Query         T0586 3NEU, Listeria innocua Clip11262, 125 residues
Match_columns 125
No_of_seqs    117 out of 8289
Neff          8.0 
Searched_HMMs 11830
Date          Sun Jun 13 15:31:51 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0586.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0586.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF00392 GntR:  Bacterial regul  99.7 6.6E-17 5.6E-21  129.3   8.2   64   14-77      1-64  (64)
  2 PF01726 LexA_DNA_bind:  LexA D  97.6 3.5E-05 2.9E-09   52.3   5.4   58   12-74      5-63  (65)
  3 PF08279 HTH_11:  HTH domain;    97.0 0.00013 1.1E-08   48.5   2.7   43   33-76     12-55  (55)
  4 PF08220 HTH_DeoR:  DeoR-like h  97.0 0.00045 3.8E-08   44.9   5.0   44   34-78     12-55  (57)
  5 PF01325 Fe_dep_repress:  Iron   97.0 0.00048   4E-08   44.8   5.0   42   33-75     19-60  (60)
  6 PF02082 Rrf2:  Transcriptional  96.7  0.0019 1.6E-07   40.8   6.4   58   22-80     11-70  (83)
  7 PF05732 RepL:  Firmicute plasm  96.6  0.0024   2E-07   40.2   6.5   48   32-80     70-117 (165)
  8 PF03444 DUF293:  Domain of unk  96.4  0.0011   9E-08   42.5   3.8   57   21-78      8-65  (78)
  9 PF04703 FaeA:  FaeA-like prote  96.4  0.0022 1.9E-07   40.4   5.3   50   16-74      3-53  (62)
 10 PF01978 TrmB:  Sugar-specific   96.2   0.002 1.7E-07   40.6   3.9   38   39-76     24-61  (68)
 11 PF04492 Phage_rep_O:  Bacterio  95.6   0.011 8.9E-07   35.9   5.6   45   28-73     46-90  (100)
 12 PF08784 RPA_C:  Replication pr  95.4  0.0083   7E-07   36.6   4.7   54   11-70     45-98  (102)
 13 PF01710 Transposase_14:  Trans  95.1   0.028 2.4E-06   33.1   6.6   89   21-119     6-94  (119)
 14 PF03428 RP-C:  Replication pro  94.7    0.05 4.3E-06   31.5   6.9   55   17-71     47-105 (177)
 15 PF08222 HTH_CodY:  CodY helix-  94.4    0.01 8.8E-07   36.0   2.9   44   39-82      6-51  (61)
 16 PF01047 MarR:  MarR family;  I  94.4   0.018 1.5E-06   34.4   4.0   36   38-73     18-53  (59)
 17 PF09339 HTH_IclR:  IclR helix-  94.1   0.024   2E-06   33.6   4.2   37   34-71     16-52  (52)
 18 PF00325 Crp:  Bacterial regula  93.6   0.028 2.3E-06   33.2   3.8   29   39-67      4-32  (32)
 19 PF03965 Pencillinase_R:  Penic  93.6    0.12 9.7E-06   29.1   6.9   92   24-117     6-110 (115)
 20 PF01022 HTH_5:  Bacterial regu  93.0   0.047   4E-06   31.6   4.2   32   37-69     16-47  (47)
 21 PF07848 PaaX:  PaaX-like prote  92.7   0.064 5.4E-06   30.8   4.5   44   36-79     22-68  (70)
 22 PF06163 DUF977:  Bacterial pro  92.0   0.071   6E-06   30.5   4.1   46   34-80     24-69  (127)
 23 PF03297 Ribosomal_S25:  S25 ri  91.7   0.065 5.5E-06   30.7   3.6   50   16-71     44-93  (105)
 24 PF09397 Ftsk_gamma:  Ftsk gamm  90.4    0.31 2.6E-05   26.2   6.0   58    9-76      2-59  (65)
 25 PF12298 Bot1p:  Eukaryotic mit  89.8    0.32 2.7E-05   26.2   5.6   55    4-65      7-61  (172)
 26 PF05043 Mga:  Mga helix-turn-h  89.2    0.68 5.8E-05   24.0   7.8   52   33-87     27-82  (87)
 27 PF04967 HTH_10:  HTH DNA bindi  88.4    0.56 4.8E-05   24.6   6.1   44   19-63      6-49  (53)
 28 PF01090 Ribosomal_S19e:  Ribos  87.4    0.45 3.8E-05   25.2   5.1   63   15-84     51-127 (139)
 29 PF07900 DUF1670:  Protein of u  87.4    0.36   3E-05   25.9   4.6   55   18-73     87-142 (220)
 30 PF01638 HxlR:  HxlR-like helix  85.8    0.57 4.8E-05   24.5   4.9   48   39-86     20-74  (90)
 31 PF09012 FeoC:  FeoC like trans  85.4    0.26 2.2E-05   26.7   3.1   37   36-73     14-50  (69)
 32 PF02002 TFIIE_alpha:  TFIIE al  84.8    0.29 2.4E-05   26.5   3.0   35   36-71     27-61  (105)
 33 PF05225 HTH_psq:  helix-turn-h  84.6    0.23 1.9E-05   27.1   2.5   29   31-61     12-40  (45)
 34 PF00356 LacI:  Bacterial regul  84.4    0.32 2.7E-05   26.2   3.1   22   39-60      1-22  (46)
 35 PF02796 HTH_7:  Helix-turn-hel  83.7    0.27 2.3E-05   26.7   2.5   32   20-59     12-43  (45)
 36 PF05584 Sulfolobus_pRN:  Sulfo  82.7    0.73 6.2E-05   23.8   4.4   33   39-71     20-52  (72)
 37 PF09681 Phage_rep_org_N:  N-te  82.0     1.5 0.00013   21.7   9.3   64   18-81     27-97  (121)
 38 PF00292 PAX:  'Paired box' dom  78.6     1.7 0.00014   21.4   5.1   62    7-76     11-72  (125)
 39 PF04079 DUF387:  Putative tran  77.7     2.1 0.00018   20.8   7.5   82   31-114     8-103 (159)
 40 PF10007 DUF2250:  Uncharacteri  77.7     1.2  0.0001   22.3   4.2   34   40-73     24-57  (92)
 41 PF01418 HTH_6:  Helix-turn-hel  77.5     0.7 5.9E-05   23.9   2.9   57   10-72     13-69  (107)
 42 PF06970 RepA_N:  Replication i  76.9     1.9 0.00016   21.1   5.0   49   13-61     25-76  (76)
 43 PF04218 CENP-B_N:  CENP-B N-te  76.3    0.27 2.3E-05   26.7   0.5   21   39-59     24-44  (53)
 44 PF09862 DUF2089:  Protein of u  75.9     1.2 9.7E-05   22.5   3.7   61   39-117    51-112 (113)
 45 PF08221 HTH_9:  RNA polymerase  74.9     1.4 0.00012   22.0   3.9   52   16-69      8-59  (62)
 46 PF10668 Phage_terminase:  Phag  73.9    0.91 7.7E-05   23.2   2.7   36   12-56      6-41  (60)
 47 PF08461 HTH_12:  Ribonuclease   73.5     1.5 0.00013   21.7   3.8   47   33-80     10-61  (66)
 48 PF01475 FUR:  Ferric uptake re  73.4    0.74 6.3E-05   23.8   2.2   36   38-73     24-64  (120)
 49 PF04433 SWIRM:  SWIRM domain;   70.2     1.8 0.00015   21.3   3.5   51   17-68     32-83  (84)
 50 PF08765 Mor:  Mor transcriptio  68.9     2.3  0.0002   20.5   3.9   50   13-66     52-101 (108)
 51 PF09170 DUF1879:  Domain of un  68.7     1.9 0.00016   21.1   3.3   82   14-95     52-151 (174)
 52 PF08280 HTH_Mga:  M protein tr  68.2     2.1 0.00018   20.8   3.5   30   34-64     17-46  (59)
 53 PF04157 EAP30:  EAP30/Vps36 fa  68.2     2.3  0.0002   20.5   3.8   71   10-81     87-168 (223)
 54 PF07453 NUMOD1:  NUMOD1 domain  67.8     1.2  0.0001   22.4   2.2   23   36-58     15-37  (37)
 55 PF00126 HTH_1:  Bacterial regu  66.9     2.1 0.00017   20.9   3.3   40   38-78     14-56  (60)
 56 PF03551 PadR:  Transcriptional  66.8     2.3 0.00019   20.6   3.5   50   21-73     10-63  (86)
 57 PF12116 SpoIIID:  Stage III sp  66.6    0.95   8E-05   23.1   1.5   28   34-62     17-45  (82)
 58 PF04297 UPF0122:  Putative hel  64.4     2.4 0.00021   20.4   3.3   28   34-62     31-58  (101)
 59 PF07638 Sigma70_ECF:  ECF sigm  62.9     3.3 0.00028   19.5   3.7   14  104-117   148-161 (185)
 60 PF07023 DUF1315:  Protein of u  62.4     3.7 0.00031   19.2   3.9   55   16-79     10-68  (93)
 61 PF01371 Trp_repressor:  Trp re  62.3     3.2 0.00027   19.6   3.6   25   39-63     51-75  (87)
 62 PF06056 Terminase_5:  Putative  59.0     3.5 0.00029   19.4   3.2   31   39-69     15-45  (58)
 63 PF03374 ANT:  Phage antirepres  57.5     4.7  0.0004   18.5   3.7   37   36-76     23-59  (111)
 64 PF01498 Transposase_5:  Transp  57.5     3.3 0.00028   19.5   2.9   36   39-77     15-55  (72)
 65 PF00376 MerR:  MerR family reg  57.3     1.9 0.00016   21.1   1.7   25   39-67      1-25  (38)
 66 PF12471 GTP_CH_N:  GTP cyclohy  56.3     5.1 0.00043   18.3   3.7   40   20-59    135-192 (194)
 67 PF08281 Sigma70_r4_2:  Sigma-7  55.7     2.9 0.00025   19.9   2.4   25   37-62     27-51  (54)
 68 PF11740 KfrA_N:  Plasmid repli  55.6     5.8 0.00049   17.9   6.1   46   15-66      3-49  (120)
 69 PF06413 Neugrin:  Neugrin;  In  54.9     3.7 0.00031   19.2   2.8   21   39-59     31-51  (225)
 70 PF09079 Cdc6_C:  CDC6, C termi  54.9     5.9  0.0005   17.8   3.9   42   30-71     15-59  (85)
 71 PF02295 z-alpha:  Adenosine de  54.7       6 0.00051   17.8   3.9   40   34-74     18-57  (66)
 72 PF05930 Phage_AlpA:  Prophage   54.3     2.2 0.00018   20.7   1.6   24   36-59      2-25  (51)
 73 PF02001 DUF134:  Protein of un  53.6     4.8 0.00041   18.4   3.2   30   31-61     52-81  (106)
 74 PF07471 Phage_Nu1:  Phage DNA   51.2     2.4  0.0002   20.5   1.3   34   39-76      4-38  (164)
 75 PF06971 Put_DNA-bind_N:  Putat  50.8     4.3 0.00036   18.8   2.6   39   13-59     12-50  (50)
 76 PF09182 PuR_N:  Bacterial puri  50.0     7.1  0.0006   17.3   4.3   42   32-74     16-63  (70)
 77 PF04539 Sigma70_r3:  Sigma-70   47.6     5.7 0.00048   17.9   2.9   28   35-62     18-45  (78)
 78 PF04182 B-block_TFIIIC:  B-blo  47.1     7.9 0.00067   17.0   3.5   48   21-72      6-53  (75)
 79 PF03811 Ins_element1:  Inserti  47.1     6.1 0.00052   17.7   2.9   34   18-59     52-85  (88)
 80 PF10264 Stork_head:  Winged he  44.3     8.7 0.00074   16.7   3.5   29   50-79     50-78  (80)
 81 PF00196 GerE:  Bacterial regul  43.9     8.8 0.00074   16.7   3.6   25   39-63     20-44  (58)
 82 PF09756 DDRGK:  DDRGK domain;   43.6     7.3 0.00062   17.2   2.9   58   18-81    100-160 (188)
 83 PF06504 RepC:  Replication pro  43.5     8.9 0.00076   16.7   5.0   67    7-73     81-153 (281)
 84 PF05402 PqqD:  Coenzyme PQQ sy  42.7     9.2 0.00078   16.6   3.5   29   40-68     49-81  (81)
 85 PF07022 Phage_CI_repr:  Bacter  42.6     3.6 0.00031   19.3   1.2   22   38-59     13-35  (66)
 86 PF07377 DUF1493:  Protein of u  42.0     9.4  0.0008   16.5   5.2   53   13-65      3-55  (111)
 87 PF03962 Mnd1:  Mnd1 family;  I  41.9     9.5  0.0008   16.5   5.0   33   44-77     22-54  (188)
 88 PF08535 KorB:  KorB domain;  I  40.9       3 0.00025   19.8   0.6   37   39-75      5-41  (93)
 89 PF03180 Lipoprotein_9:  NLPA l  40.9       8 0.00068   17.0   2.8   30   50-79    105-134 (237)
 90 PF07750 GcrA:  GcrA cell cycle  40.7     7.3 0.00062   17.2   2.5   29   36-65     18-47  (162)
 91 PF00165 HTH_AraC:  Bacterial r  38.7      11 0.00089   16.2   3.7   28   34-62      6-33  (42)
 92 PF01381 HTH_3:  Helix-turn-hel  38.2     8.1 0.00069   16.9   2.4   21   39-59     11-31  (55)
 93 PF10557 Cullin_Nedd8:  Cullin   37.9     7.6 0.00064   17.1   2.2   30   43-72     36-65  (68)
 94 PF02954 HTH_8:  Bacterial regu  37.8     9.8 0.00083   16.4   2.8   22   39-60     20-41  (42)
 95 PF05848 CtsR:  Firmicute trans  37.5      11 0.00092   16.1   3.0   63   14-78      4-69  (152)
 96 PF12481 DUF3700:  Aluminium in  37.0     6.6 0.00056   17.5   1.8   55    4-65     57-119 (124)
 97 PF07374 DUF1492:  Protein of u  36.4      11 0.00097   16.0   3.0   25   36-61     71-99  (100)
 98 PF05158 RNA_pol_Rpc34:  RNA po  34.5      12   0.001   15.8   8.2   31   40-70    104-134 (325)
 99 PF06322 Phage_NinH:  Phage Nin  34.5     8.6 0.00073   16.8   2.1   27   39-65     18-44  (64)
100 PF10141 ssDNA-exonuc_C:  Singl  33.6      13  0.0011   15.7   9.1   68   11-81     93-160 (195)
101 PF04545 Sigma70_r4:  Sigma-70,  33.5     2.5 0.00021   20.3  -0.8   27   34-61     18-44  (50)
102 PF04936 DUF658:  Protein of un  33.3     9.5  0.0008   16.5   2.1   30   39-72     16-45  (186)
103 PF07278 DUF1441:  Protein of u  31.1      14  0.0011   15.5   2.6   26   36-62      1-26  (152)
104 PF09048 Cro:  Cro;  InterPro:   29.5      15  0.0013   15.2   2.6   23   39-61     14-36  (59)
105 PF09107 SelB-wing_3:  Elongati  28.9      15  0.0013   15.2   2.8   39   33-72      7-45  (50)
106 PF05331 DUF742:  Protein of un  28.2      11  0.0009   16.2   1.7   39   36-75     55-93  (114)
107 PF10543 ORF6N:  ORF6N domain    28.2      16  0.0013   15.1   2.6   41   34-79      9-50  (88)
108 PF06353 DUF1062:  Protein of u  27.7      16  0.0013   15.0   3.9   38   30-73     98-135 (142)
109 PF04337 DUF480:  Protein of un  27.7     8.9 0.00075   16.7   1.2   34   47-81     44-77  (148)
110 PF00440 TetR_N:  Bacterial reg  27.5      16  0.0014   15.0   2.6   24   35-59     15-38  (47)
111 PF01527 Transposase_8:  Transp  27.3     6.9 0.00059   17.4   0.6   24   39-62     25-48  (76)
112 PF04645 DUF603:  Protein of un  27.2      16  0.0014   15.0   2.7   32   31-64     15-46  (181)
113 PF04760 IF2_N:  Translation in  26.9      15  0.0013   15.2   2.3   36   35-73      2-37  (54)
114 PF01399 PCI:  PCI domain;  Int  26.6     2.9 0.00024   19.9  -1.5   64   13-77     37-102 (105)
115 PF12324 HTH_15:  Helix-turn-he  23.9      16  0.0013   15.0   1.9   32   31-63     33-64  (77)
116 PF00538 Linker_histone:  linke  23.3      19  0.0016   14.5   5.3   60   13-75      3-69  (77)
117 PF05491 RuvB_C:  Holliday junc  23.3      19  0.0016   14.5   3.0   45   34-80     23-68  (76)
118 PF07514 TraI_2:  Putative heli  23.2      19  0.0016   14.5   3.3   59    9-67    239-299 (327)
119 PF06530 Phage_antitermQ:  Phag  23.2      19  0.0016   14.5   3.2   21   39-59     80-100 (125)
120 PF09904 DUF2131:  Uncharacteri  21.3      21  0.0018   14.2   3.4   39   42-80      3-47  (67)
121 PF10771 DUF2582:  Protein of u  20.8      21  0.0018   14.2   4.7   45   31-76     17-61  (65)

No 1  
>PF00392 GntR:  Bacterial regulatory proteins, gntR family;  InterPro: IPR000524   Many bacterial transcription regulation proteins bind DNA through a helix-turn-helix (HTH) motif, which can be classified into subfamilies on the basis of sequence similarities. The HTH GntR family has many members distributed among diverse bacterial groups that regulate various biological processes. It was named GntR after the Bacillus subtilis repressor of the gluconate operon . Family members include GntR, HutC, KorA, NtaR, FadR, ExuR, FarR, DgoR and PhnF. The crystal structure of the FadR protein has been determined . In general, these proteins contain a DNA-binding HTH domain at the N terminus, and an effector-binding or oligomerisation domain at the C terminus (IPR011711 from INTERPRO). The DNA-binding domain is well conserved in structure for the whole of the GntR family, consisting of a 3-helical bundle core with a small beta-sheet (wing); the GntR winged helix structure is similar to that found in several other transcriptional regulator families. The regions outside the DNA-binding domain are more variable and are consequently used to define GntR subfamilies . This entry represents the N-terminal DNA-binding domain of the GntR family.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2ra5_A 3by6_D 2ek5_C 2du9_A 1v4r_A 3bwg_A 3eet_B 1h9t_B 1hw2_B 1hw1_B ....
Probab=99.67  E-value=6.6e-17  Score=129.32  Aligned_cols=64  Identities=36%  Similarity=0.711  Sum_probs=63.2

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEE
Q ss_conf             8999999999997649899888178878999985898789999999998879167317833686
Q T0586            14 IYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFV   77 (125)
Q Consensus        14 ly~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V   77 (125)
                      +|+||+++|++.|.+|.|+||++|||+++||++|||||+|||+||..|+.+|+|++.+|+|+||
T Consensus         1 l~~~v~~~i~~~I~~g~l~~G~~lPs~~~La~~~~vSr~tvr~Al~~L~~~g~i~~~~~~G~~V   64 (64)
T PF00392_consen    1 LYEQVYEYIRRDILSGELKPGDRLPSERELAERFGVSRTTVREALKRLEEEGLIERRPGRGTFV   64 (64)
T ss_dssp             HHHHHHHHHHHHHHTTSS-TTSB---HHHHHHHHT--HHHHHHHHHHHHHTTSEEEETT---EE
T ss_pred             CHHHHHHHHHHHHHCCCCCCCCEECCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEC
T ss_conf             9899999999999849999999936899999886879899999999999889589976963679


No 2  
>PF01726 LexA_DNA_bind:  LexA DNA binding domain;  InterPro: IPR006199   This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif . This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0008992 repressor LexA activity, 0006508 proteolysis; PDB: 1lea_A 1jhh_A 1jhf_A 1leb_A.
Probab=97.63  E-value=3.5e-05  Score=52.26  Aligned_cols=58  Identities=29%  Similarity=0.563  Sum_probs=52.5

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCC-HHHHHHHHHHHHHCCEEEECCCCE
Q ss_conf             988999999999997649899888178878999985898-789999999998879167317833
Q T0586            12 KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVN-PNTVSRAYQELERAGYIYAKRGMG   74 (125)
Q Consensus        12 ~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VS-r~TVr~Al~~L~~~G~i~~~~g~G   74 (125)
                      +|...+|.++|.+.|....++     ||.+++|+.||++ ++||..-++.|+..|||.+.+|+.
T Consensus         5 T~rQ~~vL~~I~~~~~~~G~~-----Pt~rEI~~~~gl~S~~tV~~~L~~Le~kG~I~r~~~~~   63 (65)
T PF01726_consen    5 TPRQQEVLDFIKDYIREHGYP-----PTVREIAEALGLKSPSTVHKHLKALEKKGYITRDPGKA   63 (65)
T ss_dssp             -HHHHHHHHHHHHHHHH-----------HHHHHHH----SHHHHHHHHHHHHH---EE------
T ss_pred             CHHHHHHHHHHHHHHHHCCCC-----CCHHHHHHHCCCCCCHHHHHHHHHHHHCCCEECCCCCC
T ss_conf             999999999999999983889-----88999998819998099999999999982951689999


No 3  
>PF08279 HTH_11:  HTH domain;  InterPro: IPR013196   Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 . The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions.   This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon . It is also found in other proteins including regulators of amino acid biosynthsis such as LysM , and regulators of carbohydrate metabolisms such as LicR and FrvR , .; PDB: 1j5y_A 2ewn_B 1hxd_B 1bia_A 1bib_A 2dbb_B 1i1g_B 2cg4_B.
Probab=97.03  E-value=0.00013  Score=48.48  Aligned_cols=43  Identities=30%  Similarity=0.473  Sum_probs=38.4

Q ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC-EEEECCCCEEE
Q ss_conf             888178878999985898789999999998879-16731783368
Q T0586            33 GEDKLPSVREMGVKLAVNPNTVSRAYQELERAG-YIYAKRGMGSF   76 (125)
Q Consensus        33 ~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G-~i~~~~g~G~~   76 (125)
                      .+..+ |..+||+.+|||+.||++.++.|.+.| .|...+|+|++
T Consensus        12 ~~~~i-t~~eLA~~l~vS~~Ti~~~i~~L~~~g~~I~s~~~~Gy~   55 (55)
T PF08279_consen   12 NDGPI-TAKELAEELGVSRRTIRRDIKELEEEGIPIESKPGRGYR   55 (55)
T ss_dssp             CCTTS--HHHHHHHCTS-HHHHHHHHHHHHH--EB-BB-TTT---
T ss_pred             CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCCC
T ss_conf             59998-899999996979999999999999869969860789989


