Query         gi|254780955|ref|YP_003065368.1| hypothetical protein CLIBASIA_04270 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 204
No_of_seqs    127 out of 261
Neff          4.1 
Searched_HMMs 39220
Date          Mon May 30 03:14:30 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780955.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 pfam07031 consensus            100.0       0       0  444.3  17.7  153   30-201     1-153 (153)
  2 COG3814 Uncharacterized protei 100.0       0       0  414.1  15.2  157   25-204     1-157 (157)
  3 pfam04386 SspB Stringent starv 100.0 1.6E-42       0  297.1  16.0  120   30-150     1-120 (152)
  4 PRK11798 ClpXP protease specif  98.0 0.00018 4.7E-09   49.9  11.6   94   43-145    11-107 (140)
  5 COG2969 SspB Stringent starvat  95.9    0.16   4E-06   30.8   9.8   95   44-147    13-110 (155)
  6 PRK08296 hypothetical protein;  62.2      11 0.00028   18.8   3.6   40   32-71    343-382 (602)
  7 pfam03315 SDH_beta Serine dehy  57.2      14 0.00037   18.1   3.5   66   44-110    72-137 (148)
  8 pfam10274 ParcG Parkin co-regu  48.3      13 0.00033   18.4   2.1   32   23-56    136-167 (183)
  9 pfam06794 UPF0270 Uncharacteri  46.4      16 0.00041   17.7   2.3   31   29-62      2-32  (70)
 10 TIGR01349 PDHac_trf_mito pyruv  44.6      11 0.00027   18.9   1.2   41   26-71    342-382 (584)
 11 pfam01122 Cobalamin_bind Eukar  44.1      27 0.00068   16.3   3.2   34   30-66    189-222 (305)
 12 pfam08977 BOFC_N Bypass of For  43.6      16  0.0004   17.8   1.9   27   80-106    29-55  (59)
 13 COG5165 POB3 Nucleosome-bindin  42.5      28 0.00072   16.2   4.8   39  109-147   116-155 (508)
 14 pfam06057 VirJ Bacterial virul  41.9     8.2 0.00021   19.6   0.3   10   75-84     88-97  (192)
 15 pfam05798 Phage_FRD3 Bacteriop  40.7      19 0.00049   17.2   2.0   37   78-130    16-53  (75)
 16 TIGR01182 eda 2-dehydro-3-deox  38.6      32 0.00082   15.8   3.0   35   52-90     29-63  (205)
 17 PRK02967 nickel responsive reg  37.0      34 0.00087   15.6   4.6   96   24-131     7-113 (138)
 18 TIGR02249 integrase_gron integ  36.1      14 0.00037   18.1   0.8   47   23-87    167-213 (320)
 19 pfam11875 DUF3395 Domain of un  35.9      36 0.00091   15.5   4.7   72   38-135    34-115 (144)
 20 pfam02995 DUF229 Protein of un  33.1      39   0.001   15.2   5.2   85   13-126   293-398 (498)
 21 pfam09664 DUF2399 Protein of u  33.0      39   0.001   15.2   2.7   52   40-104    52-103 (155)
 22 TIGR02342 chap_CCT_delta T-com  31.4      33 0.00085   15.7   2.0   57   16-89    375-431 (526)
 23 pfam04555 XhoI Restriction end  30.3      44  0.0011   14.9   3.2   52   38-106    21-72  (196)
 24 TIGR01572 A_thl_para_3677 Arab  30.1      28 0.00071   16.2   1.4   14   59-72    242-255 (290)
 25 pfam04776 DUF626 Protein of un  29.7      32  0.0008   15.8   1.6   28   59-92     77-104 (116)
 26 PRK04966 hypothetical protein;  28.2      47  0.0012   14.7   2.3   45   29-76      2-64  (72)
 27 pfam10154 DUF2362 Uncharacteri  26.2     7.2 0.00018   20.0  -2.1   11   86-96    229-239 (501)
 28 TIGR02340 chap_CCT_alpha T-com  25.6      53  0.0013   14.4   2.3   30   16-49    371-400 (540)
 29 TIGR02439 catechol_proteo cate  25.6      38 0.00096   15.3   1.4   23   45-67    205-227 (288)
 30 PRK01002 nickel responsive reg  25.1      54  0.0014   14.3   5.2   97   24-131    10-117 (141)
 31 pfam11383 DUF3187 Protein of u  24.9      26 0.00066   16.4   0.5   66   50-117    79-145 (273)
 32 TIGR00079 pept_deformyl peptid  24.8      33 0.00084   15.7   1.0   13   88-100   152-164 (188)
 33 pfam11757 RSS_P20 Suppressor o  24.7      48  0.0012   14.6   1.9   40   15-58     86-125 (137)
 34 COG3612 Uncharacterized protei  24.3      50  0.0013   14.6   1.9   36   42-79     39-75  (157)
 35 pfam09665 RE_Alw26IDE Type II   23.9      29 0.00073   16.1   0.6   96   24-142   326-432 (511)
 36 pfam00073 Rhv picornavirus cap  22.4      48  0.0012   14.7   1.5   42   72-131   111-152 (173)
 37 KOG3913 consensus               21.4      28 0.00072   16.2   0.1   94   37-139   194-287 (356)
 38 pfam06748 DUF1217 Protein of u  21.3      57  0.0015   14.2   1.7   21   31-51     99-119 (150)
 39 cd01611 GABARAP GABARAP  (GABA  21.2      57  0.0014   14.2   1.6   33   76-108    13-47  (112)
 40 TIGR00174 miaA tRNA delta(2)-i  21.0      42  0.0011   15.0   1.0   42   16-65     57-101 (307)
 41 pfam02576 DUF150 Uncharacteriz  20.8      65  0.0017   13.8   3.4   90   30-128    37-138 (141)
 42 pfam11094 UL11 Membrane-associ  20.7      46  0.0012   14.8   1.1   10  191-200    21-30  (39)
 43 pfam02991 MAP1_LC3 Microtubule  20.7      58  0.0015   14.1   1.6   32   77-108     6-39  (104)
 44 KOG1932 consensus               20.4      67  0.0017   13.7   3.5   94   21-126   455-593 (1180)
 45 pfam11688 DUF3285 Protein of u  20.1      63  0.0016   13.9   1.7   13   35-47      7-19  (45)
 46 TIGR01722 MMSDH methylmalonate  20.0      41   0.001   15.1   0.7   27   19-45     53-82  (478)

No 1  
>pfam07031 consensus
Probab=100.00  E-value=0  Score=444.26  Aligned_cols=153  Identities=52%  Similarity=0.851  Sum_probs=131.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEECCCEEEEE
Q ss_conf             49899999999999999999999708999874699998458888775989996397537998431121807645479999
Q gi|254780955|r   30 IRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVG  109 (204)
Q Consensus        30 i~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~~FsV~  109 (204)
                      |+|++||++|||+|||++|+.|+++| |||+|||||||+|++|||+||+|||+|||+|||||||||||||+|++++|||+
T Consensus         1 i~Y~~l~~~Alr~vv~~~L~~v~~~G-lpg~hHfyItF~T~~~gV~ip~~L~~~YP~eMTIVlQhqf~dL~V~~~~FsV~   79 (153)
T pfam07031         1 IRYDKLVQDALRGVVRKVLTDVAKEG-LPGEHHFYITFLTNAPGVILPDRLKERYPEEMTIVLQHQFWDLNVTEDGFSVT   79 (153)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCEEEEEEECCCCCCCCCHHHHHHCCCCCEEEEEEEECCCEEECCCEEEE
T ss_conf             98799999999999999999999729-99873799999659999668999996498613998632232415506836999


Q ss_pred             EEECCEEEEEEEEHHHHEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             98498766899844242023067753035603467665433444565444445655664334444444555665556665
Q gi|254780955|r  110 LSFSNVPERLVIPFNAIKGFYDPSVNFELEFDVHIEHIEEKLEGGNTGKVLTSPDNFDKNQTNSVSQDSSKKKSTKKQNK  189 (204)
Q Consensus       110 LsF~g~~e~L~IPf~AIt~F~DPSV~FgLqF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  189 (204)
                      |||||+||+|+|||+||++|+||||+|||||++..++..++.+..+...                  .....++......
T Consensus        80 LsF~~~~e~l~IPf~aI~~F~DPsv~FgL~F~~~~~~~~~~~~~~~~~~------------------~~~~~~~~~~~~~  141 (153)
T pfam07031        80 LSFGGVPERLTIPFSAITKFVDPSVNFGLQFEQQENDDDEEEPDEDNDD------------------PDDEAPSPAPLTP  141 (153)
T ss_pred             EEECCEEEEEEEEHHHHHHCCCCCCCEEEEECCCCCCCCCCCCCCCCCC------------------CCCCCCCCCCCCC
T ss_conf             9849904678952688410128887757875576676556667777676------------------5567888878888


Q ss_pred             CCCCCEEEEEEC
Q ss_conf             677728983100
Q gi|254780955|r  190 NKMASVISLDNF  201 (204)
Q Consensus       190 ~~~aeVVSLD~F  201 (204)
                      .++|||||||+|
T Consensus       142 ~~~aeVVSLD~F  153 (153)
T pfam07031       142 AKGANVVSLDAF  153 (153)
T ss_pred             CCCCCEEECCCC
T ss_conf             888868857789


No 2  
>COG3814 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=100.00  E-value=0  Score=414.08  Aligned_cols=157  Identities=62%  Similarity=1.009  Sum_probs=134.0

Q ss_pred             CHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEECCC
Q ss_conf             02210498999999999999999999997089998746999984588887759899963975379984311218076454
Q gi|254780955|r   25 MNYDHIRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDN  104 (204)
Q Consensus        25 M~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~  104 (204)
                      |.+|+|+|+.|+|+|||||||++|..++..| |||+|||||||+|.+|||++|.+||++||++||||||||||||.|+|.
T Consensus         1 m~qd~i~Y~~laqealrgvvkkvL~kva~~g-Lp~dhh~yItf~T~apgV~~~s~lk~kYPeqmTIVlQ~Qfwdl~v~dt   79 (157)
T COG3814           1 MGQDHIRYDILAQEALRGVVKKVLAKVAATG-LPGDHHFYITFLTGAPGVRIPSKLKQKYPEQMTIVLQHQFWDLKVTDT   79 (157)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCEEEEEEECCCCCEECCHHHHHHCCCCEEEEEEEEEECCEECCC
T ss_conf             9522478999999999999999999875328-998737999996389823444888763850359976545401210246


