Query         gi|254780256|ref|YP_003064669.1| 50S ribosomal protein L22 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 131
No_of_seqs    114 out of 1450
Neff          5.6 
Searched_HMMs 39220
Date          Tue May 24 10:03:51 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780256.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK12279 50S ribosomal protein 100.0 2.8E-44       0  281.7  11.4  115   15-129     1-116 (311)
  2 CHL00034 rpl22 ribosomal prote 100.0 1.6E-43       0  277.3  12.4  111   16-126     1-111 (112)
  3 PRK00565 rplV 50S ribosomal pr 100.0 7.4E-43       0  273.4  12.4  111   15-125     1-111 (111)
  4 TIGR01044 rplV_bact ribosomal  100.0 1.5E-42       0  271.5   8.5  103   19-121     1-103 (103)
  5 COG0091 RplV Ribosomal protein 100.0 7.8E-41 1.4E-45  261.4  11.7  113   13-125     7-119 (120)
  6 pfam00237 Ribosomal_L22 Riboso 100.0   2E-39 5.2E-44  253.1  11.4  105   19-123     1-105 (105)
  7 cd00336 Ribosomal_L22 Ribosoma 100.0 7.2E-37 1.8E-41  238.1  11.1  105   17-121     1-105 (105)
  8 PRK04223 rpl22p 50S ribosomal  100.0 1.3E-35 3.2E-40  230.7  11.9  119    6-125     5-154 (154)
  9 TIGR01038 L22_arch ribosomal p 100.0 1.9E-31 4.9E-36  206.1   8.8  115    9-124     4-151 (151)
 10 KOG1711 consensus              100.0 2.4E-31   6E-36  205.5   8.0  113   15-127    70-183 (218)
 11 PTZ00178 60S ribosomal protein  99.9 5.3E-27 1.4E-31  179.8   9.2  120    7-127     5-156 (177)
 12 KOG3353 consensus               99.1 8.4E-13 2.1E-17   96.1  -5.2  113   12-125     4-148 (175)
 13 PRK11325 scaffold protein; Pro  67.5      11 0.00027   18.8   5.8   60   17-76     56-125 (127)
 14 TIGR03419 NifU_clost FeS clust  66.7      11 0.00029   18.7   6.0   61   17-77     50-121 (121)
 15 TIGR02871 spore_ylbJ sporulati  55.4     9.9 0.00025   19.0   2.4   39   37-75    174-212 (384)
 16 TIGR01994 SUF_scaf_2 SUF syste  36.8      35  0.0009   15.7   3.0   35   17-51     55-89  (139)
 17 pfam01024 Colicin Colicin pore  35.8      37 0.00094   15.6   3.7   45   29-73     36-83  (187)
 18 pfam01592 NifU_N NifU-like N t  33.0      41   0.001   15.4   4.5   57   17-73     53-120 (126)
 19 TIGR01803 CM-like chorismate m  28.0      47  0.0012   15.0   2.3   22   59-81     44-65  (82)
 20 TIGR02709 branched_ptb branche  26.7      44  0.0011   15.2   2.0   25   60-84     12-45  (271)
 21 TIGR02607 antidote_HigA addict  20.3      64  0.0016   14.2   1.8   42   15-56     21-62  (81)

No 1  
>PRK12279 50S ribosomal protein L22/unknown domain fusion protein; Provisional
Probab=100.00  E-value=2.8e-44  Score=281.72  Aligned_cols=115  Identities=23%  Similarity=0.339  Sum_probs=110.5

Q ss_pred             HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH-CCCCCHHHEEEEEEEECCC
Q ss_conf             123112148750889999999984798699999888658202479999999999999984-0599823369999998898
Q gi|254780256|r   15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAEN-NHDLDVDRLIVSEAYVGKS   93 (131)
Q Consensus        15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~-n~~ld~~~L~I~~~~v~~G   93 (131)
                      +|++|.+||+|+||+|+|+|+|+|||++|++|+++|.|+|+++|.+|.|+|.||+|||++ |+|+|+|+|||++|+||+|
T Consensus         1 MEAKAiaRyVRISPrKARlV~DlIRGK~V~EAlaILkFTPKKAA~iV~KvLkSAiANAe~NN~glD~D~LyVkea~VDEG   80 (311)
T PRK12279          1 MTNKVIQRNIHISHRKASLVIDLVRNKPVHEAIRILSNTPKKFAPIVLKLLNSAISNVQHNSKDMDPSKLYIYKIVANQG   80 (311)
T ss_pred             CCCEEEECCCEECHHHHHHHHHHHCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEEEEECCC
T ss_conf             96054525534167899999998879979999999840843236999999999999998610389867849999997888


Q ss_pred             CEEEEEEECCCCCCCCEECCCCEEEEEEEECCCCCC
Q ss_conf             114201025666637201785008999985172332
Q gi|254780256|r   94 VFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDEGK  129 (131)
Q Consensus        94 ~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~~k  129 (131)
                      |++|||+|||||||++|+||||||||||++..+|.+
T Consensus        81 PTLKRfrPRArGRA~rIrKRTSHITIVLSDDvner~  116 (311)
T PRK12279         81 PTMKRTLPRAKGSADQLFKRTTHLEIVLSDDVNERE  116 (311)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCHHH
T ss_conf             720143703268634301566767999788865557


No 2  
>CHL00034 rpl22 ribosomal protein L22
Probab=100.00  E-value=1.6e-43  Score=277.30  Aligned_cols=111  Identities=34%  Similarity=0.477  Sum_probs=109.2

