Query         gi|254780353|ref|YP_003064766.1| DNA topoisomerase IV subunit A [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 753
No_of_seqs    247 out of 2778
Neff          6.2 
Searched_HMMs 39220
Date          Sun May 29 16:32:45 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780353.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 TIGR01063 gyrA DNA gyrase, A s 100.0       0       0 2307.7  53.3  727   17-753     1-809 (864)
  2 PRK05561 DNA topoisomerase IV  100.0       0       0 2051.0  72.5  737   10-753     4-745 (745)
  3 PRK05560 DNA gyrase subunit A; 100.0       0       0 2030.2  68.3  730   13-753     5-752 (822)
  4 PRK13979 DNA topoisomerase IV  100.0       0       0 1965.8  68.1  734    8-753     4-853 (959)
  5 COG0188 GyrA Type IIA topoisom 100.0       0       0 1833.2  62.5  727   17-753     8-747 (804)
  6 TIGR01061 parC_Gpos DNA topois 100.0       0       0 1782.3  36.2  722   17-747     1-743 (745)
  7 TIGR01062 parC_Gneg DNA topois 100.0       0       0 1662.0  54.4  733   17-750     1-746 (747)
  8 PRK09631 DNA topoisomerase IV  100.0       0       0 1274.9  50.4  592   21-692     2-618 (626)
  9 PRK09630 DNA topoisomerase IV  100.0       0       0 1203.1  41.8  459   20-521     2-479 (479)
 10 smart00434 TOP4c DNA Topoisome 100.0       0       0 1146.5  38.4  437   20-471     1-444 (445)
 11 cd00187 TOP4c DNA Topoisomeras 100.0       0       0 1119.5  38.3  441   40-482     2-445 (445)
 12 pfam00521 DNA_topoisoIV DNA gy 100.0       0       0 1051.5  39.3  420   41-473     1-424 (428)
 13 PRK12758 DNA topoisomerase IV  100.0       0       0  860.9  50.4  603   20-690    23-653 (879)
 14 PTZ00108 DNA topoisomerase II; 100.0       0       0  496.8  32.2  439   13-486   721-1208(1506)
 15 KOG0355 consensus              100.0 6.1E-30 1.5E-34  244.7   6.6  638   13-683    72-726 (842)
 16 KOG0355 consensus              100.0   1E-37 2.6E-42  303.1 -33.2  167   17-210   644-812 (842)
 17 PRK13979 DNA topoisomerase IV   99.9 6.8E-24 1.7E-28  199.2  19.1  187  557-743   753-947 (959)
 18 PRK05560 DNA gyrase subunit A;  99.9   6E-23 1.5E-27  192.1  19.9  186  517-705   608-807 (822)
 19 TIGR01063 gyrA DNA gyrase, A s  99.9 1.3E-21 3.4E-26  181.9  15.5  180  517-699   630-857 (864)
 20 PRK05561 DNA topoisomerase IV   99.6 1.1E-12 2.7E-17  115.0  21.9  184  558-753   506-693 (745)
 21 COG0188 GyrA Type IIA topoisom  99.6 9.2E-14 2.3E-18  123.0  16.5  176  518-696   601-792 (804)
 22 TIGR01061 parC_Gpos DNA topois  99.0 2.2E-08 5.7E-13   82.5  12.8  176  515-693   539-741 (745)
 23 TIGR01062 parC_Gneg DNA topois  97.7  0.0022 5.7E-08   44.9  12.9  189  543-743   484-682 (747)
 24 pfam03989 DNA_gyraseA_C DNA gy  97.6 0.00021 5.2E-09   52.7   6.1   42  658-699     1-43  (50)
 25 PRK09630 DNA topoisomerase IV   97.4  0.0078   2E-07   40.8  12.8  106  359-465   307-427 (479)
 26 pfam03989 DNA_gyraseA_C DNA gy  96.9  0.0029 7.4E-08   44.1   6.0   46  612-657     2-49  (50)
 27 PRK09631 DNA topoisomerase IV   93.6    0.67 1.7E-05   26.3  19.8  351  310-743   221-618 (626)
 28 KOG3863 consensus               89.7     0.9 2.3E-05   25.3   5.3   61  399-462   460-531 (604)
 29 KOG0772 consensus               88.9     1.9 4.8E-05   22.9   9.2   15  659-673   470-484 (641)
 30 KOG1240 consensus               84.8     3.1 7.8E-05   21.3  11.7  113  606-718  1055-1173(1431)
 31 pfam04762 IKI3 IKI3 family. Me  79.5     4.7 0.00012   19.9  13.4  124  549-676   422-557 (918)
 32 pfam04201 TPD52 Tumour protein  79.2     2.3 5.8E-05   22.3   3.3   57  425-488    10-68  (162)
 33 PRK00215 LexA repressor; Valid  77.5     4.1  0.0001   20.4   4.2   52  636-687   147-200 (204)
 34 pfam04799 Fzo_mitofusin fzo-li  76.7     5.6 0.00014   19.4   6.3   54  434-487   112-168 (171)
 35 cd07924 PCA_45_Doxase_A The A   76.4     5.7 0.00014   19.3   5.1   32  414-445    44-75  (121)
 36 pfam03982 DAGAT Diacylglycerol  75.7    0.65 1.7E-05   26.4  -0.3   67   31-114    13-99  (297)
 37 PRK13378 protocatechuate 4,5-d  75.6       6 0.00015   19.2   5.0   32  414-445    47-78  (117)
 38 PRK13379 protocatechuate 4,5-d  74.3     6.4 0.00016   18.9   4.9   34  413-446    47-80  (119)
 39 cd07925 LigA_like_1 The A subu  74.2     6.4 0.00016   18.9   4.9   32  414-445    36-67  (106)
 40 cd07921 PCA_45_Doxase_A_like S  73.8     6.5 0.00017   18.9   4.8   32  414-445    36-67  (106)
 41 KOG4010 consensus               73.6     6.5 0.00016   18.9   4.4   52  436-487    38-94  (208)
 42 PRK13377 protocatechuate 4,5-d  72.7     6.9 0.00018   18.7   5.0   33  414-446    47-79  (129)
 43 pfam01401 Peptidase_M2 Angiote  70.7     3.1 7.9E-05   21.3   2.2   39  442-489   196-234 (595)
 44 pfam12395 DUF3658 Protein of u  69.3     2.2 5.7E-05   22.4   1.2   35   68-102    57-92  (111)
 45 pfam07746 LigA Aromatic-ring-o  68.5       8  0.0002   18.2   3.9   33  413-445    20-52  (88)
 46 cd06461 M2_ACE Peptidase famil  68.4     4.8 0.00012   19.8   2.8   57  100-158   149-206 (477)
 47 TIGR00909 2A0306 amino acid tr  66.0     4.6 0.00012   20.0   2.3   35   53-99    316-350 (451)
 48 COG3959 Transketolase, N-termi  65.9     9.4 0.00024   17.7   3.8   89   87-191    32-135 (243)
 49 cd07923 Gallate_dioxygenase_C   63.2      10 0.00027   17.3   4.7   32  414-445    28-59  (94)
 50 PHA00728 hypothetical protein   63.1     9.8 0.00025   17.5   3.5   44  441-487     4-47  (153)
 51 COG3953 SLT domain proteins [G  62.6       4  0.0001   20.5   1.4   24  114-137    66-89  (235)
 52 KOG3584 consensus               61.1      11 0.00029   17.0   5.0   36  452-487   304-343 (348)
 53 pfam03131 bZIP_Maf bZIP Maf tr  60.8      11 0.00029   17.0   5.4   47  432-487    45-91  (95)
 54 PRK10834 hypothetical protein;  60.0     3.2 8.1E-05   21.2   0.5   51   79-131    47-104 (239)
 55 pfam05133 Phage_prot_Gp6 Phage  59.8      12  0.0003   16.9   3.5   11  123-133   141-151 (435)
 56 TIGR01734 D-ala-DACP-lig D-ala  57.7     2.5 6.4E-05   22.0  -0.3  139  129-292    24-181 (513)
 57 TIGR00019 prfA peptide chain r  56.2      14 0.00035   16.5   7.4   61  426-488    32-96  (373)
 58 pfam06995 Phage_P2_GpU Phage P  56.0     4.8 0.00012   19.8   0.9   33   84-117    49-83  (121)
 59 PRK08082 consensus              54.3      11 0.00027   17.3   2.4   23  467-489   334-356 (453)
 60 COG5207 UBP14 Isopeptidase T [  53.9     1.8 4.5E-05   23.1  -1.6   50   90-140   162-221 (749)
 61 TIGR00606 rad50 rad50; InterPr  53.8      15 0.00038   16.2   4.8   11  268-278   734-744 (1328)
 62 PRK06904 replicative DNA helic  53.7      12  0.0003   17.0   2.6   22  267-288   222-243 (472)
 63 COG0576 GrpE Molecular chapero  53.5      15 0.00038   16.2   5.7   41  370-410    67-109 (193)
 64 PRK08840 replicative DNA helic  53.1      13 0.00033   16.6   2.7   71  191-289   170-240 (464)
 65 pfam03444 DUF293 Domain of unk  52.3      10 0.00026   17.5   2.0   64   50-126     2-65  (79)
 66 pfam05600 DUF773 Protein of un  52.3      16  0.0004   16.0   7.9   20  197-216   220-239 (506)
 67 COG1944 Uncharacterized conser  52.1      16  0.0004   16.0   3.6   22  180-201   167-189 (398)
 68 COG4939 Major membrane immunog  51.6      15 0.00039   16.1   2.9   47  107-153    62-113 (147)
 69 cd07321 Extradiol_Dioxygenase_  50.5      13 0.00034   16.5   2.5   33  414-446    26-58  (77)
 70 pfam03853 YjeF_N YjeF-related   50.0      16  0.0004   16.0   2.7  117   92-230    14-144 (170)
 71 TIGR02199 rfaE_dom_II rfaE bif  49.1      13 0.00034   16.5   2.3   21  267-287   123-143 (144)
 72 PRK07085 diphosphate--fructose  49.0      17 0.00044   15.7   4.0   84  305-402   240-323 (557)
 73 pfam08082 PRO8NT PRO8NT (NUC06  48.9      17 0.00044   15.7   3.1   59   50-115     4-64  (152)
 74 PRK08006 replicative DNA helic  47.9      16 0.00042   15.9   2.6   22  267-288   225-246 (471)
 75 PRK08760 replicative DNA helic  47.8      17 0.00045   15.6   2.7   21  268-288   231-251 (476)
 76 TIGR02687 TIGR02687 conserved   47.7      16 0.00041   15.9   2.5   59  331-391   389-450 (911)
 77 PRK05748 replicative DNA helic  47.7      17 0.00044   15.7   2.7   22  267-288   204-225 (448)
 78 cd04618 CBS_pair_5 The CBS dom  47.5      11 0.00028   17.2   1.6   69   47-117     6-85  (98)
 79 KOG4288 consensus               47.1      18 0.00047   15.5   3.7   14  192-205   245-258 (283)
 80 PRK08694 consensus              46.5      19 0.00048   15.4   2.8   21  268-288   220-240 (468)
 81 pfam08317 Spc7 Spc7 kinetochor  45.3      20  0.0005   15.3  12.7   15  359-373   133-147 (322)
 82 pfam01208 URO-D Uroporphyrinog  45.1      20  0.0005   15.3   3.4   12  336-347   188-199 (337)
 83 PTZ00094 serine hydroxymethylt  43.7      21 0.00053   15.1   2.9   66  418-489   382-447 (450)
 84 PRK07263 consensus              43.7      21 0.00053   15.1   2.8   50  267-331   204-253 (453)
 85 pfam07569 Hira TUP1-like enhan  43.4      21 0.00053   15.1   6.2   69  551-624    14-91  (219)
 86 KOG0831 consensus               43.3      13 0.00034   16.5   1.5   76   29-113    49-136 (334)
 87 KOG1359 consensus               43.2      13 0.00034   16.5   1.5   11  477-487   213-223 (417)
 88 KOG0650 consensus               42.9      21 0.00054   15.0   7.9   36  642-677   601-638 (733)
 89 KOG2941 consensus               42.9      21 0.00054   15.0   2.9   31  169-199   112-142 (444)
 90 KOG1446 consensus               42.8      21 0.00054   15.0  12.8   22  524-545    87-108 (311)
 91 cd02639 R3H_RRM R3H domain of   42.7      20 0.00051   15.2   2.4   25   42-69     21-46  (60)
 92 PRK07004 replicative DNA helic  42.6      21 0.00055   15.0   2.7   23  467-489   344-366 (460)
 93 TIGR00373 TIGR00373 conserved   42.3      12  0.0003   17.0   1.1   19  201-219    20-38  (168)
 94 PRK05729 valS valyl-tRNA synth  41.9      22 0.00056   14.9   4.3   53   55-117   155-211 (877)
 95 TIGR01341 aconitase_1 aconitat  41.6     5.2 0.00013   19.6  -0.8   79   29-112    20-105 (896)
 96 PRK05595 replicative DNA helic  41.1      18 0.00046   15.5   1.9   23  267-289   202-224 (444)
 97 pfam10977 DUF2797 Protein of u  40.9      22 0.00055   14.9   2.3  120  426-578   101-227 (233)
 98 pfam07798 DUF1640 Protein of u  40.9      23 0.00058   14.8   5.4   13  425-437   102-114 (177)
 99 TIGR03643 conserved hypothetic  40.6      20 0.00051   15.2   2.1   35  399-433     1-35  (72)
100 KOG2444 consensus               40.5      23 0.00059   14.8   5.6   97  522-629    34-132 (238)
101 TIGR02225 recomb_XerD tyrosine  40.2      23 0.00059   14.7   4.0   82  191-284    84-192 (305)
102 KOG0977 consensus               39.7      24  0.0006   14.7  13.0   14  179-192    82-95  (546)
103 pfam01768 Birna_VP4 Birnavirus  39.3     7.2 0.00018   18.5  -0.3   68   94-169     5-90  (264)
104 PRK08227 aldolase; Validated    38.4      25 0.00063   14.5   2.3   15  296-310   154-168 (291)
105 KOG4212 consensus               37.5      25 0.00065   14.4   4.1   60  268-332    47-109 (608)
106 cd00765 Pyrophosphate_PFK Phos  36.9      26 0.00066   14.4   4.1   86  305-404   240-325 (550)
107 pfam00416 Ribosomal_S13 Riboso  36.7      26 0.00066   14.3   2.8   41  413-453    13-60  (106)
108 COG2524 Predicted transcriptio  36.4      26 0.00067   14.3   2.2   91   50-165     4-97  (294)
109 PHA02126 hypothetical protein   35.8      20  0.0005   15.3   1.4   51  225-275    50-107 (153)
110 KOG2052 consensus               35.6      16 0.00041   15.9   1.0   16  437-452   489-504 (513)
111 COG3879 Uncharacterized protei  34.9      28  0.0007   14.1   5.3   65  443-531    58-126 (247)
112 cd00225 API3 Ascaris pepsin in  34.9      28 0.00071   14.1   3.1   42  433-474    25-66  (159)
113 TIGR01090 apt adenine phosphor  34.7      14 0.00036   16.3   0.6   49  195-253    30-80  (175)
114 COG0241 HisB Histidinol phosph  34.2     7.5 0.00019   18.4  -0.9   72  153-230    22-100 (181)
115 PRK03992 proteasome-activating  34.2      28 0.00072   14.1   6.8   15  377-391   299-313 (390)
116 KOG2264 consensus               34.2      28 0.00072   14.1   5.5   11  156-166   163-173 (907)
117 pfam04849 HAP1_N HAP1 N-termin  34.0      29 0.00073   14.0   4.9   45  444-488   244-288 (307)
118 PRK06266 transcription initiat  33.3      25 0.00064   14.4   1.7   14  206-219    31-44  (178)
119 KOG0771 consensus               33.3      29 0.00075   14.0   6.9  105  587-693   217-333 (398)
120 PRK09458 pspB phage shock prot  33.2      29 0.00075   14.0   2.0   23  447-469    47-69  (75)
121 TIGR00185 rRNA_methyl_2 RNA me  33.0      19 0.00049   15.3   1.0   40  531-570    42-84  (161)
122 COG2949 SanA Uncharacterized m  33.0      22 0.00057   14.8   1.3   77   52-132    34-117 (235)
123 TIGR02169 SMC_prok_A chromosom  32.9      30 0.00076   13.9  12.3   57  550-606  1057-1123(1202)
124 TIGR00018 panC pantoate--beta-  32.6      24 0.00061   14.6   1.5   99   68-180    19-130 (310)
125 KOG1302 consensus               32.5      30 0.00077   13.9   3.9   32   48-84     15-46  (600)
126 cd07603 BAR_ACAPs The Bin/Amph  32.5      30 0.00077   13.9   3.8   35  427-461    83-117 (200)
127 cd04585 CBS_pair_ACT_assoc2 Th  31.2      32  0.0008   13.7   2.7   39   78-117    68-109 (122)
128 pfam10985 DUF2805 Protein of u  31.1      31 0.00079   13.8   1.8   33  400-432     1-33  (73)
129 COG3546 Mn-containing catalase  31.1      24 0.00062   14.6   1.3   30  118-147    29-61  (277)
130 TIGR01882 peptidase-T peptidas  31.0      32 0.00081   13.7   3.5   58  146-216    87-170 (413)
131 pfam00465 Fe-ADH Iron-containi  30.7      32 0.00082   13.7   1.9   17  191-207    59-75  (312)
132 cd06231 Peptidase_M14-like_4 A  30.1      12  0.0003   16.9  -0.5  119   54-179    26-165 (236)
133 PRK05431 seryl-tRNA synthetase  29.8      33 0.00084   13.6   8.2   14  445-458    45-58  (422)
134 KOG1684 consensus               29.8      23 0.00058   14.8   0.9   57   88-146    64-123 (401)
135 KOG1954 consensus               29.8      33 0.00085   13.6   3.1   74   82-178    63-147 (532)
136 cd04600 CBS_pair_HPP_assoc Thi  29.7      33 0.00085   13.5   2.2   31   91-121    10-41  (124)
137 TIGR02171 Fb_sc_TIGR02171 Fibr  29.6      33 0.00085   13.5   4.9  111  516-650   514-626 (982)
138 TIGR02894 DNA_bind_RsfA transc  29.5      33 0.00085   13.5   4.7  105  365-489    47-153 (163)
139 TIGR01511 ATPase-IB1_Cu copper  29.2      34 0.00086   13.5   5.8  131  211-365    93-237 (545)
140 cd04617 CBS_pair_4 The CBS dom  29.1      20  0.0005   15.2   0.5   27   90-116    75-101 (118)
141 KOG0207 consensus               28.7      34 0.00088   13.4   4.6   85  214-307   399-494 (951)
142 COG5290 IkappaB kinase complex  28.6      35 0.00088   13.4   8.5   20   14-33    357-376 (1243)
143 COG2312 Erythromycin esterase   28.5      15 0.00039   16.1  -0.1   47   74-130    43-91  (405)
144 cd03823 GT1_ExpE7_like This fa  28.3      35 0.00089   13.4   1.7   15  459-473   321-335 (359)
145 TIGR02483 PFK_mixed phosphofru  28.2      35  0.0009   13.4   2.7   29  264-294   199-227 (339)
146 cd04793 LanC LanC is the cycla  27.9      35  0.0009   13.3   1.7   33  176-208   103-137 (382)
147 pfam05565 Sipho_Gp157 Siphovir  27.8      36 0.00091   13.3   5.2   71  443-520    55-125 (162)
148 PRK06321 replicative DNA helic  27.8      36 0.00091   13.3   2.6   21  469-489   361-381 (472)
149 cd03805 GT1_ALG2_like This fam  27.8      30 0.00076   13.9   1.3   28  460-487   357-384 (392)
150 TIGR01037 pyrD_sub1_fam dihydr  27.0      33 0.00085   13.6   1.4  102  224-341    13-131 (308)
151 cd04603 CBS_pair_KefB_assoc Th  26.9      26 0.00065   14.4   0.8   81   31-121    12-103 (111)
152 KOG2280 consensus               26.7      37 0.00095   13.2  12.2   36  167-208   162-200 (829)
153 pfam10168 Nup88 Nuclear pore c  26.7      37 0.00095   13.2   8.7   68  356-427   533-609 (717)
154 TIGR02895 spore_sigI RNA polym  26.6      37 0.00095   13.2   3.8   80  402-489    76-157 (225)
155 cd04629 CBS_pair_16 The CBS do  26.6      23  0.0006   14.7   0.5   31   91-121     9-40  (114)
156 PRK02304 adenine phosphoribosy  26.4      25 0.00064   14.4   0.7   49  194-254    33-81  (174)
157 pfam06374 NDUF_C2 NADH-ubiquin  26.3      36 0.00091   13.3   1.4   41  149-195     5-48  (117)
158 TIGR00977 LeuA_rel 2-isopropyl  26.3      38 0.00096   13.1   5.0  207   29-289   129-351 (543)
159 pfam12325 TMF_TATA_bd TATA ele  26.3      38 0.00096   13.1   8.9   45  442-486    69-113 (121)
160 pfam07914 DUF1679 Protein of u  25.9      25 0.00063   14.5   0.6   61  183-245   161-224 (413)
161 KOG0719 consensus               25.8      38 0.00098   13.1   1.9   13  477-489   226-238 (264)
162 pfam05067 Mn_catalase Manganes  25.8      32 0.00081   13.7   1.1   20  118-137    29-48  (272)
163 pfam01162 consensus             25.8      39 0.00098   13.1   1.6   20  414-433    46-65  (69)
164 PRK05636 replicative DNA helic  25.7      39 0.00099   13.1   2.5   44  355-410   224-267 (507)
165 cd07639 BAR_ACAP1 The Bin/Amph  25.6      39 0.00099   13.0   3.7   40  426-465    82-121 (200)
166 pfam12529 Xylo_C Xylosyltransf  25.3      35  0.0009   13.3   1.3   10   93-102    39-48  (180)
167 smart00787 Spc7 Spc7 kinetocho  25.3      39   0.001   13.0  13.1   46  443-488   219-264 (312)
168 TIGR02470 sucr_synth sucrose s  25.2      40   0.001   13.0   2.8   74  321-396   152-242 (790)
169 PRK09848 glucuronide transport  24.9      40   0.001   12.9   3.1   34  430-463   420-453 (457)
170 TIGR01465 cobM_cbiF precorrin-  24.7      32 0.00081   13.7   0.9   20   85-105    76-95  (252)
171 pfam10458 Val_tRNA-synt_C Valy  24.6      40   0.001   12.9   4.4   46  442-487     4-49  (66)
172 PRK06755 hypothetical protein;  24.6      40   0.001   12.9   2.2   42  477-530     9-50  (209)
173 KOG3915 consensus               24.5      41   0.001   12.9   7.1   43  441-483   527-569 (641)
174 COG2192 Predicted carbamoyl tr  24.5      41   0.001   12.9   4.0   25  266-290   161-185 (555)
175 KOG3314 consensus               23.7      42  0.0011   12.8   2.8   38   52-89     38-75  (194)
176 TIGR01034 metK S-adenosylmethi  23.7      42  0.0011   12.8   5.7  105  179-306   122-230 (393)
177 KOG3957 consensus               23.6      39 0.00099   13.0   1.2  146  224-405   152-309 (387)
178 TIGR00952 S15_bact ribosomal p  23.5      42  0.0011   12.8   1.6   30  411-440     2-37  (86)
179 pfam05400 FliT Flagellar prote  23.5      42  0.0011   12.8   3.1   36  454-489    61-96  (109)
180 cd03814 GT1_like_2 This family  23.5      42  0.0011   12.8   2.1   27  401-427   258-285 (364)
181 PRK10325 heat shock protein Gr  23.4      43  0.0011   12.7   5.5   34  372-405    72-107 (197)
182 KOG3675 consensus               23.2      43  0.0011   12.7   2.7  103   85-207    35-146 (417)
183 TIGR02041 CysI sulfite reducta  23.1      43  0.0011   12.7   3.9   59  128-201   150-222 (550)
184 TIGR03300 assembly_YfgL outer   23.1      43  0.0011   12.7  11.4   59  516-577    63-122 (377)
185 KOG2911 consensus               23.0      43  0.0011   12.7  10.5   89  391-484   290-384 (439)
186 COG2039 Pcp Pyrrolidone-carbox  23.0      40   0.001   13.0   1.2   21  189-209    38-58  (207)
187 TIGR02976 phageshock_pspB phag  22.9      43  0.0011   12.7   2.3   36  429-469    34-69  (75)
188 TIGR00501 met_pdase_II methion  22.8      15 0.00038   16.2  -1.0   27   71-97    173-199 (327)
189 cd04639 CBS_pair_26 The CBS do  22.8      31 0.00079   13.8   0.6   28   90-117    71-98  (111)
190 cd03822 GT1_ecORF704_like This  22.8      39 0.00099   13.0   1.1   28  459-487   326-353 (366)
191 cd04949 GT1_gtfA_like This fam  22.7      44  0.0011   12.7   2.5   11  356-366    82-92  (372)
192 pfam01255 Prenyltransf Putativ  22.7      44  0.0011   12.7   2.5   89  388-488    15-110 (222)
193 KOG0103 consensus               22.7      20 0.00052   15.1  -0.4  110   89-208     8-126 (727)
194 PRK10240 undecaprenyl pyrophos  22.5      44  0.0011   12.6   2.5   24  463-486    84-107 (229)
195 KOG0270 consensus               22.4      44  0.0011   12.6   8.0  161  509-684   289-457 (463)
196 TIGR02515 IV_pilus_PilQ type I  22.4      44  0.0011   12.6   3.8   84  308-411    35-123 (464)
197 cd01437 parp_like Poly(ADP-rib  22.3      45  0.0011   12.6   2.9   14  396-409   107-120 (347)
198 cd04775 HTH_Cfa-like Helix-Tur  22.2      45  0.0011   12.6   5.0   22  445-466    81-102 (102)
199 COG0216 PrfA Protein chain rel  22.0      45  0.0012   12.5  10.3   46  443-488    47-94  (363)
200 TIGR03290 CoB_CoM_SS_C CoB--Co  21.7      46  0.0012   12.5   1.5   85  188-296    54-141 (144)
201 TIGR00034 aroFGH phospho-2-deh  21.7      46  0.0012   12.5   1.8   21  415-435    18-38  (348)
202 pfam11853 DUF3373 Protein of u  21.7      46  0.0012   12.5   3.3   21  443-463    32-52  (485)
203 TIGR01051 topA_bact DNA topois  21.4      27 0.00069   14.2   0.0  132  467-604   347-503 (688)
204 TIGR03449 mycothiol_MshA UDP-N  21.4      43  0.0011   12.7   1.1   10  401-410   294-303 (405)
205 PRK11462 putative transporter;  21.1      47  0.0012   12.4   1.8   28  430-457   421-448 (460)
206 KOG0005 consensus               20.9      35 0.00089   13.4   0.5   19   47-65     33-51  (70)
207 TIGR01055 parE_Gneg DNA topois  20.9      30 0.00077   13.9   0.2  128   45-193    10-172 (647)
208 cd04469 S1_Hex1 S1_Hex1: Hex1,  20.8      48  0.0012   12.4   1.9   26  224-253    29-54  (75)
209 pfam09133 SANTA SANTA (SANT As  20.7      48  0.0012   12.4   1.7   62  528-590     6-71  (93)
210 KOG1712 consensus               20.6      48  0.0012   12.4   1.2   14  223-236    18-31  (183)
211 pfam01025 GrpE GrpE.            20.6      48  0.0012   12.3   7.2   14  518-531   135-148 (162)
212 PRK09165 replicative DNA helic  20.5      48  0.0012   12.3   2.3   61  267-331   206-269 (484)
213 cd00200 WD40 WD40 domain, foun  20.5      48  0.0012   12.3  16.2   61  610-677   146-208 (289)
214 cd07908 Mn_catalase_like Manga  20.4      32 0.00082   13.7   0.2   21  116-136    20-40  (154)
215 TIGR00746 arcC carbamate kinas  20.3      36 0.00091   13.3   0.5   11  285-295   181-191 (321)
216 PRK09956 hypothetical protein;  20.2      32  0.0008   13.7   0.2   43  167-227   113-155 (308)
217 pfam03861 ANTAR ANTAR domain.   20.1      39   0.001   13.0   0.6   22  411-432    16-37  (56)
218 TIGR01127 ilvA_1Cterm threonin  20.1      27 0.00069   14.2  -0.2   90  277-371   234-334 (381)

No 1  
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=2307.74  Aligned_cols=727  Identities=40%  Similarity=0.648  Sum_probs=702.8

Q ss_pred             EEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHH
Q ss_conf             66531999999888888899985104764112897046899999998689998980354053666542768874789999
Q gi|254780353|r   17 VKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYD   96 (753)
Q Consensus        17 i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~   96 (753)
                      |.+++|++||++|||+||||||++||||||||||||||||||||||++||++++||+||||||||||||||||||+||||
T Consensus         1 i~pv~ie~E~k~SYLdYAMSVIVsRALPDvRDGLKPVHRRiLYaM~~~Gl~~d~~~kKsARIVGDV~GkYHPHGD~aiYD   80 (864)
T TIGR01063         1 IVPVNIEEEMKRSYLDYAMSVIVSRALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSARIVGDVLGKYHPHGDSAIYD   80 (864)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCEEECCEEEEEECCCCCCCCCCHHHH
T ss_conf             94565788999998644111322211541003688504577667766278998866002428741047824898734676


Q ss_pred             HHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHH
Q ss_conf             99961001321661326788708867797100246899855999999842187861752167996324223123452676
Q gi|254780353|r   97 SLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLL  176 (753)
Q Consensus        97 a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL  176 (753)
                      ||||||||||||||||||||||||||||||||||||||||+|+|++||+|||||||||+||||||++||+||||+|||||
T Consensus        81 ~LVRMAQDFSlRYpLvDGQGNFGSiDGD~pAAMRYTEaRl~k~a~~ll~DIdKeTVdF~~NYDg~~~EP~VLPs~fPnLL  160 (864)
T TIGR01063        81 ALVRMAQDFSLRYPLVDGQGNFGSIDGDPPAAMRYTEARLTKIAEELLRDIDKETVDFVPNYDGSEKEPTVLPSRFPNLL  160 (864)
T ss_pred             HHHHHCCCHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             77650587100354416888647888882676521788888999999862043631654488886258820751241456


Q ss_pred             HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEE
Q ss_conf             42665046777751677788999999999872865320134432036778877601069889998985033415999999
Q gi|254780353|r  177 ANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARW  256 (753)
Q Consensus       177 ~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~  256 (753)
                      ||||||||||||||||||||+||||||++||+||+||++|||++||||||||||+|+ |.+||++||+||||||+||||+
T Consensus       161 vNGSsGIAVGMATNIPPHNL~Eiida~~~~i~Np~~~i~eLl~~i~GPDFPTgg~I~-G~~GI~~AY~TGRG~i~~Rar~  239 (864)
T TIGR01063       161 VNGSSGIAVGMATNIPPHNLGEIIDAILAYIDNPDISIEELLEVIKGPDFPTGGIIL-GRSGIREAYETGRGSIVIRARA  239 (864)
T ss_pred             CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCHHHHHC-CCCCHHHHHHCCCCEEEEEEEE
T ss_conf             132476000222578873368999999998718998867995607711371056430-5001377733588138999989


Q ss_pred             EEEECCC--CCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCC-CCCEEEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             9864378--840799952420021689999999986402221345776406-7660588985045458899999875420
Q gi|254780353|r  257 CVEEVGR--GSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDES-AEDVRIVLFPKNRSLDPDLLMESIFMLS  333 (753)
Q Consensus       257 ~~e~~~~--~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeS-d~~~~~vi~~~~r~~~~~~vl~~Lyk~T  333 (753)
                      +||+.++  ||.+||||||||||||++|||||||||++|||+||+|||||| ||+|+|||+++|||+.|++|||+|||+|
T Consensus       240 ~iE~~~~~~gR~~IIvTE~PYqVNKa~LiekIAeLv~ek~ieGIsdiRDESSDr~GiRiVIE~KRD~~a~VvLN~LYk~T  319 (864)
T TIGR01063       240 EIEEDSKKGGREAIIVTEIPYQVNKARLIEKIAELVREKKIEGISDIRDESSDREGIRIVIELKRDAVAEVVLNNLYKQT  319 (864)
T ss_pred             EEEECCCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCCHHHHHHHCCC
T ss_conf             99864889986248886288852026888999987400000032124425668774379999742898301542121126


Q ss_pred             CCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC--
Q ss_conf             000122331133312689722049999998999989999999999999999999999999986410789999752000--
Q gi|254780353|r  334 DMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNED--  411 (753)
Q Consensus       334 ~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s~--  411 (753)
                      +||++||+||+||++| .||+|+|+++|.+|++||.+||+|||.|+|+||++|.|||+||++|++||||||+|||+|.  
T Consensus       320 ~lQ~~Fg~NmLALv~G-~Pk~lnLk~~l~~f~~HR~~Vi~RRT~feLrKA~eRaHiL~GL~~AL~niDevI~lIr~S~~~  398 (864)
T TIGR01063       320 QLQVSFGINMLALVDG-LPKVLNLKELLEAFVEHRKDVITRRTIFELRKAEERAHILEGLLIALDNIDEVIALIRASQNT  398 (864)
T ss_pred             CCCEECCEEEEEEECC-CCCEECHHHHHHHHHHCCEEEEEEEHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCH
T ss_conf             4500148123211078-975017889999998423133552100010226557899999999997212899997427898


Q ss_pred             -CCCCCCCCC------------------------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             -011000000------------------------2577577889988789999889999766678999988776544203
Q gi|254780353|r  412 -KPKPVMVSR------------------------FSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLN  466 (753)
Q Consensus       412 -~~k~~L~~~------------------------f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~  466 (753)
                       .||+.|+++                        |+|||.||+|||||||||||+||.+||++||++|.++|++|+.||+
T Consensus       399 ~~Ak~~L~e~~W~l~di~~ll~~~~~~~l~~~g~F~l~E~QA~AILdMrL~rLTgLE~~Kl~~E~~~L~~~I~~l~~iL~  478 (864)
T TIGR01063       399 EEAKTRLVERQWELLDILPLLKLVLEVELGERGTFSLSEIQAQAILDMRLQRLTGLEREKLEEEYKELLELIADLEDILA  478 (864)
T ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
T ss_conf             89998842168607899999988767532888865448899999999887677888899999999999999999997503


Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEEC--------CCCCCC
Q ss_conf             978878999999999987417743345554200001100000011002456670599871010202--------565544
Q gi|254780353|r  467 SGKQQWNQIACEIREVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRS--------LKSHSV  538 (753)
Q Consensus       467 s~~~l~~iI~~EL~eikkkfgd~~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr--------~k~~~~  538 (753)
                      |+.+++++|++||.+++++||||     |||.|+...  ....+.||||.+|+|+|+||++|||||        |+++++
T Consensus       479 ~~~r~~~iireEL~~i~~~Fgd~-----RRT~I~~~~--~~~~D~EDLI~~E~vVvt~s~~GYvKR~p~~~Y~~Q~RGGk  551 (864)
T TIGR01063       479 SEERVLEIIREELEEIKEQFGDP-----RRTEIVAEE--SEDIDIEDLIARENVVVTLSHKGYVKRVPVSAYRSQKRGGK  551 (864)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC-----CCCHHHHCC--CCCCCCHHHHCCCCEEEEEECCCEEEECCHHHHHCCCCCCC
T ss_conf             77689999999999999973885-----321222024--32245034414787899971686478603013325766664


Q ss_pred             CCCCCCCCC-CCCCEEEEEECCCCCEEEEECCCEEEEEEHHHCCCC--CCCCCCCCCCCC-CCCCCEEEEEEE---ECCC
Q ss_conf             553223455-555401211114781789806882787551121212--344442222357-676530789998---5799
Q gi|254780353|r  539 DLSALHFKE-GDSLKIALHAHTTDRILLLSTDGKAYTLPAGNLLSG--RGHGEAIQLLID-LNHNQDIVTAFV---YDST  611 (753)
Q Consensus       539 ~~~~~~~Ke-gD~l~~~~~~~t~d~LLffTs~GkvY~l~a~~Ips~--~~kG~pI~~ll~-l~~~EkIv~~~~---~~~~  611 (753)
                      |++|+++++ +|++.++|+|+|||+||||||+|||||++||+||.+  +++|.||.|+|+ +++||+|.++++   |+++
T Consensus       552 G~~g~~~~~G~D~i~~~lvasTHD~~Lfftn~G~vY~lK~Y~iP~~~R~akG~pIvNLL~G~~~dE~I~ai~~v~~f~d~  631 (864)
T TIGR01063       552 GVSGADLKDGDDFIEQLLVASTHDYLLFFTNRGKVYRLKVYQIPEASRTAKGKPIVNLLEGLQKDERITAILSVKEFEDE  631 (864)
T ss_pred             CCCCCCCCCCCCEEEEEEEEECCCEEEEEECCCCEEEEEEEECCCCCCCCCCCHHHHHCCCCCCCCEEEEEECCCCCCCC
T ss_conf             64325312368505677883077607888188826864544178777567871288860578767668887356666855


Q ss_pred             C---EEEEEECCCCEEEEEHHHHHCCCCCCEEEEEECCCCCEEEEEECCC-CE-EEEEECCCCEEEEEHH--HCCCCCH-
Q ss_conf             8---5999974897899638874023335627885368980568896189-80-9999569938995578--7783361-
Q gi|254780353|r  612 C---KLLVVSSKGNAFIVEESEIIANTRKGKTFLKVSSEEKMKLVVKVTG-DH-VAVVGENRKLLIFSID--QIPEMSR-  683 (753)
Q Consensus       612 ~---~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~D~li~v~~~~~-d~-iiliT~~Gk~LrF~~~--eIr~~gR-  683 (753)
                      .   |++|+|++|.+||+.+++|.+.+++|+.|++|.+||+|++|..|.+ |+ |+|+|++|+++||+.+  +||+||| 
T Consensus       632 ~~~~yl~~aTk~G~vKk~~L~~F~~~rs~GiiAi~L~e~D~L~~v~~~~~~~~~v~l~s~~G~~~RF~~~~~~vR~mgR~  711 (864)
T TIGR01063       632 AYDLYLFLATKNGVVKKTSLTEFSNIRSNGIIAIKLDEGDELISVRLVDGDDEKVMLGSKNGKAVRFPEEDEEVREMGRA  711 (864)
T ss_pred             CCCEEEEEECCCCEEEEEECHHHHHHHHCCEEEEEEECCCEEEEEEEEECCCCEEEEEECCCCEEECCCCCCCHHCCCCC
T ss_conf             26617999726743887400144354527869999708968999999607886588651488479836885311002455


Q ss_pred             HHCCEEEECCCC----------------------------CEEEEEEEECCCCC-EEEEECCCCCCCCCHHHHCCCCCCC
Q ss_conf             214133421878----------------------------75689997338883-6999417756645114322544413
Q gi|254780353|r  684 GKGVRLQSYKDG----------------------------GISDVICFKICEGL-TWIDSAGRSYNRSENDLLGWLGKRG  734 (753)
Q Consensus       684 gkGVk~i~Lkd~----------------------------~~~~~~~~~~~e~~-~il~~t~~g~~k~~~~~~~~~~~Rg  734 (753)
                      ++||+||+|+++                            |.+ +.+....++. .+|++|++||||++...+|+.++||
T Consensus       712 ~~GV~Gi~L~~~~~v~~~~~~~~i~~~~~D~~~~~L~~NlD~v-v~~~~~~e~~~~lL~vt~nGyGKRt~~~~yr~~~RG  790 (864)
T TIGR01063       712 TRGVRGIKLKNEDSVISMTVLKGINSIKEDRNLEELGVNLDFV-VSLEVVSEESQKLLIVTENGYGKRTSIEEYRLQSRG  790 (864)
T ss_pred             CCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEE-EEEEEECCCCCEEEEEEECCCCEECCHHHCCCCCCC
T ss_conf             6760135406777400013443212002222465437424344-777862499837899830684200426257632656


Q ss_pred             CCCCCCCCCCCCCCCEECC
Q ss_conf             6660275526776861049
Q gi|254780353|r  735 GVGSLVPKGFPRSGKFLSS  753 (753)
Q Consensus       735 gkG~~~~k~~~K~gklV~A  753 (753)
                      |+|++.++.++|+|.||+|
T Consensus       791 g~Gv~~~~~~~r~G~vVga  809 (864)
T TIGR01063       791 GKGVKSIKITDRNGQVVGA  809 (864)
T ss_pred             CCEEEEEEEECCCCCEEEE
T ss_conf             6237889986468968789


No 2  
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=100.00  E-value=0  Score=2050.96  Aligned_cols=737  Identities=47%  Similarity=0.823  Sum_probs=708.2

Q ss_pred             CCCCCCCEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCC
Q ss_conf             66542456653199999988888889998510476411289704689999999868999898035405366654276887
Q gi|254780353|r   10 NTLVEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPH   89 (753)
Q Consensus        10 ~~~~~~~i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPH   89 (753)
                      ...+.|+|++++|+++|++||++||||||++||||||||||||||||||||||++||+|+++|+||||||||||||||||
T Consensus         4 ~~~~~e~i~~~~~~~~~~~~yl~Ya~svi~~RalPd~rDGlKPv~RRily~m~~~~l~~~~~~~KsarivG~v~GkyHPH   83 (745)
T PRK05561          4 PDPMSEGIEDLPLEEFLEERYLRYSMYVIMDRALPDVRDGLKPVQRRILYAMSELGLTPDAKFKKSARTVGDVLGKYHPH   83 (745)
T ss_pred             CCCHHCCCEEECHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCEEEEEEHHHCCCCCCC
T ss_conf             98320581572389999988999899999851277644588609999999999728999999736316641005577898


Q ss_pred             HHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEEC
Q ss_conf             47899999996100132166132678870886779710024689985599999984218786175216799632422312
Q gi|254780353|r   90 GDQSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFP  169 (753)
Q Consensus        90 Gd~s~y~a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp  169 (753)
                      ||+|||||||||||+|+||||||||||||||+||||||||||||||||++|++||+|||++||||+||||||++||+|||
T Consensus        84 GD~siY~a~vrmaQ~f~~r~plidg~GNfGsidgd~~AAmRYTE~rls~~~~~~l~di~~~tv~f~~n~D~~~~EP~vLP  163 (745)
T PRK05561         84 GDSAIYDAMVRMAQDFSYRYPLVDGQGNFGSIDGDPAAAMRYTEARLSKIAELLLEEIDEGTVDFVPNFDGTLEEPTVLP  163 (745)
T ss_pred             CHHHHHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCEEC
T ss_conf             70479999999733013157514278877899998437678898876999999996306475132058799976755430


Q ss_pred             CCCCHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCE
Q ss_conf             34526764266504677775167778899999999987286532013443203677887760106988999898503341
Q gi|254780353|r  170 SKFPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGG  249 (753)
Q Consensus       170 ~~~P~lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~  249 (753)
                      |+|||||+|||+|||||||||||||||+|||+||++||+||++|++|||+|||||||||||.|++|++||+++|+||||+
T Consensus       164 a~~PnlL~NG~~GIAvGmaTnIPpHNl~Ev~~a~i~~i~np~~t~~eL~~~i~GPDFPTGg~Ii~g~~~i~~ay~tGrG~  243 (745)
T PRK05561        164 ARFPNLLLNGATGIAVGMATDIPPHNLREVIDAAIHLIDNPDATLEELMEFVPGPDFPTGGEIITGRDGIRKAYETGRGS  243 (745)
T ss_pred             CCCCHHHCCCCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCEEEECHHHHHHHHHHCCCE
T ss_conf             46874110488624876644879976699999999874499999999983188997998838972889999999847670


Q ss_pred             EEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCC--EEEEEEEECCCCCHHHHHH
Q ss_conf             59999999864378840799952420021689999999986402221345776406766--0588985045458899999
Q gi|254780353|r  250 FRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAED--VRIVLFPKNRSLDPDLLME  327 (753)
Q Consensus       250 i~~r~k~~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~--~~~vi~~~~r~~~~~~vl~  327 (753)
                      |++||+|++|+.++|+++||||||||||||++++|+|++||++||++||+||||||||+  +|+|+++|+++++|++|||
T Consensus       244 i~iRak~~iE~~~~g~~~IvItEIPY~vnk~~liekIa~lv~~kki~gI~dvrDESdr~g~iRIVIelK~~~~d~~~vln  323 (745)
T PRK05561        244 IRVRARWEIEDLARGQWQIVITELPYQVSKAKLIEQIAEQMQAKKLPGIADVRDESDRENPVRIVIEPKSNRVDPEALMN  323 (745)
T ss_pred             EEEEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEECCCCCCCCCCEEEEEEECCCCCCHHHHHH
T ss_conf             99988999996379841799996787684899999999999708664102410366787877999997888879999999


Q ss_pred             HHHHHCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             87542000012233113331268972204999999899998999999999999999999999999998641078999975
Q gi|254780353|r  328 SIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAII  407 (753)
Q Consensus       328 ~Lyk~T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iI  407 (753)
                      +|||+|+||+||++||+||+.+++|++|||+++|++|++||++|++||++|+|+|+++|+||||||++|++|||+||+||
T Consensus       324 ~Lyk~T~Lq~sf~~N~~al~~dg~P~~l~Lk~iL~~~l~hR~~vi~rrt~~~L~Ka~~RlhIleGLliA~~~iD~VI~iI  403 (745)
T PRK05561        324 HLFATTDLESSYRVNMNVIGLDGRPRVKGLKEILSEWLDHRREVVTRRSQFRLDKVEKRLHILEGLLIAFLNIDEVIEII  403 (745)
T ss_pred             HHHHHCCCHHHCCCEEEEEECCCCCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHH
T ss_conf             99985762421371489993799755827999999999999999999999999999999999988999996768999999


Q ss_pred             HCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             20000110000002577577889988789999889999766678999988776544203978878999999999987417
Q gi|254780353|r  408 RNEDKPKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFS  487 (753)
Q Consensus       408 R~s~~~k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfg  487 (753)
                      |+|++||.+||++|+|||.||+|||+|||||||+||++++++|+++|.++|++|++||+|+++++++|++||.+++++||
T Consensus       404 R~S~dak~~L~~~f~lse~QA~AIL~mrL~rLt~LE~~kl~~E~~eL~~~I~~l~~IL~s~~~~~~iI~~EL~eik~kfg  483 (745)
T PRK05561        404 RESDEPKANLMARFGLTEIQAEAILELRLRRLAKLEEIEIRKEQDELRKEIAELEAILASERKLWKLIKKELKADAKKFG  483 (745)
T ss_pred             HCCCHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             70632667775550879999999999999998766799999999999999999999963899999999999999998638


Q ss_pred             CCCCCCCCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEE
Q ss_conf             74334555420000110000001100245667059987101020256554455322345555540121111478178980
Q gi|254780353|r  488 KSTDLGRRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLS  567 (753)
Q Consensus       488 d~~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr~k~~~~~~~~~~~KegD~l~~~~~~~t~d~LLffT  567 (753)
                      ++     |||.|++. ..+.++..|++|++|||+|++|++|||||+++++++.++.++|++|++.+++.|+|||+|+|||
T Consensus       484 d~-----RRT~I~~~-~~~~~i~~edlI~~E~v~V~lS~~GyIKr~k~~~~~~~~~~~Ke~D~v~~~~~~~T~d~LLfFT  557 (745)
T PRK05561        484 DP-----RRTPIEER-EEAKAIDEEALVPDEPVTVVLSKKGWVRRAKGHDIDPAGLGYKEGDSLLFAFEARTTDKLLFFT  557 (745)
T ss_pred             CC-----CCCCCCCC-CCCCCCCHHHHCCCCCCEEEECCCEEEEEECCCCCCCCCCCCCCCCCEEEEEEEECCCEEEEEE
T ss_conf             99-----86302267-4202378777176766189981780499844888675445677785325899980697699995


Q ss_pred             CCCEEEEEEHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCEEEEEHHHHHCCCCCCEEEEEECCC
Q ss_conf             68827875511212123444422223576765307899985799859999748978996388740233356278853689
Q gi|254780353|r  568 TDGKAYTLPAGNLLSGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKGKTFLKVSSE  647 (753)
Q Consensus       568 s~GkvY~l~a~~Ips~~~kG~pI~~ll~l~~~EkIv~~~~~~~~~~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~  647 (753)
                      |.||+|++++|+||+++++|+|+++++++++||+|+++++++++.+++++|++|++|++++++|.+.+++|+++|+|+++
T Consensus       558 n~Grvy~lkv~~IP~~r~~G~pi~nll~L~~~EkIv~vl~~~~~~~lllaTk~G~~kr~~l~e~~~~~k~G~~ai~L~~g  637 (745)
T PRK05561        558 STGRVYSLPVHELPSARGQGEPLTGLIDLEPGEEIVHVLVGDPDQKLLLASSAGYGFVVSEEDLVGRNRAGKAVINLKDG  637 (745)
T ss_pred             CCCEEEEEEHHHCCCCCCCCCCHHHCCCCCCCCEEEEEEEECCCCEEEEEECCCEEEEEEHHHHCCCCCCCEEEEEECCC
T ss_conf             79759998922087866788089880689999969999985898769999789329997869800446267188861899


Q ss_pred             CCEEEEEECCC--CEEEEEECCCCEEEEEHHHCCCCCHHHCCEEEECCCCC-EEEEEEEECCCCCEEEEECCCCCCCCCH
Q ss_conf             80568896189--80999956993899557877833612141334218787-5689997338883699941775664511
Q gi|254780353|r  648 EKMKLVVKVTG--DHVAVVGENRKLLIFSIDQIPEMSRGKGVRLQSYKDGG-ISDVICFKICEGLTWIDSAGRSYNRSEN  724 (753)
Q Consensus       648 D~li~v~~~~~--d~iiliT~~Gk~LrF~~~eIr~~gRgkGVk~i~Lkd~~-~~~~~~~~~~e~~~il~~t~~g~~k~~~  724 (753)
                      |+++++..+++  |+++++|++|+++||++++||+||||+||++|+|++++ ++++.++...+++.|++.++++++++++
T Consensus       638 Delv~~~~i~~~~d~I~lvT~~Gk~lrF~~~evr~~gRgkGVkgikLk~~D~Vv~~~vv~~~~~l~v~s~~~~g~~k~t~  717 (745)
T PRK05561        638 DKVLAPVPVEGDEDSLAAITQRGRLLVFPLSELPELSRGKGVKLIELKKEEGLADLAVLPPGDGLTLHAGKRKLTLKPKD  717 (745)
T ss_pred             CEEEEEEEECCCCCEEEEEECCCCEEEEEHHHCCCCCCCCCCCEEEECCCCEEEEEEEECCCCCEEEEECCCCCCCCCCC
T ss_conf             88988899469998899995898289979888777575468014766899989999998588834999867876345551


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCCCCEECC
Q ss_conf             43225444136660275526776861049
Q gi|254780353|r  725 DLLGWLGKRGGVGSLVPKGFPRSGKFLSS  753 (753)
Q Consensus       725 ~~~~~~~~RggkG~~~~k~~~K~gklV~A  753 (753)
                      ..+|+ ++||++|+++||+|+|+|++..+
T Consensus       718 l~~y~-~~Rgg~G~~~~k~~~k~gk~~~~  745 (745)
T PRK05561        718 LEEYR-GKRARRGSLLPRGLQRVDRLSPA  745 (745)
T ss_pred             HHHHC-CCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             67746-22477886788888878971789


No 3  
>PRK05560 DNA gyrase subunit A; Validated
Probab=100.00  E-value=0  Score=2030.24  Aligned_cols=730  Identities=39%  Similarity=0.639  Sum_probs=699.9

Q ss_pred             CCCCEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHH
Q ss_conf             42456653199999988888889998510476411289704689999999868999898035405366654276887478
Q gi|254780353|r   13 VEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQ   92 (753)
Q Consensus        13 ~~~~i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~   92 (753)
                      +.++|++++|++||++|||+||||||++|||||+||||||||||||||||+|||+|++||+||||||||||||||||||+
T Consensus         5 ~~~~i~~~~~~~~~~~~yl~Ya~svi~~RAlPdvrDGlKPv~RRily~M~~l~l~~~~~~~K~ArivG~v~gkyHPHGd~   84 (822)
T PRK05560          5 LADRIIPVNIEEEMKRSYLDYAMSVIVGRALPDVRDGLKPVHRRILYAMYELGLTPDKPYKKSARIVGDVMGKYHPHGDS   84 (822)
T ss_pred             HHCCEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCEEEEEECCCCCCCCCCCCH
T ss_conf             33444453489999988998889999851288644688508999999998728999999744206641005477898821


Q ss_pred             HHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCC
Q ss_conf             99999996100132166132678870886779710024689985599999984218786175216799632422312345
Q gi|254780353|r   93 SVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKF  172 (753)
Q Consensus        93 s~y~a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~  172 (753)
                      |||||||||||+|+||||||||||||||+||||||||||||||||++|++||+||+++||||+||||||++||+||||+|
T Consensus        85 siY~alvrmaQ~~~~r~plidg~GNfGsidgd~~AAmRYTE~rl~~~~~~ll~di~~~tV~f~~NfD~s~~EP~vLPa~~  164 (822)
T PRK05560         85 AVYDALVRMAQDFSLRYPLVDGQGNFGSIDGDPAAAMRYTEARLAKIAHELLRDIDKETVDFVPNYDGSEQEPTVLPARF  164 (822)
T ss_pred             HHHHHHHHHHHHHHHCCCEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             79999999700223047327157888899998006666788887999999985113065255048898765865256566


Q ss_pred             CHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEE
Q ss_conf             26764266504677775167778899999999987286532013443203677887760106988999898503341599
Q gi|254780353|r  173 PNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRV  252 (753)
Q Consensus       173 P~lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~  252 (753)
                      ||||+|||+|||||||||||||||+|||+||++||+||++|+++||+|||||||||||+|+ +.+||+++|+||||+|++
T Consensus       165 PnlLvNGs~GIAVGmATniPpHNL~Evi~a~~~~i~np~~t~~~L~~~i~GPDFPTGG~I~-~~~~i~~~y~tGrG~i~i  243 (822)
T PRK05560        165 PNLLVNGSSGIAVGMATNIPPHNLGEVIDACLALIDNPDITIEELMEIIPGPDFPTGGIIL-GRSGIREAYRTGRGSIIM  243 (822)
T ss_pred             CHHHCCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHCCCCCCCCCCCEEEE-CCHHHHHHHHHCCCEEEE
T ss_conf             4532057751002110588996889999999986359999999994669899799982897-848799999837670999


Q ss_pred             EEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             99999864378840799952420021689999999986402221345776406766058898504545889999987542
Q gi|254780353|r  253 RARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFML  332 (753)
Q Consensus       253 r~k~~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~  332 (753)
                      ||+|++|+.++|+++||||||||||||++++|+|++||++||++||+|+||||||+|+++|+++||+++|+.|||+|||+
T Consensus       244 R~k~~iE~~~~~r~~IvItEIPY~vnk~~liekIa~lv~~kki~gI~dirDESdr~GiRIVIelKr~~~~~~vln~Lyk~  323 (822)
T PRK05560        244 RAKAEIEEIRKGREAIIVTEIPYQVNKARLIEKIAELVKEKKIEGISDIRDESDRDGMRIVIELKRDAVPEVVLNNLYKH  323 (822)
T ss_pred             EEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHH
T ss_conf             88999998579953899996898577999999999998557544510300356877627999967989979999999860


Q ss_pred             CCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             00001223311333126897220499999989999899999999999999999999999999864107899997520000
Q gi|254780353|r  333 SDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDK  412 (753)
Q Consensus       333 T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s~~  412 (753)
                      |+||++|++||+||++| +|++|||+++|++|++||.+|++||++|+|+|+++|+||||||++|++|||+||+|||+|++
T Consensus       324 T~Lq~sf~~N~~al~~g-~P~~l~Lk~~L~~fi~hR~~vi~rr~~~~L~ka~~RlhIleGl~~a~~~iDeVI~iIR~S~~  402 (822)
T PRK05560        324 TQLQTSFGINMLALVDG-QPKLLNLKQILEAFVDHRKEVITRRTRFELRKARERAHILEGLLIALDNIDEVIALIRASPT  402 (822)
T ss_pred             CCHHHCCCCEEEEEECC-EEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHCCCC
T ss_conf             84132036117998799-87786499999999999999999999999999998899998899999587999999971898


Q ss_pred             ---CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             ---11000000257757788998878999988999976667899998877654420397887899999999998741774
Q gi|254780353|r  413 ---PKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKS  489 (753)
Q Consensus       413 ---~k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~  489 (753)
                         ||..||++|+|||.||+|||+|||||||+||+++|++|+++|.++|++|++||+|+++++++|++||.+++++||+|
T Consensus       403 ~~~Ak~~L~~~f~lse~QA~AIL~mrL~rLt~Le~~kl~~E~~eL~~~I~~l~~IL~s~~~l~~iI~~EL~eik~kygd~  482 (822)
T PRK05560        403 PAEAREGLMERYGLSEIQAQAILDMRLQRLTGLEREKIEDEYKELLAEIADLLDILASPERLMEIIREELEEIKEKFGDP  482 (822)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             78999989887588999999999989999876789999999999999999999886599999999999999999982998


Q ss_pred             CCCCCCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEECC--------CCCCCCCCCCCCCCCCCCEEEEEECCCC
Q ss_conf             33455542000011000000110024566705998710102025--------6554455322345555540121111478
Q gi|254780353|r  490 TDLGRRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRSL--------KSHSVDLSALHFKEGDSLKIALHAHTTD  561 (753)
Q Consensus       490 ~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr~--------k~~~~~~~~~~~KegD~l~~~~~~~t~d  561 (753)
                           |||.|.+..   .+++.||+|++|+++|++|++|||||+        ++++.|.++.++|++|++.+++.|+|||
T Consensus       483 -----RRT~I~~~~---~ei~~EDLI~~E~vvVtlS~~GYIKR~~~~~yr~Q~RGGkG~~g~~~ke~D~v~~~~~~~Thd  554 (822)
T PRK05560        483 -----RRTEIEAGE---GDIDDEDLIANEDVVVTLTHGGYIKRVPLDEYRAQRRGGKGKSGAGTKEDDFVEHLFVANTHD  554 (822)
T ss_pred             -----CCEEEECCC---CCCCHHHCCCCCCEEEEEECCCEEEEECHHHHHHHCCCCCCCCCCCCCCCCHHHHEEEECCCC
T ss_conf             -----860441565---656254417776469999468268861326655312677774343045565344326824788


Q ss_pred             CEEEEECCCEEEEEEHHHCCCC--CCCCCCCCCCCCCCCCCEEEEEEEE---CCCCEEEEEECCCCEEEEEHHHHHCCCC
Q ss_conf             1789806882787551121212--3444422223576765307899985---7998599997489789963887402333
Q gi|254780353|r  562 RILLLSTDGKAYTLPAGNLLSG--RGHGEAIQLLIDLNHNQDIVTAFVY---DSTCKLLVVSSKGNAFIVEESEIIANTR  636 (753)
Q Consensus       562 ~LLffTs~GkvY~l~a~~Ips~--~~kG~pI~~ll~l~~~EkIv~~~~~---~~~~~lll~Tk~G~ikr~~l~~~~~~~k  636 (753)
                      +|||||+.||||++++|+||.+  +++|.||.|+++++++|+|++++++   +++.+++|+|++|++||+++++|.+.++
T Consensus       555 ~LLfFTn~Grvy~lkv~eIPe~sr~skG~~i~nll~l~~~EkI~ail~v~~~~~~~~Lv~~Tk~G~IKRt~L~df~~~r~  634 (822)
T PRK05560        555 TLLFFTNRGRVYRLKVYELPEGSRTAKGRPIVNLLPLEPGEKITAILPVREFDDDLYLFFATKNGTVKKTALSEFSNIRS  634 (822)
T ss_pred             EEEEEECCCCEEEEEEEECCCCCCCCCCCCHHHHCCCCCCCEEEEEEECCCCCCCCEEEEEECCCCEEEECHHHCCCCCC
T ss_conf             79999369949998916745668777884899716899997367877125678885699995797279713687225552


Q ss_pred             CCEEEEEECCCCCEEEEEECCC-CEEEEEECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCCEEEEEEEECCCCCEEEEE
Q ss_conf             5627885368980568896189-8099995699389955787783361-2141334218787568999733888369994
Q gi|254780353|r  637 KGKTFLKVSSEEKMKLVVKVTG-DHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGISDVICFKICEGLTWIDS  714 (753)
Q Consensus       637 ~Gk~~ikLk~~D~li~v~~~~~-d~iiliT~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~~~~~~~~~~~e~~~il~~  714 (753)
                      +|+.+++|+++|+|++|..+++ ++++++|++|++|||++++||+||| ++||++|+|++++.+..+++. .++..++++
T Consensus       635 ~G~~AikLke~DeLv~v~l~~~~~dIil~T~~G~alRF~~~eVR~~GR~a~GVkgIkL~~gD~VV~~~vv-~~~~~iL~v  713 (822)
T PRK05560        635 NGLIAINLDEGDELIGVRLTDGDDDVLLFSANGKAIRFPEEDVRPMGRTARGVRGIKLREGDEVVSMSVL-RDEQFVLTV  713 (822)
T ss_pred             CCEEEEECCCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCCCEECCCCCEEEEEEEE-CCCCEEEEE
T ss_conf             5519998589977999998489987999978973999506657777887768431551999989999985-799879999


Q ss_pred             CCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCEECC
Q ss_conf             177566451143225444136660275526776861049
Q gi|254780353|r  715 AGRSYNRSENDLLGWLGKRGGVGSLVPKGFPRSGKFLSS  753 (753)
Q Consensus       715 t~~g~~k~~~~~~~~~~~RggkG~~~~k~~~K~gklV~A  753 (753)
                      |++||+|+++..+|+.++|||+|++++|.++|+|+||+|
T Consensus       714 Te~G~GKRt~~~eyr~~~RGgkGv~~ik~~~k~G~lv~~  752 (822)
T PRK05560        714 TENGYGKRTPAEEYRLQGRGGKGVIAIKITERNGKLVGA  752 (822)
T ss_pred             ECCCEEEECCHHHCCCCCCCCCCEEEEEECCCCCCEEEE
T ss_conf             189805305288837557787775889964888848999


No 4  
>PRK13979 DNA topoisomerase IV subunit A; Provisional,Validated
Probab=100.00  E-value=0  Score=1965.81  Aligned_cols=734  Identities=31%  Similarity=0.518  Sum_probs=684.2

Q ss_pred             CCCCC-CCCCEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCC
Q ss_conf             76665-42456653199999988888889998510476411289704689999999868999898035405366654276
Q gi|254780353|r    8 NSNTL-VEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKL   86 (753)
Q Consensus         8 ~~~~~-~~~~i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gky   86 (753)
                      +...+ -+++|++++|++||++|||+||||||++||||||||||||||||||||||++|+.|++||+|||||||||||||
T Consensus         4 ~~~~~p~~~~i~~~~i~~em~~syl~YamsVI~~RAlPDvRDGLKPVhRRiLy~M~~lg~~~~~~~~KsArivGdv~Gky   83 (959)
T PRK13979          4 KKIVIPKDNNIIKFPLEEAMPENYLPYAVEVAKDRALPDVRDGLKPVHRRILYGAYMLKAFPDKPYYKSARIVGDILGKY   83 (959)
T ss_pred             CCCCCCCCCCEEEECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCC
T ss_conf             56678986875561489999988998889987750077644688518999999998738999999841235511026477


Q ss_pred             CCCHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEE
Q ss_conf             88747899999996100132166132678870886779710024689985599999984218786175216799632422
Q gi|254780353|r   87 HPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPV  166 (753)
Q Consensus        87 hPHGd~s~y~a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~  166 (753)
                      |||||+|||||||||||+|+||||||||||||||+||||||||||||||||++|++||+|||++||||+||||||++||+
T Consensus        84 HPHGD~avYdalVrmaQ~fs~r~pLidgqGNfGSidgD~~AAmRYTEarl~~~a~~ll~di~k~tVdf~~NyD~s~~EP~  163 (959)
T PRK13979         84 HPHGDSSVYDAMVILAQNFTTRMPLIDGHGNWGSIDGDSAAAMRYTEARLTPIAMEMLRDIDKDVVDMVDNYSDSEKEPK  163 (959)
T ss_pred             CCCCCHHHHHHHHHHHCCHHHCCCCEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCC
T ss_conf             89870479999999700013127606067867899998103430688888999999983304277476148898876865


Q ss_pred             EECCCCCHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCC
Q ss_conf             31234526764266504677775167778899999999987286532013443203677887760106988999898503
Q gi|254780353|r  167 VFPSKFPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLG  246 (753)
Q Consensus       167 ~lp~~~P~lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG  246 (753)
                      ||||+|||||||||+|||||||||||||||+|||+||++||+||+++++|||+|||||||||||+|+ |.+|++++|+||
T Consensus       164 VLPa~~PnLLvNGs~GIAVGMATnIPpHNL~Evida~~a~i~np~~t~~eLm~~i~GPDFPTGGiI~-g~~gi~~aY~TG  242 (959)
T PRK13979        164 VLPARYPNLLVNGAFGIAVGLATNIPPHNLKEVIDGTLAYIDNNEITTKELMNYIKGPDLPTGGILI-GKKSLLSAYETG  242 (959)
T ss_pred             CCCCCCCHHHHCCCCCCHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHCCCCCCCCCCEEE-CCHHHHHHHHHC
T ss_conf             1357774322137740114122587997889999999999708998899998218799889984898-878799999848


Q ss_pred             CCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCC----CHHHHHHHHCCCCCEEEEEEEECCCCCH
Q ss_conf             341599999998643788407999524200216899999999864022----2134577640676605889850454588
Q gi|254780353|r  247 RGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKR----IPLLEDIRDESAEDVRIVLFPKNRSLDP  322 (753)
Q Consensus       247 ~G~i~~r~k~~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~k----i~gi~dirDeSd~~~~~vi~~~~r~~~~  322 (753)
                      ||+|++||+|++|+.++|+++||||||||||||++++|+|++||++||    ++||+|+||||||+|+++|+++||++++
T Consensus       243 rG~i~iRak~~iE~~~~gr~~IiItEiPY~vnka~lie~Iaelv~~kk~~k~i~gIsdiRDESDr~GiRIVIelKr~a~~  322 (959)
T PRK13979        243 EGKVTLRAKTTIEKLENGRLGIVITEFPYRRNKAKLLQTISEMTADKKHSKALENISDIRDESDRNGIRAVIEFKKSADE  322 (959)
T ss_pred             CCEEEEEEEEEEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEECCCCCH
T ss_conf             98399998889996178844899996687577899999999999713133668860042013677863899997688975


