Query         gi|254780412|ref|YP_003064825.1| hypothetical protein CLIBASIA_01485 [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 94
No_of_seqs    106 out of 392
Neff          5.2 
Searched_HMMs 39220
Date          Sun May 29 19:02:05 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780412.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 COG2960 Uncharacterized protei  99.8 9.1E-20 2.3E-24  146.3   9.7   82    1-82      9-90  (103)
  2 pfam04380 DUF526 Protein of un  99.8 2.8E-19 7.1E-24  143.2   9.1   70   10-79      1-70  (70)
  3 pfam05597 Phasin Poly(hydroxya  97.0  0.0081 2.1E-07   38.9   8.8   50   23-79     81-130 (132)
  4 COG3937 Uncharacterized conser  96.8  0.0098 2.5E-07   38.4   8.3   62   14-82     46-107 (108)
  5 TIGR01837 PHA_granule_1 poly(h  96.2   0.073 1.9E-06   32.8   9.4   63    9-78     57-119 (121)
  6 TIGR01834 PHA_synth_III_E poly  93.3    0.45 1.2E-05   27.8   7.0   65   12-80    266-330 (332)
  7 pfam09712 PHA_synth_III_E Poly  92.8    0.92 2.3E-05   25.9   8.0   58   10-71    235-292 (293)
  8 pfam12126 DUF3583 Protein of u  90.9     1.5 3.8E-05   24.5  10.9   78    5-85     11-88  (284)
  9 KOG4797 consensus               81.4       4  0.0001   21.8   5.2   51   30-87     46-96  (123)
 10 pfam01166 TSC22 TSC-22/dip/bun  78.0     5.3 0.00014   21.1   4.9   33   49-88     12-44  (57)
 11 pfam11853 DUF3373 Protein of u  77.4     3.5 8.9E-05   22.2   3.8   28   65-92     31-58  (485)
 12 PRK13182 racA polar chromosome  75.5     5.7 0.00015   20.9   4.5   36   55-90    118-153 (178)
 13 pfam11642 Blo-t-5 Mite allerge  71.1     8.7 0.00022   19.7   4.5   36   44-79     76-111 (112)
 14 pfam10805 DUF2730 Protein of u  70.3       6 0.00015   20.7   3.6   55   27-81     34-95  (106)
 15 pfam06698 DUF1192 Protein of u  70.1       6 0.00015   20.7   3.5   27   66-92     21-47  (58)
 16 TIGR01462 greA transcription e  69.3     6.6 0.00017   20.5   3.6   45   32-83     23-67  (155)
 17 KOG3684 consensus               65.6      12 0.00031   18.7   5.8   37   53-89    429-465 (489)
 18 PRK11239 hypothetical protein;  62.8      14 0.00035   18.4   4.2   26   63-88    188-213 (215)
 19 PHA00728 hypothetical protein   62.5      11 0.00029   19.0   3.7   28   65-92      5-32  (153)
 20 COG5509 Uncharacterized small   61.2      12  0.0003   18.9   3.6   28   65-92     25-52  (65)
 21 PRK10636 putative ABC transpor  59.0      16 0.00041   18.0   5.2   22   65-86    563-584 (638)
 22 PRK11147 ABC transporter ATPas  58.7      16 0.00042   18.0   4.2   24   65-88    568-591 (632)
 23 pfam03670 UPF0184 Uncharacteri  56.4      18 0.00045   17.7   5.5   40   45-84     20-59  (83)
 24 COG3132 Uncharacterized protei  55.8      14 0.00035   18.5   3.2   20   70-89    190-209 (215)
 25 pfam07889 DUF1664 Protein of u  54.1      19 0.00049   17.5   9.2   86    1-86     33-124 (126)
 26 pfam04966 OprB Carbohydrate-se  53.9     6.1 0.00016   20.7   1.1   38   50-87      1-38  (365)
 27 PRK00846 hypothetical protein;  51.2      20 0.00051   17.4   3.4   22   67-88      9-30  (78)
 28 TIGR03282 methan_mark_13 putat  49.8      23 0.00058   17.1   3.8   25   41-65    129-153 (352)
 29 cd04776 HTH_GnyR Helix-Turn-He  49.7      23 0.00058   17.1   5.8   35   56-90     78-112 (118)
 30 pfam07106 TBPIP Tat binding pr  48.4      24 0.00061   16.9   6.0   44   44-87     65-108 (169)
 31 PRK02119 hypothetical protein;  48.1      19 0.00049   17.5   3.0   26   58-83     30-55  (73)
 32 PRK04406 hypothetical protein;  47.6      20 0.00051   17.4   3.0   11   67-77     41-51  (75)
 33 PRK02793 hypothetical protein;  46.7      19 0.00049   17.6   2.7   24   60-83     31-54  (72)
 34 pfam01519 DUF16 Protein of unk  45.3      27 0.00068   16.6   5.5   35   45-79      7-45  (87)
 35 COG1579 Zn-ribbon protein, pos  44.5      27  0.0007   16.6   6.4   52   34-85     71-123 (239)
 36 pfam10458 Val_tRNA-synt_C Valy  44.3      28  0.0007   16.5   4.3   45   36-84     21-65  (66)
 37 TIGR01149 mtrG tetrahydrometha  44.1      28 0.00071   16.5   4.2   30   47-83     10-39  (72)
 38 pfam06447 consensus             43.0      29 0.00074   16.4   8.7   38   50-87     75-112 (407)
 39 PRK00892 lpxD UDP-3-O-[3-hydro  42.2      30 0.00076   16.3   3.4   21   65-85    322-342 (343)
 40 PRK00295 hypothetical protein;  42.1      22 0.00056   17.1   2.5   30   56-85     24-53  (68)
 41 TIGR03007 pepcterm_ChnLen poly  41.5      30 0.00078   16.3   4.8   84    7-90    267-361 (510)
 42 PRK04325 hypothetical protein;  41.1      29 0.00074   16.4   3.0   32   53-84     25-56  (74)
 43 TIGR00998 8a0101 efflux pump m  41.1      27 0.00069   16.6   2.8   36   40-75    154-192 (379)
 44 pfam06825 HSBP1 Heat shock fac  40.8      31 0.00079   16.2   5.2   21   65-85     28-48  (54)
 45 TIGR02978 phageshock_pspC phag  40.1      22 0.00057   17.1   2.3   29   62-90     88-116 (128)
 46 pfam00038 Filament Intermediat  38.8      34 0.00085   16.0  11.2   67   22-88    181-253 (312)
 47 cd04171 SelB SelB subfamily.    38.2      34 0.00087   15.9   3.2   22   41-62    110-131 (164)
 48 pfam10152 DUF2360 Predicted co  37.6      35 0.00089   15.9   3.4   37   40-83     10-46  (147)
 49 pfam08317 Spc7 Spc7 kinetochor  36.3      37 0.00093   15.7  10.9   82    8-90    166-247 (322)
 50 KOG3958 consensus               36.1      34 0.00087   16.0   2.7   17   72-88    191-207 (371)
 51 TIGR02894 DNA_bind_RsfA transc  35.5      38 0.00096   15.7   5.8   37   49-85    104-140 (163)
 52 PRK06664 fliD flagellar hook-a  33.9      40   0.001   15.5   7.4   61   29-90    602-666 (684)
 53 COG3880 Modulator of heat shoc  33.7      27 0.00068   16.6   1.8   25   46-74    147-171 (176)
 54 pfam01920 Prefoldin_2 Prefoldi  33.5      41   0.001   15.5   5.7   38   54-91     65-102 (104)
 55 pfam00509 Hemagglutinin Hemagg  33.2      41   0.001   15.4   5.3   49   29-88    371-419 (550)
 56 pfam01763 Herpes_UL6 Herpesvir  32.0      43  0.0011   15.3   7.8   57   19-86    343-399 (551)
 57 PRK09039 hypothetical protein;  32.0      43  0.0011   15.3   9.6   43   50-92    122-164 (343)
 58 TIGR02132 phaR_Bmeg polyhydrox  31.7      43  0.0011   15.3   8.4   62   10-75     35-96  (189)
 59 smart00787 Spc7 Spc7 kinetocho  31.5      44  0.0011   15.3  10.3   83    8-91    162-244 (312)
 60 COG3165 Uncharacterized protei  31.5      44  0.0011   15.3  10.3   59   23-81    139-202 (204)
 61 COG3416 Uncharacterized protei  31.2      44  0.0011   15.2   3.8   76    1-86      1-76  (233)
 62 pfam11336 DUF3138 Protein of u  29.8      47  0.0012   15.1   3.2   34   60-93     20-53  (514)
 63 pfam12269 zf-CpG_bind_C CpG bi  29.7      47  0.0012   15.1   5.3   33   58-90     29-61  (236)
 64 pfam10393 Matrilin_ccoil Trime  29.0      48  0.0012   15.0   5.4   28   60-87     15-42  (44)
 65 PRK05729 valS valyl-tRNA synth  29.0      48  0.0012   15.0   3.9   43   39-85    834-876 (877)
 66 pfam08900 DUF1845 Domain of un  28.7      49  0.0012   15.0   3.8   46   27-72    153-199 (217)
 67 pfam04012 PspA_IM30 PspA/IM30   28.5      49  0.0013   14.9   6.3   36   52-87    106-141 (220)
 68 COG1842 PspA Phage shock prote  28.5      49  0.0013   14.9   6.4   57   32-88     85-143 (225)
 69 pfam10046 BLOC1_2 Biogenesis o  28.2      50  0.0013   14.9   5.8   49   40-88     24-82  (99)
 70 KOG4571 consensus               27.7      51  0.0013   14.8   6.1   41   49-89    246-286 (294)
 71 pfam09766 FimP Fms-interacting  27.6      51  0.0013   14.8   5.5   73   18-92     37-128 (352)
 72 pfam07407 Seadorna_VP6 Seadorn  27.4      51  0.0013   14.8   3.6   37   44-80     25-61  (420)
 73 COG2193 Bfr Bacterioferritin (  27.3      52  0.0013   14.8   6.2   48   27-77     94-141 (157)
 74 KOG0241 consensus               27.0      52  0.0013   14.8   4.6   35   50-84    370-405 (1714)
 75 pfam00846 Hanta_nucleocap Hant  27.0      52  0.0013   14.8   6.5   40   48-87     32-71  (428)
 76 PRK10014 DNA-binding transcrip  26.8      53  0.0013   14.7   2.4   49    1-49      1-52  (342)
 77 COG2846 Regulator of cell morp  26.0      54  0.0014   14.7   3.3   45    4-48      3-47  (221)
 78 KOG4643 consensus               26.0      54  0.0014   14.7   3.8   41   46-86    273-315 (1195)
 79 TIGR00081 purC phosphoribosyla  25.7      55  0.0014   14.6   4.7   34   39-72    234-267 (374)
 80 KOG2802 consensus               25.7      55  0.0014   14.6   2.5   77    2-84    384-491 (503)
 81 pfam06962 rRNA_methylase Putat  25.6      34 0.00087   15.9   1.2   17   53-69      5-21  (140)
 82 pfam09340 NuA4 Histone acetylt  25.3      56  0.0014   14.6   4.4   29   60-88      4-32  (80)
 83 TIGR02169 SMC_prok_A chromosom  25.2      56  0.0014   14.6   5.6   38   52-89    787-824 (1202)
 84 TIGR02231 TIGR02231 conserved   24.6      58  0.0015   14.5   5.8   76   16-91     90-177 (558)
 85 pfam10234 Cluap1 Clusterin-ass  24.0      59  0.0015   14.4   8.5   69   20-93    136-206 (269)
 86 PRK11578 macrolide transporter  23.5      61  0.0015   14.4  12.0   51   39-89    109-159 (347)
 87 pfam11488 Lge1 Transcriptional  23.3      61  0.0016   14.3   6.0   57   33-89    156-215 (234)
 88 cd01282 HTH_MerR-like_sg3 Heli  23.1      62  0.0016   14.3   5.0   31   58-88     81-111 (112)
 89 pfam05278 PEARLI-4 Arabidopsis  22.8      63  0.0016   14.3   5.8   40   47-86    168-207 (234)
 90 COG1566 EmrA Multidrug resista  22.6      63  0.0016   14.3   5.4   28   40-67    140-167 (352)
 91 pfam07195 FliD_C Flagellar hoo  22.4      64  0.0016   14.2   8.1   61   31-92    164-229 (230)
 92 PRK00591 prfA peptide chain re  22.4      58  0.0015   14.5   1.9   27   58-84     76-102 (360)
 93 PRK10697 DNA-binding transcrip  22.3      64  0.0016   14.2   4.3   27   63-89     80-106 (119)
 94 PRK01885 greB transcription el  21.7      66  0.0017   14.1   6.4   58   23-87     14-78  (159)
 95 pfam04508 Pox_A_type_inc Viral  21.5      66  0.0017   14.1   2.7   18   67-84      3-20  (26)
 96 pfam07426 Dynactin_p22 Dynacti  21.4      67  0.0017   14.1   2.8   43    2-46     27-69  (172)
 97 PRK00226 greA transcription el  21.4      67  0.0017   14.1   7.8   58   23-87     12-76  (157)
 98 cd00187 TOP4c DNA Topoisomeras  21.2      68  0.0017   14.1  10.9   54   35-89    374-429 (445)
 99 pfam06428 Sec2p GDP/GTP exchan  20.9      68  0.0017   14.0   5.8   40   50-89     43-82  (101)
100 pfam04102 SlyX SlyX. The SlyX   20.9      69  0.0017   14.0   5.5   33   53-85     20-52  (68)
101 cd04769 HTH_MerR2 Helix-Turn-H  20.5      70  0.0018   14.0   5.1   29   61-89     82-110 (116)

No 1  
>COG2960 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=99.82  E-value=9.1e-20  Score=146.26  Aligned_cols=82  Identities=28%  Similarity=0.425  Sum_probs=79.5

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99750069999999998668887799999999999999999987398569999999999999999999999999999999
Q gi|254780412|r    1 MSFRSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQ   80 (94)
Q Consensus         1 m~~~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~k   80 (94)
                      +|...|+|.+..+++..++++++++++.|+|..+|++++++|++||||||||||+|+.|+.+||+++++|++||++||++
T Consensus         9 ~m~~~~~~e~~~~ql~e~~a~~~~~~~~evE~~~r~~~q~~lnkLDlVsREEFdvq~qvl~rtR~kl~~Leari~~LEar   88 (103)
T COG2960           9 TMIGPNRFEDIAAQLSEDAAGAAQEVRAEVEKAFRAQLQRQLNKLDLVSREEFDVQRQVLLRTREKLAALEARIEELEAR   88 (103)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             04777789999999998731000103799999999999988776022439999999999999999999999999999987