No 4  
>PF08220 HTH_DeoR:  DeoR-like helix-turn-helix domain;  InterPro: IPR001034   The deoR-type HTH domain is a DNA-binding, helix-turn-helix (HTH) domain of about 50-60 amino acids present in transcription regulators of the deoR family, involved in sugar catabolism. This family of prokaryotic regulators is named after Escherichia coli deoR, a repressor of the deo operon, which encodes nucleotide and deoxyribonucleotide catabolic enzymes. DeoR also negatively regulates the expression of nupG and tsx, a nucleoside-specific transport protein and a channel-forming protein, respectively.   DeoR-like transcription repressors occur in diverse bacteria as regulators of sugar and nucleoside metabolic systems. The effector molecules for deoR-like regulators are generally phosphorylated intermediates of the relevant metabolic pathway. The DNA-binding deoR-type HTH domain occurs usually in the N-terminal part. The C-terminal part can contain an effector-binding domain and/or an oligomerization domain. DeoR occurs as an octamer, whilst glpR and agaR are tetramers. Several operators may be bound simultaneously, which could facilitate DNA looping , . ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular
Probab=96.97  E-value=0.00045  Score=44.94  Aligned_cols=44  Identities=30%  Similarity=0.433  Sum_probs=37.7

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEEC
Q ss_conf             881788789999858987899999999988791673178336862
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVT   78 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~   78 (125)
                      ..++ |..+||+.||||..|||+-+..|+++|+|.+.+|.-..+.
T Consensus        12 ~~~~-s~~ela~~~~VS~~TiRRDl~~L~~~g~i~r~~Gg~~~~~   55 (57)
T PF08220_consen   12 HGKV-SVKELAEEFGVSEMTIRRDLNELEEQGLIRRVHGGAVLNS   55 (57)
T ss_pred             CCCE-EHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCEEEECC
T ss_conf             6989-7999999989498899998999998898899619799468


No 5  
>PF01325 Fe_dep_repress:  Iron dependent repressor, N-terminal DNA binding domain;  InterPro: IPR001367 The diphtheria toxin repressor protein (DTXR) is a member of this group . In Corynebacterium diphtheriae where it has been studied in some detail this protein acts as an iron-binding repressor of dipheteria toxin gene expression and may serve as a global regulator of gene expression. The N-terminus may be involved in iron binding and may associate with the Tox operator. Binding of DTXR to Tox operator requires a divalent metal ion such as cobalt, ferric, manganese and nickel whereas zinc shows weak activation .; GO: 0003700 transcription factor activity, 0005506 iron ion binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2h09_A 1ddn_A 1bi3_B 1g3t_A 1f5t_C 2qqb_A 2qq9_A 1bi0_A 1bi2_B 1c0w_C ....
Probab=96.96  E-value=0.00048  Score=44.77  Aligned_cols=42  Identities=26%  Similarity=0.390  Sum_probs=37.9

Q ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEE
Q ss_conf             8881788789999858987899999999988791673178336
Q T0586            33 GEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGS   75 (125)
Q Consensus        33 ~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~   75 (125)
                      .|... +..++|+.+|||+.||.++++.|.++|||...+.+|.
T Consensus        19 ~~~~v-~~~~IA~~L~vs~~TVs~ml~kL~~~Glv~~~~y~gv   60 (60)
T PF01325_consen   19 EGGPV-STSDIAERLGVSPPTVSEMLKKLEEEGLVEYEKYGGV   60 (60)
T ss_dssp             H-S---BHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEETTSBE
T ss_pred             CCCCC-CHHHHHHHHCCCCHHHHHHHHHHHHCCCEEECCCCCC
T ss_conf             69972-1999999978990789999999998899885146989


No 6  
>PF02082 Rrf2:  Transcriptional regulator;  InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulphovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis strain PCC 6803 hypothetical protein slr0846. These are small proteins of 12 to 18 kD which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 1xd7_A 1ylf_A.
Probab=96.69  E-value=0.0019  Score=40.82  Aligned_cols=58  Identities=21%  Similarity=0.463  Sum_probs=44.2

Q ss_pred             HHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC-EEE-ECCC
Q ss_conf             9999764989988817887899998589878999999999887916731783-368-6288
Q T0586            22 MKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM-GSF-VTSD   80 (125)
Q Consensus        22 l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~-G~~-V~~~   80 (125)
                      ++..+.-..-+.+..+ |..++|+.+|+|+.++++.++.|...|+|.+.+|. |-| .+.+
T Consensus        11 i~~L~~La~~~~~~~~-t~~~IA~~~~i~~~~v~kil~~L~~~Glv~s~~G~~GG~~L~~~   70 (83)
T PF02082_consen   11 IRILIYLARQPDGKPV-TSKEIAERLGISPSYVRKILQKLRKAGLVKSVRGRGGGYRLARD   70 (83)
T ss_dssp             HHHHHHHHCSTTCC----HHHHHHHHTS-HHHHHHHHHHHHHTTSEE---------EESS-
T ss_pred             HHHHHHHHHCCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCCCCCEEECCC
T ss_conf             9999999809999849-89999988890999999999999888987623678778202289


No 7  
>PF05732 RepL:  Firmicute plasmid replication protein (RepL);  InterPro: IPR008813 This family consists of Firmicute RepL proteins which are involved in plasmid replication.; GO: 0006260 DNA replication, 0006276 plasmid maintenance
Probab=96.61  E-value=0.0024  Score=40.19  Aligned_cols=48  Identities=25%  Similarity=0.424  Sum_probs=40.3

Q ss_pred             CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCC
Q ss_conf             9888178878999985898789999999998879167317833686288
Q T0586            32 KGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSD   80 (125)
Q Consensus        32 ~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~   80 (125)
                      -.+.-+.|.+++|+.+|+|+.||.++++.|++.|+|...+ .|+|.-.+
T Consensus        70 ~~N~v~~t~~~Ia~~lgiS~~Tv~r~iK~L~ek~iI~k~~-~G~Y~iNP  117 (165)
T PF05732_consen   70 SDNAVVATQKEIAEELGISKPTVSRTIKELEEKGIIKKIK-NGTYFINP  117 (165)
T ss_pred             CCCEEEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEC-CCEEEECH
T ss_conf             7983987899999997988889999999998799789823-98799883


No 8  
>PF03444 DUF293:  Domain of unknown function;  InterPro: IPR005104 This domain is always found N-terminal to a pair of cystathionine-beta-synthase (CBS) domains IPR000644 from INTERPRO. This region may be distantly related to the HrcA proteins of prokaryotes.
Probab=96.43  E-value=0.0011  Score=42.48  Aligned_cols=57  Identities=12%  Similarity=0.195  Sum_probs=44.4

Q ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC-CEEEEC
Q ss_conf             9999976498998881788789999858987899999999988791673178-336862
Q T0586            21 WMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG-MGSFVT   78 (125)
Q Consensus        21 ~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g-~G~~V~   78 (125)
                      .|...|+.-....|+.+- -+.+|+.+++|..|||.-+..|++.|+|+..|+ +|=+|-
T Consensus         8 ~IL~~lv~~Y~~~~~PVg-Sk~ia~~l~~s~aTIRN~M~~Le~lGlve~~ph~s~GriP   65 (78)
T PF03444_consen    8 EILKALVELYIETGEPVG-SKTIAEELDRSPATIRNEMADLEELGLVESQPHPSAGRIP   65 (78)
T ss_pred             HHHHHHHHHHHHCCCCCC-HHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCCCCCC
T ss_conf             999999999997399776-6999998688908899999999987983367999988783


No 9  
>PF04703 FaeA:  FaeA-like protein;  InterPro: IPR006793 This family represents a number of fimbrial protein transcription regulators found in Gram-negative bacteria. These proteins are thought to facilitate binding of the leucine-rich regulatory protein to regulatory elements, possibly by inhibiting deoxyadenosine methylation of these elements by deoxyadenosine methylase , .; GO: 0030528 transcription regulator activity, 0045449 regulation of transcription, 0009289 fimbrium; PDB: 2htj_A 2jt1_A.
Probab=96.41  E-value=0.0022  Score=40.41  Aligned_cols=50  Identities=24%  Similarity=0.354  Sum_probs=39.6

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC-CCE
Q ss_conf             99999999997649899888178878999985898789999999998879167317-833
Q T0586            16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR-GMG   74 (125)
Q Consensus        16 ~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~-g~G   74 (125)
                      ++|.++|...        +... +.+++|+.+|+|+.++|.-+..|+.+|.|...| ++|
T Consensus         3 e~Il~~i~~~--------~~p~-~t~eiA~~~gls~~qaR~~L~~L~~eG~Vk~~~~rrG   53 (62)
T PF04703_consen    3 EKILEYIKRQ--------NGPC-STREIAEALGLSIYQARYYLQKLEKEGKVKRSPVRRG   53 (62)
T ss_dssp             HCHHHHHHHH-----------B--HHHHHHHHTS-HHHHHHHHHHHHH---EEEE-----
T ss_pred             HHHHHHHHHC--------CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCCC
T ss_conf             8899999962--------7998-8999999969889999999999988797785205788


No 10 
>PF01978 TrmB:  Sugar-specific transcriptional regulator TrmB;  InterPro: IPR002831   TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively . Other members of this family are annotated as either transcriptional regulators or hypothetical proteins.  ; PDB: 2d1h_A 1sfx_A.
Probab=96.16  E-value=0.002  Score=40.65  Aligned_cols=38  Identities=26%  Similarity=0.404  Sum_probs=35.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf             87899998589878999999999887916731783368
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF   76 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~   76 (125)
                      +..+||+.+|+|++||.++++.|++.|+|+...++...
T Consensus        24 t~~eia~~~~i~~~~v~~~l~~L~~~GlV~~~~~~~~~   61 (68)
T PF01978_consen   24 TASEIAEKLGISRSTVYRILKRLEEKGLVEREKGKPKK   61 (68)
T ss_dssp             EHHHHHHHHT--HHHHHHHHHHHHH---EEEEE----E
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEE
T ss_conf             99999999890999999999999988998997685069


No 11 
>PF04492 Phage_rep_O:  Bacteriophage replication protein O      ;  InterPro: IPR006497   This set of protein sequences, defined by an N-terminal domain, represent phage lambda replication protein O and other homologous phage and prophage proteins. ; GO: 0006260 DNA replication
Probab=95.58  E-value=0.011  Score=35.92  Aligned_cols=45  Identities=27%  Similarity=0.265  Sum_probs=39.4

Q ss_pred             CCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             4989988817887899998589878999999999887916731783
Q T0586            28 TGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM   73 (125)
Q Consensus        28 ~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~   73 (125)
                      .|.=++++++ |-.++++..|+|+.+|.+|++.|...|+|.+..+.
T Consensus        46 yG~nK~~d~I-s~sq~~e~tg~~~~~V~~al~~Li~~~vi~~~G~~   90 (100)
T PF04492_consen   46 YGWNKKMDRI-SNSQIAEMTGISRDHVSRALKELIRMNVIIIEGRQ   90 (100)
T ss_pred             CCCCCCCHHE-EHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECCCE
T ss_conf             3889840040-09999988698989999999999975887644937


No 12 
>PF08784 RPA_C:  Replication protein A C terminal;  InterPro: IPR014892   This protein corresponds to the C terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1quq_A 2pqa_C 2pi2_C 1l1o_B 1z1d_A 2z6k_B 1dpu_A.
Probab=95.44  E-value=0.0083  Score=36.60  Aligned_cols=54  Identities=28%  Similarity=0.501  Sum_probs=43.8

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEC
Q ss_conf             898899999999999764989988817887899998589878999999999887916731
Q T0586            11 DKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAK   70 (125)
Q Consensus        11 ~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~   70 (125)
                      ..|+.++|++.|+.   +..-  .+=+ ++.+|++.++++...|++|+..|.++|+|++-
T Consensus        45 ~~~~~~~Vl~~i~~---~~~~--~eGv-~v~~i~~~l~~~~~~v~~a~~~L~~eG~IYsT   98 (102)
T PF08784_consen   45 LSPLQQRVLNFIKQ---SPQS--EEGV-HVDEIAQKLGMPENEVRKAIDELSDEGLIYST   98 (102)
T ss_dssp             --HHHHHHHHHHHC--------------BHHHHHHHSTS-HHHHHHHHHHHHH---EEES
T ss_pred             CCHHHHHHHHHHHH---CCCC--CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCEEECC
T ss_conf             88899999999984---4688--7871-89999999693999999999999859847266


No 13 
>PF01710 Transposase_14:  Transposase;  InterPro: IPR002622   Transposase proteins are necessary for efficient DNA transposition. This family includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily .   More information about these proteins can be found at Protein of the Month: Transposase .
Probab=95.12  E-value=0.028  Score=33.12  Aligned_cols=89  Identities=21%  Similarity=0.225  Sum_probs=52.3

Q ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999764989988817887899998589878999999999887916731783368628807899999999999999999
Q T0586            21 WMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFL  100 (125)
Q Consensus        21 ~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~~~~~~~~~~~~~~~~~~~~~  100 (125)
                      +|+..|+. .+..|.   |.++.|..||||++||.+-++ -...|.+...++.+..+  +...+......--...+   .
T Consensus         6 DlR~kvi~-~~~~G~---S~~eaA~~F~VS~~Tv~rW~k-~~~~G~~~~~~r~~~Ki--d~e~l~~~v~~~~d~tl---~   75 (119)
T PF01710_consen    6 DLRQKVIA-YVEQGM---SIREAAKRFGVSRSTVYRWLK-RRETGDLKPKPRGRKKI--DAEELKELVEENPDITL---K   75 (119)
T ss_pred             HHHHHHHH-HHHCCC---CHHHHHHHHCCCHHHHHHHHH-HHHCCCCCCCCCCCCCC--CHHHHHHHHHHCCCCCH---H
T ss_conf             99999999-999599---999999996955999999998-64113446788765402--59999999998889769---9


Q ss_pred             HHHHHCCCCHHHHHHHHHH
Q ss_conf             9999819999899999999
Q T0586           101 EEAKSIGLDDQTAIELLIK  119 (125)
Q Consensus       101 ~~~~~~~~~~~~~~~l~~~  119 (125)
                      +.+..+|++...+..++.+
T Consensus        76 Ela~~~~vs~~ti~r~Lkr   94 (119)
T PF01710_consen   76 ELAEKLGVSKSTISRALKR   94 (119)
T ss_pred             HHHHHCCCCHHHHHHHHHH
T ss_conf             9999929989999999998


No 14 
>PF03428 RP-C:  Replication protein C N-terminal domain;  InterPro: IPR005090   Proteins in this group have homology with the RepC protein of Agrobacterium Ri and Ti plasmids . They may be involved in plasmid replication and stabilisation functions.
Probab=94.66  E-value=0.05  Score=31.45  Aligned_cols=55  Identities=22%  Similarity=0.414  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHCCCCCCCCC---CCCHHHHHHHH-CCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf             99999999976498998881---78878999985-898789999999998879167317
Q T0586            17 QISDWMKKQMITGEWKGEDK---LPSVREMGVKL-AVNPNTVSRAYQELERAGYIYAKR   71 (125)
Q Consensus        17 qI~~~l~~~I~~G~l~~G~~---LPser~La~~~-~VSr~TVr~Al~~L~~~G~i~~~~   71 (125)
                      .+-+.|...--...|.+|..   .||-.+||... |+|.+|+|+.+..|.+-|+|..+.
T Consensus        47 ~vL~aLlsf~~~~d~~~~~~~iVfpSN~~La~r~~G~s~~tlrRhla~LveaGLI~r~D  105 (177)
T PF03428_consen   47 AVLDALLSFTPEDDWSGGRRPIVFPSNAQLAERLHGMSERTLRRHLARLVEAGLIVRRD  105 (177)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCEEECCHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEC
T ss_conf             99999997688634578887255208999999985999899999999999889846412


No 15 
>PF08222 HTH_CodY:  CodY helix-turn-helix domain;  InterPro: IPR013198   This family consists of the C-terminal helix-turn-helix domain found in several bacterial GTP-sensing transcriptional pleiotropic repressor CodY proteins. CodY has been found to repress the dipeptide transport operon (dpp) of Bacillus subtilis in nutrient-rich conditions . The CodY protein also has a repressor effect on many genes in Lactococcus lactis during growth in milk .; PDB: 2b0l_C.
Probab=94.43  E-value=0.01  Score=35.96  Aligned_cols=44  Identities=16%  Similarity=0.343  Sum_probs=38.2

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC--CEEEECCCHH
Q ss_conf             8789999858987899999999988791673178--3368628807
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG--MGSFVTSDKA   82 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g--~G~~V~~~~~   82 (125)
                      .-.++|++.|++++++-+|++.|+.-|+|+.+.-  +|||+.--..
T Consensus         6 taS~IAd~vGiTrSvivnaLRKlESAGVIe~rslgmkGtyikvln~   51 (61)
T PF08222_consen    6 TASKIADRVGITRSVIVNALRKLESAGVIESRSLGMKGTYIKVLND   51 (61)
T ss_dssp             -HHHHHCC----HHHHHHHHHHHHH---EEEE-------EEEE--T
T ss_pred             HHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCCCCCEEEEECCH
T ss_conf             0888888848839999999998886385311346776047531038


No 16 
>PF01047 MarR:  MarR family;  InterPro: IPR000835   The marR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the marR/slyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli marR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the marR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the marR-like regulators respond to aromatic compounds , , .   The crystal structures of marR, mexR and slyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerization. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerization, as most marR-like transcription regulators form dimers , . ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3bj6_A 2fbi_A 3e6m_E 3cjn_A 3cdh_A 2fxa_B 2fa5_B 1lnw_B 3ech_A 1jgs_A ....
Probab=94.36  E-value=0.018  Score=34.41  Aligned_cols=36  Identities=28%  Similarity=0.393  Sum_probs=33.0

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             887899998589878999999999887916731783
Q T0586            38 PSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM   73 (125)
Q Consensus        38 Pser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~   73 (125)
                      .+..+||+.++++++|+.+.++.|++.|||++.+..
T Consensus        18 ~t~~~la~~l~~~~~~vs~~i~~L~~~glI~r~~~~   53 (59)
T PF01047_consen   18 MTQSELAERLGISKSTVSRIIKRLEKKGLIEREPDP   53 (59)
T ss_dssp             EEHHHHHHHHTS-HHHHHHHHHHHHHTTSEEEEEET
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             899999999886873899999999988987872899


No 17 
>PF09339 HTH_IclR:  IclR helix-turn-helix domain;  InterPro: IPR005471   The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these subfamilies, called 'iclR', groups several proteins including: gylR, a possible activator protein for the gylABX glycerol operon in Streptomyces. iclR, the repressor of the acetate operon (also known as glyoxylate bypass operon) in Escherichia coli and Salmonella typhimurium.    These proteins have a Helix-Turn-Helix motif at the N-terminus that is similar to that of other DNA-binding proteins .; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2ia2_C 2g7u_D 2o0y_D 1mkm_B.
Probab=94.08  E-value=0.024  Score=33.56  Aligned_cols=37  Identities=30%  Similarity=0.442  Sum_probs=33.1

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf             88178878999985898789999999998879167317
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR   71 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~   71 (125)
                      +..+ +..++|+.+|++++|+.+-+..|++.|||+..|
T Consensus        16 ~~~~-t~~eia~~~gl~~st~~r~l~~L~~~g~v~~d~   52 (52)
T PF09339_consen   16 PRPL-TLSEIARALGLPKSTVHRLLQTLEEAGFVERDP   52 (52)
T ss_dssp             BSSE-EHHHHHHHTT--HHHHHHHHHHHHHT--EEE--
T ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEECC
T ss_conf             9998-999999998919999999999999991942092


No 18 
>PF00325 Crp:  Bacterial regulatory proteins, crp family;  InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA , . Within this family, the HTH motif is situated towards the C-terminus. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2gzw_A 1o3q_A 1lb2_A 1i6x_A 1ruo_B 1hw5_B 1zrf_A 1i5z_B 1j59_B 1o3s_A ....
Probab=93.63  E-value=0.028  Score=33.16  Aligned_cols=29  Identities=31%  Similarity=0.440  Sum_probs=27.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCEE
Q ss_conf             87899998589878999999999887916
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAGYI   67 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G~i   67 (125)
                      +-.+||+..|.+|.||.+.++.|.++|+|
T Consensus         4 t~~elA~~~G~tretvsR~l~~l~~~GlI   32 (32)
T PF00325_consen    4 THQELADLLGTTRETVSRILSRLRKEGLI   32 (32)
T ss_dssp             -HHHHHHHCTC-HHHHHHHHHHHHHTTSE
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCC
T ss_conf             99999988698699999999999996799


No 19 
>PF03965 Pencillinase_R:  Penicillinase repressor;  InterPro: IPR005650   Proteins in this entry are transcriptional regulators found in a variety of bacteria and a small number of archaea. Many are BlaI/MecI proteins which regulate resistance to penicillins (beta-lactams), though at least one protein (Q47839 from SWISSPROT) appears to be involved in the regulation of copper homeostasis . BlaI regulators repress the expression of penicillin-degrading enzymes (penicillinases) until the cell encounters the antiobiotic, at which point repression ceases and penicillinase expression occurs, allowing cell growth . MecI regulators repress the expression of MecA, a cell-wall biosynthetic enzyme not inhibited by penicillins at clinically achievable concentrations, until the presence of the antibiotic is detected . At this point repression ends and MecA expression occurs which, together with the switching off of the penicillin-sensitive enzymes, allows the cell to grow despite the presence of antibiotic.; GO: 0003677 DNA binding, 0016566 specific transcriptional repressor activity, 0016481 negative regulation of transcription; PDB: 1sd4_B 1xsd_A 1sd7_A 1sd6_A 2d45_A 1okr_A 1sax_A 1p6r_A 2p7c_B 2k4b_A ....
Probab=93.56  E-value=0.12  Score=29.09  Aligned_cols=92  Identities=20%  Similarity=0.233  Sum_probs=52.8

Q ss_pred             HHHHCCCCCCCCCCCCHHHHHHHHCCC----HHHHHHHHHHHHHCCEEEECCCCEEEEC----CCHHHHHHHHHHHHH--
Q ss_conf             997649899888178878999985898----7899999999988791673178336862----880789999999999--
Q T0586            24 KQMITGEWKGEDKLPSVREMGVKLAVN----PNTVSRAYQELERAGYIYAKRGMGSFVT----SDKALFDQLKKELAD--   93 (125)
Q Consensus        24 ~~I~~G~l~~G~~LPser~La~~~~VS----r~TVr~Al~~L~~~G~i~~~~g~G~~V~----~~~~~~~~~~~~~~~--   93 (125)
                      ..|+.-.|..|. + +.+++.+.++-.    ++||+-.+.+|.+.|+|.+....+.|+-    ............+..  
T Consensus         6 ~~IM~~lW~~~~-~-t~~ei~~~l~~~~~~~~sTV~t~L~rL~eKg~l~~~~~gr~~~Y~~~i~~~e~~~~~~~~~l~~~   83 (115)
T PF03965_consen    6 LEIMEILWEHGP-I-TVREIVEELKEDRDWSYSTVQTLLNRLVEKGLLTREKIGRAYIYSPLISREEYLRQELKQLLDRF   83 (115)
T ss_dssp             HHHHHHHHCHSS-E-EHHHHHHHHCTTSS--HHHHHHHHHHHHHTTSEEEEEETTCEEEEESSSHHHHHHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCC-C-CHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCEEEEECCCCEEEEECCCHHHHHHHHHHHHHHHH
T ss_conf             999999995799-7-79999999861316418789999999998898577713884588747889999999999999998


