Query         gi|254780330|ref|YP_003064743.1| 30S ribosomal protein S18 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 83
No_of_seqs    108 out of 995
Neff          5.3 
Searched_HMMs 39220
Date          Sun May 29 15:16:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780330.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK13400 30S ribosomal protein 100.0 1.4E-30 3.5E-35  192.5   6.3   74    9-82     13-86  (147)
  2 PRK00391 rpsR 30S ribosomal pr 100.0 1.2E-29   3E-34  187.2   7.3   73   10-82      5-77  (80)
  3 PRK13401 30S ribosomal protein 100.0 4.1E-29 1.1E-33  184.2   7.4   72   11-82      7-78  (79)
  4 CHL00077 rps18 ribosomal prote  99.9 3.5E-27 8.9E-32  173.4   7.4   78    3-82      2-79  (86)
  5 COG0238 RpsR Ribosomal protein  99.9   9E-27 2.3E-31  171.1   5.8   68   11-78      8-75  (75)
  6 pfam01084 Ribosomal_S18 Riboso  99.8 3.7E-21 9.5E-26  139.7   5.8   53   26-78      2-54  (54)
  7 KOG3162 consensus               99.8   3E-20 7.6E-25  134.7   5.1   66   17-82     65-131 (159)
  8 TIGR00165 S18 ribosomal protei  99.7 4.4E-17 1.1E-21  116.9   4.6   68   15-82      2-72  (73)
  9 KOG4021 consensus               99.3 5.4E-12 1.4E-16   88.5   4.6   69   12-80    102-171 (239)
 10 TIGR01370 cysRS possible cyste  64.5     5.2 0.00013   21.5   2.3   25   58-82    289-313 (325)
 11 pfam03470 zf-XS XS zinc finger  57.5     4.9 0.00013   21.7   1.2   41   21-77      1-41  (42)
 12 cd00630 RNAP_largest_subunit_C  45.6     5.5 0.00014   21.4  -0.1   31   29-59     79-109 (158)
 13 TIGR02668 moaA_archaeal probab  42.3      19 0.00048   18.4   2.2   29   52-80    131-159 (324)
 14 TIGR01857 FGAM-synthase phosph  34.0      37 0.00093   16.8   2.6   34   36-82   1103-1137(1279)
 15 TIGR01591 Fdh-alpha formate de  33.1      30 0.00077   17.3   2.0   49   30-78    249-298 (694)
 16 cd02735 RNAP_I_Rpa1_C Largest   28.9      27 0.00068   17.6   1.2   30   29-58    227-256 (309)
 17 cd02737 RNAP_IV_NRPD1_C Larges  28.8      19 0.00049   18.4   0.4   32   29-60    291-322 (381)
 18 TIGR00090 TIGR00090 iojap homo  28.6      53  0.0014   15.9   2.7   28   54-81     65-94  (155)
 19 cd06528 RNAP_A'' A'' subunit o  27.7      17 0.00042   18.7  -0.1   31   29-59    277-307 (363)
 20 TIGR01208 rmlA_long glucose-1-  24.6      19 0.00049   18.4  -0.2   46   31-77     52-97  (361)
 21 TIGR01950 SoxR redox-sensitive  20.0      41   0.001   16.5   0.7   37   41-77     19-58  (142)

No 1  
>PRK13400 30S ribosomal protein S18; Provisional
Probab=99.96  E-value=1.4e-30  Score=192.46  Aligned_cols=74  Identities=42%  Similarity=0.693  Sum_probs=70.2

Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             32277777888854350388511446889999962899848550331748999999999999999704658676
Q gi|254780330|r    9 LLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus         9 ~~~~~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      ..+..+..++|.|.||.+++..|||||+++|++||||+|||+|||+||+|++|||+|++||||||+|||||||+
T Consensus        13 ~grgrf~pRRK~C~FCaeki~~IDYKDv~lLkrFIserGKIlPRRiTG~cAKhQR~La~AIKRAR~mALLPyV~   86 (147)
T PRK13400         13 GGRGRYTPKRKICSFCAEKVSRIDYKDSAKLARYISDRGKIEPRRRTGTCARHQRALANAIKRARFIALMPFVS   86 (147)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCH
T ss_conf             88888899997483566898635755889999871637727576217858999999999999999988344548