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCE
Q ss_conf             23112148750889999999984798699999888658202479999999999999984059982336999999889811
Q gi|254780256|r   16 EANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVF   95 (131)
Q Consensus        16 e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~   95 (131)
                      |++|.+||+|+||+|+|+|+|+|||++|++|++||+|+|+++|.+|+|+|+||++||+||+|+|+|+|||+++|||+||+
T Consensus         1 E~~A~~r~ir~SprK~r~v~~~IRG~~v~~Al~~L~f~~kk~A~~i~K~l~SAvaNA~~n~~~d~~~L~V~~~~v~~G~~   80 (112)
T CHL00034          1 EVYALAKYIRMSPHKVRRVIDQIRGRSYEEALMILEFMPYRACYPILKLVYSAAANASHNMGLNKANLFISKAEVDEGPT   80 (112)
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCCCHHEEEEEEEECCCCC
T ss_conf             94898087623879999999998699199999997118633699999999999999984616881114999999899970


Q ss_pred             EEEEEECCCCCCCCEECCCCEEEEEEEECCC
Q ss_conf             4201025666637201785008999985172
Q gi|254780256|r   96 MKRFHCRGRQRIGRIVRPFSRLTVIVREVSD  126 (131)
Q Consensus        96 ~KR~~prarGRa~~i~k~~sHi~VvL~e~~~  126 (131)
                      +|||+||||||+++|+||+|||+|+|+|.+.
T Consensus        81 lKR~rprarGRa~~i~K~~sHi~Vvl~e~~k  111 (112)
T CHL00034         81 LKRFRPRAQGRSYPIKKPTCHITIVLKDISK  111 (112)
T ss_pred             CCCCCCHHCCCCCCCCCCCCEEEEEEEECCC
T ss_conf             1202841048866562553039999986547


No 3  
>PRK00565 rplV 50S ribosomal protein L22; Reviewed
Probab=100.00  E-value=7.4e-43  Score=273.38  Aligned_cols=111  Identities=51%  Similarity=0.697  Sum_probs=108.9

Q ss_pred             HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCC
Q ss_conf             12311214875088999999998479869999988865820247999999999999998405998233699999988981
Q gi|254780256|r   15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSV   94 (131)
Q Consensus        15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~   94 (131)
                      +|++|.+||+|+||+|+++|+|+|||++|+||+.||+|+|+++|.+|.|+|+||++||++|+|+|+|+|||+++|||+||
T Consensus         1 m~~~A~~k~ir~Sp~K~r~v~~~IrG~~v~eAl~~L~f~~kkaA~~i~k~L~SA~aNA~~~~~ld~~~L~I~~~~v~~G~   80 (111)
T PRK00565          1 MEAKAKARFVRISPRKARLVADLIRGKKVEEALAILKFSPKKAARLVKKVLKSAIANAENNHGLDIDELVVKEAFVDEGP   80 (111)
T ss_pred             CEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEECCCC
T ss_conf             91798718775488999999999869919999999821972047899999999999998602687010599999989998


Q ss_pred             EEEEEEECCCCCCCCEECCCCEEEEEEEECC
Q ss_conf             1420102566663720178500899998517
Q gi|254780256|r   95 FMKRFHCRGRQRIGRIVRPFSRLTVIVREVS  125 (131)
Q Consensus        95 ~~KR~~prarGRa~~i~k~~sHi~VvL~e~~  125 (131)
                      ++|||+||||||+++++||+|||+|+|+|.+
T Consensus        81 ~lKR~~prarGRa~~i~k~~sHi~vvL~e~~  111 (111)
T PRK00565         81 TLKRFRPRARGRASRIRKRTSHITVVVSERK  111 (111)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCEEEEEECCC
T ss_conf             2567698536898874488656899994389


No 4  
>TIGR01044 rplV_bact ribosomal protein L22; InterPro: IPR005727   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 model decribes bacterial and chloroplast ribosomal protein L22; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=100.00  E-value=1.5e-42  Score=271.51  Aligned_cols=103  Identities=44%  Similarity=0.636  Sum_probs=101.3

Q ss_pred             EECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEE
Q ss_conf             12148750889999999984798699999888658202479999999999999984059982336999999889811420
Q gi|254780256|r   19 AIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKR   98 (131)
Q Consensus        19 A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR   98 (131)
                      |.+|++|+||+|+|+|+|+||||+|.+||.+|+|+|+++|.+|.|+|.||+||||||+|+|+++|.|.++|||+||++||
T Consensus         1 A~~R~vR~sp~KARLV~DLirGk~v~~Al~iL~~tP~~Aa~~~~KVl~SA~ANAehN~~~D~~~L~v~~~~vD~GP~lkR   80 (103)
T TIGR01044         1 AKARFVRISPRKARLVADLIRGKSVAEALDILRFTPKKAAELIKKVLASAIANAEHNNGLDADNLVVVTIFVDEGPTLKR   80 (103)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCEEEEEEEECCCCCCCC
T ss_conf             98751021444788898873574778899987307040137899999998763205654582231587788778496000


Q ss_pred             EEECCCCCCCCEECCCCEEEEEE
Q ss_conf             10256666372017850089999
Q gi|254780256|r   99 FHCRGRQRIGRIVRPFSRLTVIV  121 (131)
Q Consensus        99 ~~prarGRa~~i~k~~sHi~VvL  121 (131)
                      |+|||+|||..|+|+||||||++
T Consensus        81 ~~PRA~GRA~~I~KrTSHi~V~V  103 (103)
T TIGR01044        81 IRPRAKGRASRIRKRTSHITVVV  103 (103)
T ss_pred             CCCHHCCCHHHCCCCCCCEEEEC
T ss_conf             13000240331268876446528


No 5  
>COG0091 RplV Ribosomal protein L22 [Translation, ribosomal structure and biogenesis]
Probab=100.00  E-value=7.8e-41  Score=261.43  Aligned_cols=113  Identities=51%  Similarity=0.648  Sum_probs=110.9