Q ss_pred             --HHHHHHHHHH-HHCCCCHHHHHHHH
Q ss_conf             --9999999999-98199998999999
Q T0586            94 --AITERFLEEA-KSIGLDDQTAIELL  117 (125)
Q Consensus        94 --~~~~~~~~~~-~~~~~~~~~~~~l~  117 (125)
                        .....++... ....++++++.+|-
T Consensus        84 ~~gs~~~ll~~l~~~~~ls~~el~~L~  110 (115)
T PF03965_consen   84 FDGSLSALLAALLDEEELSPEELEELR  110 (115)
T ss_dssp             S---HHHHHHHHHHCT-S-HHHHHHHH
T ss_pred             HCCCHHHHHHHHHHCCCCCHHHHHHHH
T ss_conf             688999999999856799999999999


No 20 
>PF01022 HTH_5:  Bacterial regulatory protein, arsR family;  InterPro: IPR001845   Bacterial transcription regulatory proteins that bind DNA via a helix-turn-helix (HTH) motif can be grouped into families on the basis of sequence similarities. One such group, termed arsR, includes several proteins that appear to dissociate from DNA in the presence of metal ions: arsR, which functions as a transcriptional repressor of an arsenic resistance operon; smtB from Synechococcus sp. (strain PCC 7942), which acts as a transcriptional repressor of the smtA gene that codes for a metallothionein; cadC, a protein required for cadmium-resistance; and hypothetical protein yqcJ from Bacillus subtilis.   The HTH motif is thought to be located in the central part of these proteins . The motif is characterised by a number of well-conserved residues: at its N-terminal extremity is a cysteine residue; a second Cys is found in arsR and cadC, but not in smtA; and at the C-terminus lie one or two histidines. These residues may be involved in metal-binding (Zn in smtB; metal-oxyanions such as arsenite, antimonite and arsenate for arsR; and cadmium for cadC) . It is believed that binding of a metal ion could induce a conformational change that would prevent the protein from binding DNA .   The crystal structure of the cyanobacterial smtB shows a fold of five alpha-helices (H) and a pair of antiparallel beta-strands (B) in the topology H1-H2-H3-H4-B1-B2-H5. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing as in other wHTH, such as the dtxR-type or the merR-type. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. Most arsR/smtB-like metalloregulators form homodimers . The dimer interface is formed by helix 5 and an N-terminal part . Two distinct metal-binding sites have been identified. The first site comprises cysteine thiolates located in the HTH in helix 3 and for some cases in the N-terminus, called the alpha3(N) site . The second metal-binding site is located in helix 5 (and C-terminus) and is called the alpha5(C) site. The alpha3N site binds large thiophilic, toxic metals including Cd, Pb, and Bi, as in S. aureus cadC. ArsR lacks the N-terminal arm and its alpha3 site coordinates smaller thiophilic ions like As and Sb. The alpha5 site contains carboxylate and imidazole ligands and interacts preferentially with biologically required metal ions including Zn, Co, and Ni. ArsR-type metalloregulators contain one of these sites, both, or other potential metal-binding sites , . Binding of metal ions to these sites leads to allosteric changes that can derepress the operator/promotor DNA. The metal-inducible operons contain one or two imperfect 12-2-12 inverted repeats, which can be recognized by multimeric arsR-type metalloregulators. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1uly_A 2cwe_A 1ku9_A 3gw2_A 2p4w_B 3f6v_A 3f6o_B 2oqg_D 2ia0_B 2zny_C ....
Probab=92.96  E-value=0.047  Score=31.63  Aligned_cols=32  Identities=41%  Similarity=0.592  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEE
Q ss_conf             788789999858987899999999988791673
Q T0586            37 LPSVREMGVKLAVNPNTVSRAYQELERAGYIYA   69 (125)
Q Consensus        37 LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~   69 (125)
                      + +..++++.+|+|++||.+-++.|++.|+|..
T Consensus        16 ~-~~~eia~~l~~s~~tvs~HL~~L~~~glV~~   47 (47)
T PF01022_consen   16 L-SVSEIAEELGISQSTVSRHLKKLEEAGLVKK   47 (47)
T ss_dssp             E-EHHHHHHHHTS-HHHHHHHHHHHHHTTSEEE
T ss_pred             C-CHHHHHHHHCCCHHHHHHHHHHHHHCCCCCC
T ss_conf             6-7999883612356589999999999808419


No 21 
>PF07848 PaaX:  PaaX-like protein;  InterPro: IPR012906   This entry describes the N-terminal region of proteins that are similar to, and nclude, the product of the paaX gene of Escherichia coli (P76086 from SWISSPROT). PaaX is a transcriptional regulator that is always found in association with operons believed to be involved in the degradation of phenylacetic acid . The gene product has been shown to bind to the promoter sites and repress their transcription . 
Probab=92.68  E-value=0.064  Score=30.77  Aligned_cols=44  Identities=16%  Similarity=0.163  Sum_probs=34.6

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC---EEEECC
Q ss_conf             17887899998589878999999999887916731783---368628
Q T0586            36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM---GSFVTS   79 (125)
Q Consensus        36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~---G~~V~~   79 (125)
                      .+.+.-.+++.||||...||-|+.+|..+||++..+.-   ++..++
T Consensus        22 ~~~~Li~l~~~~Gi~e~avR~Al~RL~~~G~l~~~r~GR~s~Y~Lt~   68 (70)
T PF07848_consen   22 WVGSLIRLLEAFGISERAVRTALSRLVKEGWLESERRGRRSYYRLTE   68 (70)
T ss_pred             EHHHHHHHHHHCCCCCHHHHHHHHHHHHCCCEEEEEECCCCEEEECC
T ss_conf             19999999998299905899999999873866757607832477488


No 22 
>PF06163 DUF977:  Bacterial protein of unknown function (DUF977);  InterPro: IPR010382   This family consists of several hypothetical bacterial proteins of unknown function.
Probab=92.04  E-value=0.071  Score=30.48  Aligned_cols=46  Identities=20%  Similarity=0.384  Sum_probs=39.5

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCC
Q ss_conf             88178878999985898789999999998879167317833686288
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSD   80 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~   80 (125)
                      .-++ +.++|...+|+||+|+++-+..|.+.|-|+..-..|.|=.+.
T Consensus        24 ~GRi-Ti~ql~~~TG~sR~T~k~~lr~Lv~~G~v~~~G~~GiFpseq   69 (127)
T PF06163_consen   24 HGRI-TIRQLVKMTGASRNTAKKYLRELVESGDVYRHGRCGIFPSEQ   69 (127)
T ss_pred             HCHH-HHHHHHHHHCCCHHHHHHHHHHHHHCCCEECCCCCCCCCCHH
T ss_conf             1630-299999997867999999999999738831168767584199


No 23 
>PF03297 Ribosomal_S25:  S25 ribosomal protein;  InterPro: IPR004977   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .    The S25 ribosomal protein is a component of the 40S ribosomal subunit.
Probab=91.70  E-value=0.065  Score=30.71  Aligned_cols=50  Identities=24%  Similarity=0.285  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf             99999999997649899888178878999985898789999999998879167317
Q T0586            16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR   71 (125)
Q Consensus        16 ~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~   71 (125)
                      ...++.|...|-      ..++-+...||+.|+|+-+.+|+||+.|+.+|+|...-
T Consensus        44 k~t~dki~kEV~------k~K~ITps~l~erlkI~~SlAr~~Lr~L~~~G~Ik~V~   93 (105)
T PF03297_consen   44 KETYDKILKEVP------KYKLITPSVLSERLKINGSLARKALRELEEKGLIKPVS   93 (105)
T ss_pred             HHHHHHHHHHHH------HCCEECHHHHHHHHHHHHHHHHHHHHHHHHCCCEEEEE
T ss_conf             999999999840------06330399987777424899999999999789989984


No 24 
>PF09397 Ftsk_gamma:  Ftsk gamma domain; PDB: 2ve8_D 2ve9_C 2j5o_A 2j5p_A.
Probab=90.37  E-value=0.31  Score=26.25  Aligned_cols=58  Identities=17%  Similarity=0.374  Sum_probs=49.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf             88898899999999999764989988817887899998589878999999999887916731783368
Q T0586             9 HADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF   76 (125)
Q Consensus         9 ~~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~   76 (125)
                      +..-|+|.++.+.+..          +.-.|..-|-..|+|..+-+.+-+..|+.+|+|.-..|+|..
T Consensus         2 ~~~D~ly~~a~~~V~~----------~~~~S~S~lQR~lrIGYnrAariid~LE~~GiVs~~~~~~~R   59 (65)
T PF09397_consen    2 DEEDPLYDEAVEFVIE----------EGKASISLLQRRLRIGYNRAARIIDQLEEEGIVSPANGSKPR   59 (65)
T ss_dssp             -TTSTTHHHHHHHHHH----------CTCESHHHHHHHHT---HHHHHHHHHHHH---BE-------E
T ss_pred             CCCCHHHHHHHHHHHH----------HCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             5210899999999998----------087579999999714799999999999988777887799898


No 25 
>PF12298 Bot1p:  Eukaryotic mitochondrial regulator protein 
Probab=89.76  E-value=0.32  Score=26.20  Aligned_cols=55  Identities=20%  Similarity=0.294  Sum_probs=45.7

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf             77776888988999999999997649899888178878999985898789999999998879
Q T0586             4 MNPTFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAG   65 (125)
Q Consensus         4 M~~~~~~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G   65 (125)
                      +|..|.+..+|.+.+.+.|-+.+..+..       |.+++|..|||+...|.-.++.-+-++
T Consensus         7 ~Np~f~~~~~lse~lr~~I~~~v~~~~~-------sv~~vS~kygi~~~RV~AIvrL~eiEk   61 (172)
T PF12298_consen    7 LNPHFRSNPVLSEELRQEIYEDVMEKGK-------SVREVSVKYGIKMQRVEAIVRLKEIEK   61 (172)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCC-------CHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             9987678776799999999999982896-------899999996977899999999999999


No 26 
>PF05043 Mga:  Mga helix-turn-helix domain;  InterPro: IPR007737 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions . The family also contains VirR like proteins which match only at the C terminus of the alignment.
Probab=89.22  E-value=0.68  Score=24.02  Aligned_cols=52  Identities=13%  Similarity=0.289  Sum_probs=40.1

Q ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHH----HHCCEEEECCCCEEEECCCHHHHHHH
Q ss_conf             88817887899998589878999999999----88791673178336862880789999
Q T0586            33 GEDKLPSVREMGVKLAVNPNTVSRAYQEL----ERAGYIYAKRGMGSFVTSDKALFDQL   87 (125)
Q Consensus        33 ~G~~LPser~La~~~~VSr~TVr~Al~~L----~~~G~i~~~~g~G~~V~~~~~~~~~~   87 (125)
                      ..+.+ +..+||+.+.||++|+.+-++.+    ..-|+--  ++.|..+..++..+...
T Consensus        27 ~~~~~-~~~~la~~l~vS~sTi~~~lk~i~~~L~~~~l~l--~~~~~~i~G~E~~iR~~   82 (87)
T PF05043_consen   27 NNEYV-SIEDLAEELYVSRSTIYRDLKKINQILKKYGLKL--KKKGLRIEGSEKNIRYF   82 (87)
T ss_pred             CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHCCEEE--CCCCEEEEECHHHHHHH
T ss_conf             48996-8999999979899999999999999999959076--38994798079999999


No 27 
>PF04967 HTH_10:  HTH DNA binding domain;  InterPro: IPR007050   Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium halobium and described as a putative bacterio-opsin activator. 
Probab=88.37  E-value=0.56  Score=24.55  Aligned_cols=44  Identities=16%  Similarity=0.324  Sum_probs=35.8

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             999999976498998881788789999858987899999999988
Q T0586            19 SDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELER   63 (125)
Q Consensus        19 ~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~   63 (125)
                      .+.|......|.|..--.. +..+||+++|||++|+.+-++.-+.
T Consensus         6 ~e~L~~A~~~GYfd~PR~~-tl~elA~~lgis~~T~~~~LRrae~   49 (53)
T PF04967_consen    6 REVLRTAYEMGYFDWPRRI-TLEELAEELGISKSTFSEHLRRAER   49 (53)
T ss_pred             HHHHHHHHHCCCCCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             9999999986887798758-8999998949999999999999999


No 28 
>PF01090 Ribosomal_S19e:  Ribosomal protein S19e;  InterPro: IPR001266   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   This family includes a number of eukaryotic and archaebacterial ribosomal proteins; mammalian S19, Drosophila S19, Ascaris lumbricoides S19g (ALEP-1) and S19s, yeast YS16 (RP55A and RP55B), Aspergillus S16 and Haloarcula marismortui HS12.; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005622 intracellular, 0005840 ribosome; PDB: 2v7f_A.
Probab=87.44  E-value=0.45  Score=25.23  Aligned_cols=63  Identities=19%  Similarity=0.266  Sum_probs=43.6

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC--------------CCHHHHHHHHHHHHHCCEEEECCCCEEEECCC
Q ss_conf             9999999999976498998881788789999858--------------98789999999998879167317833686288
Q T0586            15 YSQISDWMKKQMITGEWKGEDKLPSVREMGVKLA--------------VNPNTVSRAYQELERAGYIYAKRGMGSFVTSD   80 (125)
Q Consensus        15 y~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~--------------VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~   80 (125)
                      |.+.+.-++.-=+.|      .+ ++..|+..||              -|.+-+|.+++.|+..|+|+..++.|-.+++.
T Consensus        51 Y~RaASilRklY~~g------~v-Gv~~lr~~YGg~k~rG~rP~h~~~asg~iiR~~lQqLE~~glvek~~~~GR~lT~~  123 (139)
T PF01090_consen   51 YIRAASILRKLYIRG------PV-GVGRLRKIYGGRKRRGVRPSHFVKASGSIIRKILQQLEKAGLVEKDPKGGRRLTPK  123 (139)
T ss_dssp             HHHHHHHHHHHHH-------------HHHHHH----------TTS-------HHHHHHHHHHH---EE-------EE---
T ss_pred             HHHHHHHHHHHHHCC------CC-CHHHHHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEECCCCCCEECHH
T ss_conf             999999999998249------97-57899999787778999998646776189999999998689867769999788984


Q ss_pred             HHHH
Q ss_conf             0789
Q T0586            81 KALF   84 (125)
Q Consensus        81 ~~~~   84 (125)
                      -...
T Consensus       124 G~~~  127 (139)
T PF01090_consen  124 GRSD  127 (139)
T ss_dssp             --HH
T ss_pred             HHHH
T ss_conf             7999


No 29 
>PF07900 DUF1670:  Protein of unknown function (DUF1670);  InterPro: IPR012872   The hypothetical eukaryotic proteins found in this family are of unknown function. 
Probab=87.43  E-value=0.36  Score=25.88  Aligned_cols=55  Identities=22%  Similarity=0.413  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC-CEEEECCCC
Q ss_conf             99999999764989988817887899998589878999999999887-916731783
Q T0586            18 ISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERA-GYIYAKRGM   73 (125)
Q Consensus        18 I~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~-G~i~~~~g~   73 (125)
                      +.......|..-.|.-|--| +..+||..|++|+.||++-++.++.+ |.+.-.+|.
T Consensus        87 l~~~~ivRl~~EA~dQgalL-T~~Dla~LL~~S~~TI~~~vk~ye~~~g~vvPtRG~  142 (220)
T PF07900_consen   87 LRKHRIVRLFNEAYDQGALL-TQEDLAILLGVSPKTISRDVKEYEEEHGEVVPTRGT  142 (220)
T ss_pred             HHHHHHHHHHHHHHHCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCCCCCCC
T ss_conf             99999999999998647857-599999998889888999999999961965235762


No 30 
>PF01638 HxlR:  HxlR-like helix-turn-helix;  InterPro: IPR002577   The hxlR-type HTH domain is a domain of ~90-100 amino acids present in putative transcription regulators with a winged helix-turn-helix (wHTH) structure. The domain is named after Bacillus subtilis hxlR, a transcription activator of the hxlAB operon involved in the detoxification of formaldehyde . The hxlR-type domain forms the core of putative transcription regulators and of hypothetical proteins occurring in eubacteria as well as in archaea. The sequence and structure of hxlR-type proteins show similarities with the marR-type wHTH .     The crystal structure of ytfH resembles the DNA-binding domains of winged helix proteins, containing a three helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-H2-B1-H3-H4-B2-B3-H5-H6. This topology corresponds with that of the marR-type DNA-binding domain, wherein helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing.  ; PDB: 1z7u_A 2f2e_B 3df8_A 2hzt_C 2fsw_A 1yyv_B.
Probab=85.78  E-value=0.57  Score=24.54  Aligned_cols=48  Identities=19%  Similarity=0.243  Sum_probs=36.3

Q ss_pred             CHHHHHHHH-CCCHHHHHHHHHHHHHCCEEEECCC------CEEEECCCHHHHHH
Q ss_conf             878999985-8987899999999988791673178------33686288078999
Q T0586            39 SVREMGVKL-AVNPNTVSRAYQELERAGYIYAKRG------MGSFVTSDKALFDQ   86 (125)
Q Consensus        39 ser~La~~~-~VSr~TVr~Al~~L~~~G~i~~~~g------~G~~V~~~~~~~~~   86 (125)
                      .-.+|.+.+ |||..+..+.++.|++.|+|.+...      ..|.+++....+..
T Consensus        20 rf~el~~~l~gis~~~Ls~rL~~Le~~glv~r~~~~~~p~~v~Y~LT~~G~~l~~   74 (90)
T PF01638_consen   20 RFNELQRSLPGISPKVLSQRLKELEENGLVERRVYPEVPPRVEYSLTEKGKDLLP   74 (90)
T ss_dssp             EHHHHHHH-TTS-HHHHHHHHHHHHH---EEEEEE-SSS-EEEEEE-----CCHH
T ss_pred             CHHHHHHHCCCCCHHHHHHHHHHHHHCCCEEEEECCCCCCCCEEECCCCHHHHHH
T ss_conf             8999997740557778999999999778814654489998654756816999999


No 31 
>PF09012 FeoC:  FeoC like transcriptional regulator;  InterPro: IPR015102   This set of hypothetical proteins is found in prokaryotes. ; PDB: 2k02_A 1xn7_A.
Probab=85.40  E-value=0.26  Score=26.74  Aligned_cols=37  Identities=22%  Similarity=0.405  Sum_probs=33.2

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             17887899998589878999999999887916731783
Q T0586            36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM   73 (125)
Q Consensus        36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~   73 (125)
                      .. |..+||.+|++|+.+|+.-+..|...|.|....-.
T Consensus        14 ~~-s~~eLa~~f~~s~~~v~aMLe~l~~kG~i~k~~~~   50 (69)
T PF09012_consen   14 RV-SLSELARHFGISPDAVEAMLEQLIRKGKIEKVEDS   50 (69)
T ss_dssp             -E-EHHHHHHHTT--HHHHHHHHHHHHC---EEEEEEE
T ss_pred             CC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             81-89999999790999999999999988916873169


No 32 
>PF02002 TFIIE_alpha:  TFIIE alpha subunit;  InterPro: IPR002853 The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha P29083 from SWISSPROT and TFIIE-beta P29084 from SWISSPROT and joins the preinitiation complex after RNA polymerase II and TFIIF . This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits also .; GO: 0003702 RNA polymerase II transcription factor activity, 0006367 transcription initiation from RNA polymerase II promoter, 0005673 transcription factor TFIIE complex; PDB: 1q1h_A 1vd4_A.
Probab=84.85  E-value=0.29  Score=26.51  Aligned_cols=35  Identities=11%  Similarity=0.251  Sum_probs=31.8

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf             178878999985898789999999998879167317
Q T0586            36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR   71 (125)
Q Consensus        36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~   71 (125)
                      .+ ++.+||+.+|++..++|+.+..|.++|+|..+.
T Consensus        27 ~l-~ee~La~~l~i~~k~lR~~L~~L~e~~lv~~~~   61 (105)
T PF02002_consen   27 EL-TEEDLAELLGIKSKELRKILYKLYEDKLVKYRR   61 (105)
T ss_dssp             -B--HHHHHHTT-S-HHHHHHHHHHHHH----EEEE
T ss_pred             CC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf             90-899999890999899999999999889837898


No 33 
>PF05225 HTH_psq:  helix-turn-helix, Psq domain;  InterPro: IPR007889   This DNA-binding motif is found in four copies in the pipsqueak protein of Drosophila melanogaster . In pipsqueak this domain binds to GAGA sequence . The pipsqueak family, which includes proteins from fungi, sea urchins, nematodes, insects, and vertebrates appear to be proteins essential for sequence-specific targeting of a polycomb group protein complex .; GO: 0003677 DNA binding, 0005634 nucleus; PDB: 2cob_A.
Probab=84.64  E-value=0.23  Score=27.13  Aligned_cols=29  Identities=28%  Similarity=0.308  Sum_probs=23.4

Q ss_pred             CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9988817887899998589878999999999
Q T0586            31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQEL   61 (125)
Q Consensus        31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L   61 (125)
                      +..|. + |.++.|..|||+++|++..++.-
T Consensus        12 v~~g~-~-Si~~aA~~ygVp~sTL~~r~~g~   40 (45)
T PF05225_consen   12 VKNGK-L-SIRKAARKYGVPRSTLRRRLKGK   40 (45)
T ss_dssp             HH-------HHHHHHH----HHHHHHHHHH-
T ss_pred             HHCCC-C-CHHHHHHHHCCCHHHHHHHHCCC
T ss_conf             99099-5-79999999893989999999278


No 34 
>PF00356 LacI:  Bacterial regulatory proteins, lacI family;  InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR , . Within this family, the HTH motif is situated towards the N-terminus.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1l1m_B 2bjc_A 1lcc_A 1osl_A 2pe5_A 1lcd_A 1efa_A 1cjg_B 1lqc_A 1jwl_A ....
Probab=84.43  E-value=0.32  Score=26.19  Aligned_cols=22  Identities=23%  Similarity=0.383  Sum_probs=19.5

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             8789999858987899999999
Q T0586            39 SVREMGVKLAVNPNTVSRAYQE   60 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~   60 (125)
                      +.+++|+..|||.+||.++|..
T Consensus         1 Ti~diA~~agvS~~TVSr~Ln~   22 (46)
T PF00356_consen    1 TIKDIAKAAGVSVATVSRVLNG   22 (46)
T ss_dssp             SHHHHHHHTTSSHHHHHHHHHT
T ss_pred             CHHHHHHHHCCCHHHHHHHHCC
T ss_conf             9999998989499999999758