No 2  
>PRK00391 rpsR 30S ribosomal protein S18; Reviewed
Probab=99.96  E-value=1.2e-29  Score=187.24  Aligned_cols=73  Identities=51%  Similarity=0.869  Sum_probs=69.0

Q ss_pred             HHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             2277777888854350388511446889999962899848550331748999999999999999704658676
Q gi|254780330|r   10 LRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        10 ~~~~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      .+++...+++.|+||.++++.|||||+++|++||||+|+|+||++||+|++|||+|++|||+||+|||||||+
T Consensus         5 ~~~~~~~r~k~C~~~~~~~~~IDYKdv~lL~~Fis~~GkI~prr~TG~~~k~Qr~l~~aIKrAR~~gLLPy~~   77 (80)
T PRK00391          5 RRRRFFRRKKVCRFTAEKIEYIDYKDVELLKKFISERGKILPRRITGTSAKHQRQLATAIKRARFLALLPYVD   77 (80)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCCCCCCCHHHHHHHHHHHHHHHHHCCCCEEC
T ss_conf             4478888899898278999827876999999875888758276337879999999999999999830666102


No 3  
>PRK13401 30S ribosomal protein S18; Provisional
Probab=99.96  E-value=4.1e-29  Score=184.17  Aligned_cols=72  Identities=36%  Similarity=0.571  Sum_probs=67.6

Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             277777888854350388511446889999962899848550331748999999999999999704658676
Q gi|254780330|r   11 RRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        11 ~~~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      .++...++++|+||.++++.|||||+++|++||||+|+|+||++||+|++|||+|++|||+||+||||||++
T Consensus         7 ~~~~~~r~k~c~~~~~~i~~iDYKdv~lL~~Fis~~GkI~~rr~Tg~~ak~QR~l~~AIKrAR~laLLPy~g   78 (79)
T PRK13401          7 ARKGPTKAKKNLLDSLGVESVDYKDTATLRVFISDRGKIRSRRVTGLTVQQQRQVATAIKNAREMALLPYPG   78 (79)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCC
T ss_conf             777899888897555898856765889999874888858686027778999999999999999972788889


No 4  
>CHL00077 rps18 ribosomal protein S18
Probab=99.94  E-value=3.5e-27  Score=173.40  Aligned_cols=78  Identities=40%  Similarity=0.727  Sum_probs=65.1

Q ss_pred             CCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             76667132277777888854350388511446889999962899848550331748999999999999999704658676
Q gi|254780330|r    3 EVAPTPLLRRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus         3 ~~~p~p~~~~~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      |.+..|+.+.....+++.|++  ...+.|||||+++|++||||+|+|+|||+||+|+++||+|++|||+||+|||||||+
T Consensus         2 ~~~k~~~~k~~r~~rrk~~~~--~~~~~IDYKnv~lL~~Fise~GKIlprR~Tg~~ak~QR~l~kAIKrAR~lgLLPyv~   79 (86)
T CHL00077          2 DKSKRPFRKSKRSFRRRLPPI--QSGDRIDYKNMSLLSRFISEQGKILSRRVNRLTLKQQRLITKAIKQARILSLLPFLN   79 (86)
T ss_pred             CCCCCCCCCCCCCCCCCCCCC--CCCCCCCCCCHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHCCCEEC
T ss_conf             744466554566656679999--988867766889999875888828085207879999999999999999963478001


No 5  
>COG0238 RpsR Ribosomal protein S18 [Translation, ribosomal structure and biogenesis]
Probab=99.93  E-value=9e-27  Score=171.10  Aligned_cols=68  Identities=56%  Similarity=0.932  Sum_probs=64.4

Q ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             27777788885435038851144688999996289984855033174899999999999999970465
Q gi|254780330|r   11 RRNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLI   78 (83)
Q Consensus        11 ~~~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLl   78 (83)
                      +.+++.+++.|+||..++++|||||+++|++||||+|||+|||+||+|+++||+|+.||||||+||||
T Consensus         8 r~~~~rrrk~c~f~~~~~~~iDYKd~~~Lkrfise~GKI~prRiTG~sak~QR~la~AIKRAR~laLl   75 (75)
T COG0238           8 RAPFFRRRKVCRFTAEGIEEIDYKDVELLKRFISERGKILPRRITGTSAKHQRRLARAIKRARYLALL   75 (75)
T ss_pred             HCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             04334446436565024884672489999998562676565412352399999999999999998609


