Query         gi|254780306|ref|YP_003064719.1| DNA topoisomerase I [Candidatus Liberibacter asiaticus str. psy62]
Match_columns 837
No_of_seqs    331 out of 2557
Neff          6.3 
Searched_HMMs 39220
Date          Sun May 29 16:09:09 2011
Command       /home/congqian_1/programs/hhpred/hhsearch -i 254780306.hhm -d /home/congqian_1/database/cdd/Cdd.hhm 

 No Hit                             Prob E-value P-value  Score    SS Cols Query HMM  Template HMM
  1 PRK09138 DNA topoisomerase I;  100.0       0       0 2202.1  72.4  833    1-835     1-838 (887)
  2 PRK07941 DNA topoisomerase I;  100.0       0       0 2015.4  68.6  814    2-835    10-901 (933)
  3 PRK07561 DNA topoisomerase I;  100.0       0       0 2009.3  67.1  790    2-836     3-846 (878)
  4 PRK08780 DNA topoisomerase III 100.0       0       0 1921.4  67.0  748    2-833     4-760 (783)
  5 PRK06599 DNA topoisomerase I;  100.0       0       0 1910.7  68.0  761    1-769     1-772 (776)
  6 TIGR01051 topA_bact DNA topois 100.0       0       0 1744.4  38.9  632    3-639     1-687 (688)
  7 PRK06319 DNA topoisomerase I/S 100.0       0       0 1608.7  57.5  701    2-743     4-725 (864)
  8 PRK09137 DNA topoisomerase I;  100.0       0       0 1553.6  61.8  703    2-744     3-713 (761)
  9 PRK09001 DNA topoisomerase I;  100.0       0       0 1551.4  60.3  602    2-642     4-644 (869)
 10 PRK05582 DNA topoisomerase I;  100.0       0       0 1509.5  58.6  680    1-737     1-684 (692)
 11 PRK08413 consensus             100.0       0       0 1511.6  57.0  718    1-806     2-723 (733)
 12 PRK08938 DNA topoisomerase I;  100.0       0       0 1495.0  59.8  676    2-738     5-683 (692)
 13 PRK05823 consensus             100.0       0       0 1419.9  52.2  641    2-674     4-669 (691)
 14 COG0550 TopA Topoisomerase IA  100.0       0       0 1333.6  49.2  550    1-575     1-557 (570)
 15 PRK08620 DNA topoisomerase III 100.0       0       0 1314.2  55.1  615    1-680     2-673 (726)
 16 PRK08174 DNA topoisomerase III 100.0       0       0 1297.9  54.0  599    1-646     1-657 (670)
 17 PRK07141 DNA topoisomerase I;  100.0       0       0 1300.3  50.2  592    2-643     4-606 (622)
 18 PRK07220 DNA topoisomerase I;  100.0       0       0 1278.9  54.5  614    1-668     1-648 (740)
 19 PRK07219 DNA topoisomerase I;  100.0       0       0 1268.5  56.3  660    1-744     4-701 (769)
 20 PRK07726 DNA topoisomerase III 100.0       0       0 1173.4  53.4  598    1-640     1-664 (716)
 21 PRK09401 reverse gyrase; Revie 100.0       0       0 1187.2  42.1  513    2-570   602-1174(1176)
 22 PRK08173 DNA topoisomerase III 100.0       0       0 1153.2  54.6  698    2-766     4-783 (857)
 23 PRK09031 DNA topoisomerase III 100.0       0       0 1156.3  51.4  550    1-574     1-610 (649)
 24 PRK05776 DNA topoisomerase III 100.0       0       0 1153.4  49.3  561    3-611    11-611 (675)
 25 TIGR01056 topB DNA topoisomera 100.0       0       0 1026.6  42.2  593    1-634     3-667 (755)
 26 TIGR01057 topA_arch DNA topois 100.0       0       0 1017.6  40.6  585    5-633     1-637 (637)
 27 pfam01131 Topoisom_bac DNA top 100.0       0       0  856.1  33.5  397  130-559     2-403 (403)
 28 KOG1956 consensus              100.0       0       0  825.6  38.5  678    2-770     3-740 (758)
 29 COG1110 Reverse gyrase [DNA re 100.0       0       0  835.8  31.5  506    3-567   620-1185(1187)
 30 cd00186 TOP1Ac DNA Topoisomera 100.0       0       0  824.3  31.1  375  132-568     1-380 (381)
 31 TIGR01054 rgy reverse gyrase;  100.0       0       0  778.7  21.5  521    3-565   661-1840(1843)
 32 smart00437 TOP1Ac Bacterial DN 100.0       0       0  549.2  20.7  255  248-520     1-259 (259)
 33 COG1754 Uncharacterized C-term 100.0       0       0  519.6  18.5  247  583-835     4-258 (298)
 34 KOG1957 consensus              100.0       0       0  407.3  10.7  478    3-561     5-528 (555)
 35 cd03363 TOPRIM_TopoIA_TopoI TO 100.0 2.3E-37 5.9E-42  299.5  14.6  122    1-127     1-123 (123)
 36 cd03361 TOPRIM_TopoIA_RevGyr T 100.0 6.8E-36 1.7E-40  288.5  13.5  122    2-127     2-170 (170)
 37 PRK07941 DNA topoisomerase I;  100.0   6E-33 1.5E-37  266.4  13.6  161  659-834   638-833 (933)
 38 PRK07561 DNA topoisomerase I;  100.0 8.7E-32 2.2E-36  257.7  13.7  161  659-834   602-780 (878)
 39 PRK06599 DNA topoisomerase I;  100.0 3.5E-31   9E-36  253.1  14.6  163  657-836   599-771 (776)
 40 cd01028 TOPRIM_TopoIA TOPRIM_T 100.0 1.1E-30 2.8E-35  249.4  15.0  123    1-127     1-142 (142)
 41 cd03362 TOPRIM_TopoIA_TopoIII  100.0 1.6E-30   4E-35  248.2  14.8  124    1-127     1-151 (151)
 42 PRK09138 DNA topoisomerase I;  100.0 7.2E-30 1.8E-34  243.3  12.6  158  657-835   604-771 (887)
 43 smart00436 TOP1Bc Bacterial DN 100.0 6.4E-29 1.6E-33  236.1  10.0   88  107-194     1-89  (89)
 44 PRK08780 DNA topoisomerase III  99.9 5.5E-27 1.4E-31  221.6  12.2  165  601-775   590-770 (783)
 45 COG1754 Uncharacterized C-term  99.9 2.8E-27   7E-32  223.9   9.5  164  601-770    77-261 (298)
 46 LOAD_Toprim consensus           99.9 3.1E-25   8E-30  208.4  11.6   98    1-128     1-98  (98)
 47 pfam01751 Toprim Toprim domain  99.5   2E-13   5E-18  119.9  10.0   89    1-113     1-89  (89)
 48 smart00493 TOPRIM topoisomeras  99.4   7E-13 1.8E-17  115.7   8.8   74    1-99      1-74  (76)
 49 PRK09137 DNA topoisomerase I;   99.3 2.9E-11 7.5E-16  103.6   9.1  113  601-743   638-754 (761)
 50 PRK08413 consensus              99.3 3.7E-11 9.6E-16  102.8   8.9  107  602-737   613-722 (733)
 51 PRK06319 DNA topoisomerase I/S  99.2 5.3E-11 1.3E-15  101.6   6.9   80  602-687   645-726 (864)
 52 PRK08938 DNA topoisomerase I;   99.1 9.3E-11 2.4E-15   99.8   5.4   67  602-680   617-683 (692)
 53 PRK07219 DNA topoisomerase I;   99.0 4.6E-09 1.2E-13   87.1  11.0  113  601-743   631-746 (769)
 54 PRK05582 DNA topoisomerase I;   99.0   6E-10 1.5E-14   93.7   4.4  106  657-805   575-684 (692)
 55 PRK09001 DNA topoisomerase I;   98.8 1.5E-08 3.9E-13   83.2   5.6  146  602-764   664-815 (869)
 56 pfam01396 zf-C4_Topoisom Topoi  98.4 1.3E-07 3.2E-12   76.2   2.5   38  602-641     1-38  (39)
 57 PRK05823 consensus              98.3 3.7E-07 9.4E-12   72.8   1.9   76  657-745   603-684 (691)
 58 COG0551 TopA Zn-finger domain   98.2 3.8E-06 9.6E-11   65.2   6.4   66  597-673    12-79  (140)
 59 cd00188 TOPRIM Topoisomerase-p  97.9  0.0002 5.1E-09   52.2   9.6   72    2-98      2-73  (83)
 60 PRK08620 DNA topoisomerase III  97.4  0.0004   1E-08   50.0   6.1   61  657-737   611-672 (726)
 61 COG0551 TopA Zn-finger domain   97.3 0.00024   6E-09   51.7   3.8   72  600-684    58-130 (140)
 62 PRK00076 recR recombination pr  96.9   0.013 3.3E-07   38.6   9.2   64   61-128   122-195 (197)
 63 PRK13844 recombination protein  96.8   0.019 4.8E-07   37.4   9.4   62   62-128   127-198 (200)
 64 COG0353 RecR Recombinational D  96.7   0.041   1E-06   34.9  10.8   86    3-111    82-171 (198)
 65 COG4026 Uncharacterized protei  96.6   0.039   1E-06   35.1  10.0   80    3-112    10-94  (290)
 66 TIGR00615 recR recombination p  96.2   0.029 7.4E-07   36.0   7.4  102    3-138    85-195 (205)
 67 cd01025 TOPRIM_recR TOPRIM_rec  96.1   0.057 1.4E-06   33.8   8.4   87    2-111     2-92  (112)
 68 PRK07220 DNA topoisomerase I;   95.8   0.018 4.5E-07   37.6   4.8  114  373-506   198-312 (740)
 69 TIGR01051 topA_bact DNA topois  95.8  0.0072 1.8E-07   40.6   2.7  103  373-477   188-306 (688)
 70 PRK05776 DNA topoisomerase III  94.6    0.13 3.4E-06   31.0   6.3  113  375-506   205-319 (675)
 71 COG1658 Small primase-like pro  93.9    0.17 4.5E-06   30.2   5.6   68   59-127    43-119 (127)
 72 cd01027 TOPRIM_RNase_M5_like T  93.8    0.45 1.1E-05   27.1   7.6   68    2-97      3-70  (81)
 73 PRK07141 DNA topoisomerase I;   93.7    0.23   6E-06   29.2   6.1   58  444-505   233-294 (622)
 74 pfam01131 Topoisom_bac DNA top  93.6    0.26 6.6E-06   28.9   6.0   57  449-506   101-158 (403)
 75 PRK09031 DNA topoisomerase III  93.1    0.43 1.1E-05   27.3   6.6   56  449-505   270-327 (649)
 76 smart00437 TOP1Ac Bacterial DN  93.0    0.34 8.6E-06   28.0   5.9   93  172-269   123-219 (259)
 77 cd00186 TOP1Ac DNA Topoisomera  92.4    0.43 1.1E-05   27.3   5.8   52  453-505    69-121 (381)
 78 PRK08174 DNA topoisomerase III  92.3    0.16 4.2E-06   30.4   3.6  123  373-505   193-318 (670)
 79 TIGR01057 topA_arch DNA topois  91.4    0.75 1.9E-05   25.4   6.1   56  410-478   234-289 (637)
 80 pfam01396 zf-C4_Topoisom Topoi  91.1    0.18 4.7E-06   30.0   2.7   26  713-738     1-26  (39)
 81 PRK07726 DNA topoisomerase III  90.9    0.81 2.1E-05   25.2   5.8  117  374-506   202-320 (716)
 82 PRK04031 DNA primase; Provisio  88.6       1 2.7E-05   24.4   4.9   37  305-341   132-168 (420)
 83 TIGR02044 CueR Cu(I)-responsiv  82.1     1.2   3E-05   23.9   2.7   41  268-320     5-48  (127)
 84 PRK10046 dpiA two-component re  79.3     2.6 6.7E-05   21.3   3.6   80    1-85      5-92  (225)
 85 KOG1956 consensus               77.1   0.024 6.2E-07   36.6  -7.3  355  343-832   350-734 (758)
 86 KOG1502 consensus               76.9     5.2 0.00013   19.1   5.9   89   17-117    25-131 (327)
 87 PTZ00150 phosphoglucomutase; P  75.6     5.6 0.00014   18.9   5.9   15  552-566   449-463 (593)
 88 COG0358 DnaG DNA primase (bact  75.2     5.7 0.00015   18.8   5.1   16   75-90     55-70  (568)
 89 pfam09653 consensus             74.4       2   5E-05   22.3   1.9   49  260-319    16-64  (75)
 90 cd01029 TOPRIM_primases TOPRIM  73.6     6.2 0.00016   18.5   6.1   68    2-98      2-69  (79)
 91 TIGR01562 FdhE formate dehydro  73.0     2.8 7.1E-05   21.1   2.4   29  602-630   188-220 (312)
 92 TIGR02173 cyt_kin_arch cytidyl  71.2     2.6 6.5E-05   21.4   1.9   71    9-92     14-86  (173)
 93 smart00529 HTH_DTXR Helix-turn  71.2     6.6 0.00017   18.3   3.9   40  482-522     8-48  (96)
 94 pfam09151 DUF1936 Domain of un  66.4     3.4 8.8E-05   20.5   1.7   32  603-635     2-34  (36)
 95 cd03364 TOPRIM_DnaG_primases T  66.4     8.7 0.00022   17.4   7.1   69    2-99      2-70  (79)
 96 PRK03902 manganese transport t  64.9     9.2 0.00023   17.2   4.0   42  481-523    30-72  (142)
 97 COG0068 HypF Hydrogenase matur  64.6     7.3 0.00019   18.0   3.1   18  473-490   577-594 (750)
 98 PRK11050 manganese transport r  63.4     9.8 0.00025   17.1   4.0   39  483-522    64-103 (155)
 99 pfam09526 DUF2387 Probable met  62.5     8.1 0.00021   17.7   3.0   42  602-646     8-49  (61)
100 PRK08208 coproporphyrinogen II  62.2     6.8 0.00017   18.2   2.5   45  493-540   386-430 (436)
101 PRK06294 coproporphyrinogen II  62.1     3.5 8.9E-05   20.4   1.1   41  492-535   333-373 (374)
102 smart00347 HTH_MARR helix_turn  61.8     5.6 0.00014   18.9   2.1   50  471-524    25-81  (101)
103 PRK08599 coproporphyrinogen II  60.9     4.1  0.0001   19.9   1.2   43  482-524   327-369 (377)
104 PRK05660 coproporphyrinogen II  60.5       5 0.00013   19.2   1.6   40  484-524   332-371 (378)
105 pfam06969 HemN_C HemN C-termin  59.4     8.1 0.00021   17.7   2.5   54  466-519    54-118 (118)
106 PRK08166 NADH dehydrogenase su  59.2     4.5 0.00011   19.6   1.2   13  137-149   154-166 (858)
107 TIGR00314 cdhA CO dehydrogenas  59.0     3.3 8.4E-05   20.6   0.5   21  816-836   749-769 (795)
108 pfam07848 PaaX PaaX-like prote  58.1     8.2 0.00021   17.6   2.4   38  469-507    19-56  (70)
109 PRK08629 coproporphyrinogen II  57.4       5 0.00013   19.2   1.2   41  483-523   359-399 (424)
110 TIGR01700 PNPH purine nucleosi  57.0     8.1 0.00021   17.7   2.2   34  652-702    42-76  (259)
111 PRK08949 consensus              56.9     5.6 0.00014   18.9   1.4   41  483-524   331-371 (378)
112 PRK05799 coproporphyrinogen II  55.9     5.3 0.00013   19.1   1.1   42  483-524   327-368 (374)
113 COG1675 TFA1 Transcription ini  55.8     8.3 0.00021   17.6   2.1   31  268-306    37-67  (176)
114 PRK08898 coproporphyrinogen II  55.8     6.9 0.00018   18.2   1.7   35  490-524   353-387 (393)
115 KOG2767 consensus               55.6     5.1 0.00013   19.2   1.0   33  471-504   262-294 (400)
116 TIGR02349 DnaJ_bact chaperone   55.6     7.8  0.0002   17.8   1.9   46  597-642   183-229 (386)
117 TIGR01296 asd_B aspartate-semi  54.8      12 0.00031   16.3   2.8  101  160-293    32-148 (350)
118 PRK09129 NADH dehydrogenase su  54.7     4.7 0.00012   19.5   0.7   11   77-87     97-107 (777)
119 PRK07860 NADH dehydrogenase su  54.7     8.4 0.00022   17.5   2.0   17  135-151   165-181 (809)
120 COG1846 MarR Transcriptional r  54.4      14 0.00035   16.0   4.0   41  483-524    46-93  (126)
121 smart00532 LIGANc Ligase N fam  54.0     5.7 0.00014   18.8   1.0   27  604-635   401-427 (441)
122 TIGR00757 RNaseEG ribonuclease  53.7      13 0.00034   16.0   2.9   44  511-559   373-417 (464)
123 PRK02362 ski2-like helicase; P  51.6      15 0.00038   15.7   5.0   48  493-547   469-516 (736)
124 PRK09130 NADH dehydrogenase su  51.2      14 0.00036   15.9   2.7   16  816-831   663-678 (680)
125 TIGR01973 NuoG NADH-quinone ox  51.2      10 0.00027   16.8   2.0   27  532-558   453-482 (715)
126 PRK04017 hypothetical protein;  50.8      15 0.00039   15.6   5.1   42   60-101    52-94  (132)
127 KOG2324 consensus               49.8      12 0.00031   16.4   2.1   17  660-676   287-303 (457)
128 TIGR02390 RNA_pol_rpoA1 DNA-di  49.7      16 0.00041   15.5   6.2   15  113-127   180-194 (901)
129 PRK06266 transcription initiat  49.0      14 0.00037   15.8   2.4   29  270-306    43-71  (178)
130 COG0466 Lon ATP-dependent Lon   48.4      15 0.00038   15.7   2.4   26   55-80     29-55  (782)
131 pfam01726 LexA_DNA_bind LexA D  47.8      15 0.00039   15.6   2.4   30  480-509    32-61  (65)
132 TIGR00763 lon ATP-dependent pr  47.7      17 0.00042   15.3   2.6   17  502-518   598-619 (941)
133 PRK00574 gltX glutamyl-tRNA sy  47.7     7.5 0.00019   17.9   0.8   70  162-261    15-84  (489)
134 TIGR00354 polC DNA polymerase   47.3     9.3 0.00024   17.2   1.2  136   39-191    26-175 (1173)
135 COG2512 Predicted membrane-ass  47.1      17 0.00043   15.3   2.5   37  469-509   209-245 (258)
136 PRK08807 consensus              46.4      12  0.0003   16.4   1.7   41  483-524   339-379 (385)
137 pfam02002 TFIIE_alpha TFIIE al  46.3      15 0.00037   15.7   2.1   31  268-306    32-62  (105)
138 PRK10569 NAD(P)H-dependent FMN  46.3      18 0.00045   15.1   5.0   68    1-80      1-75  (191)
139 PRK11512 DNA-binding transcrip  45.8     4.7 0.00012   19.5  -0.5   48  471-522    55-109 (144)
140 TIGR00993 3a0901s04IAP86 chlor  45.5     9.3 0.00024   17.2   1.0  114   10-138   136-273 (772)
141 TIGR01591 Fdh-alpha formate de  45.3      13 0.00034   16.1   1.7   82  229-331   180-270 (694)
142 KOG0994 consensus               44.8      19 0.00048   14.9   3.2   26  263-288   930-955 (1758)
143 PRK03573 transcriptional regul  44.6      19 0.00048   14.9   8.2   51  471-525    47-104 (144)
144 PRK09058 coproporphyrinogen II  44.6     3.5 8.9E-05   20.4  -1.3   43  483-525   385-427 (447)
145 COG1568 Predicted methyltransf  44.3      17 0.00044   15.2   2.2   11  512-522   275-285 (354)
146 COG3383 Uncharacterized anaero  44.1      19 0.00049   14.9   2.5   39  513-553   596-650 (978)
147 cd01916 ACS_1 Acetyl-CoA synth  44.0     8.1 0.00021   17.7   0.5   12  623-634   469-480 (731)
148 pfam01978 TrmB Sugar-specific   43.7      13 0.00033   16.1   1.5   20  270-289    29-48  (68)
149 pfam10557 Cullin_Nedd8 Cullin   43.5      20  0.0005   14.8   2.6   13  495-507    51-63  (68)
150 TIGR00334 primaseG_like primas  43.1      20  0.0005   14.8   5.5   71   58-129    34-111 (176)
151 PRK00941 acetyl-CoA decarbonyl  42.6     8.7 0.00022   17.4   0.5   12  623-634   506-517 (779)
152 TIGR00014 arsC arsenate reduct  42.3      11 0.00029   16.6   1.0   53  229-291    14-67  (114)
153 TIGR02647 DNA conserved hypoth  42.1      20 0.00052   14.6   2.8   36  275-320    31-66  (77)
154 PRK08332 ribonucleotide-diphos  42.0      14 0.00037   15.8   1.5   40   48-88    399-438 (1748)
155 PRK07379 coproporphyrinogen II  41.6      21 0.00053   14.6   2.8   42  483-524   345-387 (399)
156 PRK10787 DNA-binding ATP-depen  41.5      21 0.00053   14.6   2.4   28   57-84     32-59  (784)
157 KOG1168 consensus               41.3      21 0.00053   14.6   2.6   11  165-175    34-44  (385)
158 TIGR01697 PNPH-PUNA-XAPA inosi  41.0      18 0.00045   15.1   1.8   84  654-763    48-161 (266)
159 TIGR02431 pcaR_pcaU beta-ketoa  40.9      18 0.00046   15.1   1.9   20  268-287    29-51  (252)
160 TIGR00575 dnlj DNA ligase, NAD  40.5      15 0.00039   15.6   1.5   37  259-305   238-277 (706)
161 pfam11279 DUF3080 Protein of u  40.2      21 0.00053   14.6   2.1   51  121-182    33-84  (315)
162 COG0272 Lig NAD-dependent DNA   39.8      16  0.0004   15.5   1.4   64   56-126     5-75  (667)
163 PRK09194 prolyl-tRNA synthetas  39.8      20 0.00052   14.7   2.0   43  788-832   525-567 (570)
164 COG5252 Uncharacterized conser  39.3      22 0.00057   14.3   3.8   20  694-713   190-211 (299)
165 pfam09339 HTH_IclR IclR helix-  39.2      14 0.00036   15.8   1.2   20  270-289    25-44  (52)
166 PRK13347 coproporphyrinogen II  39.2     8.3 0.00021   17.6  -0.0   36  494-529   404-439 (453)
167 TIGR01503 MthylAspMut_E methyl  38.5      22 0.00055   14.4   2.0   27  364-391   291-318 (481)
168 COG1321 TroR Mn-dependent tran  37.6      24  0.0006   14.2   3.9   38  482-520    33-71  (154)
169 TIGR00781 ccoO cytochrome c ox  37.4      17 0.00044   15.2   1.4   20  696-715   143-163 (234)
170 PRK09057 coproporphyrinogen II  37.3      21 0.00054   14.5   1.8   33  492-524   342-375 (381)
171 TIGR03129 one_C_dehyd_B formyl  36.8      16 0.00041   15.5   1.1   13  819-831   407-419 (421)
172 PRK07956 ligA NAD-dependent DN  36.3      15 0.00039   15.6   0.9   26   56-81      3-29  (668)
173 smart00346 HTH_ICLR helix_turn  36.1      25 0.00064   14.0   4.4   50  259-320    20-70  (91)
174 KOG0976 consensus               35.6      16 0.00041   15.4   1.0   22  484-505   653-674 (1265)
175 TIGR02639 ClpA ATP-dependent C  35.4      26 0.00065   13.9   3.9   52  270-336   362-422 (774)
176 KOG2337 consensus               35.4      26 0.00065   13.9   3.7   15  226-240    96-110 (669)
177 TIGR01405 polC_Gram_pos DNA po  35.2      22 0.00055   14.5   1.6   71   58-128    56-131 (1264)
178 PRK03564 formate dehydrogenase  35.0      26 0.00066   13.9   5.3   31  599-629   184-217 (307)
179 PRK11517 transcriptional regul  34.8      26 0.00067   13.8   3.6   29    1-29      1-31  (223)
180 pfam09395 consensus             34.7      26 0.00067   13.8   2.7   46  510-559     4-49  (77)
181 TIGR01381 E1_like_apg7 E1-like  34.6      26 0.00067   13.8   4.2   27  448-476   300-326 (689)
182 pfam09538 FYDLN_acid Protein o  34.6      23 0.00057   14.3   1.6   15  601-615     8-22  (104)
183 PRK08115 ribonucleotide-diphos  34.4      24 0.00062   14.1   1.7   62  686-757   730-792 (857)
184 pfam02327 BChl_A Bacteriochlor  34.3      26 0.00068   13.8   3.3   45  517-563   133-177 (357)
185 pfam10872 DUF2740 Protein of u  33.8      27 0.00069   13.7   2.0   28  367-394     3-31  (48)
186 pfam04606 Ogr_Delta Ogr/Delta-  33.0      23 0.00057   14.3   1.4   35  604-639     1-39  (47)
187 TIGR01158 SUI1_rel translation  32.3      26 0.00066   13.9   1.6   29  668-707    42-70  (111)
188 cd05569 PTS_IIB_fructose PTS_I  32.3      28 0.00073   13.6   3.6   41   67-129    49-89  (96)
189 TIGR01208 rmlA_long glucose-1-  32.2      19 0.00049   14.9   0.9   51  648-704   274-325 (361)
190 PRK10163 DNA-binding transcrip  31.6      29 0.00074   13.5   2.3   44  259-314    40-84  (271)
191 TIGR01579 MiaB-like-C MiaB-lik  31.5      29 0.00074   13.5   6.3   31   58-88     54-84  (492)
192 TIGR01743 purR_Bsub pur operon  31.4      29 0.00075   13.5   2.3   45   27-76     52-96  (269)
193 TIGR02164 torA trimethylamine-  30.9      30 0.00076   13.4   4.8   19  229-247   251-269 (847)
194 PRK08665 ribonucleotide-diphos  30.9      30 0.00076   13.4   4.7   89   58-155    28-124 (733)
195 pfam12387 Peptidase_C74 Pestiv  30.6      20 0.00052   14.6   0.8   16  490-505    85-100 (200)
196 PRK10811 rne ribonuclease E; R  30.3      21 0.00053   14.6   0.8   39   59-97    148-189 (1063)
197 TIGR01617 arsC_related conserv  29.8      27  0.0007   13.7   1.3   59  692-765    30-89  (122)
198 COG4337 Uncharacterized protei  29.6      24 0.00062   14.1   1.1   50  109-158    45-104 (206)
199 cd03765 proteasome_beta_bacter  29.5      31  0.0008   13.2   3.4   52  653-709   125-178 (236)
200 cd01304 FMDH_A Formylmethanofu  29.4      32  0.0008   13.2   2.0   29  474-502   212-251 (541)
201 pfam11834 DUF3354 Domain of un  29.4      15 0.00039   15.6   0.0   22  258-279    24-45  (69)
202 pfam09664 DUF2399 Protein of u  29.4      32 0.00081   13.2   8.2   68    3-95     22-90  (155)
203 pfam01325 Fe_dep_repress Iron   29.3      32 0.00081   13.2   1.9   29  269-305    26-54  (58)
204 PRK03353 ribB 3,4-dihydroxy-2-  29.0      32 0.00082   13.2   2.7   27   60-86     14-40  (217)
205 PRK00009 phosphoenolpyruvate c  28.8      32 0.00082   13.1   2.6   14  508-521   638-651 (916)
206 PRK05583 ribosomal protein L7A  28.7      32 0.00082   13.1   5.0   78   57-147    21-98  (104)
207 PRK09318 bifunctional 3,4-dihy  28.7      32 0.00083   13.1   2.0   23   63-86      2-24  (387)
208 smart00661 RPOL9 RNA polymeras  28.7      32 0.00083   13.1   2.4   33  604-641     2-34  (52)
209 PRK10336 DNA-binding transcrip  27.9      33 0.00085   13.0   3.6   28    1-28      1-30  (219)
210 COG0765 HisM ABC-type amino ac  27.4      34 0.00087   13.0   2.2   24  265-288   121-147 (222)
211 cd02755 MopB_Thiosulfate-R-lik  27.2      27 0.00068   13.8   0.9   41  274-322    37-86  (454)
212 PRK00215 LexA repressor; Valid  27.1      34 0.00088   12.9   2.5   32  478-509    28-59  (204)
213 PRK09880 L-idonate 5-dehydroge  27.1      23 0.00059   14.2   0.6   74  485-560   243-316 (343)
214 COG3058 FdhE Uncharacterized p  26.5      35  0.0009   12.9   4.5   30  600-629   183-216 (308)
215 PRK10427 putative fructose-lik  26.5      35  0.0009   12.9   3.3   42   67-129    53-94  (114)
216 COG0635 HemN Coproporphyrinoge  26.2      36 0.00091   12.8   1.6   58  470-527   340-408 (416)
217 PRK05978 hypothetical protein;  26.0      23 0.00059   14.2   0.4   11  603-613    35-45  (149)
218 PRK10430 DNA-binding transcrip  25.2      37 0.00094   12.7   5.4   80    1-85      2-91  (239)
219 PTZ00093 nucleoside diphosphat  25.2      37 0.00094   12.7   2.8   82  228-337    17-103 (149)
220 PRK09836 DNA-binding transcrip  25.2      37 0.00094   12.7   3.7   29    1-29      1-31  (226)
221 cd03366 TOPRIM_TopoIIA_GyrB TO  25.0      37 0.00095   12.7   3.0   78    2-95      2-95  (114)
222 TIGR00091 TIGR00091 tRNA (guan  24.8      33 0.00084   13.1   1.0   39  275-322   125-163 (216)
223 KOG0978 consensus               24.6      28  0.0007   13.7   0.6   10  601-610   642-651 (698)
224 TIGR01993 Pyr-5-nucltdase pyri  24.6      38 0.00097   12.6   3.2   43  263-307    24-67  (205)
225 TIGR01384 TFS_arch transcripti  24.5      27 0.00069   13.7   0.5   30  605-641     3-34  (111)
226 PRK10474 putative fructose-lik  24.4      38 0.00098   12.6   3.9   42   67-129    34-75  (88)
227 COG1710 Uncharacterized protei  24.3      38 0.00098   12.6   2.6   11   74-84     30-40  (139)
228 pfam08063 PADR1 PADR1 (NUC008)  24.2      33 0.00084   13.1   0.9   29  603-636    15-47  (55)
229 PRK09464 pdhR transcriptional   24.2      39 0.00098   12.6   1.9   25  480-505    41-65  (254)
230 TIGR01302 IMP_dehydrog inosine  24.2      39 0.00098   12.6   1.3   20  273-292    93-112 (476)
231 PRK01792 ribB 3,4-dihydroxy-2-  24.1      39 0.00099   12.6   3.4   53   57-128    11-63  (214)
232 TIGR01828 pyru_phos_dikin pyru  23.6      34 0.00085   13.0   0.9   40  259-312   354-397 (920)
233 cd01943 MAK32 MAK32 kinase.  M  23.6      39   0.001   12.5   3.3   12  665-676   228-239 (328)
234 COG3120 Uncharacterized protei  23.6      40   0.001   12.5   2.2   12   82-93     22-33  (149)
235 PHA00626 hypothetical protein   23.6      29 0.00073   13.5   0.5   13  604-616     2-14  (59)
236 PRK00135 scpB segregation and   23.5      40   0.001   12.5   2.1   21  493-513   113-133 (182)
237 pfam04864 Alliinase_C Allinase  23.5      18 0.00047   15.0  -0.5   28  260-287   190-217 (363)
238 pfam04475 DUF555 Protein of un  23.5      40   0.001   12.5   1.8   39  569-612    19-57  (102)
239 COG1799 Uncharacterized protei  23.5      40   0.001   12.5   1.4   30  120-149    90-121 (167)
240 PRK02888 nitrous-oxide reducta  23.4      40   0.001   12.5   2.8   36  259-310   100-136 (637)
241 COG0108 RibB 3,4-dihydroxy-2-b  23.4      40   0.001   12.5   2.8   27   61-87      5-31  (203)
242 cd04728 ThiG Thiazole synthase  23.3      26 0.00066   13.9   0.3   27  204-236     5-31  (248)
243 TIGR02041 CysI sulfite reducta  23.1      14 0.00035   16.0  -1.2   97  624-763   423-525 (550)
244 COG4904 Uncharacterized protei  23.0      40   0.001   12.4   4.0   69  485-564     3-78  (174)
245 PRK05773 3,4-dihydroxy-2-butan  23.0      41   0.001   12.4   2.7   49   62-129     4-52  (218)
246 PRK11122 artM arginine transpo  22.8      41   0.001   12.4   2.6   23  265-287   120-144 (222)
247 cd02750 MopB_Nitrate-R-NarG-li  22.6      29 0.00074   13.5   0.4   11  279-289    53-63  (461)
248 KOG3347 consensus               22.5      37 0.00094   12.7   0.9   16  536-551   152-167 (176)
249 PRK06582 coproporphyrinogen II  22.4      42  0.0011   12.3   1.4   32  492-524   353-384 (390)
250 KOG1643 consensus               22.2      42  0.0011   12.3   2.8   26  375-401   182-207 (247)
251 PRK09508 leuO leucine transcri  22.2      37 0.00095   12.7   0.9   47  473-520    36-85  (314)
252 PRK13532 nitrate reductase; Pr  22.1      39   0.001   12.5   1.0   21  268-289   340-360 (828)
253 pfam03833 PolC_DP2 DNA polymer  22.0      42  0.0011   12.3   1.3   41  447-487   395-435 (852)
254 PRK10816 DNA-binding transcrip  22.0      42  0.0011   12.3   3.7   29    1-29      1-31  (223)
255 PRK09954 hypothetical protein;  21.9      42  0.0011   12.3   1.8   23  266-288    20-42  (362)
256 PRK09249 coproporphyrinogen II  21.8      28 0.00073   13.6   0.2   44  483-526   392-438 (456)
257 TIGR02315 ABC_phnC phosphonate  21.8      43  0.0011   12.2   1.6   29  104-132   117-145 (253)
258 cd04157 Arl6 Arl6 subfamily.    21.8      43  0.0011   12.2   5.3   75   50-125    72-157 (162)
259 TIGR01968 minD_bact septum sit  21.7      43  0.0011   12.2   2.3   33  694-727   189-221 (272)
260 PRK11062 nhaR transcriptional   21.6      40   0.001   12.5   0.9   52  474-526    19-73  (296)
261 TIGR02655 circ_KaiC circadian   21.4      43  0.0011   12.2   1.1   73   63-149    74-151 (484)
262 PRK00910 ribB 3,4-dihydroxy-2-  21.4      44  0.0011   12.2   2.8   27   60-86     15-41  (218)
263 pfam01047 MarR MarR family. Th  21.4      44  0.0011   12.2   2.0   22  487-508    30-51  (59)
264 KOG0114 consensus               21.3      44  0.0011   12.2   1.5   17  138-154    68-84  (124)
265 KOG3139 consensus               21.2      44  0.0011   12.2   1.4   39  268-313   111-154 (165)
266 KOG1973 consensus               21.2      44  0.0011   12.2   1.9   27  596-634   215-241 (274)
267 PRK11123 arginine transporter   21.2      44  0.0011   12.2   2.4   25  264-288   132-159 (238)
268 pfam08772 NOB1_Zn_bind Nin one  21.0      43  0.0011   12.2   1.0   16  601-616    23-38  (73)
269 COG0055 AtpD F0F1-type ATP syn  21.0      44  0.0011   12.1   1.9   28  476-504   263-290 (468)
270 COG1339 Transcriptional regula  21.0      44  0.0011   12.1   2.0   31  267-305    23-53  (214)
271 COG1217 TypA Predicted membran  20.9      44  0.0011   12.1   1.1   16  748-763   558-573 (603)
272 TIGR01084 mutY A/G-specific ad  20.9      44  0.0011   12.1   1.6   30  483-513   124-153 (297)
273 pfam08576 DUF1764 Eukaryotic p  20.7      24 0.00062   14.1  -0.3   18  471-488    65-82  (98)
274 PRK09986 DNA-binding transcrip  20.4      45  0.0012   12.0   1.8   17  504-520    38-54  (278)
275 TIGR00100 hypA hydrogenase nic  20.4      45  0.0012   12.0   1.5   15  538-552    49-63  (128)
276 COG2022 ThiG Uncharacterized e  20.4      23  0.0006   14.2  -0.5   23  351-374    63-85  (262)
277 TIGR02169 SMC_prok_A chromosom  20.4      46  0.0012   12.0   3.4   81   59-151   563-653 (1202)
278 pfam03965 Pencillinase_R Penic  20.2      46  0.0012   12.0   3.9   77  472-563    19-97  (115)
279 cd03365 TOPRIM_TopoIIA TOPRIM_  20.1      46  0.0012   12.0   3.1   25   71-95     76-100 (120)

No 1  
>PRK09138 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=2202.08  Aligned_cols=833  Identities=58%  Similarity=0.993  Sum_probs=806.1

Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             91899779047877887508998999942511007865578676667440688776548999999999870998999469
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATD   80 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD   80 (837)
                      |||||||||+|||||++|||++|.|+||+|||||||.++++|||+++|+|.|+++++++++|+.|++++|+||+||||||
T Consensus         1 M~LvIVESPaKaktI~kyLG~~y~V~AS~GHirDLp~k~~~vd~~~~f~~~y~i~~~k~k~v~~lk~~~K~ad~v~LATD   80 (887)
T PRK09138          1 MNVVVVESPAKAKTINKYLGSDYKVLASFGHVRDLPAKDGSVDPDEDFAMSWEVDSKSAKRLKDIAKALKGADGLILATD   80 (887)
T ss_pred             CCEEEEECCHHHHHHHHHCCCCCEEEECCCCHHCCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             95899947388889998559898899616704318865585566888646789898657999999999837998998889


Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHC
Q ss_conf             97025799999999975512578871699998037989999998622646989999999999989874011378988641
Q gi|254780306|r   81 PDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKL  160 (837)
Q Consensus        81 ~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~  160 (837)
                      ||||||+|||||+++|+.+..+++++|+||||||||++||++||+|||++|++||+||+|||+|||||||+|||+|||++
T Consensus        81 pDREGEaIawhl~e~L~~k~~l~~~~vkRi~F~EITk~AI~~Al~npr~id~~LV~Aq~aRRilDrLvGf~lSp~Lwrkl  160 (887)
T PRK09138         81 PDREGEAISWHVLEVLRKKKALKDKPVERVVFNAITKSAVTDAMANPRDIDQPLVDAYLARRALDYLVGFTLSPVLWRKL  160 (887)
T ss_pred             CCCCHHHHHHHHHHHHCHHCCCCCCCEEEEEEECCCHHHHHHHHHCHHHCCHHHHHHHHHHHHHHEEECCEECHHHHHHC
T ss_conf             98341899999999856110478885368999365999999999591521888899999999987133613169999744


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCCC
Q ss_conf             46765342268999999999999641376544001223315799654223310358330331011356667776420015
Q gi|254780306|r  161 PGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKA  240 (837)
Q Consensus       161 ~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~  240 (837)
                      ++++||||||||||+||||||+||++|+|++||+|.+.|...++..|.|+|...++++++++++.++++|+.+.+.+++.
T Consensus       161 ~~~~SAGRVQSpaLrLIveRE~EI~~F~p~~Yw~i~a~~~~~~g~~f~a~l~~~~gkk~~k~~i~~~~eA~~~~~~l~~~  240 (887)
T PRK09138        161 PGARSAGRVQSVALRLVCDREAEIERFVPREYWSVAALLATPRGDEFEARLTGLDGKKLDKLDIGNGEEAEAAKAALEAA  240 (887)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCEEEEEEEEECCEECCCCCCCCHHHHHHHHHHHHCC
T ss_conf             78987651077889999984999985165436999999965889735799986267011546677889999999986069


Q ss_pred             CCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             63010000233222468521037999998876088899999999876213556721224553147554444305689999
Q gi|254780306|r  241 TYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVR  320 (837)
Q Consensus       241 ~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r  320 (837)
                      .++|.+|++|+.+++||+||+||||||+||++|||||++||++||+|||+++++|++.||||||||||++||++++..+|
T Consensus       241 ~~~V~~ve~K~~kr~Pp~PFtTSTLQQeAs~kLGfSa~~TM~iAQ~LYEg~~~~~~~~GlITYmRTDS~~lS~eai~~ar  320 (887)
T PRK09138        241 TFKVASVEAKPAKRNPPPPFTTSTLQQEASRKLGFSASRTMQIAQRLYEGVDIGGETVGLITYMRTDGVQMAPEAITAAR  320 (887)
T ss_pred             CEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCHHHHHHHH
T ss_conf             75999983342245899996467999999987199899999999999751235777505898614762201899999999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEE
Q ss_conf             76552001123763111125566688777652477302346400000199999999999999999985222110010013
Q gi|254780306|r  321 RSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVN  400 (837)
Q Consensus       321 ~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~  400 (837)
                      ++|.+.||.+|+|++||.|++|++||||||||||||++.++|+.+...|+.||++||+|||+|||||||+||++++++|+
T Consensus       321 ~~I~~~yG~~ylp~~pr~y~~K~knaQEAHEAIRPTd~~~~P~~~~~~L~~de~kLY~LIwkRtlASQM~~A~~e~ttv~  400 (887)
T PRK09138        321 DAIGERFGAAYVPEKPRFYSTKAKNAQEAHEAIRPTDFSRRPADVRRFLDADQARLYELIWKRTIASQMESAELERTTVD  400 (887)
T ss_pred             HHHHHHHCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHCCHHHEEEEEEE
T ss_conf             99998636332753230102345567667577236565558788740289889999999999999974464233789999


Q ss_pred             EEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHH
Q ss_conf             67740796399999874880588567632677763210010148864568821100110111234643101789987433
Q gi|254780306|r  401 IIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKM  480 (837)
Q Consensus       401 i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~m  480 (837)
                      |.+..+...+.|+|+|++++|+||++||.++.+++.+++++..||.|++|+.+.+.++.+.||+|+||+||||||||++|
T Consensus       401 i~~~~~~~~~~f~AsG~vi~f~Gfl~vY~e~~d~~~~de~~~~LP~l~~Gd~l~~~~i~~~q~~TkPP~RYTEASLVk~m  480 (887)
T PRK09138        401 IEAKDGGRQAGLRATGQVVKFDGFLAVYQEGRDDDDDDEDSRRLPAMSEGEALAREKVAATQHFTEPPPRYSEASLVKRM  480 (887)
T ss_pred             EEECCCCCEEEEEEEEEEEEECCEEEEECCCCCCCCCCCHHHCCCCCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHH
T ss_conf             99468871589999768997678188650456664321011028765568765676777567765899988989999999


Q ss_pred             HHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             21025665515789999973220221477122201142000022336655689889999999999986260134789999
Q gi|254780306|r  481 EEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHE  560 (837)
Q Consensus       481 E~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~  560 (837)
                      |++|||||||||+||+||++|+||.+++++|+||++|++|++||++||+++|||+|||+||++||+||+|+.+|.+||++
T Consensus       481 Ee~GIGRPSTYAsII~tL~~R~YV~~~~~~l~Pt~~G~~V~~fL~~~F~~~vdy~FTA~mE~~LD~Ia~G~~~w~~~l~~  560 (887)
T PRK09138        481 EELGIGRPSTYASILQTLRDREYVRIDKRRLIPEDKGRLVTAFLESFFERYVEYDFTADLEEKLDRISDGELDWKQVLRD  560 (887)
T ss_pred             HHCCCCCCCHHHHHHHHHHHCCCEEEECCEECCHHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf             97699986317999998871787983098766407589999999986355409175899999888987687428999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             86767665576677556667765567664102455556766114334677731368715776111234343233321001
Q gi|254780306|r  561 FWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLT  640 (837)
Q Consensus       561 Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~  640 (837)
                      ||.+|+..++++.++.+.++++.+++.+++++|+...++.+.+.||.|+.|.|.++. ||||+|+||||||+|+|++++.
T Consensus       561 Fy~~f~~~v~~~~~~~~~~v~~~l~~~l~~~~f~~~~d~~d~r~cp~c~~g~l~l~~-gk~G~figcsnypec~~t~~l~  639 (887)
T PRK09138        561 FWRDFSAAVDETKELRVTEVLDALDEELAPHIFPPREDGSDPRICPTCGTGRLSLKL-GKFGAFVGCSNYPECRYTRQLS  639 (887)
T ss_pred             HHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEC-CCCCCCCCCCCCCCCCCCCCCC
T ss_conf             976333444112111167787777765443216754467776336678887368870-5765666567886443555578


Q ss_pred             CCCCC-CCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEECC----CCCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCC
Q ss_conf             22100-00123442014689999669998269742277348----87776133789988425489999998615255157
Q gi|254780306|r  641 SNPQD-IPEMKESVLLGNDLETKESVTLRSGRFGLYVQRGD----GKDAKRCSLPKTWKSDSVDYDKAMSLLSLPREIGI  715 (837)
Q Consensus       641 ~~~~~-~~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq~Ge----~~kpkr~si~k~~~~~~itle~Al~LLsLPr~lG~  715 (837)
                      ....+ .....+++.||+||+||++|++|.||||||||+|+    .+||||+|||+++++++||||+|++||||||+||.
T Consensus       640 ~~~~~~~~~~~~~r~LG~dP~tg~~v~~k~GrfGpyvq~G~~~~~~~kpk~asl~k~~~~~~itle~Al~LlsLPr~lG~  719 (887)
T PRK09138        640 ADGGEEAAASDDPKVLGKDPETGEEVTLRSGRFGPYVQLGEATAEGKKPKRASLPKGWSPADVDLEKALALLSLPREVGK  719 (887)
T ss_pred             CCCCCCHHCCCCCCEEECCCCCCCEEEEEECCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCHHHCC
T ss_conf             87542011245783320079999758997047777586168764445754467889998010689999999817485389


Q ss_pred             CCCCCCEEEEEECCCCCEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCCCCCEEEEE
Q ss_conf             77898749991158765261678111248877514357999999998365113443445443201026789898469960
Q gi|254780306|r  716 HPETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPEGGSITVHN  795 (837)
Q Consensus       716 ~pe~g~~I~~~~GryGpYi~~~~~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~~~~i~i~~  795 (837)
                      |||+|++|+|++|||||||+|+++|+||++++++|+|+||+|++||++++..+++ +..+..|+|+||+||+|++|+|++
T Consensus       720 hpe~g~~I~a~~GrfGPYv~~~~~~~sl~~~~~~~~i~l~~A~~lia~~~~~~~~-~~~~~~~lk~lg~~p~~~~v~v~~  798 (887)
T PRK09138        720 HPETGKPISAGIGRYGPYVKHGGTYANLEKVDDVFTIGLNRAVTLLAEKQAGGGR-GRGAAAPLKTLGDHPDGGPVTVRD  798 (887)
T ss_pred             CCCCCCEEEECCCCCCCCEEECCEEECCCCCCCCEEECHHHHHHHHHHHHHCCCC-CCCCCCHHHHCCCCCCCCEEEEEC
T ss_conf             9789978998158876648889998268998986251699999999612103555-545443022237799998258845


Q ss_pred             CCCCCEEEECCEEEECCCCCCHHHCCHHHHHHHHHHHHHC
Q ss_conf             6854525367888756578896778999999999877726
Q gi|254780306|r  796 GRYGPYLHWKKINASLSKEESPDTVDLEKALKILNIKKQK  835 (837)
Q Consensus       796 GryGpYi~~gk~Na~ipk~~~~e~lt~e~a~~li~~k~~k  835 (837)
                      |||||||+||++||+|||+.|||+||+|+|++||++|++|
T Consensus       799 Gr~GpYv~~g~~Na~lpk~~~~e~~tle~a~~ll~~k~ak  838 (887)
T PRK09138        799 GRYGPYVNWGKVNATLPKGKDPEAVTLEEALALIAEKAAK  838 (887)
T ss_pred             CCCCCEEEECCEEEECCCCCCHHHCCHHHHHHHHHHHHHC
T ss_conf             8876507638478625899982128899999999987622


No 2  
>PRK07941 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=2015.43  Aligned_cols=814  Identities=36%  Similarity=0.598  Sum_probs=727.6

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCC--------------CCCCCCCCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             1899779047877887508998999942511007865--------------57867666744068877654899999999
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAK--------------KGSVLPEKEFEMIWNIDPSSQKHLQNIIH   67 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~--------------~~~v~~~~~f~p~y~v~~~~kk~~~~i~~   67 (837)
                      +|||||||+|||||++|||++|+|+||+|||||||.+              .+|||++++|.|.|+++++++++|+.|++
T Consensus        10 ~LVIVESPaKaktI~kyLG~~y~V~aS~GHIrDLp~~~~~v~~~~k~~~~~~~gvd~~~~f~p~y~v~~~kkk~v~~Lk~   89 (933)
T PRK07941         10 RLVIVESPTKARKIAPYLGSNYIVESSRGHIRDLPRAAADVPAKYKSEPWARLGVNVDADFEPLYIVSPDKKSTVAELKG   89 (933)
T ss_pred             EEEEEECCHHHHHHHHHCCCCCEEEECCCEEEECCCCCCCCCCHHCCCCHHHCCCCCCCCCCEEEEECCCHHHHHHHHHH
T ss_conf             49999182888899986598989996167601777775656410024530003315577850677889657999999999


Q ss_pred             HHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             98709989994699702579999999997551257887169999803798999999862264698999999999998987
Q gi|254780306|r   68 AVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYL  147 (837)
Q Consensus        68 ~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~l  147 (837)
                      ++|+||+||||||||||||+|||||+++|+.     +.||+||||||||++||++||+|||++|++||+||+|||+||||
T Consensus        90 ~~k~ad~V~lATDpDREGEaIawhl~e~lk~-----~~~vkRv~F~EITk~AI~~Al~npr~id~~LV~Aq~aRRilDrL  164 (933)
T PRK07941         90 LLKDVDELYLATDGDREGEAIAWHLLETLKP-----RVPVKRMVFHEITEPAILAAAENPRDLDIDLVDAQETRRILDRL  164 (933)
T ss_pred             HHHCCCEEEECCCCCCCCHHHHHHHHHHHCC-----CCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             9965998998989972404999999998389-----98747899926899999999858300169899999999999988


Q ss_pred             HHHHHCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCC------CEEEEEEEEECCEEECC
Q ss_conf             401137898864146765342268999999999999641376544001223315799------65422331035833033
Q gi|254780306|r  148 VGFNLSPILWQKLPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRN------DKFTAHLTDFNGQRIEK  221 (837)
Q Consensus       148 vG~~lSp~L~rk~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~------~~f~a~l~~~~~~~~~~  221 (837)
                      |||+|||+||++++++|||||||||||+||||||+||++|+|++||+|.+.|....+      ..|.++|..++++++..
T Consensus       165 vGf~lSp~Lw~k~~~~LSAGRVQSpaLrLIVeRE~EI~~F~p~~Yw~i~a~~~~~~~~~~~~~~~f~a~l~~~~g~~~~~  244 (933)
T PRK07941        165 YGYEVSPVLWKKVAPKLSAGRVQSVATRIIVQRERERMAFRSADYWDISAELDASVSDPAAAPPTFTARLTSVDGRRVAT  244 (933)
T ss_pred             HHHHHCHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCCCCCCCCEEEEEEEECCEEEEC
T ss_conf             64613699998626787563635478999998699998268855047999984255543246753589987436755301


Q ss_pred             ---------------CCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             ---------------10113566677764200156301000023322246852103799999887608889999999987
Q gi|254780306|r  222 ---------------KSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQK  286 (837)
Q Consensus       222 ---------------~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~  286 (837)
                                     ..+.|+++|+++.+.|++..++|.+|++|+.+++||+||+||||||+||++|||||++||+|||+
T Consensus       245 g~dfd~~~~l~~~~~~~~~de~~A~~~~~~l~~~~~~V~~ve~K~~~r~P~pPFtTSTLQQeAsrkLgfSa~~TM~iAQ~  324 (933)
T PRK07941        245 GRDFDSLGTLRKADEVLVLDEARATALAAGLQGAQLSVASVEEKPYTRRPYAPFMTSTLQQEAGRKLRFSSERTMSIAQR  324 (933)
T ss_pred             CCCCCCHHHHCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHH
T ss_conf             45555200002332011268999999999722796389988743435689899767999999987379699999999999


Q ss_pred             HHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEE-CCCCCCHH
Q ss_conf             62135567212245531475544443056899997655200112376311112556668877765247730-23464000
Q gi|254780306|r  287 LYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPND-FDFLPSKM  365 (837)
Q Consensus       287 LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~-~~~~p~~~  365 (837)
                      |||        .||||||||||++||++++..+|++|..+||++|++..+|.|++|++||||||||||||+ ...+|+.+
T Consensus       325 LYE--------~GlITYmRTDS~~LS~eai~~ar~~I~~~yG~~yl~~~~r~~~~k~knaQeAHEAIRPT~~~~~tp~~l  396 (933)
T PRK07941        325 LYE--------NGYITYMRTDSTTLSESAINAARTQARQLYGEEYVAPSPRQYTRKVKNAQEAHEAIRPAGETFATPGQL  396 (933)
T ss_pred             HHH--------CCEEEEECCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCHHHH
T ss_conf             984--------774654047876269999999999999743511268551122235567644565503463011688887


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEE-CCCEEEEEEEEEEEECCCHHHHHCCCCCCCC---CCHHH
Q ss_conf             0019999999999999999998522211001001367740-7963999998748805885676326777632---10010
Q gi|254780306|r  366 KQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATY-NDQIGHLRTTGSLLCFDGFLKVWENQYDQEK---NSEED  441 (837)
Q Consensus       366 ~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~-~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~---~~~~~  441 (837)
                      ...|+.||++||+|||+|||||||+||++++++|.|.... ....+.|+|+|++++|+||+++|.+..+++.   .++.+
T Consensus       397 ~~~L~~de~kLY~LIwkRtlASqM~~A~~~~~~v~i~~~~~~~~~~~F~asG~~i~f~Gfl~vY~e~~~~~~~~~~d~~e  476 (933)
T PRK07941        397 HRQLDGDEFRLYELIWQRTVASQMADARGTTLSLRITGTAKGGEEVVFSASGRTITFPGFLKAYVETVDELAGGEADDAE  476 (933)
T ss_pred             HCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCCCCCEEEEEEEEEEEEECCEEEEEECCCCCCCCCCCCCHH
T ss_conf             40368889999999999988753551104799999960257774179999667999888878850346532244433212


Q ss_pred             CCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHC
Q ss_conf             14886456882110011011123464310178998743321025665515789999973220221477122201142000
Q gi|254780306|r  442 ILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVT  521 (837)
Q Consensus       442 ~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~  521 (837)
                      ..||.|++|+.+.+.++.+.+|+|+||+|||||||||+||++|||||||||+||+||++|+||.+++++|+||++|++|+
T Consensus       477 ~~LP~l~~G~~l~~~~i~~~~~~TkPP~RYTEASLVk~MEe~GIGRPSTYAsII~tL~~R~YV~~~~~~l~Pt~~G~~V~  556 (933)
T PRK07941        477 SRLPNLTQGQRLDAVELTPDGHSTNPPARYTEASLVKALEELGIGRPSTYSSIIKTIQDRGYVHKKGSALVPSWVAFAVV  556 (933)
T ss_pred             HCCCCCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHHCCEEECCCCEECCHHHHHHHH
T ss_conf             10876666871001343411257689999888999999996699987128999999874535842587657547799999


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             02233665568988999999999998626013478999986767665576677556667765567664102455556766
Q gi|254780306|r  522 AFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNED  601 (837)
Q Consensus       522 ~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~  601 (837)
                      +||++||++||||+|||+||++||+||+|+.+|.+||++||++|...+.+.... ...+.+.+...+... ...  ....
T Consensus       557 ~fL~~~F~~~vdy~FTa~mE~~LD~Ia~G~~~w~~~l~~Fy~~~~~~~~~~~~~-~~~l~~~~~~~~~~i-d~~--~~~~  632 (933)
T PRK07941        557 GLLEQHFGRLVDYDFTAAMEDELDEIAAGNERRTNWLNNFYFGGDHGVADSVAR-SGGLKKLVGVNLEGI-DAR--EVNS  632 (933)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCHHHHHH-HHHHHHHHHHHHCCC-CHH--HCCC
T ss_conf             999998887748521689997652663596068999999864665440244543-222788765211005-765--5057


Q ss_pred             CEECCCCCCCCEEEEEECCCCCCC----CCCCCCCCCCCCCCCC---CCCC---------CCCCCCCCCCCCCCCCCCEE
Q ss_conf             114334677731368715776111----2343432333210012---2100---------00123442014689999669
Q gi|254780306|r  602 SRTCPECHTHSLSLKLSSKYGAFV----GCTNYPECKYTRQLTS---NPQD---------IPEMKESVLLGNDLETKESV  665 (837)
Q Consensus       602 ~~~Cp~C~~g~L~~k~~gK~G~Fi----gCSnyPeCk~t~~l~~---~~~~---------~~~~~~~~~LG~dP~~G~~I  665 (837)
                      ...|+.|....+.++ .||||+|+    +|+++++|++++....   .+.+         .....++++||.||++|++|
T Consensus       633 ~~~~~~~~g~~l~~r-~gk~G~f~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~r~LG~dP~tg~~V  711 (933)
T PRK07941        633 IKLFDDAEGRPVYVR-VGRNGPYLERMVGTGDDGEPEPQRANLPDSLTPDELTLEVAEKLFATPQEGRELGVDPETGHEI  711 (933)
T ss_pred             CCCCCCCCCCEEEEE-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEE
T ss_conf             656666789754786-1577664000247688886430215678666865343777888750567897223589999868


Q ss_pred             EEEECCCCCEE--EECCC-------------------CCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEE
Q ss_conf             99826974227--73488-------------------7776133789988425489999998615255157778987499
Q gi|254780306|r  666 TLRSGRFGLYV--QRGDG-------------------KDAKRCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQKNII  724 (837)
Q Consensus       666 ~lk~GryGpYv--q~Ge~-------------------~kpkr~si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~  724 (837)
                      +||.|||||||  |+|+.                   +||||+||||++++++||||+||+||+|||+||.||++|++|+
T Consensus       712 ~lk~GryGpyv~~~~~e~~~~~~~~~~~~~~~~~~~~~Kpk~asl~k~~~~~~itLe~Al~LlsLPR~lG~hPe~g~~I~  791 (933)
T PRK07941        712 VAKEGRFGPYVTEVLPEPEEDGAAAKTAAKKKKKETGPKPRTGSLLRSMDLQTVTLEDALKLLSLPRVVGVDPASGEEIT  791 (933)
T ss_pred             EEECCCCCCEEEEECCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCHHHCCCCCCCCEEE
T ss_conf             99417987724200477520000001101134433467877566789998020689999999708463189978998799


Q ss_pred             EEECCCCCEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCC-CCCEEEEECCCCCEEE
Q ss_conf             911587652616781112488775143579999999983651134434454432010267898-9846996068545253
Q gi|254780306|r  725 AGTGKYGYYLNHDGAYTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPE-GGSITVHNGRYGPYLH  803 (837)
Q Consensus       725 ~~~GryGpYi~~~~~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~-~~~i~i~~GryGpYi~  803 (837)
                      |++|||||||+|+++|+||++++++|+|+||+||+||+++|..++  +.++.+++|+||+||+ |++|+|++|||||||+
T Consensus       792 a~~GrfGPYlk~~~~~~sL~~~~~~~~I~l~~Av~li~~~k~~~~--~~~~~~~lk~lg~~p~~~~~i~v~~GryGpYv~  869 (933)
T PRK07941        792 AQNGRYGPYLKRGTDSRSLATEEQIFTITLDEALKIYAEPKRRGR--QAAAAPPLRELGDDPVSGKPMVIKDGRFGPYVT  869 (933)
T ss_pred             ECCCCCCCCCCCCCEEECCCCCCCCEECCHHHHHHHHHCHHHCCC--CCCCCCHHHHCCCCCCCCCCEEEECCCCCCEEE
T ss_conf             756788766640883431698887512389999999955433376--533443154448998899816994588743076


Q ss_pred             ECCEEEECCCCCCHHHCCHHHHHHHHHHHHHC
Q ss_conf             67888756578896778999999999877726
Q gi|254780306|r  804 WKKINASLSKEESPDTVDLEKALKILNIKKQK  835 (837)
Q Consensus       804 ~gk~Na~ipk~~~~e~lt~e~a~~li~~k~~k  835 (837)
                      ||++||+|||+.|||+||||+|++||++|+||
T Consensus       870 ~gk~Na~lpk~~~pe~ltle~a~~Li~~k~ak  901 (933)
T PRK07941        870 DGETNASLRKGDDVESITDARASELLADRRAR  901 (933)
T ss_pred             ECCEEECCCCCCCHHHCCHHHHHHHHHHHHHC
T ss_conf             48688516998982128999999999998732


No 3  
>PRK07561 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=2009.33  Aligned_cols=790  Identities=40%  Similarity=0.647  Sum_probs=715.4

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCC--------------CCCCCCCCCCCEEEEECCCHHHHHHHHHH
Q ss_conf             1899779047877887508998999942511007865--------------57867666744068877654899999999
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAK--------------KGSVLPEKEFEMIWNIDPSSQKHLQNIIH   67 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~--------------~~~v~~~~~f~p~y~v~~~~kk~~~~i~~   67 (837)
                      +|||||||+|||||++|||++|.|+||+|||||||.+              .+|||++++|.|.|+++++++++|+.|++
T Consensus         3 ~LVIVESPaKaktI~kyLG~~y~V~AS~GHirDLp~~~~~vp~~~k~~~~~~~gvd~~~~f~p~y~i~~~kkk~v~~Lk~   82 (878)
T PRK07561          3 TLVIVESPTKARTIRNFLPKGYRVEASMGHVRDLPNSASEIPAAVKGEKWANLGVNVEADFEPLYVVPKDKKKVVKELKD   82 (878)
T ss_pred             CEEEEECCHHHHHHHHHCCCCCEEEEECCCHHCCCCCCCCCCCHHCCCCHHHCCCCCCCCCCEEEEECCCHHHHHHHHHH
T ss_conf             48999373888999986698979996066152057764557401112303105435588952677868768999999999


Q ss_pred             HHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             98709989994699702579999999997551257887169999803798999999862264698999999999998987
Q gi|254780306|r   68 AVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYL  147 (837)
Q Consensus        68 ~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~l  147 (837)
                      ++|+||+||||||||||||+|||||+++|+.     +.+|+|+||||||++||++||+|||++|++||+||+|||+||||
T Consensus        83 ~~k~ad~V~lATDpDREGEaIawhl~e~l~~-----~~~vkRi~F~EITk~AI~~Ai~npr~id~~LV~Aq~aRRilDrl  157 (878)
T PRK07561         83 ALKGADELLLATDEDREGESISWHLLQLLKP-----KVPTKRMVFHEITKEAIQKALDNTREIDMELVHAQETRRILDRL  157 (878)
T ss_pred             HHHCCCEEEECCCCCCCCHHHHHHHHHHHCC-----CCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHH
T ss_conf             9857998998889971406999999998489-----99706899946899999999968541688889999999998864


Q ss_pred             HHHHHCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEEC-------
Q ss_conf             4011378988641467653422689999999999996413765440012233157996542233103583303-------
Q gi|254780306|r  148 VGFNLSPILWQKLPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIE-------  220 (837)
Q Consensus       148 vG~~lSp~L~rk~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~-------  220 (837)
                      |||+|||+||++++++|||||||||||+||||||+||++|+|++||+|.+.|.. ++..|.|+|.+++++++.       
T Consensus       158 VGf~lSp~Lw~k~~~~LSAGRVQSpaLrLIveRE~EI~~F~p~~Yw~i~a~~~~-~~~~f~a~l~~~~~~ki~~~~dfd~  236 (878)
T PRK07561        158 VGYTLSPLLWKKIAWGLSAGRVQSVAVRLLVQRERERRAFKSGSYWDLKAQLEK-DGSPFEAKLTTLGGQRIATGSDFDE  236 (878)
T ss_pred             HCCEECHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEC-CCCEEEEEEEEECCEEECCCCCCCC
T ss_conf             252405999975178997640189999999998999983587552899999824-8861799997318856403555542


Q ss_pred             ---------CCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCC
Q ss_conf             ---------31011356667776420015630100002332224685210379999988760888999999998762135
Q gi|254780306|r  221 ---------KKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGI  291 (837)
Q Consensus       221 ---------~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~  291 (837)
                               +.++.|+++|+++++.+++..++|.+|++|+.+++||+||+||||||+||++|||||++||++||+|||  
T Consensus       237 ~t~~~~~~~~~~~~~e~~A~~~~~~l~~~~~~V~~ve~K~~~r~PppPFtTSTLQQeAs~kLGfSa~~TM~iAQ~LYE--  314 (878)
T PRK07561        237 STGQLKAGRDVVLLDEEEAKALKERLTGKPWTVSSVEEKPTTRKPVPPFTTSTLQQEANRKLRLSARETMRCAQGLYE--  314 (878)
T ss_pred             CCCCCCCCCCCCCCCHHHHHHHHHHHCCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHH--
T ss_conf             111223454343389999999999842797699998752200379998567999999986159589999999999985--


Q ss_pred             CCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCC-CCCHHCCCCC
Q ss_conf             567212245531475544443056899997655200112376311112556668877765247730234-6400000199
Q gi|254780306|r  292 DVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDF-LPSKMKQFLD  370 (837)
Q Consensus       292 ~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~-~p~~~~~~L~  370 (837)
                            .||||||||||++||++++..+|++|...||++||++++|.|.+|++||||||||||||+..+ +|++  ..|+
T Consensus       315 ------~GlITYmRTDS~~lS~eai~~~r~~I~~~yG~~yl~~~~r~y~~k~k~aQeAHEAIRPT~~~~~~p~~--~~L~  386 (878)
T PRK07561        315 ------RGFITYMRTDSVHLSEQAIRAARSCVESMYGKEYLSPQPRQYTTKSKNAQEAHEAIRPAGETFRTPQE--TGLS  386 (878)
T ss_pred             ------CCEEEEECCCCCCCCHHHHHHHHHHHHHHCCHHHCCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCHHH--CCCC
T ss_conf             ------88378864787656999999999999874144227611200035656763561341444522258333--0899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCC--CHHHCCCCCCC
Q ss_conf             9999999999999999852221100100136774079639999987488058856763267776321--00101488645
Q gi|254780306|r  371 SDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKN--SEEDILLPYIS  448 (837)
Q Consensus       371 ~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~--~~~~~~LP~l~  448 (837)
                      .+|++||+|||+|||||||+||++++++|.+.+.+    ..|+|+|++++|+||+++|.++.++++.  ++++..||.|+
T Consensus       387 ~de~kLY~LIwkRtlASqM~~a~~~~t~v~i~~~~----~~F~asG~~i~f~G~~~vy~e~~dd~~~~~e~~~~~LP~l~  462 (878)
T PRK07561        387 GRELALYDLIWKRTVASQMAEARLTMISVELSVGD----ALFRASGKRIDFPGFFRAYVEGSDDPDAALEDQEVILPALK  462 (878)
T ss_pred             HHHHHHHHHHHHHHHHHCCCHHHEEEEEEEEEECC----EEEEEEEEEEEECCEEEEEECCCCCCCCCCCCCCCCCCCCC
T ss_conf             88999999999999986057321789999999288----69999769996178689984156762112232222277657


Q ss_pred             CCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCC
Q ss_conf             68821100110111234643101789987433210256655157899999732202214771222011420000223366
Q gi|254780306|r  449 ANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFF  528 (837)
Q Consensus       449 ~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f  528 (837)
                      +|+.+.+.++.+.+|+|+||+|||||||||+||++|||||||||+||+||++|+||.+++++|+||++|++|++||++||
T Consensus       463 ~Gd~l~~~~i~~~~~~TkPP~RYTEASLVk~MEe~GIGRPSTYAsII~tL~~R~YV~~~~~~l~Pt~~G~~V~~fL~~~F  542 (878)
T PRK07561        463 VGDHPECKSLEALGHETQPPARYTEASLVKTLEKEGIGRPSTYASIIGTIVDRGYAQLRSNALVPTFTAFAVTALLEEHF  542 (878)
T ss_pred             CCCCCEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHHCCCCEECCCCEECCHHHHHHHHHHHHHHH
T ss_conf             89832014666444562799997989999999966999871279999888627878436953353487899999999876


Q ss_pred             CCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCC
Q ss_conf             55689889999999999986260134789999867676655766775566677655676641024555567661143346
Q gi|254780306|r  529 SQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPEC  608 (837)
Q Consensus       529 ~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C  608 (837)
                      +++|||+|||+||+.||+||+|+.+|.+||++||.++......     +.+..+.+             +....+.|+.|
T Consensus       543 ~~~vdy~FTA~mE~~LD~Ia~G~~~w~~~l~~Fy~~~~~~~~~-----v~~~~~~i-------------d~~~~~~~~~~  604 (878)
T PRK07561        543 PDLVDTSFTARMEQTLDEISTGEVQWLPYLEGFYKGEKGLETQ-----VKKREGDI-------------DPGAARTVDLE  604 (878)
T ss_pred             HHHCCCHHHHHHHHHHHHHHCCCCHHHHHHHHHHCCCCCCHHH-----HHHHCCCC-------------CHHHCCCCCCC
T ss_conf             7761833079999877688669606899999984788652334-----44300345-------------85441465778


Q ss_pred             CCCCEEEEEECCCCCCCCCCCCCC-CCCCCCCCCCCCCC----------CCCCCCCCCCCCCCCCCEEEEEECCCCCEEE
Q ss_conf             777313687157761112343432-33321001221000----------0123442014689999669998269742277
Q gi|254780306|r  609 HTHSLSLKLSSKYGAFVGCTNYPE-CKYTRQLTSNPQDI----------PEMKESVLLGNDLETKESVTLRSGRFGLYVQ  677 (837)
Q Consensus       609 ~~g~L~~k~~gK~G~FigCSnyPe-Ck~t~~l~~~~~~~----------~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq  677 (837)
                      + ..+.++ .||||+|++|+++++ |+++.+....+.+.          ....++++||.||++|++|+||.||||||||
T Consensus       605 ~-~~~~~r-~gk~G~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~l~~~~~~g~r~LG~dP~tg~~V~~k~GryGpyvq  682 (878)
T PRK07561        605 G-LPCVVR-IGRFGPYLEGEREEEPIKASLPQDITPADLDPEQVEQILKQKTEGPEKLGTHPETGEPVYLLFGPYGPYVQ  682 (878)
T ss_pred             C-CCCEEE-EECCCCCEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCEEE
T ss_conf             9-862366-41676720210587653102676558654787888776412467873236689999868999358218698


Q ss_pred             ECC----CCCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEEEC-----CEECCCCCCCC
Q ss_conf             348----877761337899884254899999986152551577789874999115876526167-----81112488775
Q gi|254780306|r  678 RGD----GKDAKRCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNHD-----GAYTKLESIEQ  748 (837)
Q Consensus       678 ~Ge----~~kpkr~si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~~~-----~~~~sl~~~~~  748 (837)
                      +|+    .+||||+||||++++++||||+||+||||||+||.|||+|++|+|++|||||||+|+     ++|+||+++++
T Consensus       683 lG~~~~~~~Kpk~asl~k~~~~~~itle~Al~LlsLPr~lG~~pe~g~~I~a~~GrfGPY~~~dg~k~g~~~~sl~~~~~  762 (878)
T PRK07561        683 LGDVTEENPKPKRASLPKGVKPEDVTLEMALGLLSLPRLLGEHPETGGKIQAGLGRFGPYVVHDKGKGEKDYRSLKKEDD  762 (878)
T ss_pred             ECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCHHHCCCCCCCCEEEECCCCCCCCEEECCCCCCCCCCCCCCCCC
T ss_conf             04777667787644568999804268999999970757537887899879987678776674047766764145799887


Q ss_pred             CCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCCC-CCEEEEECCCCCEEEECCEEEECCCCCCHHHCCHHHHHH
Q ss_conf             1435799999999836511344344544320102678989-846996068545253678887565788967789999999
Q gi|254780306|r  749 VLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPEG-GSITVHNGRYGPYLHWKKINASLSKEESPDTVDLEKALK  827 (837)
Q Consensus       749 ~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~~-~~i~i~~GryGpYi~~gk~Na~ipk~~~~e~lt~e~a~~  827 (837)
                      +|+||||+||+||+++++.++     .++++++||+||++ ++|+|++|||||||+||++||+|||+.||++||+|+|++
T Consensus       763 ~~~i~l~~Av~lia~~k~~~~-----~~~~lk~lg~~p~~~~~i~v~~GRyGpYv~~gk~na~ipk~~~p~~ltle~a~~  837 (878)
T PRK07561        763 VLTVDLERALELLAMPKKGRG-----GKTPLKELGKHPEDGEPVQVYDGPYGLYVKHGKVNASLPEGKTAEDITLEEALE  837 (878)
T ss_pred             CEEECHHHHHHHHHHHHCCCC-----CCCHHHHCCCCCCCCCCEEEECCCCCEEEEECCEEECCCCCCCHHHCCHHHHHH
T ss_conf             645159999999961321465-----542366628997899835995488610688797885169999834488999999


Q ss_pred             HHHHHHHCC
Q ss_conf             998777266
Q gi|254780306|r  828 ILNIKKQKK  836 (837)
Q Consensus       828 li~~k~~kk  836 (837)
                      ||++|++++
T Consensus       838 li~~k~~~~  846 (878)
T PRK07561        838 LLAEKASSK  846 (878)
T ss_pred             HHHHHCCCC
T ss_conf             998424378


No 4  
>PRK08780 DNA topoisomerase III; Provisional
Probab=100.00  E-value=0  Score=1921.40  Aligned_cols=748  Identities=42%  Similarity=0.730  Sum_probs=699.4

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP   81 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~   81 (837)
                      +|||||||||||||++|||++|.|+||+|||||||+++++|||+++|.|.|+++++++++|+.|++++++||+|||||||
T Consensus         4 ~LVIVESPaKaktI~k~LG~~y~V~as~GHirdL~~k~~~vd~~~~f~~~y~~~~~~~k~v~~lk~~~k~ad~V~lATDp   83 (783)
T PRK08780          4 HLLIVESPAKAKTINKYLGKDFTVLASYGHVRDLVPKEGAVDPDNGFAMRYDLIDKNEKHVEAIAKAAKSADDIYLATDP   83 (783)
T ss_pred             CEEEECCHHHHHHHHHHCCCCCEEEEECCCHHHCCCHHCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf             58998270888999987296979997147463288500473756687557888887078999999998379979989898


Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHCC
Q ss_conf             70257999999999755125788716999980379899999986226469899999999999898740113789886414
Q gi|254780306|r   82 DREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLP  161 (837)
Q Consensus        82 DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~  161 (837)
                      |||||+|||||+++|+.++.++++||+|+||||||++||++||+|||++|++||+||+|||++||||||||||+||++++
T Consensus        84 DREGEaIawhl~e~l~~k~~l~~k~vkRi~F~eITk~AI~~A~~npr~id~~Lv~Aq~aRrilDrLvG~~lSp~Lw~k~~  163 (783)
T PRK08780         84 DREGEAISWHIAEILKERGLLKDKPMQRVVFTEITPRAIKEAMLKPRAIASDLVDAQQARRALDYLVGFNLSPVLWRKVQ  163 (783)
T ss_pred             CCCHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCHHHHHHHHHHHHHHHHHHHHHCCCHHHHHHHCCC
T ss_conf             70407999999999544315888863799995569999999995911102778999999998883206230188885256


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCC--
Q ss_conf             676534226899999999999964137654400122331579965422331035833033101135666777642001--
Q gi|254780306|r  162 GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKK--  239 (837)
Q Consensus       162 ~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~--  239 (837)
                      ++|||||||||||+||||||+||++|+|++||+|.|.|.. .+..|.++|...++++++++++.+++.|+++...+..  
T Consensus       164 ~~lSAGRVQSpaL~LIveRE~EI~~F~p~~Yw~i~a~~~~-~~~~f~akl~~~~~~k~~~~~~~d~~~a~~~~~~l~~~~  242 (783)
T PRK08780        164 RGLSAGRVQSPALRMIVEREEEIEAFIAREYWSIEADCAH-PSQAFNAKLIKLDGQKFEQFTITDGDTAEAARLRIQQAA  242 (783)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEC-CCCCEEEEEEEECCEEECCCCCCCHHHHHHHHHHHHHHC
T ss_conf             8866310022888889999999970388544999999824-887358999852783501167899999999999998622


Q ss_pred             -CCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCC-HHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             -56301000023322246852103799999887608889999999987621355672-1224553147554444305689
Q gi|254780306|r  240 -ATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNG-EIVGLITYMRTDGVHMSPDALE  317 (837)
Q Consensus       240 -~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~-~~~GlITYpRTDS~~ls~ea~~  317 (837)
                       ..+.|.+|++++.+++||+||+||||||+||++|||||++||++||+|||++++++ ++.||||||||||++||++++.
T Consensus       243 ~~~~~V~~v~~k~~k~~Pp~PFtTStLQqeAs~kLg~Sak~TM~iAQ~LYE~~~~~~~~~~GlITYmRTDS~~LS~eai~  322 (783)
T PRK08780        243 QGVLHVTDVASKERKRRPAPPFTTSTLQQEASRKLGFTTRKTMQVAQKLYEGVALGDEGSVGLITYMRTDSVNLSQDALA  322 (783)
T ss_pred             CCCEEEEEEEECEECCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCEEEEEECCCCCCCCCHHHHH
T ss_conf             79659999872201258999977689999999871999999999999997424256777402797347686644889999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCC
Q ss_conf             99976552001123763111125566688777652477302346400000199999999999999999985222110010
Q gi|254780306|r  318 AVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERT  397 (837)
Q Consensus       318 ~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~  397 (837)
                      .++++|...||.+|+|..+|.|++|++||||||||||||++..+|+.+...|++||++||+|||+|||||||+||+++++
T Consensus       323 ~~r~~I~~~~G~~~l~~~~r~y~~k~knaQeAHEAIRPT~~~~~p~~~~~~Ls~de~kLY~LIw~R~lASqm~~A~~~~t  402 (783)
T PRK08780        323 EIRDVIARDYGTASLPDQPNVYTTKSKNAQEAHEAVRPTSALRTPAQVARFLSDDERRLYELIWKRAVACQMIPATLNTV  402 (783)
T ss_pred             HHHHHHHHHHCHHHHCCCCHHCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHHCCHHEEEEE
T ss_conf             99999997302544121201202454565346678688610048777613699889999999999999973851268899


Q ss_pred             EEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCC--CCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHH
Q ss_conf             01367740796399999874880588567632677763--2100101488645688211001101112346431017899
Q gi|254780306|r  398 TVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQE--KNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESS  475 (837)
Q Consensus       398 ~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~--~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEas  475 (837)
                      +|.|.+..+   +.|+++|++++|+||++||.++.++.  ++++++..||.|++|+.+.+.++.+++|+|+||+||||||
T Consensus       403 ~v~i~~~~~---~~F~asG~~i~f~G~~~vy~e~~d~~~~~~~~~~~~LP~l~~Gd~l~~~~i~~~~~~TkPP~RYTEas  479 (783)
T PRK08780        403 SVDLSAGSE---HVFRATGTTVVVPGFLAVYEEGKDTKSSEDEDEGRKLPLMKEGDNVPLERIVTEQHFTQPPPRYTEAA  479 (783)
T ss_pred             EEEEECCCC---CEEEEEEEEEEECCHHHHHHCCCCCCCCCCCHHHCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCHHH
T ss_conf             999983898---58999989998557677642125555411220111277656797767899887667727999879899


Q ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHH
Q ss_conf             87433210256655157899999732202214771222011420000223366556898899999999999862601347
Q gi|254780306|r  476 LIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWK  555 (837)
Q Consensus       476 Lik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~  555 (837)
                      ||++||++|||||||||+||+||++|+||.+++++|+||++|++|++||++||+++|||+|||+||++||+||+|+.+|.
T Consensus       480 LIk~mEe~GIGRPSTyA~II~tL~~R~YV~~e~k~l~PT~~G~~V~~fL~~~F~~~vd~~FTa~mE~~LD~Ia~G~~~w~  559 (783)
T PRK08780        480 LVKALEEYGIGRPSTYASIIQTLQFRKYVEMEGRSFRPTDVGRAVSKFLSGHFTRYVDYDFTARLEDDLDAVSRGEAEWI  559 (783)
T ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHCCCCEEECCCCCCCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCHHH
T ss_conf             99999966999744279999888637868961884241289999999999863653582007999987669865972589


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             89999867676655766775566677655676641024555567661143346777313687157761112343432333
Q gi|254780306|r  556 EVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKY  635 (837)
Q Consensus       556 ~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~  635 (837)
                      +||++||.+|+..++...+..                                     .                     
T Consensus       560 ~~l~~Fy~~f~~~v~~~~~~~-------------------------------------~---------------------  581 (783)
T PRK08780        560 PLMEKFWGPFKELVEDKKDSL-------------------------------------D---------------------  581 (783)
T ss_pred             HHHHHHHHHHHHHHHHHHHCC-------------------------------------C---------------------
T ss_conf             999999887899887765301-------------------------------------3---------------------


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEECC---CCCCCCCCCCCCCCHHHCCHHHHHHHHHCCHH
Q ss_conf             210012210000123442014689999669998269742277348---87776133789988425489999998615255
Q gi|254780306|r  636 TRQLTSNPQDIPEMKESVLLGNDLETKESVTLRSGRFGLYVQRGD---GKDAKRCSLPKTWKSDSVDYDKAMSLLSLPRE  712 (837)
Q Consensus       636 t~~l~~~~~~~~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq~Ge---~~kpkr~si~k~~~~~~itle~Al~LLsLPr~  712 (837)
                                ..+..+.+.||.||+||++|++|.||||||||+|+   .+||+|+|||+++++++||||+|++||+|||.
T Consensus       582 ----------~~~~~~~r~lg~dp~~g~~v~~k~GryGpyvq~g~~~~~~kpk~~sl~~~~~~~~i~le~Al~ll~lPr~  651 (783)
T PRK08780        582 ----------KTDAGSVRVLGTDPKSGKEVSARIGRFGPMVQIGTVDDEEKPRFASLRPGQSIYSISLEEALELFKMPRA  651 (783)
T ss_pred             ----------HHHCCCCCCCCCCCCCCCEEEEEECCCCCEEEECCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHCCCHH
T ss_conf             ----------4443675204889888970599833777767514787566986331799999132789999998705242


Q ss_pred             HCCCCCCCCEEEEEECCCCCEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCCCCCEE
Q ss_conf             15777898749991158765261678111248877514357999999998365113443445443201026789898469
Q gi|254780306|r  713 IGIHPETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPEGGSIT  792 (837)
Q Consensus       713 lG~~pe~g~~I~~~~GryGpYi~~~~~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~~~~i~  792 (837)
                      ||.  ++|++|++++|||||||+|+++|+||+++++||+|+||+|++||++++..++.         +.+++|| +++|+
T Consensus       652 lG~--~~g~~i~~~~Gr~GpYv~~~~~~~sl~~~~~~~~i~l~~A~~li~~~~~~~~~---------~~~~~~~-~~~i~  719 (783)
T PRK08780        652 LGE--DKGQDVSVGIGRFGPFARRGSTYVSLKKEDDPYTIDLARAVFLIEEKEEIARN---------RVIKDFE-GSDIQ  719 (783)
T ss_pred             HCC--CCCCEEEECCCCCCCCEEECCEEECCCCCCCCEEECHHHHHHHHHHHHHCCCC---------CCCCCCC-CCCEE
T ss_conf             089--99977997768877547579888347999876452799999999703202656---------6666689-99748


Q ss_pred             EEECCCCCEEEECCEEEECCCCCCHHHCCHHHHHHHHHHHH
Q ss_conf             96068545253678887565788967789999999998777
Q gi|254780306|r  793 VHNGRYGPYLHWKKINASLSKEESPDTVDLEKALKILNIKK  833 (837)
Q Consensus       793 i~~GryGpYi~~gk~Na~ipk~~~~e~lt~e~a~~li~~k~  833 (837)
                      |++|||||||+||++||+|||+.||++||+|+|++||+++.
T Consensus       720 v~~GryGpYv~~gk~na~ipk~~~~~~ltle~a~~li~e~~  760 (783)
T PRK08780        720 VLNGRFGPYISDGKLNGKIPKDREPASLTLEEVQQLLADTG  760 (783)
T ss_pred             EECCCCCCEEEECCEEEECCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             81268864077798995058999800089999999997278


No 5  
>PRK06599 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=1910.68  Aligned_cols=761  Identities=49%  Similarity=0.861  Sum_probs=721.1

Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             91899779047877887508998999942511007865578676667440688776548999999999870998999469
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATD   80 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD   80 (837)
                      |+|||||||||||||++|||++|.|+||+|||||||.+.++|+|+++|.|.|+++++++++|+.|++++++||+||||||
T Consensus         1 MkLvIvESPsKaktI~k~LG~~y~V~as~GHi~dLp~~~~~v~~~~~f~~~y~~~~~~~k~i~~lk~l~k~ad~V~lATD   80 (776)
T PRK06599          1 MKLVIVESPAKAKTINKYLGDEFKVIASFGHIRDLPSKKGSVLPDENFAMKYDISDKAGKYVDAIVKDAKKAEAVYLATD   80 (776)
T ss_pred             CEEEEECCHHHHHHHHHHCCCCCEEEEECCCHHHCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEECCC
T ss_conf             90999817389999999709597999713737546765488676778734679897678899999999847998998989


Q ss_pred             CCCHHHHHHHHHHHHHHHHCC-CCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHH
Q ss_conf             970257999999999755125-7887169999803798999999862264698999999999998987401137898864
Q gi|254780306|r   81 PDREGEAISWHVLDVLRQKNL-IEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQK  159 (837)
Q Consensus        81 ~DREGE~Iawhi~e~l~~~~~-~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk  159 (837)
                      ||||||+|||||+++|+.+.. .+..+++|+||||||++||++||+|||++|++||+||+|||++|||||||+||+||++
T Consensus        81 pDREGEaIawhi~e~l~~~~~~~~~~~~kRi~f~eITk~AI~~Al~npr~id~~Lv~Aq~aRr~lDrlvG~~lSp~L~~k  160 (776)
T PRK06599         81 PDREGESISWHVAEVIKEKNKVKSDDFFKRVAFNEITKKAIIHAVENPRKLDTNLVNAQQARRALDYLVGFTLSPLLWRK  160 (776)
T ss_pred             CCCCHHHHHHHHHHHHCHHCCCCCCCCEEEEEEECCCHHHHHHHHHCCHHCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             97043699999999856004676777603899933899999999959320177789999999998855337455999974


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCC
Q ss_conf             14676534226899999999999964137654400122331579965422331035833033101135666777642001
Q gi|254780306|r  160 LPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKK  239 (837)
Q Consensus       160 ~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~  239 (837)
                      +++++||||||||||+|||+||+||++|+|++||+|.+.|...++..|.++|.+.++++++++++.++++|+++++.+++
T Consensus       161 ~~~~~SaGRVQSpaL~LIveRE~EI~~F~p~~Yw~v~a~~~~~~~~~f~a~l~~~~~~k~~k~~i~~~~~A~~i~~~l~~  240 (776)
T PRK06599        161 LPGCKSAGRVQSVALRLICEREDEIERFKSEEYWDISLKMQNSNNELFTAKLTHVNDQKLEKFSIINEKEAKDLTKKLKS  240 (776)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCEEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHCC
T ss_conf             37888666310799999998799998358741589999997489964777887516730031565899999999998516


Q ss_pred             CCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             56301000023322246852103799999887608889999999987621355672122455314755444430568999
Q gi|254780306|r  240 ATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAV  319 (837)
Q Consensus       240 ~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~  319 (837)
                      +.++|.+|++++.+++||+||+||||||+||++|||||++||+|||+|||++++++++.||||||||||++||++++..+
T Consensus       241 ~~~~V~~v~~k~~k~~Pp~PFtTStLQqeAs~klg~Sak~TM~iAQ~LYE~~~~~~e~~GlITYmRTDS~~LS~e~~~~~  320 (776)
T PRK06599        241 QKFHVDKIEKKQQKRQPQPPFITSSLQQEAARKLGFSAKKTMQIAQKLYEGVDIGKETIGLITYMRTDGVTLSNDAIADI  320 (776)
T ss_pred             CCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCCCCEEEEECCCCCCCCHHHHHHH
T ss_conf             97499998765421279899766899999998718889999999999985155575655258996588861399999999


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEE
Q ss_conf             97655200112376311112556668877765247730234640000019999999999999999998522211001001
Q gi|254780306|r  320 RRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTV  399 (837)
Q Consensus       320 r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v  399 (837)
                      +++|...||.+|+|..+|.|++|++||||||||||||++..+|+.+...|+.||++||+|||+|||||||++|+++.+++
T Consensus       321 ~~~I~~~~g~~yl~~~~r~~k~k~~naqeAHeAIrPT~~~~~p~~~~~~l~~de~kLY~LI~~R~lAsqm~~a~~~~~~~  400 (776)
T PRK06599        321 RKLIDKSYGDKYLPSSPRIYKSKVKNAQEAHEAIRPTNITYTPDSLKEKLEKDYYKLYELIWKRTIACQMENVIMDLVVA  400 (776)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCHHHHHHHHHHHHHHHHHCCCHHEEEEEEE
T ss_conf             99998741254333132001464434535777767877665733543016888999999999999997075016789999


Q ss_pred             EEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHH
Q ss_conf             36774079639999987488058856763267776321001014886456882110011011123464310178998743
Q gi|254780306|r  400 NIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKK  479 (837)
Q Consensus       400 ~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~  479 (837)
                      .+.+.  +..+.|+++|++++|+||++||.+..+++. ++++..||.|++|+.+.+.++.+.+|+|+||+||||||||++
T Consensus       401 ~i~~~--~~~~~~~asg~~i~f~G~~~vy~~~~~~~~-~~~~~~LP~l~~g~~l~~~~i~~~~~~TkPP~RYTEasLVk~  477 (776)
T PRK06599        401 NLASE--NKEYLAKANGSTIAFDGFYKVYRESVDDEA-EEENKMLPPLKEQEPLKTKEIIPNQHFTEPPPRYSEASLVKK  477 (776)
T ss_pred             EEEEC--CCEEEEEEEEEEEEECCCCEECCCCCCCCC-CCHHCCCCCCCCCCCCCEEEEEECCEECCCCCCCCHHHHHHH
T ss_conf             99967--953899998899973650210023355532-101113885336884202455412156279988798999999


Q ss_pred             HHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             32102566551578999997322022147712220114200002233665568988999999999998626013478999
Q gi|254780306|r  480 MEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLH  559 (837)
Q Consensus       480 mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~  559 (837)
                      ||++|||||||||+||+||++|+||.+++++|+||++|++|++||++||+++|+|+|||+||+.||+||+|+.+|.++|+
T Consensus       478 mE~~GIGRPSTyAsII~tL~~R~YV~~~~k~liPT~~G~~V~~~L~~~F~~ivd~~fTA~mE~~LD~Ia~G~~~w~~~l~  557 (776)
T PRK06599        478 LEELGIGRPSTYASILSVLQDRKYVALEKKRFIPEELGRLVTVFLVGFFKKYVEYDFTAGLENELDEIAAGKLEWKAALN  557 (776)
T ss_pred             HHHCCCCCCCCHHHHHHHHHCCCCEEECCCEECCCHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHH
T ss_conf             98569998760567787775378488428430125648999999987553512740568999867898769824999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf             98676766557667755666776556766410245555676611433467773136871577611123434323332100
Q gi|254780306|r  560 EFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQL  639 (837)
Q Consensus       560 ~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l  639 (837)
                      +||.+|+..++.+.+..+.++.+.+...+..+.+....   ..+.||+|+.|.|.++. ||||+||||||||+|+|++++
T Consensus       558 ~Fy~~f~~~i~~~~~~~~~~~~~~~~~~l~~~~~~~~~---~~~~cp~c~~g~l~~r~-gk~G~f~~cs~yp~c~~~~~~  633 (776)
T PRK06599        558 NFWSGFNHNIESVNEQKITEIISYVQKALDYHLFGENK---ESKVCPSCKTGELSLKL-GKFGAFLACSNYPECTFRKSI  633 (776)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCC---CCCCCCCCCCCCEEEEE-CCCCCCCCCCCCCCCCCCCCC
T ss_conf             99876666677777631346777787530211246666---66517878887358960-586574115798666666768


Q ss_pred             CCCCCCC-------CCCCCCCCCCCCCCCCCEEEEEECCCCCEEEECCCC---CCCCCCCCCCCCHHHCCHHHHHHHHHC
Q ss_conf             1221000-------012344201468999966999826974227734887---776133789988425489999998615
Q gi|254780306|r  640 TSNPQDI-------PEMKESVLLGNDLETKESVTLRSGRFGLYVQRGDGK---DAKRCSLPKTWKSDSVDYDKAMSLLSL  709 (837)
Q Consensus       640 ~~~~~~~-------~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq~Ge~~---kpkr~si~k~~~~~~itle~Al~LLsL  709 (837)
                      .....+.       ....++++||.||+ |.+|++|.||||||||+|+.+   ||||+|||+++++++||||+|++||+|
T Consensus       634 ~~~~~~~~~~~~~~~~~~~~~~lG~d~~-g~~v~~k~GryGpyvq~g~~~~~~kpk~~sl~~~~~~~~itle~Al~ll~l  712 (776)
T PRK06599        634 VSGNDNNENEGEPKAIPNENKVLGTDKD-GVEIYLKKGPYGPYIQLGEQEGKVKPKRSPVPASLNQNDITLEIALKLLSL  712 (776)
T ss_pred             CCCCCCCHHHHHHHHCCCCCCCCCCCCC-CCEEEEECCCCCCEEEECCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHC
T ss_conf             8765640234566633467820242989-998999248886769844777877877567889998323189999999838


Q ss_pred             CHHHCCCCCCCCEEEEEECCCCCEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCC
Q ss_conf             255157778987499911587652616781112488775143579999999983651134
Q gi|254780306|r  710 PREIGIHPETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTIDLEQAISCITEKKKIEK  769 (837)
Q Consensus       710 Pr~lG~~pe~g~~I~~~~GryGpYi~~~~~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~  769 (837)
                      ||+||.||++|++|++++|||||||+|+++|+||++++|+|+||||+||+||++||.+.+
T Consensus       713 Pr~lG~~p~~g~~i~~~~GryGpYvk~~~~~~sl~~~~~~~~i~l~~A~~li~~~k~~~~  772 (776)
T PRK06599        713 PLKIGIHKDSGEEIMIGYGKFGPYIKYMGKFISIPKKYDFLNLSLDDAMKLIEDNKAKLE  772 (776)
T ss_pred             CHHHCCCCCCCCEEEECCCCCCCEEEECCEEEECCCCCCCCCCCHHHHHHHHHHHHHHCH
T ss_conf             373199978997799877788720888998876798888743589999999998876332


