Query         gi|254780148|ref|YP_003064561.1| transcription antitermination protein NusG [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 177
No_of_seqs    123 out of 1849
Neff          8.0 
Searched_HMMs 39220
Date          Sun May 22 16:43:09 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780148.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR00922 nusG transcription t 100.0       0       0  330.6  16.5  172    5-176     1-193 (193)
  2 PRK05609 nusG transcription an 100.0       0       0  323.6  20.3  176    1-176     4-182 (183)
  3 PRK09014 rfaH transcriptional  100.0 5.6E-45       0  289.1  17.2  161    3-176     2-162 (162)
  4 COG0250 NusG Transcription ant 100.0 9.8E-45       0  287.8  17.5  177    1-177     1-178 (178)
  5 TIGR01955 RfaH transcriptional 100.0 9.7E-40 2.5E-44  257.9   5.2  160    5-174     1-162 (162)
  6 TIGR01956 NusG_myco NusG famil 100.0 6.7E-29 1.7E-33  193.0  14.9  172    4-175     1-335 (335)
  7 smart00738 NGN In Spt5p, this  100.0   7E-29 1.8E-33  192.9  10.0  105    4-108     1-105 (106)
  8 PRK08559 nusG transcription an  99.9 1.3E-24 3.2E-29  167.4  14.3  143    3-176     6-148 (153)
  9 pfam02357 NusG Transcription t  99.8 4.6E-21 1.2E-25  146.1   8.5   89    3-101     1-90  (90)
 10 TIGR00405 L26e_arch ribosomal   99.6 1.4E-14 3.6E-19  107.3  10.5  143    6-174     1-144 (151)
 11 KOG1999 consensus               98.1 9.3E-05 2.4E-09   48.5  12.3   52  123-176   408-459 (1024)
 12 pfam03439 Spt5-NGN Early trans  97.9 2.5E-05 6.3E-10   51.9   4.9   79    6-106     2-81  (82)
 13 TIGR01080 rplX_A_E ribosomal p  96.7  0.0018 4.6E-08   40.8   3.4   53  119-171    38-94  (116)
 14 pfam00467 KOW KOW motif. This   96.6  0.0022 5.5E-08   40.3   3.6   30  125-154     1-30  (32)
 15 smart00739 KOW KOW (Kyprides,   96.6  0.0021 5.4E-08   40.4   3.3   27  122-148     1-27  (28)
 16 PRK01191 rpl24p 50S ribosomal   96.6  0.0065 1.7E-07   37.5   5.7   53  119-171    43-99  (119)
 17 KOG1999 consensus               96.1   0.016 4.1E-07   35.1   5.7  133    2-162   164-296 (1024)
 18 PTZ00194 60S ribosomal protein  95.7   0.016 4.1E-07   35.1   4.2   37  120-156    44-80  (143)
 19 PRK00004 rplX 50S ribosomal pr  95.6   0.026 6.8E-07   33.8   5.1   38  122-159     3-41  (102)
 20 PRK12281 rplX 50S ribosomal pr  95.5   0.028 7.2E-07   33.6   4.9   41  120-160     4-45  (77)
 21 CHL00141 rpl24 ribosomal prote  95.3   0.037 9.5E-07   32.9   5.0   41  120-160     9-50  (90)
 22 COG0198 RplX Ribosomal protein  94.5   0.067 1.7E-06   31.4   4.6   33  122-156     4-36  (104)
 23 COG5164 SPT5 Transcription elo  93.9     0.4   1E-05   26.7   7.6   42  123-166   352-393 (607)
 24 TIGR01079 rplX_bact ribosomal   91.6    0.38 9.6E-06   26.9   4.8   38  122-159     3-41  (109)
 25 PRK06531 yajC preprotein trans  91.3    0.76 1.9E-05   25.1   6.0   49  121-177    35-83  (120)
 26 pfam11623 DUF3252 Protein of u  90.2     1.2   3E-05   24.0   6.1   50  123-174     2-53  (53)
 27 PRK00409 recombination and DNA  82.9     3.8 9.6E-05   20.9   7.7   48  121-176   633-680 (780)
 28 pfam02211 NHase_beta Nitrile h  79.3     3.9 9.8E-05   20.9   4.5   51   97-147   107-167 (220)
 29 KOG1708 consensus               77.9     3.1   8E-05   21.4   3.7   34  122-155    72-105 (236)
 30 TIGR00739 yajC preprotein tran  75.2     6.6 0.00017   19.5   5.5   49  121-176    36-84  (86)
 31 PRK11865 pyruvate ferredoxin o  75.1     3.3 8.5E-05   21.2   3.2  108    5-114   175-291 (298)
 32 PRK11864 2-ketoisovalerate fer  75.0     4.7 0.00012   20.3   3.9  108    5-114   173-289 (300)
 33 COG1862 YajC Preprotein transl  74.2       7 0.00018   19.3   5.3   45  121-174    42-86  (97)
 34 PTZ00065 60S ribosomal protein  73.6     6.1 0.00016   19.7   4.2   36  122-158     7-42  (130)
 35 pfam06003 SMN Survival motor n  67.3      10 0.00025   18.4   4.3   33  123-157    69-104 (264)
 36 TIGR01069 mutS2 MutS2 family p  66.0      11 0.00027   18.2   4.9   49  121-176   670-718 (834)
 37 cd01734 YlxS_C YxlS is a Bacil  66.0      11 0.00027   18.2   6.9   50  125-176    24-77  (83)
 38 PRK05585 yajC preprotein trans  64.3      11 0.00029   18.0   6.0   47  121-176    52-98  (107)
 39 COG2139 RPL21A Ribosomal prote  61.5      13 0.00033   17.7   6.7   52  122-175    32-93  (98)
 40 PRK11760 putative RNA 2'-O-rib  61.3      13 0.00033   17.7   6.3   27    6-32      4-30  (356)
 41 TIGR02361 dak_ATP dihydroxyace  60.5      11 0.00027   18.2   3.3   49   78-132   236-286 (627)
 42 COG2933 Predicted SAM-dependen  57.2      15 0.00039   17.3   5.7   26    6-31      4-29  (358)
 43 pfam02699 YajC Preprotein tran  55.5      16 0.00042   17.1   5.2   48  121-177    36-83  (83)
 44 PRK04333 50S ribosomal protein  55.5      16 0.00042   17.1   4.5   34  122-156     3-36  (83)
 45 TIGR02249 integrase_gron integ  53.6     7.9  0.0002   19.0   1.7   72   85-156    89-169 (320)
 46 cd01737 LSm16_N LSm16 belongs   51.7      19 0.00048   16.7   5.5   51  125-176     5-61  (62)
 47 TIGR01941 nqrF NADH:ubiquinone  50.5      10 0.00026   18.3   1.9   19  122-141   261-279 (425)
 48 COG1509 KamA Lysine 2,3-aminom  47.6      14 0.00036   17.5   2.2   70   58-131   121-201 (369)
 49 pfam02941 FeThRed_A Ferredoxin  42.0      27 0.00068   15.8   3.1   22  125-146     1-36  (67)
 50 PRK04306 50S ribosomal protein  41.3      27  0.0007   15.8   6.9   52  122-175    33-94  (97)
 51 COG2163 RPL14A Ribosomal prote  39.6      29 0.00074   15.6   4.6   32  122-154     4-35  (125)
 52 COG4873 Uncharacterized protei  36.2      33 0.00084   15.3   3.5   42  123-170    24-65  (81)
 53 pfam04943 Pox_F11 Poxvirus F11  35.1      34 0.00088   15.2   5.1  107   57-168    26-145 (366)
 54 CHL00084 rpl19 ribosomal prote  34.9      35 0.00088   15.1   5.5   45  103-148     4-55  (117)
 55 pfam10574 UPF0552 Uncharacteri  34.5      35  0.0009   15.1   6.8   37  120-162   149-188 (224)
 56 PRK10724 hypothetical protein;  33.7      36 0.00092   15.0   4.0   35  123-157    81-119 (158)
 57 TIGR01200 TIGR01200 Porphyromo  32.9      30 0.00077   15.5   2.0   38  126-163   194-234 (300)
 58 pfam08345 YscJ_FliF_C Flagella  32.6      38 0.00096   14.9   3.9   38   94-136   125-162 (162)
 59 TIGR02888 spore_YlmC_YmxH spor  32.4      38 0.00097   14.9   3.5   32  145-176    28-67  (76)
 60 KOG0107 consensus               31.6      25 0.00063   16.0   1.4   26   60-85     45-70  (195)
 61 TIGR01108 oadA oxaloacetate de  31.2      30 0.00076   15.5   1.7   76   19-110   299-390 (616)
 62 PRK00092 hypothetical protein;  30.2      42  0.0011   14.7   6.3   49  124-176    93-145 (153)
 63 COG4464 CapC Capsular polysacc  29.0      44  0.0011   14.5   3.0   11   63-73    103-113 (254)
 64 PRK08384 thiamine biosynthesis  28.4      45  0.0011   14.5   4.7   57   11-89     19-75  (310)
 65 PRK09206 pyruvate kinase; Prov  28.3      31 0.00079   15.4   1.4   74   52-138   385-458 (470)
 66 pfam01245 Ribosomal_L19 Riboso  28.1      45  0.0012   14.4   4.2   29  120-148    16-51  (113)
 67 pfam08223 PaaX_C PaaX-like pro  27.8      46  0.0012   14.4   4.5   38    3-40      6-43  (170)
 68 pfam09953 DUF2187 Uncharacteri  27.8      46  0.0012   14.4   3.2   40  124-169     5-44  (57)
 69 COG0779 Uncharacterized protei  26.7      48  0.0012   14.3   4.5   45  125-175    98-146 (153)
 70 KOG4315 consensus               26.7      29 0.00074   15.6   1.0   50  122-173   393-442 (455)
 71 pfam02576 DUF150 Uncharacteriz  25.6      50  0.0013   14.2   4.9   50  125-176    86-139 (141)
 72 PRK12289 ribosome-associated G  25.5      51  0.0013   14.2   4.1   11    3-13     18-28  (351)
 73 PRK04313 30S ribosomal protein  24.9      52  0.0013   14.1   3.6   39  119-157   168-208 (237)
 74 pfam01157 Ribosomal_L21e Ribos  24.6      52  0.0013   14.1   6.7   54  122-175    32-97  (99)
 75 pfam11572 DUF3234 Protein of u  23.6      55  0.0014   13.9   2.1   25    3-28      6-30  (102)
 76 PRK06488 sulfur carrier protei  23.4      55  0.0014   13.9   3.6   41   93-133     7-60  (65)
 77 COG1532 Predicted RNA-binding   23.0      56  0.0014   13.9   3.4   31  125-155    23-55  (57)
 78 PRK05464 Na(+)-translocating N  22.2      59  0.0015   13.8   2.1   19  122-141   251-269 (408)
 79 pfam03792 PBC PBC domain. The   22.0      20 0.00051   16.6  -0.5   35   81-115   135-169 (192)
 80 PTZ00300 pyruvate kinase; Prov  22.0      55  0.0014   14.0   1.7   81   52-141   363-443 (454)
 81 pfam04452 Methyltrans_RNA RNA   22.0      59  0.0015   13.8   4.4   13  127-139   175-187 (225)
 82 PRK05338 rplS 50S ribosomal pr  21.5      60  0.0015   13.7   5.0   30  119-148    15-51  (112)
 83 cd05697 S1_Rrp5_repeat_hs5 S1_  21.5      61  0.0015   13.7   3.5   26  120-155    42-67  (69)
 84 KOG3421 consensus               21.5      61  0.0015   13.7   2.7   33  123-156     7-39  (136)
 85 pfam12073 DUF3553 Protein of u  20.9      62  0.0016   13.6   3.9   50  123-176     1-50  (52)
 86 pfam09087 Cyc-maltodext_N Cycl  20.9      62  0.0016   13.6   1.9   20   54-73     40-59  (88)
 87 KOG3401 consensus               20.7      63  0.0016   13.6   3.6   42  119-162    45-87  (145)

No 1  
>TIGR00922 nusG transcription termination/antitermination factor NusG; InterPro: IPR001062 Bacterial transcription antitermination protein, nusG, is a component of the transcription complex and interacts with the termination factor Rho and RNA polymerase , . NusG is a bacterial transcriptional elongation factor involved in transcription termination and anti-termination .; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=100.00  E-value=0  Score=330.55  Aligned_cols=172  Identities=47%  Similarity=0.861  Sum_probs=167.6

Q ss_pred             EEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEE-CCEEE---EEECCEECEEEEEEEECCCCCHHHHH
Q ss_conf             189995288538999999999997798111432663131012772-02035---66412033099999961865224442
Q gi|254780148|r    5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVR-KGRKV---NSERRFFPGYVLIKAVMTDKVYHTIK   80 (177)
Q Consensus         5 Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~-~g~~~---~~~~plfpgYiFv~~~~~~~~~~~i~   80 (177)
                      ||||||.||+|+||+++|+++++.++++|++.+|.+|.+++...+ +|+++   .+++.+|||||||+++|++++|+.|+
T Consensus         1 WYvvq~~SG~E~~Vk~~l~~~~~~~~~~D~i~~v~vP~E~v~Ei~~~Gk~~~KI~~erK~fPGYvLv~m~l~D~~W~~v~   80 (193)
T TIGR00922         1 WYVVQTYSGYEKKVKKNLEELIELLGMTDVIFEVIVPTEEVVEIKKKGKKKTKIVVERKIFPGYVLVKMDLTDESWHLVK   80 (193)
T ss_pred             CEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEEECCCCEEEEEECCEEEEEEEEEEEECCCEEEEEEECCHHHHHHHH
T ss_conf             94886024783789999999998538886035788212233888547903201466211548648999973868898887


Q ss_pred             C----CCEEEEEECCCCCCCCCCH-----------HHHHHHHHHHHHHH--HHHCCCCCCCCCCEEEEECCCCCCCEEEE
Q ss_conf             0----3303664327886100258-----------89999997653222--10000123478977999518778971999
Q gi|254780148|r   81 D----TPKVIGFLGTGENPSPVTD-----------SEIEHIMNQVEAAV--QRPVSSVFFEVGERVCVSDGPFASFNGIV  143 (177)
Q Consensus        81 ~----t~gV~~~l~~~~~P~~i~~-----------~ei~~l~~~~~~~~--~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v  143 (177)
                      +    ||||+||||+++.|.++++           +|++.+++.+....  ..+.....|+.|+.|+|++|||++|.|.|
T Consensus        81 n~i~k~PgV~gFvG~~~~~~~~~~~~~lLP~~~~~~Ev~~il~~~~~~~~~~~p~~~~~fE~Ge~Vrv~dGPF~~F~G~V  160 (193)
T TIGR00922        81 NEIRKTPGVTGFVGSGGKPKALSEDDFLLPRKLSKEEVKNILNKLEEGKADKKPKVKIDFEVGEQVRVNDGPFANFTGTV  160 (193)
T ss_pred             HCCCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCCCCCEEE
T ss_conf             41764884400066788888777676257806328999999999874303454533432357988898038888851479


Q ss_pred             EEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             998288988999998168704788567871233
Q gi|254780148|r  144 KNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       144 ~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      .++|.+++|++|.++||||+|||||++.||||+
T Consensus       161 eev~~Ek~kLkV~VSIFGR~TPVEL~F~QVEK~  193 (193)
T TIGR00922       161 EEVDYEKSKLKVSVSIFGRETPVELEFTQVEKI  193 (193)
T ss_pred             EEEEHHCCEEEEEEECCCCCCCEEECCCEEECC
T ss_conf             888021376999997168787146051112039


No 2  
>PRK05609 nusG transcription antitermination protein NusG; Validated
Probab=100.00  E-value=0  Score=323.61  Aligned_cols=176  Identities=51%  Similarity=0.914  Sum_probs=166.5

Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHH
Q ss_conf             98861899952885389999999999977981114326631310127720203566412033099999961865224442
Q gi|254780148|r    1 MTPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIK   80 (177)
Q Consensus         1 M~~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~   80 (177)
                      |.++|||++|+||+|++|+++|++++...|++++++++|+|.++..++++|+++.+.+|||||||||+++++++.|+.|+
T Consensus         4 m~k~WYvv~tk~~~E~~v~~~L~~~~~~~~l~~~~~~v~~P~~~~~~~~~gk~~~v~~pLFPGYiFv~~~~~~~~~~~Ir   83 (183)
T PRK05609          4 MKKRWYVVQTYSGYEKKVKENLEERIKTLGMEDLIGEVLVPTEEVVEVKNGKKKVVERKFFPGYVLVKMVMTDESWHLVR   83 (183)
T ss_pred             CCCCEEEEEEECCCHHHHHHHHHHHHHHCCCCCCCCEEECCCEEEEEEECCEEEEEEEEEECCEEEEEEECCCHHHHHHH
T ss_conf             57868999977892899999999999865841022389767889999958908999998507279999644751277886


Q ss_pred             CCCEEEEEECCC---CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEE
Q ss_conf             033036643278---86100258899999976532221000012347897799951877897199999828898899999
Q gi|254780148|r   81 DTPKVIGFLGTG---ENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEV  157 (177)
Q Consensus        81 ~t~gV~~~l~~~---~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v  157 (177)
                      +|+||++||+++   .+|.|++++|++.++....++.....+...|++||+|+|++|||+|++|.|.++|.+++|+.|++
T Consensus        84 ~t~GV~~~vg~~~~~~~P~pv~~~ei~~i~~~~~~~~~~~~~~~~~~~Gd~V~I~~GPf~g~~g~v~~~d~~k~Rv~V~l  163 (183)
T PRK05609         84 NTPGVTGFVGSHGTRSKPTPLSEKEVERILNRKQEGVEKPKPKVDFEVGEVVRVTDGPFADFNGTVEEVDYEKSKLKVLV  163 (183)
T ss_pred             CCCCEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEE
T ss_conf             58981499604887787898887999999876651444565343322798999936789996899999838789999999