Q ss_pred             HHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECC
Q ss_conf             01123112148750889999999984798699999888658202479999999999999984059982336999999889
Q gi|254780256|r   13 GDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGK   92 (131)
Q Consensus        13 ~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~   92 (131)
                      ++++++|.++++|+||+|+++|+++|||+++++|+.+|+|+|+|+|+.|.|+|.||++||++|+|||+|+|||++||||+
T Consensus         7 ~~~~akA~~r~~riSpkk~r~Va~~IrG~~v~~A~~~L~~~pkKaa~~v~KvL~sA~aNAe~n~gLd~d~L~V~~i~v~~   86 (120)
T COG0091           7 PEMEAKAKARYLRISPKKARLVADLIRGKKVAEALAILEFVPKKAAKLVKKVLESAIANAENNKGLDPDKLVVSHIAVDK   86 (120)
T ss_pred             HHHHHHHHHCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECC
T ss_conf             03667764123767868999999998399499999999867488899999999999965775149986787999998478


Q ss_pred             CCEEEEEEECCCCCCCCEECCCCEEEEEEEECC
Q ss_conf             811420102566663720178500899998517
Q gi|254780256|r   93 SVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVS  125 (131)
Q Consensus        93 G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~  125 (131)
                      ||++|||+|||+||++++.+|+|||||||+|.+
T Consensus        87 gp~lKR~~pRA~GRa~~i~k~tshItvvv~e~~  119 (120)
T COG0091          87 GPVLKRFMPRARGRATRINKRTSHITVVVREKE  119 (120)
T ss_pred             CCEEEEECCCCCCCCCCCCCCCCEEEEEEEECC
T ss_conf             842220134136765632478700899996068


No 6  
>pfam00237 Ribosomal_L22 Ribosomal protein L22p/L17e. This family includes L22 from prokaryotes and chloroplasts and L17 from eukaryotes.
Probab=100.00  E-value=2e-39  Score=253.07  Aligned_cols=105  Identities=48%  Similarity=0.632  Sum_probs=103.2

Q ss_pred             EECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEE
Q ss_conf             12148750889999999984798699999888658202479999999999999984059982336999999889811420
Q gi|254780256|r   19 AIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKR   98 (131)
Q Consensus        19 A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR   98 (131)
                      |.++|+++||+|+++|+++||||+|++|++||+|+|+|+|.+|.|+|+||++||++++|+|+|+|||+++|||+||++||
T Consensus         1 A~~r~ir~S~kK~r~v~~~Irg~~v~~A~~~L~~~p~kaa~~i~k~L~sA~aNA~~~~~~d~~~L~I~~~~v~~g~~~KR   80 (105)
T pfam00237         1 AVARYIRISPKKARLVADLIRGKSVEEALAILEFVPKKAAKIILKLLKSAVANAENNKGLDPDNLYIKEIFVDKGPTLKR   80 (105)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCCCCC
T ss_conf             96153614889999999998699199999998319876899999999999998987036885684999999834870557


Q ss_pred             EEECCCCCCCCEECCCCEEEEEEEE
Q ss_conf             1025666637201785008999985
Q gi|254780256|r   99 FHCRGRQRIGRIVRPFSRLTVIVRE  123 (131)
Q Consensus        99 ~~prarGRa~~i~k~~sHi~VvL~e  123 (131)
                      ++||||||++++++|+|||+|+|+|
T Consensus        81 ~~prarGRa~~i~k~~~Hi~vvl~e  105 (105)
T pfam00237        81 FRPRARGRATPIRKRTSHITIVLSE  105 (105)
T ss_pred             CCCCCCCCCCCCCCCCCCEEEEEEC
T ss_conf             7857788887753796018999829


No 7  
>cd00336 Ribosomal_L22 Ribosomal protein L22/L17e.  L22 (L17 in eukaryotes) is a core protein of the large ribosomal subunit.  It is the only ribosomal protein that interacts with all six domains of 23S rRNA, and is one of the proteins important for directing the proper folding and stabilizing the conformation of 23S rRNA.  L22 is the largest protein contributor to the surface of the polypeptide exit channel, the tunnel through which the polypeptide product passes.  L22 is also one of six proteins located at the putative translocon binding site on the exterior surface of the ribosome.
Probab=100.00  E-value=7.2e-37  Score=238.06  Aligned_cols=105  Identities=43%  Similarity=0.495  Sum_probs=103.0

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEE
Q ss_conf             31121487508899999999847986999998886582024799999999999999840599823369999998898114
Q gi|254780256|r   17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFM   96 (131)
Q Consensus        17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~   96 (131)
                      ++|.++|+++||+|+++|+++||||+|++|+.||+|+|+++|..|.++|+||.+||++++++|+|+|||+++|||+||++
T Consensus         1 ~ka~~~~ir~S~kK~~~v~~~IrG~~v~~A~~~L~~~~~k~a~~i~k~l~sa~~nA~~~~~~d~~~L~I~~~~v~~G~~~   80 (105)
T cd00336           1 AKAKGRYLRISPKKARLVARLIRGMSVDEALAQLEFVPKKAAKIILKLLKSAEANAENNGLDDPDKLYIKHIQVNKGPTL   80 (105)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCCHHHEEEEEEEEECCCCC
T ss_conf             92202776057899999999986991999999986688518999999999999989982699857849999999048715


Q ss_pred             EEEEECCCCCCCCEECCCCEEEEEE
Q ss_conf             2010256666372017850089999
Q gi|254780256|r   97 KRFHCRGRQRIGRIVRPFSRLTVIV  121 (131)
Q Consensus        97 KR~~prarGRa~~i~k~~sHi~VvL  121 (131)
                      ||++||||||++++++++|||+|+|
T Consensus        81 kr~~~rarGR~~~~~k~~~hi~vvl  105 (105)
T cd00336          81 KRRRPRARGRANPIRKRTCHITVVL  105 (105)
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEC
T ss_conf             6768777888888626850389969


