Query         T0567 NTPase domain of the Sigma-54 transport activator, E. coli, 145 residues
Match_columns 145
No_of_seqs    117 out of 4618
Neff          7.9 
Searched_HMMs 11830
Date          Tue Jun  1 15:12:40 2010
Command       /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/bin/hhsearch -i /home/syshi_3/CASP9/HHsearch4Targetseq/seq/T0567.hhm -d /home/syshi_2/2008/ferredoxin/manualcheck/update/HHsearch/database/pfamA_24_hhmdb -o /home/syshi_3/CASP9/HHsearch4Targetseq/pfamAsearch/T0567.hhr 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PF00158 Sigma54_activat:  Sigm 100.0 1.3E-41 1.4E-45  241.2  13.0  138    3-140     1-168 (168)
  2 PF05496 RuvB_N:  Holliday junc  99.6 2.4E-15   2E-19  100.1   7.8  126    2-137    25-173 (233)
  3 PF07724 AAA_2:  AAA domain (Cd  99.3 1.7E-12 1.5E-16   84.8   7.1  112   25-136     4-170 (171)
  4 PF00004 AAA:  ATPase family as  99.2 2.1E-11 1.8E-15   78.9   9.1  105   27-142     1-129 (130)
  5 PF07728 AAA_5:  AAA domain (dy  99.1 5.2E-12 4.4E-16   82.2   0.0  103   26-134     1-139 (139)
  6 PF01078 Mg_chelatase:  Magnesi  99.0 3.1E-10 2.6E-14   72.7   6.4  138    2-145     4-203 (206)
  7 PF00308 Bac_DnaA:  Bacterial d  98.9 1.3E-09 1.1E-13   69.3   7.6  136    4-144    12-166 (218)
  8 PF00493 MCM:  MCM2/3/5 family   98.7 1.1E-09 9.2E-14   69.8   0.4  114   22-137    55-201 (326)
  9 PF07726 AAA_3:  ATPase family   98.6 1.2E-08   1E-12   64.2   4.1  104   26-134     1-129 (131)
 10 PF01637 Arch_ATPase:  Archaeal  98.4 1.2E-06   1E-10   53.4  10.0  137    3-145     1-192 (234)
 11 PF05673 DUF815:  Protein of un  98.4 6.6E-07 5.6E-11   54.8   7.7  113    2-116    28-151 (249)
 12 PF05729 NACHT:  NACHT domain;   98.3 1.7E-06 1.4E-10   52.6   8.7  112   25-145     1-151 (166)
 13 PF05621 TniB:  Bacterial TniB   98.2 1.6E-05 1.4E-09   47.4  11.1  131    9-144    41-213 (302)
 14 PF01695 IstB:  IstB-like ATP b  98.1 4.6E-07 3.9E-11   55.6   2.8  102   20-122    43-156 (178)
 15 PF00931 NB-ARC:  NB-ARC domain  97.8 2.1E-05 1.7E-09   46.8   6.3  106    8-116     3-138 (285)
 16 PF03969 AFG1_ATPase:  AFG1-lik  97.8 7.1E-05   6E-09   43.9   8.8  109   24-132    62-184 (362)
 17 PF07693 KAP_NTPase:  KAP famil  97.5  0.0014 1.2E-07   36.9  12.1  139    7-145     2-251 (325)
 18 PF03215 Rad17:  Rad17 cell cyc  97.4  0.0012   1E-07   37.3  11.1  143    3-145    21-210 (498)
 19 PF09848 DUF2075:  Uncharacteri  97.1 0.00065 5.5E-08   38.7   7.1   77   26-102     3-117 (352)
 20 PF08298 AAA_PrkA:  PrkA AAA do  96.8  0.0039 3.3E-07   34.5   8.9   45    2-46     62-110 (358)
 21 PF05707 Zot:  Zonular occluden  96.7 0.00036 3.1E-08   40.1   2.6   90   27-116     3-126 (193)
 22 PF00910 RNA_helicase:  RNA hel  96.6  0.0023 1.9E-07   35.8   6.2   59   27-91      1-64  (107)
 23 PF06414 Zeta_toxin:  Zeta toxi  96.4  0.0009 7.6E-08   38.0   3.3   91   20-113     9-128 (199)
 24 PF00437 GSPII_E:  Type II/IV s  96.3  0.0019 1.6E-07   36.2   4.5   90   12-104   125-232 (280)
 25 PF08433 KTI12:  Chromatin asso  96.3   0.014 1.2E-06   31.6   8.7   94   27-122     4-114 (270)
 26 PF01583 APS_kinase:  Adenylyls  96.2 0.00091 7.7E-08   37.9   2.4  106   25-135     3-126 (156)
 27 PF06068 TIP49:  TIP49 C-termin  96.2  0.0019 1.6E-07   36.2   4.0   39   77-116   279-317 (398)
 28 PF06309 Torsin:  Torsin;  Inte  96.1  0.0038 3.2E-07   34.6   5.2   56    2-57     26-88  (127)
 29 PF05272 VirE:  Virulence-assoc  96.1  0.0038 3.2E-07   34.6   5.2   86   22-116    50-150 (198)
 30 PF02562 PhoH:  PhoH-like prote  95.9   0.006 5.1E-07   33.5   5.6   96   23-121    18-161 (205)
 31 PF06745 KaiC:  KaiC;  InterPro  95.7    0.02 1.7E-06   30.7   7.3   38   23-60     18-56  (225)
 32 PF10236 DAP3:  Mitochondrial r  95.5   0.012 9.8E-07   32.0   5.6   41   10-50      7-50  (309)
 33 PF06048 DUF927:  Domain of unk  95.5   0.024   2E-06   30.3   7.2   78   23-104   191-269 (285)
 34 PF00270 DEAD:  DEAD/DEAH box h  95.5   0.056 4.7E-06   28.3   9.0   41   78-118   121-162 (167)
 35 PF07931 CPT:  Chloramphenicol   95.5  0.0019 1.6E-07   36.2   1.5   30   26-58      3-32  (174)
 36 PF00448 SRP54:  SRP54-type pro  95.5   0.037 3.1E-06   29.3   8.1  101   26-126     3-136 (196)
 37 PF00485 PRK:  Phosphoribulokin  95.4   0.014 1.2E-06   31.5   5.9   24   27-50      2-25  (194)
 38 PF01935 DUF87:  Domain of unkn  95.4   0.007 5.9E-07   33.2   4.1   40   23-62     22-62  (229)
 39 PF05049 IIGP:  Interferon-indu  94.2   0.018 1.5E-06   31.0   3.7   40    8-47     19-58  (376)
 40 PF02367 UPF0079:  Uncharacteri  94.1   0.012   1E-06   32.0   2.7   80   11-90      2-102 (123)
 41 PF03266 DUF265:  Protein of un  93.8   0.011 9.5E-07   32.1   2.0   88   26-116     1-135 (168)
 42 PF01745 IPT:  Isopentenyl tran  93.2   0.014 1.2E-06   31.6   1.7   30   27-59      4-33  (233)
 43 PF03029 ATP_bind_1:  Conserved  92.6  0.0091 7.7E-07   32.6   0.1   34   29-62      1-34  (238)
 44 PF00625 Guanylate_kin:  Guanyl  92.6    0.03 2.5E-06   29.8   2.7   26   24-49      2-27  (183)
 45 PF00006 ATP-synt_ab:  ATP synt  92.4    0.11   9E-06   26.8   5.4  110   24-136    15-147 (215)
 46 PF01443 Viral_helicase1:  Vira  92.3   0.022 1.8E-06   30.5   1.7   69   27-96      1-78  (226)
 47 PF03028 Dynein_heavy:  Dynein   92.3    0.27 2.3E-05   24.6  11.6   97   20-117   112-214 (707)
 48 PF05127 DUF699:  Putative ATPa  92.2   0.018 1.6E-06   30.9   1.3   50   77-134    88-138 (174)
 49 PF01580 FtsK_SpoIIIE:  FtsK/Sp  91.9   0.028 2.4E-06   29.9   1.9   37   25-61     39-79  (205)
 50 PF04851 ResIII:  Type III rest  91.8   0.095   8E-06   27.1   4.5   39    9-48     11-50  (184)
 51 PF00580 UvrD-helicase:  UvrD/R  91.7   0.046 3.9E-06   28.8   2.8   33   15-47      4-38  (533)
 52 PF08423 Rad51:  Rad51;  InterP  91.4     0.1 8.7E-06   26.9   4.4   49   25-73     44-99  (261)
 53 PF07088 GvpD:  GvpD gas vesicl  91.0   0.014 1.2E-06   31.5  -0.4   20   24-43     10-29  (484)
 54 PF00406 ADK:  Adenylate kinase  90.8   0.043 3.6E-06   29.0   1.9   17   29-45      1-17  (151)
 55 PF10443 RNA12:  RNA12 protein   90.7   0.074 6.2E-06   27.7   3.1   44   14-62      5-52  (431)
 56 PF10662 PduV-EutP:  Ethanolami  90.6   0.069 5.9E-06   27.8   2.9   24   26-49      3-26  (143)
 57 PF08303 tRNA_lig_kinase:  tRNA  90.5    0.43 3.6E-05   23.6   7.7   82   30-113     5-98  (169)
 58 PF01057 Parvo_NS1:  Parvovirus  90.5    0.07 5.9E-06   27.8   2.8   26   25-50    114-139 (271)
 59 PF03308 ArgK:  ArgK protein;    90.1   0.057 4.8E-06   28.3   2.0   39    8-46     13-51  (266)
 60 PF10412 TrwB_AAD_bind:  Type I  88.6     0.1 8.5E-06   27.0   2.4   38   23-60     14-51  (386)
 61 PF02534 TraG:  TraG/TraD famil  88.5     0.3 2.5E-05   24.4   4.8   48   25-74     45-92  (469)
 62 PF02463 SMC_N:  RecF/RecN/SMC   88.1    0.13 1.1E-05   26.3   2.8   40   77-116   159-199 (220)
 63 PF03668 ATP_bind_2:  P-loop AT  87.9    0.67 5.6E-05   22.5   7.5   21   27-47      4-24  (284)
 64 PF00735 Septin:  Septin;  Inte  87.8    0.11   9E-06   26.8   2.1   22   24-45      4-25  (281)
 65 PF07475 Hpr_kinase_C:  HPr Ser  87.0    0.13 1.1E-05   26.3   2.2   25   24-48     18-42  (171)
 66 PF06068 TIP49:  TIP49 C-termin  86.9    0.21 1.8E-05   25.2   3.2   59    3-62     26-87  (398)
 67 PF00025 Arf:  ADP-ribosylation  86.7     0.5 4.2E-05   23.2   5.1   96   22-118    11-127 (174)
 68 PF08477 Miro:  Miro-like prote  85.9    0.18 1.5E-05   25.7   2.4   22   27-48      2-23  (119)
 69 PF00009 GTP_EFTU:  Elongation   85.6    0.63 5.3E-05   22.7   5.1   92   25-118     4-135 (189)
 70 PF00488 MutS_V:  MutS domain V  85.5    0.65 5.5E-05   22.6   5.1   90   26-116    44-165 (234)
 71 PF03193 DUF258:  Protein of un  84.9    0.34 2.9E-05   24.1   3.5   24   25-48     36-59  (161)
 72 PF03205 MobB:  Molybdopterin g  84.9    0.19 1.6E-05   25.5   2.1   36   27-62      3-39  (137)
 73 PF02456 Adeno_IVa2:  Adenoviru  84.8    0.67 5.6E-05   22.5   4.9   21   25-45     86-108 (369)
 74 PF06431 Polyoma_lg_T_C:  Polyo  84.6    0.49 4.2E-05   23.2   4.2   39   10-48    141-179 (417)
 75 PF04548 AIG1:  AIG1 family;  I  83.7    0.23 1.9E-05   25.1   2.1   20   26-45      2-21  (212)
 76 PF00063 Myosin_head:  Myosin h  83.4    0.45 3.8E-05   23.5   3.6   23   22-44     83-105 (689)
 77 PF00154 RecA:  recA bacterial   83.1     1.1 9.1E-05   21.4   5.4   68   25-92     54-147 (322)
 78 PF01121 CoaE:  Dephospho-CoA k  82.8    0.26 2.2E-05   24.7   2.2   29   27-61      3-31  (180)
 79 PF01202 SKI:  Shikimate kinase  81.9    0.13 1.1E-05   26.3   0.4   25   33-60      1-25  (158)
 80 PF02374 ArsA_ATPase:  Anion-tr  80.1    0.45 3.8E-05   23.5   2.6   25   27-51      4-28  (305)
 81 PF02283 CobU:  Cobinamide kina  79.9    0.54 4.6E-05   23.0   2.9   59   27-88      1-84  (167)
 82 PF06564 YhjQ:  YhjQ protein;    79.0     1.3 0.00011   20.9   4.7   69   27-96      4-95  (243)
 83 PF04665 Pox_A32:  Poxvirus A32  78.2    0.84 7.1E-05   22.0   3.5   23   22-44     11-33  (241)
 84 PF00519 PPV_E1_C:  Papillomavi  77.4     1.4 0.00012   20.8   4.4   35   10-45    249-283 (432)
 85 PF00071 Ras:  Ras family;  Int  76.7    0.59   5E-05   22.8   2.4   20   27-46      2-21  (161)
 86 PF09439 SRPRB:  Signal recogni  75.8    0.47   4E-05   23.3   1.7   21   24-44      3-23  (181)
 87 PF12128 DUF3584:  Protein of u  74.6    0.96 8.2E-05   21.7   3.0   25   22-46     15-39  (1202)
 88 PF03796 DnaB_C:  DnaB-like hel  73.3     2.4  0.0002   19.5   7.1   38   10-48      6-43  (185)
 89 PF02223 Thymidylate_kin:  Thym  71.5     1.6 0.00014   20.4   3.6   23   29-51      1-23  (186)
 90 PF04735 Baculo_helicase:  Bacu  68.5     1.1 9.6E-05   21.3   2.2   19   26-44    881-899 (1173)
 91 PF05872 DUF853:  Bacterial pro  67.5     1.3 0.00011   21.0   2.3   36   22-57     17-52  (502)
 92 PF00265 TK:  Thymidine kinase;  67.3       3 0.00025   19.1   4.1   78   27-105     4-104 (176)
 93 PF02492 cobW:  CobW/HypB/UreG,  64.1       2 0.00017   19.9   2.8   20   27-46      3-22  (173)
 94 PF02689 Herpes_Helicase:  Heli  62.6     1.8 0.00015   20.3   2.3   20   27-46     62-81  (816)
 95 PF04670 Gtr1_RagA:  Gtr1/RagA   62.2       2 0.00017   20.0   2.5   20   27-46      2-21  (231)
 96 PF05783 DLIC:  Dynein light in  60.6     3.7 0.00031   18.6   3.6   39    9-47     25-67  (489)
 97 PF01656 CbiA:  CobQ/CobB/MinD/  58.3     3.6 0.00031   18.6   3.3   35   28-62      3-37  (194)
 98 PF00503 G-alpha:  G-protein al  56.0     1.3 0.00011   21.1   0.6   38   11-48     11-54  (350)
 99 PF01591 6PF2K:  6-phosphofruct  53.5       6  0.0005   17.4   6.0   86   23-111    11-127 (222)
100 PF02399 Herpes_ori_bp:  Origin  52.4     6.2 0.00053   17.3   4.7   35   27-61     52-87  (824)
101 PF03464 eRF1_2:  eRF1 domain 2  48.3     7.3 0.00061   17.0   5.6   51   24-74     73-124 (133)
102 PF00225 Kinesin:  Kinesin moto  47.7     3.1 0.00026   19.0   1.5   18   22-39     72-89  (333)
103 PF00350 Dynamin_N:  Dynamin fa  45.7     5.1 0.00043   17.8   2.4   19   27-45      1-19  (168)
104 PF02421 FeoB_N:  Ferrous iron   42.9     7.5 0.00063   16.9   2.9   21   26-46      2-22  (188)
105 PF07960 CBP4:  CBP4;  InterPro  39.1     6.9 0.00058   17.1   2.2   30    9-38     58-89  (128)
106 PF04275 P-mevalo_kinase:  Phos  35.2     8.8 0.00074   16.5   2.2   19   29-47      1-19  (116)
107 PF00142 Fer4_NifH:  4Fe-4S iro  35.1       9 0.00076   16.5   2.3   36   26-61      2-37  (273)
108 PF06144 DNA_pol3_delta:  DNA p  34.1      12  0.0011   15.7   3.7   38   77-114    58-99  (172)
109 PF09818 ABC_ATPase:  Predicted  33.3      12 0.00099   15.9   2.6   19   27-45    247-265 (448)
110 PF01293 PEPCK_ATP:  Phosphoeno  29.1     8.9 0.00075   16.5   1.4   18   25-42    211-228 (466)
111 PF00693 Herpes_TK:  Thymidine   27.7     8.2  0.0007   16.7   1.0   19   31-49      1-19  (281)
112 PF08283 Gemini_AL1_M:  Geminiv  22.6      11 0.00094   16.0   0.9   23   80-102    59-81  (106)
113 PF02263 GBP:  Guanylate-bindin  22.3      21  0.0017   14.5   2.8   27   19-45     13-42  (260)
114 PF10483 Hap2_elong:  Histone a  21.7      21  0.0018   14.4   8.0  119   26-145    15-161 (280)

No 1  
>PF00158 Sigma54_activat:  Sigma-54 interaction domain;  InterPro: IPR002078 Some bacterial regulatory proteins activate the expression of genes from promoters recognized by core RNA polymerase associated with the alternative sigma-54 factor. These have a conserved domain of about 230 residues involved in the ATP-dependent ,  interaction with sigma-54. About half of the proteins in which this domain is found (algB, dcdT, flbD, hoxA, hupR1, hydG, ntrC, pgtA and pilR) belong to signal transduction two-component systems  and possess a domain that can be phosphorylated by a sensor-kinase protein in their N-terminal section. Almost all of these proteins possess a helix-turn-helix DNA-binding domain in their C-terminal section. The domain which interacts with the sigma-54 factor has an ATPase activity. This may be required to promote a conformational change necessary for the interaction . The domain contains an atypical ATP-binding motif A (P-loop) as well as a form of motif B. The two ATP-binding motifs are located in the N-terminal section of the domain.; GO: 0005524 ATP binding, 0008134 transcription factor binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2bjv_A 2c98_A 2vii_A 2c99_A 2c9c_A 2bjw_A 2c96_A 3dzd_B 1ojl_E 1ny5_B ....
Probab=100.00  E-value=1.3e-41  Score=241.25  Aligned_cols=138  Identities=28%  Similarity=0.442  Sum_probs=128.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHH-------------
Q ss_conf             6658989999999999861479958987589988889999998621242678524125788988889-------------
Q T0567             3 LIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDNAPQLN-------------   69 (145)
Q Consensus         3 liG~S~~m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~~~~~-------------   69 (145)
                      +||+|++|++++++++++|.++.||||+||+||||+.+|++||..|+++++||+.+||...+...++             
T Consensus         1 liG~S~~m~~~~~~i~~~a~~~~pVlI~GE~GtGK~~~A~~IH~~s~r~~~pfi~v~c~~~~~~~~~~~LFG~~~~~~~~   80 (168)
T PF00158_consen    1 LIGKSPAMQRLREQIKRAAQSDLPVLITGESGTGKELLARAIHNASPRADGPFISVNCAALPEELLESELFGHERGAFTG   80 (168)
T ss_dssp             ----SHHHHHHHHHHHHHHTSTS-EEEE-------HHHHHHHHHHSTTCTS--EEEETTTS-HHHHHHHH---B------
T ss_pred             CEECCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEECCCCCCHHHHHHEEECCCCCCCCC
T ss_conf             98379999999999999848799889984899507799999998565237984120333123334301011555676677


Q ss_pred             ------HHHHHHCCCEEEECCHHHCCHHHHHHHHHHHHHC-----------CHHHEEEECCCCCHHHHHHCCCCCHHHHH
Q ss_conf             ------9998625874874374206877899999998721-----------40100111477687899870897656557
Q T0567            70 ------DFIALAQGGTLVLSHPEHLTREQQYHLVQLQSQE-----------HRPFRLIGIGDTSLVELAASNHIIAELYY  132 (145)
Q Consensus        70 ------~~l~~a~gGtL~l~ei~~L~~~~Q~~L~~~l~~~-----------~~~~RiI~~s~~~l~~l~~~~~~~~~L~~  132 (145)
                            ++++.|+|||||||||+.||.+.|.+|+++++++           ..++|+|++|+.++.+++.+|.|++||||
T Consensus        81 ~~~~~~G~le~A~gGTL~ldei~~L~~~~Q~~Ll~~l~~~~~~~~g~~~~~~~~~RiI~~t~~~L~~~v~~g~fr~dL~~  160 (168)
T PF00158_consen   81 ARRRKPGLLEQANGGTLFLDEIEELPLELQAKLLRLLEEGEFTRVGSNRPRPSDVRIIATTSRDLEELVEQGRFREDLYY  160 (168)
T ss_dssp             --SB----TTTT----EEEETGGGS-HHHHHHHHHHHHSSEBE------EBE----EEEE-SS-HHHHHH-----HHHHH
T ss_pred             CCCCCCCCHHHCCCCEEECCCCHHCCHHHHHHHHHHHHHCEEECCCCCCCCCCCEEEEEECCCCHHHHHHCCCCHHHHHH
T ss_conf             43347996776489758518530189999999999986023212688655657479998068899999885997599998


Q ss_pred             HHCCCEEE
Q ss_conf             55442265
Q T0567           133 CFAMTQIA  140 (145)
Q Consensus       133 ~ls~~~i~  140 (145)
                      ||++++|+
T Consensus       161 rL~~~~i~  168 (168)
T PF00158_consen  161 RLNVLPIH  168 (168)
T ss_dssp             HHTCEEEE
T ss_pred             HHCCEECC
T ss_conf             85470369


No 2  
>PF05496 RuvB_N:  Holliday junction DNA helicase ruvB N-terminus;  InterPro: IPR008824 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 N-terminal region of the proteins.; GO: 0009378 Holliday junction helicase activity, 0006281 DNA repair, 0006310 DNA recombination; PDB: 1ixr_C 1ixs_B 1hqc_A 1iqp_F.
Probab=99.57  E-value=2.4e-15  Score=100.13  Aligned_cols=126  Identities=20%  Similarity=0.278  Sum_probs=90.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCC---CCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCC-CCHHHHHHHHHHH-C
Q ss_conf             7665898999999999986147---995898758998888999999862124267852412578-8988889999862-5
Q T0567             2 ELIGRSEWINQYRRRLQQLSET---DIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTP-DNAPQLNDFIALA-Q   76 (145)
Q Consensus         2 ~liG~S~~m~~l~~~i~~~a~~---~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~-~~~~~~~~~l~~a-~   76 (145)
                      ++||+......+.-.++.+-..   -.+++++|+||+||+++|+.|.....   .+|...+... ....++...+... .
T Consensus        25 dfVGQ~~l~~~lki~i~aa~~r~~~l~h~Lf~GPPG~GKTTLA~IIA~e~~---~~~~~~sg~~i~k~~Dl~~il~~l~~  101 (233)
T PF05496_consen   25 DFVGQEHLKGNLKIFIRAAKKRGEPLDHVLFYGPPGLGKTTLARIIANEMG---VNFKITSGPVIEKPGDLAAILTNLKE  101 (233)
T ss_dssp             C----HHHHHHHHHHHHHHHTSSS---EEEEE-------HHHHHHHHHH-------EEEE----------HHHHHHT---
T ss_pred             HCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHC---CCEEECCCCCCCCHHHHHHHHHHCCC
T ss_conf             828909998635999999996499888699988986108899999986029---88006787321479999999985589


Q ss_pred             CCEEEECCHHHCCHHHHHHHHHHHHHCCH------------------HHEEEECCCCCHHHHHHCCCCCHHHHHHHCCC
Q ss_conf             87487437420687789999999872140------------------10011147768789987089765655755442
Q T0567            77 GGTLVLSHPEHLTREQQYHLVQLQSQEHR------------------PFRLIGIGDTSLVELAASNHIIAELYYCFAMT  137 (145)
Q Consensus        77 gGtL~l~ei~~L~~~~Q~~L~~~l~~~~~------------------~~RiI~~s~~~l~~l~~~~~~~~~L~~~ls~~  137 (145)
                      +.+||+|||++|++.+|+.|+..|+....                  ++-+|++|+.       .|.+.+-|..||...
T Consensus       102 ~~VLFIDEIHRlnk~~qe~Llp~mEd~~idiiiG~g~~ar~~~~~l~~FtliGATTr-------~g~ls~plr~RFgi~  173 (233)
T PF05496_consen  102 NDVLFIDEIHRLNKAQQEILLPAMEDGRIDIIIGAGPNARSVRIKLPPFTLIGATTR-------SGLLSSPLRDRFGIV  173 (233)
T ss_dssp             --EEEETTTTS--HHHHHHHHHHHHHSEEEEEB------BEEEEE----EEE---S------------S-CCCTT---E
T ss_pred             CCEEEEEHHHHCCHHHHHHHHHHHHCCEEEEEEECCCCCCEEECCCCCEEEECCCCC-------CCCCCHHHHHHCCCE
T ss_conf             978998304206988999978987458389998257676126615998258542454-------544686889555965


No 3  
>PF07724 AAA_2:  AAA domain (Cdc48 subfamily);  InterPro: IPR013093   This ATPase family, associated with various cellular activities, includes some of the AAA proteins not detected by IPR003959 from INTERPRO , .; PDB: 1um8_A 1ht1_E 1yyf_B 1ht2_H 1hqy_E 1do0_A 1g4b_F 1do2_D 1e94_F 1g4a_F ....
Probab=99.31  E-value=1.7e-12  Score=84.78  Aligned_cols=112  Identities=12%  Similarity=0.175  Sum_probs=84.2

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHCC-CCCCCCCEECCCCCCH----H--------HHHHHHHHHCCCEEEECCHHHCCH-
Q ss_conf             9589875899888899999986212-4267852412578898----8--------889999862587487437420687-
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFGR-NAQGEFVYRELTPDNA----P--------QLNDFIALAQGGTLVLSHPEHLTR-   90 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s~-~~~~~fv~~~~~~~~~----~--------~~~~~l~~a~gGtL~l~ei~~L~~-   90 (145)
                      ..+++.|++|+||+.+|+.+...-. ....+|+.+||.....    .        .-.......++|++||||||...+ 
T Consensus         4 ~~~l~~GptGvGKT~la~~la~~l~~~~~~~l~~~dms~~~~~~~~~~~i~~l~g~~~~~v~~~~~gIVllDEidKa~~~   83 (171)
T PF07724_consen    4 SNFLFLGPTGVGKTELAKALAELLFVGSERPLIRIDMSEFSEGDDVEHSISRLIGAPPGYVGYEEGGIVLLDEIDKAHPR   83 (171)
T ss_dssp             --EEEE-------HHHHHHHHHHCC-SSGCEEEEEEGGGCCSCCCCSSCSCHHHHHHHHHHHHHH--EEEEETGGGCSH-
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCEEECCCCEEEEEECHHHHCCC
T ss_conf             89999899998899999999986525886444787187764445687777788860033143366549998245541623


Q ss_pred             ----------HHHHHHHHHHHHCC-----------HHHEEEECCCCCHHHHHH--------------------CCCCCHH
Q ss_conf             ----------78999999987214-----------010011147768789987--------------------0897656
Q T0567            91 ----------EQQYHLVQLQSQEH-----------RPFRLIGIGDTSLVELAA--------------------SNHIIAE  129 (145)
Q Consensus        91 ----------~~Q~~L~~~l~~~~-----------~~~RiI~~s~~~l~~l~~--------------------~~~~~~~  129 (145)
                                ..|..|+++++.+.           .++=+|++++..-.....                    +..|.|+
T Consensus        84 ~~~~~d~~~~~Vq~~LLqile~g~l~d~~g~~id~~n~ifI~Tsn~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~PE  163 (171)
T PF07724_consen   84 SSGGRDVSGEGVQNALLQILEGGRLTDSHGRTIDFSNIIFIMTSNFGALKIIDSRRIGEAIEEEKKEQVEDLLRYGFRPE  163 (171)
T ss_dssp             -----HHHH-HHHHHHHHHHH--EEES----EEEGTTEEEEEE---SSSCGGGGTS-STTTCCHHHHHHHHHHHCCS-TT
T ss_pred             CCCCCCHHHHHHHHHHHHHCCCEEEECCCCCEEECCCEEEEEECCCCCCCHHHHHCCCCCCHHHHHHHHHHHHHCCCCHH
T ss_conf             32110030899999999980783897789978951575999967657742103330376338999998999998399967


Q ss_pred             HHHHHCC
Q ss_conf             5575544
Q T0567           130 LYYCFAM  136 (145)
Q Consensus       130 L~~~ls~  136 (145)
                      |..||..
T Consensus       164 f~~Ri~~  170 (171)
T PF07724_consen  164 FLNRIDE  170 (171)
T ss_dssp             THCT-SE
T ss_pred             HHCCCCC
T ss_conf             9766886


No 4  
>PF00004 AAA:  ATPase family associated with various cellular activities (AAA);  InterPro: IPR003959   AAA ATPases (ATPases Associated with diverse cellular Activities) form a large, functionally diverse protein family belonging to the AAA+ superfamily of ring-shaped P-loop NTPases, which exert their activity through the energy-dependent unfolding of macromolecules , . These proteins are involved in a range of processes, including protein degradation, membrane fusion, microtubule severing, peroxisome biogenesis, signal transduction and the regulation of gene expression.   AAA ATPases assemble into oligomeric assemblies (often hexamers) that form a ring-shaped structure with a central pore. These proteins produce a molecular motor that couples ATP binding and hydrolysis to changes in conformational states that can be propagated through the assembly in order to act upon a target substrate, either translocating or remodelling the substrate .     AAA ATPases contain one or two conserved ATP-binding domains, which contain two conserved motifs, A and B. These ATP-binding domains are often attached to various other functional domains. The functional variety seen between AAA ATPases is in part due to their extensive number of accessory domains and factors, and to their variable organisation within oligomeric assemblies, in addition to changes in key functional residues within the ATPase domain itself.   More information about these proteins can be found at Protein of the Month: AAA ATPases .; GO: 0005524 ATP binding; PDB: 2dhr_F 1iy0_A 1iy2_A 1iy1_A 1ixz_A 1ofi_B 1kyi_E 1ofh_A 1g3i_U 1im2_A ....
Probab=99.23  E-value=2.1e-11  Score=78.95  Aligned_cols=105  Identities=24%  Similarity=0.262  Sum_probs=76.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCC-------HHHHHHHHHHH---CCCEEEECCHHHCCHHH----
Q ss_conf             89875899888899999986212426785241257889-------88889999862---58748743742068778----
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDN-------APQLNDFIALA---QGGTLVLSHPEHLTREQ----   92 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~-------~~~~~~~l~~a---~gGtL~l~ei~~L~~~~----   92 (145)
                      |+|+|++||||+++|+.+-...   +.+|+.++|....       ...+..++..+   ....+|+||+|.+....    
T Consensus         1 vll~G~~G~GKT~~~~~~a~~~---~~~~~~i~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~vl~iDeid~l~~~~~~~~   77 (130)
T PF00004_consen    1 VLLHGPPGTGKTTLARSLAQEL---GAPFIEIDCSELIGKYIGESEKNLRSVIQKAKKSSPCVLFIDEIDNLFPKSNQSS   77 (130)
T ss_dssp             EEEE--TT---HHHHHHHHHHH---TCEEEEEETTTSCTSCHHHHHHHHHHHHHHHHHTSSEEEEEETGGGTHHHHTSST
T ss_pred             CEEECCCCCCHHHHHHHHHHHC---CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCHHHHHHHCCCCC
T ss_conf             9898979899879999998751---8864211111000012465211111110023222221365411543323103331


Q ss_pred             ------HHHHHHHHHHCCH---HHEEEECCCCCHHHHHHCCCCCHHHH-HHHCCCEEEEC
Q ss_conf             ------9999999872140---10011147768789987089765655-75544226507
Q T0567            93 ------QYHLVQLQSQEHR---PFRLIGIGDTSLVELAASNHIIAELY-YCFAMTQIACL  142 (145)
Q Consensus        93 ------Q~~L~~~l~~~~~---~~RiI~~s~~~l~~l~~~~~~~~~L~-~~ls~~~i~iP  142 (145)
                            ...|++.++....   ++.+|++++.       ...+.+.|. .|+... +.+|
T Consensus        78 ~~~~~~~~~L~~~~~~~~~~~~~i~~I~~~n~-------~~~i~~~l~~~r~~~~-~~~~  129 (130)
T PF00004_consen   78 SFSSEILNQLLKFLEKFRKKNSRIIVIGTSND-------PEKIDPALLSSRFDRR-IEVP  129 (130)
T ss_dssp             CHHHHHHHHHHHHHHHTTTTCSTEEEEEE-SS-------GGGSTHHHHHTTSEEE-EE--
T ss_pred             CCCCCCCEEEEECCCCCCCCCEEEEEEEEECC-------HHHCCHHHHHCCCEEE-EECC
T ss_conf             12332201243101245553306899984589-------4877975773868599-9767


No 5  
>PF07728 AAA_5:  AAA domain (dynein-related subfamily);  InterPro: IPR011704   This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 1f6v_A.
Probab=99.07  E-value=5.2e-12  Score=82.24  Aligned_cols=103  Identities=27%  Similarity=0.335  Sum_probs=72.1

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCC-HHHHHHHH--------------HH--HCCCEEEECCHHHC
Q ss_conf             589875899888899999986212426785241257889-88889999--------------86--25874874374206
Q T0567            26 AVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDN-APQLNDFI--------------AL--AQGGTLVLSHPEHL   88 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~-~~~~~~~l--------------~~--a~gGtL~l~ei~~L   88 (145)
                      ||+|+||+||||+.+|+.+...-   ..+++.++|.... ..++.+.+              ..  .+++++||||++..
T Consensus         1 ~vlL~G~~G~GKT~l~~~~a~~~---~~~~~~~~~~~~~~~~dl~g~~~~~~~~~~~~~~~l~~a~~~~~~l~lDEin~~   77 (139)
T PF07728_consen    1 PVLLVGPPGTGKTSLARALAKRL---GRPFVYINCSADTTPEDLIGSYDPDDGGFEWIPGPLVRAMREGGVLFLDEINRA   77 (139)
T ss_dssp             --------------------------------------------------------------------------------
T ss_pred             CCEEECCCHHHHHHHHHHHHHHH---CCCEEEEEECCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEEEEECCCCCC
T ss_conf             97899487321999999999996---997399996345146888746420443320136754002666289998983669


Q ss_pred             CHHHHHHHHHHHHHCC-------------H------HHEEEECCCCCHHHHHHCCCCCHHHHHHH
Q ss_conf             8778999999987214-------------0------10011147768789987089765655755
Q T0567            89 TREQQYHLVQLQSQEH-------------R------PFRLIGIGDTSLVELAASNHIIAELYYCF  134 (145)
Q Consensus        89 ~~~~Q~~L~~~l~~~~-------------~------~~RiI~~s~~~l~~l~~~~~~~~~L~~~l  134 (145)
                      +++.+..|..+++...             .      ++|+|++.+..-   .....+++.|..||
T Consensus        78 ~~~~~~~l~~ll~~~~~~~~~~~~~~~~~~~~~~~~~~~~iat~N~~~---~~~~~l~~al~~RF  139 (139)
T PF07728_consen   78 DPEVLESLNSLLEERRILLPEGGEEIPKEPNDLLHPNFRIIATMNPPG---GGRNELSPALLRRF  139 (139)
T ss_dssp             -----------------------------------------------------------------
T ss_pred             CHHHHHHHHHHHHCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCC
T ss_conf             999999999998369564121222111111111111111111111111---11111112223579


