Query psy9436
Match_columns 188
No_of_seqs 191 out of 423
Neff 3.6
Searched_HMMs 46136
Date Fri Aug 16 19:17:59 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9436.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9436hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PTZ00068 60S ribosomal protein 100.0 1.9E-48 4.2E-53 328.9 11.5 159 21-188 43-202 (202)
2 KOG3204|consensus 100.0 1.3E-44 2.8E-49 304.4 9.4 134 47-188 63-196 (197)
3 TIGR01077 L13_A_E ribosomal pr 99.9 2.8E-28 6.2E-33 196.4 4.8 82 45-127 61-142 (142)
4 PRK06394 rpl13p 50S ribosomal 99.9 9E-25 1.9E-29 176.9 5.7 100 23-124 44-143 (146)
5 PF00572 Ribosomal_L13: Riboso 99.5 1.3E-14 2.7E-19 115.2 3.2 76 23-99 52-127 (128)
6 TIGR01066 rplM_bact ribosomal 99.5 5.7E-14 1.2E-18 113.4 4.5 57 41-98 82-138 (140)
7 PRK09216 rplM 50S ribosomal pr 99.4 2.2E-13 4.8E-18 110.5 4.6 56 43-99 86-141 (144)
8 PLN00205 ribisomal protein L13 99.4 3.2E-13 7E-18 114.2 3.6 59 40-99 85-143 (191)
9 COG0102 RplM Ribosomal protein 99.4 2.2E-13 4.8E-18 111.4 2.3 57 44-105 87-144 (148)
10 CHL00159 rpl13 ribosomal prote 99.4 7E-13 1.5E-17 107.6 4.7 54 44-98 88-141 (143)
11 cd00392 Ribosomal_L13 Ribosoma 99.1 3.8E-11 8.2E-16 93.8 2.3 46 40-86 69-114 (114)
12 KOG3203|consensus 97.6 4.7E-05 1E-09 63.6 3.6 47 44-91 94-141 (165)
13 PF04760 IF2_N: Translation in 50.1 18 0.00038 24.0 2.5 22 113-134 3-24 (54)
14 PF09756 DDRGK: DDRGK domain; 46.3 21 0.00045 30.6 3.0 29 110-138 110-138 (188)
15 PF01726 LexA_DNA_bind: LexA D 33.3 38 0.00083 23.9 2.2 21 115-135 27-48 (65)
16 PF12324 HTH_15: Helix-turn-he 30.9 50 0.0011 24.8 2.6 26 111-136 36-61 (77)
17 PF09012 FeoC: FeoC like trans 29.7 62 0.0014 22.3 2.8 25 111-135 12-36 (69)
18 PF11524 SeleniumBinding: Sele 25.8 40 0.00087 25.7 1.3 33 109-142 16-48 (81)
19 smart00418 HTH_ARSR helix_turn 24.2 94 0.002 19.1 2.7 27 111-137 8-34 (66)
20 PF04967 HTH_10: HTH DNA bindi 23.9 67 0.0015 22.2 2.1 24 112-135 22-45 (53)
No 1
>PTZ00068 60S ribosomal protein L13a; Provisional
Probab=100.00 E-value=1.9e-48 Score=328.88 Aligned_cols=159 Identities=33% Similarity=0.499 Sum_probs=144.1
Q ss_pred ccccccccchhhHHhHhhhccCccchHHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceeccc
Q psy9436 21 TTSTKRNIGHFDRKRKQARHESKIRAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPT 100 (188)
Q Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vVP~ 100 (188)
|.++.++.-.|..-.+..++.||.. ++++++.|++|||||||||||||+++|++||+||+||+|+|+||+.+++++||+
T Consensus 43 TG~k~~~K~~y~~~lk~~~~~nP~~-g~~~~r~P~~Il~raVrGMLPkk~~~Gr~alkrLkVy~G~php~~~~k~~vvp~ 121 (202)
T PTZ00068 43 SGSLFRNKVKYEEFLRKRMNTNPRR-GPFHHRAPSDIFWRTVRGMLPHKTKRGAAALKRLKVFEGVPAPYDKVKRVVIPS 121 (202)
T ss_pred ecchhhheeeeEeeeEeeccCCCCc-chhcccCHHHHHHHHHhhhCCCCChhHHHHHhCCEEecCCCCchhccCcccccc