Q ss_pred             H---HHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9---9999875420000122331133312689722049999998999989999999999999999999999999986410
Q gi|254780353|r  323 D---LLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLN  399 (753)
Q Consensus       323 ~---~vl~~Lyk~T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~  399 (753)
                      +   .|||+|||+|+||+||++||+||++| +|++|||+++|++|++||.+||+||++|+|+|+++|+||||||++|+++
T Consensus       323 ~v~e~vLn~Lyk~T~LQ~sf~vNmlaL~~g-~P~~l~Lk~iL~~fl~hR~eVI~RRt~~~L~ka~~R~HILeGL~iAl~n  401 (959)
T PRK13979        323 DVAEKVLKYLYKKTDLQCNISFNMVALADG-KPETMGLKAIIKHYVEHQKEVVTRRTKKELEIAEKRFHIVEGFIKAIGI  401 (959)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEEEEEEECCC-CCEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             769999999997498836774589973399-1349778999999999999999999999998899899999989999978


Q ss_pred             HHHHHHHHHCCC---CCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
Q ss_conf             789999752000---01100000025775778899887899998899997666789999887765442039788789999
Q gi|254780353|r  400 IDEIIAIIRNED---KPKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIA  476 (753)
Q Consensus       400 ID~vI~iIR~s~---~~k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~  476 (753)
                      ||+||+|||+|+   +|+..||++|+|||.||+|||+|||||||+||++|+++|+++|.++|++|+.||+|+++++++|+
T Consensus       402 IDevI~iIR~S~~~~~Ak~~L~~~f~lse~QA~AILdmrL~rLT~LE~~ki~~E~~eL~~~I~~l~~IL~s~~~l~~iIk  481 (959)
T PRK13979        402 MDEIIKTIRASKSKKDASENLIEKFGFTDEQAEAILELMLYRLTGLEIKVFEKEYKELEKLIKKLEKILSSEKELLKVIK  481 (959)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHH
T ss_conf             99999999818983799998987619999999999998999987889999999999999999999999679999999999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEECC-----CCCCCCCCCCCCCCCCCC
Q ss_conf             999999874177433455542000011000000110024566705998710102025-----655445532234555554
Q gi|254780353|r  477 CEIREVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRSL-----KSHSVDLSALHFKEGDSL  551 (753)
Q Consensus       477 ~EL~eikkkfgd~~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr~-----k~~~~~~~~~~~KegD~l  551 (753)
                      +||.+++++||++     |||.|++.. .+.+++.||||++|+++|++|++|||||+     ++++.|.+++.+|++|++
T Consensus       482 ~EL~eik~kygd~-----RRT~Ii~~~-~~~~~~~EDLI~~EdvVVtlS~~GYIKR~pl~~Y~RgGkG~~g~~~ke~D~v  555 (959)
T PRK13979        482 KELKEVKEKYGDE-----RRTSIIEDD-EKAKIDIEELIVVEDVVITLSNEGFIKRIPLKSYNRSNSNVEDIEYREGDFN  555 (959)
T ss_pred             HHHHHHHHHHCCC-----CCEEEECCC-CCCCCCHHHHCCCCCEEEEEECCCEEEECCHHHHCCCCCCCCCCCCCCCCCE
T ss_conf             9999999983998-----742666563-2033657673456655999806964750458881367899778755566510


Q ss_pred             EEEEEECCCCCEEEEECCCEEEEEEHHHCCCC--CCCCCCCCCCCCC--CCCCEEEEEEEE---CCCCEEEEEECCCCEE
Q ss_conf             01211114781789806882787551121212--3444422223576--765307899985---7998599997489789
Q gi|254780353|r  552 KIALHAHTTDRILLLSTDGKAYTLPAGNLLSG--RGHGEAIQLLIDL--NHNQDIVTAFVY---DSTCKLLVVSSKGNAF  624 (753)
Q Consensus       552 ~~~~~~~t~d~LLffTs~GkvY~l~a~~Ips~--~~kG~pI~~ll~l--~~~EkIv~~~~~---~~~~~lll~Tk~G~ik  624 (753)
                      .+++.|+|||+|||||+.|+|||+++|+||.+  +++|.||.|++++  .++|+|+++++.   +++.+++|+|++|++|
T Consensus       556 ~~l~~a~THd~lLfFTn~GkvY~lKvyeIPe~sr~aKG~~i~Nll~~l~l~~E~I~~il~v~~f~~~~~lvfaTk~G~VK  635 (959)
T PRK13979        556 KFLIQSNTKDTLLIFTDKGNMYQIKGINIPEFKWKEKGERLDEIIKTIDLEEEKIIEAYSIEDFTPQKDFIFITDSGGIK  635 (959)
T ss_pred             EEEEEECCCCEEEEEECCCEEEEEEEEECCCCCCCCCCCCHHHHCCCCCCCCCEEEEEEECCCCCCCCEEEEEECCCEEE
T ss_conf             26899528963999957985999870566777700389573441055788984589977412267775499992898688


Q ss_pred             EEEHHHHHCCCCCCEEEEEECCCCCEEEEEECCC-C---EEEEEECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCCEEE
Q ss_conf             9638874023335627885368980568896189-8---099995699389955787783361-2141334218787568
Q gi|254780353|r  625 IVEESEIIANTRKGKTFLKVSSEEKMKLVVKVTG-D---HVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGISD  699 (753)
Q Consensus       625 r~~l~~~~~~~k~Gk~~ikLk~~D~li~v~~~~~-d---~iiliT~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~~~~  699 (753)
                      |+++++| ..+++|+.+++|+++|+++.|..+.+ +   .+++.|.+|+++||+.+++|+||| ++||++|+|+++|.+.
T Consensus       636 Kt~L~~f-~~~~sgiiAIkL~egDeLI~V~l~~~~~~~~~i~l~T~~G~~irf~e~~vR~mGR~a~GVrgi~L~~~D~Vv  714 (959)
T PRK13979        636 KTSLDKF-NTNYSKLMALKLKKGEELIKVKLVDRTREEKFLKIKTKKGLSFTVEEPELEPVDRNILGYQLFNLSPNDSIK  714 (959)
T ss_pred             CCCHHHC-CCCCCCCEEEECCCCCEEEEEEEECCCCCCEEEEEECCCCEEEECCCHHCCCCCCCCCCEEEEECCCCCEEE
T ss_conf             3738982-855678366666999879878973588875079996589659971420224578766675214339999898


Q ss_pred             EEEEEC--------------------------------------------------------------------------
Q ss_conf             999733--------------------------------------------------------------------------
Q gi|254780353|r  700 VICFKI--------------------------------------------------------------------------  705 (753)
Q Consensus       700 ~~~~~~--------------------------------------------------------------------------  705 (753)
                      .+.+..                                                                          
T Consensus       715 sm~i~~~~e~~~~~~~i~~~g~i~~~~~~~~~~~~~~~~~~~~~ili~~~~G~~~~~~~~~~~~~~~~g~~i~~~~~~~~  794 (959)
T PRK13979        715 KVDFCDNYEYKEFYININKKGIIKISDLKKNKSHISLKTNSSKNLLLFSDKGKVYKIPAFMLQNIEESGINISALTGDFE  794 (959)
T ss_pred             EECCCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCCEEEECCCCCEEECCHHHCCCCCCCCCCCHHHHHHHC
T ss_conf             61022444200000233420023322100111111113566311354325772330324320233555645022221210


Q ss_pred             --------------CCCCEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCEECC
Q ss_conf             --------------888369994177566451143225444136660275526776861049
Q gi|254780353|r  706 --------------CEGLTWIDSAGRSYNRSENDLLGWLGKRGGVGSLVPKGFPRSGKFLSS  753 (753)
Q Consensus       706 --------------~e~~~il~~t~~g~~k~~~~~~~~~~~RggkG~~~~k~~~K~gklV~A  753 (753)
                                    .++..+++++++||+|++...+|+.++|++.|.+   ...++|.+|++
T Consensus       795 ~~e~vi~~~~~~~~~e~~~il~vTe~G~GKRT~~~eyr~~g~~~~~~k---~~~~~~~~v~~  853 (959)
T PRK13979        795 KKESIINAISIFEFEEDLSIYFFSKKGLVKKTLLSEFKGEGNSTQVYK---FKHKEDELVSV  853 (959)
T ss_pred             CCCCEEEEEECCCCCCCCEEEEEECCCCCCCCCHHHHCCCCCCEEEEE---EEECCCCEEEE
T ss_conf             223024665203577761599993589746665677334678648999---88448978999


No 5  
>COG0188 GyrA Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=1833.17  Aligned_cols=727  Identities=42%  Similarity=0.682  Sum_probs=693.0

Q ss_pred             EEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHH
Q ss_conf             66531999999888888899985104764112897046899999998689998980354053666542768874789999
Q gi|254780353|r   17 VKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYD   96 (753)
Q Consensus        17 i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~   96 (753)
                      |.+++|+++|++||++||||||++|||||||||||||||||||||+++|++|+++|+||||+|||||||||||||+||||
T Consensus         8 i~~v~i~~e~~~syl~YAmsVIv~RALPdVRDGLKPVqRRILYaM~e~gl~~d~~~kKsAriVGdvmGkyHPHGDssiYd   87 (804)
T COG0188           8 IEPIDIEDEMKRSYLDYAMSVIVGRALPDVRDGLKPVQRRILYAMFELGLTPDKKYKKSARIVGDVMGKYHPHGDSSIYD   87 (804)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf             51265999999999988799886401775234786089998899997499989970003066775335678887168999


Q ss_pred             HHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHH
Q ss_conf             99961001321661326788708867797100246899855999999842187861752167996324223123452676
Q gi|254780353|r   97 SLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLL  176 (753)
Q Consensus        97 a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL  176 (753)
                      ||||||||||||||||||||||||+|||||||||||||||||+|.+||.||+++||||+|||||+++||+||||+|||||
T Consensus        88 alVRMAQdfs~RypLVdgqGNFGSiDgD~aAAMRYTEaRLs~ia~elL~di~kdtVdf~~NyDg~~~EP~VLPa~~PnLL  167 (804)
T COG0188          88 ALVRMAQDFSLRYPLVDGQGNFGSIDGDPAAAMRYTEARLSKIAEELLEDIDKDTVDFVPNYDGSEKEPEVLPARFPNLL  167 (804)
T ss_pred             HHHHHHHHHHHCCCCEECCCCCCCCCCCHHHHHHHHHHHCHHHHHHHHHCCCCCEEECCCCCCCCCCCCCCCCCCCCEEE
T ss_conf             99997104341576231687788999973787778886231989998744465705144079998558740346687067


Q ss_pred             HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEE
Q ss_conf             42665046777751677788999999999872865320134432036778877601069889998985033415999999
Q gi|254780353|r  177 ANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARW  256 (753)
Q Consensus       177 ~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~  256 (753)
                      +|||+|||||||||||||||.|||+||+++|+||++++++||++||||||||||+|+ |.+||+++|+||||+|++||+|
T Consensus       168 vNGssGIAVGmATnIPPHNl~Ev~da~~~li~np~~~~~~lm~~i~GPDFPTgg~I~-g~~~I~~aY~tGrG~i~vRa~~  246 (804)
T COG0188         168 VNGSSGIAVGMATNIPPHNLGEVIDALIALIDNPDATIDELMEIIKGPDFPTGGIII-GRSGIREAYETGRGSIRVRAKA  246 (804)
T ss_pred             ECCCCCEECCEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCEEE-CCHHHHHHHCCCCCEEEEEEEE
T ss_conf             606874101230577998989999999999709997467773106999899866685-4145678770078459999899


Q ss_pred             EEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCC
Q ss_conf             98643788407999524200216899999999864022213457764067660588985045458899999875420000
Q gi|254780353|r  257 CVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDME  336 (753)
Q Consensus       257 ~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq  336 (753)
                      ++|+.+.|+++||||||||||||++++|+|++|+++||+.||+++|||||++|+++++++|+++.++.+||+|||+|+||
T Consensus       247 ~iE~~~~gr~~IvItEiPyqvnka~lie~Iaelv~~kki~gis~vrDEsdr~giRivIelk~~~~~~~vln~Lfk~T~LQ  326 (804)
T COG0188         247 EIEDTKNGREQIVITEIPYQVNKAKLIEKIAELVKEKKIEGISDIRDESDREGIRIVIELKRDAVAEVVLNNLFKLTDLQ  326 (804)
T ss_pred             EEEECCCCCEEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHHHHHHHHCHHH
T ss_conf             99953788338999966970158999999999985487357300001026887079999777641789999998744187


Q ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---C
Q ss_conf             1223311333126897220499999989999899999999999999999999999999864107899997520000---1
Q gi|254780353|r  337 TRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDK---P  413 (753)
Q Consensus       337 ~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s~~---~  413 (753)
                      ++|++||+||+. ++|++++|++||++|++||+++++||++|+|+|+++|+||||||++|+++||+||+|||+|++   |
T Consensus       327 ~~f~~nm~ai~~-~~P~~~~L~~iL~~~~~hr~~vi~rR~~~~L~Ka~~R~hileGl~~a~~~iDevI~iIr~s~~~~~a  405 (804)
T COG0188         327 TSFNVNMLALVN-GRPKVLNLKEILSEFLEHRLEVVTRRTEYELNKAEERLHILEGLLIALLNIDEVIEIIRESKDKPEA  405 (804)
T ss_pred             HHHCCEEEEECC-CCCEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf             750710687317-8031537999999999999999889999999999999989988999997147889888708981678


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             10000002577577889988789999889999766678999988776544203978878999999999987417743345
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLG  493 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~~~~~  493 (753)
                      +..||++|+|||.||+|||+|||||||+||++++++|+++|.++|++|+.||+|+.++++++++||.+++++||++    
T Consensus       406 ~~~L~~~f~lse~Qa~aIl~mrL~rLt~le~~~i~~E~~~L~~~i~~l~~iL~s~~~~~~~i~~eL~~~~~k~gd~----  481 (804)
T COG0188         406 KEELMARFGLSEKQAEAILDLRLRRLTGLEEEKIEKELKELEKEIADLEKILASEERLLDIIKKELLEIKKKFGDE----  481 (804)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHCCC----
T ss_conf             9999987389678899998626777640408788889999999999999875388999999999999999871853----


Q ss_pred             CCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEECCCCCCCC---CCCCCCCCCCCCEEEEEECCCCCEEEEECCC
Q ss_conf             5542000011000000110024566705998710102025655445---5322345555540121111478178980688
Q gi|254780353|r  494 RRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRSLKSHSVD---LSALHFKEGDSLKIALHAHTTDRILLLSTDG  570 (753)
Q Consensus       494 ~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr~k~~~~~---~~~~~~KegD~l~~~~~~~t~d~LLffTs~G  570 (753)
                       |||.|......  ....|++|++|+++|++|+.||+||++...+.   .++..+|++|++...+.|+|||+++|||+.|
T Consensus       482 -Rrt~i~~~~~~--~~~~edli~~e~vvv~ls~~gyikr~~~~~~~~q~~~~~~~ke~d~~~~~~~~~t~d~ll~ft~~G  558 (804)
T COG0188         482 -RRTEIVEEEED--EIEDEDLIAEEDVVVTLSHKGYIKRVPLKGYEAQRVSGLGLKEGDFLERLFEANTHDTLLFFTSKG  558 (804)
T ss_pred             -CEEHHCCCCCC--CCCHHHHCCCCCEEEEECCCCEEEECCHHHHHHHHHHHCCCCCCCHHHHEEEECCCCEEEEECCCC
T ss_conf             -20001156532--232133133554499981653278634566433022111324340334305504664699982788


Q ss_pred             EEEEEEHHHCC--CCCCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCEEEEEHHHHHCCCCCCEEEEEECCCC
Q ss_conf             27875511212--1234444222235767653078999857998599997489789963887402333562788536898
Q gi|254780353|r  571 KAYTLPAGNLL--SGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKGKTFLKVSSEE  648 (753)
Q Consensus       571 kvY~l~a~~Ip--s~~~kG~pI~~ll~l~~~EkIv~~~~~~~~~~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~D  648 (753)
                      ++|++++|++|  +++++|+|+.++++++++|+|+.+++.+++.+++|+|++|++|++.+++|.+.+++|+.+++|+++|
T Consensus       559 ~~y~~~~~~lp~~~~~~~G~~i~~ll~~~~~E~i~~v~~~~~~~~l~~~T~~G~vK~~~l~~f~~~~~~g~~ai~L~~~d  638 (804)
T COG0188         559 RVYKLKVYELPEGSRRSRGEPIVNLLSLEKGEKITAVLPVNDDQYLFLATKKGYVKKTSLSEFKNIRSKGKIAIKLKEGD  638 (804)
T ss_pred             CEEEECCEECCCCCCCCCCHHHHHHCCCCCCCEEEEEEECCCCEEEEEEECCCCEEEEEHHHHHCCCCCCEEEEECCCCC
T ss_conf             48973130335556666781035424578885479999707860599991699479820355312356770689717776


Q ss_pred             CEEEEEECC--CCEEEEEECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCCEEEEEEEECCCCC-EEEEECCCCCCCCCH
Q ss_conf             056889618--98099995699389955787783361-21413342187875689997338883-699941775664511
Q gi|254780353|r  649 KMKLVVKVT--GDHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGISDVICFKICEGL-TWIDSAGRSYNRSEN  724 (753)
Q Consensus       649 ~li~v~~~~--~d~iiliT~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~~~~~~~~~~~e~~-~il~~t~~g~~k~~~  724 (753)
                      .+.++..+.  +++++++|++|+++||+.+++|.||| ++||++|+|++++.+..+.+ ..++. .+++++++|++|+++
T Consensus       639 ~l~~~~~~~~~~~~i~~~t~~G~~~~F~~~~v~~~gr~a~Gv~~i~l~~~d~~~~~~~-~~~~~~~~l~~t~~g~~kr~~  717 (804)
T COG0188         639 ELVSVSLTSDGDDDILLVTSNGKALRFPESEVREMGRGAKGVKGIKLKEGDKVVSLSV-VEDDEAKLLTVTERGYGKRTK  717 (804)
T ss_pred             CEEEEEECCCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCCCEEECCCCCEEEEEEE-CCCCCEEEEEEECCCCEEECC
T ss_conf             3012452157876089991487378740344221154136864064376575665320-147860589984367200041


Q ss_pred             HHHCCCCCCCCCCCCCCCCCCCC-CCEECC
Q ss_conf             43225444136660275526776-861049
Q gi|254780353|r  725 DLLGWLGKRGGVGSLVPKGFPRS-GKFLSS  753 (753)
Q Consensus       725 ~~~~~~~~RggkG~~~~k~~~K~-gklV~A  753 (753)
                      ..+|+.++||++|++.++.++|+ |.++++
T Consensus       718 ~~~~~~~~Rg~~G~~~~~~~~~~~~~~~~~  747 (804)
T COG0188         718 ISEYPVTKRGGKGVILIKGTKRNRGKVVAA  747 (804)
T ss_pred             HHHCCCCCCCCCCEECCCCCCCCCCEEEEE
T ss_conf             421342466766412454555655337764


No 6  
>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit; InterPro: IPR005741   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit A (parC) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=1782.33  Aligned_cols=722  Identities=32%  Similarity=0.543  Sum_probs=682.5

Q ss_pred             EEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHH
Q ss_conf             66531999999888888899985104764112897046899999998689998980354053666542768874789999
Q gi|254780353|r   17 VKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYD   96 (753)
Q Consensus        17 i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~   96 (753)
                      +++.+|++.|.+||-.||.|+|+||||||+|||||||||||||||+++|+++++||+||||.||+|||||||||||||||
T Consensus         1 ~~~~~Le~v~g~~F~kYaKYIIQDRALPD~RDGLKPVQRRILYaM~~~G~~fdk~YkKSAr~VGev~GkYHPHGDSSiYd   80 (745)
T TIGR01061         1 IINLPLEEVVGESFGKYAKYIIQDRALPDIRDGLKPVQRRILYAMSEDGNTFDKPYKKSARTVGEVIGKYHPHGDSSIYD   80 (745)
T ss_pred             CCCCCHHHHHHCCCCCCCCCEEECCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCCCCCCCCHHHH
T ss_conf             97875035440000000251340456665111577035778766532378668870012011102226712898644778


Q ss_pred             HHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHH
Q ss_conf             99961001321661326788708867797100246899855999999842187861752167996324223123452676
Q gi|254780353|r   97 SLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLL  176 (753)
Q Consensus        97 a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL  176 (753)
                      |||||+|+|.+|..||+.|||.||+||||||||||||||||++|.+||+||||+||.|+||||+|++||+||||.|||||
T Consensus        81 AmvRMSQ~WKn~~~lv~mHGNnGSiDGDnaAAMRYTEaRLS~iA~~LL~di~K~~V~F~~NFDDseKEP~vLP~lfPNLL  160 (745)
T TIGR01061        81 AMVRMSQDWKNNLVLVEMHGNNGSIDGDNAAAMRYTEARLSKIASELLKDIDKKTVKFIPNFDDSEKEPTVLPALFPNLL  160 (745)
T ss_pred             HHHHCCCCCCCCEEEEEEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCCEECCCCCCCCCCCCCCHHHHHHHHHH
T ss_conf             86414746334318998506667889985155432476677999999740477831033687788877742344213456


Q ss_pred             HCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEE
Q ss_conf             42665046777751677788999999999872865320134432036778877601069889998985033415999999
Q gi|254780353|r  177 ANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARW  256 (753)
Q Consensus       177 ~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~  256 (753)
                      ||||||||.||||||||||++||+||++..||.|+|++++||+++|||||||||.| ++.+||++||+||+|+|.||||+
T Consensus       161 iNGatGIaAGYATnIpPHn~~Ev~Da~i~rId~P~c~v~~L~e~~kgPDFPTGG~i-~~~~~~~~aY~tGkGk~iirak~  239 (745)
T TIGR01061       161 INGATGIAAGYATNIPPHNLNEVIDALIYRIDHPDCSVDKLMEIVKGPDFPTGGII-QGEDGIKKAYETGKGKFIIRAKI  239 (745)
T ss_pred             HHHHHHHHCCHHCCCCCCCHHHHHHHHHHHCCCCCCCHHHHHHHCCCCCCCCCCEE-ECHHHHHHHHHCCCCEEEEEEEE
T ss_conf             52013320000047788876689999986138988417889854484115887246-14154788985498139998642


Q ss_pred             EEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCC
Q ss_conf             98643788407999524200216899999999864022213457764067660588985045458899999875420000
Q gi|254780353|r  257 CVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDME  336 (753)
Q Consensus       257 ~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq  336 (753)
                      ++|-.++|++|||||||||.||||.++++|+|..-++|+.||.+|||||||+|.+|+++.|++++.+.|||+|||+|+||
T Consensus       240 ~~e~~~ng~~QI~It~IPYE~nKAnlvK~iedi~~d~kv~gi~eVrDeSDr~GlriiI~~Kk~~~~e~v~nyLyK~T~Lq  319 (745)
T TIGR01061       240 EIEVNKNGLNQIVITEIPYETNKANLVKKIEDIIVDKKVAGIEEVRDESDRKGLRIIIELKKDANAEKVLNYLYKKTDLQ  319 (745)
T ss_pred             EEEEECCCCCEEEECCCCHHHHHHHHEEEEEEEEECCEEHHHHHCCCCCCCCCCEEEEECCCCCCHHHHHHHHCCCCCCE
T ss_conf             55320588204897457467766764000002676450000010034457575546560545247556787541343543


Q ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC---CC
Q ss_conf             122331133312689722049999998999989999999999999999999999999986410789999752000---01
Q gi|254780353|r  337 TRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNED---KP  413 (753)
Q Consensus       337 ~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s~---~~  413 (753)
                      .+|+.||+||. ++.|.++||..+|++|+.|++|||.+|..|||+||++|+||+|||++|++-|||||++||+|.   ||
T Consensus       320 i~YN~n~vaI~-nr~P~lv~L~~yLd~yi~h~~evi~~~~~Ydl~ka~~R~~IveGLik~isilDeiI~~IRas~~k~DA  398 (745)
T TIGR01061       320 INYNFNMVAIA-NRTPILVGLLSYLDAYIKHSKEVIINRSLYDLEKAKKRLEIVEGLIKAISILDEIIKLIRASEDKSDA  398 (745)
T ss_pred             EEECCCCEEEC-CCCCEEECHHHHHHHHHHHHHHHEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCH
T ss_conf             86432417840-47633644016888887230232002464238889878898888999999987898877302453360


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             10000002577577889988789999889999766678999988776544203978878999999999987417743345
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLG  493 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~~~~~  493 (753)
                      |+.|+..|+||+.|||||+.|||||||+.|+-.|++|.+||.++++.|+.+|+|+..+.++|+++|.++||+|+++    
T Consensus       399 k~~Li~~f~FT~~QAEAIv~LrLY~LTnTDi~~L~~E~~eL~~~~~~l~~~i~~~k~~~~~lk~~l~~~KK~F~~~----  474 (745)
T TIGR01061       399 KENLIDKFEFTENQAEAIVSLRLYRLTNTDIFELKEEEEELEKKIKSLEEIIASEKARKKLLKKKLKELKKKFAQE----  474 (745)
T ss_pred             HHHHCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC----
T ss_conf             3431011377725799999988603732037777878999999999999987657899999899999872310575----


Q ss_pred             CCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCC-EEECCCCCCCCCC---CCCCCCCCCCEEEEEECCCCCEEEEECC
Q ss_conf             55420000110000001100245667059987101-0202565544553---2234555554012111147817898068
Q gi|254780353|r  494 RRRTTFCEVSRADKATLQQAMIEKEPITVVISNRG-WIRSLKSHSVDLS---ALHFKEGDSLKIALHAHTTDRILLLSTD  569 (753)
Q Consensus       494 ~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~G-yIKr~k~~~~~~~---~~~~KegD~l~~~~~~~t~d~LLffTs~  569 (753)
                       |||.|.+. -...++++++||+++++.|++|++| |+|+.+..++..+   .++.|++|-+.+...++|||.||+|||.
T Consensus       475 -R~s~l~~~-~~~~~i~~~~li~~~~~~v~itk~GnY~K~~S~~sf~ss~~~d~g~~~~d~l~~~~~~nttd~lL~~Ts~  552 (745)
T TIGR01061       475 -RRSKLEDE-IEKIKINEDELIEKEDLYVVITKDGNYIKRTSKRSFASSKYDDFGLKDDDILFYQTIANTTDKLLIFTSK  552 (745)
T ss_pred             -HHHHHHHH-HHHEECCHHHHHHHCCCEEEEEECCCEEHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHCCCEEEEEECC
T ss_conf             -04567511-6530104678532146407998447630001266762047311577553345354652122537887616


Q ss_pred             CEEEEEEHHHCCCCCCC--CCCCCCCCC-CCCCCEEEEEEEE---C-CCCEEEEEECCCCEEEEEHHHHHCCC---CCCE
Q ss_conf             82787551121212344--442222357-6765307899985---7-99859999748978996388740233---3562
Q gi|254780353|r  570 GKAYTLPAGNLLSGRGH--GEAIQLLID-LNHNQDIVTAFVY---D-STCKLLVVSSKGNAFIVEESEIIANT---RKGK  639 (753)
Q Consensus       570 GkvY~l~a~~Ips~~~k--G~pI~~ll~-l~~~EkIv~~~~~---~-~~~~lll~Tk~G~ikr~~l~~~~~~~---k~Gk  639 (753)
                      |++..+|+|+||+.||+  |+|+++.+. ++.+|+|+.+.+.   + +...|+++|+.|++||+++++|...+   .+..
T Consensus       553 g~~In~pvh~La~~rwkd~g~hls~~~~n~~~~E~iv~v~~~~~fdv~~~~L~l~sklg~vKriel~~l~~~~~y~sK~~  632 (745)
T TIGR01061       553 GNLINLPVHKLADIRWKDLGEHLSNKITNFDENETIVAVEILNEFDVDEAILVLASKLGMVKRIELTELDIKRNYRSKAI  632 (745)
T ss_pred             CCEEEEEEEECCCCCHHHHHHHHCCHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHCCCEEEEECCCCCCCCCCHHHHH
T ss_conf             66642130314566566899872000110210684899986132257468989987558747876032477865101223


Q ss_pred             EEEEECCCCCEEEEEECCC---CEEEEEECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCCEEEEEEEECCCCCEEEEEC
Q ss_conf             7885368980568896189---8099995699389955787783361-21413342187875689997338883699941
Q gi|254780353|r  640 TFLKVSSEEKMKLVVKVTG---DHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGISDVICFKICEGLTWIDSA  715 (753)
Q Consensus       640 ~~ikLk~~D~li~v~~~~~---d~iiliT~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~~~~~~~~~~~e~~~il~~t  715 (753)
                      .+++|+++|.++.+....+   +.|+++|+.|++|+|.++|||..|+ |+|||+|+||++|.+.++.+....+..++ .+
T Consensus       633 ~~~~L~D~d~li~a~~~~~Gh~~~i~lvS~~gy~l~F~~~Ei~~~~~~A~GvK~mkLK~~D~v~~~~i~~~~~~~vl-l~  711 (745)
T TIGR01061       633 LILKLKDEDELISAFLQKKGHDKLIILVSKLGYALLFLVEEINVVGAKAAGVKGMKLKEDDEVKSGLILEANESLVL-LT  711 (745)
T ss_pred             HHHHCCCCCCEEEEEEECCCCCCEEEEEEECCCEEEECCEEECCCCCCCCCEEEEECCCCCEEEEEEEECCCCCEEE-EE
T ss_conf             32111789543899984188844189997368357730203323144667311330576763899999827995589-97


Q ss_pred             CCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             77566451143225444136660275526776
Q gi|254780353|r  716 GRSYNRSENDLLGWLGKRGGVGSLVPKGFPRS  747 (753)
Q Consensus       716 ~~g~~k~~~~~~~~~~~RggkG~~~~k~~~K~  747 (753)
                      .+|-.|+.+..|...++|+.+|+.+.|...|.
T Consensus       712 ~~Gs~k~~~~~El~~~sRa~~~~~llRp~kk~  743 (745)
T TIGR01061       712 QRGSVKRLSISELKVTSRAATGVKLLRPLKKK  743 (745)
T ss_pred             ECCCEEEEEHHHHHHHHHHCCCCHHHCCCCCC
T ss_conf             36825651036555534311651111000047


No 7  
>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit; InterPro: IPR005742   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit A (parC) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=1661.97  Aligned_cols=733  Identities=41%  Similarity=0.737  Sum_probs=703.8

Q ss_pred             EEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHH
Q ss_conf             66531999999888888899985104764112897046899999998689998980354053666542768874789999
Q gi|254780353|r   17 VKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYD   96 (753)
Q Consensus        17 i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~   96 (753)
                      |..+++.+.+++.||.||||||.+||||+|+||||||||||+|||.+|+|.++++||||||+||||+||||||||+||||
T Consensus         1 iE~~~l~~~~~~~YL~Y~~~~IM~RaLP~i~DGLKPV~RR~~YAM~~L~L~a~a~yKKsAR~VGDVlGKyHPHGD~A~Y~   80 (747)
T TIGR01062         1 IENLDLRNFTEEAYLNYSLYVIMDRALPFIGDGLKPVQRRIVYAMSELGLNANAKYKKSARTVGDVLGKYHPHGDSAVYE   80 (747)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEECCEECCCCCCCCCCCCHHHHH
T ss_conf             97651578988888888888887423772025775146899888887164767775200102102124605896248999


Q ss_pred             HHHHHCCHHHCCCCCCCCCCCCCCCCC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHH
Q ss_conf             999610013216613267887088677-9710024689985599999984218786175216799632422312345267
Q gi|254780353|r   97 SLVRLAQPFVQRYPLISGQGNFGNIDG-DSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNL  175 (753)
Q Consensus        97 a~v~maq~~~~~~pli~g~GnfGs~~~-d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~l  175 (753)
                      |||+|||+||+|||||||||||||+|+ |++|||||||.|||++|+.||.||+++||||+||||||..||.+|||+|||+
T Consensus        81 ~~V~~AQ~FS~RYPLvDGQGN~Ga~DdP~~~AAMRYTESRl~~~s~lLl~~l~~~TvD~~~~fD~~~~EP~~lPA~lP~~  160 (747)
T TIGR01062        81 ALVLLAQPFSYRYPLVDGQGNWGAPDDPKSFAAMRYTESRLSKISELLLEELGQGTVDFRPNFDGTLLEPKILPARLPNI  160 (747)
T ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHH
T ss_conf             99986211123476201677868898742123433246678999999998618872133457887424644253112055


Q ss_pred             HHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEE
Q ss_conf             64266504677775167778899999999987286532013443203677887760106988999898503341599999
Q gi|254780353|r  176 LANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRAR  255 (753)
Q Consensus       176 L~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k  255 (753)
                      |+||++||||||||+||||||.|||+|++++||+|+++++++|++|+||||||||+|+...+.|+.+|++|||||++||.
T Consensus       161 L~NG~~GIAVGMAT~IPPHNl~E~adA~~~LiD~P~agl~d~l~~v~GPDfPT~a~II~~~~~I~~~Y~~GRGS~r~Ra~  240 (747)
T TIGR01062       161 LLNGTTGIAVGMATDIPPHNLRELADAALYLIDNPKAGLDDILNIVQGPDFPTEAEIIDKKEEIRKIYETGRGSVRMRAR  240 (747)
T ss_pred             HCCCCCCEEEECCCCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHHHCCCCCCCCCEEECCHHHHHHHHHCCCCEEEEEEE
T ss_conf             60688724752217888623799999999985288321689999734857898765747189999998569833897226


Q ss_pred             EEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCC--EEEEEEEECCCCCHHHHHHHHHHHC
Q ss_conf             99864378840799952420021689999999986402221345776406766--0588985045458899999875420
Q gi|254780353|r  256 WCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAED--VRIVLFPKNRSLDPDLLMESIFMLS  333 (753)
Q Consensus       256 ~~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~--~~~vi~~~~r~~~~~~vl~~Lyk~T  333 (753)
                      |+-|+.+.|.++||||+||||++++++|++||.++++||+|.|+|+|||||++  +|+|++++.+..|++.||++||+.|
T Consensus       241 W~KE~~syGty~ivi~~lP~Q~~~sk~i~QIA~~~~~KKlP~~~~iRDEsDH~~~iR~Vi~PR~~~~D~~~vM~~LF~~T  320 (747)
T TIGR01062       241 WKKEDGSYGTYQIVISALPHQISKSKVIEQIAIQLKDKKLPLISDIRDESDHENPIRVVIVPRSNRVDPDIVMEHLFATT  320 (747)
T ss_pred             EEECCCCCCCEEEEEECCCCCCCCHHHHHHHHHHHHHCCCCCHHHCCCCCCCCCCEEEEEECCCCCCCHHHHHHHHHHHH
T ss_conf             53014666502676522775354015889999999717887024203423677856899843887768799999986542


Q ss_pred             CCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCC
Q ss_conf             00012233113331268972204999999899998999999999999999999999999998641078999975200001
Q gi|254780353|r  334 DMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDKP  413 (753)
Q Consensus       334 ~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s~~~  413 (753)
                      +||.+|.+|||+|..+.+|.+++|.|||++|+.||+++|+||.+|+|+|...|||||+||.+|+.||||||+|||+.|+|
T Consensus       321 ~LE~~~~~N~N~IG~~~~P~V~nlLEIL~E~L~fR~~~v~RR~~Y~L~Kv~~RL~IL~~L~i~fLN~DEvIEIIR~EDeP  400 (747)
T TIGR01062       321 DLEKSYRLNMNMIGLDNKPAVKNLLEILQEWLVFRRNTVIRRLTYRLNKVLKRLHILEGLLIAFLNIDEVIEIIREEDEP  400 (747)
T ss_pred             CHHHHEEEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCC
T ss_conf             20011233224640698960454899999999855888787888779999989988764755202100101222379984


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCC
Q ss_conf             10000002577577889988789999889999766678999988776544203978878999999999987417743345
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLG  493 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~~~~~  493 (753)
                      |+.||++|+||+.||++||++|||+|.+||+.++..|+.+|+++...|++||.|+.++|+++|+|+++..++||+..-.|
T Consensus       401 K~~lM~RF~ls~~Q~e~IL~~rLR~L~KLEE~~i~~E~~~L~K~~~~L~~IL~~~~~l~~l~KKEi~~~~~~yg~ntiiG  480 (747)
T TIGR01062       401 KTILMERFKLSEIQAEAILNLRLRHLAKLEEHKIKDEQSELEKERAILEKILKSERKLNQLVKKEIQADAKKYGLNTIIG  480 (747)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCEEC
T ss_conf             28998550635899999986555565457788887656677899999999987568999999899999998740242203


Q ss_pred             CCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEECCCEEE
Q ss_conf             55420000110000001100245667059987101020256554455322345555540121111478178980688278
Q gi|254780353|r  494 RRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAY  573 (753)
Q Consensus       494 ~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr~k~~~~~~~~~~~KegD~l~~~~~~~t~d~LLffTs~GkvY  573 (753)
                      .|||.+.|.+.+....+..++++.|||||++|+-||+|+.|||..+.+++++|+||..++.+.+.|+|.++|++|+||.|
T Consensus       481 ~R~~~l~E~~~~~~~~~~t~~~~~EPvTii~S~MGWVRs~KGH~~D~~~l~YK~GD~~~~~~~~~~~~~v~~i~S~GR~y  560 (747)
T TIGR01062       481 ARRSSLEEREEAKQVSEITDMIPKEPVTIILSKMGWVRSAKGHDIDLSTLKYKAGDSEKAIIEGKSNQKVVFIDSTGRSY  560 (747)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEECCCCCCCCCCCCCCCCCCEEEEEEECCCCEEEEEECCCCEE
T ss_conf             55451356788888876653036788179982777355046656671435413686123345512775179997288526


Q ss_pred             EEEHHHCCCCCCCCCCCCCCCCCCCC-CEEEEEEEECCCCEEEEEECCCCEEEEEHHHHHCCCCCCEEEEEECCCCCEEE
Q ss_conf             75511212123444422223576765-30789998579985999974897899638874023335627885368980568
Q gi|254780353|r  574 TLPAGNLLSGRGHGEAIQLLIDLNHN-QDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKGKTFLKVSSEEKMKL  652 (753)
Q Consensus       574 ~l~a~~Ips~~~kG~pI~~ll~l~~~-EkIv~~~~~~~~~~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~D~li~  652 (753)
                      .+.+..||++++.|+|++..|.++.| ..|.+++...+++.||++|.-|+||.+..+++.+.+|.||.+|++.|+-.++.
T Consensus       561 ~l~~~~l~~a~g~G~Pl~~KL~l~~Gn~~i~~~l~~~~~Q~LL~AS~~G~GF~~~~~~liA~~k~GK~l~~lPE~~~~~~  640 (747)
T TIGR01062       561 ALDPLNLPSARGQGEPLTGKLLLPIGNATIENILMESENQKLLLASDAGYGFLVKFNDLIARNKAGKALINLPENASVLA  640 (747)
T ss_pred             EECCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEECCCCCCEEEECHHHHHHCHHCHHHCCCCCCCEEEC
T ss_conf             63112043456778722688732688623107776358853210001686247400433331100402001788861104


Q ss_pred             EEECCCCE--EEEEECCCCEEEEEHHHCCCCCHHHCCEEEECCC-------CCEEEEEEEECCCCCEEEEECCCCCCCCC
Q ss_conf             89618980--9999569938995578778336121413342187-------87568999733888369994177566451
Q gi|254780353|r  653 VVKVTGDH--VAVVGENRKLLIFSIDQIPEMSRGKGVRLQSYKD-------GGISDVICFKICEGLTWIDSAGRSYNRSE  723 (753)
Q Consensus       653 v~~~~~d~--iiliT~~Gk~LrF~~~eIr~~gRgkGVk~i~Lkd-------~~~~~~~~~~~~e~~~il~~t~~g~~k~~  723 (753)
                      |..+.++.  ++++|+.|++|.|+++++|.|.||+|+++++++.       +.+..+..+...+++.|- .+++....+.
T Consensus       641 p~~~~~~s~~~~aI~~a~R~L~F~~~~lP~l~KG~G~~~~~~~~a~A~~~~~~L~~l~~~~~Q~~L~~~-~Gk~KI~L~~  719 (747)
T TIGR01062       641 PLVVNDDSDLIVAITEAGRLLVFPIDDLPELSKGKGNKLIRIPAANAKDREELLLDLKILNKQDGLSFN-DGKRKIKLKP  719 (747)
T ss_pred             CEEECCCCCEEEEECCCCEEEEECHHHCCCCCCCCCCEEEEECCHHHCCCCCCCEEEEEECCCCCEEEC-CCCEEEEECH
T ss_conf             434237610244411367068742111776347873057750541001200010123453577732420-4822452357


Q ss_pred             HHHHCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             143225444136660275526776861
Q gi|254780353|r  724 NDLLGWLGKRGGVGSLVPKGFPRSGKF  750 (753)
Q Consensus       724 ~~~~~~~~~RggkG~~~~k~~~K~gkl  750 (753)
                      +++..+.++||++|...|++++++.++
T Consensus       720 ~~l~~~~g~RG~~G~~~~~Gl~~~~~~  746 (747)
T TIGR01062       720 EELQKFLGERGRKGTTLPRGLPKNNRV  746 (747)
T ss_pred             HHHHHHHHCCCCCCCCCCCCCCHHHCC
T ss_conf             767755304688788675454411015


No 8  
>PRK09631 DNA topoisomerase IV subunit A; Provisional
Probab=100.00  E-value=0  Score=1274.91  Aligned_cols=592  Identities=28%  Similarity=0.414  Sum_probs=486.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             19999998888888999851047641128970468999999986899989803540536665427688747899999996
Q gi|254780353|r   21 SLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVR  100 (753)
Q Consensus        21 ~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~  100 (753)
                      +|+++|++|||+||||||++|||||||||||||||||||||++|+   +++|+|||||||+|| |||||||+||||||||
T Consensus         2 ~i~~~~~~~~l~Ya~~VI~~RAlPdv~DGLKPvqRRiL~~m~~~~---~~~~~K~A~ivG~~m-kyHPHGd~siy~alV~   77 (626)
T PRK09631          2 DIKTLLKDNFLQYSSYVIKDRAIASVIDGFKPVQRRIIHSLFEMH---DGNFHKVANVVGNTM-KYHPHGDTSIYEALVN   77 (626)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHCC---CCCCCEEEEEECCCC-CCCCCCCHHHHHHHHH
T ss_conf             868999999998889998850277521488659999999998648---999857628850511-2689982479999999


Q ss_pred             HCCHHHCCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHCC
Q ss_conf             100132166132678870886-7797100246899855999999842187861752167996324223123452676426
Q gi|254780353|r  101 LAQPFVQRYPLISGQGNFGNI-DGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANG  179 (753)
Q Consensus       101 maq~~~~~~pli~g~GnfGs~-~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL~Ng  179 (753)
                      |||    |||||||||||||+ |||+||||||||||||++|.+||  ++++||||+|||||+++||+||||+|||||+||
T Consensus        78 maq----~~~lid~qGNfGsi~~gD~aAA~RYtEaRls~~a~e~l--~~~~tv~~~~nyDg~~~EP~vLP~~~PnLL~nG  151 (626)
T PRK09631         78 IAN----KDLFIEKQGNFGNLFTGDPASASRYIECRLTPLAFEVL--YSKEITSYEPSYDGRNNEPLIFPAKIPVILIQG  151 (626)
T ss_pred             HHC----CCCCEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHH--CCCCCCEECCCCCCCCCCCEEEECCCCHHHHCC
T ss_conf             856----57605278888899998834566689897799999983--787851201278987446405553573777526


Q ss_pred             CCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEEEEE
Q ss_conf             65046777751677788999999999872865320134432036778877601069889998985033415999999986
Q gi|254780353|r  180 TSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCVE  259 (753)
Q Consensus       180 ~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~~~e  259 (753)
                      |+|||||||||||||||+|||+|++++|++|++++        +|||||||+|. .     +.|+||+|+|++||+++++
T Consensus       152 ~~GIAVGmaT~IpPHNl~Evida~i~~l~~~~~~~--------~PDFPTGG~i~-~-----~~Y~tG~G~i~vRak~e~~  217 (626)
T PRK09631        152 SEGIAVGMAAKILPHNFNEILEAVKSELLGESYDL--------YPDFPTGGIVD-V-----NEYADGNGKVLVRAKIETT  217 (626)
T ss_pred             CCCHHHHHHCCCCCCCHHHHHHHHHHHHCCCCCCC--------CCCCCCCCCCC-H-----HHHHCCCEEEEEEEEEEEC
T ss_conf             74221222106899888999999998533898766--------99999875103-3-----2563486279999999981


Q ss_pred             ECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCCCCC
Q ss_conf             43788407999524200216899999999864022213457764067660588985045458899999875420000122
Q gi|254780353|r  260 EVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRF  339 (753)
Q Consensus       260 ~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq~sf  339 (753)
                      +    +++|||||||||+|+++++|+|++++++|||+ |+++||||++++++|+++ +|+++|+++||+||++|+||+||
T Consensus       218 ~----~~~ivItEiPy~v~k~~lie~I~~~~~~~ki~-I~~i~D~s~~~vrIvi~l-k~~~~~~~vln~Ly~~T~lq~sf  291 (626)
T PRK09631        218 D----EKTIVIRELPFGETTESLIASIEKAIRKNYIK-VSSINDFTAENVEIELKL-PRGVYASEVIEKLYHYTNCQVSI  291 (626)
T ss_pred             C----CCEEEEEECCCCCCHHHHHHHHHHHHHHCCCC-CCCCCCCCCCCEEEEEEE-CCCCCHHHHHHHHHHHCCHHHEE
T ss_conf             7----83599995687777899999999999725676-211414689827999998-99999899999987509713217


Q ss_pred             CCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHCCCCCCCCCC
Q ss_conf             33113331268972204999999899998999999999999999999999999998641-07899997520000110000
Q gi|254780353|r  340 PLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYL-NIDEIIAIIRNEDKPKPVMV  418 (753)
Q Consensus       340 ~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~-~ID~vI~iIR~s~~~k~~L~  418 (753)
                      |+||+||++| +|++|||+|+|++|++||.++++||++|+|+++++|+|+..+..+.+. .|+++|+.++++++....+.
T Consensus       292 ~~n~~ai~~~-~P~~l~l~eiL~~~~~h~~~vl~r~le~~l~k~~er~H~~sLe~IfIe~rIy~~Ie~~~~~e~v~~~i~  370 (626)
T PRK09631        292 SVNLLLLSDR-YPVIYTVTDIIKFHAEHLQKILKMELELERSKILEKIFSKTLEQIFIEKKIYKILETISKEEDVVSIVL  370 (626)
T ss_pred             CCEEEEEECC-EEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHH
T ss_conf             6268999899-827987999999999999999999999889989986899999999866668999884201688999999


Q ss_pred             CC---------CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             00---------257757788998878999988999976667899998877654420397887899999999998741774
Q gi|254780353|r  419 SR---------FSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKS  489 (753)
Q Consensus       419 ~~---------f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~  489 (753)
                      +.         ..+||.|+++||+|||+|||++|++|..+|+++|.++|++++..|+   .+..++++++++++++||+.
T Consensus       371 ~~l~pf~~~l~r~ite~d~~aLleirL~RIT~~didK~~eei~~L~~eI~eI~~~L~---~l~~~~I~~l~~Lk~kYG~~  447 (626)
T PRK09631        371 SELLPFKSSLSRDVTEDDVENLLKIPIRKISLFDIDKNNKDIRILNKELKSIESNIK---SIKGYAINFIDKLLAKYSKE  447 (626)
T ss_pred             HHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHCCC
T ss_conf             877767887630157999999999899885343088799999999999999986377---68999999999999873547


Q ss_pred             CCCCCCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEEC--------CCCCCCCCCCCCCCCCCCCEEEEEECCCC
Q ss_conf             3345554200001100000011002456670599871010202--------56554455322345555540121111478
Q gi|254780353|r  490 TDLGRRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRS--------LKSHSVDLSALHFKEGDSLKIALHAHTTD  561 (753)
Q Consensus       490 ~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr--------~k~~~~~~~~~~~KegD~l~~~~~~~t~d  561 (753)
                      +   .|||.|.                       +++++|+|+        +.+.+.|..|+++|++|++   +.|++||
T Consensus       448 ~---~RKTEI~-----------------------lfd~i~aKrVa~~n~Kly~nr~~GFiGtslKkdDfV---~~CSd~D  498 (626)
T PRK09631        448 Y---KRKTEIS-----------------------LIKSKNVREIATKNMKVYLNLETGFVGTSLIDGEFI---GNASYYD  498 (626)
T ss_pred             C---CCEEEEE-----------------------EECCEEEEEEECCCCEEEECCCCCEEEECCCCCCEE---EECCCCC
T ss_conf             7---7257999-----------------------764443699570233256658885561035678456---7335665


Q ss_pred             CEEEEECCCEEEEEEHHHCCCCCCCCCCC--CCCCCCCCC-CEEEEEEEECCCCEEEEEECCCCEEEEEHHHHHCCCCCC
Q ss_conf             17898068827875511212123444422--223576765-307899985799859999748978996388740233356
Q gi|254780353|r  562 RILLLSTDGKAYTLPAGNLLSGRGHGEAI--QLLIDLNHN-QDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKG  638 (753)
Q Consensus       562 ~LLffTs~GkvY~l~a~~Ips~~~kG~pI--~~ll~l~~~-EkIv~~~~~~~~~~lll~Tk~G~ikr~~l~~~~~~~k~G  638 (753)
                      +|+||++ |+.   .+.++|+..--|..+  .+++...++ +.|.+++--+.+.      ...|+||.....+..   . 
T Consensus       499 dILvF~d-G~y---kV~kV~~K~Fvgk~i~~v~v~~k~d~~~tiyn~IYrDgk~------g~~yiKRF~V~~~tr---d-  564 (626)
T PRK09631        499 KILIFKD-GSY---VLKNIEDKTFIDKKNVCVLVYDINNSKEQVFSIIYRDKLD------NFYYVKRFKIDKFIL---D-  564 (626)
T ss_pred             EEEEEEC-CEE---EEEECCCCCEECCCCEEEEEEECCCCCCEEEEEEEECCCC------CCEEEEEEEECCEEE---C-
T ss_conf             3999989-859---9998577605468837999985278765079999986998------836899988323884---2-


Q ss_pred             EEEEEECCCCCEEEEEECCCCEEEEEECCCCEE--EEEHHHCCCCCH-HHCCEEEEC
Q ss_conf             278853689805688961898099995699389--955787783361-214133421
Q gi|254780353|r  639 KTFLKVSSEEKMKLVVKVTGDHVAVVGENRKLL--IFSIDQIPEMSR-GKGVRLQSY  692 (753)
Q Consensus       639 k~~ikLk~~D~li~v~~~~~d~iiliT~~Gk~L--rF~~~eIr~~gR-gkGVk~i~L  692 (753)
                      |..--..++.++.....-..   +.-+..-+-+  -|+-+++...|| ++|+.+-+.
T Consensus       565 K~Y~l~~~~s~~l~fs~n~n---l~~~~~~k~~~~~~df~~~~iKgr~skGn~vtk~  618 (626)
T PRK09631        565 KVYEFLPENDEFLDFSLNPE---FVPFSRSKDIVKMIEIDNFMVKSRSSKGKRISSR  618 (626)
T ss_pred             CCCCCCCCCCEEEEEEECCC---CCCCCCCCCEEEEECHHHEEEECCCCCCEEEECC
T ss_conf             52245799987999997776---5745442451477321140341444555176314


No 9  
>PRK09630 DNA topoisomerase IV subunit A; Provisional
Probab=100.00  E-value=0  Score=1203.05  Aligned_cols=459  Identities=26%  Similarity=0.432  Sum_probs=408.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             31999999888888899985104764112897046899999998689998980354053666542768874789999999
Q gi|254780353|r   20 VSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLV   99 (753)
Q Consensus        20 ~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v   99 (753)
                      .+|+++|++|||+||||||++|||||+|||||||||||||||++++   +++|+|||||||+||| ||||||+|||||||
T Consensus         2 ~~i~~~~~~~yl~Ya~~vI~~RAlPdvrDGLKPVqRRiLy~m~~~~---~~~~~K~ArvvG~v~g-yHPHGd~siy~alv   77 (479)
T PRK09630          2 SDVSDLFKTHFMHYASYVILERAIPHILDGLKPVQRRLLWTLFRMD---DGKMHKVANIAGRTMA-LHPHGDAPIVEALV   77 (479)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHCCC---CCCCCEEEEEECCEEC-CCCCCHHHHHHHHH
T ss_conf             6279999999998889999851177532588609999999983068---9987134244213511-48887278999999


Q ss_pred             HHCCHHHCCCCCCCCCCCCCC-CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHC
Q ss_conf             610013216613267887088-6779710024689985599999984218786175216799632422312345267642
Q gi|254780353|r  100 RLAQPFVQRYPLISGQGNFGN-IDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLAN  178 (753)
Q Consensus       100 ~maq~~~~~~pli~g~GnfGs-~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL~N  178 (753)
                      ||||    ||||||||||||| +||||||||||||||||++|.+||  ++++||||+||||||++||+||||+|||||+|
T Consensus        78 rmaq----r~~LvdgqGNfGs~~dgd~~AAmRYtE~rls~~a~~~l--~~~dtv~f~~NyDgs~~EP~vLPa~~PnLLvN  151 (479)
T PRK09630         78 VLAN----KGYLIDTQGNFGNPLTGDPHAAARYIEARLSPLAKEVL--FNTDLMTFHDSYDGREKEPDILPAKLPLLLLH  151 (479)
T ss_pred             HHHC----CCEEEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH--CCCCCCCCCCCCCCCCCCCCEEECCCCHHHHC
T ss_conf             9856----76156467888999899804677899987589999983--55685467789899855771211457187754


Q ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEEEE
Q ss_conf             66504677775167778899999999987286532013443203677887760106988999898503341599999998
Q gi|254780353|r  179 GTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCV  258 (753)
Q Consensus       179 g~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~~~  258 (753)
                      ||+|||||||||||||||+|||+|++++|+||+++.        ||||||||+|. +.+     |+||||+|++||+|++
T Consensus       152 Gs~GIAVGmAT~IpPHNl~EvidA~i~~i~~~~~~~--------~PDFPTGGii~-~~~-----Y~tGrG~i~vRak~~~  217 (479)
T PRK09630        152 GVDGIAVGMTTKIFPHNFCELLEAQIAILNDQPFTL--------LPDFPSGGLMD-ASE-----YQDGLGSITLRASIDI  217 (479)
T ss_pred             CCCCHHHHHHHCCCCCCHHHHHHHHHHHHCCCCCCC--------CCCCCCCCEEC-HHH-----HCCCCCEEEEEEEEEE
T ss_conf             775222345525899898999999999762898775--------89999977305-466-----5578981899999999


Q ss_pred             EECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCCCC
Q ss_conf             64378840799952420021689999999986402221345776406766058898504545889999987542000012
Q gi|254780353|r  259 EEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETR  338 (753)
Q Consensus       259 e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq~s  338 (753)
                      ++    +++||||||||||++++++++|+++++++++ +|+++||||++++++++++ +|+++|+.+||+|||+|+||+|
T Consensus       218 ~~----~k~ivItEiPy~v~k~~lie~I~~~~~~~~~-~I~~i~D~s~~~~rivI~l-kr~~~~~~vl~~Lyk~T~Lq~s  291 (479)
T PRK09630        218 IN----DKTLLIKEICPSTTTETLIRSIENAAKRGII-KIDSIQDFSTDLPHIEIKL-PKGIYAKDLLPPLFEHTECQVI  291 (479)
T ss_pred             EE----CCEEEEEECCCCCCHHHHHHHHHHHHHCCCC-CCCCEEECCCCCCEEEEEC-CCCCCHHHHHHHHHHCCCHHHE
T ss_conf             71----4438997068656699999999999864876-6885113357985599847-9999999999999836962412


Q ss_pred             CCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHH---HHHHHHHHHHHHHCCC-
Q ss_conf             23311333126897220499999989999899999999999999999999---9999998---6410789999752000-
Q gi|254780353|r  339 FPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVE---ILKGLLI---AYLNIDEIIAIIRNED-  411 (753)
Q Consensus       339 f~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~Rlh---IleGl~~---a~~~ID~vI~iIR~s~-  411 (753)
                      |++||+||++| +|++++|+++|+.|++||.++++||+++.. +..+|.|   .||++.+   ++++||+||++||+++ 
T Consensus       292 f~~N~~aI~~g-~P~~l~l~eiL~~~~~~~~~~lrr~l~~~~-~~~~r~~~~k~Le~l~I~~~~~d~I~eiI~~i~~~~~  369 (479)
T PRK09630        292 LTSKPTAIYQN-KPVETSISEILKLHTEALQGYLKKELLILQ-DSLTREHYHKTLEYIFIKHKLYDTVREMLSKRKTKPS  369 (479)
T ss_pred             ECCCEEEEECC-CCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             23323788889-086666899999999987554346689998-9999999998888999987789999999998853898


Q ss_pred             --CCCCCCCCCCC--------CCHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHH
Q ss_conf             --01100000025--------775778899-8878999988999976667899998877654420397887899999999
Q gi|254780353|r  412 --KPKPVMVSRFS--------LTENQVDAI-LNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIR  480 (753)
Q Consensus       412 --~~k~~L~~~f~--------lse~QA~aI-L~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~  480 (753)
                        +++.+++..|.        ..+.||.++ ++|+|++|++||.+++++|+++|.+++++++++|+   .+++++++||+
T Consensus       370 ~ed~~~~l~~~~~~~~~~~~~~i~~q~~~~L~~l~l~kL~~Le~~k~~~El~~l~~~i~~l~~~l~---~l~kiii~eL~  446 (479)
T PRK09630        370 ASDLHNAVLHALEPFLHTLPTAPDKQATSQLASLTIKKILCFNENAYTKELAAIEKKQAAVQKDLS---QLKKYTVKYLK  446 (479)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHH
T ss_conf             999999999876566787754338999999999899987513399999999999999999999999---99999999999


Q ss_pred             HHHHHCCCCCCCCCCCCCEEECCCHHHHHHHHCCCCCCCCE
Q ss_conf             99874177433455542000011000000110024566705
Q gi|254780353|r  481 EVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKEPIT  521 (753)
Q Consensus       481 eikkkfgd~~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v~  521 (753)
                      +++++||+.   ++|||.|.++.     ..++++++.|+++
T Consensus       447 ~ikekYGd~---~eRRTeI~~~~-----~~~~~~~~~e~~v  479 (479)
T PRK09630        447 GLLERYGHL---GHRKTQITKFK-----AKKTSILKQQTLI  479 (479)
T ss_pred             HHHHHHCCC---CCCCCCCCCCC-----CHHHHCCCHHCCC
T ss_conf             999985899---87767560243-----2343024200259


No 10 
>smart00434 TOP4c DNA Topoisomerase IV. Bacterial DNA topoisomerase IV, GyrA, ParC
Probab=100.00  E-value=0  Score=1146.52  Aligned_cols=437  Identities=46%  Similarity=0.765  Sum_probs=417.8

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             31999999888888899985104764112897046899999998689998980354053666542768874789999999
Q gi|254780353|r   20 VSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLV   99 (753)
Q Consensus        20 ~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v   99 (753)
                      ++|+++|.++|++||||||.+|||||+|||||||||||||||+++|+.++++|+||||+||+|||+||||||+|+|||||
T Consensus         1 i~i~d~~~~~~~~ys~~vi~~RaiP~~~DGLKPvqRriLy~~~~~~l~~~~~~~k~a~~~g~~~~~YHpHGd~s~~~aiv   80 (445)
T smart00434        1 IDIEDFINKEYLDYSMSVINGRAIPDVRDGLKPVQRRILYAMFKRGLTPDEPKVKSARGVGDVMGKYHPHGDSSLYDAIV   80 (445)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEEEEEEHHCCCCCCCHHHHHHHHH
T ss_conf             97799998999998899876034884002787899999999997389889862788888861001788886889999999


Q ss_pred             HHCCHHHCCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHC
Q ss_conf             6100132166132678870886-779710024689985599999984218786175216799632422312345267642
Q gi|254780353|r  100 RLAQPFVQRYPLISGQGNFGNI-DGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLAN  178 (753)
Q Consensus       100 ~maq~~~~~~pli~g~GnfGs~-~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL~N  178 (753)
                      ||||+||||+||++|||||||+ |||+||||||||||||++|..||.|+|+++|+|+|||||++.||+|||++|||||||
T Consensus        81 ~mAQ~fs~n~~Ll~~~GnFGs~~~G~~aAa~RYie~rLs~~~~~~~~~~d~~~~~~~~n~Dg~~~EP~~~~p~iP~lLvN  160 (445)
T smart00434       81 RMAQDFSNNYPLLDGQGNFGSRLDGDDAAAMRYTETRLSPLARELLPDIDKDTVDFVPNYDGQEIEPTVLPPIIPNLLVN  160 (445)
T ss_pred             HHHHHHHCCCCCEECCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCEEECCCCCCCCCCCCHHCCCCCCHHEEE
T ss_conf             98474340554230588867889998203367888637799999876438780755438898726751027766730030


Q ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEEEE
Q ss_conf             66504677775167778899999999987286532013443203677887760106988999898503341599999998
Q gi|254780353|r  179 GTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCV  258 (753)
Q Consensus       179 g~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~~~  258 (753)
                      ||+||||||||+||||||.|||+||+++|++|+++.++|+.+++||||||||.++            |+|+|++||+|++
T Consensus       161 Gs~GIavG~sT~IPphN~~evi~a~~~~l~~~~~~~~~l~~~p~~pdF~gg~~~~------------g~g~~~~rg~~~~  228 (445)
T smart00434      161 GSSGIAVGMATNIPPHNLREVIDAVRRLIDNPEASIDELMMIPWGPDFPTGGEII------------GPGSYVVRGKIEI  228 (445)
T ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCEEEE------------CCCEEEEEEEEEE
T ss_conf             7874254230477887889999988766518878889996388428999816993------------3986999999999


Q ss_pred             EECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCC-CCCEEEEEEEECCCCCHHHHHHHHHHHCCCCC
Q ss_conf             64378840799952420021689999999986402221345776406-76605889850454588999998754200001
Q gi|254780353|r  259 EEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDES-AEDVRIVLFPKNRSLDPDLLMESIFMLSDMET  337 (753)
Q Consensus       259 e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeS-d~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq~  337 (753)
                      |+   ++++|+||||||++|+++++|+|+++++++|+++|.|++||| ++++.++++..+++++++.++++|||+|+||+
T Consensus       229 ~~---~~~~i~ItELP~g~~t~~~~e~i~~lv~~~ki~~i~~~~des~~~~~vrivI~lk~~~~~~~~~~~L~k~tkL~~  305 (445)
T smart00434      229 ED---GRNTIVITELPYQVNKAKLIEKIAELVKDKKIEGIIDVRDESHDRTGVRIVIELKRGAMAEVVLNGLYKLTKLQS  305 (445)
T ss_pred             EC---CCCEEEEEECCCCCCHHHHHHHHHHHHHCCCCCCCHHHHHHCCCCCCEEEEEEECCCCCHHHHHHHHHHHHHHHE
T ss_conf             87---962799994687674899999999985135666501035432887752699998899898999999998720143


Q ss_pred             CCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHCCCC----
Q ss_conf             22331133312689722049999998999989999999999999999-9999999999864107899997520000----
Q gi|254780353|r  338 RFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAID-RRVEILKGLLIAYLNIDEIIAIIRNEDK----  412 (753)
Q Consensus       338 sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~-~RlhIleGl~~a~~~ID~vI~iIR~s~~----  412 (753)
                      ||++||++|+++++|++++++|||++|++||.++++||++|+|++++ +|+|+++|++++..++|+||.++|++++    
T Consensus       306 s~s~N~~~l~~~g~p~~~~~~eIL~~f~~~R~~~~~kR~~~~L~kl~~~r~~i~~~~fi~~~~~d~ii~~~r~~~~~~~~  385 (445)
T smart00434      306 TFSINMLALFDNGKPKKYNLKEILKEFLDHRLEVYTRRKEYLLGKLEAERLHILEGLFIALSIIDEIIVLIRSSKDLAKE  385 (445)
T ss_pred             ECCEEEEEEECCCCEEEEEHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHCCCCHHHH
T ss_conf             41517999976993578525999999999999999999999999999999999886999997346577655368726999


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHH
Q ss_conf             11000000257757788998878999988999976667899998877654420397887
Q gi|254780353|r  413 PKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQ  471 (753)
Q Consensus       413 ~k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l  471 (753)
                      ++..++.+|++|+.||+|||+|||+|||++|++|+++|+++|++++++|+++|.++..+
T Consensus       386 lk~~l~~~~~~s~~q~~yLL~M~L~~LT~~e~~kL~~E~~~l~~ei~~l~~~l~~~~wl  444 (445)
T smart00434      386 AKELLMERFELSEEQADAILDMRLRRLTKLEVEKLEKELKELEKEIEDLEKILASELWL  444 (445)
T ss_pred             HHHHCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHCC
T ss_conf             99818866799999999999668998728899999999999999999998468696544


No 11 
>cd00187 TOP4c DNA Topoisomerase, subtype IIA; domain A'; bacterial DNA topoisomerase IV (C subunit, ParC), bacterial DNA gyrases (A subunit, GyrA),mammalian DNA toposiomerases II. DNA topoisomerases are essential enzymes that regulate the conformational changes in DNA topology by catalysing the concerted breakage and rejoining of DNA strands during normal cellular growth.
Probab=100.00  E-value=0  Score=1119.54  Aligned_cols=441  Identities=46%  Similarity=0.757  Sum_probs=425.6

