Query         gi|255764487|ref|YP_003065115.2| heat shock protein [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 219
No_of_seqs    122 out of 2077
Neff          7.2 
Searched_HMMs 39220
Date          Sun May 29 21:22:56 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 255764487.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK10325 heat shock protein Gr 100.0       0       0  336.0  18.4  147   36-190    51-197 (197)
  2 COG0576 GrpE Molecular chapero 100.0       0       0  323.1  17.4  151   31-189    43-193 (193)
  3 pfam01025 GrpE GrpE.           100.0 4.2E-45       0  309.3  16.6  155   24-187     8-162 (162)
  4 cd00446 GrpE GrpE is the adeni 100.0 2.8E-42       0  290.8  14.0  137   40-185     1-137 (137)
  5 KOG3003 consensus              100.0 2.4E-40 5.6E-45  278.4  16.4  155   35-191    81-235 (236)
  6 pfam11500 Cut12 Spindle-body f  66.7     8.2 0.00021   19.4   3.7   31   48-80     69-99  (151)
  7 pfam08780 NTase_sub_bind Nucle  65.4      12 0.00029   18.4   4.3   25  109-133    28-56  (123)
  8 KOG1962 consensus               56.4     9.8 0.00025   18.9   2.6   12  109-120   184-195 (216)
  9 pfam05470 eIF-3c_N Eukaryotic   38.6      31  0.0008   15.7   9.8  104   31-134    27-135 (593)
 10 TIGR00060 L18_bact ribosomal p  37.0     6.9 0.00018   19.9  -0.7   14   79-92     47-60  (118)
 11 KOG0250 consensus               34.0      37 0.00094   15.2  10.1   21  132-152   493-516 (1074)
 12 pfam04108 APG17 Autophagy prot  32.1      40   0.001   15.0   6.0   40   33-72    124-163 (410)
 13 TIGR02943 Sig70_famx1 RNA poly  30.8      42  0.0011   14.9   4.5   70   39-133     7-76  (194)
 14 PTZ00156 60S ribosomal protein  30.8      25 0.00063   16.3   1.3   49  129-186   102-150 (172)
 15 KOG3895 consensus               28.1      46  0.0012   14.6   3.0   36  119-155   204-239 (488)
 16 TIGR01364 serC_1 phosphoserine  25.9      34 0.00086   15.4   1.3   41   47-88     16-65  (391)
 17 KOG2700 consensus               25.8      51  0.0013   14.3   5.3   75   74-148   170-246 (481)
 18 pfam02963 EcoRI Restriction en  25.8      36 0.00092   15.3   1.4   53  133-190    48-100 (257)
 19 TIGR01661 ELAV_HUD_SF ELAV/HuD  25.3      33 0.00084   15.5   1.1   27  145-183   404-430 (436)
 20 TIGR02168 SMC_prok_B chromosom  24.7      53  0.0014   14.2  10.0   20   74-93    527-546 (1191)
 21 KOG0493 consensus               23.1      57  0.0015   14.0   3.5   27   43-69    254-280 (342)
 22 pfam11062 DUF2863 Protein of u  21.5      46  0.0012   14.6   1.2   30  119-148   339-368 (398)
 23 TIGR00273 TIGR00273 iron-sulfu  21.3      45  0.0011   14.7   1.1   34  123-164   105-139 (450)
 24 pfam04914 DltD_C DltD C-termin  21.0      63  0.0016   13.7   4.6   72   82-153    33-111 (130)
 25 CHL00139 rpl18 ribosomal prote  20.2      21 0.00053   16.8  -0.7   10  168-177    86-95  (109)
 26 PRK05593 rplR 50S ribosomal pr  20.1      21 0.00054   16.7  -0.7   10  168-177    92-101 (115)

No 1  
>PRK10325 heat shock protein GrpE; Provisional
Probab=100.00  E-value=0  Score=335.97  Aligned_cols=147  Identities=36%  Similarity=0.635  Sum_probs=136.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             99999999999999998899999999999999999642433432031578999999721222332101112789987644
Q gi|255764487|r   36 SLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIEG  115 (219)
Q Consensus        36 ~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~G  115 (219)
                      +.+....++|+|+|++|||+|||||+++++.++++||+++|+++||||+|||+||+.+..        ..+..+.+|++|
T Consensus        51 l~e~~~~~kD~~lR~~Ae~eN~rkR~~ke~~~~~~~a~~~~~~~lLpv~DnlerAl~~~~--------~~~~~~~~~~eG  122 (197)
T PRK10325         51 LAEAQTRERDGILRVKAEMENLRRRTELDIEKAHKFALEKFINELLPVIDSLDRALEVAD--------KANPDMSAMVEG  122 (197)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--------CCCHHHHHHHHH
T ss_conf             999999889999999998999999999999999999999999997007768999998563--------117258999999