Confidence 3445555555555444444455543 889999999999999999999999999999999999999999999999999999
Q ss_pred chhhhccCCCCCeeehhhhHHHhccchHHHHHHHHHHHHHHHHHHHHHhhhccCCchhHhhHHHHHHhHHHHHhc-chHH
Q psy9436 101 ALRTVCLKPGRSYCSVGRISHEVGWKYKTIVRHLERKRREKSIEKIKLHTVYLIPCLDCESNLTKKAGKQVKKAT-FPLT 179 (188)
Q Consensus 101 Alrv~rlkp~rKy~tLGeLs~evGWKy~~vv~~LE~KRK~ka~~~y~kK~~~~~~~~~~~~kl~~~A~k~~~k~~-~~~~ 179 (188)
|+++.+|+|+++||+|||||++|||+|+|||++||++|++++++||++|++ ..+++++|++++++++ .+++
T Consensus 122 A~r~~rl~~~~ky~~lg~ls~~vGwky~~vv~~le~krk~k~~~~~~~k~~--------~~k~~~~a~~~~~~~~~~~~~ 193 (202)
T PTZ00068 122 ALRVLRLKPERPYTVLGDLSAHVGWKYADVVAKLEEKRKERAAAYYKKKVK--------LRKAWKEARKKALAKLPKAIV 193 (202)
T ss_pred hhhhhccCCCCceeeHHHHHHHhCccHHHHHHHHHHHHHHHHHHHHHHHHH--------HHHHHHHHHHHHHHhcchHHH
Confidence 999999999999999999999999999999999999999999999999999 9999999999999988 7999
Q ss_pred HHHhhcCCC
Q psy9436 180 KQINTFGYK 188 (188)
Q Consensus 180 ~~L~~~Gy~ 188 (188)
++|++|||+
T Consensus 194 ~~l~~~gy~ 202 (202)
T PTZ00068 194 AVLKKFGYA 202 (202)
T ss_pred HHHHHcCCC
Confidence 999999995
No 2
>KOG3204|consensus
Probab=100.00 E-value=1.3e-44 Score=304.40 Aligned_cols=134 Identities=39% Similarity=0.611 Sum_probs=130.4
Q ss_pred HHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceecccchhhhccCCCCCeeehhhhHHHhccc
Q psy9436 47 VEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVGWK 126 (188)
Q Consensus 47 ~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vVP~Alrv~rlkp~rKy~tLGeLs~evGWK 126 (188)
+++--+-|..|||++||||+||||+||++|++||++|+|||+|||+++++++|.|++|++|+|++|||+||+||||||||
T Consensus 63 g~~hfr~ps~i~~~~vrgm~~~kt~rg~aal~~l~~~eGip~~~dk~~r~v~p~a~~v~~lk~~~K~c~lG~L~~eVGWk 142 (197)
T KOG3204|consen 63 GPFHFRAPSRILQKAVRGMYPHKTKRGRAALERLRVFEGIPPPYDKQKRLVVPVAFQVLRLKPYKKYCLLGRLSHEVGWK 142 (197)
T ss_pred CcchhhhHHHHHHHhhccccccCCCccHHHHHHHHHhCCCCChhhhcCCccCCcceeeecccCCceeEEeccchhhhcch
Confidence 44556889999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhccCCchhHhhHHHHHHhHHHHHhcchHHHHHhhcCCC
Q psy9436 127 YKTIVRHLERKRREKSIEKIKLHTVYLIPCLDCESNLTKKAGKQVKKATFPLTKQINTFGYK 188 (188)
Q Consensus 127 y~~vv~~LE~KRK~ka~~~y~kK~~~~~~~~~~~~kl~~~A~k~~~k~~~~~~~~L~~~Gy~ 188 (188)
||+|+++||+|||+|+++||++|++ +++++++|++|+++++++++++|+++||+
T Consensus 143 yq~vtatLEeKRKeK~~~~y~kKkq--------l~kl~~~Aekn~~kkidky~e~l~~~g~~ 196 (197)
T KOG3204|consen 143 YQAVTATLEEKRKEKAKIHYQKKKQ--------LMRLRKQAEKNVEKKIDKYTEVLKTHGLL 196 (197)
T ss_pred hHHHHHHHHHHHhHhhhhhHHHHHH--------HHHHHHHHHHHHHHhHHHHHHHHhhcccC
Confidence 9999999999999999999999999 99999999999999999999999999995
No 3
>TIGR01077 L13_A_E ribosomal protein L13, archaeal/eukaryotic. This model represents ribosomal protein of L13 from the Archaea and from the eukaryotic cytosol. Bacterial and organellar forms are represented by TIGR01066.