No 35 
>PF02796 HTH_7:  Helix-turn-helix domain of resolvase;  InterPro: IPR006120   Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur:  Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment.    Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation.   Two unrelated families of recombinases are currently known . The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second , called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1jko_C 1jkp_C 1jj8_C 1hcr_A 1jkq_C 1jj6_C 1ijw_C 1jkr_C 1zr4_B 2gm4_A ....
Probab=83.70  E-value=0.27  Score=26.66  Aligned_cols=32  Identities=22%  Similarity=0.400  Sum_probs=23.6

Q ss_pred             HHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             9999997649899888178878999985898789999999
Q T0586            20 DWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        20 ~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~   59 (125)
                      +.+.....+|       . |..++|+.|||||+||-+.+.
T Consensus        12 ~~i~~l~~~G-------~-s~~~IAk~~gvsr~TvyR~l~   43 (45)
T PF02796_consen   12 EEIRELYAQG-------M-SISEIAKRFGVSRSTVYRYLN   43 (45)
T ss_dssp             HHHHHHHH------------HHHHHHHCTS-HHHHHHHHC
T ss_pred             HHHHHHHHCC-------C-CHHHHHHHHCCCHHHHHHHHH
T ss_conf             9999999979-------9-999999998919999999974


No 36 
>PF05584 Sulfolobus_pRN:  Sulfolobus plasmid regulatory protein;  InterPro: IPR008848 This family consists of several plasmid regulatory proteins from the extreme thermophilic and acidophilic archaea Sulfolobus.
Probab=82.69  E-value=0.73  Score=23.82  Aligned_cols=33  Identities=24%  Similarity=0.388  Sum_probs=31.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC
Q ss_conf             878999985898789999999998879167317
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKR   71 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~   71 (125)
                      |..+|.+..|++++++--.+..|.++|+|++.=
T Consensus        20 tLeeL~e~Tgi~k~~llV~LsrL~k~GiI~RkW   52 (72)
T PF05584_consen   20 TLEELEEKTGIKKNELLVYLSRLAKEGIIYRKW   52 (72)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf             699999996898779999999998789266431


No 37 
>PF09681 Phage_rep_org_N:  N-terminal phage replisome organiser (Phage_rep_org_N)
Probab=81.98  E-value=1.5  Score=21.69  Aligned_cols=64  Identities=19%  Similarity=0.308  Sum_probs=48.1

Q ss_pred             HHHHHHHHHHCCCCCCC------CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCCH
Q ss_conf             99999999764989988------8178-8789999858987899999999988791673178336862880
Q T0586            18 ISDWMKKQMITGEWKGE------DKLP-SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDK   81 (125)
Q Consensus        18 I~~~l~~~I~~G~l~~G------~~LP-ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~~   81 (125)
                      ++-+++-...+|.+..+      ..+| +...||..|+.+-.||+-|+..|.+.|+|+.--+.-.++..-.
T Consensus        27 ~~I~lkLll~sgk~~~~G~L~~~~~ipyt~E~LA~~~~~~~~~V~~aL~~f~~~gmIe~~e~~~i~i~n~~   97 (121)
T PF09681_consen   27 TIIWLKLLLLSGKLNNEGKLYLSGNIPYTAEMLATIFDRPVETVRLALQVFQKLGMIEIDENGVIYITNWE   97 (121)
T ss_pred             HHHHHHHHHHHCCCCCCEEEEECCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCCEEEEECHH
T ss_conf             99999999984344788189976888986999999978878899999999987897899329908974588


No 38 
>PF00292 PAX:  'Paired box' domain;  InterPro: IPR001523   The paired box is a conserved 124 amino acid N-terminal domain of unknown function that usually, but not always, precedes a homeobox domain (see ) , . Paired box genes are expressed in alternate segments of the developing fruit fly, the observed grouping of segments into pairs depending on the position of the segment in the segmental array, and not on the identity of the segment as in the case of homeotic genes. This implies that the genes affect different processes from those altered by homeotic genes.; GO: 0007275 multicellular organismal development, 0005634 nucleus; PDB: 6pax_A 1pdn_C 1k78_E 1mdm_A 2k27_A.
Probab=78.60  E-value=1.7  Score=21.44  Aligned_cols=62  Identities=18%  Similarity=0.249  Sum_probs=47.0

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf             7688898899999999999764989988817887899998589878999999999887916731783368
Q T0586             7 TFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF   76 (125)
Q Consensus         7 ~~~~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~   76 (125)
                      -|.+.+||-..+...|.+.-..|       + +-.++|.+|+||..+|.+-+.+..+-|-|.-.+.-|..
T Consensus        11 ~f~nGRPlp~~~R~rIv~l~~~G-------~-r~~~Isr~l~VS~gcVsKIl~Ry~eTGsI~Pg~iGGsk   72 (125)
T PF00292_consen   11 VFVNGRPLPNELRQRIVELAHEG-------V-RPCDISRQLRVSHGCVSKILKRYRETGSIRPGPIGGSK   72 (125)
T ss_dssp             -------S-HHHHHHHHHHHH------------HHHHHHHHT-----HHHHHHHTTT----S--------
T ss_pred             CEECCCCCCHHHHHHHHHHHHCC-------C-CHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             00278528899999999997625-------8-77489987651476999999999986176765557999


No 39 
>PF04079 DUF387:  Putative transcriptional regulators (Ypuh-like);  InterPro: IPR005234   This family represents ScpB, which along with ScpA (IPR003768 from INTERPRO) interacts with SMC in vivo forming a complex that is required for chromosome condensation and segregation , . The SMC-Scp complex appears to be similar to the MukB-MukE-Muk-F complex in Escherichia coli , where MukB (IPR007406 from INTERPRO) is the homologue of SMC. ScpA and ScpB have little sequence similarity to MukE (IPR007385 from INTERPRO) or MukF (IPR005582 from INTERPRO), they are predicted to be structurally similar, being predominantly alpha-helical with coiled coil regions.    In general scpA and scpB form an operon in most bacterial genomes. Flanking genes are highly variable suggesting that the operon has moved throughout evolution. Bacteria containing an smc gene also contain scpA or scpB but not necessarily both. An exception is found in Deinococcus radiodurans, which contains scpB but neither smc nor scpA. In the archaea the gene order SMC-ScpA is conserved in nearly all species, as is the very short distance between the two genes, indicating co-transcription of the both in different archaeal genera and arguing that interaction of the gene products is not confined to the homologues in Bacillus subtilis. It would seem probable that, in light of all the studies, SMC, ScpA and ScpB proteins or homologues act together in chromosome condensation and segregation in all prokaryotes .  ; PDB: 1t6s_A 2z99_A.
Probab=77.72  E-value=2.1  Score=20.81  Aligned_cols=82  Identities=16%  Similarity=0.191  Sum_probs=50.1

Q ss_pred             CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC------CEEEECCCCEEEECCCHHHH---HH-----HHHHHHHHHH
Q ss_conf             9988817887899998589878999999999887------91673178336862880789---99-----9999999999
Q T0586            31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQELERA------GYIYAKRGMGSFVTSDKALF---DQ-----LKKELADAIT   96 (125)
Q Consensus        31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~------G~i~~~~g~G~~V~~~~~~~---~~-----~~~~~~~~~~   96 (125)
                      |-.|+.+ |..+|++.++ +...|++++..|..+      |+-...-+.|+.....+...   ..     ....+-...+
T Consensus         8 F~s~~pv-s~~~La~~l~-~~~~v~~~l~~L~~~y~~~~~gl~l~~~~g~y~l~tk~e~~~~v~~~~~~~~~~~LS~aal   85 (159)
T PF04079_consen    8 FASGEPV-SIKELAEILG-SEEEVREALEELQEEYEERDRGLELVEVAGGYRLQTKPEYAEYVRRLFGKPKPRKLSQAAL   85 (159)
T ss_dssp             HH-SS----HHHHHHHCT--HHHHHHHHHHHHHHHHH----EEEE------EEEE-GGGHHHHHHHHC-HHHHHHHHHHH
T ss_pred             HHCCCCC-CHHHHHHHHC-CHHHHHHHHHHHHHHHCCCCCCEEEEEECCEEEEEEHHHHHHHHHHHHCCCCCCCCCHHHH
T ss_conf             6608988-9999999859-9999999999999986308997799999999999886999999999865556688899999


Q ss_pred             HHHHHHHHHCCCCHHHHH
Q ss_conf             999999998199998999
Q T0586            97 ERFLEEAKSIGLDDQTAI  114 (125)
Q Consensus        97 ~~~~~~~~~~~~~~~~~~  114 (125)
                      +.+..-+....++..++.
T Consensus        86 EtLAiIAY~QPiTr~eIe  103 (159)
T PF04079_consen   86 ETLAIIAYKQPITRAEIE  103 (159)
T ss_dssp             HHHHHHHHH-SEEHHHHH
T ss_pred             HHHHHHHHCCCCCHHHHH
T ss_conf             999999974983899999


No 40 
>PF10007 DUF2250:  Uncharacterized protein conserved in archaea (DUF2250)
Probab=77.65  E-value=1.2  Score=22.32  Aligned_cols=34  Identities=18%  Similarity=0.322  Sum_probs=30.8

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             7899998589878999999999887916731783
Q T0586            40 VREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM   73 (125)
Q Consensus        40 er~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~   73 (125)
                      -.-+|..++++..-|+.++..|++.|+|+...|+
T Consensus        24 ak~ia~~l~~~l~eV~~~l~~Le~~GLlErv~g~   57 (92)
T PF10007_consen   24 AKMIARRLGIPLEEVRERLKKLEEMGLLERVEGS   57 (92)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCH
T ss_conf             9999999689999999999999988784321133


No 41 
>PF01418 HTH_6:  Helix-turn-helix domain, rpiR family;  InterPro: IPR000281 This domain contains a helix-turn-helix motif . Every member of this family is N-terminal to a SIS domain IPR001347 from INTERPRO. Members of this family are probably regulators of genes involved in phosphosugar metobolism.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2o3f_C.
Probab=77.54  E-value=0.7  Score=23.93  Aligned_cols=57  Identities=23%  Similarity=0.298  Sum_probs=43.3

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             889889999999999976498998881788789999858987899999999988791673178
Q T0586            10 ADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG   72 (125)
Q Consensus        10 ~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g   72 (125)
                      +=+|--.+|+++|.+....  +   ..+ |..+||+..|||.+||-+-.+.|.-.||-+-+..
T Consensus        13 ~lt~~e~~Ia~yil~~~~~--~---~~~-si~~lA~~~~vS~atv~Rf~kkLGf~gf~efk~~   69 (107)
T PF01418_consen   13 SLTPSEKKIADYILNNPDK--I---ANM-SISELAKAAGVSPATVVRFCKKLGFSGFSEFKVD   69 (107)
T ss_dssp             GS-HHHHHHHHHHHH-HHH--H---TT---HHHHHHHTT--HHHHHHHHHH------HHHHHH
T ss_pred             HCCHHHHHHHHHHHHCHHH--H---HHC-CHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             1799999999999929999--9---775-4999999979898899999999289999999999


No 42 
>PF06970 RepA_N:  Replication initiator protein A (RepA) N-terminus;  InterPro: IPR010724   This entry represents the N terminus (approximately 80 residues) of replication initiator protein A (RepA), a DNA replication initiator in plasmids . Most proteins in this entry are bacterial, but archaeal and eukaryotic members are also included.
Probab=76.86  E-value=1.9  Score=21.09  Aligned_cols=49  Identities=20%  Similarity=0.211  Sum_probs=39.6

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCC---CCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             88999999999997649899888---17887899998589878999999999
Q T0586            13 PIYSQISDWMKKQMITGEWKGED---KLPSVREMGVKLAVNPNTVSRAYQEL   61 (125)
Q Consensus        13 Ply~qI~~~l~~~I~~G~l~~G~---~LPser~La~~~~VSr~TVr~Al~~L   61 (125)
                      -+|.-+.+.+.-.+.+|.....-   -+-|..+|++.+|+|+.||.++.+.|
T Consensus        25 ilY~lL~dR~~lS~kN~wiD~~g~vY~ift~~el~~~L~~s~~~v~k~~kEL   76 (76)
T PF06970_consen   25 ILYSLLLDRMELSIKNGWIDEDGNVYIIFTNEELMEILNCSKKKVIKIKKEL   76 (76)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHHHCCCHHHHHHHHHCC
T ss_conf             9999999999876635678799998999659999999887888999999619


No 43 
>PF04218 CENP-B_N:  CENP-B N-terminal DNA-binding domain;  InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure .; GO: 0003677 DNA binding, 0000775 chromosome, pericentric region; PDB: 2elh_A 1hlv_A 1bw6_A.
Probab=76.28  E-value=0.27  Score=26.66  Aligned_cols=21  Identities=29%  Similarity=0.491  Sum_probs=19.1

Q ss_pred             CHHHHHHHHCCCHHHHHHHHH
Q ss_conf             878999985898789999999
Q T0586            39 SVREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~   59 (125)
                      |.+++|..|||+++||+..++
T Consensus        24 s~~~iAr~fgi~~sTi~~i~k   44 (53)
T PF04218_consen   24 SQREIAREFGISRSTISRILK   44 (53)
T ss_dssp             -HHHHHHHHT--CCHHHHHCC
T ss_pred             CHHHHHHHCCCCHHHHHHHHH
T ss_conf             899999891998889999998


No 44 
>PF09862 DUF2089:  Protein of unknown function(DUF2089)
Probab=75.87  E-value=1.2  Score=22.52  Aligned_cols=61  Identities=18%  Similarity=0.278  Sum_probs=37.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH-CCEEEECCCCEEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHH
Q ss_conf             8789999858987899999999988-791673178336862880789999999999999999999998199998999999
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELER-AGYIYAKRGMGSFVTSDKALFDQLKKELADAITERFLEEAKSIGLDDQTAIELL  117 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~-~G~i~~~~g~G~~V~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~  117 (125)
                      |.+++++.||||..|||.=+..+.+ -|+..          ........        .....+..+..-.++.+++++++
T Consensus        51 nlKe~ak~lgiSYpTvR~rLd~ii~~lg~~~----------~~~~~~~~--------~~~~IL~~L~~GeIs~eeA~~~L  112 (113)
T PF09862_consen   51 NLKEVAKELGISYPTVRNRLDRIIEKLGYEE----------EEEEEEND--------ERKEILDKLEKGEISVEEAIKLL  112 (113)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHHHCCCC----------CCCCCCCH--------HHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             8999999978882899999999999817987----------76654444--------69999999990997999999984


No 45 
>PF08221 HTH_9:  RNA polymerase III subunit RPC82 helix-turn-helix domain;  InterPro: IPR013197   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   This family consists of several DNA-directed RNA polymerase III polypeptides which are related to the Saccharomyces cerevisiae RPC82 protein. RNA polymerase C (III) promotes the transcription of tRNA and 5S RNA genes. In Saccharomyces cerevisiae, the enzyme is composed of 15 subunits, ranging from 10 kDa to about 160 kDa . This region is probably a DNA-binding helix-turn-helix.
Probab=74.95  E-value=1.4  Score=21.95  Aligned_cols=52  Identities=13%  Similarity=0.167  Sum_probs=40.4

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEE
Q ss_conf             999999999976498998881788789999858987899999999988791673
Q T0586            16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYA   69 (125)
Q Consensus        16 ~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~   69 (125)
                      ++.+..+...|.+--+..| ++ +.+++...-+.|+..|+.++..|.+.|++.-
T Consensus         8 ~~~FGe~~~~V~~~L~~~g-~l-tl~~i~~~t~l~~~~Vk~~L~~Liqh~~V~y   59 (62)
T PF08221_consen    8 EDHFGEIAAKVFECLLSRG-RL-TLREIVRRTKLSPSQVKKALAVLIQHNCVQY   59 (62)
T ss_pred             HHHHCHHHHHHHHHHHHCC-CC-CHHHHHHHCCCCHHHHHHHHHHHHHCCCCHH
T ss_conf             9880748999999999758-94-9999997839999999999999998086122


No 46 
>PF10668 Phage_terminase:  Phage terminase small subunit
Probab=73.88  E-value=0.91  Score=23.19  Aligned_cols=36  Identities=19%  Similarity=0.392  Sum_probs=24.9

Q ss_pred             CCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHH
Q ss_conf             988999999999997649899888178878999985898789999
Q T0586            12 KPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSR   56 (125)
Q Consensus        12 ~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~   56 (125)
                      .|-.++.++...+        .|..++ .+++|++||||.+||+.
T Consensus         6 sp~RdkA~e~y~~--------~~g~~~-~k~IAe~lgvs~~tIr~   41 (60)
T PF10668_consen    6 SPNRDKAFEIYKE--------SNGKIK-LKDIAEKLGVSESTIRK   41 (60)
T ss_pred             CCCHHHHHHHHHH--------CCCCCC-HHHHHHHHCCCHHHHHH
T ss_conf             9588999999998--------189841-99999997979999873


No 47 
>PF08461 HTH_12:  Ribonuclease R winged-helix domain;  InterPro: IPR013668   This domain is found at the amino terminus of Ribonuclease R and a number of presumed transcriptional regulatory proteins from archaea. 
Probab=73.47  E-value=1.5  Score=21.75  Aligned_cols=47  Identities=19%  Similarity=0.365  Sum_probs=34.8

Q ss_pred             CCCCCCCHHHHHHHH-----CCCHHHHHHHHHHHHHCCEEEECCCCEEEECCC
Q ss_conf             888178878999985-----898789999999998879167317833686288
Q T0586            33 GEDKLPSVREMGVKL-----AVNPNTVSRAYQELERAGYIYAKRGMGSFVTSD   80 (125)
Q Consensus        33 ~G~~LPser~La~~~-----~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~   80 (125)
                      .+..+ |-.+||+.+     .+|..+||.-++.|+.+|++..+.+.|+.+++.
T Consensus        10 ~~~P~-~~~~l~~~L~~~g~~~s~~avRrrLr~me~dG~t~~~~~~G~~ite~   61 (66)
T PF08461_consen   10 SGKPI-GRKELAEELKLRGEELSEEAVRRRLRAMERDGFTRRQGYAGRSITEK   61 (66)
T ss_pred             CCCCC-CHHHHHHHHHHHCHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCHH
T ss_conf             49998-99999999984066757999999999999878812057777606886


No 48 
>PF01475 FUR:  Ferric uptake regulator family;  InterPro: IPR002481   The Ferric uptake regulator or FUR family includes metal ion uptake regulator proteins, which bind to the operator DNA and control the transcription of metal ion-responsive genes. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2w57_A 2fu4_A 1mzb_A 2o03_A 3f8n_A 2rgv_A 2fe3_A 3eyy_A.
Probab=73.37  E-value=0.74  Score=23.77  Aligned_cols=36  Identities=28%  Similarity=0.173  Sum_probs=29.9

Q ss_pred             CCHHHHHHH-----HCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             887899998-----589878999999999887916731783
Q T0586            38 PSVREMGVK-----LAVNPNTVSRAYQELERAGYIYAKRGM   73 (125)
Q Consensus        38 Pser~La~~-----~~VSr~TVr~Al~~L~~~G~i~~~~g~   73 (125)
                      ||..++.+.     .+||++||=+++..|++.|+|......
T Consensus        24 ~sa~ei~~~l~~~~~~is~aTVYR~L~~L~e~Gli~~~~~~   64 (120)
T PF01475_consen   24 LSAEEIYDRLREKGPSISLATVYRTLDLLEEAGLIHRIELG   64 (120)
T ss_dssp             EEHHHHHHHHHHT-TT--HHHHHHHHHHHHH---EEEEE--
T ss_pred             CCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHCCEEEEEECC
T ss_conf             99999999988618999862499999999868909999918


No 49 
>PF04433 SWIRM:  SWIRM domain;  InterPro: IPR007526   The SWIRM domain is a small alpha-helical domain of about 85 amino acid residues found in eukaryotic chromosomal proteins. It is named after the proteins SWI3, RSC8 and MOIRA in which it was first recognised. This domain is predicted to mediate protein-protein interactions in the assembly of chromatin-protein complexes. The SWIRM domain can be linked to different domains, such as the ZZ-type zinc finger (IPR000433 from INTERPRO), the Myb DNA-binding domain (IPR001005 from INTERPRO), the HORMA domain (IPR003511 from INTERPRO), the amino-oxidase domain, the chromo domain (IPR000953 from INTERPRO), and the JAB1/PAD1 domain.; PDB: 2v1d_A 2com_A 2z3y_A 2iw5_A 2hko_A 2uxx_A 2dw4_A 2uxn_A 2ejr_A 2z5u_A ....
Probab=70.23  E-value=1.8  Score=21.29  Aligned_cols=51  Identities=22%  Similarity=0.296  Sum_probs=40.5

Q ss_pred             HHHHHHHHHHHCC-CCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEE
Q ss_conf             9999999997649-899888178878999985898789999999998879167
Q T0586            17 QISDWMKKQMITG-EWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIY   68 (125)
Q Consensus        17 qI~~~l~~~I~~G-~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~   68 (125)
                      +.|-.+++.|+.- ...|+..| +..+....+.+-.+-+++++.-|+..|||.
T Consensus        32 ~~Yl~iRn~il~~w~~~~~~~l-t~~~~~~~~~~d~~~~~ri~~FL~~~G~IN   83 (84)
T PF04433_consen   32 EPYLNIRNHILNEWRKNPNKYL-TKTDARRLIKIDVNKVRRIYDFLERWGYIN   83 (84)
T ss_dssp             HHHHHHHHHHHHHHHHHTTS----HHHHHHHCTSSHHHHHHHHHHHHHTT--S
T ss_pred             HHHHHHHHHHHHHHHHCCCCCE-EHHHHHHHCCCCHHHHHHHHHHHHHCCCCC
T ss_conf             8999999999999998799836-299999885237999999999999859768


No 50 
>PF08765 Mor:  Mor transcription activator family;  InterPro: IPR014875   Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C terminal contains a helix-turn-helix motif which binds DNA. ; PDB: 1rr7_A.
Probab=68.89  E-value=2.3  Score=20.53  Aligned_cols=50  Identities=16%  Similarity=0.225  Sum_probs=31.7

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCE
Q ss_conf             889999999999976498998881788789999858987899999999988791
Q T0586            13 PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGY   66 (125)
Q Consensus        13 Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~   66 (125)
                      |.-..+...+++.=+...|. |.   +.++||..||+|..+|++.++.....-.
T Consensus        52 P~~~~~~~~~Rn~~I~~~f~-G~---n~~eLArkY~lS~r~I~~Ii~~~~~~~~  101 (108)
T PF08765_consen   52 PKCDSALRALRNREIRREFN-GM---NVRELARKYGLSERWIYRIIKRQRKEER  101 (108)
T ss_dssp             ----HHHHHHHHHHHHHH---------HHHHHHH----HHHHHHHHHHHHH---
T ss_pred             CCCCHHHHHHHHHHHHHHHC-CC---CHHHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             59607889999999999838-99---7999998979669999999999888899