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEECCCC
Q ss_conf             799999999998641100013688875700577752243458977459999708817756782000248604888
Q gi|255764487|r  116 IEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSISKGKT  190 (219)
Q Consensus       116 i~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vsk~~~  190 (219)
                      |.||+++|.++|.++||++|+++|++|||++||||++++++++++|||++|+|+||+|+|||||||+|+|||+|+
T Consensus       123 v~mi~k~l~~~l~~~gv~~i~~~G~~FDP~~HeAv~~~~~~~~~~~~Iv~v~qkGY~l~~rvlRpA~V~VsK~k~  197 (197)
T PRK10325        123 IELTLKSMLDVVRKFGVEVIAETNVPLDPNVHQAIAMVESDDVAPGNVLGIMQKGYTLNGRTIRAAMVTVAKAKA  197 (197)
T ss_pred             HHHHHHHHHHHHHHCCCEEECCCCCCCCCHHHHHHEEECCCCCCCCEEEEEEECCEEECCEEECCCEEEEECCCC
T ss_conf             999999999999988935757889999806654010107899993907899657838899971064489817999


No 2  
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=100.00  E-value=0  Score=323.14  Aligned_cols=151  Identities=46%  Similarity=0.780  Sum_probs=140.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHH
Q ss_conf             03999999999999999999988999999999999999996424334320315789999997212223321011127899
Q gi|255764487|r   31 NIPEESLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLK  110 (219)
Q Consensus        31 ~~~e~~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~  110 (219)
                      ..+..+..++++++++|+|++|||+|||||++++++++++|+.++|+.+||||+|||+|||.+....       .... +
T Consensus        43 ~~i~~Le~q~~e~~~~~lr~~Ae~eN~rkR~~re~e~~~k~a~e~~~~dlLpviDnlerAl~~~~~~-------~d~~-~  114 (193)
T COG0576          43 QEIAELEAQLEELKDKYLRAQAEFENLRKRTEREREEAKKYAIEKFAKDLLPVIDNLERALEAAEDD-------KDPE-K  114 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC-------CCHH-H
T ss_conf             8999999999999999999999999999999999999999999999999888887999999712345-------4157-7


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEECCC
Q ss_conf             8764479999999999864110001368887570057775224345897745999970881775678200024860488
Q gi|255764487|r  111 SLIEGIEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSISKGK  189 (219)
Q Consensus       111 ~~~~Gi~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vsk~~  189 (219)
                      +|++||.||+++|.++|.++||+.|.+.|+.|||++|+||++++++++++|||++|+|+||+|+|||||||||+||+++
T Consensus       115 ~l~~Gvem~~~~l~~~L~k~Gv~~i~~~Ge~FDP~~HeAv~~~~~~~~~~~tVv~v~qkGY~l~dRVLRpA~V~Vak~~  193 (193)
T COG0576         115 ALLEGVEMTLDQLLDALEKLGVEEIGPEGEKFDPNLHEAVQRVESEDVEPNTVVEVLQKGYKLNDRVLRPAMVKVAKKE  193 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCEEECCCCCCCCHHHHHHEEEECCCCCCCCEEEEEEECCEEECCEECCCEEEEEECCC
T ss_conf             8999999999999999998798780788998897885510343678999994889850570648985211279972589


No 3  
>pfam01025 GrpE GrpE.
Probab=100.00  E-value=4.2e-45  Score=309.30  Aligned_cols=155  Identities=45%  Similarity=0.763  Sum_probs=142.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             22232310399999999999999999998899999999999999999642433432031578999999721222332101
Q gi|255764487|r   24 AEEKSEINIPEESLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEK  103 (219)
Q Consensus        24 ~~~~~~~~~~e~~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~  103 (219)
                      .........+..+..++++++++|+|++|||+|||||+++++.+++.|+.++|+.+||||+|+|+||+.+.+.       
T Consensus         8 ~~~~~l~~~l~~l~~e~~~~~~~~~r~~Ae~eN~rkr~~ke~~~~~~~a~~~~~~~lL~v~D~leral~~~~~-------   80 (162)
T pfam01025         8 DEEEALEEELEELEEEIEELKDRLLRLLAEFENYRKRTEREREEAKKYAIEKFAKDLLPVLDNLERALAAAKE-------   80 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC-------
T ss_conf             4799999999999999999999999999999999999999999999999999999860165269999972613-------


Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEE
Q ss_conf             11278998764479999999999864110001368887570057775224345897745999970881775678200024
Q gi|255764487|r  104 KSESVLKSLIEGIEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALV  183 (219)
Q Consensus       104 ~~~~~~~~~~~Gi~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V  183 (219)
                        .....+|++||.||+++|.++|+++||++|+|+|++|||++||||++++++++++|||++|+|+||+|+|||||||+|
T Consensus        81 --~~~~~~~~~G~~~i~~~l~~~l~~~gv~~i~~~G~~FDP~~HeAv~~~~~~~~~~~~I~~v~q~GY~l~~rvlRpA~V  158 (162)
T pfam01025        81 --NEDVKSLVEGVEMILKQLLKVLEKHGVEKIEPEGEPFDPNLHEAVSQVPSDEKPPGTVVEVLQKGYKLHDRVLRPAMV  158 (162)
T ss_pred             --CCHHHHHHHHHHHHHHHHHHHHHHCCEEEECCCCCCCCHHHHCEEEEECCCCCCCCEEEEEEECCCEECCEEECCCEE
T ss_conf             --101789999999999999999986552331677885785783011453689999298999854593879997206368