Probab=99.94 E-value=2.8e-28 Score=196.36 Aligned_cols=82 Identities=39% Similarity=0.694 Sum_probs=79.7
Q ss_pred chHHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceecccchhhhccCCCCCeeehhhhHHHhc
Q psy9436 45 RAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTVCLKPGRSYCSVGRISHEVG 124 (188)
Q Consensus 45 ~~~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vVP~Alrv~rlkp~rKy~tLGeLs~evG 124 (188)
++++++++.|++||+++||||||+++.+|+.+++||+||+|+|+||+.++++++|+|+ +.+++|.||||+|||||+.||
T Consensus 61 ~~~~~~~r~P~~il~~aVrGMLPk~~~~Gr~~~krLkvy~G~~h~~~~qk~~~~~~a~-~~~~~~~~~~~~lg~l~~~~G 139 (142)
T TIGR01077 61 RRGPFFPRAPSRIFRRTVRGMLPHKTARGRAALRRLKVYVGIPPELDKKKRVVVPEAL-VSRLSPTRKYVTLGELAKFLG 139 (142)
T ss_pred CHHHhhhcCHHHHHHHHHHHhCCCCChhHHHHHhCcEEecCCCCCccccCccccChhh-hhccCCCCceEEHHHHHHHhC
Confidence 5688999999999999999999999999999999999999999999999999999999 999999999999999999999
Q ss_pred cch
Q psy9436 125 WKY 127 (188)
Q Consensus 125 WKy 127 (188)
|||
T Consensus 140 ~k~ 142 (142)
T TIGR01077 140 WKF 142 (142)
T ss_pred CcC
Confidence 997
No 4
>PRK06394 rpl13p 50S ribosomal protein L13P; Reviewed
Probab=99.91 E-value=9e-25 Score=176.89 Aligned_cols=100 Identities=28% Similarity=0.399 Sum_probs=88.4
Q ss_pred ccccccchhhHHhHhhhccCccchHHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceecccch
Q psy9436 23 STKRNIGHFDRKRKQARHESKIRAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTAL 102 (188)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vVP~Al 102 (188)
++.|.+-.|........+.||.++++++++.|++||+++|+||||+|+.+|+.+++||+||+|+|.||..++.+++|.|+
T Consensus 44 ~K~~~~~~y~~~~~~k~~~np~~~~~~~~r~P~~il~~AV~gMLP~kn~~gr~~~~rLkvy~G~~h~~~~qkp~~~~~a~ 123 (146)
T PRK06394 44 NRERVIEKYKQRRERGSHYNPYRNGPKYPRRPDRIFKRTIRGMLPYKKPRGREALKRLKVYVGVPKELEGKEFEVIDEAD 123 (146)
T ss_pred chhhheeeEeCCCCCcccCCCCChHHhhhcCHHHHHHHHHHhcCCCCChhHHHHHhCcEEecCCCCCcccCCCEEecHHH
Confidence 34566666655555555677889999999999999999999999999999999999999999999999999999999999
Q ss_pred hhhccCCCCCeeehhhhHHHhc
Q psy9436 103 RTVCLKPGRSYCSVGRISHEVG 124 (188)
Q Consensus 103 rv~rlkp~rKy~tLGeLs~evG 124 (188)
. .++. +|+||+|||||+++|
T Consensus 124 ~-~~~~-~~k~~~lgel~~~~G 143 (146)
T PRK06394 124 L-SRLS-TIKYVTLGEVSKELG 143 (146)
T ss_pred H-hccC-CCCcEEHHHHHHHhC
Confidence 7 5776 699999999999999
No 5
>PF00572 Ribosomal_L13: Ribosomal protein L13; InterPro: IPR005822 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 L13 is one of the proteins from the large ribosomal subunit []. In Escherichia coli, L13 is known to be one of the early assembly proteins of the 50S ribosomal subunit.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome; PDB: 4A17_I 4A1E_I 4A1A_I 4A1C_I 3D5B_N 3MS1_J 1VSP_H 3PYT_J 3PYO_J 3PYV_J ....