No 6  
>PF01078 Mg_chelatase:  Magnesium chelatase, subunit ChlI;  InterPro: IPR000523 Magnesium-chelatase is a three-component enzyme that catalyses the insertion of Mg^2+ into protoporphyrin IX. This is the first unique step in the synthesis of (bacterio)chlorophyll. As a result, it is thought that Mg-chelatase has an important role in channeling intermediates into the (bacterio)chlorophyll branch in response to conditions suitable for photosynthetic growth. ChlI and BchD have molecular weights between 38-42 kDa.; GO: 0016851 magnesium chelatase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process; PDB: 1g8p_A.
Probab=98.99  E-value=3.1e-10  Score=72.71  Aligned_cols=138  Identities=18%  Similarity=0.209  Sum_probs=82.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCC-------------------------CCCCC
Q ss_conf             76658989999999999861479958987589988889999998621242-------------------------67852
Q T0567             2 ELIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNA-------------------------QGEFV   56 (145)
Q Consensus         2 ~liG~S~~m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~-------------------------~~~fv   56 (145)
                      +++|+..+    ++.++.+|.-..+|++.|++||||+++|+.++..-+.-                         ..||.
T Consensus         4 dV~GQe~a----KrAleiAAaG~h~lL~~GppGtGKSmlArrl~~iLP~l~~~E~lE~~~i~s~~g~~~~~~~~~~rPfr   79 (206)
T PF01078_consen    4 DVKGQEQA----KRALEIAAAGGHNLLMIGPPGTGKSMLARRLPSILPPLTEEEALEVTKIYSVAGLGPDEPLITRRPFR   79 (206)
T ss_dssp             G----HHH----HHHHHHHHH-----EEE--------HHHHHHHHHS--EEEE---TT--S-TT---S---EEEE----E
T ss_pred             HHCCCHHH----HHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCHHHHHHHCCCCEECCCCCCCCCCCCCCCCC
T ss_conf             72697999----99999996789976987799988999999999777973156665325510003588888734689977


Q ss_pred             EECCCCCCHHH--------HHHHHHHHCCCEEEECCHHHCCHHHHHHHHHHHHHCCH-------------HHEEEECCCC
Q ss_conf             41257889888--------89999862587487437420687789999999872140-------------1001114776
Q T0567            57 YRELTPDNAPQ--------LNDFIALAQGGTLVLSHPEHLTREQQYHLVQLQSQEHR-------------PFRLIGIGDT  115 (145)
Q Consensus        57 ~~~~~~~~~~~--------~~~~l~~a~gGtL~l~ei~~L~~~~Q~~L~~~l~~~~~-------------~~RiI~~s~~  115 (145)
                      ...-+ .+...        .-+.+..|.+|+||+||+..+++..-+.|.+-++.+..             ++.+|++.+-
T Consensus        80 ~phhs-~s~~alvGgg~~~~PGeislAH~GVLflDE~~ef~~~~le~Lr~ple~g~v~I~R~~~~~~~Pa~F~Lv~a~NP  158 (206)
T PF01078_consen   80 APHHS-ASEAALVGGGSPPRPGEISLAHRGVLFLDELPEFDRSVLEALRQPLEDGEVTISRAGGSVTYPARFQLVAAMNP  158 (206)
T ss_dssp             EE------HHHH----TTB----HHHH----EEETTGGGS-HHHHHHHHHHHH---EEE------EEE-----EE-----
T ss_pred             CCCCC-CCHHHHHCCCCCCCCCHHHHCCCCEEEEHHHHHCCHHHHHHHHHHHCCCEEEEEEECCEEEECCHHHHHHHCCC
T ss_conf             88875-67999967898889646763469889831044438999999999875896999993868997085052021086


Q ss_pred             CH---------------HH-HHHCCCCCHHHHHHHCCCEEEECCCC
Q ss_conf             87---------------89-98708976565575544226507889
Q T0567           116 SL---------------VE-LAASNHIIAELYYCFAMTQIACLPLT  145 (145)
Q Consensus       116 ~l---------------~~-l~~~~~~~~~L~~~ls~~~i~iPpL~  145 (145)
                      .+               .+ ..=.++++.-|+.|+. +.+.+|+++
T Consensus       159 cpCG~~~~~~~~C~c~~~~~~~Y~~rlsgpllDRid-l~~~~~~~~  203 (206)
T PF01078_consen  159 CPCGYYGDPDKECTCSPQQIRRYLSRLSGPLLDRID-LHVEVPPVS  203 (206)
T ss_dssp             ----------------------------------------------
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCC
T ss_conf             432321111111111111111111111111111111-111112223


No 7  
>PF00308 Bac_DnaA:  Bacterial dnaA  protein;  InterPro: IPR013317   This entry represents the central domain of bacterial DnaA proteins , ,  that play an important role in initiating and regulating chromosomal replication. DnaA is an ATP- and DNA-binding protein. It binds specifically to 9 bp nucleotide repeats known as dnaA boxes which are found in the chromosome origin of replication (oriC).   DnaA is a protein of about 50 kDa that contains two conserved regions: the first is located in the N-terminal half and corresponds to the ATP-binding domain, the second is located in the C-terminal half and could be involved in DNA-binding. The protein may also bind the RNA polymerase beta subunit, the dnaB and dnaZ proteins, and the groE gene products (chaperonins) .; PDB: 2hcb_C 1l8q_A 3bos_A 2z4r_C 2z4s_A.
Probab=98.92  E-value=1.3e-09  Score=69.30  Aligned_cols=136  Identities=16%  Similarity=0.217  Sum_probs=84.8

Q ss_pred             CCCCHHHHHHHHHHHHHHCC----CCCEEEECCCCCCHHHHHHHHHHHCCC--CCCCCCEECCCCCC--------HHHHH
Q ss_conf             65898999999999986147----995898758998888999999862124--26785241257889--------88889
Q T0567             4 IGRSEWINQYRRRLQQLSET----DIAVWLYGAPGTGRMTGARYLHQFGRN--AQGEFVYRELTPDN--------APQLN   69 (145)
Q Consensus         4 iG~S~~m~~l~~~i~~~a~~----~~pvli~Ge~GtGK~~~A~~iH~~s~~--~~~~fv~~~~~~~~--------~~~~~   69 (145)
                      +|.+.  +-....+++++..    -.|++|+|++|+||+++-++|-..-..  .....+.+++....        ....+
T Consensus        12 ~g~~N--~~a~~a~~~v~~~~~~~~npl~i~G~~G~GKTHLL~Ai~~~~~~~~~~~~v~Y~~~~~f~~~~~~~~~~~~~~   89 (218)
T PF00308_consen   12 VGDSN--ELAYAAARAVAENPGERYNPLFIYGPSGLGKTHLLQAIGNEALKNNPNKRVVYLSAEEFMNEFVSALRAGEIE   89 (218)
T ss_dssp             -------HHHHHHHHHHHCT----SSCEEEE--TT---HHHHHHHHHHHHHHCTTS-EEEEEHHHHHHHHHHHHHGGSHH
T ss_pred             CCCCH--HHHHHHHHHHHHCCCCCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEEEEHHHHHHHHHHHHHHCCHH
T ss_conf             48658--9999999999845476668469988999978999999998764148874267636999999999999832458


Q ss_pred             HHHHHH-CCCEEEECCHHHCCHHH--HHHHHHHHHHC-CHHHEEEECCCCCHHHHHHCCCCCHHHHHHHCCC-EEEECCC
Q ss_conf             999862-58748743742068778--99999998721-4010011147768789987089765655755442-2650788
Q T0567            70 DFIALA-QGGTLVLSHPEHLTREQ--QYHLVQLQSQE-HRPFRLIGIGDTSLVELAASNHIIAELYYCFAMT-QIACLPL  144 (145)
Q Consensus        70 ~~l~~a-~gGtL~l~ei~~L~~~~--Q~~L~~~l~~~-~~~~RiI~~s~~~l~~l~~~~~~~~~L~~~ls~~-~i~iPpL  144 (145)
                      .+.+.. .-..|+||+|+.+....  |..|..+++.- ..+-++|.++..+|.++.   .+.++|..||+.. .+.|.|+
T Consensus        90 ~f~~~~~~~d~l~iDDi~~l~~~~~~qe~lf~l~N~l~~~~k~lv~ts~~~P~~l~---~~~~dL~SRl~~Gl~~~i~~p  166 (218)
T PF00308_consen   90 EFKERYRSADLLLIDDIQFLAGKEETQEELFHLFNRLRESGKQLVLTSDRAPSELS---GLLPDLRSRLSWGLVVEIEPP  166 (218)
T ss_dssp             HHHHHHTTSSEEEEETGGGG---HHHHHHHHHHHHHHHCCT-EEEEE-SS-TTT-S---S--HHHHHHHH---EEE----
T ss_pred             HHHHHHHCCCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHH---HHCHHHHHHCCCCEEEECCCC
T ss_conf             99999860787776458854387799999999986432258869996798967772---316778844134417857899


No 8  
>PF00493 MCM:  MCM2/3/5 family This family extends the MCM domain of Prosite.;  InterPro: IPR001208    MCM proteins are DNA-dependent ATPases required for the initiation of eukaryotic DNA replication , , . In eukaryotes there is a family of six proteins, MCM2 to MCM7. They were first identified in yeast where most of them have a direct role in the initiation of chromosomal DNA replication by interacting directly with autonomously replicating sequences (ARS). They were thus called minichromosome maintenance proteins, MCM proteins .   This family is also present in the archebacteria in 1 to 4 copies. Methanococcus jannaschii has four members, MJ0363, MJ0961, MJ1489 and MJECL13.   The "MCM motif" contains Walker-A and Walker-B type nucleotide binding motifs. The diagnostic sequence defining the MCMs is IDEFDKM. Only Mcm2 (aka Cdc19 or Nda1) has been subjected to mutational analysis in this region, and most mutations abolish its activity . The presence of a putative ATP-binding domain implies that these proteins may be involved in an ATP-consuming step in the initiation of DNA replication in eukaryotes.   The MCM proteins bind together in a large complex . Within this complex, individual subunits associate with different affinities, and there is a tightly associated core of Mcm4 (Cdc21), Mcm6 (Mis5) and Mcm7 . This core complex in human MCMs has been associated with helicase activity in vitro , leading to the suggestion that the MCM proteins are the eukaryotic replicative helicase.   Fission yeast (Schizosaccharomyces pombe) MCMs, like those in metazoans, are found in the nucleus throughout the cell cycle. This is in contrast to the budding yeast (Saccharomyces cerevisiae) in which MCM proteins move in and out of the nucleus during each cell cycle. The assembly of the MCM complex in fission yeast is required for MCM localization, ensuring that only intact MCM complexes remain in the nucleus .; GO: 0003677 DNA binding, 0005524 ATP binding, 0008094 DNA-dependent ATPase activity, 0006270 DNA replication initiation; PDB: 3f8t_A 3f9v_A.
Probab=98.68  E-value=1.1e-09  Score=69.77  Aligned_cols=114  Identities=18%  Similarity=0.278  Sum_probs=76.0

Q ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCE--------ECCCCCCH---HHH---HHHHHHHCCCEEEECCHHH
Q ss_conf             479958987589988889999998621242678524--------12578898---888---9999862587487437420
Q T0567            22 ETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVY--------RELTPDNA---PQL---NDFIALAQGGTLVLSHPEH   87 (145)
Q Consensus        22 ~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~--------~~~~~~~~---~~~---~~~l~~a~gGtL~l~ei~~   87 (145)
                      ..+.+||+.|+|||||+.+-++++..+++..  |+.        +.++....   .+|   .+.+-.|++|+++|||++.
T Consensus        55 Rg~i~vLlvGDpgt~KSqlL~~~~~~~pr~v--~~sg~~~s~~gLTa~~~kd~~~~~~~leaGalvlAd~Gi~cIDE~dk  132 (326)
T PF00493_consen   55 RGDIHVLLVGDPGTGKSQLLKYVSKLAPRSV--YTSGKGSSAAGLTAAVVKDPVTGEWVLEAGALVLADGGICCIDEFDK  132 (326)
T ss_dssp             -----EEEE--HHHCHHHHHHCCCCT-S--B--EEEGGG-TCHHHSEEECS-------CEE---CCCC----EEECTTT-
T ss_pred             CCCEEEEEECCCCHHHHHHHHHHHHHCCCCE--EECCCCCCCCCCEEEEEEECCCCCEEEECCEEEECCCCEEEEEECCC
T ss_conf             6750289855972689999999997688636--60787654367326899952777579946707853677488600023


Q ss_pred             CCHHHHHHHHHHHHHCCH-------------HHEEEECCCCCHHH------HHHCCCCCHHHHHHHCCC
Q ss_conf             687789999999872140-------------10011147768789------987089765655755442
Q T0567            88 LTREQQYHLVQLQSQEHR-------------PFRLIGIGDTSLVE------LAASNHIIAELYYCFAMT  137 (145)
Q Consensus        88 L~~~~Q~~L~~~l~~~~~-------------~~RiI~~s~~~l~~------l~~~~~~~~~L~~~ls~~  137 (145)
                      ++.+.+..|.+.|+++..             .+-++|+++-.-..      +.++-.+.+.|+.||.-+
T Consensus       133 m~~~~~~~l~EaMEqq~isi~KaGi~~~l~ar~silAaaNP~~g~~~~~~~~~~ni~l~~~LLSRFDLi  201 (326)
T PF00493_consen  133 MSEDDRSALHEAMEQQTISIAKAGIVATLNARCSILAAANPKGGRYDPNKSLAENINLPPPLLSRFDLI  201 (326)
T ss_dssp             --CHHHHHHHHHHHSSSEEEE----EEEE-----EEEE---------TTS-CGCCT-S-CCCHCC-SEE
T ss_pred             CCHHHHHHHHHHHHHCCEEECCCCEEEEECCHHHHHHHHCCCCCCCCCCCCHHHHCCCCCCHHHHHCEE
T ss_conf             421378999999983968521342278733311567775854562267689888535555124252768


No 9  
>PF07726 AAA_3:  ATPase family associated with various cellular activities (AAA);  InterPro: IPR011703   This entry includes some of the AAA proteins not detected by the IPR003959 from INTERPRO model.; GO: 0005524 ATP binding, 0016887 ATPase activity; PDB: 2r44_A.
Probab=98.61  E-value=1.2e-08  Score=64.16  Aligned_cols=104  Identities=20%  Similarity=0.234  Sum_probs=67.6

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCC-CHHHHHHH--HH-----------HHCCCEEEECCHHHCCHH
Q ss_conf             58987589988889999998621242678524125788-98888999--98-----------625874874374206877
Q T0567            26 AVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPD-NAPQLNDF--IA-----------LAQGGTLVLSHPEHLTRE   91 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~-~~~~~~~~--l~-----------~a~gGtL~l~ei~~L~~~   91 (145)
                      ||||+|.||+||+++|+.+...   ....|.++.|+++ .+.++-+.  .+           -.-.+++++|||.+.|+.
T Consensus         1 hvLleg~PG~gKT~l~~~la~~---~~~~f~Riq~Tpdl~P~Di~G~~v~~~~~~~f~~~~gpif~~ill~DEiNRappk   77 (131)
T PF07726_consen    1 HVLLEGVPGVGKTTLAKALAKA---LGLSFKRIQFTPDLLPSDITGTPVYDPQTGEFEFRPGPIFTNILLADEINRAPPK   77 (131)
T ss_dssp             -EEEE-----HHHHHHHHHHHH---TT--EEEEE--TT--HHHH---EEE-S----EEE------SSEEEEETGGGS-HH
T ss_pred             CCCEECCCCCHHHHHHHHHHHH---CCCCCCEEEECCCCCHHHEEEEEHEECCCCCEEEECCCHHHCEEEEECCCCCCHH
T ss_conf             9543789972699999999998---4998377986898882562403110067885686268666484652043579989


Q ss_pred             HHHHHHHHHHHCCH-----------HHEEEECCCCCHHHHHHCCCCCHHHHHHH
Q ss_conf             89999999872140-----------10011147768789987089765655755
Q T0567            92 QQYHLVQLQSQEHR-----------PFRLIGIGDTSLVELAASNHIIAELYYCF  134 (145)
Q Consensus        92 ~Q~~L~~~l~~~~~-----------~~RiI~~s~~~l~~l~~~~~~~~~L~~~l  134 (145)
                      .|..|++.|.....           ++-+||+  .|+.+......+.+.+..||
T Consensus        78 tQsALLeaM~Er~Vt~~g~t~~lp~~f~ViAT--qNp~e~~Gty~LpeaqlDRF  129 (131)
T PF07726_consen   78 TQSALLEAMEERQVTIDGQTYPLPDPFFVIAT--QNPIEQEGTYPLPEAQLDRF  129 (131)
T ss_dssp             HHHHHHHHHHHSEEE----EEE--SS-EEEEE----TT---------HHHHTTS
T ss_pred             HHHHHHHHHHCCEEEECCEEEECCCCEEEEEE--CCCCCCCCCCCCCHHHHCCC
T ss_conf             99999999971868659998889998699972--48755577615988897031


No 10 
>PF01637 Arch_ATPase:  Archaeal ATPase;  InterPro: IPR011579    This domain has been found in a number of bacterial and archaeal proteins, all of which contain a conserved P-loop motif that is involved in binding ATP.; PDB: 2qen_A 2fna_B.
Probab=98.41  E-value=1.2e-06  Score=53.40  Aligned_cols=137  Identities=16%  Similarity=0.228  Sum_probs=75.2

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCC-HHH--------------
Q ss_conf             66589899999999998614799589875899888899999986212426785241257889-888--------------
Q T0567             3 LIGRSEWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDN-APQ--------------   67 (145)
Q Consensus         3 liG~S~~m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~-~~~--------------   67 (145)
                      |+|+...+.++.+.+..  ....+++|+|+.|+||+.+.+.+-..-.......+.++|.... ...              
T Consensus         1 f~GR~~el~~l~~~~~~--~~~~~~~I~G~rg~GKTsll~~~~~~~~~~~~~~i~~~~~~~~~~~~~~~~~~~~~~~~~l   78 (234)
T PF01637_consen    1 FVGREKELEELESIIES--GQSRIILIYGPRGVGKTSLLREFLEELKEKGIIVIYIDSLEESSISSLRSFISENYLKREL   78 (234)
T ss_dssp             S-S-HHHHHHHHHHHHH----SSEEEEE--TT---HHHHHHHHCCTT--EECCCHHGGTT-SHHHHHHHHHHHHHHHCHC
T ss_pred             CCCHHHHHHHHHHHHHH--HCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             98879999999999975--1476799984999989999999999887559818998434542055799999757899999


Q ss_pred             ---------------------------HHH---HHHHHC-CCEEEECCHHHCC------HHHHHHHHHHHHH--CCHHHE
Q ss_conf             ---------------------------899---998625-8748743742068------7789999999872--140100
Q T0567            68 ---------------------------LND---FIALAQ-GGTLVLSHPEHLT------REQQYHLVQLQSQ--EHRPFR  108 (145)
Q Consensus        68 ---------------------------~~~---~l~~a~-gGtL~l~ei~~L~------~~~Q~~L~~~l~~--~~~~~R  108 (145)
                                                 +..   .+.+.. .-.+++||++.+.      .+.-..|.++++.  ...++.
T Consensus        79 ~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~l~~~~~~~viiiDE~~~~~~~~~~~~~~~~~l~~~~~~~~~~~~~~  158 (234)
T PF01637_consen   79 NEALGIALPKIEIEKISSETEEDAFESLEELLEKLKKKGKKVVIIIDEFQYLDIKSEENEDLLEQLRNLIESLLSSQNLS  158 (234)
T ss_dssp             HHHHHHHCCT----EE-GTS-GG-G--HHHHHHHHHHT-SSEEEEEETGGGGG-G-----HHHHHHHHHHHH----TTEE
T ss_pred             HHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCEEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCC
T ss_conf             99986643443310001211012889999999999741782899980688862000317999999999999732357864


Q ss_pred             EEECCCC-CHHHHHHCCCCCHHHHHHHCCCEEEECCCC
Q ss_conf             1114776-878998708976565575544226507889
Q T0567           109 LIGIGDT-SLVELAASNHIIAELYYCFAMTQIACLPLT  145 (145)
Q Consensus       109 iI~~s~~-~l~~l~~~~~~~~~L~~~ls~~~i~iPpL~  145 (145)
                      +|++.+. ++...  ...-...++.+...  +.++||+
T Consensus       159 ~v~~~s~~~~~~~--~~~~~~~~~~r~~~--i~l~~l~  192 (234)
T PF01637_consen  159 LVFCGSSESLLEE--LLDQKSPLFGRFEY--IELGPLD  192 (234)
T ss_dssp             EEEE------HHH--TT-TTSTT-----E--EE-----
T ss_pred             EEEEECCHHHHHH--HHCCCCCCCCCCCE--EEECCCC
T ss_conf             8998372888887--51434710137457--9978999


No 11 
>PF05673 DUF815:  Protein of unknown function (DUF815);  InterPro: IPR008533 This domain consists of several bacterial proteins of unknown function.
Probab=98.35  E-value=6.6e-07  Score=54.81  Aligned_cols=113  Identities=12%  Similarity=0.140  Sum_probs=75.9

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCC--CCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHHHH----H
Q ss_conf             7665898999999999986147--995898758998888999999862124267852412578898888999986----2
Q T0567             2 ELIGRSEWINQYRRRLQQLSET--DIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDNAPQLNDFIAL----A   75 (145)
Q Consensus         2 ~liG~S~~m~~l~~~i~~~a~~--~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~~~~~~~l~~----a   75 (145)
                      +|+|--...+++.+..+++..-  ..+||++|++||||+.+.+++...-....-..|+++-  .+-..+..+++.    .
T Consensus        28 ~L~Gie~qk~~l~~NT~~F~~G~pAnnvLL~G~RGtGKSSlVKall~~y~~~gLRlIev~k--~~L~~Lp~i~~~l~~~p  105 (249)
T PF05673_consen   28 DLVGIERQKEALIRNTRAFLAGLPANNVLLWGARGTGKSSLVKALLNEYADQGLRLIEVDK--EDLQDLPDILDQLRDRP  105 (249)
T ss_pred             HCCCHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCEEEEEECH--HHHHHHHHHHHHHHCCC
T ss_conf             8248799999999999999749987538987599998899999999998756738999868--88867999999995799


Q ss_pred             CCCEEEECCHHHCCHHHHHHHHHH-HH----HCCHHHEEEECCCCC
Q ss_conf             587487437420687789999999-87----214010011147768
Q T0567            76 QGGTLVLSHPEHLTREQQYHLVQL-QS----QEHRPFRLIGIGDTS  116 (145)
Q Consensus        76 ~gGtL~l~ei~~L~~~~Q~~L~~~-l~----~~~~~~RiI~~s~~~  116 (145)
                      ..-+||+|++.-=..+...+-+.. ++    ..+.|+.+.+||+..
T Consensus       106 ~rFIiF~DDLsFe~~d~~yk~LKs~LeG~le~~P~NvliYATSNRR  151 (249)
T PF05673_consen  106 YRFIIFCDDLSFEEGDASYKALKSVLEGGLEARPENVLIYATSNRR  151 (249)
T ss_pred             CEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCCEEEEEECCCHH
T ss_conf             7499996889999985789999999557445789848999702477


No 12 
>PF05729 NACHT:  NACHT domain;  InterPro: IPR007111   The NACHT domain is a 300 to 400 residue predicted nucleoside triphosphatase (NTPase) domain, which is found in animal, fungal and bacterial proteins. The NACHT domain has been named after NAIP, CIITA, HET-E and TP1. It is found in association with other domains, such as the CARD domain (IPR001315 from INTERPRO), the DAPIN domain (IPR004020 from INTERPRO), the HEAT repeat (IPR004155 from INTERPRO), the WD repeat (IPR001680 from INTERPRO), the leucine-rich repeat (LRR) or the BIR repeat (IPR001370 from INTERPRO) .    The NACHT domain consists of seven distinct conserved motifs, including the ATP/GTPase specific P-loop, the Mg(2+)-binding site (Walker A and B motifs, respectively) and five more specific motifs. The unique features of the NACHT domain include the prevalence of 'tiny' residues (glycine, alanine or serine) directly C-terminal of the Mg(2+)-coordinating aspartate in the Walker B motif, in place of a second acidic residue prevalent in other NTPases. A second acidic residue is typically found in the NACHT-containing proteins two positions downstream. Furthermore, the distal motif VII contains a conserved pattern of polar, aromatic and hydrophobic residues that is not seen in any other NTPase family .
Probab=98.30  E-value=1.7e-06  Score=52.60  Aligned_cols=112  Identities=24%  Similarity=0.331  Sum_probs=61.9

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHCCCCC--C---C-CCEECCCCCCHH----HHH-------------------HHHHHH
Q ss_conf             9589875899888899999986212426--7---8-524125788988----889-------------------999862
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFGRNAQ--G---E-FVYRELTPDNAP----QLN-------------------DFIALA   75 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s~~~~--~---~-fv~~~~~~~~~~----~~~-------------------~~l~~a   75 (145)
                      .+|+|+|++|+||+++++.+-..-....  +   + .+.++|...+..    .+.                   .+....
T Consensus         1 r~l~i~G~~G~GKS~l~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~~~~   80 (166)
T PF05729_consen    1 RLLWITGEPGSGKSTLLRRLAQELKQEEPPGGEVPVVFFISLRSISESSLARSLADQLCSQLPELINNIEEVLQELLEQP   80 (166)
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCCCHHHHHHHHHCCCHHHHHHHHHHHHHHCC
T ss_conf             98999899999626999999999986043566606999985332212332040999998752101224689999999669


Q ss_pred             CCCEEEECCHHHCCHHHHH--------HHHHHHHH-CCHHHEEEECCCCCHHHHHHCCCCCHHHHHHHCC-CEEEECCCC
Q ss_conf             5874874374206877899--------99999872-1401001114776878998708976565575544-226507889
Q T0567            76 QGGTLVLSHPEHLTREQQY--------HLVQLQSQ-EHRPFRLIGIGDTSLVELAASNHIIAELYYCFAM-TQIACLPLT  145 (145)
Q Consensus        76 ~gGtL~l~ei~~L~~~~Q~--------~L~~~l~~-~~~~~RiI~~s~~~l~~l~~~~~~~~~L~~~ls~-~~i~iPpL~  145 (145)
                      ..-.+++|++|.++...+.        .|.+++.. ...+++++.++..+....         +...+.. ..+.++||+
T Consensus        81 ~~~llvlDglDe~~~~~~~~~~~~~~~~l~~ll~~~~~~~~~v~it~r~~~~~~---------l~~~~~~~~~~~l~~l~  151 (166)
T PF05729_consen   81 KRVLLVLDGLDELSREDQQSERNEVLDLLSELLPRKLPPNVKVLITSRPSALED---------LESSLESFQRIELEPLS  151 (166)
T ss_pred             CCEEEEECCHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCHHHH---------HHHHCCCCCEEEECCCC
T ss_conf             938999867788230201134679999999999734799997999985945554---------48866998789969969


No 13 
>PF05621 TniB:  Bacterial TniB protein;  InterPro: IPR008868 This family consists of several bacterial TniB NTP-binding proteins. TniB is a probable ATP-binding protein  which is involved in Tn5053 mercury resistance transposition .
Probab=98.15  E-value=1.6e-05  Score=47.36  Aligned_cols=131  Identities=15%  Similarity=0.205  Sum_probs=72.8

Q ss_pred             HHHHHHHHHHHHH----CCCCC-EEEECCCCCCHHHHHHHHHHHCC------CCCCCCCEECCCCC-CHHHH--------
Q ss_conf             9999999999861----47995-89875899888899999986212------42678524125788-98888--------
Q T0567             9 WINQYRRRLQQLS----ETDIA-VWLYGAPGTGRMTGARYLHQFGR------NAQGEFVYRELTPD-NAPQL--------   68 (145)
Q Consensus         9 ~m~~l~~~i~~~a----~~~~p-vli~Ge~GtGK~~~A~~iH~~s~------~~~~~fv~~~~~~~-~~~~~--------   68 (145)
                      ...+..++++.+-    ....| ++|+|++|+||+++.+.....-+      ....|.+.+.+.+. +...+        
T Consensus        41 ~a~~~l~~l~~L~~~p~~~r~p~lllvG~sg~GKT~ii~~f~r~~p~~~~~~~~~~PVl~v~~P~~~~~k~l~~~iL~~L  120 (302)
T PF05621_consen   41 RAIEALERLEDLLEYPRRSRMPSLLLVGDSGNGKTTIIERFRRRHPPQEDAGRTRIPVLYVQAPPKPTEKRLYSAILEAL  120 (302)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHH
T ss_conf             89999999999985542035764478769998789999999986788778888603089996899999899999999994


Q ss_pred             -----------------HHHHHHHCCCEEEECCHHHCC---HHHHHHHHHHHHHC--CHHHEEEECCCCCHHHHHHCCCC
Q ss_conf             -----------------999986258748743742068---77899999998721--40100111477687899870897
Q T0567            69 -----------------NDFIALAQGGTLVLSHPEHLT---REQQYHLVQLQSQE--HRPFRLIGIGDTSLVELAASNHI  126 (145)
Q Consensus        69 -----------------~~~l~~a~gGtL~l~ei~~L~---~~~Q~~L~~~l~~~--~~~~RiI~~s~~~l~~l~~~~~~  126 (145)
                                       ...+...+-..|.|||++.+-   ...|..++++++.-  .-++=+|.+.+.......   .-
T Consensus       121 g~P~~~r~~~~~l~~~~~~~l~~~~vr~LIIDE~h~Ll~g~~~~~~~~~n~lK~L~nel~IpiVlvGt~~a~~~i---~~  197 (302)
T PF05621_consen  121 GAPFRPRGTAAELEQRVLDLLRECGVRMLIIDEFHHLLAGSSRKQREVLNFLKYLSNELPIPIVLVGTPEALRAI---RT  197 (302)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHCCCEEEEEECCHHHCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCHHHHHHH---CC
T ss_conf             887678888999999999999974972999978355423774008999999999875258048983758999884---24


Q ss_pred             CHHHHHHHCCCEEEECCC
Q ss_conf             656557554422650788
Q T0567           127 IAELYYCFAMTQIACLPL  144 (145)
Q Consensus       127 ~~~L~~~ls~~~i~iPpL  144 (145)
                      ++.|..|+..  +.+|+.
T Consensus       198 d~Qla~Rf~~--~~lp~w  213 (302)
T PF05621_consen  198 DPQLARRFEP--FELPRW  213 (302)
T ss_pred             CHHHHHHCCC--CCCCCC
T ss_conf             5899960475--105885


No 14 
>PF01695 IstB:  IstB-like ATP binding protein;  InterPro: IPR002611   Proteins in this entry contain an ATP/GTP binding P-loop motif. They are found associated with IS21 family insertion sequences . Functionally they have not been characterised, but they may be involved in transposition .; GO: 0005524 ATP binding; PDB: 3ec2_A 3ecc_A 2qgz_A.
Probab=98.12  E-value=4.6e-07  Score=55.63  Aligned_cols=102  Identities=17%  Similarity=0.152  Sum_probs=61.3

Q ss_pred             HHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHH---------HHHHH-HHCCCEEEECCHHHCC
Q ss_conf             6147995898758998888999999862124267852412578898888---------99998-6258748743742068
Q T0567            20 LSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDNAPQL---------NDFIA-LAQGGTLVLSHPEHLT   89 (145)
Q Consensus        20 ~a~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~~~~---------~~~l~-~a~gGtL~l~ei~~L~   89 (145)
                      +......++|+|++||||+.+|.+|-...-........++.... ...+         +..+. ...--.|+|||+...+
T Consensus        43 ~~~~~~nl~l~G~~GtGKT~La~ai~~~~~~~g~~v~~~~~~~L-~~~l~~~~~~~~~~~~l~~l~~~dlLiiDDlG~~~  121 (178)
T PF01695_consen   43 FLEEGQNLILYGPPGTGKTHLAIAIAKEAIRKGYSVLFITASDL-INELKAAKDDGSYEKLLRKLARVDLLIIDDLGYEP  121 (178)
T ss_dssp             S-SS----EEE-------HHHHHHHHHHHHH----EEEEEHHHH-HHHHHHHHH----SHCCHHHHTSSCEEEET-----
T ss_pred             HHHCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCEEEEEECCC-HHHHHHHHHHHHHHHHHHHHCCCCEEEEECCCEEC
T ss_conf             76159679999478877609999999999708987099871462-44443477655689999774177881884311555


Q ss_pred             HH--HHHHHHHHHHHCCHHHEEEECCCCCHHHHHH
Q ss_conf             77--8999999987214010011147768789987
Q T0567            90 RE--QQYHLVQLQSQEHRPFRLIGIGDTSLVELAA  122 (145)
Q Consensus        90 ~~--~Q~~L~~~l~~~~~~~RiI~~s~~~l~~l~~  122 (145)
                      .+  .+..|.++++.....-.+|.+|+.++.++.+
T Consensus       122 ~~~~~~~~l~~ii~~R~~~~~tiitSN~~~~~~~~  156 (178)
T PF01695_consen  122 LTEWEAELLFEIINERYERKSTIITSNLSPSEWEE  156 (178)
T ss_dssp             --HHHCCCCHHHHHHHHHT-EEEEE-SS-CHHHHT
T ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEECCCCCHHHHH
T ss_conf             65889999999999864982679868976143553


No 15 
>PF00931 NB-ARC:  NB-ARC domain;  InterPro: IPR002182   This is the NB-ARC domain, a novel signalling motif found in bacteria and eukaryotes, shared by plant resistance gene products and regulators of cell death in animals .; GO: 0005524 ATP binding, 0006915 apoptosis; PDB: 2a5y_B 1z6t_B.
Probab=97.79  E-value=2.1e-05  Score=46.78  Aligned_cols=106  Identities=19%  Similarity=0.191  Sum_probs=60.6

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCC---CEECCCCCC--------------------
Q ss_conf             899999999998614799589875899888899999986212426785---241257889--------------------
Q T0567             8 EWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEF---VYRELTPDN--------------------   64 (145)
Q Consensus         8 ~~m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~f---v~~~~~~~~--------------------   64 (145)
                      ..++++.+.+........-|.|+|.+|+||+++|+.++..-. ....|   +++++....                    
T Consensus         3 ~~i~~l~~~L~~~~~~~~~v~I~G~gGiGKTtLa~~~~~~~~-~~~~f~~~~wv~~~~~~~~~~~~~~i~~~l~~~~~~~   81 (285)
T PF00931_consen    3 KEIEELIQRLLKNSQNVRVVAIVGMGGIGKTTLARQVANDQR-VRNHFDGVIWVSLSSEPSLEDLLEQIAKQLGIQEQSW   81 (285)
T ss_dssp             HHHHHHHHHHCCHTSSSEEEEEE-------HHHHHHHHC-CC-H---SSEEEEEE-----TTHHHHHHHHHHHTTT---S
T ss_pred             HHHHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHHHCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             899999998617899907999990880989998478776232-2332122344333333222233433222233343333


Q ss_pred             ----HHHHHHHHHHH---CCCEEEECCHHHCCHHHHHHHHHHHHHCCHHHEEEECCCCC
Q ss_conf             ----88889999862---58748743742068778999999987214010011147768
Q T0567            65 ----APQLNDFIALA---QGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDTS  116 (145)
Q Consensus        65 ----~~~~~~~l~~a---~gGtL~l~ei~~L~~~~Q~~L~~~l~~~~~~~RiI~~s~~~  116 (145)
                          .......+.+.   ..--++||+++...  ....+...+.....+.++|.||...
T Consensus        82 ~~~~~~~~~~~l~~~L~~~~~LlVlDdv~~~~--~~~~l~~~l~~~~~~s~IliTSR~~  138 (285)
T PF00931_consen   82 SEDDEEELQEQLKEALKDKRWLLVLDDVWDEE--DWEELLSFLPDFSNGSKILITSRDR  138 (285)
T ss_dssp             -TTSHHHHHHHHHHHCCCTTEEEEEECE-SHH--HH-------HCCHTT-EEEEEES-G
T ss_pred             CCCCCCCHHHHHHCCCCCCCCEEEECCCCCCC--CCCCCCCCCCCCCCCCCCCCEEECC
T ss_conf             31121100223220112333111101445433--2222223455322332222011011


No 16 
>PF03969 AFG1_ATPase:  AFG1-like ATPase;  InterPro: IPR005654   This family of proteins contains a P-loop motif and are predicted to be ATPases.
Probab=97.78  E-value=7.1e-05  Score=43.89  Aligned_cols=109  Identities=12%  Similarity=0.032  Sum_probs=66.4

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCC-----------CCCHHHHHHHHHH-HCCC-EEEECCHHHCCH
Q ss_conf             99589875899888899999986212426785241257-----------8898888999986-2587-487437420687
Q T0567            24 DIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELT-----------PDNAPQLNDFIAL-AQGG-TLVLSHPEHLTR   90 (145)
Q Consensus        24 ~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~-----------~~~~~~~~~~l~~-a~gG-tL~l~ei~~L~~   90 (145)
                      ..-|.|+|+.|+||+++.-..+...+...+.=+-+.-.           ......+.....+ ++.. .|+|||++--+.
T Consensus        62 ~~GlYl~G~VGrGKTmLMDlFy~~lp~~~K~R~HFH~FM~~vh~~l~~~~~~~dpl~~va~~la~~~~lLCfDEF~V~Di  141 (362)
T PF03969_consen   62 PRGLYLWGGVGRGKTMLMDLFYESLPIKRKRRVHFHEFMQDVHQRLHELRGQKDPLPPVAKRLAKEARLLCFDEFQVTDI  141 (362)
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCHHHHHHHHHCCCCEEEEEEEEECCH
T ss_conf             97589978888871389999999688645653104699999999999862677869999999981498899741772557