Q ss_pred             EEEC
Q ss_conf             8604
Q gi|255764487|r  184 SISK  187 (219)
Q Consensus       184 ~Vsk  187 (219)
                      +|||
T Consensus       159 ~Vsk  162 (162)
T pfam01025       159 VVSK  162 (162)
T ss_pred             EECC
T ss_conf             8679


No 4  
>cd00446 GrpE GrpE is the adenine nucleotide exchange factor of DnaK (Hsp70)-type ATPases. The GrpE dimer binds to the ATPase domain of Hsp70 catalyzing the dissociation of ADP, which enables rebinding of ATP, one step in the Hsp70 reaction cycle in protein folding. In eukaryotes, only the mitochondrial Hsp70, not the cytosolic form, is GrpE dependent.
Probab=100.00  E-value=2.8e-42  Score=290.80  Aligned_cols=137  Identities=47%  Similarity=0.852  Sum_probs=131.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             99999999999988999999999999999996424334320315789999997212223321011127899876447999
Q gi|255764487|r   40 SEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIEGIEMT  119 (219)
Q Consensus        40 ~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~Gi~mi  119 (219)
                      +++++++|+|++|||+|||||+.+++++++.|+.++|+++||||+|+|+||+++...         +...++|++||.||
T Consensus         1 ~~~~~d~~~r~~Ae~~N~rkr~~~e~~~~~~~~~~~~~~~lL~v~D~l~~al~~~~~---------~~~~~~~~~Gi~~i   71 (137)
T cd00446           1 LEELKDKLLRALAEFENYRKRTEREREEARKYAIEKFAKDLLPVLDNLERALEAAKK---------EEELKNLVEGVEMT   71 (137)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCC---------CHHHHHHHHHHHHH
T ss_conf             967899999999869999999999999999999999999615645259999982633---------13588899999999


Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEE
Q ss_conf             999999986411000136888757005777522434589774599997088177567820002486
Q gi|255764487|r  120 RREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSI  185 (219)
Q Consensus       120 ~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~V  185 (219)
                      +++|.++|+++||++|+++|++|||++||||++++++++++|+|++|+|+||+|+|||||||+|+|
T Consensus        72 ~~~l~~~L~~~gi~~i~~~g~~FDP~~HeAv~~~~~~~~~~~~I~~v~~~GY~l~~rvlRpA~V~V  137 (137)
T cd00446          72 LKQLLDVLEKHGVEKIEPEGEPFDPNLHEAVMQVPSPDVEPGTVVEVLQKGYKLGDRVLRPAMVVV  137 (137)
T ss_pred             HHHHHHHHHHCCCEEECCCCCCCCHHHHHEEEEECCCCCCCCEEEEEEECCCEECCEEEECCEEEC
T ss_conf             999999999869952245699689467104356368999939899996569386999710637469


No 5  
>KOG3003 consensus
Probab=100.00  E-value=2.4e-40  Score=278.41  Aligned_cols=155  Identities=37%  Similarity=0.660  Sum_probs=145.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             99999999999999999889999999999999999964243343203157899999972122233210111278998764
Q gi|255764487|r   35 ESLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIE  114 (219)
Q Consensus        35 ~~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~  114 (219)
                      .+.++..+|+|+|+|..||++|.|+|+.|..++++.||+++|+++||.|.|+|++|.+..+.+..  ....+..++.+++
T Consensus        81 k~~~e~~eLkdk~~rs~Ad~eNlr~R~~r~~edak~FaiQ~f~kdLleVaD~Le~a~~~v~ee~~--~~d~~~~L~~l~e  158 (236)
T KOG3003          81 KLEKEEQELKDKYLRSLAECENLRDRTIRDVEDAKKFAIQSFCKDLLEVADNLEKATECVKEESE--KEDQKKDLKDLFE  158 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHC--CCCCCHHHHHHHH
T ss_conf             88889999999999988888889999888788888899999999999988788899874342106--3200257999974


Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEECCCCC
Q ss_conf             47999999999986411000136888757005777522434589774599997088177567820002486048888
Q gi|255764487|r  115 GIEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSISKGKTQ  191 (219)
Q Consensus       115 Gi~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vsk~~~~  191 (219)
                      |+.|++++|.++|.+||++..+|+|++|||+.|||++++|...+++|||..|.+.||+||||+||||+|+|++++..
T Consensus       159 Gl~mte~ql~~vf~KhGLekldPigekFDPn~HEAvfq~p~~~k~pgtV~~v~k~Gy~L~~R~IRPA~VgV~~~~~~  235 (236)
T KOG3003         159 GLSMTEAQLKEVFAKHGLEKLDPIGEKFDPNEHEAVFQVPDAAKEPGTVALVTKKGYKLNGRVIRPAMVGVVKGGEN  235 (236)
T ss_pred             HHHHHHHHHHHHHHHCCCEECCCCCCCCCCCHHHEEEECCCCCCCCCEEEEEECCCCCCCCEEECHHHEEEECCCCC
T ss_conf             89999999999999749544178788889550222575445677997589880467401773500344145227789