Q ss_pred             HH
Q ss_conf             99
Q gi|254780412|r   81 LA   82 (94)
Q Consensus        81 l~   82 (94)
                      ++
T Consensus        89 l~   90 (103)
T COG2960          89 LA   90 (103)
T ss_pred             HC
T ss_conf             42


No 2  
>pfam04380 DUF526 Protein of unknown function (DUF526).
Probab=99.80  E-value=2.8e-19  Score=143.19  Aligned_cols=70  Identities=21%  Similarity=0.345  Sum_probs=68.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999866888779999999999999999998739856999999999999999999999999999999
Q gi|254780412|r   10 QQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQ   79 (94)
Q Consensus        10 ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~   79 (94)
                      ||+++++++++|+++++++|+++++|++++++|++||||||||||+|++|+.|+|+++++|++||++||+
T Consensus         1 ddla~~~~~~~~~~~~~~~e~e~~~r~~l~~~l~~lDlVtREEFD~q~~~l~rtR~k~~~Le~rl~~LE~   70 (70)
T pfam04380         1 DDLAKLITDALGGAQGLREEAETNVRAVLQSALSKLDLVTREEFDVQRAVLARTREKLEALEARVAALEA   70 (70)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9588998876688877889999999999999987778741999999999999999999999999997609


No 3  
>pfam05597 Phasin Poly(hydroxyalcanoate) granule associated protein (phasin). Polyhydroxyalkanoates (PHAs) are storage polyesters synthesized by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon.
Probab=96.97  E-value=0.0081  Score=38.89  Aligned_cols=50  Identities=20%  Similarity=0.346  Sum_probs=39.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             779999999999999999998739856999999999999999999999999999999
Q gi|254780412|r   23 FKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQ   79 (94)
Q Consensus        23 ~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~   79 (94)
                      +.+--+.+|..|-.++.++|+++++.||.|.+++       ..++++|.++|+.|..
T Consensus        81 a~~~wdklE~~fe~rV~~aL~rLGips~~di~~L-------~~rId~L~a~l~~L~~  130 (132)
T pfam05597        81 AEGQWDKLEQAFDERVAKALNRLGVPSRKEVEAL-------SARIDELTAQLEELAE  130 (132)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH-------HHHHHHHHHHHHHHHC
T ss_conf             8765888999999999999985699989999999-------9999999999999753


No 4  
>COG3937 Uncharacterized conserved protein [Function unknown]
Probab=96.85  E-value=0.0098  Score=38.39  Aligned_cols=62  Identities=23%  Similarity=0.364  Sum_probs=51.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999866888779999999999999999998739856999999999999999999999999999999999
Q gi|254780412|r   14 RLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLA   82 (94)
Q Consensus        14 ~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~   82 (94)
                      +++.+.+.-++.-+.+++..+..+++..+++++++++-|.+++       ++++++|+.+|..||+++-
T Consensus        46 ~~vddl~~q~k~~~~e~e~K~~r~i~~ml~~~~~~r~~~~~~l-------~~rvd~Lerqv~~Lenk~k  107 (108)
T COG3937          46 RFVDDLLRQAKEAQGELEEKIPRKIEEMLSDLEVARQSEMDEL-------TERVDALERQVADLENKLK  107 (108)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHHH-------HHHHHHHHHHHHHHHHHHC
T ss_conf             9999999998987602777636899999845020000248888-------9899999999999998761


No 5  
>TIGR01837 PHA_granule_1 poly(hydroxyalkanoate) granule-associated protein; InterPro: IPR008769   Polyhydroxyalkanoates (PHAs) are storage polyesters synthesised by various bacteria as intracellular carbon and energy reserve material. PHAs are accumulated as water-insoluble inclusions within the cells. This family consists of the phasins PhaF and PhaI which act as a transcriptional regulator of PHA biosynthesis genes. PhaF has been proposed to repress expression of the phaC1 gene and the phaIF operon..
Probab=96.19  E-value=0.073  Score=32.84  Aligned_cols=63  Identities=14%  Similarity=0.295  Sum_probs=49.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999986688877999999999999999999873985699999999999999999999999999999
Q gi|254780412|r    9 FQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIE   78 (94)
Q Consensus         9 ~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE   78 (94)
                      ++.....++.+=+.+..==+.++..|-.+++++|++|++.||+|.|++       +.+++.|..+|..|-
T Consensus        57 ~~~~~~~~~~~~d~~~~~w~~l~~~FD~R~~~~L~rL~IPs~~e~eaL-------~~k~e~L~~~~e~l~  119 (121)
T TIGR01837        57 IEEVKTKLEQVRDKVQRNWDKLEKAFDERVEQALNRLNIPSKEEVEAL-------RAKVEQLKEQVEELR  119 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH-------HHHHHHHHHHHHHHH
T ss_conf             999998888779999888988999999999999985789987769999-------999999999999884


No 6  
>TIGR01834 PHA_synth_III_E poly(R)-hydroxyalkanoic acid synthase, class III, PhaE subunit; InterPro: IPR010123   This entry represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species..
Probab=93.32  E-value=0.45  Score=27.83  Aligned_cols=65  Identities=17%  Similarity=0.334  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999998668887799999999999999999987398569999999999999999999999999999999
Q gi|254780412|r   12 ASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQ   80 (94)
Q Consensus        12 la~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~k   80 (94)
                      .+++-+..+.+...+    .......++..+..|||-||-|.|....-+.-+|-++-.|..++..++++
T Consensus       266 ~~~v~G~liNA~m~l----k~~~q~~~~~~~~~LnlPtRsEl~~~h~~i~~l~r~~~~L~~~l~~~~~~  330 (332)
T TIGR01834       266 YAKVHGKLINALMRL----KKRQQEVVEELLKALNLPTRSELDEAHQRIQELRREVKELKKRLADLEKK  330 (332)
T ss_pred             HHHHHHHHHHHHHHH----HHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             678998879899999----99999999999865389976899999999999999999999875114222


No 7  
>pfam09712 PHA_synth_III_E Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E). This entry represents the PhaE subunit of the heterodimeric class (class III) of polymerase for poly(R)-hydroxyalkanoic acids (PHAs), carbon and energy storage polymers of many bacteria. The most common PHA is polyhydroxybutyrate but about 150 different constituent hydroxyalkanoic acids (HAs) have been identified in various species.
Probab=92.84  E-value=0.92  Score=25.89  Aligned_cols=58  Identities=21%  Similarity=0.331  Sum_probs=41.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999998668887799999999999999999987398569999999999999999999999
Q gi|254780412|r   10 QQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIG   71 (94)
Q Consensus        10 ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le   71 (94)
                      ++.+++.+....+...+|..    ....++.++..|||.||.|.|.....+..+|.++-.|.
T Consensus       235 ee~~k~~g~~~nA~m~~r~~----~q~~~e~~l~~l~lPTrseld~~~kri~eLrre~r~L~  292 (293)
T pfam09712       235 EEYAQIHGRLSNAQMRLRRA----LQQVVDELLGSLGLPTRSELDTAQRRLQELRRENRALA  292 (293)
T ss_pred             HHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             89999999999999999999----99999999863899827889999999999999998752


No 8  
>pfam12126 DUF3583 Protein of unknown function (DUF3583). This domain is found in eukaryotes, and is typically between 302 and 338 amino acids in length. It is found in association with pfam00097 and pfam00643. Most members are promyelocytic leukemia proteins, and this family lies towards the C-terminus.
Probab=90.93  E-value=1.5  Score=24.52  Aligned_cols=78  Identities=14%  Similarity=0.250  Sum_probs=63.4

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             00699999999986688877999999999999999999873985699999999999999999999999999999999999
Q gi|254780412|r    5 SNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADL   84 (94)
Q Consensus         5 ~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~l   84 (94)
                      ..++|+..-..+-.|++.++..+.|.+..||++++.++.   .|-..|=+.+..|-.+.+.--+.+..++.-|++-|...
T Consensus        11 Q~~~F~~Ahaqm~SAv~qL~~vr~dteelIR~rVrqvve---hvqaqErELLE~V~~rYqR~yeEiAgqL~~ldAVLqRI   87 (284)
T pfam12126        11 QDRTFGAAHAQMCSAIGQLGRARADTEEQIRERVRQVVA---HVQAQERELLEAVNARYQRDYEEIAGQLGRLDAVLQRI   87 (284)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             776678999999999999988776299999999999999---99999999999999998740999998887899999999


Q ss_pred             H
Q ss_conf             9
Q gi|254780412|r   85 E   85 (94)
Q Consensus        85 e   85 (94)
                      .
T Consensus        88 r   88 (284)
T pfam12126        88 R   88 (284)
T ss_pred             H
T ss_conf             8


No 9  
>KOG4797 consensus
Probab=81.45  E-value=4  Score=21.81  Aligned_cols=51  Identities=18%  Similarity=0.227  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999873985699999999999999999999999999999999999996
Q gi|254780412|r   30 AESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus        30 ie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      |++.+-+-++=+-+.+-+--|||.|+++       +++-.|+.|...||..=.=|+.+
T Consensus        46 IDNKIeQAMDLVKtHLmfAVREEVe~Lk-------~qI~eL~er~~~Le~EN~lLk~~   96 (123)
T KOG4797          46 IDNKIEQAMDLVKTHLMFAVREEVEVLK-------EQIRELEERNSALERENSLLKTL   96 (123)
T ss_pred             ECHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             2148999999999999999999999999-------99999999999999987899850


No 10 
>pfam01166 TSC22 TSC-22/dip/bun family.
Probab=78.03  E-value=5.3  Score=21.06  Aligned_cols=33  Identities=24%  Similarity=0.361  Sum_probs=17.2

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6999999999999999999999999999999999999965
Q gi|254780412|r   49 RAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFI   88 (94)
Q Consensus        49 tREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~   88 (94)
                      -|||.|+++       +++..|+.|+..||..=+-|+.+.
T Consensus        12 VREEVevLk-------~~I~eL~~~~~~le~EN~~Lk~~~   44 (57)
T pfam01166        12 VREEVEVLK-------EQIKELEEKNSQLERENTLLKSLA   44 (57)
T ss_pred             HHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             999999999-------999999999999999999998609


No 11 
>pfam11853 DUF3373 Protein of unknown function (DUF3373). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=77.38  E-value=3.5  Score=22.22  Aligned_cols=28  Identities=32%  Similarity=0.532  Sum_probs=19.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999999999999999650023
Q gi|254780412|r   65 EEITAIGKRLEKIEQQLADLELFINQKE   92 (94)
Q Consensus        65 ~~~e~Le~rl~~LE~kl~~le~~~~~k~   92 (94)
                      .+|++|+++|++|++++.++.-.+++.+
T Consensus        31 qkI~~L~~ql~eLk~~~~~~~~~v~~~e   58 (485)
T pfam11853        31 QKIEALKKELAELKAQLKDLNKRVDKTE   58 (485)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999998776655566


No 12 
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=75.52  E-value=5.7  Score=20.87  Aligned_cols=36  Identities=25%  Similarity=0.305  Sum_probs=29.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999996500
Q gi|254780412|r   55 NVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQ   90 (94)
Q Consensus        55 v~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~   90 (94)
                      |+---|..-|-+++.+-++|..||.+|+.+|-..+.
T Consensus       118 VVSyQLLqHRrEiEEm~~~lq~Le~ri~klE~~~~~  153 (178)
T PRK13182        118 VVSYQLLQHRREMEEMLERIQKLEARLKKLEPIYIT  153 (178)
T ss_pred             EEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             001899987999999999999999999986155228


No 13 
>pfam11642 Blo-t-5 Mite allergen Blo t 5. This family of proteins is Blo t 5, an allergen protein from Blomia tropicalis mites. This protein shoes strong reactivity with IgE in asthmatic and rhinitis patients. The structure of the protein contains three alpha helices which form a coiled-coil.
Probab=71.10  E-value=8.7  Score=19.72  Aligned_cols=36  Identities=17%  Similarity=0.312  Sum_probs=21.0

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             739856999999999999999999999999999999
Q gi|254780412|r   44 SMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQ   79 (94)
Q Consensus        44 kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~   79 (94)
                      ++|++-|=-||...+...=.-..+.+++++|.+.++
T Consensus        76 DLnilEkfNfE~al~t~~iL~kDLk~~e~kVKaI~t  111 (112)
T pfam11642        76 DLNLLEKFNFEAALATGKVLLKDLKELAKKVKAIET  111 (112)
T ss_pred             HHHHHHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             135999826999999989999889999999887714


No 14 
>pfam10805 DUF2730 Protein of unknown function (DUF2730). This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=70.30  E-value=6  Score=20.74  Aligned_cols=55  Identities=16%  Similarity=0.379  Sum_probs=28.8

Q ss_pred             HHHHHHHH------HHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999------99999999873-985699999999999999999999999999999999
Q gi|254780412|r   27 SKEAESFA------QIKIQRTLNSM-GVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQL   81 (94)
Q Consensus        27 ~~Eie~~~------r~~~e~~l~kl-dLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl   81 (94)
                      |++++...      ..++...=.+. .|-|..++..++--+...|-++.++.++|..++-+.
T Consensus        34 kedv~~l~~~~~~~~~Rl~~lE~~v~~lPt~~dv~~L~~~itelrGe~k~l~~~i~~i~hq~   95 (106)
T pfam10805        34 REDVEKLIDIIASNDKRLTEMETKLESLPTAKDVHALKIEITELRGELKELSAQIQSISHQL   95 (106)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH
T ss_conf             98899999998877768999999985399687899999999997146999988757688899


No 15 
>pfam06698 DUF1192 Protein of unknown function (DUF1192). This family consists of several short, hypothetical, bacterial proteins of around 60 residues in length. The function of this family is unknown.
Probab=70.11  E-value=6  Score=20.75  Aligned_cols=27  Identities=19%  Similarity=0.436  Sum_probs=19.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999999999999650023
Q gi|254780412|r   66 EITAIGKRLEKIEQQLADLELFINQKE   92 (94)
Q Consensus        66 ~~e~Le~rl~~LE~kl~~le~~~~~k~   92 (94)
                      -+++|+.||+.|+..|+.+++-+.+|.
T Consensus        21 Sv~EL~~RIa~L~~EI~R~e~~~~~K~   47 (58)
T pfam06698        21 SVEELEERIALLQAEIARLEAALAKKK   47 (58)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             799999999999999999999999988