Q ss_pred             HHHHHHHHHHHHC-CHHHEEEECCCCCHHHHHHCCCCCHHHHH
Q ss_conf             7899999998721-40100111477687899870897656557
Q T0567            91 EQQYHLVQLQSQE-HRPFRLIGIGDTSLVELAASNHIIAELYY  132 (145)
Q Consensus        91 ~~Q~~L~~~l~~~-~~~~RiI~~s~~~l~~l~~~~~~~~~L~~  132 (145)
                      .--.-|-++++.- ...+.+|+||+.+|++|-..|.-+..+.-
T Consensus       142 aDAmiL~rLf~~Lf~~GvvlVaTSN~~P~dLY~~gl~R~~FlP  184 (362)
T PF03969_consen  142 ADAMILGRLFEALFARGVVLVATSNRPPEDLYKNGLQRERFLP  184 (362)
T ss_pred             HHHHHHHHHHHHHHHCCCEEEEECCCCHHHHCCCCCHHHHHHH
T ss_conf             3799999999999978989999289997897177621777799


No 17 
>PF07693 KAP_NTPase:  KAP family P-loop domain;  InterPro: IPR011646 The KAP (after Kidins220/ARMS and PifA) family of predicted NTPases are sporadically distributed across a wide phylogenetic range in bacteria and in animals. Many of the prokaryotic KAP NTPases are encoded in plasmids and tend to undergo disruption to form pseudogenes. A unique feature of all eukaryotic and certain bacterial KAP NTPases is the presence of two or four transmembrane helices inserted into the P-loop NTPase domain. These transmembrane helices anchor KAP NTPases in the membrane such that the P-loop domain is located on the intracellular side .
Probab=97.49  E-value=0.0014  Score=36.93  Aligned_cols=139  Identities=11%  Similarity=0.101  Sum_probs=84.0

Q ss_pred             CHHHHHHHHHHHHHH-CCCCCEEEECCCCCCHHHHHHHHHHHCCCC---CCCCCEECCCCCCH--HH-------------
Q ss_conf             989999999999861-479958987589988889999998621242---67852412578898--88-------------
Q T0567             7 SEWINQYRRRLQQLS-ETDIAVWLYGAPGTGRMTGARYLHQFGRNA---QGEFVYRELTPDNA--PQ-------------   67 (145)
Q Consensus         7 S~~m~~l~~~i~~~a-~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~---~~~fv~~~~~~~~~--~~-------------   67 (145)
                      ++....+-+.+.... ..+..+.|.|+-||||+++-+.+-..-...   .-.++.+|+-..+.  ..             
T Consensus         2 ~~~a~~la~~I~~~~~~~~~~Igl~G~WGsGKSs~l~~l~~~L~~~~~~~~~~v~fnaW~~~~~d~~~~~~~~~i~~~l~   81 (325)
T PF07693_consen    2 KKYAENLADLIKNPDNSDPLVIGLDGPWGSGKSSFLNMLKKELKEDNEEKFIVVYFNAWEYDGEDDLLAAFLSEISDELE   81 (325)
T ss_pred             HHHHHHHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCHHHHHHHHHHHHHHH
T ss_conf             58999999999564778984899975799999999999999975432675589998366457811199999999999998


Q ss_pred             --------------------------------------------------------------------------HHHH--
Q ss_conf             --------------------------------------------------------------------------8999--
Q T0567            68 --------------------------------------------------------------------------LNDF--   71 (145)
Q Consensus        68 --------------------------------------------------------------------------~~~~--   71 (145)
                                                                                                ...+  
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  161 (325)
T PF07693_consen   82 SEYSSKEKKLFIAKKLKALKDKFKWKGRLAKAIPLALTGLPASILLSAGISLLEELKNAAKLSEEEFLKKLKKEIEEFIE  161 (325)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             76150046788876798887667677652010246663320156888778888999987652003544322789999999


Q ss_pred             -----HHH-HCCCEEEECCHHHCCHHHHHHHHHHHHH--CCHHHEEEECCCCCHHHHHHCC--------CCCHHHHHHHC
Q ss_conf             -----986-2587487437420687789999999872--1401001114776878998708--------97656557554
Q T0567            72 -----IAL-AQGGTLVLSHPEHLTREQQYHLVQLQSQ--EHRPFRLIGIGDTSLVELAASN--------HIIAELYYCFA  135 (145)
Q Consensus        72 -----l~~-a~gGtL~l~ei~~L~~~~Q~~L~~~l~~--~~~~~RiI~~s~~~l~~l~~~~--------~~~~~L~~~ls  135 (145)
                           ++. ...=++++||+|+++++.-..+++.+..  ...++.+|.+...+.-...-+.        ..-.+....+=
T Consensus       162 ~~~~~L~~~~~riVviIDDLDR~~p~~~~~~le~Ik~~~~~~n~~fIla~D~~~l~~a~~~~~~~~~~~~~g~~yLeKii  241 (325)
T PF07693_consen  162 EIKKLLDESKKRIVVIIDDLDRCDPEEAVELLEAIKHFFDFPNVVFILAFDREILEKALESNYGSEFSEIDGRDYLEKII  241 (325)
T ss_pred             HHHHHHHCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEECHHHHHHHHHHHCCCCCCCCCHHHHHHHHC
T ss_conf             99999734787479998263337868999999999999668994899992699999988863476535444899999640


Q ss_pred             CCEEEECCCC
Q ss_conf             4226507889
Q T0567           136 MTQIACLPLT  145 (145)
Q Consensus       136 ~~~i~iPpL~  145 (145)
                      ++.+.+|+.+
T Consensus       242 q~~~~lP~~~  251 (325)
T PF07693_consen  242 QIPFSLPPPS  251 (325)
T ss_pred             CCEEECCCCC
T ss_conf             7079779988


No 18 
>PF03215 Rad17:  Rad17 cell cycle checkpoint protein;  InterPro: IPR004582    To be effective as a mechanism that preserves genomic integrity, the DNA damage checkpoint must be extremely sensitive in its ability to detect DNA damage. In Saccharomyces cerevisiae the Ddc1/Rad17/Mec3 complex and Rad24 are DNA damage checkpoint components which may promote checkpoint activation by "sensing" DNA damage directly . Rad24 shares sequence homology with RF-c, a protein that recognises DNA template/RNA primer hybrids during DNA replication. The Ddc1 complex has structural homology to proliferating-cell nuclear antigen (PCNA), which clamps onto DNA and confers processivity to DNA polymerases delta and epsilon. Rad24 is postulated to recognise DNA lesions and then recruit the Ddc1 complex to generate checkpoint signals. ; GO: 0006281 DNA repair, 0007049 cell cycle, 0005634 nucleus
Probab=97.43  E-value=0.0012  Score=37.26  Aligned_cols=143  Identities=16%  Similarity=0.138  Sum_probs=78.4

Q ss_pred             CCCCCHHHHHHHHHHHHHHCCCC---CEEEECCCCCCHHHHHHHHHHHCCC----CCCCCC----EECCCCC--------
Q ss_conf             66589899999999998614799---5898758998888999999862124----267852----4125788--------
Q T0567             3 LIGRSEWINQYRRRLQQLSETDI---AVWLYGAPGTGRMTGARYLHQFGRN----AQGEFV----YRELTPD--------   63 (145)
Q Consensus         3 liG~S~~m~~l~~~i~~~a~~~~---pvli~Ge~GtGK~~~A~~iH~~s~~----~~~~fv----~~~~~~~--------   63 (145)
                      |...-..++++++-++..-....   -++++|++|+||++..+.+...-..    +..|..    ...+...        
T Consensus        21 LaVhkkKv~eVr~wL~~~~~~~~~~~iLlLtGP~GsGKsTti~~Lakel~~~v~Ew~np~~~~~~~~~~~~~~~~~~~~~  100 (498)
T PF03215_consen   21 LAVHKKKVEEVRQWLKEMFSGRSKKRILLLTGPAGSGKSTTIKLLAKELGFEVIEWNNPSDFRSTSFEHQVSDFLSDSNQ  100 (498)
T ss_pred             HHCCHHHHHHHHHHHHHHHCCCCCCCEEEEECCCCCCHHHHHHHHHHHHCCCEEEEECCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             40355529999999999740677660799989998789999999999849756984078775562112222210001243


Q ss_pred             ----CHHHHHHHHHHH-----------CCCEEEECCHHHCC----HHHHHHHHHHHHHCCH-HHEEEECCCCC-------
Q ss_conf             ----988889999862-----------58748743742068----7789999999872140-10011147768-------
Q T0567            64 ----NAPQLNDFIALA-----------QGGTLVLSHPEHLT----REQQYHLVQLQSQEHR-PFRLIGIGDTS-------  116 (145)
Q Consensus        64 ----~~~~~~~~l~~a-----------~gGtL~l~ei~~L~----~~~Q~~L~~~l~~~~~-~~RiI~~s~~~-------  116 (145)
                          ....+..++-.+           +.-.++++|+...-    ...+..|.+++..... ++-+|.+-...       
T Consensus       101 ~~~s~~~~F~~Fll~~sky~~l~~~g~~k~lILIEDlPn~~~~~~~~fr~~L~~~l~s~~~~PlViivSe~~~~~~~~~~  180 (498)
T PF03215_consen  101 FSLSQLEQFEEFLLRASKYSSLSSSGSNKRLILIEDLPNVFHRDTERFREALRRYLASSRSLPLVIIVSECESLSGDNSQ  180 (498)
T ss_pred             CCCCHHHHHHHHHCCCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCH
T ss_conf             56237777755400443456554478874289972276422325899999999999828888759998446444666640


Q ss_pred             -HHHHHHCCCCCHHHHHHHCCCEEEECCCC
Q ss_conf             -78998708976565575544226507889
Q T0567           117 -LVELAASNHIIAELYYCFAMTQIACLPLT  145 (145)
Q Consensus       117 -l~~l~~~~~~~~~L~~~ls~~~i~iPpL~  145 (145)
                       -..+.....|.+++........|...|.|
T Consensus       181 ~~~~~t~~~Ll~~~ll~~~~v~~I~FNpIa  210 (498)
T PF03215_consen  181 DRDSFTAETLLGPELLNHPGVTIIKFNPIA  210 (498)
T ss_pred             HHHHHHHHHCCCHHHHCCCCEEEEEECCCC
T ss_conf             122212330279989608883699866887


No 19 
>PF09848 DUF2075:  Uncharacterized conserved protein (DUF2075)
Probab=97.13  E-value=0.00065  Score=38.71  Aligned_cols=77  Identities=18%  Similarity=0.272  Sum_probs=41.3

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHC-CCCCCCCCEECCCCCCH---------------------HHHHHHHHHH--------
Q ss_conf             58987589988889999998621-24267852412578898---------------------8889999862--------
Q T0567            26 AVWLYGAPGTGRMTGARYLHQFG-RNAQGEFVYRELTPDNA---------------------PQLNDFIALA--------   75 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~~s-~~~~~~fv~~~~~~~~~---------------------~~~~~~l~~a--------   75 (145)
                      -++|+|+|||||+.+|..+-..- ....+..+..-|.....                     .....++...        
T Consensus         3 v~lI~G~pGTGKTvl~~~l~~~l~~~~~~~~~~~l~~n~~~~~~l~~~l~~~~~~~~~~~~~~~~~~~i~~~~~~~~~~~   82 (352)
T PF09848_consen    3 VILITGGPGTGKTVLALNLAKELENSEKGKTVVYLSPNHPLVEVLYEALAEKLGKNRKKNLFQKPTSFINQLSIDDKEEP   82 (352)
T ss_pred             EEEEEECCCCCHHHHHHHHHHHHHCCCCCCEEEEEECCHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999489988999999999986232446558999758179999999987643020267777649999987653202478


Q ss_pred             CCCEEEECCHHHCCHHH--------HHHHHHHHHH
Q ss_conf             58748743742068778--------9999999872
Q T0567            76 QGGTLVLSHPEHLTREQ--------QYHLVQLQSQ  102 (145)
Q Consensus        76 ~gGtL~l~ei~~L~~~~--------Q~~L~~~l~~  102 (145)
                      .--.+++||.++++...        -..|..+++.
T Consensus        83 ~~dviIvDEAq~l~~~~~~~~~~~~~~~L~~l~~~  117 (352)
T PF09848_consen   83 KFDVIIVDEAQRLSTKSDQYNDFSEPNQLIELIKR  117 (352)
T ss_pred             CCEEEEEECHHHHHHHHCHHHCCCCHHHHHHHHHC
T ss_conf             74199995557776630201033328899999960


No 20 
>PF08298 AAA_PrkA:  PrkA AAA domain;  InterPro: IPR013153   This is entry is found at the N-terminus of PrkA proteins - bacterial and archaeal serine kinases approximately 630 residues in length. PrkA possesses the A-motif of nucleotide-binding proteins and exhibits distant homology to eukaryotic protein kinases . Note that many of these are hypothetical.
Probab=96.83  E-value=0.0039  Score=34.54  Aligned_cols=45  Identities=22%  Similarity=0.315  Sum_probs=38.3

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCC----CCEEEECCCCCCHHHHHHHHHH
Q ss_conf             76658989999999999861479----9589875899888899999986
Q T0567             2 ELIGRSEWINQYRRRLQQLSETD----IAVWLYGAPGTGRMTGARYLHQ   46 (145)
Q Consensus         2 ~liG~S~~m~~l~~~i~~~a~~~----~pvli~Ge~GtGK~~~A~~iH~   46 (145)
                      ++.|-...+.++....+.+|+-.    .-+++.||.|+||+++|+.+..
T Consensus        62 ~~~G~~~~i~~~V~~~~~aA~g~~~~k~il~L~GPvg~GKSsl~~~Lk~  110 (358)
T PF08298_consen   62 EFYGMEEAIERIVNYFKSAAQGLEERKQILYLLGPVGGGKSSLAERLKR  110 (358)
T ss_pred             CCCCCHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCHHHHHHHHHH
T ss_conf             2268389999999999999715784514899976898876799999999


No 21 
>PF05707 Zot:  Zonular occludens toxin (Zot);  InterPro: IPR008900 This family consists of bacterial and viral proteins which are very similar to the Zonular occludens toxin (Zot). Zot is elaborated by bacteriophage present in toxigenic strains of Vibrio cholerae. Zot is a single polypeptide chain of 44.8 kDa, with the ability to reversibly alter intestinal epithelial tight junctions, allowing the passage of macromolecules through mucosal barriers.; PDB: 2r2a_B.
Probab=96.67  E-value=0.00036  Score=40.08  Aligned_cols=90  Identities=19%  Similarity=0.417  Sum_probs=53.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCCH---------------------------HHHHHHHHHHCCCE
Q ss_conf             898758998888999999862124267852412578898---------------------------88899998625874
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDNA---------------------------PQLNDFIALAQGGT   79 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~---------------------------~~~~~~l~~a~gGt   79 (145)
                      .+++|.+|+||+..|-..|-...-..+.-|..|....+.                           ..+..+.....|+.
T Consensus         3 ~li~G~pGsGKS~~av~~~i~~~l~~gR~V~tni~gl~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~l   82 (193)
T PF05707_consen    3 YLITGKPGSGKSYEAVWMHIIPALKKGRRVYTNIPGLNLEKIPPVLGEKFRTRLIRVSDPPFEELDDDLDDWRDYPRGSL   82 (193)
T ss_dssp             EEEE-------HHHHHHHHHH-GGGS---EEE------S--EEEE--TTT-S-----S--SSSEEGGGHHHHTTSG---E
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHCCCEEEECCCCCCHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCE
T ss_conf             99986999967499999999999877999999897666434002215554333334566420445667777415788879


Q ss_pred             EEECCHHHCCHHHHH------HHHHHHHH-CCHHHEEEECCCCC
Q ss_conf             874374206877899------99999872-14010011147768
Q T0567            80 LVLSHPEHLTREQQY------HLVQLQSQ-EHRPFRLIGIGDTS  116 (145)
Q Consensus        80 L~l~ei~~L~~~~Q~------~L~~~l~~-~~~~~RiI~~s~~~  116 (145)
                      ++|||.+.+=+....      ..++++.. .+.+..+|++|...
T Consensus        83 iviDEa~~~~~~~~~~~~~~~~~i~~l~~hRh~g~diiliTQ~~  126 (193)
T PF05707_consen   83 IVIDEAHNFFPSRNWNGKKVPEIIEFLAEHRHYGWDIILITQSP  126 (193)
T ss_dssp             EEETTGGGTSB----------HHHHGGGGCCC---EEEEE----
T ss_pred             EEEECCHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCEEEECCCH
T ss_conf             99988752278986645344689999998764385089979994


No 22 
>PF00910 RNA_helicase:  RNA helicase;  InterPro: IPR000605   Helicases have been classified in 5 superfamilies (SF1-SF5). All of the proteins bind ATP and, consequently, all of them carry the classical Walker A (phosphate-binding loop or P-loop) and Walker B (Mg2+-binding aspartic acid) motifs. Superfamily 3 consists of helicases encoded mainly by small DNA viruses and some large nucleocytoplasmic DNA viruses , . Small viruses are very dependent on the host-cell machinery to replicate. SF3 helicase in small viruses is associated with an origin-binding domain. By pairing a domain that recognises the ori with a helicase, the virus can bypass the host-cell-based regulation pathway and initiate its own replication. The protein binds to the viral ori leading to origin unwinding. Cellular replication proteins are then recruited to the ori and the viral DNA is replicated.   In SF3 helicases the Walker A and Walker B motifs are separated by spacers of rather uniform, and relatively short, length. In addition to the A and B motifs this family is characterised by a third motif (C) which resides between the B motif and the C-terminus of the conserved region. This motif consists of an Asn residue preceded by a run of hydrophobic residues .   Several structures of SF3 helicases have been solved . They all possess the same core alpha/beta fold, consisting of a five-stranded parallel beta sheet flanked on both sides by several alpha helices. In contrast to SF1 and SF2 helicases, which have RecA-like core folds, the strand connectivity within the alpha/beta core domain is that of AAA+ proteins . The SF3 helicase proteins assemble into a hexameric ring.   Some proteins known to contain an SF3 helicase domain are listed below:  Polyomavirus large T antigen. It initiates DNA unwinding and replication via interactions with the viral origin of replication. Papillomavirus E1 protein. An ATP-dependent DNA helicase required for initiation of viral DNA replication. Parvovirus Rep/NS1 protein, which is also required for the initiation of viral replication. Poxviridae and other large DNA viruses D5 protein. Bacteriophage DNA primase/helicase protein. Bacterial prophage DNA primase/helicase protein.     The entry represents the core alpha/beta fold of the SF3 helicase domain found predominantly in DNA viruses.; GO: 0003723 RNA binding, 0003724 RNA helicase activity
Probab=96.59  E-value=0.0023  Score=35.82  Aligned_cols=59  Identities=17%  Similarity=0.298  Sum_probs=36.5

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCC-----CCCCCCCEECCCCCCHHHHHHHHHHHCCCEEEECCHHHCCHH
Q ss_conf             89875899888899999986212-----426785241257889888899998625874874374206877
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGR-----NAQGEFVYRELTPDNAPQLNDFIALAQGGTLVLSHPEHLTRE   91 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~-----~~~~~fv~~~~~~~~~~~~~~~l~~a~gGtL~l~ei~~L~~~   91 (145)
                      |+|+|++|+||+++|+.+-..-.     .....++..+.   +..-|.+.-   ...++++||+...+..
T Consensus         1 I~i~G~~G~GKS~la~~l~~~l~~~~~~~~~~~~y~~~~---~~~~wdgY~---~Q~vvi~DD~~~~~~~   64 (107)
T PF00910_consen    1 IWIYGPSGIGKSTLANYLAKDLLQHLGEPKKDSIYTRNP---SDDFWDGYK---GQEVVIIDDFGQDKDG   64 (107)
T ss_pred             CEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEECCC---CCCHHHCCC---CCCEEEEEECCCCCCC
T ss_conf             989898989889999999999999735678896886898---646202015---9857898605668765


No 23 
>PF06414 Zeta_toxin:  Zeta toxin;  InterPro: IPR010488   This family consists of several bacterial zeta toxin proteins. Zeta toxin is thought to be part of a postregulational killing system in bacteria. It relies on antitoxin/toxin systems that secure stable inheritance of low and medium copy number plasmids during cell division and kill cells that have lost the plasmid .; GO: 0005524 ATP binding, 0001906 cell killing; PDB: 1ly1_A 2ia5_B 1rpz_A 1rc8_A 1ltq_A 1rrc_A 1gvn_D 2p5t_B.
Probab=96.43  E-value=0.0009  Score=37.97  Aligned_cols=91  Identities=18%  Similarity=0.209  Sum_probs=47.8

Q ss_pred             HHCCCCC--EEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCC-----CHH--------------------HHHHHH
Q ss_conf             6147995--8987589988889999998621242678524125788-----988--------------------889999
Q T0567            20 LSETDIA--VWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPD-----NAP--------------------QLNDFI   72 (145)
Q Consensus        20 ~a~~~~p--vli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~-----~~~--------------------~~~~~l   72 (145)
                      +.....|  +++.|.+|+||+++|+.+.....  .+.++.+|....     ...                    ....++
T Consensus         9 ~~~~~~p~lill~G~pGsGKST~a~~l~~~~~--~~~~v~I~~D~lr~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   86 (199)
T PF06414_consen    9 YPPQERPKLILLAGPPGSGKSTLARELAEELG--RGGIVRINADELRKSLPDYDELMRDDPEEASELTEEEARRLAEELI   86 (199)
T ss_dssp             ----SS-EEEEEE-------HHHHHHHHHHT-------EEE-HHCCGGGSTTHHHHHCCHGGGCHHHHTTTHHHHHHHHH
T ss_pred             CCCCCCCEEEEEECCCCCCHHHHHHHHHHHHC--CCCEEEEEHHHHHHHCCCHHHHHHCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             46877988999889999999999999988725--6835998559998766310555530145555777999999999999


Q ss_pred             HHH--CCCEEEECCHHHCCHHHHHHHHHHHHHCCHHHEEEECC
Q ss_conf             862--58748743742068778999999987214010011147
Q T0567            73 ALA--QGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIG  113 (145)
Q Consensus        73 ~~a--~gGtL~l~ei~~L~~~~Q~~L~~~l~~~~~~~RiI~~s  113 (145)
                      +.+  +|-.+++|..-.-+..... +.+........+.++...
T Consensus        87 ~~~l~~g~~vi~d~t~~~~~~~~~-~~~~~~~~gy~v~l~~v~  128 (199)
T PF06414_consen   87 ERALENGRNVIVDGTFSNPSYREK-LIRKAKEAGYQVELVFVD  128 (199)
T ss_dssp             HHHHH----EEE---TTSSHHHHH-HHHHHHC---EEEEEEE-
T ss_pred             HHHHHCCCCCCCCCCCCCHHHHHH-HHHHHHHCCCEEEEEEEC
T ss_conf             999976998200677689999999-999999779779999945


No 24 
>PF00437 GSPII_E:  Type II/IV secretion system protein;  InterPro: IPR001482 A number of bacterial proteins, some of which are involved in a general secretion pathway (GSP) for the export of proteins (also called the type II pathway) belong to this group , . These proteins are probably located in the cytoplasm and, on the basis of the presence of a conserved P-loop region IPR001687 from INTERPRO, bind ATP.; GO: 0005524 ATP binding, 0006810 transport, 0005622 intracellular; PDB: 1p9r_A 1p9w_A 2gsz_A 2eww_A 2ewv_A 2eyu_A 2oap_1 2oaq_1 2jmz_A 2jnq_A ....
Probab=96.32  E-value=0.0019  Score=36.18  Aligned_cols=90  Identities=16%  Similarity=0.152  Sum_probs=54.1

Q ss_pred             HHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCC--------------C-CCHHHHHHHHHHH-
Q ss_conf             99999998614799589875899888899999986212426785241257--------------8-8988889999862-
Q T0567            12 QYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELT--------------P-DNAPQLNDFIALA-   75 (145)
Q Consensus        12 ~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~--------------~-~~~~~~~~~l~~a-   75 (145)
                      .+.+.++........++|.|++||||+++.+++-..-+......+.+.-.              . .....+..++..+ 
T Consensus       125 ~~~~~l~~~v~~~~~ili~G~tGSGKTT~l~al~~~~~~~~~~i~tiEd~~E~~~~~~~~~~~~~~~~~~~~~~~l~~~L  204 (280)
T PF00437_consen  125 EIAELLKQAVRGRGNILISGPTGSGKTTLLNALLREIPPDGRRIVTIEDPIELQLPGPNQVQLQTREGGITFADLLKAAL  204 (280)
T ss_dssp             HHHHHHHCHHHTT--EEEE--TT---HHHHHHHHGGSHTTTSEEEEEESSS-S--TBSSEEEEECC-GTBSHHHHHHHHT
T ss_pred             HHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHCCCCCCEEEEECCCCCCCCCCCCEEEEEECCCCCCHHHHHHHHH
T ss_conf             99999997666373799998888776589999987524566559995787523677532698872257669999999983


Q ss_pred             --CCCEEEECCHHHCCHHHHHHHHHHHHHCC
Q ss_conf             --58748743742068778999999987214
Q T0567            76 --QGGTLVLSHPEHLTREQQYHLVQLQSQEH  104 (145)
Q Consensus        76 --~gGtL~l~ei~~L~~~~Q~~L~~~l~~~~  104 (145)
                        .--.+++.|+-.  .+.... ++....++
T Consensus       205 R~~PD~IivGEiR~--~e~~~~-i~a~~tGh  232 (280)
T PF00437_consen  205 RQDPDRIIVGEIRD--PEAAEA-IQAANTGH  232 (280)
T ss_dssp             TS--SEEEESEE-S--HHHHHH-HHHHH---
T ss_pred             CCCCCEEECCCCCC--HHHHHH-HHHHHCCC
T ss_conf             76989584387786--999999-99997699


No 25 
>PF08433 KTI12:  Chromatin associated protein KTI12 ;  InterPro: IPR013641   This is a family of chromatin associated proteins which interact with the Elongator complex, a component of the elongating form of RNA polymerase II . The Elongator complex has histone acetyltransferase activity. 
Probab=96.27  E-value=0.014  Score=31.58  Aligned_cols=94  Identities=19%  Similarity=0.265  Sum_probs=45.7

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCC-------C----CCHHHHHH-HHH---H--HCCCEEEECCHHHCC
Q ss_conf             89875899888899999986212426785241257-------8----89888899-998---6--258748743742068
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELT-------P----DNAPQLND-FIA---L--AQGGTLVLSHPEHLT   89 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~-------~----~~~~~~~~-~l~---~--a~gGtL~l~ei~~L~   89 (145)
                      |+++|-|||||+++|+.|...-.......+.++-.       .    .+...... +..   +  ..|-++++|.. ..-
T Consensus         4 Iil~GlPgSGKST~A~~L~~~l~~~~~~~~~v~~~~~~~~~~~y~~~~~ek~~r~~l~~~v~r~L~~~~~VIlDat-nyi   82 (270)
T PF08433_consen    4 IILCGLPGSGKSTLAKQLAERLEAKNYRVDIVSDDSLRIDRNDYSDSQNEKQARGALKSAVKRALSKGDIVILDAT-NYI   82 (270)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCEEEEECHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECC-CCH
T ss_conf             9997799998999999999987513873899783663464422121134799999999999998646986999487-440


Q ss_pred             HHHHHHHHHHHHHCCHHHEEEECCCCCHHHHHH
Q ss_conf             778999999987214010011147768789987
Q T0567            90 REQQYHLVQLQSQEHRPFRLIGIGDTSLVELAA  122 (145)
Q Consensus        90 ~~~Q~~L~~~l~~~~~~~RiI~~s~~~l~~l~~  122 (145)
                      +.....|..+-......+.+|.. ..+++...+
T Consensus        83 k~~Ryel~~lAk~~~~~~~vv~~-~~p~e~~~~  114 (270)
T PF08433_consen   83 KGMRYELYCLAKAAGTPYCVVYV-DCPLETCRE  114 (270)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEE-CCCHHHHHH
T ss_conf             99999999999863997599997-299999999


No 26 
>PF01583 APS_kinase:  Adenylylsulphate kinase;  InterPro: IPR002891 Enzyme that catalyses the phosphorylation of adenylylsulphate to 3'-phosphoadenylylsulphate. This domain contains an ATP binding P-loop motif .; GO: 0005524 ATP binding, 0016301 kinase activity, 0016772 transferase activity, transferring phosphorus-containing groups, 0000103 sulfate assimilation; PDB: 2yvu_A 3cr8_A 1m8p_C 1i2d_B 2gks_B 1m7g_D 1m7h_C 1d6j_A 3cr7_B 2pey_B ....
Probab=96.20  E-value=0.00091  Score=37.93  Aligned_cols=106  Identities=18%  Similarity=0.189  Sum_probs=58.3

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCC----------CCCHH----HHHHHHHH----HCCCEEEECCHH
Q ss_conf             9589875899888899999986212426785241257----------88988----88999986----258748743742
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELT----------PDNAP----QLNDFIAL----AQGGTLVLSHPE   86 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~----------~~~~~----~~~~~l~~----a~gGtL~l~ei~   86 (145)
                      .-|||+|-+|+||+++|+.++..-.....+.+.+|..          ..+..    ++..+.+.    +..|.+++-..-
T Consensus         3 ~vIw~tGlsGsGKsTlA~~L~~~L~~~g~~~~~LDgD~iR~~l~~dlgfs~~dR~e~~rr~a~vA~ll~~~G~ivIva~i   82 (156)
T PF01583_consen    3 FVIWFTGLSGSGKSTLARALEKRLFERGRPVYLLDGDNIRHGLNPDLGFSREDREENIRRIAEVARLLADAGIIVIVAAI   82 (156)
T ss_dssp             -EEEEE-ETT---HHHHHHHHHHHHHTT--EEEE---HHHHHTTTT----HHHHHHHHHHHHHHHHHHHHTTSEEEEE--
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEECHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             79998897999999999999999998499987963878865679999989878999999999999999868998999427


Q ss_pred             HCCHHHHHHHHHHHHHCCHHHEEEECCCCCHHHHHHCCCCCHHHHHHHC
Q ss_conf             0687789999999872140100111477687899870897656557554
Q T0567            87 HLTREQQYHLVQLQSQEHRPFRLIGIGDTSLVELAASNHIIAELYYCFA  135 (145)
Q Consensus        87 ~L~~~~Q~~L~~~l~~~~~~~RiI~~s~~~l~~l~~~~~~~~~L~~~ls  135 (145)
                      ...++...+..+.+...  .+.-|... .+++.+.+..  ...||.+-.
T Consensus        83 sp~~~~R~~~R~~~~~~--~f~EV~v~-~~le~~~~RD--~KglY~ka~  126 (156)
T PF01583_consen   83 SPYREDREYAREIIPNE--RFIEVYVD-CPLEECERRD--PKGLYAKAR  126 (156)
T ss_dssp             --SHHHHHHHHHHHHT----EEEEEEE-S-HHHHHHHT------HHHHH
T ss_pred             CCCHHHHHHHHHHCCCC--CEEEEEEC-CCHHHHHHHC--CHHHHHHHH
T ss_conf             88889999999866868--60999847-9989998608--550787875


No 27 
>PF06068 TIP49:  TIP49 C-terminus;  InterPro: IPR010339   This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway . TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases .; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0005634 nucleus; PDB: 2cqa_A 2c9o_C.
Probab=96.19  E-value=0.0019  Score=36.16  Aligned_cols=39  Identities=21%  Similarity=0.180  Sum_probs=31.3

Q ss_pred             CCEEEECCHHHCCHHHHHHHHHHHHHCCHHHEEEECCCCC
Q ss_conf             8748743742068778999999987214010011147768
Q T0567            77 GGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDTS  116 (145)
Q Consensus        77 gGtL~l~ei~~L~~~~Q~~L~~~l~~~~~~~RiI~~s~~~  116 (145)
                      -|+||+||++-|+.+.-..|-+.++.+-.++ +|++|++-
T Consensus       279 pGVLFIDEvHMLDiEcFsfLnralEs~laPi-vI~ATNRG  317 (398)
T PF06068_consen  279 PGVLFIDEVHMLDIECFSFLNRALESELAPI-VILATNRG  317 (398)
T ss_dssp             ---EEE-SGGG-BHHHHHHHHHHTTSTT----EEEE----
T ss_pred             CCCEEEECCCCCCHHHHHHHHHHHCCCCCCE-EEEECCCC
T ss_conf             1658995133036999999999860568878-99972786


No 28 
>PF06309 Torsin:  Torsin;  InterPro: IPR010448   This family consists of several eukaryotic torsin proteins. Torsion dystonia is an autosomal dominant movement disorder characterised by involuntary, repetitive muscle contractions and twisted postures. The most severe early-onset form of dystonia has been linked to mutations in the human DYT1 (TOR1A) gene encoding a protein termed torsinA. While causative genetic alterations have been identified, the function of torsin proteins and the molecular mechanism underlying dystonia remain unknown. Phylogenetic analysis of the torsin protein family indicates these proteins share distant sequence similarity with the large and diverse family of AAA ATPase, central region containing proteins () proteins. It has been suggested that torsins play a role in effectively managing protein folding and that possible breakdown in a neuroprotective mechanism that is, in part, mediated by torsins may be responsible for the neuronal dysfunction associated with dystonia .; GO: 0005524 ATP binding, 0051085 chaperone cofactor-dependent protein folding, 0005783 endoplasmic reticulum
Probab=96.12  E-value=0.0038  Score=34.58  Aligned_cols=56  Identities=18%  Similarity=0.174  Sum_probs=39.4

Q ss_pred             CCCCCCHHHHHHHHHHHHHHCC---CCCE--EEECCCCCCHHHHHHHHHHH--CCCCCCCCCE
Q ss_conf             7665898999999999986147---9958--98758998888999999862--1242678524
Q T0567             2 ELIGRSEWINQYRRRLQQLSET---DIAV--WLYGAPGTGRMTGARYLHQF--GRNAQGEFVY   57 (145)
Q Consensus         2 ~liG~S~~m~~l~~~i~~~a~~---~~pv--li~Ge~GtGK~~~A~~iH~~--s~~~~~~fv~   57 (145)
                      ++.|+--+.+.+.+.++..-.+   +.|+  -+.|.+||||+.+|+.|...  ..-...+||.
T Consensus        26 ~lfGQhla~~~v~~al~~hl~~~~p~KpLVLSfHG~~GtGKn~va~lIA~~ly~~G~~S~~V~   88 (127)
T PF06309_consen   26 RLFGQHLAKDVVVNALKDHLSNKNPRKPLVLSFHGWTGTGKNFVARLIARNLYRSGMKSPYVH   88 (127)
T ss_pred             HCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCEE
T ss_conf             724839899999999999981899999758985389998587899999999987212786235


No 29 
>PF05272 VirE:  Virulence-associated protein E;  InterPro: IPR007936   This family contains several bacterial virulence-associated protein E like proteins.
Probab=96.11  E-value=0.0038  Score=34.58  Aligned_cols=86  Identities=19%  Similarity=0.229  Sum_probs=53.9

Q ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHHHHHCCCEEEECCHHHCCHHHHHHHHHHHH
Q ss_conf             47995898758998888999999862124267852412578898888999986258748743742068778999999987
Q T0567            22 ETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDNAPQLNDFIALAQGGTLVLSHPEHLTREQQYHLVQLQS  101 (145)
Q Consensus        22 ~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~~~~~~~l~~a~gGtL~l~ei~~L~~~~Q~~L~~~l~  101 (145)
                      +.+..+.|.|+.|+||+++-+.|   ++.    |..-+....+..+  ........-.+.++|++.+.+..+..|=.++.
T Consensus        50 k~d~vliL~G~QG~gKStf~~~L---~~~----~~~~~~~~~~~kd--~~~~l~~~~iiel~El~~~~k~~~~~lK~~iT  120 (198)
T PF05272_consen   50 KFDTVLILVGKQGIGKSTFFRKL---GPE----YFTDSLNDFDDKD--FLQQLQGKWIIELDELDGMSKAEVEALKAFIT  120 (198)
T ss_pred             CCCEEEEEECCCCCCHHHHHHHH---CHH----HCCCCCCCCCCCH--HHHHHHHCCEEEHHHHHHCCHHHHHHHHHHHC
T ss_conf             78868898889989888999986---767----4567433456757--99997514378838865234532999999854


