZ00084 40S ribosomal protein S3; Provisional
Probab=100.00 E-value=0 Score=386.84 Aligned_cols=200 Identities=22% Similarity=0.283 Sum_probs=185.5
Q ss_pred CCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCC---CEEE
Q ss_conf 2731257999989999999998774226422155325885189999737410013565348998987640358---7057
Q gi|254780255|r 24 ARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN---SEIH 100 (227)
Q Consensus 24 a~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~---~~v~ 100 (227)
+..+.|-.--....+||+||.+.|.++|+|+++|+||++.+.|+||+++||++||++|.++++|+..|++.|+ .+++
T Consensus 6 ~~~rkFv~~g~~~~~ire~l~k~L~~AG~s~ieIert~~~~~I~I~tarPG~VIGrkG~~I~~L~~~l~k~~~~~~~~v~ 85 (220)
T PTZ00084 6 SKKRKFINDGVFYAELNEFLSRELADDGYAGVELRVTPVRTEIIIRATKTREVLGEKGRRIRELTSLIQKRFNYKEGKLQ 85 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCCHHHHHHHHHHHHHHCCCCCCEE
T ss_conf 05567998556999999999988886787759999889847999996898558868854699999999998489977437
Q ss_pred EEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEECCC--CCCCE
Q ss_conf 8799813755337787999999987596368999999998532388559999703678642221578752553--24520
Q gi|254780255|r 101 LSVNEVPKPEINATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRV--PLQTL 178 (227)
Q Consensus 101 i~v~ei~~p~~~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~v--pl~t~ 178 (227)
|+|.||.+|++||+++|++||+|||+|++|||||+++++++|++||+||+|+||||| |+||||+|||++|+| |+||+
T Consensus 86 I~V~eV~~p~l~A~lvAe~IA~qLerrv~fRRA~k~ai~~~M~aGAkGikI~vSGRL-g~erARtekf~eG~v~~~g~~~ 164 (220)
T PTZ00084 86 LFAERVEVRGLCAMAQAESLRFKLLSGLPVRRAAYGIIRQVMESGAKGCEVIVSGKL-RAQRAKSMKFRDGYMISTGQPH 164 (220)
T ss_pred EEEEEECCCCCCHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCC-CHHHHHHHHHHCCEEECCCCHH
T ss_conf 999994488849899999999999746428999999999999758966799983464-5567656553156130289444
Q ss_pred EEECEEEEEEEEECCCEEEEEEEEEEC---------CCCCCCCCCCCCCHHHHHH
Q ss_conf 000305689999538266799997328---------8537721134332023332
Q gi|254780255|r 179 RAHIDYGTAVAETAYGSCGIKVYVSLR---------DEVSDSDSTIPAAEHRVVE 224 (227)
Q Consensus 179 ~a~idy~~~~a~T~~G~~GvKVwi~~~---------~~~~~~~~~~~~~~~~~~~ 224 (227)
+++|||++++|+|+||++||||||+++ ++.+||...+..+.+...|
T Consensus 165 ~~~id~a~~~a~tk~GviGVkV~Im~P~dp~g~~gp~~~lpD~i~i~~~k~~~~~ 219 (220)
T PTZ00084 165 KDFVDTATRHCQMRQGVIGVKVKIMLPYDPTGKNGPSEPLPDVITVLEPKEITAE 219 (220)
T ss_pred HHHEEEEEEEEECCCEEEEEEEEEECCCCCCCCCCCCCCCCCCEEEECCCCCCCC
T ss_conf 7533068999954872798999997798877777998899984798798644445
No 7
>TIGR01008 rpsC_E_A ribosomal protein S3; InterPro: IPR005703 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 of 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. This family describes ribosomal protein S3 of the eukaryotic cytosol and of the archaea.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015935 small ribosomal subunit.
Probab=100.00 E-value=0 Score=298.27 Aligned_cols=179 Identities=36% Similarity=0.556 Sum_probs=168.6
Q ss_pred HHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHC--CCC-CEEEEEEEEECCCCCCH
Q ss_conf 999999998774226422155325885189999737410013565348998987640--358-70578799813755337
Q gi|254780255|r 37 LKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSN--MTN-SEIHLSVNEVPKPEINA 113 (227)
Q Consensus 37 ~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~--~~~-~~v~i~v~ei~~p~~~A 113 (227)
..|.|||.++|..||+|+++|.+||-.+.|+||+++|++|||+.|..|++|++.|++ -|+ -+++|+|.+|.+|+|||
T Consensus 13 ~~idE~l~~El~~AGYsgvdv~~TPlGT~vii~AerPg~VIGr~G~rIr~LT~~l~~Rf~Fg~enPqi~V~~v~~P~L~A 92 (204)
T TIGR01008 13 LLIDEFLKKELREAGYSGVDVRKTPLGTKVIIYAERPGLVIGRGGRRIRELTEKLQKRFKFGLENPQIDVEEVENPELNA 92 (204)
T ss_pred HHHHHHHHHHHHHCCCCCCEEEECCCCCEEEEEEECCCCEECCCCCHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCCCH
T ss_conf 77888999988651777551687778967999983686377279721889999998752058999658764178989888
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEECCCCC--CCEEEECEEEEEEEEE
Q ss_conf 78799999998759636899999999853238855999970367864222157875255324--5200003056899995
Q gi|254780255|r 114 TLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRVPL--QTLRAHIDYGTAVAET 191 (227)
Q Consensus 114 ~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~vpl--~t~~a~idy~~~~a~T 191 (227)
+++|+.||..||+++.|||+.+.++..+|.+||+||+|.|||+|.| ||||+++|..|.+-- |.-..-||-++++|.+
T Consensus 93 ~v~A~~iA~~LeRG~hFRRaAY~~~rriM~aGAkGvEv~iSGKL~~-eRAr~~KF~~G~~~k~G~Pa~~lV~~g~a~a~~ 171 (204)
T TIGR01008 93 KVQAEKIARSLERGLHFRRAAYTAVRRIMEAGAKGVEVTISGKLTG-ERARTEKFAAGYLKKSGEPAEELVDKGFAIALL 171 (204)
T ss_pred HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCEEEEEEECCHHH-HHHHHHHCCCCEEEECCCCHHHHHHHHHHEEEC
T ss_conf 8999999999845347789999999999825695279998274178-778752101784898138768887766440114
Q ss_pred CCCEEEEEEEEEECCCC-------CCCCCCCC
Q ss_conf 38266799997328853-------77211343
Q gi|254780255|r 192 AYGSCGIKVYVSLRDEV-------SDSDSTIP 216 (227)
Q Consensus 192 ~~G~~GvKVwi~~~~~~-------~~~~~~~~ 216 (227)
+.|||||+|.|+++|.. +||+..+.
T Consensus 172 k~GVlGV~V~Im~Pd~~sRtGPkaLPD~v~I~ 203 (204)
T TIGR01008 172 KLGVLGVKVKIMPPDVKSRTGPKALPDEVEIK 203 (204)
T ss_pred CCCEEEEEEEEECCCCCCCCCCCCCCCEEEEE
T ss_conf 89702268888669797478888779437863
No 8
>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=100.00 E-value=2.5e-39 Score=247.12 Aligned_cols=108 Identities=48% Similarity=0.932 Sum_probs=106.1
Q ss_pred CCCCCCCEEEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCC
Q ss_conf 86457852665032062156702731257999989999999998774226422155325885189999737410013565
Q gi|254780255|r 2 GQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKG 81 (227)
Q Consensus 2 GQKvnP~g~RLg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg 81 (227)
||||||+|||||++++|+|.|||++++|+.+|+||++||+||+++|.+||||+|+|+|+.+.+.|.||+++||++||++|
T Consensus 1 GQKv~P~gfRlGi~~~w~S~Wfa~~~~y~~~l~eD~~IR~~i~~~~~~agIs~I~IeR~~~~i~V~I~tarPG~vIGk~G 80 (109)
T cd02412 1 GQKVNPLGFRLGITKDWDSRWYADKKDYAELLHEDLKIRKFIKKKLKKAGISRIEIERKADRVEVTIHTARPGIIIGKKG 80 (109)
T ss_pred CCCCCCCCEEECCCCCCCCEECCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCEEEEEEEECCCCEEECCCC
T ss_conf 98649843320436899566758824548999999999999999997689436999985773899999469955986785
Q ss_pred HHHHHHHHHHHCCCC-CEEEEEEEEECCC
Q ss_conf 348998987640358-7057879981375
Q gi|254780255|r 82 TDIEKIRKKLSNMTN-SEIHLSVNEVPKP 109 (227)
Q Consensus 82 ~~i~~l~~~L~~~~~-~~v~i~v~ei~~p 109 (227)
+++++|++.|+++++ +++.|+|.||++|
T Consensus 81 ~~Ie~L~~~L~k~~~~k~v~InI~EVk~P 109 (109)
T cd02412 81 AGIEKLRKELQKLLGNKKVRINIVEVKKP 109 (109)
T ss_pred CCHHHHHHHHHHHHCCCCEEEEEEEECCC
T ss_conf 24899999999982898538999982598
No 9
>pfam00189 Ribosomal_S3_C Ribosomal protein S3, C-terminal domain. This family contains a central domain pfam00013, hence the amino and carboxyl terminal domains are stored separately. This is a minimal carboxyl-terminal domain. Some are much longer.