No 6  
>pfam01084 Ribosomal_S18 Ribosomal protein S18.
Probab=99.83  E-value=3.7e-21  Score=139.71  Aligned_cols=53  Identities=58%  Similarity=0.913  Sum_probs=50.6

Q ss_pred             CCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             38851144688999996289984855033174899999999999999970465
Q gi|254780330|r   26 KGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLI   78 (83)
Q Consensus        26 ~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLl   78 (83)
                      .+++.+||||+++|++|+||+|+|+||++||+|++|||+|++|||+||+||||
T Consensus         2 ~~~~~idYKn~~lL~~fis~~GkI~prr~Tg~~~k~Qr~l~~aIKrAR~lgLl   54 (54)
T pfam01084         2 DKIEYIDYKDVELLRRFISERGKILPRRITGLCAKQQRKLAKAIKRARILALL   54 (54)
T ss_pred             CCCCCCCCCCHHHHHHHCCCCCEEECCCCCCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             98887288896999987699982839731888999999999999999996378


No 7  
>KOG3162 consensus
Probab=99.80  E-value=3e-20  Score=134.65  Aligned_cols=66  Identities=39%  Similarity=0.729  Sum_probs=60.9

Q ss_pred             CCCCCCCCCCCCC-CCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             8888543503885-11446889999962899848550331748999999999999999704658676
Q gi|254780330|r   17 RRKSCPLSGKGAP-RIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        17 ~~k~c~~~~~~~~-~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      ....|+.|..+++ ..+||||.||++||+|.|.|+||++||+|+++|++|++||++||.+|||||++
T Consensus        65 ~~~~c~~c~~~Vd~~~~yknv~iLsqFv~~~G~il~RkiTGLc~k~Qrki~~aI~~A~~~GlmP~~~  131 (159)
T KOG3162          65 SEPQCILCTKGVDIKLSYKNVLLLSQFVSEDGGILPRKITGLCAKNQRKIERAIKRARAAGLMPVTN  131 (159)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCCCEECCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             7666753225777322557652044440235624030100012888999999999999851665114


No 8  
>TIGR00165 S18 ribosomal protein S18; InterPro: IPR001648   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 , .   Evidence suggests that, in prokaryotes, the peptidyl transferase reaction is performed by the large subunit 23S rRNA, whereas proteins probably have a greater role in eukaryotic ribosomes. Most of the proteins lie close to, or on the surface of, the 30S subunit, arranged peripherally around the rRNA . The small subunit ribosomal proteins can be categorised as primary binding proteins, which bind directly and independently to 16S rRNA; secondary binding proteins, which display no specific affinity for 16S rRNA, but its assembly is contingent upon the presence of one or more primary binding proteins; and tertiary binding proteins, which require the presence of one or more secondary binding proteins and sometimes other tertiary binding proteins.   The small ribosomal subunit protein S18 is known to be involved in binding the aminoacyl-tRNA complex in Escherichia coli , and appears to be situated at the tRNA A-site. Experimental evidence has revealed that S18 is well exposed on the surface of the E. coli ribosome, and is a secondary rRNA binding protein . S18 belongs to a family of ribosomal proteins  that includes: eubacterial S18; metazoan mitochondrial S18, algal and plant chloroplast S18; and cyanelle S18. ; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.67  E-value=4.4e-17  Score=116.94  Aligned_cols=68  Identities=54%  Similarity=0.880  Sum_probs=64.6

Q ss_pred             CCCCCCCCCC---CCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             7788885435---0388511446889999962899848550331748999999999999999704658676
Q gi|254780330|r   15 SHRRKSCPLS---GKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        15 ~~~~k~c~~~---~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      ..+++.|+||   ..++..+||+|+++|++|+++.|+|+|+++||+|+++|++++.+|++||+++|+||++
T Consensus         2 ~~~~~~c~~~~~g~~~~~~~dy~d~~~l~~~~~~~~~~~p~~~~g~~~~~~~~~~~~~~~~~~~~l~p~~~   72 (73)
T TIGR00165         2 FRRKKYCRFTAIGELGIDHIDYKDLDLLKKFLSERGKILPRRITGTSAKYQRRLALAIKRARYLALLPFVK   72 (73)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHCCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             65432233222122357665601078898762100001310000110356788999887765544212125