Q ss_pred             EECCCEEEEEECHHHHEEC
Q ss_conf             8168704788567871233
Q gi|254780148|r  158 VIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       158 ~i~Gr~~~v~l~~~~ieki  176 (177)
                      +||||.|+|+++++|||||
T Consensus       164 ~i~Gr~~~vel~~~~veki  182 (183)
T PRK05609        164 SIFGRETPVELEFSQVEKI  182 (183)
T ss_pred             EECCCCEEEEECHHHEEEC
T ss_conf             8369961798678997966


No 3  
>PRK09014 rfaH transcriptional activator RfaH; Provisional
Probab=100.00  E-value=5.6e-45  Score=289.07  Aligned_cols=161  Identities=17%  Similarity=0.295  Sum_probs=146.3

Q ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCC
Q ss_conf             86189995288538999999999997798111432663131012772020356641203309999996186522444203
Q gi|254780148|r    3 PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDT   82 (177)
Q Consensus         3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t   82 (177)
                      ++|||++|+||+|++|+++|++         +++++|+|+.++.+.++|+++.+.+|||||||||++++++..|+.|++|
T Consensus         2 k~Wyvv~tk~~~E~ka~~~L~~---------qg~~~~~P~~~~~~~~~~k~~~~~~pLFPgYlFv~~~~~~~~~~~I~~t   72 (162)
T PRK09014          2 KSWYLLYCKRGQLQRAQEHLER---------QGVECLYPMITLEKIVRGKRTEVSEPLFPNYLFVEFDPEVIHTTTIRAT   72 (162)
T ss_pred             CCEEEEEEECCHHHHHHHHHHH---------CCCEEEEEEEEEEEEECCEEEEEEEECCCCEEEEEECCCCCCEEEEECC
T ss_conf             8599999629889999999997---------7997997779999997991899989646717999963576770104068


Q ss_pred             CEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCC
Q ss_conf             30366432788610025889999997653222100001234789779995187789719999982889889999981687
Q gi|254780148|r   83 PKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGR  162 (177)
Q Consensus        83 ~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr  162 (177)
                      +||++||++|++|++||+++|+.|+...++...   ....+++||+|+|++|||+|++|++.++|++ .|+.|++++|||
T Consensus        73 ~GV~~~v~~g~~p~~v~~~~I~~l~~~~~~~~~---~~~~~~~Gd~V~I~~GPf~g~~g~v~~~~~~-~R~~vll~~lgr  148 (162)
T PRK09014         73 RGVSHFVRFGAQPAIVPSDVIYQLKAYKPDEIV---DPETPKPGDKVIITEGAFEGIQAIYTEPDGE-ARSILLLNLLNK  148 (162)
T ss_pred             CCCCEEECCCCEECCCCHHHHHHHHHHHHCCCC---CCCCCCCCCEEEEEECCCCCCEEEEEEECCC-CCEEEEEEECCC
T ss_conf             990589778999341899999998713003554---3456999999999437999808999988687-878999620399


Q ss_pred             EEEEEECHHHHEEC
Q ss_conf             04788567871233
Q gi|254780148|r  163 VTPVELAYNQVEKI  176 (177)
Q Consensus       163 ~~~v~l~~~~ieki  176 (177)
                      .|+|+++.+|||||
T Consensus       149 ~~~v~v~~~~leKi  162 (162)
T PRK09014        149 EVKHSVDNTDFRKL  162 (162)
T ss_pred             CEEEEECHHHEEEC
T ss_conf             44899858994859


No 4  
>COG0250 NusG Transcription antiterminator [Transcription]
Probab=100.00  E-value=9.8e-45  Score=287.77  Aligned_cols=177  Identities=47%  Similarity=0.826  Sum_probs=167.2

Q ss_pred             CCCCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHH
Q ss_conf             98861899952885389999999999977981114326631310127720203566412033099999961865224442
Q gi|254780148|r    1 MTPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIK   80 (177)
Q Consensus         1 M~~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~   80 (177)
                      |.++||+++|++|+|++|+++|+++....++++++.++.+|.+++...++|++..+++++|||||||++++++++|+.|+
T Consensus         1 ~~~~Wyvv~~~sg~E~~V~~~l~~~~~~~~~~~~~~~v~vp~E~v~e~~~~~~~~~e~~~fpGYVlVem~~~~~~w~~Vr   80 (178)
T COG0250           1 LMKRWYVVQTYSGQEKKVKENLERKAELLGMEDLIFEVLVPTEEVVEVKGKRKVIVERKLFPGYVLVEMDMTDEAWHLVR   80 (178)
T ss_pred             CCCEEEEEEEECCHHHHHHHHHHHHHHHCCCCCCEEEEEECEEEEEEECCCEEEEEECCCCCCEEEEEEECCCCEEEEEE
T ss_conf             98528999943547999999999999866996302467723278998317558997126788579999982774589986


Q ss_pred             CCCEEEEEECCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEE
Q ss_conf             033036643278-8610025889999997653222100001234789779995187789719999982889889999981
Q gi|254780148|r   81 DTPKVIGFLGTG-ENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVI  159 (177)
Q Consensus        81 ~t~gV~~~l~~~-~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i  159 (177)
                      +||||+||+|++ .+|.|++++|+++++...+.....+.....|++||.|+|++|||+|+.|.|.++|.++++++|++++
T Consensus        81 ~tpgV~GfVg~~~~~P~pi~~~ei~~~l~~~~~~~~~~~~~~~~e~Gd~VrI~~GpFa~f~g~V~evd~ek~~~~v~v~i  160 (178)
T COG0250          81 NTPGVTGFVGSGGAKPVPLSEEEIEHILGFLEEEVAPKKPKVDFEPGDVVRIIDGPFAGFKAKVEEVDEEKGKLKVEVSI  160 (178)
T ss_pred             CCCCCEEEECCCCCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEECCCCCCCCEEEEEECCCCCEEEEEEEE
T ss_conf             48971798636899870268999998876401224588632467899889991667899517899984767689999997


Q ss_pred             CCCEEEEEECHHHHEECC
Q ss_conf             687047885678712339
Q gi|254780148|r  160 FGRVTPVELAYNQVEKIV  177 (177)
Q Consensus       160 ~Gr~~~v~l~~~~ieki~  177 (177)
                      |||.|||+++++||+|+-
T Consensus       161 fgr~tPVel~~~qVek~~  178 (178)
T COG0250         161 FGRPTPVELEFDQVEKLK  178 (178)
T ss_pred             ECCCEEEEEECCCEEEEC
T ss_conf             177407998601089709


No 5  
>TIGR01955 RfaH transcriptional activator RfaH; InterPro: IPR010215   This entry represents the transcriptional activator protein, RfaH . This protein is most closely related to the transcriptional termination/antitermination protein NusG (IPR001062 from INTERPRO) and contains the KOW motif (IPR005824 from INTERPRO) . This protein appears to be limited to the proteobacteria. In Escherichia coli, this gene appears to control the expression of haemolysin, sex factor and lipopolysaccharide genes.; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=100.00  E-value=9.7e-40  Score=257.94  Aligned_cols=160  Identities=25%  Similarity=0.441  Sum_probs=143.5

Q ss_pred             EEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCC-CCHHHHHCCC
Q ss_conf             189995288538999999999997798111432663131012772020356641203309999996186-5224442033
Q gi|254780148|r    5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTD-KVYHTIKDTP   83 (177)
Q Consensus         5 Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~-~~~~~i~~t~   83 (177)
                      ||+||||||+|.+|.++|+.         |.++||.|.....+.++|++..+.+||||+|+||.+|... ++|..||+|+
T Consensus         1 WYLlYcKpr~e~RA~~hL~r---------Q~~e~~~P~~~~ek~~rG~~~~v~ePLFP~YLFi~fD~~~G~~~~~irSTR   71 (162)
T TIGR01955         1 WYLLYCKPRQEQRAEEHLER---------QDVECYLPMVSVEKIKRGKKQLVEEPLFPNYLFIEFDPEKGDSWTPIRSTR   71 (162)
T ss_pred             CCCCCCCCHHHHHHHHHHHH---------CCCCCCCHHHHHHHHHHCCHHEECCCCCCCEEEEEECCCCCCCCCEEEEEE
T ss_conf             96310081457999998861---------681001005678887620201121578987326770456788121254110


Q ss_pred             EEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCC-CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCC
Q ss_conf             036643278861002588999999765322210000-1234789779995187789719999982889889999981687
Q gi|254780148|r   84 KVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVS-SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGR  162 (177)
Q Consensus        84 gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~-~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr  162 (177)
                      ||+.||++|++|++|+++.|+.|+.........+.. ...|+.||+|+|++|+|+|+||++.+-|++ .|+.++++|+||
T Consensus        72 GVS~~VrfG~~P~~v~~~~I~~l~~~~~~~~~~~~~~P~~~~~G~~V~i~~G~fag~EAIF~~~dG~-~R~~~Llnm~~~  150 (162)
T TIGR01955        72 GVSRIVRFGGHPAPVPDDLIHQLRQKELEASVPAKKTPLLFKKGDKVRITDGSFAGLEAIFLEPDGE-KRSVLLLNMIGK  150 (162)
T ss_pred             CCEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCHHHCCCCCCCCCEEEEEECCCCCCCEEEECCCCC-HHHHHHHHHHCC
T ss_conf             5144460489772236689898640343225583135657789887998628713600354078842-477665466365


Q ss_pred             EEEEEECHHHHE
Q ss_conf             047885678712
Q gi|254780148|r  163 VTPVELAYNQVE  174 (177)
Q Consensus       163 ~~~v~l~~~~ie  174 (177)
                      .++++|+.++++
T Consensus       151 ~~~~~vp~~s~~  162 (162)
T TIGR01955       151 QVKVSVPNTSVE  162 (162)
T ss_pred             EEEEEEECCCCC
T ss_conf             046886145459


No 6  
>TIGR01956 NusG_myco NusG family protein; InterPro: IPR010216   This entry represents a family of Mycoplasma proteins orthologous to the bacterial transcription termination/antitermination factor NusG. These sequences from Mycoplasma are notably diverged from those in bacterial species, and although NusA and ribosomal protein S10 (NusE) appear to be present, NusB may be absent in Mycoplasmas calling into question whether these species have a functional Nus system, which includes this family as a member.; GO: 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=99.96  E-value=6.7e-29  Score=193.05  Aligned_cols=172  Identities=28%  Similarity=0.582  Sum_probs=140.6

Q ss_pred             CEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEE---------------------------E---CCEE
Q ss_conf             618999528853899999999999779811143266313101277---------------------------2---0203
Q gi|254780148|r    4 RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSV---------------------------R---KGRK   53 (177)
Q Consensus         4 ~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~---------------------------~---~g~~   53 (177)
                      |||++.|-+|.|++|.++|++.+...+|++++.++-+-+++.+..                           .   .||.
T Consensus         1 qWYi~t~~~gnE~~Vi~niK~KV~a~~~~~~~~D~k~~K~r~~~~~~f~~~NP~~~~P~s~kN~~~~kW~t~~vdG~~~Y   80 (335)
T TIGR01956         1 QWYIVTVINGNEDEVIKNIKDKVRALGFEDKILDLKVLKEREVEEKVFDPKNPSNKAPRSMKNTASIKWETLDVDGEGKY   80 (335)
T ss_pred             CCEEEEEECCCHHHHHHHHHHHHHHCCCCCEEEEEEEEEEEEEEEEEECCCCCCCCCCCCCCCCCEEEEEEEEECCCCEE
T ss_conf             94889840787178999998887542767635525888767899998047888877776533652036999982399715


Q ss_pred             ---EEEECCEECEEEEEEEECCCCCHHHHHCCCEEEEEECCCC---CCCCCCHHHHHHHHHH------------------
Q ss_conf             ---5664120330999999618652244420330366432788---6100258899999976------------------
Q gi|254780148|r   54 ---VNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTGE---NPSPVTDSEIEHIMNQ------------------  109 (177)
Q Consensus        54 ---~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV~~~l~~~~---~P~~i~~~ei~~l~~~------------------  109 (177)
                         +..+..+||||||++|.+++++|+.||+|+|||||||+.|   +|+|||+.+.+.|...                  
T Consensus        81 ~K~kI~e~N~~~GYIyIKM~m~~~aWf~iRNT~~vTG~VGSSGkGAkPiP~s~~~~~NLf~~~~~k~I~~n~~krvlv~~  160 (335)
T TIGR01956        81 KKTKIKEKNKYNGYIYIKMIMTDDAWFLIRNTEGVTGLVGSSGKGAKPIPISDAEAENLFELKMLKGISVNKKKRVLVTQ  160 (335)
T ss_pred             EEEEEEECCCCCCEEEEEEEEECCEEEEEECCCCCCEEECCCCCCCCCCCCCHHHHHHCCHHHHHCCCCCCCCCCEEEEC
T ss_conf             57754422658970799999724714798547894367721588852664771124311106661321136666678705


Q ss_pred             --------------HHHH---------------------------HH---------------------------------
Q ss_conf             --------------5322---------------------------21---------------------------------
Q gi|254780148|r  110 --------------VEAA---------------------------VQ---------------------------------  115 (177)
Q Consensus       110 --------------~~~~---------------------------~~---------------------------------  115 (177)
                                    ++++                           ..                                 
T Consensus       161 ~~~~~~e~~~riefldsGnnf~ek~~~il~~~~~k~~~~~~~seS~e~~~~~~~~~~~~~~~~~nvE~D~~~E~~~~~~~  240 (335)
T TIGR01956       161 TAIVEMEENKRIEFLDSGNNFDEKDEYILKEKAAKTKAEKKKSESAEKVDSSNVEEVLVEANKANVEVDENVEDVALVKS  240 (335)
T ss_pred             CCCCCCHHCCEEEEECCCCCHHHHHHHHHHHHHHCHHHHHHHCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEECC
T ss_conf             74236111040424106786112335555443202134542022101245122666765332012112443114445515


Q ss_pred             --------------------------------HHCCCCCCCCCCEEEEECCCCCC--CEEEEEEECCC-CCEEEEEEEEC
Q ss_conf             --------------------------------00001234789779995187789--71999998288-98899999816
Q gi|254780148|r  116 --------------------------------RPVSSVFFEVGERVCVSDGPFAS--FNGIVKNVDEE-KSRVHVEVVIF  160 (177)
Q Consensus       116 --------------------------------~~~~~~~~~~G~~V~I~~Gpf~g--~~g~v~~i~~~-~~r~~V~v~i~  160 (177)
                                                      .......|++|..|.|..|+|.|  ..|.|.+++.+ +..++|++++|
T Consensus       241 ~Geveevti~~~VD~~~~~~~~~~~e~~~e~~~~~~~~~F~VG~~V~I~~~~~~gde~~g~I~~i~~~tk~~a~Veve~l  320 (335)
T TIGR01956       241 DGEVEEVTIAEDVDNKVLIEYLEKVELVEEKEKDDNLSKFKVGNLVEILAGSFKGDEIEGKIKKIDQETKDKAIVEVEIL  320 (335)
T ss_pred             CCCEEEEEECCCCCCCHHHCCCCCEEEEECCCCHHHHCCCCCCCEEEEEECCCCCCCEEEEEEEHHCCCCCEEEEEEEEE
T ss_conf             88346776213477101101245154531433011200133587889974675586011332120046775689999972


Q ss_pred             CCEEEEEECHHHHEE
Q ss_conf             870478856787123
Q gi|254780148|r  161 GRVTPVELAYNQVEK  175 (177)
Q Consensus       161 Gr~~~v~l~~~~iek  175 (177)
                      ||.+.|+|++.+|+.
T Consensus       321 GK~~~~~l~~~~l~l  335 (335)
T TIGR01956       321 GKLVLVDLNFKELKL  335 (335)
T ss_pred             CEEEEEECCHHHHCC
T ss_conf             707896547678079


No 7  
>smart00738 NGN In Spt5p, this domain may confer affinity for Spt4p. It possesses a RNP-like fold. In Spt5p, this domain may confer affinity for Spt4p.Spt4p
Probab=99.96  E-value=7e-29  Score=192.93  Aligned_cols=105  Identities=39%  Similarity=0.779  Sum_probs=102.1

Q ss_pred             CEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCCC
Q ss_conf             61899952885389999999999977981114326631310127720203566412033099999961865224442033
Q gi|254780148|r    4 RWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTP   83 (177)
Q Consensus         4 ~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~   83 (177)
                      +||+++|+||+|++|+++|+++....+++++++++|+|+++..+.++|+++.+.+|||||||||+++++++.|+.|++|+
T Consensus         1 nWYvv~t~~g~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~r~gk~~~~~~~lFPGYiFv~~~~~~~~~~~i~~t~   80 (106)
T smart00738        1 NWYAVRTTSGQEKRVAENLERKAEALGLEDKIVSILVPTEEVKEIRRGKKKVVERPLFPGYIFVEADLEDEVWTAIRGTP   80 (106)
T ss_pred             CEEEEEEECCHHHHHHHHHHHHHHHCCCCCCEEEEECCCEEEEEEECCCEEEEEEEECCCEEEEEEECCCCCEEEEECCC
T ss_conf             98999998980999999999987665675241799897199999847826999886218589999883877031021699


