Query         gi|254780715|ref|YP_003065128.1| 50S ribosomal protein L19 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 141
No_of_seqs    113 out of 921
Neff          4.8 
Searched_HMMs 39220
Date          Tue May 31 14:55:08 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780715.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK05338 rplS 50S ribosomal pr 100.0       0       0  313.0  11.5  112    1-117     1-112 (112)
  2 CHL00084 rpl19 ribosomal prote 100.0 1.4E-45       0  308.7  10.9  112    2-118     6-117 (117)
  3 pfam01245 Ribosomal_L19 Riboso 100.0   7E-45       0  304.0  11.6  113    1-118     1-113 (113)
  4 COG0335 RplS Ribosomal protein 100.0   1E-43       0  296.4   8.8  112    1-117     1-114 (115)
  5 KOG1698 consensus              100.0   5E-33 1.3E-37  229.0  10.2  124    2-126    75-198 (201)
  6 TIGR01024 rplS_bact ribosomal   99.9 2.4E-26   6E-31  186.9   7.8  113    1-117     1-115 (116)
  7 PRK01191 rpl24p 50S ribosomal   79.1     5.7 0.00014   20.6   8.4   76   16-101    40-117 (119)
  8 pfam03888 MucB_RseB MucB/RseB   75.6     6.2 0.00016   20.3   4.7   52   41-95     36-87  (314)
  9 PRK09455 rseB periplasmic nega  69.3     9.9 0.00025   19.0   4.7   51   42-95     21-71  (302)
 10 pfam02211 NHase_beta Nitrile h  57.8      12 0.00031   18.5   3.2   39   19-58    128-170 (220)
 11 pfam02765 Telo_bind Telomeric   54.2      19 0.00047   17.3   3.8   49   19-76     64-113 (141)
 12 cd04497 hPOT1_OB1_like hPOT1_O  51.8      20 0.00051   17.1   4.9   50   18-75     63-112 (138)
 13 cd05791 S1_CSL4 S1_CSL4: CSL4,  49.5      18 0.00045   17.5   2.9   34   25-63      5-38  (92)
 14 COG1566 EmrA Multidrug resista  49.2      22 0.00057   16.8   5.3   62   15-80    250-320 (352)
 15 COG2139 RPL21A Ribosomal prote  46.6      24 0.00062   16.6   3.5   38   21-60     30-72  (98)
 16 pfam02014 Reeler Reeler domain  45.8      25 0.00064   16.5   4.5   32   23-59     29-60  (127)
 17 TIGR02579 cas_csx3 CRISPR-asso  44.8     9.4 0.00024   19.2   0.9   15   18-32     76-90  (90)
 18 TIGR00998 8a0101 efflux pump m  44.6      26 0.00067   16.4   3.4   40   14-57    285-324 (379)
 19 pfam10447 EXOSC1 Exosome compo  40.4      20  0.0005   17.2   2.0   34   25-63      3-36  (72)
 20 COG1499 NMD3 NMD protein affec  39.8      18 0.00045   17.4   1.7   14   20-33    243-256 (355)
 21 cd05706 S1_Rrp5_repeat_sc10 S1  38.8      31 0.00078   15.9   2.8   30   16-45     40-69  (73)
 22 PRK03999 translation initiatio  38.2      33 0.00084   15.8   3.8   53   21-81      8-62  (129)
 23 TIGR01955 RfaH transcriptional  36.9      19  0.0005   17.2   1.5   60    2-70     89-149 (162)
 24 cd03451 FkbR2 FkbR2 is a Strep  36.4      35 0.00089   15.6   2.8   18   23-40     91-108 (146)
 25 cd05707 S1_Rrp5_repeat_sc11 S1  36.2      30 0.00077   16.0   2.4   29   17-45     38-66  (68)
 26 cd03454 YdeM YdeM is a Bacillu  35.6      36 0.00092   15.5   3.0   17   23-39     88-104 (140)
 27 KOG3416 consensus               35.1      20 0.00051   17.1   1.4   23   23-53     61-83  (134)
 28 cd05697 S1_Rrp5_repeat_hs5 S1_  32.5      40   0.001   15.2   3.1   23   23-45     44-66  (69)
 29 pfam08948 DUF1859 Domain of un  32.4      41   0.001   15.2   4.7   66   21-90     30-102 (126)
 30 pfam09430 DUF2012 Protein of u  32.2      19 0.00048   17.3   0.9   49   59-110    25-77  (113)
 31 PRK00006 fabZ (3R)-hydroxymyri  32.0      41   0.001   15.1   4.5   28   24-52    104-131 (149)
 32 cd03452 MaoC_C MaoC_C  The C-t  31.8      41  0.0011   15.1   2.9   16   23-38     88-103 (142)
 33 TIGR00922 nusG transcription t  30.5      44  0.0011   15.0   3.6   29   20-55    136-164 (193)
 34 pfam05641 Agenet Agenet domain  30.5      44  0.0011   15.0   4.8   38   24-67      1-38  (68)
 35 COG0361 InfA Translation initi  30.0      36 0.00091   15.5   2.0   24   21-44     44-67  (75)
 36 cd04460 S1_RpoE S1_RpoE: RpoE,  28.6      47  0.0012   14.8   3.8   42   19-61     49-90  (99)
 37 PRK10476 multidrug resistance   28.3      48  0.0012   14.7   4.3   58   17-79    254-325 (348)
 38 cd04455 S1_NusA S1_NusA: N-uti  28.1      48  0.0012   14.7   3.1   23   19-41     34-58  (67)
 39 cd01288 FabZ FabZ is a 17kD be  28.0      48  0.0012   14.7   4.4   27   24-51     88-114 (131)
 40 PRK10559 p-hydroxybenzoic acid  27.8      48  0.0012   14.7   4.9   56   16-78    197-267 (310)
 41 PRK08190 bifunctional enoyl-Co  27.6      49  0.0012   14.7   4.4   36   23-58     95-131 (465)
 42 pfam06940 DUF1287 Domain of un  27.0      50  0.0013   14.6   4.3   49   22-78    105-153 (164)
 43 TIGR00008 infA translation ini  26.9      47  0.0012   14.8   2.1   26   20-45     41-66  (69)
 44 COG0231 Efp Translation elonga  26.4      51  0.0013   14.5   4.0   52   22-81      7-59  (131)
 45 cd05685 S1_Tex S1_Tex: The C-t  26.2      52  0.0013   14.5   3.1   25   21-45     42-66  (68)
 46 TIGR02346 chap_CCT_theta T-com  25.8      53  0.0013   14.5   3.3   56    2-59    170-229 (554)
 47 TIGR02303 HpaG-C-term 4-hydrox  24.7      55  0.0014   14.3   2.2   18   17-34    219-236 (249)
 48 TIGR01652 ATPase-Plipid phosph  24.4      32 0.00083   15.8   0.9   12   23-34    202-213 (1249)
 49 TIGR01511 ATPase-IB1_Cu copper  23.7      24  0.0006   16.6   0.1   31   18-55     88-118 (545)
 50 TIGR03630 arch_S17P archaeal r  23.4      58  0.0015   14.2   2.7   21   43-66     26-46  (102)
 51 TIGR02278 PaaN-DH phenylacetic  23.4      58  0.0015   14.2   2.9   28   21-48    631-658 (690)
 52 TIGR01073 pcrA ATP-dependent D  23.1      59  0.0015   14.1   2.4   44   39-84    765-810 (811)
 53 pfam07653 SH3_2 Variant SH3 do  23.0      60  0.0015   14.1   2.4   15   22-36     16-30  (53)
 54 PRK13198 ureB urease subunit b  23.0      60  0.0015   14.1   2.6   41   17-58     87-132 (158)
 55 PRK09014 rfaH transcriptional   22.4      61  0.0016   14.0   4.7   25   24-55    110-134 (162)
 56 cd05708 S1_Rrp5_repeat_sc12 S1  22.0      62  0.0016   14.0   3.0   22   23-44     47-68  (77)
 57 PRK03598 hypothetical protein;  21.8      63  0.0016   14.0   3.9   45   19-71    249-293 (331)
 58 cd06201 SiR_like2 Cytochrome p  21.8      63  0.0016   14.0   2.9   56   19-78     79-143 (289)
 59 PRK13980 NAD synthetase; Provi  21.7      15 0.00038   17.9  -1.2   41   45-86     26-66  (264)
 60 TIGR01700 PNPH purine nucleosi  21.6      55  0.0014   14.3   1.7   13   21-33     97-109 (259)
 61 cd05790 S1_Rrp40 S1_Rrp40: Rrp  21.6      64  0.0016   13.9   2.9   34   17-54     43-76  (86)
 62 pfam11302 DUF3104 Protein of u  21.5      64  0.0016   13.9   4.8   51   22-72      4-58  (75)
 63 PRK12442 translation initiatio  21.3      64  0.0016   13.9   2.0   10   25-34     48-57  (87)
 64 pfam12148 DUF3590 Protein of u  21.1      46  0.0012   14.8   1.2   16   23-38     65-80  (85)
 65 cd05688 S1_RPS1_repeat_ec3 S1_  21.1      65  0.0017   13.9   2.9   23   23-45     44-66  (68)
 66 TIGR03516 ppisom_GldI peptidyl  20.8      66  0.0017   13.8   4.5   69   24-92     86-174 (177)
 67 pfam07154 DUF1392 Protein of u  20.6      67  0.0017   13.8   3.3   34   18-54     82-115 (150)
 68 KOG3901 consensus               20.5      31 0.00078   15.9   0.2   27   92-118    56-83  (109)

No 1  
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=100.00  E-value=0  Score=313.00  Aligned_cols=112  Identities=62%  Similarity=1.065  Sum_probs=110.1

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEEC
Q ss_conf             93589997999999760279897378998999999835887740123453543136666433886300356130289991
Q gi|254780715|r    1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPL   80 (141)
Q Consensus         1 Mnli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl   80 (141)
                      ||+|+.+|++++     ++++|+|+|||||+|+++|.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++|||
T Consensus         1 ~~ii~~ve~~~~-----k~~iP~f~~GDtV~V~~~i~EG~KeRiQ~feGvvI~~~~~G~~~tftvRki~~GvGVEr~fpl   75 (112)
T PRK05338          1 MNLIKEIEAEQL-----RKDIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRGRGLNETFTVRKISYGVGVERTFPL   75 (112)
T ss_pred             CCHHHHHHHHHH-----CCCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEEEECCCCCCEEEEEEEECCCCEEEEEEC
T ss_conf             966999999872-----446998599999999999996896388756899999737887623889996058758999977


Q ss_pred             CCCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHH
Q ss_conf             0786101222000204678768750888410220120
Q gi|254780715|r   81 YSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKEN  117 (141)
Q Consensus        81 ~SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~  117 (141)
                      |||+|++|||+++|+|||||||||||+.||+|||+|+
T Consensus        76 ~SP~i~~iev~~~gkvRRaKLyYLR~~~GK~arike~  112 (112)
T PRK05338         76 HSPRIDSIEVVRRGKVRRAKLYYLRELSGKAARIKER  112 (112)
T ss_pred             CCCCCCEEEEEEECCCHHHHHHHHHCCCCCHHEECCC
T ss_conf             7997467999980530234444350375602345359


No 2  
>CHL00084 rpl19 ribosomal protein L19
Probab=100.00  E-value=1.4e-45  Score=308.68  Aligned_cols=112  Identities=46%  Similarity=0.778  Sum_probs=108.3

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECC
Q ss_conf             35899979999997602798973789989999998358877401234535431366664338863003561302899910
Q gi|254780715|r    2 NIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLY   81 (141)
Q Consensus         2 nli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~   81 (141)
                      |+|+.+|++++     +.++|+|+|||||+|+++|.||+|+|+|.|+|+||+++++|+++|||||++++|+|||++||||
T Consensus         6 ~li~~ie~~~~-----k~~~p~f~~GDtV~V~~~i~EG~keRiQ~FeGvVIa~~~~G~~~tfTVRki~~GvGVEr~fpl~   80 (117)
T CHL00084          6 QLVKEIESEFL-----KTDLPEIRVGDTVKVGVLIQEGNKERVQAYEGTVIAKKNSGINTTITVRRVFQGIGVERVFLLH   80 (117)
T ss_pred             HHHHHHHHHHC-----CCCCCCCCCCCEEEEEEEEEECCEEEEEEEEEEEEEEECCCCCCEEEEEEECCCCCEEEEEECC
T ss_conf             99999999871-----1359983999999999999848906987888999997089998449999842787589999857