No 9  
>KOG4021 consensus
Probab=99.26  E-value=5.4e-12  Score=88.49  Aligned_cols=69  Identities=25%  Similarity=0.472  Sum_probs=61.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCCC-CEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             77777888854350388511446889999962899-8485503317489999999999999997046586
Q gi|254780330|r   12 RNVSHRRKSCPLSGKGAPRIDYKDIRLLNRFLSQR-GKIVPSRISSVSHKKQRELAKAIKRARYLGLIAY   80 (83)
Q Consensus        12 ~~~~~~~k~c~~~~~~~~~iDYKn~~lL~~Fis~~-GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy   80 (83)
                      ++...-.-+||+|++....+||+|+.||.|||++. |.++.=-.||+|.+|+..|..||..||.-|+|-|
T Consensus       102 kn~~~~gnpCPICRDeyL~~DyRN~~LlEQF~~~htg~~i~y~ktGlC~kqh~rL~~a~qkArdhG~lty  171 (239)
T KOG4021         102 KNGRFLGNPCPICRDEYLYFDYRNPGLLEQFLADHTGQPIDYLKTGLCRKQHTRLRAALQKARDHGTLTY  171 (239)
T ss_pred             HCCEECCCCCCCCCCCEEEEECCCHHHHHHHHCCCCCCCHHHHHCCHHHHHHHHHHHHHHHHHHCCEEEE
T ss_conf             1580158998752251578742677899998515899803566400379999999999997642573772


No 10 
>TIGR01370 cysRS possible cysteinyl-tRNA synthetase; InterPro: IPR016063   The prediction that proteins in this entry are cysteinyl-tRNA synthetases is supported by  but challenged by . The proteins from Deinococcus radiodurans and Methanococcus jannaschii, species lacking a conventional cysteinyl-tRNA synthetase (Cys--tRNA ligase), have been indicated to be a novel form of that enzyme, perhaps distantly related to class I tRNA ligases. The protein from Thermotoga maritima is presumed to be a second isozyme of cysteinyl-tRNA synthetase. A number of homologous but more distantly related proteins are annotated as putative alpha-1,4 polygalactosaminidases..
Probab=64.49  E-value=5.2  Score=21.53  Aligned_cols=25  Identities=32%  Similarity=0.462  Sum_probs=21.3

Q ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             8999999999999999704658676
Q gi|254780330|r   58 SHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        58 ~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      +-.+-.++.-++.+||.-|++|||.
T Consensus       289 ~~EN~~r~~d~~eka~~~G~iPYva  313 (325)
T TIGR01370       289 SFENLARVKDYAEKARAAGLIPYVA  313 (325)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCCCC
T ss_conf             0021899999999998578644123


No 11 
>pfam03470 zf-XS XS zinc finger domain. This domain is a putative nucleic acid binding zinc finger found in proteins that also contain an XS domain.
Probab=57.46  E-value=4.9  Score=21.67  Aligned_cols=41  Identities=32%  Similarity=0.442  Sum_probs=24.0

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCC
Q ss_conf             543503885114468899999628998485503317489999999999999997046
Q gi|254780330|r   21 CPLSGKGAPRIDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGL   77 (83)
Q Consensus        21 c~~~~~~~~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gL   77 (83)
                      ||||..+-.. ||+=-+||++=            +|+.+-..++   +...|.+.+|
T Consensus         1 CPfC~~kkk~-dY~~~~LlqHA------------~gvG~~~~~~---~k~ka~HrAL   41 (42)
T pfam03470         1 CPFCPGKKKQ-DYKYKELLQHA------------SGVGASSSRR---AKEKANHRAL   41 (42)
T ss_pred             CCCCCCCCCC-CCHHHHHHHHH------------HCCCCCCCCC---HHHHHHHHHH
T ss_conf             9989764333-23088999987------------4116666632---8787543410


No 12 
>cd00630 RNAP_largest_subunit_C Largest subunit of RNA polymerase (RNAP), C-terminal domain. RNA polymerase (RNAP) is a large multi-subunit complex responsible for the synthesis of RNA. It is the principal enzyme of the transcription process, and is the final target in many regulatory pathways that control gene expression in all living cells. At least three distinct RNAP complexes are found in eukaryotic nuclei, RNAP I, RNAP II, and RNAP III, for the synthesis of ribosomal RNA precursor, mRNA precursor, and 5S and tRNA, respectively. A single distinct RNAP complex is found in prokaryotes and archaea, which may be responsible for the synthesis of all RNAs. Structure studies revealed that prokaryotic and eukaryotic RNAPs share a conserved crab-claw-shape structure. The largest and the second largest subunits each make up one clamp, one jaw, and part of the cleft. The largest RNAP subunit (Rpb1) interacts with the second-largest RNAP subunit (Rpb2) to form the DNA entry and RNA exit channe
Probab=45.59  E-value=5.5  Score=21.39  Aligned_cols=31  Identities=16%  Similarity=0.249  Sum_probs=27.6

