Query         gi|254780913|ref|YP_003065326.1| cold shock protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 78
No_of_seqs    112 out of 2159
Neff          6.0 
Searched_HMMs 39220
Date          Mon May 30 00:39:50 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780913.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK09937 stationary phase/star  99.9 1.2E-25   3E-30  164.2   8.4   72    2-78      1-72  (74)
  2 COG1278 CspC Cold shock protei  99.9 5.7E-25 1.5E-29  160.3   7.7   67    2-73      1-67  (67)
  3 PRK10354 major cold shock prot  99.9 3.9E-24 9.9E-29  155.7   7.7   67    2-73      4-70  (70)
  4 PRK10943 cold shock-like prote  99.9 4.2E-24 1.1E-28  155.5   7.7   67    2-73      3-69  (69)
  5 PRK09890 cold shock protein Cs  99.9 4.2E-24 1.1E-28  155.5   7.2   67    2-73      4-70  (70)
  6 PRK09507 cspE cold shock prote  99.9 7.5E-24 1.9E-28  154.1   7.8   67    2-73      3-69  (69)
  7 LOAD_cold consensus             99.9 2.2E-23 5.6E-28  151.5   8.0   66    2-72      1-66  (67)
  8 pfam00313 CSD 'Cold-shock' DNA  99.9 1.6E-22 4.1E-27  146.6   8.4   66    3-73      1-66  (66)
  9 smart00357 CSP Cold shock prot  99.8 1.7E-20 4.3E-25  135.4   7.7   64    4-73      1-64  (64)
 10 cd04458 CSP_CDS Cold-Shock Pro  99.8 2.7E-20 6.9E-25  134.2   7.7   65    3-72      1-65  (65)
 11 TIGR02381 cspD cold shock doma  99.7 1.3E-16 3.4E-21  113.6   6.9   67    2-73      1-67  (68)
 12 KOG3070 consensus               99.5   2E-14   5E-19  101.5   4.2   64    3-71     57-124 (235)
 13 pfam08206 OB_RNB Ribonuclease   97.8 4.9E-05 1.2E-09   49.1   5.1   53   12-72      6-58  (58)
 14 PRK11642 exoribonuclease R; Pr  97.7 9.9E-05 2.5E-09   47.4   6.0   65    3-77     85-149 (813)
 15 PRK05054 exoribonuclease II; P  96.9  0.0022 5.7E-08   39.8   5.6   60    3-75     22-81  (644)
 16 TIGR02063 RNase_R ribonuclease  96.3  0.0084 2.1E-07   36.6   5.1   67    4-77     76-149 (755)
 17 pfam07497 Rho_RNA_bind Rho ter  96.0  0.0087 2.2E-07   36.5   3.8   58   13-73     11-71  (78)
 18 cd04459 Rho_CSD Rho_CSD: Rho p  95.7   0.013 3.4E-07   35.4   3.9   52   13-67      9-62  (68)
 19 PRK09376 rho transcription ter  94.7   0.036 9.1E-07   33.1   3.5   59   13-74     60-121 (416)
 20 PRK08059 general stress protei  94.3    0.13 3.3E-06   29.9   5.7   69    3-77     10-82  (119)
 21 TIGR02062 RNase_B exoribonucle  92.9    0.23 5.9E-06   28.6   4.9   59    3-74     22-80  (664)
 22 TIGR00717 rpsA ribosomal prote  92.3    0.55 1.4E-05   26.4   6.2   70    2-76    203-276 (534)
 23 PRK12608 transcription termina  92.2    0.18 4.6E-06   29.2   3.7   56   13-73     26-83  (379)
 24 PRK07400 30S ribosomal protein  91.0    0.73 1.9E-05   25.7   5.8   66    3-75    200-269 (314)
 25 COG1158 Rho Transcription term  90.2    0.27 6.9E-06   28.2   2.9   51   13-67     62-115 (422)
 26 cd04472 S1_PNPase S1_PNPase: P  90.0    0.86 2.2E-05   25.4   5.4   57    2-64      3-63  (68)
 27 PRK12678 transcription termina  90.0     0.2 5.2E-06   28.9   2.1   48    5-58    293-340 (667)
 28 cd05692 S1_RPS1_repeat_hs4 S1_  88.8     1.3 3.3E-05   24.4   5.5   57    2-64      3-63  (69)
 29 pfam00575 S1 S1 RNA binding do  88.2     1.1 2.7E-05   24.9   4.8   55    2-62      7-65  (74)
 30 cd00164 S1_like S1_like: Ribos  87.9     1.3 3.3E-05   24.4   5.1   52    4-61      2-57  (65)
 31 cd05691 S1_RPS1_repeat_ec6 S1_  87.7     1.8 4.5E-05   23.6   5.6   66    2-73      3-72  (73)
 32 COG1098 VacB Predicted RNA bin  87.1    0.68 1.7E-05   25.9   3.3   57   15-76     18-79  (129)
 33 cd04465 S1_RPS1_repeat_ec2_hs2  86.9     1.3 3.4E-05   24.3   4.6   52    3-62      4-58  (67)
 34 COG0557 VacB Exoribonuclease R  86.6    0.86 2.2E-05   25.4   3.5   65    4-76     71-136 (706)
 35 TIGR00358 3_prime_RNase VacB a  86.3    0.39 9.9E-06   27.3   1.7   64    3-75     19-83  (684)
 36 PRK00087 4-hydroxy-3-methylbut  84.9     2.6 6.6E-05   22.7   5.3   63    4-73    570-637 (670)
 37 PRK07252 hypothetical protein;  84.8     1.6 4.2E-05   23.8   4.3   67    3-75      7-77  (120)
 38 PRK08582 hypothetical protein;  83.6     3.4 8.7E-05   22.0   5.5   63    3-73      9-76  (139)
 39 PRK07899 rpsA 30S ribosomal pr  83.5     3.9  0.0001   21.7   5.7   51    3-61    212-267 (484)
 40 smart00316 S1 Ribosomal protei  83.3       3 7.5E-05   22.4   5.0   54    3-62      6-63  (72)
 41 PRK11824 polynucleotide phosph  82.7     3.8 9.7E-05   21.8   5.4   58    3-66    625-686 (694)
 42 TIGR03591 polynuc_phos polyrib  82.7     4.3 0.00011   21.5   5.7   57    3-65    622-682 (684)
 43 cd05684 S1_DHX8_helicase S1_DH  82.4     4.5 0.00011   21.4   7.1   68    3-76      4-77  (79)
 44 cd04473 S1_RecJ_like S1_RecJ_l  81.6     4.8 0.00012   21.2   6.2   52    3-64     20-71  (77)
 45 cd05689 S1_RPS1_repeat_ec4 S1_  81.0     4.2 0.00011   21.5   5.1   54    3-62      7-65  (72)
 46 PRK06676 rpsA 30S ribosomal pr  80.8     3.7 9.4E-05   21.8   4.8   13   46-58    322-334 (390)
 47 PRK05807 hypothetical protein;  80.4     4.9 0.00013   21.1   5.3   60    3-71      9-73  (136)
 48 cd05686 S1_pNO40 S1_pNO40: pNO  79.9       5 0.00013   21.1   5.2   56    3-64      7-67  (73)
 49 PRK12269 bifunctional cytidyla  78.3     6.2 0.00016   20.6   6.3   33   27-59    687-724 (863)
 50 PRK13806 rpsA 30S ribosomal pr  78.0     5.6 0.00014   20.8   5.0   49    4-58    206-258 (489)
 51 cd05688 S1_RPS1_repeat_ec3 S1_  77.5     6.5 0.00017   20.4   5.9   52    3-61      5-60  (68)
 52 cd05708 S1_Rrp5_repeat_sc12 S1  76.1     7.2 0.00018   20.2   6.0   55    2-62      5-64  (77)
 53 cd05685 S1_Tex S1_Tex: The C-t  75.5     7.5 0.00019   20.1   5.9   54    2-61      3-60  (68)
 54 COG4776 Rnb Exoribonuclease II  73.8       5 0.00013   21.1   3.8   54    3-69     22-75  (645)
 55 cd05690 S1_RPS1_repeat_ec5 S1_  72.9     7.8  0.0002   20.0   4.6   52    3-61      4-61  (69)
 56 cd04453 S1_RNase_E S1_RNase_E:  69.5      10 0.00027   19.3   5.9   58    3-64     11-75  (88)
 57 cd04452 S1_IF2_alpha S1_IF2_al  68.3      11 0.00028   19.2   5.1   57    3-64      7-69  (76)
 58 cd05697 S1_Rrp5_repeat_hs5 S1_  67.3      12  0.0003   19.0   4.7   56    1-62      2-61  (69)
 59 PRK11637 hypothetical protein;  67.2      12 0.00029   19.1   4.5   51    3-54    322-373 (404)
 60 TIGR01622 SF-CC1 splicing fact  66.4     2.2 5.6E-05   23.1   0.7   10   13-22    276-285 (531)
 61 PRK03987 translation initiatio  65.0      11 0.00029   19.1   4.1   54    4-62     13-71  (262)
 62 KOG0125 consensus               63.6       3 7.8E-05   22.3   1.0   18    9-26    129-148 (376)
 63 cd05698 S1_Rrp5_repeat_hs6_sc5  56.6      18 0.00047   17.9   5.1   56    1-62      2-61  (70)
 64 COG1093 SUI2 Translation initi  56.5     8.5 0.00022   19.8   2.3   53    5-62     17-74  (269)
 65 cd05702 S1_Rrp5_repeat_hs11_sc  54.2      19 0.00047   17.9   3.7   54    3-63      4-63  (70)
 66 cd04461 S1_Rrp5_repeat_hs8_sc7  50.9      23 0.00058   17.4   5.4   54    2-61     17-74  (83)
 67 COG0539 RpsA Ribosomal protein  47.6      26 0.00066   17.1   5.0   13   46-58    236-248 (541)
 68 pfam11604 CusF_Ec Copper bindi  46.9      19 0.00048   17.9   2.7   20   42-61     39-58  (61)
 69 COG2190 NagE Phosphotransferas  45.4      28 0.00072   16.9   4.7   45    4-53     50-100 (156)
 70 KOG0149 consensus               44.9      10 0.00026   19.4   1.1   13   10-22     50-62  (247)
 71 TIGR01661 ELAV_HUD_SF ELAV/HuD  42.9     9.5 0.00024   19.5   0.7   11   11-21    392-402 (436)
 72 COG1185 Pnp Polyribonucleotide  41.2      33 0.00084   16.5   4.8   59    3-67    623-685 (692)
 73 PTZ00162 RNA polymerase II sub  41.0      33 0.00084   16.5   4.1   41   15-59     94-148 (170)
 74 PRK09838 periplasmic copper-bi  40.7      33 0.00085   16.5   6.8   69    2-72     43-112 (114)
 75 cd05707 S1_Rrp5_repeat_sc11 S1  40.5      34 0.00086   16.5   4.3   57    1-64      2-64  (68)
 76 cd02787 MopB_CT_ydeP The MopB_  38.3      27 0.00068   17.0   2.4   29   28-59     30-58  (112)
 77 pfam04225 OapA Opacity-associa  38.2      37 0.00094   16.3   3.2   27   42-71     39-65  (85)
 78 pfam01551 Peptidase_M23 Peptid  35.6      40   0.001   16.0   3.8   51    3-54     20-71  (96)
 79 cd04485 DnaE_OBF DnaE_OBF: A s  35.6      40   0.001   16.0   4.2   67    7-75      9-79  (84)
 80 cd00210 PTS_IIA_glc PTS_IIA, P  34.5      42  0.0011   15.9   4.7   45    4-53     43-93  (124)
 81 COG1095 RPB7 DNA-directed RNA   33.4      24  0.0006   17.3   1.5   46   13-62     92-152 (183)
 82 pfam00358 PTS_EIIA_1 phosphoen  32.1      46  0.0012   15.7   5.0   45    4-53     48-98  (133)
 83 COG5569 Uncharacterized conser  29.4      46  0.0012   15.7   2.5   41   29-71     52-107 (108)
 84 COG2996 Predicted RNA-bindinin  29.1      52  0.0013   15.4   6.3   54   12-71     15-68  (287)
 85 KOG0291 consensus               29.1      52  0.0013   15.4   4.2   61    3-63    370-447 (893)
 86 TIGR01645 half-pint poly-U bin  27.9      17 0.00044   18.1   0.1   11   12-22    281-291 (791)
 87 TIGR02997 Sig70-cyanoRpoD RNA   26.8      20 0.00052   17.7   0.2   15    7-21    152-166 (336)
 88 cd04460 S1_RpoE S1_RpoE: RpoE,  26.2      59  0.0015   15.1   3.4   42   14-59     11-67  (99)
 89 KOG4208 consensus               25.9      60  0.0015   15.1   2.6   19    5-23     75-101 (214)
 90 TIGR01371 met_syn_B12ind 5-met  25.0      29 0.00073   16.8   0.8   28    7-38    119-146 (778)
 91 TIGR01628 PABP-1234 polyadenyl  24.2      30 0.00076   16.8   0.7   10   13-22    128-137 (860)
 92 TIGR02375 pseudoazurin pseudoa  23.9      55  0.0014   15.3   2.0   32   42-77     18-50  (123)
 93 TIGR02408 ectoine_ThpD ectoine  23.1      38 0.00096   16.2   1.0   12   28-39    104-115 (278)
 94 KOG0407 consensus               23.0      52  0.0013   15.4   1.8   36   29-67     26-62  (139)
 95 pfam06523 DUF1106 Protein of u  22.8      69  0.0018   14.7   4.8   56    3-58     33-89  (91)
 96 PRK07135 dnaE DNA polymerase I  22.6      70  0.0018   14.7   4.1   50   12-64    927-976 (987)
 97 TIGR02712 urea_carbox urea car  22.5      68  0.0017   14.8   2.3   34   19-55    726-762 (1226)
 98 COG4942 Membrane-bound metallo  22.4      71  0.0018   14.7   2.8   51    3-53    338-388 (420)
 99 KOG3074 consensus               21.9      72  0.0018   14.6   2.6   28   11-42    185-212 (263)
100 KOG0109 consensus               21.6      46  0.0012   15.7   1.3   20    4-23     26-45  (346)
101 TIGR02383 Hfq RNA chaperone Hf  21.3      42  0.0011   15.9   1.0   29    3-38     28-56  (61)
102 KOG4246 consensus               20.9     5.5 0.00014   20.8  -3.6   50   15-75    159-209 (1194)
103 cd04471 S1_RNase_R S1_RNase_R:  20.4      78   0.002   14.4   5.8   52    4-61      6-73  (83)

No 1  
>PRK09937 stationary phase/starvation inducible regulatory protein CspD; Provisional
Probab=99.93  E-value=1.2e-25  Score=164.15  Aligned_cols=72  Identities=35%  Similarity=0.660  Sum_probs=65.9

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECCCCCC
Q ss_conf             87762775146887465885488778837999950002358844689988999999869997111059996357889
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSSN   78 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~~~   78 (78)
                      |++|+|||||.+||||||+||   ++++|||||+|+|+..|+++|.+||+|+|++.+++++  ++|.+|..++.++.
T Consensus         1 M~~G~VKwFn~~KGyGFI~~d---~gg~DvFvH~s~i~~~G~~~L~~G~~V~f~v~~g~kG--~~A~~V~~ve~~~a   72 (74)
T PRK09937          1 MEKGTVKWFNNAKGFGFICPE---GGGEDIFAHYSTIQMDGYRTLKAGQSVQFDVHQGPKG--NHASVIVPVEVEAA   72 (74)
T ss_pred             CCCCEEEEEECCCCEEEEEEC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEECCCCCC
T ss_conf             998379788389971886207---9995599985882315884249999999999989998--51567588576667


No 2  
>COG1278 CspC Cold shock proteins [Transcription]
Probab=99.91  E-value=5.7e-25  Score=160.32  Aligned_cols=67  Identities=45%  Similarity=0.830  Sum_probs=61.3

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             877627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      |.+|+|||||+.||||||+||   +|++|||||+|+|+..|+++|.+||+|+|++++++++  ++|.||+.+
T Consensus         1 ~~~GtVKwfn~~KGfGFI~p~---~G~~DvFVH~Sai~~~g~~~L~eGQ~V~f~~~~g~kg--p~A~nv~~~   67 (67)
T COG1278           1 MATGTVKWFNATKGFGFITPE---DGGKDVFVHISAIQRAGFRTLREGQKVEFEVEQGRKG--PSAANVRAL   67 (67)
T ss_pred             CCCCEEEEEECCCCCEEECCC---CCCCCEEEEEEEECCCCCCCCCCCCEEEEEEECCCCC--CCEEEEEEC
T ss_conf             986168885089863370789---9985779980125127886557998899999528999--722678829


No 3  
>PRK10354 major cold shock protein; Provisional
Probab=99.90  E-value=3.9e-24  Score=155.68  Aligned_cols=67  Identities=39%  Similarity=0.720  Sum_probs=61.2

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             877627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      ..+|+|||||.+||||||+||   ++++|||||+|+|+.+++++|.+||+|+|++++++++  ++|.||+.|
T Consensus         4 ~~tG~VKwFn~~KGyGFI~~d---~g~~DvFvH~s~l~~~g~~~L~~Gq~V~f~~~~g~kG--~~A~nV~~l   70 (70)
T PRK10354          4 KMTGIVKWFNADKGFGFITPD---DGSKDVFVHFSAIQNDGYKSLDEGQKVSFTIESGAKG--PAAGNVTSL   70 (70)
T ss_pred             CEEEEEEEEECCCCEEEEECC---CCCCEEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEEC
T ss_conf             507999987099985998427---9984299985891704897259999999999979998--620777859


No 4  
>PRK10943 cold shock-like protein CspC; Provisional
Probab=99.90  E-value=4.2e-24  Score=155.49  Aligned_cols=67  Identities=37%  Similarity=0.728  Sum_probs=61.3

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             877627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      +.+|+|||||++||||||+|+   |+++|||||+|+|+..++++|.+||+|+|++.+++++  ++|+||+.|
T Consensus         3 ~~~G~VKwFn~~kGfGFI~~~---dg~~DvFvH~s~i~~~g~~~L~eGq~V~f~~~~g~kG--~~A~~V~~i   69 (69)
T PRK10943          3 KIKGQVKWFNESKGFGFITPA---DGSKDVFVHFSAIQGNGFKTLAEGQNVEFEIQDGQKG--PAAVNVTAI   69 (69)
T ss_pred             CEEEEEEEEECCCCEEEEEEC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CCCEEEEEC
T ss_conf             378899998399986998617---9983099993882716883239999999999979998--631887969