Probab=99.98 E-value=6.3e-33 Score=210.16 Aligned_cols=84 Identities=61% Similarity=0.924 Sum_probs=81.7
Q ss_pred HHHHHHHCCCHHHHHHHHHHHHH-HHCCCCEEEEEEECCCCCCCCCEEEEEEECCCCCCCEEEECEEEEEEEEECCCEEE
Q ss_conf 99999875963689999999985-32388559999703678642221578752553245200003056899995382667
Q gi|254780255|r 119 SIAQQLERRVVFRRAMKRAVQSA-MRFGADGVKVIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETAYGSCG 197 (227)
Q Consensus 119 ~Ia~~Lekr~~fRr~~k~~i~~~-~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~~G~~G 197 (227)
+|+.+||++++|||+++++++.+ |.++++|+||+|||||+|+||||+|+|++|++||||++++|||++.+|+|+||+||
T Consensus 1 ~ia~~Le~~~~frr~~~~~i~~i~~~~~~~GikI~isGRl~G~erAr~e~~~~G~i~l~t~~~~Idy~~~~a~Tk~G~~G 80 (85)
T pfam00189 1 RIAQQLERRISFRRAIKQAIRRIMKKAGAKGIKIQISGRLNGAERARTEKYKEGRVPLHTLRADIDYAFAEAKTKYGVIG 80 (85)
T ss_pred CHHHHHHCCHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCCHHHHHHHEEEECCCCCCEEEEEEEEEEEEEEEECCCEEE
T ss_conf 95798753448999999999999987499769999757887677623521654726883523057899999992796089
Q ss_pred EEEEE
Q ss_conf 99997
Q gi|254780255|r 198 IKVYV 202 (227)
Q Consensus 198 vKVwi 202 (227)
|||||
T Consensus 81 VKVWI 85 (85)
T pfam00189 81 VKVWI 85 (85)
T ss_pred EEEEC
T ss_conf 99989
No 10
>KOG3181 consensus
Probab=99.94 E-value=7.1e-27 Score=175.21 Aligned_cols=168 Identities=24% Similarity=0.363 Sum_probs=154.9
Q ss_pred HHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCC---EEEEEEEEECCCCCCH
Q ss_conf 9999999987742264221553258851899997374100135653489989876403587---0578799813755337
Q gi|254780255|r 37 LKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNS---EIHLSVNEVPKPEINA 113 (227)
Q Consensus 37 ~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~---~v~i~v~ei~~p~~~A 113 (227)
-.+.+|+.+.|...|+|.+++.-|+..+.|+|.+++|.-++|.+|..|.+|+...++.|+. .+.+..+++.+..++|
T Consensus 19 AELnef~treLaedGySgvEvRvtptr~eiIi~atrtq~vlGEkgrRirelt~lvqkRf~f~~~svelyaEkV~~rGLcA 98 (244)
T KOG3181 19 AELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFKFPEGSVELYAEKVANRGLCA 98 (244)
T ss_pred HHHHHHHHHHHHHCCCCCEEEEEECCCEEEEEEECCHHHHHHHCCHHHHHHHHHHHHHCCCCCCCEEEEHHHHHCCCHHH
T ss_conf 99999999999864767428994057516899831516655111141999999999871899874787466431144248
Q ss_pred HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEECCC--CCCCEEEECEEEEEEEEE
Q ss_conf 787999999987596368999999998532388559999703678642221578752553--245200003056899995
Q gi|254780255|r 114 TLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGRV--PLQTLRAHIDYGTAVAET 191 (227)
Q Consensus 114 ~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~v--pl~t~~a~idy~~~~a~T 191 (227)
...|+++.++|-.+..+||+++.++..+|.+||+||+|++||+|.| +||++.+|..|-+ +-|.....||-++.++.+
T Consensus 99 iaQaeslryKllgGlavRRA~ygvlr~vmesgAkGceviVSGKLrg-qRAKsmKF~DG~mIhSG~pv~dyi~ta~rhVll 177 (244)
T KOG3181 99 IAQAESLRYKLLGGLAVRRACYGVLRFVMESGAKGCEVIVSGKLRG-QRAKSMKFVDGLMIHSGQPVKDYIDTAVRHVLL 177 (244)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCHH-HHHHCCCCCCCEEEECCCCHHHHHHHHHHHHHH
T ss_conf 7877789999850289999999999999970677638998342405-443031024305873598078899887776543
Q ss_pred CCCEEEEEEEEEEC
Q ss_conf 38266799997328
Q gi|254780255|r 192 AYGSCGIKVYVSLR 205 (227)
Q Consensus 192 ~~G~~GvKVwi~~~ 205 (227)
.+|++||||.|+.+
T Consensus 178 rQGVlGIkVkIMlp 191 (244)
T KOG3181 178 RQGVLGIKVKIMLP 191 (244)
T ss_pred HCCEEEEEEEEECC
T ss_conf 32423478999646
No 11
>pfam00417 Ribosomal_S3_N Ribosomal protein S3, N-terminal domain. This family contains a central domain pfam00013, hence the amino and carboxyl-terminal domains are stored separately.
Probab=99.93 E-value=2.7e-26 Score=171.82 Aligned_cols=62 Identities=55% Similarity=1.004 Sum_probs=60.5
Q ss_pred CCCCCCCCEEEEEEECCCEEEEECCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCC
Q ss_conf 98645785266503206215670273125799998999999999877422642215532588
Q gi|254780255|r 1 MGQKINPILFRLGVNCTWNSRWFARGSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHK 62 (227)
Q Consensus 1 MGQKvnP~g~RLg~~k~w~S~Wfa~~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~ 62 (227)
|||||||+|||||++++|+|.|||++++|+++|+||++||+||.+++.++||++|+|+|+.+
T Consensus 1 MGQKvnP~gfRLgi~k~w~S~Wfa~~~~Y~~~l~eD~~IR~~i~~~~~~a~is~i~IeR~~~ 62 (62)
T pfam00417 1 MGQKVNPIGFRLGITRNWDSKWFANKKNYAKLLNEDLKIRNYINKNLKPAGISRIEIERKID 62 (62)
T ss_pred CCCCCCCEEEECCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCC
T ss_conf 98876975032275579968864765566899999999999999861657677799986589
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=99.79 E-value=6.4e-19 Score=129.27 Aligned_cols=83 Identities=28% Similarity=0.458 Sum_probs=79.6
Q ss_pred CCHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCC-CEEEEEEE
Q ss_conf 31257999989999999998774226422155325885189999737410013565348998987640358-70578799
Q gi|254780255|r 26 GSEYGALLHEDLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN-SEIHLSVN 104 (227)
Q Consensus 26 ~k~Y~~~L~eD~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~-~~v~i~v~ 104 (227)
.++|.+.+.+|.+||+||.+.|.+||+|+++|+|||..+.|+||+++||++||++|+.+++|++.|++.|+ .+++|+|.
T Consensus 2 kK~Fi~~~~~~~~ireyl~k~l~~Ag~s~ieIeRtp~~~~I~I~t~rPG~VIGr~G~~I~~L~~~L~~~~g~~~~~I~V~ 81 (85)
T cd02411 2 ERKFVNEGVKRTMIDEYLEKELERAGYGGMEILRTPLGTQITIYAERPGMVIGRGGKNIRELTEILETKFGLENPQIDVQ 81 (85)
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEE
T ss_conf 41698855689999999999888678655999988996699999789984777886659999999999968998659999
Q ss_pred EECC
Q ss_conf 8137
Q gi|254780255|r 105 EVPK 108 (227)
Q Consensus 105 ei~~ 108 (227)
||++
T Consensus 82 EV~n 85 (85)
T cd02411 82 EVEN 85 (85)
T ss_pred ECCC
T ss_conf 6689
No 13
>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=99.02 E-value=1.1e-09 Score=75.82 Aligned_cols=71 Identities=21% Similarity=0.389 Sum_probs=64.2
Q ss_pred HHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCC---EEEEEEEEECC
Q ss_conf 999999987742264221553258851899997374100135653489989876403587---05787998137
Q gi|254780255|r 38 KIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNS---EIHLSVNEVPK 108 (227)
Q Consensus 38 ~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~---~v~i~v~ei~~ 108 (227)
.+.+|+.+.|..+|+|.+++.+||..+.|+|++++|+.++|++|..|.+|+..|++.|+. .+.+.+..|.+
T Consensus 6 eLnEfl~reL~~~GYsGvevr~Tp~~teIiI~atrp~~ViG~kg~rIreLt~~lqkRF~~~~~~iel~~ekv~~ 79 (81)
T cd02413 6 ELNEFLTRELAEDGYSGVEVRVTPTRTEIIIRATRTQNVLGEKGRRIRELTSLVQKRFNFPEGSVELYAEKVAN 79 (81)
T ss_pred HHHHHHHHHHHHCCCCCEEEEECCCCEEEEEEECCCCEEECCCCEEHHHHHHHHHHHCCCCCCCEEEEEEEHHC
T ss_conf 88999999998678773599965886199999536515563588049999999999829999958999881220
No 14
>pfam07650 KH_2 KH domain.