Q ss_pred             CCCCCCCHHHHHHHCCCCCEECCCHHHCCCH
Q ss_conf             5114468899999628998485503317489
Q gi|254780330|r   29 PRIDYKDIRLLNRFLSQRGKIVPSRISSVSH   59 (83)
Q Consensus        29 ~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~   59 (83)
                      ..||+|+.++|..+++..|.+.|=-..|+..
T Consensus        79 i~Id~RHi~LIaD~MT~~G~i~~i~R~Gi~~  109 (158)
T cd00630          79 VSVDRRHIELIADVMTYSGGLRGVTRSGFRA  109 (158)
T ss_pred             EEECHHHHHHHHHHHHCCCCCCCCCHHHHCC
T ss_conf             3543999999999985478666672565104


No 13 
>TIGR02668 moaA_archaeal probable molybdenum cofactor biosynthesis protein A; InterPro: IPR013485    This entry consists of archaeal proteins which are predicted to be functionally equivalent to MoaA (molybdenum cofactor biosynthesis protein A) from bacteria (see IPR013483 from INTERPRO).; GO: 0046872 metal ion binding, 0006777 Mo-molybdopterin cofactor biosynthetic process.
Probab=42.27  E-value=19  Score=18.42  Aligned_cols=29  Identities=21%  Similarity=0.253  Sum_probs=26.1

Q ss_pred             CHHHCCCHHHHHHHHHHHHHHHHCCCCCC
Q ss_conf             03317489999999999999997046586
Q gi|254780330|r   52 SRISSVSHKKQRELAKAIKRARYLGLIAY   80 (83)
Q Consensus        52 rr~TG~~~k~Qr~i~~aIKrAR~~gLlPy   80 (83)
                      +.|||.....-.+|-+.|+.|...||-|-
T Consensus       131 ~kITG~~~~~~~~Vi~GI~~A~~~GL~PV  159 (324)
T TIGR02668       131 KKITGQSRDALDRVIEGIESAVDAGLTPV  159 (324)
T ss_pred             HHHCCCCCCHHHHHHHHHHHHHHCCCCCE
T ss_conf             86448998607899999999997289813


No 14 
>TIGR01857 FGAM-synthase phosphoribosylformylglycinamidine synthase; InterPro: IPR010141   This entry represents a single-molecule form of phosphoribosylformylglycinamidine synthase, also called FGAM synthase, an enzyme of purine de novo biosynthesis, which represent a second clade of the enzymes found in Clostridia, Bifidobacteria and Streptococcus species. This enzyme performs the fourth step in IMP biosynthesis (the precursor of all purines) from PRPP..
Probab=34.00  E-value=37  Score=16.80  Aligned_cols=34  Identities=26%  Similarity=0.485  Sum_probs=25.7

Q ss_pred             HHHHHHHCCCC-CEECCCHHHCCCHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             89999962899-848550331748999999999999999704658676
Q gi|254780330|r   36 IRLLNRFLSQR-GKIVPSRISSVSHKKQRELAKAIKRARYLGLIAYVN   82 (83)
Q Consensus        36 ~~lL~~Fis~~-GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLlPy~~   82 (83)
                      .+-...||.++ |-|+     |+|--.|-.|-        +|||||=+
T Consensus      1103 ~~~v~~lL~~RDGLiL-----GiCNGFQALvK--------~GLlPYG~ 1137 (1279)
T TIGR01857      1103 KEAVKKLLKERDGLIL-----GICNGFQALVK--------LGLLPYGE 1137 (1279)
T ss_pred             HHHHHHHHHHCCCEEE-----EEEHHHHHHHH--------HCCCCCCC
T ss_conf             9999999960798498-----62005678888--------24788864