Q ss_pred             EEEEEECCCCCCCCCCHHHHHHHHH
Q ss_conf             0366432788610025889999997
Q gi|254780148|r   84 KVIGFLGTGENPSPVTDSEIEHIMN  108 (177)
Q Consensus        84 gV~~~l~~~~~P~~i~~~ei~~l~~  108 (177)
                      ||++||+++++|.|||++||+.|++
T Consensus        81 gV~~fv~~~~~P~~v~~~ei~~il~  105 (106)
T smart00738       81 GVRGFVGGGGKPTPVPDDEIEKILK  105 (106)
T ss_pred             CCEEECCCCCEEEECCHHHHHHHHC
T ss_conf             9629738999853679999999738


No 8  
>PRK08559 nusG transcription antitermination protein NusG; Validated
Probab=99.93  E-value=1.3e-24  Score=167.44  Aligned_cols=143  Identities=27%  Similarity=0.413  Sum_probs=127.3

Q ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCC
Q ss_conf             86189995288538999999999997798111432663131012772020356641203309999996186522444203
Q gi|254780148|r    3 PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDT   82 (177)
Q Consensus         3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t   82 (177)
                      .+-|+++|.+|+|+.++..|.++....+++  ++.+++|..                 ++|||||+++...+.|+.++++
T Consensus         6 ~~~y~Vkt~~G~E~~Va~~L~~r~~~~~l~--I~SI~~P~~-----------------lkGYV~VEa~~~~~v~~~i~gi   66 (153)
T PRK08559          6 SMIYAVRTTAGQERNVALLLASRAEKENLD--IYSILVPPE-----------------LKGYVFVEAESKGAVEEAIRGI   66 (153)
T ss_pred             CCEEEEEECCCHHHHHHHHHHHHHHHCCCC--EEEEECCCC-----------------CCCEEEEEECCHHHHHHHHHCC
T ss_conf             818999941773999999999998626996--589985588-----------------8617999956788999998477


Q ss_pred             CEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCC
Q ss_conf             30366432788610025889999997653222100001234789779995187789719999982889889999981687
Q gi|254780148|r   83 PKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGR  162 (177)
Q Consensus        83 ~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr  162 (177)
                      ++++|++     |.++|.+||++++..       ......+++||.|+|.+|||+|+.|.|.++|.++++++|.+-.+++
T Consensus        67 ~~v~g~~-----p~~v~~~Ei~~~L~~-------~~~~~~i~~G~~V~v~~Gpfkg~~a~V~~Vd~~k~~vtV~l~~~~~  134 (153)
T PRK08559         67 PHVRGVV-----PGEISFEEVEHFLKP-------KPIVEGIKEGDIVELIAGPFKGEKARVVRVDESKEEVTVELLEAAV  134 (153)
T ss_pred             CCEEEEC-----CCCCCHHHHHHHCCC-------CCCCCCCCCCCEEEEECCCCCCCCEEEEEECCCCCEEEEEEEEECC
T ss_conf             6468564-----776798999876375-------7652346899999991357699617999981668899999996354


Q ss_pred             EEEEEECHHHHEEC
Q ss_conf             04788567871233
Q gi|254780148|r  163 VTPVELAYNQVEKI  176 (177)
Q Consensus       163 ~~~v~l~~~~ieki  176 (177)
                      .+||++..+||+.+
T Consensus       135 p~pvtv~~d~Vr~i  148 (153)
T PRK08559        135 PIPVTVRGDQVRLV  148 (153)
T ss_pred             EEEEEEECCEEEEE
T ss_conf             04689766769987


No 9  
>pfam02357 NusG Transcription termination factor nusG.
Probab=99.85  E-value=4.6e-21  Score=146.14  Aligned_cols=89  Identities=39%  Similarity=0.750  Sum_probs=76.0

Q ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEE-ECCEEEEEECCEECEEEEEEEECCCCCHHHHHC
Q ss_conf             8618999528853899999999999779811143266313101277-202035664120330999999618652244420
Q gi|254780148|r    3 PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSV-RKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKD   81 (177)
Q Consensus         3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~-~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~   81 (177)
                      ++|||++|+||+|++|+++|++         +++++|+|..+..+. ++|+++.+.+|||||||||+++++++ |..|++
T Consensus         1 ~~Wyvl~t~~~~E~~v~~~L~~---------~~~~~~~p~~~~~~~~~~g~~~~~~~plfPGYvFV~~~~~~~-~~~i~~   70 (90)
T pfam02357         1 KKWYVLRTKSGQEKKVAENLER---------QGIESFLPTEEVVEVRKNGKKKKVERPLFPGYVFVRMDLNDE-TWKIRS   70 (90)
T ss_pred             CEEEEEEEECCHHHHHHHHHHH---------CCCEEEEEEEEEEEEECCCEEEEEEEECCCCEEEEEEECCCC-HHHHHC
T ss_conf             9599999969859999999997---------199599667999999729989999997578379999874668-435336


Q ss_pred             CCEEEEEECCCCCCCCCCHH
Q ss_conf             33036643278861002588
Q gi|254780148|r   82 TPKVIGFLGTGENPSPVTDS  101 (177)
Q Consensus        82 t~gV~~~l~~~~~P~~i~~~  101 (177)
                      |+||++||++|++|.+|||+
T Consensus        71 ~~gv~~~v~~g~~p~~i~d~   90 (90)
T pfam02357        71 TPGVSGFVGFGGKPAPVPDE   90 (90)
T ss_pred             CCCCCEECCCCCEEEECCCC
T ss_conf             98902992889991128999


No 10 
>TIGR00405 L26e_arch ribosomal protein L24; InterPro: IPR011590   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 , .    This protein contains a KOW domain, shared by bacterial NusG and the L24p/L26e family of ribosomal proteins. Although called archaeal NusG in several publications, it is the only close homolog of eukaryotic L26e in archaeal genomes, shares an operon with L11 in many genomes, and has been sequenced from purified ribosomes. It is here designated as a ribosomal protein for these reasons..
Probab=99.59  E-value=1.4e-14  Score=107.28  Aligned_cols=143  Identities=26%  Similarity=0.389  Sum_probs=113.7

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCCCEE
Q ss_conf             89995288538999999999997798111432663131012772020356641203309999996186522444203303
Q gi|254780148|r    6 YIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKV   85 (177)
Q Consensus         6 yvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV   85 (177)
                      |+++|..|||+.++..|..+....+++  ++.++.|.                 =+.|||+|++.-..|....++..|+|
T Consensus         1 fAvkT~vgQEknvA~lma~~ark~~l~--vysILape-----------------sLkGYilVEaetk~D~~~~i~g~Phv   61 (151)
T TIGR00405         1 FAVKTSVGQEKNVARLMARKARKENLE--VYSILAPE-----------------SLKGYILVEAETKDDLREAIKGLPHV   61 (151)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHCCCE--EEEEECCC-----------------CCCCCEEEECCCHHHHHHHHHCCCCC
T ss_conf             930035604688999998888764880--89997475-----------------34701899706947989897528820


Q ss_pred             EEEECCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEE
Q ss_conf             6643278-861002588999999765322210000123478977999518778971999998288988999998168704
Q gi|254780148|r   86 IGFLGTG-ENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVT  164 (177)
Q Consensus        86 ~~~l~~~-~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~  164 (177)
                      .|++.+. ..-..|+=+|++.|+.-      .. .-...+.||.|.|++|||+|=.+.|.++|.++.-+++.+.=--=..
T Consensus        62 rGvV~skteGegeI~feEie~fL~P------kk-iie~I~kGd~VEiisGPFKGErAkViRvDe~keEvtlEL~eAaVPI  134 (151)
T TIGR00405        62 RGVVESKTEGEGEIDFEEIERFLTP------KK-IIESIKKGDVVEIISGPFKGERAKVIRVDESKEEVTLELLEAAVPI  134 (151)
T ss_pred             CEEECCCCCCCEEEEHHHHHHHCCC------CH-HHHCCCCCCEEEEEECCCCCCEEEEEEEECCCCEEEEEEECCCCCC
T ss_conf             1155476787313647560200584------21-4531347888899538997644689863078762667632163566


Q ss_pred             EEEECHHHHE
Q ss_conf             7885678712
Q gi|254780148|r  165 PVELAYNQVE  174 (177)
Q Consensus       165 ~v~l~~~~ie  174 (177)
                      ||++.-++|+
T Consensus       135 PvTvk~d~vr  144 (151)
T TIGR00405       135 PVTVKADQVR  144 (151)
T ss_pred             CEEECCCEEE
T ss_conf             4452487158


No 11 
>KOG1999 consensus
Probab=98.15  E-value=9.3e-05  Score=48.49  Aligned_cols=52  Identities=25%  Similarity=0.330  Sum_probs=31.9

Q ss_pred             CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             478977999518778971999998288988999998168704788567871233
Q gi|254780148|r  123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      |.+||.|.|+.|-+.|+.|.|..+|+  ..+++.-+.=+...+++++...|.|.
T Consensus       408 F~~GD~VeV~~Gel~glkG~ve~vdg--~~vti~~~~e~l~~pl~~~~~eLrKy  459 (1024)
T KOG1999         408 FSPGDAVEVIVGELKGLKGKVESVDG--TIVTIMSKHEDLKGPLEVPASELRKY  459 (1024)
T ss_pred             CCCCCEEEEEEEEECCCEEEEEECCC--CEEEEEECCCCCCCCCCCCHHHHHHH
T ss_conf             37888389962124052568996168--65998523456898611352766542


No 12 
>pfam03439 Spt5-NGN Early transcription elongation factor of RNA pol II, NGN section. Spt5p and prokaryotic NusG are shown to contain a novel 'NGN' domain. The combined NGN and KOW motif regions of Spt5 form the binding domain with Spt4. Spt5 complexes with Spt4 as a 1:1 heterodimer snf this Spt5-Spt4 complex regulates early transcription elongation by RNA polymerase II and has an imputed role in pre-mRNA processing via its physical association with mRNA capping enzymes. The Schizosaccharomyces pombe core Spt5-Spt4 complex is a heterodimer bearing a trypsin-resistant Spt4-binding domain within the Spt5 subunit.
Probab=97.86  E-value=2.5e-05  Score=51.94  Aligned_cols=79  Identities=20%  Similarity=0.284  Sum_probs=54.3

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHC-CCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCCCE
Q ss_conf             899952885389999999999977-9811143266313101277202035664120330999999618652244420330
Q gi|254780148|r    6 YIVQVYSNCEKKAVESIGGRLSRS-GLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPK   84 (177)
Q Consensus         6 yvv~t~~~~E~~v~~~L~~~~~~~-~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~g   84 (177)
                      |+++|++|+|+.++..|.++.... .-+-.++.+++|                 +=++|||||++.........++..++
T Consensus         2 ~~Vk~~~G~E~~va~~l~~k~~~~~~~~l~I~Si~~p-----------------~~lkGyIyVEA~~~~~v~~ai~gi~~   64 (82)
T pfam03439         2 WAVKCTAGQEREVAISLMNKAEALKKENLEIYSIFVP-----------------DGLKGYIYVEADRQADVERALEGLPH   64 (82)
T ss_pred             EEEECCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEC-----------------CCCCEEEEEEECCHHHHHHHHHHHHH
T ss_conf             7587389819999999999998704688745999954-----------------89846999987988999999960377


Q ss_pred             EEEEECCCCCCCCCCHHHHHHH
Q ss_conf             3664327886100258899999
Q gi|254780148|r   85 VIGFLGTGENPSPVTDSEIEHI  106 (177)
Q Consensus        85 V~~~l~~~~~P~~i~~~ei~~l  106 (177)
                      +.+.     .+..+|-+||.++
T Consensus        65 v~~~-----~~~~Vp~~E~~~~   81 (82)
T pfam03439        65 VRGV-----VMGLVPIKEMEHL   81 (82)
T ss_pred             HHCC-----CCCCCCHHHHHCC
T ss_conf             7465-----7752888997510


No 13 
>TIGR01080 rplX_A_E ribosomal protein L24; InterPro: IPR005756   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 L24 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. This entry represents the archaeal and eukaryotic branch of these proteins, known as the L26 family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=96.65  E-value=0.0018  Score=40.78  Aligned_cols=53  Identities=26%  Similarity=0.396  Sum_probs=36.8

Q ss_pred             CCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEE----EECCCEEEEEECHH
Q ss_conf             012347897799951877897199999828898899999----81687047885678
Q gi|254780148|r  119 SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEV----VIFGRVTPVELAYN  171 (177)
Q Consensus       119 ~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v----~i~Gr~~~v~l~~~  171 (177)
                      .+.+...||.|+|+-|.|+|.||.|.++|..+.++.|.=    ..=|..+.+.+..+
T Consensus        38 r~lP~RkgD~V~i~RG~fkG~EGkv~~Vd~kr~~i~ve~~t~~k~~G~~V~~~~hpS   94 (116)
T TIGR01080        38 RALPVRKGDKVRIVRGDFKGHEGKVLEVDLKRYRIYVEGVTKEKVNGTEVPVPIHPS   94 (116)
T ss_pred             CCCCCCCCCEEEEEECCCCCCCCCEEEEEEEEEEEEECCCCCCCCCCCEEEECCCCC
T ss_conf             537612398789974662587551688730388898813101023885664246766


No 14 
>pfam00467 KOW KOW motif. This family has been extended to coincide with ref. The KOW (Kyprides, Ouzounis, Woese) motif is found in a variety of ribosomal proteins and NusG.
Probab=96.62  E-value=0.0022  Score=40.32  Aligned_cols=30  Identities=47%  Similarity=0.712  Sum_probs=25.8

Q ss_pred             CCCEEEEECCCCCCCEEEEEEECCCCCEEE
Q ss_conf             897799951877897199999828898899
Q gi|254780148|r  125 VGERVCVSDGPFASFNGIVKNVDEEKSRVH  154 (177)
Q Consensus       125 ~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~  154 (177)
                      +||.|+|++|||+|..|.|.+++.++.++.
T Consensus         1 ~G~~V~V~~G~~~G~~g~I~~i~~~~~~v~   30 (32)
T pfam00467         1 KGDVVRVISGPFKGKKGKVVEVDDSKARVH   30 (32)
T ss_pred             CCCEEEEECCCCCCCCCCEEEECCCCEEEE
T ss_conf             987899934675687554899607520685


No 15 
>smart00739 KOW KOW (Kyprides, Ouzounis, Woese) motif. Motif in ribosomal proteins, NusG, Spt5p, KIN17 and T54.
Probab=96.56  E-value=0.0021  Score=40.36  Aligned_cols=27  Identities=48%  Similarity=0.642  Sum_probs=24.6

Q ss_pred             CCCCCCEEEEECCCCCCCEEEEEEECC
Q ss_conf             347897799951877897199999828
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNGIVKNVDE  148 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~  148 (177)
                      .|++|+.|+|++|||+|..|.|.+++.
T Consensus         1 ~~~~G~~V~V~~G~~~g~~g~V~~i~~   27 (28)
T smart00739        1 KFEVGDTVRVIAGPFKGKVGKVLEVDG   27 (28)
T ss_pred             CCCCCCEEEEEECCCCCCCCEEEEECC
T ss_conf             940276889972255774113898238


No 16 
>PRK01191 rpl24p 50S ribosomal protein L24P; Validated
Probab=96.55  E-value=0.0065  Score=37.46  Aligned_cols=53  Identities=28%  Similarity=0.308  Sum_probs=39.5

Q ss_pred             CCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE----EEECCCEEEEEECHH
Q ss_conf             01234789779995187789719999982889889999----981687047885678
Q gi|254780148|r  119 SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE----VVIFGRVTPVELAYN  171 (177)
Q Consensus       119 ~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~----v~i~Gr~~~v~l~~~  171 (177)
                      -......||.|.|+.|.|+|.+|.|.+++..++++.|+    ...=|..+++-++.+
T Consensus        43 Rs~~IrkgD~V~V~rG~~kG~~GkV~~V~~k~~~V~VEgv~~~K~~G~~v~~pIhpS   99 (119)
T PRK01191         43 RSLPVRKGDTVKVMRGDFKGEEGKVVEVDLKRYRIYVEGVTIKKADGTEVPYPIHPS   99 (119)
T ss_pred             CCCCEECCCEEEEEECCCCCCCCEEEEEECCCCEEEEEEEEEECCCCCEEEEEECCC
T ss_conf             744354699999955277896231899973688999943699847998786422563


No 17 
>KOG1999 consensus
Probab=96.12  E-value=0.016  Score=35.08  Aligned_cols=133  Identities=20%  Similarity=0.267  Sum_probs=83.1

Q ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHC
Q ss_conf             88618999528853899999999999779811143266313101277202035664120330999999618652244420
Q gi|254780148|r    2 TPRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKD   81 (177)
Q Consensus         2 ~~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~   81 (177)
                      .|+=|.|+|+.|.|+.++-.|-++.......+-      |.+        -+....+-=+.|||||++.--.   +...-
T Consensus       164 DP~LW~VKC~iG~Er~~a~~LMrK~i~~~~t~~------plq--------I~Sv~a~D~lkGyIYIEA~Kqs---hV~~A  226 (1024)
T KOG1999         164 DPNLWIVKCKIGREREVAFCLMRKFIELDKTDT------PLQ--------IKSVFAKDHLKGYIYIEADKQS---HVKEA  226 (1024)
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHHHCCCCC------CCE--------EEEEEECCCCCEEEEEEECHHH---HHHHH
T ss_conf             987158983366078899999999986024699------722--------7899821555216999821567---89999