No 6  
>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=100.00  E-value=0  Score=1744.40  Aligned_cols=632  Identities=46%  Similarity=0.764  Sum_probs=585.3

Q ss_pred             EEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCC------------------CCCCCCCCC--CCEEEEECCCHHHHH
Q ss_conf             899779047877887508998999942511007865------------------578676667--440688776548999
Q gi|254780306|r    3 VIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAK------------------KGSVLPEKE--FEMIWNIDPSSQKHL   62 (837)
Q Consensus         3 LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~------------------~~~v~~~~~--f~p~y~v~~~~kk~~   62 (837)
                      |||||||||||||++|||++|.|.||+|||||||.+                  .+|||+|++  |+|.|+|+++|++.|
T Consensus         1 LVIVESPAKAKTI~~YLG~~Y~V~aS~GHiRDLP~sa~~~~~~yk~~~rGa~wa~lGvd~e~~~qF~P~Y~~~~~K~~~V   80 (688)
T TIGR01051         1 LVIVESPAKAKTIKKYLGKEYEVEASMGHIRDLPKSASDVPEKYKSQERGALWARLGVDIEKNKQFEPEYVVSKGKKKVV   80 (688)
T ss_pred             CEEEECCHHHHHHHHHCCCCCEEEEECCCHHHCCCHHHCCCHHCCCCCCCCEEECCCCCCCCCCCCCCCEEECCCHHHHH
T ss_conf             95872453899998648998689972385221020001044320787343222024543213784165043546144789


Q ss_pred             HHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHH
Q ss_conf             99999987099899946997025799999999975512578871699998037989999998622646989999999999
Q gi|254780306|r   63 QNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARR  142 (837)
Q Consensus        63 ~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr  142 (837)
                      +.|++++++|++||||||+|||||||||||+++|+.+....+.=++||+|||||+.||+.||+|||+||+|||+||+|||
T Consensus        81 ~~L~~lakkA~~~yLAtD~DREGEAIaWHl~~~l~~~~~~~ddf~kR~VFnEIT~~AI~~A~~~PR~ID~~~V~AQ~ARR  160 (688)
T TIGR01051        81 KELKTLAKKADEVYLATDPDREGEAIAWHLAELLKPKLKVKDDFYKRIVFNEITKKAIRAALKNPREIDMNLVNAQQARR  160 (688)
T ss_pred             HHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHCCCCCCCCCCCCCEECCCCCHHHHHHHHHCCCCCCHHHHHHHHHHH
T ss_conf             99999987316156404888540258999999807546775643065002476778999998377202435688887765


Q ss_pred             HHHHHHHHHHCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCC------CCEEEEEEEEECC
Q ss_conf             9898740113789886414676534226899999999999964137654400122331579------9654223310358
Q gi|254780306|r  143 ALDYLVGFNLSPILWQKLPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPR------NDKFTAHLTDFNG  216 (837)
Q Consensus       143 ~lD~lvG~~lSp~L~rk~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~------~~~f~a~l~~~~~  216 (837)
                      +|||||||.||||||||+..+||||||||+|||||||||+||+.|||+.||+|.|.+...+      +..|.|+|++.+|
T Consensus       161 iLDRlVGY~lSPlLW~K~~~gLSAGRVQSVAlRLi~~RErEi~~Fvp~~YW~~~~~~~~~~~~~~~~~~~f~A~l~~~~g  240 (688)
T TIGR01051       161 ILDRLVGYKLSPLLWKKVAKGLSAGRVQSVALRLIVDREREIKRFVPEEYWTVDAKLEAKNNQKVACKETFEALLTEVNG  240 (688)
T ss_pred             HHCEEEEEEECHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCHHHHCCCCEEEEECC
T ss_conf             62122210575347731236787760565567677754789861688611798999645666311111046321241247


Q ss_pred             EEECCCC----------------HHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHH
Q ss_conf             3303310----------------113566677764200156301000023322246852103799999887608889999
Q gi|254780306|r  217 QRIEKKS----------------ISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHT  280 (837)
Q Consensus       217 ~~~~~~~----------------~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~T  280 (837)
                      +++....                +.|+.+|.++.+.|++..+.|.++++|+.+++|++||+||||||+|++||||||++|
T Consensus       241 ~kl~~~~~~D~~~g~l~~G~~v~~L~E~~A~~~~~~L~~~~~~V~~~e~K~~~~~P~~PF~TSTLQQeA~~KLGFSa~kT  320 (688)
T TIGR01051       241 KKLKAGSDFDPLTGELRPGKEVVVLNEAEATALKEQLKGEEYVVEEIEKKPKKSRPPPPFTTSTLQQEASRKLGFSAKKT  320 (688)
T ss_pred             CCCCCCCCCCCCCCCCCCCCEEEEECHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCHHHHHHHHHCCCCCCHH
T ss_conf             01132124780101268997168818699999998507864799886304330176348335418998877537951026


Q ss_pred             HHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC--CCCCCCCCCCCCCCCCEEEE-E
Q ss_conf             99998762135567212245531475544443056899997655200112376311--11255666887776524773-0
Q gi|254780306|r  281 MRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKP--RIYSSKSKNAQEAHEAIRPN-D  357 (837)
Q Consensus       281 m~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~--r~y~~k~k~aQeAHeAIrPT-~  357 (837)
                      |+|||+||||+.++.++.||||||||||++||++|++++|++|..+||++|||.+|  |+|++|.||||||||||||| +
T Consensus       321 M~iAQ~LYEGv~~~~~~~G~ITYMRTDS~~lS~~A~~eaR~~I~~~yG~~YL~~~~kLk~y~~k~KnaQeAHEAIRPtG~  400 (688)
T TIGR01051       321 MMIAQRLYEGVSLGEGTVGLITYMRTDSTRLSNEAVNEARNLIDKNYGKEYLGPKPKLKRYKSKEKNAQEAHEAIRPTGS  400 (688)
T ss_pred             HHHHHHHHCCEECCCCEEEEEECCCCCCHHHHHHHHHHHHHHHHHHCCHHCCCCCCCCCCHHHCCCCCCCHHHCCCCCCC
T ss_conf             55542331254438955899832863305789999999998888621120378874223102216875001104476431


Q ss_pred             CCCCCCHHCCCCCH---HHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCC
Q ss_conf             23464000001999---999999999999999852221100100136774079639999987488058856763267776
Q gi|254780306|r  358 FDFLPSKMKQFLDS---DQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQ  434 (837)
Q Consensus       358 ~~~~p~~~~~~L~~---de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~  434 (837)
                      +..+|++++..|+.   ||++||+|||+|||||||.||+++.++|.|.+..+...+.|+|+|+.+.|+||++||.+..|+
T Consensus       401 ~~~tP~~lk~~L~~PniD~~rLY~LIW~RfVASQM~dA~~~~~~v~l~~~~g~~~~~F~A~g~~~~FdGf~kvy~e~~dd  480 (688)
T TIGR01051       401 VFRTPEELKAELKRPNIDELRLYELIWKRFVASQMADARYDSLSVRLTAEKGSVEVVFKASGRKLLFDGFYKVYVEGSDD  480 (688)
T ss_pred             EEECHHHHHHHCCCCCHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEEEECCCEEEEEEEECCEEECCHHHHHHHCCCCC
T ss_conf             10174888522377566788888999999887448775326899999861374015897402356455236664127887


Q ss_pred             CCC--CHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEE
Q ss_conf             321--001014886456882110011011123464310178998743321025665515789999973220221477122
Q gi|254780306|r  435 EKN--SEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKIL  512 (837)
Q Consensus       435 ~~~--~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~  512 (837)
                      +.+  ++.+..||+|++||.+.+.++.+.+|+|+||||||||||||.||++||||||||||||++|||||||.+++++|+
T Consensus       481 ~~~alee~~~~LP~Lk~Gd~~~~~~~~~~~H~T~PPaRYTEASLVK~LE~~GIGRPSTYAsiis~iqdRgYv~~~~k~l~  560 (688)
T TIGR01051       481 DDEALEEKDRILPPLKEGDAVKLVEVEPNQHFTQPPARYTEASLVKELEELGIGRPSTYASIISTIQDRGYVKLENKRLV  560 (688)
T ss_pred             HHHHHCCCCCCCCCCCCCCEEEEEECCCCCCEECCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCEEEEECCCCC
T ss_conf             16752224577878888862002752314510182798652479999985778899725558867506520330244002


Q ss_pred             ECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCC
Q ss_conf             20114200002233665568988999999999998626013478999986767665576677556667765567664102
Q gi|254780306|r  513 PQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVI  592 (837)
Q Consensus       513 pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~  592 (837)
                      ||++|++|+++|++||+++||++|||.||++||+||.|+..|+.||++||.+|...|+...........   ....+...
T Consensus       561 p~~~g~~V~~~Le~hF~~~Vd~~FTA~ME~~LDeiA~gk~~w~~~L~~Fy~~F~~~v~~~~~~~~a~~~---~~~~~~~~  637 (688)
T TIGR01051       561 PTELGFAVTDLLEKHFGELVDYDFTAKMEKELDEIAEGKAEWKPVLKNFYTGFSSKVEKVVEQKIALKD---LVERKMRE  637 (688)
T ss_pred             HHHHHHHHHHHHHHHCCCCCCCHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHH---HHHHCCCC
T ss_conf             027789999998864264335502376434467885051567999961068603454224543102224---56300013


Q ss_pred             CCCCCCCCCCEECCCCCCCCEEEEEECCCC--CCCCCCCCC---CCCCCCCC
Q ss_conf             455556766114334677731368715776--111234343---23332100
Q gi|254780306|r  593 FPPKENNEDSRTCPECHTHSLSLKLSSKYG--AFVGCTNYP---ECKYTRQL  639 (837)
Q Consensus       593 ~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G--~FigCSnyP---eCk~t~~l  639 (837)
                      ........+...||+||. .+.+| .||||  +|++|||||   +|+++.++
T Consensus       638 ~~~~~~~~~~~~C~~Cg~-~~~~k-~Gk~Gne~fl~Cs~~P~~~~C~~~~~~  687 (688)
T TIGR01051       638 IDDKEKEKTSKDCPLCGS-PMVVK-LGKYGNEPFLACSNFPEKEKCKLTKSI  687 (688)
T ss_pred             CCCCCCEECCCCCCCCCC-EEEEE-ECCCCCHHHHCCCCCCCCCCCCCCCCC
T ss_conf             311220001443534687-13686-303577254317831570206877788


No 7  
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=100.00  E-value=0  Score=1608.66  Aligned_cols=701  Identities=43%  Similarity=0.713  Sum_probs=622.6

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP   81 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~   81 (837)
                      +|||||||||||||++|||++|+|+||+|||||||.+.+|||++++|.|.|+++++++++|+.|++++++||.|||||||
T Consensus         4 ~LVIVESPaKAktI~k~LG~~y~V~as~GHirdLp~~~~gvd~~~~f~p~y~~~~~k~k~i~~Lkklak~ad~V~lATDp   83 (864)
T PRK06319          4 SLIIVESPAKIKTLQKLLGEGFIFASSLGHIVDLPAKEFGIDIENDFEPDYQILPDKQEVIRKICKLAKKCDVVYLSPDP   83 (864)
T ss_pred             CEEEECCHHHHHHHHHHCCCCCEEEECCCCHHCCCCCCCCCCCCCCCCCCEEECCCHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf             38998480889999997398979995157031089855684757798641167877689999999998469979989889


Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHCC
Q ss_conf             70257999999999755125788716999980379899999986226469899999999999898740113789886414
Q gi|254780306|r   82 DREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLP  161 (837)
Q Consensus        82 DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~  161 (837)
                      |||||+|||||+++|.     .+++++|+||||||++||++||+|||++|++||+||+|||+||||||||+||+||+++.
T Consensus        84 DREGEaIawhi~~~l~-----~~~~vkRi~F~EITk~AI~~Al~npr~id~~Lv~Aq~aRr~lDrLVG~~lSplL~~k~~  158 (864)
T PRK06319         84 DREGEAIAWHIANQLP-----KNTKIQRVSFNAITKGAVTEALKHPREIDMALVNAQQARRLLDRIVGYKISPILSRKLQ  158 (864)
T ss_pred             CCCHHHHHHHHHHHCC-----CCCCCEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_conf             7152799999999738-----99982589993679999999996852027888999999999997851535499999856


Q ss_pred             --CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCC-CCEEEEEEEEECCEEECC-----------CCHHHH
Q ss_conf             --676534226899999999999964137654400122331579-965422331035833033-----------101135
Q gi|254780306|r  162 --GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPR-NDKFTAHLTDFNGQRIEK-----------KSISNK  227 (837)
Q Consensus       162 --~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~-~~~f~a~l~~~~~~~~~~-----------~~~~~~  227 (837)
                        ++|||||||||||+||||||+||++|+|++||+|.+.|.... +..|.|.|...+|+++++           ..+.++
T Consensus       159 ~~~gLSAGRVQSPaL~LIVeRE~EI~~FvP~~Yw~I~a~~~~~~~~~~F~a~l~~~~gkk~~~~~~~~~~~~e~~~i~~~  238 (864)
T PRK06319        159 RRSGISAGRVQSVALKLVVDREKAIEAFVPVEYWNIRVLLQDPKTQKTFWAHLYSVNGKKWEKEIPEGKTEDEVLLINSK  238 (864)
T ss_pred             CCCCCCCCEECCHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCEEEEEEECCCCEECCCCCCCCCCCHHCCCCCH
T ss_conf             67886744302288899999999998258864389999984177774068888501770310024433442100045889


Q ss_pred             HHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCH-HHHHHHHCCC
Q ss_conf             666777642001563010000233222468521037999998876088899999999876213556721-2245531475
Q gi|254780306|r  228 KEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGE-IVGLITYMRT  306 (837)
Q Consensus       228 ~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~-~~GlITYpRT  306 (837)
                      ++|+.+++.+++..++|.+|+.|+.+++||+||+||||||+||++|||||++||+|||+||||++++++ +.||||||||
T Consensus       239 ~~a~~i~~~l~~~~~~V~~ve~K~~k~~Pp~PFtTSTLQqeAs~klGfSakkTM~iAQ~LYEgi~l~~~g~~GlITYpRT  318 (864)
T PRK06319        239 EKADHYVELLESASYTVTRVEAKEKRRFAYPPFITSTLQQEASRHFRFSSSRTMNIAQTLYEGVDLDSEGATGLITYMRT  318 (864)
T ss_pred             HHHHHHHHHHCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEEECCC
T ss_conf             99999999853798499998742330489899566999999987559899999999999867655577676114752257


Q ss_pred             CCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHH
Q ss_conf             54444305689999765520011237631111255666887776524773023464000001999999999999999999
Q gi|254780306|r  307 DGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVA  386 (837)
Q Consensus       307 DS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~la  386 (837)
                      ||++||++++..++++|.+.||++|++..+|.|+++ +++||||||||||++..+|+.+...|+.||++||+|||+||||
T Consensus       319 DS~~ls~ea~~~~r~~I~~~~g~~yl~~~~r~~~~k-k~aQdAHEAIRPT~~~~~pe~~~~~Ls~de~kLY~LI~~RflA  397 (864)
T PRK06319        319 DSVRIDPEALKQVREYIQQTFGKEYLPSSPNVYATK-KMAQDAHEAIRPTDINLTPEKLRNKLTDDQFKLYSLIWKRFVA  397 (864)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHHHHH
T ss_conf             874359999999999999876576322256746776-6766788883556755677676410799999999999999999


Q ss_pred             HHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCC
Q ss_conf             85222110010013677407963999998748805885676326777632100101488645688211001101112346
Q gi|254780306|r  387 SQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTE  466 (837)
Q Consensus       387 sqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~Tk  466 (837)
                      |||+||+|++++|.|.+..   .+.|+|+|++++|+||++||.+..+++..++++..||.|++|+.+.+.+++.+||+|+
T Consensus       398 Sqm~~A~~~~~~v~i~~~~---~~~F~asG~~v~f~Gw~~vy~~~~~de~~~~~~~~LP~L~~Gd~l~~~~i~~~q~~Tk  474 (864)
T PRK06319        398 SQMIPAIYDTLAIQITTNK---GIDLRATGSLLKFKGFLAVYEEKRDDEGDEEENIPLPKLHEQDVLIKEEVSAEQAFTK  474 (864)
T ss_pred             HHCCHHEEEEEEEEEECCC---CEEEEEEEEEEEECCEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECEEECC
T ss_conf             7486223899999997289---7699997789986760477624357522221135688655585533245441300569


Q ss_pred             CCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             43101789987433210256655157899999732202214771222011420000223366556898899999999999
Q gi|254780306|r  467 PPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDE  546 (837)
Q Consensus       467 PP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~  546 (837)
                      ||+||||||||++||+.|||||||||+||+||++|+||.+++++|+||++|++|++||++||++|+|++|||+||++||+
T Consensus       475 PP~RYTEAsLIk~ME~~GIGRPSTyA~II~tL~~R~YV~~e~k~l~PT~lG~~V~~~L~~~f~~ivd~~fTA~mE~~LD~  554 (864)
T PRK06319        475 PLPRFTEASLVKELEKSGIGRPSTYATIMNKIQSREYTLKENQRLRPTELGKIISQFLETNFPRIMDIGFTALMEDELEL  554 (864)
T ss_pred             CCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHCCCEEEECCEECCHHHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             98998889999999717999501069999989867988101988680078999999999864643485317899988999


Q ss_pred             HHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCC
Q ss_conf             86260134789999867676655766775566677655676641024555567661143346777313687157761112
Q gi|254780306|r  547 ISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVG  626 (837)
Q Consensus       547 Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~Fig  626 (837)
                      |++|+.+|.+||++||..|...++.+.+...           ..       ...+...||+|+.|.+. ++.|++|.|||
T Consensus       555 Ia~G~~~w~~vL~~F~~~f~~~l~~a~~~~~-----------~~-------~~~~~~~Cp~Cg~~~li-k~~gk~g~F~g  615 (864)
T PRK06319        555 IADNKKPWKLLLQEFWEQFLPVVVTAEKEAF-----------IP-------RIVTEIDCPKCHKGKLV-KIWAKNRYFFG  615 (864)
T ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHHHHC-----------CC-------CCCCCCCCCCCCCCCEE-EECCCCCCEEE
T ss_conf             9738741999999999999999999986431-----------35-------55556778757887568-87146771210


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCCCCEEEEEECCCCCEEEECCCCCCCCC-CCCCCCCHHHCCHHHHH
Q ss_conf             343432333210012210000123442-0146899996699982697422773488777613-37899884254899999
Q gi|254780306|r  627 CTNYPECKYTRQLTSNPQDIPEMKESV-LLGNDLETKESVTLRSGRFGLYVQRGDGKDAKRC-SLPKTWKSDSVDYDKAM  704 (837)
Q Consensus       627 CSnyPeCk~t~~l~~~~~~~~~~~~~~-~LG~dP~~G~~I~lk~GryGpYvq~Ge~~kpkr~-si~k~~~~~~itle~Al  704 (837)
                      ||+||+|+|+.+......+.++...+. .-+.||.||.+|++|.||||.|+-+..-++.|.. +|+|.... .       
T Consensus       616 Cs~yP~C~~~~~~~~~~~~~~~~~~~~~~~~~Cp~Cg~~mv~k~gr~G~F~~Cs~YP~Ck~t~~l~k~~~~-~-------  687 (864)
T PRK06319        616 CSEYPECDYKTSEEELTFNKEDYAEDTPWDSPCPLCGGEMKVRHGRFGTFLGCENYPECRGIINIHKKGEE-G-------  687 (864)
T ss_pred             CCCCCCCCCCCCHHHCCCCCHHCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC-C-------
T ss_conf             58997656667601104562001457878998767897011313787754316998577897466666777-8-------


Q ss_pred             HHHHCCHHH-CCCCC--CCCEEEEEECCCCC-EEEECCEECCC
Q ss_conf             986152551-57778--98749991158765-26167811124
Q gi|254780306|r  705 SLLSLPREI-GIHPE--TQKNIIAGTGKYGY-YLNHDGAYTKL  743 (837)
Q Consensus       705 ~LLsLPr~l-G~~pe--~g~~I~~~~GryGp-Yi~~~~~~~sl  743 (837)
                          .++.+ ..||.  |+..|+.+.+|||- |..|.+ |..+
T Consensus       688 ----~~~~~~v~cp~~~c~g~~v~r~sr~g~~Fygc~~-yP~c  725 (864)
T PRK06319        688 ----IEQEETIPCPAIGCTGHIVKRRSRFNKIFYSCSE-YPEC  725 (864)
T ss_pred             ----CCCCCCCCCCCCCCCCEEEEEECCCCCEEECCCC-CCCC
T ss_conf             ----7656777689989898688863478984436788-9998


No 8  
>PRK09137 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=1553.64  Aligned_cols=703  Identities=49%  Similarity=0.839  Sum_probs=627.9

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP   81 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~   81 (837)
                      +|||||||||||+|++|||++|+|+||+|||+|||.+.+++|++++|.|.|++++++++||+.|++++++||+|||||||
T Consensus         3 ~LvIvEsPskAk~I~~~LG~~y~V~as~GHi~dL~~~~~~~d~~~~f~p~y~~~~~~kk~i~~lk~l~k~ad~IilAtDp   82 (761)
T PRK09137          3 NLVIVESPAKAKTIEKYLGNDFKVLASYGHVRDLPSKQGSVDPEDDFKMKYQVIERSKKHIDAIKKAAKDADNLYLATDP   82 (761)
T ss_pred             EEEEECCHHHHHHHHHHHCCCCEEEEECCCHHHCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf             49998587999999997194989999835343177645785725598444688964789999999998389989989888


Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHCC
Q ss_conf             70257999999999755125788716999980379899999986226469899999999999898740113789886414
Q gi|254780306|r   82 DREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLP  161 (837)
Q Consensus        82 DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~  161 (837)
                      |||||+|||||+++|+......++||+|+||||||++||++||+|||++|++||+||+|||++|||||||+||+||++++
T Consensus        83 DREGE~Ia~~i~~~l~~~~~~~~k~v~Ri~f~eiT~~aI~~A~~np~~~~~~Lv~A~~aR~~lD~lvG~nlS~~l~~~~~  162 (761)
T PRK09137         83 DREGEAISWHLLEVLKSKRLLKDKKVQRVVFHEITKSAVQDAIANPRDISMDLVDAQQARRALDYLVGFNLSPLLWKKIR  162 (761)
T ss_pred             CCCHHHHHHHHHHHHCCCCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHCCHHHHHHHC
T ss_conf             80500999999999672335799845999980289999999986756256878999999999999976700498886426


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCCC-
Q ss_conf             6765342268999999999999641376544001223315799654223310358330331011356667776420015-
Q gi|254780306|r  162 GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKA-  240 (837)
Q Consensus       162 ~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-  240 (837)
                      .+|||||||||||+|||+||+||++|+|++||+|.+.+.. ++..|.++|...++.+++++++.++++|+++.+.+.+. 
T Consensus       163 ~~lSaGRVQTPtL~lIveRE~EI~~F~p~~Yw~i~a~~~~-~~~~f~~~l~~~~~~~~~~~~~~~~~~a~~~~~~l~~~~  241 (761)
T PRK09137        163 RGLSAGRVQSPALRLICEREIEIEAFEAQEYWTIHADCHK-QKQKFTARLAEFNGEKLEQFDIPNEAQAHELKKALEKDA  241 (761)
T ss_pred             CCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC-CCCEEEEEEEECCCCCHHHCCCCCHHHHHHHHHHHHCCC
T ss_conf             6776574223889999999999971788405899999704-895489999850771621068789999999999984354


Q ss_pred             --CCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCC-HHHHHHHHCCCCCCCCCHHHHH
Q ss_conf             --6301000023322246852103799999887608889999999987621355672-1224553147554444305689
Q gi|254780306|r  241 --TYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNG-EIVGLITYMRTDGVHMSPDALE  317 (837)
Q Consensus       241 --~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~-~~~GlITYpRTDS~~ls~ea~~  317 (837)
                        .++|.+|++++.+++||+||+||+|||+||++|||||++||+|||+|||+|++++ ++.||||||||||++||++++.
T Consensus       242 ~~~~~V~~v~~k~~k~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~~GlITYpRTDS~~ls~~~~~  321 (761)
T PRK09137        242 NGFLTVDKITKKKRKRNPAPPFITSTLQQEAARKLGFTAKKTMSTAQKLYEGIDLGNEGAVGLITYMRTDSVNLANEALQ  321 (761)
T ss_pred             CCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCEEEEEECCCCCCCCHHHHH
T ss_conf             78639999885144058999987799999999873999999999999986354556666411588505676656899999


Q ss_pred             HHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCC
Q ss_conf             99976552001123763111125566688777652477302346400000199999999999999999985222110010
Q gi|254780306|r  318 AVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERT  397 (837)
Q Consensus       318 ~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~  397 (837)
                      .++++|..+||.+|++..+|.|+++.+|+|+||||||||++..+|+.+...|++||++||+|||+|||||||+||+|++|
T Consensus       322 ~~~~~i~~~~~~~~~~~~~~~~~~k~~~~q~AHeAI~PT~~~~~p~~~~~~Ls~de~klY~LI~~RflAs~m~~a~~~~t  401 (761)
T PRK09137        322 EIRNYIEAKYGKEYLPAKPRVYKTKSKNAQEAHEAIRPTSANRTPESVKKFLTSDQFKLYSLIWKRTVACQMAEATLDQT  401 (761)
T ss_pred             HHHHHHHHHHCHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHCCCCEEEEE
T ss_conf             99999987402222210675254567898877089288687659888762078778999999999999973850158999


Q ss_pred             EEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCC-CCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHH
Q ss_conf             01367740796399999874880588567632677763-21001014886456882110011011123464310178998
Q gi|254780306|r  398 TVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQE-KNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSL  476 (837)
Q Consensus       398 ~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~-~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasL  476 (837)
                      +|.|.+..+   +.|+++|++++|+||++||.+..+++ .+.+++..||.|++|+.+.+.++.+++|+|+||+|||||||
T Consensus       402 ~v~i~~~~~---~~F~a~g~~~~~~Gw~~vy~~~~~~~~~~~~~~~~lP~l~~g~~~~~~~~~~~~~~TkPP~ryTEasL  478 (761)
T PRK09137        402 SVDIIAGNG---HRFRATGTVIVFAGFLKVYEEGKDDDKEEEEDEKTLPPLEEGEKLKLNDLITEQHFTEPPPRYTEASL  478 (761)
T ss_pred             EEEEEECCC---EEEEEEEEEEEECCHHHHHCCCCCCCCCCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCHHHH
T ss_conf             999982797---19999879999867798740225655333322352887789998777688851457589998899999


Q ss_pred             HHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHH
Q ss_conf             74332102566551578999997322022147712220114200002233665568988999999999998626013478
Q gi|254780306|r  477 IKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKE  556 (837)
Q Consensus       477 ik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~  556 (837)
                      |++||+.|||||||||+||++|++|+||++++++|+||++|+.|+++|.++|++|++++|||+||++||+|++|+.+|.+
T Consensus       479 Ik~ME~~GIGtpsT~A~II~~L~~R~Yv~~~~k~l~pT~lG~~v~~~L~~~f~~iv~~~~Ta~mE~~Ld~Ia~G~~~~~~  558 (761)
T PRK09137        479 VKALEEYGIGRPSTYASIISTLQQREYVRLDKKRFIPTDVGRIVNKFLTEHFTKYVDYNFTAGLEDELDEIARGEKDWIP  558 (761)
T ss_pred             HHHHHHCCCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHCCCCCHHH
T ss_conf             99997379996236899999897389699659988564679999999988552315966899999988999769960899


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCC
Q ss_conf             99998676766557667755666776556766410245555676611433467773136871577611123434323332
Q gi|254780306|r  557 VLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYT  636 (837)
Q Consensus       557 ~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t  636 (837)
                      ||++||..|...++.+.+....            ...   ....+...||+|+.. |.++ .|++|.||||||||+|+|+
T Consensus       559 vl~~f~~~f~~~~~~~~~~~~~------------~~~---~~~~~~~~Cp~Cg~~-l~~r-~g~~G~F~~Cs~yP~Ck~t  621 (761)
T PRK09137        559 VLEEFWHPFIELIKEKEEDVSR------------KDV---TTEELDEKCPECGKP-LSIK-LGKRGRFIACTGYPECKYT  621 (761)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH------------CCC---CCCCCCCCCCCCCCE-EEEE-ECCCCCEEECCCCCCCCCC
T ss_conf             9999999999999999988754------------236---544457878889982-3899-5587765766798766675


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHH-CC
Q ss_conf             10012210000123442014689999669998269742277348877761337899884254899999986152551-57
Q gi|254780306|r  637 RQLTSNPQDIPEMKESVLLGNDLETKESVTLRSGRFGLYVQRGDGKDAKRCSLPKTWKSDSVDYDKAMSLLSLPREI-GI  715 (837)
Q Consensus       637 ~~l~~~~~~~~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq~Ge~~kpkr~si~k~~~~~~itle~Al~LLsLPr~l-G~  715 (837)
                      .++..+....... .+..=..||.||.++.+|.||||.|+.+...++.|...        .+.         =|... +.
T Consensus       622 ~~~~~~~~~~~~~-~~~~~~~Cp~Cg~~mv~k~gr~G~f~~Cs~yP~Ck~~~--------~~~---------k~~~~~~~  683 (761)
T PRK09137        622 RNLDEDEEEAAEE-EVVEGRKCPKCGSPLHIKQGRYGKFIGCSNYPECKHME--------PLE---------KPKDTGVT  683 (761)
T ss_pred             CCCCCCCCCCCCC-CCCCCCCCCCCCCCEEEEECCCCCEEECCCCCCCCCCC--------CCC---------CCCCCCCC
T ss_conf             7677655555566-65578869889971278614676345337998766777--------666---------76667761


Q ss_pred             CCCCCC-EEEEEECCCCC-EEEECCEECCCC
Q ss_conf             778987-49991158765-261678111248
Q gi|254780306|r  716 HPETQK-NIIAGTGKYGY-YLNHDGAYTKLE  744 (837)
Q Consensus       716 ~pe~g~-~I~~~~GryGp-Yi~~~~~~~sl~  744 (837)
                      ||+||. +|+.+.+|+|. |+.|.+ |..++
T Consensus       684 CP~C~~g~~~~r~~k~Gk~f~gC~~-yp~C~  713 (761)
T PRK09137        684 CPKCKKGELVEKKSRYGKIFYSCAR-YPKCK  713 (761)
T ss_pred             CCCCCCCCEEEEECCCCCCCCCCCC-CCCCC
T ss_conf             9899998777751799994027898-89998


No 9  
>PRK09001 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=1551.42  Aligned_cols=602  Identities=43%  Similarity=0.737  Sum_probs=553.4

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCC----------------------------------CCCCCCCCC
Q ss_conf             1899779047877887508998999942511007865----------------------------------578676667
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAK----------------------------------KGSVLPEKE   47 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~----------------------------------~~~v~~~~~   47 (837)
                      .|||||||||||||++|||++|+|+||+|||||||.+                                  .+||||+++
T Consensus         4 ~LVIVESPaKAKtI~kyLG~~y~V~aS~GHirdLp~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~li~~lGvDp~~~   83 (869)
T PRK09001          4 SLVIVESPAKAKTINKYLGNDYVVKSSVGHIRDLPTSGSASKKSAKSTSTKTAKMEKAKKKKKKERQALVNRMGVDPYHG   83 (869)
T ss_pred             CEEEECCHHHHHHHHHHCCCCCEEEECCCCEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCC
T ss_conf             29998883999999987198978997167025677655555333221112234444100232101111132237374558


Q ss_pred             CCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCC
Q ss_conf             44068877654899999999987099899946997025799999999975512578871699998037989999998622
Q gi|254780306|r   48 FEMIWNIDPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSP  127 (837)
Q Consensus        48 f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~  127 (837)
                      |.|.|+++++++++|++|++++++||.||||||||||||+|||||.++|+.    +..+++|+||||||++||++||+||
T Consensus        84 ~~~~Y~i~~~K~kvv~~Lkklak~ad~V~lATDpDREGEaIAwhl~e~l~~----~~~~~kRv~F~EITk~AI~~A~~np  159 (869)
T PRK09001         84 WKAHYEILPGKEKVVSELKKLAEKADHIYLATDLDREGEAIAWHLREVIGG----DDSRYSRVVFNEITKNAIQQAFEKP  159 (869)
T ss_pred             CCEEEEECCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHCC----CCCCEEEEEEECCCHHHHHHHHHCC
T ss_conf             633468777679999999999856998998987985604999999998658----9997058899348999999998686


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEE
Q ss_conf             64698999999999998987401137898864146765342268999999999999641376544001223315799654
Q gi|254780306|r  128 RDINLDLVNAYLARRALDYLVGFNLSPILWQKLPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKF  207 (837)
Q Consensus       128 r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f  207 (837)
                      |++|+|||+||+|||+|||||||++||+||++++++|||||||||||+||||||+||++|+|++||+|.+.|...++..|
T Consensus       160 ~~id~nlv~Aq~ARrilDrlVG~~lSplLw~k~~~gLSAGRVQSPaL~LIVeRE~EI~~FvPe~YW~I~a~~~~~~~~~~  239 (869)
T PRK09001        160 GELNIDRVNAQQARRFLDRVVGYMVSPLLWKKIARGLSAGRVQSVAVRLVVEREREIKAFVPEEYWEVHADLTTPKGEAL  239 (869)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEECCCCCEE
T ss_conf             53454568999999999999878665999986268987630477899999999999972588542589999973788579


Q ss_pred             EEEEEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             22331035833033101135666777642001563010000233222468521037999998876088899999999876
Q gi|254780306|r  208 TAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKL  287 (837)
Q Consensus       208 ~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~L  287 (837)
                      .+.+...+++.   +++.++++|+++++.+++..++|.+++.|+.+++||+||+||||||+||++|||||++||++||+|
T Consensus       240 ~~~~~~~~gk~---f~~~~~~ea~~~~~~lk~~~~~V~~ie~K~~k~~Pp~PF~TStLQqeAs~kLgfSakkTM~iAQ~L  316 (869)
T PRK09001        240 RLEVTHQNGKP---FKPVNEAQTQAAVSLLEKASYSVLEREDKPTSSKPSAPFITSTLQQAASTRLGFGVKKTMMMAQRL  316 (869)
T ss_pred             EEEEEECCCCC---CCCCCHHHHHHHHHHHCCCCEEEEEEEEEECCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHH
T ss_conf             99987117870---785789999999998527976999875002135899997789999999987299999999999999


Q ss_pred             HCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCC
Q ss_conf             21355672122455314755444430568999976552001123763111125566688777652477302346400000
Q gi|254780306|r  288 YEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQ  367 (837)
Q Consensus       288 YE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~  367 (837)
                      ||+        ||||||||||++||+++++.+|++|.+.||++|+|..++.|++| +||||||||||||++..+|+.+.+
T Consensus       317 YE~--------GlITYpRTDSt~LS~da~~~~r~~I~~~~G~~ylp~~~~~~~~k-k~aQeAHEAIrPT~v~~~~~~l~~  387 (869)
T PRK09001        317 YEA--------GYITYMRTDSTNLSQDAVNMVRGYIGDNFGKKYLPEKPNQYSSK-EGAQEAHEAIRPSDVNVKAESLKG  387 (869)
T ss_pred             HHC--------CEEEEECCCCCCCCHHHHHHHHHHHHHHHHHHHCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCHHHHCC
T ss_conf             847--------75667436765369999999999998764576354456546777-676578777224877768133124


Q ss_pred             CCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCC
Q ss_conf             19999999999999999998522211001001367740796399999874880588567632677763210010148864
Q gi|254780306|r  368 FLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYI  447 (837)
Q Consensus       368 ~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l  447 (837)
                       |+.||++||+|||+|||||||+||+|+.|+|++.+.+    +.|+|+|++++|+||++||.....    .+++..||.|
T Consensus       388 -l~~D~~kLY~LIwrRflAsqM~~A~~~~t~v~i~~~~----~~Fka~G~~v~f~Gw~~v~~~~~~----~~ed~~LP~l  458 (869)
T PRK09001        388 -MERDAQRLYELIWRQFVACQMTPAQYDSTTLTVKAGD----FELKAKGRILRFDGWTKVMPALRK----GDEDRTLPAV  458 (869)
T ss_pred             -CCHHHHHHHHHHHHHHHHHHCCHHHCCEEEEEEECCC----EEEEEEEEEEEECCEEEEECCCCC----CCCCCCCCCC
T ss_conf             -7888999999999999998474733307999998188----799997789997884154156657----5312337665


Q ss_pred             CCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCC
Q ss_conf             56882110011011123464310178998743321025665515789999973220221477122201142000022336
Q gi|254780306|r  448 SANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENF  527 (837)
Q Consensus       448 ~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~  527 (837)
                      ++|+.+.+.++.++||+|+||+||||||||++||++|||||||||+||+||++|+||..++++|+||++|+.|+++|.+|
T Consensus       459 ~~Ge~l~~~~i~~~q~~TkPP~RyTEAsLIk~MEk~GIGRPSTYA~II~tI~~RgYV~~e~k~l~pT~lG~~V~~~L~~~  538 (869)
T PRK09001        459 KVGDALTLVKLDPSQHFTKPPARFSEASLVKELEKRGIGRPSTYASIISTIQDRGYVRVENRRFYAEKMGEIVTDRLEES  538 (869)
T ss_pred             CCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHCCCCEEEECCEECCHHHHHHHHHHHHHH
T ss_conf             78998776355532115689999898999999986699974158999988863896994298976015299999999986


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCC
Q ss_conf             65568988999999999998626013478999986767665576677556667765567664102455556766114334
Q gi|254780306|r  528 FSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPE  607 (837)
Q Consensus       528 f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~  607 (837)
                      |++||||+|||+||+.||+||+|+.+|.++|++||.+|...++.+.+.....            .........+...||+
T Consensus       539 F~~i~d~~FTA~mE~~LD~Ia~G~~~w~~vl~~Fy~~f~~~l~~a~~~~~~~------------~~~~~~~~~t~~~C~~  606 (869)
T PRK09001        539 FSELMNYDFTARMEDTLDQVANGEAEWKAVLDEFFGDFTQQLEKAEKDPEEG------------GMRPNQMVLTDIDCPT  606 (869)
T ss_pred             CCHHCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHC------------CCCCCCCCCCCCCCCC
T ss_conf             5011391557999987789875985299999999999999999997204431------------6633667457863622


Q ss_pred             CCCCCEEEEEECCCCCCCCCCCCCC-----CCCCCCCCCC
Q ss_conf             6777313687157761112343432-----3332100122
Q gi|254780306|r  608 CHTHSLSLKLSSKYGAFVGCTNYPE-----CKYTRQLTSN  642 (837)
Q Consensus       608 C~~g~L~~k~~gK~G~FigCSnyPe-----Ck~t~~l~~~  642 (837)
                      ||.. +.++ .|++|.|+|||+||-     |+.|..|...
T Consensus       607 Cg~~-m~ir-~~~~G~Fl~Csgy~~~~k~~ck~t~nl~~~  644 (869)
T PRK09001        607 CGRK-MGIR-TASTGVFLGCSGYALPPKERCKTTINLVPE  644 (869)
T ss_pred             CCCH-HEEE-ECCCCEEEECCCCCCCCHHHHCCCCCCCCH
T ss_conf             4752-3023-268630886269999832320132357855


No 10 
>PRK05582 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=1509.46  Aligned_cols=680  Identities=45%  Similarity=0.746  Sum_probs=608.4

Q ss_pred             CC-EEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECC
Q ss_conf             91-89977904787788750899899994251100786557867666744068877654899999999987099899946
Q gi|254780306|r    1 MN-VIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILAT   79 (837)
Q Consensus         1 M~-LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAt   79 (837)
                      |+ |||||||||||+|++|||++|.|+||+|||+|||.+.+|++++++|.|.|++.+++++|++.|++++++||+|||||
T Consensus         1 Mk~LvIvEkPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~g~~~~~~~~P~y~~~~~~~k~i~~lk~l~k~ad~iiiAt   80 (692)
T PRK05582          1 MKNLIIVESPAKAKTIKKYLGKNYEVIASKGHIRDLPKSSLGIDIEDNYTPKYIIIKDKKELVKKIKKLAKKADKIYLAT   80 (692)
T ss_pred             CCEEEEECCHHHHHHHHHHCCCCCEEEECCCCHHHCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf             98399991879999999970969899952550643676436878777887037877667999999999986599899898


Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHH
Q ss_conf             99702579999999997551257887169999803798999999862264698999999999998987401137898864
Q gi|254780306|r   80 DPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQK  159 (837)
Q Consensus        80 D~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk  159 (837)
                      |||||||+|||||+++|+.    .+.+++|+||||||++||++||+|||++|++||+||+|||++|||||||+||+||++
T Consensus        81 DpDREGE~Ia~~i~~~l~~----~~~~~~Ri~f~eiT~~aI~~Al~n~~~~d~~l~~A~~aR~~~D~lvG~nlSr~l~~~  156 (692)
T PRK05582         81 DPDREGEAISWHVADALKK----DENELPRIVFNEITKNAIKNALKNPRKIDMNLVNAQQARRILDRLVGYKLSPLLWSK  156 (692)
T ss_pred             CCCCCHHHHHHHHHHHHCC----CCCCCEEEEECCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8871232999999999678----888733889837999999999967752368889999999999999999888999998


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCC
Q ss_conf             14676534226899999999999964137654400122331579965422331035833033101135666777642001
Q gi|254780306|r  160 LPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKK  239 (837)
Q Consensus       160 ~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~  239 (837)
                      +.++|||||||||||+|||+||+||++|+|++||+|.+.|... ...|.+.+   .+.+..+.++.++++|+.+++.+++
T Consensus       157 ~~~~lS~GRVQTPtL~lIveRe~eI~~F~p~~y~~i~~~~~~~-~~~~~~~~---~~~~~~~~~~~~~~~A~~i~~~l~~  232 (692)
T PRK05582        157 IQWGLSAGRVQSAALKLIVDREREIRAFVPEEYWTIDVIFKKD-LKAELIKL---KGKKIKKIEINNEEEAQEIINELKK  232 (692)
T ss_pred             HCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECC-CCCEEEEE---CCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf             6267775630228899999999999825676517999998228-86168885---1554533774999999999999607


Q ss_pred             CCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             56301000023322246852103799999887608889999999987621355672122455314755444430568999
Q gi|254780306|r  240 ATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAV  319 (837)
Q Consensus       240 ~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~  319 (837)
                      ..++|.+|+.++.+++||+||+||+|||+||++|||||++||++||+|||++++.+++.||||||||||++||++++..+
T Consensus       233 ~~~~V~~v~~k~~k~~Pp~pf~tstLQ~~As~~~g~sa~~Tm~iAQ~LYE~~~~~~~~~glITYpRTDS~~ls~~~~~~~  312 (692)
T PRK05582        233 ESFVVSIIEKKSKKSNPPPPFTTSTLQQDASNKLGFSPKKTMSIAQQLYEGVEIKGGQMGLITYMRTDSLRISKEAQEEA  312 (692)
T ss_pred             CCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCHHHHHHH
T ss_conf             98499998764674479899878999999998729888899999999860433467744138885467654699999999


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEE
Q ss_conf             97655200112376311112556668877765247730234640000019999999999999999998522211001001
Q gi|254780306|r  320 RRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTV  399 (837)
Q Consensus       320 r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v  399 (837)
                      +++|...||++|++..+|.|+++.+++||||||||||++..+|+.+.+.|++||++||+|||+|||||||+||+|++|+|
T Consensus       313 ~~~i~~~~g~~~l~~~~~~~~~~~k~~qdAH~AI~PT~~~~~p~~~~~~Ls~de~klY~LI~~RflAs~m~~a~~~~t~v  392 (692)
T PRK05582        313 REFIEKNYGKEYLPKKPKVYKTKEKNIQDAHEAIRPTNIEITPEIAKNYLKPDEYKLYTLIWNRFLASQMADAIFETQSI  392 (692)
T ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCHHEEEEEEE
T ss_conf             99998621143223002334456677777899944467766766765218987889999999999998485323778999


Q ss_pred             EEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHH
Q ss_conf             36774079639999987488058856763267776321001014886456882110011011123464310178998743
Q gi|254780306|r  400 NIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKK  479 (837)
Q Consensus       400 ~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~  479 (837)
                      .+.+.+    +.|+|+|++++|+||++||....+   +++....||.|++|+.+.+.++.+.+|+|+||+||||||||++
T Consensus       393 ~~~~~~----~~F~a~g~~~~~~Gw~~vy~~~~~---~~~~~~~lP~l~~g~~~~~~~~~~~e~~TkPP~ryTEasLik~  465 (692)
T PRK05582        393 RFINGK----YKFKASGRKILFDGFYKVYGYDDK---DKELSILLPNLKEGDELKLEKIESNQHFTEPPARYSEASLIKK  465 (692)
T ss_pred             EEEECC----EEEEEEEEEEEECCCEEEECCCCC---CCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCHHHHHHH
T ss_conf             999899----889984379998881677525554---4411256887778988667687832567689998799999999


Q ss_pred             HHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             32102566551578999997322022147712220114200002233665568988999999999998626013478999
Q gi|254780306|r  480 MEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLH  559 (837)
Q Consensus       480 mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~  559 (837)
                      ||+.|||||||||+||++|++|+||++++++|+||++|+.|+++|.++|++|++++|||.||+.||+|++|+.+|.+||+
T Consensus       466 ME~~GIGtpATrA~II~~L~~R~Yv~~~~k~l~pT~~G~~v~~~L~~~f~~i~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~  545 (692)
T PRK05582        466 LESLGIGRPSTYAPTISTLLSRKYVEREKKQLIPTELGFKVIEILEKHFPQIVDSEFTANMEEKLDEIAEGKADWQEVLK  545 (692)
T ss_pred             HHHCCCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             98479986045899998887467099409888475799999999988553322854899999999999859877999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf             98676766557667755666776556766410245555676611433467773136871577611123434323332100
Q gi|254780306|r  560 EFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQL  639 (837)
Q Consensus       560 ~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l  639 (837)
                      +||..|...++.+.......            .   .....+...||+|+.. |.++ .|++|.||||||||+|+||.++
T Consensus       546 ~f~~~f~~~i~~~~~~~~~~------------~---~~~~~~~~~Cp~Cg~~-l~~r-~~~~G~F~~Cs~yP~Ck~t~~~  608 (692)
T PRK05582        546 DFYYPFMEKIEEAKKEIAKQ------------K---VEDKVGERKCPKCGRE-LVIK-HGRYGEFIACSNYPKCKYTKPI  608 (692)
T ss_pred             HHHHHHHHHHHHHHHHHHHC------------C---CCCCCCCCCCCCCCCC-CEEE-ECCCCCEEECCCCCCCCCCCCC
T ss_conf             99999999999998654422------------3---4578889877567982-0267-2688962657899878897768


Q ss_pred             CCCCCCCCCCCCCCCCC-CCCCCCCEEEEEECCCCCEEEECCCCCCC--CCCCCCCCCHHHCCHHHHHHHHHCCHHHCCC
Q ss_conf             12210000123442014-68999966999826974227734887776--1337899884254899999986152551577
Q gi|254780306|r  640 TSNPQDIPEMKESVLLG-NDLETKESVTLRSGRFGLYVQRGDGKDAK--RCSLPKTWKSDSVDYDKAMSLLSLPREIGIH  716 (837)
Q Consensus       640 ~~~~~~~~~~~~~~~LG-~dP~~G~~I~lk~GryGpYvq~Ge~~kpk--r~si~k~~~~~~itle~Al~LLsLPr~lG~~  716 (837)
                      .......     ....| .||.||.+|+.|.|++|-+. +|...-|+  +.+-                   ++.+-..|
T Consensus       609 ~~~~~~~-----~~~~~~~CP~C~~~l~~r~~k~gk~F-~gCs~yp~C~~~~~-------------------~~p~~~~C  663 (692)
T PRK05582        609 EEEEKLA-----SEELDVKCPECGGKIVKRKSKKGKKF-YGCSNYPKCNFISN-------------------YEPSNEKC  663 (692)
T ss_pred             CCCCCCC-----CCCCCCCCCCCCCEEEEEECCCCCEE-EECCCCCCCCCCCC-------------------CCCCCCCC
T ss_conf             7644444-----45369979999977478854899989-97489999997738-------------------89999969


Q ss_pred             CCCCCEEEEEECCCCCEEEEC
Q ss_conf             789874999115876526167
Q gi|254780306|r  717 PETQKNIIAGTGKYGYYLNHD  737 (837)
Q Consensus       717 pe~g~~I~~~~GryGpYi~~~  737 (837)
                      |+||.++....||+|.|+.|.
T Consensus       664 p~Cg~~~~~k~~~~~~~~~c~  684 (692)
T PRK05582        664 PECGSYMVKKESKKGEYLECS  684 (692)
T ss_pred             CCCCCHHHEEECCCCCEEECC
T ss_conf             999815704745888878899


No 11 
>PRK08413 consensus
Probab=100.00  E-value=0  Score=1511.55  Aligned_cols=718  Identities=41%  Similarity=0.655  Sum_probs=634.0

Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCC-CCCEEEEECCCHHHHHHHHHHHHHHCCEEEECC
Q ss_conf             9189977904787788750899899994251100786557867666-744068877654899999999987099899946
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEK-EFEMIWNIDPSSQKHLQNIIHAVKSSTILILAT   79 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~-~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAt   79 (837)
                      .+|||||||||||+|++|||++|.|+||+|||+|||.+.+++++++ .|.|.|+++++++++++.|++++++||+|||||
T Consensus         2 k~LvIvEsPskAk~Ia~~LG~~y~V~as~GHi~dLp~~~~g~~~~~~~~~P~y~~~~~~~k~~k~lk~l~k~ad~vilAt   81 (733)
T PRK08413          2 KNLIIVESPAKAKTIKNFLGKNYEVIASKGHIRDLPKSSFGIKIEEDGFIPEYRISKDHSAIVKEIKELAKKADTIYIAT   81 (733)
T ss_pred             CEEEEEECHHHHHHHHHHHCCCCEEEECCCHHHHCCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEECC
T ss_conf             83999908799999999849397999634604228863359776678723257867768999999999985699899898


Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHH
Q ss_conf             99702579999999997551257887169999803798999999862264698999999999998987401137898864
Q gi|254780306|r   80 DPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQK  159 (837)
Q Consensus        80 D~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk  159 (837)
                      |||||||+|||||+++|+.    ...+++|+||||||++||++||+|||++|++||+||+|||++|||||||+||+||++
T Consensus        82 D~DREGE~Ia~~i~~~l~~----~~~~~~Ri~f~eiT~~aI~~Al~n~~~~d~~l~~A~~aR~~~D~lvG~nlSr~lt~~  157 (733)
T PRK08413         82 DEDREGEAIGYHIACAIGK----KPESLPRIVFHEITKNAIENALKNPRKIDMDSVNAQQARRLLDRIVGYKLSPLLSSK  157 (733)
T ss_pred             CCCCCHHHHHHHHHHHHCC----CCCCCEEEEECCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             8881531999999998678----998725899726899999999967663435668999999999998483266989998


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCC
Q ss_conf             14676534226899999999999964137654400122331579965422331035833033101135666777642001
Q gi|254780306|r  160 LPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKK  239 (837)
Q Consensus       160 ~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~  239 (837)
                      ++++|||||||||||+|||+||+||++|+|++||+|.+.|..    .+.+.+..+++.+.++.++.++++|+++++.+++
T Consensus       158 ~~~~lSaGRVQTPtL~lIveRe~eI~~F~p~~y~~i~a~~~~----~~~~~~~~~~~~~~~k~~~~~~~~a~~i~~~~~~  233 (733)
T PRK08413        158 IQKGLSAGRVQSAALKIVVDREREIRAFKPLEYFTIDALFEK----DLEAELISYKGKKIEKLSITNEKKAQEIVEELKK  233 (733)
T ss_pred             HCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC----CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHHHC
T ss_conf             548877650233788999999999972378644899999805----8624899842736110455889999999998608


Q ss_pred             CCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             56301000023322246852103799999887608889999999987621355672122455314755444430568999
Q gi|254780306|r  240 ATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAV  319 (837)
Q Consensus       240 ~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~  319 (837)
                      ..++|.+|++++.+++||+||+||+|||+||++|||||++||+|||+|||++++..++.||||||||||++||++++..+
T Consensus       234 ~~~~V~~v~~k~~~~~pP~pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~~~~~~~  313 (733)
T PRK08413        234 ESFIISSIEKKSRKIPTPPPFMTSTLQQSASSLLGFSPKKTMMIAQKLYEGVATPQGVMGVITYMRTDSLNIAKEALEAA  313 (733)
T ss_pred             CCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCCCCCCCCCCCEEECCCCCCCCCCHHHHHHH
T ss_conf             98599998763564379898566999999999809999999999999866456577766434135645432348999999


Q ss_pred             HHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEE
Q ss_conf             97655200112376311112556668877765247730234640000019999999999999999998522211001001
Q gi|254780306|r  320 RRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTV  399 (837)
Q Consensus       320 r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v  399 (837)
                      +++|.+.||.+|++..++.|.++.+++||||||||||++..+|+...+.|++||++||+|||+|||||||+||+|++|+|
T Consensus       314 ~~~i~~~~g~~~l~~~~~~~~~k~k~~q~AH~AI~PT~~~~~p~~~~~~Ls~de~klY~LI~~Rflas~m~~a~~~~t~v  393 (733)
T PRK08413        314 RELIKKDYGKDYLPAKAKVYTTKSKGAQEAHEAIRPTNLDFTPEIAAKYLKPDELKLYTLIYNRFLASQMNDAVFETQNV  393 (733)
T ss_pred             HHHHHHHHHHHHCCHHCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHCCHHHHHHHHHHHHHHHHHHCCHHEEEEEEE
T ss_conf             99999876776431111424466766522676401565455645654306887878999999999998503540789999


Q ss_pred             EEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHH
Q ss_conf             36774079639999987488058856763267776321001014886456882110011011123464310178998743
Q gi|254780306|r  400 NIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKK  479 (837)
Q Consensus       400 ~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~  479 (837)
                      .+.+.+    ..|+++|++++|+||++||...       +++..||.|++|+.+.+.++++.+|+|+||+||||||||++
T Consensus       394 ~~~~~~----~~F~a~g~~i~~~G~~~v~~~~-------~~d~~lP~l~~g~~~~~~~~~~~~~~TkPP~ryTEasLik~  462 (733)
T PRK08413        394 FVKSEK----GEFKASGRKLLFDGFYKVYGND-------DKDKLLPNLKEGDPLKLEKIESNQHFTEPPARYSEASLIKK  462 (733)
T ss_pred             EEEECC----EEEEEEEEEEEECCEEEEECCC-------CCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCHHHHHHH
T ss_conf             999899----7999999999427766653354-------43443896677986777798844446589899899999999


Q ss_pred             HHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             32102566551578999997322022147712220114200002233665568988999999999998626013478999
Q gi|254780306|r  480 MEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLH  559 (837)
Q Consensus       480 mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~  559 (837)
                      ||+.|||||||||+||++|++|+||.+++++|+||++|+.|+++|.++|++|++++|||+||+.||+|++|+.+|.+||+
T Consensus       463 ME~~GIGtpATrA~II~~L~~R~Yv~~~~k~l~pT~~G~~v~~~L~~~f~~i~~~~~Ta~~E~~Ld~Ia~G~~~~~~~l~  542 (733)
T PRK08413        463 LESLGIGRPSTYAPTISLLQSRDYVKIEKKQIIPTESAFKVIEVLEKHFSEIVDSKFTANLEEKLDEIAEDKADWQKVLK  542 (733)
T ss_pred             HHCCCCCCCCCHHHHHHHHHHCCCEEECCCEEEECHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHH
T ss_conf             97089996476889998886267299419778774699999999987560214853799999999999859865999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCC
Q ss_conf             98676766557667755666776556766410245555676611433467773136871577611123434323332100
Q gi|254780306|r  560 EFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQL  639 (837)
Q Consensus       560 ~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l  639 (837)
                      +||..|...++.+......                ......+...||+|+. .|.++ .|++|.||||||||+|+|+.++
T Consensus       543 ~f~~~f~~~i~~~~~~~~~----------------~~~~~~~~~~Cp~Cg~-~l~~~-~~r~G~F~~Cs~yP~Ck~t~~~  604 (733)
T PRK08413        543 DFYYPFMDKIEEGKKNIKS----------------QKVATPTGESCPKCGG-ELVKR-KGRYGEFIACSNFPKCKYSKNT  604 (733)
T ss_pred             HHHHHHHHHHHHHHHHHHH----------------CCCCCCCCCCCCCCCC-CCEEE-CCCCCEEEECCCCCCCCCCCCC
T ss_conf             9999999999999754231----------------1245667898743585-41133-1677406842899875554567


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEECCCCCCCCCC-CCCCCCHHHCCHHHHHHHHHCCHHHC-CCC
Q ss_conf             1221000012344201468999966999826974227734887776133-78998842548999999861525515-777
Q gi|254780306|r  640 TSNPQDIPEMKESVLLGNDLETKESVTLRSGRFGLYVQRGDGKDAKRCS-LPKTWKSDSVDYDKAMSLLSLPREIG-IHP  717 (837)
Q Consensus       640 ~~~~~~~~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq~Ge~~kpkr~s-i~k~~~~~~itle~Al~LLsLPr~lG-~~p  717 (837)
                      ........       --.+|.||.++.++.||||.|+.....++.++.- .....              .-|...| .||
T Consensus       605 ~~~~~~~~-------~~~c~~cg~~m~~k~gr~g~f~~C~~~p~ck~~~~~~~~~--------------~~~~~~~~~CP  663 (733)
T PRK08413        605 ESENKEAS-------EEVCEKCGGPMVQKFGRNGEFLACSGYPKCKNTKSLKNTP--------------NAKEVIGVKCP  663 (733)
T ss_pred             CCCCCCCC-------CCCCCCCCCHHHEEECCCCCEEECCCCCCCCCCCCCCCCC--------------CCCCCCCCCCC
T ss_conf             66543234-------5668767841321205787344347998887741255666--------------76655685689


Q ss_pred             CCCCEEEEEECCCCCEEEECCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCC-CCCEEEEEC
Q ss_conf             8987499911587652616781112488775143579999999983651134434454432010267898-984699606
Q gi|254780306|r  718 ETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPE-GGSITVHNG  796 (837)
Q Consensus       718 e~g~~I~~~~GryGpYi~~~~~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~-~~~i~i~~G  796 (837)
                      +||.+|..+.||+|.|..|.+ |..+.-...                           .+|..  ...|+ |..+..+.+
T Consensus       664 ~Cgg~l~~r~sk~GkF~gCs~-YP~C~f~~~---------------------------~~P~~--~~Cp~Cg~~~~~~~~  713 (733)
T PRK08413        664 ECGGEIVERFSRRGKFYGCSN-YPKCNFISN---------------------------YEPIN--KKCEECGYMMVKREY  713 (733)
T ss_pred             CCCCEEEEEECCCCCEECCCC-CCCCCCCCC---------------------------CCCCC--CCCCCCCCEEEEEEC
T ss_conf             999989987179997536899-999987677---------------------------89578--968789932089984


Q ss_pred             CCCCEEEECC
Q ss_conf             8545253678
Q gi|254780306|r  797 RYGPYLHWKK  806 (837)
Q Consensus       797 ryGpYi~~gk  806 (837)
                      +.|+++.|-+
T Consensus       714 ~~~~~~~C~~  723 (733)
T PRK08413        714 RKKEVHECIK  723 (733)
T ss_pred             CCCCEEECCC
T ss_conf             7898798999


No 12 
>PRK08938 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=1494.97  Aligned_cols=676  Identities=38%  Similarity=0.656  Sum_probs=605.8

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP   81 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~   81 (837)
                      +|||||||||||+|++|||++|.|+||+|||||||.+.+|||++++|.|.|.++++++++++.|++++|+||+|||||||
T Consensus         5 ~LvIvEsPskAk~I~~~LG~~y~V~as~GHi~dLp~~~~g~d~~~~~~p~y~~~~~k~~~i~~lk~~~k~ad~iilAtD~   84 (692)
T PRK08938          5 NLVIVESPAKAKTIEKYLGRKYKVVASMGHIRDLPKSQMGVDIENNYEPKYITIRGKGPVIKELKKEAKKAKKVYLASDP   84 (692)
T ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEECCCHHHHCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHCCCEEEECCCC
T ss_conf             19998885999999998394979996335174468633685767788536773575689999999998289989989898


Q ss_pred             CCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHCC
Q ss_conf             70257999999999755125788716999980379899999986226469899999999999898740113789886414
Q gi|254780306|r   82 DREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLP  161 (837)
Q Consensus        82 DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~  161 (837)
                      |||||+|||||+++|+.    ...+++|+||||||++||++||+|||++|++||+||+|||++|||||||+||+||+++.
T Consensus        85 DREGE~Ia~~i~~~l~~----~~~~~~Ri~f~eiT~~aI~~A~~n~r~~d~~l~~A~~aR~~lD~lvG~nlS~~l~~k~~  160 (692)
T PRK08938         85 DREGEAIAWHLAHILNL----DPSDKNRVVFNEITKDAVKESFKHPRAIDMDLVDAQQARRILDRLVGYSISPILWKKVK  160 (692)
T ss_pred             CCCCCHHHHHHHHHHCC----CCCCCEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHCCCHHHHHHHC
T ss_conf             71502999999998677----88875378995689999999996766035878999999998748865410889998533


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             67653422689999999999996413765440012233157996542233103583303310113566677764200156
Q gi|254780306|r  162 GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKAT  241 (837)
Q Consensus       162 ~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~  241 (837)
                      .+|||||||||||+|||+||+||++|+|++||+|.+.|.. ++..|.++|...++++   .++.++++|+.+++.+++.+
T Consensus       161 ~~lSaGRVQTPtL~lIveRe~eI~~F~p~~y~~i~a~~~~-~~~~f~a~~~~~~~~~---~~~~~~~~a~~i~~~l~~~~  236 (692)
T PRK08938        161 KGLSAGRVQSVALKLIIDRENEIKAFKPEEYWTIDGEFKK-GKKKFQASFYGVDGKK---FKLKNNDDVKEVLAKLDGDD  236 (692)
T ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEC-CCCEEEEEEEECCCCC---CCCCCHHHHHHHHHHHCCCC
T ss_conf             7877661300789999998999983688433899999980-8941899998348872---57799999999998622898


Q ss_pred             CEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCH-HHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             3010000233222468521037999998876088899999999876213556721-224553147554444305689999
Q gi|254780306|r  242 YSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGE-IVGLITYMRTDGVHMSPDALEAVR  320 (837)
Q Consensus       242 ~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~-~~GlITYpRTDS~~ls~ea~~~~r  320 (837)
                      ++|.+|++++.+++||+||+||+|||+||++|||||++||+|||+||||++++++ +.||||||||||++||++++..++
T Consensus       237 ~~V~~v~~k~~k~~PP~Pf~ts~LQq~As~~lg~sa~kTm~iAQ~LYEg~~~~~~~~~glITYpRTDS~~ls~~~~~~~~  316 (692)
T PRK08938        237 FEVTKVTKKERKRNPALPFTTSSLQQEAARKLNFRTRKTMMVAQQLYEGIDLGKQGTVGLITYMRTDSTRISPVAQNEAA  316 (692)
T ss_pred             EEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCCCCHHHHHHHH
T ss_conf             69999875034248989975799999999873999899999999987334567656556331147666403899999999


Q ss_pred             HHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEE
Q ss_conf             76552001123763111125566688777652477302346400000199999999999999999985222110010013
Q gi|254780306|r  321 RSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVN  400 (837)
Q Consensus       321 ~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~  400 (837)
                      ++|...||++|++..++.+++ .+|+|+||||||||++..+|+.+...|+.||++||+|||+|||||||+||+|++++|.
T Consensus       317 ~~i~~~~g~~~~~~~~~~~~~-~~~~qdAHeAI~PT~~~~~p~~~~~~Ls~de~klY~LI~~RflAs~m~~a~~~~t~v~  395 (692)
T PRK08938        317 QYITERYGAEYSKTHKRKVKN-KSGAQDAHEAIRPTSVMRTPESLKKYLTKDQLRLYKLIWERFVASQMTPAVLDTVKVD  395 (692)
T ss_pred             HHHHHHHHHHHHCCCCCCCCC-CCCCCCCCCCCCCCCCCCCHHHHHHCCCHHHHHHHHHHHHHHHHHHCCHHHEEEEEEE
T ss_conf             999987768651215655667-8899688258878665668656541189999999999999999985751116899999


Q ss_pred             EEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHH
Q ss_conf             67740796399999874880588567632677763210010148864568821100110111234643101789987433
Q gi|254780306|r  401 IIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKM  480 (837)
Q Consensus       401 i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~m  480 (837)
                      +.+.+    +.|+|+|++++|+||++||.+..+++ +.+++..||.|.+|+.+.+.++++++|+|+||+||||||||++|
T Consensus       396 ~~~~~----~~F~a~g~~i~~~Gw~~vy~~~~~~~-~~~~~~~LP~l~~G~~~~~~~~~~~~~~TkPP~ryTEasLIk~M  470 (692)
T PRK08938        396 LEQNG----VQFRANGSQVKFDGFMKVYVESKDDN-DSEKNKMLPDLEEGDTVKSTDIEPEQHFTQPPPRYTEARLVKTL  470 (692)
T ss_pred             EEECC----EEEEEEEEEEEECCCEEEECCCCCCC-CCHHHCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCHHHHHHHH
T ss_conf             99599----39999889996331145652445654-31233128656799877666766335426899888999999999


Q ss_pred             HHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             21025665515789999973220221477122201142000022336655689889999999999986260134789999
Q gi|254780306|r  481 EEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHE  560 (837)
Q Consensus       481 E~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~  560 (837)
                      |+.|||||||||+||++|++|+||.+++++|+||++|+.|+++|.++||+|++++|||+||+.||+|++|+.+|.++|++
T Consensus       471 E~~GIGrpsT~A~II~~L~~R~YV~~~~k~l~pT~~G~~v~~~L~~~fp~i~~~~~Ta~~E~~Ld~Ia~G~~~~~~~l~~  550 (692)
T PRK08938        471 EENGIGRPSTYAPTLDTIQKRYYVKLENKRFVPTELGEIVNELIVEFFPEIVDVEFTANMEGKLDEVEEGKEQWVKVIDE  550 (692)
T ss_pred             HHCCCCCCCCHHHHHHHHHHCCCEEECCCEEEECHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHH
T ss_conf             85799971658999999985687994297774536999999999874524349868899999999997697429999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             86767665576677556667765567664102455556766114334677731368715776111234343233321001
Q gi|254780306|r  561 FWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLT  640 (837)
Q Consensus       561 Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~  640 (837)
                      ||..|...++.+.+...            ...   .....+...||+|+..++ ++ .|++|.|||||+||+|+++.++.
T Consensus       551 f~~~f~~~l~~a~~~~~------------~~~---~~~~~~~~~Cp~Cg~~l~-~k-~gr~G~F~~Cs~yP~Ck~t~~~~  613 (692)
T PRK08938        551 FYKPFEKELEKAEEEME------------KIE---IKDEPAGFDCEVCGSPMV-IK-MGRYGKFYACSNFPDCRNTKAIV  613 (692)
T ss_pred             HHHHHHHHHHHHHHHHH------------HCC---CCCCCCCCCCCCCCCCCE-EE-ECCCCCEEECCCCCCCCCCCCCC
T ss_conf             99999999999987665------------333---566667898867886006-88-15788433478998888867766


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCC-EEEEEECCCCC-EEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCC
Q ss_conf             22100001234420146899996-69998269742-27734887776133789988425489999998615255157778
Q gi|254780306|r  641 SNPQDIPEMKESVLLGNDLETKE-SVTLRSGRFGL-YVQRGDGKDAKRCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPE  718 (837)
Q Consensus       641 ~~~~~~~~~~~~~~LG~dP~~G~-~I~lk~GryGp-Yvq~Ge~~kpkr~si~k~~~~~~itle~Al~LLsLPr~lG~~pe  718 (837)
                      ..           .-..||.||. .|..|.++.|- |.-+...++.++++..+                  | +.+.||+
T Consensus       614 ~~-----------~~~~CP~C~~g~l~~r~sk~g~~f~gCs~yp~C~~~~~~~------------------p-~~~~Cp~  663 (692)
T PRK08938        614 KE-----------IGVTCPKCHKGQVIERKSKKNRIFYGCDRYPECDFVSWDK------------------P-IGRDCPK  663 (692)
T ss_pred             CC-----------CCCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCEECCCC------------------C-CCCCCCC
T ss_conf             55-----------6882959999745755147898777489899898316788------------------7-4884999


Q ss_pred             CCCEEEEEECCCCCEEEECC
Q ss_conf             98749991158765261678
Q gi|254780306|r  719 TQKNIIAGTGKYGYYLNHDG  738 (837)
Q Consensus       719 ~g~~I~~~~GryGpYi~~~~  738 (837)
                      ||.+++...||+|.|+.|.+
T Consensus       664 Cg~~~~~~~~~~g~~~~C~n  683 (692)
T PRK08938        664 CGHYLVEKKVKKGKQVQCSN  683 (692)
T ss_pred             CCCCCEEEECCCCCEEECCC
T ss_conf             99604268557888797899


No 13 
>PRK05823 consensus
Probab=100.00  E-value=0  Score=1419.94  Aligned_cols=641  Identities=39%  Similarity=0.652  Sum_probs=553.1

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECC-------------CHHHHHHHHHHH
Q ss_conf             1899779047877887508998999942511007865578676667440688776-------------548999999999
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDP-------------SSQKHLQNIIHA   68 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~-------------~~kk~~~~i~~~   68 (837)
                      +|||||||||||+|++|||++|.|+||+|||+|||.+.++++|+ +|.|.|++.+             +++++|+.|+++
T Consensus         4 ~LvIvEsPskAk~Ia~~LG~~y~V~~s~GHl~dL~~~~~~~~~~-~~~p~~~~~~~~~~~~~~~~~~~~k~~~ik~l~~~   82 (691)
T PRK05823          4 KLLVIESPNKVKTLQKYLGDDYEIVATVGHIRELVKKNFGFDEA-DYDPKWEIITKKKKANTKKKALLSKKEIIKSIKDK   82 (691)
T ss_pred             CEEEECCHHHHHHHHHHCCCCCEEEECCCCHHHCCCCCCCCCHH-HCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHH
T ss_conf             49998686999999997095979997234086578654799955-48854210440145443211345599999999999


Q ss_pred             HHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             87099899946997025799999999975512578871699998037989999998622646989999999999989874
Q gi|254780306|r   69 VKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLV  148 (837)
Q Consensus        69 ~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lv  148 (837)
                      +++||+||||||||||||+|||||+++|+.   .++.||+|+||||||++||++||+||+++|++||+||+|||++||||
T Consensus        83 ~k~ad~viiAtD~DREGE~Ia~~i~~~l~~---~~~~~v~R~~f~eiT~~aI~~A~~n~~~~d~~L~~A~~aR~~~D~lv  159 (691)
T PRK05823         83 ASKANNIYLATDPDREGEAISWHVYDVLDE---KDKEKCKRITFNEITKKAVLDALKNPRDIDFNWVQSQFARRILDRLI  159 (691)
T ss_pred             HHCCCEEEECCCCCCCHHHHHHHHHHHHHH---CCCCCCEEEEECCCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             847998998889971502999999999622---48985069997458999999999677524787899999999999985


Q ss_pred             HHHHCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCE-------EEEEEEEECCEEECC
Q ss_conf             0113789886414676534226899999999999964137654400122331579965-------422331035833033
Q gi|254780306|r  149 GFNLSPILWQKLPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDK-------FTAHLTDFNGQRIEK  221 (837)
Q Consensus       149 G~~lSp~L~rk~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~-------f~a~l~~~~~~~~~~  221 (837)
                      |||+||+||+++. ++||||||||||+|||+||+||++|+|++||+|.+.|.......       +.+.+..........
T Consensus       160 G~nlSr~l~~~~~-~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  238 (691)
T PRK05823        160 GFKLSRLLKSKLH-ADSAGRVQSVALKFIEEREKEIRSFVPRFWWTLDVILEDNIPLVLRKIDPDLKAYLKFEKDESVSG  238 (691)
T ss_pred             HHHHHHHHHHHCC-CCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCHHHHCCCHHHHHCCCCHHHCCCCC
T ss_conf             1441068886347-877553334225789999999984689542799999726852012104702332002022213212


Q ss_pred             CCHHHHHHHHHHHHHHCCCCCEEEEEE-CCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHH
Q ss_conf             101135666777642001563010000-2332224685210379999988760888999999998762135567212245
Q gi|254780306|r  222 KSISNKKEADDLISFVKKATYSVEKIE-NKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGL  300 (837)
Q Consensus       222 ~~~~~~~~a~~~~~~~~~~~~~V~~v~-~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~Gl  300 (837)
                      .++.++++|+.+++.+.+. +.|.+++ .+..+++||+||+||+|||+||++|||||++||+|||+|||+++++|+..||
T Consensus       239 ~~~~~~~~a~~i~~~l~~~-~~v~~~~~~k~~~~~Pp~Pf~ts~LQ~~As~~lg~sa~~Tm~iAQ~LYE~~~~~g~~~gl  317 (691)
T PRK05823        239 IDFLDEESAQRVINQLSDK-FKVYSIDEPKIYSSYPKSPYTTSTLQQDAINKLGWSSKKITLIAQHLYEGVEINGEQIAL  317 (691)
T ss_pred             CCCCCHHHHHHHHHHHCCC-CEEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCCCCEE
T ss_conf             6638999999999986498-549999832510368989877799999999980987999999999974645457878655


Q ss_pred             HHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCC--CCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHH
Q ss_conf             5314755444430568999976552001123763111125--56668877765247730234640000019999999999
Q gi|254780306|r  301 ITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYS--SKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYN  378 (837)
Q Consensus       301 ITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~--~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~  378 (837)
                      ||||||||++||++++..++++|.+.||.+|++.....++  .+.+++||||||||||++..+|+.+.+.|+.||++||+
T Consensus       318 ITYpRTDS~~ls~~~~~~~~~~i~~~~g~~~~~~~~~~~~~~~~~~~~qdAH~AI~PT~~~~~p~~~~~~ls~de~klY~  397 (691)
T PRK05823        318 ISYPRTDSTRLSDQFQQEANKFIENTYGKDYLANFKVLKKIKKKEANIQDAHEAIHPIDINITPEEVKNKISKDEFLLYR  397 (691)
T ss_pred             EEECCCCCCCCCHHHHHHHHHHHHHHHHHHHHCCCCHHCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHCCCCHHHHHHHH
T ss_conf             66147887767999999999999987748653002201136666676667764402566665734541368746778999


Q ss_pred             HHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEE
Q ss_conf             99999999852221100100136774079639999987488058856763267776321001014886456882110011
Q gi|254780306|r  379 LIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATET  458 (837)
Q Consensus       379 LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~  458 (837)
                      |||+|||||||+||+|++|+|.+.+.+    ..|.++|++++++||++||.+..+++ +++....||.+++|+.+.+.++
T Consensus       398 LI~rRflAs~m~~a~~~~t~v~~~~~~----~~F~a~g~~i~~~Gw~~vy~~~~~~~-~~~~~~~Lp~l~~g~~~~~~~~  472 (691)
T PRK05823        398 LIWNRTVASLMAAAKFSKVVIRFINNN----NKFYTSSKTLLFDGYKKLYEHFYKKE-RDELYIDLNKINVGDEFKAKKI  472 (691)
T ss_pred             HHHHHHHHHHCCHHEEEEEEEEEEECC----EEEEEEEEEEEECCEEEEECCCCCCC-CCCCCCCCCCCCCCCEEEEEEE
T ss_conf             999999998485331789999999789----49999728999878688875667753-2210145776788988666688


Q ss_pred             ECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHH
Q ss_conf             01112346431017899874332102566551578999997322022147712220114200002233665568988999
Q gi|254780306|r  459 NASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTA  538 (837)
Q Consensus       459 ~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa  538 (837)
                      ++++++|+||+||||||||++||+.|||||||||+||++|++|+||++++++|+||++|+.|+++|.++|++|++++|||
T Consensus       473 ~~~e~~TkPP~ryTEasLi~~ME~~GIGtpATrA~II~~L~~R~Yv~~~~k~l~pT~~G~~l~~~L~~~~~~l~~~~~Ta  552 (691)
T PRK05823        473 DLNEHETTPPPRYTQASLIEALEKAGIGRPSTYSTMASINLERGYANLDKRAYIPTDLGEKVNQELSKHFPKIINKEFTK  552 (691)
T ss_pred             EEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEECCCEEEEHHHHHHHHHHHHHHHHHHCCHHHHH
T ss_conf             87653518999989999999999679997576899999887368289519767451899999999987525634977999


Q ss_pred             HHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEE
Q ss_conf             99999999862601347899998676766557667755666776556766410245555676611433467773136871
Q gi|254780306|r  539 DLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLS  618 (837)
Q Consensus       539 ~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~  618 (837)
                      .||+.||+|++|+.+|.+||++||..|...+..+..... .              .......+...||+|+.+.+..  .
T Consensus       553 ~~E~~Ld~I~~G~~~~~~~l~~f~~~~~~~~~~~~~~~~-~--------------~~~~~~~~~~~CP~Cg~~l~~r--~  615 (691)
T PRK05823        553 NMEESLDEIAEGKVNWKSFLKTFWPNFKEEVKLAYTSIE-K--------------VKKEKEIVGRDCPKCASDLLYR--R  615 (691)
T ss_pred             HHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHHH-H--------------CCCCCCCCCCCCCCCCCCCEEE--E
T ss_conf             999988999769988999999999999999999987776-4--------------3455777799898889820367--4


Q ss_pred             CCCC--CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCC
Q ss_conf             5776--1112343432333210012210000123442014689999669998269742
Q gi|254780306|r  619 SKYG--AFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKESVTLRSGRFGL  674 (837)
Q Consensus       619 gK~G--~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~~I~lk~GryGp  674 (837)
                      |++|  .||||||||+|+|+......+....+.    .-..||.||.+++.|.|+||.
T Consensus       616 ~~~g~~~F~~Cs~yp~Ck~~~~~~~~~~~~~~~----~~~~CP~Cg~~lv~r~~k~~k  669 (691)
T PRK05823        616 TRRGNEKFVGCSNFPKCKFTEFSEQKPLEKPEE----LEELCPECNSKLVKRKTKFNK  669 (691)
T ss_pred             CCCCCCEEEECCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCHHHHEECCCCC
T ss_conf             268886045579999887877778776666332----588599998247422023589


No 14 
>COG0550 TopA Topoisomerase IA [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=1333.58  Aligned_cols=550  Identities=50%  Similarity=0.820  Sum_probs=518.3

Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCC---CCCCCCCCCC-CCEEEEECCC-HHHHHHHHHHHHHHCCEE
Q ss_conf             9189977904787788750899899994251100786---5578676667-4406887765-489999999998709989
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPA---KKGSVLPEKE-FEMIWNIDPS-SQKHLQNIIHAVKSSTIL   75 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~---~~~~v~~~~~-f~p~y~v~~~-~kk~~~~i~~~~k~a~~i   75 (837)
                      |+|||||||+|||+|++|||++|+|+||+|||||||.   ..++++++++ |.|.|++.+. +++.++.|+.++++||.|
T Consensus         1 ~~LiIvEsPskAk~Ia~~Lg~~~~V~as~GHi~dl~~~~~~~~~~~~~~~~~~~~~~~~~~~k~~~v~~lk~~ak~ad~v   80 (570)
T COG0550           1 KRLIIVESPSKAKTIAKYLGKGYVVTASVGHLRDLPFPEEYKGWVDVDLPIFEPKYIIKPGKKKKVVKKLKKLAKKADEV   80 (570)
T ss_pred             CEEEEEECHHHHHHHHHHCCCCCEEEECCCCCCCCCCCHHCCCCCCCCCCCCCCCEECCCHHHHHHHHHHHHHHCCCCEE
T ss_conf             95999927789999998729994999756632137870211477577665566200215224579999999975549989


Q ss_pred             EECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHH
Q ss_conf             99469970257999999999755125788716999980379899999986226469899999999999898740113789
Q gi|254780306|r   76 ILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPI  155 (837)
Q Consensus        76 ilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~  155 (837)
                      |||||||||||+||||++++|+...   ..+++|+||||||++||++||+|||++|++||+||+|||++|||||||+||+
T Consensus        81 ~lAtD~DREGE~I~~~i~~~l~~~~---~~~~~R~~F~eiT~~aI~~A~~~p~~id~~lv~A~~aR~~lD~lvG~~lSr~  157 (570)
T COG0550          81 YLATDPDREGEAIGWHILEVLKLKN---PSKVKRVVFSEITKKAILSAFKNPREIDMNLVDAQLARRILDRLVGYNLSRL  157 (570)
T ss_pred             EECCCCCCCHHHHHHHHHHHHCCCC---CCCEEEEEEECCCHHHHHHHHHCHHHHCHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9898999530799999999847567---7741379984189999999995915227676889999999998853401499


Q ss_pred             HHHHCCCC-CCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHH
Q ss_conf             88641467-65342268999999999999641376544001223315799654223310358330331011356667776
Q gi|254780306|r  156 LWQKLPGA-RSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLI  234 (837)
Q Consensus       156 L~rk~~~~-lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~  234 (837)
                      ||++++.+ |||||||||||+|||+||+||++|+|++||+|.+.|..+.+. |.|.|...++++.  .++.+...|.+++
T Consensus       158 l~~~~~~~~LSaGRVQSpaL~lVveRE~EI~~F~p~~yw~i~a~~~~~~~~-f~a~~~~~~~~~~--~~~~~~~~a~~~~  234 (570)
T COG0550         158 LWKKLKRGVLSAGRVQSPALRLVVEREREIEAFVPEEYWEIKAIFEKGGGE-FSARLTEIEGKKE--GRLKDKDEAEEIV  234 (570)
T ss_pred             HHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCC-EEEEEECCCCCCC--CCCCCHHHHHHHH
T ss_conf             998605788676544551345657319999837997646999998448860-6788722564311--3455589999999


Q ss_pred             HHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHH
Q ss_conf             42001563010000233222468521037999998876088899999999876213556721224553147554444305
Q gi|254780306|r  235 SFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPD  314 (837)
Q Consensus       235 ~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~e  314 (837)
                      +.++++.+.|.++++|+.+++||+||+||||||+||++|||||++||+|||+|||+       .||||||||||++||++
T Consensus       235 ~~l~~~~~~V~~ve~k~~~~~pp~Pf~tstLQq~As~~lgfs~kktm~iAQ~LYE~-------~glITYpRTDs~~ls~~  307 (570)
T COG0550         235 NKLKGKPAKVVSVEKKPKKRSPPPPFTTSTLQQEASRKLGFSAKKTMDIAQKLYEG-------HGLITYPRTDSTRLSEE  307 (570)
T ss_pred             HHCCCCCEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHCC-------CCCEEECCCCCCCCCHH
T ss_conf             97048955999986013136898997579999999975799989999999999608-------99278257899857999


Q ss_pred             HHHHHHHHHHHH-CCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHE
Q ss_conf             689999765520-0112376311112556668877765247730234640000019999999999999999998522211
Q gi|254780306|r  315 ALEAVRRSITSH-YGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAK  393 (837)
Q Consensus       315 a~~~~r~~i~~~-~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~  393 (837)
                      ++..++.++... ||++|++..++.|.++.+++|+||||||||+ ..+|.++..   .||++||+|||+|||||||+||+
T Consensus       308 ~~~~~~~~i~~~~yg~~~l~~~~~~~~~~~~~~q~AHeAIrPT~-~~~p~~~~~---~de~klY~LI~rrflAs~m~~A~  383 (570)
T COG0550         308 ALAEARLYILAIAYGKEYLPLKPRRYPSKGKKAQEAHEAIRPTD-FETPESLKA---YDELKLYDLIWRRFLASQMPDAI  383 (570)
T ss_pred             HHHHHHHHHHHHCCHHHHCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCHHCCC---HHHHHHHHHHHHHHHHHHCCHHH
T ss_conf             99999999976320876422355557777788767887837788-788200165---55889999999999998381523


Q ss_pred             ECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCH
Q ss_conf             00100136774079639999987488058856763267776321001014886456882110011011123464310178
Q gi|254780306|r  394 FERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSE  473 (837)
Q Consensus       394 ~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytE  473 (837)
                      |++++|++.+.++    .|+|+|++++|+||++||.+.    ++++.+..||.|++||.+.+.++++.+|+|+||+||||
T Consensus       384 ~~~~~v~l~~~~~----~F~a~g~~~~~~Gw~~vy~~~----~~~~~~~~lP~l~~gd~l~~~~~~~~~~~T~PP~rytE  455 (570)
T COG0550         384 YEKTTVTLEVAGE----KFKASGKVLKFDGWLKVYGED----KDEEEDKELPELKEGDELKVEKLEVEEHFTKPPPRYTE  455 (570)
T ss_pred             HEEEEEEEEECCC----EEEEEEEEEECCCHHHHHCCC----CCCCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCH
T ss_conf             0089999994186----799974488017579860643----45643465997788984566650022442597699898


Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHH
Q ss_conf             99874332102566551578999997322022147712220114200002233665568988999999999998626013
Q gi|254780306|r  474 SSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLN  553 (837)
Q Consensus       474 asLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~  553 (837)
                      ||||++||+.|||||||||+||++|++||||.+++++|+||++|+.|+++|+++|+++++|+|||+||++||+|++|+.+
T Consensus       456 asLvk~mE~~GIGrpSTyA~iI~~L~~RgYv~~~~~~~~pT~~G~~v~~~L~~~f~~l~~~~~Ta~mE~~Ld~I~~gk~~  535 (570)
T COG0550         456 ASLVKAMEKLGIGTPSTYASIIETLQKRGYVEKKGKRLVPTELGEAVIELLEEYFPELVDPDFTAKMEEKLDEIAEGKLE  535 (570)
T ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHCCCCEEECCCEEEECHHHHHHHHHHHHHCHHHCCHHHHHHHHHHHHHHHCCCCC
T ss_conf             99999998479997001899999886277388029756775789999999987452426987899999989999859942


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             4789999867676655766775
Q gi|254780306|r  554 WKEVLHEFWEEFIEKIDSIKKL  575 (837)
Q Consensus       554 ~~~~L~~Fy~~f~~~i~~~~~~  575 (837)
                      |.+||++||..|...+......
T Consensus       536 ~~~~l~e~~~~~~~~~~~~~~~  557 (570)
T COG0550         536 WKDVLDEFKKKFSKLLEEAKKN  557 (570)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHH
T ss_conf             8999999999889999999732


No 15 
>PRK08620 DNA topoisomerase III; Provisional
Probab=100.00  E-value=0  Score=1314.15  Aligned_cols=615  Identities=25%  Similarity=0.396  Sum_probs=525.3

Q ss_pred             CC-EEEECCHHHHHHHHHHH-----------CCCCEEEEEECCCEECCCCC-------------CCCCCCCCCCEEEEEC
Q ss_conf             91-89977904787788750-----------89989999425110078655-------------7867666744068877
Q gi|254780306|r    1 MN-VIIVESPAKAKTISKYL-----------GSNYKVLSSFGHIRDLPAKK-------------GSVLPEKEFEMIWNID   55 (837)
Q Consensus         1 M~-LvIvEsP~kak~I~~~L-----------g~~y~V~as~GHirdLp~~~-------------~~v~~~~~f~p~y~v~   55 (837)
                      |+ ||||||||+||+|++||           |++|+|+||+|||+||+...             +++.|+.   ..+.++
T Consensus         2 mK~LvIaEKPs~Ak~Iak~Lg~~~k~~gy~eG~~y~Vt~s~GHl~~L~~pe~y~~~~k~W~~~dLPiiP~~---~k~~~i   78 (726)
T PRK08620          2 MKSLVLAEKPSVGRDIARVLKCNKKGNGYLEGNKYIVTWALGHLVTLADPESYDKKYKEWRLEDLPMLPKR---MKLVVI   78 (726)
T ss_pred             CCCEEEECCHHHHHHHHHHHCCCCCCCCCEECCCEEEEEECCCCCCCCCHHHCCHHHCCCCCCCCCCCCHH---CCEEEC
T ss_conf             98289983879999999985756667774668898999826666438990235612045651347767332---204454


Q ss_pred             CCHHHHHHHHHHHH--HHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCC--CCC
Q ss_conf             65489999999998--70998999469970257999999999755125788716999980379899999986226--469
Q gi|254780306|r   56 PSSQKHLQNIIHAV--KSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPR--DIN  131 (837)
Q Consensus        56 ~~~kk~~~~i~~~~--k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r--~~d  131 (837)
                      +++++|++.|++++  ++|++||||||||||||+|||||++.++     .++|++|+||||||++||++||+|++  ..+
T Consensus        79 ~~~~kq~~~ik~ll~~k~a~~IiiAtDpDREGE~Ia~~il~~~~-----~~kpikRl~fseiT~~aI~~A~~nlkp~~~~  153 (726)
T PRK08620         79 KKTSKQFNAVKSQMLRKDVKEIIIATDAGREGELVARWIIDKAG-----VKKPIKRLWISSVTDKAIKDGFKNLKPGKAY  153 (726)
T ss_pred             CCHHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHC-----CCCCEEEEEEECCCHHHHHHHHHCCCCHHHH
T ss_conf             74278999999998667999899878887334899999999837-----9997489996028999999999748981430


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEE
Q ss_conf             89999999999989874011378988641467653422689999999999996413765440012233157996542233
Q gi|254780306|r  132 LDLVNAYLARRALDYLVGFNLSPILWQKLPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHL  211 (837)
Q Consensus       132 ~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l  211 (837)
                      ++||+||+|||++|||||||+||+||.++.++|||||||||||+|||+||+||++|+|++||+|.+.+.   +  +.+.|
T Consensus       154 ~~L~~Aa~aRr~~D~lVG~nlSr~lt~k~~~~LSaGRVQTPtL~lIveRE~EI~~F~p~~Yw~i~a~~~---~--~~~~~  228 (726)
T PRK08620        154 ENLYASAVARSEADWIVGINATRALTTKYNAQLSCGRVQTPTLAMIAQREEEIKNFKPKTYYTIEATTK---G--LKLTW  228 (726)
T ss_pred             HHHHHHHHHHHHHHHHHCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEC---C--EEEEE
T ss_conf             547899999999999824000499998726766665200226699999899998089964289999964---6--06898


Q ss_pred             EEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCC
Q ss_conf             10358330331011356667776420015630100002332224685210379999988760888999999998762135
Q gi|254780306|r  212 TDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGI  291 (837)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~  291 (837)
                      ...+    .+.+++|+++|+.+++.+++..+.|.+|++++.+++||+||+||+|||+||++|||||++||+|||+|||+|
T Consensus       229 ~~~~----~~~~~~d~~~a~~i~~~l~~~~~~V~~v~~k~kk~~pP~pf~tstLQq~As~~lg~SakkTm~iAQ~LYE~~  304 (726)
T PRK08620        229 QDKK----GNSRTFNKEKAEKIVKKLKGKDGKIVEVDKKHKKSYSPGLYDLTELQRDANKRFGYSAKETLNIMQRLYEQH  304 (726)
T ss_pred             ECCC----CCCCCCCHHHHHHHHHHHHCCCEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHHCC
T ss_conf             4155----656669999999999996159859999873010048979976799999999871878899999999998658


Q ss_pred             CCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCC-------CCCCCCC-CCCCCEEEEECCCCCC
Q ss_conf             5672122455314755444430568999976552001123763111125-------5666887-7765247730234640
Q gi|254780306|r  292 DVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYS-------SKSKNAQ-EAHEAIRPNDFDFLPS  363 (837)
Q Consensus       292 ~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~-------~k~k~aQ-eAHeAIrPT~~~~~p~  363 (837)
                             ||||||||||++||++++..+++.|...++..|.+.....+.       +.+.+++ .+|||||||+....+ 
T Consensus       305 -------glITYpRTDS~~ls~d~~~~~~~~l~~~~~~~y~~~~~~~~~~~~~~~k~~~~d~kv~dH~AI~PT~~~~~~-  376 (726)
T PRK08620        305 -------KVLTYPRTDSRYISTDIVDTLKERLKACGVGEYKKLANKILKKPIKANKSFVDDSKVSDHHAIIPTEQRVNL-  376 (726)
T ss_pred             -------CEEECCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-
T ss_conf             -------603216778751788899999999998432135788887502456755444665555677684786667780-


Q ss_pred             HHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCC-CCCCHHHC
Q ss_conf             00001999999999999999999852221100100136774079639999987488058856763267776-32100101
Q gi|254780306|r  364 KMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQ-EKNSEEDI  442 (837)
Q Consensus       364 ~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~-~~~~~~~~  442 (837)
                         ..|++||++||+|||+|||||||+||+|++|+|.+.+.+    ..|+|+|++++|+||++||....++ ++++..+.
T Consensus       377 ---~~Ls~de~klY~LI~~RflAs~m~~a~~~~t~v~~~~~~----~~F~a~G~~i~~~Gw~~vy~~~~~~~~~~~~~~~  449 (726)
T PRK08620        377 ---SALSDKERKIYDLVVKRFLAVLMPPFEYEQTTVKAEVGG----ETFIAKGKVVKSLGWKEVYDNFEDDDDEDESKEQ  449 (726)
T ss_pred             ---CCCCHHHHHHHHHHHHHHHHHHCCHHEEEEEEEEEEECC----EEEEEEEEEEEECCHHHHHCCCCCCCCCCCCCCC
T ss_conf             ---008999999999999999997165125888999999789----1899998999556678762665565543210014


Q ss_pred             CCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHC-------------------CCCCCCCHHHHHHHHHHCCE
Q ss_conf             48864568821100110111234643101789987433210-------------------25665515789999973220
Q gi|254780306|r  443 LLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEI-------------------GIGRPSTYATILETLYKRKY  503 (837)
Q Consensus       443 ~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~-------------------GIGrPSTyA~II~~L~~R~Y  503 (837)
                      .||.|++|+.+.+.++...+|+|+||+||||||||++||+.                   |||||||||+||++|++|+|
T Consensus       450 ~LP~l~~Ge~l~~~~~~~~~~~TkPP~ryTEasLi~~ME~~~k~v~~~d~~l~k~l~e~~GIGtpATrA~IIe~L~~r~Y  529 (726)
T PRK08620        450 LLPKLSKGDTLKVKKINITEGETKPPARFNEGTLLSAMENPQKYMQLKDKKLAKTLGETGGLGTVATRADIIEKLFNSFL  529 (726)
T ss_pred             CCCCCCCCCEEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCEE
T ss_conf             69978889976641323222206897998989999999735535664358999987640476764417778887754105