Q ss_pred             CCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHHC
Q ss_conf             7861012220002046787687508884102201200
Q gi|254780715|r   82 SPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENT  118 (141)
Q Consensus        82 SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~~  118 (141)
                      ||+|++|||+++|+|||||||||||+.||+|||+|++
T Consensus        81 SP~i~~IeV~r~gkVRRAKLYYLR~~~GKaaRikekf  117 (117)
T CHL00084         81 SPKIASIEVLRHSKVRRAKLYYLRNRVGKATRLKQKF  117 (117)
T ss_pred             CCCCCEEEEEEECCCHHHHHHHHCCCCCHHHHCCCCC
T ss_conf             9984689999705421355564512756345114359


No 3  
>pfam01245 Ribosomal_L19 Ribosomal protein L19.
Probab=100.00  E-value=7e-45  Score=304.02  Aligned_cols=113  Identities=62%  Similarity=1.014  Sum_probs=110.5

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEEC
Q ss_conf             93589997999999760279897378998999999835887740123453543136666433886300356130289991
Q gi|254780715|r    1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPL   80 (141)
Q Consensus         1 Mnli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl   80 (141)
                      ||+|+.+|++++     ++++|+|+|||||+|+++|.||+|+|+|.|+|+||+++++|+++||||||+++|+|||++|||
T Consensus         1 ~~~i~~~e~~~~-----k~~ip~f~~GDtv~V~~~i~Eg~k~RiQ~FeGvvI~~~~~G~~~tftvRki~~g~GVEr~fpl   75 (113)
T pfam01245         1 MNLIKEIEAEQL-----KKDLPEFRVGDTVRVHVKIKEGNKERIQVFEGVVIARRGRGLNSTFTVRKISQGVGVERVFPL   75 (113)
T ss_pred             CCHHHHHHHHHH-----CCCCCCCCCCCEEEEEEEEEECCEEEEEEEEEEEEEEECCCCCEEEEEEEECCCCCEEEEEEC
T ss_conf             967999999874-----245998499999999999984881688899999999957887416999983168758999987


Q ss_pred             CCCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHHC
Q ss_conf             07861012220002046787687508884102201200
Q gi|254780715|r   81 YSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENT  118 (141)
Q Consensus        81 ~SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~~  118 (141)
                      |||+|++|||+++|||||||||||||+.||+||++|+.
T Consensus        76 ~SP~i~~IeV~r~~kvRRakLyYLR~~~GK~arike~~  113 (113)
T pfam01245        76 HSPRIDSIEVVRRGKVRRAKLYYLRDLSGKAARIKEKR  113 (113)
T ss_pred             CCCCCCEEEEEECCCHHHHHHHHHHCCCCHHHEECCCC
T ss_conf             79974679999716401455553512756134221259


No 4  
>COG0335 RplS Ribosomal protein L19 [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=1e-43  Score=296.44  Aligned_cols=112  Identities=63%  Similarity=1.083  Sum_probs=108.9

Q ss_pred             CC--HHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEE
Q ss_conf             93--5899979999997602798973789989999998358877401234535431366664338863003561302899
Q gi|254780715|r    1 MN--IIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLF   78 (141)
Q Consensus         1 Mn--li~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~f   78 (141)
                      ||  +|+++|++|+     ++++|+|+|||||+|+++|.||+|+|+|.|+|+||+++|+|+++|||||++++|+|||++|
T Consensus         1 m~~~~i~~le~~q~-----~~~iP~f~~GDtvrv~vki~Eg~keR~Q~FeGvVia~r~~G~~~tftvRkis~G~GVEr~F   75 (115)
T COG0335           1 MNIPIIQQLEQEQI-----KKDIPSFRPGDTVRVHVKIVEGSKERVQAFEGVVIARRGRGISETFTVRKISYGVGVERVF   75 (115)
T ss_pred             CCCHHHHHHHHHHH-----HHCCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEEECCCCCCCEEEEEEEECCCEEEEEE
T ss_conf             97279999999988-----8508989999889999999868807876255899998799865118999840584088997


Q ss_pred             ECCCCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHH
Q ss_conf             910786101222000204678768750888410220120
Q gi|254780715|r   79 PLYSPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKEN  117 (141)
Q Consensus        79 pl~SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~  117 (141)
                      |+|||+|++|||+++|+||||||||||++.||+|||+++
T Consensus        76 p~~SP~Ie~IeV~rrGkVRRAKLYYLR~~~GKaArIke~  114 (115)
T COG0335          76 PLHSPLIESIEVVRRGKVRRAKLYYLRERRGKAARIKEK  114 (115)
T ss_pred             ECCCCCEEEEEEEECCCEEEEEEEEEECCCCCCEEEEEC
T ss_conf             258984507999961826144467641355521056533


No 5  
>KOG1698 consensus
Probab=100.00  E-value=5e-33  Score=229.03  Aligned_cols=124  Identities=31%  Similarity=0.618  Sum_probs=117.3

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECC
Q ss_conf             35899979999997602798973789989999998358877401234535431366664338863003561302899910
Q gi|254780715|r    2 NIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLY   81 (141)
Q Consensus         2 nli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~   81 (141)
                      .+++.||+++|+..+...++|+|++||+|+|++...+ ++.++..|.|+||++++.|+++||+|||++.|+|||.+||||
T Consensus        75 ~~~e~Ldr~a~~~rr~~r~iPe~~~G~Iv~V~s~~p~-~k~k~s~f~Gi~I~R~~~Gl~atf~LRnvIagvGVEi~~pLY  153 (201)
T KOG1698          75 RIMEILDRQAVLERRKVRDIPEFKVGSIVRVTSEDPE-NKRKVSRFKGICIRRRNAGLNATFLLRNVIAGVGVEIVFPLY  153 (201)
T ss_pred             HHHHHHCHHHHHHHHHCCCCCCCCCCCEEEEEECCCC-CCCCEEEEEEEEEEECCCCCCCEEEEEEHHHCCEEEEEEECC
T ss_conf             8987637688999985456876214558999962776-677424689999972346876267720033074059998636


Q ss_pred             CCCEEEEEEEECCHHHHHHHHHHCCCCCCEEEHHHHCCCCCCCCC
Q ss_conf             786101222000204678768750888410220120012123654
Q gi|254780715|r   82 SPMIQDITVIRRGKVRRSKLYYLQDLRGKAARIKENTGKRAKALN  126 (141)
Q Consensus        82 SP~i~~Iev~r~gkvRrakLyYLR~~~gk~arik~~~~~~~~~~~  126 (141)
                      ||+|++|+|++..|+|||+||||||..+.+++++..|.+......
T Consensus       154 sP~IkeI~Vlk~~k~rra~LyYLRd~lp~lstfd~~m~~~~~~~~  198 (201)
T KOG1698         154 SPNIKEIKVLKLEKRRRAKLYYLRDALPELSTFDANMRPKKEENG  198 (201)
T ss_pred             CCCEEEEEEECHHHCCCCCHHHHHCCCCCCCCHHHCCCCCCCCCC
T ss_conf             997147898433241112013222244445834423532235578


No 6  
>TIGR01024 rplS_bact ribosomal protein L19; InterPro: IPR001857   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 L19 is one of the proteins from the large ribosomal subunit , . In Escherichia coli, L19 is known to be located at the 30S-50S ribosomal subunit interface  and may play a role in the structure and function of the aminoacyl-tRNA binding site. It belongs to a family of ribosomal proteins, including L19 from bacteria and the chloroplasts of red algae.   L19 is a protein of 120 to 130 amino-acid residues.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=99.93  E-value=2.4e-26  Score=186.94  Aligned_cols=113  Identities=61%  Similarity=0.999  Sum_probs=107.3

Q ss_pred             CCHHHHHHHHHHHHHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEE-CCCCCCEEEEE
Q ss_conf             93589997999999760279897378998999999835887740123453543136666433886300-35613028999
Q gi|254780715|r    1 MNIIDELDHEEMVRIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKI-SYGEGMNRLFP   79 (141)
Q Consensus         1 Mnli~~le~~~~~~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki-~~g~GVE~~fp   79 (141)
                      +++++.++.++.    .+.++|+|++||+++|++++.||.++|+|.|+|+||+.+++|++.||++|++ ++|+|+|+.||
T Consensus         1 ~~~~~~~~~~~~----~~~~~p~~~~gd~~~~~~~~~~g~~~~~~~~~g~~~~~~~~g~~~~~~~~~~g~~g~g~~~~f~   76 (116)
T TIGR01024         1 SNLIKELEQENQ----LKKDLPDFRPGDTVRVGVKIVEGGKERLQAFEGVVIARRGGGIGETFTVRKIGSYGVGVERIFP   76 (116)
T ss_pred             CHHHHHHHHHHH----HCCCCCCCCCCCEEEEEEEEEECCCCEEEECCCEEEEECCCCCCCEEEEEECCCCCCCCCEEEE
T ss_conf             903655444331----0012333457851468888740774100110314786417876512466422666666200100


Q ss_pred             CCCCCEEEEEEEECCHHHHHHHHHHCCCCCC-EEEHHHH
Q ss_conf             1078610122200020467876875088841-0220120
Q gi|254780715|r   80 LYSPMIQDITVIRRGKVRRSKLYYLQDLRGK-AARIKEN  117 (141)
Q Consensus        80 l~SP~i~~Iev~r~gkvRrakLyYLR~~~gk-~arik~~  117 (141)
                      +|||.+.+|++++.|++++|+|||||++.|+ ++++++.
T Consensus        77 ~~~p~~~~~~~~~~g~~~~~~~~y~~~~~g~~~~~~~~~  115 (116)
T TIGR01024        77 LHSPNIESIEVVRRGKVRRAKLYYLRERRGKAAAKIKER  115 (116)
T ss_pred             CCCCCCCEEEHHHCCCHHHHHHHHHHCCCCHHHHHHHHC
T ss_conf             136531000000003201233222220243012232104


No 7  
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=79.09  E-value=5.7  Score=20.56  Aligned_cols=76  Identities=21%  Similarity=0.210  Sum_probs=46.3

Q ss_pred             HHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEE--CCCCCCEEEEECCCCCEEEEEEEEC
Q ss_conf             60279897378998999999835887740123453543136666433886300--3561302899910786101222000
Q gi|254780715|r   16 ESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKI--SYGEGMNRLFPLYSPMIQDITVIRR   93 (141)
Q Consensus        16 ~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki--~~g~GVE~~fpl~SP~i~~Iev~r~   93 (141)
                      +..+++| ++.||+|.|.-   -..|+    -+|-|+.+...-.  .+.|-.+  .---|-+.-+|+|..++.=.++.-.
T Consensus        40 y~~Rs~~-IrkgD~V~V~r---G~~kG----~~GkV~~V~~k~~--~V~VEgv~~~K~~G~~v~~pIhpSnvvItkL~l~  109 (119)
T PRK01191         40 YGIRSLP-VRKGDTVKVMR---GDFKG----EEGKVVEVDLKRY--RIYVEGVTIKKADGTEVPYPIHPSNVMITKLDLS  109 (119)
T ss_pred             HCCCCCC-EECCCEEEEEE---CCCCC----CCCEEEEEECCCC--EEEEEEEEEECCCCCEEEEEECCCCEEEEECCCC
T ss_conf             4887443-54699999955---27789----6231899973688--9999436998479987864225631799974668


Q ss_pred             CHHHHHHH
Q ss_conf             20467876
Q gi|254780715|r   94 GKVRRSKL  101 (141)
Q Consensus        94 gkvRrakL  101 (141)
                      -+.|.++|
T Consensus       110 Dk~R~~~L  117 (119)
T PRK01191        110 DERRFKIL  117 (119)
T ss_pred             CHHHHHHH
T ss_conf             87899874


No 8  
>pfam03888 MucB_RseB MucB/RseB family. Members of this family are regulators of the anti-sigma E protein RseD.
Probab=75.64  E-value=6.2  Score=20.31  Aligned_cols=52  Identities=21%  Similarity=0.289  Sum_probs=43.1

Q ss_pred             CCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEEEEEEEECCH
Q ss_conf             7740123453543136666433886300356130289991078610122200020
Q gi|254780715|r   41 KSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGK   95 (141)
Q Consensus        41 k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~~Iev~r~gk   95 (141)
                      -.+.+.|+|+.+-.++..+.+.=.+..+.+|.-.|+...|..|..+   |+|++.
T Consensus        36 A~~~lnY~G~fvy~~~~~i~s~ri~H~~~~g~e~erL~~LdG~~rE---iiR~~d   87 (314)
T pfam03888        36 ASQQLSYEGSFVYERNGSFSSLRYRHARQDGKSYAQLLQLDGPQQE---VVRRDN   87 (314)
T ss_pred             HHHHCCEEEEEEEEECCEEEEEEEEEEECCCEEEEEEEECCCCHHE---EEEECC
T ss_conf             8875774799999919902159999995599699999954998002---899699