Q ss_pred             EEEEEEEECCEEEEEEEEHHHHEEEECCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             79999984987668998442420230677530356034676654334445654444456556643344444445556655
Q gi|254780955|r  105 HFEVGLSFSNVPERLVIPFNAIKGFYDPSVNFELEFDVHIEHIEEKLEGGNTGKVLTSPDNFDKNQTNSVSQDSSKKKST  184 (204)
Q Consensus       105 ~FsV~LsF~g~~e~L~IPf~AIt~F~DPSV~FgLqF~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  184 (204)
                      +|||+|||+|+||+|+|||+||++|+||||||.|+|++.....++.+.       ..+|.+               ..+.
T Consensus        80 gFsv~lsF~~vpe~l~iPf~Al~~FyDpsvnf~LeF~~~~~~~e~~e~-------~~~p~~---------------~~~~  137 (157)
T COG3814          80 GFSVTLSFSGVPEKLYIPFDALRGFYDPSVNFELEFDVSLNIEEEAEP-------EAEPSN---------------KAKS  137 (157)
T ss_pred             CEEEEEEECCCCEEEEEEHHHHHHHCCCCCCEEEEECCCCCCCCCCCC-------CCCCCC---------------CCCC
T ss_conf             248998857963079962588550148876579997442255445676-------555444---------------2236


Q ss_pred             CCCCCCCCCCEEEEEECCCC
Q ss_conf             56665677728983100269
Q gi|254780955|r  185 KKQNKNKMASVISLDNFRKK  204 (204)
Q Consensus       185 ~~~~~~~~aeVVSLD~FRKK  204 (204)
                      ......++++|||||+||||
T Consensus       138 ~at~~~~~p~VvsLD~FRkk  157 (157)
T COG3814         138 GATSDSEGPNVVSLDAFRKK  157 (157)
T ss_pred             CCCCCCCCCCEEEHHHHHCC
T ss_conf             66577889848873774049


No 3  
>pfam04386 SspB Stringent starvation protein B. Escherichia coli stringent starvation protein B (SspB), is thought to enhance the specificity of degradation of tmRNA-tagged proteins by the ClpXP protease. The tmRNA tag, also known as ssrA, is an 11-aa peptide added to the C terminus of proteins stalled during translation, targets proteins for degradation by ClpXP and ClpAP. SspB a cytoplasmic protein that specifically binds to residues 1-4 and 7 of the tag. Binding of SspB enhances degradation of tagged proteins by ClpX, and masks sequence elements important for ClpA interactions, inhibiting degradation by ClpA. However, more recent work has cast doubt on the importance of SspB in wild-type cells. SspB is encoded in an operon whose synthesis is stimulated by carbon, amino acid, and phosphate starvation. SspB may play a special role during nutrient stress, for example by ensuring rapid degradation of the products of stalled translation, without causing a global increase in degradation of
Probab=100.00  E-value=1.6e-42  Score=297.14  Aligned_cols=120  Identities=44%  Similarity=0.757  Sum_probs=114.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEECCCEEEEE
Q ss_conf             49899999999999999999999708999874699998458888775989996397537998431121807645479999
Q gi|254780955|r   30 IRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVG  109 (204)
Q Consensus        30 i~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~~FsV~  109 (204)
                      |+|+.|++.|||+|++.+|+.+++.| |+|+|||||||+|+++||.||++|+++||++||||+|||||||.|++++||++
T Consensus         1 ~~y~~~~~~~lRav~~w~L~~~~~~g-ld~~~~pyI~~~t~~~gV~vP~~l~~~~~~~mlnV~~~a~~~L~v~~d~~sf~   79 (152)
T pfam04386         1 ITYDSLRPYALRAVYRWVLTDVAKEG-LDNDHTPYITFDTTAPGVQVPDELVERYPQIMLNVLQHAFWDLEVGNDGFSFN   79 (152)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCC-CCCCCEEEEEEEECCCCCCCCHHHHHCCCCEEEEECHHHHHCEEECCCEEEEE
T ss_conf             97788899999999999998765348-89998379999908999187899984399479995477760516627889999


Q ss_pred             EEECCEEEEEEEEHHHHEEEECCCCCEEEEECCCCCCCCCC
Q ss_conf             98498766899844242023067753035603467665433
Q gi|254780955|r  110 LSFSNVPERLVIPFNAIKGFYDPSVNFELEFDVHIEHIEEK  150 (204)
Q Consensus       110 LsF~g~~e~L~IPf~AIt~F~DPSV~FgLqF~~~~~~~~~~  150 (204)
                      |+|+|++++|+|||+||++|+||+++|||+|+.......+.
T Consensus        80 ~rF~G~~~~i~iP~~Ai~~i~~~e~g~Gl~F~~~~~~~~~~  120 (152)
T pfam04386        80 LRFGGVPERLYVPFAAILAFYDPENGFGLQFEPEEADEDEE  120 (152)
T ss_pred             EEECCEEEEEEEEHHHEEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             99899307999744771466666678652058988777777


No 4  
>PRK11798 ClpXP protease specificity-enhancing factor; Provisional
Probab=98.01  E-value=0.00018  Score=49.87  Aligned_cols=94  Identities=15%  Similarity=0.274  Sum_probs=78.4

Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEE---ECCEEECCCEEEEEEEECCEEEEE
Q ss_conf             99999999997089998746999984588887759899963975379984311---218076454799999849876689
Q gi|254780955|r   43 LVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQ---FWDLKVLDNHFEVGLSFSNVPERL  119 (204)
Q Consensus        43 Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhq---f~dL~V~~~~FsV~LsF~g~~e~L  119 (204)
                      ++|....=+..+|+     -=||.-.+.++||.+|....    ++=.|||---   -.||.++++..+-.--|+|++..+
T Consensus        11 LiRA~yeW~~Dn~~-----TPyi~V~a~~~~v~VP~~~v----~dg~IvLNIsp~Av~~L~i~nd~isF~ARF~G~~~~i   81 (140)
T PRK11798         11 LLRALYEWLVDNGL-----TPHLLVDATYPGVQVPMEYV----KDGQIVLNISPRAVGNLQLDNDAISFNARFGGVPRQI   81 (140)
T ss_pred             HHHHHHHHHHHCCC-----CCEEEEEECCCCCCCCHHHC----CCCEEEEECCHHHHHCEEECCCEEEEEEEECCEEEEE
T ss_conf             89999999972899-----85499981799966898880----1998999779888603077587899987979915899


Q ss_pred             EEEHHHHEEEECCCCCEEEEECCCCC
Q ss_conf             98442420230677530356034676
Q gi|254780955|r  120 VIPFNAIKGFYDPSVNFELEFDVHIE  145 (204)
Q Consensus       120 ~IPf~AIt~F~DPSV~FgLqF~~~~~  145 (204)
                      .||..||.+-+-.-.+-|+-|+....
T Consensus        82 ~vP~~aV~aIyArEnG~Gm~F~~E~~  107 (140)
T PRK11798         82 YVPIAAVLAIYARENGQGMMFEPEAA  107 (140)
T ss_pred             EEEHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             97789964253010378754488766


No 5  
>COG2969 SspB Stringent starvation protein B [General function prediction only]
Probab=95.85  E-value=0.16  Score=30.78  Aligned_cols=95  Identities=13%  Similarity=0.188  Sum_probs=76.0

Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEE---CCEEECCCEEEEEEEECCEEEEEE
Q ss_conf             99999999970899987469999845888877598999639753799843112---180764547999998498766899
Q gi|254780955|r   44 VKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQF---WDLKVLDNHFEVGLSFSNVPERLV  120 (204)
Q Consensus        44 vr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf---~dL~V~~~~FsV~LsF~g~~e~L~  120 (204)
                      +|..-+-...+++-     =||--.-+.+||.+|-    .|-..=-|||---.   -+|..+.+..|-.--|+|++..+.
T Consensus        13 lRA~yeWl~DN~~T-----PhlvVd~t~~Gv~VP~----eyvkDgqIVLNvs~~Av~nL~l~Nd~vsFnARFgGvs~~v~   83 (155)
T COG2969          13 LRALYEWLLDNQLT-----PHLVVDVTLPGVKVPM----EYVRDGQIVLNIAPRAVGNLELGNDWVSFNARFGGVSRQVS   83 (155)
T ss_pred             HHHHHHHHHCCCCC-----CEEEEECCCCCCCCCH----HHCCCCEEEEEECCCCCCCEEECCCEEEEEEEECCCCEEEE
T ss_conf             99999998517987-----1389962556732787----77138859997172110366853750898666088431368


Q ss_pred             EEHHHHEEEECCCCCEEEEECCCCCCC
Q ss_conf             844242023067753035603467665
Q gi|254780955|r  121 IPFNAIKGFYDPSVNFELEFDVHIEHI  147 (204)
Q Consensus       121 IPf~AIt~F~DPSV~FgLqF~~~~~~~  147 (204)
                      ||-.|+..-+-.-.+=|.-|+....-+
T Consensus        84 vP~~avlAiYAREnG~G~~Fe~E~~~~  110 (155)
T COG2969          84 VPVGAVLAIYARENGQGMMFEPEAAYD  110 (155)
T ss_pred             EEHHHHHHHHHHHCCCCEECCCCCCCC
T ss_conf             566784314313248831307311456


No 6  
>PRK08296 hypothetical protein; Provisional
Probab=62.23  E-value=11  Score=18.77  Aligned_cols=40  Identities=18%  Similarity=0.204  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             8999999999999999999997089998746999984588
Q gi|254780955|r   32 YDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNA   71 (204)
Q Consensus        32 Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~   71 (204)
                      |..|+...=|......|..+.+-=-+.-+|||||---+.+
T Consensus       343 yr~lL~~d~r~~Fd~~L~lA~~v~p~~EdH~Fyiehw~~~  382 (602)
T PRK08296        343 YRDLLDGDERAQFDEKLGLARTVFPYVENHNFYVEHWFHS  382 (602)
T ss_pred             HHHHCCHHHHHHHHHHHHHHHHHCCCCCCCEEEEEHHHHH
T ss_conf             9985481679999999999998522457653454104789