Q ss_pred             EECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             22147712220114200002233665568988999999999998626013478999986767665576677556667765
Q gi|254780306|r  504 VIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDI  583 (837)
Q Consensus       504 V~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~  583 (837)
                      |++++++|+||++|+.|+++|..   +|++|+|||.||++||+|+.|+.+|.+||++||.-+...+++++....      
T Consensus       530 v~~~~k~l~pT~~G~~l~~~l~~---~l~~p~~TA~~E~~Ld~I~~Gk~~~~~fi~~~~~~~~~~v~~~k~~~~------  600 (726)
T PRK08620        530 IEKRGKDIKITSKGKQLLELVPE---ELKSPLLTAEWEQKLELIAKGKLKKKTFINEMKNYTKKVVNEIKNSDK------  600 (726)
T ss_pred             EEEECCEEEECHHHHHHHHHHHH---HCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHCC------
T ss_conf             87109988177689999998798---648945789999999999869998999999999999999999974014------


Q ss_pred             HHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             56766410245555676611433467773136871577611123434323332100122100001234420146899996
Q gi|254780306|r  584 LNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKE  663 (837)
Q Consensus       584 l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~  663 (837)
                                ....+..+...||+||..++.  +.||+|.|++||+ |+|+|++++...-           =+.||.||.
T Consensus       601 ----------~~~~~~~t~~~Cp~Cg~~m~~--~~gr~Gkf~~C~~-peC~~~k~~~~~~-----------~~~Cp~C~~  656 (726)
T PRK08620        601 ----------KYKHDNLTGTKCPDCGKFMLE--VKGKNGKMLVCQD-RECGHRKNVSRKT-----------NARCPNCKK  656 (726)
T ss_pred             ----------CCCCCCCCCCCCCCCCCCCEE--EECCCCCEEECCC-CCCCCCCCCHHHC-----------CCCCCCCCC
T ss_conf             ----------424577789856426832116--8589875574689-9899977710212-----------894999998


Q ss_pred             EEEEEECCCCCEEEECC
Q ss_conf             69998269742277348
Q gi|254780306|r  664 SVTLRSGRFGLYVQRGD  680 (837)
Q Consensus       664 ~I~lk~GryGpYvq~Ge  680 (837)
                      +|.+|.+++|-+..+..
T Consensus       657 ~~~~~~~~~g~~~~c~~  673 (726)
T PRK08620        657 KLELRGEGEGQIFVCVC  673 (726)
T ss_pred             EEEEEECCCCCEEEECC
T ss_conf             56898567787899738


No 16 
>PRK08174 DNA topoisomerase III; Validated
Probab=100.00  E-value=0  Score=1297.94  Aligned_cols=599  Identities=25%  Similarity=0.401  Sum_probs=516.8

Q ss_pred             CCEEEECCHHHHHHHHHHHC-----------CCCEEEEEECCCEECCCCC-------------CCCCCCCCCCEEEEECC
Q ss_conf             91899779047877887508-----------9989999425110078655-------------78676667440688776
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLG-----------SNYKVLSSFGHIRDLPAKK-------------GSVLPEKEFEMIWNIDP   56 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg-----------~~y~V~as~GHirdLp~~~-------------~~v~~~~~f~p~y~v~~   56 (837)
                      |+|||||||++||+|++|||           ++|.|+||+|||++|+..+             +.+.|+. |  .|.+.+
T Consensus         1 MkLiIaEkPs~Ak~Ia~~LG~~~k~~gy~~~~~~~Vt~~~GHl~~l~~p~~y~~~~k~w~~~~lpi~p~~-~--~~~~~~   77 (670)
T PRK08174          1 MRLFLCEKPSQGKDIARVLGATQRGEGCLSGPGVTVTWCIGHLLETAPPEAYDEQYKRWSLEQLPIIPQQ-W--KMVVKP   77 (670)
T ss_pred             CEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCCHHHCCCCCCCCCCCCCCCCCCC-C--EEEECC
T ss_conf             9599985879999999985876357762327985999846807546791234610035760117778632-2--578772


Q ss_pred             CHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHC--CCCCCHHH
Q ss_conf             5489999999998709989994699702579999999997551257887169999803798999999862--26469899
Q gi|254780306|r   57 SSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKS--PRDINLDL  134 (837)
Q Consensus        57 ~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n--~r~~d~~L  134 (837)
                      ++++|++.|++++++||+||||||||||||+|||||+++++     .++||+|+|||+||+++|++||+|  |++.+++|
T Consensus        78 ~~~~q~~~ik~l~k~ad~ii~AtD~DREGE~I~~~i~~~~~-----~~~~v~R~~fs~iT~~~I~~a~~nl~p~~~~~~L  152 (670)
T PRK08174         78 KTASQFKVVKRLLKQATELVIATDADREGEMIARELLELCG-----YRGPIQRLWLSALDDASIRKALAALKPGAETLPL  152 (670)
T ss_pred             CHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHC-----CCCCEEEEEEEECCHHHHHHHHHCCCCCHHHHHH
T ss_conf             07899999999996599999888888133699999999848-----8898278998757999999999647980330778


Q ss_pred             HHHHHHHHHHHHHHHHHHCHHHHHHC-----CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEE
Q ss_conf             99999999989874011378988641-----4676534226899999999999964137654400122331579965422
Q gi|254780306|r  135 VNAYLARRALDYLVGFNLSPILWQKL-----PGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTA  209 (837)
Q Consensus       135 v~A~~aRr~lD~lvG~~lSp~L~rk~-----~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a  209 (837)
                      ++||+|||++|||||||+||+||.+.     .+.+||||||||||+|||+||+||++|+|++||+|.+.|.. ++..|.+
T Consensus       153 ~~Aa~aR~~lD~lvG~nlSr~~t~~~~~~g~~~~lS~GRVQtPtL~lIveRE~EI~~F~p~~y~~i~~~~~~-~~~~f~a  231 (670)
T PRK08174        153 YYSALARSRADWLIGMNLSRLFTLLGRQAGYDGVLSVGRVQTPTLALVVDRDREIANFVPVPYWAIDVSLSA-GGQTFTA  231 (670)
T ss_pred             HHHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEE-CCEEEEE
T ss_conf             999999999999718553688999877507887730450124668889999999980788632899999974-8915788


Q ss_pred             EEEEECCEEECCCCHHHHHHHHHHHHHHCC-CCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             331035833033101135666777642001-5630100002332224685210379999988760888999999998762
Q gi|254780306|r  210 HLTDFNGQRIEKKSISNKKEADDLISFVKK-ATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLY  288 (837)
Q Consensus       210 ~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LY  288 (837)
                      +|...++...+.+++++++.|+.+.+.+++ ..++|.+|++++.+++||+||+||+|||+||++|||||++||+|||+||
T Consensus       232 ~~~~~~~~~d~~~r~~~~~~a~~~~~~~~~~~~~~V~~v~~k~~~~~pP~Pf~tstLQ~~As~~lg~sa~~Tm~iAQ~LY  311 (670)
T PRK08174        232 QWVPPEQYCDDEGRCLQQPVAQQAAQQIRQAGSAQVVSVETERVREGAPLPFDLGTLQEVCSKKLGLGAQETLDIAQALY  311 (670)
T ss_pred             EEECCCCCCCHHCCCCCHHHHHHHHHHHHCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             87424556212202479999999999986489759999985454247999974799999999871988889999999988


Q ss_pred             CCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCC-----CCCCCCCCCCCCCCCCCCC--CCCCEEEEECCCC
Q ss_conf             13556721224553147554444305689999765520011-----2376311112556668877--7652477302346
Q gi|254780306|r  289 EGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGD-----HYLPEKPRIYSSKSKNAQE--AHEAIRPNDFDFL  361 (837)
Q Consensus       289 E~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~-----~~l~~~~r~y~~k~k~aQe--AHeAIrPT~~~~~  361 (837)
                      |.       .||||||||||++||++++..++.+|..+++.     .+++...+.+++++.|.|+  ||||||||..   
T Consensus       312 E~-------~glITYpRTDS~~l~~~~~~~~~~~i~~l~~~~~~~~~~~~~~~~~~k~r~~n~~kv~aH~AI~PT~~---  381 (670)
T PRK08174        312 ET-------HKATTYPRTDCGYLPESMFAEVPTVLDALLKTDPSLRPLMGQLDRSQRSRAWNDKKITAHHGIIPTLE---  381 (670)
T ss_pred             HC-------CCEEEECCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC---
T ss_conf             52-------88287258787756878999999999998612715555530035333466678765456778677888---


Q ss_pred             CCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCC--CH
Q ss_conf             4000001999999999999999999852221100100136774079639999987488058856763267776321--00
Q gi|254780306|r  362 PSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKN--SE  439 (837)
Q Consensus       362 p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~--~~  439 (837)
                      +..+ ..|++||++||+|||+|||||||+||+|++|+|.+.+.+    ..|+++|++++|+||++||....+++++  ..
T Consensus       382 ~~~~-~~Ls~de~klY~LI~~RflAs~m~~a~~~~t~v~~~~~~----~~F~a~g~~i~~~Gw~~v~~~~~~~~~~~~~~  456 (670)
T PRK08174        382 PADL-SKMSEKELAVYRLIRAHYLAQFLPHHEFDRTVATFDCGG----QLLRAVGKQIVVPGWKVLFAEPLEEDDGDEAP  456 (670)
T ss_pred             CCCH-HHCCHHHHHHHHHHHHHHHHHHCCHHEEEEEEEEEEECC----CEEEEEEEEEEECCHHHHHCCCCCCCCCCCCC
T ss_conf             7880-349999999999999999998486321778899999789----38999879997477687626656653223342


Q ss_pred             HHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHH-----------------HHCCCCCCCCHHHHHHHHHHCC
Q ss_conf             10148864568821100110111234643101789987433-----------------2102566551578999997322
Q gi|254780306|r  440 EDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKM-----------------EEIGIGRPSTYATILETLYKRK  502 (837)
Q Consensus       440 ~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~m-----------------E~~GIGrPSTyA~II~~L~~R~  502 (837)
                      .+..||.|++|+.+.+.++++.+|+|+||+||||||||++|                 |+.|||||||||+||++|++|+
T Consensus       457 ~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~ryTEasLi~~M~~~~k~v~d~~l~~~LkE~~GIGtpaTrA~II~~L~~R~  536 (670)
T PRK08174        457 RSQVLPALREGQACQVADVELKALKTQPPKPYTEGTLIKAMKNVAKFVTDPRLKQKLKDTTGIGTEATRAGIIQGLLDRG  536 (670)
T ss_pred             CCCCCCCCCCCCEEEEEEEEEEECCCCCCCCCCHHHHHHHHHHHHHCCCCHHHHHHHCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             22327765689766775546520315897998989999999863003365888876310578785036999999998679


Q ss_pred             EEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             02214771222011420000223366556898899999999999862601347899998676766557667755666776
Q gi|254780306|r  503 YVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLD  582 (837)
Q Consensus       503 YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d  582 (837)
                      ||+.++++|+||++|+.|+++|..   .+++++|||.||.+||+|++|+.+|.+||.+|+..+...++.......     
T Consensus       537 Yv~~~~k~l~pT~~G~~li~~l~~---~l~~~~~Ta~~E~~Ld~I~~G~~~~~~f~~~~~~~~~~~v~~~~~~~~-----  608 (670)
T PRK08174        537 YLVKKGKALRATDAAFTLIDAVPA---AIADPGTTALWEQALDMIAAGQMTLDVFMAKQAAWVSQLVAQCGGQSL-----  608 (670)
T ss_pred             CEEECCCEEEECHHHHHHHHHHHH---HCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHCCCC-----
T ss_conf             898209876024899999997687---627967899999999999859988999999999999999998641544-----


Q ss_pred             HHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             5567664102455556766114334677731368715776111234343233321001221000
Q gi|254780306|r  583 ILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDI  646 (837)
Q Consensus       583 ~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~  646 (837)
                                   .....+..+||+|+. .|.. +.||+|.||||||||+|+||.|+..+....
T Consensus       609 -------------~~~~~~~~~CP~Cg~-~l~~-r~~k~G~F~gCs~yP~Ck~t~p~~~g~~~~  657 (670)
T PRK08174        609 -------------SIKVPPSPACPQCGA-PTRQ-RNGKSGPFWGCSRYPDCKGTLPVDSGKSKR  657 (670)
T ss_pred             -------------CCCCCCCCCCCCCCC-EEEE-EECCCCCEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             -------------457998997878997-5036-706887378699998888852289999777


No 17 
>PRK07141 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=1300.31  Aligned_cols=592  Identities=34%  Similarity=0.573  Sum_probs=515.7

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCC---CCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEEC
Q ss_conf             1899779047877887508998999942511007865---5786766674406887765489999999998709989994
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAK---KGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILA   78 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~---~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilA   78 (837)
                      +|||||||||||+|++|||++|.|+||+|||+||+..   ++++++++ |.|.|.++++++++++.|++++++||+||||
T Consensus         4 ~LiIaEkPs~ak~Ia~~LG~~y~Vt~~~GHl~~L~~~~~~~~~~~~~~-w~p~~~~~~~kk~~~k~ik~l~k~ad~viiA   82 (622)
T PRK07141          4 KLVIVESPNKVKTISKYLGSDYNVTASVGHIAKLSKSGQFGLGIDFEN-WEPLYVLDPTKKKVIKELKKAAKKAKEVYIA   82 (622)
T ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEECCCHHCCCCCCCCCCCCCHHH-CCEEEEECCCHHHHHHHHHHHHHCCCEEEEC
T ss_conf             399983879999999984939899972033541888544688877677-8675786753899999999999669999988


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHH
Q ss_conf             69970257999999999755125788716999980379899999986226469899999999999898740113789886
Q gi|254780306|r   79 TDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQ  158 (837)
Q Consensus        79 tD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~r  158 (837)
                      ||||||||+|||||+++++     +++|++|+||||||++||++||+||+++|++|++||+|||++|||||||+||+||+
T Consensus        83 tD~DREGE~I~~~i~~~~~-----~~~~v~R~~f~~iT~~aI~~A~~n~~~~~~~l~~A~~aR~~~D~lvG~nlSr~l~~  157 (622)
T PRK07141         83 TDPDREGEAIGQNLVDYLK-----LKDKYKRIKYNEITKDAILEALENPTMLDQNLINAQKTRRMLDRIIGFRLSKLMKS  157 (622)
T ss_pred             CCCCCCHHHHHHHHHHHHC-----CCCCEEEEEEECCCHHHHHHHHHCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHH
T ss_conf             8987130599999999828-----99983799982389999999985878533105589999999999706202299999


Q ss_pred             HCC---CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHH
Q ss_conf             414---67653422689999999999996413765440012233157996542233103583303310113566677764
Q gi|254780306|r  159 KLP---GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLIS  235 (837)
Q Consensus       159 k~~---~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~  235 (837)
                      +++   +.+||||||||||+|||+||+||++|+|++||.|.+.|...  ..+.+.+...+....++. +.++++++++..
T Consensus       158 ~~~~~~~~lS~GRVQTPtL~lVveRe~eI~~F~p~~y~~i~a~~~~~--~~~~~~~~~~~~~~~~~~-~~~~~~~~~~~~  234 (622)
T PRK07141        158 KLSNAPSNPSAGRVQSIALKLVIDREKEIEAFVPEKYFNLEAKIENS--NSLDAEYFNENNEAGDKN-WINEEEIDEIKA  234 (622)
T ss_pred             HHCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCCCEEEEEEEEEEECC--CCEEEEEECCCCCCHHHC-CCCHHHHHHHHH
T ss_conf             85477888776652228899999999999737870279999999348--733789703554203321-479999999999


Q ss_pred             HH-CCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHH
Q ss_conf             20-01563010000233222468521037999998876088899999999876213556721224553147554444305
Q gi|254780306|r  236 FV-KKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPD  314 (837)
Q Consensus       236 ~~-~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~e  314 (837)
                      .+ .+..++|.+++.++.+..||+||+|++||+.|    +|||++||++||+|||+++.    .||||||||||++||++
T Consensus       235 ~~~~~~~~~V~~v~~~~~~~~~p~pf~~s~l~k~~----~~sa~~tl~iaQ~LYE~~~~----~GlITYpRTDs~~ls~~  306 (622)
T PRK07141        235 EILKNKKLIVKKIKVSTRKDPKLTPFKQAVLYKKS----QYSSASVQSALQKLYEGYGD----GGLISYPRTDSTRLSQT  306 (622)
T ss_pred             HHHCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHH----CCCHHHHHHHHHHHHHHHCC----CCEEEEECCCCCCCCHH
T ss_conf             87237986999965245357998985168999885----77988999999999963165----86399767888536999


Q ss_pred             HHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHC--CCCCHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             6899997655200112376311112556668877765247730234640000--01999999999999999999852221
Q gi|254780306|r  315 ALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMK--QFLDSDQFQLYNLIWKRSVASQMASA  392 (837)
Q Consensus       315 a~~~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~--~~L~~de~klY~LI~~R~lasqm~~a  392 (837)
                      +++.++++|...||.+|++...+.    .+|+|+||||||||++..+|+...  ..|+++|++||+|||+|||||||+||
T Consensus       307 ~~~~~~~~i~~~~~~~~~~~~~k~----~~~~~~aH~AI~PT~~~~~p~~~~~~~~L~~~e~klY~LI~rrflas~~~~a  382 (622)
T PRK07141        307 FINKAKKYIEKKFGPEYVSKSIKG----FAGDQDAHEAIRPTDLELLPELAREKYDLGQIEYQIYKLIYNTTLQALMTPP  382 (622)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCC----CCCCCCCCCCCCCCCCCCCCHHHCCCCCCCHHHHHHHHHHHHHHHHHHCCHH
T ss_conf             999999999986556552243146----6676666676157886768133124457999999999999999999637666


Q ss_pred             EECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCC
Q ss_conf             10010013677407963999998748805885676326777632100101488645688211001101112346431017
Q gi|254780306|r  393 KFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYS  472 (837)
Q Consensus       393 ~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~ryt  472 (837)
                      +++.|+|.+.+.+    ..|.++|++++++||+.+|...        ++..||.+++|+.+.+.++.+++++|+||+|||
T Consensus       383 ~~~~t~v~~~~~~----~~F~~~g~~i~~~Gw~~v~~~~--------~~~~lP~l~~g~~~~~~~~~~~~~~TkPP~ryT  450 (622)
T PRK07141        383 VRKITRYTLENDK----HIFKLSYSKVTFDGYYKVTGFP--------ELKFDPKYEIGQSIEVKEFVVEDKETKPPARYN  450 (622)
T ss_pred             EEEEEEEEEEECC----EEEEEEEEEEEECCEEEECCCC--------CCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCC
T ss_conf             0054899997389----8999987999987788941675--------445599888899867768898743338998869


Q ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCH
Q ss_conf             89987433210256655157899999732202214771222011420000223366556898899999999999862601
Q gi|254780306|r  473 ESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKL  552 (837)
Q Consensus       473 EasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~  552 (837)
                      |||||++||+.|||||||||+||++|++|+||..++++|+||++|++|+++|..+||++++++|||.||+.||+|++|+.
T Consensus       451 EasLi~~Me~~gIGtpATrA~iIe~L~~R~Yv~~~~k~l~pT~~G~~l~~~L~~~~~~l~~~~~Ta~~E~~Ld~I~~G~~  530 (622)
T PRK07141        451 DGSLIEKLDDIKVGRPSTFASTVKILKDRLYVDSESKALVPTDFGKIVLEKLIIGFPEIINEKYTAQVEEELDLIAEGKI  530 (622)
T ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEECCCEEEECHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHCCCC
T ss_conf             99999998747998520299999999757738941977746374999999999861664493789999998999985998


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCC--CCCCCCCCC
Q ss_conf             347899998676766557667755666776556766410245555676611433467773136871577--611123434
Q gi|254780306|r  553 NWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKY--GAFVGCTNY  630 (837)
Q Consensus       553 ~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~--G~FigCSny  630 (837)
                      +|.+||++||..|...++.+.+...            ...   .....+...||+|++ .|.++. +++  |.|||||||
T Consensus       531 ~~~~~l~~~~~~~~~~~~~~~~~~~------------~~~---~~~~~~~~~CP~Cg~-~l~~r~-~~~g~~~F~gCs~y  593 (622)
T PRK07141        531 DYKKVLEDFWSKFENTYDDASKTME------------KTI---MEPEFLGESCPDCNG-DLVYRN-NRKGDQRFIGCSNF  593 (622)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHHHH------------HCC---CCCCCCCCCCCCCCC-CEEEEE-CCCCCCEEEECCCC
T ss_conf             6999999999999999999987554------------314---776667998878998-225787-36889869878999


Q ss_pred             CCCCCCCCCCCCC
Q ss_conf             3233321001221
Q gi|254780306|r  631 PECKYTRQLTSNP  643 (837)
Q Consensus       631 PeCk~t~~l~~~~  643 (837)
                      |+|+||.+.....
T Consensus       594 p~Ck~t~~~~~~~  606 (622)
T PRK07141        594 PNCRFTRSYEDAK  606 (622)
T ss_pred             CCCCCCEECCCCC
T ss_conf             8888811678887


No 18 
>PRK07220 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=1278.94  Aligned_cols=614  Identities=28%  Similarity=0.421  Sum_probs=516.9

Q ss_pred             CCEEEECCHHHHHHHHHHHCC---------------------CCEEEEEECCCEEC--CCCC---CCCCCCCCCCEEEEE
Q ss_conf             918997790478778875089---------------------98999942511007--8655---786766674406887
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGS---------------------NYKVLSSFGHIRDL--PAKK---GSVLPEKEFEMIWNI   54 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~---------------------~y~V~as~GHirdL--p~~~---~~v~~~~~f~p~y~v   54 (837)
                      |+||||||||+||+||++||.                     +++|+|++|||.+|  |...   ..++|.+.|.+.|..
T Consensus         1 M~LiIAEKPsvAk~IA~~Lg~~~~~~~~~~g~~~y~~~~~~~~~ivt~~~GHL~~ld~P~~y~~W~~~d~~~l~~~~~~~   80 (740)
T PRK07220          1 MHLIITEKNIAARRIAQILAPKSPKETKVSGVDVYRYEERRQETVVVGLSGHIVGIDFPEEYNNWQKVDPRDLIDAEIIT   80 (740)
T ss_pred             CEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEECCCCEEEEEECCEECCCCCCCCCCCCCCCCHHHCCCCCEEE
T ss_conf             98999778699999999858999877610586632674058817999604520356685013776727865648864576


Q ss_pred             CCCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHH
Q ss_conf             76548999999999870998999469970257999999999755125788716999980379899999986226469899
Q gi|254780306|r   55 DPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDL  134 (837)
Q Consensus        55 ~~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~L  134 (837)
                      .+.++++++.|++++++||+||||||||||||+||||++++++..  .++.+|+|+||||||++||++||+||+++|++|
T Consensus        81 ~~~~kki~~~Lk~l~k~ad~ViiAtD~DREGE~I~~e~~~i~~~~--~~~~~v~R~~fseiT~~aI~~A~~n~~~~d~~L  158 (740)
T PRK07220         81 TPTNKKIVTALRKLGKEADRVTIATDYDREGELIGVEALNIIKEV--NPDIPFDRVRFSAITKKEIERAFSNPVEVDFNL  158 (740)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEECCCCCCCCCHHHHHHHHHHHHC--CCCCEEEEEEEECCCHHHHHHHHHCCCCCCHHH
T ss_conf             676489999999998179999989889746489999999999860--899705899970589999999996875358878


Q ss_pred             HHHHHHHHHHHHHHHHHHCHHHHHHCC----CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEE
Q ss_conf             999999999898740113789886414----6765342268999999999999641376544001223315799654223
Q gi|254780306|r  135 VNAYLARRALDYLVGFNLSPILWQKLP----GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAH  210 (837)
Q Consensus       135 v~A~~aRr~lD~lvG~~lSp~L~rk~~----~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~  210 (837)
                      ++||+|||++|||||||+||+||.+++    ..|||||||||||+|||+||+||++|+|++||+|.+.|.. ++..|.++
T Consensus       159 ~~A~~aR~~lD~lvG~nlSr~lt~~~~~~g~~~LSaGRVQTPtL~lIVeRe~EI~~F~p~~Yw~i~a~~~~-~~~~~~~~  237 (740)
T PRK07220        159 ADAGEARQVIDLVWGAALTRYISLAAGRLGKMFLSVGRVQSPTLALIVDREKERNAFVPTPYWEIYAELEN-AGETFSAQ  237 (740)
T ss_pred             HHHHHHHHHHHHHHCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEC-CCCEEEEE
T ss_conf             99999999999984121658998997650677644231013889999999999984799642899999972-99049985


Q ss_pred             EEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCC
Q ss_conf             31035833033101135666777642001563010000233222468521037999998876088899999999876213
Q gi|254780306|r  211 LTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEG  290 (837)
Q Consensus       211 l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~  290 (837)
                      +        .+.++.++++|+.+.+.+. ..+.|.+|++++.+++||+||+||+|||+||+ |||||++||+|||+||| 
T Consensus       238 ~--------~~~r~~d~~~a~~i~~~l~-~~~~V~~v~~k~~~~~pP~Pf~ts~Lq~~Ask-lg~Sa~~Tm~iAQ~LYe-  306 (740)
T PRK07220        238 H--------STRRFLDKEEADRVLEKLG-KKAEVKEIEKGEKTDQPPTPFNTTGFISAASS-IGFSPANAMRIAESLYT-  306 (740)
T ss_pred             C--------CCCCCCCHHHHHHHHHHCC-CCCEEEEEEECCCCCCCCCCCCHHHHHHHHHH-CCCCHHHHHHHHHHHHC-
T ss_conf             0--------5677799999999999726-98489999835301489898767999999987-69979999999998742-


Q ss_pred             CCCCCHHHHHHHHCCCCCCCCCHHH-H-HHHHHHHHHHCCC--CCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHC
Q ss_conf             5567212245531475544443056-8-9999765520011--2376311112556668877765247730234640000
Q gi|254780306|r  291 IDVNGEIVGLITYMRTDGVHMSPDA-L-EAVRRSITSHYGD--HYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMK  366 (837)
Q Consensus       291 ~~~~~~~~GlITYpRTDS~~ls~ea-~-~~~r~~i~~~~g~--~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~  366 (837)
                             .||||||||||++++++. + ..+..+....|++  ..+....+...++.++.++||||||||+...     .
T Consensus       307 -------~GlITYpRTDS~~lp~s~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~H~AI~PT~~~~-----~  374 (740)
T PRK07220        307 -------NGYISYPRTDNTVYPESLDLRAQLEIFAEGPFGEYADKLLEKGELVPTRGKKETTDHPPIYPASLAK-----K  374 (740)
T ss_pred             -------CCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCC-----C
T ss_conf             -------8832146666540650276999999998605788899750157667786522101333435556566-----4


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCC
Q ss_conf             01999999999999999999852221100100136774079639999987488058856763267776321001014886
Q gi|254780306|r  367 QFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPY  446 (837)
Q Consensus       367 ~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~  446 (837)
                      ..|++||++||+|||+|||||||+||+|++++|.+.+.+    ..|+++|++++|+||+++|....      .++..||.
T Consensus       375 ~~L~~de~klY~LI~rRflAs~m~~a~~~~t~v~~~~~~----~~F~a~G~~i~~~Gw~~vy~~~~------~~d~~LP~  444 (740)
T PRK07220        375 SDLKEDEWKVYELVVRRFFATLAGPATWETMRLRFDIGG----EEFKANGARLLEQGWRWYYPYNR------PEDRLLPE  444 (740)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCHHEEEEEEEEEEECC----EEEEEEEEEEEECCHHHHCCCCC------CCCCCCCC
T ss_conf             559999999999999999997373543032899999899----89998658996376798617776------41001887


Q ss_pred             CCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCC
Q ss_conf             45688211001101112346431017899874332102566551578999997322022147712220114200002233
Q gi|254780306|r  447 ISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLEN  526 (837)
Q Consensus       447 l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~  526 (837)
                      |++|+.+.+.++++.+++|+||+||||||||++||+.|||||||||+||++|++|+||  ++++|+||++|++|+++|++
T Consensus       445 l~~Ge~~~~~~~~~~~k~TkPP~ryTEasLIk~ME~~GIGtpATrA~iIe~L~~R~YV--e~~~l~PT~~G~~v~~~L~~  522 (740)
T PRK07220        445 LSEGDILKVIKKEMLDKETQPPGRYGQGRLIKLMEDLGLGTKATRHEIISKLYSRAYI--HGNPIQPTNTSFAVVDALEK  522 (740)
T ss_pred             CCCCCEEEEEEEEEEEECCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCC--CCCCCCCCHHHHHHHHHHHH
T ss_conf             7789885666778873004899888989999999738998500499999999861883--28865254799999999987


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECC
Q ss_conf             66556898899999999999862601347899998676766557667755666776556766410245555676611433
Q gi|254780306|r  527 FFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCP  606 (837)
Q Consensus       527 ~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp  606 (837)
                      +|++|++|+|||.||++||+|++|+.+|.+||++|+..|...+..+.+.. .++.+.        .........+.+.||
T Consensus       523 ~~~~l~~p~~Ta~~E~~Ld~Ia~Gk~~~~~vl~e~~~~~~~~~~~~~~~~-~~i~~~--------~~~~~~~~~~~~~CP  593 (740)
T PRK07220        523 YAPTITKPDMTKLLEEDMDLIAEGKIKEDAVLEESREMLEQVFDELDKNR-EKIIES--------LQAGLREDKIIGKCS  593 (740)
T ss_pred             HCHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH-HHHHHH--------HHHCCCCCCCCCCCC
T ss_conf             23453591279999999999986999899999999999999999999989-999987--------653023677789788


Q ss_pred             CCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEE
Q ss_conf             46777313687157761112343432333210012210000123442014689999669998
Q gi|254780306|r  607 ECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKESVTLR  668 (837)
Q Consensus       607 ~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~~I~lk  668 (837)
                      +|+.+.+ +++++++|.||||||||+|+||.||.....-. . .    =..||.||.+++--
T Consensus       594 ~Cg~~l~-~r~~k~g~~FigCs~YP~C~~t~pLp~~g~~~-~-~----~~~C~~~~~~~~~~  648 (740)
T PRK07220        594 LCGSELM-VRRSKRGSRFIGCSGYPNCTFSLPLPKSGQII-V-T----DKVCEAHGLHHIKI  648 (740)
T ss_pred             CCCCCCE-EEECCCCCEEEECCCCCCCCCCEECCCCCCEE-E-C----CCCCCCCCCEEEEE
T ss_conf             8996004-77458799788589899999852269998463-4-7----88687799837999


No 19 
>PRK07219 DNA topoisomerase I; Validated
Probab=100.00  E-value=0  Score=1268.54  Aligned_cols=660  Identities=24%  Similarity=0.382  Sum_probs=535.6

Q ss_pred             CCEEEECCHHHHHHHHHHHCCC---------------------CEEEEEECCCEEC--CCCC--C-CCCCCCCCCEEEEE
Q ss_conf             9189977904787788750899---------------------8999942511007--8655--7-86766674406887
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSN---------------------YKVLSSFGHIRDL--PAKK--G-SVLPEKEFEMIWNI   54 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~---------------------y~V~as~GHirdL--p~~~--~-~v~~~~~f~p~y~v   54 (837)
                      |+||||||||+|++||++||.+                     +.|+|++|||.+|  |...  + ..++..-|...+..
T Consensus         4 MkLiIAEKPSvAr~IA~~L~~g~~k~~~~~g~~y~ef~~~g~~~~vt~~~GHl~el~~p~~y~~W~~~~l~~l~~~~~~~   83 (769)
T PRK07219          4 FRLIIAEKMDAGRRIAYFLSKGTSKQKRSKGSSYIEFESNGEKTVLIPLSGHIVEADFPSDFSDWLKSDLNLLIDARIVK   83 (769)
T ss_pred             CEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEECCCCEEEEEECCCCCCCCCCCCCCCCCCCCCHHHCCCCCEEE
T ss_conf             68999877699999999737998666556787459995179679999725422345678567877768720158864142


Q ss_pred             CCCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHH
Q ss_conf             76548999999999870998999469970257999999999755125788716999980379899999986226469899
Q gi|254780306|r   55 DPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDL  134 (837)
Q Consensus        55 ~~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~L  134 (837)
                      ....+++++.|++++++||+||||||||||||+|||||+++|+.    .+.+|+|+||||||++||++||+|||++|++|
T Consensus        84 ~~~~k~~~~~Lk~lak~ad~IilAtDpDREGE~I~~~i~~~l~~----~~~~v~Ri~f~eiT~~aI~~A~~n~~~~d~~L  159 (769)
T PRK07219         84 NVKNKRAYQTLKNFKGKADEIIIATDYDREGELIGVEALDIIKE----GKENIKRAKFSALTEKEINDAFSNTINVNYNL  159 (769)
T ss_pred             CCCCHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHCC----CCCCCEEEEEECCCHHHHHHHHHCCCCCCHHH
T ss_conf             47618999999999816999998988870434999999998522----59984689981489999999996852046889


Q ss_pred             HHHHHHHHHHHHHHHHHHCHHHHHHCC----CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEE
Q ss_conf             999999999898740113789886414----6765342268999999999999641376544001223315799654223
Q gi|254780306|r  135 VNAYLARRALDYLVGFNLSPILWQKLP----GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAH  210 (837)
Q Consensus       135 v~A~~aRr~lD~lvG~~lSp~L~rk~~----~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~  210 (837)
                      |+||+|||++|||||||+||+||.+.+    ..|||||||||||+|||+||+||++|+|++||+|.+.|..  +..|.+.
T Consensus       160 ~~A~~aRr~lD~lvG~nlSr~lt~~~~~l~~~~LSaGRVQTPtL~lIveRe~EI~~F~pe~yw~i~~~~~~--~~~f~a~  237 (769)
T PRK07219        160 ADAADARESIDLIWGAVLTRFFSIATGRLGKDFLSAGRVQTPTLAIVVKREREIRSFVPEKYWTISITFNK--NGDFDAY  237 (769)
T ss_pred             HHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEC--CCCEEEE
T ss_conf             99999999999998631068988887641456666452000778999999999983799534899999804--8826885


Q ss_pred             EEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCC
Q ss_conf             31035833033101135666777642001563010000233222468521037999998876088899999999876213
Q gi|254780306|r  211 LTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEG  290 (837)
Q Consensus       211 l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~  290 (837)
                      +         ..++.|+++|+.+++.+++..++|.+|++++.+++||+||+||+|||+|| +|||||++||+|||+||| 
T Consensus       238 ~---------~~~~~d~~~a~~i~~~l~~~~~~V~~v~~k~~~~~pP~Pf~tstLQq~As-rlg~s~~kTm~iAQ~LYe-  306 (769)
T PRK07219        238 Y---------NNELKDRDTAEKIFSEIKGMPGRVKSFDKEEYYIRRPAPFSTTEFLREAS-RIGIMPTKAMSIAEKLYM-  306 (769)
T ss_pred             C---------CCCCCCHHHHHHHHHHHHCCCCEEEEEEECCCCCCCCCCCCHHHHHHHHH-HCCCCHHHHHHHHHHHHH-
T ss_conf             4---------76668999999999997289947999972221026999978389999998-718999999999998864-


Q ss_pred             CCCCCHHHHHHHHCCCCCCCCCHHH-HHHHHHHHH----HHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHH
Q ss_conf             5567212245531475544443056-899997655----20011237631111255666887776524773023464000
Q gi|254780306|r  291 IDVNGEIVGLITYMRTDGVHMSPDA-LEAVRRSIT----SHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKM  365 (837)
Q Consensus       291 ~~~~~~~~GlITYpRTDS~~ls~ea-~~~~r~~i~----~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~  365 (837)
                             .||||||||||++++++. +..+...+.    ..|+.+++. ..+.+.++.++.++||||||||++.      
T Consensus       307 -------~GlITYpRTDS~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~-~~~~~~~~~k~~~~~H~aI~PT~~~------  372 (769)
T PRK07219        307 -------RGLISYPRTDNTVYPRSINLKSVLEKLKKSEYSMYVDEILS-QEKILPSRGRTETTDHPPIYPVSVP------  372 (769)
T ss_pred             -------CCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHC-CCCCCCCCCCCCCCCCCCCCCCCCC------
T ss_conf             -------89544677654225610329999999876467888987414-4556776444442335575646677------


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCC
Q ss_conf             00199999999999999999985222110010013677407963999998748805885676326777632100101488
Q gi|254780306|r  366 KQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLP  445 (837)
Q Consensus       366 ~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP  445 (837)
                      ...|+.||++||+|||+|||||||+||+|++++|.+.+.+    +.|+++|++++|+||++||....       .+..||
T Consensus       373 ~~~Ls~de~klY~LI~~RflAs~m~~a~~~~t~v~i~~~~----~~F~asG~~i~~~Gw~~vy~~~~-------~d~~LP  441 (769)
T PRK07219        373 KEELKGDYKRIYDLILRRFLSTLYRDGVKTVSEAEIDVNG----YDFIAEGNITTDNGWYDIYGYKS-------RDYFVP  441 (769)
T ss_pred             CHHCCHHHHHHHHHHHHHHHHHHCHHHEEEEEEEEEEECC----CEEEEEEEEEEECCHHHHHCCCC-------CCCCCC
T ss_conf             0016999999999999999998480244788999999689----58999989993558798608875-------446589


Q ss_pred             CCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCC
Q ss_conf             64568821100110111234643101789987433210256655157899999732202214771222011420000223
Q gi|254780306|r  446 YISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLE  525 (837)
Q Consensus       446 ~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~  525 (837)
                      .|++|+.+.+.++++.+|+|+||+||||||||++||+.|||||||||+||+||++|+||  ++++|+||++|++|+++|.
T Consensus       442 ~l~~g~~~~~~~~~~~~~~T~PP~ryTEasLIk~ME~~GIGrpSTyA~iI~tL~~R~YV--e~~~l~PT~lG~~v~~~l~  519 (769)
T PRK07219        442 DLEEGEVLNGRDWELQEKETKPPPRYDMSSLLKKMESLNLGTKSTRHDIIGKLISRGFI--EGNPVKPTPLGEAFIDAVI  519 (769)
T ss_pred             CCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCC--CCCCCEECHHHHHHHHHHH
T ss_conf             88889872344788763252799987999999988617998501599999999863875--0897507688999999998


Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEEC
Q ss_conf             36655689889999999999986260134789999867676655766775566677655676641024555567661143
Q gi|254780306|r  526 NFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTC  605 (837)
Q Consensus       526 ~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~C  605 (837)
                      ++|++|++++|||+||++||+|++|+.+|.+||++||..|...+..+... ..++.+.+...+        ..+.....|
T Consensus       520 ~~~~~l~~~~~Ta~~E~~Ld~I~~G~~~~~~vl~e~~~~~~~~~~~~~~~-~~~~~~~~~~~~--------~~~~~~~~c  590 (769)
T PRK07219        520 SVNSRIADPEMTAKLEMDMDKIESGTMSKDDVVNESKKMLHSVLNDFQGK-TSDVKKIINDGI--------NAGESLGRC  590 (769)
T ss_pred             HHCHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHHH--------CCCCCCCCC
T ss_conf             73545339267899999999998489879999999999999999999998-999998875432--------134445777


Q ss_pred             CCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEE--EEEECCCCCEEEECCCCC
Q ss_conf             346777313687157761112343432333210012210000123442014689999669--998269742277348877
Q gi|254780306|r  606 PECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKESV--TLRSGRFGLYVQRGDGKD  683 (837)
Q Consensus       606 p~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~~I--~lk~GryGpYvq~Ge~~k  683 (837)
                      |.|..+.+.++ .+++|.|++|++ |+|+++.++..+..-  +.. +   -.||.||.+|  +.|.|+||..-..+  ++
T Consensus       591 p~~~g~~l~~~-~~~~~~~~~c~~-p~C~~~~~~~~~g~~--~~~-~---~~Cp~Cg~~~ik~~~~g~~~~~~c~~--P~  660 (769)
T PRK07219        591 PFHDGNELFLI-KDRFTYKIRCED-ENCRIDFNIKSNGSI--QLN-D---QKCPVCGLPMIKIIRKGQSPEVKCID--PA  660 (769)
T ss_pred             CCCCCCCEEEE-ECCCCCEEECCC-CCCCCCCCCCCCCCE--EEC-C---CCCCCCCCHHHHEECCCCCCCCCCCC--CC
T ss_conf             65567520465-045550242278-776653335778850--016-8---86878895255012466687740599--98


Q ss_pred             CCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCC-EEEECCEECCCC
Q ss_conf             7613378998842548999999861525515777898749991158765-261678111248
Q gi|254780306|r  684 AKRCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGY-YLNHDGAYTKLE  744 (837)
Q Consensus       684 pkr~si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGp-Yi~~~~~~~sl~  744 (837)
                      .+.     ++.               +-.+|.||+||..++.+.+|+|- |+.|.+ |..+.
T Consensus       661 C~~-----~~~---------------~~~~~~CP~cgg~lv~r~sk~gk~F~gCs~-yP~C~  701 (769)
T PRK07219        661 CDY-----NKE---------------KEDYGECPADGGRLVLRQSRYGKRFLGCSN-YPKCT  701 (769)
T ss_pred             CCC-----CCC---------------CCCCCCCCCCCCEEEEECCCCCCEEECCCC-CCCCC
T ss_conf             878-----778---------------777722889997799863789985651799-99997


No 20 
>PRK07726 DNA topoisomerase III; Provisional
Probab=100.00  E-value=0  Score=1173.37  Aligned_cols=598  Identities=23%  Similarity=0.379  Sum_probs=490.0

Q ss_pred             CCEEEECCHHHHHHHHHHHC-----------------CCCEEEEEECCCEECCCC-------------CCCCCCCCCCCE
Q ss_conf             91899779047877887508-----------------998999942511007865-------------578676667440
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLG-----------------SNYKVLSSFGHIRDLPAK-------------KGSVLPEKEFEM   50 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg-----------------~~y~V~as~GHirdLp~~-------------~~~v~~~~~f~p   50 (837)
                      |+|||+||||+|+.||..||                 ++|.|+||+||+.+|...             .+++.|+. |  
T Consensus         1 M~LiIAEKPsvA~~iA~~l~~~k~~Gy~e~~~~~~~~~~~~vtwa~GHL~~L~~P~~y~~~~k~W~~~~LPiiP~~-f--   77 (716)
T PRK07726          1 MKLIIAEKPDQGLALASQFKYRRKDGYLEVEANELFPNGAYCTWAIGHLTQLCNPEHYHAEWKKWSLDTLPIIPER-F--   77 (716)
T ss_pred             CEEEEEECHHHHHHHHHHCCCCCCCCEEECCCCCCCCCCEEEEEECCCEEECCCHHHHCHHCCCCCHHHCCCCCHH-C--
T ss_conf             9799980889999999862877778737616654238985999971503211685562432065874426877532-2--


Q ss_pred             EEEECCCHHHHHHHHHHHHHHCC--EEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCC
Q ss_conf             68877654899999999987099--8999469970257999999999755125788716999980379899999986226
Q gi|254780306|r   51 IWNIDPSSQKHLQNIIHAVKSST--ILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPR  128 (837)
Q Consensus        51 ~y~v~~~~kk~~~~i~~~~k~a~--~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r  128 (837)
                      .|.+.+++++|++.|++|++++|  +||+|||||||||+|+|||+++++     +++|++|+|||++|++||++||+|++
T Consensus        78 ~~~~~~~~~~q~~~ik~L~~~~dv~~ii~AtD~DREGE~I~~~I~~~~~-----~~kpvkRl~~sslT~~aI~~a~~nl~  152 (716)
T PRK07726         78 QYEVTKSKYKQFNVVKQLLHNPQVTEIIHAGDAGREGELIVRNIINLCN-----VQKPMKRLWISSLTKQAIYQGFKNLL  152 (716)
T ss_pred             EEEECCCHHHHHHHHHHHHHHCCCCEEEEECCCCCCHHHHHHHHHHHHC-----CCCCEEEEEEECCCHHHHHHHHHCCC
T ss_conf             2466746699999999998648999899915887334999999999728-----99974889971389999999997077


Q ss_pred             --CCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHC-----CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEC
Q ss_conf             --46989999999999989874011378988641-----46765342268999999999999641376544001223315
Q gi|254780306|r  129 --DINLDLVNAYLARRALDYLVGFNLSPILWQKL-----PGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLET  201 (837)
Q Consensus       129 --~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~-----~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~  201 (837)
                        +.+++|++|++|||++|||||||+||+++..+     .+.+|+||||||||+|||+||+||++|+|++||+|.+.|..
T Consensus       153 ~~~~~~~L~~aa~aR~~~DwlvG~n~SR~~t~~~~~~g~~~~lS~GRVQTPtL~lIv~Re~eI~~F~p~~y~~i~a~~~~  232 (716)
T PRK07726        153 DESDTINLYYEAYTRSCADWLVGMNASRVYSILLKKKGMNDVFSAGRVQTPTLALIVKREKEIENFKSEPFWEVFATFNI  232 (716)
T ss_pred             CHHHHHHHHHHHHHHHHHHHHHCEECCHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEE
T ss_conf             61333589999999999998717510347788876427767644551111678999999999984899643899999997


Q ss_pred             CCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHH
Q ss_conf             79965422331035833033101135666777642001563010000233222468521037999998876088899999
Q gi|254780306|r  202 PRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTM  281 (837)
Q Consensus       202 ~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm  281 (837)
                       ++..|.++|...     ...++.+++.|+++.+.+.+..+.|.++++++.+.+||+||+||+||++||++|||||++||
T Consensus       233 -~~~~~~~~~~~~-----~~~r~~d~~~a~~i~~~~~~~~~~V~~v~~k~k~~~PP~pf~ls~LQ~~A~~~~g~sa~~Tl  306 (716)
T PRK07726        233 -EGKKYEGKWEKD-----NESRLKDPDMANKIAAFCQGKPAVVKEMKTERKEFQPPLLFNLSSLQATANKAFKFSPKKTL  306 (716)
T ss_pred             -CCEEEEEEEECC-----CCCCCCCHHHHHHHHHHHCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHH
T ss_conf             -891799999527-----76745899999999999648984999998424665899987789999999987298999999


Q ss_pred             HHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCC----CCCCCC-CCCCC-CCCCCCCC--CCCCCE
Q ss_conf             99987621355672122455314755444430568999976552001----123763-11112-55666887--776524
Q gi|254780306|r  282 RIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYG----DHYLPE-KPRIY-SSKSKNAQ--EAHEAI  353 (837)
Q Consensus       282 ~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g----~~~l~~-~~r~y-~~k~k~aQ--eAHeAI  353 (837)
                      ++||+|||        .||||||||||+|||++....++.++..+.+    ..+++. ..... +++..|..  .+||||
T Consensus       307 ~iAQ~LYE--------~glITYPRTDS~~ls~~~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~r~~~~~kv~dH~AI  378 (716)
T PRK07726        307 DITQKLYQ--------KGIVSYPRSDSNYVTQGEAATFPDILQKLSQFDEYKGLLPLPVESIMNNKRYVNEKKVTDHYAI  378 (716)
T ss_pred             HHHHHHHH--------CCCEEECCCCCCCCCHHHHHHHHHHHHHHHCCCCCCHHCCCCCCCHHCCCCCCCCCCCCCCCCC
T ss_conf             99999985--------6962006877764798999999999998535643101034421110014554574555677675


Q ss_pred             EEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCC
Q ss_conf             77302346400000199999999999999999985222110010013677407963999998748805885676326777
Q gi|254780306|r  354 RPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYD  433 (837)
Q Consensus       354 rPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~  433 (837)
                      |||+....+    ..|+.+|++||+|||+|||||||+||+|+.|+|...+.++   ..|+++|++++++||++||.... 
T Consensus       379 iPT~~~~~~----~~Ls~dE~kiY~LI~rRfLA~f~~~a~~~~t~v~~~~~g~---~~F~~~G~~i~~~Gw~~v~~~~~-  450 (716)
T PRK07726        379 IPTEQVTNP----SKLSGDEKKIYDLIVRRLIAAHYEVAIFDYTTIVTLVDER---AEFISKGKQQIQEGWRKVIFQDD-  450 (716)
T ss_pred             CCCCCCCCH----HHCCHHHHHHHHHHHHHHHHHHCCHHEEEEEEEEEEECCC---EEEEEEEEEEEECCHHHHCCCCC-
T ss_conf             774456891----5589999999999999999985850167559999995696---59999522998679798508776-


Q ss_pred             CCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHH-----------------CCCCCCCCHHHHHH
Q ss_conf             6321001014886456882110011011123464310178998743321-----------------02566551578999
Q gi|254780306|r  434 QEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEE-----------------IGIGRPSTYATILE  496 (837)
Q Consensus       434 ~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~-----------------~GIGrPSTyA~II~  496 (837)
                          .+++..||.|++|+.+.+.++++.+++|+||+||||||||++||.                 .|||||||||+||+
T Consensus       451 ----~~~e~~LP~l~~Ge~~~~~~~~~~e~~TkPP~ryTEatLl~aMe~~gk~v~d~el~~~lk~~~GIGTpATRA~IIe  526 (716)
T PRK07726        451 ----KDDETILPIVAEGEEGKVVKVKVKEGKTQPPKRYTEGQLITLMKTAGKYLENEELEKVLKKTEGLGTEATRAGIIT  526 (716)
T ss_pred             ----CCCCCCCCCCCCCCEEEEEEEEEEEECCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCCCHHHHHH
T ss_conf             ----6543448988999987653306642015899987999999999742101387999998754568888410899999


Q ss_pred             HHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             99732202214771222011420000223366556898899999999999862601347899998676766557667755
Q gi|254780306|r  497 TLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLR  576 (837)
Q Consensus       497 ~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~  576 (837)
                      +|++|+||++++++|+||++|+.|++.|...  .|++++|||.||..|++|+.|+.+|.+||++++.-+...++++....
T Consensus       527 ~L~~r~Yi~~~~k~l~pT~~G~~li~~l~~~--~l~~p~~Ta~wE~~L~~I~~G~~~~~~f~~~i~~~~~~~v~~~~~~~  604 (716)
T PRK07726        527 MLKDRKYIDVKKNQVYATDKGKVLIEAIGDK--ILASPEMTAKWEQRLAEIGEGTASPATFMEQTKKLSAKIIEDAVEMS  604 (716)
T ss_pred             HHHHCCCEEECCCEEEECHHHHHHHHHHCHH--HCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             9874571441098751768999999862975--43894789999999999986998999999999999999999998654


Q ss_pred             HHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCC--CCCCCCCCCC
Q ss_conf             666776556766410245555676611433467773136871577611123434--3233321001
Q gi|254780306|r  577 ISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNY--PECKYTRQLT  640 (837)
Q Consensus       577 ~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSny--PeCk~t~~l~  640 (837)
                      ......................+...+.||+|++ .+..     .|.|+|||||  |+|+|+..-.
T Consensus       605 ~~~~~~~~~~~~~~~~~~~~~~~~~ig~CP~Cg~-~v~~-----~~k~~~Cs~y~~~~C~F~i~k~  664 (716)
T PRK07726        605 EKWDFTGLDVESIERKGSKFTTGKKVGSCKKCDG-DVID-----KGTFYGCSNYNTTQCDFTISKK  664 (716)
T ss_pred             HHCCCCCCCHHHHCCCCCCCCCCCCCCCCCCCCC-EEEE-----CCEEEECCCCCCCCCCEEEECE
T ss_conf             3024344331110000343335771665999999-8377-----6758973799899999795134


No 21 
>PRK09401 reverse gyrase; Reviewed
Probab=100.00  E-value=0  Score=1187.21  Aligned_cols=513  Identities=35%  Similarity=0.535  Sum_probs=451.6

Q ss_pred             CEEEECCHHHHHHHHHHHCCC----------C---------EEEEEECCCEECCCCC--CCCCC-CCCCCEEEEECC---
Q ss_conf             189977904787788750899----------8---------9999425110078655--78676-667440688776---
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSN----------Y---------KVLSSFGHIRDLPAKK--GSVLP-EKEFEMIWNIDP---   56 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~----------y---------~V~as~GHirdLp~~~--~~v~~-~~~f~p~y~v~~---   56 (837)
                      -|||||||+||||||.|+|+-          |         .|+||.|||.||+...  .||.. ++.|.|.|..+.   
T Consensus       602 ~L~IVESP~KArTIa~FfGkps~R~~~~~~vyE~~~~d~~L~ItAs~GHv~DL~t~~g~~GV~~~~~~fiPvY~~IkrC~  681 (1176)
T PRK09401        602 ALLIVESPTKARTIANFFGRPSRRRVGGLVVYEVVTGDKILLITASGGHVYDLTTDEGYYGVLVGNGKFVPVYNSIKRCR  681 (1176)
T ss_pred             EEEEEECCCHHHHHHHHCCCCEEEEECCEEEEEEECCCEEEEEEECCCEEEECCCCCCCEEEEEECCEEEEEEHHHHHHH
T ss_conf             69999378058999987189705567887889986186589999537705761455762269963780898416676775


Q ss_pred             ----------------------CHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEC
Q ss_conf             ----------------------5489999999998709989994699702579999999997551257887169999803
Q gi|254780306|r   57 ----------------------SSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNA  114 (837)
Q Consensus        57 ----------------------~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~e  114 (837)
                                            ++.++|+.|++++++||+||||||||||||+|||||+++|+..    +++++|++|||
T Consensus       682 ~cg~qft~~~~~cP~Cgs~~i~dk~~vv~aLR~lA~EvDeVyIATDPDREGEaIAwhl~~~Lk~~----~~~ikRI~FhE  757 (1176)
T PRK09401        682 DCGHQFTDESDRCPRCGSTNIDDKEEIIEALRELALEVDEVLIATDPDTEGEKIAWDVYLLLSPY----NPNIKRIEFHE  757 (1176)
T ss_pred             HCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHHCCEEEECCCCCCCCHHHHHHHHHHHCCC----CCCCEEEEEEC
T ss_conf             35860124666688778887566899999999998755989987899856389999999983554----89833799843


Q ss_pred             CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCE
Q ss_conf             79899999986226469899999999999898740113789886414-67653422689999999999996413765440
Q gi|254780306|r  115 ITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLP-GARSAGRVQSVALRLICNRENQIESFVSEEYW  193 (837)
Q Consensus       115 iT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~-~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~  193 (837)
                      ||++||++||+|||++|+|||+||+|||++||||||+|||+||++++ .+|||||||||||+||||||+||+.   ..||
T Consensus       758 ITk~AI~~Al~npr~Id~nLV~AQ~aRRilDRlVGf~LSp~Lwkk~~~~~LSAGRVQSpaL~lIVERE~E~k~---~~~~  834 (1176)
T PRK09401        758 VTRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLQKRFGKRNLSAGRVQTPVLGWIVERYKEYKK---KKGD  834 (1176)
T ss_pred             CCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCEECHHHHHHCCCCCCCCCCCHHHHHHEEEECHHHHCC---CCCE
T ss_conf             4999999998495116988889999999999881572279999855889998661342411113351534225---3136


Q ss_pred             EEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHH
Q ss_conf             01223315799654223310358330331011356667776420015630100002332224685210379999988760
Q gi|254780306|r  194 SLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRL  273 (837)
Q Consensus       194 ~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~l  273 (837)
                      .+.+.+...  ..+..+           ..+.++++|..+.+.++  .+.|.+++.++.+++|||||+||||||+||++|
T Consensus       835 ~~~~~~~~~--~~~~~~-----------~~~~~~~~a~~~~~~l~--~~~V~~ie~k~~~~~PppPFtTStLqqeAs~kL  899 (1176)
T PRK09401        835 VLVIKLENG--VGLELK-----------GEFEDKEEAKKFYEELK--VVDVEVLEEKEEELNPLPPYTTDTLLSDASRKL  899 (1176)
T ss_pred             EEEEEECCC--CCCCEE-----------EEECCHHHHHHHHHHCC--CCEEEEEEEEEEECCCCCCCCHHHHHHHHHHHC
T ss_conf             988883367--774025-----------66377899999998426--858999860145248988965679999999876


Q ss_pred             CCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCE
Q ss_conf             88899999999876213556721224553147554444305689999765520011237631111255666887776524
Q gi|254780306|r  274 GFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAI  353 (837)
Q Consensus       274 g~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAI  353 (837)
                      ||||++||++||+|||        .||||||||||+++|+++++.++++|.+.||++|+  .||     .+++|+|||||
T Consensus       900 gfSa~kTM~iAQ~LYE--------~GLITYmRTDStrlS~~~i~~ar~yI~~~~G~~y~--~pR-----~~~~q~AHEAI  964 (1176)
T PRK09401        900 GLSAQETMRIAQDLFE--------LGLITYHRTDSTRVSDVGIEVAREYLEKRFGEEYF--VPR-----SWGEGGAHEAI  964 (1176)
T ss_pred             CCCHHHHHHHHHHHHC--------CCEEECCCCCCCCCCHHHHHHHHHHHHHHCCCCCC--CCC-----CCCCCCCCCCC
T ss_conf             9998999999999970--------78033258899866989999999999985081016--757-----67865676785


Q ss_pred             EEEECCCCCCHHC----------CCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEE-EEECC
Q ss_conf             7730234640000----------019999999999999999998522211001001367740796399999874-88058
Q gi|254780306|r  354 RPNDFDFLPSKMK----------QFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGS-LLCFD  422 (837)
Q Consensus       354 rPT~~~~~p~~~~----------~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~-~i~~~  422 (837)
                      |||++ ..|+++.          ..|+.||++||+|||+|||||||.||+++++++.+.+.+.    .|..+|. .++|+
T Consensus       965 RPT~~-~~~e~l~~~i~~~~~~~~~Lt~d~~kLY~LIw~RflASQM~~A~~~~~~v~i~~~~~----~~~~~~~~~i~~~ 1039 (1176)
T PRK09401        965 RPTRP-LDAEELERMIEEGILELSGLTKDHLRLYDLIFRRFIASQMKPAKVKKQKARIKAGGK----EQELELYVEILED 1039 (1176)
T ss_pred             CCCCC-CCHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHHHCCHHHHEEEEEEEEEECCE----EEEEEEEEEEEEC
T ss_conf             78898-986777664410210024799789999999999999975716431589999996896----8999877999877


Q ss_pred             CHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCC
Q ss_conf             85676326777632100101488645688211001101112346431017899874332102566551578999997322
Q gi|254780306|r  423 GFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRK  502 (837)
Q Consensus       423 G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~  502 (837)
                      ||+++|..            .+|.+.+|+.+.+..++..++.|+||  |||||||++||+.|||||||||+||++|++|+
T Consensus      1040 G~~~vy~~------------~l~~~~~g~~~~~~~~~~~~~~t~Pp--YTEAsLIk~MEe~GIGRPSTYAsII~tL~~R~ 1105 (1176)
T PRK09401       1040 GFNLIYPL------------KLYPREEGEGYVVVEKEFYKVPKVPL--YTQGELVEEMKERGIGRPSTYAKIVETLLRRG 1105 (1176)
T ss_pred             CHHHHCCC------------CCCCCCCCCCCCCCCCCCCCCCCCCC--CCHHHHHHHHHHCCCCCCCCHHHHHHHHHCCC
T ss_conf             73875235------------58764567600113110055897789--89899999998279998411688999886389


Q ss_pred             EE-ECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Q ss_conf             02-214771222011420000223366556898899999999999862601347899998676766557
Q gi|254780306|r  503 YV-IAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKID  570 (837)
Q Consensus       503 YV-~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~  570 (837)
                      || +.++++|+||++|+.|++||.++|+++++++|||+||+.||+|++|+.+|.+||++||++|++.++
T Consensus      1106 YVie~k~k~LiPT~lG~~V~~~L~~~F~~lv~~efTa~lE~~LD~Ia~Gk~d~~~vL~efy~el~~~le 1174 (1176)
T PRK09401       1106 YVIESKGKRLIPTKLGIKVYEYLSSRYKDLVSEERTRELEELMDKVEEGEEDYQEVLKELYEEIKELLE 1174 (1176)
T ss_pred             CEEECCCCEECCCHHHHHHHHHHHHHCCHHCCCHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             875278987681168999999999856042295027999986689976996399999999999999984


No 22 
>PRK08173 DNA topoisomerase III; Validated
Probab=100.00  E-value=0  Score=1153.21  Aligned_cols=698  Identities=25%  Similarity=0.387  Sum_probs=531.7

Q ss_pred             CEEEECCHHHHHHHHHHHCC-----------CCEEEEEECCCEECCCC-------------CCCCCCCCCCCEEEEECCC
Q ss_conf             18997790478778875089-----------98999942511007865-------------5786766674406887765
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGS-----------NYKVLSSFGHIRDLPAK-------------KGSVLPEKEFEMIWNIDPS   57 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~-----------~y~V~as~GHirdLp~~-------------~~~v~~~~~f~p~y~v~~~   57 (837)
                      .||||||||+|++|+++||.           +|+|+||+|||++|...             ++.|.|+. |.  +.++++
T Consensus         4 ~LIIAEKPSvAk~IA~~Lg~~~k~~gy~e~~~y~Vtwa~GHL~eL~~Pe~y~~~~~kW~~~~LPiiP~~-f~--l~p~~~   80 (857)
T PRK08173          4 ALIIAEKPSVANDIARALGGFTKHDDYFESDEYVLSSAVGHLLEIAAPEEYEVKRGKWSFAHLPVIPPH-FD--LNPIAK   80 (857)
T ss_pred             CEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCEEEEEECCCCCCCCCCHHCCHHHCCCCHHHCCCCCCC-CE--EEECCC
T ss_conf             299982989999999985887466875047998999754514228980014643345651106878831-32--454333


Q ss_pred             HHHHHHHHHHHHHH--CCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCC--HH
Q ss_conf             48999999999870--998999469970257999999999755125788716999980379899999986226469--89
Q gi|254780306|r   58 SQKHLQNIIHAVKS--STILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDIN--LD  133 (837)
Q Consensus        58 ~kk~~~~i~~~~k~--a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d--~~  133 (837)
                      +++|++.|++|++.  +++||+|||||||||+|+|||+++++     +++|++|+|||++|++||++||+|+|+.+  .+
T Consensus        81 ~~~q~kvi~~L~k~~dv~~II~AtD~DREGElI~~~I~~~~~-----~~kpvkRlw~sslT~~aI~~a~~nlr~~~~~~~  155 (857)
T PRK08173         81 TESRLKVLTKLIKRKDVDRLINACDAGREGELIFRLIAQHAK-----AKKPVQRLWLQSMTPQAIRDGFANLRSDEDMQP  155 (857)
T ss_pred             HHHHHHHHHHHHHHCCCCEEEECCCCCCCHHHHHHHHHHHHC-----CCCCEEEEEEECCCHHHHHHHHHCCCCCHHHHH
T ss_conf             788999999998656999899798898154699999999838-----999858899714899999999966677456689


Q ss_pred             HHHHHHHHHHHHHHHHHHHCHHHHHHCC--C---CCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEE
Q ss_conf             9999999999898740113789886414--6---7653422689999999999996413765440012233157996542
Q gi|254780306|r  134 LVNAYLARRALDYLVGFNLSPILWQKLP--G---ARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFT  208 (837)
Q Consensus       134 Lv~A~~aRr~lD~lvG~~lSp~L~rk~~--~---~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~  208 (837)
                      |++|++|||++|||||||+||+||....  +   .+|+||||||||+|||+||+||++|+|++||.|.+.|...++ .|.
T Consensus       156 L~~Aa~aR~~aDwLvG~N~SRa~T~~~~~~g~~~~lSvGRVQTPtL~lIv~Re~eI~~F~p~~Y~~i~a~f~~~~g-~~~  234 (857)
T PRK08173        156 LADAARCRSEADWLVGINGTRAMTAFNSKGGGFFLTTVGRVQTPTLSIVVEREEKIRRFVPRDYWEVRAEFVAAAG-FYE  234 (857)
T ss_pred             HHHHHHHHHHHHHEEEEEHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECCC-EEE
T ss_conf             9999999987511320340678999876417856667866277888999999999984699755999999972575-035


Q ss_pred             EEEEEECCEE------ECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHH
Q ss_conf             2331035833------0331011356667776420015630100002332224685210379999988760888999999
Q gi|254780306|r  209 AHLTDFNGQR------IEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMR  282 (837)
Q Consensus       209 a~l~~~~~~~------~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~  282 (837)
                      ++|...+-++      ....++++++.|+.+++.|.++..+|+. +.|+.++.||+||+||+||++||++|||||++||+
T Consensus       235 g~~~~~~~~~~~~~~~~~~~rl~d~~~A~~i~~~~~~~~~~V~~-e~K~~~~~pP~lf~Lt~LQ~eAn~~~g~Sa~~TL~  313 (857)
T PRK08173        235 GRWFDPKFKKDEFDPEKRASRLWSLAAAEAIVAACRGKPGTVTE-ESKPSTQLSPLLFDLTSLQREANSRFGFSAKNTLG  313 (857)
T ss_pred             EEEECCCCCCCCCHHHHHHHHHHCHHHHHHHHHHHCCCCEEEEE-EEEECCCCCCCCCCHHHHHHHHHHHCCCCHHHHHH
T ss_conf             57713234544211455554540899999999996389758998-73123678989946899999999854999999999


Q ss_pred             HHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCC-CCC------------CCCCCCCCC-CCCCCCC
Q ss_conf             99876213556721224553147554444305689999765520011-237------------631111255-6668877
Q gi|254780306|r  283 IAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGD-HYL------------PEKPRIYSS-KSKNAQE  348 (837)
Q Consensus       283 iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~-~~l------------~~~~r~y~~-k~k~aQe  348 (837)
                      |||+|||.|       |+||||||||+|||++.++.+++.+..+.+. .|.            ..+.|.|++ |+    .
T Consensus       314 iAQ~LYEkh-------klITYPRTDS~~L~ed~~~~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~kr~~dd~Kv----t  382 (857)
T PRK08173        314 LAQALYEKH-------KVLTYPRTDSRALPEDYLGTVKQTLEMLKESNNYLPHAKQILDKGWVKPNKRIFDNSKI----S  382 (857)
T ss_pred             HHHHHHCCC-------CCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCHHHHHHHHHCCCCCCCCCCCCCCCCC----C
T ss_conf             999986459-------97535787887589899999999999863453104678875223556745555687653----5


Q ss_pred             CCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHH
Q ss_conf             76524773023464000001999999999999999999852221100100136774079639999987488058856763
Q gi|254780306|r  349 AHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVW  428 (837)
Q Consensus       349 AHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy  428 (837)
                      +|||||||..  .|    ..|+++|++||+|||+||||+||+||+|+.|++.+.+.+.    .|+++|++++++||++||
T Consensus       383 dH~AIiPT~~--~p----~~Ls~~E~kiY~LI~rRfLa~f~~~a~~~~t~v~~~v~g~----~F~a~G~vi~~~GW~~vy  452 (857)
T PRK08173        383 DHFAIIPTLQ--AP----KSLSEPEQKLYDLVVKRFLAVFFPAAEFRVTTRITEVAGH----HFKTEGKVLVEPGWLAVY  452 (857)
T ss_pred             CCCCCCCCCC--CC----CCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECCC----EEEEEEEEEEECCHHHHH
T ss_conf             7777377655--64----3189999999999999999973753076668999997797----899998999246879871


Q ss_pred             CCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHH----------------HCCCCCCCCHH
Q ss_conf             26777632100101488645688211001101112346431017899874332----------------10256655157
Q gi|254780306|r  429 ENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKME----------------EIGIGRPSTYA  492 (837)
Q Consensus       429 ~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE----------------~~GIGrPSTyA  492 (837)
                      ....     .+++..||+|++|+.+.+.++++.+++|+||+||||||||++||                +.|||||||||
T Consensus       453 ~~~~-----~~ed~~Lp~l~~Ge~v~~~~~~~~ek~TkPP~ryTEatLl~aME~agk~v~D~elk~~lk~~GiGTpATRA  527 (857)
T PRK08173        453 GKEA-----QGADANLVPVQKGEKVKTDKIAAVALTTKPPARYNEATLLSAMEGAGKLVDDDELREAMAAKGLGTPATRA  527 (857)
T ss_pred             CCCC-----CCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCHHHHHHHHHHHCCCCCCHHHHHHHHHCCCCCCCHHH
T ss_conf             8656-----66546589889999766405675245168998669899999987402334889999998647899851088


Q ss_pred             HHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCC-CCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Q ss_conf             89999973220221477122201142000022336-65568988999999999998626013478999986767665576
Q gi|254780306|r  493 TILETLYKRKYVIAEKRKILPQNTGRIVTAFLENF-FSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDS  571 (837)
Q Consensus       493 ~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~-f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~  571 (837)
                      +||++|++|+||+++|+.|+||++|+.|+++|... .+.+.+|+|||.||..|++|+.|+.++.+||++.+.-....++.
T Consensus       528 ~IIe~L~~r~Yi~r~~k~l~pT~kG~~li~~l~~~~~~~l~spemTa~WE~~L~~Ie~G~~~~~~Fm~~i~~~~~~iv~~  607 (857)
T PRK08173        528 AIIEGLLGEKYLVREGRELIPTAKAFQLMTLLRGLGVKELTSPELTGEWEYKLSQIERGNLSRDAFMQEIAQMTQQIVKR  607 (857)
T ss_pred             HHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHCCCCHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             99999975786996298887876799999986403703205823799999999999859989999999999999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             67755666776556766410245555676611433467773136871577611123434323332100122100001234
Q gi|254780306|r  572 IKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKE  651 (837)
Q Consensus       572 ~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~  651 (837)
                      +.+...        +.+     + .........||+|+ |.+.     .++.+++|+   .|.|+..-......+....-
T Consensus       608 ~k~~~~--------~~~-----~-~~~~~~~~~CP~Cg-~~i~-----~~~k~y~C~---~C~f~i~k~i~gk~l~~~~~  664 (857)
T PRK08173        608 AKEYDS--------DTI-----P-GDYATLQTPCPNCG-GVVK-----ENYRRFACT---KCDFSISKIPGGRQFEIAEV  664 (857)
T ss_pred             HHHHHH--------CCC-----C-CCCCCCCCCCCCCC-CEEE-----ECCCEEECC---CCCEEEEEEECCCCCCHHHH
T ss_conf             985200--------024-----4-42233357888889-5167-----556189779---99778763207836899999


Q ss_pred             CCCCCCCCCCC--CEEEEEECC-CCCEEEECCCCCCCC-CCC-C-C---CCCHHHCCHHHHHHHHHCCHHHCCCCCCCCE
Q ss_conf             42014689999--669998269-742277348877761-337-8-9---9884254899999986152551577789874
Q gi|254780306|r  652 SVLLGNDLETK--ESVTLRSGR-FGLYVQRGDGKDAKR-CSL-P-K---TWKSDSVDYDKAMSLLSLPREIGIHPETQKN  722 (837)
Q Consensus       652 ~~~LG~dP~~G--~~I~lk~Gr-yGpYvq~Ge~~kpkr-~si-~-k---~~~~~~itle~Al~LLsLPr~lG~~pe~g~~  722 (837)
                      ..+|-. -.+|  +-..=|.|+ |-.++.+.+++.... ... + .   +-+-+.++       ++--..||.||-||.+
T Consensus       665 ~~Ll~~-~kt~~ikGF~sK~Gk~F~A~l~L~~d~~~~~k~~fdf~~~~~~~~~~~~~-------~~~~~~lg~CP~C~~~  736 (857)
T PRK08173        665 EELLRK-KEIGPLSGFRSKMGRPFSAILKLSDDETKNYKLEFDFGQDQGGEDGEAVD-------FSAQEPLGACPKCKGR  736 (857)
T ss_pred             HHHHHC-CCCCCCCCCCCCCCCCEEEEEEECCCCCCCCEEEEECCCCCCCCCCCCCC-------CCCCCCCCCCCCCCCC
T ss_conf             999977-98677667526799830179993345566632554136776655566433-------3356636789999982


Q ss_pred             EEEEECCCCC--EEE-ECCEECCCCCCCCCCCCCHHHHHHHHHHHHH
Q ss_conf             9991158765--261-6781112488775143579999999983651
Q gi|254780306|r  723 IIAGTGKYGY--YLN-HDGAYTKLESIEQVLTIDLEQAISCITEKKK  766 (837)
Q Consensus       723 I~~~~GryGp--Yi~-~~~~~~sl~~~~~~~~I~l~~Aieli~~~k~  766 (837)
                      |..+-=-||-  |+. ..+-.+.+.+..==-.|+.+++..||++.+.
T Consensus       737 v~e~~~~y~C~~~~~~~~~C~F~i~k~i~~k~i~~~~~~kLl~~gkT  783 (857)
T PRK08173        737 VFEHGMSYVCEKSVGPPKTCDFRSGKVILQQEISREQMAKLLTDGKT  783 (857)
T ss_pred             EEECCCEEECCCCCCCCCCCEEEECHHHHCCCCCHHHHHHHHHCCCC
T ss_conf             08857456515776889997179556780987899999999975991


No 23 
>PRK09031 DNA topoisomerase III; Provisional
Probab=100.00  E-value=0  Score=1156.27  Aligned_cols=550  Identities=25%  Similarity=0.396  Sum_probs=478.2

Q ss_pred             CCEEEECCHHHHHHHHHHH-------------CCCCEEEEEECCCEECCCC-------------CCCCCCCCCCCEEEEE
Q ss_conf             9189977904787788750-------------8998999942511007865-------------5786766674406887
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYL-------------GSNYKVLSSFGHIRDLPAK-------------KGSVLPEKEFEMIWNI   54 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~L-------------g~~y~V~as~GHirdLp~~-------------~~~v~~~~~f~p~y~v   54 (837)
                      |+||||||||+||+|+++|             |++++|+||+|||.+|...             ++.|.|++ |  .+.+
T Consensus         1 M~LiIAEKPs~Ar~IA~~L~~~~~k~~g~~~~g~g~~Vtw~~GHll~l~~P~~y~~~~k~W~~~~LPiiP~~-~--~~~~   77 (649)
T PRK09031          1 MRLFIAEKPSLGRAIADVLPKPHKKGDGFIECGNGDVVTWCIGHLLEQAEPDAYDPRYKRWNLEHLPIVPEK-W--QLQP   77 (649)
T ss_pred             CEEEEECCHHHHHHHHHHHCCCCCCCCCCEEECCCCEEEEECCCCCCCCCCCCCCHHHCCCCCCCCCCCCHH-C--EEEE
T ss_conf             979998486999999997276650577718847996999955644216771103654256760227857600-1--2224


Q ss_pred             CCCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCC--H
Q ss_conf             76548999999999870998999469970257999999999755125788716999980379899999986226469--8
Q gi|254780306|r   55 DPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDIN--L  132 (837)
Q Consensus        55 ~~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d--~  132 (837)
                      .+++++|++.|++++++||+||||||||||||+|+|||+++++... .++++|+|+|||+||+.||++||+|+|+.+  .
T Consensus        78 ~~~~~~ql~~ik~L~k~ad~ii~AtD~DREGElI~~eil~~~~~~~-~~~~~v~R~~~s~lt~~aI~~A~~~lr~~~~~~  156 (649)
T PRK09031         78 RPSVRKQLTVIKKLLKQADELVHAGDPDREGQLLVDEVLDYLGLSA-EKRQQVQRCLISDLNPQAVKRALDRLRSNREFI  156 (649)
T ss_pred             CCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHCCCC-CCCCCEEEEEECCCCHHHHHHHHHCCCCCHHHH
T ss_conf             6028999999999996299999886887121699999999857342-367865899952588999999997158716678


Q ss_pred             HHHHHHHHHHHHHHHHHHHHCH---HHHHHCC--CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEE
Q ss_conf             9999999999989874011378---9886414--6765342268999999999999641376544001223315799654
Q gi|254780306|r  133 DLVNAYLARRALDYLVGFNLSP---ILWQKLP--GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKF  207 (837)
Q Consensus       133 ~Lv~A~~aRr~lD~lvG~~lSp---~L~rk~~--~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f  207 (837)
                      +|++|++|||.+|||||||+|+   ++||+.+  +.||+||||||||+|||+||+||++|+|++||+|.+.|...++..|
T Consensus       157 ~L~~aa~aR~~~DwliG~n~TRa~tl~~r~~g~~~vlS~GRVQTPtL~lVveRe~eI~~F~p~~y~~i~a~~~~~~~~~f  236 (649)
T PRK09031        157 PLSVSALARARADWLYGINMTRAYTILGRKAGYQGVLSVGRVQTPVLGLVVRRDEEIENFVPKDFFEVKAHIVTPADERF  236 (649)
T ss_pred             HHHHHHHHHHHHHHHHCHHHHHHHHHHHHHCCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCEE
T ss_conf             88999999999998737003189998765416777732443310367899998999984688744899999964899627


Q ss_pred             EEEEEEECCE---EECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             2233103583---3033101135666777642001563010000233222468521037999998876088899999999
Q gi|254780306|r  208 TAHLTDFNGQ---RIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIA  284 (837)
Q Consensus       208 ~a~l~~~~~~---~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iA  284 (837)
                      .++|...+..   ..+.+++.+++.|+.+++.|.+++++|.+|+.++.+++||+||+||+||++||++|||||++||++|
T Consensus       237 ~a~w~~~~~~~~~~de~~r~~~~~~A~~i~~~i~~~~~~V~~v~~k~~k~~pP~Pf~ls~LQ~~Ask~~g~Sa~~tl~ia  316 (649)
T PRK09031        237 TAKWQPSEACEPYQDEEGRVLHRPLAENVVNRITGQPALVTSYNDKREKQSAPLPYSLSALQIDAAKRFGLSAQQVLDIC  316 (649)
T ss_pred             EEEECCCCCCCCCCCHHCCCCCHHHHHHHHHHHHCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHH
T ss_conf             99853531133343312023679999999999608983999986556634898997889999999986299999999999


Q ss_pred             HHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHH--HCCCCCCCCCC---CCCCCCCCCCC--CCCCCEEEEE
Q ss_conf             87621355672122455314755444430568999976552--00112376311---11255666887--7765247730
Q gi|254780306|r  285 QKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITS--HYGDHYLPEKP---RIYSSKSKNAQ--EAHEAIRPND  357 (837)
Q Consensus       285 Q~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~--~~g~~~l~~~~---r~y~~k~k~aQ--eAHeAIrPT~  357 (837)
                      |+|||.|       ||||||||||+|||++++..+..++..  .++.++++...   ...++++.|.+  +||||||||+
T Consensus       317 Q~LYE~~-------~lITYPRTDS~~lp~~~~~~~~~vl~~i~~~~~~~~~~~~~~~~~~k~k~~nd~kv~aH~AIiPT~  389 (649)
T PRK09031        317 QKLYETH-------KLITYPRSDCRYLPEEHFAGRHAVLNAISVHAPELLPQVEVADPDLRNRAWNDKKVDAHHAIIPTA  389 (649)
T ss_pred             HHHHHHC-------CCEECCCCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             9999718-------965016767886797999899999999985128664220114642356666776666888977887


Q ss_pred             CCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCC
Q ss_conf             23464000001999999999999999999852221100100136774079639999987488058856763267776321
Q gi|254780306|r  358 FDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKN  437 (837)
Q Consensus       358 ~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~  437 (837)
                      ....    .+.|+++|++||+|||+||||+||+||+|+.|+|++.+.++    .|.++|++++++||+.+|....++  +
T Consensus       390 ~~~~----~~~Ls~~E~klY~LI~rr~la~~~~~a~~~~t~v~~~~~~~----~F~a~g~~~~~~Gw~~~~~~~~~~--~  459 (649)
T PRK09031        390 KSSN----VNSLTENEAKVYLLIARQYLMQFYPDAVYRKCVIELDIAGG----KFIAKARFLAEAGWKTLLGKKERD--E  459 (649)
T ss_pred             CCCC----HHHCCHHHHHHHHHHHHHHHHHHCCHHEEEEEEEEEEECCC----EEEEEEEEEEECCCHHHCCCCCCC--C
T ss_conf             7789----14489999999999999999984841166238999997897----899987999556607533876665--4


Q ss_pred             CHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHH-----------------HHCCCCCCCCHHHHHHHHHH
Q ss_conf             0010148864568821100110111234643101789987433-----------------21025665515789999973
Q gi|254780306|r  438 SEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKM-----------------EEIGIGRPSTYATILETLYK  500 (837)
Q Consensus       438 ~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~m-----------------E~~GIGrPSTyA~II~~L~~  500 (837)
                      ++....||.|++|+.+.+.++++.+++|+||+||||||||++|                 |..|||||||||+||++|++
T Consensus       460 ~~~~~~LP~l~~g~~l~~~~~~~~~k~T~PP~ryTEatLl~aM~~~~r~v~d~elkk~lke~~GIGTpATrA~IIe~L~~  539 (649)
T PRK09031        460 ENDGTPLPVVAKGQELLCEKGEVVEKQTQPPKHFTDATLLSAMTGIARFVQDKELKKILRETDGLGTEATRAGIIELLFK  539 (649)
T ss_pred             CCCCCCCCCCCCCCEEEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHH
T ss_conf             10136699888999865300034257578979988799999987333234669999874125798871458999999986


Q ss_pred             CCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             22022147712220114200002233665568988999999999998626013478999986767665576677
Q gi|254780306|r  501 RKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKK  574 (837)
Q Consensus       501 R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~  574 (837)
                      |+||.++|+.|+||++|+.|+++|+.   .+.+|+|||.||.+||+|++|+.+|.+||++++..+...|+++..
T Consensus       540 R~Yv~~~gk~l~pT~~G~~Li~~L~~---~~~~p~~TA~wE~~L~~I~~G~~~~~~fm~~~~~~~~~~v~~~~~  610 (649)
T PRK09031        540 RGFLTKKGKYIHSTDAGRALIHSLPE---MATRPDMTAHWESQLTQISEKQCRYQDFMQPLVGTLYQLIDQAKR  610 (649)
T ss_pred             CCCEEECCCEEEECHHHHHHHHHHHH---HCCCCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHH
T ss_conf             78899519889776679999999888---627935699999999999859999999999999999999999860


No 24 
>PRK05776 DNA topoisomerase III; Provisional
Probab=100.00  E-value=0  Score=1153.36  Aligned_cols=561  Identities=29%  Similarity=0.447  Sum_probs=477.8

Q ss_pred             EEEECCHHHHHHHHHHHCC--------------------CCEEEEEECCCEECCCCCCCCCC-CCCCCEEEEECCCH---
Q ss_conf             8997790478778875089--------------------98999942511007865578676-66744068877654---
Q gi|254780306|r    3 VIIVESPAKAKTISKYLGS--------------------NYKVLSSFGHIRDLPAKKGSVLP-EKEFEMIWNIDPSS---   58 (837)
Q Consensus         3 LvIvEsP~kak~I~~~Lg~--------------------~y~V~as~GHirdLp~~~~~v~~-~~~f~p~y~v~~~~---   58 (837)
                      |||||||++||+||++||.                    +|.|+||+|||.+|+....+... +..|.|.|.+.+.+   
T Consensus        11 LiIAEKPsvAk~IA~~Lg~~~~~~~~~~~~~~~~~~~g~~~iVt~~~GHl~~L~~~~~~~p~~~~~w~P~~~~~~~~~~~   90 (675)
T PRK05776         11 LVIAEKPKAAKKIAEALSDKPIRCRKYGVPYWIVTNDGKKIVVAPAAGHLFGLHTDSRGFPVFDYEWKPLWEIDPSAKYT   90 (675)
T ss_pred             EEEECCHHHHHHHHHHHCCCCCCCCCCCCCEEEECCCCCEEEEEEECCEECCCCCCCCCCCCCCCCCCEEEEECCCCHHH
T ss_conf             99989889999999984889631057875313532689828999716673217853004976677877325715652007


Q ss_pred             HHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHH
Q ss_conf             89999999998709989994699702579999999997551257887169999803798999999862264698999999
Q gi|254780306|r   59 QKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAY  138 (837)
Q Consensus        59 kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~  138 (837)
                      +++++.|++++++||+||+|||||||||+|||||+++++     +.+|++|+|||+||+++|++||+||+++|++|++||
T Consensus        91 kk~~~~ik~l~k~ad~viiAtD~DREGE~I~~~I~~~~~-----~~k~v~Rl~fssiT~~~I~~A~~nl~~~d~~l~~A~  165 (675)
T PRK05776         91 KKYYELLSSLSKGASLYVNACDYDIEGSVIGYLIIKFFG-----DEKRAKRMKFSALTKQDIRRAFRNLERLDYEMINAG  165 (675)
T ss_pred             HHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHC-----CCCCEEEEEEEECCHHHHHHHHHCCCCCCHHHHHHH
T ss_conf             899999999870399999878988133899999999828-----998707899964799999999967674447788999


Q ss_pred             HHHHHHHHHHHHHHCHHHHHHCCC------CCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEE
Q ss_conf             999998987401137898864146------76534226899999999999964137654400122331579965422331
Q gi|254780306|r  139 LARRALDYLVGFNLSPILWQKLPG------ARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLT  212 (837)
Q Consensus       139 ~aRr~lD~lvG~~lSp~L~rk~~~------~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~  212 (837)
                      +|||++|||||||+||+||..+..      .+|+||||||||+|||+||+||++|+|++||.|.+.++. ++..|.+++.
T Consensus       166 ~aR~~~D~liG~nlSR~lt~~~~~~~g~~~~lSvGRVQTPtL~lIVeRe~EI~~F~p~~y~~i~~~~~~-~~~~f~~~~~  244 (675)
T PRK05776        166 LARHELDWLWGINVSRALMEAVRDATGKRVILSAGRVQSPTLVEVVEREIERNLFVPLPYYSVSITVEK-GGKEFRLKVG  244 (675)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEE-CCEEEEEEEC
T ss_conf             999999886016540999999752058766311453115999999999999982889534999999981-8878999849


Q ss_pred             EECCEEECCCCHHHHHHHHHHHHHHCCCC-CEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCC
Q ss_conf             03583303310113566677764200156-30100002332224685210379999988760888999999998762135
Q gi|254780306|r  213 DFNGQRIEKKSISNKKEADDLISFVKKAT-YSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGI  291 (837)
Q Consensus       213 ~~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~  291 (837)
                               ..+.++++|+.+++.+.+.. +.|.+|+.++.+.+||+||+||+||++||++|||||++||++||+|||  
T Consensus       245 ---------~~~~~~~ea~~~~~~l~~~~~~~V~~v~~k~k~~~PP~pf~ts~LQ~~Ask~~g~Sa~~tm~iAQ~LYe--  313 (675)
T PRK05776        245 ---------KTFEKKEEAKEIISEIRKKGYLIVVEVEEKDEILRPPPPFNLGDLQKEAARIYGFSPYKTQSIAEELYL--  313 (675)
T ss_pred             ---------CCCCCHHHHHHHHHHHHCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHC--
T ss_conf             ---------987889999999999857997599988850564379899758999999999759889999999999872--


Q ss_pred             CCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHH-----HHCCC--CCCCCCCC-CC-CCCCCCCCCCCCCEEEEECCCCC
Q ss_conf             567212245531475544443056899997655-----20011--23763111-12-55666887776524773023464
Q gi|254780306|r  292 DVNGEIVGLITYMRTDGVHMSPDALEAVRRSIT-----SHYGD--HYLPEKPR-IY-SSKSKNAQEAHEAIRPNDFDFLP  362 (837)
Q Consensus       292 ~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~-----~~~g~--~~l~~~~r-~y-~~k~k~aQeAHeAIrPT~~~~~p  362 (837)
                            .||||||||||++||++.  +++..+.     ..|+.  +.+....+ .+ ..+.+..+.||||||||+.  .|
T Consensus       314 ------~glITYPRTDS~~lp~~~--~~~~~l~~l~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aH~AI~PT~~--~~  383 (675)
T PRK05776        314 ------DALISYPRTNSQKIPPTI--DYRAILDGLSSIKSYRNLVELLLKETKGVLRPVQGSKDDPAHPAIYPTGE--KP  383 (675)
T ss_pred             ------CCCEECCCCCCCCCCCHH--HHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCC--CC
T ss_conf             ------881766887887688233--29999999974254778999875651474222556666777754033756--73


Q ss_pred             CHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHC
Q ss_conf             00000199999999999999999985222110010013677407963999998748805885676326777632100101
Q gi|254780306|r  363 SKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDI  442 (837)
Q Consensus       363 ~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~  442 (837)
                          +.|+.+|++||+|||+|||||||+||+|+.++|.+.+.+  +.+.|.++|++++++||+++|.....      ++.
T Consensus       384 ----~~Ls~de~klY~LI~rRflas~~~~a~~~~t~v~~~~~~--~~~~F~~~g~~i~~~Gw~~v~~~~~~------~~~  451 (675)
T PRK05776        384 ----KNLSKKHMKIYDLIVRRFLASFSRDAIVSKTKVTLRVPD--FDIVFKATGQRIEDKGWLKYYPFSKP------SEE  451 (675)
T ss_pred             ----CCCCHHHHHHHHHHHHHHHHHHCCHHHEEEEEEEEEECC--CCEEEEEEEEEEEECCEEEEECCCCC------CCC
T ss_conf             ----429999999999999999998486310689999999889--73599999799998880255168875------546


Q ss_pred             CCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCC
Q ss_conf             48864568821100110111234643101789987433210256655157899999732202214771222011420000
Q gi|254780306|r  443 LLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTA  522 (837)
Q Consensus       443 ~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~  522 (837)
                      .||.+++|+.+.+.++.+.+++|+||+||||||||++||+.|||||||||+||++|++|+||+.+|++|+||++|+.|++
T Consensus       452 ~LP~l~~G~~~~~~~~~~~e~~TkPP~ryTEatLi~~ME~~GIGTpATra~IIe~L~~R~Yi~~~~~~l~pT~~G~~li~  531 (675)
T PRK05776        452 KLPDLKKGEKLKIVKVSVRMSYTKPPERYTKASLLKWMESVNIGTEATRARIIETLFKRKYLRSKGGKVYATPLGIGVAE  531 (675)
T ss_pred             CCCCCCCCCEEEEEEEEEEECCCCCCCCCCHHHHHHHHHCCCCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHH
T ss_conf             59978999987888747751426999998999999998658999501689999989648969905999987445999999


Q ss_pred             CCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCC
Q ss_conf             22336655689889999999999986260134789999867676655766775566677655676641024555567661
Q gi|254780306|r  523 FLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDS  602 (837)
Q Consensus       523 ~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~  602 (837)
                      +|+++|++|++++|||+||+.||+|+.|+.++.+||+++++.+...++++... ..++.+.        +........+.
T Consensus       532 ~l~~~~~~l~~p~~Ta~~E~~L~~I~~Gk~~~~~f~~e~~~~~~~~v~~~~~~-~~~~~~~--------~~~~~~~~~~~  602 (675)
T PRK05776        532 ILQKYFPDLTSVELTRRFEEKLEKIRSGKERREEVVEEAKKTLRKLLEEFKKN-KDEVGEE--------LAYSLGLIEPP  602 (675)
T ss_pred             HHHHHHHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHH--------HHHHHCCCCCC
T ss_conf             99974365259148999999989998799999999999999999999999863-9988899--------87530255677


Q ss_pred             EECCCCCCC
Q ss_conf             143346777
Q gi|254780306|r  603 RTCPECHTH  611 (837)
Q Consensus       603 ~~Cp~C~~g  611 (837)
                      ++||.||..
T Consensus       603 g~Cp~Cg~~  611 (675)
T PRK05776        603 RKCKLCGRE  611 (675)
T ss_pred             CCCCCCCCH
T ss_conf             889876602


No 25 
>TIGR01056 topB DNA topoisomerase III; InterPro: IPR005738   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 III from bacteria and its equivalent encoded on plasmids. In Escherichia coli, topoisomerase III functions as the principal cellular decatenase, capable of unlinking replicating daughter chromosomes . Topoisomerase III requires single-stranded DNA for binding, so it is more efficient at decatenating chromosomes if the DNA circles contain a small gap. It appears that Topoisomerase III works by removing precatenanes, an alternative form that can be taken by the positive linkages that arise between the daughter chromosomes during replication. Topoisomerase III shows considerable identity to bacterial topoisomerase I, except that it lacks the zinc finger region found in the latter.   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=1026.61  Aligned_cols=593  Identities=27%  Similarity=0.449  Sum_probs=497.6

Q ss_pred             CCEEEECCHHHHHHHHHHH------------------CCCCEEEEEECCCEECCCC--------------CCCCCCCCCC
Q ss_conf             9189977904787788750------------------8998999942511007865--------------5786766674
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYL------------------GSNYKVLSSFGHIRDLPAK--------------KGSVLPEKEF   48 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~L------------------g~~y~V~as~GHirdLp~~--------------~~~v~~~~~f   48 (837)
                      |.||||||||.|+.||.+|                  |.+++||||+||+.+|...              .+.+.|+. |
T Consensus         3 ~~lvLaEKPS~ardlA~vL~~~~kkg~Gyle~sdeqlg~~~~vTWA~GHLve~a~P~~Yd~~Y~~Pw~~~~Lpl~p~~-~   81 (755)
T TIGR01056         3 MRLVLAEKPSQARDLAKVLAKKKKKGNGYLEISDEQLGDGVVVTWAVGHLVELAEPEEYDEKYKKPWRLEDLPLVPEK-W   81 (755)
T ss_pred             CEEEEEECCCHHHHHHHHHCCCCCCCCCCEEEECCCCCCCEEEEEECCCCCCCCCCCHHHHHCCCCCCCCCCCCCCCC-C
T ss_conf             526885176227899998403563788533410010188707985200010244830235660787566655667765-3


Q ss_pred             CEEEEECCCHHHHHHHHHHHHH--HCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHC
Q ss_conf             4068877654899999999987--09989994699702579999999997551257887169999803798999999862
Q gi|254780306|r   49 EMIWNIDPSSQKHLQNIIHAVK--SSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKS  126 (837)
Q Consensus        49 ~p~y~v~~~~kk~~~~i~~~~k--~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n  126 (837)
                      .  .+|.++.++||+.|+++++  ++|+||||||||||||+||..|++.|+...- .+.+|+|+|+|+++++||++||++
T Consensus        82 ~--L~v~~~~~~Qfn~ik~~L~~~~v~evviATDa~REGe~ia~~iL~~~~~~~e-k~~~v~RLw~~~~~~~ai~~A~~~  158 (755)
T TIGR01056        82 K--LVVKKKTKKQFNVIKRLLKEKEVDEVVIATDADREGELIAREILDYLKVRDE-KKVRVKRLWISSLDDKAIRKAFKK  158 (755)
T ss_pred             C--CEECHHHHHHHHHHHHHHHHCCCCEEEECCCCCCHHHHHHHHHHHHHCCCCC-CCEEEEEEEECCCCHHHHHHHHHH
T ss_conf             4--1225137888999997631137572787268863257999999987516856-530578873013787899999985


Q ss_pred             CCCC--CHHHHHHHHHHHHHHHHHHHHHCHHHHHH-----CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE
Q ss_conf             2646--98999999999998987401137898864-----1467653422689999999999996413765440012233
Q gi|254780306|r  127 PRDI--NLDLVNAYLARRALDYLVGFNLSPILWQK-----LPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLL  199 (837)
Q Consensus       127 ~r~~--d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk-----~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~  199 (837)
                      +|.-  .++|+.++.||..+|||||+|+|++++..     +.+.||+||||||||+|||.||.||+||++.+||.|.|.+
T Consensus       159 L~s~~~~~~LY~~a~AR~~ADWLvGiNltR~fT~~gReaG~~~vLsvGRVqtPtL~~v~~Re~~I~~F~~k~fy~v~A~i  238 (755)
T TIGR01056       159 LRSKSETESLYKSAVARARADWLVGINLTRAFTLLGREAGFDGVLSVGRVQTPTLAMVVKREEEIENFVAKPFYEVKATI  238 (755)
T ss_pred             CCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCEEEEEECCCCHHHHHHCCHHHCCCCCCCCCEEEEEEE
T ss_conf             27765421013664324441257765888888888886067875887301664224543002310367587741689998