No 16 
>TIGR01462 greA transcription elongation factor GreA; InterPro: IPR006359   Bacterial GreA and GreB IPR006358 from INTERPRO promote transcription elongation by stimulating an endogenous, endonucleolytic transcript cleavage activity of the RNA polymerase (RNAP) , allowing RNA transcription to continue past template-encoded arresting sites. GreA and GreB are sequence homologues and have homologues in every known bacterial genome. GreA and GreB stimulate transcript cleavage in different ways; GreA induces cleavage of 3'-RNA fragments 23 nt in length and can only prevent the formation of arrested complexes, whereas GreB induces cleavage of fragments up to 18 nt in length and can rescue pre-existing arrested complexes.    The 2.2  resolution crystal structure of Escherichia coli GreA comprises an N-terminal antiparallel alpha-helical coiled coil, and a C-terminal globular domain. While the C-terminal domain binds RNAP, the N-terminal coiled coil interacts with the transcript 3' end and is responsible for stimulating the transcript cleavage reaction . Functional differences between GreA and GreB correlate with the distribution of positively charged residues on one face of the N-terminal coiled coil.  Because members of the family outside the Proteobacteria resemble GreA more closely than GreB, the GreB clade (IPR006358 from INTERPRO) forms a plausible outgroup and the remainder of the GreA/B family, included in this family, is designated GreA. In the Chlamydias and some spirochetes, the conserved region of these proteins is found as the C-terminal region of a much larger protein.  ; GO: 0003677 DNA binding, 0003711 transcription elongation regulator activity, 0006355 regulation of transcription DNA-dependent.
Probab=69.32  E-value=6.6  Score=20.45  Aligned_cols=45  Identities=20%  Similarity=0.212  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999987398569999999999999999999999999999999999
Q gi|254780412|r   32 SFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLAD   83 (94)
Q Consensus        32 ~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~   83 (94)
                      ..+-..+..+.+.-||====|||+       ||+++..+|.||..||..|+.
T Consensus        23 peI~~~I~~AR~~GDLsENAEY~A-------AKe~Q~~~E~RI~~le~~l~~   67 (155)
T TIGR01462        23 PEISEEIKEAREHGDLSENAEYHA-------AKEEQGFIEGRIAELEDLLAN   67 (155)
T ss_pred             HHHHHHHHHHHHCCCCCCCCHHHH-------HHHHHHHHHHHHHHHHHHHHC
T ss_conf             899999999985188655600389-------999999998899999988762


No 17 
>KOG3684 consensus
Probab=65.56  E-value=12  Score=18.75  Aligned_cols=37  Identities=14%  Similarity=0.266  Sum_probs=29.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999999650
Q gi|254780412|r   53 IENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        53 Fdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~   89 (94)
                      +-..-+.+.+.+.+.++|++||+.||.++.++-..++
T Consensus       429 ~~~myd~~~~l~~~q~~le~qI~~Le~kl~~l~~~l~  465 (489)
T KOG3684         429 QNDMYDLLQELHSRQEELEKQIDTLESKLEALTASLS  465 (489)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8899999999987799999999999999999999987


No 18 
>PRK11239 hypothetical protein; Provisional
Probab=62.75  E-value=14  Score=18.44  Aligned_cols=26  Identities=19%  Similarity=0.382  Sum_probs=15.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999965
Q gi|254780412|r   63 LREEITAIGKRLEKIEQQLADLELFI   88 (94)
Q Consensus        63 ~R~~~e~Le~rl~~LE~kl~~le~~~   88 (94)
                      ...++.+||++|++|..+++.|.+.+
T Consensus       188 l~~Rv~~LE~eVa~Lk~~l~~L~a~L  213 (215)
T PRK11239        188 LQARVEALEIEVAELKQRLDSLLAHL  213 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999983


No 19 
>PHA00728 hypothetical protein
Probab=62.55  E-value=11  Score=18.98  Aligned_cols=28  Identities=29%  Similarity=0.529  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999999999999999650023
Q gi|254780412|r   65 EEITAIGKRLEKIEQQLADLELFINQKE   92 (94)
Q Consensus        65 ~~~e~Le~rl~~LE~kl~~le~~~~~k~   92 (94)
                      .+++.|.+.-++|.++|+.+|+.+|--.
T Consensus         5 teveql~keneelkkkla~leal~nne~   32 (153)
T PHA00728          5 TEVEQLKKENEELKKKLAKLEALLNNES   32 (153)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             6899999866999999999999974788


No 20 
>COG5509 Uncharacterized small protein containing a coiled-coil domain [Function unknown]
Probab=61.19  E-value=12  Score=18.92  Aligned_cols=28  Identities=11%  Similarity=0.319  Sum_probs=21.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999999999999999650023
Q gi|254780412|r   65 EEITAIGKRLEKIEQQLADLELFINQKE   92 (94)
Q Consensus        65 ~~~e~Le~rl~~LE~kl~~le~~~~~k~   92 (94)
                      --+.+|+.||+.|...|+.+++-.++|.
T Consensus        25 lsV~El~eRIalLq~EIeRlkAe~~kK~   52 (65)
T COG5509          25 LSVAELEERIALLQAEIERLKAELAKKK   52 (65)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             5188899999999999999999998610


No 21 
>PRK10636 putative ABC transporter ATP-binding protein; Provisional
Probab=59.03  E-value=16  Score=18.01  Aligned_cols=22  Identities=41%  Similarity=0.563  Sum_probs=7.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999
Q gi|254780412|r   65 EEITAIGKRLEKIEQQLADLEL   86 (94)
Q Consensus        65 ~~~e~Le~rl~~LE~kl~~le~   86 (94)
                      .+++.||++|+.||.+++.++.
T Consensus       563 ~~~~~~e~~i~~le~~~~~l~~  584 (638)
T PRK10636        563 KEIARLEKEMEKLNAQLAQAEE  584 (638)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999


No 22 
>PRK11147 ABC transporter ATPase component; Reviewed
Probab=58.73  E-value=16  Score=17.98  Aligned_cols=24  Identities=21%  Similarity=0.425  Sum_probs=9.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999965
Q gi|254780412|r   65 EEITAIGKRLEKIEQQLADLELFI   88 (94)
Q Consensus        65 ~~~e~Le~rl~~LE~kl~~le~~~   88 (94)
                      .+++.+|.+|+.||+++.++|.-+
T Consensus       568 ~~~~~~e~~i~~~e~~~~~l~~~l  591 (632)
T PRK11147        568 RELEQLPQLLEDLEAEIEALQAQV  591 (632)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999998999999999999999985


No 23 
>pfam03670 UPF0184 Uncharacterized protein family (UPF0184).
Probab=56.38  E-value=18  Score=17.73  Aligned_cols=40  Identities=18%  Similarity=0.331  Sum_probs=34.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             3985699999999999999999999999999999999999
Q gi|254780412|r   45 MGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADL   84 (94)
Q Consensus        45 ldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~l   84 (94)
                      -|=..-+||+++-.||-....-+++||.|-+.|-.+|..|
T Consensus        20 ~de~~~~Ey~aiNs~LDqin~~LD~lEqrnD~l~~qL~eL   59 (83)
T pfam03670        20 VDEFGLQEYEAINSMLDQINSALDALEERNDDLMSQLREL   59 (83)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             5300499999999999999999999998607999999999


No 24 
>COG3132 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.76  E-value=14  Score=18.47  Aligned_cols=20  Identities=30%  Similarity=0.567  Sum_probs=10.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999650
Q gi|254780412|r   70 IGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        70 Le~rl~~LE~kl~~le~~~~   89 (94)
                      ||+||++||..++.|+..++
T Consensus       190 learv~aLe~eva~L~~rld  209 (215)
T COG3132         190 LEARVEALEQEVAELRARLD  209 (215)
T ss_pred             HHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999


No 25 
>pfam07889 DUF1664 Protein of unknown function (DUF1664). The members of this family are hypothetical plant proteins of unknown function. The region featured in this family is approximately 100 amino acids long.
Probab=54.12  E-value=19  Score=17.50  Aligned_cols=86  Identities=12%  Similarity=0.249  Sum_probs=51.7

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------CCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99750069999999998668887799999999999999999987398------569999999999999999999999999
Q gi|254780412|r    1 MSFRSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGV------VRAEEIENVKRTTSHLREEITAIGKRL   74 (94)
Q Consensus         1 m~~~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldL------VtREEFdv~~~~l~k~R~~~e~Le~rl   74 (94)
                      |||-+.+=+.|.-.-++--+..+.+.=....+-+-++++..=.+||-      -+|+|....+.=+...-..++.+..-+
T Consensus        33 lMfvTkR~ms~Av~sv~KqLe~Vs~sl~~tKrhLsqRI~~vd~kld~~~eis~~i~~eV~e~~~~~~~i~~D~~~v~~~v  112 (126)
T pfam07889        33 LMFVTKRNMSDAVASVGKQLEKVSESIAATKKHLSQRIDNLDDKLDEQKEISESTRDEVTEIREDLSNIGEDVKSVQQAV  112 (126)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             56654720889999999989999999999999999988735321999999999999999999964998876999999999


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999999999
Q gi|254780412|r   75 EKIEQQLADLEL   86 (94)
Q Consensus        75 ~~LE~kl~~le~   86 (94)
                      ..||.||..+|.
T Consensus       113 ~~Le~Ki~~ie~  124 (126)
T pfam07889       113 EGLEGKLDSIEY  124 (126)
T ss_pred             HHHHHHHHHHHH
T ss_conf             989999988860


No 26 
>pfam04966 OprB Carbohydrate-selective porin, OprB family.
Probab=53.88  E-value=6.1  Score=20.69  Aligned_cols=38  Identities=11%  Similarity=0.114  Sum_probs=25.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999999996
Q gi|254780412|r   50 AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus        50 REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      ||.....+....-...+++.|..|++.||.+.+.||+.
T Consensus         1 ~edl~~~~rL~~ef~~ELa~L~Grvdgle~r~~~le~~   38 (365)
T pfam04966         1 KEGLAYAGQLQLEFDLDLAKLAGWVDGGEFRTSALERH   38 (365)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHCCCCCCEEHHHHHHCC
T ss_conf             97078998899999999999749723722066778602


No 27 
>PRK00846 hypothetical protein; Provisional
Probab=51.21  E-value=20  Score=17.43  Aligned_cols=22  Identities=23%  Similarity=0.235  Sum_probs=11.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999965
Q gi|254780412|r   67 ITAIGKRLEKIEQQLADLELFI   88 (94)
Q Consensus        67 ~e~Le~rl~~LE~kl~~le~~~   88 (94)
                      -.+||.||..||.+|+=-|-.|
T Consensus         9 d~~LE~Rl~eLE~rlaFQEqti   30 (78)
T PRK00846          9 DQALEARLVELETRVSFQEQAL   30 (78)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999999999999989


No 28 
>TIGR03282 methan_mark_13 putative methanogenesis marker 13 metalloprotein. Members of this protein family, to date, are found in a completed prokaryotic genome if and only if the species is one of the archaeal methanogens. The exact function is unknown, but likely is linked to methanogenesis or a process closely connected to it. This metal cluster-binding family is related to nitrogenase structural protein NifD and accessory protein NifE, among others.
Probab=49.77  E-value=23  Score=17.07  Aligned_cols=25  Identities=20%  Similarity=0.371  Sum_probs=21.3

Q ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             9987398569999999999999999
Q gi|254780412|r   41 TLNSMGVVRAEEIENVKRTTSHLRE   65 (94)
Q Consensus        41 ~l~kldLVtREEFdv~~~~l~k~R~   65 (94)
                      ...+.++.+.+||+-|+.||.++-+
T Consensus       129 ~A~~~G~I~~~E~eRQk~mL~~Ate  153 (352)
T TIGR03282       129 SAAEAGIIDEDEVERQKELLKKATE  153 (352)
T ss_pred             HHHHCCCCCHHHHHHHHHHHHHHHH
T ss_conf             8997598588999999999999889


No 29 
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=49.74  E-value=23  Score=17.07  Aligned_cols=35  Identities=11%  Similarity=0.284  Sum_probs=28.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999996500
Q gi|254780412|r   56 VKRTTSHLREEITAIGKRLEKIEQQLADLELFINQ   90 (94)
Q Consensus        56 ~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~   90 (94)
                      +..++.....++..|+.++..|+.-++.|+.....
T Consensus        78 l~~~l~~l~~~i~~Le~~~~~L~~~l~~L~~~~~~  112 (118)
T cd04776          78 LEKMLEKIEKRRAELEQQRRDIDAALAELDAAEER  112 (118)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999999


No 30 
>pfam07106 TBPIP Tat binding protein 1(TBP-1)-interacting protein (TBPIP). This family consists of several eukaryotic TBP-1 interacting protein (TBPIP) sequences. TBP-1 has been demonstrated to interact with the human immunodeficiency virus type 1 (HIV-1) viral protein Tat, then modulate the essential replication process of HIV. In addition, TBP-1 has been shown to be a component of the 26S proteasome, a basic multiprotein complex that degrades ubiquitinated proteins in an ATP-dependent fashion. Human TBPIP interacts with human TBP-1 then modulates the inhibitory action of human TBP-1 on HIV-Tat-mediated transactivation.
Probab=48.44  E-value=24  Score=16.94  Aligned_cols=44  Identities=20%  Similarity=0.303  Sum_probs=29.9

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             73985699999999999999999999999999999999999996
Q gi|254780412|r   44 SMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus        44 kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      .++.++-+|...+..-+...++++..|...+..|++.|..|...
T Consensus        65 ~~~~~~~eel~~~d~~i~~L~~~l~~l~~~~~~l~~el~~L~s~  108 (169)
T pfam07106        65 QFELPSDEELNKLDMEIEELREEVQLLKQDCSTLEIELKSLTSD  108 (169)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             13569988998769999999999999999999999999998758


No 31 
>PRK02119 hypothetical protein; Provisional
Probab=48.07  E-value=19  Score=17.51  Aligned_cols=26  Identities=15%  Similarity=0.222  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999
Q gi|254780412|r   58 RTTSHLREEITAIGKRLEKIEQQLAD   83 (94)
Q Consensus        58 ~~l~k~R~~~e~Le~rl~~LE~kl~~   83 (94)
                      .++.+-...++.|..++..|-.+|.+
T Consensus        30 q~v~~Qq~~i~~l~~ql~~L~~rlk~   55 (73)
T PRK02119         30 QALIQQQFVIDKMQVQLRHMANKLKD   55 (73)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999985


No 32 
>PRK04406 hypothetical protein; Provisional
Probab=47.63  E-value=20  Score=17.40  Aligned_cols=11  Identities=18%  Similarity=0.443  Sum_probs=3.4

Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999999999
Q gi|254780412|r   67 ITAIGKRLEKI   77 (94)
Q Consensus        67 ~e~Le~rl~~L   77 (94)
                      ++.|..++..|
T Consensus        41 i~~lq~qlr~L   51 (75)
T PRK04406         41 ITKMQDQMKYV   51 (75)
T ss_pred             HHHHHHHHHHH
T ss_conf             99999999999