No 5  
>PRK09890 cold shock protein CspG; Provisional
Probab=99.90  E-value=4.2e-24  Score=155.46  Aligned_cols=67  Identities=37%  Similarity=0.676  Sum_probs=61.2

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             877627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      +.+|+|||||.+||||||+||   |+++|||||+|+|+..++++|.+||+|+|++.+++++  ++|.||..|
T Consensus         4 ~~tG~VKwFn~~KGyGFI~~d---dg~~DvFvH~s~i~~~~~~~L~~Gq~V~f~v~~g~kG--~~A~~V~~L   70 (70)
T PRK09890          4 KMTGLVKWFNADKGFGFITPD---DGSKDVFVHFTAIQSNEFRTLNENQKVEFSIEQGQRG--PAAANVVTL   70 (70)
T ss_pred             CEEEEEEEECCCCCEEEECCC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CCCEEEEEC
T ss_conf             506999988399986997038---9994299986892726883329999999999979998--611438879


No 6  
>PRK09507 cspE cold shock protein CspE; Reviewed
Probab=99.90  E-value=7.5e-24  Score=154.09  Aligned_cols=67  Identities=40%  Similarity=0.757  Sum_probs=61.1

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             877627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      +.+|+|||||++||||||+||   |+++|||||+|+|+..++++|.+||+|+|++.+++++  ++|.||..|
T Consensus         3 ~i~G~VKwF~~~kGyGFI~~~---dG~~DvFvH~s~i~~~g~~~L~~Gq~V~f~v~~~~kG--~~A~~V~~l   69 (69)
T PRK09507          3 KIKGNVKWFNESKGFGFITPE---DGSKDVFVHFSAIQTNGFKTLAEGQRVEFEITNGAKG--PSAANVIAL   69 (69)
T ss_pred             CEEEEEEEEECCCCEEEEECC---CCCCCEEEEHHHCCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEEC
T ss_conf             478899998399987999707---9983299990770525786169999999999969999--851888979


No 7  
>LOAD_cold consensus
Probab=99.89  E-value=2.2e-23  Score=151.46  Aligned_cols=66  Identities=47%  Similarity=0.891  Sum_probs=60.7

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEE
Q ss_conf             87762775146887465885488778837999950002358844689988999999869997111059996
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKL   72 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~   72 (78)
                      |.+|+|||||.+||||||+||   ++++|||+|+|+|+..+++.|.+||+|+|++.+++++  ++|+||++
T Consensus         1 M~~G~VK~f~~~kGfGFI~~~---~g~~DvFvH~s~l~~~~~~~l~~G~~V~f~~~~~~kG--~~A~~V~l   66 (67)
T LOAD_cold         1 MVKGTVKWFNVKKGFGFITPE---DGGEDVFVHQSAIQGDGFRSLTEGQEVEFDIVEGPKG--PQAANVVL   66 (67)
T ss_pred             CCCEEEEEEECCCCCEEEEEC---CCCCEEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEC
T ss_conf             998699999899994788757---9982189994781404786479999999999989999--67688989


No 8  
>pfam00313 CSD 'Cold-shock' DNA-binding domain.
Probab=99.88  E-value=1.6e-22  Score=146.64  Aligned_cols=66  Identities=44%  Similarity=0.827  Sum_probs=60.2

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             77627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      .+|+|||||++||||||+|+   ++++|||+|+|+|+..+++.|.+|++|+|++.+++++  ++|.||++|
T Consensus         1 ~tG~VK~f~~~kGfGFI~~~---~~~~DiFvH~s~l~~~~~~~L~~G~~V~f~v~~~~kG--~~A~nV~~i   66 (66)
T pfam00313         1 MTGTVKWFNAKKGFGFITPE---DGDKDVFVHFSAIQGDGFRSLQEGQRVEFDIVEGTKG--PQAANVTLL   66 (66)
T ss_pred             CCEEEEEEECCCCEEEEEEC---CCCCEEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEEC
T ss_conf             94899999599996999978---9984699992681214786179999999999979998--663899989


No 9  
>smart00357 CSP Cold shock protein domain. RNA-binding domain that functions as a RNA-chaperone in bacteria and is involved in regulating translation in eukaryotes. Contains sub-family of RNA-binding domains in the Rho transcription termination factor.
Probab=99.83  E-value=1.7e-20  Score=135.39  Aligned_cols=64  Identities=44%  Similarity=0.848  Sum_probs=57.3

Q ss_pred             CCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             7627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         4 ~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      +|+|||||  ||||||+|+   ++++|||||+|+|+ .+++.|.+||+|+|++.+++.+++++|.||+.|
T Consensus         1 tG~Vk~f~--kGfGFI~~~---~g~~DvFvH~s~i~-~~~~~l~~Gd~V~f~v~~~~~~~~~~A~~v~~l   64 (64)
T smart00357        1 TGVVKWFN--KGFGFIRPD---DGGKDVFVHPSQIQ-GGLKSLREGDEVEFKVVSPRGGGKPEAENVVKL   64 (64)
T ss_pred             CCEEEEEE--CCEEEEEEC---CCCCCEEEEHHHHC-CCCCCCCCCCEEEEEEEECCCCCCCEEEEEEEC
T ss_conf             94796982--844888618---99940999869954-677744758789999998899998441898979


No 10 
>cd04458 CSP_CDS Cold-Shock Protein (CSP) contains an S1-like cold-shock domain (CSD) that is found in eukaryotes, prokaryotes, and archaea.  CSP's include the major cold-shock proteins CspA and CspB in bacteria and the eukaryotic gene regulatory factor Y-box protein. CSP expression is up-regulated by an abrupt drop in growth temperature. CSP's are also expressed under normal condition at lower level. The function of cold-shock proteins is not fully understood. They preferentially bind poly-pyrimidine region of single-stranded RNA and DNA.  CSP's are thought to bind mRNA and regulate ribosomal translation, mRNA degradation, and  the rate of transcription termination. The human Y-box protein, which contains a CSD, regulates transcription and translation of genes that contain the Y-box sequence in their promoters. This specific ssDNA-binding properties of CSD are required for the binding of Y-box protein to the promoter's Y-box sequence, thereby regulating transcription.
Probab=99.82  E-value=2.7e-20  Score=134.23  Aligned_cols=65  Identities=40%  Similarity=0.848  Sum_probs=58.1

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEE
Q ss_conf             7762775146887465885488778837999950002358844689988999999869997111059996
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKL   72 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~   72 (78)
                      .+|+|||||.+||||||+++   ++++|||||+|+|+..+++.|.+|++|+|++.+++++  ++|.+|++
T Consensus         1 ~~G~Vk~f~~~kGfGFI~~~---~~~~diF~H~s~~~~~~~~~l~~G~~V~f~~~~~~~g--~~A~~v~~   65 (65)
T cd04458           1 VTGTVKWFDDEKGFGFITPD---DGGEDVFVHISALEGDGFRSLEEGDRVEFELEEGDKG--PQAVNVRL   65 (65)
T ss_pred             CEEEEEEEECCCCEEEEEEC---CCCCCEEEEHHHHCCCCCCCCCCCCEEEEEEEECCCC--CEEEEEEC
T ss_conf             93899999799996999957---9982299995892434697479898999999989899--76899899


No 11 
>TIGR02381 cspD cold shock domain protein CspD; InterPro: IPR012751    This entry represents what appears to be a phylogenetically distinct clade, containing Escherichia coli CspD (P24245 from SWISSPROT) and related proteobacterial proteins within the larger family of cold shock domain proteins. The gene symbol cspD may have been used independently for other subfamilies of cold shock domain proteins, such as for Bacillus subtilis CspD. These proteins typically are shorter than 70 amino acids. In Escherichia coli, CspD is a stress response protein induced in stationary phase. This homodimer binds single-stranded DNA and appears to inhibit DNA replication . ; GO: 0003676 nucleic acid binding, 0006355 regulation of transcription DNA-dependent, 0006950 response to stress, 0005737 cytoplasm.
Probab=99.67  E-value=1.3e-16  Score=113.61  Aligned_cols=67  Identities=34%  Similarity=0.691  Sum_probs=59.1

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             877627751468874658854887788379999500023588446899889999998699971110599963
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      |..|+|||||..||||||.+++   ...|||.|+|.|+.+||++|+.||.|.|++.+.+++  ..|..|..+
T Consensus         1 m~~G~vkWfnn~kGfGfi~~~~---~~~d~fahys~i~~dGy~~lk~Gq~v~f~~~~~~~G--~~a~~~~~~   67 (68)
T TIGR02381         1 MEIGIVKWFNNAKGFGFISAEG---KDEDIFAHYSTIQMDGYRTLKAGQKVQFEVVQGEKG--AHATKIVPI   67 (68)
T ss_pred             CCCCCEEECCCCCCEEEEECCC---CCCCEEEEEEEEECCCCEEECCCCEEEEEEEECCCC--CCEEEEEEE
T ss_conf             9744045301665203541478---776223211100014430001474368986207888--410266760


No 12 
>KOG3070 consensus
Probab=99.49  E-value=2e-14  Score=101.50  Aligned_cols=64  Identities=39%  Similarity=0.812  Sum_probs=54.8

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCC----CCCCCCCCCCEEEEEEEECCCCCCCCCEEEE
Q ss_conf             77627751468874658854887788379999500023----5884468998899999986999711105999
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVAS----AGLFNLTEGQLVTYDYVQNDANGKYSAENLK   71 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~----~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~   71 (78)
                      .+|+|||||..+|||||+++   |+++|||||+|+|.+    .++++|.+++.|+|++++...+  ..|+++.
T Consensus        57 ~~G~~kwfnv~~G~gFi~~~---d~~~D~fvhQs~i~~~~~~~~~rs~~~~e~v~f~~~~~~~g--~~a~~vt  124 (235)
T KOG3070          57 VKGTVKWFNVGKGYGFITRD---DGPEDVFVHQSAITKYTPSEGFRSLKEGEAVPFDIQEGNKG--TEAANVT  124 (235)
T ss_pred             CCCCCEEEECCCCCCEECCC---CCCCCEEEEEEEEECCCCCCCHHHCCCCCCCCCEECCCCCC--CEEEEEC
T ss_conf             35864048636786300146---78886347864000145330011125688756100015765--3266623


No 13 
>pfam08206 OB_RNB Ribonuclease B OB domain. This family includes the N-terminal OB domain found in ribonuclease B proteins in one or two copies.
Probab=97.75  E-value=4.9e-05  Score=49.06  Aligned_cols=53  Identities=23%  Similarity=0.534  Sum_probs=41.1

Q ss_pred             CCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEE
Q ss_conf             6887465885488778837999950002358844689988999999869997111059996
Q gi|254780913|r   12 PDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKL   72 (78)
Q Consensus        12 ~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~   72 (78)
                      ..+||||+.||+   .++|||+....+..     .-.|++|..++....+++|+.+.-|++
T Consensus         6 ~~~GfGFv~~d~---~~~DifI~~~~l~~-----A~~GD~V~v~v~~~~~~~r~eG~vv~I   58 (58)
T pfam08206         6 HKKGFGFLIPDD---EEDDIFIPPEQMKK-----AMHGDRVLVRITKGDRRGRREGRIVRI   58 (58)
T ss_pred             CCCCEEEEEECC---CCCCEEECHHHHCC-----CCCCCEEEEEEECCCCCCCCCEEEEEC
T ss_conf             389009998689---98899999899745-----659999999995388899836999989


No 14 
>PRK11642 exoribonuclease R; Provisional
Probab=97.71  E-value=9.9e-05  Score=47.35  Aligned_cols=65  Identities=23%  Similarity=0.450  Sum_probs=49.1

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECCCCC
Q ss_conf             776277514688746588548877883799995000235884468998899999986999711105999635788
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSS   77 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~~   77 (78)
                      .+|+|.-  ..+||||+.+|+   +++|||++-+.+..     .-.|++|.-.+...+++|++.+..|++|+.+.
T Consensus        85 v~G~v~~--~~~GfgFv~~e~---~~eDifI~~~~l~~-----a~~GDrVlvr~~~~~r~gr~Eg~Vv~IleR~~  149 (813)
T PRK11642         85 LKGTVIG--HRDGYGFLRVEG---RKDDLYLSSEQMKT-----CIHGDQVLAQPLGADRKGRREARIVRVLVPKT  149 (813)
T ss_pred             EEEEEEE--CCCCCEEEECCC---CCCCEEECHHHHCC-----CCCCCEEEEEEECCCCCCCCCEEEEEEEECCC
T ss_conf             6899998--888777887079---87770008467432-----67999999998247788986179999995188


No 15 
>PRK05054 exoribonuclease II; Provisional
Probab=96.93  E-value=0.0022  Score=39.81  Aligned_cols=60  Identities=20%  Similarity=0.362  Sum_probs=41.3

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECCC
Q ss_conf             7762775146887465885488778837999950002358844689988999999869997111059996357
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPK   75 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~   75 (78)
                      .+|+|+-  ..|||||+.+|    +++|||++-+.+..     .-.|++|...+...  ++|..|.-++++..
T Consensus        22 v~G~~~~--~~~GfGFv~~d----~~~difI~~~~~~~-----a~~GD~V~v~v~~~--~~r~~~~~~~iv~r   81 (644)
T PRK05054         22 VEGVVKA--TEKGFGFLEVD----AKKSYFIPPPQMKK-----VMHGDRIIAVIHTE--KERESAEPEELIEP   81 (644)
T ss_pred             EEEEEEE--ECCCCEEEEEC----CCCCEEECHHHHHH-----CCCCCEEEEEEEEC--CCCCEEEEEEEEEE
T ss_conf             8999999--48963898508----98657699899944-----78999999999854--99846789999995


No 16 
>TIGR02063 RNase_R ribonuclease R; InterPro: IPR011805    This family consists of an exoribonuclease, ribonuclease R, also called VacB. It is one of the eight exoribonucleases reported in Escherichia coli and is broadly distributed throughout the bacteria. In E. coli, double mutants of this protein and polynucleotide phosphorylase are not viable. Not included in this entry are shorter, divergent forms from the Chlamydiae and the Campylobacterales (including Helicobacter pylori) and Leptospira interrogans , .; GO: 0003723 RNA binding, 0004518 nuclease activity.
Probab=96.31  E-value=0.0084  Score=36.58  Aligned_cols=67  Identities=19%  Similarity=0.512  Sum_probs=48.1

Q ss_pred             CCEEEEEECCCCEEEEEECCCC--CCCCEEEEEEEECCCCCCCCCCC--CCEEEEEEEECCCC--C-CCCCEEEEECCCC
Q ss_conf             7627751468874658854887--78837999950002358844689--98899999986999--7-1110599963578
Q gi|254780913|r    4 RGSIKWYNPDKGYGFITPEGST--ESGDDVFLHRSAVASAGLFNLTE--GQLVTYDYVQNDAN--G-KYSAENLKLVPKS   76 (78)
Q Consensus         4 ~G~VKwfn~~kGfGFI~~d~~~--d~g~DvFvH~s~i~~~g~~~l~~--G~~V~F~i~~~~~~--g-k~~A~~v~~i~~~   76 (78)
                      +|++.  -..+||||+.|+++.  +...|+|++.+.+..     .-.  ||+|.+.+....+.  | +.-|..+++|..+
T Consensus        76 ~G~~~--~~~~GfgF~~~~~~~~~~~~~d~~~~~~~~~~-----a~~G~gD~V~~~~~~~~~~~~~~~~eg~v~kil~r~  148 (755)
T TIGR02063        76 KGTVI--AHRDGFGFLRPEDDKYDEDEEDIFIPPEELNG-----AMHGLGDRVLVKITGKEDEKKGDRAEGRVIKILERA  148 (755)
T ss_pred             EEEEE--ECCCCCEEEEECCCCCCCCCCCEEECHHHHHH-----HHCCCCCEEEEEEECCCCCCCCCCCCEEEEEEECCC
T ss_conf             99999--63765137885045576556511107588866-----434899789999603643458798525899996088


Q ss_pred             C
Q ss_conf             8
Q gi|254780913|r   77 S   77 (78)
Q Consensus        77 ~   77 (78)
                      .
T Consensus       149 ~  149 (755)
T TIGR02063       149 N  149 (755)
T ss_pred             C
T ss_conf             7


No 17 
>pfam07497 Rho_RNA_bind Rho termination factor, RNA-binding domain. The Rho termination factor disengages newly transcribed RNA from its DNA template at certain, specific transcripts. It it thought that two copies of Rho bind to RNA and that Rho functions as a hexamer of protomers.
Probab=95.97  E-value=0.0087  Score=36.48  Aligned_cols=58  Identities=16%  Similarity=0.365  Sum_probs=39.1

Q ss_pred             CCCEEEEEE--CCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCC-CCEEEEEC
Q ss_conf             887465885--48877883799995000235884468998899999986999711-10599963
Q gi|254780913|r   13 DKGYGFITP--EGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKY-SAENLKLV   73 (78)
Q Consensus        13 ~kGfGFI~~--d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~-~A~~v~~i   73 (78)
                      ..|||||..  .+...+-.||||+.|.|+..+   |+.|+.|+=.+..-..+-|+ +...|..+
T Consensus        11 ~dGyGFLR~~~~~y~~~~~DvyVs~~~Irrf~---LR~GD~V~G~vR~p~~~ek~~aL~~V~~V   71 (78)
T pfam07497        11 PDGFGFLRSPDANYLPGPDDIYVSPSQIRRFN---LRTGDTIEGKIRPPKEGERYFALLKVETI   71 (78)
T ss_pred             CCCCEEEECCCCCCCCCCCCEEECHHHHHHCC---CCCCCEEEEEEECCCCCCCCEEEEEEEEE
T ss_conf             89837947786587999888788999998719---98888999998799989875210689758


No 18 
>cd04459 Rho_CSD Rho_CSD: Rho protein cold-shock domain (CSD). Rho protein is a transcription termination factor in most bacteria. In bacteria, there are two distinct mechanisms for mRNA transcription termination. In intrinsic termination, RNA polymerase and nascent mRNA are released from DNA template by an mRNA stem loop structure, which resembles the transcription termination mechanism used by eukaryotic pol III. The second mechanism is mediated by Rho factor. Rho factor terminates transcription by using energy from ATP hydrolysis to forcibly dissociate the transcripts from RNA polymerase. Rho protein contains an N-terminal S1-like domain, which binds single-stranded RNA. Rho has a C-terminal ATPase domain which hydrolyzes ATP to provide energy to strip RNA polymerase and mRNA from the DNA template. Rho functions as a homohexamer.
Probab=95.71  E-value=0.013  Score=35.44  Aligned_cols=52  Identities=23%  Similarity=0.433  Sum_probs=36.5