No 15 
>TIGR01591 Fdh-alpha formate dehydrogenase, alpha subunit; InterPro: IPR006478   This group of sequences describe a subset of formate dehydrogenase alpha chains found mainly in the archaea but also in alpha and gamma proteobacteria and a small number of Gram-positive bacteria. The alpha chain contains domains for molybdopterin dinucleotide binding and molybdopterin oxidoreductase. The holo-enzyme also contains beta and gamma subunits. The enzyme catalyzes the oxidation of formate (produced from pyruvate during anaerobic growth) to carbon dioxide with the concomitant release of two electrons and two protons. The enzyme's purpose is to allow growth on formate in some circumstances  and, in the case of FdhH in gamma proteobacteria, to pass electrons to hydrogenase (by which process acid is neutralized) . The alpha subunit of a version of nitrate reductase is closely related.; GO: 0008863 formate dehydrogenase activity, 0015942 formate metabolic process, 0009326 formate dehydrogenase complex.
Probab=33.06  E-value=30  Score=17.27  Aligned_cols=49  Identities=16%  Similarity=0.261  Sum_probs=42.6

Q ss_pred             CCCCCCHHHHHHHCCC-CCEECCCHHHCCCHHHHHHHHHHHHHHHHCCCC
Q ss_conf             1144688999996289-984855033174899999999999999970465
Q gi|254780330|r   30 RIDYKDIRLLNRFLSQ-RGKIVPSRISSVSHKKQRELAKAIKRARYLGLI   78 (83)
Q Consensus        30 ~iDYKn~~lL~~Fis~-~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gLl   78 (83)
                      ..||++.+-++.+|.. +-==.--+|||+++.+=|++|+.+-+|-..|++
T Consensus       249 R~~W~~F~E~r~~V~~~yTpE~vE~ITgV~~d~Ir~~A~~yA~a~~~Ai~  298 (694)
T TIGR01591       249 RTDWEGFEEFREIVKGKYTPEYVEKITGVPADLIREIARMYAKAGSAAIL  298 (694)
T ss_pred             HCCCCCHHHHHHHHCCCCCHHHCCCCCCCCHHHHHHHHHHHHCCCCEEEE
T ss_conf             14878537888775047875322212578888999999998358967999


No 16 
>cd02735 RNAP_I_Rpa1_C Largest subunit (Rpa1) of Eukaryotic RNA polymerase I (RNAP I), C-terminal domain. RNA polymerase I (RNAP I) is a multi-subunit protein complex responsible for the synthesis of rRNA precursor. It consists of at least 14 different subunits, and the largest one is homologous to subunit Rpb1 of yeast RNAP II and subunit beta' of bacterial RNAP. Rpa1 is also known as Rpa190 in yeast. Structure studies suggest that different RNAP complexes share a similar crab-claw-shape structure. The C-terminal domain of Rpb1, the largest subunit of RNAP II, makes up part of the foot and jaw structures of RNAP II. The similarity between this domain and the C-terminal domain of Rpb1, its counterpart in RNAP II, suggests a similar functional and structural role.
Probab=28.92  E-value=27  Score=17.56  Aligned_cols=30  Identities=13%  Similarity=0.296  Sum_probs=25.9

Q ss_pred             CCCCCCCHHHHHHHCCCCCEECCCHHHCCC
Q ss_conf             511446889999962899848550331748
Q gi|254780330|r   29 PRIDYKDIRLLNRFLSQRGKIVPSRISSVS   58 (83)
Q Consensus        29 ~~iDYKn~~lL~~Fis~~GkI~prr~TG~~   58 (83)
                      ..||||+.++|...++..|.+.|--..|+.
T Consensus       227 v~in~rHi~li~d~Mt~~G~~~~~~R~gi~  256 (309)
T cd02735         227 IAVDPRHLSLIADYMTFEGGYRPFNRIGME  256 (309)
T ss_pred             CCCCHHHHHHHHHHHCCCCCEEECCHHCCC
T ss_conf             656747766576650006857310122102