No 51 
>PF09170 DUF1879:  Domain of unknown function (DUF1879);  InterPro: IPR015253   This domain is found in a set of hypothetical eukaryotic proteins, as well as in oligonucleotide/oligosaccharide-binding fold-containing protein-1. ; PDB: 1wj5_A.
Probab=68.67  E-value=1.9  Score=21.15  Aligned_cols=82  Identities=11%  Similarity=0.230  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCCC-CCCCCHHHHHHHH--------CC--CHHHHH----HHHHHHHHCCEEEECCCC---EE
Q ss_conf             899999999999764989988-8178878999985--------89--878999----999999887916731783---36
Q T0586            14 IYSQISDWMKKQMITGEWKGE-DKLPSVREMGVKL--------AV--NPNTVS----RAYQELERAGYIYAKRGM---GS   75 (125)
Q Consensus        14 ly~qI~~~l~~~I~~G~l~~G-~~LPser~La~~~--------~V--Sr~TVr----~Al~~L~~~G~i~~~~g~---G~   75 (125)
                      +.+.|.+.|.+.=+...++.. +-++|.-.+|..=        ..  +-..|+    +|++.|+++|+|+.+.+.   =+
T Consensus        52 LsekikeFL~e~~V~~Fyq~ele~v~sL~~~a~~pv~~s~q~~~~~sts~qi~slfkeAl~lL~~~G~Vfqk~~~~D~vY  131 (174)
T PF09170_consen   52 LSEKIKEFLMENKVQNFYQKELESVESLISVASRPVSCSDQESKSSSTSKQIRSLFKEALKLLQDEGLVFQKDQNQDEVY  131 (174)
T ss_dssp             HHHHHHHHHHHHT-S-B-HHHHHT-HHHHHHHSS-------S---------HHHHHHHHHHHHHH---EE-S-------B
T ss_pred             HHHHHHHHHHHCCHHHEHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCEEEECCCCCCCEE
T ss_conf             99999999865533103088887688899763586533345778862799999999999999987795786279976517


Q ss_pred             EECCCHHHHHHHHHHHHHHH
Q ss_conf             86288078999999999999
Q T0586            76 FVTSDKALFDQLKKELADAI   95 (125)
Q Consensus        76 ~V~~~~~~~~~~~~~~~~~~   95 (125)
                      +|+..+..+......+..+.
T Consensus       132 ~Vt~~DKdLh~~il~II~ed  151 (174)
T PF09170_consen  132 YVTDQDKDLHKAILNIIQED  151 (174)
T ss_dssp             EE-SSS--------------
T ss_pred             EEECCCHHHHHHHHHHHHHH
T ss_conf             87436366899999999998


No 52 
>PF08280 HTH_Mga:  M protein trans-acting positive regulator (MGA) HTH domain;  InterPro: IPR013199   Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions .
Probab=68.23  E-value=2.1  Score=20.80  Aligned_cols=30  Identities=20%  Similarity=0.401  Sum_probs=25.9

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf             8817887899998589878999999999887
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQELERA   64 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~   64 (125)
                      ...+ +..++|+.+|+|+-||+.-+..|.+.
T Consensus        17 ~~~~-t~~ela~~l~~S~~ti~~~I~~l~~~   46 (59)
T PF08280_consen   17 NGWI-TLKELAKKLGLSERTIRNDINELNEE   46 (59)
T ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHH
T ss_conf             7979-79999999798899999999999998


No 53 
>PF04157 EAP30:  EAP30/Vps36 family;  InterPro: IPR007286   EAP30 is a subunit of the ELL complex. The ELL is an 80-kDa RNA polymerase II transcription factor. ELL interacts with three other proteins to form the complex known as ELL complex. The ELL complex is capable of increasing that catalytic rate of transcription elongation, but is unable to repress initiation of transcription by RNA polymerase II as is the case of ELL. EAP30 is thought to lead to the derepression of ELL's transcriptional inhibitory activity. ; PDB: 3cuq_A 2zme_A 1w7p_D 1u5t_B.
Probab=68.20  E-value=2.3  Score=20.52  Aligned_cols=71  Identities=18%  Similarity=0.282  Sum_probs=51.9

Q ss_pred             CCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHH--------CCCHHHHHHHHHHHHHCCE--EEECCCCE-EEEC
Q ss_conf             88988999999999997649899888178878999985--------8987899999999988791--67317833-6862
Q T0586            10 ADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKL--------AVNPNTVSRAYQELERAGY--IYAKRGMG-SFVT   78 (125)
Q Consensus        10 ~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~--------~VSr~TVr~Al~~L~~~G~--i~~~~g~G-~~V~   78 (125)
                      +..-.|.+++.+|.+....-.=..|--+ +..+|-..|        -||+..+.+|...|...|.  -..+-++| .+|.
T Consensus        87 ~~~~f~~ELa~qI~e~c~~~~~~nGGii-~L~dl~~~~nr~r~g~~lISp~Di~~A~~~l~~Lg~~~~l~~~~sg~~~v~  165 (223)
T PF04157_consen   87 GGGDFYYELAVQIVEVCLSTRKKNGGII-SLSDLYCLYNRARGGTELISPEDILKACKKLEKLGLGFKLRKIGSGVKVVQ  165 (223)
T ss_dssp             CCCHHHHHHHHHHHHHHHHHCTTSSSEE-EHHHHHHHHHHCC----T--HHHHHHHHHHHCCCT-TEEEEEETTTEEEEE
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHHCCCEE-EHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCEEEEE
T ss_conf             5006999999999999999997588856-799999999986267787599999999999998499859999668606986


Q ss_pred             CCH
Q ss_conf             880
Q T0586            79 SDK   81 (125)
Q Consensus        79 ~~~   81 (125)
                      ..+
T Consensus       166 s~~  168 (223)
T PF04157_consen  166 SVP  168 (223)
T ss_dssp             CST
T ss_pred             CCC
T ss_conf             077


No 54 
>PF07453 NUMOD1:  NUMOD1 domain;  InterPro: IPR010896   This helix-turn-helix-containing DNA-binding domain is found associated in homing nucleases . 
Probab=67.79  E-value=1.2  Score=22.44  Aligned_cols=23  Identities=26%  Similarity=0.426  Sum_probs=20.7

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHH
Q ss_conf             17887899998589878999999
Q T0586            36 KLPSVREMGVKLAVNPNTVSRAY   58 (125)
Q Consensus        36 ~LPser~La~~~~VSr~TVr~Al   58 (125)
                      ..||.++.|+.+|+|+.||++.+
T Consensus        15 ~f~Si~eAa~~l~~~~~tI~~~l   37 (37)
T PF07453_consen   15 SFSSIREAARALNISHSTISKYL   37 (37)
T ss_pred             EECCHHHHHHHHCCCHHHHHHHC
T ss_conf             97489999998099877898759


No 55 
>PF00126 HTH_1:  Bacterial regulatory helix-turn-helix protein, lysR family;  InterPro: IPR000847 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family, the lysR family, groups together a range of proteins, including ampR, catM, catR, cynR, cysB, gltC, iciA, ilvY, irgB, lysR, metR, mkaC, mleR, nahR, nhaR, nodD, nolR, oxyR, pssR, rbcR, syrM, tcbR, tfdS and trpI , , , , . The majority of these proteins appear to be transcription activators and most are known to negatively regulate their own expression. All possess a potential HTH DNA-binding motif towards their N-termini.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1ixc_B 1iz1_Q 2esn_D 1o7l_B 1b9n_A 1b9m_B 3fzv_B.
Probab=66.89  E-value=2.1  Score=20.87  Aligned_cols=40  Identities=25%  Similarity=0.296  Sum_probs=29.7

Q ss_pred             CCHHHHHHHHCCCHHHHHHHHHHHHHC---CEEEECCCCEEEEC
Q ss_conf             887899998589878999999999887---91673178336862
Q T0586            38 PSVREMGVKLAVNPNTVSRAYQELERA---GYIYAKRGMGSFVT   78 (125)
Q Consensus        38 Pser~La~~~~VSr~TVr~Al~~L~~~---G~i~~~~g~G~~V~   78 (125)
                      .|...=|+.+|+|+++|.++++.|++.   -++.+ .++|...+
T Consensus        14 gs~~~AA~~l~~s~~~vs~~i~~LE~~lg~~Lf~r-~~~~~~lT   56 (60)
T PF00126_consen   14 GSFSRAAEQLGISQSAVSRRIKRLEEELGVPLFDR-TGRGLRLT   56 (60)
T ss_dssp             S-HHHHHHHHTS-HHHHHHHHHHHHHHHTS-SEEE-----EEE-
T ss_pred             CCHHHHHHHCCCCCCHHHHHHHHHHHHHCCEEEEE-CCCCEEEC
T ss_conf             99999998708995389999999999829968998-89975489


No 56 
>PF03551 PadR:  Transcriptional regulator PadR-like family;  InterPro: IPR005149   Phenolic acids, also called substituted hydroxycinnamic acids, are abundant in the plant kingdom because they are involved in the structure of plant cell walls and are present in some vacuoles. In plant-soil ecosystems they are released as free acids by hemicellulases produced by several fungi and bacteria. Of these weak acids, the most abundant are p-coumaric, ferulic, and caffeic acids, considered to be natural toxins that inhibit the growth of microorganisms, especially at low pHs. In spite of this chemical stress, some bacteria can use phenolic acids as a sole source of carbon. For other microorganisms, these compounds induce a specific response by which the organism adapts to its environment. The ubiquitous lactic acid bacterium Lactobacillus plantarum exhibits an inducible phenolic acid decarboxylase (PAD) activity which converts these substrates into less-toxic vinyl phenol derivatives. PadR acts as a repressor of padA gene expression in the phenolic acid stress response .; PDB: 3f8b_A 3f8f_B 3f8c_A 1xma_B 3hhh_B 3elk_B 1yg2_A 2dql_A 2e1n_B 2zfw_D ....
Probab=66.77  E-value=2.3  Score=20.56  Aligned_cols=50  Identities=18%  Similarity=0.256  Sum_probs=32.9

Q ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHH----HCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             99999764989988817887899998----589878999999999887916731783
Q T0586            21 WMKKQMITGEWKGEDKLPSVREMGVK----LAVNPNTVSRAYQELERAGYIYAKRGM   73 (125)
Q Consensus        21 ~l~~~I~~G~l~~G~~LPser~La~~----~~VSr~TVr~Al~~L~~~G~i~~~~g~   73 (125)
                      .|...+..+.. .|-.|  .+.|.+.    +.+|.++|-.+++.|+++|+|+.....
T Consensus        10 ~IL~~L~~~~~-~gyei--~~~l~~~~~~~~~~s~g~iY~~L~~Le~~Gli~~~~~~   63 (86)
T PF03551_consen   10 AILGLLSEGPM-HGYEI--KKELEERYGGFWKVSPGSIYPALKRLEEEGLIESRWED   63 (86)
T ss_dssp             HHHHHHHHS-B-E--HH--HHHHHHHSTTTEE--HHHHHHHHHHHHHTTSEEEEEEE
T ss_pred             HHHHHHHHCCC-CHHHH--HHHHHHHHCCCEECCCCHHHHHHHHHHHCCCEEEEEEE
T ss_conf             99999702899-59999--99999984887242654899999999978986987653


No 57 
>PF12116 SpoIIID:  Stage III sporulation protein D
Probab=66.62  E-value=0.95  Score=23.08  Aligned_cols=28  Identities=29%  Similarity=0.401  Sum_probs=22.3

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHH-HHH
Q ss_conf             88178878999985898789999999-998
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQ-ELE   62 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~-~L~   62 (125)
                      ..+- ++|+.|+.||||.+||.+-+. +|.
T Consensus        17 ~~~a-TVR~tAk~FGVSKSTVHkDvTeRL~   45 (82)
T PF12116_consen   17 ENKA-TVRQTAKVFGVSKSTVHKDVTERLP   45 (82)
T ss_pred             HCCH-HHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             7451-6999999978529999899999997


No 58 
>PF04297 UPF0122:  Putative helix-turn-helix protein, YlxM / p13 like;  InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway .; PDB: 1s7o_B 1xsv_A.
Probab=64.42  E-value=2.4  Score=20.39  Aligned_cols=28  Identities=21%  Similarity=0.373  Sum_probs=23.3

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             88178878999985898789999999998
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQELE   62 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~~L~   62 (125)
                      .+-+ |..++|+.+||||..|...+++-.
T Consensus        31 ~eDl-SlsEIAe~~~iSRqaVyD~ikr~~   58 (101)
T PF04297_consen   31 NEDL-SLSEIAEELGISRQAVYDNIKRAE   58 (101)
T ss_dssp             TS----HHHHHHHCT--HHHHHHHHHHHH
T ss_pred             HCCC-CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             8799-899999896988999999999999


No 59 
>PF07638 Sigma70_ECF:  ECF sigma factor;  InterPro: IPR011517   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This entry represents a group of sigma factors that are able to regulate extra cellular function (ECF) . Eubacteria display considerable genetic diversity between ECF-sigma factors, but all retain two features: the ability to respond to extra-cytoplasmic functions; and regulation by anti-sigma and anti-anti-sigma factors . This family show sequence similarity to IPR007627 from INTERPRO and IPR007630 from INTERPRO.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent
Probab=62.90  E-value=3.3  Score=19.49  Aligned_cols=14  Identities=29%  Similarity=0.114  Sum_probs=6.9

Q ss_pred             HHCCCCHHHHHHHH
Q ss_conf             98199998999999
Q T0586           104 KSIGLDDQTAIELL  117 (125)
Q Consensus       104 ~~~~~~~~~~~~l~  117 (125)
                      ...|++.+|+.+.+
T Consensus       148 ~f~Glt~~EiA~~L  161 (185)
T PF07638_consen  148 YFGGLTVEEIAEAL  161 (185)
T ss_pred             HHCCCCHHHHHHHH
T ss_conf             98799999999896


No 60 
>PF07023 DUF1315:  Protein of unknown function (DUF1315);  InterPro: IPR009749   This family consists of several bacterial proteins of around 90 residues in length. The function of this family is unknown.
Probab=62.42  E-value=3.7  Score=19.22  Aligned_cols=55  Identities=11%  Similarity=0.189  Sum_probs=35.2

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC----EEEECC
Q ss_conf             9999999999764989988817887899998589878999999999887916731783----368628
Q T0586            16 SQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM----GSFVTS   79 (125)
Q Consensus        16 ~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~----G~~V~~   79 (125)
                      -.||+.|+..+..|.||-|.+| |..+-.        +--+|+-.-+....+...+..    |..+..
T Consensus        10 PevY~rL~~AVElGKWpDG~~L-T~eQre--------~~lQaVm~yq~~~n~~~e~~ti~~~G~I~~~   68 (93)
T PF07023_consen   10 PEVYERLKQAVELGKWPDGRAL-TPEQRE--------SCLQAVMLYQARHNLPEEHRTIGAGGYIDMK   68 (93)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCC-CHHHHH--------HHHHHHHHHHHHCCCCHHHEECCCCCEECCC
T ss_conf             9999999999992879898988-999999--------9999999999870898888013679766402


No 61 
>PF01371 Trp_repressor:  Trp repressor protein;  InterPro: IPR000831   The Trp repressor (TrpR) binds to at least five operators in the Escherichia coli genome, repressing gene expression. The operators at which it binds vary considerably in DNA sequence and location within the promoter; when bound to the Trp operon it recognises the sequence 5'-ACTAGT-3' and acts to prevent the initiation of transcription. The TrpR controls the trpEDCBA (trpO) operon and the genes for trpR, aroH, mtr and aroL, which are involved in the biosynthesis and uptake of the amino acid tryptophan . The repressor binds to the operators only in the presence of L-tryptophan, thereby controlling the intracellular level of its effector; the complex also regulates Trp repressor biosynthesis by binding to its own regulatory region. TrpR acts as a dimer that is composed of identical 6-helical subunits, where four of the helices form the core of the protein and intertwine with the corresponding helices from the other subunit. ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1trr_K 1tro_E 1p6z_R 1jhg_A 1co0_A 1rcs_B 3wrp_A 1zt9_B 1wrp_R 1wrt_S ....
Probab=62.33  E-value=3.2  Score=19.58  Aligned_cols=25  Identities=28%  Similarity=0.290  Sum_probs=22.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             8789999858987899999999988
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELER   63 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~   63 (125)
                      |.|++++.+|+|..||.+.=+.|..
T Consensus        51 syreI~~~tG~S~aTIsR~sr~Lk~   75 (87)
T PF01371_consen   51 SYREIAEETGASIATISRVSRCLKY   75 (87)
T ss_dssp             SHHHHHHH----HHHHHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             8999999978778899999999880


No 62 
>PF06056 Terminase_5:  Putative ATPase subunit of terminase (gpP-like);  InterPro: IPR010332   This family of proteins are annotated as ATPase subunits of phage terminase after . Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=58.99  E-value=3.5  Score=19.38  Aligned_cols=31  Identities=19%  Similarity=0.205  Sum_probs=25.8

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEE
Q ss_conf             8789999858987899999999988791673
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAGYIYA   69 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~   69 (125)
                      +..++|+.+|||+.||..=...-..+|+.-.
T Consensus        15 ~~~eIA~~Lgv~~~TV~~W~~r~~w~~~~~~   45 (58)
T PF06056_consen   15 TPKEIAEELGVSRRTVYSWKKRYGWDGLLPL   45 (58)
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHCCCCCCCH
T ss_conf             9999999988688899999997561666742


No 63 
>PF03374 ANT:  Phage antirepressor protein KilAC domain;  InterPro: IPR005039  Prophages P1 and P7 exist as unit copy DNA plasmids in the bacterial cell. Maintenance of the prophage state requires the continuous expression of two repressors: (i) C1 is a protein which negatively regulates the expression of lytic genes including the C1 inactivator gene coi, and (ii) C4 is an antisense RNA which specifically inhibits the synthesis of an anti-repressor Ant.; GO: 0003677 DNA binding
Probab=57.50  E-value=4.7  Score=18.52  Aligned_cols=37  Identities=27%  Similarity=0.523  Sum_probs=28.4

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf             17887899998589878999999999887916731783368
Q T0586            36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF   76 (125)
Q Consensus        36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~   76 (125)
                      -..+.++.|+.+|+++.   +-+..|.+.||++.+ ++|..
T Consensus        23 ~~~~i~~~AK~lgi~~~---~l~~~Lr~~~il~~~-~~~~~   59 (111)
T PF03374_consen   23 GSMTIREAAKILGIGPN---KLFKWLREKGILYRR-GSGRN   59 (111)
T ss_pred             CCEEHHHHHHHHCCCHH---HHHHHHHHCCCEEEC-CCCCC
T ss_conf             95779999999399999---999999986977856-89976


No 64 
>PF01498 Transposase_5:  Transposase;  InterPro: IPR002492   Transposase proteins are necessary for efficient DNA transposition. This family includes the amino-terminal region of Tc1, Tc1A, Tc1B and Tc2B transposases of Caenorhabditis elegans. The region encompasses the specific DNA binding and second DNA recognition domains as well as an amino-terminal region of the catalytic domain of Tc3 as described in . Tc3 is a member of the Tc1/mariner family of transposable elements.   More information about these proteins can be found at Protein of the Month: Transposase .; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated, 0015074 DNA integration, 0005634 nucleus; PDB: 3f2k_B 1u78_A.
Probab=57.49  E-value=3.3  Score=19.54  Aligned_cols=36  Identities=28%  Similarity=0.440  Sum_probs=26.8

Q ss_pred             CHHHHHHHH-----CCCHHHHHHHHHHHHHCCEEEECCCCEEEE
Q ss_conf             878999985-----898789999999998879167317833686
Q T0586            39 SVREMGVKL-----AVNPNTVSRAYQELERAGYIYAKRGMGSFV   77 (125)
Q Consensus        39 ser~La~~~-----~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V   77 (125)
                      |.++|+..+     +||.+||+++|.   ..||-...+..-.++
T Consensus        15 T~~~l~~~l~~~~~~vS~~Tv~R~L~---~~G~~~~~~~~kP~L   55 (72)
T PF01498_consen   15 TLRELARELQEEGISVSKSTVRRRLK---EMGYRKRKARKKPLL   55 (72)
T ss_dssp             -HHHHHHHT---T--S-HHHHHHHHH---H--------------
T ss_pred             CHHHHHHHHHHCCCCCCHHHHHHHHH---HCCCEEECCCCCCCC
T ss_conf             49999999986589979999999999---868920277889999


No 65 
>PF00376 MerR:  MerR family regulatory protein;  InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA , , , , , . Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N-terminus.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1r8d_B 1jbg_A 3hh0_C 3d6z_A 3d71_A 3d6y_A 1r8e_A 1exi_A 1exj_A 1q06_A ....
Probab=57.34  E-value=1.9  Score=21.13  Aligned_cols=25  Identities=28%  Similarity=0.426  Sum_probs=21.2

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCEE
Q ss_conf             87899998589878999999999887916
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAGYI   67 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G~i   67 (125)
                      |..++|+.+|||..|+|    ..+.+|+|
T Consensus         1 ti~e~a~~~gvs~~tlR----~ye~~gll   25 (38)
T PF00376_consen    1 TIGEVAKLLGVSVRTLR----YYEREGLL   25 (38)
T ss_dssp             EHHHHHHHCT--HHHHH----HHHHTTSS
T ss_pred             CHHHHHHHHCCCHHHHH----HHHHCCCC
T ss_conf             98999999896999999----99987898


No 66 
>PF12471 GTP_CH_N:  GTP cyclohydrolase N terminal 
Probab=56.33  E-value=5.1  Score=18.26  Aligned_cols=40  Identities=13%  Similarity=0.254  Sum_probs=30.7

Q ss_pred             HHHHHHHHCCCCCCCCCCCC------------------HHHHHHHHCCCHHHHHHHHH
Q ss_conf             99999976498998881788------------------78999985898789999999
Q T0586            20 DWMKKQMITGEWKGEDKLPS------------------VREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        20 ~~l~~~I~~G~l~~G~~LPs------------------er~La~~~~VSr~TVr~Al~   59 (125)
                      -.|.+.|..|.|++.-++--                  .-..|+.|||+-++.|++|-
T Consensus       135 pEi~eav~~GrL~~DG~i~~~~~G~~~VtK~AvePVWYLPGVA~RFGi~E~~LRR~LF  192 (194)
T PF12471_consen  135 PEIREAVAKGRLKPDGKIVLNSNGDVRVTKAAVEPVWYLPGVAERFGISEGELRRALF  192 (194)
T ss_pred             HHHHHHHHCCCCCCCCEEEECCCCCEEEEEEEECCCCCCHHHHHHCCCCHHHHHHHHH
T ss_conf             8899999849978887177158986889987623321361159780997999988872


No 67 
>PF08281 Sigma70_r4_2:  Sigma-70, region 4;  InterPro: IPR013249   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 2h27_D 1or7_A 2o8x_B.
Probab=55.67  E-value=2.9  Score=19.88  Aligned_cols=25  Identities=24%  Similarity=0.325  Sum_probs=21.4