No 7  
>pfam03315 SDH_beta Serine dehydratase beta chain. L-serine dehydratase (EC:4.2.1.13) is a found as a heterodimer of alpha and beta chain or as a fusion of the two chains in a single protein. This enzyme catalyses the deamination of serine to form pyruvate. This enzyme is part of the gluconeogenesis pathway.
Probab=57.21  E-value=14  Score=18.06  Aligned_cols=66  Identities=15%  Similarity=0.132  Sum_probs=36.5

Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEECCCEEEEEE
Q ss_conf             9999999997089998746999984588887759899963975379984311218076454799999
Q gi|254780955|r   44 VKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVGL  110 (204)
Q Consensus        44 vr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~~FsV~L  110 (204)
                      +...+..+...+.|.=..+.-|.|.....=+--+......+|+-|+|.+-.. ........+|||+=
T Consensus        72 ~~~~~~~i~~~~~l~l~~~~~i~f~~~~di~f~~~~~l~~HpN~m~f~a~~~-~~~l~~~~yySiGG  137 (148)
T pfam03315        72 IEARLARIREEGKLNLAGEHSIPFAPERDIVFHFKEILPFHPNGMRFTAFDD-GGELLEETYYSIGG  137 (148)
T ss_pred             HHHHHHHHHHCCEEECCCCCCEEECCCCCEEEECCCCCCCCCCEEEEEEEEC-CCEEEEEEEEECCC
T ss_conf             6899999864775502896216415027939963767999998689999919-97699999998089


No 8  
>pfam10274 ParcG Parkin co-regulated protein. This family of proteins is transcribed anti-sense along the DNA to the Parkin gene product and the two appear to be transcribed under the same promoter. The protein has predicted alpha-helical and beta-sheet domains which suggest its function is in the ubiquitin/proteasome system. Mutations in parkin are the genetic cause of early-onset and autosomal recessive juvenile parkinsonism.
Probab=48.31  E-value=13  Score=18.38  Aligned_cols=32  Identities=22%  Similarity=0.285  Sum_probs=27.2

Q ss_pred             CCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             2202210498999999999999999999997089
Q gi|254780955|r   23 TLMNYDHIRYDILAKEALRGLVKVVLSEVASIGS   56 (204)
Q Consensus        23 ~~M~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g~   56 (204)
                      +.+..|.|+|  .....++.+|.++|+..+++||
T Consensus       136 ~~n~gd~idy--~~~~~i~dlI~etL~~lE~~GG  167 (183)
T pfam10274       136 NVNLGDRIDY--RKKKNIGDLIQETLELLERNGG  167 (183)
T ss_pred             CCCCCHHHHH--HHCCCHHHHHHHHHHHHHHHCC
T ss_conf             5442116777--6124375699999999999578


No 9  
>pfam06794 UPF0270 Uncharacterized protein family (UPF0270).
Probab=46.42  E-value=16  Score=17.74  Aligned_cols=31  Identities=26%  Similarity=0.354  Sum_probs=24.4

Q ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCE
Q ss_conf             0498999999999999999999997089998746
Q gi|254780955|r   29 HIRYDILAKEALRGLVKVVLSEVASIGSLPGEHH   62 (204)
Q Consensus        29 li~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hH   62 (204)
                      +|+|+.|-.++|+|++.+-+   .+.|.=.|++.
T Consensus         2 iIP~~~L~~etL~~lIeefv---~ReGTDyG~~E   32 (70)
T pfam06794         2 IIPWQQLPPETLNNLIEEFV---LREGTDYGEDE   32 (70)
T ss_pred             CCCHHHCCHHHHHHHHHHHH---HCCCCCCCCCC
T ss_conf             27837799999999999998---62377666452


No 10 
>TIGR01349 PDHac_trf_mito pyruvate dehydrogenase complex dihydrolipoamide acetyltransferase; InterPro: IPR006257   This group of sequences represent one of several closely related clades of the dihydrolipoamide acetyltransferase subunit of the pyruvate dehydrogenase complex. It includes sequences from mitochondria and from alpha and beta branches of the proteobacteria, as well as from some other bacteria, but not the Gram-positive bacteria.; GO: 0004742 dihydrolipoyllysine-residue acetyltransferase activity, 0006090 pyruvate metabolic process, 0045254 pyruvate dehydrogenase complex.
Probab=44.61  E-value=11  Score=18.94  Aligned_cols=41  Identities=17%  Similarity=0.358  Sum_probs=31.6

Q ss_pred             HHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCC
Q ss_conf             2210498999999999999999999997089998746999984588
Q gi|254780955|r   26 NYDHIRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNA   71 (204)
Q Consensus        26 ~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~   71 (204)
                      +.+.=.|..+=++.||.++-+=|. -+|.. .|   |||+|..-+-
T Consensus       342 ~~~tg~Y~d~P~sniRk~IA~RL~-eSKq~-iP---HyYvs~~~~~  382 (584)
T TIGR01349       342 PVSTGSYEDVPLSNIRKIIAKRLL-ESKQT-IP---HYYVSVECNV  382 (584)
T ss_pred             CCCCCCEEECCCCCHHHHHHHHHH-HHHCC-CC---EEEEEEEEEH
T ss_conf             888864466788832689999998-87568-86---0799998861


No 11 
>pfam01122 Cobalamin_bind Eukaryotic cobalamin-binding protein.
Probab=44.11  E-value=27  Score=16.33  Aligned_cols=34  Identities=26%  Similarity=0.353  Sum_probs=29.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEE
Q ss_conf             4989999999999999999999970899987469999
Q gi|254780955|r   30 IRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYIT   66 (204)
Q Consensus        30 i~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyIt   66 (204)
                      .+|...+..|+|.++.++|+....+| +-|+  .|.|
T Consensus       189 ~~~~~~i~~ai~~~~~kil~~q~~~G-~iGN--~yST  222 (305)
T pfam01122       189 EGYRAEISQALKTVVEKILKSKKPNG-HIGN--IYST  222 (305)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCC-CCCC--EECH
T ss_conf             14799999999999999998637677-3253--0037


No 12 
>pfam08977 BOFC_N Bypass of Forespore C, N terminal. The N-terminal domain of 'bypass of forespore C' is composed of a four-stranded beta-sheet covered by an alpha-helix. The beta-sheet has a beta2-beta1-beta4-beta3 topology, where strands beta1 and beta2 and strands beta3 and beta4 are connected by beta-turns, whereas strands beta2 and beta3 are joined by an alpha-helix that runs across one face of the beta-sheet. This domain is similar to the third immunoglobulin G-binding domain of protein G from Streptococcus, the latter belonging to a large and diverse group of cell surface-associated proteins that bind to immunoglobulins. It has been hypothesized that this domain may be a mediator of protein-protein interactions involved in proteolytic events at the cell surface.
Probab=43.56  E-value=16  Score=17.84  Aligned_cols=27  Identities=15%  Similarity=0.327  Sum_probs=23.0

Q ss_pred             HHHHCCCEEEEEEEEEECCEEECCCEE
Q ss_conf             996397537998431121807645479
Q gi|254780955|r   80 LRKNYPEKMTIVIQNQFWDLKVLDNHF  106 (204)
Q Consensus        80 L~~~yP~emTIVlQhqf~dL~V~~~~F  106 (204)
                      .-++-|-+|||.|+-+|-|=.|+++.+
T Consensus        29 v~e~~P~~vtV~LEr~YlDGEvSeE~~   55 (59)
T pfam08977        29 VEEKEPLQVTVQLERVYLDGEVSEEII   55 (59)
T ss_pred             EEECCCCEEEEEEEEEEECCCCCHHHC
T ss_conf             774288079999999884461224222


No 13 
>COG5165 POB3 Nucleosome-binding factor SPN, POB3 subunit [Transcription / DNA replication, recombination, and repair / Chromatin structure and dynamics]
Probab=42.46  E-value=28  Score=16.16  Aligned_cols=39  Identities=23%  Similarity=0.350  Sum_probs=28.4

Q ss_pred             EEEECCEEEEEEEEHHHHEEE-ECCCCCEEEEECCCCCCC
Q ss_conf             998498766899844242023-067753035603467665
Q gi|254780955|r  109 GLSFSNVPERLVIPFNAIKGF-YDPSVNFELEFDVHIEHI  147 (204)
Q Consensus       109 ~LsF~g~~e~L~IPf~AIt~F-~DPSV~FgLqF~~~~~~~  147 (204)
                      .+-|-+.+-...||+++|+.- .|--..-++.|...++..
T Consensus       116 ~vf~~N~kp~FEIP~~~i~ntnl~~kNEv~vef~~~de~~  155 (508)
T COG5165         116 AVFFRNTKPIFEIPVDDIENTNLDIKNEVSVEFRIQDEEY  155 (508)
T ss_pred             EEEEECCCEEEEEEHHHHCCCCCCCCCEEEEEEECCCCCC
T ss_conf             2454068703771466600355544332689996044013


No 14 
>pfam06057 VirJ Bacterial virulence protein (VirJ). This family consists of several bacterial VirJ virulence proteins. VirJ is thought to be involved in the type IV secretion system. It is thought that the substrate proteins localized to the periplasm may associate with the pilus in a manner that is mediated by VirJ, and suggest a two-step process for type IV secretion in Agrobacterium.
Probab=41.85  E-value=8.2  Score=19.65  Aligned_cols=10  Identities=10%  Similarity=0.318  Sum_probs=4.9

Q ss_pred             CCCHHHHHHC
Q ss_conf             7598999639
Q gi|254780955|r   75 RISQNLRKNY   84 (204)
Q Consensus        75 ~ip~~L~~~y   84 (204)
                      .+|+.+|++-
T Consensus        88 ~LP~~~r~~v   97 (192)
T pfam06057        88 RLPPATKQRV   97 (192)
T ss_pred             HCCHHHHHHH
T ss_conf             0999998541


No 15 
>pfam05798 Phage_FRD3 Bacteriophage FRD3 protein. This family consists of bacteriophage FRD3 proteins.
Probab=40.69  E-value=19  Score=17.23  Aligned_cols=37  Identities=27%  Similarity=0.738  Sum_probs=25.8