No 8  
>PRK04223 rpl22p 50S ribosomal protein L22P; Reviewed
Probab=100.00  E-value=1.3e-35  Score=230.71  Aligned_cols=119  Identities=29%  Similarity=0.291  Sum_probs=111.5

Q ss_pred             HHHHHHHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHC-------------------------------C
Q ss_conf             576742101123112148750889999999984798699999888658-------------------------------2
Q gi|254780256|r    6 SVSKRRMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFS-------------------------------R   54 (131)
Q Consensus         6 ~~~~~~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~-------------------------------~   54 (131)
                      .++-...+++.++|.++++|+||+|+++||++||||++++|+.+|++.                               |
T Consensus         5 ~Ys~~~d~~k~akA~~~~lriS~K~~~eva~~IrGm~~~~A~~~L~~Vi~~k~~VPf~r~~~~vghr~~~~~~~~~GR~P   84 (154)
T PRK04223          5 KYSVEIDPEKTAKAMGRELPISPKHSVEIAREIRGMKLDEAKAYLEDVIALKRPVPFKRHNKKVGHRKGIWAGWKAGRYP   84 (154)
T ss_pred             ECCCCCCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             03778998622467516774056999999999869909999999999875044302574158766542212478877680


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECC
Q ss_conf             02479999999999999984059982336999999889811420102566663720178500899998517
Q gi|254780256|r   55 KRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVS  125 (131)
Q Consensus        55 kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~  125 (131)
                      +|+|+.|.|+|+||.+||+++ |||+|+|||.+++||+||++||++|||+||++++++++|||+|||+|..
T Consensus        85 ~Kaa~~ilklL~sA~aNA~~k-glD~d~L~I~~i~v~~G~~~kR~~pRA~GRa~~~~k~~~HIeivl~E~~  154 (154)
T PRK04223         85 VKAAKAILKLLENAENNAEYK-GLDTEKLVIVHIAAHKGRVIKRYMPRAFGRATPKNTETVHIEVIVEEVR  154 (154)
T ss_pred             HHHHHHHHHHHHHHHHHHHHC-CCCCHHEEEEEEEECCCCEECCCCCCCCCCCCCCCCCCCCEEEEEEECC
T ss_conf             889999999999999778754-9980133999999688842015573237887875589844799998439


No 9  
>TIGR01038 L22_arch ribosomal protein L22; InterPro: IPR005721   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 family describes the ribosomal protein of the eukaryotic cytosol and of the Archaea, variously designated as L17, L22, and L23.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0015934 large ribosomal subunit.
Probab=99.97  E-value=1.9e-31  Score=206.07  Aligned_cols=115  Identities=26%  Similarity=0.268  Sum_probs=108.1

Q ss_pred             HHHHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHC---------------------------------CC
Q ss_conf             742101123112148750889999999984798699999888658---------------------------------20
Q gi|254780256|r    9 KRRMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFS---------------------------------RK   55 (131)
Q Consensus         9 ~~~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~---------------------------------~k   55 (131)
                      +...+++.++|.++|+++|||-++.||+.|+||.++||.-+|+=.                                 |.
T Consensus         4 ~~~d~~k~A~A~G~~l~iS~K~a~E~craI~Gm~l~~A~KYLe~Vi~~~raVPFRR~~~kvGhr~G~ak~~Gw~~GRYP~   83 (151)
T TIGR01038         4 KPEDESKSAKARGRNLRISFKHAREICRAIRGMKLEEARKYLEDVIEMKRAVPFRRYNKKVGHRRGLAKKWGWTAGRYPV   83 (151)
T ss_pred             CCCCHHHHHHHHCCCCCCCCCHHHHHHHHHCCCCHHHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCH
T ss_conf             88873343431026786465547899987369636888888999998608852020167613577761205777888607


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEEC
Q ss_conf             247999999999999998405998233699999988981142010256666372017850089999851
Q gi|254780256|r   56 RIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREV  124 (131)
Q Consensus        56 k~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~  124 (131)
                      |+|+.|.|+|..|.||||++ |||+|+|+|.+|.|++||+++|+.|||.||++|....+|||.|||+|.
T Consensus        84 KaAk~~lk~L~NaeANAE~K-GLD~ekL~I~Hi~~~kGp~~rR~~PRAfGRaTP~~~~~~HIE~v~~E~  151 (151)
T TIGR01038        84 KAAKFILKVLQNAEANAEYK-GLDVEKLKIIHIQANKGPVIRRWMPRAFGRATPYNSSTTHIELVVEEK  151 (151)
T ss_pred             HHHHHHHHHHHHHHHHHHHC-CCCCCCCEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEEC
T ss_conf             89999999999999888752-899642678887414885023558742133078898971588775529


No 10 
>KOG1711 consensus
Probab=99.97  E-value=2.4e-31  Score=205.53  Aligned_cols=113  Identities=42%  Similarity=0.564  Sum_probs=109.0