Q ss_pred             CCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             78878999985898789999999998
Q T0586            37 LPSVREMGVKLAVNPNTVSRAYQELE   62 (125)
Q Consensus        37 LPser~La~~~~VSr~TVr~Al~~L~   62 (125)
                      + |..++|+.+|+|.+||+..+.+-.
T Consensus        27 ~-s~~eIA~~l~is~~tv~~~l~ra~   51 (54)
T PF08281_consen   27 L-SYKEIAEILGISESTVKSRLSRAR   51 (54)
T ss_dssp             ---HHHHHHHCTS----HHHHHHHHH
T ss_pred             C-CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             5-899999998919999999999999


No 68 
>PF11740 KfrA_N:  Plasmid replication region DNA-binding N-term
Probab=55.62  E-value=5.8  Score=17.89  Aligned_cols=46  Identities=17%  Similarity=0.302  Sum_probs=35.9

Q ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC-CCHHHHHHHHHHHHHCCE
Q ss_conf             9999999999976498998881788789999858-987899999999988791
Q T0586            15 YSQISDWMKKQMITGEWKGEDKLPSVREMGVKLA-VNPNTVSRAYQELERAGY   66 (125)
Q Consensus        15 y~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~-VSr~TVr~Al~~L~~~G~   66 (125)
                      |++|+..-...+..|.      -||...+-..+| .|.+||.+.++....+--
T Consensus         3 ~e~V~~Aa~~L~~~G~------~PTv~~VR~~lG~GS~~ti~~~lk~w~~~~~   49 (120)
T PF11740_consen    3 YEDVAAAADALLAAGK------RPTVDAVRERLGTGSMSTISKHLKEWREEQR   49 (120)
T ss_pred             HHHHHHHHHHHHHCCC------CCCHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             9999999999987489------9989999999879588999999999998753


No 69 
>PF06413 Neugrin:  Neugrin;  InterPro: IPR010487   This family consists of several mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation .
Probab=54.90  E-value=3.7  Score=19.19  Aligned_cols=21  Identities=14%  Similarity=0.431  Sum_probs=18.9

Q ss_pred             CHHHHHHHHCCCHHHHHHHHH
Q ss_conf             878999985898789999999
Q T0586            39 SVREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~   59 (125)
                      +...||+.|+||+-.||+.|+
T Consensus        31 t~~~LAe~F~vSpeaIrRILK   51 (225)
T PF06413_consen   31 TTERLAESFKVSPEAIRRILK   51 (225)
T ss_pred             CHHHHHHHCCCCHHHHHHHHH
T ss_conf             799998767999999999997


No 70 
>PF09079 Cdc6_C:  CDC6, C terminal ;  InterPro: IPR015163   The C terminal domain of CDC6 assumes a winged helix fold, with a five alpha-helical bundle (alpha15-alpha19) structure, backed on one side by three beta strands (beta6-beta8). It has been shown that this domain acts as a DNA-localisation factor, however its exact function is, as yet, unknown. Putative functions include: (1) mediation of protein-protein interactions and (2) regulation of nucleotide binding and hydrolysis. Mutagenesis studies have shown that this domain is essential for appropriate Cdc6 activity . ; PDB: 2qby_B 2v1u_A 1w5t_C 1w5s_A 1fnn_A.
Probab=54.89  E-value=5.9  Score=17.84  Aligned_cols=42  Identities=26%  Similarity=0.295  Sum_probs=32.6

Q ss_pred             CCCCCCCCCCHHHHHHHHCC---CHHHHHHHHHHHHHCCEEEECC
Q ss_conf             89988817887899998589---8789999999998879167317
Q T0586            30 EWKGEDKLPSVREMGVKLAV---NPNTVSRAYQELERAGYIYAKR   71 (125)
Q Consensus        30 ~l~~G~~LPser~La~~~~V---Sr~TVr~Al~~L~~~G~i~~~~   71 (125)
                      ....|+-...-..+|+.+|+   |.+.+..-++.|+..|+|.++.
T Consensus        15 ~~~~~~vy~~Y~~lc~~~~~~pls~~r~~~~l~~L~~~gli~~~~   59 (85)
T PF09079_consen   15 EVTTGEVYEQYEELCEKIGVDPLSQRRFSDILSELEMLGLIESER   59 (85)
T ss_dssp             SEE-HHHHHHHHHHHHHCTS----HHHHHHHHHHHHH---EEEEE
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCCEEEEE
T ss_conf             630899999999999984899998999999999998578703433


No 71 
>PF02295 z-alpha:  Adenosine deaminase z-alpha domain;  InterPro: IPR000607 Double-stranded RNA-specific adenosine deaminase () converts multiple adenosines to inosines and creates I/U mismatched base pairs in double-helical RNA substrates without apparent sequence specificity. DRADA has been found to modify adenosines in AU-rich regions more frequently, probably due to the relative ease of melting A/U base pairs compared to G/C base pairs. The protein functions to modify viral RNA genomes, and may be responsible for hypermutation of certain negative-stranded viruses. DRADA edits the mRNAs for the glutamate receptor subunits by site-selective adenosine deamination. The DRADA repeat is also found in viral E3 proteins, which contain a double-stranded RNA-binding domain.; GO: 0003723 RNA binding, 0003726 double-stranded RNA adenosine deaminase activity; PDB: 1sfu_A 1xmk_A 3eyi_A 1qbj_A 3f23_B 3f21_B 3f22_B 2acj_D 2gxb_B 1qgp_A ....
Probab=54.67  E-value=6  Score=17.79  Aligned_cols=40  Identities=20%  Similarity=0.292  Sum_probs=31.5

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCE
Q ss_conf             88178878999985898789999999998879167317833
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMG   74 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G   74 (125)
                      ++.. ..-.++..+++-..+|.++|-.|+.+|.|...++..
T Consensus        18 ~~~a-~~i~~~~~l~~~k~~vNr~LY~L~k~g~v~~~~~~P   57 (66)
T PF02295_consen   18 KSTA-TAIAKALGLSVPKKEVNRQLYRLEKSGKVCKSPGNP   57 (66)
T ss_dssp             -EEC-CHHHHHHHCTS-HHHHHHHHHHHHHTTSEEEECSSS
T ss_pred             CHHH-HHHHHHHCCCHHHHHHHHHHHHHHHCCCEECCCCCC
T ss_conf             7189-999998361252889999999999779665279979


No 72 
>PF05930 Phage_AlpA:  Prophage CP4-57 regulatory protein (AlpA);  InterPro: IPR010260   This family consists of several short bacterial and phage proteins, which are related to the Escherichia coli protein AlpA. AlpA suppresses two phenotypes of a delta lon protease mutant, overproduction of capsular polysaccharide and sensitivity to UV light . Several of the sequences in this family are thought to be DNA-binding proteins.; PDB: 1z4h_A.
Probab=54.27  E-value=2.2  Score=20.73  Aligned_cols=24  Identities=25%  Similarity=0.379  Sum_probs=19.3

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             178878999985898789999999
Q T0586            36 KLPSVREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        36 ~LPser~La~~~~VSr~TVr~Al~   59 (125)
                      ++-+..++++.+|+|++|+.+=.+
T Consensus         2 r~l~~~ev~~~lgvs~~t~y~~~~   25 (51)
T PF05930_consen    2 RLLRIKEVAELLGVSRSTLYRLIK   25 (51)
T ss_dssp             -EE-HHHHHHH-----HHHHHHHH
T ss_pred             CEECHHHHHHHHCCCHHHHHHHHH
T ss_conf             512499999998949999999977


No 73 
>PF02001 DUF134:  Protein of unknown function  DUF134;  InterPro: IPR002852   The bacterial and archaeal proteins in this family have no known function.
Probab=53.65  E-value=4.8  Score=18.45  Aligned_cols=30  Identities=17%  Similarity=0.209  Sum_probs=23.3

Q ss_pred             CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             9988817887899998589878999999999
Q T0586            31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQEL   61 (125)
Q Consensus        31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L   61 (125)
                      |.-.+.| +..+-|..+||||.|+.+.|..=
T Consensus        52 L~D~egl-~QeeAA~~MgVSR~Tf~ril~~A   81 (106)
T PF02001_consen   52 LVDYEGL-TQEEAAEQMGVSRQTFQRILKSA   81 (106)
T ss_pred             HHHHHCC-CHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             9888179-89999998497799999999999


No 74 
>PF07471 Phage_Nu1:  Phage DNA packaging protein Nu1;  InterPro: IPR010906   Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA .; PDB: 1j9i_B.
Probab=51.15  E-value=2.4  Score=20.47  Aligned_cols=34  Identities=21%  Similarity=0.312  Sum_probs=25.2

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCEE-EECCCCEEE
Q ss_conf             87899998589878999999999887916-731783368
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAGYI-YAKRGMGSF   76 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G~i-~~~~g~G~~   76 (125)
                      +-.+||+.||||..||.+-.    .+|+- ...-|+|..
T Consensus         4 nk~~lA~~~gVS~~ti~~W~----~~G~Pv~~~gg~G~~   38 (164)
T PF07471_consen    4 NKKQLAEILGVSERTITKWQ----RQGMPVVRRGGRGRE   38 (164)
T ss_dssp             EHHHHHHH----HHHHHHHT----T--------------
T ss_pred             CHHHHHHHHCCCHHHHHHHH----HCCCCEEECCCCCCC
T ss_conf             89999999798999999999----879974445889851


No 75 
>PF06971 Put_DNA-bind_N:  Putative DNA-binding protein N-terminus;  InterPro: IPR009718   This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria . They modulate transcription in response to changes in cellular NADH/NAD^(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0016564 transcription repressor activity, 0006980 redox signal response, 0016481 negative regulation of transcription, 0005737 cytoplasm; PDB: 1xcb_F 2dt5_A 2vt3_A 2vt2_B.
Probab=50.80  E-value=4.3  Score=18.78  Aligned_cols=39  Identities=21%  Similarity=0.496  Sum_probs=26.8

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             88999999999997649899888178878999985898789999999
Q T0586            13 PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        13 Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~   59 (125)
                      |+|-+.-..+.   ..|.    +.+ |-.+||+.+||+.++||+=++
T Consensus        12 p~Y~r~L~~l~---~~g~----~~i-SS~eLa~~~gi~~~qVRKDlS   50 (50)
T PF06971_consen   12 PLYLRYLKQLQ---EEGV----ERI-SSKELAEALGITPSQVRKDLS   50 (50)
T ss_dssp             HHHHHHHHHHH---H--------B---TTTHHHCCSS-HHHHHHHHH
T ss_pred             HHHHHHHHHHH---HCCC----EEE-CHHHHHHHHCCCHHHHHCCCC
T ss_conf             99999999999---8599----458-799999997979999612257


No 76 
>PF09182 PuR_N:  Bacterial purine repressor, N-terminal;  InterPro: IPR015265   The N-terminal domain of the bacterial purine repressor PuR is a winged-helix domain, a subdivision of the HTH structural family. It consists of a canonical arrangement of secondary structures: a1-b1-a2-T-a3-b2-W-b3, where a2-T-a3 is the HTH motif, a3 is the recognition helix, and W is the wing. The domain allows for recognition of a conserved CGAA sequence in the centre of a DNA PurBox, resulting in binding to the major groove of DNA . ; PDB: 1p4a_B 1o57_D.
Probab=50.03  E-value=7.1  Score=17.31  Aligned_cols=42  Identities=10%  Similarity=0.153  Sum_probs=34.2

Q ss_pred             CCCCCCCCHHHHHHHHCCCHHHHHHHHHHHH------HCCEEEECCCCE
Q ss_conf             9888178878999985898789999999998------879167317833
Q T0586            32 KGEDKLPSVREMGVKLAVNPNTVSRAYQELE------RAGYIYAKRGMG   74 (125)
Q Consensus        32 ~~G~~LPser~La~~~~VSr~TVr~Al~~L~------~~G~i~~~~g~G   74 (125)
                      .|+..+ |...+|+.|+++.+||.+-+..+.      ..|.|++.+|..
T Consensus        16 ~P~~li-~L~~F~e~~~~AKSsISEDl~iik~~~~~~~~G~leTi~GAa   63 (70)
T PF09182_consen   16 NPNKLI-SLTFFAERFGSAKSSISEDLVIIKETFEKEGLGRLETIPGAA   63 (70)
T ss_dssp             STT-----HHHHHHHHT--HHHHHHHHHHHHHHHHH-----EE------
T ss_pred             CCCCEE-CHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             997547-599999986331021476799999999875986399856877


No 77 
>PF04539 Sigma70_r3:  Sigma-70 region 3;  InterPro: IPR007624   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .  Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 1tty_A 1rp3_G 1sc5_A 1l0o_C 2a6h_F 3eql_P 2be5_P 2a6e_F 1zyr_F 2a68_F ....
Probab=47.59  E-value=5.7  Score=17.95  Aligned_cols=28  Identities=14%  Similarity=0.296  Sum_probs=24.5

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             8178878999985898789999999998
Q T0586            35 DKLPSVREMGVKLAVNPNTVSRAYQELE   62 (125)
Q Consensus        35 ~~LPser~La~~~~VSr~TVr~Al~~L~   62 (125)
                      -+-|+..++|+.+|+|..-|++++..-.
T Consensus        18 gR~Pt~eEIA~~lgis~~~v~~~~~~~~   45 (78)
T PF04539_consen   18 GREPTEEEIAEELGISEEEVRELLEASR   45 (78)
T ss_dssp             ----BHHHHHHH----HHHHHHHHHHHS
T ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHCC
T ss_conf             8898999999997888999999999746


No 78 
>PF04182 B-block_TFIIIC:  B-block binding subunit of TFIIIC;  InterPro: IPR007309 Yeast transcription factor IIIC (TFIIIC) is a multisubunit protein complex that interacts with two control elements of class III promoters called the A and B blocks. This family represents the subunit within TFIIIC involved in B-block binding .
Probab=47.08  E-value=7.9  Score=17.03  Aligned_cols=48  Identities=13%  Similarity=0.206  Sum_probs=38.6

Q ss_pred             HHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             9999976498998881788789999858987899999999988791673178
Q T0586            21 WMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG   72 (125)
Q Consensus        21 ~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g   72 (125)
                      .+-+.|....+. |.   ...+|++.+|+....+-.-.+.|.+.|+|+..+-
T Consensus         6 ~lLe~Ia~~r~~-Gi---~q~dL~k~~~~D~r~~~~~~k~L~~~gLI~k~~~   53 (75)
T PF04182_consen    6 CLLERIARSRYN-GI---TQSDLWKLFGQDPRSVFYRVKKLEDKGLIVKQQI   53 (75)
T ss_pred             HHHHHHHHHCCC-CC---CHHHHHHHHCCCCHHHHHHHHHHHHCCCEEEEEE
T ss_conf             999999967768-82---0537799858992256899999977899788883


No 79 
>PF03811 Ins_element1:  Insertion element protein;  InterPro: IPR003220 Insertion elements are mobile elements in DNA, usually encoding proteins required for transposition, for example transposases. This protein is absolutely required for transposition of insertion element 1.; GO: 0006313 transposition, DNA-mediated
Probab=47.08  E-value=6.1  Score=17.75  Aligned_cols=34  Identities=26%  Similarity=0.446  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             999999997649899888178878999985898789999999
Q T0586            18 ISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        18 I~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~   59 (125)
                      +...+.+...+|       + |.|..|..+|||.+||-+-++
T Consensus        52 ~k~~i~~l~~~G-------~-siR~iArvl~Is~~Tv~r~lK   85 (88)
T PF03811_consen   52 VKQKILELMVEG-------M-SIRDIARVLGISINTVLRWLK   85 (88)
T ss_pred             HHHHHHHHHHCC-------C-CHHHHHHHHCCCHHHHHHHHH
T ss_conf             999999998768-------5-199999986878999999986


No 80 
>PF10264 Stork_head:  Winged helix Storkhead-box1 domain
Probab=44.32  E-value=8.7  Score=16.75  Aligned_cols=29  Identities=21%  Similarity=0.398  Sum_probs=24.4

Q ss_pred             CHHHHHHHHHHHHHCCEEEECCCCEEEECC
Q ss_conf             878999999999887916731783368628
Q T0586            50 NPNTVSRAYQELERAGYIYAKRGMGSFVTS   79 (125)
Q Consensus        50 Sr~TVr~Al~~L~~~G~i~~~~g~G~~V~~   79 (125)
                      |...++.++..|..++-|+.. |.|+|+.-
T Consensus        50 s~e~~~~tL~~L~~e~kIY~t-~~GYfivt   78 (80)
T PF10264_consen   50 STEVLYNTLGTLIKERKIYHT-GEGYFIVT   78 (80)
T ss_pred             CHHHHHHHHHHHHHCCCEEEC-CCCEEEEC
T ss_conf             689999999999971632547-99668607


No 81 
>PF00196 GerE:  Bacterial regulatory proteins, luxR family;  InterPro: IPR000792   This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes.   The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers , , .   LuxR-type HTH proteins can be activated by one of four different mechanisms:   1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase , . Some proteins that belong to this category are:  Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes)   2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria : V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene)   3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE . B. subtilis gerE (transcription activator and repressor for the regulation of spore formation)   4) Multiple ligand-binding regulators, exemplified by malT . E. coli malT (activates maltose operon; MalT binds ATP and maltotriose) ; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1fse_B 2jpc_A 1x3u_A 1yio_A 1zn2_A 1p4w_A 3clo_B 1l3l_C 1h0m_B 2q0o_A ....
Probab=43.94  E-value=8.8  Score=16.71  Aligned_cols=25  Identities=20%  Similarity=0.368  Sum_probs=21.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             8789999858987899999999988
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELER   63 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~   63 (125)
                      +..++|..+|+|..||+.-...+..
T Consensus        20 ~~~eIA~~l~is~~TV~~~~~~i~~   44 (58)
T PF00196_consen   20 SNKEIAERLGISEKTVKSHRRRIMK   44 (58)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred             CCHHHHHHHCCCHHHHHHHHHHHHH
T ss_conf             8378998835452479999999999


No 82 
>PF09756 DDRGK:  DDRGK domain; PDB: 1wi9_A.
Probab=43.65  E-value=7.3  Score=17.25  Aligned_cols=58  Identities=17%  Similarity=0.295  Sum_probs=41.0

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEC---CCCEEEECCCH
Q ss_conf             99999999764989988817887899998589878999999999887916731---78336862880
Q T0586            18 ISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAK---RGMGSFVTSDK   81 (125)
Q Consensus        18 I~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~---~g~G~~V~~~~   81 (125)
                      +-....+.|...      ++-...+||..||++..-+..-++.|+..|.|.-.   +|+-.||++..
T Consensus       100 lL~~Fi~~Ik~~------k~v~l~~la~~f~l~t~~~i~ri~~L~~~~~i~Gv~DdrGk~iyis~~E  160 (188)
T PF09756_consen  100 LLQDFINYIKKK------KVVNLEDLAAEFGLKTQDVINRIQELEEQGRITGVIDDRGKFIYISQEE  160 (188)
T ss_dssp             -HHHHHHHHHH-------SEE-HHHHHHH----HHHHHHHHHHHHH-------B-----EE------
T ss_pred             HHHHHHHHHHHC------CEEEHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEECCCCCEEEECHHH
T ss_conf             999999999986------8310999998909987999999999998798446885998868855999


No 83 
>PF06504 RepC:  Replication protein C (RepC);  InterPro: IPR010522   This family consists of several bacterial replication protein C (RepC) sequences.
Probab=43.53  E-value=8.9  Score=16.67  Aligned_cols=67  Identities=15%  Similarity=0.099  Sum_probs=51.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHC------CCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             768889889999999999976498998881788789999858------9878999999999887916731783
Q T0586             7 TFHADKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLA------VNPNTVSRAYQELERAGYIYAKRGM   73 (125)
Q Consensus         7 ~~~~~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~------VSr~TVr~Al~~L~~~G~i~~~~g~   73 (125)
                      .-+...+.++|+.-.|.-+..+-.-.+=-.--|.++|+.++|      .....|++.+.+|..-.+++.+.++
T Consensus        81 ~~~p~~e~g~qLRl~Le~k~ea~~~~~~~vktS~r~La~~~Gy~~d~g~~~~~IresL~RL~~Vsv~~~~~~~  153 (281)
T PF06504_consen   81 PPEPKTEIGQQLRLFLEPKWEAVEDDAMVVKTSYRSLASELGYADDGGKNFRRIRESLERLWNVSVIVQRGGK  153 (281)
T ss_pred             CCCCCCCHHHHHHHHHCCCCCCCCCCCEEEHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHCCEEEEECCCC
T ss_conf             8888883257788651446333546542541529999998286677882089999999986286899974753


No 84 
>PF05402 PqqD:  Coenzyme PQQ synthesis protein D (PqqD);  InterPro: IPR008792 This family contains several bacterial coenzyme PQQ synthesis protein D (PqqD) sequences. This protein is required for coenzyme pyrrolo-quinoline-quinone (PQQ) biosynthesis.; GO: 0018189 pyrroloquinoline quinone biosynthetic process
Probab=42.74  E-value=9.2  Score=16.59  Aligned_cols=29  Identities=24%  Similarity=0.447  Sum_probs=19.9

Q ss_pred             HHHHHHHHCCCHHHHH----HHHHHHHHCCEEE
Q ss_conf             7899998589878999----9999998879167
Q T0586            40 VREMGVKLAVNPNTVS----RAYQELERAGYIY   68 (125)
Q Consensus        40 er~La~~~~VSr~TVr----~Al~~L~~~G~i~   68 (125)
                      ...|+++|++++.++.    .-+..|.+.|+|+
T Consensus        49 v~~L~~~Y~~~~e~~~~dv~~fL~~L~~~~lIE   81 (81)
T PF05402_consen   49 VAELAEEYDVDPEEIEQDVLAFLEQLREKGLIE   81 (81)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             999998819978999999999999999874939


No 85 
>PF07022 Phage_CI_repr:  Bacteriophage CI repressor helix-turn-helix domain;  InterPro: IPR010744   This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic .; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0016481 negative regulation of transcription; PDB: 2fjr_A 3bd1_B.
Probab=42.60  E-value=3.6  Score=19.25  Aligned_cols=22  Identities=27%  Similarity=0.332  Sum_probs=17.7

Q ss_pred             CCHHHHHHHHCCCHHHHH-HHHH
Q ss_conf             887899998589878999-9999
Q T0586            38 PSVREMGVKLAVNPNTVS-RAYQ   59 (125)
Q Consensus        38 Pser~La~~~~VSr~TVr-~Al~   59 (125)
                      -+..+||+.+|||++|+. ...+
T Consensus        13 ~~~~elA~~LgIs~stvs~~~~~   35 (66)
T PF07022_consen   13 KTDKELAEKLGISQSTVSHTWKK   35 (66)
T ss_dssp             -SCHHHHCCTT--HHHHH-HHHH
T ss_pred             CCHHHHHHHHCCCHHHHHHHHHH
T ss_conf             96999999919988885567641