Q ss_pred             HHHHHHCCC-EEEEEEEEEECCEEECCCEEEEEEEECCEEEEEEEEHHHHEEEE
Q ss_conf             899963975-37998431121807645479999984987668998442420230
Q gi|254780955|r   78 QNLRKNYPE-KMTIVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFNAIKGFY  130 (204)
Q Consensus        78 ~~L~~~yP~-emTIVlQhqf~dL~V~~~~FsV~LsF~g~~e~L~IPf~AIt~F~  130 (204)
                      +-+|.|||+ -||-|..-|||+..+.                +.=|+++++.|-
T Consensus        16 EvIRNRyPelsi~si~d~~f~~~~i~----------------i~GPle~l~~FM   53 (75)
T pfam05798        16 EVIRNRYPELSIDSVQDSKFWSIQIV----------------IEGPLEDLKKFM   53 (75)
T ss_pred             HHHHCCCCCEEEEEEECCCCCEEEEE----------------EECCHHHHHHHH
T ss_conf             99973597427776524886259999----------------856599999999


No 16 
>TIGR01182 eda 2-dehydro-3-deoxyphosphogluconate aldolase/4-hydroxy-2-oxoglutarate aldolase; InterPro: IPR000887 4-Hydroxy-2-oxoglutarate aldolase (4.1.3.16 from EC) (KHG-aldolase) catalyzes the interconversion of 4-hydroxy-2-oxoglutarate into pyruvate and glyoxylate. Phospho-2-dehydro-3-deoxygluconate aldolase (4.1.2.14 from EC) (KDPG-aldolase) catalyzes the interconversion of 6-phospho-2-dehydro-3-deoxy-D-gluconate into pyruvate and glyceraldehyde 3-phosphate. These two enzymes are structurally and functionally related . They are both homotrimeric proteins of approximately 220 amino-acid residues. They are class I aldolases whose catalytic mechanism involves the formation of a Schiff-base intermediate between the substrate and the epsilon-amino group of a lysine residue. In both enzymes, an arginine is required for catalytic activity.; GO: 0003824 catalytic activity, 0008152 metabolic process.
Probab=38.55  E-value=32  Score=15.78  Aligned_cols=35  Identities=29%  Similarity=0.312  Sum_probs=26.9

Q ss_pred             HHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEE
Q ss_conf             970899987469999845888877598999639753799
Q gi|254780955|r   52 ASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTI   90 (204)
Q Consensus        52 ~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTI   90 (204)
                      .-.||+   +-.=|||+|....=.| ..|+.++|+++.|
T Consensus        29 L~egG~---~~~EvTlRT~~A~~aI-~~l~~~~P~~~~i   63 (205)
T TIGR01182        29 LIEGGL---RVLEVTLRTPVALEAI-RALRKEVPKDALI   63 (205)
T ss_pred             HHHCCC---EEEEEEECCCCHHHHH-HHHHHHCCCCCEE
T ss_conf             986798---0898851472168999-9999728233487


No 17 
>PRK02967 nickel responsive regulator; Provisional
Probab=37.02  E-value=34  Score=15.62  Aligned_cols=96  Identities=22%  Similarity=0.304  Sum_probs=58.9

Q ss_pred             CCHHHHC-CHHHHHH--------HHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEE
Q ss_conf             2022104-9899999--------999999999999999708999874699998458888775989996397537998431
Q gi|254780955|r   24 LMNYDHI-RYDILAK--------EALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQN   94 (204)
Q Consensus        24 ~M~~Dli-~Y~~l~~--------~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQh   94 (204)
                      .|+.+|+ ..|+++.        +|.|..+|+.|..-.... -.++.-=.||+.-+|.--.+..+|.+         +||
T Consensus         7 Slp~~Ll~~~D~~i~~~Gy~sRSEaIRdliR~~l~e~~~~~-~~~~~~g~it~vYdH~~~~l~~~lt~---------iQH   76 (138)
T PRK02967          7 TLDDDLLETLDSLIARRGYQNRSEAIRDLLRAALQQEATQE-HGTQCVAVLSYVYDHEKRDLASRLVS---------TQH   76 (138)
T ss_pred             ECCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHC-CCCCEEEEEEEEEECCCHHHHHHHHH---------HHH
T ss_conf             75999999999999981999788999999999999744425-89728999999985671468999999---------988


Q ss_pred             EECCEEECCCEEEEEEEECCEEEEEEE--EHHHHEEEEC
Q ss_conf             121807645479999984987668998--4424202306
Q gi|254780955|r   95 QFWDLKVLDNHFEVGLSFSNVPERLVI--PFNAIKGFYD  131 (204)
Q Consensus        95 qf~dL~V~~~~FsV~LsF~g~~e~L~I--Pf~AIt~F~D  131 (204)
                      .|-|+.++..+  |-|.=.+--|.+.+  |-..|..|++
T Consensus        77 ~~~d~Iiss~H--vHld~~~CLEvivv~G~~~~i~~la~  113 (138)
T PRK02967         77 HHHDLSVATLH--VHLDHDDCLEVAVLKGDMGDVQHFAD  113 (138)
T ss_pred             HCCCEEEEEEE--EECCCCCCEEEEEEECCHHHHHHHHH
T ss_conf             43042988878--73377762799999557899999999


No 18 
>TIGR02249 integrase_gron integron integrase; InterPro: IPR011946    Members of this family are integrases associated with integrons (and super-integrons), which are systems for incorporating and expressing cassettes of laterally transferred DNA. Incorporation occurs at an attI site. A super-integron, as in Vibrio sp., may include over 100 cassettes. This family belongs to the phage integrase family that also includes recombinases XerC (IPR011931 from INTERPRO) and XerD (IPR011932 from INTERPRO), which are bacterial housekeeping proteins. Within this family of integron integrases, some are designated by class, e.g. IntI4, a class 4 integron integrase from Vibrio cholerae N16961.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0015074 DNA integration.
Probab=36.08  E-value=14  Score=18.06  Aligned_cols=47  Identities=17%  Similarity=0.176  Sum_probs=31.5

Q ss_pred             CCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCE
Q ss_conf             22022104989999999999999999999970899987469999845888877598999639753
Q gi|254780955|r   23 TLMNYDHIRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEK   87 (204)
Q Consensus        23 ~~M~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~e   87 (204)
                      .+||.+|       ...|+.=+..|...=+++-.-+|           +-||-||.-|+.|||+-
T Consensus       167 v~Lp~~L-------~~~L~~q~~~~~~~h~~Dl~~~G-----------~g~V~LP~AL~rKYPnA  213 (320)
T TIGR02249       167 VTLPKSL-------APPLREQLERARALHEKDLLAEG-----------YGGVYLPHALARKYPNA  213 (320)
T ss_pred             CCCHHHH-------HHHHHHHHHHHHHHHHHHHHCCC-----------CCCEEHHHHHHCCCCCC
T ss_conf             2681755-------79999999999999998640588-----------53010045542157873


No 19 
>pfam11875 DUF3395 Domain of unknown function (DUF3395). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is typically between 147 to 176 amino acids in length. This domain is found associated with pfam00226.
Probab=35.86  E-value=36  Score=15.50  Aligned_cols=72  Identities=26%  Similarity=0.355  Sum_probs=33.8

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCC------CEEEEEEEEEECCEEECCCEEEEEEE
Q ss_conf             999999999999999708999874699998458888775989996397------53799843112180764547999998
Q gi|254780955|r   38 EALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYP------EKMTIVIQNQFWDLKVLDNHFEVGLS  111 (204)
Q Consensus        38 ~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP------~emTIVlQhqf~dL~V~~~~FsV~Ls  111 (204)
                      ..|+.++.+.+..-.+.|||-=.+-.|        |..-+.......+      -.+||.||..-     .+        
T Consensus        34 ~lm~~~~~r~~~~E~~~~GLVI~~A~Y--------G~~~~~~~~~~~~~~~~~viDVTiplq~lV-----~d--------   92 (144)
T pfam11875        34 SLMGDVVERKLTREEEKGGLVILKAYY--------GNLDSIKGKAQNNDEIEEVIDVTIPLQALV-----RD--------   92 (144)
T ss_pred             HHHHHHHHHHHHHHHHCCCEEEEEEEC--------CCCCCCCCCCCCCCCCCCEEEEEEHHHHEE-----EC--------
T ss_conf             999999999999886039759999773--------676766665544457885799870320156-----17--------


Q ss_pred             ECCEEEEEEEE----HHHHEEEECCCCC
Q ss_conf             49876689984----4242023067753
Q gi|254780955|r  112 FSNVPERLVIP----FNAIKGFYDPSVN  135 (204)
Q Consensus       112 F~g~~e~L~IP----f~AIt~F~DPSV~  135 (204)
                           .+|.||    .+-+.+|+||..+
T Consensus        93 -----s~L~l~~~~~Ks~L~GF~DPcpg  115 (144)
T pfam11875        93 -----SQLVLPSGSSKSNLLGFYDPCPG  115 (144)
T ss_pred             -----CEEEECCCCCHHCCCCCCCCCCC
T ss_conf             -----77886388735217765699989


No 20 
>pfam02995 DUF229 Protein of unknown function (DUF229). Members of this family are uncharacterized. They are 500-1200 amino acids in length and share a long region conservation that probably corresponds to several domains. The Go annotation for the protein indicates that it is involved in nematode larval development and has a positive regulation on growth rate.
Probab=33.10  E-value=39  Score=15.22  Aligned_cols=85  Identities=27%  Similarity=0.488  Sum_probs=51.5

Q ss_pred             EEEEEECCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCC--------------------
Q ss_conf             045554162222022104989999999999999999999970899987469999845888--------------------
Q gi|254780955|r   13 QWFFIIKWIDTLMNYDHIRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNAR--------------------   72 (204)
Q Consensus        13 ~~~~~~~~~~~~M~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~--------------------   72 (204)
                      +=+|.+-|.... +-|.+++-..+++-++..++    ...+.|.|  ++-+-| |..+|-                    
T Consensus       293 ~p~F~~fW~~~~-sHd~~n~~~~~D~~~~~~l~----~~~~~g~l--~~tivi-~~SDHG~R~G~~r~t~~G~lEErlP~  364 (498)
T pfam02995       293 SPFFGFFWSNSL-SHDDFNYASALDEDLLKYLK----KLHERGLL--ENTIVI-FMSDHGLRFGKLRRTSQGRLEERLPF  364 (498)
T ss_pred             CCEEEEEEECCC-CCCCCHHHHHHHHHHHHHHH----HHHHCCCC--CCEEEE-EECCCCCCCCCHHHHCCCCCCCCCCE
T ss_conf             965999997874-15663267788999999999----99865963--034999-98777876665322015620002860