No 9  
>PRK09455 rseB periplasmic negative regulator of sigmaE; Provisional
Probab=69.29  E-value=9.9  Score=19.02  Aligned_cols=51  Identities=25%  Similarity=0.271  Sum_probs=41.4

Q ss_pred             CCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEEEEEEEECCH
Q ss_conf             740123453543136666433886300356130289991078610122200020
Q gi|254780715|r   42 SRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQDITVIRRGK   95 (141)
Q Consensus        42 ~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~~Iev~r~gk   95 (141)
                      .+.+.|+|+.+..++..+.+.=.+.-+.+|.-+|+.-.|..|..+   |+|++.
T Consensus        21 ~~~lnY~G~fv~~~~~~i~s~ri~H~~~~~~e~erL~~LdG~~rE---viR~~d   71 (302)
T PRK09455         21 SQSLNYELSFISINKQGIESLRYRHARLDNKPLAQLLQLDGPRRE---VIQRGN   71 (302)
T ss_pred             HHHCCEEEEEEEEECCEEEEEEEEEEECCCEEEEEEEECCCCCEE---EEEECC
T ss_conf             874781599999939925689999996599699998835998417---999599


No 10 
>pfam02211 NHase_beta Nitrile hydratase beta subunit. Nitrile hydratases EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit.
Probab=57.80  E-value=12  Score=18.47  Aligned_cols=39  Identities=23%  Similarity=0.517  Sum_probs=27.4

Q ss_pred             CCCCCCCCCCEEEEEEEEECCCCCCCEEE----EEEEEEECCCC
Q ss_conf             79897378998999999835887740123----45354313666
Q gi|254780715|r   19 RSLPKFSPGDTLCVKTIITEGDKSRIQAY----EGVCIARSGRG   58 (141)
Q Consensus        19 ~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F----~GvvI~~~~~G   58 (141)
                      ..-|.|.+||.|+|.- .....-+|+..|    .|++++.++.-
T Consensus       128 ~~~p~F~vGd~Vrv~~-~~~~gHtRlP~Y~rgk~G~I~~~~G~~  170 (220)
T pfam02211       128 DAPPRFAVGDRVRTRN-INPNGHTRLPRYVRGKTGTIVRVHGAH  170 (220)
T ss_pred             CCCCCCCCCCEEEEEE-CCCCCCCCCHHHHCCCEEEEEEEECCC
T ss_conf             9999779999899822-799975235367678745899884687


No 11 
>pfam02765 Telo_bind Telomeric single stranded DNA binding POT1/CDC13. This domain binds single stranded telomeric DNA and adopts an OB fold. It includes the proteins POT1 and CDC13 which have been shown to regulate telomere length, replication and capping.
Probab=54.22  E-value=19  Score=17.32  Aligned_cols=49  Identities=18%  Similarity=0.285  Sum_probs=30.0

Q ss_pred             CCCCCCC-CCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEE
Q ss_conf             7989737-899899999983588774012345354313666643388630035613028
Q gi|254780715|r   19 RSLPKFS-PGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNR   76 (141)
Q Consensus        19 ~~~P~f~-~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~   76 (141)
                      ..+|... +||++.++-       -++|.|.|-..+..+.+-.++|.|=  .++.|..-
T Consensus        64 e~LP~v~~~GDIi~l~r-------~~v~~~~~~~~~~~~~~~~ss~a~f--~g~~~~~~  113 (141)
T pfam02765        64 EDLPNVQSAGDIIRLHR-------VKVKLYNGKPQGVARDKNNSSWAIF--SGDLGAPF  113 (141)
T ss_pred             HHCCCCCCCCCEEEEEE-------EEEEEECCEEEEEECCCCCEEEEEE--CCCCCCCC
T ss_conf             78998677798999977-------8999998967898727884057997--18899986


No 12 
>cd04497 hPOT1_OB1_like hPOT1_OB1_like: A subfamily of OB folds similar to the first OB fold (OB1) of human protection of telomeres 1 protein (hPOT1), the single OB fold of the N-terminal domain of Schizosaccharomyces pombe POT1 (SpPOT1), and the first OB fold of the N-terminal domain of the alpha subunit (OB1Nalpha) of Oxytricha nova telomere end binding protein (OnTEBP). POT1 proteins recognize single-stranded (ss) 3-prime ends of the telomere. A 3-prime ss overhang is conserved in ciliated protozoa, yeast, and mammals. SpPOT1 is essential for telomere maintenance. It binds specifically to the ss G-rich telomeric sequence (GGTTAC) of S. pombe. hPOT1 binds specifically to ss telomeric DNA repeats ending with the sequence GGTTAG. Deletion of the S. pombe pot1+ gene results in a rapid loss of telomere sequences, chromosome mis-segregation and chromosome circularization. hPOT1 is implicated in telomere length regulation. The hPOT1 monomer consists of two closely connected OB folds (OB1-OB
Probab=51.82  E-value=20  Score=17.08  Aligned_cols=50  Identities=24%  Similarity=0.309  Sum_probs=32.1

Q ss_pred             CCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCE
Q ss_conf             2798973789989999998358877401234535431366664338863003561302
Q gi|254780715|r   18 KRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMN   75 (141)
Q Consensus        18 k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE   75 (141)
                      ...+|..++||+|.++--       ++|.|.|-..+..+. -.++|.|=+-..+.+.+
T Consensus        63 ~~~LP~v~~GDiIll~~~-------~v~~~~~~~~~~~~~-~~sswavF~g~~~~~~~  112 (138)
T cd04497          63 EESLPIVKVGDIILLRRV-------KIQSYNGKPQGISND-RGSSWAVFRGDDGVVPI  112 (138)
T ss_pred             HHHCCCCCCCCEEEEEEE-------EEEEECCEEEEEECC-CCEEEEEECCCCCCCCC
T ss_conf             656989999989999888-------999988907999778-84169998588899868


No 13 
>cd05791 S1_CSL4 S1_CSL4: CSL4, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. ScCSL4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In S. cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=49.48  E-value=18  Score=17.47  Aligned_cols=34  Identities=12%  Similarity=0.180  Sum_probs=14.7

Q ss_pred             CCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEE
Q ss_conf             789989999998358877401234535431366664338
Q gi|254780715|r   25 SPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNF   63 (141)
Q Consensus        25 ~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stf   63 (141)
                      ++||+|...+.  .-+   .|.-.--++++.++.+..+|
T Consensus         5 ~vGdiV~~rVt--rv~---~~~a~v~Il~v~~~~l~~~f   38 (92)
T cd05791           5 KVGSIVIARVT--RIN---PRFAKVDILCVGGRPLKESF   38 (92)
T ss_pred             CCCCEEEEEEE--EEC---CCEEEEEEEEECCEECCCEE
T ss_conf             89999999999--971---13789999999999837625


No 14 
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=49.19  E-value=22  Score=16.82  Aligned_cols=62  Identities=15%  Similarity=0.097  Sum_probs=44.4

Q ss_pred             HHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC-C--------CCCEEEEEEECCCCCCEEEEEC
Q ss_conf             7602798973789989999998358877401234535431366-6--------6433886300356130289991
Q gi|254780715|r   15 IESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR-G--------INKNFTVRKISYGEGMNRLFPL   80 (141)
Q Consensus        15 ~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~-G--------~~stftvRki~~g~GVE~~fpl   80 (141)
                      .++..++..+++|+-+.|++....++    ..|+|++-++... |        .++|+..=++++.+.|...|.=
T Consensus       250 nFkETqL~~~r~Gq~a~I~~da~~~~----~~~~G~v~~i~~~tg~~fsllp~~natgN~tkvvQRvPVrI~ld~  320 (352)
T COG1566         250 NFKETQLARVRPGQPAEITLDAYPGN----GVVEGIVEGIAPATGSAFSLLPAQNATGNWTKVVQRVPVRIELDP  320 (352)
T ss_pred             EEEEEECCCCCCCCEEEEEEECCCCC----EEEEEEEEEECCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEECC
T ss_conf             20011347445897089999737984----589999987447865300157874678888999976658999667


No 15 
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=46.60  E-value=24  Score=16.57  Aligned_cols=38  Identities=26%  Similarity=0.477  Sum_probs=26.8

Q ss_pred             CCCCCCCCEEEEEEEEEC----CC-CCCCEEEEEEEEEECCCCCC
Q ss_conf             897378998999999835----88-77401234535431366664
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITE----GD-KSRIQAYEGVCIARSGRGIN   60 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~e----g~-k~R~Q~F~GvvI~~~~~G~~   60 (141)
                      +-+|.+||.|.+  .|+.    |. -.|.|-..|+|+..+++...
T Consensus        30 l~ey~~Gd~V~I--~IdpSv~kGmPh~rf~G~TG~Vvg~~g~ay~   72 (98)
T COG2139          30 LQEYKVGDKVHI--DIDPSVHKGMPHPRFQGKTGTVVGVRGRAYK   72 (98)
T ss_pred             HHHCCCCCEEEE--EECCCCCCCCCCCCCCCCCEEEEECCCCEEE
T ss_conf             876079987999--8476202698775304763079841487799


No 16 
>pfam02014 Reeler Reeler domain.
Probab=45.77  E-value=25  Score=16.49  Aligned_cols=32  Identities=16%  Similarity=0.297  Sum_probs=22.9

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCC
Q ss_conf             7378998999999835887740123453543136666
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGI   59 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~   59 (141)
                      .+.||+.+.|++.-..     ...|.|..|.-++.+.
T Consensus        29 ~y~pG~~~~Vtl~~~~-----~~~F~GFllqAr~~~~   60 (127)
T pfam02014        29 SYVPGQTYTVTISKSS-----GDTFRGFLLQARNGDP   60 (127)
T ss_pred             EECCCCEEEEEEECCC-----CCCCCEEEEEEECCCC
T ss_conf             7889998999996689-----9871589999973889


No 17 
>TIGR02579 cas_csx3 CRISPR-associated protein, Csx3 family; InterPro: IPR013409    This entry is encoded in CRISPR-associated (cas) gene clusters, near CRISPR repeats, in the genomes of several different thermophiles: Archaeoglobus fulgidus (archaeal), Aquifex aeolicus (Aquificae), Dictyoglomus thermophilum (Dictyoglomi), and a thermophilic Synechococcus (Cyanobacteria). It is not yet assigned to a specific CRISPR/cas subtype (hence the x designation csx3)..
Probab=44.80  E-value=9.4  Score=19.18  Aligned_cols=15  Identities=20%  Similarity=0.328  Sum_probs=11.3

Q ss_pred             CCCCCCCCCCCEEEE
Q ss_conf             279897378998999
Q gi|254780715|r   18 KRSLPKFSPGDTLCV   32 (141)
Q Consensus        18 k~~~P~f~~GD~v~V   32 (141)
                      ....|++|+||++.+
T Consensus        76 ~SH~Pe~r~GdVi~~   90 (90)
T TIGR02579        76 SSHSPELRVGDVIDW   90 (90)
T ss_pred             EECCCCCCCCCEECC
T ss_conf             514899987743429


No 18 
>TIGR00998 8a0101 efflux pump membrane protein; InterPro: IPR005694    emrA and emrB confer resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds. EmrB encodes a highly hydrophobic 56.2-kDa peptide, with 14 potential alpha-helices to span the inner membrane. EmrA encodes a putative 42.7-kDa peptide containing a single hydrophobic domain and a large C-terminal hydrophilic domain.; GO: 0015238 drug transporter activity, 0006855 multidrug transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=44.60  E-value=26  Score=16.38  Aligned_cols=40  Identities=15%  Similarity=0.171  Sum_probs=33.3

Q ss_pred             HHHHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC
Q ss_conf             97602798973789989999998358877401234535431366
Q gi|254780715|r   14 RIESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR   57 (141)
Q Consensus        14 ~~~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~   57 (141)
                      ..++-.++...|+|.-+.|+.-...+++    .|+|.|-.+...
T Consensus       285 ANFkETqL~~vR~G~~v~i~~DlYg~dv----~F~GkV~gi~~G  324 (379)
T TIGR00998       285 ANFKETQLKNVRIGQPVTIRSDLYGSDV----VFEGKVTGISMG  324 (379)
T ss_pred             EEEECCCCCCCCCCCCEEEEEEECCCCC----EEEEEEEECCCC
T ss_conf             7520132057457872589985438980----797488422663