No 33 
>PRK02793 hypothetical protein; Provisional
Probab=46.67  E-value=19  Score=17.55  Aligned_cols=24  Identities=13%  Similarity=0.250  Sum_probs=8.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999
Q gi|254780412|r   60 TSHLREEITAIGKRLEKIEQQLAD   83 (94)
Q Consensus        60 l~k~R~~~e~Le~rl~~LE~kl~~   83 (94)
                      +.+-...++.|..++..|-.+|.+
T Consensus        31 v~~Qq~~i~~L~~ql~~L~~rLk~   54 (72)
T PRK02793         31 VTAHEMEMAKLRDHLRLLTEKLKA   54 (72)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999985


No 34 
>pfam01519 DUF16 Protein of unknown function DUF16. The function of this protein is unknown. It appears to only occur in Mycoplasma pneumoniae. The crystal structure revealed that this domain is composed of two separated homotrimeric coiled-coils.
Probab=45.32  E-value=27  Score=16.63  Aligned_cols=35  Identities=20%  Similarity=0.466  Sum_probs=20.9

Q ss_pred             CCCCCHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHH
Q ss_conf             398569999999999----99999999999999999999
Q gi|254780412|r   45 MGVVRAEEIENVKRT----TSHLREEITAIGKRLEKIEQ   79 (94)
Q Consensus        45 ldLVtREEFdv~~~~----l~k~R~~~e~Le~rl~~LE~   79 (94)
                      -+.|||.+|+.-+.-    +.|.-.++.....+|..|..
T Consensus         7 t~YVT~Kqf~efKdsn~qrltKiE~k~~~qgeqI~~l~~   45 (87)
T pfam01519         7 TGYVTHKQFDEFKDSNDQRLTKIETKLDAQGEQIRKLTQ   45 (87)
T ss_pred             CCCCHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             661209988875144226899999999999999999999


No 35 
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=44.50  E-value=27  Score=16.56  Aligned_cols=52  Identities=19%  Similarity=0.390  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHCCCCCHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999873985699-9999999999999999999999999999999999
Q gi|254780412|r   34 AQIKIQRTLNSMGVVRAE-EIENVKRTTSHLREEITAIGKRLEKIEQQLADLE   85 (94)
Q Consensus        34 ~r~~~e~~l~kldLVtRE-EFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le   85 (94)
                      ++.++.+.=.+++-||.+ ||.++..=...+..+...|+..+..|...+..++
T Consensus        71 ~r~r~~~~e~kl~~v~~~~e~~aL~~E~~~ak~r~~~le~el~~l~~~~~~l~  123 (239)
T COG1579          71 IRERIKRAEEKLSAVKDERELRALNIEIQIAKERINSLEDELAELMEEIEKLE  123 (239)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999878998861256999998788999999999999999999999999889


No 36 
>pfam10458 Val_tRNA-synt_C Valyl tRNA synthetase tRNA binding arm. This domain is found at the C-terminus of Valyl tRNA synthetases.
Probab=44.31  E-value=28  Score=16.54  Aligned_cols=45  Identities=20%  Similarity=0.394  Sum_probs=35.5

Q ss_pred             HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999873985699999999999999999999999999999999999
Q gi|254780412|r   36 IKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADL   84 (94)
Q Consensus        36 ~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~l   84 (94)
                      ..++.-|+.-++|++    |-.+|+...|.++..++.+++.|+..|+.|
T Consensus        21 ~~~~~kL~N~~Fv~k----AP~~VV~~er~kl~~~~~~~~~l~~~L~~L   65 (66)
T pfam10458        21 ERLQKKLSNPGFVAK----APAEVVEEEKAKLAEYEEQLEKLKERLSQL   65 (66)
T ss_pred             HHHHHHHCCHHHHHH----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             999987787677770----989999999999999999999999999875


No 37 
>TIGR01149 mtrG tetrahydromethanopterin S-methyltransferase, subunit G; InterPro: IPR005866    This model describes the N5-methyltetrahydromethanopterin: coenzyme M methyltransferase subunit G in methanogenic archaea. This methyltranferase is a membrane-associated enzyme complex that uses methyl-transfer reaction to drive a sodium-ion pump. Archaea have evolved energy-yielding pathways marked by one-carbon biochemistry featuring novel cofactors and enzymes. This transferase is involved in the transfer of a methyl group from N5-methyltetrahydromethanopterin to coenzyme M. In an accompanying reaction, methane is produced by two-electron reduction of the methyl moiety in methyl-coenzyme M by another enzyme methyl-coenzyme M reductase.; GO: 0030269 tetrahydromethanopterin S-methyltransferase activity, 0015948 methanogenesis, 0016021 integral to membrane.
Probab=44.07  E-value=28  Score=16.51  Aligned_cols=30  Identities=23%  Similarity=0.501  Sum_probs=19.7

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8569999999999999999999999999999999999
Q gi|254780412|r   47 VVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLAD   83 (94)
Q Consensus        47 LVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~   83 (94)
                      +|+-+||+...       +|++++|.|++---.-+++
T Consensus        10 ~~~~~ef~~~~-------~rLDeie~kveFv~~E~~Q   39 (72)
T TIGR01149        10 LVEPDEFNEVK-------KRLDEIEEKVEFVNGEVAQ   39 (72)
T ss_pred             CCCHHHHHHHH-------HHHHHHHHHHHHHHHHHHH
T ss_conf             05976699999-------8741786788789999888


No 38 
>pfam06447 consensus
Probab=42.99  E-value=29  Score=16.41  Aligned_cols=38  Identities=21%  Similarity=0.254  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999999996
Q gi|254780412|r   50 AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus        50 REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      +.|-|.+..-+...++++++|+.++..|.+++.+++..
T Consensus        75 ~~e~~~~~~~~~~~q~~l~~l~qe~~~L~~q~~~~~~~  112 (407)
T pfam06447        75 RAEREEKERDLDQNQERIASLEQENQQLREQLAAGQAN  112 (407)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999998878888999999999999999999988726


No 39 
>PRK00892 lpxD UDP-3-O-[3-hydroxymyristoyl] glucosamine N-acyltransferase; Provisional
Probab=42.16  E-value=30  Score=16.33  Aligned_cols=21  Identities=24%  Similarity=0.495  Sum_probs=13.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999
Q gi|254780412|r   65 EEITAIGKRLEKIEQQLADLE   85 (94)
Q Consensus        65 ~~~e~Le~rl~~LE~kl~~le   85 (94)
                      .++..|.+|+..||+++.++|
T Consensus       322 ~~Lp~l~k~~~~lek~~~~~~  342 (343)
T PRK00892        322 RRLDKMRKRLKALEKKVEKQE  342 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHC
T ss_conf             607999999999999998634


No 40 
>PRK00295 hypothetical protein; Provisional
Probab=42.12  E-value=22  Score=17.14  Aligned_cols=30  Identities=3%  Similarity=0.137  Sum_probs=14.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999
Q gi|254780412|r   56 VKRTTSHLREEITAIGKRLEKIEQQLADLE   85 (94)
Q Consensus        56 ~~~~l~k~R~~~e~Le~rl~~LE~kl~~le   85 (94)
                      +-.++..-.-.++.|..++..|-.++.+..
T Consensus        24 LN~~l~~Qq~~id~L~~q~~~l~~rl~~~~   53 (68)
T PRK00295         24 LNDVVVEQQRVIERLQLQMAALIKRQEEMV   53 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999988


No 41 
>TIGR03007 pepcterm_ChnLen polysaccharide chain length determinant protein, PEP-CTERM locus subfamily; InterPro: IPR014345   Members of this entry belong to the family of polysaccharide chain length determinant proteins. They are found in species that encode the PEP-CTERM/exosortase system and are predicted to act in protein sorting in a number of Gram-negative bacteria, they are also found near the epsH homologue that is the putative exosortase gene..
Probab=41.48  E-value=30  Score=16.26  Aligned_cols=84  Identities=10%  Similarity=0.124  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-----HCCCCCHHH------HHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6999999999866888779999999999999999998-----739856999------99999999999999999999999
Q gi|254780412|r    7 QFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLN-----SMGVVRAEE------IENVKRTTSHLREEITAIGKRLE   75 (94)
Q Consensus         7 ~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~-----kldLVtREE------Fdv~~~~l~k~R~~~e~Le~rl~   75 (94)
                      +-+|+|-=--++--|..-.+|.+|+..=+.+-+.+-.     .-+=..+.+      +.=++--+.++-.++++|++|.+
T Consensus       267 ~~Ld~L~l~YTd~HPdv~~~k~~Ia~L~~~~~~e~~~~~~Q~~~~~~~~~~~~~nPvyQql~~~l~~~eA~~asl~~r~~  346 (510)
T TIGR03007       267 KQLDALRLRYTDKHPDVIATKREIAQLEEQKEEELESYRKQNGEGGGSEKGSIYNPVYQQLQIELAEAEAEIASLEARVA  346 (510)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99998633630115589999999999999988999889873034555556678983137789999999999999999999


Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999996500
Q gi|254780412|r   76 KIEQQLADLELFINQ   90 (94)
Q Consensus        76 ~LE~kl~~le~~~~~   90 (94)
                      .++.+++.++...+-
T Consensus       347 ~~~~~~~~l~~~~~~  361 (510)
T TIGR03007       347 ELTARIERLESLLRT  361 (510)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999999999999753


No 42 
>PRK04325 hypothetical protein; Provisional
Probab=41.08  E-value=29  Score=16.39  Aligned_cols=32  Identities=19%  Similarity=0.343  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999
Q gi|254780412|r   53 IENVKRTTSHLREEITAIGKRLEKIEQQLADL   84 (94)
Q Consensus        53 Fdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~l   84 (94)
                      .|.+-.++.+-..+++.|..++..|-.++...
T Consensus        25 id~LN~tV~rQQqqId~L~~q~~~L~q~~~~~   56 (74)
T PRK04325         25 IDGLNATVARQQQTLDLLQAQLRLLYQQMRDA   56 (74)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999999999999999999999999998732


No 43 
>TIGR00998 8a0101 efflux pump membrane protein; InterPro: IPR005694    emrA and emrB confer resistance to carbonylcyanide m-chlorophenylhydrazone, nalidixic acid, and a number of other toxic compounds. EmrB encodes a highly hydrophobic 56.2-kDa peptide, with 14 potential alpha-helices to span the inner membrane. EmrA encodes a putative 42.7-kDa peptide containing a single hydrophobic domain and a large C-terminal hydrophilic domain.; GO: 0015238 drug transporter activity, 0006855 multidrug transport, 0009276 1-2nm peptidoglycan-based cell wall.
Probab=41.07  E-value=27  Score=16.58  Aligned_cols=36  Identities=14%  Similarity=0.302  Sum_probs=29.9

Q ss_pred             HHHHHCCCCCH---HHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99987398569---9999999999999999999999999
Q gi|254780412|r   40 RTLNSMGVVRA---EEIENVKRTTSHLREEITAIGKRLE   75 (94)
Q Consensus        40 ~~l~kldLVtR---EEFdv~~~~l~k~R~~~e~Le~rl~   75 (94)
                      ..|.+.|+|+|   ||||--++.+..+++.+++=-..|+
T Consensus       154 ~~L~~~G~I~~RkFE~l~~ar~a~~~a~A~L~aa~~~I~  192 (379)
T TIGR00998       154 VPLLKKGLISRRKFEELDHARKALLSAKAALNAAIQEIN  192 (379)
T ss_pred             HHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             889847899875444347689999999987889985433


No 44 
>pfam06825 HSBP1 Heat shock factor binding protein 1. Heat shock factor binding protein 1 (HSBP1) appears to be a negative regulator of the heat shock response.
Probab=40.83  E-value=31  Score=16.20  Aligned_cols=21  Identities=29%  Similarity=0.639  Sum_probs=15.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999
Q gi|254780412|r   65 EEITAIGKRLEKIEQQLADLE   85 (94)
Q Consensus        65 ~~~e~Le~rl~~LE~kl~~le   85 (94)
                      .|++....||+.||+-++++-
T Consensus        28 ~riDdM~~riDdLE~si~dlm   48 (54)
T pfam06825        28 SKIDEMSKRIDELEKSINDLM   48 (54)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999988836888997799999


No 45 
>TIGR02978 phageshock_pspC phage shock protein C; InterPro: IPR014320   All members of this protein are the phage shock protein PspC. The phage shock regulon is restricted to the Proteobacteria and somewhat sparsely distributed there. It is expressed, under positive control of a sigma-54-dependent transcription factor; PspF, which binds and is modulated by PspA. Stresses that induce the psp regulon include phage secretin over expression, ethanol, heat shock and protein export defects..
Probab=40.14  E-value=22  Score=17.12  Aligned_cols=29  Identities=14%  Similarity=0.516  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999996500
Q gi|254780412|r   62 HLREEITAIGKRLEKIEQQLADLELFINQ   90 (94)
Q Consensus        62 k~R~~~e~Le~rl~~LE~kl~~le~~~~~   90 (94)
                      +.+.-+..++.++..+|.+|.+.|..++=
T Consensus        88 ~p~~~L~~~~~~~~~~e~RLr~mE~yVTS  116 (128)
T TIGR02978        88 SPKQALREVKRELRRLERRLRNMERYVTS  116 (128)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHCCEEEC
T ss_conf             88899999999999988898976853206


No 46 
>pfam00038 Filament Intermediate filament protein.
Probab=38.76  E-value=34  Score=16.00  Aligned_cols=67  Identities=25%  Similarity=0.326  Sum_probs=43.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCC------CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8779999999999999999998739------856999999999999999999999999999999999999965
Q gi|254780412|r   22 AFKDISKEAESFAQIKIQRTLNSMG------VVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFI   88 (94)
Q Consensus        22 ~~~~~~~Eie~~~r~~~e~~l~kld------LVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~   88 (94)
                      .+...+.|++..++..++..-....      --+++|....+.-+...+.+++.|.++.+.|+.+|.+++...
T Consensus       181 ~~~~~~~e~e~~y~~k~~~l~~~~~~~~~~l~~~k~E~~~lr~~i~~L~~el~~l~~~~~~Le~~l~e~e~~~  253 (312)
T pfam00038       181 LAEKNRQEAEEWYKSKLEELQQAAARNGDALRSAKEEITELRRQIQSLEIELQSLKKQKASLERQLAELEERY  253 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9998799999998878899999998745779989999999999999999999999999999998999999979


