Query         gi|254780940|ref|YP_003065353.1| ribonuclease III [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 227
No_of_seqs    139 out of 3294
Neff          7.6 
Searched_HMMs 39220
Date          Mon May 30 02:29:16 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780940.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR02191 RNaseIII ribonucleas 100.0       0       0  487.5  15.7  215    9-223     1-228 (228)
  2 PRK12371 ribonuclease III; Rev 100.0       0       0  479.5  18.1  227    1-227     7-233 (235)
  3 PRK00102 rnc ribonuclease III; 100.0       0       0  443.7  17.1  221    4-224     2-226 (228)
  4 COG0571 Rnc dsRNA-specific rib 100.0       0       0  434.0  17.8  226    2-227     4-233 (235)
  5 PRK12372 ribonuclease III; Rev 100.0       0       0  431.1  16.1  216    4-222     1-219 (425)
  6 KOG1817 consensus              100.0       0       0  325.1  12.3  219    5-224   274-502 (533)
  7 smart00535 RIBOc Ribonuclease  100.0 2.5E-36 6.3E-41  243.5   6.6  127   21-148     1-127 (129)
  8 cd00593 RIBOc RIBOc. Ribonucle 100.0 6.8E-35 1.7E-39  234.7   5.3  129   21-149     1-130 (133)
  9 KOG3769 consensus               99.9 1.1E-23 2.9E-28  165.7  11.6  217    6-225    65-303 (333)
 10 pfam00636 Ribonuclease_3 RNase  99.9 1.1E-23 2.7E-28  165.8   6.8   91   41-131     1-96  (96)
 11 KOG0701 consensus               99.8 1.4E-21 3.7E-26  152.7   4.6  133    4-138   979-1174(1606)
 12 KOG0701 consensus               99.8 5.7E-20 1.4E-24  142.9   7.4  203    5-223  1370-1596(1606)
 13 KOG1817 consensus               99.8 2.8E-20 7.2E-25  144.7   4.8  135    6-140    43-232 (533)
 14 cd00048 DSRM Double-stranded R  99.6 5.2E-16 1.3E-20  118.5   7.2   68  156-223     1-68  (68)
 15 smart00358 DSRM Double-strande  99.6   2E-15 5.1E-20  114.9   7.3   67  157-224     1-67  (67)
 16 KOG3732 consensus               99.3   4E-12   1E-16   94.6   7.5   73  151-224   138-210 (339)
 17 pfam00035 dsrm Double-stranded  99.3 4.9E-12 1.3E-16   94.0   7.5   66  157-223     1-66  (66)
 18 KOG3732 consensus               99.0 5.6E-10 1.4E-14   81.4   7.0   70  155-226    38-107 (339)
 19 KOG2777 consensus               98.3 1.8E-06 4.5E-11   59.8   6.3   65  154-224    89-153 (542)
 20 KOG4334 consensus               98.1 1.3E-06 3.2E-11   60.7   2.8   63  159-223   379-441 (650)
 21 COG1939 Ribonuclease III famil  97.8 4.8E-05 1.2E-09   51.0   5.3   98   40-143    15-127 (132)
 22 KOG2334 consensus               95.2  0.0064 1.6E-07   37.9   0.8  138   75-227   299-444 (477)
 23 KOG3792 consensus               92.3   0.058 1.5E-06   32.0   1.2   48  177-225   396-443 (816)
 24 KOG3792 consensus               91.5    0.22 5.5E-06   28.5   3.4   49  174-223   520-569 (816)
 25 pfam03368 dsRNA_bind Double st  87.2     2.1 5.2E-05   22.5   5.8   63  158-226     2-77  (91)
 26 pfam11469 DUF3204 Protein of u  79.1     4.8 0.00012   20.2   4.9   84   43-145     3-90  (120)
 27 PRK07009 consensus              58.3     8.2 0.00021   18.8   2.4   82   40-126    75-172 (241)
 28 PRK06859 consensus              53.7     8.4 0.00021   18.8   1.8   82   40-126    83-180 (253)
 29 KOG2783 consensus               51.9     4.5 0.00012   20.4   0.2   42  158-199   231-272 (436)
 30 TIGR01854 lipid_A_lpxH UDP-2,3  48.8     3.3 8.4E-05   21.3  -0.9   52   58-140     8-59  (241)
 31 PRK13184 pknD serine/threonine  47.0      21 0.00055   16.2   3.1   38   41-80    551-597 (933)
 32 PRK06022 consensus              39.0      24 0.00062   15.9   2.3   80   41-125    76-169 (234)
 33 pfam04034 DUF367 Domain of unk  37.4      19 0.00048   16.6   1.5   40  109-149    61-101 (128)
 34 pfam06754 PhnG Phosphonate met  36.5      32 0.00081   15.2   4.6   36  188-223    65-102 (147)
 35 PRK06631 consensus              36.5      14 0.00035   17.4   0.7   40   81-125   136-175 (229)
 36 PRK00394 transcription factor;  34.8      34 0.00087   15.0   5.8   27  186-213   139-165 (178)
 37 TIGR02195 heptsyl_trn_II lipop  34.4      26 0.00065   15.8   1.8   24   44-67      8-31  (361)
 38 PRK08816 consensus              32.8      13 0.00034   17.5   0.2   82   40-126    75-173 (244)
 39 COG2042 Uncharacterized conser  32.0      25 0.00064   15.8   1.5   39  110-149   110-149 (179)
 40 PRK08858 consensus              31.8      22 0.00057   16.1   1.2   40   81-125   147-186 (246)
 41 PRK02287 hypothetical protein;  31.6      27 0.00068   15.7   1.5   41  108-149    99-140 (169)
 42 KOG2146 consensus               31.6      38 0.00098   14.7   3.1   73    1-81     22-110 (354)
 43 pfam11324 DUF3126 Protein of u  30.8      40   0.001   14.6   4.5   40  159-203     3-42  (63)
 44 COG4148 ModC ABC-type molybdat  30.7      19 0.00048   16.6   0.6   60    3-70     68-133 (352)
 45 cd00652 TBP_TLF TATA box bindi  30.1      41   0.001   14.5   5.5   26  187-213   138-163 (174)
 46 cd04518 TBP_archaea archaeal T  29.3      42  0.0011   14.5   5.5   27  186-213   136-162 (174)
 47 LOAD_cdc45 consensus            28.7      43  0.0011   14.4   5.5   73   61-144   338-411 (578)
 48 pfam00333 Ribosomal_S5 Ribosom  28.6      43  0.0011   14.4   6.2   39  185-223    20-62  (67)
 49 TIGR02706 P_butyryltrans phosp  28.2      44  0.0011   14.3   3.0   51   38-105   127-179 (295)
 50 pfam07125 DUF1378 Protein of u  28.0      21 0.00054   16.3   0.5   30  118-147    10-40  (59)
 51 KOG3302 consensus               27.6      45  0.0011   14.3   5.2   17  187-203   158-174 (200)
 52 TIGR02587 TIGR02587 putative i  27.5      45  0.0012   14.3   2.3   28  112-139   154-181 (284)
 53 TIGR01088 aroQ 3-dehydroquinat  26.4      18 0.00047   16.6  -0.0   18   98-116     5-22  (144)
 54 PRK05711 DNA polymerase III su  26.2      36 0.00091   14.9   1.4   40   81-125   136-175 (240)
 55 PRK10916 ADP-heptose:LPS hepto  26.2      36 0.00091   14.9   1.4   24   44-67      9-32  (348)
 56 TIGR01256 modA molybdate ABC t  25.8      42  0.0011   14.5   1.7   13  214-226   120-132 (225)
 57 PRK10422 lipopolysaccharide co  25.3      37 0.00095   14.8   1.4   10   95-104   184-193 (352)
 58 COG1737 RpiR Transcriptional r  25.2      40   0.001   14.6   1.5   44   54-97     22-66  (281)
 59 cd04516 TBP_eukaryotes eukaryo  24.8      50  0.0013   14.0   5.5   26  187-213   137-162 (174)
 60 cd01831 Endoglucanase_E_like E  24.5     9.7 0.00025   18.4  -1.7   20  199-218   145-164 (169)
 61 cd04517 TLF TBP-like factors (  24.3      52  0.0013   13.9   5.6   27  186-213   137-163 (174)
 62 pfam11940 DUF3458 Domain of un  23.5      54  0.0014   13.8   4.7   26    7-32    134-159 (408)
 63 PRK07982 consensus              22.7      29 0.00075   15.4   0.4   81   40-125    84-181 (243)
 64 pfam01418 HTH_6 Helix-turn-hel  21.8      41   0.001   14.5   1.0   41   55-97     21-64  (106)
 65 TIGR02087 LEUD_arch 3-isopropy  21.6      50  0.0013   14.0   1.4   49  161-225    27-76  (159)
 66 TIGR00677 fadh2_euk methylenet  20.7      61  0.0016   13.5   2.0   18  210-227   293-310 (312)
 67 COG0859 RfaF ADP-heptose:LPS h  20.5      49  0.0012   14.0   1.2   24   43-66      9-32  (334)
 68 pfam00352 TBP Transcription fa  20.2      62  0.0016   13.4   5.7   39  185-224    46-86  (86)
 69 PRK11557 putative DNA-binding   20.1      45  0.0011   14.3   0.9   40   55-96     21-63  (282)

No 1  
>TIGR02191 RNaseIII ribonuclease III; InterPro: IPR011907   This family consists almost exclusively of bacterial examples of ribonuclease III (RNase III). This ubiquitous enzyme specifically cleaves double-stranded rRNA and is found in all bacteria and eukaryotes . In bacteria its main role is the processing of pre-rRNAs, where the large precursor ribosomal RNA molecules are at cleaved at specific sites to produce the immediate precursors of the functional molecules. RNase III also functions in the maturation and degradation of mRNAs, and the maturaton of tRNAs. In some organisms (eg. E. coli) cells are viable without this enzyme, though they are impeded in growth, but in others (eg. B. subtilis and M. genitalium) this enzyme is essential.   The bacterial RNase III enzymes so far characterised are homodimers with a molecular mass of ~50 kDa , . The endonuclease domain is located within the N-terminal two-thirds of the protein, containing several alpha helices, but no beta strands. The double-stranded RNA binding domain is found at the C-terminal third of the protein, forming the alpha-beta(3)-alpha fold common to dsRNA-binding proteins. A signature box of 11 conserved amino acids found in the N-terminal region of RNase III may contain the active site, though this has not been proven.; GO: 0003723 RNA binding, 0004525 ribonuclease III activity, 0016075 rRNA catabolic process.
Probab=100.00  E-value=0  Score=487.46  Aligned_cols=215  Identities=45%  Similarity=0.634  Sum_probs=205.7

Q ss_pred             HHHHHCCCCCCHHHHHHHCCCHHHCCCCC-----CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             99983696589899998424612126676-----6547788745868864547877641046887899888888874433
Q gi|254780940|r    9 LEKRIGYAFANRSLLEKALTHSSISHSYQ-----ESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAET   83 (227)
Q Consensus         9 l~~~lgy~f~~~~ll~~A~th~S~~~~~~-----~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~   83 (227)
                      |+++|||+|+|+.||.+||||+||.+++.     +|||||||||||||+++||+|||++||+.+||+||++|+.|||.++
T Consensus         1 l~~~lg~~f~~~~lL~~ALTH~S~~ne~~~~~~~~~nERLEFLGDaVL~l~~~~~Lf~~~P~~~EG~Ls~~Ra~lV~~~~   80 (228)
T TIGR02191         1 LEKRLGYKFKNPELLEQALTHSSYANEHNESKKAKHNERLEFLGDAVLGLVVAEYLFKNFPDASEGELSKLRAALVSEES   80 (228)
T ss_pred             CHHHCCCCCCCHHHHHHHCCCCCHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCHHH
T ss_conf             90123888888899986201543233221146888511456788999999999999974789880258999998617488


Q ss_pred             HHHHHH-HCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCC--CCCCHHHHHCCCCCCCCC--CCC-CCCCH
Q ss_conf             454543-138772001036631237531333332669999999964155--422001221025643111--000-13452
Q gi|254780940|r   84 CSQVAR-ELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGG--IEVAGTFVDKYWKQRALK--SGK-FRRDA  157 (227)
Q Consensus        84 La~~a~-~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G--~~~~~~~i~~~~~~~~~~--~~~-~~~dp  157 (227)
                      |+.+|+ .+||++||++|++++.++++.+++||||+|||+|||||+|+|  ++.|+.||.++|.+.+..  ... ..+||
T Consensus        81 La~~A~~~~~L~~~l~LG~GE~~~gGr~r~siLaDa~EAliGAiYLD~G~e~~~a~~f~~~~~~~~~~~~~~~~~~~~D~  160 (228)
T TIGR02191        81 LAKVARKELGLGEYLLLGKGEEKSGGRRRDSILADAFEALIGAIYLDSGLELEAARKFILKLLIPRIDAIEKEEIAIKDY  160 (228)
T ss_pred             HHHHHHHHHCCCCEEEECHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             99999997188651542502543265442468999999999999841796689999999998999986655312456886


Q ss_pred             HHHHHHHHHCCCCC-CCCCCEECCCCCCCCCEEEEEEEEC-CEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             58898753202233-3343101020778884599999999-989999996898999999999999974
Q gi|254780940|r  158 KTELQEWAHAKFGV-TPEYKVTFRSGPDHDPRFTVVVEIS-GLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       158 K~~Lqe~~q~~~~~-~P~Y~~~~~~g~~~~~~f~v~v~v~-g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      ||+||||.|+++.. +|+|+++.++||+|++.|+|.|+|+ +..+|+|+|+|||+|||.||+.||++|
T Consensus       161 Kt~LQE~~Q~~~~~~~P~Y~l~~~~Gp~H~~~F~v~V~~~~~~~~g~G~G~SKKeAEQ~AA~~al~~l  228 (228)
T TIGR02191       161 KTALQEWAQARGKPELPEYRLIKEEGPDHDKEFTVEVSVNGGEPLGEGKGKSKKEAEQAAAKAALEKL  228 (228)
T ss_pred             CHHHHHHHHHCCCCCCCEEEEEECCCCCCCCEEEEEEEECCCEEEEEEEECCHHHHHHHHHHHHHHHC
T ss_conf             31789999854887672488874147889965899999738757888751776899999999999829


No 2  
>PRK12371 ribonuclease III; Reviewed
Probab=100.00  E-value=0  Score=479.54  Aligned_cols=227  Identities=55%  Similarity=0.897  Sum_probs=218.4

Q ss_pred             CCCCCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             97358899999836965898999984246121266766547788745868864547877641046887899888888874
Q gi|254780940|r    1 MSALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVS   80 (227)
Q Consensus         1 m~~~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~   80 (227)
                      |++.+++.||++|||+|+|++||.+||||+|+......|||||||||||||+++||+|||.+||+.+||+||++|+.+||
T Consensus         7 ~~~~~~~~le~~igy~F~d~~Ll~~AlTH~S~~~~~~~nyERLEFLGDaVL~lvvs~~Ly~~fP~~~EG~LT~~Rs~lV~   86 (235)
T PRK12371          7 LANKTASILEERTGHRFANKERLDRALTHSSVQAPAGGNYERLEFLGDRVLGLCVAEMLFEAFPDASEGELSVRLNALVN   86 (235)
T ss_pred             HCCCCHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHH
T ss_conf             25252999999979800888999987178686667767615553023999999999999986898883257999999971


Q ss_pred             HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCHHHH
Q ss_conf             43345454313877200103663123753133333266999999996415542200122102564311100013452588
Q gi|254780940|r   81 AETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFRRDAKTE  160 (227)
Q Consensus        81 n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~~~~~~dpK~~  160 (227)
                      +++|+.+|.++||+++++++.++....++.+++++||+|||+|||||+|+|++.|+.||.++|.+.....+....|||+.
T Consensus        87 ~~~La~iA~~lgL~~~i~~g~~~~~~~~~~~~silaD~~EAliGAiyLD~G~~~a~~fv~~~~~~~~~~~~~~~~d~Ks~  166 (235)
T PRK12371         87 AETCAAIADEIGLHDLIRTGSDVKKLTGKRLLNVRADVVEALIAVIYLDGGLEAARPFIQRYWQKRALETDAARRDAKTE  166 (235)
T ss_pred             HHHHHHHHHHCCHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCHHHH
T ss_conf             99999999875737765224462212885421088899999999999865799999999999888865214443577999