No 19 
>pfam10447 EXOSC1 Exosome component EXOSC1/CSL4. This family of proteins are components of the exosome 3'-5' exoribonuclease complex. The exosome mediates degradation of unstable mRNAs that contain AU-rich elements (AREs) within their 3' untranslated regions.
Probab=40.36  E-value=20  Score=17.16  Aligned_cols=34  Identities=15%  Similarity=0.224  Sum_probs=15.1

Q ss_pred             CCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEE
Q ss_conf             789989999998358877401234535431366664338
Q gi|254780715|r   25 SPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNF   63 (141)
Q Consensus        25 ~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stf   63 (141)
                      .+||+|...+.-.  +.   +.-..-+++..+..+..+|
T Consensus         3 ~vGdiV~arVtrv--~~---~~a~~~Il~v~~~~l~~~f   36 (72)
T pfam10447         3 KVGDIVLARVTRV--TP---RQAYCEILAVGGTALKETF   36 (72)
T ss_pred             CCCCEEEEEEEEE--CH---HEEEEEEEEECCEECCCCE
T ss_conf             8999999999997--50---1579999999999878855


No 20 
>COG1499 NMD3 NMD protein affecting ribosome stability and mRNA decay [Translation, ribosomal structure and biogenesis]
Probab=39.84  E-value=18  Score=17.44  Aligned_cols=14  Identities=43%  Similarity=1.058  Sum_probs=11.5

Q ss_pred             CCCCCCCCCEEEEE
Q ss_conf             98973789989999
Q gi|254780715|r   20 SLPKFSPGDTLCVK   33 (141)
Q Consensus        20 ~~P~f~~GD~v~V~   33 (141)
                      -+|+|++||+|.+.
T Consensus       243 rip~~~~gDiV~~~  256 (355)
T COG1499         243 RIPEFRPGDIVSVR  256 (355)
T ss_pred             ECCCCCCCCEEEEC
T ss_conf             87887988789977


No 21 
>cd05706 S1_Rrp5_repeat_sc10 S1_Rrp5_repeat_sc10: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 10 (sc10). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=38.79  E-value=31  Score=15.94  Aligned_cols=30  Identities=17%  Similarity=0.122  Sum_probs=19.5

Q ss_pred             HHCCCCCCCCCCCEEEEEEEEECCCCCCCE
Q ss_conf             602798973789989999998358877401
Q gi|254780715|r   16 ESKRSLPKFSPGDTLCVKTIITEGDKSRIQ   45 (141)
Q Consensus        16 ~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q   45 (141)
                      +.+.....|++||.|+|.+.-.+-++.|++
T Consensus        40 ~~~~~~~~~~~g~~V~v~Vl~VD~~~krI~   69 (73)
T cd05706          40 YSEALPYKFKKNDIVRACVLSVDVPNKKIA   69 (73)
T ss_pred             CCCCCHHHCCCCCEEEEEEEEEECCCCEEE
T ss_conf             013817516899999999999988899898


No 22 
>PRK03999 translation initiation factor IF-5A; Provisional
Probab=38.21  E-value=33  Score=15.76  Aligned_cols=53  Identities=17%  Similarity=0.344  Sum_probs=38.2

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC-CC-CCEEEEEEECCCCCCEEEEECC
Q ss_conf             8973789989999998358877401234535431366-66-4338863003561302899910
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR-GI-NKNFTVRKISYGEGMNRLFPLY   81 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~-G~-~stftvRki~~g~GVE~~fpl~   81 (141)
                      .-+|+.|..+.+     +|..+++.-|.   .++-|+ |- -..+.+++++.|-=.|.+||-.
T Consensus         8 ~~dlK~G~~i~i-----dg~pckVve~~---~sKpGKHG~Akvr~~~~~i~tG~k~e~~~~~~   62 (129)
T PRK03999          8 VGELKEGSYVVI-----DGEPCRIVEIS---KSKPGKHGSAKARIVAIGIFDGQKRSLVAPVD   62 (129)
T ss_pred             HHHCCCCCEEEE-----CCEEEEEEEEE---EECCCCCCCEEEEEEEEECCCCCEEEEEECCC
T ss_conf             899268999999-----99859999988---86499985369999999646797899988798


No 23 
>TIGR01955 RfaH transcriptional activator RfaH; InterPro: IPR010215   This entry represents the transcriptional activator protein, RfaH . This protein is most closely related to the transcriptional termination/antitermination protein NusG (IPR001062 from INTERPRO) and contains the KOW motif (IPR005824 from INTERPRO) . This protein appears to be limited to the proteobacteria. In Escherichia coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=36.90  E-value=19  Score=17.19  Aligned_cols=60  Identities=18%  Similarity=0.375  Sum_probs=34.8

Q ss_pred             CHHHHHHHHHHHHHHHCCCCCC-CCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECC
Q ss_conf             3589997999999760279897-37899899999983588774012345354313666643388630035
Q gi|254780715|r    2 NIIDELDHEEMVRIESKRSLPK-FSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISY   70 (141)
Q Consensus         2 nli~~le~~~~~~~~~k~~~P~-f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~   70 (141)
                      ++|++|...+..........|. |..||.|.+    .+|.=.   -||||=.  ...|-.-+..|=|+++
T Consensus        89 ~~I~~l~~~~~~~~~~~~~~P~~~~~G~~V~i----~~G~fa---g~EAIF~--~~dG~~R~~~Llnm~~  149 (162)
T TIGR01955        89 DLIHQLRQKELEASVPAKKTPLLFKKGDKVRI----TDGSFA---GLEAIFL--EPDGEKRSVLLLNMIG  149 (162)
T ss_pred             HHHHHHHHCCCCCCCCHHHCCCCCCCCCEEEE----EECCCC---CCCEEEE--CCCCCHHHHHHHHHHC
T ss_conf             89898640343225583135657789887998----628713---6003540--7884247766546636


No 24 
>cd03451 FkbR2 FkbR2 is a Streptomyces hygroscopicus protein with a hot dog fold that belongs to a conserved family of proteins found in prokaryotes and archaea but not in eukaryotes. FkbR2  has sequence similarity to (R)-specific enoyl-CoA hydratase, the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.  The function of FkbR2 is unknown.
Probab=36.40  E-value=35  Score=15.58  Aligned_cols=18  Identities=22%  Similarity=0.254  Sum_probs=14.3

Q ss_pred             CCCCCCEEEEEEEEECCC
Q ss_conf             737899899999983588
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGD   40 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~   40 (141)
                      ..++||||.+...|.+-.
T Consensus        91 PV~~GDtl~~~~eV~~~r  108 (146)
T cd03451          91 PVFHGDTLYAESEVLSKR  108 (146)
T ss_pred             CCCCCCEEEEEEEEEEEE
T ss_conf             776999999999999987


No 25 
>cd05707 S1_Rrp5_repeat_sc11 S1_Rrp5_repeat_sc11: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 11 (sc11). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=36.19  E-value=30  Score=15.99  Aligned_cols=29  Identities=24%  Similarity=0.294  Sum_probs=20.1

Q ss_pred             HCCCCCCCCCCCEEEEEEEEECCCCCCCE
Q ss_conf             02798973789989999998358877401
Q gi|254780715|r   17 SKRSLPKFSPGDTLCVKTIITEGDKSRIQ   45 (141)
Q Consensus        17 ~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q   45 (141)
                      -+..-..|.+|++|++.+.-.+-.+.|++
T Consensus        38 Vkd~~~~f~vGq~V~~kV~~iD~~~~ri~   66 (68)
T cd05707          38 LKDWKKRFKVGQLVKGKIVSIDPDNGRIE   66 (68)
T ss_pred             HCCHHHHCCCCCEEEEEEEEEECCCCEEE
T ss_conf             64998917999999999999828758673


No 26 
>cd03454 YdeM YdeM is a Bacillus subtilis protein that belongs to a family of prokaryotic proteins of unkown function.  YdeM has sequence similarity to the hot-dog fold of (R)-specific enoyl-CoA hydratase.   Other enzymes with this fold include the peroxisomal Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.
Probab=35.65  E-value=36  Score=15.50  Aligned_cols=17  Identities=35%  Similarity=0.591  Sum_probs=14.0

Q ss_pred             CCCCCCEEEEEEEEECC
Q ss_conf             73789989999998358
Q gi|254780715|r   23 KFSPGDTLCVKTIITEG   39 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg   39 (141)
                      ..++||||.+...|.+-
T Consensus        88 PV~~GDTi~~~~eV~~~  104 (140)
T cd03454          88 PVRPGDTLSVEVEVLDK  104 (140)
T ss_pred             CCCCCCEEEEEEEEEEE
T ss_conf             87689999999999993


No 27 
>KOG3416 consensus
Probab=35.07  E-value=20  Score=17.09  Aligned_cols=23  Identities=22%  Similarity=0.642  Sum_probs=13.5

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCEEEEEEEEE
Q ss_conf             7378998999999835887740123453543
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQAYEGVCIA   53 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~   53 (141)
                      -|.|||+|+.+       +.=.+.|+| |+-
T Consensus        61 ~~~PGDIirLt-------~Gy~Si~qg-~Lt   83 (134)
T KOG3416          61 LIQPGDIIRLT-------GGYASIFQG-CLT   83 (134)
T ss_pred             CCCCCCEEEEC-------CCCHHHHCC-CEE
T ss_conf             45886689963-------630434038-569


No 28 
>cd05697 S1_Rrp5_repeat_hs5 S1_Rrp5_repeat_hs5: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions. Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes H. sapiens S1 repeat 5 (hs5) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=32.52  E-value=40  Score=15.18  Aligned_cols=23  Identities=26%  Similarity=0.534  Sum_probs=17.1

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCE
Q ss_conf             73789989999998358877401
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQ   45 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q   45 (141)
                      .|++||.|++.+.-.+-++.|+.
T Consensus        44 ~fk~G~~Vk~rVl~vD~~~~ri~   66 (69)
T cd05697          44 KFKPGLKVKCRVLSVEPERKRLV   66 (69)
T ss_pred             CCCCCCEEEEEEEEEECCCCEEE
T ss_conf             08999999999999948879988


No 29 
>pfam08948 DUF1859 Domain of unknown function (DUF1859). This domain has no known function. It is predominantly found in the N-terminus of bacteriophage spike proteins.
Probab=32.38  E-value=41  Score=15.17  Aligned_cols=66  Identities=20%  Similarity=0.323  Sum_probs=45.8

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEEEEE-EEEECCCCCCCEEEEE------EECCCCCCEEEEECCCCCEEEEEE
Q ss_conf             897378998999999835887740123453-5431366664338863------003561302899910786101222
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAYEGV-CIARSGRGINKNFTVR------KISYGEGMNRLFPLYSPMIQDITV   90 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~Gv-vI~~~~~G~~stftvR------ki~~g~GVE~~fpl~SP~i~~Iev   90 (141)
                      .-+--+|.+|++.++...    -+|-|.|+ ||-+.++..+-.|++-      +|-.-.|-.--|||-||...+.-+
T Consensus        30 ~~eaiaG~~V~~DL~~~~----~T~~~sGVQ~~YID~~e~~G~~~i~v~eTGQRIt~~AG~QGYfPlL~~~~~KFv~  102 (126)
T pfam08948        30 YFDAVAGENVKYDLTYLA----DTQGFTGVQCIYIDNAENDGAFEIDVEETGQRIKCPAGKQGYFPLLVPGRAKFVA  102 (126)
T ss_pred             HHHHCCCCEEEEEEEEEE----CCCCCCEEEEEEEECCCCCCCEEEECCCCCCEEECCCCCCCCCEEECCCHHHHHH
T ss_conf             534348955999999972----2587030589998652356857996222684887457785322466066655544


No 30 
>pfam09430 DUF2012 Protein of unknown function (DUF2012). This is a eukaryotic family of uncharacterized proteins.
Probab=32.18  E-value=19  Score=17.25  Aligned_cols=49  Identities=22%  Similarity=0.331  Sum_probs=36.1