Q ss_pred             CCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECC
Q ss_conf             33036643278861002588999999765322210000123478977999518778971999998288988999998168
Q gi|254780148|r   82 TPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFG  161 (177)
Q Consensus        82 t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~G  161 (177)
                      +.||.++-.+  +-..||-.||-.++...++       ...+++|.=|||..|-++|-.|.|..++..+.+  |.|.+.=
T Consensus       227 i~gv~niy~~--~~~lVPikEM~dvLkV~K~-------~v~L~~gswVRiKrG~YKgDLAqVd~Vd~~~n~--v~lKlIP  295 (1024)
T KOG1999         227 IEGVRNIYAN--RILLVPIKEMPDVLKVVKK-------VVQLSEGSWVRIKRGKYKGDLAQVDDVDENRNR--VRLKLIP  295 (1024)
T ss_pred             HHHHHHHEEC--CEEEEEHHHHHHHHHHHHH-------HHCCCCCCEEEEECCCCCCCEEEEEEECCCCCE--EEEEEEC
T ss_conf             8520332014--1798754574445413344-------321376625887545015630125664256777--8999832


Q ss_pred             C
Q ss_conf             7
Q gi|254780148|r  162 R  162 (177)
Q Consensus       162 r  162 (177)
                      |
T Consensus       296 R  296 (1024)
T KOG1999         296 R  296 (1024)
T ss_pred             C
T ss_conf             1


No 18 
>PTZ00194 60S ribosomal protein L26; Provisional
Probab=95.67  E-value=0.016  Score=35.11  Aligned_cols=37  Identities=22%  Similarity=0.302  Sum_probs=31.2

Q ss_pred             CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE
Q ss_conf             1234789779995187789719999982889889999
Q gi|254780148|r  120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE  156 (177)
Q Consensus       120 ~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~  156 (177)
                      ..++..||.|.|..|.|+|.+|.|.+++..+.++.|.
T Consensus        44 s~pIRkgDeV~V~RG~fkG~eGKV~~V~~kk~~I~VE   80 (143)
T PTZ00194         44 AMPVRKDDEVIVKRGAFKGREGKVTACYRLKWVIHID   80 (143)
T ss_pred             CCCCCCCCEEEEEECCCCCCCCEEEEEEEEEEEEEEE
T ss_conf             1001159999998555368776599999500099995


No 19 
>PRK00004 rplX 50S ribosomal protein L24; Reviewed
Probab=95.62  E-value=0.026  Score=33.80  Aligned_cols=38  Identities=34%  Similarity=0.311  Sum_probs=33.4

Q ss_pred             CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE-EEE
Q ss_conf             34789779995187789719999982889889999-981
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE-VVI  159 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~-v~i  159 (177)
                      .+..||.|.|++|..+|-.|.|.+++.+++++.|. +++
T Consensus         3 kikkGD~V~VisGkdKGk~G~V~~v~~~~~~viVeGvN~   41 (102)
T PRK00004          3 KIKKGDTVIVIAGKDKGKQGKVLKVLPKKDKVIVEGVNI   41 (102)
T ss_pred             CEECCCEEEEEECCCCCCCEEEEEEECCCCEEEEECCEE
T ss_conf             206799999927799997368999998799999977478


No 20 
>PRK12281 rplX 50S ribosomal protein L24; Reviewed
Probab=95.52  E-value=0.028  Score=33.65  Aligned_cols=41  Identities=34%  Similarity=0.279  Sum_probs=34.6

Q ss_pred             CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE-EEEC
Q ss_conf             1234789779995187789719999982889889999-9816
Q gi|254780148|r  120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE-VVIF  160 (177)
Q Consensus       120 ~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~-v~i~  160 (177)
                      ...++.||.|.|++|.-+|-.|.|.+++++++++.|. +++-
T Consensus         4 K~kIkkGD~V~VisGkdKGk~G~Vl~v~~~~~rviVeGvN~~   45 (77)
T PRK12281          4 KLHVKKGDMVKVIAGDDKGKTGKVLAVLPKKNRVIVEGVNIR   45 (77)
T ss_pred             EEEEECCCEEEEEECCCCCCCEEEEEEECCCCEEEEECCEEE
T ss_conf             048758999999466789972789999877999999486379


No 21 
>CHL00141 rpl24 ribosomal protein L24; Validated
Probab=95.29  E-value=0.037  Score=32.91  Aligned_cols=41  Identities=22%  Similarity=0.220  Sum_probs=34.7

Q ss_pred             CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE-EEEC
Q ss_conf             1234789779995187789719999982889889999-9816
Q gi|254780148|r  120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE-VVIF  160 (177)
Q Consensus       120 ~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~-v~i~  160 (177)
                      ...+..||.|.|++|.-+|-.|.|.+++..++++.|. +++-
T Consensus         9 K~kIkkGD~V~VisGkdKGk~G~Vl~v~~~~~~viVeGvN~~   50 (90)
T CHL00141          9 KMHVKKGDTVQVISGKDKGKIGEVLKIIRKSNKVIVKGINIK   50 (90)
T ss_pred             CEEEECCCEEEEEECCCCCCCEEEEEEECCCCEEEEECCEEE
T ss_conf             406708999999166789973579999867999999795888


No 22 
>COG0198 RplX Ribosomal protein L24 [Translation, ribosomal structure and biogenesis]
Probab=94.53  E-value=0.067  Score=31.38  Aligned_cols=33  Identities=33%  Similarity=0.251  Sum_probs=27.8

Q ss_pred             CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE
Q ss_conf             34789779995187789719999982889889999
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE  156 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~  156 (177)
                      .+..||.|.|++|.++|-+|.|.++++..  +.|.
T Consensus         4 ~IrkGD~V~Vi~GkdKGk~GkVl~v~~k~--V~VE   36 (104)
T COG0198           4 KVKKGDTVKVIAGKDKGKEGKVLKVLPKK--VVVE   36 (104)
T ss_pred             CEECCCEEEEEECCCCCCCEEEEEEECCE--EEEE
T ss_conf             24369999998668899614899991573--8997


No 23 
>COG5164 SPT5 Transcription elongation factor [Transcription]
Probab=93.94  E-value=0.4  Score=26.74  Aligned_cols=42  Identities=24%  Similarity=0.401  Sum_probs=32.5

Q ss_pred             CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEE
Q ss_conf             47897799951877897199999828898899999816870478
Q gi|254780148|r  123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPV  166 (177)
Q Consensus       123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v  166 (177)
                      -..|..|+|.+||++|+-|+|+.++++  .++|.++-=.+.+.+
T Consensus       352 ~aigktVrIr~g~yKG~lGVVKdv~~~--~arVeLhs~nK~VTI  393 (607)
T COG5164         352 PAIGKTVRIRCGEYKGHLGVVKDVDRN--IARVELHSNNKFVTI  393 (607)
T ss_pred             CCCCCEEEEEECCCCCCCCEEEECCCC--EEEEEEECCCCEEEE
T ss_conf             345846899623645544246643686--489997058816986


No 24 
>TIGR01079 rplX_bact ribosomal protein L24; InterPro: IPR003256   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 L24 is one of the proteins from the large ribosomal subunit. In their mature form, these proteins have 103 to 150 amino-acid residues. This domain is found in L24 and L26 ribosomal proteins.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=91.63  E-value=0.38  Score=26.91  Aligned_cols=38  Identities=32%  Similarity=0.315  Sum_probs=32.8

Q ss_pred             CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE-EEE
Q ss_conf             34789779995187789719999982889889999-981
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE-VVI  159 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~-v~i  159 (177)
                      .++.||+|.|++|-=+|-.|.|.++.+++++|.|. +++
T Consensus         3 kiKKGD~V~VIsGKdKGK~GkVl~v~~~~~kViVEGvN~   41 (109)
T TIGR01079         3 KIKKGDTVVVISGKDKGKRGKVLKVLPKKNKVIVEGVNM   41 (109)
T ss_pred             EEEECCEEEEEECCCCCCEEEEEEEECCCCEEEEECCCE
T ss_conf             133098888886889887238999525788388831533


No 25 
>PRK06531 yajC preprotein translocase subunit YajC; Validated
Probab=91.27  E-value=0.76  Score=25.09  Aligned_cols=49  Identities=22%  Similarity=0.447  Sum_probs=32.5

Q ss_pred             CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEECC
Q ss_conf             234789779995187789719999982889889999981687047885678712339
Q gi|254780148|r  121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKIV  177 (177)
Q Consensus       121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki~  177 (177)
                      ..+++||.|. +.|   |+.|.|.++|.++.++.+.++  |  +-+.++..-|.+|+
T Consensus        35 ~~L~kGdeVv-TiG---Gl~G~V~~Vd~e~~tV~Ld~~--G--v~l~f~r~AI~~Vv   83 (120)
T PRK06531         35 NAIQKGDEVV-TIG---GLFGTVDEVDTEAKKIVLDVD--G--VYLTFELSAIKRVV   83 (120)
T ss_pred             HHCCCCCEEE-ECC---CCEEEEEEEECCCCEEEEEEC--C--EEEEEEHHHHHHHC
T ss_conf             7257999899-789---828999999278988999828--9--79999867765225


No 26 
>pfam11623 DUF3252 Protein of unknown function (DUF3252). This family of proteins has no known function. Some members are annotated as Ssl0352 however this cannot be confirmed. Currently there is no known function.
Probab=90.18  E-value=1.2  Score=23.98  Aligned_cols=50  Identities=18%  Similarity=0.191  Sum_probs=38.5

Q ss_pred             CCCCCEEEEEC--CCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHE
Q ss_conf             47897799951--87789719999982889889999981687047885678712
Q gi|254780148|r  123 FEVGERVCVSD--GPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVE  174 (177)
Q Consensus       123 ~~~G~~V~I~~--Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ie  174 (177)
                      +-||..|+|.+  -++-|++|.|.++.+  ++|-|+++=-.=.-.|++.++++|
T Consensus         2 ilPG~~V~V~n~~~~Y~gy~G~VQRvsd--~kaaVLFeggnWdKlvTf~l~~Le   53 (53)
T pfam11623         2 ILPGMTVKVKNPNDIYYGYEGQVQRVSD--GKAAVLFEGGNWDKLVTFRLSELE   53 (53)
T ss_pred             CCCCCEEEEECCCCCCHHCEEEEEEECC--CEEEEEECCCCCEEEEEEEHHHCC
T ss_conf             2599789986887760020489999419--908999569972178998755678


No 27 
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=82.92  E-value=3.8  Score=20.92  Aligned_cols=48  Identities=21%  Similarity=0.259  Sum_probs=34.8

Q ss_pred             CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             23478977999518778971999998288988999998168704788567871233
Q gi|254780148|r  121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      ..+++||.|+|.+-   |..|.|.++.+ ++.+.|.+..    ..+.++.++|+++
T Consensus       633 ~~~~~Gd~V~v~~~---~~~G~V~~i~~-~~~~~V~~g~----~k~~v~~~~l~~~  680 (780)
T PRK00409        633 EELKVGDEVKYLSL---GQKGEVLSIPD-NKEAIVQAGI----MKMKVPLSDLEKI  680 (780)
T ss_pred             CCCCCCCEEEECCC---CCEEEEEEECC-CCEEEEEECC----EEEEEEHHHCEEC
T ss_conf             79999998998579---96799999869-9819999797----6999779993137


No 28 
>pfam02211 NHase_beta Nitrile hydratase beta subunit. Nitrile hydratases EC:4.2.1.84 are unusual metalloenzymes that catalyse the hydration of nitriles to their corresponding amides. They are used as biocatalysts in acrylamide production, one of the few commercial scale bioprocesses, as well as in environmental remediation for the removal of nitriles from waste streams. Nitrile hydratases are composed of two subunits, alpha and beta, and they contain one iron atom per alpha beta unit.
Probab=79.35  E-value=3.9  Score=20.86  Aligned_cols=51  Identities=16%  Similarity=0.199  Sum_probs=33.9

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECC----------CCCCCEEEEEEEC
Q ss_conf             02588999999765322210000123478977999518----------7789719999982
Q gi|254780148|r   97 PVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDG----------PFASFNGIVKNVD  147 (177)
Q Consensus        97 ~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~G----------pf~g~~g~v~~i~  147 (177)
                      .++.+.+...+..-............|++||+|++.+-          ...|..|+|..+.
T Consensus       107 ~~~a~~v~~~l~~G~p~~R~~~~~p~F~vGd~Vrv~~~~~~gHtRlP~Y~rgk~G~I~~~~  167 (220)
T pfam02211       107 VLPADQVAAVLARGGPADRPADAPPRFAVGDRVRTRNINPNGHTRLPRYVRGKTGTIVRVH  167 (220)
T ss_pred             CCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHCCCEEEEEEEE
T ss_conf             5788899999746898778899999779999899822799975235367678745899884


No 29 
>KOG1708 consensus
Probab=77.92  E-value=3.1  Score=21.39  Aligned_cols=34  Identities=32%  Similarity=0.261  Sum_probs=24.4

Q ss_pred             CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEE
Q ss_conf             3478977999518778971999998288988999
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHV  155 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V  155 (177)
                      .|..||+|.|+.|-=+|-.|.|..+-.+++-+.|
T Consensus        72 ~ff~GDtVeVlvGkDkGkqG~Vtqv~r~~s~VvV  105 (236)
T KOG1708          72 HFFFGDTVEVLVGKDKGKQGEVTQVIRHRSWVVV  105 (236)
T ss_pred             EEECCCEEEEEECCCCCCCCEEEEEEECCCEEEE
T ss_conf             6834987999751567743138998604764897


No 30 
>TIGR00739 yajC preprotein translocase, YajC subunit; InterPro: IPR003849   This entry describes proteins of unknown function..
Probab=75.23  E-value=6.6  Score=19.46  Aligned_cols=49  Identities=16%  Similarity=0.318  Sum_probs=32.8

Q ss_pred             CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             23478977999518778971999998288988999998168704788567871233
Q gi|254780148|r  121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      ..+++||+|...+    |..|.|.++..+.+.+.+.++   -.|.+++.-+-|..+
T Consensus        36 ~~L~KGd~V~T~g----Gi~G~V~~i~e~~~~i~i~~~---~~t~~~~~K~aI~~~   84 (86)
T TIGR00739        36 ESLKKGDKVLTIG----GIIGTVTKIAENTNNIVIELN---DNTEITFSKNAIVEV   84 (86)
T ss_pred             HCCCCCCEEEECC----CEEEEEEEEECCCCEEEEEEC---CCCEEEEEHHHHHHH
T ss_conf             5279977899838----838999885238867899987---994899860342422


No 31 
>PRK11865 pyruvate ferredoxin oxidoreductase subunit beta; Provisional
Probab=75.10  E-value=3.3  Score=21.23  Aligned_cols=108  Identities=10%  Similarity=0.153  Sum_probs=65.8

Q ss_pred             EEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEE-----EEEECCEECEEEEEEEE--CCCC--C
Q ss_conf             1899952885389999999999977981114326631310127720203-----56641203309999996--1865--2
Q gi|254780148|r    5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRK-----VNSERRFFPGYVLIKAV--MTDK--V   75 (177)
Q Consensus         5 Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~-----~~~~~plfpgYiFv~~~--~~~~--~   75 (177)
                      =||.++.++.-....+.+++.++..|+.  ..++|.||..-|.....+.     .-++.-+||=|=+-.-.  .+..  .
T Consensus       175 ~YVA~~s~~~~~~l~~~i~kA~~~~G~s--~i~v~sPCp~gw~~~~~~t~~~~klAVetg~wpLye~~~g~~~~~~~p~~  252 (298)
T PRK11865        175 PYVATASIGYPEDFMKKVKKAAEVDGPA--YIQVLQPCPTGWGFPPEKTIEIGRLAVETGYWPLFEIENGKFNISYEPLH  252 (298)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHHCCCCE--EEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCCCCCCC
T ss_conf             8899982579999999999998089987--99997889566887835799999999980980489950882355678866


Q ss_pred             HHHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             244420330366432788610025889999997653222
Q gi|254780148|r   76 YHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAV  114 (177)
Q Consensus        76 ~~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~  114 (177)
                      ....+...-|..||...++..-+.+++++.|...++..-
T Consensus       253 ~~~~~~k~pv~eyL~~q~Rf~~L~~e~~~~lq~~vD~~w  291 (298)
T PRK11865        253 CLDIETRKPIEEYLKVQGRFKHLTPEDIEELQKYIDAMW  291 (298)
T ss_pred             CCCCCCCCCHHHHHHHCCCHHCCCHHHHHHHHHHHHHHH
T ss_conf             444678879999987360420189989999999999999


No 32 
>PRK11864 2-ketoisovalerate ferredoxin oxidoreductase subunit beta; Provisional
Probab=75.04  E-value=4.7  Score=20.35  Aligned_cols=108  Identities=10%  Similarity=0.125  Sum_probs=66.9