No 17 
>cd02737 RNAP_IV_NRPD1_C Largest subunit (NRPD1) of Higher plant RNA polymerase IV, C-terminal domain. Higher plants have five multi-subunit nuclear RNA polymerases: RNAP I, RNAP II and RNAP III, which are essential for viability; plus the two isoforms of the non-essential polymerase RNAP IV (IVa and IVb), which specialize in small RNA-mediated gene silencing pathways. RNAP IVa and/or RNAP IVb might be involved in RNA-directed DNA methylation of endogenous repetitive elements, silencing of transgenes, regulation of flowering-time genes, inducible regulation of adjacent gene pairs, and spreading of mobile silencing signals. NRPD1a is the largest subunit of RNAP IVa, whereas NRPD1b is the largest subunit of RNAP IVb. The full subunit compositions of RNAP IVa and RNAP IVb are not known, nor are their templates or enzymatic products. However, it has been shown that RNAP IVa and, to a lesser extent, RNAP IVb are crucial for several RNA-mediated gene silencing phenomena.
Probab=28.80  E-value=19  Score=18.36  Aligned_cols=32  Identities=9%  Similarity=0.124  Sum_probs=28.2

Q ss_pred             CCCCCCCHHHHHHHCCCCCEECCCHHHCCCHH
Q ss_conf             51144688999996289984855033174899
Q gi|254780330|r   29 PRIDYKDIRLLNRFLSQRGKIVPSRISSVSHK   60 (83)
Q Consensus        29 ~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~k   60 (83)
                      ..+||++..||..++|-.|.+.+=-..|+...
T Consensus       291 ~~v~~rHl~llad~mt~~G~~~~i~r~G~~~~  322 (381)
T cd02737         291 KSVLREHLLLVADSMTYSGEFVGLNAKGYKAQ  322 (381)
T ss_pred             CCCCHHHHHHHHHHHCCCCCEEEEECCCCCCC
T ss_conf             64218889898887335781677533020144


No 18 
>TIGR00090 TIGR00090 iojap homolog; InterPro: IPR004394 The gene iojap is a pattern-striping gene in maize, reflecting a chloroplast development defect in some cells. Maize has two RNA polymerases in plastids, but the plastid-encoded one, similar to bacterial RNA polymerases, is missing in iojap mutants. The role of iojap in chloroplast development, and the role of its bacterial orthologs modeled here, is unclear..
Probab=28.62  E-value=53  Score=15.88  Aligned_cols=28  Identities=25%  Similarity=0.310  Sum_probs=23.2

Q ss_pred             HHCCCHHHHHHHHHHHH-HHHHC-CCCCCC
Q ss_conf             31748999999999999-99970-465867
Q gi|254780330|r   54 ISSVSHKKQRELAKAIK-RARYL-GLIAYV   81 (83)
Q Consensus        54 ~TG~~~k~Qr~i~~aIK-rAR~~-gLlPy~   81 (83)
                      =||+|.+|=+.|+.+|+ .++.. |++||-
T Consensus        65 CTG~S~~qV~aiaD~~~~~~~~~hG~~~~~   94 (155)
T TIGR00090        65 CTGTSSKQVLAIADNIKKQLKEAHGLLPLG   94 (155)
T ss_pred             EECCHHHHHHHHHHHHHHHHHHHCCEEEEC
T ss_conf             306727899999999999999866822221


No 19 
>cd06528 RNAP_A'' A'' subunit of Archaeal RNA Polymerase (RNAP). Archaeal RNA polymerase (RNAP), like bacterial RNAP, is a large multi-subunit complex responsible for the synthesis of all RNAs in the cell. The relative positioning of the RNAP core is highly conserved between archaeal RNAP and the three classes of eukaryotic RNAPs. In archaea, the largest subunit is split into two polypeptides, A' and A'', which are encoded by separate genes in an operon. Sequence alignments reveal that the archaeal A'' subunit corresponds to the C-terminal one-third of the RNAPII largest subunit (Rpb1). In subunit A'', several loops in the jaw domain are shorter. The RNAPII Rpb1 interacts with the second-largest subunit (Rpb2) to form the DNA entry and RNA exit channels in addition to the catalytic center of RNA synthesis.
Probab=27.68  E-value=17  Score=18.72  Aligned_cols=31  Identities=13%  Similarity=0.269  Sum_probs=27.0

Q ss_pred             CCCCCCCHHHHHHHCCCCCEECCCHHHCCCH
Q ss_conf             5114468899999628998485503317489
Q gi|254780330|r   29 PRIDYKDIRLLNRFLSQRGKIVPSRISSVSH   59 (83)
Q Consensus        29 ~~iDYKn~~lL~~Fis~~GkI~prr~TG~~~   59 (83)
                      ..||+|++.++...++..|.+.|=.++|+..
T Consensus       277 v~In~rHi~li~d~Mt~~G~~~~i~r~g~~~  307 (363)
T cd06528         277 LDVDIRHIMLVADIMTYDGEVRQIGRHGIAG  307 (363)
T ss_pred             CCCCHHHHHHHHHHHCCCCCEEECCHHHHCC
T ss_conf             6320577877653440467142045132237