No 86 
>PF07377 DUF1493:  Protein of unknown function (DUF1493);  InterPro: IPR010862   This family consists of several bacterial proteins of around 115 residues in length. Members of this family seem to be found exclusively in Salmonella and Yersinia species and several have been described as being putative cytoplasmic proteins. The function of this family is unknown.
Probab=41.96  E-value=9.4  Score=16.51  Aligned_cols=53  Identities=11%  Similarity=0.214  Sum_probs=47.4

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf             88999999999997649899888178878999985898789999999998879
Q T0586            13 PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAG   65 (125)
Q Consensus        13 Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G   65 (125)
                      -+.+||.+.+++.+-.+.+..+..|.....|...|+++..-+.+.+....+.=
T Consensus         3 ~i~~~i~~fvr~e~g~~l~~~~~~lt~~TdL~~DL~~~gdDa~e~m~~f~~~F   55 (111)
T PF07377_consen    3 DIWKEILEFVREEIGTPLFKKKIELTPDTDLNEDLGLDGDDAEEFMEKFFERF   55 (111)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCCCCCCCCCCHHHHCCCCHHHHHHHHHHHHHHC
T ss_conf             59999999999870744357777068877478752997689999999999981


No 87 
>PF03962 Mnd1:  Mnd1 family;  InterPro: IPR005647 This family of proteins includes meiotic nuclear division protein 1 (MND1) from Saccharomyces cerevisiae. The mnd1 protein forms a complex with hop2 to promote homologous chromosome pairing and meiotic double-strand break repair .
Probab=41.90  E-value=9.5  Score=16.51  Aligned_cols=33  Identities=21%  Similarity=0.254  Sum_probs=27.1

Q ss_pred             HHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEE
Q ss_conf             9985898789999999998879167317833686
Q T0586            44 GVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFV   77 (125)
Q Consensus        44 a~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V   77 (125)
                      .+.-||+..+|.+.++.|.++|+|.... .|+-.
T Consensus        22 pK~~gI~~m~VKdvlQ~LvDDglV~~EK-iGssn   54 (188)
T PF03962_consen   22 PKVKGINSMSVKDVLQSLVDDGLVEVEK-IGSSN   54 (188)
T ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCHHHH-CCCEE
T ss_conf             6324976402999999986367621021-07755


No 88 
>PF08535 KorB:  KorB domain;  InterPro: IPR013741   This entry contains several KorB transcriptional repressor proteins. The korB gene is a major regulatory element in the replication and maintenance of broad host-range plasmid RK2. It negatively controls the replication gene trfA, the host-lethal determinants kilA and kilB, and the korA-korB operon . This domain includes the DNA-binding HTH motif . ; PDB: 1r71_B.
Probab=40.89  E-value=3  Score=19.79  Aligned_cols=37  Identities=16%  Similarity=0.141  Sum_probs=27.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEE
Q ss_conf             8789999858987899999999988791673178336
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGS   75 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~   75 (125)
                      |..++|+.+|-|+++|...+..|.--..|...-..|.
T Consensus         5 tq~eIA~~lGks~s~Vs~~L~Ll~lp~~v~~~v~~G~   41 (93)
T PF08535_consen    5 TQEEIAKRLGKSRSWVSNHLRLLDLPEDVKEAVEEGR   41 (93)
T ss_dssp             ----HHHH----HHHHHHHHGGGS--HHHHHHHH---
T ss_pred             CHHHHHHHHCCCHHHHHHHHHHHCCCHHHHHHHHCCC
T ss_conf             9999999988799999999998669999999999599


No 89 
>PF03180 Lipoprotein_9:  NLPA lipoprotein;  InterPro: IPR004872   This family of bacterial lipoproteins contains several antigenic members, that may be involved in bacterial virulence. Their precise function is unknown. However they are probably distantly related to IPR001638 from INTERPRO which are solute binding proteins. ; PDB: 1p99_A 1xs5_A.
Probab=40.87  E-value=8  Score=16.97  Aligned_cols=30  Identities=37%  Similarity=0.443  Sum_probs=25.1

Q ss_pred             CHHHHHHHHHHHHHCCEEEECCCCEEEECC
Q ss_conf             878999999999887916731783368628
Q T0586            50 NPNTVSRAYQELERAGYIYAKRGMGSFVTS   79 (125)
Q Consensus        50 Sr~TVr~Al~~L~~~G~i~~~~g~G~~V~~   79 (125)
                      .++---+||..|++.|+|..+++.|...+.
T Consensus       105 DpsN~~RAL~lLq~~GLIkLk~~~~~~~t~  134 (237)
T PF03180_consen  105 DPSNQGRALLLLQEAGLIKLKDGNGLTATV  134 (237)
T ss_dssp             SHHHHHHHHHHHHH----EE-TT------G
T ss_pred             CCCCHHHHHHHHHHCCCEEECCCCCCCCCH
T ss_conf             976586999999848957986899976784


No 90 
>PF07750 GcrA:  GcrA cell cycle regulator;  InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis . During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes . More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery .
Probab=40.74  E-value=7.3  Score=17.25  Aligned_cols=29  Identities=28%  Similarity=0.360  Sum_probs=23.5

Q ss_pred             CCCCHHHHHHHHC-CCHHHHHHHHHHHHHCC
Q ss_conf             1788789999858-98789999999998879
Q T0586            36 KLPSVREMGVKLA-VNPNTVSRAYQELERAG   65 (125)
Q Consensus        36 ~LPser~La~~~~-VSr~TVr~Al~~L~~~G   65 (125)
                      -| |-+++|++|| |||+.|.-=+++|.-.+
T Consensus        18 Gl-SasqIA~~LGgvsRNAViGK~hRLgL~~   47 (162)
T PF07750_consen   18 GL-SASQIAKQLGGVSRNAVIGKVHRLGLSG   47 (162)
T ss_pred             CC-CHHHHHHHHCCCCHHHHHHHHHHCCCCC
T ss_conf             88-8999999975520666777776436666


No 91 
>PF00165 HTH_AraC:  Bacterial regulatory helix-turn-helix proteins, AraC family;  InterPro: IPR000005   Many bacterial transcription regulation proteins bind DNA through a 'helix-turn-helix' (HTH) motif. One major subfamily of these proteins ,  is related to the arabinose operon regulatory protein AraC , . Except for celD , all of these proteins seem to be positive transcriptional factors.   Although the sequences belonging to this family differ somewhat in length, in nearly every case the HTH motif is situated towards the C-terminus in the third quarter of most of the sequences. The minimal DNA binding domain spans roughly 100 residues and comprises two HTH subdomains; the classical HTH domain and another HTH subdomain with similarity to the classical HTH domain but with an insertion of one residue in the turn-region. The N-terminal and central regions of these proteins are presumed to interact with effector molecules and may be involved in dimerization .   The known structure of MarA (P27246 from SWISSPROT) shows that the AraC domain is alpha helical and shows the two HTH subdomains both bind the major groove of the DNA. The two HTH subdomains are separated by only 27 angstroms, which causes the cognate DNA to bend.; GO: 0003700 transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1xs9_A 1bl0_A 1d5y_A 1wpk_A 2k9s_A 1zgw_A 1u8b_A.
Probab=38.70  E-value=11  Score=16.19  Aligned_cols=28  Identities=18%  Similarity=0.401  Sum_probs=23.7

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             88178878999985898789999999998
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQELE   62 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~~L~   62 (125)
                      .+.+ ++.++|..+|+|++...+.++..-
T Consensus         6 ~~~~-~i~~iA~~~g~s~~~~~r~Fk~~~   33 (42)
T PF00165_consen    6 SEPI-SIEDIAEELGYSPSYFSRLFKKEF   33 (42)
T ss_dssp             CSS---HHHHHHHTTSSHHHHHHHHHHHC
T ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             8989-799999997989999999999999


No 92 
>PF01381 HTH_3:  Helix-turn-helix;  InterPro: IPR001387   This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2ef8_B 3f6w_A 3eus_A 1x57_A 1utx_A 2gzu_A 1rio_A 1lli_A 1lmb_3 3bdn_B ....
Probab=38.19  E-value=8.1  Score=16.93  Aligned_cols=21  Identities=29%  Similarity=0.428  Sum_probs=17.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHH
Q ss_conf             878999985898789999999
Q T0586            39 SVREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~   59 (125)
                      |..++|+.+|||++||.+-.+
T Consensus        11 s~~~la~~~gis~~~i~~~e~   31 (55)
T PF01381_consen   11 SQEELARRLGISRSTISRIEN   31 (55)
T ss_dssp             -HHHHHHHHTS-HHHHHHHHT
T ss_pred             CHHHHHHHCCCCHHHHHHHHC
T ss_conf             999998864987878889976


No 93 
>PF10557 Cullin_Nedd8:  Cullin protein neddylation domain; PDB: 3dpl_C 3dqv_C 1iuy_A 2do7_A 2hye_C 1ldk_B 1u6g_A 1ldj_A.
Probab=37.87  E-value=7.6  Score=17.15  Aligned_cols=30  Identities=10%  Similarity=0.187  Sum_probs=25.5

Q ss_pred             HHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             999858987899999999988791673178
Q T0586            43 MGVKLAVNPNTVSRAYQELERAGYIYAKRG   72 (125)
Q Consensus        43 La~~~~VSr~TVr~Al~~L~~~G~i~~~~g   72 (125)
                      +...|.++...+.+++..|...|||.+..+
T Consensus        36 l~~~f~~~~~~ik~~Ie~LIekeyi~Rd~~   65 (68)
T PF10557_consen   36 LKKRFPPTVSDIKKRIEYLIEKEYIERDEN   65 (68)
T ss_dssp             TTTSS---HHHHHHHHHHHHHTTSEEEESS
T ss_pred             HHCCCCCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             746479999999999999998548871889


No 94 
>PF02954 HTH_8:  Bacterial regulatory protein, Fis family;  InterPro: IPR002197   The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences ,. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli . Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion.    In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor .    The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution ,. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as 'feelers' suitable for DNA or protein (invertase) recognition . Other proteins belonging to this subfamily include: Escherichia coli: atoC, hydG, ntrC, fhlA, tyrR,  Rhizobium spp.: ntrC, nifA, dctD  ; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1ojl_E 1fip_A 1etw_B 4fis_B 1fia_A 1etq_D 3fis_A 1f36_A 1ety_B 1etx_A ....
Probab=37.85  E-value=9.8  Score=16.40  Aligned_cols=22  Identities=14%  Similarity=0.283  Sum_probs=17.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             8789999858987899999999
Q T0586            39 SVREMGVKLAVNPNTVSRAYQE   60 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~   60 (125)
                      +..+-|+.+||||+|+.+=++.
T Consensus        20 n~~~aA~~Lgi~r~tL~~klkk   41 (42)
T PF02954_consen   20 NISKAARLLGISRSTLYRKLKK   41 (42)
T ss_dssp             -HHHHHHH----HHHHHHHHHH
T ss_pred             CHHHHHHHHCCCHHHHHHHHHH
T ss_conf             8999999979899999999984


No 95 
>PF05848 CtsR:  Firmicute transcriptional repressor of class III stress genes (CtsR);  InterPro: IPR008463 This family consists of several Firmicute transcriptional repressor of class III stress gene (CtsR) proteins. CtsR of L. monocytogenes negatively regulates the clpC, clpP and clpE genes belonging to the CtsR regulon .
Probab=37.55  E-value=11  Score=16.11  Aligned_cols=63  Identities=17%  Similarity=0.311  Sum_probs=43.8

Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHH--HHHCC-EEEECCCCEEEEC
Q ss_conf             89999999999976498998881788789999858987899999999--98879-1673178336862
Q T0586            14 IYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQE--LERAG-YIYAKRGMGSFVT   78 (125)
Q Consensus        14 ly~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~--L~~~G-~i~~~~g~G~~V~   78 (125)
                      +...|..+|+..+....  .|.-----.+||++|++.|+-+.-+++-  =.+.| +|++++|-|=|+.
T Consensus         4 iSDiIE~ylK~~L~~s~--~~~iEIkR~eLA~~F~CvPSQINYVi~TRFT~e~GY~VESkRGGGGYIR   69 (152)
T PF05848_consen    4 ISDIIEQYLKQLLEESE--EGQIEIKRNELADRFDCVPSQINYVISTRFTPERGYLVESKRGGGGYIR   69 (152)
T ss_pred             HHHHHHHHHHHHHHHCC--CCEEEEEHHHHHHHHCCCHHHCCEEEECCCCCCCCEEEEEECCCCCEEE
T ss_conf             78999999999997387--8728654888888718674661045542523778728986338986799


No 96 
>PF12481 DUF3700:  Aluminium induced protein 
Probab=37.01  E-value=6.6  Score=17.54  Aligned_cols=55  Identities=16%  Similarity=0.359  Sum_probs=30.6

Q ss_pred             CCCCCCCCCCHHHHHHHHHHHHH---HCCCCCCCCCCCCHHHHHHHHCCCHHH-----HHHHHHHHHHCC
Q ss_conf             77776888988999999999997---649899888178878999985898789-----999999998879
Q T0586             4 MNPTFHADKPIYSQISDWMKKQM---ITGEWKGEDKLPSVREMGVKLAVNPNT-----VSRAYQELERAG   65 (125)
Q Consensus         4 M~~~~~~~~Ply~qI~~~l~~~I---~~G~l~~G~~LPser~La~~~~VSr~T-----Vr~Al~~L~~~G   65 (125)
                      |....+...|+..+.+.-+ +.|   ..|.      |-..-.|-++||.|++|     |-|||+-|.+.|
T Consensus        57 lAys~~~~~~l~pR~F~~~-DdIfClF~G~------L~NL~~L~qqYGLsK~~nEa~lVIEAYrtLRDRg  119 (124)
T PF12481_consen   57 LAYSHHNQSPLRPRLFCVV-DDIFCLFQGS------LDNLCSLRQQYGLSKSANEAMLVIEAYRTLRDRG  119 (124)
T ss_pred             EEEECCCCCCCCCCEEEEE-CCEEEEEECH------HHHHHHHHHHHCCCCCCCEEEEEHHHHHHHHHCC
T ss_conf             8986488888765314641-5678998521------4438889998485667644756088887765159


No 97 
>PF07374 DUF1492:  Protein of unknown function (DUF1492);  InterPro: IPR010861   This family consists of several hypothetical, highly conserved Streptococcal and related phage proteins of around 100 residues in length. The function of this family is unknown.
Probab=36.43  E-value=11  Score=15.96  Aligned_cols=25  Identities=36%  Similarity=0.441  Sum_probs=15.0

Q ss_pred             CCCCHHHHHHHHCCCHHHH----HHHHHHH
Q ss_conf             1788789999858987899----9999999
Q T0586            36 KLPSVREMGVKLAVNPNTV----SRAYQEL   61 (125)
Q Consensus        36 ~LPser~La~~~~VSr~TV----r~Al~~L   61 (125)
                      ++ +..+.|+.+|+|++|+    ++|+..|
T Consensus        71 ~~-~~~~I~~~L~iS~~tyYr~~~kAl~~L   99 (100)
T PF07374_consen   71 KL-SWDEICEELNISRSTYYRKKRKALKEL   99 (100)
T ss_pred             CC-CHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf             59-899999998788999999999999841


No 98 
>PF05158 RNA_pol_Rpc34:  RNA polymerase Rpc34 subunit;  InterPro: IPR007832 The family comprises a subunit specific to RNA Pol III, the tRNA specific polymerase. The C34 subunit of Saccharomyces cerevisiae RNA Pol III is part of a subcomplex of three subunits which have no counterpart in the other two nuclear RNA polymerases. This subunit interacts with TFIIIB70 and therefore participates in Pol III recruitment .; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription, 0005634 nucleus; PDB: 2dk5_A 2yu3_A 2dk8_A.
Probab=34.52  E-value=12  Score=15.76  Aligned_cols=31  Identities=19%  Similarity=0.321  Sum_probs=17.1

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHCCEEEEC
Q ss_conf             7899998589878999999999887916731
Q T0586            40 VREMGVKLAVNPNTVSRAYQELERAGYIYAK   70 (125)
Q Consensus        40 er~La~~~~VSr~TVr~Al~~L~~~G~i~~~   70 (125)
                      .++|....|+..+.|.++++.|+..++|...
T Consensus       104 tk~ik~~tnL~~~~v~k~LK~Le~k~lIKsV  134 (325)
T PF05158_consen  104 TKDIKKKTNLHQNQVNKCLKSLESKKLIKSV  134 (325)
T ss_dssp             HHHHHHHCT--HHHHHHHHHHHHHTTSEEEE
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHCCCEEEE
T ss_conf             9999987499899999999999857986753


No 99 
>PF06322 Phage_NinH:  Phage NinH protein;  InterPro: IPR010454   This family consists of several phage NinH proteins. The function of this family is unknown.
Probab=34.50  E-value=8.6  Score=16.77  Aligned_cols=27  Identities=19%  Similarity=0.123  Sum_probs=21.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCC
Q ss_conf             878999985898789999999998879
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAG   65 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G   65 (125)
                      ...+.|..++++|.|||+-..-.+.+.
T Consensus        18 N~teVaR~L~c~R~TVrkY~~D~~g~~   44 (64)
T PF06322_consen   18 NQTEVARMLNCYRATVRKYARDKEGKK   44 (64)
T ss_pred             CHHHHHHHHCCHHHHHHHHHCCCCCCE
T ss_conf             689887885101887997722556624


No 100
>PF10141 ssDNA-exonuc_C:  Single-strand DNA-specific exonuclease, C terminal domain
Probab=33.59  E-value=13  Score=15.66  Aligned_cols=68  Identities=16%  Similarity=0.150  Sum_probs=52.6

Q ss_pred             CCCHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCCH
Q ss_conf             89889999999999976498998881788789999858987899999999988791673178336862880
Q T0586            11 DKPIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDK   81 (125)
Q Consensus        11 ~~Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~~   81 (125)
                      ..|--++-+...+.-.....+.-...+   .+||..+|+++.++.--++...+-|+|....|.=+.+....
T Consensus        93 g~PtRe~F~~lYk~i~~~~~~~l~~~~---~~La~~l~~~~~~l~FMi~VF~EL~FVtiedG~i~~~~~~~  160 (195)
T PF10141_consen   93 GMPTREQFAKLYKFIYQHPEFDLRKKL---MQLAKYLGWSKETLIFMIQVFFELGFVTIEDGVITVNKNPE  160 (195)
T ss_pred             CCCCHHHHHHHHHHHHHCCCCCHHHHH---HHHHHHHCCCHHHHHHHHHHHHHCCCEEEECCEEEECCCCC
T ss_conf             599899999999999967999878899---99988859799999999999987390797788886258856


No 101
>PF04545 Sigma70_r4:  Sigma-70, region 4;  InterPro: IPR007630   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .  Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif . Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription, DNA-dependent; PDB: 2p7v_B 1tlh_B 1tty_A 2a6h_F 3eql_P 2be5_P 2a6e_F 1zyr_F 2a68_F 2a69_F ....
Probab=33.52  E-value=2.5  Score=20.26  Aligned_cols=27  Identities=19%  Similarity=0.359  Sum_probs=21.2

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             8817887899998589878999999999
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQEL   61 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~~L   61 (125)
                      .+.+ |..++|+.+|+|+.||+.-++.-
T Consensus        18 ~~~~-t~~eIa~~lg~s~~~V~~~~~ra   44 (50)
T PF04545_consen   18 FEGL-TLEEIAERLGISESTVRQRLKRA   44 (50)
T ss_dssp             TST--CTCCCHHHHHHHHHHHHHHHHHH
T ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHH
T ss_conf             4999-99999989797999998999999


No 102
>PF04936 DUF658:  Protein of unknown function (DUF658);  InterPro: IPR007020   These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage. 
Probab=33.30  E-value=9.5  Score=16.49  Aligned_cols=30  Identities=20%  Similarity=0.169  Sum_probs=18.0

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             8789999858987899999999988791673178
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG   72 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g   72 (125)
                      +..++|+.|+||+++|-    .+...|.+-.+.+
T Consensus        16 t~~e~~~~~~vS~~sv~----~WvKNG~~p~~a~   45 (186)
T PF04936_consen   16 TIDEIADYFDVSRASVS----LWVKNGKDPKKAN   45 (186)
T ss_pred             CHHHHHHHHCCCHHHHH----HHHHCCCCCCCCC
T ss_conf             38999998756899999----9998388872334


No 103
>PF07278 DUF1441:  Protein of unknown function (DUF1441);  InterPro: IPR009901   This family consists of several hypothetical Enterobacterial proteins of around 160 residues in length. The function of this family is unknown.
Probab=31.12  E-value=14  Score=15.47  Aligned_cols=26  Identities=15%  Similarity=0.351  Sum_probs=21.6

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             178878999985898789999999998
Q T0586            36 KLPSVREMGVKLAVNPNTVSRAYQELE   62 (125)
Q Consensus        36 ~LPser~La~~~~VSr~TVr~Al~~L~   62 (125)
                      ++ |+.+||+.||..|.||.+=++-+.
T Consensus         1 ~~-nI~qla~~~glhRqTV~~Rl~~~~   26 (152)
T PF07278_consen    1 KL-NINQLAELFGLHRQTVAKRLKGAN   26 (152)
T ss_pred             CC-CHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             98-799999998421999999970799


No 104
>PF09048 Cro:  Cro;  InterPro: IPR000655   Bacteriophage lambda encodes two repressors: the Cro repressor that acts to turn off early gene transcription during the lytic cycle, and the lambda or cI repressor that is required to maintain lysogenic growth. Together the Cro and cI repressors form a helix-turn-helix (HTH) superfamily. The lambda Cro repressor binds to DNA as a highly flexible dimer. The crystal structure of the lambda Cro repressor  reveals a HTH DNA-binding protein with an alpha/beta fold that differs from other Cro family members, possibly by an evolutionary fold change . Most Cro proteins, such as P22 Cro and phage 434 Cro, have an all-alpha structure that is thought to be ancestral to lambda Cro, where the fourth and fifth helices are replaced by a beta-sheet, possibly as a result of secondary structure switching rather than by nonhomologous replacement . This entry represents the lambda-type Cro repressor with an alpha/beta topology.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1cop_D 2a63_A 2ovg_A 1d1m_A 6cro_A 5cro_B 1orc_A 2ecs_B 1d1l_A 3orc_A ....
Probab=29.47  E-value=15  Score=15.22  Aligned_cols=23  Identities=17%  Similarity=0.200  Sum_probs=19.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             87899998589878999999999
Q T0586            39 SVREMGVKLAVNPNTVSRAYQEL   61 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L   61 (125)
                      .....|+.|||+.+-|.+|++.=
T Consensus        14 GQak~A~~lGV~qsAISKairag   36 (59)
T PF09048_consen   14 GQAKAAKALGVTQSAISKAIRAG   36 (59)
T ss_dssp             -HHHHHHH----HHHHHHHHH--
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHC
T ss_conf             67999998297689999999828