Q ss_pred             HCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHCCCCCCCCCCCCC
Q ss_conf             10476411289704689999999868999898035405366654276887478999999961001321661326788708
Q gi|254780353|r   40 ERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFG  119 (753)
Q Consensus        40 ~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~maq~~~~~~pli~g~GnfG  119 (753)
                      +|||||++||||||||||||||++++|.++++|+||||+||+|||+||||||+|+|||||||||+||+|+||++||||||
T Consensus         2 ~RaiP~~~DGlKP~qRkiL~~~~~~~l~~~~~~~Kva~l~G~v~~~~~~HGe~sl~~aiv~mAQ~fsnn~~Ll~~~GnFG   81 (445)
T cd00187           2 GRALPDVRDGLKPVQRRILYAMFKRGLTPDKPEKKVARLVGDVAGKYHPHGDSSLYDTIVRMAQDFSNNIPLLDPQGNFG   81 (445)
T ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCCEEEEEEHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCEECCCCCC
T ss_conf             87788611488789999999999707988998515510046565046898688999999998676550575331689889


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHCCCCCHHHHHHHHCCCCCHHHH
Q ss_conf             86779710024689985599999984218786175216799632422312345267642665046777751677788999
Q gi|254780353|r  120 NIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGIAVGMATSIPSHNVQEI  199 (753)
Q Consensus       120 s~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL~Ng~~GIavG~at~ipphnl~ev  199 (753)
                      |++||+||||||||||||+++..||.++|+++|+|++||||++.||+|||+++|++|||||+||||||||+||||||.||
T Consensus        82 sr~g~~aAa~RYi~trLs~~~~~lf~~~d~~~l~y~~nyDg~~~EP~~~~p~iP~iLvNGa~GIgtG~sT~IP~hNp~ei  161 (445)
T cd00187          82 SRDGDDAAAMRYTETRLSPIARLLLPDIDDPTVDFVPNYDGQEVEPEVLPPIFPNLLVNGSSGIAVGMATNIPPHNLREV  161 (445)
T ss_pred             CCCCCCCCCHHHHHHCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHHCCCCHHHHHCCCEEEEEEECCCCCCCCHHHH
T ss_conf             99998321034565320076999864026450335358899736742205433077634661334200056788788999


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCH
Q ss_conf             99999987286532013443203677887760106988999898503341599999998643788407999524200216
Q gi|254780353|r  200 CEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQK  279 (753)
Q Consensus       200 ~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~~~e~~~~~~~~ivIteiPy~v~k  279 (753)
                      ++|++++|++|+++.+++|++++||||||||.|. +.+++.++|+||+|+|++||+|++++.+ ++++|+|||||||+|+
T Consensus       162 i~~~~~~i~~~~~~~~~l~~~~~~P~f~~~g~I~-~~~~~~~~~~tG~g~~~~rg~~~~~~~~-~~~~I~ITELP~g~~t  239 (445)
T cd00187         162 IDALRALIDNPEASIDELMEIIKGPDFPTGGIIE-GRAGIREAYETGRGRYIIRGKYEIEDDE-GRNTIEITELPYQVNK  239 (445)
T ss_pred             HHHHHHHHCCCCCCHHHHHCCCCCCCCCCCCEEE-CCCCCHHHEECCCCEEEEEEEEEEEECC-CCCEEEEEECCCCCCH
T ss_conf             9999877607776578873678899899994685-5654012123279738997899998048-8627999955887889


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCHHH
Q ss_conf             89999999986402221345776406766058898504545889999987542000012233113331268972204999
Q gi|254780353|r  280 SRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDG  359 (753)
Q Consensus       280 ~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq~sf~~N~~~l~~~~~P~~~~l~e  359 (753)
                      ++++|+|++++++||+++|+|++|+|++++.++++..+++++++.++++|||+|+||++|++||+|++.+++|+.+++.+
T Consensus       240 ~~~~e~i~~lv~~kk~~~I~d~~D~st~~~v~~vI~lk~~~~~~~~~~~L~k~tkL~~s~s~Nm~~~~~~g~p~~~~~~e  319 (445)
T cd00187         240 AKLKEKIAELVKDKKIEGISDVRDESDREGIRFVIELKRGAMAEVVLNGLYKVTKLQTTFGINMVAFDPNGRPKKLNLKE  319 (445)
T ss_pred             HHHHHHHHHHHHCCCCCCEEEEECCCCCCCEEEEEEECCCCCHHHHHHHHHHHHCHHEEECCEEEEEECCCCEEECCHHH
T ss_conf             99999999986247787466522268877247999977986668899999987150103033389993799775506999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC---CCCCHHHHHHHHHHHH
Q ss_conf             9998999989999999999999999999999999986410789999752000011000000---2577577889988789
Q gi|254780353|r  360 ILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDKPKPVMVSR---FSLTENQVDAILNLRL  436 (753)
Q Consensus       360 il~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s~~~k~~L~~~---f~lse~QA~aIL~mrL  436 (753)
                      ||+.|++||.+++.||.+|+|+++++|+|||+|+++++.+||+||++||.++++++.+++.   |+|++.||+|||+|||
T Consensus       320 IL~~f~~~R~~~y~kR~~~~L~kl~~rl~il~~~~~fi~~id~ii~~ir~~~~~k~~l~~~l~~~~~~~~q~dyLL~M~L  399 (445)
T cd00187         320 ILQEFLDHRLEVYTRRKEYELGKAEARLHILEGLLKAILNIDEVINLIRSSDEAKKALIEELEKLGFSEIQADAILDMRL  399 (445)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             99999999999999999999999999999986499999979999999985351799999998767999999999997669


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHH
Q ss_conf             9998899997666789999887765442039788789999999999
Q gi|254780353|r  437 RSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREV  482 (753)
Q Consensus       437 ~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~ei  482 (753)
                      ++||++|++++++|+++|++++++|+++|+|++++++++++||.|.
T Consensus       400 ~~LT~~e~~kL~~e~~~l~~ei~~L~~~l~~~~~~~~~~~~EL~ef  445 (445)
T cd00187         400 RRLTKLEREKLLKELKELEAEIEDLEKILASEERPKDLWKEELDEF  445 (445)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHCC
T ss_conf             9875899999999999999999999998679688999999998509


No 12 
>pfam00521 DNA_topoisoIV DNA gyrase/topoisomerase IV, subunit A.
Probab=100.00  E-value=0  Score=1051.50  Aligned_cols=420  Identities=48%  Similarity=0.790  Sum_probs=401.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCC
Q ss_conf             04764112897046899999998689998980354053666542768874789999999610013216613267887088
Q gi|254780353|r   41 RAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGN  120 (753)
Q Consensus        41 Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~maq~~~~~~pli~g~GnfGs  120 (753)
                      |||||++||||||||||||||+++++.++++|.|||++||+|||+||||||+|+|+|||+|||+|++|+||++|||||||
T Consensus         1 RaiP~~~DGLKP~qRkil~~~~~~~l~~~~~~~Kva~l~G~v~~~YHpHGe~sl~~tiv~mAQ~f~~n~~Ll~~~GnFGs   80 (428)
T pfam00521         1 RAIPDVRDGLKPVQRRILYAMFELGLNLDKKYKKVARLVGDVMGKYHPHGDASIYDALVRMAQDFVGNIPLLDGQGNFGS   80 (428)
T ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC
T ss_conf             99985234787899999999997278889986056433365663568885899999999986763156553216888888


Q ss_pred             C-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHCCCCCHHHHHHHHCCCCCHHHH
Q ss_conf             6-779710024689985599999984218786175216799632422312345267642665046777751677788999
Q gi|254780353|r  121 I-DGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANGTSGIAVGMATSIPSHNVQEI  199 (753)
Q Consensus       121 ~-~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL~Ng~~GIavG~at~ipphnl~ev  199 (753)
                      + +|++||||||||||||+++..||.++|.++|+|++||||+..||+|||++||++|||||+||||||||+||||||.||
T Consensus        81 r~~g~~~AA~RYi~trLs~~~~~if~~~d~~~l~~~~~yDg~~~EP~~y~piiP~iLvNG~~GIgtG~sT~IP~hNp~ei  160 (428)
T pfam00521        81 RLDGDKAAAMRYTEARLSKIARELFKDIDKDTVDFVPNYDGSEKEPTVLPPIIPNLLVNGASGIAVGMATNIPPHNLGEV  160 (428)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCHHCCCCCCHHHHCCCCCCEEHEECCCCCCCHHHH
T ss_conf             88898327788999757499999976426350155057898706751106655676623787301000027788888999


Q ss_pred             HHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCH
Q ss_conf             99999987286532013443203677887760106988999898503341599999998643788407999524200216
Q gi|254780353|r  200 CEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQK  279 (753)
Q Consensus       200 ~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~~~e~~~~~~~~ivIteiPy~v~k  279 (753)
                      |+||+++|++|++++   +..++||||||||.++ +.+++.++|.||+|+|++||+|++++    +++|+||||||++|+
T Consensus       161 i~~~~~~l~~~~~~~---~~~~~~P~f~~f~g~i-~~~~~~~~y~tG~G~~~~rg~~~i~~----~~~i~ITELP~g~~t  232 (428)
T pfam00521       161 IDALIALLDGPEITL---LLKIPGPDFPTGGGII-GSGGIREAYKTGRGKITVRAKIEIEE----RKTIVITELPYGVWT  232 (428)
T ss_pred             HHHHHHHHCCCCCCC---CCCCCCCCCCCCCEEE-CCCCHHHHHHCCCCEEEEEEEEEEEC----CCEEEEEECCCCCCH
T ss_conf             999999853997223---5757899799986245-66116777643883599987999940----526999944777789


Q ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCHHH
Q ss_conf             89999999986402221345776406766058898504545889999987542000012233113331268972204999
Q gi|254780353|r  280 SRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDG  359 (753)
Q Consensus       280 ~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq~sf~~N~~~l~~~~~P~~~~l~e  359 (753)
                      ++++|+|+++++++|+++ +|+||+||++++++|.++ ++++++.++++|||+|+||+||++|++++.++ .|+++++++
T Consensus       233 ~~~~e~l~~l~~~~ki~~-~di~D~Sd~~vr~vI~lk-~~~~~~~~~~~L~k~~kL~~s~s~nnm~l~d~-~pk~~s~~e  309 (428)
T pfam00521       233 EKLIESIEELVKNGKIKG-SDIRDESDRGVRIVIELK-RGADPEVVLNKLYKKTKLQSSFSTNNLVLFDG-GPKYLNLKE  309 (428)
T ss_pred             HHHHHHHHHHHHCCCCCC-CCCCCCCCCCEEEEEEEC-CCCCHHHHHHHHHHHHHHHEECCCEEEEEECC-CCCHHHHHH
T ss_conf             999999999984588787-731016788567999857-87656789999998630010046379999679-873742999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC---CCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             99989999899999999999999999999999999864107899997520000---110000002577577889988789
Q gi|254780353|r  360 ILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNEDK---PKPVMVSRFSLTENQVDAILNLRL  436 (753)
Q Consensus       360 il~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s~~---~k~~L~~~f~lse~QA~aIL~mrL  436 (753)
                      ||++|++||.++++||++|+|+++++|+|||+||++|++++|+||++||++.+   +|..|++  .|++.|++|||+|||
T Consensus       310 IL~~f~~~R~~~y~kR~~~~l~kl~~~l~iL~gl~~~~~~idfIi~iI~~s~~~~~~k~~L~~--~L~~~q~dyLL~m~L  387 (428)
T pfam00521       310 ILKEFLEHRLEVYKRRKEYLLEKLEERLHILEGLLKALNKIDFVIEVIRGSIDLNKAKKELIE--ELSEIQADYLLDMRL  387 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHHHHHHHHH--HCCHHHHHHHHHHHH
T ss_conf             999999999999999999999999999999988999998499999999768961689999999--748998999997689


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
Q ss_conf             9998899997666789999887765442039788789
Q gi|254780353|r  437 RSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWN  473 (753)
Q Consensus       437 ~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~  473 (753)
                      ++||++|++++++|+++|++++++|+++|+|+.++|.
T Consensus       388 ~~LT~~e~~kL~~e~~~l~~ei~~l~~~l~s~~~lw~  424 (428)
T pfam00521       388 RRLTKEEIEKLEKEIEELEKEIAELEKILASEKKLWI  424 (428)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH
T ss_conf             9872889999999999999999999977389999988


No 13 
>PRK12758 DNA topoisomerase IV subunit A; Provisional
Probab=100.00  E-value=0  Score=860.95  Aligned_cols=603  Identities=26%  Similarity=0.433  Sum_probs=475.3

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             31999999888888899985104764112897046899999998689998980354053666542768874789999999
Q gi|254780353|r   20 VSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLV   99 (753)
Q Consensus        20 ~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v   99 (753)
                      ..+..--+++||+||+|||.+||+|+++||||||||||||+|++|   .+.+|.|+|+|||++| +||||||+|||||||
T Consensus        23 ~~~~gmy~~wfldYasyvil~RAvp~i~DGlKPvqRril~sm~~~---~dgr~~KvAnivG~tm-~yhPHGdasi~dalv   98 (879)
T PRK12758         23 THVGGMYQNWFLDYASYVILERAVPHIEDGLKPVQRRILHSMKRL---DDGRYNKVANIVGHTM-QYHPHGDASIGDALV   98 (879)
T ss_pred             EECHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH---HCCCCCEEEEECCCCC-CCCCCCCCHHHHHHH
T ss_conf             450134788888776865335205640027853899999999861---0776302320102320-248887423899999


Q ss_pred             HHCCHHHCCCCCCCCCCCCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHC
Q ss_conf             6100132166132678870886-779710024689985599999984218786175216799632422312345267642
Q gi|254780353|r  100 RLAQPFVQRYPLISGQGNFGNI-DGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLAN  178 (753)
Q Consensus       100 ~maq~~~~~~pli~g~GnfGs~-~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL~N  178 (753)
                      +|+|    +..|||+|||||++ .||+||||||+|||||++|.+++  ++++|++|+++|||+.+||++||++||+||++
T Consensus        99 ~~~q----k~~lid~qGN~Gni~tgd~aaA~RYiE~rls~fa~ev~--fn~~~t~~~~sYDgr~kEP~~lP~kfPllL~~  172 (879)
T PRK12758         99 QLGQ----KDLLIDCQGNWGNILTGDGAAAPRYIEARLSKFALEVL--FNPKTTEWQLSYDGRKKEPVTLPVKFPLLLAQ  172 (879)
T ss_pred             HHHC----CCEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHE--ECCCCCEEEECCCCCCCCCCCCCCCCHHHHHC
T ss_conf             8624----33368647776676878722314467564207779870--38775534545687657864255211677761


Q ss_pred             CCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCC--CEEEEEEEE
Q ss_conf             665046777751677788999999999872865320134432036778877601069889998985033--415999999
Q gi|254780353|r  179 GTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGR--GGFRVRARW  256 (753)
Q Consensus       179 g~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~--G~i~~r~k~  256 (753)
                      |++||||||||+|||||+.|+|+|.++++++...++.        |||||||.+-  .    .-|..|+  |++++||+.
T Consensus       173 g~eGIAVGlstkilphNf~El~~a~i~~l~~~~~~l~--------PDF~tgG~~d--~----s~YndG~rgG~v~vRaki  238 (879)
T PRK12758        173 GVEGIAVGLSSKILPHNFNELIDASIAYLRGEEFKLY--------PDFQTGGSID--V----SNYNDGERGGRVKVRAKI  238 (879)
T ss_pred             CCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCCEEC--------CCCCCCCEEC--H----HHHHCCCCCCEEEEEEEE
T ss_conf             6762685001464887889999999999759985488--------7898875405--6----451044458548999999


Q ss_pred             EEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCC
Q ss_conf             98643788407999524200216899999999864022213457764067660588985045458899999875420000
Q gi|254780353|r  257 CVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDME  336 (753)
Q Consensus       257 ~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq  336 (753)
                      +..+    ++.|+|+||||++++++||++|..+.+.|||+ |+.|.|.+..++.+.|.+ .++.+|+..+..||++|+||
T Consensus       239 ~~~d----~~tl~I~eiP~g~tt~sLi~SI~kAn~kGKIK-Ikki~DnTa~~VEI~i~L-~~Gvs~dktidaLYAFTdCE  312 (879)
T PRK12758        239 NKLD----NKTLVITEIPYGTTTSSLIDSILKANDKGKIK-IKKVDDNTAADVEILVHL-APGVSSDKTIDALYAFTDCE  312 (879)
T ss_pred             EEEC----CCEEEEEECCCCCCHHHHHHHHHHHHHCCCCC-EEEECCCCCCCEEEEEEC-CCCCCHHHHHHHHHHHCCCE
T ss_conf             9805----96699985499875799999999998759711-466324677740699983-89998789899876303562


Q ss_pred             CCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH--HHHHHH---HHH--------HHHHH
Q ss_conf             12233113331268972204999999899998999999999999999999999--999998---641--------07899
Q gi|254780353|r  337 TRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEI--LKGLLI---AYL--------NIDEI  403 (753)
Q Consensus       337 ~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhI--leGl~~---a~~--------~ID~v  403 (753)
                      +|+|.|..+|.++ .|..+++.|+|+.-.+|-.+++++.++.+|.+.+++||.  ||-+.+   .+.        .-++|
T Consensus       313 vSISPn~cVI~dn-kP~fl~VseiLk~std~t~~LLk~ELei~l~eLeekwH~~SLErIFIEnRIYrd~~IEe~~t~E~V  391 (879)
T PRK12758        313 VSISPNCCVIDDD-KPHFLGVSEVLRISTDRTLDLLKQELEIQLEELLEQLHFASLEKIFIEERIYKDKEFEESETWEDA  391 (879)
T ss_pred             ECCCCCEEEEECC-CCEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHCCCCCHHHH
T ss_conf             2058764999899-443842899999999999999999999889999999999989999977565144000355689999


Q ss_pred             HHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf             99752000011000000257757788998878999988999976667899998877654420397887899999999998
Q gi|254780353|r  404 IAIIRNEDKPKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVK  483 (753)
Q Consensus       404 I~iIR~s~~~k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eik  483 (753)
                      ++.|...-.|-.....+ .+++.--.-.+++|++|+++++++|-.++++.|.++|++.+.-|++   +...-+.-++.++
T Consensus       392 i~~I~~gL~Pf~~~L~R-eVt~eDI~rLtEIkIkRISkFDidKa~e~I~~le~~I~eVk~nL~n---lt~YaI~yf~~Lk  467 (879)
T PRK12758        392 LLHIDDRLEPFKKQFIR-EVTEDDILRLTEIKMKRILKFNSDKAEELIARLEEDIAEVEHHLEH---IIDYTIAWFTMLK  467 (879)
T ss_pred             HHHHHHHHHHHHHHHCC-CCCHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHH
T ss_conf             99999999998886337-8888999998631377755418788999999999999999988887---8999999999999


Q ss_pred             HHCCCCCCCCCCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCE
Q ss_conf             74177433455542000011000000110024566705998710102025655445532234555554012111147817
Q gi|254780353|r  484 EIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRI  563 (753)
Q Consensus       484 kkfgd~~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr~k~~~~~~~~~~~KegD~l~~~~~~~t~d~L  563 (753)
                      ++||..+   .|||.|-.++..+..   ...+.++.+        |+-|..    |--|.++|.+.   +++.|+.-|.+
T Consensus       468 kKYGkg~---~RKTEI~~Fd~I~A~---kVa~~N~KL--------YvNRee----GFiGt~lKkdE---fv~dCSdiDDI  526 (879)
T PRK12758        468 EKYGKGF---PRRTELRNFDTIEAT---KVVEANEKL--------YINREE----GFIGTGLKKDE---FVADCSDIDDV  526 (879)
T ss_pred             HHHCCCC---CCCCEEEECCCEEHH---HHHHHHCEE--------EEECCC----CEECCCCCCCC---EEEECCCCCEE
T ss_conf             9866999---764034100315277---773531779--------982456----61101324774---44303571228


Q ss_pred             EEEECCCEEEEEEHHHCCCCCCCCCCCC--CCCCCCCCCEEEEEEEECCCCEEEEEECCCCEEEEEHHHHHCCCCCCEE-
Q ss_conf             8980688278755112121234444222--2357676530789998579985999974897899638874023335627-
Q gi|254780353|r  564 LLLSTDGKAYTLPAGNLLSGRGHGEAIQ--LLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKGKT-  640 (753)
Q Consensus       564 LffTs~GkvY~l~a~~Ips~~~kG~pI~--~ll~l~~~EkIv~~~~~~~~~~lll~Tk~G~ikr~~l~~~~~~~k~Gk~-  640 (753)
                      ++|+..|++-..++.+   ..--|..|.  ++++-.+...|-+|+--+....      .-|+||.....+.   |.-.. 
T Consensus       527 IvF~kDG~~~VtKV~d---K~FVGKdIihv~vfkK~D~rtiYN~IYrDGk~g------~syiKRF~Vtgvt---RDk~Y~  594 (879)
T PRK12758        527 IVFYRDGKYMVTKVAD---KKFVGKDIIYVAVFKKNDKRTIYNVIYRDGKSG------PSYIKRFNVTGVT---RDKEYD  594 (879)
T ss_pred             EEEECCCCEEEEECCC---CEEECCCCEEEEEEECCCCCEEEEEEEECCCCC------CEEEEEEECCCEE---ECCCCC
T ss_conf             9992388589998167---445336757999750588732889999738888------5655763124143---134024


Q ss_pred             EEEECCCCCEEEEEECC-CC-EEEE--EECCC--CEEEEEH--HHCCCCCH-HHCCEEE
Q ss_conf             88536898056889618-98-0999--95699--3899557--87783361-2141334
Q gi|254780353|r  641 FLKVSSEEKMKLVVKVT-GD-HVAV--VGENR--KLLIFSI--DQIPEMSR-GKGVRLQ  690 (753)
Q Consensus       641 ~ikLk~~D~li~v~~~~-~d-~iil--iT~~G--k~LrF~~--~eIr~~gR-gkGVk~i  690 (753)
                      ..+-..+..+.....-. |+ +++-  +..++  +-+.|+.  +++...|| ++|..+-
T Consensus       595 lt~g~~gSkvlYfsaNpNGEAE~V~v~Lr~~~~~kkl~~d~DFsdi~IKGR~skGNivT  653 (879)
T PRK12758        595 LTQGTPGSRVLYFSANPNGEAEVVTVTLKPNPRIRKLVFEKDFSEIAIKGRQSQGNILT  653 (879)
T ss_pred             CCCCCCCCEEEEEECCCCCCEEEEEEEECCCCCCCCEEEECCHHHHHCCCCCCCCEEEE
T ss_conf             66799998899995189986268999964585534156413677710014455651675


No 14 
>PTZ00108 DNA topoisomerase II; Provisional
Probab=100.00  E-value=0  Score=496.76  Aligned_cols=439  Identities=21%  Similarity=0.341  Sum_probs=337.9

Q ss_pred             CCCCEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHH--HCCCCCCH
Q ss_conf             4245665319999998888888999851047641128970468999999986899989803540536665--42768874
Q gi|254780353|r   13 VEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEV--IGKLHPHG   90 (753)
Q Consensus        13 ~~~~i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v--~gkyhPHG   90 (753)
                      .+-....+++.+.+....+-|+++= ..|+||++.|||||.||+|||+++..++..+   .|+|..+|-|  +..|| ||
T Consensus       721 ld~~~~~i~~~dFinkELi~FS~~D-~~RSIPs~~DGlKp~QRKvl~~~fkrn~~~e---iKVaQlaGyVse~saYH-HG  795 (1506)
T PTZ00108        721 VDHKEKDLSYYDFVNKELIYYSRYD-TERSIPNIMDGWKPGQRKVLYGCFKRNLKNE---CKVAQLVGYIAEHSAYH-HG  795 (1506)
T ss_pred             CCCCCCCCCHHHHHHHHHHHCCHHH-HHHHCCHHHCCCCHHHHHHHHHHHHHCCCCC---EEHHHHHHHHHHHCCCC-CC
T ss_conf             3566785438774437888642887-6512411330577124424498786347762---23215088987630467-63


Q ss_pred             HHHHHHHHHHHCCHH--HCCCCCCCCCCCCCCC--CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC---CCCEE
Q ss_conf             789999999610013--2166132678870886--7797100246899855999999842187861752167---99632
Q gi|254780353|r   91 DQSVYDSLVRLAQPF--VQRYPLISGQGNFGNI--DGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTY---NEEDS  163 (753)
Q Consensus        91 d~s~y~a~v~maq~~--~~~~pli~g~GnfGs~--~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~---D~~~~  163 (753)
                      ++|+.+|+|.|||+|  |+|.+|+.+.|+|||+  +|++|||+||++++|++++..+|..-|..    +.+|   ||...
T Consensus       796 E~SL~~tIv~mAQ~fvGsNNinlL~P~GqFGtR~~GGkDaas~RYIfT~l~~~~r~iF~~~Dd~----lL~y~~ddg~~i  871 (1506)
T PTZ00108        796 ESSLQQTIINMAQTFVGSNNINFLEPCGQFGSRKEGGKDASAARYIFTKLASSTRSIFNEYDDP----ILKYLNEEGQKI  871 (1506)
T ss_pred             HHHHHHHHHHHHHHCCCCCCHHHCCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHHCCCCCHH----HHHCCCCCCCCC
T ss_conf             8999999999987535656631045578752545588755560257663158888538933022----550203689631


Q ss_pred             EEEEECCCCCHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             42231234526764266504677775167778899999999987286532013443203677887760106988999898
Q gi|254780353|r  164 EPVVFPSKFPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESY  243 (753)
Q Consensus       164 EP~~lp~~~P~lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y  243 (753)
                      ||.++.+.+|++|||||.||++||+|+||||||.||++++.++|++.+.  ..+..+.+|  | + |.|          .
T Consensus       872 EP~~Y~PiiPmvLvNG~~GIGTGwSt~ip~ynp~dii~ni~r~l~ge~~--~~m~Pwy~g--f-~-G~i----------~  935 (1506)
T PTZ00108        872 EPQYYIPVIPTILVNGCEGIGTGYSSFIPNYNYKDIIDNIKRYINKEPL--IPMIPWYKD--F-K-GRI----------E  935 (1506)
T ss_pred             CCCEECCCCCEEEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCCCC--CCCCCCCCC--C-C-CEE----------E
T ss_conf             5430205566787337762026634778999999999999998569988--627755379--6-2-169----------9


Q ss_pred             HCCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCC-CCEEEEEEEECCCCCH
Q ss_conf             503341599999998643788407999524200216899999999864022213457764067-6605889850454588
Q gi|254780353|r  244 RLGRGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESA-EDVRIVLFPKNRSLDP  322 (753)
Q Consensus       244 ~tG~G~i~~r~k~~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd-~~~~~vi~~~~r~~~~  322 (753)
                      .+|.+++.+.|.++.-    +.+.+.|||||.++|+..+-|.+..++.+++-+.|.|++++++ ..++.+|..-. +.-.
T Consensus       936 ~~~~~~y~~~G~~~~~----~~~t~~ItELPi~~WT~~yKe~le~~~~~~~~~~i~d~~e~~t~~~V~F~i~~~~-~~~~ 1010 (1506)
T PTZ00108        936 SNGKTGYETIGIIHKI----DDDTLEINELPIKKWTQDYKEFLEELLTDEKHQLILDYIDNSSHEDICFTIKMDP-AKLK 1010 (1506)
T ss_pred             ECCCCEEEEEEEEEEE----CCCEEEEEECCCCCCHHHHHHHHHHHHCCCCCCCCCCCHHCCCCCEEEEEEEECH-HHHH
T ss_conf             8689718998799995----7987999858987626999999998750467774000043179975899999588-9989


Q ss_pred             HHHHHHHHHHCCCCCCCCC-CEEEEE-CCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHH
Q ss_conf             9999987542000012233-113331-268972204999999899998999999999999999999999999---99864
Q gi|254780353|r  323 DLLMESIFMLSDMETRFPL-NMNVLS-MGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKG---LLIAY  397 (753)
Q Consensus       323 ~~vl~~Lyk~T~Lq~sf~~-N~~~l~-~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleG---l~~a~  397 (753)
                      ...-.-|.+.-.|++++++ ||++++ .|+.-+.-+..+||++|+..|.+.+.+|..|.|.+.+..+.+|+-   |+.++
T Consensus      1011 ~~~~~gl~k~fKL~~~i~t~Nm~~Fd~~g~i~kY~~~~~Il~eF~~~Rl~~Y~kRK~~l~~~l~~~~~~l~nqaRFI~~v 1090 (1506)
T PTZ00108       1011 KAEEEGLEKVFKLKSTLTTTNMTLFDPNLKLQRYSTELDILKDFCFHRLKAYENRKSYLISKLEKEKKIISNKSKFILAI 1090 (1506)
T ss_pred             HHHHHCHHHHHCCCCEEEECCEEEECCCCCEEECCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             98760666651123134205268988999966459999999999999999999999999999999999864255656640


Q ss_pred             HH---------HHHHHHHHHCCC-CC-------C-CCCCC----------------CCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             10---------789999752000-01-------1-00000----------------025775778899887899998899
Q gi|254780353|r  398 LN---------IDEIIAIIRNED-KP-------K-PVMVS----------------RFSLTENQVDAILNLRLRSLRKLE  443 (753)
Q Consensus       398 ~~---------ID~vI~iIR~s~-~~-------k-~~L~~----------------~f~lse~QA~aIL~mrL~rLt~le  443 (753)
                      -+         =.++|+-.+... +|       + ....+                .-+++...-+|+|.|+|..||..-
T Consensus      1091 i~~~l~v~nkkk~~li~eL~~~~f~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ydYLL~M~iwsLT~Er 1170 (1506)
T PTZ00108       1091 VNNELIVNKKKKKVLVEELYRKGYDPYKDINKIKKEEIFEQELLDAADNPEDNEEIIAGISVKDYDYLLSMPIFSLTLEK 1170 (1506)
T ss_pred             CCCEEEEECCCHHHHHHHHHHCCCCCCCCHHHHHHHCCCHHHHHCCCCCCCCCHHHCCCCCCCCCHHHHCCCHHHCCHHH
T ss_conf             06758993576899999999749997741124333010002210122355442010146776784366388123200999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             9976667899998877654420397887899999999998741
Q gi|254780353|r  444 EYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIF  486 (753)
Q Consensus       444 ~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkf  486 (753)
                      .++|..|.++..+|.++|.+  .+...+|.-   +|.++-+.|
T Consensus      1171 ~~~L~~~~~~k~~El~~L~~--~s~~dlW~~---DLd~fee~~ 1208 (1506)
T PTZ00108       1171 VEDLLAQHKEKEKELEILKN--ITVETMWLK---DIEKVEEAI 1208 (1506)
T ss_pred             HHHHHHHHHHHHHHHHHHHC--CCHHHHHHH---HHHHHHHHH
T ss_conf             99999999999999999976--898999999---999999999


No 15 
>KOG0355 consensus
Probab=99.96  E-value=6.1e-30  Score=244.70  Aligned_cols=638  Identities=8%  Similarity=-0.095  Sum_probs=455.4

Q ss_pred             CCCCEEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHH
Q ss_conf             42456653199999988888889998510476411289704689999999868999898035405366654276887478
Q gi|254780353|r   13 VEENVKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQ   92 (753)
Q Consensus        13 ~~~~i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~   92 (753)
                      .+-+++++.|..|-.+.++-|+-++|-.|+.|+.+++++|+++++|+||+..+-...+.+.++++.++.+.+.+|||++.
T Consensus        72 ~~m~~i~v~i~~e~~~isv~nnGkGIPv~~H~~ek~yvpelifg~Lltssny~d~ekK~tggrngygakLcniFs~~f~~  151 (842)
T KOG0355          72 PKMNTIKVTIDKEKNEISVYNNGKGIPVTIHKVEKVYVPELIFGNLLTSSNYDDDEKKVTGGRNGYGAKLCNIFSTEFTV  151 (842)
T ss_pred             CCCCEEEEEECCCCCEEEEEECCCCCEEEECCCCCCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEECCCCCEE
T ss_conf             77652688871677679999579721312234222453478876644115678875432367775020343211454036


Q ss_pred             HHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHH-HHHHHCCCCCCCCCCCCCCCEEEEEEECCC
Q ss_conf             9999999610013216613267887088677971002468998559999-998421878617521679963242231234
Q gi|254780353|r   93 SVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAE-LILQGVDEDAVDFRDTYNEEDSEPVVFPSK  171 (753)
Q Consensus        93 s~y~a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~-~ll~di~~~~v~~~~n~D~~~~EP~~lp~~  171 (753)
                      .+||..++|||.++.+-|+.-++++|++.+.|++    ||+++++|-.+ ..+.++|.+||+++.+++-...+|. .|++
T Consensus       152 Et~d~~~~~~~kQ~w~~nm~~~~~~~i~~~~~~~----yTkitF~PDl~~F~m~eLD~Div~l~~rr~~d~a~~~-~~vk  226 (842)
T KOG0355         152 ETADREYKMAFKQTWINNMTRDEEPKIVPSTDED----YTKITFSPDLEKFKMKELDDDIVALMARRAYDLAGSV-KSVK  226 (842)
T ss_pred             EEEEHHHHHHHHHHHHCCCCCCCCCEEECCCCCC----CCEEEECCCHHHCCCHHHCCHHHHHHHHHHHHHCCCC-CCEE
T ss_conf             5300677778777652687656786552258999----5369968476752722322318876776666523442-1215


Q ss_pred             CCHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEE
Q ss_conf             52676426650467777516777889999999998728653201344320367788776010698899989850334159
Q gi|254780353|r  172 FPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFR  251 (753)
Q Consensus       172 ~P~lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~  251 (753)
                      +|..+-|++++++++||+++|| ++  -.+.....|.++..+-.|+.-...-++|++   |..........+-|+.+.++
T Consensus       227 v~ln~~~~~~~~f~~yv~~~~~-~~--~~~~~~~~ihe~~~~RwEv~~a~s~~~fqq---isfvNsI~T~kGGThVd~V~  300 (842)
T KOG0355         227 VELNGKNIPVKGFYDYVKMYLE-VL--WLNDDLKPLHEVLNFRWEVALALSDVGFQQ---VSFVNSIATTKGGTHVDYVV  300 (842)
T ss_pred             EEECCCCCCCHHHHHHHHHCCC-CC--CCCCCCHHHHCCCCHHHHHHHHHCCCCCCE---EEEECCCEECCCCCCCCHHH
T ss_conf             6516887752017788762353-22--246752222004324888865504466533---54200101047986544166


Q ss_pred             EEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             99999986437884079995242002168999999998640222134577640676605889850454588999998754
Q gi|254780353|r  252 VRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFM  331 (753)
Q Consensus       252 ~r~k~~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk  331 (753)
                      -+.+.+++++-...+.-.++++|++.+++-+.-.|..++++...++.+.-++.++...+.+...++....+...++. +-
T Consensus       301 D~iv~~l~~vvkKk~~~~~~svk~f~vkn~L~vfVN~lIENPtFesQTke~lt~~~~~fgs~~elsek~~k~~~~~~-i~  379 (842)
T KOG0355         301 DQIVAKLIDVVKKKKVKKDISVKPFQVKNHLWVFVNCLIENPTFESQTKERLTLRPKRFGSDCELSEKFTKAIELKG-VV  379 (842)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCHHHHHCCEEEEEEEEECCCCCCCCCHHHCCCCCCCCCCEEEEHHHHHHHHHHCC-HH
T ss_conf             55777888874211346654446453303569999887427663443310126663454326763167799998676-49


Q ss_pred             HCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---H
Q ss_conf             2000012233113331268972204999999899998999999999999999999999999998641078999975---2
Q gi|254780353|r  332 LSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAII---R  408 (753)
Q Consensus       332 ~T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iI---R  408 (753)
                      .+-+|.++++++..|.+. .++.++..+.+..+.+.+.....+..+-.| -+.++-|..++-.-.+...++..--|   |
T Consensus       380 esils~s~~~~~~dL~kk-~~~~~s~~e~I~KleDa~~ag~k~s~kctl-IltEgdsaksLavsGl~vvgRd~~gVfplr  457 (842)
T KOG0355         380 ESILSKSLNKYKDDLAKK-RGKLTSRSKGIPKLEDANDAGTKTSEKCTL-ILTEGDSAKSLAVSGLSVVGRDYYGVFPLR  457 (842)
T ss_pred             HHHHHHHHHHHHHHHHHH-HHHHHCCCCCHHHHHHCCCCCCCCCCCEEE-EEECCCCCHHHEECCCCCCCEEEEEECCCC
T ss_conf             999998888898765444-344433201306765233244345543168-886155203320135554660467550112


Q ss_pred             CCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHH-HHHHHHHHHHCC
Q ss_conf             0000110000002577577889988789999889999766678999988776544203978878999-999999987417
Q gi|254780353|r  409 NEDKPKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQI-ACEIREVKEIFS  487 (753)
Q Consensus       409 ~s~~~k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI-~~EL~eikkkfg  487 (753)
                      ..--...++-.+..+...|+++|+.+=..++++.+...-.--|-++   +--....+ |-+..+.+| --+..+....|.
T Consensus       458 gklLNv~e~s~kqilkn~EI~aIikIlgl~~~~~y~~~eslryg~~---mimtDQd~-dgshikgllInf~~~~~psl~~  533 (842)
T KOG0355         458 GKLLNVREASHKQILKNAEINAIIKILGLQYKKKYFDVESLRYGKL---MIMTDQDH-DGSHIKGLLINFIHHFWPSLLQ  533 (842)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCHHHE---EEEECCCC-CCCHHHHHHHHHHHHHHHHHHC
T ss_conf             3134457777988877999999999998877533133122242224---66512345-6434777889889876588635


Q ss_pred             CCCCCCCCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEEECCCCCC-------CCCCCCCCCCCCCCEEEEEECCC
Q ss_conf             74334555420000110000001100245667059987101020256554-------45532234555554012111147
Q gi|254780353|r  488 KSTDLGRRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWIRSLKSHS-------VDLSALHFKEGDSLKIALHAHTT  560 (753)
Q Consensus       488 d~~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr~k~~~-------~~~~~~~~KegD~l~~~~~~~t~  560 (753)
                      .|        -+.+.....  +..+.-+   +..-..|-.+|.|+.+...       ...+|+++...|.....|.|.-|
T Consensus       534 ~~--------fleefitpi--~k~~~~~---~~~~fys~pey~kw~~~~~~~~~~~ikyykglgts~~~e~keyf~~~~~  600 (842)
T KOG0355         534 IP--------FLEEFITPI--VKATKGK---QEVSFYSLPEYEKWKKNTDNWKSWKIKYYKGLGTSTSKEAKEYFSDLDR  600 (842)
T ss_pred             CC--------CHHHCCCCC--EEECCCC---CCEEEECCHHHHHHHHCCCCCCCCCEEEEECCCCCCHHHHHHHHHCHHH
T ss_conf             87--------421047764--5740477---4314544565788875484424422377514774547899998616001


Q ss_pred             CCEEEEECCCEEEEEEHHHCCCC--CCCCCCCCCCCCCCCCCEEEEEEEECC--CCEEEEEECCCCEEEEEHHHHHCCCC
Q ss_conf             81789806882787551121212--344442222357676530789998579--98599997489789963887402333
Q gi|254780353|r  561 DRILLLSTDGKAYTLPAGNLLSG--RGHGEAIQLLIDLNHNQDIVTAFVYDS--TCKLLVVSSKGNAFIVEESEIIANTR  636 (753)
Q Consensus       561 d~LLffTs~GkvY~l~a~~Ips~--~~kG~pI~~ll~l~~~EkIv~~~~~~~--~~~lll~Tk~G~ikr~~l~~~~~~~k  636 (753)
                      +.++|+.+.|..+....+.++..  .+++++|.++.+...+ +....+++++  +.+++|.+.+ -+..+...-+...++
T Consensus       601 h~~~F~~~~~~d~~~i~~af~k~k~~~rk~wL~~~~~~~~~-~~~~~v~~sdf~~elilf~~~~-sIp~~~dglkpgqRk  678 (842)
T KOG0355         601 HRILFKYDGGIDDEAIDMAFSKKKIDARKEWLRKYMPEYLY-KTTKFVTISDFVKELILFSNAD-SIPSLVDGLKPGQRK  678 (842)
T ss_pred             HEEEEECCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHHHCC-CCCCEEEHHHHHHHHHHHHHCC-CCHHHHHCCCCCCHH
T ss_conf             23787525750477886422310066677689986566413-6652557899999999987215-207677235866223


Q ss_pred             CCEEEEEECCCCCEEEEEECCC-CEEEEEECCCCEEEEEHHHCCCCCH
Q ss_conf             5627885368980568896189-8099995699389955787783361
Q gi|254780353|r  637 KGKTFLKVSSEEKMKLVVKVTG-DHVAVVGENRKLLIFSIDQIPEMSR  683 (753)
Q Consensus       637 ~Gk~~ikLk~~D~li~v~~~~~-d~iiliT~~Gk~LrF~~~eIr~~gR  683 (753)
                      -+..+++..+++++.++.++.. +++.....+++.+.--+..++...+
T Consensus       679 v~~~~~k~n~~~E~Kv~ql~g~v~~~s~yhhge~sl~~ti~~l~q~~~  726 (842)
T KOG0355         679 VLFTCFKRNDKREVKVAQLAGSVAEMSAYHHGEQSLMSTIVNLAQDFV  726 (842)
T ss_pred             HHHHHHHHCCCCCEEEEEECCHHHHHHHHHCCCHHHHHHHHHHHHHHC
T ss_conf             346767644766255433024788888774342769999998887505


No 16 
>KOG0355 consensus
Probab=99.96  E-value=1e-37  Score=303.14  Aligned_cols=167  Identities=29%  Similarity=0.471  Sum_probs=141.2

Q ss_pred             EEECCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHH--HCCCCCCHHHHH
Q ss_conf             665319999998888888999851047641128970468999999986899989803540536665--427688747899
Q gi|254780353|r   17 VKAVSLRFALEERYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEV--IGKLHPHGDQSV   94 (753)
Q Consensus        17 i~~~~i~~~~~~~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v--~gkyhPHGd~s~   94 (753)
                      -..+++.+.. +.|+-+++.=    +||.+.|||||.||++||++.+++...+   .|.||.+|.|  +..|| ||++|+
T Consensus       644 ~~~v~~sdf~-~elilf~~~~----sIp~~~dglkpgqRkv~~~~~k~n~~~E---~Kv~ql~g~v~~~s~yh-hge~sl  714 (842)
T KOG0355         644 TKFVTISDFV-KELILFSNAD----SIPSLVDGLKPGQRKVLFTCFKRNDKRE---VKVAQLAGSVAEMSAYH-HGEQSL  714 (842)
T ss_pred             CCEEEHHHHH-HHHHHHHHCC----CCHHHHHCCCCCCHHHHHHHHHHCCCCC---EEEEEECCHHHHHHHHH-CCCHHH
T ss_conf             5255789999-9999987215----2076772358662233467676447662---55433024788888774-342769


Q ss_pred             HHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCH
Q ss_conf             99999610013216613267887088677971002468998559999998421878617521679963242231234526
Q gi|254780353|r   95 YDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPN  174 (753)
Q Consensus        95 y~a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~  174 (753)
                      ..|+|+|||+|..                .+||++||+|++|++.+..++.--|...-. -.|=||...||++.| .+||
T Consensus       715 ~~ti~~l~q~~~g----------------kdaa~~ryi~t~l~~~tr~~f~~~dd~ll~-~~~~~~~~vep~y~p-i~p~  776 (842)
T KOG0355         715 MSTIVNLAQDFVG----------------KDAASARYIFTKLSPLTRLLFPPADDLLLK-YLNEDGQRVEPEYCP-IIPM  776 (842)
T ss_pred             HHHHHHHHHHHCC----------------CCCHHHHHHHHHCCHHHHHCCCCCCHHHHH-HHCCCCCCCCCCCCC-CEEE
T ss_conf             9999988875058----------------840236789885273654027888326766-522578671752244-1468


Q ss_pred             HHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCC
Q ss_conf             764266504677775167778899999999987286
Q gi|254780353|r  175 LLANGTSGIAVGMATSIPSHNVQEICEAALALIDNP  210 (753)
Q Consensus       175 lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~  210 (753)
                      +|+||+.||++||+|+||++|+.||++.+.+++++.
T Consensus       777 vlvngaegiGtGws~~i~n~n~~~iv~~~r~~~~~~  812 (842)
T KOG0355         777 VLVNGAEGIGTGWSTFIPNYNPREIVKNIRRLINGE  812 (842)
T ss_pred             EEEECCCCCCCCCCCCCCCCCHHHHHHHHHHHHCCC
T ss_conf             885056545567656688889899999998863699


No 17 
>PRK13979 DNA topoisomerase IV subunit A; Provisional,Validated
Probab=99.93  E-value=6.8e-24  Score=199.18  Aligned_cols=187  Identities=17%  Similarity=0.161  Sum_probs=149.0

Q ss_pred             ECCCCCEEEEECCCEEEEEEHHHCCCCCCCCCCCCCCCC-CCCCCEEEEEEE---ECCCCEEEEEECCCCEEEEEHHHHH
Q ss_conf             114781789806882787551121212344442222357-676530789998---5799859999748978996388740
Q gi|254780353|r  557 AHTTDRILLLSTDGKAYTLPAGNLLSGRGHGEAIQLLID-LNHNQDIVTAFV---YDSTCKLLVVSSKGNAFIVEESEII  632 (753)
Q Consensus       557 ~~t~d~LLffTs~GkvY~l~a~~Ips~~~kG~pI~~ll~-l~~~EkIv~~~~---~~~~~~lll~Tk~G~ikr~~l~~~~  632 (753)
                      +++.+.+++|++.|++|.++++.+.+..+.|.++..+.. +..+|+|+.++.   ++++.+++.+|++|++|||.+.+|.
T Consensus       753 ~~~~~~ili~~~~G~~~~~~~~~~~~~~~~g~~i~~~~~~~~~~e~vi~~~~~~~~~e~~~il~vTe~G~GKRT~~~eyr  832 (959)
T PRK13979        753 TNSSKNLLLFSDKGKVYKIPAFMLQNIEESGINISALTGDFEKKESIINAISIFEFEEDLSIYFFSKKGLVKKTLLSEFK  832 (959)
T ss_pred             CCCCCCEEEECCCCCEEECCHHHCCCCCCCCCCCHHHHHHHCCCCCEEEEEECCCCCCCCEEEEEECCCCCCCCCHHHHC
T ss_conf             56631135432577233032432023355564502222121022302466520357776159999358974666567733


Q ss_pred             CCCCCCEEEEEECCCCCEEEEEE-C-CCCEEEEEECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCC-EEEEEEEECCCC
Q ss_conf             23335627885368980568896-1-898099995699389955787783361-2141334218787-568999733888
Q gi|254780353|r  633 ANTRKGKTFLKVSSEEKMKLVVK-V-TGDHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGG-ISDVICFKICEG  708 (753)
Q Consensus       633 ~~~k~Gk~~ikLk~~D~li~v~~-~-~~d~iiliT~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~-~~~~~~~~~~e~  708 (753)
                      ...+.|+.+..-...+.++++.. . ++|+++++|++|+++||+.++|+.+|| ++||++|+|++++ ++.+..+..++.
T Consensus       833 ~~g~~~~~~k~~~~~~~~v~~~~~~~~~d~imliT~~G~~IR~~v~~I~~~GR~tqGV~li~L~~~dkVV~~~~i~~~~~  912 (959)
T PRK13979        833 GEGNSTQVYKFKHKEDELVSVDINEHEQKNILIITKKGMAIRFKSEAVNPMGKIASGVTGISLKDEDKVIFGSIIDENDT  912 (959)
T ss_pred             CCCCCEEEEEEEECCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCEEEEECCCCCEEEEEEEECCCCC
T ss_conf             46786489998844897899997048996389990798799987243470260368806897389987999999747777


Q ss_pred             CEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCCC
Q ss_conf             36999417756645114322544413666027552
Q gi|254780353|r  709 LTWIDSAGRSYNRSENDLLGWLGKRGGVGSLVPKG  743 (753)
Q Consensus       709 ~~il~~t~~g~~k~~~~~~~~~~~RggkG~~~~k~  743 (753)
                      ..+...++++.++..+..+..+|+|+|+|..+|-.
T Consensus       913 ~~~~~~~k~~~~~~~~~~~~~~q~~~g~g~~~~~~  947 (959)
T PRK13979        913 RKIKLKSKAKDKGEIEIEDIKLQNRAGRGNSLMPL  947 (959)
T ss_pred             CEEEEEECCCCCCEEEHHHHHHCCCCCCCCEEEEE
T ss_conf             45999973886627871131100026787247886


No 18 
>PRK05560 DNA gyrase subunit A; Validated
Probab=99.92  E-value=6e-23  Score=192.08  Aligned_cols=186  Identities=22%  Similarity=0.307  Sum_probs=155.0

Q ss_pred             CCCCEEEEECCCEEECCCCCCC------CCCCCCCCCCCCCEEEEEECCCCCEEEEECCCEEEEEEHHHCCC-C-CCCCC
Q ss_conf             6670599871010202565544------55322345555540121111478178980688278755112121-2-34444
Q gi|254780353|r  517 KEPITVVISNRGWIRSLKSHSV------DLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAGNLLS-G-RGHGE  588 (753)
Q Consensus       517 ~E~v~V~LS~~GyIKr~k~~~~------~~~~~~~KegD~l~~~~~~~t~d~LLffTs~GkvY~l~a~~Ips-~-~~kG~  588 (753)
                      ++.-.+++|++|+||+.+...+      |...++++++|.+..+..|+..+.++++|+.|++...+..++|. | .++|.
T Consensus       608 ~~~~Lv~~Tk~G~IKRt~L~df~~~r~~G~~AikLke~DeLv~v~l~~~~~dIil~T~~G~alRF~~~eVR~~GR~a~GV  687 (822)
T PRK05560        608 DDLYLFFATKNGTVKKTALSEFSNIRSNGLIAINLDEGDELIGVRLTDGDDDVLLFSANGKAIRFPEEDVRPMGRTARGV  687 (822)
T ss_pred             CCCEEEEEECCCCEEEECHHHCCCCCCCCEEEEECCCCCEEEEEEECCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCC
T ss_conf             88569999579727971368722555255199985899779999984899879999789739995066577778877684


Q ss_pred             CCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCEEEEEHHHHHCCCCCC--EEEEEECC-CCCEEEEEECCC-CEEEEE
Q ss_conf             22223576765307899985799859999748978996388740233356--27885368-980568896189-809999
Q gi|254780353|r  589 AIQLLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKG--KTFLKVSS-EEKMKLVVKVTG-DHVAVV  664 (753)
Q Consensus       589 pI~~ll~l~~~EkIv~~~~~~~~~~lll~Tk~G~ikr~~l~~~~~~~k~G--k~~ikLk~-~D~li~v~~~~~-d~iili  664 (753)
                      --   +.|.++++|+++...+++.++|++|++|++||+++++|....|.|  ...+++.+ ++.++++..+.+ |+++++
T Consensus       688 kg---IkL~~gD~VV~~~vv~~~~~iL~vTe~G~GKRt~~~eyr~~~RGgkGv~~ik~~~k~G~lv~~~~V~~~deI~li  764 (822)
T PRK05560        688 RG---IKLREGDEVVSMSVLRDEQFVLTVTENGYGKRTPAEEYRLQGRGGKGVIAIKITERNGKLVGAVPVDDDDEIMLI  764 (822)
T ss_pred             CC---EECCCCCEEEEEEEECCCCEEEEEECCCEEEECCHHHCCCCCCCCCCEEEEEECCCCCCEEEEEECCCCCEEEEE
T ss_conf             31---551999989999985799879999189805305288837557787775889964888848999991799869999


Q ss_pred             ECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCCEE-EEEEEEC
Q ss_conf             5699389955787783361-214133421878756-8999733
Q gi|254780353|r  665 GENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGIS-DVICFKI  705 (753)
Q Consensus       665 T~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~~~-~~~~~~~  705 (753)
                      |++|+++|+++++||.+|| ++||++|+|++++.+ .+..+..
T Consensus       765 T~~G~~iRi~v~~I~~~gR~t~GVrl~~L~~~d~v~~va~v~~  807 (822)
T PRK05560        765 TDAGKLIRTRVSEIRITGRNTQGVTLIRLDEGEKVVSVARVAE  807 (822)
T ss_pred             ECCCEEEEEEHHHCCCCCCCCCCEEEEECCCCCEEEEEEEECC
T ss_conf             2798799987100475675788708998599998999998078


No 19 
>TIGR01063 gyrA DNA gyrase, A subunit; InterPro: IPR005743   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   Topoisomerase II (called gyrase in bacteria) primarily introduces negative supercoils into DNA. In bacteria, topoisomerase II consists of two polypeptide subunits, gyrA and gyrB, which form a heterotetramer: (BA)2. In most eukaryotes, topoisomerase II consists of a single polypeptide, where the N- and C-terminal regions correspond to gyrB and gyrA, respectively.   This entry represents the A subunit (gyrA) as found predominantly in bacteria, but does not include the topoisomerase II enzymes composed of a single polypeptide, as are found in most eukaryotes. GyrA has two functional domains: an N-terminal that forms the covalent DNA-protein bridge that is responsible for the breaking- and rejoining function, and a C-terminal that can bind DNA non-specifically .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=99.89  E-value=1.3e-21  Score=181.95  Aligned_cols=180  Identities=21%  Similarity=0.290  Sum_probs=135.8

Q ss_pred             CCC---CEEEEECCCEEECCCCCC------CCCCCCCCCCCCCCEEEEEECCCCC-EEEEECCCEEEEEEHH--HC-C-C
Q ss_conf             667---059987101020256554------4553223455555401211114781-7898068827875511--21-2-1
Q gi|254780353|r  517 KEP---ITVVISNRGWIRSLKSHS------VDLSALHFKEGDSLKIALHAHTTDR-ILLLSTDGKAYTLPAG--NL-L-S  582 (753)
Q Consensus       517 ~E~---v~V~LS~~GyIKr~k~~~------~~~~~~~~KegD~l~~~~~~~t~d~-LLffTs~GkvY~l~a~--~I-p-s  582 (753)
                      |+.   -+++.|++|+|||.....      .|.-++++.|||++..+..|...|. +++||..|++..++..  ++ | +
T Consensus       630 d~~~~~yl~~aTk~G~vKk~~L~~F~~~rs~GiiAi~L~e~D~L~~v~~~~~~~~~v~l~s~~G~~~RF~~~~~~vR~mg  709 (864)
T TIGR01063       630 DEAYDLYLFLATKNGVVKKTSLTEFSNIRSNGIIAIKLDEGDELISVRLVDGDDEKVMLGSKNGKAVRFPEEDEEVREMG  709 (864)
T ss_pred             CCCCCEEEEEECCCCEEEEEECHHHHHHHHCCEEEEEEECCCEEEEEEEEECCCCEEEEEECCCCEEECCCCCCCHHCCC
T ss_conf             55266179997267438874001443545278699997089689999996078865886514884798368853110024


Q ss_pred             CCCCCCCCCCCCCCCCC----------------------------CEEEEEEEECCCC-EEEEEECCCCEEEEEHHHHHC
Q ss_conf             23444422223576765----------------------------3078999857998-599997489789963887402
Q gi|254780353|r  583 GRGHGEAIQLLIDLNHN----------------------------QDIVTAFVYDSTC-KLLVVSSKGNAFIVEESEIIA  633 (753)
Q Consensus       583 ~~~kG~pI~~ll~l~~~----------------------------EkIv~~~~~~~~~-~lll~Tk~G~ikr~~l~~~~~  633 (753)
                      +.+.|.-=   +.|..+                            +.++++....++. ++|.+|.+|||||++.++|..
T Consensus       710 R~~~GV~G---i~L~~~~~v~~~~~~~~i~~~~~D~~~~~L~~NlD~vv~~~~~~e~~~~lL~vt~nGyGKRt~~~~yr~  786 (864)
T TIGR01063       710 RATRGVRG---IKLKNEDSVISMTVLKGINSIKEDRNLEELGVNLDFVVSLEVVSEESQKLLIVTENGYGKRTSIEEYRL  786 (864)
T ss_pred             CCCCCEEE---EEECCCCCCCHHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEECCCCCEEEEEEECCCCEECCHHHCCC
T ss_conf             55676013---540677740001344321200222246543742434477786249983789983068420042625763


Q ss_pred             CCCCCEEEEEEC--C-CCCEEEEEECCC-CEEEEEECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCCEEE
Q ss_conf             333562788536--8-980568896189-8099995699389955787783361-2141334218787568
Q gi|254780353|r  634 NTRKGKTFLKVS--S-EEKMKLVVKVTG-DHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGISD  699 (753)
Q Consensus       634 ~~k~Gk~~ikLk--~-~D~li~v~~~~~-d~iiliT~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~~~~  699 (753)
                      ..|.|+.+..++  + +..|+++..+.+ |+++++|+.|+++|.++.+|+.+|| ++|||+++|++++.+.
T Consensus       787 ~~RGg~Gv~~~~~~~r~G~vVga~~V~~~d~lm~iT~~G~~iR~~~~~vs~~GR~t~GVrL~~l~e~d~vv  857 (864)
T TIGR01063       787 QSRGGKGVKSIKITDRNGQVVGAIAVDDDDELMLITSSGKLIRTSVQDVSIQGRNTQGVRLIRLDEDDKVV  857 (864)
T ss_pred             CCCCCCEEEEEEEECCCCCEEEEEEECCCCHHHHEECCCCEEEEEEEHHCCCCCCCCCEEEEEECCCCCEE
T ss_conf             26566237889986468968789874587400010108837997610321156535655898517876356


No 20 
>PRK05561 DNA topoisomerase IV subunit A; Validated
Probab=99.61  E-value=1.1e-12  Score=114.98  Aligned_cols=184  Identities=13%  Similarity=0.068  Sum_probs=140.9

Q ss_pred             CCCCCEEEEECCCEEEEEEHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCEEEEEHHHHHCCCCC
Q ss_conf             14781789806882787551121212344442222357676530789998579985999974897899638874023335
Q gi|254780353|r  558 HTTDRILLLSTDGKAYTLPAGNLLSGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRK  637 (753)
Q Consensus       558 ~t~d~LLffTs~GkvY~l~a~~Ips~~~kG~pI~~ll~l~~~EkIv~~~~~~~~~~lll~Tk~G~ikr~~l~~~~~~~k~  637 (753)
                      ..-+-.+.+|..|-+-+++.+....   .      -+.+.+++.+..++......+++|+|.+|.++.....++.+.+..
T Consensus       506 ~~E~v~V~lS~~GyIKr~k~~~~~~---~------~~~~Ke~D~v~~~~~~~T~d~LLfFTn~Grvy~lkv~~IP~~r~~  576 (745)
T PRK05561        506 PDEPVTVVLSKKGWVRRAKGHDIDP---A------GLGYKEGDSLLFAFEARTTDKLLFFTSTGRVYSLPVHELPSARGQ  576 (745)
T ss_pred             CCCCCEEEECCCEEEEEECCCCCCC---C------CCCCCCCCCEEEEEEEECCCEEEEEECCCEEEEEEHHHCCCCCCC
T ss_conf             6766189981780499844888675---4------456777853258999806976999957975999892208786678


Q ss_pred             CEE---EEEECCCCCEEEEEECCC-CEEEEEECCCCEEEEEHHHCCCCCHHHCCEEEECCCCCEEEEEEEECCCCCEEEE
Q ss_conf             627---885368980568896189-8099995699389955787783361214133421878756899973388836999
Q gi|254780353|r  638 GKT---FLKVSSEEKMKLVVKVTG-DHVAVVGENRKLLIFSIDQIPEMSRGKGVRLQSYKDGGISDVICFKICEGLTWID  713 (753)
Q Consensus       638 Gk~---~ikLk~~D~li~v~~~~~-d~iiliT~~Gk~LrF~~~eIr~~gRgkGVk~i~Lkd~~~~~~~~~~~~e~~~il~  713 (753)
                      |..   .+.+.+++.++++...++ ++++++|++|+..+++.+++.. .|.+|.++|+|++++..............++.
T Consensus       577 G~pi~nll~L~~~EkIv~vl~~~~~~~lllaTk~G~~kr~~l~e~~~-~~k~G~~ai~L~~gDelv~~~~i~~~~d~I~l  655 (745)
T PRK05561        577 GEPLTGLIDLEPGEEIVHVLVGDPDQKLLLASSAGYGFVVSEEDLVG-RNRAGKAVINLKDGDKVLAPVPVEGDEDSLAA  655 (745)
T ss_pred             CCCHHHCCCCCCCCEEEEEEEECCCCEEEEEECCCEEEEEEHHHHCC-CCCCCEEEEEECCCCEEEEEEEECCCCCEEEE
T ss_conf             80898806899999699999858987699997893299978698004-46267188861899889888994699988999


Q ss_pred             ECCCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCCCEECC
Q ss_conf             4177566451143225444136660275526776861049
Q gi|254780353|r  714 SAGRSYNRSENDLLGWLGKRGGVGSLVPKGFPRSGKFLSS  753 (753)
Q Consensus       714 ~t~~g~~k~~~~~~~~~~~RggkG~~~~k~~~K~gklV~A  753 (753)
                      +|.+|+..+.+..+.+.++| ++||+.++. .+.++++++
T Consensus       656 vT~~Gk~lrF~~~evr~~gR-gkGVkgikL-k~~D~Vv~~  693 (745)
T PRK05561        656 ITQRGRLLVFPLSELPELSR-GKGVKLIEL-KKEEGLADL  693 (745)
T ss_pred             EECCCCEEEEEHHHCCCCCC-CCCCCEEEE-CCCCEEEEE
T ss_conf             95898289979888777575-468014766-899989999


No 21 
>COG0188 GyrA Type IIA topoisomerase (DNA gyrase/topo II, topoisomerase IV), A subunit [DNA replication, recombination, and repair]
Probab=99.61  E-value=9.2e-14  Score=123.03  Aligned_cols=176  Identities=23%  Similarity=0.380  Sum_probs=89.7

Q ss_pred             CCCEEEEECCCEEECCCCCC------CCCCCCCCCCCCCCEEEEEEC-CCCCEEEEECCCEEEEEEHHHCCC-C-CCCCC
Q ss_conf             67059987101020256554------455322345555540121111-478178980688278755112121-2-34444
Q gi|254780353|r  518 EPITVVISNRGWIRSLKSHS------VDLSALHFKEGDSLKIALHAH-TTDRILLLSTDGKAYTLPAGNLLS-G-RGHGE  588 (753)
Q Consensus       518 E~v~V~LS~~GyIKr~k~~~------~~~~~~~~KegD~l~~~~~~~-t~d~LLffTs~GkvY~l~a~~Ips-~-~~kG~  588 (753)
                      +.-.++.|+.||+|+.+...      .+...++++++|.+.....+. ..+.++++|+.|++...+..++|. + .++|.
T Consensus       601 ~~~l~~~T~~G~vK~~~l~~f~~~~~~g~~ai~L~~~d~l~~~~~~~~~~~~i~~~t~~G~~~~F~~~~v~~~gr~a~Gv  680 (804)
T COG0188         601 DQYLFLATKKGYVKKTSLSEFKNIRSKGKIAIKLKEGDELVSVSLTSDGDDDILLVTSNGKALRFPESEVREMGRGAKGV  680 (804)
T ss_pred             CEEEEEEECCCCEEEEEHHHHHCCCCCCEEEEECCCCCCEEEEEECCCCCCEEEEEECCCEEEEEEHHHCCCCCCCCCCC
T ss_conf             60599991699479820355312356770689717776301245215787608999148737874034422115413686


Q ss_pred             CCCCCCCCCCCCEEEEEEEECCCC-EEEEEECCCCEEEEEHHHHHCCCCCCEEEEEECCCCC----EEEEEECCC-CEEE
Q ss_conf             222235767653078999857998-5999974897899638874023335627885368980----568896189-8099
Q gi|254780353|r  589 AIQLLIDLNHNQDIVTAFVYDSTC-KLLVVSSKGNAFIVEESEIIANTRKGKTFLKVSSEEK----MKLVVKVTG-DHVA  662 (753)
Q Consensus       589 pI~~ll~l~~~EkIv~~~~~~~~~-~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~D~----li~v~~~~~-d~ii  662 (753)
                      ..   +.+.+++.++++....++. +++.+|++|++|+++..+|...+|.|+..+..+..+.    ++....+.+ |+++
T Consensus       681 ~~---i~l~~~d~~~~~~~~~~~~~~~l~~t~~g~~kr~~~~~~~~~~Rg~~G~~~~~~~~~~~~~~~~~~~v~~~~~~~  757 (804)
T COG0188         681 KG---IKLKEGDKVVSLSVVEDDEAKLLTVTERGYGKRTKISEYPVTKRGGKGVILIKGTKRNRGKVVAAITVDEDDEIM  757 (804)
T ss_pred             CE---EECCCCCEEEEEEECCCCCEEEEEEECCCCEEECCHHHCCCCCCCCCCEECCCCCCCCCCEEEEEECCCCCCEEE
T ss_conf             40---643765756653201478605899843672000414213424667664124545556553377641368875389


Q ss_pred             EEECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCC
Q ss_conf             995699389955787783361-2141334218787
Q gi|254780353|r  663 VVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGG  696 (753)
Q Consensus       663 liT~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~  696 (753)
                      ++|+.|+++|...++++.+|| ++||+.+++.+++
T Consensus       758 ~~t~~g~~ir~~~~~i~~~~r~t~gv~~~~~~~~~  792 (804)
T COG0188         758 LITSRGKLIRTAVSEISITGRNTQGVKLINLDEDE  792 (804)
T ss_pred             EECCCCEEEEEECCCCCCCCCCCCCEEEEECCCCC
T ss_conf             98269638985314323124445662765317997


No 22 
>TIGR01061 parC_Gpos DNA topoisomerase IV, A subunit; InterPro: IPR005741   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit A (parC) of topoisomerase IV from Gram positive bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=98.98  E-value=2.2e-08  Score=82.53  Aligned_cols=176  Identities=19%  Similarity=0.299  Sum_probs=134.6