Q ss_pred             HCC---------------HHHEEEECCCCC
Q ss_conf             214---------------010011147768
Q T0567           102 QEH---------------RPFRLIGIGDTS  116 (145)
Q Consensus       102 ~~~---------------~~~RiI~~s~~~  116 (145)
                      ...               +.+.+|++|+.+
T Consensus       121 ~~~d~~R~~Y~~~~~~~pR~~vfigTtN~~  150 (198)
T PF05272_consen  121 RRVDTYRPPYGRRSEEFPRRCVFIGTTNND  150 (198)
T ss_pred             CCCEEEEECCCCCHHHCCEEEEEEEECCCC
T ss_conf             661456717878730287168999964887


No 30 
>PF02562 PhoH:  PhoH-like protein;  InterPro: IPR003714 PhoH is a cytoplasmic protein and predicted ATPase that is induced by phosphate starvation and belongings to the phosphate regulon (pho) in Escherichia coli .; GO: 0005524 ATP binding, 0016036 cellular response to phosphate starvation; PDB: 3b85_A.
Probab=95.95  E-value=0.006  Score=33.52  Aligned_cols=96  Identities=16%  Similarity=0.261  Sum_probs=52.2

Q ss_pred             CCCCEEEECCCCCCHHHHHH--HHHHHCCCCCCCCCEECCCCCCHH-------------------------------HHH
Q ss_conf             79958987589988889999--998621242678524125788988-------------------------------889
Q T0567            23 TDIAVWLYGAPGTGRMTGAR--YLHQFGRNAQGEFVYRELTPDNAP-------------------------------QLN   69 (145)
Q Consensus        23 ~~~pvli~Ge~GtGK~~~A~--~iH~~s~~~~~~fv~~~~~~~~~~-------------------------------~~~   69 (145)
                      ...-|++.|++||||+.+|-  +++..-......++...-......                               ..+
T Consensus        18 ~~~lv~~~G~AGTGKT~lala~a~~~l~~~~~~riii~Rp~v~~g~~lGfLpG~~~eK~~p~~~pi~D~L~~~~~~~~~~   97 (205)
T PF02562_consen   18 ENDLVFITGPAGTGKTFLALAAALQLLLNGRYRRIIITRPTVEAGEDLGFLPGDLEEKMDPYLRPIYDALEDLFGQEKIE   97 (205)
T ss_dssp             H-SEEE----------HHHHHHHHHHHHTTS-SEEEEEE-S-------------------TTTHHHHHHHTTTS-TTCHH
T ss_pred             HCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCCCHHHHHCCCCCCCHHHHHHHHHHHHHHHHHHHHCHHHHH
T ss_conf             39958997789977899999999999974888769998487224776487999878988788858999999986778899


Q ss_pred             HHHHH----------HC-----CCEEEECCHHHCCHHHHHHHHHHHHHCCHHHEEEECCCCCHHHHH
Q ss_conf             99986----------25-----874874374206877899999998721401001114776878998
Q T0567            70 DFIAL----------AQ-----GGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDTSLVELA  121 (145)
Q Consensus        70 ~~l~~----------a~-----gGtL~l~ei~~L~~~~Q~~L~~~l~~~~~~~RiI~~s~~~l~~l~  121 (145)
                      .+++.          ..     +..+++||.+.+++++=..++.-+   ..+.++|......-.++.
T Consensus        98 ~l~~~~~Iei~~l~~~RGRtl~~~~IIiDEAQN~t~~~~k~iLTR~---g~~skiVl~GD~~QiD~~  161 (205)
T PF02562_consen   98 ELLERGKIEIEPLAFMRGRTLDNSFIIIDEAQNLTPEEMKMILTRI---GEGSKIVLTGDPSQIDLP  161 (205)
T ss_dssp             HHHH---EEEEEGGGG------SEEEEE-SGGG--HHHHHHHHTT--------EEEE----------
T ss_pred             HHHHCCCEEEEEHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHHHC---CCCCEEEEECCHHHCCCC
T ss_conf             9998398699337875388766558999711179999999999981---899779994885450689


No 31 
>PF06745 KaiC:  KaiC;  InterPro: IPR014774   This entry represents a conserved region within bacterial and archaeal proteins, most of which are hypothetical. More than one copy is sometimes found in each protein in this entry. These include KaiC, which is one of the Kai proteins among which direct protein-protein association may be a critical process in the generation of circadian rhythms in cyanobacteria .    The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of this domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor.; PDB: 2w0m_A 1u9i_A 2gbl_A 2zts_B 2dr3_B.
Probab=95.66  E-value=0.02  Score=30.68  Aligned_cols=38  Identities=21%  Similarity=0.333  Sum_probs=24.4

Q ss_pred             CCCCEEEECCCCCCHHHHHHH-HHHHCCCCCCCCCEECC
Q ss_conf             799589875899888899999-98621242678524125
Q T0567            23 TDIAVWLYGAPGTGRMTGARY-LHQFGRNAQGEFVYREL   60 (145)
Q Consensus        23 ~~~pvli~Ge~GtGK~~~A~~-iH~~s~~~~~~fv~~~~   60 (145)
                      ....++|.|++||||+++|.- ++....+...+.+.+.+
T Consensus        18 ~Gs~~li~G~pGsGKT~l~~qf~~~~~~~~ge~~lyis~   56 (225)
T PF06745_consen   18 RGSVTLISGPPGSGKTTLALQFLANGAKQEGEKVLYISF   56 (225)
T ss_dssp             TT-EEEEE-------HHHHHHHHHHHHTTTT--EEEEES
T ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHHHHCCCCEEEEEE
T ss_conf             990899992799885899999999999845994699994


No 32 
>PF10236 DAP3:  Mitochondrial ribosomal death-associated protein 3
Probab=95.52  E-value=0.012  Score=32.00  Aligned_cols=41  Identities=17%  Similarity=0.264  Sum_probs=27.3

Q ss_pred             HHHHHHHHHHHHCC--CCCEEEECCCCCCHH-HHHHHHHHHCCC
Q ss_conf             99999999986147--995898758998888-999999862124
Q T0567            10 INQYRRRLQQLSET--DIAVWLYGAPGTGRM-TGARYLHQFGRN   50 (145)
Q Consensus        10 m~~l~~~i~~~a~~--~~pvli~Ge~GtGK~-~~A~~iH~~s~~   50 (145)
                      .-++.++++.....  ..-++|+|++||||+ ++|+++|.....
T Consensus         7 t~el~~~l~~~~~~~~~~r~vL~G~~GsGKS~~L~q~~~~A~~~   50 (309)
T PF10236_consen    7 TLELINQLKEADKSSKAVRIVLDGERGSGKSVLLAQAVHYAREK   50 (309)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             99999999875247885179998969987999999999999859


No 33 
>PF06048 DUF927:  Domain of unknown function (DUF927);  InterPro: IPR009270   This is a family of bacterial proteins of unknown function.
Probab=95.51  E-value=0.024  Score=30.31  Aligned_cols=78  Identities=14%  Similarity=0.118  Sum_probs=51.8

Q ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCC-CCHHHHHHHHHHHCCCEEEECCHHHCCHHHHHHHHHHHH
Q ss_conf             7995898758998888999999862124267852412578-898888999986258748743742068778999999987
Q T0567            23 TDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTP-DNAPQLNDFIALAQGGTLVLSHPEHLTREQQYHLVQLQS  101 (145)
Q Consensus        23 ~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~-~~~~~~~~~l~~a~gGtL~l~ei~~L~~~~Q~~L~~~l~  101 (145)
                      ...-+.++|+.++||++.+++.......   |. .+-... .+...++......+++.|+|||+...++..=..++-.+.
T Consensus       191 ~~~~~hl~G~SS~GKTt~~~~AaSvwG~---p~-~l~~sW~~T~n~le~~a~~~nd~~L~LDE~~~~~~~~~~~~iY~l~  266 (285)
T PF06048_consen  191 EGFGFHLYGQSSSGKTTALKLAASVWGN---PD-SLIRSWNSTANGLERTAAAHNDLPLILDEIGQADPREVGQIIYMLA  266 (285)
T ss_pred             CCEEEEEEECCCCCHHHHHHHHHHHHCC---CC-CCCCCHHHHHHHHHHHHHHCCCCCEEECHHCCCCHHHHHHHHHHHH
T ss_conf             9779999817988679999999987279---72-2002826589999999998099652510210267657999998974


Q ss_pred             HCC
Q ss_conf             214
Q T0567           102 QEH  104 (145)
Q Consensus       102 ~~~  104 (145)
                      ++.
T Consensus       267 nG~  269 (285)
T PF06048_consen  267 NGQ  269 (285)
T ss_pred             CCC
T ss_conf             887


No 34 
>PF00270 DEAD:  DEAD/DEAH box helicase;  InterPro: IPR011545   Members of this family include the DEAD and DEAH box helicases. Helicases are involved in unwinding nucleic acids. The DEAD box helicases are involved in various aspects of RNA metabolism, including nuclear transcription, pre mRNA splicing, ribosome biogenesis, nucleocytoplasmic transport, translation, RNA decay and organellar gene expression. ; GO: 0003676 nucleic acid binding, 0005524 ATP binding, 0008026 ATP-dependent helicase activity; PDB: 3ber_A 2pl3_A 1oyy_A 1oyw_A 2v1x_B 1gm5_A 2eyq_B 1wp9_A 2zja_A 2zj2_A ....
Probab=95.47  E-value=0.056  Score=28.32  Aligned_cols=41  Identities=10%  Similarity=0.138  Sum_probs=26.4

Q ss_pred             CEEEECCHHHCCHH-HHHHHHHHHHHCCHHHEEEECCCCCHH
Q ss_conf             74874374206877-899999998721401001114776878
Q T0567            78 GTLVLSHPEHLTRE-QQYHLVQLQSQEHRPFRLIGIGDTSLV  118 (145)
Q Consensus        78 GtL~l~ei~~L~~~-~Q~~L~~~l~~~~~~~RiI~~s~~~l~  118 (145)
                      +.+++||+|.+... ....+..+++.-....++|+.|....+
T Consensus       121 ~~iViDE~h~~~~~~~~~~~~~~~~~~~~~~~~v~~SAT~~~  162 (167)
T PF00270_consen  121 SLIVIDEAHLLSEQGYGSQIRRLLRRLPKNPQIVLLSATPPE  162 (167)
T ss_dssp             SEEEEESHHHHHHCCHHHHHHHHHHTSTTTSEEEEEESSSTH
T ss_pred             CCCCCHHCCCCCCCCHHHHHHHHHHHCCCCCCEEEECCCCCH
T ss_conf             402200101201322899999999852305998998428986


No 35 
>PF07931 CPT:  Chloramphenicol phosphotransferase-like protein;  InterPro: IPR012853   The members of this family are all similar to chloramphenicol 3-O phosphotransferase (CPT, Q56148 from SWISSPROT) expressed by Streptomyces venezuelae. Chloramphenicol (Cm) is a metabolite produced by this bacterium that can inhibit ribosomal peptidyl transferase activity and therefore protein production. By transferring a phosphate group to the C-3 hydroxyl group of Cm, CPT inactivates this potentially lethal metabolite , . ; PDB: 1grr_A 1qhs_A 1qhx_A 1grq_A 1qhy_A 1qhn_A.
Probab=95.47  E-value=0.0019  Score=36.24  Aligned_cols=30  Identities=23%  Similarity=0.235  Sum_probs=23.2

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEE
Q ss_conf             589875899888899999986212426785241
Q T0567            26 AVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYR   58 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~   58 (145)
                      =|+++|.+|+||+++|+.|-...+   .||+.+
T Consensus         3 iIiLnG~ssSGKSTiA~~L~~~~~---~~~~hl   32 (174)
T PF07931_consen    3 IIILNGPSSSGKSTIARALQERLP---RPWLHL   32 (174)
T ss_dssp             EEEE-----------HHHHHHHSS---S-EEEE
T ss_pred             EEEEECCCCCCHHHHHHHHHHHCC---CCEEEE
T ss_conf             999969999998999999998559---977997


No 36 
>PF00448 SRP54:  SRP54-type protein, GTPase domain;  InterPro: IPR000897    The signal recognition particle (SRP) is a multimeric protein, which along with its conjugate receptor (SR), is involved in targeting secretory proteins to the rough endoplasmic reticulum (RER) membrane in eukaryotes, or to the plasma membrane in prokaryotes , . SRP recognises the signal sequence of the nascent polypeptide on the ribosome, retards its elongation, and docks the SRP-ribosome-polypeptide complex to the RER membrane via the SR receptor. SRP consists of six polypeptides (SRP9, SRP14, SRP19, SRP54, SRP68 and SRP72) and a single 300 nucleotide 7S RNA molecule. The RNA component catalyses the interaction of SRP with its SR receptor . In higher eukaryotes, the SRP complex consists of the Alu domain and the S domain linked by the SRP RNA. The Alu domain consists of a heterodimer of SRP9 and SRP14 bound to the 5' and 3' terminal sequences of SRP RNA. This domain is necessary for retarding the elongation of the nascent polypeptide chain, which gives SRP time to dock the ribosome-polypeptide complex to the RER membrane.    This entry represents the GTPase domain of the 54 kDa SRP54 component, a GTP-binding protein that interacts with the signal sequence when it emerges from the ribosome. SRP54 of the signal recognition particle has a three-domain structure: an N-terminal helical bundle domain, a GTPase domain, and the M-domain that binds the 7s RNA and also binds the signal sequence. The extreme C-terminal region is glycine-rich and lower in complexity and poorly conserved between species. The GTPase domain is evolutionary related to P-loop NTPase domains found in a variety of other proteins .   These proteins include Escherichia coli and Bacillus subtilis ffh protein (P48), which seems to be the prokaryotic counterpart of SRP54; signal recognition particle receptor alpha subunit (docking protein), an integral membrane GTP-binding protein which ensures, in conjunction with SRP, the correct targeting of nascent secretory proteins to the endoplasmic reticulum membrane; bacterial FtsY protein, which is believed to play a similar role to that of the docking protein in eukaryotes; the pilA protein from Neisseria gonorrhoeae, the homolog of ftsY; and bacterial flagellar biosynthesis protein flhF.; GO: 0005525 GTP binding, 0008312 7S RNA binding, 0006614 SRP-dependent cotranslational protein targeting to membrane, 0016020 membrane; PDB: 2q9a_A 2q9c_B 2cnw_F 2q9b_B 2iyl_D 1rj9_A 1okk_D 2j7p_E 2px0_A 2px3_A ....
Probab=95.47  E-value=0.037  Score=29.31  Aligned_cols=101  Identities=13%  Similarity=0.120  Sum_probs=49.8

Q ss_pred             CEEEECCCCCCHHH-HHHHHHHHCCC-CCCCCCEECCCCCC------------------------HHH-HHHHHHHHC--
Q ss_conf             58987589988889-99999862124-26785241257889------------------------888-899998625--
Q T0567            26 AVWLYGAPGTGRMT-GARYLHQFGRN-AQGEFVYRELTPDN------------------------APQ-LNDFIALAQ--   76 (145)
Q Consensus        26 pvli~Ge~GtGK~~-~A~~iH~~s~~-~~~~fv~~~~~~~~------------------------~~~-~~~~l~~a~--   76 (145)
                      -+++.|++|+||++ +|+.-+....+ ..-.++..|+....                        +.+ ..+.++.+.  
T Consensus         3 vi~lvGptGvGKTTT~aKLA~~~~~~~~~v~lit~Dt~Riga~eQLk~ya~~l~vp~~~~~~~~d~~~~~~~~l~~~~~~   82 (196)
T PF00448_consen    3 VIALVGPTGVGKTTTIAKLAARLKLKGKKVALITADTYRIGAVEQLKTYAEILGVPFISARTESDPAAIAKEALEEAASR   82 (196)
T ss_dssp             EEEEE-------HHHHHHHHHHHHHTS--EEEEEESTSSHHHHHHHHHHHHHTTCEEEECTSCCCHHHHHHHHHHHHHHT
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHHHHHHCCCEECCCCCCCHHHHHHHHHHHHHHC
T ss_conf             99997998887888999999999977990699947887657999999999980982671456789999999999999967


Q ss_pred             -CCEEEECCHHHCCHHH--HHHHHHHHHHC-CHHHEEEECCCCCHHHHHHCCCC
Q ss_conf             -8748743742068778--99999998721-40100111477687899870897
Q T0567            77 -GGTLVLSHPEHLTREQ--QYHLVQLQSQE-HRPFRLIGIGDTSLVELAASNHI  126 (145)
Q Consensus        77 -gGtL~l~ei~~L~~~~--Q~~L~~~l~~~-~~~~RiI~~s~~~l~~l~~~~~~  126 (145)
                       .-.+++|=..+.+.+.  -..|-.+++.- ...+-++.+++...+.+.....|
T Consensus        83 ~~d~VLIDTaGr~~~~~~~~~el~~~~~~~~~~~~~LVlsa~~~~~~~~~~~~f  136 (196)
T PF00448_consen   83 GFDLVLIDTAGRSPRDEELMEELRKLLRVIEPDEVLLVLSATTGQEDLEQARAF  136 (196)
T ss_dssp             TSSEEEEEE-S-GSTHHHHHHHHHHHHHHHTTSEEEEEEETTB-HTHHHHHHHH
T ss_pred             CCCEEEEECCCCCCCCHHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHH
T ss_conf             999999968887757699999999984116998799996365583789999998


No 37 
>PF00485 PRK:  Phosphoribulokinase / Uridine kinase family;  InterPro: IPR006083   Phosphoribulokinase (PRK) 2.7.1.19 from EC catalyses the ATP-dependent phosphorylation of ribulose-5-phosphate to ribulose-1,5-phosphate, a key step in the pentose phosphate pathway where carbon dioxide is assimilated by autotrophic organisms . In general, plant enzymes are light-activated by the thioredoxin/ferredoxin system, while those from photosynthetic bacteria are regulated by a system that has an absolute requirement for NADH. Thioredoxin/ferredoxin regulation is mediated by the reversible oxidation/reduction of sulphydryl and disulphide groups.    Uridine kinase (pyrimidine ribonucleoside kinase) is the rate-limiting enzyme in the pyrimidine salvage pathway. It catalyzes the following reaction:  ATP + Uridine = ADP + UMP   Pantothenate kinase (2.7.1.33 from EC) catalyzes the rate-limiting step in the biosynthesis of coenzyme A, the conversion of pantothenate to D-4'-phosphopantothenate in the presence of ATP. ; GO: 0005524 ATP binding, 0016301 kinase activity, 0008152 metabolic process; PDB: 2jeo_A 2uvq_A 1uj2_B 1uei_A 1xrj_A 1ufq_B 1udw_A 1uej_B 1a7j_A 1rz3_A ....
Probab=95.43  E-value=0.014  Score=31.50  Aligned_cols=24  Identities=29%  Similarity=0.438  Sum_probs=20.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCC
Q ss_conf             898758998888999999862124
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGRN   50 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~~   50 (145)
                      |-|.|.+|+||+++|+.|...-..
T Consensus         2 IgI~G~sgSGKTTla~~L~~~l~~   25 (194)
T PF00485_consen    2 IGISGPSGSGKTTLAKRLAQILKK   25 (194)
T ss_dssp             EEEB--TT---HHHHHHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHHHHCC
T ss_conf             899899988899999999998571


No 38 
>PF01935 DUF87:  Domain of unknown function DUF87;  InterPro: IPR002789   This prokaryotic protein family has no known function. It contains several conserved aspartates and histidines that could be metal ligands.
Probab=95.38  E-value=0.007  Score=33.17  Aligned_cols=40  Identities=8%  Similarity=0.086  Sum_probs=31.4

Q ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHCC-CCCCCCCEECCCC
Q ss_conf             799589875899888899999986212-4267852412578
Q T0567            23 TDIAVWLYGAPGTGRMTGARYLHQFGR-NAQGEFVYRELTP   62 (145)
Q Consensus        23 ~~~pvli~Ge~GtGK~~~A~~iH~~s~-~~~~~fv~~~~~~   62 (145)
                      ...|++|.|.+|+||+.+++.|-.... ....+++.+|...
T Consensus        22 ~~~H~~I~G~TGsGKS~~~k~ii~~l~~~~~~~vii~Dp~g   62 (229)
T PF01935_consen   22 FNRHIAIFGTTGSGKSNLVKSIIEELARKKGIPVIIFDPHG   62 (229)
T ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             44767998589998899999999999972899789993884


No 39 
>PF05049 IIGP:  Interferon-inducible GTPase (IIGP);  InterPro: IPR007743 Interferon-inducible GTPase (IIGP) is thought to play a role in in intracellular defense. IIGP is predominantly associated with the Golgi apparatus and also localizes to the endoplasmic reticulum and exerts a distinct role in IFN-induced intracellular membrane trafficking or processing .; PDB: 1tpz_A 1tq6_A 1tq2_A 1tqd_A 1tq4_A.
Probab=94.18  E-value=0.018  Score=31.01  Aligned_cols=40  Identities=15%  Similarity=0.356  Sum_probs=32.9

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHH
Q ss_conf             8999999999986147995898758998888999999862
Q T0567             8 EWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQF   47 (145)
Q Consensus         8 ~~m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~   47 (145)
                      ..+..+++.++.......++.++|++|+||+++-.++...
T Consensus        19 ~~~~~i~~~l~~~~~~~~~iav~G~sGsGKSSfINalRgl   58 (376)
T PF05049_consen   19 EVVSKIKEALKDIENAPLNIAVTGESGSGKSSFINALRGL   58 (376)
T ss_dssp             HHHHHHHHHHHHHHH--EEEEEE-------HHHHHHH---
T ss_pred             HHHHHHHHHHHHHHCCEEEEEEECCCCCCHHHHHHHHHCC
T ss_conf             8999999999973357258999658998656999997565


No 40 
>PF02367 UPF0079:  Uncharacterised P-loop hydrolase UPF0079;  InterPro: IPR003442   This group consists of bacterial proteins, which contain a P-loop. They are probably essential to bacteria as members are found in all genomes so far sequenced and no equivalent genes have been found in the archaea and eukaryotes, suggesting the protein may be involved in cell wall biosynthesis. The sequence of YjeE, from Haemophilus influenzae, has been determined to 1.7-A resolution. The protein has a nucleotide-binding fold with a four-stranded parallel beta-sheet flanked by antiparallel beta-strands on each side. The topology of the beta-sheet is unique among P-loop proteins and has features of different families of enzymes. ADP has been shown to bind to the P-loop in the presence of Mg2+ and ATPase activity has been confirmed by kinetic measurements . ; PDB: 1fl9_A 1htw_C.
Probab=94.15  E-value=0.012  Score=31.96  Aligned_cols=80  Identities=20%  Similarity=0.255  Sum_probs=44.1

Q ss_pred             HHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHH-CCC----------------CCCCCCEECCCCCC-HHHHH--H
Q ss_conf             9999999986147995898758998888999999862-124----------------26785241257889-88889--9
Q T0567            11 NQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQF-GRN----------------AQGEFVYRELTPDN-APQLN--D   70 (145)
Q Consensus        11 ~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~-s~~----------------~~~~fv~~~~~~~~-~~~~~--~   70 (145)
                      +++=+.+.+..+...-|++.|+-|+||++++|.+-.. +..                ...+++-+|+.... ..++.  +
T Consensus         2 ~~la~~la~~l~~g~vi~L~GdLGaGKTtfvr~l~~~lG~~~~V~SPTF~l~~~Y~~~~~~i~H~DlYRl~~~~e~~~~g   81 (123)
T PF02367_consen    2 KALAKRLAKRLKPGDVILLSGDLGAGKTTFVRGLARALGIKEEVTSPTFTLVNEYEGGGFPIYHFDLYRLEDPEELEDIG   81 (123)
T ss_dssp             HH---HHHHHHSS-EEEEEE-------HHHH---------------TTTTSEEEEE----EEEEEE-TT-SSTHHHCT--
T ss_pred             HHHHHHHHHHCCCCCEEEEECCCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHEECCCCCEEEEEECCCCCCHHHHHHCC
T ss_conf             89999999878999789998888789999999999985999988799766600102899518992010389878998777


Q ss_pred             HHHH-HCCCEEEECCHHHCCH
Q ss_conf             9986-2587487437420687
Q T0567            71 FIAL-AQGGTLVLSHPEHLTR   90 (145)
Q Consensus        71 ~l~~-a~gGtL~l~ei~~L~~   90 (145)
                      +.+. ..+|..+++=.+.+..
T Consensus        82 ~~e~~~~~~i~~IEW~e~~~~  102 (123)
T PF02367_consen   82 FEEYLDEDGICLIEWPERIEE  102 (123)
T ss_dssp             -HSCSSSSEEEEEESTT----
T ss_pred             CHHHHCCCCEEEEECCCCCHH
T ss_conf             545517998999989764310


No 41 
>PF03266 DUF265:  Protein of unknown function, DUF265;  InterPro: IPR004948  This family includes hypothetical ATP-binding proteins from prokaryotes.; GO: 0005524 ATP binding, 0016740 transferase activity; PDB: 2i3b_A 1ye8_A.
Probab=93.78  E-value=0.011  Score=32.07  Aligned_cols=88  Identities=15%  Similarity=0.244  Sum_probs=49.2

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHC---CCCCCCCC--------------EECCC--------CCC-H--H-------HHHH
Q ss_conf             58987589988889999998621---24267852--------------41257--------889-8--8-------8899
Q T0567            26 AVWLYGAPGTGRMTGARYLHQFG---RNAQGEFV--------------YRELT--------PDN-A--P-------QLND   70 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~~s---~~~~~~fv--------------~~~~~--------~~~-~--~-------~~~~   70 (145)
                      +++|+|++|+||+++.+-+-..-   ...-+-|+              .++..        ..+ .  +       ..+.
T Consensus         1 ~i~iTG~pGvGKTTli~kv~~~l~~~~~~v~Gf~t~evr~~g~R~GF~iv~l~~g~~~~la~~~~~~~~~vGky~v~~~~   80 (168)
T PF03266_consen    1 HIFITGPPGVGKTTLIKKVIEELKSSGLPVGGFYTPEVREEGRRIGFDIVDLGSGERGPLARVNFVSGPRVGKYVVDVES   80 (168)
T ss_dssp             EEEEE-------HHHHHHHHHHHHH----EE--EEE--B----B---EEE------EEE-EETT---SCE----EE-HHH
T ss_pred             CEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEEEECCEECCCCCEEEEEEEECCCCCCCCCCCCCCCCCCCCCEEEEHHH
T ss_conf             98986949988999999999996157972669991156079972059999943787432110356677765773973899


Q ss_pred             H-------HHH--HCCCEEEECCHHHC---CHHHHHHHHHHHHHCCHHHEEEECCCCC
Q ss_conf             9-------986--25874874374206---8778999999987214010011147768
Q T0567            71 F-------IAL--AQGGTLVLSHPEHL---TREQQYHLVQLQSQEHRPFRLIGIGDTS  116 (145)
Q Consensus        71 ~-------l~~--a~gGtL~l~ei~~L---~~~~Q~~L~~~l~~~~~~~RiI~~s~~~  116 (145)
                      +       +..  .....+++|||..|   ++..+..+.++++.   +..+|++-..+
T Consensus        81 fe~~~~~~L~~~~~~~~liiiDEIG~mEl~s~~F~~~v~~~l~~---~~~vl~tv~~~  135 (168)
T PF03266_consen   81 FERLALPALRRALSSADLIIIDEIGKMELKSPGFQEAVEELLDS---DKPVLATVHKK  135 (168)
T ss_dssp             HHCCCCCCCHHHHHHHHEEEE------CCC-CHHHHHHHHHHCT---TSEEEEE--SS
T ss_pred             HHHHHHHHHHHCCCCCCEEEEECCCHHHHHCHHHHHHHHHHHHC---CCCEEEEEECC
T ss_conf             99999998763267899999968617776288999999999808---99799999368


No 42 
>PF01745 IPT:  Isopentenyl transferase;  InterPro: IPR002648 Isopentenyl transferase / dimethylallyl transferase synthesizes isopentenyladensosine 5'-monophosphate, a cytokinin that induces shoot formation on host plants infected with the Ti plasmid .; GO: 0004161 dimethylallyltranstransferase activity, 0009058 biosynthetic process; PDB: 2ze8_C 2ze6_A 2ze7_A 2ze5_A.
Probab=93.24  E-value=0.014  Score=31.61  Aligned_cols=30  Identities=17%  Similarity=0.317  Sum_probs=23.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCCCCCCEEC
Q ss_conf             898758998888999999862124267852412
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRE   59 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~   59 (145)
                      ++|+|++|+||+.+|-.+   +.+...|.+..|
T Consensus         4 ~lI~GpT~~GKT~~a~~L---A~~tg~pVi~lD   33 (233)
T PF01745_consen    4 YLIFGPTGSGKTSLAIAL---AQQTGWPVISLD   33 (233)
T ss_dssp             EEEE--TT---HHHHHHH---HHH---EEEE--
T ss_pred             EEEECCCCCCHHHHHHHH---HHHHCCCEEEEE
T ss_conf             999789888814999999---999799669732


No 43 
>PF03029 ATP_bind_1:  Conserved hypothetical ATP binding protein;  InterPro: IPR004130 Members of this family are found in a range of archaea and eukaryotes and have hypothesised ATP binding activity.; GO: 0000166 nucleotide binding; PDB: 1yra_B 1yrb_A 2oxr_A 1yr6_A 1yr9_A 1yr7_A 1yr8_A.
Probab=92.60  E-value=0.0091  Score=32.55  Aligned_cols=34  Identities=21%  Similarity=0.366  Sum_probs=26.4

Q ss_pred             EECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCC
Q ss_conf             8758998888999999862124267852412578
Q T0567            29 LYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTP   62 (145)
Q Consensus        29 i~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~   62 (145)
                      +.|++|+||++..+.+++.-.....+...+|.-+
T Consensus         1 ViGpaGSGKTT~~~~~~~~~~~~~~~~~~vNLDP   34 (238)
T PF03029_consen    1 VIGPAGSGKTTYCSSLSEYLESNGRKVYIVNLDP   34 (238)
T ss_dssp             -E-------TTT------TGGGT-S-EEEEE---
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCC
T ss_conf             9899999889999999999874478717996786


No 44 
>PF00625 Guanylate_kin:  Guanylate kinase;  InterPro: IPR008144   Guanylate kinase () (GK)  catalyzes the ATP-dependent phosphorylation of GMP into GDP. It is essential for recycling GMP and indirectly, cGMP. In prokaryotes (such as Escherichia coli), lower eukaryotes (such as yeast) and in vertebrates, GK is a highly conserved monomeric protein of about 200 amino acids. GK has been shown , ,  to be structurally similar to protein A57R (or SalG2R) from various strains of Vaccinia virus.   Proteins containing one or more copies of the DHR domain, an SH3 domain as well as a C-terminal GK-like domain, are collectively termed MAGUKs (membrane-associated guanylate kinase homologs) , and include Drosophila lethal(1)discs large-1 tumor suppressor protein (gene dlg1); mammalian tight junction protein Zo-1; a family of mammalian synaptic proteins that seem to interact with the cytoplasmic tail of NMDA receptor subunits (SAP90/PSD-95, CHAPSYN-110/PSD-93, SAP97/DLG1 and SAP102); vertebrate 55 kD erythrocyte membrane protein (p55); Caenorhabditis elegans protein lin-2; rat protein CASK; and human proteins DLG2 and DLG3. There is an ATP-binding site (P-loop) in the N-terminal section of GK, which is not conserved in the GK-like domain of the above proteins. However these proteins retain the residues known, in GK, to be involved in the binding of GMP.; PDB: 2j41_B 1znz_A 1znx_A 1zny_A 1znw_A 1z8f_A 1s4q_A 1kgd_A 1kjw_A 1jxm_A ....
Probab=92.57  E-value=0.03  Score=29.81  Aligned_cols=26  Identities=23%  Similarity=0.195  Sum_probs=21.3

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHHHCC
Q ss_conf             99589875899888899999986212
Q T0567            24 DIAVWLYGAPGTGRMTGARYLHQFGR   49 (145)
Q Consensus        24 ~~pvli~Ge~GtGK~~~A~~iH~~s~   49 (145)
                      ..|+.|.|++|+||+++.+.+-..-+
T Consensus         2 ~r~ivl~Gpsg~GK~tl~~~L~~~~~   27 (183)
T PF00625_consen    2 GRPIVLVGPSGSGKDTLIKRLLEEFP   27 (183)
T ss_dssp             S-EEEEE--TT--HHHHHHHHHHHCT
T ss_pred             CCEEEEECCCCCCHHHHHHHHHHHCC
T ss_conf             97899999499998999999987685


No 45 
>PF00006 ATP-synt_ab:  ATP synthase alpha/beta family, nucleotide-binding domain This Pfam entry corresponds to chains a,b,c,d,e and f;  InterPro: IPR000194   ATPases (or ATP synthases) are membrane-bound enzyme complexes/ion transporters that combine ATP synthesis and/or hydrolysis with the transport of protons across a membrane. ATPases can harness the energy from a proton gradient, using the flux of ions across the membrane via the ATPase proton channel to drive the synthesis of ATP. Some ATPases work in reverse, using the energy from the hydrolysis of ATP to create a proton gradient. There are different types of ATPases, which can differ in function (ATP synthesis and/or hydrolysis), structure (F-, V- and A-ATPases contain rotary motors) and in the type of ions they transport , .  F-ATPases (F1F0-ATPases) in mitochondria, chloroplasts and bacterial plasma membranes are the prime producers of ATP, using the proton gradient generated by oxidative phosphorylation (mitochondria) or photosynthesis (chloroplasts). V-ATPases (V1V0-ATPases) are primarily found in eukaryotic vacuoles, catalysing ATP hydrolysis to transport solutes and lower pH in organelles. A-ATPases (A1A0-ATPases) are found in Archaea and function like F-ATPases. P-ATPases (E1E2-ATPases) are found in bacteria and in eukaryotic plasma membranes and organelles, and function to transport a variety of different ions across membranes. E-ATPases are cell-surface enzymes that hydrolyse a range of NTPs, including extracellular ATP.   This entry represents the alpha and beta subunits found in the F1, V1, and A1 complexes of F-, V- and A-ATPases, respectively (sometimes called the A and B subunits in V- and A-ATPases), as well as flagellar ATPase and the termination factor Rho. The F-ATPases (or F1F0-ATPases), V-ATPases (or V1V0-ATPases) and A-ATPases (or A1A0-ATPases) are composed of two linked complexes: the F1, V1 or A1 complex contains the catalytic core that synthesizes/hydrolyses ATP, and the F0, V0 or A0 complex that forms the membrane-spanning pore. The F-, V- and A-ATPases all contain rotary motors, one that drives proton translocation across the membrane and one that drives ATP synthesis/hydrolysis , .   In F-ATPases, there are three copies each of the alpha and beta subunits that form the catalytic core of the F1 complex, while the remaining F1 subunits (gamma, delta, epsilon) form part of the stalks. There is a substrate-binding site on each of the alpha and beta subunits, those on the beta subunits being catalytic, while those on the alpha subunits are regulatory. The alpha and beta subunits form a cylinder that is attached to the central stalk. The alpha/beta subunits undergo a sequence of conformational changes leading to the formation of ATP from ADP, which are induced by the rotation of the gamma subunit, itself is driven by the movement of protons through the F0 complex C subunit .   In V- and A-ATPases, the alpha/A and beta/B subunits of the V1 or A1 complex are homologous to the alpha and beta subunits in the F1 complex of F-ATPases, except that the alpha subunit is catalytic and the beta subunit is regulatory.   The alpha/A and beta/B subunits can each be divided into three regions, or domains, centred around the ATP-binding pocket, and based on structure and function. The central domain contains the nucleotide-binding residues that make direct contact with the ADP/ATP molecule .   More information about this protein can be found at Protein of the Month: ATP Synthases . ; GO: 0015078 hydrogen ion transmembrane transporter activity, 0016469 proton-transporting two-sector ATPase complex; PDB: 3eiu_B 2c61_B 2rkw_A 3dsr_A 3b2q_A 2r9v_A 1mab_A 2f43_A 1h8e_C 2ck3_B ....
Probab=92.45  E-value=0.11  Score=26.82  Aligned_cols=110  Identities=15%  Similarity=0.223  Sum_probs=59.2