Q ss_pred             ECCCCCEEEEEEEE---ECCEEECCCCHHHHHHHHHHHHHHCCCC-CEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCC
Q ss_conf             15799654223310---3583303310113566677764200156-3010000233222468521037999998876088
Q gi|254780306|r  200 ETPRNDKFTAHLTD---FNGQRIEKKSISNKKEADDLISFVKKAT-YSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGF  275 (837)
Q Consensus       200 ~~~~~~~f~a~l~~---~~~~~~~~~~~~~~~~a~~~~~~~~~~~-~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~  275 (837)
                      .. ++..|++.|..   ....+.+..|.+++..|+.++..|.+++ +.|.+++.+..+..||++|+||+||++|+++|||
T Consensus       239 ~~-~~~~~~~~w~~sea~~~y~~~~~r~l~~~l~~~~v~~l~~~~tA~v~~~~~~~~~~~AP~~ydLs~LQ~~~~~~fg~  317 (755)
T TIGR01056       239 DK-DEEEFTAEWQPSEAAEQYKDEEERLLHEDLAERVVKDLQQKPTAVVTDLEKERKKESAPLLYDLSALQEDAAKRFGL  317 (755)
T ss_pred             EC-CCEEEEEEECCCHHHHHCCCCHHHHHHHHHHHHHHHHHCCCCCEEEEECHHHCCCCCCCCCCCHHHHHHHHHHHCCC
T ss_conf             55-85165453057043210245013554256899999860489727997112430334788544668999999733388


Q ss_pred             CHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCC--CCCCCC----CCCCCCCCCC--
Q ss_conf             89999999987621355672122455314755444430568999976552001123--763111----1255666887--
Q gi|254780306|r  276 SASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHY--LPEKPR----IYSSKSKNAQ--  347 (837)
Q Consensus       276 sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~--l~~~~r----~y~~k~k~aQ--  347 (837)
                      ||++||+|||+|||.||       |||||||||+|||++..+.+.+.+...-+..+  ++.+..    .+.+...|..  
T Consensus       318 SAk~~L~i~QkLYE~HK-------LiTYPRtDsRYL~~~~~~~l~~~l~~~~~~~~~~~~~q~~~~~~~~~~~~~nD~Kv  390 (755)
T TIGR01056       318 SAKEVLDIAQKLYETHK-------LITYPRTDSRYLPEDEKEELKEVLDALKVKAPALLPSQVKKLDEKIRNRLWNDKKV  390 (755)
T ss_pred             CHHHHHHHHHHHHHCCC-------EEECCCCCCCCCCHHHHHHHHHHHHHHCCCCHHHCCCCHHHCCCHHHCCCCCCCCC
T ss_conf             54579999985420244-------03148876566886554348888765214442331330101262223255675110


Q ss_pred             CCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHH
Q ss_conf             77652477302346400000199999999999999999985222110010013677407963999998748805885676
Q gi|254780306|r  348 EAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKV  427 (837)
Q Consensus       348 eAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~v  427 (837)
                      +|||||+||.-.    ...+.|++.|.+||+||.+||+|.+|+.++|+.|+|++.+.+.    .|.+.|++|...||+++
T Consensus       391 ~dHhAIipT~~~----~~~~~L~e~E~~vY~li~~~yl~~f~p~~~y~~T~i~~~i~k~----~F~~kG~~~~~~Gwkal  462 (755)
T TIGR01056       391 EDHHAIIPTEED----LNLSDLSEEERKVYKLIAKRYLAQFMPKAEYEETKIELEIGKE----LFEAKGKVLQENGWKAL  462 (755)
T ss_pred             CCCCCCCCCCCC----CCHHHHHHHHHHHHHHHHHHHHHHHCCHHHEEEEEEEEEECCC----EEEEEEEEEECCCCHHH
T ss_conf             344413036775----3010001777789999999999873681000036789985586----67874466631551413


Q ss_pred             HCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHH-------------------HCCCCCC
Q ss_conf             326777632100101488645688211001101112346431017899874332-------------------1025665
Q gi|254780306|r  428 WENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKME-------------------EIGIGRP  488 (837)
Q Consensus       428 y~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE-------------------~~GIGrP  488 (837)
                      |.....+++.+.++..||.|..||.+.|...+..+++|+||+||||+|||++|+                   ..||||+
T Consensus       463 l~~~~~deE~~~~~~tLP~~~kg~~~~v~~~~~~~~qT~PP~~y~e~TLL~AM~N~~~f~~Ged~~Lkk~L~e~~GLGT~  542 (755)
T TIGR01056       463 LGKKEEDEEDEDDDTTLPALQKGDELAVEKLELLEKQTKPPARYTEGTLLSAMTNPAAFVQGEDKGLKKTLKETKGLGTE  542 (755)
T ss_pred             CCCCCCCCCCCCCCCCCCHHHCCCEEEEECCEEECCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHCCCCCCC
T ss_conf             07764465568778757410058888752242302467886877626899985106876135436778887523888875


Q ss_pred             CCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf             51578999997322022147712220114200002233665568988999999999998626013478999986767665
Q gi|254780306|r  489 STYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEK  568 (837)
Q Consensus       489 STyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~  568 (837)
                      ||||.||++|++|+|+.++|+.|+.|+.|+.++..|+.+  .+..|++||.||+.|+.||.|+....+||+..-.-..+.
T Consensus       543 ATRAdIIe~L~k~~fl~~~k~~i~~T~~G~~l~~~lpG~--~l~~P~LTA~WE~~L~~ia~g~~~~~~F~~~~~~~~~q~  620 (755)
T TIGR01056       543 ATRADIIEKLFKRGFLEKKKKKIYITKKGKALLQLLPGE--LLTKPDLTAEWEQVLDEIAAGKVKSDDFIKKLKEYVKQL  620 (755)
T ss_pred             CCHHHHHHHHHCCCCEEECCCEEEECHHHHHHHHHCCCC--CCCCCCCCHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             430358888741644266285121167788998745763--467876316899999887435664278899999999999


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCC
Q ss_conf             576677556667765567664102455556766114334677731368715776111234343233
Q gi|254780306|r  569 IDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECK  634 (837)
Q Consensus       569 i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk  634 (837)
                      |++....                .............||.||.  +.++..||.|..+-|..- +|.
T Consensus       621 v~~~~~~----------------~~~~~~~~~~~~~~PeCGk--mmlkvnGkrGtmlvCqdr-ec~  667 (755)
T TIGR01056       621 VKEEKKS----------------PETIQKDAVEPVAVPECGK--MMLKVNGKRGTMLVCQDR-ECG  667 (755)
T ss_pred             HHHHHCC----------------CCEEECCCCCCCCCCCCCC--EEEEECCCCCEEEEEECC-CCC
T ss_conf             9987438----------------5114415788888864254--556760763206786055-467


No 26 
>TIGR01057 topA_arch DNA topoisomerase I; InterPro: IPR005739   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 archaea, which is more closely related to bacterial 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.    More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=1017.61  Aligned_cols=585  Identities=32%  Similarity=0.498  Sum_probs=488.7

Q ss_pred             EECCHHHHHHHHHHHCCC----------------------CEEEEEECCCEECCCCCC---CCCC--CCCCCEEEEECCC
Q ss_conf             977904787788750899----------------------899994251100786557---8676--6674406887765
Q gi|254780306|r    5 IVESPAKAKTISKYLGSN----------------------YKVLSSFGHIRDLPAKKG---SVLP--EKEFEMIWNIDPS   57 (837)
Q Consensus         5 IvEsP~kak~I~~~Lg~~----------------------y~V~as~GHirdLp~~~~---~v~~--~~~f~p~y~v~~~   57 (837)
                      |||||+.|++||..|+++                      -+|.+|+||+.-|.++.-   +.-|  |=.|.|.|+.+.+
T Consensus         1 iaEKP~~A~KIA~AL~~~~G~~kks~~gVpYye~~rdGk~i~vasavGHLfgL~~~~~k~Fg~~PvFD~eW~Pi~~~dkg   80 (637)
T TIGR01057         1 IAEKPKVAKKIAGALSDDRGVLKKSLYGVPYYEVVRDGKKIIVASAVGHLFGLAPKSRKVFGEYPVFDIEWVPIFEIDKG   80 (637)
T ss_pred             CCCCCHHHHHHHHHCCCCCCCEEECCCCCCEEEEEECCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCC
T ss_conf             98871158999862056777302116875407898779179985153315688865554358877321123305676067


Q ss_pred             H---HHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCC-CCCHH
Q ss_conf             4---8999999999870998999469970257999999999755125788716999980379899999986226-46989
Q gi|254780306|r   58 S---QKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPR-DINLD  133 (837)
Q Consensus        58 ~---kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r-~~d~~  133 (837)
                      +   ++.++.|++++++|++-|+|||.|-|||.||||++++..   ..+....+||.||+||+..|++|++||- .+|..
T Consensus        81 kgY~~~Y~~~L~~l~~~a~~y~~AcDYDiEG~lIGf~alky~C---g~~~~~A~RMkFStLt~~di~rAy~n~e~~~dyg  157 (637)
T TIGR01057        81 KGYVKKYIKALSKLAKGADEYIVACDYDIEGELIGFKALKYAC---GVEKLKAKRMKFSTLTKKDIRRAYKNPEIEIDYG  157 (637)
T ss_pred             CHHHHHHHHHHHHHCCCCCEEEEEEEECCCCCCHHHHHHHHHC---CCCCHHCCCCCCCCCCHHHHHHHHHCCCCEECHH
T ss_conf             1368999999998512354356762103565307678987508---8640001334300023799999973889443032


Q ss_pred             HHHHHHHHHHHHHHHHHHHCHHHHHHC---CCC---CCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEE
Q ss_conf             999999999989874011378988641---467---65342268999999999999641376544001223315799654
Q gi|254780306|r  134 LVNAYLARRALDYLVGFNLSPILWQKL---PGA---RSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKF  207 (837)
Q Consensus       134 Lv~A~~aRr~lD~lvG~~lSp~L~rk~---~~~---lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f  207 (837)
                      ||||+.||++|||++|.|||++|+..+   .+.   |||||||||||+++|+||+||+.|+|.|||-|.+.|.. +|+.|
T Consensus       158 ~v~AG~ARhiLDw~fGvN~SRALm~A~r~a~gr~v~LS~GRVQ~PtL~~l~eRe~EI~~F~P~pywvi~~~~~~-gG~~~  236 (637)
T TIGR01057       158 MVDAGAARHILDWYFGVNLSRALMEAIRAAAGRWVILSAGRVQGPTLAFLVEREREIKKFVPKPYWVIKALLEK-GGGVF  236 (637)
T ss_pred             HHCCCCHHHHHHHHHHHHHHHHHHHHHHHHHCCEEEEECCCCCCHHHHHHHHHHHHHHCCCCCCEEEEEEEEEC-CCCEE
T ss_conf             21113056777888534287899999999729989995176520799999988999852899830267785406-88558


Q ss_pred             EEEEEEECCEEECCCCHHHHHHHHHHHHHHCCC-CCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             223310358330331011356667776420015-6301000023322246852103799999887608889999999987
Q gi|254780306|r  208 TAHLTDFNGQRIEKKSISNKKEADDLISFVKKA-TYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQK  286 (837)
Q Consensus       208 ~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~-~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~  286 (837)
                      .|..        ++..++++++|..|.+.|+++ .+.|.+|+.+..+++||+||+|.|||+||++.|||||++|+.|||+
T Consensus       237 ~A~~--------~~~K~~~~e~a~~i~~~~~~~~~~~V~~v~~~~~~~~PP~pFdLGtLQ~EAy~~fG~sPk~Tq~IAq~  308 (637)
T TIGR01057       237 KAES--------EKEKIWKEEEAKSILEEVKKSKSAKVEEVRVKRSILKPPPPFDLGTLQREAYRVFGFSPKKTQEIAQE  308 (637)
T ss_pred             EEEC--------CCCCCCHHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCCCCCHHHHHHHHHCCCCCHHHHHHHHH
T ss_conf             7522--------57874124655568886167988423324553111683259875525899998607996446899999


Q ss_pred             HHCCCCCCCHHHHHHHHCCCCCCCCCHHH--HHHHHHHHHH--HCCC--CCCC---C--CCCCCCCCCCCCCCCCCCEEE
Q ss_conf             62135567212245531475544443056--8999976552--0011--2376---3--111125566688777652477
Q gi|254780306|r  287 LYEGIDVNGEIVGLITYMRTDGVHMSPDA--LEAVRRSITS--HYGD--HYLP---E--KPRIYSSKSKNAQEAHEAIRP  355 (837)
Q Consensus       287 LYE~~~~~~~~~GlITYpRTDS~~ls~ea--~~~~r~~i~~--~~g~--~~l~---~--~~r~y~~k~k~aQeAHeAIrP  355 (837)
                      ||+        .||||||||+|+-|+++-  ...+.+++++  .||.  +.|-   .  +|.. .+|-   ..||+||+|
T Consensus       309 LY~--------~al~SYPRT~SQKLP~~i~Y~~il~nLakn~P~yr~~~e~L~~~G~~LkPve-GkKe---DpAHPAIhp  376 (637)
T TIGR01057       309 LYE--------EALISYPRTSSQKLPKSINYRKILKNLAKNNPLYREYAERLLEKGGELKPVE-GKKE---DPAHPAIHP  376 (637)
T ss_pred             HHH--------CCCCCCCCCCCCCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHCCCCCCCCC-CCCC---CCCCCCCCC
T ss_conf             864--------2351588787667888778799999997248984689999871678878857-8779---667886005


Q ss_pred             EECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHH-CCCCCC
Q ss_conf             3023464000001999999999999999999852221100100136774079639999987488058856763-267776
Q gi|254780306|r  356 NDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVW-ENQYDQ  434 (837)
Q Consensus       356 T~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy-~~~~~~  434 (837)
                      ||.  .|.+  +.||.||.+|||||++||||.||.+|+.+..+|.|....+   ..|.+||..+...||+++| ..... 
T Consensus       377 tG~--~P~~--G~LSk~e~~vYdLIvrRfLA~F~~~Ai~~~~~V~l~~~~G---~~F~~sG~Rv~k~GWl~~YG~Y~k~-  448 (637)
T TIGR01057       377 TGE--IPSE--GELSKDEKKVYDLIVRRFLAVFSEEAIREKLKVELRIGEG---EKFKLSGKRVVKKGWLEVYGKYSKF-  448 (637)
T ss_pred             CCC--CCCC--CCCCHHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEEECCC---EEEEECCCCEEECCCCCCCCCCCCC-
T ss_conf             678--8888--8777788999989987887511510214334378982387---0698415612103630017666888-


Q ss_pred             CCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEEC
Q ss_conf             32100101488645688211001101112346431017899874332102566551578999997322022147712220
Q gi|254780306|r  435 EKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQ  514 (837)
Q Consensus       435 ~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT  514 (837)
                           ++..||+|..||.+.|..|.+..+.||||.||++||||++||..||||.||||.||+||.+||||+- ++++-.|
T Consensus       449 -----~e~~lPel~~Gd~~~V~~v~~~~~~t~pP~Ry~~ASlir~lE~~glGTkaTRA~Ii~~Ly~RgY~eG-~~~~~Vt  522 (637)
T TIGR01057       449 -----EEKELPELKRGDKIKVVRVKVEKKETKPPARYDKASLIRELEKRGLGTKATRAEIIEKLYKRGYIEG-KKSIKVT  522 (637)
T ss_pred             -----CCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHCCCEEEC-CCEEEEC
T ss_conf             -----8754888888886899998864540686876657789899872588841038999998711731541-8634652


Q ss_pred             CHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCC
Q ss_conf             11420000223366556898899999999999862601347899998676766557667755666776556766410245
Q gi|254780306|r  515 NTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDTLSSVIFP  594 (837)
Q Consensus       515 ~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~  594 (837)
                      |||..|++.|+.+||+|++.++|.++|.+|.+|-.|+.++.+|+++--..+...+++..+. ..++...+...    .-.
T Consensus       523 PLG~~vi~tl~~y~peii~~~LTR~fE~~lE~I~~Gr~~k~~Videa~~~~~kiLe~f~~~-~~~ig~el~~~----~~~  597 (637)
T TIGR01057       523 PLGEAVIETLKRYCPEIISEELTREFEKKLEDIMSGRITKDEVIDEAKKRLRKILEEFKKR-LEDIGIELAKS----LDS  597 (637)
T ss_pred             CCHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHHHHHHHHH-HHHHHHHHHHH----HCC
T ss_conf             4505899999873410068132389999988875078666789999899999988999988-99998998887----312


Q ss_pred             CC-CCCCCCEECCCCCCCCEEEEEECCC-CCCCCCCCCCCC
Q ss_conf             55-5676611433467773136871577-611123434323
Q gi|254780306|r  595 PK-ENNEDSRTCPECHTHSLSLKLSSKY-GAFVGCTNYPEC  633 (837)
Q Consensus       595 ~~-~~~~~~~~Cp~C~~g~L~~k~~gK~-G~FigCSnyPeC  633 (837)
                      .. ....+...||+||. .|.++...++ ..|+||||||+|
T Consensus       598 ~~e~K~~vvg~CP~CGG-~lv~ky~~~~~~rFvgCS~yp~c  637 (637)
T TIGR01057       598 SEEKKAKVVGKCPKCGG-KLVVKYAKKGRKRFVGCSNYPEC  637 (637)
T ss_pred             CCCCCCEEEECCCCCCC-CEEEEEECCCCCEEECCCCCCCC
T ss_conf             23324505523778887-34898606888412115788899


No 27 
>pfam01131 Topoisom_bac DNA topoisomerase. This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.
Probab=100.00  E-value=0  Score=856.11  Aligned_cols=397  Identities=42%  Similarity=0.605  Sum_probs=355.2

Q ss_pred             CCHHHHHHHHHHHHHHHHHHHHHCHHHHHHC-CCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEE
Q ss_conf             6989999999999989874011378988641-467653422689999999999996413765440012233157996542
Q gi|254780306|r  130 INLDLVNAYLARRALDYLVGFNLSPILWQKL-PGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFT  208 (837)
Q Consensus       130 ~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~-~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~  208 (837)
                      .|+|||+||+|||++|||||||+||+||++. .+++|+||||||||+|||+||+||++|+|++||.|.+.|....+. +.
T Consensus         2 ~d~nL~~A~~aR~~~D~lvG~n~Sr~~t~~~~~~~lS~GRVQtPtL~lIv~Re~eI~~F~p~~y~~i~~~~~~~~~~-~~   80 (403)
T pfam01131         2 EDENLVDAQEARRILDRLIGFNLSRALTLKGNKKVLSAGRVQTPTLGLIVEREKEIKNFVPEPYWTVEATLGKDEFA-AG   80 (403)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCCCC-CC
T ss_conf             88789999999999999972765499997248999753633889999999999999839995439999999768751-00


Q ss_pred             EEEEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             23310358330331011356667776420015630100002332224685210379999988760888999999998762
Q gi|254780306|r  209 AHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLY  288 (837)
Q Consensus       209 a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LY  288 (837)
                      .         ....+|.++++|+.+++.+++..+.|.+|+.++.+.+||+||+|++||++||++|||||++||++||+||
T Consensus        81 ~---------~~~~~~~~~~~a~~~~~~~~~~~~~v~~v~~~~~~~~pP~pf~ls~Lq~~a~~~~g~s~~~tm~iaQ~LY  151 (403)
T pfam01131        81 K---------DEEGRFFDKEEAEAIVEKIKGKTATVKSVEKKEKKEPPPLPFNTSTLQKEASRKLGFSAKKTMDIAQKLY  151 (403)
T ss_pred             C---------CCCCCCCCHHHHHHHHHHHCCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHH
T ss_conf             2---------3347769999999999986489859999876577506999857799999998753878999999999988


Q ss_pred             CCCCCCCHHHHHHHHCCCCCCCCCHHH-HHHHHHHHHHHCCCCCCCCCCCCCCCCCCC-CC-CCCCCEEEEECCCCCCHH
Q ss_conf             135567212245531475544443056-899997655200112376311112556668-87-776524773023464000
Q gi|254780306|r  289 EGIDVNGEIVGLITYMRTDGVHMSPDA-LEAVRRSITSHYGDHYLPEKPRIYSSKSKN-AQ-EAHEAIRPNDFDFLPSKM  365 (837)
Q Consensus       289 E~~~~~~~~~GlITYpRTDS~~ls~ea-~~~~r~~i~~~~g~~~l~~~~r~y~~k~k~-aQ-eAHeAIrPT~~~~~p~~~  365 (837)
                      |        .||||||||||++||+++ +..+++.|.+.||.++++..+....++..+ +| +||||||||+..  +.  
T Consensus       152 E--------~glITYpRTDs~~ls~~~~~~~~~~~l~~~~~~~~~~~~~~~~~~~~~~~~k~~aH~AI~PT~~~--~~--  219 (403)
T pfam01131       152 E--------KGLITYPRTDSTYLSEDAELAAILEYLAKRFGEEYLPYAPKLVKPKSPGNAKVGAHEAIRPTGPI--PR--  219 (403)
T ss_pred             H--------CCCEEECCCCCCCCCCHHHHHHHHHHHHHHCCHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCC--CC--
T ss_conf             6--------58345347676527825579999999984113533233000024777665556788752036777--75--


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCC
Q ss_conf             00199999999999999999985222110010013677407963999998748805885676326777632100101488
Q gi|254780306|r  366 KQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLP  445 (837)
Q Consensus       366 ~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP  445 (837)
                      ...|+.+|++||+|||+|||||||+||+|++++|.+.+.+    ..|+++|++++++||++||....      +++..+|
T Consensus       220 ~~~ls~~e~~iY~LI~~r~las~~~~a~~~~~~v~~~~~~----~~F~~~g~~~~~~Gw~~v~~~~~------~~~~~~p  289 (403)
T pfam01131       220 LPELSDDERKLYDLIVRRFLASQMPPAVYEETKVELEVGG----EEFKASGKVLLEPGWKKVYPYSK------DEDEEPP  289 (403)
T ss_pred             CCCCCHHHHHHHHHHHHHHHHHHCCHHEEEEEEEEEEECC----EEEEEEEEEECCCCHHHHHCCCC------CCCCCCC
T ss_conf             2329999999999999999998385224778999999899----79999989972576787616775------4444486


Q ss_pred             CCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCC-CCEEECCHHHHHCCCC
Q ss_conf             645688211001101112346431017899874332102566551578999997322022147-7122201142000022
Q gi|254780306|r  446 YISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEK-RKILPQNTGRIVTAFL  524 (837)
Q Consensus       446 ~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~-~~l~pT~~G~~v~~~L  524 (837)
                      .+++|+.+.+.++++.+++|+||+||||||||++||+.|||||||||+||++|++|+||.+++ ++|+||++|+.|+++|
T Consensus       290 ~~~~g~~~~~~~~~~~~~~T~PP~ryTe~sLi~~Me~~GIGtpATra~iI~~L~~R~Yi~~~k~k~l~pT~~G~~li~~l  369 (403)
T pfam01131       290 ELKEGEELTVQKVELEEKKTKPPPRYTEASLIKAMEKRGIGTPATRASIIETLLERGYVERKKNKRLVPTDLGRALIDAL  369 (403)
T ss_pred             CCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEECCCCEEEECHHHHHHHHHH
T ss_conf             41368679875778764204798765899999999857999602389999999858949974897780537899999987


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             33665568988999999999998626013478999
Q gi|254780306|r  525 ENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLH  559 (837)
Q Consensus       525 ~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~  559 (837)
                      + .|++|++|+|||.||..||+|++|+.+|.+||+
T Consensus       370 ~-~~~~l~~~~~Ta~~E~~Ld~I~~G~~~~~~~l~  403 (403)
T pfam01131       370 P-RFPDLVSPELTARLEETLDEIARGEKDYEDVLD  403 (403)
T ss_pred             H-CCCHHCCHHHHHHHHHHHHHHHCCCCCHHHHCC
T ss_conf             4-413106977899999999999869998888259


No 28 
>KOG1956 consensus
Probab=100.00  E-value=0  Score=825.57  Aligned_cols=678  Identities=27%  Similarity=0.384  Sum_probs=540.2

Q ss_pred             CEEEECCHHHHHHHHHHHCCC---------------------------CEEEEEECCCEEC--CCC---CCCCCCCCCC-
Q ss_conf             189977904787788750899---------------------------8999942511007--865---5786766674-
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSN---------------------------YKVLSSFGHIRDL--PAK---KGSVLPEKEF-   48 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~---------------------------y~V~as~GHirdL--p~~---~~~v~~~~~f-   48 (837)
                      .|.++|+++.||.++..|+.+                           -.+++..||+..|  |..   ..+..+..-| 
T Consensus         3 vl~vAekn~~ak~va~il~~g~~~~re~rSk~~kiy~f~~~~~g~~~~~~mtsvsghl~~~~f~~~~s~w~s~~~~~lf~   82 (758)
T KOG1956           3 VLCVAEKNSIAKSVASILSGGTVRRREGRSKYNKIYDFDFNLFGQNCDVTMTSVSGHLTEADFPSEYSKWQSCPPDELFD   82 (758)
T ss_pred             CCCCCCCCHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCCCCEEECCHHHHHH
T ss_conf             31113241566543000379976776540224443200044307753257752145555667744566402468899863


Q ss_pred             CEEEE-ECCCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCC
Q ss_conf             40688-77654899999999987099899946997025799999999975512578871699998037989999998622
Q gi|254780306|r   49 EMIWN-IDPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSP  127 (837)
Q Consensus        49 ~p~y~-v~~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~  127 (837)
                      .|.+. +..+.+++-+.|+++++.||.+|||||||||||+|||||.++++..+.  ...|.|++||+||+.+|..|+.||
T Consensus        83 a~~~~~~~~~~~~i~~~ir~eAr~ad~LviwtDcDREGE~Ig~eI~~v~~~~~~--~~~V~RA~Fs~it~~~I~sA~~nl  160 (758)
T KOG1956          83 APVIKSVPENAKDIAKTIREEARRADYLVIWTDCDREGENIGWEIIDVCRAVKR--LLQVRRARFSEITRSAIKSAARNL  160 (758)
T ss_pred             HHHHHCCCHHHHHHHHHHHHHHHHCCEEEEECCCCCCCHHHHHHHHHHHHHHCC--CCEEEHHHHHCCCHHHHHHHHHCC
T ss_conf             004413846666788899999742665999526885420464999999986074--213201244014699999998483


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHH--HH--HCHHHHHHCC----CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEE
Q ss_conf             6469899999999999898740--11--3789886414----67653422689999999999996413765440012233
Q gi|254780306|r  128 RDINLDLVNAYLARRALDYLVG--FN--LSPILWQKLP----GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLL  199 (837)
Q Consensus       128 r~~d~~Lv~A~~aRr~lD~lvG--~~--lSp~L~rk~~----~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~  199 (837)
                      |++|+++|+|..||++||+++|  ||  .|++|||+++    +..|+|+||.|||+|||||+.||++|+|++||+|....
T Consensus       161 reid~~~v~AvdaR~ELDlrIGa~FTRlqT~~L~r~f~~~~~~viSyG~cQfpTLgfVvdR~~eIe~FvPEefWtl~~~~  240 (758)
T KOG1956         161 REIDEKLVHAVDARIELDLRIGAAFTRLQTLLLRRKFPILGEQVISYGPCQFPTLGFVVDRYKEIENFVPEEFWTLKFKH  240 (758)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCCEEEEEEHHHHHHCCCCCCEEEEEEEE
T ss_conf             44426778888888887777545677777299986515652666544655676222220359887635875127998999


Q ss_pred             ECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCC-CCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHH
Q ss_conf             1579965422331035833033101135666777642001-563010000233222468521037999998876088899
Q gi|254780306|r  200 ETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKK-ATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSAS  278 (837)
Q Consensus       200 ~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~  278 (837)
                      ..+      +.++.++.++   ++++|..-+.-+.+.|.. ..++|.++.+|++++.||.|++|++||+.|+++|.||++
T Consensus       241 ~~~------~~~~~fnw~R---~~lfdr~s~~~~~e~c~e~k~a~Vv~~~kkpktKyrP~pl~TvELqK~~s~~lrlSak  311 (758)
T KOG1956         241 THK------GGLTEFNWKR---GHLFDRLSVVILYEICVEEKEATVVKVTKKPKTKYRPLPLDTVELQKLASRKLRLSAK  311 (758)
T ss_pred             ECC------CCEEEEEECC---CCCCCHHHHHHHHHHHHCCCCEEEEECCCCCCCCCCCCCCHHHHHHHHHHHHEECCHH
T ss_conf             625------7626776031---3410178899999987426430687435477667899764089987653554631178


Q ss_pred             HHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHH-HHHHHHHHH--HHCC---CCCCC---CCCCCCCCCCCCCCCC
Q ss_conf             9999998762135567212245531475544443056-899997655--2001---12376---3111125566688777
Q gi|254780306|r  279 HTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDA-LEAVRRSIT--SHYG---DHYLP---EKPRIYSSKSKNAQEA  349 (837)
Q Consensus       279 ~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea-~~~~r~~i~--~~~g---~~~l~---~~~r~y~~k~k~aQeA  349 (837)
                      +||+||.+||.        .|+|+||||..-..+.+. +..+.....  ..||   ...+.   ..||.    .++..+|
T Consensus       312 ~TM~iAE~ly~--------~gfisyprtetd~F~s~~~lk~lv~~qt~~~~wg~yA~~ll~~~~r~Prn----g~~~d~A  379 (758)
T KOG1956         312 HTMKIAEKLYQ--------KGFISYPRTETDNFPSDMDLKALVEKQTQDPAWGSYAQRLLQPENRNPRN----GKHNDKA  379 (758)
T ss_pred             HHHHHHHHHHH--------CCCEECCCCCCCCCCCCCCHHHHHHHHCCCCHHHHHHHHHHCCCCCCCCC----CCCCCCC
T ss_conf             89999999985--------66150242236668876863888876546814678888751568889887----7654446


Q ss_pred             CCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHC
Q ss_conf             65247730234640000019999999999999999998522211001001367740796399999874880588567632
Q gi|254780306|r  350 HEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWE  429 (837)
Q Consensus       350 HeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~  429 (837)
                      |+.|+||-+.-    -...++.|+++||+||.+||+||...+|+...|+|++....+    .|.++|..++..+|+.||.
T Consensus       380 hppihp~k~~s----~~~~~s~d~~~vye~v~rhflAc~S~dakg~et~vel~~~~E----~F~asgl~vl~~NyldVy~  451 (758)
T KOG1956         380 HPPIHPTKFTS----REANLSGDHRKVYELVVRHFLACCSQDAKGAETTVELDIAQE----RFSASGLRVLERNYLDVYP  451 (758)
T ss_pred             CCCCCCEEECC----CCCCCCCCHHHHHHHHHHHHHHHHCCCCCCCCEEEEEEEHHH----HCCCCCCCHHHCCCCCCCC
T ss_conf             89746411025----002578641789999999877763421346605999860203----0055545144326643333


Q ss_pred             CCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCC-
Q ss_conf             6777632100101488645688211001101112346431017899874332102566551578999997322022147-
Q gi|254780306|r  430 NQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEK-  508 (837)
Q Consensus       430 ~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~-  508 (837)
                      ...++      +..||.++.|+.+....++..++.|+||++||||+||+.||+.||||+||+|++|++||+|+||.+.. 
T Consensus       452 yekwe------~k~Lp~y~~ge~fq~~~lem~~g~T~~P~~ltEaeLI~lMdk~GIGtdAT~aehi~kiq~R~Yv~~~~~  525 (758)
T KOG1956         452 YEKWE------DKQLPVYEDGELFQPGELEMKDGETSPPKYLTEAELISLMDKNGIGTDATIAEHIEKIQERGYVTKKNK  525 (758)
T ss_pred             CCCCC------CCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHCCEEEECC
T ss_conf             22126------654763026662145247713676589986587999999987289973169999999886041455345


Q ss_pred             -CCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_conf             -7122201142000022336655689889999999999986260134789999867676655766775566677655676
Q gi|254780306|r  509 -RKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEKIDSIKKLRISNVLDILNDT  587 (837)
Q Consensus       509 -~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~i~~~~~~~~~~v~d~l~~~  587 (837)
                       .+|+||.+|.+|+++++..+-++-+|+|+|.||.+|+.|+.|..+|..||.+.|..|......+...     ...+.+.
T Consensus       526 ~~~~~P~~lg~aLv~gyd~~g~e~sKp~lra~mE~~Lk~Is~G~~~k~~vl~~~v~kyra~f~~~~~~-----~~~l~~~  600 (758)
T KOG1956         526 VGRFVPTFLGVALVEGYDDMGLEMSKPFLRAEMEVDLKNISDGRKDKKEVLRDIVTKYRAYFHETERK-----IGCLGES  600 (758)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHH-----HHHHHHH
T ss_conf             43107328889998767764112078677888987788742671018889999999999999999999-----9999999


Q ss_pred             HHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEE
Q ss_conf             64102455556766114334677731368715776111234343233321001221000012344201468999966999
Q gi|254780306|r  588 LSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKESVTL  667 (837)
Q Consensus       588 ~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~~I~l  667 (837)
                      +.-......                     ..-+|     ..-|+                 .++..+|-++.++.+|..
T Consensus       601 l~~y~~~~a---------------------~~~~~-----~~~p~-----------------~~Pp~~~l~~s~~~~v~p  637 (758)
T KOG1956         601 LQRYLEFIA---------------------STLTG-----PDDPE-----------------GEPPLLGLEGSTSEKVGP  637 (758)
T ss_pred             HHHHHHHCC---------------------CCCCC-----CCCCC-----------------CCCCCCCCCCCCCCCCCC
T ss_conf             999986324---------------------55668-----88888-----------------899888777887886587


Q ss_pred             EECCCCCEEEECCCCCCCCCCCCCCCC------HHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEEECCEEC
Q ss_conf             826974227734887776133789988------42548999999861525515777898749991158765261678111
Q gi|254780306|r  668 RSGRFGLYVQRGDGKDAKRCSLPKTWK------SDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNHDGAYT  741 (837)
Q Consensus       668 k~GryGpYvq~Ge~~kpkr~si~k~~~------~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~~~~~~~  741 (837)
                      +-||||+|+|+|.   .+|.+||+.++      ...+|++-|+++|..|.+.| ||+.|.++...--+-|..+++..+-.
T Consensus       638 ~cgp~p~y~~~~~---~~rg~ipp~~~~g~~~~~~~~t~~~~~~~l~~~~tn~-~p~~~~~~~~~psk~~a~~~~~p~~a  713 (758)
T KOG1956         638 KCGPKPVYRQLGK---FKRGGIPPAANAGHPKDANSITGRSALNLLRGSMTNG-HPKPGQPVVLKPSKSGATIKSRPTAA  713 (758)
T ss_pred             CCCCCCCCEECCC---CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCC
T ss_conf             8999886334254---6778989888889855465065141587741533569-99998655677545654204784335


Q ss_pred             CCCCCCCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             24887751435799999999836511344
Q gi|254780306|r  742 KLESIEQVLTIDLEQAISCITEKKKIEKS  770 (837)
Q Consensus       742 sl~~~~~~~~I~l~~Aieli~~~k~~~~~  770 (837)
                      .-+++-.+...+  +|+.|+..+....++
T Consensus       714 ~~~~~~~c~c~~--ra~~l~v~k~~~nrG  740 (758)
T KOG1956         714 TEEEEVTCGCGT--RAVKLLVAKTEPNRG  740 (758)
T ss_pred             CCCCCCCCCCCC--HHHHHHHHCCCCCCC
T ss_conf             787554568751--555332302676679


No 29 
>COG1110 Reverse gyrase [DNA replication, recombination, and repair]
Probab=100.00  E-value=0  Score=835.81  Aligned_cols=506  Identities=33%  Similarity=0.551  Sum_probs=418.7

Q ss_pred             EEEECCHHHHHHHHHHHCCC----------C---------EEEEEECCCEECCCCCC--CCCCCC-CCCEEEEEC-----
Q ss_conf             89977904787788750899----------8---------99994251100786557--867666-744068877-----
Q gi|254780306|r    3 VIIVESPAKAKTISKYLGSN----------Y---------KVLSSFGHIRDLPAKKG--SVLPEK-EFEMIWNID-----   55 (837)
Q Consensus         3 LvIvEsP~kak~I~~~Lg~~----------y---------~V~as~GHirdLp~~~~--~v~~~~-~f~p~y~v~-----   55 (837)
                      |+|||||+||+|||.|+|.-          |         .|+||.|||.||....+  ||..++ .|.|.|..+     
T Consensus       620 L~IVESPnKARTIA~FFgrPS~R~~~~~~vYEv~~gD~vL~ItAS~GHv~DLvt~~g~hGvl~~~~~~vPvY~tIKrC~d  699 (1187)
T COG1110         620 LMIVESPNKARTIASFFGRPSVRRLGGGVVYEVAIGDLVLTITASGGHVFDLVTEPGVHGVLVKDGKYVPVYDTIKRCRD  699 (1187)
T ss_pred             EEEEECCHHHHHHHHHHCCCCEEEECCEEEEEEECCCEEEEEEECCCEEEEEECCCCCCEEECCCCCEEEHHHHHHHHHH
T ss_conf             89996771888999984896235547906899961875899995387168863146521056058706862788888851


Q ss_pred             --------------------CCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECC
Q ss_conf             --------------------654899999999987099899946997025799999999975512578871699998037
Q gi|254780306|r   56 --------------------PSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAI  115 (837)
Q Consensus        56 --------------------~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~ei  115 (837)
                                          .++...++.|++++-.+|+|++|||||.|||-|||.|+..|.+.    ..+|+|+.|||+
T Consensus       700 cg~q~~~~~~~cP~Cgs~~v~d~~~~ve~lRelA~EvDeVlIgTDPDtEGEKIawDv~~~l~Py----~~nikR~eFHEV  775 (1187)
T COG1110         700 CGEQFVDSEDKCPRCGSRNVEDKTETVEALRELALEVDEILIGTDPDTEGEKIAWDVFNYLRPY----NPNVKRIEFHEV  775 (1187)
T ss_pred             CCCEECCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCEEEECCCCCCCCCHHHHHHHHHHCCC----CCCEEEEEEEEE
T ss_conf             5844044323598878832024077999999988652779981799876442578898762767----876047773232


Q ss_pred             CHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHCC-CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEE
Q ss_conf             9899999986226469899999999999898740113789886414-676534226899999999999964137654400
Q gi|254780306|r  116 TKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLP-GARSAGRVQSVALRLICNRENQIESFVSEEYWS  194 (837)
Q Consensus       116 T~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~-~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~  194 (837)
                      |+.||.+|++|||++|.|||.||..||+.||+|||.||+.||.... .+|||||||||+|++||+|+.|-+.=+.  |..
T Consensus       776 TrrAIleAl~n~r~vd~nlVkAQiVRRIeDRWIGF~LS~~Lw~~F~~~nLsAGRVQTPVLGWIV~Ry~e~~~~~~--~~~  853 (1187)
T COG1110         776 TRRAILEALKNPRDVDENLVKAQIVRRIEDRWIGFELSQKLWDVFNNKNLSAGRVQTPVLGWIVNRYEEYKEKRG--YLV  853 (1187)
T ss_pred             CHHHHHHHHHCCCCCCHHHHHHHHHHHHHHCCCCEEECHHHHHHHCCCCCCCCCCCCCCCEEEHHHHHHHHHCCC--EEE
T ss_conf             399999998390003513467776555543011426229999984766766660036640020126888764055--267


Q ss_pred             EEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHC
Q ss_conf             12233157996542233103583303310113566677764200156301000023322246852103799999887608
Q gi|254780306|r  195 LSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLG  274 (837)
Q Consensus       195 i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg  274 (837)
                      +...        +.             ..+.+...++.+...+......|..+..++.-.+|+|||||.||.++||++||
T Consensus       854 ~~~~--------~~-------------~~~~~~~~~~~~~~~~~~~~v~v~~~~e~ee~~~PlPPyTTDt~L~dAs~~L~  912 (1187)
T COG1110         854 IQLD--------LD-------------LPSGNREEVENVKRKLKLIVVEVVDVVEREEEKNPLPPYTTDTMLRDASRRLR  912 (1187)
T ss_pred             EECC--------CE-------------EECCCHHHHHHHHHHCCCCEEEEEEHHHHHHCCCCCCCCCCCHHHHHHHHHHC
T ss_conf             6213--------10-------------35266055665543204544898630234430489879670158999999848


Q ss_pred             CCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEE
Q ss_conf             88999999998762135567212245531475544443056899997655200112376311112556668877765247
Q gi|254780306|r  275 FSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIR  354 (837)
Q Consensus       275 ~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIr  354 (837)
                      +|+++||+|||.|+|        .|||||+||||++.|+..+.-++.++...+|.+|.  .||.+..     .-||||||
T Consensus       913 lsa~~~M~iaQdLFE--------~GlITYHRTDSTrVS~~Gi~vAreyl~~~~~e~~f--~pR~Wge-----~GAHEaIR  977 (1187)
T COG1110         913 LSADETMQIAQDLFE--------GGLITYHRTDSTRVSDVGIRVAREYLRKEFGEEYF--RPRSWGE-----EGAHEAIR  977 (1187)
T ss_pred             CCHHHHHHHHHHHHH--------CCCEEEEECCCCCCCHHHHHHHHHHHHHHHCCCCC--CCCCCCC-----CCCCCCCC
T ss_conf             883489999999974--------36538860577545411178899998886233125--6776566-----77621557


Q ss_pred             EEECCCCCC----------HHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCH
Q ss_conf             730234640----------0000199999999999999999985222110010013677407963999998748805885
Q gi|254780306|r  355 PNDFDFLPS----------KMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGF  424 (837)
Q Consensus       355 PT~~~~~p~----------~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~  424 (837)
                      ||......+          ++...|+.++.+||+||++|||||||.||......+.+.+.+.+   ...--.-.+...||
T Consensus       978 PtrPid~~eL~~~i~~G~i~~~~~Lt~~HlrvYdLIFrRFmASQm~pa~v~~~~~~i~~~~~~---~~~e~~ve~~~~G~ 1054 (1187)
T COG1110         978 PTRPIDVEELITLIEEGVIQLPIRLTKNHLRVYDLIFRRFMASQMRPAKVLKEKAEVKADGKD---VELEALVEILEDGF 1054 (1187)
T ss_pred             CCCCCCHHHHHHHHHCCCEECCCHHHHHHHHHHHHHHHHHHHHHCCCEEEEEEEEEEECCCCE---EEEEEHHHHHCCCH
T ss_conf             899887788999997487205521208899999999999888607860689999999648631---11110134431422


Q ss_pred             HHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEE
Q ss_conf             67632677763210010148864568821100110111234643101789987433210256655157899999732202
Q gi|254780306|r  425 LKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYV  504 (837)
Q Consensus       425 ~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV  504 (837)
                      -.+|.           -..+|.|..|+ +.+...........  +.||++++|+.|.+.|||||||||.||++|..||||
T Consensus      1055 ~~vy~-----------~~~~p~l~~g~-l~v~~~~~~~~~kv--~lytqg~vi~~MKerGIGRPSTYAkive~L~~RgYv 1120 (1187)
T COG1110        1055 ALVYP-----------TRVLPELEKGT-LKVTEVEIRKVSKV--YLYTQGEVVEEMKERGIGRPSTYAKIVETLLRRGYV 1120 (1187)
T ss_pred             HHHCC-----------CCCCCCCCCCC-EEEEEEEEEECCCC--CCCCCCHHHHHHHHCCCCCCCHHHHHHHHHHCCCEE
T ss_conf             32055-----------53357667773-14333588870464--555535299999862789970799999998637739


Q ss_pred             ECCCCC--EEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHH
Q ss_conf             214771--222011420000223366556898899999999999862601347899998676766
Q gi|254780306|r  505 IAEKRK--ILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIE  567 (837)
Q Consensus       505 ~~~~~~--l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~  567 (837)
                      ...+++  ++||.+|+.|.+||.++|+++|+.+.|.++|+.||.|+.|+.++.++|++.|+.+..
T Consensus      1121 ie~kg~~~lipTk~Gi~Vy~yL~~~~~~lVSEerTR~LEe~MD~vE~gk~dy~~vL~ely~ei~~ 1185 (1187)
T COG1110        1121 IESKGRKKLIPTKLGIEVYEYLSEKYKKLVSEERTRRLEEIMDKVEEGKADYQEVLKELYEEIKS 1185 (1187)
T ss_pred             EEECCCEEECCCCCCHHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHHHHHH
T ss_conf             98668167321411089999999850442455679999999989983644799999999999972


No 30 
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=100.00  E-value=0  Score=824.30  Aligned_cols=375  Identities=51%  Similarity=0.770  Sum_probs=339.4

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCHHHHHHCC--CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEE
Q ss_conf             899999999999898740113789886414--676534226899999999999964137654400122331579965422
Q gi|254780306|r  132 LDLVNAYLARRALDYLVGFNLSPILWQKLP--GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTA  209 (837)
Q Consensus       132 ~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~--~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a  209 (837)
                      .||++||+|||++|||||||+|+++|.+++  +.+|+||||||||+|||+||+||++|+|++||.|              
T Consensus         1 ~nL~~a~~aR~~~D~liG~n~Sr~~t~~~~~~~~lS~GRVQTPtL~lvv~Re~ei~~f~~~~y~~~--------------   66 (381)
T cd00186           1 ENLVNAQLARRILDRLVGFNLSRLLTKKLRRKGVLSAGRVQSPTLGLIVEREREIKAFVPEDYWEI--------------   66 (381)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCHHHHHHHHHHHHHHHHCCCCCCEEEE--------------
T ss_conf             966899999999999973754399999848889975664488999999988999981898552885--------------


Q ss_pred             EEEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHC
Q ss_conf             33103583303310113566677764200156301000023322246852103799999887608889999999987621
Q gi|254780306|r  210 HLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYE  289 (837)
Q Consensus       210 ~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE  289 (837)
                                                    +.++|.++++++.+.+||+||+|++||++||++|||||++||+|||+|||
T Consensus        67 ------------------------------~~~~v~~~~~k~~~~~pP~pf~l~~Lq~~a~~~~g~s~~~tl~iaQ~LYE  116 (381)
T cd00186          67 ------------------------------KEAVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAKKTMQIAQKLYE  116 (381)
T ss_pred             ------------------------------EEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCHHHHHHHHHHHHH
T ss_conf             ------------------------------34899998751586479799468999999986069599999999999986


Q ss_pred             CCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC---CCCCCCCCCCCCCCCCEEEEECCCCCCHHC
Q ss_conf             35567212245531475544443056899997655200112376311---112556668877765247730234640000
Q gi|254780306|r  290 GIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKP---RIYSSKSKNAQEAHEAIRPNDFDFLPSKMK  366 (837)
Q Consensus       290 ~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~---r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~  366 (837)
                              .||||||||||++||++++..++.++...++..++....   +....+.+++|+||||||||+....+ ...
T Consensus       117 --------~g~ITYpRTDs~~ls~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~aH~AI~PT~~~~~~-~~~  187 (381)
T cd00186         117 --------AGLITYPRTDSTRLSEEAILEAREYIQAIYGKEYLYPAPLLGRRNPKRGKKEQGAHEAIRPTKVAPTP-ELE  187 (381)
T ss_pred             --------CCEEEECCCCCCCCCHHHHHHHHHHHHHHCCCCCCCHHHHHCCCCCCCCCCCCCCCCCEECCCCCCCH-HHH
T ss_conf             --------79265326765616999999999999976473344134431256778899977896896167888885-666


Q ss_pred             CCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCC
Q ss_conf             01999999999999999999852221100100136774079639999987488058856763267776321001014886
Q gi|254780306|r  367 QFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPY  446 (837)
Q Consensus       367 ~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~  446 (837)
                      +.|+.+|++||+|||+|||||||+||+|++++|.+.+.+    ..|.++|++++++||++||....+     +++..+|.
T Consensus       188 ~~l~~~e~~iY~LI~~rfla~~~~~~~~~~t~v~~~~~~----~~F~~~g~~i~~~Gw~~v~~~~~~-----~~~~~lp~  258 (381)
T cd00186         188 ANLSEDEFKLYELIWRRFLASQMADAKYEETTVTLEIGG----EKFKASGKVLLEDGWLEVYPEEKD-----DEEEEPPP  258 (381)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHHCCCCEEEEEEEEEEECC----EEEEEEEEEEEECCHHHEECCCCC-----CCCCCCCC
T ss_conf             019999999999999999997464020368999999899----789999999976682004467787-----63235865


Q ss_pred             CCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCC
Q ss_conf             45688211001101112346431017899874332102566551578999997322022147712220114200002233
Q gi|254780306|r  447 ISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLEN  526 (837)
Q Consensus       447 l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~  526 (837)
                      +.+|+.+.+.++.+.+++|+||+||||||||++||+.|||||||||+||++|++|+||.+++++|+||++|+.|+++|.+
T Consensus       259 l~~g~~~~~~~~~~~e~~TkPP~ryTe~tLi~~Me~~GIGTpATra~IIe~L~~r~Yi~~~~~~l~~T~~G~~li~~l~~  338 (381)
T cd00186         259 LKEGDELKLEEVELEEKETQPPPRYTEASLIKLMEKRGIGRPSTYASIIETLLDRGYVEKEKKKLIPTELGFAVIELLEK  338 (381)
T ss_pred             CCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHH
T ss_conf             35697787878788877438998778999999765369987265989999998478099329999673789999999987


Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Q ss_conf             665568988999999999998626013478999986767665
Q gi|254780306|r  527 FFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWEEFIEK  568 (837)
Q Consensus       527 ~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~~f~~~  568 (837)
                      +|++|++++|||.||.+||+|++|+.+|.+||++||+.++..
T Consensus       339 ~~~~i~~p~~Ta~~E~~L~~I~~G~~~~~~~l~~~~~~~~~~  380 (381)
T cd00186         339 HFPELVDPEFTAKLEEKLDEIAEGKKDYQEVLEEFYEEFKKI  380 (381)
T ss_pred             HHHHHCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHHHHHHHH
T ss_conf             545625978999999999999879998999999999999835


No 31 
>TIGR01054 rgy reverse gyrase; InterPro: IPR005736   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.    Reverse gyrase is a type IA topoisomerase that is unique among these enzymes in its requirement for ATP. Reverse gyrase is a hyperthermophile-specific enzyme that acts as a renaturase by positively supercoiling DNA, and by annealing complementary single-strand circles . Hyperthermophilic organisms must protect themselves against heat-induced degradation, and reverse gyrase acts to reduce the rate of double-strand DNA breakage, a function that does not require ATP hydrolysis and which is independent of its positive supercoiling abilities. Reverse gyrase achieves this by recognising nicked DNA and recruiting a protein coat to the site of damage .   More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=100.00  E-value=0  Score=778.66  Aligned_cols=521  Identities=32%  Similarity=0.510  Sum_probs=390.3

Q ss_pred             EEEECCHHHHHHHHHHHCC------------------C------------C--EEEEEECCCEECCCCC----CCCCCCC
Q ss_conf             8997790478778875089------------------9------------8--9999425110078655----7867666
Q gi|254780306|r    3 VIIVESPAKAKTISKYLGS------------------N------------Y--KVLSSFGHIRDLPAKK----GSVLPEK   46 (837)
Q Consensus         3 LvIvEsP~kak~I~~~Lg~------------------~------------y--~V~as~GHirdLp~~~----~~v~~~~   46 (837)
                      |+|||||+||||||.|.|+                  |            |  .|+||.|||.||-.+.    .||..++
T Consensus       661 L~vVESPnKARTIA~FFGkP~~R~iP~~~~vYEv~~gDkilmim~~~G~V~~L~iTas~GHv~DL~t~~~~~f~GV~~~~  740 (1843)
T TIGR01054       661 LLVVESPNKARTIARFFGKPSVRKIPGGSVVYEVPVGDKILMIMAETGDVLVLVITASLGHVFDLVTDKVGGFYGVLVEN  740 (1843)
T ss_pred             EEEEECCCCHHHHHHHCCCCCCEECCCCCEEEEEEECCEEEEEECCCCCEEEEEEEEECCCHHHHCCCCCCCEEEEEEEC
T ss_conf             79982786044553430699635515985389986168289985189837899998411002110367446342115305


Q ss_pred             C-----CCEEEEECC--------------------------------CHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHH
Q ss_conf             7-----440688776--------------------------------548999999999870998999469970257999
Q gi|254780306|r   47 E-----FEMIWNIDP--------------------------------SSQKHLQNIIHAVKSSTILILATDPDREGEAIS   89 (837)
Q Consensus        47 ~-----f~p~y~v~~--------------------------------~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Ia   89 (837)
                      +     |-|.|..++                                +++..|+.|+++|.++|+|++|||||+|||-||
T Consensus       741 ~~g~~~Y~PvY~sIKrC~dcG~QfTd~~~leeli~e~cpkcgs~~~~d~~~~ve~lR~lA~EvD~v~iaTDPDtEGEKIg  820 (1843)
T TIGR01054       741 GEGAEAYVPVYTSIKRCRDCGEQFTDEEDLEELIKELCPKCGSENIEDSKSIVEILRELASEVDEVFIATDPDTEGEKIG  820 (1843)
T ss_pred             CCCCCCCEEEECCCCEECCCCCCCCCHHHHHHHHHHHHCCCCCCCCCCHHHHHHHHHHHHHHHCEEEECCCCCCCCCCHH
T ss_conf             88965420044110113358874367155899999860257875556526788999875444298887258898754089


Q ss_pred             HHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCC-----CCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHCC---
Q ss_conf             999999755125788716999980379899999986226-----469899999999999898740113789886414---
Q gi|254780306|r   90 WHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPR-----DINLDLVNAYLARRALDYLVGFNLSPILWQKLP---  161 (837)
Q Consensus        90 whi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r-----~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~---  161 (837)
                      |.|.-.+.+.    .-+|+|+.|||+|+.||++|++|||     ++|.|||+||..||+.||+|||.||+.||....   
T Consensus       821 wDl~~~~~Py----~pnv~R~eFHEVT~rAi~eAl~s~rkGeel~vd~NLVkAQvVRRI~DRWiGF~LS~~Lw~~F~Pry  896 (1843)
T TIGR01054       821 WDLALLLRPY----NPNVKRAEFHEVTKRAILEALESPRKGEELSVDENLVKAQVVRRIEDRWIGFTLSQKLWEAFNPRY  896 (1843)
T ss_pred             HHHHHHHCCC----CCCEEEECCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEEEEEEEECEEECHHHHHCCCCCH
T ss_conf             9999980887----775246214562379999986087657501000231011588898754003011547772248504


Q ss_pred             ------------CCCC--------------CCCHHHHHHHHHHHH---HH----HHHHCCCCCCEEEEEEEECCCC--CE
Q ss_conf             ------------6765--------------342268999999999---99----9641376544001223315799--65
Q gi|254780306|r  162 ------------GARS--------------AGRVQSVALRLICNR---EN----QIESFVSEEYWSLSVLLETPRN--DK  206 (837)
Q Consensus       162 ------------~~lS--------------aGRVQtp~L~lIveR---e~----eI~~F~p~~y~~i~a~~~~~~~--~~  206 (837)
                                  .-||              |||||||+|++||||   ++    |=+.  ...+..+.+. . .++  ..
T Consensus       897 CkrvleeyGekk~wLsrerCakykayynlsAGRVQTPVLGWiidRtlay~kkvWe~r~--~~~~~l~~~~-~-~d~~evP  972 (1843)
T TIGR01054       897 CKRVLEEYGEKKPWLSRERCAKYKAYYNLSAGRVQTPVLGWIIDRTLAYRKKVWEYRE--KRGSLLLFAL-E-SDDPEVP  972 (1843)
T ss_pred             HHHHHHHHCCCCCCCCHHHHHHHHHHHCCCCCEEECCCCCEEEEEEEHHCCCEEEEEE--ECCEEEEEEE-E-CCCCCCC
T ss_conf             6788874011267778556554322210358705005145067510021001001234--5133999998-2-5881023


Q ss_pred             EEEEEEEECCEEECCCCHHHHHHHHHHHHHHCCCCCEEEEEECCCC--CCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             4223310358330331011356667776420015630100002332--22468521037999998876088899999999
Q gi|254780306|r  207 FTAHLTDFNGQRIEKKSISNKKEADDLISFVKKATYSVEKIENKPI--KRNPWPAFTTSTLQQVASSRLGFSASHTMRIA  284 (837)
Q Consensus       207 f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~V~~v~~k~~--~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iA  284 (837)
                      |....           -+.|+-+|+++...+.  -.-|..+..++.  -++|||||||.||..|||++||+|+.+||+||
T Consensus       973 ~~~~~-----------~~~d~~~~~~~~~~l~--~~dV~~~~~~EEWt~~~PlPPYTTDT~L~dAn~~l~LS~~~~M~IA 1039 (1843)
T TIGR01054       973 FRLKL-----------ELDDKLEAKEFEKDLK--ELDVKVVEEKEEWTERNPLPPYTTDTMLEDANRKLGLSAKKAMKIA 1039 (1843)
T ss_pred             EEEEE-----------EEECHHHHHHHHCCCC--EEEEEEECCCEEECCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHH
T ss_conf             46433-----------5421135432202541--4665541673000368500188756789998776357978999999


Q ss_pred             HHHHCCCCCCCHHHHHHHHCCCC-----CC----------------------------------------CCC-------
Q ss_conf             87621355672122455314755-----44----------------------------------------443-------
Q gi|254780306|r  285 QKLYEGIDVNGEIVGLITYMRTD-----GV----------------------------------------HMS-------  312 (837)
Q Consensus       285 Q~LYE~~~~~~~~~GlITYpRTD-----S~----------------------------------------~ls-------  312 (837)
                      |.|+|        .||||-|-|=     ++                                        +||       
T Consensus      1040 QeLFE--------~GLITtPdtyvvlGdGrietiedivnakernvlsldldnlsikidtaikfWklrynGnlskitlsnn 1111 (1843)
T TIGR01054      1040 QELFE--------LGLITTPDTYVVLGDGRIETIEDIVNAKERNVLSLDLDNLSIKIDTAIKFWKLRYNGNLSKITLSNN 1111 (1843)
T ss_pred             HHHHH--------CCCCCCCCCEEEECCCCCHHHHHHHHHCCCCEEEEECCCCEEEEHHHHEEEEEEECCCEEEEEEECC
T ss_conf             98851--------5311288527996387103678764000121334420210121000200000002365013553035


Q ss_pred             --------------------------------------------------------------------------------
Q ss_conf             --------------------------------------------------------------------------------
Q gi|254780306|r  313 --------------------------------------------------------------------------------  312 (837)
Q Consensus       313 --------------------------------------------------------------------------------  312 (837)
                                                                                                      
T Consensus      1112 yelkatPdhCllvlrdnqlkWiPakdikendyiamPfnykverkPisllnllkylditdvliefdenstifekiaeyirn 1191 (1843)
T TIGR01054      1112 YELKATPDHCLLVLRDNQLKWIPAKDIKENDYIAMPFNYKVERKPISLLNLLKYLDITDVLIEFDENSTIFEKIAEYIRN 1191 (1843)
T ss_pred             CCCCCCCCEEEEEEECCCCEECCCCCCCCCCEEECCCCCEECCCCHHHHHHHHHHHHHHHEEEECCCCHHHHHHHHHHHH
T ss_conf             21114777058988506400024223555652634533101145136888887631411102314651388999999874


Q ss_pred             --------------------------------------------------------------------------------
Q ss_conf             --------------------------------------------------------------------------------
Q gi|254780306|r  313 --------------------------------------------------------------------------------  312 (837)
Q Consensus       313 --------------------------------------------------------------------------------  312 (837)
                                                                                                      
T Consensus      1192 niktstkykylrnrrvPlkylieWnfdldeiekeakyiyksvaGtkkiPlfklderfWyfaGlvlGdGsiqdskiriaqt 1271 (1843)
T TIGR01054      1192 NIKTSTKYKYLRNRRVPLKYLIEWNFDLDEIEKEAKYIYKSVAGTKKIPLFKLDERFWYFAGLVLGDGSIQDSKIRIAQT 1271 (1843)
T ss_pred             HHHHHHHHHHHHCCCCCHHEEEEECCCHHHHHHHHHHHHHHCCCCCCCCCEEECCHHEEEEEEEECCCCEECCEEEEECC
T ss_conf             21022322333215674000123035656665443422111035433540211110000001134166200140233237


Q ss_pred             ------------------------------------------------------HH------------------------
Q ss_conf             ------------------------------------------------------05------------------------
Q gi|254780306|r  313 ------------------------------------------------------PD------------------------  314 (837)
Q Consensus       313 ------------------------------------------------------~e------------------------  314 (837)
                                                                            +.                        
T Consensus      1272 PlkdvksildetfPflhnWisGnqviisnPiiaeileklGmrnGklnGiifslPesyinaliaGyfdtdGCfsllydkka 1351 (1843)
T TIGR01054      1272 PLKDVKSILDETFPFLHNWISGNQVIISNPIIAEILEKLGMRNGKLNGIIFSLPESYINALIAGYFDTDGCFSLLYDKKA 1351 (1843)
T ss_pred             CHHHHHHHHHHCCHHHHHHCCCCEEEEECCHHHHHHHHHCCCCCCCCEEEEECCHHHHHHHHHHCCCCCCCEEHHHHHHH
T ss_conf             63678988741011354420566268706259999987066566402157744267887887200135741100111010


Q ss_pred             -----------------------------------------------HHHHHH----HHHH------------------H
Q ss_conf             -----------------------------------------------689999----7655------------------2
Q gi|254780306|r  315 -----------------------------------------------ALEAVR----RSIT------------------S  325 (837)
Q Consensus       315 -----------------------------------------------a~~~~r----~~i~------------------~  325 (837)
                                                                     .++..+    .+++                  +
T Consensus      1352 kkhnlrmvltskrrdvlekiGiylnsiGilntlhksrevysliisnksletfkekiakylkirkeafinGyktykkehee 1431 (1843)
T TIGR01054      1352 KKHNLRMVLTSKRRDVLEKIGIYLNSIGILNTLHKSREVYSLIISNKSLETFKEKIAKYLKIRKEAFINGYKTYKKEHEE 1431 (1843)
T ss_pred             HHCCEEEEEECHHHHHHHHHHHHHHHHHHHHHHHHHHHEEEEEEECCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             00111245510145677764256645677764421100123232201167899999998876666654113444222110


Q ss_pred             HCCCCCCC------------------------------------------------------------------------
Q ss_conf             00112376------------------------------------------------------------------------
Q gi|254780306|r  326 HYGDHYLP------------------------------------------------------------------------  333 (837)
Q Consensus       326 ~~g~~~l~------------------------------------------------------------------------  333 (837)
                      .|--+.||                                                                        
T Consensus      1432 rfeCdllPvkevfkkltfekGrkeilkdskihienWykektnniPreklktvlryannsehkeflekivnGdisfvrvkk 1511 (1843)
T TIGR01054      1432 RFECDLLPVKEVFKKLTFEKGRKEILKDSKIHIENWYKEKTNNIPREKLKTVLRYANNSEHKEFLEKIVNGDISFVRVKK 1511 (1843)
T ss_pred             HHCCCCCCHHHHHHHHHHHCCHHHHHHCCCCHHHHHHHHHHCCCCHHHHHHHHHHHCCCHHHHHHHHHHCCCEEEEEEEE
T ss_conf             00123232788987642210104443103000222232220367456788887641251257888887437512799864


Q ss_pred             ------------------------------------CCCCCCC-CCCCCCC-----------------------CCCCCE
Q ss_conf             ------------------------------------3111125-5666887-----------------------776524
Q gi|254780306|r  334 ------------------------------------EKPRIYS-SKSKNAQ-----------------------EAHEAI  353 (837)
Q Consensus       334 ------------------------------------~~~r~y~-~k~k~aQ-----------------------eAHeAI  353 (837)
                                                          ++.|+=. +|..-|.                       -|||||
T Consensus      1512 veniPydGyvydlsikhnqnfisnGvishnCtYHRTDSTRVSd~Gk~~vAkEYL~~~fGGl~~e~f~pR~WGEgGAHEcI 1591 (1843)
T TIGR01054      1512 VENIPYDGYVYDLSIKHNQNFISNGVISHNCTYHRTDSTRVSDVGKMRVAKEYLEKRFGGLGEELFYPREWGEGGAHECI 1591 (1843)
T ss_pred             EECCCCCCEEEEEEEECCCCHHHCCEEECCCCEECCCCCEECCCCCEEEEHHHHHHHCCCCHHHCCCCCCCCCCCCEECC
T ss_conf             31266665268645400332000561432652102765103454660000357763237730121568834787865356


Q ss_pred             EEEECCCCCC-----------HHCCCCCHHHHHHHHHHHHHHHHHHHHHHE------------ECCCEEEEEEEECCCEE
Q ss_conf             7730234640-----------000019999999999999999998522211------------00100136774079639
Q gi|254780306|r  354 RPNDFDFLPS-----------KMKQFLDSDQFQLYNLIWKRSVASQMASAK------------FERTTVNIIATYNDQIG  410 (837)
Q Consensus       354 rPT~~~~~p~-----------~~~~~L~~de~klY~LI~~R~lasqm~~a~------------~~~~~v~i~~~~~~~~~  410 (837)
                      |||-.. .++           .+...|.....+|||||+||||||||.||.            .+...+.|...+.+   
T Consensus      1592 RPtrPl-d~~dL~~~~~~G~i~~~~~L~~~hl~lYdLIFrRFmASQMkpa~alrvvyrlrvPev~~~~~~l~~~g~e--- 1667 (1843)
T TIGR01054      1592 RPTRPL-DVEDLERLVLEGVIELEGRLRRNHLKLYDLIFRRFMASQMKPAKALRVVYRLRVPEVDTKEITLKADGKE--- 1667 (1843)
T ss_pred             CCCCCC-CHHHHHHHHHCCCEEECCHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEEECCEEEEEEEEEEECCCE---
T ss_conf             876878-9899999986392330430168998886678764133107722025677676346056789999754601---


Q ss_pred             EEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCC-CCCCHHHHHHHHHHCCCCCCC
Q ss_conf             9999874880588567632677763210010148864568821100110111234643-101789987433210256655
Q gi|254780306|r  411 HLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPP-PRYSESSLIKKMEEIGIGRPS  489 (837)
Q Consensus       411 ~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP-~rytEasLik~mE~~GIGrPS  489 (837)
                      .+.-....+.+.||-.+|.-....         .|.+..+........+..+=---+| ..|||++||+.|.+.||||||
T Consensus      1668 ~~~~~~v~~~~~Gf~l~yp~~~~~---------~~~~~k~~~~~~~~~e~~~VPKv~lkrlYt~G~iv~~MK~RGIGRPS 1738 (1843)
T TIGR01054      1668 VEEEGVVEIKERGFELVYPLKRKE---------PRLVEKGSLLIRKDKELRKVPKVYLKRLYTQGEIVKEMKERGIGRPS 1738 (1843)
T ss_pred             EEEEEEEEEEECCHHHCCCCCCCC---------CCCCCCCCCHHHHHHHCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCC
T ss_conf             311246887503202005624777---------53355664010112220407642530115631476886446775985


Q ss_pred             CHHHHHHHHHHCCEEECCCC-------CEEECCHHHHHCCCCCC--C-----------------CCCCCCHHHHHHHHHH
Q ss_conf             15789999973220221477-------12220114200002233--6-----------------6556898899999999
Q gi|254780306|r  490 TYATILETLYKRKYVIAEKR-------KILPQNTGRIVTAFLEN--F-----------------FSQYVEYDFTADLEEK  543 (837)
Q Consensus       490 TyA~II~~L~~R~YV~~~~~-------~l~pT~~G~~v~~~L~~--~-----------------f~~~~~~~fTa~~E~~  543 (837)
                      |||.||++|.+|+||...++       .|+||.+|+.|.+||.+  +                 ||.+|+.|+|.++|+.
T Consensus      1739 TYA~Iv~~Ll~R~YVvE~~~~eGrG~~~lIPTklG~~VY~YL~~~~~sadeeeyGGriaGilrr~p~lvSEd~TR~LEe~ 1818 (1843)
T TIGR01054      1739 TYAKIVEKLLERGYVVESKGKEGRGARFLIPTKLGIEVYEYLTNEKKSADEEEYGGRIAGILRRYPKLVSEDRTRELEEA 1818 (1843)
T ss_pred             HHHHHHHHHCCCCCEEEEECCCCCCCCCCCCCCCCCHHHHHHHCCCCCCCCHHCCCEEHHHHHHCCCCCCCCHHHHHHHH
T ss_conf             58999998622897787516656757521455366158876200135654101265000243314653351010689988


Q ss_pred             HHHHHCCCHHHHHHHHHHHHHH
Q ss_conf             9998626013478999986767
Q gi|254780306|r  544 LDEISTGKLNWKEVLHEFWEEF  565 (837)
Q Consensus       544 ld~Ia~G~~~~~~~L~~Fy~~f  565 (837)
                      ||.|++|+.++.+||++.|...
T Consensus      1819 MD~vE~G~~dy~~VL~~l~~~i 1840 (1843)
T TIGR01054      1819 MDKVEKGELDYLEVLEELYREI 1840 (1843)
T ss_pred             HHHHHCCCCCHHHHHHHHHHHH
T ss_conf             6355268779899999999997


No 32 
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=100.00  E-value=0  Score=549.15  Aligned_cols=255  Identities=49%  Similarity=0.718  Sum_probs=226.0

Q ss_pred             ECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHC
Q ss_conf             02332224685210379999988760888999999998762135567212245531475544443056899997655200
Q gi|254780306|r  248 ENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHY  327 (837)
Q Consensus       248 ~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~  327 (837)
                      |+|+.+++||+||+|++||++||++|||||++||++||+|||        .||||||||||++||++....++.+|..++
T Consensus         1 e~k~~~~~PP~pf~ls~Lq~~as~~~g~sa~~tl~iaQ~LYe--------~g~ITYpRTds~~l~~~~~~~~~~~i~~~~   72 (259)
T smart00437        1 EEKEKKKNPPPPFTTSTLQQEASRKLGFSAKKTMQIAQKLYE--------KGLITYPRTDSTRLSEEAVLEARNYISKHY   72 (259)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHCCCCHHHHHHHHHHHHH--------CCCEEECCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             998635789799778999999998669999999999999986--------785533476874639999999999999863


Q ss_pred             CCCCCCCC----CCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEE
Q ss_conf             11237631----11125566688777652477302346400000199999999999999999985222110010013677
Q gi|254780306|r  328 GDHYLPEK----PRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAKFERTTVNIIA  403 (837)
Q Consensus       328 g~~~l~~~----~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~  403 (837)
                      +..|+...    .+....+..++|+||||||||+....++. ...|+++|++||+|||+|||||||+||+|++++|.+.+
T Consensus        73 ~~~~~~~~~~~~~~~~~~~~~~~~~aH~AI~PT~~~~~~~~-~~~l~~~e~~lY~LI~~r~las~~~~~~~~~t~v~~~~  151 (259)
T smart00437       73 GKEYLPLAVSLLKPRKPRWGKKEQGAHEAIRPTKPIPTPEL-EKELSEDEKKLYELIWRRFLASQMPDAKYEETKVIIKI  151 (259)
T ss_pred             CHHHHHHHHHHCCCCCCCCCCCCCCCCCCEECCCCCCCHHH-HHHCCHHHHHHHHHHHHHHHHHHCCHHEEEEEEEEEEE
T ss_conf             52100255553257878889998789889873667777465-51099999999999999999985753327899999998


Q ss_pred             EECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHC
Q ss_conf             40796399999874880588567632677763210010148864568821100110111234643101789987433210
Q gi|254780306|r  404 TYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEI  483 (837)
Q Consensus       404 ~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~  483 (837)
                      .+    ..|.++|++++++||+.||....+     +++..||.+.+|+.+.+.++.+.+++|+||+||||+|||++||+.
T Consensus       152 ~~----~~F~~~g~~~~~~Gw~~v~~~~~~-----~~~~~lp~l~~g~~~~~~~~~~~~~~TkPP~~yte~tLi~~Me~~  222 (259)
T smart00437      152 GG----EKFKAKGKTLLFDGWLKVYPEEKK-----EEEIELPTLKKGDELKVEEVEVEEKKTKPPARYTEASLIKLMEKR  222 (259)
T ss_pred             CC----EEEEEEEEEEEECCHHHEECCCCC-----CCCCCCCCCCCCCEEEEEEEEEEEEECCCCCCCCHHHHHHHHHCC
T ss_conf             99----899999999986873740335656-----531328767779889998888765433899887999999987508


Q ss_pred             CCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHH
Q ss_conf             2566551578999997322022147712220114200
Q gi|254780306|r  484 GIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIV  520 (837)
Q Consensus       484 GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v  520 (837)
                      |||||||||+||++|++|+||++++++|+||++|++|
T Consensus       223 GIGtpATra~iI~~L~~R~Yi~~~~k~l~pT~~G~~l  259 (259)
T smart00437      223 GIGRPSTYAEIIETLLDRGYVTKEKKKLIPTELGIAV  259 (259)
T ss_pred             CCCCCCCHHHHHHHHHHCCCEEEECCEEEECCCEECC
T ss_conf             9985025999999897589699459999554363319


No 33 
>COG1754 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]
Probab=100.00  E-value=0  Score=519.65  Aligned_cols=247  Identities=44%  Similarity=0.791  Sum_probs=223.0

Q ss_pred             HHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCC
Q ss_conf             5567664102455556766114334677731368715776111234343233321001221000---0123442014689
Q gi|254780306|r  583 ILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDI---PEMKESVLLGNDL  659 (837)
Q Consensus       583 ~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~---~~~~~~~~LG~dP  659 (837)
                      ..+..+..++|+...+....+.||.|+.+.+.++. ||||+|++|+|||+|.++++|.....+.   .....+++||.||
T Consensus         4 ~~~~~L~~lv~~~~~D~s~~rt~~~~~~~~~slk~-GKyGpyl~~an~Pe~~~~~eL~~e~~~~l~~~~~~~~r~LG~DP   82 (298)
T COG1754           4 ALNKGLKPLVFPNREDASEPRTCPLCGTGELSLKL-GKYGPYLECANYPECTTPKELTLEVAENLEATPQGGPRVLGIDP   82 (298)
T ss_pred             HHHHHHHHHHCCCCCCCCCCCCCCCCCCCCEEEEE-CCCCCCCEECCCCCCCCHHHHCCHHCCCCCCCCCCCCCCCCCCC
T ss_conf             54544565521135776557614434666156884-25433101206866547666140001222335689975236688


Q ss_pred             CCCCEEEEEECCCCCEEE--ECCC-CCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEEE
Q ss_conf             999669998269742277--3488-7776133789988425489999998615255157778987499911587652616
Q gi|254780306|r  660 ETKESVTLRSGRFGLYVQ--RGDG-KDAKRCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNH  736 (837)
Q Consensus       660 ~~G~~I~lk~GryGpYvq--~Ge~-~kpkr~si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~~  736 (837)
                      ++|++|++|+||||||||  +|+. +||+|+|+|+++++++||||+||+||||||+||.||++|++|+|.+|||||||+|
T Consensus        83 ~tG~eI~~k~GryGPYVq~~lg~~~~kpkraSLpkg~~~e~ItLE~AL~LLsLPR~iG~hp~sge~I~ag~GRfGPyv~k  162 (298)
T COG1754          83 ETGEEIYLKNGRYGPYVQEQLGDPKPKPKRASLPKGWKPETITLEKALKLLSLPRVIGKHPDSGEEISAGLGRFGPYVKK  162 (298)
T ss_pred             CCCCEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHCCCHHHCCCCCCCCEEEECCCCCCCCEEE
T ss_conf             88856688526777615643478888854466889888312759999998738243077988886788614665763310


Q ss_pred             CCE-ECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCCC-CCEEEEECCCCCEEEECCEEEECCCC
Q ss_conf             781-1124887751435799999999836511344344544320102678989-84699606854525367888756578
Q gi|254780306|r  737 DGA-YTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPEG-GSITVHNGRYGPYLHWKKINASLSKE  814 (837)
Q Consensus       737 ~~~-~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~~-~~i~i~~GryGpYi~~gk~Na~ipk~  814 (837)
                      .++ |+||++++|+|+|+||||+.||+|++.+++     +..++++||.||++ ++|.|++|||||||+||++||+|||+
T Consensus       163 ~Gsd~~sL~~~dd~ftItL~rA~~liaEk~~~G~-----s~~alk~lg~~p~~g~pI~v~dGrfGpYv~~Gk~Na~Lpkg  237 (298)
T COG1754         163 RGSDYRSLKSEDDVFTITLDRALKLIAEKRSRGR-----SAAALKELGTHPEGGKPITVKDGRFGPYVKDGKTNATLPKG  237 (298)
T ss_pred             CCCCCCCCCCCCCEEEECHHHHHHHHHHHHCCCC-----CHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCCCCCCCCCC
T ss_conf             6842114455343266308999999974530376-----44568874458467851588447867620015303657899


Q ss_pred             CCHHHCCHHHHHHHHHHHHHC
Q ss_conf             896778999999999877726
Q gi|254780306|r  815 ESPDTVDLEKALKILNIKKQK  835 (837)
Q Consensus       815 ~~~e~lt~e~a~~li~~k~~k  835 (837)
                      .||++||+|+|++||++|+++
T Consensus       238 ~d~~sit~e~A~~LLaer~a~  258 (298)
T COG1754         238 KDPASITLEEALELLAERRAK  258 (298)
T ss_pred             CCCCCCCHHHHHHHHHHHCCC
T ss_conf             880106799999999974146


No 34 
>KOG1957 consensus
Probab=100.00  E-value=0  Score=407.28  Aligned_cols=478  Identities=23%  Similarity=0.265  Sum_probs=367.8

Q ss_pred             EEEECCHHHHHHHHHHHCC------------------------CCEEEEEECCCE--ECCCC---CCCCCCCCCCCEEEE
Q ss_conf             8997790478778875089------------------------989999425110--07865---578676667440688
Q gi|254780306|r    3 VIIVESPAKAKTISKYLGS------------------------NYKVLSSFGHIR--DLPAK---KGSVLPEKEFEMIWN   53 (837)
Q Consensus         3 LvIvEsP~kak~I~~~Lg~------------------------~y~V~as~GHir--dLp~~---~~~v~~~~~f~p~y~   53 (837)
                      |+++|+|+.|-.||+.|..                        .|+|++..||+.  |+|+|   +-.|||.+-|..--+
T Consensus         5 lmvaekpsla~sia~ils~g~~s~~kg~csvhe~~g~f~g~~~~fk~tsvcghvmsldf~~kyn~w~~vdp~elf~apt~   84 (555)
T KOG1957           5 LMVAEKPSLADSIANILSNGQASKRKGWCSVHEYDGQFRGRAARFKVTSVCGHVMSLDFPPKYNNWDKVDPAELFSAPTE   84 (555)
T ss_pred             EEEECCCHHHHHHHHHHHCCCCCCCCCCEEEEECCCCCCCCEEEEEEEEEECEEEECCCCHHCCCCCCCCHHHHHCCCCH
T ss_conf             67615845999999986477610356733566525621682336888554110586047333177332698897277400


Q ss_pred             ECC--CHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCC
Q ss_conf             776--548999999999870998999469970257999999999755125788716999980379899999986226469
Q gi|254780306|r   54 IDP--SSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDIN  131 (837)
Q Consensus        54 v~~--~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d  131 (837)
                      -..  -|-...+.|...+++||.++||.|+|+|||+|+|++++..+......+-.++|+.||+||++.|.+||.|+.+.|
T Consensus        85 kkeanpk~~m~kfl~~eargcdy~vlwldcdkegenicfevidav~~~m~~~~~~tyra~fsaitekdi~~am~~lg~p~  164 (555)
T KOG1957          85 KKEANPKMNMNKFLASEARGCDYLVLWLDCDKEGENICFEVIDAVKCVMNRSDFKTYRAHFSAITEKDIKKAMRNLGEPD  164 (555)
T ss_pred             HCCCCCHHHHHHHHHHHCCCCCEEEEEEECCCCCCEEEHHHHHHHHHHHCCCCCEEEEEEECCCCHHHHHHHHHHCCCCC
T ss_conf             00148026599987643369867999962577767220103644545540576147753313022778999998538998


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHCHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEE
Q ss_conf             89999999999989874011378988641467653422689999999999996413765440012233157996542233
Q gi|254780306|r  132 LDLVNAYLARRALDYLVGFNLSPILWQKLPGARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHL  211 (837)
Q Consensus       132 ~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l  211 (837)
                      .|...|..||+.||..|  -.        ..-.|.|.||||||+++|+|...|+.|+|+.||.+.+.+.+.+   +..+|
T Consensus       165 ~nea~svdarqeldlri--ld--------s~~isygpcqtptlgfcv~rhd~i~tfkpe~~w~l~~~~~~~~---~~lew  231 (555)
T KOG1957         165 QNEALSVDARQELDLRI--LD--------SSLISYGPCQTPTLGFCVTRHDQIQTFKPEQYWVLQTNFTTDD---LSLEW  231 (555)
T ss_pred             CCHHCCCCHHHHHHHHH--HH--------HCCEEECCCCCCCCEEEEEEHHHHHCCCCCCEEEEEEECCCCC---CCCHH
T ss_conf             32101442444302634--53--------3122106778985312455431331358540588742048887---55013


Q ss_pred             EEECCEEECCCCHHHHHHHHHHHHHHCC-CCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCC
Q ss_conf             1035833033101135666777642001-563010000233222468521037999998876088899999999876213
Q gi|254780306|r  212 TDFNGQRIEKKSISNKKEADDLISFVKK-ATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEG  290 (837)
Q Consensus       212 ~~~~~~~~~~~~~~~~~~a~~~~~~~~~-~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~  290 (837)
                              +.+|++|.+.|.-+++.++. ..+.|.+|.+|+..+.-|..++|..|.+.|                     
T Consensus       232 --------~r~rvfd~eia~~f~~~vk~~~~a~v~~vs~ke~~k~rp~alntvel~rv~---------------------  282 (555)
T KOG1957         232 --------QRGRVFDAEIARVFLNRVKECKTALVEDVSKKEARKERPCALNTVELMRVA---------------------  282 (555)
T ss_pred             --------HHCCHHHHHHHHHHHHHHHHHHHHEEHHHHHHHHHHCCCCCCCHHHEEEEE---------------------
T ss_conf             --------421113689999999998762021101045567753488421314002456---------------------


Q ss_pred             CCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEECCCCCCHHCCCCC
Q ss_conf             55672122455314755444430568999976552001123763111125566688777652477302346400000199
Q gi|254780306|r  291 IDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSSKSKNAQEAHEAIRPNDFDFLPSKMKQFLD  370 (837)
Q Consensus       291 ~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~~k~k~aQeAHeAIrPT~~~~~p~~~~~~L~  370 (837)
                                    +|..+..+..+-       .+.-+-+-|. .+    +....| +-|++|.|.....     ....+
T Consensus       283 --------------itett~y~~nfd-------~si~~~D~L~-~~----s~gtdA-gdgpPitpmr~~~-----R~m~~  330 (555)
T KOG1957         283 --------------ITETTAYPANFD-------TSIILGDTLF-EA----SFGTDA-GDGPPITPMRKCN-----RYMKS  330 (555)
T ss_pred             --------------EEECCCCCCCCC-------CCCCCCCCCC-CC----CCCCCC-CCCCCCCCCCCCC-----CCCCC
T ss_conf             --------------752245764456-------6631021001-45----456768-8999867664332-----00112


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHEECCCEEEEEEEECCCEEEEE--EEEEEEECCCHHHHHCCCCCCC-CCCHHHCCCCCC
Q ss_conf             9999999999999999852221100100136774079639999--9874880588567632677763-210010148864
Q gi|254780306|r  371 SDQFQLYNLIWKRSVASQMASAKFERTTVNIIATYNDQIGHLR--TTGSLLCFDGFLKVWENQYDQE-KNSEEDILLPYI  447 (837)
Q Consensus       371 ~de~klY~LI~~R~lasqm~~a~~~~~~v~i~~~~~~~~~~F~--asg~~i~~~G~~~vy~~~~~~~-~~~~~~~~LP~l  447 (837)
                      .|-++||..+++.|++.-+...+|..+++...++  ++  .|.  .+|+.+...||-.+.....+.+ ....++-..|..
T Consensus       331 ~dtkRLY~~vCqhf~~tp~~~~~k~it~~k~slg--de--qf~lw~~Gk~~~~~gft~fm~n~p~m~wgagcdECthPSc  406 (555)
T KOG1957         331 GDTKRLYCYVCQHFYATPQFKCKKVITTVKCSLG--DE--QFILWCTGKRLREFGFTPFMPNNPKMPWGAGCDECTHPSC  406 (555)
T ss_pred             CCCEEECCHHHHHHEECCCCCCEEEEEEEEECCC--CE--EEEECCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCCHH
T ss_conf             4300002044345212267672689866640457--74--6873157630115776635557876543457776679517


Q ss_pred             C-------CCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHH---HHHHHHCCEEECC-CCCEEECCH
Q ss_conf             5-------6882110011011123464310178998743321025665515789---9999732202214-771222011
Q gi|254780306|r  448 S-------ANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATI---LETLYKRKYVIAE-KRKILPQNT  516 (837)
Q Consensus       448 ~-------~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~I---I~~L~~R~YV~~~-~~~l~pT~~  516 (837)
                      .       .|+.+.+.++.+...+|.||-+.|++-++..||+.|||   |+|+|   |..+.+|+||..+ |++++||++
T Consensus       407 q~slSmlgiG~~vEc~~v~Lv~~qTsPkwylTcnkcisvme~hgig---tdasI~VhinsiceRnYv~Ve~gr~~~Pt~L  483 (555)
T KOG1957         407 QQSLSMLGIGQCVECESVELVLDQTSPKWYLTCNKCISVMEKHGIG---TDASIPVHINSICERNYVTVESGRALVPTPL  483 (555)
T ss_pred             HHHHHCCCCEEEEEECCEEEEECCCCCCCEEEHHHHHHHHHHHCCC---CEEEEEEEECCHHHHHEEEEECCCCCCCCCC
T ss_conf             7643025650489856689970589997413442557888762466---2125777634510131276104852477740


Q ss_pred             HHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHH
Q ss_conf             420000223366556898899999999999862601347899998
Q gi|254780306|r  517 GRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEF  561 (837)
Q Consensus       517 G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~F  561 (837)
                      |+.+..-...--|+++-+.+.+..|+.|-.++.|..++.++++.+
T Consensus       484 g~~l~~Gy~~~DP~l~lpt~r~~~es~~~lvA~G~A~~q~v~R~r  528 (555)
T KOG1957         484 GETLVRGYVKCDPELVLPTMRKEAESQLPLVAGGPADFQDVWRNR  528 (555)
T ss_pred             CHHHHCCCEEECCCEECHHHHHHHHHHCHHHHCCCCCHHHHHHCC
T ss_conf             124313746437110226688889861415417861110233121


No 35 
>cd03363 TOPRIM_TopoIA_TopoI TOPRIM_TopoIA_TopoI: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to Escherichia coli DNA topoisomerase I.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=100.00  E-value=2.3e-37  Score=299.55  Aligned_cols=122  Identities=50%  Similarity=0.798  Sum_probs=115.8

Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCC-CCEEEEECCCHHHHHHHHHHHHHHCCEEEECC
Q ss_conf             91899779047877887508998999942511007865578676667-44068877654899999999987099899946
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKE-FEMIWNIDPSSQKHLQNIIHAVKSSTILILAT   79 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~-f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAt   79 (837)
                      |+|||||||||||+|++|||++|.|+||+|||+|||.+..++++.+. |.|.|.+.++++++++.|++++++||+||+||
T Consensus         1 K~LvIvEsPskak~I~~~LG~~y~V~as~GHl~~L~~~~~~~~~~~~~~~p~~~~~~~k~k~i~~ik~l~~~ad~viiAt   80 (123)
T cd03363           1 KKLVIVESPAKAKTIKKYLGKEYEVLASVGHIRDLPKKGLGVDGEDDGFEPKYVVIPGKKKVVKELKKLAKKADEIYLAT   80 (123)
T ss_pred             CEEEEEECHHHHHHHHHHHCCCCEEEEECCCHHHCCCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECC
T ss_conf             91999958788999999819996999711502315776467775457853377966417889999999985099899848


Q ss_pred             CCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCC
Q ss_conf             997025799999999975512578871699998037989999998622
Q gi|254780306|r   80 DPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSP  127 (837)
Q Consensus        80 D~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~  127 (837)
                      |||||||+|||||+++++.     +++++|+||||||++||++||+||
T Consensus        81 D~DrEGE~I~~~i~~~~~~-----~~~~~Ri~f~~iT~~aI~~A~~nP  123 (123)
T cd03363          81 DPDREGEAIAWHLAEVLKL-----KKNVKRVVFNEITKEAIKEALKNP  123 (123)
T ss_pred             CCCCCHHHHHHHHHHHHCC-----CCCCEEEEEECCCHHHHHHHHHCC
T ss_conf             9982479999999999589-----999728999256999999999682


No 36 
>cd03361 TOPRIM_TopoIA_RevGyr TopoIA_RevGyr : The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to the ATP-dependent reverse gyrase found in archaea and thermophilic bacteria.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=100.00  E-value=6.8e-36  Score=288.50  Aligned_cols=122  Identities=31%  Similarity=0.558  Sum_probs=107.1

Q ss_pred             CEEEECCHHHHHHHHHHHCCC-------------------CEEEEEECCCEECCCCCCCCCC---CCCCCEEEE------
Q ss_conf             189977904787788750899-------------------8999942511007865578676---667440688------
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSN-------------------YKVLSSFGHIRDLPAKKGSVLP---EKEFEMIWN------   53 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~-------------------y~V~as~GHirdLp~~~~~v~~---~~~f~p~y~------   53 (837)
                      .|||||||+|||+|++|||+.                   |.|+||+|||||||.+.+++++   ++.|.|.|.      
T Consensus         2 ~LvIvEsP~kAktIa~~LG~~~~~~~~~~~~ye~~~~~~~~~V~as~GHi~dL~~~~~~~~~~~~~~~~~p~y~~~k~~~   81 (170)
T cd03361           2 ALMIVESPNKARTIANFFGRPSVRRLGGLVVYEVSTGDGVLMITASGGHVYDLVTKEGGHGVVEDDGRYVPVYDSIKRCR   81 (170)
T ss_pred             EEEEECCHHHHHHHHHHHCCCCCCCCCCCCCEEECCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHC
T ss_conf             69998278999999998388531234665412321588458999788883238876678675366756564303543200


Q ss_pred             -------------------ECCCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEEC
Q ss_conf             -------------------7765489999999998709989994699702579999999997551257887169999803
Q gi|254780306|r   54 -------------------IDPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNA  114 (837)
Q Consensus        54 -------------------v~~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~e  114 (837)
                                         +.++++++++.|++++++||+||||||||||||+||||++++|+..    +.+++|++|||
T Consensus        82 ~~~~~~~~~~~~~~~~~~~~~~~k~k~v~~lk~lak~ad~v~lATD~DREGEaIa~hi~~~l~~~----~~~~~Ri~F~e  157 (170)
T cd03361          82 DCGYQFTEDSDKCPRCGSENIDDKLETLEALRELALEVDEVLIATDPDTEGEKIAWDVYLALRPY----NKNIKRAEFHE  157 (170)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHHCCCEEEECCCCCCCHHHHHHHHHHHHCCC----CCCEEEEEECC
T ss_conf             01111112234464322233754899999999998608979985799822229999999995575----89815789746


Q ss_pred             CCHHHHHHHHHCC
Q ss_conf             7989999998622
Q gi|254780306|r  115 ITKQVVLNAMKSP  127 (837)
Q Consensus       115 iT~~aI~~A~~n~  127 (837)
                      ||++||++||+||
T Consensus       158 ITk~aI~~A~~nP  170 (170)
T cd03361         158 VTRRAILEALRNP  170 (170)
T ss_pred             CCHHHHHHHHHCC
T ss_conf             5999999999682


No 37 
>PRK07941 DNA topoisomerase I; Validated
Probab=100.00  E-value=6e-33  Score=266.37  Aligned_cols=161  Identities=35%  Similarity=0.601  Sum_probs=143.6

Q ss_pred             CCCCCEEEEEECCCCCEEEE--CCCC----CCCCCCCCCCCCHHHCCHHHHHHHHHCC---HHHCCCCCCCCEEEEEECC
Q ss_conf             99996699982697422773--4887----7761337899884254899999986152---5515777898749991158
Q gi|254780306|r  659 LETKESVTLRSGRFGLYVQR--GDGK----DAKRCSLPKTWKSDSVDYDKAMSLLSLP---REIGIHPETQKNIIAGTGK  729 (837)
Q Consensus       659 P~~G~~I~lk~GryGpYvq~--Ge~~----kpkr~si~k~~~~~~itle~Al~LLsLP---r~lG~~pe~g~~I~~~~Gr  729 (837)
                      ..+|.++.+|.||||||++.  |...    ++.|+++|.++.++++|++.|.+|+..|   |.||.||++|++|.+++||
T Consensus       638 ~~~g~~l~~r~gk~G~f~~~~~~~~~~~~~~~~~a~~~~~~~~~~~~~~~~~~~~~~~~~~r~LG~dP~tg~~V~lk~Gr  717 (933)
T PRK07941        638 DAEGRPVYVRVGRNGPYLERMVGTGDDGEPEPQRANLPDSLTPDELTLEVAEKLFATPQEGRELGVDPETGHEIVAKEGR  717 (933)
T ss_pred             CCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCCCCCCCCCCCCCCCCEEEEECCC
T ss_conf             67897547861577664000247688886430215678666865343777888750567897223589999868994179


Q ss_pred             CCCEEEE-------------------------CCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCC
Q ss_conf             7652616-------------------------781112488775143579999999983651134434454432010267
Q gi|254780306|r  730 YGYYLNH-------------------------DGAYTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGT  784 (837)
Q Consensus       730 yGpYi~~-------------------------~~~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~  784 (837)
                      |||||.-                         .-+++||++..++.+||||.|+.||+-|               |++|.
T Consensus       718 yGpyv~~~~~e~~~~~~~~~~~~~~~~~~~~~Kpk~asl~k~~~~~~itLe~Al~LlsLP---------------R~lG~  782 (933)
T PRK07941        718 FGPYVTEVLPEPEEDGAAAKTAAKKKKKETGPKPRTGSLLRSMDLQTVTLEDALKLLSLP---------------RVVGV  782 (933)
T ss_pred             CCCEEEEECCCCCCCHHHCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCC---------------HHHCC
T ss_conf             877242004775200000011011344334678775667899980206899999997084---------------63189