No 6  
>pfam11500 Cut12 Spindle-body formation-associated protein. This is the central coiled-coil region of cut12 also found in other fungi, barring S. cerevisiae. The full protein has two predicted coiled-coil regions, and one consensus phosphorylation site for p34cdc2 and two for MAP kinase. During fission yeast mitosis, the duplicated spindle pole bodies (SPBs) nucleate microtubule arrays that interdigitate to form the mitotic spindle. Cut12 is localized to the SPB throughout the cell cycle, predominantly around the inner face of the interphase SPB, adjacent to the nucleus. Cut12 associates with Fin1 and is important in this context for the activity of Plo1.
Probab=66.72  E-value=8.2  Score=19.38  Aligned_cols=31  Identities=26%  Similarity=0.374  Sum_probs=23.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999988999999999999999996424334320
Q gi|255764487|r   48 LRVIAEMENLRRRTDREKKDAQSYSIAKFARDM   80 (219)
Q Consensus        48 lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~l   80 (219)
                      .+-.++|++||-++.+|+..+++|-  ++++.+
T Consensus        69 kYWK~efesY~~~~~~Ei~kLi~yr--~~aKsy   99 (151)
T pfam11500        69 KYWKAEFDSYHSKTEREIKKLIQYK--QLAKSY   99 (151)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHH
T ss_conf             0489999999998899999999999--999999


No 7  
>pfam08780 NTase_sub_bind Nucleotidyltransferase substrate binding protein like. Nucleotidyltransferases (EC 2.7.7) comprise a large enzyme family with diverse roles in polynucleotide synthesis and modification. This domain is structurally related to kanamycin nucleotidyltransferase (KNTase) and forms a complex with HI0073, a sequence homolog of the nucleotide-binding domain of this nucleotidyltransferase superfamily.
Probab=65.39  E-value=12  Score=18.42  Aligned_cols=25  Identities=24%  Similarity=0.323  Sum_probs=11.2

Q ss_pred             HHHHHHHHHHHH----HHHHHHHHHHHHC
Q ss_conf             998764479999----9999998641100
Q gi|255764487|r  109 LKSLIEGIEMTR----REMMSTLERYGVK  133 (219)
Q Consensus       109 ~~~~~~Gi~mi~----k~l~~~L~~~GV~  133 (219)
                      ...+++.|+.++    |-|...|+..|+.
T Consensus        28 rdg~IqrFE~t~ElaWK~lK~~L~~~g~~   56 (123)
T pfam08780        28 RDGVIQRFEFTYELAWKLLKDYLEYQGIV   56 (123)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99689999999999999999999980876


No 8  
>KOG1962 consensus
Probab=56.45  E-value=9.8  Score=18.87  Aligned_cols=12  Identities=33%  Similarity=0.382  Sum_probs=4.0

Q ss_pred             HHHHHHHHHHHH
Q ss_conf             998764479999
Q gi|255764487|r  109 LKSLIEGIEMTR  120 (219)
Q Consensus       109 ~~~~~~Gi~mi~  120 (219)
                      +.+..+|+..-+
T Consensus       184 l~Kq~e~~~~Ey  195 (216)
T KOG1962         184 LKKQSEGLQDEY  195 (216)
T ss_pred             HHHHHHHCCCHH
T ss_conf             999998711089


No 9  
>pfam05470 eIF-3c_N Eukaryotic translation initiation factor 3 subunit 8 N-terminus. The largest of the mammalian translation initiation factors, eIF3, consists of at least eight subunits ranging in mass from 35 to 170 kDa. eIF3 binds to the 40 S ribosome in an early step of translation initiation and promotes the binding of methionyl-tRNAi and mRNA.
Probab=38.57  E-value=31  Score=15.65  Aligned_cols=104  Identities=13%  Similarity=0.252  Sum_probs=60.4

Q ss_pred             HHHHHHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             03999999999999-----9999999889999999999999999964243343203157899999972122233210111
Q gi|255764487|r   31 NIPEESLNQSEEFR-----DKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKS  105 (219)
Q Consensus        31 ~~~e~~~~e~~elk-----dk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~  105 (219)
                      ..++++..-++.++     +.|..+..+|+++.|.++|-+.-.-..++=+|....|--+++|-.....-+...-.-.+.+
T Consensus        27 Kr~eel~~~i~~i~na~ki~Dw~~i~~eFd~L~k~~~K~~~v~~~~~~P~fyIk~L~~LEd~v~e~~~dke~~Kkmsk~n  106 (593)
T pfam05470        27 KRFEEMTSTIKTIKNAMKINDWVSLLEEFDKLNKAYQKAKRVSENVKTPRFYIKTLVMLEDFLNELWADKEAKKKMSKNN  106 (593)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCHHHHHHCCHHH
T ss_conf             67999999999999887622399999999999999999885553489985999999999999999885757776508877


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             27899876447999999999986411000
Q gi|255764487|r  106 ESVLKSLIEGIEMTRREMMSTLERYGVKK  134 (219)
Q Consensus       106 ~~~~~~~~~Gi~mi~k~l~~~L~~~GV~~  134 (219)
                      +.++..+.+-|+=..+.+...+.++--.+
T Consensus       107 akalntlkQklkK~~k~ye~~i~~yrenP  135 (593)
T pfam05470       107 AKALNTLKQKVKKNNKQFEDDITRYREDP  135 (593)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             77789999999985077899999987296