Q ss_pred             CCCEEEEEECCC--CCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCC
Q ss_conf             887465885488--7788379999500023588446899889999998699971110
Q gi|254780913|r   13 DKGYGFITPEGS--TESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSA   67 (78)
Q Consensus        13 ~kGfGFI~~d~~--~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A   67 (78)
                      ..||||+...+.  ..+..||||+.+.|+..+   |+.|+.|+=.+..-..+-|+-|
T Consensus         9 ~dGyGFLR~~~~ny~~~~~DvyVs~~~Irrf~---LR~GD~V~G~vR~p~~~Eky~a   62 (68)
T cd04459           9 PDGFGFLRSSGYNYLPGPDDIYVSPSQIRRFN---LRTGDTVVGQIRPPKEGERYFA   62 (68)
T ss_pred             CCCCEEEECCCCCCCCCCCCEEECHHHHHHCC---CCCCCEEEEEEECCCCCCCCCC
T ss_conf             89828967898778899888789999997739---9889999997779998886410


No 19 
>PRK09376 rho transcription termination factor Rho; Provisional
Probab=94.71  E-value=0.036  Score=33.06  Aligned_cols=59  Identities=19%  Similarity=0.357  Sum_probs=39.4

Q ss_pred             CCCEEEEEE--CCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCC-CCEEEEECC
Q ss_conf             887465885--48877883799995000235884468998899999986999711-105999635
Q gi|254780913|r   13 DKGYGFITP--EGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKY-SAENLKLVP   74 (78)
Q Consensus        13 ~kGfGFI~~--d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~-~A~~v~~i~   74 (78)
                      ..||||+..  .+..-+-.||||..|.|+..+   |+.|+.|+-.+..-..+-|+ +...|..+.
T Consensus        60 ~dGyGFLR~~~~nylp~~dDiYVS~sqIrrf~---LR~GD~V~G~vR~pke~Ery~aLl~V~~VN  121 (416)
T PRK09376         60 PDGFGFLRSPDANYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKIRPPKEGERYFALLKVETVN  121 (416)
T ss_pred             CCCCEEEECCCCCCCCCCCCEEECHHHHHHHC---CCCCCEEEEEEECCCCCCCCCCEEEEEECC
T ss_conf             89865705787688899888336899999809---988888999886898888774337763228


No 20 
>PRK08059 general stress protein 13; Validated
Probab=94.34  E-value=0.13  Score=29.91  Aligned_cols=69  Identities=13%  Similarity=0.144  Sum_probs=47.0

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCCCEEEEECCCCC
Q ss_conf             77627751468874658854887788379999500023588----4468998899999986999711105999635788
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYSAENLKLVPKSS   77 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~~   77 (78)
                      .+|+|+-..+   ||..+.-   +++-+-|+|+|.|...-.    ..+..||.|.+.+..-+...+-.+..++.+.+.|
T Consensus        10 v~G~V~~I~~---fG~FV~l---~~gv~GLihiSEls~~~v~~~~~~~~vGd~V~vkVi~iD~e~~ri~LSlK~l~~~P   82 (119)
T PRK08059         10 VTGKVTGIQD---YGAFVAL---DEETQGLVHISEITHGFVKDIHDFLKVGDEVKVKVLSVDEEHGKISLSIRATEEAP   82 (119)
T ss_pred             EEEEEEEEEC---EEEEEEE---ECCCEEEEEHHHHCCCCCCCHHHHHCCCCEEEEEEEEEECCCCEEEEECCCCCCCC
T ss_conf             9999999974---0489999---43953788878824566679999705899899999999899999987503576483


No 21 
>TIGR02062 RNase_B exoribonuclease II; InterPro: IPR011804    This family consists of exoribonuclease II (RNase II), the product of the rnb gene, as found in a number of gamma proteobacteria. In Escherichia coli, it is one of eight different exoribonucleases. It is involved in mRNA degradation and tRNA precursor end processing.; GO: 0003723 RNA binding, 0008859 exoribonuclease II activity, 0006401 RNA catabolic process.
Probab=92.85  E-value=0.23  Score=28.56  Aligned_cols=59  Identities=20%  Similarity=0.405  Sum_probs=41.8

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECC
Q ss_conf             776277514688746588548877883799995000235884468998899999986999711105999635
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVP   74 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~   74 (78)
                      ..|+||-  .+|||||+..|.    .+-+|     |..-..+.+-=||+|.=.|.. + +-|.+|+==.||+
T Consensus        22 ~EGvvKa--tdkgFGFLEvDa----kksYF-----ipPp~MKkvMHGDki~A~i~~-e-~drE~AEPe~LiE   80 (664)
T TIGR02062        22 VEGVVKA--TDKGFGFLEVDA----KKSYF-----IPPPSMKKVMHGDKIVAVIKK-E-KDREVAEPEELIE   80 (664)
T ss_pred             CCEEEEE--CCCCCCCEEEEC----CCCCC-----CCCCCCCCCCCCCEEEEEEEE-C-CCCCCCCCHHHHH
T ss_conf             2316841--466752047607----64323-----786767841348827999973-5-8712148434310


No 22 
>TIGR00717 rpsA ribosomal protein S1; InterPro: IPR000110   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 S1  contains the S1 domain that has been found in a large number of RNA-associated proteins. S1 is a prominent component of the Escherichia coli ribosome and is most probably required for translation of most, if not all, natural mRNAs in E. coli in vivo . It has been suggested that S1 is a RNA-binding protein helping polynucleotide phosphorylase (PNPase, known to be phylogenetically related to S1) to degrade mRNA, or helper molecule involved in other RNase activities .    Unique among ribosomal proteins, the primary structure of S1 contains four repeating homologous stretches in the central and terminal region of the molecule. S1 is organised into at least two distinct domains; a ribosome-binding domain at the N-terminal region and a nucleic acid-binding domain at the C-terminal region . There may be a flexible region between the two domains permitting free movement of the domains relative to each other. ; GO: 0003723 RNA binding, 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=92.26  E-value=0.55  Score=26.45  Aligned_cols=70  Identities=23%  Similarity=0.241  Sum_probs=50.1

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECC----CCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEECCCC
Q ss_conf             87762775146887465885488778837999950002----3588446899889999998699971110599963578
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVA----SAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKS   76 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~----~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~   76 (78)
                      ...|.||-+.+-.|-=||..     +|-|=|+|++++.    ......+..||.|+-.+..-|+.-+.-+..++-+.+-
T Consensus       203 ~v~GvVk~iT~fGGv~Fvdl-----gg~dGLLH~~d~sWkr~~~P~e~~~~G~~~~Vkv~~~D~~~~Ri~LsLK~~~~d  276 (534)
T TIGR00717       203 VVKGVVKNITDFGGVAFVDL-----GGVDGLLHITDMSWKRVKHPSEYVKVGQEVKVKVIKFDKEKKRISLSLKQLKED  276 (534)
T ss_pred             EEEEEEEEECCCCCEEEEEC-----CCEEECCCHHHCCCCCCCCCHHHCCCCCEEEEEEEEECCCCCEEEEEEECCCCC
T ss_conf             76108888889874999981-----643320350121478878834640079889999996526576077871205888


No 23 
>PRK12608 transcription termination factor Rho; Provisional
Probab=92.22  E-value=0.18  Score=29.16  Aligned_cols=56  Identities=25%  Similarity=0.389  Sum_probs=37.1

Q ss_pred             CCCEEEEEEC--CCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             8874658854--887788379999500023588446899889999998699971110599963
Q gi|254780913|r   13 DKGYGFITPE--GSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus        13 ~kGfGFI~~d--~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      ..||||+-..  +...+-.||||..|.|+..+   |+.|+.|+=.+.. ++.|. +...|.-+
T Consensus        26 ~dGyGFLR~~~~nYlp~pdDiYVS~sqIrrf~---LR~GD~V~G~iR~-p~~ge-aL~~V~~V   83 (379)
T PRK12608         26 GKGFGFLRSPERNYLPSPDDVYVSPALIRRFG---LRTGDLVEGVIRA-PREKE-TLVRIDSV   83 (379)
T ss_pred             CCCCEEEECCCCCCCCCCCCEEECHHHHHHCC---CCCCCEEEEEECC-CCCCH-HHEEEHHC
T ss_conf             89975835898788999988100999997549---9999989998638-99874-20414523


No 24 
>PRK07400 30S ribosomal protein S1; Reviewed
Probab=91.05  E-value=0.73  Score=25.74  Aligned_cols=66  Identities=15%  Similarity=0.142  Sum_probs=33.7

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCCCEEEEECCC
Q ss_conf             77627751468874658854887788379999500023588----44689988999999869997111059996357
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYSAENLKLVPK   75 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~   75 (78)
                      .+|+|+-..   -||....-    +|-|=|+|+|.|.-...    ..++.||.|+..+..-++..+--+..++.+.+
T Consensus       200 v~G~V~~I~---~fGaFVdi----gGvdGLlHiSeiSw~rv~~p~dv~kvGd~V~vkVi~iD~e~~rIsLSiK~l~~  269 (314)
T PRK07400        200 VVGTVRGIK---PYGAFIDI----GGVSGLLHISEISHEHIETPHSVFNVNDQMKVMIIDLDAERGRISLSTKQLEP  269 (314)
T ss_pred             EEEEEEEEE---CEEEEEEE----CCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEEEEEHHHCCC
T ss_conf             999999996---40889997----89189998146165444898782679999999999973889889977666555


No 25 
>COG1158 Rho Transcription termination factor [Transcription]
Probab=90.18  E-value=0.27  Score=28.16  Aligned_cols=51  Identities=24%  Similarity=0.438  Sum_probs=36.0

Q ss_pred             CCCEEEEEECC--CCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCC-CCCC
Q ss_conf             88746588548--8778837999950002358844689988999999869997-1110
Q gi|254780913|r   13 DKGYGFITPEG--STESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG-KYSA   67 (78)
Q Consensus        13 ~kGfGFI~~d~--~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~g-k~~A   67 (78)
                      .-||||+....  ...+..||||.-|.|+..+   |+.|+.|+=.+.. ++.| |+-|
T Consensus        62 ~dGfGFLR~~~~~yl~~~~DiYvSpSQIRrf~---LrtGD~v~G~vR~-Pke~Ery~a  115 (422)
T COG1158          62 PDGFGFLRSADSSYLPGPDDIYVSPSQIRRFN---LRTGDTVEGKVRP-PKEGERYFA  115 (422)
T ss_pred             CCCCCEEECCCCCCCCCCCCEEECHHHHHHCC---CCCCCEEEEEECC-CCCCCCEEE
T ss_conf             67742440576455789776678789986506---7668877666448-876430000


No 26 
>cd04472 S1_PNPase S1_PNPase: Polynucleotide phosphorylase (PNPase), ), S1-like RNA-binding domain. PNPase  is a polyribonucleotide nucleotidyl transferase that degrades mRNA. It is a trimeric multidomain protein. The C-terminus contains the S1 domain which binds ssRNA. This family is classified based on the S1 domain. PNPase nonspecifically removes the 3' nucleotides from mRNA, but is stalled by double-stranded RNA structures such as a stem-loop. Evidence shows that a minimum of 7-10 unpaired nucleotides at the 3' end, is required for PNPase degradation. It is suggested that PNPase also dephosphorylates the RNA 5' end. This additional activity may regulate the 5'-dependent activity of RNaseE in vivo.
Probab=90.03  E-value=0.86  Score=25.37  Aligned_cols=57  Identities=19%  Similarity=0.300  Sum_probs=39.4

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCC
Q ss_conf             877627751468874658854887788379999500023588----446899889999998699971
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGK   64 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk   64 (78)
                      ..+|+|+-.-+   ||....-   ..+.+=++|+|.|...-.    ..++.||.|+..+..-+.++|
T Consensus         3 iv~G~V~~i~~---fG~FV~l---~~g~~GLiHiSeis~~~v~~~~~~~~~Gd~v~vkVi~iD~~~r   63 (68)
T cd04472           3 IYEGKVVKIKD---FGAFVEI---LPGKDGLVHISELSDERVEKVEDVLKVGDEVKVKVIEVDDRGR   63 (68)
T ss_pred             EEEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCC
T ss_conf             99999999973---2999995---7996248886893456546988907899999999999999997


No 27 
>PRK12678 transcription termination factor Rho; Provisional
Probab=89.98  E-value=0.2  Score=28.87  Aligned_cols=48  Identities=23%  Similarity=0.432  Sum_probs=37.1

Q ss_pred             CEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEE
Q ss_conf             627751468874658854887788379999500023588446899889999998
Q gi|254780913|r    5 GSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQ   58 (78)
Q Consensus         5 G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~   58 (78)
                      |.+--.|   ||||+-..+..-+-.||||..|.|+..+   |+.|+.|.=.+..
T Consensus       293 Gildi~d---~y~FlRt~~ylp~~~DvYvs~~qir~~~---Lr~GD~v~G~vr~  340 (667)
T PRK12678        293 GILDVLD---NYAFVRTSGYLPGPNDVYVSMNQVRKNG---LRRGDAITGAVRA  340 (667)
T ss_pred             EEEEEEE---CCEEEECCCCCCCCCCEEECHHHHHHHC---CCCCCEEEEEECC
T ss_conf             1789740---6116634898899877547899998719---9988987872018


No 28 
>cd05692 S1_RPS1_repeat_hs4 S1_RPS1_repeat_hs4: 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 4 (hs4) of the H. sapiens RPS1 homolog. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=88.81  E-value=1.3  Score=24.39  Aligned_cols=57  Identities=26%  Similarity=0.386  Sum_probs=39.0

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCC
Q ss_conf             877627751468874658854887788379999500023588----446899889999998699971
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGK   64 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk   64 (78)
                      ..+|+|+---+   ||....-   ..|.+=|+|+|.+.....    ..+..||.|+..+..-+.++|
T Consensus         3 vv~G~V~~I~~---fGaFV~l---~~g~~GL~HiSeis~~~v~~~~~~~~~Gd~v~vkVi~id~~~r   63 (69)
T cd05692           3 VVEGTVTRLKP---FGAFVEL---GGGISGLVHISQIAHKRVKDVKDVLKEGDKVKVKVLSIDARGR   63 (69)
T ss_pred             EEEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCC
T ss_conf             99999999985---3899996---8998899996983456557988917899999999999999996


No 29 
>pfam00575 S1 S1 RNA binding domain. The S1 domain occurs in a wide range of RNA associated proteins. It is structurally similar to cold shock protein which binds nucleic acids. The S1 domain has an OB-fold structure.
Probab=88.21  E-value=1.1  Score=24.86  Aligned_cols=55  Identities=18%  Similarity=0.181  Sum_probs=39.3

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCC----CCCCCCCCCEEEEEEEECCCC
Q ss_conf             8776277514688746588548877883799995000235----884468998899999986999
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~----g~~~l~~G~~V~F~i~~~~~~   62 (78)
                      ..+|+|+-.++   ||....-   ..+-+-|+|.|.+...    ....+..||.|.+.+..-+..
T Consensus         7 iv~G~V~~i~~---~G~fV~l---~~~~~g~v~~s~ls~~~~~~~~~~~~~G~~v~~~V~~vd~~   65 (74)
T pfam00575         7 VVKGTVTRVTK---GGAFVDL---GNGVEGFIPISEISDDRVEDPDEVLKVGDEVEVKVLKVDKE   65 (74)
T ss_pred             EEEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHHHCCCCEEEEEEEEEECC
T ss_conf             99999999987---7599997---89979999844613655567768305999999999999999


No 30 
>cd00164 S1_like S1_like: Ribosomal protein S1-like RNA-binding domain. Found in a wide variety of RNA-associated proteins. Originally identified in S1 ribosomal protein. This superfamily also contains the Cold Shock Domain (CSD), which is a homolog of the S1 domain. Both domains are members of the Oligonucleotide/oligosaccharide Binding (OB) fold.
Probab=87.91  E-value=1.3  Score=24.37  Aligned_cols=52  Identities=17%  Similarity=0.230  Sum_probs=37.6

Q ss_pred             CCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCC----CCCCCCCCCEEEEEEEECCC
Q ss_conf             76277514688746588548877883799995000235----88446899889999998699
Q gi|254780913|r    4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQNDA   61 (78)
Q Consensus         4 ~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~----g~~~l~~G~~V~F~i~~~~~   61 (78)
                      +|+|+...   .||.....   ..+.+.|+|.|.+...    ....+..||.|.+.+..-+.
T Consensus         2 ~G~V~~i~---~~G~fV~~---~~~~~gli~~s~~s~~~~~~~~~~~~~G~~V~~~Vi~vd~   57 (65)
T cd00164           2 TGKVVSIT---KFGVFVEL---EDGVEGLVHISELSDKFVKDPSEVFKVGDEVEVKVLEVDP   57 (65)
T ss_pred             EEEEEEEE---CCEEEEEE---CCCEEEEEEHHHHCCCCCCCHHHEECCCCEEEEEEEEEEC
T ss_conf             89999997---84599998---9871788988891676535951098599999999999989


No 31 
>cd05691 S1_RPS1_repeat_ec6 S1_RPS1_repeat_ec6: 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 6 (ec6) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=87.69  E-value=1.8  Score=23.63  Aligned_cols=66  Identities=15%  Similarity=0.185  Sum_probs=43.4

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             87762775146887465885488778837999950002358----8446899889999998699971110599963
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      ..+|+|+--.+ .|. |+..+    .+-+-|+|.|.+....    ...+..||.|...+..-++..+.-...++.+
T Consensus         3 iV~G~V~~i~~-~G~-fV~l~----~~v~G~ih~sels~~~~~~~~~~~~vGd~v~akIi~iD~~~~ri~LSiKal   72 (73)
T cd05691           3 IVTGKVTEVDA-KGA-TVKLG----DGVEGFLRAAELSRDRVEDATERFKVGDEVEAKITNVDRKNRKISLSIKAK   72 (73)
T ss_pred             EEEEEEEEEEC-CCE-EEEEC----CCCEEEEEHHHCCCCHHHCHHHCCCCCCEEEEEEEEEECCCCEEEEEEEEC
T ss_conf             99999999977-868-99928----996999998997821132925438999999999999978899998674245


No 32 
>COG1098 VacB Predicted RNA binding protein (contains ribosomal protein S1 domain) [Translation, ribosomal structure and biogenesis]
Probab=87.13  E-value=0.68  Score=25.91  Aligned_cols=57  Identities=32%  Similarity=0.437  Sum_probs=36.8