Probab=99.49 E-value=1.3e-14 Score=115.19 Aligned_cols=76 Identities=24% Similarity=0.205 Sum_probs=60.2
Q ss_pred ccccccchhhHHhHhhhccCccchHHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceecc
Q psy9436 23 STKRNIGHFDRKRKQARHESKIRAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVP 99 (188)
Q Consensus 23 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vVP 99 (188)
..+|..-.|.+..-.-..-...++.+++++.|+.||+++||||||+ +.+|+++|+||+||.|.|.||+.++.++||
T Consensus 52 G~k~~~k~y~~h~~~~g~~~~~~~~~~~~~~P~~i~~~aVrgMLP~-n~~g~~~l~rL~vy~g~~hp~~~~~~~~~~ 127 (128)
T PF00572_consen 52 GKKWRQKVYYRHTGYPGGLKNPTAKGLHEKDPSRILKRAVRGMLPK-NKLGREALKRLKVYPGEPHPHAAQKPVVLE 127 (128)
T ss_dssp SHHHHHHHHHHEHSSSTSCEEEECHHHHCSSHHHHHHHHHHTTSTT-SHHHHHHHTTEEEESSSSCSTTSSSCBEEE
T ss_pred CCeecceEEEeecccchhhcccchhhhhhcCHHHHHHHHHHHHCCC-ChhhhHHhhceEEECCCCCChhccCCEeCC
Confidence 3455555555422222222334678888999999999999999997 999999999999999999999999999886
No 6
>TIGR01066 rplM_bact ribosomal protein L13, bacterial type. This model distinguishes ribosomal protein L13 of bacteria and organelles from its eukarytotic and archaeal counterparts.
Probab=99.45 E-value=5.7e-14 Score=113.41 Aligned_cols=57 Identities=21% Similarity=0.212 Sum_probs=51.9
Q ss_pred cCccchHHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceec
Q psy9436 41 ESKIRAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCV 98 (188)
Q Consensus 41 ~~~~~~~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vV 98 (188)
-+.+++++++++.|++||+++|||||| |+.+|+++|+||+||+|.|.||+.++-..+
T Consensus 82 ~k~~~~~~~~~r~P~~ii~~aVrGMLP-kn~lgr~~l~rLkvy~G~~hp~~~q~p~~~ 138 (140)
T TIGR01066 82 LKSRTFEEMIARKPERVLEHAVKGMLP-KNRLGRKLFKKLKVYAGSEHPHEAQKPIVL 138 (140)
T ss_pred cccccHHHhhhcCHHHHHHHHHHhcCC-CCccHHHHHhCeEEeCCCCCChhhcCCeec
Confidence 466888999999999999999999999 799999999999999999999999875543
No 7
>PRK09216 rplM 50S ribosomal protein L13; Reviewed
Probab=99.40 E-value=2.2e-13 Score=110.51 Aligned_cols=56 Identities=25% Similarity=0.226 Sum_probs=51.1
Q ss_pred ccchHHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceecc
Q psy9436 43 KIRAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVP 99 (188)
Q Consensus 43 ~~~~~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vVP 99 (188)
.+++++++++.|++||+++||||||+ +.+|+.+|+||+||+|.|.||+.++-..++
T Consensus 86 ~~~~~~~~~r~P~~il~~aVrgMLPk-n~lgr~~~~rLkvy~G~~hp~~~q~p~~~~ 141 (144)
T PRK09216 86 EITFGELLAKKPERVIEKAVKGMLPK-NPLGRAMFKKLKVYAGAEHPHAAQQPEVLE 141 (144)
T ss_pred EecHHHHhhhCHHHHHHHHHHhcCCC-CccHHHHHhCcEEeCCCCCCccccCCEecc
Confidence 46899999999999999999999995 999999999999999999999998765543
No 8
>PLN00205 ribisomal protein L13 family protein; Provisional
Probab=99.37 E-value=3.2e-13 Score=114.21 Aligned_cols=59 Identities=14% Similarity=0.158 Sum_probs=51.9
Q ss_pred ccCccchHHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceecc
Q psy9436 40 HESKIRAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVP 99 (188)
Q Consensus 40 ~~~~~~~~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vVP 99 (188)
+.+.+++.+++++.|+.||+++|+||||+++.+|+ +++||+||+|.|.||+.++.+++.
T Consensus 85 glk~~~~~~~~~r~P~~Il~kAVrGMLPkn~lr~~-~~krLkVY~G~~hp~~~q~p~~~~ 143 (191)
T PLN00205 85 HLKERSLKDQMAKDPTEVIRKAVLRMLPRNRLRDD-RDRKLRIFAGSEHPFGDKPLEPFV 143 (191)
T ss_pred CcccccHHHHhccCHHHHHHHHHHhcCCCCchHHH-HHhCCEEECCCCCChhccCCeEec
Confidence 35678899999999999999999999999877776 789999999999999998775543
No 9
>COG0102 RplM Ribosomal protein L13 [Translation, ribosomal structure and biogenesis]
Probab=99.36 E-value=2.2e-13 Score=111.37 Aligned_cols=57 Identities=32% Similarity=0.288 Sum_probs=49.4
Q ss_pred cchHHHH-hhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceecccchhhh
Q psy9436 44 IRAVEKL-ELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCVPTALRTV 105 (188)
Q Consensus 44 ~~~~~~l-~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vVP~Alrv~ 105 (188)
.++++.+ +++|++||+++||||||+ +++|++||+||+||.|+|+|+.. .+|+++.+.
T Consensus 87 ~t~~~~~~~r~P~ri~~~AVrGMLPk-~~lGr~~~krLkVy~G~~h~~~a----q~p~~l~~~ 144 (148)
T COG0102 87 PTRGGPLAPRRPERILERAVRGMLPK-NPLGRAALKRLKVYAGIPHPHEA----QKPEALELK 144 (148)
T ss_pred cccccccccCCHHHHHHHHHhccCCC-ChhHHHHHhCceEecCCCCcccc----ccchhhhhh
Confidence 4676777 599999999999999998 99999999999999999999554 568777554
No 10
>CHL00159 rpl13 ribosomal protein L13; Validated
Probab=99.35 E-value=7e-13 Score=107.63 Aligned_cols=54 Identities=20% Similarity=0.209 Sum_probs=49.4
Q ss_pred cchHHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcccccceec
Q psy9436 44 IRAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYARRQRLCV 98 (188)
Q Consensus 44 ~~~~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd~kKr~vV 98 (188)
.++.++++++|++||+++|+|||| |+.+|+.+++||+||+|.|.||..++-.++
T Consensus 88 ~~~~~~~~r~P~~il~~aV~gMLP-kn~lgr~~~~rLkvy~G~~hph~aq~p~~~ 141 (143)
T CHL00159 88 ETFEELQNRLPNRIIEKAVKGMLP-KGPLGRKLFTKLKVYKGESHPHVAQKPIKI 141 (143)
T ss_pred ccHHHHhhcCHHHHHHHHHHhcCC-CChhHHHHHhCCEEeCCCCCCccccCCeec
Confidence 477899999999999999999999 699999999999999999999999875544
No 11
>cd00392 Ribosomal_L13 Ribosomal protein L13. Protein L13, a large ribosomal subunit protein, is one of five proteins required for an early folding intermediate of 23S rRNA in the assembly of the large subunit. L13 is situated on the bottom of the large subunit, near the polypeptide exit site. It interacts with proteins L3 and L6, and forms an extensive network of interactions with 23S rRNA. L13 has been identified as a homolog of the human breast basic conserved protein 1 (BBC1), a protein identified through its increased expression in breast cancer. L13 expression is also upregulated in a variety of human gastrointestinal cancers, suggesting it may play a role in the etiology of a variety of human malignancies.