No 10 
>TIGR00060 L18_bact ribosomal protein L18; InterPro: IPR004389   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 is the ribosomal protein L18 family. The archaebacterial and eukaryotic type rpL18 is not included in this family.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome.
Probab=36.98  E-value=6.9  Score=19.86  Aligned_cols=14  Identities=21%  Similarity=0.328  Sum_probs=8.4

Q ss_pred             HHCCHHHHHHHHHH
Q ss_conf             20315789999997
Q gi|255764487|r   79 DMLSVSDNLSRALD   92 (219)
Q Consensus        79 ~lL~v~D~lerAl~   92 (219)
                      ..|--++.|++.|.
T Consensus        47 ~tlas~Stl~~~l~   60 (118)
T TIGR00060        47 VTLASASTLEKKLK   60 (118)
T ss_pred             EEEEEHHHHHHHHH
T ss_conf             47873155668877


No 11 
>KOG0250 consensus
Probab=34.01  E-value=37  Score=15.19  Aligned_cols=21  Identities=10%  Similarity=-0.021  Sum_probs=8.4

Q ss_pred             HCCCCCCCC---CCCCCHHHHHHC
Q ss_conf             000136888---757005777522
Q gi|255764487|r  132 VKKIDAKDQ---KFNPNMHQAMFE  152 (219)
Q Consensus       132 V~~i~~~G~---~FDP~~HeAi~~  152 (219)
                      -.+++|+|.   .-+|.||-||..
T Consensus       493 ~~P~GPlG~~Vtl~~~KWa~aIE~  516 (1074)
T KOG0250         493 TPPKGPLGKYVTLKEPKWALAIER  516 (1074)
T ss_pred             CCCCCCCCCEEEECCCHHHHHHHH
T ss_conf             999887654367258088999999


No 12 
>pfam04108 APG17 Autophagy protein Apg17. Apg17 is required for activating Apg1 protein kinases.
Probab=32.05  E-value=40  Score=14.99  Aligned_cols=40  Identities=15%  Similarity=0.143  Sum_probs=22.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999889999999999999999964
Q gi|255764487|r   33 PEESLNQSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYS   72 (219)
Q Consensus        33 ~e~~~~e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a   72 (219)
                      .+.+...++...+..--+++.++|...++..+.....+..
T Consensus       124 ve~L~~~lk~~i~e~~~~~~~~d~~~~~fd~~l~~l~~~l  163 (410)
T pfam04108       124 VELLRDNLKIYIDEVPAIRAQLDNILNQFDSDLDSLQEQL  163 (410)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999898758999988627899999999999998


No 13 
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family; InterPro: IPR014289   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This group of sigma factors are part of the larger sigma-70 family. From homology, tree building, bidirectional best hits and their one-to-a-genome distribution, they appear to represent a conserved family..
Probab=30.78  E-value=42  Score=14.86  Aligned_cols=70  Identities=21%  Similarity=0.359  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             99999999999998899999999999999999642433432031578999999721222332101112789987644799
Q gi|255764487|r   39 QSEEFRDKYLRVIAEMENLRRRTDREKKDAQSYSIAKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIEGIEM  118 (219)
Q Consensus        39 e~~elkdk~lR~~AE~eN~rkR~~ke~~~~~~~a~~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~Gi~m  118 (219)
                      .+.+++-.+|| .|.++      -|+..++-+-+++.-+..-+.-.|+|                .+...++.|+-||  
T Consensus         7 ~l~~~Rr~LLr-FA~lQ------LRdh~d~AEDaVQEtLl~Al~~~~~F----------------~G~s~lkTWl~~I--   61 (194)
T TIGR02943         7 ELEDLRRDLLR-FARLQ------LRDHEDLAEDAVQETLLAALEHADSF----------------AGRSALKTWLFAI--   61 (194)
T ss_pred             HHHHHHHHHHH-HHHHC------CCCCHHHHHHHHHHHHHHHHHCCCCC----------------HHHHHHHHHHHHH--
T ss_conf             99998799999-98623------88826788899999999987357760----------------1489999999999--


Q ss_pred             HHHHHHHHHHHHHHC
Q ss_conf             999999998641100
Q gi|255764487|r  119 TRREMMSTLERYGVK  133 (219)
Q Consensus       119 i~k~l~~~L~~~GV~  133 (219)
                      ...+|+++|..-|=+
T Consensus        62 LknKiID~LR~~~R~   76 (194)
T TIGR02943        62 LKNKIIDVLRAKGRE   76 (194)
T ss_pred             HHHHHHHHHHCCCCE
T ss_conf             999999998346754


No 14 
>PTZ00156 60S ribosomal protein L11; Provisional
Probab=30.77  E-value=25  Score=16.31  Aligned_cols=49  Identities=16%  Similarity=0.234  Sum_probs=35.8