Q ss_pred             HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCHHHEEE-EEEEECCC
Q ss_conf             12311214875088999999998479869999988865820247999999999999998405998233699-99998898
Q gi|254780256|r   15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENNHDLDVDRLIV-SEAYVGKS   93 (131)
Q Consensus        15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I-~~~~v~~G   93 (131)
                      .|+.|..+.|++||+||+++|++|+||+|++||.||+|+++|+|.+|+++|.||.+||.+|+|+|+++|+| +++|+++|
T Consensus        70 ~eVya~~~~Ik~S~kK~~~l~~lirgm~v~~AL~Ql~~s~kK~a~~i~~~l~~A~~nA~~~~gl~~~~l~v~~~~t~~~g  149 (218)
T KOG1711          70 PEVYACSKSIKSSPKKVWLLARLIRGMSVEEALMQLEFSDKKAAKTIAEVLLSARANAVHNHGLDPDSLLVVAEATVGQG  149 (218)
T ss_pred             HHHHHHHHHHHHCHHHHHHHHHHHCCCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCC
T ss_conf             66899999986288999999999839979999987522067888999999999876557751999622279875103530


Q ss_pred             CEEEEEEECCCCCCCCEECCCCEEEEEEEECCCC
Q ss_conf             1142010256666372017850089999851723
Q gi|254780256|r   94 VFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDE  127 (131)
Q Consensus        94 ~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~  127 (131)
                      .++||.+++||||-++|++++|||+|+|.|.++.
T Consensus       150 ~~~Krl~~hargr~~ii~~~yvhi~v~L~e~s~~  183 (218)
T KOG1711         150 NELKRLKVHARGRFGIIRRPYVHIFVKLEEGSPP  183 (218)
T ss_pred             HHHHHEEEECCCCCCCEECCCEEEEEEEEECCCC
T ss_conf             2444302213676541001314589998306876


No 11 
>PTZ00178 60S ribosomal protein L22/L17e; Provisional
Probab=99.94  E-value=5.3e-27  Score=179.84  Aligned_cols=120  Identities=24%  Similarity=0.232  Sum_probs=110.5

Q ss_pred             HHHHHHHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHC--------------------------------C
Q ss_conf             76742101123112148750889999999984798699999888658--------------------------------2
Q gi|254780256|r    7 VSKRRMGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFS--------------------------------R   54 (131)
Q Consensus         7 ~~~~~~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~--------------------------------~   54 (131)
                      ......+++.++|...++++|++.++.+|+.|+||++++|..+|+-.                                |
T Consensus         5 s~~~~~p~k~aKArg~~lrVsfK~t~Eia~aIkGm~l~kA~~yLe~Vi~~K~~VPFrRyn~gvg~~~q~k~~g~~~GRwP   84 (177)
T PTZ00178          5 ARKPSVSSKSAKAKGSDLRVHFKNTYETARAIKGMTLRKAQQYLQDVLAKKRCVPFRRFNGGVGRTAQAKEFGQTQGRWP   84 (177)
T ss_pred             CCCCCCCCHHHHHCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCEEEEEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf             57989930445632678854406399999998498799999999999864350357874598877565221589877682


Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECCCC
Q ss_conf             0247999999999999998405998233699999988981142010256666372017850089999851723
Q gi|254780256|r   55 KRIAGEVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVSDE  127 (131)
Q Consensus        55 kk~A~~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~~~  127 (131)
                      +|+|+.|.++|++|.+||+. .|||+|+|+|.++.|++||.++|+.|||+||++|+..++|||+++|.|.++.
T Consensus        85 ~Ksa~~iL~lLkna~aNAe~-kGLD~d~L~I~hi~vnka~~~rrr~~RAhGRi~p~~s~p~hIeiil~E~~~~  156 (177)
T PTZ00178         85 EKSVVFVLSLLKNAEANAEV-KGLDPEKLVIKHVQVNRAPRGRRRTYRAHGRINPFMSSPCHVELIAAEKDER  156 (177)
T ss_pred             HHHHHHHHHHHHHHHHCCCC-CCCCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCC
T ss_conf             89999999999756740140-4887665389998863464224767654776677769980289997146555


No 12 
>KOG3353 consensus
Probab=99.11  E-value=8.4e-13  Score=96.10  Aligned_cols=113  Identities=27%  Similarity=0.237  Sum_probs=103.3

Q ss_pred             HHHHEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHC--------------------------------CCHHHH
Q ss_conf             101123112148750889999999984798699999888658--------------------------------202479
Q gi|254780256|r   12 MGDNEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFS--------------------------------RKRIAG   59 (131)
Q Consensus        12 ~~~~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~--------------------------------~kk~A~   59 (131)
                      ..++..+|...+++.+.+..+..+..|++++...|+..|.-.                                |+++|.
T Consensus         4 ~~~k~~karg~~lrv~fKn~r~~~~~i~~~~~~~a~~~l~~v~~~~~c~p~~~~~~g~g~~~q~k~~~~~~~rwpkksae   83 (175)
T KOG3353           4 NPTKSCKARGSNLRVHFKNTRETAQTIKCMELLKATVYLKDVILQKICVPFRRYNGGVGRTAQAKQWGWTQGRWPKKSAE   83 (175)
T ss_pred             CCCHHHHCCCCCEEEEECCCCCCCHHCCCCCCCCCEEEECCCHHHCCCCCCEECCCCCCCCCHHHHHCCCCCCCCCHHHH
T ss_conf             33222302655278873257644100047650222343212012200234145589868643223302354766423889


Q ss_pred             HHHHHHHHHHHHHHHCCCCCHHHEEEEEEEECCCCEEEEEEECCCCCCCCEECCCCEEEEEEEECC
Q ss_conf             999999999999984059982336999999889811420102566663720178500899998517
Q gi|254780256|r   60 EVRKTLCSAVANAENNHDLDVDRLIVSEAYVGKSVFMKRFHCRGRQRIGRIVRPFSRLTVIVREVS  125 (131)
Q Consensus        60 ~i~k~L~SA~aNA~~n~~ld~~~L~I~~~~v~~G~~~KR~~prarGRa~~i~k~~sHi~VvL~e~~  125 (131)
                      .+.-.|+.|.+||+.+ |+|.|.|+|.++.|++.|.+.|-.+||.||..++-.-.|||.+||.|.+
T Consensus        84 fll~~LkN~esnaElk-gldVDsLvIehiqvnkApKm~~rtyraHg~in~y~ssP~hie~il~~ke  148 (175)
T KOG3353          84 FLLHMLKNAESNAELK-GLDVDSLVIEHIQVNKAPKMRRRTYRAHGRINPYMSSPCHIEMILTEKE  148 (175)
T ss_pred             HHHHHHHHHHHCCCCC-CCCCCEEEEEEHHHHCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHC
T ss_conf             8899987366242113-7676646743013302413666788753532565688699999997531