Q ss_pred             HHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCC
Q ss_conf             9875320223333431010207788845999999999899999968989999999999999748899
Q gi|254780940|r  161 LQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT  227 (227)
Q Consensus       161 Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi~t  227 (227)
                      ||||||+++...|.|+++.++||+|+|+|+|.|+++|..+|+|.|+|||+||+.||++||+|+|||-
T Consensus       167 LqE~~q~~~~~~P~Y~~~~~~G~~h~~~F~v~v~i~~~~~~~G~G~SKK~AEq~AA~~aL~k~g~~k  233 (235)
T PRK12371        167 LQEWAHQQGGVTPVYRIDSRSGPDHDPLFTVEVEVKGFAPETGEGRSKRIAEQVAAEKMLEREGVWK  233 (235)
T ss_pred             HHHHHHHHCCCCCEEEEEECCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHCCCC
T ss_conf             9999997089997489830427898980899999999688998708999999999999999858866


No 3  
>PRK00102 rnc ribonuclease III; Reviewed
Probab=100.00  E-value=0  Score=443.68  Aligned_cols=221  Identities=39%  Similarity=0.561  Sum_probs=208.0

Q ss_pred             CCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
Q ss_conf             58899999836965898999984246121266--7665477887458688645478776410468878998888888744
Q gi|254780940|r    4 LRYSTLEKRIGYAFANRSLLEKALTHSSISHS--YQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSA   81 (227)
Q Consensus         4 ~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~--~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n   81 (227)
                      -++++||++|||+|+|++||.+||||+||.+.  ...|||||||||||||+++||+|||.+||+.+||+||++|+++||+
T Consensus         2 ~~~~~le~~lg~~f~~~~ll~~AlTH~S~~~~~~~~~~~erLEfLGDavL~~~vs~~L~~~~p~~~eG~LT~~R~~lV~~   81 (228)
T PRK00102          2 KDLEELQKKLGYTFKDPELLIQALTHRSYANENKGLKHNERLEFLGDAVLNLVISEYLFHRFPDLDEGDLSKLRAALVRE   81 (228)
T ss_pred             CCHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHH
T ss_conf             57999999959862888999998568172244778763489998659999999999999878899844899999998628


Q ss_pred             HHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCC--CCCCCCHHH
Q ss_conf             334545431387720010366312375313333326699999999641554220012210256431110--001345258
Q gi|254780940|r   82 ETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKS--GKFRRDAKT  159 (227)
Q Consensus        82 ~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~--~~~~~dpK~  159 (227)
                      ++|+.+|.++||++++++++++..+.++.+++++||+|||+|||||+|+|++.|+.||.++|.+.....  .....|||+
T Consensus        82 ~~La~ia~~lgL~~~i~~s~~e~~~~~~~~~~ilaD~fEA~iGAiylD~G~~~~~~fv~~~~~~~l~~~~~~~~~~d~Ks  161 (228)
T PRK00102         82 ESLAEIARELGLGEYLLLGKGEEKSGGRRRPSILADAFEALIGAIYLDSGLETARKFILKLFEPRIDEIDLGDLVKDYKT  161 (228)
T ss_pred             HHHHHHHHHCCHHHHHHHCCHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCHHH
T ss_conf             89999999659899998633687739966500888999999989996267999999999999999863110444368799


Q ss_pred             HHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             89875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  160 ELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       160 ~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      .||||||+.+...|+|+++.++||+|++.|+|+|+++|..+|+|+|+|||+||+.||++||++|.
T Consensus       162 ~Lqe~~q~~~~~~p~Y~~~~~~g~~~~~~f~v~v~i~~~~~g~G~G~SkK~Ae~~AA~~AL~~Lk  226 (228)
T PRK00102        162 RLQELLQGRGLPLPEYELVKEEGPAHDKEFTVEVIVNGKELGEGTGSSKKEAEQAAAKQALKKLK  226 (228)
T ss_pred             HHHHHHHHHCCCCCEEEEEEEECCCCCCCEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHHH
T ss_conf             99999998289998468863157999961899999999899998858999999999999999985


No 4  
>COG0571 Rnc dsRNA-specific ribonuclease [Transcription]
Probab=100.00  E-value=0  Score=434.00  Aligned_cols=226  Identities=41%  Similarity=0.592  Sum_probs=215.2

Q ss_pred             CCCCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCC--CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             73588999998369658989999842461212667--6654778874586886454787764104688789988888887
Q gi|254780940|r    2 SALRYSTLEKRIGYAFANRSLLEKALTHSSISHSY--QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLV   79 (227)
Q Consensus         2 ~~~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~--~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV   79 (227)
                      ....+..|++.+||+|+|++||.+||||+||.+++  ..|||||||||||||+++|+++||++||+.+||+||++|+.+|
T Consensus         4 ~~~~~~~l~~~lg~~f~~~~lL~~AltH~S~~~e~~~~~~nERLEFLGDavL~l~vae~Lf~~yP~~~EG~Ls~~ra~lV   83 (235)
T COG0571           4 MIKKLEALEKKLGYTFKDKELLEQALTHRSYANEHKAVENNERLEFLGDAVLGLVVAEYLFKKYPNLPEGELSKLRAALV   83 (235)
T ss_pred             CHHHHHHHHHHHCCCCCCHHHHHHHHCCCCHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHH
T ss_conf             16899999998298978989999986474122346677523888751899999999999999789998778999999997


Q ss_pred             HHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCC--CCH
Q ss_conf             443345454313877200103663123753133333266999999996415542200122102564311100013--452
Q gi|254780940|r   80 SAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKSGKFR--RDA  157 (227)
Q Consensus        80 ~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~~~~~--~dp  157 (227)
                      |+++|+.+|+.+||++|+++++++..++++.+++++||+|||+|||||+|+|++.++.|+.++|.+.+.......  +||
T Consensus        84 ~~~~La~ia~~l~l~~~l~lg~ge~~~gg~~~~silaD~~EAligAiylD~g~~~~~~~i~~l~~~~~~~~~~~~~~~D~  163 (235)
T COG0571          84 SEESLAEIARELGLGDYLRLGKGEEKSGGRRRESILADAFEALIGAIYLDSGLEAARKFILKLFLPRLEEIDAGDQFKDP  163 (235)
T ss_pred             HHHHHHHHHHHHCCCCHHHCCCCHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCH
T ss_conf             78999999998097423230577655289886239999999999999981780999999999999998631434312584


Q ss_pred             HHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCCC
Q ss_conf             5889875320223333431010207788845999999999899999968989999999999999748899
Q gi|254780940|r  158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIWT  227 (227)
Q Consensus       158 K~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi~t  227 (227)
                      |++||||+|+++...|+|+++..+||+|++.|+|.|.+++..+|+|.|+|||+|||.||+.||+++++|.
T Consensus       164 Kt~LQe~~q~~~~~~p~Y~~v~~~g~~h~~~F~v~v~v~~~~~g~G~G~skk~AEq~AA~~al~~l~~~~  233 (235)
T COG0571         164 KTRLQELLQAQGLVLPEYRLVKEEGPAHDKEFTVEVAVGGKELGTGKGRSKKEAEQAAAEQALKKLGVKE  233 (235)
T ss_pred             HHHHHHHHHHCCCCCCEEEEECCCCCCCCCEEEEEEEECCEEEEEECCCCHHHHHHHHHHHHHHHHCCCC
T ss_conf             4899999996489997479840568877866899999899457773466889999999999999860304


No 5  
>PRK12372 ribonuclease III; Reviewed
Probab=100.00  E-value=0  Score=431.10  Aligned_cols=216  Identities=35%  Similarity=0.496  Sum_probs=204.5

Q ss_pred             CCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             58899999836965898999984246121266766547788745868864547877641046887899888888874433
Q gi|254780940|r    4 LRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAET   83 (227)
Q Consensus         4 ~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~   83 (227)
                      |.++.||++|||+|+|++||.+||||+||..   .||||||||||+||+++|+++||.+||+.+||.||++|+.||+.++
T Consensus         1 MpLs~LE~rLGY~Fkd~~LL~~ALTHRS~~~---~~NERLEFLGDAVLglvIae~Ly~~fP~~~EG~LSrlRA~LV~~~t   77 (425)
T PRK12372          1 MPLSQLESRLRYEFRNAELLRQALTHRSHSA---THNERLEFLGDSVLNCAVAALLFQRFGKLDEGDLSRVRANLVKQQS   77 (425)
T ss_pred             CCHHHHHHHHCCEECCHHHHHHHHCCCCCCC---CCCCHHHCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHCHHH
T ss_conf             9868999983977688899999851657888---8871022205999999999999987889885478999999969799


Q ss_pred             HHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCC--CCCCCCHHHHH
Q ss_conf             4545431387720010366312375313333326699999999641554220012210256431110--00134525889
Q gi|254780940|r   84 CSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKS--GKFRRDAKTEL  161 (227)
Q Consensus        84 La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~--~~~~~dpK~~L  161 (227)
                      |+.+|++++|.+||++|+++..++++.+++||+|+|||+|||||+|+||+.++.||.++|.+.+..+  ....+||||+|
T Consensus        78 LAeiAr~l~Lg~~L~LG~GE~kSGGr~R~SILADA~EAlIGAIYLD~G~eaA~~~I~rlf~~~L~~i~~~~~~KD~KT~L  157 (425)
T PRK12372         78 LYEIAQALNISDGLRLGEGELRSGGFRRPSILADAFEAIIGAVFLDGGFEAAQGVIKRLYVPILDHIDPRTLGKDAKTLL  157 (425)
T ss_pred             HHHHHHHCCCCHHEEECCCHHHCCCCCCCHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHH
T ss_conf             99999976962014236740104897760089999999887963135589999999999999986089552367800899


Q ss_pred             HHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEE-EEEEECCHHHHHHHHHHHHHHH
Q ss_conf             875320223333431010207788845999999999899-9999689899999999999997
Q gi|254780940|r  162 QEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAP-AQGMDCSKRAAEQVAAAEVLKR  222 (227)
Q Consensus       162 qe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~-g~g~g~SkK~Ae~~AA~~AL~k  222 (227)
                      |||+|.++..+|+|.++..+|++|++.|+|.|.|.+..+ ..|.|.|+|.|||.||++||+.
T Consensus       158 QE~LQ~rk~~LP~Y~Vv~~~G~aH~Q~F~V~C~V~~l~~~~~G~G~SRR~AEQ~AAk~ALee  219 (425)
T PRK12372        158 QEYLQGHKIALPTYTVVATHGAAHNQQFEVECTVPKLDVKVSGSGASRRAAEQAAAKKALDE  219 (425)
T ss_pred             HHHHHHCCCCCCCEEEEEEECCCCCCEEEEEEEECCCCCEEEEEECCCHHHHHHHHHHHHHH
T ss_conf             99985179999961786315477577079998854887314742377169999999999999


No 6  
>KOG1817 consensus
Probab=100.00  E-value=0  Score=325.14  Aligned_cols=219  Identities=32%  Similarity=0.441  Sum_probs=196.6

Q ss_pred             CHHHHHHHHCCCCCCHHHHHHHCCCHHHCCC--CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
Q ss_conf             8899999836965898999984246121266--76654778874586886454787764104688789988888887443
Q gi|254780940|r    5 RYSTLEKRIGYAFANRSLLEKALTHSSISHS--YQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAE   82 (227)
Q Consensus         5 ~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~--~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~   82 (227)
                      .+-++|+++|..|.+.+++.+|||-+|....  ...+|||||||||+||++++|++||.+||+.+||.||.+|+.+|||+
T Consensus       274 p~~~~e~~~g~vF~Hirlla~aft~rs~~~n~Lt~gHNqRLEFLGDSilqlv~T~ily~kFPdhhEGhLSlLRssLVsNe  353 (533)
T KOG1817         274 PLTQFEEIIGIVFIHIRLLARAFTLRSIPFNHLTLGHNQRLEFLGDSILQLVMTEILYRKFPDHHEGHLSLLRSSLVSNE  353 (533)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCH
T ss_conf             50357998778999999999986315797125565256788886788999999999997587546436999999873627


Q ss_pred             HHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCC--CCCCCCHHHH
Q ss_conf             34545431387720010366312375313333326699999999641554220012210256431110--0013452588
Q gi|254780940|r   83 TCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALKS--GKFRRDAKTE  160 (227)
Q Consensus        83 ~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~~--~~~~~dpK~~  160 (227)
                      +.+.+|..+|+++++........ ..+.+.|.+||+|||||||+|+|.|.+.|+.|+..++.|++...  .....|||+.
T Consensus       354 tqakva~~lgf~e~li~n~~~k~-~~~lk~K~~ADlfEAfiGaLyvD~~le~~~qf~~~l~~Prl~~fi~nq~wndpksk  432 (533)
T KOG1817         354 TQAKVADDLGFHEYLITNFDLKD-FQNLKLKDYADLFEAFIGALYVDKGLEYCRQFLRVLFFPRLKEFIRNQDWNDPKSK  432 (533)
T ss_pred             HHHHHHHHHCCCHHHHHCCCHHH-HHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCHHH
T ss_conf             89999998097353440766233-33124778999999998788526880899999999831789999874011582779


Q ss_pred             HHHHHHCC------CCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             98753202------23333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  161 LQEWAHAK------FGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       161 Lqe~~q~~------~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      ||++|...      ....|.|++....||.+++.|+|.||++|+.+|+|+|+|.|.|+.+||.+||+++.
T Consensus       433 Lqq~cl~~rys~~~epdip~y~V~~~~gpa~~r~y~Vavyf~gkrlat~~G~nik~Ae~rAA~~ALe~~~  502 (533)
T KOG1817         433 LQQCCLTLRYSLGGEPDIPLYKVLGAKGPANDRNYKVAVYFKGKRLATGVGSNIKQAEMRAAMQALENLK  502 (533)
T ss_pred             HHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCCEEEEEEECCEEEEECCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9999888741568888872378723468877873589999888788624674076887789999999987


No 7  
>smart00535 RIBOc Ribonuclease III family.
Probab=100.00  E-value=2.5e-36  Score=243.54  Aligned_cols=127  Identities=42%  Similarity=0.583  Sum_probs=118.2

Q ss_pred             HHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEC
Q ss_conf             99998424612126676654778874586886454787764104688789988888887443345454313877200103
Q gi|254780940|r   21 SLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVS  100 (227)
Q Consensus        21 ~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~  100 (227)
                      ++|.+||||+|+.... +||||||||||+||+++|++|||.+||+.+||.||.+|+.+|||++|+++|.++||+++++++
T Consensus         1 ~ll~~Alth~S~~~~~-~~yerLEfLGDavL~~~v~~~l~~~~p~~~eg~lt~~r~~lvsn~~La~ia~~lgL~~~i~~~   79 (129)
T smart00535        1 SLLLRALTHASYSNEH-EHNERLEFLGDAVLELVVTEYLYKKYPDLSEGDLSRLRSALVSNETLARLAKKLGLGEFIRLG   79 (129)
T ss_pred             CHHHHHHCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHC
T ss_conf             9788976461646788-755999998999999999999998588888017999999998588999999986909997626


Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCC
Q ss_conf             663123753133333266999999996415542200122102564311
Q gi|254780940|r  101 SDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRAL  148 (227)
Q Consensus       101 ~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~  148 (227)
                      ++...+..+..++++||+|||+|||||+|+|++.|+.|+.++|.+.+.
T Consensus        80 ~~~~~~~~~~~~ki~ad~~EAliGAiyld~G~~~~~~~l~~~~~~~l~  127 (129)
T smart00535       80 RGEAISGGRDKPSILADVFEALIGAIYLDSGLEAAREFIRDLLGPRLE  127 (129)
T ss_pred             CCHHHCCCCCCCCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHH
T ss_conf             613213664466621069999999999976799999999999999986