Probab=98.81 E-value=3.6e-09 Score=72.93 Aligned_cols=54 Identities=33% Similarity=0.615 Sum_probs=51.5
Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHH
Q ss_conf 189999737410013565348998987640358705787998137553377879
Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIA 117 (227)
Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA 117 (227)
+.|++|+++||++||++|++++.|.+.|++.++.+++|++.|+++|+++|.++|
T Consensus 2 v~v~i~~srpGiiIGk~G~~I~~l~~~l~k~~~~~~~i~v~ev~~p~~~a~l~a 55 (55)
T pfam07650 2 VIVVIRTSQPGIVIGKGGSNIKKLGKELRKRFGKKVQIEVLEVKNPELLAQLGA 55 (55)
T ss_pred EEEEEEECCCCEEECCCCCCHHHHHHHHHHHHCCCCEEEEEEECCCCCCCEEEC
T ss_conf 899999189967999896039999999999879995899999538882529709
No 15
>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=98.34 E-value=1.2e-06 Score=58.43 Aligned_cols=64 Identities=41% Similarity=0.701 Sum_probs=56.7
Q ss_pred HHHHHHHHHHCCCCCEEEEECCCCCEEEEEECC--CCCCCCCCCHHHHHHHHHHHCCC-CCEEEEEE
Q ss_conf 999998774226422155325885189999737--41001356534899898764035-87057879
Q gi|254780255|r 40 REYLQCHLKQAGVAKILIERTHKNCRIIVYSAR--PGLIIGKKGTDIEKIRKKLSNMT-NSEIHLSV 103 (227)
Q Consensus 40 R~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~k--P~~iiGkkg~~i~~l~~~L~~~~-~~~v~i~v 103 (227)
|+||.+.+..+++++++|+++++...+.+++++ |+.+||++|.+++.++..+.+.+ ..++.+++
T Consensus 1 ~~~l~~~l~~~~~~~V~i~~~~~~~~~~i~~~~~~~g~~IGk~G~~l~~l~~ll~~~~~~~~~~i~v 67 (68)
T cd02409 1 REFLKKLLAPAGISGVEIERTPDRIEIIIVVARGQPGLVIGKKGQNIRALQKLLQKLLRKKRVKIDV 67 (68)
T ss_pred CHHHHHHHHHCCCCEEEEEECCCCEEEEEEECCCCCCEEECCCCHHHHHHHHHHHHHHCCCCCEEEE
T ss_conf 9578745565685569999779967999998777996489888363999999999982899843853
No 16
>COG1847 Jag Predicted RNA-binding protein [General function prediction only]
Probab=95.98 E-value=0.045 Score=31.93 Aligned_cols=103 Identities=17% Similarity=0.280 Sum_probs=74.5
Q ss_pred HHHHHHHHHHHHHCCCC-CEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCC------EEEEEEEEECCC
Q ss_conf 99999999877422642-21553258851899997374100135653489989876403587------057879981375
Q gi|254780255|r 37 LKIREYLQCHLKQAGVA-KILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNS------EIHLSVNEVPKP 109 (227)
Q Consensus 37 ~~IR~fi~k~l~~agis-~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~------~v~i~v~ei~~p 109 (227)
-.+++|+...+...|+. .|.+......+.+.|.+..++.+||++|..++.|+-......++ ++.+++......
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
T ss_conf 99999999999983986599996247579999448861023036774017999999998535059615899982068999
Q ss_pred -CCCHHHHHHHHHHHH-HCCCH---------HHHHHHHHHH
Q ss_conf -533778799999998-75963---------6899999999
Q gi|254780255|r 110 -EINATLIAQSIAQQL-ERRVV---------FRRAMKRAVQ 139 (227)
Q Consensus 110 -~~~A~~iA~~Ia~~L-ekr~~---------fRr~~k~~i~ 139 (227)
.-.-.-+|+.+|.+. +-+-+ =||++..++.
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
T ss_conf 99999999999999998509905647898788899999997
No 17
>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=95.89 E-value=0.012 Score=35.20 Aligned_cols=57 Identities=23% Similarity=0.440 Sum_probs=48.8
Q ss_pred HHHHHHHHHHCCC-CCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCC
Q ss_conf 9999987742264-22155325885189999737410013565348998987640358
Q gi|254780255|r 40 REYLQCHLKQAGV-AKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN 96 (227)
Q Consensus 40 R~fi~k~l~~agi-s~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~ 96 (227)
++|++..+..+|+ ..++++.....+.+.|.+..++.+||++|+.++.|+..+....+
T Consensus 1 k~~L~~ll~~mg~~~~v~~~~~~~~~~~~i~g~~~~~LIGk~G~tL~AlQ~L~~~~~~ 58 (77)
T cd02414 1 KEFLEEVLELMGIEADVDVEEEGDTVEVNISGDDIGLLIGKRGKTLDALQYLANLVLN 58 (77)
T ss_pred CHHHHHHHHHCCCCEEEEEEEECCEEEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf 9589999998599479999997998999994498774166898647999999999997
No 18
>cd02410 archeal_CPSF_KH The archaeal cleavage and polyadenylation specificity factor (CPSF) contains an N-terminal K homology RNA-binding domain (KH). The archeal CPSFs are predicted to be metal-dependent RNases belonging to the beta-CASP family, a subgroup enzymes within the metallo-beta-lactamase fold. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH domains are known to bind single-stranded RNA or DNA and are found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=92.91 E-value=0.72 Score=24.96 Aligned_cols=83 Identities=24% Similarity=0.452 Sum_probs=56.4
Q ss_pred HHHHHHHH-HCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHH
Q ss_conf 99998774-22642215532588518999973741001356534899898764035870578799813755337787999
Q gi|254780255|r 41 EYLQCHLK-QAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQS 119 (227)
Q Consensus 41 ~fi~k~l~-~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~ 119 (227)
+.|....+ .||+..+... +..-.|+|.+.+||+++|+.|+.++++....-.. ..-+..|-+.+..+ +.
T Consensus 56 ~~I~~ivPeeA~i~~i~FD--~~~gEV~Iea~kPg~viGk~g~~l~eI~~~tGW~--------p~v~RtPpi~S~ti-~~ 124 (145)
T cd02410 56 KIILEIVPEEAGITDIYFD--DDTGEVIIEAEKPGLVIGKGGSTLREITRETGWA--------PKVVRTPPIQSRTV-KS 124 (145)
T ss_pred HHHHHHCCCCCCCEEEEEC--CCCCEEEEEECCCEEEECCCCHHHHHHHHHHCCE--------EEEEECCCCCHHHH-HH
T ss_conf 9999858964684468974--8885799997797779727616799999973981--------57886599961789-99
Q ss_pred HHHHHHCCCHHHHHH
Q ss_conf 999987596368999
Q gi|254780255|r 120 IAQQLERRVVFRRAM 134 (227)
Q Consensus 120 Ia~~Lekr~~fRr~~ 134 (227)
|..-|..-..+|+-+
T Consensus 125 IR~~l~~~~~eRrk~ 139 (145)
T cd02410 125 IRRFLRREREERKEI 139 (145)
T ss_pred HHHHHHHHHHHHHHH
T ss_conf 999999808999999
No 19
>smart00322 KH K homology RNA-binding domain.