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHHHHHCC-----CEEEECCHHHCCHHHHH----
Q ss_conf             995898758998888999999862124267852412578898888999986258-----74874374206877899----
Q T0567            24 DIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDNAPQLNDFIALAQG-----GTLVLSHPEHLTREQQY----   94 (145)
Q Consensus        24 ~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~~~~~~~l~~a~g-----GtL~l~ei~~L~~~~Q~----   94 (145)
                      ..-++|.|++|+||+.++..+-.... ++.. | +-+..+...+..++++...+     -|.++-.-..-|+..|.    
T Consensus        15 GQr~~I~g~~g~GKT~Ll~~i~~~~~-~~~~-V-~~~iGer~~Ev~~~~~~~~~~~~~~~tvvv~~t~d~~~~~r~~~~~   91 (215)
T PF00006_consen   15 GQRILIFGGSGTGKTTLLQDIARNQD-ADVI-V-YALIGERGREVTEFVEELEGEGAMKRTVVVAATSDEPPAERYRAPY   91 (215)
T ss_dssp             --BBEEEEETT-THHHHHHHHHHHTT-TCEE-E-EEEEEEBHHHHHHHHHHHHHTTGGGGEEEEEEETTS-HHHHHHTTT
T ss_pred             CCEEEEECCCCCCCHHHHHHHHHCCC-CCEE-E-EEEECCCCCHHHHHHHHHCCCCCCCCCCEEECCCCHHHHHHHHHHH
T ss_conf             88898865888880289999985536-6504-8-9983135012788986530334444420011123203778888899


Q ss_pred             ---HHHHHHHHCCHHHEEEECCCCCHHH-----------HHHCCCCCHHHHHHHCC
Q ss_conf             ---9999987214010011147768789-----------98708976565575544
Q T0567            95 ---HLVQLQSQEHRPFRLIGIGDTSLVE-----------LAASNHIIAELYYCFAM  136 (145)
Q Consensus        95 ---~L~~~l~~~~~~~RiI~~s~~~l~~-----------l~~~~~~~~~L~~~ls~  136 (145)
                         .+++++..+..++-++.-+-..+.+           ....+.+.+++|+.++.
T Consensus        92 ~a~~~AEyfr~~G~dVll~~Dsltr~a~A~reis~~~g~~p~~~gyp~~~~~~~~~  147 (215)
T PF00006_consen   92 TALAIAEYFRDQGKDVLLLLDSLTRFARAYREISLLLGEPPGREGYPPSLFSELAR  147 (215)
T ss_dssp             HHHHHHHHHHTTT-EEEEEEETHHHHHHHHHHHHHHTT--CC-TT-BTTHHHHHHH
T ss_pred             HHHHHHHHHHHHCCCCEEEHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHH
T ss_conf             88888899988057601000234899999998876157776554425532343015


No 46 
>PF01443 Viral_helicase1:  Viral (Superfamily 1) RNA helicase;  InterPro: IPR000606 This family includes RNA helicases thought to be involved in duplex unwinding during viral RNA replication. Members of this family are found in positive-strand single stranded RNA viruses from superfamily 1. This helicase has multiple roles at different stages of viral RNA replication, as dissected by mutational analysis .; GO: 0003723 RNA binding, 0003724 RNA helicase activity, 0003968 RNA-directed RNA polymerase activity, 0019079 viral genome replication; PDB: 3gpl_B 3gp8_A 3e1s_A 1w36_D.
Probab=92.33  E-value=0.022  Score=30.53  Aligned_cols=69  Identities=19%  Similarity=0.295  Sum_probs=37.3

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCCCC-CCEECCCCCCHH-----HHHHHHHHH---CCCEEEECCHHHCCHHHHHHH
Q ss_conf             8987589988889999998621242678-524125788988-----889999862---587487437420687789999
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGRNAQGE-FVYRELTPDNAP-----QLNDFIALA---QGGTLVLSHPEHLTREQQYHL   96 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~~~~~~-fv~~~~~~~~~~-----~~~~~l~~a---~gGtL~l~ei~~L~~~~Q~~L   96 (145)
                      ++|.|.|||||+++-+.+... -....| +...+.......     .+..++...   .+.++++||...++...-..|
T Consensus         1 i~i~G~~GsGKSt~i~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~tv~~~~~~~~~~~~~~~iiDE~~~~~~~~~~~l   78 (226)
T PF01443_consen    1 IVIHGVPGSGKSTLIRKLIDD-LTVVRPTIELANEWKPDKPSKSVRTVDSFLSASIDKKGDVLIIDEASMLPPGYLLLL   78 (226)
T ss_dssp             -EEE-------CCHHHHHHHH---------HHHH---EEHHHH----------SSSS-S-SEEEE--GGG---HHHHHH
T ss_pred             CEEECCCCCHHHHHHHHHHHH-HHHHHHHHHHHHCCCCCCCCCCCEEEEEHHCCCCCCCCCEEEEECCCCCCHHHHHHH
T ss_conf             989831897399999999998-501389999987076667995761753262187878889999935146599999999


No 47 
>PF03028 Dynein_heavy:  Dynein heavy chain;  InterPro: IPR004273   Dynein is a multisubunit microtubule-dependent motor enzyme that acts as the force generating protein of eukaryotic cilia and flagella. The cytoplasmic isoform of dynein acts as a motor for the intracellular retrograde motility of vesicles and organelles along microtubules.    Dynein is composed of a number of ATP-binding large subunits, intermediate size subunits and small subunits (see IPR001372 from INTERPRO). This family represents the C-terminal region of dynein heavy chain. The dynein heavy chain also exhibits ATPase activity and microtubule binding ability and acts as a motor for the movement of organelles and vesicles along microtubules. ; GO: 0003777 microtubule motor activity, 0007018 microtubule-based movement, 0030286 dynein complex
Probab=92.31  E-value=0.27  Score=24.64  Aligned_cols=97  Identities=16%  Similarity=0.133  Sum_probs=63.8

Q ss_pred             HHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHHHHH--CCCEEEECCHHHCCHHHHHHHH
Q ss_conf             61479958987589988889999998621242678524125788988889999862--5874874374206877899999
Q T0567            20 LSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDNAPQLNDFIALA--QGGTLVLSHPEHLTREQQYHLV   97 (145)
Q Consensus        20 ~a~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~~~~~~~l~~a--~gGtL~l~ei~~L~~~~Q~~L~   97 (145)
                      -+....|+++.-.+|+.-+.-...+...-......+..+.........-+..+..|  +|++++|+|++..+.-.. .|-
T Consensus       112 ~s~~~~Pil~i~s~g~Dp~~~i~~lA~~~~~~~~~l~~islG~gq~~~A~~~i~~a~~~G~WvlLqN~HL~~~wl~-~Le  190 (707)
T PF03028_consen  112 ESSPTTPILFILSPGSDPSSEIEQLAKKKGFMNKKLQSISLGQGQGPIAEKAIKEAAKEGHWVLLQNCHLAPSWLP-ELE  190 (707)
T ss_pred             HCCCCCCEEEEECCCCCHHHHHHHHHHHHCCCCCCEEEEECCCCCHHHHHHHHHHHHHCCCEEEEECHHCCHHHHH-HHH
T ss_conf             4489986799947989879999999998275525448997899639999999999975599999970103056799-999


Q ss_pred             HHHHH----CCHHHEEEECCCCCH
Q ss_conf             99872----140100111477687
Q T0567            98 QLQSQ----EHRPFRLIGIGDTSL  117 (145)
Q Consensus        98 ~~l~~----~~~~~RiI~~s~~~l  117 (145)
                      +.+++    .+.++|+..+|..+.
T Consensus       191 ~~l~~~~~~~h~~FRLflTs~~~~  214 (707)
T PF03028_consen  191 KILENLSPEIHPNFRLFLTSEPSP  214 (707)
T ss_pred             HHHHHHCCCCCCCEEEEEEECCCC
T ss_conf             999850246788627999705765


No 48 
>PF05127 DUF699:  Putative ATPase (DUF699);  InterPro: IPR007807 This domain is about 350 amino acid residues long and appears to have a P-loop motif, suggesting this is an ATPase. This domain is often N-terminal to a GCN5-related N-acetyltransferase domain IPR000182 from INTERPRO.; PDB: 1w36_D 2zpa_B.
Probab=92.22  E-value=0.018  Score=30.90  Aligned_cols=50  Identities=10%  Similarity=0.013  Sum_probs=28.6

Q ss_pred             CCEEEECCHHHCCHHHHHHHHHHHHHCCHHHEEEECCCCCHHHHHHCCC-CCHHHHHHH
Q ss_conf             8748743742068778999999987214010011147768789987089-765655755
Q T0567            77 GGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDTSLVELAASNH-IIAELYYCF  134 (145)
Q Consensus        77 gGtL~l~ei~~L~~~~Q~~L~~~l~~~~~~~RiI~~s~~~l~~l~~~~~-~~~~L~~~l  134 (145)
                      ...+++||...+|...-.+|   ++.   .-|+|++|+.+=-+  ..|+ |.-.|..+|
T Consensus        88 ~DlliVDEAA~I~lpll~~l---l~~---~~rvi~atTi~GYE--GtGrgf~lk~~~~l  138 (174)
T PF05127_consen   88 ADLLIVDEAAMIPLPLLRKL---LKA---FPRVIFATTIHGYE--GTGRGFSLKFLQRL  138 (174)
T ss_dssp             -SCEEECTGGGS-HHHHHHH---CCC---TSEEEEEEE---GG--G-----HHHHHCCS
T ss_pred             CCEEEEECCCCCCHHHHHHH---HHH---CCEEEEEEECCCCC--CCCCHHHHHHHHHH
T ss_conf             89999978236989999999---974---89899983068730--46625999999997


No 49 
>PF01580 FtsK_SpoIIIE:  FtsK/SpoIIIE family;  InterPro: IPR002543   The FtsK/SpoIIIE domain is found extensively in a wide variety of proteins from prokaryotes and plasmids  some of which contain up to three copies.The domain contains a putative ATP binding P-loop motif. A mutation in FtsK causes a temperature sensitive block in cell division and it is involved in peptidoglycan synthesis or modification . The SpoIIIE protein is implicated in intercellular chromosomal DNA transfer . ; GO: 0000166 nucleotide binding, 0003677 DNA binding, 0005524 ATP binding, 0007049 cell cycle, 0007059 chromosome segregation, 0051301 cell division, 0016021 integral to membrane; PDB: 2ius_F 2iuu_B 2iut_B.
Probab=91.89  E-value=0.028  Score=29.91  Aligned_cols=37  Identities=19%  Similarity=0.117  Sum_probs=24.0

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHCCC----CCCCCCEECCC
Q ss_conf             95898758998888999999862124----26785241257
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFGRN----AQGEFVYRELT   61 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s~~----~~~~fv~~~~~   61 (145)
                      .+++|.|.+||||+.+.+.|-..--.    ..-.++.+|..
T Consensus        39 ~h~Li~G~tgsGKT~~l~~l~~~l~~~~~~~~~~l~iiD~k   79 (205)
T PF01580_consen   39 PHLLIAGQTGSGKTTLLRSLLASLALTHSPEEVELYIIDPK   79 (205)
T ss_dssp             -SEEEE-----------HHHHHHHHTT--TTTEEEEEE-TT
T ss_pred             CCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCEEEEEECCC
T ss_conf             86899838999868999999999999827882799997588


No 50 
>PF04851 ResIII:  Type III restriction enzyme, res subunit;  InterPro: IPR006935   There are four classes of restriction endonucleases: types I, II,III and IV. All types of enzymes recognise specific short DNA sequences and carry out the endonucleolytic cleavage of DNA to give specific double-stranded fragments with terminal 5'-phosphates. They differ in their recognition sequence, subunit composition, cleavage position, and cofactor requirements , , as summarised below:    Type I enzymes (3.1.21.3 from EC) cleave at sites remote from recognition site; require both ATP and S-adenosyl-L-methionine to function; multifunctional protein with both restriction and methylase (2.1.1.72 from EC) activities. Type II enzymes (3.1.21.4 from EC) cleave within or at short specific distances from recognition site; most require magnesium; single function (restriction) enzymes independent of methylase. Type III enzymes (3.1.21.5 from EC) cleave at sites a short distance from recognition site; require ATP (but doesn't hydrolyse it); S-adenosyl-L-methionine stimulates reaction but is not required; exists as part of a complex with a modification methylase methylase (2.1.1.72 from EC). Type IV enzymes target methylated DNA.    Type I restriction endonucleases are components of prokaryotic DNA restriction-modification mechanisms that protects the organism against invading foreign DNA. Type I enzymes have three different subunits subunits - M (modification), S (specificity) and R (restriction) - that form multifunctional enzymes with restriction (3.1.21.3 from EC), methylase (2.1.1.72 from EC) and ATPase activities , . The S subunit is required for both restriction and modification and is responsible for recognition of the DNA sequence specific for the system. The M subunit is necessary for modification, and the R subunit is required for restriction. These enzymes use S-Adenosyl-L-methionine (AdoMet) as the methyl group donor in the methylation reaction, and have a requirement for ATP. They recognize asymmetric DNA sequences split into two domains of specific sequence, one 3-4 bp long and another 4-5 bp long, separated by a nonspecific spacer 6-8 bp in length. Cleavage occurs a considerable distance from the recognition sites, rarely less than 400 bp away and up to 7000 bp away. Adenosyl residues are methylated, one on each strand of the recognition sequence. These enzymes are widespread in eubacteria and archaea. In enteric bacteria they have been subdivide into four families: types IA, IB, IC and ID.    Type III restriction endonucleases (3.1.21.5 from EC) are components of prokaryotic DNA restriction-modification mechanisms that protect the organism against invading foreign DNA. Type III enzymes are hetero-oligomeric, multifunctional proteins composed of two subunits, Res and Mod. The Mod subunit recognises the DNA sequence specific for the system and is a modification methyltransferase; as such it is functionally equivalent to the M and S subunits of type I restriction endonuclease. Res is required for restriction, although it has no enzymatic activity on its own. Type III enzymes recognize short 5-6 bp long asymmetric DNA sequences and cleave 25-27 bp downstream to leave short, single-stranded 5' protrusions. They require the presence of two inversely oriented unmethylated recognition sites for restriction to occur. These enzymes methylate only one strand of the DNA, at the N-6 position of adenosyl residues, so newly replicated DNA will have only one strand methylated, which is sufficient to protect against restriction. Type III enzymes belong to the beta-subfamily of N6 adenine methyltransferases, containing the nine motifs that characterise this family, including motif I, the AdoMet binding pocket (FXGXG), and motif IV, the catalytic region (S/D/N (PP) Y/F) , .   This entry represents the R subunit (HsdR) of type I restriction endonucleases (3.1.21.3 from EC), the Res subunit of type III endonucleases (3.1.21.5 from EC), and the B subunit of excinuclease ABC (uvrB) , , .; GO: 0003677 DNA binding, 0005524 ATP binding, 0016787 hydrolase activity; PDB: 3b6e_A 2fz4_A 2fwr_C 2gk6_A 2gk7_A 2gjk_A 1c4o_A 1d2m_A 2d7d_A 2nmv_A ....
Probab=91.83  E-value=0.095  Score=27.09  Aligned_cols=39  Identities=18%  Similarity=0.227  Sum_probs=24.3

Q ss_pred             HHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHH-HHHHC
Q ss_conf             99999999998614799589875899888899999-98621
Q T0567             9 WINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARY-LHQFG   48 (145)
Q Consensus         9 ~m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~-iH~~s   48 (145)
                      +++++...++.. .....++|.|++||||+.++-. ++...
T Consensus        11 ai~~~~~~~~~~-~~~~~~li~~~tGtGKT~~~~~~~~~l~   50 (184)
T PF04851_consen   11 AIENILKALKKK-DQKRRGLIQGPTGTGKTFTAAALIKELF   50 (184)
T ss_dssp             HHHHHHHHHHHH-STTTEEEEEE------HHHHHHHHHHHH
T ss_pred             HHHHHHHHHCCC-CCCCCEEEEECCCCCHHHHHHHHHHCCC
T ss_conf             999999873522-4578879993899988199888875012


No 51 
>PF00580 UvrD-helicase:  UvrD/REP helicase;  InterPro: IPR000212   Members of this family are helicases that catalyse ATP dependent unwinding of double stranded DNA to single stranded DNA. THe family includes both Rep and UvrD helcases. The Rep family helicases are composed of four structural domains . The Rep proteins function as dimers.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006281 DNA repair; PDB: 1qhg_A 2pjr_F 1qhh_C 3pjr_A 1pjr_A 2is2_B 2is4_A 2is1_B 2is6_A 1w36_B ....
Probab=91.66  E-value=0.046  Score=28.76  Aligned_cols=33  Identities=12%  Similarity=0.253  Sum_probs=22.6

Q ss_pred             HHHHHHHCCCCCEEEECCCCCCHHHH--HHHHHHH
Q ss_conf             99998614799589875899888899--9999862
Q T0567            15 RRLQQLSETDIAVWLYGAPGTGRMTG--ARYLHQF   47 (145)
Q Consensus        15 ~~i~~~a~~~~pvli~Ge~GtGK~~~--A~~iH~~   47 (145)
                      +|-+.+...+.|++|.|.+|||||++  .|+++..
T Consensus         4 ~Q~~ai~~~~~~~lV~A~AGSGKT~~L~~ri~~ll   38 (533)
T PF00580_consen    4 EQRKAINSPNGPLLVIAGAGSGKTTTLTHRIAYLL   38 (533)
T ss_dssp             HHHHHHHS-SSEEEEE-------HHHHHHHHHHHH
T ss_pred             HHHHHHHCCCCCEEEEECCCCCHHHHHHHHHHHHH
T ss_conf             89999858899889980898546999999999872


No 52 
>PF08423 Rad51:  Rad51;  InterPro: IPR013632   This domain is found at the C terminus of the DNA repair and recombination protein Rad51. It is critical for DNA binding . ; PDB: 1b22_A 1n0w_A 1szp_E 2zjb_B 1v5w_B 2i1q_A 2f1i_A 2f1j_A 1xu4_A 2fpk_A ....
Probab=91.42  E-value=0.1  Score=26.90  Aligned_cols=49  Identities=16%  Similarity=0.193  Sum_probs=29.7

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHCCC------CCCCCCEECCCC-CCHHHHHHHHH
Q ss_conf             95898758998888999999862124------267852412578-89888899998
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFGRN------AQGEFVYRELTP-DNAPQLNDFIA   73 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s~~------~~~~fv~~~~~~-~~~~~~~~~l~   73 (145)
                      .=.=|+||+||||+.++-.+-.....      ..+..+++|+.. .+..-+.++.+
T Consensus        44 ~ItEi~G~~gsGKTqlcl~L~v~~~l~~~~gg~~~~vvyIDTeg~f~~~Rl~qi~~   99 (261)
T PF08423_consen   44 SITEIFGESGSGKTQLCLQLAVNVQLPKEKGGLGGKVVYIDTEGTFSPERLRQIAE   99 (261)
T ss_dssp             CEEEEE--TT---HHHHHHHHHHTTSGTTT--SSEEEEEEESSS---HHHHHHHHH
T ss_pred             EEEEEEECCCCCHHHHHHHHHHHCCCCHHCCCCCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             49999937889799999999988146231068887579994699869999999998


No 53 
>PF07088 GvpD:  GvpD gas vesicle protein;  InterPro: IPR009788   This family consists of several archaeal GvpD gas vesicle proteins. GvpD is thought to be involved in the regulation of gas vesicle formation ,.; GO: 0005524 ATP binding
Probab=91.05  E-value=0.014  Score=31.54  Aligned_cols=20  Identities=30%  Similarity=0.439  Sum_probs=16.4

Q ss_pred             CCCEEEECCCCCCHHHHHHH
Q ss_conf             99589875899888899999
Q T0567            24 DIAVWLYGAPGTGRMTGARY   43 (145)
Q Consensus        24 ~~pvli~Ge~GtGK~~~A~~   43 (145)
                      ...++|.|+|||||++++=-
T Consensus        10 GktLLIkG~PGTGKTtFtL~   29 (484)
T PF07088_consen   10 GKTLLIKGEPGTGKTTFTLR   29 (484)
T ss_pred             CCEEEEECCCCCCCEEEEEE
T ss_conf             80899945899871589747


No 54 
>PF00406 ADK:  Adenylate kinase;  InterPro: IPR000850 Adenylate kinases (ADK) are phosphotransferases that catalyse the reversible reaction  AMP + MgATP = ADP + MgADP  an essential reaction for many processes in living cells. Two ADK isozymes have been identified in mammalian cells. These specifically bind AMP and favour binding to ATP over other nucleotide triphosphates (AK1 is cytosolic and AK2 is located in the mitochondria). A third ADK has been identified in bovine heart and human cells , this is a mitochondrial GTP:AMP phosphotransferase, also specific for the phosphorylation of AMP, but can only use GTP or ITP as a substrate . ADK has also been identified in different bacterial species and in yeast . Two further enzymes are known to be related to the ADK family, i.e. yeast uridine monophosphokinase and slime mold UMP-CMP kinase. Within the ADK family there are several conserved regions, including the ATP-binding domains. One of the most conserved areas includes an Arg residue, whose modification inactivates the enzyme, together with an Asp that resides in the catalytic cleft of the enzyme and participates in a salt bridge.; GO: 0005524 ATP binding, 0019205 nucleobase, nucleoside, nucleotide kinase activity, 0006139 nucleobase, nucleoside, nucleotide and nucleic acid metabolic process; PDB: 2bbw_A 2ar7_B 2ak3_B 1zd8_A 3h0k_B 1ukz_A 1uky_A 2ukd_A 1uke_A 5ukd_A ....
Probab=90.79  E-value=0.043  Score=28.96  Aligned_cols=17  Identities=41%  Similarity=0.862  Sum_probs=15.3

Q ss_pred             EECCCCCCHHHHHHHHH
Q ss_conf             87589988889999998
Q T0567            29 LYGAPGTGRMTGARYLH   45 (145)
Q Consensus        29 i~Ge~GtGK~~~A~~iH   45 (145)
                      |.|+||+||+++|+.|-
T Consensus         1 i~G~PGsGK~t~a~~l~   17 (151)
T PF00406_consen    1 IFGPPGSGKGTQAKKLA   17 (151)
T ss_dssp             EE--TT---HHHHHHHH
T ss_pred             CCCCCCCCHHHHHHHHH
T ss_conf             93899998799999999


No 55 
>PF10443 RNA12:  RNA12 protein
Probab=90.71  E-value=0.074  Score=27.67  Aligned_cols=44  Identities=14%  Similarity=0.185  Sum_probs=27.5

Q ss_pred             HHHHHHHHC--CCCCEEEECCCCCCHHHHH--HHHHHHCCCCCCCCCEECCCC
Q ss_conf             999998614--7995898758998888999--999862124267852412578
Q T0567            14 RRRLQQLSE--TDIAVWLYGAPGTGRMTGA--RYLHQFGRNAQGEFVYRELTP   62 (145)
Q Consensus        14 ~~~i~~~a~--~~~pvli~Ge~GtGK~~~A--~~iH~~s~~~~~~fv~~~~~~   62 (145)
                      .++++..-.  .+.-+++.||.||||+.+.  +.++.   +.  ....+||..
T Consensus         5 i~~Lq~wL~E~~nTFIvV~GPrGSGK~eLV~d~vL~~---r~--~~L~IDC~~   52 (431)
T PF10443_consen    5 IEQLQSWLMENPNTFIVVQGPRGSGKRELVLDHVLKD---RK--NVLVIDCKQ   52 (431)
T ss_pred             HHHHHHHHHCCCCEEEEEECCCCCCCCHHHHHHHHHC---CC--CEEEEECHH
T ss_conf             9999999826898499997999988553568888605---79--879997757


No 56 
>PF10662 PduV-EutP:  Ethanolamine utilisation - propanediol utilisation
Probab=90.65  E-value=0.069  Score=27.82  Aligned_cols=24  Identities=25%  Similarity=0.322  Sum_probs=20.4

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHCC
Q ss_conf             589875899888899999986212
Q T0567            26 AVWLYGAPGTGRMTGARYLHQFGR   49 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~~s~   49 (145)
                      -+++.|+.|+||++++++|.....
T Consensus         3 rim~iG~~g~GKTTL~q~L~g~~~   26 (143)
T PF10662_consen    3 RIMLIGPSGAGKTTLTQALNGEEI   26 (143)
T ss_pred             EEEEECCCCCCHHHHHHHHCCCCC
T ss_conf             499978998889999999748877


No 57 
>PF08303 tRNA_lig_kinase:  tRNA ligase kinase domain;  InterPro: IPR015966   This entry represents a kinase domain found in fungal tRNA ligases . Please see the following relevant references: , .; GO: 0003972 RNA ligase (ATP) activity, 0005524 ATP binding, 0006388 tRNA splicing
Probab=90.49  E-value=0.43  Score=23.58  Aligned_cols=82  Identities=20%  Similarity=0.263  Sum_probs=46.1

Q ss_pred             ECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCC-CHHHH----HHHHHHHCCCEEEECCHHHCCHHHHHHHHHHHHHCC
Q ss_conf             7589988889999998621242678524125788-98888----999986258748743742068778999999987214
Q T0567            30 YGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPD-NAPQL----NDFIALAQGGTLVLSHPEHLTREQQYHLVQLQSQEH  104 (145)
Q Consensus        30 ~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~-~~~~~----~~~l~~a~gGtL~l~ei~~L~~~~Q~~L~~~l~~~~  104 (145)
                      .+-.||||+++|.++...=+.+ +..-.-|...- ....+    ...++.+....+|+|-=.....+-++ |.+.++...
T Consensus         5 IAtiGCGKTTv~~aL~~LFgeW-gHvQnDni~~k~~~~~f~~~~l~~L~~~~~~vViaDRNNh~~reR~q-l~~~~~~~~   82 (169)
T PF08303_consen    5 IATIGCGKTTVALALSKLFGEW-GHVQNDNITGKNDKPKFIKAVLELLAKAGHPVVIADRNNHQKRERKQ-LFDDVSQLK   82 (169)
T ss_pred             ECCCCCCHHHHHHHHHHHCCCC-CCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHHHHHH-HHHHHHHHC
T ss_conf             2478766899999999976876-64235555677746799999999998579977998177732999999-999999735


Q ss_pred             H-------HHEEEECC
Q ss_conf             0-------10011147
Q T0567           105 R-------PFRLIGIG  113 (145)
Q Consensus       105 ~-------~~RiI~~s  113 (145)
                      .       ++|+|+..
T Consensus        83 ~~y~~~~~~~k~VaL~   98 (169)
T PF08303_consen   83 PDYLPYNFNVKFVALN   98 (169)
T ss_pred             CCCCCCCCCEEEEEEE
T ss_conf             5445666671799999


No 58 
>PF01057 Parvo_NS1:  Parvovirus non-structural protein NS1;  InterPro: IPR001257   Parvoviruses encode two noncapsid/non-structural proteins, NS1 and NS2. NS1 is essential for viral DNA replication . These proteins include the ATP/GTP-binding site motif A (P-loop) IPR001687 from INTERPRO.; GO: 0019079 viral genome replication; PDB: 1s9h_A 1u0j_A.
Probab=90.48  E-value=0.07  Score=27.79  Aligned_cols=26  Identities=27%  Similarity=0.497  Sum_probs=21.9

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHCCC
Q ss_conf             95898758998888999999862124
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFGRN   50 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s~~   50 (145)
                      .-++++|+++|||+.+|.+|-...+.
T Consensus       114 Nti~~~Gp~~tGK~~ia~aI~~~~~~  139 (271)
T PF01057_consen  114 NTIWFYGPASTGKTFIAQAIANAVPN  139 (271)
T ss_dssp             -EEEEE--TT---HHHHHHHHHHSS-
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHCCC
T ss_conf             46999869887689999999966785


No 59 
>PF03308 ArgK:  ArgK protein;  InterPro: IPR005129   Bacterial periplasmic transport systems require the function of a specific substrate-binding protein, located in the periplasm, and several cytoplasmic membrane transport components. In Escherichia coli K-12, the arginine-ornithine transport system requires an arginine-ornithine-binding protein and the lysine-arginine-ornithine (LAO) transport system includes a LAO-binding protein. Both periplasmic proteins can be phosphorylated by a single kinase, ArgK  resulting in reduced levels of transport activity of the periplasmic transport systems that include each of the binding proteins. The ArgK protein acts as an ATPase enzyme and as a kinase.; PDB: 2p67_A 2qm7_B 2qm8_B.
Probab=90.11  E-value=0.057  Score=28.30  Aligned_cols=39  Identities=21%  Similarity=0.248  Sum_probs=25.0

Q ss_pred             HHHHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHH
Q ss_conf             899999999998614799589875899888899999986
Q T0567             8 EWINQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQ   46 (145)
Q Consensus         8 ~~m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~   46 (145)
                      +..+++.+.+...+....-|-|+|+||.||+++...+-.
T Consensus        13 ~~~~~lL~~l~~~~g~a~viGITG~pGaGKSTl~~~L~~   51 (266)
T PF03308_consen   13 PEARELLKRLLPRTGRAHVIGITGPPGAGKSTLIDALAR   51 (266)
T ss_dssp             HHHHHHHHHHGGG----EEE--B-------HHHHHH---
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEECCCCCCHHHHHHHHHH
T ss_conf             799999999987469854999878999977999999999


No 60 
>PF10412 TrwB_AAD_bind:  Type IV secretion-system coupling protein DNA-binding domain; PDB: 1gki_F 1gl7_E 1e9r_A 1e9s_M 1gl6_B.
Probab=88.57  E-value=0.1  Score=26.96  Aligned_cols=38  Identities=16%  Similarity=0.194  Sum_probs=23.1

Q ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECC
Q ss_conf             79958987589988889999998621242678524125
Q T0567            23 TDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYREL   60 (145)
Q Consensus        23 ~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~   60 (145)
                      ...+++|.|.+||||+.+-..+-..-.......|.+|.
T Consensus        14 ~~~~~~i~G~~GsGKt~~~~~~~~~~~~~~~~~ii~D~   51 (386)
T PF10412_consen   14 ENRHILIIGTTGSGKTTLINQLLRQIRARGDRAIIYDP   51 (386)
T ss_dssp             GGG-EEEE-------HHHHHHHHH-------EEEEEEE
T ss_pred             HHCCEEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEC
T ss_conf             01828998389998899999999999976995999989


No 61 
>PF02534 TraG:  TraG/TraD family;  InterPro: IPR003688 The TRAG family are bacterial conjugation proteins. These proteins aid the transfer of DNA from the plasmid into the host bacterial chromosome although the exact mechanism of action is unknown.; GO: 0009291 unidirectional conjugation, 0016020 membrane
Probab=88.51  E-value=0.3  Score=24.41  Aligned_cols=48  Identities=15%  Similarity=0.238  Sum_probs=28.4

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHHHH
Q ss_conf             95898758998888999999862124267852412578898888999986
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDNAPQLNDFIAL   74 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~~~~~~~l~~   74 (145)
                      .++++.|++|+||+.-- .|=.. -...+.+|..|--.+.........+.
T Consensus        45 ~h~lvig~tgsGKt~~~-viP~l-l~~~~s~vv~DpKgEl~~~t~~~r~~   92 (469)
T PF02534_consen   45 SHVLVIGPTGSGKTRGF-VIPNL-LQYPGSVVVTDPKGELYEKTAGYREK   92 (469)
T ss_pred             EEEEEEECCCCCCCHHH-HHHHH-HHCCCCEEEECCCCCHHHHHHHHHHH
T ss_conf             57899947999850365-68799-85899899984774078999999986


No 62 
>PF02463 SMC_N:  RecF/RecN/SMC N terminal domain;  InterPro: IPR003395   The SMC (structural maintenance of chromosomes) family of proteins exists in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression .   This domain is found at the N terminus of SMC proteins.; GO: 0005524 ATP binding, 0006259 DNA metabolic process, 0005694 chromosome; PDB: 1f2u_C 1f2t_A 1us8_A 1ii8_A 1e69_F 1gxk_C 1gxl_C 1gxj_A 1xew_Y 1xex_A ....
Probab=88.08  E-value=0.13  Score=26.27  Aligned_cols=40  Identities=25%  Similarity=0.378  Sum_probs=33.7

Q ss_pred             CCEEEECCHH-HCCHHHHHHHHHHHHHCCHHHEEEECCCCC
Q ss_conf             8748743742-068778999999987214010011147768
Q T0567            77 GGTLVLSHPE-HLTREQQYHLVQLQSQEHRPFRLIGIGDTS  116 (145)
Q Consensus        77 gGtL~l~ei~-~L~~~~Q~~L~~~l~~~~~~~RiI~~s~~~  116 (145)
                      .+.++|||++ .|++..|.++++++.+...+.++|.+|+.+
T Consensus       159 ~pi~llDE~d~~Ld~~~~~~l~~~L~~~~~~~Q~IvtTH~~  199 (220)
T PF02463_consen  159 SPILLLDEPDAHLDPENQRKLAKLLKELSKNAQFIVTTHSP  199 (220)
T ss_dssp             -SEEEEESTTTTS-HHHHHHHHHHHHHHTTTSEEEEE-S-H
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             22222222222222222222222222222222222222222


No 63 
>PF03668 ATP_bind_2:  P-loop ATPase protein family;  InterPro: IPR005337   This is a family of putative P-loop ATPases . Many of the proteins in this family are hypothetical and kinase activity has been proposed for some family members. This family contains an ATP-binding site and could be an ATPase.
Probab=87.93  E-value=0.67  Score=22.54  Aligned_cols=21  Identities=33%  Similarity=0.540  Sum_probs=18.2

Q ss_pred             EEEECCCCCCHHHHHHHHHHH
Q ss_conf             898758998888999999862
Q T0567            27 VWLYGAPGTGRMTGARYLHQF   47 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~   47 (145)
                      |+|+|=.|+||++..+++-..
T Consensus         4 vIVTGlSGaGKS~Al~~lED~   24 (284)
T PF03668_consen    4 VIVTGLSGAGKSTALRALEDL   24 (284)
T ss_pred             EEEECCCCCCHHHHHHHHHCC
T ss_conf             999478878789999999707


No 64 
>PF00735 Septin:  Septin;  InterPro: IPR000038   Septins constitute a eukaryotic family of guanine nucleotide-binding proteins, most of which polymerise to form filaments . Members of the family were first identified by genetic screening for Saccharomyces cerevisiae mutants defective in cytokinesis . Temperature-sensitive mutations in four genes, CDC3, CDC10, CDC11 and CDC12, were found to cause cell-cycle arrest and defects in bud growth and cytokinesis. The protein products of these genes localise at the division plane between mother and daughter cells, indicating a role in mother-daughter separation during cytokinesis . Members of the family were therefore termed septins to reflect their role in septation and cell division. The identification of septin homologues in higher eukaryotes, which localise to the cleavage furrow in dividing cells, supports an orthologous function in cytokinesis. Septins have since been identified in most eukaryotes, except plants .   Septins are approximately 40-50 kDa in molecular mass, and typically comprise a conserved central core domain (more than 35% sequence identity between mammalian and yeast homologues) flanked by more divergent N- and C-termini. Most septins possess a P-loop motif in their N-terminal domain (which is characteristic of GTP-binding proteins), and a predicted C-terminal coiled-coil domain .   A number of septin interaction partners have been identified in yeast, many of which are components of the budding site selection machinery, kinase cascades or of the ubiquitination pathway. It has been proposed that septins may act as a scaffold that provides an interaction matrix for other proteins , . In mammals, septins have been shown to regulate vesicle dynamics . Mammalian septins have also been implicated in a variety of other cellular processes, including apoptosis, carcinogenesis and neurodegeneration .   This entry represents a variety of septins and homologous sequences involved in the cell division process.; GO: 0005525 GTP binding, 0007049 cell cycle; PDB: 2qag_B 2qnr_A 2qa5_A.
Probab=87.76  E-value=0.11  Score=26.81  Aligned_cols=22  Identities=23%  Similarity=0.375  Sum_probs=19.0

Q ss_pred             CCCEEEECCCCCCHHHHHHHHH
Q ss_conf             9958987589988889999998
Q T0567            24 DIAVWLYGAPGTGRMTGARYLH   45 (145)
Q Consensus        24 ~~pvli~Ge~GtGK~~~A~~iH   45 (145)
                      +..+|+.|+.|+||+++-..+-
T Consensus         4 ~fnImVvG~sG~GKSTFINsLf   25 (281)
T PF00735_consen    4 NFNIMVVGESGLGKSTFINSLF   25 (281)
T ss_dssp             EEEEEEE-------HHHHHHHH
T ss_pred             EEEEEEECCCCCCHHHHHHHHH
T ss_conf             6999998699997999999986


No 65 
>PF07475 Hpr_kinase_C:  HPr Serine kinase C-terminal domain;  InterPro: IPR011104   This family represents the C-terminal kinase domain of Hpr Serine/threonine kinase PtsK. This kinase is the sensor in a multicomponent phosphorelay system in control of carbon catabolic repression in bacteria . This kinase in unusual in that it recognises the tertiary structure of its target and is a member of a novel family unrelated to any previously described protein phosphorylating enzymes . X-ray analysis of the full-length crystalline enzyme from Staphylococcus xylosus at a resolution of 1.95 A shows the enzyme to consist of two clearly separated domains that are assembled in a hexameric structure resembling a three-bladed propeller .; GO: 0000155 two-component sensor activity, 0004672 protein kinase activity, 0005524 ATP binding, 0000160 two-component signal transduction system (phosphorelay), 0006109 regulation of carbohydrate metabolic process; PDB: 1knx_F 1ko7_A 2qmh_B 1kkm_C 1kkl_A 1jb1_A.
Probab=86.97  E-value=0.13  Score=26.34  Aligned_cols=25  Identities=28%  Similarity=0.396  Sum_probs=20.4