No 8  
>cd00593 RIBOc RIBOc. Ribonuclease III C terminal domain. This group consists of eukaryotic, bacterial and archeal ribonuclease III (RNAse III) proteins. RNAse III is a double stranded RNA-specific endonuclease. Prokaryotic RNAse III is important in post-transcriptional control of mRNA stability and translational efficiency. It is involved in the processing of ribosomal RNA precursors. Prokaryotic RNAse III also plays a role in the maturation of tRNA precursors and in the processing of phage and plasmid transcripts. Eukaryotic RNase III's participate (through direct cleavage) in rRNA processing, in processing of small nucleolar RNAs (snoRNAs) and snRNA's (components of the spliceosome). In eukaryotes RNase III or RNaseIII like enzymes such as Dicer are involved in RNAi (RNA interference) and miRNA (micro-RNA) gene silencing.
Probab=100.00  E-value=6.8e-35  Score=234.69  Aligned_cols=129  Identities=40%  Similarity=0.583  Sum_probs=118.4

Q ss_pred             HHHHHHCCCHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEE
Q ss_conf             9999842461212667-665477887458688645478776410468878998888888744334545431387720010
Q gi|254780940|r   21 SLLEKALTHSSISHSY-QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRV   99 (227)
Q Consensus        21 ~ll~~A~th~S~~~~~-~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~   99 (227)
                      .++.+||||+|+.... ..|||||||||||||+++|+.++|.+||+.+||.||++|+.+|||++|+++|.++||+++++.
T Consensus         1 ~ll~~Alth~S~~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~~g~lt~~r~~lV~n~~L~~~a~~~gl~~~i~~   80 (133)
T cd00593           1 SLLLEALTHPSYANEHGRFNNERLEFLGDAVLELVVTEYLFKKFPDLSEGDLTRLRSALVSNETLARLARELGLGKYLRL   80 (133)
T ss_pred             CHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
T ss_conf             97889764616012688743499999889999999999999858578876208999999739999999998871999860


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCC
Q ss_conf             36631237531333332669999999964155422001221025643111
Q gi|254780940|r  100 SSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQRALK  149 (227)
Q Consensus       100 ~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~~~~  149 (227)
                      ++.........+++++||+|||+|||||+|+|++.++.|+..+|.+....
T Consensus        81 ~~~~~~~~~~~~~k~~aD~~EAliGAiyld~g~~~~~~~i~~l~~~~~~~  130 (133)
T cd00593          81 GKGEEKSGGRLRPKILADVFEALIGAIYLDGGFEAARKFLLRLLGPLIEE  130 (133)
T ss_pred             CCHHHHCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHH
T ss_conf             87576548730256898999999999999647999999999999999976


No 9  
>KOG3769 consensus
Probab=99.91  E-value=1.1e-23  Score=165.67  Aligned_cols=217  Identities=21%  Similarity=0.210  Sum_probs=183.4

Q ss_pred             HHHHHHHHC-CCCCCHHHHHHHCCCHHHCCC-----------------CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             899999836-965898999984246121266-----------------76654778874586886454787764104688
Q gi|254780940|r    6 YSTLEKRIG-YAFANRSLLEKALTHSSISHS-----------------YQESYERLEFLGDRILGLLISTLLFNHFDSAK   67 (227)
Q Consensus         6 ~~~l~~~lg-y~f~~~~ll~~A~th~S~~~~-----------------~~~~~erLEflGDavL~~~v~~~l~~~~p~~~   67 (227)
                      +.+|.++|| -.|. .+.+.+|||.+|+...                 ...+|+.|--.|...+++.|++||-.+||.++
T Consensus        65 l~afg~RL~~~~is-~~~l~ka~t~~s~~~~~kv~~~~lg~~~~~~~~~~~~N~~L~~~Gk~~~~~~v~~~l~~kyPrlP  143 (333)
T KOG3769          65 LSAFGKRLQSEEIS-LSYLLKALTNLSFSYPEKVLRQQLGAETVAQVNPQYSNEELVEIGKQFLSFYVTEYLKCKYPRLP  143 (333)
T ss_pred             HHHHHHHHCCCCCC-HHHHHHHHHCCCCCCHHHHHHHHHCCHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99988774442104-99999997173200648776665321046552577550889998899999999999997556885


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCC-CCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCC
Q ss_conf             7899888888874433454543138772001036631237531-333332669999999964155422001221025643
Q gi|254780940|r   68 EGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSF-MTSIQADVVESLIAALYLDGGIEVAGTFVDKYWKQR  146 (227)
Q Consensus        68 eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~-~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~~~~~  146 (227)
                      +--+--+-+.+.+.++||++|..+|+.++++.-.-...  ... .+....+++-|++|+++.+.|++.+++||...+...
T Consensus       144 ~E~l~ai~n~ll~ee~LahiAt~lGie~l~~seeFp~~--~eisq~ess~~aI~Al~~~~~~ek~~~~v~dFI~~qi~~k  221 (333)
T KOG3769         144 EEGLHAIVNGLLGEEVLAHIATHLGIEELGLSEEFPKV--GEISQDESSRRAIGALLGSVGLEKGFNFVRDFINDQILSK  221 (333)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC--HHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
T ss_conf             89999999875218999999987538988622668994--3666788899999999832117777899999998775311


Q ss_pred             CCCCCC--CCCCHHHHHHHHHHCCCCCCCCCCEECCCCCC-CCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             111000--13452588987532022333343101020778-884599999999989999996898999999999999974
Q gi|254780940|r  147 ALKSGK--FRRDAKTELQEWAHAKFGVTPEYKVTFRSGPD-HDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       147 ~~~~~~--~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~-~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      ......  ...+|...|.+.|+..+...|+++++.++|.. -.|.|.|++|.|.+.+|+|.|+|-+.|++.||++||.++
T Consensus       222 ~L~~~~m~ql~~P~~~L~~lckr~~l~epe~Rll~esGr~S~~PvyvVgiYs~kkllGqG~Gesl~~A~e~AA~dAL~k~  301 (333)
T KOG3769         222 DLDPREMWQLQWPRRLLSRLCKRRGLKEPESRLLAESGRNSAEPVYVVGIYSGKKLLGQGQGESLKLAEEQAARDALIKL  301 (333)
T ss_pred             CCCHHHHCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCEEEEEEECCCHHHCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             02667641523669999999987487884068998716676675278886317412135852078999999999999999


Q ss_pred             CC
Q ss_conf             88
Q gi|254780940|r  224 GI  225 (227)
Q Consensus       224 gi  225 (227)
                      =.
T Consensus       302 y~  303 (333)
T KOG3769         302 YD  303 (333)
T ss_pred             HC
T ss_conf             72


No 10 
>pfam00636 Ribonuclease_3 RNase3 domain.
Probab=99.89  E-value=1.1e-23  Score=165.78  Aligned_cols=91  Identities=44%  Similarity=0.705  Sum_probs=81.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCC-----CCCCCCCCCCC
Q ss_conf             7788745868864547877641046887899888888874433454543138772001036631-----23753133333
Q gi|254780940|r   41 ERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLR-----KDVCSFMTSIQ  115 (227)
Q Consensus        41 erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~-----~~~~~~~~~il  115 (227)
                      ||||||||+||++++++|+|.+||+.+||.||.+|+.+|||++|+.+|.++||++|++.++...     .......++++
T Consensus         1 erLefLGD~vL~~~~~~~l~~~~p~~~eg~l~~~~~~lv~~~~L~~~a~~~gl~~~i~~~~~~~~~~~~~~~~~~~~k~~   80 (96)
T pfam00636         1 ERLEFLGDAVLELIVSEYLYEKYPDLSEGELTRLRSALVSNETLAKLARKLGLDKYIRRGRNALSKGEKAKSASLSPKVL   80 (96)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHCCCCCCCCHHHCCCCCCCHHH
T ss_conf             90998799999999999999878998766899999999748999999999797899860862101321221466540388


Q ss_pred             HHHHHHHHHHHHHCCC
Q ss_conf             2669999999964155
Q gi|254780940|r  116 ADVVESLIAALYLDGG  131 (227)
Q Consensus       116 ad~fEA~iGAiy~d~G  131 (227)
                      ||+|||+|||||+|+|
T Consensus        81 ad~~EAliGAiyld~g   96 (96)
T pfam00636        81 ADVFEALIGAIYLDGG   96 (96)
T ss_pred             HHHHHHHHHHHHHCCC
T ss_conf             7899999999997679


No 11 
>KOG0701 consensus
Probab=99.84  E-value=1.4e-21  Score=152.71  Aligned_cols=133  Identities=33%  Similarity=0.426  Sum_probs=109.2

Q ss_pred             CCHHHHHHHHC--CCCCCH--------HHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHH
Q ss_conf             58899999836--965898--------99998424612126676654778874586886454787764104688789988
Q gi|254780940|r    4 LRYSTLEKRIG--YAFANR--------SLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSV   73 (227)
Q Consensus         4 ~~~~~l~~~lg--y~f~~~--------~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~   73 (227)
                      ++.+.+++++.  |.|.+.        .++.+|||+.|+..  ..++||||+|||++|++.++.++|.+||+.+||.+|.
T Consensus       979 ~~~E~~e~i~n~~~~Fs~~~~~i~~~~s~LLEAlT~~~~~~--s~s~Erle~Lgds~Lk~avsr~l~L~ypd~~Egqls~ 1056 (1606)
T KOG0701         979 SDWEAVEKILNFRYVFSISLASIALSTSLLLEALTTSSCQD--SFSLERLELLGDSLLKLAVSRHLFLTYPDLDEGQLSR 1056 (1606)
T ss_pred             CCCCCCCCCCCCCEECCCCCCCCCCCHHHHHHHHHCCCCCC--CHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCHHHHH
T ss_conf             44222102344000014122311255268999860576544--2007888766778887789999997287324106899


Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEC--CCC-----------------------------CC----------------C
Q ss_conf             888887443345454313877200103--663-----------------------------12----------------3
Q gi|254780940|r   74 RFNSLVSAETCSQVARELDLASFIRVS--SDL-----------------------------RK----------------D  106 (227)
Q Consensus        74 lr~~lV~n~~La~~a~~lgl~~~l~~~--~~~-----------------------------~~----------------~  106 (227)
                      +|+.+|++++++.+|...|+..+++.+  ...                             ..                .
T Consensus      1057 lr~~~~~~~nl~~la~~~gl~~~~~~~~fep~~~~~p~~~~~~~~~~k~~~~~~~~~~~~e~~e~~~df~e~~~~~~~~~ 1136 (1606)
T KOG0701        1057 LRDVNVSNDNLARLAVKKGLYSYLRHEGFEPSRWWVPGQLDVNNVDCKDLSGDQNYILYKELDEKIKDFQEAMEKEDGDS 1136 (1606)
T ss_pred             HHHHCCCCCCHHHHHHCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             98724663102233220253544014442445111555666552001245443320012132233167887643037765


Q ss_pred             ------CCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHH
Q ss_conf             ------75313333326699999999641554220012
Q gi|254780940|r  107 ------VCSFMTSIQADVVESLIAALYLDGGIEVAGTF  138 (227)
Q Consensus       107 ------~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~  138 (227)
                            .....++.++|++||++||+|+|+|+.....+
T Consensus      1137 ~~~~~~~~~~~~ks~adl~eaLlga~~vD~~~~~~~~~ 1174 (1606)
T KOG0701        1137 RSKGGDHDWLAPKSPADLLEALLGAIYVDGGLLETFET 1174 (1606)
T ss_pred             CCCCCCCCEECCCCHHHHHHHHHHHHHHHCCCHHHHHH
T ss_conf             23332120015887899999987764322220234457


No 12 
>KOG0701 consensus
Probab=99.81  E-value=5.7e-20  Score=142.88  Aligned_cols=203  Identities=24%  Similarity=0.328  Sum_probs=138.2

Q ss_pred             CHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCC-CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             88999998369658989999842461212667-66547788745868864547877641046887899888888874433
Q gi|254780940|r    5 RYSTLEKRIGYAFANRSLLEKALTHSSISHSY-QESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAET   83 (227)
Q Consensus         5 ~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~-~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~   83 (227)
                      .+..+++.++|.|.+..++.+|+||-||..+. ..+||||||+||+|++..|++++|...|..++|.+|.+|+++|+|+-
T Consensus      1370 ~~~~~e~~l~y~f~~~~~l~~a~th~s~~~~~~~~C~qrleflgd~vld~~it~hl~~~~~~~sp~~~td~rsa~vnn~~ 1449 (1606)
T KOG0701        1370 SFGKFEEKLNYRFKLKPYLTQATTHASYIYNRITDCYQRLEFLGDAVLDYLITKHLYEDPRQHSPGVLTDLRSALVNNTI 1449 (1606)
T ss_pred             HHHHHHCCCCHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCC
T ss_conf             78765401106665410342001466312576630455677767765236665325445333472033322667641553


Q ss_pred             HHHHHHHCCCCCEEEECCCCC------------C---------CCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCC
Q ss_conf             454543138772001036631------------2---------3753133333266999999996415542200122102
Q gi|254780940|r   84 CSQVARELDLASFIRVSSDLR------------K---------DVCSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKY  142 (227)
Q Consensus        84 La~~a~~lgl~~~l~~~~~~~------------~---------~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~  142 (227)
                      .+.+|.+.++++++..-....            .         ...-.-+|.++|+||++.||||+|+|. --+-.+..+
T Consensus      1450 ~a~~av~~~~~K~~~~~~~~l~~~I~~~v~~~~q~~~~~~~~~~edievpKa~gdi~esiagai~~dsg~-~~~~~~~~~ 1528 (1606)
T KOG0701        1450 FASLAVKADLHKFIIAASPGLIHNIDRFVSFQLQSNLDSLFGWEEDIEVPKALGDIFESIAGAIKLDSGN-MMEPCIEKF 1528 (1606)
T ss_pred             CHHHHHHHCCHHHHHHHCCCCCCCHHHHHHHHHHHCCCCCCCCHHHCCCCHHHHHHHHCCCCEEECCCCC-CCCHHHHCC
T ss_conf             1256776212567776233126516778888876122457786121024044433321034400147665-410576507


Q ss_pred             CCCCCCC--CCCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHH
Q ss_conf             5643111--00013452588987532022333343101020778884599999999989999996898999999999999
Q gi|254780940|r  143 WKQRALK--SGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVL  220 (227)
Q Consensus       143 ~~~~~~~--~~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL  220 (227)
                      |..+-..  ......+|++.+-.-+++          +..     .+.-.+.|.+.+.....|.|...+.|+..|++.|+
T Consensus      1529 ~a~p~~s~~~E~~~~h~~~~~~~~~~k----------~~d-----~~~~~~tv~~~~~~~~~~~g~~~~~aK~s~~k~A~ 1593 (1606)
T KOG0701        1529 WALPPRSPIRELLELHPERALFGKCEK----------VAD-----AGKVRVTVDVFNKEVFAGEGRNYRIAKASAAKAAL 1593 (1606)
T ss_pred             CCCCCCCCHHHHCCCCCEEECCCHHHH----------HHH-----CCCEEEEEEECCCCHHHHCCHHHHHHHHHHHHHHH
T ss_conf             689985520000345540000230120----------011-----55157999841420022213123445666777999


Q ss_pred             HHC
Q ss_conf             974
Q gi|254780940|r  221 KRE  223 (227)
Q Consensus       221 ~kl  223 (227)
                      +.+
T Consensus      1594 ~ll 1596 (1606)
T KOG0701        1594 KLL 1596 (1606)
T ss_pred             HHH
T ss_conf             999


No 13 
>KOG1817 consensus
Probab=99.80  E-value=2.8e-20  Score=144.74  Aligned_cols=135  Identities=33%  Similarity=0.488  Sum_probs=111.0

Q ss_pred             HHHHHHHHCCCCCCHHHHHHHCCCHHHCCC--------------------------------------------------
Q ss_conf             899999836965898999984246121266--------------------------------------------------
Q gi|254780940|r    6 YSTLEKRIGYAFANRSLLEKALTHSSISHS--------------------------------------------------   35 (227)
Q Consensus         6 ~~~l~~~lgy~f~~~~ll~~A~th~S~~~~--------------------------------------------------   35 (227)
                      +.-||+.|||+|+|..|++.|+||||+...                                                  
T Consensus        43 l~~~e~~i~y~f~~r~~~~lal~h~s~~~~~Gt~~dh~kns~tncg~r~~~yg~~~~~~~~kr~~gin~li~imk~l~~~  122 (533)
T KOG1817          43 LDHLEELIGYTFQDRCLLQLALTHPSHKLNYGTNPDHAKNSLTNCGIRQPKYGDRKEHIMTKRKLGINTLINIMKRLGVI  122 (533)
T ss_pred             HHHHHHHHCEEECCHHHHHHHHCCCHHHHHCCCCCHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999984713121678999851842776079991565403432475775532267777777775034777887650678