Q ss_pred             -CCCCCHHHHHHCCCEEEEEEEEEECCEEECCCEEEEEEEECCEEEEEEEEHHHH
Q ss_conf             -877598999639753799843112180764547999998498766899844242
Q gi|254780955|r   73 -GVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFNAI  126 (204)
Q Consensus        73 -gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~~FsV~LsF~g~~e~L~IPf~AI  126 (204)
                       -+.+|+|+|++||+.+        .+|+...             .+|+-||+-=
T Consensus       365 l~i~lP~wfr~~yP~~~--------~nL~~N~-------------~rLts~fDlh  398 (498)
T pfam02995       365 MSIRLPPWFREKYPQAV--------ENLELNA-------------NRLTTPFDLH  398 (498)
T ss_pred             EEEEECHHHHHHHHHHH--------HHHHHHH-------------HCCCCHHHHH
T ss_conf             89991789976779999--------9999863-------------3358724689


No 21 
>pfam09664 DUF2399 Protein of unknown function C-terminus (DUF2399). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria). Just the C-terminal region is ioncluded here.
Probab=33.04  E-value=39  Score=15.21  Aligned_cols=52  Identities=21%  Similarity=0.394  Sum_probs=42.4

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEECCC
Q ss_conf             99999999999997089998746999984588887759899963975379984311218076454
Q gi|254780955|r   40 LRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDN  104 (204)
Q Consensus        40 lr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~  104 (204)
                      .+......|...++.|     ..+|-+=+=+.+|+.|..+|+.+|+..        +|...+.+=
T Consensus        52 p~~A~~~LL~~L~~~g-----~~l~Y~GDFD~~Gl~IA~~l~~ryg~~--------pWrm~~~dY  103 (155)
T pfam09664        52 PSAAALILLDRLAAAG-----ARLYYSGDFDWPGLRIANRLIARYGAR--------PWRMDAADY  103 (155)
T ss_pred             HHHHHHHHHHHHHHCC-----CEEEEECCCCHHHHHHHHHHHHHCCCC--------CCCCCHHHH
T ss_conf             7899999999998489-----869995889937999999999871995--------610789999


No 22 
>TIGR02342 chap_CCT_delta T-complex protein 1, delta subunit; InterPro: IPR012717    Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacterial, GroEL/GroES. This family consists exclusively of the CCT delta chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=31.38  E-value=33  Score=15.68  Aligned_cols=57  Identities=18%  Similarity=0.271  Sum_probs=38.8

Q ss_pred             EEECCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEE
Q ss_conf             55416222202210498999999999999999999997089998746999984588887759899963975379
Q gi|254780955|r   16 FIIKWIDTLMNYDHIRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMT   89 (204)
Q Consensus        16 ~~~~~~~~~M~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emT   89 (204)
                      -.+|+.+.+.-+   .=++=+||||| |||- |  |.+.+.+||+         .+|.|+|+-.|.+ |-.+|.
T Consensus       375 v~~RGSN~Lvi~---EAeRSlHDALC-ViRs-L--Vk~r~L~~GG---------GaPE~E~a~~L~~-~a~~~~  431 (526)
T TIGR02342       375 VLVRGSNKLVID---EAERSLHDALC-VIRS-L--VKKRALIAGG---------GAPEIEIALKLSK-LARTLK  431 (526)
T ss_pred             EEEECCCCHHHH---HHHHHHHHHHH-HHHH-H--HHCCCCCCCC---------CCCHHHHHHHHHH-HHHHHC
T ss_conf             998068602242---33221567899-9998-8--7506513886---------9528999999998-665413


No 23 
>pfam04555 XhoI Restriction endonuclease XhoI. This family consists of type II restriction enzymes (EC:3.1.21.4) that recognize the double-stranded sequence CTCGAG and cleave after C-1.
Probab=30.30  E-value=44  Score=14.92  Aligned_cols=52  Identities=21%  Similarity=0.472  Sum_probs=36.9

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEECCCEE
Q ss_conf             999999999999999708999874699998458888775989996397537998431121807645479
Q gi|254780955|r   38 EALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHF  106 (204)
Q Consensus        38 ~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~~F  106 (204)
                      ..|-+++.=++..+.+.| ||..+++     ++-..+.+|-+.|-           +--|||.|-.++-
T Consensus        21 k~mdgf~~li~~~~~~~G-l~~a~i~-----~~~~~l~lPGYfRp-----------tK~WDllVv~~g~   72 (196)
T pfam04555        21 KNMDGFAALVLDIIRANG-LAHAEIF-----QQRTALTLPGYFRP-----------TKLWDLLVVQKGV   72 (196)
T ss_pred             CCHHHHHHHHHHHHHHCC-CCHHHHH-----HCCCCCCCCCCCCC-----------CCCCCEEEEECCE
T ss_conf             236889999999999859-9777875-----24753105654244-----------5652179998893


No 24 
>TIGR01572 A_thl_para_3677 Arabidopsis paralogous family TIGR01572; InterPro: IPR006462   These sequences comprise a paralogous family of hypothetical proteins in Arabidopsis thaliana. No homologs are detected from other species. Length heterogeneity within the family is attributable partly to a 21-residue repeat present in from zero to three tandem copies. The proteins have no known function..
Probab=30.10  E-value=28  Score=16.18  Aligned_cols=14  Identities=29%  Similarity=0.361  Sum_probs=9.9

Q ss_pred             CCCEEEEEEECCCC
Q ss_conf             87469999845888
Q gi|254780955|r   59 GEHHFYITFATNAR   72 (204)
Q Consensus        59 G~hHfyItF~T~~~   72 (204)
                      +.-||||||+-=.+
T Consensus       242 ~~A~vYItF~Gl~k  255 (290)
T TIGR01572       242 KTAIVYITFKGLNK  255 (290)
T ss_pred             CCEEEEEEECCCCC
T ss_conf             75589996558898


No 25 
>pfam04776 DUF626 Protein of unknown function (DUF626). Protein of unknown function, currently only identified in Brassicaceae.
Probab=29.67  E-value=32  Score=15.84  Aligned_cols=28  Identities=32%  Similarity=0.562  Sum_probs=15.9

Q ss_pred             CCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEE
Q ss_conf             8746999984588887759899963975379984
Q gi|254780955|r   59 GEHHFYITFATNARGVRISQNLRKNYPEKMTIVI   92 (204)
Q Consensus        59 G~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVl   92 (204)
                      .+-+|||||++-+.- .+     .+.-+...||=
T Consensus        77 ~nAifYI~fk~~~~~-r~-----g~~~dr~AIVR  104 (116)
T pfam04776        77 KNAIFYITFKDSCKA-RI-----GKHVDRIAIVR  104 (116)
T ss_pred             CEEEEEEEECCCCCC-CC-----CCCCCEEEEEE
T ss_conf             015999996555566-66-----87612024563


No 26 
>PRK04966 hypothetical protein; Provisional
Probab=28.24  E-value=47  Score=14.72  Aligned_cols=45  Identities=27%  Similarity=0.316  Sum_probs=29.8

Q ss_pred             HCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCC------------------EEEEEEECCCCCCCC
Q ss_conf             049899999999999999999999708999874------------------699998458888775
Q gi|254780955|r   29 HIRYDILAKEALRGLVKVVLSEVASIGSLPGEH------------------HFYITFATNARGVRI   76 (204)
Q Consensus        29 li~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~h------------------HfyItF~T~~~gV~i   76 (204)
                      .|+|+.|-.++|++++-+   .|.+.|.=.|++                  .-.|.|...+.-+.|
T Consensus         2 iIP~~~L~~etL~~lie~---FV~REGTDYG~~E~sl~~Kv~qv~~qL~~G~a~Ivfd~~~Es~~I   64 (72)
T PRK04966          2 IIPWQDLSPETLDNLIES---FVLREGTDYGEHERSLEQKVADVKRQLQSGEAVLVWSELHETVNI   64 (72)
T ss_pred             CCCHHHCCHHHHHHHHHH---HHHCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCEEEE
T ss_conf             178377899999999999---970367777645458999999999999769989998688773761


No 27 
>pfam10154 DUF2362 Uncharacterized conserved protein (DUF2362). This is a family of proteins conserved from nematodes to humans. The function is not known.
Probab=26.19  E-value=7.2  Score=19.99  Aligned_cols=11  Identities=36%  Similarity=0.522  Sum_probs=7.3

Q ss_pred             CEEEEEEEEEE
Q ss_conf             53799843112
Q gi|254780955|r   86 EKMTIVIQNQF   96 (204)
Q Consensus        86 ~emTIVlQhqf   96 (204)
                      |--||.|--|-
T Consensus       229 ESFTIhLGsQl  239 (501)
T pfam10154       229 ESFTIHLGSQL  239 (501)
T ss_pred             CEEEEEHHHHH
T ss_conf             01687505677


No 28 
>TIGR02340 chap_CCT_alpha T-complex protein 1, alpha subunit; InterPro: IPR012715    Members of this eukaryotic family are part of the group II chaperonin complex called CCT (chaperonin containing TCP-1) or TRiC. The archaeal equivalent group II chaperonin is often called the thermosome. Both are somewhat related to the group I chaperonin of bacteria, GroEL/GroES. This family consists exclusively of the CCT alpha chain (part of a paralogous family) from animals, plants, fungi, and other eukaryotes.; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding.
Probab=25.62  E-value=53  Score=14.39  Aligned_cols=30  Identities=23%  Similarity=0.265  Sum_probs=21.4

Q ss_pred             EEECCCCCCCHHHHCCHHHHHHHHHHHHHHHHHH
Q ss_conf             5541622220221049899999999999999999
Q gi|254780955|r   16 FIIKWIDTLMNYDHIRYDILAKEALRGLVKVVLS   49 (204)
Q Consensus        16 ~~~~~~~~~M~~Dli~Y~~l~~~Alr~Vvr~~L~   49 (204)
                      -++|+.+..|.+   .-++=+||||+ |||++|+
T Consensus       371 IILRGAN~~~lD---EmeRSlHDaLc-vVkRtLE  400 (540)
T TIGR02340       371 IILRGANDFMLD---EMERSLHDALC-VVKRTLE  400 (540)
T ss_pred             EEECCCCCHHHH---HHHHHHHHHHH-HHHHHHC
T ss_conf             686166511554---66677777887-8766213