No 105
>PF09107 SelB-wing_3:  Elongation factor SelB, winged helix ;  InterPro: IPR015191   This entry represents a domain with a winged helix-type fold, which consists of a closed 3-helical bundle with a right-handed twist, and a small beta-sheet wing . Different winged helix domains share a common structure, but can differ in sequence. This entry is designated "type 3".    The winged helix motif is involved in both DNA and RNA binding. In the elongation factor SelB, the winged helix domains recognise RNA, allowing the complex to wrap around the small ribosomal subunit. In bacteria, the incorporation of the amino acid selenocysteine into proteins requires elongation factor SelB, which binds both transfer RNA (tRNA) and mRNA. SelB binds to an mRNA hairpin formed by the selenocysteine insertion sequence (SECIS) with extremely high specificity . ; GO: 0003723 RNA binding, 0003746 translation elongation factor activity, 0005525 GTP binding, 0001514 selenocysteine incorporation, 0005737 cytoplasm; PDB: 2pjp_A 2uwm_B 2ply_A 1wsu_D 1lva_A.
Probab=28.86  E-value=15  Score=15.15  Aligned_cols=39  Identities=13%  Similarity=0.166  Sum_probs=34.3

Q ss_pred             CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             8881788789999858987899999999988791673178
Q T0586            33 GEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRG   72 (125)
Q Consensus        33 ~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g   72 (125)
                      .+..+ +..++-+.+|.||-.+-.-+..|...|++.+..+
T Consensus         7 ~~~~i-~va~~rd~~g~sRK~ai~lLE~~D~~~~T~R~gd   45 (50)
T PF09107_consen    7 KNGEI-TVAEFRDALGLSRKYAIPLLEYFDREGITRRVGD   45 (50)
T ss_dssp             T---B-EHHHHHHH----HHHHHHHHHHHHHTTSEEE---
T ss_pred             CCCCC-CHHHHHHHHCCCHHHHHHHHHHHHCCCCEEEECC
T ss_conf             48957-2999999978539999999998750298786399


No 106
>PF05331 DUF742:  Protein of unknown function (DUF742);  InterPro: IPR007995   This family consists of several uncharacterised Streptomyces proteins as well as one from Mycobacterium tuberculosis. The function of these proteins is unknown.
Probab=28.25  E-value=11  Score=16.15  Aligned_cols=39  Identities=26%  Similarity=0.301  Sum_probs=34.9

Q ss_pred             CCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEE
Q ss_conf             1788789999858987899999999988791673178336
Q T0586            36 KLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGS   75 (125)
Q Consensus        36 ~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~   75 (125)
                      .+ |+.|+|..+++-.++||==+.-|.+.|+|..+.-...
T Consensus        55 p~-SVAEiAA~L~LPlgVvrVLl~DL~~~G~v~v~~p~~~   93 (114)
T PF05331_consen   55 PL-SVAEIAAHLRLPLGVVRVLLSDLLDAGLVRVRAPVPS   93 (114)
T ss_pred             CC-CHHHHHHHCCCCCCEEEEEHHHHHHCCCEEEECCCCC
T ss_conf             63-0999998619983011005776976897786079876


No 107
>PF10543 ORF6N:  ORF6N domain
Probab=28.20  E-value=16  Score=15.08  Aligned_cols=41  Identities=7%  Similarity=0.170  Sum_probs=30.8

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECC-CCEEEECC
Q ss_conf             88178878999985898789999999998879167317-83368628
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKR-GMGSFVTS   79 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~-g~G~~V~~   79 (125)
                      |.+.-+..+||+.||+-..+++++++.=.+     +-+ |..+|.-.
T Consensus         9 g~~Vmt~~~lA~lyg~~~~~i~~~~~rN~~-----rF~eg~~~f~L~   50 (88)
T PF10543_consen    9 GQRVMTDEDLAELYGVETKRINQNFKRNRD-----RFPEGDDYFQLT   50 (88)
T ss_pred             CEEEEEHHHHHHHHCCCHHHHHHHHHHHHH-----HCCCCCEEEEEC
T ss_conf             978987999999959686799999997486-----378887599972


No 108
>PF06353 DUF1062:  Protein of unknown function (DUF1062);  InterPro: IPR009412   This family consists of several hypothetical bacterial proteins of unknown function.
Probab=27.73  E-value=16  Score=15.02  Aligned_cols=38  Identities=21%  Similarity=0.249  Sum_probs=28.2

Q ss_pred             CCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             89988817887899998589878999999999887916731783
Q T0586            30 EWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM   73 (125)
Q Consensus        30 ~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~   73 (125)
                      .++..-++  .+-|++.+|+||+-+    +.|.+.|.|...+++
T Consensus        98 ~~~~~vRl--~~lLa~~L~LSrs~l----~~L~~~G~I~~~~~~  135 (142)
T PF06353_consen   98 PFPFPVRL--DRLLAEELGLSRSRL----QRLIEQGKIRSDPGK  135 (142)
T ss_pred             CCCCCCCH--HHHHHHHHCCCHHHH----HHHHHCCCEEECCCC
T ss_conf             78777529--999998838479999----999988977825740


No 109
>PF04337 DUF480:  Protein of unknown function, DUF480;  InterPro: IPR007432 This family consists of several proteins of uncharacterised function.; PDB: 3bz6_A.
Probab=27.69  E-value=8.9  Score=16.69  Aligned_cols=34  Identities=26%  Similarity=0.469  Sum_probs=28.5

Q ss_pred             HCCCHHHHHHHHHHHHHCCEEEECCCCEEEECCCH
Q ss_conf             58987899999999988791673178336862880
Q T0586            47 LAVNPNTVSRAYQELERAGYIYAKRGMGSFVTSDK   81 (125)
Q Consensus        47 ~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~V~~~~   81 (125)
                      +++|-+.|..|+..|...|++.. .+.|..|..-.
T Consensus        44 m~lse~eV~~ald~L~~~~Lv~~-~~~gsRv~ky~   77 (148)
T PF04337_consen   44 MNLSESEVQQALDELRKKGLVRE-SGFGSRVPKYE   77 (148)
T ss_dssp             ----------HHHHH-----EEE--E------EEE
T ss_pred             CCCCHHHHHHHHHHHHHCCCEEE-CCCCCCHHHHH
T ss_conf             26789999999999997847001-26775148999


No 110
>PF00440 TetR_N:  Bacterial regulatory proteins, tetR family;  InterPro: IPR001647   This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD , , . Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution . TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003700 transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1zk8_A 2oi8_A 2g7l_A 2opt_B 3b6a_F 3b6c_B 2hxo_A 2hxi_B 1z0x_B 1bjy_A ....
Probab=27.46  E-value=16  Score=14.99  Aligned_cols=24  Identities=13%  Similarity=0.480  Sum_probs=19.5

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHH
Q ss_conf             8178878999985898789999999
Q T0586            35 DKLPSVREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        35 ~~LPser~La~~~~VSr~TVr~Al~   59 (125)
                      +.+ |.+++|+..|||++++-.-+.
T Consensus        15 ~~~-t~~~ia~~agvs~~~iy~~F~   38 (47)
T PF00440_consen   15 EAV-TIRDIAERAGVSRGSIYRHFP   38 (47)
T ss_dssp             TTS-SHHHHHHHHTSBHHHHHHHSS
T ss_pred             CCC-CHHHHHHHHCCCCCCHHHHCC
T ss_conf             218-799999876479350256569


No 111
>PF01527 Transposase_8:  Transposase;  InterPro: IPR002514   Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 .   More information about these proteins can be found at Protein of the Month: Transposase .; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2rn7_A 2jn6_A.
Probab=27.33  E-value=6.9  Score=17.39  Aligned_cols=24  Identities=25%  Similarity=0.408  Sum_probs=22.3

Q ss_pred             CHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             878999985898789999999998
Q T0586            39 SVREMGVKLAVNPNTVSRAYQELE   62 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~~L~   62 (125)
                      |..++|..||||++|+..=.+...
T Consensus        25 s~~~va~~~gI~~~tl~~W~~~~~   48 (76)
T PF01527_consen   25 SVSEVAREYGISPSTLYRWVRQYR   48 (76)
T ss_dssp             HHHHHCCC----HHHHHHHHHHHH
T ss_pred             CHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             799999970533026669999986


No 112
>PF04645 DUF603:  Protein of unknown function, DUF603;  InterPro: IPR006739 This family includes several uncharacterised proteins from Borrelia species.
Probab=27.16  E-value=16  Score=14.96  Aligned_cols=32  Identities=25%  Similarity=0.289  Sum_probs=24.6

Q ss_pred             CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Q ss_conf             9988817887899998589878999999999887
Q T0586            31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQELERA   64 (125)
Q Consensus        31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~   64 (125)
                      |+.|. | +-.++|+.+||||.-|-++=+.-+.-
T Consensus        15 F~eG~-L-~D~eIA~~LGVsr~nV~kmR~Kwes~   46 (181)
T PF04645_consen   15 FKEGS-L-NDAEIAQELGVSRVNVWKMRQKWESS   46 (181)
T ss_pred             HHCCC-C-CHHHHHHHHCCHHHHHHHHHHHHHHC
T ss_conf             95388-7-57999999782199999999998813


No 113
>PF04760 IF2_N:  Translation initiation factor IF-2, N-terminal region;  InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms . Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1nd9_A.
Probab=26.87  E-value=15  Score=15.19  Aligned_cols=36  Identities=17%  Similarity=0.320  Sum_probs=23.2

Q ss_pred             CCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             817887899998589878999999999887916731783
Q T0586            35 DKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGM   73 (125)
Q Consensus        35 ~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~   73 (125)
                      +++ ++.+||+.+|++...+-+.+.  .+.|+-...+++
T Consensus         2 ~~~-rV~elAk~l~~~~~~ii~~L~--~~~Gi~~~~~~~   37 (54)
T PF04760_consen    2 EKI-RVYELAKELGVSSKEIIKKLF--KELGIMVKSHNS   37 (54)
T ss_dssp             -EE--TTHHHHHHSSSHHHHHHHH---HH------SSSS
T ss_pred             CCE-EHHHHHHHHCCCHHHHHHHHH--HHCCCCCCCCCC
T ss_conf             953-699999998929999999999--968955466357


No 114
>PF01399 PCI:  PCI domain;  InterPro: IPR000717 A homology domain of unclear function, occurs in the C-terminal region of several regulatory components of the 26S proteasome as well as in other proteins. This domain has also been called the PINT motif (Proteasome, Int-6, Nip-1 and TRIP-15) . Apparently, all of the characterised proteins containing PCI domains are parts of larger multi-protein complexes. Proteins with PCI domains include budding yeast proteasome regulatory components Rpn3(Sun2), Rpn5, Rpn6, Rpn7and Rpn9 ; mammalian proteasome regulatory components p55, p58 and p44.5, and translation initiation factor 3 complex subunits p110 and INT6 , ; Arabidopsis COP9 and FUS6/COP11 ; mammalian G-protein pathway suppressor GPS1, and several uncharacterised ORFs from plant, nematodes and mammals. The complete homology domain comprises approx. 200 residues, the highest conservation is found in the C-terminal half. Several of the proteins mentioned above have no detectable homology to the N-terminal half of the domain.; PDB: 1ufm_A 3chm_A.
Probab=26.60  E-value=2.9  Score=19.92  Aligned_cols=64  Identities=20%  Similarity=0.278  Sum_probs=47.0

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEEC--CCCEEEE
Q ss_conf             8899999999999764989988817887899998589878999999999887916731--7833686
Q T0586            13 PIYSQISDWMKKQMITGEWKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAK--RGMGSFV   77 (125)
Q Consensus        13 Ply~qI~~~l~~~I~~G~l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~--~g~G~~V   77 (125)
                      ++.+++...+....+..-+++.+.+ +...+|+.++++...|-..+..+...|.|..+  +..|+.+
T Consensus        37 ~~~~~l~~~i~~~~l~~~~~~y~~i-~~~~ia~~l~~~~~~vE~~l~~lI~~g~i~~~ID~~~~~v~  102 (105)
T PF01399_consen   37 QYVEQLKQKIRRRLLRQLSKPYSSI-SISEIAKALQISEEEVEKILINLISSGRIKAKIDQVNGVVV  102 (105)
T ss_dssp             ---HHHHHHHHHHHHHHHHHC-SEE-ECCCHHHHCTS-CHHHHHHHHCCCC---EE-EEETTTTEEE
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCC-CHHHHHHHHCCCHHHHHHHHHHHHHCCCEEEEEECCCCEEE
T ss_conf             9999999999999999999983778-89999875099878999999999986997999978999897


No 115
>PF12324 HTH_15:  Helix-turn-helix domain of alkylmercury lyase; PDB: 3f2f_A 3f0p_B 3f0o_B 3f2g_A 3fn8_A 3f2h_B 1s6l_A.
Probab=23.91  E-value=16  Score=15.03  Aligned_cols=32  Identities=9%  Similarity=0.112  Sum_probs=27.3

Q ss_pred             CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHH
Q ss_conf             998881788789999858987899999999988
Q T0586            31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQELER   63 (125)
Q Consensus        31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~   63 (125)
                      |.-|... |+.+||...|.+...|+.++..+.+
T Consensus        33 LA~G~PV-t~~~LA~atG~~ve~V~~~L~~~p~   64 (77)
T PF12324_consen   33 LADGRPV-TVETLAAATGWPVEEVRAALAQMPD   64 (77)
T ss_dssp             HT----B--HHHH-------HHHHHHHHHH-TT
T ss_pred             HHCCCCC-CHHHHHHHHCCCHHHHHHHHHHCCC
T ss_conf             9768982-6999999979899999999985768


No 116
>PF00538 Linker_histone:  linker histone H1 and H5 family;  InterPro: IPR005818 Linker histone H1 is an essential component of chromatin structure. H1 links nucleosomes into higher order structures. Histone H5 performs the same function as histone H1, and replaces H1 in certain cells. The structure of GH5, the globular domain of the linker histone H5 is known , . The fold is similar to the DNA-binding domain of the catabolite gene activator protein, CAP, thus providing a possible model for the binding of GH5 to DNA.; GO: 0003677 DNA binding, 0006334 nucleosome assembly, 0000786 nucleosome, 0005634 nucleus; PDB: 1ust_A 1uhm_A 1uss_A 1yqa_A 1ghc_A 1hst_A.
Probab=23.31  E-value=19  Score=14.50  Aligned_cols=60  Identities=15%  Similarity=0.322  Sum_probs=41.1

Q ss_pred             CHHHHHHHHHHHHHHCCCCCCCCCCCCHH-HHHHHHC--CCH----HHHHHHHHHHHHCCEEEECCCCEE
Q ss_conf             88999999999997649899888178878-9999858--987----899999999988791673178336
Q T0586            13 PIYSQISDWMKKQMITGEWKGEDKLPSVR-EMGVKLA--VNP----NTVSRAYQELERAGYIYAKRGMGS   75 (125)
Q Consensus        13 Ply~qI~~~l~~~I~~G~l~~G~~LPser-~La~~~~--VSr----~TVr~Al~~L~~~G~i~~~~g~G~   75 (125)
                      |-|.+   -|.+.|..-.=+.|.-+++.. -+.+.|+  +..    .-++.|++.+.+.|.+....|.|.
T Consensus         3 P~y~~---MI~eAI~~l~er~GsS~~aI~kyI~~~y~~~~~~~~~~~~l~~aLk~~v~~G~l~q~kG~G~   69 (77)
T PF00538_consen    3 PPYSE---MILEAITALKERKGSSRQAIKKYIESNYPVDLPPSNFKSLLKKALKKLVEKGKLVQVKGTGA   69 (77)
T ss_dssp             --HHH---HHHHHHHTTTTT---THHHHHHHHHHHSTTSSSHTTHHHHHHHHHHHHHH---EEE------
T ss_pred             CCHHH---HHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCEEEEECCCC
T ss_conf             98899---99999997588799799999999998657788768899999999999986895787403688


No 117
>PF05491 RuvB_C:  Holliday junction DNA helicase ruvB C-terminus;  InterPro: IPR008823 The RuvB protein makes up part of the RuvABC revolvasome which catalyses the resolution of Holliday junctions that arise during genetic recombination and DNA repair. Branch migration is catalysed by the RuvB protein that is targeted to the Holliday junction by the structure specific RuvA protein . This group of sequences contain this signature which is located in the C-terminal region of the proteins; it is thought to be a helicase DNA-binding domain.; GO: 0003677 DNA binding, 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1in7_A 1in5_A 1j7k_A 1in8_A 1in6_A 1in4_A 1ixr_C 1ixs_B 1hqc_A.
Probab=23.28  E-value=19  Score=14.49  Aligned_cols=45  Identities=16%  Similarity=0.268  Sum_probs=37.3

Q ss_pred             CCCCCCHHHHHHHHCCCHHHHHHHHH-HHHHCCEEEECCCCEEEECCC
Q ss_conf             88178878999985898789999999-998879167317833686288
Q T0586            34 EDKLPSVREMGVKLAVNPNTVSRAYQ-ELERAGYIYAKRGMGSFVTSD   80 (125)
Q Consensus        34 G~~LPser~La~~~~VSr~TVr~Al~-~L~~~G~i~~~~g~G~~V~~~   80 (125)
                      |-.. +...||..+|..+.|+-..|. .|-+.|+|.+.| +|-.++..
T Consensus        23 ggPV-Gl~tlA~~l~e~~~TiEdv~EPyLiq~g~i~RTp-RGR~~T~~   68 (76)
T PF05491_consen   23 GGPV-GLDTLAAALGEERDTIEDVIEPYLIQIGFIERTP-RGRVATPK   68 (76)
T ss_dssp             -------HHHHHHTTS-HHHHHHCTHHHHHH---EE-------EE-HH
T ss_pred             CCCC-CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHCC-CHHHHHHH
T ss_conf             9871-0999999987986089998518999960686388-55887899


No 118
>PF07514 TraI_2:  Putative helicase;  InterPro: IPR011119   The members of this family are restricted to the proteobacteria. Some members have been annotated as helicase, conjugative relaxase or nickase. The majority contain an HD domain, which is found in a superfamily of enzymes with a predicted or known phosphohydrolase activity. These enzymes appear to be involved in the nucleic acid metabolism, signal transduction and possibly other functions in bacteria. 
Probab=23.25  E-value=19  Score=14.49  Aligned_cols=59  Identities=12%  Similarity=0.097  Sum_probs=32.9

Q ss_pred             CCCCCHHHHHHHHHHHHH-HCCCCCCCCCC-CCHHHHHHHHCCCHHHHHHHHHHHHHCCEE
Q ss_conf             888988999999999997-64989988817-887899998589878999999999887916
Q T0586             9 HADKPIYSQISDWMKKQM-ITGEWKGEDKL-PSVREMGVKLAVNPNTVSRAYQELERAGYI   67 (125)
Q Consensus         9 ~~~~Ply~qI~~~l~~~I-~~G~l~~G~~L-Pser~La~~~~VSr~TVr~Al~~L~~~G~i   67 (125)
                      ....|+.+++.+.|+..| ..+.|++.+.= +.=-.=-..|=||++++.+....|..+|+-
T Consensus       239 ~~~~~l~~~l~~alR~ll~~~~~~~~n~~~~~~w~~~d~l~lv~k~~~d~ir~~l~~~g~~  299 (327)
T PF07514_consen  239 APGVPLERYLLDALRRLLSEEGKWNINEPGSDGWLTQDGLWLVWKTAADDIRAHLLSQGID  299 (327)
T ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCEEECCEEEEEEHHHHHHHHHHHHHCCCC
T ss_conf             8898689999999999985168668899998844736826998302699999999972998


No 119
>PF06530 Phage_antitermQ:  Phage antitermination protein Q;  InterPro: IPR010534   This family consists of several phage antitermination protein Q and related bacterial sequences. Antiterminator proteins control gene expression by recognising control signals near the promoter and preventing transcriptional termination which would otherwise occur at sites that may be a long way downstream .; GO: 0003677 DNA binding, 0030401 transcription antiterminator activity, 0045449 regulation of transcription
Probab=23.20  E-value=19  Score=14.48  Aligned_cols=21  Identities=24%  Similarity=0.343  Sum_probs=13.7

Q ss_pred             CHHHHHHHHCCCHHHHHHHHH
Q ss_conf             878999985898789999999
Q T0586            39 SVREMGVKLAVNPNTVSRAYQ   59 (125)
Q Consensus        39 ser~La~~~~VSr~TVr~Al~   59 (125)
                      |.+.+|..+++|..+||+=++
T Consensus        80 s~r~IAr~~~~s~~~ir~~l~  100 (125)
T PF06530_consen   80 SKRAIARKLKCSEGKIRKMLQ  100 (125)
T ss_pred             CHHHHHHHHCCCHHHHHHHHH
T ss_conf             899999996888889999999


No 120
>PF09904 DUF2131:  Uncharacterized protein conserved in bacteria (DUF2131)
Probab=21.34  E-value=21  Score=14.24  Aligned_cols=39  Identities=13%  Similarity=0.140  Sum_probs=32.5

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHHCCEEEE------CCCCEEEECCC
Q ss_conf             9999858987899999999988791673------17833686288
Q T0586            42 EMGVKLAVNPNTVSRAYQELERAGYIYA------KRGMGSFVTSD   80 (125)
Q Consensus        42 ~La~~~~VSr~TVr~Al~~L~~~G~i~~------~~g~G~~V~~~   80 (125)
                      .|.+.-|.-|-|++.+++.|.+-|+.-.      +.+.|+|.-.+
T Consensus         3 ~l~~~TGmPRRT~QDti~AL~dlgI~~~FvQ~G~Rn~~G~Y~i~~   47 (67)
T PF09904_consen    3 SLMELTGMPRRTAQDTIAALPDLGIECEFVQDGERNNAGYYRIRD   47 (67)
T ss_pred             HHHHHHCCCHHHHHHHHHHCCCCCEEEEEEECCCCCCCCCEEEEE
T ss_conf             177652886747999998601488189997546316787488742


No 121
>PF10771 DUF2582:  Protein of unknown function (DUF2582)
Probab=20.84  E-value=21  Score=14.17  Aligned_cols=45  Identities=16%  Similarity=0.150  Sum_probs=38.2

Q ss_pred             CCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHCCEEEECCCCEEE
Q ss_conf             9988817887899998589878999999999887916731783368
Q T0586            31 WKGEDKLPSVREMGVKLAVNPNTVSRAYQELERAGYIYAKRGMGSF   76 (125)
Q Consensus        31 l~~G~~LPser~La~~~~VSr~TVr~Al~~L~~~G~i~~~~g~G~~   76 (125)
                      |.....+ |..+|++..|.+..-+--|+--|..|+=|......|..
T Consensus        17 L~e~~~~-s~~~Lkk~~~l~~~~~~~AiGWLarE~KI~~~~~~~~~   61 (65)
T PF10771_consen   17 LNENGEW-SYKELKKATGLSDKELALAIGWLARENKIEFEEKNGEL   61 (65)
T ss_pred             HCCCCCC-CHHHHHHHHCCCHHHHHHHHHHHHCCCEEEEEECCCEE
T ss_conf             7338878-89999988498989999988888516716787308878


Done!