Q ss_pred             CCC-CCCEEEEECCCEEECCCCCCC-----------CCCCCC-CCCCCCCEEEEEECCCC----CEEEEECCCEEEEEEH
Q ss_conf             456-670599871010202565544-----------553223-45555540121111478----1789806882787551
Q gi|254780353|r  515 IEK-EPITVVISNRGWIRSLKSHSV-----------DLSALH-FKEGDSLKIALHAHTTD----RILLLSTDGKAYTLPA  577 (753)
Q Consensus       515 I~~-E~v~V~LS~~GyIKr~k~~~~-----------~~~~~~-~KegD~l~~~~~~~t~d----~LLffTs~GkvY~l~a  577 (753)
                      +.+ -+..+++|..|-+=-.+-|..           =..... +-++..+..+...+.-|    .|+++|..|.+=++..
T Consensus       539 ~~nttd~lL~~Ts~g~~In~pvh~La~~rwkd~g~hls~~~~n~~~~E~iv~v~~~~~fdv~~~~L~l~sklg~vKriel  618 (745)
T TIGR01061       539 IANTTDKLLIFTSKGNLINLPVHKLADIRWKDLGEHLSNKITNFDENETIVAVEILNEFDVDEAILVLASKLGMVKRIEL  618 (745)
T ss_pred             HHHCCCEEEEEECCCCEEEEEEEECCCCCHHHHHHHHCCHHHHHHCCCCEEEEEEECCCCCCHHHHHHHHHCCCEEEEEC
T ss_conf             52122537887616666421303145665668998720001102106848999861322574689899875587478760


Q ss_pred             HHCCCCC---CCCCCCCCCCCCCCCCEEEEEEEECC--CCEEEEEECCCCEEEEEHHHHH--CCCCCCEEEEEECCCCCE
Q ss_conf             1212123---44442222357676530789998579--9859999748978996388740--233356278853689805
Q gi|254780353|r  578 GNLLSGR---GHGEAIQLLIDLNHNQDIVTAFVYDS--TCKLLVVSSKGNAFIVEESEII--ANTRKGKTFLKVSSEEKM  650 (753)
Q Consensus       578 ~~Ips~~---~kG~pI~~ll~l~~~EkIv~~~~~~~--~~~lll~Tk~G~ikr~~l~~~~--~~~k~Gk~~ikLk~~D~l  650 (753)
                      .++...+   +|-.   ..++|.+++..++++....  ++.++++|..||+-....+|..  +....|.++|+||++|.+
T Consensus       619 ~~l~~~~~y~sK~~---~~~~L~D~d~li~a~~~~~Gh~~~i~lvS~~gy~l~F~~~Ei~~~~~~A~GvK~mkLK~~D~v  695 (745)
T TIGR01061       619 TELDIKRNYRSKAI---LILKLKDEDELISAFLQKKGHDKLIILVSKLGYALLFLVEEINVVGAKAAGVKGMKLKEDDEV  695 (745)
T ss_pred             CCCCCCCCCHHHHH---HHHHCCCCCCEEEEEEECCCCCCEEEEEEECCCEEEECCEEECCCCCCCCCEEEEECCCCCEE
T ss_conf             32477865101223---321117895438999841888441899973683577302033231446673113305767638


Q ss_pred             EEEEECCC-CEEEEEECCCCEEEEEHHHCCCCCHH-HCCEEE-ECC
Q ss_conf             68896189-80999956993899557877833612-141334-218
Q gi|254780353|r  651 KLVVKVTG-DHVAVVGENRKLLIFSIDQIPEMSRG-KGVRLQ-SYK  693 (753)
Q Consensus       651 i~v~~~~~-d~iiliT~~Gk~LrF~~~eIr~~gRg-kGVk~i-~Lk  693 (753)
                      .++..++. +.++++|+.|-+.+|+.+|+...+|+ +|+++. .++
T Consensus       696 ~~~~i~~~~~~~vll~~~Gs~k~~~~~El~~~sRa~~~~~llRp~k  741 (745)
T TIGR01061       696 KSGLILEANESLVLLTQRGSVKRLSISELKVTSRAATGVKLLRPLK  741 (745)
T ss_pred             EEEEEECCCCCEEEEEECCCEEEEEHHHHHHHHHHCCCCHHHCCCC
T ss_conf             9999982799558997368256510365555343116511110000


No 23 
>TIGR01062 parC_Gneg DNA topoisomerase IV, A subunit; InterPro: IPR005742   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit A (parC) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=97.70  E-value=0.0022  Score=44.95  Aligned_cols=189  Identities=8%  Similarity=0.058  Sum_probs=130.8

Q ss_pred             CCCCCCCCCEEEE---EECCCCCE-EEEECCCEEEEEEHHHCCCCCCCCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEE
Q ss_conf             2345555540121---11147817-8980688278755112121234444222235767653078999857998599997
Q gi|254780353|r  543 LHFKEGDSLKIAL---HAHTTDRI-LLLSTDGKAYTLPAGNLLSGRGHGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVS  618 (753)
Q Consensus       543 ~~~KegD~l~~~~---~~~t~d~L-LffTs~GkvY~l~a~~Ips~~~kG~pI~~ll~l~~~EkIv~~~~~~~~~~lll~T  618 (753)
                      ..+.|-|.-..+.   ...+...+ ++.|.-|.|=+++.|++....         ++...|+.....+....++.++|+.
T Consensus       484 ~~l~E~~~~~~~~~~t~~~~~EPvTii~S~MGWVRs~KGH~~D~~~---------l~YK~GD~~~~~~~~~~~~~v~~i~  554 (747)
T TIGR01062       484 SSLEEREEAKQVSEITDMIPKEPVTIILSKMGWVRSAKGHDIDLST---------LKYKAGDSEKAIIEGKSNQKVVFID  554 (747)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCEEEEECCCCCEEECCCCCCCCCC---------CCCCCCCCEEEEEEECCCCEEEEEE
T ss_conf             5135678888887665303678817998277735504665667143---------5413686123345512775179997


Q ss_pred             CCCCEEEEEHHHHHCCCCCCE-EEEE--ECCC-CCEEEEEECCC-CEEEEEECCCCEEEEEHHHCCCCCHHHCCEEEECC
Q ss_conf             489789963887402333562-7885--3689-80568896189-80999956993899557877833612141334218
Q gi|254780353|r  619 SKGNAFIVEESEIIANTRKGK-TFLK--VSSE-EKMKLVVKVTG-DHVAVVGENRKLLIFSIDQIPEMSRGKGVRLQSYK  693 (753)
Q Consensus       619 k~G~ikr~~l~~~~~~~k~Gk-~~ik--Lk~~-D~li~v~~~~~-d~iiliT~~Gk~LrF~~~eIr~~gRgkGVk~i~Lk  693 (753)
                      +.|..+-..-..+.+.+..|- ..+|  +.-| ..+-.+....+ +.++++|+.|+-..+..+++=...| .|=.+|+|+
T Consensus       555 S~GR~y~l~~~~l~~a~g~G~Pl~~KL~l~~Gn~~i~~~l~~~~~Q~LL~AS~~G~GF~~~~~~liA~~k-~GK~l~~lP  633 (747)
T TIGR01062       555 STGRSYALDPLNLPSARGQGEPLTGKLLLPIGNATIENILMESENQKLLLASDAGYGFLVKFNDLIARNK-AGKALINLP  633 (747)
T ss_pred             CCCCEEEECCCCCCCCCCCCCCEEEEEECCCCCCCEEEEEEECCCCCEEEECCCCCCEEEECHHHHHHCH-HCHHHCCCC
T ss_conf             2885266311204345677872268873268862310777635885321000168624740043333110-040200178


Q ss_pred             CCCEEEEEEEECCCCC-EEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCCC
Q ss_conf             7875689997338883-6999417756645114322544413666027552
Q gi|254780353|r  694 DGGISDVICFKICEGL-TWIDSAGRSYNRSENDLLGWLGKRGGVGSLVPKG  743 (753)
Q Consensus       694 d~~~~~~~~~~~~e~~-~il~~t~~g~~k~~~~~~~~~~~RggkG~~~~k~  743 (753)
                      ++..+ +.|....+.. .++..+..+.-.-.+..+.+.-+. |+|++..+.
T Consensus       634 E~~~~-~~p~~~~~~s~~~~aI~~a~R~L~F~~~~lP~l~K-G~G~~~~~~  682 (747)
T TIGR01062       634 ENASV-LAPLVVNDDSDLIVAITEAGRLLVFPIDDLPELSK-GKGNKLIRI  682 (747)
T ss_pred             CCCEE-ECCEEECCCCCEEEEECCCCEEEEECHHHCCCCCC-CCCCEEEEE
T ss_conf             88611-04434237610244411367068742111776347-873057750


No 24 
>pfam03989 DNA_gyraseA_C DNA gyrase C-terminal domain, beta-propeller. This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a beta-propeller structure. This region has been shown to bind DNA non-specifically and may stabilize the DNA-topoisomerase complex.
Probab=97.58  E-value=0.00021  Score=52.72  Aligned_cols=42  Identities=21%  Similarity=0.352  Sum_probs=36.4

Q ss_pred             CCEEEEEECCCCEEEEEHHHCCCCCH-HHCCEEEECCCCCEEE
Q ss_conf             98099995699389955787783361-2141334218787568
Q gi|254780353|r  658 GDHVAVVGENRKLLIFSIDQIPEMSR-GKGVRLQSYKDGGISD  699 (753)
Q Consensus       658 ~d~iiliT~~Gk~LrF~~~eIr~~gR-gkGVk~i~Lkd~~~~~  699 (753)
                      +++++++|++|++.||+.+++|.++| ++||++|++++++.+.
T Consensus         1 ~~~lll~T~~G~~~r~~~~~~~~~~r~~~Gv~~~~l~~~d~v~   43 (50)
T pfam03989         1 EDDLLLITSKGYVKRTPLSEFPEQGRGAKGVKAINLKEGDKVV   43 (50)
T ss_pred             CCEEEEEECCCEEEEEECHHCCCCCCCCCCEEEEECCCCCEEE
T ss_conf             9789999089989998931545468768787978879999999


No 25 
>PRK09630 DNA topoisomerase IV subunit A; Provisional
Probab=97.45  E-value=0.0078  Score=40.84  Aligned_cols=106  Identities=11%  Similarity=-0.004  Sum_probs=67.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHCCCCCCCCC-CCCCCCCHH----
Q ss_conf             99998999989999999999999999999999999986410-------789999752000011000-000257757----
Q gi|254780353|r  359 GILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLN-------IDEIIAIIRNEDKPKPVM-VSRFSLTEN----  426 (753)
Q Consensus       359 eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~-------ID~vI~iIR~s~~~k~~L-~~~f~lse~----  426 (753)
                      --|.+|+.|+.+.+....++++....+|+.--. +...+..       +|.|+++|+.....+..- ....-+...    
T Consensus       307 l~l~eiL~~~~~~~~~~lrr~l~~~~~~~~r~~-~~k~Le~l~I~~~~~d~I~eiI~~i~~~~~~ed~~~~l~~~~~~~~  385 (479)
T PRK09630        307 TSISEILKLHTEALQGYLKKELLILQDSLTREH-YHKTLEYIFIKHKLYDTVREMLSKRKTKPSASDLHNAVLHALEPFL  385 (479)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHH
T ss_conf             668999999999875543466899989999999-9988889999877899999999988538989999999998765667


Q ss_pred             --HHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHH
Q ss_conf             --788998878999988999976-667899998877654420
Q gi|254780353|r  427 --QVDAILNLRLRSLRKLEEYQI-KSELDNLLAEKEKIDSLL  465 (753)
Q Consensus       427 --QA~aIL~mrL~rLt~le~~kl-~~E~~eL~~~i~~L~~IL  465 (753)
                        |+++++++++++|+.|+..+| .-|..++.++++++++-+
T Consensus       386 ~~~~~~i~~q~~~~L~~l~l~kL~~Le~~k~~~El~~l~~~i  427 (479)
T PRK09630        386 HTLPTAPDKQATSQLASLTIKKILCFNENAYTKELAAIEKKQ  427 (479)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             877543389999999998999875133999999999999999


No 26 
>pfam03989 DNA_gyraseA_C DNA gyrase C-terminal domain, beta-propeller. This repeat is found as 6 tandem copies at the C-termini of GyrA and ParC DNA gyrases. It is predicted to form 4 beta strands and to probably form a beta-propeller structure. This region has been shown to bind DNA non-specifically and may stabilize the DNA-topoisomerase complex.
Probab=96.90  E-value=0.0029  Score=44.07  Aligned_cols=46  Identities=28%  Similarity=0.319  Sum_probs=32.2

Q ss_pred             CEEEEEECCCCEEEEEHHHHHCCCC--CCEEEEEECCCCCEEEEEECC
Q ss_conf             8599997489789963887402333--562788536898056889618
Q gi|254780353|r  612 CKLLVVSSKGNAFIVEESEIIANTR--KGKTFLKVSSEEKMKLVVKVT  657 (753)
Q Consensus       612 ~~lll~Tk~G~ikr~~l~~~~~~~k--~Gk~~ikLk~~D~li~v~~~~  657 (753)
                      .+++++|++|++++++.+++....+  +|..+++++++|+++.+..+.
T Consensus         2 ~~lll~T~~G~~~r~~~~~~~~~~r~~~Gv~~~~l~~~d~v~~~~~~~   49 (50)
T pfam03989         2 DDLLLITSKGYVKRTPLSEFPEQGRGAKGVKAINLKEGDKVVSVLVVN   49 (50)
T ss_pred             CEEEEEECCCEEEEEECHHCCCCCCCCCCEEEEECCCCCEEEEEEECC
T ss_conf             789999089989998931545468768787978879999999999917


No 27 
>PRK09631 DNA topoisomerase IV subunit A; Provisional
Probab=93.59  E-value=0.67  Score=26.32  Aligned_cols=351  Identities=11%  Similarity=0.085  Sum_probs=142.1

Q ss_pred             EEEEEEECCCCCHHHHHHHHHH--------HCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHH-------------
Q ss_conf             5889850454588999998754--------2000012233113331268972204999999899998-------------
Q gi|254780353|r  310 RIVLFPKNRSLDPDLLMESIFM--------LSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHR-------------  368 (753)
Q Consensus       310 ~~vi~~~~r~~~~~~vl~~Lyk--------~T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R-------------  368 (753)
                      .+||.+..-.++...++.+.-+        -+++...=.-++-.++ . .|+-.+-..+|...+.|-             
T Consensus       221 ~ivItEiPy~v~k~~lie~I~~~~~~~ki~I~~i~D~s~~~vrIvi-~-lk~~~~~~~vln~Ly~~T~lq~sf~~n~~ai  298 (626)
T PRK09631        221 TIVIRELPFGETTESLIASIEKAIRKNYIKVSSINDFTAENVEIEL-K-LPRGVYASEVIEKLYHYTNCQVSISVNLLLL  298 (626)
T ss_pred             EEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEE-E-ECCCCCHHHHHHHHHHHCCHHHEECCEEEEE
T ss_conf             5999956877778999999999997256762114146898279999-9-8999998999999875097132176268999


Q ss_pred             ----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHH------HHHHHHCCCCCCCCCCCCCCCC----H
Q ss_conf             ----------9999999999999999999999999986410---789------9997520000110000002577----5
Q gi|254780353|r  369 ----------REVLFRRSSFRMQAIDRRVEILKGLLIAYLN---IDE------IIAIIRNEDKPKPVMVSRFSLT----E  425 (753)
Q Consensus       369 ----------~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~---ID~------vI~iIR~s~~~k~~L~~~f~ls----e  425 (753)
                                .+++..-+.|+.+-...|+++-.+=+..-.+   ++.      +++.|++++.....+..-..--    .
T Consensus       299 ~~~~P~~l~l~eiL~~~~~h~~~vl~r~le~~l~k~~er~H~~sLe~IfIe~rIy~~Ie~~~~~e~v~~~i~~~l~pf~~  378 (626)
T PRK09631        299 SDRYPVIYTVTDIIKFHAEHLQKILKMELELERSKILEKIFSKTLEQIFIEKKIYKILETISKEEDVVSIVLSELLPFKS  378 (626)
T ss_pred             ECCEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
T ss_conf             89982798799999999999999999999988998998689999999986666899988420168899999987776788


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCH
Q ss_conf             77889988789999889999766678999988776544203978878999999999987417743345554200001100
Q gi|254780353|r  426 NQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLGRRRTTFCEVSRA  505 (753)
Q Consensus       426 ~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~~~~~~RRT~iie~~~~  505 (753)
                      .+...+-+.++.+|+.+....|           ..++.  .........+.+||.++++.+++-     ++..|.+..  
T Consensus       379 ~l~r~ite~d~~aLleirL~RI-----------T~~di--dK~~eei~~L~~eI~eI~~~L~~l-----~~~~I~~l~--  438 (626)
T PRK09631        379 SLSRDVTEDDVENLLKIPIRKI-----------SLFDI--DKNNKDIRILNKELKSIESNIKSI-----KGYAINFID--  438 (626)
T ss_pred             HHHHCCCHHHHHHHHHHHHHHH-----------HHHHH--HHHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHHHH--
T ss_conf             7630157999999999899885-----------34308--879999999999999998637768-----999999999--


Q ss_pred             HHHHHHHCCCCCCCCEEEEECCCEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEECCCEEEEEEHHHCCCCCC
Q ss_conf             00001100245667059987101020256554455322345555540121111478178980688278755112121234
Q gi|254780353|r  506 DKATLQQAMIEKEPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAGNLLSGRG  585 (753)
Q Consensus       506 ~~~~~~EdlI~~E~v~V~LS~~GyIKr~k~~~~~~~~~~~KegD~l~~~~~~~t~d~LLffTs~GkvY~l~a~~Ips~~~  585 (753)
                             ++..+.         |-.+  +    .+..                     +-.++.+-+-.+++.+......
T Consensus       439 -------~Lk~kY---------G~~~--~----RKTE---------------------I~lfd~i~aKrVa~~n~Kly~n  475 (626)
T PRK09631        439 -------KLLAKY---------SKEY--K----RKTE---------------------ISLIKSKNVREIATKNMKVYLN  475 (626)
T ss_pred             -------HHHHHH---------CCCC--C----CEEE---------------------EEEECCEEEEEEECCCCEEEEC
T ss_conf             -------999873---------5477--7----2579---------------------9976444369957023325665


Q ss_pred             CCCCCCCCCCCCCCCEEEEEEEECCCCEEEEEECCCCEEEEEHHHHHCCCCCCEEEEEECCCC--C-EEEEEECCCCEEE
Q ss_conf             444222235767653078999857998599997489789963887402333562788536898--0-5688961898099
Q gi|254780353|r  586 HGEAIQLLIDLNHNQDIVTAFVYDSTCKLLVVSSKGNAFIVEESEIIANTRKGKTFLKVSSEE--K-MKLVVKVTGDHVA  662 (753)
Q Consensus       586 kG~pI~~ll~l~~~EkIv~~~~~~~~~~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~D--~-li~v~~~~~d~ii  662 (753)
                      .|+.+.. .++.++|-|..|   ++-.+++++ ++|..+.+...+-.-.-+.-..+...+.+|  + +-.+.-.+|.   
T Consensus       476 r~~GFiG-tslKkdDfV~~C---Sd~DdILvF-~dG~ykV~kV~~K~Fvgk~i~~v~v~~k~d~~~tiyn~IYrDgk---  547 (626)
T PRK09631        476 LETGFVG-TSLIDGEFIGNA---SYYDKILIF-KDGSYVLKNIEDKTFIDKKNVCVLVYDINNSKEQVFSIIYRDKL---  547 (626)
T ss_pred             CCCCEEE-ECCCCCCEEEEC---CCCCEEEEE-ECCEEEEEECCCCCEECCCCEEEEEEECCCCCCEEEEEEEECCC---
T ss_conf             8885561-035678456733---566539999-89859999857760546883799998527876507999998699---


Q ss_pred             EEECCCCEEEEEHHHCCCCCHHHCCEEEECCCCCEEEEEEEECCCCCEEEEECCCCCCCCCHHHHCCCCCCCCCCCCCCC
Q ss_conf             99569938995578778336121413342187875689997338883699941775664511432254441366602755
Q gi|254780353|r  663 VVGENRKLLIFSIDQIPEMSRGKGVRLQSYKDGGISDVICFKICEGLTWIDSAGRSYNRSENDLLGWLGKRGGVGSLVPK  742 (753)
Q Consensus       663 liT~~Gk~LrF~~~eIr~~gRgkGVk~i~Lkd~~~~~~~~~~~~e~~~il~~t~~g~~k~~~~~~~~~~~RggkG~~~~k  742 (753)
                        +...++-||....+-   |.+.=.+.  +++.  .+..|..+.++.-. ...+.........+..+.+|+.+|.++-|
T Consensus       548 --~g~~yiKRF~V~~~t---rdK~Y~l~--~~~s--~~l~fs~n~nl~~~-~~~k~~~~~~df~~~~iKgr~skGn~vtk  617 (626)
T PRK09631        548 --DNFYYVKRFKIDKFI---LDKVYEFL--PEND--EFLDFSLNPEFVPF-SRSKDIVKMIEIDNFMVKSRSSKGKRISS  617 (626)
T ss_pred             --CCCEEEEEEEECCEE---ECCCCCCC--CCCC--EEEEEEECCCCCCC-CCCCCEEEEECHHHEEEECCCCCCEEEEC
T ss_conf             --883689998832388---42522457--9998--79999977765745-44245147732114034144455517631


Q ss_pred             C
Q ss_conf             2
Q gi|254780353|r  743 G  743 (753)
Q Consensus       743 ~  743 (753)
                      .
T Consensus       618 ~  618 (626)
T PRK09631        618 R  618 (626)
T ss_pred             C
T ss_conf             4


No 28 
>KOG3863 consensus
Probab=89.75  E-value=0.9  Score=25.34  Aligned_cols=61  Identities=34%  Similarity=0.537  Sum_probs=40.3

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHH----------HHHHHHH-HHHHHHHHHHHHHHHHHH
Q ss_conf             078999975200001100000025775778899887899----------9988999-976667899998877654
Q gi|254780353|r  399 NIDEIIAIIRNEDKPKPVMVSRFSLTENQVDAILNLRLR----------SLRKLEE-YQIKSELDNLLAEKEKID  462 (753)
Q Consensus       399 ~ID~vI~iIR~s~~~k~~L~~~f~lse~QA~aIL~mrL~----------rLt~le~-~kl~~E~~eL~~~i~~L~  462 (753)
                      ..|+||.+.+++   -..++++|.|||.|-.-|=|+|=|          |=.+|+. ..|+.|...|.++.+.|.
T Consensus       460 ~vd~IinLp~~d---Fne~ls~~~lte~QLslIrDIRRRgKNkvAAQnCRKRKLd~I~nLE~ev~~l~~eKeqLl  531 (604)
T KOG3863         460 SVDEIINLPVDD---FNEMLSKYKLTEEQLSLIRDIRRRGKNKVAAQNCRKRKLDCILNLEDEVEKLQKEKEQLL  531 (604)
T ss_pred             CHHHHCCCCHHH---HHHHHHHCCCCHHHHHHHHCCCCCCCCCHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             667653786889---999998502689887776502104565100132035677899988899998888889889


No 29 
>KOG0772 consensus
Probab=88.92  E-value=1.9  Score=22.90  Aligned_cols=15  Identities=0%  Similarity=0.158  Sum_probs=10.2

Q ss_pred             CEEEEEECCCCEEEE
Q ss_conf             809999569938995
Q gi|254780353|r  659 DHVAVVGENRKLLIF  673 (753)
Q Consensus       659 d~iiliT~~Gk~LrF  673 (753)
                      .+|++-+.+|-+-.+
T Consensus       470 NQi~~gsgdG~~~vy  484 (641)
T KOG0772         470 NQIFAGSGDGTAHVY  484 (641)
T ss_pred             HHEEEECCCCCEEEE
T ss_conf             301662379826898


No 30 
>KOG1240 consensus
Probab=84.82  E-value=3.1  Score=21.32  Aligned_cols=113  Identities=18%  Similarity=0.217  Sum_probs=73.9

Q ss_pred             EEECCC-CEEEEEECCCCEEEEEHHHHHCCCCCCEEEEEEC-CCCCEEEEEECC-CCEEEEEECCCCEEEEEHHHCCCCC
Q ss_conf             985799-8599997489789963887402333562788536-898056889618-9809999569938995578778336
Q gi|254780353|r  606 FVYDST-CKLLVVSSKGNAFIVEESEIIANTRKGKTFLKVS-SEEKMKLVVKVT-GDHVAVVGENRKLLIFSIDQIPEMS  682 (753)
Q Consensus       606 ~~~~~~-~~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk-~~D~li~v~~~~-~d~iiliT~~Gk~LrF~~~eIr~~g  682 (753)
                      ....++ .+++-.+..|.+|.=.+.++......-..-..+. ++..+..+..|. ++.+++.|++|.+..+.++....-.
T Consensus      1055 a~s~~~~s~FvsgS~DGtVKvW~~~k~~~~~~s~rS~ltys~~~sr~~~vt~~~~~~~~Av~t~DG~v~~~~id~~~~~~ 1134 (1431)
T KOG1240        1055 AVSSEHTSLFVSGSDDGTVKVWNLRKLEGEGGSARSELTYSPEGSRVEKVTMCGNGDQFAVSTKDGSVRVLRIDHYNVSK 1134 (1431)
T ss_pred             EECCCCCCEEEEECCCCEEEEEEEHHHHCCCCEEEEEEEEECCCCCEEEEEECCCCCEEEEECCCCEEEEEECCCCCCCC
T ss_conf             42489876579705886589865111216764035568871268846899851688768897278728999725434331


Q ss_pred             H-HHCCEEEECC-CCCEEEEEEEECCCCC-EEEEECCCC
Q ss_conf             1-2141334218-7875689997338883-699941775
Q gi|254780353|r  683 R-GKGVRLQSYK-DGGISDVICFKICEGL-TWIDSAGRS  718 (753)
Q Consensus       683 R-gkGVk~i~Lk-d~~~~~~~~~~~~e~~-~il~~t~~g  718 (753)
                      + +.-++..+++ +|.++..-.+...... .++..+..+
T Consensus      1135 ~~~~~~ri~n~~~~g~vv~m~a~~~~~~S~~lvy~T~~~ 1173 (1431)
T KOG1240        1135 RVATQVRIPNLKKDGVVVSMHAFTAIVQSHVLVYATDLS 1173 (1431)
T ss_pred             CEEEEEECCCCCCCCCEEEEECCCCCCCCEEEEEEEECC
T ss_conf             002333135665788368863342003652699997126


No 31 
>pfam04762 IKI3 IKI3 family. Members of this family are components of the elongator multi-subunit component of a novel RNA polymerase II holoenzyme for transcriptional elongation. This region contains WD40 like repeats.
Probab=79.52  E-value=4.7  Score=19.94  Aligned_cols=124  Identities=14%  Similarity=0.210  Sum_probs=49.6

Q ss_pred             CCCEEEEEECCCCCEEEEECCCEEEEEEHHHCCCC--CCCCCC-CCCCCCC--------CCCCEEEEEEEECCCCEEEEE
Q ss_conf             55401211114781789806882787551121212--344442-2223576--------765307899985799859999
Q gi|254780353|r  549 DSLKIALHAHTTDRILLLSTDGKAYTLPAGNLLSG--RGHGEA-IQLLIDL--------NHNQDIVTAFVYDSTCKLLVV  617 (753)
Q Consensus       549 D~l~~~~~~~t~d~LLffTs~GkvY~l~a~~Ips~--~~kG~p-I~~ll~l--------~~~EkIv~~~~~~~~~~lll~  617 (753)
                      ..+..+.-..+++.+.++++.|.++...   ++.+  +....| +...+++        ........-+.+..+..++++
T Consensus       422 ~~i~~vaf~~~~~~~avl~sdg~i~~~~---~~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~l~~~~~~~~~~~  498 (918)
T pfam04762       422 SNINDVAFSKSNSKVAVLTSDGDISIYE---LSLKARPAGSPPKLTSKFSLGSVDNSDSEVALGSLRQLAFLNDSELLVL  498 (918)
T ss_pred             CCCEEEEEECCCCEEEEEECCCCEEEEE---CCCCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCEEEEEEECCCEEEEE
T ss_conf             9603899965898899997589899998---2566777678962100201122366533355675689999569879999


Q ss_pred             ECCCCEEEEEHHHHHCCCCCCEEEEEECCCCCEEEEEECCC-CEEEEEECCCCEEEEEHH
Q ss_conf             74897899638874023335627885368980568896189-809999569938995578
Q gi|254780353|r  618 SSKGNAFIVEESEIIANTRKGKTFLKVSSEEKMKLVVKVTG-DHVAVVGENRKLLIFSID  676 (753)
Q Consensus       618 Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~D~li~v~~~~~-d~iiliT~~Gk~LrF~~~  676 (753)
                      ...+...+..+.... ..............+.++......+ +.+++-+..|+++..+.+
T Consensus       499 ~~~~~~~~~~l~~~~-~~~~~~~~~~~~~~~~~v~~~~~~~~~~~~~q~~~G~v~~l~~~  557 (918)
T pfam04762       499 SDSDNLSEIVLVDVD-DTENPLSVSSITELDGIVLILSSNDYKHVFVQTRDGKVFSLSAE  557 (918)
T ss_pred             EECCCCCEEEEEECC-CCCCCEEEEEEECCCCEEEEEEECCCCEEEEEECCCEEEEEECC
T ss_conf             967998579999825-77762356566416862899940898569999579849995058


No 32 
>pfam04201 TPD52 Tumour protein D52 family. The hD52 gene was originally identified through its elevated expression level in human breast carcinoma. Cloning of D52 homologues from other species has indicated that D52 may play roles in calcium-mediated signal transduction and cell proliferation. Two human homologues of hD52, hD53 and hD54, have also been identified, demonstrating the existence of a novel gene/protein family. These proteins have an amino terminal coiled-coil that allows members to form homo- and heterodimers with each other.
Probab=79.21  E-value=2.3  Score=22.31  Aligned_cols=57  Identities=19%  Similarity=0.242  Sum_probs=40.1

Q ss_pred             HHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             57788998878999--98899997666789999887765442039788789999999999874177
Q gi|254780353|r  425 ENQVDAILNLRLRS--LRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSK  488 (753)
Q Consensus       425 e~QA~aIL~mrL~r--Lt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd  488 (753)
                      |.-.+++-+.-+..  |+--|++.++.|+.++.++|..|+..|..+.+..       .+||.+.|.
T Consensus        10 e~~e~~~~~~~~~~~~lseee~eel~~EL~kvEeEI~tLrqvLaaKer~~-------~elKrkLGi   68 (162)
T pfam04201        10 EPKEDQNDSSSATKIVLSEAEKEELRTELAKLEEEISTLRQVLAAKEKHL-------AELKRKLGL   68 (162)
T ss_pred             CCCCHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHCC
T ss_conf             87702330035353327899999999999999999999999999999999-------999998687


No 33 
>PRK00215 LexA repressor; Validated
Probab=77.47  E-value=4.1  Score=20.38  Aligned_cols=52  Identities=19%  Similarity=0.332  Sum_probs=26.0

Q ss_pred             CCCEEEEEECCCCCEEEEEECCCCEEEEEECCCC--EEEEEHHHCCCCCHHHCC
Q ss_conf             3562788536898056889618980999956993--899557877833612141
Q gi|254780353|r  636 RKGKTFLKVSSEEKMKLVVKVTGDHVAVVGENRK--LLIFSIDQIPEMSRGKGV  687 (753)
Q Consensus       636 k~Gk~~ikLk~~D~li~v~~~~~d~iiliT~~Gk--~LrF~~~eIr~~gRgkGV  687 (753)
                      ++|..+..+-+++-.+--...+++.+.|.+.|-.  -+.|+.++++.+|+--|+
T Consensus       147 ~~G~Ivva~i~~e~tlKr~~~~~~~i~L~p~N~~y~pi~~~~~~~~I~G~vvg~  200 (204)
T PRK00215        147 RNGQIVVALIDDEATVKRFRREGGHIRLLPENPAYEPIIVDPDDVTIEGKVVGL  200 (204)
T ss_pred             CCCCEEEEEECCCCEEEEEEEECCEEEEECCCCCCCCEEECCCCEEEEEEEEEE
T ss_conf             899699999737758999999799999984899999877277837999999999


No 34 
>pfam04799 Fzo_mitofusin fzo-like conserved region. Family of putative transmembrane GTPase. The fzo protein is a mediator of mitochondrial fusion. This conserved region is also found in the human mitofusin protein.
Probab=76.73  E-value=5.6  Score=19.37  Aligned_cols=54  Identities=17%  Similarity=0.302  Sum_probs=41.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHH---HHHHHHHHHHHHCC
Q ss_conf             7899998899997666789999887765442039788789---99999999987417
Q gi|254780353|r  434 LRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWN---QIACEIREVKEIFS  487 (753)
Q Consensus       434 mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~---iI~~EL~eikkkfg  487 (753)
                      =||.+....-..++++|.++|.++|..|+.+-+.-+.+++   .+..||....+.|=
T Consensus       112 arLc~qVd~~~~~le~ei~~L~~ei~~LE~iq~~~K~LRnKA~~l~~eL~~F~~~yL  168 (171)
T pfam04799       112 ARLCQQVDVTSKDLEEEIAELTKEIQRLETIQSRSKLLRNKANLLENELEDFTKTFL  168 (171)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             999999868999999999999999999999999989998689899999999999745


No 35 
>cd07924 PCA_45_Doxase_A The A subunit of Protocatechuate 4,5-dioxygenase (LigAB) is the smaller, non-catalytic subunit. The A subunit is the non-catalytic subunit of Protocatechuate (PCA) 4,5-dioxygenase (LigAB), which is composed of A and B subunits that form a tetramer. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which  play key roles in the degradation of aromatic compounds. As a member of the Class III extradiol dioxygenase family, LigAB uses a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon.
Probab=76.44  E-value=5.7  Score=19.32  Aligned_cols=32  Identities=19%  Similarity=0.303  Sum_probs=26.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10000002577577889988789999889999
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEY  445 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~  445 (753)
                      ..+.+.+|+|||.|-+||++....+|-.+--+
T Consensus        44 e~Ay~d~~~Lteeqk~aV~~RD~~~li~lGgn   75 (121)
T cd07924          44 ERAYLDKWPMTEEQKQAVLARDYNRMLALGGN   75 (121)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999876999999999997479999992682


No 36 
>pfam03982 DAGAT Diacylglycerol acyltransferase. The terminal step of triacylglycerol (TAG) formation is catalysed by the enzyme diacylglycerol acyltransferase (DAGAT).
Probab=75.74  E-value=0.65  Score=26.40  Aligned_cols=67  Identities=25%  Similarity=0.404  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCHHHHHHHHH----HH-------------HCCCCCCCCEEEEEHHHHHHHCCCCCCHHHH
Q ss_conf             888899985104764112897046899999----99-------------8689998980354053666542768874789
Q gi|254780353|r   31 LAYALSTIKERAIPDLRDGFKPVHRRIIHA----MS-------------EMGLDFGAAFKKSARIVGEVIGKLHPHGDQS   93 (753)
Q Consensus        31 ~~ya~~vi~~Ralpd~~DGlKpvqRril~~----m~-------------~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s   93 (753)
                      +-|+.+...||.-|.- .|     ||.-|.    ++             .-.|.|++.|         +.| |||||=.+
T Consensus        13 ~~Y~~w~~~d~~tp~~-gg-----r~~~w~R~~~iwk~~~~YFPi~Lvkt~~L~p~~nY---------ifg-~hPHGil~   76 (297)
T pfam03982        13 VLYALWLFYDWNSPKR-GG-----YRSNWARNWRIWKWFANYFPVKLHKTAELPPNRNY---------LFG-YHPHGILS   76 (297)
T ss_pred             HHHHHHHHEECCCCCC-CC-----CCCHHEECCHHHHHHHHHCCCEEEECCCCCCCCCE---------EEE-ECCCCEEC
T ss_conf             9999774046788889-99-----71511013777887875188147875668998454---------888-76851032


Q ss_pred             HHHHHHHHCCH---HHCCCCCCCC
Q ss_conf             99999961001---3216613267
Q gi|254780353|r   94 VYDSLVRLAQP---FVQRYPLISG  114 (753)
Q Consensus        94 ~y~a~v~maq~---~~~~~pli~g  114 (753)
                       .+|.+.+|.+   |+--+|-+..
T Consensus        77 -~Ga~~~f~t~~~~f~~lfPgi~~   99 (297)
T pfam03982        77 -VGAFSNFSTNATGFMDKFPGIRP   99 (297)
T ss_pred             -CCHHEEECCCCCCCHHHCCCCCC
T ss_conf             -42110323455585756799987


No 37 
>PRK13378 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=75.58  E-value=6  Score=19.16  Aligned_cols=32  Identities=22%  Similarity=0.258  Sum_probs=26.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10000002577577889988789999889999
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEY  445 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~  445 (753)
                      ..+.+.+|+|||+|-+||++....+|-.+--+
T Consensus        47 e~AY~d~~~Lteeqr~aV~~RD~~~ll~lGgn   78 (117)
T PRK13378         47 EAAYCRKYGLNEEQKEAIRNRDVLQLLAAGGN   78 (117)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             99999876999999999997379999994674


No 38 
>PRK13379 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=74.34  E-value=6.4  Score=18.94  Aligned_cols=34  Identities=15%  Similarity=0.092  Sum_probs=27.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             1100000025775778899887899998899997
Q gi|254780353|r  413 PKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQ  446 (753)
Q Consensus       413 ~k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~k  446 (753)
                      ...+++.+|+|||+|.++|++.....|..+-.+=
T Consensus        47 De~Ay~d~~~LTeEqk~aV~~RDw~~li~~Ggni   80 (119)
T PRK13379         47 DAEALMQEADLTEQEKELIRARDWLGLVQYGANF   80 (119)
T ss_pred             CHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHH
T ss_conf             9999997759999999999961599999847639


No 39 
>cd07925 LigA_like_1 The A subunit of Uncharacterized proteins with similarity to Protocatechuate 4,5-dioxygenase (LigAB). The proteins of unknown function in this subfamily are similar to the A subunit of the Protocatechuate (PCA) 4,5-dioxygenase (LigAB). LigAB belongs to the class III extradiol dioxygenase family, composed of enzymes which use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Dioxygenases play key roles in the degradation of aromatic compounds. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds.
Probab=74.16  E-value=6.4  Score=18.91  Aligned_cols=32  Identities=19%  Similarity=0.224  Sum_probs=26.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10000002577577889988789999889999
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEY  445 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~  445 (753)
                      ..+.+.+|+||++|-+||++....+|-.+--+
T Consensus        36 e~Ay~d~~~Lt~eqk~aV~~RD~~~ll~~Ggn   67 (106)
T cd07925          36 EEAYCEKFGLTPEQKQAVRNRDVLRMLEAGGN   67 (106)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             99999876999999999997369999990663


No 40 
>cd07921 PCA_45_Doxase_A_like Subunit A of the Class III Extradiol dioxygenase, Protocatechuate 4,5-dioxygenase, and similar enzymes. This subfamily includes the A subunit of protocatechuate (PCA) 4,5-dioxygenase (LigAB) and two subfamilies of unknown function. The A subunit is the smaller, non-catalytic subunit of LigAB. PCA 4,5-dioxygenase catalyzes the oxidization and subsequent ring-opening of PCA (or 3,4-dihydroxybenzoic acid), which is an intermediate in the breakdown of lignin and other compounds. PCA 4,5-dioxygenase is one of the aromatic ring opening dioxygenases which play key roles in the degradation of aromatic compounds. As members of the Class III extradiol dioxygenase family, the enzymes use a non-heme Fe(II) to cleave aromatic rings between a hydroxylated carbon and an adjacent non-hydroxylated carbon. LigAB-like class III enzymes are usually composed of two subunits, designated A and B, which form a tetramer composed of two copies of each subunit.
Probab=73.83  E-value=6.5  Score=18.85  Aligned_cols=32  Identities=28%  Similarity=0.358  Sum_probs=26.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10000002577577889988789999889999
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEY  445 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~  445 (753)
                      ..+.+.+|+|||+|-+||++....+|-.+--+
T Consensus        36 e~Ay~d~~~Lt~eqk~aV~~RD~~~ll~~Ggn   67 (106)
T cd07921          36 EEAYCDKFGLTEEQKQAVLDRDWLRLLELGGN   67 (106)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             99999876999999999997369999990663


No 41 
>KOG4010 consensus
Probab=73.61  E-value=6.5  Score=18.90  Aligned_cols=52  Identities=17%  Similarity=0.307  Sum_probs=38.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHH-----HHHHHHHHCC
Q ss_conf             999988999976667899998877654420397887899999-----9999987417
Q gi|254780353|r  436 LRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIAC-----EIREVKEIFS  487 (753)
Q Consensus       436 L~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~-----EL~eikkkfg  487 (753)
                      .--|+--|.+.+..|+.++.++|..|...|+.+.+...-|+.     -|.|++..+.
T Consensus        38 ~~~LSe~Ekeelr~EL~kvEeEI~TLrqVLaAKerH~~ELKRKLGlt~~~EL~qnis   94 (208)
T KOG4010          38 FEALSEEEKEELRTELAKVEEEIVTLRQVLAAKERHAAELKRKLGLTVLKELKQNIS   94 (208)
T ss_pred             HHHHCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHH
T ss_conf             765068889999999999999999999999998888999999867416999999898


No 42 
>PRK13377 protocatechuate 4,5-dioxygenase subunit alpha; Provisional
Probab=72.72  E-value=6.9  Score=18.67  Aligned_cols=33  Identities=21%  Similarity=0.246  Sum_probs=26.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             100000025775778899887899998899997
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQ  446 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~k  446 (753)
                      ..+.+.+|+|||.|-+||++....+|-.+--+-
T Consensus        47 e~AY~d~~~Lteeqk~aV~~RD~~~li~lGgni   79 (129)
T PRK13377         47 ERAYLDEWPMTEEQKQAVLARDLNRCIALGGNI   79 (129)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHH
T ss_conf             999998769999999999973799999926739


No 43 
>pfam01401 Peptidase_M2 Angiotensin-converting enzyme. Members of this family are dipeptidyl carboxydipeptidases (cleave carboxyl dipeptides) and most notably convert angiotensin I to angiotensin II. Many members of this family contain a tandem duplication of the 600 amino acid peptidase domain, both of these are catalytically active. Most members are secreted membrane bound ectoenzymes.
Probab=70.74  E-value=3.1  Score=21.28  Aligned_cols=39  Identities=10%  Similarity=0.161  Sum_probs=20.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             999976667899998877654420397887899999999998741774
Q gi|254780353|r  442 LEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKS  489 (753)
Q Consensus       442 le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~  489 (753)
                      .|...++++.+.|-++++=|=.-      |...+..+   +.++||+.
T Consensus       196 Ye~~~f~~~~e~lw~qvkPLY~~------LHayVR~k---L~~~YG~~  234 (595)
T pfam01401       196 YESPTLEQDLERLYQELQPLYLN------LHAYVRRA---LHRHYGDQ  234 (595)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHH------HHHHHHHH---HHHHCCCC
T ss_conf             31143999999999998899999------99999999---99866621


No 44 
>pfam12395 DUF3658 Protein of unknown function. This domain family is found in bacteria, and is approximately 110 amino acids in length. The family is found in association with pfam08874. There are two completely conserved residues (D and R) that may be functionally important.
Probab=69.32  E-value=2.2  Score=22.38  Aligned_cols=35  Identities=37%  Similarity=0.525  Sum_probs=22.3

Q ss_pred             CCCCEEEEEHHHHHHHCCCC-CCHHHHHHHHHHHHC
Q ss_conf             98980354053666542768-874789999999610
Q gi|254780353|r   68 FGAAFKKSARIVGEVIGKLH-PHGDQSVYDSLVRLA  102 (753)
Q Consensus        68 ~~~~~~K~ar~vg~v~gkyh-PHGd~s~y~a~v~ma  102 (753)
                      ....|.|+||+||+|||++. +-||.=+.=-+=-|+
T Consensus        57 ~~~~~~~a~rvIg~v~g~~~~~v~D~fl~~Rir~Li   92 (111)
T pfam12395        57 ATDEFQKAARVVGEVMGHLEQLVGDTFLEYRIRELI   92 (111)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHH
T ss_conf             835445999999999986677777899999999999


No 45 
>pfam07746 LigA Aromatic-ring-opening dioxygenase LigAB, LigA subunit. This is a family of aromatic ring opening dioxygenases which catalyse the ring-opening reaction of protocatechuate and related compounds.
Probab=68.53  E-value=8  Score=18.21  Aligned_cols=33  Identities=21%  Similarity=0.229  Sum_probs=27.1

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             110000002577577889988789999889999
Q gi|254780353|r  413 PKPVMVSRFSLTENQVDAILNLRLRSLRKLEEY  445 (753)
Q Consensus       413 ~k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~  445 (753)
                      -..+++.+|+||+.|-+||++....+|..+-.+
T Consensus        20 D~eay~~~~~Lt~eqr~av~~rD~~~L~~~G~n   52 (88)
T pfam07746        20 DEEAYLDEYGLTEEQKAAVRARDWNGLIALGGN   52 (88)
T ss_pred             CHHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             999998727999999999982669999994585


No 46 
>cd06461 M2_ACE Peptidase family M2 Angiotensin converting enzyme (ACE, EC 3.4.15.1) is a membrane-bound, zinc dependent dipeptidase that catalyzes the conversion of the decapeptide angiotensin I to the potent vasopressor ocatapeptide angiotensin II, by removing two C-terminal amino acids. There are two forms of the enzyme in humans, the ubiquitous somatic ACE and the sperm-specific germinal ACE, both encoded by the same gene through transcription from alternative promoters. Somatic ACE has two tandem active sites with distinct catalytic properties, whereas germinal ACE, the function of which is largely unknown, has just a single active site. Recently, an ACE homolog, ACE2, has been identified in humans that differs from ACE; it preferentially removes carboxy-terminal hydrophobic or basic amino acids and appears to be important in cardiac function. ACE homologs (also known as members of the M2 gluzincin family) have been found in a wide variety of species, including those that neither h
Probab=68.42  E-value=4.8  Score=19.83  Aligned_cols=57  Identities=21%  Similarity=0.228  Sum_probs=43.1

Q ss_pred             HHCCHHHCCCCCCCCCCCCCCCCCCCC-CCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             610013216613267887088677971-00246899855999999842187861752167
Q gi|254780353|r  100 RLAQPFVQRYPLISGQGNFGNIDGDSA-AAYRYTEARMTQVAELILQGVDEDAVDFRDTY  158 (753)
Q Consensus       100 ~maq~~~~~~pli~g~GnfGs~~~d~~-Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~  158 (753)
                      .-||+|++-|+++.+..+-+++|-.+. -.--||..+|-+.|++.+..|.-.-  +-++|
T Consensus       149 mWaQ~W~ni~dl~~P~p~~~~~Dvt~~m~~q~~t~~~mf~~ae~FF~SLGl~~--mp~~F  206 (477)
T cd06461         149 MWAQSWSNIYDLVKPYPGKPLLDVTDAMVEQGYTAKRMFKEAEEFFTSLGLPP--MPPSF  206 (477)
T ss_pred             HHHHHHHHHHHCCCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHCCCCC--CCHHH
T ss_conf             66543665420135799988888159999859989999999999999679976--99778


No 47 
>TIGR00909 2A0306 amino acid transporter; InterPro: IPR004758 Amino acid permeases are integral membrane proteins involved in the transport of amino acids into the cell. A number of such proteins have been found to be evolutionary related , , . These proteins seem to contain up to 12 transmembrane segments. The best conserved region in this family is located in the second transmembrane segment.   Some proteins in this group are involved in the transport of the cationic amino acids (arginine,lysine and ornithine)..
Probab=65.96  E-value=4.6  Score=20.00  Aligned_cols=35  Identities=29%  Similarity=0.369  Sum_probs=23.2

Q ss_pred             HHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHH
Q ss_conf             46899999998689998980354053666542768874789999999
Q gi|254780353|r   53 VHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLV   99 (753)
Q Consensus        53 vqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v   99 (753)
                      .|=|+||||.+-|+.|.            ++.|-||.=++.-+.+++
T Consensus       316 g~~RvlFAmSRDGllP~------------slSkvH~k~~tP~~~~~~  350 (451)
T TIGR00909       316 GTSRVLFAMSRDGLLPK------------SLSKVHPKTKTPHVSILI  350 (451)
T ss_pred             HHHHHHHHHHHCCCCCC------------HHHHHCCCCCCCCHHHHH
T ss_conf             89999999986177530------------376323446875048999


No 48 
>COG3959 Transketolase, N-terminal subunit [Carbohydrate transport and metabolism]
Probab=65.90  E-value=9.4  Score=17.68  Aligned_cols=89  Identities=24%  Similarity=0.215  Sum_probs=42.5

Q ss_pred             CCCHHHHHHHHHHHHCCHHHCCCCCCCCCC-CCCCCCC----CCCCCHHHHHHHHHHH---HHHHHHHCCCCCCCCCCCC
Q ss_conf             887478999999961001321661326788-7088677----9710024689985599---9999842187861752167
Q gi|254780353|r   87 HPHGDQSVYDSLVRLAQPFVQRYPLISGQG-NFGNIDG----DSAAAYRYTEARMTQV---AELILQGVDEDAVDFRDTY  158 (753)
Q Consensus        87 hPHGd~s~y~a~v~maq~~~~~~pli~g~G-nfGs~~~----d~~Aa~RYte~rl~~~---~~~ll~di~~~~v~~~~n~  158 (753)
                      ||||..|+-|-|.-+=-. -||+   ++.. ++..+|-    +.-||+-| +|-|...   .++-|.-+.+         
T Consensus        32 H~G~SLS~~eILa~LYf~-~m~~---~p~~p~~~~RDrfiLSKGHaa~Al-Ya~Lae~G~~p~eeL~~~~~---------   97 (243)
T COG3959          32 HVGGSLSVVEILAVLYFK-IMNI---DPDDPKWPGRDRFILSKGHAAPAL-YATLAEKGYFPEEELETFRR---------   97 (243)
T ss_pred             CCCCCCHHHHHHHHHHHH-HHCC---CCCCCCCCCCCEEEEECCCCHHHH-HHHHHHCCCCCHHHHHHHCC---------
T ss_conf             757621099999999998-7266---878887777776998366413899-99999818988899997516---------


Q ss_pred             CCCEE--EEEEECCCCCHHHHCCCC-----CHHHHHHHHC
Q ss_conf             99632--422312345267642665-----0467777516
Q gi|254780353|r  159 NEEDS--EPVVFPSKFPNLLANGTS-----GIAVGMATSI  191 (753)
Q Consensus       159 D~~~~--EP~~lp~~~P~lL~Ng~~-----GIavG~at~i  191 (753)
                      +||..  -|+.  .+.|-+.+|+.|     +||||||+..
T Consensus        98 ~~srL~~Hp~~--~~~pgve~stGSLGqGLsvavGmAlg~  135 (243)
T COG3959          98 IGSRLPGHPER--NKTPGVEVSTGSLGQGLSVAVGMALGA  135 (243)
T ss_pred             CCCCCCCCCCC--CCCCCEEECCCCCCCCCHHHHHHHHHH
T ss_conf             89858899765--789865626876556610788888887


No 49 
>cd07923 Gallate_dioxygenase_C The C-terminal domain of Gallate Dioxygenase, which catalyzes the oxidization and subsequent ring-opening of gallate. Gallate Dioxygenase catalyzes the oxidization and subsequent ring-opening of gallate, an intermediate in the degradation of the aromatic compound, syringate. The reaction product of gallate dioxygenase is 4-oxalomesaconate. The amino acid sequence of the N-terminal and C-terminal regions of gallate dioxygenase exhibits homology with the sequence of the PCA 4,5-dioxygenase B (catalytic) and A subunits, respectively. This model represents the C-terminal domain, which is similar to the A subunit of PCA 4,5-dioxygenase (or LigAB). The enzyme is estimated to be a homodimer according to the Escherichia coli enzyme. Since enzymes in this subfamily have fused A and B subunits, the dimer interface may resemble the tetramer interface of classical LigAB enzymes. This enzyme belongs to the class III extradiol dioxygenase family, composed of enzymes whi
Probab=63.24  E-value=10  Score=17.32  Aligned_cols=32  Identities=16%  Similarity=0.112  Sum_probs=26.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             10000002577577889988789999889999
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEY  445 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~  445 (753)
                      ..+.+.+|+|||+|-+||++....+|-.+-.+
T Consensus        28 e~Ay~d~~~Lt~eqk~av~~RDw~~mi~~Ggn   59 (94)
T cd07923          28 PEALFDEAGLTEEERTLIRNRDWIGMIRYGVI   59 (94)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHCCCH
T ss_conf             99999876999999999996169999983764


No 50 
>PHA00728 hypothetical protein
Probab=63.12  E-value=9.8  Score=17.54  Aligned_cols=44  Identities=27%  Similarity=0.389  Sum_probs=31.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             89999766678999988776544203978878999999999987417
Q gi|254780353|r  441 KLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFS  487 (753)
Q Consensus       441 ~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfg  487 (753)
                      +.|.++++.|-++|.++.++|+.+++++..-.   -+++.++..-|.
T Consensus         4 ~teveql~keneelkkkla~leal~nne~~~~---~e~~~eiEnPYT   47 (153)
T PHA00728          4 KTEVEQLKKENEELKKKLAKLEALLNNESAEE---EEELQEIENPYT   47 (153)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCHH---HHHHHHHCCCCE
T ss_conf             46899999866999999999999974788503---566877238712


No 51 
>COG3953 SLT domain proteins [General function prediction only]
Probab=62.60  E-value=4  Score=20.46  Aligned_cols=24  Identities=46%  Similarity=0.566  Sum_probs=10.9

Q ss_pred             CCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             788708867797100246899855
Q gi|254780353|r  114 GQGNFGNIDGDSAAAYRYTEARMT  137 (753)
Q Consensus       114 g~GnfGs~~~d~~Aa~RYte~rl~  137 (753)
                      |||||=..-...+||||||+.|.-
T Consensus        66 g~~ni~Npidna~AAi~yi~~rYG   89 (235)
T COG3953          66 GQGNILNPIDNAAAAIRYIKTRYG   89 (235)
T ss_pred             CCCCHHCHHHHHHHHHHHHHHHCC
T ss_conf             740000326689999998862225


No 52 
>KOG3584 consensus
Probab=61.07  E-value=11  Score=17.05  Aligned_cols=36  Identities=17%  Similarity=0.271  Sum_probs=22.1

Q ss_pred             HHHHHHHHHHHHHHCCH----HHHHHHHHHHHHHHHHHCC
Q ss_conf             99998877654420397----8878999999999987417
Q gi|254780353|r  452 DNLLAEKEKIDSLLNSG----KQQWNQIACEIREVKEIFS  487 (753)
Q Consensus       452 ~eL~~~i~~L~~IL~s~----~~l~~iI~~EL~eikkkfg  487 (753)
                      .|-..+.+||-+.|.++    +.+++-+++||+.+|+.|.
T Consensus       304 RECRRKKKEYVKCLENRVAVLENQNKaLIEELKtLKeLYc  343 (348)
T KOG3584         304 RECRRKKKEYVKCLENRVAVLENQNKALIEELKTLKELYC  343 (348)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHH
T ss_conf             9998867689998875778875145899999998999862


No 53 
>pfam03131 bZIP_Maf bZIP Maf transcription factor. Maf transcription factors contain a conserved basic region leucine zipper (bZIP) domain, which mediates their dimerization and DNA binding property. Thus, this family is probably related to pfam00170.
Probab=60.81  E-value=11  Score=17.02  Aligned_cols=47  Identities=13%  Similarity=0.241  Sum_probs=28.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             88789999889999766678999988776544203978878999999999987417
Q gi|254780353|r  432 LNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFS  487 (753)
Q Consensus       432 L~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfg  487 (753)
                      .+=|-+|+.  +...++.|..+|..+++.|..       -...+..|...++.+|.
T Consensus        45 q~CR~KR~~--q~~~LE~e~~~L~~e~e~Lk~-------E~~~~~~E~d~~k~K~e   91 (95)
T pfam03131        45 QSCRSKRVQ--QRHELEKEKSQLQQQVEQLKQ-------ENARLRRERDALKAKYE   91 (95)
T ss_pred             HHHHHHHHH--HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHH
T ss_conf             988999999--999999999999999999999-------99999999999999998


No 54 
>PRK10834 hypothetical protein; Provisional
Probab=60.03  E-value=3.2  Score=21.23  Aligned_cols=51  Identities=24%  Similarity=0.258  Sum_probs=35.0

Q ss_pred             HHHHHC--CCCCCHHHH-HH----HHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHH
Q ss_conf             666542--768874789-99----999961001321661326788708867797100246
Q gi|254780353|r   79 VGEVIG--KLHPHGDQS-VY----DSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRY  131 (753)
Q Consensus        79 vg~v~g--kyhPHGd~s-~y----~a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RY  131 (753)
                      ||-|+|  ||++.|.-| .|    ||.+.+=+.=.-++-|+.|.  .|+.+.|.|.+||-
T Consensus        47 valVLGtak~~~~G~pn~~~~~RldaA~~LY~~GKv~~iLvSGD--n~~~~YnEp~~Mk~  104 (239)
T PRK10834         47 VGVVLGTAKYYRTGVINQYYRYRIQGAINAYNSGKVNYLLLSGD--NALQSYNEPMTMRK  104 (239)
T ss_pred             EEEEECCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEECCC--CCCCCCCCHHHHHH
T ss_conf             69994576467899819899999999999998699748986689--99888982899999


No 55 
>pfam05133 Phage_prot_Gp6 Phage portal protein, SPP1 Gp6-like. This protein forms a hole, or portal, that enables DNA passage during packaging and ejection. It also forms the junction between the phage head (capsid) and the tail proteins. During SPP1 morphogenesis, Gp6 participates in the procapsid assembly reaction. This family also includes family Phage_min_cap, pfam05126.
Probab=59.84  E-value=12  Score=16.90  Aligned_cols=11  Identities=45%  Similarity=0.492  Sum_probs=6.3

Q ss_pred             CCCCCCHHHHH
Q ss_conf             79710024689
Q gi|254780353|r  123 GDSAAAYRYTE  133 (753)
Q Consensus       123 ~d~~Aa~RYte  133 (753)
                      +.++|+.||..
T Consensus       141 ~~~~~~vr~~~  151 (435)
T pfam05133       141 RELAAAVRYYT  151 (435)
T ss_pred             CCEEEEEEEEE
T ss_conf             76359999999


No 56 
>TIGR01734 D-ala-DACP-lig D-alanine-activating enzyme; InterPro: IPR010072   This entry represents the enzyme (also called D-alanine-D-alanyl carrier protein ligase) which activates D-alanine as an adenylate via the reaction D-ala + ATP to D-ala-AMP + PPi, and further catalyses the condensation of the amino acid adenylate with the D-alanyl carrier protein (D-ala-ACP). The D-alanine is then further transferred to teichoic acid in the biosynthesis of lipoteichoic acid (LTA) and wall teichoic acid (WTA) in Gram-positive bacteria, both polysacchatides .; GO: 0016208 AMP binding, 0047473 D-alanine-poly(phosphoribitol) ligase activity, 0019350 teichoic acid biosynthetic process.
Probab=57.65  E-value=2.5  Score=21.99  Aligned_cols=139  Identities=18%  Similarity=0.216  Sum_probs=61.1

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCEEE-EE-EECCCCCHHHHCCCCCHHHHHHHH------CC--CCCHHH
Q ss_conf             246899855999999842187861752167996324-22-312345267642665046777751------67--778899
Q gi|254780353|r  129 YRYTEARMTQVAELILQGVDEDAVDFRDTYNEEDSE-PV-VFPSKFPNLLANGTSGIAVGMATS------IP--SHNVQE  198 (753)
Q Consensus       129 ~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~~~~E-P~-~lp~~~P~lL~Ng~~GIavG~at~------ip--phnl~e  198 (753)
                      -+||+.-|-.-++.+=.-|++.        -...+| |. |+=-.=|..|       ++=.|+.      ||  .|-|.|
T Consensus        24 ~~lTY~~L~~~Sd~la~~i~~~--------~l~~k~kPiivfG~~~~~Ml-------~~flg~~KsGhaYiPvD~s~P~E   88 (513)
T TIGR01734        24 QELTYQQLKEQSDRLAAFIQER--------LLPEKEKPIIVFGHMEPEML-------VAFLGSIKSGHAYIPVDTSIPLE   88 (513)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHC--------CCCCCCCCEEEECCCCHHHH-------HHHHHHHHCCCCCCCCCCCCCHH
T ss_conf             6102789999999999999860--------57666775788648868999-------99999751689643436688167


Q ss_pred             HHHHHHHHHHCCC--CCCHHHHHHCCCCCCCCCC-CCCCCHHHHHHHHHCCCCEEEEEEEEEEEECCCCCEEEEEECC--
Q ss_conf             9999999872865--3201344320367788776-0106988999898503341599999998643788407999524--
Q gi|254780353|r  199 ICEAALALIDNPE--ISIEKLLEYIIGPDFPTGG-IIVESRESIVESYRLGRGGFRVRARWCVEEVGRGSWCIVVTEI--  273 (753)
Q Consensus       199 v~~a~~~~i~~~~--~~~~~l~~~i~gPDFPTGG-~i~~~~~~i~~~y~tG~G~i~~r~k~~~e~~~~~~~~ivItei--  273 (753)
                      =|..++.-.+ |.  +.+.+|=     =|++... -|+ ..+-+.++.+.+.|.+.--..+--   +.+.+-||-|.=  
T Consensus        89 Ri~~I~~~a~-p~~vi~~~~ls-----~~~~~~~~~~~-~~~~~~~~~~~~~G~~~~~~~~V~---~dD~yYIIyTSGtT  158 (513)
T TIGR01734        89 RIEQIKEAAK-PELVIETAELS-----IDLVETETDVI-TLEALEDALTSGAGPAVDFDHAVK---GDDNYYIIYTSGTT  158 (513)
T ss_pred             HHHHHHHHCC-CCEEEEECCCC-----CCCCCCCCCEE-CHHHHHHHHHHCCCCCCCCCCCCC---CCCCEEEEEEECCC
T ss_conf             9999986338-11274311377-----53111467511-189999999706878642100005---79966899853664


Q ss_pred             --CCC--CCHHHHHHHHHHHHHH
Q ss_conf             --200--2168999999998640
Q gi|254780353|r  274 --PYQ--VQKSRLIEKIAELIIA  292 (753)
Q Consensus       274 --Py~--v~k~~~ie~I~~lv~~  292 (753)
                        |=|  ++.+.|+.-..=.+.+
T Consensus       159 G~PKGVQIS~dNL~sFtnW~~~D  181 (513)
T TIGR01734       159 GKPKGVQISHDNLVSFTNWMLED  181 (513)
T ss_pred             CCCCCEEEECCCCCHHHHHHHHC
T ss_conf             88873475200021177775302


No 57 
>TIGR00019 prfA peptide chain release factor 1; InterPro: IPR004373 This family describes peptide chain release factor 1 (PrfA, RF-1), and excludes the related peptide chain release factor 2 (PrfB, RF-2). RF-1 helps recognise and terminate translation at UAA and UAG stop codons. The mitochondrial release factors are prfA-like, although not included above the trusted cut-off for this model. RF-1 does not have a translational frameshift.; GO: 0016149 translation release factor activity codon specific, 0006415 translational termination, 0005737 cytoplasm.
Probab=56.25  E-value=14  Score=16.48  Aligned_cols=61  Identities=16%  Similarity=0.142  Sum_probs=47.5

Q ss_pred             HHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC---CHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             778899-88789999889999766678999988776544203---9788789999999999874177
Q gi|254780353|r  426 NQVDAI-LNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLN---SGKQQWNQIACEIREVKEIFSK  488 (753)
Q Consensus       426 ~QA~aI-L~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~---s~~~l~~iI~~EL~eikkkfgd  488 (753)
                      .|.++. +.-...+|  .++.....+|+.+.+.|++=+.||.   ++..|..++++||.++.++..+
T Consensus        32 d~~k~~~~~ke~~~l--~~i~~~~~~~~~~~~~~~~A~~~l~E~~~D~El~elak~El~~l~~~~~~   96 (373)
T TIGR00019        32 DQDKLRKLSKEYSQL--EEIVDKYEEYKKAQEDLKEAKELLEEKGDDKELRELAKEELEELEKEIEE   96 (373)
T ss_pred             CHHHHHHHHHHHCCH--HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             679999998862065--68999999999999999999999974258865899999999999988888


No 58 
>pfam06995 Phage_P2_GpU Phage P2 GpU. This family consists of several bacterial and phage proteins of around 130 residues in length which seem to be related to the bacteriophage P2 GpU protein which is thought to be involved in tail assembly.
Probab=56.05  E-value=4.8  Score=19.84  Aligned_cols=33  Identities=33%  Similarity=0.631  Sum_probs=15.6

Q ss_pred             CCCCCC--HHHHHHHHHHHHCCHHHCCCCCCCCCCC
Q ss_conf             276887--4789999999610013216613267887
Q gi|254780353|r   84 GKLHPH--GDQSVYDSLVRLAQPFVQRYPLISGQGN  117 (753)
Q Consensus        84 gkyhPH--Gd~s~y~a~v~maq~~~~~~pli~g~Gn  117 (753)
                      |..|||  |...-+++|-.||.. ..-+|||+|.|+
T Consensus        49 G~l~p~~~gg~~~l~~Lr~~~~~-g~p~~Lv~G~G~   83 (121)
T pfam06995        49 GVLYPEFTGGLASLDALRAMADA-GKALPLVDGNGD   83 (121)
T ss_pred             EEEEHHHCCCHHHHHHHHHHHHC-CCCEEEEECCCC
T ss_conf             99965881989999999999975-996189977983


No 59 
>PRK08082 consensus
Probab=54.30  E-value=11  Score=17.28  Aligned_cols=23  Identities=9%  Similarity=0.206  Sum_probs=14.1