Probab=99.09 E-value=3.8e-11 Score=93.85 Aligned_cols=46 Identities=33% Similarity=0.270 Sum_probs=42.3
Q ss_pred ccCccchHHHHhhchHHHHHHHhhCCCCCCCcchHHHhhccccccCC
Q psy9436 40 HESKIRAVEKLELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGI 86 (188)
Q Consensus 40 ~~~~~~~~~~l~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~Gi 86 (188)
.-...++++++++.|+.||+++|+|||| |+.+|+++|+||+||+|.
T Consensus 69 ~~~~~~~~~~~~~~P~~il~~aV~gMLP-kn~~g~~~l~rLkvy~g~ 114 (114)
T cd00392 69 GLKNPTAGPLHPRAPERILKRAVRGMLP-KNKLGRAALKRLKVYEGA 114 (114)
T ss_pred CCccCCcchhhhhCHHHHHHHHHHhcCC-CChhHHHHHhCcEEeCCC
Confidence 3466788999999999999999999999 899999999999999994
No 12
>KOG3203|consensus
Probab=97.63 E-value=4.7e-05 Score=63.60 Aligned_cols=47 Identities=17% Similarity=0.156 Sum_probs=41.0
Q ss_pred cchHHHH-hhchHHHHHHHhhCCCCCCCcchHHHhhccccccCCCCCcc
Q psy9436 44 IRAVEKL-ELFSIENARNQSESMTPHKLDRGAKALKRLKVYEGIPPKYA 91 (188)
Q Consensus 44 ~~~~~~l-~r~Pd~If~RtVRGMLPhKt~RGr~ALkRLKvy~GiP~pyd 91 (188)
.++.+.+ ++-|.+|++++|.|||| |+..++.-++||++|.|--.||+
T Consensus 94 ~~~~~q~~~rdp~~Iv~~AV~gMLP-kN~Lrr~~~~rL~lf~g~e~p~~ 141 (165)
T KOG3203|consen 94 QTTADQLADRDPCRIVRLAVYGMLP-KNLLRRRRMQRLHLFPGEEHPEK 141 (165)
T ss_pred hhHHHHHhhhCHHHHHHHHHHhhCc-cchHHHHHhheeeccCCccCchh
Confidence 4556666 79999999999999999 57888999999999999887765
No 13
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=50.13 E-value=18 Score=24.02 Aligned_cols=22 Identities=27% Similarity=0.451 Sum_probs=19.7
Q ss_pred eeehhhhHHHhccchHHHHHHH
Q psy9436 113 YCSVGRISHEVGWKYKTIVRHL 134 (188)
Q Consensus 113 y~tLGeLs~evGWKy~~vv~~L 134 (188)
.+++.+||.++|=.-++|++.|
T Consensus 3 ~i~V~elAk~l~v~~~~ii~~l 24 (54)
T PF04760_consen 3 KIRVSELAKELGVPSKEIIKKL 24 (54)
T ss_dssp EE-TTHHHHHHSSSHHHHHHHH
T ss_pred ceEHHHHHHHHCcCHHHHHHHH
Confidence 5789999999999999999999
No 14
>PF09756 DDRGK: DDRGK domain; InterPro: IPR019153 This is a family of proteins of approximately 300 residues. They contain a highly conserved DDRGK motif. The function is unknown. ; PDB: 1WI9_A.