Q ss_pred             -----CCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCC
Q ss_conf             -----766547788745868864547877641046887899888888874433454543138772001036631237531
Q gi|254780940|r   36 -----YQESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSF  110 (227)
Q Consensus        36 -----~~~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~  110 (227)
                           ....||||||+||+|.+++++.++|..+|...+|.|...|+++|.|..++.+++++.++.|+...-+....-...
T Consensus       123 ~~~~s~i~hnErle~lgdavve~~ss~hl~~~~~r~~eggLatyrta~vqnr~la~lakklrkd~fl~yahg~dl~~~~E  202 (533)
T KOG1817         123 QPTHSVIKHNERLEFLGDAVVELLSSNHLYFMFPRLEEGGLATYRTAIVQNRHLAKLAKKLRKDEFLLYAHGYDLCFETE  202 (533)
T ss_pred             CCCHHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHH
T ss_conf             87325767888999875210777777888873663002540578899997689999998877999999850732122788


Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCCHHHHH
Q ss_conf             333332669999999964155422001221
Q gi|254780940|r  111 MTSIQADVVESLIAALYLDGGIEVAGTFVD  140 (227)
Q Consensus       111 ~~~ilad~fEA~iGAiy~d~G~~~~~~~i~  140 (227)
                      -....+++|||++||+|+|+|...+.....
T Consensus       203 ~Kha~an~feavi~a~~l~g~~~~~e~lfs  232 (533)
T KOG1817         203 LKHAMANCFEAVIGAKYLDGGLVVAEKLFS  232 (533)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             777799999998588887243278999987


No 14 
>cd00048 DSRM Double-stranded RNA binding motif. Binding is not sequence specific but is highly specific for double stranded RNA. Found in a variety of proteins including dsRNA dependent protein kinase PKR, RNA helicases, Drosophila staufen protein, E. coli RNase III, RNases H1, and dsRNA dependent adenosine deaminases.
Probab=99.64  E-value=5.2e-16  Score=118.51  Aligned_cols=68  Identities=40%  Similarity=0.581  Sum_probs=65.7

Q ss_pred             CHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             52588987532022333343101020778884599999999989999996898999999999999974
Q gi|254780940|r  156 DAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       156 dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      |||+.||||||+.+...|.|.++.++||+|+++|+|.|.++|..+++|.|+|||+||+.||+.||+.|
T Consensus         1 ~pks~LqE~~q~~~~~~p~Y~~~~~~g~~h~~~F~~~v~i~~~~~~~g~g~sKK~Aeq~AA~~aL~~L   68 (68)
T cd00048           1 NPKSLLQELAQKRGKPLPEYELVEEEGPDHAPRFTVEVTVGGKITGEGEGSSKKEAKQNAAEAALRKL   68 (68)
T ss_pred             CCHHHHHHHHHHCCCCCCEEEECCCCCCCCCCEEEEEEEECCEEEECCCCCCHHHHHHHHHHHHHHHC
T ss_conf             95789999999749999979616540898773499999999988615777769999999999999849


No 15 
>smart00358 DSRM Double-stranded RNA binding motif.
Probab=99.60  E-value=2e-15  Score=114.90  Aligned_cols=67  Identities=40%  Similarity=0.568  Sum_probs=63.6

Q ss_pred             HHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             25889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  157 AKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       157 pK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      ||+.||||||+.+. .|.|.++.++||+|+++|+|.|.++|..++.|.|+|||.||+.||+.||++|.
T Consensus         1 pks~L~E~~qk~~~-~~~y~~~~~~g~~h~~~F~~~v~i~g~~~~~g~g~sKK~Ae~~AA~~al~~L~   67 (67)
T smart00358        1 PKSLLQELAQKRGL-PPEYELVKEEGPDHAPRFTVTVKVGGEYTGEGEGSSKKEAKQRAAEAALRSLK   67 (67)
T ss_pred             CCHHHHHHHHHCCC-CCEEEEEEEECCCCCCEEEEEEEECCEEEECCCCCCHHHHHHHHHHHHHHHHC
T ss_conf             94099999987798-98799997158997847999999999998435789999999999999999739


No 16 
>KOG3732 consensus
Probab=99.33  E-value=4e-12  Score=94.57  Aligned_cols=73  Identities=29%  Similarity=0.330  Sum_probs=68.1

Q ss_pred             CCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             00134525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  151 GKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       151 ~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      .....||.++|||+||++++..|+|.++.+.|++|.+.|++.|.+.+.. .+|+|.|||.|+++||+..|..+|
T Consensus       138 ~~~~~NPI~~L~e~~q~k~~k~P~yelv~E~G~~~~rEFv~q~sv~~~~-~~GkG~sKKiAKRnAAeamLe~l~  210 (339)
T KOG3732         138 YGQVLNPIGRLQELAQAKKWKLPEYELVQESGVPHRREFVIQCSVENFT-EEGKGPSKKIAKRNAAEAMLESLG  210 (339)
T ss_pred             CCCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCCCCEEEEEEEECCEE-EECCCCHHHHHHHHHHHHHHHHHC
T ss_conf             0125586999999999837899955887325777664489998750302-246785088999999999999836


No 17 
>pfam00035 dsrm Double-stranded RNA binding motif. Putative motif shared by proteins that bind to dsRNA. At least some DSRM proteins seem to bind to specific RNA targets. Exemplified by Staufen, which is involved in localization of at least five different mRNAs in the early Drosophila embryo. Also by interferon-induced protein kinase in humans, which is part of the cellular response to dsRNA.
Probab=99.33  E-value=4.9e-12  Score=94.03  Aligned_cols=66  Identities=36%  Similarity=0.534  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             2588987532022333343101020778884599999999989999996898999999999999974
Q gi|254780940|r  157 AKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       157 pK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      ||+.||||||..+. .|.|..+...|++|++.|.|.|.++|..++.|.|+|||+||+.||..||+.|
T Consensus         1 ~ks~L~e~~~~~~~-~~~~~~~~~~~~~~~~~F~~~v~v~~~~~~~g~g~sKK~A~~~AA~~aL~~L   66 (66)
T pfam00035         1 PKSLLQELCQKKGK-KPPYEYVEEEGPSHSPTFTVTVTVGGKKYGTGTGSSKKEAKQLAAEKALQKL   66 (66)
T ss_pred             CCHHHHHHHHHCCC-CCCEEEEEEECCCCCCEEEEEEEECCEEEEECCCCCHHHHHHHHHHHHHHHC
T ss_conf             94499999996295-9899999848899886599999979989874388889999999999999849


No 18 
>KOG3732 consensus
Probab=99.05  E-value=5.6e-10  Score=81.37  Aligned_cols=70  Identities=31%  Similarity=0.366  Sum_probs=63.2

Q ss_pred             CCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCCC
Q ss_conf             452588987532022333343101020778884599999999989999996898999999999999974889
Q gi|254780940|r  155 RDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGIW  226 (227)
Q Consensus       155 ~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi~  226 (227)
                      +-|.+.|||++.+.+. .|.|.+..++||.|++.|++.|.|. ...++|.|+|||.|+++||..+|..|.-+
T Consensus        38 KS~IS~l~E~~~r~~~-~v~fevl~eeGp~H~~~fv~rvtvg-~~~a~GeG~sKK~AKh~AA~~~L~~lk~l  107 (339)
T KOG3732          38 KSPISLLQEYGLRRGL-TPVYEVLREEGPPHMPNFVFRVTVG-EITATGEGKSKKLAKHRAAEALLKELKKL  107 (339)
T ss_pred             CCHHHHHHHHHHHHCC-CCCEEEEECCCCCCCCCEEEEEEEE-EEEEECCCCCHHHHHHHHHHHHHHHHHHC
T ss_conf             7708999999997089-7550542134886578768999986-46886378742688999999999998507


No 19 
>KOG2777 consensus
Probab=98.30  E-value=1.8e-06  Score=59.82  Aligned_cols=65  Identities=29%  Similarity=0.347  Sum_probs=58.6

Q ss_pred             CCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCC
Q ss_conf             34525889875320223333431010207788845999999999899999968989999999999999748
Q gi|254780940|r  154 RRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREG  224 (227)
Q Consensus       154 ~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klg  224 (227)
                      .++|.+.|.|+.+     .|.|......||.|.+.|.|.|.+||...-.| |.|||+|++.||..||+.+.
T Consensus        89 ~~npv~ll~e~~~-----~~~~~~~~~~~~~~~~~F~~~~~vdg~~~~~~-~~sKk~ak~~aa~~al~~l~  153 (542)
T KOG2777          89 GKNPVSLLHELAN-----GLFFDFVNESGPQHAPKFVMSVVVDGRWFEGG-GRSKKEAKQEAAMAALQVLF  153 (542)
T ss_pred             CCCCHHHHHHHHC-----CCCEEEECCCCCCCCCEEEEEEEECCEECCCC-CCCHHHHHHHHHHHHHHHHH
T ss_conf             6780587997750-----62434200578888860799999899873587-86237899999999999997


No 20 
>KOG4334 consensus
Probab=98.15  E-value=1.3e-06  Score=60.73  Aligned_cols=63  Identities=22%  Similarity=0.254  Sum_probs=55.5

Q ss_pred             HHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             88987532022333343101020778884599999999989999996898999999999999974
Q gi|254780940|r  159 TELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       159 ~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      -.|.||.|.-....|+|..-+.+.+  ...|..+|.+|+..+|+|+|.|||.|+..||+.+|+.|
T Consensus       379 CiLhEy~q~~lk~~pvyef~e~~n~--stpysa~v~~d~~~yGsG~g~sKK~Ak~~AAR~tLeiL  441 (650)
T KOG4334         379 CILHEYAQQCLKSLPVYEFAENDNN--STPYSAGVLPDLFPYGSGVGASKKTAKLVAARDTLEIL  441 (650)
T ss_pred             EHHHHHHHHHHHHCCEEEHHHCCCC--CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             3299999988642220003321588--98655411136500256645206777778899999975


No 21 
>COG1939 Ribonuclease III family protein [Replication, recombination, and    repair]
Probab=97.77  E-value=4.8e-05  Score=51.01  Aligned_cols=98  Identities=22%  Similarity=0.294  Sum_probs=65.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE--------EECCCCCCCCCCCC
Q ss_conf             4778874586886454787764104688789988888887443345454313877200--------10366312375313
Q gi|254780940|r   40 YERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFI--------RVSSDLRKDVCSFM  111 (227)
Q Consensus        40 ~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l--------~~~~~~~~~~~~~~  111 (227)
                      ==-|.|+||||+++.|-.|+...+.. .++.|.+.-.+.||.+..|.+-..+  .+++        +-|.+..   ....
T Consensus        15 ~laLAy~GDAV~e~yVR~~~l~~g~~-k~~~lH~~a~~~VsAk~QA~il~~~--~~~Lte~E~~I~KRgRNak---s~T~   88 (132)
T COG1939          15 GLALAYLGDAVYELYVREYLLLKGKT-KPNDLHKRATAYVSAKAQALILKAL--LEFLTEEEEEIVKRGRNAK---SGTK   88 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCC-CHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHCCCC---CCCC
T ss_conf             89999953599999999999722457-8689999999994588899999999--9986189999999701543---6789


Q ss_pred             CC-------CCHHHHHHHHHHHHHCCCCCCCHHHHHCCC
Q ss_conf             33-------332669999999964155422001221025
Q gi|254780940|r  112 TS-------IQADVVESLIAALYLDGGIEVAGTFVDKYW  143 (227)
Q Consensus       112 ~~-------ilad~fEA~iGAiy~d~G~~~~~~~i~~~~  143 (227)
                      ++       -.+.-|||++|.+|+..-.+....++...+
T Consensus        89 ~kn~dv~tYr~sTgfEAliGyLyL~~~~eRL~ell~~~i  127 (132)
T COG1939          89 PKNTDVETYRMSTGFEALIGYLYLTKQEERLEELLNKVI  127 (132)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             887976788885019999999998455999999999998


No 22 
>KOG2334 consensus
Probab=95.20  E-value=0.0064  Score=37.94  Aligned_cols=138  Identities=20%  Similarity=0.232  Sum_probs=85.0

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCC---HHHH---HHHHHHHHHCCCCCCCHHHH-HCCCCCCC
Q ss_conf             88887443345454313877200103663123753133333---2669---99999996415542200122-10256431
Q gi|254780940|r   75 FNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQ---ADVV---ESLIAALYLDGGIEVAGTFV-DKYWKQRA  147 (227)
Q Consensus        75 r~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~il---ad~f---EA~iGAiy~d~G~~~~~~~i-~~~~~~~~  147 (227)
                      ...+....+.+.+++-.+++++....+.+...... +.+.+   +|+.   |.+.     |.|   +-.+- ...|..+.
T Consensus       299 ~~~~~~~~~~~~i~k~~~i~d~~~~~~~el~~~~~-k~Rl~~~~~d~~~~~~~le-----~~~---~l~i~~r~~f~r~~  369 (477)
T KOG2334         299 GKRIQAAQTVAQICKAFEIEDIYATLKRELDTPVC-KKRLLVSPADTVNLAERLE-----DLS---ALAIHGRKIFDRPT  369 (477)
T ss_pred             HHHHHCCHHHHHHHHHHCCHHHHHHHHHHHCCCCC-CCEEEECCCHHHHHHHHHH-----HCC---CHHHHHCCCCCCCC
T ss_conf             66765305599998886014587764775156110-0024407300055766677-----501---02342011125667


Q ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEE-EECCHHHHHHHHHHHHHHHCCCC
Q ss_conf             11000134525889875320223333431010207788845999999999899999-96898999999999999974889
Q gi|254780940|r  148 LKSGKFRRDAKTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQG-MDCSKRAAEQVAAAEVLKREGIW  226 (227)
Q Consensus       148 ~~~~~~~~dpK~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g-~g~SkK~Ae~~AA~~AL~klgi~  226 (227)
                      ...  -+..||..|..||-......|.|.++...    +..|...+..+|..+-.+ +.+++|.|+|.||..+|.++|+|
T Consensus       370 ~pa--~~~~~k~~l~~~~~~~~~~~~~ye~~~~~----d~lf~si~~~~~~~~~ssi~~~n~k~aeq~aa~~~l~~s~l~  443 (477)
T KOG2334         370 DPA--KWDTPKMVLADLCVKTKANGPVYETVQRT----DKLFSSIATARGQKYNSSIWSPNKKSAEQDAAIVALRKSNLW  443 (477)
T ss_pred             CCC--CCCCHHHHHHHHHHHHCCCCCCHHHHHHH----HHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHCCCC
T ss_conf             876--78878789887435312787601355666----666677732521322123468433367888899998754762


Q ss_pred             C
Q ss_conf             9
Q gi|254780940|r  227 T  227 (227)
Q Consensus       227 t  227 (227)
                      -
T Consensus       444 e  444 (477)
T KOG2334         444 E  444 (477)
T ss_pred             H
T ss_conf             1


No 23 
>KOG3792 consensus
Probab=92.30  E-value=0.058  Score=32.04  Aligned_cols=48  Identities=35%  Similarity=0.487  Sum_probs=37.3

Q ss_pred             EECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCC
Q ss_conf             0102077888459999999998999999689899999999999997488
Q gi|254780940|r  177 VTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGI  225 (227)
Q Consensus       177 ~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi  225 (227)
                      ++...+|.|.++|+.++.+|+.. .++.|.|++.|+.-||++.|+.+|.
T Consensus       396 Lvv~t~Ps~~~~~t~e~r~~~~~-~~a~gps~~~~~wh~~~k~lq~~~~  443 (816)
T KOG3792         396 LVVDTKPSHRPRRTMEVRVNGLP-AEAEGPSKKTAKWHAARKRLQNEGR  443 (816)
T ss_pred             CEECCCCCCCCHHHHHHHHCCCC-CCCCCCCCCCCHHHHHHHHHHCCCC
T ss_conf             42126876620243566632774-1147862123038888877632589