Probab=92.63 E-value=0.095 Score=30.06 Aligned_cols=64 Identities=28% Similarity=0.372 Sum_probs=45.3
Q ss_pred CCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCE---EEEEEEEECCCCCCHHHHHHHHHHHHH
Q ss_conf 8518999973741001356534899898764035870---578799813755337787999999987
Q gi|254780255|r 62 KNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSE---IHLSVNEVPKPEINATLIAQSIAQQLE 125 (227)
Q Consensus 62 ~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~---v~i~v~ei~~p~~~A~~iA~~Ia~~Le 125 (227)
....|.+....++.+||++|.+++.+++......... .......+..+..++...+..|...++
T Consensus 3 ~~~~i~vp~~~~g~iIG~~G~~i~~i~~~~~~~I~i~~~~~~~~~v~I~g~~~~v~~a~~~i~~~i~ 69 (69)
T smart00322 3 VTIEVLIPADKVGLIIGKGGSTIKKIEEETGVKIDIPEDGSEERVVEITGPPENVEKAAELILEILE 69 (69)
T ss_pred EEEEEEECHHHCCEEECCCCCCHHHHHHHHCCEEEECCCCCCCCEEEEEECHHHHHHHHHHHHHHHC
T ss_conf 7999998978768549999845799999728889977999988789999099999999999999839
No 20
>PRK00089 era GTP-binding protein Era; Reviewed
Probab=87.06 E-value=2.4 Score=21.99 Aligned_cols=100 Identities=19% Similarity=0.240 Sum_probs=56.4
Q ss_pred EEEEECCCCHHHH---HHHHHHHHHHHHHHHHHHC-C-CCCEEEE---ECCC-C--CEEEEEECC---CCCCCCCCCHHH
Q ss_conf 1567027312579---9998999999999877422-6-4221553---2588-5--189999737---410013565348
Q gi|254780255|r 19 NSRWFARGSEYGA---LLHEDLKIREYLQCHLKQA-G-VAKILIE---RTHK-N--CRIIVYSAR---PGLIIGKKGTDI 84 (227)
Q Consensus 19 ~S~Wfa~~k~Y~~---~L~eD~~IR~fi~k~l~~a-g-is~i~I~---Rt~~-~--i~I~I~~~k---P~~iiGkkg~~i 84 (227)
.+.|+-.+..+++ -..---.||+-+..++.+. - -..++|+ -..+ . +.-.|++.+ -+++||++|+.|
T Consensus 174 ~~~~~y~~d~~Td~~~~~~v~EiIREki~~~l~~EiPY~~~V~i~~~~e~~~~~~~I~~~I~V~k~sqK~IiIGk~G~~I 253 (296)
T PRK00089 174 EGPPLYPEDQITDRPERFLAAEIIREKILRLLGDELPYSVAVEIEKFEEREDGLVRINATIYVERDSQKGIVIGKGGAKL 253 (296)
T ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCCCEEEEEEEEECCCCCCEEEEECCCHHH
T ss_conf 88656873014578488999999999999973111784279999999986887149999999877776358990785799
Q ss_pred HHHH----HHHHCCCCCEEEE--EEEEECCCCCCHHHHHH
Q ss_conf 9989----8764035870578--79981375533778799
Q gi|254780255|r 85 EKIR----KKLSNMTNSEIHL--SVNEVPKPEINATLIAQ 118 (227)
Q Consensus 85 ~~l~----~~L~~~~~~~v~i--~v~ei~~p~~~A~~iA~ 118 (227)
+++. +.|+++++.++.+ .|.--++|--++.++.+
T Consensus 254 K~Ig~~aR~~lek~~~~kV~L~L~VKV~k~W~~~~~~l~~ 293 (296)
T PRK00089 254 KKIGTEARKDIEKLLGKKVHLELWVKVKKGWRDDEKALRE 293 (296)
T ss_pred HHHHHHHHHHHHHHHCCCEEEEEEEEECCCCCCCHHHHHH
T ss_conf 9999999999999968986999999988886779899986
No 21
>PRK08406 transcription elongation factor NusA-like protein; Validated
Probab=86.74 E-value=2 Score=22.39 Aligned_cols=48 Identities=25% Similarity=0.439 Sum_probs=34.1
Q ss_pred HHHHHCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 877422642215532588518999973741001356534899898764
Q gi|254780255|r 45 CHLKQAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227)
Q Consensus 45 k~l~~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227)
..+..+..-+|.+....+.+-..+....-|..||++|.+++++++.|.
T Consensus 17 e~~T~~~~~DCi~d~~~~riiFvV~~g~mG~AIGk~G~~Ik~l~~~lg 64 (142)
T PRK08406 17 ESITGATVRDCIIDEEYDRIIFVVKEGDMGLAIGKGGENVKRLKEKLG 64 (142)
T ss_pred HHHHCCCEEEEEECCCCCEEEEEECCCHHHHHHCCCCCHHHHHHHHHC
T ss_conf 998799723568708998899998767688975879607999999858
No 22
>COG1782 Predicted metal-dependent RNase, consists of a metallo-beta-lactamase domain and an RNA-binding KH domain [General function prediction only]
Probab=86.53 E-value=2.5 Score=21.82 Aligned_cols=112 Identities=24% Similarity=0.385 Sum_probs=59.8
Q ss_pred HHHHHHH-HCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHHH
Q ss_conf 9998774-226422155325885189999737410013565348998987640358705787998137553377879999
Q gi|254780255|r 42 YLQCHLK-QAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQSI 120 (227)
Q Consensus 42 fi~k~l~-~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~I 120 (227)
.|....+ .|+|+.+.-. .+.-.|.|.+.+||++||+.|+.+..+....... ..-+..|-+....+ +.|
T Consensus 80 ~I~eivP~ea~i~~i~Fd--~~tGEViIea~KPGlvigk~g~~~reI~~~tgW~--------p~ivR~PPi~S~ti-~~i 148 (637)
T COG1782 80 IILEIVPEEAGITDIYFD--DDTGEVIIEAKKPGLVIGKGGSTLREITAETGWA--------PKIVRTPPIQSRTI-KSI 148 (637)
T ss_pred HHHHHCCCCCCCEEEEEC--CCCCEEEEEECCCCEEEECCCHHHHHHHHHHCCC--------CEEEECCCCCHHHH-HHH
T ss_conf 999748621370367861--8874499995589558824721799999974875--------30563699750669-999
Q ss_pred HHHHHCCCH-HHHHHHHHHHHHHH---CCCCEEEEEEECCCCCCCCCEEE
Q ss_conf 999875963-68999999998532---38855999970367864222157
Q gi|254780255|r 121 AQQLERRVV-FRRAMKRAVQSAMR---FGADGVKVIASGRLNGAELSRTE 166 (227)
Q Consensus 121 a~~Lekr~~-fRr~~k~~i~~~~k---~g~kGikI~isGRl~G~e~Ar~e 166 (227)
..-|.+-.- =|.++++.-.++-+ .+-.=++++--|-+. |-.|+-
T Consensus 149 r~~l~~~~~eR~~iL~~vg~rIhr~~~~~~~wvRvt~LGg~~--EVGRSa 196 (637)
T COG1782 149 REILRSERKERREILRNVGRRIHREPLVKDRWVRVTALGGFR--EVGRSA 196 (637)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEECCCH--HCCCEE
T ss_conf 999998699999999999887466850267459999612411--206256
No 23
>PRK02821 hypothetical protein; Provisional
Probab=76.63 E-value=4 Score=20.67 Aligned_cols=44 Identities=18% Similarity=0.326 Sum_probs=35.9
Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEEC
Q ss_conf 18999973741001356534899898764035870578799813
Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVP 107 (227)
Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~v~i~v~ei~ 107 (227)
+.+.++-..-|-+|||+|..++.++..+.....+++.+.+.++.
T Consensus 33 ~el~V~~eD~GkVIGk~Grta~AiRTlv~a~~~r~v~~eivd~~ 76 (77)
T PRK02821 33 LEVRVHPDDLGKVIGRGGRTATALRTLVAGIGGRGIRVDVVDTD 76 (77)
T ss_pred EEEEECHHHCCCEECCCCHHHHHHHHHHHHHCCCCCEEEEEECC
T ss_conf 99999934474454778677999999999865897369998368
No 24
>TIGR03675 arCOG00543 arCOG01782 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=70.16 E-value=8.7 Score=18.73 Aligned_cols=105 Identities=25% Similarity=0.409 Sum_probs=55.8
Q ss_pred HHHHHHHH-HCCCCCEEEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCHHHHHHH
Q ss_conf 99998774-22642215532588518999973741001356534899898764035870578799813755337787999
Q gi|254780255|r 41 EYLQCHLK-QAGVAKILIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLSVNEVPKPEINATLIAQS 119 (227)
Q Consensus 41 ~fi~k~l~-~agis~i~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~v~i~v~ei~~p~~~A~~iA~~ 119 (227)
+.|....+ .|||..+.-. +..-.|+|.+.+||+++|+.|+.++++++..-.. ..-+..|-+....+ +.
T Consensus 73 ~~i~~~vp~~a~i~~~~fd--~~~~ev~i~~~kpg~~~g~~g~~~~~i~~~~gw~--------~~v~r~p~~~s~~~-~~ 141 (630)
T TIGR03675 73 EKIKEIVPEEAGITDIYFD--DVTGEVIIEAEKPGLVIGKGGSTLREITAETGWT--------PKVVRTPPIESKTI-KN 141 (630)
T ss_pred HHHHHHCCCCCCCEEEEEC--CCCCEEEEEECCCEEEECCCCHHHHHHHHHHCCE--------EEEEECCCCCHHHH-HH
T ss_conf 9999758953584158974--8972799997796367647516799999974974--------68886599970789-99
Q ss_pred HHHHHHCCCHHHHHH-HHHHHHHHH---CCCCEEEEEEECC
Q ss_conf 999987596368999-999998532---3885599997036
Q gi|254780255|r 120 IAQQLERRVVFRRAM-KRAVQSAMR---FGADGVKVIASGR 156 (227)
Q Consensus 120 Ia~~Lekr~~fRr~~-k~~i~~~~k---~g~kGikI~isGR 156 (227)
|..-|..-..+|+-+ ++.=.++-+ .+-.-++|+.=|=
T Consensus 142 ir~~~~~~~~~r~~~l~~~g~~i~r~~~~~~~~vrit~LG~ 182 (630)
T TIGR03675 142 IREYLRSESEERKEFLRKLGRRIHRDPIFKDRWVRVTALGG 182 (630)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCC
T ss_conf 99999970799999999988874689768897499983467
No 25
>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=66.21 E-value=5.3 Score=19.99 Aligned_cols=53 Identities=28% Similarity=0.461 Sum_probs=40.9
Q ss_pred HHHHHHHHHHCCCCCEEEEEC-CCCCEEEEEECCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 999998774226422155325-88518999973741001356534899898764
Q gi|254780255|r 40 REYLQCHLKQAGVAKILIERT-HKNCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227)
Q Consensus 40 R~fi~k~l~~agis~i~I~Rt-~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227)
.+|+.+-+..+.+.++.+... .+...|.+-...-+..||++|.+++-..+.+.