No 29 
>TIGR02439 catechol_proteo catechol 1,2-dioxygenase; InterPro: IPR012801    Members of this family known so far are catechol 1,2-dioxygenases of the proteobacteria. They are distinct from catechol 1,2-dioxygenases and chlorocatechol 1,2-dioxygenases of the actinobacteria, which are quite similar to each other and resolved by separate entries. This enzyme catalyses intradiol cleavage in which catechol + O2 becomes cis,cis-muconate. Catechol is an intermediate in the catabolism of many different aromatic compounds, as is the alternative intermediate protocatechuate. In Acinetobacter lwoffii, two isozymes are present with abilities, differing somewhat, to act on catechol analogues 3-methylcatechol, 4-methylcatechol, 4-methoxycatechol, and 4-chlorocatechol.; GO: 0005506 iron ion binding, 0018576 catechol 12-dioxygenase activity, 0019614 catechol catabolic process.
Probab=25.56  E-value=38  Score=15.34  Aligned_cols=23  Identities=22%  Similarity=0.522  Sum_probs=18.3

Q ss_pred             HHHHHHHHHCCCCCCCCEEEEEE
Q ss_conf             99999999708999874699998
Q gi|254780955|r   45 KVVLSEVASIGSLPGEHHFYITF   67 (204)
Q Consensus        45 r~~L~~v~~~g~LpG~hHfyItF   67 (204)
                      -.+|....++|.=|-.-|||||=
T Consensus       205 QqlLn~LGRHG~RPAHvHFFvSA  227 (288)
T TIGR02439       205 QQLLNLLGRHGNRPAHVHFFVSA  227 (288)
T ss_pred             HHHHHHCCCCCCCCCCEEEEECC
T ss_conf             99985417888898606875658


No 30 
>PRK01002 nickel responsive regulator; Provisional
Probab=25.06  E-value=54  Score=14.33  Aligned_cols=97  Identities=20%  Similarity=0.284  Sum_probs=56.9

Q ss_pred             CCHHHHC-CHHHHHH--------HHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEE
Q ss_conf             2022104-9899999--------999999999999999708999874699998458888775989996397537998431
Q gi|254780955|r   24 LMNYDHI-RYDILAK--------EALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQN   94 (204)
Q Consensus        24 ~M~~Dli-~Y~~l~~--------~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQh   94 (204)
                      .++.+++ ..|.+++        +|+|..+|+.|..-...+...|+--=.||..-+|..-.+..+|.+         +||
T Consensus        10 Slp~~Ll~~lD~~i~~~Gy~nRSeaIRdliR~~l~~~~~~~~~~~~~~G~i~vvYdH~~~~l~~~L~~---------iqH   80 (141)
T PRK01002         10 SLPTKLLAEFDEIIEERGYASRSEAIRDAIRDYIIKHKWIHSLEGERAGTISIIYDHHYTDVMEKLTD---------IQH   80 (141)
T ss_pred             ECCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEECCCCCHHHHHHH---------HHH
T ss_conf             80999999999999980998788999999999998734302578847999999996786519999999---------977


Q ss_pred             EECCEEECCCEEEEEEEECCEEEEEEE--EHHHHEEEEC
Q ss_conf             121807645479999984987668998--4424202306
Q gi|254780955|r   95 QFWDLKVLDNHFEVGLSFSNVPERLVI--PFNAIKGFYD  131 (204)
Q Consensus        95 qf~dL~V~~~~FsV~LsF~g~~e~L~I--Pf~AIt~F~D  131 (204)
                      +|.++.++..+.-+  .=+.--|.+.+  |-..|..|++
T Consensus        81 ~~~~~I~ss~Hvhl--d~~~ClEvivv~G~~~~i~~l~~  117 (141)
T PRK01002         81 DYRKLIVATIHMHM--DHDHCMEVVLVKGDASEIRELTD  117 (141)
T ss_pred             HCCCEEEEEEEEEC--CCCCEEEEEEEECCHHHHHHHHH
T ss_conf             33060988887751--78860899999737899999999


No 31 
>pfam11383 DUF3187 Protein of unknown function (DUF3187). This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=24.92  E-value=26  Score=16.39  Aligned_cols=66  Identities=18%  Similarity=0.257  Sum_probs=46.2

Q ss_pred             HHHHCCC-CCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEECCCEEEEEEEECCEEE
Q ss_conf             9997089-9987469999845888877598999639753799843112180764547999998498766
Q gi|254780955|r   50 EVASIGS-LPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVGLSFSNVPE  117 (204)
Q Consensus        50 ~v~~~g~-LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~~FsV~LsF~g~~e  117 (204)
                      .+..+|. ---.|-|+|..-  ..||.+.+---+---.-+|..+|+|+....-.--.+..+|.||.+..
T Consensus        79 gidQNGRd~v~~~rf~I~~p--~~gi~~~dF~G~tL~~alt~Y~qYql~~~~~hglS~GgSLyyN~v~~  145 (273)
T pfam11383        79 GIGQNGRDEVDKHQFQISSP--EYGIHIEDFEGETLTSAFTLYLQYQLFQNEHHGLSIGGSLYYNNVSS  145 (273)
T ss_pred             CCCCCCCCCCCCCCEEEECC--CCCCCCCCCCCHHHHHHHHHHHHEEEECCCCCCEEEEEEEEECCCCC
T ss_conf             87866742100572687378--67875024661447888987641243048875278779999546467


No 32 
>TIGR00079 pept_deformyl peptide deformylase; InterPro: IPR000181   Peptide deformylase (PDF) is an essential metalloenzyme required for the removal of the formyl group at the N-terminus of nascent polypeptide chains in eubacteria  3.5.1.88 from EC. The enzyme acts as a monomer and binds a single zinc ion, catalysing the reaction::  N-formyl-L-methionine + H_2O = formate + methionyl peptide  Catalytic efficiency strongly depends on the identity of the bound metal .     The structure of these enzymes is known , . PDF, a member of the zinc metalloproteases family, comprises an active core domain of 147 residues and a C-terminal tail of 21 residue. The 3D fold of the catalytic core has been determined by X-ray crystallography and NMR. Overall, the structure contains a series of anti-parallel beta- strands that surround two perpendicular alpha-helices. The C-terminal helix contains the characteristic HEXXH motif of metalloenzymes, which is crucial for activity. The helical arrangement, and the way the histidine residues bind the zinc ion, is reminiscent of other metalloproteases, such as thermolysin or metzincins. However, the arrangement of secondary and tertiary structures of PDF, and the positioning of its third zinc ligand (a cysteine residue), are quite different. These discrepancies, together with notable biochemical differences, suggest that PDF constitutes a new class of zinc-metalloproteases. .; GO: 0005506 iron ion binding, 0042586 peptide deformylase activity, 0006412 translation.
Probab=24.81  E-value=33  Score=15.72  Aligned_cols=13  Identities=31%  Similarity=0.478  Sum_probs=9.7

Q ss_pred             EEEEEEEEECCEE
Q ss_conf             7998431121807
Q gi|254780955|r   88 MTIVIQNQFWDLK  100 (204)
Q Consensus        88 mTIVlQhqf~dL~  100 (204)
                      .-|||||++..|.
T Consensus       152 lA~~iQHE~DHLn  164 (188)
T TIGR00079       152 LAICIQHEMDHLN  164 (188)
T ss_pred             EEEEEEEEEECCC
T ss_conf             3588764411258


No 33 
>pfam11757 RSS_P20 Suppressor of RNA silencing P21-like. This is a large family of putative suppressors of RNA silencing proteins, P20-P25, from ssRNA positive-strand viruses such as Closterovirus, Potyvirus and Cucumovirus families. RNA silencing is one of the major mechanisms of defence against viruses, and, in response, some viruses have evolved or acquired functions for suppression of RNA silencing. These counter-defencive viral proteins with RNA silencing suppressor (RSS) activity were originally discovered in the members of plant virus genera Potyvirus and Cucumovirus. Each of the conserved blocks of amino acids found in P21-like proteins corresponds to a computer-predicted alpha-helix, with the most C-terminal element being 42 residues long. This suggests conservation of the predominantly alpha-helical secondary structure in the P21-like proteins.
Probab=24.72  E-value=48  Score=14.63  Aligned_cols=40  Identities=25%  Similarity=0.541  Sum_probs=29.0

Q ss_pred             EEEECCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             55541622220221049899999999999999999999708999
Q gi|254780955|r   15 FFIIKWIDTLMNYDHIRYDILAKEALRGLVKVVLSEVASIGSLP   58 (204)
Q Consensus        15 ~~~~~~~~~~M~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g~Lp   58 (204)
                      ||+++.+    .-...+|...++..++-++..||...++.-+|.
T Consensus        86 Ffv~k~s----sl~~~~~s~i~~~kvk~~~~aVl~dlS~e~kLD  125 (137)
T pfam11757        86 FFVMKYS----SLSHVPFSEVMRTKLKLVVKAVISDLSREHKLD  125 (137)
T ss_pred             HHHHHHC----CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             9999980----388998799998711788999999988985888


No 34 
>COG3612 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.29  E-value=50  Score=14.55  Aligned_cols=36  Identities=28%  Similarity=0.370  Sum_probs=26.2

Q ss_pred             HHHHHHHHHHHHCCCCCCC-CEEEEEEECCCCCCCCCHH
Q ss_conf             9999999999970899987-4699998458888775989
Q gi|254780955|r   42 GLVKVVLSEVASIGSLPGE-HHFYITFATNARGVRISQN   79 (204)
Q Consensus        42 ~Vvr~~L~~v~~~g~LpG~-hHfyItF~T~~~gV~ip~~   79 (204)
                      .++++++....+.|.|.+. --+.=||.|.  ||++|..
T Consensus        39 d~akr~vd~A~~eGLL~~k~~~~~p~Fd~~--~V~lP~d   75 (157)
T COG3612          39 DVAKRVVDEALAEGLLVKKGGRLAPTFDTS--GVELPLD   75 (157)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCC--CEECCCC
T ss_conf             779999999986564032275327777877--5561257


No 35 
>pfam09665 RE_Alw26IDE Type II restriction endonuclease (RE_Alw26IDE). Members of this entry are type II restriction endonucleases of the Alw26I/Eco31I/Esp3I family. characterized specificities of the three members are GGTCTC, CGTCTC and the shared subsequence GTCTC.
Probab=23.87  E-value=29  Score=16.11  Aligned_cols=96  Identities=18%  Similarity=0.238  Sum_probs=63.1