No 13 
>PRK11325 scaffold protein; Provisional
Probab=67.55  E-value=11  Score=18.79  Aligned_cols=60  Identities=18%  Similarity=0.197  Sum_probs=44.4

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHH--------HHHC--CCHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             311214875088999999998479869999988--------8658--20247999999999999998405
Q gi|254780256|r   17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALAD--------LEFS--RKRIAGEVRKTLCSAVANAENNH   76 (131)
Q Consensus        17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~--------L~f~--~kk~A~~i~k~L~SA~aNA~~n~   76 (131)
                      ++-.+..--+|--=.-.++.++.|++++||+.+        |.+.  ..+.|.+-.++|+.|+.+.+.+.
T Consensus        56 ~~F~~~GC~is~AsaS~~te~~~Gkt~~ea~~i~~~~i~e~l~lpp~r~~CA~La~~aL~~Ai~~y~~kq  125 (127)
T PRK11325         56 AKFKTYGCGSAIASSSLVTEWVKGKTLDEALAIKNTDIAEELALPPVKIHCSILAEDAIKAAIADYKSKQ  125 (127)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8897128589999999999998399799998555688998617993101799999999999999999850


No 14 
>TIGR03419 NifU_clost FeS cluster assembly scaffold protein NifU, Clostridium type. NifU and NifS form a pair of iron-sulfur (FeS) cluster biosynthesis proteins much simpler than the ISC and SUF systems. Members of this protein family are a distinct group of NifU-like proteins, found always to a NifS-like protein and restricted to species that lack a SUF system. Typically, NIF systems service a smaller number of FeS-containing proteins than do ISC or SUF. Members of this particular branch typically are found, almost half the time, near the mnmA gene, involved in the carboxymethylaminomethyl modification of U34 in some tRNAs (see GenProp0704). While other NifU proteins are associated with nitrogen fixation, this family is not.
Probab=66.69  E-value=11  Score=18.69  Aligned_cols=61  Identities=10%  Similarity=0.117  Sum_probs=45.1

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHH---------H--CCCHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             31121487508899999999847986999998886---------5--8202479999999999999984059
Q gi|254780256|r   17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLE---------F--SRKRIAGEVRKTLCSAVANAENNHD   77 (131)
Q Consensus        17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~---------f--~~kk~A~~i~k~L~SA~aNA~~n~~   77 (131)
                      ++-.+..--+|.==.-.++++|+|++++||+.+-.         +  ...+.|.+-..+|+.|+.+.+.+.|
T Consensus        50 i~F~~~GCais~AsaS~~~e~i~Gk~l~ea~~i~~~~i~~~l~~lpp~r~~CA~La~~Al~~Al~~y~~k~g  121 (121)
T TIGR03419        50 VKFKTFGCGAAIASSSMATEMIKGKTLEEAWELTNKAVAEALDGLPPVKMHCSVLAEEAIHKAINDYREKNG  121 (121)
T ss_pred             EEEEEECCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999965558899999999999849949999863548999997599931166999999999999999987269


No 15 
>TIGR02871 spore_ylbJ sporulation integral membrane protein YlbJ; InterPro: IPR014226   Members of this entry include YlbJ, from Bacillus subtilis. They are found exclusively in the Firmicutes (low-GC Gram-positive bacteria) and are known from studies in B. subtilis to be part of the sigma-E regulon . Mutation leads to a sporulation defect, confirming that members of this entry are involved in sporulation. The protein appears to be universal among endospore-forming bacteria, and in Symbiobacterium thermophilum IAM 14863, there are two ORFs encoding YlbJ that are distant from each other..
Probab=55.35  E-value=9.9  Score=19.00  Aligned_cols=39  Identities=26%  Similarity=0.215  Sum_probs=33.8

Q ss_pred             HHCCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHC
Q ss_conf             847986999998886582024799999999999999840
Q gi|254780256|r   37 MIRGKRVSDALADLEFSRKRIAGEVRKTLCSAVANAENN   75 (131)
Q Consensus        37 ~IrG~~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~~n   75 (131)
                      .++--++.+|+.-+.-..-+.-..+.++|++|+.||.++
T Consensus       174 ~~~~fS~~~AL~~l~~~~~~s~~~~G~~L~~aie~av~t  212 (384)
T TIGR02871       174 KKTEFSLKDALTGLHSIRLKSKKNIGKLLKEAIENAVKT  212 (384)
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             687665788988783235406788768999999999999