Q ss_pred             HHHHCCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEE
Q ss_conf             4110001368887570057775224345897745999970881775678200024860
Q gi|255764487|r  129 RYGVKKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSIS  186 (219)
Q Consensus       129 ~~GV~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vs  186 (219)
                      .+||.+--..|.+|||..--         +-=+..|..-++||....|=++.+.|.-.
T Consensus       102 sFGI~EhId~G~kYDP~iGI---------~Gmdv~V~l~RpG~Rv~~Rk~~~~~i~~~  150 (172)
T PTZ00156        102 GFGIQEHIDLGIKYDPSTGI---------YGMDFYVVLSRPGERVAHRKRRNSRVGKS  150 (172)
T ss_pred             EECCHHHEECCCEECCCCCE---------EEEEEEEEEECCCCEEEEHHHHCCCCCCC
T ss_conf             41522223577421686777---------65368999715874311011322558867


No 15 
>KOG3895 consensus
Probab=28.06  E-value=46  Score=14.56  Aligned_cols=36  Identities=25%  Similarity=0.493  Sum_probs=31.5

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCCCC
Q ss_conf             9999999986411000136888757005777522434
Q gi|255764487|r  119 TRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEEPH  155 (219)
Q Consensus       119 i~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~~~  155 (219)
                      +++||..++.+.|-+.|.-+-+.|=|+ |.-+.+.++
T Consensus       204 vf~Qlvki~~slG~e~fPli~qt~yPn-HK~m~s~~t  239 (488)
T KOG3895         204 VFAQLVKITKSLGPEKFPLIEQTFYPN-HKEMLSQPT  239 (488)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCEEECCC-CHHHCCCCC
T ss_conf             999999998751854455440010687-442214887


No 16 
>TIGR01364 serC_1 phosphoserine aminotransferase; InterPro: IPR003248  Phosphoserine aminotransferases (2.6.1.52 from EC) catalyse the conversion of O-phospho-L-serine and oxoglutarate to 3-phosphonooxypyruvate and L-glutamate in the major phosphorylated serine biosynthesis pathway. In bacteria it is also equired for the biosynthesis of pyridoxine. The enzyme requires pyridoxal phosphate as a cofactor, and is part of the aminotransferase class-V family.; GO: 0006564 L-serine biosynthetic process.
Probab=25.91  E-value=34  Score=15.44  Aligned_cols=41  Identities=20%  Similarity=0.235  Sum_probs=29.9

Q ss_pred             HHHHHHHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             99999889999999---------9999999999642433432031578999
Q gi|255764487|r   47 YLRVIAEMENLRRR---------TDREKKDAQSYSIAKFARDMLSVSDNLS   88 (219)
Q Consensus        47 ~lR~~AE~eN~rkR---------~~ke~~~~~~~a~~~~~~~lL~v~D~le   88 (219)
                      +.++++|+-||+..         -.++-. ..-...++.+|+||.|=||++
T Consensus        16 L~~aq~Ellnf~~~G~SVmEiSHRsk~F~-~v~~~Ae~dlR~LL~iPd~Y~   65 (391)
T TIGR01364        16 LEQAQKELLNFNGLGMSVMEISHRSKEFE-AVASEAESDLRELLNIPDNYE   65 (391)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCHHHH-HHHHHHHHHHHHHHCCCCCCE
T ss_conf             99999998657517976699853868999-999999999998824799826


No 17 
>KOG2700 consensus
Probab=25.81  E-value=51  Score=14.30  Aligned_cols=75  Identities=12%  Similarity=0.152  Sum_probs=46.4

Q ss_pred             HHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHCCCCC-CCCCCCCCHHH
Q ss_conf             433432031578999999721222332101112789987644799999999998-6411000136-88875700577
Q gi|255764487|r   74 AKFARDMLSVSDNLSRALDSAPLDLANSEKKSESVLKSLIEGIEMTRREMMSTL-ERYGVKKIDA-KDQKFNPNMHQ  148 (219)
Q Consensus        74 ~~~~~~lL~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~~Gi~mi~k~l~~~L-~~~GV~~i~~-~G~~FDP~~He  148 (219)
                      .-++-+|+-.+-+|.||+....--....--+.-..+.++..|..-=..++++.. +.+|..+.-+ .|+.+.|..+-
T Consensus       170 ~~~~qel~~~l~~f~~~~~~~~~~~~kga~gtqasf~~l~~~~~~kv~~ld~Lv~k~~gf~~~~~~TGQt~sr~~~~  246 (481)
T KOG2700         170 CLWIQELLRDLERFHRARTDVRFRGLKGATGTQASFLSLFLGDMDKVEKLDSLVTKELGFVPMYIVTGQTYSRKTDA  246 (481)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHH
T ss_conf             99899999999999986312001566521301888888633518889989999999818886554458867831578


No 18 
>pfam02963 EcoRI Restriction endonuclease EcoRI.
Probab=25.79  E-value=36  Score=15.27  Aligned_cols=53  Identities=28%  Similarity=0.406  Sum_probs=39.1