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHHHC
Q ss_conf             9958987589988889999998621
Q T0567            24 DIAVWLYGAPGTGRMTGARYLHQFG   48 (145)
Q Consensus        24 ~~pvli~Ge~GtGK~~~A~~iH~~s   48 (145)
                      ..-|+|+|+.|.||+.+|-.+...+
T Consensus        18 G~GVLi~G~SG~GKS~lal~Li~rG   42 (171)
T PF07475_consen   18 GVGVLITGPSGAGKSELALELIERG   42 (171)
T ss_dssp             ----EEE-------HHHHHHHHHTT
T ss_pred             CEEEEEECCCCCCHHHHHHHHHHCC
T ss_conf             9999998689999899999999879


No 66 
>PF06068 TIP49:  TIP49 C-terminus;  InterPro: IPR010339   This family consists of the C-terminal region of several eukaryotic and archaeal RuvB-like 1 (Pontin or TIP49a) and RuvB-like 2 (Reptin or TIP49b) proteins. The N-terminal domain contains the AAA ATPase, central region IPR003959 from INTERPRO domain. In zebrafish, the liebeskummer (lik) mutation, causes development of hyperplastic embryonic hearts. lik encodes Reptin, a component of a DNA-stimulated ATPase complex. Beta-catenin and Pontin, a DNA-stimulated ATPase that is often part of complexes with Reptin, are in the same genetic pathways. The Reptin/Pontin ratio serves to regulate heart growth during development, at least in part via the beta-catenin pathway . TBP-interacting protein 49 (TIP49) was originally identified as a TBP-binding protein, and two related proteins are encoded by individual genes, tip49a and b. Although the function of this gene family has not been elucidated, they are supposed to play a critical role in nuclear events because they interact with various kinds of nuclear factors and have DNA helicase activities. TIP49a has been suggested to act as an autoantigen in some patients with autoimmune diseases .; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0005634 nucleus; PDB: 2cqa_A 2c9o_C.
Probab=86.93  E-value=0.21  Score=25.23  Aligned_cols=59  Identities=20%  Similarity=0.169  Sum_probs=40.1

Q ss_pred             CCCCCHHHHH---HHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCC
Q ss_conf             6658989999---99999986147995898758998888999999862124267852412578
Q T0567             3 LIGRSEWINQ---YRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTP   62 (145)
Q Consensus         3 liG~S~~m~~---l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~   62 (145)
                      |||+-.+-+.   +.+.++.---...-+|+.|+|||||+-+|-+|...-. .+-||+.++.+.
T Consensus        26 lVGQ~~AReAagiiv~lIk~~k~aGraiLlaGppGtGKTAlA~aiakeLG-~~~PF~~i~gSE   87 (398)
T PF06068_consen   26 LVGQKEAREAAGIIVDLIKEGKMAGRAILLAGPPGTGKTALAMAIAKELG-EDVPFCPISGSE   87 (398)
T ss_dssp             ----HHHHHH---HHHHHHTT-----EEEEE-------HHHHHHHHHH-----S--EEE---T
T ss_pred             CCCHHHHHHHHHHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHC-CCCCEEECCHHH
T ss_conf             53539999998999999971775773899978999888999999999737-799846612544


No 67 
>PF00025 Arf:  ADP-ribosylation factor family The prints entry specific to Sar1 proteins The Prosite entry specific to Sar1 proteins;  InterPro: IPR006689   The small ADP ribosylation factor (Arf) GTP-binding proteins are major regulators of vesicle biogenesis in intracellular traffic . They are the founding members of a growing family that includes Arl (Arf-like), Arp (Arf-related proteins) and the remotely related Sar (Secretion-associated and Ras-related) proteins. Arf proteins cycle between inactive GDP-bound and active GTP-bound forms that bind selectively to effectors. The classical structural GDP/GTP switch is characterised by conformational changes at the so-called switch 1 and switch 2 regions, which bind tightly to the gamma-phosphate of GTP but poorly or not at all to the GDP nucleotide. Structural studies of Arf1 and Arf6 have revealed that although these proteins feature the switch 1 and 2 conformational changes, they depart from other small GTP-binding proteins in that they use an additional, unique switch to propagate structural information from one side of the protein to the other.     The GDP/GTP structural cycles of human Arf1 and Arf6 feature a unique conformational change that affects the beta2beta3 strands connecting switch 1 and switch 2 (interswitch) and also the amphipathic helical N-terminus. In GDP-bound Arf1 and Arf6, the interswitch is retracted and forms a pocket to which the N-terminal helix binds, the latter serving as a molecular hasp to maintain the inactive conformation. In the GTP-bound form of these proteins, the interswitch undergoes a two-residue register shift that pulls switch 1 and switch 2 up, restoring an active conformation that can bind GTP. In this conformation, the interswitch projects out of the protein and extrudes the N-terminal hasp by occluding its binding pocket.; GO: 0005525 GTP binding; PDB: 1z6x_A 2b6h_A 1e0s_A 2bao_A 2j5x_A 2a5d_A 2a5g_A 2bau_A 2a5f_A 2h57_C ....
Probab=86.73  E-value=0.5  Score=23.20  Aligned_cols=96  Identities=19%  Similarity=0.198  Sum_probs=49.9

Q ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEE---------------CCCCC--CHHHHHHHHHHHCCCEEEECC
Q ss_conf             4799589875899888899999986212426785241---------------25788--988889999862587487437
Q T0567            22 ETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYR---------------ELTPD--NAPQLNDFIALAQGGTLVLSH   84 (145)
Q Consensus        22 ~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~---------------~~~~~--~~~~~~~~l~~a~gGtL~l~e   84 (145)
                      .....|++.|..|+||+++-+.+.........|-+-.               |....  -.+.|...+..+.+=..++|-
T Consensus        11 ~~~~~ililGl~~sGKTtll~~l~~~~~~~~~pT~g~~~~~i~~~~~~~~~~D~gG~~~~r~~W~~y~~~~~~iIfVVDs   90 (174)
T PF00025_consen   11 KKEFKILILGLDGSGKTTLLYRLKTGEFSETIPTVGFNIETIKYKDYKLNFWDLGGQESFRPLWRHYYQNVDGIIFVVDS   90 (174)
T ss_dssp             TSEEEEEEE--TT---HHHHHHHHTTCEEEEESSSSSEEEEEEETTEEEEEEE----GGGGGGGGGHHTTBCEEEEEEET
T ss_pred             CCEEEEEEECCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCHHHHHHHHCCCCEEEEEEEC
T ss_conf             76589999988988705799987235653223544555314777679999984387544024799884135447999835


Q ss_pred             HH--HCCHHHHHHHHHHHHHCC-HHH-EEEECCCCCHH
Q ss_conf             42--068778999999987214-010-01114776878
Q T0567            85 PE--HLTREQQYHLVQLQSQEH-RPF-RLIGIGDTSLV  118 (145)
Q Consensus        85 i~--~L~~~~Q~~L~~~l~~~~-~~~-RiI~~s~~~l~  118 (145)
                      -|  +++ +....|.+++.... .++ -+|.....|+.
T Consensus        91 sd~~rl~-ea~~~L~~ll~~~~~~~~PvLIl~NK~D~~  127 (174)
T PF00025_consen   91 SDSERLD-EAKEELHELLNDEALKNIPVLILANKQDLP  127 (174)
T ss_dssp             T-GGGHH-HHHHHHHHHHTSGGGTTSEEEEEEESTTST
T ss_pred             CCCCCCH-HHHHHHHHHHCCHHHCCCEEEEEECCCCCC
T ss_conf             3000214-779999998511531785499993566676


No 68 
>PF08477 Miro:  Miro-like protein;  InterPro: IPR013684   Mitochondrial Rho proteins (Miro-1, Q8IXI2 from SWISSPROT, and Miro-2, Q8IXI1 from SWISSPROT), are atypical Rho GTPases. They have a unique domain organisation, with tandem GTP-binding domains and two EF hand domains (IPR002048 from INTERPRO), that may bind calcium. They are also larger than classical small GTPases. It has been proposed that they are involved in mitochondrial homeostasis and apoptosis . ; GO: 0005525 GTP binding, 0007264 small GTPase mediated signal transduction, 0005622 intracellular; PDB: 2iwr_A 2bmj_A 2zej_A 3d6t_B 3dpu_A.
Probab=85.87  E-value=0.18  Score=25.66  Aligned_cols=22  Identities=23%  Similarity=0.288  Sum_probs=18.6

Q ss_pred             EEEECCCCCCHHHHHHHHHHHC
Q ss_conf             8987589988889999998621
Q T0567            27 VWLYGAPGTGRMTGARYLHQFG   48 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s   48 (145)
                      |++.|++|+||+++.+.+....
T Consensus         2 i~V~G~~gvGKTsli~~l~~~~   23 (119)
T PF08477_consen    2 IVVLGDKGVGKTSLIRRLLGEE   23 (119)
T ss_dssp             EEEE--TT---HHHHHHHC---
T ss_pred             EEEECCCCCCHHHHHHHHHCCC
T ss_conf             9999929988999999996588


No 69 
>PF00009 GTP_EFTU:  Elongation factor Tu GTP binding domain;  InterPro: IPR000795 Elongation factors belong to a family of proteins that promote the GTP-dependent binding of aminoacyl tRNA to the A site of ribosomes during protein biosynthesis, and catalyse the translocation of the synthesised protein chain from the A to the P site. The proteins are all relatively similar in the vicinity of their C-termini, and are also highly similar to a range of proteins that includes the nodulation Q protein from Sinorhizobium meliloti, bacterial tetracycline resistance proteins  and the omnipotent suppressor protein 2 from yeast.   In both prokaryotes and eukaryotes, there are three distinct types of elongation factors, EF-1alpha (EF-Tu), which binds GTP and an aminoacyl-tRNAand delivers the latter to the A site of ribosomes; EF-1beta (EF-Ts), which interacts with EF-1a/EF-Tu to displace GDP and thus allows the regeneration of GTP-EF-1a; and EF-2 (EF-G), which binds GTP and peptidyl-tRNA and translocates the latter from the A site to the P site. In EF-1-alpha, a specific region has been shown  to be involved in a conformational change mediated by the hydrolysis of GTP to GDP. This region is conserved in both EF-1alpha/EF-Tu as well as EF-2/EF-G and thus seems typical for GTP-dependent proteins which bind non-initiator tRNAs to the ribosome. The GTP-binding protein synthesis factor family also includes the eukaryotic peptide chain release factor GTP-binding subunits  and prokaryotic peptide chain release factor 3 (RF-3) ; the prokaryotic GTP-binding protein lepA and its homolog in yeast (GUF1) and Caenorhabditis elegans (ZK1236.1); yeast HBS1 ; rat statin S1 ; and the prokaryotic selenocysteine-specific elongation factor selB . ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 1jny_A 1skq_A 1zun_B 1g7t_A 1g7s_A 1g7r_A 1zo1_I 2ywe_A 2ywf_A 2ywg_A ....
Probab=85.57  E-value=0.63  Score=22.67  Aligned_cols=92  Identities=15%  Similarity=0.155  Sum_probs=46.4

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHC-CC-------------------------------------CCCCCCEECCCCCCH-
Q ss_conf             958987589988889999998621-24-------------------------------------267852412578898-
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFG-RN-------------------------------------AQGEFVYRELTPDNA-   65 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s-~~-------------------------------------~~~~fv~~~~~~~~~-   65 (145)
                      ..|.+.|..|+||+++...|-... .-                                     ....+..+||.+... 
T Consensus         4 ~ni~i~Gh~~~GKTTL~~~L~~~~~~~~~~~~~~~~~~~~d~~~~E~~rg~Ti~~~~~~~~~~~~~~~i~liDtPGh~~f   83 (189)
T PF00009_consen    4 RNIAIIGHVDSGKTTLLEALLYRAGAISRRGSVEKGRTILDKDPEERERGITIDLSVASFEYEWNGRKINLIDTPGHEDF   83 (189)
T ss_dssp             EEEEEEESTT---HHHHHHHHHHHHCTSTTCHHHHHHCCHHSSHHHHHTTSBSSCEEEEEEECESSEEEEEEE----HHH
T ss_pred             EEEEEEECCCCCHHHHHHHHEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEECCCCCHHH
T ss_conf             49999927878754231331121002112343211221112111122234432221111111123211023022220012


Q ss_pred             -HHHHHHHHHHCCCEEEECCHHHCCHHHHHHHHHHHHHCCHHHEEEECCCCCHH
Q ss_conf             -88899998625874874374206877899999998721401001114776878
Q T0567            66 -PQLNDFIALAQGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIGIGDTSLV  118 (145)
Q Consensus        66 -~~~~~~l~~a~gGtL~l~ei~~L~~~~Q~~L~~~l~~~~~~~RiI~~s~~~l~  118 (145)
                       .+....+..++...+++|-.+-+.... ..++........+ .+++....|..
T Consensus        84 ~~~~~~~~~~~D~ailVvda~~g~~~~t-~~~~~~~~~~~~p-~iiviNK~D~~  135 (189)
T PF00009_consen   84 IKEVIRALSVADGAILVVDADDGVEPQT-EEHLKLARKLGIP-IIIVINKMDLV  135 (189)
T ss_dssp             HHHHHHHHTTBSEEEEEEETTSSS-HHH-HHHHHHHHHTT-T-EEEEEETTCGS
T ss_pred             HHHHCCCCCCCCEEEEEEEECCCCCCCC-CCCHHCCCCCCCE-EEEECCCCCCC
T ss_conf             2220112123323345553011234433-2101001234650-68752346854


No 70 
>PF00488 MutS_V:  MutS domain V C-terminus.;  InterPro: IPR000432   Mismatch repair contributes to the overall fidelity of DNA replication and is essential for combating the adverse effects of damage to the genome. It involves the correction of mismatched base pairs that have been missed by the proofreading element of the DNA polymerase complex. The post-replicative Mismatch Repair System (MMRS) of Escherichia coli involves MutS (Mutator S), MutL and MutH proteins, and acts to correct point mutations or small insertion/deletion loops produced during DNA replication . MutS and MutL are involved in preventing recombination between partially homologous DNA sequences. The assembly of MMRS is initiated by MutS, which recognises and binds to mispaired nucleotides and allows further action of MutL and MutH to eliminate a portion of newly synthesized DNA strand containing the mispaired base . MutS can also collaborate with methyltransferases in the repair of O(6)-methylguanine damage, which would otherwise pair with thymine during replication to create an O(6)mG:T mismatch . MutS exists as a dimer, where the two monomers have different conformations and form a heterodimer at the structural level . Only one monomer recognises the mismatch specifically and has ADP bound. Non-specific major groove DNA-binding domains from both monomers embrace the DNA in a clamp-like structure. Mismatch binding induces ATP uptake and a conformational change in the MutS protein, resulting in a clamp that translocates on DNA.    MutS is a modular protein with a complex structure , and is composed of:    N-terminal mismatch-recognition domain, which is similar in structure to tRNA endonuclease. Connector domain, which is similar in structure to Holliday junction resolvase ruvC. Core domain, which is composed of two separate subdomains that join together to form a helical bundle; from within the core domain, two helices act as levers that extend towards (but do not touch) the DNA. Clamp domain, which is inserted between the two subdomains of the core domain at the top of the lever helices; the clamp domain has a beta-sheet structure. ATPase domain (connected to the core domain), which has a classical Walker A motif. HTH (helix-turn-helix) domain, which is involved in dimer contacts.    Homologues of MutS have been found in many species including eukaryotes (MSH 1, 2, 3, 4, 5, and 6 proteins), archaea and bacteria, and together these proteins have been grouped into the MutS family. Although many of these proteins have similar activities to the E. coli MutS, there is significant diversity of function among the MutS family members. This diversity is even seen within species, where many species encode multiple MutS homologues with distinct functions . Inter-species homologues may have arisen through frequent ancient horizontal gene transfer of MutS (and MutL) from bacteria to archaea and eukaryotes via endosymbiotic ancestors of mitochondria and chloroplasts .    This entry represents the C-terminal region found in proteins in the MutS family of DNA mismatch repair proteins. The C-terminal region of MutS is comprised of the ATPase domain and the HTH (helix-turn-helix) domain, the latter being involved in dimer contacts. Yeast MSH3 , bacterial proteins involved in DNA mismatch repair, and the predicted protein product of the Rep-3 gene of mouse share extensive sequence similarity. Human MSH has been implicated in non-polyposis colorectal carcinoma (HNPCC) and is a mismatch binding protein. ; GO: 0005524 ATP binding, 0030983 mismatched DNA binding, 0006298 mismatch repair; PDB: 2o8f_A 2o8e_A 2o8d_A 2o8c_A 2o8b_A 1oh6_B 1ng9_B 1w7a_A 1oh5_A 1e3m_B ....
Probab=85.45  E-value=0.65  Score=22.59  Aligned_cols=90  Identities=14%  Similarity=0.084  Sum_probs=46.5

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHCCCCC-CCCC---------------EECCCCCC----------HHHHHHHHHHHCCCE
Q ss_conf             589875899888899999986212426-7852---------------41257889----------888899998625874
Q T0567            26 AVWLYGAPGTGRMTGARYLHQFGRNAQ-GEFV---------------YRELTPDN----------APQLNDFIALAQGGT   79 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~~s~~~~-~~fv---------------~~~~~~~~----------~~~~~~~l~~a~gGt   79 (145)
                      -++|+|+..+||+++-|.|-...--++ |-||               .+.+...-          -..+..++..+...+
T Consensus        44 ~~iiTGpN~~GKSt~Lk~i~l~~ilAq~G~~VPA~~a~i~~~d~I~~~~~~~d~~~~~~StF~~e~~~~~~il~~~~~~s  123 (234)
T PF00488_consen   44 ILIITGPNMGGKSTYLKQIGLIVILAQIGCFVPAKSAEIPLFDRIFTRIGDNDSLEEGLSTFMAEMKRLSNILRSATSRS  123 (234)
T ss_dssp             EEEEE--TT---HHHHHHHHHHHHHHT----BSSSEEEEE--SEEEEE-----S------HHHHHHHHHHHHHHH--TTC
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEECCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHCE
T ss_conf             99997898511568999999999998368861041369547878998256587233045707999999999998613243


Q ss_pred             -EEECCHHHCCHH--HH---HHHHHHHHHCCHHHEEEECCCCC
Q ss_conf             -874374206877--89---99999987214010011147768
Q T0567            80 -LVLSHPEHLTRE--QQ---YHLVQLQSQEHRPFRLIGIGDTS  116 (145)
Q Consensus        80 -L~l~ei~~L~~~--~Q---~~L~~~l~~~~~~~RiI~~s~~~  116 (145)
                       +++||+.+=+..  .-   ..+++.+.+. .+++.|++|+..
T Consensus       124 LvliDE~g~GT~~~eg~al~~aile~L~~~-~~~~~i~~TH~~  165 (234)
T PF00488_consen  124 LVLIDELGRGTNPEEGAALAAAILEYLLEK-NGCRVIFATHFH  165 (234)
T ss_dssp             EEEEE-------ST---HHHHHHHHHHHHT-TT-EEEEE-S-H
T ss_pred             EEEECCCCCCCCCCHHHHHHHHHHHHHHHH-CCCCEEEEECCH
T ss_conf             898446678989514389999999999863-377589996551


No 71 
>PF03193 DUF258:  Protein of unknown function, DUF258;  InterPro: IPR004881   This protein has been shown to cleave GTP, remain bound to GDP , and acts as an unusual circulary permuted GTPase that catalyzes rapid hydrolysis of GTP with a slow catalytic turnover. A role as a regulator of translation has been suggested . The Aquifex aeolicus ortholog is split into consecutive open reading frames. ; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2yv5_A 1u0l_A 1t9h_A 2rcn_A.
Probab=84.94  E-value=0.34  Score=24.10  Aligned_cols=24  Identities=25%  Similarity=0.159  Sum_probs=20.6

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHC
Q ss_conf             958987589988889999998621
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFG   48 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s   48 (145)
                      .-++|.|+.|+||+++...|...-
T Consensus        36 k~~vl~G~SGvGKSTLiN~L~~~~   59 (161)
T PF03193_consen   36 KTIVLVGPSGVGKSTLINALLGDL   59 (161)
T ss_dssp             SBEEEE-------HHHHHHH---S
T ss_pred             CEEEEECCCCCCHHHHHHHHCCHH
T ss_conf             869998899998999999873544


No 72 
>PF03205 MobB:  Molybdopterin guanine dinucleotide synthesis protein B;  InterPro: IPR004435   The majority of molybdenum-containing enzymes utilise a molybdenum cofactor (MoCF or Moco) consisting of a Mo atom coordinated via a cisdithiolene moiety to molybdopterin (MPT). MoCF is ubiquitous in nature, and the pathway for MoCF biosynthesis is conserved in all three domains of life. MoCF-containing enzymes function as oxidoreductases in carbon, nitrogen, and sulphur metabolism , .    In Escherichia coli, biosynthesis of MoCF is a three stage process. It begins with the MoaA and MoaC conversion of GTP to the meta-stable pterin intermediate precursor Z. The second stage involves MPT synthase (MoaD and MoaE), which coverts precursor Z to MPT; MoeB is involved in the recycling of MPT synthase. The final step in MoCF synthesis is the attachment of mononuclear Mo to MPT, a process that requires MoeA and which is enhanced by MogA in an Mg2 ATP-dependent manner . MoCF is the active co-factor in eukaryotic and some prokaryotic molybdoenzymes, but the majority of bacterial enzymes requiring MoCF, need a modification of MTP for it to be active; MobA is involved in the attachment of a nucleotide monophosphate to MPT resulting in the MGD co-factor, the active co-factor for most prokaryotic molybdoenzymes. Bacterial two-hybrid studies have revealed the close interactions between MoeA, MogA, and MobA in the synthesis of MoCF . Moreover the close functional association of MoeA and MogA in the synthesis of MoCF is supported by fact that the known eukaryotic homologues to MoeA and MogA exist as fusion proteins: CNX1 () of Arabidopsis thaliana (Mouse-ear cress), mammalian Gephryin (e.g. Q9NQX3 from SWISSPROT) and Drosophila melanogaster (Fruit fly) Cinnamon (P39205 from SWISSPROT) .   The MobB domain is similar to that of the urease accessory protein UreG and the hydrogenase accessory protein HypB, both GTP hydrolases involved in loading nickel into the metallocentres of their respective target enzymes. It is involved in the final step of molybdenum-cofactor biosynthesis. While its precise function has not been identified it is thought to be involved in the transfer of a guanine dinucleotide moiety to molybdopterin, as it shows GTP-binding and weak GTPase activity . The MobB protein (P32125 from SWISSPROT) from Escherichia coli, which is comprised of this domain, is a homodimer . Each molecule is composed of two distinct regions - an outer region comprised of 6 beta-strands and three alpha helices, and an inner region comprised of a two-strand beta hairpin followed by an alpha helix. These regions require interaction with the second monomer to allow proper folding to occur. The two monomers are intertwined and form an extensive 16-stranded beta-sheet. While the active site could not be positively identified, the presence of highly conserved residues suggests the substrate binding site occurs in the central solvent channel.; GO: 0005525 GTP binding, 0006777 Mo-molybdopterin cofactor biosynthetic process; PDB: 2npi_A 1np6_B 1p9n_B 2f1r_B 1xjc_A.
Probab=84.85  E-value=0.19  Score=25.51  Aligned_cols=36  Identities=22%  Similarity=0.334  Sum_probs=23.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHH-CCCCCCCCCEECCCC
Q ss_conf             898758998888999999862-124267852412578
Q T0567            27 VWLYGAPGTGRMTGARYLHQF-GRNAQGEFVYRELTP   62 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~-s~~~~~~fv~~~~~~   62 (145)
                      |.|.|..||||+++++.+-.. ..+...+-+..++..
T Consensus         3 i~vvG~k~sGKTTl~~~Li~~l~~~g~~v~~ik~~~~   39 (137)
T PF03205_consen    3 IQVVGPKGSGKTTLIRRLINYLKKRGYRVAVIKHLHH   39 (137)
T ss_dssp             EEEE-ETT---HHHHHHHHHHHHHC---EEEEEE-ST
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEECCC
T ss_conf             9998789999999999999999976997149996488


No 73 
>PF02456 Adeno_IVa2:  Adenovirus IVa2 protein;  InterPro: IPR003389 Va2 protein can interact with the adenoviral packaging signal and this interaction involves DNA sequences that have previously been demonstrated to be required for packaging . During the course of lytic infection, the adenovirus major late promoter (MLP) is induced to high levels after replication of viral DNA has started. IVa2 is a transcriptional activator of the major late promoter .; GO: 0019083 viral transcription
Probab=84.76  E-value=0.67  Score=22.54  Aligned_cols=21  Identities=29%  Similarity=0.392  Sum_probs=17.5

Q ss_pred             CC--EEEECCCCCCHHHHHHHHH
Q ss_conf             95--8987589988889999998
Q T0567            25 IA--VWLYGAPGTGRMTGARYLH   45 (145)
Q Consensus        25 ~p--vli~Ge~GtGK~~~A~~iH   45 (145)
                      .|  ..|+|++|+||+.+-|.|-
T Consensus        86 qP~I~~VYGPTG~GKSqllRNli  108 (369)
T PF02456_consen   86 QPFIGVVYGPTGSGKSQLLRNLI  108 (369)
T ss_pred             CCEEEEEECCCCCCHHHHHHHHC
T ss_conf             84489997889987799998751


No 74 
>PF06431 Polyoma_lg_T_C:  Polyomavirus large T antigen C-terminus;  InterPro: IPR010932   The oncogenic large tumour antigen (LTag) is a protein found in polyomaviruses which is essential for viral DNA replication . LTag contains three domains an N-terminal DnaJ domain which mediates protein interactions (IPR001623 from INTERPRO), a domain which binds the origin of DNA replication (IPR003133 from INTERPRO), and a C-terminal helicase domain. Replication is intitated by LTag assembling at the origin as a double hexamer that distorts and melts the origin DNA , . During elongation LTag acts as a helicase that unwinds duplex DNA at the replication forks .   This entry represents the helicase domain of LTag, which assembles into a hexameric structure containing a positively charged central channel that can bind both single- and double-stranded DNA . ATP binding and hydrolysis trigger large conformational changes which are thought to be coupled to the melting of origin DNA and the unwinding of duplex DNA . These conformational changes cause the angles and orientations between regions of a monomer to alter, creating what was described as an "iris"-like motion in the hexamer. In addition to this, six beta hairpins on the channel surface move longitudinally along the central channel, possibly serving as a motor for pulling DNA into the LTag double hexamer for unwinding.; GO: 0003677 DNA binding, 0005524 ATP binding, 0006260 DNA replication; PDB: 1svl_A 1n25_B 1svm_F 1svo_B.
Probab=84.60  E-value=0.49  Score=23.24  Aligned_cols=39  Identities=15%  Similarity=0.069  Sum_probs=25.9

Q ss_pred             HHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHC
Q ss_conf             999999999861479958987589988889999998621
Q T0567            10 INQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFG   48 (145)
Q Consensus        10 m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~s   48 (145)
                      +.++.+.+-.=-+.....++.||.-|||+++|.+|-...
T Consensus       141 i~~~Lk~~v~N~PKrRy~lFkGPVNsGKTTlAAAll~Lc  179 (417)
T PF06431_consen  141 IYEILKCMVENIPKRRYWLFKGPVNSGKTTLAAALLDLC  179 (417)
T ss_dssp             HHHHHHHHHH-BTTB-EEEEE--TT---HHHHHHHHHH-
T ss_pred             HHHHHHHHHCCCCCCEEEEEECCCCCCHHHHHHHHHHHC
T ss_conf             999999986188751368876786776377999999865


No 75 
>PF04548 AIG1:  AIG1 family;  InterPro: IPR006703   This entry represents Arabidopsis protein AIG1 which appears to be involved in plant resistance to bacteria. The Arabidopsis disease resistance gene RPS2 is involved in recognition of bacterial pathogens carrying the avirulence gene avrRpt2. AIG1 (avrRpt2-induced gene) exhibits RPS2- and avrRpt2-dependent induction early after infection with Pseudomonas syringae carrying avrRpt2 .    The pattern also recognises a number of mammalian proteins, for example the rat immune-associated nucleotide 4 protein, suggesting that the family may have a wider function. ; GO: 0005525 GTP binding; PDB: 3bb1_H 1h65_C 3def_A 3bb4_A 3bb3_A 2j3e_A.
Probab=83.67  E-value=0.23  Score=25.07  Aligned_cols=20  Identities=20%  Similarity=0.473  Sum_probs=17.9

Q ss_pred             CEEEECCCCCCHHHHHHHHH
Q ss_conf             58987589988889999998
Q T0567            26 AVWLYGAPGTGRMTGARYLH   45 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH   45 (145)
                      .|++.|.+|+||+.+...|-
T Consensus         2 ~IlLlG~TG~GKSs~~N~Il   21 (212)
T PF04548_consen    2 RILLLGKTGSGKSSTGNTIL   21 (212)
T ss_dssp             EEEEE-------HHHHHHH-
T ss_pred             EEEEECCCCCCHHHHHHHHH
T ss_conf             79998689998999999986


No 76 
>PF00063 Myosin_head:  Myosin head (motor domain);  InterPro: IPR001609   Muscle contraction is caused by sliding between the thick and thin filaments of the myofibril. Myosin is a major component of thick filaments and exists as a hexamer of 2 heavy chains , 2 alkali light chains, and 2 regulatory light chains. The heavy chain can be subdivided into the N-terminal globular head and the C-terminal coiled-coil rod-like tail, although some forms have a globular region in their C-terminal. There are many cell-specific isoforms of myosin heavy chains, coded for by a multi-gene family . Myosin interacts with actin to convert chemical energy, in the form of ATP, to mechanical energy . The 3-D structure of the head portion of myosin has been determined  and a model for actin-myosin complex has been constructed .   The globular head is well conserved, some highly-conserved regions possibly relating to functional and structural domains . The rod-like tail starts with an invariant proline residue, and contains many repeats of a 28 residue region, interrupted at 4 regularly-spaced points known as skip residues. Although the sequence of the tail is not well conserved, the chemical character is, hydrophobic, charged and skip residues occuring in a highly ordered and repeated fashion .; GO: 0003774 motor activity, 0005524 ATP binding, 0016459 myosin complex; PDB: 1mvw_J 1o19_M 1o1d_G 1m8q_P 1o1b_J 1o1a_D 1o1g_P 1o1e_P 1o1c_P 1o18_M ....
Probab=83.44  E-value=0.45  Score=23.45  Aligned_cols=23  Identities=13%  Similarity=0.463  Sum_probs=19.1

Q ss_pred             CCCCCEEEECCCCCCHHHHHHHH
Q ss_conf             47995898758998888999999
Q T0567            22 ETDIAVWLYGAPGTGRMTGARYL   44 (145)
Q Consensus        22 ~~~~pvli~Ge~GtGK~~~A~~i   44 (145)
                      ..+..++|.||.|+||+..++.+
T Consensus        83 ~~~QsIiisGeSGaGKTe~~k~~  105 (689)
T PF00063_consen   83 GRNQSIIISGESGAGKTESTKLI  105 (689)
T ss_dssp             TSEEEEEEE-------HHHHHHH
T ss_pred             CCCEEEEEECCCCCCCHHHHHHH
T ss_conf             37648996057787742679999


No 77 
>PF00154 RecA:  recA bacterial DNA recombination protein;  InterPro: IPR013765   The recA gene product is a multifunctional enzyme that plays a role in homologous recombination, DNA repair and induction of the SOS response . In homologous recombination, the protein functions as a DNA-dependent ATPase, promoting synapsis, heteroduplex formation and strand exchange between homologous DNAs . RecA also acts as a protease cofactor that promotes autodigestion of the lexA product and phage repressors. The proteolytic inactivation of the lexA repressor by an activated form of recA may cause a derepression of the 20 or so genes involved in the SOS response, which regulates DNA repair, induced mutagenesis, delayed cell division and prophage induction in response to DNA damage .    RecA is a protein of about 350 amino-acid residues. Its sequence is very well conserved , ,  among eubacterial species. It is also found in the chloroplast of plants . RecA-like proteins are found in archaea and diverse eukaryotic organisms, like fission yeast, mouse or human. In the filament visualised by X-ray crystallography, -strand 3, the loop C-terminal to -strand 2, and alpha-helix D of the core domain form one surface that packs against alpha-helix A and -strand 0 (the N-terminal domain) of an adjacent monomer during polymerisation [Lusetti and Cox, Annu. Rev. Biochem. 2002. 71:71-100.]. The core ATP-binding site domain is well conserved, with 14 invariant residues. It contains the nucleotide binding loop between -strand 1 and alpha-helix C. The Escherichia coli sequence GPESSGKT matches the consensus sequence of amino acids (G/A)XXXXGK(T/S) for the Walker A box (also referred to as the P-loop) found in a number of nucleoside triphosphate (NTP)-binding proteins. Another nucleotide binding motif, the Walker B box is found at -strand 4 in the RecA structure. The Walker B box is characterised by four hydrophobic amino acids followed by an acidic residue (usually aspartate). Nucleotide specificity and additional ATP binding interactions are contributed by the amino acid residues at -strand 2 and the loop C-terminal to that strand, all of which are greater than 90% conserved among bacterial RecA proteins.; PDB: 3cmw_A 3cmv_B 3cmu_A 3cmt_A 1u98_A 1u94_A 1xmv_A 3cmx_D 2reb_A 1xms_A ....
Probab=83.12  E-value=1.1  Score=21.42  Aligned_cols=68  Identities=15%  Similarity=0.115  Sum_probs=37.7

Q ss_pred             CCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCC-CCHHHH-------------------------HHHHHHHCCC
Q ss_conf             95898758998888999999862124267852412578-898888-------------------------9999862587
Q T0567            25 IAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTP-DNAPQL-------------------------NDFIALAQGG   78 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~-~~~~~~-------------------------~~~l~~a~gG   78 (145)
                      .-+-|+|++++||+++|-.+-.......+..+.+|... .+....                         +.++....-+
T Consensus        54 rivEI~Gp~ssGKTtLaL~~ia~~q~~g~~~afID~E~aldp~~a~~lGVDl~rLlv~qP~~gEqAl~i~e~LirSga~~  133 (322)
T PF00154_consen   54 RIVEIYGPESSGKTTLALHAIAEAQKQGGWCAFIDAEHALDPEYAASLGVDLDRLLVVQPDSGEQALEIAEQLIRSGAVD  133 (322)
T ss_dssp             -EEEEE--TT---HHHHHHHHHHHHH----EEEEESSS---HHHHHH----GGG-EEE------HHHHHHHHHHH----S
T ss_pred             CEEEEECCCCCCHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHCCCCHHHCEEECCCCHHHHHHHHHHHHCCCCCC
T ss_conf             77898457886305899999999861366179974766769799998399888875615786576999999986177865


Q ss_pred             EEEECCHHHCCHHH
Q ss_conf             48743742068778
Q T0567            79 TLVLSHPEHLTREQ   92 (145)
Q Consensus        79 tL~l~ei~~L~~~~   92 (145)
                      .+++|-+..|.+..
T Consensus       134 lVVvDSvaal~pka  147 (322)
T PF00154_consen  134 LVVVDSVAALVPKA  147 (322)
T ss_dssp             EEEEE-GCC---HH
T ss_pred             EEEEECCCCCCCHH
T ss_conf             79983365556899


No 78 
>PF01121 CoaE:  Dephospho-CoA kinase;  InterPro: IPR001977   This family contains dephospho-CoA kinases (2.7.1.24 from EC), which catalyzes the final step in CoA biosynthesis, the phosphorylation of the 3'-hydroxyl group of ribose using ATP as a phosphate donor.   The cyrstal structures of a number of the proteins in this entry have been determined, including the structure of the protein from Haemophilus influenzae to 2.0-A resolution in a comlex with ATP. The protein consists of three domains: the nucleotide-binding domain with a five-stranded parallel beta-sheet, the substrate-binding alpha-helical domain, and the lid domain formed by a pair of alpha-helices; the overall topology of the protein resembles the structures of other nucleotide kinases . ; GO: 0005524 ATP binding; PDB: 2f6r_A 2if2_C 1jjv_A 1viy_A 1n3b_A 1vht_C 1vhl_C 1t3h_A 2grj_F 1uf9_B ....
Probab=82.78  E-value=0.26  Score=24.71  Aligned_cols=29  Identities=24%  Similarity=0.235  Sum_probs=21.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCC
Q ss_conf             89875899888899999986212426785241257
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELT   61 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~   61 (145)
                      |=|+|-.||||+++++++-.      ..+..+||.
T Consensus         3 IGlTGgIgsGKStv~~~l~~------~G~~vidaD   31 (180)
T PF01121_consen    3 IGLTGGIGSGKSTVAKILKE------LGAPVIDAD   31 (180)
T ss_dssp             EEEB-------HHHHHHHHH---------EEEEHH
T ss_pred             EEEECCCCCCHHHHHHHHHH------CCCCEEEHH
T ss_conf             99978875789999999997------799699777