Q ss_pred             EEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEE-----EEEECCEECEEEEEE--EECCCCCH-
Q ss_conf             1899952885389999999999977981114326631310127720203-----566412033099999--96186522-
Q gi|254780148|r    5 WYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRK-----VNSERRFFPGYVLIK--AVMTDKVY-   76 (177)
Q Consensus         5 Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~-----~~~~~plfpgYiFv~--~~~~~~~~-   76 (177)
                      =||.++.+++-....+.+++..+..|..  ..++|.||-.-|+.....-     .-++.-+||=|=+..  +..+.... 
T Consensus       173 ~YVA~~~~a~~~~l~~~i~kA~~~~G~s--~i~v~spCp~gw~~~~~~t~~~~klAVesg~wpLye~~~g~~~~~~~~~~  250 (300)
T PRK11864        173 PYVATASIAYPEDFIRKLKKAAEIPGFK--FIHLLAPCPPGWRFDPAKTIEIARLAVETGAWPLFEYENGKFKLNPPSTT  250 (300)
T ss_pred             CEEEEEECCCHHHHHHHHHHHHCCCCCE--EEEEECCCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCEEECCCCCCC
T ss_conf             8799985569999999999997189987--99997889565886813689999999980995379977897650588755


Q ss_pred             -HHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             -44420330366432788610025889999997653222
Q gi|254780148|r   77 -HTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAV  114 (177)
Q Consensus        77 -~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~  114 (177)
                       ...+.-.-|..+|...++...+.+++++.+....+..-
T Consensus       251 ~~~~~~~~pv~eyl~~q~Rf~hL~~e~~~~~q~~vd~~w  289 (300)
T PRK11864        251 LADKKKRKPVEEYLKLQGRFKHLTEEDIKALQEEIEEEW  289 (300)
T ss_pred             CCCCCCCCCHHHHHHHCCCCHHCCHHHHHHHHHHHHHHH
T ss_conf             457778879999976274621049999999999999999


No 33 
>COG1862 YajC Preprotein translocase subunit YajC [Intracellular trafficking and secretion]
Probab=74.18  E-value=7  Score=19.30  Aligned_cols=45  Identities=20%  Similarity=0.355  Sum_probs=30.0

Q ss_pred             CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHE
Q ss_conf             234789779995187789719999982889889999981687047885678712
Q gi|254780148|r  121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVE  174 (177)
Q Consensus       121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ie  174 (177)
                      ..+++||+|. +.|   |+.|.|.+++.+.  +.|.++   ..|.+.+..+.|-
T Consensus        42 ~sL~kGD~Vv-T~g---Gi~G~V~~v~d~~--v~I~l~---~~~~i~~~k~aI~   86 (97)
T COG1862          42 NSLKKGDEVV-TIG---GIVGTVTKVGDDT--VEIELG---DGTKIKFEKEAIA   86 (97)
T ss_pred             HHCCCCCEEE-ECC---CEEEEEEEEECCC--EEEEEC---CCEEEEEEHHHHH
T ss_conf             7456899899-758---7399999970681--899978---9869999879988


No 34 
>PTZ00065 60S ribosomal protein L14; Provisional
Probab=73.61  E-value=6.1  Score=19.66  Aligned_cols=36  Identities=25%  Similarity=0.306  Sum_probs=28.7

Q ss_pred             CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEE
Q ss_conf             3478977999518778971999998288988999998
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVV  158 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~  158 (177)
                      ..++|--|.|..||.+|-.+.|..|- |..|+.|.=.
T Consensus         7 fVEvGRVv~i~~Gp~~GKL~~IVDII-D~nRvLVDGP   42 (130)
T PTZ00065          7 FVEPGRLCLITYGPDAGKLCFIVDIV-TPTRVLVDGA   42 (130)
T ss_pred             CEECCEEEEEEECCCCCCEEEEEEEE-CCCEEEECCC
T ss_conf             03426599994078889789999986-1764674087


No 35 
>pfam06003 SMN Survival motor neuron protein (SMN). This family consists of several eukaryotic survival motor neuron (SMN) proteins. The Survival of Motor Neurons (SMN) protein, the product of the spinal muscular atrophy-determining gene, is part of a large macromolecular complex (SMN complex) that functions in the assembly of spliceosomal small nuclear ribonucleoproteins (snRNPs). The SMN complex functions as a specificity factor essential for the efficient assembly of Sm proteins on U snRNAs and likely protects cells from illicit, and potentially deleterious, non-specific binding of Sm proteins to RNAs.
Probab=67.31  E-value=10  Score=18.38  Aligned_cols=33  Identities=18%  Similarity=0.441  Sum_probs=13.3

Q ss_pred             CCCCCEEEEE---CCCCCCCEEEEEEECCCCCEEEEEE
Q ss_conf             4789779995---1877897199999828898899999
Q gi|254780148|r  123 FEVGERVCVS---DGPFASFNGIVKNVDEEKSRVHVEV  157 (177)
Q Consensus       123 ~~~G~~V~I~---~Gpf~g~~g~v~~i~~~~~r~~V~v  157 (177)
                      +++||..+-+   ||  ..++|.|..||..++.++|..
T Consensus        69 wkVGD~C~A~yseDG--~~YeAtI~SId~k~gtCvV~Y  104 (264)
T pfam06003        69 WQVGDSCNAVWSEDG--NLYTATITSIDQKRGTCVVFY  104 (264)
T ss_pred             EECCCEEEEEECCCC--CCCEEEEEEECCCCCCEEEEE
T ss_conf             111885676652578--520136777526787068998


No 36 
>TIGR01069 mutS2 MutS2 family protein; InterPro: IPR005747   Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA.    MutS is a modular protein with a complex structure , and is composed of:    N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts.    Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts .    This entry represents a family of MutS proteins.; GO: 0003684 damaged DNA binding, 0005524 ATP binding, 0045005 maintenance of fidelity during DNA-dependent DNA replication.
Probab=66.04  E-value=11  Score=18.23  Aligned_cols=49  Identities=22%  Similarity=0.360  Sum_probs=35.3

Q ss_pred             CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             23478977999518778971999998288988999998168704788567871233
Q gi|254780148|r  121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      ..|++||+++|.   +.|..|.|.++......+.|.+.+|-    +.++..+|+++
T Consensus       670 ~~Fk~Gd~~~~~---~~g~kg~~~~~~~~g~~~~V~~g~~~----m~v~~~~l~~~  718 (834)
T TIGR01069       670 ADFKVGDKVKVE---SFGQKGKIVEIKGKGNKWNVTVGLLR----MKVKESELEKI  718 (834)
T ss_pred             CCCCCCCCCEEE---ECCCEEEEEEEECCCCEEEEEEEEEE----EEECHHHHHHH
T ss_conf             787357401112---15864799998056557776652104----43137888874


No 37 
>cd01734 YlxS_C YxlS is a Bacillus subtilis gene of unknown function with two domains that each have an alpha/beta fold.  The N-terminal domain is composed of two alpha-helices and a three-stranded beta-sheet, while the C-terminal domain is composed of one alpha-helix and a five-stranded beta-sheet.  This CD represents the C-terminal domain which has a fold similar to the Sm fold of proteins like Sm-D3.
Probab=66.00  E-value=11  Score=18.22  Aligned_cols=50  Identities=34%  Similarity=0.498  Sum_probs=36.7

Q ss_pred             CCCEEEEE-CCCCCC---CEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             89779995-187789---71999998288988999998168704788567871233
Q gi|254780148|r  125 VGERVCVS-DGPFAS---FNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       125 ~G~~V~I~-~Gpf~g---~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      .|..|.|. ..|..|   +.|.+.+++.  +.+.+.++.-++...+++++++|+|.
T Consensus        24 ~G~~v~v~l~~~~~g~k~f~G~L~~v~~--~~i~l~~~~~~~~~~~~i~~~~I~kA   77 (83)
T cd01734          24 VGKYVHVKLYQPIDGQKEFEGTLLGVDD--DTVTLEVDIKTRGKTVEIPLDKIAKA   77 (83)
T ss_pred             CCCEEEEEEECCCCCCEEEEEEEEEEEC--CEEEEEEECCCCCEEEEEEHHHHCEE
T ss_conf             7987999991501891899999998839--99999995277878999746982147


No 38 
>PRK05585 yajC preprotein translocase subunit YajC; Validated
Probab=64.32  E-value=11  Score=18.03  Aligned_cols=47  Identities=19%  Similarity=0.331  Sum_probs=30.1

Q ss_pred             CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             23478977999518778971999998288988999998168704788567871233
Q gi|254780148|r  121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      ..+++||+|. +.|   |+.|.|.+++++  .+.+  ++- ..+.+.+.-.-|-.|
T Consensus        52 ~~L~~Gd~Vv-T~g---Gi~G~I~~v~d~--~v~l--eia-~gv~i~~~r~aI~~V   98 (107)
T PRK05585         52 SSLAKGDEVV-TNG---GIIGKVTKVSED--FVII--ELN-DDTEIKIQKSAIAAV   98 (107)
T ss_pred             HHCCCCCEEE-ECC---CCEEEEEEEECC--EEEE--EEC-CCCEEEEEHHHHHHH
T ss_conf             8458999999-899---858999999799--8999--988-995899995896643


No 39 
>COG2139 RPL21A Ribosomal protein L21E [Translation, ribosomal structure and biogenesis]
Probab=61.45  E-value=13  Score=17.71  Aligned_cols=52  Identities=21%  Similarity=0.286  Sum_probs=36.6

Q ss_pred             CCCCCCEEEEECCC----------CCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEE
Q ss_conf             34789779995187----------7897199999828898899999816870478856787123
Q gi|254780148|r  122 FFEVGERVCVSDGP----------FASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK  175 (177)
Q Consensus       122 ~~~~G~~V~I~~Gp----------f~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~iek  175 (177)
                      .|++||.|.|.--|          |.|..|+|....+  .-..|.+..-++.-.+-+..+.|++
T Consensus        32 ey~~Gd~V~I~IdpSv~kGmPh~rf~G~TG~Vvg~~g--~ay~V~v~~G~k~K~liv~peHLk~   93 (98)
T COG2139          32 EYKVGDKVHIDIDPSVHKGMPHPRFQGKTGTVVGVRG--RAYKVEVYDGNKEKTLIVRPEHLKP   93 (98)
T ss_pred             HCCCCCEEEEEECCCCCCCCCCCCCCCCCEEEEECCC--CEEEEEEECCCCEEEEEECHHHCCC
T ss_conf             6079987999847620269877530476307984148--7799999618945899867788544


No 40 
>PRK11760 putative RNA 2'-O-ribose methyltransferase; Provisional
Probab=61.32  E-value=13  Score=17.70  Aligned_cols=27  Identities=15%  Similarity=0.220  Sum_probs=22.7

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHCCCH
Q ss_conf             899952885389999999999977981
Q gi|254780148|r    6 YIVQVYSNCEKKAVESIGGRLSRSGLD   32 (177)
Q Consensus         6 yvv~t~~~~E~~v~~~L~~~~~~~~~~   32 (177)
                      .+++|+||.|+.++.-|..+.+..++.
T Consensus         4 lllyCRpGFE~e~AaEi~~~aa~~gv~   30 (356)
T PRK11760          4 LLLYCRPGFEKECAAEITDKAAELGVF   30 (356)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHCCCC
T ss_conf             534417986389999999999963887


No 41 
>TIGR02361 dak_ATP dihydroxyacetone kinase; InterPro: IPR012734    This family consists of examples of the single chain form of dihydroxyacetone kinase (also called glycerone kinase) that uses ATP (2.7.1.29 from EC) as the phosphate donor, rather than a phosphoprotein as in Escherichia coli. This form has separable domains homologous to the K and L subunits of the E. coli enzyme, and is found in yeasts and other eukaryotes and in some bacteria, including Citrobacter freundii. The member from tomato has been shown to phosphorylate dihydroxyacetone, 3,4-dihydroxy-2-butanone, and some other aldoses and ketoses . ; GO: 0004371 glycerone kinase activity, 0005524 ATP binding.
Probab=60.45  E-value=11  Score=18.23  Aligned_cols=49  Identities=22%  Similarity=0.401  Sum_probs=33.9

Q ss_pred             HHHCCCEEEEEECCCCCCCC-CCHHHHHH-HHHHHHHHHHHHCCCCCCCCCCEEEEE
Q ss_conf             44203303664327886100-25889999-997653222100001234789779995
Q gi|254780148|r   78 TIKDTPKVIGFLGTGENPSP-VTDSEIEH-IMNQVEAAVQRPVSSVFFEVGERVCVS  132 (177)
Q Consensus        78 ~i~~t~gV~~~l~~~~~P~~-i~~~ei~~-l~~~~~~~~~~~~~~~~~~~G~~V~I~  132 (177)
                      -|++=||+.++     .|+| + ++.|.+ |+..+-+......+.+.|.+||+|.+.
T Consensus       236 GIHnEpG~~r~-----~~~pS~-~~lv~~~mLk~lLd~~D~dR~yV~~~~~~~vVLl  286 (627)
T TIGR02361       236 GIHNEPGVKRI-----SPIPSI-EDLVVKLMLKKLLDESDEDRSYVKFEEGDEVVLL  286 (627)
T ss_pred             CCCCCCCCEEE-----CCCCCH-HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEE
T ss_conf             86476664532-----466887-8999997557655787865531021799817998


No 42 
>COG2933 Predicted SAM-dependent methyltransferase [General function prediction only]
Probab=57.20  E-value=15  Score=17.27  Aligned_cols=26  Identities=12%  Similarity=0.172  Sum_probs=21.1

Q ss_pred             EEEEECCCCHHHHHHHHHHHHHHCCC
Q ss_conf             89995288538999999999997798
Q gi|254780148|r    6 YIVQVYSNCEKKAVESIGGRLSRSGL   31 (177)
Q Consensus         6 yvv~t~~~~E~~v~~~L~~~~~~~~~   31 (177)
                      .+++|+||.|+.++..|.++.+..++
T Consensus         4 l~lyCRpGFEkE~aAEi~d~Aa~l~I   29 (358)
T COG2933           4 LALYCRPGFEKECAAEITDKAAQLEI   29 (358)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHCC
T ss_conf             12331588747888999876665246


No 43 
>pfam02699 YajC Preprotein translocase subunit. See.
Probab=55.51  E-value=16  Score=17.10  Aligned_cols=48  Identities=21%  Similarity=0.404  Sum_probs=31.5

Q ss_pred             CCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEECC
Q ss_conf             234789779995187789719999982889889999981687047885678712339
Q gi|254780148|r  121 VFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKIV  177 (177)
Q Consensus       121 ~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki~  177 (177)
                      ..+++||+|. +.|   |+.|.|.++++  +.+.+.  + +..+.++++-.-|-+++
T Consensus        36 ~~L~~Gd~Vv-T~g---Gi~G~V~~i~~--~~v~le--i-~~gv~i~v~r~aI~~v~   83 (83)
T pfam02699        36 SSLKKGDEVV-TIG---GIHGKIVKVDD--DTVVLE--I-ADGVKVKVDKSAIARVL   83 (83)
T ss_pred             HHCCCCCEEE-ECC---CEEEEEEEEEC--CEEEEE--E-CCCCEEEEEHHHHHHHC
T ss_conf             8578999999-899---71999999979--999999--8-89939999969867449


No 44 
>PRK04333 50S ribosomal protein L14e; Validated
Probab=55.47  E-value=16  Score=17.10  Aligned_cols=34  Identities=24%  Similarity=0.245  Sum_probs=27.1

Q ss_pred             CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE
Q ss_conf             34789779995187789719999982889889999
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE  156 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~  156 (177)
                      ..++|--+.+..||.+|-.+.|..+- |++|+.|.
T Consensus         3 ~VEvGRV~~i~~G~~aGkl~vIVDiI-D~nrvLVd   36 (83)
T PRK04333          3 AIEVGRVCVKTAGREAGRKCVIVDII-DKNFVLVT   36 (83)
T ss_pred             CEEECEEEEEECCCCCCCEEEEEEEE-CCCEEEEE
T ss_conf             56703499993177679789999997-38879988


No 45 
>TIGR02249 integrase_gron integron integrase; InterPro: IPR011946    Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family that also includes recombinases XerC (IPR011931 from INTERPRO) and XerD (IPR011932 from INTERPRO), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration.
Probab=53.59  E-value=7.9  Score=18.97  Aligned_cols=72  Identities=18%  Similarity=0.168  Sum_probs=53.2

Q ss_pred             EEEEECCC---CCCCCCCHHHHHHHHHHHH-HHHHHHC-----CCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEE
Q ss_conf             36643278---8610025889999997653-2221000-----0123478977999518778971999998288988999
Q gi|254780148|r   85 VIGFLGTG---ENPSPVTDSEIEHIMNQVE-AAVQRPV-----SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHV  155 (177)
Q Consensus        85 V~~~l~~~---~~P~~i~~~ei~~l~~~~~-~~~~~~~-----~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V  155 (177)
                      ..+|+++.   .-|..++.+|+.+++..++ .......     +..++-++-+.||.|=.|.-.+-.|-.-++.|+|++.
T Consensus        89 ~~~~~Ra~~~~kLPvVLT~eEV~~~l~~l~eg~y~L~a~LLYGsGMRlmE~LRLRikDiDF~~~~I~vr~GKG~KdR~v~  168 (320)
T TIGR02249        89 MENFVRAKRPRKLPVVLTREEVARLLEHLEEGKYRLIAKLLYGSGMRLMECLRLRIKDIDFDYGEIRVRDGKGGKDRVVT  168 (320)
T ss_pred             HHHCCCCCCCCCCCEECCHHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHHCCCCEEEECCCEEEEEECCCCCCCCCC
T ss_conf             22220678887377335988999998425786131122231255158988875101103433766899736689886126