Q ss_pred             CCCCCCCCCCCCCHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEEEEECCCC
Q ss_conf             0013688875700577752243458977459999708817756782000248604888
Q gi|255764487|r  133 KKIDAKDQKFNPNMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALVSISKGKT  190 (219)
Q Consensus       133 ~~i~~~G~~FDP~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V~Vsk~~~  190 (219)
                      .+|+..=..+||.+-+.+....+.=+|+|-|++|--.     +--.||-+|.-||.-+
T Consensus        48 ~eIN~~L~~idp~LGqTlFv~~ssikPDGGIievKd~-----~g~wr~iLv~EaK~QG  100 (257)
T pfam02963        48 KEINEALKKIDPDLGQTLFVENASIKPDGGIVEVKDD-----YGNWRVVLVAEAKHQG  100 (257)
T ss_pred             HHHHHHHHCCCCCCCCCEEECCCCCCCCCCEEEEEEC-----CCCEEEEEEEEHHHCC
T ss_conf             9998988415834484033057752688876999806-----8988999987354247


No 19 
>TIGR01661 ELAV_HUD_SF ELAV/HuD family splicing factor; InterPro: IPR006548   These sequences represent the ELAV/HuD subfamily of splicing factors found in metazoa. HuD stands for the human paraneoplastic encephalomyelitis antigen D of which there are 4 variants in human . ELAV stands for the Drosophila Embryonic lethal abnormalvisual protein . ELAV-like splicing factors are also known in human as HuB (ELAV-like protein 2), HuC (ELAV-like protein 3, Paraneoplastic cerebellar degeneration-associated antigen) and HuR (ELAV-like protein 1). These genes are most closely related to the sex-lethal subfamily of splicing factors found in Dipteran insects (IPR006546 from INTERPRO). ; GO: 0003723 RNA binding.
Probab=25.27  E-value=33  Score=15.52  Aligned_cols=27  Identities=26%  Similarity=0.442  Sum_probs=16.1

Q ss_pred             CHHHHHHCCCCCCCCCCEEEEEECCCEEECCEEEECCEE
Q ss_conf             057775224345897745999970881775678200024
Q gi|255764487|r  145 NMHQAMFEEPHDTVPANTIIKVVQDGYAINERVLRPALV  183 (219)
Q Consensus       145 ~~HeAi~~~~~~~~~~~tVi~v~q~GY~l~~rvlRpA~V  183 (219)
                      |+.||++-+-+=            -||.|++|||-.+-+
T Consensus       404 NY~EA~~Ai~SL------------NGy~Lg~rvLQv~fk  430 (436)
T TIGR01661       404 NYDEAAMAIRSL------------NGYTLGNRVLQVSFK  430 (436)
T ss_pred             CHHHHHHHHHHH------------CCCCCCCCEEEEEEE
T ss_conf             089999999871------------474102717999985


No 20 
>TIGR02168 SMC_prok_B chromosome segregation protein SMC; InterPro: IPR011890   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression . The smc gene is often associated with scpB (IPR005234 from INTERPRO) and scpA genes, where scp stands for segregation and condensation protein. SMC was shown (in Caulobacter crescentus) to be induced early in S phase but present and bound to DNA throughout the cell cycle , , .; GO: 0005515 protein binding, 0005524 ATP binding, 0005694 chromosome.
Probab=24.74  E-value=53  Score=14.18  Aligned_cols=20  Identities=10%  Similarity=0.365  Sum_probs=7.0

Q ss_pred             HHHHHHHCCHHHHHHHHHHH
Q ss_conf             43343203157899999972
Q gi|255764487|r   74 AKFARDMLSVSDNLSRALDS   93 (219)
Q Consensus        74 ~~~~~~lL~v~D~lerAl~~   93 (219)
                      ..++.++|.|--.++.|+..
T Consensus       527 ~g~l~~~i~v~~~ye~A~e~  546 (1191)
T TIGR02168       527 VGVLSELIEVDEGYEAAIEA  546 (1191)
T ss_pred             CHHHHHHHCCCHHHHHHHHH
T ss_conf             00357652154889999999


No 21 
>KOG0493 consensus
Probab=23.08  E-value=57  Score=13.97  Aligned_cols=27  Identities=19%  Similarity=0.306  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999889999999999999999
Q gi|255764487|r   43 FRDKYLRVIAEMENLRRRTDREKKDAQ   69 (219)
Q Consensus        43 lkdk~lR~~AE~eN~rkR~~ke~~~~~   69 (219)
                      --+|+.|++|||.--|--+++.+..+-
T Consensus       254 taeQL~RLK~EF~enRYlTEqRRQ~La  280 (342)
T KOG0493         254 TAEQLQRLKAEFQENRYLTEQRRQELA  280 (342)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             499999999998660357899999999


No 22 
>pfam11062 DUF2863 Protein of unknown function (DUF2863). This bacterial family of proteins have no known function.
Probab=21.49  E-value=46  Score=14.59  Aligned_cols=30  Identities=20%  Similarity=0.389  Sum_probs=20.4

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCCHHH
Q ss_conf             999999998641100013688875700577
Q gi|255764487|r  119 TRREMMSTLERYGVKKIDAKDQKFNPNMHQ  148 (219)
Q Consensus       119 i~k~l~~~L~~~GV~~i~~~G~~FDP~~He  148 (219)
                      ...++..+|+..||+.|....+.|.|++.+
T Consensus       339 ~~~~I~~~Lre~GV~~v~~~~~~f~~EyCd  368 (398)
T pfam11062       339 PIEQIEALLRECGVTDIRRLAERFPPEYCE  368 (398)
T ss_pred             HHHHHHHHHHHCCHHHHHHHHHCCCCHHHC
T ss_conf             599999999981819999765118943331