Q ss_pred             CCC-CCCEEEEECCCCCEEEECCEEEECCCCCCHHHCCHHHHHHHHHHHHH
Q ss_conf             898-98469960685452536788875657889677899999999987772
Q gi|254780306|r  785 HPE-GGSITVHNGRYGPYLHWKKINASLSKEESPDTVDLEKALKILNIKKQ  834 (837)
Q Consensus       785 ~p~-~~~i~i~~GryGpYi~~gk~Na~ipk~~~~e~lt~e~a~~li~~k~~  834 (837)
                      ||+ |.+|.+-.|||||||+||++|+|||++.|+-+|+|++|++||++++.
T Consensus       783 hPe~g~~I~a~~GrfGPYlk~~~~~~sL~~~~~~~~I~l~~Av~li~~~k~  833 (933)
T PRK07941        783 DPASGEEITAQNGRYGPYLKRGTDSRSLATEEQIFTITLDEALKIYAEPKR  833 (933)
T ss_pred             CCCCCCEEEECCCCCCCCCCCCCEEECCCCCCCCEECCHHHHHHHHHCHHH
T ss_conf             978998799756788766640883431698887512389999999955433


No 38 
>PRK07561 DNA topoisomerase I; Validated
Probab=99.98  E-value=8.7e-32  Score=257.66  Aligned_cols=161  Identities=32%  Similarity=0.514  Sum_probs=145.2

Q ss_pred             CCCCCEEEEEECCCCCEEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHHH----CCHHHCCCCCCCCEEEEEECCCCCEE
Q ss_conf             99996699982697422773488777613378998842548999999861----52551577789874999115876526
Q gi|254780306|r  659 LETKESVTLRSGRFGLYVQRGDGKDAKRCSLPKTWKSDSVDYDKAMSLLS----LPREIGIHPETQKNIIAGTGKYGYYL  734 (837)
Q Consensus       659 P~~G~~I~lk~GryGpYvq~Ge~~kpkr~si~k~~~~~~itle~Al~LLs----LPr~lG~~pe~g~~I~~~~GryGpYi  734 (837)
                      +.++.++.+|.|||||||++.....+.++++|.++.+.+++.+.|.+|+.    -||.||.||++|++|.+++|||||||
T Consensus       602 ~~~~~~~~~r~gk~G~~i~~~~~~~~~~~~~p~~~~~~~~~~~~~~~l~~~~~~g~r~LG~dP~tg~~V~~k~GryGpyv  681 (878)
T PRK07561        602 DLEGLPCVVRIGRFGPYLEGEREEEPIKASLPQDITPADLDPEQVEQILKQKTEGPEKLGTHPETGEPVYLLFGPYGPYV  681 (878)
T ss_pred             CCCCCCCEEEEECCCCCEEEECCCCCCCCCCCCCCCCCCCCHHHHHHHHHCCCCCCCCCCCCCCCCCEEEEEECCCCCEE
T ss_conf             77898623664167672021058765310267655865478788877641246787323668999986899935821869


Q ss_pred             EECC--------EECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCC-CCCEEEEECCCCCEEEE-
Q ss_conf             1678--------1112488775143579999999983651134434454432010267898-98469960685452536-
Q gi|254780306|r  735 NHDG--------AYTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPE-GGSITVHNGRYGPYLHW-  804 (837)
Q Consensus       735 ~~~~--------~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~-~~~i~i~~GryGpYi~~-  804 (837)
                      +.|.        +++||+++.++.+||||.|++||+=|               |++|.||+ |.+|.+-.|||||||+| 
T Consensus       682 qlG~~~~~~~Kpk~asl~k~~~~~~itle~Al~LlsLP---------------r~lG~~pe~g~~I~a~~GrfGPY~~~d  746 (878)
T PRK07561        682 QLGDVTEENPKPKRASLPKGVKPEDVTLEMALGLLSLP---------------RLLGEHPETGGKIQAGLGRFGPYVVHD  746 (878)
T ss_pred             EECCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCC---------------HHHCCCCCCCCEEEECCCCCCCCEEEC
T ss_conf             80477766778764456899980426899999997075---------------753788789987998767877667404


Q ss_pred             ----CCEEEECCCCCCHHHCCHHHHHHHHHHHHH
Q ss_conf             ----788875657889677899999999987772
Q gi|254780306|r  805 ----KKINASLSKEESPDTVDLEKALKILNIKKQ  834 (837)
Q Consensus       805 ----gk~Na~ipk~~~~e~lt~e~a~~li~~k~~  834 (837)
                          |+.++|||++.|+-+|++++|++||++++.
T Consensus       747 g~k~g~~~~sl~~~~~~~~i~l~~Av~lia~~k~  780 (878)
T PRK07561        747 KGKGEKDYRSLKKEDDVLTVDLERALELLAMPKK  780 (878)
T ss_pred             CCCCCCCCCCCCCCCCCEEECHHHHHHHHHHHHC
T ss_conf             7766764145799887645159999999961321


No 39 
>PRK06599 DNA topoisomerase I; Validated
Probab=99.97  E-value=3.5e-31  Score=253.09  Aligned_cols=163  Identities=20%  Similarity=0.314  Sum_probs=137.2

Q ss_pred             CCCCCCC-EEEEEECCCCCEEEECCCCCCCCC-CCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEE
Q ss_conf             6899996-699982697422773488777613-37899884254899999986152551577789874999115876526
Q gi|254780306|r  657 NDLETKE-SVTLRSGRFGLYVQRGDGKDAKRC-SLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYL  734 (837)
Q Consensus       657 ~dP~~G~-~I~lk~GryGpYvq~Ge~~kpkr~-si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi  734 (837)
                      .||.|+. ++.+|.||||+|+++++.++.+.. ++..+... ....++...+...||.||.+|+ |.+|.+++|||||||
T Consensus       599 ~cp~c~~g~l~~r~gk~G~f~~cs~yp~c~~~~~~~~~~~~-~~~~~~~~~~~~~~~~lG~d~~-g~~v~~k~GryGpyv  676 (776)
T PRK06599        599 VCPSCKTGELSLKLGKFGAFLACSNYPECTFRKSIVSGNDN-NENEGEPKAIPNENKVLGTDKD-GVEIYLKKGPYGPYI  676 (776)
T ss_pred             CCCCCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCC-CHHHHHHHHCCCCCCCCCCCCC-CCEEEEECCCCCCEE
T ss_conf             17878887358960586574115798666666768876564-0234566633467820242989-998999248886769


Q ss_pred             EECC-------EECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCC-CCCEEEEECCCCCEEEECC
Q ss_conf             1678-------1112488775143579999999983651134434454432010267898-9846996068545253678
Q gi|254780306|r  735 NHDG-------AYTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPE-GGSITVHNGRYGPYLHWKK  806 (837)
Q Consensus       735 ~~~~-------~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~-~~~i~i~~GryGpYi~~gk  806 (837)
                      +++.       ++.||++..++.+||||.|++||.-|               |++|.||+ |.+|.+.+|||||||+||+
T Consensus       677 q~g~~~~~~kpk~~sl~~~~~~~~itle~Al~ll~lP---------------r~lG~~p~~g~~i~~~~GryGpYvk~~~  741 (776)
T PRK06599        677 QLGEQEGKVKPKRSPVPASLNQNDITLEIALKLLSLP---------------LKIGIHKDSGEEIMIGYGKFGPYIKYMG  741 (776)
T ss_pred             EECCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCC---------------HHHCCCCCCCCEEEECCCCCCCEEEECC
T ss_conf             8447778778775678899983231899999998383---------------7319997899779987778872088899


Q ss_pred             EEEECCCCCCHHHCCHHHHHHHHHHHHHCC
Q ss_conf             887565788967789999999998777266
Q gi|254780306|r  807 INASLSKEESPDTVDLEKALKILNIKKQKK  836 (837)
Q Consensus       807 ~Na~ipk~~~~e~lt~e~a~~li~~k~~kk  836 (837)
                      +|+|||++.|+-+|||++|++||+++++|.
T Consensus       742 ~~~sl~~~~~~~~i~l~~A~~li~~~k~~~  771 (776)
T PRK06599        742 KFISIPKKYDFLNLSLDDAMKLIEDNKAKL  771 (776)
T ss_pred             EEEECCCCCCCCCCCHHHHHHHHHHHHHHC
T ss_conf             887679888874358999999999887633


No 40 
>cd01028 TOPRIM_TopoIA TOPRIM_TopoIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in the type IA family of DNA topoisomerases (TopoIA).  This subgroup contains proteins similar to the Type I DNA topoisomerases: E. coli topisomerases I and III, eukaryotic topoisomerase III and, ATP-dependent reverse gyrase found in archaea and thermophilic bacteria.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA. These enzymes cleave one strand of the DNA duplex, covalently link to the 5' phosphoryl end of the DNA break and allow the other strand of the duplex to pass through the gap. Reverse gyrase is also able to insert positive supercoils in the presence of ATP and negative supercoils in the presence of AMPPNP.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general b
Probab=99.97  E-value=1.1e-30  Score=249.36  Aligned_cols=123  Identities=38%  Similarity=0.592  Sum_probs=107.8

Q ss_pred             CCEEEECCHHHHHHHHHHHCC------------CCEEEEEECCCEECCCCCCCCCC-------CCCCCEEEEECCCHHHH
Q ss_conf             918997790478778875089------------98999942511007865578676-------66744068877654899
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGS------------NYKVLSSFGHIRDLPAKKGSVLP-------EKEFEMIWNIDPSSQKH   61 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~------------~y~V~as~GHirdLp~~~~~v~~-------~~~f~p~y~v~~~~kk~   61 (837)
                      |.|||||||++|++|+++||.            +|.|+||+|||++|+........       ...+.+.|...++++++
T Consensus         1 ~~LiIaEKPs~ak~Ia~~Lg~~~~~~~~~~~~~~~~v~~~~GHl~~l~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~   80 (142)
T cd01028           1 KVLIIAEKPSKAKTIAKILGKGSKKKGFYGEGGGYVVTASVGHLLELPFPEEYVDWDKDWPLELFPFEPKYVVIPDKKKQ   80 (142)
T ss_pred             CEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCEEEEEECCCEECCCCCCCCCCCCCCCCCCCCCCCEEEEECCCHHHH
T ss_conf             98999889999999999968996556753468988999964400046881025750005865457888069989656999


Q ss_pred             HHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCC
Q ss_conf             999999987099899946997025799999999975512578871699998037989999998622
Q gi|254780306|r   62 LQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSP  127 (837)
Q Consensus        62 ~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~  127 (837)
                      ++.|++++++||+||+|||||||||+|+||++++++.    .+++++|+|||++|+++|++||+||
T Consensus        81 ~~~i~~l~~~~d~iiiAtD~DrEGE~I~~~i~~~~~~----~~~~v~R~~fsslT~~~I~~A~~nl  142 (142)
T cd01028          81 LKALKKLAKKADEIVLATDPDREGELIAWEILEVLKC----DNKPVKRAWFSEITPKAIREAFKNL  142 (142)
T ss_pred             HHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHCC----CCCCCEEEEEECCCHHHHHHHHHCC
T ss_conf             9999999861999998889982279999999999578----8999278998357999999999758


No 41 
>cd03362 TOPRIM_TopoIA_TopoIII TOPRIM_TopoIA_TopoIII: The topoisomerase-primase (TORPIM) domain found in members of the type IA family of DNA topoisomerases (Topo IA) similar to topoisomerase III.   Type IA DNA topoisomerases remove (relax) negative supercoils in the DNA by: cleaving one strand of the DNA duplex, covalently linking to the 5' phosphoryl end of the DNA break and, allowing the other strand of the duplex to pass through the gap.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  For topoisomerases the conserved glutamate is believed to act as a general base in strand joining and, as a general acid in strand cleavage. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=99.97  E-value=1.6e-30  Score=248.23  Aligned_cols=124  Identities=28%  Similarity=0.431  Sum_probs=106.7

Q ss_pred             CCEEEECCHHHHHHHHHHHCC------------------CCEEEEEECCCEECCCCC---------CCCCCCCCCCEEEE
Q ss_conf             918997790478778875089------------------989999425110078655---------78676667440688
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGS------------------NYKVLSSFGHIRDLPAKK---------GSVLPEKEFEMIWN   53 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~------------------~y~V~as~GHirdLp~~~---------~~v~~~~~f~p~y~   53 (837)
                      |.|||||||++||+|+++||.                  +|.|+||+|||++|....         ....|...+...|+
T Consensus         1 m~LiIaEKPs~Ak~IA~~Lg~~~~~~~~~~~~~~~~~~~~~~vt~~~GHl~~l~~p~~y~~~~~~~~~~~~~~~~~~~~~   80 (151)
T cd03362           1 MVLIIAEKPSVAKAIAKILGGGSKKKGKGRYYEFYGEGGGYVVTWASGHLLELDFPEEYDPWDKVWPLEDPLFPAPFKLK   80 (151)
T ss_pred             CEEEEECCHHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCEEEEEECHHHCCCCCHHHCCCCCCCCCCCCCCCCCCEEEE
T ss_conf             99999889899999999848996114765433211368988999750232144530223544357855576788771589


Q ss_pred             ECCCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCC
Q ss_conf             77654899999999987099899946997025799999999975512578871699998037989999998622
Q gi|254780306|r   54 IDPSSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSP  127 (837)
Q Consensus        54 v~~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~  127 (837)
                      +.++++++++.|++++++||+||+|||||||||+|+|||+++++.   ..+++++|+|||++|+++|++||+|+
T Consensus        81 ~~~~~~~~~~~ik~l~~~ad~ii~atD~DrEGE~I~~ei~~~~~~---~~~~~v~R~~fs~lT~~~I~~A~~nL  151 (151)
T cd03362          81 VDKGKKKQFKVLKKLAKRADEIVIATDADREGELIGREILEYAKC---VKRKPVKRAWFSSLTPKAIRRAFKNL  151 (151)
T ss_pred             ECCCHHHHHHHHHHHHHHCCEEEECCCCCCCHHHHHHHHHHHHCC---CCCCCEEEEEEECCCHHHHHHHHHCC
T ss_conf             885489999999999853998998778872045999999998488---88985689998048999999999758


No 42 
>PRK09138 DNA topoisomerase I; Validated
Probab=99.97  E-value=7.2e-30  Score=243.28  Aligned_cols=158  Identities=25%  Similarity=0.420  Sum_probs=119.5

Q ss_pred             CCCCCCC-EEEEEECCCCCEEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEE
Q ss_conf             6899996-699982697422773488777613378998842548999999861525515777898749991158765261
Q gi|254780306|r  657 NDLETKE-SVTLRSGRFGLYVQRGDGKDAKRCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLN  735 (837)
Q Consensus       657 ~dP~~G~-~I~lk~GryGpYvq~Ge~~kpkr~si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~  735 (837)
                      .||.||. .+.||.|||||||.+++-+..+..   ..+.++....+   .--.-||.||.||++|++|.+.+|||||||+
T Consensus       604 ~cp~c~~g~l~l~~gk~G~figcsnypec~~t---~~l~~~~~~~~---~~~~~~r~LG~dP~tg~~v~~k~GrfGpyvq  677 (887)
T PRK09138        604 ICPTCGTGRLSLKLGKFGAFVGCSNYPECRYT---RQLSADGGEEA---AASDDPKVLGKDPETGEEVTLRSGRFGPYVQ  677 (887)
T ss_pred             CCCCCCCCCEEEECCCCCCCCCCCCCCCCCCC---CCCCCCCCCCH---HCCCCCCEEECCCCCCCEEEEEECCCCCEEE
T ss_conf             36678887368870576566656788644355---55788754201---1245783320079999758997047777586


Q ss_pred             ECC--------EECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCC-CCCEEEEECCCCCEEEECC
Q ss_conf             678--------1112488775143579999999983651134434454432010267898-9846996068545253678
Q gi|254780306|r  736 HDG--------AYTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPE-GGSITVHNGRYGPYLHWKK  806 (837)
Q Consensus       736 ~~~--------~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~-~~~i~i~~GryGpYi~~gk  806 (837)
                      .|.        +++||++..++.+||||.|+.||+=|               |++|.||+ |.+|.+-.|||||||+||+
T Consensus       678 ~G~~~~~~~kpk~asl~k~~~~~~itle~Al~LlsLP---------------r~lG~hpe~g~~I~a~~GrfGPYv~~~~  742 (887)
T PRK09138        678 LGEATAEGKKPKRASLPKGWSPADVDLEKALALLSLP---------------REVGKHPETGKPISAGIGRYGPYVKHGG  742 (887)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHCC---------------HHHCCCCCCCCEEEECCCCCCCCEEECC
T ss_conf             1687644457544678899980106899999998174---------------8538997899789981588766488899


Q ss_pred             EEEECCCCCCHHHCCHHHHHHHHHHHHHC
Q ss_conf             88756578896778999999999877726
Q gi|254780306|r  807 INASLSKEESPDTVDLEKALKILNIKKQK  835 (837)
Q Consensus       807 ~Na~ipk~~~~e~lt~e~a~~li~~k~~k  835 (837)
                      .|+||+++.|+-+|+|++|++||++++++
T Consensus       743 ~~~sl~~~~~~~~i~l~~A~~lia~~~~~  771 (887)
T PRK09138        743 TYANLEKVDDVFTIGLNRAVTLLAEKQAG  771 (887)
T ss_pred             EEECCCCCCCCEEECHHHHHHHHHHHHHC
T ss_conf             98268998986251699999999612103


No 43 
>smart00436 TOP1Bc Bacterial DNA topoisomeraes I ATP-binding domain. Extension of TOPRIM in Bacterial DNA topoisomeraes I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase beta subunit
Probab=99.96  E-value=6.4e-29  Score=236.14  Aligned_cols=88  Identities=52%  Similarity=0.834  Sum_probs=85.0

Q ss_pred             EEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHHHHHCHHHHHHCCC-CCCCCCHHHHHHHHHHHHHHHHH
Q ss_conf             69999803798999999862264698999999999998987401137898864146-76534226899999999999964
Q gi|254780306|r  107 IQRVSFNAITKQVVLNAMKSPRDINLDLVNAYLARRALDYLVGFNLSPILWQKLPG-ARSAGRVQSVALRLICNRENQIE  185 (837)
Q Consensus       107 v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~~aRr~lD~lvG~~lSp~L~rk~~~-~lSaGRVQtp~L~lIveRe~eI~  185 (837)
                      |+|+||||||+++|++||+||+++|++|++||+||+.+|||+|||+||++|.++.. ++|+||||||||+|||+||+||+
T Consensus         1 VkR~~~~~iT~~~I~~A~~n~~~~~~~l~~a~~aR~~~D~lvG~n~sr~~t~~~~~~~lS~GRVQtP~L~liv~Re~ei~   80 (89)
T smart00436        1 IKRIEFSEITKKAIREALKNPREIDENLVNAQLARRILDRLIGFNLSRLLTKKLRKGVLSAGRVQTPTLGLIVEREREIK   80 (89)
T ss_pred             CEEEEEECCCHHHHHHHHHCCCCCCHHHHHHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHH
T ss_conf             95888707899999999977572678699999999999999676215999998477898765506779999999899998


Q ss_pred             HCCCCCCEE
Q ss_conf             137654400
Q gi|254780306|r  186 SFVSEEYWS  194 (837)
Q Consensus       186 ~F~p~~y~~  194 (837)
                      +|+|++||+
T Consensus        81 ~F~p~~y~~   89 (89)
T smart00436       81 NFVPKPYWE   89 (89)
T ss_pred             CCCCCCCCC
T ss_conf             189976369


No 44 
>PRK08780 DNA topoisomerase III; Provisional
Probab=99.95  E-value=5.5e-27  Score=221.61  Aligned_cols=165  Identities=19%  Similarity=0.281  Sum_probs=127.7

Q ss_pred             CCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCC----CCCCC--CCCC----CCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             6114334677731368715776111234343233321----00122--1000----012344201468999966999826
Q gi|254780306|r  601 DSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTR----QLTSN--PQDI----PEMKESVLLGNDLETKESVTLRSG  670 (837)
Q Consensus       601 ~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~----~l~~~--~~~~----~~~~~~~~LG~dP~~G~~I~lk~G  670 (837)
                      ..+.||+||.. +.++ .|+||+|+.|..-.+...++    +-..+  ..++    .-+..|+.||.  ++|++|.+..|
T Consensus       590 ~lg~dp~~g~~-v~~k-~GryGpyvq~g~~~~~~kpk~~sl~~~~~~~~i~le~Al~ll~lPr~lG~--~~g~~i~~~~G  665 (783)
T PRK08780        590 VLGTDPKSGKE-VSAR-IGRFGPMVQIGTVDDEEKPRFASLRPGQSIYSISLEEALELFKMPRALGE--DKGQDVSVGIG  665 (783)
T ss_pred             CCCCCCCCCCE-EEEE-ECCCCCEEEECCCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHCCCHHHCC--CCCCEEEECCC
T ss_conf             04889888970-5998-33777767514787566986331799999132789999998705242089--99977997768


Q ss_pred             CCCCEEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHHHC------CHHHCCCCCCCCEEEEEECCCCCEEEECCEECCCC
Q ss_conf             974227734887776133789988425489999998615------25515777898749991158765261678111248
Q gi|254780306|r  671 RFGLYVQRGDGKDAKRCSLPKTWKSDSVDYDKAMSLLSL------PREIGIHPETQKNIIAGTGKYGYYLNHDGAYTKLE  744 (837)
Q Consensus       671 ryGpYvq~Ge~~kpkr~si~k~~~~~~itle~Al~LLsL------Pr~lG~~pe~g~~I~~~~GryGpYi~~~~~~~sl~  744 (837)
                      ||||||++|.    +++||+++.++-+|+|+.|+.|+.-      ++.||.||  |.+|.+.+|||||||+|++.|+|||
T Consensus       666 r~GpYv~~~~----~~~sl~~~~~~~~i~l~~A~~li~~~~~~~~~~~~~~~~--~~~i~v~~GryGpYv~~gk~na~ip  739 (783)
T PRK08780        666 RFGPFARRGS----TYVSLKKEDDPYTIDLARAVFLIEEKEEIARNRVIKDFE--GSDIQVLNGRFGPYISDGKLNGKIP  739 (783)
T ss_pred             CCCCCEEECC----EEECCCCCCCCEEECHHHHHHHHHHHHHCCCCCCCCCCC--CCCEEEECCCCCCEEEECCEEEECC
T ss_conf             8775475798----883479998764527999999997032026566666689--9974881268864077798995058


Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHCCCCCCCCC
Q ss_conf             8775143579999999983651134434454
Q gi|254780306|r  745 SIEQVLTIDLEQAISCITEKKKIEKSSRKNS  775 (837)
Q Consensus       745 ~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~  775 (837)
                      ++.+|.+|||++|++||+++++..++++++.
T Consensus       740 k~~~~~~ltle~a~~li~e~~~~~~~~~~~~  770 (783)
T PRK08780        740 KDREPASLTLEEVQQLLADTGKPVRKGFGAK  770 (783)
T ss_pred             CCCCCCCCCHHHHHHHHHHCCCCCCCCCCCC
T ss_conf             9998000899999999972788877788888


No 45 
>COG1754 Uncharacterized C-terminal domain of topoisomerase IA [General function prediction only]
Probab=99.94  E-value=2.8e-27  Score=223.88  Aligned_cols=164  Identities=24%  Similarity=0.383  Sum_probs=119.6

Q ss_pred             CCEECCCCCCCCEEEEEECCCCCCCCC--CCC-CCCCC-CCCCCCCCCC------CCCCCCCCCCCCCCCCCCEEEEEEC
Q ss_conf             611433467773136871577611123--434-32333-2100122100------0012344201468999966999826
Q gi|254780306|r  601 DSRTCPECHTHSLSLKLSSKYGAFVGC--TNY-PECKY-TRQLTSNPQD------IPEMKESVLLGNDLETKESVTLRSG  670 (837)
Q Consensus       601 ~~~~Cp~C~~g~L~~k~~gK~G~FigC--Sny-PeCk~-t~~l~~~~~~------~~~~~~~~~LG~dP~~G~~I~lk~G  670 (837)
                      ..+.-|.-+  .-..-+.|+||+|+.-  ..- ++-+. ..+-..++.+      +.-+.-++.||+||++|+.|.+-+|
T Consensus        77 ~LG~DP~tG--~eI~~k~GryGPYVq~~lg~~~~kpkraSLpkg~~~e~ItLE~AL~LLsLPR~iG~hp~sge~I~ag~G  154 (298)
T COG1754          77 VLGIDPETG--EEIYLKNGRYGPYVQEQLGDPKPKPKRASLPKGWKPETITLEKALKLLSLPRVIGKHPDSGEEISAGLG  154 (298)
T ss_pred             CCCCCCCCC--CEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCHHHCCHHHHHHHHCCCHHHCCCCCCCCEEEECCC
T ss_conf             236688888--566885267776156434788888544668898883127599999987382430779888867886146


Q ss_pred             CCCCEEE-ECCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCCH----------HHCCCCCCCCEEEEEECCCCCEEEECCE
Q ss_conf             9742277-3488777613378998842548999999861525----------5157778987499911587652616781
Q gi|254780306|r  671 RFGLYVQ-RGDGKDAKRCSLPKTWKSDSVDYDKAMSLLSLPR----------EIGIHPETQKNIIAGTGKYGYYLNHDGA  739 (837)
Q Consensus       671 ryGpYvq-~Ge~~kpkr~si~k~~~~~~itle~Al~LLsLPr----------~lG~~pe~g~~I~~~~GryGpYi~~~~~  739 (837)
                      ||||||- .|.    -.+||.+.-++=+|||+.|+.|+.-.|          .||.||+.|++|.+..|||||||+|+++
T Consensus       155 RfGPyv~k~Gs----d~~sL~~~dd~ftItL~rA~~liaEk~~~G~s~~alk~lg~~p~~g~pI~v~dGrfGpYv~~Gk~  230 (298)
T COG1754         155 RFGPYVKKRGS----DYRSLKSEDDVFTITLDRALKLIAEKRSRGRSAAALKELGTHPEGGKPITVKDGRFGPYVKDGKT  230 (298)
T ss_pred             CCCCCEEECCC----CCCCCCCCCCEEEECHHHHHHHHHHHHCCCCCHHHHHHHCCCCCCCCCEEEECCCCCCCCCCCCC
T ss_conf             65763310684----21144553432663089999999745303764456887445846785158844786762001530


Q ss_pred             ECCCCCCCCCCCCCHHHHHHHHHHHHHCCCC
Q ss_conf             1124887751435799999999836511344
Q gi|254780306|r  740 YTKLESIEQVLTIDLEQAISCITEKKKIEKS  770 (837)
Q Consensus       740 ~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~  770 (837)
                      |++|++.+|+-+||+++|++||++....++.
T Consensus       231 Na~Lpkg~d~~sit~e~A~~LLaer~a~~~~  261 (298)
T COG1754         231 NATLPKGKDPASITLEEALELLAERRAKGGP  261 (298)
T ss_pred             CCCCCCCCCCCCCCHHHHHHHHHHHCCCCCC
T ss_conf             3657899880106799999999974146888


No 46 
>LOAD_Toprim consensus
Probab=99.93  E-value=3.1e-25  Score=208.44  Aligned_cols=98  Identities=35%  Similarity=0.566  Sum_probs=88.1

Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             91899779047877887508998999942511007865578676667440688776548999999999870998999469
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATD   80 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD   80 (837)
                      .+|||||||+||++|++|||+ |.|.||+||+++                         +.+..+++++++++.||||||
T Consensus         1 K~liIVEsp~k~k~I~~~l~~-~~vias~GHi~~-------------------------~~~~~~~~~~~~~~~VilATD   54 (98)
T LOAD_Toprim       1 KKIIVVEGPADAKAIERFGGD-KNVIASKGHARK-------------------------KSVLELIKLALKAKEVIIATD   54 (98)
T ss_pred             CEEEEEECHHHHHHHHHHCCC-CEEEECCCCCCC-------------------------CHHHHHHHHHHCCCEEEEECC
T ss_conf             949999284889999998599-879979588325-------------------------169999999846992999469


Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCC
Q ss_conf             970257999999999755125788716999980379899999986226
Q gi|254780306|r   81 PDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPR  128 (837)
Q Consensus        81 ~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r  128 (837)
                      ||||||+||||+.++|...    ...++|+.|||||+.||.+|++||.
T Consensus        55 pDrEGEaIa~hl~~~l~~~----~~~~~Ri~f~eitk~ai~~ai~~p~   98 (98)
T LOAD_Toprim      55 PDREGEKIAKKLLELLRGY----GGFVRRAVFLEITEEAIKEGIRKAL   98 (98)
T ss_pred             CCCCHHHHHHHHHHHHCCC----CCCEEEEEEECCCHHHHHHHHHCCC
T ss_conf             6965289999999983677----9974689980539899999997759


No 47 
>pfam01751 Toprim Toprim domain. This is a conserved region from DNA primase. This corresponds to the Toprim domain common to DnaG primases, topoisomerases, OLD family nucleases and RecR proteins. Both DnaG motifs IV and V are present in the alignment, the DxD (V) motif may be involved in Mg2+ binding and mutations to the conserved glutamate (IV) completely abolish DnaG type primase activity. DNA primase EC:2.7.7.6 is a nucleotidyltransferase it synthesizes the oligoribonucleotide primers required for DNA replication on the lagging strand of the replication fork; it can also prime the leading stand and has been implicated in cell division. This family also includes the atypical archaeal A subunit from type II DNA topoisomerases. Type II DNA topoisomerases catalyse the relaxation of DNA supercoiling by causing transient double strand breaks.
Probab=99.50  E-value=2e-13  Score=119.90  Aligned_cols=89  Identities=37%  Similarity=0.630  Sum_probs=76.4

Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             91899779047877887508998999942511007865578676667440688776548999999999870998999469
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATD   80 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD   80 (837)
                      +.|+|||+|+.+.+|+++++.++.+.++.||+.+|.                   +.++++++.|++..+++ +||+|||
T Consensus         1 ~~l~IVE~~~d~~~i~~~~~~~~~~~~~~G~~~~l~-------------------~~~~~~~~~l~~~~~~~-eViiatD   60 (89)
T pfam01751         1 KVLIIVEGPSDAIALAKAGGYKGNVVALLGHLSDVI-------------------PLTKEQLKLLKKLAKKD-EVILATD   60 (89)
T ss_pred             CEEEEECCHHHHHHHHHHCCCCEEEEEEECEECCCC-------------------CCCHHHHHHHHHHHCCC-EEEEECC
T ss_conf             989998988999999962488879998415705765-------------------54246799999862377-4999879


Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEE
Q ss_conf             970257999999999755125788716999980
Q gi|254780306|r   81 PDREGEAISWHVLDVLRQKNLIEKTKIQRVSFN  113 (837)
Q Consensus        81 ~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~  113 (837)
                      +|||||+|+||+.+.|+...    .+++|+.++
T Consensus        61 ~D~eGe~~a~~l~~~l~~~~----~~v~ri~~~   89 (89)
T pfam01751        61 PDREGEAIAWKLLELLKPLG----KKVRRIFLP   89 (89)
T ss_pred             CCHHHHHHHHHHHHHHHHCC----CCEEEEECC
T ss_conf             89489999999999831229----816999669


No 48 
>smart00493 TOPRIM topoisomerases, DnaG-type primases, OLD family nucleases and RecR proteins.
Probab=99.43  E-value=7e-13  Score=115.74  Aligned_cols=74  Identities=38%  Similarity=0.561  Sum_probs=66.3

Q ss_pred             CCEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCC
Q ss_conf             91899779047877887508998999942511007865578676667440688776548999999999870998999469
Q gi|254780306|r    1 MNVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATD   80 (837)
Q Consensus         1 M~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD   80 (837)
                      ..|+|||+|+.+.+|+++++.++.|.|+.||+.                        ++++++.|++..++ ++||+|||
T Consensus         1 ~~liIVEg~~d~~~i~~~~~~~~~~~~~~G~~~------------------------~~~~i~~l~~~~~~-~eViiatD   55 (76)
T smart00493        1 KVLIIVEGPADAIALEKAGGFGGNVVALGGHLL------------------------KKEIIKLLKRLAKK-KEVILATD   55 (76)
T ss_pred             CEEEEECCHHHHHHHHHHCCCCEEEEECCCCCC------------------------CHHHHHHHHHHHCC-CEEEEECC
T ss_conf             979998788899999985699979998215235------------------------04489999986338-97999769


Q ss_pred             CCCHHHHHHHHHHHHHHHH
Q ss_conf             9702579999999997551
Q gi|254780306|r   81 PDREGEAISWHVLDVLRQK   99 (837)
Q Consensus        81 ~DREGE~Iawhi~e~l~~~   99 (837)
                      +|||||+|+||+.+.|+..
T Consensus        56 ~D~eGe~~a~~i~~~l~~~   74 (76)
T smart00493       56 PDREGEAIAWKLAELLKPA   74 (76)
T ss_pred             CCCCHHHHHHHHHHHHHHC
T ss_conf             8944699999999987762


No 49 
>PRK09137 DNA topoisomerase I; Validated
Probab=99.27  E-value=2.9e-11  Score=103.56  Aligned_cols=113  Identities=23%  Similarity=0.374  Sum_probs=77.9

Q ss_pred             CCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-EEEEEECCCCC-EEEE
Q ss_conf             611433467773136871577611123434323332100122100001234420146899996-69998269742-2773
Q gi|254780306|r  601 DSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKE-SVTLRSGRFGL-YVQR  678 (837)
Q Consensus       601 ~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~-~I~lk~GryGp-Yvq~  678 (837)
                      ....||+|+..++ ++ .|++|.|++||+||+|+++.++...         ...-+.||+||. +|+.|.+|+|. |.-+
T Consensus       638 ~~~~Cp~Cg~~mv-~k-~gr~G~f~~Cs~yP~Ck~~~~~~k~---------~~~~~~CP~C~~g~~~~r~~k~Gk~f~gC  706 (761)
T PRK09137        638 EGRKCPKCGSPLH-IK-QGRYGKFIGCSNYPECKHMEPLEKP---------KDTGVTCPKCKKGELVEKKSRYGKIFYSC  706 (761)
T ss_pred             CCCCCCCCCCCEE-EE-ECCCCCEEECCCCCCCCCCCCCCCC---------CCCCCCCCCCCCCCEEEEECCCCCCCCCC
T ss_conf             7886988997127-86-1467634533799876677766676---------66776198999987777517999940278


Q ss_pred             CCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEE--ECCCCCEEEECCEECCC
Q ss_conf             488777613378998842548999999861525515777898749991--15876526167811124
Q gi|254780306|r  679 GDGKDAKRCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQKNIIAG--TGKYGYYLNHDGAYTKL  743 (837)
Q Consensus       679 Ge~~kpkr~si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~--~GryGpYi~~~~~~~sl  743 (837)
                      ...++.++++-.+                  | +-..||.||.++.+.  .++-|.++.|-++...-
T Consensus       707 ~~yp~C~~~~~~~------------------p-~~~~Cp~Cg~~~~~~k~~~~~g~~~~C~n~~C~~  754 (761)
T PRK09137        707 ARYPKCKYALWNP------------------P-VAEPCPKCGWPILTIKTTKRRGEEKVCPQEECDY  754 (761)
T ss_pred             CCCCCCCCCCCCC------------------C-CCCCCCCCCCCEEEEEECCCCCCEEECCCCCCCC
T ss_conf             9889998424799------------------8-8997867997015888426786279898999998


No 50 
>PRK08413 consensus
Probab=99.26  E-value=3.7e-11  Score=102.76  Aligned_cols=107  Identities=19%  Similarity=0.282  Sum_probs=79.7

Q ss_pred             CEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC-CCCCCCCEEEEEECCCCCEEEECC
Q ss_conf             1143346777313687157761112343432333210012210000123442014-689999669998269742277348
Q gi|254780306|r  602 SRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLG-NDLETKESVTLRSGRFGLYVQRGD  680 (837)
Q Consensus       602 ~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG-~dP~~G~~I~lk~GryGpYvq~Ge  680 (837)
                      ...||+|+..++.  ..|++|.|++|++||+|+.+........      .+...| .||+||.+|++|.||+|.|  +|.
T Consensus       613 ~~~c~~cg~~m~~--k~gr~g~f~~C~~~p~ck~~~~~~~~~~------~~~~~~~~CP~Cgg~l~~r~sk~GkF--~gC  682 (733)
T PRK08413        613 EEVCEKCGGPMVQ--KFGRNGEFLACSGYPKCKNTKSLKNTPN------AKEVIGVKCPECGGEIVERFSRRGKF--YGC  682 (733)
T ss_pred             CCCCCCCCCHHHE--EECCCCCEEECCCCCCCCCCCCCCCCCC------CCCCCCCCCCCCCCEEEEEECCCCCE--ECC
T ss_conf             5668767841321--2057873443479988877412556667------66556856899999899871799975--368


Q ss_pred             CC--CCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEEEC
Q ss_conf             87--7761337899884254899999986152551577789874999115876526167
Q gi|254780306|r  681 GK--DAKRCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNHD  737 (837)
Q Consensus       681 ~~--kpkr~si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~~~  737 (837)
                      ..  +.++++-.+                   -+--.||+||.+++-..++.|+++.|-
T Consensus       683 s~YP~C~f~~~~~-------------------P~~~~Cp~Cg~~~~~~~~~~~~~~~C~  722 (733)
T PRK08413        683 SNYPKCNFISNYE-------------------PINKKCEECGYMMVKREYRKKEVHECI  722 (733)
T ss_pred             CCCCCCCCCCCCC-------------------CCCCCCCCCCCEEEEEECCCCCEEECC
T ss_conf             9999998767789-------------------578968789932089984789879899


No 51 
>PRK06319 DNA topoisomerase I/SWI domain fusion protein; Validated
Probab=99.19  E-value=5.3e-11  Score=101.63  Aligned_cols=80  Identities=20%  Similarity=0.426  Sum_probs=56.7

Q ss_pred             CEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCC--CCCEEEEEECCCCCEEEEC
Q ss_conf             11433467773136871577611123434323332100122100001234420146899--9966999826974227734
Q gi|254780306|r  602 SRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLE--TKESVTLRSGRFGLYVQRG  679 (837)
Q Consensus       602 ~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~--~G~~I~lk~GryGpYvq~G  679 (837)
                      ...||+|+. .|.+| .||||.||||||||+|++|.++......   ..+......||.  ||..|+.|.+|+|- +-+|
T Consensus       645 ~~~Cp~Cg~-~mv~k-~gr~G~F~~Cs~YP~Ck~t~~l~k~~~~---~~~~~~~v~cp~~~c~g~~v~r~sr~g~-~Fyg  718 (864)
T PRK06319        645 DSPCPLCGG-EMKVR-HGRFGTFLGCENYPECRGIINIHKKGEE---GIEQEETIPCPAIGCTGHIVKRRSRFNK-IFYS  718 (864)
T ss_pred             CCCCCCCCC-CCEEE-CCCCCCCCCCCCCCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCCCEEEEEECCCCC-EEEC
T ss_conf             998767897-01131-3787754316998577897466666777---8765677768998989868886347898-4436


Q ss_pred             CCCCCCCC
Q ss_conf             88777613
Q gi|254780306|r  680 DGKDAKRC  687 (837)
Q Consensus       680 e~~kpkr~  687 (837)
                      .+..|+.-
T Consensus       719 c~~yP~c~  726 (864)
T PRK06319        719 CSEYPECS  726 (864)
T ss_pred             CCCCCCCC
T ss_conf             78899985


No 52 
>PRK08938 DNA topoisomerase I; Validated
Probab=99.12  E-value=9.3e-11  Score=99.80  Aligned_cols=67  Identities=25%  Similarity=0.443  Sum_probs=52.4

Q ss_pred             CEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEECC
Q ss_conf             1143346777313687157761112343432333210012210000123442014689999669998269742277348
Q gi|254780306|r  602 SRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKESVTLRSGRFGLYVQRGD  680 (837)
Q Consensus       602 ~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq~Ge  680 (837)
                      ...||+|+.|.+..+.+++++.|+||||||+|+|+.--            ....+.||+||.+|+.|.|++|.|+.+-+
T Consensus       617 ~~~CP~C~~g~l~~r~sk~g~~f~gCs~yp~C~~~~~~------------~p~~~~Cp~Cg~~~~~~~~~~g~~~~C~n  683 (692)
T PRK08938        617 GVTCPKCHKGQVIERKSKKNRIFYGCDRYPECDFVSWD------------KPIGRDCPKCGHYLVEKKVKKGKQVQCSN  683 (692)
T ss_pred             CCCCCCCCCCCEEEEECCCCCEEEECCCCCCCCEECCC------------CCCCCCCCCCCCCCEEEECCCCCEEECCC
T ss_conf             88295999974575514789877748989989831678------------87488499999604268557888797899


No 53 
>PRK07219 DNA topoisomerase I; Validated
Probab=99.03  E-value=4.6e-09  Score=87.10  Aligned_cols=113  Identities=16%  Similarity=0.279  Sum_probs=71.9

Q ss_pred             CCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCC-EEEEC
Q ss_conf             61143346777313687157761112343432333210012210000123442014689999669998269742-27734
Q gi|254780306|r  601 DSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKESVTLRSGRFGL-YVQRG  679 (837)
Q Consensus       601 ~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~~I~lk~GryGp-Yvq~G  679 (837)
                      ....||+||..++.+.+.|++| ++.|++ |+|+++++.             ...|.||.||.+|++|.+|+|- |+-+.
T Consensus       631 ~~~~Cp~Cg~~~ik~~~~g~~~-~~~c~~-P~C~~~~~~-------------~~~~~CP~cgg~lv~r~sk~gk~F~gCs  695 (769)
T PRK07219        631 NDQKCPVCGLPMIKIIRKGQSP-EVKCID-PACDYNKEK-------------EDYGECPADGGRLVLRQSRYGKRFLGCS  695 (769)
T ss_pred             CCCCCCCCCCHHHHEECCCCCC-CCCCCC-CCCCCCCCC-------------CCCCCCCCCCCEEEEECCCCCCEEECCC
T ss_conf             6886878895255012466687-740599-988787787-------------7772288999779986378998565179


Q ss_pred             CCCCCCCC-CCCCCCCHHHCCHHHHHHHHHCCHHHC-CCCCCCCEEEEEECCCCCEEEECCEECCC
Q ss_conf             88777613-378998842548999999861525515-77789874999115876526167811124
Q gi|254780306|r  680 DGKDAKRC-SLPKTWKSDSVDYDKAMSLLSLPREIG-IHPETQKNIIAGTGKYGYYLNHDGAYTKL  743 (837)
Q Consensus       680 e~~kpkr~-si~k~~~~~~itle~Al~LLsLPr~lG-~~pe~g~~I~~~~GryGpYi~~~~~~~sl  743 (837)
                      ..++.+.. .+|..-.+               +.+| .||.||.+++...+..|++..|-+....-
T Consensus       696 ~yP~C~~t~~lp~~~~~---------------~~~~e~Cp~Cg~~~~~~~~~~~~~~~C~~~~C~~  746 (769)
T PRK07219        696 NYPKCTVTYPLPQKGII---------------KKTGEKCPYCGAPILVLINGRRHWKFCPNIDCEY  746 (769)
T ss_pred             CCCCCCCCCCCCCCCCC---------------CCCCCCCCCCCCEEEEEECCCCCEEECCCCCCCC
T ss_conf             99999752507544764---------------5058847778983799972784300689989998


No 54 
>PRK05582 DNA topoisomerase I; Validated
Probab=98.97  E-value=6e-10  Score=93.72  Aligned_cols=106  Identities=19%  Similarity=0.329  Sum_probs=65.1

Q ss_pred             CCCCCCCEEEEEECCCCCEEEECCCCCCCCC-CCCCCCCHHHCCHHHHHHHHHCCHHHC-CCCCCCCEEEEEECCCCC-E
Q ss_conf             6899996699982697422773488777613-378998842548999999861525515-777898749991158765-2
Q gi|254780306|r  657 NDLETKESVTLRSGRFGLYVQRGDGKDAKRC-SLPKTWKSDSVDYDKAMSLLSLPREIG-IHPETQKNIIAGTGKYGY-Y  733 (837)
Q Consensus       657 ~dP~~G~~I~lk~GryGpYvq~Ge~~kpkr~-si~k~~~~~~itle~Al~LLsLPr~lG-~~pe~g~~I~~~~GryGp-Y  733 (837)
                      .||.||.++.+|.||||.|+-+..-++.+.. ++.+...             .-|...| .||.||..++.+.||+|- |
T Consensus       575 ~Cp~Cg~~l~~r~~~~G~F~~Cs~yP~Ck~t~~~~~~~~-------------~~~~~~~~~CP~C~~~l~~r~~k~gk~F  641 (692)
T PRK05582        575 KCPKCGRELVIKHGRYGEFIACSNYPKCKYTKPIEEEEK-------------LASEELDVKCPECGGKIVKRKSKKGKKF  641 (692)
T ss_pred             CCCCCCCCCEEEECCCCCEEECCCCCCCCCCCCCCCCCC-------------CCCCCCCCCCCCCCCEEEEEECCCCCEE
T ss_conf             775679820267268896265789987889776876444-------------4445369979999977478854899989


Q ss_pred             EEECCEECCCCCCCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCC-CCCEEEEECCCCCEEEEC
Q ss_conf             616781112488775143579999999983651134434454432010267898-984699606854525367
Q gi|254780306|r  734 LNHDGAYTKLESIEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPE-GGSITVHNGRYGPYLHWK  805 (837)
Q Consensus       734 i~~~~~~~sl~~~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~-~~~i~i~~GryGpYi~~g  805 (837)
                      +.|.+ |..++-...     .                      .|.  -...|. |++++.+.||+|.|+.|-
T Consensus       642 ~gCs~-yp~C~~~~~-----~----------------------~p~--~~~Cp~Cg~~~~~k~~~~~~~~~c~  684 (692)
T PRK05582        642 YGCSN-YPKCNFISN-----Y----------------------EPS--NEKCPECGSYMVKKESKKGEYLECS  684 (692)
T ss_pred             EECCC-CCCCCCCCC-----C----------------------CCC--CCCCCCCCCHHHEEECCCCCEEECC
T ss_conf             97489-999997738-----8----------------------999--9969999815704745888878899


No 55 
>PRK09001 DNA topoisomerase I; Validated
Probab=98.76  E-value=1.5e-08  Score=83.18  Aligned_cols=146  Identities=21%  Similarity=0.313  Sum_probs=84.4

Q ss_pred             CEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEECCC
Q ss_conf             11433467773136871577611123434323332100122100001234420146899996699982697422773488
Q gi|254780306|r  602 SRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKESVTLRSGRFGLYVQRGDG  681 (837)
Q Consensus       602 ~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq~Ge~  681 (837)
                      .+.||+|+..+-..- ....+.+..|+|+|+|..+.-. ...-.+....++.  =.||.||.+|.||.||||.|+.+.+ 
T Consensus       664 ~~~c~~c~~~md~yl-~d~~~k~~~c~n~p~c~g~~~e-~g~~~~~~~~~p~--~~C~kCg~~m~lk~GRfGkf~~Ct~-  738 (869)
T PRK09001        664 KRRCPKCGTAMDSYL-IDEKRKLHVCGNNPDCDGYEIE-EGEFKIKGYDGPI--VECDKCGSEMHLKTGRFGKYFGCTN-  738 (869)
T ss_pred             CCCCCCCCCCHHHHE-ECCCCEEEECCCCCCCCCEEEC-CCCCCCCCCCCCC--CCCCCCCCCCEEECCCCCCCCCCCC-
T ss_conf             454774355013212-0477447644799888865622-5620125777786--5365579854550367646431599-


Q ss_pred             CCCCCC-CCCCCC-----CHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEEECCEECCCCCCCCCCCCCHH
Q ss_conf             777613-378998-----84254899999986152551577789874999115876526167811124887751435799
Q gi|254780306|r  682 KDAKRC-SLPKTW-----KSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTIDLE  755 (837)
Q Consensus       682 ~kpkr~-si~k~~-----~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~~~~~~~sl~~~~~~~~I~l~  755 (837)
                      ++.|+. .|.++=     ..+.|.+.+          | .|+.|+...+++.|+.|+++.|.+ |......--|+--.|.
T Consensus       739 ~~Ck~trk~~~~g~~~pp~~~pi~~~~----------l-~c~k~~~~~vlr~~~~g~fla~s~-fpk~retr~p~v~e~~  806 (869)
T PRK09001        739 EECKNTRKILKNGEVAPPKEDPVPLPE----------L-KCEKSDAYFVLRDGAAGIFLAAST-FPKSRETRAPLVEELV  806 (869)
T ss_pred             CCCCCHHHHHCCCCCCCCCCCCCCCCC----------C-CCCCCCCEEEEECCCCCCCCCCCC-CCCCCCCCCCHHHHHH
T ss_conf             778567777417994999889978876----------6-566459846865255551000167-9865454783189989


Q ss_pred             HHHHHHHHH
Q ss_conf             999999836
Q gi|254780306|r  756 QAISCITEK  764 (837)
Q Consensus       756 ~Aieli~~~  764 (837)
                      +-.+.|.++
T Consensus       807 ~~~~~~~~k  815 (869)
T PRK09001        807 RFRDRLPEK  815 (869)
T ss_pred             HHHHHCCHH
T ss_conf             887646888


No 56 
>pfam01396 zf-C4_Topoisom Topoisomerase DNA binding C4 zinc finger.
Probab=98.41  E-value=1.3e-07  Score=76.24  Aligned_cols=38  Identities=53%  Similarity=1.177  Sum_probs=31.4

Q ss_pred             CEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             1143346777313687157761112343432333210012
Q gi|254780306|r  602 SRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTS  641 (837)
Q Consensus       602 ~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~  641 (837)
                      +++||+|+ +.|.++ .+|+|.|||||+||+|+||.++..
T Consensus         1 vgkCP~Cg-~~l~~r-~~r~G~F~gCs~yP~C~~t~~l~k   38 (39)
T pfam01396         1 VGKCPKCG-GDLVLK-RGKFGKFVGCSNYPECKFTKPLKK   38 (39)
T ss_pred             CCCCCCCC-CEEEEE-ECCCCEEEECCCCCCCCCEEECCC
T ss_conf             94377899-981688-368770872899989888132688


No 57 
>PRK05823 consensus
Probab=98.26  E-value=3.7e-07  Score=72.77  Aligned_cols=76  Identities=17%  Similarity=0.313  Sum_probs=48.3

Q ss_pred             CCCCCCCEEEEEECCCC--CEEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHC-CCCCCCCEEEEEECCCCC-
Q ss_conf             68999966999826974--22773488777613378998842548999999861525515-777898749991158765-
Q gi|254780306|r  657 NDLETKESVTLRSGRFG--LYVQRGDGKDAKRCSLPKTWKSDSVDYDKAMSLLSLPREIG-IHPETQKNIIAGTGKYGY-  732 (837)
Q Consensus       657 ~dP~~G~~I~lk~GryG--pYvq~Ge~~kpkr~si~k~~~~~~itle~Al~LLsLPr~lG-~~pe~g~~I~~~~GryGp-  732 (837)
                      .||.||.++.+|.|+||  +|+-+..-++.+....... .+           ..-|..++ .||.||.+++.+.||||. 
T Consensus       603 ~CP~Cg~~l~~r~~~~g~~~F~~Cs~yp~Ck~~~~~~~-~~-----------~~~~~~~~~~CP~Cg~~lv~r~~k~~k~  670 (691)
T PRK05823        603 DCPKCASDLLYRRTRRGNEKFVGCSNFPKCKFTEFSEQ-KP-----------LEKPEELEELCPECNSKLVKRKTKFNKN  670 (691)
T ss_pred             CCCCCCCCCEEEECCCCCCEEEECCCCCCCCCCCCCCC-CC-----------CCCCCCCCCCCCCCCCHHHHEECCCCCC
T ss_conf             89888982036742688860455799998878777787-76-----------6663325885999982474220235899


Q ss_pred             --EEEECCEECCCCC
Q ss_conf             --2616781112488
Q gi|254780306|r  733 --YLNHDGAYTKLES  745 (837)
Q Consensus       733 --Yi~~~~~~~sl~~  745 (837)
                        |+.|.+ |..++-
T Consensus       671 ~~f~gCs~-yP~C~~  684 (691)
T PRK05823        671 KTFIGCSN-FPKCNY  684 (691)
T ss_pred             CEEEECCC-CCCCCC
T ss_conf             87996899-999998


No 58 
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=98.22  E-value=3.8e-06  Score=65.20  Aligned_cols=66  Identities=30%  Similarity=0.684  Sum_probs=47.0

Q ss_pred             CCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCC-CEEEEEECCCC
Q ss_conf             567661143346777313687157761112343432333-210012210000123442014689999-66999826974
Q gi|254780306|r  597 ENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKY-TRQLTSNPQDIPEMKESVLLGNDLETK-ESVTLRSGRFG  673 (837)
Q Consensus       597 ~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~-t~~l~~~~~~~~~~~~~~~LG~dP~~G-~~I~lk~GryG  673 (837)
                      ....+...||+|+..++. + .+++|.|+||||||+|.+ +.+         .......-+..|+|| ..+.++.|+||
T Consensus        12 ~~~~~~~~Cp~Cg~~m~~-~-~~~~g~f~gCs~yP~C~~~~~~---------~~~~~~~~~~Cp~C~~~~~~~k~~~~~   79 (140)
T COG0551          12 KDLKTGQICPKCGKNMVK-K-FGKYGIFLGCSNYPKCDYYEPE---------KAIAEKTGVKCPKCGKGLLVLKKGRFG   79 (140)
T ss_pred             ECCCCCCCCCCCCCCEEE-E-ECCCCEEEECCCCCCCCCCCCC---------CCCCCCCCEECCCCCCCCCEEEECCCC
T ss_conf             012357607777754057-8-5458779835888655667542---------332124776677667734023434567


No 59 
>cd00188 TOPRIM Topoisomerase-primase domain. This is a nucleotidyl transferase/hydrolase domain found in type IA, type IIA and type IIB topoisomerases, bacterial DnaG-type primases, small primase-like proteins from bacteria and archaea, OLD family nucleases from bacterial and archaea, and bacterial DNA repair proteins of the RecR/M family. This domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases and in strand joining in topoisomerases and, as a general acid in strand cleavage by topisomerases and nucleases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=97.86  E-value=0.0002  Score=52.24  Aligned_cols=72  Identities=33%  Similarity=0.481  Sum_probs=59.7

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP   81 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~   81 (837)
                      .++|||+|+.+..+.++.+.+..|.++.||...                         .....+..+.+.+..|++++|+
T Consensus         2 ~viivEG~~d~~~l~~~~~~~~~~~~~~G~~~~-------------------------~~~~~~~~~~~~~~~vii~~D~   56 (83)
T cd00188           2 KLIIVEGPSDALALAQAGGYGGAVVALGGHALN-------------------------KTRELLKRLLGEAKEVIIATDA   56 (83)
T ss_pred             EEEEECCHHHHHHHHHHCCCCEEEEEEEEEECC-------------------------CHHHHHHHHHCCCCEEEEECCC
T ss_conf             799988889999999856999799997557384-------------------------3899999987689999997498


Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             70257999999999755
Q gi|254780306|r   82 DREGEAISWHVLDVLRQ   98 (837)
Q Consensus        82 DREGE~Iawhi~e~l~~   98 (837)
                      |++|+.++|++.+.+..
T Consensus        57 D~~g~~~~~~~~~~~~~   73 (83)
T cd00188          57 DREGEAIALRLLELLKS   73 (83)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             93799999999997323


No 60 
>PRK08620 DNA topoisomerase III; Provisional
Probab=97.44  E-value=0.0004  Score=49.99  Aligned_cols=61  Identities=11%  Similarity=0.097  Sum_probs=32.0

Q ss_pred             CCCCCCCEEEEEECCCCCEEEECCCCCCC-CCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEE
Q ss_conf             68999966999826974227734887776-13378998842548999999861525515777898749991158765261
Q gi|254780306|r  657 NDLETKESVTLRSGRFGLYVQRGDGKDAK-RCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLN  735 (837)
Q Consensus       657 ~dP~~G~~I~lk~GryGpYvq~Ge~~kpk-r~si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~  735 (837)
                      .||+||.+|+.+.||||.++-+.+ ++.+ +.++.+                   .+=+.||+||+.+..+.+++|-|..
T Consensus       611 ~Cp~Cg~~m~~~~gr~Gkf~~C~~-peC~~~k~~~~-------------------~~~~~Cp~C~~~~~~~~~~~g~~~~  670 (726)
T PRK08620        611 KCPDCGKFMLEVKGKNGKMLVCQD-RECGHRKNVSR-------------------KTNARCPNCKKKLELRGEGEGQIFV  670 (726)
T ss_pred             CCCCCCCCCEEEECCCCCEEECCC-CCCCCCCCCHH-------------------HCCCCCCCCCCEEEEEECCCCCEEE
T ss_conf             564268321168589875574689-98999777102-------------------1289499999856898567787899


Q ss_pred             EC
Q ss_conf             67
Q gi|254780306|r  736 HD  737 (837)
Q Consensus       736 ~~  737 (837)
                      |.
T Consensus       671 c~  672 (726)
T PRK08620        671 CV  672 (726)
T ss_pred             EC
T ss_conf             73


No 61 
>COG0551 TopA Zn-finger domain associated with topoisomerase type I [DNA replication, recombination, and repair]
Probab=97.33  E-value=0.00024  Score=51.71  Aligned_cols=72  Identities=22%  Similarity=0.470  Sum_probs=51.8

Q ss_pred             CCCEECCCCCCCCEEEEEECCCC-CCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEE
Q ss_conf             66114334677731368715776-11123434323332100122100001234420146899996699982697422773
Q gi|254780306|r  600 EDSRTCPECHTHSLSLKLSSKYG-AFVGCTNYPECKYTRQLTSNPQDIPEMKESVLLGNDLETKESVTLRSGRFGLYVQR  678 (837)
Q Consensus       600 ~~~~~Cp~C~~g~L~~k~~gK~G-~FigCSnyPeCk~t~~l~~~~~~~~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq~  678 (837)
                      .+...||.|+.+.+.++. +++| .|++|++||+|+|+........            ..|.+|.+..++.+...-++++
T Consensus        58 ~~~~~Cp~C~~~~~~~k~-~~~~~~f~~~~~~Pkc~~~~~~~~~~~------------~cp~c~~~~~~~k~~~~~~~~~  124 (140)
T COG0551          58 KTGVKCPKCGKGLLVLKK-GRFGKNFLGCSNYPKCRFTEKPKPKEK------------KCPKCGSRKLVEKKEKKKGVFL  124 (140)
T ss_pred             CCCEECCCCCCCCCEEEE-CCCCCCCCEECCCCCCCCEECCCHHHH------------HCCCCCCHHHEEEEEECCCEEE
T ss_conf             477667766773402343-456763412536886610234472444------------4865686123256651363660


Q ss_pred             CCCCCC
Q ss_conf             488777
Q gi|254780306|r  679 GDGKDA  684 (837)
Q Consensus       679 Ge~~kp  684 (837)
                      +...++
T Consensus       125 ~c~~~~  130 (140)
T COG0551         125 ECSNKP  130 (140)
T ss_pred             CCCCCH
T ss_conf             367653


No 62 
>PRK00076 recR recombination protein RecR; Reviewed
Probab=96.88  E-value=0.013  Score=38.61  Aligned_cols=64  Identities=22%  Similarity=0.421  Sum_probs=43.7

Q ss_pred             HHHHHHHHHH--HCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEE--------EECCCHHHHHHHHHCCC
Q ss_conf             9999999987--09989994699702579999999997551257887169999--------80379899999986226
Q gi|254780306|r   61 HLQNIIHAVK--SSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVS--------FNAITKQVVLNAMKSPR  128 (837)
Q Consensus        61 ~~~~i~~~~k--~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~--------f~eiT~~aI~~A~~n~r  128 (837)
                      .++.|.+.++  +.++||+||+|+-|||+-|..|.+.|+..    +.+|.|+-        +.=+....+.+||++-+
T Consensus       122 ~i~~L~~Ri~~~~v~EVIlA~~~t~EGe~Ta~yi~~~lk~~----~ikitrlA~GiP~G~~ley~D~~TL~~Al~~R~  195 (197)
T PRK00076        122 NIDELLERLADGEVKEVILATNPTVEGEATAHYIARLLKPL----GVKVTRLAHGVPVGGELEYVDEGTLSRALEGRR  195 (197)
T ss_pred             CHHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHHHC----CCEEEEEEECCCCCCCEECCCHHHHHHHHHHCC
T ss_conf             88999998657995179986489865089999999986554----970777654477785400278999999998472


No 63 
>PRK13844 recombination protein RecR; Provisional
Probab=96.78  E-value=0.019  Score=37.41  Aligned_cols=62  Identities=24%  Similarity=0.434  Sum_probs=39.3

Q ss_pred             HHHHHHHHH--HCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEE--------ECCCHHHHHHHHHCCC
Q ss_conf             999999987--099899946997025799999999975512578871699998--------0379899999986226
Q gi|254780306|r   62 LQNIIHAVK--SSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSF--------NAITKQVVLNAMKSPR  128 (837)
Q Consensus        62 ~~~i~~~~k--~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f--------~eiT~~aI~~A~~n~r  128 (837)
                      ++.|.+.++  +.++||+||+|.-|||+-|..|.+.|+.     +.+|.|+-.        .=+.+..+.+||++-+
T Consensus       127 i~~L~~ri~~~~i~EVIlA~~~t~EGe~Ta~yi~~~l~~-----~ikitrLA~GlP~G~~ley~D~~TL~~Al~~R~  198 (200)
T PRK13844        127 LDILQQIIADRKIDEVILAISPTVEGETTAHFISQMIAK-----DIKISRIGFGVPFGGELEYLDQQTLLHAFNART  198 (200)
T ss_pred             HHHHHHHHCCCCCCEEEEECCCCCCHHHHHHHHHHHHCC-----CCCEEEEEECCCCCCCCCCCCHHHHHHHHHHCC
T ss_conf             799998863799747999679996509999999998449-----972776654477785310068999999997372


No 64 
>COG0353 RecR Recombinational DNA repair protein (RecF pathway) [DNA replication, recombination, and repair]
Probab=96.73  E-value=0.041  Score=34.89  Aligned_cols=86  Identities=27%  Similarity=0.435  Sum_probs=54.1

Q ss_pred             EEEECCHHHHHHHHHHH--CCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCC--EEEEC
Q ss_conf             89977904787788750--899899994251100786557867666744068877654899999999987099--89994
Q gi|254780306|r    3 VIIVESPAKAKTISKYL--GSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSST--ILILA   78 (837)
Q Consensus         3 LvIvEsP~kak~I~~~L--g~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~--~iilA   78 (837)
                      |.|||+|+-.-.+++.-  ..-|-|+  .|||--|    .||.|++             -.++.|.+-+.+.+  +||+|
T Consensus        82 icVVe~p~Dv~a~E~~~~f~G~YhVL--~G~lspl----~gigpe~-------------l~i~~L~~Rl~~~~~~EvIlA  142 (198)
T COG0353          82 LCVVEEPKDVLALEKTGEFRGLYHVL--GGLLSPL----DGIGPED-------------LNIDELLQRLAEGSIKEVILA  142 (198)
T ss_pred             EEEECCHHHHHHHHHHCCCCEEEEEE--CCCCCCC----CCCCCCC-------------CCHHHHHHHHHCCCCCEEEEE
T ss_conf             89986649999999745257278884--5733734----5899101-------------267999999846997559996


Q ss_pred             CCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             699702579999999997551257887169999
Q gi|254780306|r   79 TDPDREGEAISWHVLDVLRQKNLIEKTKIQRVS  111 (837)
Q Consensus        79 tD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~  111 (837)
                      |+|--|||+-|..|.+.|+..    ..+|.|+-
T Consensus       143 tnpTvEGeaTA~YI~~~l~~~----~ikvtRlA  171 (198)
T COG0353         143 TNPTVEGEATALYIARLLKPL----GLKVTRLA  171 (198)
T ss_pred             CCCCCCCHHHHHHHHHHHHHC----CCEEEEEE
T ss_conf             589864368999999997535----97178776


No 65 
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=96.61  E-value=0.039  Score=35.06  Aligned_cols=80  Identities=31%  Similarity=0.514  Sum_probs=58.1

Q ss_pred             EEEECCHHHHHHHHHHH-----CCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEE
Q ss_conf             89977904787788750-----8998999942511007865578676667440688776548999999999870998999
Q gi|254780306|r    3 VIIVESPAKAKTISKYL-----GSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILIL   77 (837)
Q Consensus         3 LvIvEsP~kak~I~~~L-----g~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iil   77 (837)
                      -||||-.|-+-+|++.|     |..|.++-|            +|.|..              .+..-+.++.+||.|++
T Consensus        10 RIiVEGAsDvE~iSkalQr~aLG~eYnITis------------SIiPTT--------------~~eIA~raaeGADlvlI   63 (290)
T COG4026          10 RIIVEGASDVEVISKALQRLALGSEYNITIS------------SIIPTT--------------NVEIAKRAAEGADLVLI   63 (290)
T ss_pred             EEEEECCCHHHHHHHHHHHHHHCCCCEEEEE------------EECCCC--------------HHHHHHHHHCCCCEEEE
T ss_conf             9986065338999999988640561105888------------622675--------------19999876356877999


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             46997025799999999975512578871699998
Q gi|254780306|r   78 ATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSF  112 (837)
Q Consensus        78 AtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f  112 (837)
                      |||.||-|--.|-.+.+.|.-.-    ..+.||.+
T Consensus        64 ATDaD~~GReLA~kf~eeLrg~V----GhiERmK~   94 (290)
T COG4026          64 ATDADRVGRELAEKFFEELRGMV----GHIERMKI   94 (290)
T ss_pred             EECCCCHHHHHHHHHHHHHHHHH----HHHHEECC
T ss_conf             60576045999999999998753----04511226


No 66 
>TIGR00615 recR recombination protein RecR; InterPro: IPR000093 The bacterial protein recR seems to play a role in a recombinational process of DNA repair . It may act with recF and recO. RecR is a protein of about 200 amino acid residues. This protein contains a putative C4-type zinc finger in the N-terminal section.; GO: 0006281 DNA repair, 0006310 DNA recombination.
Probab=96.21  E-value=0.029  Score=36.04  Aligned_cols=102  Identities=29%  Similarity=0.489  Sum_probs=63.9

Q ss_pred             EEEECCHHHHHHHH---HHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHH----HHH--HCC
Q ss_conf             89977904787788---750899899994251100786557867666744068877654899999999----987--099
Q gi|254780306|r    3 VIIVESPAKAKTIS---KYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIH----AVK--SST   73 (837)
Q Consensus         3 LvIvEsP~kak~I~---~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~----~~k--~a~   73 (837)
                      +-|||.|.=+-.|+   .|.|. |-|+-  |||-  |-  -||-||+             =.++.|.+    -++  +.+
T Consensus        85 iCvV~~p~Dv~a~E~~~~f~G~-YhVL~--G~is--Pl--~Gigp~~-------------~~i~~L~~riGeRl~~~~~~  144 (205)
T TIGR00615        85 ICVVEDPKDVFALEKTKEFRGR-YHVLG--GLIS--PL--DGIGPED-------------LKIAALLKRIGERLQEESVK  144 (205)
T ss_pred             EEEECCHHHHHHHHHHHHHCCC-EEEEC--CEEC--CC--CCCCCCC-------------CCHHHHHHHHHCCCCCCCCC
T ss_conf             6874472679998765421660-14315--6417--64--5768322-------------14688998860000005797


Q ss_pred             EEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHHH
Q ss_conf             89994699702579999999997551257887169999803798999999862264698999999
Q gi|254780306|r   74 ILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNAY  138 (837)
Q Consensus        74 ~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A~  138 (837)
                      ||||||||--||||-|-.|.+.|++..  +..+|.|+            |.-=|--.|...||+.
T Consensus       145 EVIlA~nPt~EGeaTa~Yi~~~l~~~f--P~~~~tRi------------A~G~PvGg~lE~~D~~  195 (205)
T TIGR00615       145 EVILATNPTVEGEATALYIARLLRPLF--PGVKVTRI------------ASGLPVGGDLEYVDEV  195 (205)
T ss_pred             EEEEECCCCCHHHHHHHHHHHHHHHCC--CCCEEEEE------------EECCCCCCCHHHHHHH
T ss_conf             788607898413479999999986238--98378655------------4224225515667579


No 67 
>cd01025 TOPRIM_recR TOPRIM_recR: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in Escherichia coli RecR.  RecR participates in the RecFOR pathway of homologous recombinational repair in prokaryotes. This pathway provides a single-stranded DNA molecule coated with RecA to allow invasion of a homologous molecule. The RecFOR system directs the loading of RecA onto gapped DNA coated with SSB protein. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD).  In RecR sequences this glutamate in the first turn of the TOPRIM domain is semiconserved, the DXD motif is not conserved.
Probab=96.07  E-value=0.057  Score=33.83  Aligned_cols=87  Identities=25%  Similarity=0.435  Sum_probs=57.8

Q ss_pred             CEEEECCHHHHHHHHHHH--CCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHH--HCCEEEE
Q ss_conf             189977904787788750--899899994251100786557867666744068877654899999999987--0998999
Q gi|254780306|r    2 NVIIVESPAKAKTISKYL--GSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVK--SSTILIL   77 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~L--g~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k--~a~~iil   77 (837)
                      +|.|||+|+-.-.|++-=  -.-|-|+-  |++   .+.+ ++.|++             -.++.|.+.++  +.++||+
T Consensus         2 ~lcVVe~~~Dl~~iE~s~~y~G~YhVL~--G~l---spl~-g~~p~~-------------l~i~~L~~ri~~~~i~EvIl   62 (112)
T cd01025           2 KLCVVEEPRDVLAIEESGEYRGLYHVLG--GLI---SPLD-GIGPDD-------------LNIDKLLERIAKGQVKEVIL   62 (112)
T ss_pred             EEEEECCHHHHHHHHHHCCCCEEEEEEC--CCC---CCCC-CCCCCC-------------CCHHHHHHHHHCCCCEEEEE
T ss_conf             7999898999999972175656999852--634---7556-998330-------------31999999983589418999


Q ss_pred             CCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEE
Q ss_conf             4699702579999999997551257887169999
Q gi|254780306|r   78 ATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVS  111 (837)
Q Consensus        78 AtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~  111 (837)
                      ||.|.-|||+-|..|.+.|+..    +.++.|+-
T Consensus        63 A~~~t~EGe~Ta~yi~~~l~~~----~ikitrLA   92 (112)
T cd01025          63 ATNPTVEGEATALYIAKLLKDF----GVKVTRLA   92 (112)
T ss_pred             ECCCCCCCHHHHHHHHHHHHHC----CCCEEEEE
T ss_conf             7489966089999999985435----97279887


No 68 
>PRK07220 DNA topoisomerase I; Validated
Probab=95.81  E-value=0.018  Score=37.64  Aligned_cols=114  Identities=17%  Similarity=0.255  Sum_probs=66.5

Q ss_pred             HHHHHHHHHHHHHHHH-HHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCC
Q ss_conf             9999999999999985-222110010013677407963999998748805885676326777632100101488645688
Q gi|254780306|r  373 QFQLYNLIWKRSVASQ-MASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANE  451 (837)
Q Consensus       373 e~klY~LI~~R~lasq-m~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~  451 (837)
                      |--.-.||+.|...-+ +.|-.|-...+.+...  +  ..|.+....-.      +     .  +..+.+..+-.+  ++
T Consensus       198 QTPtL~lIVeRe~EI~~F~p~~Yw~i~a~~~~~--~--~~~~~~~~~~r------~-----~--d~~~a~~i~~~l--~~  258 (740)
T PRK07220        198 QSPTLALIVDREKERNAFVPTPYWEIYAELENA--G--ETFSAQHSTRR------F-----L--DKEEADRVLEKL--GK  258 (740)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECC--C--CEEEEECCCCC------C-----C--CHHHHHHHHHHC--CC
T ss_conf             138899999999999847996428999999729--9--04998505677------7-----9--999999999972--69


Q ss_pred             CCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEEC
Q ss_conf             2110011011123464310178998743321025665515789999973220221
Q gi|254780306|r  452 QLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIA  506 (837)
Q Consensus       452 ~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~  506 (837)
                      ...+.+++..++...||+.||-++|.+..-.+|++-.-| -.|-+.|.+.||+.-
T Consensus       259 ~~~V~~v~~k~~~~~pP~Pf~ts~Lq~~Asklg~Sa~~T-m~iAQ~LYe~GlITY  312 (740)
T PRK07220        259 KAEVKEIEKGEKTDQPPTPFNTTGFISAASSIGFSPANA-MRIAESLYTNGYISY  312 (740)
T ss_pred             CCEEEEEEECCCCCCCCCCCCHHHHHHHHHHCCCCHHHH-HHHHHHHHCCCCCCC
T ss_conf             848999983530148989876799999998769979999-999998742883214


No 69 
>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=95.77  E-value=0.0072  Score=40.58  Aligned_cols=103  Identities=18%  Similarity=0.215  Sum_probs=57.5

Q ss_pred             HHHHHHHHHHHHHH-HHHHHHEECCCEEEEEEEECC---CEEEEEEEEEEEECCCHHHHHCCCCCCCC------------
Q ss_conf             99999999999999-852221100100136774079---63999998748805885676326777632------------
Q gi|254780306|r  373 QFQLYNLIWKRSVA-SQMASAKFERTTVNIIATYND---QIGHLRTTGSLLCFDGFLKVWENQYDQEK------------  436 (837)
Q Consensus       373 e~klY~LI~~R~la-sqm~~a~~~~~~v~i~~~~~~---~~~~F~asg~~i~~~G~~~vy~~~~~~~~------------  436 (837)
                      |----.||+.|=-. .-|.|+.|=...+.+....++   ....|.|.  .+...|=.......-|...            
T Consensus       188 QSVAlRLi~~RErEi~~Fvp~~YW~~~~~~~~~~~~~~~~~~~f~A~--l~~~~g~kl~~~~~~D~~~g~l~~G~~v~~L  265 (688)
T TIGR01051       188 QSVALRLIVDREREIKRFVPEEYWTVDAKLEAKNNQKVACKETFEAL--LTEVNGKKLKAGSDFDPLTGELRPGKEVVVL  265 (688)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEEEEEECCCCCCCHHHHCCCCE--EEEECCCCCCCCCCCCCCCCCCCCCCEEEEE
T ss_conf             65567677754789861688611798999645666311111046321--2412470113212478010126899716881


Q ss_pred             CCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHH
Q ss_conf             10010148864568821100110111234643101789987
Q gi|254780306|r  437 NSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLI  477 (837)
Q Consensus       437 ~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLi  477 (837)
                      ++.+...|-..-.|+.+.+..++......+||+.|+=|||=
T Consensus       266 ~E~~A~~~~~~L~~~~~~V~~~e~K~~~~~P~~PF~TSTLQ  306 (688)
T TIGR01051       266 NEAEATALKEQLKGEEYVVEEIEKKPKKSRPPPPFTTSTLQ  306 (688)
T ss_pred             CHHHHHHHHHHCCCCEEEEEEEECCCCCCCCCCCCCCCHHH
T ss_conf             86999999985078647998863043301763483354189


No 70 
>PRK05776 DNA topoisomerase III; Provisional
Probab=94.59  E-value=0.13  Score=31.02  Aligned_cols=113  Identities=18%  Similarity=0.290  Sum_probs=66.4

Q ss_pred             HHHHHHHHHHHHHH-HHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCC
Q ss_conf             99999999999985-22211001001367740796399999874880588567632677763210010148864568821
Q gi|254780306|r  375 QLYNLIWKRSVASQ-MASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQL  453 (837)
Q Consensus       375 klY~LI~~R~lasq-m~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~  453 (837)
                      =.-.||+.|..+-+ +.|..|-...+.+..  ++  ..|.+...    .-|          +..++....+-.+.....+
T Consensus       205 PtL~lIVeRe~EI~~F~p~~y~~i~~~~~~--~~--~~f~~~~~----~~~----------~~~~ea~~~~~~l~~~~~~  266 (675)
T PRK05776        205 PTLVEVVEREIERNLFVPLPYYSVSITVEK--GG--KEFRLKVG----KTF----------EKKEEAKEIISEIRKKGYL  266 (675)
T ss_pred             HHHHHHHHHHHHHHHCCCCCEEEEEEEEEE--CC--EEEEEEEC----CCC----------CCHHHHHHHHHHHHCCCCE
T ss_conf             999999999999982889534999999981--88--78999849----987----------8899999999998579975


Q ss_pred             CCEEEECCCCCCCCCCCCCHHHHHHHHHH-CCCCCCCCHHHHHHHHHHCCEEEC
Q ss_conf             10011011123464310178998743321-025665515789999973220221
Q gi|254780306|r  454 IATETNASQHFTEPPPRYSESSLIKKMEE-IGIGRPSTYATILETLYKRKYVIA  506 (837)
Q Consensus       454 ~~~~~~~~~~~TkPP~rytEasLik~mE~-~GIGrPSTyA~II~~L~~R~YV~~  506 (837)
                      .+.++..+.+.+.||+.|+=++|.+.+-. .|++-. -=-+|.+.|.+.||+.-
T Consensus       267 ~V~~v~~k~k~~~PP~pf~ts~LQ~~Ask~~g~Sa~-~tm~iAQ~LYe~glITY  319 (675)
T PRK05776        267 IVVEVEEKDEILRPPPPFNLGDLQKEAARIYGFSPY-KTQSIAEELYLDALISY  319 (675)
T ss_pred             EEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHH-HHHHHHHHHHCCCCEEC
T ss_conf             999888505643798997589999999997598899-99999999872881766


No 71 
>COG1658 Small primase-like proteins (Toprim domain) [DNA replication, recombination, and repair]
Probab=93.88  E-value=0.17  Score=30.17  Aligned_cols=68  Identities=25%  Similarity=0.345  Sum_probs=39.8

Q ss_pred             HHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHH-HCCCCCCCEEE--------EEEECCCHHHHHHHHHCC
Q ss_conf             8999999999870998999469970257999999999755-12578871699--------998037989999998622
Q gi|254780306|r   59 QKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQ-KNLIEKTKIQR--------VSFNAITKQVVLNAMKSP  127 (837)
Q Consensus        59 kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~-~~~~~~~~v~R--------~~f~eiT~~aI~~A~~n~  127 (837)
                      ...+..|+.+.+. ..||+-||||+.||-|.--+.++|.- +++..+....+        +-.-++...+++.|+.+.
T Consensus        43 ~~~ie~i~~~~~~-k~VIILTD~D~~Ge~Irk~l~~~l~~~~~~~id~~~~~~~~~~~~i~gVE~~~~~~~~~~l~~~  119 (127)
T COG1658          43 LETIELIKKAQKY-KGVIILTDPDRKGERIRKKLKEYLPGAKGAFIDREIRNKLKINGKIIGVEEASSEALRKALKEV  119 (127)
T ss_pred             HHHHHHHHHHHCC-CCEEEEECCCCCHHHHHHHHHHHCCCCCCCCCCHHHHHHCCCCCCCCCCEECCHHHHHHHHHHC
T ss_conf             8899999986425-8779986898562899999999715254654148985130367552361107848899999746


No 72 
>cd01027 TOPRIM_RNase_M5_like TOPRIM_ RNase M5_like: The topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain found in Ribonuclease M5: (RNase M5) and other small primase-like proteins from bacteria and archaea.  RNase M5 catalyzes the maturation of 5S rRNA in low G+C Gram-positive bacteria. The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.
Probab=93.80  E-value=0.45  Score=27.11  Aligned_cols=68  Identities=28%  Similarity=0.415  Sum_probs=45.1

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP   81 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~   81 (837)
                      .+||||-..=...+.+++... .+..+.|..                        -..+.+..|..   ....||+.|||
T Consensus         3 evIvVEGk~D~~~l~~~~~~~-~ii~t~g~~------------------------~~~~~~~~i~~---~~~~VIIlTD~   54 (81)
T cd01027           3 EVIIVEGKNDTESLKKLGIEA-EIIETNGSI------------------------INKETIELIKK---AYRGVIILTDP   54 (81)
T ss_pred             EEEEEECCCHHHHHHHHCCCE-EEEEECCCC------------------------CCHHHHHHHHH---HCCCEEEEECC
T ss_conf             699995561899999863781-399989903------------------------45999999998---55985999689


Q ss_pred             CCHHHHHHHHHHHHHH
Q ss_conf             7025799999999975
Q gi|254780306|r   82 DREGEAISWHVLDVLR   97 (837)
Q Consensus        82 DREGE~Iawhi~e~l~   97 (837)
                      |+-||-|.--+.+.|.
T Consensus        55 D~~Gekirk~i~~~l~   70 (81)
T cd01027          55 DRKGEKIRKKLSEYLS   70 (81)
T ss_pred             CCCHHHHHHHHHHHHC
T ss_conf             9670799999999822


No 73 
>PRK07141 DNA topoisomerase I; Validated
Probab=93.74  E-value=0.23  Score=29.20  Aligned_cols=58  Identities=19%  Similarity=0.248  Sum_probs=38.0

Q ss_pred             CCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHC----CEEE
Q ss_conf             8864568821100110111234643101789987433210256655157899999732----2022
Q gi|254780306|r  444 LPYISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGRPSTYATILETLYKR----KYVI  505 (837)
Q Consensus       444 LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGrPSTyA~II~~L~~R----~YV~  505 (837)
                      +-.+..+..+.+.++...++...||..|+.++|-+..   |+. |..=-.|.+.|.+.    ||+.
T Consensus       233 ~~~~~~~~~~~V~~v~~~~~~~~~p~pf~~s~l~k~~---~~s-a~~tl~iaQ~LYE~~~~~GlIT  294 (622)
T PRK07141        233 KAEILKNKKLIVKKIKVSTRKDPKLTPFKQAVLYKKS---QYS-SASVQSALQKLYEGYGDGGLIS  294 (622)
T ss_pred             HHHHHCCCCEEEEEEEECCCCCCCCCCCCHHHHHHHH---CCC-HHHHHHHHHHHHHHHCCCCEEE
T ss_conf             9987237986999965245357998985168999885---779-8899999999996316586399


No 74 
>pfam01131 Topoisom_bac DNA topoisomerase. This subfamily of topoisomerase is divided on the basis that these enzymes preferentially relax negatively supercoiled DNA, from a 5' phospho- tyrosine linkage in the enzyme-DNA covalent intermediate and has high affinity for single stranded DNA.
Probab=93.57  E-value=0.26  Score=28.89  Aligned_cols=57  Identities=18%  Similarity=0.339  Sum_probs=45.3

Q ss_pred             CCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHH-CCCCCCCCHHHHHHHHHHCCEEEC
Q ss_conf             6882110011011123464310178998743321-025665515789999973220221
Q gi|254780306|r  449 ANEQLIATETNASQHFTEPPPRYSESSLIKKMEE-IGIGRPSTYATILETLYKRKYVIA  506 (837)
Q Consensus       449 ~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~-~GIGrPSTyA~II~~L~~R~YV~~  506 (837)
                      .+....+.+++.+++.+.||+.|+=++|.+.+-. .|+.-.-| -.|.+.|.+.|||.-
T Consensus       101 ~~~~~~v~~v~~~~~~~~pP~pf~ls~Lq~~a~~~~g~s~~~t-m~iaQ~LYE~glITY  158 (403)
T pfam01131       101 KGKTATVKSVEKKEKKEPPPLPFNTSTLQKEASRKLGFSAKKT-MDIAQKLYEKGLITY  158 (403)
T ss_pred             CCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHH-HHHHHHHHHCCCEEE
T ss_conf             4898599998765775069998577999999987538789999-999999886583453


No 75 
>PRK09031 DNA topoisomerase III; Provisional
Probab=93.12  E-value=0.43  Score=27.27  Aligned_cols=56  Identities=21%  Similarity=0.319  Sum_probs=42.0

Q ss_pred             CCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHH-HCCCCCCCCHHHHHHHHHHC-CEEE
Q ss_conf             688211001101112346431017899874332-10256655157899999732-2022
Q gi|254780306|r  449 ANEQLIATETNASQHFTEPPPRYSESSLIKKME-EIGIGRPSTYATILETLYKR-KYVI  505 (837)
Q Consensus       449 ~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE-~~GIGrPSTyA~II~~L~~R-~YV~  505 (837)
                      .|....+.+++.+++...||..|+=++|-+.+- ..|+.-- .=-.|.+.|.++ +||.
T Consensus       270 ~~~~~~V~~v~~k~~k~~pP~Pf~ls~LQ~~Ask~~g~Sa~-~tl~iaQ~LYE~~~lIT  327 (649)
T PRK09031        270 TGQPALVTSYNDKREKQSAPLPYSLSALQIDAAKRFGLSAQ-QVLDICQKLYETHKLIT  327 (649)
T ss_pred             HCCCEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHH-HHHHHHHHHHHHCCCEE
T ss_conf             08983999986556634898997889999999986299999-99999999997189650


No 76 
>smart00437 TOP1Ac Bacterial DNA topoisomerase I DNA-binding domain. Bacterial DNA topoisomerase I and III, Eukaryotic DNA topoisomeraes III, reverse gyrase alpha subunit
Probab=92.99  E-value=0.34  Score=28.03  Aligned_cols=93  Identities=23%  Similarity=0.276  Sum_probs=51.5

Q ss_pred             HHHHHHHHHHHHHHHCCC-CCCEEEEEEEECCCCCEEEEEEEEE--CCEE-ECCCCHHHHHHHHHHHHHHCCCCCEEEEE
Q ss_conf             999999999999641376-5440012233157996542233103--5833-03310113566677764200156301000
Q gi|254780306|r  172 VALRLICNRENQIESFVS-EEYWSLSVLLETPRNDKFTAHLTDF--NGQR-IEKKSISNKKEADDLISFVKKATYSVEKI  247 (837)
Q Consensus       172 p~L~lIveRe~eI~~F~p-~~y~~i~a~~~~~~~~~f~a~l~~~--~~~~-~~~~~~~~~~~a~~~~~~~~~~~~~V~~v  247 (837)
                      =.-.||+.|-..  +|-| ..|-...+.+.. ++..|.+.....  .|.+ +..  ...+++-..+-.--.+..+.|.++
T Consensus       123 ~lY~LI~~r~la--s~~~~~~~~~t~v~~~~-~~~~F~~~g~~~~~~Gw~~v~~--~~~~~~~~~lp~l~~g~~~~~~~~  197 (259)
T smart00437      123 KLYELIWRRFLA--SQMPDAKYEETKVIIKI-GGEKFKAKGKTLLFDGWLKVYP--EEKKEEEIELPTLKKGDELKVEEV  197 (259)
T ss_pred             HHHHHHHHHHHH--HHCCHHEEEEEEEEEEE-CCEEEEEEEEEEEECCHHHEEC--CCCCCCCCCCCCCCCCCEEEEEEE
T ss_conf             999999999999--85753327899999998-9989999999998687374033--565653132876777988999888


Q ss_pred             ECCCCCCCCCCCCCHHHHHHHH
Q ss_conf             0233222468521037999998
Q gi|254780306|r  248 ENKPIKRNPWPAFTTSTLQQVA  269 (837)
Q Consensus       248 ~~k~~~~~Pp~Pf~tstLQq~A  269 (837)
                      +.++.+.+||++|+-++|-+.+
T Consensus       198 ~~~~~~TkPP~~yte~tLi~~M  219 (259)
T smart00437      198 EVEEKKTKPPARYTEASLIKLM  219 (259)
T ss_pred             EEEEEECCCCCCCCHHHHHHHH
T ss_conf             8765433899887999999987


No 77 
>cd00186 TOP1Ac DNA Topoisomerase, subtype IA; DNA-binding, ATP-binding and catalytic domain of bacterial DNA topoisomerases I and III, and eukaryotic DNA topoisomerase III and eubacterial and archael reverse gyrases. Topoisomerases clevage single or double stranded DNA and then rejoin the broken phosphodiester backbone. Proposed catalytic mechanism of single stranded DNA cleavage is by phosphoryl transfer through a tyrosine nucleophile using acid/base catalysis. Tyr is activated by a nearby group (not yet identified) acting as a general base for nucleophilic attack on the 5' phosphate of the scissile bond. Arg and Lys stabilize the pentavalent transition state. Glu then acts as a proton donor for the leaving 3'-oxygen, upon cleavage of the scissile strand.
Probab=92.44  E-value=0.43  Score=27.26  Aligned_cols=52  Identities=17%  Similarity=0.424  Sum_probs=27.9

Q ss_pred             CCCEEEECCCCCCCCCCCCCHHHHHHHHH-HCCCCCCCCHHHHHHHHHHCCEEE
Q ss_conf             11001101112346431017899874332-102566551578999997322022
Q gi|254780306|r  453 LIATETNASQHFTEPPPRYSESSLIKKME-EIGIGRPSTYATILETLYKRKYVI  505 (837)
Q Consensus       453 ~~~~~~~~~~~~TkPP~rytEasLik~mE-~~GIGrPSTyA~II~~L~~R~YV~  505 (837)
                      ..+.+++.+++.+.||..|+=++|-+.+- ..|+.-. -=-.|.+.|.+.|||.
T Consensus        69 ~~v~~~~~k~~~~~pP~pf~l~~Lq~~a~~~~g~s~~-~tl~iaQ~LYE~g~IT  121 (381)
T cd00186          69 AVVVSVEKKEKKKNPPPPFTTSTLQQEASSKLGFSAK-KTMQIAQKLYEAGLIT  121 (381)
T ss_pred             EEEEEEEEEEEECCCCCCCCHHHHHHHHHHCCCCCHH-HHHHHHHHHHHCCEEE
T ss_conf             8999987515864797994689999999860695999-9999999998679265


No 78 
>PRK08174 DNA topoisomerase III; Validated
Probab=92.33  E-value=0.16  Score=30.37  Aligned_cols=123  Identities=12%  Similarity=0.111  Sum_probs=67.0

Q ss_pred             HHHHHHHHHHHHHHHH-HHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCC
Q ss_conf             9999999999999985-222110010013677407963999998748805885676326777632100101488645688
Q gi|254780306|r  373 QFQLYNLIWKRSVASQ-MASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANE  451 (837)
Q Consensus       373 e~klY~LI~~R~lasq-m~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~  451 (837)
                      |--.-.||+.|-..-+ +.|..|-...+.+...+    ..|.+...  ...++..  .+..- -.........-.++...
T Consensus       193 QtPtL~lIveRE~EI~~F~p~~y~~i~~~~~~~~----~~f~a~~~--~~~~~~d--~~~r~-~~~~~a~~~~~~~~~~~  263 (670)
T PRK08174        193 QTPTLALVVDRDREIANFVPVPYWAIDVSLSAGG----QTFTAQWV--PPEQYCD--DEGRC-LQQPVAQQAAQQIRQAG  263 (670)
T ss_pred             HHHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECC----EEEEEEEE--CCCCCCC--HHCCC-CCHHHHHHHHHHHHCCC
T ss_conf             2466888999999998078863289999997489----15788874--2455621--22024-79999999999986489


Q ss_pred             CCCCEEEECCCCCCCCCCCCCHHHHHHHHHH-CCCCCCCCHHHHHHHHHHC-CEEE
Q ss_conf             2110011011123464310178998743321-0256655157899999732-2022
Q gi|254780306|r  452 QLIATETNASQHFTEPPPRYSESSLIKKMEE-IGIGRPSTYATILETLYKR-KYVI  505 (837)
Q Consensus       452 ~~~~~~~~~~~~~TkPP~rytEasLik~mE~-~GIGrPSTyA~II~~L~~R-~YV~  505 (837)
                      ...+.+++.++....||+.|+=++|-+.+=. +|++---| -.|-+.|.+. ||+.
T Consensus       264 ~~~V~~v~~k~~~~~pP~Pf~tstLQ~~As~~lg~sa~~T-m~iAQ~LYE~~glIT  318 (670)
T PRK08174        264 SAQVVSVETERVREGAPLPFDLGTLQEVCSKKLGLGAQET-LDIAQALYETHKATT  318 (670)
T ss_pred             CEEEEEEEEEEEECCCCCCCCHHHHHHHHHHHHCCCHHHH-HHHHHHHHHCCCEEE
T ss_conf             7599999854542479999747999999998719888899-999999885288287


No 79 
>TIGR01057 topA_arch DNA topoisomerase I; InterPro: IPR005739   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 archaea, which is more closely related to bacterial 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.    More information about this protein can be found at Protein of the Month: DNA Topoisomerase .; GO: 0003677 DNA binding, 0003916 DNA topoisomerase activity, 0006265 DNA topological change, 0006268 DNA unwinding during replication, 0005694 chromosome.
Probab=91.38  E-value=0.75  Score=25.44  Aligned_cols=56  Identities=18%  Similarity=0.434  Sum_probs=40.2

Q ss_pred             EEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHH
Q ss_conf             999998748805885676326777632100101488645688211001101112346431017899874
Q gi|254780306|r  410 GHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIK  478 (837)
Q Consensus       410 ~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik  478 (837)
                      ..|.|.-     .+|+ ++       ..++....+-.++......|.+|..+...-+||+.|.=+||=+
T Consensus       234 ~~~~A~~-----~~~K-~~-------~~e~a~~i~~~~~~~~~~~V~~v~~~~~~~~PP~pFdLGtLQ~  289 (637)
T TIGR01057       234 GVFKAES-----EKEK-IW-------KEEEAKSILEEVKKSKSAKVEEVRVKRSILKPPPPFDLGTLQR  289 (637)
T ss_pred             CEEEEEC-----CCCC-CC-------HHHHHHHHHHHHCCCCCCCEEEEEEECCCCCCCCCCCCCHHHH
T ss_conf             5587522-----5787-41-------2465556888616798842332455311168325987552589


No 80 
>pfam01396 zf-C4_Topoisom Topoisomerase DNA binding C4 zinc finger.
Probab=91.07  E-value=0.18  Score=30.02  Aligned_cols=26  Identities=19%  Similarity=0.570  Sum_probs=14.0

Q ss_pred             HCCCCCCCCEEEEEECCCCCEEEECC
Q ss_conf             15777898749991158765261678
Q gi|254780306|r  713 IGIHPETQKNIIAGTGKYGYYLNHDG  738 (837)
Q Consensus       713 lG~~pe~g~~I~~~~GryGpYi~~~~  738 (837)
                      +|.+|++|.+++++.||||.|+.|.+
T Consensus         1 vgkCP~Cg~~l~~r~~r~G~F~gCs~   26 (39)
T pfam01396         1 VGKCPKCGGDLVLKRGKFGKFVGCSN   26 (39)
T ss_pred             CCCCCCCCCEEEEEECCCCEEEECCC
T ss_conf             94377899981688368770872899


No 81 
>PRK07726 DNA topoisomerase III; Provisional
Probab=90.90  E-value=0.81  Score=25.18  Aligned_cols=117  Identities=15%  Similarity=0.106  Sum_probs=67.4