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             97887899999999998741774
Q gi|254780353|r  467 SGKQQWNQIACEIREVKEIFSKS  489 (753)
Q Consensus       467 s~~~l~~iI~~EL~eikkkfgd~  489 (753)
                      ++......|...|+.+.+.++-|
T Consensus       334 ~r~~ev~~isr~LK~lAkel~ip  356 (453)
T PRK08082        334 NRQQEVSEISRTLKALARELEVP  356 (453)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             89999999999999999996997


No 60 
>COG5207 UBP14 Isopeptidase T [Posttranslational modification, protein turnover, chaperones]
Probab=53.90  E-value=1.8  Score=23.10  Aligned_cols=50  Identities=18%  Similarity=0.186  Sum_probs=20.5

Q ss_pred             HHHHHHHHHHHHCCH----HHCCCCCCCCCCCCCC------CCCCCCCCHHHHHHHHHHHH
Q ss_conf             478999999961001----3216613267887088------67797100246899855999
Q gi|254780353|r   90 GDQSVYDSLVRLAQP----FVQRYPLISGQGNFGN------IDGDSAAAYRYTEARMTQVA  140 (753)
Q Consensus        90 Gd~s~y~a~v~maq~----~~~~~pli~g~GnfGs------~~~d~~Aa~RYte~rl~~~~  140 (753)
                      |..|+|..-+..+|-    ...|.=+---.|+.|.      .+|.+-|-..|-+.- +|+|
T Consensus       162 ~~~s~~~~ni~~~~Cs~CDl~~nLW~Cl~CG~vgCGR~QyG~~GngHAlsHY~~t~-Hpla  221 (749)
T COG5207         162 GPSSIEMGNIGGLKCSLCDLKTNLWVCLSCGYVGCGRMQYGAEGNGHALSHYEETQ-HPLA  221 (749)
T ss_pred             CCCCCCCCCCCCCEECCCCCHHCEEEEEECCCCCCCCEEECCCCCCCHHHHHHCCC-CCEE
T ss_conf             99863013557732020102011478774376344503435788751333343139-9548


No 61 
>TIGR00606 rad50 rad50; InterPro: IPR004584   Rad50 is involved in recombination, recombinational repair, and/or non-homologous end joining. It is a component of an exonuclease complex with MRE11 homologs. The Saccharomyces cerevisiae Rad50/MRE11 complex possesses single-stranded endonuclease activity and ATP-dependent double-strand-specific exonuclease activity. Rad50 provides an ATP-dependent control of MRE11 by unwinding and repositioning DNA ends into the MRE11 active site. This family is distantly related to the SbcC family of bacterial proteins.    When the N- and C-terminal globular regions of Rad50 from Pyrococcus furiosus P58301 from SWISSPROT are co-expressed in Escherichia coli, they spontaneously associate to form a stable complex that possesses ATP-binding and weak ATP-hydrolysing activities. The structure formed is known as the Rad50 catalytic domain (Rad50cd1). In the presence of ATP, two Rad50cd1 molecules interact via their ATP-binding and highly conserved 'signature' motifs to form a dimer. As ATP is buried deep within this dimer interface, the two Rad50cd1 molecules may have to completely disengage after ATP hydrolysis to allow the release of ADP before binding of a new ATP molecule. ATP binding is also accompanied by a 30 rotation of two distinct domains within each Rad50cd1 part of the dimer. This rotation and dimerisation creates a positively charged surface which, potentially, could provide a DNA-binding site capable of accommodating two DNA molecules.   The Mre11-docking site within Rad50 has been mapped to two 40-residue heptad-repeat sequences that lie adjacent to the N- and C-terminal ATPase segments. A distinct region within this domain forms a conserved hydrophobic patch that is believed to be the actual Mre11-binding site and lies immediately adjacent to the putative DNA-binding site of Rad50. As Rad50 dimerises in the presence of ATP and forms a stoichiometric complex with Mre11 (one Mre11 subunit binding to one Rad50 subunit), it is possible that the MR complex forms a closely coordinated DNA-binding unit that has the potential to act on two DNA molecules simultaneously. Within this unit, ATP-dependent control of nuclease action might be achieved via Rad50 unwinding or repositioning DNA ends into the active-site of Mre11 . ; GO: 0005524 ATP binding, 0006281 DNA repair, 0030870 Mre11 complex.
Probab=53.82  E-value=15  Score=16.20  Aligned_cols=11  Identities=0%  Similarity=-0.203  Sum_probs=4.2

Q ss_pred             EEEECCCCCCC
Q ss_conf             99952420021
Q gi|254780353|r  268 IVVTEIPYQVQ  278 (753)
Q Consensus       268 ivIteiPy~v~  278 (753)
                      ++|--.|.+.+
T Consensus       734 ~~l~~~~~~~~  744 (1328)
T TIGR00606       734 EILGLAEGRQS  744 (1328)
T ss_pred             HHEEECCHHHH
T ss_conf             41010311567


No 62 
>PRK06904 replicative DNA helicase; Validated
Probab=53.69  E-value=12  Score=16.98  Aligned_cols=22  Identities=9%  Similarity=0.202  Sum_probs=14.1

Q ss_pred             EEEEECCCCCCCHHHHHHHHHH
Q ss_conf             7999524200216899999999
Q gi|254780353|r  267 CIVVTEIPYQVQKSRLIEKIAE  288 (753)
Q Consensus       267 ~ivIteiPy~v~k~~~ie~I~~  288 (753)
                      .++|--=.+.+.|+.+.-.|+.
T Consensus       222 ~LiViAaRPsmGKTa~alnia~  243 (472)
T PRK06904        222 DLIIVAARPSMGKTTFAMNLCE  243 (472)
T ss_pred             CEEEEEECCCCCHHHHHHHHHH
T ss_conf             5799973798756899999999


No 63 
>COG0576 GrpE Molecular chaperone GrpE (heat shock protein) [Posttranslational modification, protein turnover, chaperones]
Probab=53.48  E-value=15  Score=16.16  Aligned_cols=41  Identities=17%  Similarity=0.243  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             999999999999999999--99999998641078999975200
Q gi|254780353|r  370 EVLFRRSSFRMQAIDRRV--EILKGLLIAYLNIDEIIAIIRNE  410 (753)
Q Consensus       370 ~vi~rr~~~~L~k~~~Rl--hIleGl~~a~~~ID~vI~iIR~s  410 (753)
                      +-++||++-+.+++.+..  -++.-|+-+++|++..+..+...
T Consensus        67 eN~rkR~~re~e~~~k~a~e~~~~dlLpviDnlerAl~~~~~~  109 (193)
T COG0576          67 ENLRKRTEREREEAKKYAIEKFAKDLLPVIDNLERALEAAEDD  109 (193)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             9999999999999999999999999888887999999712345


No 64 
>PRK08840 replicative DNA helicase; Provisional
Probab=53.06  E-value=13  Score=16.63  Aligned_cols=71  Identities=17%  Similarity=0.160  Sum_probs=34.1

Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEEEEEECCCCCEEEEE
Q ss_conf             67778899999999987286532013443203677887760106988999898503341599999998643788407999
Q gi|254780353|r  191 IPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCVEEVGRGSWCIVV  270 (753)
Q Consensus       191 ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~~~e~~~~~~~~ivI  270 (753)
                      -.|.+..++++..+..++.-.-...+   -+  +-.|||      ...+.++ ..|   +           .  ...++|
T Consensus       170 ~~~~~~~~~~~~~~e~ie~~~~~~~~---~~--~Gi~TG------~~~LD~~-~~G---l-----------~--~G~Liv  221 (464)
T PRK08840        170 EGPQNVDSILEKTLERIELLYKSPQD---GV--TGVSTG------FTDLNKK-TAG---L-----------Q--GSDLII  221 (464)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHHCCCC---CC--CCCCCC------HHHHHHH-CCC---C-----------C--CCCEEE
T ss_conf             64001999999999999999857799---97--368889------8999875-369---8-----------7--576799


Q ss_pred             ECCCCCCCHHHHHHHHHHH
Q ss_conf             5242002168999999998
Q gi|254780353|r  271 TEIPYQVQKSRLIEKIAEL  289 (753)
Q Consensus       271 teiPy~v~k~~~ie~I~~l  289 (753)
                      --=.+.+.|+.+.-.|+.-
T Consensus       222 iaaRPsmGKTalalnia~n  240 (464)
T PRK08840        222 VAARPSMGKTTFAMNLCEN  240 (464)
T ss_pred             EEECCCCCHHHHHHHHHHH
T ss_conf             9837987368999999999


No 65 
>pfam03444 DUF293 Domain of unknown function. This domain is always found with a pair of CBS domains pfam00571. this region may be distantly related to the HrcA proteins of prokaryotes (Bateman A pers. obs.).
Probab=52.26  E-value=10  Score=17.46  Aligned_cols=64  Identities=25%  Similarity=0.402  Sum_probs=32.9

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCC
Q ss_conf             97046899999998689998980354053666542768874789999999610013216613267887088677971
Q gi|254780353|r   50 FKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSA  126 (753)
Q Consensus        50 lKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~maq~~~~~~pli~g~GnfGs~~~d~~  126 (753)
                      |-|+||.||.+.-++=...+.| .||..|. +.++ -+|-       ++=+.-|+.. -.-||+|+  =|.-.|--|
T Consensus         2 LT~~Qr~IL~aLI~lY~~~~~p-Vks~~IA-e~l~-~spg-------TIRN~M~~L~-~LGLVe~~--pgp~gGy~P   65 (79)
T pfam03444         2 LTPVQKEILQALINLYRKKGRA-VKGEEIA-DIIG-RNPG-------TVRNQMQSLK-ALGLVEGV--PGPKGGYKP   65 (79)
T ss_pred             CCHHHHHHHHHHHHHHHHCCCC-CCHHHHH-HHHC-CCHH-------HHHHHHHHHH-HCCCCCCC--CCCCCCCCC
T ss_conf             7789999999999999972998-6679999-9987-8908-------8999999999-85886578--899888765


No 66 
>pfam05600 DUF773 Protein of unknown function (DUF773). This family contains several eukaryotic sequences which are thought to be CDK5 activator-binding proteins, however, the function of this family is unknown.
Probab=52.26  E-value=16  Score=16.03  Aligned_cols=20  Identities=0%  Similarity=0.062  Sum_probs=10.4

Q ss_pred             HHHHHHHHHHHHCCCCCCHH
Q ss_conf             99999999987286532013
Q gi|254780353|r  197 QEICEAALALIDNPEISIEK  216 (753)
Q Consensus       197 ~ev~~a~~~~i~~~~~~~~~  216 (753)
                      .+++-.+.+++++++.|+.+
T Consensus       220 ~~~Lp~L~~l~~~Gnttvye  239 (506)
T pfam05600       220 KQVLPLLRHVQERGNTTVYE  239 (506)
T ss_pred             CCCCHHHHHHHHCCCCEEEE
T ss_conf             45045999998679972761


No 67 
>COG1944 Uncharacterized conserved protein [Function unknown]
Probab=52.05  E-value=16  Score=16.01  Aligned_cols=22  Identities=32%  Similarity=0.436  Sum_probs=8.8

Q ss_pred             CCCHHHHHHHHC-CCCCHHHHHH
Q ss_conf             650467777516-7778899999
Q gi|254780353|r  180 TSGIAVGMATSI-PSHNVQEICE  201 (753)
Q Consensus       180 ~~GIavG~at~i-pphnl~ev~~  201 (753)
                      .+|-|.|-+-.= --|-|-||++
T Consensus       167 tnGLAaGn~~~eA~lhgLlEviE  189 (398)
T COG1944         167 TNGLAAGNTREEAILHGLLEVIE  189 (398)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHH
T ss_conf             84112475388899999999999


No 68 
>COG4939 Major membrane immunogen, membrane-anchored lipoprotein [Function unknown]
Probab=51.57  E-value=15  Score=16.12  Aligned_cols=47  Identities=23%  Similarity=0.369  Sum_probs=31.4

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCHHHH-----HHHHHHHHHHHHHHCCCCCCC
Q ss_conf             16613267887088677971002468-----998559999998421878617
Q gi|254780353|r  107 QRYPLISGQGNFGNIDGDSAAAYRYT-----EARMTQVAELILQGVDEDAVD  153 (753)
Q Consensus       107 ~~~pli~g~GnfGs~~~d~~Aa~RYt-----e~rl~~~~~~ll~di~~~~v~  153 (753)
                      -+|-+-++.|||-|-|.|-+-+|.|-     +--++.+|+.|++-=+.+-||
T Consensus        62 ~~ydy~~k~G~~Ks~DAdy~~~mk~~~g~gp~~~f~~laD~Lve~q~p~~Vd  113 (147)
T COG4939          62 CTYDYRDKKGNIKSDDADYAGEMKYMKGQGPVQGFSTLADKLVEVQDPNEVD  113 (147)
T ss_pred             EEEEEECCCCCCCCCCHHHHHHHHHHCCCCHHHHHHHHHHHHHHCCCCCCEE
T ss_conf             8855064778736653336777777416377899999999987248945055


No 69 
>cd07321 Extradiol_Dioxygenase_3A_like Subunit A of Class III extradiol dioxygenases. Extradiol dioxygenases catalyze the incorporation of both atoms of molecular oxygen into substrates using a variety of reaction mechanisms, resulting in the cleavage of aromatic rings.  There are two major groups of dioxygenases according to the cleavage site of the aromatic ring. Intradiol enzymes cleave the aromatic ring between two hydroxyl groups, whereas extradiol enzymes cleave the aromatic ring between a hydroxylated carbon and an adjacent non-hydroxylated carbon. Extradiol dioxygenases can be divided into three classes. Class I and II enzymes are evolutionary related and show sequence similarity, with the two domain class II enzymes evolving from the class I enzyme through gene duplication. Class III enzymes are different in sequence and structure and usually have two subunits, designated A and B, which form a tetramer composed of two copies of each subunit. This model represents subunit A of c
Probab=50.53  E-value=13  Score=16.50  Aligned_cols=33  Identities=18%  Similarity=0.249  Sum_probs=26.3

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             100000025775778899887899998899997
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQ  446 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~k  446 (753)
                      ..+++++|+||+.|-+||++--...|..+..+-
T Consensus        26 ~~a~l~~~~Lt~ee~~al~~~D~~~L~~lGvn~   58 (77)
T cd07321          26 PEAVLAEYGLTPEEKAALLARDVGALYVLGVNP   58 (77)
T ss_pred             HHHHHHHCCCCHHHHHHHHCCCHHHHHHCCCCH
T ss_conf             999998769999999998856899999979969


No 70 
>pfam03853 YjeF_N YjeF-related protein N-terminus.
Probab=49.98  E-value=16  Score=16.04  Aligned_cols=117  Identities=19%  Similarity=0.310  Sum_probs=57.0

Q ss_pred             HHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHH--------------HHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             8999999961001321661326788708867797100246899--------------85599999984218786175216
Q gi|254780353|r   92 QSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEA--------------RMTQVAELILQGVDEDAVDFRDT  157 (753)
Q Consensus        92 ~s~y~a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~--------------rl~~~~~~ll~di~~~~v~~~~n  157 (753)
                      .++++.+.++-.+-..+...+-|.||.|.   |.-++.||--.              ++++-+...++-..+--+.+.+ 
T Consensus        14 ~~~a~~i~~~~~~~~~~v~il~G~GNNGG---DGlv~Ar~L~~~g~~V~v~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-   89 (170)
T pfam03853        14 RAVARVIRKLLSPAGKRVLVLCGPGNNGG---DGLAAARHLAQRGYKVTVLLLNPDEKLSEDARRALEIAKKLGGKIVS-   89 (170)
T ss_pred             HHHHHHHHHHCCCCCCEEEEEECCCCCHH---HHHHHHHHHHHCCCCEEEEEECCCCCCCHHHHHHHHHHHHCCCCEEE-
T ss_conf             99999999861877886999987998728---89999999998799079999678555999999999999986996761-


Q ss_pred             CCCCEEEEEEECCCCCHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCC
Q ss_conf             7996324223123452676426650467777516777889999999998728653201344320367788776
Q gi|254780353|r  158 YNEEDSEPVVFPSKFPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGG  230 (753)
Q Consensus       158 ~D~~~~EP~~lp~~~P~lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG  230 (753)
                      ++...  +..+  .=+-+.|-|--|+  |+.-.     +++-+..++.++...+..       +-.=|-|+|=
T Consensus        90 ~~~~~--~~~~--~~~d~iVDal~G~--Gl~~~-----l~~~~~~~i~~iN~~~~~-------visiDiPSGl  144 (170)
T pfam03853        90 LNPDE--DLSK--ALADLIIDALFGT--GLSRP-----LRGEYAELIEWINASKAP-------VLAVDIPSGL  144 (170)
T ss_pred             CCCCC--CCCC--CCCCEEEEEEEEC--CCCCC-----CCHHHHHHHHHHHCCCCC-------EEEEECCCCC
T ss_conf             58632--0125--6662899743523--67988-----988999999999738996-------7997378875


No 71 
>TIGR02199 rfaE_dom_II rfaE bifunctional protein, domain II; InterPro: IPR011914    RfaE is a protein involved in the biosynthesis of ADP-L-glycero-D-manno-heptose, a precursor for LPS inner core biosynthesis. RfaE is a bifunctional protein in Escherichia coli, and separate proteins in some other genome. Domain I (IPR011913 from INTERPRO) is suggested to act in D-glycero-D-manno-heptose 1-phosphate biosynthesis, while domain II (this family) adds ADP to yield ADP-D-glycero-D-manno-heptose .; GO: 0016773 phosphotransferase activity alcohol group as acceptor, 0016779 nucleotidyltransferase activity, 0005975 carbohydrate metabolic process.
Probab=49.10  E-value=13  Score=16.53  Aligned_cols=21  Identities=24%  Similarity=0.243  Sum_probs=13.6

Q ss_pred             EEEEECCCCCCCHHHHHHHHH
Q ss_conf             799952420021689999999
Q gi|254780353|r  267 CIVVTEIPYQVQKSRLIEKIA  287 (753)
Q Consensus       267 ~ivIteiPy~v~k~~~ie~I~  287 (753)
                      ++++=++=.+-+++++|+||.
T Consensus       123 ~V~~l~f~~g~STT~ii~ki~  143 (144)
T TIGR02199       123 QVVLLPFVEGRSTTAIIEKIL  143 (144)
T ss_pred             EEEEEEEECCCCCHHHHHHHH
T ss_conf             798985217984078999982


No 72 
>PRK07085 diphosphate--fructose-6-phosphate 1-phosphotransferase; Provisional
Probab=48.99  E-value=17  Score=15.67  Aligned_cols=84  Identities=19%  Similarity=0.173  Sum_probs=45.1

Q ss_pred             CCCCEEEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             67660588985045458899999875420000122331133312689722049999998999989999999999999999
Q gi|254780353|r  305 SAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAID  384 (753)
Q Consensus       305 Sd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~  384 (753)
                      |.+..-..|-+--|.++ +..|+-     .|||.  .|++.|.+.=..+-++|+++.+.-+    ++|.+|...  .|--
T Consensus       240 Sa~KYwHFVrlMGRsAS-HiaLEC-----aLQTh--PNi~lI~EEv~~k~~TL~~Iv~~I~----d~I~~Ra~~--Gkny  305 (557)
T PRK07085        240 SAKKYWHFIKLMGRSAS-HIALEC-----ALQTH--PNICLISEEIAEKNISLDDIVHYIA----SVIADRAAK--GKNF  305 (557)
T ss_pred             CCCCEEEEEEEECCCCH-HHHHHH-----HHHCC--CCEEEEHHHHHHCCCCHHHHHHHHH----HHHHHHHHC--CCCC
T ss_conf             15760799998168610-788888-----75138--8789767999871796999999999----999999975--9986


Q ss_pred             HHHHHHHHHHHHHHHHHH
Q ss_conf             999999999986410789
Q gi|254780353|r  385 RRVEILKGLLIAYLNIDE  402 (753)
Q Consensus       385 ~RlhIleGl~~a~~~ID~  402 (753)
                      --.-|=|||+--+-.+-.
T Consensus       306 GviLIPEGLiefIPe~k~  323 (557)
T PRK07085        306 GVILIPEGLIEFIPEMKS  323 (557)
T ss_pred             EEEEECCHHHHHCHHHHH
T ss_conf             599946238762778999


No 73 
>pfam08082 PRO8NT PRO8NT (NUC069), PrP8 N-terminal domain. The PRO8NT domain is found at the N-terminus of pre-mRNA splicing factors of PRO8 family. The NLS or nuclear localisation signal for these spliceosome proteins begins at the start and runs for 60 residues. N-terminal to this domain is a highly variable proline-rich region.
Probab=48.86  E-value=17  Score=15.66  Aligned_cols=59  Identities=25%  Similarity=0.392  Sum_probs=39.9

Q ss_pred             CCHHH-HHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHHHCCHH-HCCCCCCCCC
Q ss_conf             97046-899999998689998980354053666542768874789999999610013-2166132678
Q gi|254780353|r   50 FKPVH-RRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPF-VQRYPLISGQ  115 (753)
Q Consensus        50 lKpvq-Rril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~maq~~-~~~~pli~g~  115 (753)
                      +-|-| |+|+-   +-|-.++++|..--|+.=..+ ||-||   |+|--|-+|-|+| +.||.=|-=|
T Consensus         4 mPPEhlRKIi~---dhgDmsskkf~~dkr~~lgaL-kY~Ph---Av~KLLEnmPmPWE~~r~V~VlYH   64 (152)
T pfam08082         4 MPPEHLRKIIK---DHGDMSSKKFASDKRSYLGAL-KYMPH---ALLKLLENMPMPWEQVRYVKVLYH   64 (152)
T ss_pred             CCHHHHHHHHH---HCCCCCHHHCCHHHHHHHHHH-HHHHH---HHHHHHHCCCCCHHHHCCEEEEEE
T ss_conf             98799999997---445744011011358887677-54268---999998718985777403247886


No 74 
>PRK08006 replicative DNA helicase; Provisional
Probab=47.85  E-value=16  Score=15.86  Aligned_cols=22  Identities=9%  Similarity=0.202  Sum_probs=12.2

Q ss_pred             EEEEECCCCCCCHHHHHHHHHH
Q ss_conf             7999524200216899999999
Q gi|254780353|r  267 CIVVTEIPYQVQKSRLIEKIAE  288 (753)
Q Consensus       267 ~ivIteiPy~v~k~~~ie~I~~  288 (753)
                      .++|--=-+.+.|+.+.-.|+.
T Consensus       225 ~LiviaaRPsmGKTalalnia~  246 (471)
T PRK08006        225 DLIIVAARPSMGKTTFAMNLCE  246 (471)
T ss_pred             CEEEEEECCCCCHHHHHHHHHH
T ss_conf             3899994699876999999999


No 75 
>PRK08760 replicative DNA helicase; Provisional
Probab=47.79  E-value=17  Score=15.65  Aligned_cols=21  Identities=19%  Similarity=0.271  Sum_probs=9.7

Q ss_pred             EEEECCCCCCCHHHHHHHHHH
Q ss_conf             999524200216899999999
Q gi|254780353|r  268 IVVTEIPYQVQKSRLIEKIAE  288 (753)
Q Consensus       268 ivIteiPy~v~k~~~ie~I~~  288 (753)
                      ++|--=.+.+.|+.+.-.|+.
T Consensus       231 LiViaaRPsmGKTalalnia~  251 (476)
T PRK08760        231 LIILAARPAMGKTTFALNIAE  251 (476)
T ss_pred             EEEEEECCCCCHHHHHHHHHH
T ss_conf             799987788747899999999


No 76 
>TIGR02687 TIGR02687 conserved hypothetical protein TIGR02687; InterPro: IPR014060   Members of this family are uncharacterised proteins sporadically distributed in bacteria and archaea, about 880 amino acids in length. Proteins in this entry are encoded by genes that are repeatedly found upstream of another uncharacterised gene which encodes proteins of about 470 amino acids in length (see IPR014061 from INTERPRO)..
Probab=47.67  E-value=16  Score=15.89  Aligned_cols=59  Identities=17%  Similarity=0.347  Sum_probs=31.1

Q ss_pred             HHCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHH--HHHHHHHHHHHHHHHHHH-HHHHHHH
Q ss_conf             420000122331133312689722049999998999--989999999999999999-9999999
Q gi|254780353|r  331 MLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLA--HRREVLFRRSSFRMQAID-RRVEILK  391 (753)
Q Consensus       331 k~T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~--~R~~vi~rr~~~~L~k~~-~RlhIle  391 (753)
                      ++++|.-.|-.++.+=+.  .--+-+|.+.++.|..  ||.|-+=|...|-..+.+ +..-|+.
T Consensus       389 ~l~~~~~r~~~~~~~~~~--~~ntrslyd~~kaY~~~~y~~DqlYR~F~~~~~~~~~~~~~l~~  450 (911)
T TIGR02687       389 KLFNLKARYEDGFKAADA--AENTRSLYDLLKAYAEELYRFDQLYRKFTYYAEKVESKGAILLK  450 (911)
T ss_pred             HHHHHHHHCCCCCCHHHH--HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHH
T ss_conf             999986411237232237--77778899999999999888778888899999862204688762


No 77 
>PRK05748 replicative DNA helicase; Provisional
Probab=47.65  E-value=17  Score=15.69  Aligned_cols=22  Identities=18%  Similarity=0.229  Sum_probs=13.4

Q ss_pred             EEEEECCCCCCCHHHHHHHHHH
Q ss_conf             7999524200216899999999
Q gi|254780353|r  267 CIVVTEIPYQVQKSRLIEKIAE  288 (753)
Q Consensus       267 ~ivIteiPy~v~k~~~ie~I~~  288 (753)
                      .++|--=.+++.|+.+.-.|+.
T Consensus       204 ~LiviaaRP~mGKTa~alnia~  225 (448)
T PRK05748        204 DLIIVAARPSVGKTAFALNIAQ  225 (448)
T ss_pred             CEEEEEECCCCCHHHHHHHHHH
T ss_conf             3799984799876899999999


No 78 
>cd04618 CBS_pair_5 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=47.54  E-value=11  Score=17.17  Aligned_cols=69  Identities=23%  Similarity=0.414  Sum_probs=44.4

Q ss_pred             CCCCCHHHHHHHHHHHHCCCCCCC--CEEEEEHHH-----HHH---HCCCCCCHHHHHHHHHHHHCCHHHCCCCCCCCC-
Q ss_conf             128970468999999986899989--803540536-----665---427688747899999996100132166132678-
Q gi|254780353|r   47 RDGFKPVHRRIIHAMSEMGLDFGA--AFKKSARIV-----GEV---IGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQ-  115 (753)
Q Consensus        47 ~DGlKpvqRril~~m~~~~~~~~~--~~~K~ar~v-----g~v---~gkyhPHGd~s~y~a~v~maq~~~~~~pli~g~-  115 (753)
                      -|+--|| ++-+++|.+.|..+.-  ..+++ +-|     +|-   +--.|-|-+.|+|||.-.|-|+-.-|.|++|.. 
T Consensus         6 ~D~~l~v-k~Af~al~~ngi~~aplWds~~~-~fvGmLt~~DfI~il~lv~i~P~~sL~da~~~l~~~~ihrlPvid~~~   83 (98)
T cd04618           6 FDTKLPV-KKAFNALVENGIRSAPLWDSRKQ-QFVGMLTITDFILILRLVSIHPERSLFDAALLLLKNKIHRLPVIDPST   83 (98)
T ss_pred             EECCCCH-HHHHHHHHHCCCEEEEEECCCCC-EEEEEEEHHHHHHHHHHEECCCCCHHHHHHHHHHHCCCCCCCCCCCCC
T ss_conf             9489758-99999999869269998728876-788886479999887624448761299999999867875052164799


Q ss_pred             CC
Q ss_conf             87
Q gi|254780353|r  116 GN  117 (753)
Q Consensus       116 Gn  117 (753)
                      ||
T Consensus        84 ~~   85 (98)
T cd04618          84 GT   85 (98)
T ss_pred             CC
T ss_conf             96


No 79 
>KOG4288 consensus
Probab=47.10  E-value=18  Score=15.47  Aligned_cols=14  Identities=43%  Similarity=0.579  Sum_probs=5.6

Q ss_pred             CCCCHHHHHHHHHH
Q ss_conf             77788999999999
Q gi|254780353|r  192 PSHNVQEICEAALA  205 (753)
Q Consensus       192 pphnl~ev~~a~~~  205 (753)
                      ||-|..+|..+.+.
T Consensus       245 ppvnve~VA~aal~  258 (283)
T KOG4288         245 PPVNVESVALAALK  258 (283)
T ss_pred             CCCCHHHHHHHHHH
T ss_conf             98678999999997


No 80 
>PRK08694 consensus
Probab=46.53  E-value=19  Score=15.41  Aligned_cols=21  Identities=19%  Similarity=0.219  Sum_probs=11.6

Q ss_pred             EEEECCCCCCCHHHHHHHHHH
Q ss_conf             999524200216899999999
Q gi|254780353|r  268 IVVTEIPYQVQKSRLIEKIAE  288 (753)
Q Consensus       268 ivIteiPy~v~k~~~ie~I~~  288 (753)
                      ++|--=-+.+.|+.+.-.|+.
T Consensus       220 LiVIaaRPsmGKTalalnia~  240 (468)
T PRK08694        220 LIIVAGRPSMGKTAFSINIAE  240 (468)
T ss_pred             EEEEEECCCCCHHHHHHHHHH
T ss_conf             799961786537899999999


No 81 
>pfam08317 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=45.25  E-value=20  Score=15.27  Aligned_cols=15  Identities=27%  Similarity=0.395  Sum_probs=9.4

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999989999899999
Q gi|254780353|r  359 GILKEWLAHRREVLF  373 (753)
Q Consensus       359 eil~~f~~~R~~vi~  373 (753)
                      .-=..|++||...+.
T Consensus       133 ~aK~~WYeWR~qlle  147 (322)
T pfam08317       133 QSKKTWYEWRMKLLE  147 (322)
T ss_pred             HHHHHHHHHHHHHHH
T ss_conf             999899999999998


No 82 
>pfam01208 URO-D Uroporphyrinogen decarboxylase (URO-D).
Probab=45.14  E-value=20  Score=15.26  Aligned_cols=12  Identities=0%  Similarity=-0.175  Sum_probs=4.8

Q ss_pred             CCCCCCCEEEEE
Q ss_conf             012233113331
Q gi|254780353|r  336 ETRFPLNMNVLS  347 (753)
Q Consensus       336 q~sf~~N~~~l~  347 (753)
                      |..-+++.+.+.
T Consensus       188 qi~aGad~i~i~  199 (337)
T pfam01208       188 QIEAGADAIQIF  199 (337)
T ss_pred             HHHHCCCEEEEE
T ss_conf             998299679983


No 83 
>PTZ00094 serine hydroxymethyltransferase; Provisional
Probab=43.74  E-value=21  Score=15.11  Aligned_cols=66  Identities=12%  Similarity=0.164  Sum_probs=38.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             000257757788998878999988999976667899998877654420397887899999999998741774
Q gi|254780353|r  418 VSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKS  489 (753)
Q Consensus       418 ~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~  489 (753)
                      +..-++.|.+-..|.++=-+-|.-  -.++++   +..+.+.++.+-+.+.+. ..-+++|..++.++|--|
T Consensus       382 ~TtrGm~e~em~~ia~lI~~~i~~--~~~~~~---~~~~~~~~f~~~~~~~~~-i~~lr~~V~~~~~~fp~p  447 (450)
T PTZ00094        382 LTSRGAVEEDFEFVADFLDRAVKL--AQDIQK---EVGKKLVDFVKALEASED-IQQLRKEVVEFASQFPIP  447 (450)
T ss_pred             HHHCCCCHHHHHHHHHHHHHHHHH--HHHHHH---HHCHHHHHHHHCCCCHHH-HHHHHHHHHHHHHCCCCC
T ss_conf             883899889999999999999999--998766---501248889862045599-999999999999729999


No 84 
>PRK07263 consensus
Probab=43.68  E-value=21  Score=15.10  Aligned_cols=50  Identities=12%  Similarity=0.206  Sum_probs=26.2

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             79995242002168999999998640222134577640676605889850454588999998754
Q gi|254780353|r  267 CIVVTEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFM  331 (753)
Q Consensus       267 ~ivIteiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk  331 (753)
                      .++|=-=.+.+.|+.+.-.|+.-+-              .+.+.-|.+. +-+-..+.++..+..
T Consensus       204 dLiviaaRPsmGKTa~alnia~~iA--------------~~~~~~V~~f-SlEMs~~ql~~R~la  253 (453)
T PRK07263        204 QLIILAARPAVGKTAFVLNIAQNVG--------------TKQKKTVAIF-SLEMGAESLVDRMLA  253 (453)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHH--------------HHCCCEEEEE-ECCCCHHHHHHHHHH
T ss_conf             6899972788847899999999999--------------8559828999-246998999999999


No 85 
>pfam07569 Hira TUP1-like enhancer of split. The Hira proteins are found in a range of eukaryotes and are implicated in the assembly of repressive chromatin. These proteins also contain pfam00400.
Probab=43.37  E-value=21  Score=15.07  Aligned_cols=69  Identities=20%  Similarity=0.242  Sum_probs=34.7

Q ss_pred             CEEEEEECCCCCEEEEECCCEEEEEEHHHCCCCCCCCC--CCCCCCCC-------CCCCEEEEEEEECCCCEEEEEECCC
Q ss_conf             40121111478178980688278755112121234444--22223576-------7653078999857998599997489
Q gi|254780353|r  551 LKIALHAHTTDRILLLSTDGKAYTLPAGNLLSGRGHGE--AIQLLIDL-------NHNQDIVTAFVYDSTCKLLVVSSKG  621 (753)
Q Consensus       551 l~~~~~~~t~d~LLffTs~GkvY~l~a~~Ips~~~kG~--pI~~ll~l-------~~~EkIv~~~~~~~~~~lll~Tk~G  621 (753)
                      ...++.|+. .+|+++|..|-+|.   |++...+..-.  .+..+++.       .+.+.|+.+..- +.+.-++.-++|
T Consensus        14 ~~~~Le~~~-~~Ll~iT~~G~l~v---Wnv~~~~~~~~~~Sl~plL~~~~~~~~~~~~~~v~~~~vt-~~G~Plv~lSnG   88 (219)
T pfam07569        14 PASFLESNG-SYLLCVTSVGLLYV---WNVKTKKALLPPVSLAPLLDSSSRYSDDTSGPNVTQASVT-SSGIPLVTLSNG   88 (219)
T ss_pred             CCEEEEECC-CEEEEEECCCEEEE---EECCCCEEECCCCCHHHHHCCCCCCCCCCCCCCEEEEEEC-CCCCEEEEECCC
T ss_conf             656998179-78999925887999---9765987733730168774433345667898736899972-799558995188


Q ss_pred             CEE
Q ss_conf             789
Q gi|254780353|r  622 NAF  624 (753)
Q Consensus       622 ~ik  624 (753)
                      .++
T Consensus        89 ~~y   91 (219)
T pfam07569        89 DGY   91 (219)
T ss_pred             CEE
T ss_conf             525


No 86 
>KOG0831 consensus
Probab=43.30  E-value=13  Score=16.51  Aligned_cols=76  Identities=24%  Similarity=0.287  Sum_probs=38.1

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHH------HCCCCCCCCEEEEEHHHH---HHHCCCCCCHHHHHHHHHH
Q ss_conf             8888889998510476411289704689999999------868999898035405366---6542768874789999999
Q gi|254780353|r   29 RYLAYALSTIKERAIPDLRDGFKPVHRRIIHAMS------EMGLDFGAAFKKSARIVG---EVIGKLHPHGDQSVYDSLV   99 (753)
Q Consensus        29 ~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m~------~~~~~~~~~~~K~ar~vg---~v~gkyhPHGd~s~y~a~v   99 (753)
                      -..-|++....+|--|+-+ |     ||..|.-.      -.... --++.|-|..--   =++| |||||--+ ++|-.
T Consensus        49 ~~~ly~vw~~~d~~~~~~~-g-----~~~~~~r~~~l~k~~~~YF-Pi~L~kt~~l~p~~NYi~g-~hPHgi~~-~gaf~  119 (334)
T KOG0831          49 LAILYAVWLYYDRDTPKKG-G-----RRSNWFRNWPIWKWFCDYF-PISLIKTAELDPEKNYIFG-YHPHGILS-VGAFG  119 (334)
T ss_pred             HHHHHHHHEECCCCCCCCC-C-----CHHHHHHHHHHHHHHHHCC-CEEEEEEECCCCCCCEEEE-ECCCHHHC-CCCCC
T ss_conf             9999887501367787666-4-----1888998889999986416-4067764015876564887-65632200-01101


Q ss_pred             HHCC---HHHCCCCCCC
Q ss_conf             6100---1321661326
Q gi|254780353|r  100 RLAQ---PFVQRYPLIS  113 (753)
Q Consensus       100 ~maq---~~~~~~pli~  113 (753)
                      .|+-   +|+.-.|=+.
T Consensus       120 ~f~t~~s~~~~~fPgi~  136 (334)
T KOG0831         120 NFSTEATGFSKLFPGIR  136 (334)
T ss_pred             CCCEECCCHHHHCCCCC
T ss_conf             11022124244179887


No 87 
>KOG1359 consensus
Probab=43.20  E-value=13  Score=16.52  Aligned_cols=11  Identities=18%  Similarity=0.368  Sum_probs=5.2

Q ss_pred             HHHHHHHHHCC
Q ss_conf             99999987417
Q gi|254780353|r  477 CEIREVKEIFS  487 (753)
Q Consensus       477 ~EL~eikkkfg  487 (753)
                      +|+-.+.+|||
T Consensus       213 ~ei~~La~kYg  223 (417)
T KOG1359         213 EEISQLAKKYG  223 (417)
T ss_pred             HHHHHHHHHCC
T ss_conf             99999998629


No 88 
>KOG0650 consensus
Probab=42.94  E-value=21  Score=15.02  Aligned_cols=36  Identities=19%  Similarity=0.323  Sum_probs=24.5

Q ss_pred             EEECCCCCEEEEEEC--CCCEEEEEECCCCEEEEEHHH
Q ss_conf             853689805688961--898099995699389955787
Q gi|254780353|r  642 LKVSSEEKMKLVVKV--TGDHVAVVGENRKLLIFSIDQ  677 (753)
Q Consensus       642 ikLk~~D~li~v~~~--~~d~iiliT~~Gk~LrF~~~e  677 (753)
                      -+|..+-.-++-..+  .||++++.|..++++.|+.+-
T Consensus       601 KkL~tg~kwiS~msihp~GDnli~gs~d~k~~WfDldl  638 (733)
T KOG0650         601 KKLLTGSKWISSMSIHPNGDNLILGSYDKKMCWFDLDL  638 (733)
T ss_pred             HHHHCCCEEEEEEEECCCCCEEEEECCCCEEEEEECCC
T ss_conf             98845774644444448987078843777069997566


No 89 
>KOG2941 consensus
Probab=42.89  E-value=21  Score=15.01  Aligned_cols=31  Identities=26%  Similarity=0.256  Sum_probs=24.4

Q ss_pred             CCCCCHHHHCCCCCHHHHHHHHCCCCCHHHH
Q ss_conf             2345267642665046777751677788999
Q gi|254780353|r  169 PSKFPNLLANGTSGIAVGMATSIPSHNVQEI  199 (753)
Q Consensus       169 p~~~P~lL~Ng~~GIavG~at~ipphnl~ev  199 (753)
                      |+-+|.+.+--.-+|-.|-+--|-=||.+=-
T Consensus       112 PP~iPtliv~~~~~~l~~~KfiIDWHNy~Ys  142 (444)
T KOG2941         112 PPSIPTLIVCVLYSILTGAKFIIDWHNYGYS  142 (444)
T ss_pred             CCCCCHHHHHHHHHHHHCCEEEEEEHHHHHH
T ss_conf             9987347999999987366589970225789


No 90 
>KOG1446 consensus
Probab=42.85  E-value=21  Score=15.01  Aligned_cols=22  Identities=14%  Similarity=0.415  Sum_probs=9.7

Q ss_pred             EECCCEEECCCCCCCCCCCCCC
Q ss_conf             8710102025655445532234
Q gi|254780353|r  524 ISNRGWIRSLKSHSVDLSALHF  545 (753)
Q Consensus       524 LS~~GyIKr~k~~~~~~~~~~~  545 (753)
                      |..+-|||-.+||...+..+..
T Consensus        87 l~dNkylRYF~GH~~~V~sL~~  108 (311)
T KOG1446          87 LHDNKYLRYFPGHKKRVNSLSV  108 (311)
T ss_pred             EECCCEEEECCCCCCEEEEEEE
T ss_conf             2058169973787742777770


No 91 
>cd02639 R3H_RRM R3H domain of mainly fungal proteins which are associated with a RNA recognition motif (RRM) domain. Present in this group is the RNA-binding post-transcriptional regulator Cip2 (Csx1-interacting protein 2) involved in counteracting Csx1 function. Csx1 plays a central role in controlling gene expression during oxidative stress. The name of the R3H domain comes from the characteristic spacing of the most conserved arginine and histidine residues. The function of the domain is predicted to bind ssDNA or ssRNA in a sequence-specific manner.
Probab=42.68  E-value=20  Score=15.20  Aligned_cols=25  Identities=40%  Similarity=0.813  Sum_probs=19.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHH-HHCCCCCC
Q ss_conf             47641128970468999999-98689998
Q gi|254780353|r   42 AIPDLRDGFKPVHRRIIHAM-SEMGLDFG   69 (753)
Q Consensus        42 alpd~~DGlKpvqRril~~m-~~~~~~~~   69 (753)
                      |.|.   +|-|.||||+... +.|||.+.
T Consensus        21 ~fp~---~lsp~qRrivh~La~~lGL~h~   46 (60)
T cd02639          21 AFPS---SLSPAERRIVHLLASRLGLNHV   46 (60)
T ss_pred             ECCC---CCCHHHHHHHHHHHHHCCCCEE
T ss_conf             7599---9999999999999988199204


No 92 
>PRK07004 replicative DNA helicase; Provisional
Probab=42.62  E-value=21  Score=14.99  Aligned_cols=23  Identities=4%  Similarity=0.174  Sum_probs=12.7

Q ss_pred             CHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             97887899999999998741774
Q gi|254780353|r  467 SGKQQWNQIACEIREVKEIFSKS  489 (753)
Q Consensus       467 s~~~l~~iI~~EL~eikkkfgd~  489 (753)
                      ++......|...|+.+.+.++-|
T Consensus       344 ~r~~ei~~isr~lK~lAkel~ip  366 (460)
T PRK07004        344 NRATEISEISRSLKSLAKELDVP  366 (460)
T ss_pred             CHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             89999999999999999996997


No 93 
>TIGR00373 TIGR00373 conserved hypothetical protein TIGR00373; InterPro: IPR005241    This family of proteins is, so far, restricted to archaeal genomes. The family appears to be distantly related to the N-terminal region of the eukaryotic transcription initiation factor IIE alpha chain. .
Probab=42.29  E-value=12  Score=16.97  Aligned_cols=19  Identities=21%  Similarity=0.249  Sum_probs=9.5

Q ss_pred             HHHHHHHHCCCCCCHHHHH
Q ss_conf             9999987286532013443
Q gi|254780353|r  201 EAALALIDNPEISIEKLLE  219 (753)
Q Consensus       201 ~a~~~~i~~~~~~~~~l~~  219 (753)
                      .-+-.|+...+.|.++|-+
T Consensus        20 ~vl~~L~~kGe~Tdeeis~   38 (168)
T TIGR00373        20 EVLESLLIKGEVTDEEISK   38 (168)
T ss_pred             HHHHHHCCCCCCCHHHHHH
T ss_conf             4442220268747788888


No 94 
>PRK05729 valS valyl-tRNA synthetase; Reviewed
Probab=41.88  E-value=22  Score=14.91  Aligned_cols=53  Identities=26%  Similarity=0.437  Sum_probs=32.5

Q ss_pred             HHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHHHCC----HHHCCCCCCCCCCC
Q ss_conf             8999999986899989803540536665427688747899999996100----13216613267887
Q gi|254780353|r   55 RRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQ----PFVQRYPLISGQGN  117 (753)
Q Consensus        55 Rril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~maq----~~~~~~pli~g~Gn  117 (753)
                      ..+.--||+-||...     .-+.|     .|-|+-.+++-++=|-...    -|..+|||.|+.+-
T Consensus       155 ~~~F~~L~~kGliyr-----~~~~V-----~wcp~~~Tals~~EV~~~~~~~~~~~ikf~l~~~~~~  211 (877)
T PRK05729        155 REVFVRLYEKGLIYR-----GKRLV-----NWDPKLQTALSDLEVEYKEVKGKLWHIRYPLADGSDY  211 (877)
T ss_pred             HHHHHHHHHCCCEEE-----CCEEC-----CCCCCCCCHHHHHHHHCCCCCCCEEEEECCCCCCCCE
T ss_conf             999999998899784-----13123-----6688778843567873245667338984132478874


No 95 
>TIGR01341 aconitase_1 aconitate hydratase 1; InterPro: IPR006249   Aconitase (aconitate hydratase; 4.2.1.3 from EC) is an iron-sulphur protein that contains a [4Fe-4S]-cluster and catalyses the interconversion of isocitrate and citrate via a cis-aconitate intermediate. Aconitase functions in both the TCA and glyoxylate cycles, however unlike the majority of iron-sulphur proteins that function as electron carriers, the [4Fe-4S]-cluster of aconitase reacts directly with an enzyme substrate. In eukaryotes there is a cytosolic form (cAcn) and a mitochondrial form (mAcn) of the enzyme. In bacteria there are also 2 forms, aconitase A (AcnA) and B (AcnB). Several aconitases are known to be multi-functional enzymes with a second non-catalytic, but essential function that arises when the cellular environment changes, such as when iron levels drop , . Eukaryotic cAcn and mAcn, and bacterial AcnA have the same domain organisation, consisting of three N-terminal alpha/beta/alpha domains, a linker region, followed by a C-terminal 'swivel' domain with a beta/beta/alpha structure (1-2-3-linker-4), although mAcn is small than cAcn. However, bacterial AcnB has a different organisation: it contains an N-terminal HEAT-like domain, followed by the 'swivel' domain, then the three alpha/beta/alpha domains (HEAT-4-1-2-3) . Below is a description of some of the multi-functional activities associated with different aconitases.   Eukaryotic mAcn catalyses the second step of the mitochondrial TCA cycle, which is important for energy production, providing high energy electrons in the form of NADH and FADH2 to the mitochondrial oxidative phosphorylation pathway . The TCA cycle also provides precursors for haem and amino acid production. This enzyme has a second, non-catalytic but essential role in mitochondrial DNA (mtDNA) maintenance: mAcn acts to stabilise mtDNA, forming part of mtDNA protein-DNA complexes known as nucleoids. mAcn is thought to reversibly model nucleoids to directly influence mitochondrial gene expression in response to changes in the cellular environment. Therefore, mAcn can influence the expression of components of the oxidative phosphorylation pathway encoded in mtDNA.    Eukaryotic cAcn enzyme balances the amount of citrate and isocitrate in the cytoplasm, which in turn creates a balance between the amount of NADPH generated from isocitrate by isocitrate dehydrogenase with the amount of acetyl-CoA generated from citrate by citrate lyase. Fatty acid synthesis requires both NADPH and acetyl-CoA, as do other metabolic processes, including the need for NADPH to combat oxidative stress. The enzymatic form of cAcn predominates when iron levels are normal, but if they drop sufficiently to cause the disassembly of the [4Fe-4S]-cluster, then cAcn undergoes a conformational change from a compact enzyme to a more open L-shaped protein known as iron regulatory protein 1 (IRP1; or IRE-binding protein 1, IREBP1) , . As IRP1, the catalytic site and the [4Fe-4S]-cluster are lost, and two new RNA-binding sites appear. IRP1 functions in the post-transcriptional regulation of genes involved in iron metabolism - it binds to mRNA iron-responsive elements (IRE), 30-nucleotide stem-loop structures at the 3' or 5' end of specific transcripts. Transcripts containing an IRE include ferritin L and H subunits (iron storage), transferrin (iron plasma chaperone), transferrin receptor (iron uptake into cells), ferroportin (iron exporter), mAcn, succinate dehydrogenase, erythroid aminolevulinic acid synthetase (tetrapyrrole biosynthesis), among others. If the IRE is in the 5'-UTR of the transcript (e.g. in ferritin mRNA), then IRP1-binding prevents its translation by blocking the transcript from binding to the ribosome. If the IRE is in the 3'-UTR of the transcript (e.g. transferrin receptor), then IRP1-binding protects it from endonuclease degradation, thereby prolonging the half-life of the transcript and enabling it to be translated .   IRP2 is another IRE-binding protein that binds to the same transcripts as IRP1. However, since IRP1 is predominantly in the enzymatic cAcn form, it is IRP2 that acts as the major metabolic regulator that maintains iron homeostasis . Although IRP2 is homologous to IRP1, IPR2 lacks aconitase activity, and is known only to have a single function in the post-transcriptional regulation of iron metabolism genes . In iron-replete cells, IRP2 activity is regulated primarily by iron-dependent degradation through the ubiquitin-proteasomal system.   Bacterial AcnB is also known to be multi-functional. In addition to its role in the TCA cycle, AcnB was shown to be a post-transcriptional regulator of gene expression in Escherichia coli and Salmonella enterica , . In S.enterica, AcnB initiates a regulatory cascade controlling flagella biosynthesis through an interaction with the ftsH transcript, an alternative RNA polymerase sigma factor. This binding lowers the intracellular concentration of FtsH protease, which in turn enhances the amount of RNA polymerase sigma32 factor (normally degraded by FtsH protease), and sigma32 then increases the synthesis of chaperone DnaK, which in turn promotes the synthesis of the flagellar protein FliC. AcnB regulates the synthesis of other proteins as well, such as superoxide dismutase (SodA) and other enzymes involved in oxidative stress.   This entry represents bacterial aconitase A (AcnA), eukaryotic cytosolic aconitase (cAcn/IRP1), iron regulatory protein 2 (IRP2), and a few mitochondrial aconitases (certain mAcn proteins, but not the majority of these enzymes).   More information about these proteins can be found at Protein of the Month: Aconitase .; GO: 0051539 4 iron 4 sulfur cluster binding, 0008152 metabolic process.
Probab=41.60  E-value=5.2  Score=19.59  Aligned_cols=79  Identities=24%  Similarity=0.341  Sum_probs=51.4

Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHH-HHCCCCCC--CCEEEEEHHHHHHHCCC--CCC-HH-HHHHHHHHHH
Q ss_conf             888888999851047641128970468999999-98689998--98035405366654276--887-47-8999999961
Q gi|254780353|r   29 RYLAYALSTIKERAIPDLRDGFKPVHRRIIHAM-SEMGLDFG--AAFKKSARIVGEVIGKL--HPH-GD-QSVYDSLVRL  101 (753)
Q Consensus        29 ~y~~ya~~vi~~Ralpd~~DGlKpvqRril~~m-~~~~~~~~--~~~~K~ar~vg~v~gky--hPH-Gd-~s~y~a~v~m  101 (753)
                      +=|.||+-|+.+-++=.+ ||.+--.--|=-=. |+.+-..+  =+| |.||||   |=-|  =|= =| +|+=|||-++
T Consensus        20 ~~LPySiriLLEs~~Rn~-DG~~i~~eD~e~i~~W~~~~~~d~Ei~F-kP~RV~---mQDFTGVPAVVDLA~mR~am~~L   94 (896)
T TIGR01341        20 SKLPYSIRILLESVLRNL-DGFSIKEEDVEAILKWKKEELKDVEIAF-KPARVV---MQDFTGVPAVVDLAAMRDAMKNL   94 (896)
T ss_pred             CCCCHHHHHHHHHHHHHC-CCCCCCHHHHHHHHCCCCCCCCCCCCCC-CCCEEE---EECCCCCCHHHHHHHHHHHHHHH
T ss_conf             004147999999998763-8842067899888443113546614675-641367---52437872788889999999982


Q ss_pred             CCHHHCCCCCC
Q ss_conf             00132166132
Q gi|254780353|r  102 AQPFVQRYPLI  112 (753)
Q Consensus       102 aq~~~~~~pli  112 (753)
                      ..|-.+=-|+|
T Consensus        95 GgDp~kINP~v  105 (896)
T TIGR01341        95 GGDPEKINPLV  105 (896)
T ss_pred             CCCCCCCCCCC
T ss_conf             78812048876


No 96 
>PRK05595 replicative DNA helicase; Provisional
Probab=41.08  E-value=18  Score=15.55  Aligned_cols=23  Identities=17%  Similarity=0.195  Sum_probs=16.9

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHH
Q ss_conf             79995242002168999999998
Q gi|254780353|r  267 CIVVTEIPYQVQKSRLIEKIAEL  289 (753)
Q Consensus       267 ~ivIteiPy~v~k~~~ie~I~~l  289 (753)
                      .++|--=.+++.|+.+.-.|+.-
T Consensus       202 dLiiiaaRP~mGKTa~alnia~~  224 (444)
T PRK05595        202 DMILIAARPSMGKTTFALNIAEY  224 (444)
T ss_pred             CEEEEEECCCCCCHHHHHHHHHH
T ss_conf             77999857989807999999999


No 97 
>pfam10977 DUF2797 Protein of unknown function (DUF2797). This family of proteins has no known function.
Probab=40.92  E-value=22  Score=14.93  Aligned_cols=120  Identities=17%  Similarity=0.217  Sum_probs=56.9

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCC
Q ss_conf             77889988789999889999766678-------99998877654420397887899999999998741774334555420
Q gi|254780353|r  426 NQVDAILNLRLRSLRKLEEYQIKSEL-------DNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLGRRRTT  498 (753)
Q Consensus       426 ~QA~aIL~mrL~rLt~le~~kl~~E~-------~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~~~~~~RRT~  498 (753)
                      .||-.|++.+=|+++++=+..|.+.+       +-|..+.+.+ .+..-+.++...+.+++.++...|+...        
T Consensus       101 ~~A~~i~~v~nR~~AG~~Ev~lk~~~sDkTnWr~MLk~~~~~v-Dl~~~~~~l~~~~~~~~~~~~~~~~~~~--------  171 (233)
T pfam10977       101 VQAIPILRVPNRRLAGIVEVALKAHVADKTNWRKMLKGLVEDV-DLAAERARLLEEIAEELKELRLEYGEDA--------  171 (233)
T ss_pred             CCEEEEEECCCCCHHHHHHHHHHHHCCCCCHHHHHHCCCCCCC-CHHHHHHHHHHHHHHHHHHHHHHHCCCC--------
T ss_conf             3178999857860055889999876367415689864899886-8999999999973699999987622321--------


Q ss_pred             EEECCCHHHHHHHHCCCCCCCCEEEEECCCEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEECCCEEEEEEHH
Q ss_conf             00011000000110024566705998710102025655445532234555554012111147817898068827875511
Q gi|254780353|r  499 FCEVSRADKATLQQAMIEKEPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAG  578 (753)
Q Consensus       499 iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyIKr~k~~~~~~~~~~~KegD~l~~~~~~~t~d~LLffTs~GkvY~l~a~  578 (753)
                       ++...       +..--+.|+      ..|-.       ...++++.....+...+.+---++|+|  +.| |+.++.+
T Consensus       172 -~~~~~-------~~~~i~yPv------~~yp~-------kv~slnldk~p~~~G~L~GIKGQYLif--d~g-V~NiR~~  227 (233)
T pfam10977       172 -IEEDE-------AVFSINYPV------LEYPT-------KVKSLNLDKTPVVEGTLVGIKGQYLIL--DTG-VINIRKF  227 (233)
T ss_pred             -CCCCC-------CEEEEECCH------HCCCC-------CCCEECCCCCCCCEEEEEEEEEEEEEE--CCC-EEEEECC
T ss_conf             -23566-------338985521------12777-------651104246883114999885349996--288-6884056


No 98 
>pfam07798 DUF1640 Protein of unknown function (DUF1640). This family consists of sequences derived from hypothetical eukaryotic proteins. A region approximately 100 residues in length is featured.
Probab=40.89  E-value=23  Score=14.80  Aligned_cols=13  Identities=23%  Similarity=0.304  Sum_probs=4.7

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             5778899887899
Q gi|254780353|r  425 ENQVDAILNLRLR  437 (753)
Q Consensus       425 e~QA~aIL~mrL~  437 (753)
                      -.+|+.=|+|-|.
T Consensus       102 k~~a~~klDlNle  114 (177)
T pfam07798       102 KVTAGVRLDLNLE  114 (177)
T ss_pred             HHHHHHHHHHHHH
T ss_conf             8615257654555


No 99 
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=40.59  E-value=20  Score=15.22  Aligned_cols=35  Identities=26%  Similarity=0.507  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHH
Q ss_conf             07899997520000110000002577577889988
Q gi|254780353|r  399 NIDEIIAIIRNEDKPKPVMVSRFSLTENQVDAILN  433 (753)
Q Consensus       399 ~ID~vI~iIR~s~~~k~~L~~~f~lse~QA~aIL~  433 (753)
                      +|++||+.-=+...|-+++...|+|||.|...|.-
T Consensus         1 di~riIemAweDrt~Fe~I~~~~gl~E~evi~lMr   35 (72)
T TIGR03643         1 DIDRIIEMAWEDRTPFEAIEQQFGLSEKEVIKLMR   35 (72)
T ss_pred             CHHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHHH
T ss_conf             98899999983799899999998949999999999


No 100
>KOG2444 consensus
Probab=40.47  E-value=23  Score=14.75  Aligned_cols=97  Identities=12%  Similarity=0.101  Sum_probs=54.7

Q ss_pred             EEEECCCEEECCCCCCCCCCCCCCCCCCCCE-EEEEECCCCCEEEEECCCEEEEEEHHHCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             9987101020256554455322345555540-121111478178980688278755112121234444222235767653
Q gi|254780353|r  522 VVISNRGWIRSLKSHSVDLSALHFKEGDSLK-IALHAHTTDRILLLSTDGKAYTLPAGNLLSGRGHGEAIQLLIDLNHNQ  600 (753)
Q Consensus       522 V~LS~~GyIKr~k~~~~~~~~~~~KegD~l~-~~~~~~t~d~LLffTs~GkvY~l~a~~Ips~~~kG~pI~~ll~l~~~E  600 (753)
                      .-=|.+||++..+   .++..++.+.++++. ....+...++|++-|+.|.+|....+.      .|.+..-+..  ..|
T Consensus        34 ~~~sa~~~v~~~~---~~k~k~s~rse~~~~e~~~v~~~~~~~~vG~~dg~v~~~n~n~------~g~~~d~~~s--~~e  102 (238)
T KOG2444          34 RATSADGLVRERK---VRKHKESCRSERFIDEGQRVVTASAKLMVGTSDGAVYVFNWNL------EGAHSDRVCS--GEE  102 (238)
T ss_pred             CCCCCCCCCCCCH---HHHHHHHHHHHHHHHCCEEECCCCCEEEEECCCCEEEEECCCC------CCHHHHHHHC--CCC
T ss_conf             0036776422002---5666654222355653412203376378632441599964775------3057776502--354


Q ss_pred             EEEEEEEEC-CCCEEEEEECCCCEEEEEHH
Q ss_conf             078999857-99859999748978996388
Q gi|254780353|r  601 DIVTAFVYD-STCKLLVVSSKGNAFIVEES  629 (753)
Q Consensus       601 kIv~~~~~~-~~~~lll~Tk~G~ikr~~l~  629 (753)
                      .|..+++.- ...+.+.....|.+-.+...
T Consensus       103 ~i~~~Ip~~~~~~~~c~~~~dg~ir~~n~~  132 (238)
T KOG2444         103 SIDLGIPNGRDSSLGCVGAQDGRIRACNIK  132 (238)
T ss_pred             CCEECCCCCCCCCEEEEECCCCCEEEECCC
T ss_conf             412101405654256885257705532235


No 101
>TIGR02225 recomb_XerD tyrosine recombinase XerD; InterPro: IPR011932   Proteins in this entry are part of the wider so-called "phage" integrase fmaily which describes a number of recombinases with tyrosine active sites that transiently bind covalently to DNA. Many are associated with mobile DNA elements, including phage, transposons, and phase variation loci.   This entry represents the chromosomally-encoded polypeptide XerD, which is closely related to, and interacts with, another chromosomally-encoded polypeptide, XerC (IPR011931 from INTERPRO). These proteins are site-specific tyrosine recombinases, which act by catalyzing the cutting and rejoining of the recombining DNA molecules . They form a cyclic heterotetrameric complex composed of two molecules of XerC and two molecules of XerD. The XerC-XerD complex is essential to convert dimers of the bacterial chromosome into monomers to permit their segregation at cell division. It also contributes to the segregational stability of plasmids.   XerD is composed of two domains, an N-terminal alpha-helical domain, and a C-terminal domain composed mostly of alpha helices, with a three-stranded antiprallel beta sheet along one edge . The active site is found at the extreme C-terminal end of the polypeptide. Most of the C-terminal domain is structurally homologous to that of other "phage" integrases, but the active site regions of these enzymes are stucturally distinct.; GO: 0003677 DNA binding, 0006310 DNA recombination, 0007049 cell cycle, 0007059 chromosome segregation, 0015074 DNA integration, 0051301 cell division.
Probab=40.18  E-value=23  Score=14.72  Aligned_cols=82  Identities=18%  Similarity=0.292  Sum_probs=43.3

Q ss_pred             CCCCCHHHH-HHHHHHHHHCCC-CCCHHHHHHCCCC-CCCCCCC-----CCCCHHHHHHHHHCC----------------
Q ss_conf             677788999-999999872865-3201344320367-7887760-----106988999898503----------------
Q gi|254780353|r  191 IPSHNVQEI-CEAALALIDNPE-ISIEKLLEYIIGP-DFPTGGI-----IVESRESIVESYRLG----------------  246 (753)
Q Consensus       191 ipphnl~ev-~~a~~~~i~~~~-~~~~~l~~~i~gP-DFPTGG~-----i~~~~~~i~~~y~tG----------------  246 (753)
                      +-++||.+. +++=..--.=|+ .|++|.-..+-+| |-+|---     + .++-=+.=+|.||                
T Consensus        84 ~~~~dP~~~~~~~PK~~~~LP~vLt~~EV~~LL~~p~~~~~~~g~kr~~l-RDrAmLElLYATGlRVSELv~L~~~d~~l  162 (305)
T TIGR02225        84 LREDDPSALRIETPKVARKLPKVLTVEEVEALLAAPIDVDTPLGGKRPAL-RDRAMLELLYATGLRVSELVGLRLEDVNL  162 (305)
T ss_pred             CCCCCCHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHCCCCCCCCCCCHHH-HHHHHHHHHHHCCCCEEEEECCCHHHHHC
T ss_conf             74557336642034224578883798999999850024677676764016-54799999986488355330561665200


Q ss_pred             -CCE-EE-EEEEEEEEECCCCCEEEEEECCCCCCCHHHHHH
Q ss_conf             -341-59-999999864378840799952420021689999
Q gi|254780353|r  247 -RGG-FR-VRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIE  284 (753)
Q Consensus       247 -~G~-i~-~r~k~~~e~~~~~~~~ivIteiPy~v~k~~~ie  284 (753)
                       .|. |+ |+||       .+|.+|    +|.+-.-..+++
T Consensus       163 ~~g~~~~~v~GK-------G~KERl----VP~G~~A~~~l~  192 (305)
T TIGR02225       163 DEGVKVRKVRGK-------GSKERL----VPLGEEAIEALE  192 (305)
T ss_pred             CCCEEEEEEEEC-------CCCEEE----CCCHHHHHHHHH
T ss_conf             277379998616-------884120----220289999999


No 102
>KOG0977 consensus
Probab=39.69  E-value=24  Score=14.67  Aligned_cols=14  Identities=29%  Similarity=0.401  Sum_probs=6.2

Q ss_pred             CCCCHHHHHHHHCC
Q ss_conf             66504677775167
Q gi|254780353|r  179 GTSGIAVGMATSIP  192 (753)
Q Consensus       179 g~~GIavG~at~ip  192 (753)
                      +++||.+=|-+.++
T Consensus        82 ~ts~ik~~ye~El~   95 (546)
T KOG0977          82 ETSGIKAKYEAELA   95 (546)
T ss_pred             CCCCHHHHHHHHHH
T ss_conf             88644577542678


No 103
>pfam01768 Birna_VP4 Birnavirus VP4 protein. VP4 is a viral protease. The large RNA segment of birnaviruses codes for a polyprotein (N-VP2-VP4-VP3-C).
Probab=39.33  E-value=7.2  Score=18.52  Aligned_cols=68  Identities=22%  Similarity=0.301  Sum_probs=39.0

Q ss_pred             HHHHHHHHCCHHHCCCCCCCCCCCC-CCCCCCCCCCHHHHHHHHH--------HHH---------HHHHHHCCCCCCCCC
Q ss_conf             9999996100132166132678870-8867797100246899855--------999---------999842187861752
Q gi|254780353|r   94 VYDSLVRLAQPFVQRYPLISGQGNF-GNIDGDSAAAYRYTEARMT--------QVA---------ELILQGVDEDAVDFR  155 (753)
Q Consensus        94 ~y~a~v~maq~~~~~~pli~g~Gnf-Gs~~~d~~Aa~RYte~rl~--------~~~---------~~ll~di~~~~v~~~  155 (753)
                      +-+||--||      -||+.--+.| |.+.||.||+-||+-.--|        .++         ..+-..++  -+.|.
T Consensus         5 V~sTLfP~a------APLigaad~~i~~l~~~~Aa~gr~~~~AAsGr~~~~s~~~~sg~~~~~~s~~~~~~L~--~~~~l   76 (264)
T pfam01768         5 VLSTLFPMA------APLIGAADQFIGDLLGDNASGGRYVSHAASGRYRDVSRRWRSGSLTGDKSYSLKSRLG--EEHWL   76 (264)
T ss_pred             HHHHHCCCC------CCHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCEEEECCCC--CCCCC
T ss_conf             443433342------2012246666665316633367624423478716688877517855653113103343--11257


Q ss_pred             CCCCCCEEEEEEEC
Q ss_conf             16799632422312
Q gi|254780353|r  156 DTYNEEDSEPVVFP  169 (753)
Q Consensus       156 ~n~D~~~~EP~~lp  169 (753)
                      ||-++.--|+...+
T Consensus        77 P~e~~n~~~~~i~r   90 (264)
T pfam01768        77 PNESENYEEVEIPR   90 (264)
T ss_pred             CCCCCCCCCCCCCC
T ss_conf             64566533578888