Q ss_pred             CEE-EEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCCEEEEECCCC
Q ss_conf             746-5885488778837999950002358----8446899889999998699971110599963578
Q gi|254780913|r   15 GYG-FITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSAENLKLVPKS   76 (78)
Q Consensus        15 GfG-FI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~   76 (78)
                      -|| |+..++    |.-=+||+|.|...=    ...|.+||.|.-.+.--+..|+.. ..|+-+.+.
T Consensus        18 ~yGAFV~l~~----g~tGLVHISEIa~~fVkdI~d~L~vG~eV~vKVl~ide~GKis-LSIr~~~e~   79 (129)
T COG1098          18 PYGAFVELEG----GKTGLVHISEIADGFVKDIHDHLKVGQEVKVKVLDIDENGKIS-LSIRKLEEE   79 (129)
T ss_pred             ECCEEEEECC----CCCCEEEEHHHHHHHHHHHHHHHCCCCEEEEEEEEECCCCCCC-EEHHHHHHC
T ss_conf             4334898239----9731488357544367739988427887999997214689703-356876647


No 33 
>cd04465 S1_RPS1_repeat_ec2_hs2 S1_RPS1_repeat_ec2_hs2: 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 2 of the Escherichia coli and Homo sapiens RPS1 (ec2 and hs2, respectively). Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=86.92  E-value=1.3  Score=24.32  Aligned_cols=52  Identities=25%  Similarity=0.323  Sum_probs=36.4

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC---CCCCCCCCEEEEEEEECCCC
Q ss_conf             7762775146887465885488778837999950002358---84468998899999986999
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG---LFNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g---~~~l~~G~~V~F~i~~~~~~   62 (78)
                      .+|+|+-.+  || |||+.-    +|-..|++.|.+...-   ...+ .|+.++|.+.+-++.
T Consensus         4 v~g~I~~~~--kG-G~~v~~----~gv~~FiP~Sq~~~~~~~~~~~~-vG~~i~~~Ii~~d~~   58 (67)
T cd04465           4 VEGKVTEKV--KG-GLIVDI----EGVRAFLPASQVDLRPVEDLDEY-VGKELKFKIIEIDRE   58 (67)
T ss_pred             EEEEEEEEE--CC-CEEEEE----CCEEEEEECHHCCCCCCCCHHHH-CCCEEEEEEEEEECC
T ss_conf             999999998--57-199999----99999988025255456896897-899899999999278


No 34 
>COG0557 VacB Exoribonuclease R [Transcription]
Probab=86.58  E-value=0.86  Score=25.36  Aligned_cols=65  Identities=23%  Similarity=0.566  Sum_probs=43.6

Q ss_pred             CCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCC-CCCEEEEECCCC
Q ss_conf             7627751468874658854887788379999500023588446899889999998699971-110599963578
Q gi|254780913|r    4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGK-YSAENLKLVPKS   76 (78)
Q Consensus         4 ~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk-~~A~~v~~i~~~   76 (78)
                      .|++.+  ..+||||+.++.. ....|+|+-...+     .....|++|..++.+.++.++ +.|..+++++.+
T Consensus        71 ~~~~~~--~~~gf~f~~~~~~-~~~~d~~v~~~~~-----~~a~~gD~V~v~~~~~~~~~~~~~~~v~~il~r~  136 (706)
T COG0557          71 EGIVEA--SAKGFGFLSPDDS-KDADDIFVPKDPL-----NRALHGDRVLVELLPSDKRGRFKEAAVVRILERA  136 (706)
T ss_pred             HCEEEC--CCCCCCEECCCCC-CCCCCEEECCHHH-----HHCCCCCEEEEEECCCCCCCCCCEEEEEHHHHHH
T ss_conf             026521--3567742313667-7866578643555-----3201699899996765566666226866255553


No 35 
>TIGR00358 3_prime_RNase VacB and RNase II family 3'-5' exoribonucleases; InterPro: IPR004476   This family is defined to identify a pair of paralogous 3'->5' exoribonucleases in Escherichia coli, plus the set of proteins apparently orthologous to one or the other in other eubacteria. VacB was characterised originally as required for the expression of virulence genes, but is now recognised as the exoribonuclease RNase R (Rnr). Its paralog in Escherichia coli and Haemophilus influenzae is designated exoribonuclease II (Rnb) . Both are involved in the degradation of mRNA, and consequently have strong pleiotropic effects that may be difficult to disentangle. Both these proteins share domain-level similarity (RNB, S1) with a considerable number of other proteins, and full-length similarity scoring below the trusted cut-off to proteins associated with various phenotypes but uncertain biochemistry; it may be that these latter proteins are also 3' exoribonucleases.; GO: 0003723 RNA binding, 0004540 ribonuclease activity, 0016070 RNA metabolic process.
Probab=86.34  E-value=0.39  Score=27.27  Aligned_cols=64  Identities=25%  Similarity=0.472  Sum_probs=45.6

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCC-CCCCEEEEECCC
Q ss_conf             7762775146887465885488778837999950002358844689988999999869997-111059996357
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG-KYSAENLKLVPK   75 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~g-k~~A~~v~~i~~   75 (78)
                      .+|+++-  ..+||||+.++.  +...++|+|.+.+..     ...|+.|.+.....+..+ +..|.-++++..
T Consensus        19 ~~g~~~~--~~~~~gf~~~~~--~~~~~~~~~~~~~~~-----~~~gd~~~~~~~~~~~~~d~~~~~~~~~~~~   83 (684)
T TIGR00358        19 VKGVVKG--HNKGFGFLRPDD--GDKKDYFIPPPQLKG-----ALHGDLVLACPLGKPEKGDRREAEPVRLLEP   83 (684)
T ss_pred             HCCEEEE--CCCCCEEEEECC--CCCCEEEECCHHHHH-----HHCCCEEEEEECCCCCCCCHHHHHHHHHHHH
T ss_conf             2100220--456530133316--775236645334312-----1045424675336664432011257778777


No 36 
>PRK00087 4-hydroxy-3-methylbut-2-enyl diphosphate reductase/S1 RNA-binding domain protein; Reviewed
Probab=84.92  E-value=2.6  Score=22.67  Aligned_cols=63  Identities=25%  Similarity=0.296  Sum_probs=28.7

Q ss_pred             CCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             76277514688746-5885488778837999950002358----8446899889999998699971110599963
Q gi|254780913|r    4 RGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         4 ~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      +|+|+...   -|| |+..+    .|-|=|+|+|.+....    -..++.||.|+..+..-+...|--...++-+
T Consensus       570 ~g~V~~i~---~fGaFVel~----~gveGlih~sels~~~~~~~~~~~~~Gd~v~~kIl~id~~~krisLSiK~~  637 (670)
T PRK00087        570 LGKVVRIA---PFGAFVELE----PGVDGLVHISEISWKRIDKPEDVLSEGEEVKAKILEVDPEEKRIRLSIKEV  637 (670)
T ss_pred             EEEEEEEE---CCEEEEEEC----CCCEEEEEHHHCCCCCCCCHHHCCCCCCEEEEEEEEECCCCCEEEEEHHHC
T ss_conf             99999996---770799957----997899898994843248977748999989999999837778899784653


No 37 
>PRK07252 hypothetical protein; Provisional
Probab=84.83  E-value=1.6  Score=23.81  Aligned_cols=67  Identities=19%  Similarity=0.238  Sum_probs=41.7

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCCEEEEECCC
Q ss_conf             7762775146887465885488778837999950002358----844689988999999869997111059996357
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSAENLKLVPK   75 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~   75 (78)
                      .+|+|+---   -||..+.-   +++.+=|+|+|.|...-    ...+..||.|...+..-+...+--...++-+.+
T Consensus         7 v~G~V~~I~---~fGaFV~l---~~gv~GLiHISEis~~~v~~~~~~~kvGd~V~vkVi~ID~e~~rIsLSiK~l~e   77 (120)
T PRK07252          7 LKGTITGIK---PYGAFVAL---ENGTTGLIHISEIKTGFIDNIHQLLKVGNEVLVQVIDIDEYTKKASLSMRTLEE   77 (120)
T ss_pred             EEEEEEEEE---CCEEEEEE---CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECCCCEEECCHHHHCC
T ss_conf             999999997---54579995---799578888666010200499994789999999999986899988613633224


No 38 
>PRK08582 hypothetical protein; Provisional
Probab=83.62  E-value=3.4  Score=22.03  Aligned_cols=63  Identities=22%  Similarity=0.346  Sum_probs=41.4

Q ss_pred             CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCCCEEEEEC
Q ss_conf             776277514688746-58854887788379999500023588----446899889999998699971110599963
Q gi|254780913|r    3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYSAENLKLV   73 (78)
Q Consensus         3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i   73 (78)
                      .+|+|+---   -|| ||..    .++.+-++|+|.|...-.    ..|..||.|.-.+..-+..||. ...|+-+
T Consensus         9 v~G~V~~I~---~fGaFV~l----~~g~~GLvHISeis~~~V~~i~d~lkvGd~V~vKVi~id~~gKI-~LSiK~~   76 (139)
T PRK08582          9 LQGKVTGIT---NFGAFVEL----PEGKTGLVHISEVADNYVKDINDHLSVGDEVEVKVLNVEDDGKI-GLSIKKA   76 (139)
T ss_pred             EEEEEEEEE---CCEEEEEE----CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCCE-EEEHHHC
T ss_conf             999998996---41789995----69966788736625665689999578999999999988899970-5165554


No 39 
>PRK07899 rpsA 30S ribosomal protein S1; Reviewed
Probab=83.50  E-value=3.9  Score=21.67  Aligned_cols=51  Identities=22%  Similarity=0.304  Sum_probs=26.1

Q ss_pred             CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCC
Q ss_conf             776277514688746-5885488778837999950002358----8446899889999998699
Q gi|254780913|r    3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDA   61 (78)
Q Consensus         3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~   61 (78)
                      .+|+||..   .-|| ||..     ||-|=++|+|.|.-..    ...+..||.|+..+..-++
T Consensus       212 veG~Vk~I---t~fGAFVDL-----GGVDGLvHiSEiSW~Rv~~Psev~~vGd~V~VkVl~iD~  267 (484)
T PRK07899        212 RKGVVSSI---VNFGAFVDL-----GGVDGLVHVSELSWKHIDHPSEVVEVGDEVTVEVLDVDL  267 (484)
T ss_pred             EEEEEEEE---CCCEEEEEE-----CCEEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECC
T ss_conf             99999982---164689995-----572378981340356779989957799879999987747


No 40 
>smart00316 S1 Ribosomal protein S1-like RNA-binding domain.
Probab=83.28  E-value=3  Score=22.37  Aligned_cols=54  Identities=17%  Similarity=0.206  Sum_probs=39.0

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCC----CCCCCCCCCEEEEEEEECCCC
Q ss_conf             776277514688746588548877883799995000235----884468998899999986999
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~----g~~~l~~G~~V~F~i~~~~~~   62 (78)
                      .+|+|.-.++   +|++..-   .++-+-|+|.|.+...    ....+..|+.|.+.+..-+..
T Consensus         6 v~g~V~~v~~---~g~~v~i---~~~~~g~l~~~~l~~~~~~~~~~~~~~G~~v~~~V~~~~~~   63 (72)
T smart00316        6 VEGTVTEITP---FGAFVDL---GNGVEGLIPISELSDKRVKDPEEVLKVGDEVKVKVLSVDEE   63 (72)
T ss_pred             EEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEEEECC
T ss_conf             9999999978---7399997---69989999807505555478468363898999999999999


No 41 
>PRK11824 polynucleotide phosphorylase/polyadenylase; Provisional
Probab=82.73  E-value=3.8  Score=21.75  Aligned_cols=58  Identities=22%  Similarity=0.303  Sum_probs=40.3

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCC
Q ss_conf             77627751468874658854887788379999500023588----44689988999999869997111
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYS   66 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~   66 (78)
                      .+|+|+.--+   ||-.+--   -.|+|-++|+|.|.....    ..|++||.|...+..-+++||..
T Consensus       625 y~g~V~~i~~---fGafve~---~pg~~GLlHiSel~~~rv~~v~d~~~~Gd~i~Vk~~~id~~Gri~  686 (694)
T PRK11824        625 YEGKVVRIVD---FGAFVEI---LPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKRGRIR  686 (694)
T ss_pred             EEEEEEEEEE---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCEE
T ss_conf             9999999984---4189996---799806888002465234686451168988999999898999866


No 42 
>TIGR03591 polynuc_phos polyribonucleotide nucleotidyltransferase. Members of this protein family are polyribonucleotide nucleotidyltransferase, also called polynucleotide phosphorylase. Some members have been shown also to have additional functions as guanosine pentaphosphate synthetase and as poly(A) polymerase (see model TIGR02696 for an exception clade, within this family).
Probab=82.68  E-value=4.3  Score=21.47  Aligned_cols=57  Identities=23%  Similarity=0.316  Sum_probs=39.6

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCC
Q ss_conf             77627751468874658854887788379999500023588----4468998899999986999711
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKY   65 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~   65 (78)
                      .+|+|+---   -||-.+--   -.|+|=++|+|.|.....    ..|++||.|...+..-+++||.
T Consensus       622 y~g~V~~i~---~fGafve~---~pg~~GLlHiSel~~~rv~~v~dv~~~Gd~i~Vk~~~id~~Gri  682 (684)
T TIGR03591       622 YEGKVVRIM---DFGAFVEI---LPGKDGLVHISEIANERVEKVEDVLKEGDEVKVKVLEIDKQGRI  682 (684)
T ss_pred             EEEEEEEEE---ECEEEEEE---CCCCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEECCCCCC
T ss_conf             999999998---44089996---79981478700136534468645216898899999978899982


No 43 
>cd05684 S1_DHX8_helicase S1_DHX8_helicase: The  N-terminal S1 domain of human ATP-dependent RNA helicase DHX8, a DEAH (Asp-Glu-Ala-His) box polypeptide.  The DEAH-box RNA helicases are thought to play key roles in pre-mRNA splicing and DHX8 facilitates nuclear export of spliced mRNA by releasing the RNA from the spliceosome. DHX8 is also known as HRH1 (human RNA helicase 1) in Homo sapiens and PRP22 in Saccharomyces cerevisiae.
Probab=82.40  E-value=4.5  Score=21.36  Aligned_cols=68  Identities=22%  Similarity=0.328  Sum_probs=43.7

Q ss_pred             CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCCC-----CCCCCCCEEEEEEEECCCCCCCCCEEEEECCCC
Q ss_conf             776277514688746-58854887788379999500023588-----446899889999998699971110599963578
Q gi|254780913|r    3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAGL-----FNLTEGQLVTYDYVQNDANGKYSAENLKLVPKS   76 (78)
Q Consensus         3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g~-----~~l~~G~~V~F~i~~~~~~gk~~A~~v~~i~~~   76 (78)
                      .+|+|+..-   -|| ||..++ ...+.|=++|+|.|...+.     ..++.||.|...+..-++ +| -...++-+.+.
T Consensus         4 ~~G~V~~i~---~fGaFV~l~~-~~~~~~GLvHiSeis~~~~~~~~~~~~~~G~~V~vkVi~id~-~k-i~LS~K~~~~~   77 (79)
T cd05684           4 YKGKVTSIM---DFGCFVQLEG-LKGRKEGLVHISQLSFEGRVANPSDVVKRGQKVKVKVISIQN-GK-ISLSMKDVDQD   77 (79)
T ss_pred             EEEEEEEEE---EEEEEEEEEC-CCCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEEC-CE-EEEEEEECCCC
T ss_conf             999998997---5339999967-889806789956815755558988936799999999999869-98-88722613467


No 44 
>cd04473 S1_RecJ_like S1_RecJ_like: The S1 domain of the archaea-specific RecJ-like exonuclease. The function of this family is not fully understood. In Escherichia coli, RecJ degrades single-stranded DNA in the 5'-3' direction and participates in homologous recombination and mismatch repair.
Probab=81.62  E-value=4.8  Score=21.19  Aligned_cols=52  Identities=19%  Similarity=0.277  Sum_probs=36.6

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCC
Q ss_conf             77627751468874658854887788379999500023588446899889999998699971
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGK   64 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk   64 (78)
                      .+|+|...-   -||--..-   ..+.+=++|+|.+..    .+++|+.|.-.+..-+++||
T Consensus        20 y~G~V~~v~---~fGaFV~l---~~~~~GLiHiS~l~~----~~~vGD~V~VkV~~I~~~Gk   71 (77)
T cd04473          20 YKGKVNGVA---KYGVFVDL---NDHVRGLIHRSNLLR----DYEVGDEVIVQVTDIPENGN   71 (77)
T ss_pred             EEEEEEEEE---ECCEEEEC---CCCCEEEEEEHHCCC----CCCCCCEEEEEEEEECCCCC
T ss_conf             999998896---62889992---699879689316668----78999999999999999997


No 45 
>cd05689 S1_RPS1_repeat_ec4 S1_RPS1_repeat_ec4: 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 4 (ec4) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=80.96  E-value=4.2  Score=21.49  Aligned_cols=54  Identities=19%  Similarity=0.185  Sum_probs=36.2

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCC-----CCCCCCCCCEEEEEEEECCCC
Q ss_conf             776277514688746588548877883799995000235-----884468998899999986999
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASA-----GLFNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~-----g~~~l~~G~~V~F~i~~~~~~   62 (78)
                      .+|+|+--.   -||....   -+.|-|=++|+|.|.-.     ....++.||.|++.+.+-++.
T Consensus         7 v~G~V~~It---~fG~FV~---i~~g~eGLvHiSelsw~~~~~~p~~~~~~Gd~v~vkIl~iD~e   65 (72)
T cd05689           7 LFGKVTNLT---DYGCFVE---LEEGVEGLVHVSEMDWTNKNIHPSKVVSLGDEVEVMVLDIDEE   65 (72)
T ss_pred             EEEEEEEEE---CCEEEEE---ECCCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEEECC
T ss_conf             999998994---7623999---6699389999766316546679636038999999999999599


No 46 
>PRK06676 rpsA 30S ribosomal protein S1; Reviewed
Probab=80.81  E-value=3.7  Score=21.84  Aligned_cols=13  Identities=38%  Similarity=0.496  Sum_probs=4.8

Q ss_pred             CCCCCEEEEEEEE
Q ss_conf             6899889999998
Q gi|254780913|r   46 LTEGQLVTYDYVQ   58 (78)
Q Consensus        46 l~~G~~V~F~i~~   58 (78)
                      ++.||.|...+..
T Consensus       322 ~~~Gd~V~~~Vl~  334 (390)
T PRK06676        322 LEEGQEVKVKVLE  334 (390)
T ss_pred             CCCCCEEEEEEEE
T ss_conf             7899999999999