No 47 
>cd04171 SelB SelB subfamily.  SelB is an elongation factor needed for the co-translational incorporation of selenocysteine.  Selenocysteine is coded by a UGA stop codon in combination with a specific downstream mRNA hairpin.  In bacteria, the C-terminal part of SelB recognizes this hairpin, while the N-terminal part binds GTP and tRNA in analogy with elongation factor Tu (EF-Tu).  It specifically recognizes the selenocysteine charged tRNAsec, which has a UCA anticodon, in an EF-Tu like manner. This allows insertion of selenocysteine at in-frame UGA stop codons.  In E. coli SelB binds GTP, selenocysteyl-tRNAsec, and a stem-loop structure immediately downstream of the UGA codon (the SECIS sequence).  The absence of active SelB prevents the participation of selenocysteyl-tRNAsec in translation.  Archaeal and animal mechanisms of selenocysteine incorporation are more complex.  Although the SECIS elements have different secondary structures and conserved elements between archaea and eukaryo
Probab=38.24  E-value=34  Score=15.94  Aligned_cols=22  Identities=18%  Similarity=0.232  Sum_probs=16.4

Q ss_pred             HHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             9987398569999999999999
Q gi|254780412|r   41 TLNSMGVVRAEEIENVKRTTSH   62 (94)
Q Consensus        41 ~l~kldLVtREEFdv~~~~l~k   62 (94)
                      ++||+|+|.+|+++....-+.+
T Consensus       110 vlNK~D~v~~~~~~~~~~~i~~  131 (164)
T cd04171         110 VLTKADLVDEDWLELVEEEIRE  131 (164)
T ss_pred             EEECCCCCCHHHHHHHHHHHHH
T ss_conf             3463425797899999999999


No 48 
>pfam10152 DUF2360 Predicted coiled-coil domain-containing protein (DUF2360). This is the conserved 140 amino acid region of a family of proteins conserved from nematodes to humans. One C. elegans member is annotated as a Daf-16-dependent longevity protein 1 but this could not be confirmed. The function is unknown.
Probab=37.62  E-value=35  Score=15.88  Aligned_cols=37  Identities=19%  Similarity=0.311  Sum_probs=20.2

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99987398569999999999999999999999999999999999
Q gi|254780412|r   40 RTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLAD   83 (94)
Q Consensus        40 ~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~   83 (94)
                      ++||++..+--+-|--       .-.++..||..+.-||+||+-
T Consensus        10 ~FLNrFs~~CE~KL~~-------~e~~LQ~lE~~l~ILEaKL~S   46 (147)
T pfam10152        10 QFLNRFSAVCESKLVE-------AERSLQQLETTLSLLEAKLAS   46 (147)
T ss_pred             HHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999999999999999-------999999999999999999746


No 49 
>pfam08317 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=36.27  E-value=37  Score=15.75  Aligned_cols=82  Identities=15%  Similarity=0.271  Sum_probs=49.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999986688877999999999999999999873985699999999999999999999999999999999999996
Q gi|254780412|r    8 FFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus         8 ~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      .+..-..++.+..+.+..-...+..-+.. ++.....++...++|....+.-+...-.++++....+..++.++..++..
T Consensus       166 ~L~~~~~~l~~~~p~l~~~~~~L~~e~~~-l~~~~~e~~~~D~~eL~~~r~eL~~~~~~i~~~~~~l~el~~el~~l~~~  244 (322)
T pfam08317       166 LLNKDLNLINSIKPKLRKKLQALKEEIAN-LRQLADELNLCDPLELEKARQELRSLSVKISEKRKQLEELQQELQELTIA  244 (322)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99989999988899999999999999999-99736555217999999999999999999999998999999999999999


Q ss_pred             HHH
Q ss_conf             500
Q gi|254780412|r   88 INQ   90 (94)
Q Consensus        88 ~~~   90 (94)
                      |..
T Consensus       245 ie~  247 (322)
T pfam08317       245 IEA  247 (322)
T ss_pred             HHH
T ss_conf             999


No 50 
>KOG3958 consensus
Probab=36.13  E-value=34  Score=15.95  Aligned_cols=17  Identities=24%  Similarity=0.618  Sum_probs=10.3

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999965
Q gi|254780412|r   72 KRLEKIEQQLADLELFI   88 (94)
Q Consensus        72 ~rl~~LE~kl~~le~~~   88 (94)
                      +|++.||++|..+|..+
T Consensus       191 akVA~LE~Rlt~lE~vv  207 (371)
T KOG3958         191 AKVAELEKRLTELETVV  207 (371)
T ss_pred             HHHHHHHHHHHHHHHHH
T ss_conf             88999999999999997


No 51 
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family; InterPro: IPR014243    This entry represents a set of transcription factors found in some endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria). In some species these proteins are encoded multiple times. The best characterised protein in this entry is the prespore-specific transcription factor RsfA from Bacillus subtilis, previously known as YwfN. Expression of RsfA is controlled by sigma factor F, and it seems to improve the efficiency of sporulation by fine-tuning the expression of genes in the sigma F regulon, particularly the timing of their expression . It also negatively regulates spoIIR and its own synthesis. A paralog in B. subtilis is designated YlbO, though its function is not known. A highly variable linker region separates two very strongly conserved sequence regions within the protein. .
Probab=35.52  E-value=38  Score=15.67  Aligned_cols=37  Identities=27%  Similarity=0.413  Sum_probs=25.4

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6999999999999999999999999999999999999
Q gi|254780412|r   49 RAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLE   85 (94)
Q Consensus        49 tREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le   85 (94)
                      .+-|=+.++.=....+.+++.|++++..|+++..-.+
T Consensus       104 l~~E~~~L~~~~~~Lq~~ne~L~~el~~L~~~~~~~e  140 (163)
T TIGR02894       104 LQKENERLKKELESLQKRNEELEKELEKLEKRQSTIE  140 (163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9989999999999999999999999999999846789


No 52 
>PRK06664 fliD flagellar hook-associated protein FliD; Validated
Probab=33.94  E-value=40  Score=15.51  Aligned_cols=61  Identities=11%  Similarity=0.208  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHH
Q ss_conf             99999999999999873985699999999999999999999999999999999----999996500
Q gi|254780412|r   29 EAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQL----ADLELFINQ   90 (94)
Q Consensus        29 Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl----~~le~~~~~   90 (94)
                      .+-..+...+..++..-+++.--. +-+..-+.+...+++.|+.|++.+|.++    +.+|..+.+
T Consensus       602 G~a~~l~~~l~~~~~~~G~i~~~~-~~l~~~i~~~~~~i~~~~~rl~~~e~ry~~QF~ame~~~~~  666 (684)
T PRK06664        602 GVAKMLLEYLKPYTQAGGIVYNKV-KSLDEKIANNNKKVEEYEKKLESRERKLKGKFLTMDQTVKK  666 (684)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             499999999998765686453066-67999998999999999999999999999999999999999


No 53 
>COG3880 Modulator of heat shock repressor CtsR, McsA [Signal transduction    mechanisms]
Probab=33.65  E-value=27  Score=16.63  Aligned_cols=25  Identities=24%  Similarity=0.458  Sum_probs=18.8

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             98569999999999999999999999999
Q gi|254780412|r   46 GVVRAEEIENVKRTTSHLREEITAIGKRL   74 (94)
Q Consensus        46 dLVtREEFdv~~~~l~k~R~~~e~Le~rl   74 (94)
                      ++|-|||||--..    .|.++.+|+.+.
T Consensus       147 ~~i~~EefEeAA~----iRDqIr~Lk~k~  171 (176)
T COG3880         147 DLIEREEFEEAAV----IRDQIRALKAKN  171 (176)
T ss_pred             HHHHHHHHHHHHH----HHHHHHHHHHHC
T ss_conf             9998888899999----999999988543


No 54 
>pfam01920 Prefoldin_2 Prefoldin subunit. This family includes prefoldin subunits that are not detected by pfam02996.
Probab=33.47  E-value=41  Score=15.47  Aligned_cols=38  Identities=29%  Similarity=0.481  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             99999999999999999999999999999999965002
Q gi|254780412|r   54 ENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQK   91 (94)
Q Consensus        54 dv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~k   91 (94)
                      ..+.........++..|+.++..+++.+.+++..+.++
T Consensus        65 ~~L~~~~e~i~~~i~~le~q~~~~~~~~~~lk~~l~~~  102 (104)
T pfam01920        65 EELEERKETLEKEIKTLEKQLEKLEKELEELKEELYKL  102 (104)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999999999887


No 55 
>pfam00509 Hemagglutinin Hemagglutinin. Hemagglutinin from influenza virus causes membrane fusion of the viral membrane with the host membrane. Fusion occurs after the host cell internalises the virus by endocytosis. The drop of pH causes release of a hydrophobic fusion peptide and a large conformational change leading to membrane fusion.
Probab=33.18  E-value=41  Score=15.44  Aligned_cols=49  Identities=16%  Similarity=0.286  Sum_probs=33.5

Q ss_pred             HHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999998739856999999999999999999999999999999999999965
Q gi|254780412|r   29 EAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFI   88 (94)
Q Consensus        29 Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~   88 (94)
                      .+=..+-..+.+.+.||+    +.|+++       ..+...||.||..|++++.+..+.+
T Consensus       371 ~AId~It~KlN~iiek~N----~qf~~i-------~~EF~evE~rI~~l~~~v~D~~~D~  419 (550)
T pfam00509       371 KAIDQITGKLNSLIEKMN----TQFEAI-------EKEFSELERRINNLNKKVDDGITDI  419 (550)
T ss_pred             HHHHHHHHHHHHHHHHHH----HHHHHH-------HHHHHHHHHHHHHHHHHHCCCCEEH
T ss_conf             999988778888999877----678887-------7789999999999997630100010


No 56 
>pfam01763 Herpes_UL6 Herpesvirus UL6 like. This family consists of various proteins from the herpesviridae that are similar to herpes simplex virus type I UL6 virion protein. UL6 is essential for cleavage and packaging of the viral genome.
Probab=31.96  E-value=43  Score=15.31  Aligned_cols=57  Identities=21%  Similarity=0.297  Sum_probs=46.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             68887799999999999999999987398569999999999999999999999999999999999999
Q gi|254780412|r   19 ASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLEL   86 (94)
Q Consensus        19 a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~   86 (94)
                      ..++.+++|+-+-+++--.++..+|.+       ||    -++..++.++.++.|+..+|..|.....
T Consensus       343 ~~~~~~~~r~~V~n~V~kcLe~qIn~q-------F~----tIe~Lk~~n~~~~~kl~~~e~~L~r~~~  399 (551)
T pfam01763       343 AETTRQAFRKSVSNSVNKCLEGQINEQ-------FD----TIEDLKEENEDLLKKLRELESELSRLRE  399 (551)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHH-------HH----HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             762778999999987999879999999-------99----9999999999999999999999999887


No 57 
>PRK09039 hypothetical protein; Validated
Probab=31.96  E-value=43  Score=15.31  Aligned_cols=43  Identities=16%  Similarity=0.378  Sum_probs=32.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999999999999999999999999999999999650023
Q gi|254780412|r   50 AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKE   92 (94)
Q Consensus        50 REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~k~   92 (94)
                      +++-+.+++....++.+++.|..+|.+|..+|+.+...++..+
T Consensus       122 ~~~L~~~~~~s~~a~~qi~~Ln~Qi~aLr~qL~~l~~~L~~~e  164 (343)
T PRK09039        122 NQALDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASE  164 (343)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999988999999999999999999999999999999999


No 58 
>TIGR02132 phaR_Bmeg polyhydroxyalkanoic acid synthase, PhaR subunit; InterPro: IPR011729   This entry describes a protein, PhaR, localized to polyhydroxyalkanoic acid (PHA) inclusion granules in Bacillus cereus and related species. PhaR is required for PHA biosynthesis along with PhaC and may be a regulatory subunit ..
Probab=31.67  E-value=43  Score=15.28  Aligned_cols=62  Identities=18%  Similarity=0.209  Sum_probs=50.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999986688877999999999999999999873985699999999999999999999999999
Q gi|254780412|r   10 QQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLE   75 (94)
Q Consensus        10 ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~   75 (94)
                      .++|.++|+.+    ++-=--...+...-.++|...++-|+|+.=-+..+....-++++.||..++
T Consensus        35 EEyS~~MG~VL----~lNL~YQ~A~N~~T~~YL~QVNVPTKED~A~VA~LVIN~E~KV~~~EE~l~   96 (189)
T TIGR02132        35 EEYSALMGSVL----DLNLFYQKALNDVTKRYLEQVNVPTKEDVARVASLVINLEEKVDLLEEFLD   96 (189)
T ss_pred             HHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             48999978898----788999999999876676515898554687688887546888889988864


No 59 
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=31.54  E-value=44  Score=15.27  Aligned_cols=83  Identities=19%  Similarity=0.268  Sum_probs=48.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999986688877999999999999999999873985699999999999999999999999999999999999996
Q gi|254780412|r    8 FFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus         8 ~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      .+..-..++.+..+.+..-...+..-+.. ++.....++=...+|.+..+.-+...-.++......+..++.++.+++..
T Consensus       162 ~L~~~~~~l~~i~p~l~~~~~~L~~e~~~-L~~~~~e~~~~d~~eL~~lk~~L~~~~~ei~~~~~~l~e~~~~l~~l~~~  240 (312)
T smart00787      162 LLMKELELLNSIKPKLRDRKDALEEELRQ-LKQLEDELEDCDPTELDRAKEKLKKLLQEIMIKVKKLEELEEELQELESK  240 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999988899999999999999999-99768888718999999999999999999999999999999999999999


Q ss_pred             HHHC
Q ss_conf             5002
Q gi|254780412|r   88 INQK   91 (94)
Q Consensus        88 ~~~k   91 (94)
                      |+..
T Consensus       241 I~~~  244 (312)
T smart00787      241 IEDL  244 (312)
T ss_pred             HHHH
T ss_conf             9989


No 60 
>COG3165 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.46  E-value=44  Score=15.26  Aligned_cols=59  Identities=15%  Similarity=0.192  Sum_probs=30.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH-----CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7799999999999999999987-----3985699999999999999999999999999999999
Q gi|254780412|r   23 FKDISKEAESFAQIKIQRTLNS-----MGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQL   81 (94)
Q Consensus        23 ~~~~~~Eie~~~r~~~e~~l~k-----ldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl   81 (94)
                      +.+....+...+++.-+.+-.-     --+|.+.|...-.+-+...|.-.+.|++|++.||.+.
T Consensus       139 l~~~~~~l~~~~~~~q~~~Ae~iTEE~r~~v~~~ela~f~~evd~lr~~~~rL~~RL~rLe~k~  202 (204)
T COG3165         139 LRSGSRFLKHGLKQLQRNLAEAITEEWRMAVGPLELADFAEEVDALRDAVERLEARLERLERKA  202 (204)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9998999999999999999999868764368868999999999999999999999999999763