No 104
>PRK08227 aldolase; Validated
Probab=38.36  E-value=25  Score=14.53  Aligned_cols=15  Identities=7%  Similarity=-0.115  Sum_probs=7.7

Q ss_pred             HHHHHHHHCCCCCEE
Q ss_conf             134577640676605
Q gi|254780353|r  296 PLLEDIRDESAEDVR  310 (753)
Q Consensus       296 ~gi~dirDeSd~~~~  310 (753)
                      ..+..+.+|.++-++
T Consensus       154 ~~lg~v~~e~~~~Gm  168 (291)
T PRK08227        154 KNIIQLVDAGLRYGM  168 (291)
T ss_pred             HHHHHHHHHHHHCCC
T ss_conf             999999999998299


No 105
>KOG4212 consensus
Probab=37.51  E-value=25  Score=14.43  Aligned_cols=60  Identities=22%  Similarity=0.294  Sum_probs=37.1

Q ss_pred             EEEECCCCCCCHHHHHHHHHHHHHHC--CCHHHHHHHHCCCC-CEEEEEEEECCCCCHHHHHHHHHHH
Q ss_conf             99952420021689999999986402--22134577640676-6058898504545889999987542
Q gi|254780353|r  268 IVVTEIPYQVQKSRLIEKIAELIIAK--RIPLLEDIRDESAE-DVRIVLFPKNRSLDPDLLMESIFML  332 (753)
Q Consensus       268 ivIteiPy~v~k~~~ie~I~~lv~~~--ki~gi~dirDeSd~-~~~~vi~~~~r~~~~~~vl~~Lyk~  332 (753)
                      ..||.|||.+.-.+    +.+||++|  .++-+.=+-|+|-+ .+.-||+.|. ..+.++-++.|-||
T Consensus        47 vfItNIpyd~rWqd----LKdLvrekvGev~yveLl~D~~GK~rGcavVEFk~-~E~~qKa~E~lnk~  109 (608)
T KOG4212          47 VFITNIPYDYRWQD----LKDLVREKVGEVEYVELLFDESGKARGCAVVEFKD-PENVQKALEKLNKY  109 (608)
T ss_pred             EEEECCCCHHHHHH----HHHHHHHHCCCEEEEEEECCCCCCCCCCEEEEEEC-HHHHHHHHHHHHHC
T ss_conf             78865753211376----99999974473586652013478857734798507-77899999986443


No 106
>cd00765 Pyrophosphate_PFK Phosphofructokinase, a key regulatory enzyme in glycolysis, catalyzes the phosphorylation of fructose-6-phosphate to fructose-1,6-biphosphate. The members belong to a subfamily of the PFKA family (cd00363) and include pyrophosphate-dependent phosphofructokinases. These are found in bacteria as well as plants. These may be dimeric nonallosteric enzymes as in bacteria or allosteric heterotetramers as in plants.
Probab=36.85  E-value=26  Score=14.36  Aligned_cols=86  Identities=20%  Similarity=0.210  Sum_probs=43.0

Q ss_pred             CCCCEEEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             67660588985045458899999875420000122331133312689722049999998999989999999999999999
Q gi|254780353|r  305 SAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAID  384 (753)
Q Consensus       305 Sd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~  384 (753)
                      |.+.--..|-+--|.++ +..|+-     .|||.  .|++.|.+.=.-+-++|.++.+.-+    ++|.+|...  .|-=
T Consensus       240 Sa~KYwHFIklMGRsaS-HiaLEc-----aLQTh--PNi~lI~EEv~~k~~TL~~Iv~~I~----d~I~~Ra~~--Gkny  305 (550)
T cd00765         240 STGKYWHFVKLMGRSAS-HIALEC-----ALKTH--PNICIISEEVSAQKQTLKNITDYMV----DVICKRAEL--GYNF  305 (550)
T ss_pred             CCCCEEEEEEEECCCCC-HHHHHH-----HHHCC--CCEEEEHHHHHHCCCCHHHHHHHHH----HHHHHHHHC--CCCC
T ss_conf             04760799998168610-788877-----66228--9899867998864796999999999----999999975--9986


Q ss_pred             HHHHHHHHHHHHHHHHHHHH
Q ss_conf             99999999998641078999
Q gi|254780353|r  385 RRVEILKGLLIAYLNIDEII  404 (753)
Q Consensus       385 ~RlhIleGl~~a~~~ID~vI  404 (753)
                      --.-|=|||+--+-.+-..|
T Consensus       306 GviLIPEGLiefIPe~k~Li  325 (550)
T cd00765         306 GVVLVPEGLIEFIPEVKELI  325 (550)
T ss_pred             EEEEECCHHHHHCHHHHHHH
T ss_conf             49995605887688899999


No 107
>pfam00416 Ribosomal_S13 Ribosomal protein S13/S18. This family includes ribosomal protein S13 from prokaryotes and S18 from eukaryotes.
Probab=36.73  E-value=26  Score=14.35  Aligned_cols=41  Identities=17%  Similarity=0.204  Sum_probs=33.2

Q ss_pred             CCCCCCCCCCCCHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             11000000257757788998-------878999988999976667899
Q gi|254780353|r  413 PKPVMVSRFSLTENQVDAIL-------NLRLRSLRKLEEYQIKSELDN  453 (753)
Q Consensus       413 ~k~~L~~~f~lse~QA~aIL-------~mrL~rLt~le~~kl~~E~~e  453 (753)
                      -..+|..-|++...+|.+|+       ++++..||.-|.++|.+..++
T Consensus        13 v~~ALt~I~GIG~~~A~~Ic~~lgi~~~~k~~~Lt~~qi~~l~~~i~~   60 (106)
T pfam00416        13 IEIALTYIKGIGRRKANQILKKAGVDKDKRVGELTEEEIDRIRDIISN   60 (106)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             644411210528999999999919597757154999999999999975


No 108
>COG2524 Predicted transcriptional regulator, contains C-terminal CBS domains [Transcription]
Probab=36.38  E-value=26  Score=14.31  Aligned_cols=91  Identities=18%  Similarity=0.213  Sum_probs=49.0

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCH
Q ss_conf             97046899999998689998980354053666542768874789999999610013216613267887088677971002
Q gi|254780353|r   50 FKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAY  129 (753)
Q Consensus        50 lKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~  129 (753)
                      |-|+||-||+|.-.|=-..++ ..|+- -+.++++ -||-       +.=++-|... -.-|++|.  -|-.+|=.|-.-
T Consensus         4 LT~~QkeIL~aLi~LY~~~~r-~IKge-eIA~~l~-rnpG-------TVRNqmq~Lk-aLgLVegv--pGPkGGY~PT~k   70 (294)
T COG2524           4 LTSSQKEILQALINLYRRKKR-PIKGE-EIAEVLN-RNPG-------TVRNQMQSLK-ALGLVEGV--PGPKGGYKPTSK   70 (294)
T ss_pred             CCHHHHHHHHHHHHHHHHCCC-CCCHH-HHHHHHC-CCCC-------HHHHHHHHHH-HCCCCCCC--CCCCCCCCCCHH
T ss_conf             218899999999999985378-85559-9999874-5961-------6999999988-52752256--689889653389


Q ss_pred             HHHHHHHHHHHHHHH--HHCCCCCCCCCCCC-CCCEEEE
Q ss_conf             468998559999998--42187861752167-9963242
Q gi|254780353|r  130 RYTEARMTQVAELIL--QGVDEDAVDFRDTY-NEEDSEP  165 (753)
Q Consensus       130 RYte~rl~~~~~~ll--~di~~~~v~~~~n~-D~~~~EP  165 (753)
                      -|          +.|  +.++.+  --+|+| ||...|-
T Consensus        71 AY----------e~L~iqt~~~~--~~Vpi~~~G~~v~~   97 (294)
T COG2524          71 AY----------EALSIQTLETE--FVVPIYKDGNVVED   97 (294)
T ss_pred             HH----------HHHCCCCCCCC--EEEEEEECCEEEEE
T ss_conf             99----------87445777751--48889876828501


No 109
>PHA02126 hypothetical protein
Probab=35.82  E-value=20  Score=15.26  Aligned_cols=51  Identities=31%  Similarity=0.457  Sum_probs=32.8

Q ss_pred             CCCCCCCCCCCHHHHHHHHHCCCCEEE-------EEEEEEEEECCCCCEEEEEECCCC
Q ss_conf             788776010698899989850334159-------999999864378840799952420
Q gi|254780353|r  225 DFPTGGIIVESRESIVESYRLGRGGFR-------VRARWCVEEVGRGSWCIVVTEIPY  275 (753)
Q Consensus       225 DFPTGG~i~~~~~~i~~~y~tG~G~i~-------~r~k~~~e~~~~~~~~ivIteiPy  275 (753)
                      ..|.|+.|+.+.+-|.++-..|-.+-+       .|-|+++|-+++----|.+||+|.
T Consensus        50 qlpggalivadrd~i~~~r~~~~nk~rmldtlsfcrdkmhfell~rppviif~t~~~~  107 (153)
T PHA02126         50 QLPGGALIVADRDIITSIRRAGGNKPRMLDTLSFCRDKMHFELLGRPPVIIFNTQTPL  107 (153)
T ss_pred             CCCCCEEEEECHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHCCCCEEEEECCCCH
T ss_conf             4898438995478899886236897425677887654466876189988999536756


No 110
>KOG2052 consensus
Probab=35.57  E-value=16  Score=15.88  Aligned_cols=16  Identities=19%  Similarity=0.164  Sum_probs=7.6

Q ss_pred             HHHHHHHHHHHHHHHH
Q ss_conf             9998899997666789
Q gi|254780353|r  437 RSLRKLEEYQIKSELD  452 (753)
Q Consensus       437 ~rLt~le~~kl~~E~~  452 (753)
                      -|||.|-+.|-..++.
T Consensus       489 aRltALriKKtl~~l~  504 (513)
T KOG2052         489 ARLTALRIKKTLAKLS  504 (513)
T ss_pred             HHHHHHHHHHHHHHHH
T ss_conf             4556788999999986


No 111
>COG3879 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=34.94  E-value=28  Score=14.15  Aligned_cols=65  Identities=14%  Similarity=0.267  Sum_probs=42.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHH----HHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCHHHHHHHHCCCCCC
Q ss_conf             999766678999988776544203978----8789999999999874177433455542000011000000110024566
Q gi|254780353|r  443 EEYQIKSELDNLLAEKEKIDSLLNSGK----QQWNQIACEIREVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKE  518 (753)
Q Consensus       443 e~~kl~~E~~eL~~~i~~L~~IL~s~~----~l~~iI~~EL~eikkkfgd~~~~~~RRT~iie~~~~~~~~~~EdlI~~E  518 (753)
                      |...+++...+|..+++.|++-++|-.    .-.+.|.++|..++..-|.-                        -+.-+
T Consensus        58 e~~s~Q~~~~~L~~ev~~~~~~~~s~~~~~~t~~~~ie~~l~~l~~~aG~v------------------------~V~G~  113 (247)
T COG3879          58 ELRSLQKKVNTLAAEVEDLENKLDSVRRSVLTDDAALEDRLEKLRMLAGSV------------------------PVTGP  113 (247)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCC------------------------CCCCC
T ss_conf             989999999999999999999998877767769999999999998885557------------------------77478


Q ss_pred             CCEEEEECCCEEE
Q ss_conf             7059987101020
Q gi|254780353|r  519 PITVVISNRGWIR  531 (753)
Q Consensus       519 ~v~V~LS~~GyIK  531 (753)
                      -++|||+..||.=
T Consensus       114 Gl~ITi~d~~~~~  126 (247)
T COG3879         114 GLVITIDDPGYSP  126 (247)
T ss_pred             CEEEEECCCCCCC
T ss_conf             5799965898786


No 112
>cd00225 API3 Ascaris pepsin inhibitor-3 (API3); protein inhibitor that reversibly inhibits aspartic proteinase cathepsin E, and gastric enzymes pepsin and gastricsin.
Probab=34.92  E-value=28  Score=14.15  Aligned_cols=42  Identities=17%  Similarity=0.275  Sum_probs=26.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHH
Q ss_conf             878999988999976667899998877654420397887899
Q gi|254780353|r  433 NLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQ  474 (753)
Q Consensus       433 ~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~i  474 (753)
                      ..+||.||.-|..++.+-.++...-.++++.+|..+.+-|+.
T Consensus        25 g~~lReLt~~Eq~Ela~y~~e~~~yK~~~k~~l~er~~~~~~   66 (159)
T cd00225          25 GFPLRELTPDEQQELAQYVEDVADYKEEVKQALKERQEGLKL   66 (159)
T ss_pred             CCCHHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             622221888899999999999999999999999999988887


No 113
>TIGR01090 apt adenine phosphoribosyltransferase; InterPro: IPR005764    Adenine phosphoribosyltransferase (APRTase, 2.4.2.7 from EC) is a widely distributed enzyme, and its deficiency in humans causes the accumulation of 2,8-dihydroxyadenine. It is the sole catalyst for adenine recycling in most eukaryotes.  AMP + diphosphate = adenine + 5-phospho-alpha-D-ribose 1-diphosphate  ; GO: 0003999 adenine phosphoribosyltransferase activity, 0006168 adenine salvage.
Probab=34.69  E-value=14  Score=16.33  Aligned_cols=49  Identities=22%  Similarity=0.370  Sum_probs=33.4

Q ss_pred             CHHHHHHHHHHHHHCCC--CCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             88999999999872865--320134432036778877601069889998985033415999
Q gi|254780353|r  195 NVQEICEAALALIDNPE--ISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVR  253 (753)
Q Consensus       195 nl~ev~~a~~~~i~~~~--~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r  253 (753)
                      -++.+|+.+...+++-+  ++.+    +|=|||=  =|-|. |   -.=||++|-|=+-||
T Consensus        30 ~f~~~id~l~~~~~~~~~~id~d----~iVG~Ea--RGFif-G---~~LA~~LgvGFVPVR   80 (175)
T TIGR01090        30 LFRFLIDLLVERYKDANGEIDAD----LIVGLEA--RGFIF-G---AALAYKLGVGFVPVR   80 (175)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCEE----EEECCCC--CHHHH-H---HHHHHHHCCCEEEEE
T ss_conf             89999999999998607951513----6876766--72577-8---899997089806754


No 114
>COG0241 HisB Histidinol phosphatase and related phosphatases [Amino acid transport and metabolism]
Probab=34.23  E-value=7.5  Score=18.39  Aligned_cols=72  Identities=19%  Similarity=0.409  Sum_probs=37.1

Q ss_pred             CCCCCCCCCEEEEEEECCC-------CCHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCC
Q ss_conf             7521679963242231234-------526764266504677775167778899999999987286532013443203677
Q gi|254780353|r  153 DFRDTYNEEDSEPVVFPSK-------FPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPD  225 (753)
Q Consensus       153 ~~~~n~D~~~~EP~~lp~~-------~P~lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPD  225 (753)
                      +|+.+.|.-.-+|-+.||.       +..+++---+|||.|+-|..   ++...-+.....+..-...++   .+.-+|+
T Consensus        22 ~yv~~~~~~~~~~g~i~al~~l~~~gy~lVvvTNQsGi~rgyf~~~---~f~~~~~~m~~~l~~~gv~id---~i~~Cph   95 (181)
T COG0241          22 DYVDSLDDFQFIPGVIPALLKLQRAGYKLVVVTNQSGIGRGYFTEA---DFDKLHNKMLKILASQGVKID---GILYCPH   95 (181)
T ss_pred             CCCCCHHHHCCCCCHHHHHHHHHHCCCEEEEEECCCCCCCCCCCHH---HHHHHHHHHHHHHHHCCCCCC---EEEECCC
T ss_conf             4338699912274589999998867976999987777556676689---999899999999997497036---4998788


Q ss_pred             CCCCC
Q ss_conf             88776
Q gi|254780353|r  226 FPTGG  230 (753)
Q Consensus       226 FPTGG  230 (753)
                      +|.++
T Consensus        96 ~p~~~  100 (181)
T COG0241          96 HPEDN  100 (181)
T ss_pred             CCCCC
T ss_conf             98777


No 115
>PRK03992 proteasome-activating nucleotidase; Provisional
Probab=34.22  E-value=28  Score=14.07  Aligned_cols=15  Identities=33%  Similarity=0.490  Sum_probs=6.8

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             999999999999999
Q gi|254780353|r  377 SFRMQAIDRRVEILK  391 (753)
Q Consensus       377 ~~~L~k~~~RlhIle  391 (753)
                      .+.+-..+.|.+|++
T Consensus       299 ~iplPd~~~R~~Ilk  313 (390)
T PRK03992        299 EVPLPDEEGRLEILK  313 (390)
T ss_pred             EECCCCHHHHHHHHH
T ss_conf             708949999999999


No 116
>KOG2264 consensus
Probab=34.20  E-value=28  Score=14.06  Aligned_cols=11  Identities=18%  Similarity=0.105  Sum_probs=6.4

Q ss_pred             CCCCCCEEEEE
Q ss_conf             16799632422
Q gi|254780353|r  156 DTYNEEDSEPV  166 (753)
Q Consensus       156 ~n~D~~~~EP~  166 (753)
                      |+-+..+.||-
T Consensus       163 P~~~pr~l~pp  173 (907)
T KOG2264         163 PLQIPRELEPP  173 (907)
T ss_pred             CCCCCCCCCCC
T ss_conf             55576568984


No 117
>pfam04849 HAP1_N HAP1 N-terminal conserved region. This family represents an N-terminal conserved region found in several huntingtin-associated protein 1 (HAP1) homologues. HAP1 binds to huntingtin in a polyglutamine repeat-length-dependent manner. However, its possible role in the pathogenesis of Huntington's disease is unclear. This family also includes a similar N-terminal conserved region from hypothetical protein products of ALS2CR3 genes found in the human juvenile amyotrophic lateral sclerosis critical region 2q33-2q34.
Probab=34.02  E-value=29  Score=14.04  Aligned_cols=45  Identities=16%  Similarity=0.348  Sum_probs=37.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             997666789999887765442039788789999999999874177
Q gi|254780353|r  444 EYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSK  488 (753)
Q Consensus       444 ~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd  488 (753)
                      +.+++...+.+..+-++|...|..-...-..+..||.+++++|..
T Consensus       244 i~dLq~r~k~l~~EnEEL~~~L~~~ke~Q~~L~~El~el~~rY~E  288 (307)
T pfam04849       244 IVDLQKKCKSYALENEELQQHLAAAKDAQRQLQAELQELQDKYAE  288 (307)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999988548999999999899899999999999999999


No 118
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=33.33  E-value=25  Score=14.44  Aligned_cols=14  Identities=36%  Similarity=0.527  Sum_probs=6.4

Q ss_pred             HHHCCCCCCHHHHH
Q ss_conf             87286532013443
Q gi|254780353|r  206 LIDNPEISIEKLLE  219 (753)
Q Consensus       206 ~i~~~~~~~~~l~~  219 (753)
                      +.+..++|.++|.+
T Consensus        31 l~~~~evTDEeiAe   44 (178)
T PRK06266         31 LIKKGEVTDEEIAE   44 (178)
T ss_pred             CCCCCCCCHHHHHH
T ss_conf             26546578999999


No 119
>KOG0771 consensus
Probab=33.26  E-value=29  Score=13.96  Aligned_cols=105  Identities=15%  Similarity=0.181  Sum_probs=48.2

Q ss_pred             CCCCCCCCCCCCCCEEEEEEE-ECC-CCEEEEEECCCCEEEEEHHHHHCCCCCCEEEEEEC---CCCCEEEEEECC--CC
Q ss_conf             442222357676530789998-579-98599997489789963887402333562788536---898056889618--98
Q gi|254780353|r  587 GEAIQLLIDLNHNQDIVTAFV-YDS-TCKLLVVSSKGNAFIVEESEIIANTRKGKTFLKVS---SEEKMKLVVKVT--GD  659 (753)
Q Consensus       587 G~pI~~ll~l~~~EkIv~~~~-~~~-~~~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk---~~D~li~v~~~~--~d  659 (753)
                      |-++...-+.+.+|.+-.+-- .++ ...+.+++..+.++++..-+.....+ + .+..+.   ..++-++...+.  |.
T Consensus       217 g~~~a~~t~~~k~~~~~~cRF~~d~~~~~l~laa~~~~~~~v~~~~~~~w~~-~-~~l~~~~~~~~~~siSsl~VS~dGk  294 (398)
T KOG0771         217 GAALARKTPFSKDEMFSSCRFSVDNAQETLRLAASQFPGGGVRLCDISLWSG-S-NFLRLRKKIKRFKSISSLAVSDDGK  294 (398)
T ss_pred             CCHHHHCCCCCCCHHHHHCEECCCCCCCEEEEEEECCCCCCEEEEEEEEECC-C-CCCCHHHHHHCCCCCEEEEECCCCC
T ss_conf             8602114876643043311101248775489998617888446887545326-6-4220112331257503688758884


Q ss_pred             EEEEEECCCCEEEEEHHHCCCC--C-HHH-C-CEEEECC
Q ss_conf             0999956993899557877833--6-121-4-1334218
Q gi|254780353|r  660 HVAVVGENRKLLIFSIDQIPEM--S-RGK-G-VRLQSYK  693 (753)
Q Consensus       660 ~iiliT~~Gk~LrF~~~eIr~~--g-Rgk-G-Vk~i~Lk  693 (753)
                      -+++.|..|-++.+...++...  - ++- | |.+..+-
T Consensus       295 f~AlGT~dGsVai~~~~~lq~~~~vk~aH~~~VT~ltF~  333 (398)
T KOG0771         295 FLALGTMDGSVAIYDAKSLQRLQYVKEAHLGFVTGLTFS  333 (398)
T ss_pred             EEEEECCCCCEEEEEECEEEEEEEEHHHHEEEEEEEEEC
T ss_conf             799860678589999000055675132402056668986


No 120
>PRK09458 pspB phage shock protein B; Provisional
Probab=33.18  E-value=29  Score=13.96  Aligned_cols=23  Identities=4%  Similarity=0.346  Sum_probs=17.3

Q ss_pred             HHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             66678999988776544203978
Q gi|254780353|r  447 IKSELDNLLAEKEKIDSLLNSGK  469 (753)
Q Consensus       447 l~~E~~eL~~~i~~L~~IL~s~~  469 (753)
                      +-+..+.+.++|+.|+.||+.+.
T Consensus        47 L~~~A~~m~eRI~tLE~ILDae~   69 (75)
T PRK09458         47 LTEKAEKMRERIQTLEAILDAEH   69 (75)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCC
T ss_conf             99999999999999999972669


No 121
>TIGR00185 rRNA_methyl_2 RNA methyltransferase, TrmH family, group 2; InterPro: IPR004440 The RNA methyltransferase, TrmH family, group 2 are part of the trmH (spoU) family of rRNA methylases that are involved in tRNA and rRNA base modification.; GO: 0008173 RNA methyltransferase activity, 0009451 RNA modification.
Probab=33.02  E-value=19  Score=15.31  Aligned_cols=40  Identities=23%  Similarity=0.340  Sum_probs=27.7

Q ss_pred             ECCCCCCCCCCC-CCCCCCCCCEEEEEECCCCC--EEEEECCC
Q ss_conf             025655445532-23455555401211114781--78980688
Q gi|254780353|r  531 RSLKSHSVDLSA-LHFKEGDSLKIALHAHTTDR--ILLLSTDG  570 (753)
Q Consensus       531 Kr~k~~~~~~~~-~~~KegD~l~~~~~~~t~d~--LLffTs~G  570 (753)
                      |+++|.+.+... +.+...+....++.+...++  |.+||.+|
T Consensus        42 K~L~RAGLdyw~fv~~~~H~s~E~fle~~~~~~~nlf~lT~~G   84 (161)
T TIGR00185        42 KRLKRAGLDYWEFVQLFYHKSWEEFLEAEKPQKGNLFLLTKKG   84 (161)
T ss_pred             CEEEECCCCCCCCEEEEECCCHHHHHHHCCCCCEEEEEEEECC
T ss_conf             1423147874452323562556888863389971688884038


No 122
>COG2949 SanA Uncharacterized membrane protein [Function unknown]
Probab=32.99  E-value=22  Score=14.83  Aligned_cols=77  Identities=27%  Similarity=0.349  Sum_probs=44.3

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHC--CCCCCHHHHHH-----HHHHHHCCHHHCCCCCCCCCCCCCCCCCC
Q ss_conf             046899999998689998980354053666542--76887478999-----99996100132166132678870886779
Q gi|254780353|r   52 PVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIG--KLHPHGDQSVY-----DSLVRLAQPFVQRYPLISGQGNFGNIDGD  124 (753)
Q Consensus        52 pvqRril~~m~~~~~~~~~~~~K~ar~vg~v~g--kyhPHGd~s~y-----~a~v~maq~~~~~~pli~g~GnfGs~~~d  124 (753)
                      -++|-|-|+-.  ++..+..-.=-+|-||-|+|  ||-+.|.--.|     +|.+.+=+.=+.+|.|+.|.  .++..-+
T Consensus        34 ~~dr~i~~~t~--~~i~~~~~~lP~r~vgvVLGtsky~~~g~~N~yy~~Ri~aA~~ly~~gKV~~LLlSGD--N~~~sYn  109 (235)
T COG2949          34 IADRWISWATA--GLIYDDIQDLPARQVGVVLGTSKYLAKGPPNRYYTYRIDAAIALYKAGKVNYLLLSGD--NATVSYN  109 (235)
T ss_pred             HHHHHHHHHHC--CCCCCCHHHCCCCCEEEEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCEEEEEEECC--CCCCCCC
T ss_conf             98788776534--7621685458862048997223002479955768999999999986477049998168--7753465


Q ss_pred             CCCCHHHH
Q ss_conf             71002468
Q gi|254780353|r  125 SAAAYRYT  132 (753)
Q Consensus       125 ~~Aa~RYt  132 (753)
                      .|-+|+=-
T Consensus       110 Ep~tM~kd  117 (235)
T COG2949         110 EPRTMRKD  117 (235)
T ss_pred             CHHHHHHH
T ss_conf             45899999


No 123
>TIGR02169 SMC_prok_A chromosome segregation protein SMC; InterPro: IPR011891   The SMC (structural maintenance of chromosomes) family of proteins, exist in virtually all organisms including both bacteria and archaea. The SMC proteins are essential for successful chromosome transmission during replication and segregation of the genome in all organisms and form three types of heterodimer (SMC1SMC3, SMC2SMC4, SMC5SMC6), which are core components of large multiprotein complexes. The best known complexes are cohesin, which is responsible for sister-chromatid cohesion, and condensin, which is required for full chromosome condensation in mitosis.     SMCs are generally present as single proteins in bacteria, and as at least six distinct proteins in eukaryotes. The proteins range in size from approximately 110 to 170 kDa, and share a five-domain structure, with globular N- and C-terminal (IPR003395 from INTERPRO) domains separated by a long (circa 100 nm or 900 residues) coiled coil segment in the centre of which is a globular ''hinge'' domain, characterised by a set of four highly conserved glycine residues that are typical of flexible regions in a protein. The amino-terminal domain contains a 'Walker A' nucleotide-binding domain (GxxGxGKS/T), which by mutational studies has been shown to be essential in several proteins. The carboxy-terminal domain contains a sequence (the DA-box) that resembles a 'Walker B' motif (XXXXD, where X is any hydrophobic residue), and a LSGG motif with homology to the signature sequence of the ATP-binding cassette (ABC) family of ATPases .    All SMC proteins appear to form dimers, either forming homodimers with themselves, as in the case of prokaryotic SMC proteins, or heterodimers between different but related SMC proteins. The dimers are arranged in an antiparallel alignment. This orientation brings the N- and C-terminal globular domains (from either different or identical protamers) together, which unites an ATP binding site (Walker A motif) within the N-terminal domain with a Walker B motif (DA box) within the C-terminal domain, to form a potentially functional ATPase. Protein interaction and microscopy data suggest that SMC dimers form a ring-like structure which might embrace DNA molecules. Non-SMC subunits associate with the SMC amino- and carboxy-terminal domains. The sequence homology within the carboxy-terminal domain is relatively high within the SMC1-SMC4 group, whereas SMC5 and SMC6 show some divergence in both of these sequences.   SMCs share not only sequence similarity but also structural similarity with ABC proteins. SMC proteins function together with other proteins in a range of chromosomal transactions, including chromosome condensation, sister-chromatid cohesion, recombination, DNA repair and epigenetic silencing of gene expression .    This family represents the SMC protein of archaea and a few bacteria (Aquifex, Synechocystis, etc); the SMC of other bacteria is described by IPR011890 from INTERPRO. The N- and C-terminal domains of this protein are well conserved, but the central hinge region is skewed in composition and highly divergent ..
Probab=32.90  E-value=30  Score=13.92  Aligned_cols=57  Identities=12%  Similarity=0.147  Sum_probs=32.1

Q ss_pred             CCEEEEEECCC-CCEEEEEC-CCEEEEEEHH-HCC--C-----CCCCCCCCCCCCCCCCCCEEEEEE
Q ss_conf             54012111147-81789806-8827875511-212--1-----234444222235767653078999
Q gi|254780353|r  550 SLKIALHAHTT-DRILLLST-DGKAYTLPAG-NLL--S-----GRGHGEAIQLLIDLNHNQDIVTAF  606 (753)
Q Consensus       550 ~l~~~~~~~t~-d~LLffTs-~GkvY~l~a~-~Ip--s-----~~~kG~pI~~ll~l~~~EkIv~~~  606 (753)
                      |+..+-..|.| .+|.-+=| .|..+-+--. +=|  +     .+.+|.|+..+=.|+.|||=++++
T Consensus      1057 F~~aF~~IN~~f~~iF~~LSP~G~g~L~Le~PdDPF~GGl~l~a~P~~K~vqrleAMSGGEKSLtAL 1123 (1202)
T TIGR02169      1057 FMEAFEAINENFKEIFAELSPGGTGELILENPDDPFAGGLELKAKPKGKPVQRLEAMSGGEKSLTAL 1123 (1202)
T ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCEEEECCCCCCCCCCCCEEEEEECCCCEEEHHHCCCCHHHHHHH
T ss_conf             9999999999999999853889824654358887436871788873788502022103838999999


No 124
>TIGR00018 panC pantoate--beta-alanine ligase; InterPro: IPR003721 D-Pantothenate is synthesized via four enzymes from ketoisovalerate, which is an intermediate of branched-chain amino acid synthesis . Pantoate-beta-alanine ligase, also know as pantothenate synthase, (6.3.2.1 from EC) catalyzes the formation of pantothenate from pantoate and alanine in the pantothenate biosynthesis pathway .; GO: 0004592 pantoate-beta-alanine ligase activity, 0015940 pantothenate biosynthetic process.
Probab=32.64  E-value=24  Score=14.61  Aligned_cols=99  Identities=26%  Similarity=0.392  Sum_probs=53.2

Q ss_pred             CCCCEEEEEHHHHHH--HCCCCCCHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             989803540536665--427688747899999996100132166132678870886779710024689985599999984
Q gi|254780353|r   68 FGAAFKKSARIVGEV--IGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQ  145 (753)
Q Consensus        68 ~~~~~~K~ar~vg~v--~gkyhPHGd~s~y~a~v~maq~~~~~~pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~  145 (753)
                      ..++|+|+   ||-|  ||..| .|-.|+-+-.+.=+-- .-=.-.|+|- +||--. |=.+=||=.|-=+.     +++
T Consensus        19 ~eGrfrk~---vGfVPTMG~LH-~GH~sL~~~a~~End~-vvvSIFVNP~-QFgp~E-Dl~~YPR~l~~D~~-----l~E   86 (310)
T TIGR00018        19 REGRFRKT---VGFVPTMGALH-EGHLSLIDRAVKENDL-VVVSIFVNPL-QFGPNE-DLEAYPRDLEEDLA-----LLE   86 (310)
T ss_pred             HCCCEEEE---EECCCCCCCHH-HHHHHHHHHHHHHCCE-EEEEEEECCC-CCCCCC-CHHHCCCCHHHHHH-----HHH
T ss_conf             16850123---31226731015-6789999999866885-8999975787-888875-45445798589999-----998


Q ss_pred             HCCCCCCCCCCCC-----CCC-----EEEEEEECCC-CCHHHHCCC
Q ss_conf             2187861752167-----996-----3242231234-526764266
Q gi|254780353|r  146 GVDEDAVDFRDTY-----NEE-----DSEPVVFPSK-FPNLLANGT  180 (753)
Q Consensus       146 di~~~~v~~~~n~-----D~~-----~~EP~~lp~~-~P~lL~Ng~  180 (753)
                      .+.=+.| |.|+-     +|.     ++.-.++|.+ +-.. +-|+
T Consensus        87 ~lgVd~~-FaP~~~~mYP~~~PldieE~~~~~~~p~~ls~~-LeGa  130 (310)
T TIGR00018        87 KLGVDVV-FAPKVHEMYPDGAPLDIEEQKTTVLVPKALSEV-LEGA  130 (310)
T ss_pred             HCCCCEE-ECCCCEEECCCCCCCCCCCCEEEEECCCCCCCC-CCCC
T ss_conf             3896588-557214407886232113754478617654100-1678


No 125
>KOG1302 consensus
Probab=32.55  E-value=30  Score=13.88  Aligned_cols=32  Identities=25%  Similarity=0.393  Sum_probs=18.5

Q ss_pred             CCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHC
Q ss_conf             2897046899999998689998980354053666542
Q gi|254780353|r   48 DGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIG   84 (753)
Q Consensus        48 DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~g   84 (753)
                      -|++++-||-|...-+-  .|+   +|+-=+--+.||
T Consensus        15 ~~lq~~a~~eL~~lLds--~pG---~K~lvlD~dL~~   46 (600)
T KOG1302          15 QGLQEVARRELISLLDS--LPG---KKELVLDPDLMG   46 (600)
T ss_pred             HHHHHHHHHHHHHHHHC--CCC---CEEEEECCCCCC
T ss_conf             88799999999999964--898---615886300156


No 126
>cd07603 BAR_ACAPs The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. This subfamily is composed of ACAPs (ArfGAP with Coiled-coil, ANK repeat and PH domain containing proteins), which are Arf GTPase activating proteins (GAPs) containing an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. Vertebrates contain at least three members, ACAP1, ACAP2, and ACAP3. ACAP1 and ACAP2 are Arf6-specific GAPs, involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration, by mediating Arf6 signaling. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=32.45  E-value=30  Score=13.87  Aligned_cols=35  Identities=11%  Similarity=0.193  Sum_probs=13.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             78899887899998899997666789999887765
Q gi|254780353|r  427 QVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKI  461 (753)
Q Consensus       427 QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L  461 (753)
                      |++.++--||.++.+-++...++..+...+..++|
T Consensus        83 q~~~~v~~pL~~f~k~dl~~vKe~KK~FdK~s~~y  117 (200)
T cd07603          83 QAQRTVSTQLQNFVKEDIKKVKESKKHFEKISDDL  117 (200)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999973689999888999878889


No 127
>cd04585 CBS_pair_ACT_assoc2 This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains in  the acetoin utilization proteins in bacteria. Acetoin is a product of fermentative metabolism in many prokaryotic and eukaryotic microorganisms.  They produce acetoin as an external carbon storage compound and then later reuse it as a carbon and energy source during their stationary phase and sporulation. In addition these CBS domains are associated with a downstream ACT domain, which is linked to a wide range of metabolic enzymes that are regulated by amino acid concentration. Pairs of ACT domains bind specifically to a particular amino acid leading to regulation of the linked enzyme. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The i
Probab=31.18  E-value=32  Score=13.72  Aligned_cols=39  Identities=21%  Similarity=0.368  Sum_probs=18.3

Q ss_pred             HHHHHHCCCCC---CHHHHHHHHHHHHCCHHHCCCCCCCCCCC
Q ss_conf             36665427688---74789999999610013216613267887
Q gi|254780353|r   78 IVGEVIGKLHP---HGDQSVYDSLVRLAQPFVQRYPLISGQGN  117 (753)
Q Consensus        78 ~vg~v~gkyhP---HGd~s~y~a~v~maq~~~~~~pli~g~Gn  117 (753)
                      -|+++|- -+|   +.|.++++|+-.|.+.--.+.|.+|.+|.
T Consensus        68 ~v~~im~-~~~~tv~~~~~l~~a~~~m~~~~i~~lpVvd~~g~  109 (122)
T cd04585          68 KVSDIMT-RDPITVSPDASVEEAAELMLERKISGLPVVDDQGR  109 (122)
T ss_pred             CHHHHCC-CCCEEEECCCCHHHHHHHHHHCCCCEEEEEECCCE
T ss_conf             9999577-89889938866999999998759878999958998


No 128
>pfam10985 DUF2805 Protein of unknown function (DUF2805). This is a bacterial family of proteins with unknown function.
Probab=31.14  E-value=31  Score=13.79  Aligned_cols=33  Identities=24%  Similarity=0.466  Sum_probs=22.2

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             789999752000011000000257757788998
Q gi|254780353|r  400 IDEIIAIIRNEDKPKPVMVSRFSLTENQVDAIL  432 (753)
Q Consensus       400 ID~vI~iIR~s~~~k~~L~~~f~lse~QA~aIL  432 (753)
                      ||+||+.-=+-..|-+++...|+|+|.|...|.
T Consensus         1 i~riIeMAweDrt~FeaI~~~~gl~E~eVi~lM   33 (73)
T pfam10985         1 ISRIIEMAWEDRTPFEAIERQFGLSEKEVIKLM   33 (73)
T ss_pred             CHHHHHHHHCCCCCHHHHHHHHCCCHHHHHHHH
T ss_conf             939999998269989999999895999999999


No 129
>COG3546 Mn-containing catalase [Inorganic ion transport and metabolism]
Probab=31.08  E-value=24  Score=14.58  Aligned_cols=30  Identities=20%  Similarity=0.247  Sum_probs=20.2

Q ss_pred             CCCCCCCCCCCHHHHHHHHHHH---HHHHHHHC
Q ss_conf             0886779710024689985599---99998421
Q gi|254780353|r  118 FGNIDGDSAAAYRYTEARMTQV---AELILQGV  147 (753)
Q Consensus       118 fGs~~~d~~Aa~RYte~rl~~~---~~~ll~di  147 (753)
                      ||-.+|.-+|||||..-+++--   ..+||.||
T Consensus        29 lGG~~GElsaamqYl~Q~fn~r~~~~~dll~DI   61 (277)
T COG3546          29 LGGAFGELSAAMQYLFQGFNVRDAKYKDLLMDI   61 (277)
T ss_pred             HCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             679624799999998753466753799999986


No 130
>TIGR01882 peptidase-T peptidase T; InterPro: IPR010161   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This entry represents metallopeptidases belonging to MEROPS peptidase family M20 (clan MH), subfamily M20B. They are tripeptide aminopeptidases commonly known as Peptidase T, which have a substrate preference for hydrophobic peptides.; GO: 0008270 zinc ion binding, 0016285 cytosol alanyl aminopeptidase activity, 0045148 tripeptide aminopeptidase activity, 0006518 peptide metabolic process, 0005737 cytoplasm.
Probab=31.02  E-value=32  Score=13.70  Aligned_cols=58  Identities=34%  Similarity=0.545  Sum_probs=37.4

Q ss_pred             HCCCCCCC--CCCCCCCCEE------EEEEECCCCCHHHH--------------CCC---CCHHHHHHHHCCCCCHHHHH
Q ss_conf             21878617--5216799632------42231234526764--------------266---50467777516777889999
Q gi|254780353|r  146 GVDEDAVD--FRDTYNEEDS------EPVVFPSKFPNLLA--------------NGT---SGIAVGMATSIPSHNVQEIC  200 (753)
Q Consensus       146 di~~~~v~--~~~n~D~~~~------EP~~lp~~~P~lL~--------------Ng~---~GIavG~at~ipphnl~ev~  200 (753)
                      |..-+-|.  -..||||..+      |=+.=|-.||||==              -||   +|||             |+.
T Consensus        87 DFn~enVnPQI~enYDGes~i~lgd~eftLdP~~fPnL~~YKGqTlittdGtTLLG~d~K~Gia-------------EiM  153 (413)
T TIGR01882        87 DFNAENVNPQILENYDGESVIQLGDLEFTLDPEDFPNLKKYKGQTLITTDGTTLLGADDKAGIA-------------EIM  153 (413)
T ss_pred             CCCCCCCCCCEEECCCCCCEEEECCEEEEECCCCCCCCCCCCCCEEEECCCCCCCCCCCCCCHH-------------HHH
T ss_conf             2256787775520368850455065017627221764225887678851686111665334288-------------999


Q ss_pred             HHHHHHHH-CCCCCCHH
Q ss_conf             99999872-86532013
Q gi|254780353|r  201 EAALALID-NPEISIEK  216 (753)
Q Consensus       201 ~a~~~~i~-~~~~~~~~  216 (753)
                      -+.-+||+ +|++.--+
T Consensus       154 T~adYL~~ihPe~kHG~  170 (413)
T TIGR01882       154 TLADYLLNIHPEVKHGK  170 (413)
T ss_pred             HHHHHHHHCCCCCCCCE
T ss_conf             99999850489610373


No 131
>pfam00465 Fe-ADH Iron-containing alcohol dehydrogenase.
Probab=30.74  E-value=32  Score=13.67  Aligned_cols=17  Identities=18%  Similarity=0.137  Sum_probs=5.6

Q ss_pred             CCCCCHHHHHHHHHHHH
Q ss_conf             67778899999999987
Q gi|254780353|r  191 IPSHNVQEICEAALALI  207 (753)
Q Consensus       191 ipphnl~ev~~a~~~~i  207 (753)
                      +.||-..|-++.+....
T Consensus        59 v~~~p~~~~v~~~~~~~   75 (312)
T pfam00465        59 VEPNPTLEEVDEAAAAA   75 (312)
T ss_pred             CCCCCCHHHHHHHHHHH
T ss_conf             27999999999999999


No 132
>cd06231 Peptidase_M14-like_4 A functionally uncharacterized subgroup of the M14 family of metallocarboxypeptidases (MCPs). The M14 family are zinc-binding carboxypeptidases (CPs) which hydrolyze single, C-terminal amino acids from polypeptide chains, and have a recognition site for the free C-terminal carboxyl group, which is a key determinant of specificity. Two major subfamilies of the M14 family, defined based on sequence and structural homology, are the A/B and N/E subfamilies. Enzymes belonging to the A/B subfamily are normally synthesized as inactive precursors containing preceding signal peptide, followed by an N-terminal pro-region linked to the enzyme; these proenzymes are called procarboxypeptidases. The A/B enzymes can be further divided based on their substrate specificity; Carboxypeptidase A-like (CPA-like) enzymes favor hydrophobic residues while carboxypeptidase B-like (CPB-like) enzymes only cleave the basic residues lysine or arginine. The A forms have slightly differe
Probab=30.11  E-value=12  Score=16.90  Aligned_cols=119  Identities=14%  Similarity=0.109  Sum_probs=58.5

Q ss_pred             HHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHCC-----CCCCCCCCCC-CCC---C--
Q ss_conf             6899999998689998980354053666542768874789999999610013216-----6132678870-886---7--
Q gi|254780353|r   54 HRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQR-----YPLISGQGNF-GNI---D--  122 (753)
Q Consensus        54 qRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~maq~~~~~-----~pli~g~Gnf-Gs~---~--  122 (753)
                      ++..||++.-.+-.++   +.+.=|.|-|-| |-|-|-.++.+=+-..|.+|.-+     +|+|.+.|-= +++   +  
T Consensus        26 ~~ypL~~~~s~~~~~~---~P~vLItgGvHG-~E~aGv~gaL~fL~~~a~~~~~~~nl~v~PcvnP~Gye~~~R~N~~g~  101 (236)
T cd06231          26 QSYPLYALKSRGWDSD---LPRVLITAGIHG-DEPAGPLGALEFLRAAALELAQDVNLSVYPCINPSGFEAITRWNRNGI  101 (236)
T ss_pred             CCCCEEEEECCCCCCC---CCEEEEECCCCC-CCCCHHHHHHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCCCCC
T ss_conf             4363689954776788---985999524146-665228999999998889874477389996428110222454686456


Q ss_pred             --------CCCCCCHHHHHHHHHHHH--HHHHHHCCCCCCCCCCCCCCCEEEEEEECCCCCHHHHCC
Q ss_conf             --------797100246899855999--999842187861752167996324223123452676426
Q gi|254780353|r  123 --------GDSAAAYRYTEARMTQVA--ELILQGVDEDAVDFRDTYNEEDSEPVVFPSKFPNLLANG  179 (753)
Q Consensus       123 --------~d~~Aa~RYte~rl~~~~--~~ll~di~~~~v~~~~n~D~~~~EP~~lp~~~P~lL~Ng  179 (753)
                              +.++.-.|+...-+....  -.+.=|+-+ |++ .+-+|.++-.|. +|++.=.-++++
T Consensus       102 DpNRsF~~~sp~~E~~~l~~~~~~~~~~~~~~idLHE-d~~-s~dty~yefrpa-~aaRdg~~~~~~  165 (236)
T cd06231         102 DPNRSFRSESPSPEVRLLMEWLRRLGAAFDLHIDLHE-DTE-STDTYNYEFRPA-LAARDGLPARAW  165 (236)
T ss_pred             CCCHHHCCCCCCHHHHHHHHHHHHCCCCEEEEEEECC-CCC-CCCCCCEEECCC-CCCCCCHHHHHC
T ss_conf             8314431489618999999999863887458998056-788-788111024765-456645233312


No 133
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=29.83  E-value=33  Score=13.56  Aligned_cols=14  Identities=21%  Similarity=0.256  Sum_probs=4.4

Q ss_pred             HHHHHHHHHHHHHH
Q ss_conf             97666789999887
Q gi|254780353|r  445 YQIKSELDNLLAEK  458 (753)
Q Consensus       445 ~kl~~E~~eL~~~i  458 (753)
                      +.++.|.+++.++|
T Consensus        45 e~Lr~erN~iSK~I   58 (422)
T PRK05431         45 EELQAERNALSKEI   58 (422)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999999


No 134
>KOG1684 consensus
Probab=29.79  E-value=23  Score=14.79  Aligned_cols=57  Identities=19%  Similarity=0.139  Sum_probs=25.8

Q ss_pred             CCHHHHHHHHHHHHCCHHHCCCCCCCCCCCCC---CCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             87478999999961001321661326788708---867797100246899855999999842
Q gi|254780353|r   88 PHGDQSVYDSLVRLAQPFVQRYPLISGQGNFG---NIDGDSAAAYRYTEARMTQVAELILQG  146 (753)
Q Consensus        88 PHGd~s~y~a~v~maq~~~~~~pli~g~GnfG---s~~~d~~Aa~RYte~rl~~~~~~ll~d  146 (753)
                      -|=+-++|-.++-..++-  .+-+|--.|+-|   +-+||-.|+.+-.-.+=++.+...|.+
T Consensus        64 leMv~~~~~~L~~we~s~--~~k~vIlkgs~~raFCAGgDI~~~ae~~~d~~~~~~~~fF~~  123 (401)
T KOG1684          64 LEMVLSIYPKLVEWEKSP--LVKLVILKGSGGRAFCAGGDIKAVAESIKDKETPEVKKFFTE  123 (401)
T ss_pred             HHHHHHHHHHHHHHCCCC--CCEEEEEECCCCCEEECCCCHHHHHHHHHCCCCHHHHHHHHH
T ss_conf             888998899887540277--721899916898601458657889887624895588999999


No 135
>KOG1954 consensus
Probab=29.77  E-value=33  Score=13.55  Aligned_cols=74  Identities=18%  Similarity=0.295  Sum_probs=52.1

Q ss_pred             HHCCCCCCHHHHHHHHHHHHCCHH-HC--------CCCCCCCCCCC-CCCCCCC-CCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             542768874789999999610013-21--------66132678870-8867797-1002468998559999998421878
Q gi|254780353|r   82 VIGKLHPHGDQSVYDSLVRLAQPF-VQ--------RYPLISGQGNF-GNIDGDS-AAAYRYTEARMTQVAELILQGVDED  150 (753)
Q Consensus        82 v~gkyhPHGd~s~y~a~v~maq~~-~~--------~~pli~g~Gnf-Gs~~~d~-~Aa~RYte~rl~~~~~~ll~di~~~  150 (753)
                      .||.|- -|-++.---|  +-|+| ++        -+-.+-+|||= ||++|.. ++-++|++..|++++..++.-    
T Consensus        63 l~GqyS-tGKTtfi~yL--le~dypg~riGpEPTtd~Fi~vM~G~~e~~ipGnal~vd~~~pF~gL~~FG~aflnR----  135 (532)
T KOG1954          63 LVGQYS-TGKTTFIRYL--LEQDYPGLRIGPEPTTDRFIAVMHGDEEGSIPGNALVVDAKKPFRGLNKFGNAFLNR----  135 (532)
T ss_pred             EEECCC-CCHHHHHHHH--HHCCCCCCCCCCCCCCCEEEEEEECCCCCCCCCCEEEECCCCCHHHHHHHHHHHHHH----
T ss_conf             972466-6603999998--717787554689997530689985586566678625646877516566667999998----


Q ss_pred             CCCCCCCCCCCEEEEEEECCCCCHHHHC
Q ss_conf             6175216799632422312345267642
Q gi|254780353|r  151 AVDFRDTYNEEDSEPVVFPSKFPNLLAN  178 (753)
Q Consensus       151 ~v~~~~n~D~~~~EP~~lp~~~P~lL~N  178 (753)
                                      ..++++||-++-
T Consensus       136 ----------------f~csqmp~~vLe  147 (532)
T KOG1954         136 ----------------FMCSQLPNQVLE  147 (532)
T ss_pred             ----------------HHHHCCCHHHHH
T ss_conf             ----------------877338756550


No 136
>cd04600 CBS_pair_HPP_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the HPP motif domain. These proteins are integral membrane proteins with four transmembrane spanning helices. The function of these proteins is uncertain, but they are thought to be transporters. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=29.71  E-value=33  Score=13.54  Aligned_cols=31  Identities=19%  Similarity=0.434  Sum_probs=19.0

Q ss_pred             HHHHHHHHHHHCCHHHCCCCCCCCCCCC-CCC
Q ss_conf             7899999996100132166132678870-886
Q gi|254780353|r   91 DQSVYDSLVRLAQPFVQRYPLISGQGNF-GNI  121 (753)
Q Consensus        91 d~s~y~a~v~maq~~~~~~pli~g~Gnf-Gs~  121 (753)
                      |+++.+|+-.|.+.--..+|.+|.+|.+ |-+
T Consensus        10 ~~tl~~a~~~m~~~~~~~lpVvd~~g~lvGii   41 (124)
T cd04600          10 DTSLEEAWALLRRHRIKALPVVDGDRRLVGIV   41 (124)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEEECCCCEEEEE
T ss_conf             39799999999972997899995698088885


No 137
>TIGR02171 Fb_sc_TIGR02171 Fibrobacter succinogenes paralogous family TIGR02171.
Probab=29.62  E-value=33  Score=13.53  Aligned_cols=111  Identities=11%  Similarity=0.138  Sum_probs=59.4

Q ss_pred             CCCCCEEEEECCCEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEEECCCEEEEEEHHHCCCCCCCCCCCCCCCC
Q ss_conf             56670599871010202565544553223455555401211114781789806882787551121212344442222357
Q gi|254780353|r  516 EKEPITVVISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPAGNLLSGRGHGEAIQLLID  595 (753)
Q Consensus       516 ~~E~v~V~LS~~GyIKr~k~~~~~~~~~~~KegD~l~~~~~~~t~d~LLffTs~GkvY~l~a~~Ips~~~kG~pI~~ll~  595 (753)
                      .++.|-+.|+++|-=|.+=..==|.+|..|=.       ..=.+|.+||+.+++|+...-=+.  |++-          .
T Consensus       514 gEQACNaSLakDGs~RTLFLDFGG~TG~~Fvg-------~kYgvHERlLVaDS~GkLV~~vaa--P~Gy----------t  574 (982)
T TIGR02171       514 GEQACNASLAKDGSKRTLFLDFGGSTGRAFVG-------QKYGVHERLLVADSKGKLVRAVAA--PAGY----------T  574 (982)
T ss_pred             CCHHHCCCHHCCCCCCEEEEECCCCCCHHHHC-------CCCCCEEEEEEECCCCCEEEEECC--CCCC----------C
T ss_conf             21020001320776732688568861045404-------775102244563147761332267--8888----------8


Q ss_pred             CCCCCEEEEEEEECCCCEEEE--EECCCCEEEEEHHHHHCCCCCCEEEEEECCCCCE
Q ss_conf             676530789998579985999--9748978996388740233356278853689805
Q gi|254780353|r  596 LNHNQDIVTAFVYDSTCKLLV--VSSKGNAFIVEESEIIANTRKGKTFLKVSSEEKM  650 (753)
Q Consensus       596 l~~~EkIv~~~~~~~~~~lll--~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~D~l  650 (753)
                      ++--|=|.+|+..+.....+.  +-.+|-=+|+-|=++..     ..++.|-|+|+|
T Consensus       575 FDHtEWV~GmlnGe~~N~aVAtLtn~nGaH~KiALiNl~~-----~~v~eLVEGdEL  626 (982)
T TIGR02171       575 FDHTEWVLGMLNGERSNLAVATLTNVNGAHKKIALINLSD-----SKVTELVEGDEL  626 (982)
T ss_pred             CCCHHHEEEEECCCCCCEEEEEEECCCCCCCEEEEEECCC-----CCEEEEECCCCC
T ss_conf             4411320212147885479996626866643488998378-----847998616877


No 138
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family; InterPro: IPR014243    This entry represents a set of transcription factors found in some endospore-forming bacteria within the Firmicutes (low-GC Gram-positive bacteria). In some species these proteins are encoded multiple times. The best characterised protein in this entry is the prespore-specific transcription factor RsfA from Bacillus subtilis, previously known as YwfN. Expression of RsfA is controlled by sigma factor F, and it seems to improve the efficiency of sporulation by fine-tuning the expression of genes in the sigma F regulon, particularly the timing of their expression . It also negatively regulates spoIIR and its own synthesis. A paralog in B. subtilis is designated YlbO, though its function is not known. A highly variable linker region separates two very strongly conserved sequence regions within the protein. .
Probab=29.54  E-value=33  Score=13.52  Aligned_cols=105  Identities=18%  Similarity=0.282  Sum_probs=63.7

Q ss_pred             HHHHH-HHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHH
Q ss_conf             99989-9999999999999999-999999999864107899997520000110000002577577889988789999889
Q gi|254780353|r  365 LAHRR-EVLFRRSSFRMQAIDR-RVEILKGLLIAYLNIDEIIAIIRNEDKPKPVMVSRFSLTENQVDAILNLRLRSLRKL  442 (753)
Q Consensus       365 ~~~R~-~vi~rr~~~~L~k~~~-RlhIleGl~~a~~~ID~vI~iIR~s~~~k~~L~~~f~lse~QA~aIL~mrL~rLt~l  442 (753)
                      |.||= -+|+++++-.++.|++ |.|---.--..-.-|..||....+-.+.                   ...+.+|- .
T Consensus        47 CGFRWNa~VRk~Y~~aI~lAKK~RK~~KRak~~~~lTl~~VI~FLq~~~~~-------------------~~~~~~l~-~  106 (163)
T TIGR02894        47 CGFRWNAVVRKRYEEAIELAKKQRKERKRAKKAESLTLQDVISFLQNLKTT-------------------NPSDQALQ-K  106 (163)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHH-------------------HHHHHHHH-H
T ss_conf             025335787585899999998861478864378626878899999998887-------------------79999999-8


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             99976667899998877654420397887899999999998741774
Q gi|254780353|r  443 EEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKS  489 (753)
Q Consensus       443 e~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~  489 (753)
                      |.++|.+|...|++++++|++=|..-......|.++-..+.+...-.
T Consensus       107 E~~~L~~~~~~Lq~~ne~L~~el~~L~~~~~~~eEDY~~L~~IMdRA  153 (163)
T TIGR02894       107 ENERLKKELESLQKRNEELEKELEKLEKRQSTIEEDYETLIDIMDRA  153 (163)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             99999999999999999999999999998467899999999999887


No 139
>TIGR01511 ATPase-IB1_Cu copper-translocating P-type ATPase; InterPro: IPR006403   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.   P-ATPases (sometime known as E1-E2 ATPases) (3.6.3.- from EC) are found in bacteria and in a number of eukaryotic plasma membranes and organelles . P-ATPases function to transport a variety of different compounds, including ions and phospholipids, across a membrane using ATP hydrolysis for energy. There are many different classes of P-ATPases, each of which transports a specific type of ion: H^+, Na^+, K^+, Mg^2+, Ca^2+, Ag^+ and Ag^2+, Zn^2+, Co^2+, Pb^2+, Ni^2+, Cd^2+, Cu^+ and Cu^2+. P-ATPases can be composed of one or two polypeptides, and can usually assume two main conformations called E1 and E2.   This entry represents P-type ATPases that specialise in cation and copper transport; those transporting copper (3.6.3.4 from EC) have been classified as belonging to the IB subfamily , , . These proteins are involved in a variety of processes in both prokaryotes and eukaryotes. Some of these P-ATPases import copper into cells, such as in Arabidopsis sp., which require copper to create functional hormone receptors for ethylene signalling. Other P-ATPases are involved in copper export out of cells, such as occurs with the efflux of hepatic copper into the bile in eukaryotes. In bacteria, some of these P-ATPases play a role in osmotic adaptation. Certain copper ATPases have been implicated in both Wilson and Menkes diseases .   More information about this protein can be found at Protein of the Month: ATP Synthases .; GO: 0004008 copper-exporting ATPase activity, 0005524 ATP binding, 0046872 metal ion binding, 0046873 metal ion transmembrane transporter activity, 0030001 metal ion transport, 0016020 membrane.
Probab=29.19  E-value=34  Score=13.48  Aligned_cols=131  Identities=17%  Similarity=0.304  Sum_probs=80.5

Q ss_pred             CCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCC--------CEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHH
Q ss_conf             5320134432036778877601069889998985033--------41599999998643788407999524200216899
Q gi|254780353|r  211 EISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGR--------GGFRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRL  282 (753)
Q Consensus       211 ~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~--------G~i~~r~k~~~e~~~~~~~~ivIteiPy~v~k~~~  282 (753)
                      ++...|.++.-||--+|+=|+|+.|.+.+.|.--||-        |.-.+=|....    .|.=.+-+|..+    +..+
T Consensus        93 ~l~~GD~~~V~pG~k~PvDG~v~~G~S~vDES~~TGEs~PV~K~~Gd~ViaGt~N~----~G~L~~~~t~~g----~~t~  164 (545)
T TIGR01511        93 ELQPGDIVKVLPGEKIPVDGTVIEGESEVDESLVTGESLPVPKKVGDTVIAGTVNG----TGSLVVKATKVG----EDTT  164 (545)
T ss_pred             HCCCCCEEEECCCCCCCCCCEEECCCCEEHHHHHCCCCCCEECCCCCEEEEEEEEC----CCEEEEEEEECC----CCCH
T ss_conf             41888889975789564040785132022245555888665027888799988846----848999998417----7660


Q ss_pred             HHHHHHHHHHCCCH--HHHHHHHCCCCCEEEEEEEECCCCCHHH----HHHHHHHHCCCCCCCCCCEEEEECCCCCCCCC
Q ss_conf             99999986402221--3457764067660588985045458899----99987542000012233113331268972204
Q gi|254780353|r  283 IEKIAELIIAKRIP--LLEDIRDESAEDVRIVLFPKNRSLDPDL----LMESIFMLSDMETRFPLNMNVLSMGRVPQVMP  356 (753)
Q Consensus       283 ie~I~~lv~~~ki~--gi~dirDeSd~~~~~vi~~~~r~~~~~~----vl~~Lyk~T~Lq~sf~~N~~~l~~~~~P~~~~  356 (753)
                      +-+|.++|++-+-.  -|..+-|-=           .+=..|-+    ++-.+.=.+.|+...++ | ++-   +|=-||
T Consensus       165 La~I~~lv~~AQ~~Ka~~~~lADk~-----------a~~fvP~v~~~A~~Tf~~W~~Al~~avtV-l-iIA---CPCALG  228 (545)
T TIGR01511       165 LAQIVELVRQAQQSKAPIQRLADKV-----------AGYFVPVVIAIAILTFVIWLFALETAVTV-L-IIA---CPCALG  228 (545)
T ss_pred             HHHHHHHHHHHHHCCCHHHHHHHHH-----------HHHHHHHHHHHHHHHHHHHHHHHHHHHHE-E-EEE---CCCHHH
T ss_conf             8999999999840281156889999-----------99999999999999999999999875113-5-774---667004


Q ss_pred             HHHHHHHHH
Q ss_conf             999999899
Q gi|254780353|r  357 LDGILKEWL  365 (753)
Q Consensus       357 l~eil~~f~  365 (753)
                      |=-=+-..+
T Consensus       229 LA~Ptv~~V  237 (545)
T TIGR01511       229 LATPTVIMV  237 (545)
T ss_pred             HHHHHHHHH
T ss_conf             799999999


No 140
>cd04617 CBS_pair_4 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic genera
Probab=29.12  E-value=20  Score=15.24  Aligned_cols=27  Identities=19%  Similarity=0.341  Sum_probs=12.2

Q ss_pred             HHHHHHHHHHHHCCHHHCCCCCCCCCC
Q ss_conf             478999999961001321661326788
Q gi|254780353|r   90 GDQSVYDSLVRLAQPFVQRYPLISGQG  116 (753)
Q Consensus        90 Gd~s~y~a~v~maq~~~~~~pli~g~G  116 (753)
                      -|.++++|+-.|.+.---+.|.+|..|
T Consensus        75 pd~~v~~A~~~M~~~~i~~LPVVd~~~  101 (118)
T cd04617          75 PEESVLEAAKKLIEHQVDSLPVVEKVD  101 (118)
T ss_pred             CCCCHHHHHHHHHHCCCCEECEEECCC
T ss_conf             999399999999982999856794399


No 141
>KOG0207 consensus
Probab=28.72  E-value=34  Score=13.42  Aligned_cols=85  Identities=18%  Similarity=0.386  Sum_probs=56.8

Q ss_pred             CHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCC--------CCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHH
Q ss_conf             013443203677887760106988999898503--------341599999998643788407999524200216899999
Q gi|254780353|r  214 IEKLLEYIIGPDFPTGGIIVESRESIVESYRLG--------RGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEK  285 (753)
Q Consensus       214 ~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG--------~G~i~~r~k~~~e~~~~~~~~ivIteiPy~v~k~~~ie~  285 (753)
                      ..++.+..||--+|.-|.++.|...+.+-.-||        +|+..+-|....    +|.-.+-.|-.|=...    +.+
T Consensus       399 ~gdivkV~pG~kiPvDG~Vv~Gss~VDEs~iTGEs~PV~Kk~gs~ViaGsiN~----nG~l~VkaT~~g~dtt----la~  470 (951)
T KOG0207         399 VGDIVKVKPGEKIPVDGVVVDGSSEVDESLITGESMPVPKKKGSTVIAGSINL----NGTLLVKATKVGGDTT----LAQ  470 (951)
T ss_pred             CCCEEEECCCCCCCCCCEEEECCEEECHHHCCCCCEECCCCCCCEEEEEEECC----CCEEEEEEEECCCCCH----HHH
T ss_conf             18889988898236662899574563053404873004567898566456658----8459999873466354----999


Q ss_pred             HHHHHHHCC---CHHHHHHHHCCCC
Q ss_conf             999864022---2134577640676
Q gi|254780353|r  286 IAELIIAKR---IPLLEDIRDESAE  307 (753)
Q Consensus       286 I~~lv~~~k---i~gi~dirDeSd~  307 (753)
                      |..||++-.   -+ |..+.|.-..
T Consensus       471 IvkLVEEAQ~sKap-iQq~aDkia~  494 (951)
T KOG0207         471 IVKLVEEAQLSKAP-IQQLADKIAG  494 (951)
T ss_pred             HHHHHHHHHCCCCH-HHHHHHHHHH
T ss_conf             99999998706630-8889998651


No 142
>COG5290 IkappaB kinase complex, IKAP component [Transcription]
Probab=28.64  E-value=35  Score=13.42  Aligned_cols=20  Identities=15%  Similarity=0.037  Sum_probs=12.1

Q ss_pred             CCCEEECCHHHHHHHHHHHH
Q ss_conf             24566531999999888888
Q gi|254780353|r   14 EENVKAVSLRFALEERYLAY   33 (753)
Q Consensus        14 ~~~i~~~~i~~~~~~~y~~y   33 (753)
                      .+.|..+.+...|...+-.|
T Consensus       357 ~~~I~~V~f~~k~~~~~s~~  376 (1243)
T COG5290         357 GERILRVFFSEKKTHHGSEY  376 (1243)
T ss_pred             CCEEEEEEEEHHHHCCCCCC
T ss_conf             87389998314440388656


No 143
>COG2312 Erythromycin esterase homolog [General function prediction only]
Probab=28.51  E-value=15  Score=16.08  Aligned_cols=47  Identities=30%  Similarity=0.456  Sum_probs=31.3

Q ss_pred             EEEHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCC--CCCCCCCHH
Q ss_conf             540536665427688747899999996100132166132678870886--779710024
Q gi|254780353|r   74 KSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQRYPLISGQGNFGNI--DGDSAAAYR  130 (753)
Q Consensus        74 K~ar~vg~v~gkyhPHGd~s~y~a~v~maq~~~~~~pli~g~GnfGs~--~~d~~Aa~R  130 (753)
                      +-+|||+  +|-=- ||+..+|.+=+||-+.      ||+-+| |+++  .-|.|.+++
T Consensus        43 ~~~RiV~--LGE~s-HGt~e~~~~k~rm~r~------Lvee~G-f~~iA~EA~~~d~~a   91 (405)
T COG2312          43 TDARIVL--LGEPS-HGTGEFFAFKARMFRA------LVEELG-FRAIAFEADFPDAQA   91 (405)
T ss_pred             CCCEEEE--ECCCC-CCCCHHHHHHHHHHHH------HHHHHC-CCEEEECCCCHHHHH
T ss_conf             6773898--43777-7740789999999999------999838-626874168377888