No 47 
>PRK05807 hypothetical protein; Provisional
Probab=80.40  E-value=4.9  Score=21.13  Aligned_cols=60  Identities=28%  Similarity=0.411  Sum_probs=40.1

Q ss_pred             CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCCCCCEEEE
Q ss_conf             776277514688746-58854887788379999500023588----4468998899999986999711105999
Q gi|254780913|r    3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGKYSAENLK   71 (78)
Q Consensus         3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk~~A~~v~   71 (78)
                      .+|+|+-.-   -|| ||..+     |.+=+||+|.|...-.    ..|.+||.|...+..-+.+||. ...++
T Consensus         9 v~G~V~~I~---~fGaFV~l~-----g~~GLvHISEis~~~Vk~i~d~lk~Gd~V~vkVl~iD~~gkI-~LSiK   73 (136)
T PRK05807          9 LEGTVVNIT---NFGAFVEVE-----GKTGLVHISEVADTYVKDIREHLKEQDKVKVKVISIDDNGKI-SLSIK   73 (136)
T ss_pred             EEEEEEEEE---CCEEEEEEC-----CEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEECCCCCC-EEEHH
T ss_conf             999999997---244799978-----927689856707764369999678999999999998999981-43322


No 48 
>cd05686 S1_pNO40 S1_pNO40: pNO40 , S1-like RNA-binding domain. pNO40 is a nucleolar protein of unknown function with an N-terminal S1 RNA binding domain, a CCHC type zinc finger, and clusters of basic amino acids representing a potential nucleolar targeting signal.  pNO40 was identified through a yeast two-hybrid interaction screen of a human kidney cDNA library using the pinin (pnn) protein as bait. pNO40 is thought to play a role in ribosome maturation and/or biogenesis.
Probab=79.91  E-value=5  Score=21.09  Aligned_cols=56  Identities=20%  Similarity=0.355  Sum_probs=37.3

Q ss_pred             CCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCCCC
Q ss_conf             776277514688746-58854887788379999500023588----446899889999998699971
Q gi|254780913|r    3 HRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDANGK   64 (78)
Q Consensus         3 ~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~gk   64 (78)
                      .+|+|+.--   -|| ||..++.   +.|=++|+|.|...-.    ..|+.||.|.-.+..-+.++|
T Consensus         7 ~~G~V~~i~---~fGAFV~i~g~---~~~GLvHiSeis~~rv~~~~dvv~vGd~V~Vkvi~id~~~k   67 (73)
T cd05686           7 FKGEVASVT---EYGAFVKIPGC---RKQGLVHKSHMSSCRVDDPSEVVDVGEKVWVKVIGREMKDK   67 (73)
T ss_pred             EEEEEEEEE---ECCEEEEECCC---CCCEEEEEECCCCCCCCCHHHHCCCCCEEEEEEEEECCCCC
T ss_conf             999998997---53239990898---84355995605412028999955799999999998868998


No 49 
>PRK12269 bifunctional cytidylate kinase/ribosomal protein S1; Provisional
Probab=78.29  E-value=6.2  Score=20.57  Aligned_cols=33  Identities=21%  Similarity=0.250  Sum_probs=15.3

Q ss_pred             CCCEEEEEEEECCC--C---CCCCCCCCCEEEEEEEEC
Q ss_conf             88379999500023--5---884468998899999986
Q gi|254780913|r   27 SGDDVFLHRSAVAS--A---GLFNLTEGQLVTYDYVQN   59 (78)
Q Consensus        27 ~g~DvFvH~s~i~~--~---g~~~l~~G~~V~F~i~~~   59 (78)
                      ++-|-|+|.|+|.=  .   ..+..+.|+.|++.+..-
T Consensus       687 ~gIDGlvH~sDlSW~~~~~~~~~~~kkGd~ve~kVL~I  724 (863)
T PRK12269        687 EGIDGFLHVDDLSWVKRTRPADHELEVGKEIECMVIEC  724 (863)
T ss_pred             CCCEEEEEHHHCCCCCCCCCHHHHCCCCCEEEEEEEEE
T ss_conf             99367898210676787726566257898799999997


No 50 
>PRK13806 rpsA 30S ribosomal protein S1; Provisional
Probab=78.03  E-value=5.6  Score=20.82  Aligned_cols=49  Identities=16%  Similarity=0.259  Sum_probs=19.7

Q ss_pred             CCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEE
Q ss_conf             762775146887465885488778837999950002358----8446899889999998
Q gi|254780913|r    4 RGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQ   58 (78)
Q Consensus         4 ~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~   58 (78)
                      +|+|+-..+   ||-.+.-   ..|-|-|+|+|.|.-..    ...+..||.|...+..
T Consensus       206 ~G~V~~i~~---~GaFVdl---~~GvdGllHiSeiSw~rv~~p~~~~~vGd~v~vkVl~  258 (489)
T PRK13806        206 EGTVTRLAP---FGAFVEI---APGVEGMVHISELSWSRVQQADEAVSVGDRVRVKVLG  258 (489)
T ss_pred             CEEEEEECC---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHEECCCCEEEEEEEE
T ss_conf             429999757---5389993---7980799983555865668888945169889999999


No 51 
>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=77.52  E-value=6.5  Score=20.44  Aligned_cols=52  Identities=21%  Similarity=0.246  Sum_probs=35.8

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCC
Q ss_conf             77627751468874658854887788379999500023588----446899889999998699
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDA   61 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~   61 (78)
                      .+|+|+-..   -||....-   + +-+-|+|+|.|.....    ..++.||.|...+..-++
T Consensus         5 v~g~V~~i~---~fG~FV~l---~-gi~Glihisels~~~~~~~~~~~k~Gd~v~~kVi~iD~   60 (68)
T cd05688           5 VEGTVKSIT---DFGAFVDL---G-GVDGLLHISDMSWGRVKHPSEVVNVGDEVEVKVLKIDK   60 (68)
T ss_pred             EEEEEEEEE---CCEEEEEE---C-CEEEEEECHHHCCCCCCCHHHHCCCCCEEEEEEEEEEC
T ss_conf             999999995---63889997---9-98999984364666668988914799999999999999


No 52 
>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=76.09  E-value=7.2  Score=20.21  Aligned_cols=55  Identities=18%  Similarity=0.306  Sum_probs=36.8

Q ss_pred             CCCCEEEEEECCCCEEEEE-ECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCC
Q ss_conf             8776277514688746588-54887788379999500023588----4468998899999986999
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFIT-PEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~-~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~   62 (78)
                      ..+|+|+--.   -||... .++   .+-+=|+|+|.|.....    ..++.||.|...+.+-+..
T Consensus         5 ~v~G~V~~i~---~fG~FV~l~g---~~i~GLvHiSels~~~~~~~~~~~~~Gd~V~vkVl~iD~e   64 (77)
T cd05708           5 KIDGTVRRVE---DYGVFIDIDG---TNVSGLCHKSEISDNRVADASKLFRVGDKVRAKVLKIDAE   64 (77)
T ss_pred             EEEEEEEEEE---CEEEEEEECC---CCEEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECC
T ss_conf             9999999996---4178999678---9807998878817565689889168999999999999899


No 53 
>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=75.50  E-value=7.5  Score=20.12  Aligned_cols=54  Identities=19%  Similarity=0.210  Sum_probs=36.8

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCC
Q ss_conf             87762775146887465885488778837999950002358----8446899889999998699
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDA   61 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~   61 (78)
                      ..+|+|+-..   -||-...   ...+-|=++|+|.|....    ...++.||.|...+..-+.
T Consensus         3 iv~G~V~~i~---~fG~FV~---l~~~~~GLvhisels~~~~~~~~~~~~vGd~v~~kVi~id~   60 (68)
T cd05685           3 VLEGVVTNVT---DFGAFVD---IGVKQDGLIHISKMADRFVSHPSDVVSVGDIVEVKVISIDE   60 (68)
T ss_pred             EEEEEEEEEE---CEEEEEE---ECCCCEEEEECHHHCCCCCCCHHHCCCCCCEEEEEEEEEEC
T ss_conf             9999999996---5289999---14997899981897678767986857999999999999989


No 54 
>COG4776 Rnb Exoribonuclease II [Transcription]
Probab=73.80  E-value=5  Score=21.07  Aligned_cols=54  Identities=20%  Similarity=0.370  Sum_probs=35.5

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEE
Q ss_conf             7762775146887465885488778837999950002358844689988999999869997111059
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAEN   69 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~   69 (78)
                      ..|+||-  .+|||||+..|    ..+-+|+---.     .+.+.-|+++.--+...  +-|.+|+-
T Consensus        22 vEGvVK~--tekgfGFLEvD----~qkSYFIpPp~-----MKkvMHGDkIiA~i~te--~erE~aEP   75 (645)
T COG4776          22 VEGVVKA--TEKGFGFLEVD----AQKSYFIPPPQ-----MKKVMHGDKIIAVIHTE--KERESAEP   75 (645)
T ss_pred             CCEEEEE--CCCCCEEEEEC----CCCCCCCCCHH-----HHHHCCCCEEEEEEEEC--CCCCCCCH
T ss_conf             0105740--45641028875----76540138878-----86521567589998742--74010586


No 55 
>cd05690 S1_RPS1_repeat_ec5 S1_RPS1_repeat_ec5: 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 5 (ec5) of the Escherichia coli RPS1. Autoantibodies to double-stranded DNA from patients with systemic lupus erythematosus cross-react with the human RPS1 homolog.
Probab=72.87  E-value=7.8  Score=20.01  Aligned_cols=52  Identities=23%  Similarity=0.244  Sum_probs=35.6

Q ss_pred             CCCEEEEEECCCCEEE-EEECCCCCCCCEEEEEEEECCCC-----CCCCCCCCCEEEEEEEECCC
Q ss_conf             7762775146887465-88548877883799995000235-----88446899889999998699
Q gi|254780913|r    3 HRGSIKWYNPDKGYGF-ITPEGSTESGDDVFLHRSAVASA-----GLFNLTEGQLVTYDYVQNDA   61 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGF-I~~d~~~d~g~DvFvH~s~i~~~-----g~~~l~~G~~V~F~i~~~~~   61 (78)
                      .+|+|+-.-   -||. |..    +++-|=++|+|.+.-.     ....++.||.|+..+..-+.
T Consensus         4 v~G~V~~i~---~fG~FV~l----~~gieGLvHiselsw~~~~~~~~~~~~~Gd~V~vkVl~iD~   61 (69)
T cd05690           4 VSGKIKSIT---DFGIFVGL----DGGIDGLVHISDISWTQRVRHPSEIYKKGQEVEAVVLNIDV   61 (69)
T ss_pred             EEEEEEEEC---CCEEEEEE----CCCCEEEEEHHHHCCCCCCCCHHHCCCCCCEEEEEEEEEEC
T ss_conf             999999991---31899997----69965999948824566667976825899999999999979


No 56 
>cd04453 S1_RNase_E S1_RNase_E: RNase E and RNase G, S1-like RNA-binding domain. RNase E is an essential endoribonuclease in the processing and degradation of RNA. In addition to its role in mRNA degradation, RNase E has also been implicated in the processing of rRNA, and the maturation of tRNA, 10Sa RNA and the M1 precursor of RNase P. RNase E associates with PNPase (3' to 5' exonuclease), Rhl B (DEAD-box RNA helicase) and enolase (glycolytic enzyme)  to form the RNA degradosome. RNase E tends to cut mRNA within single-stranded regions that are rich in A/U nucleotides. The N-terminal region of RNase E contains the catalytic site. Within the conserved N-terminal domain of RNAse E and RNase G, there is an S1-like subdomain, which is an ancient single-stranded RNA-binding domain. S1 domain is an RNA-binding module originally identified in the ribosomal protein S1. The S1 domain is required for RNA cleavage by RNase E. RNase G is paralogous to RNase E with an N-terminal catalytic domain th
Probab=69.48  E-value=10  Score=19.31  Aligned_cols=58  Identities=28%  Similarity=0.271  Sum_probs=42.2

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC-------CCCCCCCCEEEEEEEECCCCCC
Q ss_conf             7762775146887465885488778837999950002358-------8446899889999998699971
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG-------LFNLTEGQLVTYDYVQNDANGK   64 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g-------~~~l~~G~~V~F~i~~~~~~gk   64 (78)
                      ..|+|+-..+.=.==||...    .+++-|+|++++....       -..|.+||.|-.++...+.+.|
T Consensus        11 Y~GkV~~v~p~i~AAFVdiG----~~k~gfL~~~d~~~~~~~~~~~~~~~l~~G~~ilVQV~Ke~~~~K   75 (88)
T cd04453          11 YLGRVKKIVPGLQAAFVDIG----LGKNGFLHLSDILPAYFKKHKKIAKLLKEGQEILVQVVKEPIGTK   75 (88)
T ss_pred             EEEEEEEECCCCCEEEEECC----CCCCEEEECHHCCHHHHCCCCCHHHHCCCCCEEEEEEEECCCCCC
T ss_conf             99999886668748999658----986899990345723513578877837799999999976687997


No 57 
>cd04452 S1_IF2_alpha S1_IF2_alpha: The alpha subunit of translation Initiation Factor 2, S1-like RNA-binding domain. S1-like RNA-binding domains are found in a wide variety of RNA-associated proteins. Eukaryotic and archaeal Initiation Factor 2 (e- and aIF2, respectively) are heterotrimeric proteins with three subunits (alpha, beta, and gamma). IF2 plays a crucial role in the process of translation initiation. The IF2 gamma subunit contains a GTP-binding site. The IF2 beta and gamma subunits together are thought to be responsible for binding methionyl-initiator tRNA. The ternary complex consisting of IF2, GTP, and the methionyl-initiator tRNA binds to the small subunit of the ribosome, as part of a pre-initiation complex that scans the mRNA to find the AUG start codon. The IF2-bound GTP is hydrolyzed to GDP when the methionyl-initiator tRNA binds the AUG start codon, at which time the IF2 is released with its bound GDP. The large ribosomal subunit then joins with the small subunit to c
Probab=68.29  E-value=11  Score=19.16  Aligned_cols=57  Identities=11%  Similarity=0.023  Sum_probs=38.0

Q ss_pred             CCCEEEEEECCCCEEEE-EECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCC-CCC
Q ss_conf             77627751468874658-854887788379999500023588----446899889999998699-971
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFI-TPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDA-NGK   64 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI-~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~-~gk   64 (78)
                      .+|+|+--.   -||.. ..+.  -+|.+=|+|+|.|...-.    ..++.||.|...+..-++ +++
T Consensus         7 v~G~V~~i~---~~GafV~l~e--~~g~eGlihiSEis~~~v~~~~d~~~~G~~v~~kVi~vD~~k~~   69 (76)
T cd04452           7 VVVTVKSIA---DMGAYVSLLE--YGNIEGMILLSELSRRRIRSIRKLVKVGRKEVVKVIRVDKEKGY   69 (76)
T ss_pred             EEEEEEEEE---CCEEEEEECC--CCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEECCCCE
T ss_conf             999999997---3469999733--69919999979968451159999558999999999999789999


No 58 
>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=67.30  E-value=12  Score=19.05  Aligned_cols=56  Identities=13%  Similarity=0.112  Sum_probs=38.4

Q ss_pred             CCCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCC
Q ss_conf             987762775146887465885488778837999950002358----84468998899999986999
Q gi|254780913|r    1 MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus         1 mm~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~   62 (78)
                      +..+|+|+...   -||....   -.++-|=++|.|.+....    ......||.|.+.+..-+..
T Consensus         2 ~iv~G~V~~i~---~fG~fV~---l~~~i~Glv~~s~lsd~~v~~p~~~fk~G~~Vk~rVl~vD~~   61 (69)
T cd05697           2 QVVKGTIRKLR---PSGIFVK---LSDHIKGLVPPMHLADVRLKHPEKKFKPGLKVKCRVLSVEPE   61 (69)
T ss_pred             CEEEEEEEEEC---CCEEEEE---ECCCEEEEEEHHHHCCCCCCCHHHCCCCCCEEEEEEEEEECC
T ss_conf             99999999973---8427999---579906998789908652069889089999999999999488


No 59 
>PRK11637 hypothetical protein; Provisional
Probab=67.15  E-value=12  Score=19.07  Aligned_cols=51  Identities=14%  Similarity=0.176  Sum_probs=34.6

Q ss_pred             CCCEEEEEECCCCEEEEE-ECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEE
Q ss_conf             776277514688746588-5488778837999950002358844689988999
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFIT-PEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTY   54 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~-~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F   54 (78)
                      ..|+|.+=+.-+|||-++ .|+ .++=--++-|.|.|...--..+..||.+-.
T Consensus       322 ~~G~Vv~a~~~~gyG~~ViIdH-G~g~~TlYah~s~l~v~~Gq~V~~Gq~Ig~  373 (404)
T PRK11637        322 ADGRVILADWLQGYGLVVVVEH-GKGDMSLYGYNQSALVSVGAQVRAGQPIAL  373 (404)
T ss_pred             CCEEEEEEEECCCCCCEEEEEC-CCCCEEECCCCCCCCCCCCCEECCCCEEEE
T ss_conf             1769999114088885799986-994657152889588899799899996987


No 60 
>TIGR01622 SF-CC1 splicing factor, CC1-like family; InterPro: IPR006509   These sequences represent a subfamily of RNA splicing factors including the Pad-1 protein (Neurospora crassa), CAPER (mouse) and CC1.3 (human). All are characterised by an N-terminal arginine-rich, low complexity domain followed by three (or in the case of 4 human paralogs, two) RNA recognition domains. These splicing factors are closely related to the U2AF splicing factor family (IPR006529 from INTERPRO). ; GO: 0003723 RNA binding, 0006397 mRNA processing, 0005634 nucleus.
Probab=66.41  E-value=2.2  Score=23.10  Aligned_cols=10  Identities=60%  Similarity=1.075  Sum_probs=7.7

Q ss_pred             CCCEEEEEEC
Q ss_conf             8874658854
Q gi|254780913|r   13 DKGYGFITPE   22 (78)
Q Consensus        13 ~kGfGFI~~d   22 (78)
                      .||||||+--
T Consensus       276 SkGyGFiqF~  285 (531)
T TIGR01622       276 SKGYGFIQFR  285 (531)
T ss_pred             CCCCCEEEEC
T ss_conf             3254005511


No 61 
>PRK03987 translation initiation factor IF-2 subunit alpha; Validated
Probab=64.96  E-value=11  Score=19.08  Aligned_cols=54  Identities=30%  Similarity=0.370  Sum_probs=35.2