Q ss_pred             CCCEEEEEEECCCCCCEEEEECCCCCE----EEEEEEECCHHHHHHHHHHCCCCCC
Q ss_conf             643388630035613028999107861----0122200020467876875088841
Q gi|254780715|r   59 INKNFTVRKISYGEGMNRLFPLYSPMI----QDITVIRRGKVRRSKLYYLQDLRGK  110 (141)
Q Consensus        59 ~~stftvRki~~g~GVE~~fpl~SP~i----~~Iev~r~gkvRrakLyYLR~~~gk  110 (141)
                      .+.||+++|+-.|.-   ...++||..    -.|+|...|+.|.-+++|.....+.
T Consensus        25 ~dGsF~f~nVp~Gsy---~ldv~~~~~~F~pvRVdV~~~g~~~~~~~~~~~~~~~~   77 (113)
T pfam09430        25 RDGSFVFHNVPAGSY---LLEVESPGYRFEPVRVDVSAKGKVRAVQLNIVETYEVN   77 (113)
T ss_pred             CCCEEEECCCCCEEE---EEEEECCCCEECCEEEEEECCCCCCCEEEEECCCCCCC
T ss_conf             687799738998338---99984698280578999946986464687732354576


No 31 
>PRK00006 fabZ (3R)-hydroxymyristoyl-ACP dehydratase; Reviewed
Probab=32.00  E-value=41  Score=15.13  Aligned_cols=28  Identities=25%  Similarity=0.494  Sum_probs=18.9

Q ss_pred             CCCCCEEEEEEEEECCCCCCCEEEEEEEE
Q ss_conf             37899899999983588774012345354
Q gi|254780715|r   24 FSPGDTLCVKTIITEGDKSRIQAYEGVCI   52 (141)
Q Consensus        24 f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI   52 (141)
                      ..|||++.++.++.. .+...-.|.|.+-
T Consensus       104 V~PGd~l~i~~~l~~-~~~~~~~~~~~a~  131 (149)
T PRK00006        104 VVPGDQLILEVEFLK-KRRGIGKFKGVAK  131 (149)
T ss_pred             CCCCCEEEEEEEEEE-EECCEEEEEEEEE
T ss_conf             799999999999999-6589999999999


No 32 
>cd03452 MaoC_C MaoC_C  The C-terminal hot dog fold of the MaoC (monoamine oxidase C) dehydratase regulatory protein. Orthologs of MaoC include PaaZ [Escherichia coli] and PaaN [Pseudomonas putida], which are putative ring-opening enzymes involved in phenylacetic acid degradation. The C-terminal domain of MaoC has sequence similarity to (R)-specific enoyl-CoA hydratase,Hydratase-Dehydrogenase-Epimerase (HDE) protein, and the fatty acid synthase beta subunit.  MaoC also has an N-terminal PutA domain like that found in the E. coli PutA proline dehydrogenase and other members of the aldehyde dehydrogenase family.
Probab=31.84  E-value=41  Score=15.11  Aligned_cols=16  Identities=31%  Similarity=0.480  Sum_probs=13.3

Q ss_pred             CCCCCCEEEEEEEEEC
Q ss_conf             7378998999999835
Q gi|254780715|r   23 KFSPGDTLCVKTIITE   38 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~e   38 (141)
                      ..++||||.+.+.|.+
T Consensus        88 PV~~GDTi~~~~~V~e  103 (142)
T cd03452          88 PVYPGDTIQVRLTCKR  103 (142)
T ss_pred             CCCCCCEEEEEEEEEE
T ss_conf             9899999999999999


No 33 
>TIGR00922 nusG transcription termination/antitermination factor NusG; InterPro: IPR001062 Bacterial transcription antitermination protein, nusG, is a component of the transcription complex and interacts with the termination factor Rho and RNA polymerase , . NusG is a bacterial transcriptional elongation factor involved in transcription termination and anti-termination .; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=30.49  E-value=44  Score=14.97  Aligned_cols=29  Identities=17%  Similarity=0.338  Sum_probs=22.3

Q ss_pred             CCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEEC
Q ss_conf             989737899899999983588774012345354313
Q gi|254780715|r   20 SLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARS   55 (141)
Q Consensus        20 ~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~   55 (141)
                      .--+|-+|+.|+|    .+|   -.+.|.|.|..+.
T Consensus       136 ~~~~fE~Ge~Vrv----~dG---PF~~F~G~Veev~  164 (193)
T TIGR00922       136 VKIDFEVGEQVRV----NDG---PFANFTGTVEEVD  164 (193)
T ss_pred             CCCCCCCCCEEEE----ECC---CCCCCCEEEEEEE
T ss_conf             3432357988898----038---8888514798880


No 34 
>pfam05641 Agenet Agenet domain. This domain is related to the TUDOR domain pfam00567. The function of the agenet domain is unknown. This family currently only matches one of the two Agenet domains in the FMR proteins.
Probab=30.46  E-value=44  Score=14.97  Aligned_cols=38  Identities=21%  Similarity=0.302  Sum_probs=26.6

Q ss_pred             CCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEE
Q ss_conf             37899899999983588774012345354313666643388630
Q gi|254780715|r   24 FSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRK   67 (141)
Q Consensus        24 f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRk   67 (141)
                      |+.||.|.|... .+|-  +-.-|.+.+|...+..   +|.|+=
T Consensus         1 f~~G~~VEV~s~-~~g~--~gaWf~a~Vi~~~~~~---~~~V~Y   38 (68)
T pfam05641         1 FSKGSEVEVSSE-EEGF--EGAWFRAKVLKELGED---KYKVEY   38 (68)
T ss_pred             CCCCCEEEEEEC-CCCC--CEEEEEEEEEEECCCC---EEEEEE
T ss_conf             979999999755-8887--4078899999977998---799996


No 35 
>COG0361 InfA Translation initiation factor 1 (IF-1) [Translation, ribosomal structure and biogenesis]
Probab=30.03  E-value=36  Score=15.51  Aligned_cols=24  Identities=29%  Similarity=0.329  Sum_probs=13.9

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCC
Q ss_conf             897378998999999835887740
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRI   44 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~   44 (141)
                      .--+.|||.|.|..+-..-+|.|+
T Consensus        44 ~i~I~~GD~V~Ve~~~~d~~kg~I   67 (75)
T COG0361          44 RIRILPGDVVLVELSPYDLTKGRI   67 (75)
T ss_pred             EEEECCCCEEEEEECCCCCCCCCE
T ss_conf             488579999999745665333558


No 36 
>cd04460 S1_RpoE S1_RpoE: RpoE, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. RpoE is subunit E of archaeal RNA polymerase. Archaeal cells contain a single RNA polymerase made up of 12 subunits, which are homologous to the 12 subunits (RPB1-12) of eukaryotic RNA polymerase II. RpoE is homologous to Rpa43 of eukaryotic RNA polymerase I, RPB7 of eukaryotic RNA polymerase II, and Rpc25 of eukaryotic RNA polymerase III. RpoE is composed of two domains, the N-terminal RNP (ribonucleoprotein) domain and the C-terminal S1 domain. This S1 domain binds ssRNA and ssDNA. This family is classified based on the C-terminal S1 domain. The function of RpoE is not fully understood. In eukaryotes, RPB7 and RPB4 form a heterodimer that reversibly associates with the RNA polymerase II core.
Probab=28.56  E-value=47  Score=14.76  Aligned_cols=42  Identities=12%  Similarity=0.175  Sum_probs=25.8

Q ss_pred             CCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCC
Q ss_conf             7989737899899999983588774012345354313666643
Q gi|254780715|r   19 RSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINK   61 (141)
Q Consensus        19 ~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~s   61 (141)
                      +.--.|+.||.|+|.+.-..-++.++ .|.-+=+..+.-|+++
T Consensus        49 r~~~~~~~GD~V~vrV~~V~~~~r~i-~~~~IgLtmrqp~lGk   90 (99)
T cd04460          49 ETKRVLKVGDVVRARIVAVSLKERRP-RESKIGLTMRQPGLGK   90 (99)
T ss_pred             CCCCEECCCCEEEEEEEEEECCCCCC-CCCEEEECCCCCCCCC
T ss_conf             27869847999999999980620676-7646650224788987


No 37 
>PRK10476 multidrug resistance protein MdtN; Provisional
Probab=28.28  E-value=48  Score=14.73  Aligned_cols=58  Identities=16%  Similarity=0.238  Sum_probs=35.1

Q ss_pred             HCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCC------C-----C---CCEEEEEEECCCCCCEEEEE
Q ss_conf             02798973789989999998358877401234535431366------6-----6---43388630035613028999
Q gi|254780715|r   17 SKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGR------G-----I---NKNFTVRKISYGEGMNRLFP   79 (141)
Q Consensus        17 ~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~------G-----~---~stftvRki~~g~GVE~~fp   79 (141)
                      ...++..+++|+-+.|++-...|     +.|.|.|.++...      +     +   ++|..-=|+.+.+.|-..|.
T Consensus       254 ~Et~l~~v~~Gq~v~I~~Da~p~-----~~f~G~V~sI~~g~~~~~~~~~~~~lp~~natgn~~Kv~QRvPVrI~~d  325 (348)
T PRK10476        254 RETDLKNIRVGDCATVYSMIDRG-----RPIEGKVDSIGWGVLPDDGGNVPRGLPYVPRSINWVRVAQRFPVRIMLD  325 (348)
T ss_pred             CHHHHCCCCCCCEEEEEEECCCC-----CEEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEEC
T ss_conf             27782527998989999976899-----7899999998878778100555445899799987688878985999988


No 38 
>cd04455 S1_NusA S1_NusA: N-utilizing substance A protein (NusA), S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. NusA is a transcription elongation factor containing an N-terminal catalytic domain and three RNA binding domains (RBD's). The RBD's include one S1 domain and two KH domains that form an RNA binding surface. DNA transcription by RNA polymerase (RNAP) includes three phases - initiation, elongation, and termination. During initiation, sigma factors bind RNAP and target RNAP to specific promoters. During elongation, N-utilization substances (NusA, B, E, and G) replace sigma factors and regulate pausing, termination, and antitermination. NusA is cold-shock-inducible.
Probab=28.15  E-value=48  Score=14.72  Aligned_cols=23  Identities=17%  Similarity=0.468  Sum_probs=15.4

Q ss_pred             CCCC--CCCCCCEEEEEEEEECCCC
Q ss_conf             7989--7378998999999835887
Q gi|254780715|r   19 RSLP--KFSPGDTLCVKTIITEGDK   41 (141)
Q Consensus        19 ~~~P--~f~~GD~v~V~~~i~eg~k   41 (141)
                      ..+|  .|++||.|++.+.-.+-..
T Consensus        34 eqip~E~~~~Gdrik~~i~~V~~~~   58 (67)
T cd04455          34 EQIPGESYRPGDRIKAYVLEVRKTS   58 (67)
T ss_pred             HCCCCCCCCCCCEEEEEEEEEEECC
T ss_conf             9578866399998999999987469


No 39 
>cd01288 FabZ FabZ is a 17kD beta-hydroxyacyl-acyl carrier protein (ACP) dehydratase that primarily catalyzes the dehydration of beta-hydroxyacyl-ACP to trans-2-acyl-ACP, the third step in the elongation phase of the bacterial/ plastid, type II, fatty-acid biosynthesis pathway.
Probab=28.04  E-value=48  Score=14.71  Aligned_cols=27  Identities=22%  Similarity=0.442  Sum_probs=18.6

Q ss_pred             CCCCCEEEEEEEEECCCCCCCEEEEEEE
Q ss_conf             3789989999998358877401234535
Q gi|254780715|r   24 FSPGDTLCVKTIITEGDKSRIQAYEGVC   51 (141)
Q Consensus        24 f~~GD~v~V~~~i~eg~k~R~Q~F~Gvv   51 (141)
                      ..|||++.+..++.. .+.++-.|.|.+
T Consensus        88 V~PGd~l~i~~~~~~-~~~~~~~~~~~~  114 (131)
T cd01288          88 VVPGDQLILEVELLK-LRRGIGKFKGKA  114 (131)
T ss_pred             CCCCCEEEEEEEEEE-EECCEEEEEEEE
T ss_conf             899999999999999-769999999999


No 40 
>PRK10559 p-hydroxybenzoic acid efflux subunit AaeA; Provisional
Probab=27.83  E-value=48  Score=14.68  Aligned_cols=56  Identities=13%  Similarity=0.169  Sum_probs=34.6