No 144
>cd03823 GT1_ExpE7_like This family is most closely related to the GT1 family of glycosyltransferases. ExpE7 in Sinorhizobium meliloti has been shown to be involved in the biosynthesis of galactoglucans (exopolysaccharide II).
Probab=28.32  E-value=35  Score=13.38  Aligned_cols=15  Identities=7%  Similarity=0.138  Sum_probs=6.9

Q ss_pred             HHHHHHHCCHHHHHH
Q ss_conf             765442039788789
Q gi|254780353|r  459 EKIDSLLNSGKQQWN  473 (753)
Q Consensus       459 ~~L~~IL~s~~~l~~  473 (753)
                      +.+..+|+++++..+
T Consensus       321 ~ai~~ll~d~~~~~~  335 (359)
T cd03823         321 AALERLIDDPDLLER  335 (359)
T ss_pred             HHHHHHHCCHHHHHH
T ss_conf             999999849999999


No 145
>TIGR02483 PFK_mixed phosphofructokinase; InterPro: IPR012829    Members of this family that are characterised, save one, are phosphofructokinases dependent on pyrophosphate (2.7.1.90 from EC) rather than ATP (2.7.1.11 from EC). The exception is one of three phosphofructokinases from Streptomyces coelicolor. Family members are both bacterial and archaeal.; GO: 0005524 ATP binding, 0008443 phosphofructokinase activity, 0006002 fructose 6-phosphate metabolic process, 0006096 glycolysis.
Probab=28.22  E-value=35  Score=13.36  Aligned_cols=29  Identities=28%  Similarity=0.565  Sum_probs=23.1

Q ss_pred             CCEEEEEECCCCCCCHHHHHHHHHHHHHHCC
Q ss_conf             8407999524200216899999999864022
Q gi|254780353|r  264 GSWCIVVTEIPYQVQKSRLIEKIAELIIAKR  294 (753)
Q Consensus       264 ~~~~ivIteiPy~v~k~~~ie~I~~lv~~~k  294 (753)
                      |-..|.|=|+||.++  +++++|.+.-..+|
T Consensus       199 GAd~ILIPE~P~d~~--~v~~~v~~r~~~G~  227 (339)
T TIGR02483       199 GADVILIPEIPFDID--SVCEKVRERFARGK  227 (339)
T ss_pred             CCCEEEECCCCCCHH--HHHHHHHHHHHCCC
T ss_conf             876789786048889--99999999987266


No 146
>cd04793 LanC LanC is the cyclase enzyme of the lanthionine synthetase. Lanthinoine is a lantibiotic, a unique class of peptide antibiotics. They are ribosomally synthesized as precursor peptides and then post-translationally modified to contain thioether cross-links called lanthionines (Lans) or methyllanthionines (MeLans) in addition to  2,3-didehydroalanine (Dha) and (Z)-2,3-didehydrobutyrine (Dhb). These unusual amino acids are introduced by the dehydration of serine and threonine residues, followed by thioether formation via addition of cysteine thiols, catalysed by LanB and LanC or LanM. LanC, the cyclase component, is a zinc metalloprotein, whose bound metal has been proposed to activate the thiol substrate for nucleophilic addition.
Probab=27.94  E-value=35  Score=13.34  Aligned_cols=33  Identities=21%  Similarity=0.245  Sum_probs=20.1

Q ss_pred             HHCCCCCHHHHHHHHCCCC--CHHHHHHHHHHHHH
Q ss_conf             6426650467777516777--88999999999872
Q gi|254780353|r  176 LANGTSGIAVGMATSIPSH--NVQEICEAALALID  208 (753)
Q Consensus       176 L~Ng~~GIavG~at~ipph--nl~ev~~a~~~~i~  208 (753)
                      +++|.+||+.-+-....++  -+..|.+.+..+.+
T Consensus       103 ~i~G~sGi~~yLL~~~~~~~~~~~~i~~~L~~l~~  137 (382)
T cd04793         103 VISGLSGIGRYLLLRHEPDSELLREILDYLVYLTE  137 (382)
T ss_pred             CCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             12778999999985046781689999999999998


No 147
>pfam05565 Sipho_Gp157 Siphovirus Gp157. This family contains both viral and bacterial proteins which are related to the Gp157 protein of the Streptococcus thermophilus SFi bacteriophages. It is thought that bacteria possessing the gene coding for this protein have an increased resistance to the bacteriophage.
Probab=27.80  E-value=36  Score=13.31  Aligned_cols=71  Identities=18%  Similarity=0.110  Sum_probs=28.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCHHHHHHHHCCCCCCCC
Q ss_conf             999766678999988776544203978878999999999987417743345554200001100000011002456670
Q gi|254780353|r  443 EEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKEPI  520 (753)
Q Consensus       443 e~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v  520 (753)
                      +.+-+.+|.+.|.+..+.++.       ...-+++.|....+.-|...--..--|.-+-.......+.+|+.||++-+
T Consensus        55 ~~~~~k~e~krl~erkk~~en-------k~~~LK~yl~~~m~~~g~~kikt~~~tis~rk~~~sv~I~de~~iP~ey~  125 (162)
T pfam05565        55 DIEAIKAEIKRLAERKKSIEN-------KVKRLKDYLEEAMEATGIKKIKTPLFTVSIRKSKPSVEIEDEAKIPAEYF  125 (162)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHCCCCEEECCCEEEEEECCCCCEECCCHHHCCHHHH
T ss_conf             899999999999999999998-------99999999999999809867763767999737899132489566889985


No 148
>PRK06321 replicative DNA helicase; Provisional
Probab=27.79  E-value=36  Score=13.31  Aligned_cols=21  Identities=5%  Similarity=0.186  Sum_probs=10.6

Q ss_pred             HHHHHHHHHHHHHHHHHCCCC
Q ss_conf             887899999999998741774
Q gi|254780353|r  469 KQQWNQIACEIREVKEIFSKS  489 (753)
Q Consensus       469 ~~l~~iI~~EL~eikkkfgd~  489 (753)
                      ......|...|+.+.+.++-|
T Consensus       361 ~~~i~~isr~lK~lAkel~vp  381 (472)
T PRK06321        361 QTEISEISRMLKNLARELNIP  381 (472)
T ss_pred             HHHHHHHHHHHHHHHHHHCCC
T ss_conf             999999999999999997997


No 149
>cd03805 GT1_ALG2_like This family is most closely related to the GT1 family of glycosyltransferases.  ALG2, a 1,3-mannosyltransferase, in yeast catalyzes the mannosylation of Man(2)GlcNAc(2)-dolichol diphosphate and Man(1)GlcNAc(2)-dolichol diphosphate to form Man(3)GlcNAc(2)-dolichol diphosphate. A deficiency of this enzyme causes an abnormal accumulation of Man1GlcNAc2-PP-dolichol and Man2GlcNAc2-PP-dolichol, which is associated with a type of congenital disorders of glycosylation (CDG), designated CDG-Ii, in humans.
Probab=27.76  E-value=30  Score=13.89  Aligned_cols=28  Identities=29%  Similarity=0.146  Sum_probs=13.0

Q ss_pred             HHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             6544203978878999999999987417
Q gi|254780353|r  460 KIDSLLNSGKQQWNQIACEIREVKEIFS  487 (753)
Q Consensus       460 ~L~~IL~s~~~l~~iI~~EL~eikkkfg  487 (753)
                      .+..+|.|++...+.=.+=..-++++|+
T Consensus       357 ~i~~ll~d~~lr~~mg~~ar~~v~~~Fs  384 (392)
T cd03805         357 AMLKLANDPDLADRMGAAGRKRVKEKFS  384 (392)
T ss_pred             HHHHHHCCHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999978999999999999999998669


No 150
>TIGR01037 pyrD_sub1_fam dihydroorotate dehydrogenase family protein; InterPro: IPR005720   Dihydroorotate dehydrogenase (1.3.3.1 from EC) (DHOdehase) catalyzes the fourth step in the de novo biosynthesis of pyrimidine, the conversion of dihydroorotate into orotate. DHOdehase is a ubiquitous FAD flavoprotein. In bacteria (gene pyrD), DHOdease is located on the inner side of the cytosolic membrane. In some yeasts, such as in Saccharomyces cerevisiae (gene URA1, subfamily 2), it is a cytosolic protein while in other eukaryotes it is found in the mitochondria .    This describes dihydroorotate dehydrogenases subfamily 1 that includes a number of uncharacterised proteins and a domain of dihydropyrimidine dehydrogenase.; GO: 0004158 dihydroorotate oxidase activity, 0006207 'de novo' pyrimidine base biosynthetic process, 0005737 cytoplasm.
Probab=27.04  E-value=33  Score=13.55  Aligned_cols=102  Identities=19%  Similarity=0.279  Sum_probs=62.6

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEEEEEECCCCCEEEEEECCCCCC-------CHH--HHHHHHHHHHHHCC
Q ss_conf             778877601069889998985033415999999986437884079995242002-------168--99999999864022
Q gi|254780353|r  224 PDFPTGGIIVESRESIVESYRLGRGGFRVRARWCVEEVGRGSWCIVVTEIPYQV-------QKS--RLIEKIAELIIAKR  294 (753)
Q Consensus       224 PDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~~~e~~~~~~~~ivIteiPy~v-------~k~--~~ie~I~~lv~~~k  294 (753)
                      |=|+--|..=.+.+.++-+++.|=|.++..+--.-|..++..  =-|-|+|++.       |..  ++.++         
T Consensus        13 P~~lASG~~G~~~~~l~~~~~~gaGAVvTKs~g~~pr~Gy~n--PtiVE~~~G~lNAiGL~NPG~e~fl~E---------   81 (308)
T TIGR01037        13 PVILASGVMGSGVEALRRIDRSGAGAVVTKSIGLEPRPGYRN--PTIVEVPCGLLNAIGLQNPGVEAFLEE---------   81 (308)
T ss_pred             CCEEECCCCCCCHHHHHHHHCCCCCEEEECCEECCCCCCCCC--CEEEECCCCEEEECCCCCHHHHHHHHH---------
T ss_conf             610221103662889998750588637862133158885443--807981785575235898217999986---------


Q ss_pred             CHHHHHHHHCCCC-CEEEEEEEECCCCCHHHH---HHHHH---H-HCCCCCCCCC
Q ss_conf             2134577640676-605889850454588999---99875---4-2000012233
Q gi|254780353|r  295 IPLLEDIRDESAE-DVRIVLFPKNRSLDPDLL---MESIF---M-LSDMETRFPL  341 (753)
Q Consensus       295 i~gi~dirDeSd~-~~~~vi~~~~r~~~~~~v---l~~Ly---k-~T~Lq~sf~~  341 (753)
                         +.++++|-++ ++|+++=.-  +.++|..   -.+|=   + ---+|-+.||
T Consensus        82 ---~~~~~~e~~t~dvr~I~svy--G~~~EEfa~va~~~e~A~~y~~~~ELN~SC  131 (308)
T TIGR01037        82 ---LKDVREEVPTHDVRLIASVY--GESEEEFAEVAEKLEDADPYVDAYELNVSC  131 (308)
T ss_pred             ---HHHHHHCCCCCCEEEEEEEC--CCCCHHHHHHHHHHHHHHHHHEEEECCCCC
T ss_conf             ---32566438987528999831--888225899999872113440000104777


No 151
>cd04603 CBS_pair_KefB_assoc This cd contains two tandem repeats of the cystathionine beta-synthase (CBS pair) domains associated with the KefB (Kef-type K+ transport systems) domain which is involved in inorganic ion transport and metabolism. CBS is a small domain originally identified in cystathionine beta-synthase and subsequently found in a wide range of different proteins. CBS domains usually come in tandem repeats, which associate to form a so-called Bateman domain or a CBS pair which is reflected in this model. The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown.
Probab=26.94  E-value=26  Score=14.40  Aligned_cols=81  Identities=21%  Similarity=0.185  Sum_probs=52.6

Q ss_pred             HHHHHHHHHH---CCCCCCCCCCCHHH----HHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCC---CCHHHHHHHHHHH
Q ss_conf             8888999851---04764112897046----899999998689998980354053666542768---8747899999996
Q gi|254780353|r   31 LAYALSTIKE---RAIPDLRDGFKPVH----RRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLH---PHGDQSVYDSLVR  100 (753)
Q Consensus        31 ~~ya~~vi~~---Ralpd~~DGlKpvq----Rril~~m~~~~~~~~~~~~K~ar~vg~v~gkyh---PHGd~s~y~a~v~  100 (753)
                      |.-|+..+.+   ||+|=|-++.||+-    +-+|-.      .++.   -+---|+++|- .-   -|-|+++.||+-.
T Consensus        12 L~~a~~~~~e~~~~~i~VVD~~~k~vG~it~~Dll~~------~~~~---~~~~~V~d~m~-~~v~~i~~~~~v~dalr~   81 (111)
T cd04603          12 LREAIKMINELGARAVVVVDEENKVLGQVTLSDLLEI------GPND---YETLKVCEVYI-VPVPIVYCDSKVTDLLRI   81 (111)
T ss_pred             HHHHHHHHHHCCCCEEEEECCCCCEEEEEEHHHHHHH------CHHH---HHCCCHHHHHC-CCCCCCCCCCCHHHHHHH
T ss_conf             9999999987699768998899968899889998643------8445---53243877515-677463899768999999


Q ss_pred             HCCHHHCCCCCCCCCCCC-CCC
Q ss_conf             100132166132678870-886
Q gi|254780353|r  101 LAQPFVQRYPLISGQGNF-GNI  121 (753)
Q Consensus       101 maq~~~~~~pli~g~Gnf-Gs~  121 (753)
                      |.|.-.-+.|.+|+.|.| |.+
T Consensus        82 ~~~~~~~~l~VVD~~grlvGiI  103 (111)
T cd04603          82 FRETEPPVVAVVDKEGKLVGTI  103 (111)
T ss_pred             HHHCCCCEEEEECCCCCEEEEE
T ss_conf             8744998899993899799999


No 152
>KOG2280 consensus
Probab=26.71  E-value=37  Score=13.18  Aligned_cols=36  Identities=14%  Similarity=-0.006  Sum_probs=15.9

Q ss_pred             EECCCCCHHHHCCCCCHHHHHHHHCCC---CCHHHHHHHHHHHHH
Q ss_conf             312345267642665046777751677---788999999999872
Q gi|254780353|r  167 VFPSKFPNLLANGTSGIAVGMATSIPS---HNVQEICEAALALID  208 (753)
Q Consensus       167 ~lp~~~P~lL~Ng~~GIavG~at~ipp---hnl~ev~~a~~~~i~  208 (753)
                      -+|. +|+..++-     .-|+..=|+   |-+-+|..+....+.
T Consensus       162 ~~~d-iP~~~~~~-----~~Wt~~~~~~~~~~ll~v~~~v~~~~~  200 (829)
T KOG2280         162 KMPD-IPYNELPK-----SCWTVFQPHRQSTILLDVDVAVGLHIC  200 (829)
T ss_pred             HCCC-CCCCCCCC-----CCEEEECCCCCCEEEEEECHHHHCCCC
T ss_conf             1799-99766897-----522773698764256652123221300


No 153
>pfam10168 Nup88 Nuclear pore component. Nup88 can be divided into two structural domains; the N-terminal two-thirds of the protein has no obvious structural motifs but is the region for binding to Nup98, one of the components of the nuclear pore. the C-terminal end is a predicted coiled-coil domain. Nup88 is overexpressed in tumour cells.
Probab=26.66  E-value=37  Score=13.17  Aligned_cols=68  Identities=19%  Similarity=0.237  Sum_probs=31.0

Q ss_pred             CHHHHHH---HHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHCCCCCCCCCCCCC-CCCHH
Q ss_conf             4999999---8999-98999999999999999999999999998----64107899997520000110000002-57757
Q gi|254780353|r  356 PLDGILK---EWLA-HRREVLFRRSSFRMQAIDRRVEILKGLLI----AYLNIDEIIAIIRNEDKPKPVMVSRF-SLTEN  426 (753)
Q Consensus       356 ~l~eil~---~f~~-~R~~vi~rr~~~~L~k~~~RlhIleGl~~----a~~~ID~vI~iIR~s~~~k~~L~~~f-~lse~  426 (753)
                      +-.|.++   .=.+ ||.+.+.|...-+ +.+++|.+.|.....    -+..+.+-.+.|++   -...|.++| .++++
T Consensus       533 s~~E~leLL~qAtqvlReeyl~khd~ar-eEi~kRV~~L~~qK~~QL~eL~~l~eer~~l~e---~Ae~LAekyEei~dk  608 (717)
T pfam10168       533 PPEECLQLLSRATQVFREQYLLKHDLAR-EEFQRRVKLLQLQKEKQLEDIQDCREERKSLSE---RAEKLAEKFEEAKYN  608 (717)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHH
T ss_conf             9899999999999999999988889999-999999999999999999999999999999999---999999998887887


Q ss_pred             H
Q ss_conf             7
Q gi|254780353|r  427 Q  427 (753)
Q Consensus       427 Q  427 (753)
                      |
T Consensus       609 Q  609 (717)
T pfam10168       609 Q  609 (717)
T ss_pred             H
T ss_conf             9


No 154
>TIGR02895 spore_sigI RNA polymerase sigma-I factor; InterPro: IPR014244   The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes.   With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognized by the major sigma factors , .    This entry represents the transcription factor Sigma-I. This protein is found in endospore-forming species in the Firmicutes lineage of bacteria, such as Bacillus subtilis, but is not universally present among such species. Sigma-I was shown to be induced by heat shock  in B. subtilis and is suggested by its phylogenetic profile to be connected to the program of sporulation .; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, 0006355 regulation of transcription DNA-dependent.
Probab=26.64  E-value=37  Score=13.17  Aligned_cols=80  Identities=23%  Similarity=0.288  Sum_probs=60.1

Q ss_pred             HHHHHHHCCCC--CCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHH
Q ss_conf             99997520000--1100000025775778899887899998899997666789999887765442039788789999999
Q gi|254780353|r  402 EIIAIIRNEDK--PKPVMVSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEI  479 (753)
Q Consensus       402 ~vI~iIR~s~~--~k~~L~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL  479 (753)
                      .||.-||....  .-.-|.+.|.=+|.|++--|+|.+.    +|.-+-+-|...-..||.++++.|.    +|++--.||
T Consensus        76 r~IDy~R~n~k~~~~~~l~e~y~n~E~~~~~~~~~~~~----~e~y~~~i~~~~RrlEILey~~~L~----~f~I~f~eL  147 (225)
T TIGR02895        76 RVIDYIRKNQKYKNLVYLDEDYDNSEENDENSLEIKVS----LEEYKNEIENENRRLEILEYKKLLK----QFGIEFVEL  147 (225)
T ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHH----HHHHHHHHHHHHHHHHHHHHHHHHH----HHCCCHHHH
T ss_conf             98888874111221167677656403577548999999----9999987588866899999999998----738707687


Q ss_pred             HHHHHHCCCC
Q ss_conf             9998741774
Q gi|254780353|r  480 REVKEIFSKS  489 (753)
Q Consensus       480 ~eikkkfgd~  489 (753)
                      -+..=|+.|.
T Consensus       148 v~~SPKH~d~  157 (225)
T TIGR02895       148 VKVSPKHRDA  157 (225)
T ss_pred             HCCCCCHHHH
T ss_conf             4107776889


No 155
>cd04629 CBS_pair_16 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=26.57  E-value=23  Score=14.68  Aligned_cols=31  Identities=26%  Similarity=0.495  Sum_probs=19.9

Q ss_pred             HHHHHHHHHHHCCHHHCCCCCCCCCCCC-CCC
Q ss_conf             7899999996100132166132678870-886
Q gi|254780353|r   91 DQSVYDSLVRLAQPFVQRYPLISGQGNF-GNI  121 (753)
Q Consensus        91 d~s~y~a~v~maq~~~~~~pli~g~Gnf-Gs~  121 (753)
                      |+++++|+-.|++.--...|.+|.+|.+ |-+
T Consensus         9 ~~tl~~a~~~m~~~~~~~~pVvd~~~~lvGii   40 (114)
T cd04629           9 DMSVTEAVEKLLKSKISGGPVVDDNGNLVGFL   40 (114)
T ss_pred             CCCHHHHHHHHHHHCCCEEEEECCCCEEEEEE
T ss_conf             29999999999971997899994899299999


No 156
>PRK02304 adenine phosphoribosyltransferase; Provisional
Probab=26.40  E-value=25  Score=14.45  Aligned_cols=49  Identities=27%  Similarity=0.492  Sum_probs=27.7

Q ss_pred             CCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEE
Q ss_conf             7889999999998728653201344320367788776010698899989850334159999
Q gi|254780353|r  194 HNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRA  254 (753)
Q Consensus       194 hnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~  254 (753)
                      .-+.++++.+.....+.++      .+|-|+|  ..|.+. +   -.=+|+.|.|-+.+|=
T Consensus        33 ~~~~~~~~~l~~~~~~~~v------D~IvgiE--arGfi~-a---~alA~~l~~p~v~iRK   81 (174)
T PRK02304         33 EALREVIDALVERYKDADI------DKIVGIE--ARGFIF-G---AALAYKLGIGFVPVRK   81 (174)
T ss_pred             HHHHHHHHHHHHHHCCCCC------CEEEEEC--CCCEEC-C---HHHHHHHCCCEEEEEC
T ss_conf             9999999999998434899------8999986--555210-1---5889982998799972


No 157
>pfam06374 NDUF_C2 NADH-ubiquinone oxidoreductase subunit b14.5b (NDUFC2). This family consists of several NADH-ubiquinone oxidoreductase subunit b14.5b proteins (EC:1.6.5.3).
Probab=26.33  E-value=36  Score=13.31  Aligned_cols=41  Identities=24%  Similarity=0.457  Sum_probs=29.4

Q ss_pred             CCCCCCCCCCCCCEEEEEEECC--CC-CHHHHCCCCCHHHHHHHHCCCCC
Q ss_conf             7861752167996324223123--45-26764266504677775167778
Q gi|254780353|r  149 EDAVDFRDTYNEEDSEPVVFPS--KF-PNLLANGTSGIAVGMATSIPSHN  195 (753)
Q Consensus       149 ~~~v~~~~n~D~~~~EP~~lp~--~~-P~lL~Ng~~GIavG~at~ipphn  195 (753)
                      .+...|.||      |...||+  .. |+++--|..|..+||-+|---|-
T Consensus         5 ~~pl~~lpd------ea~~LppP~i~np~~~~~G~~G~~~al~~N~~~rR   48 (117)
T pfam06374         5 NDPLEFLPD------EARSLPPPKLWDPRLIACGLLGYCSGLFDNWGRRR   48 (117)
T ss_pred             CCCCCCCCC------CCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             877354884------22448897654764224358999999998876248


No 158
>TIGR00977 LeuA_rel 2-isopropylmalate synthase/homocitrate synthase family protein; InterPro: IPR005675    This model represents largely uncharacterised proteins related to 2-isopropylmalate synthases and homocitrate synthases but phylogenetically distinct. ; GO: 0046912 transferase activity transferring acyl groups acyl groups converted into alkyl on transfer, 0019752 carboxylic acid metabolic process.
Probab=26.33  E-value=38  Score=13.13  Aligned_cols=207  Identities=25%  Similarity=0.365  Sum_probs=109.1

Q ss_pred             HHH-HHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHHHCCHHHC
Q ss_conf             888-8889998510476411289704689999999868999898035405366654276887478999999961001321
Q gi|254780353|r   29 RYL-AYALSTIKERAIPDLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLAQPFVQ  107 (753)
Q Consensus        29 ~y~-~ya~~vi~~Ralpd~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~maq~~~~  107 (753)
                      +|| .|+-.||.|-  -+--||-|-=.-.-|-++.- ....++.+-=-+-.=|-++    ||   .|++-.-..-+.+. 
T Consensus       129 ~YLk~~~~~VIyDA--EHfFDGYkaN~eYAL~~L~~-A~~aGAdwlVlcDTNGGTL----P~---~I~EI~~~Vk~~~g-  197 (543)
T TIGR00977       129 AYLKRYADEVIYDA--EHFFDGYKANPEYALKTLKV-AEKAGADWLVLCDTNGGTL----PH---EIEEITKKVKKSLG-  197 (543)
T ss_pred             HHHHHHCCEEEEEC--CCCCCCCCCCHHHHHHHHHH-HHHCCCCEEEEEECCCCCC----CH---HHHHHHHHHHHHHC-
T ss_conf             99987212256302--00246345786899999999-9846982899950787998----50---47899999998617-


Q ss_pred             CCCCCCCCC----CCCCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCC--CCCCCCEEEEEEECCCCCHHHHCCC
Q ss_conf             661326788----70886-7797100246899855999999842187861752--1679963242231234526764266
Q gi|254780353|r  108 RYPLISGQG----NFGNI-DGDSAAAYRYTEARMTQVAELILQGVDEDAVDFR--DTYNEEDSEPVVFPSKFPNLLANGT  180 (753)
Q Consensus       108 ~~pli~g~G----nfGs~-~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~--~n~D~~~~EP~~lp~~~P~lL~Ng~  180 (753)
                          +|||.    |.|=- -.|+-.|          +|+.|+. ..+..+.-.  =|==|...=-.-||+.+|||-+-  
T Consensus       198 ----ldg~sdk~p~lGIHAHNDS~~A----------VANsL~A-V~~GA~~V~GTING~GER~GNANLCs~IPNL~LK--  260 (543)
T TIGR00977       198 ----LDGQSDKDPQLGIHAHNDSETA----------VANSLLA-VEAGATQVQGTINGLGERCGNANLCSVIPNLQLK--  260 (543)
T ss_pred             ----CCCCCCCCCCCCEEEECCCHHH----------HHHHHHH-HHHCCCEECCEECCCCCCCCCCCHHHHCCCHHHH--
T ss_conf             ----7865556766652555563078----------9999999-9734315422042555565764111110010210--


Q ss_pred             CCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEEE---
Q ss_conf             50467777516777889999999998728653201344320367788776010698899989850334159999999---
Q gi|254780353|r  181 SGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWC---  257 (753)
Q Consensus       181 ~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~~---  257 (753)
                          .||- -||+-||..+.+.....-+=-+....+=|.|+=---|                 . -||.|.+.|.-.   
T Consensus       261 ----l~~d-vI~~E~L~~L~~~a~lvaEi~n~~~~~~~PyVG~~AF-----------------A-HKGGvHvSAv~r~p~  317 (543)
T TIGR00977       261 ----LGYD-VIPKENLKKLTEVARLVAEIVNLPLDENMPYVGESAF-----------------A-HKGGVHVSAVKRNPK  317 (543)
T ss_pred             ----CCCC-CCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCC-----------------C-CCCCEEEEEEECCCC
T ss_conf             ----2664-5686667889989999999854885346782366322-----------------0-258657765505887


Q ss_pred             -EE----ECCCCCEEEEEECCCCCCCHHHHHHHHHHH
Q ss_conf             -86----437884079995242002168999999998
Q gi|254780353|r  258 -VE----EVGRGSWCIVVTEIPYQVQKSRLIEKIAEL  289 (753)
Q Consensus       258 -~e----~~~~~~~~ivIteiPy~v~k~~~ie~I~~l  289 (753)
                       .|    ++-.++..|+|.|+   ..++.+++|+.+.
T Consensus       318 TYEHI~P~LVGN~R~I~vSe~---aG~SNvl~K~~~~  351 (543)
T TIGR00977       318 TYEHIDPELVGNKRKIVVSEL---AGKSNVLEKLKEF  351 (543)
T ss_pred             CCCCCCCCCCCCEEEEEEECC---CCCHHHHHHHHHH
T ss_conf             423458643177137998235---5731489999870


No 159
>pfam12325 TMF_TATA_bd TATA element modulatory factor 1 TATA binding. This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family.
Probab=26.29  E-value=38  Score=13.12  Aligned_cols=45  Identities=20%  Similarity=0.373  Sum_probs=39.2

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             999976667899998877654420397887899999999998741
Q gi|254780353|r  442 LEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIF  486 (753)
Q Consensus       442 le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkf  486 (753)
                      -+...++.++.+|..+-..+-.+++-+.....-++..+.++|+-|
T Consensus        69 ~~~~~l~~~l~~l~~r~~t~LellGEK~E~vEEL~~Dv~DlK~my  113 (121)
T pfam12325        69 KEIEELEAELEDLEQRYETTLELLGEKSERVEELRADVVDLKEMY  113 (121)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCHHHHHHHHHHHHHHHHHHHH
T ss_conf             689999999999999999999996627899999996799999999


No 160
>pfam07914 DUF1679 Protein of unknown function (DUF1679). The region featured in this family is found in a number of C. elegans proteins, in one case as a repeat. In many of the family members, this region is associated with the CHK region described by SMART as being found in ZnF_C4 and HLH domain-containing kinases. In fact, one member of this family is annotated as being a member of the nuclear hormone receptor family, and contains regions typical of such proteins (Interpro:IPR000536, Interpro:IPR008946, and Interpro:IPR001628).
Probab=25.93  E-value=25  Score=14.50  Aligned_cols=61  Identities=18%  Similarity=0.195  Sum_probs=41.0

Q ss_pred             HHHHHHHHCCCCCHHHHHHHHHHHHH-CCCCCCHHHHHHCCCCCCCC--CCCCCCCHHHHHHHHHC
Q ss_conf             46777751677788999999999872-86532013443203677887--76010698899989850
Q gi|254780353|r  183 IAVGMATSIPSHNVQEICEAALALID-NPEISIEKLLEYIIGPDFPT--GGIIVESRESIVESYRL  245 (753)
Q Consensus       183 IavG~at~ipphnl~ev~~a~~~~i~-~~~~~~~~l~~~i~gPDFPT--GG~i~~~~~~i~~~y~t  245 (753)
                      ..++|-.|+||..|-.|++++..+-- .-..|.+|. +.+.||||.-  =+... +.++++.+|..
T Consensus       161 ~~~~~y~ni~~deL~~vv~~iA~fqA~~~~LseEE~-k~i~g~df~~~~~~~~~-~~~~~~~~f~~  224 (413)
T pfam07914       161 HTRHMYENIPADELIPVLRAIATFQALGESLSEEEK-KSANGADFLEQMFETFM-SEEGLKGIFDQ  224 (413)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHH-HHCCCHHHHHHHHHHHH-HHHHHHHHHHH
T ss_conf             687254898989999999999999986434998997-53567579999999872-36779999999


No 161
>KOG0719 consensus
Probab=25.84  E-value=38  Score=13.07  Aligned_cols=13  Identities=8%  Similarity=0.253  Sum_probs=7.1

Q ss_pred             HHHHHHHHHCCCC
Q ss_conf             9999998741774
Q gi|254780353|r  477 CEIREVKEIFSKS  489 (753)
Q Consensus       477 ~EL~eikkkfgd~  489 (753)
                      .=|..+.++||-.
T Consensus       226 sl~~SL~~kY~~~  238 (264)
T KOG0719         226 SLLDSLEEKYGGN  238 (264)
T ss_pred             HHHHHHHHHHCCC
T ss_conf             9999999986666


No 162
>pfam05067 Mn_catalase Manganese containing catalase. Catalases are important antioxidant metalloenzymes that catalyse disproportionation of hydrogen peroxide, forming dioxygen and water. Two families of catalases are known, one having a heme cofactor, and this family that is a structurally distinct family containing non-heme manganese.
Probab=25.83  E-value=32  Score=13.68  Aligned_cols=20  Identities=30%  Similarity=0.396  Sum_probs=13.0

Q ss_pred             CCCCCCCCCCCHHHHHHHHH
Q ss_conf             08867797100246899855
Q gi|254780353|r  118 FGNIDGDSAAAYRYTEARMT  137 (753)
Q Consensus       118 fGs~~~d~~Aa~RYte~rl~  137 (753)
                      ||-.+|.-.|||||..-+.+
T Consensus        29 ~GG~~GElsaamqYl~Q~~~   48 (272)
T pfam05067        29 LGGQFGELSAAMRYLFQGFN   48 (272)
T ss_pred             HCCCCHHHHHHHHHHHHHHC
T ss_conf             57972499999999998727


No 163
>pfam01162 consensus
Probab=25.76  E-value=39  Score=13.06  Aligned_cols=20  Identities=15%  Similarity=0.508  Sum_probs=12.4

Q ss_pred             CCCCCCCCCCCHHHHHHHHH
Q ss_conf             10000002577577889988
Q gi|254780353|r  414 KPVMVSRFSLTENQVDAILN  433 (753)
Q Consensus       414 k~~L~~~f~lse~QA~aIL~  433 (753)
                      +..+++.|+|++..|+.+++
T Consensus        46 ~~r~~~~ygL~~~dA~~L~~   65 (69)
T pfam01162        46 RERLVKEYGLSEEDAQTLVS   65 (69)
T ss_pred             HHHHHHHHCCCHHHHHHHHC
T ss_conf             99999993969999999972


No 164
>PRK05636 replicative DNA helicase; Provisional
Probab=25.72  E-value=39  Score=13.05  Aligned_cols=44  Identities=20%  Similarity=0.378  Sum_probs=24.9

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             04999999899998999999999999999999999999998641078999975200
Q gi|254780353|r  355 MPLDGILKEWLAHRREVLFRRSSFRMQAIDRRVEILKGLLIAYLNIDEIIAIIRNE  410 (753)
Q Consensus       355 ~~l~eil~~f~~~R~~vi~rr~~~~L~k~~~RlhIleGl~~a~~~ID~vI~iIR~s  410 (753)
                      ..+.+++..|++.            +++..+.-....|+-.-+..+|.++.=++.+
T Consensus       224 ~~~~d~l~~~~~~------------ie~~~~~~g~~~Gi~TGf~~LD~~t~Gl~~G  267 (507)
T PRK05636        224 AVLADILDETMAE------------IEMLESDGGIATGIPTGFKDLDDLTNGLRGG  267 (507)
T ss_pred             EEHHHHHHHHHHH------------HHHHHHCCCCCEEEECCCHHHHHHHCCCCCC
T ss_conf             5699999999999------------9999857999525658808899755088835


No 165
>cd07639 BAR_ACAP1 The Bin/Amphiphysin/Rvs (BAR) domain of ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 1. BAR domains are dimerization, lipid binding and curvature sensing modules found in many different proteins with diverse functions. ACAP1 (ArfGAP with Coiled-coil, ANK repeat and PH domain containing protein 1), also called centaurin beta-1, is an Arf6-specific GTPase activating protein (GAP) which mediates Arf6 signaling. Arf6 is involved in the regulation of endocytosis, phagocytosis, cell adhesion and migration. ACAP1 also participates in the cargo sorting and recycling of the transferrin receptor and integrin beta1. It may also play a role in innate immune responses. ACAP1 contains an N-terminal BAR domain, followed by a Pleckstrin homology (PH) domain, an Arf GAP domain, and C-terminal ankyrin (ANK) repeats. BAR domains form dimers that bind to membranes, induce membrane bending and curvature, and may also be involved in protein-protein interactions.
Probab=25.58  E-value=39  Score=13.03  Aligned_cols=40  Identities=13%  Similarity=0.144  Sum_probs=21.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             7788998878999988999976667899998877654420
Q gi|254780353|r  426 NQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLL  465 (753)
Q Consensus       426 ~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL  465 (753)
                      .||+..+--||.++.+-++...++..+...+.-+.|..-|
T Consensus        82 ~q~~~~l~~pL~~F~k~dl~~vKe~kK~FdK~s~~~d~al  121 (200)
T cd07639          82 EATQFSFKQQLQLLVKEDLRGFRDARKEFERGAESLEAAL  121 (200)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999886899998868988779999999


No 166
>pfam12529 Xylo_C Xylosyltransferase C terminal. This domain family is found in eukaryotes, and is typically between 169 and 183 amino acids in length. The family is found in association with pfam02485. There is a single completely conserved residue G that may be functionally important. Xylosyltransferases are enzymes involved in the biosynthesis of the glycosaminoglycan linker region in proteoglycans.
Probab=25.29  E-value=35  Score=13.34  Aligned_cols=10  Identities=70%  Similarity=1.016  Sum_probs=5.5

Q ss_pred             HHHHHHHHHC
Q ss_conf             9999999610
Q gi|254780353|r   93 SVYDSLVRLA  102 (753)
Q Consensus        93 s~y~a~v~ma  102 (753)
                      ++|+++.|||
T Consensus        39 t~~~Sl~Rla   48 (180)
T pfam12529        39 TVYHSLARLA   48 (180)
T ss_pred             HHHHHHHHHH
T ss_conf             6888889999


No 167
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=25.26  E-value=39  Score=12.99  Aligned_cols=46  Identities=17%  Similarity=0.241  Sum_probs=29.7

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9997666789999887765442039788789999999999874177
Q gi|254780353|r  443 EEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSK  488 (753)
Q Consensus       443 e~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd  488 (753)
                      ++.....+..++.++.+.++.-++........+..++.+..+....
T Consensus       219 ei~~~~~~l~e~~~~l~~l~~~I~~~~~~k~e~~~~I~~ae~~~~~  264 (312)
T smart00787      219 EIMIKVKKLEELEEELQELESKIEDLTNKKSELNTEIAEAEKKLEQ  264 (312)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999999999999999999999998999999999999999999987


No 168
>TIGR02470 sucr_synth sucrose synthase; InterPro: IPR012820    This entry represents sucrose synthase an enzyme that despite its name, generally uses rather produces sucrose. Sucrose plus UDP (or ADP) becomes D-fructose plus UDP-glucose (or ADP-glucose), which is then available for cell wall (or starch) biosynthesis. The enzyme is homologous to sucrose phosphate synthase, which catalyses the penultimate step in sucrose synthesis. Sucrose synthase is found, so far, exclusively in plants and cyanobacteria.; GO: 0016157 sucrose synthase activity.
Probab=25.18  E-value=40  Score=12.98  Aligned_cols=74  Identities=19%  Similarity=0.269  Sum_probs=35.2

Q ss_pred             CHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHH----HHHHHHHHH-------------HH
Q ss_conf             8899999875420000122331133312689722049999998999989999----999999999-------------99
Q gi|254780353|r  321 DPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVL----FRRSSFRMQ-------------AI  383 (753)
Q Consensus       321 ~~~~vl~~Lyk~T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi----~rr~~~~L~-------------k~  383 (753)
                      +++.=+..||.+-.+-.-=+.+| .| .++.+.+-.|...|..=.+|-..+=    =...+++|+             +.
T Consensus       152 ~~~~w~~~Ll~FLr~H~y~G~~L-ml-nd~i~~~~~L~~~L~~A~~~ls~lp~~tPY~eF~~~lQ~lGfE~GWGdTA~Rv  229 (790)
T TIGR02470       152 DKESWMEPLLNFLRVHNYNGEQL-ML-NDRIQSVSALQSQLRKAEEFLSALPPDTPYSEFEFELQELGFEPGWGDTAERV  229 (790)
T ss_pred             CHHHHHHHHHHHHHHHHHCCCCC-CC-CCCCCCHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHH
T ss_conf             83146799999985442168401-13-44566578999999999999845887674478988987448888853068999


Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999999986
Q gi|254780353|r  384 DRRVEILKGLLIA  396 (753)
Q Consensus       384 ~~RlhIleGl~~a  396 (753)
                      .+-+|+|.-++-|
T Consensus       230 ~Et~~lL~~lL~a  242 (790)
T TIGR02470       230 RETLHLLLDLLEA  242 (790)
T ss_pred             HHHHHHHHHHHCC
T ss_conf             9999999998528


No 169
>PRK09848 glucuronide transporter; Provisional
Probab=24.90  E-value=40  Score=12.94  Aligned_cols=34  Identities=21%  Similarity=0.186  Sum_probs=23.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9988789999889999766678999988776544
Q gi|254780353|r  430 AILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDS  463 (753)
Q Consensus       430 aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~  463 (753)
                      +++-|..++||+-...++++|+++-++.-+++.+
T Consensus       420 ~~~~~~~Y~Lt~~~~~eI~~eL~~rr~~~~~~~~  453 (457)
T PRK09848        420 AFVIIWFYPLTDKKFKEIVVEIDNRKKVQQQLIS  453 (457)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9999986158899999999999999998765330


No 170
>TIGR01465 cobM_cbiF precorrin-4 C11-methyltransferase; InterPro: IPR006362   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.   This entry represents CobM and CibF precorrin-4 C11-methyltransferase (2.1.1.133 from EC), both as stand-alone enzymes and when CobJ forms part of a bifunctional enzyme. In the aerobic pathway, CobM catalyses the methylation of precorrin-4 at C-11 to yield precorrin-5. The extruded acyl group is then removed in the subsequent step catalysed by CobF. In the anaerobic pathway, CibF catalyses the methylation of cobalt-precorrin-4 to cobalt-precoriin-5 .    Nomenclature note: occasionally precorrin-4 C11-methyltransferase is one of two methyltransferases often referred to as precorrin-3 methylase (the other is precorrin-3 methylase (the other is precorrin-4 C11-methyltransferase, 2.1.1.131 from EC). ; GO: 0046026 precorrin-4 C11-methyltransferase activity, 0009236 cobalamin biosynthetic process.
Probab=24.66  E-value=32  Score=13.69  Aligned_cols=20  Identities=35%  Similarity=0.689  Sum_probs=10.3

Q ss_pred             CCCCCHHHHHHHHHHHHCCHH
Q ss_conf             768874789999999610013
Q gi|254780353|r   85 KLHPHGDQSVYDSLVRLAQPF  105 (753)
Q Consensus        85 kyhPHGd~s~y~a~v~maq~~  105 (753)
                      ..| =||-|||+||.=+-|.+
T Consensus        76 RLH-sGDPsIYGA~~EQ~~~L   95 (252)
T TIGR01465        76 RLH-SGDPSIYGAIAEQMQLL   95 (252)
T ss_pred             EEE-CCCHHHHHHHHHHHHHH
T ss_conf             985-08755776699999999


No 171
>pfam10458 Val_tRNA-synt_C Valyl tRNA synthetase tRNA binding arm. This domain is found at the C-terminus of Valyl tRNA synthetases.
Probab=24.64  E-value=40  Score=12.91  Aligned_cols=46  Identities=22%  Similarity=0.185  Sum_probs=31.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             9999766678999988776544203978878999999999987417
Q gi|254780353|r  442 LEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFS  487 (753)
Q Consensus       442 le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfg  487 (753)
                      -|...|..|++.|..+++.++.-|+++.-+.+.=.+-...-++++.
T Consensus         4 ~E~~RL~Kel~kl~~~i~~~~~kL~N~~Fv~kAP~~VV~~er~kl~   49 (66)
T pfam10458         4 KERARLEKELAKLQKEIERLQKKLSNPGFVAKAPAEVVEEEKAKLA   49 (66)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHCCHHHHHHHHHHHH
T ss_conf             8999899999999999999998778767777098999999999999


No 172
>PRK06755 hypothetical protein; Validated
Probab=24.57  E-value=40  Score=12.90  Aligned_cols=42  Identities=21%  Similarity=0.302  Sum_probs=22.7

Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCEEECCCHHHHHHHHCCCCCCCCEEEEECCCEE
Q ss_conf             999999874177433455542000011000000110024566705998710102
Q gi|254780353|r  477 CEIREVKEIFSKSTDLGRRRTTFCEVSRADKATLQQAMIEKEPITVVISNRGWI  530 (753)
Q Consensus       477 ~EL~eikkkfgd~~~~~~RRT~iie~~~~~~~~~~EdlI~~E~v~V~LS~~GyI  530 (753)
                      +||.+++..|..      |.=.-  ...  ....  --..++|..+.+|-.|-=
T Consensus         9 ~eL~~v~~el~~------RgW~~--gTs--GNlS--~~~~~dpl~fliTaSGkd   50 (209)
T PRK06755          9 NELKDVKSELAL------RDWFY--GTK--ISLS--LCTSKEPLTFLVNVEGRD   50 (209)
T ss_pred             HHHHHHHHHHHH------CCCCC--CCC--CCEE--EEECCCCCEEEEECCCCC
T ss_conf             999999999985------89877--778--7668--894589867999678776


No 173
>KOG3915 consensus
Probab=24.54  E-value=41  Score=12.90  Aligned_cols=43  Identities=14%  Similarity=0.212  Sum_probs=29.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHH
Q ss_conf             8999976667899998877654420397887899999999998
Q gi|254780353|r  441 KLEEYQIKSELDNLLAEKEKIDSLLNSGKQQWNQIACEIREVK  483 (753)
Q Consensus       441 ~le~~kl~~E~~eL~~~i~~L~~IL~s~~~l~~iI~~EL~eik  483 (753)
                      .+|..+|+-|+-.-++-.+.|++.|..+.+++.++.+.|+.-|
T Consensus       527 q~Ek~ELkmd~lrerelreslekql~~ErklR~~~qkr~kkEk  569 (641)
T KOG3915         527 QLEKTELKMDFLRERELRESLEKQLAMERKLRAIVQKRLKKEK  569 (641)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8889999999999999999999999999999999999988888


No 174
>COG2192 Predicted carbamoyl transferase, NodU family [Posttranslational modification, protein turnover, chaperones]
Probab=24.51  E-value=41  Score=12.89  Aligned_cols=25  Identities=8%  Similarity=-0.044  Sum_probs=14.2

Q ss_pred             EEEEEECCCCCCCHHHHHHHHHHHH
Q ss_conf             0799952420021689999999986
Q gi|254780353|r  266 WCIVVTEIPYQVQKSRLIEKIAELI  290 (753)
Q Consensus       266 ~~ivIteiPy~v~k~~~ie~I~~lv  290 (753)
                      .--+|.+.|+--+-.-+...|.++.
T Consensus       161 ~~~~i~~~~~~~SLG~fY~~~T~~l  185 (555)
T COG2192         161 QLTPIAQSRGIDSLGLFYAAFTELL  185 (555)
T ss_pred             EEEEEEEECCCCHHHHHHHHHHHHH
T ss_conf             0689875058642889999999982


No 175
>KOG3314 consensus
Probab=23.69  E-value=42  Score=12.78  Aligned_cols=38  Identities=26%  Similarity=0.472  Sum_probs=17.4

Q ss_pred             HHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCC
Q ss_conf             04689999999868999898035405366654276887
Q gi|254780353|r   52 PVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPH   89 (753)
Q Consensus        52 pvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPH   89 (753)
                      |+-+-.+-||-.+|-.-+..+.+|.---|.|-|-|||-
T Consensus        38 P~Vkfl~~am~k~~c~~~d~~isc~~C~~~~~GGy~~~   75 (194)
T KOG3314          38 PIVKFLMEAMEKSGCRVGDNFISCVVCTGPVAGGYTPG   75 (194)
T ss_pred             CHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCCCCC
T ss_conf             38999999999738876677457766899756774688


No 176
>TIGR01034 metK S-adenosylmethionine synthetase; InterPro: IPR002133   S-adenosylmethionine synthetase (MAT, 2.5.1.6 from EC) is the enzyme that catalyzes the formation of S-adenosylmethionine (AdoMet) from methionine and ATP . AdoMet is an important methyl donor for transmethylation and is also the propylamino donor in polyamine biosynthesis.   In bacteria there is a single isoform of AdoMet synthetase (gene metK), there are two in budding yeast (genes SAM1 and SAM2) and in mammals while in plants there is generally a multigene family.   The sequence of AdoMet synthetase is highly conserved throughout isozymes and species. The active sites of both the Escherichia coli and rat liver MAT reside between two subunits, with contributions from side chains of residues from both subunits, resulting in a dimer as the minimal catalytic entity. The side chains that contribute to the ligand binding sites are conserved between the two proteins. In the structures of complexes with the E. coli enzyme, the phosphate groups have the same positions in the (PPi plus Pi) complex and the (ADP plus Pi) complex, and are located at the bottom of a deep cavity with the adenosyl group nearer the entrance .; GO: 0004478 methionine adenosyltransferase activity, 0005524 ATP binding, 0006730 one-carbon compound metabolic process.
Probab=23.66  E-value=42  Score=12.78  Aligned_cols=105  Identities=25%  Similarity=0.268  Sum_probs=49.3

Q ss_pred             CCCCHHHHHHHHCCCC---CHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEE
Q ss_conf             6650467777516777---8899999999987286532013443203677887760106988999898503341599999
Q gi|254780353|r  179 GTSGIAVGMATSIPSH---NVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRAR  255 (753)
Q Consensus       179 g~~GIavG~at~ipph---nl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k  255 (753)
                      |=+||-+|||||=-|-   -+..++..+...+.  +..-+--++|++ ||==|==.|         -|+.+||.+.....
T Consensus       122 GDQGimFGYAt~ET~~~MPlpi~lAH~l~~~~~--~~Rk~g~lpwLR-PD~KsQVt~---------~Ye~~~~aviPV~v  189 (393)
T TIGR01034       122 GDQGIMFGYATNETPELMPLPITLAHKLLKRAA--ELRKSGTLPWLR-PDGKSQVTI---------EYEDNKGAVIPVRV  189 (393)
T ss_pred             CCEEEEEEEECCCHHCCCCHHHHHHHHHHHHHH--HHHHCCCCCCCC-CCCCEEEEE---------EEECCCCEEEEEEE
T ss_conf             840578544224000008777999999999999--851227888546-897058898---------98468951777653


Q ss_pred             EEEEECCCCCEEEEE-ECCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHCCC
Q ss_conf             998643788407999-524200216899999999864022213457764067
Q gi|254780353|r  256 WCVEEVGRGSWCIVV-TEIPYQVQKSRLIEKIAELIIAKRIPLLEDIRDESA  306 (753)
Q Consensus       256 ~~~e~~~~~~~~ivI-teiPy~v~k~~~ie~I~~lv~~~ki~gi~dirDeSd  306 (753)
                                ..||+ +.=-..++-..|-+.|.|-|-..-++ =..+.||--
T Consensus       190 ----------~~iv~S~QH~p~iS~~~Lr~~i~E~iI~p~lp-~~~~ld~~t  230 (393)
T TIGR01034       190 ----------DTIVISTQHDPDISQKELREAIIEEIIKPVLP-DAEYLDEKT  230 (393)
T ss_pred             ----------EEEEEEECCCCCCCHHHHHHHHHHHCCCCCCC-CHHHCCCCC
T ss_conf             ----------08999853798547799999987511222438-520056688


No 177
>KOG3957 consensus
Probab=23.65  E-value=39  Score=13.04  Aligned_cols=146  Identities=17%  Similarity=0.237  Sum_probs=66.2

Q ss_pred             CCCCCCCCCCCC--HHHHHHHHHCCCCEEEEEEEEEEEECCCCCEEEEEECCCCCCCHHHHHHHHH--HHHHHCC---CH
Q ss_conf             778877601069--8899989850334159999999864378840799952420021689999999--9864022---21
Q gi|254780353|r  224 PDFPTGGIIVES--RESIVESYRLGRGGFRVRARWCVEEVGRGSWCIVVTEIPYQVQKSRLIEKIA--ELIIAKR---IP  296 (753)
Q Consensus       224 PDFPTGG~i~~~--~~~i~~~y~tG~G~i~~r~k~~~e~~~~~~~~ivIteiPy~v~k~~~ie~I~--~lv~~~k---i~  296 (753)
                      -||.|||....+  ...+.+-++||||-+. -+..              +|  =++.-++++-+--  -+.+.++   ..
T Consensus       152 aDfAgGgL~aa~gI~~AL~~RtrtgkGqvi-D~~m--------------~e--g~ayl~S~v~~~y~~s~~ea~R~~~~~  214 (387)
T KOG3957         152 ADFAGGGLYAAGGILAALYQRTRTGKGQVI-DCNM--------------LE--GVAYLLSFVQKNYLQSLWEADRYGTAH  214 (387)
T ss_pred             HHHCCCHHHHHHHHHHHHHHHHCCCCCEEE-EECH--------------HH--HHHHHHHHHHHHHHHHHCCCCCCCCCC
T ss_conf             442365068999999999998416885488-7215--------------67--689999999997652000354312336


Q ss_pred             -HHHHHHHCCCCCEEEEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             -3457764067660588985045458899999875420000122331133312689722049999998999989999999
Q gi|254780353|r  297 -LLEDIRDESAEDVRIVLFPKNRSLDPDLLMESIFMLSDMETRFPLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRR  375 (753)
Q Consensus       297 -gi~dirDeSd~~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq~sf~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr  375 (753)
                       ++-=++-.-.++|.++..   -..+|+ .-..|++.--           +.....|++++-.+=+..|++-|+-.    
T Consensus       215 G~~~~Y~tykTkDG~fmav---ga~epQ-F~~~l~~ll~-----------~~~d~~p~~~tn~~rvtnr~E~~kil----  275 (387)
T KOG3957         215 GSIPPYQTYKTKDGYFMAV---GALEPQ-FYELLKKLLG-----------LKLDENPKQFTNPDRVTNRVELRKIL----  275 (387)
T ss_pred             CCCCCCEEEECCCCEEEEE---CCCCHH-HHHHHHHHHC-----------CCCCCCHHHCCCCCCCCCHHHHHHHH----
T ss_conf             7876512455268539972---366678-9999998607-----------66322402216854221009999999----


Q ss_pred             HHHHHHHHHHHH-HHHHHHH---HHHHHHHHHHH
Q ss_conf             999999999999-9999999---86410789999
Q gi|254780353|r  376 SSFRMQAIDRRV-EILKGLL---IAYLNIDEIIA  405 (753)
Q Consensus       376 ~~~~L~k~~~Rl-hIleGl~---~a~~~ID~vI~  405 (753)
                      .+--++|.++.| .|-||--   .-+.+|.||.+
T Consensus       276 ~e~f~~kT~~eW~~iFeG~d~cV~PVl~~~EV~~  309 (387)
T KOG3957         276 EEVFLEKTRAEWSQIFEGQDACVTPVLDIHEVFH  309 (387)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCCCCCCCCHHHHCC
T ss_conf             9999898799999985579876533357877433


No 178
>TIGR00952 S15_bact ribosomal protein S15; InterPro: IPR005290   Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites , . About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits.    Many of ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome , .   This family includes specifically bacterial, chloroplast, and mitochondrial ribosomal protein S15. The homologous proteins of Archaea and Eukarya are designated S13.     Escherichia coli ribosomal protein S15 has been shown to regulate the expression of its own mRNA by a feedback mechanism at the translational level. The translational operator overlaps the ribosome binding site and folds into two mutually exclusive structures, one consisting of two stem-loops (I and II) and the other one forming a pseudoknot. The two structures, which seem to be energetically equivalent are in dynamic equilibrium, and the pseudoknot is stabilized by binding of S15. However, binding of S15 does not prevent 30 S subunit binding but traps the subunit into an incompetent translation initiation complex. Repression can be alleviated by 16 S rRNA, which is able to displace the bound S15, thus allowing translation to proceed .; GO: 0003735 structural constituent of ribosome, 0006412 translation, 0005840 ribosome.
Probab=23.53  E-value=42  Score=12.76  Aligned_cols=30  Identities=30%  Similarity=0.525  Sum_probs=20.9

Q ss_pred             CCCCCCCCCCCCCCHHH-----HH-HHHHHHHHHHH
Q ss_conf             00110000002577577-----88-99887899998
Q gi|254780353|r  411 DKPKPVMVSRFSLTENQ-----VD-AILNLRLRSLR  440 (753)
Q Consensus       411 ~~~k~~L~~~f~lse~Q-----A~-aIL~mrL~rLt  440 (753)
                      .+.|+.+|+.|+..|.-     ++ |||.=|+.+||
T Consensus         2 ~e~K~~ii~~f~~hE~DTGS~~VQiAlLT~rI~~Lt   37 (86)
T TIGR00952         2 KERKQEIIKEFQLHEKDTGSPEVQIALLTERINQLT   37 (86)
T ss_pred             HHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             124899999854589985588999999999998887


No 179
>pfam05400 FliT Flagellar protein FliT. This family contains several bacterial flagellar FliT proteins. The flagellar proteins FlgN and FliT have been proposed to act as substrate specific export chaperones, facilitating incorporation of the enterobacterial hook-associated axial proteins (HAPs) FlgK/FlgL and FliD into the growing flagellum. In Salmonella typhimurium flgN and fliT mutants, the export of target HAPs is reduced, concomitant with loss of unincorporated flagellin into the surrounding medium.
Probab=23.53  E-value=42  Score=12.76  Aligned_cols=36  Identities=11%  Similarity=0.258  Sum_probs=30.2

Q ss_pred             HHHHHHHHHHHHCCHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             998877654420397887899999999998741774
Q gi|254780353|r  454 LLAEKEKIDSLLNSGKQQWNQIACEIREVKEIFSKS  489 (753)
Q Consensus       454 L~~~i~~L~~IL~s~~~l~~iI~~EL~eikkkfgd~  489 (753)
                      ......-++.||.++..++.++...+.++.+.++..
T Consensus        61 ~~~~~~lL~~IL~nda~IR~Ll~prl~~Ls~li~q~   96 (109)
T pfam05400        61 QEQKRELLQKILDNEAEIKDLLQPRLDELSQLIGQS   96 (109)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999879999998899999999999887


No 180
>cd03814 GT1_like_2 This family is most closely related to the GT1 family of glycosyltransferases. Glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltransferases. GTB proteins have distinct N- and C- terminal domains each containing a typical Rossmann fold. The two domains have high structural homology despite minimal sequence homolog
Probab=23.49  E-value=42  Score=12.76  Aligned_cols=27  Identities=22%  Similarity=0.255  Sum_probs=11.5

Q ss_pred             HHHHHHHHCCCC-CCCCCCCCCCCCHHH
Q ss_conf             899997520000-110000002577577
Q gi|254780353|r  401 DEIIAIIRNEDK-PKPVMVSRFSLTENQ  427 (753)
Q Consensus       401 D~vI~iIR~s~~-~k~~L~~~f~lse~Q  427 (753)
                      +++.++++++|= .-+..-+.|+++-..
T Consensus       258 ~el~~~~~~adi~v~pS~~E~fg~~~lE  285 (364)
T cd03814         258 EELAAAYASADVFVFPSRTETFGLVVLE  285 (364)
T ss_pred             HHHHHHHHHCCCCCCCCCCCCCCHHHHH
T ss_conf             9999999824756788653457657999


No 181
>PRK10325 heat shock protein GrpE; Provisional
Probab=23.36  E-value=43  Score=12.74  Aligned_cols=34  Identities=18%  Similarity=0.327  Sum_probs=19.3

Q ss_pred             HHHHHHHHHHHHHHHH--HHHHHHHHHHHHHHHHHH
Q ss_conf             9999999999999999--999999986410789999
Q gi|254780353|r  372 LFRRSSFRMQAIDRRV--EILKGLLIAYLNIDEIIA  405 (753)
Q Consensus       372 i~rr~~~~L~k~~~Rl--hIleGl~~a~~~ID~vI~  405 (753)
                      ++||+.-+...+.+..  .++.-||-+++|++..+.
T Consensus        72 ~rkR~~ke~~~~~~~a~~~~~~~lLpv~DnlerAl~  107 (197)
T PRK10325         72 LRRRTELDIEKAHKFALEKFINELLPVIDSLDRALE  107 (197)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999997007768999998


No 182
>KOG3675 consensus
Probab=23.19  E-value=43  Score=12.72  Aligned_cols=103  Identities=23%  Similarity=0.332  Sum_probs=59.3

Q ss_pred             CCCCC-HHHHHHHHHHHHCCHHHCCCCCCCCCCCCCCC---CCCCCCCHHHHHHHHHHH---HHHHHHHCCCCCCCCCCC
Q ss_conf             76887-47899999996100132166132678870886---779710024689985599---999984218786175216
Q gi|254780353|r   85 KLHPH-GDQSVYDSLVRLAQPFVQRYPLISGQGNFGNI---DGDSAAAYRYTEARMTQV---AELILQGVDEDAVDFRDT  157 (753)
Q Consensus        85 kyhPH-Gd~s~y~a~v~maq~~~~~~pli~g~GnfGs~---~~d~~Aa~RYte~rl~~~---~~~ll~di~~~~v~~~~n  157 (753)
                      +|--| --.++|+++...-|.  .|-|       +|++   .|=-|+--.=+-+|.+.+   |+.++..+     +|.+-
T Consensus        35 ~Y~~hf~kgP~~e~~igFIqt--yrdp-------~G~r~efEgfVA~vNKe~saKF~~LV~~AE~~l~~l-----Pw~~~  100 (417)
T KOG3675          35 KYVHHFSKGPWYEGLIGFIQT--YRDP-------AGSRGEFEGFVAVVNKEMSAKFSWLVNNAEQLLPEL-----PWIYA  100 (417)
T ss_pred             HHHHHHHCCCHHHHHHHHHHH--CCCC-------CCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC-----CCCHH
T ss_conf             555554127515435455420--4665-------566200000565530454456788765476541117-----85155


Q ss_pred             CCCCEEEEEEECCCCCH--HHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHH
Q ss_conf             79963242231234526--764266504677775167778899999999987
Q gi|254780353|r  158 YNEEDSEPVVFPSKFPN--LLANGTSGIAVGMATSIPSHNVQEICEAALALI  207 (753)
Q Consensus       158 ~D~~~~EP~~lp~~~P~--lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i  207 (753)
                      |.-    |.+|+.-|-.  +|.=+.+||+.|.  |||.++=.+--.......
T Consensus       101 ~ek----d~Fl~pDftsLdvlafagsGipAGI--NIpNy~dirq~egfKnv~  146 (417)
T KOG3675         101 LEK----DLFLAPDFTQLDVLAFAGSGIPAGI--NIPNYTDIRQQEGFKNVA  146 (417)
T ss_pred             HHH----CCCCCCCHHHHHHHHHHCCCCCCCC--CCCCCCHHHHHHHHHHHH
T ss_conf             533----0036898067777765057755556--778752898988899999


No 183
>TIGR02041 CysI sulfite reductase (NADPH) hemoprotein, beta-component; InterPro: IPR011786    Sulphite reductase (NADPH) catalyzes a six electron reduction of sulphite to sulphide in prokaryotic organisms. It is a complex oligomeric enzyme composed of two different peptides with a subunit composition of alpha(8)-beta(4). The alpha component, encoded by cysJ, is a flavoprotein containing both FMN and FAD, while the beta component, encoded by cysI, is a siroheme, iron-sulphur protein.; GO: 0004783 sulfite reductase (NADPH) activity, 0050661 NADP binding, 0051539 4 iron 4 sulfur cluster binding, 0008652 amino acid biosynthetic process, 0009337 sulfite reductase complex (NADPH).
Probab=23.15  E-value=43  Score=12.71  Aligned_cols=59  Identities=27%  Similarity=0.397  Sum_probs=30.7

Q ss_pred             CHHHHHHHHHHHHHHHHH------H--CCCCCCCCCCCCCC--CEEEEE----EECCCCCHHHHCCCCCHHHHHHHHCCC
Q ss_conf             024689985599999984------2--18786175216799--632422----312345267642665046777751677
Q gi|254780353|r  128 AYRYTEARMTQVAELILQ------G--VDEDAVDFRDTYNE--EDSEPV----VFPSKFPNLLANGTSGIAVGMATSIPS  193 (753)
Q Consensus       128 a~RYte~rl~~~~~~ll~------d--i~~~~v~~~~n~D~--~~~EP~----~lp~~~P~lL~Ng~~GIavG~at~ipp  193 (753)
                      +-=|+-|  .++|++||-      +  +|.+-|-=.|.=|+  .+.||.    |||=+|=.=             --|||
T Consensus       150 ~e~YewA--kkiSehLLPrTRAY~EIWLD~~KV~gtp~~e~~l~~~EPiyG~~YLPRKFKt~-------------v~~PP  214 (550)
T TIGR02041       150 REVYEWA--KKISEHLLPRTRAYHEIWLDEEKVAGTPEGEEFLQEEEPIYGKTYLPRKFKTG-------------VVIPP  214 (550)
T ss_pred             HHHHHHH--HHHHHHHCCCCCCCEEEEECCCEECCCCCHHHHHHCCCCCCCCCCCCCCCEEE-------------EEECC
T ss_conf             9999999--98766517765444146533442147763122321368876887788520133-------------66189


Q ss_pred             CCHHHHHH
Q ss_conf             78899999
Q gi|254780353|r  194 HNVQEICE  201 (753)
Q Consensus       194 hnl~ev~~  201 (753)
                      ||=.+|-.
T Consensus       215 ~NDvDvya  222 (550)
T TIGR02041       215 INDVDVYA  222 (550)
T ss_pred             CCCCEEEE
T ss_conf             88711132


No 184
>TIGR03300 assembly_YfgL outer membrane assembly lipoprotein YfgL. Members of this protein family are YfgL, a lipoprotein component of a complex that acts protein insertion into the bacterial outer membrane. Other members of this complex are NlpB, YfiO, and YaeT. This protein contains multiple copies of a repeat that, in other contexts, are associated with binding of the coenzyme PQQ.
Probab=23.09  E-value=43  Score=12.70  Aligned_cols=59  Identities=12%  Similarity=0.113  Sum_probs=28.1

Q ss_pred             CCCCCEEEEECCCEEECCCCCC-CCCCCCCCCCCCCCEEEEEECCCCCEEEEECCCEEEEEEH
Q ss_conf             5667059987101020256554-4553223455555401211114781789806882787551
Q gi|254780353|r  516 EKEPITVVISNRGWIRSLKSHS-VDLSALHFKEGDSLKIALHAHTTDRILLLSTDGKAYTLPA  577 (753)
Q Consensus       516 ~~E~v~V~LS~~GyIKr~k~~~-~~~~~~~~KegD~l~~~~~~~t~d~LLffTs~GkvY~l~a  577 (753)
                      .....+.+.+.+|.+.++...+ ...-...+  ++.+ ..-.+-..+.+.+-|..|.+|.+.+
T Consensus        63 v~~~~vy~~~~~G~v~Ald~~tG~~~W~~~~--~~~i-~~g~~v~~~~v~vgt~~G~l~Ald~  122 (377)
T TIGR03300        63 VAGGKVYAADADGTVVALDAETGKRLWRVDL--DERL-SGGVGADGGLVFVGTEKGEVIALDA  122 (377)
T ss_pred             EECCEEEEECCCCEEEEEECCCCCEEEEEEC--CCCE-EEEEEEECCEEEEEECCCEEEEEEC
T ss_conf             9899999984997599999658948878886--9981-5603882999999909975999997