No 16 
>TIGR01994 SUF_scaf_2 SUF system FeS assembly protein, NifU family; InterPro: IPR011341   Iron-sulphur (FeS) clusters are important cofactors for numerous proteins involved in electron transfer, in redox and non-redox catalysis, in gene regulation, and as sensors of oxygen and iron. These functions depend on the various FeS cluster prosthetic groups, the most common being [2Fe-2S] and [4Fe-4S] . FeS cluster assembly is a complex process involving the mobilisation of Fe and S atoms from storage sources, their assembly into [Fe-S] form, their transport to specific cellular locations, and their transfer to recipient apoproteins. So far, three FeS assembly machineries have been identified, which are capable of synthesising all types of [Fe-S] clusters: ISC (iron-sulphur cluster), SUF (sulphur assimilation), and NIF (nitrogen fixation) systems.   The ISC system is conserved in eubacteria and eukaryotes (mitochondria), and has broad specificity, targeting general FeS proteins , . It is encoded by the isc operon (iscRSUA-hscBA-fdx-iscX). IscS is a cysteine desulphurase, which obtains S from cysteine (converting it to alanine) and serves as a S donor for FeS cluster assembly. IscU and IscA act as scaffolds to accept S and Fe atoms, assembling clusters and transfering them to recipient apoproteins. HscA is a molecular chaperone and HscB is a co-chaperone. Fdx is a [2Fe-2S]-type ferredoxin. IscR is a transcription factor that regulates expression of the isc operon. IscX (also known as YfhJ) appears to interact with IscS and may function as an Fe donor during cluster assembly .   The SUF system is an alternative pathway to the ISC system that operates under iron starvation and oxidative stress. It is found in eubacteria, archaea and eukaryotes (plastids). The SUF system is encoded by the suf operon (sufABCDSE), and the six encoded proteins are arranged into two complexes (SufSE and SufBCD) and one protein (SufA). SufS is a pyridoxal-phosphate (PLP) protein displaying cysteine desulphurase activity. SufE acts as a scaffold protein that accepts S from SufS and donates it to SufA . SufC is an ATPase with an unorthodox ATP-binding cassette (ABC)-like component. No specific functions have been assigned to SufB and SufD. SufA is homologous to IscA , acting as a scaffold protein in which Fe and S atoms are assembled into [FeS] cluster forms, which can then easily be transferred to apoproteins targets.   In the NIF system, NifS and NifU are required for the formation of metalloclusters of nitrogenase in Azotobacter vinelandii, and other organisms, as well as in the maturation of other FeS proteins. Nitrogenase catalyses the fixation of nitrogen. It contains a complex cluster, the FeMo cofactor, which contains molybdenum, Fe and S. NifS is a cysteine desulphurase. NifU binds one Fe atom at its N-terminal, assembling an FeS cluster that is transferred to nitrogenase apoproteins . Nif proteins involved in the formation of FeS clusters can also be found in organisms that do not fix nitrogen .   This family represents SufU, NifU-like proteins that are part of the SUF system, one of the two different proteins proposed to act as a scaffold on which the Fe-S cluster is built and from which it is transferred.; GO: 0005506 iron ion binding, 0005515 protein binding, 0051536 iron-sulfur cluster binding, 0016226 iron-sulfur cluster assembly.
Probab=36.82  E-value=35  Score=15.74  Aligned_cols=35  Identities=23%  Similarity=0.305  Sum_probs=25.8

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHH
Q ss_conf             31121487508899999999847986999998886
Q gi|254780256|r   17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLE   51 (131)
Q Consensus        17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~   51 (131)
                      ++=....--||.==+-.++++|+|++|.||+..-+
T Consensus        55 ~~F~G~GCsIS~ASaSmM~e~i~Gk~~~eA~~~~~   89 (139)
T TIGR01994        55 IAFEGEGCSISQASASMMTELIKGKTVEEALKLVE   89 (139)
T ss_pred             EEEECCCCHHHHHHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             88735767089988999999745989889999999


No 17 
>pfam01024 Colicin Colicin pore forming domain.
Probab=35.77  E-value=37  Score=15.64  Aligned_cols=45  Identities=27%  Similarity=0.289  Sum_probs=28.4

Q ss_pred             HHHHHHHHHHCCC---CHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999984798---69999988865820247999999999999998
Q gi|254780256|r   29 QKLNLVAAMIRGK---RVSDALADLEFSRKRIAGEVRKTLCSAVANAE   73 (131)
Q Consensus        29 ~K~r~va~~IrG~---~v~eAl~~L~f~~kk~A~~i~k~L~SA~aNA~   73 (131)
                      +=.+.+++.++|+   +++||+..++=...-...-+-+.=+.|+.||-
T Consensus        36 ~lA~elA~~~KGKkIRn~~dAl~s~eK~~~n~nkK~~~~Dr~AI~nAl   83 (187)
T pfam01024        36 KLARELADDAKGKKIRSVDEALASFEKYKANLNKKINAADRDAIANAL   83 (187)
T ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCHHCCHHHHHHHHHHH
T ss_conf             999999987067713789999999999872820214561199999999


No 18 
>pfam01592 NifU_N NifU-like N terminal domain. This domain is found in NifU in combination with pfam01106. This domain is found on isolated in several bacterial species. The nif genes are responsible for nitrogen fixation. However this domain is found in bacteria that do not fix nitrogen, so it may have a broader significance in the cell than nitrogen fixation. These proteins appear to be scaffold proteins for iron-sulfur clusters.
Probab=32.99  E-value=41  Score=15.37  Aligned_cols=57  Identities=16%  Similarity=0.093  Sum_probs=40.3

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHH-----HH------CCCHHHHHHHHHHHHHHHHHH
Q ss_conf             3112148750889999999984798699999888-----65------820247999999999999998
Q gi|254780256|r   17 ANAIASMLRVSPQKLNLVAAMIRGKRVSDALADL-----EF------SRKRIAGEVRKTLCSAVANAE   73 (131)
Q Consensus        17 ~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L-----~f------~~kk~A~~i~k~L~SA~aNA~   73 (131)
                      ++-.+..--+|-==+-.+++++.|++++||..+-     ++      ...+.+.+-..+|++|+.+-.
T Consensus        53 i~F~~~GCais~AsaS~l~e~i~Gk~~~ea~~i~~~~i~~~lg~l~~~r~~Ca~La~~al~~av~~y~  120 (126)
T pfam01592        53 AKFKTFGCGSAIASSSALTELVKGKTLDEALKITNTDIAEELGGLPPVKMHCSVLGDDALKAAIADYK  120 (126)
T ss_pred             EEEEEECCHHHHHHHHHHHHHHCCCCHHHHHHCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             89986376888999999999986993999986169999999737999740089999999999999817