Probab=46.33 E-value=21 Score=30.56 Aligned_cols=29 Identities=7% Similarity=0.297 Sum_probs=22.0
Q ss_pred CCCeeehhhhHHHhccchHHHHHHHHHHH
Q psy9436 110 GRSYCSVGRISHEVGWKYKTIVRHLERKR 138 (188)
Q Consensus 110 ~rKy~tLGeLs~evGWKy~~vv~~LE~KR 138 (188)
.+|.|.|.+||.++|-+.+++|+.+..-.
T Consensus 110 ~~Kvv~ledla~~f~l~t~~~i~ri~~L~ 138 (188)
T PF09756_consen 110 EHKVVNLEDLAAEFGLRTQDVINRIQELE 138 (188)
T ss_dssp H-SEE-HHHHHHHH-S-HHHHHHHHHHHH
T ss_pred HcceeeHHHHHHHcCCCHHHHHHHHHHHH
Confidence 37999999999999999999999887643
No 15
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=33.34 E-value=38 Score=23.87 Aligned_cols=21 Identities=38% Similarity=0.618 Sum_probs=14.3
Q ss_pred ehhhhHHHhccc-hHHHHHHHH
Q psy9436 115 SVGRISHEVGWK-YKTIVRHLE 135 (188)
Q Consensus 115 tLGeLs~evGWK-y~~vv~~LE 135 (188)
++-||+..+|++ ...|-..|+
T Consensus 27 t~rEIa~~~g~~S~~tv~~~L~ 48 (65)
T PF01726_consen 27 TVREIAEALGLKSTSTVQRHLK 48 (65)
T ss_dssp -HHHHHHHHTSSSHHHHHHHHH
T ss_pred CHHHHHHHhCCCChHHHHHHHH
Confidence 577999999999 544444443
No 16
>PF12324 HTH_15: Helix-turn-helix domain of alkylmercury lyase; InterPro: IPR024259 Alkylmercury lyase (EC:4.99.1.2) cleaves the carbon-mercury bond of organomercurials such as phenylmercuric acetate. This entry represents the N-terminal helix-turn-helix domain.; PDB: 3FN8_B 3F2G_B 3F0P_A 3F2F_B 3F2H_A 3F0O_B 1S6L_A.
Probab=30.91 E-value=50 Score=24.84 Aligned_cols=26 Identities=15% Similarity=0.385 Sum_probs=19.6
Q ss_pred CCeeehhhhHHHhccchHHHHHHHHH
Q psy9436 111 RSYCSVGRISHEVGWKYKTIVRHLER 136 (188)
Q Consensus 111 rKy~tLGeLs~evGWKy~~vv~~LE~ 136 (188)
-.=++..+||..+||..++|...|+.
T Consensus 36 G~PVt~~~LA~a~g~~~e~v~~~L~~ 61 (77)
T PF12324_consen 36 GQPVTVEQLAAALGWPVEEVRAALAA 61 (77)
T ss_dssp TS-B-HHHHHHHHT--HHHHHHHHHH
T ss_pred CCCcCHHHHHHHHCCCHHHHHHHHHh
Confidence 45678999999999999999999975
No 17
>PF09012 FeoC: FeoC like transcriptional regulator; InterPro: IPR015102 This entry contains several transcriptional regulators, including FeoC, which contain a HTH motif. FeoC acts as a [Fe-S] dependent transcriptional repressor []. ; PDB: 1XN7_A 2K02_A.