No 24 
>KOG3792 consensus
Probab=91.45  E-value=0.22  Score=28.54  Aligned_cols=49  Identities=27%  Similarity=0.321  Sum_probs=43.1

Q ss_pred             CCCEECCCC-CCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             431010207-78884599999999989999996898999999999999974
Q gi|254780940|r  174 EYKVTFRSG-PDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       174 ~Y~~~~~~g-~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      .|+++.+.| -.|+++|..+|.++|++ +.|.+.+++.|...|+-.|++++
T Consensus       520 k~El~set~~gs~~~R~v~gV~rvG~~-akG~~~~gd~a~~~a~Lca~~pt  569 (816)
T KOG3792         520 KYELPSETGTGSHDKRFVKGVMRVGIL-AKGLLLNGDRAVELALLCAEKPT  569 (816)
T ss_pred             CEECCCCCCCCCCCCCEEEEEEEEEHH-HCCCCCCCHHHHHHHHHHCCCCC
T ss_conf             210454467888886035543430010-00444464178889887515766


No 25 
>pfam03368 dsRNA_bind Double stranded RNA binding domain. This domain is a divergent double stranded RNA-binding domain. It is found in members of the Dicer protein family which function in RNA interference, an evolutionarily conserved mechanism for gene silencing using double-stranded RNA (dsRNA) molecules.
Probab=87.23  E-value=2.1  Score=22.51  Aligned_cols=63  Identities=24%  Similarity=0.164  Sum_probs=40.6

Q ss_pred             HHHHHHHHHC-----CCCCCCCCCEECCCCCCCCCEEEEEEEECC-----EEEEEEEECCHHHHHHHHHHHHHHH---CC
Q ss_conf             5889875320-----223333431010207788845999999999-----8999999689899999999999997---48
Q gi|254780940|r  158 KTELQEWAHA-----KFGVTPEYKVTFRSGPDHDPRFTVVVEISG-----LAPAQGMDCSKRAAEQVAAAEVLKR---EG  224 (227)
Q Consensus       158 K~~Lqe~~q~-----~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g-----~~~g~g~g~SkK~Ae~~AA~~AL~k---lg  224 (227)
                      .+.|..||.+     -....|+|.+...+     +.|.|+|.+--     ...|. .-.|++.|++.||-+|.++   +|
T Consensus         2 i~lL~~yCa~LP~d~f~~~~P~~~~~~~~-----~~~~~~v~LP~~splr~i~g~-~~~~~~~Ak~~aAf~ac~~L~~~G   75 (91)
T pfam03368         2 ISLLHRYCAKLPSDPFTKLKPEFSVEPDE-----GGYVCTVILPLNSPVREIVGP-PMKSKRLAKQSAAFEACKKLHELG   75 (91)
T ss_pred             HHHHHHHHHCCCCCCCCCCCEEEEEEECC-----CCEEEEEECCCCCCCCEEECC-CCCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             78999998218998655774169999659-----917999987899985735877-331189999999999999999868


Q ss_pred             CC
Q ss_conf             89
Q gi|254780940|r  225 IW  226 (227)
Q Consensus       225 i~  226 (227)
                      .+
T Consensus        76 ~L   77 (91)
T pfam03368        76 EL   77 (91)
T ss_pred             CC
T ss_conf             76


No 26 
>pfam11469 DUF3204 Protein of unknown function (DUF3204). This archaeal family of proteins has no known function.
Probab=79.07  E-value=4.8  Score=20.23  Aligned_cols=84  Identities=20%  Similarity=0.218  Sum_probs=49.5

Q ss_pred             HHHHHHHHHHHHHHHHHH--HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHH
Q ss_conf             887458688645478776--410468878998888888744334545431387720010366312375313333326699
Q gi|254780940|r   43 LEFLGDRILGLLISTLLF--NHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVE  120 (227)
Q Consensus        43 LEflGDavL~~~v~~~l~--~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fE  120 (227)
                      |.-+||+.++|++|--|-  .-+|...          -|-|.+|+---..-||...+.   +      +....-.+|.-|
T Consensus         3 Lak~GDSLiNfl~SlALse~lG~Ptg~----------rVPnasLaiale~agL~~~~~---P------Rtdkh~kGd~aE   63 (120)
T pfam11469         3 LAKLGDSLINFLVSLALTELLGKPTGV----------RVPNASLAIALESSGLSKLGK---P------RTDKHAKGDAAE   63 (120)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCC----------CCCCHHHHHHHHHHHHHHCCC---C------CCCCCCCCHHHH
T ss_conf             777738999999999999993898878----------788739999999870651389---7------657677518999


Q ss_pred             HHHHHHHHCCCCC--CCHHHHHCCCCC
Q ss_conf             9999996415542--200122102564
Q gi|254780940|r  121 SLIAALYLDGGIE--VAGTFVDKYWKQ  145 (227)
Q Consensus       121 A~iGAiy~d~G~~--~~~~~i~~~~~~  145 (227)
                      |+++--|+.+-+.  .+-.++..-+.+
T Consensus        64 A~iAyAWleg~is~eEavEil~~nl~~   90 (120)
T pfam11469        64 ALLAYAWLKGSISCEEAVEILYTNLDD   90 (120)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHCCCH
T ss_conf             999999980535199999999964745


No 27 
>PRK07009 consensus
Probab=58.29  E-value=8.2  Score=18.84  Aligned_cols=82  Identities=12%  Similarity=0.113  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHH---------HHHHHHHHHHHCCCCCH------HHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEECCCC
Q ss_conf             477887458688---------64547877641046887------89988888887-443345454313877200103663
Q gi|254780940|r   40 YERLEFLGDRIL---------GLLISTLLFNHFDSAKE------GELSVRFNSLV-SAETCSQVARELDLASFIRVSSDL  103 (227)
Q Consensus        40 ~erLEflGDavL---------~~~v~~~l~~~~p~~~e------G~lt~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~~  103 (227)
                      -|-+||+||++|         +|+-.++--..+|.+.+      ..|..-|...- ...+|-.+|+.++++..=+.--++
T Consensus        75 ~efl~Fi~~a~LVaHNA~FD~~FLn~EL~r~G~~~~~~~~~~viDTL~lAR~~~Pg~~~sLdaLc~R~~I~~~~r~~HgA  154 (241)
T PRK07009         75 DQIRDFVQDAELIIHNAPFDLGFLDAEFALLGLPPFTEHCAGVIDTLVQAKQMFPGKRNSLDALCDRFGISNAHRTLHGA  154 (241)
T ss_pred             HHHHHHHCCCEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCC
T ss_conf             99999966992788676999999999999839973102444476799999997899987889999982869887330242


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             12375313333326699999999
Q gi|254780940|r  104 RKDVCSFMTSIQADVVESLIAAL  126 (227)
Q Consensus       104 ~~~~~~~~~~ilad~fEA~iGAi  126 (227)
                      ..     ...+||+++=++.|+-
T Consensus       155 L~-----Da~lLa~vyl~mtgGq  172 (241)
T PRK07009        155 LL-----DSELLAEVYLAMTRGQ  172 (241)
T ss_pred             HH-----HHHHHHHHHHHHHCCC
T ss_conf             87-----7999999999983897


No 28 
>PRK06859 consensus
Probab=53.69  E-value=8.4  Score=18.76  Aligned_cols=82  Identities=12%  Similarity=0.107  Sum_probs=43.9

Q ss_pred             HHHHHHHHHHHH---------HHHHHHHHHHHCCCCCH------HHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEECCCC
Q ss_conf             477887458688---------64547877641046887------89988888887-443345454313877200103663
Q gi|254780940|r   40 YERLEFLGDRIL---------GLLISTLLFNHFDSAKE------GELSVRFNSLV-SAETCSQVARELDLASFIRVSSDL  103 (227)
Q Consensus        40 ~erLEflGDavL---------~~~v~~~l~~~~p~~~e------G~lt~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~~  103 (227)
                      .|-++|+||++|         +|+=.++--...|...+      ..|..-|...- ...+|-.+|+.++++..-|.--++
T Consensus        83 ~efl~Fi~~a~LVaHNa~FD~~FLn~El~r~g~~~~~~~~~~viDTL~lAR~~~Pg~~~sLdaLc~r~~id~~~R~~HgA  162 (253)
T PRK06859         83 QEFIDYIKGAELLIHNAPFDVGFMDYEFRKLNLNVKTDDICLVTDTLQMARQMYPGKRNNLDALCDRLGIDNSKRTLHGA  162 (253)
T ss_pred             HHHHHHHCCCEEEEECHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCH
T ss_conf             99999967997999571888999999999749996532200113399999987879977999999973998766330132


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             12375313333326699999999
Q gi|254780940|r  104 RKDVCSFMTSIQADVVESLIAAL  126 (227)
Q Consensus       104 ~~~~~~~~~~ilad~fEA~iGAi  126 (227)
                      ..     ...+|||++=++.|+-
T Consensus       163 ll-----Da~lLa~VYl~mtGGQ  180 (253)
T PRK06859        163 LL-----DAEILADVYLMMTGGQ  180 (253)
T ss_pred             HH-----HHHHHHHHHHHHCCCC
T ss_conf             88-----8999999999872675


No 29 
>KOG2783 consensus
Probab=51.95  E-value=4.5  Score=20.41  Aligned_cols=42  Identities=21%  Similarity=0.248  Sum_probs=24.1

Q ss_pred             HHHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEE
Q ss_conf             588987532022333343101020778884599999999989
Q gi|254780940|r  158 KTELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLA  199 (227)
Q Consensus       158 K~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~  199 (227)
                      |..|--++.--++...+|+-+...-|-..|.|..+|+..|..
T Consensus       231 k~~l~~L~~~Lf~~~~~~rwV~~yfpft~ps~eleI~~~~~w  272 (436)
T KOG2783         231 KQTLEGLCDELFGKEVEYRWVDAYFPFTHPSWELEIYFKGEW  272 (436)
T ss_pred             HHHHHHHHHHHCCCHHHEEHEEEECCCCCCCEEEEEEECCCC
T ss_conf             999988999862604411011057666898758999965876


No 30 
>TIGR01854 lipid_A_lpxH UDP-2,3-diacylglucosamine hydrolase; InterPro: IPR010138   This entry represents LpxH, or UDP-2,3-diacylglucosamine hydrolase (or pyrophosphatase), which is an essential enzyme in Escherichia coli that catalyses the fourth step in lipid A biosynthesis. This reaction involves pyrophosphate bond hydrolysis of the precursor UDP-2,3-diacylglucosamine to yield 2,3-diacylglucosamine 1-phosphate and UMP . Several Gram-negative bacteria have homologues of LpxH and/or LpxH2, while others have only distant orthologues of LpxH or LpxH2, or lack these enzymes altogether .; GO: 0016462 pyrophosphatase activity, 0009245 lipid A biosynthetic process, 0005737 cytoplasm.
Probab=48.81  E-value=3.3  Score=21.27  Aligned_cols=52  Identities=15%  Similarity=-0.049  Sum_probs=29.8

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCHH
Q ss_conf             77641046887899888888874433454543138772001036631237531333332669999999964155422001
Q gi|254780940|r   58 LLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAALYLDGGIEVAGT  137 (227)
Q Consensus        58 ~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGAiy~d~G~~~~~~  137 (227)
                      ||-..-|+.++++|.=|++...                           +.+..-=||+|+|||.||    |-+.+....
T Consensus         8 HL~~~~P~iTa~Fl~FL~~~A~---------------------------G~AdALYILGDLFeaWIG----DD~~~~l~~   56 (241)
T TIGR01854         8 HLSEERPDITALFLDFLREEAR---------------------------GKADALYILGDLFEAWIG----DDDPSALAR   56 (241)
T ss_pred             CCCCCCCHHHHHHHHHHHHHCC---------------------------CCCHHHHHHCCHHHCEEC----CCCCCHHHH
T ss_conf             5882460789999999875233---------------------------400002210120001146----897217999


Q ss_pred             HHH
Q ss_conf             221
Q gi|254780940|r  138 FVD  140 (227)
Q Consensus       138 ~i~  140 (227)
                      =|.
T Consensus        57 ~va   59 (241)
T TIGR01854        57 SVA   59 (241)
T ss_pred             HHH
T ss_conf             999


No 31 
>PRK13184 pknD serine/threonine-protein kinase; Reviewed
Probab=47.05  E-value=21  Score=16.25  Aligned_cols=38  Identities=16%  Similarity=0.294  Sum_probs=23.1

Q ss_pred             HHHHHHHHHHHHHHHHHH---------HHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             778874586886454787---------7641046887899888888874
Q gi|254780940|r   41 ERLEFLGDRILGLLISTL---------LFNHFDSAKEGELSVRFNSLVS   80 (227)
Q Consensus        41 erLEflGDavL~~~v~~~---------l~~~~p~~~eG~lt~lr~~lV~   80 (227)
                      --||+||.|..---..+|         -+++||+.+|  +.+++..+|.
T Consensus       551 apleylgkalvyq~~~~~~eeik~~~la~kry~~hp~--i~~l~~h~~~  597 (933)
T PRK13184        551 APLEYLGKALVYQRLGEYNEEIKSLLLALKRYSQHPE--IPRLKDHVVY  597 (933)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCC--CHHHHHHHHH
T ss_conf             7578888899998730078999999999975679987--3678989999


No 32 
>PRK06022 consensus
Probab=39.03  E-value=24  Score=15.93  Aligned_cols=80  Identities=15%  Similarity=0.151  Sum_probs=38.3

Q ss_pred             HHHHHHHHHHH---------HHHHHHHHHHHCCCCCHHH-H-H--HHHHHHH-HHHHHHHHHHHCCCCCEEEECCCCCCC
Q ss_conf             77887458688---------6454787764104688789-9-8--8888887-443345454313877200103663123
Q gi|254780940|r   41 ERLEFLGDRIL---------GLLISTLLFNHFDSAKEGE-L-S--VRFNSLV-SAETCSQVARELDLASFIRVSSDLRKD  106 (227)
Q Consensus        41 erLEflGDavL---------~~~v~~~l~~~~p~~~eG~-l-t--~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~~~~~  106 (227)
                      +-++|+||++|         +|+-.++--...|...... + |  .-|...- ...+|-.+|+.++++.--|.--++.. 
T Consensus        76 ~fl~Fi~~a~LVaHNA~FD~gFLn~El~r~G~~~~~~~~viDTL~LAR~~~Pg~~~sLdaLc~r~~Id~~~R~~HgAL~-  154 (234)
T PRK06022         76 EFLEFFDGARLVAHNATFDLGFINAEFARLGQPEITSERVVDTLALARRKHPMGPNSLDALCRRYGIDNSHRTKHGALL-  154 (234)
T ss_pred             HHHHHHCCCEEEEECHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCCCHH-
T ss_conf             9999818985999557872999999999859987778887469999998688998898999998399977735376288-


Q ss_pred             CCCCCCCCCHHHHHHHHHH
Q ss_conf             7531333332669999999
Q gi|254780940|r  107 VCSFMTSIQADVVESLIAA  125 (227)
Q Consensus       107 ~~~~~~~ilad~fEA~iGA  125 (227)
                          -..+||+++=.+.|+
T Consensus       155 ----Da~lLa~VyleL~GG  169 (234)
T PRK06022        155 ----DSELLAEVYIELIGG  169 (234)
T ss_pred             ----HHHHHHHHHHHHCCC
T ss_conf             ----899999999997288


No 33 
>pfam04034 DUF367 Domain of unknown function (DUF367).
Probab=37.36  E-value=19  Score=16.59  Aligned_cols=40  Identities=30%  Similarity=0.412  Sum_probs=27.9