Q ss_pred             HHHHHHHHHHHHHHH-HHHHEECCCEEEEEEEECCCEEEEEEEEEEEECCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCC
Q ss_conf             999999999999985-2221100100136774079639999987488058856763267776321001014886456882
Q gi|254780306|r  374 FQLYNLIWKRSVASQ-MASAKFERTTVNIIATYNDQIGHLRTTGSLLCFDGFLKVWENQYDQEKNSEEDILLPYISANEQ  452 (837)
Q Consensus       374 ~klY~LI~~R~lasq-m~~a~~~~~~v~i~~~~~~~~~~F~asg~~i~~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~  452 (837)
                      --.-.||+.|..+-+ +.|..|-...+.+...+    ..|.+....  .... ++.     +.   +....+-....|..
T Consensus       202 TPtL~lIv~Re~eI~~F~p~~y~~i~a~~~~~~----~~~~~~~~~--~~~~-r~~-----d~---~~a~~i~~~~~~~~  266 (716)
T PRK07726        202 TPTLALIVKREKEIENFKSEPFWEVFATFNIEG----KKYEGKWEK--DNES-RLK-----DP---DMANKIAAFCQGKP  266 (716)
T ss_pred             HHHHHHHHHHHHHHHHCCCCCEEEEEEEEEECC----EEEEEEEEC--CCCC-CCC-----CH---HHHHHHHHHHCCCC
T ss_conf             167899999999998489964389999999789----179999952--7767-458-----99---99999999964898


Q ss_pred             CCCEEEECCCCCCCCCCCCCHHHHHHHHH-HCCCCCCCCHHHHHHHHHHCCEEEC
Q ss_conf             11001101112346431017899874332-1025665515789999973220221
Q gi|254780306|r  453 LIATETNASQHFTEPPPRYSESSLIKKME-EIGIGRPSTYATILETLYKRKYVIA  506 (837)
Q Consensus       453 ~~~~~~~~~~~~TkPP~rytEasLik~mE-~~GIGrPSTyA~II~~L~~R~YV~~  506 (837)
                      ..+.+++.+++...||..|+=++|-+.+- ..|+.-.-| -.|.+.|.++||+.-
T Consensus       267 ~~V~~v~~k~k~~~PP~pf~ls~LQ~~A~~~~g~sa~~T-l~iAQ~LYE~glITY  320 (716)
T PRK07726        267 AVVKEMKTERKEFQPPLLFNLSSLQATANKAFKFSPKKT-LDITQKLYQKGIVSY  320 (716)
T ss_pred             EEEEEEEEEEEECCCCCCCCHHHHHHHHHHHCCCCHHHH-HHHHHHHHHCCCEEE
T ss_conf             499999842466589998778999999998729899999-999999985696200


No 82 
>PRK04031 DNA primase; Provisional
Probab=88.62  E-value=1  Score=24.35  Aligned_cols=37  Identities=30%  Similarity=0.391  Sum_probs=18.7

Q ss_pred             CCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCCCCCCC
Q ss_conf             7554444305689999765520011237631111255
Q gi|254780306|r  305 RTDGVHMSPDALEAVRRSITSHYGDHYLPEKPRIYSS  341 (837)
Q Consensus       305 RTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~r~y~~  341 (837)
                      -.||..|.++.....|.-=...||.+-||..|.+.++
T Consensus       132 ~~~~~~i~~ev~~~~~~~~~~~yg~~~lpagp~v~~s  168 (420)
T PRK04031        132 IPDSKEIIEEVREAVRVEEIIEYGPEKLPAGPNVDDS  168 (420)
T ss_pred             CCCHHHHHHHHHHHHHHHHHHEECCCCCCCCCCCCCC
T ss_conf             8219999999998860364411165678999897888


No 83 
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator; InterPro: IPR011789    This entry represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system . This protein is a member of the MerR family of transcriptional activators and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue .; GO: 0003677 DNA binding, 0005507 copper ion binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription.
Probab=82.13  E-value=1.2  Score=23.90  Aligned_cols=41  Identities=24%  Similarity=0.447  Sum_probs=32.6

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHH-HCCCCCCC--CCHHHHHHHH
Q ss_conf             98876088899999999876213556721224553-14755444--4305689999
Q gi|254780306|r  268 VASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLIT-YMRTDGVH--MSPDALEAVR  320 (837)
Q Consensus       268 ~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlIT-YpRTDS~~--ls~ea~~~~r  320 (837)
                      ++++.-|+|+|-.     +|||.       .|||+ =+||||-|  +++.+++..+
T Consensus         5 ~~AK~tglssK~I-----R~YE~-------kGLi~Pp~Rse~GYR~Y~~~h~~~L~   48 (127)
T TIGR02044         5 QVAKLTGLSSKSI-----RYYEE-------KGLIPPPLRSEGGYRTYTDKHVDELR   48 (127)
T ss_pred             HHHCCCCCCHHHH-----HHHHH-------HCCCCCCCCCCCCCCCCCHHHHHHHH
T ss_conf             7750147726889-----88776-------32679988688888563876788889


No 84 
>PRK10046 dpiA two-component response regulator DpiA; Provisional
Probab=79.35  E-value=2.6  Score=21.34  Aligned_cols=80  Identities=16%  Similarity=0.307  Sum_probs=47.0

Q ss_pred             CCEEEEC-CHHHHHHHHHHHCC--CCEEEEEECCCEE---CCCC-CCC-CCCCCCCCEEEEECCCHHHHHHHHHHHHHHC
Q ss_conf             9189977-90478778875089--9899994251100---7865-578-6766674406887765489999999998709
Q gi|254780306|r    1 MNVIIVE-SPAKAKTISKYLGS--NYKVLSSFGHIRD---LPAK-KGS-VLPEKEFEMIWNIDPSSQKHLQNIIHAVKSS   72 (837)
Q Consensus         1 M~LvIvE-sP~kak~I~~~Lg~--~y~V~as~GHird---Lp~~-~~~-v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a   72 (837)
                      |+++||| -|..+..++.||..  +|.|+++.+-..+   +-.. ... |..|     .+-..-+.-..++.|+..-..+
T Consensus         5 i~VLIVEDd~~v~~~l~~~L~~~~gf~~V~~A~~~~eA~~~l~~~~pDLvLLD-----i~LPd~~Glell~~lr~~~~~~   79 (225)
T PRK10046          5 LTLLIVEDETPLAEMHAEYIRHIPGFSQILLAGNLAQARMMIERFKPGLILLD-----NYLPDGRGINLLHELVQAHYPG   79 (225)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHHCCCCEEEEE-----CCCCCCCHHHHHHHHHHHCCCC
T ss_conf             86999959899999999999728995499998999999999973599999982-----8989997999999999648799


Q ss_pred             CEEEECCCCCCHH
Q ss_conf             9899946997025
Q gi|254780306|r   73 TILILATDPDREG   85 (837)
Q Consensus        73 ~~iilAtD~DREG   85 (837)
                      +-|++-.-.|.|=
T Consensus        80 ~VI~iTA~~d~~~   92 (225)
T PRK10046         80 DVVFTTAASDMET   92 (225)
T ss_pred             CEEEEECCCCHHH
T ss_conf             8899968999999


No 85 
>KOG1956 consensus
Probab=77.12  E-value=0.024  Score=36.59  Aligned_cols=355  Identities=18%  Similarity=0.162  Sum_probs=174.6

Q ss_pred             CCCCCCCCCCEEEEECC-CCCCHHCCCCCHHHHHHHHHHHHHHHHHHHHHHE-ECCCEEEEEEEECCCEEEEEEEEEEEE
Q ss_conf             66887776524773023-4640000019999999999999999998522211-001001367740796399999874880
Q gi|254780306|r  343 SKNAQEAHEAIRPNDFD-FLPSKMKQFLDSDQFQLYNLIWKRSVASQMASAK-FERTTVNIIATYNDQIGHLRTTGSLLC  420 (837)
Q Consensus       343 ~k~aQeAHeAIrPT~~~-~~p~~~~~~L~~de~klY~LI~~R~lasqm~~a~-~~~~~v~i~~~~~~~~~~F~asg~~i~  420 (837)
                      ...+|.||+|++|++.. +.|......+..+--..|.++|-|-.+.||.++. |+-..-.+-+...   ..+++.-+.+.
T Consensus       350 t~~~~wg~yA~~ll~~~~r~Prng~~~d~Ahppihp~k~~s~~~~~s~d~~~vye~v~rhflAc~S---~dakg~et~ve  426 (758)
T KOG1956         350 TQDPAWGSYAQRLLQPENRNPRNGKHNDKAHPPIHPTKFTSREANLSGDHRKVYELVVRHFLACCS---QDAKGAETTVE  426 (758)
T ss_pred             CCCCHHHHHHHHHHCCCCCCCCCCCCCCCCCCCCCCEEECCCCCCCCCCHHHHHHHHHHHHHHHHC---CCCCCCCEEEE
T ss_conf             468146788887515688898877654446897464110250025786417899999998777634---21346605999


Q ss_pred             CCCHHHHHCCCCCCCCCCHHHCCCCCCCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHH-HCCCC--C-C--CCHHHH
Q ss_conf             5885676326777632100101488645688211001101112346431017899874332-10256--6-5--515789
Q gi|254780306|r  421 FDGFLKVWENQYDQEKNSEEDILLPYISANEQLIATETNASQHFTEPPPRYSESSLIKKME-EIGIG--R-P--STYATI  494 (837)
Q Consensus       421 ~~G~~~vy~~~~~~~~~~~~~~~LP~l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE-~~GIG--r-P--STyA~I  494 (837)
                      +++...+|...-           |-.+..|. +.+-..+--+  ++--|.|.++.++.--| +++=|  . |  =|-|+.
T Consensus       427 l~~~~E~F~asg-----------l~vl~~Ny-ldVy~yekwe--~k~Lp~y~~ge~fq~~~lem~~g~T~~P~~ltEaeL  492 (758)
T KOG1956         427 LDIAQERFSASG-----------LRVLERNY-LDVYPYEKWE--DKQLPVYEDGELFQPGELEMKDGETSPPKYLTEAEL  492 (758)
T ss_pred             EEEHHHHCCCCC-----------CCHHHCCC-CCCCCCCCCC--CCCCCCCCCCCCCCCCEEEECCCCCCCCCCCCHHHH
T ss_conf             860203005554-----------51443266-4333322126--654763026662145247713676589986587999


Q ss_pred             HHHHHHCCEE---------EC--CCCCEEE-CCHHHHHCCCCCCCCCCCCCHHHHHHH-HHHHHHHHCCCHHHHHHHHHH
Q ss_conf             9999732202---------21--4771222-011420000223366556898899999-999999862601347899998
Q gi|254780306|r  495 LETLYKRKYV---------IA--EKRKILP-QNTGRIVTAFLENFFSQYVEYDFTADL-EEKLDEISTGKLNWKEVLHEF  561 (837)
Q Consensus       495 I~~L~~R~YV---------~~--~~~~l~p-T~~G~~v~~~L~~~f~~~~~~~fTa~~-E~~ld~Ia~G~~~~~~~L~~F  561 (837)
                      |..+-+-|-=         ++  +.+...- ...|+             +.|.|-+.+ -.-+|.+  |-..|+..|..-
T Consensus       493 I~lMdk~GIGtdAT~aehi~kiq~R~Yv~~~~~~~~-------------~~P~~lg~aLv~gyd~~--g~e~sKp~lra~  557 (758)
T KOG1956         493 ISLMDKNGIGTDATIAEHIEKIQERGYVTKKNKVGR-------------FVPTFLGVALVEGYDDM--GLEMSKPFLRAE  557 (758)
T ss_pred             HHHHHHCCCCCCHHHHHHHHHHHHHCCEEEECCCCC-------------CCCHHHHHHHHHHHHHH--HHHCCCHHHHHH
T ss_conf             999987289973169999999886041455345431-------------07328889998767764--112078677888


Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCCEEEEEECCCCCCCCCC-CCCCCCCCCCCC
Q ss_conf             6767665576677556667765567664102455556766114334677731368715776111234-343233321001
Q gi|254780306|r  562 WEEFIEKIDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHSLSLKLSSKYGAFVGCT-NYPECKYTRQLT  640 (837)
Q Consensus       562 y~~f~~~i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCS-nyPeCk~t~~l~  640 (837)
                      .+.-.++|.....    +-...+.+.                              ..+|..++--+ +--.|. ..-|.
T Consensus       558 mE~~Lk~Is~G~~----~k~~vl~~~------------------------------v~kyra~f~~~~~~~~~l-~~~l~  602 (758)
T KOG1956         558 MEVDLKNISDGRK----DKKEVLRDI------------------------------VTKYRAYFHETERKIGCL-GESLQ  602 (758)
T ss_pred             HHHHHHHHCCCCC----CHHHHHHHH------------------------------HHHHHHHHHHHHHHHHHH-HHHHH
T ss_conf             9877887426710----188899999------------------------------999999999999999999-99999


Q ss_pred             CCCCCCCCCCCCCCCCCCCCCCCEEEEEECCCCCEEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHHHCCHHHCCCCCCC
Q ss_conf             22100001234420146899996699982697422773488777613378998842548999999861525515777898
Q gi|254780306|r  641 SNPQDIPEMKESVLLGNDLETKESVTLRSGRFGLYVQRGDGKDAKRCSLPKTWKSDSVDYDKAMSLLSLPREIGIHPETQ  720 (837)
Q Consensus       641 ~~~~~~~~~~~~~~LG~dP~~G~~I~lk~GryGpYvq~Ge~~kpkr~si~k~~~~~~itle~Al~LLsLPr~lG~~pe~g  720 (837)
                                  +-+..+.++.         +|       ...|      .                ..|..+|.|+.++
T Consensus       603 ------------~y~~~~a~~~---------~~-------~~~p------~----------------~~Pp~~~l~~s~~  632 (758)
T KOG1956         603 ------------RYLEFIASTL---------TG-------PDDP------E----------------GEPPLLGLEGSTS  632 (758)
T ss_pred             ------------HHHHHCCCCC---------CC-------CCCC------C----------------CCCCCCCCCCCCC
T ss_conf             ------------9986324556---------68-------8888------8----------------8998887778878


Q ss_pred             CEEEEEECCCCCEEEECCE-ECCCCC------CCCCCCCCHHHHHHHHHHHHHCCCCCCCCCCCCCHHCCCCCC-CCCEE
Q ss_conf             7499911587652616781-112488------775143579999999983651134434454432010267898-98469
Q gi|254780306|r  721 KNIIAGTGKYGYYLNHDGA-YTKLES------IEQVLTIDLEQAISCITEKKKIEKSSRKNSKNQGHVIGTHPE-GGSIT  792 (837)
Q Consensus       721 ~~I~~~~GryGpYi~~~~~-~~sl~~------~~~~~~I~l~~Aieli~~~k~~~~~~~~~~~~~~~~lg~~p~-~~~i~  792 (837)
                      +.|-..-|++|+|...++. -.+++.      ..+.-.|++.-|++++..+.               ..| ||+ +.+++
T Consensus       633 ~~v~p~cgp~p~y~~~~~~~rg~ipp~~~~g~~~~~~~~t~~~~~~~l~~~~---------------tn~-~p~~~~~~~  696 (758)
T KOG1956         633 EKVGPKCGPKPVYRQLGKFKRGGIPPAANAGHPKDANSITGRSALNLLRGSM---------------TNG-HPKPGQPVV  696 (758)
T ss_pred             CCCCCCCCCCCCCEECCCCCCCCCCCCCCCCCCCCCCCCCCHHHHHHHHCCC---------------CCC-CCCCCCCCC
T ss_conf             8658789998863342546778989888889855465065141587741533---------------569-999986556


Q ss_pred             EEECCCCCEEEECCEEEECCCCCCHHHCCHHHHHHHHHHH
Q ss_conf             9606854525367888756578896778999999999877
Q gi|254780306|r  793 VHNGRYGPYLHWKKINASLSKEESPDTVDLEKALKILNIK  832 (837)
Q Consensus       793 i~~GryGpYi~~gk~Na~ipk~~~~e~lt~e~a~~li~~k  832 (837)
                      .+--+-|..++.--+-++-+++..+--.|  +|..|+-.|
T Consensus       697 ~~psk~~a~~~~~p~~a~~~~~~~c~c~~--ra~~l~v~k  734 (758)
T KOG1956         697 LKPSKSGATIKSRPTAATEEEEVTCGCGT--RAVKLLVAK  734 (758)
T ss_pred             CCCCCCCCCCCCCCCCCCCCCCCCCCCCC--HHHHHHHHC
T ss_conf             77545654204784335787554568751--555332302


No 86 
>KOG1502 consensus
Probab=76.89  E-value=5.2  Score=19.12  Aligned_cols=89  Identities=22%  Similarity=0.313  Sum_probs=48.4

Q ss_pred             HHHCCCCEEEEEE---------CCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC------
Q ss_conf             7508998999942---------5110078655786766674406887765489999999998709989994699------
Q gi|254780306|r   17 KYLGSNYKVLSSF---------GHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP------   81 (837)
Q Consensus        17 ~~Lg~~y~V~as~---------GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~------   81 (837)
                      ..|-.||.|.+++         .|+++|+...     +.  ...|+.   --.-...+.+++++||.|++...|      
T Consensus        25 ~LL~rGY~V~gtVR~~~~~k~~~~L~~l~~a~-----~~--l~l~~a---DL~d~~sf~~ai~gcdgVfH~Asp~~~~~~   94 (327)
T KOG1502          25 LLLSRGYTVRGTVRDPEDEKKTEHLRKLEGAK-----ER--LKLFKA---DLLDEGSFDKAIDGCDGVFHTASPVDFDLE   94 (327)
T ss_pred             HHHHCCCEEEEEECCCCHHHHHHHHHHCCCCC-----CC--CEEEEC---CCCCCCHHHHHHHCCCEEEEECCCCCCCCC
T ss_conf             99868998999970863056589998651575-----44--258852---435513599997078789991766787778


Q ss_pred             CCHHHHHHHHH---HHHHHHHCCCCCCCEEEEEEECCCH
Q ss_conf             70257999999---9997551257887169999803798
Q gi|254780306|r   82 DREGEAISWHV---LDVLRQKNLIEKTKIQRVSFNAITK  117 (837)
Q Consensus        82 DREGE~Iawhi---~e~l~~~~~~~~~~v~R~~f~eiT~  117 (837)
                      |-|-|+|-=-+   ..+|+.+.  ..+.|+|++|.+=+-
T Consensus        95 ~~e~~li~pav~Gt~nVL~ac~--~~~sVkrvV~TSS~a  131 (327)
T KOG1502          95 DPEKELIDPAVKGTKNVLEACK--KTKSVKRVVYTSSTA  131 (327)
T ss_pred             CCHHHHHHHHHHHHHHHHHHHH--CCCCCCEEEEECCHH
T ss_conf             7477663178888999999986--058722699961478


No 87 
>PTZ00150 phosphoglucomutase; Provisional
Probab=75.62  E-value=5.6  Score=18.88  Aligned_cols=15  Identities=33%  Similarity=0.437  Sum_probs=8.1

Q ss_pred             HHHHHHHHHHHHHHH
Q ss_conf             134789999867676
Q gi|254780306|r  552 LNWKEVLHEFWEEFI  566 (837)
Q Consensus       552 ~~~~~~L~~Fy~~f~  566 (837)
                      ++-.+.|++.|..+.
T Consensus       449 ~tL~d~L~eiy~~yG  463 (593)
T PTZ00150        449 LTFHEYLENIREEIG  463 (593)
T ss_pred             CCHHHHHHHHHHHHC
T ss_conf             999999999999839


No 88 
>COG0358 DnaG DNA primase (bacterial type) [DNA replication, recombination, and repair]
Probab=75.21  E-value=5.7  Score=18.81  Aligned_cols=16  Identities=19%  Similarity=0.268  Sum_probs=9.1

Q ss_pred             EEECCCCCCHHHHHHH
Q ss_conf             9994699702579999
Q gi|254780306|r   75 LILATDPDREGEAISW   90 (837)
Q Consensus        75 iilAtD~DREGE~Iaw   90 (837)
                      ++++-=|..=|-+|+|
T Consensus        55 ~yhCFGCg~~Gd~i~F   70 (568)
T COG0358          55 FYHCFGCGAGGDAIKF   70 (568)
T ss_pred             EEEECCCCCCCCHHHH
T ss_conf             6984168998517778


No 89 
>pfam09653 consensus
Probab=74.37  E-value=2  Score=22.28  Aligned_cols=49  Identities=24%  Similarity=0.313  Sum_probs=31.2

Q ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHH
Q ss_conf             103799999887608889999999987621355672122455314755444430568999
Q gi|254780306|r  260 FTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAV  319 (837)
Q Consensus       260 f~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~  319 (837)
                      |++++.|+ .-+...=.+..+...||+||+        .||||-|  |.-||.+..++.+
T Consensus        16 F~l~S~~e-GIKvH~dA~p~~i~Aa~RLf~--------KGLitq~--DGGYLT~lG~e~a   64 (75)
T pfam09653        16 FPLDSTQE-GIKVHSDAAPELIAAAKRLFD--------KGLITQP--DGGYLTSLGHDAA   64 (75)
T ss_pred             CCCCCHHC-CCCCCCCCCHHHHHHHHHHHH--------CCCCCCC--CCCCCCHHHHHHH
T ss_conf             89711003-640136699999999999998--------5882188--8885407678899


No 90 
>cd01029 TOPRIM_primases TOPRIM_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of bacterial DnaG-type primases and their homologs. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function. The prototypical bacterial primase. Escherichia coli DnaG is a single subunit enzyme.
Probab=73.57  E-value=6.2  Score=18.52  Aligned_cols=68  Identities=24%  Similarity=0.309  Sum_probs=44.1

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP   81 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~   81 (837)
                      .++|||.+.-|=++..+-+  ..|.++.|--             +           ...++.   .+.+....||+|.|.
T Consensus         2 ~v~i~EG~~Dals~~~~g~--~~~va~~G~~-------------~-----------~~~~~~---~l~~~~~~vii~~D~   52 (79)
T cd01029           2 EVIIVEGYMDVLALHQAGI--KNVVAALGTA-------------N-----------TEEQLR---LLKRFARTVILAFDN   52 (79)
T ss_pred             EEEEEECHHHHHHHHHCCC--CCCCCCCCCC-------------C-----------CHHHHH---HHHCCCCCEEEEECC
T ss_conf             3999964799999997186--5442588767-------------7-----------499999---985557765999688


Q ss_pred             CCHHHHHHHHHHHHHHH
Q ss_conf             70257999999999755
Q gi|254780306|r   82 DREGEAISWHVLDVLRQ   98 (837)
Q Consensus        82 DREGE~Iawhi~e~l~~   98 (837)
                      |..|..-+.+..+.+..
T Consensus        53 D~aG~~~~~~~~~~~~~   69 (79)
T cd01029          53 DEAGKKAAARALELLLA   69 (79)
T ss_pred             CHHHHHHHHHHHHHHHH
T ss_conf             89999999999999997


No 91 
>TIGR01562 FdhE formate dehydrogenase accessory protein FdhE; InterPro: IPR006452   This family of sequences describe an accessory protein required for the assembly of formate dehydrogenase of certain proteobacteria although not present in the final complex . The exact nature of the function of FdhE in the assembly of the complex is unknown, but considering the presence of selenocysteine, molybdopterin, iron-sulphur clusters and cytochrome b556, it is likely to be involved in the insertion of cofactors. .
Probab=72.97  E-value=2.8  Score=21.13  Aligned_cols=29  Identities=21%  Similarity=0.589  Sum_probs=16.6

Q ss_pred             CEECCCCCCCCE-EEEEEC--CCC-CCCCCCCC
Q ss_conf             114334677731-368715--776-11123434
Q gi|254780306|r  602 SRTCPECHTHSL-SLKLSS--KYG-AFVGCTNY  630 (837)
Q Consensus       602 ~~~Cp~C~~g~L-~~k~~g--K~G-~FigCSny  630 (837)
                      ...||.||+.-+ ...+.|  ..| .|+.||-.
T Consensus       188 R~~CPaCGs~PvasMv~~g~~~~GlRYlsCslC  220 (312)
T TIGR01562       188 RTLCPACGSRPVASMVRIGHKAEGLRYLSCSLC  220 (312)
T ss_pred             CCCCCCCCCCCHHHHHCCCCCCCCHHHHCCCCC
T ss_conf             522367877861666203676553122200000


No 92 
>TIGR02173 cyt_kin_arch cytidylate kinase, putative; InterPro: IPR011892    Proteins in this family are believed to be cytidylate kinase. Members of this family are found in the archaea and in spirochaetes, and differ considerably from the common bacterial form of cytidylate kinase described by IPR003136 from INTERPRO.; GO: 0004127 cytidylate kinase activity, 0005524 ATP binding, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=71.24  E-value=2.6  Score=21.40  Aligned_cols=71  Identities=23%  Similarity=0.368  Sum_probs=46.7

Q ss_pred             HHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCC-CCCCCEEEEECCC-HHHHHHHHHHHHHHCCEEEECCCCCCHHH
Q ss_conf             047877887508998999942511007865578676-6674406887765-48999999999870998999469970257
Q gi|254780306|r    9 PAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLP-EKEFEMIWNIDPS-SQKHLQNIIHAVKSSTILILATDPDREGE   86 (837)
Q Consensus         9 P~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~-~~~f~p~y~v~~~-~kk~~~~i~~~~k~a~~iilAtD~DREGE   86 (837)
                      -|.||.||+-||=.| |  |.||||+|..+. |.+. |+...   +-.|+ -|++=+.++..+.+...||+      ||-
T Consensus        14 tTvA~~lA~~Lsl~~-i--SaG~iRelA~~~-Gldl~E~~~a---ee~~eIDk~iD~~~~E~A~~~~nvvl------Esr   80 (173)
T TIGR02173        14 TTVAKILAEKLSLKL-I--SAGDIRELAEKM-GLDLAESKYA---EENPEIDKKIDRRIREIAEKEKNVVL------ESR   80 (173)
T ss_pred             HHHHHHHHHHCCCCE-E--CCCHHHHHHHHC-CCCHHHHHHH---CCCCCCCHHHHHHHHHHHCCCCCEEE------EEH
T ss_conf             789999998639831-2--020078898642-9887773443---05863116753788554304896688------520


Q ss_pred             HHHHHH
Q ss_conf             999999
Q gi|254780306|r   87 AISWHV   92 (837)
Q Consensus        87 ~Iawhi   92 (837)
                      +=||-+
T Consensus        81 lagW~~   86 (173)
T TIGR02173        81 LAGWIL   86 (173)
T ss_pred             HHHHHC
T ss_conf             543311


No 93 
>smart00529 HTH_DTXR Helix-turn-helix diphteria tox regulatory element. iron dependent repressor
Probab=71.19  E-value=6.6  Score=18.34  Aligned_cols=40  Identities=28%  Similarity=0.367  Sum_probs=26.6

Q ss_pred             HCCCCCCCCHHHHHHHHHHCCEEECCC-CCEEECCHHHHHCC
Q ss_conf             102566551578999997322022147-71222011420000
Q gi|254780306|r  482 EIGIGRPSTYATILETLYKRKYVIAEK-RKILPQNTGRIVTA  522 (837)
Q Consensus       482 ~~GIGrPSTyA~II~~L~~R~YV~~~~-~~l~pT~~G~~v~~  522 (837)
                      .+|+-+| |-...++.|.+.|||..++ +.+.-|+.|+....
T Consensus         8 ~L~vs~~-sVs~~l~~L~~~Gli~~~~y~~i~LT~~G~~~A~   48 (96)
T smart00529        8 RLNVSPP-TVTQMLKKLEKDGLVEYEPYRGITLTEKGRRLAR   48 (96)
T ss_pred             HHCCCCH-HHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHH
T ss_conf             8499916-7999999999888988749989788987999999


No 94 
>pfam09151 DUF1936 Domain of unknown function (DUF1936). This domain is found in a set of hypothetical Archaeal proteins. Its exact function has not, as yet, been defined. It possesses a zinc ribbon fold.
Probab=66.39  E-value=3.4  Score=20.45  Aligned_cols=32  Identities=31%  Similarity=0.725  Sum_probs=20.4

Q ss_pred             EECCCCCCCCEEEEEECCCC-CCCCCCCCCCCCC
Q ss_conf             14334677731368715776-1112343432333
Q gi|254780306|r  603 RTCPECHTHSLSLKLSSKYG-AFVGCTNYPECKY  635 (837)
Q Consensus       603 ~~Cp~C~~g~L~~k~~gK~G-~FigCSnyPeCk~  635 (837)
                      ..||+|+-|.|.-.-..|.- ..+-||| |.|.|
T Consensus         2 hlcpkcgvgvlepvydekgeikvfrcsn-pacdy   34 (36)
T pfam09151         2 HLCPKCGVGVLEPVYDEKGEIKVFRCSN-PACDY   34 (36)
T ss_pred             CCCCCCCCCCEEEECCCCCCEEEEECCC-CCCCC
T ss_conf             6477456110032005777388997279-76665


No 95 
>cd03364 TOPRIM_DnaG_primases TOPRIM_DnaG_primases: The topoisomerase-primase (TORPIM) nucleotidyl transferase/hydrolase domain found in the active site regions of proteins similar to Escherichia coli DnaG. Primases synthesize RNA primers for the initiation of DNA replication. DnaG type primases are often closely associated with DNA helicases in primosome assemblies.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in nucleotide polymerization by primases. The DXD motif may co-ordinate Mg2+, a cofactor required for full catalytic function.  E. coli DnaG is a single subunit enzyme.
Probab=66.38  E-value=8.7  Score=17.44  Aligned_cols=69  Identities=23%  Similarity=0.347  Sum_probs=48.1

Q ss_pred             CEEEECCHHHHHHHHHHHCCCCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             18997790478778875089989999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP   81 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~   81 (837)
                      +++|||.+--+=+...+ |-.. ++|++|-=                        -...|++.|++.   +++|+++.|.
T Consensus         2 ~viivEG~~D~i~~~~~-G~~n-~VA~~Gt~------------------------~t~~q~~~L~~~---~~~vil~~D~   52 (79)
T cd03364           2 KVILVEGYMDVIALHQA-GIKN-VVASLGTA------------------------LTEEQAELLKRL---AKEVILAFDG   52 (79)
T ss_pred             EEEEEECHHHHHHHHHC-CCCC-EEECCCCC------------------------CCHHHHHHHHCC---CCCEEEEECC
T ss_conf             89999677999999985-9962-56256654------------------------719999977231---5867999789


Q ss_pred             CCHHHHHHHHHHHHHHHH
Q ss_conf             702579999999997551
Q gi|254780306|r   82 DREGEAISWHVLDVLRQK   99 (837)
Q Consensus        82 DREGE~Iawhi~e~l~~~   99 (837)
                      |.-|..=++.+.+.|...
T Consensus        53 D~AG~~Aa~r~~~~l~~~   70 (79)
T cd03364          53 DEAGQKAALRALELLLKL   70 (79)
T ss_pred             CHHHHHHHHHHHHHHHHC
T ss_conf             889999999999999977


No 96 
>PRK03902 manganese transport transcriptional regulator; Provisional
Probab=64.89  E-value=9.2  Score=17.24  Aligned_cols=42  Identities=26%  Similarity=0.491  Sum_probs=32.6

Q ss_pred             HHCCCCCCCCHHHHHHHHHHCCEEECCC-CCEEECCHHHHHCCC
Q ss_conf             2102566551578999997322022147-712220114200002
Q gi|254780306|r  481 EEIGIGRPSTYATILETLYKRKYVIAEK-RKILPQNTGRIVTAF  523 (837)
Q Consensus       481 E~~GIGrPSTyA~II~~L~~R~YV~~~~-~~l~pT~~G~~v~~~  523 (837)
                      +.+|+ .|||-...|..|.+.|||..+. +.+.-|+.|+.+...
T Consensus        30 ~~L~V-s~~SVs~mikkL~~~Glv~~~~y~~i~LT~~G~~~A~~   72 (142)
T PRK03902         30 EALSV-HPSSVTKMVQKLDKDEYLIYEKYRGLVLTPKGKKIGKR   72 (142)
T ss_pred             HHHCC-CCHHHHHHHHHHHHCCCCEECCCCCEEECHHHHHHHHH
T ss_conf             99789-95339999999998799245589875689879999999


No 97 
>COG0068 HypF Hydrogenase maturation factor [Posttranslational modification, protein turnover, chaperones]
Probab=64.61  E-value=7.3  Score=17.99  Aligned_cols=18  Identities=33%  Similarity=0.440  Sum_probs=11.6

Q ss_pred             HHHHHHHHHHCCCCCCCC
Q ss_conf             899874332102566551
Q gi|254780306|r  473 ESSLIKKMEEIGIGRPST  490 (837)
Q Consensus       473 EasLik~mE~~GIGrPST  490 (837)
                      +-.+++.+-+.||-.|-|
T Consensus       577 ~~~~l~~~~e~gin~p~t  594 (750)
T COG0068         577 ELKVLAQALEKGINAPLT  594 (750)
T ss_pred             HHHHHHHHHHHCCCCCCC
T ss_conf             578899998714687310


No 98 
>PRK11050 manganese transport regulator MntR; Provisional
Probab=63.40  E-value=9.8  Score=17.05  Aligned_cols=39  Identities=21%  Similarity=0.342  Sum_probs=21.2

Q ss_pred             CCCCCCCCHHHHHHHHHHCCEEECCC-CCEEECCHHHHHCC
Q ss_conf             02566551578999997322022147-71222011420000
Q gi|254780306|r  483 IGIGRPSTYATILETLYKRKYVIAEK-RKILPQNTGRIVTA  522 (837)
Q Consensus       483 ~GIGrPSTyA~II~~L~~R~YV~~~~-~~l~pT~~G~~v~~  522 (837)
                      +|+- |+|-+.+|.+|.+.|||..+. +.+.-|+.|+.+..
T Consensus        64 LgVs-~pSVt~mlkrL~~~GlV~~~~Y~~I~LT~~G~~~A~  103 (155)
T PRK11050         64 LGVS-QPTVAKMLKRLARDGLVEMRPYRGVFLTPEGEKLAQ  103 (155)
T ss_pred             HCCC-CHHHHHHHHHHHHCCCEEECCCCCEEECHHHHHHHH
T ss_conf             0999-331999999998789988718988468977999999


No 99 
>pfam09526 DUF2387 Probable metal-binding protein (DUF2387). Members of this family are small proteins, about 70 residues in length, with a basic triplet near the N-terminus and a probable metal-binding motif CPXCX(18)CXXC. Members are found in various proteobacteria.
Probab=62.55  E-value=8.1  Score=17.68  Aligned_cols=42  Identities=26%  Similarity=0.585  Sum_probs=23.1

Q ss_pred             CEECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             114334677731368715776111234343233321001221000
Q gi|254780306|r  602 SRTCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTSNPQDI  646 (837)
Q Consensus       602 ~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~~~~~  646 (837)
                      +-.||+|+.-.-.....-..-.++.|-   .|.|+......+.+.
T Consensus         8 GAvCP~C~~~D~i~~~~~~~~~~~eCV---~Cg~~e~~~~~~~e~   49 (61)
T pfam09526         8 GAVCPKCSAMDTIRMWRENGVEYVECV---SCGYTDQQTDEPVEL   49 (61)
T ss_pred             CCCCCCCCCCCEEEEEECCCCEEEEEC---CCCCCCCCCCCCCCC
T ss_conf             541898756537988723994699977---899981268886442


No 100
>PRK08208 coproporphyrinogen III oxidase; Validated
Probab=62.16  E-value=6.8  Score=18.23  Aligned_cols=45  Identities=11%  Similarity=0.201  Sum_probs=35.0

Q ss_pred             HHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHH
Q ss_conf             899999732202214771222011420000223366556898899999
Q gi|254780306|r  493 TILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADL  540 (837)
Q Consensus       493 ~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~  540 (837)
                      .-|+.+++.|.|+.++++|..|+.|+.+.+.+-   ..+++++-++.+
T Consensus       386 ~~l~~l~~~GLl~~~~~~l~LT~~G~~~~d~I~---~~F~s~~v~~~~  430 (436)
T PRK08208        386 PELEEFIDQGWCYQNGSRVRLTETGLAYSDCLG---PVFISPEVRKMM  430 (436)
T ss_pred             HHHHHHHHCCCEEEECCEEEECHHHHHHHHHHH---HHHCCHHHHHHH
T ss_conf             999999978888970999999975889999999---987698889999


No 101
>PRK06294 coproporphyrinogen III oxidase; Provisional
Probab=62.14  E-value=3.5  Score=20.40  Aligned_cols=41  Identities=5%  Similarity=0.060  Sum_probs=30.8

Q ss_pred             HHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHH
Q ss_conf             78999997322022147712220114200002233665568988
Q gi|254780306|r  492 ATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYD  535 (837)
Q Consensus       492 A~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~  535 (837)
                      ...++.+.++|+++.++++|..|+.|+.+.+.+-   .++++..
T Consensus       333 ~~~l~~~~~~Gll~~~~~~l~LT~~G~l~~d~I~---~~ll~~s  373 (374)
T PRK06294        333 LELTMQPSIQGLFTQNDQILSLNKQGRLFHDTIA---EEIMGSS  373 (374)
T ss_pred             HHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHH---HHHHCCC
T ss_conf             9999999988988984999999942627999999---9985001


No 102
>smart00347 HTH_MARR helix_turn_helix multiple antibiotic resistance protein.
Probab=61.84  E-value=5.6  Score=18.86  Aligned_cols=50  Identities=28%  Similarity=0.373  Sum_probs=34.6

Q ss_pred             CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCC-------CEEECCHHHHHCCCC
Q ss_conf             178998743321025665515789999973220221477-------122201142000022
Q gi|254780306|r  471 YSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKR-------KILPQNTGRIVTAFL  524 (837)
Q Consensus       471 ytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~-------~l~pT~~G~~v~~~L  524 (837)
                      -|...|...|   |+- +||-+.+|..|.++|||.+...       .+..|+.|..+.+-+
T Consensus        25 ~t~~~la~~l---~~~-~~~vs~~v~~L~~~glv~r~~~~~D~R~~~i~LT~~G~~~~~~~   81 (101)
T smart00347       25 LSVSELAKRL---GVS-PSTVTRVLDRLEKKGLIRRLPSPEDRRSVLVSLTEEGRELIEEL   81 (101)
T ss_pred             CCHHHHHHHH---CCC-HHHHHHHHHHHHCCCCEEEEECCCCCCEEEEEECHHHHHHHHHH
T ss_conf             7999999998---968-87999999999458938982189998858989998999999999


No 103
>PRK08599 coproporphyrinogen III oxidase; Provisional
Probab=60.88  E-value=4.1  Score=19.92  Aligned_cols=43  Identities=7%  Similarity=0.186  Sum_probs=35.0

Q ss_pred             HCCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCC
Q ss_conf             1025665515789999973220221477122201142000022
Q gi|254780306|r  482 EIGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFL  524 (837)
Q Consensus       482 ~~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L  524 (837)
                      ..|+.-...++..|+.|+++|+|..+++++..|+.|+.+.+.+
T Consensus       327 ~fg~~~~~~~~~~l~~l~~~Gll~~~~~~i~lT~~G~~~~~~I  369 (377)
T PRK08599        327 KFGQSFEEVFGETIQELQEQGLLEEDDDFVRLTKKGKFLGNEV  369 (377)
T ss_pred             HHCCCHHHHHHHHHHHHHHCCCEEECCCEEEECHHHHHHHHHH
T ss_conf             9892999999999999997798998099999998489999999


No 104
>PRK05660 coproporphyrinogen III oxidase; Provisional
Probab=60.54  E-value=5  Score=19.23  Aligned_cols=40  Identities=15%  Similarity=0.205  Sum_probs=31.5

Q ss_pred             CCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCC
Q ss_conf             25665515789999973220221477122201142000022
Q gi|254780306|r  484 GIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFL  524 (837)
Q Consensus       484 GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L  524 (837)
                      |+.- ..+...|+.++++|++..++.++..|+.|+.+.+.+
T Consensus       332 g~~~-~~~~~~l~~l~~~Gll~~~~~~l~lT~~G~l~~n~I  371 (378)
T PRK05660        332 GLPE-SVIRPQLDEAIAQGYLTETEDYWQITEHGKLFLNDL  371 (378)
T ss_pred             CCCH-HHHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHH
T ss_conf             9799-999999999997998898399999997789999999


No 105
>pfam06969 HemN_C HemN C-terminal region. Members of this family are all oxygen-independent coproporphyrinogen-III oxidases (HemN). This enzyme catalyses the oxygen-independent conversion of coproporphyrinogen-III to protoporphyrinogen-IX, one of the last steps in haem biosynthesis. The function of this domain is unclear, but comparison to other proteins containing a radical SAM domain (pfam04055) suggest it may be a substrate binding domain.
Probab=59.44  E-value=8.1  Score=17.66  Aligned_cols=54  Identities=19%  Similarity=0.298  Sum_probs=34.9

Q ss_pred             CCCCCCCHHHHHHHHHHCCCC-----------CCCCHHHHHHHHHHCCEEECCCCCEEECCHHHH
Q ss_conf             643101789987433210256-----------655157899999732202214771222011420
Q gi|254780306|r  466 EPPPRYSESSLIKKMEEIGIG-----------RPSTYATILETLYKRKYVIAEKRKILPQNTGRI  519 (837)
Q Consensus       466 kPP~rytEasLik~mE~~GIG-----------rPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~  519 (837)
                      .|..+..|.-+...+-..||=           =..-+...|+.++++|+|..+++.|.+|+.|+.
T Consensus        54 s~~d~~~e~ii~~LR~~~Gi~~~~~~~~~g~~~~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G~l  118 (118)
T pfam06969        54 SPEDRLRERLILGLRLTEGLDLAAFEQRFGLDFEEEYEPLLEKLQEDGLLELDDGRLRLTPRGRL  118 (118)
T ss_pred             CHHHHHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCEEEECCEEEECCCCCC
T ss_conf             98999999999999985890899999998949999879999999988998973999997868569


No 106
>PRK08166 NADH dehydrogenase subunit G; Validated
Probab=59.19  E-value=4.5  Score=19.60  Aligned_cols=13  Identities=23%  Similarity=0.296  Sum_probs=6.0

Q ss_pred             HHHHHHHHHHHHH
Q ss_conf             9999999898740
Q gi|254780306|r  137 AYLARRALDYLVG  149 (837)
Q Consensus       137 A~~aRr~lD~lvG  149 (837)
                      .+.+=|+.|=+.|
T Consensus       154 C~rCvR~c~ei~g  166 (858)
T PRK08166        154 CYRCVRYYKDYAG  166 (858)
T ss_pred             CCHHHHHHHHHCC
T ss_conf             7556551786548


No 107
>TIGR00314 cdhA CO dehydrogenase/acetyl-CoA synthase complex, epsilon subunit; InterPro: IPR004460 Acetyl-CoA decarbonylase/synthase (ACDS) is a multienzyme complex (carbon monoxide dehydrogenase is a synonym). The ACDS complex carries out an unusual reaction involving the reversible cleavage and synthesis of acetyl-CoA in methanogens. The family contains the 4Fe-4S ferredoxin domain [C-x(2)-C-x(2)-C-x(3)-C-[PEG]] between residues 448-462 of the model.; GO: 0018492 carbon-monoxide dehydrogenase (acceptor) activity, 0006084 acetyl-CoA metabolic process.
Probab=58.98  E-value=3.3  Score=20.61  Aligned_cols=21  Identities=29%  Similarity=0.153  Sum_probs=10.1

Q ss_pred             CHHHCCHHHHHHHHHHHHHCC
Q ss_conf             967789999999998777266
Q gi|254780306|r  816 SPDTVDLEKALKILNIKKQKK  836 (837)
Q Consensus       816 ~~e~lt~e~a~~li~~k~~kk  836 (837)
                      |+==..-++.++.|++|-.+|
T Consensus       749 DlPl~~k~~~lk~LEek~gWK  769 (795)
T TIGR00314       749 DLPLVMKDELLKVLEEKYGWK  769 (795)
T ss_pred             CCCHHHHHHHHHHHHHHHCCC
T ss_conf             775577999999987651788


No 108
>pfam07848 PaaX PaaX-like protein. This family contains proteins that are similar to the product of the paaX gene of Escherichia coli. This protein is involved in the regulation of expression of a group of proteins known to participate in the metabolism of phenylacetic acid. In fact, some members of this family are annotated by InterPro as containing a winged helix DNA-binding domain (Interpro:IPR009058).
Probab=58.12  E-value=8.2  Score=17.64  Aligned_cols=38  Identities=24%  Similarity=0.294  Sum_probs=30.0

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECC
Q ss_conf             101789987433210256655157899999732202214
Q gi|254780306|r  469 PRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAE  507 (837)
Q Consensus       469 ~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~  507 (837)
                      ....-++||+.||..||.-++.|++ +.-|..+|.++.+
T Consensus        19 g~i~~~sLi~ll~~~Gi~~~avRtA-lsRl~~~GwL~~~   56 (70)
T pfam07848        19 GAIWLGSLIRLLAGFGISERLVRTA-LSRLVKAGWLVRE   56 (70)
T ss_pred             CEEEHHHHHHHHHHCCCCHHHHHHH-HHHHHHCCCEEEE
T ss_conf             8374899999999839981789999-9999764864667


No 109
>PRK08629 coproporphyrinogen III oxidase; Provisional
Probab=57.39  E-value=5  Score=19.21  Aligned_cols=41  Identities=7%  Similarity=0.114  Sum_probs=33.9

Q ss_pred             CCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCC
Q ss_conf             02566551578999997322022147712220114200002
Q gi|254780306|r  483 IGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAF  523 (837)
Q Consensus       483 ~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~  523 (837)
                      -|+-=...|+.-|+.+++.|+++.++++|..|+.|+.+.+.
T Consensus       359 fG~~~~~~~~~~i~~l~~~GLl~~~~~~lrLT~kG~ll~n~  399 (424)
T PRK08629        359 FGVNLDTALFKEMLLLKLIGAIKNDPGDLIVTDFGKYLGVV  399 (424)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCEEECCCEEEECCCHHHHHHH
T ss_conf             89599999999999999889989819999999047899999


No 110
>TIGR01700 PNPH purine nucleoside phosphorylase I, inosine and guanosine-specific; InterPro: IPR011270   This entry represents a family of bacterial and metazoan purine phosphorylases acting primarily on inosine and guanosine and not acting on adenosine. PNP-I refers to the nomenclature from Bacillus stearothermophilus  where PHP-II refers to the nucleotidase acting on adenosine as the primary substrate. The bacterial enzymes (PUNA) are typified by the Bacillus PupG protein  which is involved in the metabolism of nucleosides as a carbon source. Several metazoan enzymes (PNPH) are well characterised including the human  and bovine  enzymes which have been crystallised. ; GO: 0004731 purine-nucleoside phosphorylase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=56.99  E-value=8.1  Score=17.67  Aligned_cols=34  Identities=24%  Similarity=0.447  Sum_probs=26.0

Q ss_pred             CCCCCCCCCCCCEEEEEECCCCCEEEECCCCCCCCCCCCCC-CCHHHCCHHH
Q ss_conf             42014689999669998269742277348877761337899-8842548999
Q gi|254780306|r  652 SVLLGNDLETKESVTLRSGRFGLYVQRGDGKDAKRCSLPKT-WKSDSVDYDK  702 (837)
Q Consensus       652 ~~~LG~dP~~G~~I~lk~GryGpYvq~Ge~~kpkr~si~k~-~~~~~itle~  702 (837)
                      .-++|.  -.|++|.+..|||=+|               ++ ++++.+|+=-
T Consensus        42 ~lvfG~--L~G~~Vv~mQGRFH~Y---------------EGny~~~~VTFPV   76 (259)
T TIGR01700        42 NLVFGI--LGGKPVVAMQGRFHLY---------------EGNYDMAKVTFPV   76 (259)
T ss_pred             CEEEEE--ECCEEEEEECCCCCCC---------------CCCCCHHHHCHHH
T ss_conf             377556--7796799831886566---------------7887766604356


No 111
>PRK08949 consensus
Probab=56.88  E-value=5.6  Score=18.88  Aligned_cols=41  Identities=12%  Similarity=0.196  Sum_probs=32.9

Q ss_pred             CCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCC
Q ss_conf             025665515789999973220221477122201142000022
Q gi|254780306|r  483 IGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFL  524 (837)
Q Consensus       483 ~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L  524 (837)
                      .|+. ...+...|+.+++.||+..++..+..|+.|+.+.+.+
T Consensus       331 ~G~~-~~~~~~~l~~l~~~Gll~~~~~~l~lT~~G~l~~n~I  371 (378)
T PRK08949        331 TGLT-ESVIRPQIDEAIAQGYLTETEDYWQITEHGKLFLNSL  371 (378)
T ss_pred             HCCC-HHHHHHHHHHHHHCCCEEECCCEEEECHHHHHHHHHH
T ss_conf             7989-9999999999997898396299999998789999999


No 112
>PRK05799 coproporphyrinogen III oxidase; Provisional
Probab=55.89  E-value=5.3  Score=19.06  Aligned_cols=42  Identities=14%  Similarity=0.286  Sum_probs=35.3

Q ss_pred             CCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCC
Q ss_conf             025665515789999973220221477122201142000022
Q gi|254780306|r  483 IGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFL  524 (837)
Q Consensus       483 ~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L  524 (837)
                      .|+.-...+...++.+.++|++..++.++..|+.|+.+.+.+
T Consensus       327 fg~~~~~~~~~~l~~l~~~Gll~~~~~~i~lT~~G~~~~d~i  368 (374)
T PRK05799        327 FGKNIYEVYGEVINKYIKEGLLIEKEGRIYLSERGIEISNSI  368 (374)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCEEECCCEEEECHHHHHHHHHH
T ss_conf             892999999999999997599898099999997789999999


No 113
>COG1675 TFA1 Transcription initiation factor IIE, alpha subunit [Transcription]
Probab=55.83  E-value=8.3  Score=17.57  Aligned_cols=31  Identities=35%  Similarity=0.536  Sum_probs=22.6

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             988760888999999998762135567212245531475
Q gi|254780306|r  268 VASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRT  306 (837)
Q Consensus       268 ~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRT  306 (837)
                      +-+..+|+....+-++.+.|||        .|+|+|.|.
T Consensus        37 ela~~l~i~~~~vrriL~~L~e--------~~li~~~k~   67 (176)
T COG1675          37 ELAELLGIKKNEVRRILYALYE--------DGLISYRKK   67 (176)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH--------CCCEEEEEE
T ss_conf             9988867639999999999985--------792688860


No 114
>PRK08898 coproporphyrinogen III oxidase; Provisional
Probab=55.82  E-value=6.9  Score=18.18  Aligned_cols=35  Identities=17%  Similarity=0.172  Sum_probs=29.6

Q ss_pred             CHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCC
Q ss_conf             15789999973220221477122201142000022
Q gi|254780306|r  490 TYATILETLYKRKYVIAEKRKILPQNTGRIVTAFL  524 (837)
Q Consensus       490 TyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L  524 (837)
                      .+...|+.+++.|.|+.++.++..|+.|+.+.+.+
T Consensus       353 ~~~~~l~~l~~~GLl~~~~~~i~lT~~G~~~~n~I  387 (393)
T PRK08898        353 AIEPQLAAAEQRGLLERDPTRIRPTPLGQRFLNDL  387 (393)
T ss_pred             HHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHH
T ss_conf             99999999997898998099999997589999999


No 115
>KOG2767 consensus
Probab=55.59  E-value=5.1  Score=19.20  Aligned_cols=33  Identities=24%  Similarity=0.401  Sum_probs=18.0

Q ss_pred             CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEE
Q ss_conf             1789987433210256655157899999732202
Q gi|254780306|r  471 YSESSLIKKMEEIGIGRPSTYATILETLYKRKYV  504 (837)
Q Consensus       471 ytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV  504 (837)
                      -+.-.|++.++++-|--. ----+.+.|++-.||
T Consensus       262 ~~~kEi~~~a~~l~i~~k-~p~vl~~~Lf~e~iv  294 (400)
T KOG2767         262 KSDKEIVKEAERLDIKNK-APLVLAEVLFDEKIV  294 (400)
T ss_pred             CCHHHHHHHHHHHHHCCC-CHHHHHHHHHHHHHH
T ss_conf             027999999888763135-428999998626899


No 116
>TIGR02349 DnaJ_bact chaperone protein DnaJ; InterPro: IPR012724    Molecular chaperones are a diverse family of proteins that function to protect proteins in the intracellular milieu from irreversible aggregation during synthesis and in times of cellular stress. The bacterial molecular chaperone DnaK is an enzyme that couples cycles of ATP binding, hydrolysis, and ADP release by an N-terminal ATP-hydrolizing domain to cycles of sequestration and release of unfolded proteins by a C-terminal substrate binding domain. Dimeric GrpE is the co-chaperone for DnaK, and acts as a nucleotide exchange factor, stimulating the rate of ADP release 5000-fold . DnaK is itself a weak ATPase; ATP hydrolysis by DnaK is stimulated by its interaction with another co-chaperone, DnaJ. Thus the co-chaperones DnaJ and GrpE are capable of tightly regulating the nucleotide-bound and substrate-bound state of DnaK in ways that are necessary for the normal housekeeping functions and stress-related functions of the DnaK molecular chaperone cycle.   Besides stimulating the ATPase activity of DnaK through its J-domain, DnaJ also associates with unfolded polypeptide chains and prevents their aggregation . Thus, DnaK and DnaJ may bind to one and the same polypeptide chain to form a ternary complex. The formation of a ternary complex may result in cis-interaction of the J-domain of DnaJ with the ATPase domain of DnaK. An unfolded polypeptide may enter the chaperone cycle by associating first either with ATP-liganded DnaK or with DnaJ. DnaK interacts with both the backbone and side chains of a peptide substrate; it thus shows binding polarity and admits only L-peptide segments. In contrast, DnaJ has been shown to bind both L- and D-peptides and is assumed to interact only with the side chains of the substrate.  DnaJ comprises a 70-residue N-terminal domain (the J-domain); a 30-residue glycine-rich region (the G-domain); a central domain containing 4 repeats of a CxxCxGxG motif (the CRR-domain); and a 120-170 residue C-terminal region. The J- and CRR-domains are found in many prokaryotic and eukaryotic proteins , either together or separately.    This entry mostly consists of bacterial forms of DnaJ. The three components of the DnaK-DnaJ-GrpE system are typically encoded by consecutive genes. DnaJ homologues occur in many genomes, typically not encoded near DnaK and GrpE-like genes. Most such proteins are not included in this family, though some chloroplast homologues are included; GO: 0005524 ATP binding, 0051082 unfolded protein binding, 0006457 protein folding, 0009408 response to heat.
Probab=55.57  E-value=7.8  Score=17.76  Aligned_cols=46  Identities=22%  Similarity=0.515  Sum_probs=30.0

Q ss_pred             CCCCCCEECCCCC-CCCEEEEEECCCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             5676611433467-773136871577611123434323332100122
Q gi|254780306|r  597 ENNEDSRTCPECH-THSLSLKLSSKYGAFVGCTNYPECKYTRQLTSN  642 (837)
Q Consensus       597 ~~~~~~~~Cp~C~-~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~~  642 (837)
                      +.+..+++||.|+ .|.+......=+|.|-.-+-.|+|.-.-.+..+
T Consensus       183 ~~g~~~~tC~~C~G~Gqv~~~~~t~fG~f~~~~tC~~C~G~G~ii~~  229 (386)
T TIGR02349       183 KPGTDPKTCPTCGGTGQVRRQQGTPFGFFQQQQTCPTCGGEGKIIKE  229 (386)
T ss_pred             CCCCCCEECCCCCCEEEEEEECCCEEEEEEEEEECCCCCCEEEEEEC
T ss_conf             08888547877897589999714065899985877885842389633


No 117
>TIGR01296 asd_B aspartate-semialdehyde dehydrogenase; InterPro: IPR005986   Bacteria, plants and fungi metabolise aspartic acid to produce four amino acids - lysine, threonine, methionine and isoleucine - in a series of reactions known as the aspartate pathway. Additionally, several important metabolic intermediates are produced by these reactions, such as diaminopimelic acid, an essential component of bacterial cell wall biosynthesis, and dipicolinic acid, which is involved in sporulation in Gram-positive bacteria. Members of the animal kingdom do not posses this pathway and must therefore acquire these essential amino acids through their diet. Research into improving the metabolic flux through this pathway has the potential to increase the yield of the essential amino acids in important crops, thus improving their nutritional value. Additionally, since the enzymes are not present in animals, inhibitors of them are promising targets for the development of novel antibiotics and herbicides. For more information see .   Aspartate-semialdehyde dehydrogenase, the second enzyme in the aspartate pathway, converts aspartyl phosphate to aspartate-semialdehyde, the branch point intermediate between the lysine and threonine/methionine pathways. Based on sequence alignments, the aspartate-semialdehyde dehydrogenase family appears to have two distinct subgroups, one found in most bacteria (Gram-positve and Gram-negative), while the other is found primarily in organisms lacking peptidoglycan (archaea,fungi and some bacteria). Most studies have been performed on enzymes isolated from Gram-negative bacteria , , , . The N-terminal domain forms the active site and NADP-binding pocket, while C-terminal domain is primarily involved in hydrophobic intersubunit contacts. The catalytic mechanism involves the formation of a covalent thioester acyl-enzyme intermediate mediated through nucleophilic attack by an active site cysteine residue on the substrate aspartyl phosphate. Release of inorganic phosphate is followed by hydride transfer from NADPH to yield the product. The recently described archaeal structure suggests that the two subgroups of aspartate semi-aldehyde dehydrogenase share similar structures and have an identical catalytic mechanism, despite their relatively low sequence identity . Unlike the bacterial enzymes, the archaeal enzyme utilised both NAD and NADP as cofactor.   This entry represents the subgroup of aspartate-semialdehyde dehydrogenase most commonly found in bacteria. Note that some bacteria, such as Chlamydia, contain the enzyme from the other subgroup (IPR005676 from INTERPRO) instead.; GO: 0004073 aspartate-semialdehyde dehydrogenase activity, 0009086 methionine biosynthetic process, 0009088 threonine biosynthetic process.
Probab=54.84  E-value=12  Score=16.34  Aligned_cols=101  Identities=20%  Similarity=0.231  Sum_probs=44.3

Q ss_pred             CCCCCCCCCHHHHHHHHHHHHHHHHHHCCCC-CCEE--EEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHH
Q ss_conf             1467653422689999999999996413765-4400--122331579965422331035833033101135666777642
Q gi|254780306|r  160 LPGARSAGRVQSVALRLICNRENQIESFVSE-EYWS--LSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISF  236 (837)
Q Consensus       160 ~~~~lSaGRVQtp~L~lIveRe~eI~~F~p~-~y~~--i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~  236 (837)
                      ++...|+||.=+-     -++|.+|+.-.++ .|-.  |.--|       |.|            +.=.+++.|-++...
T Consensus        32 ~AS~RS~G~~~~F-----~gke~~v~~~~~~n~F~gekidIAl-------FSA------------GgsvSke~aP~a~k~   87 (350)
T TIGR01296        32 LASERSAGRKVTF-----KGKELEVEEAKKENSFEGEKIDIAL-------FSA------------GGSVSKEFAPKAAKA   87 (350)
T ss_pred             HCCCCCCCCEEEE-----CCCEEEEECCCCCCCCCCCEEEEEE-------ECC------------CHHHHHHHHHHHHCC
T ss_conf             1056788857851-----2753660101001488877033456-------515------------313348887888608


Q ss_pred             -H------------CCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCC
Q ss_conf             -0------------01563010000233222468521037999998876088899999999876213556
Q gi|254780306|r  237 -V------------KKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDV  293 (837)
Q Consensus       237 -~------------~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~  293 (837)
                       +            .+-++.|-+|..+..+..++.=       --||  =.-|.=+.|.+..=||...++
T Consensus        88 g~~VIDntS~fR~D~dVPLVVPEVN~~~~~~~~~kg-------IIAN--PNCstIqmv~~LkPl~~~~~i  148 (350)
T TIGR01296        88 GVIVIDNTSAFRMDPDVPLVVPEVNLEDLKEFNKKG-------IIAN--PNCSTIQMVVVLKPLHDEAKI  148 (350)
T ss_pred             CCEEEECCCCCCCCCCCCEEECCCCHHHHHCCCCCC-------CEEC--CCCCHHHHHHHHHHHHHHCCE
T ss_conf             757981762000578986344377847763478888-------1458--860077798840465630674


No 118
>PRK09129 NADH dehydrogenase subunit G; Validated
Probab=54.68  E-value=4.7  Score=19.46  Aligned_cols=11  Identities=27%  Similarity=0.178  Sum_probs=6.4

Q ss_pred             ECCCCCCHHHH
Q ss_conf             94699702579
Q gi|254780306|r   77 LATDPDREGEA   87 (837)
Q Consensus        77 lAtD~DREGE~   87 (837)
                      -+.=+|+-||.
T Consensus        97 dc~~c~~~g~c  107 (777)
T PRK09129         97 DCPICDQGGEC  107 (777)
T ss_pred             CCCCCCCCCCC
T ss_conf             78868888876


No 119
>PRK07860 NADH dehydrogenase subunit G; Validated
Probab=54.66  E-value=8.4  Score=17.53  Aligned_cols=17  Identities=24%  Similarity=0.084  Sum_probs=10.5

Q ss_pred             HHHHHHHHHHHHHHHHH
Q ss_conf             99999999989874011
Q gi|254780306|r  135 VNAYLARRALDYLVGFN  151 (837)
Q Consensus       135 v~A~~aRr~lD~lvG~~  151 (837)
                      +..+.+=|..|-+.|-.
T Consensus       165 I~C~RCVR~c~ev~G~~  181 (809)
T PRK07860        165 VLCARCTRFSDQIAGDP  181 (809)
T ss_pred             CCCCHHHHHHHHHCCCC
T ss_conf             62818999998644874


No 120
>COG1846 MarR Transcriptional regulators [Transcription]
Probab=54.40  E-value=14  Score=15.98  Aligned_cols=41  Identities=20%  Similarity=0.275  Sum_probs=29.1

Q ss_pred             CCCCCCCCHHHHHHHHHHCCEEECCCC-------CEEECCHHHHHCCCC
Q ss_conf             025665515789999973220221477-------122201142000022
Q gi|254780306|r  483 IGIGRPSTYATILETLYKRKYVIAEKR-------KILPQNTGRIVTAFL  524 (837)
Q Consensus       483 ~GIGrPSTyA~II~~L~~R~YV~~~~~-------~l~pT~~G~~v~~~L  524 (837)
                      .|+ ++||-..+|..|.++|||.+...       .+..|+.|+.+..-+
T Consensus        46 l~~-~~~~vt~~l~~Le~~glv~r~~~~~DrR~~~l~lT~~G~~~~~~~   93 (126)
T COG1846          46 LGL-DRSTVTRLLKRLEDKGLIERLRDPEDRRAVLVRLTEKGRELLEQL   93 (126)
T ss_pred             HCC-CHHHHHHHHHHHHHCCCEEEECCCCCCCEEEEEECHHHHHHHHHH
T ss_conf             787-888899999999988993674388886312435562159999997


No 121
>smart00532 LIGANc Ligase N family.
Probab=54.01  E-value=5.7  Score=18.83  Aligned_cols=27  Identities=30%  Similarity=0.739  Sum_probs=11.3

Q ss_pred             ECCCCCCCCEEEEEECCCCCCCCCCCCCCCCC
Q ss_conf             43346777313687157761112343432333
Q gi|254780306|r  604 TCPECHTHSLSLKLSSKYGAFVGCTNYPECKY  635 (837)
Q Consensus       604 ~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~  635 (837)
                      .||.|+.. |. +  .....++-|.| +.|..
T Consensus       401 ~CP~C~s~-l~-~--~~~~~~~~C~n-~~C~a  427 (441)
T smart00532      401 HCPSCGSE-LV-R--EEGEVDIRCPN-PLCPA  427 (441)
T ss_pred             CCCCCCCE-EE-E--CCCCEEEECCC-CCCHH
T ss_conf             89899798-38-4--38987898899-98989


No 122
>TIGR00757 RNaseEG ribonuclease, Rne/Rng family; InterPro: IPR004659   The eubacterial degradosome is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria .    The components of the RNA degradosome in E. coli (EBI-1169250 from INTACT) are:  Ribonuclease E (Rne), P21513 from SWISSPROT, IPR004659 from INTERPRO ATP-dependent RNA helicase (RhlB), P0A8J8 from SWISSPROT, IPR000629 from INTERPRO Polynucleotide phosphorylase (Pnp), , IPR012162 from INTERPRO Enolase (Eno), P0A6P9 from SWISSPROT, IPR000941 from INTERPRO       Associated components:   The chaperone protein DnaK (,IPR012725 from INTERPRO) associates to abnormal complexes in which the canonical components RhlB and PNPase are not present or present in limiting amount and could be involved in repairing such incorrectly assembled degradosomes. Polyphosphate kinase (Ppk), P0A7B1 from SWISSPROT, IPR003414 from INTERPRO appears to maintain an appropriate microenvironment, removing inhibitory polyphosphate and NDPs and regenerating ATP.   Subunit composition of the E. coli degradosome(see: http://biocyc.org/ECOLI/NEW-IMAGE?type=POLYPEPTIDE&object=CPLX0-2381): [(Ppk)4][(Rne)4][(RhlB)2][(Pnp)3][(Eno)2]      In vitro a "minimal" degradosome composed of only RNase E, PNPase and RhlB degrades malEF REP RNA in an ATP-dependent manner in vitro, with activity equivalent to purified whole degradosomes. RNase E enzymatic function is dispensible, whereas PNPase must be catalytically active and incorporated into the degradosome for degradation to occur . RNase E provides the organizational structure for the degradosome . It is tethered to the cytoplasmic membrane via its amino-terminus and its carboxy-terminal half, which is largly unstructured and poorly conserved, cooridnates the binding of PNPase, RhlB and enolase. The loss of this portion of the protein prevents degradation of a number of degradosome substrates, including the ptsG and mukB mRNAs and RNA I , , .    Ribonuclease E 3.1.4 from EC is responsible for maturing 5S rRNA from its precursors from all the rRNA genes. It also cleaves RNA I, a molecule that controls the replication of ColE1 plasmid DNA. It is the major endoribonuclease participating in mRNA turnover in Escherichia coli, and initiates decay of RNAs by cutting them internally near their 5'-end. It is able to remove poly A tails by an endonucleolytic process. Ribonuclease G is smaller than RNase E lacking the C-terminal region. It is involved in processing of the 5' end of 16S rRNA, and may be involved in chromosome segregation and cell division too.   RNase E is a major subunit the eubacterial degradosome. It is a large, multiprotein, multienzyme complex involved in RNA processing and degradation in Escherichia coli and other proteobacteria . It consists of the RNA degradation enzymes RNase E (Rne) and PNPase (Pnp), as well as the ATP-dependent RNA helicase (RhlB) and the metabolic enzyme enolase (Eno) , , .; GO: 0004540 ribonuclease activity, 0006396 RNA processing, 0005737 cytoplasm.
Probab=53.71  E-value=13  Score=16.04  Aligned_cols=44  Identities=18%  Similarity=0.214  Sum_probs=29.5

Q ss_pred             EEECCH-HHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             222011-4200002233665568988999999999998626013478999
Q gi|254780306|r  511 ILPQNT-GRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLH  559 (837)
Q Consensus       511 l~pT~~-G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~  559 (837)
                      |.--++ |.+|+||.     |+.+.+=-..+++.|.+.-+....+..+..
T Consensus       373 LrLRnlGGiiiiDFI-----DM~~~k~~~~vl~~l~~~l~~DraR~~i~~  417 (464)
T TIGR00757       373 LRLRNLGGIIIIDFI-----DMKSEKNRRRVLERLKEALSRDRARIQILG  417 (464)
T ss_pred             HHHCCCCCEEEEEEE-----CCCCHHHHHHHHHHHHHHHHCCCCCCCHHH
T ss_conf             521015847999510-----698866689999999999861663100110


No 123
>PRK02362 ski2-like helicase; Provisional
Probab=51.58  E-value=15  Score=15.67  Aligned_cols=48  Identities=19%  Similarity=0.275  Sum_probs=35.6

Q ss_pred             HHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             8999997322022147712220114200002233665568988999999999998
Q gi|254780306|r  493 TILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEI  547 (837)
Q Consensus       493 ~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~I  547 (837)
                      +.++.|.+.++|+.++..+.||++|+++...       +++|.-.+.+-+.|...
T Consensus       469 ~~l~~L~~~~~i~~~~~~~~~T~lG~avs~~-------yldp~~a~~i~~~L~~~  516 (736)
T PRK02362        469 DVLEFLRRNGMVEEDGDALRATRLGSLVSRL-------YIDPLSAALIIDGLRDA  516 (736)
T ss_pred             HHHHHHHHCCCEECCCCEEEECHHHHHHHHH-------CCCHHHHHHHHHHHHHH
T ss_conf             9999999786957059878446789999980-------59988999999999986


No 124
>PRK09130 NADH dehydrogenase subunit G; Validated
Probab=51.22  E-value=14  Score=15.85  Aligned_cols=16  Identities=0%  Similarity=0.034  Sum_probs=8.6

Q ss_pred             CHHHCCHHHHHHHHHH
Q ss_conf             9677899999999987
Q gi|254780306|r  816 SPDTVDLEKALKILNI  831 (837)
Q Consensus       816 ~~e~lt~e~a~~li~~  831 (837)
                      .--+-|+.+|-++-..
T Consensus       663 sr~S~tM~~cs~~~~~  678 (680)
T PRK09130        663 ARASATMAECSALASG  678 (680)
T ss_pred             HHCCHHHHHHHHHHHC
T ss_conf             6602999998855432


No 125
>TIGR01973 NuoG NADH-quinone oxidoreductase, chain G; InterPro: IPR010228   This entry represents the G subunit (one of 14 subunits, A to N) of the NADH-quinone oxidoreductase complex I which generally couples NADH and ubiquinone oxidation/reduction in bacteria and mammalian mitochondria while translocating protons, but may act on NADPH and/or plastoquinone in cyanobacteria and plant chloroplasts. This family does not contain related subunits from formate dehydrogenase complexes.; GO: 0016651 oxidoreductase activity acting on NADH or NADPH, 0051536 iron-sulfur cluster binding.
Probab=51.17  E-value=10  Score=16.82  Aligned_cols=27  Identities=22%  Similarity=0.164  Sum_probs=20.0

Q ss_pred             CCHHHHHHHHHHHHHHH---CCCHHHHHHH
Q ss_conf             89889999999999986---2601347899
Q gi|254780306|r  532 VEYDFTADLEEKLDEIS---TGKLNWKEVL  558 (837)
Q Consensus       532 ~~~~fTa~~E~~ld~Ia---~G~~~~~~~L  558 (837)
                      -.+...+.+++.|+.|+   .|.-.|..++
T Consensus       453 ~~~~~~g~~~~~L~~ia~~~~~~~~~~~~~  482 (715)
T TIGR01973       453 NLVFHPGLSPKKLDDIAEASSGAHSDDQVV  482 (715)
T ss_pred             CCHHHHCCHHHHHHHHHHHHHHCCCHHHHH
T ss_conf             332340500347999999997427100001


No 126
>PRK04017 hypothetical protein; Provisional
Probab=50.81  E-value=15  Score=15.59  Aligned_cols=42  Identities=24%  Similarity=0.299  Sum_probs=31.9

Q ss_pred             HHHHHHHHHH-HHCCEEEECCCCCCHHHHHHHHHHHHHHHHCC
Q ss_conf             9999999998-70998999469970257999999999755125
Q gi|254780306|r   60 KHLQNIIHAV-KSSTILILATDPDREGEAISWHVLDVLRQKNL  101 (837)
Q Consensus        60 k~~~~i~~~~-k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~  101 (837)
                      ..+..+...+ +...+||+-||-||-|+-++-.+.+.|...+.
T Consensus        52 ~~l~~ia~~~~~~~~~vIlL~DwDr~G~~L~~kl~~~L~~~g~   94 (132)
T PRK04017         52 LPLFEIALRASRLKKEVIILTDFDRKGEELAKKLSEYLQGYGI   94 (132)
T ss_pred             CCHHHHHHHHHHCCCEEEEEEECCCCHHHHHHHHHHHHHHCCC
T ss_conf             4099999999855983999971363217999999999986899


No 127
>KOG2324 consensus
Probab=49.78  E-value=12  Score=16.35  Aligned_cols=17  Identities=24%  Similarity=0.313  Sum_probs=10.1

Q ss_pred             CCCCEEEEEECCCCCEE
Q ss_conf             99966999826974227
Q gi|254780306|r  660 ETKESVTLRSGRFGLYV  676 (837)
Q Consensus       660 ~~G~~I~lk~GryGpYv  676 (837)
                      .+|+|-+|..|=||.=|
T Consensus       287 ~~gKpe~l~MgCyGIGV  303 (457)
T KOG2324         287 VEGKPEFLHMGCYGIGV  303 (457)
T ss_pred             ECCCCCEEEECCEECCH
T ss_conf             05984068740200048


No 128
>TIGR02390 RNA_pol_rpoA1 DNA-directed RNA polymerase subunit A'; InterPro: IPR012758   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.    This family consists of the archaeal A' subunit of the DNA-directed RNA polymerase. The example from Methanococcus jannaschii contains an intein.; GO: 0003677 DNA binding, 0003899 DNA-directed RNA polymerase activity, 0008270 zinc ion binding, 0006350 transcription.
Probab=49.69  E-value=16  Score=15.46  Aligned_cols=15  Identities=7%  Similarity=0.071  Sum_probs=10.9

Q ss_pred             ECCCHHHHHHHHHCC
Q ss_conf             037989999998622
Q gi|254780306|r  113 NAITKQVVLNAMKSP  127 (837)
Q Consensus       113 ~eiT~~aI~~A~~n~  127 (837)
                      -=||++.|++=|++-
T Consensus       180 ~KLTP~eiRErLEki  194 (901)
T TIGR02390       180 VKLTPSEIRERLEKI  194 (901)
T ss_pred             EECCCHHHHHHHHCC
T ss_conf             442817999975168


No 129
>PRK06266 transcription initiation factor E subunit alpha; Validated
Probab=48.98  E-value=14  Score=15.79  Aligned_cols=29  Identities=31%  Similarity=0.567  Sum_probs=17.9

Q ss_pred             HHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             8760888999999998762135567212245531475
Q gi|254780306|r  270 SSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRT  306 (837)
Q Consensus       270 s~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRT  306 (837)
                      +..+|+..-.+=++...|||        .||+||-|.
T Consensus        43 Ae~~gi~lN~VRk~LY~Lye--------~~La~yrR~   71 (178)
T PRK06266         43 AEQTGIKLNTVRKILYKLYD--------AGLADYKRE   71 (178)
T ss_pred             HHHHCCCHHHHHHHHHHHHH--------CCCCEEEEE
T ss_conf             99969978999999999985--------764136665


No 130
>COG0466 Lon ATP-dependent Lon protease, bacterial type [Posttranslational modification, protein turnover, chaperones]
Probab=48.38  E-value=15  Score=15.68  Aligned_cols=26  Identities=19%  Similarity=0.312  Sum_probs=17.8

Q ss_pred             CCCHHHHHHHHHHHHHHC-CEEEECCC
Q ss_conf             765489999999998709-98999469
Q gi|254780306|r   55 DPSSQKHLQNIIHAVKSS-TILILATD   80 (837)
Q Consensus        55 ~~~~kk~~~~i~~~~k~a-~~iilAtD   80 (837)
                      .-+..+-++.|..+++.- ..|.+++-
T Consensus        29 ~vgr~~si~ale~a~~~~~k~i~l~~q   55 (782)
T COG0466          29 FVGREKSIKALEEAMKNDQKYILLVTQ   55 (782)
T ss_pred             ECCCHHHHHHHHHHHHCCCCEEEEEEE
T ss_conf             727753799999997278877999981


No 131
>pfam01726 LexA_DNA_bind LexA DNA binding domain. This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins. The aligned region contains a variant form of the helix-turn-helix DNA binding motif. This domain is found associated with pfam00717 the auto-proteolytic domain of LexA EC:3.4.21.88.
Probab=47.83  E-value=15  Score=15.56  Aligned_cols=30  Identities=17%  Similarity=0.409  Sum_probs=20.6

Q ss_pred             HHHCCCCCCCCHHHHHHHHHHCCEEECCCC
Q ss_conf             321025665515789999973220221477
Q gi|254780306|r  480 MEEIGIGRPSTYATILETLYKRKYVIAEKR  509 (837)
Q Consensus       480 mE~~GIGrPSTyA~II~~L~~R~YV~~~~~  509 (837)
                      ++..|+--|||-...|..|.++||+.+..+
T Consensus        32 ~~~~g~~S~s~v~~~l~~Le~kG~I~r~~~   61 (65)
T pfam01726        32 AQALGLRSPNAAEEHLKALERKGYIERDPG   61 (65)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHCCCEECCCC
T ss_conf             999389980999999999999839634899


No 132
>TIGR00763 lon ATP-dependent protease La; InterPro: IPR004815   Proteolytic enzymes that exploit serine in their catalytic activity are ubiquitous, being found in viruses, bacteria and eukaryotes . They include a wide range of peptidase activity, including exopeptidase, endopeptidase, oligopeptidase and omega-peptidase activity. Over 20 families (denoted S1 - S66) of serine protease have been identified, these being grouped into clans on the basis of structural similarity and other functional evidence . Structures are known for members of the clans and the structures indicate that some appear to be totally unrelated, suggesting different evolutionary origins for the serine peptidases .   Not withstanding their different evolutionary origins, there are similarities in the reaction mechanisms of several peptidases. Chymotrypsin, subtilisin and carboxypeptidase C have a catalytic triad of serine, aspartate and histidine in common: serine acts as a nucleophile, aspartate as an electrophile, and histidine as a base . The geometric orientations of the catalytic residues are similar between families, despite different protein folds . The linear arrangements of the catalytic residues commonly reflect clan relationships. For example the catalytic triad in the chymotrypsin clan (PA) is ordered HDS, but is ordered DHS in the subtilisin clan (SB) and SDH in the carboxypeptidase clan (SC) , .   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 signature defines the bacterial and eukaryotic lon proteases, which are ATP-dependent serine peptidases belonging to the MEROPS peptidase family S16 (lon protease family, clan SF). This family of sequences does not include the archaeal lon homologs, IPR004663 from INTERPRO. In the eukaryotes the majority of the proteins are located in the mitochondrial matrix , . In yeast, Pim1, is located in the mitochondrial matrix, is required for mitochondrial function, is constitutively expressed but is increased after thermal stress, suggesting that Pim1 may play a role in the heat shock response .; GO: 0004176 ATP-dependent peptidase activity, 0005524 ATP binding, 0006510 ATP-dependent proteolysis.
Probab=47.75  E-value=17  Score=15.34  Aligned_cols=17  Identities=24%  Similarity=0.460  Sum_probs=10.1

Q ss_pred             CEEECCC-----CCEEECCHHH
Q ss_conf             2022147-----7122201142
Q gi|254780306|r  502 KYVIAEK-----RKILPQNTGR  518 (837)
Q Consensus       502 ~YV~~~~-----~~l~pT~~G~  518 (837)
                      ||+.-+|     +.|+|..+..
T Consensus       598 GY~~~EK~~IA~~yLiP~~~~~  619 (941)
T TIGR00763       598 GYTEEEKLEIAKKYLIPKALED  619 (941)
T ss_pred             CCCHHHHHHHHHHCCHHHHHHH
T ss_conf             8876789999985471367987


No 133
>PRK00574 gltX glutamyl-tRNA synthetase; Reviewed
Probab=47.69  E-value=7.5  Score=17.90  Aligned_cols=70  Identities=14%  Similarity=0.261  Sum_probs=37.1

Q ss_pred             CCCCCCCHHHHHHHHHHHHHHHHHHCCCCCCEEEEEEEECCCCCEEEEEEEEECCEEECCCCHHHHHHHHHHHHHHCCCC
Q ss_conf             67653422689999999999996413765440012233157996542233103583303310113566677764200156
Q gi|254780306|r  162 GARSAGRVQSVALRLICNRENQIESFVSEEYWSLSVLLETPRNDKFTAHLTDFNGQRIEKKSISNKKEADDLISFVKKAT  241 (837)
Q Consensus       162 ~~lSaGRVQtp~L~lIveRe~eI~~F~p~~y~~i~a~~~~~~~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~~~~~~  241 (837)
                      |-|-+|-+-|.....+.-|                     ..|..|-.++-..|..|      ..++..+.|.+.++=-.
T Consensus        15 G~lHiG~~rtAl~n~l~Ar---------------------~~~G~fiLRIEDTD~~R------~~~~~~~~I~~~L~wlg   67 (489)
T PRK00574         15 GYLHIGNARTALFNYLFAK---------------------HNNGKFILRIEDTDQER------NVEGGEESQLENLKWLG   67 (489)
T ss_pred             CCCCHHHHHHHHHHHHHHH---------------------HCCCEEEEEECCCCCCC------CCHHHHHHHHHHHHHCC
T ss_conf             8422478999999999999---------------------64998999867789877------87699999999999879


Q ss_pred             CEEEEEECCCCCCCCCCCCC
Q ss_conf             30100002332224685210
Q gi|254780306|r  242 YSVEKIENKPIKRNPWPAFT  261 (837)
Q Consensus       242 ~~V~~v~~k~~~~~Pp~Pf~  261 (837)
                      ..   ..+.+...-|..||-
T Consensus        68 l~---~DE~p~~~g~~gPY~   84 (489)
T PRK00574         68 ID---WDEGPDKGGEYGPYR   84 (489)
T ss_pred             CC---CCCCCCCCCCCCCCC
T ss_conf             88---877877788888835


No 134
>TIGR00354 polC DNA polymerase II, large subunit DP2; InterPro: IPR004475 This family represents the large subunit, DP2, of a two subunit novel archaebacterial replicative DNA polymerase first characterised for Pyrococcus furiosus. The structure of DP2 appears to be organised as a ~950 residue component separated from a ~300 residue component by a ~150 residue intein. The other subunit, DP1, has sequence similarity to the eukaryotic DNA polymerase delta small subunit.; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0006308 DNA catabolic process.
Probab=47.27  E-value=9.3  Score=17.22  Aligned_cols=136  Identities=21%  Similarity=0.191  Sum_probs=65.0

Q ss_pred             CCCCCCCCCCCEEEEECCCHHH---HHHH---HHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEE
Q ss_conf             5786766674406887765489---9999---999987099899946997025799999999975512578871699998
Q gi|254780306|r   39 KGSVLPEKEFEMIWNIDPSSQK---HLQN---IIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSF  112 (837)
Q Consensus        39 ~~~v~~~~~f~p~y~v~~~~kk---~~~~---i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f  112 (837)
                      .-|.||+..  +.   +|=+++   .|.-   ++.+|+...++   -.-||==|.||+.|..-+-.....+..|-.|   
T Consensus        26 kkGlDp~~~--vE---IPlAkdmAeRVEgLvgp~G~A~RI~EL---eeg~lgrE~~af~iA~EIvegkfg~~dPeek---   94 (1173)
T TIGR00354        26 KKGLDPELE--VE---IPLAKDMAERVEGLVGPKGVAKRIKEL---EEGDLGREEVAFKIAKEIVEGKFGEFDPEEK---   94 (1173)
T ss_pred             HCCCCCCCC--CC---CCHHHHHHHHHHHHCCCHHHHHHHHHH---HCCCCCHHHHHHHHHHHHHCCCCCCCCHHHH---
T ss_conf             257688887--46---503554777766431842377677776---5088653589999999985257887674678---


Q ss_pred             ECCCHHHHHHHHHCCCCCCHHHHHH---HHHH-HHHHHHHHHHHCHHHHHHCC-CCCCCCC---HHHHHHHHHHHHHHHH
Q ss_conf             0379899999986226469899999---9999-99898740113789886414-6765342---2689999999999996
Q gi|254780306|r  113 NAITKQVVLNAMKSPRDINLDLVNA---YLAR-RALDYLVGFNLSPILWQKLP-GARSAGR---VQSVALRLICNRENQI  184 (837)
Q Consensus       113 ~eiT~~aI~~A~~n~r~~d~~Lv~A---~~aR-r~lD~lvG~~lSp~L~rk~~-~~lSaGR---VQtp~L~lIveRe~eI  184 (837)
                      -+.-++||+-|++=+.   +..|.|   +.|| |+ |.=  |.-|..|.-..+ +-.|||=   |-|+-++==|.|-.+|
T Consensus        95 Ek~ad~AvRTAlAilT---EGvVAAPlEGIArVrI-k~n--~D~~~yLavYyAGPIRSAGGTAqalSVLvaDyvR~a~gl  168 (1173)
T TIGR00354        95 EKKADQAVRTALAILT---EGVVAAPLEGIARVRI-KKN--FDKSEYLAVYYAGPIRSAGGTAQALSVLVADYVRKAVGL  168 (1173)
T ss_pred             HHHHHHHHHHHHHHHH---CCCEECCCCCEEEEEE-ECC--CCCCCEEEEEECCCCCCCHHHHHHHHHHHHHHHHHHHCC
T ss_conf             9999899999999972---3310047665034665-027--898623688853876560369999999999899876237


Q ss_pred             HHCCCCC
Q ss_conf             4137654
Q gi|254780306|r  185 ESFVSEE  191 (837)
Q Consensus       185 ~~F~p~~  191 (837)
                      ..++|.+
T Consensus       169 dRYkPtE  175 (1173)
T TIGR00354       169 DRYKPTE  175 (1173)
T ss_pred             CCCCCCH
T ss_conf             8878655


No 135
>COG2512 Predicted membrane-associated trancriptional regulator    [Transcription]
Probab=47.07  E-value=17  Score=15.27  Aligned_cols=37  Identities=30%  Similarity=0.490  Sum_probs=29.7

Q ss_pred             CCCCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCC
Q ss_conf             10178998743321025665515789999973220221477
Q gi|254780306|r  469 PRYSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKR  509 (837)
Q Consensus       469 ~rytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~  509 (837)
                      .|-+++.|.+++   |+=++ |=.-|+..|-+||||+++++
T Consensus       209 Gri~Q~eL~r~l---glskt-TvsR~L~~LEk~GlIe~~K~  245 (258)
T COG2512         209 GRITQAELRRAL---GLSKT-TVSRILRRLEKRGLIEKEKK  245 (258)
T ss_pred             CEEEHHHHHHHH---CCCHH-HHHHHHHHHHHCCCEEEEEE
T ss_conf             978699988860---99767-79999999986895688870


No 136
>PRK08807 consensus
Probab=46.37  E-value=12  Score=16.40  Aligned_cols=41  Identities=15%  Similarity=0.273  Sum_probs=30.9

Q ss_pred             CCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCC
Q ss_conf             025665515789999973220221477122201142000022
Q gi|254780306|r  483 IGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFL  524 (837)
Q Consensus       483 ~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L  524 (837)
                      .|+.-.. +..-+..+.++|++..++.++.+|+.|+.+.+.+
T Consensus       339 ~G~~~~~-~~~~l~~~~~~Gll~~~~~ri~LT~~G~~~~n~V  379 (385)
T PRK08807        339 TGLAAEV-IEAPLARAVAQGWLRRQDGRVVPTELGRRFTNDV  379 (385)
T ss_pred             HCCCHHH-HHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHH
T ss_conf             7969999-9999999997899897499999996388999999


No 137
>pfam02002 TFIIE_alpha TFIIE alpha subunit. The general transcription factor TFIIE has an essential role in eukaryotic transcription initiation together with RNA polymerase II and other general factors. Human TFIIE consists of two subunits TFIIE-alpha and TFIIE-beta, and joins the preinitiation complex after RNA polymerase II and TFIIF. This family consists of the conserved amino terminal region of eukaryotic TFIIE-alpha and proteins from archaebacteria that are presumed to be TFIIE-alpha subunits.
Probab=46.32  E-value=15  Score=15.74  Aligned_cols=31  Identities=23%  Similarity=0.441  Sum_probs=26.2

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCC
Q ss_conf             988760888999999998762135567212245531475
Q gi|254780306|r  268 VASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRT  306 (837)
Q Consensus       268 ~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRT  306 (837)
                      +.+..+|+....+=+++.+|||        .||++|.|.
T Consensus        32 dLa~~l~~~~n~vRkiL~~L~e--------~~lv~~~r~   62 (105)
T pfam02002        32 DLAELLGIDLNELRKLLYRLYD--------ARLVKYRRR   62 (105)
T ss_pred             HHHHHHCCCHHHHHHHHHHHHH--------CCCEEEEEE
T ss_conf             9999978988899999999987--------886588976


No 138
>PRK10569 NAD(P)H-dependent FMN reductase; Provisional
Probab=46.29  E-value=18  Score=15.10  Aligned_cols=68  Identities=22%  Similarity=0.356  Sum_probs=39.4

Q ss_pred             CCEEEE-CCH---HHHHHHHHHHCC---CCEEEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCC
Q ss_conf             918997-790---478778875089---9899994251100786557867666744068877654899999999987099
Q gi|254780306|r    1 MNVIIV-ESP---AKAKTISKYLGS---NYKVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSST   73 (837)
Q Consensus         1 M~LvIv-EsP---~kak~I~~~Lg~---~y~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~   73 (837)
                      ||+|++ =||   |+.+.+.+++..   ..-+....-+++|||...+ +.  .+|.        . ..+..+.+.+..||
T Consensus         1 MkIV~IsGS~s~~SrT~~L~~~v~~~L~~~g~ev~~i~l~dl~~~~l-l~--~~~~--------~-p~v~~~~~~V~~AD   68 (191)
T PRK10569          1 MRVITLAGSPRFPSRSSVLLEYAREWLQGLDVEVYHWNLQDFAAEDL-LY--ARFD--------S-PAVKTFTEQLQQAD   68 (191)
T ss_pred             CEEEEEECCCCCCCHHHHHHHHHHHHHHHCCCEEEEEEHHHCCCHHH-HC--CCCC--------C-HHHHHHHHHHHHCC
T ss_conf             95999958999997499999999999986698589986331680654-01--6789--------9-89999999998589


Q ss_pred             EEEECCC
Q ss_conf             8999469
Q gi|254780306|r   74 ILILATD   80 (837)
Q Consensus        74 ~iilAtD   80 (837)
                      -+|+||=
T Consensus        69 ~lIVaTP   75 (191)
T PRK10569         69 GLIVATP   75 (191)
T ss_pred             EEEEECC
T ss_conf             7999676


No 139
>PRK11512 DNA-binding transcriptional repressor MarR; Provisional
Probab=45.80  E-value=4.7  Score=19.45  Aligned_cols=48  Identities=13%  Similarity=0.187  Sum_probs=25.7

Q ss_pred             CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCCC-------CEEECCHHHHHCC
Q ss_conf             178998743321025665515789999973220221477-------1222011420000
Q gi|254780306|r  471 YSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEKR-------KILPQNTGRIVTA  522 (837)
Q Consensus       471 ytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~-------~l~pT~~G~~v~~  522 (837)
                      .|.+.|-+.|   ||- +||-+.+|..|..+|||++.-+       .+..|+.|..+.+
T Consensus        55 ~t~~eLa~~l---~id-~~tvt~~ldrLe~~GlI~R~~~p~DrR~~~v~LT~~G~~l~~  109 (144)
T PRK11512         55 ITPVELKKVL---SVD-LGALTRMLDRLVCKGWVERLPNPNDKRGVLVKLTTSGAAICE  109 (144)
T ss_pred             CCHHHHHHHH---CCC-HHHHHHHHHHHHHCCCEEECCCCCCCCEEEEEECHHHHHHHH
T ss_conf             7999999997---888-878999999999787966357987762478788977999999


No 140
>TIGR00993 3a0901s04IAP86 chloroplast protein import component Toc86/159, G and M domains; InterPro: IPR005690    Two integral outer envelope GTPases, Toc34 and Toc86, are proposed to regulate the recognition and translocation of nuclear-encoded preproteins during the early stages of protein import into chloroplasts. The long precursor of the 86K protein is proposed to have three domains. The N-terminal A-domain is acidic, repetitive, weakly conserved, readily removed by proteolysis during chloroplast isolation, and not required for protein translocation . The other domains are designated G (GTPase) and M (membrane anchor); this family includes most of the G domain and all of M.; GO: 0015450 P-P-bond-hydrolysis-driven protein transmembrane transporter activity, 0006886 intracellular protein transport, 0009707 chloroplast outer membrane.
Probab=45.49  E-value=9.3  Score=17.20  Aligned_cols=114  Identities=21%  Similarity=0.328  Sum_probs=60.0

Q ss_pred             HHHHHHHHHHCCCCEEEEEECC----CEECCCCCCCCCCC----CCCCEEEEECCCHHHHHHHHHHHHHHC-CEEEECCC
Q ss_conf             4787788750899899994251----10078655786766----674406887765489999999998709-98999469
Q gi|254780306|r   10 AKAKTISKYLGSNYKVLSSFGH----IRDLPAKKGSVLPE----KEFEMIWNIDPSSQKHLQNIIHAVKSS-TILILATD   80 (837)
Q Consensus        10 ~kak~I~~~Lg~~y~V~as~GH----irdLp~~~~~v~~~----~~f~p~y~v~~~~kk~~~~i~~~~k~a-~~iilAtD   80 (837)
                      .|.-||...||.--..+.+||-    |+|.-.-=-||.+.    -+..+.|.=-....|++..+|+++|++ --|||--|
T Consensus       136 GKSATINSI~~e~~~s~dAf~~~T~~V~~i~G~V~Gv~i~viDTPGL~~s~~dQs~N~K~L~sVK~~~KK~PPDIVLY~D  215 (772)
T TIGR00993       136 GKSATINSIFGEVKASIDAFGLGTTSVQEIEGLVDGVKIRVIDTPGLKSSASDQSKNEKILSSVKKLIKKNPPDIVLYVD  215 (772)
T ss_pred             CCCHHHHHHHCCEEEEEECCCCCCCEEEEEEEEEEEEEEEEEECCCCCHHHHHHHHCHHHHHHHHHHHCCCCCCEEEEEC
T ss_conf             72010111123500120101466644776666771079999757887555543330206888888863179696698600


Q ss_pred             CCCHHHHHHHHHHHHHHHHCCCCCCCEEE---------EEEECCCHHHHHHHHHCCCC------CCHHHHHHH
Q ss_conf             97025799999999975512578871699---------99803798999999862264------698999999
Q gi|254780306|r   81 PDREGEAISWHVLDVLRQKNLIEKTKIQR---------VSFNAITKQVVLNAMKSPRD------INLDLVNAY  138 (837)
Q Consensus        81 ~DREGE~Iawhi~e~l~~~~~~~~~~v~R---------~~f~eiT~~aI~~A~~n~r~------~d~~Lv~A~  138 (837)
                        |=         + ++.+. .++.|.-|         ||+|.|-  .+.+|-.-|=+      ..++++=||
T Consensus       216 --RL---------D-~Q~RD-~~dlPlLRti~~~lGpsIW~N~IV--~LTHAAS~PPDg~~Gt~~SYD~FVaQ  273 (772)
T TIGR00993       216 --RL---------D-LQTRD-LNDLPLLRTITDVLGPSIWKNAIV--TLTHAASAPPDGPNGTPLSYDVFVAQ  273 (772)
T ss_pred             --CC---------C-CCCCC-CCCCCHHHHHHHHHCCHHHHHHHH--HHHHCCCCCCCCCCCCCCCEEEEEEC
T ss_conf             --22---------3-33465-667744757775616101320432--11100368767888884200001100