No 79 
>PF01202 SKI:  Shikimate kinase;  InterPro: IPR000623 Shikimate kinase () catalyzes the fifth step in the biosynthesis of aromatic amino acids from chorismate (the so-called shikimate pathway) . The enzyme catalyzes the following reaction:  ATP + shikimate = ADP + shikimate-3-phosphate  The protein is found in bacteria (gene aroK or aroL), plants and fungi (where it is part of a multifunctional enzyme that catalyses five consecutive steps in this pathway). In 1994, the 3D structure of shikimate kinase was predicted to be very close to that of adenylate kinase, suggesting a functional similarity as well as an evolutionary relationship . This prediction has since been confirmed experimentally. The protein is reported to possess an alpha/beta fold, consisting of a central sheet of five parallel beta-strands flanked by alpha-helices. Such a topology is very similar to that of adenylate kinase .; GO: 0004765 shikimate kinase activity, 0005524 ATP binding; PDB: 1e6c_A 2shk_B 1shk_A 1zui_A 1zuh_A 2dft_C 1l4u_A 2iyz_A 2iyr_A 1l4y_A ....
Probab=81.90  E-value=0.13  Score=26.31  Aligned_cols=25  Identities=28%  Similarity=0.410  Sum_probs=18.6

Q ss_pred             CCCCHHHHHHHHHHHCCCCCCCCCEECC
Q ss_conf             9988889999998621242678524125
Q T0567            33 PGTGRMTGARYLHQFGRNAQGEFVYREL   60 (145)
Q Consensus        33 ~GtGK~~~A~~iH~~s~~~~~~fv~~~~   60 (145)
                      +|+||+++++.+..   +-.-+|+..|-
T Consensus         1 ~G~GKTTvg~~LA~---~Lg~~fiD~D~   25 (158)
T PF01202_consen    1 PGSGKTTVGRLLAE---RLGLPFIDLDD   25 (158)
T ss_dssp             TT---HHHHHHHHH---HHT-EEEEHHH
T ss_pred             CCCCHHHHHHHHHH---HHCCCEEECHH
T ss_conf             99988999999999---83998681567


No 80 
>PF02374 ArsA_ATPase:  Anion-transporting ATPase;  InterPro: IPR003348   This ATPase is involved in the removal of arsenate, antimonite, and arsenate from the cell.    In Escherichia coli an anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773. This ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. Maintenance of a low intracellular concentration of oxyanion produces resistance to the toxic agents. The pump is composed of two polypeptides, the products of the arsA and arsB genes. This two-subunit enzyme produces resistance to arsenite and antimonite. A third gene, arsC, expands the substrate specificity to allow for arsenate pumping and resistance .   The ArsA and ArsB proteins form a membrane-bound pump that functions as an oxyanion-translocating ATPase. The ArsC protein is an arsenate reductase that reduces arsenate to arsenite, which is subsequently pumped out of the cell .; GO: 0005524 ATP binding, 0006820 anion transport, 0016020 membrane; PDB: 1f48_A 1ii0_A 1ihu_A 1ii9_B 2ph1_A.
Probab=80.08  E-value=0.45  Score=23.46  Aligned_cols=25  Identities=20%  Similarity=0.163  Sum_probs=19.4

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCCC
Q ss_conf             8987589988889999998621242
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGRNA   51 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~~~   51 (145)
                      +++.|.-|+||+++|.++.....+.
T Consensus         4 i~~~GKGGVGKTT~aaA~A~~~A~~   28 (305)
T PF02374_consen    4 IFFGGKGGVGKTTVAAATALALARR   28 (305)
T ss_dssp             EEEE-------HHHHHHHHHHHHH-
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHC
T ss_conf             9993788874489999999999837


No 81 
>PF02283 CobU:  Cobinamide kinase / cobinamide phosphate guanyltransferase;  InterPro: IPR003203 This family is composed of a group of bifunctional cobalbumin biosynthesis enzymes which display cobinamide kinase and cobinamide phosphate guanyltransferase activity. The crystal structure of the enzyme reveals the molecule to be a trimer with a propeller-like shape .; PDB: 1cbu_C 1c9k_C.
Probab=79.88  E-value=0.54  Score=23.04  Aligned_cols=59  Identities=17%  Similarity=0.191  Sum_probs=36.1

Q ss_pred             EEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCCCCHHHHHHHH------------------------HHHC-CCEEE
Q ss_conf             8987589988889999998621242678524125788988889999------------------------8625-87487
Q T0567            27 VWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTPDNAPQLNDFI------------------------ALAQ-GGTLV   81 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~~~~~~~l------------------------~~a~-gGtL~   81 (145)
                      +||+|...|||+.+|.-+-....   ++.+.+-.+...+.++...+                        .... ++++.
T Consensus         1 ~lv~GG~rSGKS~~AE~la~~~~---~~~~YiAT~~~~D~Em~~RI~~H~~~R~~~w~t~E~p~~l~~~l~~~~~~~~vL   77 (167)
T PF02283_consen    1 ILVTGGARSGKSAFAEQLAAQLG---GRVVYIATAQAFDEEMQERIARHRARRPAGWTTIEEPLDLAEALKELSKGDVVL   77 (167)
T ss_dssp             EEEE-------HHHHHHH--------SCEEEEESSHHHHHHHHHHHHHHH----TCEEEEE-SS-GGGTS-TTS-T-EEE
T ss_pred             CEEECCCCCCHHHHHHHHHHHCC---CCCEEEECCCCCCHHHHHHHHHHHHHCCCCCEEEECHHHHHHHHHHCCCCCEEE
T ss_conf             97837888667999999998338---985899858989989999999999858999759973210999997348999899


Q ss_pred             ECCHHHC
Q ss_conf             4374206
Q T0567            82 LSHPEHL   88 (145)
Q Consensus        82 l~ei~~L   88 (145)
                      +|.+..|
T Consensus        78 lDclt~w   84 (167)
T PF02283_consen   78 LDCLTLW   84 (167)
T ss_dssp             EE-HHHH
T ss_pred             EECHHHH
T ss_conf             9456999


No 82 
>PF06564 YhjQ:  YhjQ protein;  InterPro: IPR009504   This family consists of several bacterial YhjQ proteins. The function of this family is unknown.
Probab=79.03  E-value=1.3  Score=20.94  Aligned_cols=69  Identities=16%  Similarity=0.135  Sum_probs=41.7

Q ss_pred             EEEECCC-CCCHHHHHHHHHHHCCCCCCCCCEECCCCCCH----------------------HHHHHHHHHHCCCEEEEC
Q ss_conf             8987589-98888999999862124267852412578898----------------------888999986258748743
Q T0567            27 VWLYGAP-GTGRMTGARYLHQFGRNAQGEFVYRELTPDNA----------------------PQLNDFIALAQGGTLVLS   83 (145)
Q Consensus        27 vli~Ge~-GtGK~~~A~~iH~~s~~~~~~fv~~~~~~~~~----------------------~~~~~~l~~a~gGtL~l~   83 (145)
                      +.|.|.. |.||+++|..+-..-.+...+.+.+|+.+.+.                      ..|....-+...|..|+.
T Consensus         4 i~i~s~rGGvG~TTltA~LA~aL~~~g~~VlaID~dp~NlLrlhfgl~~~~~~G~a~a~l~~~~W~~~~~~~~~gl~~lP   83 (243)
T PF06564_consen    4 IAIVSVRGGVGRTTLTANLAWALQRLGEPVLAIDLDPQNLLRLHFGLPFSQRDGWARALLDGEDWRQAAYRSSDGLDFLP   83 (243)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHCCCCEEEEECCCCHHCCEECCCCCCCCCCHHHHHCCCCCHHHHHCCCCCCCEEEC
T ss_conf             99971788877899999999999976995699965841101521289966566078987089988995121769986967


Q ss_pred             CHHHCCHHHHHHH
Q ss_conf             7420687789999
Q T0567            84 HPEHLTREQQYHL   96 (145)
Q Consensus        84 ei~~L~~~~Q~~L   96 (145)
                       ...++.+.+..+
T Consensus        84 -fG~l~~~~~~~~   95 (243)
T PF06564_consen   84 -FGQLNAAERLAF   95 (243)
T ss_pred             -CCCCCHHHHHHH
T ss_conf             -899999999879


No 83 
>PF04665 Pox_A32:  Poxvirus A32 protein;  InterPro: IPR006758   The A32 protein is thought to be an ATPase involved in viral DNA packaging .; GO: 0005524 ATP binding
Probab=78.23  E-value=0.84  Score=22.01  Aligned_cols=23  Identities=22%  Similarity=0.407  Sum_probs=17.7

Q ss_pred             CCCCCEEEECCCCCCHHHHHHHH
Q ss_conf             47995898758998888999999
Q T0567            22 ETDIAVWLYGAPGTGRMTGARYL   44 (145)
Q Consensus        22 ~~~~pvli~Ge~GtGK~~~A~~i   44 (145)
                      ..+-.+.+.|.+||||+++...+
T Consensus        11 ~~~f~~viiG~sGSGKTt~i~~L   33 (241)
T PF04665_consen   11 SDPFRIVIIGKSGSGKTTLIKSL   33 (241)
T ss_pred             CCCCEEEEECCCCCCHHHHHHHH
T ss_conf             78750999889999889999999


No 84 
>PF00519 PPV_E1_C:  Papillomavirus helicase;  InterPro: IPR001177   Papillomaviruses are a large family of DNA tumour viruses which give rise to warts in their host species. The helicase E1 protein is an ATP-dependent DNA helicase required for initiation of viral DNA replication . It forms a complex with the viral E2 protein, which is a site-specific DNA-binding transcriptional activator. The E1-E2 complex binds to the replication origin which contains binding sites for both proteins .   The E1 protein is a 70 kDa polypeptide with a central DNA-binding domain and a C-terminal ATPase/helicase domain. It binds specific 18 bp DNA sequences at the origin of replication, melts the DNA duplex and functions as a 3' to 5' helicase . In addition to E2 it also interacts with DNA polymerase alpha and replication protein A to effect DNA replication. The DNA-binding domain forms a five-stranded antiparallel beta sheet bordered by four loosely packed alpha helices on one side and two tightly packed helices on the other . Two structural modules within this domain, an extended loop and a helix, contain conserved residues and are critical for DNA binding. In solution E1 is a monomer, but binds DNA as a dimer. Recruitment of more E1 subunits to the complex leads to melting of the origin and ultimately to the formation of an E1 hexamer with helicase activity .   The entry represents the C-terminal region of E1, containing both the DNA-binding and ATPase/helical domains.; GO: 0003677 DNA binding, 0004003 ATP-dependent DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 1tue_H 1r9w_A 2v9p_A 2gxa_E 1ksx_M 1ksy_A 1f08_B.
Probab=77.42  E-value=1.4  Score=20.84  Aligned_cols=35  Identities=20%  Similarity=0.355  Sum_probs=22.6

Q ss_pred             HHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHH
Q ss_conf             999999999861479958987589988889999998
Q T0567            10 INQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLH   45 (145)
Q Consensus        10 m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH   45 (145)
                      +..++..++.. +...=++|+|+|.|||+.++-.+-
T Consensus       249 l~alk~~L~g~-PKknCivi~GPPnTGKS~F~mSLi  283 (432)
T PF00519_consen  249 LSALKDFLKGI-PKKNCIVIYGPPNTGKSMFCMSLI  283 (432)
T ss_dssp             HHHHHHHH----TTSSEEEEE--TT---HHHHHHHH
T ss_pred             HHHHHHHHHCC-CCCCEEEEECCCCCCHHHHHHHHH
T ss_conf             99999998268-755589998999976518999999


No 85 
>PF00071 Ras:  Ras family;  InterPro: IPR013753   Many members of the Ras superfamily of GTPases have been implicated in the regulation of hematopoietic cells, with roles in growth, survival, differentiation, cytokine production, chemotaxis, vesicle-trafficking, and phagocytosis. The Ras superfamily of proteins now includes over 150 small GTPases (distinguished from the large, heterotrimeric GTPases, the G-proteins). It comprises six subfamilies, the Ras, Rho, Ran, Rab, Arf, and Kir/Rem/Rad subfamilies . They exhibit remarkable overall amino acid identities, especially in the regions interacting with the guanine nucleotide exchange factors that catalyze their activation .  ; PDB: 1yzu_B 1yzt_B 1z08_B 2ot3_B 1z0i_A 3clv_A 1ek0_A 2efh_D 2efe_B 2efd_B ....
Probab=76.73  E-value=0.59  Score=22.82  Aligned_cols=20  Identities=20%  Similarity=0.348  Sum_probs=16.3

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q ss_conf             89875899888899999986
Q T0567            27 VWLYGAPGTGRMTGARYLHQ   46 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~   46 (145)
                      |++.|++|+||+.+.+.+-.
T Consensus         2 i~~vG~~~vGKtsli~~~~~   21 (161)
T PF00071_consen    2 IVVVGDSGVGKTSLINRLLN   21 (161)
T ss_dssp             EEEE--TT---HHHHHHHHH
T ss_pred             EEEECCCCCCHHHHHHHHHC
T ss_conf             89999799899999999973


No 86 
>PF09439 SRPRB:  Signal recognition particle receptor beta subunit; PDB: 2ged_A 1nrj_B 2fh5_B 2go5_2.
Probab=75.83  E-value=0.47  Score=23.33  Aligned_cols=21  Identities=29%  Similarity=0.373  Sum_probs=16.4

Q ss_pred             CCCEEEECCCCCCHHHHHHHH
Q ss_conf             995898758998888999999
Q T0567            24 DIAVWLYGAPGTGRMTGARYL   44 (145)
Q Consensus        24 ~~pvli~Ge~GtGK~~~A~~i   44 (145)
                      ...|||.|+.|+||+.+-..+
T Consensus         3 ~~~vll~Gp~gsGKTaLf~~L   23 (181)
T PF09439_consen    3 RPTVLLVGPSGSGKTALFSQL   23 (181)
T ss_dssp             --EEEEE--TT---HHHHHHH
T ss_pred             CCEEEEECCCCCCHHHHHHHH
T ss_conf             753999887998899999999


No 87 
>PF12128 DUF3584:  Protein of unknown function (DUF3584)
Probab=74.58  E-value=0.96  Score=21.68  Aligned_cols=25  Identities=24%  Similarity=0.323  Sum_probs=21.1

Q ss_pred             CCCCCEEEECCCCCCHHHHHHHHHH
Q ss_conf             4799589875899888899999986
Q T0567            22 ETDIAVWLYGAPGTGRMTGARYLHQ   46 (145)
Q Consensus        22 ~~~~pvli~Ge~GtGK~~~A~~iH~   46 (145)
                      ..+.+|.|+|-.|.||+++-|+|=.
T Consensus        15 ~ldG~t~~~GTNG~GKTTLlRlIp~   39 (1202)
T PF12128_consen   15 DLDGNTHFIGTNGVGKTTLLRLIPF   39 (1202)
T ss_pred             ECCCCEEEECCCCCCHHHHHHHHHH
T ss_conf             3389716743788869999999997


No 88 
>PF03796 DnaB_C:  DnaB-like helicase C terminal domain;  InterPro: IPR007694   The hexameric helicase DnaB unwinds the DNA duplex at the Escherichia coli chromosome replication fork. Although the mechanism by which DnaB both couples ATP hydrolysis to translocation along DNA and denatures the duplex is unknown, a change in the quaternary structure of the protein involving dimerization of the N-terminal domain has been observed and may occur during the enzymatic cycle. This C-terminal domain contains an ATP-binding site and is therefore probably the site of ATP hydrolysis. ; GO: 0003678 DNA helicase activity, 0005524 ATP binding, 0006260 DNA replication; PDB: 2q6t_B 1q57_E 1e0j_F 1cr1_A 1e0k_F 1cr0_A 1cr2_A 1cr4_A 3bgw_E 3bh0_A ....
Probab=73.27  E-value=2.4  Score=19.53  Aligned_cols=38  Identities=18%  Similarity=0.170  Sum_probs=23.0

Q ss_pred             HHHHHHHHHHHHCCCCCEEEECCCCCCHHHHHHHHHHHC
Q ss_conf             999999999861479958987589988889999998621
Q T0567            10 INQYRRRLQQLSETDIAVWLYGAPGTGRMTGARYLHQFG   48 (145)
Q Consensus        10 m~~l~~~i~~~a~~~~pvli~Ge~GtGK~~~A~~iH~~s   48 (145)
                      +..+-+.+.-+ ....=++|.|.||.||+.+|.-+-...
T Consensus         6 ~~~LD~~~~G~-~~G~l~vi~g~pg~GKT~~~~~i~~~~   43 (185)
T PF03796_consen    6 FPSLDKITGGL-RPGELIVIGGRPGMGKTTFALNIALNA   43 (185)
T ss_dssp             -HHHHHHH-----TT-EEEEEESTT-HHHHHHHHHHHHH
T ss_pred             HHHHHHHHCCC-CCCCEEEEEECCCCCHHHHHHHHHHHH
T ss_conf             48899884397-878579998468888169999999999


No 89 
>PF02223 Thymidylate_kin:  Thymidylate kinase;  InterPro: IPR000062   Thymidylate kinase (2.7.4.9 from EC; dTMP kinase) catalyzes the phosphorylation of thymidine 5'-monophosphate (dTMP) to form thymidine 5'-diphosphate (dTDP) in the presence of ATP and magnesium:   ATP + thymidine 5'-phosphate = ADP + thymidine 5'-diphosphate    Thymidylate kinase is an ubiquitous enzyme of about 25 Kd and is important in the dTTP synthesis pathway for DNA synthesis. The function of dTMP kinase in eukaryotes comes from the study of a cell cycle mutant, cdc8, in Saccharomyces cerevisiae Saccharomyces cerevisiae. Structural and functional analyses suggest that the cDNA codes for authentic human dTMP kinase. The mRNA levels and enzyme activities corresponded to cell cycle progression and cell growth stages. ; GO: 0004798 thymidylate kinase activity, 0005524 ATP binding, 0006233 dTDP biosynthetic process, 0006235 dTTP biosynthetic process; PDB: 2ccj_B 2ccg_A 2cck_B 2pbr_B 3hjn_A 4tmk_A 5tmp_A 2v54_B 2w0s_B 1nn0_A ....
Probab=71.53  E-value=1.6  Score=20.44  Aligned_cols=23  Identities=26%  Similarity=0.408  Sum_probs=17.4

Q ss_pred             EECCCCCCHHHHHHHHHHHCCCC
Q ss_conf             87589988889999998621242
Q T0567            29 LYGAPGTGRMTGARYLHQFGRNA   51 (145)
Q Consensus        29 i~Ge~GtGK~~~A~~iH~~s~~~   51 (145)
                      |.|-.|+||++.++.++..-...
T Consensus         1 ~EGiDGsGKtT~~~~L~~~l~~~   23 (186)
T PF02223_consen    1 FEGIDGSGKTTQAKLLKEALEER   23 (186)
T ss_dssp             EE--TT---HHHHHHHHHHHCCT
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             98998899999999999999872


No 90 
>PF04735 Baculo_helicase:  Baculovirus DNA helicase;  InterPro: IPR006824 This is a family of Baculovirus DNA helicases, which are essential for the initiation of viral DNA replication and may contribute to other functions, such as controlling the switch to the late phase and leading to the inhibition of host protein synthesis.; GO: 0003678 DNA helicase activity, 0019079 viral genome replication
Probab=68.52  E-value=1.1  Score=21.30  Aligned_cols=19  Identities=26%  Similarity=0.536  Sum_probs=17.3

Q ss_pred             CEEEECCCCCCHHHHHHHH
Q ss_conf             5898758998888999999
Q T0567            26 AVWLYGAPGTGRMTGARYL   44 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~i   44 (145)
                      -+.|.|+||+||+.+-+.+
T Consensus       881 clyL~g~PnsGKSSffeLL  899 (1173)
T PF04735_consen  881 CLYLTGKPNSGKSSFFELL  899 (1173)
T ss_pred             EEEECCCCCCCHHHHHHHH
T ss_conf             9992488999703499996


No 91 
>PF05872 DUF853:  Bacterial protein of unknown function (DUF853);  InterPro: IPR008571 Members of this family have a P-loop containing nucleotide triphosphate hydrolases fold. This family is restricted to bacterial proteins, none of which have currently been characterised.
Probab=67.48  E-value=1.3  Score=21.00  Aligned_cols=36  Identities=19%  Similarity=0.134  Sum_probs=21.4

Q ss_pred             CCCCCEEEECCCCCCHHHHHHHHHHHCCCCCCCCCE
Q ss_conf             479958987589988889999998621242678524
Q T0567            22 ETDIAVWLYGAPGTGRMTGARYLHQFGRNAQGEFVY   57 (145)
Q Consensus        22 ~~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~   57 (145)
                      ..+.|=||.|.+||||+..-+.+.+.=.++.-|.+.
T Consensus        17 ~~NRHGLIaGATGTGKTvTLq~lAE~fS~~GVPVf~   52 (502)
T PF05872_consen   17 MANRHGLIAGATGTGKTVTLQVLAEQFSRAGVPVFL   52 (502)
T ss_pred             HHHHCCEEECCCCCCCCHHHHHHHHHHHHCCCCEEE
T ss_conf             740103552256788410599999998655994897


No 92 
>PF00265 TK:  Thymidine kinase;  InterPro: IPR001267   Thymidine kinase (TK) (2.7.1.21 from EC) is an ubiquitous enzyme that catalyzes the ATP-dependent phosphorylation of thymidine. Two different families of TK have been identified ,  and are included in this family; one family groups together TK from herpesviruses as well as cellular thymidylate kinases and the second family groups TK from various sources that include, vertebrates, bacteria, the Bacteriophage T4, poxviruses, African swine fever virus (ASFV) and Fish lymphocystis disease virus (FLDV). The major capsid protein of insect iridescent viruses also belongs to this family. The Prosite pattern recognises only the cellular type of thymidine kinases.; GO: 0004797 thymidine kinase activity, 0005524 ATP binding; PDB: 2j87_C 1w4r_G 1xbt_H 2orv_A 1xx6_B 2ja1_A 2j9r_A 2uz3_D 2b8t_B 2qpo_C ....
Probab=67.27  E-value=3  Score=19.06  Aligned_cols=78  Identities=14%  Similarity=0.249  Sum_probs=42.1

Q ss_pred             EEEECCCCCCHHH-HHHHHHHHCCCCCCCCCEEC--------------------CCCCCHHHHHHHHHHHC--CCEEEEC
Q ss_conf             8987589988889-99999862124267852412--------------------57889888899998625--8748743
Q T0567            27 VWLYGAPGTGRMT-GARYLHQFGRNAQGEFVYRE--------------------LTPDNAPQLNDFIALAQ--GGTLVLS   83 (145)
Q Consensus        27 vli~Ge~GtGK~~-~A~~iH~~s~~~~~~fv~~~--------------------~~~~~~~~~~~~l~~a~--gGtL~l~   83 (145)
                      .+++|+..+||++ +-+.+|.........++..+                    |.......+.+......  -.++++|
T Consensus         4 ~~i~GpMfSGKS~~Li~~~~~~~~~~~kv~~~kp~~D~R~~~~~I~sr~g~~~~~~~~~~~~~~~i~~~~~~~~d~I~ID   83 (176)
T PF00265_consen    4 EFITGPMFSGKSTELIRRAHRYEIAGKKVLVFKPAIDTRYGENKIVSRDGIEIEAIVDPIDNFEEIIKYLENDYDVIAID   83 (176)
T ss_dssp             EEEE--TT---HHHHHHHHHHHHCTT-BEEEEEESTSCCCCSSEEEHHHCCEEEEESSEESSGGGGHGGCCTTBSEEEEC
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHCCCEEEEEEECCCCCCCCCEEECCCCCCCCCEECCCCCHHHHHHHHHCCCCEEEEC
T ss_conf             99988888824899999999998789979999845447789985986889855543226236999999885489999980


Q ss_pred             CHHHCCHHHHHHHHHHHHHCCH
Q ss_conf             7420687789999999872140
Q T0567            84 HPEHLTREQQYHLVQLQSQEHR  105 (145)
Q Consensus        84 ei~~L~~~~Q~~L~~~l~~~~~  105 (145)
                      |++-++ ++=..+.+.+.+...
T Consensus        84 EaQFf~-~~i~~~~~~~~~~g~  104 (176)
T PF00265_consen   84 EAQFFD-EQIVQLCDILADKGI  104 (176)
T ss_dssp             SGGGST-TTHHHHHHHHHH---
T ss_pred             CHHHCC-HHHHHHHHHHHHCCC
T ss_conf             056273-789999999997799


No 93 
>PF02492 cobW:  CobW/HypB/UreG, nucleotide-binding domain;  InterPro: IPR003495   Cobalamin (vitamin B12) is a structurally complex cofactor, consisting of a modified tetrapyrrole with a centrally chelated cobalt. Cobalamin is usually found in one of two biologically active forms: methylcobalamin and adocobalamin. Most prokaryotes, as well as animals, have cobalamin-dependent enzymes, whereas plants and fungi do not appear to use it. In bacteria and archaea, these include methionine synthase, ribonucleotide reductase, glutamate and methylmalonyl-CoA mutases, ethanolamine ammonia lyase, and diol dehydratase . In mammals, cobalamin is obtained through the diet, and is required for methionine synthase and methylmalonyl-CoA mutase .    There are at least two distinct cobalamin biosynthetic pathways in bacteria :  Aerobic pathway that requires oxygen and in which cobalt is inserted late in the pathway ; found in Pseudomonas denitrificans and Rhodobacter capsulatus. Anaerobic pathway in which cobalt insertion is the first committed step towards cobalamin synthesis ; found in Salmonella typhimurium, Bacillus megaterium, and Propionibacterium freudenreichii shermanii.     Either pathway can be divided into two parts: (1) corrin ring synthesis (differs in aerobic and anaerobic pathways) and (2) adenosylation of corrin ring, attachment of aminopropanol arm, and assembly of the nucleotide loop (common to both pathways) . There are about 30 enzymes involved in either pathway, where those involved in the aerobic pathway are prefixed Cob and those of the anaerobic pathway Cbi. Several of these enzymes are pathway-specific: CbiD, CbiG, and CbiK are specific to the anaerobic route of S. typhimurium, whereas CobE, CobF, CobG, CobN, CobS, CobT, and CobW are unique to the aerobic pathway of P. denitrificans.   CobW proteins are generally found proximal to the trimeric cobaltochelatase subunit CobN, which is essential for vitamin B12 (cobalamin) biosynthesis . They contain a P-loop nucleotide-binding loop in the N-terminal domain and a histidine-rich region in the C-terminal portion suggesting a role in metal binding, possibly as an intermediary between the cobalt transport and chelation systems. CobW might be involved in cobalt reduction leading to cobalt(I) corrinoids.   This entry represents CobW-like proteins, including P47K (P31521 from SWISSPROT), a Pseudomonas chlororaphis protein needed for nitrile hydratase expression , and urease accessory protein UreG, which acts as a chaperone in the activation of urease upon insertion of nickel into the active site . ; PDB: 2hf9_B 2hf8_B 1nij_A.
Probab=64.10  E-value=2  Score=19.95  Aligned_cols=20  Identities=25%  Similarity=0.277  Sum_probs=16.4

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q ss_conf             89875899888899999986
Q T0567            27 VWLYGAPGTGRMTGARYLHQ   46 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~   46 (145)
                      ++|+|-.|+||+++-+.+-.
T Consensus         3 ~iitGfLGsGKTTll~~ll~   22 (173)
T PF02492_consen    3 TIITGFLGSGKTTLLNHLLK   22 (173)
T ss_dssp             EEEE-------HHHHHHHHH
T ss_pred             EEEECCCCCHHHHHHHHHHH
T ss_conf             99983898849999999998


No 94 
>PF02689 Herpes_Helicase:  Helicase;  InterPro: IPR003840 Helicases from the Herpesviridae are responsible for the unwinding of DNA and are essential for replication and completion of the viral life cycle.; GO: 0004386 helicase activity, 0005524 ATP binding, 0019079 viral genome replication
Probab=62.56  E-value=1.8  Score=20.27  Aligned_cols=20  Identities=25%  Similarity=0.473  Sum_probs=18.0

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q ss_conf             89875899888899999986
Q T0567            27 VWLYGAPGTGRMTGARYLHQ   46 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~   46 (145)
                      .||+|-+|+||++.-..+|+
T Consensus        62 yLITGtAGaGKSTsIq~L~~   81 (816)
T PF02689_consen   62 YLITGTAGAGKSTSIQTLAE   81 (816)
T ss_pred             EEEECCCCCCCHHHHHHHHH
T ss_conf             99953788872208999986


No 95 
>PF04670 Gtr1_RagA:  Gtr1/RagA G protein conserved region;  InterPro: IPR006762   GTR1 was first identified in Saccharomyces cerevisiae as a suppressor of a mutation in RCC1. RCC1 catalyzes guanine nucleotide exchange on Ran, a well characterised nuclear Ras-like small G protein that plays an essential role in the import and export of proteins and RNAs across the nuclear membrane through the nuclear pore complex. RCC1 is located inside the nucleus, bound to chromatin. The concentration of GTP within the cell is ~30 times higher than the concentration of GDP, thus resulting in the preferential production of the GTP form of Ran by RCC1 within the nucleus.   Gtr1p is located within both the cytoplasm and the nucleus and has been reported to play a role in cell growth. Biochemical analysis revealed that Gtr1 is in fact a G protein of the Ras family. The RagA/B proteins are the human homologues of Gtr1 and Rag A and Gtr1p belong to the sixth subfamily of the Ras-like small GTPase superfamily . ; GO: 0005525 GTP binding, 0005634 nucleus, 0005737 cytoplasm; PDB: 2q3f_B.
Probab=62.21  E-value=2  Score=19.98  Aligned_cols=20  Identities=20%  Similarity=0.458  Sum_probs=17.8

Q ss_pred             EEEECCCCCCHHHHHHHHHH
Q ss_conf             89875899888899999986
Q T0567            27 VWLYGAPGTGRMTGARYLHQ   46 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH~   46 (145)
                      ||+.|..|+||+.+=+.|.+
T Consensus         2 iLLMG~~~sGKsSm~~iIF~   21 (231)
T PF04670_consen    2 ILLMGLSGSGKSSMRSIIFS   21 (231)
T ss_dssp             EEEE--TT---HHHHHHHHC
T ss_pred             EEEECCCCCCCHHHHHHHHC
T ss_conf             79972799983025989876


No 96 
>PF05783 DLIC:  Dynein light intermediate chain (DLIC);  InterPro: IPR008467 This family consists of several eukaryotic dynein light intermediate chain proteins. The light intermediate chains (LICs) of cytoplasmic dynein consist of multiple isoforms, which undergo post-translational modification to produce a large number of species. DLIC1 is known to be involved in assembly, organisation, and function of centrosomes and mitotic spindles when bound to pericentrin. DLIC2 is a subunit of cytoplasmic dynein 2 that may play a role in maintaining Golgi organisation by binding cytoplasmic dynein 2 to its Golgi-associated cargo .; GO: 0003774 motor activity
Probab=60.56  E-value=3.7  Score=18.56  Aligned_cols=39  Identities=15%  Similarity=0.198  Sum_probs=25.5

Q ss_pred             HHHHHHHHHHHHH----CCCCCEEEECCCCCCHHHHHHHHHHH
Q ss_conf             9999999999861----47995898758998888999999862
Q T0567             9 WINQYRRRLQQLS----ETDIAVWLYGAPGTGRMTGARYLHQF   47 (145)
Q Consensus         9 ~m~~l~~~i~~~a----~~~~pvli~Ge~GtGK~~~A~~iH~~   47 (145)
                      ....+...+..-+    .....|++.|..|+||+++...+...
T Consensus        25 LWssiL~eV~~~~~~klps~K~IlVLG~~~sGKsTLi~kLq~~   67 (489)
T PF05783_consen   25 LWSSILSEVSTRSSSKLPSEKNILVLGSKGSGKSTLINKLQGR   67 (489)
T ss_pred             HHHHHHHHHHHHHCCCCCCCCEEEEECCCCCCHHHHHHHHCCC
T ss_conf             9999999986420135888872899678987518889885387


No 97 
>PF01656 CbiA:  CobQ/CobB/MinD/ParA nucleotide binding domain;  InterPro: IPR002586 This entry consists of various cobyrinic acid a,c-diamide synthases. These include CbiA and CbiP from Salmonella typhimurium ., and CobQ from Rhodobacter capsulatus . These amidases catalyse amidations to various side chains of hydrogenobyrinic acid or cobyrinic acid a,c-diamide in the biosynthesis of cobalamin (vitamin B12) from uroporphyrinogen III. Vitamin B12 is an important cofactor and an essential nutrient for many plants and animals and is primarily produced by bacteria .; GO: 0042242 cobyrinic acid a,c-diamide synthase activity, 0009236 cobalamin biosynthetic process; PDB: 2oze_A 3cwq_A 3ez6_B 3ez7_A 3ez2_B 3ezf_A 3ez9_B 1dah_A 1dag_A 1bs1_A ....
Probab=58.32  E-value=3.6  Score=18.59  Aligned_cols=35  Identities=23%  Similarity=0.149  Sum_probs=24.1

Q ss_pred             EEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCCC
Q ss_conf             98758998888999999862124267852412578
Q T0567            28 WLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELTP   62 (145)
Q Consensus        28 li~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~~   62 (145)
                      +..+..|+||+++|..+-..-.+...+...+||..
T Consensus         3 v~~~kGGvGKTt~a~~la~~la~~g~~Vl~iD~D~   37 (194)
T PF01656_consen    3 VTSTKGGVGKTTIAANLAQALARKGKRVLLIDLDP   37 (194)
T ss_dssp             EEESSTT-HHHHHHHHHHHHHHHTT--EEEEECCT
T ss_pred             EECCCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCC
T ss_conf             98489998789999999999864302324435787


No 98 
>PF00503 G-alpha:  G-protein alpha subunit;  InterPro: IPR001019   Guanine nucleotide binding proteins (G proteins) are membrane-associated, heterotrimeric proteins composed of three subunits: alpha (IPR001019 from INTERPRO), beta (IPR001632 from INTERPRO) and gamma (IPR001770 from INTERPRO) . G proteins and their receptors (GPCRs) form one of the most prevalent signalling systems in mammalian cells, regulating systems as diverse as sensory perception, cell growth and hormonal regulation . At the cell surface, the binding of ligands such as hormones and neurotransmitters to a GPCR activates the receptor by causing a conformational change, which in turn activates the bound G protein on the intracellular-side of the membrane. The activated receptor promotes the exchange of bound GDP for GTP on the G protein alpha subunit. GTP binding changes the conformation of switch regions within the alpha subunit, which allows the bound trimeric G protein (inactive) to be released from the receptor, and to dissociate into active alpha subunit (GTP-bound) and beta/gamma dimer. The alpha subunit and the beta/gamma dimer go on to activate distinct downstream effectors, such as adenylyl cyclase, phosphodiesterases, phospholipase C, and ion channels. These effectors in turn regulate the intracellular concentrations of secondary messengers, such as cAMP, diacylglycerol, sodium or calcium cations, which ultimately lead to a physiological response, usually via the downstream regulation of gene transcription. The cycle is completed by the hydrolysis of alpha subunit-bound GTP to GDP, resulting in the re-association of the alpha and beta/gamma subunits and their binding to the receptor, which terminates the signal . The length of the G protein signal is controlled by the duration of the GTP-bound alpha subunit, which can be regulated by RGS (regulator of G protein signalling) proteins (IPR000342 from INTERPRO) or by covalent modifications .   There are several isoforms of each subunit, many of which have splice variants, which together can make up hundreds of combinations of G proteins. The specific combination of subunits in heterotrimeric G proteins affects not only which receptor it can bind to, but also which downstream target is affected, providing the means to target specific physiological processes in response to specific external stimuli , . G proteins carry lipid modifications on one or more of their subunits to target them to the plasma membrane and to contribute to protein interactions.   This family consists of the G protein alpha subunit, which acts as a weak GTPase. G protein classes are defined based on the sequence and function of their alpha subunits, which in mammals fall into four main categories: G(S)alpha, G(Q)alpha, G(I)alpha and G(12)alpha; there are also fungal and plant classes of alpha subunits. The alpha subunit consists of two domains: a GTP-binding domain and a helical insertion domain (IPR011025 from INTERPRO). The GTP-binding domain is homologous to Ras-like small GTPases, and includes switch regions I and II, which change conformation during activation. The switch regions are loops of alpha-helices with conformations sensitive to guanine nucleotides. The helical insertion domain is inserted into the GTP-binding domain before switch region I and is unique to heterotrimeric G proteins. This helical insertion domain functions to sequester the guanine nucleotide at the interface with the GTP-binding domain and must be displaced to enable nucleotide dissociation.; GO: 0004871 signal transducer activity, 0019001 guanyl nucleotide binding, 0007186 G-protein coupled receptor protein signaling pathway; PDB: 2ode_A 2ihb_A 2v4z_A 1shz_D 1gp2_A 1as2_A 1gfi_A 1cip_A 1svk_A 1as3_A ....
Probab=56.02  E-value=1.3  Score=21.07  Aligned_cols=38  Identities=24%  Similarity=0.427  Sum_probs=24.9