Q ss_pred             CCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCC-CCCCCCC
Q ss_conf             3133333266999999996415542200122102-5643111
Q gi|254780940|r  109 SFMTSIQADVVESLIAALYLDGGIEVAGTFVDKY-WKQRALK  149 (227)
Q Consensus       109 ~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~-~~~~~~~  149 (227)
                      -+++-.|+ +.||+.+|+|+-+-.+.++.++..| |.+....
T Consensus        61 YGKP~kLs-~vEAlAAaLyI~G~~~~A~~lL~~FkWG~~Fl~  101 (128)
T pfam04034        61 YGKPCKLS-CVEALAAALYIVGFKDEASELLSKFKWGHTFLE  101 (128)
T ss_pred             CCCCCCCC-HHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHH
T ss_conf             68876212-799999999994999999999850897178999


No 34 
>pfam06754 PhnG Phosphonate metabolism protein PhnG. This family consists of several bacterial phosphonate metabolism protein PhnG sequences. In Escherichia coli, the phn operon encodes proteins responsible for the uptake and breakdown of phosphonates. The exact function of PhnG is unknown, however it is thought likely that along with six other proteins PhnG makes up the the C-P (carbon-phosphorus) lyase.
Probab=36.49  E-value=32  Score=15.19  Aligned_cols=36  Identities=19%  Similarity=0.183  Sum_probs=27.5

Q ss_pred             EEEEEEEECCEEEEEEE--ECCHHHHHHHHHHHHHHHC
Q ss_conf             59999999998999999--6898999999999999974
Q gi|254780940|r  188 RFTVVVEISGLAPAQGM--DCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       188 ~f~v~v~v~g~~~g~g~--g~SkK~Ae~~AA~~AL~kl  223 (227)
                      +-.|.|.+++-.+|-|.  |.+|+.||.-|--+||-|-
T Consensus        65 VTRc~VrL~~G~~G~~yv~GRdk~~AelaA~~DALlQ~  102 (147)
T pfam06754        65 VTRAAVRLASGTVGHSYVLGRDKRHAELAALIDALLQD  102 (147)
T ss_pred             EEEEEEEECCCCEEEEEEECCCHHHHHHHHHHHHHHCC
T ss_conf             88899994899756887635899999999999998479


No 35 
>PRK06631 consensus
Probab=36.46  E-value=14  Score=17.43  Aligned_cols=40  Identities=13%  Similarity=0.086  Sum_probs=23.9

Q ss_pred             HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             433454543138772001036631237531333332669999999
Q gi|254780940|r   81 AETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAA  125 (227)
Q Consensus        81 n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGA  125 (227)
                      ..+|..+|+.++++.--+..-++..     -..++|++|=++.|+
T Consensus       136 ~~sLdaLc~r~~I~~s~r~~H~AL~-----DA~llA~Vyl~l~gG  175 (229)
T PRK06631        136 KYNLDALCKRFKVDNSGRQLHGALK-----DAALLAEVYVELTGG  175 (229)
T ss_pred             CCCHHHHHHHCCCCCCCCCCCCCHH-----HHHHHHHHHHHHHCC
T ss_conf             8899999998499999855568689-----999999999997178


No 36 
>PRK00394 transcription factor; Reviewed
Probab=34.80  E-value=34  Score=15.02  Aligned_cols=27  Identities=33%  Similarity=0.380  Sum_probs=18.1

Q ss_pred             CCEEEEEEEECCEEEEEEEECCHHHHHH
Q ss_conf             8459999999998999999689899999
Q gi|254780940|r  186 DPRFTVVVEISGLAPAQGMDCSKRAAEQ  213 (227)
Q Consensus       186 ~~~f~v~v~v~g~~~g~g~g~SkK~Ae~  213 (227)
                      +|.-++-++..|+.+-+|. +|..++++
T Consensus       139 ~pk~~~liF~sGkivitGa-ks~~~~~~  165 (178)
T PRK00394        139 DPKVVVLLFGSGKLVITGA-KSEEDAEK  165 (178)
T ss_pred             CCCEEEEEECCCEEEEECC-CCHHHHHH
T ss_conf             9978999977984999866-99999999


No 37 
>TIGR02195 heptsyl_trn_II lipopolysaccharide heptosyltransferase II; InterPro: IPR011910    This family consists of examples of ADP-heptose:LPS heptosyltransferase II, an enzyme of LPS inner core region biosynthesis. LPS, composed of lipid A, a core region, and O antigen, is found in the outer membrane of Gram-negative bacteria.; GO: 0016757 transferase activity transferring glycosyl groups, 0009103 lipopolysaccharide biosynthetic process.
Probab=34.44  E-value=26  Score=15.79  Aligned_cols=24  Identities=21%  Similarity=0.409  Sum_probs=18.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             874586886454787764104688
Q gi|254780940|r   44 EFLGDRILGLLISTLLFNHFDSAK   67 (227)
Q Consensus        44 EflGDavL~~~v~~~l~~~~p~~~   67 (227)
                      .|+||+|+.-..=.-|.++||+..
T Consensus         8 sWVGDmvMaQ~Lf~~Lk~~yP~~~   31 (361)
T TIGR02195         8 SWVGDMVMAQSLFRLLKKRYPDAV   31 (361)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             736555676899999998589838


No 38 
>PRK08816 consensus
Probab=32.78  E-value=13  Score=17.52  Aligned_cols=82  Identities=17%  Similarity=0.151  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHHH---------HHHHHHHHHH--HCCCCC-----HHHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEECCC
Q ss_conf             477887458688---------6454787764--104688-----789988888887-44334545431387720010366
Q gi|254780940|r   40 YERLEFLGDRIL---------GLLISTLLFN--HFDSAK-----EGELSVRFNSLV-SAETCSQVARELDLASFIRVSSD  102 (227)
Q Consensus        40 ~erLEflGDavL---------~~~v~~~l~~--~~p~~~-----eG~lt~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~  102 (227)
                      -|-++|+||++|         +|+=.++-..  .+|...     ...|..-|...= ...+|-.+|+.++++..=|.--+
T Consensus        75 ~efl~Fi~ds~LVaHNa~FDi~FLn~El~r~g~~~~~~~~~~~v~DTl~lAr~~~Pg~~nsLDaLc~r~~id~~~R~~Hg  154 (244)
T PRK08816         75 DEFLAYIDGAELIIHNAAFDLGFLDNELSLLGDQYGRIVDRATVVDTLMMARERYPGQRNSLDALCKRLGVDNSHRQLHG  154 (244)
T ss_pred             HHHHHHHCCCEEEEECCHHHHHHHHHHHHHHCCCCCCCCCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCC
T ss_conf             99999828998999663652989999999848875676431010438999998787997789999997497887735014


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHHH
Q ss_conf             312375313333326699999999
Q gi|254780940|r  103 LRKDVCSFMTSIQADVVESLIAAL  126 (227)
Q Consensus       103 ~~~~~~~~~~~ilad~fEA~iGAi  126 (227)
                      +..     ...+|||++=++.|+-
T Consensus       155 ALl-----Da~lLa~VYl~mtgGq  173 (244)
T PRK08816        155 ALL-----DAQILADVYIALTSGQ  173 (244)
T ss_pred             HHH-----HHHHHHHHHHHHCCCC
T ss_conf             888-----7999999999974786


No 39 
>COG2042 Uncharacterized conserved protein [Function unknown]
Probab=32.00  E-value=25  Score=15.82  Aligned_cols=39  Identities=28%  Similarity=0.372  Sum_probs=27.2

Q ss_pred             CCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCC-CCCCCCC
Q ss_conf             133333266999999996415542200122102-5643111
Q gi|254780940|r  110 FMTSIQADVVESLIAALYLDGGIEVAGTFVDKY-WKQRALK  149 (227)
Q Consensus       110 ~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~-~~~~~~~  149 (227)
                      +++=.| .+.||+++|+|+-+-.+.+..++..| |.+..+.
T Consensus       110 Gkp~kL-ss~EAlaAaLYI~G~~deA~~lls~F~WG~~Fle  149 (179)
T COG2042         110 GKPFKL-SSAEALAAALYIVGFKDEASELLSKFKWGHTFLE  149 (179)
T ss_pred             CCCCHH-CHHHHHHHHHHHHCCHHHHHHHHHHCCCCHHHHH
T ss_conf             875010-4499999999982769799999842760188999


No 40 
>PRK08858 consensus
Probab=31.80  E-value=22  Score=16.14  Aligned_cols=40  Identities=13%  Similarity=0.042  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             433454543138772001036631237531333332669999999
Q gi|254780940|r   81 AETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAA  125 (227)
Q Consensus        81 n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGA  125 (227)
                      ..+|-.+|+.++++.-=|.--++..     -..+||+++=++.|+
T Consensus       147 ~~sLdaLc~r~~Id~s~R~~HgALl-----Da~lLa~Vyl~mtgG  186 (246)
T PRK08858        147 RNNLDVLCERYGIDNSHRTLHGALL-----DAEILADVYLLMTGG  186 (246)
T ss_pred             CCCHHHHHHHCCCCCCCCCCCCHHH-----HHHHHHHHHHHHCCC
T ss_conf             8888999998198988834023088-----899999999997289


No 41 
>PRK02287 hypothetical protein; Provisional
Probab=31.59  E-value=27  Score=15.67  Aligned_cols=41  Identities=29%  Similarity=0.355  Sum_probs=27.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHCC-CCCCCCC
Q ss_conf             53133333266999999996415542200122102-5643111
Q gi|254780940|r  108 CSFMTSIQADVVESLIAALYLDGGIEVAGTFVDKY-WKQRALK  149 (227)
Q Consensus       108 ~~~~~~ilad~fEA~iGAiy~d~G~~~~~~~i~~~-~~~~~~~  149 (227)
                      +-+++-.|+ +.||+.+|+|+-+-.+.+..++..| |.+....
T Consensus        99 NYGkP~kLs-~vEAlAAaLyI~G~~~~A~~lL~~FkWG~~Fl~  140 (169)
T PRK02287         99 NYGKPCKLS-SVEAFAAALYILGYKEEAEKILSKFKWGHTFLE  140 (169)
T ss_pred             CCCCCCCCC-HHHHHHHHHHHCCCHHHHHHHHHCCCCCHHHHH
T ss_conf             668876212-799999999994999999999850897278999


No 42 
>KOG2146 consensus
Probab=31.56  E-value=38  Score=14.70  Aligned_cols=73  Identities=21%  Similarity=0.276  Sum_probs=39.0

Q ss_pred             CCCCCHHH-HHHHHCCCCCCHHHHHHHCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCC------------
Q ss_conf             97358899-99983696589899998424612126676654778874586886454787764104688------------
Q gi|254780940|r    1 MSALRYST-LEKRIGYAFANRSLLEKALTHSSISHSYQESYERLEFLGDRILGLLISTLLFNHFDSAK------------   67 (227)
Q Consensus         1 m~~~~~~~-l~~~lgy~f~~~~ll~~A~th~S~~~~~~~~~erLEflGDavL~~~v~~~l~~~~p~~~------------   67 (227)
                      |+.++|.+ |++++...=-|.++|.-=+|-        .-||-|-|--|-|++||....=-..+|+-.            
T Consensus        22 mkqmKF~~~lekkVDmsKvnleVlkPWItk--------rvneilgfEDdVViefvynqLee~k~ldpkkmQiNlTGFLng   93 (354)
T KOG2146          22 MKQMKFPACLEKKVDMSKVNLEVLKPWITK--------RVNEILGFEDDVVIEFVYNQLEEAKNLDPKKMQINLTGFLNG   93 (354)
T ss_pred             HHHCCCHHHHHHHCCHHHCCHHHHHHHHHH--------HHHHHHCCCCCHHHHHHHHHHHHHCCCCCHHEEEEEEHHCCC
T ss_conf             986353777765312433034453389988--------788763664203599988777651278813146521000254


Q ss_pred             ---HHHHHHHHHHHHHH
Q ss_conf             ---78998888888744
Q gi|254780940|r   68 ---EGELSVRFNSLVSA   81 (227)
Q Consensus        68 ---eG~lt~lr~~lV~n   81 (227)
                         -.+|-+|.+.|+++
T Consensus        94 rnAreFmgeLW~LliS~  110 (354)
T KOG2146          94 RNAREFMGELWSLLISE  110 (354)
T ss_pred             CCHHHHHHHHHHHHHHH
T ss_conf             20899999999998720


No 43 
>pfam11324 DUF3126 Protein of unknown function (DUF3126). This family of proteins with unknown function appear to be restricted to Alphaproteobacteria.
Probab=30.77  E-value=40  Score=14.61  Aligned_cols=40  Identities=25%  Similarity=0.233  Sum_probs=25.8

Q ss_pred             HHHHHHHHCCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEE
Q ss_conf             889875320223333431010207788845999999999899999
Q gi|254780940|r  159 TELQEWAHAKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQG  203 (227)
Q Consensus       159 ~~Lqe~~q~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g  203 (227)
                      .+||.|+++.++. |...+.....++    =.|+|+++++.+|.-
T Consensus         3 ~klq~yLr~~F~n-~~i~v~~r~k~~----DSaEV~~~~EFiGvi   42 (63)
T pfam11324         3 KKLQAYLKRKFGN-PTLRVKARPKKG----DSAEVYIGDEFIGVL   42 (63)
T ss_pred             HHHHHHHHHHHCC-CCEEEECCCCCC----CCEEEEECCEEEEEE
T ss_conf             8999999997199-965997679999----876998589899999


No 44 
>COG4148 ModC ABC-type molybdate transport system, ATPase component [Inorganic ion transport and metabolism]
Probab=30.66  E-value=19  Score=16.59  Aligned_cols=60  Identities=25%  Similarity=0.510  Sum_probs=36.2

Q ss_pred             CCCHHHHHHHHCCCCCCHHHHHHHCCCHHHCCCCCCCHH----HH-HHHHHHHHHHHHHHHHHHHCCC-CCHHH
Q ss_conf             358899999836965898999984246121266766547----78-8745868864547877641046-88789
Q gi|254780940|r    3 ALRYSTLEKRIGYAFANRSLLEKALTHSSISHSYQESYE----RL-EFLGDRILGLLISTLLFNHFDS-AKEGE   70 (227)
Q Consensus         3 ~~~~~~l~~~lgy~f~~~~ll~~A~th~S~~~~~~~~~e----rL-EflGDavL~~~v~~~l~~~~p~-~~eG~   70 (227)
                      ++.+..=+.++||-|+|-+|    |-|=|...+.  .|-    +. +|  |.+.++.-..+|..+||. ++-|+
T Consensus        68 ~i~lp~~~RriGYVFQDARL----FpH~tVrgNL--~YG~~~~~~~~f--d~iv~lLGI~hLL~R~P~~LSGGE  133 (352)
T COG4148          68 GIFLPPEKRRIGYVFQDARL----FPHYTVRGNL--RYGMWKSMRAQF--DQLVALLGIEHLLDRYPGTLSGGE  133 (352)
T ss_pred             CCCCCHHHHEEEEEEECCCC----CCCEEEECCH--HHHCCCCCHHHH--HHHHHHHCCHHHHHCCCCCCCCCH
T ss_conf             74467546113567400201----6651773220--010143536779--999998484867850877567615


No 45 
>cd00652 TBP_TLF TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA. New members of the TBP family, called TBP-like proteins (TBLP, TLF, TLP) or TBP-related factors (TRF1, TRF2,TRP), are similar to the core domain of TBPs, with identical or chemically similar amino acids at many
Probab=30.12  E-value=41  Score=14.55  Aligned_cols=26  Identities=19%  Similarity=0.333  Sum_probs=16.3

Q ss_pred             CEEEEEEEECCEEEEEEEECCHHHHHH
Q ss_conf             459999999998999999689899999
Q gi|254780940|r  187 PRFTVVVEISGLAPAQGMDCSKRAAEQ  213 (227)
Q Consensus       187 ~~f~v~v~v~g~~~g~g~g~SkK~Ae~  213 (227)
                      +.-++-++..|+.+-+|. +|..++++
T Consensus       138 pk~~~liF~sGkvvitGa-ks~~~~~~  163 (174)
T cd00652         138 PKVVLLIFVSGKIVITGA-KSREDIYE  163 (174)
T ss_pred             CCEEEEEECCCEEEEECC-CCHHHHHH
T ss_conf             978999977987999747-99999999


No 46 
>cd04518 TBP_archaea archaeal TATA box binding protein (TBP): TBPs are transcription factors present in archaea and eukaryotes, that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=29.31  E-value=42  Score=14.46  Aligned_cols=27  Identities=22%  Similarity=0.346  Sum_probs=17.9