Q ss_pred             CCEEEEEECCCCEEEE-EECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCC
Q ss_conf             7627751468874658-85488778837999950002358----84468998899999986999
Q gi|254780913|r    4 RGSIKWYNPDKGYGFI-TPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus         4 ~G~VKwfn~~kGfGFI-~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~   62 (78)
                      .|+|+--.   -||.. ..+.  -+|.+-|+|+|.|...-    ...|++||.|...+..-++.
T Consensus        13 ~~~V~~i~---~~Ga~v~l~e--y~~~eG~i~isEis~~~v~~i~d~~k~G~~v~~kVi~vd~~   71 (262)
T PRK03987         13 VGTVKEVK---DFGAFVTLDE--YPGKEGFIHISEVASGWVKNIRDYVKEGQKVVCKVIRVDPK   71 (262)
T ss_pred             EEEEEEEE---CCEEEEEECC--CCCCCEEEEHHHCCHHHHHCHHHHCCCCCEEEEEEEEECCC
T ss_conf             99999995---6679999356--59931678879834677519998515898899999988387


No 62 
>KOG0125 consensus
Probab=63.59  E-value=3  Score=22.30  Aligned_cols=18  Identities=39%  Similarity=0.861  Sum_probs=12.7

Q ss_pred             EEEC--CCCEEEEEECCCCC
Q ss_conf             5146--88746588548877
Q gi|254780913|r    9 WYNP--DKGYGFITPEGSTE   26 (78)
Q Consensus         9 wfn~--~kGfGFI~~d~~~d   26 (78)
                      -||+  .|||||+|-|...|
T Consensus       129 IfNERGSKGFGFVTmen~~d  148 (376)
T KOG0125         129 IFNERGSKGFGFVTMENPAD  148 (376)
T ss_pred             EECCCCCCCCCEEEECCHHH
T ss_conf             86367777523487228246


No 63 
>cd05698 S1_Rrp5_repeat_hs6_sc5 S1_Rrp5_repeat_hs6_sc5: 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 6 (hs6) and S. cerevisiae S1 repeat 5 (sc5). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=56.59  E-value=18  Score=17.93  Aligned_cols=56  Identities=21%  Similarity=0.230  Sum_probs=38.3

Q ss_pred             CCCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCC----CCCCCCCEEEEEEEECCCC
Q ss_conf             9877627751468874658854887788379999500023588----4468998899999986999
Q gi|254780913|r    1 MVHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGL----FNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus         1 mm~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~----~~l~~G~~V~F~i~~~~~~   62 (78)
                      |..+|+|+-..   -||-+..-   .++-+-|+|.|.+.....    ..+..||.|...+..-+..
T Consensus         2 ~vv~G~V~~i~---~~G~fV~~---~~~i~Glvp~seis~~~v~~p~~~f~~Gq~V~v~Vl~vd~~   61 (70)
T cd05698           2 LKTHGTIVKVK---PNGCIVSF---YNNVKGFLPKSELSEAFIKDPEEHFRVGQVVKVKVLSCDPE   61 (70)
T ss_pred             CEEEEEEEEEE---CCCEEEEE---CCCCEEEEEHHHHCCCCCCCHHHHCCCCCEEEEEEEEEECC
T ss_conf             99999999998---17189994---89969998989928320289899377999999999998089


No 64 
>COG1093 SUI2 Translation initiation factor 2, alpha subunit (eIF-2alpha) [Translation, ribosomal structure and biogenesis]
Probab=56.53  E-value=8.5  Score=19.79  Aligned_cols=53  Identities=30%  Similarity=0.422  Sum_probs=36.1

Q ss_pred             CEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCC
Q ss_conf             6277514688746-5885488778837999950002358----84468998899999986999
Q gi|254780913|r    5 GSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus         5 G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~   62 (78)
                      |+|+-   -..|| |+..|.  -+|.+-|+|+|.+...-    ...+++||+|-+.+..-+++
T Consensus        17 ~tV~~---V~~~GA~v~L~E--Y~g~Eg~ihiSEvas~wVknIrd~vkegqkvV~kVlrVd~~   74 (269)
T COG1093          17 GTVKQ---VADYGAYVELDE--YPGKEGFIHISEVASGWVKNIRDYVKEGQKVVAKVLRVDPK   74 (269)
T ss_pred             EEEEE---EECCCCEEEEEC--CCCEEEEEEHHHHHHHHHHHHHHHHHCCCEEEEEEEEECCC
T ss_conf             99998---604642798420--59962267789987789988999861698699999888687


No 65 
>cd05702 S1_Rrp5_repeat_hs11_sc8 S1_Rrp5_repeat_hs11_sc8: 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 11 (hs11) and S. cerevisiae S1 repeat 8 (sc8). Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=54.18  E-value=19  Score=17.92  Aligned_cols=54  Identities=13%  Similarity=0.055  Sum_probs=34.9

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCC------CCCCCCCCCCEEEEEEEECCCCC
Q ss_conf             77627751468874658854887788379999500023------58844689988999999869997
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVAS------AGLFNLTEGQLVTYDYVQNDANG   63 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~------~g~~~l~~G~~V~F~i~~~~~~g   63 (78)
                      .+|+|+.-.   .||....-   .++-.=++|+|.+-.      .....+++||.|+..+.- -+..
T Consensus         4 v~g~V~sik---~~~l~V~L---~d~~~GrVhiSei~D~~~~~k~P~~~~k~Gq~V~~rViG-~~d~   63 (70)
T cd05702           4 VKAKVKSVK---PTQLNVQL---ADNVHGRIHVSEVFDEWPDGKNPLSKFKIGQKIKARVIG-GHDA   63 (70)
T ss_pred             EEEEEEEEE---CCEEEEEE---CCCCEEEEEHHHCCCCCCCCCCHHHHCCCCCEEEEEEEE-EECC
T ss_conf             999999994---67089996---899577898455213555556946856899999999997-6546


No 66 
>cd04461 S1_Rrp5_repeat_hs8_sc7 S1_Rrp5_repeat_hs8_sc7: Rrp5 Homo sapiens S1 repeat 8 (hs8) and Saccharomyces cerevisiae S1 repeat 7 (sc7)-like domains. 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 S. cerevisiae Rrp5 and 14 S1 repeats in H. 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 8 and S. cerevisiae S1 repeat 7. Rrp5 is found in eukaryotes but not in prokaryotes or archaea.
Probab=50.95  E-value=23  Score=17.41  Aligned_cols=54  Identities=24%  Similarity=0.297  Sum_probs=37.3

Q ss_pred             CCCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCC
Q ss_conf             87762775146887465885488778837999950002358----8446899889999998699
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDA   61 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~   61 (78)
                      ..+|+|+...+   ||..+.-   .++-+=|+|.|.+....    ...+..||.|...+..-+.
T Consensus        17 iv~G~V~~i~~---~G~FV~l---~~~v~Glv~~s~ls~~~~~~~~~~~~vGq~V~~~V~~iD~   74 (83)
T cd04461          17 VVHGYVRNITP---YGVFVEF---LGGLTGLAPKSYISDEFVTDPSFGFKKGQSVTAKVTSVDE   74 (83)
T ss_pred             EEEEEEEEEEC---CEEEEEE---CCCCEEEEEHHHCCCCCCCCHHHHCCCCCEEEEEEEEEEC
T ss_conf             99999999927---8199995---6994899899996864226989945599999999999958


No 67 
>COG0539 RpsA Ribosomal protein S1 [Translation, ribosomal structure and biogenesis]
Probab=47.61  E-value=26  Score=17.10  Aligned_cols=13  Identities=15%  Similarity=0.253  Sum_probs=5.1

Q ss_pred             CCCCCEEEEEEEE
Q ss_conf             6899889999998
Q gi|254780913|r   46 LTEGQLVTYDYVQ   58 (78)
Q Consensus        46 l~~G~~V~F~i~~   58 (78)
                      ++.||.|...+..
T Consensus       236 vkvGd~VkvkVi~  248 (541)
T COG0539         236 VKVGDEVKVKVIS  248 (541)
T ss_pred             CCCCCEEEEEEEE
T ss_conf             3569889999999


No 68 
>pfam11604 CusF_Ec Copper binding periplasmic protein CusF. CusF is a periplasmic protein involved in copper and silver resistance in Escherichia coil. CusF forms a five-stranded beta-barrel OB fold. Cu(I) binds to H36, M47 and M49 which are conserved residues in the protein.
Probab=46.93  E-value=19  Score=17.89  Aligned_cols=20  Identities=25%  Similarity=0.529  Sum_probs=15.7

Q ss_pred             CCCCCCCCCEEEEEEEECCC
Q ss_conf             88446899889999998699
Q gi|254780913|r   42 GLFNLTEGQLVTYDYVQNDA   61 (78)
Q Consensus        42 g~~~l~~G~~V~F~i~~~~~   61 (78)
                      -+..|.+|++|.|++.+...
T Consensus        39 ~l~~l~~G~~V~F~~~~~~~   58 (61)
T pfam11604        39 DLAGLKPGDKVRFEFEKGDD   58 (61)
T ss_pred             HHHCCCCCCEEEEEEEECCC
T ss_conf             87449999989999997889


No 69 
>COG2190 NagE Phosphotransferase system IIA components [Carbohydrate transport and metabolism]
Probab=45.37  E-value=28  Score=16.90  Aligned_cols=45  Identities=20%  Similarity=0.434  Sum_probs=30.0

Q ss_pred             CCEE-EEEECCCCEEEEEECCCCCCCCEEEEEEE----ECCCCCCC-CCCCCCEEE
Q ss_conf             7627-75146887465885488778837999950----00235884-468998899
Q gi|254780913|r    4 RGSI-KWYNPDKGYGFITPEGSTESGDDVFLHRS----AVASAGLF-NLTEGQLVT   53 (78)
Q Consensus         4 ~G~V-Kwfn~~kGfGFI~~d~~~d~g~DvFvH~s----~i~~~g~~-~l~~G~~V~   53 (78)
                      .|+| .-|...-.||+.+     +.|-++++|+-    .|...|+. .+++||+|.
T Consensus        50 dG~v~~iFpTkHAigi~t-----~~GvEiLiHiGiDTV~L~GegF~~~v~~Gd~Vk  100 (156)
T COG2190          50 DGTVVLIFPTKHAIGIET-----DEGVEILIHIGIDTVKLNGEGFESLVKEGDKVK  100 (156)
T ss_pred             CCEEEEEEECCCEEEEEC-----CCCCEEEEEECEEEEEECCCCEEEEEECCCEEC
T ss_conf             858999851784799983-----899599999564058688932478750799881


No 70 
>KOG0149 consensus
Probab=44.91  E-value=10  Score=19.38  Aligned_cols=13  Identities=46%  Similarity=0.807  Sum_probs=9.8

Q ss_pred             EECCCCEEEEEEC
Q ss_conf             1468874658854
Q gi|254780913|r   10 YNPDKGYGFITPE   22 (78)
Q Consensus        10 fn~~kGfGFI~~d   22 (78)
                      =...|||||+|--
T Consensus        50 t~rskGyGfVTf~   62 (247)
T KOG0149          50 TGRSKGYGFVTFR   62 (247)
T ss_pred             CCCCCCEEEEEEE
T ss_conf             7642324568861


No 71 
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor; InterPro: IPR006548   These sequences represent the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human . ELAV stands for the Drosophila Embryonic lethal abnormalvisual protein . ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (IPR006546 from INTERPRO). ; GO: 0003723 RNA binding.
Probab=42.90  E-value=9.5  Score=19.54  Aligned_cols=11  Identities=55%  Similarity=1.011  Sum_probs=5.6

Q ss_pred             ECCCCEEEEEE
Q ss_conf             46887465885
Q gi|254780913|r   11 NPDKGYGFITP   21 (78)
Q Consensus        11 n~~kGfGFI~~   21 (78)
                      |.=|||||++=
T Consensus       392 n~CKGygFVsM  402 (436)
T TIGR01661       392 NKCKGYGFVSM  402 (436)
T ss_pred             CCCCCCEEEEC
T ss_conf             85121123524


No 72 
>COG1185 Pnp Polyribonucleotide nucleotidyltransferase (polynucleotide phosphorylase) [Translation, ribosomal structure and biogenesis]
Probab=41.22  E-value=33  Score=16.53  Aligned_cols=59  Identities=22%  Similarity=0.277  Sum_probs=41.4

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCC----CCCCCCCCEEEEEEEECCCCCCCCC
Q ss_conf             7762775146887465885488778837999950002358----8446899889999998699971110
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAG----LFNLTEGQLVTYDYVQNDANGKYSA   67 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g----~~~l~~G~~V~F~i~~~~~~gk~~A   67 (78)
                      ..|+|+.-.+   ||--+-   --.|+|-++|+|.+....    -..|++||.|...+..-++.||...
T Consensus       623 y~G~V~ri~~---fGaFv~---l~~gkdgl~hiS~~~~~rv~kv~dvlk~Gd~v~Vkv~~iD~~Gri~l  685 (692)
T COG1185         623 YEGTVVRIVD---FGAFVE---LLPGKDGLVHISQLAKERVEKVEDVLKEGDEVKVKVIEIDKQGRIRL  685 (692)
T ss_pred             EEEEEEEEEE---CCEEEE---ECCCCCEEEEEHHHHHHHHHCCCCEEECCCEEEEEEEEECCCCCCCC
T ss_conf             9988999864---125898---33896206874353345553204535448659999963366677032


No 73 
>PTZ00162 RNA polymerase II subunit 7; Provisional
Probab=40.97  E-value=33  Score=16.51  Aligned_cols=41  Identities=20%  Similarity=0.366  Sum_probs=27.3

Q ss_pred             CEEEEEECCCCCCCCEEEEEEEECCCC--------------CCCCCCCCCEEEEEEEEC
Q ss_conf             746588548877883799995000235--------------884468998899999986
Q gi|254780913|r   15 GYGFITPEGSTESGDDVFLHRSAVASA--------------GLFNLTEGQLVTYDYVQN   59 (78)
Q Consensus        15 GfGFI~~d~~~d~g~DvFvH~s~i~~~--------------g~~~l~~G~~V~F~i~~~   59 (78)
                      -|||...-++    -|+|+|.|.+..+              .-+.|+.|+.|.+.++-.
T Consensus        94 ~~G~fv~~GP----l~~fv~~s~i~~d~~yd~~~~~~~~~~~~~~i~kgd~VR~rIvg~  148 (170)
T PTZ00162         94 KLGFFAQAGP----LKIFVSRTAIPPNFVYDSDSAYPCFSDGTISIKPQSEVRLRLQGI  148 (170)
T ss_pred             CCEEEEEECC----EEEEEEHHHCCCCCEECCCCCCCEECCCCCEECCCCEEEEEEEEE
T ss_conf             4079999128----089989899998648978998604827883888899999999998


No 74 
>PRK09838 periplasmic copper-binding protein; Provisional
Probab=40.70  E-value=33  Score=16.48  Aligned_cols=69  Identities=13%  Similarity=0.177  Sum_probs=36.7

Q ss_pred             CCCCEEEEEECCCCEEEEEECCC-CCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEEE
Q ss_conf             87762775146887465885488-778837999950002358844689988999999869997111059996
Q gi|254780913|r    2 VHRGSIKWYNPDKGYGFITPEGS-TESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLKL   72 (78)
Q Consensus         2 m~~G~VKwfn~~kGfGFI~~d~~-~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~~   72 (78)
                      +-+|+|+-.|.+.|-=-|.-+-- +-+-+-.=.-+..-...-+..|++|++|.|+.++.  ++.+.-.+|++
T Consensus        43 ~~~G~V~~ID~~~~kVTI~H~pI~aL~WPaMTM~F~v~~~~~l~~lk~Gd~V~F~Fvq~--G~~~~l~~I~~  112 (114)
T PRK09838         43 SATGVVKGIDLESKKITIHHEPIPAVNWPEMTMRFTITPQTKMSEIKTGDKVAFNFVQQ--GNLSLLQDIKV  112 (114)
T ss_pred             EEEEEEEEEECCCCEEEEECCCCCCCCCCCCEEEEECCCHHHHHCCCCCCEEEEEEEEE--CCEEEEEEEEE
T ss_conf             73479999826799799825861306998635763338956760599999899999963--99779999886


No 75 
>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=40.48  E-value=34  Score=16.46  Aligned_cols=57  Identities=32%  Similarity=0.343  Sum_probs=37.5

Q ss_pred             CCCCCEEEEEECCCCEE-EEEECCCCCCCCEEEEEEEECCCC----CCCCCCCCCEEEEEEEECCC-CCC
Q ss_conf             98776277514688746-588548877883799995000235----88446899889999998699-971
Q gi|254780913|r    1 MVHRGSIKWYNPDKGYG-FITPEGSTESGDDVFLHRSAVASA----GLFNLTEGQLVTYDYVQNDA-NGK   64 (78)
Q Consensus         1 mm~~G~VKwfn~~kGfG-FI~~d~~~d~g~DvFvH~s~i~~~----g~~~l~~G~~V~F~i~~~~~-~gk   64 (78)
                      |..+|+||.-.   -|| |+...    .+.|-++|+|.|...    -...+..||.|.-.+..-+. .+|
T Consensus         2 ~~v~G~V~~i~---~~G~FV~l~----~~~~glVhiselsd~fVkd~~~~f~vGq~V~~kV~~iD~~~~r   64 (68)
T cd05707           2 DVVRGFVKNIA---NNGVFVTLG----RGVDARVRVSELSDSYLKDWKKRFKVGQLVKGKIVSIDPDNGR   64 (68)
T ss_pred             CEEEEEEEEEC---CCCEEEEEC----CCCEEEEEHHHHCHHHHCCHHHHCCCCCEEEEEEEEEECCCCE
T ss_conf             99899999803---640799917----9967999959917235649989179999999999998287586


No 76 
>cd02787 MopB_CT_ydeP The MopB_CT_ydeP CD includes a group of related uncharacterized bacterial molybdopterin-binding oxidoreductase-like domains with a putative molybdopterin cofactor binding site. This CD is of the conserved molybdopterin_binding C-terminal (MopB_CT) region present in many, but not all, MopB homologs.
Probab=38.26  E-value=27  Score=17.02  Aligned_cols=29  Identities=28%  Similarity=0.423  Sum_probs=22.2

Q ss_pred             CCEEEEEEEECCCCCCCCCCCCCEEEEEEEEC
Q ss_conf             83799995000235884468998899999986
Q gi|254780913|r   28 GDDVFLHRSAVASAGLFNLTEGQLVTYDYVQN   59 (78)
Q Consensus        28 g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~   59 (78)
                      ...||+|-.+++..|   |++|++|...-..+
T Consensus        30 R~vVfMNp~D~~~lG---l~~Gd~V~l~S~~g   58 (112)
T cd02787          30 RDVVFMNPDDIARLG---LKAGDRVDLESAFG   58 (112)
T ss_pred             EEEEEECHHHHHHCC---CCCCCEEEEEEECC
T ss_conf             259998899999829---99999999998538