T Consensus 2 ~~fi~nal~Pa~v~~V~i~~~~~~~~~V~V~~~~~~~AIGk~G~Nvrla~~l~g 55 (61)
T cd02134 2 AEFIRNALSPAKVTSVTVLDDEEKRARVVVPDDQLGLAIGKGGQNVRLASKLLG 55 (61)
T ss_pred HHHHHHHCCCCEEEEEEECCCCCCEEEEEECHHHHHHHHCCCCEEHHHHHHHHC
T ss_conf 789986369875579884478773799998857843876678670999999779
No 26
>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=62.18 E-value=6.3 Score=19.51 Aligned_cols=29 Identities=41% Similarity=0.691 Sum_probs=24.5
Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 18999973741001356534899898764
Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227)
Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227)
+++.+-...-|.+||++|..|+++++.-.
T Consensus 2 ~rilvP~~~vG~vIGk~G~~I~~i~~~sg 30 (65)
T cd02396 2 LRLLVPSSQAGSIIGKGGSTIKEIREETG 30 (65)
T ss_pred EEEEEEHHHEEEEECCCCHHHHHHHHHHC
T ss_conf 89998746722899799878999999849
No 27
>COG1159 Era GTPase [General function prediction only]
Probab=58.91 E-value=14 Score=17.46 Aligned_cols=79 Identities=27% Similarity=0.398 Sum_probs=45.9
Q ss_pred HHHHHHHHHHHC--CCCCEEEEECC---CC---CEEEEEE---CCCCCCCCCCCHHHHHH----HHHHHCCCCCEEEEEE
Q ss_conf 999999877422--64221553258---85---1899997---37410013565348998----9876403587057879
Q gi|254780255|r 39 IREYLQCHLKQA--GVAKILIERTH---KN---CRIIVYS---ARPGLIIGKKGTDIEKI----RKKLSNMTNSEIHLSV 103 (227)
Q Consensus 39 IR~fi~k~l~~a--gis~i~I~Rt~---~~---i~I~I~~---~kP~~iiGkkg~~i~~l----~~~L~~~~~~~v~i~v 103 (227)
|||=+..++... ....++|++.. ++ +.-.|++ +.-+++||++|+.|+++ +++++++++.++.+.+
T Consensus 196 iREk~~~~l~eElPhsv~VeIe~~~~~~~~~~~I~a~I~Ver~sQK~IiIGk~G~~iK~IG~~AR~~ie~l~~~kV~L~L 275 (298)
T COG1159 196 IREKLLLLLREELPHSVAVEIEEFEEREKGLLKIHATIYVERESQKGIIIGKNGAMIKKIGTAARKDIEKLLGCKVYLEL 275 (298)
T ss_pred HHHHHHHHCCCCCCCEEEEEEEEEEECCCCEEEEEEEEEEECCCCCCEEECCCCHHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf 99999985244268137999999775689859999999982277643598788199999999999999998499669999
Q ss_pred --EEECCCCCCHHHHH
Q ss_conf --98137553377879
Q gi|254780255|r 104 --NEVPKPEINATLIA 117 (227)
Q Consensus 104 --~ei~~p~~~A~~iA 117 (227)
.--+++.-+...+.
T Consensus 276 ~VKVk~~W~~~~~~l~ 291 (298)
T COG1159 276 WVKVKKNWRDDEEALR 291 (298)
T ss_pred EEEECCCCCCCHHHHH
T ss_conf 9997456111889999
No 28
>PRK01064 hypothetical protein; Provisional
Probab=54.91 E-value=17 Score=17.07 Aligned_cols=47 Identities=30% Similarity=0.375 Sum_probs=32.5
Q ss_pred ECCCCCEEE--EEECCCCCCCCCCCHHHHHHHHHHHC---CCCCEEEEEEEE
Q ss_conf 258851899--99737410013565348998987640---358705787998
Q gi|254780255|r 59 RTHKNCRII--VYSARPGLIIGKKGTDIEKIRKKLSN---MTNSEIHLSVNE 105 (227)
Q Consensus 59 Rt~~~i~I~--I~~~kP~~iiGkkg~~i~~l~~~L~~---~~~~~v~i~v~e 105 (227)
...+.+.+. +.-..-|-+|||+|..++.++..+.. ..++++.+.+.+
T Consensus 25 ~~~~~~~~~l~V~~~D~GkVIGk~GrtakAIRtlv~aaa~k~~~rv~leI~d 76 (78)
T PRK01064 25 QGTHTIIYELTVAKPDIGKIIGKEGRTIKAIRTLLVSVASRNNVKVSLEIME 76 (78)
T ss_pred ECCCEEEEEEEECCCCCCCEECCCCHHHHHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf 4798799999999001855878887469999999999734699789999962
No 29
>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=52.10 E-value=9.8 Score=18.42 Aligned_cols=28 Identities=43% Similarity=0.627 Sum_probs=23.6
Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHH
Q ss_conf 1899997374100135653489989876
Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKL 91 (227)
Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L 91 (227)
..+.+-...-+.+||++|.+|+++++.-
T Consensus 2 ~~i~ip~~~~g~vIG~~G~~I~~I~~~~ 29 (64)
T cd00105 2 ERVLVPSSLVGRIIGKGGSTIKEIREET 29 (64)
T ss_pred EEEEECHHHCCEEECCCCCHHHHHHHHC
T ss_conf 8999736654267998981347999975
No 30
>COG4808 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.57 E-value=6.6 Score=19.43 Aligned_cols=59 Identities=27% Similarity=0.323 Sum_probs=46.2
Q ss_pred EEEECCCCCCCCCEEEEEEECCCCCCCEEEECEEEEEEEEEC--------------CCEEEEEEEEEECCCCC
Q ss_conf 997036786422215787525532452000030568999953--------------82667999973288537
Q gi|254780255|r 151 VIASGRLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAETA--------------YGSCGIKVYVSLRDEVS 209 (227)
Q Consensus 151 I~isGRl~G~e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~T~--------------~G~~GvKVwi~~~~~~~ 209 (227)
=..+|-|||.|++-+-.|+--.|--|+....|-|+.--|.|+ .++-||+-.|-|.|-.-
T Consensus 30 ktf~~nlnG~ei~~TytYKgDkVlkQsse~ki~Y~slga~tKeeA~Kml~~~s~kykni~Gv~ekidY~D~yA 102 (152)
T COG4808 30 KTFSGNLNGTEIKITYTYKGDKVLKQSSENKILYASLGAKTKEEAAKMLEPLSAKYKNIAGVEEKLDYKDTYA 102 (152)
T ss_pred HEEECCCCCEEEEEEEEECCCCHHHHHCHHEEEHHHHCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCC
T ss_conf 2251035772889999962760433311110231540686489999998888998657866302400302110
No 31
>PRK12328 nusA transcription elongation factor NusA; Provisional
Probab=49.42 E-value=19 Score=16.80 Aligned_cols=34 Identities=15% Similarity=0.123 Sum_probs=13.1
Q ss_pred CCCCCCEEEE--CEEEEEEEEECCCEEEEEEEEEECC
Q ss_conf 5324520000--3056899995382667999973288
Q gi|254780255|r 172 RVPLQTLRAH--IDYGTAVAETAYGSCGIKVYVSLRD 206 (227)
Q Consensus 172 ~vpl~t~~a~--idy~~~~a~T~~G~~GvKVwi~~~~ 206 (227)
++|-..++.. |.-....+.+ -.--|.++-+++..
T Consensus 171 qip~E~y~~Gdrik~~i~~V~~-~~~~gpqI~lSRt~ 206 (375)
T PRK12328 171 RIKGEKFKVGDVVKAVLRRVKI-DKKNGIKLELSRTS 206 (375)
T ss_pred CCCCCCCCCCCEEEEEEEEEEC-CCCCCCEEEEECCC
T ss_conf 3886558999869999999872-78999589996798
No 32
>PRK00045 hemA glutamyl-tRNA reductase; Reviewed
Probab=47.38 E-value=19 Score=16.79 Aligned_cols=39 Identities=18% Similarity=0.128 Sum_probs=30.5
Q ss_pred HHHHHHHHHHHHHHCCCCCEEEEECCCCCEEEEEECCCC
Q ss_conf 999999999877422642215532588518999973741
Q gi|254780255|r 36 DLKIREYLQCHLKQAGVAKILIERTHKNCRIIVYSARPG 74 (227)
Q Consensus 36 D~~IR~fi~k~l~~agis~i~I~Rt~~~i~I~I~~~kP~ 74 (227)
|-.+.+++.......++..+.|-.|.+++.|+.++..|.