Q ss_pred             HHCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEE---------------EEEEECCCCCCEEEE
Q ss_conf             602798973789989999998358877401234535431366664338---------------863003561302899
Q gi|254780715|r   16 ESKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNF---------------TVRKISYGEGMNRLF   78 (141)
Q Consensus        16 ~~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stf---------------tvRki~~g~GVE~~f   78 (141)
                      ++..++..+++|+.+.|..   .+ ..+  .|.|.|.++- .|.++.|               .-=|+.+-+.|-..+
T Consensus       197 fkETqL~~ir~Gq~v~I~~---~~-p~~--~f~G~V~si~-~g~~~~~s~~~~~~LP~~NatgnwvKv~QRvPVrI~l  267 (310)
T PRK10559        197 MEETKLEGVRPGYRAEITP---LG-SNR--VLKGTVDSVA-AGVTNASSTRDSKGMATIDSNLEWVRLAQRVPVRIRL  267 (310)
T ss_pred             ECHHHCCCCCCCCEEEEEE---EC-CCC--EEEEEEEEEC-CCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEEEEEE
T ss_conf             0522125389999799999---17-998--8999999887-4446632367523389968988748677874179997


No 41 
>PRK08190 bifunctional enoyl-CoA hydratase/phosphate acetyltransferase; Validated
Probab=27.60  E-value=49  Score=14.66  Aligned_cols=36  Identities=25%  Similarity=0.384  Sum_probs=27.4

Q ss_pred             CCCCCCEEEEEEEEECCCC-CCCEEEEEEEEEECCCC
Q ss_conf             7378998999999835887-74012345354313666
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDK-SRIQAYEGVCIARSGRG   58 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k-~R~Q~F~GvvI~~~~~G   58 (141)
                      ..++||+|.+++.+.|-.. .|.-.|.-.|....+.-
T Consensus        95 PV~iGDtvtatVtV~ek~~~k~~V~L~~~~~nq~G~~  131 (465)
T PRK08190         95 PVRIGDTITVTVTVREKRPEKRIVLLDCRCTNQDGEV  131 (465)
T ss_pred             CCCCCCEEEEEEEEEEECCCCCEEEEEEEEECCCCCE
T ss_conf             8889998999999999717889899997999069979


No 42 
>pfam06940 DUF1287 Domain of unknown function (DUF1287). This family consists of several hypothetical bacterial proteins of around 200 residues in length. The function of this family is unknown. This family is related to pfam00877.
Probab=27.02  E-value=50  Score=14.59  Aligned_cols=49  Identities=16%  Similarity=0.374  Sum_probs=32.3

Q ss_pred             CCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEE
Q ss_conf             973789989999998358877401234535431366664338863003561302899
Q gi|254780715|r   22 PKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYGEGMNRLF   78 (141)
Q Consensus        22 P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~f   78 (141)
                      -++.|||+|.-  .. .|+-    .--|+|..+++.. +.-+.+.|+-.|.--|-+.
T Consensus       105 ~~yqpGDIV~w--~l-~~~~----~HIgIVsd~~~~~-g~p~viHNig~g~~eeD~L  153 (164)
T pfam06940       105 EDYQPGDIVTW--ML-PGNL----PHIGIVSDRRRAD-GVPLVIHNIGAGPREEDIL  153 (164)
T ss_pred             HHCCCCCEEEE--EC-CCCC----CEEEEEECCCCCC-CCEEEEEECCCCCCHHHHH
T ss_conf             66689787999--77-9997----4589983466888-9858999478885214443


No 43 
>TIGR00008 infA translation initiation factor IF-1; InterPro: IPR004368 This family consists of translation initiation factor IF-1 as found in bacteria and chloroplasts. This protein, about 70 residues in length, consists largely of an S1 RNA binding domain (IPR003029 from INTERPRO).; GO: 0003743 translation initiation factor activity, 0006413 translational initiation.
Probab=26.90  E-value=47  Score=14.76  Aligned_cols=26  Identities=23%  Similarity=0.298  Sum_probs=19.2

Q ss_pred             CCCCCCCCCEEEEEEEEECCCCCCCE
Q ss_conf             98973789989999998358877401
Q gi|254780715|r   20 SLPKFSPGDTLCVKTIITEGDKSRIQ   45 (141)
Q Consensus        20 ~~P~f~~GD~v~V~~~i~eg~k~R~Q   45 (141)
                      +.-.+-|||-|.|.+.-.+-.++|+-
T Consensus        41 ~~iriLpGD~V~ve~SpYdl~~GRI~   66 (69)
T TIGR00008        41 NYIRILPGDKVKVELSPYDLTRGRII   66 (69)
T ss_pred             CEEEECCCCEEEEEECCCCCCCCCEE
T ss_conf             51755479878998713648775087


No 44 
>COG0231 Efp Translation elongation factor P (EF-P)/translation initiation factor 5A (eIF-5A) [Translation, ribosomal structure and biogenesis]
Probab=26.45  E-value=51  Score=14.53  Aligned_cols=52  Identities=12%  Similarity=0.279  Sum_probs=31.9

Q ss_pred             CCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCC-CCEEEEEEECCCCCCEEEEECC
Q ss_conf             97378998999999835887740123453543136666-4338863003561302899910
Q gi|254780715|r   22 PKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGI-NKNFTVRKISYGEGMNRLFPLY   81 (141)
Q Consensus        22 P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~-~stftvRki~~g~GVE~~fpl~   81 (141)
                      -+|++|.++..     +|...++.-++=   .+-|+|- -..+-++++..|.-+|.+|+--
T Consensus         7 ~~lr~G~~i~~-----dg~~~~V~~~~~---~KpGKg~a~vrvk~k~l~tG~~~e~~f~~~   59 (131)
T COG0231           7 SELRKGLYIVI-----DGEPYVVVEISH---VKPGKGGAFVRVKLKNLFTGKKVEKTFKAD   59 (131)
T ss_pred             HHCCCCCEEEE-----CCEEEEEEEEEE---CCCCCCCCEEEEEEEECCCCCEEEEEECCC
T ss_conf             77268779998-----996899999787---269999857999999845898999997578


No 45 
>cd05685 S1_Tex S1_Tex: The C-terminal S1 domain of a transcription accessory factor called Tex, which has been characterized in Bordetella pertussis and Pseudomonas aeruginosa. The tex gene is essential in Bortella pertusis and is named for its role in toxin expression. Tex has two functional domains, an N-terminal domain homologous to the Escherichia coli maltose repression protein, which is a poorly defined transcriptional factor, and a C-terminal S1 RNA-binding domain. Tex is found in prokaryotes, eukaryotes, and archaea.
Probab=26.20  E-value=52  Score=14.50  Aligned_cols=25  Identities=32%  Similarity=0.405  Sum_probs=16.7

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCE
Q ss_conf             8973789989999998358877401
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQ   45 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q   45 (141)
                      ...|++||.|++.+.-.+-.+.|+.
T Consensus        42 ~~~~~vGd~v~~kVi~id~e~~ri~   66 (68)
T cd05685          42 SDVVSVGDIVEVKVISIDEERGRIS   66 (68)
T ss_pred             HHCCCCCCEEEEEEEEEECCCCEEE
T ss_conf             6857999999999999989999887


No 46 
>TIGR02346 chap_CCT_theta T-complex protein 1, theta subunit; InterPro: IPR012721    Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT theta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=25.79  E-value=53  Score=14.45  Aligned_cols=56  Identities=21%  Similarity=0.400  Sum_probs=39.9

Q ss_pred             CHHHHHHHHHHHHHHHC----CCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCC
Q ss_conf             35899979999997602----79897378998999999835887740123453543136666
Q gi|254780715|r    2 NIIDELDHEEMVRIESK----RSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGI   59 (141)
Q Consensus         2 nli~~le~~~~~~~~~k----~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~   59 (141)
                      |+|.+|-.+.+-...-+    -.+|-|.+ |.||| .++--|+=...+...|+||.+.-.|.
T Consensus       170 dfL~~LvA~Ac~~v~P~~~~~GeiPyFnV-DniRV-~Ki~Ggs~~~S~v~~GmV~~reaeG~  229 (554)
T TIGR02346       170 DFLAQLVAKACITVLPKNPENGEIPYFNV-DNIRV-SKILGGSISNSEVLKGMVFKREAEGS  229 (554)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCC-CCEEE-EEECCCCCCCCEEEECCEECCCCCCC
T ss_conf             88999999887412788889886551145-60132-23207863477588511763178843


No 47 
>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=24.75  E-value=55  Score=14.33  Aligned_cols=18  Identities=22%  Similarity=0.556  Sum_probs=10.9

Q ss_pred             HCCCCCCCCCCCEEEEEE
Q ss_conf             027989737899899999
Q gi|254780715|r   17 SKRSLPKFSPGDTLCVKT   34 (141)
Q Consensus        17 ~k~~~P~f~~GD~v~V~~   34 (141)
                      .-|-+-+++|||.|++.+
T Consensus       219 TPKG~~dv~pGD~v~~ei  236 (249)
T TIGR02303       219 TPKGLSDVKPGDVVRLEI  236 (249)
T ss_pred             CCCCCCCCCCCCEEEEEE
T ss_conf             888752235587899977


No 48 
>TIGR01652 ATPase-Plipid phospholipid-translocating P-type ATPase, flippase; InterPro: IPR006539    These sequences represent the P-type ATPase responsible for transporting phospholipids from one leaflet of bilayer membranes to the other . These ATPases are found only in eukaryotes. ; GO: 0000287 magnesium ion binding, 0004012 phospholipid-translocating ATPase activity, 0005524 ATP binding, 0015914 phospholipid transport, 0016021 integral to membrane.
Probab=24.41  E-value=32  Score=15.78  Aligned_cols=12  Identities=33%  Similarity=0.470  Sum_probs=9.3

Q ss_pred             CCCCCCEEEEEE
Q ss_conf             737899899999
Q gi|254780715|r   23 KFSPGDTLCVKT   34 (141)
Q Consensus        23 ~f~~GD~v~V~~   34 (141)
                      +++|||+|+|+-
T Consensus       202 ~~~VGDivKv~~  213 (1249)
T TIGR01652       202 DLRVGDIVKVKK  213 (1249)
T ss_pred             EEEECCEEEECC
T ss_conf             024155789757


No 49 
>TIGR01511 ATPase-IB1_Cu copper-translocating P-type ATPase; InterPro: IPR006403   ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , .  F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.   P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H^+, Na^+, K^+, Mg^2+, Ca^2+, Ag^+ and Ag^2+, Zn^2+, Co^2+, Pb^2+, Ni^2+, Cd^2+, Cu^+ and Cu^2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.   This entry represents P-type ATPases that specialise in cation and copper transport; those transporting copper (3.6.3.4 from EC) have been classified as belonging to the IB subfamily , , . These proteins are involved in a variety of processes in both prokaryotes and eukaryotes. Some of these P-ATPases import copper into cells, such as in Arabidopsis sp., which require copper to create functional hormone receptors for ethylene signalling. Other P-ATPases are involved in copper export out of cells, such as occurs with the efflux of hepatic copper into the bile in eukaryotes. In bacteria, some of these P-ATPases play a role in osmotic adaptation. Certain copper ATPases have been implicated in both Wilson and Menkes diseases .   More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0004008 copper-exporting ATPase activity, 0005524 ATP binding, 0046872 metal ion binding, 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0016020 membrane.
Probab=23.68  E-value=24  Score=16.64  Aligned_cols=31  Identities=26%  Similarity=0.492  Sum_probs=21.4

Q ss_pred             CCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEEC
Q ss_conf             27989737899899999983588774012345354313
Q gi|254780715|r   18 KRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARS   55 (141)
Q Consensus        18 k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~   55 (141)
                      .-++-++++||+|+|    ..|.|-   +-.|++|.=+
T Consensus        88 ~v~v~~l~~GD~~~V----~pG~k~---PvDG~v~~G~  118 (545)
T TIGR01511        88 DVPVAELQPGDIVKV----LPGEKI---PVDGTVIEGE  118 (545)
T ss_pred             CCCHHHCCCCCEEEE----CCCCCC---CCCCEEECCC
T ss_conf             723644188888997----578956---4040785132


No 50 
>TIGR03630 arch_S17P archaeal ribosomal protein S17P. This model describes exclusively the archaeal ribosomal protein S17P. It excludes homologous ribosomal proteins S11 from eukaryotes and S17 from bacteria.
Probab=23.44  E-value=58  Score=14.17  Aligned_cols=21  Identities=38%  Similarity=0.534  Sum_probs=16.1

Q ss_pred             CCEEEEEEEEEECCCCCCCEEEEE
Q ss_conf             401234535431366664338863
Q gi|254780715|r   43 RIQAYEGVCIARSGRGINKNFTVR   66 (141)
Q Consensus        43 R~Q~F~GvvI~~~~~G~~stftvR   66 (141)
                      |=|.|+|+|++-+   ++.|+++.
T Consensus        26 rGril~G~VvS~K---m~KTvvV~   46 (102)
T TIGR03630        26 RGQILEGVVVSDK---MNKTVVVE   46 (102)
T ss_pred             EEEEEEEEEEECC---CCCEEEEE
T ss_conf             6789999999787---99639999