No 77 
>pfam04225 OapA Opacity-associated protein A LysM-like domain. This family includes the Haemophilus influenzae opacity-associated protein. This protein is required for efficient nasopharyngeal mucosal colonisation, and its expression is associated with a distinctive transparent colony phenotype. OapA is thought to be a secreted protein, and its expression exhibits high-frequency phase variation. This is a LysM-like domain.
Probab=38.15  E-value=37  Score=16.25  Aligned_cols=27  Identities=30%  Similarity=0.425  Sum_probs=19.8

Q ss_pred             CCCCCCCCCEEEEEEEECCCCCCCCCEEEE
Q ss_conf             884468998899999986999711105999
Q gi|254780913|r   42 GLFNLTEGQLVTYDYVQNDANGKYSAENLK   71 (78)
Q Consensus        42 g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~   71 (78)
                      .+..|++||.|+|.+-   ..|+.++..|.
T Consensus        39 ~Ls~Lk~Gq~v~~~~n---~~G~l~~L~i~   65 (85)
T pfam04225        39 PLSNIKSGQLVRIKLN---AQGRVDELQIE   65 (85)
T ss_pred             CHHHCCCCCEEEEEEC---CCCCEEEEEEE
T ss_conf             0544589999999999---99988999981


No 78 
>pfam01551 Peptidase_M23 Peptidase family M23. Members of this family are zinc metallopeptidases with a range of specificities. The peptidase family M23 is included in this family, these are Gly-Gly endopeptidases. Peptidase family M23 are also endopeptidases. This family also includes some bacterial lipoproteins, for which no proteolytic activity has been demonstrated. This family also includes leukocyte cell-derived chemotaxin 2 (LECT2) proteins. LECT2 is a liver-specific protein which is thought to be linked to hepatocyte growth although the exact function of this protein is unknown.
Probab=35.62  E-value=40  Score=16.02  Aligned_cols=51  Identities=16%  Similarity=0.212  Sum_probs=31.7

Q ss_pred             CCCEEEEEECCCCEEEE-EECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEE
Q ss_conf             77627751468874658-85488778837999950002358844689988999
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFI-TPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTY   54 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI-~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F   54 (78)
                      ..|+|..-...++||-. ..+. .++-.-+|.|.+.+.-.--..+++||.+-.
T Consensus        20 ~~G~V~~~~~~~~~G~~v~i~h-~~g~~~~Y~hl~~~~V~~G~~V~~G~~IG~   71 (96)
T pfam01551        20 ADGVVVFAGYLGGYGNLVIIDH-GNGYETLYAHLSKILVKVGQRVKAGQVIGT   71 (96)
T ss_pred             ECEEEEEEEECCCCCEEEEEEE-CCCCEEEECCCEEEEECCCCCHHHCCEEEE
T ss_conf             3679999898399885999993-898769983644677958989013999998


No 79 
>cd04485 DnaE_OBF DnaE_OBF: A subfamily of OB folds corresponding to the C-terminal OB-fold nucleic acid binding domain of Thermus aquaticus and Escherichia coli type C replicative DNA polymerase III alpha subunit (DnaE). The DNA polymerase holoenzyme of E. coli contains two copies of this replicative polymerase, each of which copies a different DNA strand. This group also contains Bacillus subtilis DnaE. Replication in B. subtilis and Staphylococcus aureus requires two different type C polymerases, polC and DnaE, both of which are thought to be included in the DNA polymerase holoenzyme. At the B. subtilis replication fork, polC appears to be involved in leading strand synthesis and DnaE in lagging strand synthesis.
Probab=35.61  E-value=40  Score=16.02  Aligned_cols=67  Identities=16%  Similarity=0.159  Sum_probs=39.7

Q ss_pred             EEEEECCCC--EEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCC--CCCCCEEEEECCC
Q ss_conf             775146887--46588548877883799995000235884468998899999986999--7111059996357
Q gi|254780913|r    7 IKWYNPDKG--YGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDAN--GKYSAENLKLVPK   75 (78)
Q Consensus         7 VKwfn~~kG--fGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~--gk~~A~~v~~i~~   75 (78)
                      +|..-..+|  |+|++.++. .|.-|+-+--..+.... ..|.+++.|-+...-..+.  -+..|.++..+.+
T Consensus         9 ~k~~~tk~G~~~a~~tleD~-~g~~e~~~F~~~~~~~~-~~l~~~~~v~i~g~v~~~~~~~~l~~~~i~~l~~   79 (84)
T cd04485           9 VRRRRTKKGKRMAFVTLEDL-TGSIEVVVFPETYEKYR-DLLKEDALLLVEGKVERRDGGLRLIAERIEDLED   79 (84)
T ss_pred             EEEEECCCCCEEEEEEEECC-CCCEEEEECHHHHHHHH-HHHCCCCEEEEEEEEEEECCEEEEEEEEEEEHHH
T ss_conf             89985579998999999437-87499999699999988-8744698899999999969989999999467899


No 80 
>cd00210 PTS_IIA_glc PTS_IIA, PTS system, glucose/sucrose specific IIA subunit. The bacterial phosphoenolpyruvate: sugar phosphotransferase system (PTS) is a multi-protein system involved in the regulation of a variety of metabolic and transcriptional processes. This family is one of four structurally and functionally distinct group IIA PTS system cytoplasmic enzymes, necessary for the uptake of carbohydrates across the cytoplasmic membrane and their phosphorylation.
Probab=34.47  E-value=42  Score=15.91  Aligned_cols=45  Identities=24%  Similarity=0.474  Sum_probs=29.1

Q ss_pred             CCEEEE-EECCCCEEEEEECCCCCCCCEEEEEEE----ECCCCCCC-CCCCCCEEE
Q ss_conf             762775-146887465885488778837999950----00235884-468998899
Q gi|254780913|r    4 RGSIKW-YNPDKGYGFITPEGSTESGDDVFLHRS----AVASAGLF-NLTEGQLVT   53 (78)
Q Consensus         4 ~G~VKw-fn~~kGfGFI~~d~~~d~g~DvFvH~s----~i~~~g~~-~l~~G~~V~   53 (78)
                      .|+|.. |...-.||+-+.     +|-+|++|+-    .|...|+. .+++||+|.
T Consensus        43 ~G~V~~v~~T~HAigi~t~-----~G~evLiHiGiDTV~L~G~gF~~~v~~Gd~V~   93 (124)
T cd00210          43 DGTIVQIFPTKHAIGIESD-----SGVEILIHIGIDTVKLNGEGFTSHVEEGQRVK   93 (124)
T ss_pred             CEEEEEECCCCCEEEEEEC-----CCCEEEEEEEECCCCCCCCCEEEEECCCCEEC
T ss_conf             9799998678969999968-----99899999730420148953189974889998


No 81 
>COG1095 RPB7 DNA-directed RNA polymerase, subunit E' [Transcription]
Probab=33.35  E-value=24  Score=17.32  Aligned_cols=46  Identities=20%  Similarity=0.114  Sum_probs=29.5

Q ss_pred             CCCEEEEEECCCCCCCCEEEEEEEECCCC---------------CCCCCCCCCEEEEEEEECCCC
Q ss_conf             88746588548877883799995000235---------------884468998899999986999
Q gi|254780913|r   13 DKGYGFITPEGSTESGDDVFLHRSAVASA---------------GLFNLTEGQLVTYDYVQNDAN   62 (78)
Q Consensus        13 ~kGfGFI~~d~~~d~g~DvFvH~s~i~~~---------------g~~~l~~G~~V~F~i~~~~~~   62 (78)
                      ..-||+-+.=+    --|.|+|.|.|-..               .-+.+..|+.|.+.|+-....
T Consensus        92 ~~~~G~fV~ig----p~dglvh~sqi~dd~~~~d~~~~~~~g~~tk~~i~~gd~VR~RIv~~s~~  152 (183)
T COG1095          92 VVEFGAFVRIG----PLDGLVHVSQIMDDYIDYDEKNKVLIGEETKRVLKVGDKVRARIVGVSLK  152 (183)
T ss_pred             EEECCEEEEEC----CCCCCCCHHHCCCCCCCCCCCCCEEEECCCCEEEECCCEEEEEEEEEECC
T ss_conf             96144699963----62221138666575325275554124036515884198899999996146


No 82 
>pfam00358 PTS_EIIA_1 phosphoenolpyruvate-dependent sugar phosphotransferase system, EIIA 1.
Probab=32.12  E-value=46  Score=15.69  Aligned_cols=45  Identities=20%  Similarity=0.437  Sum_probs=28.8

Q ss_pred             CCEEEE-EECCCCEEEEEECCCCCCCCEEEEEEE----ECCCCCCC-CCCCCCEEE
Q ss_conf             762775-146887465885488778837999950----00235884-468998899
Q gi|254780913|r    4 RGSIKW-YNPDKGYGFITPEGSTESGDDVFLHRS----AVASAGLF-NLTEGQLVT   53 (78)
Q Consensus         4 ~G~VKw-fn~~kGfGFI~~d~~~d~g~DvFvH~s----~i~~~g~~-~l~~G~~V~   53 (78)
                      .|+|.. |...-.||+-+.     +|-++++|+-    .|...|+. .+++||+|.
T Consensus        48 ~G~V~~v~~T~HAigi~~~-----~G~eiLiHiGiDTV~L~G~gF~~~v~~Gd~V~   98 (133)
T pfam00358        48 DGTIVQIFPTKHAIGIESD-----GGVEILIHVGIDTVKLNGEGFESHVEEGDRVK   98 (133)
T ss_pred             CEEEEEECCCCCEEEEEEC-----CCCEEEEEECCCCEECCCCCEEEEECCCCEEC
T ss_conf             9799998689979999968-----99899999864522338963189975899998


No 83 
>COG5569 Uncharacterized conserved protein [Function unknown]
Probab=29.43  E-value=46  Score=15.69  Aligned_cols=41  Identities=32%  Similarity=0.536  Sum_probs=26.3

Q ss_pred             CEEEEEEEECCC---------------CCCCCCCCCCEEEEEEEECCCCCCCCCEEEE
Q ss_conf             379999500023---------------5884468998899999986999711105999
Q gi|254780913|r   29 DDVFLHRSAVAS---------------AGLFNLTEGQLVTYDYVQNDANGKYSAENLK   71 (78)
Q Consensus        29 ~DvFvH~s~i~~---------------~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~   71 (78)
                      +.|=+|.-.|..               .-+..|++|+.|+|..+.  .+|++-..+|+
T Consensus        52 kKVTl~He~i~~l~mp~MTM~F~Vkd~a~ls~lKeGdkV~fvfer--v~gk~tv~qvk  107 (108)
T COG5569          52 KKVTLHHEPIKNLNMPAMTMVFRVKDQAKLSGLKEGDKVEFVFER--VNGKLTVQQVK  107 (108)
T ss_pred             CEEEEECCCHHHCCCCCEEEEEEECCHHHHHCCCCCCCEEEEEEE--ECCEEEEEEEC
T ss_conf             567886251533799640799996557776434567727889875--38978888705


No 84 
>COG2996 Predicted RNA-bindining protein (contains S1 and HTH domains) [General function prediction only]
Probab=29.09  E-value=52  Score=15.39  Aligned_cols=54  Identities=20%  Similarity=0.250  Sum_probs=32.7

Q ss_pred             CCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCCCCCEEEE
Q ss_conf             688746588548877883799995000235884468998899999986999711105999
Q gi|254780913|r   12 PDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGKYSAENLK   71 (78)
Q Consensus        12 ~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk~~A~~v~   71 (78)
                      ....||.--..  ..++..|++|.+....   ..+..|+.|++=+ -.+..+++.|.-..
T Consensus        15 ~~~~~g~fL~~--~~~~~~ilL~k~~~~~---~e~evGdev~vFi-Y~D~~~rl~aTt~~   68 (287)
T COG2996          15 EFSDFGYFLDA--GEDGTTILLPKSEPEE---DELEVGDEVTVFI-YVDSEDRLIATTRE   68 (287)
T ss_pred             EEECEEEEEEC--CCCCEEEECCCCCCCC---CCCCCCCEEEEEE-EECCCCCEEHEEEC
T ss_conf             85221489966--8886078625667767---8511376899999-98887763010104


No 85 
>KOG0291 consensus
Probab=29.06  E-value=52  Score=15.39  Aligned_cols=61  Identities=20%  Similarity=0.337  Sum_probs=34.5

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEE-------C---------C-CCCCCCCCCCCEEEEEEEECCCCC
Q ss_conf             77627751468874658854887788379999500-------0---------2-358844689988999999869997
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSA-------V---------A-SAGLFNLTEGQLVTYDYVQNDANG   63 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~-------i---------~-~~g~~~l~~G~~V~F~i~~~~~~g   63 (78)
                      .-|+||-||...||=|+|-+....+-.-+-+|++.       |         + -..+|+...-.+++|..+-.++.|
T Consensus       370 eDgKVKvWn~~SgfC~vTFteHts~Vt~v~f~~~g~~llssSLDGtVRAwDlkRYrNfRTft~P~p~QfscvavD~sG  447 (893)
T KOG0291         370 EDGKVKVWNTQSGFCFVTFTEHTSGVTAVQFTARGNVLLSSSLDGTVRAWDLKRYRNFRTFTSPEPIQFSCVAVDPSG  447 (893)
T ss_pred             CCCCEEEEECCCCEEEEEECCCCCCEEEEEEEECCCEEEEEECCCEEEEEEECCCCEEEEECCCCCEEEEEEEECCCC
T ss_conf             778378985368638999525887447999996287899962387178434103320243127886036688875888


No 86 
>TIGR01645 half-pint poly-U binding splicing factor, half-pint family; InterPro: IPR006532   The proteins contain three RNA recognition motifs and have been characterised as poly-pyrimidine tract binding proteins associated with RNA splicing factors , , . In the case of PUF60, in complex with p54, and in the presence of U2AF, it facilitates association of U2 snRNP with pre-mRNA . .
Probab=27.89  E-value=17  Score=18.06  Aligned_cols=11  Identities=55%  Similarity=0.969  Sum_probs=7.4

Q ss_pred             CCCCEEEEEEC
Q ss_conf             68874658854
Q gi|254780913|r   12 PDKGYGFITPE   22 (78)
Q Consensus        12 ~~kGfGFI~~d   22 (78)
                      .-||||||..+
T Consensus       281 ~HkGfGFiEf~  291 (791)
T TIGR01645       281 KHKGFGFIEFE  291 (791)
T ss_pred             CCCCCCCHHHH
T ss_conf             85431000110


No 87 
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family.
Probab=26.79  E-value=20  Score=17.70  Aligned_cols=15  Identities=33%  Similarity=0.806  Sum_probs=11.1

Q ss_pred             EEEEECCCCEEEEEE
Q ss_conf             775146887465885
Q gi|254780913|r    7 IKWYNPDKGYGFITP   21 (78)
Q Consensus         7 VKwfn~~kGfGFI~~   21 (78)
                      |==|||+|||=|=|.
T Consensus       152 VEKFDPtrGYKFSTY  166 (336)
T TIGR02997       152 VEKFDPTRGYKFSTY  166 (336)
T ss_pred             CCCCCCCCCCCCCCH
T ss_conf             233577778863301


No 88 
>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=26.23  E-value=59  Score=15.10  Aligned_cols=42  Identities=24%  Similarity=0.246  Sum_probs=25.5

Q ss_pred             CCEEEEEECCCCCCCCEEEEEEEECCCCCC---------------CCCCCCCEEEEEEEEC
Q ss_conf             874658854887788379999500023588---------------4468998899999986
Q gi|254780913|r   14 KGYGFITPEGSTESGDDVFLHRSAVASAGL---------------FNLTEGQLVTYDYVQN   59 (78)
Q Consensus        14 kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~---------------~~l~~G~~V~F~i~~~   59 (78)
                      ..||+-+.-++    -|=++|+|.|..+-+               +.++.||.|.-.+..-
T Consensus        11 t~fG~FV~L~~----ieGLvHiS~l~dD~~~fd~~~~~liG~r~~~~~~~GD~V~vrV~~V   67 (99)
T cd04460          11 VDFGAFVRIGP----VDGLLHISQIMDDYISYDPKNKRLIGEETKRVLKVGDVVRARIVAV   67 (99)
T ss_pred             EECCEEEEECC----CEEEEEHHHCCCCEEEECHHHCEEEECCCCCEECCCCEEEEEEEEE
T ss_conf             82566999328----1068993675784399812446898512786984799999999998


No 89 
>KOG4208 consensus
Probab=25.85  E-value=60  Score=15.06  Aligned_cols=19  Identities=32%  Similarity=0.730  Sum_probs=13.3

Q ss_pred             CEEEEEEC--------CCCEEEEEECC
Q ss_conf             62775146--------88746588548
Q gi|254780913|r    5 GSIKWYNP--------DKGYGFITPEG   23 (78)
Q Consensus         5 G~VKwfn~--------~kGfGFI~~d~   23 (78)
                      |+|+.|-.        .|||+||.-+.
T Consensus        75 g~v~r~rlsRnkrTGNSKgYAFVEFEs  101 (214)
T KOG4208          75 GTVTRFRLSRNKRTGNSKGYAFVEFES  101 (214)
T ss_pred             CEEEEEEEECCCCCCCCCCEEEEEECC
T ss_conf             836999842244467767537887356


No 90 
>TIGR01371 met_syn_B12ind 5-methyltetrahydropteroyltriglutamate--homocysteine S-methyltransferase; InterPro: IPR006276   This group represents cobalamin-independent methionine synthase. A family of uncharacterised archaeal proteins having substantial homology to the C-terminal region of this family, are not included in this group, though they are contained in a larger family of vitamin-B12 independent methionine synthase.; GO: 0003871 5-methyltetrahydropteroyltriglutamate-homocysteine S-methyltransferase activity, 0009086 methionine biosynthetic process.
Probab=25.04  E-value=29  Score=16.85  Aligned_cols=28  Identities=32%  Similarity=0.631  Sum_probs=19.2