No 19 
>TIGR01803 CM-like chorismate mutase related enzymes; InterPro: IPR008241   Isochorismate pyruvate-lyase (IPL; PchB) catalyses the second reaction in the pyochelin biosynthetic pathway of Pseudomonas aeruginosa, conversion of isochorismate to salicylate plus pyruvate (following the initial PchA-dependent conversion of chorismate to isochorismate) . This enzyme can also carry out the chorismate mutase (CM) reaction, but with a low catalytic efficiency. It is unlikely that PchB plays a significant role in aromatic amino acid biosynthesis. This enzyme is a stand-alone version of a chorismate mutase domain of the AroQ class.   The three types of CM are AroQ class, Prokaryotic type (e.g., IPR008239 from INTERPRO and others); AroQ class, Eukaryotic type (IPR008238 from INTERPRO); and AroH class (IPR008243 from INTERPRO). They fall into two structural folds (AroQ class and AroH class) which are completely unrelated . The two types of the AroQ structural class (the Escherichia coli CM dimer and the yeast CM monomer) can be structurally superimposed, and the topology of the four-helix bundle forming the active site is conserved .   The PchB-type of chorismate mutase domain, while sharing conserved residues and the predicted secondary structure with the other subgroups of the AroQ class (Prokaryotic type), has isochorismate pyruvate-lyase (IPL) as a primary catalytic activity. PchB can still use the same active site either for the IPL or for the CM reaction. It has been suggested that PchB was derived from an AroQ-class CM by a gene duplication event followed by selection for efficient IPL function in the course of the evolution of the pyochelin siderophore pathway, with only residual CM activity remaining. It can be further speculated that contemporary CMs may already possess (weak) IPL activity .   For additional information please see , , ..
Probab=27.96  E-value=47  Score=15.02  Aligned_cols=22  Identities=27%  Similarity=0.199  Sum_probs=17.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCHH
Q ss_conf             99999999999999840599823
Q gi|254780256|r   59 GEVRKTLCSAVANAENNHDLDVD   81 (131)
Q Consensus        59 ~~i~k~L~SA~aNA~~n~~ld~~   81 (131)
                      .-|..+..+|.=||+. +||||+
T Consensus        44 ~RvA~v~~naaR~A~e-~GlDp~   65 (82)
T TIGR01803        44 ERVAEVKENAARYAAE-LGLDPD   65 (82)
T ss_pred             HHHHHHHHHHHHHHHH-CCCCHH
T ss_conf             4689862877766786-389988


No 20 
>TIGR02709 branched_ptb branched-chain phosphotransacylase; InterPro: IPR014081   This entry distinguishes branched-chain phosphotransacylases like that of Enterococcus faecalis from closely related subfamilies of phosphate butyryltransferase 2.3.1.19 from EC, (IPR014079 from INTERPRO) and phosphate acetyltransferase 2.3.1.8 from EC, (IPR004614 from INTERPRO). Members of this family and of IPR014079 from INTERPRO show considerable cross reactivity, and the occurrence of a member of either family proximate to an apparent leucine dehydrogenase will suggest activity on branched chain-acyl-CoA compounds..
Probab=26.69  E-value=44  Score=15.18  Aligned_cols=25  Identities=32%  Similarity=0.474  Sum_probs=11.1

Q ss_pred             HHHHHHHHHHHHHHH---------CCCCCHHHEE
Q ss_conf             999999999999984---------0599823369
Q gi|254780256|r   60 EVRKTLCSAVANAEN---------NHDLDVDRLI   84 (131)
Q Consensus        60 ~i~k~L~SA~aNA~~---------n~~ld~~~L~   84 (131)
                      .|..+++.|...|++         |.+||.++||
T Consensus        12 eilqlvkkalkeaeqPlqfivfdtnenldtenlW   45 (271)
T TIGR02709        12 EILQLVKKALKEAEQPLQFIVFDTNENLDTENLW   45 (271)
T ss_pred             HHHHHHHHHHHHHCCCEEEEEEECCCCCCHHHHH
T ss_conf             7999999987631287068997155554512431


No 21 
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family; InterPro: IPR013430    Proteins in this entry form a distinct group of helix-turn-helix proteins, which are strictly bacterial and nearly always shorter than 110 amino acids. They include the characterised member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is encoded by the upstream member of the gene pair.; GO: 0003677 DNA binding.
Probab=20.31  E-value=64  Score=14.23  Aligned_cols=42  Identities=24%  Similarity=0.123  Sum_probs=36.6

Q ss_pred             HEEEEECCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHCCCH
Q ss_conf             123112148750889999999984798699999888658202
Q gi|254780256|r   15 NEANAIASMLRVSPQKLNLVAAMIRGKRVSDALADLEFSRKR   56 (131)
Q Consensus        15 ~e~~A~~k~ir~Sp~K~r~va~~IrG~~v~eAl~~L~f~~kk   56 (131)
                      -++.+.++.+.+|+.-+..|++.=+|.+.|-|+-.-+|.-..
T Consensus        21 ~s~~~LA~~LgVsr~~~sriv~~~~~iT~dmALRL~~~lG~s   62 (81)
T TIGR02607        21 LSVRALAKALGVSRSTLSRIVNGRRGITADMALRLAKALGTS   62 (81)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHCCCCCCHHHHHHHHHHHCCC
T ss_conf             068999987099978888887448998888999999973898


Done!