No 51 
>TIGR02278 PaaN-DH phenylacetic acid degradation protein paaN; InterPro: IPR011966    This enzyme is proposed to act in the ring-opening step of phenylacetic acid degradation  which follows ligation of the acid with coenzyme A (by PaaF) and hydroxylation by a multicomponent non-heme iron hydroxylase complex (PaaGHIJK). Gene symbols have been standardised in . This enzyme is related to aldehyde dehydrogenases..
Probab=23.40  E-value=58  Score=14.17  Aligned_cols=28  Identities=18%  Similarity=0.380  Sum_probs=19.8

Q ss_pred             CCCCCCCCEEEEEEEEECCCCCCCEEEE
Q ss_conf             8973789989999998358877401234
Q gi|254780715|r   21 LPKFSPGDTLCVKTIITEGDKSRIQAYE   48 (141)
Q Consensus        21 ~P~f~~GD~v~V~~~i~eg~k~R~Q~F~   48 (141)
                      |-...+||+|+|.+.++.-...+...++
T Consensus       631 l~PV~~dDsi~V~LT~Krk~p~~~~~~g  658 (690)
T TIGR02278       631 LEPVKPDDSIQVRLTVKRKTPRKEKEYG  658 (690)
T ss_pred             CCCCCCCCCEEEEEEEEECCCCCCCCCC
T ss_conf             3567998845899842203777786667


No 52 
>TIGR01073 pcrA ATP-dependent DNA helicase PcrA; InterPro: IPR005751    The DNA helicase PcrA is found mainly in Gram-positive bacteria and belongs to a superfamily of helicases, together with Rep and UvrD helicases from Escherichia coli. The action of the 3'5' bacterial DNA helicase is based upon two separate but coupled activities, ssDNA translocation and duplex destabilisation, and is driven by energy derived from the continuous ATP-binding and hydrolysis events that take place in the active-site cleft. The resulting conformational changes that accompany these events underpin the coupling process and allow the helicase to translocate along the DNA, destabilising the duplex and separating the two strands in an active process .; GO: 0004003 ATP-dependent DNA helicase activity, 0006268 DNA unwinding during replication, 0005737 cytoplasm.
Probab=23.14  E-value=59  Score=14.14  Aligned_cols=44  Identities=20%  Similarity=0.449  Sum_probs=34.7

Q ss_pred             CCCCC-CEEEEEEEEEECCCCCCCEEEEEEECCC-CCCEEEEECCCCC
Q ss_conf             88774-0123453543136666433886300356-1302899910786
Q gi|254780715|r   39 GDKSR-IQAYEGVCIARSGRGINKNFTVRKISYG-EGMNRLFPLYSPM   84 (141)
Q Consensus        39 g~k~R-~Q~F~GvvI~~~~~G~~stftvRki~~g-~GVE~~fpl~SP~   84 (141)
                      |+|-. -+.=.|+|++++|+|-++...+-  +.+ +||-+..+-|-|.
T Consensus       765 GDrv~H~~fG~GTVv~v~G~G~~~el~i~--FP~P~gvK~Ll~~FAPi  810 (811)
T TIGR01073       765 GDRVSHKKFGVGTVVSVKGKGDDAELDIA--FPSPIGVKRLLAAFAPI  810 (811)
T ss_pred             CCCCCCCCCCEEEEEEEEECCCCCCEEEE--CCCCCCHHHHCCCCCCC
T ss_conf             86103430000589888505557512542--67885412011334889


No 53 
>pfam07653 SH3_2 Variant SH3 domain. SH3 (Src homology 3) domains are often indicative of a protein involved in signal transduction related to cytoskeletal organisation. First described in the Src cytoplasmic tyrosine kinase. The structure is a partly opened beta barrel.
Probab=22.99  E-value=60  Score=14.12  Aligned_cols=15  Identities=20%  Similarity=0.113  Sum_probs=11.5

Q ss_pred             CCCCCCCEEEEEEEE
Q ss_conf             973789989999998
Q gi|254780715|r   22 PKFSPGDTLCVKTII   36 (141)
Q Consensus        22 P~f~~GD~v~V~~~i   36 (141)
                      -.|+.||+|.|.-..
T Consensus        16 L~f~~Gdii~v~~~~   30 (53)
T pfam07653        16 LTLKKGDVVKVLDKD   30 (53)
T ss_pred             CCCCCCCEEEEEEEC
T ss_conf             789899999999954


No 54 
>PRK13198 ureB urease subunit beta; Reviewed
Probab=22.96  E-value=60  Score=14.11  Aligned_cols=41  Identities=24%  Similarity=0.494  Sum_probs=28.7

Q ss_pred             HCCCCC-----CCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCC
Q ss_conf             027989-----737899899999983588774012345354313666
Q gi|254780715|r   17 SKRSLP-----KFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRG   58 (141)
Q Consensus        17 ~k~~~P-----~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G   58 (141)
                      ...++|     .|-|||+..|.+ |.-|.+.++.-|-|+|=.--+.|
T Consensus        87 ~RLdIPAGtavRFEPG~~k~V~L-V~~gG~r~v~GfngLv~Gw~g~~  132 (158)
T PRK13198         87 KRLNISSTTAIRFEPGDETEVPL-IPFGGKQTLYGFNNLVDGWTGEG  132 (158)
T ss_pred             CCCCCCCCCEEEECCCCEEEEEE-EECCCCEEEEECCCCCCCCCCCC
T ss_conf             53176787737528898479999-98078458982585323666886


No 55 
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=22.39  E-value=61  Score=14.04  Aligned_cols=25  Identities=20%  Similarity=0.473  Sum_probs=11.6

Q ss_pred             CCCCCEEEEEEEEECCCCCCCEEEEEEEEEEC
Q ss_conf             37899899999983588774012345354313
Q gi|254780715|r   24 FSPGDTLCVKTIITEGDKSRIQAYEGVCIARS   55 (141)
Q Consensus        24 f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~   55 (141)
                      |.+||.|+|.    +|.   .+-|+|+++..+
T Consensus       110 ~~~Gd~V~I~----~GP---f~g~~g~v~~~~  134 (162)
T PRK09014        110 PKPGDKVIIT----EGA---FEGIQAIYTEPD  134 (162)
T ss_pred             CCCCCEEEEE----ECC---CCCCEEEEEEEC
T ss_conf             9999999994----379---998089999886


No 56 
>cd05708 S1_Rrp5_repeat_sc12 S1_Rrp5_repeat_sc12: Rrp5 is a trans-acting factor important for biogenesis of both the 40S and 60S eukaryotic ribosomal subunits. Rrp5 has two distinct regions, an N-terminal region containing tandemly repeated S1 RNA-binding domains (12 S1 repeats in Saccharomyces cerevisiae Rrp5 and 14 S1 repeats in Homo sapiens Rrp5) and a C-terminal region containing tetratricopeptide repeat (TPR) motifs thought to be involved in protein-protein interactions.  Mutational studies have shown that each region represents a specific functional domain. Deletions within the S1-containing region inhibit pre-rRNA processing at either site A3 or A2, whereas deletions within the TPR region confer an inability to support cleavage of A0-A2. This CD includes S. cerevisiae S1 repeat 12 (sc12). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=21.98  E-value=62  Score=13.99  Aligned_cols=22  Identities=32%  Similarity=0.534  Sum_probs=14.8

Q ss_pred             CCCCCCEEEEEEEEECCCCCCC
Q ss_conf             7378998999999835887740
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRI   44 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~   44 (141)
                      .|++||.|+|.+.-.+..+.|+
T Consensus        47 ~~~~Gd~V~vkVl~iD~e~~rI   68 (77)
T cd05708          47 LFRVGDKVRAKVLKIDAEKKRI   68 (77)
T ss_pred             HCCCCCEEEEEEEEEECCCCEE
T ss_conf             1689999999999998999999


No 57 
>PRK03598 hypothetical protein; Provisional
Probab=21.82  E-value=63  Score=13.97  Aligned_cols=45  Identities=24%  Similarity=0.251  Sum_probs=30.1

Q ss_pred             CCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCCCCCEEEEEEECCC
Q ss_conf             79897378998999999835887740123453543136666433886300356
Q gi|254780715|r   19 RSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRGINKNFTVRKISYG   71 (141)
Q Consensus        19 ~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G~~stftvRki~~g   71 (141)
                      .+++.+++|+.+.|++.-..+     +.|.|.|-.+.-   .+.||-+++..+
T Consensus       249 ~~i~~v~~Gq~v~i~~da~p~-----~~f~G~V~~Isp---~a~~tp~~~~t~  293 (331)
T PRK03598        249 RNLGQAQPGRKVLVYTDGRPD-----KPYHGQIGFVSP---TAEFTPKTVETP  293 (331)
T ss_pred             HHHHHCCCCCEEEEEEECCCC-----CEEEEEEEEECC---CCCCCCCCCCCC
T ss_conf             999528899989999946999-----689999999856---443678755566


No 58 
>cd06201 SiR_like2 Cytochrome p450- like alpha subunits of E. coli sulfite reductase (SiR) multimerize with beta subunits to catalyze the NADPH dependent reduction of sulfite to sulfide.  Beta subunits have an Fe4S4 cluster and a siroheme, while the alpha subunits (cysJ gene) are of the cytochrome p450 (CyPor) family having FAD and FMN as prosthetic groups and utilizing NADPH.  Cypor (including cyt -450 reductase, nitric oxide synthase, and methionine synthase reductase) are ferredoxin reductase (FNR)-like proteins with an additional N-terminal  FMN domain and a connecting sub-domain inserted within the flavin binding portion of the FNR-like domain. The connecting domain orients the N-terminal FMN domain with the C-terminal FNR domain. NADPH cytochrome p450 reductase (CYPOR) serves as an electron donor in several oxygenase systems and is a component of nitric oxide synthases and methionine synthase reductases. CYPOR transfers two electrons from NADPH to the heme of cytochrome p450 via F
Probab=21.78  E-value=63  Score=13.96  Aligned_cols=56  Identities=20%  Similarity=0.530  Sum_probs=33.3

Q ss_pred             CCCCCCCCCCEEEEEEEEECCC-CCCC--------EEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEE
Q ss_conf             7989737899899999983588-7740--------1234535431366664338863003561302899
Q gi|254780715|r   19 RSLPKFSPGDTLCVKTIITEGD-KSRI--------QAYEGVCIARSGRGINKNFTVRKISYGEGMNRLF   78 (141)
Q Consensus        19 ~~~P~f~~GD~v~V~~~i~eg~-k~R~--------Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~f   78 (141)
                      ..+|.|.+||.+.|.   .++. ..|.        .-+.-+|+.++..|+.|+++-. .--|--|.-.+
T Consensus        79 ~~~p~f~aGDLl~i~---Pp~~~~~R~YSiAs~~~dg~~~l~Vr~~~~GlcS~~L~~-L~~Gd~i~~~i  143 (289)
T cd06201          79 KGLPSFEAGDLLGIL---PPGSDVPRFYSLASSSSDGFLEICVRKHPGGLCSGYLHG-LKPGDTIKAFI  143 (289)
T ss_pred             CCCCCCCCCCEEEEC---CCCCCCCCCCCCCCCCCCCEEEEEEEECCCCCCHHHHHC-CCCCCEEEEEE
T ss_conf             668888877732334---899998752240436999979999996799743677715-99989899998


No 59 
>PRK13980 NAD synthetase; Provisional
Probab=21.69  E-value=15  Score=17.89  Aligned_cols=41  Identities=20%  Similarity=0.312  Sum_probs=31.6

Q ss_pred             EEEEEEEEEECCCCCCCEEEEEEECCCCCCEEEEECCCCCEE
Q ss_conf             123453543136666433886300356130289991078610
Q gi|254780715|r   45 QAYEGVCIARSGRGINKNFTVRKISYGEGMNRLFPLYSPMIQ   86 (141)
Q Consensus        45 Q~F~GvvI~~~~~G~~stftvRki~~g~GVE~~fpl~SP~i~   86 (141)
                      .-|.|+||+.. .|++|+.+.-=.+.-.|-|+++-+..|...
T Consensus        26 ~g~kg~VlGlS-GGIDSavva~La~~Alg~~~v~~v~mP~~~   66 (264)
T PRK13980         26 AGFKGVVLGLS-GGIDSAVVAYLAVKALGKENVLALLMPYRV   66 (264)
T ss_pred             HCCCEEEEECC-CCHHHHHHHHHHHHHCCCCCEEEEECCCCC
T ss_conf             09980999798-688899999999985496606899898999