Q ss_pred             HHHHHHHHHH---HCCCCCEEEECCCCCCHHHHHH---HHHHHC
Q ss_conf             9999999986---1479958987589988889999---998621
Q T0567            11 NQYRRRLQQL---SETDIAVWLYGAPGTGRMTGAR---YLHQFG   48 (145)
Q Consensus        11 ~~l~~~i~~~---a~~~~pvli~Ge~GtGK~~~A~---~iH~~s   48 (145)
                      +++-+++++-   .....-+|+.|...|||+++.+   .||..+
T Consensus        11 ~~Idk~l~~~k~~~~~~iKlLLLG~gESGKSTi~KQmrii~~~g   54 (350)
T PF00503_consen   11 KEIDKQLKKEKKKEKREIKLLLLGAGESGKSTILKQMRIIHGNG   54 (350)
T ss_dssp             HHHHHHHHHHCCHHCEEEEEEEE-HTTHHHHHHHHHHHHHHTHH
T ss_pred             HHHHHHHHHHHHHHHHHHHEEEECCCCCCHHHHHHHHHHHHCCC
T ss_conf             99999999989875401226653157764287998898761676


No 99 
>PF01591 6PF2K:  6-phosphofructo-2-kinase;  InterPro: IPR013079   6-Phosphofructo-2-kinase (, ) is a bifunctional enzyme that catalyses both the synthesis and the degradation of fructose-2, 6-bisphosphate. The fructose-2,6-bisphosphatase reaction involves a phosphohistidine intermediate. The catalytic pathway is:  ATP + D-fructose 6-phosphate = ADP + D-fructose 2,6-bisphosphate   D-fructose 2,6-bisphosphate + H_2O = 6-fructose 6-phosphate + P_i  The enzyme is important in the regulation of hepatic carbohydrate metabolism and is found in greatest quantities in the liver, kidney and heart. In mammals, several genes often encode different isoforms, each of which differs in its tissue distribution and enzymatic activity . The family described here bears a resemblance to the ATP-driven phospho-fructokinases, however, they share little sequence similarity, although a few residues seem key to their interaction with fructose 6-phosphate .   This domain forms the N-terminal region of this enzyme, while IPR013078 from INTERPRO forms the C-terminal domain.; PDB: 2dwo_A 2dwp_A 2i1v_B 2axn_A 3bif_A 2bif_A 1bif_A 1k6m_A.
Probab=53.54  E-value=6  Score=17.43  Aligned_cols=86  Identities=15%  Similarity=0.223  Sum_probs=45.4

Q ss_pred             CCCCEEEECCCCCCHHHHHHHHHHHCCCCC---CCCCE----------------ECCCCCCHH------------HHHHH
Q ss_conf             799589875899888899999986212426---78524----------------125788988------------88999
Q T0567            23 TDIAVWLYGAPGTGRMTGARYLHQFGRNAQ---GEFVY----------------RELTPDNAP------------QLNDF   71 (145)
Q Consensus        23 ~~~pvli~Ge~GtGK~~~A~~iH~~s~~~~---~~fv~----------------~~~~~~~~~------------~~~~~   71 (145)
                      ...-|.+.|=|++||+++|+.|-..-....   .-|-.                .+.......            ++..+
T Consensus        11 ~klvVvmVGLPArGKS~ia~kL~ryL~w~g~~~kvFnvG~yRR~~~~~~~~~~ff~p~n~~~~~~R~~~a~~~l~d~~~~   90 (222)
T PF01591_consen   11 GKLVVVMVGLPARGKSYIAKKLCRYLNWLGVKTKVFNVGNYRRKLSGAPADAEFFDPNNEEAVKLREQIARAALEDMLNF   90 (222)
T ss_dssp             --EEEEEE--TT---HHHHHHHHHHHHH----EEEEE---HHHHHCSS-S-GGGGSTT-HHHHHHHHHHHHHHHHHHHHH
T ss_pred             CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCEEEEHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98899997888887778999999998545898547568887664402565211369988889999999999999999999


Q ss_pred             HHHHCCCEEEECCHHHCCHHHHHHHHHHHHHCCHHHEEEE
Q ss_conf             9862587487437420687789999999872140100111
Q T0567            72 IALAQGGTLVLSHPEHLTREQQYHLVQLQSQEHRPFRLIG  111 (145)
Q Consensus        72 l~~a~gGtL~l~ei~~L~~~~Q~~L~~~l~~~~~~~RiI~  111 (145)
                      +....|.+-++| .-.-+.+....+.+.+....  +++++
T Consensus        91 l~~~~G~VaI~D-AtN~T~~rR~~i~~~~~~~~--~~vlF  127 (222)
T PF01591_consen   91 LNEEGGQVAIFD-ATNSTRERRKWILEEFRERG--IKVLF  127 (222)
T ss_dssp             HHT----EEEEE-S---SHHHHHHHHHHHHHCT---EEEE
T ss_pred             HHHCCCEEEEEE-CCCCCHHHHHHHHHHHHHCC--CEEEE
T ss_conf             964897299997-88899999999999987639--82999


No 100
>PF02399 Herpes_ori_bp:  Origin of replication binding protein;  InterPro: IPR003450 This family represents the Herpesviridae origin of replication binding protein, probably involved in DNA replication.; GO: 0003688 DNA replication origin binding, 0005524 ATP binding, 0006260 DNA replication
Probab=52.42  E-value=6.2  Score=17.33  Aligned_cols=35  Identities=11%  Similarity=0.134  Sum_probs=24.6

Q ss_pred             EEEECCCCCCHHH-HHHHHHHHCCCCCCCCCEECCC
Q ss_conf             8987589988889-9999986212426785241257
Q T0567            27 VWLYGAPGTGRMT-GARYLHQFGRNAQGEFVYRELT   61 (145)
Q Consensus        27 vli~Ge~GtGK~~-~A~~iH~~s~~~~~~fv~~~~~   61 (145)
                      +++.-+.||||++ +-+++-+.-...+..++.+.|.
T Consensus        52 ~vVKApMGSGKTTaLi~wL~~~l~~~d~~vLvvShR   87 (824)
T PF02399_consen   52 LVVKAPMGSGKTTALIKWLQDALGAPDESVLVVSHR   87 (824)
T ss_pred             EEEECCCCCCCHHHHHHHHHHHHHCCCCCEEEEEHH
T ss_conf             899878888748999999998721789818998479


No 101
>PF03464 eRF1_2:  eRF1 domain 2;  InterPro: IPR005141    This domain is found in the release factor eRF1 which terminates protein biosynthesis by recognizing stop codons at the A site of the ribosome and stimulating peptidyl-tRNA bond hydrolysis at the peptidyl transferase centre. The crystal structure of human eRF1 is known . The overall shape and dimensions of eRF1 resemble a tRNA molecule with domains 1, 2, and 3 of eRF1 corresponding to the anticodon loop, aminoacyl acceptor stem, and T stem of a tRNA molecule, respectively. The position of the essential GGQ motif at an exposed tip of domain 2 suggests that the Gln residue coordinates a water molecule to mediate the hydrolytic activity at the peptidyl transferase centre. A conserved groove on domain 1, 80 A from the GGQ motif, is proposed to form the codon recognition site .   This domain is also found in other proteins which may also be involved in translation termination ; PDB: 2vgn_A 2vgm_A 2qi2_A 3e1y_D 2hst_A 1dt9_A.
Probab=48.30  E-value=7.3  Score=16.96  Aligned_cols=51  Identities=12%  Similarity=0.160  Sum_probs=41.2

Q ss_pred             CCCEEEECCCCCCHHHHHHHHHHHCCCCC-CCCCEECCCCCCHHHHHHHHHH
Q ss_conf             99589875899888899999986212426-7852412578898888999986
Q T0567            24 DIAVWLYGAPGTGRMTGARYLHQFGRNAQ-GEFVYRELTPDNAPQLNDFIAL   74 (145)
Q Consensus        24 ~~pvli~Ge~GtGK~~~A~~iH~~s~~~~-~~fv~~~~~~~~~~~~~~~l~~   74 (145)
                      +...+|.+-||--|+.++++++...++.. ..++.+++..-....+.+.+..
T Consensus        73 ~~~~iiiaGPGf~k~~F~~~~~~~~~~~~~~~~~~~~~s~~~~~gl~EvL~~  124 (133)
T PF03464_consen   73 KVKCIIIAGPGFTKDDFYEYLKLEAPRKKKKKIVVVHTSSGGEHGLREVLKR  124 (133)
T ss_dssp             T-SEEEEEE-TTHHHHHHHHHHHHHHHHT-T-EEEEE-SSS----HHHHHHC
T ss_pred             CCCEEEEECCHHHHHHHHHHHHHHHHHHCCCEEEEEECCCCCHHHHHHHHHH
T ss_conf             5558999898899999999888766762288799998798867899999996


No 102
>PF00225 Kinesin:  Kinesin motor domain;  InterPro: IPR001752   Kinesin , ,  is a microtubule-associated force-producing protein that may play a role in organelle transport. The kinesin motor activity is directed toward the microtubule's plus end. Kinesin is an oligomeric complex composed of two heavy chains and two light chains. The maintenance of the quaternary structure does not require interchain disulphide bonds.   The heavy chain is composed of three structural domains: a large globular N-terminal domain which is responsible for the motor activity of kinesin (it is known to hydrolyze ATP, to bind and move on microtubules), a central alpha-helical coiled coil domain that mediates the heavy chain dimerization; and a small globular C-terminal domain which interacts with other proteins (such as the kinesin light chains), vesicles and membranous organelles.   A number of proteins have been recently found that contain a domain similar to that of the kinesin 'motor' domain , :  Drosophila melanogaster claret segregational protein (ncd). Ncd is required for normal chromosomal segregation in meiosis, in females, and in early mitotic divisions of the embryo. The ncd motor activity is directed toward the microtubule's minus end. Homo sapiens CENP-E . CENP-E is a protein that associates with kinetochores during chromosome congression, relocates to the spindle midzone at anaphase, and is quantitatively discarded at the end of the cell division. CENP-E is probably an important motor molecule in chromosome movement and/or spindle elongation. H. sapiens mitotic kinesin-like protein-1 (MKLP-1), a motor protein whose activity is directed toward the microtubule's plus end. Saccharomyces cerevisiae KAR3 protein, which is essential for Saccharomyces cerevisiae nuclear fusion during mating. KAR3 may mediate microtubule sliding during nuclear fusion and possibly mitosis. S. cerevisiae CIN8 and KIP1 proteins which are required for the assembly of the mitotic spindle. Both proteins seem to interact with spindle microtubules to produce an outwardly directed force acting upon the poles. Aspergillus nidulans bimC, which plays an important role in nuclear division. A. nidulans klpA. Caenorhabditis elegans unc-104, which may be required for the transport of substances needed for neuronal cell differentiation. C. elegans osm-3. Xenopus laevis Eg5, which may be involved in mitosis. Arabidopsis thaliana KatA, KatB and katC. Chlamydomonas reinhardtii FLA10/KHP1 and KLP1. Both proteins seem to play a role in the rotation or twisting of the microtubules of the flagella. Caenorhabditis elegans hypothetical protein T09A5.2.    The kinesin motor domain is located in the N-terminal part of most of the above proteins, with the exception of KAR3, klpA, and ncd where it is located in the C-terminal section.   The kinesin motor domain contains about 330 amino acids. An ATP-binding motif of type A is found near position 80 to 90, the C-terminal half of the domain is involved in microtubule-binding.; GO: 0003777 microtubule motor activity, 0005524 ATP binding, 0007018 microtubule-based movement, 0005875 microtubule associated complex; PDB: 1goj_A 3kin_D 2kin_B 1mkj_A 2p4n_K 1bg2_A 2nr8_A 3cnz_A 3cob_C 1sdm_A ....
Probab=47.72  E-value=3.1  Score=18.96  Aligned_cols=18  Identities=22%  Similarity=0.630  Sum_probs=14.2

Q ss_pred             CCCCCEEEECCCCCCHHH
Q ss_conf             479958987589988889
Q T0567            22 ETDIAVWLYGAPGTGRMT   39 (145)
Q Consensus        22 ~~~~pvli~Ge~GtGK~~   39 (145)
                      -.+.-|+-+|.+||||+.
T Consensus        72 G~n~~i~aYGqtgSGKTy   89 (333)
T PF00225_consen   72 GYNATIFAYGQTGSGKTY   89 (333)
T ss_dssp             --EEEEEEE--TT---HH
T ss_pred             CCCEEEECCCCCCCCCCE
T ss_conf             982367636778888843


No 103
>PF00350 Dynamin_N:  Dynamin family;  InterPro: IPR001401   Membrane transport between compartments in eukaryotic cells requires proteins that allow the budding and scission of nascent cargo vesicles from one compartment and their targeting and fusion with another. Dynamins are large GTPases that belong to a protein superfamily  that, in eukaryotic cells, includes classical dynamins, dynamin-like proteins, OPA1, Mx proteins, mitofusins and guanylate-binding proteins/atlastins , , , , and are involved in the scission of a wide range of vesicles and organelles. They play a role in many processes including budding of transport vesicles, division of organelles, cytokinesis and pathogen resistance.     The minimal distinguishing architectural features that are common to all dynamins and are distinct from other GTPases are the structure of the large GTPase domain (300 amino acids) and the presence of two additional domains; the middle domain and the GTPase effector domain (GED), which are involved in oligomerization and regulation of the GTPase activity.   This entry represents the GTPase domain, containing the GTP-binding motifs that are needed for guanine-nucleotide binding and hydrolysis. The conservation of these motifs is absolute except for the the final motif in guanylate-binding proteins. The GTPase catalytic activity can be stimulated by oligomerisation of the protein, which is mediated by interactions between the GTPase domain, the middle domain and the GED.; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2aka_B 1jwy_B 1jx2_B 2qpt_A 2j69_D 2j68_A.
Probab=45.71  E-value=5.1  Score=17.79  Aligned_cols=19  Identities=21%  Similarity=0.163  Sum_probs=17.0

Q ss_pred             EEEECCCCCCHHHHHHHHH
Q ss_conf             8987589988889999998
Q T0567            27 VWLYGAPGTGRMTGARYLH   45 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH   45 (145)
                      |.+.|+.++||+++-.+|-
T Consensus         1 I~vvG~~saGKStlINaLl   19 (168)
T PF00350_consen    1 IAVVGQFSAGKSTLINALL   19 (168)
T ss_dssp             EEEE--TT---HHHHHHHH
T ss_pred             CEEECCCCCCHHHHHHHHH
T ss_conf             9897479896899999997


No 104
>PF02421 FeoB_N:  Ferrous iron transport protein B;  InterPro: IPR011619    Escherichia coli has an iron(II) transport system (feo) which may make an important contribution to the iron supply of the cell under anaerobic conditions. FeoB has been identified as part of this transport system and may play a role in the transport of ferrous iron. FeoB is a large 700-800 amino acid integral membrane protein. The N terminus contains a P-loop motif suggesting that iron transport may be ATP dependent .; GO: 0005525 GTP binding, 0015093 ferrous iron transmembrane transporter activity, 0015684 ferrous iron transport, 0009276 1-2nm peptidoglycan-based cell wall, 0016021 integral to membrane
Probab=42.94  E-value=7.5  Score=16.89  Aligned_cols=21  Identities=29%  Similarity=0.328  Sum_probs=18.2

Q ss_pred             CEEEECCCCCCHHHHHHHHHH
Q ss_conf             589875899888899999986
Q T0567            26 AVWLYGAPGTGRMTGARYLHQ   46 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~   46 (145)
                      -|.+.|.|.+||+++-..+-.
T Consensus         2 ~ialvG~PN~GKStlfN~LtG   22 (188)
T PF02421_consen    2 RIALVGNPNVGKSTLFNALTG   22 (188)
T ss_pred             EEEEECCCCCCHHHHHHHHHC
T ss_conf             899978999889999999968


No 105
>PF07960 CBP4:  CBP4;  InterPro: IPR012420   The CBP4 gene in Saccharomyces cerevisiae is essential for the expression and activity of ubiquinol-cytochrome c reductase , . This family appears to be fungal specific. 
Probab=39.11  E-value=6.9  Score=17.09  Aligned_cols=30  Identities=17%  Similarity=0.404  Sum_probs=24.2

Q ss_pred             HHHHHHHHHHHHHCCCCCEEEECCCCC--CHH
Q ss_conf             999999999986147995898758998--888
Q T0567             9 WINQYRRRLQQLSETDIAVWLYGAPGT--GRM   38 (145)
Q Consensus         9 ~m~~l~~~i~~~a~~~~pvli~Ge~Gt--GK~   38 (145)
                      ..+.+..+++..|.+|.||+..|+.++  .+.
T Consensus        58 Efde~v~~lKe~skSdkpIW~~~~iesp~E~~   89 (128)
T PF07960_consen   58 EFDEFVKILKETSKSDKPIWKAGPIESPWEKK   89 (128)
T ss_pred             HHHHHHHHHHHHHCCCCCHHHCCCCCCCHHHH
T ss_conf             99999999999700478622326755827788


No 106
>PF04275 P-mevalo_kinase:  Phosphomevalonate kinase ;  InterPro: IPR005919    Phosphomevalonate kinase (2.7.4.2 from EC) catalyzes the phosphorylation of 5-phosphomevalonate into 5-diphosphomevalonate, an essential step in isoprenoid biosynthesis via the mevalonate pathway. In an example of nonorthologous gene displacement, two different types of phosphomevalonate kinase are found - the higher eukaryotic form and the ERG8 type. This model represents the form of the enzyme found in animals.  ; GO: 0004631 phosphomevalonate kinase activity, 0006695 cholesterol biosynthetic process, 0005737 cytoplasm; PDB: 3ch4_B.
Probab=35.19  E-value=8.8  Score=16.52  Aligned_cols=19  Identities=21%  Similarity=0.146  Sum_probs=16.7

Q ss_pred             EECCCCCCHHHHHHHHHHH
Q ss_conf             8758998888999999862
Q T0567            29 LYGAPGTGRMTGARYLHQF   47 (145)
Q Consensus        29 i~Ge~GtGK~~~A~~iH~~   47 (145)
                      |.|..++||..+|..+...
T Consensus         1 ~sGKrksGKDy~a~~l~~~   19 (116)
T PF04275_consen    1 FSGKRKSGKDYCAERLVSR   19 (116)
T ss_dssp             EE--TT---HHHHHHHHHH
T ss_pred             CCCCCCCCCHHHHHHHHHH
T ss_conf             9987667715899999999


No 107
>PF00142 Fer4_NifH:  4Fe-4S iron sulfur cluster binding proteins, NifH/frxC family;  InterPro: IPR000392 Nitrogen fixing bacteria possess a nitrogenase enzyme complex  that comprises 2 components, which catalyse the reduction of molecular nitrogen to ammonia , : component I (nitrogenase MoFe protein or dinitrogenase) contains 2 molecules each of 2 non-identical subunits; component II (nitrogenase Fe protein or dinitrogenase reductase) is a homodimer, the monomer being coded for by the nifH gene . Component II has 2 ATP-binding domains and one 4Fe-4S cluster per homodimer: it supplies energy by ATP hydrolysis, and transfers electrons from reduced ferredoxin or flavodoxin to component I for the reduction of molecular nitrogen to ammonia . There are a number of conserved regions in the sequence of these proteins: in the N-terminal section there is an ATP-binding site motif 'A' (P-loop) IPR001687 from INTERPRO and in the central section there are two conserved cysteines which have been shown, in nifH, to be the ligands of the 4Fe-4S cluster.; GO: 0005524 ATP binding, 0016491 oxidoreductase activity, 0006118 electron transport; PDB: 2afi_H 1g1m_A 2afk_E 1nip_B 2c8v_A 1de0_A 1fp6_B 1g20_F 1m1y_H 1m34_H ....
Probab=35.12  E-value=9  Score=16.46  Aligned_cols=36  Identities=17%  Similarity=0.182  Sum_probs=22.4

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHCCCCCCCCCEECCC
Q ss_conf             589875899888899999986212426785241257
Q T0567            26 AVWLYGAPGTGRMTGARYLHQFGRNAQGEFVYRELT   61 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv~~~~~   61 (145)
                      .+-|+|.-|.||++++.-+-..-.........+.|.
T Consensus         2 ~IAiyGKGGIGKSTts~Nlsaala~~G~rVl~iGCD   37 (273)
T PF00142_consen    2 KIAIYGKGGIGKSTTSSNLSAALAEMGKRVLQIGCD   37 (273)
T ss_dssp             EEEEE-------HHHHHHHHHHHHH----EEEE-E-
T ss_pred             EEEEECCCCCCCCHHHHHHHHHHHHHCCCEEEEECC
T ss_conf             389975898676746689999998611315787402


No 108
>PF06144 DNA_pol3_delta:  DNA polymerase III, delta subunit;  InterPro: IPR010372   DNA polymerase III, delta subunit (2.7.7.7 from EC) is required for, along with delta' subunit, the assembly of the processivity factor beta(2) onto primed DNA in the DNA polymerase III holoenzyme-catalysed reaction . The delta subunit is also known as HolA.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0009360 DNA polymerase III complex; PDB: 1xxh_A 1jql_B 1jqj_C 3gli_A 3glf_F 3glh_A 1xxi_A 3glg_A 1jr3_D.
Probab=34.08  E-value=12  Score=15.70  Aligned_cols=38  Identities=11%  Similarity=0.098  Sum_probs=23.8

Q ss_pred             CCEEEECCH----HHCCHHHHHHHHHHHHHCCHHHEEEECCC
Q ss_conf             874874374----20687789999999872140100111477
Q T0567            77 GGTLVLSHP----EHLTREQQYHLVQLQSQEHRPFRLIGIGD  114 (145)
Q Consensus        77 gGtL~l~ei----~~L~~~~Q~~L~~~l~~~~~~~RiI~~s~  114 (145)
                      .-.+++++.    +..+...+..|.+++++...++.+|..+.
T Consensus        58 ~klvii~~~~~l~~~~~~~~~~~l~~~l~~~~~~~~lii~~~   99 (172)
T PF06144_consen   58 KKLVIIKNANFLKSKKSKKEIKELEEYLENPPPDTVLIIISP   99 (172)
T ss_dssp             SEEEEEE----------TTHHHHHHHH----BSSEEEEEE--
T ss_pred             CEEEEEECCCCCCCCCCHHHHHHHHHHHHCCCCCEEEEEEEC
T ss_conf             759999767533332448899999999846899879999926


No 109
>PF09818 ABC_ATPase:  Predicted ATPase of the ABC class
Probab=33.32  E-value=12  Score=15.85  Aligned_cols=19  Identities=21%  Similarity=0.170  Sum_probs=17.3

Q ss_pred             EEEECCCCCCHHHHHHHHH
Q ss_conf             8987589988889999998
Q T0567            27 VWLYGAPGTGRMTGARYLH   45 (145)
Q Consensus        27 vli~Ge~GtGK~~~A~~iH   45 (145)
                      .+|+|..+.||+++-++|.
T Consensus       247 tlivGgg~hGKSTLL~Al~  265 (448)
T PF09818_consen  247 TLIVGGGYHGKSTLLEALE  265 (448)
T ss_pred             EEEECCCCCCHHHHHHHHH
T ss_conf             9998899877899999998


No 110
>PF01293 PEPCK_ATP:  Phosphoenolpyruvate carboxykinase The Prosite pattern is specific to the ATP binding region;  InterPro: IPR001272    Phosphoenolpyruvate carboxykinase (PEPCK) catalyses the first committed (rate-limiting) step in hepatic gluconeogenesis, namely the reversible decarboxylation of oxaloacetate to phosphoenolpyruvate (PEP) and carbon dioxide, using either ATP or GTP as a source of phosphate. The ATP-utilising (4.1.1.49 from EC) and GTP-utilising (4.1.1.32 from EC) enzymes form two divergent subfamilies, which have little sequence similarity but which retain conserved active site residues. ATP-utilising PEPCKs are monomers or oligomers of identical subunits found in certain bacteria, yeast, trypanosomatids, and plants, while GTP-utilising PEPCKs are mainly monomers found in animals and some bacteria . Both require divalent cations for activity, such as magnesium or manganese. One cation interacts with the enzyme at metal binding site 1 to elicit activation, while the second cation interacts at metal binding site 2 to serve as a metal-nucleotide substrate. In bacteria, fungi and plants, PEPCK is involved in the glyoxylate bypass, an alternative to the tricarboxylic acid cycle.    PEPCK helps to regulate blood glucose levels. The rate of gluconeogenesis can be controlled through transcriptional regulation of the PEPCK gene by cAMP (the mediator of glucagon and catecholamines), glucocorticoids and insulin. In general, PEPCK expression is induced by glucagon, catecholamines and glucocorticoids during periods of fasting and in response to stress, but is inhibited by (glucose-induced) insulin upon feeding . With type II diabetes, this regulation system can fail, resulting in increased gluconeogenesis that in turn raises glucose levels .   PEPCK consists of an N-terminal and a catalytic C-terminal domain, with the active site and metal ions located in a cleft between them. Both domains have an alpha/beta topology that is partly similar to one another , . Substrate binding causes PEPCK to undergo a conformational change, which accelerates catalysis by forcing bulk solvent molecules out of the active site . PCK uses an alpha/beta/alpha motif for nucleotide binding, this motif differing from other kinase domains. GTP-utilising PEPCK has a PEP-binding domain and two kinase motifs to bind GTP and magnesium.   This entry represents ATP-utilising phosphoenolpyruvate carboxykinase enzymes.; GO: 0004612 phosphoenolpyruvate carboxykinase (ATP) activity, 0005524 ATP binding, 0006094 gluconeogenesis; PDB: 1j3b_B 2pc9_C 1xkv_B 1ygg_A 1ylh_A 2olq_A 2pxz_X 1ayl_A 1k3d_A 1aq2_A ....
Probab=29.07  E-value=8.9  Score=16.48  Aligned_cols=18  Identities=28%  Similarity=0.464  Sum_probs=15.2

Q ss_pred             CCEEEECCCCCCHHHHHH
Q ss_conf             958987589988889999
Q T0567            25 IAVWLYGAPGTGRMTGAR   42 (145)
Q Consensus        25 ~pvli~Ge~GtGK~~~A~   42 (145)
                      -..+++|=.||||+++..
T Consensus       211 d~alfFGLSGTGKTTLS~  228 (466)
T PF01293_consen  211 DVALFFGLSGTGKTTLSA  228 (466)
T ss_dssp             -EEEEE-------HHHHS
T ss_pred             CEEEEEEECCCCCCCCCC
T ss_conf             889999717789751014


No 111
>PF00693 Herpes_TK:  Thymidine kinase from herpesvirus;  InterPro: IPR001889   The thymidine kinase from Herpesviridae catalyses the reaction: ATP + THYMIDINE = ADP + THYMIDINE 5'-PHOSPHATE.  The enzyme is not subject to feedback inhibition by its product and the crystal structure of the enzyme from Human herpesvirus 1 (HHV-1) has been reported .; GO: 0004797 thymidine kinase activity, 0005524 ATP binding, 0006230 TMP biosynthetic process; PDB: 1e2j_A 2ki5_B 1e2p_B 1kim_B 1vtk_A 1e2n_B 1of1_B 2vtk_A 1ki3_A 1e2l_A ....
Probab=27.70  E-value=8.2  Score=16.67  Aligned_cols=19  Identities=32%  Similarity=0.350  Sum_probs=14.3

Q ss_pred             CCCCCCHHHHHHHHHHHCC
Q ss_conf             5899888899999986212
Q T0567            31 GAPGTGRMTGARYLHQFGR   49 (145)
Q Consensus        31 Ge~GtGK~~~A~~iH~~s~   49 (145)
                      |..|.||++.++.+-....
T Consensus         1 G~~GvGKTT~~~~l~~~~~   19 (281)
T PF00693_consen    1 GAMGVGKTTTLKALAEALP   19 (281)
T ss_dssp             -------HHHHHTTHHCCT
T ss_pred             CCCCCCHHHHHHHHHHHCC
T ss_conf             9987578999999997358


No 112
>PF08283 Gemini_AL1_M:  Geminivirus rep protein central domain;  InterPro: IPR001191 Geminiviruses are characterised by a genome of circular single-stranded DNA encapsidated in twinned (geminate) quasi-isometric particles, from which the group derives its name . Most geminiviruses can be divided into two subgroups on the basis of host range and/or insect vector: i.e.those that infect dicotyledenous plants and are transmitted by the same whitefly species, and those that infect monocotyledenous plants and are transmitted by different leafhopper vectors. The genomes of the whitefly-transmitted African cassava mosaic virus, Tomato golden mosaic virus (TGMV) and Bean golden mosaic virus (BGMV) possess a bipartite genome. By contrast, only a single DNA component has been identified for the leafhopper-transmitted Maize streak virus (MSV) and Wheat dwarf virus (WDV) , . Beet curly top virus (BCTV), and Tobacco yellow dwarf virus belong to a third possible subgroup. Like MSV and WDV, BCTV is transmitted by a specific leafhopper species, yet like the whitefly-transmitted geminiviruses it has a host range confined to dicotyledenous plants.   Sequence comparison of the whitefly-transmitted Squash leaf curl virus (SqLCV) and Tomato yellow leaf curl virus (TYLCV) with the genomic components of TGMV and BGMV reveals a close evolutionary relationship , , . Amino acid sequence alignments of Potato yellow mosaic viral (PYMV) proteins with those encoded by other geminiviruses show that PYMV is closely related to geminiviruses isolated from the New World, especially in the putative coat protein gene regions . Comparison of MSV DNA-encoded proteins with those of other geminiviruses infecting monocotyledonous plants, including Panicum streak virus  and Miscanthus streak virus (MiSV) , reveal high levels of similarity.    ; GO: 0005198 structural molecule activity, 0019028 viral capsid
Probab=22.63  E-value=11  Score=15.97  Aligned_cols=23  Identities=17%  Similarity=0.030  Sum_probs=15.0

Q ss_pred             EEECCHHHCCHHHHHHHHHHHHH
Q ss_conf             87437420687789999999872
Q T0567            80 LVLSHPEHLTREQQYHLVQLQSQ  102 (145)
Q Consensus        80 L~l~ei~~L~~~~Q~~L~~~l~~  102 (145)
                      .-+.+....|++.|.++-+.+..
T Consensus        59 f~~ssf~~vpeel~~W~~~nv~~   81 (106)
T PF08283_consen   59 FPLSSFDQVPEELQEWADENVYD   81 (106)
T ss_pred             CCCHHHCCCCHHHHHHHHHHCCC
T ss_conf             76376525878999999985336


No 113
>PF02263 GBP:  Guanylate-binding protein, N-terminal domain;  InterPro: IPR015894   Guanylate-binding protein is a GTPase that is induced by interferon (IFN)-gamma. GTPases induced by IFN-gamma are key to the protective immunity against microbial and viral pathogens. These GTPases are classified into three groups: the small 47-kd GTPases, the Mx proteins, and the large 65- to 67-kd GTPases. Guanylate-binding proteins (GBP) fall into the last class. In humans, there are seven GBPs (hGBP1-7) . Structurally, hGBP1 consists of two domains: a compact globular N-terminal domain harbouring the GTPase function, and an alpha-helical finger-like C-terminal domain (IPR003191 from INTERPRO). Human GBP1 is secreted from cells without the need of a leader peptide, and has been shown to exhibit antiviral activity against Vesicular stomatitis virus and Encephalomyocarditis virus, as well as being able to regulate the inhibition of proliferation and invasion of endothelial cells in response to IFN-gamma .; GO: 0003924 GTPase activity, 0005525 GTP binding; PDB: 2b92_B 2b8w_A 2bc9_A 1dg3_A 2d4h_A 1f5n_A.
Probab=22.34  E-value=21  Score=14.52  Aligned_cols=27  Identities=26%  Similarity=0.167  Sum_probs=19.7

Q ss_pred             HHHCCCCC---EEEECCCCCCHHHHHHHHH
Q ss_conf             86147995---8987589988889999998
Q T0567            19 QLSETDIA---VWLYGAPGTGRMTGARYLH   45 (145)
Q Consensus        19 ~~a~~~~p---vli~Ge~GtGK~~~A~~iH   45 (145)
                      .+...+.|   |-|.|+..|||+.+...+-
T Consensus        13 ~l~~~~~~V~vVsv~G~~rtGKSfLlN~l~   42 (260)
T PF02263_consen   13 ILEQIDQPVVVVSVVGPYRTGKSFLLNQLL   42 (260)
T ss_dssp             HHHT--S-EEEEEEE--TT---HHHHHHH-
T ss_pred             HHHCCCCCEEEEEEECCCCCCHHHHHHHHH
T ss_conf             986469987999987589887489999984


No 114
>PF10483 Hap2_elong:  Histone acetylation protein 2
Probab=21.67  E-value=21  Score=14.45  Aligned_cols=119  Identities=14%  Similarity=0.118  Sum_probs=65.5

Q ss_pred             CEEEECCCCCCHHHHHHHHHHHCCCCCCCCC---------------EECCCCCCHHHHHHHHHHH---------CCCEEE
Q ss_conf             5898758998888999999862124267852---------------4125788988889999862---------587487
Q T0567            26 AVWLYGAPGTGRMTGARYLHQFGRNAQGEFV---------------YRELTPDNAPQLNDFIALA---------QGGTLV   81 (145)
Q Consensus        26 pvli~Ge~GtGK~~~A~~iH~~s~~~~~~fv---------------~~~~~~~~~~~~~~~l~~a---------~gGtL~   81 (145)
                      -+++.-=.=+|+-.+=.+|+....+ +...+               .++|...+..++.+.+..+         ....++
T Consensus        15 ~L~~Dsl~q~a~~ll~e~i~~a~~~-~~~V~~vsfEt~~~p~~~d~fi~~~~~s~~~i~~~i~~~~~~~~~~~~~~~lVi   93 (280)
T PF10483_consen   15 TLVLDSLEQSARPLLREFIRRAKLR-NEHVIFVSFETLNKPEYVDSFIDARSKSPADIIKEIKSALPSSQNKSKKRFLVI   93 (280)
T ss_pred             EEEEECCCCCCHHHHHHHHHHHHCC-CCEEEEEEEECCCCCCCCCCHHHCCCCCHHHHHHHHHHHCCCCCCCCCCCEEEE
T ss_conf             9998553454748999999987368-984999987647886556602204579989999999873155567778753899


Q ss_pred             ECCHHHCCHHHHHHHHHHHHHCC--HHHEEEECCCCCH-HH-HHHCCCCCHHHHHHHCCCEEEECCCC
Q ss_conf             43742068778999999987214--0100111477687-89-98708976565575544226507889
Q T0567            82 LSHPEHLTREQQYHLVQLQSQEH--RPFRLIGIGDTSL-VE-LAASNHIIAELYYCFAMTQIACLPLT  145 (145)
Q Consensus        82 l~ei~~L~~~~Q~~L~~~l~~~~--~~~RiI~~s~~~l-~~-l~~~~~~~~~L~~~ls~~~i~iPpL~  145 (145)
                      ||-+..|....-..+..++..-.  ..+.++++.+.|+ .. ......-.-.+...++...+.+.|++
T Consensus        94 IDSln~ll~~~~~~l~~fLssl~~~p~~slv~~~H~Dl~~~~~~~~~P~~l~lL~ylATtvi~v~p~~  161 (280)
T PF10483_consen   94 IDSLNPLLRHSPTQLSSFLSSLLSHPQSSLVGTYHSDLTPPSQSPYYPSPLSLLSYLATTVITVEPLS  161 (280)
T ss_pred             EECCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEECCCCCCCCCCCCCCCHHHHHHHHHEEEEEECCCC
T ss_conf             96386777520789999998506799728999975545676667778668999987647899963567


Done!