Probab=29.65 E-value=62 Score=22.33 Aligned_cols=25 Identities=24% Similarity=0.360 Sum_probs=18.2
Q ss_pred CCeeehhhhHHHhccchHHHHHHHH
Q psy9436 111 RSYCSVGRISHEVGWKYKTIVRHLE 135 (188)
Q Consensus 111 rKy~tLGeLs~evGWKy~~vv~~LE 135 (188)
+.-+++++||+++|+..+.|-.-||
T Consensus 12 ~~~~S~~eLa~~~~~s~~~ve~mL~ 36 (69)
T PF09012_consen 12 RGRVSLAELAREFGISPEAVEAMLE 36 (69)
T ss_dssp S-SEEHHHHHHHTT--HHHHHHHHH
T ss_pred cCCcCHHHHHHHHCcCHHHHHHHHH
Confidence 5678999999999999887766665
No 18
>PF11524 SeleniumBinding: Selenium binding protein; InterPro: IPR021603 Selenium is an important nutrient which needs to be regulated since lack of the nutrient leads to cell abnormalities and high concentrations are toxic.SeBP regulates the level of free selenium in the cell by sequestering the nutrient during transport. SeBP acts as a pentamer and delivers the selenium to the selenophosphate synthetase enzyme []. Each subunit is composed of an alpha helix on top of a four stranded twisted ss sheet, stabilised by hydrogen bonds []. members of this entry are restricted to the archaeal Methanococcales.; PDB: 2JZ7_D.
Probab=25.78 E-value=40 Score=25.70 Aligned_cols=33 Identities=24% Similarity=0.448 Sum_probs=27.2
Q ss_pred CCCCeeehhhhHHHhccchHHHHHHHHHHHHHHH
Q psy9436 109 PGRSYCSVGRISHEVGWKYKTIVRHLERKRREKS 142 (188)
Q Consensus 109 p~rKy~tLGeLs~evGWKy~~vv~~LE~KRK~ka 142 (188)
|+-.-|++|=+|..+- ...++++.||++-|++.
T Consensus 16 PGiely~~gIvS~~~e-nvd~li~~lee~vk~k~ 48 (81)
T PF11524_consen 16 PGIELYYLGIVSEASE-NVDELIKKLEEKVKAKG 48 (81)
T ss_dssp TTS--EEEEEEEEBSS-SHHHHHHHHHHHHHHTT
T ss_pred CCeEEEeehhHHHHHh-hHHHHHHHHHHHHHhCC
Confidence 7888999999999888 88999999999877764
No 19
>smart00418 HTH_ARSR helix_turn_helix, Arsenical Resistance Operon Repressor.
Probab=24.24 E-value=94 Score=19.14 Aligned_cols=27 Identities=19% Similarity=0.289 Sum_probs=21.1
Q ss_pred CCeeehhhhHHHhccchHHHHHHHHHH
Q psy9436 111 RSYCSVGRISHEVGWKYKTIVRHLERK 137 (188)
Q Consensus 111 rKy~tLGeLs~evGWKy~~vv~~LE~K 137 (188)
...+++++|+.++|+....+...|+.-
T Consensus 8 ~~~~~~~~i~~~l~is~~~v~~~l~~L 34 (66)
T smart00418 8 EGELCVCELAEILGLSQSTVSHHLKKL 34 (66)
T ss_pred cCCccHHHHHHHHCCCHHHHHHHHHHH
Confidence 456789999999999887776666543
No 20
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=23.88 E-value=67 Score=22.16 Aligned_cols=24 Identities=21% Similarity=0.387 Sum_probs=20.1
Q ss_pred CeeehhhhHHHhccchHHHHHHHH
Q psy9436 112 SYCSVGRISHEVGWKYKTIVRHLE 135 (188)
Q Consensus 112 Ky~tLGeLs~evGWKy~~vv~~LE 135 (188)
+=+++++||.++|-.-..+...|-
T Consensus 22 R~~tl~elA~~lgis~st~~~~LR 45 (53)
T PF04967_consen 22 RRITLEELAEELGISKSTVSEHLR 45 (53)
T ss_pred CcCCHHHHHHHhCCCHHHHHHHHH
Confidence 457899999999999888877763
Done!