Q ss_pred             E
Q ss_conf             9
Q gi|254780148|r  156 E  156 (177)
Q Consensus       156 ~  156 (177)
                      +
T Consensus       169 L  169 (320)
T TIGR02249       169 L  169 (320)
T ss_pred             C
T ss_conf             8


No 46 
>cd01737 LSm16_N LSm16 belongs to a family of Sm-like proteins that associate with RNA to form the core domain of the ribonucleoprotein particles involved in a variety of RNA processing events including pre-mRNA splicing, telomere replication, and mRNA degradation. Members of this family share a highly conserved Sm fold, containing an N-terminal helix followed by a strongly bent five-stranded antiparallel beta-sheet, that associates with other Sm proteins to form hexameric and heptameric ring structures.   LSm16 has, in addition to its N-terminal Sm-like domain, a C-terminal Yjef_N-type rossman fold domain of unknown function.
Probab=51.72  E-value=19  Score=16.73  Aligned_cols=51  Identities=22%  Similarity=0.377  Sum_probs=37.2

Q ss_pred             CCCEEEEECCCCCC-CEEEEEEECCCCCEEEEEEEECCC-----EEEEEECHHHHEEC
Q ss_conf             89779995187789-719999982889889999981687-----04788567871233
Q gi|254780148|r  125 VGERVCVSDGPFAS-FNGIVKNVDEEKSRVHVEVVIFGR-----VTPVELAYNQVEKI  176 (177)
Q Consensus       125 ~G~~V~I~~Gpf~g-~~g~v~~i~~~~~r~~V~v~i~Gr-----~~~v~l~~~~ieki  176 (177)
                      .|..|-|..||=.| |.|.|+.++.... ...+-.-|+-     ...|++...+|+.+
T Consensus         5 iG~~VSI~C~~~lGv~QG~I~~v~~~~q-tItl~~~f~ngi~~~~~EVtl~a~dI~~L   61 (62)
T cd01737           5 LGSIVSINCGETLGVYQGLVSAVDQESQ-TISLAFPFHNGVKCLVPEVTFRAGDIREL   61 (62)
T ss_pred             EEEEEEEEECCCCCEEEEEEEEECCCCC-EEEEEECCCCCCCCCCCEEEEEHHHHHHC
T ss_conf             4068999867985288889998576663-89984056688658883599983564333


No 47 
>TIGR01941 nqrF NADH:ubiquinone oxidoreductase, Na(+)-translocating, F subunit; InterPro: IPR010205   This entry represents the NqrF subunit of the six-protein, Na(+)-pumping NADH-quinone reductase of a number of marine and pathogenic Gram-negative bacteria.; GO: 0016655 oxidoreductase activity acting on NADH or NADPH quinone or similar compound as acceptor, 0051537 2 iron 2 sulfur cluster binding, 0006814 sodium ion transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane.
Probab=50.55  E-value=10  Score=18.28  Aligned_cols=19  Identities=32%  Similarity=0.698  Sum_probs=15.7

Q ss_pred             CCCCCCEEEEECCCCCCCEE
Q ss_conf             34789779995187789719
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNG  141 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g  141 (177)
                      .+++||+| .++|||-.+-.
T Consensus       261 sLKpGDKv-~~sGPfGefF~  279 (425)
T TIGR01941       261 SLKPGDKV-TVSGPFGEFFA  279 (425)
T ss_pred             ECCCCCEE-EEECCCCCCEE
T ss_conf             44798777-99778885302


No 48 
>COG1509 KamA Lysine 2,3-aminomutase [Amino acid transport and metabolism]
Probab=47.61  E-value=14  Score=17.48  Aligned_cols=70  Identities=17%  Similarity=0.379  Sum_probs=47.3

Q ss_pred             CCEECEEEEEEEE-------CCCC----CHHHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             1203309999996-------1865----2244420330366432788610025889999997653222100001234789
Q gi|254780148|r   58 RRFFPGYVLIKAV-------MTDK----VYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVG  126 (177)
Q Consensus        58 ~plfpgYiFv~~~-------~~~~----~~~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G  126 (177)
                      .+++..|.|=+--       ++.+    ...-|+.+|-+..+|-+||.|..+++.+++.|+..+.+.....    .+..|
T Consensus       121 C~vyCRyCfRr~~~~~~~~~~~~~~~~~al~YIa~hPeI~eVllSGGDPL~ls~~~L~~ll~~L~~IpHv~----iiRi~  196 (369)
T COG1509         121 CAVYCRYCFRRRFVGQDNQGFNKEEWDKALDYIAAHPEIREVLLSGGDPLSLSDKKLEWLLKRLRAIPHVK----IIRIG  196 (369)
T ss_pred             CCCEEEECCCCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHEEEECCCCCCCCCHHHHHHHHHHHHCCCCEE----EEEEE
T ss_conf             64521000134555666566788999999999973951651774078756368899999999875489646----99862


Q ss_pred             CEEEE
Q ss_conf             77999
Q gi|254780148|r  127 ERVCV  131 (177)
Q Consensus       127 ~~V~I  131 (177)
                      .++-|
T Consensus       197 TR~pv  201 (369)
T COG1509         197 TRLPV  201 (369)
T ss_pred             CCCCE
T ss_conf             46743


No 49 
>pfam02941 FeThRed_A Ferredoxin thioredoxin reductase variable alpha chain.
Probab=41.95  E-value=27  Score=15.81  Aligned_cols=22  Identities=32%  Similarity=0.548  Sum_probs=14.6

Q ss_pred             CCCEEEEECC--------------CCCCCEEEEEEE
Q ss_conf             8977999518--------------778971999998
Q gi|254780148|r  125 VGERVCVSDG--------------PFASFNGIVKNV  146 (177)
Q Consensus       125 ~G~~V~I~~G--------------pf~g~~g~v~~i  146 (177)
                      +||+|+|.+-              .++|++|+|..+
T Consensus         1 vGdrVrV~~sv~VyhhP~hr~~~fDl~G~eGeV~~~   36 (67)
T pfam02941         1 VGDRVRVKTSVVVYHHPEHRGPAFDLKGMEGEIKQY   36 (67)
T ss_pred             CCCEEEECCCEEEEECCCCCCCCCCCCCCEEEEEEE
T ss_conf             997489810189985865358874446777777567


No 50 
>PRK04306 50S ribosomal protein L21e; Reviewed
Probab=41.30  E-value=27  Score=15.75  Aligned_cols=52  Identities=21%  Similarity=0.162  Sum_probs=35.5

Q ss_pred             CCCCCCEEEEEC-C---------CCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEE
Q ss_conf             347897799951-8---------77897199999828898899999816870478856787123
Q gi|254780148|r  122 FFEVGERVCVSD-G---------PFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK  175 (177)
Q Consensus       122 ~~~~G~~V~I~~-G---------pf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~iek  175 (177)
                      .|++||.|.|.- +         -|.|..|.|....+  .-..|.+..-++.-.+-+-.+.|.+
T Consensus        33 ~f~~GD~V~I~idpsv~kGmPh~ryhGkTG~V~~~~g--~a~~V~v~~g~k~K~i~vr~eHlr~   94 (97)
T PRK04306         33 EFEEGDKVHIVIDPSVHKGMPHPRFHGKTGTVVGKRG--RAYIVEVKDGGKEKTLIARPEHLRP   94 (97)
T ss_pred             HCCCCCEEEEEECCCCCCCCCCCEECCCCEEEEEECC--EEEEEEEEECCEEEEEEECHHHCCC
T ss_conf             4779988999868862069985404687559993145--3999999979905899958768166


No 51 
>COG2163 RPL14A Ribosomal protein L14E/L6E/L27E [Translation, ribosomal structure and biogenesis]
Probab=39.55  E-value=29  Score=15.59  Aligned_cols=32  Identities=28%  Similarity=0.397  Sum_probs=22.1

Q ss_pred             CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEE
Q ss_conf             347897799951877897199999828898899
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVH  154 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~  154 (177)
                      .+.+|.-|.++.|-|+|-.++|.++-+++ .+.
T Consensus         4 ~l~~GrVvvv~~GR~aGkk~VIv~~iDd~-~v~   35 (125)
T COG2163           4 SLEVGRVVVVTAGRFAGKKVVIVKIIDDN-FVL   35 (125)
T ss_pred             CCCCCEEEEEECCEECCCEEEEEEECCCC-EEE
T ss_conf             56387699996250279549999982278-799


No 52 
>COG4873 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=36.21  E-value=33  Score=15.27  Aligned_cols=42  Identities=33%  Similarity=0.545  Sum_probs=31.2

Q ss_pred             CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECH
Q ss_conf             478977999518778971999998288988999998168704788567
Q gi|254780148|r  123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAY  170 (177)
Q Consensus       123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~  170 (177)
                      -++|+.+...+|    +.|.|++++. ++ +.|.+.++..-..++++.
T Consensus        24 a~vgniief~dg----l~g~vek~ne-ns-vivdlt~menf~dl~l~e   65 (81)
T COG4873          24 AKVGNIIEFKDG----LTGVVEKVNE-NS-VIVDLTIMENFRDLELDE   65 (81)
T ss_pred             ECCCCEEEECCC----CEEEEEEECC-CC-EEEEEEEECCCCCCCCCH
T ss_conf             100646887045----4011124058-84-899875101130059961


No 53 
>pfam04943 Pox_F11 Poxvirus F11 protein. The protein F11 is an early virus protein.
Probab=35.10  E-value=34  Score=15.16  Aligned_cols=107  Identities=11%  Similarity=0.099  Sum_probs=56.2

Q ss_pred             ECCEECEEEEEEEECCCCCHHHHHC----CCEEE--EEECCCCCCCCCCHHHHHHHHHHHHHHHHHH------CCCCCCC
Q ss_conf             4120330999999618652244420----33036--6432788610025889999997653222100------0012347
Q gi|254780148|r   57 ERRFFPGYVLIKAVMTDKVYHTIKD----TPKVI--GFLGTGENPSPVTDSEIEHIMNQVEAAVQRP------VSSVFFE  124 (177)
Q Consensus        57 ~~plfpgYiFv~~~~~~~~~~~i~~----t~gV~--~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~------~~~~~~~  124 (177)
                      ..|..-+++||.....+.....+.+    +.-.+  ..+.++-+|.+|++.-++.++....--....      .+...|.
T Consensus        26 ~~~vL~dsvfi~~~di~~~~~~vs~l~~~~~~~~~~~~~~y~~kkV~i~~~~l~~l~D~eg~Fev~d~~lvkL~HGn~f~  105 (366)
T pfam04943        26 DNPVLVDSVFISIMDIENLLNDVSSLTDSTGSKTKSTLFTYSWKKVPVDSIKLRFLLDAEGYFEVSDCFLVKLEHGNGFM  105 (366)
T ss_pred             CCCEEEEEEEEEECCHHHHCCCHHHHCCCCCCCCCCCCCCCCEEEECCCHHHHHHHHCCCCCEEHHHEEEEEEECCCCCC
T ss_conf             98367544678504376520405540178755321244323136612566777665122475211246899961367512


Q ss_pred             CCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECC-CEEEEEE
Q ss_conf             8977999518778971999998288988999998168-7047885
Q gi|254780148|r  125 VGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFG-RVTPVEL  168 (177)
Q Consensus       125 ~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~G-r~~~v~l  168 (177)
                      .|..   -.|-..||.++|. +. ..|++-+.++-.- ..+.++.
T Consensus       106 ~~~~---~~~~s~gF~A~IC-Ik-NeG~Sgi~V~~t~~l~~~m~~  145 (366)
T pfam04943       106 KGAL---YVDNSAGFTAVIC-IK-NEGRSGIMVNHTNVLQTNMQE  145 (366)
T ss_pred             CCCC---CCCCCCCEEEEEE-EC-CCCEEEEEECCCCCEEEEEEE
T ss_conf             4751---1587455079999-73-787058873797513555430


No 54 
>CHL00084 rpl19 ribosomal protein L19
Probab=34.93  E-value=35  Score=15.15  Aligned_cols=45  Identities=18%  Similarity=0.381  Sum_probs=24.6

Q ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCCEEEE----ECCC---CCCCEEEEEEECC
Q ss_conf             99999765322210000123478977999----5187---7897199999828
Q gi|254780148|r  103 IEHIMNQVEAAVQRPVSSVFFEVGERVCV----SDGP---FASFNGIVKNVDE  148 (177)
Q Consensus       103 i~~l~~~~~~~~~~~~~~~~~~~G~~V~I----~~Gp---f~g~~g~v~~i~~  148 (177)
                      |+.+....+.... ...-+.|.+||+|+|    .+|.   ..-|+|.|.....
T Consensus         4 m~~li~~ie~~~~-k~~~p~f~~GDtV~V~~~i~EG~keRiQ~FeGvVIa~~~   55 (117)
T CHL00084          4 LQQLVKEIESEFL-KTDLPEIRVGDTVKVGVLIQEGNKERVQAYEGTVIAKKN   55 (117)
T ss_pred             HHHHHHHHHHHHC-CCCCCCCCCCCEEEEEEEEEECCEEEEEEEEEEEEEEEC
T ss_conf             8999999999871-135998399999999999984890698788899999708


No 55 
>pfam10574 UPF0552 Uncharacterized protein family UPF0552. This family of proteins has no known function.
Probab=34.55  E-value=35  Score=15.11  Aligned_cols=37  Identities=27%  Similarity=0.398  Sum_probs=23.6

Q ss_pred             CCCCCCCCEEEEE---CCCCCCCEEEEEEECCCCCEEEEEEEECCC
Q ss_conf             1234789779995---187789719999982889889999981687
Q gi|254780148|r  120 SVFFEVGERVCVS---DGPFASFNGIVKNVDEEKSRVHVEVVIFGR  162 (177)
Q Consensus       120 ~~~~~~G~~V~I~---~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr  162 (177)
                      ...|+.|+.||+.   +|||..-.+   ++|.  +.+.. .++-|-
T Consensus       149 ~~ele~G~evRlKT~GDgpFi~Sla---KlD~--~tvtk-cNFAGD  188 (224)
T pfam10574       149 KTELELGQEVRLKTRGDGPFIFSLA---KMDS--GTVTK-CNFAGD  188 (224)
T ss_pred             CCCCCCCCEEEEEECCCCCCEEEEE---EECC--CCEEE-EECCCC
T ss_conf             0141368758998517874144443---2025--71577-631577


No 56 
>PRK10724 hypothetical protein; Provisional
Probab=33.69  E-value=36  Score=15.02  Aligned_cols=35  Identities=20%  Similarity=0.461  Sum_probs=21.2

Q ss_pred             CCCCCEE--EEECCCCCCCEEE--EEEECCCCCEEEEEE
Q ss_conf             4789779--9951877897199--999828898899999
Q gi|254780148|r  123 FEVGERV--CVSDGPFASFNGI--VKNVDEEKSRVHVEV  157 (177)
Q Consensus       123 ~~~G~~V--~I~~Gpf~g~~g~--v~~i~~~~~r~~V~v  157 (177)
                      +.++..+  ..++|||+.++|.  +..++.+..++...+
T Consensus        81 ~~~~~~I~~~lv~GPFk~L~~~W~F~~~~~~~c~V~f~l  119 (158)
T PRK10724         81 LTSNQSILMQLVDGPFKKLIGGWKFTPLSQEACRIEFHL  119 (158)
T ss_pred             ECCCCEEEEEECCCCHHHEEEEEEEEECCCCCEEEEEEE
T ss_conf             438762545554797022057789997799958999999


No 57 
>TIGR01200 TIGR01200 Porphyromonas gingivalis paralogous family TIGR01200; InterPro: IPR005901    This family of proteins of unknown function is found in Porphyromonas gingivalis (Bacteroides gingivalis)..
Probab=32.94  E-value=30  Score=15.50  Aligned_cols=38  Identities=24%  Similarity=0.481  Sum_probs=26.5

Q ss_pred             CCEEEEECCC--CCCCEEEEEEECC-CCCEEEEEEEECCCE
Q ss_conf             9779995187--7897199999828-898899999816870
Q gi|254780148|r  126 GERVCVSDGP--FASFNGIVKNVDE-EKSRVHVEVVIFGRV  163 (177)
Q Consensus       126 G~~V~I~~Gp--f~g~~g~v~~i~~-~~~r~~V~v~i~Gr~  163 (177)
                      -+.+.+-+||  |.|+-|.|..|.+ ++..+-++.-+.|..
T Consensus       194 ~EDIal~~GPYiF~GLPGLI~~I~~~~~EYvF~~~~~~g~I  234 (300)
T TIGR01200       194 SEDIALSDGPYIFRGLPGLIVAIRSDDGEYVFELNGMQGEI  234 (300)
T ss_pred             CCCCCCCCCCEEECCCCEEEEEEECCCCCEEEEEHHHHHCC
T ss_conf             12656898587415887048997248983201001243102


No 58 
>pfam08345 YscJ_FliF_C Flagellar M-ring protein C-terminal. This domain is found in bacterial flagellar M-ring (FliF) proteins together with the YscJ/FliF domain (pfam01514).
Probab=32.65  E-value=38  Score=14.92  Aligned_cols=38  Identities=29%  Similarity=0.303  Sum_probs=27.8