No 61 
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.18  E-value=44  Score=15.23  Aligned_cols=76  Identities=13%  Similarity=0.146  Sum_probs=29.0

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99750069999999998668887799999999999999999987398569999999999999999999999999999999
Q gi|254780412|r    1 MSFRSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQ   80 (94)
Q Consensus         1 m~~~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~k   80 (94)
                      |+.--.++++++-.....+--.      +-+...-.++.+.+.+--  +--=+=||+.+++-  .-+..+..+|.+||++
T Consensus         1 MtpeE~qlle~lf~rlk~a~~~------~rD~~Ae~lI~~~~~~qP--~a~Y~laQ~vliqE--~ALk~a~~~i~eLe~r   70 (233)
T COG3416           1 MTPEEKQLLENLFHRLKKAEAN------ERDPQAEALIAEAVAKQP--DAAYYLAQRVLIQE--QALKKASTQIKELEKR   70 (233)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCC------CCCHHHHHHHHHHHHCCC--CHHHHHHHHHHHHH--HHHHHHHHHHHHHHHH
T ss_conf             9878999999999998642467------777489999999985499--54899999999999--9999999999999999


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780412|r   81 LADLEL   86 (94)
Q Consensus        81 l~~le~   86 (94)
                      ++.++.
T Consensus        71 i~~lq~   76 (233)
T COG3416          71 IAILQA   76 (233)
T ss_pred             HHHHHC
T ss_conf             999841


No 62 
>pfam11336 DUF3138 Protein of unknown function (DUF3138). This family of proteins with unknown function appear to be restricted to Proteobacteria.
Probab=29.79  E-value=47  Score=15.08  Aligned_cols=34  Identities=21%  Similarity=0.308  Sum_probs=21.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9999999999999999999999999996500237
Q gi|254780412|r   60 TSHLREEITAIGKRLEKIEQQLADLELFINQKEK   93 (94)
Q Consensus        60 l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~k~~   93 (94)
                      +.-+-.++.+|.+++.+|.++..++.+-+.-|+.
T Consensus        20 a~s~a~~ikalqaq~~~lq~q~~~l~a~laak~~   53 (514)
T pfam11336        20 AASDASQIKALQAQLTALQQQVNELRAALAAKPA   53 (514)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             2589999999999999999999999998614876


No 63 
>pfam12269 zf-CpG_bind_C CpG binding protein zinc finger C terminal domain. This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=29.75  E-value=47  Score=15.08  Aligned_cols=33  Identities=21%  Similarity=0.451  Sum_probs=17.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999996500
Q gi|254780412|r   58 RTTSHLREEITAIGKRLEKIEQQLADLELFINQ   90 (94)
Q Consensus        58 ~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~   90 (94)
                      ..+.+.|.+......+|++|+.+-.+|++.|++
T Consensus        29 ~~Le~Ir~kq~~~~~~L~eLe~~~~eL~~iI~r   61 (236)
T pfam12269        29 KALERIRKKQQVARTRLQELERRHQELETIISR   61 (236)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999999998


No 64 
>pfam10393 Matrilin_ccoil Trimeric coiled-coil oligomerisation domain of matrilin. This short domain is a coiled coil structure and has a single cysteine residue at the start which is likely to form a di-sulfide bridge with a corresponding cysteine in an upstream EGF (pfam00008) domain thereby spanning a VWA (pfam00092) domain. All three domains can be associated together as in the cartilage matrix protein matrilin, where this domain is likely to be responsible for oligomerisation.
Probab=29.01  E-value=48  Score=15.00  Aligned_cols=28  Identities=21%  Similarity=0.358  Sum_probs=15.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999996
Q gi|254780412|r   60 TSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus        60 l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      =.+..+.+.+|..||++.-++|..+|-.
T Consensus        15 Q~kv~~~lq~Lt~KLe~vtkrl~~lEnr   42 (44)
T pfam10393        15 QRKVEELLQKLTQKLEAVTKRLEALENR   42 (44)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999998751


No 65 
>PRK05729 valS valyl-tRNA synthetase; Reviewed
Probab=28.97  E-value=48  Score=14.99  Aligned_cols=43  Identities=26%  Similarity=0.461  Sum_probs=25.0

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99998739856999999999999999999999999999999999999
Q gi|254780412|r   39 QRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLE   85 (94)
Q Consensus        39 e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le   85 (94)
                      +.-|+.-+.|.+    |=.++...-+++++.++.+++.+++.|+.|+
T Consensus       834 ~~kLsN~~Fi~k----AP~~VV~~ek~Kl~~~~~~i~~i~~~L~~Lk  876 (877)
T PRK05729        834 EKKLSNEGFVAK----APEEVVEKEREKLAEYQEKLEKLKERLARLK  876 (877)
T ss_pred             HHHHCCHHHHHH----CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             977678566673----8999999999999999999999999999725


No 66 
>pfam08900 DUF1845 Domain of unknown function (DUF1845). This family of proteins are functionally uncharacterized.
Probab=28.69  E-value=49  Score=14.96  Aligned_cols=46  Identities=7%  Similarity=0.053  Sum_probs=26.9

Q ss_pred             HHHHHHHHHHHHHHHHH-HCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999998-73985699999999999999999999999
Q gi|254780412|r   27 SKEAESFAQIKIQRTLN-SMGVVRAEEIENVKRTTSHLREEITAIGK   72 (94)
Q Consensus        27 ~~Eie~~~r~~~e~~l~-kldLVtREEFdv~~~~l~k~R~~~e~Le~   72 (94)
                      -++....+|.....+.+ +.==|||++|..+.+...++.++.-.|..
T Consensus       153 l~~g~~~vR~vf~~~~~Yr~~gvtR~D~~~nn~~~~~A~e~~G~lp~  199 (217)
T pfam08900       153 LDEGGRLVRRVFGLVQRYRFSGVTRDDFAANNARAQAAIERMGELPQ  199 (217)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHCCHHHHHHHHHCCCCCH
T ss_conf             99988999999998877513797788788578999999998389998


No 67 
>pfam04012 PspA_IM30 PspA/IM30 family. This family includes PspA a protein that suppresses sigma54-dependent transcription. The PspA protein, a negative regulator of the Escherichia coli phage shock psp operon, is produced when virulence factors are exported through secretins in many Gram-negative pathogenic bacteria and its homologue in plants, VIPP1, plays a critical role in thylakoid biogenesis, essential for photosynthesis. Activation of transcription by the enhancer-dependent bacterial sigma(54) containing RNA polymerase occurs through ATP hydrolysis-driven protein conformational changes enabled by activator proteins that belong to the large AAA(+) mechanochemical protein family. It has been shown that PspA directly and specifically acts upon and binds to the AAA(+) domain of the PspF transcription activator.
Probab=28.54  E-value=49  Score=14.94  Aligned_cols=36  Identities=11%  Similarity=0.377  Sum_probs=20.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999996
Q gi|254780412|r   52 EIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus        52 EFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      .++.+...+.+.+..+..|+.+|..+..+...|.+.
T Consensus       106 q~~~~~~~~~~L~~~l~~le~ki~e~k~k~~~L~Ar  141 (220)
T pfam04012       106 QLTQQRSAVEQLRKQLAALETKIQQLKAKKTALKAR  141 (220)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999999999999999999


No 68 
>COG1842 PspA Phage shock protein A (IM30), suppresses sigma54-dependent transcription [Transcription / Signal transduction mechanisms]
Probab=28.53  E-value=49  Score=14.94  Aligned_cols=57  Identities=9%  Similarity=0.270  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHHCCCCC--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999998739856--999999999999999999999999999999999999965
Q gi|254780412|r   32 SFAQIKIQRTLNSMGVVR--AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFI   88 (94)
Q Consensus        32 ~~~r~~~e~~l~kldLVt--REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~   88 (94)
                      ...+..+++.-+--+.+.  ..++..+...+.+.+..+..|+.+|..++++...+.+..
T Consensus        85 ~LAr~al~~~~~le~~~~~~~~~~~~~~~~~~~l~~~~~~Le~Ki~e~~~~~~~l~ar~  143 (225)
T COG1842          85 DLAREALEEKQSLEDLAKALEAELQQAEEQVEKLKKQLAALEQKIAELRAKKEALKARK  143 (225)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999899999999999999999999999999999999999999999999798


No 69 
>pfam10046 BLOC1_2 Biogenesis of lysosome-related organelles complex-1 subunit 2. Members of this family of proteins play a role in cellular proliferation, as well as in the biogenesis of specialized organelles of the endosomal-lysosomal system.
Probab=28.23  E-value=50  Score=14.91  Aligned_cols=49  Identities=29%  Similarity=0.429  Sum_probs=33.4

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHH----------HHHHHHHHHHHHHH
Q ss_conf             99987398569999999999999999999999999----------99999999999965
Q gi|254780412|r   40 RTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRL----------EKIEQQLADLELFI   88 (94)
Q Consensus        40 ~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl----------~~LE~kl~~le~~~   88 (94)
                      +.|.+|+-++-.+|.-+..++...+..++.|..+-          +.+|.+++.||...
T Consensus        24 ~LLe~mN~~~~~kY~~~~~~a~~l~~~~~~L~~ky~~l~pyl~qId~Ie~~V~~LE~~a   82 (99)
T pfam10046        24 KLLEKMNENTALKYKKMRQSAKGLRVEIEALNQKYEELKPYLQQIDAIEQQVTTLEEAV   82 (99)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999879999999999999998999999999988877899999999998999999999


No 70 
>KOG4571 consensus
Probab=27.69  E-value=51  Score=14.85  Aligned_cols=41  Identities=15%  Similarity=0.210  Sum_probs=32.5

Q ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             69999999999999999999999999999999999999650
Q gi|254780412|r   49 RAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        49 tREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~   89 (94)
                      -|.|-+.+..-+.-.-.++++|..|+..||.-|.-++-+|-
T Consensus       246 kRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~  286 (294)
T KOG4571         246 KRAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLIL  286 (294)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             89999888878777888779999999999999999999999


No 71 
>pfam09766 FimP Fms-interacting protein. This entry carries part of the crucial 144 N-terminal residues of the FmiP protein, which is essential for the binding of the protein to the cytoplasmic domain of activated Fms-molecules in M-CSF induced haematopoietic differentiation of macrophages. The C-terminus contains a putative nuclear localisation sequence and a leucine zipper which suggest further, as yet unknown, nuclear functions. The level of FMIP expression might form a threshold that determines whether cells differentiate into macrophages or into granulocytes.
Probab=27.61  E-value=51  Score=14.84  Aligned_cols=73  Identities=18%  Similarity=0.194  Sum_probs=42.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHH----------------HHHHHHHHHHHHHHH---HHHHHHHHHH
Q ss_conf             668887799999999999999999987398569999----------------999999999999999---9999999999
Q gi|254780412|r   18 CASDAFKDISKEAESFAQIKIQRTLNSMGVVRAEEI----------------ENVKRTTSHLREEIT---AIGKRLEKIE   78 (94)
Q Consensus        18 ~a~~~~~~~~~Eie~~~r~~~e~~l~kldLVtREEF----------------dv~~~~l~k~R~~~e---~Le~rl~~LE   78 (94)
                      +.+--...+.+||.+-....-  -=..++||+-|||                |--..|+.|..-++.   .|.++..+|+
T Consensus        37 NLlYE~~HL~KEI~~C~~FkS--~d~~i~Lv~~eEF~~~ap~~i~~~~~~~~d~H~~~L~RL~~EL~qRK~L~~~~~~L~  114 (352)
T pfam09766        37 NLLYEKSHLEKEIKRCLDFKS--KDEEIELVPEEEFYSDAPEDISRPEKTPLDEHNLMLARLEWELEQRKELCEKLKELE  114 (352)
T ss_pred             HHHHHHHHHHHHHHHHHCCCC--CCCCCCCCCHHHHHHHCHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999999999870223--699835677799998571310564567888699999999999999999999999999


Q ss_pred             HHHHHHHHHHHHCC
Q ss_conf             99999999650023
Q gi|254780412|r   79 QQLADLELFINQKE   92 (94)
Q Consensus        79 ~kl~~le~~~~~k~   92 (94)
                      ..-..+.-.|.+|.
T Consensus       115 ~~K~~l~~~i~~k~  128 (352)
T pfam09766       115 SEKEKLLQDIEKKK  128 (352)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999999


No 72 
>pfam07407 Seadorna_VP6 Seadornavirus VP6 protein. This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=27.36  E-value=51  Score=14.81  Aligned_cols=37  Identities=16%  Similarity=0.402  Sum_probs=26.0

Q ss_pred             HCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7398569999999999999999999999999999999
Q gi|254780412|r   44 SMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQ   80 (94)
Q Consensus        44 kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~k   80 (94)
                      .+.=|+-+|.-++++--+|...++++|..++..||.-
T Consensus        25 elegvsfdelaalreenaklkkenealktkihrlesd   61 (420)
T pfam07407        25 ELEGVSFDELAALREENAKLKKENEALKTKIHRLESD   61 (420)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             1457658998988876455654528887667544146


No 73 
>COG2193 Bfr Bacterioferritin (cytochrome b1) [Inorganic ion transport and metabolism]
Probab=27.28  E-value=52  Score=14.80  Aligned_cols=48  Identities=19%  Similarity=0.162  Sum_probs=30.0

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999987398569999999999999999999999999999
Q gi|254780412|r   27 SKEAESFAQIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKI   77 (94)
Q Consensus        27 ~~Eie~~~r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~L   77 (94)
                      -.++....|..+.-.=+.-|.|||+.|+.+.   .-+-+-++-||.++.-+
T Consensus        94 E~~a~~~lk~~i~~~e~~~Dyvsrdl~~~iL---~deEEHid~LetqL~li  141 (157)
T COG2193          94 EYEARDALKEAIAYCEEVQDYVSRDLLEEIL---ADEEEHIDWLETQLDLI  141 (157)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCHHHHHHHHHH---CCHHHHHHHHHHHHHHH
T ss_conf             8999999999999998605633899999998---16077799999999999


No 74 
>KOG0241 consensus
Probab=27.03  E-value=52  Score=14.78  Aligned_cols=35  Identities=17%  Similarity=0.399  Sum_probs=24.9

Q ss_pred             HHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999-9999999999999999999999
Q gi|254780412|r   50 AEEIENVKRTTSH-LREEITAIGKRLEKIEQQLADL   84 (94)
Q Consensus        50 REEFdv~~~~l~k-~R~~~e~Le~rl~~LE~kl~~l   84 (94)
                      |||.|-++.+|.. .+++...|+.+++++|+-+.++
T Consensus       370 ReEve~lr~qL~~ae~~~~~el~e~l~esekli~ei  405 (1714)
T KOG0241         370 REEVEKLREQLEQAEAMKLPELKEKLEESEKLIKEI  405 (1714)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             999999999986543110467899999999999999