No 141
>TIGR01591 Fdh-alpha formate dehydrogenase, alpha subunit; InterPro: IPR006478   This group of sequences describe a subset of formate dehydrogenase alpha chains found mainly in the archaea but also in alpha and gamma proteobacteria and a small number of Gram-positive bacteria. The alpha chain contains domains for molybdopterin dinucleotide binding and molybdopterin oxidoreductase. The holo-enzyme also contains beta and gamma subunits. The enzyme catalyzes the oxidation of formate (produced from pyruvate during anaerobic growth) to carbon dioxide with the concomitant release of two electrons and two protons. The enzyme's purpose is to allow growth on formate in some circumstances  and, in the case of FdhH in gamma proteobacteria, to pass electrons to hydrogenase (by which process acid is neutralized) . The alpha subunit of a version of nitrate reductase is closely related.; GO: 0008863 formate dehydrogenase activity, 0015942 formate metabolic process, 0009326 formate dehydrogenase complex.
Probab=45.25  E-value=13  Score=16.08  Aligned_cols=82  Identities=20%  Similarity=0.203  Sum_probs=36.6

Q ss_pred             HHHHHHHHH--CCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHH-------HHHHHHCCCCCCCHHHH
Q ss_conf             667776420--015630100002332224685210379999988760888999999-------99876213556721224
Q gi|254780306|r  229 EADDLISFV--KKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMR-------IAQKLYEGIDVNGEIVG  299 (837)
Q Consensus       229 ~a~~~~~~~--~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~-------iAQ~LYE~~~~~~~~~G  299 (837)
                      -++.+.++.  +++.+.|.++-+.+.-++.-       ++.+..=.++=..+=++-       |-|.||..        -
T Consensus       180 v~~~l~~AKk~nGaKiiV~DpR~t~taksah-------i~AD~~i~~k~GTdial~na~a~viI~egL~Dk--------~  244 (694)
T TIGR01591       180 VASKLMRAKKRNGAKIIVIDPRKTETAKSAH-------IIADLFIPLKPGTDIALLNAVANVIIEEGLYDK--------E  244 (694)
T ss_pred             HHHHHHHHHHHCCCEEEEECCCCCCHHHHHH-------HCCCEEEECCCCHHHHHHHHHHHEEECCCCCCH--------H
T ss_conf             8999999985089789997588860232211-------101106517997089999732002422786166--------8


Q ss_pred             HHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCC
Q ss_conf             55314755444430568999976552001123
Q gi|254780306|r  300 LITYMRTDGVHMSPDALEAVRRSITSHYGDHY  331 (837)
Q Consensus       300 lITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~  331 (837)
                      ||- -|||-..     .++.|+.|+..|-.++
T Consensus       245 Fi~-~R~~W~~-----F~E~r~~V~~~yTpE~  270 (694)
T TIGR01591       245 FIE-KRTDWEG-----FEEFREIVKGKYTPEY  270 (694)
T ss_pred             HHH-HHCCCCC-----HHHHHHHHCCCCCHHH
T ss_conf             897-5148785-----3788877504787532


No 142
>KOG0994 consensus
Probab=44.84  E-value=19  Score=14.94  Aligned_cols=26  Identities=27%  Similarity=0.290  Sum_probs=11.5

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             79999988760888999999998762
Q gi|254780306|r  263 STLQQVASSRLGFSASHTMRIAQKLY  288 (837)
Q Consensus       263 stLQq~As~~lg~sa~~Tm~iAQ~LY  288 (837)
                      -|+|..++=+-||+-.+.-..|+.-+
T Consensus       930 ~t~~ivC~C~~GY~G~RCe~CA~~~f  955 (1758)
T KOG0994         930 RTQQIVCHCQEGYSGSRCEICADNHF  955 (1758)
T ss_pred             CCCCEEEECCCCCCCCCHHHHCCCCC
T ss_conf             32232342146766540123123456


No 143
>PRK03573 transcriptional regulator SlyA; Provisional
Probab=44.60  E-value=19  Score=14.92  Aligned_cols=51  Identities=22%  Similarity=0.346  Sum_probs=36.2

Q ss_pred             CCHHHHHHHHHHCCCCCCCCHHHHHHHHHHCCEEECCC-------CCEEECCHHHHHCCCCC
Q ss_conf             17899874332102566551578999997322022147-------71222011420000223
Q gi|254780306|r  471 YSESSLIKKMEEIGIGRPSTYATILETLYKRKYVIAEK-------RKILPQNTGRIVTAFLE  525 (837)
Q Consensus       471 ytEasLik~mE~~GIGrPSTyA~II~~L~~R~YV~~~~-------~~l~pT~~G~~v~~~L~  525 (837)
                      -|...|-+.   .||-+| |=+.+|..|.++|||.+..       +.+..|+.|..+.+-+.
T Consensus        47 ~tq~eLa~~---l~v~~~-t~tr~ld~LE~~GlI~R~~~~~DrR~~~i~LT~~G~~l~~~~~  104 (144)
T PRK03573         47 QSQIQLAKA---IGIEQP-SLVRTLDQLEEKGLISRQTCASDRRAKRIKLTEKAEPLISEME  104 (144)
T ss_pred             CCHHHHHHH---HCCCHH-HHHHHHHHHHHCCCEEEECCCCCCCEEEEEECHHHHHHHHHHH
T ss_conf             899999999---798783-6999999999888978622867675467678887999999999


No 144
>PRK09058 coproporphyrinogen III oxidase; Provisional
Probab=44.60  E-value=3.5  Score=20.41  Aligned_cols=43  Identities=14%  Similarity=0.085  Sum_probs=34.6

Q ss_pred             CCCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCC
Q ss_conf             0256655157899999732202214771222011420000223
Q gi|254780306|r  483 IGIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLE  525 (837)
Q Consensus       483 ~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~  525 (837)
                      .+.|.....+..++.+++.|.|..++..|..|+.|+.+.+.+-
T Consensus       385 ~~~~~~~~~~~~l~~~~~~GLv~~~~~~l~LT~~Gr~~~~~Ia  427 (447)
T PRK09058        385 LRTPHAVALAPLLAQWQQAGLVELSSDCLRLTLAGRFWAVNLA  427 (447)
T ss_pred             CCCCHHHHHHHHHHHHHHCCCEEEECCEEEECCCCCCHHHHHH
T ss_conf             2655699999999999978998996999999977666999999


No 145
>COG1568 Predicted methyltransferases [General function prediction only]
Probab=44.30  E-value=17  Score=15.20  Aligned_cols=11  Identities=27%  Similarity=0.468  Sum_probs=4.3

Q ss_pred             EECCHHHHHCC
Q ss_conf             22011420000
Q gi|254780306|r  512 LPQNTGRIVTA  522 (837)
Q Consensus       512 ~pT~~G~~v~~  522 (837)
                      ..++.|..+++
T Consensus       275 lIn~~gvVITd  285 (354)
T COG1568         275 LINEMGVVITD  285 (354)
T ss_pred             HHHHCCEEHHH
T ss_conf             98743764076


No 146
>COG3383 Uncharacterized anaerobic dehydrogenase [General function prediction only]
Probab=44.15  E-value=19  Score=14.87  Aligned_cols=39  Identities=26%  Similarity=0.433  Sum_probs=20.7

Q ss_pred             ECCHHHHHCCCCCCCCCCCCCHHHHHHHH----------------HHHHHHHCCCHH
Q ss_conf             20114200002233665568988999999----------------999998626013
Q gi|254780306|r  513 PQNTGRIVTAFLENFFSQYVEYDFTADLE----------------EKLDEISTGKLN  553 (837)
Q Consensus       513 pT~~G~~v~~~L~~~f~~~~~~~fTa~~E----------------~~ld~Ia~G~~~  553 (837)
                      ..+.|- +-+.|..+ ..|-|..+.++.|                ++||.|.+|++.
T Consensus       596 a~DmGs-lP~~LPGy-q~isdd~~R~kFE~~wGv~i~~ePGl~~~~Mlea~~~G~~~  650 (978)
T COG3383         596 ACDMGS-LPDVLPGY-QPISDDAVRAKFEEAWGVKIPREPGLDNPEMLEAIEEGKLK  650 (978)
T ss_pred             CCCCCC-CCCCCCCC-CCCCCHHHHHHHHHHHCCCCCCCCCCCCHHHHHHHHCCCEE
T ss_conf             244566-86658775-21565889999999758877998888728999998628615


No 147
>cd01916 ACS_1 Acetyl-CoA synthase (ACS), also known as acetyl-CoA decarbonylase, is found in acetogenic and methanogenic organisms and is responsible for the synthesis and breakdown of acetyl-CoA.  ACS forms a heterotetramer with carbon monoxide dehydrogenase (CODH) consisting of two ACS and two CODH subunits. CODH reduces carbon dioxide to carbon monoxide and ACS then synthesizes acetyl-CoA from carbon monoxide, CoA, and a methyl group donated by another protein (CoFeSP).  ACS has three structural domains, an N-terminal rossman fold domain with a helical region at its N-terminus which interacts with CODH, and two alpha + beta fold domains.  A Ni-Fe-S center referred to as the A-cluster is located in the C-terminal domain. A large cavity exists between the three domains which may bind CoA.
Probab=44.03  E-value=8.1  Score=17.68  Aligned_cols=12  Identities=58%  Similarity=1.265  Sum_probs=10.1

Q ss_pred             CCCCCCCCCCCC
Q ss_conf             111234343233
Q gi|254780306|r  623 AFVGCTNYPECK  634 (837)
Q Consensus       623 ~FigCSnyPeCk  634 (837)
                      .|+||||||+..
T Consensus       469 a~vGC~Nypng~  480 (731)
T cd01916         469 ALVGCSNYPNGT  480 (731)
T ss_pred             EEECCCCCCCCC
T ss_conf             995078898861


No 148
>pfam01978 TrmB Sugar-specific transcriptional regulator TrmB. One member of this family, TrmB, has been shown to be a sugar-specific transcriptional regulator of the trehalose/maltose ABC transporter in Thermococcus litoralis.
Probab=43.70  E-value=13  Score=16.11  Aligned_cols=20  Identities=15%  Similarity=0.253  Sum_probs=10.5

Q ss_pred             HHHHCCCHHHHHHHHHHHHC
Q ss_conf             87608889999999987621
Q gi|254780306|r  270 SSRLGFSASHTMRIAQKLYE  289 (837)
Q Consensus       270 s~~lg~sa~~Tm~iAQ~LYE  289 (837)
                      ++..|++-.++-++.++|.+
T Consensus        29 a~~~~i~r~~vY~~L~~L~~   48 (68)
T pfam01978        29 AEESGVPRSKVYEVLRSLEK   48 (68)
T ss_pred             HHHHCCCHHHHHHHHHHHHH
T ss_conf             99959889899999999998


No 149
>pfam10557 Cullin_Nedd8 Cullin protein neddylation domain. This is the neddylation site of cullin proteins which are a family of structurally related proteins containing an evolutionarily conserved cullin domain. With the exception of APC2, each member of the cullin family is modified by Nedd8 and several cullins function in Ubiquitin-dependent proteolysis, a process in which the 26S proteasome recognizes and subsequently degrades a target protein tagged with K48-linked poly-ubiquitin chains. Cullins are molecular scaffolds responsible for assembling the ROC1/Rbx1 RING-based E3 ubiquitin ligases, of which several play a direct role in tumorigenesis. Nedd8/Rub1 is a small ubiquitin-like protein, which was originally found to be conjugated to Cdc53, a cullin component of the SCF (Skp1-Cdc53/CUL1-F-box protein) E3 Ub ligase complex in Saccharomyces cerevisiae, and Nedd8 modification has now emerged as a regulatory pathway of fundamental importance for cell cycle control and for embryogenes
Probab=43.48  E-value=20  Score=14.79  Aligned_cols=13  Identities=23%  Similarity=0.649  Sum_probs=7.8

Q ss_pred             HHHHHHCCEEECC
Q ss_conf             9999732202214
Q gi|254780306|r  495 LETLYKRKYVIAE  507 (837)
Q Consensus       495 I~~L~~R~YV~~~  507 (837)
                      |+.|++|+|+.++
T Consensus        51 Ie~LIekeYl~R~   63 (68)
T pfam10557        51 IESLIEKEYLERD   63 (68)
T ss_pred             HHHHHHHHHHHCC
T ss_conf             9999987888318


No 150
>TIGR00334 primaseG_like primase homolog; InterPro: IPR004466 This family of orthologous proteins shows a weak but significant similarity to the central region of the DnaG-type DNA primase. The region of similarity is termed the Toprim (topoisomerase-primase) domain and is also shared by RecR, OLD family nucleases, and type IA and II topoisomerases..
Probab=43.14  E-value=20  Score=14.76  Aligned_cols=71  Identities=20%  Similarity=0.342  Sum_probs=46.9

Q ss_pred             HHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHH-------CCCCCCCEEEEEEECCCHHHHHHHHHCCCC
Q ss_conf             489999999998709989994699702579999999997551-------257887169999803798999999862264
Q gi|254780306|r   58 SQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQK-------NLIEKTKIQRVSFNAITKQVVLNAMKSPRD  129 (837)
Q Consensus        58 ~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~-------~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~  129 (837)
                      +...++.++...+ ...+++.+|||..|+.|-..+.+.+...       .....+..+.+-..+.+..++..++.+...
T Consensus        34 ~~~~~~~~~~~~~-~~~~~~~~dpd~~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~g~~~~~~~~~~~~l~~~~~  111 (176)
T TIGR00334        34 KDETINLLKKALK-KKGVILLLDPDKPGEKIRKKLEEHLGGYENCFLPKALLKPKNTKKIGVEEASKTALIAALENVGT  111 (176)
T ss_pred             HHHHHHHHHHHHH-HCCEEEEECCCCCHHHHHHHHHHHHCCHHHHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHHHHH
T ss_conf             5788999998775-36736875687322689999998614212333314551333332111123218899999864444


No 151
>PRK00941 acetyl-CoA decarbonylase/synthase complex subunit alpha; Validated
Probab=42.65  E-value=8.7  Score=17.41  Aligned_cols=12  Identities=67%  Similarity=1.370  Sum_probs=10.3

Q ss_pred             CCCCCCCCCCCC
Q ss_conf             111234343233
Q gi|254780306|r  623 AFVGCTNYPECK  634 (837)
Q Consensus       623 ~FigCSnyPeCk  634 (837)
                      .|+||+|||+..
T Consensus       506 a~vGC~Nypng~  517 (779)
T PRK00941        506 AFVGCSNYPNGG  517 (779)
T ss_pred             EEECCCCCCCCC
T ss_conf             995178898861


No 152
>TIGR00014 arsC arsenate reductase; InterPro: IPR006659   This entry describes a distinct clade, including ArsC itself, of the broader family of ArsC and related proteins. This clade is almost completely restricted to the proteobacteria. An anion-translocating ATPase has been identified as the product of the arsenical resistance operon of resistance plasmid R773 . When expressed in Escherichia coli this ATP-driven oxyanion pump catalyses extrusion of the oxyanions arsenite, antimonite and arsenate. The pump is composed of two polypeptides, the products of the arsA and arsB genes. The pump alone produces resistance to arsenite and antimonite. This protein, ArsC, catalyzes the reduction of arsenate to arsenite, and thus extends resistance to include arsenate. ; GO: 0008794 arsenate reductase (glutaredoxin) activity, 0006118 electron transport.
Probab=42.30  E-value=11  Score=16.55  Aligned_cols=53  Identities=23%  Similarity=0.281  Sum_probs=35.0

Q ss_pred             HHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCH-HHHHHHHHHHHCCC
Q ss_conf             6677764200156301000023322246852103799999887608889-99999998762135
Q gi|254780306|r  229 EADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSA-SHTMRIAQKLYEGI  291 (837)
Q Consensus       229 ~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa-~~Tm~iAQ~LYE~~  291 (837)
                      ++-++++.- +-.-+|...=+        -||+.|.||+-. ++||.|+ ++.|+.=..+|-..
T Consensus        14 ~tLalL~dk-gi~P~vV~YL~--------~pp~~seL~~~~-~~LG~~~ar~~~R~ke~~y~eL   67 (114)
T TIGR00014        14 QTLALLEDK-GIEPEVVKYLK--------NPPTKSELKALL-AKLGISSAREMIRTKEELYKEL   67 (114)
T ss_pred             HHHHHHHHC-CCCCEEEECCC--------CCCCHHHHHHHH-HHCCCCHHHHHCCCCCCCCCCC
T ss_conf             999999856-99954741458--------974868899999-8708970363011765210004


No 153
>TIGR02647 DNA conserved hypothetical protein TIGR02647; InterPro: IPR013468    Proteins in this entry are found, so far, only in the Gammaproteobacteria. Their function is currently unknown. The location on the chromosome is usually not far from housekeeping genes. Some proteins have been annotated in public databases as DNA-binding protein inhibitors, putative transcriptional regulators, or hypothetical DNA binding proteins..
Probab=42.10  E-value=20  Score=14.65  Aligned_cols=36  Identities=31%  Similarity=0.415  Sum_probs=24.9

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHH
Q ss_conf             8899999999876213556721224553147554444305689999
Q gi|254780306|r  275 FSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVR  320 (837)
Q Consensus       275 ~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r  320 (837)
                      -........|++|||+        ||+|=|  |.-||.+..++.+.
T Consensus        31 ~A~~~~~aA~~RL~~K--------~L~~Qp--DGGYLT~~G~~~ae   66 (77)
T TIGR02647        31 TASPAAVAAAKRLYEK--------GLTDQP--DGGYLTSLGLEAAE   66 (77)
T ss_pred             HHHHHHHHHHHHHHHC--------CCCCCC--CCCCHHHHHHHHHH
T ss_conf             1037899999988733--------775579--97501354448899


No 154
>PRK08332 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=41.99  E-value=14  Score=15.80  Aligned_cols=40  Identities=25%  Similarity=0.301  Sum_probs=18.2

Q ss_pred             CCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCCCCHHHHH
Q ss_conf             44068877654899999999987099899946997025799
Q gi|254780306|r   48 FEMIWNIDPSSQKHLQNIIHAVKSSTILILATDPDREGEAI   88 (837)
Q Consensus        48 f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~DREGE~I   88 (837)
                      |.|-+.+.|+- +++..-.+.+|..|-+|-.--.|..=|.|
T Consensus       399 ~~~~~~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~~~~~~  438 (1748)
T PRK08332        399 WHPFFVITPDF-KIVEKRADELKEGDILIGGMPDDDDYEFI  438 (1748)
T ss_pred             CCCCEEECCCC-CHHHHHHHHHCCCCEEECCCCCCCCHHHH
T ss_conf             86517856863-11564444540377665378887540123


No 155
>PRK07379 coproporphyrinogen III oxidase; Provisional
Probab=41.62  E-value=21  Score=14.60  Aligned_cols=42  Identities=10%  Similarity=0.180  Sum_probs=32.9

Q ss_pred             CCCCCCCCHHHHHHHHHHCCEEECCCCCEEECC-HHHHHCCCC
Q ss_conf             025665515789999973220221477122201-142000022
Q gi|254780306|r  483 IGIGRPSTYATILETLYKRKYVIAEKRKILPQN-TGRIVTAFL  524 (837)
Q Consensus       483 ~GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~-~G~~v~~~L  524 (837)
                      .|..-...+...++.+.++|.+..+++++..|+ .|+.+.+.+
T Consensus       345 fg~~~~~~~~~~l~~l~~~Gll~~~~~~i~LT~p~G~l~~n~I  387 (399)
T PRK07379        345 FGQEIVEKILQCLQPYFQQGWVELTGGRLRLTDPEGFLFSNTV  387 (399)
T ss_pred             HCCCHHHHHHHHHHHHHHCCCEEEECCEEEEECCCCEEEHHHH
T ss_conf             8967899999999999967988997999999487835429899


No 156
>PRK10787 DNA-binding ATP-dependent protease La; Provisional
Probab=41.49  E-value=21  Score=14.58  Aligned_cols=28  Identities=11%  Similarity=0.265  Sum_probs=17.3

Q ss_pred             CHHHHHHHHHHHHHHCCEEEECCCCCCH
Q ss_conf             5489999999998709989994699702
Q gi|254780306|r   57 SSQKHLQNIIHAVKSSTILILATDPDRE   84 (837)
Q Consensus        57 ~~kk~~~~i~~~~k~a~~iilAtD~DRE   84 (837)
                      +..+-++.|..+.+.-..|++.+--|-+
T Consensus        32 GR~kSI~AlE~A~~~d~~I~LVaQKD~~   59 (784)
T PRK10787         32 GREKSIRCLEAAMDHDKKIMLVAQKEAS   59 (784)
T ss_pred             CCHHHHHHHHHHHHCCCEEEEEECCCCC
T ss_conf             8889999999999649979999756888


No 157
>KOG1168 consensus
Probab=41.34  E-value=21  Score=14.56  Aligned_cols=11  Identities=27%  Similarity=0.005  Sum_probs=4.1

Q ss_pred             CCCCHHHHHHH
Q ss_conf             53422689999
Q gi|254780306|r  165 SAGRVQSVALR  175 (837)
Q Consensus       165 SaGRVQtp~L~  175 (837)
                      |-+-.-|++++
T Consensus        34 s~~~~~S~~~~   44 (385)
T KOG1168          34 SQLFFPSELFR   44 (385)
T ss_pred             CCCCCCHHHHH
T ss_conf             02457507666


No 158
>TIGR01697 PNPH-PUNA-XAPA inosine guanosine and xanthosine phosphorylase family; InterPro: IPR011268   This entry describes a subset of the phosphorylase family. The entry excludes the methylthioadenosine phosphorylases (MTAP, IPR010044 from INTERPRO), which are believed to play a specific role in the recycling of methionine from methylthioadenosine.    This entry consists of three clades of purine phosphorylases based on a neighbour-joining tree using the MTAP family as an out group. The highest-branching clade (IPR011269 from INTERPRO) consists of a group of sequences from both Gram-positive and Gram-negative bacteria which have been shown to act as purine nucleotide phosphorylases but whose physiological substrate and role in vivo remain unknown . Of the two remaining clades, one is xanthosine phosphorylase (XAPA, IPR010943 from INTERPRO); it is limited to certain gammaproteobacteria and constitutes a special purine phosphorylase found in a specialised operon for xanthosine catabolism . The enzyme also acts on the same purines (inosine and guanosine) as the other characterised members of this subfamily, but is only induced when xanthosine must be degraded. The remaining and largest clade consists of purine nucleotide phosphorylases (PNPH, IPR011270 from INTERPRO) from metazoa  and bacteria  which act primarily on guanosine and inosine, and do not act on adenosine. Sequences from Clostridium and Thermotoga fall between these last two clades and are uncharacterised with respect to substrate range. ; GO: 0004731 purine-nucleoside phosphorylase activity, 0006139 nucleobase nucleoside nucleotide and nucleic acid metabolic process.
Probab=41.00  E-value=18  Score=15.14  Aligned_cols=84  Identities=14%  Similarity=0.324  Sum_probs=46.2

Q ss_pred             CCCCCCCCCC--EEEEEECCCCCEEEECCCCCCCCCCCCCC-CCHHHCCHHHHHHHHHC---------------CHHHCC
Q ss_conf             0146899996--69998269742277348877761337899-88425489999998615---------------255157
Q gi|254780306|r  654 LLGNDLETKE--SVTLRSGRFGLYVQRGDGKDAKRCSLPKT-WKSDSVDYDKAMSLLSL---------------PREIGI  715 (837)
Q Consensus       654 ~LG~dP~~G~--~I~lk~GryGpYvq~Ge~~kpkr~si~k~-~~~~~itle~Al~LLsL---------------Pr~lG~  715 (837)
                      ++|.  -.|+  ||.+..|||=+|               ++ .+++.+|+=  ++++.+               -+++..
T Consensus        48 v~G~--Lgg~rvpV~~m~GRfH~Y---------------EGn~d~~~vt~P--vR~mk~lGv~~lvvTNAAGg~n~~~~~  108 (266)
T TIGR01697        48 VFGR--LGGKRVPVVVMQGRFHYY---------------EGNYDMAAVTFP--VRVMKLLGVEILVVTNAAGGLNADFKP  108 (266)
T ss_pred             EEEE--ECCEEEEEEEEECCCCCC---------------CCCCCHHHHHHH--HHHHHHCCCEEEEEECCCCCCCCCCCC
T ss_conf             7776--657114688850772356---------------789666677689--999986692089997466120678898


Q ss_pred             CCCCCCEEEEE-----ECC--CCCEEEEC-----CEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             77898749991-----158--76526167-----81112488775143579999999983
Q gi|254780306|r  716 HPETQKNIIAG-----TGK--YGYYLNHD-----GAYTKLESIEQVLTIDLEQAISCITE  763 (837)
Q Consensus       716 ~pe~g~~I~~~-----~Gr--yGpYi~~~-----~~~~sl~~~~~~~~I~l~~Aieli~~  763 (837)
                          |.-|.+.     .|+  +-|=|-++     .-|.+|   -+.+|-+|=+.+.=+|+
T Consensus       109 ----GdLm~i~DHIN~~~~ag~nPLvGpN~~~FG~RFp~l---~~AYD~~lr~~~~~~A~  161 (266)
T TIGR01697       109 ----GDLMIIKDHINLPGLAGFNPLVGPNDDEFGTRFPDL---SNAYDKELRALAKDVAK  161 (266)
T ss_pred             ----CCEEEEECHHHCCCCCCCCCCCCCCCCCCCCCCCCC---CCHHHHHHHHHHHHHHH
T ss_conf             ----537997112114400047878698885557899876---64567999999999998


No 159
>TIGR02431 pcaR_pcaU beta-ketoadipate pathway transcriptional regulators, PcaR/PcaU/PobR family; InterPro: IPR012794    Members of this family are IclR-type transcriptional regulators with similar DNA binding sites, able to bind at least three different metabolites related to protocatechuate metabolism. Beta-ketoadipate is the inducer for PcaR, p-hydroxybenzoate for PobR, and protocatechuate for PcaU.; GO: 0003677 DNA binding, 0016563 transcription activator activity, 0045941 positive regulation of transcription, 0046278 protocatechuate metabolic process.
Probab=40.91  E-value=18  Score=15.06  Aligned_cols=20  Identities=15%  Similarity=0.165  Sum_probs=11.5

Q ss_pred             HHHHHHCCC---HHHHHHHHHHH
Q ss_conf             988760888---99999999876
Q gi|254780306|r  268 VASSRLGFS---ASHTMRIAQKL  287 (837)
Q Consensus       268 ~As~~lg~s---a~~Tm~iAQ~L  287 (837)
                      +++++=|+|   |.|.|-..|+|
T Consensus        29 ~vA~~TGL~RAaARR~LLTL~~L   51 (252)
T TIGR02431        29 DVAEATGLTRAAARRFLLTLVEL   51 (252)
T ss_pred             HHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             99987589947988899846562


No 160
>TIGR00575 dnlj DNA ligase, NAD-dependent; InterPro: IPR001679   DNA ligase (polydeoxyribonucleotide synthase) is the enzyme that joins two DNA fragments by catalyzing the formation of an internucleotide ester bond between phosphate and deoxyribose. It is active during DNA replication, DNA repair and DNA recombination. There are two forms of DNA ligase: one requires ATP (6.5.1.1 from EC), the other NAD (6.5.1.2 from EC).   This family is predominantly composed of NAD-dependent bacterial DNA ligases. They are proteins of about 75 to 85 Kd whose sequence is well conserved , . They also show similarity to yicF, an Escherichia coli hypothetical protein of 63 Kd.; GO: 0003911 DNA ligase (NAD+) activity, 0006260 DNA replication, 0006281 DNA repair.
Probab=40.54  E-value=15  Score=15.61  Aligned_cols=37  Identities=22%  Similarity=0.419  Sum_probs=27.8

Q ss_pred             CCCHHHHHHHHHHHHCCC-HHHHHHHHH--HHHCCCCCCCHHHHHHHHCC
Q ss_conf             210379999988760888-999999998--76213556721224553147
Q gi|254780306|r  259 AFTTSTLQQVASSRLGFS-ASHTMRIAQ--KLYEGIDVNGEIVGLITYMR  305 (837)
Q Consensus       259 Pf~tstLQq~As~~lg~s-a~~Tm~iAQ--~LYE~~~~~~~~~GlITYpR  305 (837)
                      ||.|-..--..=++|||. .....+.++  ++=|          .|.|-+
T Consensus       238 ~~~t~~~~L~~L~~~GF~TV~~~~~~~~ln~~~e----------V~~~~~  277 (706)
T TIGR00575       238 PFRTQYEALAWLKKLGFPTVNPHIRLCKLNSIEE----------VLEYYE  277 (706)
T ss_pred             CCCCHHHHHHHHHHCCCCCCHHHHHHHCCCCHHH----------HHHHHH
T ss_conf             8677899999998638842012577630389889----------999999


No 161
>pfam11279 DUF3080 Protein of unknown function (DUF3080). Some members in this family of proteins are annotated as lipoproteins however this cannot be confirmed. Currently this family has no known function.
Probab=40.25  E-value=21  Score=14.60  Aligned_cols=51  Identities=20%  Similarity=0.171  Sum_probs=32.0

Q ss_pred             HHHHHCCCCCCHHHHHHHHHHH-HHHHHHHHHHCHHHHHHCCCCCCCCCHHHHHHHHHHHHHH
Q ss_conf             9998622646989999999999-9898740113789886414676534226899999999999
Q gi|254780306|r  121 LNAMKSPRDINLDLVNAYLARR-ALDYLVGFNLSPILWQKLPGARSAGRVQSVALRLICNREN  182 (837)
Q Consensus       121 ~~A~~n~r~~d~~Lv~A~~aRr-~lD~lvG~~lSp~L~rk~~~~lSaGRVQtp~L~lIveRe~  182 (837)
                      +....+.-+++.+|.|+..-|. .|--+||=           ++-|-||||+|.-+|++|.+-
T Consensus        33 r~~~~~~~~~~i~lld~~~L~~C~L~~liae-----------rNs~LGk~~~~s~rl~ye~~f   84 (315)
T pfam11279        33 RELLLDIPDLTIGLLDFLSLRHCGLFVLIAE-----------RNSILGKVQDPSQRLDYELRF   84 (315)
T ss_pred             HHHCCCCCCCCCCHHHHHHHCCCCCHHHHHH-----------HCCCCCCCCCHHHHHHHHHHH
T ss_conf             4431789866764999986368950779998-----------624313576888988999999


No 162
>COG0272 Lig NAD-dependent DNA ligase (contains BRCT domain type II) [DNA replication, recombination, and repair]
Probab=39.81  E-value=16  Score=15.53  Aligned_cols=64  Identities=19%  Similarity=0.248  Sum_probs=35.2

Q ss_pred             CCHHHHHHHHHHHHHHCCEEEECCC----CCCHHHHHHHHHHHHHH---HHCCCCCCCEEEEEEECCCHHHHHHHHHC
Q ss_conf             6548999999999870998999469----97025799999999975---51257887169999803798999999862
Q gi|254780306|r   56 PSSQKHLQNIIHAVKSSTILILATD----PDREGEAISWHVLDVLR---QKNLIEKTKIQRVSFNAITKQVVLNAMKS  126 (837)
Q Consensus        56 ~~~kk~~~~i~~~~k~a~~iilAtD----~DREGE~Iawhi~e~l~---~~~~~~~~~v~R~~f~eiT~~aI~~A~~n  126 (837)
                      .+.++.+..|+++++..+.-|.--|    +|-|=-.....+. .|+   +.....+.|..|+=      .++..+|..
T Consensus         5 ~~~~~~i~~L~~~L~~~~~~Yyv~d~P~VsD~eYD~L~reL~-~lE~~~Pel~~~dSPtqrVG------~~~~~~F~k   75 (667)
T COG0272           5 AEAQEEIEELRELLNKHDYRYYVLDAPSVSDAEYDQLYRELQ-ELEEKHPELITPDSPTQRVG------AAPLNAFKK   75 (667)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCHHHHHHHHHHHH-HHHHHCCCCCCCCCCCCCCC------CCCHHCCCC
T ss_conf             789999999999999977887226999798589999999999-99986877678999965557------430100453


No 163
>PRK09194 prolyl-tRNA synthetase; Provisional
Probab=39.76  E-value=20  Score=14.65  Aligned_cols=43  Identities=14%  Similarity=0.122  Sum_probs=31.0

Q ss_pred             CCCEEEEECCCCCEEEECCEEEECCCCCCHHHCCHHHHHHHHHHH
Q ss_conf             984699606854525367888756578896778999999999877
Q gi|254780306|r  788 GGSITVHNGRYGPYLHWKKINASLSKEESPDTVDLEKALKILNIK  832 (837)
Q Consensus       788 ~~~i~i~~GryGpYi~~gk~Na~ipk~~~~e~lt~e~a~~li~~k  832 (837)
                      |-|+.|--|+=  .++.|..-....+.-..+.++++++++.|.+.
T Consensus       525 GiP~~vvvGkk--~l~~g~vEvk~R~~~~~~~v~~~el~~~v~~l  567 (570)
T PRK09194        525 GIPHRIVVGKR--GLAEGIVEYKNRRTGEKEEVKLDELVEFLKEL  567 (570)
T ss_pred             CCCEEEEECCC--CCCCCEEEEEEECCCCEEEECHHHHHHHHHHH
T ss_conf             89979999267--40158599999068975886199999999998


No 164
>COG5252 Uncharacterized conserved protein, contains CCCH-type Zn-finger protein [General function prediction only]
Probab=39.34  E-value=22  Score=14.35  Aligned_cols=20  Identities=20%  Similarity=0.416  Sum_probs=12.3

Q ss_pred             CHHHCCHHHHHHHH--HCCHHH
Q ss_conf             84254899999986--152551
Q gi|254780306|r  694 KSDSVDYDKAMSLL--SLPREI  713 (837)
Q Consensus       694 ~~~~itle~Al~LL--sLPr~l  713 (837)
                      .-.+|+||.-|++-  +||..|
T Consensus       190 tq~eislEefIE~eR~~L~~~L  211 (299)
T COG5252         190 TQVEISLEEFIELERQSLPEKL  211 (299)
T ss_pred             CCCCCCHHHHHHHHHCCCCCCC
T ss_conf             5542019999998860278767


No 165
>pfam09339 HTH_IclR IclR helix-turn-helix domain.
Probab=39.18  E-value=14  Score=15.81  Aligned_cols=20  Identities=35%  Similarity=0.496  Sum_probs=12.2

Q ss_pred             HHHHCCCHHHHHHHHHHHHC
Q ss_conf             87608889999999987621
Q gi|254780306|r  270 SSRLGFSASHTMRIAQKLYE  289 (837)
Q Consensus       270 s~~lg~sa~~Tm~iAQ~LYE  289 (837)
                      ++.+|++...+-++.+.|=+
T Consensus        25 a~~~gl~kstv~RlL~tL~~   44 (52)
T pfam09339        25 ARRTGLPKSTAHRLLQTLVE   44 (52)
T ss_pred             HHHHCCCHHHHHHHHHHHHH
T ss_conf             99989199999999999998


No 166
>PRK13347 coproporphyrinogen III oxidase; Provisional
Probab=39.16  E-value=8.3  Score=17.57  Aligned_cols=36  Identities=22%  Similarity=0.182  Sum_probs=29.0

Q ss_pred             HHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCC
Q ss_conf             999997322022147712220114200002233665
Q gi|254780306|r  494 ILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFS  529 (837)
Q Consensus       494 II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~  529 (837)
                      -++.+.++|.|+.++.+|..|+.|+.+.+.+-..|.
T Consensus       404 ~l~~l~~~GLl~~~~~~l~lT~~Gr~l~~~Ia~~Fd  439 (453)
T PRK13347        404 RLEPLAADGLVTIDGGGIRVTPEGRPLIRAVAAAFD  439 (453)
T ss_pred             HHHHHHHCCCEEEECCEEEECHHHHHHHHHHHHHHH
T ss_conf             999999789889989999999708999999999999


No 167
>TIGR01503 MthylAspMut_E methylaspartate mutase, E subunit; InterPro: IPR006396   Glutamate mutase (methylaspartate mutase) catalyses the reversible interconversion of L-glutamate and L-threo-3-methylaspartate, the first step in the pathway of glutamate fermentation . Catalysis is initiated using the cobalamin cofactor. The E subunit is the catalytic subunit (MutE) . ; GO: 0016866 intramolecular transferase activity, 0031419 cobalamin binding, 0019670 anaerobic glutamate catabolic process.
Probab=38.49  E-value=22  Score=14.44  Aligned_cols=27  Identities=11%  Similarity=0.178  Sum_probs=17.7

Q ss_pred             HHCCCCCHHHHHHHHHHHHH-HHHHHHHH
Q ss_conf             00001999999999999999-99985222
Q gi|254780306|r  364 KMKQFLDSDQFQLYNLIWKR-SVASQMAS  391 (837)
Q Consensus       364 ~~~~~L~~de~klY~LI~~R-~lasqm~~  391 (837)
                      +=.+....||.|-|-+|.-- |+| -|..
T Consensus       291 QWmGGFP~dE~kAf~vIs~ataiA-~l~~  318 (481)
T TIGR01503       291 QWMGGFPEDESKAFGVISLATAIA-ALSG  318 (481)
T ss_pred             CCCCCCCHHHHHHHHHHHHHHHHH-HHHC
T ss_conf             277996256788877899999999-8737


No 168
>COG1321 TroR Mn-dependent transcriptional regulator [Transcription]
Probab=37.61  E-value=24  Score=14.16  Aligned_cols=38  Identities=18%  Similarity=0.260  Sum_probs=29.1

Q ss_pred             HCCCCCCCCHHHHHHHHHHCCEEECCC-CCEEECCHHHHH
Q ss_conf             102566551578999997322022147-712220114200
Q gi|254780306|r  482 EIGIGRPSTYATILETLYKRKYVIAEK-RKILPQNTGRIV  520 (837)
Q Consensus       482 ~~GIGrPSTyA~II~~L~~R~YV~~~~-~~l~pT~~G~~v  520 (837)
                      .+++- |+|-+.++..|.+.|||..++ +.+.-|+.|...
T Consensus        33 ~L~Vs-p~sVt~ml~rL~~~GlV~~~~y~gi~LT~~G~~~   71 (154)
T COG1321          33 RLKVS-PPSVTEMLKRLERLGLVEYEPYGGVTLTEKGREK   71 (154)
T ss_pred             HHCCC-CHHHHHHHHHHHHCCCEEEECCCCEEECCCHHHH
T ss_conf             85899-2789999999987899788458886788354899


No 169
>TIGR00781 ccoO cytochrome c oxidase, cbb3-type, subunit II; InterPro: IPR003468   Cytochrome cbb3 oxidases are found almost exclusively in Proteobacteria, and represent a distinctive class of proton-pumping respiratory haem-copper oxidases (HCO) that lack many of the key structural features that contribute to the reaction cycle of the intensely studied mitochondrial cytochrome c oxidase (CcO) . Cytochrome cbb3 oxidases are required both to support symbiotic nitrogen fixation, whilst ensuring that the oxygen-labile nitrogenase is not compromised. Cytochrome cbb3 oxidases consist of four subunits: FixN (or CcoN), FixO (or CcoO), FixP (or CcoP) and FixQ (or CcoQ). The catalytic core is comprised of subunits FixN, FixO and FixP, where FixN acts as the catalytic subunit, and Fix O and FixP are membrane-bound mono- and di-haem cytochromes c, respectively. The FixQ subunit protects the core complex in the presence of oxygen from proteolytic degradation . This entry represents the mono-haem FixO subunit.; GO: 0004129 cytochrome-c oxidase activity, 0006118 electron transport.
Probab=37.36  E-value=17  Score=15.18  Aligned_cols=20  Identities=25%  Similarity=0.531  Sum_probs=11.3

Q ss_pred             HHCCHHHHHHHHHCCHHH-CC
Q ss_conf             254899999986152551-57
Q gi|254780306|r  696 DSVDYDKAMSLLSLPREI-GI  715 (837)
Q Consensus       696 ~~itle~Al~LLsLPr~l-G~  715 (837)
                      ..+|.+.+..-++=-+.| |+
T Consensus       143 ~~~d~~~~~~~~~~~~~VfGv  163 (234)
T TIGR00781       143 KKVDVDTVVAELKAQKKVFGV  163 (234)
T ss_pred             CCCCHHHHHHHHHHCCCCCCC
T ss_conf             888599999988640031256


No 170
>PRK09057 coproporphyrinogen III oxidase; Provisional
Probab=37.27  E-value=21  Score=14.54  Aligned_cols=33  Identities=15%  Similarity=0.252  Sum_probs=27.2

Q ss_pred             HHHHHHHHHCCEEECCCC-CEEECCHHHHHCCCC
Q ss_conf             789999973220221477-122201142000022
Q gi|254780306|r  492 ATILETLYKRKYVIAEKR-KILPQNTGRIVTAFL  524 (837)
Q Consensus       492 A~II~~L~~R~YV~~~~~-~l~pT~~G~~v~~~L  524 (837)
                      ..-++.+.+.|+++.+++ +|.+|+.|+.+.+.+
T Consensus       342 ~~~l~~l~~~Gll~~~~~~rl~lT~~G~~l~d~v  375 (381)
T PRK09057        342 PARLALLIEEGLIERDGDSRLRATPAGRLVLDAV  375 (381)
T ss_pred             HHHHHHHHHCCCEEEECCCEEEECHHHHHHHHHH
T ss_conf             9999999978997980898699997887999999


No 171
>TIGR03129 one_C_dehyd_B formylmethanofuran dehydrogenase subunit B. Members of this largely archaeal protein family are subunit B of the formylmethanofuran dehydrogenase. Nomenclature in some bacteria may reflect inclusion of the formyltransferase described by TIGR03119 as part of the complex, and therefore call this protein formyltransferase/hydrolase complex Fhc subunit C. Note that this model does not distinguish tungsten (FwdB) from molybdenum-containing (FmdB) forms of this enzyme.
Probab=36.81  E-value=16  Score=15.45  Aligned_cols=13  Identities=23%  Similarity=0.023  Sum_probs=4.6

Q ss_pred             HCCHHHHHHHHHH
Q ss_conf             7899999999987
Q gi|254780306|r  819 TVDLEKALKILNI  831 (837)
Q Consensus       819 ~lt~e~a~~li~~  831 (837)
                      .-+.-+.+..|++
T Consensus       407 ~~sd~~i~~~ia~  419 (421)
T TIGR03129       407 EPSDEEILKKILE  419 (421)
T ss_pred             CCCHHHHHHHHHH
T ss_conf             8799999999982


No 172
>PRK07956 ligA NAD-dependent DNA ligase LigA; Validated
Probab=36.32  E-value=15  Score=15.60  Aligned_cols=26  Identities=8%  Similarity=0.272  Sum_probs=18.4

Q ss_pred             CCHHHHHHHHHHHHHHCCEEEECC-CC
Q ss_conf             654899999999987099899946-99
Q gi|254780306|r   56 PSSQKHLQNIIHAVKSSTILILAT-DP   81 (837)
Q Consensus        56 ~~~kk~~~~i~~~~k~a~~iilAt-D~   81 (837)
                      .+.++.+..|++.+..++..|-.. +|
T Consensus         3 ~~~~~~i~~L~~~i~~~n~~YY~~~~p   29 (668)
T PRK07956          3 EEAKKRIEELREELNHHAYAYYVLDNP   29 (668)
T ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCC
T ss_conf             799999999999999999986438998


No 173
>smart00346 HTH_ICLR helix_turn_helix isocitrate lyase regulation.
Probab=36.12  E-value=25  Score=14.00  Aligned_cols=50  Identities=26%  Similarity=0.410  Sum_probs=28.8

Q ss_pred             CCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHC-CCCCCCCCHHHHHHHH
Q ss_conf             2103799999887608889999999987621355672122455314-7554444305689999
Q gi|254780306|r  259 AFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYM-RTDGVHMSPDALEAVR  320 (837)
Q Consensus       259 Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYp-RTDS~~ls~ea~~~~r  320 (837)
                      |.+.+.    .++.+|++..-+.++.+.|-+        .||+.+- .|..-.+....+.-..
T Consensus        20 ~~sl~e----ia~~~~l~ksT~~RlL~tL~~--------~G~l~~~~~~~~Y~lG~~~~~lg~   70 (91)
T smart00346       20 GLTLAE----LAERLGLSKSTAHRLLNTLQE--------LGYVEQDGQNGRYRLGPKVLELGQ   70 (91)
T ss_pred             CCCHHH----HHHHHCCCHHHHHHHHHHHHH--------CCCEEEECCCCEEEECHHHHHHHH
T ss_conf             989999----999989099999999999998--------899688499997753099999999


No 174
>KOG0976 consensus
Probab=35.55  E-value=16  Score=15.42  Aligned_cols=22  Identities=27%  Similarity=0.389  Sum_probs=17.5

Q ss_pred             CCCCCCCHHHHHHHHHHCCEEE
Q ss_conf             2566551578999997322022
Q gi|254780306|r  484 GIGRPSTYATILETLYKRKYVI  505 (837)
Q Consensus       484 GIGrPSTyA~II~~L~~R~YV~  505 (837)
                      -.|||||||++++....|.|+.
T Consensus       653 klgrrstl~st~sE~dts~ymr  674 (1265)
T KOG0976         653 KLGRRSTLASTFSEADTSDYMR  674 (1265)
T ss_pred             CCCCHHHHHHHHHHHHHHHHHC
T ss_conf             6577178888878877777623


No 175
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit ClpA; InterPro: IPR013461    Proteins in this entry are related to ClpA () from Escherichia coli. ClpA is an ATP-dependent chaperone and part of the ClpAP protease that participates in regulatory protein degradation and the dissolution and degradation of protein aggregates . ClpA recognises sequences in specific proteins, which it then unfolds in an ATP-dependent manner and transports into the degradation chamber of the associated ClpP protein , . A small adaptor-like protein, ClpS, modulates the activity of ClpA and is an important regulatory factor for this protein . It protects ClpA from autodegradation and appears to redirect its activity away from soluble proteins and toward aggregated proteins..
Probab=35.41  E-value=26  Score=13.92  Aligned_cols=52  Identities=35%  Similarity=0.488  Sum_probs=35.2

Q ss_pred             HHHHC------CCHHHHHHHHHHH---HCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHHHHHHCCCCCCCCCC
Q ss_conf             87608------8899999999876---2135567212245531475544443056899997655200112376311
Q gi|254780306|r  270 SSRLG------FSASHTMRIAQKL---YEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRSITSHYGDHYLPEKP  336 (837)
Q Consensus       270 s~~lg------~sa~~Tm~iAQ~L---YE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~i~~~~g~~~l~~~~  336 (837)
                      ||||.      =|...|..|.+.|   ||.            ||-   +++|++++..+-.+-..-.-+.+||++.
T Consensus       362 sRRFQKIDv~EPs~eet~~ILkGLk~~YE~------------fH~---V~Y~~eal~~Av~LS~ryI~DRfLPDKA  422 (774)
T TIGR02639       362 SRRFQKIDVGEPSIEETVKILKGLKEQYEE------------FHH---VKYSDEALEAAVELSARYINDRFLPDKA  422 (774)
T ss_pred             CCCCCEECCCCCCHHHHHHHHHHHHHHHHC------------CCC---EECCHHHHHHHHHHHHHHCCCCCCCCHH
T ss_conf             654233117957888999999865542013------------250---1138699999999988860257898543


No 176
>KOG2337 consensus
Probab=35.37  E-value=26  Score=13.91  Aligned_cols=15  Identities=20%  Similarity=0.366  Sum_probs=8.0

Q ss_pred             HHHHHHHHHHHHCCC
Q ss_conf             356667776420015
Q gi|254780306|r  226 NKKEADDLISFVKKA  240 (837)
Q Consensus       226 ~~~~a~~~~~~~~~~  240 (837)
                      -+++|+++-+.++..
T Consensus        96 l~~ea~eiwesi~sG  110 (669)
T KOG2337          96 LEQEAEEIWESIKSG  110 (669)
T ss_pred             HHHHHHHHHHHHCCC
T ss_conf             999999999863048


No 177
>TIGR01405 polC_Gram_pos DNA polymerase III, alpha subunit, Gram-positive type; InterPro: IPR006308   These are the polypeptide chains of DNA polymerase III. Full-length homologs of this protein are restricted to the Gram-positive lineages, including the Mycoplasmas. This protein is designated alpha chain and given the gene symbol polC, but is not a full-length homolog of other polC genes. The N-terminal region of about 200 amino acids is rich in low-complexity sequence and poorly alignable. ; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication, 0005737 cytoplasm.
Probab=35.23  E-value=22  Score=14.46  Aligned_cols=71  Identities=17%  Similarity=0.128  Sum_probs=37.4

Q ss_pred             HHHHHHHHHHHH-HHCCEEEECCCCCCHHHHHHHHHHHHHH--HHCCCCCCC--EEEEEEECCCHHHHHHHHHCCC
Q ss_conf             489999999998-7099899946997025799999999975--512578871--6999980379899999986226
Q gi|254780306|r   58 SQKHLQNIIHAV-KSSTILILATDPDREGEAISWHVLDVLR--QKNLIEKTK--IQRVSFNAITKQVVLNAMKSPR  128 (837)
Q Consensus        58 ~kk~~~~i~~~~-k~a~~iilAtD~DREGE~Iawhi~e~l~--~~~~~~~~~--v~R~~f~eiT~~aI~~A~~n~r  128 (837)
                      -.+.+..|+.-. =++.--+------|+++.+.-.|.++-.  ...-..+.|  .+||.||-=|+=+=..|+.++.
T Consensus        56 D~~~~~~~K~~~wv~~~g~~~~~~~~~~~~~~~~~I~~i~~~~~~~r~D~~k~~~KRVEL~~HTkMS~mDaI~s~~  131 (1264)
T TIGR01405        56 DKEKFDGIKIGKWVRVRGKIELDKFSRDLQMIIKDIEEIETSAEAERKDKAKEIEKRVELHFHTKMSQMDAITSVQ  131 (1264)
T ss_pred             HHHHHHHHCCCCCEEEEEEEEEECCCCCCEEEEECCCCCCCCCCCCCCCCCCCCCCCEEEECCHHHHHHCCCCCHH
T ss_conf             0577734203773599998875221200058775021246772214655553557534541121201010457889


No 178
>PRK03564 formate dehydrogenase accessory protein FdhE; Provisional
Probab=35.01  E-value=26  Score=13.87  Aligned_cols=31  Identities=19%  Similarity=0.644  Sum_probs=19.2

Q ss_pred             CCCCEECCCCCCCCE--EEEEECCCC-CCCCCCC
Q ss_conf             766114334677731--368715776-1112343
Q gi|254780306|r  599 NEDSRTCPECHTHSL--SLKLSSKYG-AFVGCTN  629 (837)
Q Consensus       599 ~~~~~~Cp~C~~g~L--~~k~~gK~G-~FigCSn  629 (837)
                      +...+.||.||..-+  .++..++.| .|+-||-
T Consensus       184 ~~~~~~CPvCGs~Pvasvv~~g~~~G~RyL~Csl  217 (307)
T PRK03564        184 GEQRQYCPVCGSMPVSSVVQIGTTQGLRYLHCNL  217 (307)
T ss_pred             CCCCCCCCCCCCCCCEEEEEECCCCCEEEEECCC
T ss_conf             7778859988987514557506878706886487


No 179
>PRK11517 transcriptional regulatory protein YedW; Provisional
Probab=34.77  E-value=26  Score=13.85  Aligned_cols=29  Identities=14%  Similarity=0.331  Sum_probs=23.6

Q ss_pred             CCEEEEC-CHHHHHHHHHHHC-CCCEEEEEE
Q ss_conf             9189977-9047877887508-998999942
Q gi|254780306|r    1 MNVIIVE-SPAKAKTISKYLG-SNYKVLSSF   29 (837)
Q Consensus         1 M~LvIvE-sP~kak~I~~~Lg-~~y~V~as~   29 (837)
                      |++.||| -|..+..|..+|. .||.|.++.
T Consensus         1 MkILiVEDd~~l~~~l~~~L~~~g~~V~~a~   31 (223)
T PRK11517          1 MKILLIEDNQRTQEWVTQGLSEAGYVIDAVS   31 (223)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             9899996989999999999998899999989


No 180
>pfam09395 consensus
Probab=34.74  E-value=26  Score=13.84  Aligned_cols=46  Identities=26%  Similarity=0.436  Sum_probs=32.1

Q ss_pred             CEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHH
Q ss_conf             12220114200002233665568988999999999998626013478999
Q gi|254780306|r  510 KILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLH  559 (837)
Q Consensus       510 ~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~  559 (837)
                      ..-||.-|++  +||..+.+. ||-++ -.||+.|.+|++-...-+++++
T Consensus         4 sYCPTTCGIA--DFLs~Yqt~-vdkdL-q~lE~~L~qieN~Tsea~~lIk   49 (77)
T pfam09395         4 SYCPTTCGIA--DFLSTYQTT-VDKDL-QTLEDILHQIENKTSEAKELIK   49 (77)
T ss_pred             CCCCCCHHHH--HHHHHHHHH-HHHHH-HHHHHHHHHHHCCCHHHHHHHH
T ss_conf             6598501089--999985010-66799-9999999999800267999999


No 181
>TIGR01381 E1_like_apg7 E1-like protein-activating enzyme Gsa7p/Apg7p; InterPro: IPR006285   This is a family of eukaryotic proteins found in animals, plants, and yeasts that includes Apg7p (YHR171W) from Saccharomyces cerevisiae and GSA7 from Pichia pastoris. Members are about 650 to 700 residues in length and include a central domain of about 150 residues shared with the ThiF/MoeB/HesA family of proteins. A low level of similarity to ubiquitin-activating enzyme E1 is described in a paper on peroxisome autophagy mediated by GSA7, and is the basis of the name ubiquitin activating enzyme E1-like protein. Members of the family appear to be involved in protein lipidation events analogous to ubiquitination and required for membrane fusion events during autophagy. .
Probab=34.63  E-value=26  Score=13.83  Aligned_cols=27  Identities=26%  Similarity=0.459  Sum_probs=11.3

Q ss_pred             CCCCCCCCEEEECCCCCCCCCCCCCHHHH
Q ss_conf             56882110011011123464310178998
Q gi|254780306|r  448 SANEQLIATETNASQHFTEPPPRYSESSL  476 (837)
Q Consensus       448 ~~g~~~~~~~~~~~~~~TkPP~rytEasL  476 (837)
                      ...+++....+.+-..  -=|.|.-+.|.
T Consensus       300 na~gKl~P~s~dl~~~--~DP~rLa~~sV  326 (689)
T TIGR01381       300 NANGKLVPKSVDLAKE--VDPKRLAERSV  326 (689)
T ss_pred             CCCCCCCCEEEEHHHC--CCHHHHHHHHH
T ss_conf             3578877604210011--58167887641


No 182
>pfam09538 FYDLN_acid Protein of unknown function (FYDLN_acid). Members of this family are bacterial proteins with a conserved motif [KR]FYDLN, sometimes flanked by a pair of CXXC motifs, followed by a long region of low complexity sequence in which roughly half the residues are Asp and Glu, including multiple runs of five or more acidic residues. The function of members of this family is unknown.
Probab=34.60  E-value=23  Score=14.33  Aligned_cols=15  Identities=40%  Similarity=0.862  Sum_probs=9.5

Q ss_pred             CCEECCCCCCCCEEE
Q ss_conf             611433467773136
Q gi|254780306|r  601 DSRTCPECHTHSLSL  615 (837)
Q Consensus       601 ~~~~Cp~C~~g~L~~  615 (837)
                      +.|.||.|+.-+.-+
T Consensus         8 ~kr~c~~c~~~fydl   22 (104)
T pfam09538         8 TKRTCPTCGKRFYDL   22 (104)
T ss_pred             CCCCCCCCCCCCCCC
T ss_conf             765478888821127


No 183
>PRK08115 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=34.37  E-value=24  Score=14.08  Aligned_cols=62  Identities=13%  Similarity=0.100  Sum_probs=33.6

Q ss_pred             CCCCCCCCC-HHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEEECCEECCCCCCCCCCCCCHHHH
Q ss_conf             133789988-425489999998615255157778987499911587652616781112488775143579999
Q gi|254780306|r  686 RCSLPKTWK-SDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTIDLEQA  757 (837)
Q Consensus       686 r~si~k~~~-~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~~~~~~~sl~~~~~~~~I~l~~A  757 (837)
                      -.||.|+++ |++.|.|+.-++.-+--.+|--   |-.|.-.=       ..+..--||..+++-++-.++..
T Consensus       730 DsSISKTINlPndATvEDV~~vY~~AY~~GCK---GVTVYRDG-------SR~~QVLsl~~Ee~~~~~~~~~~  792 (857)
T PRK08115        730 DSSISKTVNAPKGYTVEQVEKVYERLYRGGAK---GGTVYVDG-------SRDAQVLSLKAEENDLDEGDDPT  792 (857)
T ss_pred             CCCCCCCEECCCCCCHHHHHHHHHHHHHCCCC---EEEEECCC-------CCCCEEEEEECCCCCCHHHHCCC
T ss_conf             34010433288988999999999999976997---79994278-------77611576422033301220444


No 184
>pfam02327 BChl_A Bacteriochlorophyll A protein. Bacteriochlorophyll A protein is involved in the energy transfer system of green photosynthetic bacteria. The protein forms a homotrimer, with each monomer unit containing seven molecules of bacteriochlorophyll A.
Probab=34.32  E-value=26  Score=13.80  Aligned_cols=45  Identities=22%  Similarity=0.369  Sum_probs=34.0

Q ss_pred             HHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             42000022336655689889999999999986260134789999867
Q gi|254780306|r  517 GRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHEFWE  563 (837)
Q Consensus       517 G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~Fy~  563 (837)
                      |+..-+.|.+.  .+-+.++--.||..++.|..|-.++.+++++||.
T Consensus       133 GrqfHDi~mkV--PlDnndlIdTWeg~~~a~~~~gaNF~dwIrdfWf  177 (357)
T pfam02327       133 GRQFHDIIMKV--PLDNNDLIDTWEGFQKAIQGGGANFGDWIREFWF  177 (357)
T ss_pred             CCCHHHEEEEC--CCCCHHHHHHHHHHHHHHHCCCCCHHHHHHHHEE
T ss_conf             74110047855--7996348899999999875489645665566234


No 185
>pfam10872 DUF2740 Protein of unknown function (DUF2740). This family of proteins with unknown function has a highly conserved sequence.
Probab=33.77  E-value=27  Score=13.73  Aligned_cols=28  Identities=29%  Similarity=0.288  Sum_probs=19.0

Q ss_pred             CCCCHHHHHHHHHH-HHHHHHHHHHHHEE
Q ss_conf             01999999999999-99999985222110
Q gi|254780306|r  367 QFLDSDQFQLYNLI-WKRSVASQMASAKF  394 (837)
Q Consensus       367 ~~L~~de~klY~LI-~~R~lasqm~~a~~  394 (837)
                      ..|++|+-+|-.-| ..||+.|+-.|..+
T Consensus         3 kqlspdqdklhknilrdrflssfkqpgrf   31 (48)
T pfam10872         3 KQLSPDQDKLHKNILRDRFLSSFKQPGRF   31 (48)
T ss_pred             CCCCCCHHHHHHHHHHHHHHHHHCCCCHH
T ss_conf             55694587999999999999971485369


No 186
>pfam04606 Ogr_Delta Ogr/Delta-like zinc finger. This is a viral family of phage zinc-binding transcriptional activators, which also contains cryptic members in some bacterial genomes. The P4 phage delta protein contains two such domains attached covalently, while the P2 phage Ogr proteins possess one domain but function as dimers. All the members of this family have the following consensus sequence: C-X(2)-C-X(3)-A-(X)2-R-X(15)-C-X(4)-C-X(3)-F. This family also includes zinc fingers in recombinase proteins.
Probab=33.04  E-value=23  Score=14.32  Aligned_cols=35  Identities=26%  Similarity=0.412  Sum_probs=20.6

Q ss_pred             ECCCCCCCCEEEEEECC----CCCCCCCCCCCCCCCCCCC
Q ss_conf             43346777313687157----7611123434323332100
Q gi|254780306|r  604 TCPECHTHSLSLKLSSK----YGAFVGCTNYPECKYTRQL  639 (837)
Q Consensus       604 ~Cp~C~~g~L~~k~~gK----~G~FigCSnyPeCk~t~~l  639 (837)
                      .||.|+...........    .-.|..|+|. +|.++-..
T Consensus         1 ~CP~Cg~~a~irts~~~s~~~~e~Y~qC~N~-~Cg~tfv~   39 (47)
T pfam04606         1 RCPHCGAKARIRTSRRLSALVRELYYQCTNP-ECGHTFVT   39 (47)
T ss_pred             CCCCCCCCEEEEEHHHCCHHHHEEEEECCCC-CCCCEEEE
T ss_conf             9598898389968356297553138880896-45968999


No 187
>TIGR01158 SUI1_rel translation initation factor SUI1, putative; InterPro: IPR005872    This family of archaeal and bacterial proteins is homologous to the eukaryotic translation intiation factor SUI1 involved in directing the ribosome to the proper start site of translation by functioning in concert with eIF-2 and the initiator tRNA-Met.; GO: 0003743 translation initiation factor activity, 0006412 translation.
Probab=32.30  E-value=26  Score=13.86  Aligned_cols=29  Identities=21%  Similarity=0.298  Sum_probs=20.4

Q ss_pred             EECCCCCEEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHH
Q ss_conf             8269742277348877761337899884254899999986
Q gi|254780306|r  668 RSGRFGLYVQRGDGKDAKRCSLPKTWKSDSVDYDKAMSLL  707 (837)
Q Consensus       668 k~GryGpYvq~Ge~~kpkr~si~k~~~~~~itle~Al~LL  707 (837)
                      +.||||           |.++|=++++.++++|+.--+-|
T Consensus        42 ~~GR~G-----------K~VTiI~Gld~~~~~L~~LAk~L   70 (111)
T TIGR01158        42 TRGRKG-----------KGVTIIEGLDLSDIDLKELAKEL   70 (111)
T ss_pred             ECCCCC-----------CEEEEEECCCCCHHHHHHHHHHH
T ss_conf             036757-----------54788615783367899999987


No 188
>cd05569 PTS_IIB_fructose PTS_IIB_fructose: subunit IIB of enzyme II (EII) of the fructose-specific phosphoenolpyruvate:carbohydrate phosphotransferase system (PTS). In this system, EII (also referred to as FruAB) is a fructose-specific permease made up of two proteins (FruA and FruB) each containing 3 domains. The FruA protein contains two tandem nonidentical IIB domains and a C-terminal IIC transmembrane domain. Both IIB domains of FruA are included in this alignment. The FruB protein (also referred to as diphosphoryl transfer protein) contains a IIA domain, a domain of unknown function, and an Hpr-like domain called FPr (fructose-inducible HPr). This familiy also includes the IIB domains of several fructose-like PTS permeases including the Frv permease encoded by the frvABXR operon, the Frw permease encoded by the frwACBD operon, the Frx permease encoded by the hrsA gene,  and the Fry permease encoded by the fryABC (ypdDGH) operon. FruAB takes up exogenous fructose, releasing the 1-p
Probab=32.27  E-value=28  Score=13.56  Aligned_cols=41  Identities=22%  Similarity=0.336  Sum_probs=28.2

Q ss_pred             HHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCC
Q ss_conf             998709989994699702579999999997551257887169999803798999999862264
Q gi|254780306|r   67 HAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRD  129 (837)
Q Consensus        67 ~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~  129 (837)
                      ..+..||.||+|+|-+-+++-              ...+|+.|.        .+.+++.+|..
T Consensus        49 ~~I~~Ad~VIiA~d~~i~~~R--------------F~gk~~~~~--------~~~~ai~~~~~   89 (96)
T cd05569          49 EDIAEADAVILAADVPVDDER--------------FAGKRVYEV--------SVAEAIKDAEA   89 (96)
T ss_pred             HHHHHCCEEEEEECCCCCHHH--------------CCCCEEEEE--------CHHHHHHCHHH
T ss_conf             999859999999367675431--------------499769997--------48999878999


No 189
>TIGR01208 rmlA_long glucose-1-phosphate thymidylyltransferase; InterPro: IPR005908    Synonym: dTDP-D-glucose synthase     This group of proteins comprises a tightly conserved but broadly distributed subfamily of known and putative bacterial glucose-1-phosphate thymidylyltransferases (2.7.7.24 from EC). It is well characterised in several species as the first of four enzymes involved in the biosynthesis of dTDP-L-rhamnose, a cell wall constituent and a feedback inhibitor of the enzyme.  dTTP + alpha-D-glucose 1-phosphate = diphosphate + dTDP-glucose     The family of known and putative glucose-1-phosphate thymidyltransferases shows a deep split into a short form (see IPR005907 from INTERPRO) and a long form described by this model. The homotetrameric short form is found in numerous bacterial species that incorporate dTDP-L-rhamnose, which it helps synthesize, into the cell wall. It is subject to feedback inhibition. The long form, in contrast, is found in many species for which it serves as a sugar-activating enzyme for antibiotic biosynthesis and or other, unknown pathways, and in which dTDP-L-rhamnose is not necessarily produced. .
Probab=32.19  E-value=19  Score=14.87  Aligned_cols=51  Identities=14%  Similarity=0.313  Sum_probs=34.2

Q ss_pred             CCCCCCCCCCCCCCCCEEEEEECCC-CCEEEECCCCCCCCCCCCCCCCHHHCCHHHHH
Q ss_conf             1234420146899996699982697-42277348877761337899884254899999
Q gi|254780306|r  648 EMKESVLLGNDLETKESVTLRSGRF-GLYVQRGDGKDAKRCSLPKTWKSDSVDYDKAM  704 (837)
Q Consensus       648 ~~~~~~~LG~dP~~G~~I~lk~Gry-GpYvq~Ge~~kpkr~si~k~~~~~~itle~Al  704 (837)
                      ...+|-.+|      +++++++.-| |||..+|+.-.-+.+++=.++=+++..++-+-
T Consensus       274 ~i~GPa~IG------~d~~I~nsGyiGPYtSig~~~~I~d~~vE~S~vldes~I~~v~  325 (361)
T TIGR01208       274 VIRGPAVIG------EDCIIENSGYIGPYTSIGEGVVIRDAEVEHSIVLDESVIEGVE  325 (361)
T ss_pred             EEECCEEEC------CCCEEECCCCCCCEEEECCCEEEECCCCCCEEEECCCEEEEHH
T ss_conf             787060877------9527826861177077257538741630203564421143103


No 190
>PRK10163 DNA-binding transcriptional repressor AllR; Provisional
Probab=31.59  E-value=29  Score=13.48  Aligned_cols=44  Identities=18%  Similarity=0.178  Sum_probs=29.1

Q ss_pred             CCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCC-CCHH
Q ss_conf             2103799999887608889999999987621355672122455314755444-4305
Q gi|254780306|r  259 AFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVH-MSPD  314 (837)
Q Consensus       259 Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~-ls~e  314 (837)
                      |.+++.|    ++.+|++...+.++.+.|=+        .||+.+-..+..| |...
T Consensus        40 ~ltl~ei----a~~lglpksT~~RlL~tL~~--------~G~v~~d~~~~~Y~lG~~   84 (271)
T PRK10163         40 SSSVSDI----SLNLDLPLSTTFRLLKVLQA--------ADFVYQDSQLGWWHIGLG   84 (271)
T ss_pred             CCCHHHH----HHHHCCCHHHHHHHHHHHHH--------CCCEEEECCCCCEECCHH
T ss_conf             9799999----99979199999999999996--------898898489991764789


No 191
>TIGR01579 MiaB-like-C MiaB-like tRNA modifying enzyme; InterPro: IPR006467   This clade of sequences is closely related to MiaB, a modifier of isopentenylated adenosine-37 of certain eukaryotic and bacterial tRNAs (see IPR006463 from INTERPRO). Sequence alignments suggest that these sequences perform the same chemical transformation as MiaB, perhaps on a different (or differently modified) tRNA base substrate. This clade represents a subfamily that spans low GC Gram-positive bacteria, alpha and epsilon proteobacteria, Campylobacter, Porphyromonas, Aquifex, Thermotoga, Chlamydia, Treponema and Fusobacterium , , ..
Probab=31.53  E-value=29  Score=13.48  Aligned_cols=31  Identities=3%  Similarity=0.146  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHHHHHCCEEEECCCCCCHHHHH
Q ss_conf             4899999999987099899946997025799
Q gi|254780306|r   58 SQKHLQNIIHAVKSSTILILATDPDREGEAI   88 (837)
Q Consensus        58 ~kk~~~~i~~~~k~a~~iilAtD~DREGE~I   88 (837)
                      .+..|+.++..=++|--|+=-|=+-.+++.+
T Consensus        54 ~R~~ir~~~r~NP~A~iivTGC~AQ~~~~~l   84 (492)
T TIGR01579        54 ARRAIRRAKRENPKAKIIVTGCYAQLNPKEL   84 (492)
T ss_pred             HHHHHHHHHHCCCCEEEEEECCCCCCCHHHH
T ss_conf             9999999982099559999623112687999


No 192
>TIGR01743 purR_Bsub pur operon repressor; InterPro: IPR010078   This entry represents the pur operon repressor PurR of low-GC Gram-positive bacteria. This homodimeric repressor contains a large region homologous to phosphoribosyltransferases and is inhibited by 5-phosphoribosyl 1-pyrophosphate.; GO: 0003677 DNA binding, 0016564 transcription repressor activity, 0016481 negative regulation of transcription, 0045982 negative regulation of purine base metabolic process.
Probab=31.37  E-value=29  Score=13.46  Aligned_cols=45  Identities=11%  Similarity=0.310  Sum_probs=21.1

Q ss_pred             EEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEE
Q ss_conf             94251100786557867666744068877654899999999987099899
Q gi|254780306|r   27 SSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILI   76 (837)
Q Consensus        27 as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~ii   76 (837)
                      -.+|||.-.|.=.|||.    |-|... ..++++.+++|++.+++.+.|+
T Consensus        52 ~~~G~~~T~~GAaGGv~----YiP~~~-~~~~~~fv~~l~~~l~~s~Ri~   96 (269)
T TIGR01743        52 FDIGKLETVPGAAGGVK----YIPEVS-EKEAKEFVEELCEKLSESERIL   96 (269)
T ss_pred             CCCCEEEEECCCCCCEE----EECCCC-CHHHHHHHHHHHHHHCCCCCCC
T ss_conf             68864786147889705----845646-0456889999998622888403


No 193
>TIGR02164 torA trimethylamine-N-oxide reductase TorA; InterPro: IPR011887   Trimethylamine N-oxide (TMAO) is a major low molecular mass compound found in marine fishes and invertebrates where it is thought to act as an osmoprotectant . It has the useful biological function of protecting proteins against denaturation induced by stresses such as high concentrations of urea . Several bacterial species are capable of anaerobic growth using TMAO as the terminal electron acceptor of a respiratory transport chain where it is reduced to the volatile compound trimethylamine . Bacteria which reduce TMAO fall into three ecological niches: marine bacteria, photosynthetic bacteria living in ponds and, surprisingly, enterobacteria.   The TMAO reductase torA is an inducible, periplasmic, molydopterin-containing enzyme enzyme which shows a high level of substrate specificity . The crystal structure of the Shewenella massilia enzyme (O87948 from SWISSPROT) has been determined to 2.5 A resolution . This protein has the same overall structure as dimethylsulphoxide (DMSO) reductase, being a spherical protein composed of four domains, with a freely accessible, funnel-like cavity leading to the metal-ion redox centre.; GO: 0030151 molybdenum ion binding, 0050626 trimethylamine-N-oxide reductase (cytochrome c) activity, 0042597 periplasmic space.
Probab=30.89  E-value=30  Score=13.40  Aligned_cols=19  Identities=16%  Similarity=0.064  Sum_probs=9.6

Q ss_pred             HHHHHHHHHCCCCCEEEEE
Q ss_conf             6677764200156301000
Q gi|254780306|r  229 EADDLISFVKKATYSVEKI  247 (837)
Q Consensus       229 ~a~~~~~~~~~~~~~V~~v  247 (837)
                      -.+++.+.+......|.+|
T Consensus       251 Yl~QLK~KV~~g~i~Vis~  269 (847)
T TIGR02164       251 YLAQLKAKVAAGEINVISV  269 (847)
T ss_pred             HHHHHHHHHHCCCEEEEEE
T ss_conf             9999999984197169986


No 194
>PRK08665 ribonucleotide-diphosphate reductase subunit alpha; Validated
Probab=30.87  E-value=30  Score=13.40  Aligned_cols=89  Identities=13%  Similarity=0.211  Sum_probs=43.3

Q ss_pred             HHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHC----CCCCCHH
Q ss_conf             489999999998709989994699702579999999997551257887169999803798999999862----2646989
Q gi|254780306|r   58 SQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKS----PRDINLD  133 (837)
Q Consensus        58 ~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n----~r~~d~~  133 (837)
                      -...+..+-..+..++..+ ++..|+|  ..+-.++++|......   |-.+.|||+=|+..   -+.+    |-+-+++
T Consensus        28 p~~~~~RVA~~la~~e~~~-~~~~~~~--~~~~~fy~~l~~~~f~---p~sPtl~naG~~~~---qlssCFv~~v~Dsl~   98 (733)
T PRK08665         28 PEDMFRRVARTIAAAELKY-DSKADVE--ALADRFYDLMTSLEFL---PNSPTLMNAGRELG---QLSACFVLPVGDSIE   98 (733)
T ss_pred             HHHHHHHHHHHHHHHHCCC-CCHHHHH--HHHHHHHHHHHCCCEE---CCCCCCCCCCCCCC---CCCEEEECCCCCCHH
T ss_conf             9999999999998641015-8844299--9999999999859841---69974427999999---855179526899988


Q ss_pred             -HHHHH-HHHHHHH--HHHHHHHCHH
Q ss_conf             -99999-9999989--8740113789
Q gi|254780306|r  134 -LVNAY-LARRALD--YLVGFNLSPI  155 (837)
Q Consensus       134 -Lv~A~-~aRr~lD--~lvG~~lSp~  155 (837)
                       ..++. ++-++.-  ==+|+++|.+
T Consensus        99 ~I~~~~~~~a~i~k~GGG~G~~~S~l  124 (733)
T PRK08665         99 EIFDAVKHAALIHKSGGGTGFSFSRL  124 (733)
T ss_pred             HHHHHHHHHHHHHCCCCEEEEECCCC
T ss_conf             99999999999862377420102354


No 195
>pfam12387 Peptidase_C74 Pestivirus NS2 peptidase. The pestivirus NS2 peptidase is responsible for single cleavage between NS2 and NS3 of the bovine viral diarrhea virus polyprotein, a cleavage that is correlated with cytopathogenicity. The peptidase is activated by its interaction with 'J-domain protein interacting with viral protein' - Jiv.
Probab=30.60  E-value=20  Score=14.64  Aligned_cols=16  Identities=6%  Similarity=0.276  Sum_probs=8.9

Q ss_pred             CHHHHHHHHHHCCEEE
Q ss_conf             1578999997322022
Q gi|254780306|r  490 TYATILETLYKRKYVI  505 (837)
Q Consensus       490 TyA~II~~L~~R~YV~  505 (837)
                      .-+-+|..|++-+...
T Consensus        85 ~~SR~iAalIElNW~~  100 (200)
T pfam12387        85 FLSRLIAALIELNWAF  100 (200)
T ss_pred             HHHHHHHHHHHHHHCC
T ss_conf             9999999999863000


No 196
>PRK10811 rne ribonuclease E; Reviewed
Probab=30.34  E-value=21  Score=14.61  Aligned_cols=39  Identities=21%  Similarity=0.394  Sum_probs=22.4

Q ss_pred             HHHHHHHHHHHH--HCCEEEECCCC-CCHHHHHHHHHHHHHH
Q ss_conf             899999999987--09989994699-7025799999999975
Q gi|254780306|r   59 QKHLQNIIHAVK--SSTILILATDP-DREGEAISWHVLDVLR   97 (837)
Q Consensus        59 kk~~~~i~~~~k--~a~~iilAtD~-DREGE~Iawhi~e~l~   97 (837)
                      ++.++.+-.-+.  +--.+|+=|-. ++.-|.|.|.+-.+++
T Consensus       148 R~rLkeiL~~L~~Peg~GlIVRTAa~g~s~eeL~~Dl~~Ll~  189 (1063)
T PRK10811        148 RTELKEALASLELPEGMGLIVRTAGVGKSAEALQWDLSFRLK  189 (1063)
T ss_pred             HHHHHHHHHHCCCCCCCEEEEECCCCCCCHHHHHHHHHHHHH
T ss_conf             999999997135788826999757689999999999999999


No 197
>TIGR01617 arsC_related conserved hypothetical protein; InterPro: IPR006504   These sequences are a part of the Arsenate reductase family of sequences. The family includes a glutaredoxin-dependent arsenate reductase that works together with an arsenite exporter. It also includes an uncharacterised family associated with nitrogenase system genes in a number of phylogenetically distant species. The function of this group of sequences seems unlikely to be arsenate reductase, although that assignment has been given to a number of members of this family. .
Probab=29.77  E-value=27  Score=13.69  Aligned_cols=59  Identities=17%  Similarity=0.275  Sum_probs=38.0

Q ss_pred             CCCHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEEECCEECCCC-CCCCCCCCCHHHHHHHHHHHH
Q ss_conf             98842548999999861525515777898749991158765261678111248-877514357999999998365
Q gi|254780306|r  692 TWKSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNHDGAYTKLE-SIEQVLTIDLEQAISCITEKK  765 (837)
Q Consensus       692 ~~~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~~~~~~~sl~-~~~~~~~I~l~~Aieli~~~k  765 (837)
                      .+.-+.+|-|.-..+|+.   +    ++|-+=+.+        .++.+|+.|+ ..+...+++.++|++||++.-
T Consensus        30 ~~~~~~~~~e~l~~~l~~---~----~~g~~~l~n--------t~g~~~r~L~i~~~~~~~~~~~~~~~Ll~~~~   89 (122)
T TIGR01617        30 DLKEDTPTREELKEILSL---L----EDGIDPLLN--------TRGQSYRALDILKNKFEELSDKEALELLAEDP   89 (122)
T ss_pred             ECCCCCCCHHHHHHHHHH---H----HHHHHHHHH--------CCCHHHHHCCCCHHHHHCCCHHHHHHHHHHCH
T ss_conf             034589787899999874---0----100123330--------23112442588345664278889999987271


No 198
>COG4337 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.61  E-value=24  Score=14.08  Aligned_cols=50  Identities=34%  Similarity=0.436  Sum_probs=29.3

Q ss_pred             EEEEECCCHHHHHHHHHCCCC----CCH-----HHHH-HHHHHHHHHHHHHHHHCHHHHH
Q ss_conf             999803798999999862264----698-----9999-9999999898740113789886
Q gi|254780306|r  109 RVSFNAITKQVVLNAMKSPRD----INL-----DLVN-AYLARRALDYLVGFNLSPILWQ  158 (837)
Q Consensus       109 R~~f~eiT~~aI~~A~~n~r~----~d~-----~Lv~-A~~aRr~lD~lvG~~lSp~L~r  158 (837)
                      -++-+.||++.|..|-..=.+    |..     .... -.+|-+.+|--+||++.|+|.+
T Consensus        45 ~~vn~aiTe~eVLaAQkAWGEALvaIS~ty~a~G~a~AkaLA~~VlD~AYGYq~GpVLFK  104 (206)
T COG4337          45 LVVNNAITEEEVLAAQKAWGEALVAISDTYQAQGIAAAKALANQVLDQAYGYQQGPVLFK  104 (206)
T ss_pred             HHHHCCCCHHHHHHHHHHHHHHHHHHHHHHHHCCHHHHHHHHHHHHHHHHCCCCCCEEEE
T ss_conf             677434568999999998887787753566531558899999998887624234765640


No 199
>cd03765 proteasome_beta_bacterial Bacterial proteasome, beta subunit. The 20S proteasome, multisubunit proteolytic complex, is the central enzyme of nonlysosomal protein degradation in both the cytosol and nucleus. It is composed of 28 subunits arranged as four homoheptameric rings that stack on top of one another forming an elongated alpha-beta-beta-alpha cylinder with a central cavity. The proteasome alpha and beta subunits are members of the N-terminal nucleophile (Ntn)-hydrolase superfamily. Their N-terminal threonine residues are exposed as a nucleophile in peptide bond hydrolysis. Mammals have 7 alpha and 7 beta proteasome subunits while archaea have one of each.
Probab=29.49  E-value=31  Score=13.23  Aligned_cols=52  Identities=15%  Similarity=0.097  Sum_probs=28.6

Q ss_pred             CCCCCCCCCCCEEEEEECCCCCEEEECCCCCCCCCCCCCCCCHHHCCHHHHHHHH--HC
Q ss_conf             2014689999669998269742277348877761337899884254899999986--15
Q gi|254780306|r  653 VLLGNDLETKESVTLRSGRFGLYVQRGDGKDAKRCSLPKTWKSDSVDYDKAMSLL--SL  709 (837)
Q Consensus       653 ~~LG~dP~~G~~I~lk~GryGpYvq~Ge~~kpkr~si~k~~~~~~itle~Al~LL--sL  709 (837)
                      ++.=+.|+ |.  |+.-.+--||+|+||.+.+|-. |--.++ .+.+|++|.++.  |+
T Consensus       125 ~LflIYpe-GN--fIeas~dtPf~QIGEtKYGKPI-LDR~i~-~~~sl~~A~K~aLvSf  178 (236)
T cd03765         125 RLFLIYPQ-GN--FIEATPDTPFLQIGETKYGKPI-LDRVIT-PDTSLEDAAKCALVSM  178 (236)
T ss_pred             EEEEEECC-CC--EEECCCCCCEEEECCCCCCCCE-EEEECC-CCCCHHHHHHHHHHHH
T ss_conf             38999369-86--1860699965885465679853-885357-9999999999877712


No 200
>cd01304 FMDH_A Formylmethanofuran dehydrogenase (FMDH) subunit A;  Methanogenic bacteria and archea derive the energy for autotrophic growth from methanogenesis, the reduction of CO2 with molecular hydrogen as the electron donor. FMDH catalyzes the first step in methanogenesis, the formyl-methanofuran synthesis. In this step, CO2 is bound to methanofuran and subsequently reduced to the formyl state with electrons derived from hydrogen.
Probab=29.43  E-value=32  Score=13.23  Aligned_cols=29  Identities=38%  Similarity=0.638  Sum_probs=22.3

Q ss_pred             HHHHHHHHHCC-----------CCCCCCHHHHHHHHHHCC
Q ss_conf             99874332102-----------566551578999997322
Q gi|254780306|r  474 SSLIKKMEEIG-----------IGRPSTYATILETLYKRK  502 (837)
Q Consensus       474 asLik~mE~~G-----------IGrPSTyA~II~~L~~R~  502 (837)
                      .+|++..|++|           +|-|-.|.++++|+..-+
T Consensus       212 ~~L~~a~e~LglPH~lHvH~nNLG~PGN~~ttl~T~~~~e  251 (541)
T cd01304         212 KGLAEANEELGLPHSIHVHCNNLGVPGNYETTLETMKAAE  251 (541)
T ss_pred             HHHHHHHHHCCCCCCEEHHHHHCCCCCCHHHHHHHHHHCC
T ss_conf             9999999865999603201231799987266776444204


No 201
>pfam11834 DUF3354 Domain of unknown function (DUF3354). This domain is functionally uncharacterized. This domain is found in eukaryotes. This presumed domain is about 60 amino acids in length.
Probab=29.41  E-value=15  Score=15.55  Aligned_cols=22  Identities=23%  Similarity=0.407  Sum_probs=15.9

Q ss_pred             CCCCHHHHHHHHHHHHCCCHHH
Q ss_conf             5210379999988760888999
Q gi|254780306|r  258 PAFTTSTLQQVASSRLGFSASH  279 (837)
Q Consensus       258 ~Pf~tstLQq~As~~lg~sa~~  279 (837)
                      .|-++..|...|+.+||+++.+
T Consensus        24 lP~sleeLl~ia~~Kfg~~~~~   45 (69)
T pfam11834        24 LPDSLEELLEIAGKKFGFSPTK   45 (69)
T ss_pred             CCCCHHHHHHHHHHHCCCCCCE
T ss_conf             9857999999999980998518


No 202
>pfam09664 DUF2399 Protein of unknown function C-terminus (DUF2399). Proteins in this entry are encoded within a conserved gene four-gene neighbourhood found sporadically in a phylogenetically broad range of bacteria including: Nocardia farcinica, Symbiobacterium thermophilum, and Streptomyces avermitilis (Actinobacteria), Geobacillus kaustophilus (Firmicutes), Azoarcus sp. EbN1 and Ralstonia solanacearum (Beta-proteobacteria). Just the C-terminal region is ioncluded here.
Probab=29.37  E-value=32  Score=13.22  Aligned_cols=68  Identities=21%  Similarity=0.231  Sum_probs=47.0

Q ss_pred             EEEECCHHHHHHHHHHHCCCCE-EEEEECCCEECCCCCCCCCCCCCCCEEEEECCCHHHHHHHHHHHHHHCCEEEECCCC
Q ss_conf             8997790478778875089989-999425110078655786766674406887765489999999998709989994699
Q gi|254780306|r    3 VIIVESPAKAKTISKYLGSNYK-VLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPSSQKHLQNIIHAVKSSTILILATDP   81 (837)
Q Consensus         3 LvIvEsP~kak~I~~~Lg~~y~-V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~~kk~~~~i~~~~k~a~~iilAtD~   81 (837)
                      +.|||-|+....+...+|..-. .+-+.|..                         +...+.-|..+++.--.++-.+|-
T Consensus        22 V~V~ENP~V~s~a~d~~~~~~~pLvCt~Gqp-------------------------~~A~~~LL~~L~~~g~~l~Y~GDF   76 (155)
T pfam09664        22 VYVCENPAVFSAAADRLGARCAPLVCTSGQP-------------------------SAAALILLDRLAAAGARLYYSGDF   76 (155)
T ss_pred             EEEEECHHHHHHHHHHCCCCCCCEEECCCCH-------------------------HHHHHHHHHHHHHCCCEEEEECCC
T ss_conf             9998198999999986478898868689987-------------------------899999999998489869995889


Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             70257999999999
Q gi|254780306|r   82 DREGEAISWHVLDV   95 (837)
Q Consensus        82 DREGE~Iawhi~e~   95 (837)
                      |-||=.||-++...
T Consensus        77 D~~Gl~IA~~l~~r   90 (155)
T pfam09664        77 DWPGLRIANRLIAR   90 (155)
T ss_pred             CHHHHHHHHHHHHH
T ss_conf             93799999999987


No 203
>pfam01325 Fe_dep_repress Iron dependent repressor, N-terminal DNA binding domain. This family includes the Diphtheria toxin repressor. DNA binding is through a helix-turn-helix motif.
Probab=29.35  E-value=32  Score=13.22  Aligned_cols=29  Identities=28%  Similarity=0.379  Sum_probs=20.0

Q ss_pred             HHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCC
Q ss_conf             8876088899999999876213556721224553147
Q gi|254780306|r  269 ASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMR  305 (837)
Q Consensus       269 As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpR  305 (837)
                      -+.+||.|+.-+-...++|-+        .|||.|-+
T Consensus        26 iA~~L~Vs~~SVt~mlkkL~~--------~GlV~~e~   54 (58)
T pfam01325        26 LAERLNVSPSTVSEMLKKLEK--------DGYVVYEP   54 (58)
T ss_pred             HHHHHCCCCHHHHHHHHHHHH--------CCCEEEEC
T ss_conf             999959992529999999998--------89978532


No 204
>PRK03353 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=28.97  E-value=32  Score=13.17  Aligned_cols=27  Identities=22%  Similarity=0.453  Sum_probs=21.3

Q ss_pred             HHHHHHHHHHHHCCEEEECCCCCCHHH
Q ss_conf             999999999870998999469970257
Q gi|254780306|r   60 KHLQNIIHAVKSSTILILATDPDREGE   86 (837)
Q Consensus        60 k~~~~i~~~~k~a~~iilAtD~DREGE   86 (837)
                      ..|....+.++.-.-|++.-|.|||+|
T Consensus        14 ~~Ie~Ai~al~~G~~Viv~Dd~dREnE   40 (217)
T PRK03353         14 ERVEAALDALREGRGVLVLDDEDRENE   40 (217)
T ss_pred             CHHHHHHHHHHCCCEEEEEECCCCCCC
T ss_conf             159999999987995999838998764


No 205
>PRK00009 phosphoenolpyruvate carboxylase; Reviewed
Probab=28.76  E-value=32  Score=13.15  Aligned_cols=14  Identities=21%  Similarity=0.449  Sum_probs=7.7

Q ss_pred             CCCEEECCHHHHHC
Q ss_conf             77122201142000
Q gi|254780306|r  508 KRKILPQNTGRIVT  521 (837)
Q Consensus       508 ~~~l~pT~~G~~v~  521 (837)
                      ++.+.-|+-|.++.
T Consensus       638 ~g~ir~TEQGEvI~  651 (916)
T PRK00009        638 KGRIRVTEQGEVIR  651 (916)
T ss_pred             CCCEEEEECCCCHH
T ss_conf             68436653465377


No 206
>PRK05583 ribosomal protein L7Ae family protein; Provisional
Probab=28.73  E-value=32  Score=13.14  Aligned_cols=78  Identities=10%  Similarity=0.089  Sum_probs=45.1

Q ss_pred             CHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHH
Q ss_conf             54899999999987099899946997025799999999975512578871699998037989999998622646989999
Q gi|254780306|r   57 SSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVN  136 (837)
Q Consensus        57 ~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~  136 (837)
                      +.....+.|++  .++..|++|+|...-..-=   +...+..    .+.|+..    ..|++.+-.|+...+-.-....|
T Consensus        21 G~~~v~~~ik~--~k~~LVi~A~Das~~tkkk---~~~~c~~----~~Vp~~~----~~tk~eLg~aiGk~~r~vvaI~D   87 (104)
T PRK05583         21 GYNKCEEAVKK--NKIYLFIISNDISENSKNK---FKKYCEK----YNIPYIE----SFSKEELGYALGRDEIKILGVKD   87 (104)
T ss_pred             CHHHHHHHHHH--CCEEEEEEECCCCHHHHHH---HHHHHHC----CCCCEEE----ECCHHHHHHHHCCCCEEEEEEEC
T ss_conf             68999999994--9857999956778658999---9999853----6988898----53899999985889816999957


Q ss_pred             HHHHHHHHHHH
Q ss_conf             99999998987
Q gi|254780306|r  137 AYLARRALDYL  147 (837)
Q Consensus       137 A~~aRr~lD~l  147 (837)
                      ++.|++++-.+
T Consensus        88 ~gfAk~l~~l~   98 (104)
T PRK05583         88 KNMANKLLKLW   98 (104)
T ss_pred             HHHHHHHHHHH
T ss_conf             77999999999


No 207
>PRK09318 bifunctional 3,4-dihydroxy-2-butanone 4-phosphate synthase/GTP cyclohydrolase II protein; Provisional
Probab=28.69  E-value=32  Score=13.14  Aligned_cols=23  Identities=30%  Similarity=0.424  Sum_probs=17.4

Q ss_pred             HHHHHHHHHCCEEEECCCCCCHHH
Q ss_conf             999999870998999469970257
Q gi|254780306|r   63 QNIIHAVKSSTILILATDPDREGE   86 (837)
Q Consensus        63 ~~i~~~~k~a~~iilAtD~DREGE   86 (837)
                      .++.+.++.-.-||+- |.|||.|
T Consensus         2 ee~i~~~~~Gk~vivv-DedREnE   24 (387)
T PRK09318          2 EELREAFLEGKPVILI-DRNRENE   24 (387)
T ss_pred             HHHHHHHHCCCEEEEE-ECCCCCH
T ss_conf             7799999879929999-3898760


No 208
>smart00661 RPOL9 RNA polymerase subunit 9.
Probab=28.67  E-value=32  Score=13.14  Aligned_cols=33  Identities=21%  Similarity=0.527  Sum_probs=19.8

Q ss_pred             ECCCCCCCCEEEEEECCCCCCCCCCCCCCCCCCCCCCC
Q ss_conf             43346777313687157761112343432333210012
Q gi|254780306|r  604 TCPECHTHSLSLKLSSKYGAFVGCTNYPECKYTRQLTS  641 (837)
Q Consensus       604 ~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk~t~~l~~  641 (837)
                      -||+|+..  .....++.+.-+.|+   .|.|..+...
T Consensus         2 FCp~C~n~--l~p~~~~~~~~~~C~---~C~y~~~~~~   34 (52)
T smart00661        2 FCPKCGNM--LIPKEGKEKRRFVCR---KCGYEEPIEQ   34 (52)
T ss_pred             CCCCCCCE--EEEEECCCCEEEECC---CCCCCCCCCC
T ss_conf             78652888--768536995389748---9998436688


No 209
>PRK10336 DNA-binding transcriptional regulator QseB; Provisional
Probab=27.93  E-value=33  Score=13.05  Aligned_cols=28  Identities=18%  Similarity=0.202  Sum_probs=23.1

Q ss_pred             CCEEEEC-CHHHHHHHHHHHC-CCCEEEEE
Q ss_conf             9189977-9047877887508-99899994
Q gi|254780306|r    1 MNVIIVE-SPAKAKTISKYLG-SNYKVLSS   28 (837)
Q Consensus         1 M~LvIvE-sP~kak~I~~~Lg-~~y~V~as   28 (837)
                      |++.||| -|.-+..|..+|. .||.|.++
T Consensus         1 mkILlVEDd~~l~~~l~~~L~~~g~~V~~a   30 (219)
T PRK10336          1 MRILLIEDDMLIGDGIKTGLSKMGFSVDWF   30 (219)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEE
T ss_conf             989999389999999999999879999998


No 210
>COG0765 HisM ABC-type amino acid transport system, permease component [Amino acid transport and metabolism]
Probab=27.44  E-value=34  Score=12.99  Aligned_cols=24  Identities=38%  Similarity=0.304  Sum_probs=20.3

Q ss_pred             HHHHHHHHHCCCHHHHHHH---HHHHH
Q ss_conf             9999887608889999999---98762
Q gi|254780306|r  265 LQQVASSRLGFSASHTMRI---AQKLY  288 (837)
Q Consensus       265 LQq~As~~lg~sa~~Tm~i---AQ~LY  288 (837)
                      =|.||++-+|+|..+||+-   =|-+.
T Consensus       121 GQ~EAA~aLGls~~q~~r~IIlPQAlr  147 (222)
T COG0765         121 GQWEAARALGLTYWQTMRYVILPQALR  147 (222)
T ss_pred             HHHHHHHHCCCCHHHHHHHEEHHHHHH
T ss_conf             689999985999866866300235699


No 211
>cd02755 MopB_Thiosulfate-R-like The MopB_Thiosulfate-R-like CD contains thiosulfate-, sulfur-, and polysulfide-reductases, and other related proteins. Thiosulfate reductase catalyzes the cleavage of sulfur-sulfur bonds in thiosulfate. Polysulfide reductase is a membrane-bound enzyme that catalyzes the reduction of polysulfide using either hydrogen or formate as the electron donor. Members of the MopB_Thiosulfate-R-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=27.16  E-value=27  Score=13.78  Aligned_cols=41  Identities=22%  Similarity=0.232  Sum_probs=19.7