Q ss_pred             CCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEE-EEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEEC
Q ss_conf             202210498999999999999999999997089998746999-9845888877598999639753799843112180764
Q gi|254780955|r   24 LMNYDHIRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYI-TFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVL  102 (204)
Q Consensus        24 ~M~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyI-tF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~  102 (204)
                      .+.+|...|.+++.+.+...++ +|..+..+|     ||+|+ ||++-            .|     ---+.-|.+|.++
T Consensus       326 ~~~~~a~~ls~~lr~n~~~~m~-iL~~i~~nG-----~~~fL~t~L~~------------~Y-----a~y~y~Fe~l~~~  382 (511)
T pfam09665       326 SNDETAKRLSKLLRDNRDTYMR-ILWYILSNG-----HAFFLATFLKP------------EY-----ALYDYTFEGLIIS  382 (511)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHH-HHHHHHHCC-----HHHHHHHHCCC------------HH-----HHCCCEECCCCCC
T ss_conf             7828899999999985899999-999999654-----49999997070------------33-----2011011255367


Q ss_pred             CC---EEEEEEEEC-------CEEEEEEEEHHHHEEEECCCCCEEEEECC
Q ss_conf             54---799999849-------87668998442420230677530356034
Q gi|254780955|r  103 DN---HFEVGLSFS-------NVPERLVIPFNAIKGFYDPSVNFELEFDV  142 (204)
Q Consensus       103 ~~---~FsV~LsF~-------g~~e~L~IPf~AIt~F~DPSV~FgLqF~~  142 (204)
                      +.   .-++.-++.       .+.-++.|-|.|+..|+.---.=++.+..
T Consensus       383 ~~~~~~~~i~~~~~~T~~~~~~~aR~iRIAFesL~dY~~KEnRn~~~v~~  432 (511)
T pfam09665       383 NHLGQIKSIYKDRRLTKYADSQKARRIRIAFESLKDYNSKENRNAKEVLT  432 (511)
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             76202432215730455667876568777799999888664110465334


No 36 
>pfam00073 Rhv picornavirus capsid protein. CAUTION: This alignment is very weak. It can not be generated by clustalw. If a representative set is used for a seed, many so-called members are not recognized. The family should probably be split up into sub-families. Capsid proteins of picornaviruses. Picornaviruses are non-enveloped plus-strand ssRNA animal viruses with icosahedral capsids. They include rhinovirus (common cold) and poliovirus. Common structure is an 8-stranded beta sandwich. Variations (one or two extra strands) occur.
Probab=22.44  E-value=48  Score=14.67  Aligned_cols=42  Identities=29%  Similarity=0.505  Sum_probs=26.1

Q ss_pred             CCCCCCHHHHHHCCCEEEEEEEEEECCEEECCCEEEEEEEECCEEEEEEEEHHHHEEEEC
Q ss_conf             887759899963975379984311218076454799999849876689984424202306
Q gi|254780955|r   72 RGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFNAIKGFYD  131 (204)
Q Consensus        72 ~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~~FsV~LsF~g~~e~L~IPf~AIt~F~D  131 (204)
                      ||...|...     ++.+ +--||||||.-            +-..+|+|||=++..+..
T Consensus       111 ~g~~~p~~~-----~qa~-~~ph~~~~~~~------------n~~~~~~vPyis~~~~~~  152 (173)
T pfam00073       111 PGAPKPTSR-----WQAT-LNPHQFWNLGT------------NSSARLSVPYVSIAPAYS  152 (173)
T ss_pred             CCCCCCCCH-----HHHH-CCCEEEEECCC------------CCEEEEEECCCCCCCCCC
T ss_conf             888899898-----9961-08668894798------------985899976161657666


No 37 
>KOG3913 consensus
Probab=21.42  E-value=28  Score=16.15  Aligned_cols=94  Identities=13%  Similarity=0.129  Sum_probs=60.3

Q ss_pred             HHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCHHHHHHCCCEEEEEEEEEECCEEECCCEEEEEEEECCEE
Q ss_conf             99999999999999997089998746999984588887759899963975379984311218076454799999849876
Q gi|254780955|r   37 KEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQNLRKNYPEKMTIVIQNQFWDLKVLDNHFEVGLSFSNVP  116 (204)
Q Consensus        37 ~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~~L~~~yP~emTIVlQhqf~dL~V~~~~FsV~LsF~g~~  116 (204)
                      ++|=|.+|++.|+.--|=-|+.|.--+=--.+.-.+==.+.+.||+||-.-..+..-..=..         ....+....
T Consensus       194 NeaGR~av~~~m~~~CKCHGvSGSC~~KTCW~~lp~Fr~vG~~Lk~KYd~A~~V~~~~~~~~---------~~~~~~~~~  264 (356)
T KOG3913         194 NEAGRKAVKKNMRRECKCHGVSGSCTVKTCWKQLPDFREVGDYLKEKYDGAIKVTVNNRGRR---------SAPALRPEK  264 (356)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHEEEEECCCCCC---------CCCCCCCCC
T ss_conf             49899999986542364167155215364986576689999999998641168765267766---------665445555


Q ss_pred             EEEEEEHHHHEEEECCCCCEEEE
Q ss_conf             68998442420230677530356
Q gi|254780955|r  117 ERLVIPFNAIKGFYDPSVNFELE  139 (204)
Q Consensus       117 e~L~IPf~AIt~F~DPSV~FgLq  139 (204)
                      ++...|-..=..|.|+|-+|=..
T Consensus       265 ~~~~~~~~~dLVYle~SPdfC~~  287 (356)
T KOG3913         265 PRFKPPTETDLVYLEDSPDYCER  287 (356)
T ss_pred             CCCCCCCCCCEEEECCCCHHHCC
T ss_conf             55689998742885699714315


No 38 
>pfam06748 DUF1217 Protein of unknown function (DUF1217). This family represents a conserved region that is found within bacterial proteins, most of which are hypothetical. Some members contain multiple copies.
Probab=21.33  E-value=57  Score=14.18  Aligned_cols=21  Identities=43%  Similarity=0.513  Sum_probs=17.6

Q ss_pred             CHHHHHHHHHHHHHHHHHHHH
Q ss_conf             989999999999999999999
Q gi|254780955|r   31 RYDILAKEALRGLVKVVLSEV   51 (204)
Q Consensus        31 ~Y~~l~~~Alr~Vvr~~L~~v   51 (204)
                      =|+.|-..+||.||+.+|..=
T Consensus        99 ~~~iL~d~~L~~v~~talgLp  119 (150)
T pfam06748        99 AYDILADPALREVALTALGLP  119 (150)
T ss_pred             HHHHHCCHHHHHHHHHHHCCC
T ss_conf             999987888999999992999


No 39 
>cd01611 GABARAP GABARAP  (GABA-receptor-associated protein) belongs ot a large family of proteins that mediate intracellular membrane trafficking and/or fusion.  GABARAP binds not only to GABA, type A but also to tubulin, gephrin, and ULK1.  Orthologues of GABARAP include Gate-16 (golgi-associated ATPase enhancer), LC3 (microtubule-associated protein light chain 3), and ATG8 (autophagy protein 8).  ATG8 is a ubiquitin-like protein that is conjugated to the membrane phospholipid, phosphatidylethanolamine as part of a ubiquitin-like conjugation system essential for autophagosome-formation.
Probab=21.16  E-value=57  Score=14.18  Aligned_cols=33  Identities=18%  Similarity=0.493  Sum_probs=21.8

Q ss_pred             CCHHHHHHCCCEEEEEEEE-EECCE-EECCCEEEE
Q ss_conf             5989996397537998431-12180-764547999
Q gi|254780955|r   76 ISQNLRKNYPEKMTIVIQN-QFWDL-KVLDNHFEV  108 (204)
Q Consensus        76 ip~~L~~~yP~emTIVlQh-qf~dL-~V~~~~FsV  108 (204)
                      -+.+++++||+-+-||++- .=.+| ..+...|-|
T Consensus        13 es~~i~~KyPdrIPVIve~~~~s~lp~ldk~KfLV   47 (112)
T cd01611          13 EVERIRAKYPDRIPVIVERYPKSDLPDLDKKKYLV   47 (112)
T ss_pred             HHHHHHHHCCCCCEEEEEECCCCCCCCCCCCEEEE
T ss_conf             99999997899766999987899970026856972


No 40 
>TIGR00174 miaA tRNA delta(2)-isopentenylpyrophosphate transferase; InterPro: IPR002627 tRNA isopentenyltransferases 2.5.1.8 from EC also known as tRNA delta(2)-isopentenylpyrophosphate transferases or IPP transferases. These enzymes modify both cytoplasmic and mitochondrial tRNAs at A(37) to give isopentenyl A(37) .; GO: 0004811 tRNA isopentenyltransferase activity, 0005524 ATP binding, 0008033 tRNA processing.
Probab=21.04  E-value=42  Score=15.03  Aligned_cols=42  Identities=21%  Similarity=0.514  Sum_probs=27.2

Q ss_pred             EEECCCCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCCCCC---CCCEEEE
Q ss_conf             5541622220221049899999999999999999999708999---8746999
Q gi|254780955|r   16 FIIKWIDTLMNYDHIRYDILAKEALRGLVKVVLSEVASIGSLP---GEHHFYI   65 (204)
Q Consensus        16 ~~~~~~~~~M~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g~Lp---G~hHfyI   65 (204)
                      |.|.++|-.-.-..-+|...+.++|+        .+.+.|-+|   |+.+|||
T Consensus        57 ~l~Dildp~e~y~~~~F~~~~~~~~~--------~i~~~Gkipl~VGGT~lY~  101 (307)
T TIGR00174        57 HLIDILDPSESYSAADFQTQALNAIA--------DITARGKIPLLVGGTGLYL  101 (307)
T ss_pred             EEEECCCCCCCCCCHHHHHHHHHHHH--------HHHHCCCCEEEECCHHHHH
T ss_conf             58513471200370889999999999--------9985698348868578899