No 75 
>pfam00846 Hanta_nucleocap Hantavirus nucleocapsid protein.
Probab=26.98  E-value=52  Score=14.77  Aligned_cols=40  Identities=25%  Similarity=0.292  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             5699999999999999999999999999999999999996
Q gi|254780412|r   48 VRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus        48 VtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      |-++-=|+.+..+..-+..+.+|+.+|++|..+|+++-+.
T Consensus        32 ~e~dPDdvnk~~l~~R~~~v~~l~~Kl~elkrqlAd~v~~   71 (428)
T pfam00846        32 VEVDPDDVNKSTLQSRRAAVSALEAKLAELKRQLADRIAT   71 (428)
T ss_pred             HCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             5479636668999999999999999999999999999985


No 76 
>PRK10014 DNA-binding transcriptional repressor MalI; Provisional
Probab=26.76  E-value=53  Score=14.75  Aligned_cols=49  Identities=10%  Similarity=0.196  Sum_probs=34.6

Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             99750069999999998668887799---99999999999999998739856
Q gi|254780412|r    1 MSFRSNQFFQQASRLASCASDAFKDI---SKEAESFAQIKIQRTLNSMGVVR   49 (94)
Q Consensus         1 m~~~~n~~~ddla~~~~~a~~~~~~~---~~Eie~~~r~~~e~~l~kldLVt   49 (94)
                      |+.+.+.-+.|+|+.++-..+|++-+   +..+-.-.|.++..+..++|.+.
T Consensus         1 m~~~kkvTi~dIA~~aGVS~aTVSrvLn~~~~Vs~eTr~rV~~aa~elgY~p   52 (342)
T PRK10014          1 MATAKKITIHDVALAAGVSVSTVSLVLSGKGRISTATGERVNQAIEELGFVR   52 (342)
T ss_pred             CCCCCCCCHHHHHHHHCCCHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCC
T ss_conf             9999988799999998969999999977989999999999999999948997


No 77 
>COG2846 Regulator of cell morphogenesis and NO signaling [Cell division and chromosome partitioning]
Probab=26.04  E-value=54  Score=14.66  Aligned_cols=45  Identities=11%  Similarity=0.129  Sum_probs=19.2

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             500699999999986688877999999999999999999873985
Q gi|254780412|r    4 RSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMGVV   48 (94)
Q Consensus         4 ~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kldLV   48 (94)
                      ..++.+.|++--+-+|...+.+..=++=---+..++++..+.+++
T Consensus         3 ~~dq~lg~la~~iP~A~~iFr~y~iDFCCGG~~~L~~Aa~~k~l~   47 (221)
T COG2846           3 YRDQPLGDLAISIPRAAEIFRSYDIDFCCGGKVTLERAAAEKGLD   47 (221)
T ss_pred             CCCCHHHHHHHHCCCHHHHHHHCCCCEECCCHHHHHHHHHHCCCC
T ss_conf             311439999995743899999839862058719999999983898


No 78 
>KOG4643 consensus
Probab=26.01  E-value=54  Score=14.66  Aligned_cols=41  Identities=22%  Similarity=0.311  Sum_probs=29.4

Q ss_pred             CCCCHHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHH
Q ss_conf             9856999999999999999999--9999999999999999999
Q gi|254780412|r   46 GVVRAEEIENVKRTTSHLREEI--TAIGKRLEKIEQQLADLEL   86 (94)
Q Consensus        46 dLVtREEFdv~~~~l~k~R~~~--e~Le~rl~~LE~kl~~le~   86 (94)
                      +-|--|||+.+++-++++|.+.  ..|+..|-.+.++|.++..
T Consensus       273 N~vLleekeMLeeQLq~lrarse~~tleseiiqlkqkl~dm~~  315 (1195)
T KOG4643         273 NRVLLEEKEMLEEQLQKLRARSEGATLESEIIQLKQKLDDMRS  315 (1195)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             6989999999999999988524568717889999887789998


No 79 
>TIGR00081 purC phosphoribosylaminoimidazole-succinocarboxamide synthase; InterPro: IPR001636   Phosphoribosylaminoimidazole-succinocarboxamide synthase (6.3.2.6 from EC) (SAICAR synthetase) catalyzes the seventh step in the de novo purine biosynthetic pathway; the ATP-dependent conversion of 5'-phosphoribosyl-5-aminoimidazole-4-carboxylic acid and aspartic acid to SAICAR .   In bacteria (purC), fungi (ADE1) and plants (Pur7), SAICAR synthetase is a monofunctional protein; in animals it is the N-terminal domain of a bifunctional enzyme that also catalyse phosphoribosylaminoimidazole carboxylase (AIRC) activity (see ). ; GO: 0004639 phosphoribosylaminoimidazolesuccinocarboxamide synthase activity, 0006164 purine nucleotide biosynthetic process.
Probab=25.67  E-value=55  Score=14.62  Aligned_cols=34  Identities=18%  Similarity=0.336  Sum_probs=27.6

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999873985699999999999999999999999
Q gi|254780412|r   39 QRTLNSMGVVRAEEIENVKRTTSHLREEITAIGK   72 (94)
Q Consensus        39 e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~   72 (94)
                      ++...-+++||+|+++.+++.+.+..+.+..+-.
T Consensus       234 ~s~a~~~~~~~~e~~~~~Kela~~~n~~l~~~~~  267 (374)
T TIGR00081       234 ESYAEALGLATEEELERIKELALKVNEVLKRLFD  267 (374)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             7799882367888999999999999899999997


No 80 
>KOG2802 consensus
Probab=25.66  E-value=55  Score=14.62  Aligned_cols=77  Identities=12%  Similarity=0.252  Sum_probs=46.8

Q ss_pred             CCCCCHHHHHHHHHHHHHH-HHHHH----------------HHHHHHHHHHHHHHHHHHHCCCCCHHHHHHH--------
Q ss_conf             9750069999999998668-88779----------------9999999999999999987398569999999--------
Q gi|254780412|r    2 SFRSNQFFQQASRLASCAS-DAFKD----------------ISKEAESFAQIKIQRTLNSMGVVRAEEIENV--------   56 (94)
Q Consensus         2 ~~~~n~~~ddla~~~~~a~-~~~~~----------------~~~Eie~~~r~~~e~~l~kldLVtREEFdv~--------   56 (94)
                      |+..|||+|-+..+.-|++ |+.-.                ++.|++=+-|-..+++|.      |+||+-.        
T Consensus       384 s~tgnPIyD~~GSivvGaLLGmVe~diyDvK~~diG~g~vRfKAE~DFdGr~vtrsYL~------kqd~akml~e~~~~~  457 (503)
T KOG2802         384 SITGNPIYDSLGSIVVGALLGMVENDIYDVKATDIGLGKVRFKAEVDFDGRVVTRSYLE------KQDFAKMLQEIQEVK  457 (503)
T ss_pred             HHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCEEECCCEEEEEEEECCCCHHHHHHHHH------HHHHHHHHHHHHHCC
T ss_conf             72189786542037898888777776541322340464168887852672216897872------889999999998209


Q ss_pred             ------HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             ------9999999999999999999999999999
Q gi|254780412|r   57 ------KRTTSHLREEITAIGKRLEKIEQQLADL   84 (94)
Q Consensus        57 ------~~~l~k~R~~~e~Le~rl~~LE~kl~~l   84 (94)
                            .-|+..-.+=++.|-+.++-||+.|.++
T Consensus       458 ~~e~le~fml~~GEnivd~lG~EvDRlEkel~~~  491 (503)
T KOG2802         458 TPEELETFMLKHGENIVDTLGAEVDRLEKELKKR  491 (503)
T ss_pred             CHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9899999999734489987635778999999874


No 81 
>pfam06962 rRNA_methylase Putative rRNA methylase. This family contains a number of putative rRNA methylases. Note that many family members are hypothetical proteins.
Probab=25.57  E-value=34  Score=15.94  Aligned_cols=17  Identities=6%  Similarity=0.206  Sum_probs=13.9

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999
Q gi|254780412|r   53 IENVKRTTSHLREEITA   69 (94)
Q Consensus        53 Fdv~~~~l~k~R~~~e~   69 (94)
                      ||+|.+-+..||.++..
T Consensus         5 FDIQ~~Ai~~T~~rL~~   21 (140)
T pfam06962         5 FDIQEEALENTKEKLEQ   21 (140)
T ss_pred             EECHHHHHHHHHHHHHH
T ss_conf             96099999999999996


No 82 
>pfam09340 NuA4 Histone acetyltransferase subunit NuA4. The NuA4 histone acetyltransferase (HAT) multisubunit complex is responsible for acetylation of histone H4 and H2A N-terminal tails in yeast. NuA4 complexes are highly conserved in eukaryotes and play primary roles in transcription, cellular response to DNA damage, and cell cycle control.
Probab=25.30  E-value=56  Score=14.58  Aligned_cols=29  Identities=24%  Similarity=0.257  Sum_probs=20.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999965
Q gi|254780412|r   60 TSHLREEITAIGKRLEKIEQQLADLELFI   88 (94)
Q Consensus        60 l~k~R~~~e~Le~rl~~LE~kl~~le~~~   88 (94)
                      |..+-.+=..|+..++.||.+|-++|+--
T Consensus         4 L~~ll~kK~~Le~~L~~lE~qIY~~Et~Y   32 (80)
T pfam09340         4 LKELLQKKKKLEKELAALERQIYDKETEY   32 (80)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999


No 83 
>TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression .    This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent ..
Probab=25.24  E-value=56  Score=14.57  Aligned_cols=38  Identities=39%  Similarity=0.599  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999999999999650
Q gi|254780412|r   52 EIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        52 EFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~   89 (94)
                      +-...+..+.....++..++..++.++..|.++|...+
T Consensus       787 ~~~~~~~e~~~l~~~i~~~e~~~~~~~~~l~~le~~~~  824 (1202)
T TIGR02169       787 ELENVKSELKELEAEIEELEEKLAKLEEALEDLEASLS  824 (1202)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             88889999999999999999999999998852651101


No 84 
>TIGR02231 TIGR02231 conserved hypothetical protein; InterPro: IPR011935    This family consists of proteins over 500 amino acids long in Caenorhabditis elegans and several bacteria (Pseudomonas aeruginosa, Nostoc sp. PCC 7120, Leptospira interrogans, etc.). The function is unknown..
Probab=24.58  E-value=58  Score=14.49  Aligned_cols=76  Identities=21%  Similarity=0.340  Sum_probs=50.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH---HHHHHHHCCCCCHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9866888779999999999999---999998739856999---------9999999999999999999999999999999
Q gi|254780412|r   16 ASCASDAFKDISKEAESFAQIK---IQRTLNSMGVVRAEE---------IENVKRTTSHLREEITAIGKRLEKIEQQLAD   83 (94)
Q Consensus        16 ~~~a~~~~~~~~~Eie~~~r~~---~e~~l~kldLVtREE---------Fdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~   83 (94)
                      +.+..+.++..++.+++.+-..   +..-+.+-+.++|++         |+.+.....++..+.-..+.++.+|++|+++
T Consensus        90 ~~~~~~~l~~~~~~L~K~~~~~~~~~~~~~~~sg~~~~~~~~~~~~~~~f~~~~~~~~~~~~~~r~~~~~~~el~~~~~~  169 (558)
T TIGR02231        90 LEDRGDALKALKSNLDKFLEDIREGLTEPIKDSGVLKRNEPDLKELKQLFDFVGSEIERLLTEDREVERRIRELEKQLSE  169 (558)
T ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCEEEECCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             77788899985301025677774201467321523561576568999999988999999988877899999999999999


Q ss_pred             HHHHHHHC
Q ss_conf             99965002
Q gi|254780412|r   84 LELFINQK   91 (94)
Q Consensus        84 le~~~~~k   91 (94)
                      |+.-++..
T Consensus       170 L~~el~~~  177 (558)
T TIGR02231       170 LENELRAL  177 (558)
T ss_pred             HHHHHHHH
T ss_conf             99999874


No 85 
>pfam10234 Cluap1 Clusterin-associated protein-1. This protein is conserved from worms to humans. The protein of 413 amino acids contains a central coiled-coil domain, possibly the region that binds to clusterin. Cluap1 expression is highest in the nucleus and gradually increases during late S to G2/M phases of the cell cycle and returns to the basal level in the G0/G1 phases. In addition, it is upregulated in colon cancer tissues compared to corresponding non-cancerous mucosa. It thus plays a crucial role in the life of the cell.
Probab=24.02  E-value=59  Score=14.42  Aligned_cols=69  Identities=19%  Similarity=0.362  Sum_probs=39.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHH-HCCCCCHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             888779999999999999999998-73985699999-999999999999999999999999999999996500237
Q gi|254780412|r   20 SDAFKDISKEAESFAQIKIQRTLN-SMGVVRAEEIE-NVKRTTSHLREEITAIGKRLEKIEQQLADLELFINQKEK   93 (94)
Q Consensus        20 ~~~~~~~~~Eie~~~r~~~e~~l~-kldLVtREEFd-v~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~~k~~   93 (94)
                      ++...-+++|++  +|..-+..++ .+++.+   +| +++..+.....+++.+.+.+..+..--+.|+.-|.+|.+
T Consensus       136 A~L~dlL~kE~~--lr~~R~~a~~r~~el~~---iEk~l~~~i~~~~~~~~~~~~~l~~~~~de~~Le~KIekkk~  206 (269)
T pfam10234       136 AALYDLLGKELD--LRESRQKALSRPLELAE---VEKALKEAIKNLAARLQQLQAELDNLKSDEANLEAKIERKKQ  206 (269)
T ss_pred             HHHHHHHHHHHH--HHHHHHHHHCCCCCHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999975898--99999999817667899---999999999999999999999999877378779989999888


No 86 
>PRK11578 macrolide transporter subunit MacA; Provisional
Probab=23.46  E-value=61  Score=14.36  Aligned_cols=51  Identities=12%  Similarity=0.246  Sum_probs=38.3

Q ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999987398569999999999999999999999999999999999999650
Q gi|254780412|r   39 QRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        39 e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~   89 (94)
                      ...|.+.+.+++.+||--+.=+...+.+++.+++++...++.|...+..+.
T Consensus       109 ~~~L~~~~~is~~~~d~a~~~~~~~~a~l~~~~a~~~~~~a~l~~a~~~l~  159 (347)
T PRK11578        109 QQRLAKTQAVSQQDLDTAATEMAVKQAQIGTIDAQIKRNQASLDTAKTNLD  159 (347)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999987576247889887879998764588999999999999999987652