Q ss_pred             CCCHHHHHHHHHHHHCCCCCCCHHHHHHHHC--CC----CCC--CCC-HHHHHHHHHH
Q ss_conf             8889999999987621355672122455314--75----544--443-0568999976
Q gi|254780306|r  274 GFSASHTMRIAQKLYEGIDVNGEIVGLITYM--RT----DGV--HMS-PDALEAVRRS  322 (837)
Q Consensus       274 g~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYp--RT----DS~--~ls-~ea~~~~r~~  322 (837)
                      |+.-.+-....|.+|-        ..=|+||  |+    |..  .+| +||++.+.+-
T Consensus        37 G~lC~kG~~~~~~~~~--------pdRl~~Pl~R~g~rG~G~~~~iSWdeAl~~ia~k   86 (454)
T cd02755          37 GKLCARGNAGIQLLYD--------PDRLKKPLIRVGERGEGKFREASWDEALQYIASK   86 (454)
T ss_pred             CEECHHHHHHHHHHCC--------CCHHCCCEEECCCCCCCCEEEECHHHHHHHHHHH
T ss_conf             5677735646887459--------7541288885666888987882799999999999


No 212
>PRK00215 LexA repressor; Validated
Probab=27.12  E-value=34  Score=12.95  Aligned_cols=32  Identities=16%  Similarity=0.376  Sum_probs=25.2

Q ss_pred             HHHHHCCCCCCCCHHHHHHHHHHCCEEECCCC
Q ss_conf             43321025665515789999973220221477
Q gi|254780306|r  478 KKMEEIGIGRPSTYATILETLYKRKYVIAEKR  509 (837)
Q Consensus       478 k~mE~~GIGrPSTyA~II~~L~~R~YV~~~~~  509 (837)
                      .-++..||--|||-...++.|.++||+.+..+
T Consensus        28 EI~~~~g~~S~~tV~~~l~~Le~kG~i~r~~~   59 (204)
T PRK00215         28 EIADALGLRSPSAVHEHLKALERKGFIRRDPG   59 (204)
T ss_pred             HHHHHHCCCCCHHHHHHHHHHHHCCCEECCCC
T ss_conf             99998099981899999999987978870699


No 213
>PRK09880 L-idonate 5-dehydrogenase; Provisional
Probab=27.05  E-value=23  Score=14.22  Aligned_cols=74  Identities=16%  Similarity=0.178  Sum_probs=32.4

Q ss_pred             CCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHHHHHCCCHHHHHHHHH
Q ss_conf             5665515789999973220221477122201142000022336655689889999999999986260134789999
Q gi|254780306|r  485 IGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLDEISTGKLNWKEVLHE  560 (837)
Q Consensus       485 IGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld~Ia~G~~~~~~~L~~  560 (837)
                      .|.|++...-++-+..+|-+..-+-.-.+.+  +-...++.+...=+-++.++.+|+..|+.|++|+.+...++..
T Consensus       243 ~G~~~~~~~al~~~r~gG~iv~vG~~~~~~~--~~~~~l~~kei~i~Gs~~~~~~~~~~l~li~~g~i~~~~lIt~  316 (343)
T PRK09880        243 SGHPSSVNTCLEVTRAKGVMVQVGMGGAMPE--FPMMTLISKEISLKGSFRFTSEFNTAVSWLANGVINPLPLLSA  316 (343)
T ss_pred             CCCHHHHHHHHHHCCCCEEEEEEECCCCCCC--CCHHHHHHCCCEEEEECCCHHHHHHHHHHHHCCCCCHHHEEEE
T ss_conf             1999999999973779839999972798887--0899998588499990486799999999998599980455887


No 214
>COG3058 FdhE Uncharacterized protein involved in formate dehydrogenase formation [Posttranslational modification, protein turnover, chaperones]
Probab=26.54  E-value=35  Score=12.87  Aligned_cols=30  Identities=23%  Similarity=0.606  Sum_probs=17.5

Q ss_pred             CCCEECCCCCCCCE-EEEEEC--CCC-CCCCCCC
Q ss_conf             66114334677731-368715--776-1112343
Q gi|254780306|r  600 EDSRTCPECHTHSL-SLKLSS--KYG-AFVGCTN  629 (837)
Q Consensus       600 ~~~~~Cp~C~~g~L-~~k~~g--K~G-~FigCSn  629 (837)
                      .....||.||+--+ +....|  -.| .|+.||-
T Consensus       183 e~~~~CPvCGS~PvaSmV~~g~~~~GlRYL~Csl  216 (308)
T COG3058         183 ESRQYCPVCGSMPVASMVQIGETEQGLRYLHCSL  216 (308)
T ss_pred             CCCCCCCCCCCCCCCEEEEECCCCCCCHHHHHHH
T ss_conf             6641077768877431346347533430212066


No 215
>PRK10427 putative fructose-like phosphotransferase EIIB subunit 3; Provisional
Probab=26.48  E-value=35  Score=12.87  Aligned_cols=42  Identities=14%  Similarity=0.412  Sum_probs=28.1

Q ss_pred             HHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCC
Q ss_conf             998709989994699702579999999997551257887169999803798999999862264
Q gi|254780306|r   67 HAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRD  129 (837)
Q Consensus        67 ~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~  129 (837)
                      ..++.||.||+|+|-+-+|.       +.+      ..+|+.++        .+.+|+.+|..
T Consensus        53 ~dI~~AD~VIiA~D~~i~~~-------eRF------~Gk~v~~~--------~v~~ai~~p~~   94 (114)
T PRK10427         53 EDIRRADVVLLITDIELAGA-------ERF------EHCRYVQC--------SIYAFLREPQR   94 (114)
T ss_pred             HHHHHCCEEEEEECCCCCCC-------CCC------CCCEEEEE--------CHHHHHHCHHH
T ss_conf             99986999999845877851-------014------99878992--------58998879999


No 216
>COG0635 HemN Coproporphyrinogen III oxidase and related Fe-S oxidoreductases [Coenzyme metabolism]
Probab=26.18  E-value=36  Score=12.83  Aligned_cols=58  Identities=10%  Similarity=0.141  Sum_probs=38.1

Q ss_pred             CCCHHHHHHHHHHCCCCC-----------CCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCC
Q ss_conf             017899874332102566-----------5515789999973220221477122201142000022336
Q gi|254780306|r  470 RYSESSLIKKMEEIGIGR-----------PSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENF  527 (837)
Q Consensus       470 rytEasLik~mE~~GIGr-----------PSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~  527 (837)
                      ++.|.-+...|...|+--           -+-....+..+.+.|++..++..+..|+.|+.+.+.+...
T Consensus       340 ~~~e~~i~gLr~~~gv~~~~~~~~~~~~~~~~~~~~l~~~~~~Gll~~~~~~~~lt~~g~~~~~~i~~~  408 (416)
T COG0635         340 LIREALILGLRLNFGVDLAELEERFGIFKFAEILELLAELIADGLLELDGDRLRLTEKGRLLLRSIAEA  408 (416)
T ss_pred             HHHHHHHHHHHHHCCCCHHHHHHHHCCCHHHHHHHHHHHHHHCCCEEECCCEEEECCCHHHHHHHHHHH
T ss_conf             999999986577448678999998486056667999999986896896398799885306479999999


No 217
>PRK05978 hypothetical protein; Provisional
Probab=25.99  E-value=23  Score=14.22  Aligned_cols=11  Identities=36%  Similarity=0.939  Sum_probs=9.0

Q ss_pred             EECCCCCCCCE
Q ss_conf             14334677731
Q gi|254780306|r  603 RTCPECHTHSL  613 (837)
Q Consensus       603 ~~Cp~C~~g~L  613 (837)
                      +.||.|+.|.|
T Consensus        35 ~rCP~CG~G~L   45 (149)
T PRK05978         35 GRCPHCGEGKL   45 (149)
T ss_pred             CCCCCCCCCHH
T ss_conf             75989999415


No 218
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=25.24  E-value=37  Score=12.71  Aligned_cols=80  Identities=14%  Similarity=0.264  Sum_probs=50.8

Q ss_pred             CCEEEEC-CHHHHHHHHHHHC--CCCEEEEEECCCEE---CC-CCCCCCC---CCCCCCEEEEECCCHHHHHHHHHHHHH
Q ss_conf             9189977-9047877887508--99899994251100---78-6557867---666744068877654899999999987
Q gi|254780306|r    1 MNVIIVE-SPAKAKTISKYLG--SNYKVLSSFGHIRD---LP-AKKGSVL---PEKEFEMIWNIDPSSQKHLQNIIHAVK   70 (837)
Q Consensus         1 M~LvIvE-sP~kak~I~~~Lg--~~y~V~as~GHird---Lp-~~~~~v~---~~~~f~p~y~v~~~~kk~~~~i~~~~k   70 (837)
                      |+++||| -|..+..+..||.  .+|.|.++.+-..+   +- .....+|   .|     .|-...+.-+.++.|+..-.
T Consensus         2 irVLIVEDD~~v~~~~~~~l~~~~gf~vv~~a~t~~eA~~~l~~~~~~~DLILLD-----i~mPd~~Glell~~lR~~~~   76 (239)
T PRK10430          2 INVLIVDDDAMVAELNRRYVAQIPGFQCCGTASTLEKAKEIIFNSDTPIDLILLD-----IYMQQENGLDLLPVLHEAGC   76 (239)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCCEEEEEECCHHHHHHHHHCCCCCCCEEEEC-----CCCCCCCHHHHHHHHHHHCC
T ss_conf             8799992989999999999851899089999899999999996579998589978-----99999978999999998589


Q ss_pred             HCCEEEECCCCCCHH
Q ss_conf             099899946997025
Q gi|254780306|r   71 SSTILILATDPDREG   85 (837)
Q Consensus        71 ~a~~iilAtD~DREG   85 (837)
                      .++.|++-...|.+-
T Consensus        77 ~~~VI~ITa~~d~~~   91 (239)
T PRK10430         77 KSDVIVISSAADAAT   91 (239)
T ss_pred             CCEEEEEEECCCHHH
T ss_conf             981999972688999


No 219
>PTZ00093 nucleoside diphosphate kinase; Provisional
Probab=25.20  E-value=37  Score=12.70  Aligned_cols=82  Identities=13%  Similarity=0.179  Sum_probs=45.7

Q ss_pred             HHHHHHHHHHCCCCCEEEEEECCCCCCCCCCCCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCC
Q ss_conf             66677764200156301000023322246852103799999887608889999999987621355672122455314755
Q gi|254780306|r  228 KEADDLISFVKKATYSVEKIENKPIKRNPWPAFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMRTD  307 (837)
Q Consensus       228 ~~a~~~~~~~~~~~~~V~~v~~k~~~~~Pp~Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTD  307 (837)
                      ....+|++.+....|.|...+.-                       .++    ...|..+|+.|+-.-.-..|++||-..
T Consensus        17 ~l~g~Ii~~i~~~Gf~I~~~k~~-----------------------~lt----~e~a~~fY~~h~gkpff~~Lv~~mtSG   69 (149)
T PTZ00093         17 GLVGEIIKRFEKKGYKLVALKFL-----------------------QPT----TEQAEEHYKEHKSKPFFPGLVSYISSG   69 (149)
T ss_pred             CCHHHHHHHHHHCCCEEEEEEEE-----------------------CCC----HHHHHHHHHHHCCCCCHHHHHHHHCCC
T ss_conf             88799999999879989998742-----------------------589----999999999971883288899986789


Q ss_pred             CCCC-----CHHHHHHHHHHHHHHCCCCCCCCCCC
Q ss_conf             4444-----30568999976552001123763111
Q gi|254780306|r  308 GVHM-----SPDALEAVRRSITSHYGDHYLPEKPR  337 (837)
Q Consensus       308 S~~l-----s~ea~~~~r~~i~~~~g~~~l~~~~r  337 (837)
                       .-+     .++++...|+++...-..+-.|.+.|
T Consensus        70 -Pvvalvleg~naI~~~R~l~GpT~p~~a~p~tIR  103 (149)
T PTZ00093         70 -PVVCMVWEGKNVVKSGRVLLGATNPADSAPGTIR  103 (149)
T ss_pred             -CEEEEEEECCCHHHHHHHHHCCCCCCCCCCCCHH
T ss_conf             -8799996278889999998589996768998828


No 220
>PRK09836 DNA-binding transcriptional activator CusR; Provisional
Probab=25.19  E-value=37  Score=12.70  Aligned_cols=29  Identities=24%  Similarity=0.289  Sum_probs=23.4

Q ss_pred             CCEEEEC-CHHHHHHHHHHHC-CCCEEEEEE
Q ss_conf             9189977-9047877887508-998999942
Q gi|254780306|r    1 MNVIIVE-SPAKAKTISKYLG-SNYKVLSSF   29 (837)
Q Consensus         1 M~LvIvE-sP~kak~I~~~Lg-~~y~V~as~   29 (837)
                      |++.||| -|..+..|..+|. .||.|.++.
T Consensus         1 MkILiVEDd~~l~~~l~~~L~~~G~~v~~a~   31 (226)
T PRK09836          1 MKLLIVEDEKKTGEYLTKGLTEAGFVVDLAD   31 (226)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             9899993999999999999987899999989


No 221
>cd03366 TOPRIM_TopoIIA_GyrB TOPRIM_TopoIIA_GyrB: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to the Escherichia coli GyrB subunit. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA.  These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings.  DNA gyrase is more effective at relaxing supercoils than decatentating DNA.  DNA gyrase in addition inserts negative supercoils in the presence of ATP.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleava
Probab=24.97  E-value=37  Score=12.67  Aligned_cols=78  Identities=19%  Similarity=0.278  Sum_probs=40.5

Q ss_pred             CEEEECCHHHHHHHHHHHCCCC-EEEEEECCCEECCCCCCCCCCCCCCCEEEEECCC---HHHHHHHHHHHH--------
Q ss_conf             1899779047877887508998-9999425110078655786766674406887765---489999999998--------
Q gi|254780306|r    2 NVIIVESPAKAKTISKYLGSNY-KVLSSFGHIRDLPAKKGSVLPEKEFEMIWNIDPS---SQKHLQNIIHAV--------   69 (837)
Q Consensus         2 ~LvIvEsP~kak~I~~~Lg~~y-~V~as~GHirdLp~~~~~v~~~~~f~p~y~v~~~---~kk~~~~i~~~~--------   69 (837)
                      -|+|||--|-+-.+...-...| -|.+-.|-+..         +       |....+   +-+-+..|.+.+        
T Consensus         2 eL~l~EGDSA~g~a~~~Rd~~~qgv~PLrGK~lN---------v-------~~~~~~ki~~N~Ei~~l~~~lGl~~~~~~   65 (114)
T cd03366           2 ELYIVEGDSAGGSAKQGRDRRFQAILPLRGKILN---------V-------EKARLDKILKNEEIRALITALGTGIGEDF   65 (114)
T ss_pred             EEEEECCCCCHHHHHCCCCCCCEEEEECCCCCHH---------H-------HHCCHHHHHCCHHHHHHHHHHCCCCCCCC
T ss_conf             2899727674055652178786899870785000---------6-------42878788629679999999687878645


Q ss_pred             --H--HCCEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             --7--0998999469970257999999999
Q gi|254780306|r   70 --K--SSTILILATDPDREGEAISWHVLDV   95 (837)
Q Consensus        70 --k--~a~~iilAtD~DREGE~Iawhi~e~   95 (837)
                        +  .-..|+++||+|.-|--|.=-++..
T Consensus        66 d~~~LRYgkIiImtDaD~DG~HI~~Lli~f   95 (114)
T cd03366          66 DLEKLRYHKIIIMTDADVDGAHIRTLLLTF   95 (114)
T ss_pred             CHHHCCCCEEEEEECCCCCCHHHHHHHHHH
T ss_conf             400078786999968998806899999999


No 222
>TIGR00091 TIGR00091 tRNA (guanine-N(7)-)-methyltransferase; InterPro: IPR004395   This predicted S-adenosylmethionine-dependent methyltransferase is found in a single copy in most Bacteria . It is also found, with a short amino-terminal extension in eukaryotes. Its function is unknown. In Escherichia coli, this protein flanks the DNA repair protein MutY, also called micA.; GO: 0008168 methyltransferase activity.
Probab=24.81  E-value=33  Score=13.10  Aligned_cols=39  Identities=23%  Similarity=0.355  Sum_probs=26.8

Q ss_pred             CCHHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCHHHHHHHHHH
Q ss_conf             889999999987621355672122455314755444430568999976
Q gi|254780306|r  275 FSASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSPDALEAVRRS  322 (837)
Q Consensus       275 ~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~ea~~~~r~~  322 (837)
                      .++.=.-.++|.|=+|        |+| |++||...|.+..+..+.+.
T Consensus       125 ~~~~Fl~~~~~~L~~~--------G~i-~~~TD~~~lfE~mL~~l~~~  163 (216)
T TIGR00091       125 TQPHFLKEVANVLKKG--------GVI-ELKTDNEPLFEDMLKVLSEN  163 (216)
T ss_pred             CCHHHHHHHHHHCCCC--------CEE-EEECCCHHHHHHHHHHHHHC
T ss_conf             5678999999970459--------689-99707846789999999653


No 223
>KOG0978 consensus
Probab=24.61  E-value=28  Score=13.67  Aligned_cols=10  Identities=30%  Similarity=0.790  Sum_probs=7.1

Q ss_pred             CCEECCCCCC
Q ss_conf             6114334677
Q gi|254780306|r  601 DSRTCPECHT  610 (837)
Q Consensus       601 ~~~~Cp~C~~  610 (837)
                      ..-+||.|+.
T Consensus       642 ~~LkCs~Cn~  651 (698)
T KOG0978         642 ELLKCSVCNT  651 (698)
T ss_pred             HCEECCCCCC
T ss_conf             5102877667


No 224
>TIGR01993 Pyr-5-nucltdase pyrimidine 5'-nucleotidase; InterPro: IPR010237   This family of proteins includes the SDT1/SSM1 gene from yeast, which has been shown to code for a pyrimidine (UMP/CMP) 5'nucleotidase. The family spans plants, fungi and bacteria. These enzymes are members of the haloacid dehalogenase (HAD) superfamily of hydrolases, specifically the IA subfamily..
Probab=24.60  E-value=38  Score=12.62  Aligned_cols=43  Identities=14%  Similarity=0.390  Sum_probs=32.6

Q ss_pred             HHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHH-CCCC
Q ss_conf             79999988760888999999998762135567212245531-4755
Q gi|254780306|r  263 STLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITY-MRTD  307 (837)
Q Consensus       263 stLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITY-pRTD  307 (837)
                      ..+|.-..++||+|+.+.-.+-+.+|-.+..+  .+||+.- +-=|
T Consensus        24 ~~i~~F~~~~L~l~~eeA~~L~~~yY~~YG~t--l~GL~~~gh~i~   67 (205)
T TIGR01993        24 RNITEFVAAKLKLSEEEARKLRKDYYKEYGTT--LAGLMILGHEID   67 (205)
T ss_pred             HHHHHHHHHHCCCCHHHHHHHHHHHHHHHHHH--HHHHHHHCCCCC
T ss_conf             99999999870899889999999987857589--999998579978


No 225
>TIGR01384 TFS_arch transcription factor S; InterPro: IPR006288   DNA-directed RNA polymerases 2.7.7.6 from EC (also known as DNA-dependent RNA polymerases) are responsible for the polymerisation of ribonucleotides into a sequence complementary to the template DNA. In eukaryotes, there are three different forms of DNA-directed RNA polymerases transcribing different sets of genes. Most RNA polymerases are multimeric enzymes and are composed of a variable number of subunits. The core RNA polymerase complex consists of five subunits (two alpha, one beta, one beta-prime and one omega) and is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme . The core RNA polymerase complex forms a "crab claw"-like structure with an internal channel running along the full length . The key functional sites of the enzyme, as defined by mutational and cross-linking analysis, are located on the inner wall of this channel.   RNA synthesis follows after the attachment of RNA polymerase to a specific site, the promoter, on the template DNA strand. The RNA synthesis process continues until a termination sequence is reached. The RNA product, which is synthesised in the 5' to 3'direction, is known as the primary transcript. Eukaryotic nuclei contain three distinct types of RNA polymerases that differ in the RNA they synthesise:  RNA polymerase I: located in the nucleoli, synthesises precursors of most ribosomal RNAs. RNA polymerase II: occurs in the nucleoplasm, synthesises mRNA precursors.  RNA polymerase III: also occurs in the nucleoplasm, synthesises the precursors of 5S ribosomal RNA, the tRNAs, and a variety of other small nuclear and cytosolic RNAs.  Eukaryotic cells are also known to contain separate mitochondrial and chloroplast RNA polymerases. Eukaryotic RNA polymerases, whose molecular masses vary in size from 500 to 700 kD, contain two non-identical large (>100 kDa) subunits and an array of up to 12 different small (less than 50 kDa) subunits.   These sequences are the archaeal DNA-directed RNA polymerase, subunit M (also known as transcription factor S), a protein related in size and sequence to certain eukaryotic RNA polymerase small subunits, and in sequence and function to the much larger eukaryotic transcription factor IIS (TFIIS). Although originally suggested to be a subunit of the archaeal RNA polymerase, it elutes separately from active polymerase in gel filtration experiments and acts, like TFIIs, as an induction factor for RNA cleavage by RNA polymerase . ; GO: 0003677 DNA binding, 0003700 transcription factor activity, 0003899 DNA-directed RNA polymerase activity, 0006350 transcription.
Probab=24.46  E-value=27  Score=13.71  Aligned_cols=30  Identities=33%  Similarity=0.915  Sum_probs=14.1

Q ss_pred             CCCCCCCCEEEEEECCCC--CCCCCCCCCCCCCCCCCCC
Q ss_conf             334677731368715776--1112343432333210012
Q gi|254780306|r  605 CPECHTHSLSLKLSSKYG--AFVGCTNYPECKYTRQLTS  641 (837)
Q Consensus       605 Cp~C~~g~L~~k~~gK~G--~FigCSnyPeCk~t~~l~~  641 (837)
                      ||+||+-++=-|   +.|  .| -|.   .|.|=.+++.
T Consensus         3 CPKCgs~M~P~K---~~Gkn~~-~C~---~CGYE~~~T~   34 (111)
T TIGR01384         3 CPKCGSLMVPDK---KNGKNKY-KCR---KCGYEKEITK   34 (111)
T ss_pred             CCCCCCCCCCCC---CCCCCEE-ECC---CCCCCCCCCC
T ss_conf             786697158543---0695011-628---8887330466


No 226
>PRK10474 putative fructose-like phosphotransferase EIIB subunit 2; Provisional
Probab=24.39  E-value=38  Score=12.59  Aligned_cols=42  Identities=26%  Similarity=0.310  Sum_probs=28.8

Q ss_pred             HHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCC
Q ss_conf             998709989994699702579999999997551257887169999803798999999862264
Q gi|254780306|r   67 HAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRD  129 (837)
Q Consensus        67 ~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~  129 (837)
                      ..++.||.||+|.|-+-+++       +.+      ..+|+.++        .+.+|+.+|..
T Consensus        34 ~dI~~AD~VIiA~Dv~i~~~-------eRF------~gK~v~~~--------~v~~aI~~p~~   75 (88)
T PRK10474         34 EDVASADMVILTKDIGIKFE-------ERF------AGKTIVRV--------NISDAVKRADA   75 (88)
T ss_pred             HHHHHCCEEEEEECCCCCCH-------HHC------CCCEEEEE--------CHHHHHHCHHH
T ss_conf             99985999999843877822-------323------99857993--------48999879999


No 227
>COG1710 Uncharacterized protein conserved in archaea [Function unknown]
Probab=24.32  E-value=38  Score=12.59  Aligned_cols=11  Identities=27%  Similarity=0.492  Sum_probs=4.9

Q ss_pred             EEEECCCCCCH
Q ss_conf             89994699702
Q gi|254780306|r   74 ILILATDPDRE   84 (837)
Q Consensus        74 ~iilAtD~DRE   84 (837)
                      +|++-.-|+||
T Consensus        30 eiyinlr~tr~   40 (139)
T COG1710          30 EIYINLRPTRE   40 (139)
T ss_pred             EEEEEECCCHH
T ss_conf             27886045489


No 228
>pfam08063 PADR1 PADR1 (NUC008) domain. This domain is found in poly(ADP-ribose)-synthetases. The function of this domain is unknown.
Probab=24.21  E-value=33  Score=13.07  Aligned_cols=29  Identities=31%  Similarity=0.854  Sum_probs=17.2

Q ss_pred             EECCCCCCCCEEEEEECCCCCCCCCCCC----CCCCCC
Q ss_conf             1433467773136871577611123434----323332
Q gi|254780306|r  603 RTCPECHTHSLSLKLSSKYGAFVGCTNY----PECKYT  636 (837)
Q Consensus       603 ~~Cp~C~~g~L~~k~~gK~G~FigCSny----PeCk~t  636 (837)
                      ..||.|+++.+...  +. +  +.|++|    -.|.|+
T Consensus        15 ~~Cp~C~~~~~~~~--~~-~--Y~C~G~~sewtkC~~~   47 (55)
T pfam08063        15 GPCPTCSGGQLVFN--GD-A--YVCTGYISEWTKCTYS   47 (55)
T ss_pred             CCCCCCCCCEEEEC--CC-C--EEECCCCCCCCCCEEE
T ss_conf             87987899707888--97-2--5865357852112416


No 229
>PRK09464 pdhR transcriptional regulator PdhR; Reviewed
Probab=24.18  E-value=39  Score=12.57  Aligned_cols=25  Identities=16%  Similarity=0.384  Sum_probs=9.5

Q ss_pred             HHHCCCCCCCCHHHHHHHHHHCCEEE
Q ss_conf             32102566551578999997322022
Q gi|254780306|r  480 MEEIGIGRPSTYATILETLYKRKYVI  505 (837)
Q Consensus       480 mE~~GIGrPSTyA~II~~L~~R~YV~  505 (837)
                      ++..|++|++=| .=|..|...|+|+
T Consensus        41 A~~lgVSR~~VR-EAL~~L~~~GlV~   65 (254)
T PRK09464         41 AKQFDVSRPSLR-EAIQRLEAKGLLL   65 (254)
T ss_pred             HHHHCCCCHHHH-HHHHHHHHCCCEE
T ss_conf             998689955999-9999999889989


No 230
>TIGR01302 IMP_dehydrog inosine-5'-monophosphate dehydrogenase; InterPro: IPR005990    Synonyms: Inosine-5'-monophosphate dehydrogenase, Inosinic acid dehydrogenase     IMP dehydrogenase (1.1.1.205 from EC,IMPDH) catalyzes the rate-limiting reaction of de novo GTP biosynthesis, the NAD-dependent reduction of IMP into XMP .  Inosine 5-phosphate + NAD+ + H2O = xanthosine 5-phosphate + NADH     IMP dehydrogenase is associated with cell proliferation and is a possible target for cancer chemotherapy. Mammalian and bacterial IMPDHs are tetramers of identical chains. There are two IMP dehydrogenase isozymes in humans . IMP dehydrogenase nearly always contains a long insertion that has two CBS domains within it and adopts a TIM barrel structure.; GO: 0003938 IMP dehydrogenase activity, 0006177 GMP biosynthetic process.
Probab=24.17  E-value=39  Score=12.57  Aligned_cols=20  Identities=20%  Similarity=0.150  Sum_probs=9.8

Q ss_pred             HCCCHHHHHHHHHHHHCCCC
Q ss_conf             08889999999987621355
Q gi|254780306|r  273 LGFSASHTMRIAQKLYEGID  292 (837)
Q Consensus       273 lg~sa~~Tm~iAQ~LYE~~~  292 (837)
                      +=++|..|..-+.+|=|.+.
T Consensus        93 ~t~~P~~tv~~~~~l~~~~g  112 (476)
T TIGR01302        93 VTISPETTVEDVLELMERKG  112 (476)
T ss_pred             EEECCCCHHHHHHHHCCCCC
T ss_conf             68479851899997322157


No 231
>PRK01792 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=24.09  E-value=39  Score=12.56  Aligned_cols=53  Identities=25%  Similarity=0.386  Sum_probs=34.6

Q ss_pred             CHHHHHHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCC
Q ss_conf             548999999999870998999469970257999999999755125788716999980379899999986226
Q gi|254780306|r   57 SSQKHLQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPR  128 (837)
Q Consensus        57 ~~kk~~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r  128 (837)
                      .+.+.|+.-.+.++.-.-|++--|.|||+|.      +++             +.-.-+|++.|.-.+.+-+
T Consensus        11 ~~~~~V~~Ai~alr~G~~Viv~Dd~dREnEg------Dlv-------------~aAe~~T~e~i~fm~~~~~   63 (214)
T PRK01792         11 TSEERVINAINAFKQGNGVLVLDDEDRENEG------DLI-------------FPAETITPEQMAKLIRYGS   63 (214)
T ss_pred             CHHHHHHHHHHHHHCCCEEEEEECCCCCCCC------CEE-------------EEHHHCCHHHHHHHHHHCC
T ss_conf             9788999999999879969998289987640------679-------------6855499999999999589


No 232
>TIGR01828 pyru_phos_dikin pyruvate, phosphate dikinase; InterPro: IPR010121   Pyruvate phosphate dikinase (PPDK, or pyruvate orthophosphate dikinase) is found in plants, bacteria and archaea. The amino acid sequence identity between bacterial and plant enzymes is high, and they are similar in sequence to other PEP-utilizing enzymes. PPDK catalyses the reversible conversion of ATP and pyruvate to AMP and PEP (phosphoenolpyruvate). In bacteria such as Clostridium symbiosum, PPDK uses Mg2+ and NH4+ ions as cofactors . The enzyme has three domains: the N- and C-terminal domains each have an active site centre that catalyses a different step in the reaction, and the middle domain has a carrier histidine residue that moves between the two active centres.   In plants, PPDK is localised predominantly in chloroplast stroma where it catalyses the rate-limiting step in the C4 photosynthetic pathway, namely the synthesis of PEP, which acts as the primary CO2 acceptor in C4 photosynthesis . PPDK activity in C4 plants is strictly regulated by light, its activity decreasing in darkness. This response is regulated by phosphorylation and dephosphorylation of the enzyme using ADP; such regulation is not seen in the bacterial form of the enzyme. PPDK is also found in C3 plants, but it is not known to have a photosynthetic role .; GO: 0050242 pyruvate phosphate dikinase activity.
Probab=23.64  E-value=34  Score=13.03  Aligned_cols=40  Identities=30%  Similarity=0.401  Sum_probs=30.1

Q ss_pred             CCCHHHHHHHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHH----HCCCCCCCCC
Q ss_conf             21037999998876088899999999876213556721224553----1475544443
Q gi|254780306|r  259 AFTTSTLQQVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLIT----YMRTDGVHMS  312 (837)
Q Consensus       259 Pf~tstLQq~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlIT----YpRTDS~~ls  312 (837)
                      +|.   ||-...   +-||+-+.+||=.|++        .|+||    =||=+...|.
T Consensus       354 LYm---LQTR~G---KRTA~AA~rIAvDmv~--------Eg~It~eeA~~Rv~p~~ld  397 (920)
T TIGR01828       354 LYM---LQTRNG---KRTAKAAVRIAVDMVK--------EGLITKEEAIMRVEPESLD  397 (920)
T ss_pred             EEE---EECCCC---CCCHHHHHHHHHHHHH--------CCCCCHHHHHHCCCHHHHH
T ss_conf             013---335552---2355889999999873--------5887757864215747875


No 233
>cd01943 MAK32 MAK32 kinase.  MAK32 is a protein found primarily in fungi that is necessary for the structural stability of L-A particles.  The L-A virus particule is a specialized compartment for the transcription and replication of double-stranded RNA, known to infect yeast and other fungi.  MAK32 is part of the host machinery used by the virus to multiply.
Probab=23.63  E-value=39  Score=12.49  Aligned_cols=12  Identities=58%  Similarity=1.104  Sum_probs=4.3

Q ss_pred             EEEEECCCCCEE
Q ss_conf             999826974227
Q gi|254780306|r  665 VTLRSGRFGLYV  676 (837)
Q Consensus       665 I~lk~GryGpYv  676 (837)
                      |++|.|.+|.++
T Consensus       228 vVIK~G~~Ga~~  239 (328)
T cd01943         228 VVLRCGKLGCYV  239 (328)
T ss_pred             EEEEECCCCEEE
T ss_conf             999617875599


No 234
>COG3120 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.57  E-value=40  Score=12.49  Aligned_cols=12  Identities=42%  Similarity=0.548  Sum_probs=9.2

Q ss_pred             CCHHHHHHHHHH
Q ss_conf             702579999999
Q gi|254780306|r   82 DREGEAISWHVL   93 (837)
Q Consensus        82 DREGE~Iawhi~   93 (837)
                      -||||+|-.++-
T Consensus        22 hreGE~iTRyie   33 (149)
T COG3120          22 HREGELITRYIE   33 (149)
T ss_pred             HCCCCHHHHHHH
T ss_conf             305541599999


No 235
>PHA00626 hypothetical protein
Probab=23.56  E-value=29  Score=13.52  Aligned_cols=13  Identities=23%  Similarity=0.920  Sum_probs=10.2

Q ss_pred             ECCCCCCCCEEEE
Q ss_conf             4334677731368
Q gi|254780306|r  604 TCPECHTHSLSLK  616 (837)
Q Consensus       604 ~Cp~C~~g~L~~k  616 (837)
                      .||+|+.|.+-..
T Consensus         2 scpkcgsgniake   14 (59)
T PHA00626          2 SCPKCGSGNIAKE   14 (59)
T ss_pred             CCCCCCCCCHHHH
T ss_conf             8875688641244


No 236
>PRK00135 scpB segregation and condensation protein B; Reviewed
Probab=23.54  E-value=40  Score=12.48  Aligned_cols=21  Identities=29%  Similarity=0.414  Sum_probs=17.0

Q ss_pred             HHHHHHHHCCEEECCCCCEEE
Q ss_conf             899999732202214771222
Q gi|254780306|r  493 TILETLYKRKYVIAEKRKILP  513 (837)
Q Consensus       493 ~II~~L~~R~YV~~~~~~l~p  513 (837)
                      .+|.+|.+||.|...|++=.|
T Consensus       113 ~~i~~LlergLI~~~Gr~~~~  133 (182)
T PRK00135        113 GALQTLLAKGLIKEAGRKEVP  133 (182)
T ss_pred             HHHHHHHHCCCEEECCCCCCC
T ss_conf             999999986995887606999


No 237
>pfam04864 Alliinase_C Allinase. Allicin is a thiosulphinate that gives rise to dithiines, allyl sulphides and ajoenes, the three groups of active compounds in Allium species. Allicin is synthesized from sulfoxide cysteine derivatives by alliinase (EC:4.4.1.4), whose C-S lyase activity cleaves C(beta)-S(gamma) bonds. It is thought that this enzyme forms part of a primitive plant defence system.
Probab=23.53  E-value=18  Score=14.98  Aligned_cols=28  Identities=32%  Similarity=0.489  Sum_probs=9.9

Q ss_pred             CCHHHHHHHHHHHHCCCHHHHHHHHHHH
Q ss_conf             1037999998876088899999999876
Q gi|254780306|r  260 FTTSTLQQVASSRLGFSASHTMRIAQKL  287 (837)
Q Consensus       260 f~tstLQq~As~~lg~sa~~Tm~iAQ~L  287 (837)
                      |++|-+--.|..|+||-.-+--.+||++
T Consensus       190 FTlSK~TGHAGsRiGWALVKD~~VakkM  217 (363)
T pfam04864       190 FTMSKYTGHAGSRFGWALVKDEEVAKKM  217 (363)
T ss_pred             EEECCCCCCCCCCEEEEEECCHHHHHHH
T ss_conf             9861223676252347886379999999


No 238
>pfam04475 DUF555 Protein of unknown function (DUF555). Family of uncharacterized, hypothetical archaeal proteins.
Probab=23.52  E-value=40  Score=12.48  Aligned_cols=39  Identities=31%  Similarity=0.466  Sum_probs=17.6

Q ss_pred             HHHHHHHHHHHHHHHHHHHHHHCCCCCCCCCCCCEECCCCCCCC
Q ss_conf             57667755666776556766410245555676611433467773
Q gi|254780306|r  569 IDSIKKLRISNVLDILNDTLSSVIFPPKENNEDSRTCPECHTHS  612 (837)
Q Consensus       569 i~~~~~~~~~~v~d~l~~~~~~~~~~~~~~~~~~~~Cp~C~~g~  612 (837)
                      +++.....+.+....++..+.   |-  +.......||.|+...
T Consensus        19 ~dDAI~iAIseaGkrLn~~l~---~V--eIevG~~~cP~Cge~~   57 (102)
T pfam04475        19 VDDAIGVAISEAGKRLNPKLD---FV--EIEVGSTACPKCGEEL   57 (102)
T ss_pred             HHHHHHHHHHHHHHHHCCCCC---EE--EEECCCCCCCCCCCCC
T ss_conf             788999999999886498988---79--9825751088767866


No 239
>COG1799 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=23.46  E-value=40  Score=12.47  Aligned_cols=30  Identities=27%  Similarity=0.598  Sum_probs=13.2

Q ss_pred             HHHHHHCCCCCCHHH--HHHHHHHHHHHHHHH
Q ss_conf             999986226469899--999999999898740
Q gi|254780306|r  120 VLNAMKSPRDINLDL--VNAYLARRALDYLVG  149 (837)
Q Consensus       120 I~~A~~n~r~~d~~L--v~A~~aRr~lD~lvG  149 (837)
                      |-..|.+-+-+-.||  .+-.+|||++|+|-|
T Consensus        90 ia~~lk~~k~Vvinl~~m~~~qArRivDFlaG  121 (167)
T COG1799          90 IADYLKNRKAVVINLQRMDPAQARRIVDFLAG  121 (167)
T ss_pred             HHHHHHCCCEEEEEEEECCHHHHHHHHHHHCC
T ss_conf             99998459649987031898998899988600


No 240
>PRK02888 nitrous-oxide reductase; Validated
Probab=23.39  E-value=40  Score=12.46  Aligned_cols=36  Identities=17%  Similarity=0.300  Sum_probs=19.3

Q ss_pred             CCCHHHHHHHHHHHHCCCHHHHHHHHHH-HHCCCCCCCHHHHHHHHCCCCCCC
Q ss_conf             2103799999887608889999999987-621355672122455314755444
Q gi|254780306|r  259 AFTTSTLQQVASSRLGFSASHTMRIAQK-LYEGIDVNGEIVGLITYMRTDGVH  310 (837)
Q Consensus       259 Pf~tstLQq~As~~lg~sa~~Tm~iAQ~-LYE~~~~~~~~~GlITYpRTDS~~  310 (837)
                      -|+.     ++..-|||+- +++++... +..          .-.|+--|+-|
T Consensus       100 VF~~-----~~~~GwG~t~-ESk~vL~~~~~~----------~~~~~wGDtHH  136 (637)
T PRK02888        100 VFNR-----DSATGWGITN-ESKKVLGEGLLP----------QGKYLNGDLHH  136 (637)
T ss_pred             EECC-----CCCCCCCCCH-HHHHHHHCCCCC----------CCCCCCCCCCC
T ss_conf             2457-----8653557765-578886266556----------76403687578


No 241
>COG0108 RibB 3,4-dihydroxy-2-butanone 4-phosphate synthase [Coenzyme metabolism]
Probab=23.39  E-value=40  Score=12.46  Aligned_cols=27  Identities=30%  Similarity=0.543  Sum_probs=21.4

Q ss_pred             HHHHHHHHHHHCCEEEECCCCCCHHHH
Q ss_conf             999999998709989994699702579
Q gi|254780306|r   61 HLQNIIHAVKSSTILILATDPDREGEA   87 (837)
Q Consensus        61 ~~~~i~~~~k~a~~iilAtD~DREGE~   87 (837)
                      .+......++.-.-|++--|.|||+|.
T Consensus         5 ~ie~ai~al~~G~~Viv~DdedREnEg   31 (203)
T COG0108           5 RVEEAIEALRAGKPVIVVDDEDRENEG   31 (203)
T ss_pred             HHHHHHHHHHCCCEEEEECCCCCCCCC
T ss_conf             299999999879869997388877860


No 242
>cd04728 ThiG Thiazole synthase (ThiG) is the tetrameric enzyme that is involved in the formation of the thiazole moiety of thiamin pyrophosphate, an essential ubiquitous cofactor that plays an important role in carbohydrate and amino acid metabolism. ThiG catalyzes the formation of thiazole from 1-deoxy-D-xylulose 5-phosphate (DXP) and dehydroglycine, with the help of the sulfur carrier protein ThiS that carries the sulfur needed for thiazole assembly on its carboxy terminus (ThiS-COSH).
Probab=23.29  E-value=26  Score=13.86  Aligned_cols=27  Identities=11%  Similarity=0.105  Sum_probs=11.4

Q ss_pred             CCEEEEEEEEECCEEECCCCHHHHHHHHHHHHH
Q ss_conf             965422331035833033101135666777642
Q gi|254780306|r  204 NDKFTAHLTDFNGQRIEKKSISNKKEADDLISF  236 (837)
Q Consensus       204 ~~~f~a~l~~~~~~~~~~~~~~~~~~a~~~~~~  236 (837)
                      +..|..+|.-      ..+++.|.+...+.++.
T Consensus         5 g~~f~SRLil------GTgky~s~~~~~~ai~a   31 (248)
T cd04728           5 GKTFSSRLLL------GTGKYPSPAIMKEAIEA   31 (248)
T ss_pred             CEEEECCEEE------ECCCCCCHHHHHHHHHH
T ss_conf             9887743378------64899999999999999


No 243
>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=23.07  E-value=14  Score=15.97  Aligned_cols=97  Identities=21%  Similarity=0.376  Sum_probs=48.5

Q ss_pred             CCCCCCCCCCCCCCCCCCCCCC--CCC--CCCCCCCCCCCCCCCEEEEEEC--CCCCEEEECCCCCCCCCCCCCCCCHHH
Q ss_conf             1123434323332100122100--001--2344201468999966999826--974227734887776133789988425
Q gi|254780306|r  624 FVGCTNYPECKYTRQLTSNPQD--IPE--MKESVLLGNDLETKESVTLRSG--RFGLYVQRGDGKDAKRCSLPKTWKSDS  697 (837)
Q Consensus       624 FigCSnyPeCk~t~~l~~~~~~--~~~--~~~~~~LG~dP~~G~~I~lk~G--ryGpYvq~Ge~~kpkr~si~k~~~~~~  697 (837)
                      =++|-.+|.|--.    --+++  ++.  .+-++++-+|--..+.|++|..  |.|          .-|+.|      .+
T Consensus       423 smaCValPTCpLA----MAEAER~LP~Fi~~~~~i~~k~Gl~~~~I~~R~tGCPNG----------C~R~~L------AE  482 (550)
T TIGR02041       423 SMACVALPTCPLA----MAEAERYLPDFIDKLDNIMEKHGLADEEIVLRITGCPNG----------CGRPYL------AE  482 (550)
T ss_pred             CCCEECCCCCHHH----HHHHHHHHHHHHHHHHHHHHHCCCCCCEEEEEECCCCCH----------HHHHHH------HH
T ss_conf             7744446775236----999974558999999999996088876078985279863----------257768------77


Q ss_pred             CCHHHHHHHHHCCHHHCCCCCCCCEEEEEECCCCCEEEECCEECCCCCCCCCCCCCHHHHHHHHHH
Q ss_conf             489999998615255157778987499911587652616781112488775143579999999983
Q gi|254780306|r  698 VDYDKAMSLLSLPREIGIHPETQKNIIAGTGKYGYYLNHDGAYTKLESIEQVLTIDLEQAISCITE  763 (837)
Q Consensus       698 itle~Al~LLsLPr~lG~~pe~g~~I~~~~GryGpYi~~~~~~~sl~~~~~~~~I~l~~Aieli~~  763 (837)
                      |            =-||+          ..|||--||-=+..-..|++--. .+||..+-+.-|.+
T Consensus       483 i------------gLvGK----------apGRYNL~lGG~~~G~Rl~~lYr-ENitE~eIL~~L~~  525 (550)
T TIGR02041       483 I------------GLVGK----------APGRYNLYLGGNRRGSRLPRLYR-ENITEEEILAELDE  525 (550)
T ss_pred             H------------HHHCC----------CCCCHHHHCCCCCCCCCCHHHHH-CCCCHHHHHHHHHH
T ss_conf             4------------33326----------64401000167878862313432-06898899999999


No 244
>COG4904 Uncharacterized protein conserved in archaea [Function unknown]
Probab=23.03  E-value=40  Score=12.41  Aligned_cols=69  Identities=22%  Similarity=0.434  Sum_probs=27.7

Q ss_pred             CCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHHHHHHHHHH-------HHHCCCHHHHHH
Q ss_conf             5665515789999973220221477122201142000022336655689889999999999-------986260134789
Q gi|254780306|r  485 IGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFTADLEEKLD-------EISTGKLNWKEV  557 (837)
Q Consensus       485 IGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fTa~~E~~ld-------~Ia~G~~~~~~~  557 (837)
                      +|||.-|+++-.-+         ..-|.+..+|.-.-+.|++. |. +|.+.++.+-..+.       .-..-+.-|..+
T Consensus         3 ~~r~~fyl~vs~If---------~~ll~~~a~g~D~~~~ld~~-~~-~d~~l~~~l~~evr~~~~~kDl~k~~~~v~~k~   71 (174)
T COG4904           3 NLRPTFYLGVSNIF---------SALLLSKATGDDIDDGLDDI-PP-ADEKLVAELKEEVRSLSCRKDLTKAAKLVWRKT   71 (174)
T ss_pred             CCCHHHHHHHHHHH---------HHHCCHHHCCCCHHHHHHCC-CC-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_conf             76048999999999---------98726030375155663037-71-106799999999976587732579999999999


Q ss_pred             HHHHHHH
Q ss_conf             9998676
Q gi|254780306|r  558 LHEFWEE  564 (837)
Q Consensus       558 L~~Fy~~  564 (837)
                      |++||+.
T Consensus        72 ~~~FYEn   78 (174)
T COG4904          72 VEAFYEN   78 (174)
T ss_pred             HHHHHHH
T ss_conf             9999997


No 245
>PRK05773 3,4-dihydroxy-2-butanone 4-phosphate synthase; Validated
Probab=22.96  E-value=41  Score=12.40  Aligned_cols=49  Identities=18%  Similarity=0.228  Sum_probs=31.0

Q ss_pred             HHHHHHHHHHCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCC
Q ss_conf             99999998709989994699702579999999997551257887169999803798999999862264
Q gi|254780306|r   62 LQNIIHAVKSSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRD  129 (837)
Q Consensus        62 ~~~i~~~~k~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~  129 (837)
                      |++..+.+++-.-|++--|.|||+|.      +++             +.-.-+|++.|.--+.+.+-
T Consensus         4 Ie~ai~alr~G~~Viv~DdedREnEg------Dlv-------------~aAe~vtpe~i~fm~r~a~G   52 (218)
T PRK05773          4 IEEARKALRQGRPVLIYDGDGREEEV------DMV-------------FYAGAVTWKSVYWLRKNAGG   52 (218)
T ss_pred             HHHHHHHHHCCCEEEEEECCCCCCCC------CEE-------------EEHHHCCHHHHHHHHHHCCC
T ss_conf             89999999879969998489987760------668-------------67654999999999980897


No 246
>PRK11122 artM arginine transporter permease subunit ArtM; Provisional
Probab=22.82  E-value=41  Score=12.38  Aligned_cols=23  Identities=30%  Similarity=0.286  Sum_probs=19.2

Q ss_pred             HHHHHHHHHCCCHHHHHHHH--HHH
Q ss_conf             99998876088899999999--876
Q gi|254780306|r  265 LQQVASSRLGFSASHTMRIA--QKL  287 (837)
Q Consensus       265 LQq~As~~lg~sa~~Tm~iA--Q~L  287 (837)
                      =|.||++-+|||..++|+|-  |-+
T Consensus       120 GQ~EAA~slGls~~q~~rIilPQa~  144 (222)
T PRK11122        120 GQWQSCSALGMSKKQTLAILLPYAF  144 (222)
T ss_pred             HHHHHHHHCCCCHHHHHHHHHHHHH
T ss_conf             7999999869899999998999999


No 247
>cd02750 MopB_Nitrate-R-NarG-like Respiratory nitrate reductase A (NarGHI), alpha chain (NarG) and related proteins. Under anaerobic conditions in the presence of nitrate, E. coli synthesizes the cytoplasmic membrane-bound quinol-nitrate oxidoreductase (NarGHI), which reduces nitrate to nitrite and forms part of a redox loop generating a proton-motive force. Found in prokaryotes and some archaea, NarGHI usually functions as a heterotrimer. The alpha chain contains the molybdenum cofactor-containing Mo-bisMGD catalytic subunit. Members of the MopB_Nitrate-R-NarG-like CD belong to the molybdopterin_binding (MopB) superfamily of proteins.
Probab=22.63  E-value=29  Score=13.49  Aligned_cols=11  Identities=18%  Similarity=0.241  Sum_probs=4.8

Q ss_pred             HHHHHHHHHHC
Q ss_conf             99999987621
Q gi|254780306|r  279 HTMRIAQKLYE  289 (837)
Q Consensus       279 ~Tm~iAQ~LYE  289 (837)
                      +-+...|.+|-
T Consensus        53 KG~~~~~~~y~   63 (461)
T cd02750          53 RGASFSWYLYS   63 (461)
T ss_pred             CHHHHHHHHCC
T ss_conf             73442876459


No 248
>KOG3347 consensus
Probab=22.51  E-value=37  Score=12.71  Aligned_cols=16  Identities=13%  Similarity=0.214  Sum_probs=6.3

Q ss_pred             HHHHHHHHHHHHHCCC
Q ss_conf             9999999999986260
Q gi|254780306|r  536 FTADLEEKLDEISTGK  551 (837)
Q Consensus       536 fTa~~E~~ld~Ia~G~  551 (837)
                      .+..|+..++.|-++.
T Consensus       152 ~~Eem~~ni~ri~~w~  167 (176)
T KOG3347         152 TKEEMESNISRILNWT  167 (176)
T ss_pred             CHHHHHHHHHHHHHHH
T ss_conf             7899999899999999


No 249
>PRK06582 coproporphyrinogen III oxidase; Provisional
Probab=22.43  E-value=42  Score=12.33  Aligned_cols=32  Identities=9%  Similarity=0.248  Sum_probs=25.6

Q ss_pred             HHHHHHHHHCCEEECCCCCEEECCHHHHHCCCC
Q ss_conf             789999973220221477122201142000022
Q gi|254780306|r  492 ATILETLYKRKYVIAEKRKILPQNTGRIVTAFL  524 (837)
Q Consensus       492 A~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L  524 (837)
                      ...++.+.+.|+|+.++ ++..|+.|+.+.+.+
T Consensus       353 ~~~l~~l~~~gLi~~d~-~i~LT~kG~ll~n~I  384 (390)
T PRK06582        353 MNNLKHYQALDLIRLDE-NIYLTDKGLMLHSYI  384 (390)
T ss_pred             HHHHHHHHHCCCEEECC-EEEECHHHHHHHHHH
T ss_conf             89999999797989899-899996688899999


No 250
>KOG1643 consensus
Probab=22.19  E-value=42  Score=12.30  Aligned_cols=26  Identities=15%  Similarity=0.157  Sum_probs=14.9

Q ss_pred             HHHHHHHHHHHHHHHHHHEECCCEEEE
Q ss_conf             999999999999852221100100136
Q gi|254780306|r  375 QLYNLIWKRSVASQMASAKFERTTVNI  401 (837)
Q Consensus       375 klY~LI~~R~lasqm~~a~~~~~~v~i  401 (837)
                      -+-.-| |+++++-..++.-..+.|..
T Consensus       182 EVh~~i-R~wl~~~vs~~Va~~~RIiY  207 (247)
T KOG1643         182 EVHAEI-RKWLKSNVSDAVASSTRIIY  207 (247)
T ss_pred             HHHHHH-HHHHHHCCHHHHHHCEEEEE
T ss_conf             999999-99986311166653337896


No 251
>PRK09508 leuO leucine transcriptional activator; Reviewed
Probab=22.17  E-value=37  Score=12.68  Aligned_cols=47  Identities=17%  Similarity=0.386  Sum_probs=17.9

Q ss_pred             HHHHHHHHHHCCCCCCCCHHHHHHHHH---HCCEEECCCCCEEECCHHHHH
Q ss_conf             899874332102566551578999997---322022147712220114200
Q gi|254780306|r  473 ESSLIKKMEEIGIGRPSTYATILETLY---KRKYVIAEKRKILPQNTGRIV  520 (837)
Q Consensus       473 EasLik~mE~~GIGrPSTyA~II~~L~---~R~YV~~~~~~l~pT~~G~~v  520 (837)
                      +.|.-++-|.+|+--|| -+.-|..|.   +-.-..+.++.+.||+.|..+
T Consensus        36 ~~svtrAA~~L~vSQpA-vS~aL~rLr~~~gd~LFvR~grg~~pT~~a~~L   85 (314)
T PRK09508         36 EQNITRAAHNLGMSQPA-VSNAVARLKVMFNDELFVRYGRGIQPTARARQL   85 (314)
T ss_pred             CCCHHHHHHHHCCCHHH-HHHHHHHHHHHHCCEEEEECCCCEEHHHHHHHH
T ss_conf             29999999997898669-999999999981995488349935429989999


No 252
>PRK13532 nitrate reductase; Provisional
Probab=22.10  E-value=39  Score=12.53  Aligned_cols=21  Identities=24%  Similarity=0.363  Sum_probs=15.0

Q ss_pred             HHHHHHCCCHHHHHHHHHHHHC
Q ss_conf             9887608889999999987621
Q gi|254780306|r  268 VASSRLGFSASHTMRIAQKLYE  289 (837)
Q Consensus       268 ~As~~lg~sa~~Tm~iAQ~LYE  289 (837)
                      .|+..-|.++...-++| ++|-
T Consensus       340 ~aa~itGvp~e~I~~~A-~~~a  360 (828)
T PRK13532        340 KTAKMSGVPKEQLEQLA-KLYA  360 (828)
T ss_pred             HHHHHHCCCHHHHHHHH-HHHH
T ss_conf             99998794999999999-9984


No 253
>pfam03833 PolC_DP2 DNA polymerase II large subunit DP2.
Probab=22.03  E-value=42  Score=12.27  Aligned_cols=41  Identities=22%  Similarity=0.234  Sum_probs=26.7

Q ss_pred             CCCCCCCCCEEEECCCCCCCCCCCCCHHHHHHHHHHCCCCC
Q ss_conf             45688211001101112346431017899874332102566
Q gi|254780306|r  447 ISANEQLIATETNASQHFTEPPPRYSESSLIKKMEEIGIGR  487 (837)
Q Consensus       447 l~~g~~~~~~~~~~~~~~TkPP~rytEasLik~mE~~GIGr  487 (837)
                      +-.||.|.--.=-++...+-.|+-|++-=-++.|++.|.+.
T Consensus       395 ~~lGeili~~Gdf~enn~~l~p~~y~~eww~qel~~a~~~~  435 (852)
T pfam03833       395 LDLGEILIAYGDFLENNHPLLPASYCEEWWIQELPAALKGN  435 (852)
T ss_pred             EECCCEEEECHHHHHCCCCCCCCCCCHHHHHHHHHHHCCCC
T ss_conf             87576765002575379868888667899999998602467


No 254
>PRK10816 DNA-binding transcriptional regulator PhoP; Provisional
Probab=22.02  E-value=42  Score=12.27  Aligned_cols=29  Identities=21%  Similarity=0.226  Sum_probs=23.2

Q ss_pred             CCEEEEC-CHHHHHHHHHHHC-CCCEEEEEE
Q ss_conf             9189977-9047877887508-998999942
Q gi|254780306|r    1 MNVIIVE-SPAKAKTISKYLG-SNYKVLSSF   29 (837)
Q Consensus         1 M~LvIvE-sP~kak~I~~~Lg-~~y~V~as~   29 (837)
                      |+.+||| -++-+..|..+|. .+|.|.++.
T Consensus         1 mkILivEdd~~~~~~l~~~L~~~g~~V~~a~   31 (223)
T PRK10816          1 MRVLVVEDNALLRHHLKVQLQDAGHQVDAAE   31 (223)
T ss_pred             CEEEEEECCHHHHHHHHHHHHHCCCEEEEEC
T ss_conf             9899995989999999999997899999989


No 255
>PRK09954 hypothetical protein; Provisional
Probab=21.90  E-value=42  Score=12.25  Aligned_cols=23  Identities=22%  Similarity=0.108  Sum_probs=12.9

Q ss_pred             HHHHHHHHCCCHHHHHHHHHHHH
Q ss_conf             99988760888999999998762
Q gi|254780306|r  266 QQVASSRLGFSASHTMRIAQKLY  288 (837)
Q Consensus       266 Qq~As~~lg~sa~~Tm~iAQ~LY  288 (837)
                      |||-..+||.|=.-+-..--.|-
T Consensus        20 q~ela~~lgisrs~va~hi~~l~   42 (362)
T PRK09954         20 QNEIADILQISRSRVAAHIMDLM   42 (362)
T ss_pred             HHHHHHHHCCCHHHHHHHHHHHH
T ss_conf             99999997987999999999887


No 256
>PRK09249 coproporphyrinogen III oxidase; Provisional
Probab=21.81  E-value=28  Score=13.56  Aligned_cols=44  Identities=23%  Similarity=0.256  Sum_probs=30.1

Q ss_pred             CCCCCCCCHHHH---HHHHHHCCEEECCCCCEEECCHHHHHCCCCCC
Q ss_conf             025665515789---99997322022147712220114200002233
Q gi|254780306|r  483 IGIGRPSTYATI---LETLYKRKYVIAEKRKILPQNTGRIVTAFLEN  526 (837)
Q Consensus       483 ~GIGrPSTyA~I---I~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~  526 (837)
                      .||--..-++..   ++.+.++|.|+.++..|..|+.|+.+.+.+-.
T Consensus       392 ~g~~~~~~f~~~~~~L~~l~~~GLl~~~~~~l~lT~~Gr~l~r~Ia~  438 (456)
T PRK09249        392 FGIDFAEYFAEELELLAPLEDDGLVELDEDGITVTPTGRLLVRNIAM  438 (456)
T ss_pred             HCCCHHHHHHHHHHHHHHHHHCCCEEEECCEEEECHHHHHHHHHHHH
T ss_conf             69899999999999999999799899989999999406799999999


No 257
>TIGR02315 ABC_phnC phosphonate ABC transporter, ATP-binding protein; InterPro: IPR012693   ABC transporters belong to the ATP-Binding Cassette (ABC) superfamily, which uses the hydrolysis of ATP to energize diverse biological systems. ABC transporters are minimally constituted of two conserved regions: a highly conserved ATP binding cassette (ABC) and a less conserved transmembrane domain (TMD). These regions can be found on the same protein or on two different ones. Most ABC transporters function as a dimer and therefore are constituted of four domains, two ABC modules and two TMDs.   ABC transporters are involved in the export or import of a wide variety of substrates ranging from small ions to macromolecules. The major function of ABC import systems is to provide essential nutrients to bacteria. They are found only in prokaryotes and their four constitutive domains are usually encoded by independent polypeptides (two ABC proteins and two TMD proteins). Prokaryotic importers require additional extracytoplasmic binding proteins (one or more per systems) for function. In contrast, export systems are involved in the extrusion of noxious substances, the export of extracellular toxins and the targeting of membrane components. They are found in all living organisms and in general the TMD is fused to the ABC module in a variety of combinations. Some eukaryotic exporters encode the four domains on the same polypeptide chain .    The ABC module (approximately two hundred amino acid residues) is known to bind and hydrolyze ATP, thereby coupling transport to ATP hydrolysis in a large number of biological processes. The cassette is duplicated in several subfamilies. Its primary sequence is highly conserved, displaying a typical phosphate-binding loop: Walker A, and a magnesium binding site: Walker B. Besides these two regions, three other conserved motifs are present in the ABC cassette: the switch region which contains a histidine loop, postulated to polarize the attaching water molecule for hydrolysis, the signature conserved motif (LSGGQ) specific to the ABC transporter, and the Q-motif (between Walker A and the signature), which interacts with the gamma phosphate through a water bond. The Walker A, Walker B, Q-loop and switch region form the nucleotide binding site , , .   The 3D structure of a monomeric ABC module adopts a stubby L-shape with two distinct arms. ArmI (mainly beta-strand) contains Walker A and Walker B. The important residues for ATP hydrolysis and/or binding are located in the P-loop. The ATP-binding pocket is located at the extremity of armI. The perpendicular armII contains mostly the alpha helical subdomain with the signature motif. It only seems to be required for structural integrity of the ABC module. ArmII is in direct contact with the TMD. The hinge between armI and armII contains both the histidine loop and the Q-loop, making contact with the gamma phosphate of the ATP molecule. ATP hydrolysis leads to a conformational change that could facilitate ADP release. In the dimer the two ABC cassettes contact each other through hydrophobic interactions at the antiparallel beta-sheet of armI by a two-fold axis , , , , , .   Proteins known to belong to this family are classified in several functional subfamilies depending on the substrate used (for further information see http://www.tcdb.org/tcdb/index.php?tc=3.A.1).     Phosphonates are a class of phosphorus-containing organic compound with a stable direct C-P bond rather than a C-O-P linkage. A number of bacterial species have operons, typically about 14 genes in size, with genes for ATP-dependent transport of phosphonates, degradation, and regulation of the expression of the system. Members of this protein family are the ATP-binding cassette component of tripartite ABC transporters of phosphonates.; GO: 0005524 ATP binding, 0015416 phosphonate transmembrane-transporting ATPase activity, 0015716 phosphonate transport, 0016020 membrane.
Probab=21.80  E-value=43  Score=12.24  Aligned_cols=29  Identities=10%  Similarity=0.060  Sum_probs=16.1

Q ss_pred             CCCEEEEEEECCCHHHHHHHHHCCCCCCH
Q ss_conf             87169999803798999999862264698
Q gi|254780306|r  104 KTKIQRVSFNAITKQVVLNAMKSPRDINL  132 (837)
Q Consensus       104 ~~~v~R~~f~eiT~~aI~~A~~n~r~~d~  132 (837)
                      .++.=|.+|.-.+++.-.+||+.+..++.
T Consensus       117 ~~~~~~~~~~~F~~~dk~~Al~~L~rVGl  145 (253)
T TIGR02315       117 YKSTWRSLLGRFSEEDKERALSLLERVGL  145 (253)
T ss_pred             CCHHHHHHHCCCCHHHHHHHHHHHHHCCH
T ss_conf             45034556325899899999987652387


No 258
>cd04157 Arl6 Arl6 subfamily.  Arl6 (Arf-like 6) forms a subfamily of the Arf family of small GTPases.  Arl6 expression is limited to the brain and kidney in adult mice, but it is expressed in the neural plate and somites during embryogenesis, suggesting a possible role for Arl6 in early development.  Arl6 is also believed to have a role in cilia or flagella function.  Several proteins have been identified that bind Arl6, including Arl6 interacting protein (Arl6ip), and SEC61beta, a subunit of the heterotrimeric conducting channel SEC61p.  Based on Arl6 binding to these effectors, Arl6 is also proposed to play a role in protein transport, membrane trafficking, or cell signaling during hematopoietic maturation.  At least three specific homozygous Arl6 mutations in humans have been found to cause Bardet-Biedl syndrome, a disorder characterized by obesity, retinopathy, polydactyly, renal and cardiac malformations, learning disabilities, and hypogenitalism.  Older literature suggests that A
Probab=21.78  E-value=43  Score=12.24  Aligned_cols=75  Identities=19%  Similarity=0.234  Sum_probs=45.6

Q ss_pred             EEEEECCCHHHHHHHHH----HHHH-------HCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHH
Q ss_conf             06887765489999999----9987-------099899946997025799999999975512578871699998037989
Q gi|254780306|r   50 MIWNIDPSSQKHLQNII----HAVK-------SSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQ  118 (837)
Q Consensus        50 p~y~v~~~~kk~~~~i~----~~~k-------~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~  118 (837)
                      ..|+++......+...+    .++.       +..-+|+|.--|..+.....+|.+.|..... .+.+++=.-.|++|.+
T Consensus        72 iI~VvDssd~~~~~~~~~~l~~ll~~~~~~~~~~PiLI~~NK~D~~~~~~~~ei~~~l~l~~~-~~~~~~i~~~SA~tG~  150 (162)
T cd04157          72 IIFVIDSSDRLRLVVVKDELELLLNHPDIKHRRVPILFFANKMDLPDALTAVKITQLLGLENI-KDKPWHIFASNALTGE  150 (162)
T ss_pred             EEEEEECCCHHHHHHHHHHHHHHHHCHHHCCCCCEEEEEEECCCCCCCCCHHHHHHHHCHHHH-CCCCEEEEEEECCCCC
T ss_conf             899970763888999999999997176551798459999814778899999999988586652-4896499997897897


Q ss_pred             HHHHHHH
Q ss_conf             9999986
Q gi|254780306|r  119 VVLNAMK  125 (837)
Q Consensus       119 aI~~A~~  125 (837)
                      .|.+||.
T Consensus       151 Gi~e~f~  157 (162)
T cd04157         151 GLDEGVQ  157 (162)
T ss_pred             CHHHHHH
T ss_conf             9899999


No 259
>TIGR01968 minD_bact septum site-determining protein MinD; InterPro: IPR010223   This entry describes the bacterial and chloroplast form of MinD, a multifunctional cell division protein that guides correct placement of the septum. In Escherichia coli, the cell division site is determined by the cooperative activity of min operon products MinC, MinD, and MinE . MinD is a membrane-associated ATPase and is a septum site-determining factor through the activation and regulation of MinC and MinE. MinD is also known to undergo a rapid pole-to-pole oscillation movement in vivo as observed by fluorescent microscopy. In plants, chloroplast division requires the dimerisation of stromal MinD . The homologous archaeal MinD proteins, with many archaeal genomes having two or more forms, are described by a separate model.; GO: 0016887 ATPase activity, 0000918 selection of site for barrier septum formation.
Probab=21.67  E-value=43  Score=12.22  Aligned_cols=33  Identities=33%  Similarity=0.645  Sum_probs=25.7

Q ss_pred             CHHHCCHHHHHHHHHCCHHHCCCCCCCCEEEEEE
Q ss_conf             8425489999998615255157778987499911
Q gi|254780306|r  694 KSDSVDYDKAMSLLSLPREIGIHPETQKNIIAGT  727 (837)
Q Consensus       694 ~~~~itle~Al~LLsLPr~lG~~pe~g~~I~~~~  727 (837)
                      .-|-++.+|..+.||+| -+|.=||+..-|.+.|
T Consensus       189 ~G~Mlsi~Dv~~~L~i~-LiGviPeD~~iI~stN  221 (272)
T TIGR01968       189 KGDMLSIDDVLEILSIP-LIGVIPEDEEIIVSTN  221 (272)
T ss_pred             CCCCCCHHHHHHHCCCC-CEEEECCCCCEEEEEC
T ss_conf             68982789999860886-1686329986576645


No 260
>PRK11062 nhaR transcriptional activator NhaR; Provisional
Probab=21.64  E-value=40  Score=12.46  Aligned_cols=52  Identities=19%  Similarity=0.327  Sum_probs=26.4

Q ss_pred             HHHHHHHHHCCCCCCCCHHHHHHHHHH---CCEEECCCCCEEECCHHHHHCCCCCC
Q ss_conf             998743321025665515789999973---22022147712220114200002233
Q gi|254780306|r  474 SSLIKKMEEIGIGRPSTYATILETLYK---RKYVIAEKRKILPQNTGRIVTAFLEN  526 (837)
Q Consensus       474 asLik~mE~~GIGrPSTyA~II~~L~~---R~YV~~~~~~l~pT~~G~~v~~~L~~  526 (837)
                      +|+-++=|.+++- +||-+.-|..|-+   ..-.++.++.+.+|+.|..+.++-+.
T Consensus        19 gs~~~Aa~~L~~t-q~~vS~qi~~LE~~lg~~Lf~R~~r~~~lT~~G~~~~~~a~~   73 (296)
T PRK11062         19 GSVVGAAEALFLT-PQTITGQIKALEERLQGKLFKRKGRGLEPTELGELVFRYADK   73 (296)
T ss_pred             CCHHHHHHHHCCC-CHHHHHHHHHHHHHHCCCCEEECCCCEEECHHHHHHHHHHHH
T ss_conf             9999999996898-179999999999995991099889982885899999999999


No 261
>TIGR02655 circ_KaiC circadian clock protein KaiC; InterPro: IPR013503    The circadian clock protein KaiC, is encoded in the kaiABC operon that controls circadian rhythms and may be universal in Cyanobacteria. Each member contains two copies of the KaiC domain, which is also found in other proteins. KaiC performs autophosphorylation and acts as its own transcriptional repressor. Kai proteins (KaiA and KaiC) appear to positively and negatively regulate kaiBC transcription which is consistent with a transcription/translation oscillatory (TTO) feedback model, believed to be at the core of all self-sustained circadian timers. However, the cyanobacterial circadian clock is able to function without de novo synthesis of clock gene mRNAs and the clock proteins, and the period is accurately determined without TTO feedback and the system is also temperature-compensated. It has been demonstrated that these three purified proteins form a temperature-compensated molecular oscillator in vitro that exhibits rhythmic phosphorylation and dephosphorylation of KaiC.    A negative-stain electron microscopy study of Synechococcus elongatus and Thermosynechococcus elongatus BP-1 KaiAKaiC complexes in combination with site-directed mutagenesis reveals that KaiA binds exclusively to the CII half of the KaiC hexamer. The EM-based model of the KaiAKaiC complex reveals proteinprotein interactions at two sites: the known interaction of the flexible C-terminal KaiC peptide with KaiA, and a second postulated interaction between the apical region of KaiA and the ATP binding cleft on KaiC. This model brings KaiA mutation sites that alter clock period or abolish rhythmicity into contact with KaiC and suggests how KaiA might regulate KaiC phosphorylation . ; GO: 0000287 magnesium ion binding, 0003677 DNA binding, 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0042752 regulation of circadian rhythm, 0045449 regulation of transcription.
Probab=21.41  E-value=43  Score=12.20  Aligned_cols=73  Identities=26%  Similarity=0.478  Sum_probs=45.8

Q ss_pred             HHHHHHHHHCCEEEECCCCCCHHHHHH--HHH---HHHHHHHCCCCCCCEEEEEEECCCHHHHHHHHHCCCCCCHHHHHH
Q ss_conf             999999870998999469970257999--999---999755125788716999980379899999986226469899999
Q gi|254780306|r   63 QNIIHAVKSSTILILATDPDREGEAIS--WHV---LDVLRQKNLIEKTKIQRVSFNAITKQVVLNAMKSPRDINLDLVNA  137 (837)
Q Consensus        63 ~~i~~~~k~a~~iilAtD~DREGE~Ia--whi---~e~l~~~~~~~~~~v~R~~f~eiT~~aI~~A~~n~r~~d~~Lv~A  137 (837)
                      -.|.+++.+....|+-.-||-||+-|+  |.+   .|.+++.  ..+-..+|+.+.++|  +|-..++.          +
T Consensus        74 W~l~~l~~~~klfildasPdP~Gq~~~G~fdls~lier~~ya--i~ky~a~rv~ids~t--~vfqqy~a----------~  139 (484)
T TIGR02655        74 WDLQKLVDEGKLFILDASPDPEGQDVVGEFDLSALIERINYA--IRKYKAKRVSIDSVT--AVFQQYDA----------V  139 (484)
T ss_pred             CHHHHHHHCCCEEEEECCCCCCCCEEEECCCHHHHHHHHHHH--HHHHHCCEEEHHHHH--HHHHHHHH----------H
T ss_conf             007888515967999668899755144031078999999999--876410000034666--56764212----------5


Q ss_pred             HHHHHHHHHHHH
Q ss_conf             999999898740
Q gi|254780306|r  138 YLARRALDYLVG  149 (837)
Q Consensus       138 ~~aRr~lD~lvG  149 (837)
                      ...||.+=||+-
T Consensus       140 ~vvrre~frl~a  151 (484)
T TIGR02655       140 SVVRREIFRLVA  151 (484)
T ss_pred             HHHHHHHHHHHH
T ss_conf             678899999999


No 262
>PRK00910 ribB 3,4-dihydroxy-2-butanone 4-phosphate synthase; Provisional
Probab=21.35  E-value=44  Score=12.18  Aligned_cols=27  Identities=30%  Similarity=0.527  Sum_probs=21.2

Q ss_pred             HHHHHHHHHHHHCCEEEECCCCCCHHH
Q ss_conf             999999999870998999469970257
Q gi|254780306|r   60 KHLQNIIHAVKSSTILILATDPDREGE   86 (837)
Q Consensus        60 k~~~~i~~~~k~a~~iilAtD~DREGE   86 (837)
                      ..|....+.++.-.-|++--|.|||+|
T Consensus        15 s~Ie~Ai~al~~Gk~Viv~DdedREnE   41 (218)
T PRK00910         15 TRVENALQALREGRGVLLLDDEDRENE   41 (218)
T ss_pred             CHHHHHHHHHHCCCEEEEEECCCCCCH
T ss_conf             529999999988995999978998761


No 263
>pfam01047 MarR MarR family. The Mar proteins are involved in the multiple antibiotic resistance, a non-specific resistance system. The expression of the mar operon is controlled by a repressor, MarR. A large number of compounds induce transcription of the mar operon. This is thought to be due to the compound binding to MarR, and the resulting complex stops MarR binding to the DNA. With the MarR repression lost, transcription of the operon proceeds. The structure of MarR is known and shows MarR as a dimer with each subunit containing a winged-helix DNA binding motif.
Probab=21.35  E-value=44  Score=12.18  Aligned_cols=22  Identities=23%  Similarity=0.323  Sum_probs=13.3

Q ss_pred             CCCCHHHHHHHHHHCCEEECCC
Q ss_conf             6551578999997322022147
Q gi|254780306|r  487 RPSTYATILETLYKRKYVIAEK  508 (837)
Q Consensus       487 rPSTyA~II~~L~~R~YV~~~~  508 (837)
                      .|+|-+.+|..|.++|||.+..
T Consensus        30 ~~~~vs~~i~~Le~~glv~R~~   51 (59)
T pfam01047        30 DRSTVTRVLDRLEKKGLIERSR   51 (59)
T ss_pred             CHHHHHHHHHHHHHCCCEEECC
T ss_conf             8654999999998897988627


No 264
>KOG0114 consensus
Probab=21.31  E-value=44  Score=12.17  Aligned_cols=17  Identities=35%  Similarity=0.632  Sum_probs=9.2

Q ss_pred             HHHHHHHHHHHHHHHCH
Q ss_conf             99999989874011378
Q gi|254780306|r  138 YLARRALDYLVGFNLSP  154 (837)
Q Consensus       138 ~~aRr~lD~lvG~~lSp  154 (837)
                      +.||.+.|.|.|||+.+
T Consensus        68 ~dAk~A~dhlsg~n~~~   84 (124)
T KOG0114          68 FDAKKACDHLSGYNVDN   84 (124)
T ss_pred             HHHHHHHHHHCCCCCCC
T ss_conf             66899999841553478


No 265
>KOG3139 consensus
Probab=21.24  E-value=44  Score=12.16  Aligned_cols=39  Identities=26%  Similarity=0.210  Sum_probs=25.1

Q ss_pred             HHHHHHCCC-----HHHHHHHHHHHHCCCCCCCHHHHHHHHCCCCCCCCCH
Q ss_conf             988760888-----9999999987621355672122455314755444430
Q gi|254780306|r  268 VASSRLGFS-----ASHTMRIAQKLYEGIDVNGEIVGLITYMRTDGVHMSP  313 (837)
Q Consensus       268 ~As~~lg~s-----a~~Tm~iAQ~LYE~~~~~~~~~GlITYpRTDS~~ls~  313 (837)
                      ++.+..|++     ..-|..-|.+|||+       -|++++=|+..-|+..
T Consensus       111 d~m~~~g~~eVvLeTe~~n~~A~~LY~s-------LGF~r~~r~~~YYlng  154 (165)
T KOG3139         111 DAMRSRGYSEVVLETEVTNLSALRLYES-------LGFKRDKRLFRYYLNG  154 (165)
T ss_pred             HHHHHCCCCEEEEECCCCCHHHHHHHHH-------CCCEEECCEEEEEECC
T ss_conf             9999779968998324334189999885-------4946733124789778


No 266
>KOG1973 consensus
Probab=21.24  E-value=44  Score=12.16  Aligned_cols=27  Identities=30%  Similarity=0.784  Sum_probs=16.9

Q ss_pred             CCCCCCCEECCCCCCCCEEEEEECCCCCCCCCCCCCCCC
Q ss_conf             556766114334677731368715776111234343233
Q gi|254780306|r  596 KENNEDSRTCPECHTHSLSLKLSSKYGAFVGCTNYPECK  634 (837)
Q Consensus       596 ~~~~~~~~~Cp~C~~g~L~~k~~gK~G~FigCSnyPeCk  634 (837)
                      ..+.+....|+ |          ..||.+|||.| |+|.
T Consensus       215 d~~e~~yC~Cn-q----------vsyg~Mi~CDn-~~C~  241 (274)
T KOG1973         215 DPDEPTYCICN-Q----------VSYGKMIGCDN-PGCP  241 (274)
T ss_pred             CCCCCEEEEEC-C----------CCCCCCCCCCC-CCCC
T ss_conf             89987688716-7----------66565022079-9998


No 267
>PRK11123 arginine transporter permease subunit ArtQ; Provisional
Probab=21.19  E-value=44  Score=12.15  Aligned_cols=25  Identities=24%  Similarity=0.070  Sum_probs=19.8

Q ss_pred             HHHHHHHHHHCCCHHHHHHH---HHHHH
Q ss_conf             99999887608889999999---98762
Q gi|254780306|r  264 TLQQVASSRLGFSASHTMRI---AQKLY  288 (837)
Q Consensus       264 tLQq~As~~lg~sa~~Tm~i---AQ~LY  288 (837)
                      .=|.||++-+|||..++|.-   =|-+-
T Consensus       132 ~GQ~EAa~alGms~~q~~r~IilPQa~r  159 (238)
T PRK11123        132 VGQWESGQALGLSKSAIFFRLVMPQMWR  159 (238)
T ss_pred             HHHHHHHHHCCCCHHHHHHHHHHHHHHH
T ss_conf             9999999984989999999999899999


No 268
>pfam08772 NOB1_Zn_bind Nin one binding (NOB1) Zn-ribbon like. This domain corresponds to a zinc ribbon and is found on the RNA binding protein NOB1.
Probab=21.05  E-value=43  Score=12.22  Aligned_cols=16  Identities=25%  Similarity=0.644  Sum_probs=10.9

Q ss_pred             CCEECCCCCCCCEEEE
Q ss_conf             6114334677731368
Q gi|254780306|r  601 DSRTCPECHTHSLSLK  616 (837)
Q Consensus       601 ~~~~Cp~C~~g~L~~k  616 (837)
                      +..-||+||...|...
T Consensus        23 ~k~FCpkCGn~TL~rv   38 (73)
T pfam08772        23 TKQFCPKCGNATLRRV   38 (73)
T ss_pred             CCCCCCCCCCCCEEEE
T ss_conf             6612753699901699


No 269
>COG0055 AtpD F0F1-type ATP synthase, beta subunit [Energy production and conversion]
Probab=20.97  E-value=44  Score=12.12  Aligned_cols=28  Identities=29%  Similarity=0.354  Sum_probs=14.5

Q ss_pred             HHHHHHHCCCCCCCCHHHHHHHHHHCCEE
Q ss_conf             87433210256655157899999732202
Q gi|254780306|r  476 LIKKMEEIGIGRPSTYATILETLYKRKYV  504 (837)
Q Consensus       476 Lik~mE~~GIGrPSTyA~II~~L~~R~YV  504 (837)
                      |+-.|-.. .|--.|-|+=+..||+|=--
T Consensus       263 lLGr~PSa-vGYQpTLatemg~lQERIts  290 (468)
T COG0055         263 LLGRMPSA-VGYQPTLATEMGQLQERITS  290 (468)
T ss_pred             HHCCCCCC-CCCCCHHHHHHHHHHHHHHC
T ss_conf             84569641-45674067788889999753


No 270
>COG1339 Transcriptional regulator of a riboflavin/FAD biosynthetic operon [Transcription / Coenzyme metabolism]
Probab=20.96  E-value=44  Score=12.12  Aligned_cols=31  Identities=29%  Similarity=0.338  Sum_probs=22.7

Q ss_pred             HHHHHHHCCCHHHHHHHHHHHHCCCCCCCHHHHHHHHCC
Q ss_conf             998876088899999999876213556721224553147
Q gi|254780306|r  267 QVASSRLGFSASHTMRIAQKLYEGIDVNGEIVGLITYMR  305 (837)
Q Consensus       267 q~As~~lg~sa~~Tm~iAQ~LYE~~~~~~~~~GlITYpR  305 (837)
                      ++.++++|.|.+.+.+..+.|=+        .|||+=-+
T Consensus        23 ~ela~~l~~S~qta~R~l~~le~--------~~~I~R~~   53 (214)
T COG1339          23 SELAKRLGVSSQTAARKLKELED--------EGYITRTI   53 (214)
T ss_pred             HHHHHHHCCCCHHHHHHHHHHCC--------CCCEEEEE
T ss_conf             99998857470778899886411--------78478883


No 271
>COG1217 TypA Predicted membrane GTPase involved in stress response [Signal transduction mechanisms]
Probab=20.90  E-value=44  Score=12.11  Aligned_cols=16  Identities=25%  Similarity=0.503  Sum_probs=10.8

Q ss_pred             CCCCCCHHHHHHHHHH
Q ss_conf             5143579999999983
Q gi|254780306|r  748 QVLTIDLEQAISCITE  763 (837)
Q Consensus       748 ~~~~I~l~~Aieli~~  763 (837)
                      .|...+||+|++.|+.
T Consensus       558 ~p~~msLE~Ale~i~d  573 (603)
T COG1217         558 PPIRMTLERALEFIAD  573 (603)
T ss_pred             CCCCCCHHHHHHHCCC
T ss_conf             8410669999854587


No 272
>TIGR01084 mutY A/G-specific adenine glycosylase; InterPro: IPR005760    The DNA repair enzyme MutY plays an important role in the prevention of DNA mutations resulting from the presence of the oxidatively damaged lesion 7,8-dihydro-8-oxo-2'-deoxyguanosine (8-OxoG). 8-OxoG can mispair with 2'-deoxycytidine 5'-triphosphate or with 2'-deoxyadenosine triphosphate during DNA replication, forming C*8-oxoG and A*8-oxoG mispairs. Human MutY is responsible for recognition and removal of the inappropriately inserted adenine in an A=8-oxoG mispair. If unrepaired, the A=8-oxoG mispairs can result in deleterious C:G to A:T transversions.    Multiple forms of mammalian MutY are formed by alternative splicing and locate to the nucleus or mitochondrion, where they have been shown to interact with several other proteins involved in the repair of DNA damage . The HhH-GPD domain within the protein binds the phosphate backbone of the substrate.   This family represents bacterial MutY and a limited number of murine homologs. In rat, the Escherichia coli MutY DNA glycosylase homolog (MYH) is induced in response to mitochondrial DNA damage . ; GO: 0019104 DNA N-glycosylase activity, 0006284 base-excision repair, 0005622 intracellular.
Probab=20.88  E-value=44  Score=12.11  Aligned_cols=30  Identities=27%  Similarity=0.306  Sum_probs=25.5

Q ss_pred             CCCCCCCCHHHHHHHHHHCCEEECCCCCEEE
Q ss_conf             0256655157899999732202214771222
Q gi|254780306|r  483 IGIGRPSTYATILETLYKRKYVIAEKRKILP  513 (837)
Q Consensus       483 ~GIGrPSTyA~II~~L~~R~YV~~~~~~l~p  513 (837)
                      .|||| ||=+.|.+--.++.+-..+||-...
T Consensus       124 ~GVG~-yTAgAils~a~~~~~p~~DGNV~RV  153 (297)
T TIGR01084       124 PGVGR-YTAGAILSFAYNKPVPILDGNVKRV  153 (297)
T ss_pred             CCCCH-HHHHHHHHHHHCCCCCCCCCCHHHH
T ss_conf             89762-1799999987268762015407889


No 273
>pfam08576 DUF1764 Eukaryotic protein of unknown function (DUF1764). This is a family of eukaryotic proteins of unknown function. This family contains many hypothetical proteins.
Probab=20.71  E-value=24  Score=14.06  Aligned_cols=18  Identities=33%  Similarity=0.453  Sum_probs=8.9

Q ss_pred             CCHHHHHHHHHHCCCCCC
Q ss_conf             178998743321025665
Q gi|254780306|r  471 YSESSLIKKMEEIGIGRP  488 (837)
Q Consensus       471 ytEasLik~mE~~GIGrP  488 (837)
                      +-++-.|=.||++|||.|
T Consensus        65 ~~dg~~iy~~~el~~~~~   82 (98)
T pfam08576        65 TEDGLPIYTEEELKIGNP   82 (98)
T ss_pred             CCCCCEECCHHHHCCCCC
T ss_conf             577863446999288887


No 274
>PRK09986 DNA-binding transcriptional activator XapR; Provisional
Probab=20.44  E-value=45  Score=12.04  Aligned_cols=17  Identities=24%  Similarity=0.497  Sum_probs=7.5

Q ss_pred             EECCCCCEEECCHHHHH
Q ss_conf             22147712220114200
Q gi|254780306|r  504 VIAEKRKILPQNTGRIV  520 (837)
Q Consensus       504 V~~~~~~l~pT~~G~~v  520 (837)
                      +.+.++.+.+|+-|..+
T Consensus        38 f~R~~r~v~LT~~G~~l   54 (278)
T PRK09986         38 FIRHSRSVALTHAGKIL   54 (278)
T ss_pred             EEECCCCEEECHHHHHH
T ss_conf             99999977089889999


No 275
>TIGR00100 hypA hydrogenase nickel insertion protein HypA; InterPro: IPR000688   Bacterial membrane-bound nickel-dependent hydrogenases requires a number of accessory proteins which are involved in their maturation. The exact role of these proteins is not yet clear, but some seem to be required for the incorporation of the nickel ions . One of these proteins is generally known as hypA. It is a protein of about 12 to 14 kDa that contains, in its C-terminal region, four conserved cysteines that form a zinc-finger like motif. Escherichia coli has two proteins that belong to this family, hypA and hybF. A homologue, MJ0214, has also been found in a number of archaeal species, including the genome of Methanococcus jannaschii. ; GO: 0016151 nickel ion binding, 0006464 protein modification process.
Probab=20.38  E-value=45  Score=12.03  Aligned_cols=15  Identities=13%  Similarity=0.366  Sum_probs=7.4

Q ss_pred             HHHHHHHHHHHCCCH
Q ss_conf             999999999862601
Q gi|254780306|r  538 ADLEEKLDEISTGKL  552 (837)
Q Consensus       538 a~~E~~ld~Ia~G~~  552 (837)
                      ..+.-.+|-+++|..
T Consensus        49 ~~l~FaFev~~~gT~   63 (128)
T TIGR00100        49 EQLQFAFEVVREGTV   63 (128)
T ss_pred             HHHHHHHHHHCCCCE
T ss_conf             999888987246742


No 276
>COG2022 ThiG Uncharacterized enzyme of thiazole biosynthesis [Nucleotide transport and metabolism]
Probab=20.36  E-value=23  Score=14.21  Aligned_cols=23  Identities=13%  Similarity=0.293  Sum_probs=12.1

Q ss_pred             CCEEEEECCCCCCHHCCCCCHHHH
Q ss_conf             524773023464000001999999
Q gi|254780306|r  351 EAIRPNDFDFLPSKMKQFLDSDQF  374 (837)
Q Consensus       351 eAIrPT~~~~~p~~~~~~L~~de~  374 (837)
                      +.|+|.++...|+. .+.-+.+|.
T Consensus        63 ~~l~~~~~~~LPNT-aGc~taeEA   85 (262)
T COG2022          63 DLLIPLGVTLLPNT-AGCRTAEEA   85 (262)
T ss_pred             HHHHHCCCEECCCC-CCCCCHHHH
T ss_conf             77411386767876-455889999


No 277
>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=20.35  E-value=46  Score=12.03  Aligned_cols=81  Identities=21%  Similarity=0.273  Sum_probs=40.0

Q ss_pred             HHHHHHHHHHHH-HCCEEEECCCCCCHHHHHHHHHHHHHHHHCCCCCCCEEEEEEECCCHHHHH---HH---HHCCCCCC
Q ss_conf             899999999987-099899946997025799999999975512578871699998037989999---99---86226469
Q gi|254780306|r   59 QKHLQNIIHAVK-SSTILILATDPDREGEAISWHVLDVLRQKNLIEKTKIQRVSFNAITKQVVL---NA---MKSPRDIN  131 (837)
Q Consensus        59 kk~~~~i~~~~k-~a~~iilAtD~DREGE~Iawhi~e~l~~~~~~~~~~v~R~~f~eiT~~aI~---~A---~~n~r~~d  131 (837)
                      ..++..|..++- ..+.||..+|.+-. ++|     ++|+...      .-|++|==|++=.-.   +-   +...+-||
T Consensus       563 e~Y~~A~E~AaG~RL~~VVV~dd~vA~-~aI-----~~LK~~k------~GRaTFLPLNkmr~~~~~~~~s~~~~~G~id  630 (1202)
T TIGR02169       563 ERYALAIEVAAGNRLNNVVVEDDAVAK-EAI-----ELLKRRK------AGRATFLPLNKMRSKKARRDLSILAEDGVID  630 (1202)
T ss_pred             HHHHHHHHHHHHHHCCCEEECCHHHHH-HHH-----HHHHHCC------CCCCCCCCHHHCCCCCCCCCCCCCCCCCCCE
T ss_conf             999999999974122685415758999-999-----9999707------8987656614305642357666554578526


Q ss_pred             --HHHHHH-HHHHHHHHHHHHHH
Q ss_conf             --899999-99999989874011
Q gi|254780306|r  132 --LDLVNA-YLARRALDYLVGFN  151 (837)
Q Consensus       132 --~~Lv~A-~~aRr~lD~lvG~~  151 (837)
                        +|||+= .+=+.+.-|.+|=|
T Consensus       631 fA~dLv~FD~ky~~af~yvfgDT  653 (1202)
T TIGR02169       631 FAVDLVEFDPKYEPAFKYVFGDT  653 (1202)
T ss_pred             EEHHHHHHHHHHHHHHHHHHCCH
T ss_conf             31000102377888888886132


No 278
>pfam03965 Pencillinase_R Penicillinase repressor. The penicillinase repressor negatively regulates expression of the penicillinase gene. The N-terminal region of this protein is involved in operator recognition, while the C-terminal is responsible for dimerization of the protein.
Probab=20.17  E-value=46  Score=12.00  Aligned_cols=77  Identities=21%  Similarity=0.274  Sum_probs=41.8

Q ss_pred             CHHHHHHHHHHC-CCCCCCCHHHHHHHHHHCCEEECCCCCEEECCHHHHHCCCCCCCCCCCCCHHHH-HHHHHHHHHHHC
Q ss_conf             789987433210-256655157899999732202214771222011420000223366556898899-999999999862
Q gi|254780306|r  472 SESSLIKKMEEI-GIGRPSTYATILETLYKRKYVIAEKRKILPQNTGRIVTAFLENFFSQYVEYDFT-ADLEEKLDEIST  549 (837)
Q Consensus       472 tEasLik~mE~~-GIGrPSTyA~II~~L~~R~YV~~~~~~l~pT~~G~~v~~~L~~~f~~~~~~~fT-a~~E~~ld~Ia~  549 (837)
                      |=..++..|.+. +. -++|-++++..|.++|||..++.       |+.-+     |.|.+-.-++. ..+.+-+|.+-.
T Consensus        19 t~~ei~~~l~~~~~~-~~tTv~T~L~rL~~KG~l~~~~~-------gr~~~-----Y~p~v~~~~~~~~~~~~~~~~~f~   85 (115)
T pfam03965        19 TVKEVVEELPEPRDW-AYSTVKTLLTRLVKKGLLSREKD-------GRAYI-----YSPLVSREEAVASAVKQLLDRLFG   85 (115)
T ss_pred             CHHHHHHHHCCCCCC-CHHHHHHHHHHHHHCCCEEEEEC-------CCCEE-----EEECCCHHHHHHHHHHHHHHHHHC
T ss_conf             799999985145688-57289999999997786268733-------99479-----874688999999999999999979


Q ss_pred             CCHHHHHHHHHHHH
Q ss_conf             60134789999867
Q gi|254780306|r  550 GKLNWKEVLHEFWE  563 (837)
Q Consensus       550 G~~~~~~~L~~Fy~  563 (837)
                      |.  ..+++..|..
T Consensus        86 gs--~~~lv~~l~~   97 (115)
T pfam03965        86 GS--VGALVANFVE   97 (115)
T ss_pred             CC--HHHHHHHHHH
T ss_conf             89--9999999986


No 279
>cd03365 TOPRIM_TopoIIA TOPRIM_TopoIIA: topoisomerase-primase (TOPRIM) nucleotidyl transferase/hydrolase domain of the type found in proteins of the type IIA family of DNA topoisomerases similar to Saccharomyces cerevisiae Topoisomerase II. TopoIIA enzymes cut both strands of the duplex DNA to remove (relax) both positive and negative supercoils in DNA.  These enzymes covalently attach to the 5' ends of the cut DNA, separate the free ends of the cleaved strands, pass another region of the duplex through this gap, then rejoin the ends. These proteins also catenate/ decatenate duplex rings.  The TOPRIM domain has two conserved motifs, one of which centers at a conserved glutamate and the other one at two conserved aspartates (DxD). This glutamate and two aspartates, cluster together to form a highly acid surface patch. The conserved glutamate may act as a general base in strand joining and as a general acid in strand cleavage by topisomerases.  The DXD motif may co-ordinate Mg2+, a cofact
Probab=20.11  E-value=46  Score=12.00  Aligned_cols=25  Identities=24%  Similarity=0.389  Sum_probs=18.0

Q ss_pred             HCCEEEECCCCCCHHHHHHHHHHHH
Q ss_conf             0998999469970257999999999
Q gi|254780306|r   71 SSTILILATDPDREGEAISWHVLDV   95 (837)
Q Consensus        71 ~a~~iilAtD~DREGE~Iawhi~e~   95 (837)
                      .-..|+++||+|-.|-.|.=-++..
T Consensus        76 RYgkIiI~tDaDvDG~HI~~Llltf  100 (120)
T cd03365          76 RYGRLMIMTDQDHDGSHIKGLLINF  100 (120)
T ss_pred             CCCEEEEEECCCCCHHHHHHHHHHH
T ss_conf             8885899878988657899999999


Done!