No 23 
>TIGR00273 TIGR00273 iron-sulfur cluster binding protein; InterPro: IPR004452 Members of this family have a perfect 4Fe-4S binding motif C-x(2)-C-x(2)-C-x(3)-CP followed by either a perfect or imperfect (the first Cys replaced by Ser) second copy. Members probably bind two 4fe-4S iron-sulphur clusters..
Probab=21.30  E-value=45  Score=14.67  Aligned_cols=34  Identities=12%  Similarity=0.414  Sum_probs=26.3

Q ss_pred             HHHHHHHHHHCCCCC-CCCCCCCCHHHHHHCCCCCCCCCCEEE
Q ss_conf             999986411000136-888757005777522434589774599
Q gi|255764487|r  123 MMSTLERYGVKKIDA-KDQKFNPNMHQAMFEEPHDTVPANTII  164 (219)
Q Consensus       123 l~~~L~~~GV~~i~~-~G~~FDP~~HeAi~~~~~~~~~~~tVi  164 (219)
                      |-.+|++.|++.+++ +|+        -|.++.+.+.|...||
T Consensus       105 Ln~~L~~~G~~v~ETDLGE--------lI~Q~~d~d~P~H~Vv  139 (450)
T TIGR00273       105 LNEVLEKKGIEVVETDLGE--------LILQLDDNDPPSHIVV  139 (450)
T ss_pred             HHHHHHHCCCEEEEECCCE--------EEEEEECCCCCEEEEE
T ss_conf             1488876597799800430--------7887745888427885


No 24 
>pfam04914 DltD_C DltD C-terminal region. DltD is and integral membrane protein involved in the biosynthesis of D-alanyl-lipoteichoic acid. This is important in controlling the net ionic charge in lipoteichoic acid (LTA). This family is found in bacteria of the Bacillus/Clostridium group. DltD binds Dcp and ligates it with D-alanine. DltD does not ligate acyl carrier protein (ACP) with D-alanine. It also has thioesterase activity for mischarged D-alanyl-acyl carrier protein (ACP). DltD is thought to be responsible for discriminating between Dcp involved in the D-alanylation of LTA, and ACP involved in fatty acid biosynthesis. This family consists of the C-terminal region of DltD.
Probab=20.96  E-value=63  Score=13.70  Aligned_cols=72  Identities=17%  Similarity=0.103  Sum_probs=42.6

Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH-------HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHCC
Q ss_conf             15789999997212223321011127899876-------4479999999999864110001368887570057775224
Q gi|255764487|r   82 SVSDNLSRALDSAPLDLANSEKKSESVLKSLI-------EGIEMTRREMMSTLERYGVKKIDAKDQKFNPNMHQAMFEE  153 (219)
Q Consensus        82 ~v~D~lerAl~~~~~~~~~~~~~~~~~~~~~~-------~Gi~mi~k~l~~~L~~~GV~~i~~~G~~FDP~~HeAi~~~  153 (219)
                      |=..+|.+.|.........+.----+....|+       +..+-.++++..+++++|+..++-....++|.+++=.+|+
T Consensus        33 pEy~Dlql~L~~~~~~~~~vlfVi~PvNgkWydytGl~k~~r~~~y~KI~~~~~~~Gf~i~Dls~~~y~pYfm~DtiHl  111 (130)
T pfam04914        33 PEYNDLQLVLDQFAKAGADVLFVIPPVNGKWYDYTGLSKEMRQQYYKKIKYQLKSQGFNIADLSDDGYEPYFMQDTIHL  111 (130)
T ss_pred             CCHHHHHHHHHHHHHCCCCEEEEECCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHCCCEEEECCCCCCCCCEEEECCCC
T ss_conf             4406899999999984994189854777058887089999999999999999998798387244578987635423325


No 25 
>CHL00139 rpl18 ribosomal protein L18; Validated
Probab=20.18  E-value=21  Score=16.78  Aligned_cols=10  Identities=20%  Similarity=0.415  Sum_probs=7.3

Q ss_pred             CCCEEECCEE
Q ss_conf             0881775678
Q gi|255764487|r  168 QDGYAINERV  177 (219)
Q Consensus       168 q~GY~l~~rv  177 (219)
                      +.||+|||||
T Consensus        86 Rggy~YHGrV   95 (109)
T CHL00139         86 RGGKLYHGRI   95 (109)
T ss_pred             CCCCCCHHHH
T ss_conf             8998422199


No 26 
>PRK05593 rplR 50S ribosomal protein L18; Reviewed
Probab=20.12  E-value=21  Score=16.72  Aligned_cols=10  Identities=40%  Similarity=0.780  Sum_probs=7.9

Q ss_pred             CCCEEECCEE
Q ss_conf             0881775678
Q gi|255764487|r  168 QDGYAINERV  177 (219)
Q Consensus       168 q~GY~l~~rv  177 (219)
                      +.||+|||||
T Consensus        92 R~g~~YHGrv  101 (115)
T PRK05593         92 RGGYKYHGRV  101 (115)
T ss_pred             CCCCCCCHHH
T ss_conf             8998422399


Done!