T Consensus 25 ~~~~~~~l~~l~~~~~i~e~vvLSTCNR~EiY~~~~~~~ 63 (429)
T PRK00045 25 PDELKEALKSLLASPSVLEAVILSTCNRTEIYAVVDDFH 63 (429)
T ss_pred HHHHHHHHHHHHCCCCCCEEEEEECCCCEEEEEEECCCC
T ss_conf 889999999986179981599995578239999958854
No 33
>PRK00468 hypothetical protein; Provisional
Probab=42.15 E-value=27 Score=15.89 Aligned_cols=62 Identities=18% Similarity=0.257 Sum_probs=36.2
Q ss_pred HHHHHHHHHCCCCCEEEE--ECCCCCEEE--EEECCCCCCCCCCCHHHHHHHHHHHC---CCCCEEEEEE
Q ss_conf 999987742264221553--258851899--99737410013565348998987640---3587057879
Q gi|254780255|r 41 EYLQCHLKQAGVAKILIE--RTHKNCRII--VYSARPGLIIGKKGTDIEKIRKKLSN---MTNSEIHLSV 103 (227)
Q Consensus 41 ~fi~k~l~~agis~i~I~--Rt~~~i~I~--I~~~kP~~iiGkkg~~i~~l~~~L~~---~~~~~v~i~v 103 (227)
+||-+.+-+. =..+.+. .....+.+. +....-|-+|||+|..++.++..+.- ..++++.+++
T Consensus 6 e~iv~~LVd~-Pd~V~V~~~~~~~~~~~~l~V~~~D~GkVIGk~GrtakAIRtll~aaa~k~~~rv~leI 74 (75)
T PRK00468 6 ETIAKALVDN-PDAVQVNEIEGEQSIILELKVAPEDMGKVIGKQGRIAKAIRTVVKAAAIKENKRVVVEI 74 (75)
T ss_pred HHHHHHHCCC-CCEEEEEEEECCCEEEEEEEECHHHCCCEECCCCHHHHHHHHHHHHHHCCCCCEEEEEE
T ss_conf 9999984899-88389999967987999999993558646677871499999999997435897799997
No 34
>TIGR01953 NusA transcription termination factor NusA; InterPro: IPR010213 This entry describes NusA, or N utilisation 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 Escherichia coli of phage lambda antitermination protein N with the N-utilisation substance, consisting of NusA, NusB, NusE (ribosomal protein S10), and NusG . This entry represents a region of NusA shared by all bacterial forms, and includes the S1 (IPR003029 from INTERPRO) and KH RNA binding domains. Proteobacterial forms have an additional C-terminal region, not included in this entry, with two repeats of 50-residue domain rich in acidic amino acids.; GO: 0003723 RNA binding, 0030528 transcription regulator activity.
Probab=40.37 E-value=29 Score=15.72 Aligned_cols=29 Identities=34% Similarity=0.504 Sum_probs=12.2
Q ss_pred CEEEEEE-CCCC-----CCCCCCCHHHHHHHHHHH
Q ss_conf 1899997-3741-----001356534899898764
Q gi|254780255|r 64 CRIIVYS-ARPG-----LIIGKKGTDIEKIRKKLS 92 (227)
Q Consensus 64 i~I~I~~-~kP~-----~iiGkkg~~i~~l~~~L~ 92 (227)
.+|-+++ ..|+ ..+|.+|..+..+.+.|.
T Consensus 253 ~KiAV~SH~d~~iDPvGAcvG~~G~Ri~~i~~EL~ 287 (366)
T TIGR01953 253 TKIAVESHNDENIDPVGACVGPKGSRIQAISKELN 287 (366)
T ss_pred CEEEEEEECCCCCCEEEEEECCCCCCHHHHHHHHC
T ss_conf 13578850789987046588898865433388747
No 35
>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=36.23 E-value=20 Score=16.63 Aligned_cols=28 Identities=32% Similarity=0.488 Sum_probs=22.3
Q ss_pred EEEEEECCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 8999973741001356534899898764
Q gi|254780255|r 65 RIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227)
Q Consensus 65 ~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227)
.|.+-....+.|||++|..+++|++.-.
T Consensus 3 ~i~vp~~~h~~iIG~~G~~i~~i~~~~~ 30 (62)
T cd02394 3 EVEIPKKLHRFIIGKKGSNIRKIMEETG 30 (62)
T ss_pred EEEECHHHCCCEECCCCCCHHHHHHHHC
T ss_conf 8998978819758899973999999859
No 36
>pfam00013 KH_1 KH domain. KH motifs can bind RNA in vitro. Autoantibodies to Nova, a KH domain protein, cause paraneoplastic opsoclonus ataxia. Q4R966.1/333-392;
Probab=36.01 E-value=25 Score=16.08 Aligned_cols=28 Identities=39% Similarity=0.649 Sum_probs=21.8
Q ss_pred EEEEEECCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 8999973741001356534899898764
Q gi|254780255|r 65 RIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227)
Q Consensus 65 ~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227)
.+.+-...-+.+||++|..+++|++...
T Consensus 3 ~v~vp~~~~~~iIG~~G~~i~~I~~~t~ 30 (57)
T pfam00013 3 EILIPSSLVGRIIGKGGSNIKEIREETG 30 (57)
T ss_pred EEEECHHHCCEEECCCCCHHHHHHHHCC
T ss_conf 9998755420689989647699999739
No 37
>KOG2192 consensus
Probab=33.25 E-value=15 Score=17.31 Aligned_cols=35 Identities=29% Similarity=0.518 Sum_probs=20.3
Q ss_pred ECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 25885189999737410013565348998987640
Q gi|254780255|r 59 RTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSN 93 (227)
Q Consensus 59 Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~ 93 (227)
+.|-.+.+.||.+.-|-+||+.|+.|++|+++-+.
T Consensus 120 ~~pce~rllihqs~ag~iigrngskikelrekcsa 154 (390)
T KOG2192 120 PSPCELRLLIHQSLAGGIIGRNGSKIKELREKCSA 154 (390)
T ss_pred CCCHHHHHHHHHHHCCCEECCCCHHHHHHHHHHHH
T ss_conf 98522221332441353343674057888876425
No 38
>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=31.79 E-value=22 Score=16.39 Aligned_cols=31 Identities=19% Similarity=0.244 Sum_probs=24.6
Q ss_pred CCCEEEEEECCCCCCCCCCCHHHHHHHHHHH
Q ss_conf 8518999973741001356534899898764
Q gi|254780255|r 62 KNCRIIVYSARPGLIIGKKGTDIEKIRKKLS 92 (227)
Q Consensus 62 ~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~ 92 (227)
.-..+.|...+-+.+||..|..|+.+.+.-.
T Consensus 2 ~i~~~~I~~dkIg~vIGpGGk~Ik~I~e~tg 32 (61)
T cd02393 2 RIETMKIPPDKIRDVIGPGGKTIKKIIEETG 32 (61)
T ss_pred EEEEEEECHHHHHHHCCCCCHHHHHHHHHHC
T ss_conf 4899996989987644886089999999889
No 39
>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=30.43 E-value=42 Score=14.77 Aligned_cols=64 Identities=19% Similarity=0.348 Sum_probs=39.7
Q ss_pred EEECCCCCCCCCCCHHHHHHHHHHHCCCCCEEEEE----EEEEC--CCCCCHHHHHHHHHHHHHCCCHHHHHHH
Q ss_conf 99737410013565348998987640358705787----99813--7553377879999999875963689999
Q gi|254780255|r 68 VYSARPGLIIGKKGTDIEKIRKKLSNMTNSEIHLS----VNEVP--KPEINATLIAQSIAQQLERRVVFRRAMK 135 (227)
Q Consensus 68 I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~v~i~----v~ei~--~p~~~A~~iA~~Ia~~Lekr~~fRr~~k 135 (227)
|=..+-|.+||+.|+.++.|.+.+.- ++.++ ..++. ..+..+.+-|..+...+-++.+.-+|++
T Consensus 4 IP~~Rig~lIGk~G~~~k~Iee~~~~----~i~ids~tg~V~i~~~~~Dp~~~~KA~d~I~Ai~rGf~pe~A~~ 73 (172)
T TIGR03665 4 IPKDRIGVLIGKGGETKKEIEERTGV----KLDIDSETGEVKIEEEDEDPLAVMKAREVVKAIGRGFSPEKALK 73 (172)
T ss_pred CCHHHEEEEECCCCCHHHHHHHHHCC----EEEEECCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf 87356355556870139999999798----79984686348835788998999999999999876999899998
No 40
>COG0195 NusA Transcription elongation factor [Transcription]
Probab=30.22 E-value=42 Score=14.75 Aligned_cols=36 Identities=25% Similarity=0.497 Sum_probs=24.1
Q ss_pred EEECCCC-CEEEEEECCC-CCCCCCCCHHHHHHHHHHH
Q ss_conf 5325885-1899997374-1001356534899898764
Q gi|254780255|r 57 IERTHKN-CRIIVYSARP-GLIIGKKGTDIEKIRKKLS 92 (227)
Q Consensus 57 I~Rt~~~-i~I~I~~~kP-~~iiGkkg~~i~~l~~~L~ 92 (227)
+.|.+.. ..+++-...| |..+|++|..++.+.+.|.