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCC
Q ss_conf             6100258899999976532221000012347897799951877
Q gi|254780148|r   94 NPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCVSDGPF  136 (177)
Q Consensus        94 ~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I~~Gpf  136 (177)
                      .+.|+++++++.|...+......     .-..||.|.|..-||
T Consensus       125 ~~~~~s~ee~~~i~~lV~~AiG~-----d~~RGD~v~V~~~~F  162 (162)
T pfam08345       125 AYVPRSPEELAQIEALVKSAVGF-----DAARGDSVTVVSMPF  162 (162)
T ss_pred             CCCCCCHHHHHHHHHHHHHHCCC-----CCCCCCEEEEEECCC
T ss_conf             34667999999999999996088-----877899899994689


No 59 
>TIGR02888 spore_YlmC_YmxH sporulation protein, YlmC/YmxH family; InterPro: IPR014238   Proteins in this entry belong to the broader family of PRC-barrel domain proteins, but are found only in endospore-forming bacteria within the Firmicutes (low-GC, Gram-positive bacteria). Most species encode two of these proteins, though their function is unknown. In Bacillus subtilis, which encodes YlmC and YmxH, YmxH is strongly induced by the mother cell-specific sigma-E factor ..
Probab=32.41  E-value=38  Score=14.90  Aligned_cols=32  Identities=22%  Similarity=0.532  Sum_probs=25.7

Q ss_pred             EECCCCCEEEEE--------EEECCCEEEEEECHHHHEEC
Q ss_conf             982889889999--------98168704788567871233
Q gi|254780148|r  145 NVDEEKSRVHVE--------VVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       145 ~i~~~~~r~~V~--------v~i~Gr~~~v~l~~~~ieki  176 (177)
                      .+|.+++|..-+        +.+|++...++++.++|.||
T Consensus        28 ~ID~~~G~I~~lIip~~g~~~glf~~~~~~~IpW~~IkKI   67 (76)
T TIGR02888        28 EIDEEDGKIESLIIPGKGKKFGLFSKGEEIEIPWKAIKKI   67 (76)
T ss_pred             EEECCCCEEEEEEECCCCEEEECEECCCCEEECCHHCEEE
T ss_conf             9808999598988718970522100687548663002780


No 60 
>KOG0107 consensus
Probab=31.58  E-value=25  Score=16.04  Aligned_cols=26  Identities=8%  Similarity=0.111  Sum_probs=21.3

Q ss_pred             EECEEEEEEEECCCCCHHHHHCCCEE
Q ss_conf             03309999996186522444203303
Q gi|254780148|r   60 FFPGYVLIKAVMTDKVYHTIKDTPKV   85 (177)
Q Consensus        60 lfpgYiFv~~~~~~~~~~~i~~t~gV   85 (177)
                      .=|||-||+++...+....++.+.|-
T Consensus        45 nPPGfAFVEFed~RDA~DAvr~LDG~   70 (195)
T KOG0107          45 NPPGFAFVEFEDPRDAEDAVRYLDGK   70 (195)
T ss_pred             CCCCCEEEECCCCCCHHHHHHHCCCC
T ss_conf             48984677616852388888641785


No 61 
>TIGR01108 oadA oxaloacetate decarboxylase alpha subunit; InterPro: IPR005776    This family describes the bacterial oxaloacetate decarboxylase alpha subunit and its equivalents in archaea . The oxaloacetate decarboxylase Na+ pump is the paradigm of the family of Na+ transport decarboxylases that present in bacteria and archaea. It a multi subunit enzyme consisting of a peripheral alpha-subunit and integral membrane subunits beta and gamma. The energy released by the decarboxylation reaction of oxaloacetate is coupled to Na+ ion pumping across the membrane.; GO: 0008948 oxaloacetate decarboxylase activity, 0006814 sodium ion transport.
Probab=31.16  E-value=30  Score=15.54  Aligned_cols=76  Identities=24%  Similarity=0.488  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEE--------------EEEEECCCCCHHHH-HCCC
Q ss_conf             99999999977981114326631310127720203566412033099--------------99996186522444-2033
Q gi|254780148|r   19 VESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYV--------------LIKAVMTDKVYHTI-KDTP   83 (177)
Q Consensus        19 ~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYi--------------Fv~~~~~~~~~~~i-~~t~   83 (177)
                      ..||.+++..||..|..-+|.   +++.+.|.+-          ||+              |++. +.-|.|..| +.|.
T Consensus       299 ~SNL~~QLkEQna~DkLd~VL---~EiPrVreDL----------GYpPLVTPTSQIVGtQAvlNV-L~GERYk~iT~ET~  364 (616)
T TIGR01108       299 LSNLESQLKEQNALDKLDEVL---EEIPRVREDL----------GYPPLVTPTSQIVGTQAVLNV-LTGERYKTITKETK  364 (616)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH---HHCCCCHHHC----------CCCCCCCCCCCEEEEEEEEEE-EECCCHHHHHHHHH
T ss_conf             889999998623755788887---4157412326----------765697787521345667742-31451148899999


Q ss_pred             EEEEEEC-CCCCCCCCCHHHHHHHHHHH
Q ss_conf             0366432-78861002588999999765
Q gi|254780148|r   84 KVIGFLG-TGENPSPVTDSEIEHIMNQV  110 (177)
Q Consensus        84 gV~~~l~-~~~~P~~i~~~ei~~l~~~~  110 (177)
                      ++..  | +|..|+||..+-+++++...
T Consensus       365 ~~~k--G~YGrtPApi~~~L~~k~L~~e  390 (616)
T TIGR01108       365 DYVK--GEYGRTPAPIDAELVKKILGDE  390 (616)
T ss_pred             HHHC--CCCCCCCCCCCHHHHHHHHCCC
T ss_conf             9848--8988879777989999861444


No 62 
>PRK00092 hypothetical protein; Reviewed
Probab=30.19  E-value=42  Score=14.67  Aligned_cols=49  Identities=31%  Similarity=0.461  Sum_probs=34.7

Q ss_pred             CCCCEEEEE-CCCCCC---CEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             789779995-187789---71999998288988999998168704788567871233
Q gi|254780148|r  124 EVGERVCVS-DGPFAS---FNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       124 ~~G~~V~I~-~Gpf~g---~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      ..|..|+|. .-|..|   +.|.+.+++.+.    +.++.=|+...+++++++|+|.
T Consensus        93 ~~G~~v~v~l~~~~~~~k~~~G~L~~~~~~~----i~l~~~~~~~~~~i~~~~I~ka  145 (153)
T PRK00092         93 FVGREVKVKLREPIDGRKKFQGRLLAVDGET----VTLEVEGKPKVVEIPLDNIAKA  145 (153)
T ss_pred             HCCCEEEEEEECCCCCCEEEEEEEEEEECCE----EEEEECCCCEEEEEEHHHHEEE
T ss_conf             6693899999446689649999999884998----9999889706999736981089


No 63 
>COG4464 CapC Capsular polysaccharide biosynthesis protein [Carbohydrate transport and metabolism / Cell envelope biogenesis, outer membrane]
Probab=29.03  E-value=44  Score=14.55  Aligned_cols=11  Identities=36%  Similarity=0.570  Sum_probs=7.5

Q ss_pred             EEEEEEEECCC
Q ss_conf             09999996186
Q gi|254780148|r   63 GYVLIKAVMTD   73 (177)
Q Consensus        63 gYiFv~~~~~~   73 (177)
                      .|++|++.++.
T Consensus       103 kYlLIEF~~~~  113 (254)
T COG4464         103 KYLLIEFPMNH  113 (254)
T ss_pred             CEEEEECCCCC
T ss_conf             34999746886


No 64 
>PRK08384 thiamine biosynthesis protein ThiI; Provisional
Probab=28.42  E-value=45  Score=14.49  Aligned_cols=57  Identities=12%  Similarity=0.187  Sum_probs=32.1

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCHHHCCEEEEECCCCEEEECCEEEEEECCEECEEEEEEEECCCCCHHHHHCCCEEEEEE
Q ss_conf             2885389999999999977981114326631310127720203566412033099999961865224442033036643
Q gi|254780148|r   11 YSNCEKKAVESIGGRLSRSGLDHLVTEITIPSERVVSVRKGRKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFL   89 (177)
Q Consensus        11 ~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~P~~~~~~~~~g~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV~~~l   89 (177)
                      +...|+...+|+++.+...+++..          .....            .|.+++..+..++.-..+..++|+.++-
T Consensus        19 R~~fe~~L~~NIk~~L~~~~~~~~----------~v~~~------------~gri~v~~~~~~~~~~~l~~vfGI~s~s   75 (310)
T PRK08384         19 RRWFERILMNNIREALVSEGIEYK----------EVFAK------------HGRVIVRTNRAEEAKEVLVRVFGIVSLS   75 (310)
T ss_pred             HHHHHHHHHHHHHHHHHHCCCCCE----------EEEEE------------CCEEEEECCCHHHHHHHHHHCCCCCEEE
T ss_conf             899999999999999986699824----------89997------------4799997598799999998659977170


No 65 
>PRK09206 pyruvate kinase; Provisional
Probab=28.32  E-value=31  Score=15.43  Aligned_cols=74  Identities=15%  Similarity=0.105  Sum_probs=37.8

Q ss_pred             EEEEEECCEECEEEEEEEECCCCCHHHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEE
Q ss_conf             03566412033099999961865224442033036643278861002588999999765322210000123478977999
Q gi|254780148|r   52 RKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCV  131 (177)
Q Consensus        52 ~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I  131 (177)
                      ++....+|--|=|.|.   .++.....+.-..||.-++-....    +.   +.+.....+.   ......++.||.|.+
T Consensus       385 ~~is~~RP~~pI~a~t---~~~~~~r~l~l~~Gv~p~~~~~~~----~~---~~~~~~~~~~---~~~~g~~~~GD~vVv  451 (470)
T PRK09206        385 RSVRKYFPDATILALT---TNEKTAHQLVLSKGVVPQLVKEIA----ST---DDFYRLGKEL---ALQSGLAQKGDVVVM  451 (470)
T ss_pred             HHHHHCCCCCCEEEEC---CCHHHHHHHHECCCEEEEEECCCC----CH---HHHHHHHHHH---HHHCCCCCCCCEEEE
T ss_conf             9997039999889988---988999975652583899927889----99---9999999999---998699899898999


Q ss_pred             ECCCCCC
Q ss_conf             5187789
Q gi|254780148|r  132 SDGPFAS  138 (177)
Q Consensus       132 ~~Gpf~g  138 (177)
                      ++|++.+
T Consensus       452 ~~G~~~~  458 (470)
T PRK09206        452 VSGALVP  458 (470)
T ss_pred             ECCCCCC
T ss_conf             7777789


No 66 
>pfam01245 Ribosomal_L19 Ribosomal protein L19.
Probab=28.09  E-value=45  Score=14.45  Aligned_cols=29  Identities=31%  Similarity=0.466  Sum_probs=18.6

Q ss_pred             CCCCCCCCEEEE----ECCC---CCCCEEEEEEECC
Q ss_conf             123478977999----5187---7897199999828
Q gi|254780148|r  120 SVFFEVGERVCV----SDGP---FASFNGIVKNVDE  148 (177)
Q Consensus       120 ~~~~~~G~~V~I----~~Gp---f~g~~g~v~~i~~  148 (177)
                      -+.|.+||.|+|    .+|.   ..-|+|++.....
T Consensus        16 ip~f~~GDtv~V~~~i~Eg~k~RiQ~FeGvvI~~~~   51 (113)
T pfam01245        16 LPEFRVGDTVRVHVKIKEGNKERIQVFEGVVIARRG   51 (113)
T ss_pred             CCCCCCCCEEEEEEEEEECCEEEEEEEEEEEEEEEC
T ss_conf             998499999999999984881688899999999957


No 67 
>pfam08223 PaaX_C PaaX-like protein C-terminal domain. This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid.
Probab=27.84  E-value=46  Score=14.42  Aligned_cols=38  Identities=18%  Similarity=0.378  Sum_probs=32.4

Q ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHHCCCHHHCCEEEE
Q ss_conf             86189995288538999999999997798111432663
Q gi|254780148|r    3 PRWYIVQVYSNCEKKAVESIGGRLSRSGLDHLVTEITI   40 (177)
Q Consensus         3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~~~~~~~~~~v~~   40 (177)
                      -+|.++.+.|..+....+.|++++...|++....-+|+
T Consensus         6 G~W~lv~~spe~~r~~R~~lr~~L~~lGFg~l~~glwi   43 (170)
T pfam08223         6 GSWHLVVLSPESDRAARDALRRELEWLGFGELAPGLWI   43 (170)
T ss_pred             CEEEEEEECCCCCHHHHHHHHHHHHHCCCCCCCCCEEE
T ss_conf             62689885886589999999999998789718899678


No 68 
>pfam09953 DUF2187 Uncharacterized protein conserved in bacteria (DUF2187). This domain, found in various hypothetical bacterial proteins, has no known function.
Probab=27.82  E-value=46  Score=14.42  Aligned_cols=40  Identities=30%  Similarity=0.558  Sum_probs=29.1

Q ss_pred             CCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEEC
Q ss_conf             7897799951877897199999828898899999816870478856
Q gi|254780148|r  124 EVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELA  169 (177)
Q Consensus       124 ~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~  169 (177)
                      ++|+.+...+|    +.|+|++++. + -+.|.+.++..-..++++
T Consensus         5 ~vG~iiEFk~G----l~GiVeKvNe-N-SVIVdlT~Men~~~L~le   44 (57)
T pfam09953         5 EVGNIIEFKNG----LQGIVEKVNE-N-SVIVDLTYMENFRDLDLE   44 (57)
T ss_pred             CCCCEEEECCC----CEEEEEEECC-C-CEEEEEEEECCCHHCCCC
T ss_conf             00667997264----2010013047-8-389998853360014877


No 69 
>COG0779 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.71  E-value=48  Score=14.30  Aligned_cols=45  Identities=31%  Similarity=0.499  Sum_probs=31.2

Q ss_pred             CCCEEEEEC----CCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEE
Q ss_conf             897799951----877897199999828898899999816870478856787123
Q gi|254780148|r  125 VGERVCVSD----GPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEK  175 (177)
Q Consensus       125 ~G~~V~I~~----Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~iek  175 (177)
                      .|..|.|.-    .-=+-++|.+..++.+.    +-+++-|+.  ++++++.|.|
T Consensus        98 ~G~~Vkv~l~~~~~~~k~~~G~i~~~d~~~----v~~~~~~k~--v~Ip~~~i~k  146 (153)
T COG0779          98 IGEKVKVKLRLPIEGRKKFEGKIVAVDGET----VTLEVDGKE--VEIPFSDIAK  146 (153)
T ss_pred             CCCEEEEEEECCCCCCEEEEEEEEEECCCE----EEEEECCEE--EEEECCCCHH
T ss_conf             695899999654488407889999972986----999977848--9987563112


No 70 
>KOG4315 consensus
Probab=26.69  E-value=29  Score=15.60  Aligned_cols=50  Identities=24%  Similarity=0.218  Sum_probs=34.1

Q ss_pred             CCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHH
Q ss_conf             3478977999518778971999998288988999998168704788567871
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQV  173 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~i  173 (177)
                      +-..|++|.|+.|+-+|..|...+-|.++.+..+.+  .--.-.|++.+++|
T Consensus       393 pr~~Ge~vmvv~gkhkg~~g~llskd~~Ke~~~v~~--~a~ndvv~~~~D~v  442 (455)
T KOG4315         393 PRRGGEKVMVVSGKHKGVYGSLLSKDLDKETGVVRL--VATNDVVTVYLDQV  442 (455)
T ss_pred             CCCCCCEEEEEECCCCCCHHHHHHHHHHHHHCCEEC--CCCCCHHHHHHHHH
T ss_conf             313596468985365661232220122222030211--45563245658779


No 71 
>pfam02576 DUF150 Uncharacterized BCR, YhbC family COG0779.
Probab=25.58  E-value=50  Score=14.18  Aligned_cols=50  Identities=32%  Similarity=0.493  Sum_probs=33.1

Q ss_pred             CCCEEEEE-CCCCC---CCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             89779995-18778---971999998288988999998168704788567871233
Q gi|254780148|r  125 VGERVCVS-DGPFA---SFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       125 ~G~~V~I~-~Gpf~---g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      .|..|.|. ..+..   -+.|.+.+++.+  .+.+.++--.+...+++++++|+|.
T Consensus        86 ~G~~v~v~l~~~~~~~k~~~G~L~~~~~~--~i~l~~~~~~~~~~~~i~~~~I~kA  139 (141)
T pfam02576        86 IGKLVKVSLKEPIEGRKNFTGKLLEVDGD--TVTIEVDDKRRKKEVEIPFADIKKA  139 (141)
T ss_pred             CCCEEEEEEECCCCCEEEEEEEEEEEECC--EEEEEECCCCCCEEEEEEHHHHHHC
T ss_conf             59489999924669938999999988699--9999985871226899737995233


No 72 
>PRK12289 ribosome-associated GTPase; Reviewed
Probab=25.47  E-value=51  Score=14.16  Aligned_cols=11  Identities=18%  Similarity=0.404  Sum_probs=7.9

Q ss_pred             CCEEEEEECCC
Q ss_conf             86189995288
Q gi|254780148|r    3 PRWYIVQVYSN   13 (177)
Q Consensus         3 ~~Wyvv~t~~~   13 (177)
                      .+||-|++-.+
T Consensus        18 ~~fY~V~~d~~   28 (351)
T PRK12289         18 ANFYQVRLDQP   28 (351)
T ss_pred             CCEEEEEECCC
T ss_conf             86799995467