No 60 
>TIGR01700 PNPH purine nucleoside phosphorylase I, inosine and guanosine-specific; InterPro: IPR011270   This entry represents a family of bacterial and metazoan purine phosphorylases acting primarily on inosine and guanosine and not acting on adenosine. PNP-I refers to the nomenclature from Bacillus stearothermophilus  where PHP-II refers to the nucleotidase acting on adenosine as the primary substrate. The bacterial enzymes (PUNA) are typified by the Bacillus PupG protein  which is involved in the metabolism of nucleosides as a carbon source. Several metazoan enzymes (PNPH) are well characterised including the human  and bovine  enzymes which have been crystallised. ; GO: 0004731 purine-nucleoside phosphorylase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=21.60  E-value=55  Score=14.33  Aligned_cols=13  Identities=23%  Similarity=0.531  Sum_probs=7.0

Q ss_pred             CCCCCCCCEEEEE
Q ss_conf             8973789989999
Q gi|254780715|r   21 LPKFSPGDTLCVK   33 (141)
Q Consensus        21 ~P~f~~GD~v~V~   33 (141)
                      .|+|++||++-|.
T Consensus        97 N~~F~~GDlmlI~  109 (259)
T TIGR01700        97 NTEFKVGDLMLIR  109 (259)
T ss_pred             CCCCCCCCEEEEC
T ss_conf             7776677778971


No 61 
>cd05790 S1_Rrp40 S1_Rrp40: Rrp40 S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Rrp4 protein is a subunit of the exosome complex. The exosome plays a central role in 3' to 5' RNA processing and degradation in eukarytes and archaea. Its functions include the removal of incorrectly processed RNA and the maintenance of proper levels of mRNA, rRNA and a number of small RNA species. In Saccharomyces cerevisiae, the exosome includes nine core components, six of which are homologous to bacterial RNase PH. These form a hexameric ring structure. The other three subunits (RrP4, Rrp40, and Csl4) contain an S1 RNA binding domain and are part of the "S1 pore structure".
Probab=21.57  E-value=64  Score=13.94  Aligned_cols=34  Identities=21%  Similarity=0.435  Sum_probs=21.8

Q ss_pred             HCCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEE
Q ss_conf             02798973789989999998358877401234535431
Q gi|254780715|r   17 SKRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIAR   54 (141)
Q Consensus        17 ~k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~   54 (141)
                      .|++.|.+++||.|=-  ++...++.-  --|=.|+.-
T Consensus        43 TKknrP~L~~GdlVYa--RV~~a~~~~--e~EL~Cvd~   76 (86)
T cd05790          43 TKRNRPNLNVGDLVYA--RVVKANRDM--EPELSCVDS   76 (86)
T ss_pred             CCCCCCCCCCCCEEEE--EEEECCCCC--CEEEEEECC
T ss_conf             6556887887889999--998748999--704898888


No 62 
>pfam11302 DUF3104 Protein of unknown function (DUF3104). This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=21.49  E-value=64  Score=13.93  Aligned_cols=51  Identities=27%  Similarity=0.417  Sum_probs=34.5

Q ss_pred             CCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEECCCC----CCCEEEEEEECCCC
Q ss_conf             9737899899999983588774012345354313666----64338863003561
Q gi|254780715|r   22 PKFSPGDTLCVKTIITEGDKSRIQAYEGVCIARSGRG----INKNFTVRKISYGE   72 (141)
Q Consensus        22 P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~~~~G----~~stftvRki~~g~   72 (141)
                      ..+++||+|-|.-.-..+.+....-.-|-||...+..    ..+-|-|-++=.|+
T Consensus         4 L~Vk~Gd~ViV~~~~~~~~~~~~dWWmg~Vi~~~ggar~P~~~tlFQVadVDtG~   58 (75)
T pfam11302         4 LSVKPGDTVIVEANQENGQKDSKDWWMGQVIHCEGGARDPRVPTLFQVADVDTGE   58 (75)
T ss_pred             EEECCCCEEEEECCCCCCCCCCCCCEEEEEEECCCCCCCCCCCCCEEEEECCCCC
T ss_conf             3627998999914844577789981789999816854489998417999837993


No 63 
>PRK12442 translation initiation factor IF-1; Reviewed
Probab=21.29  E-value=64  Score=13.90  Aligned_cols=10  Identities=20%  Similarity=0.411  Sum_probs=3.8

Q ss_pred             CCCCEEEEEE
Q ss_conf             7899899999
Q gi|254780715|r   25 SPGDTLCVKT   34 (141)
Q Consensus        25 ~~GD~v~V~~   34 (141)
                      -+||.|.|.+
T Consensus        48 l~GD~V~VEl   57 (87)
T PRK12442         48 LAGDRVTLEL   57 (87)
T ss_pred             CCCCEEEEEE
T ss_conf             6899899998


No 64 
>pfam12148 DUF3590 Protein of unknown function (DUF3590). This domain is found in eukaryotes, and is typically between 83 and 97 amino acids in length. It is found in association with pfam00097, pfam02182, pfam00628, pfam00240. There are two conserved sequence motifs: RAR and NYN. The domain is part of the protein NIRF which has zinc finger and ubiquitinating domains. The function of this domain is likely to be mainly structural, however this has not been confirmed.
Probab=21.11  E-value=46  Score=14.81  Aligned_cols=16  Identities=19%  Similarity=0.221  Sum_probs=9.3

Q ss_pred             CCCCCCEEEEEEEEEC
Q ss_conf             7378998999999835
Q gi|254780715|r   23 KFSPGDTLCVKTIITE   38 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~e   38 (141)
                      ++.+||+|.|.|.+.+
T Consensus        65 ~L~vG~~VmvNYN~d~   80 (85)
T pfam12148        65 ELEVGQVVMVNYNPDE   80 (85)
T ss_pred             HCCCCCEEEEECCCCC
T ss_conf             8775649999758798


No 65 
>cd05688 S1_RPS1_repeat_ec3 S1_RPS1_repeat_ec3: Ribosomal protein S1 (RPS1) domain. RPS1 is a component of the small ribosomal subunit thought to be involved in the recognition and binding of mRNA's during translation initiation. The bacterial RPS1 domain architecture consists of 4-6 tandem S1 domains. In some bacteria, the tandem S1 array is located C-terminal to a 4-hydroxy-3-methylbut-2-enyl diphosphate reductase (HMBPP reductase) domain. While RPS1 is found primarily in bacteria, proteins with tandem RPS1-like domains have been identified in plants and humans, however these lack the N-terminal HMBPP reductase domain. This CD includes S1 repeat 3 (ec3) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=21.09  E-value=65  Score=13.88  Aligned_cols=23  Identities=26%  Similarity=0.439  Sum_probs=15.2

Q ss_pred             CCCCCCEEEEEEEEECCCCCCCE
Q ss_conf             73789989999998358877401
Q gi|254780715|r   23 KFSPGDTLCVKTIITEGDKSRIQ   45 (141)
Q Consensus        23 ~f~~GD~v~V~~~i~eg~k~R~Q   45 (141)
                      .|++||.|.+.+.-.+..+.|++
T Consensus        44 ~~k~Gd~v~~kVi~iD~~k~rIs   66 (68)
T cd05688          44 VVNVGDEVEVKVLKIDKERKRIS   66 (68)
T ss_pred             HCCCCCEEEEEEEEEECCCCEEC
T ss_conf             14799999999999999979864


No 66 
>TIGR03516 ppisom_GldI peptidyl-prolyl isomerase, gliding motility-associated. Members of this protein family are exclusive to the Bacteroidetes phylum (previously Cytophaga-Flavobacteria-Bacteroides). GldI is a FKBP-type peptidyl-prolyl cis-trans isomerase (pfam00254) linked to a type of rapid surface gliding motility found in certain Bacteroidetes, such as Flavobacterium johnsoniae and Cytophaga hutchinsonii. Knockout of this gene abolishes the gliding phenotype. Gliding motility appears closely linked to chitin utilization in the model species Flavobacterium johnsoniae. This family is only found in Bacteroidetes containing the suite of genes proposed to confer the gliding motility phenotype.
Probab=20.79  E-value=66  Score=13.84  Aligned_cols=69  Identities=17%  Similarity=0.129  Sum_probs=37.4

Q ss_pred             CCCCCEEEEEEEEECCCCC-------C--CEEEEE--EEEE-----E--CCCCCCCEEEEEEEC-CC-CCCEEEEECCCC
Q ss_conf             3789989999998358877-------4--012345--3543-----1--366664338863003-56-130289991078
Q gi|254780715|r   24 FSPGDTLCVKTIITEGDKS-------R--IQAYEG--VCIA-----R--SGRGINKNFTVRKIS-YG-EGMNRLFPLYSP   83 (141)
Q Consensus        24 f~~GD~v~V~~~i~eg~k~-------R--~Q~F~G--vvI~-----~--~~~G~~stftvRki~-~g-~GVE~~fpl~SP   83 (141)
                      =..||+|.|+|.+..-+.+       +  .+...|  -+|.     .  =..|-..+|.+=-.. +| .|-.-.+|-+||
T Consensus        86 P~~gd~V~~~Y~~~~ldG~~~~ss~~~gp~~f~v~~~~vi~G~~egl~lm~~Ge~~~~~iPs~LaYG~~G~~~~I~pn~~  165 (177)
T TIGR03516        86 PEFGDLVTFEYDIRALDGDVIYSEEELGPQTYKVDQQDLFSGLRDGLKLMKEGETATFLFPSHKAYGYYGDQNKIGPNLP  165 (177)
T ss_pred             CCCCCEEEEEEEEEECCCCEEEEECCCCCEEEEECCCCCCHHHHHHHHHCCCCCEEEEEECCHHCCCCCCCCCCCCCCCC
T ss_conf             99999899999999768988874034686569855656464899999855789789999573004466788995496985


Q ss_pred             CEEEEEEEE
Q ss_conf             610122200
Q gi|254780715|r   84 MIQDITVIR   92 (141)
Q Consensus        84 ~i~~Iev~r   92 (141)
                      ++-.|+++.
T Consensus       166 Lif~v~Ll~  174 (177)
T TIGR03516       166 IISTVTLLN  174 (177)
T ss_pred             EEEEEEEEE
T ss_conf             999999973


No 67 
>pfam07154 DUF1392 Protein of unknown function (DUF1392). This family consists of several hypothetical cyanobacterial proteins of around 150 residues in length which seem to be specific to Anabaena species. The function of this family is unknown.
Probab=20.61  E-value=67  Score=13.81  Aligned_cols=34  Identities=29%  Similarity=0.514  Sum_probs=23.2

Q ss_pred             CCCCCCCCCCCEEEEEEEEECCCCCCCEEEEEEEEEE
Q ss_conf             2798973789989999998358877401234535431
Q gi|254780715|r   18 KRSLPKFSPGDTLCVKTIITEGDKSRIQAYEGVCIAR   54 (141)
Q Consensus        18 k~~~P~f~~GD~v~V~~~i~eg~k~R~Q~F~GvvI~~   54 (141)
                      ..+-|.|.-||.|.+... .+|.|.|+  ..|+.+-.
T Consensus        82 tv~kp~F~LGd~V~~~f~-~~~pkqRl--IlGv~lv~  115 (150)
T pfam07154        82 TLSKPAFALGDRVLLRFA-SHGPKQRL--ILGVSLVN  115 (150)
T ss_pred             ECCCCCEECCCEEEEEEC-CCCCCEEE--EEEEEEEC
T ss_conf             306872224778999845-99984579--99899862


No 68 
>KOG3901 consensus
Probab=20.52  E-value=31  Score=15.93  Aligned_cols=27  Identities=33%  Similarity=0.454  Sum_probs=21.9

Q ss_pred             ECCHHH-HHHHHHHCCCCCCEEEHHHHC
Q ss_conf             002046-787687508884102201200
Q gi|254780715|r   92 RRGKVR-RSKLYYLQDLRGKAARIKENT  118 (141)
Q Consensus        92 r~gkvR-rakLyYLR~~~gk~arik~~~  118 (141)
                      ++||++ -.=+|+||.-+.|.+|+++-.
T Consensus        56 ~rgk~~veD~~f~lRkDpkK~~Rv~eLL   83 (109)
T KOG3901          56 KRGKVKVEDFKFLLRKDPKKLGRVKELL   83 (109)
T ss_pred             CCCCEEHHHHHHHHHHCHHHHHHHHHHH
T ss_conf             4675008889999970858886899999


Done!