No 185
>KOG2911 consensus
Probab=23.02  E-value=43  Score=12.69  Aligned_cols=89  Identities=17%  Similarity=0.262  Sum_probs=56.7

Q ss_pred             HHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             99998641078999975200001100000025775778899887899998899-99766678999988776544203978
Q gi|254780353|r  391 KGLLIAYLNIDEIIAIIRNEDKPKPVMVSRFSLTENQVDAILNLRLRSLRKLE-EYQIKSELDNLLAEKEKIDSLLNSGK  469 (753)
Q Consensus       391 eGl~~a~~~ID~vI~iIR~s~~~k~~L~~~f~lse~QA~aIL~mrL~rLt~le-~~kl~~E~~eL~~~i~~L~~IL~s~~  469 (753)
                      |-+...+.+++.|+.-|-+|.+-+.-|.+ |+-.-.--++|+.    +--+.| .+.+.+|..+...+-++.+.+|++-.
T Consensus       290 er~~~~l~~l~~vl~~Id~s~~nkvvl~A-yksGs~alK~il~----~~~s~ekVed~Ldev~et~d~~~EV~~~la~~~  364 (439)
T KOG2911         290 ERKVSSLNNLETVLSQIDNSQTNKVVLQA-YKSGSEALKAILA----QGGSTEKVEDVLDEVNETLDRQEEVEDALASYN  364 (439)
T ss_pred             HHHHHHHHHHHHHHHHHHHHCCCHHHHHH-HHHHHHHHHHHHH----CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             99999999999999988762110899999-9976999999985----268704599999999998865999999984589


Q ss_pred             HH-----HHHHHHHHHHHHH
Q ss_conf             87-----8999999999987
Q gi|254780353|r  470 QQ-----WNQIACEIREVKE  484 (753)
Q Consensus       470 ~l-----~~iI~~EL~eikk  484 (753)
                      .-     ..-|-+||.++.-
T Consensus       365 ~~~~d~~de~lEkEL~~L~~  384 (439)
T KOG2911         365 VNNIDFEDEDLEKELEDLEA  384 (439)
T ss_pred             CCCCCCCHHHHHHHHHHHHH
T ss_conf             88876246999999999974


No 186
>COG2039 Pcp Pyrrolidone-carboxylate peptidase (N-terminal pyroglutamyl peptidase) [Posttranslational modification, protein turnover, chaperones]
Probab=23.01  E-value=40  Score=12.97  Aligned_cols=21  Identities=14%  Similarity=0.088  Sum_probs=13.3

Q ss_pred             HHCCCCCHHHHHHHHHHHHHC
Q ss_conf             516777889999999998728
Q gi|254780353|r  189 TSIPSHNVQEICEAALALIDN  209 (753)
Q Consensus       189 t~ipphnl~ev~~a~~~~i~~  209 (753)
                      .-+.|--+++..+++...|+.
T Consensus        38 ~~~lP~~f~~s~~~l~~~i~~   58 (207)
T COG2039          38 GRILPVVFKKSIDALVQAIAE   58 (207)
T ss_pred             EEECCCCHHHHHHHHHHHHHH
T ss_conf             998574188899999999985


No 187
>TIGR02976 phageshock_pspB phage shock protein B; InterPro: IPR009554   This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages . Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one ..
Probab=22.87  E-value=43  Score=12.67  Aligned_cols=36  Identities=14%  Similarity=0.299  Sum_probs=25.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCHH
Q ss_conf             89988789999889999766678999988776544203978
Q gi|254780353|r  429 DAILNLRLRSLRKLEEYQIKSELDNLLAEKEKIDSLLNSGK  469 (753)
Q Consensus       429 ~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~L~~IL~s~~  469 (753)
                      +.+-+.=.++|+.     +.+..+.|.++|+.||.||.++.
T Consensus        34 ~~l~~~d~~~L~~-----L~~~A~Rl~~Ri~tLE~iLd~e~   69 (75)
T TIGR02976        34 ASLSTDDLQLLQE-----LYAKADRLEERIDTLERILDAEH   69 (75)
T ss_pred             CCCCHHHHHHHHH-----HHHHHHHHHHHHHHHHHHHHCCC
T ss_conf             1115799999999-----99999899999999999872048


No 188
>TIGR00501 met_pdase_II methionine aminopeptidase, type II; InterPro: IPR002468   Metalloproteases are the most diverse of the four main types of protease, with more than 50 families identified to date. In these enzymes, a divalent cation, usually zinc, activates the water molecule. The metal ion is held in place by amino acid ligands, usually three in number. The known metal ligands are His, Glu, Asp or Lys and at least one other residue is required for catalysis, which may play an electrophillic role. Of the known metalloproteases, around half contain an HEXXH motif, which has been shown in crystallographic studies to form part of the metal-binding site . The HEXXH motif is relatively common, but can be more stringently defined for metalloproteases as 'abXHEbbHbc', where 'a' is most often valine or threonine and forms part of the S1' subsite in thermolysin and neprilysin, 'b' is an uncharged residue, and 'c' a hydrophobic residue. Proline is never found in this site, possibly because it would break the helical structure adopted by this motif in metalloproteases .   Peptidases are grouped into clans and families. Clans are groups of families for which there is evidence of common ancestry. Each clan is identified with two letters, the first representing the catalytic type of the families included in the clan (with the letter 'P' being used for a clan containing families of more than one of the catalytic types serine, threonine and cysteine). Some families cannot yet be assigned to clans, and when a formal assignment is required, such a family is described as belonging to clan A-, C-, M-, S-, T- or U-, according to the catalytic type. Some clans are divided into subclans because there is evidence of a very ancient divergence within the clan, for example MA(E), the gluzincins, and MA(M), the metzincins.   Families are grouped by their catalytic type, the first character representing the catalytic type: A, aspartic; C, cysteine; G, glutamic acid; M, metallo; S, serine; T, threonine; and U, unknown. The serine, threonine and cysteine peptidases utilise the amino acid as a nucleophile and form an acyl intermediate - these peptidases can also readily act as transferases. In the case of aspartic, glutamic and metallopeptidases, the nucleophile is an activated water molecule.    This group of metallopeptidases belong to MEROPS peptidase family M24 (clan MG), subfamily M24A.   Methionine aminopeptidase (3.4.11.18 from EC) (MAP) is responsible for the removal of the amino-terminal (initiator) methionine from nascent eukaryotic cytosolic and cytoplasmic prokaryotic proteins if the penultimate amino acid is small and uncharged. All MAP studied to date are monomeric proteins that require cobalt ions for activity. Two subfamilies of MAP enzymes are known to exist , . While being evolutionary related, they only share a limited amount of sequence similarity mostly clustered around the residues shown, in the Escherichia coli MAP , to be involved in cobalt-binding. The first family consists of enzymes from prokaryotes as well as eukaryotic MAP-1, while the second group (IPR002467 from INTERPRO) is made up of archaeal MAP and eukaryotic MAP-2 and includes proteins which do not seem to be MAP, but that are clearly evolutionary related such as mouse proliferation-associated protein 1 and fission yeast curved DNA-binding protein. ; GO: 0004239 methionyl aminopeptidase activity, 0006508 proteolysis.
Probab=22.83  E-value=15  Score=16.15  Aligned_cols=27  Identities=15%  Similarity=0.267  Sum_probs=11.9

Q ss_pred             CEEEEEHHHHHHHCCCCCCHHHHHHHH
Q ss_conf             803540536665427688747899999
Q gi|254780353|r   71 AFKKSARIVGEVIGKLHPHGDQSVYDS   97 (753)
Q Consensus        71 ~~~K~ar~vg~v~gkyhPHGd~s~y~a   97 (753)
                      +||=|.+.+|++|-.|--|+-.|||--
T Consensus       173 g~kP~~NL~GHs~~rY~~H~G~SiPn~  199 (327)
T TIGR00501       173 GVKPISNLTGHSMARYLLHAGLSIPNV  199 (327)
T ss_pred             CCCCCCCCCCCCCCHHHHCCCCCCEEE
T ss_conf             433422273564001543589500034


No 189
>cd04639 CBS_pair_26 The CBS domain, named after human CBS, is a small domain originally identified in cystathionine beta-synthase and is subsequently found in a wide range of different proteins. CBS domains usually occur in tandem repeats. They associate to form a so-called Bateman domain or a CBS pair based on crystallographic studies in bacteria.  The CBS pair was used as a basis for this cd hierarchy since the human CBS proteins can adopt the typical core structure and form an intramolecular CBS pair.  The interface between the two CBS domains forms a cleft that is a potential ligand binding site. The CBS pair coexists with a variety of other functional domains and this has been used to help in its classification here.  It has been proposed that the CBS domain may play a regulatory role, although its exact function is unknown. Mutations of conserved residues within this domain are associated with a variety of human hereditary diseases, including congenital myotonia, idiopathic gener
Probab=22.78  E-value=31  Score=13.76  Aligned_cols=28  Identities=18%  Similarity=0.253  Sum_probs=12.6

Q ss_pred             HHHHHHHHHHHHCCHHHCCCCCCCCCCC
Q ss_conf             4789999999610013216613267887
Q gi|254780353|r   90 GDQSVYDSLVRLAQPFVQRYPLISGQGN  117 (753)
Q Consensus        90 Gd~s~y~a~v~maq~~~~~~pli~g~Gn  117 (753)
                      -|.++++|+-+|.+.-.-+.|.+|.+|.
T Consensus        71 ~~~~l~~~~~~m~~~~~~~lpVVd~~g~   98 (111)
T cd04639          71 PSATLDAVLRLMQQGGAPAVPVVDGSGR   98 (111)
T ss_pred             CCCCHHHHHHHHHHCCCCEEEEECCCCE
T ss_conf             9994999999999589988989957992


No 190
>cd03822 GT1_ecORF704_like This family is most closely related to the GT1 family of glycosyltransferases. ORF704 in E. coli has been shown to be involved in the biosynthesis of O-specific mannose homopolysaccharides.
Probab=22.75  E-value=39  Score=13.05  Aligned_cols=28  Identities=25%  Similarity=0.266  Sum_probs=13.5

Q ss_pred             HHHHHHHCCHHHHHHHHHHHHHHHHHHCC
Q ss_conf             76544203978878999999999987417
Q gi|254780353|r  459 EKIDSLLNSGKQQWNQIACEIREVKEIFS  487 (753)
Q Consensus       459 ~~L~~IL~s~~~l~~iI~~EL~eikkkfg  487 (753)
                      +.+..+|+|++...+ +.+.-.+..++|.
T Consensus       326 ~ai~~ll~d~~~r~~-l~~~a~~~a~~~s  353 (366)
T cd03822         326 EAIRRLLADPELAQA-LRARAREYARAMS  353 (366)
T ss_pred             HHHHHHHCCHHHHHH-HHHHHHHHHHHCC
T ss_conf             999999879999999-9999999999799


No 191
>cd04949 GT1_gtfA_like This family is most closely related to the GT1 family of glycosyltransferases and is named after gtfA in Streptococcus gordonii, where it plays a role in the O-linked glycosylation of GspB, a cell surface glycoprotein involved in platelet binding.  In general glycosyltransferases catalyze the transfer of sugar moieties from activated donor molecules to specific acceptor molecules, forming glycosidic bonds. The acceptor molecule can be a lipid, a protein, a heterocyclic compound, or another carbohydrate residue. This group of glycosyltransferases is most closely related to the previously defined glycosyltransferase family 1 (GT1). The members of this family may transfer UDP, ADP, GDP, or CMP linked sugars. The diverse enzymatic activities among members of this family reflect a wide range of biological functions. The protein structure available for this family has the GTB topology, one of the two protein topologies observed for nucleotide-sugar-dependent glycosyltra
Probab=22.73  E-value=44  Score=12.65  Aligned_cols=11  Identities=9%  Similarity=0.184  Sum_probs=4.1

Q ss_pred             CHHHHHHHHHH
Q ss_conf             49999998999
Q gi|254780353|r  356 PLDGILKEWLA  366 (753)
Q Consensus       356 ~l~eil~~f~~  366 (753)
                      +..|+...|++
T Consensus        82 ~~~eL~~~fl~   92 (372)
T cd04949          82 NEEELFAFFLD   92 (372)
T ss_pred             CHHHHHHHHHH
T ss_conf             89999999999


No 192
>pfam01255 Prenyltransf Putative undecaprenyl diphosphate synthase. Previously known as uncharacterized protein family UPF0015, a single member of this family has been identified as an undecaprenyl diphosphate synthase.
Probab=22.72  E-value=44  Score=12.65  Aligned_cols=89  Identities=13%  Similarity=0.109  Sum_probs=38.5

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCCCCCCCCC-------CCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999999986410789999752000011000-------0002577577889988789999889999766678999988776
Q gi|254780353|r  388 EILKGLLIAYLNIDEIIAIIRNEDKPKPVM-------VSRFSLTENQVDAILNLRLRSLRKLEEYQIKSELDNLLAEKEK  460 (753)
Q Consensus       388 hIleGl~~a~~~ID~vI~iIR~s~~~k~~L-------~~~f~lse~QA~aIL~mrL~rLt~le~~kl~~E~~eL~~~i~~  460 (753)
                      ...+|.......+-+|++....   ....-       .+.|+=+....+++.++=.+.|.+        +..++.+ ..-
T Consensus        15 ~~~~Gh~~G~~~~~~i~~~c~~---~gI~~lTvyaFStEN~~R~~~Ev~~L~~l~~~~l~~--------~~~~~~~-~~i   82 (222)
T pfam01255        15 PRTEGHRAGAEALREILEWCLE---LGIKYLTLYAFSTENWKRPKEEVDFLMELLEEKLRR--------LLEDLHK-NGV   82 (222)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHH---CCCCEEEEHHHCHHHCCCCHHHHHHHHHHHHHHHHH--------HHHHHHH-CCE
T ss_conf             8779999999999999999998---699989726417875499989999999999999999--------9999998-693


Q ss_pred             HHHHHCCHHHHHHHHHHHHHHHHHHCCC
Q ss_conf             5442039788789999999999874177
Q gi|254780353|r  461 IDSLLNSGKQQWNQIACEIREVKEIFSK  488 (753)
Q Consensus       461 L~~IL~s~~~l~~iI~~EL~eikkkfgd  488 (753)
                      --.++++.+.+-.-+.+.+.++.+.-.+
T Consensus        83 ki~~iG~~~~Lp~~l~~~i~~~e~~T~~  110 (222)
T pfam01255        83 RVRVIGDLSLLPEDLRKAIEDAEEATKN  110 (222)
T ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHHCC
T ss_conf             8999526556898999999999997157


No 193
>KOG0103 consensus
Probab=22.71  E-value=20  Score=15.13  Aligned_cols=110  Identities=17%  Similarity=0.245  Sum_probs=66.3

Q ss_pred             CHHHHHHHHHHHHC------CHHHCCC-CCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCC-
Q ss_conf             74789999999610------0132166-132678870886779710024689985599999984218786175216799-
Q gi|254780353|r   89 HGDQSVYDSLVRLA------QPFVQRY-PLISGQGNFGNIDGDSAAAYRYTEARMTQVAELILQGVDEDAVDFRDTYNE-  160 (753)
Q Consensus        89 HGd~s~y~a~v~ma------q~~~~~~-pli~g~GnfGs~~~d~~Aa~RYte~rl~~~~~~ll~di~~~~v~~~~n~D~-  160 (753)
                      .|..++|=|++|.+      .++|+|- |.+.+-|--+-..|..+++.--+-.+-+.-.   ++.+-      -.-|++ 
T Consensus         8 ~Gn~nc~iavAr~~gIe~i~nd~Snr~TPa~vsfg~K~R~~G~aak~~~~~n~kntv~~---~KRl~------Gr~f~dP   78 (727)
T KOG0103           8 LGNENCYIAVARQGGIEVVANDYSNRETPAIVSFGPKNRFIGVAAKNQQTTNVKNTVSN---FKRLI------GRKFSDP   78 (727)
T ss_pred             CCCCCEEEEEECCCCCEEEEECCCCCCCCCEEEECCCCCEEEECCCCCEEECCCCCCHH---HHHHH------CCCCCCH
T ss_conf             26654344320217733553043334575223225665245431564222020026336---66550------4234783


Q ss_pred             -CEEEEEEECCCCCHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHH
Q ss_conf             -632422312345267642665046777751677788999999999872
Q gi|254780353|r  161 -EDSEPVVFPSKFPNLLANGTSGIAVGMATSIPSHNVQEICEAALALID  208 (753)
Q Consensus       161 -~~~EP~~lp~~~P~lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~  208 (753)
                       -..|+.-+|..+- .+.||..||.|-+.-..+|+-+..|.......++
T Consensus        79 ~~q~~~~~~~~~vv-~~~dg~vgi~v~ylge~~~ft~~Qv~Am~l~klk  126 (727)
T KOG0103          79 EVQREIKSLPRSVV-QLKDGDVGIKVEYLGEKHPFTPEQVLAMLLTKLK  126 (727)
T ss_pred             HHHHCCCCCCHHEE-ECCCCCCCEEEHCCCCCCCCCHHHHHHHHHHHHH
T ss_conf             76531000653205-6688870002110267889973899999999989


No 194
>PRK10240 undecaprenyl pyrophosphate synthase; Provisional
Probab=22.49  E-value=44  Score=12.62  Aligned_cols=24  Identities=8%  Similarity=0.192  Sum_probs=12.3

Q ss_pred             HHHCCHHHHHHHHHHHHHHHHHHC
Q ss_conf             420397887899999999998741
Q gi|254780353|r  463 SLLNSGKQQWNQIACEIREVKEIF  486 (753)
Q Consensus       463 ~IL~s~~~l~~iI~~EL~eikkkf  486 (753)
                      .++++.+.+-+-+.+.+.++.+.=
T Consensus        84 ~~iGd~~~Lp~~l~~~i~~~e~~T  107 (229)
T PRK10240         84 RIIGDTSRFNSRLQERIRKSEALT  107 (229)
T ss_pred             EEEECCCCCCHHHHHHHHHHHHHH
T ss_conf             996441006758999999999974


No 195
>KOG0270 consensus
Probab=22.41  E-value=44  Score=12.61  Aligned_cols=161  Identities=13%  Similarity=0.098  Sum_probs=70.5

Q ss_pred             HHHHCCCCCCCCEE-EEECCCEEECCCCCCCCCCCCCCCCCCCCEEEEEECCCCCE--EEEECCCEEEEEEHHHCCCCCC
Q ss_conf             01100245667059-98710102025655445532234555554012111147817--8980688278755112121234
Q gi|254780353|r  509 TLQQAMIEKEPITV-VISNRGWIRSLKSHSVDLSALHFKEGDSLKIALHAHTTDRI--LLLSTDGKAYTLPAGNLLSGRG  585 (753)
Q Consensus       509 ~~~EdlI~~E~v~V-~LS~~GyIKr~k~~~~~~~~~~~KegD~l~~~~~~~t~d~L--LffTs~GkvY~l~a~~Ips~~~  585 (753)
                      +..-+.-+.+|.++ +=|.+|+++-...+...-++...|-.-.+. .+.-+-|...  ++=|+.|.+|++.      .|+
T Consensus       289 Vq~l~wh~~~p~~LLsGs~D~~V~l~D~R~~~~s~~~wk~~g~VE-kv~w~~~se~~f~~~tddG~v~~~D------~R~  361 (463)
T KOG0270         289 VQTLEWHPYEPSVLLSGSYDGTVALKDCRDPSNSGKEWKFDGEVE-KVAWDPHSENSFFVSTDDGTVYYFD------IRN  361 (463)
T ss_pred             EEEEEECCCCCEEEEECCCCCEEEEEECCCCCCCCCEEEECCCEE-EEEECCCCCEEEEEECCCCEEEEEE------CCC
T ss_conf             258873278861898415564478653357655673577405257-8983478841588764786288653------378


Q ss_pred             CCCCCCCCCCCCCCCEEEEEEEECCCCEEE--EEECCCCEEEEEHHHHHCCCCCCEEEEEECCCCCEEEEEEC-CCC--E
Q ss_conf             444222235767653078999857998599--99748978996388740233356278853689805688961-898--0
Q gi|254780353|r  586 HGEAIQLLIDLNHNQDIVTAFVYDSTCKLL--VVSSKGNAFIVEESEIIANTRKGKTFLKVSSEEKMKLVVKV-TGD--H  660 (753)
Q Consensus       586 kG~pI~~ll~l~~~EkIv~~~~~~~~~~ll--l~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~~D~li~v~~~-~~d--~  660 (753)
                      .|.|+..+---  ++. ++.+.++....-+  ..+..+++|.-.+..-....-.+ .-+++.-    ..|+.+ ...  .
T Consensus       362 ~~~~vwt~~AH--d~~-ISgl~~n~~~p~~l~t~s~d~~Vklw~~~~~~~~~v~~-~~~~~~r----l~c~~~~~~~a~~  433 (463)
T KOG0270         362 PGKPVWTLKAH--DDE-ISGLSVNIQTPGLLSTASTDKVVKLWKFDVDSPKSVKE-HSFKLGR----LHCFALDPDVAFT  433 (463)
T ss_pred             CCCCEEEEEEC--CCC-CCEEEECCCCCCCEEECCCCCEEEEEEECCCCCCCCCC-CCCCCCC----EEECCCCCCCCEE
T ss_conf             88852688751--687-32478347788610323665259999604888761123-2100021----1102458776358


Q ss_pred             EEEEECCCCEEEEEHHHCCCCCHH
Q ss_conf             999956993899557877833612
Q gi|254780353|r  661 VAVVGENRKLLIFSIDQIPEMSRG  684 (753)
Q Consensus       661 iiliT~~Gk~LrF~~~eIr~~gRg  684 (753)
                      +++-..++.+..++...-+...|+
T Consensus       434 la~GG~k~~~~vwd~~~~~~V~ka  457 (463)
T KOG0270         434 LAFGGEKAVLRVWDIFTNSPVRKA  457 (463)
T ss_pred             EEECCCCCEEEEEECCCCHHHHHH
T ss_conf             994474652777541357267775


No 196
>TIGR02515 IV_pilus_PilQ type IV pilus secretin PilQ; InterPro: IPR013355    A number of proteins homologous to PilQ are involved in type IV pilus formation, competence for transformation, type III secretion, and type II secretion (also referred to as the main terminal branch of the general secretion pathway). Members of this family include PilQ itself, which is a component of the type IV pilus structure, from a number of species. In Haemophilus influenzae, the member of this family is associated with the uptake of exogenous DNA, rather than with formation of a type IV pilus - the surface structure required for this may be considered an unusual, incomplete type IV pilus structure.; GO: 0009297 pilus biogenesis, 0009306 protein secretion.
Probab=22.40  E-value=44  Score=12.61  Aligned_cols=84  Identities=12%  Similarity=0.222  Sum_probs=37.4

Q ss_pred             CEEEEEEEECCCCCHHHHHHHHHHHCCCCCCC---CCCEEEEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             60588985045458899999875420000122---331133312689722049999998999989999999999999999
Q gi|254780353|r  308 DVRIVLFPKNRSLDPDLLMESIFMLSDMETRF---PLNMNVLSMGRVPQVMPLDGILKEWLAHRREVLFRRSSFRMQAID  384 (753)
Q Consensus       308 ~~~~vi~~~~r~~~~~~vl~~Lyk~T~Lq~sf---~~N~~~l~~~~~P~~~~l~eil~~f~~~R~~vi~rr~~~~L~k~~  384 (753)
                      .|-+=  ++-+++.=+..|.-..|-=.|-..=   .=|.+-+    .|    ..||...     .     +.+-+.++..
T Consensus        35 ~G~it--LrL~nVPWDQALDivLk~KgL~~r~~~s~GNi~~i----AP----~~el~~~-----e-----~~~l~~~~~~   94 (464)
T TIGR02515        35 QGNIT--LRLKNVPWDQALDIVLKSKGLDKRRESSDGNIIYI----AP----ADELAAR-----E-----KDELEAKKQI   94 (464)
T ss_pred             CEEEE--EEECCCCHHHHHHHHHHHCCCCCEEEECCCCEEEE----CC----HHHHHHH-----H-----HHHHHHHHHH
T ss_conf             21388--85178986899889875358652451127886997----58----7998899-----9-----9999999999


Q ss_pred             HHHHHH--HHHHHHHHHHHHHHHHHHCCC
Q ss_conf             999999--999986410789999752000
Q gi|254780353|r  385 RRVEIL--KGLLIAYLNIDEIIAIIRNED  411 (753)
Q Consensus       385 ~RlhIl--eGl~~a~~~ID~vI~iIR~s~  411 (753)
                      +.++=|  |-+-+=|.+-+++=++|+.++
T Consensus        95 ~~l~~L~te~i~lnYa~A~di~k~l~~~~  123 (464)
T TIGR02515        95 ENLEPLQTELIQLNYAKASDIAKVLTGDR  123 (464)
T ss_pred             HHHCCCCCCEEEEEECCHHHHHHHHHCCC
T ss_conf             85116421207885237899999972124


No 197
>cd01437 parp_like Poly(ADP-ribose) polymerase (parp) catalytic domain catalyses the covalent attachment of ADP-ribose units from NAD+ to itself and to a limited number of other DNA binding proteins,  which decreases their affinity for DNA. Poly(ADP-ribose) polymerase is a regulatory component induced by DNA damage. The carboxyl-terminal region is the most highly conserved region of the protein. Experiments have shown that a carboxyl 40 kDa fragment is still catalytically active. Poly(ADP-ribose)-like polymerases (PARPS 1-3, VPARP, tankyrase) catalyze the addition of up to 100 ADP_ribose units from NAD+. PARPs 1 and 2 are localized in the nucleaus, bind DNA, and are activated  by DNA damage. VPARP is part of the vault ribonucleoprotein complex. Tankyrases regulates telomere length through interactions with telomere repeat binding factor 1.
Probab=22.27  E-value=45  Score=12.59  Aligned_cols=14  Identities=14%  Similarity=0.332  Sum_probs=6.1

Q ss_pred             HHHHHHHHHHHHHC
Q ss_conf             64107899997520
Q gi|254780353|r  396 AYLNIDEIIAIIRN  409 (753)
Q Consensus       396 a~~~ID~vI~iIR~  409 (753)
                      ++.+|.-+.++++.
T Consensus       107 ~L~die~A~~ll~~  120 (347)
T cd01437         107 ALRDIEIASKLLKD  120 (347)
T ss_pred             HHHHHHHHHHHHHH
T ss_conf             99999999999974


No 198
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=22.23  E-value=45  Score=12.58  Aligned_cols=22  Identities=14%  Similarity=0.382  Sum_probs=12.0

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHC
Q ss_conf             9766678999988776544203
Q gi|254780353|r  445 YQIKSELDNLLAEKEKIDSLLN  466 (753)
Q Consensus       445 ~kl~~E~~eL~~~i~~L~~IL~  466 (753)
                      ..++++.++|.+..+.|+.+|+
T Consensus        81 ~~i~~~I~~L~~~r~~L~~llG  102 (102)
T cd04775          81 QSLNREIQRLRQQQQVLAAILG  102 (102)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHC
T ss_conf             9999999999999999998739


No 199
>COG0216 PrfA Protein chain release factor A [Translation, ribosomal structure and biogenesis]
Probab=21.95  E-value=45  Score=12.54  Aligned_cols=46  Identities=13%  Similarity=0.135  Sum_probs=39.1

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHCC--HHHHHHHHHHHHHHHHHHCCC
Q ss_conf             9997666789999887765442039--788789999999999874177
Q gi|254780353|r  443 EEYQIKSELDNLLAEKEKIDSLLNS--GKQQWNQIACEIREVKEIFSK  488 (753)
Q Consensus       443 e~~kl~~E~~eL~~~i~~L~~IL~s--~~~l~~iI~~EL~eikkkfgd  488 (753)
                      ++.....|++.+.+++++.+.+|++  +..+.....+|+.+++++...
T Consensus        47 ~iv~~~~~~~~~~~~l~~a~~~l~~~~D~em~ema~~Ei~~~~~~~~~   94 (363)
T COG0216          47 PIVEKYREYKKAQEDLEDAKEMLAEEKDPEMREMAEEEIKELEAKIEE   94 (363)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999999999983568878999999999999998999


No 200
>TIGR03290 CoB_CoM_SS_C CoB--CoM heterodisulfide reductase, subunit C. The last step in methanogenesis leaves two coenzymes of methanogenesis, CoM and CoB, linked by a disulfide bond. Members of this protein family are the C subunit of the enzyme that reduces the heterodisulfide to CoB-SH and CoM-SH. Similar enzyme complex subunits are found in various other species, but likely act on a different substrate.
Probab=21.74  E-value=46  Score=12.51  Aligned_cols=85  Identities=16%  Similarity=0.144  Sum_probs=50.7

Q ss_pred             HHHCCCC--CHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCCCCCCCCCCHHHHHHHHHCCCCEEEEEEEEEEEECCCCC
Q ss_conf             7516777--88999999999872865320134432036778877601069889998985033415999999986437884
Q gi|254780353|r  188 ATSIPSH--NVQEICEAALALIDNPEISIEKLLEYIIGPDFPTGGIIVESRESIVESYRLGRGGFRVRARWCVEEVGRGS  265 (753)
Q Consensus       188 at~ipph--nl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFPTGG~i~~~~~~i~~~y~tG~G~i~~r~k~~~e~~~~~~  265 (753)
                      =+...|-  ++.+|+.++..+.-.......         .         -.+....+|+||++--.-+      +...-+
T Consensus        54 C~~~CP~gV~~~~vI~~lR~~A~~~G~~~~---------~---------~~~~~~~i~~~GhaVp~n~------~~~e~r  109 (144)
T TIGR03290        54 CQERCPRDVKITDIIKALRNLAAKKGFMAK---------A---------HRKTASFVLKTGHAVPIND------EIKELR  109 (144)
T ss_pred             HHHHCCCCCCHHHHHHHHHHHHHHCCCCCH---------H---------HHHHHHHHHHHCCCCCCCH------HHHHHH
T ss_conf             401348999889999999999998599879---------9---------9999999999687788658------999999


Q ss_pred             EEEEEECCCCCCCH-HHHHHHHHHHHHHCCCH
Q ss_conf             07999524200216-89999999986402221
Q gi|254780353|r  266 WCIVVTEIPYQVQK-SRLIEKIAELIIAKRIP  296 (753)
Q Consensus       266 ~~ivIteiPy~v~k-~~~ie~I~~lv~~~ki~  296 (753)
                      ..+=-+|+|+.+.+ .+.+|.|..++++-++.
T Consensus       110 ~~~gl~~~ppt~~~~~~~~~~~~~i~~~~~~~  141 (144)
T TIGR03290       110 KELGLDEIPPTTHKYPEALEEVQKLIKALEFD  141 (144)
T ss_pred             HHCCCCCCCCHHHHCHHHHHHHHHHHHHCCHH
T ss_conf             98599889950430898899999999973533


No 201
>TIGR00034 aroFGH phospho-2-dehydro-3-deoxyheptonate aldolase; InterPro: IPR006219   Members of this group catalyze the first enzymatic reaction of the shikimate pathway. The common (shikimate) pathway links metabolism of carbohydrates to biosynthesis of aromatic amino acids phenylalanine, tyrosine, tryptophan, and derivatives in microorganisms and in plants. In a sequence of seven enzymatic reactions, D-erythrose 4-phosphate (E4P), an intermediate of the pentose phosphate pathway, and phosphoenol pyruvate (PEP), a glycolytic intermediate, are converted to chorismate. The pathway begins with the stereospecific condensation of E4P and PEP to yield 7-phospho 2-dehydro 3-deoxy-D-arabino-heptulosonate (DAHP), catalyzed by 3-deoxy-7-phosphoheptulonate synthase (DAHPS) (EC 2.5.1.54, formerly EC 4.1.2.15). The divalent metal cation requirement of this enzyme can be satisfied by a broad range of metals . A Cys residue in a Cys-X-X-His motif has been identified as part of a metal binding site . In Escherichia coli, the enzyme exists in three isoforms, each specifically inhibited by one of the three aromatic amino acids.   DAHP synthetases fall into two classes, class I (represented by this entry) and class II (represented by PIRSF015573 from PIRSF). Class I was believed to be limited to microorganisms and class II to plants. However, a more recent study showed that class II also contains enzymes from a microbial eukaryote and several bacteria . Brick and Woodard  proposed that the difference between the two classes lies in their metal ion requirement for activity. Whereas class I requires no metal cation, class II is dependent on a metal cation for activity. However, recently a class I DAHP synthase from Thermotoga maritima has been purified, characterised, and shown to be a metalloenzyme .   The three-dimentional structures of DAHP synthases have been determined , , , , . The DAHPS(Phe) monomer is a (beta/alpha)8 barrel with an additional N-terminal beta strand and helices and an extra beta sheet near the C terminus . The active site is located in a cleft at the carboxyl end of the barrel . The allosteric feedback inhibition binding site of DAHPS(Phe) is composed of residues from two adjacent subunits of a tight dimer and is at least 20 angstroms away from the closest active site .   The absence of the shikimate pathway in animals makes it an attractive target for nontoxic herbicidal, antimicrobial, and antifungal agents. The nontoxic herbicide glyphosphate competitively inhibits 3-phosphoshikimate 1-carboxyvinyltransferase, the sixth enzymatic reaction of the pathway.; GO: 0003849 3-deoxy-7-phosphoheptulonate synthase activity, 0009073 aromatic amino acid family biosynthetic process.
Probab=21.74  E-value=46  Score=12.51  Aligned_cols=21  Identities=24%  Similarity=0.472  Sum_probs=13.2

Q ss_pred             CCCCCCCCCCHHHHHHHHHHH
Q ss_conf             000000257757788998878
Q gi|254780353|r  415 PVMVSRFSLTENQVDAILNLR  435 (753)
Q Consensus       415 ~~L~~~f~lse~QA~aIL~mr  435 (753)
                      ..|.++|-+|+.|++.|-.-|
T Consensus        18 ~~L~~~~P~t~~~~~~v~~~R   38 (348)
T TIGR00034        18 AELAAKFPLTPKQAENVAQSR   38 (348)
T ss_pred             HHHHHHCCCCHHHHHHHHHHH
T ss_conf             999974787887999999889


No 202
>pfam11853 DUF3373 Protein of unknown function (DUF3373). This family of proteins are functionally uncharacterized. This protein is found in bacteria. Proteins in this family are typically between 472 to 574 amino acids in length.
Probab=21.65  E-value=46  Score=12.50  Aligned_cols=21  Identities=24%  Similarity=0.329  Sum_probs=12.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHH
Q ss_conf             999766678999988776544
Q gi|254780353|r  443 EEYQIKSELDNLLAEKEKIDS  463 (753)
Q Consensus       443 e~~kl~~E~~eL~~~i~~L~~  463 (753)
                      ++++|++|.++|+++.++++.
T Consensus        32 kI~~L~~ql~eLk~~~~~~~~   52 (485)
T pfam11853        32 KIEALKKELAELKAQLKDLNK   52 (485)
T ss_pred             HHHHHHHHHHHHHHHHHHHHH
T ss_conf             999999999999999998776


No 203
>TIGR01051 topA_bact DNA topoisomerase I; InterPro: IPR005733   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type I topoisomerases are ATP-independent enzymes (except for reverse gyrase), and can be subdivided according to their structure and reaction mechanisms: type IA (bacterial and archaeal topoisomerase I, topoisomerase III and reverse gyrase) and type IB (eukaryotic topoisomerase I and topoisomerase V). These enzymes are primarily responsible for relaxing positively and/or negatively supercoiled DNA, except for reverse gyrase, which can introduce positive supercoils into DNA.     This entry describes topoisomerase I from bacteria, which is more closely related to archaeal than to eukaryotic topoisomerase I . Topoisomerase I is the major enzyme for relaxing negatively supercoiled DNA, and its presence is balanced by reverse gyrase, which can introduce negative supercoils. Prokaryotic topoisomerase I folds in an unusual way to give 4 distinct domains, enclosing a hole large enough to accommodate a double-stranded DNA segment. A tyrosine at the active site, which lies at the interface of 2 domains, is involved in transient breakage of a DNA strand, and the formation of a covalent protein-DNA intermediate through a 5-phosphotyrosine linkage. The structure reveals a plausible mechanism by which this and related enzymes could catalyse the passage of one DNA strand through a transient break in another strand . Topoisomerase I require Mg2+ as a cofactor for catalysis to take place.    More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003917 DNA topoisomerase type I activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=21.43  E-value=27  Score=14.22  Aligned_cols=132  Identities=16%  Similarity=0.203  Sum_probs=59.5

Q ss_pred             CHHHHHHHHHHHHHH-HHHHCCCCCCCCCC--CCCEEECCCHHHHHHHHCCCCCCCC-EEEEECCCEEE-CCCC---CCC
Q ss_conf             978878999999999-98741774334555--4200001100000011002456670-59987101020-2565---544
Q gi|254780353|r  467 SGKQQWNQIACEIRE-VKEIFSKSTDLGRR--RTTFCEVSRADKATLQQAMIEKEPI-TVVISNRGWIR-SLKS---HSV  538 (753)
Q Consensus       467 s~~~l~~iI~~EL~e-ikkkfgd~~~~~~R--RT~iie~~~~~~~~~~EdlI~~E~v-~V~LS~~GyIK-r~k~---~~~  538 (753)
                      |-.++-+--++|.+. |.+.||++..-.++  |.---   ..  ....|..-+=.|. .|+++=+- +| .+++   ...
T Consensus       347 DS~~lS~~A~~eaR~~I~~~yG~~YL~~~~kLk~y~~---k~--KnaQeAHEAIRPtG~~~~tP~~-lk~~L~~PniD~~  420 (688)
T TIGR01051       347 DSTRLSNEAVNEARNLIDKNYGKEYLGPKPKLKRYKS---KE--KNAQEAHEAIRPTGSVFRTPEE-LKAELKRPNIDEL  420 (688)
T ss_pred             CCHHHHHHHHHHHHHHHHHHCCHHCCCCCCCCCCHHH---CC--CCCCCHHHCCCCCCCEEECHHH-HHHHCCCCCHHHH
T ss_conf             3057899999999988886211203788742231022---16--8750011044764311017488-8522377566788


Q ss_pred             CCC--------CCCCCC--CCCCEEEEEECCCCCEEEEECCCEEEEEEHHHC--CCCCCC--C--CCCCCCCC-CCCCCE
Q ss_conf             553--------223455--555401211114781789806882787551121--212344--4--42222357-676530
Q gi|254780353|r  539 DLS--------ALHFKE--GDSLKIALHAHTTDRILLLSTDGKAYTLPAGNL--LSGRGH--G--EAIQLLID-LNHNQD  601 (753)
Q Consensus       539 ~~~--------~~~~Ke--gD~l~~~~~~~t~d~LLffTs~GkvY~l~a~~I--ps~~~k--G--~pI~~ll~-l~~~Ek  601 (753)
                      ..-        .-.+.+  .|.+...+.|.+...=+-|.-.|+-...+.|.=  ..++..  +  +--...|+ |..||.
T Consensus       421 rLY~LIW~RfVASQM~dA~~~~~~v~l~~~~g~~~~~F~A~g~~~~FdGf~kvy~e~~dd~~~alee~~~~LP~Lk~Gd~  500 (688)
T TIGR01051       421 RLYELIWKRFVASQMADARYDSLSVRLTAEKGSVEVVFKASGRKLLFDGFYKVYVEGSDDDDEALEEKDRILPPLKEGDA  500 (688)
T ss_pred             HHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEECCEEECCHHHHHHHCCCCCHHHHHCCCCCCCCCCCCCCE
T ss_conf             88899999988744877532689999986137401589740235645523666412788716752224577878888862


Q ss_pred             EEE
Q ss_conf             789
Q gi|254780353|r  602 IVT  604 (753)
Q Consensus       602 Iv~  604 (753)
                      |-.
T Consensus       501 ~~~  503 (688)
T TIGR01051       501 VKL  503 (688)
T ss_pred             EEE
T ss_conf             002


No 204
>TIGR03449 mycothiol_MshA UDP-N-acetylglucosamine: 1L-myo-inositol-1-phosphate 1-alpha-D-N-acetylglucosaminyltransferase. Members of this protein family, found exclusively in the Actinobacteria, are MshA, the glycosyltransferase of mycothiol biosynthesis. Mycothiol replaces glutathione in these species.
Probab=21.38  E-value=43  Score=12.71  Aligned_cols=10  Identities=20%  Similarity=0.607  Sum_probs=4.0

Q ss_pred             HHHHHHHHCC
Q ss_conf             8999975200
Q gi|254780353|r  401 DEIIAIIRNE  410 (753)
Q Consensus       401 D~vI~iIR~s  410 (753)
                      +++....+.+
T Consensus       294 ~~~~~~~~~a  303 (405)
T TIGR03449       294 EELVHVYRAA  303 (405)
T ss_pred             HHHHHHHHHC
T ss_conf             9999999957


No 205
>PRK11462 putative transporter; Provisional
Probab=21.14  E-value=47  Score=12.43  Aligned_cols=28  Identities=21%  Similarity=0.135  Sum_probs=18.8

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             9988789999889999766678999988
Q gi|254780353|r  430 AILNLRLRSLRKLEEYQIKSELDNLLAE  457 (753)
Q Consensus       430 aIL~mrL~rLt~le~~kl~~E~~eL~~~  457 (753)
                      +++-++-|+||+-...++++|+++-+++
T Consensus       421 ~ii~~~~Y~L~~~~~~eI~~eL~~~~~~  448 (460)
T PRK11462        421 AIIAKRYYSLTTHNLKTVMEQLAQGKRR  448 (460)
T ss_pred             HHHHHHEECCCHHHHHHHHHHHHHHHHH
T ss_conf             9999952359899999999999999884


No 206
>KOG0005 consensus
Probab=20.93  E-value=35  Score=13.38  Aligned_cols=19  Identities=32%  Similarity=0.630  Sum_probs=15.2

Q ss_pred             CCCCCHHHHHHHHHHHHCC
Q ss_conf             1289704689999999868
Q gi|254780353|r   47 RDGFKPVHRRIIHAMSEMG   65 (753)
Q Consensus        47 ~DGlKpvqRril~~m~~~~   65 (753)
                      ..|.-|+|.|++|+-.+++
T Consensus        33 keGIPp~qqrli~~gkqm~   51 (70)
T KOG0005          33 KEGIPPQQQRLIYAGKQMN   51 (70)
T ss_pred             HCCCCCHHHHHHHCCCCCC
T ss_conf             2189916663210230025


No 207
>TIGR01055 parE_Gneg DNA topoisomerase IV, B subunit; InterPro: IPR005737   DNA topoisomerases regulate the number of topological links between two DNA strands (i.e. change the number of superhelical turns) by catalysing transient single- or double-strand breaks, crossing the strands through one another, then resealing the breaks. These enzymes have several functions: to remove DNA supercoils during transcription and DNA replication; for strand breakage during recombination; for chromosome condensation; and to disentangle intertwined DNA during mitosis , . DNA topoisomerases are divided into two classes: type I enzymes (5.99.1.2 from EC; topoisomerases I, III and V) break single-strand DNA, and type II enzymes (5.99.1.3 from EC; topoisomerases II, IV and VI) break double-strand DNA .   Type II topoisomerases are ATP-dependent enzymes, and can be subdivided according to their structure and reaction mechanisms: type IIA (topoisomerase II or gyrase, and topoisomerase IV) and type IIB (topoisomerase VI). These enzymes are responsible for relaxing supercoiled DNA as well as for introducing both negative and positive supercoils .   This entry represents subunit B (parE) of topoisomerase IV from Gram negative bacteria. Topoisomerase IV primarily decatenates DNA and relaxes positive supercoils, which is important in bacteria, where the circular chromosome becomes catenated, or linked, during replication . Topoisomerase IV consists of two polypeptide subunits, parC (subunit A), which is homologous to gyrA of topoisomerase II, and parE (subunit B), which is homologous to gyrB of topoisomerase II.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003918 DNA topoisomerase (ATP-hydrolyzing) activity, 0005524 ATP binding, 0006265 DNA topological change, 0005694 chromosome.
Probab=20.88  E-value=30  Score=13.85  Aligned_cols=128  Identities=22%  Similarity=0.287  Sum_probs=64.3

Q ss_pred             CCCCCCCHHHHHHHHHHHHCCCCCCCCEEEEEHHHHHHHCCCCCCHHHHHHHHHHHHC--------CHHHCC-------C
Q ss_conf             4112897046899999998689998980354053666542768874789999999610--------013216-------6
Q gi|254780353|r   45 DLRDGFKPVHRRIIHAMSEMGLDFGAAFKKSARIVGEVIGKLHPHGDQSVYDSLVRLA--------QPFVQR-------Y  109 (753)
Q Consensus        45 d~~DGlKpvqRril~~m~~~~~~~~~~~~K~ar~vg~v~gkyhPHGd~s~y~a~v~ma--------q~~~~~-------~  109 (753)
                      .|-+||-|||||  =+||--|-..+++.    ..+-||+       |-|+=+|+..-|        ||.|..       +
T Consensus        10 ~VL~gLEPVr~R--PGMY~GGtD~~~~~----HL~~EV~-------DN~~DEA~AGfA~~i~v~lH~D~Si~v~D~GRG~   76 (647)
T TIGR01055        10 EVLDGLEPVRKR--PGMYTGGTDTTRPN----HLVQEVI-------DNSVDEALAGFASKIEVILHQDQSIEVIDNGRGM   76 (647)
T ss_pred             HHHCCCCCCCCC--CCCEECCCCCCCCH----HHHHHHH-------HHHHHHHHCCCCEEEEEEECCCCEEEEEECCCCC
T ss_conf             220168773428--87201786565301----3455544-------3335555406530788998289617998888303


Q ss_pred             CCCCCCCCC-CCCCCCCCCCHHHHHHHHH---HHHHH--------------HHHHCCCCCCCCCCCCCCCEEEEEE-ECC
Q ss_conf             132678870-8867797100246899855---99999--------------9842187861752167996324223-123
Q gi|254780353|r  110 PLISGQGNF-GNIDGDSAAAYRYTEARMT---QVAEL--------------ILQGVDEDAVDFRDTYNEEDSEPVV-FPS  170 (753)
Q Consensus       110 pli~g~Gnf-Gs~~~d~~Aa~RYte~rl~---~~~~~--------------ll~di~~~~v~~~~n~D~~~~EP~~-lp~  170 (753)
                      | ||-|-.| |-      .|.--+=|+|+   +||+.              ...-+. +.|+-.-.=+|....-.+ ==+
T Consensus        77 P-vD~HP~~P~~------sa~EvILt~LHaG~KFSN~~Y~~sGGLHGVGISVVNALS-~~~~i~V~~~G~~Y~~af~~G~  148 (647)
T TIGR01055        77 P-VDIHPKEPGV------SAVEVILTKLHAGGKFSNKNYEFSGGLHGVGISVVNALS-KRVKIKVKRQGKLYSIAFENGA  148 (647)
T ss_pred             C-CCCCCCCCCC------CEEEEEEEECCCCCCCCCCCCCCCCCEECCHHHHEEECC-CEEEEEEEECCEEEEHHHHCCC
T ss_conf             4-4278888888------623556430057852114440136860021432022013-2367899746704320221575


Q ss_pred             CCCHHHHCCCCC-HHHHHHHHCCC
Q ss_conf             452676426650-46777751677
Q gi|254780353|r  171 KFPNLLANGTSG-IAVGMATSIPS  193 (753)
Q Consensus       171 ~~P~lL~Ng~~G-IavG~at~ipp  193 (753)
                      ++-.|-+-|++| =..|-+-+--|
T Consensus       149 K~~dL~~~~~~GkR~~GT~v~F~P  172 (647)
T TIGR01055       149 KVTDLEVVGTCGKRLTGTSVHFTP  172 (647)
T ss_pred             CHHHHHHHHCCCCCCCCCEEEECC
T ss_conf             110233211267765563577316


No 208
>cd04469 S1_Hex1 S1_Hex1: Hex1, S1-like RNA-binding domain. Hex1 protein is the major component of the Woronin body in filamentous fungi. The Woronin body is a dense vesicle and plays a vital role in filamentous fungi cell integrity. When cell damage occurs, Woronin bodies seal the septal pore to prevent further cytoplasmic bleeding. Hex1 protein self-assembles to form the solid core of the Woronin body vesicle. The Hex1 sequence and structure are similar to eukaryotic initiation factor 5A (eIF5A), suggesting they share a common ancestor during evolution. All members of the EF superfamily to which Hex1 belongs, contain an S1 domain, which has been shown to bind RNA or single-stranded DNA and often interacts with the ribosome.
Probab=20.79  E-value=48  Score=12.38  Aligned_cols=26  Identities=23%  Similarity=0.466  Sum_probs=16.7

Q ss_pred             CCCCCCCCCCCCHHHHHHHHHCCCCEEEEE
Q ss_conf             778877601069889998985033415999
Q gi|254780353|r  224 PDFPTGGIIVESRESIVESYRLGRGGFRVR  253 (753)
Q Consensus       224 PDFPTGG~i~~~~~~i~~~y~tG~G~i~~r  253 (753)
                      |=++.++..    .-|.+||+.||||+++-
T Consensus        29 pVidqs~L~----~Rl~~Afe~grgsVR~L   54 (75)
T cd04469          29 PVIDQSNLW----TRLKTAFESGRGSVRVL   54 (75)
T ss_pred             EEECCCHHH----HHHHHHHHCCCCCEEEE
T ss_conf             233153589----99999976489839999


No 209
>pfam09133 SANTA SANTA (SANT Associated). The SANTA domain (SANT Associated domain) is approximately 90 amino acids in length and is conserved in Eukaryota. It is sometimes found in association with the SANT domain (pfam00249, also known as Myb-like DNA-binding domain) implying a putative function in regulating chromatin remodelling. Sequence analysis has showed that the SANTA domain is likely to form four central beta-sheets with three flanking alpha- helixes. Many conserved hydrophobic residues are present which implying a possible role in protein-protein interactions.
Probab=20.67  E-value=48  Score=12.36  Aligned_cols=62  Identities=13%  Similarity=0.156  Sum_probs=36.7

Q ss_pred             CEEECCCCCCCCCCCCCCCCCC---CCEEEEEECCCCCEEEEECCCEEEEEEHH-HCCCCCCCCCCC
Q ss_conf             1020256554455322345555---54012111147817898068827875511-212123444422
Q gi|254780353|r  528 GWIRSLKSHSVDLSALHFKEGD---SLKIALHAHTTDRILLLSTDGKAYTLPAG-NLLSGRGHGEAI  590 (753)
Q Consensus       528 GyIKr~k~~~~~~~~~~~KegD---~l~~~~~~~t~d~LLffTs~GkvY~l~a~-~Ips~~~kG~pI  590 (753)
                      =|+|+..+. ..+.|....++.   ...+...+.-++.-.+.|..|..|.|... +.+..+..|-|.
T Consensus         6 Wwlk~~~~~-i~V~G~~~~~~~~~~~~~S~~IvkR~~~~~l~T~dG~~~~L~G~in~~~~~~nGfs~   71 (93)
T pfam09133         6 WWLKKNNKD-LCVEGFRTEENTGMILFHSNFIVKRHSSTTLETVDGITYVLVGFIDRSRMLKNGFPS   71 (93)
T ss_pred             HHHHHCCCC-EEEEEEEECCCCCEEEEECHHHHEEECCCEEEECCCEEEEEECCCCHHHHHHCCCCH
T ss_conf             566433784-799858613564148880155410012437992587099994656888898859998


No 210
>KOG1712 consensus
Probab=20.59  E-value=48  Score=12.38  Aligned_cols=14  Identities=43%  Similarity=0.847  Sum_probs=9.0

Q ss_pred             CCCCCCCCCCCCCH
Q ss_conf             67788776010698
Q gi|254780353|r  223 GPDFPTGGIIVESR  236 (753)
Q Consensus       223 gPDFPTGG~i~~~~  236 (753)
                      =||||.-|+...+.
T Consensus        18 ~pdFPk~GI~F~Di   31 (183)
T KOG1712          18 VPDFPKKGIMFQDI   31 (183)
T ss_pred             CCCCCCCCEEHHHH
T ss_conf             78999886002000


No 211
>pfam01025 GrpE GrpE.
Probab=20.59  E-value=48  Score=12.35  Aligned_cols=14  Identities=14%  Similarity=0.230  Sum_probs=9.8

Q ss_pred             CCCEEEEECCCEEE
Q ss_conf             67059987101020
Q gi|254780353|r  518 EPITVVISNRGWIR  531 (753)
Q Consensus       518 E~v~V~LS~~GyIK  531 (753)
                      +..++-+-+.||.-
T Consensus       135 ~~~I~~v~q~GY~l  148 (162)
T pfam01025       135 PGTVVEVLQKGYKL  148 (162)
T ss_pred             CCEEEEEEECCCEE
T ss_conf             29899985459387


No 212
>PRK09165 replicative DNA helicase; Provisional
Probab=20.53  E-value=48  Score=12.34  Aligned_cols=61  Identities=18%  Similarity=0.068  Sum_probs=28.1

Q ss_pred             EEEEECCCCCCCHHHHHHHHHHHHHH-CCCHHHHHHHHCC--CCCEEEEEEEECCCCCHHHHHHHHHH
Q ss_conf             79995242002168999999998640-2221345776406--76605889850454588999998754
Q gi|254780353|r  267 CIVVTEIPYQVQKSRLIEKIAELIIA-KRIPLLEDIRDES--AEDVRIVLFPKNRSLDPDLLMESIFM  331 (753)
Q Consensus       267 ~ivIteiPy~v~k~~~ie~I~~lv~~-~ki~gi~dirDeS--d~~~~~vi~~~~r~~~~~~vl~~Lyk  331 (753)
                      .++|--=-+.+.|+.+.-.|+.-+-. -....   ..+.+  ...+..|.+. +-+-..+.++..+..
T Consensus       206 dLiIIAARPsmGKTafaLniA~n~A~~~~~~~---~~~~~~~~~~g~~V~~F-SLEMs~~ql~~Rlls  269 (484)
T PRK09165        206 DLIILAGRPSMGKTALATNIAFNAAKAYLREA---QPDGSKKAVNGGVVGFF-SLEMSAEQLATRILS  269 (484)
T ss_pred             CEEEEEECCCCCHHHHHHHHHHHHHHHHHCCC---CCCCCCCCCCCCEEEEE-ECCCCHHHHHHHHHH
T ss_conf             37999607999778999999999998741022---22332113689848999-477999999999999


No 213
>cd00200 WD40 WD40 domain, found in a number of eukaryotic proteins that cover a wide variety of functions including adaptor/regulatory modules in signal transduction, pre-mRNA processing and cytoskeleton assembly; typically contains a GH dipeptide 11-24 residues from its N-terminus and the WD dipeptide at its C-terminus and is 40 residues long, hence the name WD40; between GH and WD lies a conserved core; serves as a stable propeller-like platform to which proteins can bind either stably or reversibly; forms a propeller-like structure with several blades where each blade is composed of a four-stranded anti-parallel b-sheet; instances with few detectable copies are hypothesized to form larger structures by dimerization; each WD40 sequence repeat forms the first three strands of one blade and the last strand in the next blade; the last C-terminal WD40 repeat completes the blade structure of the first WD40 repeat to create the closed ring propeller-structure; residues on the top and botto
Probab=20.52  E-value=48  Score=12.34  Aligned_cols=61  Identities=10%  Similarity=0.183  Sum_probs=24.4

Q ss_pred             CCCEEEEEECCCCEEEEEHHHHHCCCCCCEEEEEECC-CCCEEEEEECC-CCEEEEEECCCCEEEEEHHH
Q ss_conf             9985999974897899638874023335627885368-98056889618-98099995699389955787
Q gi|254780353|r  610 STCKLLVVSSKGNAFIVEESEIIANTRKGKTFLKVSS-EEKMKLVVKVT-GDHVAVVGENRKLLIFSIDQ  677 (753)
Q Consensus       610 ~~~~lll~Tk~G~ikr~~l~~~~~~~k~Gk~~ikLk~-~D~li~v~~~~-~d~iiliT~~Gk~LrF~~~e  677 (753)
                      .+.+++..+.+|.++....+.       +.....+.. .+.+..+.... +..++..+..|.+..|+...
T Consensus       146 ~~~~i~~~~~dg~v~i~d~~~-------~~~~~~~~~h~~~i~~i~~~~~~~~~~~~~~d~~i~i~d~~~  208 (289)
T cd00200         146 DGTFVASSSQDGTIKLWDLRT-------GKCVATLTGHTGEVNSVAFSPDGEKLLSSSSDGTIKLWDLST  208 (289)
T ss_pred             CCCEEEEECCCCEEEEEECCC-------CCEEEEEEECCCCCEEEEECCCCCCCEEECCCCEEEEEECCC
T ss_conf             998999973899799999999-------949899986155632688889998147415999899999999


No 214
>cd07908 Mn_catalase_like Manganese catalase-like protein, ferritin-like diiron-binding domain. This uncharacterized bacterial protein family has a ferritin-like domain similar to that of the manganese catalase protein of Lactobacillus plantarum and the bll3758 protein of Bradyrhizobium japonicum.  Ferritin-like, diiron-carboxylate proteins participate in a range of functions including iron regulation, mono-oxygenation, and reactive radical production. These proteins are characterized by the fact that they catalyze dioxygen-dependent oxidation-hydroxylation reactions within diiron centers; one exception is manganese catalase, which catalyzes peroxide-dependent oxidation-reduction within a dimanganese center. Diiron-carboxylate proteins are further characterized by the presence of duplicate metal ligands, glutamates and histidines (ExxH) and two additional glutamates within a four-helix bundle. Outside of these conserved residues there is little obvious homology. Members include bacterio
Probab=20.35  E-value=32  Score=13.66  Aligned_cols=21  Identities=10%  Similarity=0.325  Sum_probs=16.4

Q ss_pred             CCCCCCCCCCCCCHHHHHHHH
Q ss_conf             870886779710024689985
Q gi|254780353|r  116 GNFGNIDGDSAAAYRYTEARM  136 (753)
Q Consensus       116 GnfGs~~~d~~Aa~RYte~rl  136 (753)
                      -+||..+|.-.|+|||..-++
T Consensus        20 ~~~gG~~gElsA~~qYl~q~~   40 (154)
T cd07908          20 DDYAGTNSELTAISQYIYQHL   40 (154)
T ss_pred             HHHCCCCHHHHHHHHHHHHHH
T ss_conf             984896168999999999897


No 215
>TIGR00746 arcC carbamate kinase; InterPro: IPR003964   The arginine dihydrolase (AD) pathway is found in many prokaryotes and some primitive eukaryotes. The three- enzyme anaerobic pathway breaks down L-arginine to form 1 mol of ATP, carbon dioxide and ammonia. In simpler bacteria, the first enzyme, arginine deiminase, can account for up to 100f total cell protein .   Carbamate kinase is involved in the last step of the AD pathway, converting carbamoyl phosphate and ADP into ammonia, carbon dioxide and ATP . The second step of the pathway involves the degradation of L-citrulline to carbamoyl phosphate and L-ornithine, using ornithine carbamoyltransferase .    The crystal structure of Enterococcus faecium carbamate kinase has been determined to 2.8A resolution . The enzyme exists as a homodimer of two 33kDa subunits. The hallmark of the dimer is a 16-stranded beta-sheet, surrounded by alpha-helices. Each subunit contains an active site within a large crevice.; GO: 0008804 carbamate kinase activity, 0006525 arginine metabolic process.
Probab=20.27  E-value=36  Score=13.32  Aligned_cols=11  Identities=27%  Similarity=0.208  Sum_probs=5.2

Q ss_pred             HHHHHHHHCCC
Q ss_conf             99998640222
Q gi|254780353|r  285 KIAELIIAKRI  295 (753)
Q Consensus       285 ~I~~lv~~~ki  295 (753)
                      .|..||+++.|
T Consensus       181 ~Ik~L~e~g~i  191 (321)
T TIGR00746       181 VIKTLVENGVI  191 (321)
T ss_pred             HHHHHHHCCEE
T ss_conf             78998648827


No 216
>PRK09956 hypothetical protein; Provisional
Probab=20.18  E-value=32  Score=13.72  Aligned_cols=43  Identities=21%  Similarity=0.318  Sum_probs=25.3

Q ss_pred             EECCCCCHHHHCCCCCHHHHHHHHCCCCCHHHHHHHHHHHHHCCCCCCHHHHHHCCCCCCC
Q ss_conf             3123452676426650467777516777889999999998728653201344320367788
Q gi|254780353|r  167 VFPSKFPNLLANGTSGIAVGMATSIPSHNVQEICEAALALIDNPEISIEKLLEYIIGPDFP  227 (753)
Q Consensus       167 ~lp~~~P~lL~Ng~~GIavG~at~ipphnl~ev~~a~~~~i~~~~~~~~~l~~~i~gPDFP  227 (753)
                      -||..+|.|+-||-.+       ..| +.++     ..-+     ....++.+.+..++||
T Consensus       113 ~LP~IiPiv~YhG~~~-------p~p-~s~~-----~~d~-----f~~~~la~~l~~~~y~  155 (308)
T PRK09956        113 RVPLVVPLLFYHGETS-------PYP-YSLN-----WLDE-----FDDPQLARQLYTEAFP  155 (308)
T ss_pred             CCCCEEEEEEECCCCC-------CCC-CCCC-----HHHH-----CCCHHHHHHHCCCCCE
T ss_conf             6884236887758778-------877-8634-----9986-----2788999974557860


No 217
>pfam03861 ANTAR ANTAR domain. ANTAR (AmiR and NasR transcription antitermination regulators) is an RNA-binding domain found in bacterial transcription antitermination regulatory proteins. The majority of the domain consists of a coiled-coil.
Probab=20.11  E-value=39  Score=13.02  Aligned_cols=22  Identities=23%  Similarity=0.453  Sum_probs=17.1

Q ss_pred             CCCCCCCCCCCCCCHHHHHHHH
Q ss_conf             0011000000257757788998
Q gi|254780353|r  411 DKPKPVMVSRFSLTENQVDAIL  432 (753)
Q Consensus       411 ~~~k~~L~~~f~lse~QA~aIL  432 (753)
                      +.||-.||..+++||.||-..|
T Consensus        16 ~~AkgiLm~~~~~~e~~A~~~L   37 (56)
T pfam03861        16 EQAKGILMERRGLSEEEAFELL   37 (56)
T ss_pred             HHHHHHHHHHHCCCHHHHHHHH
T ss_conf             9999999988691999999999


No 218
>TIGR01127 ilvA_1Cterm threonine dehydratase; InterPro: IPR005789    Serine and threonine dehydratases ,  are functionally and structurally related pyridoxal-phosphate dependent enzymes. L-serine dehydratase () and D-serine dehydratase () catalyze the dehydratation of L-serine (respectively D-serine) into ammonia and pyruvate. Threonine dehydratase () (TDH) catalyzes the dehydratation of threonine into alpha-ketobutarate and ammonia. In Escherichia coli and other microorganisms, two classes of TDH are known to exist. One is involved in the biosynthesis of isoleucine, the other in hydroxamino acid catabolism. Threonine synthase () is also a pyridoxal-phosphate enzyme, it catalyzes the transformation of homoserine-phosphate into threonine. It has been shown  that threonine synthase is distantly related to the serine/threonine dehydratases. In all these enzymes, the pyridoxal-phosphate group is attached to a lysine residue.    A form of threonine dehydratase with two copies of the C-terminal domain  is described by . This model describes a phylogenetically distinct which branches with the catabolic threonine dehydratase of E. coli; many members are designated as catabolic for this reason. However, the catabolic form lacks any  domain. Many members of this model are found in species with other isoleucine biosynthetic enzymes.; GO: 0004794 L-threonine ammonia-lyase activity.
Probab=20.08  E-value=27  Score=14.22  Aligned_cols=90  Identities=16%  Similarity=0.178  Sum_probs=36.0

Q ss_pred             CCHHHHHHHHHHHHHHCCCH-------HHHHHHH-CCC-CCEEEEEEEEC-CCCCHHHHHHHHHHHCCCCCCCCC-CEEE
Q ss_conf             21689999999986402221-------3457764-067-66058898504-545889999987542000012233-1133
Q gi|254780353|r  277 VQKSRLIEKIAELIIAKRIP-------LLEDIRD-ESA-EDVRIVLFPKN-RSLDPDLLMESIFMLSDMETRFPL-NMNV  345 (753)
Q Consensus       277 v~k~~~ie~I~~lv~~~ki~-------gi~dirD-eSd-~~~~~vi~~~~-r~~~~~~vl~~Lyk~T~Lq~sf~~-N~~~  345 (753)
                      |+-+.+-.-|--|.+..|+-       |++-+=. --| .+|+.|.+-.+ -+.|+..+-.-.+|  .|..+... -..+
T Consensus       234 V~eeEIA~A~~~LLEr~Ki~aEGAGA~gvAA~L~~K~~~~kG~K~~~v~SGGNID~~~l~~iI~k--GL~~~GR~v~I~~  311 (381)
T TIGR01127       234 VDEEEIAKAILLLLERAKIVAEGAGAVGVAAVLEDKVDYVKGKKVAVVVSGGNIDLNLLEKIILK--GLVKSGRKVRIET  311 (381)
T ss_pred             ECHHHHHHHHHHHHCCCCEEECCCHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCHHHHHHHHHH--HHHCCCCEEEEEE
T ss_conf             47377999999986077478827458999999975403689828999985477686677788655--2220583699999


Q ss_pred             EECCCCCCCCCHHHHHHHHHHHHHHH
Q ss_conf             31268972204999999899998999
Q gi|254780353|r  346 LSMGRVPQVMPLDGILKEWLAHRREV  371 (753)
Q Consensus       346 l~~~~~P~~~~l~eil~~f~~~R~~v  371 (753)
                      +..++ |=.  |++++..--+.|.++
T Consensus       312 ~~~D~-PG~--L~~ll~~~A~~~aNi  334 (381)
T TIGR01127       312 VIPDR-PGA--LYKLLEVIAEERANI  334 (381)
T ss_pred             EEECC-CCC--HHHHHHHHHHHCCCE
T ss_conf             98238-986--699999999816978


Done!