T Consensus 69 i~rd~r~av~~~~~~~d~vG~~iG~~G~rvk~i~~eLg 106 (190)
T COG0195 69 VARDPRAAVVSNVVKIDPVGACIGKRGSRVKAVSEELG 106 (190)
T ss_pred EEECCCCCEEEEECCCCCHHHHCCCCCHHHHHHHHHHC
T ss_conf 98267550399615768445421777628999999868
No 41
>TIGR02539 SepCysS Sep-tRNA:Cys-tRNA synthase; InterPro: IPR013375 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology . The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric . Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices , and are mostly dimeric or multimeric, containing at least three conserved regions , , . However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases; these synthetases are further divided into three subclasses, a, b and c, according to sequence homology. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases . Many archaeal species lack cysteinyl-tRNA synthetase, an essential enzyme that provides Cys-tRNA(Cys) in other organisms. Instead, in a two step pathway, tRNA-Cys is acylated with O-phosphoserine (Sep) to form Sep-tRNA(Cys), which is subsequently converted to Cys-tRNA(Cys) . This pathway is also thought to function as the sole route of cysteine biosynthesis in these organisms. Several other archaeal species use both this pathway and direct tRNA(Cys) aminoacylation to synthesize Cys-tRNA(Cys), but this pathway appears to be the only route for cysteine biosynthesis. Proteins in this entry catalyse the second step in this pathway using pyridoxal phosphate and a sulphur donor to synthesize Cys from Sep while attached to the tRNA..
Probab=29.77 E-value=25 Score=16.10 Aligned_cols=38 Identities=24% Similarity=0.373 Sum_probs=29.6
Q ss_pred CCCCCCCCEEEEEEECCCCCCCEEEECEEEEEEEE------ECCCEEEEEE
Q ss_conf 67864222157875255324520000305689999------5382667999
Q gi|254780255|r 156 RLNGAELSRTECYLEGRVPLQTLRAHIDYGTAVAE------TAYGSCGIKV 200 (227)
Q Consensus 156 Rl~G~e~Ar~e~~~~G~vpl~t~~a~idy~~~~a~------T~~G~~GvKV 200 (227)
=||+| |.-||+|++...-..||=..+-| -+=||||++=
T Consensus 182 LLNCA-------Y~vGRmPv~~ke~~~DFiVGSGHKSMAASaP~GvLa~~e 225 (381)
T TIGR02539 182 LLNCA-------YTVGRMPVSAKEIKADFIVGSGHKSMAASAPCGVLAMSE 225 (381)
T ss_pred EECCC-------CEEEEECCCCCCCCCCEEEECCCCHHHHCCCEEECCCCC
T ss_conf 21245-------052100315777787677806851322126600214542
No 42
>TIGR02303 HpaG-C-term 4-hydroxyphenylacetate degradation bifunctional isomerase/decarboxylase, C-terminal subunit; InterPro: IPR012684 This entry represents one of two subunits/domains of the bifunctional isomerase/decarboxylase involved in 4-hydroxyphenylacetate degradation . In Escherichia coli and some other species, this enzyme is encoded by a single polypeptide containing both this domain and the closely related N-terminal domain (IPR012686 from INTERPRO). In other species such as Pasteurella multocida, these domains are found as two separate proteins (usually as tandem genes). Together, these domains carry out the decarboxylation of 5-oxopent-3-ene-1,2,5-tricarboxylic acid (OPET) to 2-hydroxy-2,4-diene-1,7-dioate (HHDD) and the subsequent isomerization to 2-oxohept-3-ene-1,7-dioate (OHED).; GO: 0008704 5-carboxymethyl-2-hydroxymuconate delta-isomerase activity, 0018800 5-oxopent-3-ene-125-tricarboxylate decarboxylase activity.
Probab=29.63 E-value=11 Score=18.02 Aligned_cols=65 Identities=18% Similarity=0.268 Sum_probs=40.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHC------------C--CCCEEEEECCCCCEEEEEECCCCCCCCCCC-----HHHHHHHHH
Q ss_conf 799998999999999877422------------6--422155325885189999737410013565-----348998987
Q gi|254780255|r 30 GALLHEDLKIREYLQCHLKQA------------G--VAKILIERTHKNCRIIVYSARPGLIIGKKG-----TDIEKIRKK 90 (227)
Q Consensus 30 ~~~L~eD~~IR~fi~k~l~~a------------g--is~i~I~Rt~~~i~I~I~~~kP~~iiGkkg-----~~i~~l~~~ 90 (227)
..-+-.|+.||+|++++|+.. | |.+++=..-+.++.+.-|+ -|.+-...+ .++-.|.+.
T Consensus 125 GYTiaNDya~RDYleNyYRPnlRvK~Rdt~~P~GPw~VD~~dveDp~nL~LrtyV--NGEL~Q~G~T~dMiF~va~LiEy 202 (249)
T TIGR02303 125 GYTIANDYAIRDYLENYYRPNLRVKNRDTLTPIGPWIVDKEDVEDPMNLALRTYV--NGELTQEGNTSDMIFSVAYLIEY 202 (249)
T ss_pred CCHHCCHHHHCCCCCCCCCCCCEECCCCCCCCCCCEEEEECCCCCCCCCEEEEEE--EEEEEECCCCCHHHHCHHHHHHH
T ss_conf 4100001121000011338981033767644378847851236785567133677--13786468742112046789998
Q ss_pred HHCCCC
Q ss_conf 640358
Q gi|254780255|r 91 LSNMTN 96 (227)
Q Consensus 91 L~~~~~ 96 (227)
||.++=
T Consensus 203 lS~~mT 208 (249)
T TIGR02303 203 LSEFMT 208 (249)
T ss_pred HHHCCC
T ss_conf 631024
No 43
>COG1104 NifS Cysteine sulfinate desulfinase/cysteine desulfurase and related enzymes [Amino acid transport and metabolism]
Probab=29.20 E-value=44 Score=14.65 Aligned_cols=41 Identities=17% Similarity=0.126 Sum_probs=33.8
Q ss_pred EECCCCCCCEEEECEEEEEEEEECCCEEEEEEEEEECCCCC
Q ss_conf 52553245200003056899995382667999973288537
Q gi|254780255|r 169 LEGRVPLQTLRAHIDYGTAVAETAYGSCGIKVYVSLRDEVS 209 (227)
Q Consensus 169 ~~G~vpl~t~~a~idy~~~~a~T~~G~~GvKVwi~~~~~~~ 209 (227)
..|++|+.--...||+.+..++.-||.=||=.-..++++.+
T Consensus 181 a~Gkipi~~~~~~vD~ls~SaHK~~GpkGiGaLyv~~~~~~ 221 (386)
T COG1104 181 AVGKIPIDLEELGVDLLSFSAHKFGGPKGIGALYVRPGVRL 221 (386)
T ss_pred HCCCEECCCCCCCCCEEEEEHHHCCCCCCEEEEEECCCCCC
T ss_conf 25760046021576568731121369984279998799873
No 44
>PRK09202 nusA transcription elongation factor NusA; Validated
Probab=28.17 E-value=46 Score=14.54 Aligned_cols=15 Identities=33% Similarity=0.753 Sum_probs=5.5
Q ss_pred CCCCCHHHHHHHHHH
Q ss_conf 135653489989876
Q gi|254780255|r 77 IGKKGTDIEKIRKKL 91 (227)
Q Consensus 77 iGkkg~~i~~l~~~L 91 (227)
+|-+|..+..+.+.|
T Consensus 252 VG~rGsRI~~I~~EL 266 (428)
T PRK09202 252 VGMRGSRIQAISNEL 266 (428)
T ss_pred ECCCCCCHHHHHHHH
T ss_conf 778864299999874
No 45
>KOG1676 consensus
Probab=25.24 E-value=38 Score=15.04 Aligned_cols=24 Identities=38% Similarity=0.739 Sum_probs=11.2
Q ss_pred EEEEECCCCCCCCCCCHHHHHHHH
Q ss_conf 999973741001356534899898
Q gi|254780255|r 66 IIVYSARPGLIIGKKGTDIEKIRK 89 (227)
Q Consensus 66 I~I~~~kP~~iiGkkg~~i~~l~~ 89 (227)
|.|=..|-|+|||+.|+.+++|++
T Consensus 143 I~IPa~k~GlIIGKgGETikqlqe 166 (600)
T KOG1676 143 ILIPANKCGLIIGKGGETIKQLQE 166 (600)
T ss_pred ECCCCCCEEEEECCCCCHHHHHHH
T ss_conf 024754200376168607778775
No 46
>TIGR02799 thio_ybgC tol-pal system-associated acyl-CoA thioesterase; InterPro: IPR014166 The tol-pal system consists of five critical genes. Inner membrane proteins TolQ and TolR convert proton motive force to energy that is transduced through TolA to an outer membrane complex of TolB and Pal. The system is known to be required to maintain outer membrane integrity. In a system with several homologous parts, ExbB and ExbD transduces energy through TonB to a variety of outer membrane proteins, many of which are siderophore receptors. The tol-pal system therefore may also be involved in transport. This family consists of a protein nearly always found in operons with the genes of the tol-pal system. The significance of this thioesterase to the tol-pal system is unclear, but either of two observations may be relevant. First, Pal, or peptidoglycan-associated lipoprotein, has a conserved N-terminal cleavage and acylation that makes it a lipoprotein. Second, the tol-pal system is implicated not only in the import of certain organics but also in the maintenance of outer membrane integrity (by an unknown mechanism) ..