No 20 
>TIGR01208 rmlA_long glucose-1-phosphate thymidylyltransferase; InterPro: IPR005908    Synonym: dTDP-D-glucose synthase     This group of proteins comprises a tightly conserved but broadly distributed subfamily of known and putative bacterial glucose-1-phosphate thymidylyltransferases (2.7.7.24 from EC). It is well characterised in several species as the first of four enzymes involved in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme.  dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose     The family of known and putative glucose-1-phosphate thymidyltransferases shows a deep split into a short form (see IPR005907 from INTERPRO) and a long form described by this model. The homotetrameric short form is found in numerous bacterial species that incorporate dTDP-L-rhamnose, which it helps synthesize, into the cell wall. It is subject to feedback inhibition. The long form, in contrast, is found in many species for which it serves as a sugar-activating enzyme for antibiotic biosynthesis and or other, unknown pathways, and in which dTDP-L-rhamnose is not necessarily produced. .
Probab=24.60  E-value=19  Score=18.39  Aligned_cols=46  Identities=20%  Similarity=0.283  Sum_probs=39.0

Q ss_pred             CCCCCHHHHHHHCCCCCEECCCHHHCCCHHHHHHHHHHHHHHHHCCC
Q ss_conf             14468899999628998485503317489999999999999997046
Q gi|254780330|r   31 IDYKDIRLLNRFLSQRGKIVPSRISSVSHKKQRELAKAIKRARYLGL   77 (83)
Q Consensus        31 iDYKn~~lL~~Fis~~GkI~prr~TG~~~k~Qr~i~~aIKrAR~~gL   77 (83)
                      +-+.+.+-.+.++. .|....-++|-.-...|.=||+||..||..||
T Consensus        52 vg~~~~e~i~~~~g-~g~~fg~kityI~Q~~plGlAHAv~~A~~fGl   97 (361)
T TIGR01208        52 VGPETGEEIKEIVG-EGERFGAKITYIVQGEPLGLAHAVYVARDFGL   97 (361)
T ss_pred             ECCCCCHHHEEEEC-CCCCCCEEEEEEECCCCCHHHHHHHHHHHHCC
T ss_conf             46988212202324-88302328989822787604676457888478


No 21 
>TIGR01950 SoxR redox-sensitive transcriptional activator SoxR; InterPro: IPR010211   SoxR is a MerR-family homodimeric transcription factor with a 2Fe-2S cluster in each monomer. The motif CIGCGCxxxxxC is conserved. Oxidation of the iron-sulphur cluster activates SoxR. The physiological role in Escherichia coli is response to oxidative stress. It is activated by superoxide, singlet oxygen, nitric oxide (NO), and hydrogen peroxide. In Escherichia coli, SoxR increases expression of transcription factor SoxS; different downstream targets may exist in other species.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0005506 iron ion binding, 0006118 electron transport, 0006355 regulation of transcription DNA-dependent, 0006979 response to oxidative stress.
Probab=20.05  E-value=41  Score=16.55  Aligned_cols=37  Identities=24%  Similarity=0.451  Sum_probs=31.4

Q ss_pred             HHCCCCCEECCCHHHCCCHHHHHHHHH---HHHHHHHCCC
Q ss_conf             962899848550331748999999999---9999997046
Q gi|254780330|r   41 RFLSQRGKIVPSRISSVSHKKQRELAK---AIKRARYLGL   77 (83)
Q Consensus        41 ~Fis~~GkI~prr~TG~~~k~Qr~i~~---aIKrAR~~gL   77 (83)
                      +|==..|=|.+.|-.|+.+++.|.+-+   -||-|+.+|+
T Consensus        19 HFYE~KGLI~S~Rn~GnQRRy~Rd~LRRVa~Ik~AQ~vGi   58 (142)
T TIGR01950        19 HFYESKGLIHSVRNAGNQRRYKRDVLRRVAVIKVAQRVGI   58 (142)
T ss_pred             HHHHHCCCEECCCCCCCCCCCCCCHHHHHHHHHHHHHCCC
T ss_conf             6541035610113688834232001115674332332589


Done!