No 87 
>pfam11488 Lge1 Transcriptional regulatory protein LGE1. This family of proteins is conserved in yeasts where it is involved in the ubiquitination of histones H2A and H2B. This ubiquitination step is a vital one in the regulation of the transcriptional activity of RNA polymerase II. In S. cerevisiae, Rad6 and Bre1 are present in a complex, also containing Lge1, that is required for H2B ubiquitination. Bre1 is the H2B ubiquitin ligase that interacts with acidic activators, such as Gal4, and recruits Rad6 and its binding partner Lge1 to target promoters. In S. pombe the equivalent protein to Lge1 appears to be Shf1.
Probab=23.31  E-value=61  Score=14.34  Aligned_cols=57  Identities=19%  Similarity=0.156  Sum_probs=30.8

Q ss_pred             HHHHHHHHHHHHCCC---CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999987398---569999999999999999999999999999999999999650
Q gi|254780412|r   33 FAQIKIQRTLNSMGV---VRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        33 ~~r~~~e~~l~kldL---VtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~   89 (94)
                      .++....-||+=|++   -|.+.|+-...-+...-.+|+.|+.++..||--++.||+.+.
T Consensus       156 ~i~~~~~P~I~Im~idd~~t~e~le~~~~e~~~~d~~L~~~~~~~~k~e~~~~~le~q~~  215 (234)
T pfam11488       156 KIKNFNNPWINIMDIDDEPTQEKLEERYKELEELDQKLEELQLKKLKLELELALLETQAA  215 (234)
T ss_pred             CCCCCCCCHHEEEECCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             675556641001105673148899998766888899999999999999999999988876


No 88 
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.13  E-value=62  Score=14.32  Aligned_cols=31  Identities=16%  Similarity=0.413  Sum_probs=21.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999965
Q gi|254780412|r   58 RTTSHLREEITAIGKRLEKIEQQLADLELFI   88 (94)
Q Consensus        58 ~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~   88 (94)
                      ++....+.++..++++++.|+.-.+.|+..+
T Consensus        81 ~~~~~l~~kl~ei~~~I~~L~~lr~~L~~~l  111 (112)
T cd01282          81 DLLAVLRRELARIDRQIADLTRSRDRLDAYL  111 (112)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999999999975


No 89 
>pfam05278 PEARLI-4 Arabidopsis phospholipase-like protein (PEARLI 4). This family contains several phospholipase-like proteins from Arabidopsis thaliana which are homologous to PEARLI 4.
Probab=22.76  E-value=63  Score=14.27  Aligned_cols=40  Identities=18%  Similarity=0.441  Sum_probs=25.3

Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             8569999999999999999999999999999999999999
Q gi|254780412|r   47 VVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLEL   86 (94)
Q Consensus        47 LVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~   86 (94)
                      +-.|.|.+.+.+=+.+--.++..-.+|+.++-.+|.+||.
T Consensus       168 ~~~k~EmE~~~~eL~~kEKevke~r~~v~e~~~~Lg~LEm  207 (234)
T pfam05278       168 LLKKQEMEKQEAELVRKEKEVKEFREKVEEMAGRLGELEM  207 (234)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8778899999999999999999999999999988877777


No 90 
>COG1566 EmrA Multidrug resistance efflux pump [Defense mechanisms]
Probab=22.63  E-value=63  Score=14.25  Aligned_cols=28  Identities=21%  Similarity=0.358  Sum_probs=21.8

Q ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             9998739856999999999999999999
Q gi|254780412|r   40 RTLNSMGVVRAEEIENVKRTTSHLREEI   67 (94)
Q Consensus        40 ~~l~kldLVtREEFdv~~~~l~k~R~~~   67 (94)
                      ..|.+-+.|||+|+|-.+.-+..++..+
T Consensus       140 ~~L~~~g~vs~~~~~~a~~a~~~A~A~~  167 (352)
T COG1566         140 AELAQRGVVSREELDRARAALQAAEAAL  167 (352)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             9887567443999998888999998888


No 91 
>pfam07195 FliD_C Flagellar hook-associated protein 2 C-terminus. The flagellar hook-associated protein 2 (HAP2 or FliD) forms the distal end of the flagella, and plays a role in mucin specific adhesion of the bacteria. This alignment covers the C-terminal region of this family of proteins.
Probab=22.44  E-value=64  Score=14.23  Aligned_cols=61  Identities=15%  Similarity=0.352  Sum_probs=32.1

Q ss_pred             HHHHHHHHHHHHHHC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHCC
Q ss_conf             999999999999873-9856999999999999999999999999999999----9999999650023
Q gi|254780412|r   31 ESFAQIKIQRTLNSM-GVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQ----QLADLELFINQKE   92 (94)
Q Consensus        31 e~~~r~~~e~~l~kl-dLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~----kl~~le~~~~~k~   92 (94)
                      -..+...++.++..- +.++-.. +.+..-+.....+++.|+.|++..+.    +-+.+|..+++=+
T Consensus       164 ~~~l~~~l~~~~~~~~G~l~~~~-~~l~~~~~~~~~~i~~l~~rl~~~~~~~~~qf~~me~~i~~mn  229 (230)
T pfam07195       164 AKRLDDSLKPYTGSGNGILASRE-DSLNKQIKRLNKQIEDLDRRLDTLEARLKAQFTAMDDLMSKMN  229 (230)
T ss_pred             HHHHHHHHHHHHCCCCCEEHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             99999999998478986405688-8899999999999999999999999999999999999999847


No 92 
>PRK00591 prfA peptide chain release factor 1; Validated
Probab=22.35  E-value=58  Score=14.50  Aligned_cols=27  Identities=30%  Similarity=0.500  Sum_probs=18.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999
Q gi|254780412|r   58 RTTSHLREEITAIGKRLEKIEQQLADL   84 (94)
Q Consensus        58 ~~l~k~R~~~e~Le~rl~~LE~kl~~l   84 (94)
                      ++..-+.+++..|++++..||.+|..+
T Consensus        76 el~e~a~~El~~l~~~l~~lE~eL~~l  102 (360)
T PRK00591         76 EMREMAKEELKELEERLEELEEELKIL  102 (360)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             899999999999999999999999998


No 93 
>PRK10697 DNA-binding transcriptional activator PspC; Provisional
Probab=22.27  E-value=64  Score=14.21  Aligned_cols=27  Identities=22%  Similarity=0.415  Sum_probs=14.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999650
Q gi|254780412|r   63 LREEITAIGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        63 ~R~~~e~Le~rl~~LE~kl~~le~~~~   89 (94)
                      .+..+..+..+++.+|.+|.+.|..++
T Consensus        80 p~~~l~~i~~~~~~~E~RLr~ME~YVT  106 (119)
T PRK10697         80 SSELLDEVDRELAAGEQRLREMERYVT  106 (119)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             999999999999999999999988873


No 94 
>PRK01885 greB transcription elongation factor GreB; Reviewed
Probab=21.73  E-value=66  Score=14.14  Aligned_cols=58  Identities=10%  Similarity=0.213  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHH-------HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             779999999999-------99999999873985699999999999999999999999999999999999996
Q gi|254780412|r   23 FKDISKEAESFA-------QIKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus        23 ~~~~~~Eie~~~-------r~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      ...++.|++...       ...+..+-+.-||=--=||++       +++++..|++||..|+.+|+.-+-.
T Consensus        14 ~~kL~~El~~L~~~~r~~~~~~i~~Ar~~GDlsENaeY~a-------Ake~q~~le~rI~~Le~~L~~A~ii   78 (159)
T PRK01885         14 YERLKQELDYLWREERPEVTQKVSWAASLGDRSENADYIY-------GKKRLREIDRRVRFLTKRLENLKVV   78 (159)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHH-------HHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9999999999874530458999999998599430263899-------9999999999999999998733035


No 95 
>pfam04508 Pox_A_type_inc Viral A-type inclusion protein repeat. The repeat is found in the A-type inclusion protein of the Poxvirus family.
Probab=21.54  E-value=66  Score=14.12  Aligned_cols=18  Identities=28%  Similarity=0.626  Sum_probs=9.0

Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999
Q gi|254780412|r   67 ITAIGKRLEKIEQQLADL   84 (94)
Q Consensus        67 ~e~Le~rl~~LE~kl~~l   84 (94)
                      ++.+..+|..|+++|.+-
T Consensus         3 ldr~r~~I~dLek~L~~c   20 (26)
T pfam04508         3 LDRLRRRISDLEKQLSDC   20 (26)
T ss_pred             HHHHHHHHHHHHHHHHHH
T ss_conf             889999988899999998


No 96 
>pfam07426 Dynactin_p22 Dynactin subunit p22. This family contains p22, the smallest subunit of dynactin, a complex that binds to cytoplasmic dynein and is a required activator for cytoplasmic dynein-mediated vesicular transport. Dynactin localizes to the cleavage furrow and to the midbodies of dividing cells, suggesting that it may function in cytokinesis. Family members are approximately 170 residues long and seem to be restricted to mammals.
Probab=21.39  E-value=67  Score=14.10  Aligned_cols=43  Identities=9%  Similarity=0.097  Sum_probs=19.7

Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             975006999999999866888779999999999999999998739
Q gi|254780412|r    2 SFRSNQFFQQASRLASCASDAFKDISKEAESFAQIKIQRTLNSMG   46 (94)
Q Consensus         2 ~~~~n~~~ddla~~~~~a~~~~~~~~~Eie~~~r~~~e~~l~kld   46 (94)
                      +..++++.|.++++-....+++.  ++|--+.+--+++....=+|
T Consensus        27 ~~~~~~v~d~L~~vq~~l~~a~s--kRerik~l~kki~eL~kYLD   69 (172)
T pfam07426        27 TGEPRKVAEGLVKIQVALGNIAN--KRERVKILYKKIEDLLKYLD   69 (172)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHC--CHHHHHHHHHHHHHHHHHCC
T ss_conf             78984177899999999999861--35999999997899998669


No 97 
>PRK00226 greA transcription elongation factor GreA; Reviewed
Probab=21.35  E-value=67  Score=14.09  Aligned_cols=58  Identities=19%  Similarity=0.320  Sum_probs=40.2

Q ss_pred             HHHHHHHHHHHHH-------HHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7799999999999-------9999999873985699999999999999999999999999999999999996
Q gi|254780412|r   23 FKDISKEAESFAQ-------IKIQRTLNSMGVVRAEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELF   87 (94)
Q Consensus        23 ~~~~~~Eie~~~r-------~~~e~~l~kldLVtREEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~   87 (94)
                      ..-+++|++....       ..+..+-+.-||=--=||++       +++++..+++||..|+..|+..+..
T Consensus        12 ~~~L~~El~~L~~~~r~~i~~~i~~Ar~~GDlsENaeY~a-------Ake~q~~~e~rI~~Le~~L~~A~ii   76 (157)
T PRK00226         12 YEKLEEELEELKTVERPEIIEAIAEAREHGDLSENAEYHA-------AKEEQGFIEGRIRELEDKLSNAEVI   76 (157)
T ss_pred             HHHHHHHHHHHHHCCHHHHHHHHHHHHHCCCCCCCHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999999999987236899999999998699640576999-------9999999999999999999850145


No 98 
>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
Probab=21.15  E-value=68  Score=14.07  Aligned_cols=54  Identities=17%  Similarity=0.283  Sum_probs=41.6

Q ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999987398569999999999999--999999999999999999999999650
Q gi|254780412|r   35 QIKIQRTLNSMGVVRAEEIENVKRTTSH--LREEITAIGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        35 r~~~e~~l~kldLVtREEFdv~~~~l~k--~R~~~e~Le~rl~~LE~kl~~le~~~~   89 (94)
                      +..+...+.++++ +.+.||.+..|=..  |+++++.|++.++.+++.++.++..++
T Consensus       374 k~~l~~~l~~~~~-~~~q~dyLL~M~L~~LT~~e~~kL~~e~~~l~~ei~~L~~~l~  429 (445)
T cd00187         374 KKALIEELEKLGF-SEIQADAILDMRLRRLTKLEREKLLKELKELEAEIEDLEKILA  429 (445)
T ss_pred             HHHHHHHHHHCCC-CHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9999999876799-9999999997669987589999999999999999999999867


No 99 
>pfam06428 Sec2p GDP/GTP exchange factor Sec2p. In Saccharomyces cerevisiae, Sec2p is a GDP/GTP exchange factor for Sec4p, which is required for vesicular transport at the post-Golgi stage of yeast secretion.
Probab=20.91  E-value=68  Score=14.03  Aligned_cols=40  Identities=23%  Similarity=0.362  Sum_probs=21.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999999999999999999999999650
Q gi|254780412|r   50 AEEIENVKRTTSHLREEITAIGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        50 REEFdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le~~~~   89 (94)
                      |-|-.+...--.++++.+..-+.-|+.|..+|.+|+.++-
T Consensus        43 r~e~~~~e~kn~qL~eqL~e~e~ll~slQ~QL~~LK~v~~   82 (101)
T pfam06428        43 RKEREAVEIKNEKLEEQLKEKETLLDSLQAQLKELKQVMQ   82 (101)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999998899999997699899999999999999999


No 100
>pfam04102 SlyX SlyX. The SlyX protein has no known function. It is short less than 80 amino acids and is found close to the slyD gene. The SlyX protein has a conserved PPH(Y/W) motif at its C-terminus. The protein may be a coiled-coil structure.
Probab=20.86  E-value=69  Score=14.03  Aligned_cols=33  Identities=18%  Similarity=0.441  Sum_probs=26.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999999999999999999999999999999
Q gi|254780412|r   53 IENVKRTTSHLREEITAIGKRLEKIEQQLADLE   85 (94)
Q Consensus        53 Fdv~~~~l~k~R~~~e~Le~rl~~LE~kl~~le   85 (94)
                      .|-+-.++.+-..+++.|+.++..|..++.+++
T Consensus        20 ie~Ln~vv~~Qq~~i~~L~~~l~~L~~rl~~~~   52 (68)
T pfam04102        20 IEELNQVVAEQQRQIDRLQRQLRLLVERLKEVE   52 (68)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             999999999999999999999999999999742


No 101
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.45  E-value=70  Score=13.97  Aligned_cols=29  Identities=24%  Similarity=0.401  Sum_probs=18.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999999999999999999999650
Q gi|254780412|r   61 SHLREEITAIGKRLEKIEQQLADLELFIN   89 (94)
Q Consensus        61 ~k~R~~~e~Le~rl~~LE~kl~~le~~~~   89 (94)
                      .-...+.+.++++++.|+.....++....
T Consensus        82 ~~l~~~~~~i~~qI~~L~~~~~~L~~~~~  110 (116)
T cd04769          82 QALEDKKQEIRAQITELQQLLARLDAFEA  110 (116)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999


Done!