No 41 
>pfam02576 DUF150 Uncharacterized BCR, YhbC family COG0779.
Probab=20.84  E-value=65  Score=13.79  Aligned_cols=90  Identities=13%  Similarity=0.235  Sum_probs=48.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEECCCCCCCCCH----HHHHHCCCEEEEEEEE------EECC-
Q ss_conf             4989999999999999999999970899987469999845888877598----9996397537998431------1218-
Q gi|254780955|r   30 IRYDILAKEALRGLVKVVLSEVASIGSLPGEHHFYITFATNARGVRISQ----NLRKNYPEKMTIVIQN------QFWD-   98 (204)
Q Consensus        30 i~Y~~l~~~Alr~Vvr~~L~~v~~~g~LpG~hHfyItF~T~~~gV~ip~----~L~~~yP~emTIVlQh------qf~d-   98 (204)
                      ++-+...  .+-..+...|..   ...+|++-    +.--..||+.=|=    +.+.---+.+.|.+..      +|.. 
T Consensus        37 v~iddc~--~~Sr~i~~~Ld~---~d~~~~~y----~LEVSSPGi~RpL~~~~~f~~~~G~~v~v~l~~~~~~~k~~~G~  107 (141)
T pfam02576        37 VTLDDCE--EVSRAISALLDV---EDPIPEAY----FLEVSSPGLERPLKTERHFARFIGKLVKVSLKEPIEGRKNFTGK  107 (141)
T ss_pred             CCHHHHH--HHHHHHHHHHCC---CCCCCCCE----EEEEECCCCCCCCCCHHHHHHHCCCEEEEEEECCCCCEEEEEEE
T ss_conf             7899999--999999877512---66667755----99995899998348889999865948999992466993899999


Q ss_pred             -EEECCCEEEEEEEECCEEEEEEEEHHHHEE
Q ss_conf             -076454799999849876689984424202
Q gi|254780955|r   99 -LKVLDNHFEVGLSFSNVPERLVIPFNAIKG  128 (204)
Q Consensus        99 -L~V~~~~FsV~LsF~g~~e~L~IPf~AIt~  128 (204)
                       +.++++.+.+.+.=+...+.+.|||+.|..
T Consensus       108 L~~~~~~~i~l~~~~~~~~~~~~i~~~~I~k  138 (141)
T pfam02576       108 LLEVDGDTVTIEVDDKRRKKEVEIPFADIKK  138 (141)
T ss_pred             EEEEECCEEEEEECCCCCCEEEEEEHHHHHH
T ss_conf             9988699999998587122689973799523


No 42 
>pfam11094 UL11 Membrane-associated tegument protein. The UL11 gene product of herpes simplex virus is a membrane-associated tegument protein that is incorporated into the HSV virion and functions in viral envelopment. UL11 is acylated which is crucial for lipid raft association.
Probab=20.72  E-value=46  Score=14.78  Aligned_cols=10  Identities=40%  Similarity=0.551  Sum_probs=7.7

Q ss_pred             CCCCEEEEEE
Q ss_conf             7772898310
Q gi|254780955|r  191 KMASVISLDN  200 (204)
Q Consensus       191 ~~aeVVSLD~  200 (204)
                      .++||||||+
T Consensus        21 ~~GevvsL~a   30 (39)
T pfam11094        21 SSGEVVSLDA   30 (39)
T ss_pred             CCCCEEEECH
T ss_conf             5886898723


No 43 
>pfam02991 MAP1_LC3 Microtubule associated protein 1A/1B, light chain 3. Light chain 3 is proposed to function primarily as a subunit of microtubule associated proteins 1A and 1B and that its expression may regulate microtubule binding activity.
Probab=20.71  E-value=58  Score=14.13  Aligned_cols=32  Identities=25%  Similarity=0.624  Sum_probs=20.5

Q ss_pred             CHHHHHHCCCEEEEEEEEEE-CCE-EECCCEEEE
Q ss_conf             98999639753799843112-180-764547999
Q gi|254780955|r   77 SQNLRKNYPEKMTIVIQNQF-WDL-KVLDNHFEV  108 (204)
Q Consensus        77 p~~L~~~yP~emTIVlQhqf-~dL-~V~~~~FsV  108 (204)
                      +.+++++||+-+-||++-.= .+| ..+...|-|
T Consensus         6 s~~i~~KyPdriPVIve~~~~~~lp~ldk~KfLV   39 (104)
T pfam02991         6 SEKIREKYPDRIPVIIEKASGSDLPDIDKKKYLV   39 (104)
T ss_pred             HHHHHHHCCCCCEEEEEECCCCCCCCCCCCEEEE
T ss_conf             9999987899776999987889872347746872


No 44 
>KOG1932 consensus
Probab=20.39  E-value=67  Score=13.73  Aligned_cols=94  Identities=19%  Similarity=0.180  Sum_probs=55.4

Q ss_pred             CCCCCHHHHCCHHHHHHHHHHHHHHHHHHHHHHCC---------CCCCCCEEEEEEECCCCCCCCCHHHH----------
Q ss_conf             22220221049899999999999999999999708---------99987469999845888877598999----------
Q gi|254780955|r   21 IDTLMNYDHIRYDILAKEALRGLVKVVLSEVASIG---------SLPGEHHFYITFATNARGVRISQNLR----------   81 (204)
Q Consensus        21 ~~~~M~~Dli~Y~~l~~~Alr~Vvr~~L~~v~~~g---------~LpG~hHfyItF~T~~~gV~ip~~L~----------   81 (204)
                      ....|..+.|+-+..+     .|+.++|..+.+.-         .++|-.-++|++.-+-.|-.|+--++          
T Consensus       455 ~~~~m~~~~i~~e~~~-----q~f~kv~~~~~~~~~k~~~~~Wv~~~g~~~~r~~~~~N~k~~~Ie~~i~Q~v~~~~~A~  529 (1180)
T KOG1932         455 LLQRMSGNRINEELSF-----QVFNKVLELASKMLLKSFFQTWVYGLGVPILRLGQRFNVKGKDIEMGIDQWVRTGGHAP  529 (1180)
T ss_pred             HHHHHHHCCCCCCHHH-----HHHHHHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCCCCCHHHHHHHHHCCCCC
T ss_conf             8898731323413799-----99999987620567778888777535870699999985035523278887765236554


Q ss_pred             --------------------------HHCCCEEEEEEEEEECCEEECCCEEEEEEEECCEEEEEEEEHHHH
Q ss_conf             --------------------------639753799843112180764547999998498766899844242
Q gi|254780955|r   82 --------------------------KNYPEKMTIVIQNQFWDLKVLDNHFEVGLSFSNVPERLVIPFNAI  126 (204)
Q Consensus        82 --------------------------~~yP~emTIVlQhqf~dL~V~~~~FsV~LsF~g~~e~L~IPf~AI  126 (204)
                                                ++|+--|||.+|-      ++-. |.-+|--.|--.++-||+++=
T Consensus       530 ~sv~~~~n~~rna~~~~~~qD~~~g~~~~~GpmtIrv~E------lDGt-feH~lqi~~~~~k~dI~chsK  593 (1180)
T KOG1932         530 FSVFSDFNRKRNALEHEIKQDYTAGNEKYTGPMTIRVQE------LDGT-FEHTLQIDGDFTKLDIQCHSK  593 (1180)
T ss_pred             EEEECCCCHHHHHHHHHCCCCCCCCCCEECCCEEEEEEE------ECCC-CEEEEEECCCCCCCCEEECCC
T ss_conf             022222000122332000356567774543534899996------0674-102588557620030152340


No 45 
>pfam11688 DUF3285 Protein of unknown function (DUF3285). This family of proteins with unknown function appears to be restricted to Cyanobacteria.
Probab=20.08  E-value=63  Score=13.90  Aligned_cols=13  Identities=31%  Similarity=0.378  Sum_probs=10.0

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999999
Q gi|254780955|r   35 LAKEALRGLVKVV   47 (204)
Q Consensus        35 l~~~Alr~Vvr~~   47 (204)
                      .+.-||||.||+-
T Consensus         7 yvKLAMRNMVRKg   19 (45)
T pfam11688         7 YVKLAMRNMVRKG   19 (45)
T ss_pred             HHHHHHHHHHHHC
T ss_conf             9999999999806


No 46 
>TIGR01722 MMSDH methylmalonate-semialdehyde dehydrogenase; InterPro: IPR010061   These proteins are involved in valine catabolism, methylmalonate-semialdehyde dehydrogenase catalyzes the irreversible NAD+- and CoA-dependent oxidative decarboxylation of methylmalonate semialdehyde to propionyl-CoA. Methylmalonate-semialdehyde dehydrogenase has been characterised in both prokaryotes ,  and eukaryotes , functioning as a mammalian tetramer and a bacterial homodimer. Although similar in monomeric molecular mass and enzymatic activity, the N-terminal sequence in Pseudomonas aeruginosa does not correspond with the N-terminal sequence predicted for rat liver. Sequence homology to a variety of prokaryotic and eukaryotic aldehyde dehydrogenases places MMSDH in the aldehyde dehydrogenase (NAD+) superfamily making MMSDH's CoA requirement unique among known ALDHs. Methylmalonate semialdehyde dehydrogenase is closely related to betaine aldehyde dehydrogenase, 2-hydroxymuconic semialdehyde dehydrogenase, and class 1 and 2 aldehyde dehydrogenase .    In Bacillus, a highly homologous protein to methylmalonic acid semialdehyde dehydrogenase, groups out from the main MMSDH clade with Listeria and Sulfolobus. This Bacillus protein has been suggested to be located in an iol operon and/or involved in myo-inositol catabolism, converting malonic semialdehyde to acetyl CoA ad CO2 . The preceding enzymes responsible for valine catabolism are present in Bacillus, Listeria, and Sulfolobus.; GO: 0004491 methylmalonate-semialdehyde dehydrogenase (acylating) activity, 0006573 valine metabolic process.
Probab=20.03  E-value=41  Score=15.11  Aligned_cols=27  Identities=30%  Similarity=0.473  Sum_probs=15.2

Q ss_pred             CCCCCCCHHH---HCCHHHHHHHHHHHHHH
Q ss_conf             1622220221---04989999999999999
Q gi|254780955|r   19 KWIDTLMNYD---HIRYDILAKEALRGLVK   45 (204)
Q Consensus        19 ~~~~~~M~~D---li~Y~~l~~~Alr~Vvr   45 (204)
                      .|.+++.++-   |+||+.|+.+.+..+=|
T Consensus        53 ~W~~ts~~~R~~vllRyqaLlkeh~dEiA~   82 (478)
T TIGR01722        53 AWKETSVAERARVLLRYQALLKEHRDEIAK   82 (478)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             102477656679999999998840789999


Done!