Q ss_pred             CCEEEEEEEECCEEEEEEEECCHHHHHH
Q ss_conf             8459999999998999999689899999
Q gi|254780940|r  186 DPRFTVVVEISGLAPAQGMDCSKRAAEQ  213 (227)
Q Consensus       186 ~~~f~v~v~v~g~~~g~g~g~SkK~Ae~  213 (227)
                      +|.-++-++..|+.+-+|. +|..+++.
T Consensus       136 ~pk~~~liF~SGKivitGa-ks~~~~~~  162 (174)
T cd04518         136 EPKVVLLLFSSGKMVITGA-KSEEDAKR  162 (174)
T ss_pred             CCCEEEEEECCCEEEEECC-CCHHHHHH
T ss_conf             9978999987984999867-99999999


No 47 
>LOAD_cdc45 consensus
Probab=28.74  E-value=43  Score=14.40  Aligned_cols=73  Identities=18%  Similarity=0.191  Sum_probs=33.7

Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCC-HHHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf             4104688789988888887443345454313877200103663123753133333-266999999996415542200122
Q gi|254780940|r   61 NHFDSAKEGELSVRFNSLVSAETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQ-ADVVESLIAALYLDGGIEVAGTFV  139 (227)
Q Consensus        61 ~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~il-ad~fEA~iGAiy~d~G~~~~~~~i  139 (227)
                      ++|..++..    +|..+  .+.|.+.|.++||.++...+-. ..-+.+.  ++- +|+++|+.+-+  ++|-+.-+.|.
T Consensus       338 Q~y~~Md~~----lK~~L--~~~l~k~a~~ygL~~l~~~sF~-r~~Gyk~--~lsAsD~v~a~~AlL--E~~~~~~~~~~  406 (578)
T LOAD_cdc45      338 QTYEAMDLS----LKREL--VSMLEKSADKYGLTDIIYQGFT-RTLGFRD--KLAASDVVEALSALL--EMGTARRRSGT  406 (578)
T ss_pred             HHHHHCCHH----HHHHH--HHHHHHHHHHCCCCCEEECCEE-EEECCCC--CEEHHHHHHHHHHHH--HCCCCCCCCHH
T ss_conf             455427999----99999--9999998876699752526456-7852665--202899999989998--33854456588


Q ss_pred             HCCCC
Q ss_conf             10256
Q gi|254780940|r  140 DKYWK  144 (227)
Q Consensus       140 ~~~~~  144 (227)
                      .+||.
T Consensus       407 ~nFw~  411 (578)
T LOAD_cdc45      407 SNFYE  411 (578)
T ss_pred             HHHHH
T ss_conf             89999


No 48 
>pfam00333 Ribosomal_S5 Ribosomal protein S5, N-terminal domain.
Probab=28.55  E-value=43  Score=14.38  Aligned_cols=39  Identities=13%  Similarity=0.041  Sum_probs=27.0

Q ss_pred             CCCEEEEEEEECCE--E--EEEEEECCHHHHHHHHHHHHHHHC
Q ss_conf             88459999999998--9--999996898999999999999974
Q gi|254780940|r  185 HDPRFTVVVEISGL--A--PAQGMDCSKRAAEQVAAAEVLKRE  223 (227)
Q Consensus       185 ~~~~f~v~v~v~g~--~--~g~g~g~SkK~Ae~~AA~~AL~kl  223 (227)
                      ....|.+-|.+++.  .  +|.|.+..-..|-++|-..|-++|
T Consensus        20 r~~~f~alvvVGn~~G~vG~G~gKa~ev~~Ai~KA~~~Ak~nm   62 (67)
T pfam00333        20 RRFSFRALVVVGDKNGHVGLGEGKAKEVPGAIRKAIEDAKLNL   62 (67)
T ss_pred             CCEEEEEEEEEECCCCCEEEEEEECCCHHHHHHHHHHHHHHCC
T ss_conf             6115899999977998397746643618999999999998676


No 49 
>TIGR02706 P_butyryltrans phosphate butyryltransferase; InterPro: IPR014079   Members of this family are phosphate butyryltransferase enzymes, also called phosphotransbutyrylase. In general, this enzyme is found in butyrate-producing anaerobic bacteria, encoded next to the gene for butyrate kinase. Together, these two enzymes represent what may be the less common of two pathways for butyrate production from butyryl-CoA. The alternative is transfer of the CoA group to acetate by butyryl-CoA:acetate CoA transferase. This entry does not include the homologue from Thermotoga maritima, whose activity on butyryl-CoA is only 30 0f its activity with acetyl-CoA..
Probab=28.21  E-value=44  Score=14.34  Aligned_cols=51  Identities=18%  Similarity=0.275  Sum_probs=34.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCC--CCEEEECCCCCC
Q ss_conf             65477887458688645478776410468878998888888744334545431387--720010366312
Q gi|254780940|r   38 ESYERLEFLGDRILGLLISTLLFNHFDSAKEGELSVRFNSLVSAETCSQVARELDL--ASFIRVSSDLRK  105 (227)
Q Consensus        38 ~~~erLEflGDavL~~~v~~~l~~~~p~~~eG~lt~lr~~lV~n~~La~~a~~lgl--~~~l~~~~~~~~  105 (227)
                      +.|+||=||-         +-=|..||++.+      +..+|+|..=  +|+..|+  ++--.++.-|--
T Consensus       127 P~~dRLl~lT---------DaAfN~yP~Lk~------K~~ii~NaV~--VAha~Gi~~PkVA~l~AVEvV  179 (295)
T TIGR02706       127 PGFDRLLFLT---------DAAFNIYPELKD------KVQIINNAVK--VAHAIGIEVPKVAVLAAVEVV  179 (295)
T ss_pred             CCCCHHHHHH---------HHHHCCCCCHHH------HHHHHHHHHH--HHHCCCCCCCCEEEECCEEEE
T ss_conf             9855143231---------266502878789------9999764755--023217886861153026356


No 50 
>pfam07125 DUF1378 Protein of unknown function (DUF1378). This family consists of hypothetical bacterial and phage proteins of around 59 residues in length. Bacterial members of this family seem to be specific to Enterobacteria. The function of this family is unknown.
Probab=27.96  E-value=21  Score=16.26  Aligned_cols=30  Identities=27%  Similarity=0.526  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHH-CCCCCCCHHHHHCCCCCCC
Q ss_conf             69999999964-1554220012210256431
Q gi|254780940|r  118 VVESLIAALYL-DGGIEVAGTFVDKYWKQRA  147 (227)
Q Consensus       118 ~fEA~iGAiy~-d~G~~~~~~~i~~~~~~~~  147 (227)
                      -|...|.++|+ .+|+.+++.++.+-+....
T Consensus        10 YFCtvVc~lYL~sGGYk~iR~~~rrkID~~A   40 (59)
T pfam07125        10 YFCTVVCALYLVSGGYKVIRNYIRRKIDDAA   40 (59)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf             9999999999983439999999999875999


No 51 
>KOG3302 consensus
Probab=27.64  E-value=45  Score=14.28  Aligned_cols=17  Identities=18%  Similarity=0.536  Sum_probs=10.5

Q ss_pred             CEEEEEEEECCEEEEEE
Q ss_conf             45999999999899999
Q gi|254780940|r  187 PRFTVVVEISGLAPAQG  203 (227)
Q Consensus       187 ~~f~v~v~v~g~~~g~g  203 (227)
                      +.-+..+++.|.++-+|
T Consensus       158 pkv~l~IF~tG~Vvvtg  174 (200)
T KOG3302         158 PKVVLLIFVTGKVVVTG  174 (200)
T ss_pred             CCEEEEEECCCEEEEEE
T ss_conf             86899992377799970


No 52 
>TIGR02587 TIGR02587 putative integral membrane protein TIGR02587; InterPro: IPR013416    This entry is found in Nostoc sp. PCC 7120, Agrobacterium tumefaciens, Rhizobium meliloti, and Gloeobacter violaceus in a conserved two-gene neighbourhood. Proteins containing this entry appear to span the membrane seven times..
Probab=27.45  E-value=45  Score=14.26  Aligned_cols=28  Identities=25%  Similarity=0.287  Sum_probs=23.1

Q ss_pred             CCCCHHHHHHHHHHHHHCCCCCCCHHHH
Q ss_conf             3333266999999996415542200122
Q gi|254780940|r  112 TSIQADVVESLIAALYLDGGIEVAGTFV  139 (227)
Q Consensus       112 ~~ilad~fEA~iGAiy~d~G~~~~~~~i  139 (227)
                      +--++|+|--+|||+++.-+...+++.+
T Consensus       154 ~gyl~eLf~~~vGAl~ls~NiAPTeEv~  181 (284)
T TIGR02587       154 YGYLAELFLMLVGALFLSLNIAPTEEVV  181 (284)
T ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCHHHH
T ss_conf             0359999999999999984279831189


No 53 
>TIGR01088 aroQ 3-dehydroquinate dehydratase, type II; InterPro: IPR001874 3-dehydroquinate dehydratase (4.2.1.10 from EC), or dehydroquinase, catalyzes the conversion of 3-dehydroquinate into 3-dehydroshikimate. It is the third step in the shikimate pathway for the biosynthesis of aromatic amino acids from chorismate. Two classes of dehydroquinases exist, known as types I and II. Class-II enzymes are homododecameric enzymes of about 17 kDa. They are found in some bacteria such as actinomycetales ,  and some fungi where they act in a catabolic pathway that allows the use of quinic acid as a carbon source.; GO: 0003855 3-dehydroquinate dehydratase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=26.41  E-value=18  Score=16.65  Aligned_cols=18  Identities=6%  Similarity=-0.164  Sum_probs=6.9

Q ss_pred             EECCCCCCCCCCCCCCCCH
Q ss_conf             1036631237531333332
Q gi|254780940|r   98 RVSSDLRKDVCSFMTSIQA  116 (227)
Q Consensus        98 ~~~~~~~~~~~~~~~~ila  116 (227)
                      +-||+..+-+.|+ |.+++
T Consensus         5 lnGPNLN~LG~RE-P~~YG   22 (144)
T TIGR01088         5 LNGPNLNMLGLRE-PGVYG   22 (144)
T ss_pred             ECCCCCCCCCCCC-CCCCC
T ss_conf             2088747578746-53247


No 54 
>PRK05711 DNA polymerase III subunit epsilon; Provisional
Probab=26.18  E-value=36  Score=14.89  Aligned_cols=40  Identities=10%  Similarity=0.091  Sum_probs=23.6

Q ss_pred             HHHHHHHHHHCCCCCEEEECCCCCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             433454543138772001036631237531333332669999999
Q gi|254780940|r   81 AETCSQVARELDLASFIRVSSDLRKDVCSFMTSIQADVVESLIAA  125 (227)
Q Consensus        81 n~~La~~a~~lgl~~~l~~~~~~~~~~~~~~~~ilad~fEA~iGA  125 (227)
                      ..+|-.+|+.++++.--|.--++..     -..++|++|=++.|+
T Consensus       136 ~~sLdaLc~r~~I~~s~R~~HgAL~-----Da~llA~Vyl~l~gG  175 (240)
T PRK05711        136 RNSLDALCKRYGIDNSHRTLHGALL-----DAEILAEVYLAMTGG  175 (240)
T ss_pred             CCCHHHHHHHCCCCCCCCCCCCHHH-----HHHHHHHHHHHHCCC
T ss_conf             8899999998098988756576488-----899999999997178


No 55 
>PRK10916 ADP-heptose:LPS heptosyltransferase II; Provisional
Probab=26.16  E-value=36  Score=14.90  Aligned_cols=24  Identities=17%  Similarity=0.314  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             874586886454787764104688
Q gi|254780940|r   44 EFLGDRILGLLISTLLFNHFDSAK   67 (227)
Q Consensus        44 EflGDavL~~~v~~~l~~~~p~~~   67 (227)
                      -++||.|+..-+...|-++||+..
T Consensus         9 ~~iGDvvlttP~l~aLr~~~P~a~   32 (348)
T PRK10916          9 SWVGDMMMSQSLYRTLKARYPQAI   32 (348)
T ss_pred             CCHHHHHHHHHHHHHHHHHCCCCE
T ss_conf             764699999999999998789988


No 56 
>TIGR01256 modA molybdate ABC transporter, periplasmic molybdate-binding protein; InterPro: IPR005950   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     This entry describes the molybdate ABC transporter periplasmic binding protein in bacteria and archae. Several of the periplasmic receptors constitute a diverse class of binding proteins that differ widely in size, sequence and ligand specificity. It has been shown experimentally by radioactive labeling that ModA represents a hydrophylioc periplasmic-binding protein in Gram-negative organisms and its counterpart in Gram-positive organisms is a lipoprotein. The other components of the system include ModB, an integral membrane protein and ModC, the ATP-binding subunit. Almost all of them display a common beta/alpha folding motif and have similar tertiary structures consisting of two globular domains.; GO: 0015412 molybdate transmembrane-transporting ATPase activity, 0015689 molybdate ion transport, 0030288 outer membrane-bounded periplasmic space.
Probab=25.84  E-value=42  Score=14.47  Aligned_cols=13  Identities=54%  Similarity=1.038  Sum_probs=8.2

Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             9999999974889
Q gi|254780940|r  214 VAAAEVLKREGIW  226 (227)
Q Consensus       214 ~AA~~AL~klgi~  226 (227)
                      .||.++|+++|+|
T Consensus       120 ~~A~E~L~~lgl~  132 (225)
T TIGR01256       120 AAAKEVLQKLGLW  132 (225)
T ss_pred             HHHHHHHHHCCCC
T ss_conf             9999999707976


No 57 
>PRK10422 lipopolysaccharide core biosynthesis protein; Provisional
Probab=25.25  E-value=37  Score=14.76  Aligned_cols=10  Identities=10%  Similarity=0.478  Sum_probs=4.2

Q ss_pred             CEEEECCCCC
Q ss_conf             2001036631
Q gi|254780940|r   95 SFIRVSSDLR  104 (227)
Q Consensus        95 ~~l~~~~~~~  104 (227)
                      +|+.++++..
T Consensus       184 ~~ivi~pga~  193 (352)
T PRK10422        184 NYVVIQPTAR  193 (352)
T ss_pred             CEEEEECCCC
T ss_conf             8799967899


No 58 
>COG1737 RpiR Transcriptional regulators [Transcription]
Probab=25.25  E-value=40  Score=14.57  Aligned_cols=44  Identities=20%  Similarity=0.187  Sum_probs=31.5

Q ss_pred             HHHHHHHHHCCCCCHHHHHHH-HHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             547877641046887899888-88887443345454313877200
Q gi|254780940|r   54 LISTLLFNHFDSAKEGELSVR-FNSLVSAETCSQVARELDLASFI   97 (227)
Q Consensus        54 ~v~~~l~~~~p~~~eG~lt~l-r~~lV~n~~La~~a~~lgl~~~l   97 (227)
                      -|.+|+..+.+....+....+ ...=||..++.+.|+++|+..|=
T Consensus        22 ~iA~yil~~~~~~~~~si~elA~~a~VS~aTv~Rf~~kLGf~Gf~   66 (281)
T COG1737          22 KIADYILANPDEVALLSIAELAERAGVSPATVVRFARKLGFEGFS   66 (281)
T ss_pred             HHHHHHHHCHHHHHHCCHHHHHHHHCCCHHHHHHHHHHCCCCCHH
T ss_conf             999999939678856149999988199888999999985999889


No 59 
>cd04516 TBP_eukaryotes eukaryotic TATA box binding protein (TBP): Present in archaea and eukaryotes, TBPs are transcription factors that recognize promoters and initiate transcription. TBP has been shown to be an essential component of three different transcription initiation complexes: SL1, TFIID and TFIIIB, directing transcription by RNA polymerases I, II and III, respectively. TBP binds directly to the TATA box promoter element, where it nucleates polymerase assembly, thus defining the transcription start site. TBP's binding in the minor groove induces a dramatic DNA bending while its own structure barely changes. The conserved core domain of TBP, which binds to the TATA box, has a bipartite structure, with intramolecular symmetry generating a saddle-shaped structure that sits astride the DNA.
Probab=24.85  E-value=50  Score=13.97  Aligned_cols=26  Identities=23%  Similarity=0.356  Sum_probs=16.6