No 73 
>PRK04313 30S ribosomal protein S4e; Validated
Probab=24.88  E-value=52  Score=14.10  Aligned_cols=39  Identities=18%  Similarity=0.246  Sum_probs=29.9

Q ss_pred             CCCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEE--EEEE
Q ss_conf             01234789779995187789719999982889889--9999
Q gi|254780148|r  119 SSVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRV--HVEV  157 (177)
Q Consensus       119 ~~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~--~V~v  157 (177)
                      ....|++|..+-|+.|-=.|..|.|.++....+..  .|.+
T Consensus       168 ~~i~fe~G~~~~itgG~n~G~vG~I~~I~~~~~s~~~~V~~  208 (237)
T PRK04313        168 DHIPFEEGNLAMITGGKHVGEIGKIVEIQVTPSSKPNIVTL  208 (237)
T ss_pred             EEEECCCCCEEEEECCEEEEEEEEEEEEEECCCCCCCEEEE
T ss_conf             67852799899997880525899998899605777518999


No 74 
>pfam01157 Ribosomal_L21e Ribosomal protein L21e.
Probab=24.64  E-value=52  Score=14.07  Aligned_cols=54  Identities=20%  Similarity=0.269  Sum_probs=32.5

Q ss_pred             CCCCCCEEEEEC-C---------CCCCCEEEEEEECCCCCEEEEEEEECCCE--EEEEECHHHHEE
Q ss_conf             347897799951-8---------77897199999828898899999816870--478856787123
Q gi|254780148|r  122 FFEVGERVCVSD-G---------PFASFNGIVKNVDEEKSRVHVEVVIFGRV--TPVELAYNQVEK  175 (177)
Q Consensus       122 ~~~~G~~V~I~~-G---------pf~g~~g~v~~i~~~~~r~~V~v~i~Gr~--~~v~l~~~~iek  175 (177)
                      .|++||.|.|.- +         -|.|..|.|.++.....=..+.+.+-++.  -.+-+-.++|.+
T Consensus        32 ~f~~GD~V~I~idpsv~kGMPh~~yhGkTG~V~nv~~~~~G~~~~~~V~~~~~~K~i~vr~eHlk~   97 (99)
T pfam01157        32 EYKVGDYVDIKINGSVQKGMPHKRFHGKTGRVYNVTPGAVGVAVNKKVRDGILEKRINVRPEHIRP   97 (99)
T ss_pred             HCCCCCEEEEEECCCEECCCCCCEECCCCEEEEEECCCCEEEEEEEEECCCCEEEEEEECHHHCCC
T ss_conf             436998899963486006997422158864799845860799999997588320899971677146


No 75 
>pfam11572 DUF3234 Protein of unknown function (DUF3234). This bacterial family of proteins has no known function. Some members in this family of proteins are annotated as TTHA0547 however this cannot be confirmed.
Probab=23.62  E-value=55  Score=13.95  Aligned_cols=25  Identities=36%  Similarity=0.671  Sum_probs=20.2

Q ss_pred             CCEEEEEECCCCHHHHHHHHHHHHHH
Q ss_conf             86189995288538999999999997
Q gi|254780148|r    3 PRWYIVQVYSNCEKKAVESIGGRLSR   28 (177)
Q Consensus         3 ~~Wyvv~t~~~~E~~v~~~L~~~~~~   28 (177)
                      ..|||+---|| |.-|.+.|.++++.
T Consensus         6 ~TWYVLEgdPG-EHLVvEaLG~RLS~   30 (102)
T pfam11572         6 GTWYVLEGDPG-EHLVVEALGERLSG   30 (102)
T ss_pred             CEEEEECCCCC-CEEHHHHHHHHHHH
T ss_conf             14898628996-10089998516656


No 76 
>PRK06488 sulfur carrier protein ThiS; Validated
Probab=23.42  E-value=55  Score=13.93  Aligned_cols=41  Identities=5%  Similarity=0.123  Sum_probs=24.5

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHH-------------CCCCCCCCCCEEEEEC
Q ss_conf             8610025889999997653222100-------------0012347897799951
Q gi|254780148|r   93 ENPSPVTDSEIEHIMNQVEAAVQRP-------------VSSVFFEVGERVCVSD  133 (177)
Q Consensus        93 ~~P~~i~~~ei~~l~~~~~~~~~~~-------------~~~~~~~~G~~V~I~~  133 (177)
                      +++..++..-+..++..++......             .....+..||+|.|+.
T Consensus         7 Ge~~e~~a~tl~~Ll~elg~~~~~vAvAvN~~~Vpr~~~~~~~L~eGDriEIv~   60 (65)
T PRK06488          7 GEEIETAATTLALLLAELGYEGNWLATAVNGELVHSEARAQFVLHEGDRIEILS   60 (65)
T ss_pred             CEEEEECHHHHHHHHHHCCCCCCCEEEEECCEEECHHHHCCCCCCCCCEEEEEC
T ss_conf             977770086899999972988880899989998742450545179999999964


No 77 
>COG1532 Predicted RNA-binding protein [General function prediction only]
Probab=22.97  E-value=56  Score=13.87  Aligned_cols=31  Identities=29%  Similarity=0.515  Sum_probs=21.3

Q ss_pred             CCCEEEEEC--CCCCCCEEEEEEECCCCCEEEE
Q ss_conf             897799951--8778971999998288988999
Q gi|254780148|r  125 VGERVCVSD--GPFASFNGIVKNVDEEKSRVHV  155 (177)
Q Consensus       125 ~G~~V~I~~--Gpf~g~~g~v~~i~~~~~r~~V  155 (177)
                      .|+.|+..+  |.-+-++|.++++|-+..++.+
T Consensus        23 ~~e~V~a~Dilgd~ke~~G~vkriDldehkI~l   55 (57)
T COG1532          23 TEEGVVARDILGDEKEFEGQVKRIDLDEHKIEL   55 (57)
T ss_pred             ECCCEEEEECCCCCEEECCEEEEEECCCCEEEE
T ss_conf             258399986038721742248999746638996


No 78 
>PRK05464 Na(+)-translocating NADH-quinone reductase subunit F; Provisional
Probab=22.20  E-value=59  Score=13.78  Aligned_cols=19  Identities=37%  Similarity=0.791  Sum_probs=15.3

Q ss_pred             CCCCCCEEEEECCCCCCCEE
Q ss_conf             34789779995187789719
Q gi|254780148|r  122 FFEVGERVCVSDGPFASFNG  141 (177)
Q Consensus       122 ~~~~G~~V~I~~Gpf~g~~g  141 (177)
                      .+++||+|.+. |||-.|--
T Consensus       251 ~LK~GD~V~is-GP~G~Ffl  269 (408)
T PRK05464        251 SLKPGDKVTIS-GPFGEFFA  269 (408)
T ss_pred             CCCCCCEEEEE-CCCCCEEE
T ss_conf             38999889997-78644275


No 79 
>pfam03792 PBC PBC domain. The PBC domain is a member of the TALE (three-amino-acid loop extension) superclass of homeodomain proteins.
Probab=22.03  E-value=20  Score=16.59  Aligned_cols=35  Identities=23%  Similarity=0.409  Sum_probs=25.8

Q ss_pred             CCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             03303664327886100258899999976532221
Q gi|254780148|r   81 DTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQ  115 (177)
Q Consensus        81 ~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~  115 (177)
                      -|.+|..+|+..++..||+..||++|.+.+.....
T Consensus       135 Ft~hV~nLLreQsrtRPIs~kEiErmv~iI~~KF~  169 (192)
T pfam03792       135 FTQHVMNLLREQSRTRPISQREIERMVNIISRKFN  169 (192)
T ss_pred             HHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             99999999998535689988999999999999999


No 80 
>PTZ00300 pyruvate kinase; Provisional
Probab=22.03  E-value=55  Score=13.95  Aligned_cols=81  Identities=16%  Similarity=0.096  Sum_probs=43.2

Q ss_pred             EEEEEECCEECEEEEEEEECCCCCHHHHHCCCEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCEEEE
Q ss_conf             03566412033099999961865224442033036643278861002588999999765322210000123478977999
Q gi|254780148|r   52 RKVNSERRFFPGYVLIKAVMTDKVYHTIKDTPKVIGFLGTGENPSPVTDSEIEHIMNQVEAAVQRPVSSVFFEVGERVCV  131 (177)
Q Consensus        52 ~~~~~~~plfpgYiFv~~~~~~~~~~~i~~t~gV~~~l~~~~~P~~i~~~ei~~l~~~~~~~~~~~~~~~~~~~G~~V~I  131 (177)
                      ++....+|-.|=|.|-   .+......+.-..||.-++-.......  ++.++.+....-+.   .......+.||.|.+
T Consensus       363 ~~vs~~RP~~pI~a~t---~~~~~~r~l~l~~GV~p~~~~~~~~~~--~~~~~~~i~~a~~~---~~~~g~~~~GD~vVv  434 (454)
T PTZ00300        363 RLVAKYRPNCPIVCVT---TRLQTCRQLNITQGVESVFFDAERLGH--DEGKEQRVAMGVGF---AKSKGYVQSGDLMVV  434 (454)
T ss_pred             HHHHHHCCCCCEEEEC---CCHHHHHHHHEECCEEEEEECCCCCCC--CCCHHHHHHHHHHH---HHHCCCCCCCCEEEE
T ss_conf             9999659799999989---879999865660585999866634676--56999999999999---997799889998999


Q ss_pred             ECCCCCCCEE
Q ss_conf             5187789719
Q gi|254780148|r  132 SDGPFASFNG  141 (177)
Q Consensus       132 ~~Gpf~g~~g  141 (177)
                      ++|+.. -.|
T Consensus       435 v~g~~~-~~G  443 (454)
T PTZ00300        435 VHADHK-VKG  443 (454)
T ss_pred             EECCCC-CCC
T ss_conf             934899-997


No 81 
>pfam04452 Methyltrans_RNA RNA methyltransferase. RNA methyltransferases modify nucleotides during ribosomal RNA maturation in a site-specific manner. The Escherichia coli member is specific for U1498 methylation.
Probab=22.02  E-value=59  Score=13.76  Aligned_cols=13  Identities=31%  Similarity=0.468  Sum_probs=5.5

Q ss_pred             CEEEEECCCCCCC
Q ss_conf             7799951877897
Q gi|254780148|r  127 ERVCVSDGPFASF  139 (177)
Q Consensus       127 ~~V~I~~Gpf~g~  139 (177)
                      ..+.+.=||=-||
T Consensus       175 ~~i~i~IGPEGGf  187 (225)
T pfam04452       175 GKVLLIIGPEGGF  187 (225)
T ss_pred             CCEEEEECCCCCC
T ss_conf             8458998898899


No 82 
>PRK05338 rplS 50S ribosomal protein L19; Provisional
Probab=21.55  E-value=60  Score=13.70  Aligned_cols=30  Identities=27%  Similarity=0.413  Sum_probs=19.6

Q ss_pred             CCCCCCCCCEEEE----ECCC---CCCCEEEEEEECC
Q ss_conf             0123478977999----5187---7897199999828
Q gi|254780148|r  119 SSVFFEVGERVCV----SDGP---FASFNGIVKNVDE  148 (177)
Q Consensus       119 ~~~~~~~G~~V~I----~~Gp---f~g~~g~v~~i~~  148 (177)
                      .-+.|.+||.|+|    .+|.   ..-|+|++.....
T Consensus        15 ~iP~f~~GDtV~V~~~i~EG~KeRiQ~feGvvI~~~~   51 (112)
T PRK05338         15 DIPEFRPGDTVRVHVKVVEGNKERIQAFEGVVIARRG   51 (112)
T ss_pred             CCCCCCCCCEEEEEEEEEECCCEEEEEEEEEEEEEEC
T ss_conf             6998599999999999996896388756899999737


No 83 
>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=21.49  E-value=61  Score=13.69  Aligned_cols=26  Identities=27%  Similarity=0.319  Sum_probs=20.2

Q ss_pred             CCCCCCCCEEEEECCCCCCCEEEEEEECCCCCEEEE
Q ss_conf             123478977999518778971999998288988999
Q gi|254780148|r  120 SVFFEVGERVCVSDGPFASFNGIVKNVDEEKSRVHV  155 (177)
Q Consensus       120 ~~~~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V  155 (177)
                      ...|++||.|+          +.|.++|.+++|+.+
T Consensus        42 ~~~fk~G~~Vk----------~rVl~vD~~~~ri~L   67 (69)
T cd05697          42 EKKFKPGLKVK----------CRVLSVEPERKRLVL   67 (69)
T ss_pred             HHCCCCCCEEE----------EEEEEEECCCCEEEE
T ss_conf             89089999999----------999999488799886


No 84 
>KOG3421 consensus
Probab=21.48  E-value=61  Score=13.69  Aligned_cols=33  Identities=33%  Similarity=0.319  Sum_probs=22.9

Q ss_pred             CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEE
Q ss_conf             4789779995187789719999982889889999
Q gi|254780148|r  123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVE  156 (177)
Q Consensus       123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~  156 (177)
                      .++|.-+-+..||..|--..|..++++ +|+.+.
T Consensus         7 veVGrva~v~~G~~~GkL~AIVdviDq-nr~lvD   39 (136)
T KOG3421           7 VEVGRVALVSFGPDAGKLVAIVDVIDQ-NRALVD   39 (136)
T ss_pred             EEECEEEEEEECCCCCEEEEEEEEECC-HHHHCC
T ss_conf             000349999706777608999986253-235304


No 85 
>pfam12073 DUF3553 Protein of unknown function (DUF3553). This family of proteins is functionally uncharacterized. This protein is found in bacteria. Proteins in this family are about 60 amino acids in length. This protein has two conserved sequence motifs: GQVQS and TVNF.
Probab=20.89  E-value=62  Score=13.62  Aligned_cols=50  Identities=24%  Similarity=0.230  Sum_probs=33.1

Q ss_pred             CCCCCEEEEECCCCCCCEEEEEEECCCCCEEEEEEEECCCEEEEEECHHHHEEC
Q ss_conf             478977999518778971999998288988999998168704788567871233
Q gi|254780148|r  123 FEVGERVCVSDGPFASFNGIVKNVDEEKSRVHVEVVIFGRVTPVELAYNQVEKI  176 (177)
Q Consensus       123 ~~~G~~V~I~~Gpf~g~~g~v~~i~~~~~r~~V~v~i~Gr~~~v~l~~~~ieki  176 (177)
                      |+||+.|+--+-|==| .|.|.++-.  +|++|.++=.|+.+ ++.+.-.+++|
T Consensus         1 lePG~~V~~P~~pdWG-iGQVQS~I~--~kvTVNFe~~GK~v-I~~~~i~L~~v   50 (52)
T pfam12073         1 LEPGMLVRHPDQPDWG-VGQVQSNIG--GRITVNFEHAGKVV-IDGSRVALELV   50 (52)
T ss_pred             CCCCCEEECCCCCCCC-CCEEEEECC--CEEEEECCCCCCEE-EECCEEEEEEE
T ss_conf             9897787689998777-002554308--87899323677589-81566889990


No 86 
>pfam09087 Cyc-maltodext_N Cyclomaltodextrinase, N-terminal. Members of this family assume a beta-sandwich structure composed of the eight antiparallel beta-strands. A ten residue linker is also present at the C-terminal end, which connects the N terminal domain to a distal domain in the protein. This domain participates in oligomerisation of the protein, wherein the N-terminal domain of one subunit contacts the active centre of the other subunit, and is also required for binding of cyclodextrin to substrate.
Probab=20.87  E-value=62  Score=13.61  Aligned_cols=20  Identities=10%  Similarity=0.290  Sum_probs=14.2

Q ss_pred             EEEECCEECEEEEEEEECCC
Q ss_conf             56641203309999996186
Q gi|254780148|r   54 VNSERRFFPGYVLIKAVMTD   73 (177)
Q Consensus        54 ~~~~~plfpgYiFv~~~~~~   73 (177)
                      ..+.+.==|+|+||..+..+
T Consensus        40 ~~v~~~enpNYLFv~L~i~~   59 (88)
T pfam09087        40 KSVVKTDNPNYLFVNLDISE   59 (88)
T ss_pred             EEEEECCCCCEEEEEEEECC
T ss_conf             99896589988999989557


No 87 
>KOG3401 consensus
Probab=20.69  E-value=63  Score=13.59  Aligned_cols=42  Identities=21%  Similarity=0.211  Sum_probs=30.2

Q ss_pred             CCCCCCCCCEEEEECCCCCC-CEEEEEEECCCCCEEEEEEEECCC
Q ss_conf             01234789779995187789-719999982889889999981687
Q gi|254780148|r  119 SSVFFEVGERVCVSDGPFAS-FNGIVKNVDEEKSRVHVEVVIFGR  162 (177)
Q Consensus       119 ~~~~~~~G~~V~I~~Gpf~g-~~g~v~~i~~~~~r~~V~v~i~Gr  162 (177)
                      ....+..+|.|.|..|-+.| .+|.+.++...  +..+-++...+
T Consensus        45 rs~pir~ddev~v~rg~~kG~q~G~v~~vyrK--k~~iyie~v~~   87 (145)
T KOG3401          45 RSMPIRKDDEVQVVRGHFKGFQIGKVSQVYRK--KYVIYIERVQR   87 (145)
T ss_pred             CCCCEEECCEEEEEECCCCCCCCCEEHHHHHH--HHEEEEEEEEE
T ss_conf             40314643379997413344110300243453--20022366778


Done!