Probab=24.22 E-value=19 Score=16.82 Aligned_cols=26 Identities=27% Similarity=0.077 Sum_probs=16.9
Q ss_pred CCCCCCCEEEEEEECCCCCCCEEEECE
Q ss_conf 786422215787525532452000030
Q gi|254780255|r 157 LNGAELSRTECYLEGRVPLQTLRAHID 183 (227)
Q Consensus 157 l~G~e~Ar~e~~~~G~vpl~t~~a~id 183 (227)
|+=-|||||||.+.==+.. ++.++=+
T Consensus 24 L~F~ERARTEwLR~lG~~Q-~l~~~~g 49 (127)
T TIGR02799 24 LKFMERARTEWLRALGFEQ-TLLEETG 49 (127)
T ss_pred HHHHCCCCHHHHHHCCCCC-HHHHCCC
T ss_conf 2010323137786357210-3575499
No 47
>TIGR00284 TIGR00284 dihydropteroate synthase-related protein; InterPro: IPR005236 The proteins of this family have been found so far only in the four archaeal species. The central region of the proteins shows considerable homology to the amino-terminal half of dihydropteroate synthases. .
Probab=23.43 E-value=57 Score=14.02 Aligned_cols=45 Identities=29% Similarity=0.482 Sum_probs=20.4
Q ss_pred HHHHHHHHCCCCCEEEEECC--CCCEEEEEEC--CCCCCC-CCCCHHHHH
Q ss_conf 99987742264221553258--8518999973--741001-356534899
Q gi|254780255|r 42 YLQCHLKQAGVAKILIERTH--KNCRIIVYSA--RPGLII-GKKGTDIEK 86 (227)
Q Consensus 42 fi~k~l~~agis~i~I~Rt~--~~i~I~I~~~--kP~~ii-Gkkg~~i~~ 86 (227)
+++....+.|+.+|+|.|.. ..+..+-|.. .|.++| ||++.+|-+
T Consensus 440 ~iep~~d~tG~akI~vd~erkn~~i~~~~~~~~~ep~~~i~Gkkp~si~r 489 (529)
T TIGR00284 440 EIEPEMDDTGYAKIEVDRERKNEEIVAVFYIARREPKVTIKGKKPKSILR 489 (529)
T ss_pred CCCCHHHCCCCEEEEEEECCCCCCEEEEEECCCCCCEEEEECCCCHHHHH
T ss_conf 68700104774699985002255258999848885148884478637999
No 48
>COG1837 Predicted RNA-binding protein (contains KH domain) [General function prediction only]
Probab=23.43 E-value=57 Score=14.02 Aligned_cols=50 Identities=26% Similarity=0.401 Sum_probs=32.6
Q ss_pred CEEEEECCCC--CEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCC---CEEEEEE
Q ss_conf 2155325885--189999737410013565348998987640358---7057879
Q gi|254780255|r 54 KILIERTHKN--CRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTN---SEIHLSV 103 (227)
Q Consensus 54 ~i~I~Rt~~~--i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~---~~v~i~v 103 (227)
++..+-..+. +.+.++...-|-+|||+|..++.++..|+.... +++.+.+
T Consensus 20 ~V~~~~~~~~~~~~l~v~~~D~GkvIGk~GRti~AIRTll~a~~~~~~~~v~i~i 74 (76)
T COG1837 20 RVDEEEGEKTVTIELRVAPEDMGKVIGKQGRTIQAIRTLLSAVGSKDSKRVVVEI 74 (76)
T ss_pred EEEEEECCCEEEEEEEECCCCCCCEECCCCHHHHHHHHHHHHHCCCCCEEEEEEE
T ss_conf 8999816974999999872004635667870599999999984225743999995
No 49
>COG1855 ATPase (PilT family) [General function prediction only]
Probab=21.05 E-value=63 Score=13.74 Aligned_cols=14 Identities=36% Similarity=0.411 Sum_probs=5.5
Q ss_pred EEEEEEECCCCCCC
Q ss_conf 59999703678642
Q gi|254780255|r 148 GVKVIASGRLNGAE 161 (227)
Q Consensus 148 GikI~isGRl~G~e 161 (227)
-+++-.-=||-|.-
T Consensus 344 DF~vyaDmRLAGVG 357 (604)
T COG1855 344 DFQVYADLRLAGVG 357 (604)
T ss_pred CEEEEEEEECCCCC
T ss_conf 61676650011575
No 50
>PRK00092 hypothetical protein; Reviewed
Probab=21.01 E-value=63 Score=13.74 Aligned_cols=123 Identities=23% Similarity=0.306 Sum_probs=66.6
Q ss_pred HHHHHHHHHHHHHCCCCCE--EEEECCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHCCCCCE---EEEEEEEECCCCC
Q ss_conf 9999999987742264221--5532588518999973741001356534899898764035870---5787998137553
Q gi|254780255|r 37 LKIREYLQCHLKQAGVAKI--LIERTHKNCRIIVYSARPGLIIGKKGTDIEKIRKKLSNMTNSE---IHLSVNEVPKPEI 111 (227)
Q Consensus 37 ~~IR~fi~k~l~~agis~i--~I~Rt~~~i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~~~~~~---v~i~v~ei~~p~~ 111 (227)
-.|.+.+.-.....|+.-+ ++........+.|+..+++-+ .-.....+...++..+... ..=+..||.+|.+
T Consensus 4 e~i~~li~pvv~~~G~~L~dve~~~~~~~~~lrI~ID~~~gv---~lddc~~vSr~is~~LD~~d~i~~~Y~LEVSSPGi 80 (153)
T PRK00092 4 EQLTELIEPVVEGLGYELVGVEFVKAGRPSTLRIYIDSDGGI---TLDDCEDVSRQLSAVLDVEDPIPDAYTLEVSSPGL 80 (153)
T ss_pred HHHHHHHHHHHHHCCCEEEEEEEEECCCCEEEEEEEECCCCC---CHHHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCC
T ss_conf 999999999998779999999999189973999999889991---89999998899887526365678755999967999
Q ss_pred CHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCEEEEEEECC
Q ss_conf 3778799999998759636899999999853238855999970367864222157875255
Q gi|254780255|r 112 NATLIAQSIAQQLERRVVFRRAMKRAVQSAMRFGADGVKVIASGRLNGAELSRTECYLEGR 172 (227)
Q Consensus 112 ~A~~iA~~Ia~~Lekr~~fRr~~k~~i~~~~k~g~kGikI~isGRl~G~e~Ar~e~~~~G~ 172 (227)
+-.+.... -|++..-+.+.-..+....|-+ .+.|+|.+++-....-..+|.
T Consensus 81 ~RpL~~~~---------~f~~~~G~~v~v~l~~~~~~~k-~~~G~L~~~~~~~i~l~~~~~ 131 (153)
T PRK00092 81 DRPLKTAE---------HFRRFVGREVKVKLREPIDGRK-KFQGRLLAVDGETVTLEVEGK 131 (153)
T ss_pred CCCCCCHH---------HHHHHCCCEEEEEEECCCCCCE-EEEEEEEEEECCEEEEEECCC
T ss_conf 97326989---------9998669389999944668964-999999988499899998897
No 51
>KOG2190 consensus
Probab=20.40 E-value=65 Score=13.66 Aligned_cols=30 Identities=40% Similarity=0.595 Sum_probs=23.0
Q ss_pred CEEEEEECCCCCCCCCCCHHHHHHHHHHHC
Q ss_conf 189999737410013565348998987640
Q gi|254780255|r 64 CRIIVYSARPGLIIGKKGTDIEKIRKKLSN 93 (227)
Q Consensus 64 i~I~I~~~kP~~iiGkkg~~i~~l~~~L~~ 93 (227)
+++..++...|-+||++|..++++++.-+.
T Consensus 45 ~RlL~~~kevG~IIGk~G~~vkkir~~t~s 74 (485)
T KOG2190 45 YRLLCHVKEVGSIIGKKGDIVKKIRKETES 74 (485)
T ss_pred EEEEECCCCCEEEECCCCHHHHHHHHCCCC
T ss_conf 799721554414874675788887644556
Done!