Q ss_pred             CEEEEEEEECCEEEEEEEECCHHHHHH
Q ss_conf             459999999998999999689899999
Q gi|254780940|r  187 PRFTVVVEISGLAPAQGMDCSKRAAEQ  213 (227)
Q Consensus       187 ~~f~v~v~v~g~~~g~g~g~SkK~Ae~  213 (227)
                      +.-++-++..|+.+-+|. +|..+++.
T Consensus       137 ~~~~~liF~sGkvvitGa-ks~~~~~~  162 (174)
T cd04516         137 PKIVLLIFVSGKIVLTGA-KSREEIYQ  162 (174)
T ss_pred             CCEEEEEECCCEEEEECC-CCHHHHHH
T ss_conf             988999967987999767-99999999


No 60 
>cd01831 Endoglucanase_E_like Endoglucanase E-like members of the SGNH hydrolase family; Endoglucanase E catalyzes the endohydrolysis of 1,4-beta-glucosidic linkages in cellulose, lichenin and cereal beta-D-glucans.
Probab=24.49  E-value=9.7  Score=18.37  Aligned_cols=20  Identities=5%  Similarity=-0.077  Sum_probs=13.8

Q ss_pred             EEEEEEECCHHHHHHHHHHH
Q ss_conf             99999968989999999999
Q gi|254780940|r  199 APAQGMDCSKRAAEQVAAAE  218 (227)
Q Consensus       199 ~~g~g~g~SkK~Ae~~AA~~  218 (227)
                      .+|.+.++|...-++.|.+-
T Consensus       145 ~~g~~~HPs~~gh~kmA~~L  164 (169)
T cd01831         145 DIGCDWHPTVAGHQKIAKHL  164 (169)
T ss_pred             CCCCCCCCCHHHHHHHHHHH
T ss_conf             76898894999999999999


No 61 
>cd04517 TLF TBP-like factors (TLF; also called TLP, TRF, TRP), which are found in most metazoans. TLFs and TBPs have well-conserved core domains; however, they only share about 60% similarity. TLFs, like TBPs, interact with TFIIA and TFIIB, which are part of the basal transcription machinery. Yet, in contrast to TBPs, TLFs seem not to interact with the TATA-box and even have a negative effect on the transcription of TATA-containing promoters. Recent results indicate that TLFs are involved in the transcription via TATA-less promoters.
Probab=24.29  E-value=52  Score=13.90  Aligned_cols=27  Identities=22%  Similarity=0.297  Sum_probs=16.6

Q ss_pred             CCEEEEEEEECCEEEEEEEECCHHHHHH
Q ss_conf             8459999999998999999689899999
Q gi|254780940|r  186 DPRFTVVVEISGLAPAQGMDCSKRAAEQ  213 (227)
Q Consensus       186 ~~~f~v~v~v~g~~~g~g~g~SkK~Ae~  213 (227)
                      ++.-++-++..|+.+-+|. +|..+++.
T Consensus       137 ~pk~~~lIF~sGkvvitGa-ks~~e~~~  163 (174)
T cd04517         137 GPRATLSIFSTGSVTVTGA-RSMEDVRE  163 (174)
T ss_pred             CCCEEEEEECCCEEEEECC-CCHHHHHH
T ss_conf             9968999967977999806-99899999


No 62 
>pfam11940 DUF3458 Domain of unknown function (DUF3458). This presumed domain is functionally uncharacterized. This domain is found in bacteria, archaea and eukaryotes. This domain is typically between 402 to 419 amino acids in length. This domain is found associated with pfam01433. This domain has a conserved FSAPV sequence motif.
Probab=23.47  E-value=54  Score=13.80  Aligned_cols=26  Identities=12%  Similarity=0.013  Sum_probs=13.5

Q ss_pred             HHHHHHHCCCCCCHHHHHHHCCCHHH
Q ss_conf             99999836965898999984246121
Q gi|254780940|r    7 STLEKRIGYAFANRSLLEKALTHSSI   32 (227)
Q Consensus         7 ~~l~~~lgy~f~~~~ll~~A~th~S~   32 (227)
                      .++...|.=.--|+.+..++||=||.
T Consensus       134 ~a~~~~L~d~~lD~a~~A~~L~LPse  159 (408)
T pfam11940       134 DAFRALLADESLDPAFRALLLTLPSE  159 (408)
T ss_pred             HHHHHHHCCCCCCHHHHHHHHCCCCH
T ss_conf             99999975987799999998639997


No 63 
>PRK07982 consensus
Probab=22.69  E-value=29  Score=15.42  Aligned_cols=81  Identities=11%  Similarity=0.119  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHH-------HHHHHHHHHHH----CCCCCH-----HHHHHHHHHHH-HHHHHHHHHHHCCCCCEEEECCC
Q ss_conf             477887458688-------64547877641----046887-----89988888887-44334545431387720010366
Q gi|254780940|r   40 YERLEFLGDRIL-------GLLISTLLFNH----FDSAKE-----GELSVRFNSLV-SAETCSQVARELDLASFIRVSSD  102 (227)
Q Consensus        40 ~erLEflGDavL-------~~~v~~~l~~~----~p~~~e-----G~lt~lr~~lV-~n~~La~~a~~lgl~~~l~~~~~  102 (227)
                      .|-++|+||++|       ++-.-++=+.+    .|....     ..|..-|...- ...+|-.+|+.++++..-|.--+
T Consensus        84 ~efl~Fi~~a~LVaHNA~FD~~FLn~El~r~g~~~~~~~~~~~v~DTL~lAR~~~Pg~~~sLDaLc~R~~Id~s~R~~Hg  163 (243)
T PRK07982         84 DEFLDYIRGAELVIHNAAFDIGFMDYEFSLLKRDIPKTNTFCKVTDSLALARKMFPGKRNSLDALCDRYEIDNSKRTLHG  163 (243)
T ss_pred             HHHHHHHCCCEEEEECCHHHHHHHHHHHHHCCCCCCCCCCCCCEEEHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCCC
T ss_conf             99999967998999733888999999999708898861012431349999888788986899999875487765655233


Q ss_pred             CCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             31237531333332669999999
Q gi|254780940|r  103 LRKDVCSFMTSIQADVVESLIAA  125 (227)
Q Consensus       103 ~~~~~~~~~~~ilad~fEA~iGA  125 (227)
                      +..     ...+||+++=++.|+
T Consensus       164 ALl-----Da~lLAeVYl~ltgG  181 (243)
T PRK07982        164 ALL-----DAQILAEVYLAMTGG  181 (243)
T ss_pred             HHH-----HHHHHHHHHHHHCCC
T ss_conf             377-----488999999997289


No 64 
>pfam01418 HTH_6 Helix-turn-helix domain, rpiR family. This domain contains a helix-turn-helix motif. The best characterized member of this family is RpiR, a regulator of the expression of rpiB gene.
Probab=21.78  E-value=41  Score=14.51  Aligned_cols=41  Identities=22%  Similarity=0.299  Sum_probs=26.6

Q ss_pred             HHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHHHHHCCCCCEE
Q ss_conf             47877641046---88789988888887443345454313877200
Q gi|254780940|r   55 ISTLLFNHFDS---AKEGELSVRFNSLVSAETCSQVARELDLASFI   97 (227)
Q Consensus        55 v~~~l~~~~p~---~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~l   97 (227)
                      |++|+..+...   ++-.++.  ...-||..+..+.|+++|+..|-
T Consensus        21 ia~yil~~~~~~~~~si~~lA--~~~~vS~atv~Rf~kklG~~Gf~   64 (106)
T pfam01418        21 IADYILASPDNAIHLSIAELA--KAAGVSEASVVRFCRKLGFSGFS   64 (106)
T ss_pred             HHHHHHHCHHHHHHCCHHHHH--HHHCCCHHHHHHHHHHHCCCCHH
T ss_conf             999999299999883399999--89699899999999995899899


No 65 
>TIGR02087 LEUD_arch 3-isopropylmalate dehydratase, small subunit; InterPro: IPR011827   3-isopropylmalate dehydratase (or isopropylmalate isomerase; 4.2.1.33 from EC) catalyses the stereo-specific isomerisation of 2-isopropylmalate and 3-isopropylmalate, via the formation of 2-isopropylmaleate. This enzyme performs the second step in the biosynthesis of leucine, and is present in most prokaryotes and many fungal species. The prokaryotic enzyme is a heterodimer composed of a large (LeuC) and small (LeuD) subunit, while the fungal form is a monomeric enzyme. Both forms of isopropylmalate are related and are part of the larger aconitase family . Aconitases are mostly monomeric proteins which share four domains in common and contain a single, labile [4Fe-4S] cluster. Three structural domains (1, 2 and 3) are tightly packed around the iron-sulphur cluster, while a fourth domain (4) forms a deep active-site cleft. The prokaryotic enzyme is encoded by two adjacent genes, leuC and leuD, corresponding to aconitase domains 1-3 and 4 respectively , . LeuC does not bind an iron-sulphur cluster. It is thought that some prokaryotic isopropylamalate dehydrogenases can also function as homoaconitase 4.2.1.36 from EC, converting cis-homoaconitate to homoisocitric acid in lysine biosynthesis . Homoaconitase has been identified in higher fungi (mitochondria) and several archaea and one thermophilic species of bacteria, Thermus thermophilus .     This entry is most closely related to the 3-isopropylmalate dehydratase IPR004431 from INTERPRO. It also includes members, which cluster with other genes of leucine biosynthesis.    The structure of the Pyrococcus horikoshii small subunit (O59393 from SWISSPROT) has recently been determined . As expected the structure of this polypeptide is similar to that of aconitase domain 4, though one alpha helix is replaced by a short loop with relatively high temperature factor values. This loop region is thought to be important for substrate recognition. Unlike other aconitase family proteins, this subunit formed a tetramer through disulphide linkages, though it is not expected to interfere with its interaction with the large subunit. These disulphide linkages would be expected to confer thermostability on the enzyme, reflecting the thermophilic lifestyle of the organism.; GO: 0003861 3-isopropylmalate dehydratase activity, 0009098 leucine biosynthetic process, 0009316 3-isopropylmalate dehydratase complex.
Probab=21.64  E-value=50  Score=13.99  Aligned_cols=49  Identities=35%  Similarity=0.473  Sum_probs=25.3

Q ss_pred             HHHHHH-CCCCCCCCCCEECCCCCCCCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHHHHHCCC
Q ss_conf             987532-02233334310102077888459999999998999999689899999999999997488
Q gi|254780940|r  161 LQEWAH-AKFGVTPEYKVTFRSGPDHDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEVLKREGI  225 (227)
Q Consensus       161 Lqe~~q-~~~~~~P~Y~~~~~~g~~~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~AL~klgi  225 (227)
                      +||+.+ +.-+..|+|--.-..|         .|.|=|+-  -|+|+|.-+     |-.|||+.||
T Consensus        27 ~~eLA~haM~g~~PeF~~kvr~G---------DviVAGkN--FGcGSSREQ-----A~~ALK~aGv   76 (159)
T TIGR02087        27 PDELASHAMEGIDPEFAKKVREG---------DVIVAGKN--FGCGSSREQ-----AALALKAAGV   76 (159)
T ss_pred             HHHHHHHCCCCCCCCHHHHCCCC---------CEEEECCC--CCCCCCHHH-----HHHHHHHCCE
T ss_conf             78899870558996313407899---------78871416--477887788-----9999974790


No 66 
>TIGR00677 fadh2_euk methylenetetrahydrofolate reductase; InterPro: IPR004621 The enzyme activities methylenetetrahydrofolate reductase (1.5.1.20 from EC) and 5,10-methylenetetrahydrofolate reductase (FADH) (1.7.99.5 from EC) differ in that the former (assigned in many eukaryotes) is defined to use NADP+ as an acceptor, while the latter (assigned in many bacteria) is flexible with respect to the acceptor. Both convert 5-methyltetrahydrofolate to 5,10-methylenetetrahydrofolate. From a larger set of proteins assigned as one or the other, this family describes the subset of proteins found in eukaryotes, and currently designated methylenetetrahydrofolate reductase (1.5.1.20 from EC). This protein is an FAD-containing flavoprotein.; GO: 0004489 methylenetetrahydrofolate reductase (NADPH) activity, 0006555 methionine metabolic process.
Probab=20.72  E-value=61  Score=13.46  Aligned_cols=18  Identities=28%  Similarity=0.302  Sum_probs=14.6

Q ss_pred             HHHHHHHHHHHHHCCCCC
Q ss_conf             999999999999748899
Q gi|254780940|r  210 AAEQVAAAEVLKREGIWT  227 (227)
Q Consensus       210 ~Ae~~AA~~AL~klgi~t  227 (227)
                      .=-++|+.+.|++||+|+
T Consensus       293 lNlEKA~~~Il~rLg~l~  310 (312)
T TIGR00677       293 LNLEKAALMILERLGLLD  310 (312)
T ss_pred             CCHHHHHHHHHHHCCCCC
T ss_conf             017789999998478877


No 67 
>COG0859 RfaF ADP-heptose:LPS heptosyltransferase [Cell envelope biogenesis, outer membrane]
Probab=20.47  E-value=49  Score=14.05  Aligned_cols=24  Identities=33%  Similarity=0.411  Sum_probs=11.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             887458688645478776410468
Q gi|254780940|r   43 LEFLGDRILGLLISTLLFNHFDSA   66 (227)
Q Consensus        43 LEflGDavL~~~v~~~l~~~~p~~   66 (227)
                      +.++||.|+...+-..|-+.||+.
T Consensus         9 ~~~iGD~vlt~p~~~~lk~~~P~a   32 (334)
T COG0859           9 LSKLGDVVLTLPLLRTLKKAYPNA   32 (334)
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             574013776999999999878997


No 68 
>pfam00352 TBP Transcription factor TFIID (or TATA-binding protein, TBP).
Probab=20.23  E-value=62  Score=13.39  Aligned_cols=39  Identities=26%  Similarity=0.337  Sum_probs=25.7

Q ss_pred             CCCEEEEEEEECCEEEEEEEECCHHHHHHHHHHHH--HHHCC
Q ss_conf             88459999999998999999689899999999999--99748
Q gi|254780940|r  185 HDPRFTVVVEISGLAPAQGMDCSKRAAEQVAAAEV--LKREG  224 (227)
Q Consensus       185 ~~~~f~v~v~v~g~~~g~g~g~SkK~Ae~~AA~~A--L~klg  224 (227)
                      ++|.-++-++..|+.+.+|. +|..++++.+.+-+  |+++|
T Consensus        46 ~~pk~t~liF~SGkivitGa-ks~~~~~~a~~~i~~~L~~~g   86 (86)
T pfam00352        46 REPKATALIFSSGKVVITGA-KSEEDAKKAVRKIAPILKKLG   86 (86)
T ss_pred             CCCCEEEEEECCCEEEEECC-CCHHHHHHHHHHHHHHHHHCC
T ss_conf             78854999983885999842-999999999999999999758


No 69 
>PRK11557 putative DNA-binding transcriptional regulator; Provisional
Probab=20.07  E-value=45  Score=14.29  Aligned_cols=40  Identities=20%  Similarity=0.269  Sum_probs=24.1

Q ss_pred             HHHHHHHHCC---CCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCE
Q ss_conf             4787764104---68878998888888744334545431387720
Q gi|254780940|r   55 ISTLLFNHFD---SAKEGELSVRFNSLVSAETCSQVARELDLASF   96 (227)
Q Consensus        55 v~~~l~~~~p---~~~eG~lt~lr~~lV~n~~La~~a~~lgl~~~   96 (227)
                      |++|+..+..   .++-.+|.  ...-||..+..+.|+++|+..|
T Consensus        21 IA~yIl~n~~~v~~~si~eLA--~~~~vS~aTVvRf~kkLGf~Gf   63 (282)
T PRK11557         21 LADYLLLQPDTARHLSSQQLA--NEAGVSQSSVVKFAQKLGYKGF   63 (282)
T ss_pred             HHHHHHCCHHHHHHCCHHHHH--HHHCCCHHHHHHHHHHHCCCCH
T ss_conf             999998098999765699999--8969998899999999389989


Done!