Q ss_pred             EEEEECCCCEEEEEECCCCCCCCEEEEEEEEC
Q ss_conf             77514688746588548877883799995000
Q gi|254780913|r    7 IKWYNPDKGYGFITPEGSTESGDDVFLHRSAV   38 (78)
Q Consensus         7 VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i   38 (78)
                      +||||.  .|=+|+|+-..  ...+-++.+.+
T Consensus       119 tKWFnT--NYHYiVPE~~~--~~~F~L~~~k~  146 (778)
T TIGR01371       119 TKWFNT--NYHYIVPELSP--ATEFKLTSNKP  146 (778)
T ss_pred             ECCCCC--CCCEEECCCCC--CCEEEECCCHH
T ss_conf             224367--74303113589--74143240005


No 91 
>TIGR01628 PABP-1234 polyadenylate binding protein, human types 1, 2, 3, 4 family; InterPro: IPR006515   These eukaryotic proteins recognize the poly-A of mRNA and consist of four tandem RNA recognition domains at the N terminus followed by a PABP-specific domain at the C terminus. The protein is involved in the transport of mRNAs from the nucleus to the cytoplasm . There are four paralogs in Homo sapiens which are expressed in testis , platelets (Q13310 from SWISSPROT ), broadly expressed (P11940 from SWISSPROT ) and of unknown tissue range (Q15097 from SWISSPROT). ; GO: 0003723 RNA binding.
Probab=24.19  E-value=30  Score=16.77  Aligned_cols=10  Identities=50%  Similarity=1.125  Sum_probs=5.2

Q ss_pred             CCCEEEEEEC
Q ss_conf             8874658854
Q gi|254780913|r   13 DKGYGFITPE   22 (78)
Q Consensus        13 ~kGfGFI~~d   22 (78)
                      .||||||.-+
T Consensus       128 SrGYgFV~fE  137 (860)
T TIGR01628       128 SRGYGFVHFE  137 (860)
T ss_pred             CCCCCEEECC
T ss_conf             0354134023


No 92 
>TIGR02375 pseudoazurin pseudoazurin; InterPro: IPR012745   Pseudoazurin, also called cupredoxin, is a small, blue periplasmic protein with a single bound copper atom. Pseudoazurin is related to plastocyanins. Several examples of pseudoazurin are encoded by a neighbouring gene for, or have been shown to transfer electrons to, copper-containing nitrite reductases (IPR012746 from INTERPRO) of the same species.; GO: 0005507 copper ion binding.
Probab=23.89  E-value=55  Score=15.28  Aligned_cols=32  Identities=22%  Similarity=0.497  Sum_probs=20.3

Q ss_pred             CCCCCCCCCEEEEEEEECCCCCCCCCEEE-EECCCCC
Q ss_conf             88446899889999998699971110599-9635788
Q gi|254780913|r   42 GLFNLTEGQLVTYDYVQNDANGKYSAENL-KLVPKSS   77 (78)
Q Consensus        42 g~~~l~~G~~V~F~i~~~~~~gk~~A~~v-~~i~~~~   77 (78)
                      .+-.+.+||.|.|  +..+++  ..+..| ..+|+++
T Consensus        18 A~i~a~pGDtv~F--vPtDKG--HNve~iKgm~P~GA   50 (123)
T TIGR02375        18 AYIKAAPGDTVTF--VPTDKG--HNVETIKGMIPEGA   50 (123)
T ss_pred             CEEEECCCCEEEE--ECCCCC--CCHHCCCCCCCCCH
T ss_conf             3366538976877--528887--67000023365221


No 93 
>TIGR02408 ectoine_ThpD ectoine hydroxylase; InterPro: IPR012774    Both ectoine and hydroxyectoine are compatible solvents that serve as protectants against osmotic and thermal stresses. A number of genomes synthesize ectoine. This enzyme allows conversion of ectoine to hydroxyectoine, which may be more effective for some purposes, and is found in a subset of ectoine-producing organisms.; GO: 0016725 oxidoreductase activity acting on CH or CH2 groups.
Probab=23.06  E-value=38  Score=16.20  Aligned_cols=12  Identities=42%  Similarity=0.944  Sum_probs=8.9

Q ss_pred             CCEEEEEEEECC
Q ss_conf             837999950002
Q gi|254780913|r   28 GDDVFLHRSAVA   39 (78)
Q Consensus        28 g~DvFvH~s~i~   39 (78)
                      |.|||||+|=|-
T Consensus       104 GSdVYvHQsRiN  115 (278)
T TIGR02408       104 GSDVYVHQSRIN  115 (278)
T ss_pred             CCCEEEEEEEEC
T ss_conf             561244321100


No 94 
>KOG0407 consensus
Probab=22.99  E-value=52  Score=15.42  Aligned_cols=36  Identities=28%  Similarity=0.521  Sum_probs=22.0

Q ss_pred             CEEEEEEEECCCCC-CCCCCCCCEEEEEEEECCCCCCCCC
Q ss_conf             37999950002358-8446899889999998699971110
Q gi|254780913|r   29 DDVFLHRSAVASAG-LFNLTEGQLVTYDYVQNDANGKYSA   67 (78)
Q Consensus        29 ~DvFvH~s~i~~~g-~~~l~~G~~V~F~i~~~~~~gk~~A   67 (78)
                      .|-|||++++.... +-.+.-|.+|.-+   .+...+++|
T Consensus        26 ndtfvhitdlsg~eti~rvtggmkvkad---rdesspyaa   62 (139)
T KOG0407          26 NDTFVHVTDLSGKETIVRVTGGMKVKAD---RDESSPYAA   62 (139)
T ss_pred             CCCEEEEECCCCCEEEEEEECCEEEECC---CCCCCHHHH
T ss_conf             6616998615785688985076278604---566886899


No 95 
>pfam06523 DUF1106 Protein of unknown function (DUF1106). This family consists of several hypothetical bacterial proteins found in Escherichia coli and Citrobacter rodentium. The function of this family is unknown.
Probab=22.82  E-value=69  Score=14.72  Aligned_cols=56  Identities=14%  Similarity=0.261  Sum_probs=37.9

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEE-EEEECCCCCCCCCCCCCEEEEEEEE
Q ss_conf             7762775146887465885488778837999-9500023588446899889999998
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFL-HRSAVASAGLFNLTEGQLVTYDYVQ   58 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFv-H~s~i~~~g~~~l~~G~~V~F~i~~   58 (78)
                      .+|.|--+.-.+|-=++...-..+...-||+ |.....-+.++.+-+.+.++|.++-
T Consensus        33 lrgivlt~kcs~g~iylsi~~~pnnr~hiflyhkk~yi~dklkeifpde~iefsiey   89 (91)
T pfam06523        33 LRGIVLTFKCSKGIIYLSIKVNPNNRKHIFLYHKKDYIFDKLKEIFPDEAIEFSIEY   89 (91)
T ss_pred             EEEEEEEEEECCCEEEEEEEECCCCCCEEEEEEECCHHHHHHHHHCCCCCEEEEEEE
T ss_conf             023899999469689999996899863489996042577779875899763899984


No 96 
>PRK07135 dnaE DNA polymerase III DnaE; Validated
Probab=22.64  E-value=70  Score=14.70  Aligned_cols=50  Identities=12%  Similarity=0.169  Sum_probs=36.9

Q ss_pred             CCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCCC
Q ss_conf             68874658854887788379999500023588446899889999998699971
Q gi|254780913|r   12 PDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANGK   64 (78)
Q Consensus        12 ~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~gk   64 (78)
                      ..+++.|++.++ ..+.-+++|--..+.+  ++.|+.|+.+.+.+.-..++|.
T Consensus       927 ~~~~~af~~l~D-~tg~~e~~vf~~~~ek--yr~l~~g~~~~~~v~~~~~~~~  976 (987)
T PRK07135        927 KNKEYKKVIFAD-DTVEIKIFVNDNNLEK--YRLLKTGKIYEVIIFFKKPGGN  976 (987)
T ss_pred             CCCCEEEEEEEC-CCCCEEEEECHHHHHH--HHCCCCCCEEEEEEEEECCCCC
T ss_conf             897579999986-8865899986899998--7626469879999999658984


No 97 
>TIGR02712 urea_carbox urea carboxylase; InterPro: IPR014084   Members of this family are ATP-dependent urea carboxylases, including characterised members from Oleomonas sagaranensis (alpha class Proteobacterium) and yeasts such as Saccharomyces cerevisiae (Baker's yeast). The allophanate hydrolase domain of the yeast enzyme is not included in this entry and is represented by an adjacent gene in Oleomonas sagaranensis. The fusion of urea carboxylase and allophanate hydrolase is designated urea amidolyase. The enzyme from O. sagaranensis was shown to be highly active on acetamide and formamide as well as urea..
Probab=22.52  E-value=68  Score=14.78  Aligned_cols=34  Identities=29%  Similarity=0.517  Sum_probs=24.2

Q ss_pred             EEECCCCCCCCEEEEEEEECCCCC---CCCCCCCCEEEEE
Q ss_conf             885488778837999950002358---8446899889999
Q gi|254780913|r   19 ITPEGSTESGDDVFLHRSAVASAG---LFNLTEGQLVTYD   55 (78)
Q Consensus        19 I~~d~~~d~g~DvFvH~s~i~~~g---~~~l~~G~~V~F~   55 (78)
                      |+||+++=||   ||=--.|..+.   .-=|++||+|.|.
T Consensus       726 LgpDGPSLGG---FVCpAvv~~AELWK~GQlKPGD~vrF~  762 (1226)
T TIGR02712       726 LGPDGPSLGG---FVCPAVVAEAELWKVGQLKPGDTVRFV  762 (1226)
T ss_pred             ECCCCCCCCC---CCCCEEECCCCEECCCEECCCCEEEEE
T ss_conf             0775786767---114238312452413433688816887


No 98 
>COG4942 Membrane-bound metallopeptidase [Cell division and chromosome partitioning]
Probab=22.37  E-value=71  Score=14.67  Aligned_cols=51  Identities=10%  Similarity=0.157  Sum_probs=29.0

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEE
Q ss_conf             776277514688746588548877883799995000235884468998899
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVT   53 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~   53 (78)
                      .-|+|-+=+.-+|||-++.-+..+|---|+-+...|....-..+..|+.|-
T Consensus       338 AdG~VvyA~~l~GYG~vvIldhG~gy~slyg~~~~i~v~~G~~V~AGepIa  388 (420)
T COG4942         338 ADGRVVYADWLRGYGLVVILDHGGGYHSLYGGNQSILVNPGQFVKAGEPIA  388 (420)
T ss_pred             CCCEEEECHHHCCCCEEEEEECCCCCEEEECCCCEEEECCCCEEECCCCHH
T ss_conf             695699543325675699997488537886166422106897755697153


No 99 
>KOG3074 consensus
Probab=21.93  E-value=72  Score=14.62  Aligned_cols=28  Identities=29%  Similarity=0.330  Sum_probs=19.8

Q ss_pred             ECCCCEEEEEECCCCCCCCEEEEEEEECCCCC
Q ss_conf             46887465885488778837999950002358
Q gi|254780913|r   11 NPDKGYGFITPEGSTESGDDVFLHRSAVASAG   42 (78)
Q Consensus        11 n~~kGfGFI~~d~~~d~g~DvFvH~s~i~~~g   42 (78)
                      -+.|+|+|+.=  .  +..-+|+.+|.|+..+
T Consensus       185 vDnk~F~Fd~G--~--N~~G~f~riSEVk~n~  212 (263)
T KOG3074         185 VDNKRFLFDVG--K--NKRGVFVRISEVKSNG  212 (263)
T ss_pred             EECCEEEEECC--C--CCCCCEEEEEEECCCC
T ss_conf             71450687437--7--8755257888742788


No 100
>KOG0109 consensus
Probab=21.60  E-value=46  Score=15.68  Aligned_cols=20  Identities=30%  Similarity=0.446  Sum_probs=15.0

Q ss_pred             CCEEEEEECCCCEEEEEECC
Q ss_conf             76277514688746588548
Q gi|254780913|r    4 RGSIKWYNPDKGYGFITPEG   23 (78)
Q Consensus         4 ~G~VKwfn~~kGfGFI~~d~   23 (78)
                      -|+|---|-.|.|||+..++
T Consensus        26 ygkVlECDIvKNYgFVHiEd   45 (346)
T KOG0109          26 YGKVLECDIVKNYGFVHIED   45 (346)
T ss_pred             HCCEEEEEEECCCCEEEEEC
T ss_conf             17467632450311378403


No 101
>TIGR02383 Hfq RNA chaperone Hfq; InterPro: IPR005001    This entry represents the RNA-binding pleiotropic regulator Hfq, a small, Sm-like protein of bacteria. It helps pair regulatory non-coding RNAs with complementary mRNA target regions. It enhances the elongation of poly(A) tails on mRNA. It appears also to protect RNase E recognition sites (A/U-rich sequences with adjacent stem-loop structures) from cleavage. Being pleiotropic, it differs in some of its activities in different species. Hfq binds the non-coding regulatory RNA DsrA (see Rfam:RF00014) in the few species known to have it: Escherichia coli, Shigella flexneri, Salmonella spp. In Azorhizobium caulinodans, an hfq mutant is unable to express nifA, and Hfq is called NrfA, for nif regulatory factor (see ). The name Hfq reflects phenomenology as a host factor for phage Q-beta RNA replication.   The Hfq protein is conserved in a wide range of bacteria and varies in length from 70 to 100 amino acids. In all cases, a conserved Sm motif is located in the N-terminal halves of the molecules. The Hfq protein of E. coli is an 11 kDa polypeptide that forms a hexameric ring-shaped structure. Structural studies have suggested that the beta-4 strand in one molecule dimerises with the beta-5 strand of a neighbouring subunit to form the hexamer. These two strands move with a concerted mobility which may explain the stability of the entire structure .   The architecture of the Hfq-RNA complex suggests two, not mutually exclusive, mechanisms by which Hfq might exert its function as modulator of RNA-RNA interactions. First, when Hfq binds single-stranded RNA, the target site is unwound in a circular manner. This would greatly destabilise surrounding RNA structures that are located several nucleotides on either side of the binding site, thereby permitting new RNA-RNA interactions. Secondly, the repetition of identical BPs on the Hfq hexamer implies that the binding surface can accommodate more than just a single RNA target. This would allow simultaneous binding of two RNA strands and could greatly enhance interaction between the strands .; GO: 0003723 RNA binding, 0006355 regulation of transcription DNA-dependent.
Probab=21.31  E-value=42  Score=15.92  Aligned_cols=29  Identities=21%  Similarity=0.408  Sum_probs=16.5

Q ss_pred             CCCEEEEEECCCCEEEEEECCCCCCCCEEEEEEEEC
Q ss_conf             776277514688746588548877883799995000
Q gi|254780913|r    3 HRGSIKWYNPDKGYGFITPEGSTESGDDVFLHRSAV   38 (78)
Q Consensus         3 ~~G~VKwfn~~kGfGFI~~d~~~d~g~DvFvH~s~i   38 (78)
                      .+|.|+|||.     |-+.-  ..+|+-=+|..=||
T Consensus        28 l~G~i~sFD~-----FtVlL--~~~g~Q~LiYKHAI   56 (61)
T TIGR02383        28 LKGVIKSFDN-----FTVLL--ESQGKQQLIYKHAI   56 (61)
T ss_pred             CCCEEEEECC-----EEEEE--CCCCEEEEEEEEEE
T ss_conf             0518997221-----79987--20992688997666


No 102
>KOG4246 consensus
Probab=20.87  E-value=5.5  Score=20.85  Aligned_cols=50  Identities=24%  Similarity=0.406  Sum_probs=29.4

Q ss_pred             CEEEEEECCCCCCCCEEEEEEEECCCCCCCCCCCCCEEEEEEEECCCCC-CCCCEEEEECCC
Q ss_conf             7465885488778837999950002358844689988999999869997-111059996357
Q gi|254780913|r   15 GYGFITPEGSTESGDDVFLHRSAVASAGLFNLTEGQLVTYDYVQNDANG-KYSAENLKLVPK   75 (78)
Q Consensus        15 GfGFI~~d~~~d~g~DvFvH~s~i~~~g~~~l~~G~~V~F~i~~~~~~g-k~~A~~v~~i~~   75 (78)
                      -||||-        .||||..|+++..   ....|++|--+.-.++.-. |+.|..|+.++.
T Consensus       159 tygfVD--------~dvffQls~~~g~---hp~vgD~V~vea~Ynpsmpfkwnaqriq~l~~  209 (1194)
T KOG4246         159 TYGFVD--------QDVFFQLSKMQGL---HPSVGDAVNVEADYNPSMPFKWNAQRIQHLGG  209 (1194)
T ss_pred             CCCCCC--------HHHHHHHHHHHCC---CCCCCCCEEEECCCCCCCCCCCCHHHHHHCCC
T ss_conf             324410--------7889999887067---87511000132256888874401799875045


No 103
>cd04471 S1_RNase_R S1_RNase_R: RNase R C-terminal S1 domain. RNase R is a processive 3' to 5' exoribonuclease, which is a homolog of RNase II. RNase R degrades RNA with secondary structure having a 3' overhang of at least 7 nucleotides. RNase R and PNPase play an important role in the degradation of RNA with extensive secondary structure, such as rRNA, tRNA, and certain mRNA which contains repetitive extragenic palindromic sequences. The C-terminal S1 domain binds ssRNA.
Probab=20.36  E-value=78  Score=14.43  Aligned_cols=52  Identities=17%  Similarity=0.174  Sum_probs=30.0

Q ss_pred             CCEEEEEECCCCEEE-EEECCCCCCCCEEEEEEEECCCCC---------------CCCCCCCCEEEEEEEECCC
Q ss_conf             762775146887465-885488778837999950002358---------------8446899889999998699
Q gi|254780913|r    4 RGSIKWYNPDKGYGF-ITPEGSTESGDDVFLHRSAVASAG---------------LFNLTEGQLVTYDYVQNDA   61 (78)
Q Consensus         4 ~G~VKwfn~~kGfGF-I~~d~~~d~g~DvFvH~s~i~~~g---------------~~~l~~G~~V~F~i~~~~~   61 (78)
                      +|+|.-.+   -||+ +..+.   .+-|=|+|.|.|...-               -+.+.-||+|.-.+..-+.
T Consensus         6 ~g~I~~v~---~~GiFV~l~~---~~ieGli~~~~l~~d~y~~d~~~~~l~g~~~~~~~~lGd~v~V~i~~vd~   73 (83)
T cd04471           6 DGVISGVT---SFGLFVELDN---LTVEGLVHVSTLGDDYYEFDEENHALVGERTGKVFRLGDKVKVRVVRVDL   73 (83)
T ss_pred             EEEEEEEE---EEEEEEEEEC---CCEEEEEECCCCCCCCEEECCCCEEEECCCCCCEEECCCEEEEEEEEEEC
T ss_conf             99999898---3069999828---87399998221456722447402189813477599789999999999943


Done!